title: BMDM_HSA_18hr_rep5

value: HSA (control protein)


title: G45_rep1

status: Public on Mar 01 2012

type: genomic

city: Pullman

first: Devendra

middle: H

last: Shah

state: WA

address: 100 Dairy Rd

department: Veterinary Microbiology and Pathology

country: USA

institute: Washington State University

description: The raw data file (slide_4067_CGH_400PMT_07212011.gpr available as a Series Supplementary file) contains 3 arrays, all of which are for G45 (rep 1, 2, and 3 corresponds to Block1, Block2, and Block3 portion of the raw data in the file).

hyb_protocol: Labeled DNA was resuspended in 135 μl of hybridization buffer consisting of 4× SSC (60 mM NaCl, 0.6 mM Na-citrate; pH 7.0) and 5× Denhardt’s solution (0.1% Ficoll, 0.1% polyvinylpyrrolidone, 0.1% bovine serum albumin), and heat denatured before being added to the slide for overnight hybridizations at 50°C. Each array on the slide was preblocked at 50°C for 30 min with 1% BSA in 5X SSC and 0.1% SDS. Slides were washed three times with TNT buffer (100 mM Tris-HCl [pH 7.5], 150 mM NaCl, 0.05% Tween 20), and the remaining steps were performed according to the manufacturer’s instructions for the TSA kit (Perkin Elmer). Finally, biotinyl tyramide was washed from the slide, and 2 μg streptavidin/ml conjugated to Alexa Fluor 555 (Invitrogen) was added in 1× SSC and 5× Denhardt’s solution and incubated for 1 h. The slides were then washed with TNT 3X for 1 min each and dried by spinning on a slide microfuge for 15 seconds.

scan_protocol: Slides were scanned using a Genepix400B scanner (Axon Instruments) and the images were quantified using Genepix Pro software

data_processing: Each spot was corrected by subtracting local background values and each “corrected” spot intensity was used to calculate a median signal intensity for each array. Inferior spot intensities (empty spots or those where signal intensity was less than 2 times the background) were reset to an arbitrary number (50) and were not used in the median calculation. The array median intensity was then used for within array normalization. The data was log2 transformed followed by quantile normalization between arrays

label: Biotin

molecule: genomic DNA

organism: Salmonella enterica subsp. enterica serovar Enteritidis

source_name: Strain G45

label_protocol: 1 μg of genomic DNA was nick translated in the presence of biotin-dATP using the BioNick labeling system (Invitrogen) according to manufacturer’s instructions.

growth_protocol: Frozen stocks of cultures were grown on Luria-Bertani (LB) agar incubated at 37°C for overnight. For all the experiments, a single colony from the overnight culture was inoculated into LB broth and grown at 37°C for 16 h with shaking at 200 rpm.

extract_protocol: Genomic DNA was extracted using the Qiagen DNeasy kit as per manufacturers instructions.

treatment_protocol: There is no treatment.

tag: strain

tag: phage type

tag: pathogenicity/invasiveness

value: Low

tag: mlva type


title: G1_rep2

description: The raw data file (Slide_4057_CGH_PMT500_07212011.gpr available as a Series Supplementary file) contains 3 arrays, all of which are for G1 (rep 1, 2, and 3 corresponds to Block1, Block2, and Block3 portion of the raw data in the file).

source_name: Strain G1

value: High/Medium


title: G1_rep1


title: G1_rep3


title: fie-RNA-2

type: mixed

city: Berkeley

first: Toshiro

last: Nishimura

state: CA

address: 211 Koshland Hall

department: Plant and Microbial Biology

institute: University of California at Berkeley

hyb_protocol: The hybridization and data extraction were performed at the Fred Hutchinson Cancer Research Center DNA array facility according to standard NimbleGen protocols (www.nimblegen.com).

scan_protocol: Standard NimbleGen protocol.

data_processing: Standard NimbleGen protocol.

molecule: total RNA

organism: Arabidopsis thaliana

source_name: fie - total RNA

label_protocol: ChIP-chip was performed according to the NimbleGen protocol (Roche, www.nimblegen.com). IP and Input DNA were amplified using the Sigma Whole Genome Amplification kit and labeled with CY5 and CY3, respectively according to the NimbleGen protocol (www.nimblegen.com). Combined samples, which include 10ug of CY5-labeled IP and 10ug of CY3-labeled Input DNA, were hybridized with NimbleGen HD2 arrays.

growth_protocol: Short day growth conditions for 14 days

extract_protocol: ChIP experiment was performed on WT, emf1, emf2, transgenic FIE, and transgenic plants harboring the EMF1-3FLAG construct grown in short day growth conditions for 14 days. Plants were vacuum infiltrated in 1% formaldehyde solution for half an hour to cross-link the chromatin. Tissues were ground in liquid nitrogen, nuclei isolated, and chromatin extracted. Chromatin was sheared by sonication to 0.5-2 kb fragments. For immunoprecipitated chromatin (IP), monoclonal anti-FLAG mouse antibody (Sigma F1804) and polyclonal anti-H3K27me3 antibody (Upstate, rabbit IgG, 07-449) were added to fragmented chromatin to precipitate EMF1-bound and H3K27me3 modified chromatin, respectively. Cross-linking was reversed with 5M NaCl and DNA precipitated by 100% EtOH. For global gene expression studies, total RNA was extracted from 14-day-old WT and mutants using trizol and converted into cDNA. Genomic DNA from WT and cDNA from mutants and WT were labeled with CY3, and CY5, respectively, and combined to hybridize.

tag: ecotype

value: Columbia

tag: genotype

value: fie

tag: chip antibody

source_name: Input DNA (control genomic DNA)

tag: genotype/variation

value: WT

tag: sample type

value: input DNA (control)


title: BMDM_HSA_18hr_rep3

type: RNA

city: South Bend

first: Manuel

last: Galvan

state: IN

address: 1234 Notre Dame Ave

department: Microbiology and Immunology

institute: Indiana University School of Medicine-South Bend

description: This sample is of wildtype Bone Marrow Derived Macrophages

hyb_protocol: Hybridization was performed using  hybridization buffer containing alignment oligos and unique sample tracking controls (Roche NimbleGen Systems Inc, Madison, WI USA) following their standard operating protocol See wwwnimblegencom

scan_protocol: Scanning was performed using a NimbleGen MS 200 Microarray Scanner following their standard operating protocol See wwwnimblegencom

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 25 (Roche NimbleGen, Inc)

organism: Mus musculus

source_name: C57Bl/6 Bone Marrow Derived Macrophages wildtype

label_protocol: Labeling was performed using  NimbleGen One-color (Cy3) DNA labeling kit (Roche NimbleGen Systems Inc, Madison, WI USA) following their standard operating protocol See wwwnimblegencom

growth_protocol: Bone marrow derived macrophages obtained from C57Bl/6 mice were cultured in serum free HL-1 media  37°C at 5% C02 for 4 or 18 hrs in the presence or absence of M avium or apoptotic Jurkat cells

extract_protocol: Total RNA was extracted using the Trizol method (Sigma, St Louis, MO, USA)  and DNA was removed by DNase digestion with the RNase-Free DNase (Qiagen) RNA quality and concentration was determined by analysis with an Agilent 2100 bioanalyzer at the University of Notre Dame Genomics Core Facility (University of Notre Dame, Notre Dame, USA)

value: Wildtype

tag: cell type

value: Bone Marrow Derived Macrophages (BMDM)

tag: treatment

tag: time


title: BMDM_HSA_18hr_rep2


title: K27-fie-3

source_name: H3K27me3 ChIP DNA

value: polyclonal anti-H3K27me3 antibody (Upstate, rabbit IgG, 07-449)


title: emf2-RNA-1

source_name: emf2 - total RNA


title: BMDM_HSA_18hr_rep4


title: fie-RNA-1


title: C45_rep2

description: The raw data file (Slide_4068_CGH_PMT400_07212011.gpr available as a Series Supplementary file) contains 3 arrays, all of which are for C45 (rep 1, 2, and 3 corresponds to Block1, Block2, and Block3 portion of the raw data in the file).

source_name: Strain C45


title: BMDM_HSA_18hr_rep1


title: C45_rep3


title: C45_rep1


title: emf2-RNA-2


title: BMDM_C1q & LPS & apoptotic Jurkat_4hr_rep5

value: C1q & LPS & apoptotic Jurkat


title: BMDM_C1q & LPS & apoptotic Jurkat_4hr_rep4


title: emf1-RNA-1

source_name: emf1 - total RNA


title: BMDM_C1q & LPS & apoptotic Jurkat_4hr_rep3


title: K27-WT-3


title: C19_rep2

description: The raw data file (slide_4069_CGH_400PMT_07212011.gpr available as a Series Supplementary file) contains 3 arrays, all of which are for C19 (rep 1, 2, and 3 corresponds to Block1, Block2, and Block3 portion of the raw data in the file).

source_name: Strain C19


title: WT-RNA-2

source_name: WT - total RNA


title: WT-RNA-1


title: BMDM_C1q & LPS & apoptotic Jurkat_4hr_rep1


title: BMDM_C1q &  LPS & apoptotic Jurkat_4hr_rep2


title: K27-emf1-2


title: K27-emf2-1


title: K27-fie-2


title: emf1-RNA-3


title: K27-fie-1


title: K27-emf2-2


title: K27-emf1-1


title: emf1-RNA-2


title: BMDM_HSA & LPS & apoptotic Jurkat_4hr_rep5

value: HSA (control protein) & LPS & apoptotic Jurkat


title: BC8_rep2

description: The raw data file (Slide_4058_CGH_PMT500_07212011.gpr available as a Series Supplementary file) contains 3 arrays, all of which are for BC8 (rep 1, 2, and 3 corresponds to Block1, Block2, and Block3 portion of the raw data in the file).

hyb_protocol: Labeled DNA was resuspended in 135 μl of hybridization buffer consisting of 4× SSC (60 mM NaCl, 0.6 mM Na-citrate; pH 7.0) and 5× Denhardt’s solution (0.1% Ficoll, 0.1% polyvinylpyrrolidone, 0.1% bovine serum albumin), and heat denatured before being added to the slide for overnight hybridizations at 50°C. Each array on the slide was preblocked at 50°C for 30 min with 1% BSA in 5X SSC and 0.1% SDS. Slides were washed three times with TNT buffer (100 mM Tris-HCl [pH 7.5], 150 mM NaCl, 0.05% Tween 20), and the remaining steps were performed according to the manufacturer’s instructions for the TSA kit (Perkin Elmer). Finally, biotinyl tyramide was washed from the slide,  and 2 μg streptavidin/ml conjugated to Alexa Fluor 555 (Invitrogen) was added in 1× SSC and 5× Denhardt’s solution and incubated for 1 h. The slides were then washed with TNT 3X for 1 min each and dried by spinning on a slide microfuge for 15 seconds.

scan_protocol: Slides were scanned using a Genepix400B scanner (Axon Instruments) and the images were quantified using Genepix Pro software.

data_processing: Each spot was corrected by subtracting local background values and each “corrected” spot intensity was used to calculate a median signal intensity for each array.  Inferior spot intensities (empty spots or those where signal intensity was less than 2 times the background) were reset to an arbitrary number (50) and were not used in the median calculation.  The array median intensity was then used for within array normalization.  The data was log2 transformed followed by quantile normalization between arrays

source_name: Strain BC8

value: High


title: BMDM_HSA & LPS & apoptotic Jurkat_4hr_rep4


title: C19_rep1


title: K27-emf1-3


title: BC8-rep1


title: BMDM_HSA & LPS & apoptotic Jurkat_4hr_rep3


title: BMDM_HSA & LPS & apoptotic Jurkat_4hr_rep1


title: BMDM_C1q & LPS_4hr_rep5

value: C1q & LPS


title: 148/92_1

city: Helsinki

first: Panu

last: Somervuo

address: Viikinkaari 4

country: Finland

institute: University of Helsinki

hyb_protocol: Agilent (Santa Clara, USA) 8x15K CGH protocol, 65°C for 18-20 h.

scan_protocol: GenePix 4200 AL (Axon Instruments) using pixel resolution of 5 µm, line average 2.

data_processing: Image analysis with GenePix Pro 6.0, bad spots were manually flagged (flag-value -100). Data preprocessing in R with limma package: background subtraction with normexp and offset 50. Normalization factor was determined by the location of the main mode of log-ratio distribution between the sample and reference strain. Separate normalization factors were calculated between each sample and all reference hybridizations. Normalized log2-intensity was determined by subtracting the sample-specific median normalization factor from the original log2-intensity.

organism: Clostridium perfringens

source_name: feces food poisoning

label_protocol: DNA was labeled using the BioPrime labeling kit (Invitrogen, Carlsbad, CA) according to the instructions of the manufacturer. Labeled DNA was purified with the DNA purification kit (QIAquick PCR Purification Kit, Qiagen, Hilden, Germany).

growth_protocol: Strains were grown in a tryptose-peptone-glucose-yeast medium (Difco Laboratories, Detroit, Mich.) under anaerobic conditions at 37°C 16 h.

extract_protocol: DNA was extracted as described by Hyytiä et al. (1999) and Keto-Timonen et al. (2003). In brief, the cells were lysed in TE containing lysozyme and mutanolysin. Lysis was completed by adding proteinase K,  NaCl, EDTA, and sodium dodecyl sulfate.  Phenol-chloroform-isoamyl alcohol and chloroform-2-pentanol extractions were performed, and DNA was ethanol precipitated and resuspended in TE. RNA was removed by RNase , followed by the addition of NaCl, chloroform-2-pentanol extraction, and ethanol precipitation. DNA concentrations were determined with a BioPhotometer (Eppendorf, Hamburg, Germany).

tag: cpe positive

value: negative


title: BMDM_C1q & LPS_4hr_rep4


title: BMDM_HSA & LPS & apoptotic Jurkat_4hr_rep2


title: 1534/86_2


title: 1534/86_1


title: 344/91_1

source_name: food


title: BC8_rep3


title: BMDM_C1q & LPS_4hr_rep3


title: BMDM_C1q & LPS_4hr_rep2


title: 148/92_2


title: C19_rep3


title: EMF1_IP-1

source_name: EMF1 ChIP DNA

value: anti-FLAG mouse antibody (Sigma F1804)


title: strain13_2

source_name: reference


title: EMF1_IP-2


title: strain13_3


title: strain13_1


title: d9033/97_1


title: d9033/97_2


title: strain13_4


title: cps50a_1

source_name: pig feces


title: BMDM_HSA & LPS_4hr_rep4

value: HSA (control protein) & LPS


title: BMDM_HSA & LPS_4hr_rep3


title: BMDM_HSA & M avium (1:1000)_4hr_rep5

value: HSA (control protein) & M avium (1:1000)


title: K27-WT-2


title: BMDM_C1q & LPS_4hr_rep1


title: BMDM_HSA & LPS_4hr_rep2


title: BMDM_HSA & LPS_4hr_rep5


title: K27-WT-1


title: cps3c_1


title: BMDM_HSA & M avium (1:1000)_4hr_rep4


title: BMDM_HSA & M avium (1:1000)_4hr_rep1


title: BMDM_HSA & M avium (1:1000)_4hr_rep3


title: 344/91_2


title: cps3c_2


title: BMDM_HSA & M avium (1:1000)_4hr_rep2


title: BMDM_HSA & LPS_4hr_rep1


title: cps131-3a_1


title: cps12km_2


title: cps217b_1


title: BMDM_C1q & M avium (1:500)_4hr_rep4


title: cps2a_1


title: BMDM_C1q & M avium (1:500)_4hr_rep5


title: cps2a_2


title: cpn7c_2

source_name: cattle feces


title: cps12km_1


title: BMDM_C1q & M avium (1:500)_4hr_rep3


title: BMDM_C1q & M avium (1:500)_4hr_rep2


title: BMDM_HSA & M avium (1:500)_4hr_rep5

value: HSA (control protein) & M avium (1:500)


title: cpn17a_1


title: cpn7c_1


title: cpn29a_1


title: cpn29a_2


title: cpn35d_2


title: BMDM_HSA & M avium (1:500)_4hr_rep4


title: cpn35d_1


title: BMDM_HSA & M avium (1:500)_4hr_rep3


title: BMDM_C1q & M avium (1:500)_4hr_rep1


title: BMDM_C1q_4hr_rep5


title: cpn16b_1


title: BMDM_HSA & M avium (1:500)_4hr_rep1


title: BMDM_HSA & M avium (1:500)_4hr_rep2


title: BMDM_C1q_4hr_rep4


title: cpm7a_1

source_name: soil


title: cpm42a_2


title: cpm4b_1


title: cpm42a_1


title: BMDM_C1q_4hr_rep1


title: BMDM_C1q_4hr_rep3


title: BMDM_HSA_4hr_rep3

value: HSA (control protein)


title: BMDM_C1q_4hr_rep2


title: BMDM_HSA_4hr_rep4


title: BMDM_HSA_4hr_rep1


title: BMDM_HSA_4hr_rep5


title: BMDM_HSA_4hr_rep2


title: cpi57-2_1

source_name: human feces


title: cpli8b2_1

source_name: sludge


title: cpi39k-2a_2


title: cpi39k-2a_1


title: cpi39k-1a_2


title: cpli8b2_2


title: cpi18-6_2


title: cpi18-6_1


title: serous ovarian cancer 294

city: Niigata

first: Kosuke

last: Yoshihara

address: 1-757 Asahimachi-dori

department: Obstetrics and Gynecology

country: Japan

institute: Niigata University

hyb_protocol: Cy3-labeled cRNAs (1.65 µg) were hybridized for 17 hours at 65°C to an Agilent Whole Human Genome Oligo Microarray in a rotating Agilent hybridization oven.

scan_protocol: The hybridized microarray was washed and then scanned in Cy3 channel with the Agilent DNA Microarray Scanner (model G2565AA).

data_processing: Signal intensity per spot was generated from the scanned image with Feature Extraction Software ver.9.1 (Agilent Technologies) in the default settings.

organism: Homo sapiens

source_name: high-grade serous ovarian cancer

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the Quick Amp Labering Kit, one-color (Agilent Technologies) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).

extract_protocol: Total RNA was extracted from tissue samples using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer's recommendations. RNA was examined with a 2100 Bioanalyzer (Agilent Technologies Inc., Palo Alto, CA, USA) using an RNA 6000 Nano LabChip (Agilent Technologies)

tag: tissue

value: tumor

tag: grading

tag: Stage

value: IIIc

tag: surgery status

value: optimal

tag: taxane

tag: platinum

tag: pfs (m)

tag: rec (1)

tag: os (m)

tag: death (1)


title: cpb(bp70-6/4)_1

source_name: broiler feces

tag: strain


title: cpi57-2_2


title: cpb(bp70-6/4)_2


title: H.zea_infected_rep1

city: Brisbane

first: Quan

middle: Hoang

last: Nguyen

state: Queensland

address: Queensland Bioscience Precinct (Building 80) The University of Queensland. 306 Carmody Road. St

department: Australian Institute for Bioengineering and Nanotechnology

country: Australia

institute: The University of Queensland

description:
Helicoverpa zea cell line (HzAM1) infected by Helicoverpa armigera single-capsid nucleopolyhedrovirus (HaSNPV). The Helicoverpa zea cell line, designated as BCIRL-NZ-AM1, was isolated from pupal ovarian tissue by McIntosh and Ignoffo (1983). The HaNPV, (Strain: H25EA1 isolated by CSIRO), was used for infections. This is an Australian wildtype field isolate.
Gene expression of H. zea cell line at 18 hours post infection by HaSNPV

hyb_protocol: Hybridization and washing was performed using the in situ Hybridization Plus kit (Agilent) and following the manufacturer's instructions. Arrays were hybridised at 65 dgrees C for 17 hours rotating at 10rpm.

scan_protocol: Arrays were scanned on an Agilent scanner. The scan resolution was 3um.

data_processing:
Data were extracted from images using Feature Extraction Software Version 10.7.3.1. The extraction protocol was GE1_107_Sep09. Normalization was performed between arrays using the Quantile method by R statistics with the Limma package. Correction for multiple hypothesis testing in the linear model was performed using Benjamini-Hochberg method. The emperical bayes method within limma was used for significant events detection, with false discovery rate lower than 5%. The normalized data is not included in the gProcessedSignal column in the raw Agilent feature extraction files.
The full 180,000 probes were used for validating de novo assembled sequences (total 29,856 assembled sequences) from RNAseq short reads. This full array allows for the orientation of assembled sequence and the best probe that gives well above background signal for that sequence. As a result, 27,400 probes were obtained and the data from these validated 27,400 probes were used to analyze differential expression. The full data set is contained in the data tables below, and a matrix containing the set of 27,400 validated probes is linked as a supplementary file on the Series record.

organism: Helicoverpa zea

source_name: H.zea cells infected by HaSNPV virus at 18 hour post infection

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 100 ng RNA using the One-Color Low RNA Input Low Input Quick Amp kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA) and assessed by Agilent 2100 bioanalyzer

growth_protocol: H.zea cells were typically cultivated in 250 ml Erlenmeyer flasks containing 50-100 ml of VPM3 medium at 28 degree C, and grown on an orbital shaker operating at 120 rpm. Cells were routinely passaged twice a week, with a seeding cell density of 2-4x1E5 cells/ml.

extract_protocol: Samples containing 5x1E5 H. zea (HzAM1) cells (Mcintosh and Ignoffo, 1983), grown in shaker-flask suspension cultures using serum free insect medium (VPM3), were collected for total RNA extraction and DNA removal using the Qiagen RNAeasy extraction and on-column DNAse kit (Qiagen, Hilden, Germany).

treatment_protocol: Briefly, 5x1E9 caterpillar purified OB are digested with an alkaline solution for 30 minutes, neutralized by the addition of VPM3,  filter sterilized and inoculated to a total culture volume of 100 ml containing H.zea cells at 5x105 cells/ml. Passage 1, (P1), BV harvested at 4 d.p.i. was used for P2 virus production at 17 pfu/cell.

tag: cell line

value: Helicoverpa zea cell line (HzAM1)

tag: virus


title: serous ovarian cancer 292


title: cpb(bp70-5/1)_1


title: cpi39k-1a_1


title: serous ovarian cancer 298R

value: IV

value: suboptimal


title: H.zea_uninfected_rep1

description:
Helicoverpa zea cell line (HzAM1).  The Helicoverpa zea cell line, designated as BCIRL-NZ-AM1, was isolated from pupal ovarian tissue by McIntosh and Ignoffo (1983).
Gene expression of H. zea cell line not being infected by HaSNPV virus

source_name: H.zea cells not infected


title: serous ovarian cancer 297R


title: H.zea_uninfected_rep2

description:
Helicoverpa zea cell line (HzAM1).  The Helicoverpa zea cell line, designated as BCIRL-NZ-AM1, was isolated from pupal ovarian tissue by McIntosh and Ignoffo (1983).
Gene expression of H. zea cell line not being infected by virus


title: serous ovarian cancer 291


title: cpb(bp70-3/4)_1


title: serous ovarian cancer 289

value: IIIb


title: cpb(bp70-1/1)_1


title: H.zea_infected_rep2

description:
Helicoverpa zea cell line (HzAM1) infected by Helicoverpa armigera single-capsid nucleopolyhedrovirus (HaSNPV).  The Helicoverpa zea cell line, designated as BCIRL-NZ-AM1, was isolated from pupal ovarian tissue by McIntosh and Ignoffo (1983). The HaNPV, (Strain: H25EA1 isolated by CSIRO), was used for infections. This is an Australian wildtype field isolate.
Gene expression of H. zea cell line at 18 hours post infection by HaSNPV


title: cpb(bp70-2/4)_1


title: atcc13124_4


title: serous ovarian cancer 288


title: serous ovarian cancer 287


title: atcc13124_1


title: serous ovarian cancer 285


title: sids14os_2


title: atcc13124_2


title: sids15ps_1


title: serous ovarian cancer 286


title: atcc13124_3


title: sids14os_1


title: serous ovarian cancer 280


title: 721/84_2


title: cpli4-1_2


title: serous ovarian cancer 283


title: serous ovarian cancer 284


title: 721/84_1


title: serous ovarian cancer 281


title: serous ovarian cancer 282


title: sids15ps_2


title: serous ovarian cancer 274


title: serous ovarian cancer 231


title: serous ovarian cancer 277


title: cpli4-1_1


title: cpli3-1_2


title: serous ovarian cancer 229


title: serous ovarian cancer 226


title: serous ovarian cancer 278


title: cps253-c2a_1


title: cpi75-1_2


title: cpi75-1_1


title: serous ovarian cancer 230


title: cpli3-1_1


title: cpi75k-3_1


title: cpi75k-2a_2


title: serous ovarian cancer 224


title: cpi75k-2a_1


title: serous ovarian cancer 213


title: serous ovarian cancer 207


title: serous ovarian cancer 206


title: cpi53k-r1_1


title: cpi63k-r5_1


title: serous ovarian cancer 198


title: cpi75k-3_2


title: serous ovarian cancer 222


title: serous ovarian cancer 203


title: cpi53k-r1_2


title: serous ovarian cancer 197


title: serous ovarian cancer 205


title: serous ovarian cancer 196


title: serous ovarian cancer 200


title: serous ovarian cancer 195R


title: cpi63k-r5_2


title: serous ovarian cancer 192


title: cpi103k-3_1


title: aad1930/04a_1


title: aad1527a_2


title: aad1930/04a_2


title: cpi26k-r2_1


title: serous ovarian cancer 109R


title: cpr16_2


title: 149/92_1


title: 149/92_2


title: cpi26k-r2_2


title: cpi103k-3_2


title: serous ovarian cancer 106


title: cpr16_1


title: serous ovarian cancer 97d

scan_protocol: The hybridized microarray was washed and then scanned in Cy3 channel with the Agilent DNA Microarray Scanner (model G2565CA).

data_processing: Signal intensity per spot was generated from the scanned image with Feature Extraction Software ver.10.1 (Agilent Technologies) in the default settings.

value: high-grade serous ovarian cancer tumor


title: serous ovarian cancer 111R


title: 1533/86_1


title: serous ovarian cancer 94d


title: serous ovarian cancer 93d


title: serous ovarian cancer 110


title: serous ovarian cancer 95d


title: cpr12_2


title: serous ovarian cancer 89d


title: 1533/86_2


title: aad1527a_1


title: serous ovarian cancer 88d


title: serous ovarian cancer 108


title: serous ovarian cancer 92d


title: serous ovarian cancer 86d


title: serous ovarian cancer 90d


title: cpm77b_2


title: cpr11_1


title: cpm77e_1


title: cpm77b_1


title: cpr12_1


title: cpr11_2


title: cpli2-1_1


title: cpli3-1_3


title: cpli2-1_2


title: cpli6-1_1


title: cpi75-4_1


title: serous ovarian cancer 77d


title: serous ovarian cancer 69d


title: cpi75-4_2


title: serous ovarian cancer 80d


title: serous ovarian cancer 72d


title: serous ovarian cancer 79d


title: cpi75k-4_2


title: cpi57k-4_2


title: serous ovarian cancer 84d


title: cpi75k-4_1


title: serous ovarian cancer 66d


title: serous ovarian cancer 642d


title: serous ovarian cancer 68d

value: IIIa


title: serous ovarian cancer 7d


title: serous ovarian cancer 643d


title: cpi57k-4_1


title: serous ovarian cancer 637d


title: serous ovarian cancer 644d


title: serous ovarian cancer 641d2


title: serous ovarian cancer 636d2R


title: cpi57k-1_4


title: serous ovarian cancer 64d


title: serous ovarian cancer 634d2


title: cpi57k-1_1


title: cpi39-1a_2


title: cpi18-4_2


title: serous ovarian cancer 633d2R


title: cpi18-2_2


title: cpi57k-1_3


title: serous ovarian cancer 628d2


title: cpi57k-1_2


title: cpi18-2_1


title: cpi18-4_1


title: cpi18-1b_2


title: serous ovarian cancer 635d2


title: serous ovarian cancer 62d


title: cpi18-1b_1


title: aad1900a_2


title: serous ovarian cancer 623d2


title: cpi39-1a_1


title: aad1900a_1


title: serous ovarian cancer 616d2


title: aad1863c_2


title: serous ovarian cancer 611d


title: serous ovarian cancer 630d2


title: serous ovarian cancer 610d2


title: aad1863c_1


title: 955/85_2

value: chromosomal


title: serous ovarian cancer 612d2


title: serous ovarian cancer 621d2


title: ghh_All_Cell_Types_replicate_3

city: New York

first: Adam

last: Paré

state: NY

address: 1275 York Avenue

department: Developmental Biology

institute: Memorial Sloan Kettering Cancer Center

description: Gene expression in 48-h-old ghh (FGSC #13563) mutant Neurospora colonies

hyb_protocol: A custom Agilent 8x22K Neurospora crassa Array was used. These arrays were identical to those available from the FGSC (Kasuga and Glass, Euk. Cell, 2008; Kasuga et al. Nuc. Acid Res. 2005) except that the probes were shortened from 70mers to 60mers by removal of the first 10 nucleotides. Hybridization of 1 microgram Cy3-labeled cRNA to each array, washing, and scanning were performed according to Agilent's specifications. Hybridizations were carried out for 18 h at 42°C in a shaking incubator.

scan_protocol: Processed slides were scanned using an Agilent Scanner with the scan resolution set to 5 µM. Agilent's Feature Extraction 9.5.3 Software was utilized for spot-finding.

data_processing: All samples were normalized simultaneously using a multiple-loess technique as described elsewhere (Sasik et al., 2004).

organism: Neurospora crassa

source_name: 48-h-old ghh (FGSC #13563) mutant Neurospora colonies _replicate_3

label_protocol: For each sample, 500 ng of total RNA were converted into fluorescently labeled Cy3-labeled cRNA using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent).

growth_protocol: Seeder slants of wild-type (FGSC #2489) and ghh (FGSC #13563) strains were grown for 3 days at 30°C under a 12 h light/dark cycle, and conidia were harvested in 1 ml H20. As the csp phenotype makes homogenous resuspension of ghh conidia impossible, accurate conidial counts of the suspensions could not be obtained. Therefore, plates and flasks were innoculated with approximately equivalent masses of conidia suspended in water. As Neurospora comes to confluence very quickly on plates, and growth in liquid culture for short periods of time should not be nutrient limiting, we believe the number of starting conidia was not crucial to these experiments. The following collection procedures were carried out in triplicate for both wild-type and ghh samples. 1) “ALL” samples were collected by densely plating conidia on minimal Vogel’s agar medium + 1.5% sucrose in 10 cm Petri dishes that had been overlain with disks of cellophane (VWR, 100357-652). After 48 h at 30°C under a 12 h light/dark cycle, the plates were densely covered with conidiating colonies. Samples were scraped off the cellophane using cell-scrapers, submerged in 5 ml Trizol (Invitrogen), and quickly frozen in liquid nitrogen. 2) “AHC” samples were collected by densely plating conidia on minimal Vogel’s agar medium + 1.5% sucrose in a deep 10 cm Petri dishes. Disks of medium gauge wire mesh were suspended ~0.5 cm above the surface of the agar using a ring of plastic tubing around the periphery of each Petri dish. After 48 h at 30°C under a 12 h light/dark cycle, the aerial hyphae and conidia had grown abundantly through the mesh. The mesh disks were carefully peeled off, and the adherent cells were harvested in H20 using cell-scrapers. Samples were dried by vacuum filtration, removed from the filter paper using cell-scrapers, submerged in 5 ml Trizol, and quickly frozen in liquid nitrogen. 3) “MYC” samples were collected by inoculating 25 ml of liquid Vogel’s medium + 1.5% sucrose in 125 ml Erlenmeyer flasks with sponge stoppers. After 28 h at 28°C with constant shaking in the dark, log-phase mycelial mats were recovered by vacuum filtration, removed from the filter paper using cell-scrapers, and frozen in 2 ml Trizol with liquid nitrogen.

extract_protocol: To obtain total RNA from the Neurospora samples for microarray analysis, we followed a protocol similar to that reported elsewhere (Kasuga and Glass, Euk. Cell, 2008). Samples in Trizol were thawed and quickly homogenized by vortexing and passing through a P1000 pipet tip multiple times to break up large clumps. Approximately 100 µl of cells were placed in an eppendorf tube with 1 ml Trizol and 200 mg of 0.5 mm Zirconia/Silica Beads (Biospec). Samples were disrupted twice with a MiniBeadBeater (Biospec) at maximum speed for 30 s each time. RNA was then extracted using standard Trizol procedures and resuspended in 100 µl H20. RNA was quantified in 10 mM Tris pH 7.5, and 50 µg of total RNA was cleaned further using the RNeasy miniprep kit (Qiagen). RNA integrity was assayed by gel electrophoresis, RT-PCR against several developmentally dynamic genes [80], and Bioanalyzer (Agilent) analysis

treatment_protocol: The experimental and control samples differed only in their genotypes: grainy-head homolog strain FGSC #13563 vs. wild-type strain FGSC #2489.

tag: cell type

value: All Cell Types


title: 955/85_1


title: wt_All_Cell_Types_replicate_1

description: Gene expression in 48-h-old wild-type (FGSC #2489) Neurospora colonies

source_name: 48-h-old wild-type (FGSC #2489) Neurospora colonies _replicate_1


title: serous ovarian cancer 609dR


title: wt_All_Cell_Types_replicate_2

source_name: 48-h-old wild-type (FGSC #2489) Neurospora colonies _replicate_2


title: serous ovarian cancer 613d2


title: wt_All_Cell_Types_replicate_3

source_name: 48-h-old wild-type (FGSC #2489) Neurospora colonies _replicate_3


title: serous ovarian cancer 606d


title: 954/84_1

source_name: feces food poisoning


title: ghh_All_Cell_Types_replicate_1

source_name: 48-h-old ghh (FGSC #13563) mutant Neurospora colonies _replicate_1


title: 948/85_2

source_name: food


title: serous ovarian cancer 61d


title: serous ovarian cancer 601d


title: ghh_All_Cell_Types_replicate_2

source_name: 48-h-old ghh (FGSC #13563) mutant Neurospora colonies _replicate_2


title: serous ovarian cancer 60d


title: serous ovarian cancer 608d2


title: Pig 40 ASC osteogenic differentiation 7 day of differentiation

city: Corvallis

first: Massimo

last: Bionaz

state: OR

address: 316A Withycombe Hall

department: Animal and Rangeland Sciences

institute: Oregon State University

description: A mixture of total RNA from 4 porcine tissues (32% liver, 32% jujenum, 24% kidney, and 10% mammary tissue) were used as reference (Cy5 in Ch1 and Cy3 in Ch2)

hyb_protocol: Same amount of labelled cDNA from sample and reference were hybridised using 80 μL of the hybridization buffer #1 (Ambion).  Slides placed in humidified slide chambers (Corning) in water bath for 40 h at 45 °C. Prior scanning the microarray were washed for 5 min by agitation 3 times with wash buffers in the following order: 1×SSC and 0.2% SDS solution preheated at 42°C, 0.1×SSC and 0.2% SDS solution, and 0.1×SSC solution. Lastly, slides were inserted into a 50 mL tube, spin-dried and gassed with Argon to preserve dye from bleaching.

scan_protocol: Arrays were scanned with a ScanArray 4000 (GSI-Lumonics) dual-laser confocal scanner and images were processed and edited using GenePix 6.0 (Axon Instruments).

data_processing: Array quality was assessed using an in-house parser written in Perl language. Spots that received a -100 flag by GenePix 6.0 were removed from further analysis and background intensity was subtracted from the foreground intensity. Spots on the slide were considered “good” if the median intensity of sample was ≥3 standard deviation above median background for each channel (i.e., dye). Spots were flagged “present” when both dyes passed the criteria, “marginal” if only one dye passed the criteria, or “absent” when both dyes failed to pass the criteria. Statistical analysis was conducted on oligos that were flagged as “present” and “marginal”. Data from a total of 82 microarrays were normalized for dye and array effects (i.e., Lowess normalization and array centering and scaling) before statistical analysis.

organism: Sus scrofa

source_name: ASC  at 7 day of osteogenic differentiation

label_protocol: Labelled with Cy3 and Cy5 during cDNA synthesis from total RNA using Superscript III Kit (Invitrogen).

growth_protocol: Cells were plated in 75 cm2 Corning cell culture flasks at 7.5 X 105 cells in 15 mL of culture medium and incubated at 39°C and 5% CO2 in 100% humidified air. The culture medium used was high glucose Dulbecco's Modified Eagle's Medium supplemented with 10% Fetal Bovine Serum, antibiotic and antimycotic. Medium was changed every other day and the cells were maintained in culture for 3 passages before starting the adipogenic and osteogenic differentiation.

extract_protocol: At 0, 2, 7, and 21 days of differentiation cells were trypsinized and total RNA was isolated using the RNeasy Mini Kit (Qiagen) according to the manufacturer’s protocol. Any residual genomic DNA was eliminated by treatment with RNase-Free DNase Set (Qiagen). RNA concentration was measured with a NanoDrop ND-1000 spectrophotometer.

treatment_protocol: Adipose and bone marrow derived stem cells were induced to differentiate towards bone and adipose with specific differentiation media. The medium for the osteogenic differentiation consisted of high glucose DMEM supplemented with 100 nM dexamethasone, 10 mM b-glycerophosphate, 0.05 mM ascorbic acid-2-phosphate, 10% FBS, 1% Penicillin G-Streptomycin, and 5.0 mg/L Amphotericin B. The adipogenic medium consisted of basic high glucose DMEM supplemented with 1.0 mM dexamethasone, 0.5 mM isobutylmethylxanthine, 10 mM insulin, 200 mM indomethacin, 10% FBS, 1% Penicillin G-Streptomycin, and 5.0 mg/L Amphotericin B.

tag: animal id

value: Pig 40

value: adipose

value: ASC Mesenchymal Stem cells

tag: protocol

value: osteogenic differentiation

value: 7 days

source_name: reference

tag: reference composition


title: 954/84_2

tag: cpe positive


title: Pig 40 ASC osteogenic differentiation 21 day of differentiation

source_name: ASC  at 21 day of osteogenic differentiation

tag: tissue

tag: time

value: 21 days

value: A mixture of total RNA from 4 porcine tissues (32% liver, 32% jujenum, 24% kidney, and 10% mammary tissue)


title: Pig 40 ASC 0 day of differentiation

source_name: ASC  at 0 day of  differentiation

value: control

value: 0 days


title: serous ovarian cancer 599d

tag: grading

tag: Stage

value: IIIc

tag: surgery status


title: wt_Mycelia_replicate_3

description: Gene expression in the Mycelia of 28-h-old wild-type (FGSC #2489) Neurospora colonies

source_name: Mycelia of 28-h-old wild-type (FGSC #2489) Neurospora colonies _replicate_3

value: Mycelia


title: wt_Mycelia_replicate_1

source_name: Mycelia of 28-h-old wild-type (FGSC #2489) Neurospora colonies _replicate_1


title: ghh_Mycelia_replicate_3

description: Gene expression in the Mycelia of 28-h-old ghh (FGSC #13563) mutant Neurospora colonies

source_name: Mycelia of 28-h-old ghh (FGSC #13563) mutant Neurospora colonies _replicate_3


title: serous ovarian cancer 6d

source_name: high-grade serous ovarian cancer

value: optimal

tag: taxane

tag: platinum

tag: pfs (m)


title: wt_Mycelia_replicate_2

source_name: Mycelia of 28-h-old wild-type (FGSC #2489) Neurospora colonies _replicate_2


title: Pig 40 ASC osteogenic differentiation 2 day of differentiation

source_name: ASC  at 2 day of osteogenic differentiation

value: 2 days


title: 834/87_2


title: 945/85_2


title: Pig 22 ASC osteogenic differentiation 21 day of differentiation

value: Pig 22


title: serous ovarian cancer 596d

value: high-grade serous ovarian cancer tumor

tag: rec (1)

tag: os (m)

tag: death (1)


title: 948/85_1

tag: strain

value: chromosomal


title: 945/85_1


title: serous ovarian cancer 595d

value: suboptimal


title: ghh_Mycelia_replicate_2

source_name: Mycelia of 28-h-old ghh (FGSC #13563) mutant Neurospora colonies _replicate_2

tag: cell type


title: 834/87_1


title: ghh_Mycelia_replicate_1

source_name: Mycelia of 28-h-old ghh (FGSC #13563) mutant Neurospora colonies _replicate_1


title: Pig 22 ASC 0 day of differentiation

tag: animal id


title: 497/86_2


title: Pig 12 ASC osteogenic differentiation 21 day of differentiation

value: Pig 12

tag: protocol


title: Pig 22 ASC osteogenic differentiation 2 day of differentiation

value: adipose

tag: reference composition


title: serous ovarian cancer 590d


title: wt_Aerial_Hyphae_&_Conidia_replicate_3

description: Gene expression in the Aerial Hyphae & Conida of 48-h-old wild-type (FGSC #2489) Neurospora colonies

source_name: Aerial Hyphae & Conida of 48-h-old wild-type (FGSC #2489) Neurospora colonies _replicate_3

value: Aerial Hyphae & Conidia


title: wt_Aerial_Hyphae_&_Conidia_replicate_2

source_name: Aerial Hyphae & Conida of 48-h-old wild-type (FGSC #2489) Neurospora colonies _replicate_2


title: 497/86_1

source_name: feces food poisoning

tag: cpe positive


title: serous ovarian cancer 592d

tag: tissue

value: IV


title: Pig 22 ASC osteogenic differentiation 7 day of differentiation

value: ASC Mesenchymal Stem cells

value: osteogenic differentiation

tag: time

value: 7 days


title: serous ovarian cancer 589d

tag: grading


title: Pig 12 ASC osteogenic differentiation 2 day of differentiation

value: A mixture of total RNA from 4 porcine tissues (32% liver, 32% jujenum, 24% kidney, and 10% mammary tissue)


title: 346/91_2


title: 346/91_1


title: serous ovarian cancer 587d

tag: Stage


title: wt_Aerial_Hyphae_&_Conidia_replicate_1

source_name: Aerial Hyphae & Conida of 48-h-old wild-type (FGSC #2489) Neurospora colonies _replicate_1


title: serous ovarian cancer 591d

tag: surgery status


title: Pig 12 ASC osteogenic differentiation 7 day of differentiation


title: ghh_Aerial_Hyphae_&_Conidia_replicate_3

description: Gene expression in the Aerial Hyphae & Conida of 48-h-old ghh (FGSC #13563) mutant Neurospora colonies

source_name: Aerial Hyphae & Conida of 48-h-old ghh (FGSC #13563) mutant Neurospora colonies _replicate_3


title: serous ovarian cancer 586d

tag: taxane


title: ghh_Aerial_Hyphae_&_Conidia_replicate_2

source_name: Aerial Hyphae & Conida of 48-h-old ghh (FGSC #13563) mutant Neurospora colonies _replicate_2


title: ghh_Aerial_Hyphae_&_Conidia_replicate_1

source_name: Aerial Hyphae & Conida of 48-h-old ghh (FGSC #13563) mutant Neurospora colonies _replicate_1


title: Pig 40 BMSC osteogenic differentiation 21 day of differentiation

source_name: BMSC at 21 day of osteogenic differentiation

value: Pig 40

value: bone

value: BMSC Mesenchymal Stem cells

value: 21 days

source_name: reference


title: Pig 12 ASC 0 day of differentiation

source_name: ASC  at 0 day of  differentiation

value: control

value: 0 days


title: serous ovarian cancer 585d

value: high-grade serous ovarian cancer tumor

value: IIIc

tag: platinum


title: serous ovarian cancer 584d

value: optimal

tag: pfs (m)


title: 310/85_2

source_name: food

value: chromosomal


title: 318/86_1


title: 318/86_2


title: serous ovarian cancer 582d

value: suboptimal

tag: rec (1)


title: 26/86_2


title: DK21_plus_120h_2

city: Seoul

first: Won

middle: Kyong

last: Cho

address: 5103-ho, 200-dong, Daehak-dong, Kwanak-gu

department: Department of Agricultural Biotechnology and Center for Fungal Pathogenesis

country: South Korea

institute: Seoul National University

description: This sample is of FgV1-DK21 infected Fusarium graminearum. It is the second of three virus infected biological replicates used in this experiment and is harvested at 120 hrs.

hyb_protocol: Hybridization was performed by NimbleGen Systems Inc., Madison, WI, USA following their standard operating protocol. See www.nimblegen.com.

scan_protocol: Scanning was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See 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: Fusarium graminearum

source_name: Fusarium graminearum infected with FgV1-DK21 at 120 hpi

label_protocol: Labeling was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

growth_protocol: Virus-free and FgV1-DK21-infected F. graminearum strains were maintained on potato dextrose agar (PDA) at 25°C with 12 h light–dark cycle. Freshly grown mycelia from PDA media plate were inoculated in 50 or 200 ml of complete media (CM) broth and incubated at 25°C for 36 hrs or 120 hrs in an orbital shaker (150 rpm). Hyphae were collected by filtering through 3MM paper, washed with distilled water, dried by blotting with paper towels and frozen at -80°C.

extract_protocol: Frozen mycelia were pulverized with mortar and pestle using liquid nitrogen for nucleic acid extraction. Total RNAs were extracted by Iso-RNA Lysis reagent (5 PRIME, Germany). Extracted total RNA was treated with DNase I (Takara, Japan) to remove genomic DNA according to instructions provided by the manufacturer. The total RNA sample were precipitated with ethanol and resuspended in DEPC-treated water finally.

treatment_protocol: There is no special treatment in F. graminearum.

tag: anamorph

value: Fusarium graminearum

value: hyphae


title: 310/85_1


title: Pig 40 BMSC osteogenic differentiation 7 day of differentiation

source_name: BMSC at 7 day of osteogenic differentiation


title: Pig 40 BMSC 0 day of differentiation

source_name: BMSC at 0 day of  differentiation


title: Pig 22 BMSC osteogenic differentiation 21 day of differentiation

value: Pig 22


title: DK21_plus_120h_3

description: This sample is of FgV1-DK21 infected Fusarium graminearum. It is the third of three virus infected biological replicates used in this experiment and is harvested at 120 hrs.


title: 26/86_1


title: serous ovarian cancer 58d

source_name: high-grade serous ovarian cancer

tag: os (m)

tag: death (1)


title: Pig 40 BMSC osteogenic differentiation 2 day of differentiation

source_name: BMSC at 2 day of osteogenic differentiation

tag: cell type

value: osteogenic differentiation

value: 2 days


title: serous ovarian cancer 581d


title: Pig 22 BMSC osteogenic differentiation 7 day of differentiation

tag: animal id

value: 7 days

value: A mixture of total RNA from 4 porcine tissues (32% liver, 32% jujenum, 24% kidney, and 10% mammary tissue)


title: 20/85_2

tag: strain


title: DK21_plus_120h_1

description: This sample is of FgV1-DK21 infected Fusarium graminearum. It is the first of three virus infected biological replicates used in this experiment and is harvested at 120 hrs.


title: DK21_minus_120h_3

description: This sample is of wild-type Fusarium graminearum. It is the third of three wild-type biological replicates used in this experiment and is harvested together with virus infected samples at 120 hrs.

source_name: Virus free Fusarium graminearum at 120 hpi


title: DK21_minus_120h_2

description: This sample is of wild-type Fusarium graminearum. It is the second of three wild-type biological replicates used in this experiment and is harvested together with virus infected samples at 120 hrs.


title: 20/85_1


title: serous ovarian cancer 578d


title: serous ovarian cancer 576d

value: IV


title: DK21_minus_120h_1

description: This sample is of wild-type Fusarium graminearum. It is the first of three wild-type biological replicates used in this experiment and is harvested together with virus infected samples at 120 hrs.


title: Pig 22 BMSC osteogenic differentiation 2 day of differentiation

value: bone

value: BMSC Mesenchymal Stem cells

tag: protocol

tag: reference composition


title: DK21_plus_36h_3

description: This sample is of FgV1-DK21 infected Fusarium graminearum. It is the third of three virus infected biological replicates used in this experiment and is harvested at 36 hrs.

source_name: Fusarium graminearum infected with FgV1-DK21 at 36 h


title: Pig 22 BMSC 0 day of differentiation

tag: tissue

value: control


title: Pig 12 BMSC osteogenic differentiation 7 day of differentiation

value: Pig 12

tag: time


title: serous ovarian cancer 579d

value: high-grade serous ovarian cancer tumor

tag: grading


title: 1293/86_2

tag: cpe positive


title: Pig 12 BMSC osteogenic differentiation 2 day of differentiation


title: serous ovarian cancer 575d

tag: Stage

value: IIIc

tag: surgery status


title: 1293/86_1


title: cpr20_1


title: serous ovarian cancer 573d

tag: taxane

tag: platinum


title: DK21_minus_36h_3

description: This sample is of wild-type Fusarium graminearum. It is the third of three wild-type biological replicates used in this experiment and is harvested together with virus infected samples at 36 hrs.

source_name: Fusarium graminearum virus free at 36 h


title: cpr20_2


title: cpr19_2


title: Pig 40 ASC adipogenic differentiation 7 day of differentiation

source_name: ASC  at 7 day of adipogenic differentiation

value: Pig 40

value: adipose

value: ASC Mesenchymal Stem cells

value: adipogenic differentiation


title: Pig 12 BMSC 0 day of differentiation

value: 0 days


title: DK21_plus_36h_2

description: This sample is of FgV1-DK21 infected Fusarium graminearum. It is the second of three virus infected biological replicates used in this experiment and is harvested at 36 hrs.

value: Fusarium graminearum

value: hyphae


title: DK21_minus_36h_2

description: This sample is of wild-type Fusarium graminearum. It is the second of three wild-type biological replicates used in this experiment and is harvested together with virus infected samples at 36 hrs.


title: DK21_plus_36h_1

description: This sample is of FgV1-DK21 infected Fusarium graminearum. It is the first of three virus infected biological replicates used in this experiment and is harvested at 36 hrs.


title: Pig 40 ASC adipogenic differentiation 2 day of differentiation

source_name: ASC  at 2 day of adipogenic differentiation

value: 2 days


title: DK21_minus_36h_1

description: This sample is of wild-type Fusarium graminearum. It is the first of three wild-type biological replicates used in this experiment and is harvested together with virus infected samples at 36 hrs.


title: Pig 40 ASC adipogenic differentiation 21 day of differentiation

description: A mixture of total RNA from 4 porcine tissues (32% liver, 32% jujenum, 24% kidney, and 10% mammary tissue) were used as reference (Cy5 in Ch1 and Cy3 in Ch2)

source_name: ASC  at 21 day of adipogenic differentiation

value: 21 days


title: cpr19_1

value: chromosomal


title: serous ovarian cancer 57d

value: optimal

tag: pfs (m)

tag: rec (1)


title: serous ovarian cancer 570d

value: suboptimal

tag: os (m)


title: cpr18_2


title: serous ovarian cancer 571d

value: IV

tag: death (1)


title: Pig 22 ASC adipogenic differentiation 21 day of differentiation

value: Pig 22

tag: cell type

value: A mixture of total RNA from 4 porcine tissues (32% liver, 32% jujenum, 24% kidney, and 10% mammary tissue)


title: serous ovarian cancer 569d

value: high-grade serous ovarian cancer tumor


title: Pig 22 ASC adipogenic differentiation 7 day of differentiation

tag: animal id

value: 7 days


title: cpr18_1

tag: strain


title: Pig 22 ASC adipogenic differentiation 2 day of differentiation

tag: protocol


title: cpr17_2


title: serous ovarian cancer 566d2


title: C. remanei_rep3_stage10

city: Haifa

first: Itai

last: Yanai

address: Technion City

department: Biology

country: Israel

institute: Technion - Israel Institute of Technology

description: C. remanei_rep3_stage10

hyb_protocol: The hybridization and washing of the microarrays were performed following the Agilent protocol for single-channel arrays.

scan_protocol: Agilent Microarray Scanner was used to scan the slides

data_processing: Feature Extraction was used for data processing with protocol GE1_105_Dec08

molecule: polyA RNA

organism: Caenorhabditis remanei

source_name: C. remanei,stage10

label_protocol: 6μg of RNA was labeled with Cy-3 and 1.65μg of labeled aRNA was incubated on each microarray. Each embryonic stage was measured in independent biological triplicates.

growth_protocol: Standard C. elegans techniques were followed to grow worms (Stiernagle 2006).

extract_protocol: RNA was extracted from embryos using Trizol. Each sample comprised 48 individually staged embryos. Total RNA was amplified by two round of in vitro transcription (IVT)and cy3 labeled using the MessageAmpII kit (Ambion). We also added to this reaction RNA from a Spike-in kit (Agilent) that included 10 different species of RNA at various concentrations.

treatment_protocol: For the embryo collection of all species adult hermaphrodites or females were collected and cut to obtain embryos. Embryos were washed with a bleach solution (70% DDW, 20% bleach, 10% 5M KOH) for 30 seconds and subsequently with a 5% BSA solution for 30 seconds. 4-cell embryos were collected,washed 4 times in clear DDW and incubated at 20°C for the appropriate time for each species to reach stages 1-10. After incubation embryos were frozen in liquid nitrogen and kept at -80°C until RNA extraction.

tag: developmental stage

value: Juvenile L1 larvae


title: cpr17_1


title: serous ovarian cancer 565d2

tag: tissue


title: cpr15_2


title: C. remanei_rep3_stage9

description: C. remanei_rep3_stage9

source_name: C. remanei,stage9

value: Movement


title: serous ovarian cancer 567d2

value: IIIc


title: C. remanei_rep3_stage8

description: C. remanei_rep3_stage8

source_name: C. remanei,stage8

value: Comma stage


title: serous ovarian cancer 564d


title: cpr15_1


title: cpr14_2


title: Pig 12 ASC adipogenic differentiation 21 day of differentiation

value: Pig 12

value: adipose

value: ASC Mesenchymal Stem cells

value: adipogenic differentiation

tag: time

source_name: reference

tag: reference composition


title: Pig 12 ASC adipogenic differentiation 7 day of differentiation


title: Pig 40 BMSC adipogenic differentiation 21 day of differentiation

source_name: BMSC at 21 day of adipogenic differentiation

value: Pig 40

value: bone

value: BMSC Mesenchymal Stem cells

value: 21 days


title: Pig 12 ASC adipogenic differentiation 2 day of differentiation

value: 2 days


title: Pig 40 BMSC adipogenic differentiation 7 day of differentiation

source_name: BMSC at 7 day of adipogenic differentiation


title: serous ovarian cancer 561d2

tag: grading

value: optimal


title: serous ovarian cancer 560d2

tag: Stage

value: IV


title: C. remanei_rep3_stage6

description: C. remanei_rep3_stage6

source_name: C. remanei,stage6

value: 7th AB division


title: C. remanei_rep3_stage7

description: C. remanei_rep3_stage7

source_name: C. remanei,stage7

value: Ventral enclosure stage


title: cpr14_1

source_name: food

tag: cpe positive

value: chromosomal


title: C. remanei_rep3_stage5

description: C. remanei_rep3_stage5

source_name: C. remanei,stage5

value: 6th AB division


title: Pig 40 BMSC adipogenic differentiation 2 day of differentiation

source_name: BMSC at 2 day of adipogenic differentiation

value: A mixture of total RNA from 4 porcine tissues (32% liver, 32% jujenum, 24% kidney, and 10% mammary tissue)


title: Pig 22 BMSC adipogenic differentiation 21 day of differentiation

value: Pig 22


title: serous ovarian cancer 56d

source_name: high-grade serous ovarian cancer

value: high-grade serous ovarian cancer tumor

value: IIIc

tag: surgery status

value: suboptimal

tag: taxane


title: serous ovarian cancer 559d2

tag: platinum

tag: pfs (m)


title: C. remanei_rep3_stage3

description: C. remanei_rep3_stage3

source_name: C. remanei,stage3

value: 4th AB division


title: C. remanei_rep3_stage4

description: C. remanei_rep3_stage4

source_name: C. remanei,stage4

value: 5th AB division


title: serous ovarian cancer 558d2

tag: rec (1)

tag: os (m)


title: cpr13_1


title: cpr13_2


title: C. remanei_rep3_stage2

description: C. remanei_rep3_stage2

source_name: C. remanei,stage2

value: E-cell division


title: serous ovarian cancer 557d2

tag: death (1)


title: cpli73b_2

source_name: sludge


title: Pig 22 BMSC adipogenic differentiation 7 day of differentiation

tag: animal id

value: bone

tag: cell type

value: BMSC Mesenchymal Stem cells

value: adipogenic differentiation

value: 7 days


title: C. remanei_rep2_stage10

description: C. remanei_rep2_stage10

value: Juvenile L1 larvae


title: cpli73b_1

tag: strain


title: serous ovarian cancer 555d2

value: IV

value: optimal


title: cpi76k-4_2

source_name: human feces

value: chromosomal


title: cpi76k-4_1


title: Pig 12 BMSC adipogenic differentiation 21 day of differentiation

value: Pig 12

tag: protocol

value: 21 days


title: C. remanei_rep3_stage1

description: C. remanei_rep3_stage1

source_name: C. remanei,stage1

tag: developmental stage

value: 4-cell stage


title: Pig 12 BMSC adipogenic differentiation 7 day of differentiation

tag: tissue

tag: time

value: A mixture of total RNA from 4 porcine tissues (32% liver, 32% jujenum, 24% kidney, and 10% mammary tissue)


title: Pig 12 BMSC adipogenic differentiation 2 day of differentiation

value: 2 days

tag: reference composition


title: C. remanei_rep2_stage8

description: C. remanei_rep2_stage8

value: Comma stage


title: C. remanei_rep2_stage9

description: C. remanei_rep2_stage9

source_name: C. remanei,stage9

value: Movement


title: Pig 22 BMSC adipogenic differentiation 2 day of differentiation

value: Pig 22


title: C. remanei_rep2_stage7

description: C. remanei_rep2_stage7

value: Ventral enclosure stage


title: Cow 7313 300d relative to parturition

description: A mixture of total RNA from 5 bovine tissues (mammary, liver, muscle, adipsoe, and placenta) were used as reference.

hyb_protocol: Labelled cDNA hybridised using 80 μL of the hybridization buffer #1 (Ambion).  Slides placed in humidified slide chambers (Corning) in water bath for 40 h at 42 °C. Prior scanning the microarray were washed for 5 min by agitation 3 times with wash buffers in the following order: 1×SSC and 0.2% SDS solution preheated at 42°C, 0.1×SSC and 0.2% SDS solution, and 0.1×SSC solution. Lastly, slides were inserted into a 50 mL tube, spin-dried and gassed with Argon to preserve dye from bleaching.

data_processing: Array quality was assessed using an in-house parser written in Perl language. Spots that received a -100 flag by GenePix 6.0 were removed from further analysis and background intensity was subtracted from the foreground intensity. Spots on the slide were considered “good” if the median intensity was ≥3 standard deviation above median background for each channel (i.e., dye). Spots were flagged “present” when both dyes passed the criteria, “marginal” if only one dye passed the criteria, or “absent” when both dyes failed to pass the criteria. Statistical analysis was conducted on oligos that were flagged as “present” and “marginal”. Data from a total of 124 microarrays were normalized for dye and array effects (i.e., Loess normalization and array centering and scaling) before statistical analysis.

organism: Bos taurus

label_protocol: Labelled with Cy3 and Cy5 during cDNA synthesis from total RNA using Superscript III Kit (Invitrogen) as manufacturers instructions.

growth_protocol: Cows were maintain in a normal farm management

extract_protocol: Biopsy tissue was weighted (~0.5-1.0 g) and immediately subjected to RNA extraction using ice-cold TRIZol. Genomic DNA was removed from RNA with DNAse (Qiagen) using RNeasy Mini Kit columns (Qiagen)

tag: breed

value: Holstein dairy cow

value: Mammary biopsy of cow at 300 day relative to parturition

value: Bovine tissue reference (mammary, liver, muscle, adipsoe, and placenta)

value: Holstein dairy cows


title: C. remanei_rep2_stage6

description: C. remanei_rep2_stage6

value: 7th AB division


title: serous ovarian cancer 554d2

value: high-grade serous ovarian cancer tumor

tag: grading

tag: Stage

value: IIIc

value: suboptimal


title: serous ovarian cancer 553d2

value: IIIb

tag: surgery status

value: optimal

tag: taxane


title: serous ovarian cancer 551d2

tag: platinum

tag: pfs (m)


title: WS5041 (mir 58(n4640); alg 1(tm492); opIs205). Replicate 3

city: Cambridge

first: Marko

last: Jovanovic

state: MA

address: 7 Cambridge Center

department: Core Group (Regev group) member

institute: Broad Institute of MIT and Harvard

description: TAP::ALG-1 associated RNA (RIP)

hyb_protocol: According to Affymetrix protocol

scan_protocol: Arrays were scanned on an Affymetrix 3000 7G scanner, according to manufacturer instructions.

data_processing: Microarray data were preprocessed using the rma algorithm of the Bioconductor package affy (Gautier et al. 2004). 15880 identifiers out of the total of 22625 identifiers passed the log2 signal threshold of 4.644 (=linear signal threshold of 25) and were further considered. To identify transcripts that were specifically enriched by association to TAP::ALG 1 isolated from WS4303 animals compared to WS5041 animals, we performed a two class paired Significance Analysis of Microarrays (SAM) (Tusher et al. 2001).

label: biotin

organism: Caenorhabditis elegans

source_name: mir-58(n4640) mutant expressing TAP::ALG-1

label_protocol: 100 ng of RNA were amplified by the MessageAmp™ aRNA Kit (Ambion) in a two cycle protocol and labeled as recommended by the vendor.

growth_protocol: For synchronized late L4 stage cultures of transgenic animals, eggs were isolated by bleaching (Stiernagle 2006). The purified eggs were allowed to hatch overnight on large unseeded NGM plates. Synchronized L1 larvae were then spotted onto large NGM plates seeded with OP50 and grown at 25°C until late L4 stage (36 hours).

extract_protocol: RNA Immunopurifications (RIPs) have been described previously (Gerber et al. 2004). We have adapted the protocol accordingly. In brief, after harvesting, worms were separated from the bacteria by several washes in ice-cold buffer A (20 mM Tris–HCl [pH 8.0], 140 mM KCl, 1.8 mM MgCl2, 0.1% Nonidet P-40 (NP-40), 0.1 mg/ml heparin) and frozen in liquid nitrogen and stored at -80°C until further use. 1 ml of frozen worm pellet was resuspended in 5 ml buffer B (buffer A plus 1.5 mM dithiothreitol (DTT), 1 mM phenylmethylsulfonylfluoride, 0.5 µg/ml leupeptin, 0.8 µg/ml pepstatin, 20 U/ml DNase I, 100 U/ml RNaseOUT (Invitrogen), and 0.2 mg/ml heparin). The resuspended worms were drop wise refrozen in liquid nitrogen and homogenized by a TissueLyser instrument (Qiagen) by 4 cycles of 4 minutes each with a setting of 30 Hertz; the metal chars (50 ml) containing the samples were always refrozen in liquid nitrogen between the cycles. The worm lysates were clarified by sequential centrifugation steps and the purified extracts were incubated on a rotor with 400-µl slurry (50% (v/v)) IgG–agarose beads (Sigma) for 2 h at 4°C. The beads were washed four times for 15 min at 4°C with buffer C (20 mM Tris–HCl (pH 8.0), 140 mM KCl, 1.8 mM MgCl2, 1 mM DTT, 0.01% NP-40, 10 U/ml RNasin). ALG-1 was released from the beads by incubation with 100 U of TEV protease (Invitrogen) for 90 min at 25°C. RNA was isolated from the TEV eluates (IP fraction) by extraction with the miRVana kit (Ambion) according to the vendor’s instructions. RNA was quantified with a Nanodrop device (Witeg AG).

treatment_protocol: The coding sequence for the N-terminal tandem affinity purification (TAP)-tag was amplified from plasmid pBS1761 (Rigaut et al. 1999) by PCR. The alg-1 genomic sequence was amplified from genomic C. elegans DNA by PCR. The sequences were tagged with the following restriction sites: 5’AscI:TAP-tag:3’FseI; 5’FseI:alg-1(genomic+3’UTR):3’PacI. The tagged fragments were subcloned into the pCR2.1 TOPO vector (Invitrogen). Both constructs were then inserted into pLN022 (Neukomm et al. 2011) to generate the final expression vector pMJ001, where TAP::ALG-1 expression is under the control of the ubiquitous eft-3 promoter. Low copy transgenic animals were generated by bombardment as previously described (Praitis et al. 2001). The protocol was adapted as follows: unc-119(ed3) mutant worms were grown in liquid culture. pMJ001 was precipitated onto gold beads and shot at unc-119(ed3) mutant worms using a Biolistic PDS-1000 bombardment apparatus (Bio-Rad). Bombarded worms were distributed onto large seeded plates and left to starve. Starved worms were chunked onto fresh seeded plates and screened for unc–119(+) transgenic animals. Rescued worms that expressed TAP::ALG-1 were kept and analyzed. All further experiments were done with the integrant opIs205[Peft-3::TAPtag::alg-1(genomics+3’UTR); unc-119(+)]. The transgenic line carrying opIs205 was crossed into alg-1(tm492) mutant animals to generate the strain WS4303 (alg-1(tm492); opIs205). The opIs205 transgene successfully rescued the reduced brood size of homozygous alg-1(tm492) mutant animals, proving the functionality of our transgene (data not shown).WS4303 was also crossed into mir-58(n4640) animals to generate the strain WS5041 (mir-58(n4640); alg-1(tm492); opIs205).

tag: genotype

tag: transgene

value: opIs205[Peft 3::TAPtag::alg 1(genomics+3’UTR); unc 119(+)] integrated by bombardment

value: synchronized, late L4

value: whole animal


title: Cow 7313 120d relative to parturition

treatment_protocol: Cows were maintain in a normal farm management

value: Mammary biopsy of cow at 120 day relative to parturition


title: serous ovarian cancer 552d2

tag: rec (1)

tag: os (m)

tag: death (1)


title: WS4303 (alg 1(tm492); opIs205). Replicate 2

description: TAP::ALG-1 associated RNA (RIP)

source_name: NO miRNA mutation (WT) expressing TAP::ALG-1

tag: strain


title: Cow 7313 240d relative to parturition

value: Mammary biopsy of cow at 240 day relative to parturition


title: Cow 7313 60d relative to parturition

value: Mammary biopsy of cow at 60 day relative to parturition


title: WS4303 (alg 1(tm492); opIs205). Replicate 3

description: TAP::ALG-1 associated RNA (RIP)

tag: developmental stage


title: Cow 7313 30d relative to parturition

value: Mammary biopsy of cow at 30 day relative to parturition


title: serous ovarian cancer 55d

tag: tissue


title: serous ovarian cancer 548d

value: IV


title: serous ovarian cancer 547d


title: C. remanei_rep2_stage5

description: C. remanei_rep2_stage5

value: 6th AB division


title: WS4303 (alg 1(tm492); opIs205). Replicate 1

description: TAP::ALG-1 associated RNA (RIP)


title: C. remanei_rep2_stage3

description: C. remanei_rep2_stage3

value: 4th AB division


title: C. remanei_rep2_stage4

description: C. remanei_rep2_stage4

value: 5th AB division


title: C. remanei_rep2_stage1

description: C. remanei_rep2_stage1

value: 4-cell stage


title: WS5041 (mir 58(n4640); alg 1(tm492); opIs205). Replicate 2

description: TAP::ALG-1 associated RNA (RIP)


title: C. remanei_rep2_stage2

description: C. remanei_rep2_stage2

value: E-cell division


title: serous ovarian cancer 549d2

value: high-grade serous ovarian cancer tumor

value: IIIc


title: Cow 7313 1d relative to parturition

value: Holstein dairy cow

value: Mammary biopsy of cow at 1 day relative to parturition

value: Bovine tissue reference (mammary, liver, muscle, adipsoe, and placenta)

value: Holstein dairy cows


title: serous ovarian cancer 546d

value: suboptimal


title: serous ovarian cancer 556d2


title: Cow 7313 -30d relative to parturition

value: Mammary biopsy of cow at -30 day relative to parturition


title: Cow 7277 30d relative to parturition


title: Cow 7313 -15d relative to parturition

value: Mammary biopsy of cow at -15 day relative to parturition


title: WS5041 (mir 58(n4640); alg 1(tm492); opIs205). Replicate 1

description: TAP::ALG-1 associated RNA (RIP)

value: opIs205[Peft 3::TAPtag::alg 1(genomics+3’UTR); unc 119(+)] integrated by bombardment

value: synchronized, late L4

value: whole animal


title: Cow 7313 15d relative to parturition

value: Mammary biopsy of cow at 15 day relative to parturition


title: serous ovarian cancer 544d

value: IV


title: serous ovarian cancer 543d


title: C. remanei_rep1_stage8

description: C. remanei_rep1_stage8

source_name: C. remanei,stage8

value: Comma stage


title: C. remanei_rep1_stage10

description: C. remanei_rep1_stage10

source_name: C. remanei,stage10

value: Juvenile L1 larvae


title: C. remanei_rep1_stage9

description: C. remanei_rep1_stage9

value: Movement


title: C. remanei_rep1_stage7

description: C. remanei_rep1_stage7

value: Ventral enclosure stage


title: serous ovarian cancer 542d

value: high-grade serous ovarian cancer tumor


title: Cow 7277 15d relative to parturition

value: Holstein dairy cow


title: C. remanei_rep1_stage6

description: C. remanei_rep1_stage6

source_name: C. remanei,stage6

value: 7th AB division


title: Preoptic area-anterior hypothalamus_Vinclozolin_Female_biological rep4

first: Michael

middle: K

last: Skinner

address: Abelson 507

department: SBS

institute: WSU

description:
Treatment-Sex Group: POAH-F-Vin
Marina-POAH-Vin-Fm-4-022310-142.CEL
Preoptic area-anterior hypothalamus from F3-generation Vincozolin lineage female 11 months old rat brain

hyb_protocol: Following fragmentation, ssDNA were hybridized  on Affymetrix Rat Gene 1.0 ST Array according to standard Affymetrix protocol. Chips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data for each of the 12 studied  male or female brain areas (F-Amy, F-CngCTX, F-EnCTX, F-Hipp, F-OlfB, F-POAH ,M-Amy, M-CngCTX, M-EnCTX, M-Hipp, M-OlfB, M-POAH) were pre-processed and analyzed as a separate group (12 groups,  9-12 chips per group) with Partek Genomic Suite 6.5 beta software (Partek Inc. St. Louis MO) in August-October of 2010 using RMA GC-content adjusted algorithm background correction, quintile normalization, median polish methods for probesets summarization, and log values of probes signals using base 2.

organism: Rattus norvegicus

source_name: Preoptic area-anterior hypothalamus from F3-generation Vincozolin lineage female rat brain

label_protocol: Biotin-labeled ssDNA were prepared according to the standard Affymetrix protocol from at least 300 ng total RNA (GeneChip® Whole Transcript (WT) Sense Target Labeling Assay Manual, 2005-2209, Affymetrix).

growth_protocol: Male and female rats of the F3 generation of Vinclozolin (Vinclozolin-Lineage) and DMSO Control (Control-Lineage) Lineages were selected out of litters from untreated F2 generation mothers at Washington State University according to established protocols (Anway et al., 2005).  On postnatal day (PND) 22, one day after weaning, animals were shipped to the University of Texas.  Upon arriving at the University of Texas, one animal from each Lineage (Control and Vinclozolin) was pair-housed (one control and one vinclozolin animal) and remained in these dyads throughout the duration of the behavioral study.  All rats were sacrificed at age of 11 months and certain brain areas samples were collected as 3 mm tissue punches and put into Trizol™ reagent (Invitrogen, USA) and kept at -20 degrees Celsius until RNA isolation.

extract_protocol: RNA was isolated from individual animal tissue homogenate in 750 ul Trizol™ reagent (Invitrogen, USA), according to manufacturer’s instructions.

treatment_protocol: Gestating outbred Sprague-Dawley mother rats were given intraperitoneal injections of Vinclozolin (100mg/kg/day) or vehicle (DMSO, Control) from embryonic day 8-14 (E8-E14) of gestation (i.e. F0 generation) [Cupp AS, et al., 2003].  Male and female rats of the F3 generation of Vinclozolin and Control lineages were selected out of litters from untreated F2 generation.  One animal from each lineage (Control and Vinclozolin) were pair-housed (one control and one vinclozolin animal) and remained in these dyads throughout the duration of the behavioral study until sacrifice at age of 11 months.

tag: rna prep date

tag: scan date

tag: animal id

tag: vin/con rats dyad group

value: Sprague-Dawley rat

tag: gender

value: Female

tag: generation

tag: lineage

value: Vincozolin

value: Preoptic area-anterior hypothalamus

tag: age

value: 11 months


title: C. remanei_rep1_stage5

description: C. remanei_rep1_stage5

value: 6th AB division


title: Cow 7277 1d relative to parturition

tag: breed

value: Mammary biopsy of cow at 1 day relative to parturition

value: Bovine tissue reference (mammary, liver, muscle, adipsoe, and placenta)

value: Holstein dairy cows


title: serous ovarian cancer 54d

tag: grading

tag: Stage

value: IIIb

tag: surgery status

value: optimal

tag: taxane

tag: platinum

tag: pfs (m)


title: Preoptic area-anterior hypothalamus_Vinclozolin_Female_biological rep6

description:
Treatment-Sex Group: POAH-F-Vin
Marina-POAH-Vin-Fm-6-022310-144.CEL
Preoptic area-anterior hypothalamus from F3-generation Vincozolin lineage female 11 months old rat brain

tag: strain


title: Preoptic area-anterior hypothalamus_Vinclozolin_Female_biological rep5

description:
Treatment-Sex Group: POAH-F-Vin
Marina-POAH-Vin-Fm-5-022310-143.CEL
Preoptic area-anterior hypothalamus from F3-generation Vincozolin lineage female 11 months old rat brain

tag: tissue


title: serous ovarian cancer 541d

value: IV

value: suboptimal

tag: rec (1)

tag: os (m)

tag: death (1)


title: C. remanei_rep1_stage4

description: C. remanei_rep1_stage4

tag: developmental stage

value: 5th AB division


title: Preoptic area-anterior hypothalamus_Vinclozolin_Female_biological rep2

description:
Treatment-Sex Group: POAH-F-Vin
Marina-POAH-Vin-Fm-2-022310-140.CEL
Preoptic area-anterior hypothalamus from F3-generation Vincozolin lineage female 11 months old rat brain

tag: rna prep date

tag: scan date

tag: animal id

tag: vin/con rats dyad group

tag: gender


title: Cow 7277 -15d relative to parturition

tag: breed

value: Mammary biopsy of cow at -15 day relative to parturition


title: Preoptic area-anterior hypothalamus_Vinclozolin_Female_biological rep3

description:
Treatment-Sex Group: POAH-F-Vin
Marina-POAH-Vin-Fm-3-022310-141.CEL
Preoptic area-anterior hypothalamus from F3-generation Vincozolin lineage female 11 months old rat brain

tag: generation

tag: lineage

tag: age


title: serous ovarian cancer 539d

value: high-grade serous ovarian cancer tumor

tag: grading

tag: Stage

tag: surgery status

tag: taxane

tag: platinum


title: Preoptic area-anterior hypothalamus_Vinclozolin_Female_biological rep1

description:
Treatment-Sex Group: POAH-F-Vin
Marina-POAH-Vin-Fm-1-022310-139.CEL
Preoptic area-anterior hypothalamus from F3-generation Vincozolin lineage female 11 months old rat brain

tag: strain

tag: tissue


title: Preoptic area-anterior hypothalamus_Control_Female_biological rep3

description:
Treatment-Sex Group: POAH-F-Con
Marina-POAH-Con-Fm-3-022310-135.CEL
Preoptic area-anterior hypothalamus from F3-generation control lineage (vehicle) female 11 months old rat brain

source_name: Preoptic area-anterior hypothalamus from F3-generation control lineage (vehicle) female rat brain

value: control (vehicle)


title: serous ovarian cancer 538d

tag: pfs (m)

tag: rec (1)

tag: os (m)

tag: death (1)


title: C. remanei_rep1_stage3

description: C. remanei_rep1_stage3

tag: developmental stage

value: 4th AB division


title: serous ovarian cancer 536d

value: IIIc


title: Preoptic area-anterior hypothalamus_Control_Female_biological rep5

description:
Treatment-Sex Group: POAH-F-Con
Marina-POAH-Con-Fm-5-022310-137.CEL
Preoptic area-anterior hypothalamus from F3-generation control lineage (vehicle) female 11 months old rat brain

tag: rna prep date

tag: scan date

tag: animal id

tag: vin/con rats dyad group

value: Sprague-Dawley rat

tag: gender

value: Female


title: Cow 7273 120d relative to parturition

tag: breed

value: Holstein dairy cow

value: Mammary biopsy of cow at 120 day relative to parturition


title: C. remanei_rep1_stage2

description: C. remanei_rep1_stage2

value: E-cell division


title: Preoptic area-anterior hypothalamus_Control_Female_biological rep6

description:
Treatment-Sex Group: POAH-F-Con
Marina-POAH-Con-Fm-6-022310-138.CEL
Preoptic area-anterior hypothalamus from F3-generation control lineage (vehicle) female 11 months old rat brain

tag: generation

tag: lineage

value: Preoptic area-anterior hypothalamus

tag: age

value: 11 months


title: Cow 7277 -30d relative to parturition

value: Mammary biopsy of cow at -30 day relative to parturition

value: Bovine tissue reference (mammary, liver, muscle, adipsoe, and placenta)

value: Holstein dairy cows


title: Preoptic area-anterior hypothalamus_Control_Female_biological rep2

description:
Treatment-Sex Group: POAH-F-Con
Marina-POAH-Con-Fm-2-022310-134.CEL
Preoptic area-anterior hypothalamus from F3-generation control lineage (vehicle) female 11 months old rat brain


title: serous ovarian cancer 535d

tag: grading

tag: Stage

value: IIIa

tag: surgery status

value: optimal

tag: taxane

tag: platinum


title: Cow 7273 240d relative to parturition

value: Mammary biopsy of cow at 240 day relative to parturition


title: Cow 7273 60d relative to parturition

value: Mammary biopsy of cow at 60 day relative to parturition


title: Preoptic area-anterior hypothalamus_Vinclozolin_Male_biological rep11

description:
Treatment-Sex Group: POAH-M-Vin
Marina-POAH-Vin-M-11-022210-131.CEL
Preoptic area-anterior hypothalamus from F3-generation Vincozolin lineage male 11 months old rat brain

source_name: Preoptic area-anterior hypothalamus from F3-generation Vincozolin lineage male rat brain

tag: strain

value: Male

value: Vincozolin

tag: tissue


title: C. japonica_rep3_stage10

description: C. japonica_rep3_stage10

organism: Caenorhabditis japonica

source_name: C. japonica, stage10

tag: developmental stage

value: Juvenile L1 larvae


title: C. remanei_rep1_stage1

description: C. remanei_rep1_stage1

value: 4-cell stage


title: Cow 7273 15d relative to parturition

value: Mammary biopsy of cow at 15 day relative to parturition


title: Preoptic area-anterior hypothalamus_Control_Female_biological rep1

description:
Treatment-Sex Group: POAH-F-Con
Marina-POAH-Con-Fm-1-022310-133.CEL
Preoptic area-anterior hypothalamus from F3-generation control lineage (vehicle) female 11 months old rat brain

tag: rna prep date

value: Sprague-Dawley rat

value: Female

value: control (vehicle)


title: serous ovarian cancer 537d2

source_name: high-grade serous ovarian cancer

value: high-grade serous ovarian cancer tumor

value: IIIc

value: suboptimal

tag: pfs (m)

tag: rec (1)

tag: os (m)

tag: death (1)


title: Preoptic area-anterior hypothalamus_Vinclozolin_Male_biological rep8

description:
Treatment-Sex Group: POAH-M-Vin
Marina-POAH-Vin-M-8-022210-128.CEL
Preoptic area-anterior hypothalamus from F3-generation Vincozolin lineage male 11 months old rat brain

tag: scan date

tag: animal id

tag: vin/con rats dyad group

tag: gender

value: Preoptic area-anterior hypothalamus

value: 11 months


title: Cow 7273 30d relative to parturition

tag: breed

value: Holstein dairy cow

value: Mammary biopsy of cow at 30 day relative to parturition

value: Bovine tissue reference (mammary, liver, muscle, adipsoe, and placenta)

value: Holstein dairy cows


title: Cow 7273 -15d relative to parturition

value: Mammary biopsy of cow at -15 day relative to parturition


title: serous ovarian cancer 531d2

tag: grading

tag: Stage

value: IV


title: C. japonica_rep3_stage7

description: C. japonica_rep3_stage7

source_name: C. japonica, stage7

value: Ventral enclosure stage


title: serous ovarian cancer 533d

tag: surgery status

value: optimal

tag: taxane


title: C. japonica_rep3_stage9

description: C. japonica_rep3_stage9

source_name: C. japonica, stage9

value: Movement


title: Preoptic area-anterior hypothalamus_Vinclozolin_Male_biological rep9

description:
Treatment-Sex Group: POAH-M-Vin
Marina-POAH-Vin-M-9-022210-129.CEL
Preoptic area-anterior hypothalamus from F3-generation Vincozolin lineage male 11 months old rat brain

tag: strain

value: Sprague-Dawley rat

value: Male

tag: generation

tag: lineage

value: Vincozolin

tag: age


title: Cow 7273 1d relative to parturition

value: Mammary biopsy of cow at 1 day relative to parturition


title: C. japonica_rep3_stage5

description: C. japonica_rep3_stage5

source_name: C. japonica, stage5

tag: developmental stage

value: 6th AB division


title: C. japonica_rep3_stage6

description: C. japonica_rep3_stage6

source_name: C. japonica, stage6

value: 7th AB division


title: serous ovarian cancer 529d

tag: tissue

value: high-grade serous ovarian cancer tumor

value: IIIc

tag: platinum

tag: pfs (m)

tag: rec (1)


title: C. japonica_rep3_stage4

description: C. japonica_rep3_stage4

source_name: C. japonica, stage4

value: 5th AB division


title: serous ovarian cancer 534d

tag: os (m)

tag: death (1)


title: Preoptic area-anterior hypothalamus_Vinclozolin_Male_biological rep7

description:
Treatment-Sex Group: POAH-M-Vin
Marina-POAH-Vin-M-7-022210-127.CEL
Preoptic area-anterior hypothalamus from F3-generation Vincozolin lineage male 11 months old rat brain

tag: rna prep date

tag: scan date

tag: animal id

tag: vin/con rats dyad group

tag: gender

value: Preoptic area-anterior hypothalamus

value: 11 months


title: Preoptic area-anterior hypothalamus_Control_Male_biological rep10

description:
Treatment-Sex Group: POAH-M-Con
Marina-POAH-Con-M-10-022210-124.CEL
Preoptic area-anterior hypothalamus from F3-generation control lineage (vehicle) male 11 months old rat brain

source_name: Preoptic area-anterior hypothalamus from F3-generation control lineage (vehicle) male rat brain

value: control (vehicle)


title: Preoptic area-anterior hypothalamus_Control_Male_biological rep11

description:
Treatment-Sex Group: POAH-M-Con
Marina-POAH-Con-M-11-022210-125.CEL
Preoptic area-anterior hypothalamus from F3-generation control lineage (vehicle) male 11 months old rat brain


title: Cow 7273 -30d relative to parturition

description: A mixture of total RNA from 5 bovine tissues (mammary, liver, muscle, adipsoe, and placenta) were used as reference.

tag: breed

value: Holstein dairy cow

value: Mammary biopsy of cow at -30 day relative to parturition

value: Bovine tissue reference (mammary, liver, muscle, adipsoe, and placenta)

value: Holstein dairy cows


title: C. japonica_rep3_stage8

description: C. japonica_rep3_stage8

source_name: C. japonica, stage8

value: Comma stage


title: serous ovarian cancer 528d2

tag: grading

tag: Stage

tag: surgery status

value: optimal

tag: taxane


title: serous ovarian cancer 53d

value: IV

value: suboptimal


title: Cow 7265 30d relative to parturition

value: Mammary biopsy of cow at 30 day relative to parturition


title: Cow 7265 15d relative to parturition

value: Mammary biopsy of cow at 15 day relative to parturition


title: C. japonica_rep3_stage3

description: C. japonica_rep3_stage3

source_name: C. japonica, stage3

tag: developmental stage

value: 4th AB division


title: serous ovarian cancer 527d2

tag: tissue

value: high-grade serous ovarian cancer tumor


title: Cow 7264 240d relative to parturition

value: Mammary biopsy of cow at 240 day relative to parturition


title: Cow 7265 -15d relative to parturition

value: Mammary biopsy of cow at -15 day relative to parturition


title: serous ovarian cancer 525d2

value: IIIc

tag: platinum


title: Preoptic area-anterior hypothalamus_Control_Male_biological rep7

description:
Treatment-Sex Group: POAH-M-Con
Marina-POAH-Con-M-7-022210-121.CEL
Preoptic area-anterior hypothalamus from F3-generation control lineage (vehicle) male 11 months old rat brain

tag: strain

value: Sprague-Dawley rat

value: Male

tag: generation

tag: lineage

value: Preoptic area-anterior hypothalamus

tag: age

value: 11 months


title: serous ovarian cancer 526d2

tag: pfs (m)

tag: rec (1)

tag: os (m)

tag: death (1)


title: Cow 7264 300d relative to parturition

value: Holstein dairy cow

value: Mammary biopsy of cow at 300 day relative to parturition

value: Bovine tissue reference (mammary, liver, muscle, adipsoe, and placenta)


title: serous ovarian cancer 522d2


title: C. japonica_rep3_stage2

description: C. japonica_rep3_stage2

source_name: C. japonica, stage2

value: E-cell division


title: Cow 7265 1d relative to parturition

value: Mammary biopsy of cow at 1 day relative to parturition

value: Holstein dairy cows


title: Entorhinal cortex_Vinclozolin_Female_biological rep6

description:
Treatment-Sex Group: EnCTX-F-Vin
Marina-EnCTX-Vin-Fm-6-021210-120.CEL
Entorhinal cortex from F3-generation Vincozolin lineage female 11 months old rat brain

source_name: Entorhinal cortex from F3-generation Vincozolin lineage female rat brain

tag: rna prep date

tag: scan date

tag: animal id

tag: vin/con rats dyad group

tag: gender

value: Female

value: Vincozolin

value: Entorhinal cortex


title: Entorhinal cortex_Vinclozolin_Female_biological rep5

description:
Treatment-Sex Group: EnCTX-F-Vin
Marina-EnCTX-Vin-Fm-5-021210-119.CEL
Entorhinal cortex from F3-generation Vincozolin lineage female 11 months old rat brain


title: Preoptic area-anterior hypothalamus_Control_Male_biological rep9

description:
Treatment-Sex Group: POAH-M-Con
Marina-POAH-Con-M-9-022210-123.CEL
Preoptic area-anterior hypothalamus from F3-generation control lineage (vehicle) male 11 months old rat brain

value: control (vehicle)


title: C. japonica_rep3_stage1

description: C. japonica_rep3_stage1

source_name: C. japonica, stage1

value: 4-cell stage


title: Cow 7264 120d relative to parturition

tag: breed

value: Mammary biopsy of cow at 120 day relative to parturition


title: Entorhinal cortex_Vinclozolin_Female_biological rep4

description:
Treatment-Sex Group: EnCTX-F-Vin
Marina-EnCTX-Vin-Fm-4-021210-118.CEL
Entorhinal cortex from F3-generation Vincozolin lineage female 11 months old rat brain


title: serous ovarian cancer 523d2

value: high-grade serous ovarian cancer tumor

tag: grading

tag: Stage

value: IV

tag: surgery status

value: optimal

tag: taxane


title: C. japonica_rep2_stage10

description: C. japonica_rep2_stage10

tag: developmental stage

value: Juvenile L1 larvae


title: Preoptic area-anterior hypothalamus_Control_Male_biological rep8

description:
Treatment-Sex Group: POAH-M-Con
Marina-POAH-Con-M-8-022210-122.CEL
Preoptic area-anterior hypothalamus from F3-generation control lineage (vehicle) male 11 months old rat brain

tag: strain

value: Sprague-Dawley rat

value: Male

tag: generation

tag: lineage

tag: tissue

value: Preoptic area-anterior hypothalamus

value: 11 months


title: serous ovarian cancer 521d2

value: IIIc

value: suboptimal

tag: platinum

tag: pfs (m)

tag: rec (1)

tag: os (m)


title: C. japonica_rep2_stage9

description: C. japonica_rep2_stage9

value: Movement


title: serous ovarian cancer 520d2

tag: death (1)


title: C. japonica_rep2_stage7

description: C. japonica_rep2_stage7

value: Ventral enclosure stage


title: C. japonica_rep2_stage8

description: C. japonica_rep2_stage8

value: Comma stage


title: Cow 7264 60d relative to parturition

value: Holstein dairy cow

value: Mammary biopsy of cow at 60 day relative to parturition

value: Bovine tissue reference (mammary, liver, muscle, adipsoe, and placenta)

value: Holstein dairy cows


title: Entorhinal cortex_Vinclozolin_Female_biological rep3

description:
Treatment-Sex Group: EnCTX-F-Vin
Marina-EnCTX-Vin-Fm-3-021210-117.CEL
Entorhinal cortex from F3-generation Vincozolin lineage female 11 months old rat brain

tag: rna prep date

tag: scan date

tag: animal id

tag: vin/con rats dyad group

value: Female

value: Vincozolin

value: Entorhinal cortex

tag: age


title: serous ovarian cancer 519d2

value: high-grade serous ovarian cancer tumor

tag: grading

tag: Stage

tag: surgery status


title: C. japonica_rep2_stage6

description: C. japonica_rep2_stage6

tag: developmental stage

value: 7th AB division


title: Entorhinal cortex_Vinclozolin_Female_biological rep2

description:
Treatment-Sex Group: EnCTX-F-Vin
Marina-EnCTX-Vin-Fm-2-021210-116.CEL
Entorhinal cortex from F3-generation Vincozolin lineage female 11 months old rat brain

tag: strain

value: Sprague-Dawley rat

tag: gender

tag: generation


title: Entorhinal cortex_Vinclozolin_Female_biological rep1

description:
Treatment-Sex Group: EnCTX-F-Vin
Marina-EnCTX-Vin-Fm-1-021210-115.CEL
Entorhinal cortex from F3-generation Vincozolin lineage female 11 months old rat brain

tag: lineage

tag: tissue


title: serous ovarian cancer 518d

value: optimal

tag: taxane

tag: platinum

tag: pfs (m)

tag: rec (1)


title: serous ovarian cancer 516d

value: IV

tag: os (m)

tag: death (1)


title: Cow 7264 -30d relative to parturition

tag: breed

value: Mammary biopsy of cow at -30 day relative to parturition


title: Cow 7264 -15d relative to parturition

value: Mammary biopsy of cow at -15 day relative to parturition


title: Entorhinal cortex_Control_Female_biological rep5

description:
Treatment-Sex Group: EnCTX-F-Con
Marina-EnCTX-Con-Fm-5-021210-113.CEL
Entorhinal cortex from F3-generation control lineage (vehicle) female 11 months old rat brain

source_name: Entorhinal cortex from F3-generation control lineage (vehicle) female rat brain

tag: rna prep date

tag: scan date

tag: animal id

tag: vin/con rats dyad group

value: control (vehicle)

tag: age

value: 11 months


title: Cow 7257 120d relative to parturition

value: Mammary biopsy of cow at 120 day relative to parturition


title: Entorhinal cortex_Control_Female_biological rep4

description:
Treatment-Sex Group: EnCTX-F-Con
Marina-EnCTX-Con-Fm-4-021210-112.CEL
Entorhinal cortex from F3-generation control lineage (vehicle) female 11 months old rat brain

tag: strain


title: C. japonica_rep2_stage5

description: C. japonica_rep2_stage5

tag: developmental stage

value: 6th AB division


title: Cow 7257 60d relative to parturition

value: Holstein dairy cow

value: Mammary biopsy of cow at 60 day relative to parturition


title: Entorhinal cortex_Control_Female_biological rep6

description:
Treatment-Sex Group: EnCTX-F-Con
Marina-EnCTX-Con-Fm-6-021210-114.CEL
Entorhinal cortex from F3-generation control lineage (vehicle) female 11 months old rat brain

tag: gender

tag: generation


title: C. japonica_rep2_stage3

description: C. japonica_rep2_stage3

value: 4th AB division


title: Cow 7264 30d relative to parturition

value: Mammary biopsy of cow at 30 day relative to parturition

value: Bovine tissue reference (mammary, liver, muscle, adipsoe, and placenta)

value: Holstein dairy cows


title: serous ovarian cancer 514d2

tag: tissue

value: high-grade serous ovarian cancer tumor

tag: grading

tag: Stage

value: IIIc

tag: surgery status

value: suboptimal


title: Cow 7264 1d relative to parturition

value: Mammary biopsy of cow at 1 day relative to parturition


title: serous ovarian cancer 511d

tag: taxane

tag: platinum

tag: pfs (m)

tag: rec (1)


title: serous ovarian cancer 510d2

tag: os (m)

tag: death (1)


title: Entorhinal cortex_Control_Female_biological rep3

description:
Treatment-Sex Group: EnCTX-F-Con
Marina-EnCTX-Con-Fm-3-021210-111.CEL
Entorhinal cortex from F3-generation control lineage (vehicle) female 11 months old rat brain

tag: rna prep date

tag: scan date

tag: animal id

value: Sprague-Dawley rat

value: Female

tag: lineage

value: Entorhinal cortex


title: C. japonica_rep2_stage4

description: C. japonica_rep2_stage4

tag: developmental stage

value: 5th AB division


title: C. japonica_rep2_stage2

description: C. japonica_rep2_stage2

value: E-cell division


title: serous ovarian cancer 513d


title: C. japonica_rep1_stage10

description: C. japonica_rep1_stage10

value: Juvenile L1 larvae


title: Cow 7257 30d relative to parturition

tag: breed


title: C. japonica_rep1_stage9

description: C. japonica_rep1_stage9

value: Movement


title: Entorhinal cortex_Control_Female_biological rep1

description:
Treatment-Sex Group: EnCTX-F-Con
Marina-EnCTX-Con-Fm-1-021210-109.CEL
Entorhinal cortex from F3-generation control lineage (vehicle) female 11 months old rat brain

tag: vin/con rats dyad group

tag: strain

tag: gender

tag: generation

value: control (vehicle)

tag: age

value: 11 months


title: C. japonica_rep2_stage1

description: C. japonica_rep2_stage1

value: 4-cell stage


title: Cow 7264 15d relative to parturition

value: Holstein dairy cow

value: Mammary biopsy of cow at 15 day relative to parturition


title: serous ovarian cancer 512d

tag: tissue

tag: grading

tag: Stage

tag: surgery status

tag: taxane


title: Entorhinal cortex_Control_Female_biological rep2

description:
Treatment-Sex Group: EnCTX-F-Con
Marina-EnCTX-Con-Fm-2-021210-110.CEL
Entorhinal cortex from F3-generation control lineage (vehicle) female 11 months old rat brain


title: Cow 7257 15d relative to parturition

value: Bovine tissue reference (mammary, liver, muscle, adipsoe, and placenta)

value: Holstein dairy cows


title: serous ovarian cancer 51d

value: high-grade serous ovarian cancer tumor

value: IIIc

tag: platinum

tag: pfs (m)

tag: rec (1)

tag: os (m)

tag: death (1)


title: Entorhinal cortex_Vinclozolin_Male_biological rep7

description:
Treatment-Sex Group: EnCTX-M-Vin
Marina-EnCTX-Vin-M-7-021110-103.CEL
Entorhinal cortex from F3-generation Vincozolin lineage male 11 months old rat brain

source_name: Entorhinal cortex from F3-generation Vincozolin lineage male rat brain

tag: rna prep date

tag: scan date

tag: animal id

value: Male

tag: lineage

value: Vincozolin


title: Entorhinal cortex_Vinclozolin_Male_biological rep8

description:
Treatment-Sex Group: EnCTX-M-Vin
Marina-EnCTX-Vin-M-8-021110-104.CEL
Entorhinal cortex from F3-generation Vincozolin lineage male 11 months old rat brain

tag: vin/con rats dyad group

tag: strain

value: Sprague-Dawley rat

tag: gender


title: Entorhinal cortex_Vinclozolin_Male_biological rep9

description:
Treatment-Sex Group: EnCTX-M-Vin
Marina-EnCTX-Vin-M-9-021110-105.CEL
Entorhinal cortex from F3-generation Vincozolin lineage male 11 months old rat brain

tag: generation

tag: tissue

value: Entorhinal cortex

tag: age


title: Entorhinal cortex_Vinclozolin_Male_biological rep10

description:
Treatment-Sex Group: EnCTX-M-Vin
Marina-EnCTX-Vin-M-10-021110-106.CEL
Entorhinal cortex from F3-generation Vincozolin lineage male 11 months old rat brain


title: C. japonica_rep1_stage7

description: C. japonica_rep1_stage7

tag: developmental stage

value: Ventral enclosure stage


title: serous ovarian cancer 508d2

tag: grading

tag: Stage

value: IV

tag: surgery status

value: optimal

tag: taxane


title: serous ovarian cancer 507d2

tag: platinum

tag: pfs (m)

tag: rec (1)

tag: os (m)


title: C. japonica_rep1_stage8

description: C. japonica_rep1_stage8

value: Comma stage


title: Cow 7257 -15d relative to parturition

description: A mixture of total RNA from 5 bovine tissues (mammary, liver, muscle, adipsoe, and placenta) were used as reference.

tag: breed

value: Mammary biopsy of cow at -15 day relative to parturition


title: C. japonica_rep1_stage5

description: C. japonica_rep1_stage5

value: 6th AB division


title: serous ovarian cancer 509d

tag: death (1)


title: Cow 7257 -30d relative to parturition

value: Mammary biopsy of cow at -30 day relative to parturition


title: Cow 7251 300d relative to parturition

value: Holstein dairy cow

value: Mammary biopsy of cow at 300 day relative to parturition


title: serous ovarian cancer 505d


title: Cow 7251 240d relative to parturition

value: Mammary biopsy of cow at 240 day relative to parturition

value: Bovine tissue reference (mammary, liver, muscle, adipsoe, and placenta)


title: Cow 7257 1d relative to parturition

value: Mammary biopsy of cow at 1 day relative to parturition

value: Holstein dairy cows


title: serous ovarian cancer 504d2

value: high-grade serous ovarian cancer tumor

value: suboptimal


title: C. japonica_rep1_stage2

description: C. japonica_rep1_stage2

value: E-cell division


title: C. japonica_rep1_stage6

description: C. japonica_rep1_stage6

value: 7th AB division


title: serous ovarian cancer 503d

value: IIIc


title: Entorhinal cortex_Control_Male_biological rep11

description:
Treatment-Sex Group: EnCTX-M-Con
Marina-EnCTX-Con-M-11-021110-101.CEL
Entorhinal cortex from F3-generation control lineage (vehicle) male 11 months old rat brain

source_name: Entorhinal cortex from F3-generation control lineage (vehicle) male rat brain

tag: rna prep date

tag: scan date

tag: animal id

tag: vin/con rats dyad group

value: Sprague-Dawley rat

value: Male

tag: lineage

value: control (vehicle)

value: Entorhinal cortex

value: 11 months


title: Cow 7251 120d relative to parturition

value: Mammary biopsy of cow at 120 day relative to parturition


title: C. japonica_rep1_stage3

description: C. japonica_rep1_stage3

value: 4th AB division


title: C. japonica_rep1_stage4

description: C. japonica_rep1_stage4

value: 5th AB division


title: Entorhinal cortex_Control_Male_biological rep10

description:
Treatment-Sex Group: EnCTX-M-Con
Marina-EnCTX-Con-M-10-021110-100.CEL
Entorhinal cortex from F3-generation control lineage (vehicle) male 11 months old rat brain

tag: strain

tag: gender

tag: generation

tag: tissue

tag: age


title: Entorhinal cortex_Control_Male_biological rep12

description:
Treatment-Sex Group: EnCTX-M-Con
Marina-EnCTX-Con-M-12-021110-102.CEL
Entorhinal cortex from F3-generation control lineage (vehicle) male 11 months old rat brain


title: Entorhinal cortex_Control_Male_biological rep8

description:
Treatment-Sex Group: EnCTX-M-Con
Marina-EnCTX-Con-M-8-021110-98.CEL
Entorhinal cortex from F3-generation control lineage (vehicle) male 11 months old rat brain


title: serous ovarian cancer 502d2

tag: grading

tag: Stage

tag: surgery status

tag: taxane


title: Entorhinal cortex_Control_Male_biological rep9

description:
Treatment-Sex Group: EnCTX-M-Con
Marina-EnCTX-Con-M-9-021110-99.CEL
Entorhinal cortex from F3-generation control lineage (vehicle) male 11 months old rat brain


title: C. japonica_rep1_stage1

description: C. japonica_rep1_stage1

tag: developmental stage

value: 4-cell stage


title: Cow 7251 30d relative to parturition

tag: breed

value: Holstein dairy cow

value: Mammary biopsy of cow at 30 day relative to parturition

value: Bovine tissue reference (mammary, liver, muscle, adipsoe, and placenta)


title: serous ovarian cancer 501d

value: high-grade serous ovarian cancer tumor

tag: platinum

tag: pfs (m)

tag: rec (1)

tag: os (m)

tag: death (1)


title: Cow 7251 60d relative to parturition

value: Mammary biopsy of cow at 60 day relative to parturition

value: Holstein dairy cows


title: C. elegans_rep3_stage9

description: C. elegans_rep3_stage9

source_name: C. elegans, stage9

value: Movement


title: Entorhinal cortex_Control_Male_biological rep7

description:
Treatment-Sex Group: EnCTX-M-Con
Marina-EnCTX-Con-M-7-021110-97.CEL
Entorhinal cortex from F3-generation control lineage (vehicle) male 11 months old rat brain

tag: rna prep date

tag: scan date

tag: animal id

tag: vin/con rats dyad group

tag: lineage


title: serous ovarian cancer 500d

tag: tissue

value: IIIc

value: suboptimal


title: C. elegans_rep3_stage10

description: C. elegans_rep3_stage10

source_name: C. elegans, stage10

value: Juvenile L1 larvae


title: Cow 7251 15d relative to parturition

value: Mammary biopsy of cow at 15 day relative to parturition


title: Cow 7251 1d relative to parturition

value: Mammary biopsy of cow at 1 day relative to parturition


title: Cingulate cortex_Vinclozolin_Female_biological rep5

description:
Treatment-Sex Group: CngCTX-F-Vin
Marina-CngCTX-Vin-FM-5-121009-95.CEL
Cingulate cortex from F3-generation Vincozolin lineage female 11 months old rat brain

source_name: Cingulate cortex from F3-generation Vincozolin lineage female rat brain

tag: strain

value: Sprague-Dawley rat

tag: gender

value: Female

tag: generation

value: Vincozolin

value: Cingulate cortex

tag: age

value: 11 months


title: Cow 7251 -15d relative to parturition

value: Holstein dairy cow

value: Mammary biopsy of cow at -15 day relative to parturition


title: Cingulate cortex_Vinclozolin_Female_biological rep4

description:
Treatment-Sex Group: CngCTX-F-Vin
Marina-CngCTX-Vin-FM-4-121009-94.CEL
Cingulate cortex from F3-generation Vincozolin lineage female 11 months old rat brain