title: Ssa_Diet 1 (ctrl)_56d_replicate 2

source_name: Ssa_Diet 1 (ctrl)_56d_replicate 2


title: Ssa_Diet 1 (ctrl)_14d_replicate 5

status: Public on Dec 31 2012

type: RNA

city: Moncton

first: Francis

last: LeBlanc

state: NB

address: 343 University Ave.

department: Aquatic Animal Health

country: Canada

institute: Fisheries & Oceans Canada

hyb_protocol: Microarray hybridizations were performed using Agilent’s 4 x 44K Atlantic salmon microarray slides containing 4 grids with the same ~ 44 000 features (Design ID 025055), using a one-color approach.  All hybridizations, including washes and drying steps were carried out on a HS4800 automated hybridization station using quad chambers (Tecan, Männedorf, Switzerland). Briefly, slides were initially washed with Agilent’s aOligo aCGH Prehybridization buffer for 1 min at 65°C and injected with a 60 µl of hybridization mix containing 30 µl of fragmentation mix and 30 µl of Agilent’s 2x GEx hybridization Buffer Hi-RPM per chamber.  The injected material was hybridized for 17 hour at 65°C.  Following hybridization slides were washed twice with Agilent’s gene expression wash buffer 1 at 23°C for 1 min, twice with Agilent’s gene expression wash buffer 2 with 0.01 wash buffer additive at 37°C for 1 min and then dried under nitrogen.

scan_protocol: Microarray slides were scanned at a resolution of 5 µm using Agilent’s High Resolution Microarray Scanner (Agilent, CA, USA) using a 20-bit data format and automatic PMT adjustment.

data_processing: The resulting TIFF images were quantified using Agilent’s Feature Extraction software (Agilent, CA, USA). Numerical intensities, descriptive statistics and flag value were computed for each spot and exported in a text file. Spots were considered flagged it they were saturated, not uniform, below background levels and if the background was not uniform. Genes that had a flag on more than 1/3 of the slides used for a particular statistical analysis were filtered out.  The gProcessedSignal values (foreground value minus background value) for each spot were then log2 transformed and normalized between arrays using a median centering approach found in BRBArrayTool version 4.1.0 Beta_2 Release (developed by Dr. Richard Simon and BRB-ArrayTools Development Team).  Statistical analysis was performed on log2 transformed and normalized gProcessedSignal value.

molecule: total RNA

organism: Salmo salar

source_name: Ssa_Diet 1 (ctrl)_14d_replicate 5

label_protocol: RNA amplification and labeling for microarray was performed using the one-color Low Input Quick Amp Labeling kit (Agilent, CA, USA) and following the manufacturer’s recommendations. Briefly, 200 ng of each RNA sample was reverse transcribed, amplified and labeled using Cy3 dyes resulting in Cy3 labeled amplified RNA (aRNA). Purification of the labeled aRNA was performed using NucleoSpin RNA clean up columns (Macherey-Nagel, CA, USA) following the manufacturer’s recommendations. Following purification, labeled aRNA samples were then quantified using the NanoDrop 8000 to verify the yield of aRNA and the labeling efficiency. 1.65 µg of each purified aRNA was prepared for hybridization using the fragmentation step described in Agilent’s Low Input Quick Amp labeling kit protocol. Briefly each aRNA was fragmented by mixing 1.65 µg of aRNA in a volume of 22.8 µl, with 6 µl of 10X blocking agent and 1.2 µl of 25X fragmentation buffer and heating the mix at 60°C for 30 min.

extract_protocol: Total RNA from RNAlater preserved salmon liver samples was extracted using TRI reagent (Molecular Research Center, OH, USA) followed by column purification using the NucleoSpin RNA II (Macherey-Nagel, PA, USA) and following the manufacturer’s protocol.  An on column DNase digestion step was performed on each sample.  RNA quantification was performed using a NanoDrop 8000 (Thermo Scientific, DE, USA) and RNA quality and integrity was assessed with the Experion automated electrophoresis system (Bio-Rad, TX, USA).  Only RNA samples with RNA Quality Indicator (RQI) values above 8 were used for analysis.  RNA’s were stored at -70ºC in DEPC treated water containing an RNase inhibitor (Qiagen, ON, Canada) until needed.

tag: diet

value: control

tag: tissue

value: Liver

tag: time


title: MDA231_Fibro-2_Hs

city: Houston

first: Sangbae

last: Kim

state: TX

address: 1 Baylor plaza

department: HGSC

country: USA

institute: Baylor Colleage of Medicine

description: To export to gene expression data based on unique gene, we used Sample Gene Profile option of Illumina BeadStudio software. The whole 48697 probes on the Human-6 beadChip ver. 2 were used.

hyb_protocol: Labeled, amplified material (750 ng per array) was hybridized to the Illumina HumanHT-12 V3.0 expression beadchip according to the Manufacturer's instructions (Illumina, Inc., San Diego, CA).

scan_protocol: Arrays were scanned with an Illumina Bead array Reader confocal scanner (BeadStation 500GXDW; Illumina, Inc., San Diego, CA) according to the Manufacturer's instructions

data_processing: Array data processing were performed on Illumina BeadStudio software. We normalized gene expression data using Quantile normalization and log2 transformatoin. To export to a data matrix, Sample Gene Profile option of this software was used.

label: Biotin

organism: Homo sapiens

source_name: MDA-MB-231, NIH 3T3

label_protocol: Biotin-labeled cRNA samples for hybridization were prepared according to Illumina's recommended sample labeling procedure: 500 ng of total RNA was used for cDNA synthesis, followed by an amplification/labeling step (in vitro transcription) to synthesize biotin-labeled cRNA using the Illumina. TotalPrep RNA Amplification kit (Ambion Inc., Austin, TX). cRNA concentrations using spectrophotometer (Nanodrop, ND-1000)

extract_protocol: Total RNA was isolated from tissues with mirVana RNA Isolation labeling kit (Ambion Inc) according to the manufacturer protocol. RNA quality and integrity were confirmed by ExperionTM Automated Electrophoresis System (BIO-RAD)

tag: protocol

value: co-culture of MDA-MB-231 and astrocyte cells


title: 5 minutes after Notch activation vs unactivated pool trial 3

city: Cambridge

first: Sarah

last: Bray

address: Downing Street

department: PDN

country: United Kingdom

institute: University  of Cambridge

description: 5' Notch activation trial 3

hyb_protocol: Co-hybridisation of sample vs reference control to long oligonucleotides microarrays (Flychip FL003; GEO platform accession GPL8244) was performed for 16 hours at 51°C using a GeneTac hybridisation station (Digilab Genomic Solutions Inc). Post hybridisation washes were performed according to the slide manufacturer’s recommendation.  Detailed protocols for array spotting, labelling, hybridisation and washes are available at http://www.flychip.org.uk/protocols/.

scan_protocol: Operating instructions for the Genepix 4000B dual laser scanner (http://www.flychip.org.uk/protocols/imaging/)

data_processing: Spot finding and quantitation via the Dapple package. The R package limma (SMYTH and SPEED 2003) was used to normalize the arrays. For each array, the background intensity level of the array image was first adjusted before loess normalization was applied to the MA values of the array. The intensities of the two channels of all 72 arrays (4 replicates at 18 time points) were then quantile normalized, such that the intensities all had the same empirical distribution. Missing values arise because genes are not expressed or there is poor quality on the array.

organism: Drosophila melanogaster

source_name: reference pool - trial 3

label_protocol: 45 µg of sample or reference pool RNA was mixed with 1.5 µM anchored oligo(dT)23 (Sigma) and incubated at 65°C for 10 minutes. Reverse transcription was performed in the presence of 1nmol fluorescently labelled Cy3- or Cy5-dCTP (GE Healthcare) and 20U RNAsin (Promega) with 400U SuperScript III (Life Technologies) at 46°C for 2 hours. The product was purified using Sephadex G50 columns (GE Healthcare). Samples from trials #1 and #3 were labelled with Cy5 and trails #2 and #4 as dye-swap with Cy3.

growth_protocol: DmD8 cells were cultured in Schneiders medium (Invitrogen) supplemented with 10% FBS (Sigma), 5ug/ml insulin (Sigma) and 5% penicillin / streptomycin (Sigma) according to standard protocols.

extract_protocol: RNA was extracted from cells by removing media and incubating cells in TRI-reagent (Ambion) for 5 minutes. RNA was then purified by extracting with chloroform and precipitating with isopropanol before resuspension in DEPC treated water. DNA was removed by treating with DNase (DNA-free kit - Ambion). For each trial 50 µg of the untreated RNA sample of each time point was pooled to create a trial specific reference sample.

treatment_protocol: Notch signalling was initiated by replacing cell media with 2mM EDTA in PBS. For control samples, media was replaced with fresh media to mimic the addition and removal of EDTA in corresponding experimental samples.

tag: cell line

value: pool of unactivated cells from 0-150 minutes

tag: time trial

source_name: 5' after Notch activation - trial 3

treatment_protocol: Notch signalling was initiated by replacing cell media with 2mM EDTA in PBS. Cells were stimulated for 0 minutes before washing out EDTA using normal culture media.

value: 5 minutes after a 5 minute activation with EDTA


title: Ssa_Diet 1 (ctrl)_14d_replicate 6

source_name: Ssa_Diet 1 (ctrl)_14d_replicate 6


title: Ssa_Diet 1 (ctrl)_56d_replicate 3

source_name: Ssa_Diet 1 (ctrl)_56d_replicate 3


title: Ssa_Diet 1 (ctrl)_14d_replicate 4

source_name: Ssa_Diet 1 (ctrl)_14d_replicate 4


title: 0 minutes after Notch activation vs unactivated pool trial 4

description: 0' Notch activation trial 4 - dye swap

source_name: 0' after Notch activation - trial 4

extract_protocol: RNA was extracted from cells by removing media and incubating cells in TRI-reagent (Ambion) for 5 minutes. RNA was then purified by extracting with chloroform and precipitating with isopropanol before resuspension in DEPC treated water. DNA was removed by treating with DNase (DNA-free kit - Ambion).

value: 0 minutes after a 5 minute activation with EDTA

source_name: reference pool - trial 4


title: YP97-19052

type: genomic

city: Gotenburg

first: Marta

last: Persson

address: Box 425

country: Sweden

institute: Sahlgrenska Cancer Center

hyb_protocol: Oligoarray control targets (Cot-1 DNA and Blocking agent) and hybridization buffer (Agilent oligo aCGH/ChIP-on-Chip Hybridization Kit) were added, the samples were denatured and applied to microarrays (Agilent Human Genome CGH Microarray 44K and 244K 60-mer oligonucleotide arrays) as recommended by the manufacturer. The arrays were enclosed in a rotating hybridization oven at 65°C for 40 h. After hybridization, the slides were sequentially washed and dried.

scan_protocol: The arrays were scanned on an Agilent  Microarray Confocal Scanner (G2567AA) and the images were quantified with Agilent Feature Extraction Software (v.7.5) using the intensity-dependent linear normalization method.

data_processing: Data analysis was carried out using Nexus Copy Number software v.4.1 (BioDiscovery Inc., El Segundo, CA, USA), which uses the Rank segmentation algorithm to define non-random regions of CNAs across the genome. Sex chromosomes were excluded from the analysis. The significance threshold for segmentation was set to p=1.0E-7 and the thresholds of log2 ratio values for gain and loss were 0.4 and −0.3, respectively; the thresholds for high copy number gain/amplification and homozygous deletion were 1.0 and −1.0, respectively.

molecule: genomic DNA

source_name: Mucoepidermoid carcinoma

label_protocol: 3.0 µg of genomic tumor DNA and sex-matched reference DNA (pooled peripheral blood cells from 5 normal female and male genomes) were digested with AluI and Rsa1 (Promega, Madisaon, WI) and labeled with Cy3-dUTP and Cy5-dUTP (Perkin-Elmer Life and Analytical Sciences Inc., Wellesley, MA, USA).

extract_protocol: Genomic DNA was isolated from FFPE tissue using the standard phenol-chloroform method and from fresh frozen tissue using the QIAamp DNA Mini Kit (Qiagen GmbH, Hilden, Germany) according to the manufacturer instructions.

treatment_protocol: Fresh frozen tumor material from 15 MECs and paraffin embedded tumor material from 13 MECs were retrieved from the department of Pathology at Haartman Institute in Helsinki, the department of pathology at Sahlgrenska University Hospital in Gothenburg and the department of Oral Pathology at Guy's Hospital in London. The tumors were classified as low grade and high grade according to the histologic classification of salivary gland tumours by WHO.

tag: fusion status

value: Neg

tag: grade

value: High Grade

source_name: Normal tissue

tag: sample type

value: reference

tag: gender

value: F


title: YP97-17066

value: M


title: YP01-10210

value: Pos

value: Low Grade


title: YP96-15636


title: MDA231_Fibro-1_Hs


title: Ssa_Diet 1 (ctrl)_14d_replicate 1

source_name: Ssa_Diet 1 (ctrl)_14d_replicate 1


title: YP04-28078


title: MDA231_Astro-2_Hs

source_name: MDA-MB-231, astrocytes


title: 0 minutes after Notch activation vs unactivated pool trial 3

description: 0' Notch activation trial 3

source_name: 0' after Notch activation - trial 3


title: MDA231_Astro-3_Hs


title: MDA231_Astro-1_Hs


title: Ssa_Diet 1 (ctrl)_14d_replicate 2

source_name: Ssa_Diet 1 (ctrl)_14d_replicate 2


title: Ssa_Diet 1 (ctrl)_14d_replicate 3

source_name: Ssa_Diet 1 (ctrl)_14d_replicate 3


title: MDA231_Astro-4_Hs


title: 0 minutes after Notch activation vs unactivated pool trial 2

description: 0' Notch activation trial 2 - dye swap

source_name: 0' after Notch activation - trial 2

source_name: reference pool - trial 2


title: YP04-19660


title: 0 minutes after Notch activation vs unactivated pool trial 1

description: 0' Notch activation trial 1

source_name: reference pool - trial 1

source_name: 0' after Notch activation - trial 1


title: YP05-14190


title: Stable Plaque, biological rep 5

city: Newcastle upon Tyne

first: Kelvin

last: Lee

state: Tyne and Wear

address: International Centre for Life, Central Parkway

department: Cardiovascular Research

institute: Institute of Genetic Medicine, University of Newcastle upon Tyne

description: Gene expression data from macrophages isolated from stable plaques of Asymptomatic patients

hyb_protocol: Standard Affymetrix Protocol using the GeneChip Two-Cycle Target Labelling Kit

scan_protocol: Standard Affymetrix protocols using the Affymetrix 3000 GeneChip Scanner and GCOS ver.1.3 to generate RAW probe data in .cel files.

data_processing:
The RAW microarray data were analyzed using the GeneSpring GX 7.3.1 analysis package.  Raw microarray signal data were pre-processed and normalized using GCRMA, and normalised to the median.  Affymetrix external control probesets and probesets that were called absent in more than 6 of the 11 samples and were prefiltered out. The resulting 25538 of the 54675 probesets were analysed using ANOVA with corrections for the error of multiple testing by the Benjamini and Hochberg method.
RAW values in matrix file were the log transformed GCRMA processed signal intensity values. NORMALIZED values in the matrix file were the ratios of the log transformed GCRMA processed signal intensity values to the median. The ABS_CALL were the absent and present calls generated by the standard Affymetrix algorithm using GCOS ver.1.3 without any alteration from the default value of Tau.  File matrix_NORMALIZED_RAW_ABSCALL.txt is linked as a supplementary file on the Series record.

source_name: Macrophages, LMDed from Stable Carotid Atheromatous Plaque

label_protocol: Twenty to sixty nanograms of total RNA were subjected to two cycles of linear amplification using the Affymetrix GeneChip Two-Cycle Target Labeling Kit.

extract_protocol: RNA was isolated using the Qiagen RNeasy Micro kit. RNA quality and quantity was assessed by RIN score using the RNA6000 Pico Labchip (Agilent Bioanalyser 2100, Agilent).  Only samples with RIN scores of 6 and above were considered suitable for microarray analysis.

tag: age

value: female

tag: days from last symptom

tag: symptom event

tag: radiological stenosis

tag: plaque histology

value: Stable Thick Fibrous Cap Atheroma

tag: cell type

value: macrophage


title: YP03-18414


title: 5h oocysts Replicate 2-2

city: College Station

first: haili

last: zhang

address: Texas A&M University 4467 TAMU

department: VTPB

institute: TAMU

description: 5h Biological replicate 2 of 2.Technique replicate 2-2.

hyb_protocol: Arrays were incubated at 65°C for 17 h in Agilent's microarray hybridization chambers. After hybridization, arrays were washed according to the Agilent protocol.

scan_protocol: Scanned on an Agilent G2505C scanner. Images were quantified using Agilent Feature Extraction Software (version 10.7.1.1).

data_processing: Agilent Featxure Extraction Software (version 10.7.1.1) was used for background subtraction and LOWESS normalization.

organism: Cryptosporidium parvum

source_name: 5h control oocysts

label_protocol: A 100 ng of total RNA was reverse transcribed into cDNA using the two-color microarray-based gene expression analysis low input quick amp labeling kit (Agilent Technologies). The synthesized cDNA was transcribed into cRNA and labelled with either cyanine 3 or cyanine 5-labelled nucleotide (Perkin Elmer, Wellesley, MA).

growth_protocol: Fresh oocysts of C. parvum( Iowa strain) were purchased from Bunch Grass Farm( Deary, Idaho). The oocysts were stored in PBS solution.

extract_protocol: Following UV-C treatment, 350ul of lysis buffer were added to each sample and samples were freezed immediately in liquid nitrogen and disrupted using a mortar and pestle. Total RNA was then isolated using an RNeasy isolation kit (Qiagen, Valencia, CA). All of DNA was removed from the samples using RNase-free DNase set (Qiagen, Valecia, CA) according to the manufacture’s protocol.

treatment_protocol: Before UV treatment, the oocysts were further purified by a Percoll based gradient centrifugation method and surface-sterilized with 10% bleach for 7 min on ice, followed by washes with PBS for 5 times. To reduce the effects of temperature change on the expression, oocysts were placed at room temperature for overnight. Oocysts were divided into 8 groups (9x107oocysts/group), in which four groups were treated with 2.8mj/cm^2  dose of UV by placed in a stratalinker UV crosslinker equipped with FG8T5 germicidal lamps( Stratagene). The remaining 4 groups were served as controls (two groups each) that received no treatment, but were simply placed outside of the UV Crosslinker for 0.5 h and 5.0 h.

tag: time point

source_name: 5h UV treated oocysts


title: 5h oocysts Replicate 2-1

description: 5h Biological replicate 2 of 2.Technique replicate 2-1.


title: Stable Plaque, biological rep 4

value: male


title: YP03-16568


title: 5 minutes after Notch activation vs unactivated pool trial 1

description: 5' Notch activation trial 1

source_name: 5' after Notch activation - trial 1


title: Stable Plaque, biological rep 6

value: Stable Fibrocalcific Plaque


title: Stable Plaque, biological rep 3


title: 5h oocysts Replicate 1-1

description: 5h Biological replicate 1 of 2.Technique replicate 1-1.


title: 5h oocysts Replicate 1-2

description: 5h Biological replicate 1 of 2.Technique replicate 1-2.


title: YP97-7050


title: Stable Plaque, biological rep 2


title: 0.5h oocysts Replicate 2-2

description: 0.5h Biological replicate 2 of 2.Technique replicate 2-2.

source_name: 0.5h control oocysts

source_name: 0.5h UV treated oocysts


title: noTBMDM_Challenge_rep2

city: Beijing

first: Xiangmei

last: Zhou

address: No.2 Yuanmingyuan Xilu, Haidian District

department: College of Veterinary Medicine

country: China

institute: China Agricultural University

description:
6+
Gene expression after 6hr of challenge

hyb_protocol: Each Slide was hybridized with 1.65μg Cy3-labeled cRNA using Gene Expression Hybridization Kit (Cat#5188-5242, Agilent technologies, Santa Clara, CA, US) in Hybridization Oven (Cat#G2545A, Agilent technologies, Santa Clara, CA, US), according to the manufacture's instructions. After 17 hours hybridization, slides were washed in staining dishes (Cat#121, Thermo Shandon, MA, USA) with Gene Expression Wash Buffer Kit (Cat#5188-5327, Agilent technologies, US), followed the manufacturer's instructions.

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2565CA, Agilent technologies, US) with default settings, Dye channel: Green ,Scan resolution=5μm, PMT 100%, 10% 16bit.

data_processing: Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US) Raw data were normalized by Quantile algorithm, Gene Spring Software 11.0 (Agilent technologies, Santa Clara, CA, US).

organism: Bos taurus

source_name: MDM from TB-free cattle_challenged by M.bovis_6h

label_protocol: Total RNA was amplified and labeled by Low Input Quick Amp Labeling Kit, One-Color (Cat#5190-2305, Agilent technologies, Santa Clara, CA, US), followed the manufacturer’s instructions. Labeled cRNA were purified by RNeasy mini kit (Cat#74106, QIAGEN, Germany).

growth_protocol: Cows were recruited from a farm in Shandong province in China and were performed single intradermal tuberculin test and the INF-gamma release test (Bovigam, Prionics AG).

extract_protocol: TRIzol treated samples were purified by PureLink RNA Mini Kit (Ambion, USA). The quality and quantity of total RNA was examined by NanoDrop and Agilent Bioanalyzer 2100 (Agilent technologies, USA). Total RNA was further purified by Rneasy micro kit (QIAGEN, Germany)

treatment_protocol: PBMCs were isolated using 1.078 Optiprep （Axis-shield, Oslo, Norway) density gradient according to Application Sheet C08. Monocytes were allowed to adhere to plastic cell flasks for 24 hours and derived to macrophages after 5 days. Macrophages were challenged by M. bovis at MOI of 10 and unattached bacteria are washed out by PBS after 2 hours. At 6 hour, TRIzol (Invitrogen, USA) was added to each sample.

value: monocytes derived macrophages

tag: tb-infection status

value: TB-free cattle

tag: challenged with

value: M. bovis at MOI 10


title: 0.5h oocysts Replicate 2-1

description: 0.5h Biological replicate 2 of 2.Technique replicate 2-1.


title: noTBMDM_unChallenge_rep3

description:
8-
Gene expression at 6 hour

source_name: MDM from TB-free cattle_unchallenged_6h

tag: tissue

value: none (unchallenged)


title: Stable Plaque, biological rep 1

value: CVA(lacunar)


title: Ruptured Plaque, biological rep 5

description: Gene expression data from macrophages isolated from ruptured plaques of Symptomatic patients

source_name: Macrophages, LMDed from Ruptured Carotid Atheromatous Plaque

value: CVA

value: Ruptured Thin Fibrous Cap Atheroma


title: TBMDM_unChallenge_rep2

description:
5-
Gene expression at 6 hour

source_name: MDM from TB-infected cattle_unchallenged_6h

value: TB-infected cattle


title: TBMDM_Challenge_rep3

description:
7+
Gene expression after 6hr of challenge

source_name: MDM from TB-infected cattle_challenged by M.bovis_6h


title: noTBMDM_Challenge_rep3

description:
8+
Gene expression after 6hr of challenge


title: MDA-MB-231 Cells: shMUC4 Transfected vs. Control SCR  rep2

city: Omaha

first: Partha

last: Mukhopadhyay

state: Nebraska

address: 985870 Nebraska Medical Center

department: Biochemistry and Molecular Biology

institute: University of Nebraska Medical Center

description: Biological replicate 2

hyb_protocol: This was done using Slide hyb#2 (cat#AM8862, Ambion, USA) kit following manufacturer's procedure

scan_protocol: Microarrays were scanned with the GenePix 4000B Scanner (Axon Instruments, Foster City, CA, US). Images were quantified using GenePix Pro Software (version 6.1).

data_processing:
LOWESS normalized, background subtracted data obtained from log2 of processed Red signal/processed Green signal. BRB ArrayTools software was used.

Background adjustment; Intensity filter: Exclude the spot if at least one of the two intensities is below the minimum of 100
Lowess normalization
Over 50% missing removed
Control spots removed: empty|CGAM Control|IH Control|GAM Control|Ambion Control|ETQ Control|ITQ Control|Antisense Control|Cy3 Control|IHL Control|Phx Control|Cy5 Control|NA

source_name: Pooled equal amount of total RNA from three populations of independently grown MDA-MB-231-SCR cells

label_protocol: This was done using Amino Allyl MessageAmpTM II aRNA Amplification kit (Cat#AM 1753, Ambion, USA) using manufacturer's procedure

growth_protocol: After stable transfection and clone selection, control MDA-MB-231-SCR and MUC4 knockdown MDA-MB-231-shMUC4 cells were maintained in complete α-MEM media with the addition of 1-3 μg/ml puromycin.

extract_protocol: Total RNA was isolated using RNeasy Mini Kit columns as described by the manufacturer (Qiagen, Valencia, CA, US).

tag: passage

value: below 20 passages

tag: transfection

value: pSUPER-retro-puro-shMUC4 and selected using puromycin as selection marker

source_name: Pooled equal amount of total RNA from three populations of independently grown MDA-MB-231-shRNA cells

value: Below 20 passages

value: pSUPER-retro-puro-SCR and selected using puromycin as selection marker


title: TBMDM_unChallenge_rep3

description:
7-
Gene expression at 6 hour


title: noTBMDM_unChallenge_rep2

description:
6-
Gene expression at 6 hour


title: TBMDM_Challenge_rep2

description:
5+
Gene expression after 6hr of challenge


title: noTBMDM_Challenge_rep1

description:
2+
Gene expression after 6hr of challenge


title: 0.5h oocysts Replicate1-1

description: 0.5h Biological replicate 1 of 2.Technique replicate 1-1.


title: Sigmaringen Sediment freeze-dried

city: Karlsruhe

first: Jens

middle: C

last: Otte

address: Postfach 3640

department: Institute of Toxicology and Genetics

country: Germany

institute: Karlsruhe Institute of Technology

description:
This record represents all technological and biological replicates (i.e. from the same and different biological source, respectively) that were performed with this particular freeze-dried sediment at this particular concentration. The Dye-Swap Design was utilized.
Sigmaringen_sediment_1_zp8-65.high.gpr: test=Cy5, reference=Cy3
Sigmaringen_sediment_1_zp8-65.low.gpr: test=Cy5, reference=Cy3
Sigmaringen_sediment_1_zp8-65.medium.gpr: test=Cy5, reference=Cy3
Sigmaringen_sediment_1_zp8-66.high.gpr: test=Cy3, reference=Cy5
Sigmaringen_sediment_1_zp8-66.low.gpr: test=Cy3, reference=Cy5
Sigmaringen_sediment_1_zp8-66.medium.gpr: test=Cy3, reference=Cy5
Sigmaringen_sediment_2_zp8-69.high.gpr: test=Cy5, reference=Cy3
Sigmaringen_sediment_2_zp8-69.low.gpr: test=Cy5, reference=Cy3
Sigmaringen_sediment_2_zp8-69.medium.gpr: test=Cy5, reference=Cy3
Sigmaringen_sediment_2_zp8-70.high.gpr: test=Cy3, reference=Cy5
Sigmaringen_sediment_2_zp8-70.low.gpr: test=Cy3, reference=Cy5
Sigmaringen_sediment_2_zp8-70.medium.gpr: test=Cy3, reference=Cy5
Sigmaringen_sediment_3_zp8-74.high.gpr: test=Cy5, reference=Cy3
Sigmaringen_sediment_3_zp8-74.low.gpr: test=Cy5, reference=Cy3
Sigmaringen_sediment_3_zp8-74.medium.gpr: test=Cy5, reference=Cy3
Sigmaringen_sediment_3_zp8-88.high.gpr: test=Cy3, reference=Cy5
Sigmaringen_sediment_3_zp8-88.low.gpr: test=Cy3, reference=Cy5
Sigmaringen_sediment_3_zp8-88.medium.gpr: test=Cy3, reference=Cy5

hyb_protocol: 1) Removal of unincorporated nucleotides over Microcon 30 spin columns (Millipore, Bedford, MA). 2) The concentrated probes were hybridized to the microarray in 1xDIG Easy-Hyb buffer (Hoffmann-La Roche, Basel, CH) overnight at 42 C. 3) Cover slips were removed from the slides by flushing with 4xSSC. 4) Slides were washed in pre-warmed wash buffer 1 (2xSSC, 0.1% SDS) for 5 minutes at 42 C. 5) Washing in buffer 2 (0.1xSSC, 0.1% SDS) for 10 minutes at room temperature. 6) Washing in 0.1xSSC four times for 1 min at room temperature. 7) The slides were briefly dipped into 0.01xSSC at room temperature. 8) Centrifugation for 7 min at 800 rpm in an Eppendorf 5810R centrifuge.

scan_protocol: 1) Scanned on a GenePix 4000B dual-laser scanner from Molecular Devices. 2) Both channels (532 nm for Cy3, and 635 nm for Cy5) were scanned in parallel. 3) Data was stored as 16-bit TIFF files. 4) The channels for Cy3 and Cy5 were balanced in each scan for approximately the same intensity profile. 5) Each array was scanned three times (low, medium and high scan) with different signal amplification factors (voltage settings of the photomultiplier tubes), but with the same laser power. For the low scan, no spot was saturated; in the high scan, the signal amplification for Cy5 was set to approximately 80% of maximum and Cy3 amplification was adjusted to this. The settings used in the medium scan lie between the low and the high scan. The absolute intensity values span the range from 0 to 65536. Signal intensities from low, medium, and high scans were mapped onto the same scale by an affine transformation. Transformation parameters are estimated based on a least-squares optimization. Averaging the transformed intensities gives the consensus signals, which are independent of the voltage settings of the photomultiplier tube. 6) Raw data was retrieved with GenePix Pro 6.0 software from Axon Instruments. 7) Data processing was performed. 8) The scans were performed with a resolution of 10 um.

data_processing: 1) Raw data are retrieved with GenePix. 2) Quality control on spot level. 3) Local background correction. 4) Averaging of the two spots for each gene. 5) Consensus signals are calculated from low, medium and high scan based on a Least Squares Algorithm. 6) Log transformation. 7) Locally weighted regression smoother (LOESS). 8) Scaling to a common MAD. 9) t-test. 10) Adjustment of p-values for multiplicity. 11) Quality control on array level.

organism: Danio rerio

source_name: mRNA from zebrafish embryos exposed to freeze-dried sediment from Sigmaringen, Germany

label_protocol: Labeled cDNA was synthesized from 1-2 ug mRNA using the Amersham direct cDNA labeling kit (Amersham Europe, Freiburg, Germany).

growth_protocol: As described in Westerfield, 1993.

extract_protocol: 1) Total RNA was isolated using the Nucleospin RNA L Kit (Macherey-Nagel, Dueren, Germany). 2) mRNA was extracted with the Ambion Purist Kit (Austin, TX).

treatment_protocol: Zebrafish wild type strains AB, ABO and Tuebingen were kept and bred. 400 embryos were exposed for each treatment (negative control, freeze-dried sediment). Fertilized eggs were collected after spawning and exposed for 96 hpf at 27 °C for each treatment. The concentration of the exposure was selected as 300 mg sediment per ml test medium. No solvent was added. Embryos were grown in embryo medium (60 µg/ml Instant Ocean, Red Sea, Houston, TX; pH 6.73, Ca 0.8 mg/l; K 0.6 mg/l; Mg 2 mg/l; Na 16 mg/l; S 2 mg/l). Each treatment and control was performed in triplicates; each represents a full biological replicate.

tag: strain

value: AB, ABO, and Tübingen

tag: genotype

value: wild type

value: 96 hours post-fertilization

tag: developmental stage

value: embryo

value: whole body

tag: treatment

value: freeze-dried sediment from Sigmaringen

source_name: mRNA from zebrafish embryos NOT exposed to freeze-dried sediment from Sigmaringen, Germany

value: negative control


title: Ruptured Plaque, biological rep 4

tag: gender

value: female

value: AFugax

value: macrophage


title: Ruptured Plaque, biological rep 3

tag: age

value: male

value: TIA


title: Acetonic soxhlet extraction control

description:
This record represents all technological and biological replicates (i.e. from the same and different biological source, respectively) that were performed with this particular sediment extract at this particular concentration. The Dye-Swap Design was utilized.
extraction_control_1_zp8-92.high.gpr: test=Cy5, reference=Cy3
extraction_control_1_zp8-92.low.gpr: test=Cy5, reference=Cy3
extraction_control_1_zp8-92.medium.gpr: test=Cy5, reference=Cy3
extraction_control_1_zp8-97.high.gpr: test=Cy3, reference=Cy5
extraction_control_1_zp8-97.low.gpr: test=Cy3, reference=Cy5
extraction_control_1_zp8-97.medium.gpr: test=Cy3, reference=Cy5
extraction_control_2_zp8-85.high.gpr: test=Cy5, reference=Cy3
extraction_control_2_zp8-85.low.gpr: test=Cy5, reference=Cy3
extraction_control_2_zp8-85.medium.gpr: test=Cy5, reference=Cy3
extraction_control_2_zp8-86.high.gpr: test=Cy3, reference=Cy5
extraction_control_2_zp8-86.low.gpr: test=Cy3, reference=Cy5
extraction_control_2_zp8-86.medium.gpr: test=Cy3, reference=Cy5
extraction_control_3_zp8-23.high.gpr: test=Cy5, reference=Cy3
extraction_control_3_zp8-23.low.gpr: test=Cy5, reference=Cy3
extraction_control_3_zp8-23.medium.gpr: test=Cy5, reference=Cy3
extraction_control_3_zp8-77.high.gpr: test=Cy3, reference=Cy5
extraction_control_3_zp8-77.low.gpr: test=Cy3, reference=Cy5
extraction_control_3_zp8-77.medium.gpr: test=Cy3, reference=Cy5

source_name: mRNA from zebrafish embryos exposed to the soxhlet extraction control

treatment_protocol: Zebrafish wild type strains AB, ABO and Tuebingen were kept and bred. 400 embryos were exposed for each treatment (negative control, sediment extract). Fertilized eggs were collected after spawning and exposed for 96 hpf at 27 °C for each treatment. The concentration of the exposure was selected as equivalent to 30 mg SEQ (sediment equivalent) per ml test medium in a solvent concentration of 0.15 % DMSO (vol/vol). Embryos were grown in embryo medium (60 μg/ml Instant Ocean, Red Sea, Houston, TX; pH 6.73, Ca 0.8 mg/l; K 0.6 mg/l; Mg 2 mg/l; Na 16 mg/l; S 2 mg/l). Each treatment and control was performed in triplicates; each represents a full biological replicate.

value: soxhlet extraction control

source_name: mRNA from zebrafish embryos NOT exposed to the soxhlet extraction control


title: Ruptured Plaque, biological rep 2

tag: days from last symptom

value: Ruptured Thin Fibrous Cap Atheroma


title: MDA-MB-231 Cells: shMUC4 Transfected vs. Control SCR  rep1

description: Biological replicate 1

tag: cell line

value: below 20 passages

value: pSUPER-retro-puro-shMUC4 and selected using puromycin as selection marker


title: Ehingen Sediment freeze-dried

description:
This record represents all technological and biological replicates (i.e. from the same and different biological source, respectively) that were performed with this particular freeze-dried sediment at this particular concentration. The Dye-Swap Design was utilized.
Ehingen_sediment_1_zp8-71.high_2.gpr: test=Cy5, reference=Cy3
Ehingen_sediment_1_zp8-71.low.gpr: test=Cy5, reference=Cy3
Ehingen_sediment_1_zp8-71.medium.gpr: test=Cy5, reference=Cy3
Ehingen_sediment_1_zp8-72.high_2.gpr: test=Cy3, reference=Cy5
Ehingen_sediment_1_zp8-72.low.gpr: test=Cy3, reference=Cy5
Ehingen_sediment_1_zp8-72.medium.gpr: test=Cy3, reference=Cy5
Ehingen_sediment_2_zp8-41.high_4.gpr: test=Cy5, reference=Cy3
Ehingen_sediment_2_zp8-41.low.gpr: test=Cy5, reference=Cy3
Ehingen_sediment_2_zp8-41.medium.gpr: test=Cy5, reference=Cy3
Ehingen_sediment_2_zp8-42.high_2.gpr: test=Cy3, reference=Cy5
Ehingen_sediment_2_zp8-42.low.gpr: test=Cy3, reference=Cy5
Ehingen_sediment_2_zp8-42.medium_2.gpr: test=Cy3, reference=Cy5
Ehingen_sediment_3_zp8-89.high.gpr: test=Cy5, reference=Cy3
Ehingen_sediment_3_zp8-89.low.gpr: test=Cy5, reference=Cy3
Ehingen_sediment_3_zp8-89.medium.gpr: test=Cy5, reference=Cy3
Ehingen_sediment_3_zp8-90.high_2.gpr: test=Cy3, reference=Cy5
Ehingen_sediment_3_zp8-90.low.gpr: test=Cy3, reference=Cy5
Ehingen_sediment_3_zp8-90.medium.gpr: test=Cy3, reference=Cy5

source_name: mRNA from zebrafish embryos exposed to freeze-dried sediment from Ehingen, Germany

treatment_protocol: Zebrafish wild type strains AB, ABO and Tuebingen were kept and bred. 400 embryos were exposed for each treatment (negative control, freeze-dried sediment) . Fertilized eggs were collected after spawning and exposed for 96 hpf at 27 °C for each treatment. The concentration of the exposure was selected as 37.5 mg sediment per ml test medium. No solvent was added. Embryos were grown in embryo medium (60 μg/ml Instant Ocean, Red Sea, Houston, TX; pH 6.73, Ca 0.8 mg/l; K 0.6 mg/l; Mg 2 mg/l; Na 16 mg/l; S 2 mg/l). Each treatment and control was performed in triplicates; each represents a full biological replicate.

value: freeze-dried sediment from Ehingen

source_name: mRNA from zebrafish embryos NOT exposed to freeze-dried sediment from Ehingen, Germany


title: freeze-dried sediment control - silica dust

description:
This record represents all technological and biological replicates (i.e. from the same and different biological source, respectively) that were performed with this particular freeze-dried sediment at this particular concentration. The Dye-Swap Design was utilized.
silica_dust_1_zp8-26.high.gpr: test=Cy5, reference=Cy3
silica_dust_1_zp8-26.low.gpr: test=Cy5, reference=Cy3
silica_dust_1_zp8-26.medium.gpr: test=Cy5, reference=Cy3
silica_dust_1_zp8-27.high.gpr: test=Cy3, reference=Cy5
silica_dust_1_zp8-27.low.gpr: test=Cy3, reference=Cy5
silica_dust_1_zp8-27.medium.gpr: test=Cy3, reference=Cy5
silica_dust_2_zp8-21.high.gpr: test=Cy5, reference=Cy3
silica_dust_2_zp8-21.low.gpr: test=Cy5, reference=Cy3
silica_dust_2_zp8-21.medium.gpr: test=Cy5, reference=Cy3
silica_dust_2_zp8-22.high.gpr: test=Cy3, reference=Cy5
silica_dust_2_zp8-22.low.gpr: test=Cy3, reference=Cy5
silica_dust_2_zp8-22.medium.gpr: test=Cy3, reference=Cy5

source_name: mRNA from zebrafish embryos exposed to silica dust, Germany

treatment_protocol: Zebrafish wild type strains AB, ABO and Tuebingen were kept and bred. 400 embryos were exposed for each treatment (negative control, freeze-dried sediment). Fertilized eggs were collected after spawning and exposed for 96 hpf at 27 °C for each treatment. The concentration of the exposure was selected as 600 mg silica dust per ml test medium. No solvent was added. Embryos were grown in embryo medium (60 µg/ml Instant Ocean, Red Sea, Houston, TX; pH 6.73, Ca 0.8 mg/l; K 0.6 mg/l; Mg 2 mg/l; Na 16 mg/l; S 2 mg/l). Each treatment and control was performed in duplicates; each represents a full biological replicate.

value: AB, ABO, and Tübingen

value: silica dust

source_name: mRNA from zebrafish embryos NOT exposed to silica dust, Germany


title: Lauchert Sediment freeze-dried

description:
This record represents all technological and biological replicates (i.e. from the same and different biological source, respectively) that were performed with this particular freeze-dried sediment at this particular concentration. The Dye-Swap Design was utilized.
Lauchert_sediment_1_zp8-63.high.gpr: test=Cy5, reference=Cy3
Lauchert_sediment_1_zp8-63.low.gpr: test=Cy5, reference=Cy3
Lauchert_sediment_1_zp8-63.medium.gpr: test=Cy5, reference=Cy3
Lauchert_sediment_1_zp8-64.high.gpr: test=Cy3, reference=Cy5
Lauchert_sediment_1_zp8-64.low.gpr: test=Cy3, reference=Cy5
Lauchert_sediment_1_zp8-64.medium.gpr: test=Cy3, reference=Cy5
Lauchert_sediment_2_zp8-67.high.gpr: test=Cy5, reference=Cy3
Lauchert_sediment_2_zp8-67.low.gpr: test=Cy5, reference=Cy3
Lauchert_sediment_2_zp8-67.medium.gpr: test=Cy5, reference=Cy3
Lauchert_sediment_2_zp8-68.high.gpr: test=Cy3, reference=Cy5
Lauchert_sediment_2_zp8-68.low.gpr: test=Cy3, reference=Cy5
Lauchert_sediment_2_zp8-68.medium.gpr: test=Cy3, reference=Cy5
Lauchert_sediment_3_zp8-43.high.gpr: test=Cy5, reference=Cy3
Lauchert_sediment_3_zp8-43.low.gpr: test=Cy5, reference=Cy3
Lauchert_sediment_3_zp8-43.medium.gpr: test=Cy5, reference=Cy3
Lauchert_sediment_3_zp8-44.high.gpr: test=Cy3, reference=Cy5
Lauchert_sediment_3_zp8-44.low.gpr: test=Cy3, reference=Cy5
Lauchert_sediment_3_zp8-44.medium.gpr: test=Cy3, reference=Cy5
Lauchert_sediment_4_zp8-25.high.gpr: test=Cy5, reference=Cy3
Lauchert_sediment_4_zp8-25.low.gpr: test=Cy5, reference=Cy3
Lauchert_sediment_4_zp8-25.medium.gpr: test=Cy5, reference=Cy3
Lauchert_sediment_4_zp8-33.high.gpr: test=Cy3, reference=Cy5
Lauchert_sediment_4_zp8-33.low.gpr: test=Cy3, reference=Cy5
Lauchert_sediment_4_zp8-33.medium.gpr: test=Cy3, reference=Cy5

source_name: mRNA from zebrafish embryos exposed to freeze-dried sediment from Lauchert, Germany

treatment_protocol: Zebrafish wild type strains AB, ABO and Tuebingen were kept and bred. 400 embryos were exposed for each treatment (negative control, freeze-dried sediment). Fertilized eggs were collected after spawning and exposed for 96 hpf at 27 °C for each treatment. The concentration of the exposure was selected as 300 mg sediment per ml test medium. No solvent was added. Embryos were grown in embryo medium (60 µg/ml Instant Ocean, Red Sea, Houston, TX; pH 6.73, Ca 0.8 mg/l; K 0.6 mg/l; Mg 2 mg/l; Na 16 mg/l; S 2 mg/l). Each treatment and control was performed four times; each represents a full biological replicate.

value: wild type

value: 96 hours post-fertilization

value: freeze-dried sediment from Lauchert

source_name: mRNA from zebrafish embryos NOT exposed to freeze-dried sediment from Lauchert, Germany


title: noTBMDM_unChallenge_rep1

description:
2-
Gene expression at 6 hour

value: monocytes derived macrophages

value: TB-free cattle

value: none (unchallenged)


title: 0.5h oocysts Replicate1-2

description: 0.5h Biological replicate 1 of 2.Technique replicate 1-2.

source_name: 0.5h UV treated oocysts

source_name: 0.5h control oocysts


title: Sigmaringen Sediment Extract

description:
This record represents all technological and biological replicates (i.e. from the same and different biological source, respectively) that were performed with this particular sediment extract at this particular concentration. The Dye-Swap Design was utilized.
Sigmaringen_extract_1_zp8-95.high.gpr: test=Cy5, reference=Cy3
Sigmaringen_extract_1_zp8-95.low.gpr: test=Cy5, reference=Cy3
Sigmaringen_extract_1_zp8-95.medium.gpr: test=Cy5, reference=Cy3
Sigmaringen_extract_1_zp8-96.high.gpr: test=Cy3, reference=Cy5
Sigmaringen_extract_1_zp8-96.low.gpr: test=Cy3, reference=Cy5
Sigmaringen_extract_1_zp8-96.medium.gpr: test=Cy3, reference=Cy5
Sigmaringen_extract_2_zp8-30.high.gpr: test=Cy5, reference=Cy3
Sigmaringen_extract_2_zp8-30.low.gpr: test=Cy5, reference=Cy3
Sigmaringen_extract_2_zp8-30.medium.gpr: test=Cy5, reference=Cy3
Sigmaringen_extract_2_zp8-75.high.gpr: test=Cy3, reference=Cy5
Sigmaringen_extract_2_zp8-75.low.gpr: test=Cy3, reference=Cy5
Sigmaringen_extract_2_zp8-75.medium.gpr: test=Cy3, reference=Cy5
Sigmaringen_extract_3_zp8-73.high.gpr: test=Cy5, reference=Cy3
Sigmaringen_extract_3_zp8-73.low.gpr: test=Cy5, reference=Cy3
Sigmaringen_extract_3_zp8-73.medium.gpr: test=Cy5, reference=Cy3
Sigmaringen_extract_3_zp8-91.high.gpr: test=Cy3, reference=Cy5
Sigmaringen_extract_3_zp8-91.low.gpr: test=Cy3, reference=Cy5
Sigmaringen_extract_3_zp8-91.medium.gpr: test=Cy3, reference=Cy5

source_name: mRNA from zebrafish embryos exposed to sediment extract from Sigmaringen, Germany

treatment_protocol: Zebrafish wild type strains AB, ABO and Tuebingen were kept and bred. 400 embryos were exposed for each treatment (negative control, sediment extract). Fertilized eggs were collected after spawning and exposed for 96 hpf at 27 °C for each treatment. Concentrations of the sediment extracts were selected as 10 mg sediment equivalent (SEQ) per ml test medium for the site Sigmaringen in a solvent concentration of 0.05 % DMSO (vol/vol). Embryos were grown in embryo medium (60 μg/ml Instant Ocean, Red Sea, Houston, TX; pH 6.73, Ca 0.8 mg/l; K 0.6 mg/l; Mg 2 mg/l; Na 16 mg/l; S 2 mg/l). Each treatment and control was performed in triplicates; each represents a full biological replicate.

value: embryo

value: whole body

value: sediment extract from Sigmaringen

source_name: mRNA from zebrafish embryos NOT exposed to sediment extract from Sigmaringen, Germany

value: negative control


title: Lauchert Sediment Extract

description:
This record represents all technological and biological replicates (i.e. from the same and different biological source, respectively) that were performed with this particular sediment extract at this particular concentration. The Dye-Swap Design was utilized.
Lauchert_extract_1_zp8-93.high.gpr: test=Cy5, reference=Cy3
Lauchert_extract_1_zp8-93.low.gpr: test=Cy5, reference=Cy3
Lauchert_extract_1_zp8-93.medium.gpr: test=Cy5, reference=Cy3
Lauchert_extract_1_zp8-94.high.gpr: test=Cy3, reference=Cy5
Lauchert_extract_1_zp8-94.low.gpr: test=Cy3, reference=Cy5
Lauchert_extract_1_zp8-94.medium.gpr: test=Cy3, reference=Cy5
Lauchert_extract_2_zp8-98.high.gpr: test=Cy5, reference=Cy3
Lauchert_extract_2_zp8-98.low.gpr: test=Cy5, reference=Cy3
Lauchert_extract_2_zp8-98.medium.gpr: test=Cy5, reference=Cy3
Lauchert_extract_2_zp8-99.high.gpr: test=Cy3, reference=Cy5
Lauchert_extract_2_zp8-99.low.gpr: test=Cy3, reference=Cy5
Lauchert_extract_2_zp8-99.medium.gpr: test=Cy3, reference=Cy5
Lauchert_extract_3_zp8-76.high.gpr: test=Cy5, reference=Cy3
Lauchert_extract_3_zp8-76.low.gpr: test=Cy5, reference=Cy3
Lauchert_extract_3_zp8-76.medium.gpr: test=Cy5, reference=Cy3
Lauchert_extract_3_zp8-80.high.gpr: test=Cy3, reference=Cy5
Lauchert_extract_3_zp8-80.low.gpr: test=Cy3, reference=Cy5
Lauchert_extract_3_zp8-80.medium.gpr: test=Cy3, reference=Cy5

source_name: mRNA from zebrafish embryos exposed to sediment extract from Lauchert, Germany

treatment_protocol: Zebrafish wild type strains AB, ABO and Tuebingen were kept and bred. 400 embryos were exposed for each treatment (negative control, sediment extract). Fertilized eggs were collected after spawning and exposed for 96 hpf at 27 °C for each treatment. Concentrations of the sediment extracts were selected as 30 mg sediment equivalent (SEQ) per ml test medium for the site Lauchert in a solvent concentration of 0.15 % DMSO (vol/vol). Embryos were grown in embryo medium (60 μg/ml Instant Ocean, Red Sea, Houston, TX; pH 6.73, Ca 0.8 mg/l; K 0.6 mg/l; Mg 2 mg/l; Na 16 mg/l; S 2 mg/l). Each treatment and control was performed in triplicates; each represents a full biological replicate.

value: sediment extract from Lauchert

source_name: mRNA from zebrafish embryos NOT exposed to sediment extract from Lauchert, Germany


title: shSCM, replicate 3

city: Boston

first: Joseph

middle: Daniel

last: Fleming

state: MA

address: 240 Longwood Ave

department: Biological Chemistry and Molecular Pharmacology

institute: Harvard Medical School

description: HeLaS3 cells treated with shSCM (control)

hyb_protocol: Following fragmentation, 12.5 ug of fragmented aRNA was hybridized as per manufacturer's protocol for the U133 plus 2.0 arrays. Intruments used were Affymetrix GeneChip Fluidics Station 450, Affymetrix GeneChip Hybridization Oven 640.

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

data_processing: Arrays were RMA normalized (Irizarry et al. 2003), gene expression levels calculated, differential expression determined using the following R packages from the Bioconductor project: affy (Gautier et al. 2004), limma (Smyth 2004).

label: biotin

source_name: HeLaS3 cells

label_protocol: Biotinylated aRNA were prepared using the 3’ IVT Express Kit (Affymetrix, USA).

growth_protocol: HeLaS3 cells were grown as adherent cells in alpha-MEM media supplemented with 5% fetal bovin serum with penn/strep.

extract_protocol: Trizol extraction and Qiagen RNeasy kit purification performed according to the manufacturer's instructions.

treatment_protocol: HeLaS3 cells were transduced with shSCM (control) or shNF-YA viral supernatants, in triplicate, and cells collected after 48 hr of incubation.

value: shSCM

tag: genotype/variation

value: control


title: TBMDM_Challenge_rep1

description:
1+
Gene expression after 6hr of challenge

source_name: MDM from TB-infected cattle_challenged by M.bovis_6h

value: TB-infected cattle

value: M. bovis at MOI 10


title: TBMDM_unChallenge_rep1

description:
1-
Gene expression at 6 hour

source_name: MDM from TB-infected cattle_unchallenged_6h


title: PBMC response to tetanus toxoid TT 38

city: Dummerstorf

first: Klaus

last: Wimmers

address: Wilhelm-Stahl-Allee 2

institute: Leibniz Institute for Farm Animal Biology (FBN)

description: PBMC response to tetanus toxoid

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 42C on Affymetrix GeneChip Porcine Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: Scanning using the GeneChip scanner 3000 were performed according to Affymetrix protocols

data_processing: Data were analysed with Affymetrix GCOS 1.1.1 software using global scaling to a target signal of 500 and Affymetrix Expression Console 1.1

organism: Sus scrofa

source_name: PBMC

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 0.5 ug total RNA (Expression Analysis Technical Manual, 2009, Affymetrix).

extract_protocol: Total RNA was isolated using TRI Reagent (Sigma, Taufkirchen, Germany) according to the manufacturer’s protocol. After DNaseI treatment the RNA was cleaned up using the RNeasy Kit (Qiagen, Hilden, Germany).

treatment_protocol: vaccination, 1 ml (30 IU) of tetanus toxoid (Equilis Tetanus-Vaccine)

tag: first or second vaccination, 14 day interval

value: 2nd vaccination

tag: time after vaccination

tag: one of 3 rna pools, 6 animals each

value: b


title: PBMC response to tetanus toxoid TT 39

description: PBMC response to tetanus toxoid

value: c


title: shNFYA, replicate 1

description: HeLaS3 cells treated with shNF-YA

value: shNFYA

value: NF-YA knockdown


title: shSCM, replicate 2


title: shSCM, replicate 1


title: shNFYA, replicate 3

description: HeLaS3 cells treated with shNF-YA


title: Sediment Extract Iffezheim core sample

description: This file contains all technological and biological replicates (i.e. from the same and different biological source, repspectively) that were performed with this particular toxin at this particular concentration. The Dye-Swap Designe was utilised.

scan_protocol: 1) Scanned on an GenePix 4000B dual-laser scanner from Molecular Devices 2) Both channels (532 nm for Cy3 and 635 nm for Cy5) were scanned in parallel 3) Data was stored as 16-bit TIFF files 4) The channels for Cy3 and Cy5 were balanced in each scan for approximately the same intensity profile. 5) Each array was scanned three times (low, medium and high scan) with different signal amplification factors (voltage settings of the photomultiplier tubes), but with the same laser power. For the low scan no spot was saturated; in the high scan the signal amplification for Cy5 was set to approximately 80% of maximum and Cy3 amplification was adjusted to this. The settings used in the medium scan lie between the low and the high scan. The absolute intensity values span the range from 0 to 65536. Signal intensities from low, medium, and high scans were mapped onto the same scale by an affine transformation. Transformation parameters are estimated based on a least-squares optimization. Averaging the transformed intensities gives the consensus signals, which are independent of the voltage settings of the photomultiplier tube. 6) Raw data was retrieved with GenePix Pro 6.0 software from Axon Instruments . 7) Data processing was performed 8) The scans were performed with a resolution of 10 um.

data_processing: 1) Raw data are retrieved with GenePix 2) Quality control on spot level 3) Local background correction. 4) Averaging of the two spots for each gene. 5) Consensus signals are calculated from low, medium and high scan based on a Least Squares Algorithm. 6) Log transformation. 7) locally weighted regression smoother (LOESS). 8) Scaling to a common MAD. 9) t-test 10) adjustment of p-values for multiplicity 11) Quality control on array level.

label: Cy5, Cy3

molecule: polyA RNA

source_name: mRNA from zebrafish embryos that were exposed sediment extract from Iffezheim, Germany

growth_protocol: as described in Westerfield 1993

treatment_protocol: Zebrafish wild type strains AB, ABO and Tuebingen were kept and bred. 600 embryos were exposed for each treatment (negative control, sediment extract) to guarantee for about 400 surviving embryos after exposure, given a maximum embryotoxicity of approx. 30%. Fertilised eggs were collected after spawning and exposed for 120 hpf at 27 °C for each treatment. Concentrations of the sediment extracts were selected as 20 mg sediment equivalent (SEQ) per ml test medium for the site Reckingen in a solvent concentration of 0.1 % DMSO (vol/vol). Eggs for negative controls were treated with embryo water only (60 μg/ml Instant Ocean, Red Sea, Houston, TX; pH 6.73, Ca 0.8 mg/l; K 0.6 mg/l; Mg 2 mg/l; Na 16 mg/l; S 2 mg/l). Each treatment and control has been replicated and represent full biological replicates.

tag: strains

value: zebrafish from AB,ABO, and Tübingen

value: 120 hours post fertilisation

value: whole body mRNA

label: Cy3, Cy5

source_name: mRNA from zebrafish embryos that were NOT exposed sediment extract from Iffezheim, Germany


title: PBMC response to tetanus toxoid TT 37

description: PBMC response to tetanus toxoid

value: a


title: PBMC response to tetanus toxoid TT 36

description: PBMC response to tetanus toxoid


title: Ruptured Plaque, biological rep 1

description: Gene expression data from macrophages isolated from ruptured plaques of Symptomatic patients

source_name: Macrophages, LMDed from Ruptured Carotid Atheromatous Plaque

value: male

tag: symptom event

value: CVA

tag: radiological stenosis

tag: plaque histology

value: Ruptured Thin Fibrous Cap Atheroma

tag: cell type

value: macrophage


title: Ehingen Sediment Extract

description:
This record represents all technological and biological replicates (i.e. from the same and different biological source, respectively) that were performed with this particular sediment extract at this particular concentration. The Dye-Swap Design was utilized.
Ehingen_extract_1_zp8-32.high_2.gpr: test=Cy5, reference=Cy3
Ehingen_extract_1_zp8-32.low.gpr: test=Cy5, reference=Cy3
Ehingen_extract_1_zp8-32.medium.gpr: test=Cy5, reference=Cy3
Ehingen_extract_1_zp8-87.high_2.gpr: test=Cy3, reference=Cy5
Ehingen_extract_1_zp8-87.low.gpr: test=Cy3, reference=Cy5
Ehingen_extract_1_zp8-87.medium.gpr: test=Cy3, reference=Cy5
Ehingen_extract_2_zp8-18.high_4.gpr: test=Cy5, reference=Cy3
Ehingen_extract_2_zp8-18.low.gpr: test=Cy5, reference=Cy3
Ehingen_extract_2_zp8-18.medium.gpr: test=Cy5, reference=Cy3
Ehingen_extract_2_zp8-28.high_2.gpr: test=Cy3, reference=Cy5
Ehingen_extract_2_zp8-28.low.gpr: test=Cy3, reference=Cy5
Ehingen_extract_2_zp8-28.medium_2.gpr: test=Cy3, reference=Cy5
Ehingen_extract_3_zp8-29.high.gpr: test=Cy5, reference=Cy3
Ehingen_extract_3_zp8-29.low.gpr: test=Cy5, reference=Cy3
Ehingen_extract_3_zp8-29.medium.gpr: test=Cy5, reference=Cy3
Ehingen_extract_3_zp8-36.high_2.gpr: test=Cy3, reference=Cy5
Ehingen_extract_3_zp8-36.low.gpr: test=Cy3, reference=Cy5
Ehingen_extract_3_zp8-36.medium.gpr: test=Cy3, reference=Cy5

source_name: mRNA from zebrafish embryos exposed to sediment extract from Ehingen, Germany

treatment_protocol: Zebrafish wild type strains AB, ABO and Tuebingen were kept and bred. 400 embryos were exposed for each treatment (negative control, sediment extract). Fertilized eggs were collected after spawning and exposed for 96 hpf at 27 °C for each treatment. Concentrations of the sediment extracts were selected as 10 mg sediment equivalent (SEQ) per ml test medium for the site Ehingen in a solvent concentration of 0.05 % DMSO (vol/vol). Embryos were grown in embryo medium (60 μg/ml Instant Ocean, Red Sea, Houston, TX; pH 6.73, Ca 0.8 mg/l; K 0.6 mg/l; Mg 2 mg/l; Na 16 mg/l; S 2 mg/l). Each treatment and control was performed in triplicates; each represents a full biological replicate.

tag: strain

value: AB, ABO, and Tübingen

value: wild type

value: 96 hours post-fertilization

value: embryo

tag: tissue

value: whole body

value: sediment extract from Ehingen

source_name: mRNA from zebrafish embryos NOT exposed to sediment extract from Ehingen, Germany

value: negative control


title: shNFYA, replicate 2

description: HeLaS3 cells treated with shNF-YA

value: shNFYA


title: Sediment Extract Reckingen surface sample

source_name: mRNA from zebrafish embryos that were exposed sediment extract from Reckingen, Germany

source_name: mRNA from zebrafish embryos that were NOT exposed sediment extract from Reckingen, Germany


title: PBMC response to tetanus toxoid TT 35

description: PBMC response to tetanus toxoid

value: 2nd vaccination

value: b


title: PBMC response to tetanus toxoid TT 34

description: PBMC response to tetanus toxoid


title: CL1-0 cells expressing FDFT1

city: Taipei

first: Michael

last: Hsiao

address: 128 Academia Road, Section 2, Nankang, Taipei 115, Taiwan

department: Genomics Research Center

country: Taiwan

institute: Academia Sinica

hyb_protocol: Following fragmentation, 20 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Human Genome U133 PLUS 2.0 . GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: CL1-0_FDFT overexpression

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: Cells were cultured in 5% CO2 incubator at 37C.

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

treatment_protocol: Cell were selected with puromycin for two weeks.  Stably transduced cells were use for this experiment.

value: expressing FDFT1 vector

tag: tissue origin

value: Lung  adenocarcinoma

value: Type II alveolar cell


title: 2M1 - 10b3

city: Singapore

first: Jia Kai

last: Lim

address: 31 Biopolis Way #04-01, Nanos

country: Singapore

institute: Institute of Bioengineering and Nanotechnology

description: Invasive subline of U87 derived from an in vivo experimental lung metastasis assay which is subsequently propagated in vitro

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.

source_name: U87-2M1_miR-10b silencing

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 0.25 ug total RNA

growth_protocol: DMEM, 10% FBS, 5% L-glutamine, 5% Penicillin-streptomycin, maintained in hypoxia

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

treatment_protocol: Cells were cultured under routine conditions as described above, and detached from culture plates using trypsin, pelleted and lysed in TRIzol immediately.

value: Invasive subline derived from U87 glioma cells

tag: passage

value: passage 4 cells

tag: tranduced with

value: baculoviral miR-10b decoy vector


title: CL1-0 cells expressing control vector

source_name: CL1-0_control vector

value: expressing control vector


title: PBMC response to tetanus toxoid TT 32

description: PBMC response to tetanus toxoid


title: PBMC response to tetanus toxoid TT 33

description: PBMC response to tetanus toxoid

value: c


title: HeDiPig30

description: Gene expression data from teat tissue of peripubertal pigs of commercial dam lines

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 42°C on Affymetrix GeneChip Porcine Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

data_processing: Data were analysed with Affymetrix GCOS 1.1.1 software using global scaling to a target signal of 500.

source_name: teat, mesenchymal tissue, non-affected

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 500 ng total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Animals were grown according to standard procedures described in Richtlinien für die Stationsprüfung auf Mastleistung, Schlachtkörperwert und Fleischbeschaffenheit beim Schwein, ZDS, 2004. Teat tissue taken at slaughter, mean end weight of 110 kg.

treatment_protocol: no experimental treatment

value: teat, mesenchymal tissue

tag: teat type

value: normal teat

tag: animal type

value: non-affected

tag: breed

value: Pietrain x (Large White x German Landrace)


title: HeDiPig29

source_name: teat, mesenchymal tissue, affected

value: inverted teat

value: affected


title: 2M1 - 10b2

tag: cell line


title: PBMC response to tetanus toxoid TT 29

description: PBMC response to tetanus toxoid

tag: first or second vaccination, 14 day interval


title: 2M1 - 10b1


title: HeDiPig28


title: 2M1 - ctr2

source_name: U87-2M1_vector control

value: baculoviral control decoy vector


title: 2M1 - ctr3


title: 2M1 - ctr1


title: HeDiPig27

value: Large White x German Landrace


title: PBMC response to tetanus toxoid TT 28

description: PBMC response to tetanus toxoid

value: 2nd vaccination

tag: time after vaccination

value: a


title: PBMC response to tetanus toxoid TT 31

description: PBMC response to tetanus toxoid

tag: one of 3 rna pools, 6 animals each


title: U87-2M1-3

source_name: U87-2M1 glioma cells derived from U87 cells subjected to an in vivo experimental lung metastasis assay and propagated in vitro

growth_protocol: DMEM, 10% FBS, 5% L-glutamine, 5% Penicillin-streptomycin

value: Invasive subline U87-2M1 derived from U87

value: Passage 4 cells, maintained under hypoxia


title: U87-2M1-2


title: HeDiPig26


title: PBMC response to tetanus toxoid TT 26

description: PBMC response to tetanus toxoid

value: b


title: U87-2M1-1


title: HeDiPig25


title: U87-3

source_name: U87 glioma cells from ATCC cultivated in vitro according to ATCC's protocol

value: U87 glioma cells

value: Late passage cells


title: PBMC response to tetanus toxoid TT 30

description: PBMC response to tetanus toxoid


title: U87-2


title: HeDiPig23


title: PBMC response to tetanus toxoid TT 23

description: PBMC response to tetanus toxoid


title: 5hmC neurons 4/4

city: Duarte

first: Xiwei

last: Wu

state: CA

address: 1500 E. Duarte Rd.

department: Computational and Quantitative Medicine

institute: City of Hope National Medical Center

description: Cells were isolated by FACs sorting from nmouse cortex using GFP/RFP reported system at 15.5E embryonic development. GFP+ (under Nestin promoter), RFP - (Under Dbx promoter)

hyb_protocol: According to NimbleGen Kit

scan_protocol: Follow NimbleScan's default using Agilent Scanner

data_processing: Cy5/Cy3 log2 ratio scaled by NimbleScan software v2.5 with Tukey Biweight mean

organism: Mus musculus

source_name: 5hmC enriched DNA fraction after pull-down with 5hmC antibodies.  DNA was isolated from neurons

label_protocol: According to standard NimbleGen Protocol

extract_protocol: For MIRA, sonicated DNA was incubated with MBD2b-GST and MBD3L1-His overnight at +4C. Methylated DNA was captured by using magnetic GST beads, purified and amplified by using LM-PCR. For ChIp-ChIp experiments, cells were fixed with 1% formaldehyde in PBS1x for 10 minutes at RT and briefly quest by adding of 0.125M Glycine.  Sonicated chromatin was incubated with appropriate antibodies overnight and captured by A/G agarose beads. Purified decrosslinked DNA was amplified by LM-PCR procedure. For hMeDIP, linker ligated DNA was denatured and incubated with 5hmC antibodies overnight at +4C with further purification with A/G plus beads and genome amplification by LM-PCR. For 5hmC enrichment with Hydroxymethyl Collector (Active Motif), sonicated DNA was glycosylated, labeled with biotin and purified according manufacturer instructions with further genome amplification by LM-PCR.

treatment_protocol: no treatment

value: neurons, cortex

tag: age

tag: enrichment method

value: hMeDIP

tag: antibody

source_name: Input DNA from neurons

value: none, Input


title: PBMC response to tetanus toxoid TT 27

description: PBMC response to tetanus toxoid

source_name: PBMC

value: c


title: PBMC response to tetanus toxoid TT 25

description: PBMC response to tetanus toxoid


title: HeDiPig24

value: teat, mesenchymal tissue

value: normal teat

value: non-affected


title: U87-1


title: PBMC response to tetanus toxoid TT 24

description: PBMC response to tetanus toxoid


title: PBMC response to tetanus toxoid TT 22

description: PBMC response to tetanus toxoid


title: HeDiPig21

value: inverted teat

value: affected


title: H3K4me3 neurons 4/4

source_name: H3K4me3 ChIp DNA from neurons

value: ChIp


title: BT-474, pair_3, 32°C, date: 08.02.2010

city: Braunschweig

first: Robert

last: Geffers

address: Inhoffenstr. 7

department: Dep. Molecular Bacteriology

institute: HCI - Helmholtz Centre for Infection Research

description: Sample ID: RLT-018,  Description: Serie_c, BT-474, pair_3, 32°C, date: 08.02.2010

hyb_protocol: Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at conditions recommended by the manufacturer. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Affymetrix GCS 3000.

data_processing: RMA summarization

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 microg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: RNAeasy

tag: condition

value: p53 status on

tag: source tissue

value: human ductal breast cancer

tag: treatment


title: H3K27me3 neurons 4/4

source_name: H3K27me3 ChIp DNA from neurons

tag: cell type


title: 5hmC NPC 4/4

source_name: 5hmC enriched DNA fraction after pull-down with 5hmC antibodies.  DNA was isolated from NPC

value: neural progenitor cells, cortex

source_name: Input DNA from NPC


title: PBMC response to tetanus toxoid TT 21

description: PBMC response to tetanus toxoid

value: 2nd vaccination


title: H3K36me3 neurons 4/4

source_name: H3K36me3 ChIp DNA from neurons


title: BT-474, pair_3, 37°C, date 08.0122010

description: Sample ID: RLT-017,  Description: Serie_C, BT-474, pair_3, 37°C, date 08.0122010

value: p53 status off


title: PBMC response to tetanus toxoid TT 20

description: PBMC response to tetanus toxoid

value: b


title: HeDiPig20

tag: tissue

value: Large White x German Landrace


title: HeDiPig22


title: H3K27me3 NPC 4/4

source_name: H3K27me3 ChIp DNA from NPC


title: H3K4me3 neurons 3/4

value: neurons, cortex


title: BT-474, pair_2, 37°C, date 01.02.2010

description: Sample ID: RLT-013,  Description: Serie_C, BT-474, pair_2, 37°C, date 01.02.2010


title: 5mC neurons 4/4

source_name: methylated DNA fraction enriched by MIRA. DNA was isolated from neurons

value: MIRA


title: PBMC response to tetanus toxoid TT 19

description: PBMC response to tetanus toxoid

value: a


title: BT-474, pair_2, 32°C, date: 01.02.2010

description: Sample ID: RLT-014,  Description: Serie_c, BT-474, pair_2, 32°C, date: 01.02.2010


title: BT-474, pair_1, 32°C, date: 25.01.2010

description: Sample ID: RLT-008,  Description: Serie_c, BT-474, pair_1, 32°C, date: 25.01.2010


title: HeDiPig18

value: German Landrace


title: PBMC response to tetanus toxoid TT 18

description: PBMC response to tetanus toxoid

value: 1st vaccination

value: c


title: 5hmC NPC 3/4

value: hMeDIP

value: none, Input


title: H3K4me3 NPC 4/4

source_name: H3K4me3 ChIp DNA from NPC


title: HeDiPig17

value: teat, mesenchymal tissue

value: normal teat

value: non-affected


title: 5hmC neurons 3/4


title: H3K36me3 NPC 3/4

source_name: H3K36me3 ChIp DNA from NPC

value: ChIp


title: H3K27me3 neurons 3/4


title: PBMC response to tetanus toxoid TT 17

description: PBMC response to tetanus toxoid


title: HeDiPig16

source_name: teat, mesenchymal tissue, non-affected


title: BT-474, pair_1, 37°C, date 25.01.2010

description: Sample ID: RLT-007,  Description: Serie_C, BT-474, pair_1, 37°C, date 25.01.2010

value: human ductal breast cancer


title: H3K36me3 NPC 4/4

value: neural progenitor cells, cortex


title: PBMC response to tetanus toxoid TT 16

description: PBMC response to tetanus toxoid


title: 5mC NPC 4/4

source_name: methylated DNA fraction enriched by MIRA. DNA was isolated from NPC


title: HeDiPig15

source_name: teat, epithelial tissue, non-affected

value: teat, epithelial tissue

value: Pietrain x (Large White x German Landrace)


title: H3K4me3 NPC 3/4


title: H3K36me3 neurons 3/4


title: HeDiPig14

source_name: teat, epithelial tissue, affected

value: inverted teat

value: affected


title: HeDiPig13


title: MCF-7, pair_3, 32°C, date: 08.02.2010

description: Sample ID: RLT-016,  Description: Serie_B, MCF-7, pair_3, 32°C, date: 08.02.2010

value: p53 status on


title: HeDiPig12

value: Large White x German Landrace


title: MCF-7, pair_3, 37°C, date: 08.02.2010

description: Sample ID: RLT-015,  Description: Serie_B, MCF-7, pair_3, 37°C, date: 08.02.2010


title: PBMC response to tetanus toxoid TT 13

description: PBMC response to tetanus toxoid

value: a


title: H3K27me3 NPC 3/4


title: PBMC response to tetanus toxoid TT 12

description: PBMC response to tetanus toxoid

value: 1st vaccination


title: MCF-7, pair_2, 32°C, date: 01.02.2010

description: Sample ID: RLT-012,  Description: Serie_B, MCF-7, pair_2, 32°C, date: 01.02.2010


title: 5mC NPC 3/4

value: MIRA


title: HeDiPig11


title: MCF-7, pair_2, 37°C. date: 01.02.2010

description: Sample ID: RLT-011,  Description: Serie_B, MCF-7, pair_2, 37°C. date: 01.02.2010


title: MCF-7, pair_1, 32°C, date: 25.01.2010

description: Sample ID: RLT-006,  Description: Serie_B, MCF-7, pair_1, 32°C, date: 25.01.2010


title: PBMC response to tetanus toxoid TT 14

description: PBMC response to tetanus toxoid

value: b


title: 5mC neurons 3/4

value: neurons, cortex

value: none, Input


title: MCF-7, pair_1, 37°C, date: 25.01.2010

description: Sample ID: RLT-005,  Description: Serie_B, MCF-7, pair_1, 37°C, date: 25.01.2010


title: PBMC response to tetanus toxoid TT 10

description: PBMC response to tetanus toxoid


title: HeDiPig10

value: normal teat


title: IPH-926, pair_3, 32°C, date: 25.01.2010

description: Sample ID: RLT-010,  Description: Serie_A, IPH-926, pair_3, 32°C, date: 25.01.2010

value: human lobular breast cancer


title: HeDiPig8


title: PBMC response to tetanus toxoid TT 15

description: PBMC response to tetanus toxoid

value: c


title: HeDiPig9

value: non-affected


title: PBMC response to tetanus toxoid TT 09

description: PBMC response to tetanus toxoid


title: HeDiPig7


title: HeDiPig19

source_name: teat, mesenchymal tissue, affected

value: teat, mesenchymal tissue

value: German Landrace


title: 5hmC NPC 2/4

value: neural progenitor cells, cortex

value: hMeDIP


title: IPH-926, pair_3, 37°C, date 25.01.2010

description: Sample ID: RLT-009,  Description: Serie_A, IPH-926, pair_3, 37°C, date 25.01.2010

value: p53 status off


title: PBMC response to tetanus toxoid TT 08

description: PBMC response to tetanus toxoid


title: IPH-926, pair_2, 32°C, date: 22.12.2009

description: Sample ID: RLT-004,  Description: Serie_A, IPH-926, pair_2, 32°C, date: 22.12.2009

value: p53 status on


title: PBMC response to tetanus toxoid TT 07

description: PBMC response to tetanus toxoid


title: HeDiPig6

description: Gene expression data from teat tissue of peripubertal pigs of commercial dam lines

value: teat, epithelial tissue

value: inverted teat

value: affected

value: Large White x German Landrace


title: PBMC response to tetanus toxoid TT 06

description: PBMC response to tetanus toxoid

value: 1st vaccination


title: IPH-926, pair_2, 37°C, date 22.12.2009

description: Sample ID: RLT-003,  Description: Serie_A, IPH-926, pair_2, 37°C, date 22.12.2009


title: HeDiPig5


title: HeDiPig4


title: IPH-926, pair_1, 32°C, date: 24.11.2009

description: Sample ID: RLT-002,  Description: Serie_A, IPH-926, pair_1, 32°C, date: 24.11.2009


title: H3K36me3 neurons 2/4

description: Cells were isolated by FACs sorting from nmouse cortex using GFP/RFP reported system at 15.5E embryonic development. GFP+ (under Nestin promoter), RFP - (Under Dbx promoter)

value: neurons, cortex

value: ChIp


title: PBMC response to tetanus toxoid TT 11

description: PBMC response to tetanus toxoid

value: b


title: PBMC response to tetanus toxoid TT 04

description: PBMC response to tetanus toxoid

value: a


title: IPH-926, pair_1, 37°C, date:24.11.2009

description: Sample ID: RLT-001,  Description: Serie_A, IPH-926, pair_1, 37°C, date:24.11.2009

value: human lobular breast cancer


title: 5hmC neurons 2/4

source_name: 5hmC enriched DNA fraction after pull-down with 5hmC antibodies.  DNA was isolated from neurons

value: none, Input


title: Melanocyte (expression) Mel.24

first: Arthur

last: Li

address: 1500 E Duarte Rd

institute: City of Hope

description: melanocyte

hyb_protocol: The hybridization cocktails containing 2.5 ug of the fragmented, end-labeled cDNA were applied to the GeneChip® Human Gene 1.0 ST arrays. Hybridization was performed for 16 hours, and the arrays were washed and stained with the GeneChip Fluidics Station 450 using FS450_0007 script.

scan_protocol: Arrays were scanned using the Affymetrix GCS 3000 7G and GeneChip Operating Software v. 1.4 to produce CEL intensity files.

data_processing:
Data were background corrected with GC bin, quantile normalized and summarized by interPLIER algorithm with Affymetrix Expression Console.
Expression Console processed intensity at linear scale

source_name: melanocyte

label_protocol: One µg of each sample was processed using the Affymetrix GeneChip Whole Transcript Sense Target Labeling Assay (https://www.affymetrix.com/support/downloads/manuals/wt_sensetarget_label_manual.pdf

growth_protocol: For control purposes, normal human melanocytes from healthy donors were obtained from commercial sources, and cultured in M-254-500 complete medium according to the manufacturer’s instructions (Invitrogen Corp., Carlsbad, CA). When reaching near confluence, all cultures were harvested by trypsinization, and subjected to genomic DNA- and RNA isolation using standard phenol/chloroform extraction and ethanol precipitation method, and the RNeasy kit (Qiagen, Valencia, CA), respectively. The isolated DNA and RNA samples were kept at –80°C until further analysis.

extract_protocol: Genomic DNA- and RNA were isolated using standard phenol/chloroform extraction and ethanol precipitation method, and the RNeasy kit (Qiagen, Valencia, CA), respectively.

treatment_protocol: The MRC-5 cells were transduced in triplicate, with rAAVintA,  rAAVpp65N, rAAVpp65NLSKO and incubated for 48hrs at 37C.

tag: braf mutational status

value: Wild-type

value: melanocyte


title: Melanocyte (expression) Mel.23

description: melanocyte


title: HeDiPig2

value: normal teat

value: non-affected

value: German Landrace


title: H3K4me3 NPC 2/4

value: neural progenitor cells, cortex


title: H3K27me3 neurons 2/4

source_name: Input DNA from neurons


title: PBMC response to tetanus toxoid TT 03

description: PBMC response to tetanus toxoid

source_name: PBMC

value: c


title: Melanocyte (expression) Mel.22

description: melanocyte


title: H3K27me3 NPC 2/4


title: HeDiPig1

value: teat, epithelial tissue


title: PBMC response to tetanus toxoid TT 05

description: PBMC response to tetanus toxoid


title: HeDiPig3

value: affected


title: PBMC response to tetanus toxoid TT 01

description: PBMC response to tetanus toxoid


title: PBMC response to tetanus toxoid TT 02

description: PBMC response to tetanus toxoid


title: Melanocyte (expression) Mel.21

description: melanocyte


title: IPEC J2 2000 bl_2

description: genome wide gene expression of untreated and DON-treated IPEC-J2 cells

source_name: polarized intestinal porcine epithelial cell line IPEC‑J2

growth_protocol: IPEC‑J2 cells (ACC701, DSMZ) were cultured in Dulbecco’s modified eagle medium (DMEM/Ham’s F-12 (1:1)) supplemented with 5 % fetal calf serum (FCS), 1 % insulin-transferrin-selenium (ITS), 16 mmol/L HEPES (all PAN-Biotech, Germany) and 5 ng/mL epidermal growth factor (EGF; BD Biosciences, Germany) and incubated at 39°C and 5 % CO2. The cells were routinely seeded at a density of 0.5*105/mL with 7.5 mL in plastic tissue culture flasks (25 cm2 Nunc, Denmark) and passaged every 3‑4 d for a maximum of 20 times (passages 78‑98). For the use in experiments, cells were seeded at a density of 2.0 x 105/ well in uncoated 6‑well 1 µm pore-sized ThinCert™ membrane inserts (Greiner bio-one, Germany) and cultured for 7 d.

treatment_protocol: either a low DON concentration of 200 ng/ml or a high DON concentration of 2000 ng/mL was applied from either the apical or the basolateral compartment of ThinCert® membrane inserts for 72 h

tag: treatment group

value: DON-treated

tag: application route

value: basolateral

tag: don concentration


title: IPEC J2 2000 bl_1


title: Melanoma (expression) Mel.14

description: Tissue Same from Melanoma Tumor 14

source_name: Melanoma Tumor 14

value: melanoma


title: Melanoma (expression) Mel.12

description: Tissue Same from Melanoma Tumor 12

source_name: Melanoma Tumor 12

value: Mutant

tag: braf mutation


title: 5mC NPC 2/4

value: MIRA

source_name: Input DNA from NPC


title: H3K4me3 neurons 2/4

source_name: H3K4me3 ChIp DNA from neurons

value: neurons, cortex

value: ChIp


title: Melanoma (expression) Mel.10

description: Tissue Same from Melanoma Tumor 10

source_name: Melanoma Tumor 10


title: IPEC J2 2000 ap_3

value: apical


title: Su(H)_100min_rep3

hyb_protocol: 34 µg labeled sample DNA and 34 µg labeled control DNA were combined, dried in a speed vac with medium heat and resuspended in 12.3 µl water.  For each hybridisation, 29.5µl 2X Hybridization Buffer, 11.8µl Hybridization Component A and 1.2µl Alignment Oligo (NimbleGen Hybridization Kit) were combined and 31.7µl added to each hybridisation sample. Samples were incubated at +95°C for 5 minutes, 42°C for 5 minutes and 41 µl loaded onto the array. The hybridisation was performed to NimbleGen D. melanogaster ChIP-chip 2.1M Whole-Genome Tiling Arrays in the Nimbelegen hybridisation station at 42°C (mix mode B) for 18 hours. Post-hybridisation washes were performed according to the NimbleGen Wash Buffer Kit instructions.

scan_protocol: Arrays were scanned on an Axon 4000B scanner per manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html).

data_processing: Arrays were processed using NimbleGen's standard protocol for Nimblescan 2.4 ChIP data extraction to create raw data. One replicate at 10 min for Su(H) samples was discarded due to quality issues. This results in a total of 20 arrays. Quantile normalization was applied to the 2 or 3 arrays at each of the 7 time points. Since DNA samples for the first 3 time points and the last 4 time points were collected separately, there was a prominent batch effect in the Su(H) samples. We applied batch effect correction (Johnson et al. 2007) to these arrays.

source_name: Total input after 100 min. Notch activation

label_protocol: In duplicate reactions: 1 μg of amplified DNA with 30 µl 2.5X Random Primers Solution (BioPrime DNA labelling kit, Life Technologies) was incubated at 100°C for 5 minutes and then cooled on ice. The samples were labelled as technical dye-swap replicates using the BioPrime DNA labelling kit (Life Technologies) in the presence of 4.5nmol fluorescently labelled Cy3- or Cy5-dCTP (GE Healthcare) and 72 U of Klenow at 37°C. After 2 hours the reactions were stopped with 7.5 µl Stop Buffer (BioPrime DNA labelling kit, Life Technologies). Duplicate reactions were pooled into single tubes and then precipitated with 165 µl Isopropanol and 0.2M sodium chloride and washed with cold 80% ethanol. The DNA was resuspened in 50 µl water and quantified on a Nanodrop spectrophotometer (Thermo Scientific).

extract_protocol: Chromatin was crosslinked by fixing cells for 10 minutes with 1% formaldehyde (Sigma) at room temperature before addition of Glycine (Sigma) (0.2M final concentration) to stop the crosslinking reaction.  Cells were then detached from plates and washed twice with PBS, keeping samples at 4°C at all times.  Chromatin was released from cells by incubation with nuclear lysis buffer (50mM Tris-HCl pH 8.1, 10mM EDTA, 1% SDS, 1X complete protease inhibitor (Roche) for 10 minutes on ice.  Crosslinked chromatin was fragmented by sonication to an average length of roughly 500bp.  Chromatin was then precleared by addition of rabbit IgG and protein G agarose beads (Santa Cruz Biotechnology) in IP dilution buffer (IPDB) (20mM Tris-HCl pH 8.1, 150mM NaCl, 2mM EDTA, 1% Triton X-100, 0.01% SDS, 1X complete protease inhibitor (Roche) and incubation at 4°C for 5 hours with gentle agitation.  2µg Su(H) antibody (Santa Cruz Biotechnology) per sample was preincubated with protein G agarose beads in IPDB for 5 hours at 4°C with gentle agitation.  Precleared chromatin was precipitated by addition of protein G agarose beads with prebound Su(H) antibody and incubation at 4°C overnight with gentle agitation.  Beads with chromatin bound were washed twice with wash buffer 1 (20mM Tris-HCl pH 8.1, 50mM NaCl, 2mM EDTA, 1% Triton X-100, 0.1% SDS), twice with wash buffer 2 (10mM Tris-HCl pH 8.1, 250mM LiCl, 1mM EDTA, 1% NP-40, 1% deoxycholic acid) and once with TE pH 8.0.  Chromatin was then eluted from the agarose beads by incubation with elution buffer (100mM NaHCO3, 1% SDS) for 10 minutes with vigorous shaking before decrosslinking (of precipitated samples and total input) by incubating at 65°C for 5 hours with NaCl (0.27M final concentration).  Remaining proteins were removed by incubating with proteinase-K at 55°C overnight.  DNA was then purified by phenol/chloroform extraction and ethanol precipitation. Binding relative to input was quantified by qPCR.  For array analysis, DNA fragments and total input samples were amplified by ligation mediated PCR and labelled before hybridisation to tiling arrays.

treatment_protocol: Notch signalling was initiated by replacing cell media with 2mM EDTA in PBS for 5 minutes. The EDTA was then washed out using normal culture media and the cells were collected after 100 minutes.

tag: cell line

value: Notch stimulation

tag: time point

value: 100 min

tag: chip antibody

source_name: Su(H) ChIP DNA after 100 min. Notch activation

value: Su(H) antibody

tag: antibody vendor

value: Santa Cruz Biotechnology


title: IPEC J2 2000 ap_2


title: IPEC J2 2000 bl_3


title: Melanoma (expression) Mel.7

description: Tissue Same from Melanoma Tumor 7

source_name: Melanoma Tumor 7

value: Wild-type


title: Su(H)_60min_rep3

source_name: Total input after 60 min. Notch activation

treatment_protocol: Notch signalling was initiated by replacing cell media with 2mM EDTA in PBS for 5 minutes. The EDTA was then washed out using normal culture media and the cells were collected after 60 minutes.

value: 60 min

source_name: Su(H) ChIP DNA after 60 min. Notch activation


title: H3K36me3 NPC 2/4

source_name: H3K36me3 ChIp DNA from NPC

value: neural progenitor cells, cortex

tag: age

value: none, Input


title: IPEC J2 2000 ap_1


title: Su(H)_40min_rep3

source_name: Total input after 40 min. Notch activation

treatment_protocol: Notch signalling was initiated by replacing cell media with 2mM EDTA in PBS for 5 minutes. The EDTA was then washed out using normal culture media and the cells were collected after 40 minutes.

value: 40 min

source_name: Su(H) ChIP DNA after 40 min. Notch activation


title: IPEC J2 200 bl_3

value: DON-treated

value: 200 ng/mL


title: Melanoma (expression) Mel.6

description: Tissue Same from Melanoma Tumor 6

source_name: Melanoma Tumor 6

value: melanoma


title: Su(H)_60min_rep2


title: Melanoma (expression) Mel.8

description: Tissue Same from Melanoma Tumor 8

source_name: Melanoma Tumor 8


title: Melanoma (expression) Mel.5

description: Tissue Same from Melanoma Tumor 5

source_name: Melanoma Tumor 5

value: Mutant


title: 5mC neurons 2/4

source_name: methylated DNA fraction enriched by MIRA. DNA was isolated from neurons

tag: enrichment method

value: MIRA

source_name: Input DNA from neurons


title: Su(H)_60min_rep1


title: Su(H)_40min_rep2


title: Su(H)_40min_rep1


title: IPEC J2 200 bl_1

source_name: polarized intestinal porcine epithelial cell line IPEC‑J2

value: basolateral


title: IPEC J2 200 bl_2


title: Melanoma (expression) Mel.3

description: Tissue Same from Melanoma Tumor 3

source_name: Melanoma Tumor 3


title: Su(H)_100min_rep2


title: Melanoma (expression) Mel.2

description: Tissue Same from Melanoma Tumor 2

source_name: Melanoma Tumor 2


title: 5hmC NPC 1/4

source_name: 5hmC enriched DNA fraction after pull-down with 5hmC antibodies.  DNA was isolated from NPC

value: hMeDIP

tag: antibody

source_name: Input DNA from NPC


title: Su(H)_30min_rep1

source_name: Su(H) ChIP DNA after 30 min. Notch activation

treatment_protocol: Notch signalling was initiated by replacing cell media with 2mM EDTA in PBS for 5 minutes. The EDTA was then washed out using normal culture media and the cells were collected after 30 minutes.

value: 30 min

source_name: Total input after 30 min. Notch activation


title: IPEC J2 200 ap_3

value: apical


title: IPEC J2 200 ap_2


title: crpvsYPIII_GEO_sample04

first: Ann

middle: Kathrin

last: Heroven

state: Niedersachsen

department: Molecular Infection Biology

institute: Helmholtz Centre for Infection Research

description: Biological replicate 4 of 4.

hyb_protocol: 300ng of each Cy3- and Cy5-labelled RNA and hybridized to the microarray at 65°C for 17 hours using the Agilent Hybridization Chamber according to the Agilent instructions

scan_protocol: The array were scanned at a resolution of 5μm using the Axon GenePix Personal 4100A microarray scanner (Axon instruments) and features were extracted using GenePix Pro 6

data_processing: The data were processed by R16 in combination with Bioconductor. Thereby, preprocessing was based on the marray package employing initially the read.GenePix function. Control code for probe selection was adapted due to Agilent purposes and quality control was performed to check for hybridization artifacts as well as to avoid large scale differences between the microarrays of one experiment. Lowess normalization was applied for two-color intensity-dependent normalization within each microarray and if necessary supplemented by scale normalization between different microarrays. Further diagnostic plots showing normalization results were created for quality assessment. Afterwards, differentially expressed genes were obtained using the limma package and the lmFit function for linear modeling, eBayes for significance calculations and topTable for the extraction of the differential expressed genes. Since every gene on the microarray was represented at least by three probes, overall fold-changes were summarized on the calculation of the median value for all mating probes

organism: Yersinia pseudotuberculosis YPIII

source_name: YPIII pIB1 wild type

label_protocol: RNA samples were labelled either with Cy3 (mutant) or Cy5 (wild type) using the ULS fluorescent labelling kit (Kreatech, Germany)

growth_protocol: Y. pseudotuberculosis strains were grown in LB medium at 25°C to stationary phase (OD600 = 3.5)

extract_protocol: RNA extraction was performed using the SV Total RNA Isolation System (Promega)

tag: strain

value: YPIII pIB1 wild type

source_name: YPIII pIB1 crp mutant

value: YPIII pIB1 crp mutant


title: 5hmC neurons 1/4

source_name: 5hmC enriched DNA fraction after pull-down with 5hmC antibodies.  DNA was isolated from neurons

value: neurons, cortex


title: H3K4me3 neurons 1/4

source_name: H3K4me3 ChIp DNA from neurons

value: ChIp


title: Melanoma (expression) Mel.4

description: Tissue Same from Melanoma Tumor 4

source_name: Melanoma Tumor 4

value: Wild-type


title: H3K36me3 NPC 1/4

source_name: H3K36me3 ChIp DNA from NPC

value: neural progenitor cells, cortex


title: Su(H)_20min_rep3

source_name: Total input after 20 min. Notch activation

treatment_protocol: Notch signalling was initiated by replacing cell media with 2mM EDTA in PBS for 5 minutes. The EDTA was then washed out using normal culture media and the cells were collected after 20 minutes.

value: Notch stimulation

value: 20 min

source_name: Su(H) ChIP DNA after 20 min. Notch activation

value: Su(H) antibody

value: Santa Cruz Biotechnology


title: IPEC J2 200 ap_1

value: DON-treated

value: 200 ng/mL


title: Su(H)_100min_rep1

source_name: Su(H) ChIP DNA after 100 min. Notch activation

value: 100 min

source_name: Total input after 100 min. Notch activation


title: Su(H)_10min_rep1

source_name: Su(H) ChIP DNA after 10 min. Notch activation

treatment_protocol: Notch signalling was initiated by replacing cell media with 2mM EDTA in PBS for 5 minutes. The EDTA was then washed out using normal culture media and the cells were collected after 10 minutes.

value: 10 min

source_name: Total input after 10 min. Notch activation


title: crpvsYPIII_GEO_sample03

description: Biological replicate 3 of 4.


title: crpvsYPIII_GEO_sample02

description: Biological replicate 2 of 4.


title: IPEC J2 K_3

source_name: polarized intestinal porcine epithelial cell line IPEC‑J2

value: control


title: H3K36me3 neurons 1/4

source_name: H3K36me3 ChIp DNA from neurons

source_name: Input DNA from neurons

value: none, Input


title: iCFB subclone 50, biological repeat 2

first: Chun

middle: Ying

last: Yu

address: 128 Academia Road, Section 2

department: Genomic Research center

institute: Academia sinica

description:
iCFB50-2
Gene expression data from iCFB cells.

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

scan_protocol: Chips were scanned with an Affymetrix GeneChip Scanner 7G.

data_processing: Global scaling was used as the normalization method.

source_name: induced pluripotency cells from foreskin cells, subclone 50

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA.

growth_protocol: Pluripotent cells were grown on MEF feeders in DMEM/F12 medium plus 20% Knockout Serum Replacement and bFGF. The parental cells were grown in DMDM plus 10% FBS.

treatment_protocol: None.

tag: subclone

tag: gender

value: male


title: Su(H)_30min_rep3

source_name: Total input after 30 min. Notch activation

tag: treatment

value: 30 min

source_name: Su(H) ChIP DNA after 30 min. Notch activation


title: Su(H)_20min_rep1


title: IPEC J2 K_2


title: Su(H)_0min_rep3

source_name: Total input after 0 min. Notch activation

treatment_protocol: Notch signalling was initiated by replacing cell media with 2mM EDTA in PBS for 5 minutes. The EDTA was then washed out using normal culture media and the cells were collected after 0 minutes.

value: 0 min

source_name: Su(H) ChIP DNA after 0 min. Notch activation


title: H3K4me3 NPC 1/4

source_name: H3K4me3 ChIp DNA from NPC

tag: cell type

source_name: Input DNA from NPC


title: crpvsYPIII_GEO_sample01

description: Biological replicate 1 of 4.

source_name: YPIII pIB1 wild type

value: YPIII pIB1 wild type

source_name: YPIII pIB1 crp mutant

value: YPIII pIB1 crp mutant


title: Su(H)_10min_rep2


title: iCFB subclone 50, biological repeat 1

description:
iCFB50-1
Gene expression data from iCFB cells.

value: induced pluripotency cells from foreskin cells


title: IPEC J2 K_1


title: iCFB subclone 46, biological repeat 1

description:
iCFB46-1
Gene expression data from iCFB cells.

source_name: induced pluripotency cells from foreskin cells, subclone 46


title: Su(H)_30min_rep2


title: H3K27me3 neurons 1/4

source_name: H3K27me3 ChIp DNA from neurons

value: neurons, cortex

value: ChIp


title: primary foreskin cells, biological repeat 2

description:
foreskin2
Gene expression data from foreskin cells.

source_name: adult foreskin cells

value: primary foreskin cells

tag: developmental stage

value: adult


title: HeDiPig_F12

data_processing:
Data were analysed with Affymetrix GCOS 1.1.1 software using global scaling to a target signal of 500.
by PLIER algorithm

source_name: milk line from fetus taken at 91 day post conception

tag: tissue

value: nipple

tag: breed

value: Pietrain

value: 91 dpc


title: HeDiPig_F13


title: HeDiPig_F14


title: primary foreskin cells, biological repeat 1

description:
foreskin1
Gene expression data from foreskin cells.


title: Su(H)_0min_rep2

value: Notch stimulation

value: Su(H) antibody

value: Santa Cruz Biotechnology


title: Su(H)_20min_rep2

source_name: Su(H) ChIP DNA after 20 min. Notch activation

value: 20 min

source_name: Total input after 20 min. Notch activation


title: igra subclone 2, biological repeat 2

description:
iGra2-2
Gene expression data from iGra cells.

source_name: induced pluripotency cells from granulosa cells, subclone 2

value: female


title: HeDiPig_F11

source_name: milk line from fetus taken at 63 day post conception

value: 63 dpc


title: HeDiPig_F10


title: Su(H)_0min_rep1

value: 0 min


title: 5mC NPC 1/4

source_name: methylated DNA fraction enriched by MIRA. DNA was isolated from NPC

value: neural progenitor cells, cortex

value: MIRA

value: none, Input


title: HeDiPig_F9


title: igra subclone 1, biological repeat 2

description:
iGra1-2
Gene expression data from iGra cells.

source_name: induced pluripotency cells from granulosa cells, subclone 1


title: RpoD binding site identification experiment 3

city: La Jolla

first: Bernhard

last: Palsson

address: 417 Powell-Focht Bioengineering Hall, 9500 Gilman Dr.

institute: University of California, San Diego

description: ChIP-chip for RpoD binding site identification in Klebsiella pneumoniae MGH 78578

hyb_protocol: The labeled ChIP DNA was precipitated with 0.1 volume 5M NaCl and 1 volume isopropanol, and hybridized in 45 ul of buffer containing 20% formamide, 1.2 M betaine, 0.1 ug/ul herring sperm DNA and 10 ug of human COT1 DNA (Invitrogen). Arrays were hybridized in Maui hybridization stations for 16-18 h at 42C, and then washed in 42C 0.2% SDS/0.2x SSC, room temperature 0.2x SSC, and 0.05x SSC. Hybridization buffers and washes were completed using manufacturer's protocols (http://www.nimblegen.com/products/lit/lit.html)

data_processing: Arrays were processed using Nimblegen's standard protocol for Nimblescan 2.4 ChIP data extraction.

organism: Klebsiella pneumoniae subsp. pneumoniae MGH 78578

source_name: RpoD ChIP DNA

label_protocol: Labling was done according to manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html).

growth_protocol: Cells were cultured to mid-log phase (OD~0.6) in glucose M9 minimal media

extract_protocol: Cells were grown in 2 g/L glucose M9 minimal media at 37  C. When the cultures reached an appropriate OD, the cells were cross-linked by 1% formaldehyde at room temperature for 30 min. Following quenching the unused formaldehyde with 125 mM glycine at room temperature for 5 min, the cross-linked cells were harvested by centrifugation and washed 3 times with 50 mL of ice-cold TBS. The washed cells were resuspended in 0.5 ml of lysis buffer composed of 50 mM Tris-HCl (pH 7.5), 100 mM NaCl, 1 mM EDTA, protease inhibitor mixture (Sigma) and 1 kU Ready-Lyse lysozyme (Epicentre). The cells were incubated at room temperature for 30 min and then treated with 0.5 ml of 2  IP buffer composed of 100 mM Tris-HCl (pH 7.5), 200 mM NaCl, 1 mM EDTA, 2% (vol/vol) Triton X-100, and protease inhibitor mixture (Sigma). The lysate was then sonicated 4 times for 20 sec each in an ice bath to fragment the chromatin complexes. Cell debris was removed by centrifugation at 13,000 rpm at 4  C for 10 min. To immunoprecipitate the protein-DNA complexes, the antibody was then added into the cell extract. For the control (mock-IP), 2 ug of normal mouse IgG (Upstate) was added into the cell extract. They were then incubated overnight at 4  C, and 50   l of the Dynabeads Pan mouse IgG magnetic beads (Invitrogen) was added into the mixture. After 5-h incubation at 4  C, the beads were washed twice with the IP buffer [50 mM Tris-HCl (pH 7.5), 140 mM NaCl, 1 mM EDTA, 1% (vol/vol) Triton X-100, and protease inhibitor mixture], once with the wash buffer I [50 mM Tris-HCl (pH 7.5), 500 mM NaCl, 1% (vol/vol) Triton X-100, and 1 mM EDTA], once with wash buffer II [10 mM Tris-HCl buffer (pH 8.0), 250 mM LiCl, 1% (vol/vol) Triton X-100, and 1 mM EDTA], and once with TE buffer [10 mM Tris-HCl (pH 8.0), 1 mM EDTA] in order. After removing the TE buffer, the beads were resuspended in 200 ul of elution buffer [50 mM Tris-HCl (pH 8.0), 10 mM EDTA and 1% SDS] and incubated overnight at 65  C for reverse cross-linking. After reversal of the cross-links, RNAs were removed by incubation with 200uL of TE buffer with 1uL of RNaseA (Qiagen) for 2 h at 37  C. Proteins in the DNA sample were then removed by incubation with 4uL of proteinase K solution (Invitrogen) for 2 h at 55  C. The sample was then purified with a PCR purification kit (Qiagen).

tag: phenotype

value: pathogenic, capsular

value: anti-sigmaD

tag: vendor/catalog

value: neoclone #W0004

source_name: Mock IP DNA

value: normal mouse IgG


title: RpoS binding site identification experiment 3

description: ChIP-chip for RpoS binding site identification in Klebsiella pneumoniae MGH 78578

source_name: RpoS ChIP DNA

growth_protocol: Cells were cultured to stationary phase (OD~1.3) in glucose M9 minimal media

value: anti-sigmaS

value: neoclone #W0009


title: RpoS binding site identification experiment 2


title: igra subclone 1, biological repeat 1

description:
iGra1-1
Gene expression data from iGra cells.

value: induced pluripotency cells from granulosa cells


title: 5mC neurons 1/4

source_name: methylated DNA fraction enriched by MIRA. DNA was isolated from neurons

value: neurons, cortex

source_name: Input DNA from neurons


title: iCFB subclone 46, biological repeat 2

description:
iCFB46-2
Gene expression data from iCFB cells.

value: induced pluripotency cells from foreskin cells

value: male


title: H3K27me3 NPC 1/4

source_name: H3K27me3 ChIp DNA from NPC

value: ChIp

source_name: Input DNA from NPC


title: RpoD binding site identification experiment 2


title: primary granulosa cells, biological repeat 2

description:
Gra2
Gene expression data from granulosa cells.

source_name: granulosa cells

value: primary granulosa cells

value: female


title: RpoS binding site identification experiment 1


title: HeDiPig_F8

description: Gene expression data from teat tissue of peripubertal pigs of commercial dam lines

value: nipple

value: German landrace

value: 91 dpc