title: H3K36 methyltransferase SETD2 regulates lymphoid and neural development [seq]

first: Richard

last: Koche

state: New York

institute: Memorial Sloan Kettering Cancer Center

summary: We study the role of loss of Setd2 and H3K36me3 in early B cell development through NGS methods including RNA, ChIP and ATAC Seq of sorted B cell populations of control and Setd2KO primary B cells from mice.

overall_design: From age-matched littermate controls and Setd2KO mouse, we sorted early proB cells (B220+CD43+CD19-Cd25-IgM-) and performed ATAC-seq, RNA-Seq, and ChIP-seq using an antibody against H3K36me3.

first: S

middle: H

last: Chu

first: Scott

middle: A

last: Armstrong


title: Quantification, dynamic visualization, and validation of bias in ATAC-seq data with ataqv

status: Public on Mar 23 2020

city: Ann Arbor

first: Stephen

last: Parker

state: MI

address: 100 Washtenaw Avenue

country: USA

institute: University of Michigan

type: Genome binding/occupancy profiling by high throughput sequencing

summary: The assay for transposase-accessible chromatin using sequencing (ATAC-seq) has become the preferred method for mapping chromatin accessibility, due to its simplicity, speed, and low input material requirements. However, it can be difficult to evaluate data quality, particularly when processing many samples. Here, we present ataqv, a computational toolkit for efficiently measuring, visualizing, and comparing ATAC-seq quality control results. We perform controlled ATAC-seq experiments and utilize ataqv to show that the ratio of Tn5 transposase to nuclei and sequencing flowcell cluster density induce reproducible technical bias in ATAC-seq results, significantly changing the fragment length distribution and enrichment of reads in promoter and enhancer chromatin states.

overall_design: ATAC-seq was performed using seven different concentrations of Tn5 transposase, on DNA isolated from GM12878 cells. In one experiment ('PCR-constant'), the same number of PCR cycles were used for each library and n = 6 different nuclear isolations were performed, resulting in 42 total libraries. In another experiment ('PCR-constant'), the number of PCR cycles for each library was selected via qPCR, n = 3 different nuclear isolations were performed (resulting in 21 separate libraries), and each library was sequenced one a sequencing run with low cluster density ('low') as well as on a run with high cluster density ('high')

first: Peter

last: Orchard

first: Yasuhiro

last: Kyono

first: John

last: Hensley

first: Jacob

middle: O

last: Kitzman

middle: C


title: Next Generation Sequencing Facilitates Quantitative Analysis of the Role of Transcriptional Factor FoxM1 in Muscle Satellte Cells

city: Chongqing

first: Zhe

last: Chen

address: 1 Yixueyuan Road, Yuzhong District

country: China

institute: Chongqing Medical University

type: Expression profiling by high throughput sequencing

summary:
Purpose:To identify genes and the molecular pathways involved in the transcriptional factor FoxM1 regulating muscle satellite cells (SCs) in mice, we performed RNA-Sequence of SCs in qiuescent state (homeostatic condition) or activated state (48 hours-post injury).
Methods: mRNA  profiles of SCs in FoxM1fl/fl (floxp) and FoxM1fl/fl,Pax7Cre/+ (cKO) in quiescent state (Qfloxp or QcKO) or activated state (Afloxp or AcKO) were generated by deep sequencing, in triplicate, using Illumina HiSeq 2000. Activated state was induced by Bacl2 injection (48 hours-post injury).
Results:Using an optimized data analysis workflow, we mapped about 9 million sequence reads per sample to the mouse genome (build mm10) and identified 13776 transcripts in SCs (the floxp  and  cKO group) with BWA workflow.
Conclusions: Our results represent the first detailed analysis of SCs transcriptomes in FoxM1-knockout mice and found that FoxM1 regulated multiple mRNA pathways in SCs.

overall_design: The mRNA  profiles of SCs in Control and FoxM1-knockout mice (under hemostatic or injured condition) were generated by deep sequencing, in triplicate, using Illumina HiSeq 2000.

first: Yu

last: Hou


title: miRNA expression profiles in non-aggressive, invasive and metastatic papillary thyroid cancer

city: Adana

first: Esra

last: Gov

state: Turkey

address: Gültepe Mahallesi, Çatalan Caddesi

department: Bioengineering

country: Turkey

institute: Adana Alparslan Türkeş Science and Technology University

summary:
Paillary thyroid cancer (PTC) is the most common type of thyroid malignancy. Extrathyroidal invasion (ETİ), lymph node metastasis, and distance organ metastasis is poor prognostic factor in PTC. The metastasis is still a leading cause of papillary thyroid cancer death. The early detection of metastatic signature is crucial for identification of thyroid cancer prognosis and personalized therapeutic strategies.
In the present study, we  present thyroid cancer metastasis and invasivenes related miRNAs identified by comprehensive miRNA expression profiling of formalin-fixed paraffin embedded (FFPE) thyroid tissues obtained from patients belonging to intrathyroidal, invasive and metastatic thyroid carcinoma groups

overall_design: The formalin-fixed paraffin embedded (FFPE) carcinoma tissues of PTC patients from three different groups were included in the study: (i) non-aggressive tumors  patients having carcinoma size <2 cm, intrathyroidal, with no lymphovascular invasion (group A, n=3); (ii) patients with minimal invasion of extrathyroidal soft tissue (group B, n=3); (iii) patients with distant organ metastasis (group C, n=3). FFPE tissues of the follow-up and treatment patients of the Kocaeli University Faculty of Medicine Endocrinology and Metabolism Clinic, between the years of 2003-2016, were obtained from the pathology archive of Kocaeli University Faculty of Medicine.  Tumor histopathologic features such as histological subtype, extrathyroidal invasion, vascular and perineural invasion were evaluated by a clinopathological outcome blind pathologist. Groups were similar in age and gender.

first: Ozlem

last: Zeynep Akyay


title: mRNA expression profiles in non-aggressive, invasive and metastatic papillary thyroid cancer


title: Characterisation of epigenomic changes during chondrogenesis

city: NEWCASTLE UPON TYNE

first: David

last: Young

address: Centre For Life

country: United Kingdom

institute: Newcastle University

summary: Epigenetic mechanisms are known to regulate gene expression during chondrogenesis. In this study, we have characterised the epigenome during in vitro differentiation of human mesenchymal stem cells (hMSCs) into chondrocytes. Chromatin immunoprecipitation followed by next-generation sequencing (ChIP-seq) was used to assess a range of N-terminal post-transcriptional modifications (marks) to histone H3 lysines (H3K4me3, H3K4me1, H3K27ac, H3K27me3 and H3K36me3) in both hMSCs and differentiated chondrocytes. Chromatin states were characterised using histone ChIP-seq and cis-regulatory elements were identified in chondrocytes.

overall_design: Histone ChIP-seq (H3K4me3, H3K4me1, H3K27ac, H3K27me3, H3K36me3) in hMSC and differentiated chondrocytes at day 14. Input samples were sequenced for each cell type. Experiments were performed with 2 replicates.

first: Kathleen

last: Cheung

first: Matthew

middle: J

last: Barter


title: Inducible knock-out of BCL6 in lymphoma cells results in tumor stasis

city: Vienna

first: Daniel

last: Gerlach

address: Dr.-Boehringer-Gasse 5-11

department: Global Computational Biology and Digital Sciences

country: Austria

institute: Boehringer Ingelheim RCV GmbH & Co KG

summary: Diffuse large B-cell lymphoma (DLBCL) is the most common type of non-Hodgkin lymphomas worldwide and is characterized by a high diversity of genetic and molecular alterations. Chromosomal translocations and mutations leading to deregulated expression of the transcriptional repressor BCL6 occur in a significant fraction of DLBCL patients. An oncogenic role of BCL6 in the initiation of DLBCL has been shown as the constitutive expression of BCL6 in mice recapitulates the pathogenesis of human DLBCL. However, the role of BCL6 in tumor maintenance remains poorly investigated due to the absence of suitable genetic models and limitations of pharmacological inhibitors. Here, we have utilized tetracycline-inducible CRISPR/Cas9 mutagenesis to study the consequences of BCL6 deletion in established DLBCL models in culture and in vivo. We show that BCL6 knock-out in SU-DHL-4 cells in vitro results in an anti-proliferative response 4-7 days after Cas9 induction that was characterized by cell cycle (G1) arrest. Conditional BCL6 deletion in established DLBCL tumors in vivo induced a significant tumor growth inhibition with initial tumor stasis followed by slow tumor growth kinetics. Our findings support a role of BCL6 in the maintenance of lymphoma growth and showcase the utility of inducible CRISPR/Cas9 systems for probing oncogene addiction.

overall_design: For the generation of dox-inducible cell lines, SU-DHL-4 cells were modified to express the rtTA3 using lentiviral transduction of MSCV-rtTA3-IRES-EcoR-PGK-Puro followed by selection with Puromycin. The resulting cell line was transduced with a TRE3G promoter-driven Cas9-GFP cassette (pRRL-TRE3G-Cas9-P2A-GFP). Single cell clones were picked, expanded and tested for Cas9 induction and promoter leakiness as described. A selected SU-DHL-4 Cas9 clone was infected with a vector allowing for U6 promoter driven constitutive expression of negative control and BCL6 targeting sgRNAs and in addition contains an EF-1alpha short (EF1as) promoter driven mCherry fluorescence marker. Editing efficiency was confirmed in a bulk depletion assay as described before. mCherry+ cells (sgRNA expressing cells) were single cell sorted using a Sony Sorter SH800.  For treatment of SU-DHL-4 cells to induce Cas9 expression, doxycycline (Sigma #D9891) was dissolved in sterile water and was added to the cell culture medium at a final concentration of 100 ng/ml if not indicated differently. Subsequently cells were harvested for total RNA isolation using TriZol (Ambion) and further purified using miRNAeasy columns (Qiagen). Approximately 500ng of total RNA were subjected to library preparation using the TruSeq RNA Library Prep Kit v2 with polyA selection as recommended by the manufacturer (Illumina) without generating stranded information. Library were multiplexed and sequenced on a NextSeq 500 system using paired-end sequencing with 76 cycles.

first: Stefanie

last: Schlager

first: Roland

last: Varecka

first: Norbert

last: Schweifer

first: Tilman

last: Voss


title: miRNA and mRNA expression profiles in non-aggressive, invasive and metastatic papillary thyroid cancer

type:
Non-coding RNA profiling by array
Expression profiling by array

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

platform_organism:
Homo sapiens
synthetic construct

overall_design: Refer to individual Series


title: Next Generation Sequencing Facilitates Quantitative Analysis of Original and RCHO-resistant OCI-LY8 cell Transcriptomes

status: Public on Mar 30 2020

city: Shanghai

first: Jianfeng

state: Shanghai

address: 270 Dong'an Road

institute: Fudan University Shanghai Cancer Center

summary: The goal of this study is to screen the differential genes between original and RCHO-resistant OCI-LY8 cells, then analyze the significant pathways.

overall_design: The total RNA of each group was pooled from 3 different passages separately. RNA-seq was performed using the proton sequencing process.

first: Weiguo

last: Hu


title: Dysregulation of lncRNAs and circRNAs in mouse testes after exposure to triptolide

city: Nanchang

first: Xiaoning

last: Zhang

address: 999 Xuefu R.D., Nanchang

institute: Nanchang University

type: Non-coding RNA profiling by high throughput sequencing

summary: Triptolide has been shown to exert various pharmacological effects on systemic autoimmune diseases and cancers. However, its severe toxicity, especially reproduction toxicity, prevents wide clinical use for those people with fertility needs. Noncoding RNAs including lncRNAs and cicrRNAs are regulatory molecules that mediate a wide variety of physiological activities, which are critical for spermatogenesis, and their dysregulation might lead to male infertility. However, whether they are involved in triptolide-induced reproduction toxicity is fully unknown. Here, after exposure of mice to triptolide for 35 day, the total RNAs were used to investigate lncRNAs/cicrRNAs/mRNAs expression profiles by strand-specific RNA sequencing at the transcriptome level to help determine any RNA-related mechanisms in triptolide-induced toxicity. The results showed that triptolide significantly decreased the testicular weight, damaged testis and sperm morphology, reduced sperm motility and density. Furthermore, there's a remarkable deformity in sperm head and tail in triptolide-exposed mice. At the transcriptome level, the triptolide-treated mice exhibited aberrant expression profiles for lncRNAs/cicrRNAs/mRNAs, many of them were dysregulated. Gene ontology and pathway analyses revealed that the functions of differentially expressed lncRNA targets, cicrRNAs cognate genes and mRNAs were closely linked with many processes involved in spermatogenesis. Additionally, many newly identified lncRNAs /cicrRNAs displayed inducible expression, suggesting that they might be good candidate markers for triptolide-induced male reproductive toxicity. This study gives us an insight into understanding the reproductive system toxicity of triptolide and reminds us to strengthen the research on increasing efficacy and decreasing toxicity of triptolide.

overall_design: LncRNA profiles of testis were generated by stranded-specific RNA-seq, using Illumina HiSeq™ X Ten platform with PE150.

first: Suping

last: Xiong


title: Gene expression profile of human colorectal carcinoma HCT 116 cell line treated with imipramine

city: Murcia

first: Antonio

last: Parrado

address: Ctra. Madrid-Cartagena, s/n

country: Spain

institute: Hospital Clinico Universitario Virgen de la Arrixaca

summary: The study aim is to evaluate to what extent imipramine treatment of HCT-116 colorectal cell lines does affect fascin1-related or cytoskeleton-associated functions

overall_design: Gene expression signatures of HCT-116 cells treated with 20 µM imipramine and treated with 0.1% DMSO as control treatment were compared

first: Begoña

last: Alburquerque-González

first: Silvia

last: Montoro-García

first: Pablo

last: Conesa-Zamora


title: Giardia lamblia WB: 5'5npac control vs pPTop3b

city: Taipei

first: Chin-Hung

last: Sun

address: Department of Parasitology, College of Medicine, National Taiwan University

department: Department of Parasitology

country: Taiwan

summary: Transcriptional profiling of Giardia lamblia WB comparing control 5'5npac cells with pPTop3b cells.

overall_design: Two-condition experiment 5'5npac cells with pPTop3b cells.


title: Transcriptomic analyses between Lycium barbarum and Lycium ruthenicum

city: WuHan

first: Guosong

last: Jiang

state: Hubei Province

address: Jiefang Road, No. 1277

department: Department of Urology

institute: Union Hospital, Tongji Medical College, Huazhong University of Science and Technology

summary: Lycium barbarum, a member of the Solanaceae family, has been used for more than 2000 years in the traditional Chinese medicine. L. ruthenicum, endemic to northwestern China, is also used as medicine and has had a great influence on the development of Minority Medicine. Previous studies revealed there are many differences between two species, including morphological and phytochemical differences. However, the molecular mechanism of formation of its fruit and associated medicinal and nutritional components is unexplored. In the present studies, for transcriptomic analyses, fruits from 5 developmental stages L. barbarum and L. ruthenicum were collected. KEGG analyses for the DEGs between L. barbarum and L. ruthenicum, revealed that molecular mechanism of fruit formation were distinct obviously during the development process. Moreover, we found that multiple DEGs enriched in “Phenylpropanoid biosynthesis (ID: ko00940”, “Flavonoid biosynthesis” (ID: ko00941) were up-regulated in L. ruthenicum at different developmental stages of fruit. It suggested that biotic and abiotic stress might be responsible for high abundance of antioxidant capacities in L. ruthenicum.

sample_organism:
Lycium barbarum
Lycium ruthenicum

platform_organism:
Lycium barbarum
Lycium ruthenicum

overall_design: Comparative study on development of wolfberry by transcriptomic analyses from Lycium barbarum and Lycium ruthenicum

first: Jianhua

last: Zhao


title: Expression profiles of RNA during osteogenic differentiation of human mesenchymal stem cells under normal ground condition and simulated microgravity

city: Hangzhou

first: Liang

last: Li

state: Zhejiang

address: number 866 of Yuhangtang road, West Lake Dist

department: College of Life Sciences

institute: Zhejiang University

summary: In this study, hMSCs were osteogenically induced for 0, 2, 7 and 14 days under normal ground gravity and simulated microgravity, followed by analysis of the differences in transcriptome expression during osteogenic differentiation by RNA sequencing.

overall_design: The 3rd passage of hMSCs were cultured in T12.5 flasks and filled with osteogenic medium and fixed on a cell culture vessel for RPM exposure, while hMSCs grown in NG condition were also filled with osteogenic medium and were statically placed in the same CO2 incubator. The medium was changed twice a week. Cells induced for 0, 2, 7, and 14 days were used to study the effects of SMG.


title: Transcriptional gender specific changes in the APP/PS1 mouse model of Alzheimer’s disease pathology

city: Beerse

first: An

last: De Bondt

address: Turnhoutseweg 30

country: Belgium

institute: Janssen Pharmaceutica

summary: The prevalence of Alzheimer’s disease is significantly higher in women than in men, with recent estimates suggesting that two thirds of AD patients are females. However, the reason for this is unclear and complex, with the fact that women live longer than men being a likely contributor to the observed disparity. Given the complexity of AD and the restrictions in studying any gender-linked biological differences in patients, an established alternative is to study animal models of a disease. To determine if there are gender differences in the response of animals to amyloid deposit, a key pathological feature of AD, we did a genome-wide expression study on tissue obtained from the hippocampus and prefrontal cortex of male and female APP/PS1 mice at 8 months of age, a time at which significant cortical and hippocampal amyloid deposition is present. Amyloid deposit has previously been demonstrated in this model to be independent of gender. Regardless of the tissue sampled, we observed similar pathways affected in male and female mice. Focusing on major neurotransmitter and ionic pathways within the central nervous system reveal more profound gene expression changes in the prefrontal cortex and more restricted changes in the hippocampus. While the changes in the prefrontal cortex involved the same amount of genes in either gender only 60% of these are shown to overlap. In the hippocampus, distinctively fewer changes were observed in female mice than in male mice. By using pre-menopausal mice to investigation the gender differences in response to amyloid deposition, the effect of menopause and changes in progesterone and estrogen levels were eliminated in our study. While previous studies have focused on the genome-wide changes in AD models, the present study contributes to the existing literature on the gene changes in special relation to gender effect in AD.

overall_design: This study includes 58 samples. There are 8 groups considered, each with at least 6 biological replicates.

first: Tutu

last: Oyelami

first: Ilse

last: Van den Wyngaert

first: Kirsten

last: Van Hoorde

last: Dewachter

first: John

last: Kemp


title: Transcriptome analysis of human embryonic stem cell differentiation to endothelial cells

city: Edinburgh

first: Julie

last: Rodor

address: 47 Little France Crescent

department: Centre for Cardiovascular Science

institute: UNIVERSITY OF EDINBURGH

summary: Deep RNA sequencing was performed during human embryonic stem cell (hESC) differentiation to endothelial cells (ECs), via mesodermal precursors. Our work focused on long non-coding RNAs (lncRNAs) regulated during EC differentiation as lncRNA are known regulators of cell differentiation, physiology and disease. EC-enriched lncRNAs were screened for binding sites for the transcription factor ERG, important for endothelial cell identity and function. The LINC00961 gene, first annotated as a lncRNA but now reassigned as a protein coding gene for the SPAAR micropeptide, was potently activated during differentiation. Using primary ECs, we studied the role of LINC00961 locus after depletion and gain of function experiments and showed its effect on EC adhesion, tube formation, migration and proliferation. We showed that LINC00961 functions as a bona fide non-coding RNA in ECs, at least in part, through binding to TMSB4X.

overall_design: We used an embryoid body based directed differentiation protocol developed in our laboratory to generate ECs directly via mesodermal precursors (MP) (Boulberdaa et al, 2016 Mol Ther). To ensure the purity of specific cell lineages, we included purification steps based on mesodermal (CD326low/CD56+) and endothelial specific cell surface (CD31+/CD144+) markers to enrich target populations. Our RNAseq analysis includes the following populations: the d0 H9 human embryonic stem cells (ESC - 4 replicates), the day3 mesoderm population (CD326lowCD56+ purified from embryoid bodies) (MP - 4 replicates) and the day 3 remaining cell population (non-MP - 4 replicates), the day 7 selected endothelial cells (CD144+CD31+) (EC - 2 replicates) and the day 7 remaining population (non-EC - 2 replicates). We also included in our analysis Human Saphenous Vein Endothelial Cells (HSVEC - 4 replicates) as a control of mature endothelial cell population. RNA-seq was performed (45 million paired end reads per sample) on ribosomal RNAs depleted libraries.

first: Helen

middle: L

last: Spencer

first: Rachel

last: Sanders

first: Mounia

last: Boulberdaa

first: Graeme

last: Birdsey

first: Joanne

last: Mountford

first: Costanza

last: Emmanueli

first: Anna

last: Randi

first: Andrea

last: Caporali

first: Mairi

last: Brittan

first: Andrew

last: Baker


title: Zscan4 binds nucleosomal microsatellite DNA and protects mouse two-cell embryos from DNA damage [ATAC-seq]

status: Public on Mar 22 2020

city: Stanford

first: Tomek

last: Swigut

state: CA

address: 265 Campus Dr

department: Chemical and Systems Biology

institute: Stanford University

summary: ATAC-seq from mouse ESC with stably integrated Zscan4c-GFP reporter.

overall_design: Measured genome-wide chromatin accessibility status in 2C-like cells by performing ATAC-seq in the GFP positive population sorted from the Zprom::GFP reporter mouse ESC line. There is one sample analyzed.

first: Rajini

last: Srinivasan

first: Joanna

last: Wysocka


title: RNA-seq of Histamine stimulated HUVECs infected with shNT or shH1R

city: Beijing

first: Jiayi

last: Chen

address: 27 Tai-Ping Road

institute: National Center of Biomedical Analysis

summary: To investigate the mechanism of histamine H1 receptor (H1R)- mediated proliferation and angiogenesis of endothelial cells, mRNA profiles of HUVEC cells transduced with shNT or shH1R under histamine treatment for 9 hrs were generated by deep sequencing, in replicate, using Illumina GAIIx.  We identified the upregulation of genes in several pathways including angiogenesis, proliferation and migration that could be responsible for the increased tube formation in histamine treated shNT expressing HUVEC cells

overall_design: mRNA profile of shNT or shH1R expressing HUVEC cells under histamine treatment for 9 hrs were generated by deep sequencing, in replicate, using  Illumina HiSeq 2500 .

first: Jjiayi


title: Transcriptional responses to TNF following HFol treatment of wild type and GCN2 depleted synoviocytes

city: Boston

first: John

middle: N

last: Hutchinson

state: Massachusetts

address: 201 Wachusett Street

institute: Diamond Age Data Science

summary:
We report the effects of Hfol on TNF induction of inflammatory genes in wild type cells versus cells depleted of GCN2
RNA-seq analysis of wild type or GCN2-depleted established fibroblast like synoviocytes (K4 cells) treated with TNFa in the presence or absence of Halofuginone (HF).

overall_design: To test the requirement for the protein kinase GCN2 in the effects of  the aminoacyl tRNA synthetase (AARS) inhibitor HF, wild type K4 cells or cells depleted of GCN2 by stable infection with a  lentiviral shRNA directed against GCN2 cells in culture were treated, using duplicate samples for each condition, for 16 hours with HF and 8 hours with  TNFa.

first: Tracy

last: Keller

first: Malcolm

last: Whitman


title: Expression data from small intestine of NFKBIA-KO mice versus wild type

city: Berlin

first: Marina

last: Kolesnichenko

address: Robert-Rössle-Str. 10

country: Germany

institute: Max-Delbrück-Center

summary: The IkB-Kinase (IKK)-NF-kB signaling pathway plays a multifaceted role in Inflammatory Bowel Disease: One the one hand it protects cells from apoptosis, but on the other, it activates transcription of numerous inflammatory cytokines and chemokines. To examine the role of constitutive NF-kB signaling in intestinal epithelium cells (IEC), we generated a mouse model with a tissue-specific knockout of the direct inhibitor of NF-kB, IkBα.  We demonstrate that in IκBαIEC-KO mice, constitutive activation of NF-kB in epithelium leads to abnormal intestinal development, enlarged peyer’s patches, loss of Paneth cells, and spontaneous inflammation. We performed expression analysis of IκBαIEC-KO mice compared to wildtype by using the Affymetrix array Clariom S mouse.

overall_design:
We utilized the Cre-loxP recombination system to generate a mouse line that allows tissue-selective deletion of IκBα. The targeting construct was designed in a way that Cre-mediated recombination results in deletion of the promoter region containing essential regulatory NF-κB binding sites, the core promoter, and the first two exons. To achieve tissue specific knockout, mice were crossed to Villin-Cre bearing mice.
IκBαIEC-KO mice (Villin-Cre x floxed IκBα) were genotyped, depletion of IκBα was confirmed in each case by qRT-PCR on RNA extracted from bulk small intestine.  Mice between 8-11 weeks of age were used for experiments. For each knockout mouse, a littermate sibling control was taken for comparison. For RNA  extraction, duodenum was snap-frozen in liquid nitrogen and homogenized. RNA was extracted using Trizol reagent according to manufacturer’s instructions (Thermo Fisher). Preparation of cDNA, fragmentation and labeling was performed with the GeneChIPTM WT PLUS reagent kit (ThermoFisher Scientific). Samples were hybridized to the mouse Clariom™ S Assay (ThermoFisher Scientific).

first: Eva

last: Kärgel

first: Claus

last: Scheidereit


title: Transcriptional responses of fibroblast like synoviocytes to TNFa in the presence or absence of Halofuginone (HF)


title: Zscan4 binds nucleosomal microsatellite DNA and protects mouse two-cell embryos from DNA damage [ChIP-seq]

summary: Genome-wide binding analysis of Zscan4 showed sequence-specific occupancy at (CA)n microsatellite repeats in 2C-like cells. Genome-wide occupancy profiling of FACT subunit SSRP1 in curaxin-treated mouse ESC demonstrated re-localization from transcription start sites to Zscan4 binding sites.

overall_design: We profiled SSRP1 binding sites by performing ChIP-seq using an SSRP1 antibody in control or curaxin-treated mouse ESC. There are twelve samples analyzed and two replicates for each treatment. We also identified direct targets of Zscan4 in 2C-like cells by performing ChIP-seq using a GFP antibody in 2C-like cells (GFP positive population) from the Zprom::GFP-Zscan4 reporter line and control Zprom::GFP line, and profiled genomic occupancy of endogenous Zscan4 using a Zscan4 antibody in the Zprom::GFP line (GFP positive population and control GFP negative population). There are eight samples analyzed.


title: Transcriptional responses to TNF following HFl treatment of primary rheumatoid arthritis fibroblast like synoviocytes (RA-FLS)

summary:
We report the effects of Hfol on TNF induction of inflammatory genes in wild type cells versus cells depleted of GCN2
RNA-seq analysis of primary rheumatoid arthritis fibroblast like synoviocytes (RA-FLS) treated with TNFa in the presence or absence of Halofuginone (HF).

overall_design: To test the effect of the aminoacyl tRNA synthetase (AARS) inhibitor HF on inflammatory responses in RA-FLS, cells in culture were treated, using duplicate samples for each condition, for 16 hours with HF and 8 or 24 hours with  TNFa.

first: Yeonjin

last: Kim


title: Genomic profiles of crocidolite-induced malignant peritoneal mesotheliomas developed in mice

city: Nagoya

first: Shinya

last: Toyokuni

state: Aichi

address: 65 Tsuruma-Cho, Showa-Ku

department: Pathology

country: Japan

institute: Nagoya University

type: Genome variation profiling by genome tiling array

summary: Intraperitoneal injection of crocidolite initiates malignant peritoneal mesothelioma (MM) in mice. We performed high-resolution comparative genomic hybridization to identify characterstics in the genomic profiles of crocidolite-induced MM in the mice.

overall_design: The carcinogenesis protocol was performed for five groups of wild type, Dmt1-transgenic, Mth1-knockout, Mutyh-knockout and Ogg1-knockout mice. Genomes of 20 malignant mesotheliomas were profiled on Agilent 180K mouse genome CGH microarrays.

first: Yasumasa

last: Okazaki

first: Satomi

last: Funahashi

last: Akatsuka


title: Temporo-spatial distribution and transcriptional profile of retinal microglia in the oxygen-induced retinopathy mouse model

city: Freiburg

first: Clemens

last: Lange

address: Kilianstraße 5

department: Klinik für Augenheilkunde

institute: Uniklinik Freiburg

summary: Myeloid cells such as resident retinal microglia or infiltrating blood-derived macrophages accumulate in areas of retinal ischemia and neovascularization (RNV) and modulate neovascular eye disease. Their temporo-spatial distribution and biological function in this process, however, remain unclarified. We determined the extent of microglia proliferation and macrophage infiltration in areas of ischemia and RNV using Cx3cr1CreERT2:Rosa26-tdTomato mice and assessed the transcriptional profile of microglia in the oxygen-induced retinopathy (OIR) mouse model. We show that microglia are the predominant myeloid cell population in areas of RNV. Thirty percent of retinal microglia were EdU-positive indicating considerable expansion of local microglia. RNA-Seq revealed an enrichment of processes related to cell division and chemokine receptor binding. We propose that activated retinal MG alter their transcriptional profile, exhibit proliferative ability and are by far the most frequent myeloid cell population in areas of RNV in the OIR model thus presenting a potential target for future therapeutic approaches.

overall_design: Examination of the transcriptional profile of retinal microglia cells in the healthy retina and in the oxygen-induced retinopathy model

first: Myriam

last: Boeck

first: Adrian

last: Thien

first: Julian

last: Wolf

first: Nora

last: Hagemeyer

first: Yannik

last: Laich

first: Dilmurat

last: Yussuf

first: Rolf

last: Backofen

first: Peipei

last: Zhang

first: Stefaniya

last: Boneva

first: Andreas

last: Stahl

first: Ingo

last: Hilgendorf

first: Hansjürgen

last: Agostini

first: Marco

last: Prinz

first: Peter

last: Wieghofer

first: Günther

last: Schlunck

first: Anja

last: Schlecht


title: Genomic profiles of tremolite-induced malignant peritoneal mesotheliomas developed in rats

first: Shinya

last: Toyokuni

summary: Intraperitoneal injection of tremolite initiates mesothelial injury and chronic inflammation that causes the development of malignant mesothelioma (MM). We performed high-resolution comparative genomic hybridization to identify characteristics in the genomic profiles of tremolite-induced MMs in rats.

overall_design: The carcinogenesis protocol was performed by intraperitoneal injection of 10 mg of tremolite  in F1 hybrid (crossing Brown-Norway and Fischer344) rats. Genomes of 8 malignant peritoneal mesothelioma were profiled on Agilent 180K rat genome CGH microarrays.

first: Okazaki

last: Yasumasa

first: Akatsuka

last: Shinya

first: Toyokuni


title: Molecular classification and therapeutic targets in extrahepatic cholangiocarcinoma

city: Barcelona

first: Robert

last: Montal

address: Rosselló 153

institute: IDIBAPS

summary:
Genome-wide expression analysis of 182 extrahepatic cholangiocarcinoma and 38 non-tumoral bile duct samples as part of a integrated study of gene expression and targeted DNA-sequencing in patients with extrahepatic cholangiocarcinoma
We used whole-genome transcriptome to conduct an unsupervised molecular classification of extrahepatic cholangiocarcinoma

overall_design: Formalin-fixed paraffin-embedded samples (primary extrahepatic cholangiocarcinoma and non-tumor bile duct) from patients treated with surgical resection

first: Josep

middle: M

last: Llovet


title: Abscisic acid transcriptional response of the maize epigenetic mutant, mop1-1

city: Bothell

first: Thelma

middle: F

last: Madzima

state: WA

address: 18115 Campus Way NE

department: Division of Biological Sciences

institute: University of Washington Bothell

type: Methylation profiling by high throughput sequencing

summary:
MOP1-dependent and ABA-responsive pathways act within complex, connected transcriptional regulatory networks to mediate tissue-specific growth and responses to abiotic stress in maize
Purpose: To identify genome-wide ABA-induced, MOP1-dependent and independent transcriptional responses
Methods:  mRNA profiles of Mop1 wildtype and mop1-1 mutant V3 stage maize seedlings  were subjected to ABA and MS treatments for 8 hours. The trimmed sequence reads were analyzed at the gene level using HISAT2, stringite, and edgeR.
Results: we mapped ~23 million, 150 bp, paired-end sequence reads per sample to the B73 version 4 maize genome and identified 3,242 genes in four pairwise-comparisons to be differentially expressed genes (DEGs) with a fold change ≥2 and FDR <0.05, 1,561 DEGs were found to be unique to one genotype/treatment comparison.
Conclusions: Our study represents the first analysis of ABA in maize seedlings in the RdDM (mop1-1) mutant, with biological replicates, and generated by RNA-seq technology. We identified common targets of MOP1 and ABA transcriptional regulation.

overall_design: RNA-seq and Sequence Capture Bisulfite-seq was preformed on homozgyous Mop1 wildtype and mop1-1 mutant V3 seedling shoots with and without exogenous 50 µM ABA treatment  for 7 (SeqCap) or 8 hours (RNA-seq).

first: Karen

last: McGinnis

first: Stefania

last: Vendramin

first: Ji

last: Huang

last: Crisp


title: Loss of Apc impairs Lgr5+ intestinal stem cell fate programs [RRBS]

city: Montpellier

first: Philippe

last: Jay

address: 141 rue de la Cardonille

country: France

institute: CNRS-Inserm-University

summary: Loss of APC is the main driving alteration associated with colorectal cancer (CRC) development. We investigate the immediate outcome of this genetic event on the transcriptomic and DNA methylation profiles of Lgr5+ intestinal stem cells (ISCs), considered as the cell-of-origin of CRC. RNA-seq analyses show that the sequential deletion of Apc alleles  has a rapid impact on the transcriptional profiles of ISCs. Indeed, Apc loss-of-function dictates an altered cell fate program at transcriptional level, resuting in an impaired commitment of those cells to differentiation. Reduced-representation bisufite sequencing (RRBS) on the genomic DNA (gDNA) also shows that focal alterations occur in the DNA methylations profiles of ISCs at this stage, and functionally contribute to altered cell fate in those cells. This study sheds light on the earliest events in CRC development, proving evidences on the role exerted by DNA methylation changes associated with Apc inactivation in the homeostatic rupture at CRC initation.

overall_design: Lgr5+-GFP+ Intestinal stem cells were FACS-sorted from 4 Apc+/+ : , 4 ApcFlox/+, : and 4 ApcFlox/Flox : Lgr5-CreERT2-ires-eGFP mice 15 days after the activation of the Cre recombinase by tamoxifen administration to study the impact of the mutation on gene expression and DNA methylation profiles.

first: Michael

last: Weber


title: Loss of Apc impairs Lgr5+ intestinal stem cell fate programs [RNA-seq]


title: Loss of Apc impairs Lgr5+ intestinal stem cell fate programs

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

overall_design: Refer to individual Series


title: NONO-mediated alternative splicing of SETMAR inhibits lymphatic metastasis in bladder cancer

status: Public on Mar 21 2020

city: Guangzhou

first: Ruihui

last: Xie

state: Guangdong

address: 107 Yan Jiang West Road

institute: Sun Yat-sen Memorial Hospital, SYSU

summary: To explore the molecular mechanism underlying NONO-mediated lymphatic metastasis inhibition in bladder cancer, a genome-wide RNA-sequencing was conducted to compare gene expression profiles of UM-UC-3 cells with NONO knockdown and control.

overall_design: Bladder cancer cell line UM-UC-3 was transfected with the control siRNA or two independent NONO siRNAs for 48h. The RNA of the transfected cells was extracted and sequenced on an Illumina Hiseq 2500 platform and 100 bp paired-end reads were generated.

first: Xu

last: Chen

first: Tianxin

last: Lin

first: Jian


title: Podocyte-specific deletion of tubular sclerosis complex 2 causes focal segmental glomerular sclerosis and progressive renal failure

city: Shinjuku-ku, Tokyo

first: Hiroyuki

last: Unoki-Kubota

address: 1-21-1 Toyama

department: Department of Diabetic Complications, Diabetes Research Center, Research Institute

institute: National Center for Global Health and Medicine

summary: Obesity can initiate and accelerate the progression of kidney diseases. However, it remains unclear how obesity affects renal dysfunction. Here, we show that a newly generated podocyte-specific tubular sclerosis complex 2 (Tsc2) knockout mouse model (Tsc2∆podocyte) develops proteinuria and dies due to end-stage renal dysfunction by 10 weeks of age. Tsc2∆podocyte mice exhibit an increased glomerular size and focal segmental glomerulosclerosis, including podocyte foot process effacement, mesangial sclerosis and proteinaceous casts. Podocytes isolated from Tsc2∆podocyte mice show nuclear factor, erythroid derived 2, like 2-mediated increased oxidative stress response on microarray analysis and their autophagic activity is lowered through the mammalian target of rapamycin (mTOR)—unc-51-like kinase 1 pathway. Rapamycin attenuated podocyte dysfunction and extends survival in Tsc2∆podocyte mice. Additionally, mTOR complex 1 (mTORC1) activity is increased in podocytes of renal biopsy specimens obtained from obese patients with chronic kidney disease. Our work shows that mTORC1 hyperactivation in podocytes leads to severe renal dysfunction and that inhibition of mTORC1 activity in podocytes could be a key therapeutic target for obesity-related kidney diseases.

overall_design: To explore the molecular mechanism of podocyte dysfunction in Tsc2∆podocyte mice, we conducted microarray analysis using the total RNA of primary podocytes isolated from Tsc2∆podocyte and control Tsc2flox/flox mice with or without rapamycin treatment (n = 4/each group).

first: Wakiko

last: Iwata

first: Hideki

last: Kato

first: Akira

last: Shimizu

first: Michihiro

last: Matsumoto

first: Toshiyuki

last: Imasawa

first: Arisa

last: Igarashi

first: Kenji

first: Tetsuo

last: Noda

first: Yasuo

last: Terauchi

first: Masaomi

last: Nangaku

first: Masato

last: Kasuga

first: Yasushi

last: Kaburagi


title: Fibroblast-specific genome-scale modelling predicts an imbalance in amino acid metabolism in Refsum disease

city: Leiden

first: Agnieszka

last: Wegrzyn

address: Einsteinweg 55

country: Netherlands

institute: Leiden University

summary:
In this study, we reconstructed a fibroblast-specific genome-scale model based on the recently published, FAD-curated model, based on Recon3D reconstruction.
To constrain the model we used transcriptomics, and proteomics data, which we obtained from healthy controls and Refsum disease patient fibroblasts incubated with phytol, a precursor of phytanic acid.
Using this model, we investigated the metabolic phenotype of Refsum disease at the genome-scale, and we studied the effect of phytanic acid on cell metabolism. We identified 20 metabolites that were predicted to discriminate between Healthy and Refsum disease patients, several of which with a link to amino acid metabolism.

overall_design: Comparison between control and Refsum disease patient cell lines (and models) metabolism, with or without exposure to phytol.

middle: B

first: Katharina

last: Herzog

first: Albert

last: Gerding

first: Marcel

last: Kwiatkowski

first: Justina

last: Wolters

first: Amalia

last: Dolga

first: Alida

last: van Lint

first: Ronald

last: Wanders

first: Hans

middle: R

last: Waterham

first: Barbara

last: Bakker


title: Characterization of Ewing sarcoma resistance to the EWS-FLI1 inhibitor YK-4-279

city: Washington

first: Garrett

middle: Thomas

last: Graham

state: DC

address: 3970 Reservoir Rd NW

department: Oncology

institute: Georgetown University Medical Center

summary: Ewing sarcoma (ES) is the second most common pediatric malignancy of the bones and soft tissue, but few advances in therapeutic options have been made over the past several decades. A characteristic feature of ES that and an attractive therapeutic targets is the EWS-FLI1 fusion protein. A small molecule inhibitor of EWS-FLI1, YK-4-279 was as a targeted therapy option for Ewing sarcoma patients. A YK-4-279 analog, TK216, is currently in clinical trial. With any targeted therapy, there is always the risk that tumors will become resistant and stop responding to treatment. Here, we investigated resistance mechanisms to YK-4-279 (YK) by developing ES cell lines specifically resistant to YK. We found that expression of the cell surface protein CD99 was elevated in YK-resistant cells. Increased CD99 expression occurs within five days of YK treatment in vivo. When CD99 expression is reduced by shRNA, resistant cells regain sensitivity to YK but reducing CD99 expression in non-resistant cells does not affect sensitivity. Little is known about CD99 function in the context of Ewing sarcoma, but the data presented here indicates the function of CD99 is altered upon acquisition of YK resistance, and that CD99 serves a critical function in developed resistance to YK-4-279. RNA sequencing analysis yielded candidate genes that may also be involved in the YK resistance mechanism. We identified a potential modulator of CD99 function, ANO1, a member of the ANO family and a participant in membrane-bound ion channel activity. CD99 has previously been linked with membrane-associated ion channels. A functional association between the two proteins remains to be investigated.

overall_design: Three samples each of A4573, TC-71, A4573-R, and TC-71-R

first: Erin

last: Conn

first: Sarah

last: Hour

first: David

middle: V

last: Allegakoen

first: Jeff

last: Petro

first: Marilyn

last: Kouassi-Brou

middle: T

first: Saravana

middle: P

last: Selvanathan

first: Haydar

last: Çelik

first: Jeffrey

last: Toretsky

first: Aykut

last: Üren


title: H3K4me2 Chromatin Immunoprecipitation sequencing analysis of chicken Embryonic stem cells, Primordial germ cells and Spermatogonial stem cells

city: Yangzhou

first: Chen

last: Zhang

address: wenhui road

institute: Yangzhou university

summary: We report the chromatin status in chicken Embryonic stem cells（ESCs）, Primordial germ cells (PGCs) and Spermatogonial stem cells (SSCs). H3K4me2 antibody was used to collect DNA sequences through CHIP experiments, and the DNA was analyzed by next-generation sequencing. We mapped the genome-wide chromatin maps of chicken ESCs, PGCs, and SSCs. We found that the entire genome of H3K4me2 in ESCs, PGCs, and SSCs was erased and then reconstructed. Most of the enriched genes were related to the cell lineage. It is mainly enriched in distal intergenic. H3K4me2 in the promoter first enriches in ESCs, then decreases in PGCs. The enrichment rebuilds in SSCs. This study provides a basis for analyzing the differences of chromatin status in ESCs, PGCs, and SSCs.

overall_design: Examination of H3K4me2 modifications in 3 cell types.

first: Bichun

last: Li

first: Qisheng

last: Zuo

first: Yani


title: Kdm5b depletion in embryonic stem cells does not induce intragenic promoters or affect transcription [HELP-tagging]

city: Bronx

first: Andrew

last: Johnston

state: NY

address: 1301 Morris Park Avenue

department: Genetics

institute: Albert Einstein College of Medicine

summary: The application of massively-parallel sequencing (MPS) technology to understanding how the genome is regulated is of major importance, as we now appreciate sequence variants associated with common heritable diseases to be enriched at regulatory elements in the genome.  There is, however, an enormous challenge inherent to these studies, which are much more varied as assays and in terms of analytical approaches than the approaches  used to define the sequence variants themselves.  For example, there areis a plethora of assays that test 5-methylcytosine genome-wide, numerous different analytical approaches to defineing peaks from chromatin immunoprecipitation sequencing (ChIP-seq), and increasingly diverse aspects of genomic regulation being studied.  The extremely large data sets generated do not lend themselves to distribution without some degree of pre-processing, and the hardware requirements for running these analyses are often substantial.  We have highlighted these concerns previously, but the central concern for our field is that genomics research is especially prone to poor reproducibility, and is a prime candidate for implementation of measures that could help to address this general problem.To illustrate the practical issues involved in genomics reproducibility, we sought to analyze our and three previoulsy published studies of the histone demethylase KDM5B using the same analytical approaches.

overall_design: Cytosine methylation profile of mouse embryonic stem (mES) cells after knock down of Kdm5b

first: Maria-Paz

last: Ramos

middle: D

first: John

last: Greally


title: Kdm5b depletion in embryonic stem cells does not induce intragenic promoters or affect transcription [RNA-Seq]

overall_design: mRNA profile of mES cells after Kdm5b knock down


title: Kdm5b depletion in embryonic stem cells does not induce intragenic promoters or affect transcription


title: Expression data from D. melanogaster raised on glucose-enriched or unmodified holidic food II

status: Public on Mar 20 2020

city: Edmonton

first: Edan

last: Foley

state: Alberta

address: 114 ST and 87 AVE

department: Medical Microbiology and Immunology

country: Canada

institute: University of Alberta

summary:
We used microarrays to examine transcriptional profiles of female flies raised on either a glucose-enriched (100 g/L) or unmodified holidic diet.
We found several diet-dependent effects including increased growth pathway and immunity expression in flies raised on a glucose-enriched diet.

overall_design: Newly eclosed w1118 females were raised for 10 days at 25˚C on either a glucose-enriched (100g/L) or unmodified holidic diet. RNA was extracted from samples of 5 whole flies or 10 dissected midguts in triplicate.

first: Anthony

last: Galenza


title: RNA helicase Belle (DDX3) non-autonomously suppresses germ cell tumorigenesis in the testes of Drosophila via regulation of multiple mRNAs

city: Moscow

first: Alexei

middle: A.

last: Kotov

address: 26 Vavilov Street

country: Russia

institute: Koltzov Institute of Developmental Biology of the Russian Academy of Sciences

summary: DEAD-box RNA helicases DDX3 are important developmental regulators of multiple aspects of RNA metabolism of eukaryotes. belle, a single DDX3 ortholog in Drosophila, is essential for fly viability, fertility, and germline stem cell maintenance. Here we showed that RNAi belle knockdown in testis cyst cells caused a disruption of adhesion between germ cells and cyst cells and a generation of tumor-like clusters of stem-like germ cells. Ectopic expression of β-integrin in cyst cells rescued early stages of spermatogenesis in the belle knockdown testes, indicating that integrin adhesion complexes are required for interaction between somatic and germ cells in cyst. To address in details Belle functions in spermatogenesis we performed CLIP-seq analysis and identified multiple mRNAs which interacted with Belle in the testes. A set of Belle targets includes mRNAs of factors that are essential for preventing tumor-like cluster formation of early germ cells and ensuring of sustained gametogenesis.

overall_design: CLIP-seq to identify target genes of belle (DDX3) in Drosophila testes


title: microRNA microarray profile in the plasma of mild cognitive impairment due to Alzheimer's disease

city: Shanghai

first: Haining

last: He

address: 600 South Wan Ping Road

department: Department of Geriatric Psychiatry

institute: Shanghai Mental Health Center

summary: To explore the microRNAs associated with pathology of early Alzheimer's disease, we detected the microRNA profiles in the plasma of subjects with mild cognitive impairment due to Alzheimer's disease and gender-, age-, education-matched normal control elderly.

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus

overall_design: We recruited five mild cognitive impairment due to Alzheimer's disease subjects and five gender-, age-, education-matched normal aging elderly. Blood samples of all participants were collected after fasting for 12 hours. Then plasma was saperated, and the RNA was extracted for the microRNA microarray analysis.

first: Tao

last: Wang


title: Effects of SF3B1 mutation on blast cells from patients with MDS

city: Cleveland

first: Hyunmin

last: Kim

state: Ohio

address: 10900 Euclid Ave.

department: Department of Genetics and Genome Sciences

institute: Case Western Reserve University

overall_design:
Here we isolated bone marrow blast cells from 7 patients with myelodysplastic syndrome (MDS): 4 patients with the SF3B1 -K700E mutation and 3 patients without SF3B1, U2AF1, or SRSF2 mutations (WT). RNA was prepared and RNAseq performed to determine the effects of SF3B1-K700E on gene expression and pre-mRNA splicing.
WT (n=3), K700E (n=4)

first: Scott

last: Alper

first: Aik-Choon

last: Tan

first: Daniel

last: Pollyea


title: Differential gene expression in the esophageal epithelium of WT mice, p63KO mice and p63KO;Villin-Cdx2 mice

city: Camden

first: Xiaoxin

middle: Luke

last: Chen

state: NJ

address: 403 Haddon Ave

institute: Coriell Institute for Medical Research

summary: We aimed to determine the effects of p63KO and p63KO/Cdx2 overexpression on gene expression profiles in the mouse esophageal epithelium (P0).

overall_design: WT mice; p63 KO mice; p63KO/Villin-Cdx2 mice

first: Caizhi

last: Huang


title: A transcriptional roadmap for 2C-like to pluripotent state transition  [single cells]

city: Doha

first: Mohamed Nadhir

last: Djekidel

state: Doha

address: Gharafa

department: Translational Medicine Department

country: Qatar

institute: Sidra Medicine

summary: In mouse embryonic stem cell (ESC) culture, a small proportion of cells display totipotent features by expressing a set of genes that are only active in 2-cell-stage embryos. These 2-cell-like (2C-like) cells spontaneously transit back into pluripotent state. We previously dissected the transcriptional dynamics of pluripotent to 2C-like transition and identified factors that modulate the transition. However, how 2C-like cells transits back to the pluripotent state and what factors drive this process remains largely unknown. To address these questions, we examined the transcriptional dynamics during the reverse transition from the 2C-like state to ESCs and identified an intermediate state involved in the transition. Interestingly, we found that mESCs exit from the 2C-like state through a molecular path characterized by a two-wave upregulation of pluripotent genes different from the one observed during the 2C-like entry transition. We also showed that nonsense-mediated mRNA decay (NMD) targets Dux mRNA and affects 2C-like state maintenance, suggesting that Dux degradation contributes to the reversal of 2C-like state.

overall_design: Here we performed bulk RNA-seq on 24h Dux-induced 2C-Like cells (D1 2C+) and the cells obtained after 24h from D1 2C+ cells, D2 2C-negative, and D2 2C-positive cells. We also perfomred single cell RNA-seq on cells obtained from Dux-induced 2C-like at 0h and 24h.

first: Xudong

last: Fu

first: Yi

last: Zhang


title: Expression data from D. melanogaster raised on glucose-enriched or unmodified holidic food

summary: We used RNA-seq to determine transcriptional profiles of whole flies raised on either a glucose-enriched or unmodified holidic diet.

overall_design: Newly eclosed w1118 males were raised for 20 days at 25˚C on either a glucose-enriched (50g/L) or unmodified holidic diet. Thre transcriptome of whole flies was sequenced.


title: Differential DNA methylation encodes proliferation and senescence programs in human adipose-derived mesenchymal stem cells

status: Public on Mar 19 2020

city: Stanford

first: Mark

middle: Emile

last: Pepin

address: 870 Quarry Road

department: Cardiovascular Medicine

institute: Stanford University

summary: Adipose tissue-derived mesenchymal stem cells (ASC’s) constitute a vital population of multipotent cells capable of differentiating into end-organ tissues. However, scientific endeavors to harness the regenerative potential of ASC’s for regenerative medicine are currently limited by an incomplete understanding of the mechanisms that determine cell-lineage commitment and stemness. In the current study, we used reduced representation bisulfite sequencing (RRBS) analysis to identify epigenetic gene targets and cellular processes that are responsive to 5-azathioprine, a potent inducer of DNA methylation. In this manner, we describe specific changes to DNA methylation of ASCs to identify the critical pathways associated with ASC differentiation  . We identified 4,797 differentially-methylated regions (FDR < 0.05) associated with 3,625 genes. Gene set enrichment analysis of the differentially-methylated target promoters identified phagocytosis, type 2 diabetes mellitus, and metabolic pathways as disproportionately hypomethylated, whereas adipocyte differentiation was the top most-enriched pathway to represent genes with hyper-methylated promoters. Interestingly, ZNF11 and ELK4 gene response elements were identified as genomic features most affected by DNA hypo- and hyper-methylation, respectively. Although further validation is needed, the implications of this pilot analysis provide the basis for understanding how epigenetic mechanisms influence the metabolic phenotype, and ultimately regenerative capacity, of ASC’s.

middle: E

first: Giuditta

last: Benincasa

first: Teresa

last: Infante

first: Marco

last: Miceli

first: Simona

last: Ceccarelli

first: Francesca

last: Megiorni

first: Eleni

last: Anastasiadou

first: Giovanni

last: Della Valle

first: Gerardo

last: Fatone

first: Ludovico

last: Docimo

last: Nicoletti

first: Cinzia

last: Marchese

first: Adam

last: Wende

first: Claudio

last: Napoli


title: A transcriptional roadmap for 2C-like to pluripotent state transition

last: Djekidel


title: Effect of UV irradiation on Sulfolobus acidocaldarius and involvement of the general transcription factor TFB3   in early UV response

city: Bielefeld

first: Andreas

last: Albersmeier

address: Universitätsstr. 27

institute: Bielefeld University

summary: Extremophilic archaea like all organisms experience potentially life-threatening conditions including UV light, which induces severe DNA damage. Since the alternative general transcription factor (GTF) TFB3 has been proposed to play a key role in UV stress response in the thermoacidophilic crenarchaeon Sulfolobus acidocaldarius, we investigated the expression of TFB3 on protein level including in vivo protein-protein interaction studies, tfb3 reporter gene assays and creation of a tfb3 insertion mutant to study early differential gene expression upon UV treatment (after 45 and 90 minutes).   Our results allowed differentiating between the TFB3-dependent and TFB3-independent early UV response in S. acidocaldarius. The early TFB3-independent UV response includes the repression of nucleotide biosynthesis and transport, replication and cell cycle progression in order to allow DNA repair. The TFB3-dependent UV response is characterized by the early induction of TFB3, which is a prerequisite for the following TFB3-dependent expression of genes involved in ups pili formation and the Ced DNA importer. Both structures facilitate the transfer of DNA to allow repair via homologous recombination. The fact, that all genes are downregulated in the tfb3 mutant compared to the reference strain, confirms the hypothesis that TFB3 acts as an activator of transcription.

overall_design: Differential gene expression analysis for transcriptomes of S. acidocaldarius MW001pyrEF+ and the insertion mutant S. acidocaldarius MW001 tfb3::pyrEF, both before, 45min and 90 min after UV-treatment; Three biological replicates per sample

first: Frank

last: Schult

first: Thuong

last: Le

first: Bernadette

last: Rauch

first: Patrick

last: Blumenkamp

first: Alexander

last: Goesmann

first: Jörn

last: Kalinowski

first: Sonja

last: Albers

first: Bettina

last: Siebers


title: Microarray profiling analysis of lncRNAs expression in gastric cancer specimens

city: Shenyang

first: Yong

last: Zhou

state: Liaoning

address: 4 Chongshan Road

institute: the Fourth Affiliated Hospital of China Medical University

summary:
Growing evidence has indicated that LncRNA CYTOR involved in the initiation and progression of malignancy, such as gastric cancer, hepatocellular carcinoma, renal cell carcinoma, and colorectal cancer. Nevertheless, the mechanisms of CYTOR in the development of metastatic gastric cancer remains unknown. In the current study, the authors clarified the association of CYTOR/miR-103/RAB10 was implicated in cancer metastasis. CYTOR expression evaluated in metastatic gastric cancer biopsies compared to the primary cases. Moreover, CYTOR expression correlated with the invasiveness, lymph node metastasis, and advanced stages of gastric cancer. Downregulation of CYTOR by shRNA hampered proliferation and migration, while induced cell apoptosis significantly. MicroRNA miR-103 was related to CYTOR expression negatively. Furthermore, dual-luciferase reporter assay confirmed that CYTOR sponged miR-103 and diminished miR-103 expression. Expression of Ras-related protein RAB10 was downregulated by miR-103, leading to the attenuation of cell migration and proliferation. The deregulated CYTOR cells were produced and subsequently injected into mice subcutaneously. The tumor growth decreased significantly in the CYTOR knockdown group, compared to the vehicle group. Briefly, the present findings suggested that CYTOR -miR-103-RAB10 was a novel promising pathway for conquering gastric cancer progression.
Long noncoding RNA  profiling by array

overall_design: Three paired of gastric cancer samples were collected in the current study. Microarray-based LncRNA expression profiles were gained with custom Prime PCR LncRNA Array.


title: Kdm5b depletion in embryonic stem cells does not induce intragenic promoters or affect transcription [ChIP-Seq]

first: Andrew

last: Johnston

summary: The application of massively-parallel sequencing (MPS) technology to understanding how the genome is regulated is of major importance, as we now appreciate sequence variants associated with common heritable diseases to be enriched at regulatory elements in the genome.  There is, however, an enormous challenge inherent to these studies, which are much more varied as assays and in terms of analytical approaches than the approaches  used to define the sequence variants themselves.  For example, there are a plethora of assays that test 5-methylcytosine genome-wide, numerous different analytical approaches to defineing peaks from chromatin immunoprecipitation sequencing (ChIP-seq), and increasingly diverse aspects of genomic regulation being studied.  The extremely large data sets generated do not lend themselves to distribution without some degree of pre-processing, and the hardware requirements for running these analyses are often substantial.  We have highlighted these concerns previously, but the central concern for our field is that genomics research is especially prone to poor reproducibility, and is a prime candidate for implementation of measures that could help to address this general problem. To illustrate the practical issues involved in genomics reproducibility, we sought to analyze our data and data from three previoulsy published studies of the histone demethylase KDM5B using the same analytical approaches. In particular we compared the results of our ChIP-seq experiments to previous H3K4me3 and Kdm5b ChIP-seq data in the public database: GSE31966 and GSE53087 (only samples GSM1282126, GSM1282127, GSM1282129, GSM1282131, and GSM1282132). Re-analyzed (ChIP-seq) data from GSE31966 and GSE53087 are linked below as supplementary files.

overall_design: Examination of H3K4me3 localization by ChIP-seq in mES cell after the knock down of Kdm5b

first: Maria-Paz

last: Ramos

first: John

last: Greally


title: Characterization of antibiotic resistance and host-microbiome interactions in the human upper respiratory tract during influenza infection

city: New York

first: Elodie

last: Ghedin

state: New York

address: 12 Waverly Place

department: Biology

institute: NYU

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

overall_design: Refer to individual Series


title: Pattern of Islr knockout mouse colon gene expression

city: Beijing

first: Jiu

middle: zhi

last: Xu

state: Beijing

address: Yuanmingyuan West Road NO.2

department: College of Biological sciences

institute: China Agricultural University

summary: To further understand different gene expression of islr knockout mouse colon and normal colon, we have employed colon samples microarray expression profiling as a discovery platform to identify different genes with Islr knockout mouse colon and normal colon. Comparison with normal colon, significantly upgene is 779 and downgene is 996 in knockout group.

overall_design: 3 control and 3 Islr knockout mice colon samples were flow separated into Trizol, the samples were taken to lab on ice, mRNA were extracted with Trizol, good quality mRNA were chosen as microarray analysis in CapitalBio technology.

first: Jiuzhi

first: Zhengquan

last: Yu


title: Transcriptional response of springtail (Folsomia candida) exposed to decabromodiphenyl ether-contaminated soil

status: Public on Mar 18 2020

first: Qianqian

last: Zhang

state: (Click to Select US State)

address: Shuangqing Road

institute: Research Center for Eco-Environmental Sciences

summary: To assess the effects of decabromodiphenyl ether (BDE209) on gene transcription of Folsomia candida and explore the mechanisms of toxicity, we detected changes in gene transcription of F. candida exposed to BDE209 (0.81 mg/kg) in soil for 2, 7 and 14 days. We identified 16 and 771 significantly differentially expressed genes after 2 and 7 days of exposure respectively, and no significantly regulated genes were shared among the two time points. No genes were affected after 14 days of exposure. Our results suggeted that BDE209 affected the transcription of genes involved in moulting, neural signal transmission and detoxification.

overall_design: Thirty adult springtails (23-day old) were exposed to BDE209-polluted soil or solvent control soil in 100 mL glass beakers for 2, 7 or 14 days.

first: Min

last: Qiao


title: Novel RvD6 stereoisomer induces corneal nerve regeneration and wound healing post-injury by modulating trigeminal transcriptomic signature

city: San Diego

first: Thang

middle: Luong

last: Pham

state: California

address: 4445 Eastgate Mall, Suite 200

institute: BioTuring

summary: We performed the RNA-seq analysis to unravel the underlying mechanism of corneal nerve regeneration after treatment with our identified RvD6 isomer and RvD6 standard.

overall_design: There are three groups of treatment: (i) vehicle, (ii) RvD6-standard, and (iii) RvD6-isomer. Each group has five samples. The vehicle group is considered as reference for the differential gene expression analysis using DEseq2 algorithm.

first: Azucena

middle: H

last: Kakazu

first: Jiucheng

last: He

first: Bokkyoo

last: Jun

first: Nicolas

middle: G

last: Bazan

first: Haydee


title: Lgr5-negative cancer cells seed metastases in colorectal cancer

city: Amsterdam

first: Lennart

last: Kester

address: Plesmanlaan 121

institute: Netherlands Cancer Institute

summary: Cancer stem cells (CSCs) are a minority population of cancer cells that display stem cell-like multipotent and self-renewal properties. They give rise to the bulk of cancer cells with limited replicative potential. In colorectal cancer (CRC), CSCs are marked by expression of the leucine-rich repeat-containing G-protein receptor 5 (Lgr5). Since CSCs display multipotent and self-renewal properties, this population is thought to seed metastases. Here, we used a mouse model and human xenografts to investigate the cell-of-origin of metastases. Surprisingly, we found that most CRC cells that disseminated and entered the blood circulation were Lgr5-. Lgr5- cancer cells arriving at the metastatic site formed lesions in which Lgr5+ CSCs appeared. This plasticity could occur independently of stemness-inducing factors, and was an indispensable event for the outgrowth of metastases, since neutralization of this plasticity prevented metastatic outgrowth. Combined, our study shows that most metastases are seeded by Lgr5- cancer cells, and that these cells have a niche-independent and intrinsic capacity to become CSCs and restore epithelial hierarchy.

overall_design: Single-cell mRNA sequencing of genetically engineered colorectal tumor organoids and mouse derived tumors.

first: A

last: Fumagalli

first: K

last: Oost

first: L

first: J

last: van Rheenen


title: Myc-mediated SDHA Acetylation Triggers Epigenetic Regulation of Gene Expression and Tumorigenesis.

city: He Fei

first: Shi-Ting

last: Li

state: An Hui

address: No.443, Huangshan Road

department: Innovation Center for Cell Biology

institute: University of Science and Technology of China

summary: Trimethylated H3K4 (H3K4me3), which is often found surrounding the transcriptional start site of active genes, is strongly enriched in the promoter regions of Myc-targeted genes. Succinate, which inhibits JmjC domain-containing histone demethylases (JHDMs), can induce H3K4me3 level of the promoter regions. It's interesting to ask whether Myc can mediate H3K4me3 by regulating cellular succinate level. Here, We used ChIP-seq to study Myc modulates H3K4me3 by altering succinate levels, dimethyl succinate (DMS), a membrane-permeable succinate analog, was introduced to treat CA46 cells with high or depleted Myc expression. And we also performed RNA-seq assays in Myc expressed or depleted CA46 cells with or without DMS treatment.

overall_design: CA46 cells were infected with viruses expressing non-targeting control (NTC) or Myc shRNA for 48h in presence of methyl succinate (DMS) and followed by H3K4me3 ChIP-seq to address whether succinate can induce H3K4me3 level of the promoter regions in CA46 cells with depleted Myc expression. For the CA46 cells’ ChIP-seq experiments with spike-in control, Drosophila chromatin (Active Motif 53083) and a Drosophila-specific antibody (Active Motif 61686) were used for each reaction. The D. melanogaster-specific antibody is used to immunoprecipitate D. melanogaster chromatin from each reaction, which is then used as a reference for normalization during data analysis. And ChIP-seq was sequenced at Novogene (Tianjin, China) on the Illumina novaseq6000 platform. Meanwhile, we also performed RNA extraction from these cell samples and sequenced on Illumina novaseq6000 platform.

first: Shengqi

last: Shen

first: Ping

last: Gao

first: Huafeng


title: Human bone-marrow-derived mesenchymal stem cells: control vs. cells undergoing chondrogenesis

first: Mingjian

last: Huang

address: 768 Shuangliao Road

institute: Xin Hua Hospital Affliated to Shanghai Jiao Tong University School of Medicien (SJTUSM)

type:
Expression profiling by array
Non-coding RNA profiling by array

summary: Long non-coding RNAs profiling of human mesenchymal stem cells comparing undifferentiated HMSCs with differentiated HMSCs during chondrogenesis. The chondrogenic differentiation of HMSCs was induced by chondrogenic medium. The chondrogenic marker genes (Col2a1, Sox9 and ACAN) has been detected upregulating during this process by Q-PCR. The aim of this study is to determine key lncRNAs regulating the chondrogenic differentiation process.

overall_design: Two-condition experiment, chondrogenesis vs. hMSCs. Biological replicates: each sample contains the mixture of cell sources from three parallel experiments.

first: Jing


title: Gene expression profiles of the standardized uptake value in 18F-fluorodeoxyglucose positron emission tomography in tripple negative breast cancer

city: Daejeon

first: Seon-Kyu

last: Kim

address: 125 Gwahak-ro, Yuseong-gu, Daejeon 305-806, Korea

department: Personalized Genomic Medicine Research Center

country: South Korea

institute: Korea Research Institutue of Bioscience & Biotechnology

summary: The standardized uptake value (SUV), an indicator of the glucose uptake degree in 18F-fluorodeoxyglucose positron emission tomography (FDG-PET), has been used as a prognostic factor in malignant tumors. We aimed to identify a signature reflecting prognostic SUV characteristics in triple negative breast cancer (TNBC). Transcriptome profiling was performed to identify a signature associated with the SUV in TNBC patients who underwent preoperative FDG-PET. We defined a signature significantly associated with the SUV (|r| > .35; P < .01). The SUV signature showed independent clinical utility for predicting BRC prognosis. Integrative analysis demonstrated a significance of the signature in predicting the response to immunotherapy and revealed that a signaling axis defined by TP53-FOXM1 and its downstream effectors in glycolysis-gluconeogenesis, including LDHA, might be important mediators in the FDG-PET process. Our results reveal characteristics of glucose uptake captured by FDG-PET, supporting an understanding of glucose metabolism as well as poor prognosis in TNBC patients with a high SUV.

overall_design: We prospectively collected tumor tissues from specimens of surgically resected breast cancer at the Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul, Korea, between July 1997 and December 2007. A total of 84 patients with triple negative breast cancer were enrolled for gene expression profiling.

first: Sun-Hee

last: Leem

first: In-Sun

last: Chu

first: Joon

last: Jeong

first: SungGwe

last: Ahn


title: Benzo[a]pyrene and dibenzo[def,p]chrysene in 3D primary human bronchial epithelial cells [miRNA-seq]

city: Corvallis

first: Susan

middle: C.

last: Tilton

state: OR

address: 1007 ALS Bldg

department: AG Envr & Molec Toxicology

institute: Oregon State University

summary: In this study, we assess potential differences in mechanism of action for two PAHs, benzo[a]pyrene (BAP) and dibenzo-[def,p]chrysene (DBC), in a primary human 3D bronchial epithelial culture (HBEC) model based on short-term biosignatures identified from global transcriptional profiling.

overall_design: Fully differentiated bronchial epithelial cells (n=4 replicates) were treated with 500 µg/ml (19.80 nanomoles) benzo[a]pyrene (BAP), 10 µg/ml (0.35 nanomoles) dibenzo[def,p]chrysene (DBC) or acetone vehicle control for 48 hrs and isolated mRNA were sequenced on Illumina HiSeq 3000.

middle: C


title: Parallel social information processing circuits are differentially impacted in autism

city: Baltimore

first: Loyal

middle: A

last: Goff

state: MD

address: 733 N. Broadway Avenue

department: Institute of Genetic Medicine

institute: Johns Hopkins University

summary: Parallel processing circuits are thought to dramatically expand the network capabilities of the nervous system. Magnocellular and parvocellular oxytocin neurons have been proposed to subserve two parallel streams of social information processing, which allow a single molecule to encode a diverse array of ethologically distinct behaviors, although to date direct evidence to support this hypothesis is lacking. Here we provide the first comprehensive characterization of magnocellular and parvocellular oxytocin neurons, validated across anatomical, projection target, electrophysiological, and transcriptional criteria. We next used novel multiple feature selection tools in Fmr1 KO mice to provide direct evidence that normal functioning of the parvocellular but not magnocellular oxytocin pathway is required for autism-relevant social reward behavior. Finally, we demonstrate that autism risk genes are uniquely enriched in parvocellular oxytocin neurons. Taken together these results provide the first evidence that oxytocin pathway specific pathogenic mechanisms account for social impairments across a broad range of autism etiologies.

overall_design: 146 SMART-Seq2 full-length cDNA scRNA-Seq libraries from enriched oxytocinergic neurons from P23 OT-2A-Flp::fdGFP+ mouse hypothalamus paraventricular nucleus.  Cells were sequenced to an average depth of 1,424,499 ±77,731 paired-end 50bp reads per neuron on the Illumina HiSeq 2500 platform. 21 parvocellular OT neurons and 215 magnocelluar OT neurons are represented.

first: Eastman

middle: M

last: Lewis

first: Genevieve

middle: L

last: Stein-O'Brien

first: Alejandra

last: Patino

first: Romain

last: Nardou

first: Cooper

last: Grossman

first: Matthew

last: Brown

first: Bidii

last: Bangamwabo

first: Ndeye

last: Ndiaye

first: Daniel

last: Giovinazzo

first: Ian

last: Dardani

first: Connie

last: Jiang

first: Gül

last: Dölen


title: Myc-mediated SDHA Acetylation Triggers Epigenetic Regulation of Gene Expression and Tumorigenesis

first: Shi-Ting

last: Li

summary: Trimethylated H3K4 (H3K4me3), which is often found surrounding the transcriptional start site of active genes, is strongly enriched in the promoter regions of Myc-targeted genes. Succinate, which inhibits JmjC domain-containing histone demethylases (JHDMs), can induce H3K4me3 level of the promoter regions. It's interesting to ask whether Myc can mediate H3K4me3 by inhibiting SDH activity and inducing cellular succinate level. Here, We used ChIP-seq to study Myc modulates H3K4me3 by altering succinate levels, dimethyl succinate (DMS), a membrane-permeable succinate analog, was introduced to treat P493-6 cells with high or depleted Myc expression. And we performed RNA-seq assays in Myc expressed or depleted P493-6 cells with or without DMS treatment. Besides, we also performed RNA-seq assays in Myc expressed or depleted P493-6 cells with or without 3-nitropropionic acid (3-NPA, SDH enzyme inhibitor) treatment.

overall_design: P493-6 cells were treated with tetracycline (tet) or without for 48h in presence of methyl succinate (DMS) and followed by H3K4me3 ChIP-seq to address whether succinate can induce H3K4me3 level of the promoter regions in P493-6 cells with depleted Myc expression. Meanwhile, we also performed RNA extraction and sequenced on Illumina novaseq (Homo sapiens). Moreover, we also treated P493-6 cell with tet or without for 48h in presence of 3-nitropropionic acid (3-NPA, SDH enzyme inhibitor), followed by extracting RNA and sequenced on Illumina novaseq (Homo sapiens).

first: Shengqi

last: Shen

first: Ping

last: Gao

first: Huafeng

last: Zhang


title: Effects of treatment with bovine oviductal extracellular vesicles on the transcriptome of bovine day 7 in vitro produced embryos

city: Lindau

first: Stefan

middle: Michael

last: Bauersachs

state: Zurich

address: Eschikon 27 EHB 23.1

department: Department for Farm Animals

country: Switzerland

institute: University of Zurich

summary: Oviductal extracellular vesicles (oEVs) are emerging as key players in gamete/embryo-oviduct interactions contributing to successful pregnancy. Various positive effects of oEVs on gametes and early embryos have been found in vitro. To find out if these effects are associated with changes of embryonic gene expression, the embryonic transcriptome was analyzed after supplementation of bovine embryos with bovine oEVs during in vitro culture (IVC) in comparison to corresponding controls without oEVs. Embryos were cultured during 7 days of IVC with fresh oEVs, oEVs frozen after isolation from oviductal fluid or without oEVs (control), since a previous study showed different effects of fresh and frozen oEVs. Five pools of 10-14 embryos were analyzed for each group by low-input Illumina RNA-sequencing. Analysis of differential gene expression revealed 221 differentially expressed genes (DEGs) for the comparison of frozen oEVs vs control, 67 DEGs for fresh vs frozen oEVs, and only minor differences for the comparison fresh oEVs vs control (28 DEGs). An integrative analysis with the previously studied mRNA and small ncRNA content of bovine oEVs suggested direct effects of oEVs content on the embryonic transcriptome for the supplementation with frozen oEVs, i.e., increase of transcripts found in higher concentrations in oEVs and decrease of transcripts which are potential targets of miRNAs found in oEVs.

overall_design: Supplementation of bovine embryos during in vitro culture with fresh or frozen bovine oviductal EVs and untreated controls, low-input total RNA-seq of 5 replicates (pools of 8-14 embryos) per group using Illumina HiSeq 2500

first: Carmen

last: Almiñana Brines


title: Global epigenomic analysis of primary effusion lymphoma identifies MYC super-enhancers and enhancer RNAs associated with KSHV infection

status: Public on Mar 17 2020

city: Los Angeles

first: Angela

last: Park

state: CA

address: 1501 San Pablo St, ZNI 521

department: Molecular Microbiology and Immunology

country: USA

institute: University of Southern California

summary: Enhancers play indispensable roles in cell proliferation and survival through spatiotemporally regulating gene transcription. In addition, active enhancers and super-enhancers often produce noncoding enhancer RNAs (eRNAs) that precisely control RNA polymerase II activity. Kaposi’s sarcoma-associated herpesvirus (KSHV) is a human oncogenic gamma-2 herpesvirus that causes Kaposi’s sarcoma and lymphoproliferative diseases of B-cell origin such as primary effusion lymphoma (PEL). It is well characterized that KSHV utilizes host epigenetic and nuclear machineries to control the switch between two life cycles, latency and lytic replication. However, how KSHV impacts the host epigenome at different stages of viral life cycle is not well understood. Using the analysis of global run-on sequencing (GRO-seq) and chromatin-immunoprecipitation sequencing (ChIP-seq), we profiled the dynamics of host transcriptional regulatory elements during latency and lytic replication of KSHV-infected PEL cells. This study showed that a number of critical host genes for KSHV latency, including MYC proto-oncogene, were under the control of super-enhancers and eRNAs that were globally repressed upon viral reactivation. A combination of circular chromosome conformation capture combined with sequencing (4C-seq), GRO-seq and ChIP-seq indicated that the eRNA-expressing super-enhance regions were located at downstream of the MYC gene in KSHV-infected PELs. Treatment of an epigenetic drug to block enhancer function or shRNA-mediated depletion of the eRNA expression significantly reduced MYC mRNA expression in KSHV-infected PELs. Finally, while cellular IRF4 acted upon the eRNAs and super-enhancers for MYC expression during latency, the KSHV viral IRF4 repressed cellular IRF4 expression upon reactivation, decreasing MYC expression and thereby, facilitating lytic replication. Taken together, these data suggest that KSHV acts as an epigenetic driver that modifies host epigenomic status by effectively regulating enhancer function upon reactivation.

overall_design: Epigenomic profile of KSHV-infected primary effusion lymphoma cell line during latency and lytic replication

first: Soohwan

last: Oh

first: Kyle

last: Jung

first: Un-Yung

last: Choi

first: Hye-Ra

last: Lee

first: Michael

last: Rosenfeld

first: Jae

middle: U


title: MacroH2A deletion causes neuronal developmental deficits and autism-like behavior in mice

first: Jianwei

last: Jiao

address: 1 Beichen West Road

department: State Key Laboratory of Reproductive Biology

country: China

institute: Institute of Zoology, Chinese Academy of Sciences

summary:
Purpose:To further understand how MacroH2A regulates the proliferation of neural progenitor cells, RNA-seq was used to analyze genome-wide changes in the cerebral cortex and littermate wild type of E13.5 MacroH2A knockout mice
Methods: Total RNA was extracted from wild-type E13.5 brain tissue and knock-out E13.5 brain tissue. Specifically, the Agilent 2100 Bioanalyzer was used for quality control and quantification. Total RNA was then converted to cDNA and combined with the library. Illumina HiSeq 2500 platform in Annoroad Genomics uses RNA sequencing analysis
Results: Approximately  one thousand transcripts showed differential expression between the wild-type(WT) and knock-out mice brain cortex, with a fold change ≥1.5 and p value <0.05.Geneontology analysis of the up-regulated genes showed obvious enrichment of biological processes related to development and proliferation.The down-regulated genes exhibited enrichment of biological processes related to the negative regulation of cell proliferation and developmental process. These results reflected human MacroH2A plays a role in brain neuron development.

overall_design: Total mRNA profiles of E13.5 wild type (WT) and knock-out(KO) mice were generated by deep sequencing using Illumina HiSeq 2500.

first: Hongyan

last: Ma


title: Employing proximity-dependent ligation techniques to estimate EcR/Usp molecular partners in Drosophila

city: Moscow

first: Nadezhda

last: Vorobyeva

address: Vavilova 34/5

institute: Institute of Gene Biology RAS

summary: The subject of the current study is the finding of possible molecular partners of Drosophila EcR receptor. Two labelling enzymes (BioID2 and APEX2) were fused to EcR or Usp to biotin label the surrounding proteins. All fused proteins were expressed using the Act5C promoter in Drosophila S2 cells. To ensure functionality of the generated proteins, we verified their ability to bind EcR and Usp sites in the Drosophila genome with the ChIP-Seq. Our results demonstrate that EcR and Usp fusions can be recruited to genomic sites endogenous for the EcR/Usp proteins. Conversely, unfused BioID2 and APEX2 enzymes do not bind to EcR/Usp sites. A more in-depth study was conducted to clarify the association of EcR/Usp with one of the detected proteins, CP190, a well-described cofactor of Drosophila insulators. ChIP-Seq experiments revealed an enrichment of CP190 binding on transcription start and end sites of 20E-dependent genes but not at EcR/Usp-bound enhancers.

overall_design: ChIP-Seqs by anti-3xFLAG antibodies were performed after 1 hour treatment with 20-hydroxyecdysone (20E) in S2 Schneider cells stably expressing 3xFLAG-EcR, 3xFLAG-EcR-BioID2, 3xFLAG-EcR-APEX2, 3xFLAG-Usp, 3xFLAG-Usp-APEX2, 3xFLAG-Usp-BioID2, 3xFLAG-BioID2, 3xFLAG-APEX2. ChIP-Seq by anti-CP190 and Rpb3 antibodies were performed after 1 hour treatment with 20E and in sham-treated (DMSO) S2 Schneider cells stably expressing 3xFLAG-EcR. ChIP-Seq by anti-CP190 antibodies were performed on white prepupae (Oregon-Modencode).

first: N


title: Transcriptiomics of cDC2 from young adult and aged mice after immunisation

city: Cambridge

first: Felix

last: Krueger

address: Granta Park

department: Bioinformatics

institute: Altos Labs

summary: Antigen-bearing cDC2 isolated from 2 or 23 month old mice 22hrs after immunisation with EaGFP in IFA

overall_design: 2 or 23 month old male C57BL/6 mice were immunised subcutaneously in the hind flank with EaGFP in IFA, 22 hours later the inguinal lymph nodes were taken and GFP+MHCIICD11c+CD11b+Lineage-CD172a+CD24- cDC2 cells were flow sorted into lysis buffer for transcriptomic analysis

first: Danika

last: Hill

first: Alexandre

last: Bignon

first: Michelle

last: Linterman


title: Reversion of Alzheimer’s disease signatures

city: Sabadell

first: Antoni

last: Berenguer-LLergo

state: Barcelona

address: Parc del Taulí, 1

department: A8G2 Group - Rheumatology Service

institute: Parc Taulí Research and Innovation Institute (I3PT)

summary:
Chemical Checker (CC) is a resource that provides processed, harmonized and integrated bioactivity data on 800,000 small molecules. In the CC, bioactivity data are expressed in a vector format, which naturally extends the notion of chemical similarity between compounds to similarities between bioactivity signatures of different kinds. We experimentally validate that CC signatures can be used to reverse and mimic biological signatures of disease models and genetic perturbations.
We developed cellular models of Alzheimer’s disease (AD) by introducing familial AD (fAD) mutations into SH-SY5Y cells. Using CRISPR/Cas9-induced homology-directed repair, we obtained clones harboring the fAD PSEN1-M146V or the APP-V717F mutations. Three compounds (noscapine - 10 uM, palbociclib - 0.4 uM and AG-494 - 10uM) reverted fAD signatures. We confirmed that genes up-regulated in SH-SY5Y fAD mutants were indeed downregulated upon treatment with the drugs, and vice versa. Moreover, the three drug treatments significantly reverted a subset of genes strongly linked to AD, including the recovery of the expression levels of GRIN2D, a glutamate receptor involved in synaptic transmission and BIN1, a gene involved in synaptic vesicle endocytosis and strongly associated with AD risk.

overall_design: Affymetrix PrimeView arrays were used to analyze the whole-genome expression profile of wild-type or mutated SH-SY5Y cells treated with vehicle (DMSO) or the indicated drugs. Three independent experiments were performed.

first: Eduardo

last: Pauls

first: Patrick

last: Aloy


title: RNAseq to profile transcriptomes in bone marrow-derived macrophages from TKO (mir-106a~363-/- mir-106b~25-/- mir-17~92flox/flox Lyz2-Cre) and WT(Lyz2-Cre) mice stimulated with LPS for 3 hours.

first: Xiang

last: Zhang

address: Tsinghuayuan Street

institute: Tsinghua University

summary: We performed the transcriptomic analysis of RNA-seq of BMDMs generated from WT and TKO mice and stimulated with 10 ng/ml LPS for 3 h to identify gene expression changes.

overall_design: BMDMs from WT and TKO mice were stimulated with 10 ng/ml LPS for 3h and then were lysed. RNA was extracted, polyA enriched and prepared for sequencing libraries.


title: Characterization of antibiotic resistance and host-microbiome interactions in the human upper respiratory tract during influenza infection [human host RNA-seq]

first: Christian

last: Forst

address: One Gustave L. Levy Place

department: Genetics and Genomic Sciences

institute: Icahn School of Medicine at Mount Sinai

summary: Antibiotic resistance genes expressed in the upper respiratory tract of patients infected with influenza viruses were associated with the microbial community and microbial activities. Interactions between the host systemic responses to influenza infection and ARG expression highlight the importance of antibiotic resistance in viral-bacterial co-infection.

overall_design: Transcriptome profile from PBMCs of 37 human subjects 1-2 days post illness onset with influenza-like symptoms (Initial) and 30-45 days later (Final). The specific influenza strains were verified by RT-PCR.

first: Lingdi

middle: V

first: Aubree

last: Gordon

first: Gabrielle

last: Gussin

first: Adam

middle: B

last: Geber

first: Porfirio

middle: J

last: Fernandez

first: Tao

last: Ding

first: Lauren

last: Lashua

first: Minghui

last: Wang

first: Angel

last: Balmaseda

first: Richard

last: Bonneau

first: Bin

first: Elodie

last: Ghedin


title: Gene expression associated with morphological changes in osteoblasts.

city: Suita

first: Daisuke

last: Okuzaki

state: Osaka

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

institute: Osaka univ.

summary: In the field of bone-tissue engineering, bone morphogenetic protein (BMP)-2 plays a central role because of its potent bone-induction ability. However, the widespread use of BMP-2 is prevented by its dose-dependent inflammation-related side effects. One reason why optimising BMP-induced bone formation is challenging is that this induction process in vivo remains poorly elucidated. Here, RNA-sequencing was performed to identify changes in gene expression in OBs. Out of 23,284 genes, 182 genes showed an adjusted fold-change of >2.0 and an FPKM >0.1 from Day 10 to Day 14. Among the 182 genes, 32 genes associated with ‘organisation of cytoskeleton’ were upregulated on Day 14.

overall_design: We examined the differences in gene expression in osteoblasts between Day 10 and Day 14, a period during which active morphological change and mineralisation were observed. Fluorescence-activated cell sorting was used to isolate ECFP+ osteoblasts in the lesions where ectopic bone formation was occurring, and transcriptome profiling through RNA-sequencing was performed to identify changes in gene expression in osteoblasts.

first: Kunihiko

last: Hashimoto

first: Masaru

last: Ishii


title: Re-expression of TAZ in human myeloma cell line KMM1

city: Saint John

first: Tony

last: Reiman

state: NB

address: 100 Tucker Park Rd

institute: University of New Brunswick

summary: We report RNAseq analysis of KMM1 cells after re-introduction of the TAZ transcriptional co-activator

overall_design: KMM1 cells expressing TAZ were compared to KMM1 cells expressing empty vector control WPI

first: Stacy

last: Grieve

first: Gabriel

last: Wajnberg

first: Miranda

last: Lees

first: Simi

last: Chacko

first: Nicolas

last: Crapoulet


title: Rheumatoid arthritis associated microRNA in peripheral blood mononuclear cells

city: Suzhou

first: Xingbo

last: Mo

address: Renai Road

institute: Soochow University

summary: Genome wide microRNA profiling in peripheral blood mononuclear cells from rheumatoid arthritis (RA) patients and healthy controls. The Affymetrix miRNA 4.0 chip was used to obtain RNA profiles in  28 RA patients and 18 healthy controls.

overall_design: To identify novel rheumatoid arthritis (RA) associated microRNAs and comprehensively understand their underlying pathologic mechanism, we compared the Affymetrix miRNA 4.0 microarray data from PBMCs of 28 RA patients with that of 18 healthy controls.

first: Shu-Feng

last: Lei

first: Xiao-Wei

last: Zhu

first: Long-Fei

last: Wu

first: Xing-Bo


title: Next-Generation Sequencing Characterization of Hematopoietic Stem and Progenitors Cells in Murine Systemic Lupus Erythematosus

city: Athens

first: Maria

last: Grigoriou

state: Papagou

address: Soranou Efesiou 4

country: Greece

institute: BRFAA

summary:
Purpose: Next-generation sequencing (NGS) technology was exploited to map genome-wide expression profile of hematopoietic stem and progenitor cells (HSPCs) in mouse model of Systemic Lupus Erythematosus (SLE).
Methods: Total RNA was extracted as described by manufacturer (NucleoSpin® RNA XS) and mRNA libraries were generated using the Illumina TruSeq Sample Preparation kit v2. Single-end 75-bp mRNA sequencing was performed on Illumina NextSeq 500 platform. Quality of sequencing was assessed using FastQC software. Raw reads in fastq format were collected and aligned to the mouse genome (mm10 version) using STAR 2.6 algorithm. Gene quantification was performed using HTSeq and differential expression analysis was performed using edgeR package.
Results: Transcriptomic analysis of F1-L LSK indicates activation as they respond to type I IFN, displayed increased proliferation and replicative stress, and profoundly prefer to differentiate towards myeloid/granulocytic lineage. Gene expression analysis of F1-L CMPs suggests arrest of differentiation at the level of myeloid progenitors as key regulators including Cebpa, Cebpe, Irf8 are suppressed.
Conclusions: Our study suggests deregulation of differentiation at the level of CMPs and “priming” of LSK cells towards granulocytic branch proposing an alternative granulopoiesis route. This comparison indicates an arrest at the progenitor stage both in murine lupus hematopoiesis as important regulators for terminal differentiation are downregulated.

overall_design: Murine BM-derived LSK and CMP mRNA profiles of F1-P and F1-L (LSK mRNA profiles from their age-matched C57BL/6 counterparts) were generated by deep sequencing, in triplicate.

last: Grgioriou

first: Aggelos

last: Banos


title: DNA methylation analysis for target regions in swim-up sperm

city: Fukuoka

first: Hiromitsu

last: Araki

address: 744 Motooka Nishi-Ku

institute: Kyushu University

summary: Increasing evidence indicates that paternal dietary conditions influence the metabolic disorders of offspring. Previous studies suggested the involvement of epigenetic regulation for such phenomena, but the mechanism remains elusive. To reveal the molecular function of  stress-dependent epigenetic regulator ATF7 in paternal inheritance of dietry effect on offpring phenotype, we analyzed ATF7-binding profiles in testicular germ cells by ChIP-seq, DNA methylation profiles in sperm by TGBS, small RNA expression profiles in HRCS by RNA-seq,and whole expression profiles in offspring liver by expression array analysis, using wild-type and ATF7 heterozygous mutant mice.

overall_design: Examination of DNA methylation status in sperm samples collected from wild-type and ATF7 heterozygous mutant mice fed with control diet or low-protein diet

first: Keisuke

last: Yoshida

first: Fumihito

last: Miura

first: Takashi

last: Ito


title: Next Generation Sequencing Facilitates Quantitative Analysis of SMMC7721 shYTHDF2 and shCtrl transcriptomes.

city: Shanghai

first: Zhenjun

last: Zhao

state: Shanghai

address: 1630 Dongfang Road, Puundong New District, Shanghai, China

institute: Renji Hospital, Shanghai Jiao Tong University, School of Medicine

summary: Dynamic N6-methyladenosine (m6A) modification was previously identified as a ubiquitous post-transcriptional regulation that affected mRNA homeostasis. However, the m6A-related epitranscriptomic alterations and functions remain elusive in human diseases such as cancer. Here we show that hypoxia restrains the ‘reader’ protein YTH domain family 2 (YTHDF2), to stabilize the methylated oncogene mRNAs in inflammation-associated liver cancer. YTHDF2 silenced in human cancer cells or depleted in mouse hepatocytes evoked pro-inflammatory responses and accelerated tumor growth and metastatic progression. Under hypoxia, YTHDF2 processed the decay of m6A-containing interleukin 11 (IL11) and serpin family E member 2 (SERPINE2) mRNAs, which were responsible for the inflammation-mediated malignancy. Reciprocally, YTHDF2 transcription succumbed to hypoxia-inducible factor-2α (HIF-2α). Administration of a HIF-2α antagonist (PT2385) restored YTHDF2-programed epigenetic machinery and repressed liver cancer. Hence, our findings provide a new insight into the mechanism by which hypoxia adapts m6A-mRNA editing to promote cancer.

overall_design: mRNA profile of SMMC7721-shYTHDF2 and SMMC7721-shCtrl were generated by deep sequencing.

first: Jiajie

last: Hou


title: Neural Lineage Progression Controlled by a Temporal Proliferation Program along the Apical-basial Axis

city: linkoping

first: shahrzad

last: Bahrampour

address: Campus HU: Lab 1, floor 13

department: IKE

country: Sweden

institute: Linkoping University

summary: This project is focused on understanding how the early driver factors act along the A-P axis. We have recently found that neural stem cells in the brain divide for longer, and bud off daughters that divide more, hence generating larger lineages that those found in the nerve cord. Intriguingly, the early factors are expressed at a higher level in the brain, and her functional studies indicate that this provides a driving input that contributes to the generation of the large brain lineages.

overall_design: We generated  quadruple UASs combination: ase, Kr;SoxN, wor (denoted UAS-Quad), and  and sextuple UASs combination: hb, ase, Kr ; SoxN, nub, wor (denoted UAS-Hexa).   To get the transcriptomic view of the effects of the Quad and Hexa misexpressions, we have run RNAseq analysis for to two separate set of experiments: 1 (control VS UAS-Quad) and 2(Control VS UAS-Hexa).  UAS-Quad and UAS-Hexa misexpressions were driven from Insc-Gal4, and for the control, we have used the heterozygous Insc-Gal4 over plus.   Within each experiment, we have three biological replicates per genotype (control and misexpressions).   In total, we have had 9 samples (3 per each experiment).

first: Shahrzad

first: Stefan

last: Thor