title: Patient 5 AIA-9

source_name: Patient 5 AIA-9_PBMC

tag: drug response

value: Non-R

tag: response rate

tag: % fall

value: F

value: sm

tag: bmi


title: Colony 1-1 (cy5) - Colony 2-2 (cy3)

status: Public on Apr 08 2013

type: RNA

city: Miami

first: Anthony

middle: John

last: Bellantuono

state: FL

department: Biological Sciences

country: USA

institute: Florida International University

hyb_protocol: Static hybridizations were performed using formamide-based hybribization buffer (Genisphere).  Prehybridization used 1 μg Human Cot-1 DNA for 90 minutes. Hybridization with cDNA was performed for 14 hours at 47°C. Arrays were washed in 65°C 2x SSC/0.2% SDS for 15 minutes, 2x SSC at room temperature for 15 minutes, and 0.2x SSC at room temperature for 15 minutes. Dye capture with Array 900 3DNA capture reagents (Genisphere) was performed at 50°C for 4 hours, followed by washing. Arrays were dipped in DyeSaver II (Genisphere).

scan_protocol: Scanning was performed on a GenePix Personal 4100A (Axon Instruments) microarray scanner using GenePix Pro 4.1.

data_processing: Following gridding and quality control using GenePix Pro 4.1 (Axon Instruments), background-subtracted mean intensity values were log- and lowess-transformed using R/Maanova version 1.18 (Wu and Churchill 2008). A fixed-effect ANOVA model was fit to the normalized data. Empirical-Bayes Fs statistic was used to test for differentially expressed genes at each sampling time. P-values for each clone were calculated from 500 permutations of residual shuffling. False discovery rate adjustments were implemented using jsFDR (Storey 2002, J Roy Stat Soc B), using an adjusted p-value threshold of less than 0.05.

molecule: total RNA

organism: Acropora millepora

source_name: Colony 1, within-colony biological replicate 1

label_protocol: cDNA probe synthesis was performed from 2.5 μg high-quality total RNA using Superscript II Reverse Transcriptase (Invitrogen) and the 3DNA Array 350 kit (Genisphere) according to the manufacturer’s guidelines. Two primers were used, which consisted of a Cy3 and Cy5 specific capture sequence and a poly-T tail. In order to make each sample specific for Cy3 and Cy5, each sample was reverse transcribed separately using only one primer.

extract_protocol: Coral fragments were immediately frozen in liquid nitrogen upon sampling. Frozen coral fragments were homogenized in Trizol Reagent (Invitrogen). Trizol RNA extraction protocol was followed as per manufacturer’s protocol through phase separation, after which  the aqueous phase was recovered, mixed with an equal volume of absolute ethanol, and processed with an RNeasy Mini kit (QIAGEN). RNA integrity was assessed with the use of a Bioanalyzer (Agilent); only high integrity RNA was used for cDNA synthesis and subsequent hybridization.

tag: genotype/variation

value: intron 4-500 haplotype 1

source_name: Colony 2, within-colony biological replicate 2


title: Patient 4 AIA-8

city: Bucheon-si

first: Seung-Woo

last: Shin

state: Gyeonggi-do

address: 1174 Jung-dong, Wonmi-gu

department: Genome research Center for Allergy and Respiratory Diseases

country: South Korea

institute: Soon Chun Hyang University hospital

hyb_protocol: The purified cDNA was resuspended in 100 uL of hybridization solution containing 5% SSC, 0.1% SDS, 30% formamide, 20 ug of Human Cot-1 DNA, 20 ug of poly A RNA, and 20 ug of Yeast tRNA (Invitrogen). The hybridization mixtures were heated at 100C for 2 to 3 min and directly pipetted onto microarrays. The arrays were hybridized at 42C for 12 to 16 h in a humidified hybridization chamber (Genomictree, Korea). The hybridized microarrays were washed with 2% SSC/0.1% SDS for 5 min, 0.1% SSC/0.1% SDS for 10 min, and 0.1% SSC for 2 min twice. The washed microarrays were immediately dried using a microarray centrifuge (Genomictree, Korea).

scan_protocol: Axon 4000B scanner (Molecular Devices, CA, USA). The signals and the background fluorescence intensities were calculated for each probe by averaging the intensities of every pixel inside the probe spot region using GenePix Pro 4.0 software (Molecular Devices). Spots of poor quality or indistinguishable signal level from the background were excluded.

data_processing: To analyze differentially expressed genes between ATA and AERD samples, the Cross gene error model for replicates was activated. Gene expression data was normalized in two ways: LOWESS and per gene normalization.  In per gene normalization, the data from a given gene was normalized to the median expression level of the gene across all samples.

organism: Homo sapiens

source_name: Patient 4 AIA-8_PBMC

label_protocol: Briefly, each 50 ug of total RNA was mixed with 2 ug of oligo-24N (dT) (GenoTech, Korea) in 15.4 uL of RNase free water and incubated at 65C for 10 min. After incubation, the single-stranded cDNA was synthesized in the presence of Cy3-dUTP or Cy5-dUTP (1 mM each, NEN Life Science Products, Boston, USA) at 42C for 2 h. Total RNA from test samples and common reference RNA pooled from 10 normal samples were labeled with Cy5 and Cy3, respectively. Both Cy3- and Cy5-labeled cDNA were purified using PCR purification kit (Qiagen) as recommended by the manufacturer.

extract_protocol: Total RNA was isolated from PBMC using a modified guanidinium thiocyanate–phenol–chloroform extraction method.

tag: condition

value: AERD

tag: onset of asthma (age)

tag: wbc

tag: blood eosinophil percentage

tag: Sex

value: M

tag: birthday

tag: age

tag: smoke

value: es

tag: height

tag: weight

tag: fvc%

source_name: common reference RNA

tag: common reference

value: RNA pooled from 10 normal samples


title: Colony 1 (cy5) - Colony 4 (cy3)

source_name: Colony 1

source_name: Colony 4

value: intron 4-500 haplotype 2


title: Patient 1 AIA-3

source_name: Patient 1 AIA-3_PBMC

value: NS


title: Wild-type_Liver_2

city: Indianapolis

first: Keith

middle: M

last: Goldstein

state: IN

address: Lilly Corporate Center

department: Investigative Toxicology

institute: Eli Lilly & Co.

description: Male wild-type Sprague-Dawley rats 8-11 weeks old

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Rat Genome 230 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 following Affymetrix standard procedures.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 30007G using GeneChip Operating Software to generate raw and averaged image files (.DAT and .CEL).

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. The trimmed mean target intensity of each array was set to 1500.

label: Biotin

organism: Rattus norvegicus

label_protocol: Biotinylated cRNA were prepared using a modified MessageAmp procedure (Life Technologies, Inc.) from 1 ug total RNA.

extract_protocol: RNA was isolated using Qiagen RNeasy columns according to the manufacturer's protocol

treatment_protocol: SAGE knockout of Mdr1a, Mrp2, Bcrp (www.sageresearchmodels.com)

tag: strain

value: Sprague Dawley

tag: gender

value: male

value: Wild-type

tag: tissue

value: Liver


title: Patient 2 AIA-5

source_name: Patient 2 AIA-5_PBMC

tag: % fall

value: ns

tag: bmi


title: monocytes_T14_rep3

city: Kiel

first: Frank

last: Döring

address: Heinrich-Hecht-Platz 10

department: Human Nutrition and Food Science

country: Germany

institute: Christian-Albrechts-University Kiel

description: after 2-week Q10H2 supplementation

hyb_protocol: 15 µg of fragmented cRNA was hybridized to a Human Genome U133+ 2.0 Array for 16 hr at 45 °C at 60 rpm. Arrays were washed on GeneChip®  Fluidics station 450 (Affymetrix) and stained with streptavidin-phycoerythrin

scan_protocol: Microarrays were scanned with a GeneChip® Scanner 3000 7G (Affymetrix).

data_processing: Expression data was normalized with Affymetrix GeneChip Operating Software (GCOS) 1.4 using mean value (global normalization).

label: biotin

label_protocol: Biotinylated cRNA was prepared with the MessageAmp™ II-Biotin Enhanced Kit (Ambion/Applied Biosystems) according to the manufacturer´s instructions.

growth_protocol: Based on clinical laboratory tests, all study participants fulfilled the following inclusion criteria: 1) no history of gastrointestinal, hepatic, cardiovascular or renal disease; 2) no supplemental vitamin use for > 2 weeks before the start of the study; 3) non- or occasional smoking (< 3 cigarettes/d); and 4) perpetuation of usual nutrition habits.

extract_protocol: Fasting blood samples were taken before (T0) and after (T14) supplementation with Q10H2 from all study participants as well as 4 weeks after study completion (T42, washout period) from 9 subjects, respectively.

treatment_protocol: 53 healthy male volunteers received 150 mg Q10H2 daily in form of three softgel capsules with each principal meal (a´ 50 mg) for 14 days.

tag: disease state

value: healthy


title: monocytes_T14_rep2

description: after 2-week Q10H2 supplementation


title: Wild-type_Liver_3

tag: genotype/variation


title: Patient 3 AIA-7

source_name: Patient 3 AIA-7_PBMC

tag: condition

tag: onset of asthma (age)

tag: wbc

value: SM

value: nd


title: Wild-type_Liver_4


title: monocytes_T0_rep1

description: before Q10H2 supplementation


title: monocytes_T14_rep1

description: after 2-week Q10H2 supplementation


title: iOPC, biological rep2

status: Public on Apr 07 2013

city: Stanford

first: Samuele

last: Marro

state: California

address: 256 Campus Drive

institute: Stanford University

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Rat Genome 230 2.0 Arrays. GeneChips were washed and stained in the Affymetrix GeneChip Fluidics Station 450.

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

data_processing: CEL files were imported by Partek, pre-background adjustment for GC content was automatically performed by the software as well as RMA background correction and quantile normalization.

source_name: iOPCs three weeks after infection

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Primary rat embryonic fibroblasts were isolated as previously described (TV, nature) and plated in MEF media (DMEM high glucose, calf serum, sodium pyruvate, non-essential amino acids, penicillin/streptomycin and β-mercaptoethanol). Before being used for experiments, primary fibroblasts were passaged three times. Cortical OPCs and OLs were purified by sequential immunopanning as described previously (Chan et al., 2004). DMEM (Invitrogen) contained human transferrin (100 μg/ml), bovine serum albumin (100 μg/ml), putrescine (16 μg/ml), progesterone (60 ng/ml), sodium selenite (40 ng/ml), N-acetyl-L-cysteine (5 μg/ml), D-biotin (10 ng/ml), forskolin (4.2 μg/ml), bovine insulin (5 μg/ml) (all from Sigma), glutamine (2 mM), sodium pyruvate (1 mM), penicillin– streptomycin (100 U each) (all from Invitrogen), Trace Elements B (1×; Mediatech, Herndon, VA), and CNTF (10 ng/ml, Pepro Tech); proliferation medium also contained OPC mitogens PDGF-AA (10 ng/ml) and NT-3 (1 ng/ml) (both from PeproTech); differentiation medium also contained triiodothyronine (T3) (40 ng/ml; Sigma) without OPC mitogens.

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

value: Sprague-Dawley

tag: cell type

value: induced oligodendrocyte precursor cells (iOPCs)


title: monocytes_T0_rep3

description: before Q10H2 supplementation


title: Fibroblast, biological rep2

source_name: Rat embryonic fibroblasts

value: embryonic fibroblasts


title: OL, day six, biological rep1

source_name: OPC six days after differentiation

value: oligodendroglia (OL)


title: OL, day six, biological rep2


title: OL, day three, biological rep2

source_name: OPC three days after differentiation


title: OPC, day zero

source_name: Primary OPC from neonatal brain

value: neonatal brain

value: primary oligodendrocyte precursor cells (OPCs)


title: iOPC, biological rep1


title: OL, day three, biological rep1


title: Fibroblast, biological rep1


title: monocytes_T0_rep2

description: before Q10H2 supplementation


title: Full-length_cjejuni_416826 6

status: Public on Apr 06 2013

type: protein

city: Potsdam

first: Sebastian

last: Hoppe

address: Am Mühlenberg 13

department: Bioanalytics and Biosensorics

institute: Fraunhofer Institute for Cell Therapy and Immunology

description:
slide416826 Ch6
Recombinant protein (cDNA library).
HaloTag-fusion proteins derived from Campylobacter jejuni cDNA and expressed in Acella E. coli overexpression strains.

hyb_protocol: Fusion proteins were spotted and coupled to the microarray surface for one hour at room temperature with 70% humidity. Slides were washed three times with PBSI (PBS + 0.01% Igepal). Incubation with primary antibody (rabbit polyclonal to C. jejuni) and secondary antibody (goat polyclonal to rabbit, Chromeo-546 conjugated) were performed for 1.5 h each, with washing (three times) with PBSI after each incubation step. Slides were dried with nitrogen and scanned afterwards. Primary antibody: anti-Campylobacter jejuni (Abd Serotec 1744-9035, Lot#110810).

scan_protocol: Fluorescent array images were collected for Cy3 with a GenePix 4200A fluorescent scanner. Image intensity data were extracted and analyzed using Origin Pro 8G.

data_processing:
From the raw data, the corrected median fluorescent intensities (F532 median - B532) were used. Then, relative fluorescence intensities (rfis) were calculated by subtracting each corresponding compartment by the compartment incubated only with secondary antibody. This acknowledges the presence of unspecific interactions of the secondary antibody to the samples. Next, the normalized value was calculated by dividing the rfi of each sample with the median signal of all sample spots within a compartment. Next, a median value was calculated for each set of sample replicates and these median values were used to calculate a Q-value = [median normalized rfi (sample)]/[median normalized rfi(positive control)]for each positive reference used. Additionally, the error was calculated by error propagation according to Gauss. If the Q-value of the positive reference (taking the error into account) was below that of any negative control, the test was discarded.

Raw data file: GSE45520_416826.gpr

molecule: protein

organism: Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819

source_name: crude lysate Acella E. coli + recombinantly expressed proteins

extract_protocol: Fusion proteins were extracted from cultures using the EasyLyse Bacterial protein extraction kit (Epicentre).


title: Full-length_cjejuni_416826 4

description:
slide416826 Ch4
Recombinant protein (cDNA library).
HaloTag-fusion proteins derived from Campylobacter jejuni cDNA and expressed in Acella E. coli overexpression strains.

hyb_protocol: Fusion proteins were spotted and coupled to the microarray surface for one hour at room temperature with 70% humidity. Slides were washed three times with PBSI (PBS + 0.01% Igepal). Incubation with primary antibody (rabbit polyclonal to C. jejuni) and secondary antibody (goat polyclonal to rabbit, Chromeo-546 conjugated) were performed for 1.5 h each, with washing (three times) with PBSI after each incubation step. Slides were dried with nitrogen and scanned afterwards. Primary antibody: anti-Campylobacter jejuni (Abcam ab22542, Lot#203685).


title: Full-length_cjejuni_416826 5

description:
slide416826 Ch5
Recombinant protein (cDNA library).
HaloTag-fusion proteins derived from Campylobacter jejuni cDNA and expressed in Acella E. coli overexpression strains.


title: Full-length_cjejuni_416826 3

description:
slide416826 Ch3
Recombinant protein (cDNA library).
HaloTag-fusion proteins derived from Campylobacter jejuni cDNA and expressed in Acella E. coli overexpression strains.


title: Full-length_cjejuni_416826 2

description:
slide416826 Ch2
Recombinant protein (cDNA library).
HaloTag-fusion proteins derived from Campylobacter jejuni cDNA and expressed in Acella E. coli overexpression strains.

hyb_protocol: Fusion proteins were spotted and coupled to the microarray surface for one hour at room temperature with 70% humidity. Slides were washed three times with PBSI (PBS + 0.01% Igepal). Incubation with primary antibody (rabbit polyclonal to C. jejuni) and secondary antibody (goat polyclonal to rabbit, Chromeo-546 conjugated) were performed for 1.5 h each, with washing (three times) with PBSI after each incubation step. Slides were dried with nitrogen and scanned afterwards. Primary antibody: anti-Campylobacter jejuni (Acris AP24002PU-N, Lot#3F17910).


title: Full-length_cjejuni_416826 1

description:
slide416826 Ch1
Recombinant protein (cDNA library).
HaloTag-fusion proteins derived from Campylobacter jejuni cDNA and expressed in Acella E. coli overexpression strains.


title: Full-length_cjejuni_416033 6

description:
slide416033 Ch6
Recombinant protein (cDNA library).
HaloTag-fusion proteins derived from Campylobacter jejuni cDNA and expressed in Acella E. coli overexpression strains.

data_processing:
From the raw data, the corrected median fluorescent intensities (F532 median - B532) were used. Then, relative fluorescence intensities (rfis) were calculated by subtracting each corresponding compartment by the compartment incubated only with secondary antibody. This acknowledges the presence of unspecific interactions of the secondary antibody to the samples. Next, the normalized value was calculated by dividing the rfi of each sample with the median signal of all sample spots within a compartment. Next, a median value was calculated for each set of sample replicates and these median values were used to calculate a Q-value = [median normalized rfi (sample)]/[median normalized rfi(positive control)]for each positive reference used. Additionally, the error was calculated by error propagation according to Gauss. If the Q-value of the positive reference (taking the error into account) was below that of any negative control, the test was discarded.

Raw data file: GSE45520_416033.gpr


title: Full-length_cjejuni_416033 4

description:
slide416033 Ch4
Recombinant protein (cDNA library).
HaloTag-fusion proteins derived from Campylobacter jejuni cDNA and expressed in Acella E. coli overexpression strains.


title: Full-length_cjejuni_416033 5

description:
slide416033 Ch5
Recombinant protein (cDNA library).
HaloTag-fusion proteins derived from Campylobacter jejuni cDNA and expressed in Acella E. coli overexpression strains.


title: Full-length_cjejuni_416033 3

description:
slide416033 Ch3
Recombinant protein (cDNA library).
HaloTag-fusion proteins derived from Campylobacter jejuni cDNA and expressed in Acella E. coli overexpression strains.


title: mouse 2 tamox treated

city: Berkeley

first: Kwan

last: Chow

state: CA

address: 439 LSA

institute: UC Berkeley

description: pDC differentiated in Gfi1 and Gfi1b-deficient background

hyb_protocol: Following fragmentation, 5 ug of fragmented cRNA was hybridized for 18 hr at 45C on GeneChip Mouse Gene 1.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: data was processed using GenePattern (Broad Institute) platform with floor threshold set as 20 and ceiling threshold set as 20000

organism: Mus musculus

source_name: ex vivo differentiated pDCs

label_protocol: Integrity of total RNAs were checked with Bioanalyzer. Biotinylated cRNA were prepared from the total RNA according to the manufacturer's recommendation (NuGen, San Carlos, CA) from 200ng of total RNA.

growth_protocol: total bone marrow cells were cultured in RPMI 1640 medium supplemented with 10% (vol/vol) FCS, L-glutamine (2 mM), penicillin (100 g/ml), streptomycin (100 g/ml), 2-mercaptoethanol (50 mM), and 25ng/ml Flt-3L.

extract_protocol: B220+CD11c+ pDCs were sorted, total RNA was extracted using TRIZOL reagent, then purified with QIAGEN RNAeasy mini kit columns

treatment_protocol: Half the cells were treated with 1uM tamoxifen during differentiation, the other half untreated

tag: genotype

value: Gfi1f/f; Gfi1bf/f; ERCre

tag: agent

value: 1uM tamoxifen


title: mouse 3 tamox treated


title: mouse 1 tamox treated


title: Full-length_cjejuni_416033 2

description:
slide416033 Ch2
Recombinant protein (cDNA library).
HaloTag-fusion proteins derived from Campylobacter jejuni cDNA and expressed in Acella E. coli overexpression strains.


title: Full-length_cjejuni_416033 1

description:
slide416033 Ch1
Recombinant protein (cDNA library).
HaloTag-fusion proteins derived from Campylobacter jejuni cDNA and expressed in Acella E. coli overexpression strains.


title: Immunoscreening C. jejuni 4, replicate 2

description:
slide416366
Recombinant protein (cDNA library).
Crude lysate Acella E. coli + recombinantly expressed proteins.

data_processing: From the raw data, the corrected median fluorescent intensities (F532 median - B532) were used. Then, relative fluorescence intensities (rfis) were calculated by subtracting the fluorescent intensities of the top compartment by the ones from the bottom compartment. This acknowledges the presence of unspecific interactions of the secondary antibody to the samples. If these values were negative, they were set to zero prior to contrast calculation; otherwise, the contrast formula will not work properly. Next, the contrast method was applied by calculating the contrast for each spot of the top compartment. C = [rfi(sample) - median rfi(negative reference)]/[rfi(sample) + median rfi(negative reference)].

source_name: HaloTag-fusion proteins derived from Campylobacter jejuni cDNA and expressed in Acella E. coli overexpression strains


title: Immunoscreening C. jejuni 4, replicate 3

description:
slide416367
Recombinant protein (cDNA library).
Crude lysate Acella E. coli + recombinantly expressed proteins.


title: mouse 2 untreated

description: pDC differentiated in wildtype condition


title: mouse 3 untreated


title: SATB1 WT HSC #2

city: Bronx

first: Boris

last: Bartholdy

state: NY

address: 1300 Morris Park Ave

department: Cell Biology

institute: Albert Einstein College of Medicine

hyb_protocol: Following fragmentation, ~5 microg of cRNA were hybridized for 16 hr at 45C on GeneChip® Mouse Gene 1.0 ST microarrays (Affymetrix). GeneChips were washed and stained in an Affymetrix Fluidics Station.

scan_protocol: GeneChip® Scanner 3000 7G system (Affymetrix) according to standard protocols.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings. CEL files were generated and processed/normalized using the R package Affy to generate probeset-level signal intensity data.

source_name: sorted HSC from murine bone marrow, SATB1 WT

label_protocol: Biotinylated cRNA were prepared using the GeneChip® WT terminal labeling kit (Affymetrix) according to the manufacturer's instructions.

growth_protocol: Uncultured primary cells.

extract_protocol: Total RNA was extracted using Qiagen's RNeasy Micro kit according to the manufacturer's instructions. After checking the quality of RNA with an Agilent 2100 Bioanalyzer, total RNA was amplified utilizing the Single Primer Isothermal Amplification (SPIA®Nugen Ovation pico WTA) system according to the manufacturer's instructions.

treatment_protocol: No treatment.

tag: strain/background

value: SATB1 wild-type


title: SATB1 KO HSC #2

source_name: sorted HSC from murine bone marrow, SATB1 KO

value: SATB1 knockout


title: mouse 1 untreated


title: SATB1 WT HSC #1


title: Immunoscreening C. jejuni 4, replicate 1

description:
slide416304
Recombinant protein (cDNA library).
Crude lysate Acella E. coli + recombinantly expressed proteins.


title: SATB1 KO HSC #1


title: Chicken Abdominal fat, high (HG) versus low (LG) growth lines, 11 week of age, replicate 4

city: Newark

first: Larry

middle: Albert

last: Cogburn

state: DE

address: 531 South College Ave.

department: Animal and Food Sciences

institute: University of Delaware

hyb_protocol: A cDNA spotted glass slide (Del-Mar 14K Chicken Integrated Systems microarray) was pre-treated for 45 min at 42 degrees Celsius in pre-hybridization solution containing 5x SSC, 0.1 % SDS and 1 % BSA and followed by dipping for 5 min in deionized water and dry spinning for 5 min at 1,000 x g. The labeled cDNA was dried down (Speed Vac) and reconstituted prior to hybridization in a 30 microliter volume of pre-warm DIG Easy Hyb solution (Roche Diagnostics; Indianapolis, IN). The two target samples (Alexa 555 and Alexa 647 labeled) were pooled and mixed with 2.5 microliter of 10 mg/ml Yeast tRNA, 2.5 microliter of 10 mg/ml salmon testes DNA (Sigma, Louis, MO) and 2.5 microliter of 1 microgram/microliter of pSport 6.1(Invitrogen) vector (PCR amplified product from “empty” pSport 6.1 vector sequence). The target mixture was denatured for 2 min at 94 degrees Celsius, cooled at room temperature, carefully loaded onto the middle of a pre-treated mircoarray slide held in a hybridization chamber (Corning #2551, Lowell, MA) and overlaid with a 22 x 65 mm LifterSlip (Erie Scientific, Portsmouth, NH). The sealed hybridization chamber was incubated overnight (approximately 16 hours) at 42 degrees Celsius in a water bath under a light-tight box. On the following day, slides were sequentially washed with 1 x SSC, 0.2% SDS, and 0.5% DTT at 50 degrees C for 10 min, then 0.1 x SSC, 0.2% SDS, and 0.5% DTT for 5 min at room temperature, and finally 0.1 x SSC and 0.5% DTT for 1 min at room temperature, with nitrogen gas bubbled through each of the washes to prevent interference from ozone. The slides were subsequently rinsed in dH2O and dried by centrifugation. Slides were stored until scanning in individual 50 ml tubes covered in aluminum foil and filled with nitrogen gas.

scan_protocol: Each microarray slide was scanned using a GenePix 4000B microarray scanner (Molecular Devices; Sunnyvale, CA) set at 635 nm for Alexa647 and 532 nm for Alexa555 after adjustment of the PMT count ratio (635/532) to 1. Two high-resolution TIFF images (embedded in a single file) were generated for each slide.

data_processing: Image analysis was performed on high-resolution TIFF images using GenePix Pro 4.1 (Molecular Devices, Sunnyvale, CA). The results of image analysis [GenePix Report (GPR) files] were automatically merged with Excel files containing the clone identification number/plate address and gene name/function (from the highest BLAST score). Fluorescence intensities were analyzed with the linear mixed model (MIXED) procedure in SAS (SAS Institute Inc., Cary, NC, USA).

label: Alexa Flour 647

organism: Gallus gallus

label_protocol: Twenty micrograms of total RNA were indirectly labeled using SuperScript Plus Indirect cDNA Labeling System (Invitrogen, Carlsbad, CA). Briefly, the first strand cDNA synthesis was performed in a 30 microliter final volume containing 1x first-strand buffer, 5 micrograms of anchored oligo(dT)20, DTT, dNTP mix (including aminoallyl- and aminohexyl-modified nucleotides), 40 U of RNaseOUT and 800 U of SuperScript III reverse transcriptase with an incubation at 46 degrees Celsius for 3 hours. The original RNA was destroyed by NaOH hydrolysis and followed by neutralization with HCl. The cDNAs were purified using a low-elution volume spin cartridge (Invitrogen; Carlsbad, CA) and labeled with either Alexa Fluor 555 or Alexa Fluor 647 succinimidyl ester in the dark at room temperature for 2 hours. After purification of labeled cDNAs with a low-elution-volume spin cartridge, the efficiency of dye incorporation was determined using the Microarray Module on the NanoDrop ND-1000 spectrophotometer and the Base:Dye Ratio Calculator on the Invitrogen website.

growth_protocol: Standard broiler chicken growth protocol

extract_protocol: Total RNA was extracted using a RNeasy Midi kit according to the manufacturer’s protocol (Qiagen; Valencia, CA). The RNA concentration was determined with a NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies; Wilmington, DE). RNA integrity was examined using a RNA 6000 Nano Assay kit and the Model 2100 Bioanalyzer (Agilent Technologies; Palo Alto, CA).

treatment_protocol: Divergently selected on body weight (HG genotype).

value: abdominal adipose

value: HG cockerel

tag: age

value: 11 week of age

label: Alexa Flour 555

value: LG cockerel


title: 51 year old human aortic valve leaflets

city: Boeblingen

first: Shannon

last: Layland

address: Nobelstrasse 12

institute: Fraunhofer IGB

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Data normalized with variance stabilizing normalization (VSN)

source_name: aortic valve leaflets

label_protocol: illumina standard labeling

extract_protocol: Total RNA was extracted from FFPE tissues with RNeasy FFPE-kit (#74404 and #73504) and from cryopreserved tissue with Microarray RNeasy Kit (#76163) from Qiagen. Quality control was performed with the Agilent BioAnalyzer 2100.

value: 51 year old

tag: pretreatment

value: Cryopreservation


title: Chicken Abdominal fat, high (HG) versus low (LG) growth lines, 11 week of age, replicate 2


title: Chicken Abdominal fat, high (HG) versus low (LG) growth lines, 11 week of age, replicate 3


title: Chicken Abdominal fat, high (HG) versus low (LG) growth lines, 9 week of age, replicate 4

value: 9 week of age


title: Chicken Abdominal fat, high (HG) versus low (LG) growth lines, 11 week of age, replicate 1


title: Chicken Abdominal fat, high (HG) versus low (LG) growth lines, 9 week of age, replicate 3


title: 17 year old human aortic valve leaflets

value: 17 year old


title: Chicken Abdominal fat, high (HG) versus low (LG) growth lines, 9 week of age, replicate 1


title: 53 year old human aortic valve leaflets

value: 53 year old


title: Chicken Abdominal fat, high (HG) versus low (LG) growth lines, 7 week of age, replicate 4

value: 7 week of age


title: Chicken Abdominal fat, high (HG) versus low (LG) growth lines, 7 week of age, replicate 3


title: Chicken Abdominal fat, high (HG) versus low (LG) growth lines, 7 week of age, replicate 2


title: 55 year old human aortic valve leaflets

value: 55 year old


title: 18 year old human aortic valve leaflets

value: 18 year old


title: 14 week human fetal semilunar valve

source_name: fetal semilunar valve leaflets

value: fetal 14 week

value: FFPE


title: Chicken Abdominal fat, high (HG) versus low (LG) growth lines, 5 week of age, replicate 4

value: 5 week of age


title: Chicken Abdominal fat, high (HG) versus low (LG) growth lines, 7 week of age, replicate 1


title: Chicken Abdominal fat, high (HG) versus low (LG) growth lines, 5 week of age, replicate 3


title: Chicken Abdominal fat, high (HG) versus low (LG) growth lines, 9 week of age, replicate 2


title: 15 week human fetal semilunar valve 2

value: fetal 15 week


title: 14 year old human aortic valve leaflets

value: 14 year old


title: 15 week human fetal semilunar valve 1


title: 19 year old human aortic valve leaflets

value: 19 year old


title: 50 year old human aortic valve leaflets

value: 50 year old


title: 10 week human fetal semilunar valve

value: fetal 10 week


title: 12 week human fetal semilunar valve 1

value: fetal 12 week


title: Chicken Abdominal fat, high (HG) versus low (LG) growth lines, 5 week of age, replicate 2

value: abdominal adipose

value: HG cockerel

value: LG cockerel


title: 9 week human fetal semilunar valve

value: fetal 9 week


title: 12 week human fetal semilunar valve 2


title: 17 week human fetal semilunar valve

value: fetal 17 week


title: Chicken Abdominal fat, high (HG) versus low (LG) growth lines, 5 week of age, replicate 1


title: Chicken Abdominal fat, high (HG) versus low (LG) growth lines, 3 week of age, replicate 4

value: 3 week of age


title: Chicken Abdominal fat, high (HG) versus low (LG) growth lines, 3 week of age, replicate 3


title: Chicken Abdominal fat, high (HG) versus low (LG) growth lines, 3 week of age, replicate 2


title: Chicken Abdominal fat, high (HG) versus low (LG) growth lines, 1 week of age, replicate 4

value: 1 week of age


title: Chicken Abdominal fat, high (HG) versus low (LG) growth lines, 3 week of age, replicate 1


title: Cultured P12 Müller glia, GFP

city: SEATTLE

first: THOMAS

middle: A

last: REH

state: WA

address: 1959 NE PACIFIC STREET

department: BIOLOGICAL STRUCTURE

institute: UNIVERSITY OF WASHINGTON

description: Pooled retinas from 1 litter of P12 WT mice were cultured and infected with Gfp

hyb_protocol: Following fragmentation, cRNA were hybridized on Mouse Gene 1.0 ST Array, washed, and stained as per manufacturer guidelines.

scan_protocol: Genechips were scanned using Affymetrix GeneChip Scanner 3000

data_processing: The data were analyzed with Affymetrix Expression Console Software

source_name: Dissociated P12 WT Müller glial cultures GFP-infected 4dpi

label_protocol: Cy3 RNA were prepared according to the standard Affymetrix protocol from total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: Total RNA was extracted using Picopure RNA Isolation kit (Invitrogen, per manufacturer's instructions) or TRIzol (manufacturer's instructions) and followed with RNA cleaup kit (Qiagen)

value: Müller glia

value: WT

value: GFP

tag: days post-infection


title: Chicken Abdominal fat, high (HG) versus low (LG) growth lines, 1 week of age, replicate 3


title: alascan_spec, rep4

description:
Spec_11_1
Alanine scan of 11mer oligopeptide from cj0669.

hyb_protocol: Slides were blocked using SuperBlock (Pierce) for 2 h at room temperature with mild shaking. Incubation with primary antibody (rabbit polyclonal to C. jejuni or S. enterica) was performed overnight at 4°C with mild shaking in a humidity chamber. Secondary antibody (goat polyclonal to rabbit, Chromeo-546 conjugated) was incubated for 1.5 h with mild shaking at room temperature in the dark. After each incubation step, the slides were washed three times with PBSI (PBS + 0.05% IGEPAL). Slides were dried with nitrogen and scanned afterwards. Primary antibody: anti-Salmonella (Abcam ab35156, Lot# GR44107).

scan_protocol: Fluorescent array images were collected for Cy3 with a GenePix 4000A fluorescent scanner and a PMT gain of 500. Image intensity data were extracted and analyzed using Origin Pro 8G.

data_processing:
From the raw data, the corrected median fluorescent intensities (F532 median - B532) were used. Then, relative fluorescence intensities (rfis) were calculated by subtracting the fluorescent intensities of the chamber incubated with secondary antibody from the other chambers. This was done for all of the samples except the positive control rabbit IgG, as the secondary antibody (goat antibody to rabbit IgG) is supposed to bind at this site. This acknowledges the presence of unspecific interactions of the secondary antibody to the samples.

Raw data file: GSE45556_A11.gpr

source_name: cj0669 peptide

tag: strain


title: alascan_spec, rep3

description:
Spec_10_2
Alanine scan of 11mer oligopeptide from cj0669.

hyb_protocol: Slides were blocked using SuperBlock (Pierce) for 2 h at room temperature with mild shaking. Incubation with primary antibody (rabbit polyclonal to C. jejuni or S. enterica) was performed overnight at 4°C with mild shaking in a humidity chamber. Secondary antibody (goat polyclonal to rabbit, Chromeo-546 conjugated) was incubated for 1.5 h with mild shaking at room temperature in the dark. After each incubation step, the slides were washed three times with PBSI (PBS + 0.05% IGEPAL). Slides were dried with nitrogen and scanned afterwards. Primary antibody: anti-E. coli (MicroMol #322).

data_processing:
From the raw data, the corrected median fluorescent intensities (F532 median - B532) were used. Then, relative fluorescence intensities (rfis) were calculated by subtracting the fluorescent intensities of the chamber incubated with secondary antibody from the other chambers. This was done for all of the samples except the positive control rabbit IgG, as the secondary antibody (goat antibody to rabbit IgG) is supposed to bind at this site. This acknowledges the presence of unspecific interactions of the secondary antibody to the samples.

Raw data file: GSE45556_A10.gpr


title: alascan_spec, rep5

description:
Spec_11_2
Alanine scan of 11mer oligopeptide from cj0669.


title: Hes5-GFP, P0

description: Dissociated retinas from P0 Hes5-GFP+ mice were FAC-sorted

source_name: FAC-sorted P0 Hes5-GFP+ progenitors

value: Progenitors

value: No infection


title: Hes5-GFP, P7

description: Dissociated retinas from P7 Hes5-GFP+ mice were FAC-sorted

source_name: FAC-sorted P7 Hes5-GFP+ progenitors/Müller glia

value: Progenitors/Müller glia


title: alascan_spec, rep1

description:
Spec_6_2
Alanine scan of 11mer oligopeptide from cj0669.

data_processing:
From the raw data, the corrected median fluorescent intensities (F532 median - B532) were used. Then, relative fluorescence intensities (rfis) were calculated by subtracting the fluorescent intensities of the chamber incubated with secondary antibody from the other chambers. This was done for all of the samples except the positive control rabbit IgG, as the secondary antibody (goat antibody to rabbit IgG) is supposed to bind at this site. This acknowledges the presence of unspecific interactions of the secondary antibody to the samples.

Raw data file: GSE45556_A6.gpr


title: Chicken Abdominal fat, high (HG) versus low (LG) growth lines, 1 week of age, replicate 1

tag: genotype:


title: Cultured P12 Müller glia, Ascl1

description: Pooled retinas from 1 litter of P12 WT mice were cultured and infected with Ascl1

source_name: Dissociated P12 WT Müller glial cultures ASCL1-infected 4dpi


title: Hes5-GFP, P10

description: Dissociated retinas from P10 Hes5-GFP+ mice were FAC-sorted

source_name: FAC-sorted P10 Hes5-GFP+ Müller glia


title: Chicken Abdominal fat, high (HG) versus low (LG) growth lines, 1 week of age, replicate 2

tag: tissue


title: Hes5-GFP, P14

description: Dissociated retinas from P14 Hes5-GFP+ mice were FAC-sorted

source_name: FAC-sorted P14 Hes5-GFP+ Müller glia


title: Hes5-GFP, P21

description: Dissociated retinas from P21 Hes5-GFP+ mice were FAC-sorted

source_name: FAC-sorted P21 Hes5-GFP+ Müller glia


title: alascan_spec, rep2

description:
Spec_10_1
Alanine scan of 11mer oligopeptide from cj0669.


title: alascan, rep5

description:
8_2
Alanine scan of 11mer oligopeptide from cj0669.

hyb_protocol: Slides were blocked using SuperBlock (Pierce) for 2 h at room temperature with mild shaking. Incubation with primary antibody (rabbit polyclonal to C. jejuni or S. enterica) was performed overnight at 4°C with mild shaking in a humidity chamber. Secondary antibody (goat polyclonal to rabbit, Chromeo-546 conjugated) was incubated for 1.5 h with mild shaking at room temperature in the dark. After each incubation step, the slides were washed three times with PBSI (PBS + 0.05% IGEPAL). Slides were dried with nitrogen and scanned afterwards. Primary antibody: anti-Campylobacter jejuni (Acris AP24002PU-N, Lot#3F17910).

data_processing:
From the raw data, the corrected median fluorescent intensities (F532 median - B532) were used. Then, relative fluorescence intensities (rfis) were calculated by subtracting the fluorescent intensities of the chamber incubated with secondary antibody from the other chambers. This was done for all of the samples except the positive control rabbit IgG, as the secondary antibody (goat antibody to rabbit IgG) is supposed to bind at this site. This acknowledges the presence of unspecific interactions of the secondary antibody to the samples.

Raw data file: GSE45556_A8.gpr


title: alascan, rep3

description:
7_2
Alanine scan of 11mer oligopeptide from cj0669.

data_processing:
From the raw data, the corrected median fluorescent intensities (F532 median - B532) were used. Then, relative fluorescence intensities (rfis) were calculated by subtracting the fluorescent intensities of the chamber incubated with secondary antibody from the other chambers. This was done for all of the samples except the positive control rabbit IgG, as the secondary antibody (goat antibody to rabbit IgG) is supposed to bind at this site. This acknowledges the presence of unspecific interactions of the secondary antibody to the samples.

Raw data file: GSE45556_A7.gpr


title: alascan, rep4

description:
8_1
Alanine scan of 11mer oligopeptide from cj0669.

hyb_protocol: Slides were blocked using SuperBlock (Pierce) for 2 h at room temperature with mild shaking. Incubation with primary antibody (rabbit polyclonal to C. jejuni or S. enterica) was performed overnight at 4°C with mild shaking in a humidity chamber. Secondary antibody (goat polyclonal to rabbit, Chromeo-546 conjugated) was incubated for 1.5 h with mild shaking at room temperature in the dark. After each incubation step, the slides were washed three times with PBSI (PBS + 0.05% IGEPAL). Slides were dried with nitrogen and scanned afterwards. Primary antibody: anti-Campylobacter jejuni (Abd Serotec 1744-9035, Lot#110810).


title: Epitopset2_spec, rep5

description:
S2_11_2
15mer oligopeptides with an overlap of 11 residues comprising the entire sequence of a set of proteins from C. jejuni NCTC 11168.

hyb_protocol: Slides were blocked using SuperBlock (Pierce) for 2 h at room temperature with mild shaking. Incubation with primary antibody (rabbit polyclonal to C. jejuni, E. coli or S. enterica) was performed overnight at 4°C with mild shaking in a humidity chamber. Secondary antibody (goat polyclonal to rabbit, Chromeo-546 conjugated) was incubated for 1.5 h with mild shaking at room temperature in the dark. After each incubation step, the slides were washed three times with PBSI (PBS + 0.05% IGEPAL). Slides were dried with nitrogen and scanned afterwards. Primary antibody: anti-E. coli (MicroMol #322).

data_processing:
From the raw data, the corrected median fluorescent intensities (F532 median - B532) were used. Then, relative fluorescence intensities (rfis) were calculated by subtracting the fluorescent intensities of the chamber incubated with secondary antibody from the other chambers. This was done for all of the samples except for the positive control rabbit IgG, as the secondary antibody (goat antibody to rabbit IgG) is supposed to bind at this site. This acknowledges the presence of unspecific interactions of the secondary antibody to the samples.

Raw data file: GSE45542_S2_11.gpr

source_name: oligopeptide


title: alascan, rep2

description:
7_1
Alanine scan of 11mer oligopeptide from cj0669.


title: Cyp17i_Cre.Input.saline.3

city: Pullman

first: Ryan

last: Evanoff

department: School of Molecular Biosciences

institute: Washington State University

description: total RNA

hyb_protocol: Fragmented, biotin labeled cDNA was hybridized for 16 hr at 45C on GeneChip Mouse Gene ST 1.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

data_processing: Array output was normalized using the RMA algorithm, and data analysis was conducted using GeneSpring (Version 11.0.2; Agilent Technologies).

source_name: Cyp17i_Cre:Ribotag mouse testes - input sample, saline treated

label_protocol: Approximately 100 ng total RNA from each sample was used to generate cDNA using the Ovation RNA Amplification System V2 (NuGEN, San Carlos, CA) according to the manufacturer's instructions.  3.75ug of the cDNA was then fragmented and labelled using the Encore Biotin Module (NuGEN, San Carlos, CA) according to the manufacturer's instructions.

extract_protocol: Total RNA was extracted using the Rneasy kit from Qiagen according to the manufacturer's protocol.

treatment_protocol: For in vivo LH treatment experiments, mice were injected with the GnRH antagonist acyline for 4 days before a single injection of purified human LH. After treatment, testes were homogenized and polysomes were immunoprecipitated by utilizing an anti-HA antibody. RNA was extracted, labelled, and hybridized to Mouse Gene ST 1.0 arrays.

value: mouse testes

tag: sample type

value: input

tag: antibody

tag: treatment

value: saline


title: Epitopset2_spec, rep4

description:
S2_11_1
15mer oligopeptides with an overlap of 11 residues comprising the entire sequence of a set of proteins from C. jejuni NCTC 11168.

hyb_protocol: Slides were blocked using SuperBlock (Pierce) for 2 h at room temperature with mild shaking. Incubation with primary antibody (rabbit polyclonal to C. jejuni, E. coli or S. enterica) was performed overnight at 4°C with mild shaking in a humidity chamber. Secondary antibody (goat polyclonal to rabbit, Chromeo-546 conjugated) was incubated for 1.5 h with mild shaking at room temperature in the dark. After each incubation step, the slides were washed three times with PBSI (PBS + 0.05% IGEPAL). Slides were dried with nitrogen and scanned afterwards. Primary antibody: anti-Salmonella (Abcam ab35156, Lot# GR44107).


title: Cyp17i_Cre.IP.saline.1

description: polysome associated RNA

molecule: other

source_name: Cyp17i_Cre:Ribotag mouse testes - IP sample, saline treated

tag: genotype/variation

value: IP

value: anti-HA


title: Cyp17i_Cre.IP.Acyline.LH.1h.1

description: polysome associated RNA

source_name: Cyp17i_Cre:Ribotag mouse testes - IP sample, acyline treated + LH treated 1 hour


title: Cyp17i_Cre.IP.Acyline.2

description: polysome associated RNA

source_name: Cyp17i_Cre:Ribotag mouse testes - IP sample, acyline treated

value: acyline


title: Cyp17i_Cre.Input.saline.1

description: total RNA


title: Cyp17i_Cre.IP.saline.3

description: polysome associated RNA


title: Cyp17i_Cre.Input.saline.2

description: total RNA


title: Cyp17i_Cre.IP.Acyline.LH.4h.1

description: polysome associated RNA

source_name: Cyp17i_Cre:Ribotag mouse testes - IP sample, acyline treated + LH treated 4 hours


title: Epitopset2_spec, rep2

description:
S2_10_1
15mer oligopeptides with an overlap of 11 residues comprising the entire sequence of a set of proteins from C. jejuni NCTC 11168.

data_processing:
From the raw data, the corrected median fluorescent intensities (F532 median - B532) were used. Then, relative fluorescence intensities (rfis) were calculated by subtracting the fluorescent intensities of the chamber incubated with secondary antibody from the other chambers. This was done for all of the samples except for the positive control rabbit IgG, as the secondary antibody (goat antibody to rabbit IgG) is supposed to bind at this site. This acknowledges the presence of unspecific interactions of the secondary antibody to the samples.

Raw data file: GSE45542_S2_10.gpr


title: Full-length_cjejuni_1001 Ch5

description:
slide1001 Ch5
Recombinant protein (cDNA library).
HaloTag-fusion proteins derived from Campylobacter jejuni cDNA and expressed in Acella E. coli overexpression strains.

data_processing:
From the raw data, the corrected median fluorescent intensities (F532 median - B532) were used. Then, relative fluorescence intensities (rfis) were calculated by subtracting each corresponding compartment by the compartment incubated only with secondary antibody. This acknowledges the presence of unspecific interactions of the secondary antibody to the samples. Next, the normalized value was calculated by dividing the rfi of each sample with the median signal of all sample spots within a compartment. Next, a median value was calculated for each set of sample replicates and these median values were used to calculate a Q-value = [median normalized rfi (sample)]/[median normalized rfi(positive control)]for each positive reference used. Additionally, the error was calculated by error propagation according to Gauss. If the Q-value of the positive reference (taking the error into account) was below that of any negative control, the test was discarded.

Raw data file: GSE45520_1001.gpr

source_name: crude lysate Acella E. coli + recombinantly expressed proteins


title: Cyp17i_Cre.IP.Acyline.LH.4h.2

description: polysome associated RNA


title: Cyp17i_Cre.IP.saline.2

description: polysome associated RNA


title: Cyp17i_Cre.IP.Acyline.LH.1h.2

description: polysome associated RNA


title: Cyp17i_Cre.IP.Acyline.1

description: polysome associated RNA


title: Epitopset2_spec, rep3

description:
S2_10_2
15mer oligopeptides with an overlap of 11 residues comprising the entire sequence of a set of proteins from C. jejuni NCTC 11168.


title: Full-length_cjejuni_1001 Ch6

description:
slide1001 Ch6
Recombinant protein (cDNA library).
HaloTag-fusion proteins derived from Campylobacter jejuni cDNA and expressed in Acella E. coli overexpression strains.


title: alascan, rep1

description:
6_1
Alanine scan of 11mer oligopeptide from cj0669.


title: AMH_Cre.IP.saline.3

description: polysome associated RNA

source_name: AMH_Cre:Ribotag mouse testes - IP sample, saline treated


title: Full-length_cjejuni_1001 Ch4

description:
slide1001 Ch4
Recombinant protein (cDNA library).
HaloTag-fusion proteins derived from Campylobacter jejuni cDNA and expressed in Acella E. coli overexpression strains.


title: Epitopset2_spec, rep1

description:
S2_6_2
15mer oligopeptides with an overlap of 11 residues comprising the entire sequence of a set of proteins from C. jejuni NCTC 11168.

data_processing:
From the raw data, the corrected median fluorescent intensities (F532 median - B532) were used. Then, relative fluorescence intensities (rfis) were calculated by subtracting the fluorescent intensities of the chamber incubated with secondary antibody from the other chambers. This was done for all of the samples except for the positive control rabbit IgG, as the secondary antibody (goat antibody to rabbit IgG) is supposed to bind at this site. This acknowledges the presence of unspecific interactions of the secondary antibody to the samples.

Raw data file: GSE45542_S2_6.gpr


title: AMH_Cre.IP.saline.5

description: polysome associated RNA


title: AMH_Cre.IP.saline.4

description: polysome associated RNA


title: AMH_Cre.IP.saline.2

description: polysome associated RNA


title: AMH_Cre.IP.Centro.T.1

description: polysome associated RNA

source_name: AMH_Cre:Ribotag mouse testes - input sample, centrorelix treated + testosterone treated

value: cetrorelix+Testosterone


title: AMH_Cre.IP.saline.1

description: polysome associated RNA


title: AMH_Cre.IP.Centro.T.2

description: polysome associated RNA


title: Epitopset2, rep5

description:
S2_8_2
15mer oligopeptides with an overlap of 11 residues comprising the entire sequence of a set of proteins from C. jejuni NCTC 11168.

hyb_protocol: Slides were blocked using SuperBlock (Pierce) for 2 h at room temperature with mild shaking. Incubation with primary antibody (rabbit polyclonal to C. jejuni, E. coli or S. enterica) was performed overnight at 4°C with mild shaking in a humidity chamber. Secondary antibody (goat polyclonal to rabbit, Chromeo-546 conjugated) was incubated for 1.5 h with mild shaking at room temperature in the dark. After each incubation step, the slides were washed three times with PBSI (PBS + 0.05% IGEPAL). Slides were dried with nitrogen and scanned afterwards. Primary antibody: anti-Campylobacter jejuni (Acris AP24002PU-N, Lot#3F17910).

data_processing:
From the raw data, the corrected median fluorescent intensities (F532 median - B532) were used. Then, relative fluorescence intensities (rfis) were calculated by subtracting the fluorescent intensities of the chamber incubated with secondary antibody from the other chambers. This was done for all of the samples except for the positive control rabbit IgG, as the secondary antibody (goat antibody to rabbit IgG) is supposed to bind at this site. This acknowledges the presence of unspecific interactions of the secondary antibody to the samples.

Raw data file: GSE45542_S2_8.gpr


title: Full-length_cjejuni_1001 Ch2

description:
slide1001 Ch2
Recombinant protein (cDNA library).
HaloTag-fusion proteins derived from Campylobacter jejuni cDNA and expressed in Acella E. coli overexpression strains.


title: Full-length_cjejuni_1001 Ch3

description:
slide1001 Ch3
Recombinant protein (cDNA library).
HaloTag-fusion proteins derived from Campylobacter jejuni cDNA and expressed in Acella E. coli overexpression strains.


title: Epitopset2, rep3

description:
S2_7_2
15mer oligopeptides with an overlap of 11 residues comprising the entire sequence of a set of proteins from C. jejuni NCTC 11168.

data_processing:
From the raw data, the corrected median fluorescent intensities (F532 median - B532) were used. Then, relative fluorescence intensities (rfis) were calculated by subtracting the fluorescent intensities of the chamber incubated with secondary antibody from the other chambers. This was done for all of the samples except for the positive control rabbit IgG, as the secondary antibody (goat antibody to rabbit IgG) is supposed to bind at this site. This acknowledges the presence of unspecific interactions of the secondary antibody to the samples.

Raw data file: GSE45542_S2_7.gpr


title: Full-length_cjejuni_1001 Ch1

description:
slide1001 Ch1
Recombinant protein (cDNA library).
HaloTag-fusion proteins derived from Campylobacter jejuni cDNA and expressed in Acella E. coli overexpression strains.


title: Full-length_cjejuni_1000 Ch6

description:
slide1000 Ch6
Recombinant protein (cDNA library).
HaloTag-fusion proteins derived from Campylobacter jejuni cDNA and expressed in Acella E. coli overexpression strains.

data_processing:
From the raw data, the corrected median fluorescent intensities (F532 median - B532) were used. Then, relative fluorescence intensities (rfis) were calculated by subtracting each corresponding compartment by the compartment incubated only with secondary antibody. This acknowledges the presence of unspecific interactions of the secondary antibody to the samples. Next, the normalized value was calculated by dividing the rfi of each sample with the median signal of all sample spots within a compartment. Next, a median value was calculated for each set of sample replicates and these median values were used to calculate a Q-value = [median normalized rfi (sample)]/[median normalized rfi(positive control)]for each positive reference used. Additionally, the error was calculated by error propagation according to Gauss. If the Q-value of the positive reference (taking the error into account) was below that of any negative control, the test was discarded.

Raw data file: GSE45520_1000.gpr


title: AMH_Cre.IP.Centro.1

description: polysome associated RNA

source_name: AMH_Cre:Ribotag mouse testes - input sample, centrorelix treated

value: cetrorelix


title: Epitopset2, rep4

description:
S2_8_1
15mer oligopeptides with an overlap of 11 residues comprising the entire sequence of a set of proteins from C. jejuni NCTC 11168.

hyb_protocol: Slides were blocked using SuperBlock (Pierce) for 2 h at room temperature with mild shaking. Incubation with primary antibody (rabbit polyclonal to C. jejuni, E. coli or S. enterica) was performed overnight at 4°C with mild shaking in a humidity chamber. Secondary antibody (goat polyclonal to rabbit, Chromeo-546 conjugated) was incubated for 1.5 h with mild shaking at room temperature in the dark. After each incubation step, the slides were washed three times with PBSI (PBS + 0.05% IGEPAL). Slides were dried with nitrogen and scanned afterwards. Primary antibody: anti-Campylobacter jejuni (Abd Serotec 1744-9035, Lot#110810).


title: Epitopset2, rep2

description:
S2_7_1
15mer oligopeptides with an overlap of 11 residues comprising the entire sequence of a set of proteins from C. jejuni NCTC 11168.


title: Full-length_cjejuni_1000 Ch5

description:
slide1000 Ch5
Recombinant protein (cDNA library).
HaloTag-fusion proteins derived from Campylobacter jejuni cDNA and expressed in Acella E. coli overexpression strains.

hyb_protocol: Fusion proteins were spotted and coupled to the microarray surface for one hour at room temperature with 70% humidity. Slides were washed three times with PBSI (PBS + 0.01% Igepal). Incubation with primary antibody (rabbit polyclonal to C. jejuni) and secondary antibody (goat polyclonal to rabbit, Chromeo-546 conjugated) were performed for 1.5 h each, with washing (three times) with PBSI after each incubation step. Slides were dried with nitrogen and scanned afterwards. Primary antibody: anti-Campylobacter jejuni (Abd Serotec 1744-9035, Lot#110810).


title: AMH_Cre.IP.Centro.2

description: polysome associated RNA


title: Epitopset2, rep1

description:
S2_6_1
15mer oligopeptides with an overlap of 11 residues comprising the entire sequence of a set of proteins from C. jejuni NCTC 11168.


title: Immunoscreening C. jejuni 3, replicate 3

description:
slide1722
Recombinant protein (cDNA library).
Crude lysate Acella E. coli + recombinantly expressed proteins.

data_processing: From the raw data, the corrected median fluorescent intensities (F532 median - B532) were used. Then, relative fluorescence intensities (rfis) were calculated by subtracting the fluorescent intensities of the top compartment by the ones from the bottom compartment. This acknowledges the presence of unspecific interactions of the secondary antibody to the samples. If these values were negative, they were set to zero prior to contrast calculation; otherwise, the contrast formula will not work properly. Next, the contrast method was applied by calculating the contrast for each spot of the top compartment. C = [rfi(sample) - median rfi(negative reference)]/[rfi(sample) + median rfi(negative reference)].

source_name: HaloTag-fusion proteins derived from Campylobacter jejuni cDNA and expressed in Acella E. coli overexpression strains


title: AMH_Cre.IP.Acyline.FSH_1h.1

description: polysome associated RNA

source_name: AMH_Cre:Ribotag mouse testes - IP sample, acyline treated + FSH treated  for 1 hour


title: Full-length_cjejuni_1000 Ch4

description:
slide1000 Ch4
Recombinant protein (cDNA library).
HaloTag-fusion proteins derived from Campylobacter jejuni cDNA and expressed in Acella E. coli overexpression strains.

hyb_protocol: Fusion proteins were spotted and coupled to the microarray surface for one hour at room temperature with 70% humidity. Slides were washed three times with PBSI (PBS + 0.01% Igepal). Incubation with primary antibody (rabbit polyclonal to C. jejuni) and secondary antibody (goat polyclonal to rabbit, Chromeo-546 conjugated) were performed for 1.5 h each, with washing (three times) with PBSI after each incubation step. Slides were dried with nitrogen and scanned afterwards. Primary antibody: anti-Campylobacter jejuni (Abcam ab22542, Lot#203685).


title: Epitopset1_spec, rep3

description:
7_1
15mer oligopeptides with an overlap of 11 residues comprising the entire sequence of a set of proteins from C. jejuni NCTC 11168.

data_processing:
From the raw data, the corrected median fluorescent intensities (F532 median - B532) were used. Then, relative fluorescence intensities (rfis) were calculated by subtracting the fluorescent intensities of the chamber incubated with secondary antibody from the other chambers. This was done for all of the samples except for the positive control rabbit IgG, as the secondary antibody (goat antibody to rabbit IgG) is supposed to bind at this site. This acknowledges the presence of unspecific interactions of the secondary antibody to the samples.

Raw data file: GSE45542_7.gpr


title: Immunoscreening C. jejuni 3, replicate 2

description:
slide1681
Recombinant protein (cDNA library).
Crude lysate Acella E. coli + recombinantly expressed proteins.

hyb_protocol: Fusion proteins were spotted and coupled to the microarray surface for one hour at room temperature with 70% humidity. Slides were washed three times with PBSI (PBS + 0.01% Igepal). Incubation with primary antibody (rabbit polyclonal to C. jejuni) and secondary antibody (goat polyclonal to rabbit, Chromeo-546 conjugated) were performed for 1.5 h each, with washing (three times) with PBSI after each incubation step. Slides were dried with nitrogen and scanned afterwards. Primary antibody: anti-Campylobacter jejuni (Acris AP24002PU-N, Lot#3F17910).


title: Epitopset1_spec, rep4

description:
7_2
15mer oligopeptides with an overlap of 11 residues comprising the entire sequence of a set of proteins from C. jejuni NCTC 11168.


title: AMH_Cre.IP.Acyline.FSH_4h.2

description: polysome associated RNA

source_name: AMH_Cre:Ribotag mouse testes - IP sample, acyline treated + FSH treated  for 4 hours


title: AMH_Cre.IP.Acyline.FSH_1h.2

description: polysome associated RNA


title: AMH_Cre.IP.Acyline.2

description: polysome associated RNA

source_name: AMH_Cre:Ribotag mouse testes - IP sample, acyline treated


title: AMH_Cre.Input.saline.5

description: total RNA

source_name: AMH_Cre:Ribotag mouse testes - input sample, saline treated


title: AMH_Cre.IP.Acyline.FSH_4h.1

description: polysome associated RNA


title: AMH_Cre.IP.Acyline.1

description: polysome associated RNA


title: AMH_Cre.Input.saline.4

description: total RNA


title: Full-length_cjejuni_1000 Ch3

description:
slide1000 Ch3
Recombinant protein (cDNA library).
HaloTag-fusion proteins derived from Campylobacter jejuni cDNA and expressed in Acella E. coli overexpression strains.


title: AMH_Cre.Input.saline.2

description: total RNA


title: AMH_Cre.Input.saline.3

description: total RNA


title: Full-length_cjejuni_1000 Ch2

description:
slide1000 Ch2
Recombinant protein (cDNA library).
HaloTag-fusion proteins derived from Campylobacter jejuni cDNA and expressed in Acella E. coli overexpression strains.


title: Full-length_cjejuni_1000 Ch1

description:
slide1000 Ch1
Recombinant protein (cDNA library).
HaloTag-fusion proteins derived from Campylobacter jejuni cDNA and expressed in Acella E. coli overexpression strains.


title: Epitopset1_spec, rep1

description:
6_1
15mer oligopeptides with an overlap of 11 residues comprising the entire sequence of a set of proteins from C. jejuni NCTC 11168.

data_processing:
From the raw data, the corrected median fluorescent intensities (F532 median - B532) were used. Then, relative fluorescence intensities (rfis) were calculated by subtracting the fluorescent intensities of the chamber incubated with secondary antibody from the other chambers. This was done for all of the samples except for the positive control rabbit IgG, as the secondary antibody (goat antibody to rabbit IgG) is supposed to bind at this site. This acknowledges the presence of unspecific interactions of the secondary antibody to the samples.

Raw data file: GSE45542_6.gpr


title: AMH_Cre.Input.saline.1

description: total RNA


title: Immunoscreening C. jejuni 2, replicate 2

description:
slide416372
Recombinant protein (cDNA library).
Crude lysate Acella E. coli + recombinantly expressed proteins.


title: Immunoscreening C. jejuni 2, replicate 3

description:
slide416373
Recombinant protein (cDNA library).
Crude lysate Acella E. coli + recombinantly expressed proteins.


title: Epitopset1_spec, rep2

description:
6_2
15mer oligopeptides with an overlap of 11 residues comprising the entire sequence of a set of proteins from C. jejuni NCTC 11168.


title: Epitopset1, rep4

description:
5_2
15mer oligopeptides with an overlap of 11 residues comprising the entire sequence of a set of proteins from C. jejuni NCTC 11168.

data_processing:
From the raw data, the corrected median fluorescent intensities (F532 median - B532) were used. Then, relative fluorescence intensities (rfis) were calculated by subtracting the fluorescent intensities of the chamber incubated with secondary antibody from the other chambers. This was done for all of the samples except for the positive control rabbit IgG, as the secondary antibody (goat antibody to rabbit IgG) is supposed to bind at this site. This acknowledges the presence of unspecific interactions of the secondary antibody to the samples.

Raw data file: GSE45542_5.gpr


title: Full-length_cjejuni_2447 2

description:
slide2447 Ch2
Recombinant protein (cDNA library).
HaloTag-fusion proteins derived from Campylobacter jejuni cDNA and expressed in Acella E. coli overexpression strains.

data_processing:
From the raw data, the corrected median fluorescent intensities (F532 median - B532) were used. Then, relative fluorescence intensities (rfis) were calculated by subtracting each corresponding compartment by the compartment incubated only with secondary antibody. This acknowledges the presence of unspecific interactions of the secondary antibody to the samples. Next, the normalized value was calculated by dividing the rfi of each sample with the median signal of all sample spots within a compartment. Next, a median value was calculated for each set of sample replicates and these median values were used to calculate a Q-value = [median normalized rfi (sample)]/[median normalized rfi(positive control)]for each positive reference used. Additionally, the error was calculated by error propagation according to Gauss. If the Q-value of the positive reference (taking the error into account) was below that of any negative control, the test was discarded.

Raw data file: GSE45520_2447.gpr


title: Full-length_cjejuni_2447 1

description:
slide2447 Ch1
Recombinant protein (cDNA library).
HaloTag-fusion proteins derived from Campylobacter jejuni cDNA and expressed in Acella E. coli overexpression strains.


title: Immunoscreening C. jejuni 1, replicate 3

description:
slide415965
Recombinant protein (cDNA library).
Crude lysate Acella E. coli + recombinantly expressed proteins.


title: Immunoscreening C. jejuni 2, replicate 1

description:
slide415799
Recombinant protein (cDNA library).
Crude lysate Acella E. coli + recombinantly expressed proteins.


title: Epitopset1, rep1

description:
4_1
15mer oligopeptides with an overlap of 11 residues comprising the entire sequence of a set of proteins from C. jejuni NCTC 11168.

data_processing:
From the raw data, the corrected median fluorescent intensities (F532 median - B532) were used. Then, relative fluorescence intensities (rfis) were calculated by subtracting the fluorescent intensities of the chamber incubated with secondary antibody from the other chambers. This was done for all of the samples except for the positive control rabbit IgG, as the secondary antibody (goat antibody to rabbit IgG) is supposed to bind at this site. This acknowledges the presence of unspecific interactions of the secondary antibody to the samples.

Raw data file: GSE45542_4.gpr


title: Full-length_cjejuni_2009 2

description:
slide2009 Ch2
Recombinant protein (cDNA library).
HaloTag-fusion proteins derived from Campylobacter jejuni cDNA and expressed in Acella E. coli overexpression strains.

data_processing:
From the raw data, the corrected median fluorescent intensities (F532 median - B532) were used. Then, relative fluorescence intensities (rfis) were calculated by subtracting each corresponding compartment by the compartment incubated only with secondary antibody. This acknowledges the presence of unspecific interactions of the secondary antibody to the samples. Next, the normalized value was calculated by dividing the rfi of each sample with the median signal of all sample spots within a compartment. Next, a median value was calculated for each set of sample replicates and these median values were used to calculate a Q-value = [median normalized rfi (sample)]/[median normalized rfi(positive control)]for each positive reference used. Additionally, the error was calculated by error propagation according to Gauss. If the Q-value of the positive reference (taking the error into account) was below that of any negative control, the test was discarded.

Raw data file: GSE45520_2009.gpr


title: Immunoscreening C. jejuni 1, replicate 2

description:
slide415964
Recombinant protein (cDNA library).
Crude lysate Acella E. coli + recombinantly expressed proteins.


title: Full-length_cjejuni_2009 1

description:
slide2009 Ch1
Recombinant protein (cDNA library).
HaloTag-fusion proteins derived from Campylobacter jejuni cDNA and expressed in Acella E. coli overexpression strains.


title: Immunoscreening C. jejuni 1, replicate 1

description:
slide415800
Recombinant protein (cDNA library).
Crude lysate Acella E. coli + recombinantly expressed proteins.


title: Myocytes_7days_rep3

city: Poznań

first: Tomasz

middle: Jan

last: Kolanowski

address: Strzeszyńska 32

department: Biology of Reproduction and Stem Cells

country: Poland

institute: Institute of Human Genetics PAS

description: Cells after 7 days of differentiation medium (treated with 2% horse serum).

hyb_protocol: Array hybridisation and washing were conducted according to manufacturer’s protocol using high-density arrays GeneChip Human Gene 1.0 ST (Affymetrix, Santa Clara, CA).

scan_protocol: After washing, microarrays were scanned using the GeneChip Scanner 3000 (Affymetrix, Santa Clara, CA).

data_processing: The CEL files obtained were analysed with the Expression Console software (Affymetrix, Santa Clara, CA) by using Robust Multi-chip Analysis (RMA) to correct the background. For subsequent analysis and feature extraction Subio software (Subio, Japan) was used.

source_name: myoblasts isolated from human skeletal musce

label_protocol: The single stranded DNA was generated using the Ambion WT Expression Kit (Ambion, Austin, USA), followed by fragmentation and labelling of cDNA using the Affymetrix GeneChip WT Terminal Labelling Kit (Affymetrix, Santa Clara, CA).

growth_protocol: The myoblast medium was based on DMEM (Dulbecco Modified Eagle Medium) (with 4.5 g/l glucose, Lonza, Basel, Switzerland ) supplemented with 20% FBS (Fetal Bovine Serum; Lonza, Basel, Switzerland), 1% Ultraglutamine (Lonza, Basel, Switzerland) and antibiotics ( Lonza, Basel, Switzerland). Various concentrations of bFGF (basic Fibroblast Growth Factor; Sigma-Aldrich, St. Louis, USA) were added to the stimulated myoblasts to sustain in vitro proliferation. The cells were passaged at 75% confluence to avoid spontaneous myoblast fusion.

extract_protocol: RNA was obtained from in vitro cultured myoblasts and myocytes using the TriReagent (Sigma-Aldrich, St. Louis, USA) according to the manufacturer’s protocol. Evaluation of RNA integrity and quantity was conducted using the BioAnalyser (Agilent, Santa Clara, USA) and the NanoDrop spectrophotometer (Nanodrop, Wilmington, USA). The samples were prepared in triplicate.

value: differentiated myoblasts


title: Myoblasts_24hrs_rep3

value: undifferentated myoblasts


title: Myocytes_7days_rep1


title: Epitopset1, rep2

description:
4_2
15mer oligopeptides with an overlap of 11 residues comprising the entire sequence of a set of proteins from C. jejuni NCTC 11168.


title: Myoblasts_24hrs_rep1


title: Myocytes_7days_rep2


title: Myoblasts_24hrs_rep2


title: peripheral white blood cell 4014

status: Public on Apr 05 2013

city: Milwaukee

first: Yi

last: Zhang

state: WI

address: 8701 W Watertown Plank Rd

department: Medicine

institute: Medical College of Wisconsin

hyb_protocol: A total of 1.5 µg aRNA was hybridized to Illumina HumanWG-6 version 2 or version 3 chips accoriding to manufacturer’s instructions

scan_protocol: scanned using the Illumina  BeadArrayTM 500GX Reader with Illumina BeadScan image data acquisition software (version 2.3.0.13)

data_processing: Illumina GenomeStudio software (version 2010.3) was used for preliminary data analysis with standard background normalization.

source_name: peripheral white blood cell

label_protocol: Biotin-16-UTP (Roche) labeled aRNA was synthesized using Ambion’s proprietary MEGAscript in vitro transcription IVT) technology and T7 RNA Polymerase. Purification of aRNA samples was carried out using QIAGEN’s RNeasy 96 protocol for RNA cleanup using spin technology.

extract_protocol: 2.5ml blood was collected into a PAXgene® Blood RNA Tube (BD, Franklin Lakes, NJ) following an overnight fast. Total RNA was isolated from each tube using the PAXgene Blood RNA Kit (Qiagen, Valencia, CA) and anti-sense RNA (aRNA) was synthesized using the MessageAmp II-Biotin aRNA kit (Ambion, Austin, TX)

tag: race

value: Caucasian

tag: Sex

value: M


title: peripheral white blood cell 2084

value: F

tag: leptin

tag: adiponectin

tag: fatmass(kg)

tag: fatmass(pct)

tag: leanmass(kg)

tag: leanmass(pct)


title: peripheral white blood cell 4043


title: peripheral white blood cell 3080


title: peripheral white blood cell 2081

tag: age


title: peripheral white blood cell 14054


title: peripheral white blood cell 4438


title: peripheral white blood cell 4025


title: peripheral white blood cell 4709


title: peripheral white blood cell 2080


title: peripheral white blood cell 10200


title: peripheral white blood cell 2082


title: peripheral white blood cell 1210


title: peripheral white blood cell 14053


title: peripheral white blood cell 4708


title: peripheral white blood cell 4707


title: peripheral white blood cell 2083


title: peripheral white blood cell 4696


title: peripheral white blood cell 4711


title: peripheral white blood cell 4686


title: peripheral white blood cell 4710


title: peripheral white blood cell 4689


title: peripheral white blood cell 6012


title: peripheral white blood cell 4688


title: peripheral white blood cell 4678


title: peripheral white blood cell 4706


title: peripheral white blood cell 4687


title: peripheral white blood cell 1359


title: Immunoscreening C. jejuni 3, replicate 1

description:
slide416040
Recombinant protein (cDNA library).
Crude lysate Acella E. coli + recombinantly expressed proteins.


title: peripheral white blood cell 4593


title: peripheral white blood cell 4505


title: peripheral white blood cell 4432


title: peripheral white blood cell 4609


title: peripheral white blood cell 4677


title: peripheral white blood cell 4675


title: peripheral white blood cell 4610


title: Epitopset1, rep3

description:
5_1
15mer oligopeptides with an overlap of 11 residues comprising the entire sequence of a set of proteins from C. jejuni NCTC 11168.

source_name: oligopeptide


title: peripheral white blood cell 4607


title: peripheral white blood cell 4430


title: peripheral white blood cell 4437


title: peripheral white blood cell 4443


title: peripheral white blood cell 4442


title: peripheral white blood cell 4418


title: peripheral white blood cell 4420


title: peripheral white blood cell 4434


title: peripheral white blood cell 4419


title: peripheral white blood cell 4431


title: peripheral white blood cell 4422


title: peripheral white blood cell 4424


title: peripheral white blood cell 4428


title: peripheral white blood cell 4592


title: peripheral white blood cell 4435


title: peripheral white blood cell 4436


title: peripheral white blood cell 4423


title: peripheral white blood cell 4417


title: peripheral white blood cell 4416


title: peripheral white blood cell 4063


title: peripheral white blood cell 4059


title: peripheral white blood cell 4421


title: peripheral white blood cell 4011


title: peripheral white blood cell 4441


title: peripheral white blood cell 4058


title: peripheral white blood cell 4062


title: peripheral white blood cell 3961


title: peripheral white blood cell 3958


title: peripheral white blood cell 4010


title: peripheral white blood cell 3963


title: peripheral white blood cell 3722


title: peripheral white blood cell 3962


title: peripheral white blood cell 4060


title: peripheral white blood cell 4009


title: peripheral white blood cell 4008


title: peripheral white blood cell 3647


title: peripheral white blood cell 3653


title: peripheral white blood cell 3651


title: peripheral white blood cell 3959


title: peripheral white blood cell 3649


title: peripheral white blood cell 3718


title: peripheral white blood cell 3957


title: peripheral white blood cell 3646


title: peripheral white blood cell 3402


title: peripheral white blood cell 3336


title: peripheral white blood cell 3631


title: peripheral white blood cell 3398


title: peripheral white blood cell 3648


title: peripheral white blood cell 3634


title: peripheral white blood cell 3633


title: peripheral white blood cell 3632


title: peripheral white blood cell 3401


title: peripheral white blood cell 3396


title: peripheral white blood cell 3271


title: peripheral white blood cell 3248


title: peripheral white blood cell 3241


title: peripheral white blood cell 3112


title: peripheral white blood cell 3110


title: peripheral white blood cell 3134


title: peripheral white blood cell 3249


title: peripheral white blood cell 3105


title: peripheral white blood cell 3103


title: peripheral white blood cell 3247


title: peripheral white blood cell 2195


title: peripheral white blood cell 2188


title: peripheral white blood cell 3108


title: peripheral white blood cell 3111


title: peripheral white blood cell 2068


title: peripheral white blood cell 2075


title: peripheral white blood cell 2073


title: peripheral white blood cell 3109


title: peripheral white blood cell 3104


title: peripheral white blood cell 2071


title: peripheral white blood cell 3107


title: peripheral white blood cell 2065


title: peripheral white blood cell 2196


title: peripheral white blood cell 2189


title: peripheral white blood cell 2186


title: peripheral white blood cell 2072


title: peripheral white blood cell 2074


title: peripheral white blood cell 2064


title: peripheral white blood cell 2067


title: peripheral white blood cell 2061


title: peripheral white blood cell 2041


title: peripheral white blood cell 2063


title: peripheral white blood cell 2070


title: peripheral white blood cell 2042


title: peripheral white blood cell 2043


title: peripheral white blood cell 2045


title: peripheral white blood cell 2062


title: peripheral white blood cell 3652


title: peripheral white blood cell 2044


title: peripheral white blood cell 2040


title: peripheral white blood cell 1990


title: peripheral white blood cell 1958


title: peripheral white blood cell 1953


title: peripheral white blood cell 1944


title: peripheral white blood cell 2039


title: peripheral white blood cell 1940


title: peripheral white blood cell 1959


title: peripheral white blood cell 1957


title: peripheral white blood cell 1942


title: peripheral white blood cell 1885


title: peripheral white blood cell 1935


title: peripheral white blood cell 1938


title: peripheral white blood cell 1882


title: peripheral white blood cell 1880


title: peripheral white blood cell 1884


title: peripheral white blood cell 1939


title: peripheral white blood cell 1881


title: peripheral white blood cell 1826


title: peripheral white blood cell 1821


title: peripheral white blood cell 1937


title: peripheral white blood cell 1879


title: peripheral white blood cell 1886


title: peripheral white blood cell 1536


title: peripheral white blood cell 1819


title: peripheral white blood cell 1715


title: peripheral white blood cell 1822


title: peripheral white blood cell 1535


title: peripheral white blood cell 1712


title: peripheral white blood cell 1533


title: peripheral white blood cell 1531


title: peripheral white blood cell 1818


title: peripheral white blood cell 1716


title: peripheral white blood cell 1820


title: peripheral white blood cell 1711


title: peripheral white blood cell 1534


title: peripheral white blood cell 1710


title: peripheral white blood cell 1532


title: peripheral white blood cell 1528


title: peripheral white blood cell 1530


title: peripheral white blood cell 1460


title: peripheral white blood cell 1527


title: peripheral white blood cell 1459


title: peripheral white blood cell 1461


title: peripheral white blood cell 1361


title: peripheral white blood cell 1360


title: peripheral white blood cell 1356


title: peripheral white blood cell 1332


title: peripheral white blood cell 1328


title: peripheral white blood cell 1324


title: peripheral white blood cell 1326


title: peripheral white blood cell 1317


title: peripheral white blood cell 1329


title: peripheral white blood cell 1331


title: peripheral white blood cell 1325


title: peripheral white blood cell 1358


title: peripheral white blood cell 1323


title: peripheral white blood cell 1310


title: peripheral white blood cell 1309


title: peripheral white blood cell 1311


title: peripheral white blood cell 1308


title: peripheral white blood cell 1262


title: peripheral white blood cell 1315


title: peripheral white blood cell 1313


title: peripheral white blood cell 1267


title: peripheral white blood cell 1208


title: peripheral white blood cell 1257


title: peripheral white blood cell 1261


title: peripheral white blood cell 1271


title: peripheral white blood cell 1256


title: peripheral white blood cell 1268


title: peripheral white blood cell 1263


title: peripheral white blood cell 1204


title: peripheral white blood cell 1202


title: peripheral white blood cell 1201


title: peripheral white blood cell 1207


title: peripheral white blood cell 1333


title: peripheral white blood cell 1199


title: peripheral white blood cell 1194


title: peripheral white blood cell 1198


title: peripheral white blood cell 1191


title: peripheral white blood cell 1196


title: peripheral white blood cell 1270


title: peripheral white blood cell 1200


title: peripheral white blood cell 1195


title: peripheral white blood cell 1713


title: peripheral white blood cell 1190


title: peripheral white blood cell 1167


title: peripheral white blood cell 1193


title: peripheral white blood cell 1171


title: peripheral white blood cell 1164


title: peripheral white blood cell 896


title: peripheral white blood cell 1162


title: peripheral white blood cell 1166


title: peripheral white blood cell 1189


title: peripheral white blood cell 1168


title: peripheral white blood cell 728


title: peripheral white blood cell 893


title: peripheral white blood cell 1163


title: peripheral white blood cell 721


title: peripheral white blood cell 712


title: peripheral white blood cell 725


title: peripheral white blood cell 709


title: peripheral white blood cell 895


title: peripheral white blood cell 894


title: peripheral white blood cell 705


title: peripheral white blood cell 701


title: peripheral white blood cell 702


title: peripheral white blood cell 1159


title: peripheral white blood cell 724


title: peripheral white blood cell 711


title: peripheral white blood cell 703


title: peripheral white blood cell 704


title: peripheral white blood cell 707


title: peripheral white blood cell 710


title: peripheral white blood cell 700


title: peripheral white blood cell 697


title: peripheral white blood cell 698


title: peripheral white blood cell 696


title: peripheral white blood cell 706


title: peripheral white blood cell 699


title: peripheral white blood cell 694


title: peripheral white blood cell 676


title: peripheral white blood cell 678


title: peripheral white blood cell 695


title: peripheral white blood cell 662


title: peripheral white blood cell 677


title: peripheral white blood cell 660


title: peripheral white blood cell 679


title: peripheral white blood cell 649


title: peripheral white blood cell 653


title: peripheral white blood cell 655


title: peripheral white blood cell 642


title: peripheral white blood cell 643


title: peripheral white blood cell 651


title: peripheral white blood cell 654


title: peripheral white blood cell 635


title: peripheral white blood cell 636


title: peripheral white blood cell 640


title: peripheral white blood cell 638


title: peripheral white blood cell 641


title: peripheral white blood cell 511


title: peripheral white blood cell 510


title: peripheral white blood cell 282


title: peripheral white blood cell 508


title: peripheral white blood cell 507


title: peripheral white blood cell 512


title: peripheral white blood cell 513


title: peripheral white blood cell 283


title: peripheral white blood cell 509


title: peripheral white blood cell 279


title: peripheral white blood cell 281


title: peripheral white blood cell 278


title: peripheral white blood cell 130


title: peripheral white blood cell 639


title: blastomere 6 from embryo 5 E6.C6

type: genomic

city: Brussels

first: Claudia

last: Spits

address: Laarbeeklaan 103

department: Research Group of Reproduction and Genetics

country: Belgium

institute: Vrije Universiteit Brussel

description: frozen-thawed day-4 embryo

hyb_protocol: Array-CGH was carried out using 24Sure Cytochip microarrays following the standard protocol (BlueGnome 24Sure Protocol, www.cytochip.com).

scan_protocol: The slides were  scanned using an Agilent dual laser DNA microarray scanner G2566AA (Agilent technologies, Palo Alto, CA, USA).

data_processing: The scan images were analysed using BlueFuse Software (BlueGnome).

molecule: genomic DNA

source_name: blastomere 6 from embryo 5

extract_protocol: Blastomeres were collected  and the genomic DNA  was amplified using the SurePlex DNA Amplification System (BlueGnome, Cambridge, UK), according to the manufacturer’s instructions.

treatment_protocol: All blastomeres from nine top-quality day-4 embryos frozen at day 3 of development and four fresh top-quality day-4 embryos that had one-cell biopsy on day 3 for preimplantation genetic diagnosis (PGD) were collected and arrayed.

value: day 4 embryo

tag: cell type

value: blastomere

value: blastomere from frozen-thawed day-4 embryo

source_name: Control genomic DNA

tag: gender

value: male


title: blastomere 2 from embryo 5 E6.C2

description: frozen-thawed day-4 embryo

source_name: blastomere 2 from embryo 5

label_protocol: Array-CGH was carried out using 24Sure Cytochip microarrays following the standard protocol (BlueGnome 24Sure Protocol, www.cytochip.com).


title: peripheral white blood cell 280


title: peripheral white blood cell 128


title: peripheral white blood cell 131


title: peripheral white blood cell 129


title: blastomere 12 from embryo 4 E4.C12

description: frozen-thawed day-4 embryo

source_name: blastomere 12 from embryo 4


title: peripheral white blood cell 126


title: peripheral white blood cell 127


title: peripheral white blood cell 125


title: blastomere 1 from embryo 5 E6.C1

description: frozen-thawed day-4 embryo

source_name: blastomere 1 from embryo 5


title: blastomere 5 from embryo 4 E4.C5

description: frozen-thawed day-4 embryo

source_name: blastomere 5 from embryo 4


title: blastomere 13 from embryo 4 E4.C13

description: frozen-thawed day-4 embryo

source_name: blastomere 13 from embryo 4


title: blastomere 9 from embryo 8 E9.C9

description: frozen-thawed day-4 embryo

source_name: blastomere 9 from embryo 8


title: blastomere 8 from embryo 8 E9.C8

description: frozen-thawed day-4 embryo

source_name: blastomere 8 from embryo 8


title: peripheral white blood cell 93


title: peripheral white blood cell 68


title: peripheral white blood cell 98


title: peripheral white blood cell 97


title: blastomere 7 from embryo 8 E9.C7

description: frozen-thawed day-4 embryo

source_name: blastomere 7 from embryo 8


title: peripheral white blood cell 65


title: peripheral white blood cell 69


title: peripheral white blood cell 96


title: peripheral white blood cell 94


title: peripheral white blood cell 95


title: blastomere 5 from embryo 8 E9.C5

description: frozen-thawed day-4 embryo

source_name: blastomere 5 from embryo 8


title: blastomere 6 from embryo 8 E9.C6

description: frozen-thawed day-4 embryo

source_name: blastomere 6 from embryo 8


title: blastomere 3 from embryo 8 E9.C3

description: frozen-thawed day-4 embryo

source_name: blastomere 3 from embryo 8


title: blastomere 28 from embryo 8 E9.C28

description: frozen-thawed day-4 embryo

source_name: blastomere 28 from embryo 8


title: blastomere 25 from embryo 8 E9.C25

description: frozen-thawed day-4 embryo

source_name: blastomere 25 from embryo 8


title: blastomere 26 from embryo 8 E9.C26

description: frozen-thawed day-4 embryo

source_name: blastomere 26 from embryo 8


title: blastomere 24 from embryo 8 E9.C24

description: frozen-thawed day-4 embryo

source_name: blastomere 24 from embryo 8


title: blastomere 22 from embryo 8 E9.C22

description: frozen-thawed day-4 embryo

source_name: blastomere 22 from embryo 8


title: blastomere 20 from embryo 8 E9.C20

description: frozen-thawed day-4 embryo

source_name: blastomere 20 from embryo 8

source_name: Control genomic DNA


title: blastomere 2 from embryo 8 E9.C2

description: frozen-thawed day-4 embryo

source_name: blastomere 2 from embryo 8


title: blastomere 27 from embryo 8 E9.C27

description: frozen-thawed day-4 embryo

source_name: blastomere 27 from embryo 8


title: blastomere 12 from embryo 8 E9.C12

description: frozen-thawed day-4 embryo

source_name: blastomere 12 from embryo 8


title: blastomere 11 from embryo 8 E9.C11

description: frozen-thawed day-4 embryo

source_name: blastomere 11 from embryo 8


title: blastomere 4 from embryo 8 E9.C4

description: frozen-thawed day-4 embryo

source_name: blastomere 4 from embryo 8


title: blastomere 10 from embryo 8 E9.C10

description: frozen-thawed day-4 embryo

source_name: blastomere 10 from embryo 8


title: blastomere 18 from embryo 8 E9.C18

description: frozen-thawed day-4 embryo

source_name: blastomere 18 from embryo 8


title: blastomere 15 from embryo 8 E9.C15

description: frozen-thawed day-4 embryo

source_name: blastomere 15 from embryo 8


title: blastomere 21 from embryo 8 E9.21

description: frozen-thawed day-4 embryo

source_name: blastomere 21 from embryo 8


title: blastomere 17 from embryo 8 E9.C17

description: frozen-thawed day-4 embryo

source_name: blastomere 17 from embryo 8


title: blastomere 9 from embryo 7 E8.C9

description: frozen-thawed day-4 embryo

source_name: blastomere 9 from embryo 7


title: blastomere 16 from embryo 8 E9.C16

description: frozen-thawed day-4 embryo

source_name: blastomere 16 from embryo 8


title: blastomere 1 from embryo 8 E9.C1

description: frozen-thawed day-4 embryo

source_name: blastomere 1 from embryo 8


title: blastomere 5 from embryo 7 E8.C5

description: frozen-thawed day-4 embryo

source_name: blastomere 5 from embryo 7


title: blastomere 4 from embryo 7 E8.C4

description: frozen-thawed day-4 embryo

source_name: blastomere 4 from embryo 7


title: blastomere 7 from embryo 7 E8.C7

description: frozen-thawed day-4 embryo

source_name: blastomere 7 from embryo 7


title: blastomere 14 from embryo 8 E9.C14

description: frozen-thawed day-4 embryo

source_name: blastomere 14 from embryo 8

source_name: Control genomic DNA


title: blastomere 6 from embryo 7 E8.C6

description: frozen-thawed day-4 embryo

source_name: blastomere 6 from embryo 7


title: blastomere 15 from embryo 7 E8.C15

description: frozen-thawed day-4 embryo

source_name: blastomere 15 from embryo 7


title: blastomere12  from embryo 7 E8.C12

description: frozen-thawed day-4 embryo

source_name: blastomere12  from embryo 7


title: blastomere 17 from embryo 7 E8.C17

description: frozen-thawed day-4 embryo

source_name: blastomere 17 from embryo 7


title: blastomere 1 from embryo 7 E8.C1

description: frozen-thawed day-4 embryo

source_name: blastomere 1 from embryo 7


title: blastomere 14 from embryo 7 E8.C14

description: frozen-thawed day-4 embryo

source_name: blastomere 14 from embryo 7


title: blastomere 13 from embryo 7 E8.C13

description: frozen-thawed day-4 embryo

source_name: blastomere 13 from embryo 7


title: blastomere 11 from embryo 7 E8.C11

description: frozen-thawed day-4 embryo

source_name: blastomere 11 from embryo 7


title: blastomere 9 from embryo 6 E7.C9

description: frozen-thawed day-4 embryo

source_name: blastomere 9 from embryo 6


title: blastomere 2 from embryo 6 E7.C2

description: frozen-thawed day-4 embryo

source_name: blastomere 2 from embryo 6


title: blastomere 5 from embryo 6 E7.C5

description: frozen-thawed day-4 embryo

source_name: blastomere 5 from embryo 6


title: blastomere 3 from embryo 6 E7.C3

description: frozen-thawed day-4 embryo

source_name: blastomere 3 from embryo 6


title: blastomere 6 from embryo 6 E7.C6

description: frozen-thawed day-4 embryo

source_name: blastomere 6 from embryo 6


title: blastomere 7 from embryo 6 E7.C7

description: frozen-thawed day-4 embryo

source_name: blastomere 7 from embryo 6


title: blastomere 11 from embryo 6 E7.C11

description: frozen-thawed day-4 embryo

source_name: blastomere 11 from embryo 6


title: blastomere 10 from embryo 6 E7.C10

description: frozen-thawed day-4 embryo

source_name: blastomere 10 from embryo 6


title: blastomere 9 from embryo 5 E6.C9

description: frozen-thawed day-4 embryo

source_name: blastomere 9 from embryo 5

source_name: Control genomic DNA


title: blastomere 7 from embryo 5 E6.C7

description: frozen-thawed day-4 embryo

source_name: blastomere 7 from embryo 5


title: blastomere 1 from embryo 6 E7.C1

description: frozen-thawed day-4 embryo

source_name: blastomere 1 from embryo 6


title: blastomere 8 from embryo 6 E7.C8

description: frozen-thawed day-4 embryo

source_name: blastomere 8 from embryo 6


title: blastomere 3 from embryo 5 E6.C3

description: frozen-thawed day-4 embryo

source_name: blastomere 3 from embryo 5


title: blastomere 17 from embryo 5 E6.C17

description: frozen-thawed day-4 embryo

source_name: blastomere 17 from embryo 5


title: blastomere 16 from embryo 5 E6.C16

description: frozen-thawed day-4 embryo

source_name: blastomere 16 from embryo 5


title: blastomere 12 from embryo 6 E7.C12

description: frozen-thawed day-4 embryo

source_name: blastomere 12 from embryo 6


title: blastomere 19 from embryo 6 E7.C19

description: frozen-thawed day-4 embryo

source_name: blastomere 19 from embryo 6


title: blastomere 17 from embryo 6 E7.C17

description: frozen-thawed day-4 embryo

source_name: blastomere 17 from embryo 6


title: blastomere 15 from embryo 6 E7.C15

description: frozen-thawed day-4 embryo

source_name: blastomere 15 from embryo 6


title: blastomere 4 from embryo 5 E6.C4

description: frozen-thawed day-4 embryo

source_name: blastomere 4 from embryo 5


title: blastomere 12 from embryo 5 E6.C12

description: frozen-thawed day-4 embryo

source_name: blastomere 12 from embryo 5


title: blastomere 11 from embryo 5 E6.C11

description: frozen-thawed day-4 embryo

source_name: blastomere 11 from embryo 5


title: blastomere 10 from embryo 5 E6.C10

description: frozen-thawed day-4 embryo

source_name: blastomere 10 from embryo 5


title: blastomere 13 from embryo 5 E6.C13

description: frozen-thawed day-4 embryo

source_name: blastomere 13 from embryo 5


title: blastomere 16 from embryo 6 E7.C16

description: frozen-thawed day-4 embryo

source_name: blastomere 16 from embryo 6


title: blastomere 15 from embryo 5 E6.C15

description: frozen-thawed day-4 embryo

source_name: blastomere 15 from embryo 5

source_name: Control genomic DNA


title: blastomere 14 from embryo 5 E6.C14

description: frozen-thawed day-4 embryo

source_name: blastomere 14 from embryo 5


title: blastomere 8 from embryo 4 E4.C8

description: frozen-thawed day-4 embryo

source_name: blastomere 8 from embryo 4


title: blastomere 8 from embryo 5 E6.C8

description: frozen-thawed day-4 embryo

source_name: blastomere 8 from embryo 5


title: blastomere 5 from embryo 5 E6.C5

description: frozen-thawed day-4 embryo

source_name: blastomere 5 from embryo 5


title: blastomere 7 from embryo 4 E4.C7

description: frozen-thawed day-4 embryo

source_name: blastomere 7 from embryo 4


title: blastomere 2 from embryo 4 E4.C2

description: frozen-thawed day-4 embryo

source_name: blastomere 2 from embryo 4


title: blastomere 3 from embryo 4 E4.C3

description: frozen-thawed day-4 embryo

source_name: blastomere 3 from embryo 4


title: blastomere 4 from embryo 4 E4.C4

description: frozen-thawed day-4 embryo

source_name: blastomere 4 from embryo 4


title: blastomere 6 from embryo 4 E4.C6

description: frozen-thawed day-4 embryo

source_name: blastomere 6 from embryo 4


title: blastomere 9 from embryo 4 E4.C9

description: frozen-thawed day-4 embryo

source_name: blastomere 9 from embryo 4


title: blastomere 11 from embryo 4 E4.C11

description: frozen-thawed day-4 embryo

source_name: blastomere 11 from embryo 4


title: blastomere 10 from embryo 4 E4.C10

description: frozen-thawed day-4 embryo

source_name: blastomere 10 from embryo 4


title: blastomere 1 from embryo 4 E4.C1

description: frozen-thawed day-4 embryo

source_name: blastomere 1 from embryo 4


title: blastomere 12 from embryo 3 E3.C12

description: frozen-thawed day-4 embryo

source_name: blastomere 12 from embryo 3


title: blastomere 9 from embryo 3 E3.C9

description: frozen-thawed day-4 embryo

source_name: blastomere 9 from embryo 3


title: blastomere 8 from embryo 3 E3.C8

description: frozen-thawed day-4 embryo

source_name: blastomere 8 from embryo 3


title: blastomere 3 from embryo 3 E3.C3

description: frozen-thawed day-4 embryo

source_name: blastomere 3 from embryo 3

source_name: Control genomic DNA


title: blastomere 4 from embryo 3 E3.C4

description: frozen-thawed day-4 embryo

source_name: blastomere 4 from embryo 3


title: blastomere 7 from embryo 3 E3.C7

description: frozen-thawed day-4 embryo

source_name: blastomere 7 from embryo 3


title: blastomere 5 from embryo 2 E2.C5

description: frozen-thawed day-4 embryo

source_name: blastomere 5 from embryo 2


title: blastomere 11 from embryo 3 E3.C11

description: frozen-thawed day-4 embryo

source_name: blastomere 11 from embryo 3


title: blastomere 6 from embryo 3 E3.C6

description: frozen-thawed day-4 embryo

source_name: blastomere 6 from embryo 3


title: blastomere 10 from embryo 3 E3.C10

description: frozen-thawed day-4 embryo

source_name: blastomere 10 from embryo 3


title: blastomere 5 from embryo 3 E3.C5

description: frozen-thawed day-4 embryo

source_name: blastomere 5 from embryo 3


title: blastomere 6 from embryo 2 E2.C6

description: frozen-thawed day-4 embryo

source_name: blastomere 6 from embryo 2


title: blastomere 8 from embryo 2 E2.C8

description: frozen-thawed day-4 embryo

source_name: blastomere 8 from embryo 2


title: blastomere 3 from embryo 2 E2.C3

description: frozen-thawed day-4 embryo

source_name: blastomere 3 from embryo 2


title: blastomere 18 from embryo 2 E2.C18

description: frozen-thawed day-4 embryo

source_name: blastomere 18 from embryo 2


title: blastomere 2 from embryo 2 E2.C2

description: frozen-thawed day-4 embryo

source_name: blastomere 2 from embryo 2


title: blastomere 4 from embryo 2 E2.C4

description: frozen-thawed day-4 embryo

source_name: blastomere 4 from embryo 2


title: blastomere 1 from embryo 3 E3.C1

description: frozen-thawed day-4 embryo

source_name: blastomere 1 from embryo 3