title: CNC-Control-3

city: Amherst

first: Dominique

last: Alfandari

address: 661 North pleasant street

department: Vet & Animal Sciences

institute: University of Massachusetts

description:
10 ng of MO at the one cell stage.
CMO2 (expt DA2).

hyb_protocol: Labeled cDNA were incorporated into a hybridization solution from the Affymetrix GeneChip Hybridization Kit. Each sample was hybridized in separate arrays for 20 hours at 450C.

scan_protocol: All arrays were treated by the MIT core facility. http://openwetware.org/wiki/BioMicroCenter:Microarrays.

data_processing: Initial data analysis was generated with the Affymetrix Expression Console and an R package was used to assess data quality.  Sample normalization was done using the gcrma method.

label: Biotin

organism: Xenopus laevis

source_name: Xenopus laevis CNC from stage 17 embryos injected with control morpholino.

label_protocol: Total RNA quality control was performed with the Bioanalyzer 2100 (Agilent). Double stranded cDNA was generated and labeled with the Ovation RNA Amplification System and Encore Biotin Module (NuGen), respectively. Purification was performed using the Qiagen PCR Purification Kit

growth_protocol: Embryos were injected at the one cell stage and grown at 15C until stage 15 to 17.

extract_protocol: RNA extraction was performed as previously described using guanidium thioisocyanate, phenol chlorophorm and lithium chloride precipitation. P. Chomczynski, N. Sacchi, Anal. Biochem. 162, 156 (1987).

treatment_protocol: Cranial neural crest cells were dissected and imediately extracted.

value: Stage 15-17 embryos

value: cranial neural crest explant

tag: agent

value: control morpholino


title: CNC-MO13+C13-3

status: Public on Feb 22 2011

type: RNA

state: MA

country: USA

description:
10 ng of MO at the one cell stage plus 300pg of mRNA.
MO13+C13-2 (expt DA2).

molecule: total RNA

source_name: Xenopus laevis CNC from stage 17 embryos injected with a morpholino to ADAM13 and a GFP-fusion protein containing the ADAM13 cytoplasmic domain.

tag: developmental stage

tag: tissue


title: CNC-MO13-3

description:
10 ng of MO at the one cell stage.
MO13-2 (expt DA2).

source_name: Xenopus laevis CNC from stage 17 embryos injected with a morpholino to ADAM13.

value: a morpholino to ADAM13


title: tooth germs treated by 5E1, biological rep1

city: Seoul

first: Sung-Won

last: Cho

address: Seongsanno 250, Seodaemun-gu

department: Oral Biology

country: South Korea

institute: Yonsei University College of Dentistry

description: Gene expression data from tooth germs at 24hours after injection time.

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45℃ on GeneChip Mouse Genome 430 2.0 array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000.

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

label: biotin

organism: Mus musculus

source_name: tooth germs affected by 5E1, biological rep1

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, Affymetrix, P/N 702232 Rev. 3).

growth_protocol: Embryos were collected from pregnant mice at 24 hours after injection.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions. And then, extracted total RNA was purified using RNeasy min elute kit manufacturer's instructions.

treatment_protocol: A single injection of 5E1 (10 mg/kg body weight), 40-1a (10 mg/kg body weight), cyclopamine (10 mg/kg body weight) or PBS (1 ml) was administered intraperitoneally to pregnant ICR mice at the stage of embryonic day 14. After one day tooth germs were dissected from mandibles in embryos.

tag: strain

value: ICR

value: mandibular molar tooth germs, embryos

tag: antibody transfer to embryo

value: intraperitoneal 5E1 injection to pregnant mice

tag: injection time

value: embryonic day 14

tag: sampling time

value: at 24 hours after injection


title: phoB mutant_0.0066mM

city: tokushima

first: Haruyuki

last: Nakayama-Imaohji

address: 3-18-15 kuramoto-cho

country: Japan

institute: Tokushima University

description: delta PhoB 0.006

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

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

data_processing: The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis), quantile normalization, and background correction as implemented in the ArrayStar software (DNASTAR)

organism: Bacteroides fragilis

source_name: Bacteroides fragilis

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

growth_protocol: Bacteroides fragilis strains were grown to mid-log phase (O.D.600nm 0.4-0.6) in defined minimal media (Varel, V.H et al. Appl. Microbiol.28(2):251-257, 1974.) supplemented with 6.6 mM or 0.0066 mM of KH2PO4.

extract_protocol: Total RNAs were extracted using hot-phenol method.

tag: genotype/variation

value: BF1576 (phoB) mutant

tag: culture condition

value: Pi-limiting (0.0066mM Pi) condition


title: proband 12

type: genomic

city: Baltimore

first: Jonathan

last: Pevsner

state: MD

address: 707 N. Broadway

institute: Kennedy Krieger Institute

description: Genomic DNA extracted from cell lines was genotyped using Infinium HumanHap550-v3 Genotyping BeadChips (Illumina).

hyb_protocol: RA1 resuspended DNA was loaded onto BeadChips arrays. After overnight incubation at 48¡C, single-base extension and allele-specific staining was performed on a Teflow chamber rack system (Tecan, Maennedorf, Switzerland).

scan_protocol: After allele-specific staining BeadChip arrays were coated with XC4/ethanol , dried for 1 hour and scanned on a BeadArray Reader (Illumina).

data_processing: Genomic DNA extracted from cell lines was genotyped using Infinium HumanHap550-v3 or HumanHap300-2 Genotyping BeadChips (Illumina).

label: C-Bio and A-DNP

molecule: genomic DNA

organism: Homo sapiens

source_name: Lymphoblastoid cells

label_protocol: 750ng of genomic DNA was whole-genome amplified in an overnight reaction at 37¡C using amplification master mix (WG-AMM) and primer/neutralization mix (WG-MP1). After incubation the amplified DNA was fragmented with fragmentation mix (WG-FRG), precipitated with isopropanol and precipitation mix (PA1) and resuspended in hybridization buffer (RA1).

extract_protocol: Extraction of genomic DNA from cell lines was performed using a Qiagen or Gentra PurGene kit.

tag: gender

value: male


title: tooth germs treated by 5E1, biological rep2

source_name: tooth germs affected by 5E1, biological rep2


title: CNC-MO13+C13-2

description:
10 ng of MO at the one cell stage plus 300pg of mRNA.
MO13+C13-5 (expt DA5).

value: a morpholino to ADAM13 and a GFP-fusion protein containing the ADAM13 cytoplasmic domain


title: tooth germs treated by 40-1a, biological rep1

source_name: tooth germs affected by 40-1a, biological rep1

value: intraperitoneal 40-1a injection to pregnant mice


title: mouse embryonic fibroblast-shRNA TNC-rep1

city: Basel

first: florence

last: Brellier

address: Maulbeerstrasse 66

country: Switzerland

institute: FMI

description: mouse embryonic fibroblast expanded from a wild-type mouse, stably transfected with tenascin-C shRNA- clone 1

hyb_protocol: Affymetrix GeneChip arrays were hybridized following the GeneChip Whole Transcript (WT) Sense Target Labeling Assay Manual (Affymetrix) with a hybridization time of 16h. The Affymetrix Fluidics protocol FS450_0007 was used for washing.

scan_protocol: Scanning was performed with Affymetrix GCC Scan Control v. 3.0.1 on a GeneChip® Scanner 3000 with autoloader.

data_processing: Probesets were summarized and probeset-level values normalized with justRMA() function from R (version 2.8.0) / Bioconductor (version 2.4) package affy using the CDF environment MoGene-1_0-st-v1.r3.cdf and annotation from Netaffx (www.netaffx.com).

label_protocol: RNA was processed the WT cDNA Syntehsis & Amplification kit and labeling was performed with the WT Terminal Labeling kit from Affymetrix according to the manufacturer's instructions.

growth_protocol: 50 000 MEFs were seeded in wells of 6-well plates and cultured for 2 days in DMEM 10% fetal calf serum

extract_protocol: total RNA was extracted with RNeasy from Qiagen

treatment_protocol: No particular treatment was applied

tag: cell type

value: mouse embryonic fibroblast

tag: immortalization

value: spontaneous


title: phoB mutant_6.6mM

description: delta PhoB 6.6

value: Pi-excess (6.6mM Pi) condition


title: mouse embryonic fibroblast-shRNA TNC-rep2

description: mouse embryonic fibroblast expanded from a wild-type mouse, stably transfected with tenascin-C shRNA- clone 2


title: WT_0.0066mM

description: Wild 0.006

organism: Bacteroides fragilis YCH46

source_name: Bacteroides fragilis strain YCH46

value: Wild-type


title: CNC-Control-2

description:
10 ng of MO at the one cell stage.
CMO5 (expt DA5).

value: Stage 15-17 embryos

value: cranial neural crest explant


title: OVE26_8W_4_7

city: New York

first: Ann

middle: Marie

last: Schmidt

state: NY

department: Department of Surgery

institute: Columbia University

description: Glomeruli of OVE26 Diabetic mouse

hyb_protocol: 10 μg of RNA dissolved in 300 μL of buffer was hybridized to Mouse Genome 430. 2.0 GeneChips (Affymetrix). All samples were prepared with the two-cycle protocol recommended by the manufacturer.

scan_protocol: Arrays were scanned on an Affymetrix Scanner 3000-7G scanner with GCOS software. Scanning was peformed according to the protocol described in the Affymetrix GeneChip® Expression Analysis Technical Manual, November 2004 Edition.

data_processing: Data was normalized using the GCRMA algorithm.

source_name: Glomeruli from diabetic male OVE26 mouse sacrificed at 8 weeks

label_protocol: The RNA was amplified, biotin labeled and fragmented using the Gene Chip 3’IVT Express Kit (Affymetrix). Yield of fragmented samples was tested by Nanodrop and RNA size was assessed by Bioanalyzer using the Agilent RNA 6000 Pico kit.

growth_protocol: Mice were maintained at all times on a 12-hour light-dark cycle in a pathogen-free environment with free access to rodent chow and water.

extract_protocol: RNA was isolated from ~1000 isolated glomeruli per mouse using the RNaqueous kit (Ambion, Austin, TX) including a DNase step. Total RNA concentration was assessed by NanoDrop Spectrophotometer (NanoDrop Technologies) and quality was assessed on a 2100 Bioanalyzer system (Agilent Technologies) using the Agilent RNA 6000 Nano kit. All of our samples had an RNA integrity score >8, and there was no indication of RNA degradation or contamination with DNA.

treatment_protocol: Mice were fed Purina mouse diet 5053.

tag: sample type

value: ove26 mice

value: Male

tag: age

value: 8 weeks

value: glomerulus

tag: disease state

value: Diabetic


title: OVE26_8W_1_4

description: Glomeruli of OVE26 diabetic mouse


title: OVE26_8W_2_5

description: Glomeruli of OVE26 Diabetic mouse


title: mouse embryonic fibroblast-TNCKO-rep1

description: mouse embryonic fibroblast expanded from a tenascin-C knock-out mouse- clone 1

value: tenascin-C knock-out mouse


title: OVE26_8W_3_6

description: Glomeruli of OVE26 Diabetic mouse


title: proband 15

value: female


title: mouse embryonic fibroblast-TNCKO-rep2

description: mouse embryonic fibroblast expanded from a tenascin-C knock-out mouse- clone 2


title: proband 18

description: Genomic DNA extracted from cell lines was genotyped using Infinium HumanHap300-2 Genotyping BeadChips (Illumina).


title: mouse embryonic fibroblast-wild-type-rep3

description: mouse embryonic fibroblast expanded from a wild-type mouse- clone 3

value: wild-type


title: tooth germs treated by 40-1a, biological rep2

source_name: tooth germs affected by 40-1a, biological rep2

value: ICR

value: mandibular molar tooth germs, embryos

value: embryonic day 14

value: at 24 hours after injection


title: CNC-MO13+C13-1

description:
10 ng of MO at the one cell stage plus 300pg of mRNA.
MO13+C13-4 (expt DA4).

value: a morpholino to ADAM13 and a GFP-fusion protein containing the ADAM13 cytoplasmic domain


title: WT_6.6mM

description: Wild 6.6

value: Pi-excess (6.6mM Pi) condition


title: mouse embryonic fibroblast-wild-type-rep2

description: mouse embryonic fibroblast expanded from a wild-type mouse- clone 2

value: mouse embryonic fibroblast

value: spontaneous


title: CNC-MO13-1

description:
10 ng of MO at the one cell stage.
MO13-4 (expt DA4).

value: Stage 15-17 embryos

value: cranial neural crest explant

value: a morpholino to ADAM13


title: proband 8


title: FVB_8W_2_2

description: Glomeruli of FVB Non-diabetic mouse

source_name: Glomeruli from nondiabetic male FVB mouse sacrificed at 8 weeks

value: fvb control

value: fvb/nj

value: Male

value: 8 weeks

value: Nondiabetic


title: proband 40

value: female


title: S2_NeuN_negative

status: Public on Feb 21 2011

city: Wako

first: Kazuya

last: Iwamoto

address: 2-1 Hirosawa

department: Brain Science Institute

institute: RIKEN

description:
Affymetrix Human Promoter Array 1.0R
test: S2_MeCl_M1.CEL, S2_MeCl_M2.CEL, S2_MeCl_M3.CEL
ctrl: Satsu2_M1.CEL, Satsu2_M2.CEL, Satsu2_M3.CEL

hyb_protocol: Labeled DNA was hybridzed per array using the Affymetrix hybridization kit, according to the manufacturer's protocol.

scan_protocol: Arrays were scanned on an Affymetrix Scanner 3000.

data_processing:
Data was analyzed with MAT software (bandwidth, 300; max gap, 300; minimum number of probes, 10)
Bar files were generated by MAT software and contain MAT scores in each probe.  Three bed files (see Series supplementary files) contain high quality methylated regions in the neuronal, non-neuronal, or both fractions. After the consideration of effect of restriction enzymes, they are extracted based on the commonly methylated regions in all the relevant samples and that MAT score p values < 0.0001 in each sample.

label_protocol: Samples (7.5 ug of DNA) were enzymatically fragmented and labeled using the WT Labeling Kit (Affymetrix) to add biotinylated compound to the ends of the fragments.

extract_protocol: NeuN+ and NeuN- nuclei fraction was isolated using NeuN-based cell sorting method. After isolation of genomic DNA from each fraction, enrichment of methylated DNA with a Methylcollector and unmethylated DNA by McrBC treatment was performed. Three unrelated Japanese male prefrontal cortex samples were used. Treated DNA was amplified according to the Affymetrix immunoprecipitation protocol.

tag: subject

value: subject 2

tag: marker

value: NeuN negative

tag: treatment

value: methylated DNA (methyl collector)

source_name: unmethylated DNA from NeuN negative nuclei (frontal cortex)

value: unmethylated DNA (McrBC)


title: mouse embryonic fibroblast-wild-type-rep1

description: mouse embryonic fibroblast expanded from a wild-type mouse- clone 1

value: wild-type


title: S3_NeuN_positive

description:
Affymetrix Human Promoter Array 1.0R
test: S3_MeCl_P1.CEL, S3_MeCl_P2.CEL, S3_MeCl_P3.CEL
ctrl: Satsu3_P1.CEL, Satsu3_P2.CEL, Satsu3_P3.CEL

value: subject 3

value: NeuN positive

source_name: unmethylated DNA from NeuN positive nuclei (frontal cortex)


title: S6_NeuN_negative

description:
Affymetrix Human Promoter Array 1.0R
test: S6_MeCl_M1.CEL, S6_MeCl_M2.CEL, S6_MeCl_M3.CEL
ctrl: Satsu6_M1.CEL, Satsu6_M2.CEL, Satsu6_M3.CEL

source_name: methylated DNA from NeuN negative nuclei (frontal cortex)

value: subject 6


title: S2_NeuN_positive

description:
Affymetrix Human Promoter Array 1.0R
test: S2_MeCl_P1.CEL, S2_MeCl_P2.CEL, S2_MeCl_P3.CEL
ctrl: Satsu2_P1.CEL, Satsu2_P2.CEL, Satsu2_P3.CEL

source_name: methylated DNA from NeuN positive nuclei (frontal cortex)


title: proband 5

description: Genomic DNA extracted from cell lines was genotyped using Infinium HumanHap550-v3 Genotyping BeadChips (Illumina).


title: proband 6

source_name: Fibroblasts

value: male


title: fus3-3 vs. wild-type (Col-0), 12 DAF, Seed 2

city: Nagoya

first: Akiko

last: Yamamoto

address: Furo-cho

department: Bioscience and Biotechnology Center

institute: Nagoya University

description: Transcriptomes were compared between fus3 mutant and wild-type developing seeds.

hyb_protocol: Agilent Arabidopsis2 oligo microarray hybridization protocol.

scan_protocol: Dual-laser Microarray scanner Agilent Technologies.

data_processing: Agilent Feature Extraction software version A.7.5.1

organism: Arabidopsis thaliana

source_name: wild-type (Col-0), 12 DAF

label_protocol: Agilent Low RNA Input Linear Amplification Kit.

growth_protocol: 16h light/8h dark, 22°C.

extract_protocol: The total RNA was extracted using Concert Plant RNA Reagent (Invitrogen) and was followed by purification using RNeasy Mini Kit (Qiagen).

tag: ecotype

tag: genotype

value: seed

value: 12 days after flowering (DAF)

tag: developmental stage

value: green cotyledon stage

value: no treatment

tag: replicate

value: 2 of 3

source_name: fus3-3 mutant, 12 DAF

value: fus3-3 mutant


title: fus3-3 vs. wild-type (Col-0), 12 DAF, Seed 1 (dye-swap)

tag: tissue

value: 1 of 3 (dye-swap)


title: S3_NeuN_negative

description:
Affymetrix Human Promoter Array 1.0R
test: S3_MeCl_M1.CEL, S3_MeCl_M2.CEL, S3_MeCl_M3.CEL
ctrl: Satsu3_M1.CEL, Satsu3_M2.CEL, Satsu3_M3.CEL


title: S6_NeuN_positive

description:
Affymetrix Human Promoter Array 1.0R
test: S6_MeCl_P1.CEL, S6_MeCl_P2.CEL, S6_MeCl_P3.CEL
ctrl: Satsu6_P1.CEL, Satsu6_P2.CEL, Satsu6_P3.CEL


title: proband 22

value: female


title: proband 7


title: FVB_8W_3_3

description: Glomeruli of FVB Non-diabetic mouse

value: fvb control

tag: strain

value: fvb/nj

value: Male

value: 8 weeks

value: glomerulus

value: Nondiabetic


title: proband 4


title: fus3-3 vs. wild-type (Col-0), 12 DAF, Seed 1

value: wild-type

value: 1 of 3


title: fus3-3 vs. wild-type (Col-0), 12 DAF, Seed 2 (dye-swap)

value: 2 of 3 (dye-swap)


title: CNC-MO13-2

description:
10 ng of MO at the one cell stage.
MO13-5 (expt DA5).

source_name: Xenopus laevis CNC from stage 17 embryos injected with a morpholino to ADAM13.

value: Stage 15-17 embryos

value: cranial neural crest explant

tag: agent

value: a morpholino to ADAM13


title: FVB_8W_1_1

description: Glomeruli of FVB Non-diabetic mouse


title: fus3-3 vs. wild-type (Col-0), 8 DAF, Seed 3 (dye-swap)

data_processing: Agilent Feature Extraction software version A.7.1.1.

source_name: fus3-3 mutant, 8 DAF

value: seed

value: 8 days after flowering (DAF)

value: bent cotyledon stage

value: no treatment

value: 3 of 3 (dye-swap)

source_name: wild-type (Col-0), 8 DAF


title: fus3-3 vs. wild-type (Col-0), 12 DAF, Seed 3 (dye-swap)

value: fus3-3 mutant

value: 12 days after flowering (DAF)

value: green cotyledon stage


title: fus3-3 vs. wild-type (Col-0), 12 DAF, Seed 3

value: 3 of 3


title: fus3-3 vs. wild-type (Col-0), 8 DAF, Seed 3


title: proband 3

source_name: Lymphoblastoid cells

value: male


title: proband 1


title: fus3-3 vs. wild-type (Col-0), 8 DAF, Seed 2 (dye-swap)


title: Transgenic ER-FUS3, 6h, ESTR ABA, 2

description: ER-FUS3 transgenic plants were used to identify the genes up-regulated in young seedlings of Arabidopsis in response to ectopic expression of FUS3.

source_name: ER-FUS3 transgenic plant (Col-0), untreated

growth_protocol: Seeds of an ER8-FUS3 transgenic line were plated on 0.6% agar plates with the same composition as below and kept for 3 days at 4°C, then shifted to 22°C under continuous light, cultured for 4 days. The transgenic plant seedlings with expanded cotyledons were transferred from the plates to a 10 ml liquid medium [half-strength MS salt mixture, pH 5.7, B5 vitamins, and 1% (w/v) sucrose] in a 100 ml Erlenmyer flask (100 seedlings per flask), cultured for additional 3 days.

extract_protocol: The total RNA was extracted by RNeasy Mini Kit (Qiagen) and was purified again using the same kit.

value: ER-FUS3 transgenic

value: seedling

value: 7 days

tag: treatment time

value: 2 of 2

source_name: ER-FUS3 transgenic plant (Col-0), ESTR and ABA, 6h

value: 4μM estrogen (ESTR) & 100μM abscisic acid (ABA)


title: CNC-Control-1

description:
10 ng of MO at the one cell stage.
CMO4 (expt DA4).

source_name: Xenopus laevis CNC from stage 17 embryos injected with control morpholino.

value: Stage 15-17 embryos

value: cranial neural crest explant

value: control morpholino


title: fus3-3 vs. wild-type (Col-0), 8 DAF, Seed 1

value: wild-type

value: seed

value: 8 days after flowering (DAF)

value: 1 of 3


title: proband 9

tag: gender

value: female


title: Transgenic ER-FUS3, 36h, ABA, 2

value: no treatment

source_name: ER-FUS3 transgenic plant (Col-0), ABA, 36h

value: 100μM abscisic acid (ABA)


title: fus3-3 vs. wild-type (Col-0), 8 DAF, Seed 2

value: bent cotyledon stage

value: 2 of 3

value: fus3-3 mutant


title: Transgenic ER-FUS3, 12h, ESTR ABA, 2

value: ER-FUS3 transgenic

value: seedling

source_name: ER-FUS3 transgenic plant (Col-0), ESTR and ABA, 12h


title: Transgenic ER-FUS3, 36h, ESTR ABA, 2

value: 7 days

value: 2 of 2

source_name: ER-FUS3 transgenic plant (Col-0), ESTR and ABA, 36h


title: proband 2


title: Transgenic ER-FUS3, 48h, ABA, 2

source_name: ER-FUS3 transgenic plant (Col-0), ABA, 48h


title: Transgenic ER-FUS3, 48h, ESTR ABA, 2

source_name: ER-FUS3 transgenic plant (Col-0), ESTR and ABA, 48h

value: 4μM estrogen (ESTR) & 100μM abscisic acid (ABA)


title: Transgenic ER-FUS3, 3h, ESTR ABA, 2

source_name: ER-FUS3 transgenic plant (Col-0), ESTR and ABA, 3h


title: Transgenic ER-FUS3, 36h, ESTR, 2

source_name: ER-FUS3 transgenic plant (Col-0), ESTR, 36h

value: 4μM estrogen (ESTR)


title: fus3-3 vs. wild-type (Col-0), 8 DAF, Seed 1 (dye-swap)

value: 1 of 3 (dye-swap)


title: Transgenic ER-FUS3, 12h, ABA, 2

source_name: ER-FUS3 transgenic plant (Col-0), ABA, 12h


title: Transgenic ER-FUS3, 24h, ABA, 2

source_name: ER-FUS3 transgenic plant (Col-0), ABA, 24h


title: Transgenic ER-FUS3, 12h, ESTR, 2

source_name: ER-FUS3 transgenic plant (Col-0), ESTR, 12h


title: Transgenic ER-FUS3, 24h, ESTR ABA, 2

source_name: ER-FUS3 transgenic plant (Col-0), ESTR and ABA, 24h


title: Transgenic ER-FUS3, 48h, ESTR, 2

source_name: ER-FUS3 transgenic plant (Col-0), ESTR, 48h


title: Transgenic ER-FUS3, 6h, ABA, 2

source_name: ER-FUS3 transgenic plant (Col-0), ABA, 6h


title: ERalpha ChIP-chip (replicate 2)

city: Dallas

first: W. Lee

last: Kraus

state: TX

address: 5323 Harry Hines Blvd.

institute: UT Southwestern Medical Center

hyb_protocol: see NimbleGen website

scan_protocol: see NimbleGen website

data_processing: Genomic data analysis was performed using the statistical programming language R (R Development Core Team, version 2.6.1). All data processing scripts are available upon request. The log2 ratio data from each of the arrays was subjected to lowess normalization.

source_name: input

label_protocol: see NimbleGen website

extract_protocol: HeLa-ER cells were grown to ~80 to 90% confluence, treated with 100nM E2 for 45 min, cross-linked with 10mM DMS in PBS for 10min at 37°C followed by crosslinking with 1% paraformaldehyde in PBS for 10 min. at 37°C, and quenched in 125 mM glycine in PBS for 5 min. at 4°C.  The cells were collected by centrifugation and sonicated in Lysis Buffer [Tris•HCl pH 7.9, 10 mM EDTA, 50 mM NaCl, 1% SDS, and 1x protease inhibitor cocktail (Roche, cat no. 04 693 124 001)] to generate chromatin fragments of ~500 bp in length.  The material was clarified by centrifugation, diluted 10-fold in Dilution Buffer (20 mM Tris•HCl pH 7.9, 2 mM EDTA, 150 mM NaCl, 0.5% Triton X-100, 1x protease inhibitor cocktail), and pre-cleared by incubation with protein A-agarose beads.  The pre-cleared, chromatin-containing supernatant was used in immunoprecipitation reactions with an antibody against ERalpha, or without antibody as a control.  The immunoprecipitated genomic DNA was cleared of protein and residual RNA by digestion with proteinase K and RNase H, respectively.  The DNA was then extracted with phenol:chloroform:isoamyl alcohol and precipitated with ethanol.   The material was then amplified with LM-PCR.

tag: cell line

value: HeLa-ER

tag: antibody

value: none (input)

source_name: IP

value: custom made rabbit polyclonal ERa antibody (Kraus WL, Kadonaga JT, Genes Dev. 1998 Feb 1;12(3):331-42)


title: Transgenic ER-FUS3, 3h, ABA, 2

source_name: ER-FUS3 transgenic plant (Col-0), untreated

source_name: ER-FUS3 transgenic plant (Col-0), ABA, 3h


title: Transgenic ER-FUS3, 24h, ESTR, 2

source_name: ER-FUS3 transgenic plant (Col-0), ESTR, 24h


title: SM3B

city: Memphis

first: Katherine

middle: S

last: Barker

state: TN

address: 881 Madison Avenue, Room 305

department: Clinical Pharmacy

institute: University of Tennessee Health Science Center

description: clinical isolate with hyperactive PDR1 allele

hyb_protocol: The cRNA pellet was suspended in 10 µl of RNase-free water, and 10 µg was fragmented at 95°C for 35 min in 200 mM Tris-acetate (pH 8.1), 500 mM potassium acetate, and 150 mM magnesium acetate. The fragmented cRNA was hybridized for 16 h at 45°C to an Affymetrix custom expression array (CAN07a520619F; manufactured by Affymetrix) for C. albicans. Arrays were washed at 25°C with 6x SSPE (1x SSPE is 0.18 M NaCl, 10 mM NaH2PO4, and 1 mM EDTA [pH 7.7]) and 0.01% Tween 20 followed by a stringent wash at 50°C with 100 mM MES (morpholineethanesulfonic acid), 0.1 M NaCl, and 0.01% Tween 20. Affymetrix Fluidics Station 450 was used for hybridizations and washes according to standard EukGE-WS2v5 protocol. The arrays were then stained with phycoerythrin-conjugated streptavidin (Molecular Probes).

scan_protocol: The fluorescence intensities were determined using a GCS 3000 high-resolution confocal laser scanner (Affymetrix).

data_processing:
The scanned images were analyzed using software resident in the GeneChip operating system, version 2.0 (Affymetrix). Sample loading and variations in staining were standardized by scaling the average of the fluorescent intensities of all genes on an array to a constant target intensity of 250. The signal intensity for each gene was calculated as the average intensity difference, represented by (PM –MM)/number of probe pairs, where PM and MM denote perfectly matched and mismatched probes, respectively.
Probe sets were deleted from subsequent analysis if they were called absent by the Affymetrix criterion and displayed an absolute value below 20 in all experiments. The expression value of each gene was normalized to the median expression of all genes in each chip as well as to the median expression for that gene across all chips in the study. A pairwise comparison of gene expression was performed for each matched experiment.

organism: Nakaseomyces glabratus

source_name: SM3 isolate

label_protocol: First- and second-strand cDNA was synthesized from 15 µg total RNA, using a SuperScript double-stranded cDNA synthesis kit (Invitrogen) and an oligo-dT24-T7 primer (Proligo) according to the manufacturers' instructions. cRNA was synthesized and labeled with biotinylated UTP and CTP by in vitro transcription, using T7 promoter-coupled double-stranded cDNA as a template and a BioArray HighYield RNA transcript labeling kit (Enzo Diagnostics). Double-stranded cDNA synthesized from the previous steps was washed twice with 70% ethanol and suspended in 22 µl of RNase-free water. The cDNA was incubated as recommended with reaction buffer, biotin-labeled ribonucleotides,dithiothreitol, RNase inhibitor mix, and T7 RNA polymerase for 5 h at 37°C. The labeled cRNA was separated from unincorporatedribonucleotides with a Chroma Spin-100 column (Clontech) and was ethanol precipitated at –20°C overnight.

growth_protocol: Cells were grown overnight at 30deg Celsius in YPD (1% yeast extract, 2% peptone, and 1% dextrose) with agitation, and these saturated cultures were used to seed 20ml YPD cultures (OD600= 0.2) which were grown with agitation for 3hrs at 30deg Celsius.

extract_protocol: RNA was isolated from frozen cell pellets using the hot-phenol method (Schmitt, M. E., T. A. Brown, and B. L. Trumpower. 1990. Nucleic Acids Res. 18:3091-3092.). Briefly, cells were resuspended in 12 ml AE buffer (50 mM sodium acetate [pH 5.2] and 10 mM EDTA) at room temperature, after which 800 µl 25% sodium dodecyl sulfate and 12 ml acid phenol (Fisher Scientific, Houston, TX) were added. The cell lysate was then incubated for 10 min at 65°C with vigorous shaking each minute, cooled on ice for 5 min, and subjected to centrifugation for 15 min at 11,952 x g. The supernatants were transferred to new tubes containing 15 ml chloroform, mixed, and subjected to centrifugation at 200 x g for 10 min. RNA was precipitated from the resultingaqueous layer by mixing that portion in new tubes with 1 volume of isopropanol and 0.1 volume of 2 M sodium acetate [pH 5.0] and subjecting the mixture to centrifugation at 17,211 x g for 35 min at 4°C. The supernatants were removed, the pellet was resuspended in 10 ml 70% ethanol, and the RNA was collected by centrifugation at 17,211 x g for 20 min at 4°C. The supernatants were again removed, and the RNA was resuspended in 50 to 200 µl diethyl pyrocarbonate-treated water. The RNA was stored at –80°C until needed.


title: Transgenic ER-FUS3, 6h, ESTR, 2

source_name: ER-FUS3 transgenic plant (Col-0), ESTR, 6h


title: SM1-delta-pdr1/PDR1-SM3B

description: clinical isolate in which PDR1 gene was replaced by PDR1 allele from SM3

source_name: SM1Dpdr1/PDR1-SM3 strain


title: Transgenic ER-FUS3, 6h, No treatment, 2

source_name: ER-FUS3 transgenic plant (Col-0), untreated, 6h


title: Transgenic ER-FUS3, 3h, ESTR, 2

source_name: ER-FUS3 transgenic plant (Col-0), ESTR, 3h


title: 6856-2

description: clinical isolate with wildtype PDR1 allele

source_name: 6856 isolate


title: SM1-delta-pdr1/PDR1-6955B

description: clinical isolate in which PDR1 gene was replaced by PDR1 allele from 6955

source_name: SM1Dpdr1/PDR1-6955 strain


title: SM1-delta-pdr1/PDR1-SM1B

description: clinical isolate in which PDR1 gene was replaced by PDR1 allele from SM1

source_name: SM1Dpdr1/PDR1-SM1 strain


title: Transgenic ER-FUS3, 48h, No treatment, 2

source_name: ER-FUS3 transgenic plant (Col-0), untreated, 48h


title: proband 10

source_name: Lymphoblastoid cells

value: male


title: Transgenic ER-FUS3, 12h, No treatment, 2

source_name: ER-FUS3 transgenic plant (Col-0), untreated, 12h


title: SM1B

source_name: SM1 isolate


title: Transgenic ER-FUS3, 3h, No treatment, 2

source_name: ER-FUS3 transgenic plant (Col-0), untreated, 3h


title: SM1-delta-pdr1/PDR1-6856A

description: clinical isolate in which PDR1 gene was replaced by PDR1 allele from 6856

source_name: SM1Dpdr1/PDR1-6856 strain


title: Transgenic ER-FUS3, 48h, ESTR ABA, 1

data_processing: Agilent Feature Extraction software version A.6.1.1.

source_name: ER-FUS3 transgenic plant (Col-0), untreated

value: 1 of 2

source_name: ER-FUS3 transgenic plant (Col-0), ESTR and ABA, 48h


title: Transgenic ER-FUS3, 36h, No treatment, 2

value: no treatment

source_name: ER-FUS3 transgenic plant (Col-0), untreated, 36h


title: 6955-2

source_name: 6955 isolate


title: SM1-delta-pdr1/PDR1-6856B


title: ERalpha ChIP-chip (replicate 1)

source_name: input

source_name: IP


title: Transgenic ER-FUS3, 0h, No treatment, 2

source_name: ER-FUS3 transgenic plant (Col-0), untreated, 0h


title: Transgenic ER-FUS3, 24h, No treatment, 2

source_name: ER-FUS3 transgenic plant (Col-0), untreated, 24h


title: SM1-delta-pdr1/PDR1-6955A


title: 6955-1


title: SM1-delta-pdr1/PDR1-SM1A


title: SM1-delta-pdr1/PDR1-SM3A

source_name: SM1Dpdr1/PDR1-SM3 strain


title: Transgenic ER-FUS3, 3h, ESTR ABA, 1

source_name: ER-FUS3 transgenic plant (Col-0), ESTR and ABA, 3h


title: SM3A

source_name: SM3 isolate


title: Transgenic ER-FUS3, 36h, ESTR ABA, 1

source_name: ER-FUS3 transgenic plant (Col-0), ESTR and ABA, 36h


title: Transgenic ER-FUS3, 24h, ESTR ABA, 1

source_name: ER-FUS3 transgenic plant (Col-0), ESTR and ABA, 24h


title: 6856-1

source_name: 6856 isolate


title: Transgenic ER-FUS3, 24h, ABA, 1

source_name: ER-FUS3 transgenic plant (Col-0), ABA, 24h

value: 100μM abscisic acid (ABA)


title: Transgenic ER-FUS3, 6h, ESTR ABA, 1

source_name: ER-FUS3 transgenic plant (Col-0), ESTR and ABA, 6h


title: Transgenic ER-FUS3, 3h, ABA, 1

source_name: ER-FUS3 transgenic plant (Col-0), ABA, 3h


title: Transgenic ER-FUS3, 12h, ESTR ABA, 1

source_name: ER-FUS3 transgenic plant (Col-0), untreated

source_name: ER-FUS3 transgenic plant (Col-0), ESTR and ABA, 12h


title: Transgenic ER-FUS3, 36h, ABA, 1

source_name: ER-FUS3 transgenic plant (Col-0), ABA, 36h


title: Transgenic ER-FUS3, 12h, ABA, 1

source_name: ER-FUS3 transgenic plant (Col-0), ABA, 12h


title: SM1A

source_name: SM1 isolate


title: Transgenic ER-FUS3, 48h, ESTR, 1

source_name: ER-FUS3 transgenic plant (Col-0), ESTR, 48h


title: Transgenic ER-FUS3, 6h, ABA, 1

source_name: ER-FUS3 transgenic plant (Col-0), ABA, 6h


title: Transgenic ER-FUS3, 48h, ABA, 1

source_name: ER-FUS3 transgenic plant (Col-0), ABA, 48h


title: Transgenic ER-FUS3, 12h, ESTR, 1

source_name: ER-FUS3 transgenic plant (Col-0), ESTR, 12h


title: Transgenic ER-FUS3, 36h, ESTR, 1

source_name: ER-FUS3 transgenic plant (Col-0), ESTR, 36h


title: Transgenic ER-FUS3, 24h, ESTR, 1

source_name: ER-FUS3 transgenic plant (Col-0), ESTR, 24h


title: Transgenic ER-FUS3, 6h, ESTR, 1

source_name: ER-FUS3 transgenic plant (Col-0), ESTR, 6h


title: Transgenic ER-FUS3, 3h, ESTR, 1

source_name: ER-FUS3 transgenic plant (Col-0), ESTR, 3h


title: C2-dnMEK5-4.5day-rep1

city: Kyoto

first: Eisuke

last: Nishida

address: Kitashirakawa, Sakyo-ku

department: Department of Cell and Developmental Biology

institute: Graduate School of Biostudies, Kyoto University

description: C2C12 cells were placed in DM and infected with adenovirus containing dnMEK5 1 day of differentiation. Cells were collected at 4.5 days of differentiation.

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45 degrees C on Mouse Genome 430 2.0 array. GeneChips were washed and stained in the Affymetrix Fluidics Styation 450.

scan_protocol: GeneChips were scanned using an Affymetrix GeneChip Scanner.

data_processing: The data were analyzed with the GCRMA algorithm (GeneSpring GX 11.0.2).

source_name: dnMEK5-infected C2C12 cells in DM

label_protocol: Biotinylated cRNA were prepared according to the Affymetrix protocol (One-Cycle Target Labeling Assays) from 5 ug total RNA.

growth_protocol: C2C12 cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM) containing 15% fetal bovine serum (FBS) (growth medium; GM). To induce differentiation, growth medium was replaced with DMEM containing 3% horse serum (differentiation medium; DM) when cells were 90-100% confluent.

extract_protocol: Total RNA was prepared using the RNeasy Mini Kit (Qiagen) according to the manufacturer’s instructions.

treatment_protocol: C2C12 cells were infected with adenovirus containing lacZ or dnMEK5 1 day after differentiation. For each experiment, five samples were used: cells in growth medium (0 day), lacZ-infected cells at two time points (lacZ- 2.5 day and lacZ- 4.5 day) and dnMEK5-infected cells at two time points (dnMEK5- 2.5 day and dnMEK5- 4.5 day).

tag: medium

value: differentiation

tag: infection

tag: time

value: 4 .5 days


title: C2-lacZ-2.5day-rep2

description: C2C12 cells were placed in DM and infected with adenovirus containing lacZ 1 day of differentiation. Cells were collected at 2.5 days of differentiation.

source_name: lacZ-infected C2C12 cells in DM

value: lacZ

value: 2.5 days


title: C2-dnMEK5-2.5day-rep2

description: C2C12 cells were placed in DM and infected with adenovirus containing dnMEK5 1 day of differentiation. Cells were collected at 2.5 days of differentiation.


title: C2-dnMEK5-4.5day-rep2


title: C2-lacZ-2.5day-rep1


title: C2-dnMEK5-2.5day-rep1


title: C2-lacZ-4.5day-rep2

description: C2C12 cells were placed in DM and infected with adenovirus containing lacZ 1 day of differentiation. Cells were collected at 4.5 days of differentiation.


title: C2-0day-rep2

description: C2C12 cells grown in GM.

source_name: C2C12 cells in GM

value: growth

value: 0 days


title: C2-0day-rep1

description: C2C12 cells grown in GM.


title: C2-lacZ-4.5day-rep1


title: Transgenic ER-FUS3, 48h, No treatment, 1

value: ER-FUS3 transgenic

value: seedling

tag: age

value: 7 days

source_name: ER-FUS3 transgenic plant (Col-0), untreated, 48h


title: Transgenic ER-FUS3, 36h, No treatment, 1

source_name: ER-FUS3 transgenic plant (Col-0), untreated, 36h


title: Transgenic ER-FUS3, 6h, No treatment, 1

source_name: ER-FUS3 transgenic plant (Col-0), untreated, 6h


title: Transgenic ER-FUS3, 12h, No treatment, 1

source_name: ER-FUS3 transgenic plant (Col-0), untreated, 12h


title: Transgenic ER-FUS3, 24h, No treatment, 1

source_name: ER-FUS3 transgenic plant (Col-0), untreated, 24h


title: TKO KSL2

city: Chiba

first: ATSUSHI

last: IWAMA

address: 1-8-1 Inohana, Chuo-ku

department: Department of Cellular and Molecular Medicine

institute: Graduate School of Medicine, Chiba University

description: Gene expression data from  KSL hematopoietic stem/progenitor cells from 4-week-old Bmi1-/-Ink4a-/-Arf-/- mice

hyb_protocol: standard Affymetrix protocol

scan_protocol: GeneChips were scanned using Affymetrix GeneChip Scanner 3000 7G.

data_processing: needs updated

label_protocol: Biotinylated cRNA were prepared  from the purified total RNA equivalent to 10,000 cells according to the standard Affymetrix protocol.

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

value: Hematopoietic stem/progenitor cells

value: 4-week-old C57BL/6 mice


title: DKO KSL1

description: Gene expression data from  KSL hematopoietic stem/progenitor cells from 4-week-old Ink4a-/-Arf-/- mice

source_name: Ink4a-/-Arf-/- KSL


title: SKO KSL1

description: Gene expression data from  KSL hematopoietic stem/progenitor cells from 4-week-old Bmi1-/- mice

source_name: Bmi1-/- KSL


title: Xenopus_control-morpholino_rep1

description:
control-MO
Xenopus embryos injected with control-morpholino.

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45 degrees on the GeneChip Xenopus laevis Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

data_processing: The data were analyzed with the MAS 5.0 algorithm using GeneChip Operating Software (GCOS) v. 1.4.

source_name: control-morpholino-injected Xenopus laevis embryos

label_protocol: Biotinylated cRNA were prepared according to the Affymetrix protocol (Two-Cycle Target Labeling Assays) from 100 ng total RNA.

growth_protocol: Xenopus eggs were obtained by in vitro fertilization and were dejellied in 2% cysteine, pH 7.8.

extract_protocol: Total RNA was prepared using TRIzol (Invitrogen) and purified through RNeasy columns (Qiagen), according to the manufacturers' instructions.

treatment_protocol: We radially injected control-morpholino (80 ng) or xSGK1-morpholinos (morpholino1 40 ng and morpholino2 40 ng) into 4-cell embryos, and cultured the embryos until stage 12.

value: whole embryo

value: stage 12

value: control morpholino


title: Xenopus_control-morpholino_rep2

description:
control-MO2
Xenopus embryos injected with control-morpholino.


title: Xenopus_xSGK1-morpholinos_rep2

description:
xSGK1-MO2
Xenopus embryos injected with xSGK1-morpholinos.

source_name: xSGK1-morpholinos-injected Xenopus laevis embryos

value: xSGK1 morpholinos


title: Xenopus_xSGK1-morpholinos_rep1

description:
xSGK1-MO
Xenopus embryos injected with xSGK1-morpholinos.


title: WT KSL 2

description: Gene expression data from  KSL hematopoietic stem/progenitor cells from 4-week-old wild-type mice

source_name: Wild-type KSL

value: Wild type


title: Transgenic ER-FUS3, 3h, No treatment, 1

description: ER-FUS3 transgenic plants were used to identify the genes up-regulated in young seedlings of Arabidopsis in response to ectopic expression of FUS3.

value: no treatment

value: 1 of 2

source_name: ER-FUS3 transgenic plant (Col-0), untreated, 3h


title: TKO KSL1


title: P a PAO1 LB 0.1 mg/ml IAN 5h suspension cells

status: Public on Feb 20 2011

city: Gyeongsan-Si

first: Jintae

last: Lee

state: Gyeongsangbuk-Do

address: 214-1 Daedong

department: Chemical engineering

institute: Yeungnam University

description: In the present study, we performed global gene expression analyses using Affymetrix GeneChip® P. aeruginosa Genome arrays. The sample preparation was performed according to the instructions and recommendations provided by the manufacturer. RNA extracted from suspension cells of P. aeruginosa PAO1 wild type after 5 h of growth in LB and 0.1 % DMSO at 37oC

hyb_protocol: Following affymetrix protocol.  Fragmented end-labeled cDNA was hybridized to the GeneChip® P. aeruginosa Genome arrays for 16 hours at 50 ℃ and 60 rpm as described in the Gene Chip Whole Transcript (WT) Sense Target Labeling Assay Manual (Affymetrix).

scan_protocol: Following affymetrix protocol. After hybridization, the chips were stained and washed in a Genechip Fluidics Station 450(Affymetrix) and scanned by using a Genechip Array scanner 3000 7G (Affymetrix).

data_processing: MAS 5.0 Expression Analysis Defalut Setting

organism: Pseudomonas aeruginosa

label_protocol: Per RNAsample, 300 ng were used as input into the Affymetrix procedure as recommended by protocol (http://www.affymetrix.com). Briefly, 300 ng of total RNA from each sample was converted to double-strand cDNA Using a random hexamer incorporating a T7 promoter, amplified RNA( cRNA) was generated from the double-stranded cDNA template though an IVT( in-vitro transcription) reaction and purified with the Affymetrix sample cleanup module. cDNA was regenerated through a random-primed reverse transcription using a dNTP mix containing dUTP. The cDNA was then fragmented by UDG and APE 1 restriction endonucleases and end-labeled by terminal transferase reaction incorporating a biotinylated dideoxynucleotide.

extract_protocol: To lyse the cells, 1.0 mL RLT buffer (Qiagen, Inc., Valencia, CA) and 0.2 mL 0.1 mm zirconia/silica beads (Biospec) were added to the cell pellets. The tubes were closed tightly and vortexed for 50 seconds. The total RNA was isolated by following the protocol of the RNeasy Mini Kit (Qiagen) including an on-column DNase digestion with RNase-free DNase I (Qiagen). RNA quality was assessed by Agilent 2100 bioanalyser using the RNA 6000 Nano Chip (Agilent Technologies, Amstelveen, The Netherlands), and quantity was determined by ND-1000 Spectrophotometer (NanoDrop Technologies, Inc., DE, USA).

tag: culture condition

value: suspension cells

tag: genotype/variation

value: wild type

value: 5 h of growth in LB and at 0.1 mg/ml IAN 37oC


title: WT KSL 1


title: DKO KSL2


title: P a PAO1 LB DMSO 5h suspension cells

source_name: P a PAO1 LB DMSO 5h suspension cells

tag: treatment

value: 5 h of growth in LB and 0.1 % DMSO at 37oC


title: Transgenic ER-FUS3, 0h, No treatment, 1

tag: ecotype

tag: genotype

source_name: ER-FUS3 transgenic plant (Col-0), untreated, 0h


title: control CD4+CD8+ normal thymocytes

status: Public on Feb 19 2011

city: Boston

first: Xiaoyu

last: Li

address: 44 Binney Street

institute: Dana-Farber Cancer Institute

hyb_protocol: The Hy3™-labeled sample and the Hy5™-labeled reference pool RNA were mixed and hybridized to the miRCURYTM LNA array version 8.1 (Exiqon). The hybridization was performed according to the miRCURYTM LNA array manual using a Tecan HS4800 hybridization station (Tecan, Austria).

scan_protocol: The miRCURYTM LNA array microarray slides were scanned by a ScanArray 4000 XL scanner (Packard Biochip Technologies). Image analysis was carried out using the ImaGene 7.0 software (BioDiscovery, Inc.USA).

data_processing:
The quantified signals were normalized using the global Lowess (LOcally WEighted Scatterplot Smoothing) regression algorithm  (LOcally WEighted Scatterplot Smoothing) regression algorithm
Expression ratios were determined for microarray data by computing the background-corrected fluorescent signal from the query sample (Q)/reference sample (R). Ratiometric data were transformed to log 2 to produce a continuous spectrum of up- and down-regulated values

source_name: control CD4+CD8+ normal thymocytes

label_protocol: Equal amounts of each sample were used to generate a reference pool. For each array to be hybridized,  total RNA from each sample and the reference pool were labeled with Hy3™ and Hy5™ fluorescent label, respectively, using the miRCURYTM LNA Array labeling kit (Exiqon, Denmark) following the manufacturer's instructions.

extract_protocol: Total RNA was purified using Trizol reagent (Invitrogen) according to the manufacturer’s instructions

tag: genetic background

value: Balb/c

tag: cell type

value: control CD4+CD8+ normal thymocytes

source_name: Pool of all RNA samples

value: pool of control CD4+CD8+ normal thymocytes, non-malignant ICN1-expressing CD4+CD8+ cells, and tumor ICN1-expressing CD4+CD8+ cells


title: tumor ICN1-expressing CD4+CD8+ cells

source_name: tumor ICN1-expressing CD4+CD8+ cells

value: tumor ICN1-expressing CD4+CD8+ cells


title: non-malignant ICN1-expressing CD4+CD8+ cells


title: Donor 1 M01-3

city: seoul

first: Eun Ju

address: 28 yongon dong

institute: seoul natonal university

description: Gene expression of M01-3

hyb_protocol: cRNA were hybridized on Human Genome Array.

scan_protocol: standard Affymetrix protocol

data_processing: MAS 5.0 normalization using Genowiz 4.0TM (Ocimum Biosolutions, India)

source_name: M01 hUCB-MSC

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

growth_protocol: Briefly, mononuclear cells were isolated by centrifugation (400G, 50 min) in a Ficoll hypaque gradient (density 1.077g/cm3, Sigma). These cells were cultured in alpha-minimum essential medium (alpha-MEM, Gibco BRL), supplemented with 10% FBS (Gibco BRL), 10,000 units/ml penicillin G sodium, 10,000㎍/ml streptomycin sulfate, and 25㎍/ml amphotericin B (Invitrogen Co.) at a concentration 5.0 x 106 cells/cm2. Cultures were maintained in a humidified 37℃ cell incubator with 5% CO2 with a change of culture medium twice a week. Three weeks later, monolayer of fibroblast-like adherent cells were trypsinized (0.25% trypsin, HyClone), washed, resuspended in culture medium and subcultured at a concentration of 1.0 x 105 cells/cm2.

extract_protocol: Total RNA was isolated by using TRIzol Reagent (Invitrogen, Carlsbad, CA). The RNA were extracted with chloroform (Sigma Chemical, St. Louis, MO, USA) and followed by ethanol precipitation. RNA was quantified using NanoDrop® ND-1000 spectrophotometer(NanoDrop Technologies, Inc., Wilmington, DE, USA). And RNA quality was assessed using Agilent RNA Nano 6000 LabChip kits and Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA).

treatment_protocol: Total RNAs from M01 or M02 hUCB-MSCs were isolated using TRIzol (Invitrogen, Carlsbad) and the RNeasy Mini kit (Qiagen, Valencia).

value: hUCB-MSC

value: female

tag: donor


title: E2 LY294002

city: Tucson

first: Parker

middle: B

last: Antin

state: AZ

address: 1656 E. Mabel Street

department: Cell Biology and Anatomy

institute: University of Arizona

description: Analysis used preingression epiblast (E2 region) microdissected from control  or LY294002 tretated embryos

hyb_protocol: The arrays were baked at 90C for 90 minutes prior to use. Pre-treatment of slides was accomplished by incubation of slides in pre-hybridization solution (5xSSC, 0.1%SDS, and 1% BSA) for 45 min at 42C. Slides were then dipped in 2x SSC and 0.2x SSC for 5 min each. Slides were dried by centrifugation (5 min at 1000 x g). An aliquot of 5 µg of labeled, purified aRNA was fragmented in 1x fragmentation buffer (Ambion, Austin, TX) for 15 min at 70C. Stop solution was added to terminate the reaction, and samples were dried again in the SpeedVac. Pre-warmed DIG Easy Hyb solution (Roche Diagnostics Corporation, Indianapolis, IN) was used to reconstitute the samples in a 30 µL volume. Reference aRNA samples used within the same day were pooled and aliquoted. One reference pool (30 µL) and one sample (target) (30 µL) were mixed and 2.5 µL of 10mg/mL yeast tRNA and 2.5 µL of 10mg/mL salmon testes DNA (Sigma, St. Louis, MO) were added. The target/reference mixture (65 µL) was heated to 94C for 2 min for denaturation, cooled at room temperature, and loaded to the middle of a pre-treated slide held in a hybridization chamber (Corning #2551, Lowell, MA), which was overlaid with a 22 x 65 mm LifterSlip (Erie Scientific, Portsmouth, NH). Slides were then incubated for 14-16h at 42C inside a light-tight sealed box in a water bath. Following incubation, the cover slip was removed by flushing with wash solution #1 (1x SSC, 0.2% SDS, 0.5% DTT). Sequential washes were as follows: Ten min at 42C in pre-warmed wash solution #1, five min at room temp in wash solution #2 (0.1x SSC, 0.2% SDS, 0.5% DTT), and one min at room temperature in wash solution #3 (0.1x SSC, 0.5% DTT). Slides were then washed with ddH2O and dried by centrifugation. Slides were stored in 50 mL conical tubes covered in foil in the presence of nitrogen gas until scanning

scan_protocol: For each slide, a high-resolution TIFF image file was generated usingan  Array WorX white light microarray scanner by Applied Precision and analyzed with the SotWorX tracker software package by Molecular Ware. The TIFF image was acquired at 9.756 micron resolution by sequentially scanning at two wavelengths [555 nm (green) and 647 nm (red). The software was used at default setting using high siganal to noise.

data_processing: Each TIFF image was further analyzed with GenePix Pro software, generating a GenePix Report (gpr) file. GenePix report files were converted to .mev files using Express Converter software freely available from The Institute for Genomic Research (TIGR) website. Converted files were Lowess normalized using Microarray Data Analysis System (MIDAS) software.

organism: Gallus gallus

source_name: Preingression epiblast (E2 region) isolated from embryos treated with LY294002

label_protocol: Dye labeling was accomplished according to the instructions for dye labeling and labeled aRNA cleanup with the SuperScript Plus Indirect cDNA Labeling System Kit (Invitrogen #L1014-06).Twenty micrograms of aRNA was dried to a minimal volume (not overdryed) in a SpeedVac concentrator to a volume of 3ul. 5µL of coupling buffer was added, followed by 2ul of Alexa Fluor Reactive Dye resuspended in DMSO . aRNA with dye was incubated in the dark for two h at room temperature for coupling. Labeled cDNA was purified according to manufacturer's instructions. The incorporation of dye and concentration of aRNA were quantified with the NanoDrop spectrophotometer (Wilmington, DE) and incorporation efficiency was determined using the calculator available at www.ambion.com/tools/dye

growth_protocol: Embryos were explanted into New Culture for control and xperimental treatments

extract_protocol: Total RNA extracted using Trizol according to manufacturer's instructions. RNA was amplified by combining 2ug of RNA, 2 ul random hexamers to 18ul in DEPC treated water.  The reaction mixture was incubated at 70 degrees C for 5 mnutes and then placed on ice.  6ul of first strand buffer, 1.5ul of 0.1M DTT, 1.5ul dNTP mix, 1 RNaseOUT (40U/ul), Superscript III RT (400U/ul) was added and the mixture was incubated at 46 degrees C for 3 h.

treatment_protocol: 100uM SU5402, 100uM LY294002 or 100uMU0126 was added to experimental embryos

tag: developmental stage

value: HH Stage 5-6 embryos

tag: tissue

source_name: Preingression epiblast (E2 region) isolated from control embryos

value: untreated


title: E2 versus E3

description: Analysis used preingression epiblast (E2 region) versus lateral epiblast (E3) region

source_name: Preingression epiblast (E2 region)

value: Preingression epiblast (E2 region) isolated from embryos

source_name: Lateral epiblast (E3 region) from control embryos


title: E2 U0126

description: Analysis used preingression epiblast  (E2 region) microdissected from control  or U0126 tretated embryos

source_name: Preingression epiblast (E2 region) isolated from embryos treated with  U0126

value: Preingression epiblast (E2 region) isolated from control embryos


title: Donor 2 M02-3

description: Gene expression of M02-3

source_name: M02 hUCB-MSC

tag: gender

value: male


title: Donor 2 M02-2

description: Gene expression of M02-2


title: Donor 1 M01-1

description: Gene expression of M01-1


title: Transcriptional profiling between Hypoxic and Normoxic mesenchymal stem cells

city: Taipei

first: Chih

middle: Chien

last: Tsai

address: No. 201, Sec. 2, Shih-Pai Road, Taipei 112, Taiwan

country: Taiwan

institute: Taipei Vaterans General Hospital

description: Normoxic and Hypoxic mesenchymal stem cells, untreated, harvested after 12 days

hyb_protocol: Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequential.

scan_protocol: Scanned by Aligent microarray scanner (G2565ba, Agilent Technologies, USA)

data_processing: Agilent Feature extraction 9.1 software (Agilent Technologies,USA) and eGenomix V1.0 was used for quantification, background subtraction and rank-consistency-filtering LOWESS normalization. The fold changes converted from “normalized log2 ratio (Cy5/Cy3) Hypo/Nor” are contained in the RANK column.

source_name: Normoxic D12 Mesenchymal stem cells

label_protocol: 10 µg of total RNA were primed with DNA primer at 70°C for 10 min, then reversed transcribed at 42°C for 1 h in the presence of 400 U SuperScript II Rnase H-reverse transcriptase (Invitrogen), and 100 µM each dATP, dTTP, dGTP, with 25 µM dCTP, 25 µM Cy3-label(Nor) and Cy5-label(Hypo).

growth_protocol: MSCs were kept in normoxia (21% O2) or hypoxia (1% O2) for 12 days.

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

value: Bone marrow

value: Mesenchymal stem cells

source_name: Hypoxic D12 Mesenchymal stem cells


title: GnRH treated LbetaT2 cells Expt2

status: Public on Feb 18 2011

city: La Jolla

first: Nick

last: Webster

state: CA

address: 9500 Gilman Drive

department: Medicine

institute: UCSD

description: miRNA expression

hyb_protocol: Labeled probes were hybridized to NCODE miRNA microarrays in a Maui hybridization station for 24 h

scan_protocol: Arrays were scanned on a Molecular Devices Genepix 4000B

data_processing: mean of ratio (635/532) then miRNAs with signals < 2x background were excluded.  Signals for the remaining miRNAs were median-centered and analyzed using Prism (Graphpad software) using a Z-test.

source_name: LbetaT2 gonadotrope cells

label_protocol: RNA from unstimulated cells was labeled with Cy3 and RNA from GnRH stimulated cells with Cy5 using the NCODE labelling kit following manufacturers instructions

growth_protocol: Mouse LbetaT2 cells at passages 13-19 were cultured in monolayers with DMEM containing 10 % FBS, penicillin/streptomycin, and Gluta-max in a humidified 10 % CO2 atmosphere at 37˚C.

extract_protocol: Total RNA was purified with RNA-Bee (Tel-test, TX) according to manufacturer’s protocol, the mRNAs were enriched from total RNA using the ribosomal RNA reduction kit (Invitrogen)

treatment_protocol: Cells were starved in DMEM containing 0.5% FBS, penicillin/streptomycin, and Gluta-max for 24 h then treated with 100 nM GnRH for 2 h

value: LbetaT2 gonadotrope cells

value: 100 nM GnRH treated


title: E2 SU5402

description: Analysis used preingression epiblast  (E2 region) microdissected from control  or SU5402 tretated embryos

source_name: Preingression epiblast (E2 region) isolated from embryos treated with SU5402


title: Donor 2 M02-1

description: Gene expression of M02-1


title: 03 - mdx/MMP-2-/- mice at 1 month of age

city: Matsumoto

first: daigo

last: miyazaki

address: 3-1-1 Asahi

department: Department of Medicine (Neurology and Rheumatology)

institute: Shinshu University School of Medicine

description: Tibialis anterior muscle from mdx/MMP-2-/- mice at 1 month of age.

hyb_protocol: 12.5 μg of the fragmented cRNA were then hybridized with the mouse Genome 430 2.0 array (Affymetrix). Hybridization was allowed to proceed 16 hours, followed by automated washing and staining in the Fluidics Station 450 (Affymetrix).

scan_protocol: The GeneChips were scanned with an Affymetrix GeneChip Scanner 3000 and the data acquired via the Microarray Suite version 5.0 (MAS 5.0).

data_processing: The data were analyzed with MAS 5.0 using Affymetrix Expression Console software with default analysis settings.

source_name: skeletal muscle, mdx/MMP-2-/-, 1 month

label_protocol: Total RNA (100ng) from each sample was used to synthesize double-stranded cDNA (One-Cycle cDNA Synthesis Kit, Affymetrix). The double-stranded cDNA samples were subsequently reverse transcribed, amplified, and biotin-labeled according to the Affymetrix standard protocol.

extract_protocol: Total RNA was isolated from the skeletal muscle using the RNeasy mini kit (Qiagen, Hilden, Germany) according to the manufacturer’s instructions. RNA quality was checked using an Agilent 2100 Bioanalyzer (Agilent Technologies, Wilmington DE) before cDNA synthesis.

tag: strain

value: tibialis anterior muscle

value: 1 month


title: MCF7-ERbeta cells, vehicle treated, 24 hours, replicate 2

city: Rochester

first: John

last: Hawse

state: MN

address: 200 1st St. SW

department: Biochemistry and Molecular Biology

institute: Mayo Clinic

description: Replicate 2

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The raw data was pre-processed by Illumina's beadstudio without backgroud subtraction and gene level profile was obtained. This data was exported, log2 ransformed and normalized using fast lowess normalization in R

source_name: ER-beta expressing MCF7 cells

growth_protocol: MCF7 cells were cultured in phenol red-free Dulbecco’s modified Eagle’s medium/F12 (DMEM/F12) medium containing 10% (v/v) Fetal Bovine Serum (FBS) and 1% (v/v) antibiotic-antimycotic (AA) solution  in a humidified 37°C incubator with 5% CO2.  MCF7 cells stably expressing ERβ were generated using an S-tagged-Flag-tagged ERβ expression construct (pIRES2-EGFP) and were cultured in identical medium containin 300 microL/mL G418.

extract_protocol: Total RNA was isolated using Trizol reagent.

treatment_protocol: All cell treatments were conducted in phenol red-free DMEM/F12 medium containing 10% triple charcoal stripped FBS and 1% antibiotic-antimycotic.

value: estrogen-receptor beta expressing cells

tag: agent

value: ethanol vehicle

tag: cell line

value: breast cancer cells


title: Donor 1 M01-2

description: Gene expression of M01-2


title: 01 - mdx mice at 1 month of age

description: Tibialis anterior muscle from mdx mice at 1 month of age.

source_name: skeletal muscle, mdx, 1 month

value: mdx


title: MCF7 parental cells, 1nM estradiol + 40nM endoxifen treated, 24 hours, replicate 2

description: Replicate 2

source_name: Parental MCF7 cells

value: parental cells

value: 1nM estradiol + 40nM endoxifen


title: MCF7 parental cells, 1nM estradiol + 40nM endoxifen treated, 24 hours, replicate 1

description: Replicate 1


title: MCF7-ERbeta cells, 1nM estradiol + 40nM endoxifen treated, 24 hours, replicate 1

description: Replicate 1


title: MCF7 parental cells, 1nM estradiol treated, 24 hours, replicate 1

description: Replicate 1

value: 1nM estradiol


title: MCF7 parental cells, vehicle treated, 24 hours, replicate 1

description: Replicate 1


title: MCF7 parental cells, 1nM estradiol treated, 24 hours, replicate 2

description: Replicate 2


title: MCF7-ERbeta cells, 1nM estradiol treated, 24 hours, replicate 2

description: Replicate 2


title: 04 - mdx/MMP-2-/- mice at 3 months of age

description: Tibialis anterior muscle from mdx/MMP-2-/- mice at 3 months of age.

source_name: skeletal muscle, mdx/MMP-2-/-, 3 months

value: 3 months


title: MCF7-ERbeta cells, 1nM estradiol treated, 24 hours, replicate 1

description: Replicate 1


title: MCF7 parental cells, vehicle treated, 24 hours, replicate 2

description: Replicate 2


title: MCF7-ERbeta cells, vehicle treated, 24 hours, replicate 1

description: Replicate 1


title: GnRH treated LbetaT2 cells Expt1

description: miRNA expression

value: untreated


title: MCF7-ERbeta cells, 1nM estradiol + 40nM endoxifen treated, 24 hours, replicate 2

description: Replicate 2


title: 02 - mdx mice at 3 months of age

description: Tibialis anterior muscle from mdx mice at 3 months of age.

source_name: skeletal muscle, mdx, 3 months


title: 8994_Child (Illumina HumanHap550)

status: Public on Feb 17 2011

city: Vancouver

first: Tracy

last: Tucker

address: Box 153 4480 Oak Street

country: Canada

institute: University of British Columbia

hyb_protocol: DNA was hybridized overnight to a Beadchip placed in a humidified chamber

scan_protocol: Beadchips were imaged using a two-color confocal laser system with 0.8-μm resolution to identify both SNP alleles

data_processing: The intensities for each allele were extracted and normalized, and values for genotypes, allelic ratio (B-allele frequency) and logR ratio were calculated using an Illumina-supplied cluster file, which is based on a set of about 100 HapMap reference samples. The normalization algorithm adjusts for nominal offset, cross-talk, and intensity variations observed in the two-color channels. CNV detection was done using PennCNV [20] with a threshold of 5 SNP-minimum per bin

label_protocol: DNA from the proband in each trio was used for hybridization on the Illumina Human Hap550 Beadchips according to the manufacturer’s instructions

extract_protocol: Genomic DNA was extracted from blood samples using the Puregene DNA kit

tag: developmental state

value: Developmental Delay

tag: family

tag: phenotype

value: idiopathic MR

value: Female


title: 9313_Child (Illumina HumanHap550)

value: Male


title: 8327_Child (Illumina HumanHap550)


title: 8160_Child (Illumina HumanHap550)

value: unknown


title: 8135_Child (Illumina HumanHap550)


title: 9390_Child (Illumina HumanHap550)


title: 9609_Child (Illumina HumanHap550)


title: 8612_Child (Illumina HumanHap550)


title: 7093_Child (Illumina HumanHap550)


title: 6942_Child (Illumina HumanHap550)


title: 7581_Child (Illumina HumanHap550)


title: 8960_Child (Illumina HumanHap550)


title: 6932_Child (Illumina HumanHap550)


title: 4821_Child (Illumina HumanHap550)


title: 5993_Child (Illumina HumanHap550)


title: 7531_Child (Illumina HumanHap550)


title: 6428_Child (Illumina HumanHap550)


title: 2894_Child (Illumina HumanHap550)


title: 1056_Child (Illumina HumanHap550)


title: 2332_Child (Illumina HumanHap550)


title: 1780_Child (Illumina HumanHap550)


title: 8994_Child_Mother (Agilent 244K)

hyb_protocol: 3 day hyb at 65C in Agilent Hyb Oven

scan_protocol: 5um scan with Agilent Scanner  and Agilent Scanner Control Software v7.0

data_processing: Captured images were analysed with Feature Extraction v 9.1 and CGH Analytics 3.5.14 using the ADM-1 algorithm to identify regions with consistently high or low log2 ratio. This algorithm does not rely on a window size but rather samples immediately adjacent probes and uses the average normalized log2 ratios of all probes in a genomic interval to determine the deviation of the log2 ratio from its expected value of zero. A user-defined stringency threshold of 6, the recommended default value, was set.  Two other methods were also used to assist in the aberration calls. A centralization process was performed that assumes the log2 ratio values are centered at zero and re-centers the data by finding a constant value to add to or subtract from all log2 values. The program uses a default of a 10 probe window to average the log2 ratios. Also, a “fuzzy zero” method, which applies a global error mode to all aberrant intervals identified by the ADM-1 algorithm, was used to avoid erroneous aberration calls when the errors were correlated.

source_name: peripheral blood

label_protocol: 3 μg of high-quality genomic DNA were digested with RsaI and AluI and labeled with Cyanine-3 or Cyanine-5 using a random priming method. Two arrays were used for each trio, one in which the child’s DNA was hybridized against the father’s DNA, and another in which the child’s DNA was hybridized against the mother’s DNA. Equal amounts of the child’s and one parent’s DNA were labeled with opposite fluorochromes and hybridized to the array

value: peripheral blood

tag: family member

value: Child

value: Mother


title: 7484_Child (Illumina HumanHap550)


title: 3519_Child (Illumina HumanHap550)


title: 9609_Child_Father (Agilent 244K)

value: Father


title: 9609_Child_Mother (Agilent 244K)


title: 2714_Child (Illumina HumanHap550)


title: 1815_Child (Illumina HumanHap550)


title: 2377_Child (Illumina HumanHap550)


title: 9390_Child_Father (Agilent 244K)


title: 2569_Child (Illumina HumanHap550)


title: 9313_Child_Father (Agilent 244K)


title: 9313_Child_Mother (Agilent 244K)


title: 9390_Child_Mother (Agilent 244K)


title: 8612_Child_Mother (Agilent 244K)


title: 8612_Child_Father (Agilent 244K)


title: 8960_Child_Father (Agilent 244K)


title: 8960_Child_Mother (Agilent 244K)


title: 8160_Child_Father (Agilent 244K)


title: 3094_Child (Illumina HumanHap550)


title: 1511_Child (Illumina HumanHap550)


title: 8327_Child_Mother (Agilent 244K)


title: 8327_Child_Father (Agilent 244K)


title: 8135_Child_Mother (Agilent 244K)


title: 8994_Child_Father (Agilent 244K)


title: 3921_Child (Illumina HumanHap550)


title: 8160_Child_Mother (Agilent 244K)


title: 8135_Child_Father (Agilent 244K)


title: 7581_Child_Mother (Agilent 244K)


title: 7484_Child_Mother (Agilent 244K)


title: 7484_Child_Father (Agilent 244K)


title: 7531_Child_Mother (Agilent 244K)


title: 7531_Child_Father (Agilent 244K)


title: 7093_Child_Mother (Agilent 244K)


title: 7581_Child_Father (Agilent 244K)


title: 7093_Child_Father (Agilent 244K)


title: 6942_Child_Mother (Agilent 244K)


title: 6932_Child_Mother (Agilent 244K)


title: 6942_Child_Father (Agilent 244K)


title: 6932_Child_Father (Agilent 244K)


title: 7531_Father (Mapping250K_Sty)

hyb_protocol: hybridized to GeneChip® Human Mapping 250K Nsp or 250K Sty arrays in an Affymetrix Hybridization Oven 640

scan_protocol: images were obtained using an Affymetrix GeneChip® Scanner 3000 7G and GeneChip® Operating Software version 1.4

data_processing:
CNVs were detected using the Copy Number Analysis Tool (CNAT) (release cn-1.5.6_v3.2), which incorporates a Bayesian Robust Linear Model with the Mahalanobis distance classifier (BRLMM) algorithm to perform quantile normalization, followed by regression to reduce the PCR bias due to GC content and fragment length
An HMM-based algorithm implemented in CNAT4 was used to estimate copy number for each SNP in the context of its surrounding SNPs. The Gaussian bandwidth was set to 0 Kb and a minimum of 5 probes was required to detect a CNV. The findings were visualized using GeneChip Genotyping Analysis Software (GTYPE) from Affymetrix.

label_protocol: DNA samples were processed according to the instructions provided in the Affymetrix GeneChip® Mapping 500K Assay Manual

value: unaffected


title: 6428_Child_Mother (Agilent 244K)


title: 6428_Child_Father (Agilent 244K)


title: 9390_Father (Mapping250K_Sty)


title: 9609_Father (Mapping250K_Sty)


title: 4821_Child_Father (Agilent 244K)


title: 9609_Child (Mapping250K_Sty)


title: 7531_Mother (Mapping250K_Sty)


title: 9609_Mother (Mapping250K_Sty)


title: 5993_Child_Mother (Agilent 244K)


title: 7581_Mother (Mapping250K_Sty)


title: 9390_Mother (Mapping250K_Sty)


title: 7531_Child (Mapping250K_Sty)


title: 4821_Child_Mother (Agilent 244K)


title: 5993_Child_Father (Agilent 244K)


title: 7581_Father (Mapping250K_Sty)


title: 7484_Mother (Mapping250K_Sty)


title: 7484_Child (Mapping250K_Sty)


title: 3921_Child_Mother (Agilent 244K)


title: 7484_Father (Mapping250K_Sty)


title: 9390_Child (Mapping250K_Sty)


title: 6428_Mother (Mapping250K_Sty)


title: 6428_Father (Mapping250K_Sty)


title: 3921_Child_Father (Agilent 244K)


title: 7093_Child (Mapping250K_Sty)


title: 3519_Child_Mother (Agilent 244K)


title: 5993_Mother (Mapping250K_Sty)


title: 7093_Mother (Mapping250K_Sty)


title: 7093_Father (Mapping250K_Sty)


title: 7581_Child (Mapping250K_Sty)


title: 5993_Father (Mapping250K_Sty)


title: 3094_Child_Mother (Agilent 244K)


title: 6428_Child (Mapping250K_Sty)


title: 3519_Child_Father (Agilent 244K)


title: 5993_Child (Mapping250K_Sty)


title: 2377_Child_Mother (Agilent 244K)


title: 3094_Child_Father (Agilent 244K)


title: 2894_Child_Mother (Agilent 244K)


title: 2714_Child_Father (Agilent 244K)


title: 2714_Child_Mother (Agilent 244K)


title: 2377_Child_Father (Agilent 244K)


title: 2569_Child_Father (Agilent 244K)


title: 2332_Child_Father (Agilent 244K)


title: 2894_Child_Father (Agilent 244K)


title: 2569_Child_Mother (Agilent 244K)


title: 2332_Child_Mother (Agilent 244K)


title: 3519_Mother (Mapping250K_Sty)


title: 3921_Father (Mapping250K_Sty)


title: 3921_Child (Mapping250K_Sty)


title: 3519_Father (Mapping250K_Sty)


title: 1815_Child_Mother (Agilent 244K)


title: 3921_Mother (Mapping250K_Sty)


title: 3094_Mother (Mapping250K_Sty)


title: 3094_Father (Mapping250K_Sty)


title: 3094_Child (Mapping250K_Sty)


title: 2714_Father (Mapping250K_Sty)


title: 1780_Child_Father (Agilent 244K)


title: 1815_Child_Father (Agilent 244K)


title: 1780_Child_Mother (Agilent 244K)


title: 1815_Mother (Mapping250K_Sty)


title: 2714_Child (Mapping250K_Sty)


title: ARV1 mutant, rep 1C

first: Stephen

middle: L

last: Sturley

address: 630 West 168th Street, PH1512 East

department: Department of Pediatrics

description:
Yeast_ARV1-1C
Ye6100 array format

hyb_protocol: The biotin-labeled and fragmented cRNA was hybridized to the YE6100 or S98 Yeast GeneChip arrays (Affymetrix), washed, and stained according to the manufacturer's instructions.

scan_protocol: The arrays were scanned using the Hewlett-Packard Gene Array Scanner (Affymetrix) at a wavelength of 570 nm.

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

organism: Saccharomyces cerevisiae

source_name: Yeast ARV1 mutant strain

label_protocol: Synthesis of biotin-labeled cRNA was carried out by in vitro transcription using Enzo Bioarray RNA transcript labeling kit (Enzo Diagnostics), according to the manufacturer's instructions.

growth_protocol: Cells grown to mid-logarithmic stage (A600=0.5-0.6) in YEPD.

extract_protocol: Total RNA was extracted and poly(A)+ RNA was purified from total RNA by Oligotex oligo(dT) selection according to manufacturer's instructions (Qiagen).

tag: mating type

value: MATa

tag: genotype/variation

value: ARV1 mutant


title: ARV1 mutant, rep 2C

description:
Yeast_ARV1-2C
Ye6100 array format


title: 1815_Father (Mapping250K_Sty)


title: Control, rep 1/2C

description:
Yeast_Control-1/2C
Ye6100 array format

source_name: Yeast control strain

value: control


title: 1511_Child_Father (Agilent 244K)


title: ARV1 mutant, rep 1D

description:
Yeast_ARV1-1D
Ye6100 array format


title: 1056_Child_Father (Agilent 244K)


title: ARV1 mutant, rep 2D

description:
Yeast_ARV1-2D
Ye6100 array format


title: 1815_Child (Mapping250K_Sty)


title: 3519_Child (Mapping250K_Sty)


title: 1056_Child_Mother (Agilent 244K)


title: 1511_Child_Mother (Agilent 244K)


title: 1056_Mother (Mapping250K_Sty)


title: ARV1 mutant, rep 2B

description:
Yeast_ARV1-2B
Ye6100 array format


title: ARV1 mutant, rep 2A

description:
Yeast_ARV1-2A
Ye6100 array format


title: 2714_Mother (Mapping250K_Sty)


title: Control, rep 1/2B

description:
Yeast_Control-1/2B
Ye6100 array format


title: Control, rep 1/2A

description:
Yeast_Control-1/2A
Ye6100 array format


title: 1056_Father (Mapping250K_Sty)


title: 1056_Child (Mapping250K_Sty)


title: 1780_Child (Mapping250K_Sty)


title: ARV1 mutant, rep 1A

description:
Yeast_ARV1-1A
Ye6100 array format


title: 1780_Mother (Mapping250K_Sty)


title: ARV1 mutant, rep 1B

description:
Yeast_ARV1-1B
Ye6100 array format


title: dcl1-15 torpedo stage embryos, biological replicate 3

city: Ithaca

first: Matthew

middle: R

last: Willmann

address: B18 Weill Hall, 237 Tower Road

department: School of Integrative Plant Science

institute: Cornell University

description:
Gene expression data from dcl1-15/dcl1-15 torpedo-stage embryos.
Ws backcrossed to Landsberg erecta 6-7 times; dcl1-15/dcl1-15 embryos from DCL1/dcl1-15 plants

hyb_protocol: Affymetrix ATH1 GeneChips were hybridized with 3.75 ug of biotin-labeled cDNA at a concentration of 17 ng/ul in the hybridization coctail.  Hybridization was carried out for 16-18 hours at 45oC.  Washing and staining were done using a GeneChip Fluidics Station 450.

scan_protocol: The GeneChips were scanned using a 7G Affymetrix GeneChip Scanner.

data_processing: The data were gcRMA-normalized in R using the gcrma package and filtered to remove all probesets that did not have a MAS5.0 present call in at least one of the six arrays.

source_name: Arabidopsis thaliana torpedo staged dcl1-15/dcl1-15 embryos

label_protocol: Biotin-labeled cDNA targets were made from 50 ng starting RNA that was reverse-transcribed and amplified using the OvationTM RNA Amplification SystemV2 and fragmented and labeled using the FL-OvationTM cDNA Biotin Module V2 (NuGEN Technologies, San Carlos, CA) per the manufacturer’s instructions.

growth_protocol: Seeds from a DCL1/dcl1-15 plant were sown in Fafard #2 soil in 96-well flats.  The flats were placed at 4oC for five days before being put in a Conviron growth chamber at a constant 23oC under a two-to-one ratio of T8 Sylvania Octron 4100K Ecologic and GroLite WS fluorescent lamps (Interlectric) at ~125 μmol m-2 s-1.  Upon fruiting, 300 mutant embryos were collected from siliques where the non-mutant siblings were at the torpedo stage.  Three hundred torpedo-stage wild-type embryos isolated from wild-type siblings were used as controls.

extract_protocol: The embryos were ground in liquid nitrogen microcentrifuge tubes using a pestle attached to an electric drill.  RNA was extracted from the tissue using the RNeasy Micro kit (Qiagen, Valencia, CA) according to the directions for extracting RNA from tissues, with modifications, as follow.  The samples were ground in 350 μl RLT alone and then with 25 μl of Plant RNA Isolation Aid (Ambion, Austin, TX) added.  The samples were homogenized by passing the material over a Qiashredder column (Qiagen).  The rest of the RNeasy Micro protocol was performed according to the instructions, including the on-column DNA digestion.  The eluted RNA was precipitated overnight at -20oC in 0.1 μg/μl glycogen, 0.6 M ammonium acetate, and 70% EtOH, spun at 4oC for 50 minutes at 18,000 x G, and eluted in 10 ml water.

treatment_protocol: 300 wild-type torpedo stage or mutant embryos from siliques with torpedo stage embryos were removed from the ovules using forceps and immediately placed in microcentrifuge tubes in liquid nitrogen.  Collections of wild-type and mutant embryos were done in alternating batches of 10 embryos per sample in order to minimize the effect of collection time, until 300 per sample had been reached.

value: dcl1-15 mutant

value: dcl1-15 embryos segregating from siliques with wild-type torpedo-staged embryos


title: 9313_Child (Mapping250_Sty)


title: dcl1-15 torpedo stage embryos, biological replicate 1


title: wild-type torpedo stage embryos, biological replicate 3

description:
Gene expression data from DCL1/DCL1 torpedo-stage embryos.
Ws backcrossed to Landsberg erecta 6-7 times; wild-type embryos from DCL1/DCL1 plants segregating from a DCL1/dcl1-15 parent

source_name: Arabidopsis thaliana torpedo staged DCL1/DCL1 embryos

value: wild type

value: torpedo stage embryo


title: dcl1-15 torpedo stage embryos, biological replicate 2


title: wild-type torpedo stage embryos, biological replicate 2


title: 9313_Child_Father (Mapping250_Sty)


title: wild-type torpedo stage embryos, biological replicate 1


title: 8994_Child (Mapping250_Sty)

value: Developmental Delay


title: 9313_Child_Mother (Mapping250_Sty)


title: 8994_Child_Mother (Mapping250_Sty)


title: 8994_Child_Father (Mapping250_Sty)


title: ExVivoHybridomacell_4hr_5ug/ml_rep1

city: Nanjing

first: Pu

middle: Yan

last: Chen

address: No. 1, Weigang

country: China

institute: Nanjing Agriculture University

description: Gene expression after 4hr in 5ug/ml BSP-II-treated hybridoma cell

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >20.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Mouse Genome microarrays (G2505B) for 17 hours at 65℃ in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37℃ GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565BA) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The resulting text files extracted from Agilent Feature Extraction Software (version 10.5.1.1) were imported into the Agilent GeneSpring GX software (version 11.0) for further analysis. The microarray data sets were normalized in GeneSpring GX using the Agilent FE one-color scenario (mainly median normalization)

source_name: Hybridoma cell, 4hr, 5ug/ml, replicate 1

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 1 ug RNA usingQuick Amp Labeling Kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Hybridoma cells were cultured with RPMI 1640 supplemented with 20% heat-inactivated fetal bovine serum (Invitrogen) at 37℃ with 5% CO2.

extract_protocol: Total RNAs are harvested using TRIzol (Invitrogen) and the RNeasy kit (Qiagen) according to manufacturer’s instructions, including a DNase digestion step. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Hybridoma cell was treated by BSP-II with RPMI 1640 medium supplemented with 20% heat-inactivated fetal bovine serum. The cultures were incubated for 4 hours at 37 ºC in a humidified incubator with 5% CO2.

tag: condition

value: 4hr in 5ug/ml BSP-II

value: Hybridoma cell


title: 8960_Child_Mother (Mapping250_Sty)


title: 1780_Father (Mapping250K_Sty)


title: 8612_Child (Mapping250_Sty)

value: idiopathic MR

value: Female


title: 8327_Child_Mother (Mapping250_Sty)

value: peripheral blood


title: 8327_Child (Mapping250_Sty)

value: Child


title: Control, rep 1/2D

city: New York

institute: Columbia University

description:
Yeast_Control-1/2D
Ye6100 array format


title: 8960_Child_Father (Mapping250_Sty)


title: 8612_Child_Father (Mapping250_Sty)


title: 8160_Child (Mapping250_Sty)

value: unknown


title: 8160_Child_Father (Mapping250_Sty)

value: Father


title: 8135_Child_Father (Mapping250_Sty)

value: unaffected


title: 8327_Child_Father (Mapping250_Sty)


title: 8160_Child_Mother (Mapping250_Sty)

value: Mother


title: 8135_Child_Mother (Mapping250_Sty)


title: 8135_Child (Mapping250_Sty)

value: Male


title: 6942_Child_Father (Mapping250_Sty)


title: 8612_Child_Mother (Mapping250_Sty)


title: 6942_Child_Mother (Mapping250_Sty)


title: 6932_Child_Father (Mapping250_Sty)


title: 6932_Child (Mapping250_Sty)


title: 6932_Child_Mother (Mapping250_Sty)


title: 6942_Child (Mapping250_Sty)


title: 8960_Child (Mapping250_Sty)


title: 4821_Child_Mother (Mapping250_Sty)


title: 2894_Child (Mapping250_Sty)


title: 2894_Child_Mother (Mapping250_Sty)


title: 4821_Child (Mapping250_Sty)


title: 4821_Child_Father (Mapping250_Sty)


title: 2569_Child_Mother (Mapping250_Sty)


title: 8960_Child_Mother (GenomeWideSNP_6)

data_processing:
CNVs were identified using the Genotyping Console 3.0.1 program.
Since this program cannot perform pair-wise comparisons, we compared the results of each sample to a reference dataset generated by the combined results for the 30 parents in the 15 trios studied on the platform.


title: 9313_Child_Mother (GenomeWideSNP_6)


title: 2894_Child_Father (Mapping250_Sty)


title: 9313_Child_Father (GenomeWideSNP_6)


title: 8994_Child (GenomeWideSNP_6)


title: 8994_Child_Mother (GenomeWideSNP_6)


title: 2569_Child (Mapping250_Sty)


title: 8960_Child (GenomeWideSNP_6)


title: 8327_Child_Mother (GenomeWideSNP_6)


title: 2332_Child_Mother (Mapping250_Sty)


title: 2332_Child_Father (Mapping250_Sty)


title: 8994_Child_Father (GenomeWideSNP_6)


title: 2569_Child_Father (Mapping250_Sty)


title: 2377_Child_Mother (Mapping250_Sty)


title: 9313_Child (GenomeWideSNP_6)


title: 8960_Child_Father (GenomeWideSNP_6)


title: 8327_Child_Father (GenomeWideSNP_6)


title: 2377_Child_Father (Mapping250_Sty)


title: 8160_Child_Mother (GenomeWideSNP_6)


title: Patient 379 DCIS (mRNA)

first: Bethany

last: Hannafon

address: 650 Albany Street

department: Medicine/Section of Hematology and Oncology

institute: Boston University School of Medicine

description: Gene expression data from case 379 ductal carcinoma in situ

hyb_protocol: 10 µg of fragmented cRNA and hybridization controls were hybridized to each U133A GeneChip (Affymetrix) for 16 hours and then washed and stained according to the standard antibody amplification for eukaryotic targets protocol (Affymetrix)

scan_protocol: The stained arrays were scanned using a G2500 Scanner (Agilent)

data_processing: Images from the scanned chips were quantified and scaled using Affymetrix Microarray Suite 5.0 (Affymetrix), and the unnormalized data were then rescaled to a target of 100 to remove bias.

source_name: ductal carcinoma in situ epithelium

label_protocol: To convert the RNA to cDNA, the purified total RNA was linearly amplified for two rounds using the MessageAMP aRNA Kit (Ambion, Austin, TX), in which the first round is based on an oligo-dT primer and T7 RNA polymerase. For second round amplification, cDNA for each sample was in vitro transcribed (IVT) to biotin-labeled cRNA with the IVT labeling kit (Affymetrix, Santa Clara, CA).

extract_protocol: On average, ~50 10 um-thick cryostat sections were prepared for the extraction of total RNA by laser-capture microdissection from normal or DCIS epithelial regions, which were identified by a surgical pathologist (AdlM) using every 7th section stained by Hematoxylin and Eosin. Total RNA was extracted from the captured epithelium using the Picopure RNA Isolation Kit (Arcturus Engineering) according to manufacturer's protocol with additional DNAse treatment step.

treatment_protocol: Primary patient breast tissue was snap-frozen in liquid nitrogen, embedded in optimal cutting temperature compound and stored at -80C

tag: sample type

value: laser capture microdissected human breast

value: ductal carcinoma in situ epithelium

value: female

tag: age


title: 2332_Child (Mapping250_Sty)


title: P_NY84

first: Yujin

last: Hoshida

address: 5323 Harry Hines Blvd

institute: University of Texas Southwestern Medical Center

hyb_protocol: Refer to the Illumina beadarray Assay System Manual

data_processing: For each probe, replicate mesurements were averaged after removing outliers. After subtracting background signal intensities, data were then normalized using the cubic spline algorithm.

source_name: Human hepatocellular carcinoma

extract_protocol: Using formalin-fixed, paraffin-embedded HCC tissues, total RNA was extracted using TRIzol (Invitrogen).

value: hepatocellular carcinoma

tag: vascular invasion

value: No

tag: used for qpcr of microrna in chr19q13.41

value: Yes


title: 8327_Child (GenomeWideSNP_6)

value: Developmental Delay


title: 8612_Child (GenomeWideSNP_6)


title: Patient 446B DCIS (mRNA)

description: Gene expression data from case 446B ductal carcinoma in situ


title: 8612_Child_Mother (GenomeWideSNP_6)


title: 1511_Child_Father (Mapping250_Sty)


title: 1511_Child (Mapping250_Sty)


title: P_NY65

scan_protocol: Refer to the Illumina beadarray Assay System Manual


title: P_NY643

label_protocol: Refer to the Illumina beadarray Assay System Manual


title: P_NY641


title: 8160_Child_Father (GenomeWideSNP_6)


title: 8135_Child_Father (GenomeWideSNP_6)


title: P_NY637


title: P_NY635


title: 8612_Child_Father (GenomeWideSNP_6)


title: 8160_Child (GenomeWideSNP_6)


title: P_NY633


title: P_NY673


title: 8135_Child_Mother (GenomeWideSNP_6)


title: 1511_Child_Mother (Mapping250_Sty)


title: 6942_Child_Father (GenomeWideSNP_6)


title: 6942_Child_Mother (GenomeWideSNP_6)


title: P_NY639


title: 8135_Child (GenomeWideSNP_6)


title: 6942_Child (GenomeWideSNP_6)


title: P_NY631


title: 2377_Child (Mapping250_Sty)


title: P_NY627


title: P_NY625


title: 6932_Child_Mother (GenomeWideSNP_6)


title: P_NY617


title: 6932_Child_Father (GenomeWideSNP_6)


title: P_NY615


title: P_NY611


title: P_NY607


title: P_NY609


title: P_NY629


title: P_NY605


title: P_NY599


title: P_NY601


title: P_NY603


title: P_NY597


title: 6932_Child (GenomeWideSNP_6)


title: expended blastocyst vs hatched blastocyst 3

city: Québec City

first: Marc-André

last: Sirard

state: Quebec

address: Offfice 2732, 2440 Hochelaga Blvd.

department: Sciences Animales

institute: Université Laval

description: Biological replicate 3 of 3. Expended blastocysts vsHatched blastocysts. 3 stage loop design

hyb_protocol: Hybridization of the labeled aRNA to the Bluechip was performed at 50°C for 18 h in SlideHyb Glass Array Hybridization Buffer #1 (Ambion, Austin, Tx, USA) using a Slide Booster apparatus (Advalytix, Concord, MA, USA). To discard unhybridized probes, slides were washed twice at RT in 2X SSC/0.5% SDS for 15 min and twice in 0.5X SSC/0.5% SDS for 15 min, the washing solutions were previously incubated at 50°C. Finally, slides were dipped 3 times in 1X SSC and 3 times in H2O before being centrifuged at 1200g for 5 minutes.

scan_protocol: The scan was then performed using the VersArray ChipReader System (Bio-Rad Laboratories) and image processing with the ArrayPro Analyzer software (Media Cybernetics, San Diego, CA, USA).

data_processing: The net intensity of each spot was evaluated after local background subtraction. The comparison of the three different blastocyst stages was done in a loop design experiment using dye swap.

label: Alexa555, Alexa647

organism: Bos taurus

source_name: In-vitro produced blastocyst

label_protocol: From each pool, an aliquot of 2.5 µg aRNA was labeled using DY555/ULS and DY647/ULS (KREATECH Biotechnology, Amsterdam, The Netherlands) according to the manufacturer's protocol. The probe was then purified with Picopure RNA isolation kit (Molecular Devices) to remove the non-reacted ULS dyes.

growth_protocol: Bovine ovaries were collected at a commercial slaughterhouse and maintained in a thermoflask at about 35C° while transported to the laboratory in a 0.9% NaCl (w/v) aqueous solution containing antibiotics and antimycotic agents (100.000 IU/l penicillin, 100 mg/l streptomycin and 250 μg/l amphotericin B, all from Invitrogen, Burlington, ON, Canada). Cumulus-oocyte complexes (COCs) from follicles with a diameter ranging between 3 and 6 mm were collected by follicular liquid aspiration using an 18G needle attached to a 10ml syringe and then decanted for 5 min in a 50 ml Falcon centrifuge tube. The COCs were selected based on their morphological properties. Those with at least 5 compact layers of cumulus and an homogenous cytoplasm were harvested and washed three times in a Hepes-buffered Tyrode  medium (TLH) supplemented with 5% (v/v) bovine serum (HyClone), 0.2 mM pyruvic acid (Sigma-Aldrich, Oakville, ON, Canada) and 50 µg/ml gentamicin (Sigma-Aldrich).  After being selected and washed as described above, COCs were maturated in vitro as groups of 10 COCs and were placed in droplets, each one consisting of 50 µl of maturation medium. The maturation medium was composed of modified synthetic oviductal fluid (SOF) (Holm et al., 1999) with 5% (v/v) fetal bovine serum (FBS) (HyClone), MEM nonessential amino acids (Invitrogen), MEM essential amino acids (Invitrogen), 0.33 mM pyruvic acid, 1 mM glutamine (Sigma-Aldrich), 50 µg/ml gentamicin, 0.1 µg/ml FSH (Gonal F; Serono) and 1 µg/ml 17β-estradiol (Sigma-Aldrich). The droplets containing COCs were then covered with mineral oil (Sigma-Aldrich), to avoid their evaporation and incubated for 24 hours in a humidified atmosphere of 95% air at 38.5°C.  After 24 h of in vitro maturation, COCs were collected and washed twice in TLH medium before being transferred in groups of 5 into 48 µl droplets under mineral oil. The droplets consisted of modified Tyrode lactate medium (TL) supplemented with 0.6% (w/v) free fatty acid BSA (Sigma-Aldrich), 0.2 mM pyruvic acid, 2 µg/ml heparin and 50 µg/ml gentamycin. Oocytes were transferred 15 min prior to semen addition and 2 µl of PHE (1 mM hypotaurine, 2 mM penicillamine, 250 mM epinephrine (Sigma-Aldrich)) were added to each droplet to stimulate sperm motility. The semen used consisted of a cryopreserved mixture of ejaculates from three bulls (Centre d'Insémination Artificielle du Québec; CIAQ, St-Hyacinthe, Qc, Canada). The spermatozoa previously stored in liquid nitrogen were thawed for 1 min in 35°C water, added to a discontinuous Percoll gradient (45% over a 90% Percoll (Sigma-Aldrish)), and centrifuged at 700 x g for 30 min at 26°C. The supernatant containing the cryoprotectant and the dead spermatozoa was discarded and the pellet was then resuspended in 1 ml of modified TL and centrifuged at 250 x g for 5 min at 26°C. The recuperated spermatozoa were counted on a hemocytometer and resuspended in IVF medium to obtain a final concentration of 1 x 106 cells/ml. Their motility and their viability were also checked under the microscope. Finally, 2 µl of the sperm suspension were added to the droplets containing the maturated COCs. The fertilization medium was incubated at 38.5°C for 15-18 h in a humidified atmosphere of 95% air. The eventually fertilized oocytes were mechanically denuded by repeated pipetting. To assure the complete removal of the cumulus cells, oocytes were washed 3 times in the first culture medium (SOF1). Groups of 20-30 embryos were then transferred to 50 µl culture medium droplets. The embryo culture was initially performed in SOF1 under mineral oil at 38.5°C in 5% CO2 in a reduced oxygen atmosphere (7%) with high humidity. After 72 h of in vitro culture SOF1 medium was replaced by SOF2. The SOF1 medium consisted of 5% of FBS, MEM nonessential amino acids, 1 mM glutamine, 10µM EDTA, 0.33 mM pyruvic acid and 50 µg/ml gentamicin. The SOF2 medium contained 5 % FBS, MEM nonessential amino acids, MEM essential amino acids, 1 mM glutamine, 0.33 mM pyruvic acid and 50 µg/ml gentamicin. Embryos were maintained in culture until they reached the blastocyst stage. At this point of development, three “sub-stages” can be distinguished corresponding to the early, expanded and hatched blastocysts, which were collected respectively at the 7th, the 8th and the 9th day of culture. In each group, the fast and the slow developing embryos were separated according to their cleavage kinetics. Embryos were washed three times in PBS, collected in pools with a minimum volume of buffer, frozen and stored at -80°C until RNA extraction. Pools were done in triplicate and contained 10 blastocysts from the 3 different sub-stages.

extract_protocol: Total RNA was extracted from blastocysts (early, expanded and hatched) using the Picopure RNA extraction kit (Molecular Devices, Sunnyvale, CA, USA). To avoid genomic DNA contamination, DNase I treatment was performed directly on the column as described by the manufacturer’s protocol. Total RNA was recuperated in 11 µl of elution buffer and stored at -80°C. Before proceeding to its amplification, total RNA quantification and integrity assessment were realized using an Agilent 2100 bioanalyzer (Agilent Technologies, Waldbronn, Germany) according to its users' manual recommendations. The RNA was amplified by two successive rounds of T7-based linear amplification using the RiboAmp HS RNA Amplification kit (Molecular Devices Corporation, Sunnyvale USA) following the manufacturer's instructions. The amplified antisense RNA (aRNA) was quantified with a ND-1000 nanodrop (NanoDrop Technologies, Wilmington, USA) and stored at -80°C.

tag: developmental stage

value: Expended stage

tag: cell type

value: blastocyst

label: Alexa647, Alexa563

value: Hatched stage


title: P_NY595

city: Dallas

tag: tissue


title: expended blastocyst vs hatched blastocyst 1

description: Biological replicate 1 of 3. Expended blastocysts vsHatched blastocysts. 3 stage loop design

label: Alexa647, Alexa561


title: expended blastocyst vs hatched blastocyst 2

description: Biological replicate 2 of 3. Expended blastocysts vsHatched blastocysts. 3 stage loop design

label: Alexa647, Alexa562


title: P_NY619


title: P_NY593


title: 4821_Child_Mother (GenomeWideSNP_6)

value: peripheral blood


title: early blastocyst vs hatched blastocyst 3

description: Biological replicate 3 of 3. Early blastocysts vs Hatched blastocysts. 3 stage loop design

value: Early stage

label: Alexa647, Alexa560


title: P_NY589


title: P_NY591


title: early blastocyst vs hatched blastocyst 2

description: Biological replicate 2 of 3. Early blastocysts vs Hatched blastocysts. 3 stage loop design

label: Alexa647, Alexa559


title: P_NY587


title: early blastocyst vs hatched blastocyst 1

description: Biological replicate 1 of 3. Early blastocysts vs Hatched blastocysts. 3 stage loop design

label: Alexa647, Alexa558


title: early blastocyst vs expended blastocyst 3

description: Biological replicate 2 of 3. Early blastocysts vs Expended blastocysts. 3 stage loop design

label: Alexa647, Alexa557


title: 2894_Child_Mother (GenomeWideSNP_6)


title: early blastocyst vs expended blastocyst 2

label: Alexa647, Alexa556


title: P_NY579


title: 2569_Child_Mother (GenomeWideSNP_6)


title: P_NY575


title: P_NY585


title: P_NY583


title: P_NY571


title: 2569_Child_Father (GenomeWideSNP_6)


title: early blastocyst vs expended blastocyst 1

description: Biological replicate 1 of 3. Early blastocysts vs Expended blastocysts. 3 stage loop design

label: Alexa647, Alexa555


title: P_NY573


title: P_NY577


title: infected with Helicobacter felis; 8 month post infection A

first: Steven

last: Head

address: 10550 N Torrey Pines Rd

institute: The Scripps Research Institute

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on the v2 GeneChip 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 RMA Express using the default settings (Background Adjust - Yes, Normalization - Quantile, Summarization Method - Median Polish, Store Residuals - unchecked).

source_name: mouse stomach infected with Helicobacter felis; 8 month post infection

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

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

tag: Sex

value: unknown

tag: strain

value: FVB/N

tag: disease state

value: infected with Helicobacter felis

value: stomach


title: infected with Helicobacter felis; 8 month post infection B


title: infected with Helicobacter felis; 9 month post infection A

source_name: mouse stomach infected with Helicobacter felis; 9 month post infection


title: 2894_Child (GenomeWideSNP_6)

tag: developmental state

value: idiopathic MR

value: Child

tag: gender

value: Male


title: 2377_Child_Mother (GenomeWideSNP_6)

value: unaffected

tag: family

value: Mother


title: 2377_Child_Father (GenomeWideSNP_6)

tag: family member

value: Father


title: infected with Helicobacter felis; 6 month post infection B

source_name: mouse stomach infected with Helicobacter felis; 6 month post infection


title: infected with Helicobacter felis; 6 month post infection C


title: infected with Helicobacter felis; 6 month post infection D


title: infected with Helicobacter felis; 4 month post infection B

source_name: mouse stomach infected with Helicobacter felis; 4 month post infection


title: P_NY567

value: hepatocellular carcinoma

value: No

value: Yes


title: 2332_Child_Father (GenomeWideSNP_6)


title: P_NY559


title: 2569_Child (GenomeWideSNP_6)

value: Developmental Delay

tag: phenotype


title: P_NY561


title: infected with Helicobacter felis; 6 month post infection A


title: infected with Helicobacter felis; 4 month post infection A


title: P_NY563


title: P_NY565


title: P_NY569


title: 2332_Child_Mother (GenomeWideSNP_6)


title: P_NY557


title: infected with Helicobacter felis; 2 month post infection C

source_name: mouse stomach infected with Helicobacter felis; 2 month post infection


title: infected with Helicobacter felis; 2 month post infection B


title: P_NY553


title: P_NY551


title: infected with Helicobacter felis; 2 month post infection D


title: 1511_Child_Mother (GenomeWideSNP_6)


title: non-infected control timepoint 8 months B

source_name: mouse stomach non-infected control timepoint 8 months

value: healthy


title: infected with Helicobacter felis; 2 month post infection A


title: 1511_Child_Father (GenomeWideSNP_6)

value: peripheral blood