title: 5_spiked_MDA-MB-468_d1_b


title: hipp_control_adjuvant_day39_102_rep7

status: Public on Nov 21 2014

type: RNA

city: Vancouver

first: Michael

middle: S.

last: Kobor

state: BC

address: 950 West 28th Avenue

department: Medical Genetics

country: Canada

institute: Centre for Molecular Medicine and Therapeutics / University of British Columbia

description: Sample name: 5398636051_B

hyb_protocol: Gene expression was analyzed for both the PFC and HPC using the Illumina RatRef-12 Expression BeadChip microarray, which has 12 arrays per chip. PFC and HPC samples were run separately on different dates, due a limit of processing 8 chips (96 arrays) per batch. 750 ng of cRNA was applied to each array, with one sample per array. Experimental groups were counter-balanced across the arrays, such that chip batch was not confounded with any experimental treatment group, amplification batch, or dissection batch. Additional arrays included an amplification replicate and several hybridization replicates, yielding a total of 96 arrays run per tissue. Microarrays were scanned on the Illumina iScan, and bead-level expression data was collected.

scan_protocol: Standard Illumina scanning protocol

data_processing: Detection p-values were identified using calculateDetection in the R package beadArray. Data were then filtered to remove non-gene probes and processed by quantile normalization using the normalizeIllumina function of the beadArray package in R.

molecule: total RNA

organism: Rattus norvegicus

source_name: hippocampus, control diet, adjuvant injected, day 39 post injection

label_protocol: To generate cRNA for microarray analysis, 250 ng of total RNA from each sample was amplified using the Ambion Illumina TotalPrep RNA Amplification kit, in batches of ~24 samples at a time. Samples were distributed across amplification batches such that batch was not confounded with experimental treatment group.

extract_protocol: Brains were gradually thawed to 4 °C, and the prefrontal cortex (PFC) and hippocampus (HPC) were dissected using RNase-free technique. Dissected tissues were placed in RNAlater and stored at -20 °C. Total RNA and DNA were simultaneously extracted from the dissected tissues using the Qiagen AllPrep DNA/RNA Mini kit, and a DNase digestion step was included in the RNA extraction process. RNA integrity was determined using the Agilent BioAnalyzer mRNA Nano assay, and no samples were excluded due to low RNA integrity. Only one sample was excluded at this stage (PF hippocampus from the Day 39 Adjuvant group), due to suspected contamination.

treatment_protocol: Breeding and prenatal alcohol exposure: Rats were obtained from the Animal Care Center at the University of British Columbia, and were group- housed 1-2 weeks before breeding, with ad libitum access to standard lab chow (Jamieson’s Pet Food Distributors, Ltd., Delta, BC, Canada). Details of the procedures for breeding and handling have been published previously (Glavas et al. 2007). Briefly, females and males were co-housed in stainless steel cages with mesh front and floors, and wax paper under the cages was checked daily for the presence of vaginal plugs, which indicated day 1 of gestation. Thereafter pregnant dams were singly housed, and were assigned to one of three groups – a control group (C; fed laboratory chow ad libitum), pair-fed group (PF; liquid-control diet, with maltose-dextrin isocalorically substituted for ethanol, in the amount consumed by an ethanol- consuming partner, matched for g/kg body weight/day of gestation), or an ethanol-fed group (E; ad libitum access to liquid ethanol diet, with 36% calories derived from ethanol). All animals had ad libitum access to water, and diets were fed from gestation days 1-21 (Weinberg/Kiever Ethanol Diet #710324, Weinberg/Kiever Control Diet #710109, Dyets Inc., Bethlehem, PA). After gestational day 21, all animals were given laboratory chow and water ad libitum. Litters were weighed and culled at birth to 5 males and 5 females, when possible. Following weaning (on postnatal day 22) female offspring were group-housed by litter (2-3 rats per cage) until the start of testing.  Induction of adjuvant-induced arthritis: Details of the postnatal induction of adjuvant-induced arthritis in these animals have been previously published (Zhang et al. 2012). Briefly, female offspring (50-65 days of age) from the C, PF, and E groups were divided into two postnatal treatment groups, in which animals received an intradermal injection at the base of the tail of either 0.1 ml of 12 mg/ml suspension of complete Freund’s adjuvant (CFA) (Adjuvant group), or 0.1ml saline (Saline group). All animals were single-housed after injection, and monitored for clinical signs of arthritis, from the onset of AA through to resolution. To evaluate clinical signs of arthritis, animals were lightly anesthetized with isofluorane, and paws were scored for severity of redness and swelling, on days 7, 10, and every other day afterwards, following injection (results published previously in Zhang et al., 2012).  Termination of animals: Animals were terminated in two cohorts for analysis of gene expression. One cohort was terminated on day 16 post-injection (at the peak of adjuvant-induced arthritis), and another on day 39 post-injection (during resolution phase of arthritis). Each cohort contained 27 adjuvant-injected animals (9 each of C, PF, and E) and 15-18 saline-injected animals (5-6 each of C, PF, and E). For termination, animals were singly removed from their colony room, exposed to CO2 for 30 seconds, and then quickly decapitated. Brains were rapidly removed, immediately frozen on dry ice, wrapped in foil, and stored at -70 °C.

tag: gender

value: female

tag: strain

value: Sprague Dawley

tag: developmental stage

value: adult

tag: tissue

value: hippocampus

tag: prenatal diet

value: control

tag: adult treatment

value: adjuvant injection

tag: termination time point (post injection)

value: day 39

tag: animal id

tag: sample type

value: sample


title: hipp_ethanol_adjuvant_day16_55_rep8

description: Sample name: 5398636051_F

source_name: hippocampus, ethanol diet, adjuvant injected, day 16 post injection

value: ethanol

value: day 16


title: hipp_pairfed_saline_day16_47_hybridizationrep11

description: Sample name: 5398636050_F

source_name: hippocampus, pairfed diet, adjuvant injected, day 16 post injection, array hybrization replicate

value: pairfed

value: saline injection

value: hybridization replicate


title: hipp_control_adjuvant_day16_81_rep3

description: Sample name: 5398636050_B

source_name: hippocampus, control diet, adjuvant injected, day 16 post injection


title: hipp_ethanol_adjuvant_day16_82_rep7

description: Sample name: 5398636050_L


title: hipp_ethanol_saline_day16_70_rep5

description: Sample name: 5398636050_C

source_name: hippocampus, ethanol diet, saline injected, day 16 post injection


title: 25_spiked_MDA-MB-468_d1_b

city: Milan

first: Maurizio

last: Callari

address: Via Amadeo, 42

country: Italy

institute: Fondazione IRCCS Istituto Nazionale dei Tumori

description: healthy donor1 blood spiked with 25 MDA-MB-468 cells

hyb_protocol: cRNA were hybridazed onto Illumina HumanHT-12 WG-DASL V4.0 R2 expression beadchip according to the standard Illumina protocol.

scan_protocol: Illumina BeadArray Reader was used for scanning the arrays and Illumina BeadScan was used for image acquisition and recovery of primary data.

data_processing:
Raw data were generated using the Illumina BeadStudio 3.8 software and analyzed with R/Bioconductor. For each gene, only the probe with higher interquartile range was selected.
According with the characteristics of the study, data normalization was not applicable

organism: Homo sapiens

source_name: breast cancer

label_protocol: Flourescently labeled cRNA were prepared according to the standard Illumina protocol.

extract_protocol: Total RNA extraction was performed according to the manufacturer’s instructions and RNA was eluted in 5 or 10 ul of RNase-free water (Ambion), depending on the experimental setting.

tag: experiment

value: spiked cells

tag: cell line

tag: cell number 5ml

tag: donor

tag: replicate

value: b

value: blood


title: hipp_pairfed_saline_day16_71_rep5

description: Sample name: 5398636049_L

source_name: hippocampus, pairfed diet, saline injected, day 16 post injection


title: hipp_pairfed_adjuvant_day16_50_rep2

description: Sample name: 5398636050_H

source_name: hippocampus, pairfed diet, adjuvant injected, day 16 post injection


title: hipp_pairfed_adjuvant_day16_83_rep3

description: Sample name: 5398636051_D


title: hipp_control_adjuvant_day39_129_rep3

description: Sample name: 5398636050_A


title: 50_spiked_MDA-MB-468_d1_b

description: healthy donor1 blood spiked with 50 MDA-MB-468 cells


title: 100_RNA_MCF7_b

description: 100 ng of RNA deriving from MCF7 cells

value: RNA

tag: rna quantity (ng)


title: hipp_ethanol_saline_day39_88_rep4

description: Sample name: 5430261013_G

source_name: hippocampus, ethanol diet, saline injected, day 39 post injection

value: female


title: hipp_control_adjuvant_day16_57_rep2

description: Sample name: 5398636049_K

value: Sprague Dawley


title: 5_spiked_MCF7_d1_b

description: healthy donor1 blood spiked with 5 MCF7 cells


title: 25_spiked_MCF7_d1_b

description: healthy donor1 blood spiked with 25 MCF7 cells


title: 10_spiked_MCF7_d1_b

description: healthy donor1 blood spiked with 10 MCF7cells


title: Control_blood_d1_AW_Yes_b

description: healthy donor blood treated with AdnaWash

value: blood with AdnaWash

value: a


title: hipp_ethanol_adjuvant_day16_79_rep6

description: Sample name: 5398636049_I

value: adult

value: hippocampus


title: 50_spiked_MCF7_d2_a

description: healthy donor2 blood spiked with 50 MCF7 cells


title: 100_RNA_MDA-MB-468_a2

description: 100 ng of RNA deriving from MDA-MB-468 cells


title: hipp_pairfed_adjuvant_day16_80_rep9

description: Sample name: 5398636049_A

value: adjuvant injection


title: 5_spiked_MDA-MB-468_d1_a

description: healthy donor1 blood spiked with 5 MDA-MB-468 cells


title: hipp_ethanol_adjuvant_day39_127_rep7

description: Sample name: 5398636051_A

source_name: hippocampus, ethanol diet, adjuvant injected, day 39 post injection

value: day 39

value: sample


title: hipp_ethanol_saline_day16_52_rep4

description: Sample name: 5398636049_H

value: ethanol

value: day 16


title: hipp_pairfed_saline_day16_47_hybridizationrep10

description: Sample name: 5398636049_D

value: pairfed

value: saline injection


title: hipp_control_adjuvant_day39_117_rep4

description: Sample name: 5398636045_L

value: control


title: hipp_ethanol_adjuvant_day39_100_rep1

description: Sample name: 5398636049_G


title: hipp_control_adjuvant_day39_87_rep5

description: Sample name: 5398636049_C


title: hipp_control_saline_day16_48_rep4

description: Sample name: 5398636045_G

source_name: hippocampus, control diet, saline injected, day 16 post injection


title: hipp_pairfed_adjuvant_day16_44_rep1

description: Sample name: 5398636049_E


title: 10_spiked_MDA-MB-468_d1_a

description: healthy donor1 blood spiked with 10 MDA-MB-468 cells

value: spiked cells


title: hipp_pairfed_adjuvant_day39_107_hybridizationrep8

description: Sample name: 5398636049_B

source_name: hippocampus, pairfed diet, adjuvant injected, day 39 post injection, array hybrization replicate

value: hybridization replicate


title: hipp_pairfed_adjuvant_day39_107_hybridizationrep7

description: Sample name: 5398636045_J


title: hipp_pairfed_adjuvant_day16_74_rep8

description: Sample name: 5398636045_H


title: hipp_control_saline_day16_78_rep5

description: Sample name: 5398636049_F


title: hipp_control_adjuvant_day16_84_rep9

description: Sample name: 5398636045_I


title: hipp_pairfed_adjuvant_day39_107_rep7

description: Sample name: 5398636045_E

source_name: hippocampus, pairfed diet, adjuvant injected, day 39 post injection


title: hipp_ethanol_adjuvant_day39_106_rep5

description: Sample name: 5398636049_J


title: hipp_ethanol_adjuvant_day16_73_rep5

description: Sample name: 5398636045_K


title: hipp_ethanol_adjuvant_day39_97_rep4

description: Sample name: 5398636045_D


title: hipp_ethanol_saline_day39_124_rep6

description: Sample name: 5398636045_F


title: 25_spiked_MDA-MB-468_d1_a

value: blood


title: 50_spiked_MDA-MB-468_d1_a


title: 100_RNA_MCF7_a

description: 100 ng of RNA deriving from MCF7 cells

value: RNA


title: hipp_control_adjuvant_day16_51_rep1

description: Sample name: 5398636045_C

value: female

value: Sprague Dawley


title: 71_cx_30_bx1 none

city: San Francisco

first: Linda

last: Giudice

state: CA

address: 513 Parnassus Ave. HSE 1619

department: OBGYN and RS

country: USA

institute: University of California, San Francisco

hyb_protocol: Microarrays were hybridized, washed, and stained according to the protocol described in WT Sense Target Labeling Assay Manual from Affymetrix (Version 4; FS450_0007) at the UCSF Gladstone Genomics Core Facility.

scan_protocol: Microarrays were scanned according to the protocol described in WT Sense Target Labeling Assay Manual from Affymetrix (Version 4; FS450_0007) at the UCSF Gladstone Genomics Core Facility.

data_processing: For each sample, intensity values for all probe sets in the GeneChip operating software (Affymetrix) were imported into GeneSpring GX version 12.6 (Agilent Technologies, Santa Clara, CA) and processed using the robust multiarray analysis algorithm for background adjustment, normalization, and log2 transformation of perfect-match values. The intensity values in each condition and tissue type were normalized to the median of all samples. Genes lists were generated using two-way ANOVA and Benjamini-Hochberg multiple testing correction for false discovery rate, and filtered with a ≥1.5 fold change cut-off and P≥0.05.

label: biotin

source_name: Cervical transformation zone, control

label_protocol: RNA was reverse transcribed/amplified into cDNA using the NuGEN Ovation Pico WTA V2 kit, followed by fragmentation and labeling using NuGEN Encore Biotin Module for hybridization to Affymetrix Human Gene 1.0 ST arrays.

growth_protocol: Tissue biopsies were flash frozen immediately following procedure and stored at -80C until TRIzol extraction.

extract_protocol: RNA was extracted from frozen tissues using TRIzol Reagent (Life Technologies, Grand Island, NY) and purified using the NucleoSpin RNA II kit (Macherey-Nagel, Bethlehem, PA) as described. Total RNA as well as protein (abs260/abs280) and organic compound (abs260/abs230) contamination were measured using the Nanodrop (Thermo Fisher Scientific Inc., Waltham, MA, USA).

treatment_protocol: Cervical transformation zone and endometrial biopsies were obtained from 3 groups of volunteers: those using no hormonal contraceptives, DMPA users, or LNG-IUS users. DMPA and LNG-IUS groups had used these contraceptives for at least 6 months.

value: cervical transformation zone

tag: hormonal contraceptive treatment

value: no treatment (mid-secretory phase)


title: 63_cx_21_bx2 none


title: Cortex tissue from SHARP1/2 double null mutant mice (DKO) harvested at ZT16 replicate 1

city: Munich

first: Moritz

middle: J

last: Rossner

address: Nussbaumstr. 7

department: Psychiatry

country: Germany

description: Expression data from adult mouse cortex

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip U74v2 Mouse Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station according to manufacturer protocols.

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

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: Mus musculus

source_name: Cortex tissue ZT16

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Mice were group housed under 12h light 12 dark conditions in standard cages and harvested at indicated timepoints.

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

treatment_protocol: Mice were anesthetized, immediatley decapitated and cortical tissue (bregma 0 to -2mm) was isolated using a ‘rodent brain matrix’ 1 mm coronal slicer.

value: cortex

tag: time

tag: genotype

value: SHARP1/2 null mutant

tag: age

value: 4 months


title: 50_spiked_MCF7_d1_a

description: healthy donor1 blood spiked with 50 MCF7 cells

value: a


title: Cortex tissue from SHARP1/2 double null mutant mice (DKO) harvested at ZT16 replicate 2

description: Expression data from adult mouse cortex

tag: strain


title: 1_RNA_MDA-MB-468_b

description: 1 ng of RNA deriving from MDA-MB-468 cells

value: b


title: hipp_pairfed_saline_day16_65_rep4

description: Sample name: 5398636045_A

tag: gender

tag: developmental stage

value: adult

tag: tissue

value: hippocampus

value: day 16

value: sample


title: 23_Cx_7_bx3 none


title: 51_cx_16_bx1 none


title: 28_Cx_10_bx3 none


title: hipp_ethanol_saline_day16_46_rep3

description: Sample name: 5398636045_B

tag: prenatal diet

value: ethanol

tag: adult treatment

value: saline injection

tag: termination time point (post injection)


title: Cortex tissue from SHARP1/2 double null mutant mice (DKO) harvested at ZT4 replicate 2

description: Expression data from adult mouse cortex

source_name: Cortex tissue ZT4


title: 100_spiked_MCF7_b

description: healthy donor1 blood spiked with 100 MCF7 cells

tag: experiment

tag: sample type

value: spiked cells

value: blood


title: 50_spiked_MCF7_d1_b

tag: cell line

tag: cell number 5ml


title: Cortex tissue from WT mice harvested at ZT16 replicate 2

description: Expression data from adult mouse cortex

value: wildtype


title: Cortex tissue from SHARP1/2 double null mutant mice (DKO) harvested at ZT4 replicate 1

description: Expression data from adult mouse cortex


title: 50_spiked_MCF7_b

tag: donor

tag: replicate


title: 25_spiked_MCF7_d1_a


title: 5_spiked_MCF7_d1_a


title: 200_spiked_MCF7_b

description: healthy donor1 blood spiked with 200 MCF7 cells


title: 21_Cx_4_bx3 none

tag: hormonal contraceptive treatment


title: 0.5_RNA_MDA-MB-468_b

description: 0,5 ng of RNA deriving from MDA-MB-468 cells

value: RNA

tag: rna quantity (ng)


title: Cortex tissue from WT mice harvested at ZT16 replicate 1

description: Expression data from adult mouse cortex

tag: time

tag: genotype


title: 10_RNA_MDA-MB-468_b

description: 10 ng of RNA deriving from MDA-MB-468 cells


title: 10_spiked_MCF7_d1_a

description: healthy donor1 blood spiked with 10 MCF7 cells


title: Cortex tissue from WT mice harvested at ZT4 replicate 2

description: Expression data from adult mouse cortex

tag: strain

tag: age


title: 50_spiked_MDA-MB-468_b


title: Cortex tissue from WT mice harvested at ZT4 replicate 1

description: Expression data from adult mouse cortex


title: 100_spiked_MDA-MB-468_b

description: healthy donor1 blood spiked with 100 MDA-MB-468 cells


title: 100_RNA_MDA-MB-468_b


title: Control_blood_AW_No_b

description: healthy donor1 blood untreated with AdnaWash

value: blood without AdnaWash


title: 1_RNA_MDA-MB-468_a


title: 100_RNA_MDA-MB-468_a


title: 61.PR-39-EF

source_name: Endometrium, LNG-IUS

value: endometrium

value: levonorgestrel intrauterine device


title: 100_spiked_MCF7_a


title: 55.PR-31-EF


title: 60.PR-38-EF

source_name: Endometrium, DMPA

value: depot medroxyprogesterone acetate


title: 66.PR-44-EF


title: Control_blood_AW_No_a


title: 59.PR-36-EF


title: 56.PR-32-EF


title: 0.5_RNA_MDA-MB-468_a


title: 200_spiked_MDA-MB-468_b

description: healthy donor1 blood spiked with 200 MDA-MB-468 cells


title: 50_spiked_MCF7_a


title: 50_spiked_MDA-MB-468_a

description: healthy donor1 blood spiked with 50 MDA-MB-468 cells


title: 58.PR-35-EF


title: 10_RNA_MDA-MB-468_a


title: 64.PR-42-EF


title: Control_blood_AW_Yes_b

description: healthy donor1 blood treated with AdnaWash

value: blood with AdnaWash


title: 63.PR-41-EF


title: 57.PR-34-EF


title: 54.PR-29-EF


title: 65.PR-43-EF


title: 200_spiked_MCF7_a

value: a


title: 53.PR-27-EF


title: Control_blood_AW_Yes_a


title: 100_spiked_MDA-MB-468_a


title: 51.PR-25-EF


title: 49.PR-20-EF


title: 200_spiked_MDA-MB-468_a


title: Input

type: genomic

city: Lausanne

first: Nicolas

last: Lonfat

address: EPFL-SV-ISREC-UPDUB- Station 19

department: School of Life Sciences

country: Switzerland

institute: EPFL - Ecole Polytechnique Fédérale de Lausanne

hyb_protocol: 1μg of DNA was hybridzed per array for 16 hours at 45° at 60rpm using the Affymetrix hybridization kit.

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

data_processing:
Data were quantile normalized within ChIP replicate groups against input and scaled to medial feature intensity of 100 using TAS software (Affymetrix). PM-MM pairs mapping within a sliding window of 250 bp was used.
bar files of normalized signals are generated by TAS software (Affymetrix).

molecule: genomic DNA

source_name: Input DNA from E12.5 mouse limbs

label_protocol: 1 ug of ChIP was fragmented and labeled using GeneChip WT Double-Stranded DNA Terminal Labeling Kit (Affymetrix).

extract_protocol: ChIP was carried out according to (Lee et al., 2006) on pool of 20 genital tubercles dissected at E15.5 or E13.5, fixed for 15 minutes in 1% formaldehyde and using 4μl of anti-H3K27me3 (Millipore, 17-622) or H3K27ac (abcam ab4729) antibodies, immunoprecipated with EZview Red protein G/A affinity Gel beads from Sigma. ChIP were amplified using ligation mediated-PCR, then fragmented, labeled and hybridized to custom tiling array (Lee et al., 2006).

tag: antibody

tag: developmental stage

value: Embryo

value: Forelimb/ autopod


title: GT E13-5 H3K27Ac

source_name: H3K27Ac ChIP DNA from E13.5 mouse genital tubercle

tag: tissue

value: Genital tubercle


title: 52.PR-26-EF


title: 48.PR-12-EF


title: Kidney_UPEC132ΔR049_infected_8h_rep2

city: Tianjin

first: Dongjing

last: Yang

address: 6, Huayue Road

department: Tianjin Institute for Preventive Medicine

country: China

institute: Tianjin Centers for Disease Control and Prevention

description: This sample is of kidney from BALB/c mouse at 4 h post-infection by UPEC132ΔR049. It is the second of two biological replicates used in this experiment, each from separate mouse.

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

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

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

source_name: Mouse kidney of UPEC132ΔR049 group at 8h post-infection

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

extract_protocol: Total RNA was extracted using the the RNeasy Plus kit (Qiagen Inc., Valencia, CA, USA) and the RNAprotect reagent (Qiagen) and DNA was removed by on-column DNase digestion with the RNase-Free DNase set (Qiagen). RNA quality and concentration was determined by analysis with agarose gel electrophoresis and spectrophotometer at CapitalBio Corporation (Beijing, China).

value: 4 h

tag: infection

value: E. coli UPEC132 delta R049

tag: genetic background

value: BALB/c

value: kidney

tag: gender

value: female

value: 8 weeks

tag: weight


title: Kidney_UPEC132ΔR049_infected_4h_rep1

description: This sample is of kidney from BALB/c mouse at 4 h post-infection by UPEC132ΔR049. It is the first of two biological replicates used in this experiment, each from separate mouse.

source_name: Mouse kidney of UPEC132ΔR049 group at 4h post-infection


title: 45.PR-08-EF

source_name: Endometrium, control

value: no treatment (mid-secretory phase)


title: 46.PR-09-EF


title: Kidney_PBS_infected_rep2

description: This sample is of kidney from BALB/c mouse infected by PBS. It is the second of two biological replicates used in this experiment, each from separate mouse.

source_name: Mouse kidney of PBS group

value: PBS


title: Kidney_PBS_infected_rep1

description: This sample is of kidney from BALB/c mouse infected by PBS. It is the first of two biological replicates used in this experiment, each from separate mouse.


title: Kidney_UPEC132_infected_8h_rep1

description: This sample is of kidney from BALB/c mouse at 8 h post-infection by UPEC132. It is the first of two biological replicates used in this experiment, each from separate mouse.

source_name: Mouse kidney of UPEC132 group at 8h post-infection

value: 8 h

value: E. coli UPEC132


title: Kidney_UPEC132ΔR049_infected_8h_rep1

description: This sample is of kidney from BALB/c mouse at 8 h post-infection by UPEC132ΔR049. It is the first of two biological replicates used in this experiment, each from separate mouse.


title: GT E15-5 H3K27Ac

source_name: H3K27Ac ChIP DNA from E15.5 mouse genital tubercle


title: GT E15-5 H3K27Me3

source_name: H3K27Me3 ChIP DNA from E15.5 mouse genital tubercle


title: 47.PR-11-EF

value: endometrium

value: levonorgestrel intrauterine device


title: 41.PR-01-EF


title: 40.PR-44-CF

source_name: Cervical transformation zone, DMPA

value: cervical transformation zone

value: depot medroxyprogesterone acetate


title: 44.PR-07-EF


title: 42.PR-05-EF


title: 43.PR-06-EF


title: 39.PR-43-CF


title: Kidney_UPEC132_infected_4h_rep2

description: This sample is of kidney from BALB/c mouse at 4 h post-infection by UPEC132. It is the second of two biological replicates used in this experiment, each from separate mouse.

source_name: Mouse kidney of UPEC132 group at 4h post-infection


title: 38.PR-42-CF


title: Kidney_UPEC132_infected_8h_rep2

description: This sample is of kidney from BALB/c mouse at 8 h post-infection by UPEC132. It is the second of two biological replicates used in this experiment, each from separate mouse.


title: Kidney_UPEC132_infected_4h_rep1

description: This sample is of kidney from BALB/c mouse at 4 h post-infection by UPEC132. It is the first of two biological replicates used in this experiment, each from separate mouse.


title: Kidney_UPEC132ΔR049_infected_4h_rep2


title: 36.PR-40-CF


title: 37.PR-41-CF

source_name: Cervical transformation zone, LNG-IUS


title: 35.PR-38-CF


title: 32.PR-35-CF


title: 33.PR-36-CF


title: 31.PR-34-CF


title: 34.PR-37-CF


title: 29.PR-32-CF


title: 25.PR-27-CF


title: 28.PR-31-CF


title: 23.PR-25-CF


title: 24.PR-26-CF


title: P5+WT H3.3, biological rep1

city: New York

first: Viviane

last: Tabar

state: New York

address: 1275 York Avenue

department: Department of Neurosurgery

institute: Memorial Sloan-Kettering Cancer Center

description:
Gene expression data from NPCs expressing constitutively active PDGFRA (D842V), sh-p53 and WT H3.3
P5W-1

hyb_protocol: Following fragmentation, 10ug of cRNA were hybridized for 16 hours at 45 deg C on GeneChip Human U133 PLUS 2.0 Genome Array. Gene Chips were washed washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data was normalized by robust multichip analysis (RMA) using GenePattern analysis platform.

source_name: Human ES-derived NPCs

label_protocol: Biotinylated cRNA was prepared according to standard Affymetrix protocol from 2 micrograms total RNA.

growth_protocol: Human ES cells (WA-09) were differentiated to NPCs using Dual smad inhibition protocol. NPCs were maintained on dishes coated with 10 μg/ml polyornithine, 2 μg/ml laminin and 1 μg/ml fibronectin, in N2 medium supplemented with EGF (20 ng/ml) and FGF2 (20 ng/ml) and B-27 supplement without vitamin A.

extract_protocol: Cells were lysed directly in Trizol (Life Technologies). RNA was extracted using chloroform and ethanol precipitation.

treatment_protocol: NPCs were lentivirally transduced with a combination of constitutively active PDGFRA (D842V), sh-p53, and WT or K27M mutant form of histone H3.3 variant.

tag: cell type

value: Human ES-derived NPCs

tag: expression construct

value: CA-PDGFRA + sh-p53 + WT H3.3


title: 27.PR-30-CF


title: 30.PR-33-CF


title: P5+K27M mutant, biological rep2

description:
Gene expression data from NPCs expressing constitutively active PDGFRA (D842V), sh-p53 and H3.3-K27M
P5K-2

value: CA-PDGFRA + sh-p53 + H3.3-K27M


title: P5, biological rep2

description:
Gene expression data from NPCs expressing constitutively active PDGFRA (D842V) and sh-p53
P5-2

value: CA-PDGFRA + sh-p53


title: 26.PR-29-CF


title: 19.PR-20-CF


title: 21.PR-22-CF


title: 22.PR-23-CF


title: P5+K27M mutant, biological rep3

description:
Gene expression data from NPCs expressing constitutively active PDGFRA (D842V), sh-p53 and H3.3-K27M
P5K-3


title: 18.PR-19-CF


title: 14.PR-14-CF


title: P5, biological rep3

description:
Gene expression data from NPCs expressing constitutively active PDGFRA (D842V) and sh-p53
P5-3


title: 15.PR-15-CF


title: P5+K27M mutant, biological rep1

description:
Gene expression data from NPCs expressing constitutively active PDGFRA (D842V), sh-p53 and H3.3-K27M
P5K-1


title: K27M mutant, biological rep3

description:
Gene expression data from NPCs expressing H3.3-K27M
K27M-3


title: P5+WT H3.3, biological rep2

description:
Gene expression data from NPCs expressing constitutively active PDGFRA (D842V), sh-p53 and WT H3.3
P5W-2


title: 13.PR-13-CF

source_name: Cervical transformation zone, control


title: 16.PR-17-CF


title: 17.PR-18-CF


title: WT H3.3, biological rep1

description:
Gene expression data from NPCs expressing WT H3.3
WT-1

value: WT H3.3


title: K27M mutant, biological rep2

description:
Gene expression data from NPCs expressing H3.3-K27M
K27M-2


title: WT H3.3, biological rep2

description:
Gene expression data from NPCs expressing WT H3.3
WT-2


title: K27M mutant, biological rep1

description:
Gene expression data from NPCs expressing H3.3-K27M
K27M-1


title: Mock NPCs, biological rep3

description:
Gene expression data from mock-infected NPCs
Mock-3

value: Mock


title: P5, biological rep1

description:
Gene expression data from NPCs expressing constitutively active PDGFRA (D842V) and sh-p53
P5-1


title: 09.PR-09-CF


title: 11.PR-11-CF


title: 12.PR-12-CF


title: 07.PR-07-CF


title: 04.PR-04-CF


title: Mock NPCs, biological rep1

description:
Gene expression data from mock-infected NPCs
Mock-1


title: overexpressing-MYCN-rep1_SHSY5Y_THZ1

city: Boston

first: Rani

last: George

state: MA

address: 450 Brookline Ave

department: Pediatric Oncology

institute: Dana Farber Cancer Institute

description: Gene expression data

hyb_protocol: Following fragmentation, 12.5 ug of aRNA were hybridized at 45C for 16 hr at 60RPM on GeneChip Arrays (PrimeView). GeneChips were washed and stained in the Affymetrix Fluidics Station 450 according to the manurfacturer's instructions, using the buffers provided in the Affymetrix GeneChip Hybridization, Wash and Stain Kit.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 and images were extracted with Affymetrix GeneChip Expression Console. A CDF containing the ERCC probes was provided by Affymetrix.

data_processing: A CDF provided by Affymetrix, which contained the ERCC probes (PrimeView_withERCC_binary.cdf) was used instead of the standard PrimeView cdf. The data were analyzed with Bioconductor using the MAS5 normalization method. Then, these data were renormalized to the external spike-ins. See manuscript for additional details.

label_protocol: Biotinylated aRNA was prepared according to the standard Affymetrix protocol from 100 ng total RNA (GeneChip 3' IVT Express Kit User Manual, 2009, Affymetrix).

growth_protocol: RPMI 1640 + FBS.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions. External spike-in RNAs (ERCC ExFold RNA Spike-In kit, Ambion, 4456739) were added based on cell number. See manuscript for details.

treatment_protocol: 100 nM THZ1 or DMSO for 6hrs. 1 uM Actinomycin D for 6hrs.

value: Neuroblastoma


title: TN-05

city: Brussels

first: David

last: Brown

address: Boulevard de Waterloo 127

country: Belgium

institute: Institut Jules Bordet

hyb_protocol: Hybridization was done according to the standard Affymetrix protocol (GeneChip Expression Analysis Technical Manual, Rev. 5, Affymetrix)

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner

data_processing: The probe level intensities were background adjusted using the Robust multi-array analysis (RMA) method followed by quantile normalization as impletemented in the R/Bioconductor package frma. Probe level annotations were obtained from Affymetrix’s website. In particular, we used release 31 of the NetAffx annotation files.

source_name: Breast tumor

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol (GeneChip Expression Analysis Technical Manual, Rev. 5, Affymerrix)

extract_protocol: RNA was isolated by the Trizol method (Invitrogen) according to manufacturers’ instructions.

tag: er

tag: pgr

tag: grade

value: breast cancer tumor


title: Mock NPCs, biological rep2

description:
Gene expression data from mock-infected NPCs
Mock-2


title: 03.PR-03-CF

tag: hormonal contraceptive treatment


title: TN-26


title: TN-25


title: TN-23


title: 10.PR-10-CF


title: 06.PR-06-CF


title: 05.PR-05-CF


title: TN-03


title: TN-28


title: TN-24


title: TN-21


title: TN-22


title: overexpressing-MYCN-rep1_SHSY5Y

description: Gene expression data


title: overexpressing-MYCN-rep2_SHSY5Y_THZ1

description: Gene expression data


title: 01.PR-01-CF


title: TN-20


title: overexpressing-MYCN-rep2_SHSY5Y

description: Gene expression data


title: 08.PR-08-CF


title: high-MYCN-rep1_kelly_shMYCN

description: Gene expression data

source_name: Kelly


title: 02.PR-02-CF


title: high-MYCN-rep2_kelly_shMYCN

description: Gene expression data


title: TN-02


title: 1_CMA03/06_rep1

city: MILAN

first: Luca

last: Agnelli

address: Venezian 1

department: Department of Advanced Diagnostics

institute: IRCCS Istituto Nazionale dei Tumori

description: Gene expression profiling data of CMA03/06 cells cultured in absence of IL-6 for 24 hours, replicate 1

hyb_protocol: The fragmented labeled single-stranded DNA target was hybridized for 16 hr 30 minutes at 45°C on GeneChip® Gene 1.0 ST array according to the standard Affymetrix protocol. The arrays were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: The Gene 1.0 ST arrays were scanned using the GeneChip® Scanner 3000 7G (Affymetrix Inc., Santa Clara, CA).

data_processing: Log2-transformed expression values were extracted from CEL files and normalized using NetAffx Transcript Cluster Annotations, Release 30 and robust multi-array average (RMA) procedure in Expression Console software (Affymetrix Inc.). The expression values of transcript cluster ID specific for loci representing naturally occurring read-through transcriptions or mapped to more than one chromosomal location were summarized as median value for each sample. The supervised gene expression analyses were performed using Rank Product method by the RankProd R package available on Bioconductor repository (http://www.bioconductor.org/): the up-regulated or down-regulated genes were selected from the lists generated by RankProd using a filter on percentage of false positive predictions (pfp < 0.005) and a second filter on the difference in gene expression value (fold change > 2).

source_name: IL-6-independent variant of CMA03, CMA03/06

label_protocol: 5.5 micrograms of single-stranded DNA target obtained from 100 ng of purified total RNA was fragmented and then labeled using the WT Terminal Labeling Kit according to the standard Affymetrix protocol (GeneChip® Whole Transcript (WT) Sense Target Labeling Assay Manual).

growth_protocol: CMA03/06 cells were cultured in Iscove's modified Dulbecco's medium (IMDM) supplemented with 10% fetal calf serum (FCS).

extract_protocol: Cell pellets were resuspended in TRIzol Reagent (Life Technologies, Inc., Rockville, MD, USA), total RNA was then purified using the RNeasy® total RNA Isolation Kit (Qiagen, Valencia, CA).

treatment_protocol: CMA03/06 cells were cultured in absence of IL-6 for 24 hours.

tag: cell line


title: 3_CMA03_IL6-_rep3

description: Gene expression profiling data of CMA03 cells cultured in absence of IL-6 for 24 hours, replicate 3

source_name: IL-6-dependent human myeloma cell line obtained from a peritoneal effusion of a patient with refractory myeloma, CMA03

growth_protocol: CMA03 cells were cultured in Iscove's modified Dulbecco's medium (IMDM) supplemented with 10% fetal calf serum (FCS) in absence of IL-6.

treatment_protocol: CMA03 cells were cultured in absence of IL-6 for 24 hours.

tag: treatment


title: TN-19


title: TN-16


title: high-MYCN-rep2_kelly_shGFP

description: Gene expression data


title: TN-01


title: 1_CMA03_IL6-_rep1

description: Gene expression profiling data of CMA03 cells cultured in absence of IL-6 for 24 hours, replicate 1


title: low-MYCN-rep2_SHSY5Y_THZ1

description: Gene expression data


title: 1_CMA03_IL6+_rep1

description: Gene expression profiling data of CMA03 cells cultured in presence of IL-6 for 24 hours, replicate 1

growth_protocol: CMA03 cells were cultured in Iscove's modified Dulbecco's medium (IMDM) supplemented with 10% fetal calf serum (FCS) and 20 U/mL recombinant human IL-6 (R&D System, Minneapolis, MN, USA).

treatment_protocol: CMA03 cells were cultured in presence of IL-6 for 24 hours.


title: TN-17


title: LUMB-03


title: TN-18


title: low-MYCN-rep3_SHSY5Y_THZ1

description: Gene expression data


title: low-MYCN-rep3_SHSY5Y_DMSO

description: Gene expression data


title: TN-15


title: high-MYCN-rep2_kelly_ActD

description: Gene expression data


title: 2_CMA03/06_rep2

description: Gene expression profiling data of CMA03/06 cells cultured in absence of IL-6 for 24 hours, replicate 2


title: 3_CMA03_IL6+_rep3

description: Gene expression profiling data of CMA03 cells cultured in presence of IL-6 for 24 hours, replicate 3

value: CMA -03


title: 3_CMA03/06_rep3

description: Gene expression profiling data of CMA03/06 cells cultured in absence of IL-6 for 24 hours, replicate 3


title: high-MYCN-rep1_kelly_ActD

description: Gene expression data


title: high-MYCN-rep1_kelly_shGFP

description: Gene expression data


title: 2_CMA03_IL6-_rep2

description: Gene expression profiling data of CMA03 cells cultured in absence of IL-6 for 24 hours, replicate 2


title: 2_CMA03_IL6+_rep2

description: Gene expression profiling data of CMA03 cells cultured in presence of IL-6 for 24 hours, replicate 2


title: low-MYCN-rep1_SHSY5Y_THZ1

description: Gene expression data


title: LUMB-05


title: LUMB-21


title: LUMB-19


title: LUMB-23


title: low-MYCN-rep2_SHSY5Y_DMSO

description: Gene expression data


title: LUMB-18


title: high-MYCN-rep1_IMR32_THZ1

description: Gene expression data


title: high-MYCN-rep3_IMR32_DMSO

description: Gene expression data


title: LUMB-15


title: low-MYCN-rep1_SHSY5Y_DMSO

description: Gene expression data


title: high-MYCN-rep3_IMR32_THZ1

description: Gene expression data


title: LUMB-17


title: high-MYCN-rep2_IMR32_DMSO

description: Gene expression data


title: LUMA-04


title: LUMA-33


title: LUMA-29


title: high-MYCN-rep2_kelly_THZ1

description: Gene expression data


title: high-MYCN-rep1_kelly_THZ1

description: Gene expression data


title: LUMA-31


title: high-MYCN-rep1_IMR32_DMSO

description: Gene expression data


title: LUMB-20


title: LUMA-32


title: LUMB-01


title: high-MYCN-rep2_kelly_DMSO

description: Gene expression data


title: high-MYCN-rep3_kelly_DMSO

description: Gene expression data


title: high-MYCN-rep3_kelly_THZ1

description: Gene expression data


title: high-MYCN-rep1_kelly_DMSO

description: Gene expression data


title: AAA_ATLO - 2

city: Lille

last: Hot

address: 1 rue du professeur Calmette

department: Center for Infection and Immunity of Lille

country: France

institute: Institut Pasteur de Lille

description: Microdissceted areas

hyb_protocol: The miRNA Complete Hybridization Kit (Agilent Technologies) required 100 ng of total RNA per sample. Purified labeled miRNAs were prepared with 10 × Blocking Agent and 2 × Hi-RPM hybridization buffer and incubated with the array in hybridization chambers (Agilent) for 20 hours at 55 °C.

scan_protocol: SureScan microarray scanner (Agilent Technologies).

data_processing: Raw data were acquired with Feature Extraction Software (Version 10.7.3.1). Calculation of the total gene signal for each miRNA replicated probe subtracted background signals. We used the R package script AgiMicroRna for normalization.

source_name: Patient T20

label_protocol: The miRNA Complete Labeling Kit (Agilent Technologies) required 100 ng of total RNA per sample. After dephosphorylation, they were labeled with Cyanine 3-pCp at 16°C for 2 hours, with a T4 ligase. Micro Bio-Spin 6 chromatography columns (Bio-Rad Laboratories, Hercules, CA) were used to purify the labeled RNA.

extract_protocol: RNA was extracted from 10 mm2 of LCM-isolated areas with 200 μL TRI Reagent® (Ambion), according to the manufacturer’s instructions. RNA quality (RNA integrity number, RIN) and quantity were systematically checked for each sample with Pico 6000 Chips and then Small RNA Chips  on the BioAnalyzer 1200 (Agilent Technologies) and using the NanoDrop 2000 (Thermo Scientific), respectively and according to the manufacturer's instructions.

treatment_protocol: Human abdominal aortic aneurysm biopsy samples were harvested during open surgery treatment. Human abdominal non aneurysmal aortas were harvested during multiretrieval organs, with the written consent of their families and the authorization of the French Biomedicine Agency (PFS 11-004).

value: Abdominal aortic aneurysm

value: ATLO


title: LUMA-28


title: Total mRNAs from Ler (heat stress) set 2

city: Uppsala

first: Emilio

last: Gutierrez Beltran

state: Sweden

address: Almas Allé 5

department: Department of Plant Biology

country: Sweden

institute: Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, SLU (Biocenter)

description:
heat stress (39ºC, 40 min)
Total mRNAs

hyb_protocol: For the hybridisation the Agilent Gene Expression Hybridisation Kit (Agilent Technologies) is used following the manufacture‘s protocol. For example 600 ng cRNA are hybridised on a 8x60K microarray at 65 ◦C for 17 h using Agilent‘s recommended hybridisation chamber and oven. Finally the microarray is washed once with the Agilent Gene Expression Wash Buffer 1 for one minute at ambient temperature followed by a second wash with preheated (37 ◦C) Gene Expression Wash Buffer 2 for one minute. Washed miroarray can be scanned.

scan_protocol: Fluorescence signals on microarray are detected by the SureScan Microarray Scanner (Agilent Technologies) at a resolution of 3 micron for SurePrint G3 Gene Expression Microarrays and 5 micron for HD Microarray formats, generating a 20 bit TIFF file respectively.

data_processing: Prior to normalisation the following processing steps are performed: ������1.removal of signals from control probes; 2. mean of signals from replicate probes and 3. mean of signals from all probes of a target.  Data of all samples are quantile normalised using the ranked median quantiles according to Bolstad et al. “A comparison of normalisation methods for high density oligonucleotide array data based on variance and bias”, Bioinformatics, 2003, Oxford Univ Press. Briefly, the mean signal of each target is ranked relative to all other targets. The ranked signal value is replaced with the median quantile value of the same rank. So the highest value in all samples becomes the mean of the highest values, the second highest value becomes the mean of the second highest values, and so on.

organism: Arabidopsis thaliana

source_name: roots

label_protocol: The Low Input QuickAmp Labeling Kit (Agilent Technologies) is used for generation of fluorescent cRNA (complementary RNA). By default cRNA is amplified by using oligo-dT primer and labeled with cyanine 3-CTP following the manufacture‘s protocol.

extract_protocol: Uncapped mRNA purification was performed as previously described, using T4 RNA ligase (Ambion) to add an RNA adaptor to the uncapped mRNA (Jiao et al., 2008; Jiao and Riechmann, 2012). Total mRNA was isolated using Rneasy mini kit (Qiagen).

value: Five-day old seedlings

tag: genotype

value: Landsberg erecta (Ler) ecotype.

value: heat stress (39ºC, 40 min)

value: root


title: high-MYCN-rep2_IMR32_THZ1

description: Gene expression data


title: LUMA-27


title: AAA_ATLO - 1

description: Microdissceted areas

source_name: Patient T6


title: LUMA-26


title: Total mRNAs from tsn1tsn2 (heat stress) set 2

description:
heat stress (39ºC, 40 min)
Total mRNAs

value: tsn1tsn2 double mutant


title: LUMA-24


title: LUMA-23


title: Total mRNAs from tsn1tsn2 (control) set 2

description:
control  (23ºC)
Total mRNAs

value: control  (23ºC)


title: LUMA-25


title: SE1457 wild type strain after 6 hours of growth replicate 3

type: mixed

city: Geneva

first: FRANCOIS

last: Patrice

state: Ge 4

address: Rue Gabrielle-Perret-Gentil, 4

department: Service of Infectious Diseases

institute: Genomic Research Laboratory

description: Staphylococcus epidermidis strain SE1457 WT versus Staphylococcus epidermidis gDNA pool

hyb_protocol: A mixture of RNA from WT or DssrABstrains and gDNA pool was diluted in 50 µl Agilent hybridization buffer, and hybridized at a temperature of 60°C for 17 hours in a dedicated hybridization oven

scan_protocol: 100% PMT using Agilent scanner

data_processing: Local background-subtracted signals were corrected for unequal dye incorporation or unequal load of labelled product. The algorithm consisted of a rank consistency filter and a curve fit using the default LOWESS (locally weighted linear regression) method

organism: Staphylococcus epidermidis

source_name: S. epidermidis SE1457 WT

label_protocol: Incorporation during reverse transcription

growth_protocol: 4, 6 or 12 hours growth in Tryptic Soy Broth

extract_protocol: Wash with 0.85% NaCl (ice-cold) and lyzed/homogenized using 0.1 mm Ziconia-silica beads inMini-Beadbeater (Biospec,Bartlesville,OK, USA). Total RNA was isolated using the RNeasyMini kit (QIAGEN, Hilden, Germany) according to the manufacturer’s instructions including a DNase treatment.

treatment_protocol: For anaerobic incubation, the overnight bacterial culture was diluted 1:200 into fresh BM media in sealed bottles supplied continuously with nitrogen and cultured at 37℃ with orbital agitation (200 rpm). Bacteria cells were harvested at 4h, 6h and 12h, respectively.

tag: strain

tag: genotype/variation

value: wild type

tag: growth time

value: 6 h

source_name: gDNA pool

tag: reference

value: Staphylococcus epidermidis gDNA mixture


title: LUMA-21

tag: tissue


title: Total mRNAs from Col (control) set 2

description:
control  (23ºC)
Total mRNAs

tag: developmental stage

value: Columbia (Col) ecotype


title: SE1457 wild type strain after 6 hours of growth replicate 2


title: Total mRNAs from Col (heat stress) set 2

description:
heat stress (39ºC, 40 min)
Total mRNAs


title: Total mRNAs from Ler (control) set 2

description:
control  (23ºC)
Total mRNAs


title: SE1457 wild type strain after 6 hours of growth replicate 1


title: LUMA-22


title: Total mRNAs from tsn1tsn2 (heat stress) set 1

description:
heat stress (39ºC, 40 min)
Total mRNAs


title: LUMA-20


title: LUMA-19


title: SE1457 ssrA mutant strain after 12 hours of growth replicate 3

description: Staphylococcus epidermidis strain SE1457 DssrA versus Staphylococcus epidermidis gDNA pool

source_name: S. epidermidis SE1457DsaeRS

value: ssrA mutant


title: SE1457 ssrA mutant strain after 12 hours of growth replicate 2


title: LUMA-18


title: SE1457 ssrA mutant strain after 6 hours of growth replicate 3


title: Total mRNAs from Col (control) set 1

description:
control  (23ºC)
Total mRNAs


title: Total mRNAs from tsn1tsn2 (control) set 1

description:
control  (23ºC)
Total mRNAs


title: HER2-03


title: Total mRNAs from Col (heat stress) set 1

description:
heat stress (39ºC, 40 min)
Total mRNAs


title: SE1457 ssrA mutant strain after 12 hours of growth replicate 1


title: HER2-24


title: Total mRNAs from Ler (heat stress) set 1

description:
heat stress (39ºC, 40 min)
Total mRNAs


title: SE1457 ssrA mutant strain after 6 hours of growth replicate 2


title: SE1457 ssrA mutant strain after 6 hours of growth replicate 1


title: HER2-25


title: SE1457 ssrA mutant strain after 4 hours of growth replicate 3

value: 4 h


title: HER2-23


title: Total mRNAs from Ler (control) set 1

description:
control  (23ºC)
Total mRNAs


title: Uncapped mRNAs from Col (control) set 2

description:
control  (23ºC)
uncapped mRNAs


title: Uncapped mRNAs from tsn1tsn2 (heat stress) set 2

description:
heat stress (39ºC, 40 min)
uncapped mRNAs


title: HER2-22


title: Uncapped mRNAs from Ler (control) set 2

description:
control  (23ºC)
uncapped mRNAs


title: SE1457 ssrA mutant strain after 4 hours of growth replicate 2


title: Uncapped mRNAs from Ler (heat stress) set 2


title: SE1457 ssrA mutant strain after 4 hours of growth replicate 1


title: Uncapped mRNAs from tsn1tsn2 (heat stress) set 1


title: Uncapped mRNAs from tsn1tsn2 (control) set 2

description:
control  (23ºC)
uncapped mRNAs


title: HER2-02


title: HER2-19


title: HER2-18


title: Uncapped mRNAs from Ler (control) set 1

description:
control  (23ºC)
uncapped mRNAs


title: Uncapped mRNAs from Ler (heat stress) set 1


title: HER2-16


title: Uncapped mRNAs from Col (heat stress) set 2


title: Uncapped mRNAs from Col (heat stress) set 1


title: HER2-15


title: HER2-20


title: HER2-13


title: HER2-14


title: HER2-21


title: Uncapped mRNAs from tsn1tsn2 (control) set 1

description:
control  (23ºC)
uncapped mRNAs


title: Uncapped mRNAs from Col (control) set 1

description:
control (23ºC)
uncapped mRNAs

value: control (23ºC)


title: Rottweiler-BI_12282_ARRAY127874

status: Public on Nov 20 2014

city: Cambridge

first: Hyun Ji

last: Noh

address: 7 Cambridge Center

department: Genome Sequencing and Analysis

institute: Broad Institute

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000.

data_processing:
The array image was acquired using Affymetrix GeneChip® Operating Software.
Genotype Call (SNP call): AA, AB, BB, NC, and NoCall; 'Signal' = Summarized signal

label: Biotin

organism: Canis lupus familiaris

source_name: blood

label_protocol: As per manufacturer (Affymetrix)

extract_protocol: Genomic DNA was extracted from blood using the Puregene DNA purification Kit (Gentra Systems) protocol.

value: blood


title: Leonberger-BI_03730_ARRAY127954


title: Rottweiler-BI_12281_ARRAY127858


title: Leonberger-BI_02542_ARRAY128002


title: Leonberger-BI_03734_ARRAY127986


title: Rottweiler-BI_12337_ARRAY127922


title: Leonberger-BI_03735_ARRAY127970


title: Rottweiler-BI_12274_ARRAY128000


title: Rottweiler-BI_12276_ARRAY127826


title: Rottweiler-BI_12270_ARRAY127984


title: Rottweiler-BI_12279_ARRAY127842


title: TibetanTerrier-BI_08467_ARRAY127888


title: TibetanTerrier-BI_08469_ARRAY127920


title: TibetanTerrier-BI_08464_ARRAY127840


title: TibetanTerrier-BI_08468_ARRAY127904


title: TibetanTerrier-BI_08466_ARRAY127872


title: TibetanTerrier-BI_08463_ARRAY127824


title: TibetanTerrier-BI_08462_ARRAY127998


title: TibetanTerrier-BI_08461_ARRAY127982


title: Rottweiler-BI_12286_ARRAY127906


title: Rottweiler-BI_12283_ARRAY127890


title: LPS stimulated macrophage replicate 2

city: Seoul

first: Yi Rang

address: 101, daehak-ro Jongro-gu

department: Microbiology and Immunology

country: South Korea

institute: Seoul National University College of Medicine

description: Biological replicate 2 of 2. Comparing set of LPS stimulated macrophages from wildtype and CDK5R1 knockout mice.

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 on an Agilent G2565AA scanner.

data_processing: Agilent Feature Extraction Software (v 9.3.2.1) was used for background subtraction and LOWESS normalization.

source_name: bone marrow cell derived macrophages

label_protocol: 10 µg of total RNA were primed with 2 µl of 100 µM T16N2 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 RTase (Invitrogen), and 100 µM each dATP, dTTP, dGTP, with 25 µM dCTP, 25 µM Cy3-label

growth_protocol: Isolated bone marrow cells were cultured for 7 days in RPMI medium supplemented with 10% FBS, 10 units/ml penicillin, 10 µg/ml streptomycin and 2 mM L-glutamine. To enrich the macrophage population, we supplemented 25 ng/ml murine GM-CSF.

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

treatment_protocol: Macrophages were stimulated with E.coli LPS (100 ng/ml) for 6 hours.

tag: gender

value: male

value: wildtype

value: bone marrow

tag: age

value: 6 wks of age

value: primary bone marrow derived macrophages

value: CDK5R1 knockout


title: TibetanTerrier-BI_08460_ARRAY127966


title: basal macrophage replicate 1

description: Biological replicate 1 of 2. Comparing set of basal macrophages from wildtype and CDK5R1 knockout mice.


title: LPS stimulated macrophage replicate 1

description: Biological replicate 1 of 2. Comparing set of LPS stimulated macrophages from wildtype and CDK5R1 knockout mice.


title: basal macrophage replicate 2

description: Biological replicate 2 of 2. Comparing set of basal macrophages from wildtype and CDK5R1 knockout mice.


title: TibetanTerrier-BI_08459_ARRAY127950


title: TibetanTerrier-BI_08457_ARRAY127918


title: TibetanTerrier-BI_08456_ARRAY127902


title: TibetanTerrier-BI_08455_ARRAY127886


title: TibetanTerrier-BI_08451_ARRAY127822


title: TibetanTerrier-BI_08453_ARRAY127854


title: TibetanTerrier-BI_08452_ARRAY127838


title: TibetanTerrier-BI_08454_ARRAY127870


title: GoldenRetriever-BI_03714_ARRAY414360


title: Poodle-BI_13028_ARRAY187366


title: Poodle-BI_16989_ARRAY187334


title: Poodle-BI_13025_ARRAY187318


title: Poodle-BI_16973_ARRAY187302


title: Poodle-BI_16968_ARRAY187286


title: Poodle-BI_13019_ARRAY187270


title: Poodle-BI_13012_ARRAY187254


title: Poodle-BI_16951_ARRAY187222


title: Poodle-BI_13009_ARRAY187238


title: Poodle-BI_16953_ARRAY187206


title: Poodle-BI_16952_ARRAY187380


title: Poodle-BI_16950_ARRAY187364


title: Replication timing of wildtype naïve mouse embryonic stem cells

city: Tallahassee

first: Benjamin

last: Pope

state: FL

address: 319 Stadium Dr

department: Biological Science

institute: Florida State University

hyb_protocol: Standard NimbleGen protocol (www.nimblegen.com/products/lit/index.html). Briefly, Cy3 and Cy5 labeled DNA samples (34 ug each) were co-hybridized to Nimblegen CGH arrays containing one oligonucleotide probe every 5.8 kb across the mouse genome.

scan_protocol: GenePix 4000B scanner (Molecular Devices) and GenePix software were used per NimbleGen's standard protocol (www.nimblegen.com/products/lit/index.html).

data_processing: NimbleScan software was used to obtain .pair raw data per manufacturer's instructions. Raw early/late data (i.e. from .pair files) were loess-normalized to remove signal intensity-dependent bias, and scaled to a reference data set to have the same median absolute deviation (limma package, R/Bioconductor).The early/late ratios were used to generate a smoothed profile (i.e. processed data) using local polynomial smoothing (loess, 300-kb span) for each chromosome using basic functions in the statistical language R. Processed data sets can be graphically displayed (and are also downloadable) on our web site (http://www.replicationdomain.org). Further details can be found in Hiratani et al [PLoS Biology (2008) 6: e245].

source_name: Early-replicating DNA of wildtype naïve mouse embryonic stem cells

label_protocol: Standard NimbleGen protocol (www.nimblegen.com/products/lit/index.html). Briefly, randomly-amplified BrdU-immunoprecipitated DNA samples (1 ug each) were Cy3- or Cy5-labeled by Klenow reaction using end-labeled Cy3- or Cy5-random 9-mers.

growth_protocol: 1:1 Neurobasal (Gibco 12348-017): DMEM/F12 (Gibco 311331-028) with 1x glutamax (Gibco 35050-038), 1x pen/strep (Gibco 14140-122), 1x NEAA (Gibco 11140-035), 1x Na-pyruvate (Gibco 11360-039), 1x N2 (Gibco 17502-048), 1x B27 (Gibco 17504-044), B-Mercaptoethanol and LIF (as usual in ES cell culture), 1 uM MEK1 inhibitor (Gibco PD-0325901), and 3 uM GSK inhibitor (Gibco CHIRON99021)

extract_protocol: Replication timing data were obtained by hybridizing early and late replication intermediates to NimbleGen oligonucleotide arrays, as described in Hiratani et al [PLoS Biology (2008) 6: e245]. Briefly, replication intermediates are prepared from cells that are first pulse-labeled with BrdU and then sorted into early (1st half of S) and late (2nd half of S) stages of S-phase by flow cytometry, followed by anti-BrdU immunoprecipitation of the BrdU-substituted (nascent) replication intermediates that were synthesized either early or late during S-phase. Samples were labeled after unbiased amplification of recovered DNA by whole-genome amplification (WGA; Sigma, GenomePlex). Further details can be found in Hiratani et al [PLoS Biology (2008) 6: e245].

value: naïve embryonic stem cells

source_name: Late-replicating DNA of wildtype naïve mouse embryonic stem cells


title: Poodle-BI_16949_ARRAY187348


title: Poodle-BI_16946_ARRAY187300


title: Poodle-BI_16948_ARRAY187332


title: Poodle-BI_13015_ARRAY187382


title: Poodle-BI_16945_ARRAY187284


title: Poodle-BI_16944_ARRAY187268


title: Poodle-BI_16947_ARRAY187316


title: Replication timing of Suz12 knockout naïve mouse embryonic stem cells

source_name: Early-replicating DNA of Suz12 knockout naïve mouse embryonic stem cells

source_name: Late-replicating DNA of Suz12 knockout naïve mouse embryonic stem cells


title: Poodle-BI_16941_ARRAY187220


title: Poodle-BI_16943_ARRAY187252


title: Poodle-BI_16942_ARRAY187236


title: Poodle-BI_16929_ARRAY187346


title: Poodle-BI_16931_ARRAY187378


title: Poodle-BI_16930_ARRAY187362


title: Poodle-BI_16939_ARRAY187314


title: Poodle-BI_16940_ARRAY187330


title: Poodle-BI_16938_ARRAY187298


title: Poodle-BI_16937_ARRAY187282


title: Poodle-BI_16928_ARRAY187266


title: Poodle-BI_16936_ARRAY187250


title: Poodle-BI_16933_ARRAY187202


title: Poodle-BI_16934_ARRAY187218


title: Poodle-BI_16924_ARRAY187328


title: Poodle-BI_16925_ARRAY187344


title: Poodle-BI_16923_ARRAY187296


title: Poodle-BI_13016_ARRAY187280


title: Poodle-BI_13018_ARRAY187248


title: Poodle-BI_13006_ARRAY187216


title: Poodle-BI_13013_ARRAY187264


title: Poodle-BI_13010_ARRAY187232


title: Poodle-BI_13020_ARRAY187312


title: Poodle-BI_16932_ARRAY187204


title: Poodle-BI_16921_ARRAY187374


title: FinnishSpitz-BI_16788_ARRAY187342


title: FinnishSpitz-BI_16752_ARRAY187310


title: FinnishSpitz-BI_16751_ARRAY187278


title: Poodle-BI_16935_ARRAY187234


title: FinnishSpitz-BI_16779_ARRAY187262


title: FinnishSpitz-BI_16792_ARRAY187214


title: FinnishSpitz-BI_16790_ARRAY187326


title: FinnishSpitz-BI_16772_ARRAY187246


title: FinnishSpitz-BI_16670_ARRAY187230


title: FinnishSpitz-BI_16784_ARRAY187198


title: FinnishSpitz-BI_16789_ARRAY187372


title: Poodle-BI_16927_ARRAY187376


title: Poodle-BI_13014_ARRAY187358


title: Poodle-BI_16926_ARRAY187360


title: FinnishSpitz-BI_16753_ARRAY187340


title: FinnishSpitz-BI_16786_ARRAY187356


title: FinnishSpitz-BI_16780_ARRAY187324


title: FinnishSpitz-BI_16769_ARRAY187308


title: Poodle-BI_16922_ARRAY187200


title: FinnishSpitz-BI_16771_ARRAY187276


title: FinnishSpitz-BI_16781_ARRAY187260


title: FinnishSpitz-BI_16776_ARRAY187244


title: FinnishSpitz-BI_16750_ARRAY187292


title: FinnishSpitz-BI_16767_ARRAY187294


title: FinnishSpitz-BI_16777_ARRAY187228


title: FinnishSpitz-BI_16793_ARRAY187196


title: FinnishSpitz-BI_16763_ARRAY187370


title: FinnishSpitz-BI_16756_ARRAY187354


title: FinnishSpitz-BI_16774_ARRAY187338


title: FinnishSpitz-BI_16757_ARRAY187306


title: FinnishSpitz-BI_16761_ARRAY187274


title: FinnishSpitz-BI_16748_ARRAY187210


title: FinnishSpitz-BI_16778_ARRAY187258


title: FinnishSpitz-BI_16766_ARRAY187226


title: FinnishSpitz-BI_16765_ARRAY187242


title: FinnishSpitz-BI_16775_ARRAY187368


title: FinnishSpitz-BI_16782_ARRAY187194


title: FinnishSpitz-BI_16783_ARRAY187320


title: FinnishSpitz-BI_16787_ARRAY187336


title: FinnishSpitz-BI_16791_ARRAY187304


title: FinnishSpitz-BI_16785_ARRAY187288


title: FinnishSpitz-BI_16762_ARRAY187272


title: FinnishSpitz-BI_16759_ARRAY187290


title: FinnishSpitz-BI_16768_ARRAY187240


title: FinnishSpitz-BI_16764_ARRAY187224


title: FinnishSpitz-BI_16758_ARRAY187208


title: FinnishSpitz-BI_16755_ARRAY187256


title: FinnishSpitz-BI_16773_ARRAY187192


title: GoldenRetriever-BI_09217_ARRAY231366


title: GoldenRetriever-BI_12684_ARRAY231382


title: GoldenRetriever-BI_09199_ARRAY231318


title: FinnishSpitz-BI_16760_ARRAY187322


title: GoldenRetriever-BI_09218_ARRAY231350


title: GoldenRetriever-BI_02636_ARRAY231428


title: GoldenRetriever-BI_02178_ARRAY231364


title: GoldenRetriever-BI_09140_ARRAY231302


title: GoldenRetriever-BI_01957_ARRAY231348


title: GoldenRetriever-BI_22751_ARRAY231300


title: GoldenRetriever-BI_21420_ARRAY231284


title: GoldenRetriever-BI_22321_ARRAY231410


title: GoldenRetriever-BI_21448_ARRAY231346


title: GoldenRetriever-BI_22302_ARRAY231378


title: GoldenRetriever-BI_21694_ARRAY231362


title: GoldenRetriever-BI_21441_ARRAY231330


title: GoldenRetriever-BI_20702_ARRAY231314


title: Rottweiler-BI_12338_ARRAY127938


title: GoldenRetriever-BI_22320_ARRAY231394


title: GoldenRetriever-BI_19927_ARRAY231298


title: GoldenRetriever-BI_19920_ARRAY231282


title: GoldenRetriever-BI_18299_ARRAY231266


title: GoldenRetriever-BI_15753_ARRAY231408


title: GoldenRetriever-BI_15756_ARRAY231424


title: GoldenRetriever-BI_14412_ARRAY231392


title: GoldenRetriever-BI_12671_ARRAY231360


title: GoldenRetriever-BI_12709_ARRAY231376


title: GoldenRetriever-BI_16275_ARRAY231250


title: Wolf-BI_22815_ARRAY231288

organism: Canis lupus


title: DobermanPinscher-BI_20892_ARRAY231310


title: Wolf-BI_22803_ARRAY231240


title: Wolf-BI_22810_ARRAY231272


title: DobermanPinscher-BI_20888_ARRAY231246


title: GoldenRetriever-BI_01949_ARRAY231332


title: GoldenRetriever-BI_01913_ARRAY231252


title: ShetlandSheepdog-BI_07104_ARRAY152002


title: ShetlandSheepdog-BI_07110_ARRAY152018


title: ShetlandSheepdog-BI_07094_ARRAY151922


title: ShetlandSheepdog-BI_07095_ARRAY151938


title: ShetlandSheepdog-BI_07111_ARRAY152034


title: ShetlandSheepdog-BI_07091_ARRAY151890


title: ShetlandSheepdog-BI_07099_ARRAY151970


title: ShetlandSheepdog-BI_07103_ARRAY151986


title: ShetlandSheepdog-BI_07081_ARRAY151874


title: ShetlandSheepdog-BI_07080_ARRAY151858


title: ShetlandSheepdog-BI_07098_ARRAY151954


title: ShetlandSheepdog-BI_07069_ARRAY152016


title: ShetlandSheepdog-BI_07059_ARRAY151968


title: ShetlandSheepdog-BI_07070_ARRAY152032


title: ShetlandSheepdog-BI_07067_ARRAY151984


title: ShetlandSheepdog-BI_07068_ARRAY152000


title: Boxer-BI_04914_ARRAY151936


title: Boxer-BI_04913_ARRAY151920


title: Boxer-BI_07318_ARRAY151904


title: ShetlandSheepdog-BI_13397_ARRAY151872


title: ShetlandSheepdog-BI_13396_ARRAY151856


title: Boxer-BI_07366_ARRAY151888


title: EnglishCockerSpaniel-BI_06835_ARRAY152030


title: EnglishCockerSpaniel-BI_06780_ARRAY152014


title: EnglishCockerSpaniel-BI_06925_ARRAY151998


title: EnglishCockerSpaniel-BI_06843_ARRAY151966


title: EnglishCockerSpaniel-BI_06883_ARRAY151982


title: EnglishCockerSpaniel-BI_06818_ARRAY151918


title: EnglishCockerSpaniel-BI_06838_ARRAY151950


title: ShetlandSheepdog-BI_07092_ARRAY151906


title: EnglishCockerSpaniel-BI_06824_ARRAY151934


title: EnglishCockerSpaniel-BI_06747_ARRAY151902


title: EnglishCockerSpaniel-BI_13390_ARRAY151996


title: EnglishCockerSpaniel-BI_13386_ARRAY151964


title: EnglishCockerSpaniel-BI_13393_ARRAY151854


title: EnglishCockerSpaniel-BI_13385_ARRAY151948


title: EnglishCockerSpaniel-BI_13391_ARRAY152012


title: EnglishCockerSpaniel-BI_13384_ARRAY151932


title: EnglishCockerSpaniel-BI_13381_ARRAY151884


title: EnglishCockerSpaniel-BI_13378_ARRAY151852


title: EnglishCockerSpaniel-BI_13380_ARRAY151868


title: EnglishCockerSpaniel-BI_13377_ARRAY152026


title: EnglishCockerSpaniel-BI_13382_ARRAY151900


title: Basenji-BI_13711_ARRAY152010


title: KerryBlueTerrier-BI_13708_ARRAY151962


title: KerryBlueTerrier-BI_13707_ARRAY151946


title: ChineseCrested-BI_13705_ARRAY151914


title: Basenji-BI_13710_ARRAY151994


title: EnglishCockerSpaniel-BI_13394_ARRAY151870


title: PembrokeWelshCorgi-BI_13797_ARRAY151882


title: PembrokeWelshCorgi-BI_13796_ARRAY151866


title: EnglishCockerSpaniel-BI_13395_ARRAY151886


title: Basenji-BI_13709_ARRAY151978


title: KerryBlueTerrier-BI_13706_ARRAY151930


title: ChineseCrested-BI_13704_ARRAY151898


title: PembrokeWelshCorgi-BI_13795_ARRAY151850


title: EnglishCockerSpaniel-BI_13388_ARRAY151980


title: PembrokeWelshCorgi-BI_13794_ARRAY152024


title: PembrokeWelshCorgi-BI_13812_ARRAY151992


title: PembrokeWelshCorgi-BI_13810_ARRAY151960


title: EnglishCockerSpaniel-BI_13383_ARRAY151916


title: PembrokeWelshCorgi-BI_13806_ARRAY151896


title: EnglishCockerSpaniel-BI_13392_ARRAY152028


title: PembrokeWelshCorgi-BI_13807_ARRAY151912


title: PembrokeWelshCorgi-BI_13805_ARRAY151880


title: PembrokeWelshCorgi-BI_13803_ARRAY151848


title: PembrokeWelshCorgi-BI_13793_ARRAY152022


title: PembrokeWelshCorgi-BI_13804_ARRAY151864


title: PembrokeWelshCorgi-BI_13801_ARRAY151990


title: PembrokeWelshCorgi-BI_13799_ARRAY151958


title: PembrokeWelshCorgi-BI_13813_ARRAY152008


title: PembrokeWelshCorgi-BI_13792_ARRAY151926


title: PembrokeWelshCorgi-BI_13790_ARRAY151894


title: PembrokeWelshCorgi-BI_13811_ARRAY151976


title: PembrokeWelshCorgi-BI_13788_ARRAY151862


title: PembrokeWelshCorgi-BI_13786_ARRAY152020


title: PembrokeWelshCorgi-BI_13785_ARRAY152004


title: PembrokeWelshCorgi-BI_13787_ARRAY151846


title: PembrokeWelshCorgi-BI_13782_ARRAY151956


title: PembrokeWelshCorgi-BI_13808_ARRAY151928


title: PembrokeWelshCorgi-BI_13789_ARRAY151878


title: PembrokeWelshCorgi-BI_13781_ARRAY151940


title: PembrokeWelshCorgi-BI_13791_ARRAY151910


title: PembrokeWelshCorgi-BI_13780_ARRAY151924


title: PembrokeWelshCorgi-BI_13809_ARRAY151944


title: PembrokeWelshCorgi-BI_13777_ARRAY151876


title: PembrokeWelshCorgi-BI_13783_ARRAY151972


title: PembrokeWelshCorgi-BI_13778_ARRAY151892


title: Rottweiler-BI_05749_ARRAY127772


title: PembrokeWelshCorgi-BI_13779_ARRAY151908


title: Rottweiler-BI_05747_ARRAY127740


title: Akita-BI_05418_ARRAY127708


title: Akita-BI_05417_ARRAY127692


title: PembrokeWelshCorgi-BI_13800_ARRAY151974


title: Mastiff-BI_03706_ARRAY127690


title: Mastiff-BI_03226_ARRAY127674


title: Mastiff-BI_02569_ARRAY127658


title: Mastiff-BI_05414_ARRAY127642


title: Mastiff-BI_05412_ARRAY127784


title: Mastiff-BI_03471_ARRAY127768


title: Mastiff-BI_05411_ARRAY127800


title: Rottweiler-BI_05755_ARRAY127720


title: Mastiff-BI_03473_ARRAY127752


title: Mastiff-BI_05413_ARRAY127816


title: Rottweiler-BI_05753_ARRAY127736


title: Rottweiler-BI_05754_ARRAY127704


title: EnglishBulldog-BI_03422_ARRAY127672


title: Pekingese-BI_05745_ARRAY127782


title: PembrokeWelshCorgi-BI_13776_ARRAY151860


title: Rottweiler-BI_03657_ARRAY127656


title: Rottweiler-BI_05752_ARRAY127820


title: Pekingese-BI_05743_ARRAY127766


title: Pekingese-BI_05742_ARRAY127734


title: EnglishBulldog-BI_05466_ARRAY127688


title: Pekingese-BI_05739_ARRAY127686


title: Rottweiler-BI_05751_ARRAY127804


title: Pekingese-BI_05738_ARRAY127670


title: AustralianCattleDog-BI_05732_ARRAY127654


title: Pekingese-BI_05740_ARRAY127702


title: AustralianCattleDog-BI_05731_ARRAY127638


title: AustralianCattleDog-BI_05729_ARRAY127812


title: AustralianCattleDog-BI_05728_ARRAY127796


title: AustralianCattleDog-BI_05727_ARRAY127780


title: AustralianCattleDog-BI_05726_ARRAY127764


title: AustralianCattleDog-BI_05724_ARRAY127732


title: AustralianCattleDog-BI_05737_ARRAY127716


title: Rottweiler-BI_12289_ARRAY127814


title: GermanShortHairedPointer-BI_05714_ARRAY127684


title: AustralianCattleDog-BI_05723_ARRAY127700


title: GermanShortHairedPointer-BI_05711_ARRAY127636


title: Pekingese-BI_05744_ARRAY127750


title: GermanShortHairedPointer-BI_05712_ARRAY127652


title: GermanShortHairedPointer-BI_05713_ARRAY127668


title: GermanShortHairedPointer-BI_05710_ARRAY127810


title: GermanShortHairedPointer-BI_05721_ARRAY127778


title: GermanShortHairedPointer-BI_05709_ARRAY127794


title: GermanShortHairedPointer-BI_05708_ARRAY127762


title: GermanShortHairedPointer-BI_05707_ARRAY127746


title: GermanShortHairedPointer-BI_05706_ARRAY127730


title: EnglishSetter-BI_05678_ARRAY127698


title: EnglishSetter-BI_05675_ARRAY127650


title: EnglishSetter-BI_05677_ARRAY127682


title: EnglishSetter-BI_05674_ARRAY127634


title: EnglishSetter-BI_05672_ARRAY127792


title: EnglishSetter-BI_05679_ARRAY127714


title: EnglishSetter-BI_05671_ARRAY127776


title: EnglishSetter-BI_05673_ARRAY127808


title: Pug-BI_05664_ARRAY127744


title: Pug-BI_05663_ARRAY127728


title: Pug-BI_05662_ARRAY127712


title: Pug-BI_05659_ARRAY127664


title: BassetHound-BI_05645_ARRAY127774


title: Pug-BI_05665_ARRAY127632


title: Pug-BI_05661_ARRAY127696


title: Pug-BI_05658_ARRAY127648


title: Pug-BI_05660_ARRAY127680


title: Pug-BI_05656_ARRAY127790


title: Pug-BI_05657_ARRAY127806


title: BassetHound-BI_05655_ARRAY127742


title: BassetHound-BI_05646_ARRAY127710


title: BassetHound-BI_05643_ARRAY127694


title: BassetHound-BI_05640_ARRAY127662


title: BassetHound-BI_05642_ARRAY127678


title: BassetHound-BI_05644_ARRAY127758


title: BassetHound-BI_05647_ARRAY127726


title: BassetHound-BI_05641_ARRAY127646


title: EnglishSetter-BI_05670_ARRAY127760


title: BassetHound-BI_05654_ARRAY127630


title: Greyhound-BI_15216_ARRAY164582


title: Greyhound-BI_15217_ARRAY164550


title: Greyhound-BI_15212_ARRAY164566


title: Greyhound-BI_15214_ARRAY164502


title: Greyhound-BI_15215_ARRAY164518


title: Greyhound-BI_15207_ARRAY164486


title: Greyhound-BI_15208_ARRAY164454


title: FinnishSpitz-BI_16749_ARRAY187212


title: Greyhound-BI_15204_ARRAY164438


title: Greyhound-BI_15203_ARRAY164596


title: Greyhound-BI_15209_ARRAY164422


title: Greyhound-BI_15211_ARRAY164564


title: ChineseCrested-BI_13199_ARRAY164462


title: ChineseCrested-BI_13198_ARRAY164446


title: Greyhound-BI_15205_ARRAY164580


title: Greyhound-BI_15206_ARRAY164598


title: ChineseCrested-BI_13195_ARRAY164572


title: ChineseCrested-BI_13196_ARRAY164588


title: ChineseCrested-BI_13197_ARRAY164414


title: ChineseCrested-BI_13185_ARRAY164430


title: ChineseCrested-BI_13194_ARRAY164540


title: EnglishSetter-BI_05676_ARRAY127666


title: ChineseCrested-BI_13205_ARRAY164508


title: ChineseCrested-BI_13207_ARRAY164476


title: ChineseCrested-BI_13208_ARRAY164460


title: ChineseCrested-BI_13192_ARRAY164444


title: ChineseCrested-BI_13204_ARRAY164556


title: ChineseCrested-BI_13209_ARRAY164586


title: ChineseCrested-BI_13206_ARRAY164492


title: ChineseCrested-BI_13210_ARRAY164412


title: ChineseCrested-BI_13211_ARRAY164428


title: ChineseCrested-BI_13182_ARRAY164538


title: ChineseCrested-BI_13213_ARRAY164506


title: Greyhound-BI_15210_ARRAY164452


title: ChineseCrested-BI_13191_ARRAY164490


title: ChineseCrested-BI_13217_ARRAY164474


title: ChineseCrested-BI_13183_ARRAY164458


title: ChineseCrested-BI_13200_ARRAY164426


title: ChineseCrested-BI_13215_ARRAY164410


title: ChineseCrested-BI_13201_ARRAY164442


title: ChineseCrested-BI_13202_ARRAY164584


title: ChineseCrested-BI_13186_ARRAY164472


title: ChineseCrested-BI_13219_ARRAY164568


title: ChineseCrested-BI_13184_ARRAY164488


title: ChineseCrested-BI_13216_ARRAY164536


title: ChineseCrested-BI_13203_ARRAY164504


title: ChineseCrested-BI_13188_ARRAY164440


title: ChineseCrested-BI_13187_ARRAY164456


title: GoldenRetriever-BI_12366_ARRAY134506


title: ChineseCrested-BI_13218_ARRAY164552


title: ChineseCrested-BI_13189_ARRAY164424


title: ChineseCrested-BI_13190_ARRAY164408


title: GoldenRetriever-BI_11094_ARRAY134426


title: Pekingese-BI_05741_ARRAY127718


title: GoldenRetriever-BI_06499_ARRAY134410


title: ChineseCrested-BI_13181_ARRAY164554


title: GoldenRetriever-BI_09375_ARRAY134394


title: GoldenRetriever-BI_11096_ARRAY134536


title: GoldenRetriever-BI_03672_ARRAY134378


title: GoldenRetriever-BI_12972_ARRAY134436


title: GoldenRetriever-BI_02021_ARRAY134546


title: GoldenRetriever-BI_02660_ARRAY134404


title: GoldenRetriever-BI_02165_ARRAY134452


title: GoldenRetriever-BI_01933_ARRAY134388


title: GoldenRetriever-BI_09450_ARRAY134554


title: ChineseCrested-BI_13180_ARRAY164570


title: GoldenRetriever-BI_12968_ARRAY134490


title: GoldenRetriever-BI_12229_ARRAY134466


title: GoldenRetriever-BI_02325_ARRAY134498


title: GoldenRetriever-BI_02630_ARRAY134420


title: SharPei-BI_12344_ARRAY134434


title: GoldenRetriever-BI_12973_ARRAY134514


title: GoldenRetriever-BI_02875_ARRAY134474


title: GoldenRetriever-BI_11117_ARRAY134442


title: SharPei-BI_12343_ARRAY134450


title: SharPei-BI_12345_ARRAY134418


title: SharPei-BI_12936_ARRAY134386


title: GoldenRetriever-BI_03195_ARRAY134482


title: SharPei-BI_12937_ARRAY134370


title: SharPei-BI_12938_ARRAY134544


title: Greyhound-BI_15213_ARRAY164470


title: SharPei-BI_12935_ARRAY134402


title: SharPei-BI_12941_ARRAY134496


title: SharPei-BI_12942_ARRAY134480


title: SharPei-BI_12943_ARRAY134464


title: SharPei-BI_12947_ARRAY134400


title: SharPei-BI_12948_ARRAY134384


title: SharPei-BI_12949_ARRAY134368


title: GoldenRetriever-BI_02209_ARRAY134530


title: SharPei-BI_12950_ARRAY134542


title: SharPei-BI_12951_ARRAY134526


title: SharPei-BI_12952_ARRAY134510


title: SharPei-BI_12953_ARRAY134494


title: SharPei-BI_12954_ARRAY134478


title: SharPei-BI_12955_ARRAY134462


title: SharPei-BI_12956_ARRAY134446


title: Dachshund-BI_07015_ARRAY134492


title: SharPei-BI_12958_ARRAY134414


title: SharPei-BI_12959_ARRAY134398


title: SharPei-BI_12957_ARRAY134430


title: SharPei-BI_12939_ARRAY134528


title: Dachshund-BI_06945_ARRAY134428


title: Dachshund-BI_06939_ARRAY134460


title: Dachshund-BI_06946_ARRAY134412


title: Dachshund-BI_06934_ARRAY134382


title: Dachshund-BI_06937_ARRAY134508


title: Dachshund-BI_07018_ARRAY134540


title: Dachshund-BI_06955_ARRAY134380


title: Dachshund-BI_07016_ARRAY134366


title: Dachshund-BI_06948_ARRAY134396


title: GoldenRetriever-BI_02354_ARRAY127612


title: GoldenRetriever-BI_03123_ARRAY127580


title: Dachshund-BI_06942_ARRAY134444


title: GoldenRetriever-BI_02654_ARRAY127564


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