title: Prostate Cancer_NUGEN TEST07

first: M. Simo

last: Arredouani

address: 330 Brookline Ave.

department: Surgery

institute: Beth Israel Deaconess Medical Center

description: NUGEN TEST07

hyb_protocol: cRNA (15 μg) was fragmented and hybridized to arrays according to the manufacturer's (Ambion® | Life Technologies) protocols.

scan_protocol: GeneArray Scanner G2500A (Hewlett-Packard)

data_processing: BioConductor R packages

source_name: malignant tissue_TMPRSS2:ERG fusion negative

label_protocol: Biotin-UTP was incorporated during the overnight in vitro transcription step according to the manufacturer's (Ambion® | Life Technologies) protocol.

growth_protocol: A biopsy punch was used to select the PCa tissues from the OCT prostate sample blocks.

extract_protocol: Total RNA was isolated using Trizol reagent. RNA was quantified by NanoDrop ND-1000 spectrophotometer, and quality was evaluated with Agilent RNA 6000 NanoChip and the 2100 Bioanalyzer, with 28S/18S ratios and RIN determined by 2100 Expert software.

treatment_protocol: Benign or PCa tissues were homogenized using a TissueLyser (Qiagen) at 28 Hz for 5 min.

tag: tissue type

value: Malignant prostate tissue

value: ERG fusion status:negative


title: Embryo at E8.5, caudal neural epithelium 2

status: Public on Mar 18 2014

type: RNA

city: Cincinnati

first: Rebekah

last: Karns

state: OH

address: 3333 Burnet Ave

department: Gastroenterology, Hepatology, & Nutrition

country: USA

institute: Cincinnati Children's Hospital Medical Center

description: Gene expression of the caudal neural epithelium at E8.5

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: Data were analyzed in Genespring v 7.3.1. A standard workflow for microarray analysis included removal of probesets that did not map uniquely to the mm9 ENSEMBL genome and the identification of genes, transcripts, and probesets whose RMA- measured expression level was at least 6.2 in at least one sample

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: embryo_E8.5_caudal neural epithelium

label_protocol: Biotynilated cRNA were prepared according to the standard Affymetrix protocol

growth_protocol: Embryos were collected from CD1 outbred mice with the day of vaignal plug designated E0.5.  Embryos were flash frozen, cryostat section were made a processed.  Laser capture microdissection was carried out with an Arcturus Veritas.

extract_protocol: RNA was purified using the ZR RNA MicroPrep kit (Zymo). Nugen RiboSpia Ovation Pico WTA System V2 was used for aplification.

tag: strain

tag: embryonic stage

tag: tissue

value: caudal neural epithelium


title: Embryo at E8.5, caudal neural epithelium 4


title: temporary ponds family 2 Ålgrundet JB003-4204D

city: Victoria

first: Nik

last: Veldhoen

state: BC

address: PO Box 3055 STN CSC

department: Biochemistry & Microbiology

country: Canada

institute: University of Victoria

hyb_protocol: Prepare a MAGEX slide by hydration in WB2 buffer (1xSSC, 0.1% SDS) at ambient temperature followed by incubation in PB1 buffer (5xSSC, 0.2% BSA, 0.2% SDS) for 45 minutes at 48°C. Rinse the slide with water followed by immersion in isopropanol at ambient temperature and centrifuge dry. Place a Lifterslip CS/3 (Erie Scientific Company) over each array region on the slide. Combine the Cy labeled sample (5.5ul of 15 pmol/ul Cy3 label) and reference (1 ul of 2 pmol/ul Cy5 label) cDNA and briefly denature at 95°C for 3 min followed by immediate incubation on ice. Prepare a 33 ul hybridization mix containing 5xSSC, 25% deionized formamide, 0.02% BSA, 1ug A45 oligonucleotide, 0.1% SDS, 5% Dextran, and 6.5 ul of the combined Cy3-labeled sample and Cy5-labeled reference cDNA. Briefly warm the hybridization solution at 37°C and then place onto the MAGEX array and incubate the prepared slide in a Hybex incubator at 42°C for 18 hrs. Hybridized slides were washed once with WB1 buffer (1xSSC, 0.1% SDS) at 48°C for 5 min; twice with WB2 buffer (0.1x SSC, 0.1% SDS) at 48°C for 10 min; and once with WB3 (0.01x SSC, 0.1% SDS) at 48°C for 10 min. Dry the slides by centrifugation at 200 x g and store in a desiccator prior to data collection.

scan_protocol: Scanning was done on a Packard Bioscience Scan Array Express Micro array scanner with the Cy3 PMT gain at 80% and Cy5 PMT gain at 70%. Laser strength was set at 90% for both channels. MAGEX 2008 microarray slides were scanned at 5 um resolution with an X=0 mm, Y=11.73 mm, W=22 mm, and H=52.38mm.

data_processing: Data was aquired from raw scanned MAGEX 2008 array images using ImaGene v9.0.

organism: Rana temporaria

source_name: liver, constant water

label_protocol: Amplified cDNA (500 ng) was random labeled with 2 ul of 1 mM Cy3-dCTP (GE Healthcare) using the DecaLabel DNA Labeling Kit (Fermentas Canada).

growth_protocol: Rana temporaria eggs were collected from six islands within the Gulf of Bothnia, northern Sweden. For each island, samples of 20–50 eggs were taken from a maximum of 10 clutches and transported to the laboratory. Each clutch was assumed to represent one female, as female R. temporaria lay only one egg clump per season. Eggs from each female were kept in separate containers filled with aged tap water. The eggs were stored in thermo-constant laboratory conditions and kept cool (4 °C) until all eggs were collected. When all eggs were collected, the temperature of the laboratory was set to 22 °C for the remainder of the experiment. A light : dark cycle of 18 h : 6 h was employed. The tadpoles were fed ad libitum every fourth day on a mixture (1 : 2) of finely ground fish food and rabbit chow. The food mass was 15 mg per tadpole at the beginning of the experiment, increased to 30 mg at day 9, 45 mg at day 13, 60 mg at day 17, and 75 mg from day 21 and to the end of the experiment. Water was replaced every fourth day, prior to feeding.

extract_protocol: Total RNA was extracted from RNAlater (Life Technologies) preserved liver tissue using TRIzol (Life Technologies) and a Retsch MM301 mixer mill with a 3mm tungsten carbide bead and 1 ug used to prepare amplified cDNA using the SMARTer cDNA synthesis kit (Clontech Laboratories). SMARTer cDNA samples were purified using the GeneJET PCR Purification Kit (Fermentas Canada).

treatment_protocol: Tadpoles originating from each island were raised to Gosner stage 23 (active swimming) (Gosner, 1960) and then one set was reared in constant water while a second set was reared under reduced water conditions. Four tadpoles from each female (two allocated to each treatment) were randomly chosen and placed into individual plastic containers (9.5 cm × 9.5 cm, height 10 cm). The containers were filled with 750 mL of tap water, previously aged and aerated together with dried deciduous leaves. The leaves were removed when the water was transferred to the experimental containers. The tadpoles were subjected to one of two treatments, either constant water level (C) or simulated pool drying (D). In the simulated drying treatment the initial water volume of 750 mL was lowered by 33% every fourth day, starting at day 5 and continued until day 25, after which the water volume in the D treatment was kept constant at 66 mL. The water temperature did not differ between the two treatments. The experiment was terminated at Gosner stage 37 (front legs visible), after which tadpoles were weighed. Liver samples were obtained from individuals in all groups at a fixed time point 14 days post commencement of water adjustment and when animals had reached Gosner stage 37.

tag: island of origin

value: Ålgrundet

tag: family

value: liver

tag: treatment

value: constant water

tag: developmental stage

value: Gosner Stage 37


title: Prostate Cancer_MS 36C9

city: Boston

state: MA

description: MS 36C9

organism: Homo sapiens

source_name: malignant tissue_TMPRSS2:ERG fusion positive

value: ERG fusion status:positive


title: Prostate Cancer_MS 36A6

description: MS 36A6


title: Embryo at E8.5, caudal neural epithelium 1


title: Prostate Cancer_MS 36A1

description: MS 36A1


title: Embryo at E8.5, caudal neural epithelium 3


title: e8.5 paraxial mesoderm rep. 2

source_name: Embryonic paraxial mesoderm from E8.5

value: Paraxial mesoderm


title: Prostate Cancer_MS 36C4

description: MS 36C4


title: Prostate Cancer_MS 36C8

description: MS 36C8


title: Prostate Cancer_MS 36C1

description: MS 36C1


title: Embryo at E8.5, floor plate neural epithelium 1

description: Gene expression of the floor plate neural epithelium at E8.5

source_name: embryo_E8.5_floor plate neural epithelium

value: floor plate neural epithelium


title: Prostate Cancer_MS 36C3

description: MS 36C3


title: Prostate Cancer_NUGEN TEST05

description: NUGEN TEST05


title: e8.5 paraxial mesoderm rep. 3


title: temporary ponds family 9 Ålgrundet JB003-4200D


title: e8.5 paraxial mesoderm rep. 1


title: Prostate Cancer_MS 36D7

description: MS 36D7


title: Prostate Cancer_MS 36C2

description: MS 36C2


title: Prostate Cancer_MS 36D8

description: MS 36D8


title: temporary ponds family 1 Ålgrundet JB003-4159U


title: temporary ponds family 4 Ålgrundet JB003-4158D


title: Normal_MS 36D2

description: MS 36D2

source_name: benign tissue

value: Benign prostate tissue


title: permanent ponds family 4 Stora Fjäderägg JB003-4163U

value: Stora Fjäderägg


title: permanent ponds family 2 Stora Fjäderägg JB003-4159D


title: permanent ponds family 9 Stora Fjäderägg JB003-4230D


title: permanent ponds family 6 Stora Fjäderägg JB003-4319D


title: permanent ponds family 10 Stora Fjäderägg JB003-4229U


title: permanent ponds family 1 Stora Fjäderägg JB003-4321D


title: e8.5 neural crest rep. 2

source_name: Embryonic neural crest from E8.5

value: Neural crest


title: permanent ponds family 9 Öster Hällskär JB003-4300U

value: Öster Hällskär


title: e8.5 neural crest rep. 1


title: e8.5 neuroepithilium rep. 1

source_name: Embryonic neuroepithilium from E8.5

value: Neuroepithilium


title: e8.5 neural crest rep. 5


title: Δ hupB mutant_0.02 µg Fe / mL

city: Hyderabad

first: Manjula

last: Sritharan

state: Andhra Pradesh

address: Prof. CR Rao Road

department: Animal Sciences

country: India

institute: University of Hyderabad

description: LI- H37Rv ∆ hupB

hyb_protocol: The labeled cRNA samples were hybridized on to an Agilent Custom Mycobacterium tuberculosis 8x15k Array designed by Genotypic Technology Private Limited. (AMADID: 20181). 600 ng of cy3 labeled samples were fragmented and hybridized. Fragmentation of labeled cRNA and hybridization were done using the Gene Expression Hybridization kit of Agilent (Part Number 5188-5242). Hybridization was carried out in Agilent’s Surehyb Chambers at 65º C for 16 hours. The hybridized slides were washed using Agilent Gene Expression wash buffers (Part No: 5188-5327)

scan_protocol: Scanned on an Agilent G2505C scanner and Images were quantified using Agilent Feature Extraction Software (version 10.5.1.1)

data_processing: Data extraction from Images was done using Feature Extraction software  and Percentile Shift Normalization of the data was done in GeneSpring GX (Gene Based Analysis was performed)

organism: Mycobacterium tuberculosis

source_name: RNA isolated from low iron grown H37Rv ∆ hupB mutant

label_protocol: Poly (A)-tails were added to the 3’-end of RNA by using A-plus Poly (A) polymerase tailing kit (Epicentre Biotechnologies).Then the samples were labeled using Agilent Quick Amp Kit PLUS (Part number: 5190-0442). Five hundred nanograms each of the samples were incubated with reverse trancription mix at 42°C and converted to double stranded cDNA primed by oligodT with a T7 polymerase promoter. The cleaned up double stranded cDNA were used as template for aRNA generation. cRNA was generated by in vitro transcription and the dye Cy3 CTP(Agilent) was incorporated during this step. The cDNA synthesis and in vitro transcription steps were carried out at 40°C. Labeled cRNA was cleaned up and quality assessed for yields and specific activity.

growth_protocol: Actively growing culture of WT H37Rv and H37Rv ∆ hupB in Middlebrook 7H9 medium were re-suspended in iron-free Proskauer and Beck medium and diluted to get a cell suspension equivalent to McFarland 4 and 1 mL of this was used to inoculate two identical sets of six flasks each.  Each flask contained 100 mL Proskauer & Beck medium to which 1 mL of salt solution containing (16.8 mM Mg2+, 5.01 μM Mn2+ and 17 μM Zn2+) was added. Iron was added at a final concentration of 0.02 μg Fe / ml (0.36 μM of Fe) for low iron growth and 8 μg Fe / ml for high iron growth (144 μM of Fe). 300 ug / mL hygromycin was added to the flasks inoculated with the mutant strain. The cultures were incubated in an orbital shaker (150 rpm) at 37°C.

extract_protocol: The cell pellet, obtained by centrifugation at 4000 rpm for 10 min at RT was re-suspended in 1 ml Trizol (InVitrogen), transferred to ribolyzer tube and ribolyzed for 45 sec (set at power 6.5). 400 µL chloroform was added, mixed by inverting the tube and centrifuged for 5 min at 14,000 rpm. The clear upper layer containing the RNA was transferred to a new tube and added 0.8 volumes of isopropanol and 0.3 volumes of 3 M sodium acetate. The tubes were mixed well by inverting the tube and the RNA was allowed to precipitate overnight at -20°C. The RNA pellet, obtained by centrifugation for 10 min at 14,000 rpm was washed with 70% ethanol, air-dried and dissolved in 100 µL of RNAse - free water. The sample was purified by treatment with DNase I (TURBO DNA - free kit from Ambion (Austin, USA) and passing through RNeasy column (Qiagen (Hilden, Germany) using manufacturer's instructions. Absence of DNA was confirmed by PCR amplification against a positive control and the integrity of RNA was checked on 2% Tris-acetate agarose gel.

treatment_protocol: The organisms were allowed to grow till mid-log phase, when the OD 600 nm was ~0.4 when sufficient carboxymycobactin was detected in the spent growth medium of low iron cultures. An equal volume of guanidine thiocyanate (GTC; Sigma Aldrich Pvt. Ltd. MO, USA) solution was added to the culture and mixed well before proceeding to extraction of RNA  The cell pellet, obtained by centrifugation at 4000 rpm for 10 min at RT was re-suspended in 1 ml Trizol, transferred to ribolyzer tube and ribolyzed for 45 sec (set at power 6.5). 400 µL chloroform was added, mixed by inverting the tube and centrifuged for 5 min at 14,000 rpm. The clear upper layer containing the RNA was transferred to a new tube and added 0.8 volumes of isopropanol and 0.3 volumes of 3 M sodium acetate. The tubes were mixed well by inverting the tube and the RNA was allowed to precipitate overnight at -20°C. The RNA pellet, obtained by centrifugation for 10 min at 14,000 rpm was washed with 70% ethanol, air-dried and dissolved in 100 µL of RNAse - free water. The sample was purified by treatment with DNase I and passing through RNeasy column using manufacturer's instructions. Absence of DNA was confirmed by PCR amplification against a positive control and the integrity of RNA was checked on 2% Tris-acetate agarose gel.  before proceeding to extraction of RNA  The cell pellet, obtained by centrifugation at 4000 rpm for 10 min at RT was re-suspended in 1 ml Trizol, transferred to ribolyzer tube and ribolyzed for 45 sec (set at power 6.5). 400 µL chloroform was added, mixed by inverting the tube and centrifuged for 5 min at 14,000 rpm. The clear upper layer containing the RNA was transferred to a new tube and added 0.8 volumes of isopropanol and 0.3 volumes of 3 M sodium acetate. The tubes were mixed well by inverting the tube and the RNA was allowed to precipitate overnight at -20°C. The RNA pellet, obtained by centrifugation for 10 min at 14,000 rpm was washed with 70% ethanol, air-dried and dissolved in 100 µL of RNAse - free water. The sample was purified by treatment with DNase I and passing through RNeasy column using manufacturer's instructions. Absence of DNA was confirmed by PCR amplification against a positive control and the integrity of RNA was checked on 2% Tris-acetate agarose gel.

tag: genotype

value: low iron supplemented Proskauer & Beck medium

tag: growth

value: H37Rv ∆ hupB mutant


title: Wild type_0.02 µg Fe / mL

source_name: RNA isolated from low iron grown WT H37RV

value: WT H37Rv


title: e8.5 neuroepithilium rep. 3


title: A549 treated with heptanal_C7_3

city: Seoul

first: Yoon

last: Cho

address: hwarang-ro 14

country: South Korea

institute: KIST

description:
mRNA expression after 48 h in heptanal treated human cells
C7-IC20_3

hyb_protocol: After checking labeling efficiency, fragmentation of cRNA was performed by adding 10X blocking agent and 25X fragmentation buffer and incubating at 60oC for 30 min. The fragmented cRNA was resuspended with 2X hybridization buffer and directly pipetted onto assembled Agilent’s Canine Oligo Microarray (44K). The arrays hybridized at 65oC for 17 hours using Agilent Hybridization oven (Agilent Technology, USA). The hybridized microarrays were washed as the manufacturer’s washing protocol (Agilent Technology, USA).

scan_protocol: The hybridized images were scanned using Agilent’s DNA microarray scanner and quantified with Feature Extraction Software (Agilent Technology, Palo Alto, CA).

data_processing: All data normalization and selection of fold-changed genes were performed using GeneSpringGX 7.3 (Agilent Technology, USA). The averages of normalized ratios were calculated by dividing the average of normalized signal channel intensity by the average of normalized control channel intensity. Functional annotation of genes was performed according to Gene OntologyTM Consortium (http://www.geneontology.org/index.shtml) by GeneSpringGX 7.3. Gene classification was based on searches done by BioCarta (http://www.biocarta.com/), GenMAPP (http://www.genmapp.org/), DAVID (http://david.abcc.ncifcrf.gov/), and Medline databases (http://www.ncbi.nlm.nih.gov/).

source_name: Human alveolar adenocarcinoma cells (A549), 48 h, 1% of total volume

label_protocol: Amplified and labeled cRNA was purified on cRNA Cleanup Module (Agilent Technology) according to the manufacturer’s protocol. Labeled cRNA target was quantified using ND-1000 spectrophotometer (NanoDrop Technologies, Inc., Wilmington, DE).

growth_protocol: The human alveolar epithelial cell line A549 was purchased from Korean Cell Line Bank (KCLB, Seoul, Korea) and was maintained under a humidified atmosphere of 5% CO2 and 95% air at 37°C. The culture medium was 90% Roswell Park Memorial Institute (RPMI) 1640 supplemented with 10% FBS, sodium bicarbonate (Sigma), sodium pyruvate (GIBCO), and penicillin and streptomycin (GIBCO). The culture medium was refreshed every 2 to 3 days.

extract_protocol: Total RNA was extracted from treated A549 cells using TRIzol reagent.

treatment_protocol: The cells were treated with each compounds at 1.0% of final solvent (DMSO) concentration in dish. The A549 cells were seeded at a density of 25 × 104 cells/mL for RNA extraction. After incubation for 24 h at 37°C, the cells were treated with each compounds for 48 h.

tag: cell line

value: Lung

tag: agent

value: heptanal


title: e8.5 neuroepithilium rep. 2


title: e8.5 neural crest rep. 4


title: A549 treated with nonanal_C9_1

description:
mRNA expression after 48 h in nonanal treated human cells
C9-IC20_1

value: nonanal


title: A549 treated with octanal_C8_2

description:
mRNA expression after 48 h in octanal treated human cells
C8-IC20_2

value: octanal


title: A549 treated with octanal_C8_3

description:
mRNA expression after 48 h in octanal treated human cells
C8-IC20_3


title: permanent ponds family 10 Öster Hällskär JB003-4227U

value: liver

value: constant water


title: A549 treated with nonanal_C9_3

description:
mRNA expression after 48 h in nonanal treated human cells
C9-IC20_3


title: A549 treated with octanal_C8_1

description:
mRNA expression after 48 h in octanal treated human cells
C8-IC20_1


title: A549 treated with nonanal_C9_2

description:
mRNA expression after 48 h in nonanal treated human cells
C9-IC20_2


title: Vehicle Treated 3

city: Cambridge

first: John

last: Keilty

state: Massachusetts

address: 780 Memorial Drive

department: Informatics

institute: Infinity Pharmaceuticals

description: mRNA Expression

hyb_protocol: Samples were hybridized  according to the manufacturer's instructions

scan_protocol: Slides were scanned on the Agilent G2505C DNA Microarray Scanner using standard settings

data_processing: The scanned images were analyzed with Agilent Feature Extraction Software using default parameters to obtain background subtracted values.   Non-uniform outliers were excluded.

source_name: Chondrosarcoma Tumor

label_protocol: Total RNA were labeled using the QuickPrime Labeling Kit (Agilent) according to the manufacturer's instructions.

extract_protocol: RNA was isolated from tumor tissue using the Ambion RNAqueous 4PCR kit

tag: gender

value: male


title: permanent ponds family 3 Öster Hällskär JB003-4204U

value: Gosner Stage 37


title: Vehicle Treated 4

description: mRNA Expression


title: Wild type_8.0 µg Fe / mL

source_name: RNA isolated from high iron grown WT H37Rv

value: high iron supplemented Proskauer & Beck medium


title: permanent ponds family 5 Öster Hällskär JB003-4319U


title: permanent ponds family 1 Stora Fjäderägg JB003-4231D

source_name: liver, decreasing water

value: decreasing water


title: WT+H2O2

city: Guangzhou

first: Chi Kwan

last: Tsang

address: Building #3, 613 Huangpu avenue west

department: Clinical Neuroscience Institute

country: China

institute: Jinan University

description: Gene expression data from early log phase of cells at OD = 0.4

hyb_protocol: Samples were prepared for hybridization to the Affymetrix Yeast Genome 2.0 arrays using the Affymetrix GeneChip Hybridization, Wash and Stain Kit. Modifications were made to the Affymetrix protocol using the cocktail assembly for Mini Arrays.  Samples were hybridized overnight in an Affymetrix GeneChip Hybridization Oven 640.

scan_protocol: Samples were then processed on the GeneChip Fluidics Station 450 and GeneChip Scanner 3000 7G.

data_processing: Data were analyzed with Genesifter software, Analysis Edition (Perkin Elmer) for background correction and GC-RMA was used as the normalization method.

label: Biotin

organism: Saccharomyces cerevisiae

source_name: Yeast wild type cells with H2O2 treatment

label_protocol: RNA samples were amplified and reverse-transcribed using the NuGEN Ovation Pico WTA System V2 with 50ng RNA according to the manufacturer’s protocol. The yield of resulting cDNA was measured on the Caliper LabChip DS, and product sizing was evaluated on the Bioanalyzer. 5µg of each sample was fragmented and labeled with the Nugen Encore Biotin Module following the manufacturer’s protocol.

growth_protocol: Cells were grown in yeast synthetic complete drop out (SC-Leu) medium at 30 °C on shaker to early log phase (OD600 ~0.4).

extract_protocol: Cells were resuspended in TES solution (10 mM Tris-HCl [pH 7.5], 10 mM EDTA, 0.5% SDS), and incubated with acidic phenol (pH 4.5; Sigma) for 1 hr at 65 °C. Samples were placed on ice for 10 min and centrifuged for 5 min at 13,000 rpm at 4 °C. Aqueous phases were extracted again with phenol and chloroform. RNA was precipitated in 100% ethanol for at least 2 h at -20 °C, centrifuged at 13,000 rpm for 15 min at 4°C, washed with 70% ethanol, and resuspended in water. Residual DNA was removed by DNase digestion using the RNase-Free DNase Set (Qiagen). RNA samples were further purified by RNeasy Kit (Qiagen).

treatment_protocol: Cells were treated with 0.4 mM H2O2 for 20 min.

tag: ploidy

value: Haploid


title: permanent ponds family 2 Öster Hällskär JB003-4158U


title: Vehicle Treated 2

description: mRNA Expression


title: Mutant+H2O2

description: Gene expression data from early log phase of cells

source_name: Yeast sod1Δ mutant with H2O2 treatment


title: A549 treated with heptanal_C7_2

description:
mRNA expression after 48 h in heptanal treated human cells
C7-IC20_2


title: WT-H2O2

source_name: Yeast wild type cells without H2O2 treatment


title: permanent ponds family 1 Öster Hällskär JB003-4192D


title: Prostate Cancer_MS 36D6

description: MS 36D6

source_name: malignant tissue_TMPRSS2:ERG fusion negative

value: Malignant prostate tissue

value: ERG fusion status:negative


title: e8.5 neural crest rep. 3

value: Neural crest


title: A549 treated with hexanal_C6_1

description:
mRNA expression after 48 h in hexanal treated human cells
C6-IC20_1

value: hexanal


title: A549 treated with heptanal_C7_1

description:
mRNA expression after 48 h in heptanal treated human cells
C7-IC20_1


title: Mutant-H2O2

source_name: Yeast sod1Δ mutant without H2O2 treatment


title: A549 treated with hexanal_C6_3

description:
mRNA expression after 48 h in hexanal treated human cells
C6-IC20_3


title: A549 treated with hexanal_C6_2

description:
mRNA expression after 48 h in hexanal treated human cells
C6-IC20_2


title: IPI-926 Treated 4

description: mRNA Expression

source_name: IPI-926 Chondrosarcoma Tumor


title: Vehicle Treated 1

description: mRNA Expression


title: IPI-926 Treated 3

description: mRNA Expression


title: A549 treated with pentanal_C5_2

description:
mRNA expression after 48 h in pentanal treated human cells
C5-IC20_2

value: pentanal


title: A549 treated with pentanal_C5_1

description:
mRNA expression after 48 h in pentanal treated human cells
C5-IC20_1


title: A549 treated with butanal_C4_3

description:
mRNA expression after 48 h in butanal treated human cells
C4-IC20_3

value: butanal


title: IPI-926 Treated 2

description: mRNA Expression


title: A549 treated with pentanal_C5_3

description:
mRNA expression after 48 h in pentanal treated human cells
C5-IC20_3

value: Lung


title: rdr6-15 biological replicate1

city: Cold Spring Harbor

first: Kate

middle: M

last: Creasey

state: NY

address: 1 Bungtown Road

department: Plant Sciences

institute: Cold Spring Harbor Laboratory

description: Expression data from Arabidopsis inflorescence

hyb_protocol: Hybridized for 16 hours at 45oC on GeneChip Arabidopsis Genome Array

scan_protocol: GeneChip scanned with the Affymetrix GeneChip Scanner 3000.

data_processing: RMA normalized data in the Sample data tables. Further processed data were derived from GeneSpring. 20 percentile to filter for low intensity and high saturated probes. P-value cut-off 0.05. Fold change cut-off log2.

organism: Arabidopsis thaliana

source_name: Arabidopsis stages 9 to 12 inflorescence

label_protocol: Biotynlated aRNA were prepared according to the standard ATH1 affymetrix protocol for 6 ug total RNA.

growth_protocol: Plants were grown under standard long day growth conditions.

extract_protocol: Total RNA was isolated from pooled inflorescence tissue (n = 3) and TRIzol (Invitrogen).

treatment_protocol: Inflorescence tissue isolated on dry ice.

value: plant inflorescence

tag: genotype/variation


title: A549 treated with butanal_C4_2

description:
mRNA expression after 48 h in butanal treated human cells
C4-IC20_2


title: IPI-926 Treated 1

description: mRNA Expression


title: A549 treated with propanal_C3_3

description:
mRNA expression after 48 h in propanal treated human cells
C3-IC20_3

value: propanal


title: ddm1-2 rdr6-15 biological replicate2


title: A549 treated with propanal_C3_2

description:
mRNA expression after 48 h in propanal treated human cells
C3-IC20_2


title: rdr6-15 biological replicate2


title: ddm1-2 rdr6-15 biological replicate1


title: Col-0 biological replicate2


title: ddm1-2 biological replicate1


title: A549 treated with butanal_C4_1

description:
mRNA expression after 48 h in butanal treated human cells
C4-IC20_1


title: A549 treated with DMSO_C-3_2 (control for C9)

description:
mRNA expression after 48 h in DMSO (vehicle control) treated human cells
C-3_2

value: DMSO (vehicle control)


title: Col-0 biological replicate1


title: ddm1-2 biological replicate2


title: A549 treated with propanal_C3_1

description:
mRNA expression after 48 h in propanal treated human cells
C3-IC20_1


title: A549 treated with DMSO_C-3_1 (control for C9)

description:
mRNA expression after 48 h in DMSO (vehicle control) treated human cells
C-3_1


title: A549 treated with DMSO_C-3_3 (control for C9)

description:
mRNA expression after 48 h in DMSO (vehicle control) treated human cells
C-3_3


title: A549 treated with DMSO_C-2_1 (control for C7, C8)

description:
mRNA expression after 48 h in DMSO (vehicle control) treated human cells
C-2_1


title: A549 treated with DMSO_C-1_1 (control for C3, C4, C5, C6)

description:
mRNA expression after 48 h in DMSO (vehicle control) treated human cells
C-1_1


title: A549 treated with DMSO_C-2_2 (control for C7, C8)

description:
mRNA expression after 48 h in DMSO (vehicle control) treated human cells
C-2_2


title: Pooled CD107neg Rep1

city: Singapore

first: Vivek

last: Tanavde

state: Singapore

address: 30 Biopolis Street, #07-01, Matrix

department: Genome and Gene Expression Data Analysis Division

country: Singapore

institute: Bioinformatics Institute, A*STAR, Singapore

description:
4290076073_E
Replicate 1

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Quantile normalized and chip batch effect removed using Partekmicroarray analysis software

source_name: NK cell

label_protocol: NK cells from individual or pooled donors sorted for CD107 were used. CD107+ & CD107- cells were used. See treatment protocol. The RNA was labeled using standard Illumina labeling protocol

growth_protocol: PBMCs were isolated from healthy donors and NK cells isolated using negative magnetic depletion following Miltenyi Biotech standard protocol

extract_protocol: Total RNA was extracted using Trizol reagent and sample amplification was performed using the Illumina® TotalPrep RNA amplification kit according to the manufacturer’s instructions.

treatment_protocol: NK cells were stimulated with K562 tumor cells for 4 hours in presence of brefeldin, then FACS sorted on CD107 surface expression using NK markers CD56+, CD3-.

value: adult

tag: status

value: healthy

tag: cell type

value: NK

tag: sort population

tag: donors

value: Pooled donors


title: A549 treated with DMSO_C-1_2 (control for C3, C4, C5, C6)

description:
mRNA expression after 48 h in DMSO (vehicle control) treated human cells
C-1_2


title: LNCap ERG-2

scan_protocol: Arrays were scanned with the GeneChip Scanner 3000 and GeneChip Operating Software acquired raw fluorescence signal.

data_processing: Scanned array images were analyzed by dChip and CEL file data were normalized using RMAexpress.

source_name: LNCap ERG

growth_protocol: Cells were grown in regular RMPI 10% culture medium.

extract_protocol: RNA extracted using Trizol.

treatment_protocol: LNCap-ERG and LNCap-Vector were seeded and cultured overnight before RNA extraction.

value: LNCap

value: human prostate tumor cells

tag: transfected with

value: LNCap Lentivirus ERG


title: A549 treated with DMSO_C-2_3 (control for C7, C8)

description:
mRNA expression after 48 h in DMSO (vehicle control) treated human cells
C-2_3

tag: tissue


title: Pooled CD107neg Rep2

description:
4290076073_F
Replicate 2


title: Donor1 CD107neg Rep3

description:
4403835009_C
Replicate 3

value: Single donor


title: Pooled CD107pos Rep2

description:
4403835009_D
Replicate 2


title: U937_GFP

status: Public on Mar 17 2014

city: Suzhou

first: Chun

last: Zhang

institute: Suzhou Institute of Biomedical Engineering and Technology, Chinise Academy of Sciences

hyb_protocol: Hybridized on the specific miRCURY™ LNA Array (v.18.0, Exiqon, Denmark) platform.

scan_protocol: Images on the chip were scanned using an Axon GenePix 4000B microarray scanner (Axon Instruments, Foster City, CA, USA) and imported into GenePix Pro 6.0 software (Axon) for grid alignment and data extraction

data_processing: MiRNAs with intensities >50 were used to calculate the normalization factor. Expression data were normalized using the median normalization. After normalization, average values of replicate spots of each miRNA were used for statistical analysis; differentially expressed miRNAs were identified through fold change filtering.

label_protocol: labeled using the miRCURY™ Hy3™/Hy5™ Power labeling kit

growth_protocol: The U937 cells were cultured in RPMI1640 medium (Gibco, Grand Island, NY, USA) containing 10% fetal bovine serum under 5% CO2 at 37 °C, infected with viral IDLVs stock at 5:1 multiplicity of infection (MOI), refreshed with medium 6 h later and incubated for 64 h.

extract_protocol: total RNAs were purified using TRIzol and a miRNeasy mini kit.

treatment_protocol: After 64 h, the cells were collected,  mixed with TRIzol (1 ml) and frozen at －80°C until RNA were extracted

value: macrophages

value: expressing expressing GFP protein (control)


title: A549 treated with DMSO_C-1_3 (control for C3, C4, C5, C6)

description:
mRNA expression after 48 h in DMSO (vehicle control) treated human cells
C-1_3


title: Donor1 CD107neg Rep1

description:
4290076073_C
Replicate 1


title: Pooled CD107pos Rep3

description:
4403835009_E
Replicate 3


title: LNCap Vector-2

source_name: LNCap Vector

value: LNCap Lentivirus Vector


title: Donor1 CD107neg Rep2

description:
4403835009_B
Replicate 2


title: polygamy female virgin 3

city: Columbia

first: Brian

last: Hollis

state: SC

address: 715 Sumter Street

department: Department of Biological Sciences

institute: University of South Carolina

description: RMA processed expression values in pair files

hyb_protocol: Hybridization was performed by Florida State University NimbleGen Systems Inc. approved facility following their standard protocol [www.nimblegen.com]

scan_protocol: Scanning was performed by Florida State University NimbleGen Systems Inc. approved facility following their standard protocol [www.nimblegen.com]

data_processing: The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.4.27 (Roche NimbleGen, Inc.).

organism: Drosophila melanogaster

source_name: whole fly, polygamous, female, virgin

label_protocol: Labeling was performed by Florida State University NimbleGen Systems Inc. approved facility following their standard protocol [www.nimblegen.com]

growth_protocol: standard cornmeal medium

extract_protocol: Total RNA extracted with Molecular Research Center RNAzol [http://www.mrcgene.com/] by their standard protocol

treatment_protocol: Six independent, experimentally-evolved populations experiencing 65 generations of monogamy (3 populations) or polygamy (3 populations)

tag: subject

value: female

tag: mating status

value: virgin

value: polygamous virgin

value: whole organism

tag: genetic background

value: IV


title: monogamy female virgin 3

source_name: whole fly, monogamous, female, virgin

tag: treatment

value: monogamous virgin


title: Donor1 CD107pos Rep1

description:
4290076073_A
Replicate 1

tag: developmental stage

value: adult


title: polygamy female virgin 1


title: LNCap Vector-1


title: U937_Hsp16.3

value: expressing Mycobacterium tuberculosis Hsp16.3 and GFP


title: polygamy female virgin 2


title: Pooled CD107pos Rep1

description:
4290076073_D
Replicate 1

value: healthy

value: NK


title: polygamy male virgin 2

source_name: whole fly, polygamous, male, virgin

value: male


title: LNCap ERG-1

value: LNCap

value: human prostate tumor cells


title: Donor1 CD107pos Rep2

description:
4290076073_B
Replicate 2

value: Single donor


title: polygamy male virgin 3


title: monogamy male virgin 2

source_name: whole fly, monogamous, male, virgin


title: H5-DM3

city: Dallas

first: Damien

last: Chaussabel

state: TX

address: 3434 Live Oak

institute: Baylor Institute for Immunology Research

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Arrays were scanned using the Illumina HiScan and the standard Illumina scanning protocol.

data_processing: The data were preprocessed using R, which included the following steps: quantile normalization, flooring all intensities <10 to 10, log2 transformation, and PALO (present at least once) filter. PALO, which selects only transcripts with detection p-values < 0.01 in at least one sample, was performed to reduce background noise.

source_name: neutrophils

label_protocol: Standard Illumina labeling protocol.

extract_protocol: RNA was extracted using the QIAGEN MicroRNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with the Agilent Bioanalyser.

tag: experiment

value: III

tag: activators

value: Uninfected plasma

tag: sample id

tag: age (years)

value: Female

tag: bacterial identification

tag: day of blood collection

tag: severity

value: neutrophila


title: H5-DM9

tag: gender

tag: cell type


title: Pooled CD107neg Rep3

description:
4403835009_F
Replicate 3

tag: status

tag: sort population

tag: donors

value: Pooled donors


title: monogamy male virgin 3

tag: subject

value: virgin

tag: tissue


title: H5-DM5

value: Male


title: H5-DM7


title: Donor1 CD107pos Rep3

description:
4403835009_A
Replicate 3


title: H5-HC1


title: monogamy female virgin 1

value: female

tag: mating status

value: whole organism

tag: genetic background

value: IV


title: H5-HC9


title: H5-DM10


title: polygamy male virgin 1

tag: treatment

value: polygamous virgin


title: ES H3K9ac ChIP replicate 1

type: genomic

city: Basel

first: Fabio

last: Mohn

address: Maulbeerstrasse 66

country: Switzerland

institute: Friedrich Miescher Institute for Biomedical Research

hyb_protocol: According to Nimblegen standard guidelines for HD2.1 oligonucleotide tiling arrays

data_processing:
Arrays were processed using Nimblegen's standard protocol for Nimblescan 2.4 ChIP data extraction
median normalized, scaled, log2 (ChIP/Input) ratio. Calculated using the R Limma package

molecule: genomic DNA

source_name: H3K9ac ChIP DNA from mouse ES cells

growth_protocol: embryonic stem cells were cultured as described previously (Bibel et al, Nat Neuroscience, 2007)

extract_protocol: ChIP experiments were performed as described before (F. Mohn et al., Mol Cell 30, 755 (Jun 20, 2008)), starting with 70 µg of chromatin and 5 µg of specific antibodies. The material was amplified using whole genome amplification kit (Sigma) before labeling for hybridization.

treatment_protocol: ChIP experiments were performed as described before (Mohn et al, Mol Cell, 2008), starting with 70 µg of chromatin and 5 µg of specific antibodies. The material was amplified using whole genome amplification kit (Sigma) before labeling for hybridization.

tag: genotype/variation

value: wildtype

value: embryonic stem cells

tag: strain

tag: chip antibody

value: anti-H3K9ac (Abcam ab4441)

source_name: Genomic input DNA from mouse ES cells

value: none (input control)


title: monogamy male virgin 1

value: male

value: monogamous virgin


title: H5-HC2

tag: experiment

value: III

tag: activators

tag: sample id

tag: age (years)


title: H5-DM6

value: Uninfected plasma

tag: gender

tag: bacterial identification

tag: day of blood collection

tag: severity


title: H5-Bp25

tag: donors

value: Septic plasma

value: Female

value: Burkholderia pseudomallei

value: Severe

tag: cell type


title: H5-DM1

value: neutrophila


title: H5-Ot21

value: Staphylococcus aureus

value: Non-severe


title: H5-HC5

value: Male


title: monogamy female virgin 2

tag: subject

value: female

value: virgin

tag: tissue

value: whole organism

value: IV


title: H5-DM8


title: ES H3K64ac ChIP replicate 2

scan_protocol: According to Nimblegen standard guidelines for HD2.1 oligonucleotide tiling arrays

source_name: H3K64ac ChIP DNA from mouse ES cells

value: wildtype

value: embryonic stem cells

value: anti-H3K64ac (Active Motif, cat. no. 39-545, lot 32908001; described in Di Cerbo et al., eLife 2014)

value: none (input control)


title: H5-HC8

value: III

value: Uninfected plasma


title: H5-Ot32

value: Septic plasma

value: Female

value: Escherichia coli


title: H5-Bp16

value: Burkholderia pseudomallei

value: Severe

value: neutrophila


title: H5-HC3

value: Male


title: H5-DM4


title: H5-Bp36

value: Non-severe


title: H5-HC6


title: H5-Ot58

value: Acinetobacter baumannii


title: H5-DM2


title: H5-Ot1

value: Acinetobactor baumannii


title: H5-Ot18

value: Klebsiella pneumoniae


title: H5-Bp6


title: H5-Bp35


title: H5-HC4


title: H5-Bp2


title: H5-HC7


title: H5-Ot48

value: Acinetobacter Iwoffii


title: H5-Bp27


title: H5-Bp4


title: H5-Ot5

value: Escherichia coli (ESBL)


title: H5-Ot16


title: H5-Bp29


title: H5-Ot38


title: H5-Bp32


title: ES H3K64ac ChIP replicate 1

label_protocol: According to Nimblegen standard guidelines for HD2.1 oligonucleotide tiling arrays

value: wildtype

value: embryonic stem cells

value: anti-H3K64ac (Active Motif, cat. no. 39-545, lot 32908001; described in Di Cerbo et al., eLife 2014)


title: H5-Bp3

value: III


title: H5-Ot30

value: Septic plasma

value: Viridans Streptococci


title: H5-Ot45

value: Staphylococcus aureus


title: H5-Bp9

value: Burkholderia pseudomallei


title: H5-Ot20

value: Enterococus spp.


title: H5-Ot7

value: Female

value: Candida albicans

value: Severe

value: neutrophila


title: H5-Ot27

value: Klebsiella spp.

value: Non-severe


title: H5-Ot52

value: Citrobacter freundii


title: H5-Ot2

value: Male

value: Salmonella spp. (serotype B)


title: H5-Med1

value: Medium alone


title: H3-HC23

value: II

value: Uninfected plasma

value: neutrophil


title: H3-HC10


title: H3-HC11


title: H5-Bp23

value: III

value: Septic plasma


title: H5-Ot53

value: Staphylococcus aureus


title: H3-HC7


title: H3-HC25


title: H3-HC20


title: H3-HC8


title: H5-Bp1

value: Burkholderia pseudomallei


title: H5-Ot10


title: H3-HC15

value: Female


title: H3-HC13


title: H3-HC21


title: H5-Med2


title: H3-Ot7


title: H3-Ot18

value: Enterococcus spp.


title: H5-Bp39

value: Severe


title: H5-Ot49

value: Acinetobacter baumannii

value: neutrophila


title: H3-HC14


title: H5-Ot8

value: Corynbacterium spp.


title: H3-Ot19

value: Klebsiella pneumoniae


title: H3-BP8

value: Male

value: Non-severe


title: H3-HC12


title: H3-HC18


title: H3-HC22


title: H3-Ot11

value: Enterobacter cloacae


title: H3-HC17

value: II


title: H3-HC24

value: Uninfected plasma


title: H3-BP10

value: neutrophil


title: H3-BP17


title: H3-Ot26

value: Escherichia coli


title: H3-BP26

value: Septic plasma


title: H3-BP20


title: H3-BP9


title: H3-BP22


title: H3-Ot8

value: Citrobacter freundii


title: H3-BP14

value: Burkholderia pseudomallei


title: H3-BP19


title: H3-Ot15

value: Sphingobacterium spp.

value: Non-severe**


title: H3-Ot22

value: Staphylococcus aureus

value: Severe


title: H3-BP24


title: H3-BP25


title: H3-BP11


title: H3-Ot12

value: Female

value: Streptococcus pyrogenes


title: H3-Med2

value: Medium alone


title: H3-BP7

value: Male


title: H3-Ot9

value: Sphingomonas spp.


title: H3-Ot20


title: H3-Ot24


title: H3-Ot13


title: H3-BP12


title: H3-Ot10

value: Non-severe


title: H3-Med1

value: II


title: H3-BP13


title: H1-PMN-HC2

value: I

value: Uninfected plasma


title: H2-PMN-Ot2

value: Streptococcus pnumoniae

value: neutrophil


title: H3-LPS1

value: LPS


title: H2-PMN-Ot5

value: Septic plasma

value: Pseudomonas aeruginosa


title: H1-PMN-Ot5


title: H1-PMN-HC3


title: H2-PMN-Ot4

value: Klebsiella pneumoniae


title: H1-PMN-Ot2


title: H2-PMN-Bp3

value: Burkholderia pseudomallei


title: H2-PMN-HC3


title: H1-PMN-HC6


title: H2-PMN-Bp4

value: Severe


title: H2-PMN-Ot1


title: H2-PMN-HC5


title: pob3-7, biological rep. 3

city: Seville

first: Andrés

last: Aguilera

address: Av. Américo Vespucio 24

department: Genome BIology

country: Spain

institute: CABIMER, Universidad de Sevilla

description: Asynchronous cultures exponentially growing in YEPD 4 h after a 26-to-30ºC temperature shift

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip® Yeast Genome 2.0 Array. GeneChips were washed and stained in the GeneChip® Fluidics Station 450 according to GeneChip® Expression AnalysisTechnical Manual, Affymetrix, 2004.

scan_protocol: Microarrays were scanned using GeneChip® Scanner 3000 7G

data_processing: The data were normalized by RMA (Robust Microarray Average) to allow direct comparison between expression values in different experiments. Statistical analysis was performed by LIMMA (Linear Models for Microarray Analysis) using the program affylmGUI. Genes showing at least 2-fold expression change compared to wild-type strain with a p-value FDR < 0.01, were considered as altered. Expression values were obtained with the anti-log of RMA values.

source_name: Mutant pob3-7

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA One-Cycle Target Labeling Assays (GeneChip® Expression AnalysisTechnical Manual, Affymetrix, 2004).

growth_protocol: Each strain was grown to mid-log phase in liquid YPAD medium at 26 ºC and shifed to 30°C during 4 hours

extract_protocol: Total RNA were isolated with the RNeasy Midi kit (QIAGEN)

tag: genotype


title: H2-PMN-Bp1


title: H1-PMN-LPS1


title: H2-PMN-Bp2


title: H1-PMN-Bp3


title: H1-PMN-Bp4


title: H2-PMN-HC1


title: H2-PMN-HC2


title: H1-PMN-Bp1


title: pob3-7, biological rep. 2


title: pob3-7, biological rep. 1


title: spt16-11, biological rep. 3

source_name: Mutant spt16-11


title: H1-PMN-HC5


title: H1-PMN-Ot4

value: Female


title: spt16-11, biological rep. 2


title: spt16-11, biological rep. 1


title: H1-PMN-HC4


title: WT, biological rep. 3

source_name: Wild type W303-1ARb


title: H1-PMN-Bp2


title: WT, biological rep. 2


title: H1-PMN-Bp6


title: WT, biological rep. 1


title: H2-PMN-LPS1


title: H2-PMN-HC4


title: H1-PMN-Ot1


title: H2-PMN-M1


title: H1-PMN-Ot6

value: Escherichia coli (ESBL)


title: H1-PMN-M1

value: Medium alone


title: Liver_Wildtype_PFNA Vehicle_Rep3

city: Research Triangle Park

first: Mitch

last: Rosen

state: NC

address: MD 72

institute: U.S. EPA

hyb_protocol: Standard Affymetrix procedures

scan_protocol: Standard Affymetrix procedures

data_processing: Normalized expression of probe level data was calculated using the Robust Multiarray Average function (RMA) implemented in Bioconductor's affy-package

source_name: Liver

label_protocol: Standard Affymetrix procedures

growth_protocol: PPARα-null (Null) mice (129S4/SvJae-PPARαtm1Gonz/J, stock #003580) and wild-type (WT) mice (129S1/SvlmJ, stock #002448) were purchased from The Jackson Laboratory (Bar Harbor, ME) and maintained as an inbred colony on the 129/Sv background at the U.S. EPA, Research Triangle Park, NC.  Animals were housed 4 per cage and allowed to acclimate for a period of one week prior to the conduct of the study.  Food and municipal tap water were provided ad libitum.  Animal facilities were controlled for temperature (20-24°C), relative humidity (40-60%), and kept under a 12 hr light-dark cycle.

extract_protocol: Total RNA was extracted and transcribed to cDNA

treatment_protocol: At the end of the dosing period, animals were euthanized by CO2 asphyxiation and tissue collected from the left lobe of the liver for preparation of total RNA.  Livers were removed 24-hrs after the last dose and were rapidly snap-frozen in liquid nitrogen and stored at -70°C until analysis.

value: Wildtype

tag: Sex

value: Male

tag: age

value: 6-9 months

tag: genetic background

tag: compound

value: Vehicle

tag: route

value: Gavage

tag: dose

value: 0 mg/kg, 7 days

value: liver


title: H2-PMN-Bp6

tag: experiment

value: I

tag: activators

tag: sample id

value: neutrophil


title: H2-PMN-Ot3

value: Septic plasma

tag: age (years)

tag: gender

tag: bacterial identification

value: Enterococus faecium


title: H2-PMN-Ot6

tag: donors

tag: day of blood collection

tag: severity


title: Liver_Wildtype_PFNA Vehicle_Rep2

tag: tissue


title: H1-PMN-HC1

value: Uninfected plasma

tag: cell type


title: H2-PMN-HC6


title: Liver_Wildtype_PFNA Vehicle_Rep1

tag: genotype

tag: Sex


title: Liver_Wildtype_PFNA_3 mg/kg_Rep1

tag: age

tag: genetic background

value: PFNA

value: 3 mg/kg, 7 days


title: Liver_Wildtype_PFNA_3 mg/kg_Rep3

tag: compound

tag: route


title: Liver_Wildtype_PFNA_3 mg/kg_Rep2

tag: dose


title: Liver_Wildtype_PFNA Vehicle_Rep4


title: H1-PBMC-Bp5

source_name: PBMC

tag: experiment

tag: activators

value: Burkholderia pseudomallei

value: Non-severe

value: PBMC


title: Liver_Wildtype_PFNA_3 mg/kg_Rep4

value: Wildtype


title: H2-PBMC-HC2

tag: sample id

tag: age (years)

value: Male


title: H3-HC16

value: II

tag: gender

value: Female

tag: bacterial identification


title: H1-PMN-Ot3

tag: donors

tag: day of blood collection

value: Severe


title: Liver_Wildtype_PFNA_1 mg/kg_Rep2

value: 6-9 months

value: Gavage

value: 1 mg/kg, 7 days

tag: tissue


title: Liver_Wildtype_PFNA_1 mg/kg_Rep3

value: liver


title: Liver_Wildtype_PFNA_1 mg/kg_Rep1


title: Liver_PPARα Knockout_PFNA Vehicle_Rep2

value: PPARα-null

value: Vehicle

value: 0 mg/kg, 7 days


title: Liver_PPARα Knockout_PFNA Vehicle_Rep3


title: H1-PBMC-Bp2

value: I

value: Septic plasma

tag: severity

tag: cell type


title: Liver_PPARα Knockout_PFNA Vehicle_Rep4

tag: genotype

tag: Sex


title: Liver_PPARα Knockout_PFNA Vehicle_Rep1

tag: age

tag: genetic background


title: H2-PBMC-HC5

value: Uninfected plasma


title: H1-PBMC-Ot4

value: Klebsiella pneumoniae


title: H1-PBMC-Bp4

value: Burkholderia pseudomallei

value: PBMC


title: H2-PBMC-Bp3

value: Male


title: Liver_PPARα Knockout_PFNA_3 mg/kg_Rep4

tag: compound

value: PFNA

tag: route

value: 3 mg/kg, 7 days


title: Liver_PPARα Knockout_PFNA_3 mg/kg_Rep3

tag: dose


title: H1-PBMC-Bp1

tag: experiment

tag: activators

value: Severe


title: Liver_PPARα Knockout_PFNA_3 mg/kg_Rep2

value: 6-9 months


title: H1-PBMC-HC2

tag: sample id

tag: age (years)


title: H2-PBMC-Ot3

tag: gender

value: Female

tag: bacterial identification

value: Enterococus faecium


title: H1-PBMC-HC1

tag: donors

tag: day of blood collection


title: H1-PBMC-Ot1

value: Streptococcus pnumoniae

tag: severity


title: H2-PBMC-M1

value: Medium alone

tag: cell type


title: Liver_PPARα Knockout_PFNA_1 mg/kg_Rep4

tag: genotype

value: PPARα-null

value: Gavage

value: 1 mg/kg, 7 days

tag: tissue

value: liver


title: Liver_PPARα Knockout_PFNA_3 mg/kg_Rep1

tag: Sex

tag: age


title: H2-PBMC-Ot5

value: I

value: Septic plasma

value: Pseudomonas aeruginosa


title: Liver_PPARα Knockout_PFNA_1 mg/kg_Rep3

tag: genetic background

tag: compound


title: Liver_PPARα Knockout_PFNA_1 mg/kg_Rep1

tag: route

tag: dose


title: H2-PBMC-HC1

tag: experiment

tag: activators

value: Uninfected plasma

value: PBMC


title: H1-PBMC-M1

tag: sample id

tag: age (years)


title: H1-PBMC-HC4

tag: gender

tag: bacterial identification


title: H1-PBMC-HC5

tag: donors

value: Male

tag: day of blood collection


title: H2-PBMC-Ot6

value: Escherichia coli (ESBL)

tag: severity

tag: cell type


title: H2-PBMC-Bp1

value: Burkholderia pseudomallei

value: Severe


title: Liver_Wildtype_PFHxS_10 mg/kg_Rep4

tag: genotype

value: Wildtype

value: 6-9 months

value: PFHxS

value: 10 mg/kg, 7 days

tag: tissue


title: Liver_Wildtype_PFHxS_3 mg/kg_Rep3

tag: Sex

tag: age

value: 3 mg/kg, 7 days


title: H1-PBMC-Bp6


title: Liver_Wildtype_PFHxS_10 mg/kg_Rep2

tag: genetic background

tag: compound

value: Gavage


title: H2-PBMC-Bp6


title: Liver_Wildtype_PFHxS_3 mg/kg_Rep2

tag: route

tag: dose


title: Liver_Wildtype_PFHxS_10 mg/kg_Rep3


title: Liver_Wildtype_PFHxS_10 mg/kg_Rep1


title: Liver_Wildtype_PFHxS_3 mg/kg_Rep4


title: H1-PBMC-HC3

tag: experiment

tag: activators

value: Female


title: H2-PBMC-Ot1

tag: sample id

tag: age (years)

value: Streptococcus pnumoniae


title: Liver_Wildtype_PFHxS_3 mg/kg_Rep1

value: liver


title: H2-PBMC-LPS1

value: I

value: LPS

tag: gender

tag: bacterial identification


title: H2-PBMC-HC4

tag: donors

value: Uninfected plasma

tag: day of blood collection


title: H1-PBMC-Ot6

value: Septic plasma

tag: severity

tag: cell type

value: PBMC


title: Liver_Wildtype_PFHxS Vehicle_Rep2

tag: genotype

value: Male

value: Vehicle

value: 0 mg/kg, 7 days

tag: tissue


title: Liver_PPARα Knockout_PFHxS_3 mg/kg_Rep4

value: PPARα-null

tag: Sex

tag: age


title: H2-PBMC-Ot4

value: Klebsiella pneumoniae

value: Severe


title: H1-PBMC-LPS1


title: Liver_PPARα Knockout_PFHxS_3 mg/kg_Rep3

value: 6-9 months

tag: genetic background

tag: compound

value: PFHxS


title: H1-PBMC-Ot3

value: Enterococus faecium


title: Liver_Wildtype_PFHxS Vehicle_Rep1

value: Wildtype

tag: route

value: Gavage

tag: dose


title: Liver_Wildtype_PFHxS Vehicle_Rep4

value: liver


title: H2-PBMC-Bp5

tag: experiment

value: I

tag: activators

value: Burkholderia pseudomallei

value: Non-severe


title: Liver_Wildtype_PFHxS Vehicle_Rep3


title: H1-PBMC-Ot5

value: Septic plasma

tag: sample id

tag: age (years)

value: Female

value: Pseudomonas aeruginosa


title: Liver_PPARα Knockout_PFHxS_10 mg/kg_Rep4

value: Male

value: 10 mg/kg, 7 days


title: Liver_PPARα Knockout_PFHxS_3 mg/kg_Rep2

value: PPARα-null

value: 3 mg/kg, 7 days


title: H2-PBMC-HC6

value: Uninfected plasma

tag: gender

tag: bacterial identification

value: PBMC


title: Liver_PPARα Knockout_PFHxS_10 mg/kg_Rep3

value: 6-9 months

value: PFHxS


title: H1-PBMC-Bp3

tag: donors

tag: day of blood collection

value: Severe


title: H2-PMN-Bp5

tag: severity

tag: cell type

value: neutrophil


title: H1-PMN-Bp5


title: H2-PBMC-HC3


title: H1-PBMC-Ot2

value: Streptococcus pnumoniae


title: Liver_PPARα Knockout_PFHxS_10 mg/kg_Rep1

tag: genotype

value: Gavage

tag: tissue

value: liver


title: Liver_PPARα Knockout_PFHxS_3 mg/kg_Rep1

tag: Sex

tag: age


title: Liver_PPARα Knockout_PFHxS_10 mg/kg_Rep2

tag: genetic background

tag: compound


title: H1-PBMC-HC6

value: I


title: H2-PBMC-Bp4

value: Septic plasma

value: Burkholderia pseudomallei


title: Liver_PPARα Knockout_PFHxS Vehicle_Rep4

value: Vehicle

tag: route

tag: dose

value: 0 mg/kg, 7 days


title: Liver_PPARα Knockout_PFHxS Vehicle_Rep3

value: Male


title: H2-PBMC-Bp2

tag: experiment

tag: activators


title: H1-DC-HC6

source_name: dendritic cells

tag: sample id

tag: age (years)

value: dendritic cells


title: H2-DC-HC6

tag: gender

tag: bacterial identification


title: H2-PBMC-Ot2

tag: donors

value: Female

tag: day of blood collection


title: Liver_PPARα Knockout_PFHxS Vehicle_Rep2

value: PPARα-null


title: H2-DC-HC5

value: Uninfected plasma

tag: severity

tag: cell type


title: H1-DC-HC4


title: Liver_RC23_72hr_DEHP_Rep2

city: Bracknell

first: Richard

last: Currie

address: Jealotts Hill

country: United Kingdom

institute: Syngenta International Research Centre

source_name: DEHP, B6C3F1, liver, 72 hours

growth_protocol: B6C3F1 male mice (7–10 weeks old on arrival) were obtained from Harlan Olac Ltd. (Bicester, UK). Upon arrival at the laboratory, all animals were allowed at least 5 days to acclimatize. Animals were housed at up to 5/cage and received RM1 (Rat and Mouse No 1; Special Diet Services Ltd., Witham, UK) and water ad libitum.

treatment_protocol: Mice were killed by an overdose of anesthetic (Halothane Ph.Eur. vapor) followed by exsanguination via cardiac puncture. The tissue samples for RNA analysis were collected in RNase-free tubes prior to being snap frozen in liquid nitrogen and stored at −70°C.

tag: strain

tag: tissue

value: Liver

value: DEHP

value: Oral gavage

value: 1150 mg/kg/day

tag: time

value: 72 hours


title: H2-DC-HC1


title: H2-DC-HC3


title: H2-DC-HC4


title: Liver_PPARα Knockout_PFHxS Vehicle_Rep1

tag: genotype

tag: Sex

tag: age

value: 6-9 months

tag: genetic background

value: Gavage


title: Liver_RC24_72hr_DEHP_Rep3

tag: compound

tag: route

tag: dose


title: H1-DC-Ot5

tag: experiment

value: I

tag: activators

tag: sample id

tag: age (years)

value: Pseudomonas aeruginosa

value: Severe


title: H1-DC-HC3

tag: donors

tag: gender

tag: bacterial identification

tag: day of blood collection


title: Liver_RC7_72hr_Corn oil_Rep1

source_name: B6C3F1, liver, 72 hours

tag: strain

tag: tissue

value: Corn oil

value: 0 mg/kg/day


title: Liver_RC8_72hr_DEHP_Rep1

value: Male

tag: time


title: Liver_RC22_72hr_Corn oil_Rep3

tag: Sex


title: H1-DC-HC5

tag: severity

tag: cell type

value: dendritic cells


title: H1-DC-HC2


title: H2-DC-Ot6

value: Septic plasma

value: Female

value: Escherichia coli (ESBL)


title: Liver_RC21_72hr_Corn oil_Rep2

value: Liver

tag: compound


title: Liver_RC20_24hr_DEHP_Rep3

source_name: DEHP, B6C3F1, liver, 24 hours

value: DEHP

tag: route

value: 24 hours


title: H2-DC-HC2

value: Uninfected plasma


title: H1-DC-HC1


title: H1-DC-Bp4

value: Burkholderia pseudomallei


title: Liver_RC19_24hr_DEHP_Rep2

value: Oral gavage

tag: dose


title: H1-DC-Bp1

tag: experiment


title: H2-DC-Bp3

tag: activators


title: H1-DC-Bp6

tag: sample id


title: H1-DC-Ot1

tag: age (years)

value: Streptococcus pnumoniae


title: Liver_RC17_24hr_Corn oil_Rep2

source_name: B6C3F1, liver, 24 hours

value: 0 mg/kg


title: Liver_RC18_24hr_Corn oil_Rep3


title: H2-DC-Bp5

value: I

tag: donors

value: Non-severe


title: H2-DC-Ot2

tag: gender

value: Severe


title: H2-DC-Ot5

tag: bacterial identification

value: Pseudomonas aeruginosa


title: Liver_RC6_24hr_DEHP_Rep1

value: Male


title: Liver_PPARα Knockout_PFNA_1 mg/kg_Rep2

tag: genotype

value: PPARα-null

tag: age

value: 6-9 months

tag: genetic background

value: PFNA

value: Gavage

value: 1 mg/kg, 7 days

value: liver


title: H2-DC-Ot3

value: Septic plasma

value: Female

value: Enterococus faecium

tag: day of blood collection

value: dendritic cells


title: H1-DC-Bp5

value: Burkholderia pseudomallei


title: H2-DC-Ot1

value: Streptococcus pnumoniae


title: H1-DC-Bp2

value: I


title: Liver_RC14_8hr_DEHP_Rep2

source_name: DEHP, B6C3F1, liver, 8 hours

tag: strain

tag: tissue

value: Liver

tag: Sex

value: DEHP

value: Oral gavage

tag: time

value: 8 hours


title: H1-DC-Ot3

tag: severity

value: Severe

tag: cell type


title: H2-DC-Bp1

tag: experiment

value: Male


title: Liver_RC4_8hr_DEHP_Rep1

tag: compound

tag: route

tag: dose


title: H1-DC-Ot2

tag: donors

tag: activators

tag: sample id

tag: age (years)


title: Liver_RC15_8hr_DEHP_Rep3


title: H1-DC-Bp3

tag: gender

tag: bacterial identification


title: Liver_RC5_24hr_Corn oil_Rep1

value: Corn oil

value: 0 mg/kg

value: 24 hours


title: H2-DC-Bp4

tag: day of blood collection


title: Liver_RC14_8hr_Corn oil_Rep3

source_name: B6C3F1, liver, 8 hours

tag: strain


title: Liver_RC13_8hr_Corn oil_Rep2

tag: tissue


title: H2-DC-Ot4

value: Klebsiella pneumoniae


title: Rrm3-Flag-spt16-td

description: Asynchronous cultures exponentially growing in YPGal without CuSO4 75 m after a 26-to-37ºC temperature and 2% rafinose-to-2% galactose containing medium shift.

hyb_protocol: Approximately 10 μg of DNA was hybridzed per array using the Affymetrix hybridization kit. The arrays were hybridized for 16 hours at 45° at 60 rpm using an Affymetrix hybridization oven. The probe was removed from these arrays and reused to hybridize the remaining three arrays.

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

data_processing:
Primary data analyses were carried out using the Affymetrix TAS 1.1.02 software to obtain hybridization intensity, signal log2 ratio value and change P-value for each locus. For the discrimination of positive and negative signals for the binding, we compared the chromatin-immunprecipitated fraction with the supernatant fraction by using two criteria. First, the reliability of binding ratio was judged by change P-value (P ≤ 0.01). Second, clusters consisting of at least twenty-five contiguous probe-sets (max. gap 250bp, min run. 100bp) that filled the above criterion were selected.
Locus identification, raw signal intensity, detection signal log ratio, and change p-value was obtained using the Affymetrix TAS 1.1.02 software.

source_name: Rrm3-Flag ChIP DNA from WSDR-8C, asynchronous culture

label_protocol: Chromatin-immunprecipitated DNA was purified and amplified by random priming as described (Katou et al. 2003): A total of 10 μg of amplified DNA was digested with DNaseI to a mean size of 100 bp and purified, and the fragments were end-labeled with biotin-N6-ddATP.

growth_protocol: Yeast WRBb-9B, WSRBb-2D and WPRBb-10D cells were grown in YEPD to mid-log phase at 30°C. Yeast WDRB-18A and WSDR-8C were grown in 2% rafinose containing medium to mid-log phase at 26ºC and shifed to YPGal medium at 37ºC during 75 minutes.

extract_protocol: ChIP was carried out as previously described (Katou et al. 2003, 2006): We disrupted 1.5 × 107  cells by Multi-beads shocker (MB400U, Yasui Kikai) using glass beads. Anti-FLAG monoclonal antibody M2 (Sigma-Aldrich) was used for ChIP.

tag: chip antibody

value: anti-Flag

tag: genotype

value: MATa ade2-1 ura3-1  leu2-3,112  his3-11,15 can1-100 RRM3-FLAG::KAN ubr1Δ::GAL-UBR1::HIS3 spt16-td

tag: cell cycle stage

value: asynchronous

source_name: Input DNA from WSDR-8C, asynchronous culture

value: supernatant


title: H2-DC-Bp2

value: Septic plasma

value: Burkholderia pseudomallei

tag: severity

tag: cell type

value: dendritic cells


title: Liver_RC12_2hr_DEHP_Rep3

source_name: DEHP, B6C3F1, liver, 2 hours

value: Liver

tag: Sex

tag: compound

tag: time

value: 2 hours


title: H1-DC-Ot4

tag: experiment

value: I

tag: donors

value: Female


title: Rrm3-Flag-WT-td

source_name: Rrm3-Flag ChIP DNA from WDRB-18A, asynchronous culture

value: MATa ade2-1 ura3-1  leu2-3,112  his3-11,15 can1-100 RRM3-FLAG::KAN ura3::URA3/GPD-TK (7x) ubr1Δ::GAL-UBR1::HIS3

source_name: Input DNA fromWDRB-18A, asynchronous culture


title: Rrm3-Flag-pob3-7

source_name: Rrm3-Flag ChIP DNA from WPRBb-10D, asynchronous culture

value: MATa ade2-1 ura3-1  leu2-3,112  his3-11,15 can1-100 bar1∆ RRM3-FLAG::KAN ura3::URA3/GPD-TK (7x) pob3-7

source_name: Input DNA fromWPRBb-10D, asynchronous culture


title: H1-DC-Ot6

tag: activators

tag: sample id

value: Escherichia coli (ESBL)

value: Severe


title: Liver_RC3_8hr_Corn oil_Rep1

value: Male

value: Corn oil

tag: route

value: Oral gavage

tag: dose

value: 0 mg/kg

value: 8 hours


title: Rrm3-Flag-WT

description: Asynchronous cultures exponentially growing in YEPD at 30ºC

source_name: Rrm3-Flag ChIP DNA from WRBb-9B, asynchronous culture

value: anti-Flag

value: MATa ade2-1 ura3-1  leu2-3,112  his3-11,15 can1-100 bar1∆ RRM3-FLAG::KAN ura3::URA3/GPD-TK (7x)

value: asynchronous

source_name: Input DNA fromWRBb-9B, asynchronous culture

value: supernatant


title: H2-DC-Bp6

value: Septic plasma

tag: age (years)

tag: gender

tag: bacterial identification

value: Burkholderia pseudomallei

tag: day of blood collection

value: dendritic cells


title: Rrm3-Flag-spt16-11

source_name: Rrm3-Flag ChIP DNA from WSRBb-2D, asynchronous culture

tag: strain

tag: chip antibody

tag: genotype

value: MATa ade2-1 ura3-1  leu2-3,112  his3-11,15 can1-100 bar1∆ RRM3-FLAG::KAN ura3::URA3/GPD-TK (7x) spt16-11

source_name: Input DNA fromWSRBb-2D, asynchronous culture


title: H2-DC-LPS1

source_name: dendritic cells

value: I

value: LPS

tag: severity

tag: cell type


title: H1-DC-M1

value: Medium alone


title: H1-DC-LPS1


title: H2-DC-M1


title: Liver_RC1_2hr_Corn oil_Rep1

source_name: B6C3F1, liver, 2 hours

tag: tissue

value: Liver

tag: Sex

tag: compound

value: 2 hours


title: Liver_RC2_2hr_DEHP_Rep1

value: Male

value: DEHP

tag: time


title: WX_S98_117-1-T0

city: Las Vegas

first: Wilson

last: Xu

state: NV

address: One Breakthrough Way

institute: Nevada Cancer Institute

description: Wild-type strain.

hyb_protocol: Affymetrix Yeast Genome S98 arrays were used as a DNA microarray. The probe was hybridized to a DNA microarray at 45oC for 18 h according to the Affymetrix user’s manual (Affymetrix, Santa Clara, USA).

scan_protocol: The washing and staining of arrays were performed using a GeneChip Fluidics Station 400. The scanning of arrays was carried out using a GeneChip scanner (Affymetrix).

data_processing: Acquisition and quantification of array images as well as primary data analysis were performed by using the Affymetrix software package microarray suite 5.0. Data were used for all probe sets representing transcripts, called “present” by microarray suite 5.0, in at least three arrays. The transcription analysis was performed with RNA prepared from three WT (Y117) and three H2B (K123R) (Y118) cultures. Each of the three WT RNA preparations was compared with three mutant RNA preparations, generating in total 6 comparisons. The fold changes were calculated by using the average of the 6 comparisons.

source_name: Stationary yeast (WT) grown to OD2.0 in fresh YPD

label_protocol: cDNA synthesis, cRNA synthesis, and labeling were performed according to the Affymetrix user’s manual (Affymetrix, Santa Clara, USA).

growth_protocol: For microarray analyses, early stationary phase cultures of Y117 and Y118 in triplicates were innoculated in 150 ml of yeast rich media YPD (OD600 = 0.3) in 500-ml flasks and shaked (about 300 rpm) at 30oC for 7 hours until OD600 reaches 2.

extract_protocol: RNA was extracted with Ribo-Pure-Yeast kit (Ambion) according to the manufacturer's manual and was then used for genome-wide profiling experiments with the Affymetrix GeneChip system (MSKCC Genome Core).

tag: mutation

value: WT


title: Liver_RC9_2hr_Corn oil_Rep2

value: Corn oil

value: Oral gavage

value: 0 mg/kg


title: WX_S98_118-2-T0

description: The strain has a point mutation at histone H2B (K123R).

source_name: Stationary yeast (H2B K123R) grown to OD2.0 in fresh YPD

value: histone H2B (K123R)


title: Liver_RC10_2hr_Corn oil_Rep3


title: Liver_RC11_2hr_DEHP_Rep2


title: WX_S98_118-3-T0


title: WX_S98_117-2-T0

description: Wild-type strain.


title: S2-G1-6

status: Public on Mar 15 2014

city: Kansas City

first: Chris

middle: W

last: Seidel

state: MO

department: Genomics

institute: Stowers Institute

hyb_protocol: Following fragmentation, 5 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome 2.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: Array intensities were processed and normalized using the RMA algorithm in the affy library (version affy_1.36.1) from bioconductor in R version 2.15.2.

molecule: polyA RNA

source_name: S2 cells, G1

label_protocol: Biotinylated cRNA was prepared from 100 ng Total RNA using MessageAmp III aRNA Kit from Ambion.

growth_protocol: Drosophila larvae were raised at 25°C at low density until the 3rd instar wandering stage, washed and dissected in PBS (pH 7.4). For S2 cell FACS, low-passage cells (fewer than 30 passages) were used to count and check for viability using a Vi-Cell XR Cell Viability Analyzer (Beckman Coulter) before experiments.

extract_protocol: Cells were sorted directly into RNAprotect Cell Reagent (QIAGEN) and total RNA was extracted using QIAGEN RNeasy Plus Micro Kit according to manufacturer instructions.

treatment_protocol: Wing discs and S2 cells were subject to cytometric analysis and partitioned into G1 and G2/M populations. Robust gating was applied based on 2C and 4C peak positions.

tag: cell cycle stage

tag: replicate

value: S2 cells


title: WX_S98_117-3-T0

description: Wild-type strain.


title: WX_S98_118-1-T0


title: MCF7 YC-1

city: Barcelona

first: Miguel Angel

last: Pujana

address: Gran Via 199

institute: Institut Catala d'Oncologia IDIBELL

hyb_protocol: Affymetrix GeneChip Expression Analysis Technical Manual (P/N 702232 Rev 2).

data_processing: The data were analyzed with Partek Genomics Suite using Affymetrix default analysis settings and global scaling as normalization method.

source_name: MCF7 cell line treated

label_protocol: FL-Ovation cDNA Biotin Module V2 from NuGen Technologies Inc.

growth_protocol: MCF7 cells were cultured and maintained in RPMI medium containing 10% FBS and 2 mM glutamine and LTED cells were cultured and maintained in RPMI medium containing 10% DCC-FBS (estrogen depleted) and 2 mM glutamine.

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

treatment_protocol: MCF7 cells were treated with YC-1 (20 micrograms/L) and LTED cells were treated with YC-1 (2 micrograms/L) or vehicle (DMSO) for 48 hours.

tag: cell line source

value: Breast cancer

tag: agent

value: YC-1 (20 micrograms/L)

tag: cell line


title: LTED YC-1

scan_protocol: Affymetrix GeneChip Expression Analysis Technical Manual (P/N 702232 Rev 2).

source_name: LTED cell line treated

value: YC-1 (2 micrograms/L)

value: LTED


title: LTED

source_name: LTED cell line


title: S2-G1-5


title: S2-G2-6

source_name: S2 cells, G2


title: znua_cy3 vs wt_cy5 rep3

status: Public on Mar 16 2014

first: Todd

middle: C.

last: Hoopman

address: 5323 Harry Hines Blvd.

department: Microbiology

institute: University of Texas Southwestern Medical Center

hyb_protocol: Equivalent amounts of the Cy3- and Cy5-labeled cDNA samples were mixed, lyophilized, and then dissolved in 21 microliters of H2O. After denaturation for 3 minutes at 94 degrees Celsius these samples were kept on ice until they were used for DNA hybridization. The hybridization mixture containing 15 microliters of 4X hybridization buffer (GE Healthcare), 24 microliters of formamide (40% volume/volume), and 21 microliters of the Cy3- and Cy5-labeled cDNA. The mixture was added to a DNA microarray slide and incubated at 50 degrees Celsius overnight (~ 16 hours). After hybridization the slides were washed twice in 6X SSPE containing 0.01% Tween 20 at 50 degrees Celsius for 5 min, twice in 0.8X SSPE containing 0.001% Tween 20 at 50 degrees Celsius for 5 min, and twice in 0.8X SSPE at room temperature.

scan_protocol: The slides were dried by centrifugation at 900 x g in loosely capped 50-ml conical tubes for 3 minutes. Microarray slides were scanned with a GenePix 4100A microarray reader (Molecular Devices, Sunnyvale, CA) and analyzed with GenePix 4.0 software (Molecular Devices).

data_processing: The Acuity 4.0 software package (Molecular Devices) was utilized to analyze the microarray data. Raw data were first normalized using a ratio-based normalization method to equalize the means and medians of the features to 1 and exclude ratios that were less than 0.1 or greater than 10. Features that were flagged by the software as bad, absent, or not found were also excluded from further analysis. Secondly, a Lowess-based normalization was applied to the microarray data prior to final analysis. The RNA isolated from the in vitro broth-grown O35E wild-type cells was utilized as the baseline gene expression template. To identify those genes in the znuA mutant strain that exhibited n vitro broth-grown wild-type cells, a threshold of twofold-increased or decreased expression over the baseline was utilized.

organism: Moraxella catarrhalis

source_name: strain O35E

label_protocol: Five micrograms of total RNA from the O35E cells grown in BHI were mixed with 3.0 micrograms of M. catarrhalis genome directed primers and dried in the Speed-Vac. Once lyophilized the sample was reconstituted with 11 microliters of H2O and heated at 70 degrees Celsius for 5 minutes. The mixture was then cooled to room temperature for 10 minutes. cDNA synthesis was then performed with the Ambion Amino Allyl cDNA synthesis kit per the manufacturer's instructions RNA hydrolysis was accomplished with the addition of 15 microliters of sodium hydroxide (0.1M) and the sample was maintained at 70 degrees Celsius for 15 minutes. 15 microliters of hydrochloric acid (0.1M) was then added and the amino allyl-labeled cDNA was purified with a QIAGEN QIAquick gel extraction kit. After purification, Cy3 dye (GE Heathcare) was added and labelling occured per the manufacturers instructions. The CyDye-labeled cDNA sample was purified by using Microcon YM30 columns. A NanoDrop spectrophotometer was used to measure the concentration of the CyDye-labeled cDNA sample.

growth_protocol: Bacterial cells were grown in BHI broth to and OD600=0.900

extract_protocol: The contents of each flask underwent total RNA extraction with the Ambion Ribopure Bacteria kit as per manufacturer's instructions and then were treated with DNase I from a MessageClean kit as per manufacturer's instructions.

value: wild-type

source_name: znuA mutant of strain O35E

label_protocol: Five micrograms of total RNA from the O35E.znuA cells grown in BHI were mixed with 3.0 micrograms of M. catarrhalis genome directed primers and dried in the Speed-Vac. Once lyophilized the sample was reconstituted with 11 microliters of H2O and heated at 70 degrees Celsius for 5 minutes. The mixture was then cooled to room temperature for 10 minutes. cDNA synthesis was then performed with the Ambion Amino Allyl cDNA synthesis kit per the manufacturer's instructions RNA hydrolysis was accomplished with the addition of 15 microliters of sodium hydroxide (0.1M) and the sample was maintained at 70 degrees Celsius for 15 minutes. 15 microliters of hydrochloric acid (0.1M) was then added and the amino allyl-labeled cDNA was purified with a QIAGEN QIAquick gel extraction kit. After purification, Cy5 dye (GE Heathcare) was added and labelling occured per the manufacturers instructions. The CyDye-labeled cDNA sample was purified by using Microcon YM30 columns. A NanoDrop spectrophotometer was used to measure the concentration of the CyDye-labeled cDNA sample.

value: znuA mutant


title: znua_cy3 vs wt_cy5 rep2

data_processing: The Acuity 4.0 software package (Molecular Devices) was utilized to analyze the microarray data. Raw data were first normalized using a ratio-based normalization method to equalize the means and medians of the features to 1 and exclude ratios that were less than 0.1 or greater than 10. Features that were flagged by the software as bad, absent, or not found were also excluded from further analysis. Secondly, a Lowess-based normalization was applied to the microarray data prior to final analysis. The RNA isolated from the in vitro broth-grown O35E wild-type cells exposed to hydrogen peroxide was utilized as the baseline gene expression template. To identify those genes in the wild-type strain that exhibited an altered expression profile upon exposure to hydrogen peroxide relative to the in vitro broth-grown oxyR mutant cells exposed to hydrogen peroxide, a threshold of twofold-increased or decreased expression over the baseline was utilized.

treatment_protocol: Bacterial cells were grown in BHI broth to and OD600=0.900

label_protocol: Five micrograms of total RNA from the O35E cells grown in BHI were mixed with 3.0 micrograms of M. catarrhalis genome directed primers and dried in the Speed-Vac. Once lyophilized the sample was reconstituted with 11 microliters of H2O and heated at 70 degrees Celsius for 5 minutes. The mixture was then cooled to room temperature for 10 minutes. cDNA synthesis was then performed with the Ambion Amino Allyl cDNA synthesis kit per the manufacturer's instructions RNA hydrolysis was accomplished with the addition of 15 microliters of sodium hydroxide (0.1M) and the sample was maintained at 70 degrees Celsius for 15 minutes. 15 microliters of hydrochloric acid (0.1M) was then added and the amino allyl-labeled cDNA was purified with a QIAGEN QIAquick gel extraction kit. After purification, Cy5 dye (GE Heathcare) was added and labelling occured per the manufacturers instructions. The CyDye-labeled cDNA sample was purified by using Microcon YM30 columns. A NanoDrop spectrophotometer was used to measure the concentration of the CyDye-labeled cDNA sample.


title: S2-G2-5


title: S2-G1-4


title: S2-G2-4


title: WD-G1-3

source_name: Wing Disk, G1

value: OreR Wing Disc


title: WD-G2-3

source_name: Wing Disk, G2


title: znua_cy5 vs wt_cy3 rep2


title: MCF7 control

source_name: MCF7 cell line


title: znua_cy5 vs wt_cy3 rep3


title: WD-G2-4


title: MC2Ao-RIP317-ARS121-YJL9177_1-rep

city: Santa Barbara

last: Richardson

state: CA

address: UCSB

department: Molecular, Cellular, and Developmental Biology

institute: UCSB

hyb_protocol: Hybridization was performed in 3X SSC + 25mM HEPES pH7.0 + 0.25% SDS at 63C for 18-48

scan_protocol: Arrays were scanned with an Axon 3000B scanner using GenePixPro6.0.

data_processing: Data were filtered in GenePix to flag as bad features that had : (1) obvious defects; (2) saturated pixels; (3) regression r^2 values less than 0.5; (4) fewer than 55% of their pixels with flourescence intensity greater than 2 standard deviations above background. BLAST analysis was used to generate a filter that would flag as bad elements whose PCR product were excessively repetitive. Raw Cy5/Cy3 median of ratios values were normalized such that the average ratio was equal to 2.  VALUE is the log2 of the normalized ratio of Cy5 to Cy3; note that to convert to usable copy number profiles raise two to the indicated value.

source_name: YJL9177 S Phase

label_protocol: Amino-allyl-dUTP incorporation with Klenow.  Chemical coupling of dye to aa-dUTP labelled DNA.

growth_protocol: Cells grown as described in Richardson CD and Li JJ PLoS Genetics 2014.  Ch1 samples taken from replicating (S phase) or re-replicating (M phase + 3/6 hour induced).  Ch2 samples taken from M phase arrested DNA.

extract_protocol: DNA was purified by organic extraction and ethanol precipitation, or by more extensive methods when large quantities were needed.  See Richardson CD and Li JJ PloS Genetics 2014.

tag: phase

value: replicating (S phase)

source_name: YJL7695 M phase arrested DNA

value: M phase arrested

tag: sample type

value: Non-rereplicating reference DNA


title: MC2Ao-RIP317-ARS1-YJL9076_2-rerep3hr

source_name: YJL9076 M phase + Induced 3hr

tag: strain

value: re-replicating (M phase + Induced 3hr)


title: znua_cy5 vs wt_cy3 rep1


title: MC2Ao-RIP1238-ARS1238(63bp)-YJL10292-rerep6hr

source_name: YJL10292 M phase + Induced 6hr

value: re-replicating (M phase + Induced 6hr)


title: MC2Ao-RIP1238-ARS1238(73bp)-YJL10289-rerep6hr

source_name: YJL10289 M phase + Induced 6hr


title: WD-G1-4


title: MC2Ao-RIP1238-ARS301-YJL10001-rerep3hr

source_name: YJL10001 M phase + Induced 3hr


title: MC2Ao-RIP317-ARS121-YJL9078_1-rerep3hr

source_name: YJL9078 M phase + Induced 3hr


title: znua_cy3 vs wt_cy5 rep1


title: MC2Ao-RIP1238-ARS1238(58bp)-YJL10294-rerep6hr

source_name: YJL10294 M phase + Induced 6hr


title: MC2Ao-RIP1238-ARS1238(73bp)-YJL10290-rerep6hr

source_name: YJL10290 M phase + Induced 6hr


title: MC2Ao-RIP1238-ARS1238(63bp)-YJL10291-rerep6hr

source_name: YJL10291 M phase + Induced 6hr


title: WD-G1-2


title: WD-G2-2


title: MC2Ao-RIP317-ARS121-YJL9078_2-rerep3hr


title: MC2Ao-RIP317-ARS1-YJL9076_1-rerep3hr


title: MC2Ao-RIP1238-ARS301-YJL10002-rerep3hr

source_name: YJL10002 M phase + Induced 3hr


title: MC2Ao-RIP1238-ARS1238(53bp)-YJL10158-rerep6hr

source_name: YJL10158 M phase + Induced 6hr


title: MC2Ao-RIP1238-ARS1238(45bp)-YJL10296-rerep6hr

source_name: YJL10296 M phase + Induced 6hr


title: MC2Ao-RIP1238-ARS1238(53bp)-YJL10159-rerep6hr

source_name: YJL10159 M phase + Induced 6hr


title: MC2Ao-RIP1238-ARS1238(45bp)-YJL10295-rerep6hr

source_name: YJL10295 M phase + Induced 6hr


title: MC2Ao-RIP1238-ARS1238(58bp)-YJL10293-rerep6hr

source_name: YJL10293 M phase + Induced 6hr


title: MC2Ao-RIP1238-ARS1238(153bp)-YJL10288-rerep6hr

source_name: YJL10288 M phase + Induced 6hr


title: MC2Ao-RIP1238-ARS1238(21bp)-YJL10299-rerep6hr

source_name: YJL10299 M phase + Induced 6hr


title: MC2Ao-RIP1238-ARS121-YJL9999-rerep3hr

source_name: YJL9999 M phase + Induced 3hr

source_name: YJL7695 M phase arrested DNA


title: MC2Ao-RIP1238-ARS121-YJL10000-rerep3hr

source_name: YJL10000 M phase + Induced 3hr


title: MC2Ao-RIP1238-ARS1238(27bp)-YJL10297-rerep6hr

source_name: YJL10297 M phase + Induced 6hr


title: MC2Ao-ARS317 -sir4del-YJL6903-rerep3hr

source_name: YJL6903 M phase + Induced 3hr

value: MC2Ao-ARS317 -sir4∆


title: MC2Ao-ARS317 -sir2del-YJL6896-rerep3hr

source_name: YJL6896 M phase + Induced 3hr

value: MC2Ao-ARS317 -sir2∆


title: MC2Ao-ARS317 -sir1del-YJL6893-rerep3hr

source_name: YJL6893 M phase + Induced 3hr

value: MC2Ao-ARS317 -sir1∆


title: MC2Ao-RIP1238-ARS1238(21bp)-YJL10300-rerep6hr

source_name: YJL10300 M phase + Induced 6hr


title: MC2Ao-ARS317-YJL3758_2-rerep3hr

source_name: YJL3758 M phase + Induced 3hr


title: MC2Ao-ARS317 -sir1del-YJL6894-rerep3hr

source_name: YJL6894 M phase + Induced 3hr


title: MC2Ao-ARS317 -sir2del-YJL6897-rerep3hr

source_name: YJL6897 M phase + Induced 3hr


title: MC2Ao-ARS317-YJL3759_2-rerep6hr

source_name: YJL3759 M phase + Induced 6hr


title: MC2Ao-ARS317-YJL3759_1-rerep3hr

source_name: YJL3759 M phase + Induced 3hr


title: MC2Ao-RIP1238-ARS1238(153bp)-YJL10287-rerep6hr

source_name: YJL10287 M phase + Induced 6hr


title: MC2Ao-ARS317-YJL3758_1-rerep3hr


title: MC2Ao-ARS317 -sir3del-YJL6899-rerep3hr

source_name: YJL6899 M phase + Induced 3hr

value: MC2Ao-ARS317 -sir3∆


title: MC2Ao-ARS317 -sir3del-YJL6900-rerep3hr

source_name: YJL6900 M phase + Induced 3hr


title: MC2Ao-ars1238del-YJL9152_8-rerep6hr

source_name: YJL9152 M phase + Induced 6hr


title: MC2Ao-ARS317 -sir4del-YJL6902-rerep3hr

source_name: YJL6902 M phase + Induced 3hr


title: MC2Ao-ARS317-YJL3758_3-rerep6hr

source_name: YJL3758 M phase + Induced 6hr

source_name: YJL7695 M phase arrested DNA


title: MC2Ao-ars1238del-YJL9152_7-rerep3hr

source_name: YJL9152 M phase + Induced 3hr


title: MC2Ao-ars1238del-YJL9152_5-rerep3hr


title: MC2Ao-ars1238del-YJL9152_6-rerep3hr


title: MC2Ao-ARS317-YJL3758_4-rerep3hr


title: MC2Ao-ars1238del-YJL9152_9-rerep6hr


title: MC2Ao-ARS317-YJL3758_5-rerep3hr


title: MC2Ao-ars1238del-YJL9152_4-rerep3hr


title: MC2Ao-ars1238del-YJL9152_2-rerep3hr


title: MC2Ao-ars1238del-YJL9152_3-rerep3hr


title: MC2Ao-317(+92to-106)-YJL8402-rerep3hr

source_name: YJL8402 M phase + Induced 3hr


title: MC2Ao-ars1238del-YJL9152_1-rerep3hr


title: MC2Ao-317(+300to+34)-YJL7717_1-rerep3hr

source_name: YJL7717 M phase + Induced 3hr


title: MC2Ao-317(+300to+34)-YJL7717_2-rerep3hr


title: MC2Ao-317(+294to-106)-YJL8257-rerep3hr

source_name: YJL8257 M phase + Induced 3hr


title: MC2Ao-317(+300to-106)-YJL7700-rerep3hr

source_name: YJL7700 M phase + Induced 3hr


title: MC2Ao-317(+52to-106)-YJL8405-rerep3hr

source_name: YJL8405 M phase + Induced 3hr


title: MC2Ao-317(+52to-106)-YJL10444-rerep3hr

source_name: YJL10444 M phase + Induced 3hr


title: MC2Ao-317(+92to-106)-YJL8401-rerep3hr

source_name: YJL8401 M phase + Induced 3hr


title: MC2Ao-317(+52to-106)-YJL10445-rerep3hr

source_name: YJL10445 M phase + Induced 3hr


title: MC2Ao-317(+52to-106)-YJL8404-rerep3hr

source_name: YJL8404 M phase + Induced 3hr


title: MC2Ao-317(+251to-106)-YJL8387-rerep3hr

source_name: YJL8387 M phase + Induced 3hr


title: MC2Ao-317(+167to-106)HMRE-A-YJL8526_2-rerep3hr

source_name: YJL8526 M phase + Induced 3hr


title: MC2Ao-317(+153to-106)Linker9,17-YJL8830_2-rerep3hr

source_name: YJL8830 M phase + Induced 3hr


title: MC2Ao-317(+167to-106)HMRE-E-YJL8538_1-rerep3hr

source_name: YJL8538 M phase + Induced 3hr


title: MC2Ao-317(+200to-106)-YJL8392-rerep3hr

source_name: YJL8392 M phase + Induced 3hr


title: MC2Ao-317(+300to-106)-YJL7701-rerep3hr

source_name: YJL7701 M phase + Induced 3hr


title: MC2Ao-317(+167to-106)-YJL8395-rerep3hr

source_name: YJL8395 M phase + Induced 3hr

source_name: YJL7695 M phase arrested DNA


title: MC2Ao-317(+167to-106)HMRE-A-YJL8526_1-rerep3hr


title: MC2Ao-317(+294to-106)-YJL8256-rerep3hr

source_name: YJL8256 M phase + Induced 3hr


title: MC2Ao-317(+153to-106)Linker9,15-YJL8773_2-rerep3hr

source_name: YJL8773 M phase + Induced 3hr


title: MC2Ao-317(+167to-106)-YJL8396-rerep3hr

source_name: YJL8396 M phase + Induced 3hr


title: MC2Ao-317(+153to-106)Linker9,17-YJL8830_1-rerep3hr


title: MC2Ao-317(+200to-106)-YJL8393-rerep3hr

source_name: YJL8393 M phase + Induced 3hr


title: MC2Ao-317(+167to-106)HMRE-E-YJL8538_2-rerep3hr


title: MC2Ao-317(+153to-106)Linker9,13-YJL8836_2-rerep3hr

source_name: YJL8836 M phase + Induced 3hr


title: MC2Ao-317(+153to-106)Linker9,15-YJL8773_1-rerep3hr


title: MC2Ao-317(+251to-106)-YJL8386-rerep3hr

source_name: YJL8386 M phase + Induced 3hr


title: MC2Ao-317(+153to-106)Linker9,11,15-YJL8771_1-rerep3hr

source_name: YJL8771 M phase + Induced 3hr


title: MC2Ao-317(+153to-106)Linker9,13-YJL8836_1-rerep3hr


title: MC2Ao-317(+153to-106)Linker9,11,15-YJL8771_2-rerep3hr


title: MC2Ao-317(+153to-106)Linker7-YJL8653_1-rerep3hr

source_name: YJL8653 M phase + Induced 3hr


title: MC2Ao-317(+153to-106)Linker8-YJL8977_2-rerep3hr

source_name: YJL8977 M phase + Induced 3hr


title: MC2Ao-317(+153to-106)Linker7-YJL8653_2-rerep3hr


title: MC2Ao-317(+153to-106)Linker9,11-YJL8777_1-rerep3hr

source_name: YJL8777 M phase + Induced 3hr


title: MC2Ao-317(+153to-106)Linker8-YJL8977_1-rerep3hr


title: MC2Ao-317(+153to-106)Linker32-YJL8995_2-rerep3hr

source_name: YJL8995 M phase + Induced 3hr


title: MC2Ao-317(+153to-106)Linker9-YJL8656_1-rerep3hr

source_name: YJL8656 M phase + Induced 3hr


title: MC2Ao-317(+153to-106)Linker9-YJL8656_2-rerep3hr


title: MC2Ao-317(+153to-106)Linker5-YJL8650_1-rerep3hr

source_name: YJL8650 M phase + Induced 3hr


title: MC2Ao-317(+153to-106)Linker4-YJL8975_1-rerep3hr

source_name: YJL8975 M phase + Induced 3hr


title: MC2Ao-317(+153to-106)Linker32-YJL8995_1-rerep3hr


title: MC2Ao-317(+153to-106)Linker5-YJL8650_2-rerep3hr


title: MC2Ao-317(+153to-106)Linker9,11-YJL8777_2-rerep3hr


title: MC2Ao-317(+153to-106)Linker6-YJL9016_1-rerep3hr

source_name: YJL9016 M phase + Induced 3hr


title: MC2Ao-317(+153to-106)Linker4-YJL8975_2-rerep3hr


title: MC2Ao-317(+153to-106)Linker31-YJL8692_2-rerep3hr

source_name: YJL8692 M phase + Induced 3hr


title: MC2Ao-317(+153to-106)Linker6-YJL9016_2-rerep3hr

source_name: YJL7695 M phase arrested DNA


title: MC2Ao-317(+153to-106)Linker3-YJL8647_2-rerep3hr

source_name: YJL8647 M phase + Induced 3hr


title: MC2Ao-317(+153to-106)Linker30-YJL9022_2-rerep3hr

source_name: YJL9022 M phase + Induced 3hr


title: MC2Ao-317(+153to-106)Linker33-YJL8695_2-rerep3hr

source_name: YJL8695 M phase + Induced 3hr


title: MC2Ao-317(+153to-106)Linker30-YJL9022_1-rerep3hr


title: MC2Ao-317(+153to-106)Linker33-YJL8695_1-rerep3hr


title: MC2Ao-317(+153to-106)Linker29-YJL8689_2-rerep3hr

source_name: YJL8689 M phase + Induced 3hr


title: MC2Ao-317(+153to-106)Linker28-YJL8993_1-rerep3hr

source_name: YJL8993 M phase + Induced 3hr


title: MC2Ao-317(+153to-106)Linker28-YJL8993_2-rerep3hr


title: MC2Ao-317(+153to-106)Linker27-YJL8671_2-rerep3hr

source_name: YJL8671 M phase + Induced 3hr


title: MC2Ao-317(+153to-106)Linker29-YJL8689_1-rerep3hr


title: MC2Ao-317(+153to-106)Linker27-YJL8671_1-rerep3hr


title: MC2Ao-317(+153to-106)Linker3-YJL8647_1-rerep3hr


title: MC2Ao-317(+153to-106)Linker23-YJL8665_1-rerep3hr

source_name: YJL8665 M phase + Induced 3hr


title: MC2Ao-317(+153to-106)Linker23-YJL8665_2-rerep3hr


title: MC2Ao-317(+153to-106)Linker24-YJL9020_1-rerep3hr

source_name: YJL9020 M phase + Induced 3hr


title: MC2Ao-317(+153to-106)Linker26-YJL8991_2-rerep3hr

source_name: YJL8991 M phase + Induced 3hr


title: MC2Ao-317(+153to-106)Linker20-YJL8987_2-rerep3hr

source_name: YJL8987 M phase + Induced 3hr


title: MC2Ao-317(+153to-106)Linker21-YJL8686_2-rerep3hr

source_name: YJL8686 M phase + Induced 3hr


title: MC2Ao-317(+153to-106)Linker22-YJL8989_1-rerep3hr

source_name: YJL8989 M phase + Induced 3hr


title: MC2Ao-317(+153to-106)Linker25-YJL8668_2-rerep3hr

source_name: YJL8668 M phase + Induced 3hr


title: MC2Ao-317(+153to-106)Linker21,23-YJL8828_1-rerep3hr

source_name: YJL8828 M phase + Induced 3hr


title: MC2Ao-317(+153to-106)Linker21-YJL8686_1-rerep3hr


title: MC2Ao-317(+153to-106)Linker26-YJL8991_1-rerep3hr


title: MC2Ao-317(+153to-106)Linker22-YJL8989_2-rerep3hr


title: MC2Ao-317(+153to-106)Linker21,23-YJL8828_2-rerep3hr


title: MC2Ao-RIP1238-ARS1238(27bp)-YJL10298-rerep6hr

source_name: YJL10298 M phase + Induced 6hr


title: MC2Ao-317(+153to-106)Linker20-YJL8987_1-rerep3hr


title: MC2Ao-317(+153to-106)Linker2-YJL8973_2-rerep3hr

source_name: YJL8973 M phase + Induced 3hr


title: MC2Ao-317(+153to-106)Linker25-YJL8668_1-rerep3hr

source_name: YJL7695 M phase arrested DNA


title: MC2Ao-317(+153to-106)Linker18-YJL8985_2-rerep3hr

source_name: YJL8985 M phase + Induced 3hr


title: MC2Ao-317(+153to-106)Linker19-YJL8662_1-rerep3hr

source_name: YJL8662 M phase + Induced 3hr


title: MC2Ao-317(+153to-106)Linker18-YJL8985_1-rerep3hr


title: MC2Ao-317(+153to-106)Linker24-YJL9020_2-rerep3hr


title: MC2Ao-317(+153to-106)Linker17-YJL9175_2-rep

source_name: YJL9175 S Phase


title: MC2Ao-317(+153to-106)Linker19-YJL8662_2-rerep3hr


title: MC2Ao-317(+153to-106)Linker17-YJL9175_1-rep


title: MC2Ao-317(+153to-106)Linker17-YJL8683_1-rerep3hr

source_name: YJL8683 M phase + Induced 3hr


title: MC2Ao-317(+153to-106)Linker16-YJL9018_2-rerep3hr

source_name: YJL9018 M phase + Induced 3hr


title: MC2Ao-317(+153to-106)Linker14-YJL8983_2-rerep3hr

source_name: YJL8983 M phase + Induced 3hr


title: MC2Ao-317(+153to-106)Linker15-YJL8659_1-rerep3hr

source_name: YJL8659 M phase + Induced 3hr


title: MC2Ao-317(+153to-106)Linker17-YJL8683_2-rerep3hr


title: MC2Ao-317(+153to-106)Linker15,17-YJL8834_2-rerep3hr

source_name: YJL8834 M phase + Induced 3hr


title: MC2Ao-317(+153to-106)Linker15-YJL8659_2-rerep3hr


title: MC2Ao-317(+153to-106)Linker13-YJL8680_2-rerep3hr

source_name: YJL8680 M phase + Induced 3hr


title: MC2Ao-317(+153to-106)Linker12-YJL8981_1-rerep3hr

source_name: YJL8981 M phase + Induced 3hr


title: MC2Ao-317(+153to-106)Linker16-YJL9018_1-rerep3hr


title: MC2Ao-317(+153to-106)Linker13-YJL8680_1-rerep3hr


title: MC2Ao-317(+153to-106)Linker11,17-YJL8832_2-rerep3hr

source_name: YJL8832 M phase + Induced 3hr


title: MC2Ao-317(+153to-106)Linker11-YJL8677_1-rerep3hr

source_name: YJL8677 M phase + Induced 3hr


title: MC2Ao-317(+153to-106)Linker11-YJL8677_2-rerep3hr


title: MC2Ao-317(+153to-106)Linker13,17-YJL8826_1-rerep3hr

source_name: YJL8826 M phase + Induced 3hr


title: MC2Ao-317(+153to-106)Linker10-YJL8979_2-rerep3hr

source_name: YJL8979 M phase + Induced 3hr


title: MC2Ao-317(+153to-106)Linker13,17-YJL8826_2-rerep3hr


title: MC2Ao-317(+153to-106)DTransversion-YJL10328-rerep6hr

source_name: YJL10328 M phase + Induced 6hr


title: MC2Ao-317(+153to-106)Linker1-YJL8644_1-rerep3hr

source_name: YJL8644 M phase + Induced 3hr


title: MC2Ao-317(+153to-106)Linker11,15-YJL8775_1-rerep3hr

source_name: YJL8775 M phase + Induced 3hr

source_name: YJL7695 M phase arrested DNA


title: MC2Ao-317(+153to-106)Linker11,17-YJL8832_1-rerep3hr


title: MC2Ao-317(+153to-106)Linker14-YJL8983_1-rerep3hr


title: MC2Ao-317(+153to-106)Linker12-YJL8981_2-rerep3hr


title: MC2Ao-317(+153to-106)Linker11,15-YJL8775_2-rerep3hr


title: MC2Ao-317(+153to-106)Linker2-YJL8973_1-rerep3hr

source_name: YJL8973 M phase + Induced 3hr


title: MC2Ao-317(+153to-106)Linker10-YJL8979_1-rerep3hr


title: MC2Ao-317(+153to-106)CTransversion-YJL10326-rerep6hr

source_name: YJL10326 M phase + Induced 6hr


title: MC2Ao-317(+153to-106)D1Transversion-YJL10334-rerep6hr

source_name: YJL10334 M phase + Induced 6hr


title: MC2Ao-317(+153to-106)CTransversion-YJL10325-rerep6hr

source_name: YJL10325 M phase + Induced 6hr


title: MC2Ao-317(+153to-106)D2Transversion-YJL10335-rerep6hr

source_name: YJL10335 M phase + Induced 6hr


title: MC2Ao-317(+153to-106)D1Transversion-YJL10333-rerep6hr

source_name: YJL10333 M phase + Induced 6hr


title: MC2Ao-317(+153to-106)C2Transversion-YJL10332-rerep6hr

source_name: YJL10332 M phase + Induced 6hr


title: MC2Ao-317(+153to-106)C-DTransversion-YJL10322-rerep6hr

source_name: YJL10322 M phase + Induced 6hr


title: MC2Ao-317(+153to-106)D2Transversion-YJL10336-rerep6hr

source_name: YJL10336 M phase + Induced 6hr


title: MC2Ao-317(+153to-106)C1Transversion-YJL10330-rerep6hr

source_name: YJL10330 M phase + Induced 6hr


title: MC2Ao-317(+153to-106)DTransversion-YJL10327-rerep6hr

source_name: YJL10327 M phase + Induced 6hr


title: MC2Ao-317(+153to-106)C1Transversion-YJL10329-rerep6hr

source_name: YJL10329 M phase + Induced 6hr


title: MC2Ao-317(+153to-106)C2Transversion-YJL10331-rerep6hr

source_name: YJL10331 M phase + Induced 6hr


title: MC2Ao-317(+153to-106)C-DScramble-YJL10323-rerep6hr

source_name: YJL10323 M phase + Induced 6hr


title: MC2Ao-317(+153to-106)C-DTransversion-YJL10321-rerep6hr

source_name: YJL10321 M phase + Induced 6hr


title: MC2Ao-317(+153to-106)C-DScramble-YJL10324-rerep6hr

source_name: YJL10324 M phase + Induced 6hr


title: MC2Ao-317(+153to-106)-YJL8398_9-rerep3hr

source_name: YJL8398 M phase + Induced 3hr

source_name: YJL7695 M phase arrested DNA


title: MC2Ao-317(+153to-106)-YJL8398_4-rerep3hr


title: MC2Ao-317(+153to-106)-YJL8398_7-rerep3hr


title: MC2Ao-317(+153to-106)C-DReverse-YJL10319-rerep6hr

source_name: YJL10319 M phase + Induced 6hr


title: MC2Ao-317(+153to-106)-YJL8398_6-rerep3hr


title: MC2Ao-317(+153to-106)C-DReverse-YJL10320-rerep6hr

source_name: YJL10320 M phase + Induced 6hr


title: MC2Ao-317(+153to-106)-YJL8398_5-rerep3hr


title: MC2Ao-317(+153to-106)-YJL8398_8-rerep3hr


title: MC2Ao-317(+153to-106)-YJL8398_2-rerep3hr


title: MC2Ao-317(+153to-106)-YJL8399-rerep6hr

source_name: YJL8399 M phase + Induced 6hr


title: MC2Ao-317(+153to-106)-YJL8398_3-rerep3hr


title: MC2Ao-317(+153to-106)Linker1-YJL8644_2-rerep3hr

source_name: YJL8644 M phase + Induced 3hr


title: MC2Ao-317(+153to-106)-YJL8398_17-rerep3hr


title: MC2Ao-317(+153to-106)-YJL8398_18-rerep3hr


title: MC2Ao-317(+153to-106)-YJL8398_19-rerep3hr


title: MC2Ao-317(+153to-106)-YJL8398_14-rerep3hr


title: MC2Ao-317(+153to-106)Linker31-YJL8692_1-rerep3hr

source_name: YJL8692 M phase + Induced 3hr


title: MC2Ao-317(+153to-106)-YJL8398_15-rerep3hr


title: MC2Ao-317(+153to-106)-YJL8398_11-rerep3hr


title: MC2Ao-317(+153to-106)-YJL8398_16-rerep3hr


title: MC2Ao-317(+153to-106)-fkh1delkfh2del-YJL8750-rerep3hr

source_name: YJL8750 M phase + Induced 3hr


title: MC2Ao-317(+153to-106)-fkh2del-YJL8701-rerep3hr

source_name: YJL8701 M phase + Induced 3hr


title: MC2Ao-317(+153to-106)-YJL8398_13-rerep6hr

source_name: YJL8398 M phase + Induced 6hr


title: MC2Ao-317(+153to-106)-YJL8398_1-rerep3hr


title: MC2Ao-317(+153to-106)-fkh2del-YJL8702-rerep3hr

source_name: YJL8702 M phase + Induced 3hr


title: MC2Ao-317(+153to-106)-YJL8398_10-rerep3hr


title: MC2Ao-317(+143to-106)-YJL8553_2-rerep3hr

source_name: YJL8553 M phase + Induced 3hr


title: MC2Ao-317(+153to-106)-fkh1del-YJL8745-rerep3hr

source_name: YJL8745 M phase + Induced 3hr


title: MC2Ao-317(+123to-106)-YJL8559_1-rerep3hr

source_name: YJL8559 M phase + Induced 3hr


title: MC2Ao-317(+113to-106)-YJL8562_2-rerep3hr

source_name: YJL8562 M phase + Induced 3hr


title: MC2Ao-317(+123to-106)-YJL8559_2-rerep3hr


title: MC2Ao-317(+143to-106)-YJL8553_1-rerep3hr


title: MC2Ao-317(+153to-106)-fkh1delkfh2del-YJL8749-rerep3hr

source_name: YJL8749 M phase + Induced 3hr


title: MC2Ao-317(+133to-106)-YJL8556_1-rerep3hr

source_name: YJL8556 M phase + Induced 3hr


title: MC2Ao-317(+153to-106)-fkh1del-YJL8746-rerep3hr

source_name: YJL8746 M phase + Induced 3hr


title: MC2Ao-317(+103to-106)-YJL8565_2-rerep3hr

source_name: YJL8565 M phase + Induced 3hr

source_name: YJL7695 M phase arrested DNA


title: MC2Ao-1238(+83to-100)-YJL9708-rerep6hr

source_name: YJL9708 M phase + Induced 6hr


title: MC2Ao-317(+103to-106)-YJL8565_1-rerep3hr


title: MC2Ao-317(+153to-106)-YJL8398_12-rerep3hr

source_name: YJL8398 M phase + Induced 3hr


title: MC2Ao-1238(+83to-100)-YJL9707-rerep6hr

source_name: YJL9707 M phase + Induced 6hr


title: MC2Ao-1238(+133to-100)linkerH-YJL10285-rerep6hr

source_name: YJL10285 M phase + Induced 6hr


title: MC2Ao-1238(+133to-100)linkerG-YJL10284-rerep6hr

source_name: YJL10284 M phase + Induced 6hr


title: MC2Ao-317(+133to-106)-YJL8556_2-rerep3hr


title: MC2Ao-1238(+133to-100)linkerH-YJL10286-rerep6hr

source_name: YJL10286 M phase + Induced 6hr


title: MC2Ao-1238(+133to-100)linkerF-YJL10282-rerep6hr

source_name: YJL10282 M phase + Induced 6hr


title: MC2Ao-317(+113to-106)-YJL8562_1-rerep3hr


title: MC2Ao-1238(+133to-100)linkerF-YJL10281-rerep6hr

source_name: YJL10281 M phase + Induced 6hr


title: MC2Ao-1238(+133to-100)linkerE-YJL10280-rerep6hr

source_name: YJL10280 M phase + Induced 6hr


title: MC2Ao-1238(+133to-100)linkerC-YJL10276-rerep6hr

source_name: YJL10276 M phase + Induced 6hr


title: MC2Ao-1238(+133to-100)linkerC-YJL10275-rerep6hr

source_name: YJL10275 M phase + Induced 6hr


title: MC2Ao-1238(+133to-100)linkerA-YJL10272-rerep6hr

source_name: YJL10272 M phase + Induced 6hr


title: MC2Ao-1238(+133to-100)linkerG-YJL10283-rerep6hr

source_name: YJL10283 M phase + Induced 6hr


title: MC2Ao-1238(+133to-100)linkerB-YJL10273-rerep6hr

source_name: YJL10273 M phase + Induced 6hr


title: MC2Ao-1238(+133to-100)-YJL9566-rerep6hr

source_name: YJL9566 M phase + Induced 6hr


title: MC2Ao-1238(+133to-100)linkerD-YJL10277-rerep6hr

source_name: YJL10277 M phase + Induced 6hr


title: MC2Ao-1238(+133to-100)linkerD-YJL10278-rerep6hr

source_name: YJL10278 M phase + Induced 6hr

source_name: YJL7695 M phase arrested DNA


title: MC2Ao-1238(+133to-100)linkerE-YJL10279-rerep6hr

source_name: YJL10279 M phase + Induced 6hr


title: MC2A-ARS317-YJL8923-rerep3hr

source_name: YJL8923 M phase + Induced 3hr


title: MC2Ao-YJL9220_3-rep

source_name: YJL9220 S Phase


title: MC2Ao-YJL9220_5-rep


title: MC2Ao-YJL9220_2-rep


title: MC2Ao-YJL9220_4-rep


title: MC2Ao-1238(+133to-100)-YJL9567-rerep6hr

source_name: YJL9567 M phase + Induced 6hr


title: MC2Ao-1238(+133to-100)linkerB-YJL10274-rerep6hr

source_name: YJL10274 M phase + Induced 6hr


title: MC2Ao-YJL9220_6-rep


title: MC2Ao-RIPxx(linker6)-ARS317-YJL9248_2-rep

source_name: YJL9248 S Phase


title: MC2Ao-YJL9220_1-rep


title: MC2A-ARS317-YJL8924-rerep3hr

source_name: YJL8924 M phase + Induced 3hr


title: MC2Ao-RIPxx(linker6)-ARS301-YJL9233_2-rep

source_name: YJL9233 S Phase


title: MC2Ao-RIPxx(linker6)-ARS317-YJL9248_1-rep


title: MC2Ao-1238(+133to-100)linkerA-YJL10271-rerep6hr

source_name: YJL10271 M phase + Induced 6hr


title: MC2Ao-RIPxx(linker6)-ARS121-YJL9229_2-rep

source_name: YJL9229 S Phase


title: MC2Ao-RIPxx(linker6)-ARS301-YJL9233_1-rep


title: MC2Ao-RIPxx-ARS301-YJL9225_1-rerep3hr

source_name: YJL9225 M phase + Induced 3hr