title: Single cell analyses reveals a non-canonical EZH2 activity as main driver of RA resistance in PLZF/RARA leukemia [ChIP-seq]

first: Estelle

last: Duprez

summary: Resistance to treatment is due to the heterogeneity of the tumor which contains a subset of cancer cells that escape treatment and are responsible for the relapse. We took advantage of the PLZF/RARA retinoic acid (RA) resistant acute promyelocytic leukemia (APL) model to catch relapse-initiating cell features and their vulnerabilities. By developing an integrative single-cell multi-omics analysis (scRNA-seq and scATAC-seq), we uncovered transcriptional and chromatin heterogeneity of the PLZF/RARA APL blasts. We highlighted a subset of cells insensitive to RA-induced differentiation with a strong DNA repair signature ("Rep" cluster) and exhibiting a fine tuned transcriptional network targeting the histone methyltransferase Ezh2. Combining epigenomic profiling with mouse-derived models for Ezh2 catalytic inhibition or total KO, we revealed an independent methyltransferase Ezh2 activity linked to RA resistance. These findings demonstrate the power of single-cell multi-omics integration to highlight paths to sensitize therapy-resistant leukemia cells

overall_design: ChIPseq for H3K27ac, H3K27me3, H3K4me3, H3K4me1 performed on murine purified promyelocytes expressing the PLZF/RARA  oncogonic fusion

first: Mathilde

last: Poplineau

first: Mazuel

last: Adrien


title: Gene expression analysis in mice with knockout of Xbp1 in intestinal epithelial cells during graft-versus-host disease

status: Public on Aug 22 2022

city: Freiburg

first: Geoffroy

last: Andrieux

address: Breisacherstr 153

country: Germany

institute: University clinics Freiburg

summary: We analyzed gene expression in mice with a deletion of Xbp1 in their intestinal epithelial cells and their littermates during graft-versus-host disease. Xbp1 is a central transcription factor that mediates the unfolded protein response following endoplasmic reticulum stress.

overall_design: Villin-Cre Xbp1 fl/fl mice (Knock-out, KO) and Xbp1 fl/fl (wildtype, WT) littermates underwent allogeneic hematopoietic cell transplantation in a major-mismatch-model with total body irradiation as a conditioning treatment. On day 14 after transplantation, RNA from the small intestine of recipient mice was isolated and Affymetrix microarrays were performed.

first: Petya

last: Apostolova

first: Eileen

last: Haring

first: Melanie

last: Boerries


title: Single cell analyses reveals a non-canonical EZH2 activity as main driver of RA resistance in PLZF/RARA leukemia [scATAC-seq]

city: Marseille

address: 27 Boulevard Lei Roure

country: France

institute: CRCM

type: Genome binding/occupancy profiling by high throughput sequencing

overall_design: Single-cell ATAC-seq performed on murine purified promyelocytes expressing the PLZF/RARA  oncogenic fusion


title: CDK9 and PP2A regulate RNA polymerase II transcription termination and coupled RNA maturation

city: Leicester

first: Michael

last: Tellier

state: Select State

address: Lancaster Road

department: Department of Molecular and Cell Biology

country: United Kingdom

institute: University of Leicester

type: Expression profiling by high throughput sequencing

summary: CDK9 is a kinase critical for the productive transcription of protein-coding genes by RNA polymerase II (pol II). As part of P-TEFb, CDK9 phosphorylates the carboxyl-terminal domain (CTD) of pol II and elongation factors, which allows pol II to elongate past the early elongation checkpoint (EEC) encountered soon after initiation. We show that, in addition to halting pol II at the EEC, loss of CDK9 activity causes premature termination of transcription across the last exon, loss of polyadenylation factors from chromatin, and loss of polyadenylation of nascent transcripts. Inhibition of the phosphatase PP2A abrogates the premature termination and loss of polyadenylation caused by CDK9 inhibition, indicating that this kinase/phosphatase pair regulates transcription elongation and RNA processing at the end of protein-coding genes. We also confirm the splicing factor SF3B1 as a target of CDK9 and show that SF3B1 in complex with polyadenylation factors is lost from chromatin after CDK9 inhibition. These results emphasize the important roles that CDK9 plays in coupling transcription elongation and termination to RNA maturation downstream of the EEC.

overall_design: mNET-seq of total RNA polymerase II in HeLa cells treated with DMSO or the CDK9 inhibitor, DRB, for 5, 10, 15, or 30 minutes. Nuclear 3'seq in HeLa cells treated for 30 minutes with DMSO or DRB, or for 30 minutes with TNFα followed by 30 minutes with DMSO or DRB. Mouse spiked-in total RNA polymerase II ChIP-seq in HeLa cells treated with DMSO; the CDK9 inhibitor, DRB; the PP2A inhibitor, Calyculin A (CA); or DRB & CA for 30 minutes.

first: Justyna

last: Zaborowska

first: Jonathan

last: Neve

first: Takayuki

last: Nojima

first: Svenja

last: Hester

first: Marjorie

last: Fournier

first: Andre

last: Furger

first: Shona

last: Murphy


title: Fetal origin of sex-bias brain aging

city: Columbia

first: Susanta

middle: K.

last: Behura

state: Missouri

address: 920 East Campus Drive

department: Division of Animal Sciences

country: USA

institute: Univeristy of Missouri

type: Methylation profiling by high throughput sequencing

summary: DNA methylation plays crucial roles during fetal development as well as aging. Whether the aging of the brain is programmed at the fetal stage remains untested. To test this hypothesis, mouse epigenetic clock (epiclock) was profiled in fetal (gestation day 15), postnatal (day 5), and aging (week 70) brain of male and female C57BL/6J inbred mice. Data analysis showed that on week 70, the female brain was epigenetically younger than the male brain. Predictive modeling by neural network identified specific methylations in the brain at the developing stages that were predictive of epigenetic state of the brain during aging. Transcriptomic analysis showed coordinated changes in the expression of epiclock genes in the fetal brain relative to the placenta. Whole-genome bisulfite sequencing identified sites that were methylated both in the placenta and fetal brain in a sex-specific manner. Epiclock genes and genes associated with specific signaling pathways, primarily the gonadotropin-releasing hormone receptor (GnRHR) pathway, were associated with the sex-bias methylations in the placenta as well as the fetal brain. Transcriptional crosstalk among the epiclock and GnRHR pathway genes was evident in the placenta that was maintained in the brain during development as well as aging. Collectively, these findings suggest that sex differences in the aging of the brain are of fetal origin and epigenetically linked to the placenta.

overall_design: The day 15 placenta and brain of male and female fetuses of wild-type (C57BL/6) mice were analyzed by whole-genome bisulfite sequencing (WGBS).

first: Maliha

last: Islam

first: Monica

last: Strawn

middle: K


title: 3D chromatin organization changes modulate adipogenesis and osteogenesis [RNA-seq]

city: Xi'an

first: Ruohan

last: Hao

state: Shaanxi

address: No.28 West Xianning Road

country: China

institute: Xi'an Jiaotong University

summary: Human mesenchymal stem cells (hMSCs) can be differentiated into adipocytes and osteoblasts. While the transcriptomic and epigenomic changes during adipogenesis and osteogenesis have been characterized, what happens to the chromatin loops is hardly known. Here we induced hMSCs to adipogenic and osteogenic differentiation, and performed 2 kb resolution Hi-C experiments for loop detection and generated RNA-seq, histone modification ChIP-seq and ATAC-seq data for integrative analysis before and after differentiation. We quantitatively identified differential contact loops and unique loops. After integrating with multi-omics data, we demonstrate that strengthened loops after differentiation are associated with gene expression activation. Specially, unique loops are linked with cell fate determination. We also proposed loop-mediated regulatory networks and identified IRS2 and RUNX2 as being activated by cell-specific loops to facilitate adipocytes and osteoblasts commitment, respectively. These results are expected to help better understand the long-range regulation in controlling hMSC differentiation, and provide novel targets for studying adipocytes and osteoblasts determination.

overall_design: Hi-C experiment was conducted to reveal 3D chromatin changes before and after human mesenchymal stem cells differentiation into adipocytes and osteoblasts. Comprehensively profiling of gene expression, enhancer activity and chromatin accessibility using RNA-seq, H3K4me1 and H3K27ac ChIP-seq, and ATAC-seq were estimated at the same time.

first: Ruo-Han

first: Yan

last: Guo

first: Jing

first: Yu

last: Rong

first: Shi

last: Yao

first: Yi-Xiao

last: Chen

first: Shan-Shan

last: Dong

first: Dong-Li

last: Zhu

first: Hao

first: Tie-Lin

last: Yang


title: 3D chromatin organization changes modulate adipogenesis and osteogenesis

summary: This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: 3D chromatin organization changes modulate adipogenesis and osteogenesis [ChIP-seq]


title: 3D chromatin organization changes modulate adipogenesis and osteogenesis [ATAC-seq]


title: 3D chromatin organization changes modulate adipogenesis and osteogenesis [Hi-C]


title: Early host-micorbe interactionin a peri-implant mucosa-biofilm model

city: Hannover

first: Carina

last: Mikolai

address: Carl-Neuberg-Str. 1

department: Department of Prosthetic Dentistry and Biomedical Materials Science

institute: Hannover Medical School

summary: Oral health is associated with a symbiotic microbial community and host-microbe homeostasis is maintained by the controlled immune response. Various factors can disrupt this homeostasis. Dysbiosis, which is characterized by increased immune response and a shift in the microbiome, contributes the pathogenesis of peri-implantitis. Peri-implant mucosa and commensal bacteria play important roles in the maintenance of host-microbe homeostasis, but little is known about how they interact. We have therefore investigated the early host-microbe interaction between a commensal multispecies biofilm (Streptococcus oralis, Actinomyces naeslundii, Veillonella dispar, Porphyromonas gingivalis) and peri-implant mucosa at 24 and 48 h. Our in vitro peri-implant mucosa-biofilm model contained organotypic oral mucosa, implant material and biofilm. After 24 h, the biofilm induced a modest innate immune response in the peri-implant mucosa by the upregulation of 5 genes related to immune and inflammatory response and the increased secretion of IL-6 and CCL20. This controlled immune response protected tissue integrity and the peri-implant mucosa remained intact. The secreted antibacterial proteins human β-Defensins-1, -2, and CCL20 controlled the overgrowth of the biofilm by reducing its volume - without affecting the live/dead ratio or bacterial distribution. Thus, host-microbe homeostasis was established within the first 24 h. In contrast, host-microbe homeostasis was disrupted after 48 h. The mucosa was damaged and detached from the implant, due to the induced downregulation of cell adhesion related genes. The immune response was enhanced by upregulation of additional genes related to the immune and inflammatory response and increased secretion of IL-1β, TNF-α, and CCL20. Moreover, bacterial distribution was altered, with an increased proportion of V. dispar. The disrupted host-microbe homeostasis could lead to incipient dysbiosis. This deeper understanding of the early host-microbe interaction at the peri-implant site may provide the basis for new strategies to improve the prevention and therapy of peri-implant diseases.

overall_design: Multispecies biofilm induced gene expression in an organotypic peri-implant mucosa was analyzed after 24 and 48 h. Four peri-implant mucosa models for each condition were used which were produced in three independent experiments.

first: Andreas

last: Winkel

first: Meike

last: Stiesch


title: Expression data from human regulatory T cells of short chain fatty acid propionic acid treated MS patients

first: Ori

last: Staszewski

address: Breisacher Str. 64

department: Institute of Neuropathology

institute: University Medical Center Freiburg

summary:
Short chain fatty acids were shown to affect regulatory immune response in context of autoimmune diseases like multiple sclerosis (MS). Recent studys in an animal model of MS revealed significant impact of short chain fatty acid propionate (PA) on the differentiation towards regulatory Tcells (Treg). In a translational proof of concept study PA was administered to relapse remitting MS patients. We observed an increase of Treg in peripheral blood as well as functional improvement in Treg suppressive capacity beside a decrease of proinflammatory Thelper1 and 17 cells.
To investigate underlying mechanisms of the observed shift in immune cell balance, intensive transcriptomic analysis on isolated Treg from whole blood PBMC of PA treated relapse remitting MS patients was performed at baseline, 14 days and 90 days of treatment.

overall_design: PA was supplemented on daily basis in three new diagnosed relapse remitting MS patients for 90 consecutive days. Blood was collcected in EDTA tubes with subsequent PBMC isolation by density gradient centrifugation. Treg were isolated by MACS technology, stored in RNA protect reagent and immediatly frozen on -80°C for subsequent microarray analysis to compare all three timepoints of treatment.

first: A

last: Haghikia

first: M

last: Prinz

first: R

last: Gold

last: Duscha

first: O

first: N

last: Dokalis


title: Endovascular Device for Endothelial Cell Sampling

status: Public on Aug 21 2022

city: Stockholm

first: Mikael

last: Sandell

state: Solna

address: Akademiska stråket 1

department: Clinical Neuroscience

country: Sweden

institute: Karolinska Institutet

summary: We have developed an endovascular catheter-based device for sampling of the endothelium, intended for RNA-seq analysis. With an outer diameter of 0.23 mm it is capable of reaching peripheral vessels for endothelial sampling, and favourably compares to other approaches with stent retrievers or similar tools. Here, we have collected samples from liver and kidney vessels from swine and performed RNA-sequencing to validate the sample quality.

overall_design: Various samples were extracted for comparison. 3 blood samples, 10 endothelial samples with the new device (5 from liver, 5 from kidney), 4 negative control samples from a wire without the novel device attached as well as 4 positive control samples extracted surgically from a blood vessel.

first: Arvin

last: Chireh

first: Staffan

last: Holmin

first: Niclas

last: Roxhed


title: TNF-R1 Co-opts TLR4 Pathway Components CD14, TRAM and TRIF to Drive TNF-Induced Inflammation and Toxicity

city: Medford

first: rebecca

last: batorsky

state: MA

address: 419 Boston Ave

institute: Tufts University

summary: We report the application of single-cell-sequencing technology for the profiling of TRIF-dependent changes in immune cell populations, and TRIF-dependent cellular responses in the spleens of mice 4 hours after intravenous injection with recombinant murine TNF.

overall_design: Examination of the effect of TRIF-deficiency on cellular responses in the spleens of TNF-injected mice

first: Alexander

last: Poltorak

first: Rebecca

last: Batorsky


title: HDAC complex non-enzymatic inhibitor confers therapeutic effects with minimal transcriptomic changes

city: Cambridge

first: Samira

last: Ibrahim

address: 400 Technology Square

institute: Ragon Institute

summary: Targeting the biological function of an HDAC complex identifies a protein interaction inhibitor that solves the longstanding specificity issue associated with enzymatic inhibition.

overall_design: Neuroblastoma cells were treated with HDAC inhibitors for scRNA-seq

first: Julien

last: Olivet

first: SoonGang

last: Choi

first: Salvador

last: Sierra

first: Tina

middle: M

last: OÕGrady

first: Mario

last: de la Fuente Revenga

first: Florent

last: Laval

first: Vladimir

middle: V

last: Botchkarev Jr.

first: Christoph

last: Gorgulla

first: Paul

middle: W

last: Coote

first: JŽrŽmy

last: Blavier

first: Ezekiel

middle: A

last: Geffken

first: Jimit

last: Lakhani

first: Kijun

last: Song

first: Zoe

middle: C

last: Yeoh

first: Bin

last: Hu

first: Anthony

last: Varca

first: Jonathan

last: Bruyr

first: Tasneem

last: Jivanjee

first: Joshua

middle: D

last: Bromley

first: Sarah

last: Nyquist

first: Aaron

last: Richardson

first: Hong

last: Yue

first: Yang

last: Wang

first: Natalia

last: Calonghi

first: Alessandra

last: Stefan

first: Kerstin

last: Spirohn

first: Didier

last: Vertommen

first: Maria

middle: F

last: Baietti

first: Irma

last: Lemmens

first: Hyuk-Soo

last: Seo

first: Mikhail

middle: G

last: Dozmorov

first: Luc

last: Willems

first: Jan

last: Tavernier

first: Kalyan

last: Das

first: Eleonora

last: Leucci

first: Alejandro

last: Hochkoeppler

first: Zhen-Yu

last: Jim Sun

first: Michael

last: Calderwood

first: Tong

last: Hao

first: Alex


title: PDS5A and PDS5B differentially affect gene expression without altering cohesin localization across the genome [RNA-seq]

city: Chapel Hill

first: Jill

last: Dowen

state: NC

address: 250 Bell Tower Drive

institute: University of North Carolina at Chapel Hill

summary:
Purpose: Cohesin is an important structural regulator of the genome. Whether cohesin HEAT repeat accessory proteins PDS5A and PDS5B differentially contribute to cohesin function remains unclear. The purpose of this study is to interrogate how PDS5A and PDS5B affect cohesin localization and gene expression in mouse embronic stem cells (mESCs)
Method: The role of PDS5A and PDS5B in gene regulation was assessed by performing RNA-seq in wildtype and CRISPR-Cas9 genome edited PDS5 knockout mouse embryonic stem cells (mESCs). The redundancy of the PDS5s was addressed by using siRNA against PDS5B in a PDS5A-knockout background. Whether PDS5 and STAG proteins have selective roles in gene expression was addressed by using siRNA against STAG1 and STAG2 in a PDS5A-KO background

overall_design: RNA-seq was performed in wild type mESCs, PDS5-knockout CRISPR-Cas9 genome edited mESCs, and PDS5A-knockout mESCs with siRNA depletion of PDS5B, STAG1, or STAG2, all in triplicate.

first: Nicole

middle: L

last: Arruda

first: Audra

last: Bryan


title: Deleterious effects of high sucrose diet on intestinal homeostasis in mice

city: Vandoeuvre-lès-Nancy

first: Sebastien

last: Hergalant

address: Faculté de Médecine. 9 avenue de la forêt de Haye

department: Bioinformatics

institute: INSERM

summary:
Objective Western Diet (WD) appears to be an important factor associated with inflammatory bowel diseases (IBD). Refined sugars represent up to 40% of caloric intake in industrialized countries. Unlike fats, the impact of dietary sugar on healthy and inflamed intestine remains poorly described.    Design We investigated the effects of a high sucrose diet (HSD) on dextran sulfate sodium (DSS)-induced colitis and on healthy intestine in mice. Several techniques ranging from macroscopic to molecular were used in vivo and direct effect of sugars was examined in cellulo on Caco-2 cell distinguishing differential effect of fructose and glucose.
Results During established colitis in mice, HSD aggravated inflammation by increasing gut permeability, raising immune cells in spleen and impairing autophagy process in colonic mucosa. On healthy intestine, HSD caused spontaneous endoscopic lesions, systemic broad immunosuppression and dysregulation of stress-related genes, associated with gut microbiota dysbiosis. Global reprogramming of colonic transcriptome was detected in HSD-fed mice and amazingly, functional annotations demonstrated association with IBD and “colitis” without DSS-treatment. In vitro, low dose of fructose as well as high dose of glucose induced alteration of junctions confirming the deleterious effects of sugar on intestine. These effects seem to be partially reversible on microbiome and transcriptome of mice after switching back to normal diet.   Conclusions Our results demonstrated for the first time that under pathological conditions mimicking pre-diabetes (mild hyperglycemia-associated with overweight), a pre-IBD state is established and depending on host sensitivity, in colitis conditions, this exacerbates the inflammation severity by disturbing cell-cell junction organization and autophagy process.

overall_design: 37 samples divided in 4 diet groups : Control Diet (CD), High Sucrose Diet (HSD) during 8 weeks or 16 weeks and HSD+CD (HSD 8 weeks + CD 8 weeks) and subdivided in two groups DSS-treated and not (DSS+/DSS-) ; CD DSS- ; N = 5 ; biological replicates / CD DSS+ ; N = 4 ; biological replicates / HSD8 DSS- ; N = 5 ; biological replicates / HSD8 DSS+ ; N = 5 ; biological replicates / HSD16 DSS- ; N = 5 ; biological replicates / HSD16 DSS+ ; N = 4 ; biological replicates / HSD+CD DSS- ; N = 5 ; biological replicates / HSD+CD DSS+ ; N = 4 ; biological replicates.

first: Djésia

last: Arnone

first: Sébastien

first: Laurent

last: Peyrin-Biroulet


title: Chronic exposure to butyl-paraben causes photosensitivity disruption and memory impairment in adult zebrafish

city: Nowon-gu

first: Kitae

last: Kim

address: Gongneung-ro

country: South Korea

institute: Seoul national university of science and technology

summary: Limited studies on neurotoxicity following chronic exposure to butyl-paraben (BuP) have been conducted. In this study, neurobehavior in zebrafish adults was assessed using a novel tank test, photomotor response tests, and T-maze tests after exposure to BuP for 28 days at the concentrations of 0, 0.01, 0.1, and 1.0 mg/L. To comprehensively understand the underlying molecular perturbations in the brain, alterations in transcripts, neurotransmitters, and neurosteroids were measured. We found that BuP penetrated the blood-brain barrier and impaired neurobehavior in photosensitivity at 1.0 mg/L and in memory at 0.1 and 1.0 mg/L. RNA-seq analysis showed that phototransduction, tight junctions, and neuroactive ligand receptor activity were significantly affected, which explains the observed abnormal neurobehaviors. Neurosteroid analysis revealed that BuP increased cortisol levels in a concentration-dependent manner and specifically reduced allopregnanolone levels at all tested concentrations, suggesting that cortisol and allopregnanolone are significant neurosteroid markers associated with photosensitivity and memory deficits. Collectively, we demonstrated that BuP can cross the blood-brain and modulates the levels of transcripts, associated with phototransduction and circadian rhythm, and neurosteroidal cortisol and allopregnanolone, resulting in abnormal neurobehavioral responses to light stimulation and learning and memory.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for control and butylparaben treated groups.

first: Jiwon

first: Seong

middle: S

first: Kyu-Seok

last: Hwang

first: Hae-Chul

last: Park

first: Sung-Hee

last: Cho

first: Myung

last: Bae

first: Ki-Tae


title: Impacts of Gestational FireMaster 550 (FM 550) Exposure on the Neonatal Cortex are Sex Specific and Largely Attributable to the Organophosphate Esters

status: Public on Aug 20 2022

city: Raleigh

first: Heather

last: Patisaul

state: North Carolina

institute: North Carolina State University

summary: To investigate the potential underlying neurotoxic effect of developmental exposure to flame retardant mixture, Fire Master 550, or it brominated and organophosphate we performed gene expression profiling in PND1 rat prefrontal cortex.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for PND1 prefrontal cortex of  male and females following developmental exposure.

first: Shannah

last: Witchey

first: Michael

last: Doyle

first: Jacob

last: Fredenburg

first: Genevieve

last: St. Armour

first: Brian

last: Horman

first: Melanie

middle: T

last: Odenkirk

first: David

last: Aylor

first: Erin

last: Baker

middle: B


title: PDS5A and PDS5B differentially affect gene expression without altering cohesin localization across the genome

first: Jill

last: Dowen


title: A novel mechanism of bacteria to adapt to nutrient deprivation via the ribosome silencing factor RsfS (reference number: NMICROBIOL-19112987)

city: guangzhou

first: zhang

last: hong

state: guangdong province

address: Huangpu Boulavard West Jinan uinversity

institute: zhanghong

summary: The factor RsfS is present in almost all bacteria and organelles. RsfS is important under conditions of nutrient downshifts leading to decreasing growth rates. A common feature of these conditions is a strong reduction of the translation capacity revealed by polysomal fraction decrease and a vast appearance of vacant 70S ribosomes, which might cause a devastating energy drain by stimulating the activity of GTPase proteins e.g. EF-G with idle ribosomes. Here we show that RsfS blocks association of free ribosomal subunits and induces dissociation exclusively of vacant ribosomes rather than of programmed ribosomes carrying tRNAs. As a consequence, RsfS reduces the abundance of the cellular translational apparatus, and the EF-G dependent burst of GTP cleavage in the presence of vacant 70S ribosomes as well as with 30S and 50S subunits is decreased. These observations hint to a regulatory role of RsfS by utilizing cellular resource in an economic way under conditions, where the amino acids are limited and energy has to be saved.

overall_design: Ribo-seq of E. coli strain BW25113 and BW25113_ΔRsfS in M9 minimal medium.

first: Hong

last: Zhang

first: Gong


title: Bulk RNA-Seq for MDSCs

city: Kansas City

first: Shiyuan

middle: (Cynthia)

last: Chen

state: MO

department: Computational Biology

institute: Stowers Institute for Medical Research

summary: Myeloid-derived suppressor cells (MDSCs) as a population of myeloid cells enriched in cancer patients with immunosuppressive function. Further studies have determined that MDSCs are comprised of two groups: polymorphonuclear-MDSCs (G-MDSCs) and monocytic-MDSCs (M-MDSCs). We used a microbeads kit (Miltenyi) to isolate G-MDSCs and M-MDSCs with markers Ly6c2-Ly6g+CD11b+ and Ly6c2+Ly6g-CD11b+, respectively. And then using bulk RNA-seq to anlysis the enrichment gene expression in G-or M-MDSC which from wild type, APCmin mutant adenoma and immune deffiency mice.

overall_design: We isolate MDSCs from bone marrow (C57BL/6 WT mice), intestine (APCmin/+ mutant mice) and spleen (APCmin/+ mutant mice and BALB/c immune-diffency mice). Including bone marrow single cells (WT), (G+M)-MDSCs from spleen (BALB/c immune-diffency mice), Intestine single cells (APCmin/+ mutant mice), (G+M)-MDSCs from intestine (APCmin/+ mutant mice), (G+M)-MDSCs from spleen (APCmin/+ mutant mice),  G-MDSCs from bone marrow (C57BL/6 WT), Spleen (APCmin/+ mutant mice and BALB/c immune-diffency mice) and M-MDSCs from bone marrow (C57BL/6 WT), Spleen (APCmin/+ mutant mice and BALB/c immune-diffency mice). Total 39 samples were analyzed including three replicates for each group.


title: PDS5A and PDS5B differentially affect gene expression without altering cohesin localization across the genome [ChIP-seq]

summary:
Purpose: Cohesin is an important structural regulator of the genome. Whether cohesin HEAT repeat accessory proteins PDS5A and PDS5B differentially contribute to cohesin function remains unclear. The purpose of this study is to interrogate how PDS5A and PDS5B affect cohesin localization and gene expression in mouse embronic stem cells (mESCs)
Method: Genome wide binding patterns of PDS5A, PDS5B, and cohesin in wildtype cells as well as in PDS5 CRISPR/Cas9 genome edited knockout cells were assessed via chromatin immunoprecipitation followed by high throughput sequencing (ChIP-seq). The redundancy of the PDS5 subunits was addressed by using siRNA against PDS5B in a PDS5A-knockout background.

overall_design: ChIP-seq was performed in wildtype mESCs in duplicate for PDS5A, PDS5B, and RAD21. ChIP-seq was performed in CRISPR-Cas9 genome edited PDS5 deletion mESCs in duplicate for the reciprocal PDS5 and RAD21. ChIP-seq was performed in wildtype and PDS5A-KO cells after being treated with either siGLO transfection control or siPds5b.

first: Nicole

last: Arruda

first: Audra

last: Bryan


title: Analysis of transgenerational effects on DNA copy number aberrations in male mice exposed to continuous 1mGy/day gamma-rays for 400 days (Secondary screening for 1mGyO familly).

city: Rokkasho-mura,Kamikita-gun,

first: Keiji

last: OGURA

state: Aomori

address: Takahoko, Hacchasawa,

department: Department of Radiobiology

country: Japan

institute: Institute for Environmental Science

type: Genome variation profiling by genome tiling array

summary:
Transgenerational effects of continuous low dose-rate (LDR) gamma-ray irradiation have not been well studied. Recent advances in DNA technology enabled us to examine a whole genome at molecular level. Here we adopted one of these techniques called oligo-microarray comparative genome hybridization (CGH) and studied trans-generational effects on DNA copy number aberrations (CNAs).  C57BL/6JNrs male mice were exposed to LDR gamma-rays (0.05 mGy/day) for 400 days (total dose: 20 mGy) from 8 weeks of age. Progeny from 0.05 mGy/day irradiated mice had significantly lower frequencies of genomic aberrations than the progeny of non-irradiated mice.This study investigated the De novo mutation by comparing the parents and children using 15 LDR gamma-rays (0.05 mGy/day) irradiated male family and 25 non irradiated male family.
This is a secondary screening.
This study was performed under contract with the Aomori Prefectural Government, Japan.

overall_design: Two-condition experiment, C57 Black/J6Nrs tail tissue non-irradiated male (1mGyOM), female (1mGyOF) and their progenies (1mGyO1 to 1mGyO8) vs. reference male mouse.  We irradiated and non-irradiated male mice (C57BL/6JNrs) for 400 days and cross to non- irradiated female mice (C57BL/6JNrs) and got F1 mice. After they dead the DNA were prepared from their tails.  At first, primary screening using １M oligo-microarray was performed. The array was mounted autosomal fragment at intervals of an average about 2kb.  Two-condition experiment, mice tail tissue irradiated or non-irradiated male, female and their progenies vs. reference male mouse. This reference male mouse was from the same colony used in this experiment. Twice by changing the labeling color Cy3 and Cy5, performed CGH and extracting probes showed either aberration.  Identification the chromosomal location of the probe. Probes adjacent to the probe with aberration were set at high density. The candidate probes in one family was designed in a single 4x 244k or 8x 60k oligo-microarray and performed secondary screening. Extracting the flanking probes showed either aberration when labeled with Cy3 and Cy5 and identification the chromosomal location of the probe.  Finally, we performed TaqMan® Copy Number Assays to verify the mutations.

first: Ogura

last: Keiji


title: Analysis of transgenerational effects on DNA copy number aberrations in male mice exposed to continuous 1mGy/day gamma-rays for 400 days (Primary screening for 1mGyO familly).

summary:
Transgenerational effects of continuous low dose-rate (LDR) gamma-ray irradiation have not been well studied.  Recent advances in DNA technology enabled us to examine a whole genome at molecular level. Here we adopted one of these techniques called oligo-microarray comparative genome hybridization (CGH) and studied trans-generational effects on DNA copy number aberrations (CNAs).  C57BL/6J male mice were exposed to LDR gamma-rays (1 mGy/day) for 400 days (total dose: 400 mGy) from 8 weeks of age.  Progeny from 1 mGy/day irradiated mice had significantly lower frequencies of genomic aberrations than the progeny of non-irradiated mice.This study investigated the De novo mutation by comparing the parents and children using 15 LDR gamma-rays (1 mGy/day) irradiated male family and 25 non irradiated male family.
This is a primary screening.
This study was performed under contract with the Aomori Prefectural Government, Japan.

overall_design: Two-condition experiment, C57 Black/J6Nrs tail tissue non-irradiated male (1mGyOM), female (1mGyOF) and their progenies (1mGyO1 to 1mGyO8) vs. reference male mouse. This reference male mouse was from the same colony used in this experiment. Twice by changing the labeling color Cy3 and Cy5, performed CGH and extracting probes showed either aberration.  Identification the chromosomal location of the probe. Probes adjacent to the probe with aberration were set at high density. The candidate probes in one family was designed in a single 4x 244k or 8x 60k oligo-microarray and performed secondary screening. Extracting the flanking probes showed either aberration when labeled with Cy3 and Cy5 and identification the chromosomal location of the probe.  Finally, we performed TaqMan® Copy Number Assays to verify the mutations.


title: Analysis of transgenerational effects on DNA copy number aberrations in male mice exposed to continuous 1mGy/day gamma-rays for 400 days (Primary screening for 1mGyN familly).

overall_design: Two-condition experiment, C57 Black/J6Nrs tail tissue non-irradiated male (1mGyNM), female (1mGyNF) and their progenies (1mGyN1 to 1mGyN6) vs. reference male mouse. This reference male mouse was from the same colony used in this experiment. Twice by changing the labeling color Cy3 and Cy5, performed CGH and extracting probes showed either aberration.  Identification the chromosomal location of the probe. Probes adjacent to the probe with aberration were set at high density. The candidate probes in one family was designed in a single 4x 244k or 8x 60k oligo-microarray and performed secondary screening. Extracting the flanking probes showed either aberration when labeled with Cy3 and Cy5 and identification the chromosomal location of the probe.  Finally, we performed TaqMan® Copy Number Assays to verify the mutations.


title: Analysis of transgenerational effects on DNA copy number aberrations in male mice exposed to continuous 1mGy/day gamma-rays for 400 days (Secondary screening for 1mGyM familly).

overall_design: Two-condition experiment, C57 Black/J6Nrs tail tissue non-irradiated male (1mGyMM), female (1mGyMF) and their progenies (1mGyM1 to 1mGyM7) vs. reference male mouse.  We irradiated and non-irradiated male mice (C57BL/6JNrs) for 400 days and cross to non- irradiated female mice (C57BL/6JNrs) and got F1 mice. After they dead the DNA were prepared from their tails.  At first, primary screening using １M oligo-microarray was performed. The array was mounted autosomal fragment at intervals of an average about 2kb.  Two-condition experiment, mice tail tissue irradiated or non-irradiated male, female and their progenies vs. reference male mouse. This reference male mouse was from the same colony used in this experiment. Twice by changing the labeling color Cy3 and Cy5, performed CGH and extracting probes showed either aberration.  Identification the chromosomal location of the probe. Probes adjacent to the probe with aberration were set at high density. The candidate probes in one family was designed in a single 4x 244k or 8x 60k oligo-microarray and performed secondary screening. Extracting the flanking probes showed either aberration when labeled with Cy3 and Cy5 and identification the chromosomal location of the probe.  Finally, we performed TaqMan® Copy Number Assays to verify the mutations.


title: Analysis of transgenerational effects on DNA copy number aberrations in male mice exposed to continuous 1mGy/day gamma-rays for 400 days (Secondary screening for 1mGyL familly).

overall_design: Two-condition experiment, C57 Black/J6Nrs tail tissue non-irradiated male (1mGyLM), female (1mGyLF) and their progenies (1mGyL1 to 1mGyL6) vs. reference male mouse.  We irradiated and non-irradiated male mice (C57BL/6JNrs) for 400 days and cross to non- irradiated female mice (C57BL/6JNrs) and got F1 mice. After they dead the DNA were prepared from their tails.  At first, primary screening using １M oligo-microarray was performed. The array was mounted autosomal fragment at intervals of an average about 2kb.  Two-condition experiment, mice tail tissue irradiated or non-irradiated male, female and their progenies vs. reference male mouse. This reference male mouse was from the same colony used in this experiment. Twice by changing the labeling color Cy3 and Cy5, performed CGH and extracting probes showed either aberration.  Identification the chromosomal location of the probe. Probes adjacent to the probe with aberration were set at high density. The candidate probes in one family was designed in a single 4x 244k or 8x 60k oligo-microarray and performed secondary screening. Extracting the flanking probes showed either aberration when labeled with Cy3 and Cy5 and identification the chromosomal location of the probe.  Finally, we performed TaqMan® Copy Number Assays to verify the mutations.


title: Transcription profiling of PfSPZ Malaria Vaccine trial subjects receiving a 3-dose regimen in a malaria endemic region

city: Bethesda

first: Robert

last: Morrison

state: MD

address: 29 Lincoln Drive

department: NIAID

institute: NIH

summary: The Sanaria® PfSPZ Vaccine can confer sterilizing protection against liver stage infection by Plasmodium falciparum (Pf) in malaria naïve individuals. The vaccine consists of aseptically purified irradiated Pf sporozoites. Vaccinees received 3 doses of 1.8 X 106 irradiated sporozoites. Efficacy was measured by challenged by controlled human malaria infections (CHMI),  and against naturally occurring Pf Infections in Malian adults during the malaria transmission season

overall_design: 32 samples from 2 time points, pre-vaccination (Day -7) and post-vaccination (Day 116), for 16 Malian adult participants who all received 3 doses of the PfSPZ vaccine. All subjects remained uninfected after CHMI and 9 participants remained uninfected during the subsequent malaria season

first: Patrick

middle: E

last: Duffy

first: Irfan

last: Zaidi


title: Analysis of transgenerational effects on DNA copy number aberrations in male mice exposed to continuous 1mGy/day gamma-rays for 400 days (Secondary screening for 1mGyN familly).

overall_design: Two-condition experiment, C57 Black/J6Nrs tail tissue non-irradiated male (1mGyNM), female (1mGyNF) and their progenies (1mGyN1 to 1mGyN6) vs. reference male mouse.  We irradiated and non-irradiated male mice (C57BL/6JNrs) for 400 days and cross to non- irradiated female mice (C57BL/6JNrs) and got F1 mice. After they dead the DNA were prepared from their tails.  At first, primary screening using １M oligo-microarray was performed. The array was mounted autosomal fragment at intervals of an average about 2kb.  Two-condition experiment, mice tail tissue irradiated or non-irradiated male, female and their progenies vs. reference male mouse. This reference male mouse was from the same colony used in this experiment. Twice by changing the labeling color Cy3 and Cy5, performed CGH and extracting probes showed either aberration.  Identification the chromosomal location of the probe. Probes adjacent to the probe with aberration were set at high density. The candidate probes in one family was designed in a single 4x 244k or 8x 60k oligo-microarray and performed secondary screening. Extracting the flanking probes showed either aberration when labeled with Cy3 and Cy5 and identification the chromosomal location of the probe.  Finally, we performed TaqMan® Copy Number Assays to verify the mutations.


title: Analysis of transgenerational effects on DNA copy number aberrations in male mice exposed to continuous 1mGy/day gamma-rays for 400 days (Secondary screening for 1mGyK familly).

overall_design: Two-condition experiment, C57 Black/J6Nrs tail tissue non-irradiated male (1mGyKM), female (1mGyKF) and their progenies (1mGyK1 to 1mGyK7) vs. reference male mouse.  We irradiated and non-irradiated male mice (C57BL/6JNrs) for 400 days and cross to non- irradiated female mice (C57BL/6JNrs) and got F1 mice. After they dead the DNA were prepared from their tails.  At first, primary screening using １M oligo-microarray was performed. The array was mounted autosomal fragment at intervals of an average about 2kb.  Two-condition experiment, mice tail tissue irradiated or non-irradiated male, female and their progenies vs. reference male mouse. This reference male mouse was from the same colony used in this experiment. Twice by changing the labeling color Cy3 and Cy5, performed CGH and extracting probes showed either aberration.  Identification the chromosomal location of the probe. Probes adjacent to the probe with aberration were set at high density. The candidate probes in one family was designed in a single 4x 244k or 8x 60k oligo-microarray and performed secondary screening. Extracting the flanking probes showed either aberration when labeled with Cy3 and Cy5 and identification the chromosomal location of the probe.  Finally, we performed TaqMan® Copy Number Assays to verify the mutations.


title: Analysis of transgenerational effects on DNA copy number aberrations in male mice exposed to continuous 1mGy/day gamma-rays for 400 days (Primary screening for 1mGyM familly).

overall_design: Two-condition experiment, C57 Black/J6Nrs tail tissue non-irradiated male (1mGyMM), female (1mGyMF) and their progenies (1mGyM1 to 1mGyM7) vs. reference male mouse. This reference male mouse was from the same colony used in this experiment. Twice by changing the labeling color Cy3 and Cy5, performed CGH and extracting probes showed either aberration.  Identification the chromosomal location of the probe. Probes adjacent to the probe with aberration were set at high density. The candidate probes in one family was designed in a single 4x 244k or 8x 60k oligo-microarray and performed secondary screening. Extracting the flanking probes showed either aberration when labeled with Cy3 and Cy5 and identification the chromosomal location of the probe.  Finally, we performed TaqMan® Copy Number Assays to verify the mutations.


title: Analysis of transgenerational effects on DNA copy number aberrations in male mice exposed to continuous 1mGy/day gamma-rays for 400 days (Primary screening for 1mGyL familly).

overall_design: Two-condition experiment, C57 Black/J6Nrs tail tissue non-irradiated male (1mGyLM), female (1mGyLF) and their progenies (1mGyL1 to 1mGyL6) vs. reference male mouse. This reference male mouse was from the same colony used in this experiment. Twice by changing the labeling color Cy3 and Cy5, performed CGH and extracting probes showed either aberration.  Identification the chromosomal location of the probe. Probes adjacent to the probe with aberration were set at high density. The candidate probes in one family was designed in a single 4x 244k or 8x 60k oligo-microarray and performed secondary screening. Extracting the flanking probes showed either aberration when labeled with Cy3 and Cy5 and identification the chromosomal location of the probe.  Finally, we performed TaqMan® Copy Number Assays to verify the mutations.


title: Analysis of transgenerational effects on DNA copy number aberrations in male mice exposed to continuous 1mGy/day gamma-rays for 400 days (Primary screening for 1mGyK familly).

overall_design: Two-condition experiment, C57 Black/J6Nrs tail tissue non-irradiated male (1mGyKM), female (1mGyKF) and their progenies (1mGyK1 to 1mGyK7) vs. reference male mouse. This reference male mouse was from the same colony used in this experiment. Twice by changing the labeling color Cy3 and Cy5, performed CGH and extracting probes showed either aberration.  Identification the chromosomal location of the probe. Probes adjacent to the probe with aberration were set at high density. The candidate probes in one family was designed in a single 4x 244k or 8x 60k oligo-microarray and performed secondary screening. Extracting the flanking probes showed either aberration when labeled with Cy3 and Cy5 and identification the chromosomal location of the probe.  Finally, we performed TaqMan® Copy Number Assays to verify the mutations.


title: Analysis of transgenerational effects on DNA copy number aberrations in male mice exposed to continuous 1mGy/day gamma-rays for 400 days (Secondary screening for 1mGyI familly).

overall_design: Two-condition experiment, C57 Black/J6Nrs tail tissue non-irradiated male (1mGyIM), female (1mGyIF) and their progenies (1mGyI1 to 1mGyI6) vs. reference male mouse.  We irradiated and non-irradiated male mice (C57BL/6JNrs) for 400 days and cross to non- irradiated female mice (C57BL/6JNrs) and got F1 mice. After they dead the DNA were prepared from their tails.  At first, primary screening using １M oligo-microarray was performed. The array was mounted autosomal fragment at intervals of an average about 2kb.  Two-condition experiment, mice tail tissue irradiated or non-irradiated male, female and their progenies vs. reference male mouse. This reference male mouse was from the same colony used in this experiment. Twice by changing the labeling color Cy3 and Cy5, performed CGH and extracting probes showed either aberration.  Identification the chromosomal location of the probe. Probes adjacent to the probe with aberration were set at high density. The candidate probes in one family was designed in a single 4x 244k or 8x 60k oligo-microarray and performed secondary screening. Extracting the flanking probes showed either aberration when labeled with Cy3 and Cy5 and identification the chromosomal location of the probe.  Finally, we performed TaqMan® Copy Number Assays to verify the mutations.


title: Analysis of transgenerational effects on DNA copy number aberrations in male mice exposed to continuous 1mGy/day gamma-rays for 400 days (Secondary screening for 1mGyJ familly).

overall_design: Two-condition experiment, C57 Black/J6Nrs tail tissue non-irradiated male (1mGyJM), female (1mGyJF) and their progenies (1mGyJ1 to 1mGyJ6) vs. reference male mouse.  We irradiated and non-irradiated male mice (C57BL/6JNrs) for 400 days and cross to non- irradiated female mice (C57BL/6JNrs) and got F1 mice. After they dead the DNA were prepared from their tails.  At first, primary screening using １M oligo-microarray was performed. The array was mounted autosomal fragment at intervals of an average about 2kb.  Two-condition experiment, mice tail tissue irradiated or non-irradiated male, female and their progenies vs. reference male mouse. This reference male mouse was from the same colony used in this experiment. Twice by changing the labeling color Cy3 and Cy5, performed CGH and extracting probes showed either aberration.  Identification the chromosomal location of the probe. Probes adjacent to the probe with aberration were set at high density. The candidate probes in one family was designed in a single 4x 244k or 8x 60k oligo-microarray and performed secondary screening. Extracting the flanking probes showed either aberration when labeled with Cy3 and Cy5 and identification the chromosomal location of the probe.  Finally, we performed TaqMan® Copy Number Assays to verify the mutations.


title: Analysis of transgenerational effects on DNA copy number aberrations in male mice exposed to continuous 1mGy/day gamma-rays for 400 days (Primary screening for 1mGyJ familly).

overall_design: Two-condition experiment, C57 Black/J6Nrs tail tissue non-irradiated male (1mGyJM), female (1mGyJF) and their progenies (1mGyJ1 to 1mGyJ6) vs. reference male mouse. This reference male mouse was from the same colony used in this experiment. Twice by changing the labeling color Cy3 and Cy5, performed CGH and extracting probes showed either aberration.  Identification the chromosomal location of the probe. Probes adjacent to the probe with aberration were set at high density. The candidate probes in one family was designed in a single 4x 244k or 8x 60k oligo-microarray and performed secondary screening. Extracting the flanking probes showed either aberration when labeled with Cy3 and Cy5 and identification the chromosomal location of the probe.  Finally, we performed TaqMan® Copy Number Assays to verify the mutations.


title: Analysis of transgenerational effects on DNA copy number aberrations in male mice exposed to continuous 1mGy/day gamma-rays for 400 days (Secondary screening for 1mGyH familly).

overall_design: Two-condition experiment, C57 Black/J6Nrs tail tissue non-irradiated male (1mGyHM), female (1mGyHF) and their progenies (1mGyH1 to 1mGyH6) vs. reference male mouse.  We irradiated and non-irradiated male mice (C57BL/6JNrs) for 400 days and cross to non- irradiated female mice (C57BL/6JNrs) and got F1 mice. After they dead the DNA were prepared from their tails.  At first, primary screening using １M oligo-microarray was performed. The array was mounted autosomal fragment at intervals of an average about 2kb.  Two-condition experiment, mice tail tissue irradiated or non-irradiated male, female and their progenies vs. reference male mouse. This reference male mouse was from the same colony used in this experiment. Twice by changing the labeling color Cy3 and Cy5, performed CGH and extracting probes showed either aberration.  Identification the chromosomal location of the probe. Probes adjacent to the probe with aberration were set at high density. The candidate probes in one family was designed in a single 4x 244k or 8x 60k oligo-microarray and performed secondary screening. Extracting the flanking probes showed either aberration when labeled with Cy3 and Cy5 and identification the chromosomal location of the probe.  Finally, we performed TaqMan® Copy Number Assays to verify the mutations.


title: Analysis of transgenerational effects on DNA copy number aberrations in male mice exposed to continuous 1mGy/day gamma-rays for 400 days (Primary screening for 1mGyH familly).

overall_design: Two-condition experiment, C57 Black/J6Nrs tail tissue non-irradiated male (1mGyHM), female (1mGyHF) and their progenies (1mGyH1 to 1mGyH6) vs. reference male mouse. This reference male mouse was from the same colony used in this experiment. Twice by changing the labeling color Cy3 and Cy5, performed CGH and extracting probes showed either aberration.  Identification the chromosomal location of the probe. Probes adjacent to the probe with aberration were set at high density. The candidate probes in one family was designed in a single 4x 244k or 8x 60k oligo-microarray and performed secondary screening. Extracting the flanking probes showed either aberration when labeled with Cy3 and Cy5 and identification the chromosomal location of the probe.  Finally, we performed TaqMan® Copy Number Assays to verify the mutations.


title: Analysis of transgenerational effects on DNA copy number aberrations in male mice exposed to continuous 1mGy/day gamma-rays for 400 days (Secondary screening for 1mGyG familly).

overall_design: Two-condition experiment, C57 Black/J6Nrs tail tissue non-irradiated male (1mGyGM), female (1mGyGF) and their progenies (1mGyG1 to 1mGyG8) vs. reference male mouse.  We irradiated and non-irradiated male mice (C57BL/6JNrs) for 400 days and cross to non- irradiated female mice (C57BL/6JNrs) and got F1 mice. After they dead the DNA were prepared from their tails.  At first, primary screening using １M oligo-microarray was performed. The array was mounted autosomal fragment at intervals of an average about 2kb.  Two-condition experiment, mice tail tissue irradiated or non-irradiated male, female and their progenies vs. reference male mouse. This reference male mouse was from the same colony used in this experiment. Twice by changing the labeling color Cy3 and Cy5, performed CGH and extracting probes showed either aberration.  Identification the chromosomal location of the probe. Probes adjacent to the probe with aberration were set at high density. The candidate probes in one family was designed in a single 4x 244k or 8x 60k oligo-microarray and performed secondary screening. Extracting the flanking probes showed either aberration when labeled with Cy3 and Cy5 and identification the chromosomal location of the probe.  Finally, we performed TaqMan® Copy Number Assays to verify the mutations.


title: Analysis of transgenerational effects on DNA copy number aberrations in male mice exposed to continuous 1mGy/day gamma-rays for 400 days (Primary screening for 1mGyI familly).

overall_design: Two-condition experiment, C57 Black/J6Nrs tail tissue non-irradiated male (1mGyIM), female (1mGyIF) and their progenies (1mGyI1 to 1mGyI6) vs. reference male mouse. This reference male mouse was from the same colony used in this experiment. Twice by changing the labeling color Cy3 and Cy5, performed CGH and extracting probes showed either aberration.  Identification the chromosomal location of the probe. Probes adjacent to the probe with aberration were set at high density. The candidate probes in one family was designed in a single 4x 244k or 8x 60k oligo-microarray and performed secondary screening. Extracting the flanking probes showed either aberration when labeled with Cy3 and Cy5 and identification the chromosomal location of the probe.  Finally, we performed TaqMan® Copy Number Assays to verify the mutations.


title: Analysis of transgenerational effects on DNA copy number aberrations in male mice exposed to continuous 1mGy/day gamma-rays for 400 days (Secondary screening for 1mGyF familly).

overall_design: Two-condition experiment, C57 Black/J6Nrs tail tissue non-irradiated male (1mGyFM), female (1mGyFF) and their progenies (1mGyF1 to 1mGyF7) vs. reference male mouse.  We irradiated and non-irradiated male mice (C57BL/6JNrs) for 400 days and cross to non- irradiated female mice (C57BL/6JNrs) and got F1 mice. After they dead the DNA were prepared from their tails.  At first, primary screening using １M oligo-microarray was performed. The array was mounted autosomal fragment at intervals of an average about 2kb.  Two-condition experiment, mice tail tissue irradiated or non-irradiated male, female and their progenies vs. reference male mouse. This reference male mouse was from the same colony used in this experiment. Twice by changing the labeling color Cy3 and Cy5, performed CGH and extracting probes showed either aberration.  Identification the chromosomal location of the probe. Probes adjacent to the probe with aberration were set at high density. The candidate probes in one family was designed in a single 4x 244k or 8x 60k oligo-microarray and performed secondary screening. Extracting the flanking probes showed either aberration when labeled with Cy3 and Cy5 and identification the chromosomal location of the probe.  Finally, we performed TaqMan® Copy Number Assays to verify the mutations.


title: Analysis of transgenerational effects on DNA copy number aberrations in male mice exposed to continuous 1mGy/day gamma-rays for 400 days (Primary screening for 1mGyG familly).

overall_design: Two-condition experiment, C57 Black/J6Nrs tail tissue non-irradiated male (1mGyGM), female (1mGyGF) and their progenies (1mGyG1 to 1mGyG8) vs. reference male mouse.This reference male mouse was from the same colony used in this experiment. Twice by changing the labeling color Cy3 and Cy5, performed CGH and extracting probes showed either aberration.  Identification the chromosomal location of the probe. Probes adjacent to the probe with aberration were set at high density. The candidate probes in one family was designed in a single 4x 244k or 8x 60k oligo-microarray and performed secondary screening. Extracting the flanking probes showed either aberration when labeled with Cy3 and Cy5 and identification the chromosomal location of the probe.  Finally, we performed TaqMan® Copy Number Assays to verify the mutations.


title: Analysis of transgenerational effects on DNA copy number aberrations in male mice exposed to continuous 1mGy/day gamma-rays for 400 days (Secondary screening for 1mGyE familly).

overall_design: Two-condition experiment, C57 Black/J6Nrs tail tissue non-irradiated male (1mGyEM), female (1mGyEF) and their progenies (1mGyE1 to 1mGyE6) vs. reference male mouse.  We irradiated and non-irradiated male mice (C57BL/6JNrs) for 400 days and cross to non- irradiated female mice (C57BL/6JNrs) and got F1 mice. After they dead the DNA were prepared from their tails.  At first, primary screening using １M oligo-microarray was performed. The array was mounted autosomal fragment at intervals of an average about 2kb.  Two-condition experiment, mice tail tissue irradiated or non-irradiated male, female and their progenies vs. reference male mouse. This reference male mouse was from the same colony used in this experiment. Twice by changing the labeling color Cy3 and Cy5, performed CGH and extracting probes showed either aberration.  Identification the chromosomal location of the probe. Probes adjacent to the probe with aberration were set at high density. The candidate probes in one family was designed in a single 4x 244k or 8x 60k oligo-microarray and performed secondary screening. Extracting the flanking probes showed either aberration when labeled with Cy3 and Cy5 and identification the chromosomal location of the probe.  Finally, we performed TaqMan® Copy Number Assays to verify the mutations.


title: Analysis of transgenerational effects on DNA copy number aberrations in male mice exposed to continuous 1mGy/day gamma-rays for 400 days (Primary screening for 1mGyF familly).

overall_design: Two-condition experiment, C57 Black/J6Nrs tail tissue non-irradiated male (1mGyFM), female (1mGyFF) and their progenies (1mGyF1 to 1mGyF7) vs. reference male mouse. This reference male mouse was from the same colony used in this experiment. Twice by changing the labeling color Cy3 and Cy5, performed CGH and extracting probes showed either aberration.  Identification the chromosomal location of the probe. Probes adjacent to the probe with aberration were set at high density. The candidate probes in one family was designed in a single 4x 244k or 8x 60k oligo-microarray and performed secondary screening. Extracting the flanking probes showed either aberration when labeled with Cy3 and Cy5 and identification the chromosomal location of the probe.  Finally, we performed TaqMan® Copy Number Assays to verify the mutations.


title: Analysis of transgenerational effects on DNA copy number aberrations in male mice exposed to continuous 1mGy/day gamma-rays for 400 days (Primary screening for 1mGyE familly).

overall_design: Two-condition experiment, C57 Black/J6Nrs tail tissue non-irradiated male (1mGyEM), female (1mGyEF) and their progenies (1mGyE1 to 1mGyE6) vs. reference male mouse. This reference male mouse was from the same colony used in this experiment. Twice by changing the labeling color Cy3 and Cy5, performed CGH and extracting probes showed either aberration.  Identification the chromosomal location of the probe. Probes adjacent to the probe with aberration were set at high density. The candidate probes in one family was designed in a single 4x 244k or 8x 60k oligo-microarray and performed secondary screening. Extracting the flanking probes showed either aberration when labeled with Cy3 and Cy5 and identification the chromosomal location of the probe.  Finally, we performed TaqMan® Copy Number Assays to verify the mutations.


title: Analysis of transgenerational effects on DNA copy number aberrations in male mice exposed to continuous 1mGy/day gamma-rays for 400 days (Secondary screening for 1mGyD familly).

overall_design: Two-condition experiment, C57 Black/J6Nrs tail tissue non-irradiated male (1mGyDM), female (1mGyDF) and their progenies (1mGyD1 to 1mGyD8) vs. reference male mouse.  We irradiated and non-irradiated male mice (C57BL/6JNrs) for 400 days and cross to non- irradiated female mice (C57BL/6JNrs) and got F1 mice. After they dead the DNA were prepared from their tails.  At first, primary screening using １M oligo-microarray was performed. The array was mounted autosomal fragment at intervals of an average about 2kb.  Two-condition experiment, mice tail tissue irradiated or non-irradiated male, female and their progenies vs. reference male mouse. This reference male mouse was from the same colony used in this experiment. Twice by changing the labeling color Cy3 and Cy5, performed CGH and extracting probes showed either aberration.  Identification the chromosomal location of the probe. Probes adjacent to the probe with aberration were set at high density. The candidate probes in one family was designed in a single 4x 244k or 8x 60k oligo-microarray and performed secondary screening. Extracting the flanking probes showed either aberration when labeled with Cy3 and Cy5 and identification the chromosomal location of the probe.  Finally, we performed TaqMan® Copy Number Assays to verify the mutations.


title: Analysis of transgenerational effects on DNA copy number aberrations in male mice exposed to continuous 1mGy/day gamma-rays for 400 days (Primary screening for 1mGyD familly).

overall_design: Two-condition experiment, C57 Black/J6Nrs tail tissue non-irradiated male (1mGyDM), female (1mGyDF) and their progenies (1mGyD1 to 1mGyD8) vs. reference male mouse.This reference male mouse was from the same colony used in this experiment. Twice by changing the labeling color Cy3 and Cy5, performed CGH and extracting probes showed either aberration.  Identification the chromosomal location of the probe. Probes adjacent to the probe with aberration were set at high density. The candidate probes in one family was designed in a single 4x 244k or 8x 60k oligo-microarray and performed secondary screening. Extracting the flanking probes showed either aberration when labeled with Cy3 and Cy5 and identification the chromosomal location of the probe.  Finally, we performed TaqMan® Copy Number Assays to verify the mutations.


title: Analysis of transgenerational effects on DNA copy number aberrations in male mice exposed to continuous 1mGy/day gamma-rays for 400 days (Primary screening for 1mGyC familly).

overall_design: Two-condition experiment, C57 Black/J6Nrs tail tissue non-irradiated male (1mGyCM), female (1mGyCF) and their progenies (1mGyC1 to 1mGyC6) vs. reference male mouse.This reference male mouse was from the same colony used in this experiment. Twice by changing the labeling color Cy3 and Cy5, performed CGH and extracting probes showed either aberration.  Identification the chromosomal location of the probe. Probes adjacent to the probe with aberration were set at high density. The candidate probes in one family was designed in a single 4x 244k or 8x 60k oligo-microarray and performed secondary screening. Extracting the flanking probes showed either aberration when labeled with Cy3 and Cy5 and identification the chromosomal location of the probe.  Finally, we performed TaqMan® Copy Number Assays to verify the mutations.


title: Analysis of transgenerational effects on DNA copy number aberrations in male mice exposed to continuous 1mGy/day gamma-rays for 400 days (Secondary screening for 1mGyC familly).

overall_design: Two-condition experiment, C57 Black/J6Nrs tail tissue non-irradiated male (1mGyCM), female (1mGyCF) and their progenies (1mGyC1 to 1mGyC6) vs. reference male mouse.  We irradiated and non-irradiated male mice (C57BL/6JNrs) for 400 days and cross to non- irradiated female mice (C57BL/6JNrs) and got F1 mice. After they dead the DNA were prepared from their tails.  At first, primary screening using １M oligo-microarray was performed. The array was mounted autosomal fragment at intervals of an average about 2kb.  Two-condition experiment, mice tail tissue irradiated or non-irradiated male, female and their progenies vs. reference male mouse. This reference male mouse was from the same colony used in this experiment. Twice by changing the labeling color Cy3 and Cy5, performed CGH and extracting probes showed either aberration.  Identification the chromosomal location of the probe. Probes adjacent to the probe with aberration were set at high density. The candidate probes in one family was designed in a single 4x 244k or 8x 60k oligo-microarray and performed secondary screening. Extracting the flanking probes showed either aberration when labeled with Cy3 and Cy5 and identification the chromosomal location of the probe.  Finally, we performed TaqMan® Copy Number Assays to verify the mutations.


title: Analysis of transgenerational effects on DNA copy number aberrations in male mice exposed to continuous 1mGy/day gamma-rays for 400 days (Secondary screening for 1mGyB familly).

overall_design: Two-condition experiment, C57 Black/J6Nrs tail tissue non-irradiated male (1mGyBM), female (1mGyBF) and their progenies (1mGyB1 to 1mGyB7) vs. reference male mouse.  We irradiated and non-irradiated male mice (C57BL/6JNrs) for 400 days and cross to non- irradiated female mice (C57BL/6JNrs) and got F1 mice. After they dead the DNA were prepared from their tails.  At first, primary screening using １M oligo-microarray was performed. The array was mounted autosomal fragment at intervals of an average about 2kb.  Two-condition experiment, mice tail tissue irradiated or non-irradiated male, female and their progenies vs. reference male mouse. This reference male mouse was from the same colony used in this experiment. Twice by changing the labeling color Cy3 and Cy5, performed CGH and extracting probes showed either aberration.  Identification the chromosomal location of the probe. Probes adjacent to the probe with aberration were set at high density. The candidate probes in one family was designed in a single 4x 244k or 8x 60k oligo-microarray and performed secondary screening. Extracting the flanking probes showed either aberration when labeled with Cy3 and Cy5 and identification the chromosomal location of the probe.  Finally, we performed TaqMan® Copy Number Assays to verify the mutations.


title: Analysis of transgenerational effects on DNA copy number aberrations in male mice exposed to continuous 0.05mGy/day gamma-rays for 400 days (Secondary screening for 0.05mGyO familly).

overall_design: Two-condition experiment, C57BL/6JNrs tail tissue non-irradiated male (0.05 mGyOM), female (0.05 mGyOF) and their progenies (0.05 mGyO1 to 0.05 mGyO7) vs. reference male mouse.  We irradiated and non-irradiated male mice (C57BL/6JNrs) for 400 days and cross to non- irradiated female mice (C57BL/6JNrs) and got F1 mice. After they dead the DNA were prepared from their tails.  At first, primary screening using １M oligo-microarray was performed. The array was mounted autosomal fragment at intervals of an average about 2kb.  Two-condition experiment, mice tail tissue irradiated or non-irradiated male, female and their progenies vs. reference male mouse. This reference male mouse was from the same colony used in this experiment. Twice by changing the labeling color Cy3 and Cy5, performed CGH and extracting probes showed either aberration.  Identification the chromosomal location of the probe. Probes adjacent to the probe with aberration were set at high density. The candidate probes in one family was designed in a single 4x 244k or 8x 60k oligo-microarray and performed secondary screening. Extracting the flanking probes showed either aberration when labeled with Cy3 and Cy5 and identification the chromosomal location of the probe.  Finally, we performed TaqMan® Copy Number Assays to verify the mutations.


title: Analysis of transgenerational effects on DNA copy number aberrations in male mice exposed to continuous 1mGy/day gamma-rays for 400 days (Primary screening for 1mGyB familly).


title: Analysis of transgenerational effects on DNA copy number aberrations in male mice exposed to continuous 1mGy/day gamma-rays for 400 days (Primary screening for 1mGyA familly).

overall_design: Two-condition experiment, C57 Black/J6Nrs tail tissue non-irradiated male (1mGyAM), female (1mGyAF) and their progenies (1mGyA1 to 1mGyA6) vs. reference male mouse.  We irradiated and non-irradiated male mice (C57BL/6JNrs) for 400 days and cross to non- irradiated female mice (C57BL/6JNrs) and got F1 mice. After they dead the DNA were prepared from their tails.  At first, primary screening using １M oligo-microarray was performed. The array was mounted autosomal fragment at intervals of an average about 2kb.  Two-condition experiment, mice tail tissue irradiated or non-irradiated male, female and their progenies vs. reference male mouse. This reference male mouse was from the same colony used in this experiment. Twice by changing the labeling color Cy3 and Cy5, performed CGH and extracting probes showed either aberration.  Identification the chromosomal location of the probe. Probes adjacent to the probe with aberration were set at high density. The candidate probes in one family was designed in a single 4x 244k or 8x 60k oligo-microarray and performed secondary screening. Extracting the flanking probes showed either aberration when labeled with Cy3 and Cy5 and identification the chromosomal location of the probe.  Finally, we performed TaqMan® Copy Number Assays to verify the mutations.


title: Analysis of transgenerational effects on DNA copy number aberrations in male mice exposed to continuous 0.05mGy/day gamma-rays for 400 days (Primary screening for 0.05mGyO familly).

summary:
Transgenerational effects of continuous low dose-rate (LDR) gamma-ray irradiation have not been well studied. Recent advances in DNA technology enabled us to examine a whole genome at molecular level. Here we adopted one of these techniques called oligo-microarray comparative genome hybridization (CGH) and studied trans-generational effects on DNA copy number aberrations (CNAs).  C57BL/6JNrs male mice were exposed to LDR gamma-rays (0.05 mGy/day) for 400 days (total dose: 20 mGy) from 8 weeks of age. Progeny from 0.05 mGy/day irradiated mice had significantly lower frequencies of genomic aberrations than the progeny of non-irradiated mice.This study investigated the De novo mutation by comparing the parents and children using 15 LDR gamma-rays (0.05 mGy/day) irradiated male family and 25 non irradiated male family.
This is a primary screening.
This study was performed under contract with the Aomori Prefectural Government, Japan.


title: Analysis of transgenerational effects on DNA copy number aberrations in male mice exposed to continuous 0.05mGy/day gamma-rays for 400 days (Secondary screening for 0.05mGyN familly).

overall_design: Two-condition experiment, C57BL/6JNrs tail tissue non-irradiated male (0.05 mGyNM), female (0.05 mGyNF) and their progenies (0.05 mGyN1 to 0.05 mGyN7) vs. reference male mouse.  We irradiated and non-irradiated male mice (C57BL/6JNrs) for 400 days and cross to non- irradiated female mice (C57BL/6JNrs) and got F1 mice. After they dead the DNA were prepared from their tails.  At first, primary screening using １M oligo-microarray was performed. The array was mounted autosomal fragment at intervals of an average about 2kb.  Two-condition experiment, mice tail tissue irradiated or non-irradiated male, female and their progenies vs. reference male mouse. This reference male mouse was from the same colony used in this experiment. Twice by changing the labeling color Cy3 and Cy5, performed CGH and extracting probes showed either aberration.  Identification the chromosomal location of the probe. Probes adjacent to the probe with aberration were set at high density. The candidate probes in one family was designed in a single 4x 244k or 8x 60k oligo-microarray and performed secondary screening. Extracting the flanking probes showed either aberration when labeled with Cy3 and Cy5 and identification the chromosomal location of the probe.  Finally, we performed TaqMan® Copy Number Assays to verify the mutations.


title: Analysis of transgenerational effects on DNA copy number aberrations in male mice exposed to continuous 0.05mGy/day gamma-rays for 400 days (Primary screening for 0.05mGyM familly).

overall_design: Two-condition experiment, C57BL/6JNrs tail tissue non-irradiated male (0.05 mGyMM), female (0.05 mGyMF) and their progenies (0.05 mGyM1 to 0.05 mGyM7) vs. reference male mouse.  We irradiated and non-irradiated male mice (C57BL/6JNrs) for 400 days and cross to non- irradiated female mice (C57BL/6JNrs) and got F1 mice. After they dead the DNA were prepared from their tails.  At first, primary screening using １M oligo-microarray was performed. The array was mounted autosomal fragment at intervals of an average about 2kb.  Two-condition experiment, mice tail tissue irradiated or non-irradiated male, female and their progenies vs. reference male mouse. This reference male mouse was from the same colony used in this experiment. Twice by changing the labeling color Cy3 and Cy5, performed CGH and extracting probes showed either aberration.  Identification the chromosomal location of the probe. Probes adjacent to the probe with aberration were set at high density. The candidate probes in one family was designed in a single 4x 244k or 8x 60k oligo-microarray and performed secondary screening. Extracting the flanking probes showed either aberration when labeled with Cy3 and Cy5 and identification the chromosomal location of the probe.  Finally, we performed TaqMan® Copy Number Assays to verify the mutations.


title: Analysis of transgenerational effects on DNA copy number aberrations in male mice exposed to continuous 0.05mGy/day gamma-rays for 400 days (Secondary screening for 0.05mGyL familly).

overall_design: Two-condition experiment, C57BL/6JNrs tail tissue non-irradiated male (0.05 mGyLM), female (0.05 mGyLF) and their progenies (0.05 mGyL1 to 0.05 mGyL6) vs. reference male mouse.  We irradiated and non-irradiated male mice (C57BL/6JNrs) for 400 days and cross to non- irradiated female mice (C57BL/6JNrs) and got F1 mice. After they dead the DNA were prepared from their tails.  At first, primary screening using １M oligo-microarray was performed. The array was mounted autosomal fragment at intervals of an average about 2kb.  Two-condition experiment, mice tail tissue irradiated or non-irradiated male, female and their progenies vs. reference male mouse. This reference male mouse was from the same colony used in this experiment. Twice by changing the labeling color Cy3 and Cy5, performed CGH and extracting probes showed either aberration.  Identification the chromosomal location of the probe. Probes adjacent to the probe with aberration were set at high density. The candidate probes in one family was designed in a single 4x 244k or 8x 60k oligo-microarray and performed secondary screening. Extracting the flanking probes showed either aberration when labeled with Cy3 and Cy5 and identification the chromosomal location of the probe.  Finally, we performed TaqMan® Copy Number Assays to verify the mutations.


title: Analysis of transgenerational effects on DNA copy number aberrations in male mice exposed to continuous 0.05mGy/day gamma-rays for 400 days (Secondary screening for 0.05mGyM familly).


title: Analysis of transgenerational effects on DNA copy number aberrations in male mice exposed to continuous 0.05mGy/day gamma-rays for 400 days (Secondary screening for 0.05mGyK familly).

overall_design: Two-condition experiment, C57BL/6JNrs tail tissue non-irradiated male (0.05 mGyKM), female (0.05 mGyKF) and their progenies (0.05 mGyK1 to 0.05 mGyK7) vs. reference male mouse.  We irradiated and non-irradiated male mice (C57BL/6JNrs) for 400 days and cross to non- irradiated female mice (C57BL/6JNrs) and got F1 mice. After they dead the DNA were prepared from their tails.  At first, primary screening using １M oligo-microarray was performed. The array was mounted autosomal fragment at intervals of an average about 2kb.  Two-condition experiment, mice tail tissue irradiated or non-irradiated male, female and their progenies vs. reference male mouse. This reference male mouse was from the same colony used in this experiment. Twice by changing the labeling color Cy3 and Cy5, performed CGH and extracting probes showed either aberration.  Identification the chromosomal location of the probe. Probes adjacent to the probe with aberration were set at high density. The candidate probes in one family was designed in a single 4x 244k or 8x 60k oligo-microarray and performed secondary screening. Extracting the flanking probes showed either aberration when labeled with Cy3 and Cy5 and identification the chromosomal location of the probe.  Finally, we performed TaqMan® Copy Number Assays to verify the mutations.


title: Analysis of transgenerational effects on DNA copy number aberrations in male mice exposed to continuous 0.05mGy/day gamma-rays for 400 days (Primary screening for 0.05mGyN familly).


title: Analysis of transgenerational effects on DNA copy number aberrations in male mice exposed to continuous 0.05mGy/day gamma-rays for 400 days (Primary screening for 0.05mGyL familly).


title: Analysis of transgenerational effects on DNA copy number aberrations in male mice exposed to continuous 1mGy/day gamma-rays for 400 days (Secondary screening for 1mGyA familly).

overall_design: Two-condition experiment, C57BL/6JNrs tail tissue non-irradiated male (1 mGyDM), female (1 mGyDF) and their progenies (1 mGyA1 to 1 mGyA6) vs. reference male mouse.  We irradiated and non-irradiated male mice (C57BL/6JNrs) for 400 days and cross to non- irradiated female mice (C57BL/6JNrs) and got F1 mice. After they dead the DNA were prepared from their tails.  At first, primary screening using １M oligo-microarray was performed. The array was mounted autosomal fragment at intervals of an average about 2kb.  Two-condition experiment, mice tail tissue irradiated or non-irradiated male, female and their progenies vs. reference male mouse. This reference male mouse was from the same colony used in this experiment. Twice by changing the labeling color Cy3 and Cy5, performed CGH and extracting probes showed either aberration.  Identification the chromosomal location of the probe. Probes adjacent to the probe with aberration were set at high density. The candidate probes in one family was designed in a single 4x 244k or 8x 60k oligo-microarray and performed secondary screening. Extracting the flanking probes showed either aberration when labeled with Cy3 and Cy5 and identification the chromosomal location of the probe.  Finally, we performed TaqMan® Copy Number Assays to verify the mutations.


title: Analysis of transgenerational effects on DNA copy number aberrations in male mice exposed to continuous 0.05mGy/day gamma-rays for 400 days (Primary screening for 0.05mGyK familly).


title: Analysis of transgenerational effects on DNA copy number aberrations in male mice exposed to continuous 0.05mGy/day gamma-rays for 400 days (Secondary screening for 0.05mGyJ familly).

overall_design: Two-condition experiment, C57BL/6JNrs tail tissue non-irradiated male (0.05 mGyJM), female (0.05 mGyJF) and their progenies (0.05 mGyJ1 to 0.05 mGyJ6) vs. reference male mouse.  We irradiated and non-irradiated male mice (C57BL/6JNrs) for 400 days and cross to non- irradiated female mice (C57BL/6JNrs) and got F1 mice. After they dead the DNA were prepared from their tails.  At first, primary screening using １M oligo-microarray was performed. The array was mounted autosomal fragment at intervals of an average about 2kb.  Two-condition experiment, mice tail tissue irradiated or non-irradiated male, female and their progenies vs. reference male mouse. This reference male mouse was from the same colony used in this experiment. Twice by changing the labeling color Cy3 and Cy5, performed CGH and extracting probes showed either aberration.  Identification the chromosomal location of the probe. Probes adjacent to the probe with aberration were set at high density. The candidate probes in one family was designed in a single 4x 244k or 8x 60k oligo-microarray and performed secondary screening. Extracting the flanking probes showed either aberration when labeled with Cy3 and Cy5 and identification the chromosomal location of the probe.  Finally, we performed TaqMan® Copy Number Assays to verify the mutations.


title: Analysis of transgenerational effects on DNA copy number aberrations in male mice exposed to continuous 0.05mGy/day gamma-rays for 400 days (Secondary screening for 0.05mGyH familly).

overall_design: Two-condition experiment, C57BL/6JNrs tail tissue non-irradiated male (0.05 mGyHM), female (0.05 mGyHF) and their progenies (0.05 mGyH1 to 0.05 mGyH7) vs. reference male mouse.  We irradiated and non-irradiated male mice (C57BL/6JNrs) for 400 days and cross to non- irradiated female mice (C57BL/6JNrs) and got F1 mice. After they dead the DNA were prepared from their tails.  At first, primary screening using １M oligo-microarray was performed. The array was mounted autosomal fragment at intervals of an average about 2kb.  Two-condition experiment, mice tail tissue irradiated or non-irradiated male, female and their progenies vs. reference male mouse. This reference male mouse was from the same colony used in this experiment. Twice by changing the labeling color Cy3 and Cy5, performed CGH and extracting probes showed either aberration.  Identification the chromosomal location of the probe. Probes adjacent to the probe with aberration were set at high density. The candidate probes in one family was designed in a single 4x 244k or 8x 60k oligo-microarray and performed secondary screening. Extracting the flanking probes showed either aberration when labeled with Cy3 and Cy5 and identification the chromosomal location of the probe.  Finally, we performed TaqMan® Copy Number Assays to verify the mutations.


title: Analysis of transgenerational effects on DNA copy number aberrations in male mice exposed to continuous 0.05mGy/day gamma-rays for 400 days (Secondary screening for 0.05mGyI familly).

overall_design: Two-condition experiment, C57BL/6JNrs tail tissue non-irradiated male (0.05 mGyIM), female (0.05 mGyIF) and their progenies (0.05 mGyI1 to 0.05 mGyI7) vs. reference male mouse.  We irradiated and non-irradiated male mice (C57BL/6JNrs) for 400 days and cross to non- irradiated female mice (C57BL/6JNrs) and got F1 mice. After they dead the DNA were prepared from their tails.  At first, primary screening using １M oligo-microarray was performed. The array was mounted autosomal fragment at intervals of an average about 2kb.  Two-condition experiment, mice tail tissue irradiated or non-irradiated male, female and their progenies vs. reference male mouse. This reference male mouse was from the same colony used in this experiment. Twice by changing the labeling color Cy3 and Cy5, performed CGH and extracting probes showed either aberration.  Identification the chromosomal location of the probe. Probes adjacent to the probe with aberration were set at high density. The candidate probes in one family was designed in a single 4x 244k or 8x 60k oligo-microarray and performed secondary screening. Extracting the flanking probes showed either aberration when labeled with Cy3 and Cy5 and identification the chromosomal location of the probe.  Finally, we performed TaqMan® Copy Number Assays to verify the mutations.


title: Analysis of transgenerational effects on DNA copy number aberrations in male mice exposed to continuous 0.05mGy/day gamma-rays for 400 days (Primary screening for 0.05mGyH familly).


title: Analysis of transgenerational effects on DNA copy number aberrations in male mice exposed to continuous 0.05mGy/day gamma-rays for 400 days (Primary screening for 0.05mGyJ familly).


title: Analysis of transgenerational effects on DNA copy number aberrations in male mice exposed to continuous 0.05mGy/day gamma-rays for 400 days (Secondary screening for 0.05mGyG familly).

overall_design: Two-condition experiment, C57BL/6JNrs tail tissue non-irradiated male (0.05 mGyGM), female (0.05 mGyGF) and their progenies (0.05 mGyG1 to 0.05 mGyG6) vs. reference male mouse.  We irradiated and non-irradiated male mice (C57BL/6JNrs) for 400 days and cross to non- irradiated female mice (C57BL/6JNrs) and got F1 mice. After they dead the DNA were prepared from their tails.  At first, primary screening using １M oligo-microarray was performed. The array was mounted autosomal fragment at intervals of an average about 2kb.  Two-condition experiment, mice tail tissue irradiated or non-irradiated male, female and their progenies vs. reference male mouse. This reference male mouse was from the same colony used in this experiment. Twice by changing the labeling color Cy3 and Cy5, performed CGH and extracting probes showed either aberration.  Identification the chromosomal location of the probe. Probes adjacent to the probe with aberration were set at high density. The candidate probes in one family was designed in a single 4x 244k or 8x 60k oligo-microarray and performed secondary screening. Extracting the flanking probes showed either aberration when labeled with Cy3 and Cy5 and identification the chromosomal location of the probe.  Finally, we performed TaqMan® Copy Number Assays to verify the mutations.


title: Analysis of transgenerational effects on DNA copy number aberrations in male mice exposed to continuous 0.05mGy/day gamma-rays for 400 days (Secondary screening for 0.05mGyF familly).

overall_design: Two-condition experiment, C57BL/6JNrs tail tissue non-irradiated male (0.05 mGyFM), female (0.05 mGyFF) and their progenies (0.05 mGyF1 to 0.05 mGyF6) vs. reference male mouse.  We irradiated and non-irradiated male mice (C57BL/6JNrs) for 400 days and cross to non- irradiated female mice (C57BL/6JNrs) and got F1 mice. After they dead the DNA were prepared from their tails.  At first, primary screening using １M oligo-microarray was performed. The array was mounted autosomal fragment at intervals of an average about 2kb.  Two-condition experiment, mice tail tissue irradiated or non-irradiated male, female and their progenies vs. reference male mouse. This reference male mouse was from the same colony used in this experiment. Twice by changing the labeling color Cy3 and Cy5, performed CGH and extracting probes showed either aberration.  Identification the chromosomal location of the probe. Probes adjacent to the probe with aberration were set at high density. The candidate probes in one family was designed in a single 4x 244k or 8x 60k oligo-microarray and performed secondary screening. Extracting the flanking probes showed either aberration when labeled with Cy3 and Cy5 and identification the chromosomal location of the probe.  Finally, we performed TaqMan® Copy Number Assays to verify the mutations.


title: Analysis of transgenerational effects on DNA copy number aberrations in male mice exposed to continuous 0.05mGy/day gamma-rays for 400 days (Secondary screening for 0.05mGyD familly).

overall_design: Two-condition experiment, C57BL/6JNrs tail tissue non-irradiated male (0.05 mGyDM), female (0.05 mGyDF) and their progenies (0.05 mGyD1 to 0.05 mGyD8) vs. reference male mouse.  We irradiated and non-irradiated male mice (C57BL/6JNrs) for 400 days and cross to non- irradiated female mice (C57BL/6JNrs) and got F1 mice. After they dead the DNA were prepared from their tails.  At first, primary screening using １M oligo-microarray was performed. The array was mounted autosomal fragment at intervals of an average about 2kb.  Two-condition experiment, mice tail tissue irradiated or non-irradiated male, female and their progenies vs. reference male mouse. This reference male mouse was from the same colony used in this experiment. Twice by changing the labeling color Cy3 and Cy5, performed CGH and extracting probes showed either aberration.  Identification the chromosomal location of the probe. Probes adjacent to the probe with aberration were set at high density. The candidate probes in one family was designed in a single 4x 244k or 8x 60k oligo-microarray and performed secondary screening. Extracting the flanking probes showed either aberration when labeled with Cy3 and Cy5 and identification the chromosomal location of the probe.  Finally, we performed TaqMan® Copy Number Assays to verify the mutations.


title: Analysis of transgenerational effects on DNA copy number aberrations in male mice exposed to continuous 0.05mGy/day gamma-rays for 400 days (Primary screening for 0.05mGyD familly).


title: Analysis of transgenerational effects on DNA copy number aberrations in male mice exposed to continuous 0.05mGy/day gamma-rays for 400 days (Secondary screening for 0.05mGyC familly).

overall_design: Two-condition experiment, C57BL/6JNrs tail tissue non-irradiated male (0.05 mGyCM), female (0.05 mGyCF) and their progenies (0.05 mGyC1 to 0.05 mGyC6) vs. reference male mouse.  We irradiated and non-irradiated male mice (C57BL/6JNrs) for 400 days and cross to non- irradiated female mice (C57BL/6JNrs) and got F1 mice. After they dead the DNA were prepared from their tails.  At first, primary screening using １M oligo-microarray was performed. The array was mounted autosomal fragment at intervals of an average about 2kb.  Two-condition experiment, mice tail tissue irradiated or non-irradiated male, female and their progenies vs. reference male mouse. This reference male mouse was from the same colony used in this experiment. Twice by changing the labeling color Cy3 and Cy5, performed CGH and extracting probes showed either aberration.  Identification the chromosomal location of the probe. Probes adjacent to the probe with aberration were set at high density. The candidate probes in one family was designed in a single 4x 244k or 8x 60k oligo-microarray and performed secondary screening. Extracting the flanking probes showed either aberration when labeled with Cy3 and Cy5 and identification the chromosomal location of the probe.  Finally, we performed TaqMan® Copy Number Assays to verify the mutations.


title: Analysis of transgenerational effects on DNA copy number aberrations in male mice exposed to continuous 0.05mGy/day gamma-rays for 400 days (Secondary screening for 0.05mGyB familly).

overall_design: Two-condition experiment, C57BL/6JNrs tail tissue non-irradiated male (0.05 mGyBM), female (0.05 mGyBF) and their progenies (0.05 mGyB1 to 0.05 mGyB8) vs. reference male mouse.  We irradiated and non-irradiated male mice (C57BL/6JNrs) for 400 days and cross to non- irradiated female mice (C57BL/6JNrs) and got F1 mice. After they dead the DNA were prepared from their tails.  At first, primary screening using １M oligo-microarray was performed. The array was mounted autosomal fragment at intervals of an average about 2kb.  Two-condition experiment, mice tail tissue irradiated or non-irradiated male, female and their progenies vs. reference male mouse. This reference male mouse was from the same colony used in this experiment. Twice by changing the labeling color Cy3 and Cy5, performed CGH and extracting probes showed either aberration.  Identification the chromosomal location of the probe. Probes adjacent to the probe with aberration were set at high density. The candidate probes in one family was designed in a single 4x 244k or 8x 60k oligo-microarray and performed secondary screening. Extracting the flanking probes showed either aberration when labeled with Cy3 and Cy5 and identification the chromosomal location of the probe.  Finally, we performed TaqMan® Copy Number Assays to verify the mutations.


title: Analysis of transgenerational effects on DNA copy number aberrations in male mice exposed to continuous 0.05mGy/day gamma-rays for 400 days (Primary screening for 0.05mGyF familly).


title: Analysis of transgenerational effects on DNA copy number aberrations in male mice exposed to continuous 0.05mGy/day gamma-rays for 400 days (Primary screening for 0.05mGyB familly).

overall_design: Two-condition experiment, C57BL/6JNrs tail tissue non-irradiated male (0.05 mGyBM), female (0.05 mGyBF) and their progenies (0.05 mGyA1 to 0.05 mGyB8) vs. reference male mouse.  We irradiated and non-irradiated male mice (C57BL/6JNrs) for 400 days and cross to non- irradiated female mice (C57BL/6JNrs) and got F1 mice. After they dead the DNA were prepared from their tails.  At first, primary screening using １M oligo-microarray was performed. The array was mounted autosomal fragment at intervals of an average about 2kb.  Two-condition experiment, mice tail tissue irradiated or non-irradiated male, female and their progenies vs. reference male mouse. This reference male mouse was from the same colony used in this experiment. Twice by changing the labeling color Cy3 and Cy5, performed CGH and extracting probes showed either aberration.  Identification the chromosomal location of the probe. Probes adjacent to the probe with aberration were set at high density. The candidate probes in one family was designed in a single 4x 244k or 8x 60k oligo-microarray and performed secondary screening. Extracting the flanking probes showed either aberration when labeled with Cy3 and Cy5 and identification the chromosomal location of the probe.  Finally, we performed TaqMan® Copy Number Assays to verify the mutations.


title: Analysis of transgenerational effects on DNA copy number aberrations in male mice exposed to continuous 0.05mGy/day gamma-rays for 400 days (Primary screening for 0.05mGyE familly).

overall_design: Two-condition experiment, C57BL/6JNrs tail tissue non-irradiated male (0.05 mGyEM), female (0.05 mGyEF) and their progenies (0.05 mGyE1 to 0.05 mGyE6) vs. reference male mouse.  We irradiated and non-irradiated male mice (C57BL/6JNrs) for 400 days and cross to non- irradiated female mice (C57BL/6JNrs) and got F1 mice. After they dead the DNA were prepared from their tails.  At first, primary screening using １M oligo-microarray was performed. The array was mounted autosomal fragment at intervals of an average about 2kb.  Two-condition experiment, mice tail tissue irradiated or non-irradiated male, female and their progenies vs. reference male mouse. This reference male mouse was from the same colony used in this experiment. Twice by changing the labeling color Cy3 and Cy5, performed CGH and extracting probes showed either aberration.  Identification the chromosomal location of the probe. Probes adjacent to the probe with aberration were set at high density. The candidate probes in one family was designed in a single 4x 244k or 8x 60k oligo-microarray and performed secondary screening. Extracting the flanking probes showed either aberration when labeled with Cy3 and Cy5 and identification the chromosomal location of the probe.  Finally, we performed TaqMan® Copy Number Assays to verify the mutations.


title: Analysis of transgenerational effects on DNA copy number aberrations in male mice exposed to continuous 0.05mGy/day gamma-rays for 400 days (Secondary screening for 0.05mGyA familly).

overall_design: Two-condition experiment, C57BL/6JNrs tail tissue non-irradiated male (0.05 mGyAM), female (0.05 mGyAF) and their progenies (0.05 mGyA1 to 0.05 mGyA6) vs. reference male mouse.  We irradiated and non-irradiated male mice (C57BL/6JNrs) for 400 days and cross to non- irradiated female mice (C57BL/6JNrs) and got F1 mice. After they dead the DNA were prepared from their tails.  At first, primary screening using １M oligo-microarray was performed. The array was mounted autosomal fragment at intervals of an average about 2kb.  Two-condition experiment, mice tail tissue irradiated or non-irradiated male, female and their progenies vs. reference male mouse. This reference male mouse was from the same colony used in this experiment. Twice by changing the labeling color Cy3 and Cy5, performed CGH and extracting probes showed either aberration.  Identification the chromosomal location of the probe. Probes adjacent to the probe with aberration were set at high density. The candidate probes in one family was designed in a single 4x 244k or 8x 60k oligo-microarray and performed secondary screening. Extracting the flanking probes showed either aberration when labeled with Cy3 and Cy5 and identification the chromosomal location of the probe.  Finally, we performed TaqMan® Copy Number Assays to verify the mutations.


title: Analysis of transgenerational effects on DNA copy number aberrations in male mice exposed to continuous 0.05mGy/day gamma-rays for 400 days (Primary screening for 0.05mGyC familly).


title: Analysis of transgenerational effects on DNA copy number aberrations in male mice exposed to continuous 0.05mGy/day gamma-rays for 400 days (Primary screening for 0.05mGyI familly).


title: Methylome analysis for prediction of long and short survival in glioblastoma patients from the Nordic phase 3 trial

city: Linköping

first: Malgorzata

last: Lysiak

state: Östergötland

institute: Linköping University

summary: Genome wide DNA methylation profiling of glioblastoma tumor samples from the Nordic randomised, phase 3 trial. For this study samples were selected based on their good prognostic markers (type of surgery, performance status) from three treatment arms (temozolomide (TMZ) vs. hypofractionated radiation 34Gy vs. radiation 60Gy), and based on the MGMT methylation status. From each group half of the patients had short survival and the other half had long survival.

overall_design: 59 samples FFPE samples, histologically described as glioblastoma. DNA was extracted with Maxwell FFPE DNA Purification Kit (Promega) and quantified using Quantus (Promega), after which it was bisullfite converted with EZ DNA methylation kit (Zymo Research). The quality was assessed with the Illumina Infinium HD FFPE QC Assay Protocol and methylome analysis was done with the Infinium MethylationEPIC BeadChip Kit (Illumina) complemented by the Infinium HD FFPE DNA Restore Kit.

first: Jyotirmoy

last: Das

first: Annika

last: Malmström

first: Peter

last: Söderkvist


title: p53 drives cytokine expression in melanoma to support proliferation and migration

city: Pittsburgh

first: Jacob

last: Stewart-Ornstein

state: PA

address: UPMC Hillman Cancer Center, 5117 Centre Avenue

department: computational and systems biology

institute: University of Pittsburgh, School of Medicine

summary: This study aims to define if p53 in melanoma is playing non-canonical roles.  Using RNAseq we find evidence that p53 regulates cytokine signaling in multiple melanoma cell lines.

overall_design: Melanoma cells are treated with various p53 activating agents (non-genotoxic, DNA damage) and gene expression measured.  P53 is deleted from melanoma cell lines and gene expression is measured.


title: Analysis of transgenerational effects on DNA copy number aberrations in male mice exposed to continuous 0.05mGy/day gamma-rays for 400 days (Primary screening for 0.05mGyG familly).


title: Analysis of transgenerational effects on DNA copy number aberrations in male mice exposed to continuous 0.05mGy/day gamma-rays for 400 days (Secondary screening for 0.05mGyE familly).