title: P057N


title: P070T

status: Public on Oct 05 2012

type: RNA

city: Lund

first: Rolf

last: Søkilde

address: Scheelevägen 2

department: Department of Oncology

country: Sweden

institute: Lund University, Sweden

hyb_protocol: Hybridization was performed in the hybridization station (Tecan Group Ltd., Männedorf, Switzerland) for 16 hours, followed by stringency washes. Subsequently, slides were dried and scanned.

scan_protocol: The arrays were scanned by the Agilent scanner (Agilent Technologies, Santa Clara, CA, USA) to generate Tagged Image File Format (TIFF) images. The analysis was performed using the relevant GenePix® Array Lists (GAL files) (www.exiqon.com). Image analysis: The intensities were converted to digital values using Imagene version 7.0 software. The quality control of the spots was performed by the software and adjusted manually.

data_processing: Data processing and normalization: Low-level analysis was performed in the R statistical computing environment, including importing and pre-processing of the data using the LIMMA package (available at http://bioconductor.org). After excluding flagged spots from the analysis, the “normexp” background correction method, plus offset=50 was applied. The intensities were log2 transformed and quantile normalized as implemented in LIMMA. Log2 intensities (single channel analysis) of four intra-slide replicates were averaged.

molecule: total RNA

organism: Homo sapiens

source_name: rectal, tumor

label_protocol: One µg of total RNA from each sample was labeled using the miRCURY™ LNA microRNA Power labeling kit (Exiqon) following a two-step protocol: First, Calf Intestinal Alkaline Phosphatase (CIAP) was applied to remove terminal 5'phosphates; second, fluorescent labels were attached enzymatically to the 3'-end of the microRNAs. Sample-specific RNA was labeled with Hy3 (green channel) fluorophore.

extract_protocol: RNA was extracted using TRIZOL (Invitrogen, Carlsbad, CA). Nucleic acid quantity, quality and purity were determined using a spectrophotometer (Nanodrop, Rockland, DE) and a 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA).

tag: tissue

value: rectal tumor

tag: t (tumor) or n (normal)

value: T

tag: patient identifier


title: P056N

source_name: rectal, normal

value: normal rectal mucosa

value: N


title: P067T


title: P066T


title: Cologne_251275011633

type: genomic

city: Genova

first: PAOLA

last: SCARUFFI

state: GE

address: LARGO R. BENZI, 10

country: Italy

institute: "San Martino" Hospital

description: aCGH analysis

hyb_protocol: Labelled DNAs were hybridized to whole-genome oligonucleotide 2x105K or 4x44K microarrays (Agilent Technologies) following the manufacture's instructions ("Agilent Oligonucleotide Array-Based CGH for Genomic DNA Analysis protocol”, v. 5.0 (Agilent Technologies). Briefly, fluorescent-labeled reference and tumor DNAs (3 ug each) were mixed with 50 ug of human Cot-1 DNA (Invitrogen Life Technologies) and control targets (Agilent Technologies). Slides were hybridized in SureHyb gasket (Agilent Technologies) placed in rotisserie (20 RPM rotation speed) in hybridization oven at 65°C for 40 hrs. After hybridization, the slides were washed with Oligo aCGH Wash Buffer 1(Agilent Technologies) at room temperature for 5 min, with Oligo aCGH Wash Buffer 2 (Agilent Technologies) at 37°C for 1 min, with the Stabilization solution (Agilent) for 1 minute at room temperature, then dried immediately by rinsing slides into Drying solution (Agilent) for 30 seconds.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using the following settings: Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel 1 is set to Red & Green, Red PMT is set to 100%, Green PMT is set to 100% . Microarray performance was assessed by QC metric tool.

data_processing:
The scanned TIFF images were loaded into the Feature Extraction (v9.5 Agilent technologies), Feature Extraction files were analyzed by CGH Analytics Software (v. 3.5.14 Agilent Technologies) applying Z-Score algorithm.

Z-score data is not available for GEO submission.

molecule: genomic DNA

source_name: tumor sample

label_protocol: We followed the "Agilent Oligonucleotide Array-Based CGH for Genomic DNA Analysis protocol”, v. 5.0 (Agilent Technologies). Briefly, 2 ug of sample and reference genomic DNAs (for reference were used Human Genomic DNA: male Cat G1471, female Cat G1521, Promega, Madison, WI)  were separately digested with AluI/RsaI restriction enzyme mix (Promega). Fragmented DNA was labeled by direct enzymatic incorporation of fluorescent tags. Genomic DNA was labeled with Cy3-dUTP or Cy5-dUTP (Perkin Elmer) using the Random-Primed Bioprime DNA Labeling kit (Invitrogen Life Technologies). Briefly, 50 ul reaction mix containing dATP, dGTP and dTTP (120 ueach), dUTP (60 uM) and Cy3-dUTP (60 uM) or Cy5-dUTP (60 uM) was incubated with Klenow Fragment (40 units) at 37°C for 2 hrs. Unincorporated nucleotides were removed on Microcon YM-30 filters (Millipore) according to the manufacturer’s protocol. Dye incorporations of post-labeling products were measured by NanoDrop 1000 (ThermoScientific) and the parameters that predicted successful hybridization were a minimum Cy3 incorporation of 0.5 pmol/ul and Cy5 incorporation of 0.3 pmol/ul.

extract_protocol: Genomic DNA was extracted overnight with lysis buffer containing K proteinase (0.2 mg/ml) followed by standard phenol/chloroform extraction. DNA content and quality were measured by Biophotometer (Eppendorf)

value: Neuroblastoma

tag: tumor stage

tag: patient nationality

value: German

tag: gender

tag: group

value: long-survivor

source_name: reference

value: Normal Reference DNA


title: P072T


title: Cologne_251275011612

description: aCGH analysis


title: P065T


title: P071T


title: Cologne_251275011600

description: aCGH analysis


title: Cologne_251275011608

description: aCGH analysis


title: Cologne_251270010270

description: aCGH analysis


title: BT373_A

city: Candiolo

first: Enzo

last: Medico

state: TO

address: Strada Prov. 142, km 3,95

department: Oncology

institute: Candiolo Cancer Institute, University of Torino

description:
glioblastoma stem cells cultured as neurospheres, patient 6
10 - BT 373 - EXP 233

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard scanning on a Illumina Beadstation 500

data_processing: Raw data were processed and cubic-spline normalized with Illumina Genome Studio

label: biotin-SA Cy3

label_protocol: Biotinylated cRNA was prepared using the Illumina TotalPrep RNA Amplification Kit (Ambion) according to the manufacturer’s recommendations

growth_protocol: standard neurobasal medium for the growth of neurospheres (DMEM/F12, B27, EGF and bFGF)

extract_protocol: RNA extraction was performed using Trizol plus RNA purification kit (Invitrogen). RNA qualitative and quantitative assessment was performed using the Bioanalyzer 2100 (Agilent Tecnologies).

treatment_protocol: No treatment

tag: tissue type

value: Neurosphere

tag: glioblastoma subtype

value: Classical

tag: egfr status

value: EGFR AMP

value: IV

tag: age

value: M

tag: localization

value: F dx


title: BT379_A

description:
glioblastoma stem cells cultured as neurospheres, patient 9
3 - BT 379 - EXP 244

value: Mesenchymal

value: EGFR WT

value: FTP dx


title: P057T

value: rectal tumor


title: BT358_B

description:
glioblastoma stem cells cultured as neurospheres, patient 12
28 - BT358 - EXP 247

value: F


title: BT379_B

description:
glioblastoma stem cells cultured as neurospheres, patient 9
4 - BT 379 - EXP 244


title: P064N

value: normal rectal mucosa


title: BT358_A

description:
glioblastoma stem cells cultured as neurospheres, patient 12
21 - BT 358 - EXP 247


title: BT373_B

description:
glioblastoma stem cells cultured as neurospheres, patient 6
12 - BT 373 - EXP 233


title: BT347_B

description:
glioblastoma stem cells cultured as neurospheres, patient 10
6 - BT 347 - EXP 244

value: T sx


title: 1045

description: aCGH analysis

value: Neuroblastoma

value: Italian

value: male


title: P037N

value: N


title: BT347_A

description:
glioblastoma stem cells cultured as neurospheres, patient 10
5 - BT 347 - EXP 244

value: Neurosphere


title: P033N


title: P036N


title: P032N


title: P020N


title: P030N


title: P056T

value: T


title: P023N


title: P060T


title: P019N


title: P031N


title: P011N


title: P073T


title: BT337_B

description:
glioblastoma stem cells cultured as neurospheres, patient 14
25 - BT 337 - EXP 247

value: Proneural

value: FTP sx


title: P009N


title: BT334_B

description:
glioblastoma stem cells cultured as neurospheres, patient 7
14 - BT 334 - EXP 233

value: Classical

value: EGFR AMP

value: IV

value: M

value: FT dx


title: P037T

value: rectal tumor


title: BT334_A

description:
glioblastoma stem cells cultured as neurospheres, patient 7
13 - BT 334 - EXP 233


title: P036T


title: BT337_A

description:
glioblastoma stem cells cultured as neurospheres, patient 14
24 - BT 337 - EXP 247

value: EGFR WT


title: BT332_B

description:
glioblastoma stem cells cultured as neurospheres, patient 18
10 - BT 332 - EXP 267

value: PO sx


title: P033T


title: BT332_A

description:
glioblastoma stem cells cultured as neurospheres, patient 18
9 - BT 332 - EXP 267


title: Sgo1-3V5 ChIP from metaphase-I arrested CUP-CLB3 cells

city: Cambridge

first: Elcin

last: Unal

state: MA

address: 500 Main Street 76-561

department: Koch Institute

country: USA

institute: Massachusetts Institute of Technology HHMI

description: Sgo1ChIP CUP-CLB3 metaphase I

hyb_protocol: Samples were co-hybridized to custom Agilent arrays in 1X Agilent hybridization buffer at 65°C for 16 hours. Samples were washed according to manufacturer's instructions.

scan_protocol: Agilent scanner using the AgilentHD_CGH protocol (5μM resolution, 100% PMT for each laser).

data_processing: Cy3 and Cy5 levels and background were calculated using Agilent Feature Extractor software. Background normalization, log2 ratios for each experiment and scale normalizations across each set of experiments were calculated using the sma package in R (Yang, et al., 2001), a computer language and environment for statistical computing (v2.1.0, http://www.r-project.org).

organism: Saccharomyces cerevisiae

source_name: meiotic budding yeast cells depleted of Cdc20 for metaphase-I arrest, 7 hrs in SPO-medium

label_protocol: Half of the immunoprecipitated DNA or one tenth of the input DNA was labeled with Cy3- or Cy5-dUTP (GE Healthcare) by random priming using 4 µg random nonamer oligo (Integrated DNA Technologies) and 10 units of Klenow (New England Biolabs). Unincorporated dye was removed using microcon columns (30-kDa MW cutoff, Millipore).

growth_protocol: Cells were grown to saturation in YPD at room temperature, diluted in BYTA (1% yeast extract, 2% tryptone, 1% potassium acetate, 50mM potassium phthalate) to OD600 = 0.25, and grown overnight at 30°C. Cells were resuspended in sporulation medium (0.3% potassium acetate [pH 7], 0.02% raffinose, 0h) to OD600 = 1.85 and sporulated at 30°C.

extract_protocol: 400 OD600 units of cells were fixed for 15 min at room temperature in 1% formaldehyde. The formaldehyde was quenched by addition of 125 mM glycine. Samples were processed as previously described (Vader et al., 2011). Before immunoprecipitation, one twentieth of the sample was removed as the input sample. Rec8-13myc was immunoprecipitated using 2-5μg of  anti-myc antibody (9E11)  for 12-16h at 4°C, followed by 2h in combination with 50μl of 50% slurry Protein G beads (Roche). Pds5 was immunoprecipitated with 1.3μl of rabbit anti-Pds5 antibody 12-16h at 4°C, followed by 2h in combination with 50μl of 50% slurry Protein A beads (Roche). Sgo1-3V5 was immunoprecipitated with 40-50μl of 50% slurry anti-V5 agarose affinity gel (Sigma) for 12-16h at 4°C.

tag: strain

tag: genotype/variation

tag: chip antibody

value: 50% slurry anti-V5 agarose affinity gel

tag: chip antibody vendor

value: Sigma

tag: chip antibody cat. #

tag: sample type

value: input


title: Sgo1-3V5 ChIP from metaphase-I arrested wild-type cells

description: Sgo1ChIP wild-type metaphase I

value: wild-type


title: P032T

tag: tissue

tag: t (tumor) or n (normal)


title: BT328_B

description:
glioblastoma stem cells cultured as neurospheres, patient 11
10 - BT 328 - EXP 244

value: Mesenchymal

tag: tumor stage

value: F sx


title: Sgo1-3V5 ChIP from prophase-I arrested wild-type cells

description: Sgo1ChIP wild-type prophase I

source_name: meiotic budding yeast cells depleted of Ndt80 for pachytene arrest, 5 hrs in SPO-medium


title: 917

description: aCGH analysis

value: Neuroblastoma

tag: patient nationality

value: Italian

value: male

value: long-survivor

value: Normal Reference DNA


title: BT328_A

description:
glioblastoma stem cells cultured as neurospheres, patient 11
9 - BT 328 - EXP 244

value: Neurosphere

value: IV

tag: gender


title: BT326_A

description:
glioblastoma stem cells cultured as neurospheres, patient 15
1 - BT 326 - EXP 267

value: Classical

value: EGFR AMP

value: M


title: P031T

value: rectal tumor

value: T

tag: patient identifier


title: Sgo1-3V5 ChIP from prophase-I arrested CUP-CLB3 cells

description: Sgo1ChIP CUP-CLB3 prophase I

value: 50% slurry anti-V5 agarose affinity gel

value: Sigma


title: BT314_A

description:
glioblastoma stem cells cultured as neurospheres, patient 8
1 - BT 314 - EXP 244

tag: tissue type

value: Proneural

value: EGFR WT

value: T sx


title: P030T


title: Pds5 ChIP from metaphase-I arrested wild-type cells

description: Pds5ChIP wild-type metaphase I

source_name: meiotic budding yeast cells depleted of Cdc20 for metaphase I arrest, 7 hrs in SPO-medium

value: wild-type

value: rabbit anti-Pds5 antibody (kindly provided by Vincent Guacci)

value: input


title: BT314_B

description:
glioblastoma stem cells cultured as neurospheres, patient 8
2 - BT 314 - EXP 244

tag: glioblastoma subtype


title: Pds5 ChIP from metaphase-I arrested CUP-CLB3 cells

description: Pds5ChIP CUP-CLB3 metaphase I


title: P019T


title: BT326_B

description:
glioblastoma stem cells cultured as neurospheres, patient 15
2 - BT 326 - EXP 267

tag: egfr status

value: F sx


title: Rec8-13myc ChIP from prophase-I arrested wild-type cells

description: Rec8ChIP wild-type prophase I

value: rat anti-myc antibody [9E11]

value: Abcam


title: P012T


title: BT308_A

description:
glioblastoma stem cells cultured as neurospheres, patient 4
7 - BT 308 - EXP 233

value: Neurosphere

value: IV

tag: age


title: P009T


title: P011T


title: BT308_B

description:
glioblastoma stem cells cultured as neurospheres, patient 4
8 - BT 308 - EXP 233

tag: localization


title: P023T


title: BT302_A

description:
glioblastoma stem cells cultured as neurospheres, patient 3
5 - BT 302 - EXP 233

value: Mesenchymal

value: F

value: FP dx


title: Rec8-13myc ChIP from prophase-I arrested CUP-CLB3 cells

description: Rec8ChIP CUP-CLB3 prophase I

tag: strain


title: BT299_B

description:
glioblastoma stem cells cultured as neurospheres, patient 17
8 - BT 299 - EXP 267

value: Classical

value: M

value: TPO sx


title: S. mansoni infected 2 (technical replicate) vs. reference

city: Antwerp

first: Leela Rani

last: Avula

state: Antwerp

address: Groenenborgerlaan 171

department: Dept of Veterinary Sciences

country: Belgium

institute: University of Antwerp

description: technical replicate

hyb_protocol: The two-colour microarray-based gene expression analysis protocol (version 5.7, http://www.agilent.com) was followed to hybridize the samples. A hybridis ation sample volume of 100 µl was applied on each array containing a total of 825 ng of test sample hybridized against the complementarily labeled reference. Hybridized rrays were then incubated at 65°C for 17 h in rotating hybridization chamber.

scan_protocol: The slides were scanned in the Genepix personal 4100A scanner at a wavelength of 532 nm and 635 nm for red and green channels respectively.

data_processing: The photomultiplier tube voltages were adjusted to obtain an overall green/red ratio of one. Images were processed using the GenePix Pro 4.1 software (Axon Instruments) for the identification and quantification of the fluorescent signal intensities of the spots. Statistical analysis was performed using the R package limma. The median background signal was subtracted from the median foreground signal, after which the data were normalized using vsn. Linear models were fitted to intensity ratios, after which probes were ranked in order of evidence of differential expression using an empirical Bayes method. The two inflammation models were contrasted against the Controls and probes were considered differentially expressed when p<0.05 and log2FC>1 or log2FC<−1.

organism: Mus musculus

source_name: S.mansoni-infected ileum

label_protocol: The two-colour microarray-based gene expression analysis protocol (version 5.7, http://www.agilent.com) was followed to construct and fluorescently label cRNA from total RNA extracts. Each Control sample was labeled in Cy5, each S.mansoni-infected sample in Cy3 and each TNBS-treated sample was labeled in Cy5. Additionally one dye flipped technical replicate each was used for Control and S.mansoni-infected samples.

growth_protocol: Adult female C57BL/6J mice were given a standard pellet diet plus water ad libitum, while being housed in a 12 h/12 h light/dark cycle at constant temperature (22˚C).

extract_protocol: Total RNA extracted using Trizol method following manufacturer's instructions

treatment_protocol: Mice were infected with S.mansoni according to the method of Yolles et al.. TNBS-ileitis was induced by laparotomy using a modified procedure of Pontell et al.. After this surgery, animals were maintained in a controlled environment for 24 h. The S.mansoni-infected animals were sacrificed 8 weeks post infection at the acute stage of intestinal schistosomiasis. TNBS-treated animals were sacrificed 24 h post induction at the acute stage of ileitis. All control and inflamed animals were age matched at the time of tissue retrieval. All animals were euthanized by cervical dislocation, full thickness terminal ileal tissue was dissected out and rinsed with Krebs solution. Pieces of ileum weighing around 100 mg each were snap-frozen in liquid nitrogen and stored at -80°C for RNA extraction.

value: ileum

tag: disease state

value: inflamed (intestinal schistosomiasis)

value: female

source_name: reference (Control pool)

value: reference (Control pool)


title: BT297_B

description:
glioblastoma stem cells cultured as neurospheres, patient 13
23 - BT 297 - EXP 247

value: EGFR AMP

value: T sx


title: TNBS treated 3 (biological replicate) vs. reference

description: biological replicate

source_name: TNBS-treated ileum

value: inflamed (TNBS-ileits)


title: BT299_A

description:
glioblastoma stem cells cultured as neurospheres, patient 17
7 - BT 299 - EXP 267

value: EGFR WT


title: reference vs. Control 2 (technical replicate)

description: technical replicate

source_name: Control ileum

value: healthy control


title: BT302_B

description:
glioblastoma stem cells cultured as neurospheres, patient 3
6 - BT 302 - EXP 233

value: Neurosphere


title: BT275_A

description:
glioblastoma stem cells cultured as neurospheres, patient 2
3 - BT 275 - EXP 233

value: IV

value: P dx


title: BT297_A

description:
glioblastoma stem cells cultured as neurospheres, patient 13
22 - BT 297 - EXP 247


title: MC58 wild type with zinc supplementation compared to mc58 zur knock out mutant 5

city: Wuerzburg

first: Biju Joseph

last: Ampattu

address: Josef-Schneider Str 2

department: Department of Microbiology

country: Germany

institute: University of Wuerzburg

description: MC58 zur knock out versus MC58 with Zn supplement_Replicate3_dye swap

hyb_protocol: The labelled DNA were mixed together in hybridization buffer (3 x SSC and 0.1% SDS) and hybridized onto prehybridized microarray slides using a Tecan Hybridization station.

scan_protocol: The slides were scanned using a Genepix Pro scanner with settings to avoid more than 10% of the spots being saturated.

data_processing: Raw data generated after flagging for obvious cases of stray background and spots with a signal to noise ratio of less than 3 were further analyses using the R package limma. Loess normalization was used for within slide and Rquantile normalization was used for between slide normalization.

organism: Neisseria meningitidis

source_name: RNA from strain MC58 grown in RPMI with Zinc supplementation (0.5 uM ZnSO4)

label_protocol: 10 µg of test RNA and 10 µg of reference RNA were labelled with Cy3 dCTP and Cy5 dCTP using reverse transcriptase (Invitrogen)and random nonamers and the labelled DNA was precipitated and purified.

growth_protocol: The strains were grown in RPMI 1640 medium to a mid log phase with and without Zinc supplementation and harvested for RNA isolation.

extract_protocol: Total RNA extracted using RNeasy kit from Qiagen following manufacturer's instructions

tag: genotype

value: wild type

tag: treatment

value: 0.5 uM ZnSO4

value: RNA isolated from the RPMI + 0.5 µM ZnSO4 grown strain using RNeasy kit from Qiagen

source_name: RNA from strain MC58 zur knock out grown in RPMI

value: zur KO

value: RNA isolated from the adherent strain using RNeasy kit from Qiagen


title: BT273_B2

description:
glioblastoma stem cells cultured as neurospheres, patient 1
12 - BT 273 - EXP 233

value: Classical

value: M

value: FTP dx


title: TNBS treated 1 (biological replicate) vs. reference

description: biological replicate

value: ileum

value: female

value: reference (Control pool)


title: reference vs. S. mansoni infected 3 (biological replicate)

description: biological replicate

value: inflamed (intestinal schistosomiasis)


title: BT273_B

description:
glioblastoma stem cells cultured as neurospheres, patient 1
2 - BT 273 - EXP 233

value: EGFR AMP


title: BT275_B

description:
glioblastoma stem cells cultured as neurospheres, patient 2
4 - BT 275 - EXP 233

value: F


title: BT205_B

description:
glioblastoma stem cells cultured as neurospheres, patient 5
11 - BT 205 - EXP 233

value: Neurosphere

value: Mesenchymal

value: EGFR WT

value: T dx


title: MC58 wild type with zinc supplementation compared to mc58 zur knock out mutant 4

description: MC58 zur knock out versus MC58 with Zn supplement_Replicate3

source_name: RNA from strain MC58 grown in RPMI with Zinc supplementation (0.5 µM ZnSO4)

value: wild type

value: 0.5 uM ZnSO4


title: MC58 wild type compared to mc58 zur knock out mutant 6

description: MC58 zur knock out versus MC58 wild type_Replicate_3_dye swap

source_name: RNA from strain MC58 grown in RPMI

value: zur KO


title: Control 3 (biological replicate) vs. reference

description: biological replicate

value: healthy control


title: TNBS treated 2 (biological replicate) vs. reference

description: biological replicate

value: inflamed (TNBS-ileits)


title: reference vs. S. mansoni infected 1 (biological replicate)

description: biological replicate


title: MC58 wild type compared to mc58 zur knock out mutant 5

description: MC58 zur knock out versus MC58 wild type_Replicate3

value: RNA isolated from the adherent strain using RNeasy kit from Qiagen


title: reference vs. S. mansoni infected 2 (biological replicate)

description: biological replicate


title: BT273_A

description:
glioblastoma stem cells cultured as neurospheres, patient 1
1 - BT 273 - EXP 233

value: Classical

value: IV

value: M

value: FTP dx


title: Control 2 (biological replicate) vs. reference

description: biological replicate

value: ileum

value: female

value: reference (Control pool)


title: BT205_A

description:
glioblastoma stem cells cultured as neurospheres, patient 5
9 - BT 205 - EXP 233

value: Neurosphere


title: Control 1 (biological replicate) vs. reference

description: biological replicate


title: BT168_A

description:
glioblastoma stem cells cultured as neurospheres, patient 16
5 - BT 168 - EXP 267

value: Mesenchymal

value: EGFR AMP

value: F

value: PO sx


title: BT168_B

description:
glioblastoma stem cells cultured as neurospheres, patient 16
6 - BT 168 - EXP 267


title: MC58 wild type with zinc supplementation compared to mc58 zur knock out mutant 2

description: MC58 zur knock out versus MC58 with Zn supplement_Replicate2

value: RNA isolated from the RPMI grown strain using RNeasy kit from Qiagen

value: wild type

value: 0.5 uM ZnSO4

value: RNA isolated from the RPMI + 0.5 µM ZnSO4 grown strain using RNeasy kit from Qiagen


title: XOct-25 overexpression-experiment 2

city: Higashi-hiroshima

first: Atsushi

last: Suzuki

state: Hiroshima

address: Kagamiyama 1-3-1

department: Graduate School of Science

country: Japan

institute: Hiroshima University

description: Analysis of the experimental sample overexpressing XOct-25 (dexamethasone treated) in comparison with control sample (dexamethasone non-treated)

hyb_protocol: Microarray hybridization buffer ver2 (Amersham Biosciences) was used for hybridization.  Hybridization and washing were carried out according to the manufacturer’s protocol.

scan_protocol: Scanning was performed on a GenePix 4000B (Axon, Union City, CA) to generate two 16-bit TIFF images corresponding to the Cy3 and Cy5 channels.

data_processing: After image analysis using GenePix Pro 4.1 (Axon), the data were analysed with the statistical program Cyber-T （http://cybert.microarray.ics.uci.edu/）.

organism: Xenopus laevis

source_name: ectodermal explants isolated at blastula stage and cultured until gastrula stage

label_protocol: Using total RNAs, T7 RNA polymerase-based mRNA amplification was carried out with a RiboAmp RNA Amplification Kit (Arcturus). Five µg of amplified antisense RNA from each sample was labelled with Cy3- or Cy5-dCTP (Cyscribe Post Labeling Reactive Dye; Amersham Biosciences) using random primers and SuperScriptII reverse transcriptase (Invitrogen). Samples were purified using CyScribe GFX Purification Kit (Amersham Biosciences) before hybridization.

growth_protocol: Xenopus eggs were obtained by artificial fertilization and dejellied with 3.5% cysteine (pH 8.0). Embryos were cultured in 0.5X MMR containing 3.5% Ficoll and staged according to Nieuwkoop and Faber (1967).

extract_protocol: Total RNA from about 100 ectodermal explants was purified using the AGPC method.

treatment_protocol: Eight-cell stage embryos were microinjected with 1 ng of mRNA encoding GR-XOct-25, a hormone-inducible version of XOct-25.  Ectodermal explants were isolated at stage 9, treated with or without 2 M of dexamethazone (DEX) until the sibling embryos reached stage 10.5, and used for RNA extraction.

tag: cell type

value: embryonic ectodermal cells

tag: expression

value: XOct-25 overexpressed (dexamethasone treated)

value: Control (cultured in the absence of dexamethasone )


title: MC58 wild type compared to mc58 zur knock out mutant 3

description: MC58 zur knock out versus MC58 wild type_Replicate2

value: zur KO

tag: sample type


title: XOct-25 overexpression-experiment 1


title: MC58 wild type compared to mc58 zur knock out mutant 4

description: MC58 zur knock out versus MC58 wild type_Replicate_2_dye swap

value: RNA isolated from the adherent strain using RNeasy kit from Qiagen


title: MC58 wild type with zinc supplementation compared to mc58 zur knock out mutant 3

description: MC58 zur knock out versus MC58 with Zn supplement_Replicate2_dye swap


title: HA-Fbxl10 cell, Replicate 3

city: Bonn

first: Andreas

last: Janzer

address: Sigmund Freud St. 25

department: Pathology

institute: University of Bonn

hyb_protocol: Affymetrix protocoll

scan_protocol: GeneChip 3000 7G(Affymetrix) was used. Array images were analysed for defects with the Expression Console software (Affymetrix).

data_processing: Raw data were normalized by GC RMA algorithm.GeneSpring GX 10.0 software (Agilent Technologies, Böblingen, Germany) was used for filtering and statistical data analysis. An unpaired T test FDR corrected by Benjamini Hochberg was carried out between control and experimental samples to test for differential   expression.

label: biotin

source_name: Cell line

label_protocol: Affymetrix protocoll

extract_protocol: RNA was extracted using PureLink RNA Micro scale kit (Invitrogen). Microarray was performed with 300ng RNA. RNA integrety was tested with Agilent 2100 Bioanalyzer (Agilent Technologies).

value: MEF derived stable cell line

tag: genotype/variation

value: Tet-off HA-Fbxl10


title: MC58 wild type with zinc supplementation compared to mc58 zur knock out mutant 1

description: MC58 zur knock out versus MC58 with Zn supplement_Replicate1


title: HA-Fbxl10 cell, Replicate 2


title: 3999

city: Dallas

first: Lianghao

last: Ding

state: TX

address: 5323 Harry Hines Blvd

institute: UT Southwestern Medical Center

description: Radiation-induced AML mouse vs normal CBA mouse

hyb_protocol: 31 μg of the labeled DNA is prepared for hybridization and placed on the human or mouse 720K whole genome array and hybridized at 42ºC for ~72 hours using a Maui hybridization system.

scan_protocol: The arrays are washed and scanned at 2 μM resolution on a NimbleGen MS 200 High Resolution Scanner.

data_processing: Data was processed through NimbleScan 2.6 with default settings. Data was analyzed as Cy5 vs Cy3

source_name: Spleen tumor DNA from AML mouse

label_protocol: Labeling reactions were prepared using the Roche NimbleGen Labeling Protocol for aCGH (Version 7.0). 1 μg of test DNA and reference DNA is labeled with Cyanine 5-Random Nonamers and Cyanine 3-Random Nonamers by Exo-Klenow fragment. Labeled DNA is then purified by isopropanol precipitation and the labeling efficiency determined by the NanoDrop spectrophotometer.

extract_protocol: Spleen tissues were flash-frozen in liquid nitrogen. Isolation of genomic DNA was peroformed using Dneasy Blood & tissue Kit from Qiagen according to the manufracturer's protocol. DNA quality and concentration was determined on the NanoDrop spectrophotometer.

tag: tissue

value: Spleen Tumor

tag: pathology

value: Acute Myeloid Leukemia

value: CBA

source_name: Input of CBA mouse DNA from Jackson's Lab


title: HA-Fbxl10 cell, Replicate 1


title: GSNO vs control

city: Richmond

first: Janina

middle: P

last: Lewis

state: VA

address: 521 North 11th Street

department: Philips Institute of OCMB

institute: Virginia Commonwealth University

description: control wild type W83 strain grown anaerobically vs control wild type W83 strain grown anaerobically and exposed to GSNO

hyb_protocol: Differentially labeled cDNAs were hybridized to glass genomic microarrays (obtained from J. Craig Venter Institute [JCVI]) containing 70 mer oligonucleotide probes for all predicted open reading frames (ORFs) present on the P. gingivalis genome. Microarray hybridization and washing were done as decsribed by Genisphere (Genisphere, Hatfield, PA, USA). Dithiothreitol (DTT, 0.1mM) was added to washes following teh final hybridization, and the slides were protected from the impact of ozone by the application of DyeSaver (Genisphere, Hatfield, PA). The microarrays were scanned with an Axon 4200A microarray scanner (Molecular Devices, Downington, PA) to detect the hybridized cDNAs.

scan_protocol: Scanned on an Axon 4200A microarray scanner. Images were quantified using GenePix software (v 6.0).

data_processing: Images of microarrays were inspected for quality, quantized using GenePix v6.0 software (Molecular Devices, Downington, PA) and the gpr files were analyzed for significant differences using the Significance Analysis for Oral Pathogen Microarrays (SAOPMD) tools available at the Bioinformatics Resource for Oral Pathogens (BROP) website provided by The Forsyth Institute (www.brop.org). Normalized, background subttracted data obtained from log2 processed Red signal/ processed Green signal.  LIMMA was used. LIMMA (Linear Models for Microarray Analysis) package for statistical inference. LIMMA includes pre-processing capabilities for two-colour spotted microarrays, such as background subtraction.  Data were analysed for significant differences using teh SAOMPD.  SAOMPD combined all the repeats within and between arrays and generates statistics.  Data were obtained from four technical repeats for each condition tested.

organism: Porphyromonas gingivalis

source_name: Bacterial cells

label_protocol: 10 ug of total RNA was primed with random DNA primer at 70C for 10min, then reverse transcribed for 1hr at 42C in the presence of ArrayScript reverse transcriptase (Applied Biosystems/Ambion/ Austin, Texas). The cDNA was labeled with dyes (Cy3 and Cy5, GE Healthcare) using Array 900 MPX kit from Genisphere (Genisphere, Hatfield, PA).

growth_protocol: Bacterial cells were grown anaerobically in Mycoplasma broth to mid logarythmic phase (OD660 = 0.4 - 0.6)

extract_protocol: Total RNA was extracted using Qiagen protocol

treatment_protocol: Bacterial cells were exposed to 200nM of nitrite (NaNO2) or 20nM of S-nitrosoglutathione (GSNO) for 90 min

value: Wild type strain W83

value: control

value: GSNO


title: MC58 wild type compared to mc58 zur knock out mutant 2

description: MC58 zur knock out versus MC58 wild type_Replicate1_dye swap

value: RNA isolated from the RPMI grown strain using RNeasy kit from Qiagen


title: Control cell, Replicate 3

value: Tet-off control cells


title: 3861


title: 5342


title: Nitrite vs control

description: Control wild type W83 strain grown anaerobically vs control wild type W83 strain grown anaerobically and exposed to nitrite

value: nitrite


title: MYB shRNA-C

status: Public on Oct 04 2012

city: Memphis

first: Jian

last: Xu

state: Tennessee

address: 262 Danny Thomas Place, MS 345

institute: St. Jude Children's Research Hospital

description: Ex vivo erythroid differentiation of magnetically-sorted CD34+ HSPCs

hyb_protocol: Standard Affymetrix protocol.

scan_protocol: Standard Affymetrix protocol.

data_processing: We RMA-normalized the arrays using the affy package from Bioconductor in R, and further eliminated batch effects using ComBat.

source_name: Adult Day5 ProEs

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol.

growth_protocol: Primary maturing adult erythroblasts were generated ex vivo using a serum-free two-phase liquid culture system.

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

treatment_protocol: CD34+ cells were transduced with shRNA lentiviruses, selected, and differentiated into proerythroblasts.

value: ex vivo differentiating ProEs

tag: developmental stage

value: adult bone marrow

tag: transfection

value: shRNAs against MYB


title: MC58 wild type compared to mc58 zur knock out mutant 1

description: MC58 zur knock out versus MC58 wild type_Replicate1

value: wild type


title: MYB shRNA-D


title: Control cell, Replicate 2


title: Control shRNA-C

value: control shRNAs


title: 3777


title: Control cell, Replicate 1


title: 3364


title: MYB shRNA-A


title: 4228

hyb_protocol: 31 μg of the labeled DNA is prepared for hybridization and placed on the human or mouse 385K whole genome array and hybridized at 42ºC for ~72 hours using a Maui hybridization system.


title: Control shRNA-D


title: 3272


title: MYB shRNA-B


title: 3286


title: Control shRNA-B


title: 3512


title: 3208


title: 3269


title: IRF6 shRNA-C

value: shRNAs against IRF6


title: 3416


title: 3189


title: IRF6 shRNA-B


title: IRF2 shRNA-B

value: shRNAs against IRF2


title: 3048


title: 3250


title: 2704


title: 3192


title: IRF2 shRNA-A


title: Fetal day5-C

source_name: Fetal Day5 ProEs

value: 2-trimester fetal liver


title: Adult-day7-B

source_name: Adult Day7 ProEs

growth_protocol: Primary maturing fetal or adult erythroblasts were generated ex vivo using a serum-free two-phase liquid culture system.


title: Adult day5-B


title: Fetal day5-B


title: Adult-day5-C


title: Adult-day5-B


title: Adult-day7-A


title: Adult day5-A


title: 3173

value: Spleen Tumor


title: Adult-day5-A


title: Control shRNA-A


title: Adult day5-C


title: 2816

value: Acute Myeloid Leukemia


title: Adult-day3-A

source_name: Adult Day3 ProEs


title: IRF2 shRNA-C


title: Adult-day7-C


title: Fetal-day7-B

source_name: Fetal Day7 ProEs


title: Fetal-day7-A


title: Adult-day0-A

source_name: Adult CD34+ HSPCs

value: primary HSPCs isolated from G-CSF mobilized peripheral blood mononuclear cells from healthy donors


title: Adult-day0-C


title: Adult-day3-C


title: Fetal-day5-A


title: Fetal-day5-B


title: Fetal-day3-A

source_name: Fetal Day3 ProEs


title: flat adenoma 136

city: Amsterdam

first: Daoud

last: Sie

address: De Boelelaan 1117

country: Netherlands

institute: Vrije Universiteit Medical Center

description:
raw data ch1: US22502676_252252210215_S01_CGH_105_Dec08_1_3.txt
raw data ch2: US22502676_252252210215_S01_CGH_105_Dec08_1_1.txt
FLAT_ADE_136

hyb_protocol: Hybridization protocol available via www.agilent.com

scan_protocol: Slides were scanned using the Agilent G2505B micro-array scanner. Image data acquisition was performed in feature extraction software v10.5 (Agilent Technologies) using the Agilent CGH-105_Dec08 protocol with default settings

data_processing: Median Signal intensity minus median Background intensity; excluding negative values. To overcome potential wave bias due to differences in GC-content of the different chromosomal regions, a smoothing algorithm was applied on our dataset as described by van de Wiel et al, Bioinformatics 2009; 25(9):1099-1104.

source_name: Colorectal tissue, macrodissected [test]

label_protocol: DNA labeling protocol according to Enzo Life Sciences.

extract_protocol: Laser capture microdissection was performed on haematoxylin stained tissue section to obtain the dysplastic cells. Tissues were incubated overnight 37°C in 1M NaSCN. Subsequently, samples were treated with proteinase K for 5 days. DNA was extracted using the DNA Qiagen micro kit (Qiagen).

tag: gender

value: F

tag: paris classification

value: IIa

source_name: FFPE colon DNA pool from healthy individuals [reference]

tag: reference description

value: Pooled DNA (FFPE) of 10 healthy individuals was used as reference in the aCGH experiments; across array CGH comparisons were made as described by Buffart et al, Genes, Chromosomes & Cancer 2008, 47(11):994-1004


title: polypoid adenoma 139

description:
raw data ch1: US22502676_252252210215_S01_CGH_105_Dec08_1_4.txt
raw data ch2: US22502676_252252210215_S01_CGH_105_Dec08_1_4.txt
POLY_ADE_139

value: Ip


title: Fetal-day5-C


title: polypoid adenoma 137

description:
raw data ch1: US22502676_252252210215_S01_CGH_105_Dec08_1_2.txt
raw data ch2: US22502676_252252210215_S01_CGH_105_Dec08_1_4.txt
POLY_ADE_137


title: Fetal-day0-B

source_name: Fetal CD34+ HSPCs

value: primary HSPCs isolated from 2-trimester fetal liver


title: polypoid adenoma 145

description:
raw data ch1: US22502676_252252210216_S01_CGH_105_Dec08_1_3.txt
raw data ch2: US22502676_252252210216_S01_CGH_105_Dec08_1_4.txt
POLY_ADE_145

value: M


title: Fetal day5-A

value: ex vivo differentiating ProEs


title: polypoid adenoma 134

description:
raw data ch1: US22502676_252252210215_S01_CGH_105_Dec08_1_1.txt
raw data ch2: US22502676_252252210215_S01_CGH_105_Dec08_1_1.txt
POLY_ADE_134


title: Fetal-day3-B


title: flat adenoma 130

description:
raw data ch1: US22502676_252252210214_S01_CGH_105_Dec08_1_2.txt
raw data ch2: US22502676_252252210214_S01_CGH_105_Dec08_1_4.txt
FLAT_ADE_130


title: flat adenoma 133

description:
raw data ch1: US22502676_252252210214_S01_CGH_105_Dec08_1_1.txt
raw data ch2: US22502676_252252210214_S01_CGH_105_Dec08_1_4.txt
FLAT_ADE_133


title: Fetal-day0-C


title: Fetal-day0-A


title: IRF6 shRNA-A

value: adult bone marrow


title: Adult-day3-B


title: polypoid adenoma 135

description:
raw data ch1: US22502676_252252210215_S01_CGH_105_Dec08_1_2.txt
raw data ch2: US22502676_252252210215_S01_CGH_105_Dec08_1_1.txt
POLY_ADE_135


title: polypoid adenoma 141

description:
raw data ch1: US22502676_252252210216_S01_CGH_105_Dec08_1_3.txt
raw data ch2: US22502676_252252210216_S01_CGH_105_Dec08_1_4.txt
POLY_ADE_141


title: Adult-day0-B


title: flat adenoma 127

description:
raw data ch1: US22502676_252252210211_S01_CGH_105_Dec08_1_4.txt
raw data ch2: US22502676_252252210055_S01_CGH_105_Dec08_1_1.txt
FLAT_ADE_127


title: flat adenoma 132

description:
raw data ch1: US22502676_252252210214_S01_CGH_105_Dec08_1_4.txt
raw data ch2: US22502676_252252210214_S01_CGH_105_Dec08_1_4.txt
FLAT_ADE_132


title: flat adenoma 128

description:
raw data ch1: US22502676_252252210214_S01_CGH_105_Dec08_1_2.txt
raw data ch2: US22502676_252252210214_S01_CGH_105_Dec08_1_1.txt
FLAT_ADE_128


title: flat adenoma 126

description:
raw data ch1: US22502676_252252210211_S01_CGH_105_Dec08_1_3.txt
raw data ch2: US22502676_252252210055_S01_CGH_105_Dec08_1_1.txt
FLAT_ADE_126


title: polypoid adenoma 144

description:
raw data ch1: US22502676_252252210216_S01_CGH_105_Dec08_1_2.txt
raw data ch2: US22502676_252252210216_S01_CGH_105_Dec08_1_4.txt
POLY_ADE_144


title: flat adenoma 129

description:
raw data ch1: US22502676_252252210214_S01_CGH_105_Dec08_1_3.txt
raw data ch2: US22502676_252252210214_S01_CGH_105_Dec08_1_1.txt
FLAT_ADE_129


title: flat adenoma 131

description:
raw data ch1: US22502676_252252210214_S01_CGH_105_Dec08_1_3.txt
raw data ch2: US22502676_252252210214_S01_CGH_105_Dec08_1_4.txt
FLAT_ADE_131


title: flat adenoma 121

description:
raw data ch1: US22502676_252252210213_S01_CGH_105_Dec08_1_4.txt
raw data ch2: US22502676_252252210055_S01_CGH_105_Dec08_1_1.txt
FLAT_ADE_121


title: flat adenoma 107

description:
raw data ch1: US22502676_252252210056_S01_CGH_105_Dec08_1_2.txt
raw data ch2: US22502676_252252210056_S01_CGH_105_Dec08_1_1.txt
FLAT_ADE_107


title: flat adenoma 125

description:
raw data ch1: US22502676_252252210211_S01_CGH_105_Dec08_1_2.txt
raw data ch2: US22502676_252252210055_S01_CGH_105_Dec08_1_1.txt
FLAT_ADE_125


title: flat adenoma 117

description:
raw data ch1: US22502676_252252210213_S01_CGH_105_Dec08_1_2.txt
raw data ch2: US22502676_252252210055_S01_CGH_105_Dec08_1_1.txt
FLAT_ADE_117


title: flat adenoma 108

description:
raw data ch1: US22502676_252252210056_S01_CGH_105_Dec08_1_3.txt
raw data ch2: US22502676_252252210056_S01_CGH_105_Dec08_1_1.txt
FLAT_ADE_108


title: flat adenoma 116

description:
raw data ch1: US22502676_252252210213_S01_CGH_105_Dec08_1_1.txt
raw data ch2: US22502676_252252210055_S01_CGH_105_Dec08_1_1.txt
FLAT_ADE_116


title: flat adenoma 119

description:
raw data ch1: US22502676_252252210213_S01_CGH_105_Dec08_1_2.txt
raw data ch2: US22502676_252252210055_S01_CGH_105_Dec08_1_1.txt
FLAT_ADE_119


title: flat adenoma 120

description:
raw data ch1: US22502676_252252210213_S01_CGH_105_Dec08_1_3.txt
raw data ch2: US22502676_252252210055_S01_CGH_105_Dec08_1_1.txt
FLAT_ADE_120


title: flat adenoma 105

description:
raw data ch1: US22502676_252252210056_S01_CGH_105_Dec08_1_2.txt
raw data ch2: US22502676_252252210056_S01_CGH_105_Dec08_1_1.txt
FLAT_ADE_105


title: flat adenoma 122

description:
raw data ch1: US22502676_252252210211_S01_CGH_105_Dec08_1_1.txt
raw data ch2: US22502676_252252210055_S01_CGH_105_Dec08_1_1.txt
FLAT_ADE_122


title: flat adenoma 123

description:
raw data ch1: US22502676_252252210211_S01_CGH_105_Dec08_1_2.txt
raw data ch2: US22502676_252252210055_S01_CGH_105_Dec08_1_1.txt
FLAT_ADE_123


title: flat adenoma 124

description:
raw data ch1: US22502676_252252210211_S01_CGH_105_Dec08_1_3.txt
raw data ch2: US22502676_252252210055_S01_CGH_105_Dec08_1_1.txt
FLAT_ADE_124


title: R_UB3.Cel

city: St Louis

first: Joseph

middle: D

last: Dougherty

state: Missouri

address: 4566 Scott Ave, box 8232

department: Genetics and Psychiatry

institute: Washington University

hyb_protocol: Standard Affymetrix Protocols

scan_protocol: Standard Affymetrix Protocols

data_processing: Within replicates GCRMA normalization, using R and Bioconductor. Custom Cdfs: Mouse4302_Mm_ENTREZG, following recommendations as in Pubmed: 20308160

label: Biotin

source_name: Total RNA from Recruited Tumor

label_protocol: Affymetric 2 cycle amplification

growth_protocol: For first dataset, dissected cortex from adult mice For second dataset, dissected tumors from mice.

extract_protocol: Trizol followed by Qiagen RNeasy Minelute. Translating Ribosome Affinity Purification protocol (see Pubmed: [19013281])

treatment_protocol: Either wildtype or induction of tumor (for tumor samples).

value: mix of c57/bl6j, FVB, and Swiss-Webster

value: Total RNA from Recruited Tumor

tag: rna subtype

value: Total RNA

tag: dataset

value: dataset 2


title: R_UB2.Cel

tag: strain


title: R_IP1.Cel

source_name: Olig2 cells from Recruited Tumor

value: Olig2 cells from Recruited Tumor

value: Ribosome bound RNA


title: R_IP2.Cel


title: R_IP3.Cel


title: flat adenoma 102

description:
raw data ch1: US22502676_252252210055_S01_CGH_105_Dec08_1_4.txt
raw data ch2: US22502676_252252210055_S01_CGH_105_Dec08_1_4.txt
FLAT_ADE_102


title: flat adenoma 103

description:
raw data ch1: US22502676_252252210055_S01_CGH_105_Dec08_1_3.txt
raw data ch2: US22502676_252252210055_S01_CGH_105_Dec08_1_1.txt
FLAT_ADE_103


title: P_UB3.Cel

source_name: Total RNA from Pdgf Tumor

value: Total RNA from Pdgf Tumor


title: flat adenoma 104

description:
raw data ch1: US22502676_252252210056_S01_CGH_105_Dec08_1_1.txt
raw data ch2: US22502676_252252210056_S01_CGH_105_Dec08_1_1.txt
FLAT_ADE_104


title: P_UB2.Cel


title: flat adenoma 99

description:
raw data ch1: US22502676_252252210055_S01_CGH_105_Dec08_1_2.txt
raw data ch2: US22502676_252252210055_S01_CGH_105_Dec08_1_1.txt
FLAT_ADE_99


title: flat adenoma 101

description:
raw data ch1: US22502676_252252210055_S01_CGH_105_Dec08_1_2.txt
raw data ch2: US22502676_252252210055_S01_CGH_105_Dec08_1_4.txt
FLAT_ADE_101


title: flat adenoma 100

description:
raw data ch1: US22502676_252252210055_S01_CGH_105_Dec08_1_3.txt
raw data ch2: US22502676_252252210055_S01_CGH_105_Dec08_1_1.txt
FLAT_ADE_100


title: flat adenoma 98

description:
raw data ch1: US22502676_252252210055_S01_CGH_105_Dec08_1_1.txt
raw data ch2: US22502676_252252210055_S01_CGH_105_Dec08_1_1.txt
FLAT_ADE_98


title: polypoid adenoma 97

description:
raw data ch1: US22502676_252252210158_S01_CGH_105_Dec08_1_2.txt
raw data ch2: US22502676_252252210158_S01_CGH_105_Dec08_1_1.txt
POLY_ADE_97


title: polypoid adenoma 96

description:
raw data ch1: US22502676_252252210158_S01_CGH_105_Dec08_1_3.txt
raw data ch2: US22502676_252252210158_S01_CGH_105_Dec08_1_4.txt
POLY_ADE_96


title: P_IP3.Cel

source_name: Olig2 cells from Pdgf Tumor

value: Olig2 cells from Pdgf Tumor


title: polypoid adenoma 95

description:
raw data ch1: US22502676_252252210158_S01_CGH_105_Dec08_1_4.txt
raw data ch2: US22502676_252252210158_S01_CGH_105_Dec08_1_4.txt
POLY_ADE_95


title: P_UB1.Cel


title: polypoid adenoma 93

description:
raw data ch1: US22502676_252252210158_S01_CGH_105_Dec08_1_2.txt
raw data ch2: US22502676_252252210158_S01_CGH_105_Dec08_1_1.txt
POLY_ADE_93


title: P_IP2.Cel


title: polypoid adenoma 94

description:
raw data ch1: US22502676_252252210158_S01_CGH_105_Dec08_1_3.txt
raw data ch2: US22502676_252252210158_S01_CGH_105_Dec08_1_4.txt
POLY_ADE_94


title: P_C_UB3.Cel

source_name: Total RNA from Pdgf Cre Tumor

value: Total RNA from Pdgf Cre Tumor


title: P_C_UB2.Cel


title: P_IP1.Cel


title: polypoid adenoma 89

description:
raw data ch1: US22502676_252252210157_S01_CGH_105_Dec08_1_4.txt
raw data ch2: US22502676_252252210157_S01_CGH_105_Dec08_1_4.txt
POLY_ADE_89


title: P_C_UB1.Cel


title: P_C_IP3.Cel

source_name: Olig2 cells from Pdgf Cre Tumor

value: Olig2 cells from Pdgf Cre Tumor


title: P_C_IP2.Cel


title: polypoid adenoma 88

description:
raw data ch1: US22502676_252252210157_S01_CGH_105_Dec08_1_3.txt
raw data ch2: US22502676_252252210157_S01_CGH_105_Dec08_1_4.txt
POLY_ADE_88


title: P_C_IP1.Cel


title: polypoid adenoma 84

description:
raw data ch1: US22502676_252252210156_S01_CGH_105_Dec08_1_4.txt
raw data ch2: US22502676_252252210156_S01_CGH_105_Dec08_1_4.txt
POLY_ADE_84


title: polypoid adenoma 82

description:
raw data ch1: US22502676_252252210156_S01_CGH_105_Dec08_1_2.txt
raw data ch2: US22502676_252252210156_S01_CGH_105_Dec08_1_4.txt
POLY_ADE_82


title: polypoid adenoma 87

description:
raw data ch1: US22502676_252252210157_S01_CGH_105_Dec08_1_3.txt
raw data ch2: US22502676_252252210157_S01_CGH_105_Dec08_1_1.txt
POLY_ADE_87


title: polypoid adenoma 92

description:
raw data ch1: US22502676_252252210158_S01_CGH_105_Dec08_1_1.txt
raw data ch2: US22502676_252252210158_S01_CGH_105_Dec08_1_1.txt
POLY_ADE_92

value: F


title: polypoid adenoma 83

description:
raw data ch1: US22502676_252252210156_S01_CGH_105_Dec08_1_3.txt
raw data ch2: US22502676_252252210156_S01_CGH_105_Dec08_1_4.txt
POLY_ADE_83

value: Pooled DNA (FFPE) of 10 healthy individuals was used as reference in the aCGH experiments; across array CGH comparisons were made as described by Buffart et al, Genes, Chromosomes & Cancer 2008, 47(11):994-1004


title: polypoid adenoma 81

description:
raw data ch1: US22502676_252252210156_S01_CGH_105_Dec08_1_3.txt
raw data ch2: US22502676_252252210156_S01_CGH_105_Dec08_1_1.txt
POLY_ADE_81

value: Ip


title: polypoid adenoma 91

description:
raw data ch1: US22502676_252252210157_S01_CGH_105_Dec08_1_2.txt
raw data ch2: US22502676_252252210157_S01_CGH_105_Dec08_1_1.txt
POLY_ADE_91


title: polypoid adenoma 90

description:
raw data ch1: US22502676_252252210157_S01_CGH_105_Dec08_1_2.txt
raw data ch2: US22502676_252252210157_S01_CGH_105_Dec08_1_4.txt
POLY_ADE_90


title: polypoid adenoma 86

description:
raw data ch1: US22502676_252252210157_S01_CGH_105_Dec08_1_1.txt
raw data ch2: US22502676_252252210157_S01_CGH_105_Dec08_1_1.txt
POLY_ADE_86


title: polypoid adenoma 80

description:
raw data ch1: US22502676_252252210156_S01_CGH_105_Dec08_1_1.txt
raw data ch2: US22502676_252252210156_S01_CGH_105_Dec08_1_1.txt
POLY_ADE_80


title: polypoid adenoma 78

description:
raw data ch1: US22502676_252252210155_S01_CGH_105_Dec08_1_3.txt
raw data ch2: US22502676_252252210155_S01_CGH_105_Dec08_1_4.txt
POLY_ADE_78


title: polypoid adenoma 85

description:
raw data ch1: US22502676_252252210156_S01_CGH_105_Dec08_1_2.txt
raw data ch2: US22502676_252252210156_S01_CGH_105_Dec08_1_4.txt
POLY_ADE_85


title: polypoid adenoma 77

description:
raw data ch1: US22502676_252252210155_S01_CGH_105_Dec08_1_2.txt
raw data ch2: US22502676_252252210155_S01_CGH_105_Dec08_1_4.txt
POLY_ADE_77


title: Olig2_IP2.Cel

source_name: Cortical Oligodendroglia

value: Cortical Oligodendroglia

value: dataset 1


title: Olig2_IP1.Cel


title: polypoid adenoma 79

description:
raw data ch1: US22502676_252252210155_S01_CGH_105_Dec08_1_3.txt
raw data ch2: US22502676_252252210155_S01_CGH_105_Dec08_1_1.txt
POLY_ADE_79


title: Cortex_UB3.cel

source_name: Cortex

value: Cortex


title: Cortex_UB2.cel


title: polypoid adenoma 76

description:
raw data ch1: US22502676_252252210155_S01_CGH_105_Dec08_1_4.txt
raw data ch2: US22502676_252252210155_S01_CGH_105_Dec08_1_4.txt
POLY_ADE_76


title: Olig2_IP3.Cel


title: Cortex_UB4.cel


title: flat adenoma 69

description:
raw data ch1: US22502676_252252210153_S01_CGH_105_Dec08_1_2.txt
raw data ch2: US22502676_252252210153_S01_CGH_105_Dec08_1_1.txt
FLAT_ADE_69

value: M

value: IIa


title: flat adenoma 70

description:
raw data ch1: US22502676_252252210154_S01_CGH_105_Dec08_1_1.txt
raw data ch2: US22502676_252252210154_S01_CGH_105_Dec08_1_1.txt
FLAT_ADE_70


title: Cortex_UB1.cel

value: mix of c57/bl6j, FVB, and Swiss-Webster


title: R_UB1.Cel

value: Total RNA from Recruited Tumor

value: Total RNA


title: Pdgfra_Jd340_IP3.cel

source_name: Cortical Oligodendrocyte Progenitor Cells


title: EHEC grown in fresh medium for 1 h

city: College Station

first: Tarun

last: Bansal

address: 3122 TAMU

department: Chemical Engineering

institute: Texas A & M University

hyb_protocol: Following affymetrix protocol, hybridization cocktail was prepared including 1X hybrization buffer, 50 pM B2 Control Oligo, 0.1 mg/mL Herring Sperm DNA, 0.5 mg/mL BSA, and at least 1 ug fragmented and labelled cDNA. After loading of hybridization cocktail in Affymetrix E. coli Genome 2.0 Array, the hybridization was performed at 45ºC, with 60 rpm for 16 hours. After hybridization, the probe array was washed and stained using Affymetrix Genechip Fluidics Station 450 and Genome Chip Operating Software (GCOS).

scan_protocol: Following affymetrix protocol, after washing and staining, the probe array was scanned using Affymetrix Genechip scanner GCS3000 7G system and Genome Chip Operating Software (GCOS).

data_processing: MAS 5.0 Expression Analysis Default Setting was used to analyze data.

organism: Escherichia coli O157:H7 str. EDL933

source_name: EHEC grown in fresh medium for 1 h

label_protocol: Following affymetrix protocol, cDNA was synthesized first using Promega M-MLV Reverse transcriptase (cat# M1705). After removing RNA, DNA fragmentation was performed to obtain and 50-200 base cDNA fragments. The fragmented cDNA was labelled with Biotin-ddUTP using Enzo BioArray Terminal Labeling Kit (Affymetrix, P/N 900181).

growth_protocol: Overnight cultures of EHEC were diluted in LB medium to a turbidity of 0.1 at 600 nm. The cells were allowed to grow to a turbidity of 1.0 at 600 nm at 37°C and the EHEC cells were then resuspended in either fresh or conditioned medium.  Total RNA was isolated from the cell pellets (173) and RNA quality was assessed using gel electrophoresis. Escherichia coli Genome 2.0 arrays (Affymetrix, Santa Clara, CA, USA) containing 10,208 probe sets for all 20,366 genes present in four strains of E. coli, including EHEC, were used to profile changes in gene expression using RNA samples for each treatment.

extract_protocol: Total RNA was isolated from the cell pellets using Rneasy Mini Kit (Qiagen, Catalog 74104) and RNA quality was assessed using gel electrophoresis.

treatment_protocol: EHEC cells were resuspended in either fresh or conditioned medium.The cultures were then allowed to grow for 1 h or 3 h before cell pellets were collected by centrifugation and stored at -80°C.

tag: medium type

value: fresh medium

tag: time point

value: 1 h


title: Pdgfra_Jd340_IP2.cel

value: Cortical Oligodendrocyte Progenitor Cells

value: Ribosome bound RNA


title: EHEC grown in conditioned medium for 1 h

value: conditioned medium


title: EHEC grown in fresh medium for 3 h

source_name: EHEC grown in fresh medium for 3 h

value: 3 h


title: EHEC grown in conditioned medium for 3 h


title: flat adenoma 68

description:
raw data ch1: US22502676_252252210153_S01_CGH_105_Dec08_1_3.txt
raw data ch2: US22502676_252252210153_S01_CGH_105_Dec08_1_4.txt
FLAT_ADE_68


title: flat adenoma 72

description:
raw data ch1: US22502676_252252210154_S01_CGH_105_Dec08_1_3.txt
raw data ch2: US22502676_252252210154_S01_CGH_105_Dec08_1_1.txt
FLAT_ADE_72

value: F

value: LST-F


title: flat adenoma 73

description:
raw data ch1: US22502676_252252210154_S01_CGH_105_Dec08_1_3.txt
raw data ch2: US22502676_252252210154_S01_CGH_105_Dec08_1_1.txt
FLAT_ADE_73

value: Pooled DNA (FFPE) of 10 healthy individuals was used as reference in the aCGH experiments; across array CGH comparisons were made as described by Buffart et al, Genes, Chromosomes & Cancer 2008, 47(11):994-1004


title: flat adenoma 71

description:
raw data ch1: US22502676_252252210154_S01_CGH_105_Dec08_1_2.txt
raw data ch2: US22502676_252252210154_S01_CGH_105_Dec08_1_1.txt
FLAT_ADE_71


title: polypoid adenoma 74

description:
raw data ch1: US22502676_252252210155_S01_CGH_105_Dec08_1_1.txt
raw data ch2: US22502676_252252210155_S01_CGH_105_Dec08_1_1.txt
POLY_ADE_74

value: Ip


title: flat adenoma 118

description:
raw data ch1: US22502676_252252210213_S01_CGH_105_Dec08_1_3.txt
raw data ch2: US22502676_252252210055_S01_CGH_105_Dec08_1_1.txt
FLAT_ADE_118


title: Cortex_UB5.cel

value: dataset 1


title: polypoid adenoma 75

description:
raw data ch1: US22502676_252252210155_S01_CGH_105_Dec08_1_2.txt
raw data ch2: US22502676_252252210155_S01_CGH_105_Dec08_1_4.txt
POLY_ADE_75


title: Aldh1L1_IP1.cel

source_name: Cortical Astrocytes

value: Cortical Astrocytes


title: Aldh1L1_IP2.cel


title: Aldh1L1_IP3.cel


title: Cnp1_JD368_IP1.cel

source_name: Cortical Mature Oligodendrocytes

value: Cortical Mature Oligodendrocytes


title: flat adenoma 66

description:
raw data ch1: US22502676_252252210153_S01_CGH_105_Dec08_1_2.txt
raw data ch2: US22502676_252252210153_S01_CGH_105_Dec08_1_1.txt
FLAT_ADE_66

value: M

value: IIc


title: flat adenoma 63

description:
raw data ch1: US22502676_252252210035_S01_CGH_105_Dec08_1_2.txt
raw data ch2: US22502676_252252210035_S01_CGH_105_Dec08_1_1.txt
FLAT_ADE_63

value: IIa


title: Pdgfra_Jd340_IP1.cel

value: mix of c57/bl6j, FVB, and Swiss-Webster


title: flat adenoma 58

description:
raw data ch1: MAF_252252210064_S01_CGH-v4_10_Apr08_1_4.txt
raw data ch2: MAF_252252210064_S01_CGH-v4_10_Apr08_1_4.txt
FLAT_ADE_58


title: Snap25_JD362_IP2.cel

source_name: Cortical Neurons

value: Cortical Neurons


title: Cnp1_JD368_IP3.cel


title: Snap25_JD362_IP1.cel


title: Snap25_JD362_IP3.cel


title: flat adenoma 61

description:
raw data ch1: US22502676_252252210035_S01_CGH_105_Dec08_1_4.txt
raw data ch2: US22502676_252252210035_S01_CGH_105_Dec08_1_4.txt
FLAT_ADE_61

source_name: Colorectal tissue, macrodissected [test]


title: flat adenoma 64

description:
raw data ch1: US22502676_252252210035_S01_CGH_105_Dec08_1_3.txt
raw data ch2: US22502676_252252210035_S01_CGH_105_Dec08_1_1.txt
FLAT_ADE_64

source_name: FFPE colon DNA pool from healthy individuals [reference]


title: flat adenoma 60

description:
raw data ch1: US22502676_252252210035_S01_CGH_105_Dec08_1_2.txt
raw data ch2: US22502676_252252210035_S01_CGH_105_Dec08_1_1.txt
FLAT_ADE_60


title: flat adenoma 56

description:
raw data ch1: MAF_252252210064_S01_CGH-v4_10_Apr08_1_2.txt
raw data ch2: MAF_252252210064_S01_CGH-v4_10_Apr08_1_1.txt
FLAT_ADE_56

value: LST-G


title: flat adenoma 59

description:
raw data ch1: US22502676_252252210035_S01_CGH_105_Dec08_1_1.txt
raw data ch2: US22502676_252252210035_S01_CGH_105_Dec08_1_1.txt
FLAT_ADE_59


title: flat adenoma 55

description:
raw data ch1: MAF_252252210064_S01_CGH-v4_10_Apr08_1_1.txt
raw data ch2: MAF_252252210064_S01_CGH-v4_10_Apr08_1_1.txt
FLAT_ADE_55


title: Cnp1_JD368_IP2.cel


title: flat adenoma 54

description:
raw data ch1: MAF_252252210064_S01_CGH-v4_10_Apr08_1_3.txt
raw data ch2: MAF_252252210064_S01_CGH-v4_10_Apr08_1_4.txt
FLAT_ADE_54


title: flat adenoma 65

description:
raw data ch1: US22502676_252252210153_S01_CGH_105_Dec08_1_1.txt
raw data ch2: US22502676_252252210153_S01_CGH_105_Dec08_1_1.txt
FLAT_ADE_65


title: flat adenoma 50

description:
raw data ch1: US22502676_252252210034_S01_CGH_105_Dec08_1_2.txt
raw data ch2: US22502676_252252210034_S01_CGH_105_Dec08_1_1.txt
FLAT_ADE_50


title: flat adenoma 53

description:
raw data ch1: US22502676_252252210034_S01_CGH_105_Dec08_1_3.txt
raw data ch2: US22502676_252252210034_S01_CGH_105_Dec08_1_1.txt
FLAT_ADE_53


title: flat adenoma 51

description:
raw data ch1: US22502676_252252210034_S01_CGH_105_Dec08_1_3.txt
raw data ch2: US22502676_252252210034_S01_CGH_105_Dec08_1_1.txt
FLAT_ADE_51


title: HepG2 siRNF43 biological rep3

city: Hangzhou

first: Chunyang

last: Xing

address: 79# Qingchun Road

country: China

institute: First Affiliated Hospital, School of Medicine, Zhejiang University

description: Gene expression data from HepG2 cells transfected with RNF43 siRNA

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip U133 plus 2.0 array Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: Raw data were normalized by MAS 5.0 algorithm

source_name: HepG2 transfected with RNF43 siRNA

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

growth_protocol: HepG2 cells were cultured in Dulbecco's modified Eagle medium (DMEM, Gibco-Invitrogen, Carlsbad, CA, USA) supplemented with 10% fetal bovine serum (SAFC Biosciences, Lenexa, KS, USA), 100 units/mL penicillin and 100 mg/mL streptomycin (Sigma-Aldrich, St. Louis, MO, USA).

extract_protocol: Total RNA was extracted using the RNeasy kit (Qiagen, Hilden, Germany) according to the manufacturer's instructions.

treatment_protocol: HepG2 cells were transfected with RNF43 siRNA or negative control siRNA using Lipofectamine 2000 (Invitrogen, Carlsbad, CA, USA) following the manufacturer's instructions. The sequence of siRNA: ( RNF43 siRNA: Sense 5’-CAGAACAGAAAGCUAUUAUTT -3’,Antisense 5’-AUAAUAGCUUUCUGUUCUGTT -3’. Negative control siRNA: Sense 5’-UUCUCCGAACGUGUCACGUTT -3’, Antisense 5’-ACGUGACACGUUCGGAGAATT -3’).

tag: cell line

tag: treatment


title: HepG2 siRNF43 biological rep2


title: HepG2 siRNF43 biological rep1


title: flat adenoma 67

description:
raw data ch1: US22502676_252252210153_S01_CGH_105_Dec08_1_4.txt
raw data ch2: US22502676_252252210153_S01_CGH_105_Dec08_1_4.txt
FLAT_ADE_67


title: flat adenoma 52

description:
raw data ch1: US22502676_252252210034_S01_CGH_105_Dec08_1_2.txt
raw data ch2: US22502676_252252210034_S01_CGH_105_Dec08_1_1.txt
FLAT_ADE_52


title: flat adenoma 49

description:
raw data ch1: US22502676_252252210034_S01_CGH_105_Dec08_1_1.txt
raw data ch2: US22502676_252252210034_S01_CGH_105_Dec08_1_1.txt
FLAT_ADE_49


title: flat adenoma 41

description:
raw data ch1: US22502676_252252210053_S01_CGH_105_Dec08_1_2.txt
raw data ch2: US22502676_252252210053_S01_CGH_105_Dec08_1_1.txt
FLAT_ADE_41


title: HepG2 siNC biological rep2

description: Gene expression data from HepG2 cells transfected with negative control siRNA

source_name: HepG2 transfected with negative control siRNA

value: control


title: flat adenoma 44

description:
raw data ch1: US22502676_252252210054_S01_CGH_105_Dec08_1_2.txt
raw data ch2: US22502676_252252210054_S01_CGH_105_Dec08_1_1.txt
FLAT_ADE_44


title: flat adenoma 42

description:
raw data ch1: US22502676_252252210053_S01_CGH_105_Dec08_1_3.txt
raw data ch2: US22502676_252252210053_S01_CGH_105_Dec08_1_1.txt
FLAT_ADE_42


title: flat adenoma 40

description:
raw data ch1: US22502676_252252210053_S01_CGH_105_Dec08_1_4.txt
raw data ch2: US22502676_252252210053_S01_CGH_105_Dec08_1_4.txt
FLAT_ADE_40


title: polypoid adenoma 46

description:
raw data ch1: US22502676_252252210054_S01_CGH_105_Dec08_1_4.txt
raw data ch2: US22502676_252252210054_S01_CGH_105_Dec08_1_4.txt
POLY_ADE_46


title: HepG2 siNC biological rep1


title: Karpas422_EZH2i_day6_rep1

city: Shanghai

first: Shannon

last: Chuai

state: Shanghai

address: Building 8, Lane 898 Halei Road, Pudong New Aera

institute: Novartis

description: Timecourse gene expression profiling of DLBCL cell line Karpas422 after EZH2 inhibitor treatment

hyb_protocol: According to Affymetrix protocol

scan_protocol: According to Affymetrix protocol

data_processing: The gene expression data was normalized using the Robust Multiarray Averaging (RMA) method and log2 transformed before comparisons using R 2.10.1. The EZH2 inhibitor-treated cells were then compared to their corresponding DMSO-treated control groups to obtain the significantly differentially expressed gene lists using two-tailed student t test at each time point.

source_name: Karpas422, EZH2i, day6, rep1

label_protocol: According to Affymetrix protocol

extract_protocol: According to Trizol protocol

tag: genotype

value: EZH2 Y641N

tag: disease

value: DLBCL


title: polypoid adenoma 38

description:
raw data ch1: US22502676_252252210053_S01_CGH_105_Dec08_1_2.txt
raw data ch2: US22502676_252252210053_S01_CGH_105_Dec08_1_1.txt
POLY_ADE_38


title: Karpas422_DMSO_day6_rep3

source_name: Karpas422, DMSO, day6, rep3


title: Karpas422_EZH2i_day6_rep2

source_name: Karpas422, EZH2i, day6, rep2


title: Karpas422_DMSO_day6_rep1

source_name: Karpas422, DMSO, day6, rep1


title: Karpas422_EZH2i_day3_rep2

source_name: Karpas422, EZH2i, day3, rep2


title: HepG2 siNC biological rep3


title: Karpas422_DMSO_day6_rep2

source_name: Karpas422, DMSO, day6, rep2


title: polypoid adenoma 39

description:
raw data ch1: US22502676_252252210053_S01_CGH_105_Dec08_1_3.txt
raw data ch2: US22502676_252252210053_S01_CGH_105_Dec08_1_1.txt
POLY_ADE_39


title: flat adenoma 32

description:
raw data ch1: US22502676_252252210052_S01_CGH_105_Dec08_1_2.txt
raw data ch2: US22502676_252252210052_S01_CGH_105_Dec08_1_1.txt
FLAT_ADE_32


title: Karpas422_EZH2i_day3_rep1

source_name: Karpas422, EZH2i, day3, rep1


title: Karpas422_EZH2i_day6_rep3

source_name: Karpas422, EZH2i, day6, rep3


title: Karpas422_EZH2i_day3_rep3

source_name: Karpas422, EZH2i, day3, rep3


title: polypoid adenoma 34

description:
raw data ch1: US22502676_252252210052_S01_CGH_105_Dec08_1_4.txt
raw data ch2: US22502676_252252210052_S01_CGH_105_Dec08_1_4.txt
POLY_ADE_34


title: flat adenoma 37

description:
raw data ch1: US22502676_252252210053_S01_CGH_105_Dec08_1_1.txt
raw data ch2: US22502676_252252210053_S01_CGH_105_Dec08_1_1.txt
FLAT_ADE_37


title: shCTR biological replicate 3

city: Barcelona

first: Luciano

last: Di Croce

address: Dr. Aiguader, 88

country: Spain

institute: Centre for Genomic Regulation

hyb_protocol: After fragmentation, 1650 ng of labeled cRNA from each sample was hybridized in in situ hybridization oven (Agilent) for 17 h at 65ºC and washed during 1 min at rt in Gene Expression Wash Buffer 1 (Agilent) and 1 min at 37 ºC with Gene Expression Wahs buffer 2 (Agilent).

scan_protocol: Scanned on an Agilent G2539A scanner at 5um resolution and 100%PMT The intensity data of each individual hybridization were extracted and the quality was assessed with the Feature Extraction software 10.7 (Agilent).

data_processing: Raw data was corrected for background noise using the normexp method. Quantile normalization was applied to assure comparability across samples.

source_name: embryonic stem cell

label_protocol: 500 ng of total RNA from each sample were amplified by Oligo-dT-T7 reverse transcription and labeled by in vitro transcription with T7 RNA polymerase in the presence of Cy3-CTP using the Quick Amp Labeling kit (Agilent) and purified using RNAeasy columns (Qiagen, Hilden, Germany)

extract_protocol: Total RNAs were prepared with Qiagen Rneasy minikit according to manufacturer’s protocol

value: embryonic stem cell

value: shCTR


title: flat adenoma 30

description:
raw data ch1: US22502676_252252210154_S01_CGH_105_Dec08_1_4.txt
raw data ch2: US22502676_252252210156_S01_CGH_105_Dec08_1_1.txt
FLAT_ADE_30


title: Karpas422_DMSO_day3_rep2

source_name: Karpas422, DMSO, day3, rep2


title: flat adenoma 29

description:
raw data ch1: US22502676_252252210071_S01_CGH_105_Dec08_1_3.txt
raw data ch2: US22502676_252252210071_S01_CGH_105_Dec08_1_1.txt
FLAT_ADE_29


title: Karpas422_DMSO_day3_rep3

source_name: Karpas422, DMSO, day3, rep3


title: flat adenoma 26

description:
raw data ch1: US22502676_252252210071_S01_CGH_105_Dec08_1_4.txt
raw data ch2: US22502676_252252210071_S01_CGH_105_Dec08_1_4.txt
FLAT_ADE_26


title: flat adenoma 27

description:
raw data ch1: US22502676_252252210071_S01_CGH_105_Dec08_1_2.txt
raw data ch2: US22502676_252252210071_S01_CGH_105_Dec08_1_4.txt
FLAT_ADE_27


title: shCTR biological replicate 1


title: Karpas422_EZH2i_day2_rep3

source_name: Karpas422, EZH2i, day2, rep3


title: shCTR biological replicate 4


title: shCTR biological replicate 2


title: Karpas422_DMSO_day3_rep1

source_name: Karpas422, DMSO, day3, rep1


title: flat adenoma 28

description:
raw data ch1: US22502676_252252210071_S01_CGH_105_Dec08_1_2.txt
raw data ch2: US22502676_252252210071_S01_CGH_105_Dec08_1_1.txt
FLAT_ADE_28

source_name: Colorectal tissue, macrodissected [test]

source_name: FFPE colon DNA pool from healthy individuals [reference]


title: flat adenoma 25

description:
raw data ch1: US22502676_252252210071_S01_CGH_105_Dec08_1_3.txt
raw data ch2: US22502676_252252210071_S01_CGH_105_Dec08_1_1.txt
FLAT_ADE_25


title: Karpas422_EZH2i_day2_rep2

source_name: Karpas422, EZH2i, day2, rep2


title: Karpas422_EZH2i_day2_rep1

source_name: Karpas422, EZH2i, day2, rep1


title: sh4 biological replicate 1


title: sh4 biological replicate 2


title: sh4 biological replicate 3


title: shCTR 72 RA biological replicate 3

value: 72 hours with 1uM retinoic acid


title: shCTR 72 RA biological replicate 4


title: Karpas422_DMSO_day2_rep3

source_name: Karpas422, DMSO, day2, rep3


title: shCTR 72 RA biological replicate 2


title: flat adenoma 22

description:
raw data ch1: US22502676_252252210070_S01_CGH_105_Dec08_1_3.txt
raw data ch2: US22502676_252252210070_S01_CGH_105_Dec08_1_4.txt
FLAT_ADE_22

value: F

value: Pooled DNA (FFPE) of 10 healthy individuals was used as reference in the aCGH experiments; across array CGH comparisons were made as described by Buffart et al, Genes, Chromosomes & Cancer 2008, 47(11):994-1004


title: flat adenoma 19

description:
raw data ch1: US22502676_252252210070_S01_CGH_105_Dec08_1_3.txt
raw data ch2: US22502676_252252210070_S01_CGH_105_Dec08_1_4.txt
FLAT_ADE_19


title: flat adenoma 23

description:
raw data ch1: US22502676_252252210070_S01_CGH_105_Dec08_1_2.txt
raw data ch2: US22502676_252252210070_S01_CGH_105_Dec08_1_1.txt
FLAT_ADE_23


title: Karpas422_DMSO_day2_rep2

source_name: Karpas422, DMSO, day2, rep2


title: Karpas422_DMSO_day2_rep1

source_name: Karpas422, DMSO, day2, rep1


title: Karpas422_EZH2i_day1_rep3

source_name: Karpas422, EZH2i, day1, rep3


title: flat adenoma 17

description:
raw data ch1: US22502676_252252210159_S01_CGH_105_Dec08_1_4.txt
raw data ch2: US22502676_252252210159_S01_CGH_105_Dec08_1_1.txt
FLAT_ADE_17

value: LST-F


title: Karpas422_DMSO_day1_rep3

source_name: Karpas422, DMSO, day1, rep3


title: S. mutans ∆nox mutant pH7 replicate 4

city: Rochester

first: Roberta

middle: C

last: Faustoferri

state: NY

address: 601 Elmwood Ave. Box 611

department: Center for Oral Biology

institute: University of Rochester Medical Center

description: ∆nox pH7-4

hyb_protocol: The slides were hybridized in a mixture containing equal amounts of labeled test and reference cDNA as described by the protocol from the Pathogen Functional Genomics Research Center (PFGRC) for 16 h at 42°C in a MAUI hybridization chamber (BioMicro Systems, Salt Lake City, UT).  Hybridized slides were washed and scanned using a GenePix 4000b scanner (Molecular Devices, Inc., Sunnyvale, CA).

scan_protocol: Hybridized slides were washed using the method described by the Pathogen Functional Genomics Research Center (PFGRC) and scanned using a GenePix 4000b scanner (Molecular Devices, Inc., Sunnyvale, CA).

data_processing: Data were analyzed using software available at the J. Craig Venter Institute PFGRC website. The 'IA' and 'IB' in the raw data .MEV files correspond to "Cy3" and "Cy5," respectively.  Single-channel images of the slides were loaded into Spotfinder and overlaid.  MIDAS software was used to normalize the spot intensity data using LOWESS and iterative log mean centering with default setting, followed by in-slide replicate analysis.  Statistical analysis was carried out with BRB array tools (http://linus.nci.nih.gov/BRB-ArrayTools.html) with a cutoff P-value of 0.01 and a ≥2-fold change of expression.

organism: Streptococcus mutans UA159

source_name: ∆nox mutant strain, steady-state pH7

label_protocol: Once RNA was purified as described above, cDNA was generated from 2µg RNA per sample as described by the protocol available from the Pathogen Functional Genomics Research Center (PFGRC) using Invitrogen Superscript III Reverse Transcriptase (Life Technologies, Carlsbad, CA) to increase cDNA yields.  Purified cDNAs were coupled to Cy3 (experimental samples) or Cy5 (reference cDNA).

growth_protocol: S. mutans UA159 (parent strain) and MU1020 (∆nox) were grown in continuous culture to steady-state pH values of 7 with or without supplemented oxygen in a BioFlo2000 fermentor at a dilution rate of 0.24h-1 in non-limiting glucose concentrations.

extract_protocol: RNA was isolated from homogenized S. mutans cells grown in continuous culture in TY + 1% glucose medium to steady-state pH value of 7 with or without supplemented oxygen, by repeated hot acid-phenol: chloroform extractions, and the nucleic acid was precipitated with 1 volume ice-cold isopropanol and one-tenth volume 3M sodium acetate (pH 5) at –20°C overnight.  RNA pellets were resuspended in 80 mL nuclease-free H2O, and treated with DNase I (Ambion) at 37°C for 30 minutes.  RNA concentrations were determined using a Nanodrop ND-1000 Spectrophotometer (Thermo Fisher Scientific, Waltham, MA), and 1 µL samples were run on an agarose gel to verify RNA integrity.  The RNA was purified again using the RNeasy mini kit (Qiagen), including a second on-column DNase treatment that was performed as recommended by the supplier.  Final RNA concentrations were determined spectrophotometrically.

tag: genotype/variation

value: ∆nox mutant (MU1020)

source_name: parent strain_mid-log

tag: growth stage

value: mid-log


title: sh4 72 RA biological replicate 4

tag: tissue


title: S. mutans ∆nox mutant pH7 replicate 2

description: ∆nox pH7-2


title: S. mutans ∆nox mutant pH7 replicate 3

description: ∆nox pH7-3


title: flat adenoma 16

description:
raw data ch1: US22502676_252252210159_S01_CGH_105_Dec08_1_3.txt
raw data ch2: US22502676_252252210159_S01_CGH_105_Dec08_1_1.txt
FLAT_ADE_16


title: flat adenoma 15

description:
raw data ch1: US22502676_252252210159_S01_CGH_105_Dec08_1_2.txt
raw data ch2: US22502676_252252210159_S01_CGH_105_Dec08_1_1.txt
FLAT_ADE_15


title: Karpas422_EZH2i_day1_rep1

description: Timecourse gene expression profiling of DLBCL cell line Karpas422 after EZH2 inhibitor treatment

source_name: Karpas422, EZH2i, day1, rep1


title: flat adenoma 13

description:
raw data ch1: US22502676_252252210159_S01_CGH_105_Dec08_1_2.txt
raw data ch2: US22502676_252252210159_S01_CGH_105_Dec08_1_1.txt
FLAT_ADE_13


title: sh4 72 RA biological replicate 3

source_name: embryonic stem cell


title: Karpas422_DMSO_day1_rep1

source_name: Karpas422, DMSO, day1, rep1


title: Karpas422_DMSO_day1_rep2

source_name: Karpas422, DMSO, day1, rep2


title: shCTR 72 RA biological replicate 1


title: Karpas422_EZH2i_day1_rep2

source_name: Karpas422, EZH2i, day1, rep2


title: sh4 72 RA biological replicate 1


title: flat adenoma 12

description:
raw data ch1: US22502676_252252210159_S01_CGH_105_Dec08_1_1.txt
raw data ch2: US22502676_252252210159_S01_CGH_105_Dec08_1_1.txt
FLAT_ADE_12


title: flat adenoma 11

description:
raw data ch1: US22502676_252252210069_S01_CGH_105_Dec08_1_3.txt
raw data ch2: US22502676_252252210069_S01_CGH_105_Dec08_1_4.txt
FLAT_ADE_11

value: M


title: VVM-GC-4

city: Philadelphia

first: Young

middle: Shin

last: Lee

state: PA

address: 3307 N. Broad Street AHB 557

department: Fels Institute for Cancer Research and Molecular Biology

institute: Temple University

description: Gene expression data from granulosa cells isolated from ovarian follicle following in vivo maturation (w/ FSH + hCG stimulation)

hyb_protocol: The biotin-labeled cRNA samples were fragmented and 10 µg of the fragmented cRNAs were hybridized onto Affymetrix Rhesus Genome GeneChip arrays.  Hybridization, washing and staining of the GeneChip arrays were performed using an automated fluidics station at the University of Pennsylvania Microarray Core Facility.

scan_protocol: GeneChips were scanned using GCS3000 laser scanner.

data_processing: Probe hybridization intensity data were imported into the Affymetrix Expression Console Software and summarized using the Robust Multichip Analysis (RMA) algorithm with a global background correction and a quantile normalization.

organism: Macaca mulatta

source_name: Granulosa cells from COC matured in vivo (FSH stimulation + in vivo maturation with hCG stimulation)

label_protocol: 50 ng of total RNA was subjected to two rounds of cDNA synthesis and in-vitro transcription labeling to achieve a linear amplification (Eukaryotic Small Sample Target Labeling Assay, Affymetrix GeneChip Expression Analysis Technical Manual) with minor modifications (initial 5 µl volume for annealing and reverse transcription for 30 min at 42°C followed by 30 min at 45°C).

extract_protocol: Total RNA was extracted from granulosa cells using PicoPure RNA purification kit (MDS Analytical Technologies)

tag: cell type

value: Granulosa cells

tag: maturation

value: In vivo maturation


title: S. mutans UA159 parent strain + 8.4% O2 pH7 replicate 4

description: UA159 + O2 pH7-4

source_name: parent strain with oxygen, steady-state pH7

value: parent

value: 8.4% O2 supplemented


title: PR knockout

city: Urbana

first: Shanmugasundaram

last: Nallasamy

state: IL

address: 2001 S Lincoln Ave

department: Comparative Biosciences

institute: University of illinois at Urbana-Champaign

description:
Mouse, ovary, ovulation, progesterone receptor, contraception, Ulipristal acetate
PRKO

hyb_protocol: 10 micrograms of labeled aRNA were hybridized to a Mouse Genome 430 2.0 Affymetrix 3' Expression Analysis Array.  Wash and stain were performed on Affymetrix Fluidics Station 450 with protocol EukGE_WS2v5 using Affymetrix GeneChip Command Console Fluidics Control software and solutions prepared by Keck Center,Comparative and Functional Genomics Unit, Roy J. Carver Biotechnology Center, University of Illinois at Urbana-Champaign.

scan_protocol: Arrays were scanned on Affymetrix GeneChip Scanner model 3000 7G Plus using GeneChip Command Console Scan Control software to generate DAT and CEL files.

data_processing: To generate quality control metrics the Keck Center  generated CHP files using the MAS5 algorithm with Affymetrix Expression Console version 1_1.

source_name: Ovaries from PRKO mice

label_protocol: The Keck Center Comparative and Functional Genomics Unit, Roy J. Carver Biotechnology Center, University of Illinois at Urbana-Champaign prepared amplified, biotin-labeled, fragmented antisense RNA from 100 nanograms of sample total RNA using the Affymetrix 3' Express Kit (Affymetrix, Inc., Santa Clara, CA) according to manufacturer’s instructions.

growth_protocol: Mice were maintained in the designated animal care facility at University of Illinois at Urbana-Champaign according to the institutional guidelines for the care and use of laboratory animals.

extract_protocol: Total RNA was extracted from ovaries using Trizol reagent and RNA was cleaned up by the Qiagen RNAeasy  kit according to the manufacturer's instructions.

treatment_protocol: Microarray analyses were performed using total RNA samples prepared from WT or PRKO mice. Mice were treated with PMSG for 48 h followed by hCG.  Ovaries were collected at 11 h and total RNA was analyzed using Affymetrix mouse arrays (GeneChip Mouse Genome 430 2.0 Array; Affymetrix, Inc., Santa Clara, CA)

tag: age

value: ovary

tag: genetic background

value: PR knockout


title: S. mutans ∆nox mutant pH7 replicate 1

description: ∆nox pH7-1


title: flat adenoma 10

description:
raw data ch1: US22502676_252252210069_S01_CGH_105_Dec08_1_4.txt
raw data ch2: US22502676_252252210069_S01_CGH_105_Dec08_1_4.txt
FLAT_ADE_10

source_name: Colorectal tissue, macrodissected [test]

tag: gender

tag: paris classification

value: IIc

source_name: FFPE colon DNA pool from healthy individuals [reference]

tag: reference description


title: S. mutans UA159 parent strain + 8.4% O2 pH7 replicate 3

description: UA159 + O2 pH7-3


title: wild type

description:
Mouse, ovary, ovulation, progesterone receptor, contraception, Ulipristal acetate
WT

source_name: Ovaries from wt mice

value: wild type


title: VVM-GC-3


title: Vehicle treated (OIL)

description:
Mouse, ovary, ovulation, progesterone receptor, contraception, Ulipristal acetate
Vehicle/oil treated control

source_name: Ovaries from mice treated with vehicle (oil)

treatment_protocol: Microarray analyses were performed using total RNA samples prepared from vehicle or UPA-treated mice. Mice were treated with PMSG for 48 h followed by hCG. Two hour after hCG treatment, mice were administered with UPA or vehicle. Ovaries were collected at 11 h and total RNA was analyzed using Affymetrix mouse arrays (GeneChip Mouse Genome 430 2.0 Array; Affymetrix, Inc., Santa Clara, CA)

value: oil vehicle


title: flat adenoma 9

description:
raw data ch1: US22502676_252252210069_S01_CGH_105_Dec08_1_3.txt
raw data ch2: US22502676_252252210069_S01_CGH_105_Dec08_1_4.txt
FLAT_ADE_9

value: IIa


title: Ulipristal/CDB treated

description:
Mouse, ovary, ovulation, progesterone receptor, contraception, Ulipristal acetate
Ulipristal/CDB treated

source_name: Ovaries from mice treated with CDB

value: Ulipristal acetate


title: S. mutans UA159 parent strain + 8.4% O2 pH7 replicate 2

description: UA159 + O2 pH7-2


title: S. mutans UA159 parent strain pH7 replicate 3

description: UA159 pH7-3

source_name: parent strain, steady-state pH7


title: VVM-GC-2


title: S. mutans UA159 parent strain + 8.4% O2 pH7 replicate 1

description: UA159 + O2 pH7-1


title: flat adenoma 14

description:
raw data ch1: US22502676_252252210159_S01_CGH_105_Dec08_1_3.txt
raw data ch2: US22502676_252252210159_S01_CGH_105_Dec08_1_1.txt
FLAT_ADE_14

value: F

value: LST-G


title: wildTypeRep1

city: Houston

first: kaifu

last: chen

address: 1 Baylor plaza, suite 450A

institute: Baylor College of Medicine

hyb_protocol: manufacturer's protocol

scan_protocol: manufacturer's protocol

data_processing: Probe value were extracted from .CEL files by the RMA package, differential analysis carried out based on the Limma package.

source_name: wild type

label_protocol: manufacturer's protocol

growth_protocol: Both the wild-type BY4741 and an isogenic fun30∆ mutant were grown in 10 ml of synthetic complete medium until log phase.

extract_protocol: Cells were collected and resuspended in 400 µl of TES solution (10 mM Tris-HCl pH 7.5, 10 mM EDTA, 0.5% SDS). Cells were lysed by vortexing with glass beads after adding 400 μl of acidic phenol to the cell suspension. Cell lysates were clarified by centrifugation at 13,000 rpm for 10 min at 4°C. Protein in the supernatant was extracted once with an equal volume of phenol:chloroform (1:1) solution, followed by extraction once with an equal volume of chloroform. The resulting supernatant was mixed with three volumes of 100% ethanol and 0.1 volume of 3M NaOAc (pH 5.2) and incubated at -80°C for 2 hrs. Total RNA was precipitated by centrifugation at 13,000 rpm for 20 min at 4°C followed by washing once with 70% ethanol.  After a brief air dry (5 min), RNA was dissolved in 50 μl of DEPC-treated water and analyzed with an Affimatrix microarray.  l

tag: strain


title: S. mutans UA159 parent strain pH7 replicate 2

description: UA159 pH7-2


title: VVM-GC-1


title: wildTypeRep2


title: Fun30KOrep2


title: Fun30KOrep1


title: S. mutans UA159 parent strain pH7 replicate 1

description: UA159 pH7-1


title: sh4 biological replicate 4

value: embryonic stem cell

tag: transfection


title: flat adenoma 8

description:
raw data ch1: US22502676_252252210069_S01_CGH_105_Dec08_1_2.txt
raw data ch2: US22502676_252252210069_S01_CGH_105_Dec08_1_4.txt
FLAT_ADE_8

value: LST-F

value: Pooled DNA (FFPE) of 10 healthy individuals was used as reference in the aCGH experiments; across array CGH comparisons were made as described by Buffart et al, Genes, Chromosomes & Cancer 2008, 47(11):994-1004


title: isu1Δ::URA3 integration vs pRS416

description: Integration at ISU1

hyb_protocol: Common priming sites on Cy5- or Cy3-labelled barcode PCR products were masked by pre-incubation with an ∼48-fold excess of complementary oligonucleotides and then hybridized to a “Hopkins TAG-array” in 5 ml of hybridization buffer (1 M NaCl; 10 mM Tris·HCl, pH 7.5; 0.5% Triton X-100; 1 mM DTT) in a hybridization chamber at 42 °C for an overnight.

scan_protocol: A hybridized array is carefully removed from the hybridization chamber by grabbing one end with Teflon coated forceps. The array is slowly dipped into and pulled out of a 50-ml conical tube containing 50 ml of 6 × SSPE (0.9 M NaCl; 60 mM NaH2PO4; 6 mM EDTA; adjust to pH 7.4) with 0.05% Triton X-100 and 1 mM DDT for 5 times and then similarly washed in 50 ml of 0.06 × SSPE containing 1 mM DDT (also in a 50-ml conical tube). After the final dip into the 0.06 × SSPE buffer, the slide is very slowly pulled out of the washing solution to avoid residual liquid stuck on the slide.  Each slide is then immediately scanned with a Genepix 4000B instrument. Laser power settings and photomultiplier tube (detector) voltages were set to ensure that signal intensities are maximized but with no more than a few saturated features. Scanner resolution was 10 μm/pixel. For each scan, the result was saved as a multi-color image file (“.tif”).

data_processing: Image files were processed with GenePix Pro software package version 6.0 to generate the raw data as GPR files.  To generate the final reported results, raw data of each experment was further processed using Microsoft Excel.  Background-subtracted values (“F532 Median – B532” or “F635 Median – B635”) of median signal intensity of all barcodes in both control (pRS416) and experimental (isu1Δ::URA3 integration) samples were summed up and compared with each other to obtain a global normalization factor. For each barcode, a control/experiment signal intensity ratio was subsequently obtained by taking into account of this global normalization factor.

source_name: pRS416-transformed pool

label_protocol: PCR primers used to amplify barcodes were labeled at the 5' with either Cy5 or Cy3.

growth_protocol: A homozygous diploid deletion mutant library was transformed with a circular plasmid pRS416, an isu1Δ::URA3 integration cassette, Transformants were grown on solid SC-Ura medium for 2 days at 30°C.  Transformation with the plasmid was used as a control.

extract_protocol: Genomic DNA was purified using a Yeast genomic DNA purification kit (Zymoresearch) following the manufacturer's instructions.

value: pRS416-transformed pool

source_name: isu1Δ::URA3-transformed pool

value: isu1Δ::URA3-transformed pool


title: sod2Δ::URA3 integration vs pRS416

description: Integration at SOD2

data_processing: Image files were processed with GenePix Pro software package version 6.0 to generate the raw data as GPR files.  To generate the final reported results, raw data of each experment was further processed using Microsoft Excel.  Background-subtracted values (“F532 Median – B532” or “F635 Median – B635”) of median signal intensity of all barcodes in both control (pRS416) and experimental (sod2Δ::URA3 integration) samples were summed up and compared with each other to obtain a global normalization factor. For each barcode, a control/experiment signal intensity ratio was subsequently obtained by taking into account of this global normalization factor.

source_name: sod2Δ::URA3-transformed pool

growth_protocol: A homozygous diploid deletion mutant library was transformed with a circular plasmid pRS416,  an sod2Δ::URA3 integration cassette. Transformants were grown on solid SC-Ura medium for 2 days at 30°C.  Transformation with the plasmid was used as a control.

value: sod2Δ::URA3-transformed pool


title: flat adenoma 5

description:
raw data ch1: US22502676_252252210067_S01_CGH_105_Dec08_1_3.txt
raw data ch2: US22502676_252252210067_S01_CGH_105_Dec08_1_4.txt
FLAT_ADE_5

value: M


title: PM-GC-3

description: Gene expression data from granulosa cells isolated before maturation (FSH-stimulation only)

source_name: Granulosa cells from immature COC (FSH-stimulation only)

value: Granulosa cells

value: Pre-maturation


title: PM-GC-2


title: flat adenoma 6

description:
raw data ch1: US22502676_252252210067_S01_CGH_105_Dec08_1_4.txt
raw data ch2: US22502676_252252210067_S01_CGH_105_Dec08_1_4.txt
FLAT_ADE_6


title: PM-GC-4


title: PM-GC-1


title: flat adenoma 7

description:
raw data ch1: US22502676_252252210069_S01_CGH_105_Dec08_1_2.txt
raw data ch2: US22502676_252252210069_S01_CGH_105_Dec08_1_1.txt
FLAT_ADE_7


title: flat adenoma 24

description:
raw data ch1: US22502676_252252210071_S01_CGH_105_Dec08_1_1.txt
raw data ch2: US22502676_252252210071_S01_CGH_105_Dec08_1_1.txt
FLAT_ADE_24


title: flat adenoma 3

description:
raw data ch1: US22502676_252252210067_S01_CGH_105_Dec08_1_3.txt
raw data ch2: US22502676_252252210067_S01_CGH_105_Dec08_1_1.txt
FLAT_ADE_3


title: flat adenoma 2

description:
raw data ch1: US22502676_252252210067_S01_CGH_105_Dec08_1_2.txt
raw data ch2: US22502676_252252210067_S01_CGH_105_Dec08_1_1.txt
FLAT_ADE_2


title: Surgery 4-PBS-8 h (data for dynamic bayesian analysis)

status: Public on Oct 03 2012

first: Leslie

middle: Garry

last: Adams

address: 402 Raymond Stotzer Blvd.

department: Veterinary Pathobiology

institute: Texas A&M University

hyb_protocol: cDNA from bovine experimental samples (i.e. from MAP and MAA infected and PBS control loops) were co-hybridized against cDNA generated from the bovine reference RNA sample 13K bovine 70mer oligoarray.  Prior to hybridization, the microarrays were denatured by exposing to steam from boiling water for three seconds, UV cross-linked and then immersed in pre-hybridization buffer [5X sodium chloride, sodium citrate buffer (SSC), 0.1% sodium dodecyl sulfate (SDS) (Ambion, Austin, TX), 1% bovine serum albumin (BSA)] at 42ºC for a minimum of 45 min followed by four washes in RNase-, DNase-free, distilled water, immersion in 100% isopropanol for 10 seconds, and dried by centrifugation. Slides were hybridized at 42ºC for approximately 40 hours in a dark humid chamber (Corning, Corning, NY) and washed for 10 min at 42ºC with low stringency buffer [1 X SSC, 0.2% SDS] followed by two 5-min washes in a higher stringency buffer [0.1 X SSC, 0.2% SDS and 0.1 X SSC] at room temperature in dark with mild agitation.

scan_protocol: Immediately after washing, the slides were scanned using a commercial laser scanner (GenePix 4100; Axon Instruments Inc., Foster City, CA). Scans were performed using the autoscan feature with the percent saturated pixels set at 0.03%

data_processing: log2 ratio of experiment/reference channel.  Prior to computing the ratio, we performed global scaling across all arrays and then a Lowess correction on an array basis.

organism: Bos taurus

source_name: Ileal mucosa inoculated with PBS, tissue collected at 8 H post infection

label_protocol: Total RNA was reverse transcribed using Superscript III reverse transcriptase (Invitrogen, Carlsbad, CA) and labeled with amino-allyl-UTP (Ambion, Austin, TX).  Cy3 (Reference)  and Cy5 (Experimental, i.e. PBS, MAp or MAA inoculated loop) dye esters were covalently linked to the amino-allyl group by incubating the samples with the dye esters in 0.1M sodium carbonate buffer.

growth_protocol: Mycobacterium avium subsp. paratuberculosis (ATCC 19698 from American Type Culture Collection, Manassas, VA),  was grown aerobically in 7H9 broth (Difco Laboratories, Detroit, MI) supplemented with 2.5% (vol/vol) glycerol (Sigma Chemical Co., St. Louis, MO), oleic acid-albumin-dextrose-catalase (Difco Laboratories, Detroit, MI), 0.05% Tween 80 (Sigma Chemical Co., MO), and 2 mg of Mycobactin J (Allied Monitor, Inc., Fayette, MO.).  Mycobacterium avium subsp. avium (ATCC 35716 from American Type Culture Collection, Manassas, VA) was grown in 7H9 broth supplemented with 2.5% (vol/vol) glycerol, oleic acid-albumin-dextrose-catalase and 0.05% Tween 80.

extract_protocol: Total RNA was extracted after dissection of the ileal loops obtained at 30 min and at 1, 2, 4, 8, and 12 hours post-infection.  A 6 mm biopsy punch was used to collect tissue pieces of Peyer’s patch from the excised loop. The mucosa of the samples were immediately dissected, the tissue pieces finely minced with a scalpel blade, and two biopsy punches (0.1 mg of tissue) transferred to 1 ml of Trizol reagent (Molecular Research Center, Cincinnati, OH).  Tissues were further disrupted with an RNase, DNase free plastic disposable pestle.  The RNA extraction was performed using the recommended protocol from the manufacturer. The resultant RNA pellet was re-suspended in DEPC-treated water (Ambion, Austin, TX).  Genomic DNA was removed by RNase-free DNase I treatment (DNA-free, Ambion) according to the manufacture’s instructions, and samples were stored at −80ºC until used. The quality of the RNA was initially assessed by measurement of the lambda 260/280 ratio and agarose gel electrophoresis. RNA concentration was quantified by measuring absorbance at lambda 260nm using a NanoDrop® ND-1000 (NanoDrop, Wilmington, DW), and the RNA quality was determined using a Nano-Chip® on an Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA). Samples were characterized by distinct 18S and 28S rRNA peaks and RNA size distribution. Ten micrograms of RNA was used as starting material for each array.  Reference RNA was a pool of Madin-Darby bovine kidney and  bovine B lymphocyte cell lines and fresh bovine brain cortex and cerebellum.  Total RNA was isolated from Madin-Darby bovine kidney (MDBK) and bovine B lymphocyte (BL-3) cell lines (American Type Culture Collection, Manassas, VA) and fresh bovine brain cortex and cerebellum collected from surgery calves following euthanasia at the conclusion of each experiment.  Cell lines were grown in 150 cm2 cell culture flasks with Eagle’s minimum essential medium (E-MEM) (ATCC) supplemented with 10% heat-inactivated fetal bovine serum (HI-FBS). Tissues were homogenized in ice-cold Tri-reagent® (Ambion, Austin, TX). RNA concentration and quality from each sample was determined before and after pooling the samples. Total RNA isolated from three samples was pooled together in equal amounts, aliquoted and stored at −80ºC until needed.

treatment_protocol: Cows were infected (ligated ileal loops) with PBS, a virulent strain of Mycobacterium avium (subsp. paratuberculosis) or an avirulent M. avium strain (subsp. avium) for 30 min, 1h, 2h, 4h, 8h, or 12h. The experiment was performed in quadruplicate (except for the avirulent infections at 2 and 8 hours, which were performed three times each). Post-infection, RNA was collected, processed, and then hybridized to custom bovine gene expression arrays, each of which represented 13,258 transcripts spotted in duplicate.  There were therefore 70 arrays in total.

tag: male calf

tag: 3 to 6 weeks of age

tag: outbred

tag: distal ileum

source_name: reference RNA

tag: A mixture of equal parts total RNA from Madin-Darby bovine kidney (MDBK) and bovine B lymphocyte (BL-3) cell lines and fresh bovine brain cortex and cerebellum.

tag: cell lines were purchased from the American Type Culture Collection (ATCC), fresh bovine brain and cerebellum was collected from surgery calves immediately following euthanasia by barbituate overdose at the conclusion of bovine ligated ileal loop surgery.


title: Surgery 4-MAA-8 h (data for dynamic bayesian analysis)

source_name: Ileal mucosa inoculated with MAA, tissue collected 8 H post infection


title: Surgery 4-MAA-2 h (data for dynamic bayesian analysis)

source_name: Ileal mucosa inoculated with MAA, tissue collected 2 H post infection


title: Surgery 4-MAP-12 h (data for dynamic bayesian analysis)

source_name: Ileal mucosa inoculated with MAP, tissue collected at 12 H post infection


title: Surgery 4-PBS-12 h (data for dynamic bayesian analysis)

source_name: Ileal mucosa inoculated with PBS, tissue collected at 12 H post infection


title: Surgery 4-MAA-30 min (data for dynamic bayesian analysis)

source_name: Ileal mucosa inoculated with MAA, tissue collected at 30 min post infection


title: Surgery 3-PBS-12 h (data for dynamic bayesian analysis)


title: Surgery 4-MAP-2 h (data for dynamic bayesian analysis)

source_name: Ileal mucosa inoculated with MAP, tissue collected at 2 H post infection


title: Surgery 4-MAA-1 h (data for dynamic bayesian analysis)

source_name: Ileal mucosa inoculated with MAA, tissue collected at 1H post infection


title: Surgery 4-PBS-4 h (data for dynamic bayesian analysis)

source_name: Ileal mucosa inoculated with PBS, tissue collected at 4 H post infection


title: Surgery 4-MAP-4 h (data for dynamic bayesian analysis)

source_name: Ileal mucosa inoculated with MAP, tissue collected at 4 H post infection


title: Surgery 3-MAA-8 h (data for dynamic bayesian analysis)


title: Surgery 4-MAP-30 min (data for dynamic bayesian analysis)

source_name: Ileal mucosa inoculated with MAP, tissue collected at 30 min post infection


title: Surgery 3-MAA-12 h (data for dynamic bayesian analysis)

source_name: Ileal mucosa inoculated with MAA, tissue collected at 12 H post infection


title: Surgery 4-MAA-4 h (data for dynamic bayesian analysis)

source_name: Ileal mucosa inoculated with MAA, tissue collected 4 H post infection


title: Surgery 3-MAP-12 h (data for dynamic bayesian analysis)


title: Surgery 4-PBS-2 h (data for dynamic bayesian analysis)

source_name: Ileal mucosa inoculated with PBS, tissue collected at 2 H post infection


title: Surgery 4-MAA-12 h (data for dynamic bayesian analysis)


title: Surgery 4-MAP-1 h (data for dynamic bayesian analysis)

source_name: Ileal mucosa inoculated with MAP, tissue collected at 1H post infection


title: Surgery 4-PBS-1 h (data for dynamic bayesian analysis)

source_name: Ileal mucosa inoculated with PBS, tissue collected at 1H post infection


title: Surgery 4-MAP-8 h (data for dynamic bayesian analysis)

source_name: Ileal mucosa inoculated with MAP, tissue collected at 8 H post infection


title: Surgery 4-PBS-30 min (data for dynamic bayesian analysis)

source_name: Ileal mucosa inoculated with PBS, tissue collected at 30 min post infection

source_name: reference RNA


title: Surgery 3-MAA-4 h (data for dynamic bayesian analysis)


title: Surgery 3-MAP-2 h (data for dynamic bayesian analysis)


title: Surgery 3-PBS-8 h (data for dynamic bayesian analysis)

source_name: Ileal mucosa inoculated with PBS, tissue collected at 8 H post infection


title: Surgery 3-MAA-2 h (data for dynamic bayesian analysis)

source_name: Ileal mucosa inoculated with MAA, tissue collected 2 H post infection


title: Surgery 3-MAP-4 h (data for dynamic bayesian analysis)


title: Surgery 3-PBS-4 h (data for dynamic bayesian analysis)


title: Surgery 3-PBS-2 h (data for dynamic bayesian analysis)


title: Surgery 3-MAP-8 h (data for dynamic bayesian analysis)


title: Surgery 3-MAA-1 h (data for dynamic bayesian analysis)


title: Surgery 3-MAP-30 min (data for dynamic bayesian analysis)


title: Surgery 2-MAP-4 h (data for dynamic bayesian analysis)


title: Surgery 2-MAP-8 h (data for dynamic bayesian analysis)


title: Surgery 2-MAA-8 h (data for dynamic bayesian analysis)

source_name: Ileal mucosa inoculated with MAA, tissue collected 8 H post infection