title: cFDcontrol_12hpfuvcmd_16hpfsort_rep5

city: Stanford

first: James

last: Chen

state: CA

address: 269 Campus Dr

department: Chemical and Systems Biology

institute: Stanford University

description: These are control embryonic cells form notochord with WT morphology.

data_processing: The raw data (.pair file) was subjected to RMA, quantile normalization, background correction, and generation of gene expression calls from probe sets (.calls file) by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See ww.nimblegen.com.

organism: Danio rerio

source_name: cFD injected, 12 hpf irradiated in chordamesoderm, 16 hpf collected

label_protocol: Average cDNA length was 400 bp, as determined by capillary electrophoresis (Agilent Bioanalyzer DNA 1000 kit).  Cy3 labeling was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

growth_protocol: Zebrafish embryos were collected by natural mating and maintained in E3 media at 28.5°C.  Following localized irradiation with 360-nm light, embryos were cultured to 16 hpf.

extract_protocol: Linear acrylamide (5 µL of a 5 mg/mL solution; Ambion) was added to the chilled 1-mL TRIzol solution containing the sorted cells, RNA pellet was obtained according to manufacturer’s protocol, and resuspended in water (2.8 µL). Isolated RNA was reverse transcribed and amplified with a WTA2 TransPlex Complete Whole Transcriptome Amplification kit (Sigma) using a miniaturized procedure and manufacturer-recommended incubation steps. The RNA solution was mixed with library synthesis buffer (0.5 µL) and incubated to anneal primers. Pre-made library synthesis mix (0.5 µL library synthesis buffer, 0.5 µL library synthesis enzyme, and 0.78 µL water) was then added, and the RNA was reverse-transcribed. Amplification master mix (70 µL; 8 µL amplification mix, 1.6 µL dNTP, 0.8 µL amplification enzyme, and 63.5 µL water) was added to the cDNA, and after 22 PCR cycles the amplified cDNA was isolated using a QIAquick PCR purification kit (Qiagen) in 30 µL EB solution.

treatment_protocol:
Embryos were dechorinated with pronase, and transferred to calcium-free Ringer’s solution (100 μL for 25-30 embryos; 116 mM NaCl, 2.6 mM KCl, 5 mM HEPES, pH 7.0), homogenized with a 200-μL pipette tip, and incubated for 5 min at room temperature.  Embryonic homogenate was transferred to a 1.2-mL solution of 1X PBS containing trypsin (0.25%, Gibco, 15090-046), collagenase P (30 μg, Roche), and 1 mM EDTA, incubated for 15 min at 28.5 °C with further triturating every 5 min. Trypsin digestion was quenched with stop solution (200 μL; 1X PBS containing 30% (v/v) calf serum and 6 mM CaCl2), and cells were collected by centrifugation (400 x g, 5 min, 4 °C). After aspirating the supernatant, cells were resuspended in chilled suspension solution (700 μL; DMEM containing 1% (v/v) calf serum, 0.8 mM CaCl2, 50 U/mL penicillin, and 0.05 mg/ml streptomycin), centrifuged again, and resuspended once more in chilled suspension solution.
The cell suspension was filtered into FACS sample tubes through a 40-μm cell strainer (BD Biosciences).  Irradiated, fluorescent cells from the dissociated embryos were purified using a BD FACSAria sorter using a 100-μm nozzle. Chilled cells were periodically vortexed to prevent settling, and the signal threshold was set to 2,000 to prevent contamination of the sorted cells with embryonic debris. Forward and side scatter gates were used to isolate viable, individual cells from embryonic debris, and FL1-Area (Ex: 488 nm; Em: 530 nm) intensities were used to identify green fluorescent cells, that were sorted directly into 1 mL of chilled TRIzol (Invitrogen) in siliconized microcentrifuge tubes. Approximately 8,000 cells were collected from each group of 25-30 locally irradiated embryos.

value: AB


title: cFDcontrol_12hpfuvcmd_16hpfsort_rep4

status: Public on Mar 01 2012

type: RNA

country: USA

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.

molecule: total RNA

tag: strain


title: DMEM-HI + S. boydii PCM, biological rep2

city: Baltimore

first: Jason

last: Sahl

state: MD

address: 801 West Baltimore St.

department: School of Medicine

institute: University of Maryland

description: Expression in minimal media plus PCM from obligate pathogen

hyb_protocol: A hybridization mixture was prepared that contained labeled cDNA, 7.8% DMSO and OligoB2 mixture (Affymetrix, P/N 900301) according to the manufacturers protocols.  GeneChips were prepared by pre-hybridization for 10 minutes at 45ºC with the kit pre-hybridization solution; samples were denatured at 95ºC for 1 minute, equilibrated to 45ºC, centrifuged, and transferred to prepared arrays.  Hybridization was continued in a rotating incubator for 16h at 60 rpm and 45ºC.  Post-hybridization, the hybridization cocktail was recovered and the arrays washed and stained using the standard Affymetrix ProkGE-WS2v3_450 fluidics protocol and GeneChip Hybridization, Wash and Stain Kit reagents (Affymetrix, P/N 900720).

scan_protocol: Chips were scanned with the Affymetrix GCOS software

data_processing: Array data was processed with the Simpleaffy bioconductor package in R

label: biotin

organism: Escherichia coli O139:H28 str. E24377A

source_name: E24377A grown in DMEM-HI glucose + PCM from Shigella boydii (10% v/v)

label_protocol: Digested cDNA was end-labeled with Biotin-11-ddATP (Perkin Elmer, P/N NEL548001EA) using Terminal Deoxynucleotidyl Transferase, and verified by gel shift assay, according to Affymetrix standard protocols

growth_protocol: Single colonies were grown overnight at 37C and 225 rpm in 5 ml LB.  The next day, cultures were diluted 1:100 in 25 ml LB, grown at 37C at 225 rpm

extract_protocol: Cultures were either extracted using the RiboPure RNA kit from ambion, or a acid phenol/lithium chloride method

tag: treatment


title: Amygdaloid nuclei_Control_Female_biological rep6

city: Pullman

first: Michael

middle: K

last: Skinner

state: WA

address: Abelson 507

department: SBS

institute: WSU

description:
Treatment-Sex Group: Amy-F-Con
Marina-Amy-Con-Fm-6_111709-18(3D).CEL
Amygdaloid nuclei from F3-generation control lineage (vehicle) 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: Amygdaloid nuclei from F3-generation control lineage (vehicle) 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: control (vehicle)

tag: tissue

value: Amygdaloid nuclei

tag: age

value: 11 months


title: serous ovarian cancer 306d

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 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.

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)

value: high-grade serous ovarian cancer tumor

tag: grading

tag: Stage

value: IIIc

tag: surgery status

value: suboptimal

tag: taxane

tag: platinum

tag: pfs (m)

tag: rec (1)

tag: os (m)

tag: death (1)


title: PA01_cell_28℃_rep1

city: Shanghai

first: daqiang

last: wu

address: 800 Dongchuan Road

department: School of life science and biotechnology

country: China

institute: Shanghaijiaotong University

description: gene expression at 28℃

hyb_protocol: Each Slide was hybridized with 1.65μg Cy3-labeled cRNA using Gene Expression Hybridization Kit (Agilent technologies, Santa Clara, CA, US)Hybridization Oven (Agilent technologies, Santa Clara, CA, US), according to the manufacturer’s instructions. After 17 hours hybridization, slides were washed in staining dishes with Gene Expression Wash Buffer Kit( Agilent technologies, Santa Clara, CA, US), Stabilization and Drying Solution (Agilent technologies, Santa Clara, CA, US)followed the manufacturer’s instructions。

scan_protocol: Scanned on an Agilent G2505B scanner.

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent technologies, Santa Clara, CA, US) using default parameters.

organism: Pseudomonas aeruginosa

source_name: Cells, 28℃,replicate 1

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared using the  Low RNA Input Linear Amplification  kit (Agilent technologies, Santa Clara, CA, US) according to the manufacturer's instructions,and purified by RNeasy mini kit ( QIAGEN, GmBH, Germany).

growth_protocol: Cells were grown to OD600=5.0-6.0 (late exponential phase) in LB medium at 28℃ and 37℃, respectively.

extract_protocol: Total RNA was extracted using TRIzol reagent (Invitrogen,Carlsbad, CA, USA).

tag: growth phase

value: late exponential phase

tag: temperature


title: PA01_cell_28℃_rep2

description: gene expression at 28℃

source_name: Cells, 28℃,replicate 2


title: LB + bile salts, OD600=0.8

description: Expression in bile salts at high growth density

source_name: E24377A grown in LB + bile salts (3% w/v) at OD600=0.8

tag: treatment


title: DMEM-HI + S. boydii PCM, biological rep1

source_name: E24377A grown in DMEM-HI glucose + PCM from Shigella boydii  (10% v/v)


title: Amygdaloid nuclei_Vinclozolin_Female_biological rep2

description:
Treatment-Sex Group: Amy-F-Vin
Marina-Amy-Vin-Fm-2_111709-20(1C).CEL
Amygdaloid nuclei from F3-generation Vincozolin lineage female 11 months old rat brain

source_name: Amygdaloid nuclei 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: strain

tag: gender

value: Vincozolin


title: serous ovarian cancer 303d

tag: tissue

tag: grading

tag: Stage

value: optimal


title: Amygdaloid nuclei_Control_Female_biological rep3

description:
Treatment-Sex Group: Amy-F-Con
Marina-Amy-Con-Fm-3_111709-15(3C).CEL
Amygdaloid nuclei from F3-generation control lineage (vehicle) female 11 months old rat brain

tag: generation

tag: lineage

tag: age


title: PA01_cell_28℃_rep3

description: gene expression at 28℃

source_name: Cells, 28℃,replicate 3


title: serous ovarian cancer 305d2

tag: surgery status

tag: taxane

tag: platinum

tag: pfs (m)

tag: rec (1)

tag: os (m)


title: Amygdaloid nuclei_Vinclozolin_Female_biological rep3

description:
Treatment-Sex Group: Amy-F-Vin
Marina-Amy-Vin-Fm-3_111709-21(2B).CEL
Amygdaloid nuclei from F3-generation Vincozolin lineage female 11 months old rat brain

tag: rna prep date

tag: scan date


title: cFDcontrol_12hpfuvcmd_16hpfsort_rep2


title: serous ovarian cancer 304d

tag: death (1)


title: serous ovarian cancer 300d

value: IV


title: serous ovarian cancer 302d


title: Amygdaloid nuclei_Control_Female_biological rep4

description:
Treatment-Sex Group: Amy-F-Con
Marina-Amy-Con-Fm-4_111709-16(1B).CEL
Amygdaloid nuclei from F3-generation control lineage (vehicle) female 11 months old rat brain

tag: animal id

tag: vin/con rats dyad group

tag: strain


title: cFDcontrol_12hpfuvcmd_16hpfsort_rep3


title: LB + bile salts, OD600=0.2, biological rep1

description: Expression in bile salts at low growth density

source_name: E24377A grown in LB + bile salts (3% w/v) at OD600=0.2

tag: treatment


title: NtlacMO_cFD_12hpfUVcmd_16hpfsort_rep5

description: These embryonic cells lost Ntla, preculding notochord differentiation.

source_name: ntla cMO and cFD injected, 12 hpf irradiated in chordamesoderm, 16 hpf collected


title: cFDcontrol_12hpfuvcmd_16hpfsort_rep1


title: NtlacMO_cFD_12hpfUVcmd_16hpfsort_rep3


title: Amygdaloid nuclei_Control_Female_biological rep5

description:
Treatment-Sex Group: Amy-F-Con
Marina-Amy-Con-Fm-5_111709-17(2C).CEL
Amygdaloid nuclei from F3-generation control lineage (vehicle) female 11 months old rat brain

tag: gender

tag: tissue


title: Amygdaloid nuclei_Control_Female_biological rep2

description:
Treatment-Sex Group: Amy-F-Con
Marina-Amy-Con-Fm-2_111709-14(2D).CEL
Amygdaloid nuclei from F3-generation control lineage (vehicle) female 11 months old rat brain

tag: generation

tag: lineage


title: serous ovarian cancer 301d

tag: grading

tag: Stage

value: IIIb

tag: surgery status


title: serous ovarian cancer 299d

tag: taxane

tag: platinum

tag: pfs (m)


title: NtlacMO_cFD_12hpfUVcmd_16hpfsort_rep4


title: Hippocampus_Control_Male_biological rep8

description:
Treatment-Sex Group: Hip-M-Con
Marina-Hipp-Con-M-8-112409-26.CEL
Hippocampus from F3-generation control lineage (vehicle) male 11 months old rat brain

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

tag: rna prep date

value: Male

value: Hippocampus

tag: age


title: LB + bile salts, OD600=0.2, biological rep2

value: grown in LB + bile salts (3% w/v) at OD600=0.2


title: LB, biological rep1

description: Baseline expression profile

source_name: E24377A grown in LB

value: grown in LB


title: serous ovarian cancer 27d

tag: rec (1)

tag: os (m)

tag: death (1)


title: serous ovarian cancer 269d


title: DMEM-HI + E.coli HS PCM 1%, biological rep2

description: Expression in PCM from human commensal, lower concentration

source_name: E24377A grown in DMEM-HI glucose + PCM from E.coli HS (1% v/v)


title: DMEM-HI + E.coli HS PCM 1%, biological rep1

value: grown in DMEM-HI glucose + PCM from E.coli HS (1% v/v)


title: Amygdaloid nuclei_Control_Female_biological rep1

description:
Treatment-Sex Group: Amy-F-Con
Marina-Amy-Con-Fm-1_111709-13(1A).CEL
Amygdaloid nuclei from F3-generation control lineage (vehicle) female 11 months old rat brain

tag: scan date

tag: animal id

tag: vin/con rats dyad group

tag: strain

value: Sprague-Dawley rat

value: Female


title: Amygdaloid nuclei_Vinclozolin_Male_biological rep10

description:
Treatment-Sex Group: Amy-M-Vin
Marina-Amy-Vin-M-11_111309-11(2A).CEL
Amygdaloid nuclei from F3-generation Vincozolin lineage male 11 months old rat brain

source_name: Amygdaloid nuclei from F3-generation Vincozolin lineage male rat brain

tag: gender

tag: generation

tag: tissue

value: Amygdaloid nuclei


title: Amygdaloid nuclei_Vinclozolin_Male_biological rep11

description:
Treatment-Sex Group: Amy-M-Vin
Marina-Amy-Vin-M-12_111309-12(3B).CEL
Amygdaloid nuclei from F3-generation Vincozolin lineage male 11 months old rat brain

tag: lineage

value: 11 months


title: serous ovarian cancer 268d

value: high-grade serous ovarian cancer tumor

tag: grading

tag: Stage

tag: surgery status


title: LB, biological rep2

description: Baseline expression profile

tag: treatment


title: DMEM-HI + E.coli HS PCM, biological rep2

description: Expression in PCM from human commensal

source_name: E24377A grown in DMEM-HI glucose + PCM from E.coli HS (10% v/v)


title: NtlacMO_cFD_12hpfUVcmd_16hpfsort_rep1

value: AB


title: NtlacMO_cFD_12hpfUVcmd_16hpfsort_rep2


title: DMEM-HI + E.coli HS PCM, biological rep1

description: Expression in PCM from human commensal

value: grown in DMEM-HI glucose + PCM from E.coli HS (10% v/v)


title: serous ovarian cancer 266d

value: IIIc

value: suboptimal

tag: taxane

tag: platinum

tag: pfs (m)


title: Amygdaloid nuclei_Vinclozolin_Male_biological rep12

description:
Treatment-Sex Group: Amy-M-Vin
Marina-Amy-Vin-M10_111309-10(1D).CEL
Amygdaloid nuclei from F3-generation Vincozolin lineage male 11 months old rat brain

tag: rna prep date

value: Vincozolin

tag: age


title: DMEM-LO, biological rep2

description: Baseline expression profile

source_name: E24377A grown in DMEM-Lo glucose

value: grown in DMEM-Lo glucose


title: serous ovarian cancer 267d

value: optimal

tag: rec (1)

tag: os (m)

tag: death (1)


title: Amygdaloid nuclei_Vinclozolin_Male_biological rep7

description:
Treatment-Sex Group: Amy-M-Vin
Marina-Amy-Vin-M7_111309-7(1C).CEL
Amygdaloid nuclei from F3-generation Vincozolin lineage male 11 months old rat brain

tag: scan date

tag: animal id

tag: vin/con rats dyad group

tag: strain

value: Male


title: DMEM-LO, biological rep1

description: Baseline expression profile


title: cFDcontrol_6hpfuvshield_9hpfsort_rep5

description: These are control embryonic cells that form both notochord and floor plate.

source_name: cFD injected, 6 hpf irradiated in shield, 9 hpf collected

growth_protocol: Zebrafish embryos were collected by natural mating and maintained in E3 media at 28.5°C.  Following localized irradiation with 360-nm light, embryos were cultured to 9 hpf.

treatment_protocol:
Embryos were dechorinated with pronase, and transferred to calcium-free Ringer’s solution (100 μL for 25-30 embryos; 116 mM NaCl, 2.6 mM KCl, 5 mM HEPES, pH 7.0), homogenized with a 200-μL pipette tip, and incubated for 5 min at room temperature.  Embryonic homogenate was transferred to a 1.2-mL solution of 1X PBS containing trypsin (0.25%, Gibco, 15090-046) and 1 mM EDTA, incubated for 15 min at 28.5 °C with further triturating every 5 min. Trypsin digestion was quenched with stop solution (200 μL; 1X PBS containing 30% (v/v) calf serum and 6 mM CaCl2), and cells were collected by centrifugation (400 x g, 5 min, 4 °C). After aspirating the supernatant, cells were resuspended in chilled suspension solution (700 μL; DMEM containing 1% (v/v) calf serum, 0.8 mM CaCl2, 50 U/mL penicillin, and 0.05 mg/ml streptomycin), centrifuged again, and resuspended once more in chilled suspension solution.
The cell suspension was filtered into FACS sample tubes through a 40-μm cell strainer (BD Biosciences).  Irradiated, fluorescent cells from the dissociated embryos were purified using a BD FACSAria sorter using a 100-μm nozzle. Chilled cells were periodically vortexed to prevent settling, and the signal threshold was set to 2,000 to prevent contamination of the sorted cells with embryonic debris. Forward and side scatter gates were used to isolate viable, individual cells from embryonic debris, and FL1-Area (Ex: 488 nm; Em: 530 nm) intensities were used to identify green fluorescent cells, that were sorted directly into 1 mL of chilled TRIzol (Invitrogen) in siliconized microcentrifuge tubes. Approximately 8,000 cells were collected from each group of 25-30 locally irradiated embryos.


title: serous ovarian cancer 264d

tag: tissue


title: Amygdaloid nuclei_Vinclozolin_Male_biological rep8

description:
Treatment-Sex Group: Amy-M-Vin
Marina-Amy-Vin-M-8_111309-8(2B).CEL
Amygdaloid nuclei from F3-generation Vincozolin lineage male 11 months old rat brain

tag: gender

tag: generation

tag: lineage


title: cFDcontrol_6hpfuvshield_9hpfsort_rep4


title: serous ovarian cancer 262d

tag: grading

tag: Stage

tag: surgery status


title: cFDcontrol_6hpfuvshield_9hpfsort_rep3


title: Amygdaloid nuclei_Control_Male_biological rep12

description:
Treatment-Sex Group: Amy-M-Con
Marina-Amy-Con-M-12_111309-6(3D).CEL
Amygdaloid nuclei from F3-generation control lineage (vehicle) male 11 months old rat brain

source_name: Amygdaloid nuclei from F3-generation control lineage (vehicle) male rat brain

value: control (vehicle)


title: Amygdaloid nuclei_Vinclozolin_Male_biological rep9

description:
Treatment-Sex Group: Amy-M-Vin
Marina-Amy-Vin-M-9_111309-9(3A).CEL
Amygdaloid nuclei from F3-generation Vincozolin lineage male 11 months old rat brain


title: cFDcontrol_6hpfuvshield_9hpfsort_rep1


title: serous ovarian cancer 260d

source_name: high-grade serous ovarian cancer

value: IIIb

tag: taxane

tag: platinum

tag: pfs (m)


title: serous ovarian cancer 257d

tag: rec (1)


title: Amygdaloid nuclei_Control_Male_biological rep11

description:
Treatment-Sex Group: Amy-M-Con
Marina-Amy-Con-M-11_111309-5(2C).CEL
Amygdaloid nuclei from F3-generation control lineage (vehicle) male 11 months old rat brain

tag: rna prep date

tag: age


title: DMEM-HI, biological rep1

description: Baseline expression profile

source_name: E24377A grown in DMEM-HI glucose

tag: treatment

value: grown in DMEM-HI glucose


title: NtlacMO_cFD_6hpfUVshield_9hpfsort_rep4

description: These embryonic cells lost Ntla and form exclusively floor plate.

source_name: ntla cMO and cFD injected, 6 hpf irradiated in shield, 9 hpf collected


title: DMEM-HI + bile salts, biological rep2

description: Expression in minimal media and bile salts

source_name: E24377A grown in DMEM-HI glucose + bile salts (3% w/v)


title: NtlacMO_cFD_6hpfUVshield_9hpfsort_rep5


title: DMEM-HI + bile salts, biological rep1

value: grown in DMEM-HI glucose + bile salts (3% w/v)


title: Amygdaloid nuclei_Control_Male_biological rep10

description:
Treatment-Sex Group: Amy-M-Con
Marina-Amy-Con-M-10_111309-4(1B).CEL
Amygdaloid nuclei from F3-generation control lineage (vehicle) male 11 months old rat brain

tag: scan date

tag: animal id

value: Sprague-Dawley rat


title: LB + bile salts, biological rep2

description: Expression in bile salts

source_name: E24377A grown in LB + bile salts (3% w/v)

value: grown in LB + bile salts (3% w/v)


title: serous ovarian cancer 25d

tag: os (m)

tag: death (1)


title: Amygdaloid nuclei_Control_Male_biological rep8

description:
Treatment-Sex Group: Amy-M-Con
Marina-Amy-Con-M-8_111309-2(2D).CEL
Amygdaloid nuclei from F3-generation control lineage (vehicle) male 11 months old rat brain

tag: vin/con rats dyad group

tag: strain

tag: gender

tag: tissue

value: Amygdaloid nuclei


title: serous ovarian cancer 249d

tag: grading

tag: Stage


title: Amygdaloid nuclei_Control_Male_biological rep7

description:
Treatment-Sex Group: Amy-M-Con
Marina-Amy-Con-M-7_111309-1(1A).CEL
Amygdaloid nuclei from F3-generation control lineage (vehicle) male 11 months old rat brain

tag: generation

tag: lineage

value: 11 months


title: serous ovarian cancer 23d

value: high-grade serous ovarian cancer tumor

tag: surgery status

tag: taxane

tag: platinum

tag: pfs (m)


title: kidney outer medulla_dDAVP 5ng/h_3d_rep3

city: Berlin

first: Alexander

last: Paliege

address: Philippstr. 12

department: Anatomy

country: Germany

institute: Charité

description: Gene expression data from Brattleboro rat kidney outer medulla after 3d dDAVP treatment 5ng/h.

hyb_protocol: Hybridization (16h x 45°C) was processed according to the standard Affymetrix protocol.

scan_protocol: Affymetrix GeneArray Scanner3000

data_processing: The data were analyzed with a commercial software called JMP Genomics, version 4, from SAS. Gene expression profiling was performed using arrays of rat230_2 -type from Affymetrix. A Custom CDF Version 9 with Unigene based gene definitions was used to annotate the arrays. The Raw fluorescence intensity values were normalized by Robust Multichip Average (RMA). This includes the quantile normalization, a Background-Correction and a median-Polish algorithm.

source_name: Brattleboro rat kidney outer medulla_dDAVP 5ng/h_ 3d

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

growth_protocol: Young adult (8 weeks) male Brattleboro rats were obtained from the local colony in the Charité-Universitätsmedizin Berlin. Animals were kept on a 12h light and dark cycle and had free access to standard rat chow and tap water throughout the study.

extract_protocol: Total RNA was isolated from the outer medulla of dDAVP and vehicle treated Brattleboro rats using the Qiagen RNeasy mini kit following the manufacturer's protocol (Qiagen, Hilden, Germany).

treatment_protocol: Rats were randomly divided into 2 groups (n = 3 per group) and treated for 3 days with either 1-desamino-8-D-Arg vasopressin (dDAVP; 5ng/h; Sigma Aldrich, Germany) or vehicle via osmotic minipump (ALZET minipump model 2001, Charles River, Sulzfeld, Germany). After three days animals were sacrificed and the kidneys removed. The outer medulla was isolated and used for cDNA generation.

value: Brattleboro

value: male

tag: age

value: young adult (8 weeks)

value: kidney

tag: kidney zone

value: outer medulla


title: DMEM-HI + 2348/69 PCM, biological rep2

description: Expression in PCM from enteric pathogen

source_name: E24377A grown in DMEM-HI glucose + PCM from EPEC E2348/69 (10% v/v)

tag: treatment


title: NtlacMO_cFD_6hpfUVshield_9hpfsort_rep3

value: AB


title: NtlacMO_cFD_6hpfUVshield_9hpfsort_rep2


title: E_faecalis_OG1RF_wild-type_N_medium_rep1

city: Rancagua

first: Mauricio

middle: Alejandro

last: Latorre

state: VI

address: Av. Libertador Bernardo OHiggins 611

department: ICI

country: Chile

institute: Universidad de OHiggins

description:
GEO_GLOPEZ2011_Efae_V583_EXP_growth_medium_N_strain_E_faecalis_OG1RF_wild-type_rep1
This sample is of wild-type Enterococcus faecalis OG1RF, correspond to the first of two biological replicates used in this experiment, each from separate cultures.
The Nimblegen platform is based on Enterococcus faecalis V583 (wild type strain). We made a cross hybridation.
SAMPLE 1

data_processing: All data was processes automatically using DNASTAR software Array star 3.0. See www.dnastar.com.

organism: Enterococcus faecalis OG1RF

source_name: controls sample_N medium growth

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

growth_protocol: Enterococcus faeclis OG1RF wild-type was grown to mid-log phase (O.D600nm 1.0), aerobically estandar condition at 37°C in N medium (Peptone 1 % (Difco), yeast extract 0.5 % (Difco), Na2HPO4 1 % (Merck) and glucose 1 % (Oxoid), Odermatt A, Solioz M. J Biol Chem 1995, 270(9).  In treatment cultures, strain was gowth at the same condition by adding Fe (Fe-NTA 0.5 mM) to the control medium.

extract_protocol: The RNA was extracted using a Qiagen RNeasy mini kit (Qiagen). Residual contaminating genomic DNA was removed with RQ1 RNase-free DNase (Promega) treatment according to the manufacturer’s protocol. The integrity of the RNA was assessed by gel electrophoresis.

treatment_protocol: All Fe-treated cells were exposed for 6 hours prior to harvesting (at mid-log phase, OD600nm 1.0); the untreated cells were collected simultaneously.

tag: genotype

value: wild type

tag: phenotype

value: normal


title: LB + bile salts, biological rep1

description: Expression in bile salts


title: serous ovarian cancer 20d

value: IIIc

value: optimal

tag: rec (1)

tag: os (m)

tag: death (1)


title: DMEM-HI + 2348/69 PCM, biological rep1

description: Expression in PCM from enteric pathogen

value: grown in DMEM-HI glucose + PCM from EPEC E2348/69 (10% v/v)


title: kidney outer medulla_dDAVP 5ng/h_3d_rep1

tag: strain

tag: gender

tag: tissue


title: serous ovarian cancer 22d

tag: grading

tag: Stage

value: suboptimal


title: serous ovarian cancer 2d

tag: surgery status


title: kidney outer medulla_vehicle_3d_rep3

description: Gene expression data from Brattleboro rat kidney outer medulla after vehicle treatment.

source_name: Brattleboro rat kidney outer medulla_vehicle_ 3d


title: GC_F3-Vin_biological rep2

description:
Gene expression data from Granulosa cell from 6 months old ovary of F3 vinclozolin lineage rat
For each mRNA microarray replica, mRNA from 4 different samples of granulosa cell originated from 4 different rats were combined - equal amount of mRNA from each.

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 4500.

data_processing: The data were analyzed with Partek Genomic Suite 6.5 beta software  (Partek Inc., St. Louis, MO) 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.  Granulosa cell preparation date batch effect was removed.

source_name: Granulosa cell from 6 months old F3 vinclozolin lineage rat ovary

growth_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].  Subsequent  F2 and F3 generations wee obtained from F1 rats.

extract_protocol: RNA was isolated from granulosa cells of rat ovaries after lysis in 1 ml Trizol™ reagent (Sigma-Aldritch, USA), according to manufacturer’s instructions.

treatment_protocol: Granulosa cell were isolated from 6 months old female rats of F3 generation of vinclozolin and control lineages as described earlier (Peters et al., 1999).

tag: cell preparation date batch

value: Sprague-Dawley

value: Female

tag: cell

value: granulosa cell

tag: developmental stage

value: Ovary  from 6 months old rat

tag: lineage

value: F3 vinclozolin


title: DMEM-HI, biological rep2

description: Baseline expression profile

value: grown in DMEM-HI glucose


title: kidney outer medulla_dDAVP 5ng/h_3d_rep2

value: Brattleboro

value: male

tag: age

tag: kidney zone


title: GC_F3-Vin_biological rep3


title: serous ovarian cancer 186d

value: high-grade serous ovarian cancer tumor

tag: taxane

tag: platinum

tag: pfs (m)


title: serous ovarian cancer 185d

tag: rec (1)

tag: os (m)


title: LB + glucose, biological rep2

description: Expression in the presence of glucose

source_name: E24377A grown in LB + glucose at OD600=0.5

tag: treatment

value: grown in LB + glucose at OD600=0.5


title: kidney outer medulla_vehicle_3d_rep2

tag: strain

tag: gender

value: young adult (8 weeks)

value: kidney

value: outer medulla


title: GC_F3-Vin_biological rep1


title: kidney outer medulla_vehicle_3d_rep1

tag: tissue


title: LB + glucose, biological rep1

description: Expression in the presence of glucose


title: Amygdaloid nuclei_Control_Male_biological rep9

description:
Treatment-Sex Group: Amy-M-Con
Marina-Amy-Con-M-9_111309-3(3C).CEL
Amygdaloid nuclei 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

value: Sprague-Dawley rat

value: Male

tag: generation

value: control (vehicle)

value: Amygdaloid nuclei

value: 11 months


title: GC_F3-Control_biological rep3

description:
Gene expression data from Granulosa cell from 6 months old ovary of F3 control lineage rat
For each mRNA microarray replica, mRNA from 4 different samples of granulosa cell originated from 4 different rats were combined - equal amount of mRNA from each.

source_name: Granulosa cell from 6 months old F3 control lineage rat ovary

tag: cell preparation date batch

value: Sprague-Dawley

value: Female

tag: cell

tag: developmental stage

tag: lineage

value: F3 control


title: C. brenneri_rep3_stage10

city: Haifa

first: Itai

last: Yanai

address: Technion City

department: Biology

country: Israel

institute: Technion - Israel Institute of Technology

description: C. brenneri_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 brenneri

source_name: C. brenneri, 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.

value: Juvenile L1 larvae


title: serous ovarian cancer 184d

tag: grading

tag: Stage

value: IIIc

tag: surgery status

value: optimal

tag: taxane

tag: platinum

tag: death (1)


title: serous ovarian cancer 178d

value: IV

tag: pfs (m)

tag: rec (1)

tag: os (m)


title: C. brenneri_rep3_stage9

description: C. brenneri_rep3_stage9

source_name: C. brenneri, stage9

value: Movement


title: NtlacMO_cFD_6hpfUVshield_9hpfsort_rep1

tag: strain

value: AB


title: mammary gland , J50, Génistéine + Vinclozoline, biological rep1

city: 91400 Orsay

first: Florent

last: Dumont

state: Ile de France

address: 17 avenue des sciences

country: France

institute: Université Paris-Saclay

hyb_protocol: cDNA is then hybridized to GeneChip® rat  Gene (Affymetrix) at 45°C for 17 hours

scan_protocol: After overnight hybridization, chips are washed on the fluidic station FS450 following specific protocols (Affymetrix) and scanned using the GCS3000 7G

data_processing: Raw data were preprocessing using the Robust Multichip Algorithm

source_name: pool of 5 RNA

label_protocol: cDNA is end labelled with biotin using Terminal Transferase (using the WT terminal labelling kit of Affymetrix)

growth_protocol: Females and males Wistar Han rats at eight weeks of age (Harlan France Sarl, Gannat, France) were maintained in an animal facility and fed a purified diet (phytoestrogen-free, INRA, France) and water ad libitum. Procedures for handling and experimentation followed ethical guidelines. At gestational day 1, determined by the presence of intravaginal sperm plug, the dams were randomly divided into groups of 15. From the first gestational day (GD1) until the weaning (PND 21), each pregnant female were orally gavaged once daily with genistein (G), vinclozoline (V) alone or in combination (GV) at 1 mg/kg body weight/day, as previously described. At weaning, immature rats were dispatched. Female offspring were randomized (one female per litter), identified by implanted chips, and fed the purified diet until sacrifice (PND 35 and PND 50). Twenty pubertal or cycling female offspring animals per treatment group were used for subsequent analysis

extract_protocol: Total RNA was extracted from individual mammary glands with Trizol extraction.

treatment_protocol: Females and males Wistar Han rats at eight weeks of age (Harlan France Sarl, Gannat, France) were maintained in an animal facility and fed a purified diet (phytoestrogen-free, INRA, France) and water ad libitum. Procedures for handling and experimentation followed ethical guidelines and were previously described [37, Reprod Toxicol]. At gestational day 1, determined by the presence of intravaginal sperm plug, the dams were randomly divided into groups of 15. From the first gestational day (GD1) until the weaning (PND 21), each pregnant female were orally gavaged once daily with genistein (G), vinclozoline (V) alone or in combination (GV) at 1 mg/kg body weight/day, as previously described ( ). At weaning, immature rats were dispatched. Female offspring were randomized (one female per litter), identified by implanted chips, and fed the purified diet until sacrifice (PND 35 and PND 50) (Fig. 1). Twenty pubertal or cycling female offspring animals per treatment group were used for subsequent analysis.

tag: tissue

value: mammary gland

value: Wistar Han

tag: treatment

value: Génistéine + Vinclozoline


title: serous ovarian cancer 183d

value: high-grade serous ovarian cancer tumor

value: suboptimal


title: mammary gland , J50, Génistéine + Vinclozoline, biological rep2


title: serous ovarian cancer 18d


title: GC_F3-Control_biological rep1

tag: gender

value: granulosa cell

value: Ovary  from 6 months old rat


title: serous ovarian cancer 171d


title: mammary gland , J50, Génistéine, biological rep2

value: Génistéine


title: C. brenneri_rep3_stage5

description: C. brenneri_rep3_stage5

source_name: C. brenneri, stage5

value: 6th AB division


title: serous ovarian cancer 174d


title: C. brenneri_rep3_stage4

description: C. brenneri_rep3_stage4

source_name: C. brenneri, stage4

value: 5th AB division


title: serous ovarian cancer 173d

source_name: high-grade serous ovarian cancer


title: GC_F3-Control_biological rep2

tag: cell preparation date batch

value: Sprague-Dawley

value: Female

value: F3 control


title: mammary gland , J50, Génistéine, biological rep1


title: serous ovarian cancer 17d

value: IIIb

value: optimal


title: C. brenneri_rep3_stage8

description: C. brenneri_rep3_stage8

source_name: C. brenneri, stage8

value: Comma stage


title: mammary gland , J50, Vinclozoline, biological rep2

value: Vinclozoline


title: C. brenneri_rep3_stage6

description: C. brenneri_rep3_stage6

source_name: C. brenneri, stage6

value: 7th AB division


title: C. brenneri_rep3_stage7

description: C. brenneri_rep3_stage7

source_name: C. brenneri, stage7

value: Ventral enclosure stage


title: C. brenneri_rep3_stage3

description: C. brenneri_rep3_stage3

source_name: C. brenneri, stage3

value: 4th AB division


title: mammary gland , J50, control untreated, biological rep2

value: mammary gland

value: Wistar Han


title: serous ovarian cancer 16d

value: high-grade serous ovarian cancer tumor

value: IIIc


title: serous ovarian cancer 160d

value: suboptimal


title: mammary gland , J50, control untreated, biological rep1


title: serous ovarian cancer 156d


title: C. brenneri_rep3_stage2

description: C. brenneri_rep3_stage2

source_name: C. brenneri, stage2

value: E-cell division


title: serous ovarian cancer 15d


title: C. brenneri_rep2_stage9

description: C. brenneri_rep2_stage9

value: Movement


title: mammary gland , J35, Génistéine + Vinclozoline, biological rep2

value: Génistéine + Vinclozoline


title: serous ovarian cancer 150d


title: cFDcontrol_6hpfuvshield_9hpfsort_rep2

source_name: cFD injected, 6 hpf irradiated in shield, 9 hpf collected

value: AB


title: mammary gland , J35, Vinclozoline, biological rep2


title: mammary gland , J50, Vinclozoline, biological rep1


title: serous ovarian cancer 155d


title: serous ovarian cancer 148d


title: C. brenneri_rep2_stage10

description: C. brenneri_rep2_stage10

value: Juvenile L1 larvae


title: mammary gland , J35, Vinclozoline, biological rep1


title: C. brenneri_rep2_stage4

description: C. brenneri_rep2_stage4

value: 5th AB division


title: mammary gland , J35, control untreated, biological rep2


title: serous ovarian cancer 146d

value: IIIb


title: C. brenneri_rep2_stage6

description: C. brenneri_rep2_stage6


title: C. brenneri_rep3_stage1

description: C. brenneri_rep3_stage1

source_name: C. brenneri, stage1

value: 4-cell stage


title: mammary gland , J35, Génistéine, biological rep2

value: Génistéine


title: serous ovarian cancer 143d


title: C. brenneri_rep2_stage3

description: C. brenneri_rep2_stage3


title: MGUS clinical sample 6

type: genomic

city: Tokyo

first: Masanori

last: Nojima

state: Tokyo

address: 4-6-1, Shirokanedai, Minato-ku

department: The Institution of Medical Science

institute: The University of Tokyo

description:
Sample name: MGUS6
Methylation levels listed in the 'Characteristics' field were deteremined by bisulfite-pyrosequencing.

hyb_protocol: Labeled DNA was mixed with 25 μg of Cot-1 DNA (Invitrogen), denatured at 95°C for 3 minutes, and incubated at 37°C for 30 minutes. The probe mixture was then hybridized for 40 hours at 65°C to SurePrint G3 Human CGH Microarray Kit 8x60K (G4450A, Agilent Technologies)

scan_protocol: After washing, the array was scanned with an Agilent G2565BA Microarray Scanner

data_processing: The fluorescent signals were acquired using Feature Extraction software (Agilent Technologies)

molecule: genomic DNA

source_name: MGUS clinical sample 6

label_protocol: Using Genomic DNA Enzymatic Labeling kit (Agilent Technologies), sample DNA and reference DNA were labeled with Cy5 and Cy3

growth_protocol: Clinical samples

extract_protocol: We extracted DNA from CD138 positive cells using QIAamp DNA Blood Mini Kit, and isolated mononuclear cells from samples using Fillo-Paque (StemCell Technologies), and then separated CD138 positive cells using CD138 MicroBeads (MiltenyBiotec)

tag: sample type

value: clinical sample

value: male

tag: place

value: Hiroshima

tag: cell type

value: CD138+ cells

tag: methylation line-1

tag: methylation alu yb8

tag: methylation alu ya5

tag: methylation satellite-α

tag: survival (days)

tag: prognosis

source_name: Human Genomic DNA: Male (Promega)

value: reference


title: C. brenneri_rep2_stage8

description: C. brenneri_rep2_stage8

tag: developmental stage

value: Comma stage


title: serous ovarian cancer 144d

value: high-grade serous ovarian cancer tumor

tag: grading

tag: Stage

value: IV

tag: surgery status

tag: taxane

tag: platinum

tag: pfs (m)

tag: rec (1)

tag: death (1)


title: C. brenneri_rep2_stage5

description: C. brenneri_rep2_stage5

value: 6th AB division


title: mammary gland , J35, Génistéine + Vinclozoline, biological rep1

tag: tissue

value: mammary gland

tag: strain

value: Wistar Han

tag: treatment


title: serous ovarian cancer 145d

value: IIIc

value: suboptimal

tag: os (m)


title: mammary gland , J35, Génistéine, biological rep1


title: serous ovarian cancer 140d


title: mammary gland , J35, control untreated, biological rep1


title: C. brenneri_rep2_stage7

description: C. brenneri_rep2_stage7

value: Ventral enclosure stage


title: MGUS clinical sample 5

description:
Sample name: MGUS5
Methylation levels listed in the 'Characteristics' field were deteremined by bisulfite-pyrosequencing.

source_name: MGUS clinical sample 5

tag: sample type

tag: gender

tag: place

tag: cell type

tag: methylation line-1

tag: methylation alu yb8

tag: methylation alu ya5


title: Leaves of Vaniglia Sanguigno, technical rep3

city: New Delhi

first: Vajinder

last: Kumar

state: Delhi

address: LBS Builduing, Pusa Campus IARI

department: Biotechnology

country: India

institute: National Research Center on Plant Biotechnology

hyb_protocol: Following fragmentation, 12 µg of aRNA were hybridized for 16 h at 45°C on GeneChip Citrus Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: The data were analyzed with Robin using Affymetrix default analysis settings and RMA normalization method.

organism: Citrus sinensis

source_name: Young leaves

label_protocol: Biotinylated cRNA were prepared according to the GeneChip 3' IVT express kit from 100-250 ng total RNA (Affymetrix user manual P/N 702646 Rev. 7).

growth_protocol: Ovules were harvested in the month of February or March from field grown citrus plants maintained at Punjab Agricultural University Regional Station, Abohar, Punjab, India.

extract_protocol: Whole flowers were harvested and ovaries were excised preventing the damage to ovules. Ovules were excised with needles and transferred to screw cap cryo vials and immediately stored in liquid nitrogen till RNA isolation. RNA was isolated using SV Total RNA isolation System (Cat. Z3100) of Promega.

treatment_protocol: No treatment was given to the plants

tag: cultivar

value: Vaniglia Sanguigno

tag: cultivar type

value: Polyembryonic

value: Young leaves


title: C. brenneri_rep2_stage1

description: C. brenneri_rep2_stage1

tag: developmental stage

value: 4-cell stage


title: C. brenneri_rep2_stage2

description: C. brenneri_rep2_stage2

value: E-cell division


title: serous ovarian cancer 139d

tag: grading

tag: Stage

tag: surgery status

value: optimal

tag: taxane

tag: platinum

tag: pfs (m)


title: MGUS clinical sample 3

description:
Sample name: MGUS3
Methylation levels listed in the 'Characteristics' field were deteremined by bisulfite-pyrosequencing.

source_name: MGUS clinical sample 3

value: clinical sample

value: female

value: Hiroshima

value: CD138+ cells

tag: methylation satellite-α

tag: survival (days)

tag: prognosis

source_name: Human Genomic DNA: Female (Promega)


title: NimbleGen: Human cerebral cortex H2

city: Los Angeles

first: Jinkai

last: Wang

address: 650 Charles E. Young Drive South, CHS 33-228

institute: University of California, Los Angeles

description: Human cerebral cortex DNA methylation

hyb_protocol: Follow standard NimbleGen protocols

scan_protocol: The Scanning was performed with the Axon GenePix 4000B microarray scanner

data_processing: Between array normalization was conducted using Limma package implemented in R, and the probes that were not unique in the respective genomes were removed from the analyses.

source_name: MeDIP DNA from human cerebral cortex

label_protocol: Follow standard NimbleGen protocols

extract_protocol: Genomic DNA from cerebral cortex tissues was extracted using DNeasy Blood & Tissue Kit (Qiagen) and fragmented by ultrasonic wave according to the manufacturer’s instructions

treatment_protocol: Post-mortem brain samples from cerebral cortex were collected

tag: gender

value: Male

tag: age (year)

source_name: Input DNA from human cerebral cortex


title: Leaves of Vaniglia Sanguigno, technical rep2

tag: tissue


title: serous ovarian cancer 134d

value: high-grade serous ovarian cancer tumor

value: IIIa

tag: rec (1)

tag: os (m)

tag: death (1)


title: C. brenneri_rep1_stage9

description: C. brenneri_rep1_stage9

source_name: C. brenneri, stage9

value: Movement


title: MGUS clinical sample 4

description:
Sample name: MGUS4
Methylation levels listed in the 'Characteristics' field were deteremined by bisulfite-pyrosequencing.

source_name: MGUS clinical sample 4

tag: sample type

value: male

tag: place

tag: cell type

tag: methylation line-1

tag: methylation alu yb8

tag: methylation alu ya5

value: reference


title: Initial Fruit Set stage ovules of Temple, technical rep3

source_name: ovules having functional sexual embryos

tag: cultivar

value: Temple

tag: cultivar type

value: Monoembryonic

value: ovules

tag: developmental stage

value: Initial Fruit Set stage


title: NimbleGen: Human cerebral cortex H1

description: Human cerebral cortex DNA methylation


title: MGUS clinical sample 2

description:
Sample name: MGUS2
Methylation levels listed in the 'Characteristics' field were deteremined by bisulfite-pyrosequencing.

source_name: MGUS clinical sample 2

tag: methylation satellite-α

tag: survival (days)


title: C. brenneri_rep1_stage10

description: C. brenneri_rep1_stage10

source_name: C. brenneri, stage10

value: Juvenile L1 larvae


title: NimbleGen: Human cerebral cortex H3

description: Human cerebral cortex DNA methylation

tag: gender


title: serous ovarian cancer 130d

source_name: high-grade serous ovarian cancer

tag: grading

tag: Stage

value: IIIc

tag: surgery status

value: suboptimal

tag: taxane

tag: platinum

tag: pfs (m)


title: C. brenneri_rep1_stage7

description: C. brenneri_rep1_stage7

source_name: C. brenneri, stage7

value: Ventral enclosure stage


title: C. brenneri_rep1_stage6

description: C. brenneri_rep1_stage6

source_name: C. brenneri, stage6

value: 7th AB division


title: Leaves of Vaniglia Sanguigno, technical rep1

value: Vaniglia Sanguigno

value: Polyembryonic

tag: tissue

value: Young leaves


title: serous ovarian cancer 132d

value: high-grade serous ovarian cancer tumor

value: optimal

tag: rec (1)

tag: os (m)

tag: death (1)


title: C. brenneri_rep1_stage5

description: C. brenneri_rep1_stage5

source_name: C. brenneri, stage5

value: 6th AB division


title: serous ovarian cancer 123d


title: serous ovarian cancer 125Rd

value: IV


title: Initial Fruit Set stage ovules of Temple, technical rep1


title: MGUS clinical sample 1

description:
Sample name: MGUS1
Methylation levels listed in the 'Characteristics' field were deteremined by bisulfite-pyrosequencing.

source_name: MGUS clinical sample 1

tag: sample type

value: clinical sample

value: female

tag: place

value: Hiroshima

tag: cell type

value: CD138+ cells

tag: methylation line-1

tag: methylation alu yb8

tag: methylation alu ya5

tag: prognosis

value: reference


title: Initial Fruit Set stage ovules of Temple, technical rep2

tag: cultivar

value: Temple

tag: cultivar type

value: Monoembryonic

value: ovules

tag: developmental stage

value: Initial Fruit Set stage


title: serous ovarian cancer 129d

tag: grading

tag: Stage

value: IIIc

tag: surgery status

tag: taxane


title: Initial Fruit Set stage ovules of Vaniglia Sanguigno, technical rep3

source_name: ovules having functional sexual and nucellar embryos

value: Vaniglia Sanguigno

tag: tissue


title: MM clinical sample 65

description:
Sample name: MM65
Methylation levels listed in the 'Characteristics' field were deteremined by bisulfite-pyrosequencing.

source_name: MM clinical sample 65

tag: gender

tag: methylation satellite-α

tag: survival (days)


title: MM clinical sample 66

description:
Sample name: MM66
Methylation levels listed in the 'Characteristics' field were deteremined by bisulfite-pyrosequencing.

source_name: MM clinical sample 66

tag: sample type

tag: place

value: Censored


title: C. brenneri_rep1_stage4

description: C. brenneri_rep1_stage4

source_name: C. brenneri, stage4

value: 5th AB division


title: MM clinical sample 67

description:
Sample name: MM67
Methylation levels listed in the 'Characteristics' field were deteremined by bisulfite-pyrosequencing.

source_name: MM clinical sample 67

tag: cell type

tag: methylation line-1

source_name: Human Genomic DNA: Female (Promega)


title: Initial Fruit Set stage ovules of Vaniglia Sanguigno, technical rep2

value: Polyembryonic


title: Initial Fruit Set stage ovules of Vaniglia Sanguigno, technical rep1


title: Post Anthesis stage ovules of Temple, technical rep3

source_name: ovules containing sexual embryos only

value: Post Anthesis stage


title: MM clinical sample 64

description:
Sample name: MM64
Methylation levels listed in the 'Characteristics' field were deteremined by bisulfite-pyrosequencing.

source_name: MM clinical sample 64

tag: methylation alu yb8

tag: methylation alu ya5


title: serous ovarian cancer 120d

value: high-grade serous ovarian cancer tumor

value: suboptimal

tag: platinum

tag: pfs (m)

tag: rec (1)

tag: os (m)

tag: death (1)


title: serous ovarian cancer 122d

tag: grading

tag: Stage

tag: surgery status


title: C. brenneri_rep1_stage2

description: C. brenneri_rep1_stage2

source_name: C. brenneri, stage2

tag: developmental stage

value: E-cell division


title: serous ovarian cancer 12d

tag: tissue

value: optimal

tag: taxane


title: Post Anthesis stage ovules of Temple, technical rep2

tag: cultivar

tag: cultivar type


title: MM clinical sample 62

description:
Sample name: MM62
Methylation levels listed in the 'Characteristics' field were deteremined by bisulfite-pyrosequencing.

source_name: MM clinical sample 62

tag: sample type

value: clinical sample

tag: gender

value: female

tag: place

value: Hiroshima

tag: cell type

tag: methylation satellite-α

tag: survival (days)

tag: prognosis


title: C. brenneri_rep1_stage1

description: C. brenneri_rep1_stage1

source_name: C. brenneri, stage1

value: 4-cell stage


title: MM clinical sample 60

description:
Sample name: MM60
Methylation levels listed in the 'Characteristics' field were deteremined by bisulfite-pyrosequencing.

source_name: MM clinical sample 60

value: male

value: CD138+ cells

tag: methylation line-1

tag: methylation alu yb8

tag: methylation alu ya5

source_name: Human Genomic DNA: Male (Promega)

value: reference


title: Post Anthesis stage ovules of Vaniglia Sanguigno, technical rep3

source_name: ovules containing nucellar embryos along side sexual embryos

value: ovules


title: WS5041 total vs. WS4303 total (3 replicates)

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: M = log2 Ratio (mir-58 / wt)

hyb_protocol: The Cy3- and Cy5-labeled cDNA samples were mixed and competitively hybridized to Long-oligo whole-genome C. elegans arrays, produced by the Genome Sequencing Center at Washington University in St. Louis (http://genome.wustl.edu/genome/celegans/microarray/ma_gen_info.cgi) according to the manufacturer’s instructions.

scan_protocol: Microarrays were scanned with an Axon Instruments Scanner 4200A (Molecular Devices). Scanning parameters were adjusted to similar fluorescent intensities for Arabidopsis thaliana spots in both channels. Data were collected with the GENEPIX 5.1 Program (Molecular Devices). Spots with abnormal morphology were excluded from further analysis.

data_processing: Data were collected with the GENEPIX 5.1 Program (Molecular Devices). Spots with abnormal morphology were excluded from further analysis. Differential expression computation was done by using the Bioconductor package limma (Smyth 2005). All identifiers that passed the quality control filter (average signal intensity > 250 (A (log2 of signal intensity) > 7.966)) are listed.

organism: Caenorhabditis elegans

source_name: mir-58(n4640) mutant background

label_protocol: Labeling was performed as described in (Gerber et al. 2004) with a few adjustments. In brief, equal amounts of a pool of ten synthetically prepared Arabidopsis thaliana RNAs (Stratagene, for a manual see - http://genome.wustl.edu/genome/celegans/microarray/protocol_workflow/spot_report_oligo_array_validation_manual.pdf) were added to each RNA sample prior to labeling and served as a control for the labeling procedure. cDNA was synthesized with amino-allyl dUTP in addition to the four natural dNTPs using a 1:1 mixture of oligo(dT) and random nonamer primers. cDNAs synthesized from total RNA (10 µg) derived from the WS4303 and WS5041 extracts  were labeled with Cy5 and Cy3 fluorescent dyes, respectively.

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: 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 a 0.1ml aliquot of the purified extracts was used for total RNA isolation. RNA was isolated 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. WS4303 was also crossed into mir-58(n4640) mutant animals to generate the strain WS5041 (mir-58(n4640); alg-1(tm492); opIs205).

tag: strain

tag: genotype

tag: transgene

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

value: synchronized, late L4

tag: total rna amount

value: 10 μg

source_name: NO miRNA mutation (wild type)


title: MM clinical sample 61

description:
Sample name: MM61
Methylation levels listed in the 'Characteristics' field were deteremined by bisulfite-pyrosequencing.

source_name: MM clinical sample 61

value: Dead


title: C. brenneri_rep1_stage3

description: C. brenneri_rep1_stage3

source_name: C. brenneri, stage3

tag: developmental stage

value: 4th AB division


title: Post Anthesis stage ovules of Vaniglia Sanguigno, technical rep2

tag: cultivar

value: Vaniglia Sanguigno

value: Polyembryonic

tag: tissue

value: Post Anthesis stage


title: C. brenneri_rep1_stage8

description: C. brenneri_rep1_stage8

source_name: C. brenneri, stage8

value: Comma stage


title: Post Anthesis stage ovules of Vaniglia Sanguigno, technical rep1

tag: cultivar type


title: serous ovarian cancer 116d

source_name: high-grade serous ovarian cancer

value: high-grade serous ovarian cancer tumor

tag: grading

tag: Stage

value: IIIc

tag: surgery status

value: suboptimal

tag: taxane

tag: platinum

tag: pfs (m)

tag: rec (1)

tag: os (m)

tag: death (1)


title: serous ovarian cancer 115d

value: IIIb


title: Pre Anthesis stage ovules of Temple, technical rep3

source_name: ovules with no nucellar embryony

value: Temple

value: Monoembryonic

value: Pre Anthesis stage


title: Post Anthesis stage ovules of Temple, technical rep1

value: ovules


title: serous ovarian cancer 117d

value: optimal


title: C. elegans, whole animal, mixed-stage, strain WS4303 (alg 1(tm492); opIs205). Replicate 3

description: TAP::ALG-1 IP (3)

data_processing: Data were collected with the GENEPIX 5.1 Program (Molecular Devices). Spots with abnormal morphology were excluded from further analysis. Arrays were computer normalized by the GENEPIX 5.1 Program (default setting of the program was used: for normalization only oligo probes that had a Cy3 to Cy5 ratio between 0.1 – 10 were considered) and exported to Acuity 4.0 for further analysis. The data were filtered for signal over background levels greater than 3 in the channel measuring cDNA from total extract (Cy3 channel), and only features that met these criteria in 80% (= at least 5 out of 6) of the arrays were analyzed further. Log2 ratios (immunopurified (IP) RNA over total RNA from extract) were calculated for each gene. Microarrays generated from WS4303 animals were compared to microarrays generated from N2 mock control animals by a Student’s two sample t-test.

source_name: strong TAP::ALG-1 expression_WS4303_input RNA

label_protocol: RNA isolated from WS4303 and N2 (mock control) animals was analyzed for each IP sample and for each total worm extract sample. Three independent biological replicates have been performed. Long-oligo whole-genome C. elegans arrays, produced by the Genome Sequencing Center at Washington University in St. Louis (http://genome.wustl.edu/genome/celegans/microarray/ma_gen_info.cgi), were used for analysis of the mixed-stage samples. Microarray analysis was performed as described in (Gerber et al. 2004) with a few adjustments. In brief, equal amounts of a pool of ten synthetically prepared Arabidopsis thaliana RNAs (Stratagene, for a manual see - http://genome.wustl.edu/genome/celegans/microarray/protocol_workflow/spot_report_oligo_array_validation_manual.pdf) were added to each RNA sample prior to labeling and served as a control for the labeling procedure. cDNA was synthesized with amino-allyl dUTP in addition to the four natural dNTPs using a 1:1 mixture of oligo(dT) and random nonamer primers. cDNAs synthesized from total RNA (9 - 15 µg) derived from the extract and 1 µg of affinity-isolated RNA (or up to 50% of the isolated RNA if less than 2 µg have been isolated) were labeled with Cy3 and Cy5 fluorescent dyes, respectively.

growth_protocol: For the generation of a large population of mixed-stage animals, the worms were grown in liquid culture at 20°C as described previously (Stiernagle 2006).

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 (purified fraction - IP) and from extracts (input – total RNA) 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.

tag: strain

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

value: mixed-stage (from embryo to adult)

value: 12 μg

source_name: strong TAP::ALG-1 expression_WS4303_IP RNA

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

tag: ip rna amount


title: MM clinical sample 58

description:
Sample name: MM58
Methylation levels listed in the 'Characteristics' field were deteremined by bisulfite-pyrosequencing.

source_name: MM clinical sample 58

tag: sample type

value: clinical sample

tag: gender

value: female

tag: place

value: Hiroshima

tag: cell type

value: CD138+ cells

tag: methylation line-1

tag: methylation alu yb8

tag: methylation alu ya5

tag: methylation satellite-α

tag: survival (days)

tag: prognosis

value: Censored

source_name: Human Genomic DNA: Female (Promega)

value: reference


title: serous ovarian cancer 119d

tag: tissue

value: high-grade serous ovarian cancer tumor

tag: grading

tag: Stage

value: IIIc

tag: surgery status

tag: taxane

tag: platinum


title: serous ovarian cancer 11d

value: IIIb

tag: pfs (m)

tag: rec (1)

tag: os (m)

tag: death (1)


title: C. elegans, whole animal, mixed-stage, strain WS4303 (alg 1(tm492); opIs205). Replicate 2

description: TAP::ALG-1 IP (2)

tag: strain

tag: genotype

tag: transgene

tag: developmental stage

tag: total rna amount

value: 9 μg

tag: ip rna amount


title: MM clinical sample 59

description:
Sample name: MM59
Methylation levels listed in the 'Characteristics' field were deteremined by bisulfite-pyrosequencing.

source_name: MM clinical sample 59

tag: sample type

tag: gender

value: male

tag: place

tag: cell type

tag: methylation line-1

tag: methylation alu yb8

tag: methylation alu ya5

tag: methylation satellite-α

tag: survival (days)

tag: prognosis


title: C. elegans, whole animal, mixed-stage, strain WS4303 (alg 1(tm492); opIs205). Replicate 1

description: TAP::ALG-1 IP (1)

value: 1 μg


title: Pre Anthesis stage ovules of Temple, technical rep2

tag: cultivar

value: Temple

tag: cultivar type

value: Monoembryonic

tag: tissue

value: ovules

value: Pre Anthesis stage


title: MM clinical sample 57

description:
Sample name: MM57
Methylation levels listed in the 'Characteristics' field were deteremined by bisulfite-pyrosequencing.

source_name: MM clinical sample 57


title: MM clinical sample 55

description:
Sample name: MM55
Methylation levels listed in the 'Characteristics' field were deteremined by bisulfite-pyrosequencing.

source_name: MM clinical sample 55


title: MM clinical sample 56

description:
Sample name: MM56
Methylation levels listed in the 'Characteristics' field were deteremined by bisulfite-pyrosequencing.

source_name: MM clinical sample 56


title: Pre Anthesis stage ovules of Vaniglia Sanguigno, technical rep3

source_name: ovules showing initiation of nucellar embryony

value: Vaniglia Sanguigno

value: Polyembryonic


title: serous ovarian cancer 10d

tag: grading

tag: Stage

tag: surgery status

value: optimal

tag: taxane

tag: platinum

tag: pfs (m)

tag: rec (1)

tag: os (m)

tag: death (1)


title: 36hBD (pooled)

city: Seattle

first: Laura

last: Buttitta

address: 1100 Fairview Ave. N.

institute: Fred Hutchinson Cancer Research Center

description: This sample is a pooled sample of replicates 36B and 36D of w1118 wings at 36h APF

hyb_protocol: Hybridization was performed by the FHCRC microarray facility, follwing Nimblegen standard hybridization protocol (see www.nimblegen.com)

scan_protocol: Scanning was performed by the FHCRC microarray facility, follwing Nimblegen standard scanning 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

organism: Drosophila melanogaster

source_name: dissected wing

label_protocol: Labeling was performed by the FHCRC microarray facility, follwing Nimblegen standard operating protocol (see www.nimblegen.com)

growth_protocol: Drosophila were grown on standard cornmeal, molasses media under uncrowded conditions (less than 50 larvae per vial) at 25oC until dissection

extract_protocol: 10 wings of the indicated stages were dissected and total RNA was extracted using a Qiagen RNAeasy kit.

tag: genotype

value: w1118;+;+ (Bloomington Stock #3605)

tag: developmental stage

value: wandering 3rd larval instar


title: C. elegans, whole animal, mixed-stage, strain N2 (wild type). Replicate 3

description: wild type IP (3)

source_name: NO TAP::ALG-1 expression_mock sample_input RNA

tag: strain

value: N2 = wild type

tag: transgene

value: no transgene

value: mixed-stage (from embryo to adult)

tag: total rna amount

value: 15 μg

source_name: NO TAP::ALG-1 expression_mock sample_IP RNA

tag: ip rna amount


title: C. elegans, whole animal, mixed-stage, strain N2 (wild type). Replicate 1

description: wild type IP (1)

value: 12 μg


title: Pre Anthesis stage ovules of Temple, technical rep1

tag: cultivar

tag: cultivar type


title: MM clinical sample 53

description:
Sample name: MM53
Methylation levels listed in the 'Characteristics' field were deteremined by bisulfite-pyrosequencing.

source_name: MM clinical sample 53

tag: sample type

value: clinical sample

tag: gender

value: female

tag: place

value: Hiroshima

tag: cell type

value: CD138+ cells

tag: methylation line-1

tag: methylation alu yb8

tag: methylation alu ya5

tag: methylation satellite-α

tag: survival (days)

tag: prognosis

value: Censored

value: reference


title: Pre Anthesis stage ovules of Vaniglia Sanguigno, technical rep2

tag: tissue

value: ovules

tag: developmental stage

value: Pre Anthesis stage


title: MM clinical sample 52

description:
Sample name: MM52
Methylation levels listed in the 'Characteristics' field were deteremined by bisulfite-pyrosequencing.

source_name: MM clinical sample 52


title: 36hC

description: This sample is one of three independent replicates of w1118 wings at 36h APF

tag: genotype

value: 36 hours after pupa formation


title: C. elegans, whole animal, mixed-stage, strain N2 (wild type). Replicate 2

description: wild type IP (2)

tag: strain

tag: transgene

tag: total rna amount


title: 36hD


title: 24hE

description: This sample is one of four independent replicates of w1118 wings at 24h APF


title: 24hD

value: 24 hours after pupa formation


title: MM clinical sample 54

description:
Sample name: MM54
Methylation levels listed in the 'Characteristics' field were deteremined by bisulfite-pyrosequencing.

source_name: MM clinical sample 54


title: 24hB

value: w1118;+;+ (Bloomington Stock #3605)


title: MM clinical sample 51

description:
Sample name: MM51
Methylation levels listed in the 'Characteristics' field were deteremined by bisulfite-pyrosequencing.

source_name: MM clinical sample 51

value: male

source_name: Human Genomic DNA: Male (Promega)


title: 36hB


title: MM clinical sample 49

description:
Sample name: MM49
Methylation levels listed in the 'Characteristics' field were deteremined by bisulfite-pyrosequencing.

source_name: MM clinical sample 49


title: Pre Anthesis stage ovules of Vaniglia Sanguigno, technical rep1

tag: cultivar

value: Vaniglia Sanguigno

tag: cultivar type

value: Polyembryonic


title: MM clinical sample 50

description:
Sample name: MM50
Methylation levels listed in the 'Characteristics' field were deteremined by bisulfite-pyrosequencing.

source_name: MM clinical sample 50

tag: sample type

tag: gender

value: Dead


title: Fetal DN3 biological rep. 3

city: Stevenage

first: Nikolai

middle: Nikolaevich

last: Belyaev

address: Gunnels Wood Road

department: Refractory Respiratory Inflammation

country: United Kingdom

institute: GlaxoSmithKline

description: Gene expression data from irreversibly committed T-cell progenitors in the fetal thymus.

hyb_protocol: The biotinylated cRNA was cleaned up by the Sample Cleanup Modules (Affymetrix), fragmented by metal-induced hydrolysis and hybridised to the Mouse 430A_2.0 GeneChip for 16hours at 45oC and 60rpm.

scan_protocol: GeneChips were scanned by the Affymetrix GeneChip Scanner.

data_processing: Data was normalised by the GC-RMA algorithm in GeneSpring GX 11.0. The data is unfiltered and is expressed as Log2 Normalized Intensity values.

organism: Mus musculus

source_name: Lin neg.CD44-CD25+ fetal thymocyte progenitors

extract_protocol: Total RNA from 80 x 10^3 cells from each population was extracted with Trizol according to manufacturer's protocol. Subsequently, RNA was cleaned up using the Qiagen RNeasy Micro Kit following the Clean Up protocol

tag: age


title: MM clinical sample 48

description:
Sample name: MM48
Methylation levels listed in the 'Characteristics' field were deteremined by bisulfite-pyrosequencing.

source_name: MM clinical sample 48

tag: place

tag: cell type

tag: methylation line-1

source_name: Human Genomic DNA: Female (Promega)


title: 18hD

description: This sample is one of four independent replicates of w1118 wings at 18h APF


title: 24hA


title: Fetal DN3 biological rep. 2


title: Fetal DN3 biological rep. 1


title: Fetal DN2 biological rep. 3

description: Gene expression data from an intermediate progenitor stage during T-cell differentiation in the fetal thymus.

source_name: Lin neg.CD44+CD25+ fetal thymocyte progenitors


title: MM clinical sample 47

description:
Sample name: MM47
Methylation levels listed in the 'Characteristics' field were deteremined by bisulfite-pyrosequencing.

source_name: MM clinical sample 47

tag: methylation alu yb8

tag: methylation alu ya5

tag: methylation satellite-α


title: MM clinical sample 44

description:
Sample name: MM44
Methylation levels listed in the 'Characteristics' field were deteremined by bisulfite-pyrosequencing.

source_name: MM clinical sample 44

tag: survival (days)

tag: prognosis


title: Fetal ETP biological rep. 2

description: Gene expression data from the most immature stage of T-cell differentiation in the fetal thymus.

source_name: Lin neg.CD44+CD25-c-kit+ fetal thymocyte progenitors


title: MM clinical sample 43

description:
Sample name: MM43
Methylation levels listed in the 'Characteristics' field were deteremined by bisulfite-pyrosequencing.

source_name: MM clinical sample 43


title: Fetal DN2 biological rep. 2


title: 18hC

source_name: dissected wing

tag: genotype

tag: developmental stage

value: wandering 3rd larval instar


title: 18hB


title: Fetal DN2 biological rep. 1

tag: strain


title: Fetal ETP biological rep. 3


title: MM clinical sample 46

description:
Sample name: MM46
Methylation levels listed in the 'Characteristics' field were deteremined by bisulfite-pyrosequencing.

source_name: MM clinical sample 46


title: 6hA

description: This sample is one of four independent replicates of w1118 wings at 6h APF


title: 18hA


title: MM clinical sample 42

description:
Sample name: MM42
Methylation levels listed in the 'Characteristics' field were deteremined by bisulfite-pyrosequencing.

source_name: MM clinical sample 42


title: 6hD


title: MM clinical sample 45

description:
Sample name: MM45
Methylation levels listed in the 'Characteristics' field were deteremined by bisulfite-pyrosequencing.

source_name: MM clinical sample 45


title: MM clinical sample 63

description:
Sample name: MM63
Methylation levels listed in the 'Characteristics' field were deteremined by bisulfite-pyrosequencing.

source_name: MM clinical sample 63


title: 2hD

description: This sample is one of four independent replicates of w1118 wings at 2h APF


title: MM clinical sample 40

description:
Sample name: MM40
Methylation levels listed in the 'Characteristics' field were deteremined by bisulfite-pyrosequencing.

source_name: MM clinical sample 40


title: Adult DN3 biological rep. 1

description: Gene expression data from irreversibly committed T-cell progenitors in the adult thymus.

source_name: Lin neg.CD44-CD25+ adult thymocyte progenitors

value: Female

value: 4-6 weeks


title: 6hE


title: Adult DN3 biological rep. 2


title: MM clinical sample 41

description:
Sample name: MM41
Methylation levels listed in the 'Characteristics' field were deteremined by bisulfite-pyrosequencing.

source_name: MM clinical sample 41

value: clinical sample

source_name: Human Genomic DNA: Male (Promega)


title: Adult DN2 biological rep. 3

description: Gene expression data from an intermediate progenitor stage during T-cell differentiation in the adult thymus.

source_name: Lin neg.CD44+CD25+ adult thymocyte progenitors


title: 6hB


title: Adult DN3 biological rep. 3


title: MM clinical sample 39

description:
Sample name: MM39
Methylation levels listed in the 'Characteristics' field were deteremined by bisulfite-pyrosequencing.

source_name: MM clinical sample 39

value: female

value: Hiroshima


title: MM clinical sample 38

description:
Sample name: MM38
Methylation levels listed in the 'Characteristics' field were deteremined by bisulfite-pyrosequencing.

source_name: MM clinical sample 38

value: CD138+ cells

source_name: Human Genomic DNA: Female (Promega)


title: 2hE


title: 2hC


title: Adult DN2 biological rep. 1


title: Adult DN2 biological rep. 2


title: Adult ETP biological rep. 3

description: Gene expression data from the most immature stage of T-cell differentiation in the adult thymus.

source_name: Lin neg.CD44+CD25-c-kit+ adult thymocyte progenitors


title: MM clinical sample 37

description:
Sample name: MM37
Methylation levels listed in the 'Characteristics' field were deteremined by bisulfite-pyrosequencing.

source_name: MM clinical sample 37

value: reference


title: L3_4

description: This sample is one of four independent replicates of w1118 wings at L3


title: MM clinical sample 36

description:
Sample name: MM36
Methylation levels listed in the 'Characteristics' field were deteremined by bisulfite-pyrosequencing.

source_name: MM clinical sample 36


title: 2hB


title: L3_3


title: Adult ETP biological rep. 2


title: MM clinical sample 35

description:
Sample name: MM35
Methylation levels listed in the 'Characteristics' field were deteremined by bisulfite-pyrosequencing.

source_name: MM clinical sample 35

value: Censored


title: MM clinical sample 33

description:
Sample name: MM33
Methylation levels listed in the 'Characteristics' field were deteremined by bisulfite-pyrosequencing.

source_name: MM clinical sample 33

value: Sapporo


title: wt_embryos_st16-17_rep1

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 during late-stage embryogenesis of wild-type Drosophila embryos

hyb_protocol: The Agilent 4x44K Drosophila Array (Platform GPL7300) was used (Agilent-018972). 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).

source_name: late stage-16 and early stage-17 Drosophila  (y; cn, bw, sp; +) embryos; total RNA; replicate 1

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: Parental flies were raised under standard laboratory conditions, and the laid embryos were allowed to develop at 25°C until appropriately staged. Homozygous grainy head embryos were selected (against the CKG fluorescent balancer chromosome) using fluorescent microscopy; we also used gut auto-fluorescence as a morphologic guide to ensure proper staging. Wild-type embryos were raised identically; they were also properly staged using gut auto-fluorescence as a guide.

extract_protocol: Whole embryos were collected and stored frozen in Trizol (Invitrogen). For each replicate, ~500 whole embryos were ground (in Trizol) in microfuge tubes with a pestle according to the manufacturer's recommendations. For each sample, 50 µg of RNA was further cleaned using the Qiagen RNeasy miniprep kit, according to the manufacturer's recommendations. Sample integrity was assayed using gel electrophoresis, RT-PCR, and BioAnalyzer (Agilent) analysis.

treatment_protocol: The experimental and control embryos differed only in their genotypes: homozygous grainy head mutant (+; cn, grhIM, bw, sp; +) vs. wild-type (y; cn, bw, sp; +) embryos

value: whole embryos (500 pooled)

tag: Stage

value: pre-larval

tag: genotype/variation

value: (y; cn, bw, sp; +)


title: L3_1

source_name: dissected wing

value: w1118;+;+ (Bloomington Stock #3605)


title: Adult ETP biological rep. 1


title: grhIM_embryos_st16-17_rep2

description: Gene expression during late-stage embryogenesis of grh-deficient Drosophila embryos

source_name: late stage-16 and early stage-17 Drosophila  (+; cn, grhIM, bw, sp; +) embryos; total RNA; replicate 2

value: (+; cn, grhIM, bw, sp; +)


title: L3_2


title: MM clinical sample 31

description:
Sample name: MM31
Methylation levels listed in the 'Characteristics' field were deteremined by bisulfite-pyrosequencing.

source_name: MM clinical sample 31


title: MM clinical sample 32

description:
Sample name: MM32
Methylation levels listed in the 'Characteristics' field were deteremined by bisulfite-pyrosequencing.

source_name: MM clinical sample 32


title: grhIM_embryos_st16-17_rep1

source_name: late stage-16 and early stage-17 Drosophila  (+; cn, grhIM, bw, sp; +) embryos; total RNA; replicate 1


title: Dismal River - rep 5

city: Alachua

first: Barbara

middle: Joan

last: Carter

state: FL

address: 12085 Research Drive

department: R&D

institute: Applied Food Technologies

hyb_protocol: Fragmentation of the cRNA was performed using Agilent’s Gene Expression Hybridization Kit. A final volume of 50µl per sample was hybridized to the microarrays for 17h at 65ºC.

scan_protocol: Agilent DNA microarray scanner and raw images were processed using Agilent Feature Extraction Software v9.5.

data_processing: Microarray data were imported into JMP Genomics v4.1. Raw intensity data were subjected to a log2 transformation followed by Loess normalization. Gene probes differentially regulated between the sites were identified by one-way ANOVA (p<0.05; fold change >1.5). Functional enrichment analysis was performed using the Gene Ontology (GO) annotations provided by EcoArray Inc. Differentially regulated genes that were over-represented in the biological process GO category were determined by Fisher Exact Test (p<0.05, no post hoc correction). The most significant genes (p<0.01; fold change > 1.5) were subjected to a hierarchical clustering analysis using Cluster 3.0 and visualized in Java TreeView.

organism: Pimephales promelas

source_name: Liver

label_protocol: Microarray hybridizations were performed according to the manufacturer’s instructions. Briefly, RNA samples were used for the synthesis/amplification of cyanine 3 (Cy3) labeled cRNA using Agilent’s Low RNA Input Fluorescent Linear Amplification Kit. The resulting cRNA probes were purified with RNeasy purification columns (Qiagen). The amplification yield and Cy3 incorporation were evaluated using the NanoDrop spectrophotometer and samples with a specific activity >8 pmol Cy3/µl were used on the arrays.

extract_protocol: Total RNA was isolated from male livers (n = 3-5 per site) using the RNeasy Plus Mini Kit (Qiagen, Valencia, CA) according to manufacturer’s protocol and quantified on a NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE).  RNA integrity was determined using a BioAnalyzer 2100 (Agilent, Palo Alto, CA).  The average RNA integrity number (RIN) was 7.6.

treatment_protocol:
Adult fathead minnows were caged at each of the aforementioned sites during the summer of 2007 as described in Sellin et al.6  At each site, 36 sexually-mature fish (21 males and 15 females) were divided equally into three cages and deployed for seven days.  Three polar organic chemical integrative samplers (POCIS, Environmental Sampling Technologies, Inc, St. Joseph, MO) and a temperature logger (Onset, Bourne, MA) were also placed at each site.  The 7-day deployments were initiated within a three-day period, from June 4-6, with retrievals occurring from June 11-13.
Following the 7-day deployments, fish were euthanized with tricaine methanesulfonate (MS-222) and body mass was determined.  Livers and gonads were dissected from each fish, weighed and flash frozen in liquid nitrogen.  Hepatosomatic (HSI) and gonadosomatic (GSI) indices were calculated by dividing the mass of the tissues into the body mass of the fish, then multiplying by 100.  Male livers were sent to EcoArray, Inc. (Gainesville, FL) where they were transferred to vials containing RNA Later (Ambion, Austin, TX) for storage at -20ºC until further analysis.

tag: tissue

value: liver

tag: environment type

value: low-impact agricultural site

tag: environment

value: Dismal River

value: Adult male - caged

value: male

value: adult


title: MM clinical sample 34

description:
Sample name: MM34
Methylation levels listed in the 'Characteristics' field were deteremined by bisulfite-pyrosequencing.

source_name: MM clinical sample 34

tag: sample type

value: clinical sample

tag: gender

value: female


title: Non-vaccinated, challenged, day 5, mild, replicate 4

city: Ames

first: Susan

middle: J

last: Lamont

state: IA

address: 2255 Kildee Hall

department: Animal Science

institute: Iowa State University

hyb_protocol: Blocking agent, fragment buffer and hybridization buffer were added to 825ng of Cy3 and 825ng Cy5 labeled cRNA.  Samples were applied to a gasket slide and hybridized to the microarray slide.  After hybridization, slides were washed in wash buffer then a stabilization agent

scan_protocol: Slides scanned using GenePix 4100A scanner Images quantified using GenePix Pro v6.0

data_processing: Probes with an average Signal to Noise ratio of less than 3 over all slides were excluded from further study, where SNR is (Median Foreground - Median Background) / Standard Deviation of Background.  Median background was subtracted from median foreground, LOWESS normalization was done using R program

organism: Gallus gallus

source_name: Chicken PBL non-vaccinated, non-challenged, day 1

label_protocol: 400ng of total RNA was primed by adding T7 Promoter primer and incubating at 65C for 10 minutes.  RNA was reverse-transcribed into cDNA by using RT enzyme and dNTP mix, incubating at 40C for 2 hours followed by 65C for 15 minutes.  cDNA was transcribed into cRNA which was labeled with either Cy3 or Cy5 dye, then purified using RNeasy kit.

extract_protocol: Total RNA extracted using MagMax-96 for microarrays

treatment_protocol: Male broilers chicks were vaccinated/non-vaccinated at 2 weeks of age and challenged/non-challenged at 4 weeks of age.  Necropsies took place 1 and 5 days post-challenge, at which time blood was taken and lesion scores assessed.

tag: Sex

tag: cell type

value: peripheral blood leukocytes

tag: vaccine status

value: Non-vaccinated

tag: challenge status

value: Non-challenged

tag: time

value: Day 1

tag: pathology

tag: infection

value: uninfected

source_name: Chicken PBL non-vaccinated, challenged, day 5, mild

value: Challenged

value: Day 5

value: Mild

value: Avian Pathogenic Escherichia coli


title: MM clinical sample 30

description:
Sample name: MM30
Methylation levels listed in the 'Characteristics' field were deteremined by bisulfite-pyrosequencing.

source_name: MM clinical sample 30

tag: place

value: Sapporo

value: CD138+ cells

tag: methylation line-1

tag: methylation alu yb8

tag: methylation alu ya5

tag: methylation satellite-α

tag: survival (days)

tag: prognosis

value: Censored

source_name: Human Genomic DNA: Male (Promega)

value: reference


title: Osteoblasts_Hu_2

city: Brisbane

first: Stefan

last: Thor

state: QLD

address: Skerman Bldg (65) room 506  Faculty of Medicine

department: School of Biomedical Sciences

country: Australia

institute: The University of Queensland

hyb_protocol: Hybridization according to Affymetrix HuGene 1.0ST protocol 2009

scan_protocol: According to protocol. Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
CEL-files imported into Agilent GeneSpring GX11 and 11.5. Quantile normalization, baseline to median of all samples using RMA16 (core). Data exported as tab-delimited txt showing transcript cluster id and normalized intensity values.
Affymetrix.ExonExprChip.HuGene-1_0-st-v1

source_name: osteoblasts, primary, P3-5, reference

label_protocol: Labelled according to Affymetrix HuGene 1.0ST protocol 2009.

growth_protocol: all cells cultured and expanded in T75 plastic culture flasks.

extract_protocol: Cultures were trypsinized, RNA extracted with Macherey-Nagel Total RNA isolation kit (filter-column kit). Checked with NanoDrop and Agilent BioAnalyzer 2000.

treatment_protocol: control and reference cultures maintained in specified media and split when confluent. Differentiated fibroblasts kept in induction media for 4 weeks without passaging.

value: osteoblasts, primary

tag: medium

value: osteoblast maintenance

tag: group

value: osteo-ref


title: Dismal River - rep 3

tag: tissue

value: liver

tag: environment type

value: low-impact agricultural site

tag: environment

value: Dismal River

tag: sample type

value: Adult male - caged

tag: gender

value: male

tag: developmental stage

value: adult


title: Non-vaccinated, challenged, day 1, mild, replicate 4

tag: Sex

tag: cell type

value: peripheral blood leukocytes

tag: vaccine status

value: Non-vaccinated

tag: challenge status

value: Non-challenged

tag: time

value: Day 1

tag: pathology

value: uninfected

source_name: Chicken PBL non-vaccinated, challenged, day 1, mild

value: Challenged


title: MM clinical sample 29

description:
Sample name: MM29
Methylation levels listed in the 'Characteristics' field were deteremined by bisulfite-pyrosequencing.

source_name: MM clinical sample 29

value: clinical sample

tag: place

value: Sapporo

value: CD138+ cells

tag: methylation line-1

tag: methylation alu yb8

tag: methylation alu ya5

tag: methylation satellite-α

value: Censored


title: Vaccinated, non-challenged, day 1, replicate 4

tag: infection

source_name: Chicken PBL vaccinated, non-challenged, day 1

value: Vaccinated


title: wt_embryos_st16-17_rep2

source_name: late stage-16 and early stage-17 Drosophila  (y; cn, bw, sp; +) embryos; total RNA; replicate 2

value: whole embryos (500 pooled)

tag: Stage

value: pre-larval

tag: genotype/variation

value: (y; cn, bw, sp; +)


title: Fib_OsteoMedium_1

source_name: dermal fibroblasts in osteogenic medium 28d

value: dermal fibroblasts

tag: medium

value: osteogenic

tag: group

value: osteo-test


title: Fibroblasts_Hu_P6_2

source_name: dermal fibroblasts P6, controls

value: DMEM, 10% FCS

value: fib-control


title: Dismal River - rep 2

tag: tissue

value: liver

tag: environment type

value: low-impact agricultural site

tag: environment

value: Dismal River

tag: sample type

value: Adult male - caged

tag: gender

value: male

tag: developmental stage

value: adult


title: Non-vaccinated, challenged, day 1, severe, replicate 4

tag: Sex

tag: cell type

value: peripheral blood leukocytes

tag: vaccine status

value: Non-vaccinated

tag: challenge status

value: Non-challenged

tag: time

value: Day 1

tag: pathology

value: uninfected

source_name: Chicken PBL non-vaccinated, challenged, day 1, severe

value: Challenged

value: Severe

value: Avian Pathogenic Escherichia coli


title: MM clinical sample 27

description:
Sample name: MM27
Methylation levels listed in the 'Characteristics' field were deteremined by bisulfite-pyrosequencing.

source_name: MM clinical sample 27

value: clinical sample

tag: place

value: Sapporo

value: CD138+ cells

tag: methylation line-1

tag: methylation alu yb8

tag: methylation alu ya5

tag: methylation satellite-α

tag: survival (days)

tag: prognosis

value: Censored

value: reference


title: Dismal River - rep 1

tag: tissue

value: liver

tag: environment type

value: low-impact agricultural site

tag: environment

value: Dismal River


title: MM clinical sample 26

description:
Sample name: MM26
Methylation levels listed in the 'Characteristics' field were deteremined by bisulfite-pyrosequencing.

source_name: MM clinical sample 26

tag: sample type

tag: gender

value: male

value: Dead


title: Fib_OsteoMedium_2

tag: cell type

value: dermal fibroblasts

tag: medium

value: osteogenic

tag: group

value: osteo-test


title: MM clinical sample 28

description:
Sample name: MM28
Methylation levels listed in the 'Characteristics' field were deteremined by bisulfite-pyrosequencing.

source_name: MM clinical sample 28


title: Fibroblasts_Hu_P6_1

value: DMEM, 10% FCS

value: fib-control


title: Vaccinated, challenged, day 1, replicate 4

tag: Sex

value: peripheral blood leukocytes

tag: vaccine status

value: Non-vaccinated

tag: challenge status

value: Non-challenged

tag: time

value: Day 1

tag: infection

value: uninfected

source_name: Chicken PBL vaccinated, challenged, day 1

value: Vaccinated

value: Challenged


title: MM clinical sample 23

description:
Sample name: MM23
Methylation levels listed in the 'Characteristics' field were deteremined by bisulfite-pyrosequencing.

source_name: MM clinical sample 23

value: clinical sample

value: female

tag: place

value: Sapporo

value: CD138+ cells

tag: methylation line-1

tag: methylation alu yb8

tag: methylation alu ya5

source_name: Human Genomic DNA: Female (Promega)

value: reference


title: Osteoblasts_Hu_1

value: osteoblasts, primary

value: osteoblast maintenance

value: osteo-ref


title: Non-vaccinated, challenged, day 5, severe, replicate 4

source_name: Chicken PBL non-vaccinated, non-challenged, day 1

value: male

tag: pathology

source_name: Chicken PBL non-vaccinated, challenged, day 5, severe

value: Day 5

value: Severe

value: Avian Pathogenic Escherichia coli