title: FACS sorted resident macrophages from the colons of 6 weeks old CX3CR1cre:IL10Raflox/flox mice_SJ67

city: Rehovot

first: Gilgi

last: Friedlander

address: Hertzel st

country: Israel

institute: Weizmann Institute of Science

scan_protocol: According to Affymetrix standard protocols, using Affymetrix GeneChip 3000 7G plus scanner

data_processing: RMA was carried out using Partek Genomic Suite 6.5 (Inc. St. Charles, MO; www.partek.com)

source_name: FACS sorted resident macrophages_CX3CR1cre:IL10Raflox/flox

growth_protocol: All mice were maintained under specific pathogen-free conditions and handled according to protocols approved by the Weizmann Institute and the Institute Pasteur Animal Care Committee as per international guidelines.

extract_protocol: Total RNA was extracted with the miRNeasy Mini Kit (Qiagen) for samples 1-2 and with the RNeasy Micro Kit (Qiagen) for samples 3-7. RNA purity was assessed with ND-1000 Nanodrop (Peqlab) and BioAnalyzer 2100 (Agilent).

treatment_protocol: Cells were sorted from the digested tissue and were sorted using a FACSAria machine (BD).

tag: strain background

value: macrophage-restricted interleukin-10 receptor deficient; CX3CR1cre:IL10Raflox/flox

value: 6 weeks

value: colon; lamina propria

value: FACS sorted resident macrophages


title: DC_B6.CD11-Cre.FasKi_Rep3

status: Public on May 09 2014

type: RNA

city: Chicago

first: Aly

middle: Azeem

last: Khan

state: IL

address: 6045 S. Kenwood Ave.

country: USA

institute: University of Chicago

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol.

data_processing: Data was processed with GenomeStudio using Illumina default analysis settings.

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: Splenic DCs

label_protocol: Total RNA was processed using the Illumina Totalprep kit (Ambion, Life Technologies, Carlsbad, CA) according to the manufacturer’s protocol.

extract_protocol: Total RNA was extracted using guanidinium cesium chloride gradient ultracentrifugation (Chirgwin et al., 1979).

tag: genetic background

tag: cell type

value: Splenic DCs

tag: genotype


title: DC_B6.FasKI_Rep2


title: DC_B6.FasKI_Rep3


title: normal-weight male child with FTO allele TT NW29

type: genomic

city: Footscray

first: Sarah

middle: Amandine Caroline

last: Voisin

state: VIC

address: Ballarat Road

department: Institute for Health and Sport

country: Australia

institute: Victoria University

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation27 Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using Illumina's iScan reader using standard recommended Illumina scanner settings

data_processing: Genomestudio2009.2 toghether with the methylumi and limma packages from Bioconductor. Probes with detection P-value>0.01 were removed from further analysis together with probes from the sex chromosomes.

label: Cy5 and Cy3

molecule: genomic DNA

organism: Homo sapiens

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from pheripheral whole blood using QiaGen Maxiprep kit

tag: gender

value: male

tag: age

tag: weight category

value: normal-weight

tag: tanner stage

tag: fto allele

value: TT


title: muscle_20-24h_rep3

city: San Francisco

first: Charlie

last: Kim

state: CA

address: 1001 Potrero Ave

department: Medicine

institute: University of California, San Francisco

hyb_protocol: 825 ng of each aRNA hybridized to custom Agilent 4x44k microarrays as per manufacturer's instructions

scan_protocol: Molecular Devices Genepix 4000B scanner at 5 um resolution

data_processing: Software: GenePix 6.0. Ratio normalized, filters: 'B532' <= 350 AND 'B635' <= 350) AND 'F532 % Sat.' <= 60 AND 'F635 % Sat.' <= 60 AND 'F532 CV' <= 80 AND 'F635 CV' <= 80 AND 'Flags' >= 0 AND 'Dia.' >= 50 AND 'Dia.' <= 80 AND ('% > B532+2SD' >= 70 OR '% > B635+2SD' >= 70) AND 'Substance Name' begins with 'f' AND 'Circularity' >= 60

organism: Drosophila melanogaster

source_name: pooled reference amplified RNA from whole animals and sorted populations

label_protocol: 1.5 ug of aRNA coupled to Cy5 (or Cy3 for common pooled reference aRNA) as per standard protocols

growth_protocol: Timed larvae collections on grape juice agar plates

extract_protocol: Dissociated cells isolated by FACS.  Up to 10k cells sorted into Ambion RNAqueous Micro kit lysis buffer.  RNA isolated as per manufacturer's instructions with DNase treatment.  RNA amplified in two rounds with Ambion Aminoallyl MessageAmp II kit.

tag: tissue

value: Whole animal

source_name: Amplified RNA from FACS-sorted muscle cells 20-24h AEL

value: Muscle

tag: marker

value: Mhc

tag: age (hours after egg laying)


title: PNS-md_44-48h_rep2

source_name: Amplified RNA from FACS-sorted PNS neurons (md subset) 44-48h AEL

value: PNS md neurons


title: obese male child with FTO allele TT O31

value: obese


title: FACS sorted resident macrophages from the colons of 6 weeks old CX3CR1cre:IL10Raflox/flox mice_SJ54

hyb_protocol: According to Affymetrix standard protocols

tag: genotype/variation


title: normal-weight male child with FTO allele AA NW30

value: AA


title: FACS sorted resident macrophages from the colons of 6 weeks old CX3CR1gfp/+ mice_SJ68

source_name: FACS sorted resident macrophages_CX3CR1gfp/+

label_protocol: According to Affymetrix standard protocols

value: wild type; Cx3cr1gfp/+


title: obese male child with FTO allele TT O30


title: obese male child with FTO allele TT O27


title: muscle_20-24h_rep1


title: FACS sorted resident macrophages from the colons of 6 weeks old CX3CR1gfp/+ mice_SJ56


title: muscle_20-24h_rep2


title: obese male child with FTO allele AA O28


title: epithelial_116-120h_rep2

source_name: Amplified RNA from FACS-sorted epithelial cells 116-120h AEL

value: Epithelia

value: arm


title: epithelial_116-120h_rep1


title: epithelial_116-120h_rep3


title: FACS sorted CX3CR1hi macrophages from the colons of 6 weeks old CX3CR1gfp/+ mice_SJ38

source_name: FACS sorted CX3CR1hi macrophages_CX3CR1gfp/+

value: FACS sorted CX3CR1hi macrophages


title: epithelial_92-96h_rep2

source_name: Amplified RNA from FACS-sorted epithelial cells 92-96h AEL


title: obese male child with FTO allele TT O20


title: epithelial_92-96h_rep3


title: normal-weight male child with FTO allele TT NW16


title: FACS sorted CX3CR1hi macrophages from the colons of 6 weeks old IL10-/- CX3CR1gfp/+ mice_SJ41

source_name: FACS sorted CX3CR1hi macrophages_IL10-/- CX3CR1gfp/+

value: Interleukin-10 deficient; IL10-/- CX3CR1gfp/+

value: 6 weeks


title: epithelial_116-120h_rep4


title: normal-weight male child with FTO allele AA NW15


title: obese male child with FTO allele AA O19


title: obese male child with FTO allele AA O17


title: normal-weight male child with FTO allele TT NW25


title: obese male child with FTO allele TT O21


title: FACS sorted resident macrophages from the colons of 6 weeks old CX3CR1gfp/+ mice_SJ55

value: colon; lamina propria

value: FACS sorted resident macrophages


title: KAP_WT, biological replicate 2

city: Ann Arbor

first: Tom

middle: Klaus

last: Kerppola

state: Michigan

address: 1150 West Medical Center Drive

department: Biological Chemistry

institute: University of Michigan

hyb_protocol: Following fragmentation, 3.7 ug of cDNA were hybridized for 20 hr at 48C on Mouse Gene 1.1 ST Array Strips using the Affymetrix Gene Atlas system (software version 1.0.4.267)

scan_protocol: Arrays were scanned using the Affymetrix Gene Atlas system

data_processing: Data was analyzed using the affy Bioconductor package implemented in the R-statistical environment. RMA was used to normalize the data and fit log2 transformed expression values

source_name: Mouse ES cells wild type

label_protocol: Biotinylated cDNA were prepared according to the Ambion WT kit protocol from 250 ng total RNA (GeneAtlas™ WT Expression Kit User Manual P/N 702935 Rev. 3)

growth_protocol: All cells were cultured on irradiated MEFs under the conditions described

extract_protocol: Total RNA was isolated from cells using the RNeasy Mini Kit (Qiagen). The integrity of RNA was analyzed by RNA 6000 Nano Bioanalyzer. The transcripts were reverse transcribed and the labeled cDNAs were analyzed by hybridization to the Affymetrix Mouse Gene ST 1.1 array following the manufacturer’s instructions.  The changes in hybridization signals were quantified using software provided by Affymetrix.

treatment_protocol: The cells were treated with 4-hydroxy-tamoxifen (+OHT) or with vehicle (ethanol) (−OHT) for 24 hours followed by 48 hours culture without tamoxifen

value: wild type

tag: treatment


title: epithelial_92-96h_rep1


title: KAP_KO, biological replicate 1

source_name: Mouse ES cells KAP1 fl/fl knockout

value: KAP1 fl/fl


title: epithelial_20-24h_rep4

source_name: Amplified RNA from FACS-sorted epithelial cells 20-24h AEL


title: KAP_KO, biological replicate 2


title: normal-weight male child with FTO allele AA NW24

value: male

value: normal-weight


title: obese male child with FTO allele AA O23


title: normal-weight male child with FTO allele TT NW13

value: TT


title: normal-weight male child with FTO allele TT NW17


title: normal-weight male child with FTO allele TT NW18


title: epithelial_20-24h_rep3

value: Whole animal


title: SOX9 overexpression vector replicate 3

city: Geneva

first: Phil

middle: Fang

last: Cheng

address: Rue Gabrielle-Perret-Gentil 4

department: Oncology

country: Switzerland

institute: Hopitaux universitaires de Geneve

description: Gene expression data of M010817 transfected with SOX9 overexpression vector

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Affymetri Scanner 3000 7G

data_processing: The data were analyzed in R using the affy package and normalized with Robust Multiarray Averaging (RMA).

source_name: M010817 transfected with pLenti6.2-SOX9 vector

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 500 ng total RNA (Genechip 3' IVT PLUS Reagent Kit, Affymetrix).

growth_protocol: Melanoma cells were grown in RPMI 1640 with 10% FCS, 5 mM glutamine, and 1 mM sodium pyruvate.

extract_protocol: RNA was extracted by Trizol (Invitrogen) according to manufacturer's instructions.

treatment_protocol: Lentiviral transfection with control vector or SOX9 overexpression vector for 48 hours, then selected with blasticidine (4ng/mL) for one week.

tag: cell line

value: melanoma

value: transfected with pLenti6.2-SOX9 vector


title: KAP_WT, biological replicate 1


title: normal-weight male child with FTO allele AA NW20

value: AA


title: obese male child with FTO allele TT O18

value: obese


title: Control vector replicate 2

description: Gene expression data of M010817 transfected with control vector

source_name: M010817 transfected with pLenti6.2 eGFP vector

value: transfected with pLenti6.2 eGFP vector


title: SOX9 overexpression vector replicate 2


title: SOX9 overexpression vector replicate 1


title: obese male child with FTO allele AA O22


title: Control vector replicate 3


title: dTAT 5μM, 1h+ 24h after incubation

city: College Station

first: Jean-Philippe

last: Pellois

state: Texas

address: 300 Olsen Blvd

department: Biochemistry and Biophysics

institute: Texas A&M university

description: replicate 1

hyb_protocol: Biotin labeled cRNA are hybridized with Illumina Beadchips using Illumina standard protocol

scan_protocol: The beadchips are scanned using Illumina HiScanSQ scanner

data_processing: The data is analyzed using Illumina GenomeStudio software

source_name: Dermal fibroblast

label_protocol: The RNA samples are labeled with Biotin using Illumina TotalPrep RNA Amplification Kit

extract_protocol: Total RNAs were isolated with Trizol reagent (Invitrogen)

value: Normal human primary fibroblast

value: neonatal

value: foreskin


title: epithelial_20-24h_rep1

value: Epithelia

value: arm


title: control no peptide, 1h+ 24h after incubation

description: replicate 1


title: staurosporine 100nM 1h

description: replicate 1


title: control no peptide, 1h+ 1h after incubation

description: replicate 1


title: Control vector replicate 1


title: epithelial_20-24h_rep2


title: CaSki, TGF-b1, rep2

city: Kyoto

first: Budiman

last: Kharma

state: Kyoto

address: 54 Kawahara-cho, Shogoin, Sakyo-ku

department: Gynecology and Obstetrics

country: Japan

institute: Kyoto University Graduate School of Medicine

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Human GeneChip U133 Plus2 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the  GeneArray Scanner System 3000.

data_processing:
The data were analyzed using Affymetrix Expression Console with default analysis settings and global scaling as normalization method using RMA Express.
affymetrix-algorithm-name = rma
affymetrix-algorithm-version = 1.0
program-name = Expression Console
program-version = 1.3.1.187

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA.

growth_protocol: Human cervical squamous cell carcinoma cell lines, CaSki (a CSCC cell line), was maintained in RPMI1640 supplemented with 10% heat-inactivated fetal bovine serum and penicillin–streptomycin.

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

treatment_protocol: recombinant TGF-b1 (2 ng/mL, Peprotech, Rocky Hill, NJ), and medium without recombinant TGF-b1 as a negative control.

value: CaSki

value: human cervical squamous cell carcinoma cells

tag: treated with

value: 2ng/ml recombinant TGF-b1


title: CaSki, TGF-b1, rep1


title: whole_116-120h_rep3

source_name: Amplified RNA from whole larvae 116-120h AEL

value: Whole larvae


title: CaSki, TGF-b1, rep3


title: CaSki, non-treated, rep2

value: none (untreated control)


title: whole_116-120h_rep2


title: dTAT 5μM, 1h+ 1h after incubation

description: replicate 1


title: CaSki, non-treated, rep3


title: whole_92-96h_rep3

source_name: Amplified RNA from whole larvae 92-96h AEL


title: dTAT 5μM, 1h incubation

description: replicate 1


title: CaSki, non-treated, rep1


title: control no peptide, 1h incubation

description: replicate 1


title: whole_116-120h_rep1


title: SW-480_3D_rep4

city: Duesseldorf

first: Karl

last: Koehrer

address: Universitaetsstr. 1

department: BMFZ

country: Germany

institute: University of Duesseldorf

description: 8SW480_3D_US45103065_252800411144_S01_GE1_107_Sep09_1_2

hyb_protocol: After fragmentation, labeled cRNA was hybridized to Agilent Human 8x60K High Density Oligonucleotide Microarrays for 17h at 65°C according to the manufacturers´ protocol (One-Color Microarray-Based Gene Expression Analysis, Low Input Quick Amp Labeling, Vers. 6.5; Agilent Technologies)

scan_protocol: Microarray slides were scanned as described in the manufacturers´ protocol (Scanner G2505C, Agilent Technologies).

data_processing: Signal intensities on 20 bit tiff images were calculated by Feature Extraction software (FE, Vers. 10.7.1.1; Agilent Technologies) using scan protocol GE1_107_Sep09 / grid 028004_D_F_20100430. Data analyses were conducted with GeneSpring GX (Vers. 10.5; Agilent Technologies). Probe signal intensities were quantile normalized across all samples to reduce inter-array variability. Input data pre-processing was concluded by baseline transformation to the median of all samples.

source_name: SW-480_3D culture Matrigel on top_7 days

label_protocol: Synthesis of cDNA and subsequent fluorescent labeling of cRNA was performed according to the manufacturers´ protocol (One-Color Microarray-Based Gene Expression Analysis, Low Input Quick Amp Labeling, Vers. 6.5; Agilent Technologies). Briefly, 100 ng of total RNA were converted to cDNA, followed by in vitro transcription and incorporation of Cy3 labeled nucleotides into newly synthesized cRNA

growth_protocol: For 3D-culture, cells were plated in the Matrigel (BioCoat Matrigel Basement Membrane, growth factor reduced, BD Biosciences, Heidelberg, Germany) on-top assay at a density of 18000 cells per well in 24 well plates. Spheres were cultured for 7 days before recovering from Matrigel. Medium was changed every other day in 3D cultures. For 2D-culture, cells were maintained under standard tissue-culture conditions in RPMI 1640 + GlutaMAX-I (Gibco/Invitrogen, Darmstadt, Germany) containing 10 % fetal calf serum (Gibco/ Invitrogen) and were harvested after seven days at a confluency of around 80%.

extract_protocol: 3D-spheres were recovered from the Matrigel Basement Membrane by removing the medium from the Matrigel cell culture and incubation in 400 µl/well dispase (BD Biosciences, Heidelberg, Germany), preheated at 37°C, and incubated for 2 h at 37°C and 5% CO2. The activation of the dispase was stopped with 10 mM EDTA in 1xPBS. Spheres were centrifuged and washed with 1xPBS. 2D cultured cells were also washed with PBS and scraped off the culture dish. Total RNA was isolated using RNeasy Mini Kit (Qiagen) according to manufacturer's instructions. RNA was diluted in 50-80 µl nuclease free and sterile water. RNA concentration was measured spectrophotometrically at 260 nm and RNA quality was assessed using the Agilent 2100 Bioanalyzer.

value: colorectal cancer cells

tag: culture condition

value: 3D culture Matrigel on top_7 days


title: NF6003_40DAP seeds Replicate 1

city: BEAUCOUZE

first: Sandra

last: Pelletier

address: 42, rue Georges Morel - BP 60057

country: France

institute: INRA

hyb_protocol: The hybridization performed on a NimbleGen Hybridization System 4 (mix mode B) at 42° overnigth. Afterwards, the slide were washed, dried, and scanned.

scan_protocol: Slides were scanned at 532/635nm at 2 μm resolution and high sensitivity with a Roche-NimbleGen MS200. NimbleScan Software v2.4 was used to extract pair-data files from the scanned images.

data_processing: All statistical analyses on the gene expression data were performed using the R language, version 2.5.1 (R Development Core Team, 2011) and the package LIMMA (Smyth G.K., 2005) from the Bioconductor project. For the processing step, data were normalized by the lowess method in LIMMA.

organism: Medicago truncatula

label_protocol: 400 ng of total RNAs were amplified using the Ambion messageAmp II (Ambion, Austin TX) following manufacturer's instructions. 5µg of each aRNAs were retrotranscribed with 400U of Superscript II reverse-transcriptase (Invitrogen Corp., Carlsbad, CA) and labelled with 1,5mmol of Cyanine-3 (Cy3) or Cyanine-5 (Cy5) (Interchim, France), then purified with NucleoSpin Gel and PCR Clean-up column kits (Macherey-Nagel, GmbH & Co. KG, Germany). Purified labeled cDNA were quantified using NanoDrop ND-1000 (Nanodrop Technologies, DE, USA). Labelled samples were combined as 30 pmol for each dye and co-hybridized to the Medtr_v1 12x135K arrays.

growth_protocol: Plants of M. truncatula Gaertn. (A17) were grown in a sterile mix of vermiculite and soil in a growth chamber at 24°C/21°C, 16 h photoperiod at 200 µM m-2 s-2.

extract_protocol: Total RNA was extracted by using a modified cetyltrimethylammonium bromide method (Verdier et al., 2008)

tag: tissus

value: seeds

value: R108 ecotype

value: abi3 -

tag: phenotype

value: intolerant to desiccation

value: 40 days after pollination stage


title: CMP with high-ROS levels rep3

city: Bunkyo-ku

first: Akihito

last: Shinohara

state: Tokyo

department: Hematology and Oncology, Graduate school of medicine

institute: The University of Tokyo

description: Gene expression data from murine CMP

hyb_protocol: Labeled probes were hybridized to the Mouse Genome 430 2.0 Array (Affymetrix).

scan_protocol: These were scanned with the GeneChip Scanner 3000 7G and FS450_0004 protocol.

data_processing: Expression data were extracted from image files using Affymetrix GeneChip Operating Software 1.0, and normalization and expression calculations were performed using dChip (www.dchip.org)

source_name: common myeloid progenitor cells (CMP) from murine bone marrow

label_protocol: Amplification and biotin labeling of fragmented cDNA were performed using the NuGen Ovation Biotin labeling system (NuGEN Technologies, Inc.).

extract_protocol: Total RNA was isolated from sorted CMP using the RNeasy Micro Kit (Qiagen), and the integrity of isolated RNA was determined using the RNA 6000 Pico Kit (Agilent Inc.).

treatment_protocol: Murine bone marrow cells were flushed from femurs, tibiae and ilia.The cells were sorted according to ROS content (cells with high or low ROS levels comprised 15 % to 20 % of total CMP) using FACS with H2-DCFDA staining.

tag: strain

tag: cell type

value: common myeloid progenitor cells with high-ROS levels


title: SW-480_3D_rep3

description: 50SW480_3D_US45103065_252800411144_S01_GE1_107_Sep09_2_4


title: whole_68-72h_rep3

source_name: pooled reference amplified RNA from whole animals and sorted populations

value: Whole animal

source_name: Amplified RNA from whole larvae 68-72h AEL


title: NF6003_40DAP seeds Replicate 2

tag: genetic background

tag: genotype


title: whole_92-96h_rep1


title: SW-480_3D_rep1

description: 22SW480_3D_US45103065_252800411144_S01_GE1_107_Sep09_1_4


title: LOVO_3D_rep4

description: 53Lovo_3D_US45103065_252800411154_S01_GE1_107_Sep09_2_4

source_name: LOVO_3D culture Matrigel on top_7 days

value: LOVO


title: R108_40DAP seeds Replicate 2

value: Wild-type

value: tolerant to desiccation

tag: age


title: NF6003_40DAP seeds Replicate 3


title: SW-480_3D_rep2

description: 36SW480_3D_US45103065_252800411144_S01_GE1_107_Sep09_2_2


title: NF6003_32DAP seeds Replicate 2

value: 32 days after pollination stage


title: R108_40DAP seeds Replicate 3


title: R108_40DAP seeds Replicate 1


title: CMP with high-ROS levels rep2

description: Gene expression data from murine CMP


title: NF6003_32DAP seeds Replicate 3


title: CMP with low-ROS levels rep2

description: Gene expression data from murine CMP

value: common myeloid progenitor cells with low-ROS levels


title: CMP with high-ROS levels rep1

description: Gene expression data from murine CMP


title: CMP with low-ROS levels rep1

description: Gene expression data from murine CMP


title: CMP with low-ROS levels rep3

description: Gene expression data from murine CMP


title: whole_68-72h_rep1


title: whole_92-96h_rep2


title: whole_44-48h_rep3

source_name: Amplified RNA from whole larvae 44-48h AEL


title: whole_20-24h_rep2

source_name: Amplified RNA from whole larvae 20-24h AEL


title: whole_20-24h_rep3


title: whole_44-48h_rep1


title: GF re-conventionalised (CONV-D)_liver_biological rep 5

city: Cork

first: John

middle: Andrew

last: Mac Sharry

state: Cork

address: College Road

department: APC, Biosciences Instiute

country: Ireland

institute: UCC

hyb_protocol: controls BioB, BioC, BioD and Cre and PolyA (Lys, Phe, Thr and Dap) (peformed by contract company ALMAC)

scan_protocol: ALMAC

data_processing:
Expression console v1.1, RMA- sketch,  HCA (hierarchical cluster analysis) and PCA (Principal component analysis) using Partek Genomics Suite (peformed by contract company ALMAC)
probe group file: MoEx-1_0-st-v1.r2.pgf (ALMAC generated)
meta-probeset file: MoEx-1_0-st-v1.r2.dt1.mm9.full (ALMAC generated)
Almac Diagnostics applies hierarchical clustering analysis and principal components analysis (PCA) using Partek Genomics Suite to assess the integrity of expression data prior to any downstream analysis.     The data was pre-processed using Robust Multichip Algorithm (RMA) based on standard RMA background correction, quantile normalisation and median polish summarisation (Bolstad et al. 2003) on the gene core probes. The pre-processed data matrix of all samples with Log2 expressions for each sample and each gene probeset is provided for ileum and liver datasets. Furthermore, the data matrix of exon data is also provided. Clustering was performed using Euclidean as the distance metric and Ward’s method for linkage. (ALMAC)

source_name: GF CONV-D

label_protocol: biotin (ALMAC)

extract_protocol: The Ileum and Liver were removed and the RNA extracted (RNAeasy plus universal  kit (Qiagen) and quantified (nanopdrop)

treatment_protocol: Germ free Swiss Webster mice were monocolonised with EC containing the bacterial gene, Bile salt hydroalse. The treatment groups and relevant controls were;1.  Germ Free(GF) n=4 , 2.  GF and EC n=4, 3. GF and EC +BSH1 n=4, 4. GF and EC+ BSH2 n=4,  5.  GF re-conventionalised (CONV-D) n= 5

value: Swiss Webster

value: Liver


title: whole_44-48h_rep2

value: Whole larvae


title: HT-29_3D_rep1

description: 23HT29_3D_US45103065_252800411145_S01_GE1_107_Sep09_1_4

source_name: HT-29_3D culture Matrigel on top_7 days

value: colorectal cancer cells


title: LOVO_3D_rep1

description: 11Lovo_3D_US45103065_252800411154_S01_GE1_107_Sep09_1_2

value: 3D culture Matrigel on top_7 days


title: NF6003_32DAP seeds Replicate 1

value: seeds


title: High fat diet 3

city: Shanghai

first: Yan

last: Lu

address: 197, Ruijin No.2 Road

department: Department of Endocrine and Metabolic Diseases

country: China

institute: Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China

hyb_protocol: 10 micrograms of fragmented RNAs were employed for each chip hybridization. Hyridization and wash protocols were as described in Affymetrix Technical Manual, GENE EXPRESSION MONITORING, GeneChip® Expression Analysis 701021 Rev. 5. Hybridization buffer contains 100 mM MES(2-(N-Morpholino)ethanesulfonic acid sodium salt), 1M [Na+], 20 mM EDTA, 0.01% Tween-20. Hybridization was performed at 45 celsius for 16 hours.

scan_protocol: Affymetrix GeneChip Scanner 3000 with GCOS GeneChip Operating software Version 1.2.0.037

data_processing: Gene expression levels were normalized using the robust multiarray average (RMA) procedure using Affymetrix Expression Console software Version 1.0.

label: Biotin

source_name: High fat diet

label_protocol: Biotin-labeled RNAs were prepared from 10 micrograms of total RNAs using the Affymetrix One-cycle protocol. Quantity and quality of unfragmented RNAs and fragmented RNA were analyzed using a Bioanalyzer (Agilent).

growth_protocol: Male C57BL/6 mice aged 8 weeks were fed a normal diet (ND) or high-fat-diet (HFD) containing 60 Kcal% of fat for 12 weeks. Then mice were sacrificed and total RNAs were isoloated from hepatic tissues.

extract_protocol: Total RNAs were extracted from liver tissues using the standard TRIzol method according to the manufacturer’s instructions (Invitrogen, Shanghai)

treatment_protocol: Mice were housed at 21±1°C with a humidity of 55±10% and a 12-hour light–dark cycle.

tag: stain

tag: gender

value: Male

value: 8 weeks

value: liver


title: Normal diet 3

source_name: Normal diet

tag: tissue


title: whole_68-72h_rep2

tag: marker


title: High fat diet 2


title: DLD-1_3D_rep1

description: 24DLD-1_3D_US45103065_252800411146_S01_GE1_107_Sep09_1_4

source_name: DLD-1_3D culture Matrigel on top_7 days


title: High fat diet 1


title: whole_20-24h_rep1

tag: age (hours after egg laying)


title: Normal diet 1


title: PBMC_WY_subj5

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

country: Netherlands

institute: Wageningen University

hyb_protocol: Hybridization and washing of the Affymetrix GeneChip Human Gene 1.1 ST peg arrays were performed on a GeneTitan Instrument (Affymetrix, Santa Clara, CA) according to the manufacturer's recommendations.

scan_protocol: Arrays were scanned on an Affymetrix GeneTitan instrument (Affymetrix, Santa Clara, CA).

data_processing: Expression estimates were calculated applying the RMA algorithm in the Bioconductor library 'Oligo' (v1.24.0).

source_name: Peripheral blood mononuclear cells, 13hr incubation with 50 uM WY14,643, subject 5

label_protocol: One hundred nanogram of RNA was used for whole transcript cDNA synthesis with the Ambion WT expression kit [catalog number 4411974] (Applied Biosystems/Life Technologies, Nieuwekerk a/d IJssel, The Netherlands).

growth_protocol: Peripheral blood mononuclear cells from ten healthy Caucasian male blood donors, aged 30, 31, 34, 35, 43, 52, 62, 64, 65 and 66 years, were isolated directly after arrival of the buffy coat (max. 8 hours after donation) by Ficol-paque Plus density gradient centrifugation (Amersham Biosciences, Roosendaal, the Netherlands).  All donors gave full written informed consent.

extract_protocol: Total RNA was isolated using RNeasy micro kit from Qiagen. RNA integrity was checked on chip analysis (Agilent 2100 bioanalyzer, Agilent Technologies, Amsterdam, the Netherlands) according to the manufacturer's instructions. RNA was judged as suitable for array hybridization only if samples exhibited intact bands corresponding to the 18S and 28S ribosomal RNA subunits, and displayed no chromosomal peaks or RNA degradation products (RNA Integrity Number > 8.0).

treatment_protocol: Peripheral blood mononuclear cells were incubated in RPMI1640 medium with 2 mmol/L L-glutamine, 10% fetal bovine serum and antibiotics (penicillin and streptomycin) in the presence of 5% CO2 at 37°C at 1.0 × 10^6 cells per ml with either WY14,643 (50 μM) or vehicle (DMSO, 0.05%). After 13 hrs of exposure the cell suspensions were transferred to 15ml tubes and centrifuged for 5 minutes at 1,600rpm at 4°C. The two cell pellets per donor were re-suspended in ice-cold PBS, and each transferred to separate eppendorf tubes for RNA and DNA isolation and again centrifuged for 5 minutes at 5,000rpm at 4°C. After removing the supernatant, pellets for DNA isolation were snap frozen  on dry-ice  and stored at -80°C. The pellets for RNA isolation were resuspended in 700 μL of  Buffer RPE with added B-mercaptoethanol according to manufacturer’s instructions (Qiagen) and passed five times through a 23G needle before freezing at -80°C.

value: male

tag: subject

value: 62 yr

tag: age group

value: old

value: cultured peripheral blood mononuclear cells


title: R108_32DAP seeds Replicate 3

value: R108 ecotype

value: Wild-type


title: HT-29_3D_rep3

description: 9HT29_3D_US45103065_252800411145_S01_GE1_107_Sep09_1_2

tag: cell line


title: DLD-1_3D_rep3

description: 52DLD-1_3D_US45103065_252800411146_S01_GE1_107_Sep09_2_4


title: GF re-conventionalised (CONV-D)_liver_biological rep 4


title: LOVO_3D_rep2

description: 25Lovo_3D_US45103065_252800411225_S01_GE1_107_Sep09_1_1

value: LOVO


title: DLD-1_3D_rep2

description: 38DLD-1_3D_US45103065_252800411146_S01_GE1_107_Sep09_2_2


title: R108_32DAP seeds Replicate 1

value: tolerant to desiccation

value: 32 days after pollination stage


title: LOVO_3D_rep3

description: 39Lovo_3D_US45103065_252800411154_S01_GE1_107_Sep09_2_2


title: PBMC_WY_subj7

source_name: Peripheral blood mononuclear cells, 13hr incubation with 50 uM WY14,643, subject 7

value: 66 yr

tag: treatment


title: HT-29_3D_rep2

description: 37HT29_3D_US45103065_252800411145_S01_GE1_107_Sep09_2_2

tag: culture condition


title: Normal diet 2


title: PBMC_WY_subj8

source_name: Peripheral blood mononuclear cells, 13hr incubation with 50 uM WY14,643, subject 8

value: 64 yr


title: PBMC_WY_subj12

source_name: Peripheral blood mononuclear cells, 13hr incubation with 50 uM WY14,643, subject 12

value: 31 yr

value: young


title: COLO206F_3D_rep4

description: 56Colo206F_3D_US45103065_252800411265_S01_GE1_107_Sep09_2_4

source_name: COLO206F_3D culture Matrigel on top_7 days

value: colorectal cancer cells

value: 3D culture Matrigel on top_7 days


title: PBMC_WY_subj4

source_name: Peripheral blood mononuclear cells, 13hr incubation with 50 uM WY14,643, subject 4

value: 52 yr


title: PBMC_WY_subj6

source_name: Peripheral blood mononuclear cells, 13hr incubation with 50 uM WY14,643, subject 6

value: 65 yr


title: PBMC_WY_subj10

source_name: Peripheral blood mononuclear cells, 13hr incubation with 50 uM WY14,643, subject 10

value: male

value: 30 yr


title: R108_32DAP seeds Replicate 2

tag: tissus

value: seeds


title: GF re-conventionalised (CONV-D)_liver_biological rep 2

value: Swiss Webster

value: Liver


title: COLO206F_3D_rep3

description: 42Colo206F_3D_US45103065_252800411267_S01_GE1_107_Sep09_2_3


title: PBMC_WY_subj3

source_name: Peripheral blood mononuclear cells, 13hr incubation with 50 uM WY14,643, subject 3

value: 34 yr

value: cultured peripheral blood mononuclear cells


title: GF re-conventionalised (CONV-D)_liver_biological rep 3


title: PBMC_Ctrl_subj12

source_name: Peripheral blood mononuclear cells, 13hr incubation with 0.05% DMSO (control), subject 12


title: GF re-conventionalised (CONV-D)_liver_biological rep 1


title: PBMC_Ctrl_subj10

source_name: Peripheral blood mononuclear cells, 13hr incubation with 0.05% DMSO (control), subject 10


title: COLO206F_3D_rep2

description: 28Colo206F_3D_US45103065_252800412034_S01_GE1_107_Sep09_1_4


title: COLO205_3D_rep3

description: 55Colo205_3D_US45103065_252800411225_S01_GE1_107_Sep09_2_4

source_name: COLO205_3D culture Matrigel on top_7 days


title: PBMC_WY_subj1

source_name: Peripheral blood mononuclear cells, 13hr incubation with 50 uM WY14,643, subject 1

value: 43 yr


title: PBMC_Ctrl_subj7

source_name: Peripheral blood mononuclear cells, 13hr incubation with 0.05% DMSO (control), subject 7

value: old


title: GF and EC+BSH2_liver_biological rep 4

source_name: GF and EC+BSH2


title: PBMC_Ctrl_subj6

source_name: Peripheral blood mononuclear cells, 13hr incubation with 0.05% DMSO (control), subject 6


title: COLO206F_3D_rep1

description: 14Colo206F_3D_US45103065_252800412034_S01_GE1_107_Sep09_1_1


title: GF and EC+BSH2_liver_biological rep 3


title: GF and EC+BSH1_liver_biological rep 4

source_name: GF and EC+BSH1


title: PBMC_Ctrl_subj8

source_name: Peripheral blood mononuclear cells, 13hr incubation with 0.05% DMSO (control), subject 8


title: CACO-2_3D_rep3

description: 54Calo_3D_US45103065_252800411155_S01_GE1_107_Sep09_2_4

source_name: CACO-2_3D culture Matrigel on top_7 days


title: COLO205_3D_rep1

description: 13Colo205_3D_US45103065_252800411156_S01_GE1_107_Sep09_1_2


title: PBMC_Ctrl_subj5

source_name: Peripheral blood mononuclear cells, 13hr incubation with 0.05% DMSO (control), subject 5

value: 62 yr


title: CACO-2_3D_rep2

description: 26Calo_3D_US45103065_252800411225_S01_GE1_107_Sep09_1_2


title: GF and EC+BSH2_liver_biological rep 1


title: PBMC_Ctrl_subj4

source_name: Peripheral blood mononuclear cells, 13hr incubation with 0.05% DMSO (control), subject 4


title: GF and EC+BSH1_liver_biological rep 3


title: GF and EC+BSH1_liver_biological rep 2


title: F4/80(high), CD11b(high) peritoneal resident macrophages_naive_biological rep 3

city: CARDIFF

first: Peter

last: Giles

address: Heath Park

country: United Kingdom

institute: Cardiff University

description: Cells were isolated by lavage with ice-cold PBS, 0.5% BSA, 5mM EDTA and cells were stained immediately via the common protocol.

hyb_protocol: 15μg fragmented cDNA was then hybridised overnight to the Affymetrix MOE430 2.0 GeneChips

scan_protocol: GeneChips were scanned using the Agilent Gene Array Scanner controlled by GCOS 1.2

data_processing: The data were analyzed with Affymetrix Expression Console 1.2 using the MAS 5.0 algorithm and global scaling (TGT 100) as the normalization method.

source_name: Tissue resident macrophage, naive

label_protocol: 100ng RNA was amplified and labeled using the GeneChip® Two-Cycle Target Labeling and Control Reagents from Affymetrix.

extract_protocol: RNA was extracted using TriZol reagent performed according to the manufacturer's instructions.

treatment_protocol: Cells were blocked with 5% heated-rabbit serum, 0.5%BSA in PBS, 5mM EDTA (on ice) and then stained by the addition of fluorescently-labeled antibodies for 1 hour on ice. Free-antibody was removed by 2 washes with 0.5% BSA in PBS with 5mM EDTA before purifying the target populations on a MoFlo cell sorter. RNA was then extracted from purified cells.

value: Female

value: Peritoneal cavity

value: 7-8 weeks


title: COLO205_3D_rep2

description: 27Colo205_3D_US45103065_252800411156_S01_GE1_107_Sep09_1_4

value: colorectal cancer cells


title: GF and EC+BSH2_liver_biological rep 2


title: GF and EC+BSH1_liver_biological rep 1


title: Ly-6B+Ly-6G- bone marrow monocyte_biological rep 3

description: Bones were flushed with ice-cold PBS, 0.5% BSA, 5mM EDTA and marrow was passed through a 40um cell strainer.  Red blood cells were lysed with ACK buffer at room temperature and then cells were stained via the common protocol.

source_name: bone marrow monocyte, naive

value: Bone marrow


title: GF+ EC_liver_biological rep 4

source_name: GF+ EC


title: SW-480_2D_rep3

description: 29SW480_2D_US45103065_252800411144_S01_GE1_107_Sep09_2_1

source_name: SW-480_2D culture_7 days until 70-80% confluence


title: PBMC_Ctrl_subj3

source_name: Peripheral blood mononuclear cells, 13hr incubation with 0.05% DMSO (control), subject 3

value: young


title: Ly-6B+Ly-6G- bone marrow monocyte_biological rep 1


title: SW-480_2D_rep4

description: 43SW480_2D_US45103065_252800411144_S01_GE1_107_Sep09_2_3

value: 2D culture_7 days until 70-80% confluence


title: F4/80(high), CD11b(high) peritoneal resident macrophages_naive_biological rep 2


title: SW-480_2D_rep1

description: 15SW480_2D_US45103065_252800412034_S01_GE1_107_Sep09_1_2


title: PBMC_Ctrl_subj1

source_name: Peripheral blood mononuclear cells, 13hr incubation with 0.05% DMSO (control), subject 1

value: male


title: CACO-2_3D_rep1

description: 12Calo_3D_US45103065_252800411155_S01_GE1_107_Sep09_1_2

value: 3D culture Matrigel on top_7 days


title: F4/80(high), CD11b(high) peritoneal resident macrophages_naive_biological rep 1


title: SW-480_2D_rep2

description: 1SW480_2D_US45103065_252800411144_S01_GE1_107_Sep09_1_1


title: Ly-6B+/low, Ly-6G- inflammation-associated monocyte/macrophage_18 hours_biological rep 3

source_name: Inflammatory monocyte/macrophage, 18 hours after zymosan


title: GF+ EC_liver_biological rep 2


title: LOVO_2D_rep4

description: 4Lovo_2D_US45103065_252800411154_S01_GE1_107_Sep09_1_1

source_name: LOVO_2D culture_7 days until 70-80% confluence

value: LOVO


title: PBMC_Ctrl_subj2

source_name: Peripheral blood mononuclear cells, 13hr incubation with 0.05% DMSO (control), subject 2

value: 35 yr


title: GF+ EC_liver_biological rep 1

value: Swiss Webster

value: Liver


title: GF+ EC_liver_biological rep 3


title: Ly-6B+Ly-6G- bone marrow monocyte_biological rep 2


title: Ly-6B+/low, Ly-6G- inflammation-associated monocyte/macrophage_18 hours_biological rep 1


title: LOVO_2D_rep3

description: 46Lovo_2D_US45103065_252800411154_S01_GE1_107_Sep09_2_3


title: HT-29_2D_rep3

description: 30HT29_2D_US45103065_252800411145_S01_GE1_107_Sep09_2_1

source_name: HT-29_2D culture_7 days until 70-80% confluence


title: GF control_liver_biological rep 4

source_name: GF control


title: F4/80+, CD11b+ inflammation-associated macrophages_72 hours_biological rep 3

source_name: Inflammatory macrophage, 72 hours after zymosan


title: GF control_liver_biological rep 3


title: GF re-conventionalised (CONV-D)_lleum_biological rep 5

source_name: GF CONV-D

value: Ileum


title: LOVO_2D_rep1

description: 18Lovo_2D_US45103065_252800411154_S01_GE1_107_Sep09_1_3


title: PBMC_WY_subj2

source_name: Peripheral blood mononuclear cells, 13hr incubation with 50 uM WY14,643, subject 2

value: cultured peripheral blood mononuclear cells


title: GF control_liver_biological rep 2


title: GF re-conventionalised (CONV-D)_lleum_biological rep 2


title: F4/80+, CD11b+ inflammation-associated macrophages_72 hours_biological rep 2


title: GF re-conventionalised (CONV-D)_lleum_biological rep 3


title: DLD-1_2D_rep4

description: 45DLD-1_2D_US45103065_252800411146_S01_GE1_107_Sep09_2_3

source_name: DLD-1_2D culture_7 days until 70-80% confluence


title: Ly-6B+, Ly-6G- inflammation-associated monocyte_4 hours_biological rep 3

source_name: Inflammatory monocyte, 4 hours after zymosan


title: F4/80(high), Ly-6B- inflammation-associated macrophages_168 hours_biological rep 2

source_name: Ly-6B- Inflammatory macrophage, 168 hours after zymosan


title: DLD-1_2D_rep3

description: 3DLD-1_2D_US45103065_252800411146_S01_GE1_107_Sep09_1_1


title: HT-29_2D_rep2

description: 2HT29_2D_US45103065_252800411145_S01_GE1_107_Sep09_1_1


title: LOVO_2D_rep2

description: 32Lovo_2D_US45103065_252800411154_S01_GE1_107_Sep09_2_1


title: GF control_liver_biological rep 1


title: F4/80(high), Ly-6B- inflammation-associated macrophages_168 hours_biological rep 3


title: GF re-conventionalised (CONV-D)_lleum_biological rep 1


title: F4/80(high), Ly-6B- inflammation-associated macrophages_168 hours_biological rep 1


title: Ly-6B+, Ly-6G- inflammation-associated monocyte_4 hours_biological rep 2


title: GF re-conventionalised (CONV-D)_lleum_biological rep 4


title: Ly-6B+, Ly-6G- inflammation-associated monocyte_4 hours_biological rep 1


title: DLD-1_2D_rep2

description: 31DLD-1_2D_US45103065_252800411146_S01_GE1_107_Sep09_2_1


title: HT-29_2D_rep1

description: 16HT29_2D_US45103065_252800411145_S01_GE1_107_Sep09_1_3


title: F4/80+, CD11b+ inflammation-associated macrophages_72 hours_biological rep 1

description: Cells were isolated by lavage with ice-cold PBS, 0.5% BSA, 5mM EDTA and cells were stained immediately via the common protocol.


title: F4/80(med-high), Ly-6B+ inflammation-associated macrophages_168 hours_biological rep 3

source_name: Ly-6B+ Inflammatory macrophage, 168 hours after zymosan


title: GF and EC+BSH2_lleum_biological rep 4

source_name: GF and EC+BSH2


title: F4/80(med-high), Ly-6B+ inflammation-associated macrophages_168 hours_biological rep 2


title: GF and EC+BSH2_lleum_biological rep 1


title: GF and EC+BSH2_lleum_biological rep 3


title: DLD-1_2D_rep1

description: 17DLD-1_2D_US45103065_252800411146_S01_GE1_107_Sep09_1_3


title: COLO206F_2D_rep3

description: 7Colo206F_2D_US45103065_252800411267_S01_GE1_107_Sep09_1_1

source_name: COLO206F_2D culture_7 days until 70-80% confluence


title: GF and EC+BSH1_lleum_biological rep 4

source_name: GF and EC+BSH1


title: GF and EC+BSH1_lleum_biological rep 3


title: GF and EC+BSH1_lleum_biological rep 2


title: COLO205_2D_rep4

description: 6Colo205_2D_US45103065_252800411156_S01_GE1_107_Sep09_1_1

source_name: COLO205_2D culture_7 days until 70-80% confluence


title: GF and EC+BSH2_lleum_biological rep 2


title: GF+ EC_lleum_biological rep 4

source_name: GF+ EC


title: GF and EC+BSH1_lleum_biological rep 1


title: F4/80(med-high), Ly-6B+ inflammation-associated macrophages_168 hours_biological rep 1


title: COLO205_2D_rep2

description: 34Colo205_2D_US45103065_252800411156_S01_GE1_107_Sep09_2_1


title: COLO206F_2D_rep2

description: 49Colo206F_2D_US45103065_252800411267_S01_GE1_107_Sep09_2_4


title: COLO205_2D_rep3

description: 48Colo205_2D_US45103065_252800412034_S01_GE1_107_Sep09_2_1


title: COLO205_2D_rep1

description: 20Colo205_2D_US45103065_252800411156_S01_GE1_107_Sep09_1_3


title: nac rep3

city: Portland

first: Georgiana

last: Purdy

state: Or

address: 3181 SW Sam Jackson Park Rd

department: Molecular Microbiology and Immunology

institute: OHSU

hyb_protocol: Array hybridization was performed at the Institute for Bioinformatics and Evolutionary Studies, Genomic Resources Laboratory, University of Idaho, Moscow, ID, USA, (http://cores.ibest.uidaho.edu/genomics-resources-core/services/microarrays) following their standard operating procedures. Hybridization and washes used NimbleGen reagents

scan_protocol: Scanning with an Roche Nimblegen MS200  scanner in accordance with the protocols provided by NimbleGen was performed at the Institute for Bioinformatics and Evolutionary Studies, Genomic Resources Laboratory, University of Idaho, Moscow, ID, USA, (http://cores.ibest.uidaho.edu/genomics-resources-core/services/microarrays).

data_processing: NimbleScan software (NimbleGen. Madison, WI) was used to align a chip-specific grid to control features and extract raw intensity data for each probe and each array. Chip images were then visually checked for each array and verified not to contain any significant spatial artifacts. Raw intensity data was then read into the R statistical computing environment and checked for quality. Further, chip intensity distributions, boxplots and hierarchical clusters were compared and checked for any unusual global patterns.  Each array was then background corrected and normalized using the quantile normalization procedure and finally each probeset was summarized using the median polish procedure as described with the robust multichip average (RMA) procedure (Rafael. A. et al., Nucleic Acids Research  31(4):e15; Irizarry et al. Biostatistics 4(2):249), Bolstad et al. Bioinformatics 19(2):185.

organism: Shigella flexneri

source_name: nac mutant S. flexneri, 4 h post infection

label_protocol: cDNA was synthesized from RNA using the Invitrogen SuperScript Double-Stranded cDNA synthesis kit. cDNA quality and concentration was determined by analysis with an Agilent 2100 bioanalyzer and a Nanodrop ND-1000. cDNA labeling with Cy-5 was performed using the NimbleGen labeling kit at the Institute for Bioinformatics and Evolutionary Studies, Genomic Resources Laboratory, University of Idaho, Moscow, ID, USA, (http://cores.ibest.uidaho.edu/genomics-resources-core/services/microarrays) following their standard operating procedures.

growth_protocol: Henle cells (Intestine 407 cells; American Type Culture Collection, Manassas, VA) were infected with S. flexneri at an MOI of 100:1 as described previously (Hong M, et al. Infect. Immun. 66:4700–4710). During infection, Henle cells were maintained in Henle medium [Minimum Essential Medium (Invitrogen, Carlsbad, CA) supplemented with 1X nonessential amino acid solution (Invitrogen), and 10% fetal bovine serum (Invitrogen)] in a 5% CO2 atmosphere at 37°C. Gentamycin was added to the media to kill extracellular bacteria at 45 min post-invasion. RNA was isolated 4 hours post-infection

extract_protocol: S. flexneri RNA was isolated from infected Henle cells using a modification of the methods described by Eriksson S, et al. 2003 Mol. Microbiol. 47:103–118. Briefly, infected Henle cells were lysed on ice for 30 minutes in 0.1% SDS, 1% acidic phenol, 19% ethanol in water to stabilize bacterial RNA. Cellular lysates were centrifuged, and bacterial pellets were frozen at -80 oC. RNA was subsequently isolated using RNeasy columns (Qiagen). RNA was eluted in 35 µl RNAse free water then treated with DNAse (Ambion) to ensure adequate removal of genomic DNA contamination. RNA quality and concentration was determined by analysis with an Agilent 2100 bioanalyzer and a Nanodrop ND-1000.

tag: genotype/variation

value: nac


title: ntrBC rep2

source_name: ntrBC mutant S. flexneri, 4 h post infection

value: ntrBC


title: ntrBC rep1


title: ntrBC rep3


title: nac rep2


title: nac rep1


title: WT rep3

source_name: Wild type S. flexneri, 4 h post infection

value: WT


title: WT rep1


title: CACO-2_2D_rep1

description: 19Calo_2D_US45103065_252800411155_S01_GE1_107_Sep09_1_3

source_name: CACO-2_2D culture_7 days until 70-80% confluence


title: GF control_lleum_biological rep 2

source_name: GF control

tag: strain


title: GF+ EC_lleum_biological rep 3


title: GF control_lleum_biological rep 3


title: WT rep2


title: CACO-2_2D_rep3

description: 5Calo_2D_US45103065_252800411155_S01_GE1_107_Sep09_1_1

tag: cell type


title: GF control_lleum_biological rep 1


title: nuo-6(qm200);ced-4(n1162) double mutant young adults, biological rep 1

status: Public on May 08 2014

city: Montreal

first: Siegfried

last: Hekimi

state: Quebec

address: 1205 ave Docteur Penfield

department: Biology

country: Canada

institute: McGill University

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip C. elegans Genome Array.

scan_protocol: GeneChips were scanned using a GeneChip Scanner 3000Dx

data_processing: FlexArray Software was used to processes the raw Affymetrix data. Samples were normalized using the GC-RMA algorithm.

organism: Caenorhabditis elegans

label_protocol: Biotinylated cRNA was prepared using the GeneChip 3' IVT Express Kit (Affymetrix) according to manufacturer's protocol

growth_protocol: Worms were grown using a 4-hour synchronized lay from gravid mothers. Worms were grown until young adult stage.

extract_protocol: Worm total RNA was extracted using a Qiagen Tissue Mini Kit (Trizol) according to manufacturer's protocol

treatment_protocol: Worms were hand picked and washed three times with M9 buffer

tag: strain background

value: Bristol N2

value: hermaphrodite

tag: developmental stage

value: young adult


title: COLO206F_2D_rep1

description: 35Colo206F_2D_US45103065_252800411267_S01_GE1_107_Sep09_2_1

value: colorectal cancer cells


title: CACO-2_2D_rep2

description: 47Calo_2D_US45103065_252800411155_S01_GE1_107_Sep09_2_3


title: Ly-6B+/low, Ly-6G- inflammation-associated monocyte/macrophage_18 hours_biological rep 2

source_name: Inflammatory monocyte/macrophage, 18 hours after zymosan

value: Female

value: Peritoneal cavity

tag: age

value: 7-8 weeks


title: GF+ EC_lleum_biological rep 2


title: GF control_lleum_biological rep 4


title: nuo-6(qm200);ced-4(n1162) double mutant young adults, biological rep 3


title: ced-4(n1162) young adults, biological rep 3

source_name: whole young adult_ced-4(n1162)

value: ced-4(n1162) mutant


title: ced-4(n1162) young adults, biological rep 2


title: GF+ EC_lleum_biological rep 1


title: nuo-6(qm200) young adults, biological rep 2

source_name: whole young adult_nuo-6(qm200)

value: nuo-6(qm200) mutant


title: isp-1(qm150) ced-4(n1162) double mutant young adults, biological rep 2

source_name: whole young adult_isp-1(qm150) ced-4(n1162)

value: isp-1(qm150) ced-4(n1162) mutant


title: nuo-6(qm200) young adults, biological rep 1


title: ced-4(n1162) young adults, biological rep 1


title: Wild type young adults treated with 0.1mM paraquat, biological rep 2

source_name: whole young adult_Bristol N2_0.1mM Paraquat

value: wild type

tag: treated with

value: 0.1mM paraquat


title: Wild type young adults treated with 0.1mM paraquat, biological rep 1

tag: gender


title: Wild type young adults treated with 0.1mM paraquat, biological rep 3


title: isp-1(qm150) ced-4(n1162) double mutant young adults, biological rep 1


title: nuo-6(qm200) young adults, biological rep 3


title: isp-1(qm150) young adults, biological rep 3

source_name: whole young adult_isp-1(qm150)

value: isp-1(qm150) mutant


title: Wild type young adults, biological rep 3

source_name: whole young adult_Bristol N2


title: Wild type young adults, biological rep 4


title: isp-1(qm150) young adults, biological rep 1


title: isp-1(qm150) ced-4(n1162) double mutant young adults, biological rep 3


title: Wild type young adults, biological rep 2


title: Wild type young adults, biological rep 1


title: 034-p1  HsO3I-086_339469

city: Luxembourg

first: Yvan

last: Devaux

address: 120 route d'Arlon

country: Luxembourg

institute: LIH

description: Date: 2008/03/12

hyb_protocol: Agilent : 80 pmol at 60 degree_C during 17 hours

scan_protocol: Scanned on an GenePix 4000B fluorescent scanner Image intensity data were extracted with GenePix Pro 6.0 analysis software

data_processing:
Lowess non linear normalization
the mean of the replicated probes

label_protocol: Ambion

extract_protocol: Qiagen

tag: tissue

value: blood

tag: phenotype

value: vasospasm

value: male

tag: age (y)

tag: FISHer grade

tag: disease state

value: subarachnoid-hemorrhage

tag: individual

value: PAXgene

source_name: Ref

extract_protocol: Trizol

value: pooled blood

value: various

value: male and female

value: Ref

value: Trizol


title: 034-p1  HsO3I-087_339470

description: Date: 2008/03/12


title: nuo-6(qm200);ced-4(n1162) double mutant young adults, biological rep 2

value: Bristol N2

value: hermaphrodite

value: young adult


title: 056-p1 HsO4A-032_346153

description: Date: 2008/10/06

value: no vasospasm

value: female


title: 056-p1 HsO4A-077_345930

description: Date: 2008/09/16


title: 056-p1 HsO4A-041_346106

description: Date: 2008/10/06


title: 056-p1 HsO4A-078_345933

description: Date: 2008/09/16


title: 034-p1 HsO3I-085_339467

description: Date: 2008/03/12


title: 049-p1 HsO4A-023_346352

description: Date: 2008/09/29


title: isp-1(qm150) young adults, biological rep 2


title: 049-p1 HsO4A-028_346357

description: Date: 2008/09/23


title: 026-p1  HsO4A-079_346369

description: Date: 2008/09/16


title: 049-p1 HsO4A-022_346351

description: Date: 2008/09/29


title: 056-p1  HsO4A-034_346371

description: Date: 2008/10/06


title: 104-p1  HsO4F-119_359220

description: Date: 2009/02/04


title: 034-p1 HsO3I-088_339228

description: Date: 2008/03/12


title: 026-p1  HsO4A-080_346368

description: Date: 2008/09/16


title: 049-p1 HsO4A-031_346108

description: Date: 2008/09/23


title: 033-p1  HsO4A-021_346425

description: Date: 2008/09/23


title: 033-p1  HsO4A-029_346358

description: Date: 2008/09/23


title: 125-p1  HsO4F-110_359218

description: Date: 2010/02/24


title: 168-p1  HsO4F-097_359060

description: Date: 2010/05/04


title: 104-p1  HsO4F-117_359223

description: Date: 2009/02/04


title: 049-p1  HsO4A-024_346353

description: Date: 2008/09/29


title: 172-p1  HsO4F-108_359151

description: Date: 2010/03/15


title: 093-p1  HsO4F-116_359224

description: Date: 2009/01/22


title: 179-p1  HsO4F-101_359170

description: Date: 2010/03/24


title: 179-p1  HsO4F-102_359171

description: Date: 2010/03/24


title: 157-p1  HsO4F-078_359511

description: Date: 2010/04/19


title: 049-p1  HsO4A-025_346354

description: Date: 2008/09/29


title: 125-p1  HsO4F-111_358966

description: Date: 2010/02/24


title: 093-p1  HsO4F-118_359221

description: Date: 2009/01/22


title: 056-p1  HsO4A-033_346154

description: Date: 2008/10/06


title: 168-p1  HsO4F-095_359165

description: Date: 2010/05/04


title: 157-p1  HsO4F-080_359513

description: Date: 2010/04/19


title: 140-p1  HsO4F-075_359472

description: Date: 2010/04/14


title: 128-p1  HsO4F-089_359516

description: Date: 2009/02/19


title: 172-p1  HsO4F-109_359217

description: Date: 2010/03/15


title: 128-p1  HsO4F-032_359198

description: Date: 2009/02/19


title: 140-p1  HsO4F-076_359473

description: Date: 2010/04/14


title: 194-p1  HsO4F-071_359468

description: Date: 2010/04/13


title: 175-p1  HsO4F-061_359273

description: Date: 2010/05/27


title: 175-p1  HsO4F-079_359512

description: Date: 2010/05/27


title: 194-p1  HsO4F-072_359469

description: Date: 2010/04/13


title: 173-p1  HsO4F-062_359271

description: Date: 2010/05/25


title: 129-p1  HsO4F-054_359360

description: Date: 2010/02/24


title: 129-p1  HsO4F-053_359361

description: Date: 2010/02/24


title: 173-p1  HsO4F-063_359305

description: Date: 2010/05/25


title: 067-p1  HsO4F-044_359192

description: Date: 2009/01/13


title: 145-p1  HsO4F-051_359364

description: Date: 2010/03/01


title: 114-p1  HsO4F-040_359143

description: Date: 2009/02/05


title: 145-p1  HsO4F-052_359363

description: Date: 2010/03/01


title: 114-p1  HsO4F-038_359142

description: Date: 2009/02/05


title: 169-p1  HsO4F-034_359200

description: Date: 2010/05/18


title: 169-p1  HsO4F-033_359199

description: Date: 2010/05/18


title: 158-p1  HsO4F-106_359123

description: Date: 2010/03/08


title: 111-p1  HsO4F-092_359168

description: Date: 2009/02/25


title: 061-p1  HsO4F-029_359188

description: Date: 2009/02/18


title: 067-p1  HsO4F-045_359191

description: Date: 2009/01/13


title: 061-p1  HsO4F-028_359187

description: Date: 2009/02/18


title: 149-p1  HsO4F-021_359144

description: Date: 2010/04/21


title: 143-p1  HsO4F-018_359005

description: Date: 2010/04/26


title: 143-p1  HsO4F-064_359304

description: Date: 2010/04/26


title: 158-p1  HsO4F-048_358969

description: Date: 2010/03/08


title: 111-p1  HsO4F-031_359197

description: Date: 2009/02/25


title: 149-p1  HsO4F-020_359467

description: Date: 2010/04/21


title: 120-p1  HsO4F-012_359074

description: Date: 2009/02/12


title: 128-p1 HsO4F-091_359169

description: Date: 2009/02/19


title: 129-p1 HsO4F-056_359356

description: Date: 2010/02/24


title: 129-p1 HsO4F-055_359359

description: Date: 2010/02/24


title: 168-p1 HsO4F-096_358951

description: Date: 2010/05/04


title: 212-p1  HsO5A-063_372180

description: Date: 2010/06/07


title: 120-p1  HsO4F-013_359075

description: Date: 2009/02/12


title: 192-p1  HsO5A-075_372608

description: Date: 2010/06/01


title: 212-p1  HsO5A-062_372179

description: Date: 2010/06/07


title: 197-p1  HsO5A-058_372134

description: Date: 2010/06/03


title: 197-p1  HsO5A-061_372181

description: Date: 2010/06/03


title: 192-p1  HsO5A-076_372607

description: Date: 2010/06/01


title: 218-p1  HsO5A-048_372414

description: Date: 2010/06/09


title: 218-p1  HsO5A-066_372176

description: Date: 2010/06/09


title: 218-p1 HsO5A-068_372149

description: Date: 2010/06/09


title: 218-p1 HsO5A-067_372148

description: Date: 2010/06/09


title: 212-p1 HsO5A-065_372178

description: Date: 2010/06/07


title: 192-p1 HsO5A-074_372603

description: Date: 2010/06/01


title: 197-p1 HsO5A-059_372129

description: Date: 2010/06/03


title: 192-p1 HsO5A-077_372037

description: Date: 2010/06/01


title: 197-p1 HsO5A-078_372036

description: Date: 2010/06/03


title: 111-p1 HsO4F-114_358962

description: Date: 2009/02/25


title: 179-p1 HsO4F-104_359121

description: Date: 2010/03/24


title: 172-p1 HsO4F-107_359125

description: Date: 2010/05/04


title: 172-p1 HsO4F-100_359057

description: Date: 2010/05/04


title: 125-p1 HsO4F-112_358965

description: Date: 2009/02/26


title: 125-p1 HsO4F-113_358963

description: Date: 2009/02/26


title: 168-p1 HsO4F-098_359059

description: Date: 2010/05/04


title: 158-p1 HsO4F-105_359122

description: Date: 2010/03/08


title: 128-p1 HsO4F-093_359167

description: Date: 2009/02/19


title: 169-p1 HsO4F-099_359058

description: Date: 2010/05/18


title: 149-p1 HsO4F-082_359054

description: Date: 2010/04/21


title: 093-p1 HsO4F-115_358961

description: Date: 2009/01/22


title: 114-p1 HsO4F-084_359052

description: Date: 2009/02/25


title: 111-p1 HsO4F-094_359166

description: Date: 2009/02/25


title: 157-p1 HsO4F-081_359055

description: Date: 2010/04/19


title: 149-p1 HsO4F-083_359053

description: Date: 2010/04/21


title: 140-p1 HsO4F-073_359470

description: Date: 2010/04/14


title: 140-p1 HsO4F-074_359471

description: Date: 2010/04/14


title: 157-p1 HsO4F-077_359475

description: Date: 2010/04/19


title: 194-p1 HsO4F-069_359172

description: Date: 2010/04/13


title: 145-p1 HsO4F-057_359025

description: Date: 2010/03/01


title: 175-p1 HsO4F-059_359021

description: Date: 2010/05/27


title: 194-p1 HsO4F-070_359365

description: Date: 2010/04/13


title: 175-p1 HsO4F-058_359023

description: Date: 2010/05/27


title: 145-p1 HsO4F-050_359019

description: Date: 2010/03/01


title: 067-p1 HsO4F-047_358968

description: Date: 2009/01/13


title: 158-p1 HsO4F-049_359018

description: Date: 2010/03/08


title: 104-p1 HsO4F-042_359194

description: Date: 2009/02/04


title: 067-p1 HsO4F-046_358967

description: Date: 2009/01/13


title: 093-p1 HsO4F-043_359193

description: Date: 2009/01/22


title: 114-p1 HsO4F-039_359141

description: Date: 2009/02/25


title: 173-p1 HsO4F-037_359138

description: Date: 2010/05/25


title: 104-p1 HsO4F-041_359196

description: Date: 2009/02/04


title: 173-p1 HsO4F-036_359137

description: Date: 2010/05/25


title: 169-p1 HsO4F-035_359136

description: Date: 2010/05/18


title: 143-p1 HsO4F-016_359003

description: Date: 2010/04/26


title: NormalControl_B626a

city: Gainesville

first: Xin

last: Qi

state: FL

address: 1600 SW Archer Rd

department: Medicinal Chemistry

institute: University of Florida

hyb_protocol: 0.6 ug of Cy3-labelled cRNA (specific activity > 8 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (GPL17077) for 17 hours at 65 °C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried using Agilent stabilization and drying solution.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 1x60k array slides (Scan Area 61X21 mm, Scan resolution 3 um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The data were analyzed by GeneSpring GX (Agilent) using one parameter of subtype, whose values are Luminal A, Luminal B, Triple Negative and normal. Genes were filtered with one-way ANOVA (p<0.05) and fold change >= 2.0.

source_name: Breast tissue

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 100ng RNA using the One-Color Low Input Quick Amp labeling kit (Agilent, Valencia, CA) according to the manufacturer's instructions, followed by RNeasy Mini Kit (Qiagen, Valencia, CA) purification.  Dye incorporation and cRNA yield were checked with the NanoDrop Spectrophotometer (NanoDrop Technologies, Inc).

extract_protocol: Total RNAs were extracted using Qiagen RNeasy Mini Kit, QIAshredder kit and RNase-Free DNase Set kit (Qiagen, Valencia, CA) following manufacturer's recommendations. The protocol includes homogenization of tissue by grinding in mortor with liquid nitrogen and binding to the RNeasy Mini spin column, then DNase were used to get rid of trace amount of DNA. RNAs were quantified using a NanoDrop-2000 spectrophotometer and their qualities were monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

tag: tissue type

value: normal breast

tag: cancer subtype


title: 143-p1 HsO4F-017_359004

description: Date: 2010/04/26


title: NormalControl_N186b


title: NormalControl_N700a


title: NormalControl_N949a


title: NormalControl_N513c


title: 061-p1 HsO4F-022_359145

description: Date: 2009/02/18


title: 120-p1 HsO4F-015_359002

description: Date: 2009/02/12


title: NormalControl_N655a


title: 061-p1 HsO4F-011_359073

description: Date: 2009/02/18


title: 120-p1 HsO4F-014_359001

description: Date: 2009/02/12


title: NormalControl_N114a


title: 179-p1 HsO4F-103_359120

description: Date: 2010/03/24


title: Brain metastasis_Patient65

city: Houston

first: Guo

last: Chen

state: TX

address: 7435 Fannin Street

department: Melanoma Medical Oncology

institute: The University of Texas MD Anderson Cancer Center

description: 340k MIP array

hyb_protocol: As per manufacturer (Affymetrix)

scan_protocol: As per manufacturer (Affymetrix)

data_processing:
Copy number data were generated from CEL files by OncoScan 2.0 service (Affymetrix)
Copy number data normalized to reference samples

source_name: Brain metastasis,Patient65

label_protocol: As per manufacturer (Affymetrix)

extract_protocol: Genomic DNA was extracted from formalin-fixed and paraffin-embedded (FFPE) metastatic melanomas using QIAamp DNA FFPE Tissue kit (Qiagen)

tag: a/t array

tag: g/c array

value: Female

value: Brain metastasis


title: Brain metastasis_Patient67

description: 340k MIP array

source_name: Brain metastasis,Patient67

value: Male


title: Brain metastasis_Patient80

description: 340k MIP array

source_name: Brain metastasis,Patient80


title: Brain metastasis_Patient66

description: 340k MIP array

source_name: Brain metastasis,Patient66


title: Brain metastasis_Patient45

description: 340k MIP array

source_name: Brain metastasis,Patient45


title: Brain metastasis_Patient64

description: 340k MIP array

source_name: Brain metastasis,Patient64


title: Brain metastasis_Patient63

description: 340k MIP array

source_name: Brain metastasis,Patient63


title: Brain metastasis_Patient62

description: 340k MIP array

source_name: Brain metastasis,Patient62


title: Extracranial metastasis_Patient57

description: 340k MIP array

source_name: Extracranial metastasis,Patient57

value: Extracranial metastasis


title: Extracranial metastasis_Patient24

description: 340k MIP array

source_name: Extracranial metastasis,Patient24


title: 212-p1 HsO5A-064_372177

description: Date: 2010/06/07

value: subarachnoid-hemorrhage

value: blood

value: vasospasm


title: Brain metastasis_Patient79

description: 340k MIP array

source_name: Brain metastasis,Patient79


title: Extracranial metastasis_Patient29

description: 340k MIP array

source_name: Extracranial metastasis,Patient29


title: Extracranial metastasis_Patient12

description: 340k MIP array

source_name: Extracranial metastasis,Patient12


title: Extracranial metastasis_Patient09

description: 340k MIP array

source_name: Extracranial metastasis,Patient09


title: Extracranial metastasis_Patient05

description: 340k MIP array

source_name: Extracranial metastasis,Patient05


title: Extracranial metastasis_Patient11

description: 340k MIP array

source_name: Extracranial metastasis,Patient11


title: Extracranial metastasis_Patient26 tech rep

description: 340k MIP array

source_name: Extracranial metastasis,Patient26


title: Extracranial metastasis_Patient10

description: 340k MIP array

source_name: Extracranial metastasis,Patient10


title: Extracranial metastasis_Patient04

description: 340k MIP array

source_name: Extracranial metastasis,Patient04


title: Extracranial metastasis_Patient61

description: 340k MIP array

source_name: Extracranial metastasis,Patient61


title: Brain metastasis_Patient13

description: 340k MIP array

source_name: Brain metastasis,Patient13


title: Brain metastasis_Patient14

description: 340k MIP array

source_name: Brain metastasis,Patient14


title: Brain metastasis_Patient10

description: 340k MIP array

source_name: Brain metastasis,Patient10


title: Extracranial metastasis_Patient02

description: 340k MIP array

source_name: Extracranial metastasis,Patient02


title: Brain metastasis_Patient09

description: 340k MIP array

source_name: Brain metastasis,Patient09


title: Brain metastasis_Patient11

description: 340k MIP array

source_name: Brain metastasis,Patient11


title: Brain metastasis_Patient03

description: 340k MIP array

source_name: Brain metastasis,Patient03


title: Brain metastasis_Patient15

description: 340k MIP array

source_name: Brain metastasis,Patient15


title: Extracranial metastasis_Patient01

description: 340k MIP array

source_name: Extracranial metastasis,Patient01


title: Normal tissue_Patient29

description: 340k MIP array

source_name: Normal tissue,Patient29

value: Normal tissue


title: Brain metastasis_Patient04

description: 340k MIP array

source_name: Brain metastasis,Patient04


title: Normal tissue_Patient74

description: 340k MIP array

source_name: Normal tissue,Patient74


title: Normal tissue_Patient26

description: 340k MIP array

source_name: Normal tissue,Patient26


title: Normal tissue_Patient21

description: 340k MIP array

source_name: Normal tissue,Patient21


title: Normal tissue_Patient72

description: 340k MIP array

source_name: Normal tissue,Patient72


title: Extracranial metastasis_Patient28

description: 340k MIP array

source_name: Extracranial metastasis,Patient28


title: Normal tissue_Patient17

description: 340k MIP array

source_name: Normal tissue,Patient17


title: Normal tissue_Patient13

description: 340k MIP array

source_name: Normal tissue,Patient13


title: Normal tissue_Patient76

description: 340k MIP array

source_name: Normal tissue,Patient76


title: Extracranial metastasis_Patient03

description: 340k MIP array

source_name: Extracranial metastasis,Patient03


title: Normal tissue_Patient10

description: 340k MIP array

source_name: Normal tissue,Patient10


title: Normal tissue_Patient09

description: 340k MIP array

source_name: Normal tissue,Patient09


title: Normal tissue_Patient11

description: 340k MIP array

source_name: Normal tissue,Patient11


title: Normal tissue_Patient73

description: 340k MIP array

source_name: Normal tissue,Patient73


title: Normal tissue_Patient14

description: 340k MIP array

source_name: Normal tissue,Patient14


title: Normal tissue_Patient16

description: 340k MIP array

source_name: Normal tissue,Patient16


title: Normal tissue_Patient58

description: 340k MIP array

source_name: Normal tissue,Patient58


title: Normal tissue_Patient12

description: 340k MIP array

source_name: Normal tissue,Patient12


title: Normal tissue_Patient08

description: 340k MIP array

source_name: Normal tissue,Patient08


title: Normal tissue_Patient75

description: 340k MIP array

source_name: Normal tissue,Patient75


title: Normal tissue_Patient06

description: 340k MIP array

source_name: Normal tissue,Patient06


title: Normal tissue_Patient04

description: 340k MIP array

source_name: Normal tissue,Patient04


title: Autoimmune LPR8 4M 2

type: other

city: Phoenix

first: Phillip

last: Stafford

state: AZ

address: 1001 S. McAllister

department: Center for Innovations in Medicine

institute: Biodesign Institute

description: Goat anti-mouse IgG biotinylated secondary antibody was added followed by streptavidin conjugated with AlexaFluor 555.

hyb_protocol: Each slide was blocked with buffer containing mercaptohexanol for one hour followed by a one hour incubation with 1/500 dilution of each serum sample.  The slides were washed with TBST and then incubated with 6.67μM of goat anti-mouse IgG biotinylated secondary antibody at 37oC for one hour.  5nM of streptavidin conjugated with AlexaFluor 555 was added to the slides, the slides were washed and then spun dry before scanning.

scan_protocol: A Perkin Elmer Scan Array laser Scanner was used to scanned the slides (543nm emission, 565 nm absorption, 75% PMT, 100% laser power).

data_processing: GenePix Pro 6.0 was used to produce a gpr file that was analyzed in GeneSpring 7.3.1.

label: Alexafluor 555

molecule: other

source_name: mouse serum

label_protocol: Mouse IgG bound to the arrays were detected using goat anti-mouse IgG biotinylated secondary antibody followed by streptavidin conjugated with AlexaFluor 555.

growth_protocol: Mice were house under standard laboratory conditions.

extract_protocol: Blood samples were collected via cardiac exsanguination or tail vein blood collection.

treatment_protocol: Mice were subjected to different behavior tests.

tag: strain

value: MRL/lpr

tag: Sex

tag: sample type

value: serum


title: Autoimmune LPR10 4M 2


title: Autoimmune LPR9 4M 2


title: Normal tissue_Patient05

description: 340k MIP array

source_name: Normal tissue,Patient05


title: Extracranial metastasis_Patient16

description: 340k MIP array

source_name: Extracranial metastasis,Patient16


title: Normal tissue_Patient03

description: 340k MIP array

source_name: Normal tissue,Patient03


title: Extracranial metastasis_Patient13

description: 340k MIP array

source_name: Extracranial metastasis,Patient13


title: Extracranial metastasis_Patient26

description: 340k MIP array

source_name: Extracranial metastasis,Patient26


title: Brain metastasis_Patient78

description: 340k MIP array

source_name: Brain metastasis,Patient78


title: Normal tissue_Patient01

description: 340k MIP array

source_name: Normal tissue,Patient01


title: Autoimmune LPR4 4M 2


title: Autoimmune LPR5 4M 2


title: Normal tissue_Patient15

description: 340k MIP array

source_name: Normal tissue,Patient15


title: Brain metastasis_Patient12

description: 340k MIP array

source_name: Brain metastasis,Patient12


title: Extracranial metastasis_Patient21

description: 340k MIP array

source_name: Extracranial metastasis,Patient21


title: Autoimmune LPR2 4M 2


title: Extracranial metastasis_Patient77

description: 340k MIP array

source_name: Extracranial metastasis,Patient77


title: Extracranial metastasis_Patient15

description: 340k MIP array

source_name: Extracranial metastasis,Patient15


title: Extracranial metastasis_Patient08

description: 340k MIP array

source_name: Extracranial metastasis,Patient08


title: Autoimmune LPR6 4M 2


title: Brain metastasis_Patient01

description: 340k MIP array

source_name: Brain metastasis,Patient01


title: Autoimmune LPR1 4M 2


title: Extracranial metastasis_Patient58

description: 340k MIP array

source_name: Extracranial metastasis,Patient58


title: Autoimmune LPR6 4M 2 #2


title: Autoimmune LPR7 4M 2


title: Autoimmune LPR8 1.5M 2


title: Autoimmune LPR7 1.5M 2


title: Brain metastasis_Patient05

description: 340k MIP array

source_name: Brain metastasis,Patient05


title: Brain metastasis_Patient16

description: 340k MIP array

source_name: Brain metastasis,Patient16


title: Autoimmune LPR10 1.5M 2

source_name: mouse serum


title: Autoimmune LPR8 1.5M #2 2


title: Autoimmune LPR9 1.5M 2


title: Autoimmune LPR4 1.5M 2


title: Autoimmune MRL/mp 557 4M

value: MRL/mp


title: Autoimmune LPR3 1.5M 2


title: Autoimmune LPR5 1.5M 2


title: Autoimmune LPR6 1.5M 2


title: Autoimmune MRL/mp 502 4M


title: Autoimmune MRL/mp 561 4M


title: Autoimmune LPR2 1.5M 2


title: Autoimmune LPR1 1.5M 2


title: Autoimmune MRL/mp 478 4M


title: Autoimmune MRL/mp 560 4M


title: Autoimmune MRL/mp 423 4M


title: Autoimmune MRL/mp 422 4M


title: Control C3H/HeJ 6


title: Control C3H/HeJ 8


title: Autoimmune MRL/mp 421 4M


title: Control C3H/HeJ 9


title: Control C3H/HeJ 7


title: Control C3H/HeJ 5


title: Control C3H/HeJ 4


title: Control C3H/HeJ 2


title: Control C3H/HeJ 3


title: genomic dna from ovarian_Tyknu_d10_mock

city: Baltimore

first: Stephen

last: Baylin

state: Maryland

address: 1650 Orleans St CRB I RM 541

institute: Johns Hopkins UniversityJohns Hopkins Medical Institutions

hyb_protocol: Bisulfite-converted DNA was analyzed using Illumina’s Infinium Human Methylation450 Beadchip Kit (WG-314-1001) by following manufacturer’s manual. Beadchip contains 485,577 CpG loci in human genome. Briefly, 4 ul of bisulfite-converted DNA was added to a 0.8 ml 96-well storage plate (Thermo Scientific), denatured in 0.014N sodium hydroxide, neutralized and amplified with kit-provided reagents and buffer at 37C for 20-24 hours. Samples were fragmented using kit-provided reagents and buffer at 37C for one hour and precipitated by adding 2-propanol. Re-suspended samples were denatured in a 96-well plate heat block at 95C for 20 minutes. 12 ul of each sample was loaded onto a 12-sample chip and the chips were assembled into hybridization chamber as instructed in the manual. After incubation at 48C for 16-20 hours, chips were briefly washed and then assembled and placed in a fluid flow-through station for primer-extension and staining procedures.

scan_protocol: Polymer-coated chips were image-processed in Illumina’s iScan scanner.

data_processing:
Data were extracted using Methylation Module of GenomeStudio v1.0 Software. The 'signal_intensities.txt' contains unmethylated and methylated signal intensities. Methylation status of each CpG site was presented as b (beta) value based on following definition:
b  value = (signal intensity of methylation-detection probe)/(signal intensity of methylation- detection probe + signal intensity of non-methylation-detection probe + 100).

growth_protocol: Breast, colon, and ovarian cancer cell lines were maintained under ATCC recommended growth conditions.

extract_protocol: Genomic DNA was extracted and purified from cell pellets using the Qiagen DNeasy Kit according to the manufacturer's instructions.

treatment_protocol: Cell lines were treated with 500 nM 5-azacitidine for 72 hours while in log-growth phase, changing the media and drug every 24 hours for AZA treatment. Cells were harvested at 1, 3, 7, 10, 14, or 21 days following initial application of drug.

tag: cell line

value: Tyknu

tag: cell type

value: ovarian cancer cell line

tag: sample group


title: genomic dna from ovarian_Tyknu_d10_Aza

label_protocol: Bisulfite-converted DNA was analyzed using Illumina’s Infinium Human Methylation450 Beadchip Kit (WG-314-1001) by following manufacturer’s manual. Beadchip contains 485,577 CpG loci in human genome. Briefly, 4 ul of bisulfite-converted DNA was added to a 0.8 ml 96-well storage plate (Thermo Scientific), denatured in 0.014N sodium hydroxide, neutralized and amplified with kit-provided reagents and buffer at 37C for 20-24 hours. Samples were fragmented using kit-provided reagents and buffer at 37C for one hour and precipitated by adding 2-propanol. Re-suspended samples were denatured in a 96-well plate heat block at 95C for 20 minutes. 12 ul of each sample was loaded onto a 12-sample chip and the chips were assembled into hybridization chamber as instructed in the manual. After incubation at 48C for 16-20 hours, chips were briefly washed and then assembled and placed in a fluid flow-through station for primer-extension and staining procedures.


title: genomic dna from ovarian_SKOV3_d3_mock


title: genomic dna from ovarian_OVKATE_d10_Aza

value: OVKATE


title: genomic dna from ovarian_OVKATE_d3_Aza


title: genomic dna from ovarian_SKOV3_d10_mock


title: genomic dna from ovarian_OVKATE_d10_mock


title: genomic dna from ovarian_SKOV3_d10_Aza


title: genomic dna from ovarian_SKOV3_d3_Aza


title: genomic dna from ovarian_Tyknu_d3_Aza


title: genomic dna from ovarian_Tyknu_d3_mock


title: Autoimmune LPR7 4M 2 #2


title: Autoimmune LPR#2 1 Slide 2 4M


title: genomic dna from ovarian_OVCAR5_d10_Mock


title: genomic dna from ovarian_OVKATE_d3_mock


title: genomic dna from ovarian_OVCAR5_d10_Aza


title: genomic dna from ovarian_OVCAR3_d10_AZA


title: genomic dna from ovarian_OVCAR3_d10_Mock


title: genomic dna from ovarian_OVCAR5_d3_Aza


title: genomic dna from ovarian_OVCAR3_d3_AZA


title: genomic dna from ovarian_OVCAR5_d3_Mock


title: genomic dna from ovarian_OVCAR3_d3_Mock


title: genomic dna from ovarian_OV2008_d10_Aza


title: genomic dna from ovarian_OV2008_d10_mock


title: genomic dna from ovarian_OV2008_d3_Aza


title: Control C3H/HeJ 1


title: genomic dna from ovarian_OV2008_d3_mock


title: genomic dna from ovarian_OAW28_d10_Aza


title: genomic dna from ovarian_OAW28_d3_Aza


title: genomic dna from ovarian_OAW28_d10_mock


title: genomic dna from ovarian_OAW28_d3_mock


title: genomic dna from ovarian_Kuramochi_d10_mock

value: Kuramochi


title: genomic dna from ovarian_Kuramochi_d3_mock


title: genomic dna from ovarian_Hey_d10_Aza

value: Hey


title: genomic dna from ovarian_Kuramochi_d3_Aza


title: Brain metastasis_Patient17

description: 340k MIP array

source_name: Brain metastasis,Patient17

tag: gender


title: Brain metastasis_Patient06

description: 340k MIP array

source_name: Brain metastasis,Patient06

tag: tissue


title: genomic dna from ovarian_Hey_d10_mock


title: Autoimmune LPR#1 1 Slide 2 4M


title: Autoimmune LPR#5 1 Slide 1 4M


title: Autoimmune LPR#2 1 Slide 1 4M


title: Autoimmune LPR#5 1 Slide 3 4M


title: Autoimmune LPR#4 1 Slide 2 4M


title: Autoimmune LPR#4 1 Slide 3 4M


title: Autoimmune LPR#1 1 Slide 3 4M


title: Autoimmune LPR#5 1 Slide 2 4M


title: genomic dna from ovarian_Hey_d3_Aza


title: genomic dna from ovarian_Hey_d3_mock


title: genomic dna from ovarian_Es2_d10_Aza


title: Autoimmune LPR#2 1 Slide 3 4M


title: genomic dna from ovarian_ES2_d10_mock


title: Autoimmune LPR #3 1 Slide 1 4M


title: Autoimmune LPR#4 1 Slide 1 4M


title: genomic dna from ovarian_ES2_d3_mock


title: genomic dna from ovarian_Es2_d3_Aza


title: genomic dna from ovarian_Kuramochi_d10_Aza


title: genomic dna from ovarian_EF027_d10_mock


title: genomic dna from ovarian_CAOV3_d10_AZA


title: genomic dna from ovarian_CAOV3_d3_AZA


title: genomic dna from ovarian_CAOV3_d3_Mock2


title: genomic dna from ovarian_A2780_d10_AZA


title: genomic dna from ovarian_EF027_d3_mock


title: genomic dna from colon_COLO205_AZA_D10

value: colon cancer cell line


title: genomic dna from colon_COLO205_AZA_D14


title: genomic dna from ovarian_EF027_d10_Aza


title: genomic dna from colon_COLO205_AZA_D7


title: genomic dna from ovarian_A2780_d3_Mock


title: Autoimmune LPR #3 1 Slide 2 4M

value: Female


title: genomic dna from colon_COLO205_Mock_D3


title: genomic dna from colon_SKCO1_AZA_D21


title: genomic dna from colon_COLO205_AZA_D3


title: genomic dna from colon_COLO205_AZA_D21


title: genomic dna from colon_SKCO1_AZA_D14


title: genomic dna from ovarian_A2780_d3_AZA


title: Autoimmune LPR#1 1 Slide 1 4M


title: genomic dna from ovarian_EF027_d3_Aza


title: genomic dna from colon_SKCO1_AZA_D10


title: genomic dna from ovarian_CAOV3_d10_Mock


title: genomic dna from colon_SW620_AZA_D14


title: genomic dna from colon_SW620_AZA_D10


title: genomic dna from colon_SKCO1_AZA_D7


title: genomic dna from ovarian_A2780_d10_Mock


title: genomic dna from colon_SW620_AZA_D21


title: genomic dna from colon_SW620_AZA_D7


title: genomic dna from colon_SKCO1_Mock_D3


title: genomic dna from colon_SW620_AZA_D3


title: genomic dna from colon_CACO2_AZA_D21


title: genomic dna from colon_CACO2_AZA_D14


title: genomic dna from colon_SW620_Mock_D3


title: genomic dna from colon_CACO2_AZA_D7


title: Autoimmune MRL/mp 510 4M


title: genomic dna from colon_SW480_AZA_D14


title: genomic dna from colon_SW480_AZA_D10


title: genomic dna from colon_SW480_AZA_D3


title: genomic dna from colon_CACO2_Mock_D3


title: genomic dna from colon_SW480_AZA_D7


title: genomic dna from colon_SW480_Mock_D3


title: genomic dna from colon_SW48_Aza_14


title: genomic dna from colon_SW48_Mock_3


title: genomic dna from colon_SW48_Aza_3


title: genomic dna from colon_SKCO1_AZA_D3


title: genomic dna from colon_SNUC1_Aza_14


title: genomic dna from colon_SNUC1_Aza_10


title: genomic dna from colon_SNUC1_Mock_3


title: genomic dna from colon_SNUC1_Aza_3


title: genomic dna from colon_CACO2_AZA_D10


title: genomic dna from colon_CACO2_AZA_D3


title: genomic dna from colon_RKO_AZA_D21

value: RKO


title: genomic dna from colon_RKO_AZA_D10


title: genomic dna from colon_RKO_AZA_D14


title: genomic dna from colon_SW48_Aza_10


title: genomic dna from colon_SW480_AZA_D21


title: genomic dna from colon_RKO_AZA_D3


title: genomic dna from colon_RKO_AZA_D7


title: genomic dna from colon_Lovo_AZA_Day21

value: Lovo


title: genomic dna from colon_RKO_Mock_D3


title: genomic dna from colon_Lovo_AZA_Day14


title: _8_Cy3 (HX12)

city: Golden

first: Shihui

last: YANG

state: CO

address: 1617 Cole Blvd

department: National Bioenergy Center

institute: National Renewable Energy Lab

hyb_protocol: The labeling, hybridization, and scanning following NimbleGen company's protocols.

data_processing:
Raw data: ORF/gene-level .calls files.
Statistical analysis was done with JMP Genomics 4.0 software (SAS Institute, Cary, NC). The data were subsequently normalized using the standard normalization algorithm (Loess) within JMP Genomics. An analysis of variance (ANOVA) was performed to determine differential expression levels between conditions and time points using the FDR testing method (p < 0.05).

organism: Acetivibrio thermocellus ATCC 27405

growth_protocol: Batch fermentations were conducted in approximately 5 L of MTC medium with switchgrass as carbon source as described previously (Yang et al., 2008).

extract_protocol: RNA was isolated essentially described previously (Yang et al. 2010. PNAS. 107:10395–10400). Briefly, samples were harvested by centrifugation and the TRIzol reagent (Invitrogen, Carlsbad, CA) was used to extract total cellular RNA. Each total RNA preparation was treated with RNase-free DNase I (Ambion, Austin, TX) to digest residual chromosomal DNA and subsequently purified with the Qiagen RNeasy Mini kit in accordance with the instructions from the manufacturer. Total cellular RNA was quantified at OD260 and OD280 with a NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE) and the RNA quality was checked with Agilent Bioanalyzer (Agilent, CA). The purified RNA with good quality from each sample was used as the template to generate ds-cDNA using Invitrogen ds-cDNA synthesis kit (Invitrogen, CA).

tag: time point

tag: array


title: genomic dna from colon_Lovo_AZA_Day10


title: _7_Cy3 (HX12)

scan_protocol: The labeling, hybridization, and scanning following NimbleGen company's protocols.


title: _10_Cy3 (HX12)

label_protocol: The labeling, hybridization, and scanning following NimbleGen company's protocols.


title: _9_Cy3 (HX12)


title: _6_Cy3 (HX12)


title: _11_Cy3 (HX12)


title: genomic dna from colon_Lovo_AZA_Day7


title: _5_Cy3 (HX12)


title: _4_Cy3 (HX12)


title: genomic dna from colon_Lovo_AZA_Day3


title: _1_Cy3 (HX12)


title: genomic dna from colon_Lovo_Mock_Day1


title: _2_Cy3 (HX12)


title: genomic dna from colon_HT29_Aza_14


title: _3_Cy3 (HX12)


title: genomic dna from colon_HT29_Aza_3


title: genomic dna from colon_HCT116_AZA_D21


title: genomic dna from colon_HCT116_AZA_D14


title: genomic dna from colon_HT29_Mock_3


title: genomic dna from colon_HCT116_AZA_D10


title: genomic dna from colon_HCT116_AZA_D7


title: genomic dna from colon_HCT116_AZA_D3


title: genomic dna from colon_HCT116_Mock_D3


title: genomic dna from colon_HT29_Aza_10


title: genomic dna from colon_DLD1_AZA_Day21


title: genomic dna from colon_DLD1_AZA_Day14


title: genomic dna from colon_DLD1_AZA_Day10


title: genomic dna from colon_DLD1_AZA_Day7


title: genomic dna from colon_DLD1_Mock_Day1


title: 36HPI-EV71 Infected3

city: Brisbane

first: Edmund

last: Lui

state: qld

address: 2 George Street, Brisbane QLD 4000

institute: Queensland University of Technology

description: miRNA profile of EV71 infected HT29 cells at 36hpi

hyb_protocol: Labelled samples will subsequently be processed according to manufacturer's instructions for the Affymetrix miRNA Array 2.0 (Affymetrix, Santa Clara, CA).

scan_protocol: After hybridisation for 16 h at 48°C, the arrays will be washed and stained in an Affymetrix Fluidics station 450, then scanned in an Affymetrix 3000 7G scanner

data_processing: Raw data for the microarray was analysed with Partek® Genomics Suite (Partek Incorporated, Saint Louis, USA) where p<0.05 is considered significant.

source_name: 36HPI-EV71 Infected 3

label_protocol: The extracted total RNA was labelled with FlashTag™ Biotin HSR RNA Labeling Kits for the Affymetrix GeneChip miRNA array according to manufacturer’s instruction.

growth_protocol: HT29 cells were seeded at a concentration of 5 × 105 cells/ml in 6-well plates and incubated for 24h at 37°C with 5% CO2.

extract_protocol: The respective infected cells were harvest at 36 hours posts infection (hpi). The total cellular RNA of HT29 cells were extracted using the miRNeasy mini kit (Qiagen, Hilden, Germany) in accordance to the manufacturer’s instructions.

treatment_protocol: Cells were washed twice with phosphate buffered saline (PBS) and infected with EV71 at multiplicity of infection (MOI) of 1 or nil respectively


title: 36HPI-Control 1

description: miRNA profile of control

source_name: 36HPI-Control 1


title: genomic dna from colon_COLO320_Aza_14


title: 36HPI-Control 2

description: miRNA profile of control

source_name: 36HPI-Control 2


title: 36HPI-EV71 Infected2

source_name: 36HPI-EV71 Infected 2


title: 36HPI-Control 3

description: miRNA profile of control

source_name: 36HPI-Control 3


title: AcR_MM_NaAc_F5_190h

hyb_protocol: The ds-cDNA was sent to NimbleGen for labeling, hybridization, and scanning following company's protocols.

data_processing: Statistical analysis was done with JMP Genomics 4.0 software (SAS Institute, Cary, NC). The data were subsequently normalized using the standard normalization algorithm within JMP Genomics. An analysis of variance (ANOVA) was performed to determine differential expression levels between conditions and time points using the FDR testing method (p < 0.05).

organism: Zymomonas mobilis subsp. mobilis ZM4 = ATCC 31821

growth_protocol: Batch fermentations were conducted in approximately 4 L of MM medium in 7.5-L BioFlo110 bioreactors (New Brunswick Scientific, Edison, NJ) fitted with agitation, pH, temperature and DOT probes and controls as described previously (Yang et al., 2008).

extract_protocol: RNA was isolated essentially described previously [26]. Briefly, samples were harvested by centrifugation and the TRIzol reagent (Invitrogen, Carlsbad, CA) was used to extract total cellular RNA. Each total RNA preparation was treated with RNase-free DNase I (Ambion, Austin, TX) to digest residual chromosomal DNA and subsequently purified with the Qiagen RNeasy Mini kit in accordance with the instructions from the manufacturer. Total cellular RNA was quantified at OD260 and OD280 with a NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE) and the RNA quality was checked with Agilent Bioanalyzer (Agilent, CA). The purified RNA with good quality from each sample was used as the template to generate ds-cDNA using Invitrogen ds-cDNA synthesis kit (Invitrogen, CA).

tag: time

tag: growth phase

value: Stationary

tag: genotype

value: Zymomonas mobilis subsp. mobilis ZM4 acetate-tolerant mutant AcR


title: ZM4_MM_NaAc_F3_148h

scan_protocol: The ds-cDNA was sent to NimbleGen for labeling, hybridization, and scanning following company's protocols.

value: Exponential

value: Zymomonas mobilis subsp. mobilis ZM4


title: ZM4_MM_NaAc_F3_190h

label_protocol: The ds-cDNA was sent to NimbleGen for labeling, hybridization, and scanning following company's protocols.


title: genomic dna from colon_COLO320_Aza_10


title: AcR_MM_NaAc_F5_166h


title: ZM4_MM_NaAc_F2_190h


title: AcR_MM_NaAc_F5_148h


title: ZM4_MM_NaAc_F2_148h


title: ZM4_MM_NaAc_F3_166h


title: AcR_MM_NaAc_F6_190h


title: AcR_MM_NaAc_F6_166h


title: ZM4_MM_NaAc_F2_130h


title: genomic dna from colon_DLD1_AZA_Day3


title: AcR_MM_NaAc_F6_148h


title: ZM4_MM_NaAc_F2_166h


title: 36HPI-EV71 Infected1

source_name: 36HPI-EV71 Infected 1


title: ZM4_MM_NaAc_F3_130h


title: genomic dna from colon_COLO201_AZA_D3


title: genomic dna from colon_COLO201_AZA_D10


title: genomic dna from colon_COLO201_AZA_D7


title: genomic dna from colon_COLO320_Mock_3


title: genomic dna from colon_COLO201_Mock_D3


title: genomic dna from breast_HCC1937_AZA_day10

value: breast cancer cell line


title: genomic dna from colon_COLO320_Aza_3


title: genomic dna from colon_COLO201_AZA_D21


title: genomic dna from breast_HCC1937_AZA_day7


title: AcR_MM_NaAc_F5_130h


title: genomic dna from colon_COLO201_AZA_D14


title: AcR_MM_NaAc_F6_130h


title: KT2440(pCAR1DpmrDphu)-biofilm

city: Tokyo

first: Hideaki

last: Nojiri

address: 1-1-1 Yayoi, Bunkyo-ku

department: Biotechnology Research Center

description: This is an Affymetrix custom-commercial tiling array that covers thePseudomonas putida KT2440 chromosome (RefSeq: NC_002947) at 11-bp density.  BPMAP files are provided as supplementary files. KT2440b520511FR-3.bpmap represents  the forward strand of KT2440 chromosome, and KT2440b520511FF-3.bpmap represents the reverse strand of KT2440 chromosome.

hyb_protocol: Labeled cDNA was mixed with 50 pM control oligonucleotide B2 (Affymetrix), 1× Hybridization Mix (Affymetrix), and 7% DMSO in a total volume of 200 µl and denatured at 95˚C for 5 min. Per array, 200 µl of the hybridization cocktail was hybridized at 50˚C for 16 h with a rotation rate of 60 rpm using a GeneChip Hybridization Oven 640 (Affymetrix). Chips were washed and stained using a Hybridization, Wash, and Stain Kit (Affymetrix) according to the the modified FleX450-0005 protocol (for chromosomal tiling array, changed temperature of ‘the Post Hyb Wash #2” to 50˚C) of GeneChip Fluidics station 450 (Affymetrix).

scan_protocol: Arrays were scanned on an Affymetrix Scanner 3000 7G

data_processing:
The CEL files were generated using Affymetrix GCOS. Data was quantile normalized and analyzed with Affymetrix Tiling Analysis Software v1.1, which uses non-parametric quantile normalization and a Hodges-Lehmann estimator for fold enrichment.The intensities were linearly scaled so that the median was 100. Each CEL file was converted into the BAR files using KT2440b520511FR-3.bpmap for the forward strand and KT2440b520511FF-3.bpmap for the reverse strand; the BAR files with F indicate the forward strand and with R indicate the reverse strand of KT2440 chromosome. Bandwidth: 30, Threshold: 0, MaxGap: 30, MinRun, 30.
KT2440b520511FR-3.bpmap
KT2440b520511FF-3.bpmap

organism: Pseudomonas putida

source_name: cDNA prepared from LB culture of KT2440(pCAR1dpmrdphu)

label_protocol: Single-strand cDNA was synthesized in 60 µl of 1× First Strand Buffer (Invitrogen, Carlsbad, CA) containing 12  µg of total RNA, 360ng of actinomycin D (A1410, SIGMA, St.Louis, USA), 750 ng of random primers (Invitrogen), 1500 units of SuperScript II (Invitrogen), 60 units of RNaseOUT (Invitrogen), 10 mM DTT (Invitrogen), 0.5 mM dATP, 0.5 mM dCTP, 0.5 mM dGTP, 0.4 mM dTTP, and 0.1 mM dUTP (Roche Applied Science, Mannheim, Germany). After the RNA and random primers were denatured at 70˚C for 10 min and annealed at 25˚C for 10 min, the remaining reagents were added, and the reaction mixture was then incubated at 25˚C for 10 min, 37˚C for 60 min, 42˚C for 60 min, and 70˚C for 10 min. After cDNA synthesis, template RNA was degraded with one-third volume of 1N NaOH at 65˚C for 30 min; one-third volume of 1N HCl was added to neutralize the reaction mixture before cleanup. The cDNA was purified using a QIAquick PCR Purification Kit (Qiagen). The cDNA was fragmented and labeled using GeneChip WT Double-Stranded DNA Terminal Labeling Kit (Affymetrix). The purified single-stranded cDNA (~5 µg) was fragmented in 48 µl of 1× cDNA Fragmentation Buffer containing 15 units of Uracil DNA Glycosylase (UDG) and 225 units of Apurinic/apyrimidinic Endonuclease 1 (APE1) at 37˚C for 60 min, and incubated at 93˚C for 2 min. The fragmented cDNA was labeled in 60 µl of 1× TdT Buffer containing 60 units of Terminal Deoxynucleotidyl Transferase (TdT) and 0.083 mM GeneChip DNA Labeling Reagent at 37˚C for 60 min, and incubated at 70˚C for 2 min.

growth_protocol: Each strain was grown in 5 ml of LB at 300 strokes/min for 14-14.5 h (pre-culture) and then washed and transferred into 100-ml of NMM-4 buffer (Miyakoshi et al. Transcriptome analysis of Pseudomonas putida KT2440 harboring the completely sequenced IncP-7 plasmid pCAR1. J Bacteriol 2007 Oct;189(19):6849-60. PMID: 17675379) supplemented with 0.1% succinate adjusting its turbidity (600 nm) at 0.05. The resultant culture was incubated on a rotary shaker at 120 rpm and cell growth was monitored in by measuring its turbidity (600 nm).

extract_protocol: Cells were treated with RNA Protect Bacteria reagent (Qiagen, CA, USA) to stabilize RNA of them.Total RNA was extracted using NucleoSpin RNA II (Macherey-Nagel GmbH & Co. KG, Düren, Germany). The eluted RNA was treated with RQ1 RNase-free DNase (Promega, Madison, WI) at 37˚C for 30 min. After inactivation of DNase by the addition of the provided stop reagent and subsequent incubation at 65˚C for 10 min, total RNA was repurified using NucleoSpin RNA Clean-up (Macherey-Nagel).

tag: genotype/variation