title: Cryptic introns in lncRNAs recruit conserved Pir2/ARS2 protein to promote gene repression [smRNA-seq]

city: Bethesda

first: Shiv

last: Grewal

address: NCI bldg 37 Rm 6068 9000 Rockville Pike

department: LBMB

institute: NCI

summary: Long non-coding RNAs (lncRNAs) dynamically regulate gene expression during development and in response to environmental conditions.  In S. pombe, lncRNAs repress the expression of nearby genes via a mechanism involving silencing effector proteins.  In this study, we find that invasion of a lncRNA into the neighboring gene results in inclusion of a cryptic intron that is required for its repressive activity.  We show that cryptic introns are targeted by the conserved protein Pir2/ARS2 in association with splicing factors, which provide a scaffold for the recruitment of RNA degradation factors and chromatin modifying activities.

overall_design: smRNA-seq of WT, pir2-1, rrp6D, pir2-1 rrp6D, cwf10-1 rrp6D mutants in Schizosaccharomyces pombe.

first: Gobi

last: Thillainadesan

first: Hua

last: Xiao

first: Sahana

last: Holla

first: Jothy

last: Dhakshnamoorthy

middle: I


title: Cryptic introns in lncRNAs recruit conserved Pir2/ARS2 protein to promote gene repression [RIP-seq]

status: Public on Apr 07 2020

state: MD

country: USA

overall_design: RIP-seq of untagged WT cells and Pir2-GFP.


title: Widespread and tissue-specific expression of endogenous retroelements in human somatic tissues

status: Public on Apr 09 2020

city: Montréal

first: Claude

last: Perreault

state: Québec

address: 2950, Chemin de Polytechnique

country: Canada

institute: Institute for Research in Immunology and Cancer

type: Expression profiling by high throughput sequencing

summary: Endogenous retroelements (ERE) constitute about 42% of the human genome and have been implicated in common human diseases such as autoimmunity and cancer. Despite evidence that some EREs can be expressed at the RNA and protein levels in specific contexts, a systems-level evaluation of their expression in human tissues is lacking. We report that all human tissues express EREs but the breadth and magnitude of ERE expression are very heterogeneous from one tissue to another. ERE expression was particularly high in two MHC-I-deficient tissues (ESCs and testis) and one MHC-I-expressing tissue, mTECs. In mutant mice, we report that the exceptional expression of EREs in mTECs was AIRE-independent. MS analyses identified 103 non-redundant ERE-derived MAPs (ereMAPs) in B-LCLs. These ereMAPs preferentially derived from sense translation of intronic EREs. Notably, detailed analyses of their amino acid composition revealed that ERE-derived MAPs presented homology to viral MAPs. This study shows that ERE expression in somatic tissues is more pervasive and heterogeneous than anticipated. The high and diversified expression of EREs in mTECs and their ability to generate MAPs suggest that EREs may play an important role in the establishment of self-tolerance. The viral-like properties of ERE-derived MAPs suggest that those not expressed in mTECs can be highly immunogenic.

overall_design: mRNA sequencing was performed on IFN-g treated OVCAR-3 cells.

first: Jean-David

last: Larouche


title: Cryptic introns in lncRNAs recruit conserved Pir2/ARS2 protein to promote gene repression [ChIP-seq]

type: Genome binding/occupancy profiling by high throughput sequencing

overall_design: ChIP-seq of Pir2-GFP in Schizosaccharomyces pombe.


title: Cryptic introns in lncRNAs recruit conserved Pir2/ARS2 protein to promote gene repression [RNA-Seq]

overall_design: RNA-seq of WT, pir2-1 mutant in Schizosaccharomyces pombe.


title: Chronic expression of p16INK4a in the epidermis induces Wnt-mediated hyperplasia and promotes tumor initiation

status: Public on Apr 06 2020

city: Jerusalem

first: Ittai

last: Ben-Porath

address: Ein-Kerem

department: Department of Developmental Biology and Cancer Research

country: Israel

institute: The Hebrew University Faculty of Medicine

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

overall_design: Refer to individual Series


title: Chronic expression of p16INK4a in the epidermis induces Wnt-mediated hyperplasia and promotes tumor initiation (2)

summary: In this study we examine the outcomes of p16INK4a activation in the adult epidermis. We found that prolonged expression of p16INK4a induces epidermal hyperplasia and dysplasia. We also found that continued p16INK4a expression increased the number of epidermal papillomas that developed after carcinogen treatment. Profling of p16INK4a- expressing cells showed elevated levels of Wnt-pathway ligands and targets, and pharmacologic or genetic Wnt inhibition suppressed p16-induced hyperplasia. In human actinic keratosis, a precursor of squamous cell carcinoma, p16-expressing cells are typically found adjacent to dividing cells, consistent with paracrine interaction. These findings reveal that in addition to its cell-autonomous role in blocking cell proliferation, p16 can induce hyperplasia through paracrine stimulation, suggesting that its activity contributes to the formation of early premalignant epidermal lesions.

overall_design: Expression profiles of papillomas excised from K5-rtTA/tet-p16 and tet-p16 control mice.

first: Narmen

last: Azazmeh


title: Cryptic introns in lncRNAs recruit conserved Pir2/ARS2 protein to promote gene repression

type: Non-coding RNA profiling by high throughput sequencing


title: Dissecting the cellular specificity of smoking effects and reconstructing lineages in the human airway epithelium

city: Denver

first: Nathan

last: Jackson

state: CO

address: 1400 Jackson St.

department: Center for Genes, Environment, and Health

institute: National Jewish Health

summary: Cigarette smoke first interacts with the lung through the cellularly diverse airway epithelium and goes on to drive development of most chronic lung diseases. Here, through single cell RNA-sequencing analysis of the tracheal epithelium from smokers and nonsmokers, we generate a comprehensive atlas of epithelial cell types and states, connect these into lineages, and define cell-specific responses to smoking. Our analysis infers multi-state lineages that develop into surface mucus secretory and ciliated cells and then contrasts these to the unique specification of submucosal gland (SMG) cells. Accompanying knockout studies reveal that tuft-like cells are the likely progenitor of both pulmonary neuroendocrine cells and CFTR-rich ionocytes. Our smoking analysis finds that all cell types, including protected stem and SMG populations, are affected by smoking through both pan-epithelial smoking response networks and hundreds of cell-specific response genes, redefining the penetrance and cellular specificity of smoking effects on the human airway epithelium.

overall_design: For the in vivo dataset, we sequenced a total of 68,370 (36,248 after QC) epithelial cells from across 15 human tracheal donors (6 heavy smokers, 6 never-smokers, 2 light smokers, and 1 pediatric subject). For the in vitro dataset we sequenced a total of 8,722 (5,976 after QC) epithelial cells sampled from 20 time points along the differentiation process taken by air-liquid interface (ALI) cultures seeded from primary basal cells of 3 human tracheal donors (from ALI seed day to day 32 post-airlift)

first: Katherine

middle: C

last: Goldfarbmuren

middle: D

first: Satria

middle: P

last: Sajuthi

last: Dyjack

first: Katie

middle: S

last: Li

first: Cydney

middle: L

last: Rios

first: Elizabeth

middle: G

last: Plender

first: Michael

middle: T

last: Montgomery

first: Jamie

last: Everman

first: Preston

middle: E

last: Bratcher

first: Eszter

middle: K

last: Vladar

first: Max

middle: A

last: Seibold


title: Chronic expression of p16INK4a in the epidermis induces Wnt-mediated hyperplasia and promotes tumor initiation (1)

overall_design: Expression profiles of GFP+ and GFP- epidermal keratincytes isolated from K5-rtTA/tet-GFP/tet-p16 and GFP+ cells from control (GFP only) K5-rtTA/tet-GFP mice, after 6 months of induction.


status: Public on Apr 05 2020

city: Pleasanton

first: Juan

middle: Pablo

last: Romero

state: CA

address: 6230 Stoneridge Mall Rd

department: Computational Biology

institute: 10x Genomics

summary: Single-cell RNA-seq of engineered healthy human kidney organoids. These data are part of a larger investigation (data not provided here) showing that SARS-CoV-2 can directly infect engineered human blood vessel organoids and human kidney organoids which can be inhibited by human recombinant soluble ACE2 (hrsACE2), demonstrating that hrsACE2 can significantly block early stages of SARS-CoV-2 infections.

overall_design: Single-cell RNA-seq of engineered human kidney organoids

first: Vanessa

last: Monteil

first: Heysoo

last: Kwon

first: Patricia

last: Prado

first: Reiner

last: Wimmer

first: Martin

last: Stahl

first: Alexandra

last: Leopoldi

first: Elena

last: Garreta

first: Carmen

last: Hurtado del Pozo

first: Felipe

last: Prosper

first: Gerald

last: Wirnsberger

first: Haibo

last: Zhang

first: Arthur

last: Slutsky

first: Ryan

last: Conder

first: Nuria

last: Montserrat

first: Ali

last: Mirazimi

first: Josef

middle: M

last: Penninger


title: Gene expression analysis of EB differentiation by RNA-Sequencing

city: Boston

first: Aref

last: Ebrahimi

state: MA

address: 1 Joslin Pl

department: Islet Cell and Regenerative Biology

institute: Harvard Medical School - Joslin

summary: RNA sequencing was performed using shLacZ and shDis3l2 undifferentiated mESCs as well as EB differentiated cells

overall_design: RNA samples were extracted from undifferentiated and differentiated cells, and cDNA libraries were prepared using Illumina pipeline.

first: Mehdi

last: Pirouz


title: Single cell 3' RNA sequencing of 6 Belgian colorectal cancer patients

city: Seoul

first: Yourae

last: Hong

address: 81, Irwon-ro

department: Samsung Genome Institute

country: South Korea

institute: Samsung Medical Center

summary: For the understanding of intrinsic cancer cell signatures and the surrounding microenvironment, we provide single-cell 3’ RNA sequencing data on 27,414 cells from 6 CRC patients in core and border tumor regions, as well as in matched normal mucosa. Analysis of primary colorectal cancer and normal mucosa samples depicts a comprehensive cellular landscape of colorectal cancer and potential cellular interactions, which would be a valuable resource for the development of therapeutic strategies.

overall_design:
Single-cell 3' mRNA sequencing data were obtained from 6 Belgian patients in core and border tumor regions, as well as in matched normal mucosa. To remove low-quality cells, we applied filtering criteria using nUMI, nGene and percent of mitochondrial genes. 29,003 cells have passed the criteria. To eliminate cells of an ambiguous identity, we combined the Seurat multiCCA and RCA pipelines for initial clustering and cell type identification, and removed discordant cells from 2 methods. After defining the global cell type, cells with a number of genes exceeding the outliers were removed to eliminate potential doublets. 27,414 cells have passed the final criteria.
Raw data was deposited at ArrayExpress, accession number : E-MTAB-8410

first: Hakki

last: Etlioglu

first: Valentina

last: Pomella

first: Ben

last: van den Bosch

first: Jasper

last: Vanhecke

first: Sabine

last: Tejpar

first: Bram

last: Boeckx

first: Diether

last: Lambrechts


title: Ribosome Footprinting (RiboSeq) analysis of mRNA translation in Dis3l2 knockout mESCs

status: Public on Apr 04 2020

first: Qi

last: Liu

state: MASSACHUSETTS

address: Boston, 02115.USA

institute: Boston Children's Hospital

summary: Input mRNAs and ribosome protected fragments (RPFs) from Heterozygout (Control) and Dis3l2 knockout (KO) mESCs cultures were analyzed by TruSeq Ribo Profile (Illumina) library preparation and high throughput sequencing

overall_design: mESCs were cultured in LIF/Serum condition. Input mRNAs and RPFs were isolated, ribosomal RNAs were depleted and cDNA libraries were prepared according to the TruSeq Ribo Profile pipeline (Illumina)

first: Richard

last: Gregory


title: RNA m6A methylation regulates sorafenib-resistance in liver cancer through FOXO3-mediated autophagy

status: Public on Apr 03 2020

city: Guangzhou

first: Guohui

last: Wan

state: Guangdong

address: 132# Waihuan Dong Road, High Education Mega Center

country: China

institute: Sun-yat sen University


title: RNA m6A methylation regulates sorafenib-resistance in liver cancer through FOXO3-mediated autophagy [m6A RIP-seq]

summary: N6-methyladenosine (m6A) is a type of nucleotide modification abundant in mRNA, which regulates mRNA stability, splicing and translation. However, its physiological role in intratumoral microenvironment and drug resistancehave not been fully understood. We demonstrated that METTL3,a primary m6A methyltransferase, was significantly down-regulated in human sorafenib-resistant hepatocellular carcinoma (HCC). Depletion of METTL3 under hypoxia promoted sorafenib-resistance and angiogenesis and exacerbated progression by activating autophagy-associated pathway. Mechanistically, we identified FOXO3 as a key downstream target of the METTL3-mediated m6A modification. The m6A modification of FOXO3 at the 3'-untranslated region increased FOXO3 mRNA stability. Analysis of clinical samples showed that METTL3levels aretightly correlated with FOXO3levels in patients with HCC, and suppression of FOXO3 predicted poor clinical outcomes. Importantly, METTL3-depletion significantly enhanced sorafenib-resistance of HCC via a METTL3-FOXO3 axis, whereasoverexpression of FOXO3 restored the m6A-dependent sorafenib-sensitivity. Collectively, our work revealedthe critical function of the METTL3-mediated m6A modification in HCC in hypoxic tumor microenvironment, and provided insights into the molecular mechanism of the m6A modification in the resistance of HCC to sorafenib therapy.

overall_design: We examined m6A abundance of SMMC-7721 mRNA under hypoxia using m6A-RNA immunoprecipitation sequencing.

first: Ziyou

last: Lin


title: Attenuated epigenetic suppression of muscle stem cell necroptosis is required for efficient regeneration of dystrophic muscle [RNA-seq 3]

status: Public on Apr 02 2020

city: Bad Nauheim

first: Carsten

last: Kuenne

address: Ludwigstrasse 43

department: Bioinformatics

country: Germany

institute: Max Planck Institute for Heart and Lung Research

summary: We performed a thorough study to analyze the epigenetic regulation of genes enabling programmed cell death as part of the chronic muscle regeneration.

overall_design: RNA-seq experiment of quiescent satellite cells of muscular dystrophy (mdx, 3 replicates) and wild type (2 replicates) mice.

first: Krishnamoorthy

last: Sreenivasan

first: Stefan

last: Guenther


title: Attenuated epigenetic suppression of muscle stem cell necroptosis is required for efficient regeneration of dystrophic muscle [RNA-seq 2]

summary: We performed a thorough study to analyze the epigenetic suppression of genes enabling programmed cell death as part of the muscle regeneration program.

overall_design: RNA-seq experiment of activated satellite cells (ASC) of WT MuSCs that were co-cultured in a transwell assay.WT, mdx and mdx/Ripk3mKO MuSCs were grown in the upper transwell; in the lower well single WT MuSCs were grown in monolayer. 72 hrs post conditioning, samples were harvested for RNAseq analysis.


title: Dbf4-Dependent Kinase (DDK)-Mediated Proteolysis of CENP-A Prevents Mislocalization of CENP-A in Saccharomyces cerevisiae

city: Worcester

last: Baker

address: 55 Lake Avenue North

department: Microbiology & Physiological Systems

institute: University of Massachusetts Medical School

summary: Restricting the localization of the centromeric histone H3 variant CENP-A to centromeres is essential to prevent chromosomal instability (CIN). Mislocalization of overexpressed CENP-A contributes to CIN in yeast, fly, and human cells. CENP-A is overexpressed in many cancers. Therefore, defining mechanisms that prevent CENP-A mislocalization will help us understand how CENP-A overexpression contributes to CIN in cancer. A genome-wide screen to characterize essential genes required for growth when CENP-A is overexpressed identified the replication initiation Dbf4-Dependent Kinase (DDK) complex. We show that DDK regulates ubiquitin-mediated proteolysis of Cse4 and prevents mislocalization of Cse4 independently of its role in DNA replication.

overall_design: Cse4 ChIP-seq was carried out in wild-type and cdc7-7 yeast strains overexpressing epitope-tagged Cse4 or tagged Cse4 expressed from the endogenous promoter. Samples of input and immunoprecipitated DNA were analyzed.

first: Jessica

middle: R

last: Eisenstatt

first: Lars

last: Boeckmann

first: Wei-Chun

last: Au

first: Valerie

last: Garcia

first: Levi

last: Bursch

first: Josefina

last: Ocampo

first: Michael

last: Costanzo

last: Weinreich

first: Robert

last: Sclafani

first: Anastasia

last: Baryshnikova

first: Chad

last: Myers

first: Charles

last: Boone

first: David

middle: J

last: Clark

first: Munira

last: Basrai


title: Attenuated epigenetic suppression of muscle stem cell necroptosis is required for efficient regeneration of dystrophic muscle

last: Kuenne


title: RNA m6A methylation regulates sorafenib-resistance in liver cancer through FOXO3-mediated autophagy [RNA-seq]

first: Guohui

last: Wan

overall_design: We examined differentially expressed genes between HCC tissue and sorafenib-resistant HCC tissue from patients via transcriptome sequencing.

first: Ziyou

last: Lin


title: Role of NCOR1 in CD4+ T cells

city: Vienna

first: Wilfried

last: Ellmeier

address: Lazarettgase 19

department: Institute of Immunology

country: Austria

institute: Medical University of Vienna


title: RNA-Seq to evaluate detaining intron splicing upon O-GlcNAc perturbation

first: Zhi-Wei

last: Tan

state: Massachusetts

address: Dept. of Microbiology, Harvard Medical School HIM, Room 1018D, 4 Blackfan Circle Boston, MA 02115

institute: Harvard University

summary: We report the effect of splicing upon O-GlcNAc perturbation with OGT inhibitor or OGA inhibitor. We found that splicing is acutely affected through our phosphoproteomics data when cells are treated with OGT inhibitor. By obtaining the various splicing events that are affected by OGT or OGA inhibition, we found that O-GlcNAc is a major regulator of detained introns splicing. At early time point, we observed highly specific splicing of OGT/OGA detained introns to buffer O-GlcNAc changes. At longer time point, ~80% of the total detained introns are affected by O-GlcNAc perturbation, while the rest of canonical splicing events are only minimally affected (~ 5%).

overall_design: Examination of gene changes and splicing changes with either OGT inhibitor or OGA inhibitor

first: Paul

last: Boutz


title: Single cell RNA sequencing of colorectal cancer with diverse tissue dissociation protocols or fresh vs. frozen cell preparations.

first: Yourae

last: Hong

summary: To evaluate 3 different tissue dissociation protocols or fresh vs. frozen cell preparations, we performed single-cell RNA sequencing on cancer or distant normal tissue dissociates from 2 colorectal cancer patients. Total 18,409 cells from 10 sample preparations were analyzed (5 primary colorectal cancer and 5 matched normal mucosa). The results suggest highly consistent cellular proportions were recovered with different sample preparation methods.

overall_design:
Ten batches of single cell RNA sequencing data were obtained from 2 patients, with 5 different sample preparations for primary colorectal cancer or matched normal mucosa respectively. For one patient, 3 different tissue dissociation protocols were applied for cancer and matched normal mucosa. For another freshly prepared or frozen-thawed cell stocks were tested for cancer and matched normal mucosa. After sequencing, we applied filtering criteria using nUMI, nGene and percent of mitochondrial genes to eliminate low-quality cells and 18,409 cells passed the filtering criteria.
****raw data files have not been provided due to patient privacy issues and will be available in EGA as controlled access****

first: Hae-Ock

last: Lee

first: Yong-Beom

last: Cho

first: Woong-Yang

last: Park


title: HOX13-dependent chromatin accessibility underlies the transition towards the digit development program[ATAC-Seq]

city: LAUSANNE

first: ALEXANDRE

last: MAYRAN

state: Waadt

address: Station 19

country: Switzerland

institute: EPFL

summary: Pioneer factors are transcription factors able to recognize their target site even concealed in “closed” chromatin, eventually eliciting the switch to accessible targets for other transcription factors and the transcriptional machinery. As such, pioneer factors play a key role in switching cell fate. Here, we provide evidence that HOXA13 and HOXD13 (HOX13 hereafter), two transcription factors of the Hox family of developmental genes, act as pioneer factors in the developing limb. We show that Hox13 function is mandatory for switching a series of target loci to an accessible chromatin state, allowing the binding of other transcription factors. These target loci include an enhancer previously identified as essential for the pentadactyl state, providing evidence that the pioneer activity of HOX13 is key for digit patterning. Based on the data reported here and previous studies, we propose that, during the fin-to-limb transition, the implementation of digit-specific enhancer elements had required an ancestral pioneer function of the HOX13 TFs.

overall_design: ATAC-Seq:  e11.5 mouse proximal forelimb WT, e11.5 mouse distal forelimb WT, e11.5 mouse distal forelimb HOX13KO.

first: Alexandre

last: Mayran

first: Rushikesh

last: Sheth

first: Claudia

last: Gentile


title: Attenuated epigenetic suppression of muscle stem cell necroptosis is required for efficient regeneration of dystrophic muscle [RNA-seq 1]

first: Carsten

summary: We performed a thorough study to analyze the epigenetic suppression of genes enabling programmed cell death as part of the muscle regeneration program. RNAseq analysis here serves as a method to compare the differentially deregulated genes upon knockdown of Chd4 in MuSCs using Adenoviral CRE recombination.

overall_design: Lox-cre recombination was used to create a deletion mutant of the CHD4 chromatin modifier (exons 12-21). A pseudo "infection" with GFP was used as control. Each of the two conditions was replicated using four mice.

first: Krishnamoorthy

last: Sreenivasan

first: Diana

last: Mesquita

first: Stefan

last: Guenther


title: Attenuated epigenetic suppression of muscle stem cell necroptosis is required for efficient regeneration of dystrophic muscle [ATAC-Seq]

last: Kuenne

summary: We performed a thorough study to analyze the epigenetic suppression of genes enabling programmed cell death as part of the muscle regeneration program. ATACseq analysis here serves as a method to compare the chromatin state and accessibilty of MuSCs in their quiescent state.

overall_design: ATAC-seq experiment of quiescent satellite cells of muscular dystrophy (mdx) and wild type mice. Each of the two conditions was replicated using three mice.


title: Single-cell RNA sequencing of healthy and dystrophic murine skeletal muscle

city: Berlin

first: Jordi

last: Camps

address: Müllerstraße 178

institute: Bayer AG

summary: Fibrosis and fat replacement in the skeletal muscle is a major complication that leads to a loss of mobility in chronic muscle disorders, such as muscular dystrophy. However, our current knowledge on the in vivo properties of adipogenic stem and precursor cells remains unclear, mainly due to the high cell heterogeneity in skeletal muscles. For this purpose, we used single-cell RNA-sequencing to decomplexify interstitial cell populations in healthy and dystrophic skeletal muscles. We identified a CD142 (F3) positive cell subpopulation in mice and humans that is responsible for the inhibition of adipogenesis. Furthermore, we found a completely altered composition of interstitial cells in muscular dystrophy, with a near absence of the CD142-positive cells. The novel discovery of these adipo-regulatory cells in the skeletal muscle aids our understanding regarding the aberrant fat deposition in muscular dystrophy, paving the way for treatments that potentially sustain ambulation in patients with muscular dystrophy.

overall_design: Hindlimb muscles of wild-type (C57BL6, n=1) and dystrophic (Sgcb-null, n=1) mice were digested and sorted as CD45-negative and CD31-negative single-cells in 96w plates. A total of 384 cells were processed into a single-cell library with SMART-seq2.

first: Maurilio

last: Sampaolesi


title: Genetic Deletion of Socs3 in Smooth Muscle Cells Ameliorates Aortic Dissection in Mice

status: Public on Apr 01 2020

city: Kurume

first: Hiroki

last: Aoki

state: Fukuoka

address: 67 Asahimachi

department: Cardiovascular Research Institute

country: Japan

institute: Kurume University

summary: Objective—We aimed to elucidate how the inflammatory response is involved in AD progression and the associated tissue destruction, focusing on the role of Jak/Stat signaling in smooth muscle cells (SMCs). Background—Aortic dissection (AD) is caused by disruption of the intima-media complex and tearing of the medial layer of the aorta. AD is life-threatening due to progressive destruction of the aorta, resulting in critical damage to organs. Recent studies reveal that the inflammatory response, including Jak/Stat signaling, is important in AD pathogenesis. However, it remains unclear how Jak/Stat signaling is involved in the tissue destruction in AD. Methods—Immunohistochemical analysis of human AD tissue revealed activation of signal transducer and activator of transcription 3 (Stat3) in medial SMCs. Stat3 activation was recapitulated in a mouse model of AD induced via β-aminopropionitrile and angiotensin II infusion. We also created a knockout mouse strain (smSocs3-KO) by deleting Socs3, a negative regulator of Jak/Stat signaling, specifically in mouse SMCs. Results—Compared to wild-type mice, smSocs3-KO mice developed a less severe AD phenotype that was associated with proinflammatory response at baseline, increased fibroblast and collagen deposition, and reinforced aortic tensile strength. Cell culture experiments revealed that Stat3 activation in SMCs caused secretion of factors that can stimulate fibroblast growth. Conclusions—Our present findings suggested that, although an acute inflammatory response is detrimental in AD, chronic activation of the SMC-mediated proinflammatory response was protective against aortic destruction in AD.

overall_design: To achieve the smooth muscle-specific deletion of Socs3 (smSocs3-KO), we crossed mice that were homozygous for the floxed allele of Socs3 (Socs3fl/fl) and backcrossed to C57BL/6J for three generations, with SM22-Cre mice (JAX Mice, stock # 004746) that carried a Cre recombinase transgene under control of the smooth muscle SM22 promoter. Socs3fl/fl littermate mice lacking the SM22-Cre transgene served as wild type (WT) controls. As a mouse model of aortic dissection, BAPN (150 mg/kg/day) and angiotensin II (AngII; 1000 ng/kg/min) were simultaneously administered to mice with (smSocs3-KO) or without (WT) SM22-Cre transgene using osmotic minipumps (Alzet model 1002). Aortic samples were obtained with or without 3 days of BAPN+AngII infusion.

first: Saki

last: Hirakata

first: Satoko

last: Ohno-Urabe

first: Michihide

last: Nishihara

first: Aya

last: Furusho

first: Norifumi

last: Nishida

first: Sohei

last: Ito

first: Makiko

last: Hayashi

first: Hideo

last: Yasukawa

first: Tsutomu

last: Imaizumi

first: Sinichi

last: Hiromatsu

first: Hiroyuki

last: Tanaka

first: Yoshihiro

last: Fukumoto


title: Condensation of nucleoid during environmental adaptation is regulated by dynamic HU interactions

first: Subhash

last: Verma

address: 37 Convent Dr

department: National Cancer Institute

institute: National Institutes of Health

summary: Nucleoid remodeling facilitated by DNA supercoiling results in changes in nucleoid configuration and involves nucleoid-associated proteins (NAPs) and structural maintenance of chromosomes (SMC) proteins among others.   Changes in nucleoid configurations regulated by NAPs are synchronized with cellular adaptation and influence the simultaneous expression of several genes. HU, a ubiquitous bacterial histone-like protein, is among the most conserved and abundant NAPs in eubacteria. In Escherichia coli, HU forms dimers by HUα self-association (HUαα) or by HUα-HUβ interactions (HUαβ). HUα is mostly expressed during lag and early exponential growth phase and HUβ is expressed only during the later exponential and stationary phase, pointing to distinct HUαα/DNA and HUαβ/DNA packaging of the nucleoid in regulating expression patterns during growth and stasis. Mutations or the deletion of HU transform the E. coli nucleoid to a different form and alter overall transcription program; thus, HU interactions with DNA directly affect global gene regulation. Recently, analysis of high-resolution contact maps of the E. coli nucleoid revealed an important role of HU to promote long-range DNA-DNA contacts within the nucleoid.  Yet, the molecular connections between HU-DNA interactions and changes in nucleoid architecture that regulate gene expression globally remain unknown. Here, we explored the higher-order E. coli nucleoid organization by soft x-ray tomography (SXT) and revealed an effect of HU surface charges in overall nucleoid organization and rearrangements. We also studied global transcription by next-generation RNA sequencing (RNA-Seq) and found a link between nucleoid rearrangement and changes in global transcription. To determine the functional relationships of observed nucleoid rearrangement and HU-DNA interactions, we also characterized the overall organization of HU nucleoprotein complexes in solution by small angle x-ray scattering (SAXS). We found that HUαα-mediated DNA networks are different at different ionic strengths and pHs. By means of macromolecular crystallography, we additionally elucidate HUαα dependent molecular switches that modulate DNA networking. This integrative structural study explains how HUαα regulates dynamic transformations of the nucleoid by DNA bridging to control nucleoid rearrangement and global gene regulation.

overall_design: Three biological replicates were analyzed for each of 12 conditions

first: Sankar

last: Adhya

first: Soumya

last: Remesh

first: Michal

last: Hammel


title: Effect of rapamycin on gene expresssion in mouse model of aortic dissection

first: Hiroki

last: Aoki

summary: Aortic dissection (AD) is a medical emergency that leads to sudden death. Effective medical therapy is not available because molecular mechanism of AD is poorly understood. We performed the transcriptome analysis in mouse AD model that was created by infusion of beta-aminopropionitrile, a collagen crosslink inhibitor, and angiotensin II. Bayesian network analysis of the transcriptome revealed several distinct gene clusters that were tightly co-regulated during AD development. Functional annotation analysis revealed that each gene cluster has distinct function, namely, cell proliferation, inflammation, cell locomotion and adhesion, and muscle differentiation. Among the gene clusters, cell proliferation cluster was the first to be activated during AD development. Cell proliferation before AD development was confirmed by immunoblotting of G1 cyclins. Immunostaining for Ki67 and cell markers revealed the proliferation of smooth muscle cells, fibroblasts, and monocytes in aortic tissue before AD development. Treatment of mice with rapamycin, an mTOR inhibitor, suppressed cell proliferative response in AD model. Rapamycin completely prevented AD when given before AD development, and effectively suppressed progression when given after AD development. Interestingly, transcriptome analysis showed that rapamycin strongly suppressed cell proliferation and muscle differentiation clusters, but its effect on inflammation cluster was modest. We concluded that mTOR constitutes an essential part of the molecular pathogenesis of AD by regulating cell proliferation, and represents a new therapeutic target.

overall_design: Aortic dissection model was created by continuous infusion of 150 mg/kg/day beta-aminopropionitrile, a collagen crosslink inhibitor, and 1 ug/kg/min angiotensin II (B+A). Rapamycin (2 mg/kg/day) or dimethylsulfoxide (DMSO, vehicle) was intraperitoneally administored to mice once a day. Four experimental groups were set; DMSO alone (Pre), rapamycin alone, B+A+DMSO, and B+A+rapamycin, each of which contained 3 mice. Aortic samples were obtained at 3 days of experiment.

last: Hayashi-Hori

first: Yohei

last: Hashimoto

first: Ryohei

last: Majima


title: Molecular diversity of auditory critical period plasticity revealed by single-nucleus RNA sequencing

first: Brian

last: Kalish

address: 220 Longwood Ave

department: Neurobiology

summary: Auditory experience drives neural circuit refinement during auditory circuit development, but little is known about the genetic regulation of this developmental process. The primary auditory cortex (A1) exhibits a critical period for thalamocortical connectivity between postnatal days P12 and P15, during which tone exposure alters the tonotopic topography of A1. We hypothesized that a coordinated, multicellular transcriptional program governs this window for patterning of the auditory cortex. To test this idea, we generated a multicellular map of gene expression by performing droplet-based, single-nucleus RNA sequencing (snRNA-seq) of A1 across three developmental time points spanning the tonotopic critical period (P10, P15, P20). We also tone-reared mice (7 kHz pips) during the 3-day critical period and carried out snRNA-seq of A1 at P15 and P20. Using semi-supervised clustering and marker genes, we identified and profiled neuronal (glutamatergic and GABAergic) and non-neuronal (oligodendrocytes, microglia, astrocytes, and endothelial) cell types in A1 under these different conditions to identify candidate genes that might regulate auditory critical period plasticity. By comparing normally reared and tone-reared mice, we identified hundreds of genes in both glutamatergic and GABAergic cells with altered expression as a result of sensory manipulation in the critical period. In addition, we identified previously unknown effects of developmental tone exposure on interneuron developmental trajectories. This single-cell transcriptomic resource of the developing auditory cortex will provide a powerful discovery platform for future characterization of mediators of tonotopic plasticity.

overall_design: Five conditions, each with two bioreplicates: P10 normally reared, P15 normally reared, P15 tone reared, P20 normally reared, P20 tone reared.

first: Michael

last: Greenberg


title: Gene expression and exon splicing of two Ewing sarcoma cell lines (TC-32, RDES), transiently transfected with shControl or two different shRNA against SOX6

city: Heidelberg

first: Thomas

middle: Georg Philipp

last: Grunewald

address: Im Neuenheimer Feld 280

department: Division of Translational Pediatric Sarcoma Research

institute: German Cancer Research Center (DKFZ)

summary: In this dataset, we include the gene expression and exon splicing variants of two Ewing sarcoma cell lines (RDES and TC-32) after knockdown of the transcription factor SOX6 in order to obtain differentially expressed genes and different exon splicing variants.

overall_design: 12 samples were normalised (log2) with Affymetrix Expression Console Software (v1.4) using SST-RMA algorithm. They were annotated on gene and exon level with the library for Clariom D Array (human).

first: Aruna

last: Marchetto

first: Julia

last: Gerke

last: Grünewald


title: RNAseq Suv39h1 injected single embryo

city: Munich

first: Elias

middle: Rafael

last: Ruiz-Morales

state: Baviera

address: Marchioninistrasse 25

department: Institute of Epigenetics and Stem Cells

institute: Helmholtz Zentrum Muenchen

summary: Suv39h1wt or mut mRNA was injected into the zygote and cultured for the indicated timepoints

overall_design: title code: A-D = experiment, 1-4 = time of collection (48h, 65h, 75, 90h), N,1,2 = mRNA microinjected, embryonic stage (E2 = 2-cell etc. B= blastocyst, M= morula)

first: Adam

last: Burton


title: Genomic-wide Spi-C binding in mouse 38B9 cells

city: London

first: Rodney

middle: Peter

last: DeKoter

state: Ontario

address: 1151 Richmond St

department: Microbiology and Immunology

institute: Western University

summary: We determined the genome-wide binding of the ETS transcription factor Spi-C with target genes using chromatin immunoprecipitation and next generation sequencing (ChIP-seq)

overall_design: Mouse Ableson-transformed 38B9 B cells were infected with retroviral vectors encoding 3XFLAG-tagged mouse Spi-C. Infected cells were enriched to 100% GFP positive. Anti-FLAG chromatin immunoprecipitation was performed on chromatin prepared from formaldehyde-fixed 38B9-Spi-C cells.


title: Comparison of mRNA profiles of AGO2 sufficent and deficient pancreatic tissue in the LSL KRASG12D mouse model of pancreatic cancer

status: Public on Mar 31 2020

city: Ann Arbor

first: Arul

last: Chinnaiyan

state: MI

address: 1500 E. Medical Center Drive

department: Pathology

institute: University of Michigan

summary:
Purpose:  The goals of this study are to compare NGS-derived transcripts to compare the expression of transcripts between AGO2 sufficent PDAC tissue and AGO2 deficient senescent PanINs in the mouse model
Methods: mRNA profiles of 500 day-old AGO2+/+;KRASG12D;p48Cre and AGO2fl/fl;KRASG12D;p48Cre pancreatic tissue were generated in duplicates
Results: mRNA transcripts were further analyzed using GSEA tools for mouse transcript quantitation

overall_design: Pancreatic tissue mRNA profiles of AGO2+/+;KRASG12D;p48Cre and AGO2fl/fl;KRASG12D;p48Cre mice at 500-day time point were generated by deep sequencing.

first: Pankaj

last: Vats


title: 5' droplet-based single cell RNA sequencing of human colorectal cancer and normal organoids

city: Hong Kong

first: Suet Yi

last: Leung

address: Queen Mary Hospital, Pokfulam Road

department: Department of Pathology

country: Hong Kong

institute: The University of Hong Kong

summary: Using 5' droplet-based single cell sequencing, we profiled single cells dervied from human colorectal cancer organoids carrying either APC mutation or RSPO fusion, and paired normal colon organoids for the later.

overall_design:
Colorectal cancer and normal organoids were cultured in standard colon organoid medium or specified culture conditions to achieve differentiated state. Organoids were then FACS-sorted to obtain single cells and were subjected to sequencing.
The raw data files have not been included due to privacy concerns.


title: Gene expression profiling of sciatic nerves from rats with diabetic peripheral neuropathy

city: Ningbo

first: yiji

last: tu

state: Zhejiang

address: 1059 East Zhongshan Road, Yinzhou District

institute: Ningbo 6th hospital

summary: To identify the key genes and pathways which might play critical roles in the pathogenesis of experimental DPN via microarray analysis. Adult male Sprague-Dawley rats (initial weight 250-300g, from the department of laboratory animal science of Fudan University) were randomly assigned into two groups: control rats and diabetic rats. Diabetes was induced with a single intraperitoneal injection of STZ (55mg/kg). Control rats were performed with a single intraperitoneal injection of 0.9% saline solution. Glucose level was evaluated using Sannuo strips on tail vein blood at day 3 after STZ injection and verified again at day 7 after STZ injection. Only rats with blood glucose level 16.7 mmol/L were considered diabetic.Six weeks after diabetes induction, nerve tissue samples (about 1cm long) were harvested from the right sciatic nerve of rats in control (n=3) and diabetic (n=3) groups for total RAN isolation. Microarray hybridization was then performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technologies). Quantile normalization and subsequent data processing were performed using the GeneSpring GX v12.1 software package (Agilent Technologies). The univariate t-test with a fold-change >2 and P value < 0.001 was applied to identify the DEGs between control rats and diabetic rats. Credibility of the microarray data was validated through qRT-PCR on 4 genes. Total RNA was independently extracted from the right sciatic nerve of rats in both groups (n=3) 6 weeks after diabetes induction.

first: Yiji

last: Tu


title: Detection of CNVs in patients with syndromic intellectual disability

city: Vilnius

first: Živilė

last: Maldžienė

address: Santariškių str. 2

country: Lithuania

institute: Vilnius University

type:
Genome variation profiling by SNP array
SNP genotyping by SNP array

summary: Illumina whole genome SNP (single nucleotide polymorphism) microarray analysis  was carried out on the patient in order to determine copy number variations and to assess their disease etiopathogenesis.

overall_design: A SNP-CGH test was carried out on the patient in order to determine copy number variations and to assess their disease etiopathogenesis. This approach consists of three main steps. First, the SNP genotyping consists from DNA amplification,First, the SNP genotyping consists from DNA amplification, fragmentation, precipitation, resuspendation, DNA hybridization on SNP chips, washing, dyeing and scanning of SNP chips. Second, primary analysis of results includes project establishment using Genotyping Module v1.9 software, genome visualisation tool of GenomeStudio™ Genotyping Module v1.9 software and QuantiSNP v2.1 software for determining CNVs. The third step includes biocomputational analysis of CNVs in Genome browser of GenomeStudio™ Genotyping Module v1.9 software and in DGV, Decipher and in others databases.

first: Beata

last: Aleksiūnienė


title: Temporal Transcriptomic Analysis of Human Primary Keratinocytes Exposed to β-naphthoflavone Highlights the Protective Efficacy of Skin to Environmental Pollutants

city: LONGJUMEAU

first: Angela

last: PATATIAN

address: 1CHEMIN DE SAULXIER

department: ESSONNE

country: France

institute: GENEX

summary: The skin covers almost the entire body and plays an important role in detoxification and elimination of xenobiotics. These processes are initiated following the binding of xenobiotics to the aryl hydrocarbon receptor (AhR), which leads to the expression of several detoxification enzymes. To gain some insights on their impacts on skin cells over time, a temporal transcriptional analysis using gene expression arrays was performed in human primary epidermal keratinocyte (HEK) cells exposed for 6, 24 and 48h to β-naphthoflavone (βNF), a potent agonist of AhR. Our results demonstrated that expression of genes related to xenobiotic, inflammation, and extracellular matrix remodeling was increased upon βNF treatment from 6h onwards. In contrast, the anti-oxidative response was seen mainly starting at 24h. While some of the genes controlled by the epidermal differentiation complex was induced as soon as 6h, expression of most of the S100 related genes located within the same chromosomal locus and keratin genes was increased at later times (24 and 48h). Altogether our transcriptomic data highlight that following βNF exposure, HEK cells elicited a protective xenobiotic response together with the activation of inflammation and keratinocyte regeneration. Later on these processes were followed by the stimulation of anti-oxidant activity and terminal differentiation.

overall_design: Neonatal human epidermal keratinocytes (HEKn) are primary cells derived from neonatal foreskins. They are supplied by the American Type Culture Collection (ATCC) in the form of 5 × 10 5 viable cells vials from different donors in order to have a constant homogeneity of cell populations. These cells were cultured in a specific medium (Epilife, Life Technologies) supplemented with a plant-derived supplement (HKSdaFREE and HKGE, AvantBio) that replaces the sera of animal origin more commonly used in cell culture. The cells were cultured at 37 ° C in an incubator (5% CO2 / 95% air). Total RNA was extracted from keratinocyte using RNeasy Mini Plus Kits (Qiagen). Total RNA were used for reverse transcription, amplification and Cy3 labeling, using the Low Input Labeling kit, one-color (Agilent Technologies). All cRNAs were hybridized to human whole genome oligo microarrays (Agilent Technologies v2 (AMADID 039494), which contains 60.000 probes, derived from the National Center for Biotechnology Information Reference Sequence (NCBI) RefSeq. Microarray data were quantified (GeneExtraction Feature V11.0,1) and normalized with R tools (Bioconductor).

first: P

last: Quantin

first: A

last: Patatian

first: M

last: Floreani

last: Benech

first: C

last: Egles

first: H

last: Ficheux


title: GPR56/ADGRG1 is associated with response to antidepressant treatment

city: Montreal

first: Gustavo

last: Turecki

state: Quebec

address: 6875 Boulevard LaSalle

department: Psychiatry

institute: McGill University

summary: It remains unclear why many patients with depression do not respond to antidepressant treatment. In three cohorts of individuals with depression and treated with serotonin-norepinephrine reuptake inhibitor (N=424) we show that responders, but not non-responders, display an increase of GPR56 mRNA in the blood. In a small group of subjects we also show that GPR56 is also downregulated in the PFC of individuals with depression that died by suicide. In mice, we show that chronic stress induced Gpr56 downregulation in the blood and prefrontal cortex (PFC), which is accompanied by depression-like behaviour, and can be reversed by antidepressant treatment. Gpr56 knockdown in mouse PFC was is associated with depressive-like behaviors, executive dysfunction and poor response to antidepressant treatment. GPR56 peptide agonists had antidepressant-like effects and up-regulated AKT/GSK3/EIF4 pathways. Our findings uncover a potential role of GPR56 in antidepressant response.

overall_design:
Analysis of changes in gene expression over 8 weeks in patients with MDD treated with duloxetine or placebo

Please note that the 'characteristics: response' values 1 and 0 represent True (1) and False (0), respectively, indicating whether the subjects responded (1) or not (0) to the treatment.

first: Laura

last: Fiori

first: Raoul

last: Belzeaux

first: Jean-François

last: Théroux


title: ANDROGEN RECEPTOR WITH SHORT POLYGLUTAMINE TRACT PREFERABLY ENHANCES WNT/BETA-CATENIN MEDIATED PROSTATE TUMORIGENESIS

city: Duarte

first: Zijie

last: Sun

address: 1500 E. Duarte Rd.

department: Cancer Biology

institute: City of Hope

summary: Polyglutamine (polyQ) tract polymorphism within the human androgen receptor (AR) shows population heterogeneity.  African American men possess short polyQ tracts significantly more frequently than Caucasian American men.  The length of polyQ tracts is inversely correlated with the risk of prostate cancer, age of onset, and aggressiveness at diagnosis.  Aberrant activation of Wnt signaling also reveals frequently in advanced prostate cancer, and an enrichment of androgen and Wnt signaling activation has been observed in African American patients.  Here, we investigated aberrant expression of AR bearing different polyQ tracts and stabilized β-catenin in prostate tumorigenesis using newly generated mouse models.  We observed an early onset oncogenic transformation, accelerated tumor cell growth, and aggressive tumor phenotypes in the compound mice bearing short polyQ tract AR and stabilized β-catenin.  RNA sequencing analysis showed a robust enrichment of Myc-regulated downstream genes in tumor samples bearing short polyQ AR versus those with longer polyQ tract AR.  Upstream regulator analysis further identified Myc as the top candidate of transcriptional regulators in tumor cells from the above mouse samples with short polyQ tract AR and β-catenin.  Chromatin immunoprecipitation analyses revealed increased recruitment of b-catenin and AR on the c-Myc gene regulatory locus in the tumor tissues expressing stabilized b-catenin and shorter polyQ tract AR.  These data demonstrate a promotional role of aberrant activation of Wnt/b-catenin in combination with short polyQ AR expression in prostate tumorigenesis and provide mechanistic insight into aggressive prostatic tumor development that is frequently observed in African American patients.

overall_design: Two replicates were included in each group.

middle: Z


title: Expression data from IEC6 cells after treatment with Na2S3

city: Okinawa

first: Sayomi

last: Higa-Nakamine

address: 207 Uehara, Nishihara

department: Department of Biochemistry

institute: Graduate School of Medicine, University of the Ryukyus

summary:
Analysis of IEC6 cells treated with Na2S3
In this dataset, we include the expression data obtained from IEC6 cells after treatment with Na2S3. We confirmed that IEC6 cells expressed Kruppel-like transcription factor 4 (KLF4). Results provide insight into the effect of Na2S3 on MAP kinase pathway.

overall_design: IEC6 cells were treated with 100 uM Na2S3 for 60min.

first: Kaoru

last: Arakaki

first: Hideyuki

last: Yamamoto


title: Bone marrow LysM-Cre mediated TFEB overexpression significantly affected the response of bone marrow-derived macrophages to tumor material, decreasing both the expression of typical M2-like macrophage associated genes and inflammatory response genes.

city: Columbia

first: Diego

last: Altomare

state: SC

address: 715 Sumter Street, Room 617

department: Department of Drug Discovery and Biomedical Sciences

institute: University of South Carolina

summary: In order to examine the effects of TFEB overexpression in macrophages on anti-tumor immunity, 8 week-old, female LysM-Double-Cre x TFEB transgene+ (TFEBtg) and LysM-Double-Cre x TFEB transgene- (WT) mice were sacrificed and their bone marrow was differentiated into macrophages using recombinant M-CSF. After one week of differentiation, macrophages were replated and treated with either DMEM only or DMEM supplemented with tumor-conditioned medium (serum-free DMEM supernatant exposed to EO771 tumor cells) and tumor lysate for 24 hours. Macrophages were then collected and gene expression was analyzed using whole genome microarray. TFEBtg macrophages expressed significantly less typical M2-like macrophage genes, such as Arg1 and IL-10, than WT macrophages when exposed to tumor-conditioned medium and lysate. TFEB overexpression also decreased the expression of pro-inflammatory genes such as IL-1β, IL-6, and NLRP3 as well as genes involved in PGE2 synthesis, such as COX2, HIF-1α, MIF, and cPLA2. RT-qPCR was used to confirm the expression of the genes listed and many others. Ingenuity Pathway Analysis was also performed in order to analyze the expression of genes clustered by functional relationships. Mice treated to increase TFEB expression demonstrated decreased breast tumor growth.

overall_design: Four-condition, one-color experiment. Microarray analysis of  LysM-Double-Cre x TFEB transgene+ and LysM-Double-Cre x TFEB transgene- mouse gene expression was performed on bone marrow-derived macrophage RNA. 3 biological replicates per each experimental group.

first: Hodge

last: Johnie

first: Dapin

last: Fan


title: NicE-seq in Suv39h2 knockdown 8-cell stage

first: Adam

last: Burton

address: Marchioninistr. 25

department: IES

institute: Helmholtz Munchen

summary:
Determination of accessible chromatin regions in the 8-cell stage mouse embryo after Suv39h2 knockdown
The study aimed to address a potential function of H3K9me3 in early mouse development by assessing its impact on chromatin compaction. The histone methyltransferase responsible for de novo H3K9me3 at fertilization Suv39h2, was knocked down by microinjection of dsRNA targeting Suv39h2 in the early zygote. Embryos were then cultured until the 8-cell stage of development. They were then fixed and chromatin compaction was assessed by NicE-seq in pools of 10 8-cell stage embryos.

overall_design: Mouse zygotes were microinjected with double stranded RNA (approx 400bp) targeting N-terminal Suv39h2 or Lacz as control. They were cultured until the 8-cell stage and pools of 10 were fixed in 1% PFA. NicE-seq (nicking enzyme assisted sequencing) was applied accoridng to Ponnaluri et al., 2017.


title: Analysis of the translocating RNA-binding protein HNRNPU using MY-CLIP

city: Fujisawa

first: Masato

last: Yugami

state: Kanagawa

address: 26-1, Muraoka-Higashi 2-chome

department: Research

institute: Takeda Pharmaceutical Company

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

overall_design: Refer to individual Series


title: HNRNPU MY-CLIP study using cytoplasmic or whole lysates

summary: Comparison of MY-CLIP between using cytoplasmic fraction and whole cell lysate for PMA/Ca2+ ionophore stimuated HeLa cells

overall_design: UV-irradiated HeLa cells stimulated by PMA/Ca2+ ionophore were fractionated, and then subjected to HNRNPU MY-CLIP to identify HNRNPU binding positions on RNA

first: Masto

last: Yano


title: RNAseq in PMA/Ca2+ ionophore stimulated HeLa cells transfected with negative control siRNA and siRNA against HNRNPU

summary: We sequenced mRNA from cultured HeLa cells transfected with control or HNRNPU siRNA to compare gene expression level in PMA/Ca2+ ionophore stimulated condition

overall_design: mRNA profiles obtained from 3 different control and 3 siRNA against HNRNPU treated HeLa cells were generated by  sequencing using Illumina MiSeq.


title: MY-CLIP verification study

summary: Comparison between BrdU-CLIP and MY-CLIP for HNRNPU, and MY-CLIP performance for HNRNPC

overall_design: UV-irradiated HeLa cell samples were subjected to HNRNPU BrdU-CLIP and MY-CLIP to compare each productivity of the CLIP libraries,  and HNRNPC MY-CLIP to validate its performance by comparison with previous reported HNRNPC CLIP study by using illumina MiSeq


title: RNA sequencing analysis of wildtye and Acc2 iKO mice heart in chow and HFD

city: SEATTLE

first: Rong

last: Tian

state: WA

address: 850 Republican Street, Room N130

institute: University of Washington

summary: Here, we show that short term HFD feeding did not change the cardiac function in normal (Con) and increased FAO mice (ACC2 iKO). RNA sequencing analysis show that ACC2 can have small but significant genetic perturbations impact on the global transcriptome under chow and HFD condition. Most of fatty acid degradation and PPAR signaling pathway related gene transcription levels were decreased by knocking out ACC2. Intriguingly, cardiac transcriptome analysis of several lipotoxicity mouse models showed an opposite regulation direction of PPAR signaling pathway and fatty acid degradation genes. Finally, fatty acid degradation gene transcription was found back to normal in iKO-HFD mouse hearts compared to Con-chow mice hearts. These results suggest that fatty acid availability may play an important role in PPAR signaling regulation regardless the fatty acid oxidation rate, at least in mice heart.

overall_design: ACC2 flox/flox-MerCreMer+ (ACC2-f/f-MCM+) mice were mated with ACC2f/f to produce both study and control littermates. At 8 weeks of age, both ACC2f/f-MCM+ and ACC2f/f (CON) mice received an intraperitoneal injection of tamoxifen (20 mg/kg) for 5 days, which was sufficient to cause ACC2 deletion in ACC2f/f-MCM+ (iKO). Four weeks after the last injection of tamoxifen, male CON and iKO mice were subjected to chow or High fat diet for 16 weeks. Illumina HiSeq 2000 at a read length of 100nt single end.

first: Zhenglong

last: Liu

first: Dan

last: Shao


title: Endogenous expression of CD83 in Foxp3+ T cells essentially contributes to differentiation and function of murine Foxp3+ effector regulatory T cells

city: Bonn

first: Joachim

last: Schultze

state: NRW

address: Carl-Troll-Strasse 31

department: Genomics and Immunoregulation

institute: LIMES (Life and Medical Sciences Center Genomics and Immunoregulation)

summary: Foxp3-positive regulatory T (Treg) cells are crucial players for the maintenance of immune homeostasis and keep immune responses in check. Upon activation, Treg are transferred into an effector state expressing transcripts essential for their suppressive activity, migration and survival. However, how different intrinsic and environmental factors control differentiation is still not completely understood. Here, we present for the first time data suggesting that Treg intrinsic expression of CD83 is essential for Treg differentiation upon activation. Interestingly, mice with Treg intrinsic CD83 deficiency are characterized by a pro-inflammatory phenotype. Furthermore, the loss of CD83 expression by Treg leads to the downregulation of Treg specific differentiation markers and the induction of an inflammatory profile. In addition, Treg specific conditional knockout mice showed aggravated autoimmunity and an impaired resolution of inflammation. Altogether, CD83 expression in Treg cells is an essential factor for the development and function of effector Treg cells upon activation.

overall_design: Whole genome transcript levels were measured in 3h activated versus non-activated (anti-CD3/-CD28) splenic sorted Treg total RNA preparations from 6 mice of two different genotypes (in general three 9-10-week-old mice per genotype)

first: Marina

last: Doebbeler

first: Christina

last: Koenig

first: Lena

last: Krzyzak

first: Christine

last: Seitz

first: Alina

last: Butterhof

last: Kuhnt

first: Katarzyna

last: Kuzcera

last: Sandrock

first: Elisabeth

last: Zinser

first: Ilka

last: Knippertz

first: Stefan

last: Wirtz

last: Riegel

first: Petra

last: Hoffmann

first: Lars

last: Nitschke

first: Thomas

last: Winkler

first: Dmitry

last: Kopelyanskiy

last: Ulas

first: Alexander

last: Steinkasserer

first: Matthias

last: Lechmann


title: Epigenome analysis of human blood and saliva samples

city: Kumamoto

first: Kazuya

last: Iwamoto

address: 1-1-1 Honjo, Chuo-ku

department: Faculty of Life Sciences

institute: Kumamoto University

type: Methylation profiling by genome tiling array

summary: Genome-wide DNA methylation profiling of human blood and saliva samples. The Illumina Infinium HumanMethylation 450k BeadChip was used to obtain DNA methylation profiles across approximately 480,000 CpGs in blood and saliva samples provided from 22 persons, and saliva samples from 3 persons.

overall_design: Bisulfite converted DNA from the 44 samples (saliva and blood) and 12 samples (saliva only) were analyzed by the hybridization to the Illumina Infinium HumanMethylation 450k BeadChip.

first: Yui

last: Murata

first: Ayaka

last: Fujii

first: Miki

last: Bundo


title: Differential gene expression profiling by deletion of GFI1 super-enhancer (GFI1-SE-KO) upon treatment of a LSD1 inhibitor NCD38 in HEL cells

city: Otsu

first: Goichi

last: Tatsumi

address: Seta Tsukinowa-cho

institute: Shiga University of Medical Science

summary: Activation of GFI1-super-enhancer (GFI1-SE) by a LSD1 inhibitor NCD38 was relevant to myeloid differentiation and antileukemia effect in human erythroleukemia cells (HEL cells). Thus, we investigated the role of GFI1-SE upon NCD38 treatment in HEL cells. We established three independent sublines with bi-allelic deletion of GFI1-SE (CCE2 #114, #141, and #216) using CRISPR-Cas9 genome editing system in HEL cells and a classical limiting dilution method. Control sublines (Ctrl C1, C2, and C5) were established by transfection of parent vector and limiting dilution. After treatment of each subline with DMSO or NCD38 (LSD1i) for 24 hours, these gene expression profiling data were obtained.

overall_design: Two target-specific oligonucleotides were designed to cleave upstream and downstream sites of the GFI1-SE, and were inserted into the entry site of the CRISPR-CAS9 genome editing vector (pX330-U6-Chimeric_BB-CBh-hSpCas9, Addgene, plasmid ID: 42230). Oligonucleotides for site-specific chromatin cleavage of target regions were designed using a bioinformatics tool (https://chopchop.rc.fas.harvard.edu/). Both vectors were transfected into HEL cells using the Amaxa nucleofection technology. After limiting dilution and genotype screening, three independent sublines with bi-allelic deletion of the GFI1-SE (delGFI1-SE) were established. For control sublines, the parent (non-inserted) CRISPR-CAS9 genome editing vector was used. After treatment of each subline with DMSO or NCD38 (LSD1i) for 24 hours, these gene expression profiling data were obtained.

first: Masahiro

last: Kawahara


title: Transcriptome analysis uncovers a link between copper metabolism, and both fungal fitness and antifungal sensitivity in the opportunistic yeast Candida albicans

status: Public on Mar 30 2020

city: Québec

first: Faiza

last: Tebbji

address: 2705 Boulevard Laurier

institute: CHU Québec

summary: Copper homeostasis is an important determinant for virulence of many human pathogenic fungi such as the highly prevalent yeast Candida albicans. However, beyond the copper transporter Ctr1, little is known regarding other genes or biological process that are affected by copper. To gain insight into the cellular processes that are modulated by copper abundance in C. albicans, we monitored the global gene expression dynamic under both copper depletion and excess using RNA-seq.

overall_design: Examination of the effect of copper depletion and excess.

first: Inès

last: Khemiri

first: Faïza

first: Adnane

last: Sellam


title: RNA-seq 2-cell Suv392 knockdown

city: Munich

first: Adam

last: Burton

summary: Suv39h2 knockdown mouse 2-cell stage

overall_design: Zygotes microinjected with dsSuv39h2, RNAseq in pools of 5x 2-cell stage at the 2-cell stage

first: Quirze

last: Rovira


title: L. lactis cultures: control vs acetaldehyde-induced

city: Groningen

first: Jhonatan

middle: Alejandro

last: HernandezValdes

address: Nijenborgh 7

department: Molecular Genetics

country: Netherlands

institute: University of Groningen

summary: Transcriptome analysis of Lactococcus lactis cultures comparing control non-induced and induced with acetaldehyde

overall_design: Two-condition experiment, control vs induced: biological replicates 3 control and 3 induced.

last: Hernandez-Valdes


title: L. lactis cultures: control vs diacetyl-induced

summary: Transcriptome analysis of Lactococcus lactis cultures comparing control non-induced and induced with diacetyl


title: Unique Properties of a Subset of Human Pluripotent Stem Cells With High Capacity for Self-Renewal [FAST-ATAC]

city: Bar Harbor

first: Christopher

middle: Lee

last: Baker

state: ME

address: 600 Main Street

institute: The Jackson Laboratory

summary: Archetypal human pluripotent stem cells (hPSC) are widely considered to be equivalent in developmental status to mouse epiblast stem cells, which correspond to pluripotent cells at a late post-implantation stage of embryogenesis. Heterogeneity within hPSC cultures complicates this interspecies comparison. Here we show that a subpopulation of archetypal hPSC enriched for high self-renewal capacity (ESR) has distinct properties relative to the bulk of the population, including a cell cycle with a very low G1 fraction and a metabolomic profile that reflects a combination of oxidative phosphorylation and glycolysis. ESR cells are capable of differentiation into primordial germ cell-like cells. Global DNA methylation levels in the ESR subpopulation are lower than those in mouse epiblast stem cells. Chromatin accessibility analysis revealed a unique set of open chromatin sites in ESR cells. RNA-seq at the subpopulation and single cell levels shows that, unlike mouse epiblast stem cells, the ESR subset of hPSC displays no lineage priming, and that it can be clearly distinguished from gastrulating and extraembryonic cell populations in the primate embryo. ESR hPSC correspond to an earlier stage of post-implantation development than mouse epiblast stem cells.

overall_design: hESC were FACS sorted using a panel of CD9, GCTM2 and EPCAM expression. The total population was surveyed for hESC cultured under defined conditions of matrigel and mTESR1 with and without the treatment of protein kinase c inhibitors. The triple-high sub-population of cells represents those hESC cultured under defined conditions expressing the highest level of markers.

first: K

middle: X

last: Lau

first: E

last: Mason

first: J

last: Kie

first: D

middle: P

last: De Souza

last: Kloehn

last: Tull

first: M

last: McConville

first: A

last: Keniry

first: T

last: Beck

last: Blewitt

last: Ritchie

first: S

middle: H

last: Naik

last: Zalcenstein

first: O

last: Korn

last: Su

first: I

last: Romero

first: C

last: Spruce

middle: C

last: McGarr

last: Wells

middle: F

last: Pera


title: Synthetic lethal and resistance interactions with BET bromodomain inhibitors [ChIP-Seq]

city: Boston

first: Kornelia

last: Polyak

address: 450 Brookline Ave

department: Medical Oncology

institute: Dana-Farber Cancer Institute

summary: BET bromodomain inhibitors (BBDI) are promising therapeutic agents in triple-negative breast cancer (TNBC). However, not all tumors respond and acquired resistance emerges rapidly even in the responders. Using CRISPR and small molecule inhibitor screens combined with comprehensive molecular profiling of BBDI response and resistance in TNBC cell lines, we identified numerous synthetic lethal interactions with BBDIs as well as genes that when deleted confer resistance. The most prominent and consistent synergy was observed with CDK4/6 inhibitors and paclitaxel. We also uncovered functional similarities and differences between BBD proteins BRD2, BRD4, and BRD7, whereas deletion of BRD2 and BRD4 enhances sensitivity to BBDIs, BRD7 loss leads to resistance. Lastly, single cell RNA-seq and cellular barcoding analysis of BBDI responses in sensitive and resistant cell lines highlight heterogeneity among samples and demonstrate that BBDI resistance can be both pre-existing and acquired.

overall_design: ChIP-Seq of parental and JQ1 resistant breast cancer cell lines

first: Shaokun

last: Shu

first: Hua-Jun

last: Wu

first: Franziska

last: Michor


title: Synthetic lethal and resistance interactions with BET bromodomain inhibitors [scRNA-Seq]

overall_design: scRNA-Seq of parental and JQ1 resistant breast cancer cell lines


title: Single cell transcriptomics identifies stem cell-derived graft composition in a model of Parkinson’s disease.

city: Lund

first: Johan

last: Jakobsson

address: Solvegatan 17

country: Sweden

institute: Lund University

summary: Cell replacement is a long-standing and realistic goal for the treatment of Parkinson’s disease (PD). Cells for transplantation can be obtained from fetal brain tissue or from stem cells.  However, after transplantation dopamine (DA) neurons are a minor component of grafts and it has remained difficult to determine the identity of other cell types. Here, we report analysis by single cell RNA sequencing (scRNA-seq) combined with comprehensive histological analyses to characterize intracerebral grafts from human embryonic stem cells (hESCs) and fetal tissue after functional maturation in a pre-clinical rat PD model. We show that neurons and astrocytes are major components in both fetal and stem cell-derived grafts. Additionally, we identify a cell type closely resembling a class of newly identified perivascular-like cells in stem cell-derived grafts. Thus, this study uncovers previously unknown cellular diversity in a clinically relevant cell replacement PD model.

overall_design: single cell RNA sequencing of hESCs derived cells that were transplanted in rat model of PD for 12 months using two different (with and without FACS sorting) strategies.

first: Katarina

last: Tiklova

first: Sara

last: Nolbrant

first: Alessandro

last: Fiorenzano

first: Åsa

middle: K

last: Björklund

first: Yogita

last: Sharma

first: Andreas

last: Heuer

first: Linda

last: Gillberg

first: Deirdre

middle: B

last: Hoban

first: Tiago

last: Cardoso

first: Andrew

last: Adler

first: Marcella

last: Birtele

first: Hilda

last: Lundén-Miguel

first: Nikolaos

last: Volakakis

first: Agnete

last: Kirkeby

first: Thomas

last: Perlmann

first: Malin

last: Parmar


title: A molecular network regulating the pro-inflammatory phenotype of human memory T lymphocytes (ATAC-seq)

city: Milan

first: Chiara

last: Balestrieri

address: Via Olgettina 58

department: Center for Omics Sciences

country: Italy

institute: IRCCS San Raffaele Scientific Institute

summary: Understanding the mechanisms that modulate T helper lymphocyte functions is crucial to decipher normal and pathogenic immune responses in humans. To identify molecular determinants influencing the pathogenicity of T cells, we separated ex vivo-isolated primary human memory T lymphocytes based on their ability to produce high levels of inflammatory cytokines. We found that the inflammatory, cytokine-producing phenotype of memory T lymphocytes was defined by a specific core gene signature and was mechanistically regulated by the constitutive activation of the NF-kB pathway and by the expression of the transcriptional repressor BHLHE40. BHLHE40 attenuated the expression of anti-inflammatory factors, including miR-146a, a negative regulator of NF-kB activation, and ZC3H12D, an RNase of the Regnase-1 family able to degrade inflammatory transcripts. Our data reveal a molecular network regulating the pro-inflammatory phenotype of human memory T lymphocytes, with the potential to contribute to disease.

overall_design: Primary human T effector memory cells (TEM) were obtained from 3 donors. TEM cells were PE-labelled for GM-CSF expression with a GM-CSF Cytokine Secretion Assay (Miltenyi Biotec) and sorted for PE+/-.

first: Stefan

last: Emming

first: Niccolò

last: Bianchi

last: Polletti

first: Gioacchino

last: Natoli

first: Silvia

last: Monticelli


title: Synthetic lethal and resistance interactions with BET bromodomain inhibitors [RNA-Seq]

first: Kornelia

last: Polyak

overall_design: RNA-Seq of parental and JQ1 resistant breast cancer cell lines

first: Shaokun

last: Shu

first: Hua-Jun

last: Wu

first: Franziska

last: Michor


title: Synthetic lethal and resistance interactions with BET bromodomain inhibitors [Barcode_seq]

overall_design: Barcode-seq of parental and JQ1 resistant breast cancer cell lines


title: Synthetic lethal and resistance interactions with BET bromodomain inhibitors [ATAC-Seq]

overall_design: ATAC-Seq of parental and JQ1 resistant breast cancer cell lines


title: A molecular network regulating the pro-inflammatory phenotype of human memory T lymphocytes (Nanostring II)

overall_design: Primary human T effector memory cells (Tem) were obtained from 6 donors. Tem cells were PE-labelled for GM-CSF expression with a GM-CSF Cytokine Secretion Assay (Miltenyi Biotec) and sorted for PE+/-. Total RNA of was extracted and 100 ng of RNA were used for the hybridization reagents of the nCounter® Human miRNA Expression Assay (Nanostring). Samples were run on a Nanostring Sprint Profiler and analysed using Nsolver 3.0.

first: Niccolo

first: Michele

last: Chirichella


title: A molecular network regulating the pro-inflammatory phenotype of human memory T lymphocytes (Nanostring I)

overall_design: Primary human T memory cells (Tmem) were obtained from 3 donors. Tmem were were activated with plate-bound aCD3 and aCD28 for 2 days, removed from stimuli and lentivirally transduced with lv-Bhlhe40 or lv-empty. Cells were cultured for 10 more days and from day 5 on the media was supplemented with IL-2 (50U, provided by the institute). During this time cells were selected twice with puromycin (2 ug/ml, Sigma-Aldrich) for 24h.


title: A molecular network regulating the pro-inflammatory phenotype of human memory T lymphocytes (Nanostring III)

overall_design: Primary human T central memory cells (TCM) were obtained from 6 donors. TCM cells were PE-labelled for GM-CSF expression with a GM-CSF Cytokine Secretion Assay (Miltenyi Biotec) and sorted for PE+/-. RNA of 2 donors was combined and extracted. 50 ng of RNA were used for the hybridization reagents of the Nanostring Human Immunology panel v2 (Nanostring). Samples were run on a Nanostring Sprint Profiler and analysed using Nsolver 3.0.


title: A molecular network regulating the pro-inflammatory phenotype of human memory T lymphocytes (ChIP-Seq)

overall_design: Jurkat T cells were lentivirally transduced either with a construct harboring Bhlhe40 or an empty vector (pLvx-EF1a-FlagHA-IRES-ZsGreen backbone)

first: Sara

last: Pollett


title: A molecular network regulating the pro-inflammatory phenotype of human memory T lymphocytes (RNA-Seq)

overall_design: Primary human T central memory cells (TEM) were obtained from 9 donors. TEM cells were PE-labelled for GM-CSF expression with a GM-CSF Cytokine Secretion Assay (Miltenyi Biotec) and sorted for PE+/-. Total RNA of 3 donors was combined and extracted.


title: Division of Labor Between PCNA Loaders in DNA Replication and Sister Chromatid Cohesion Establishment [Affymetrix ChIP-chip]

status: Public on Mar 29 2020

city: London

first: Hon Wing

last: Liu

address: 1 Midland Road

country: United Kingdom

institute: Francis Crick Institute

type: Genome binding/occupancy profiling by genome tiling array

summary:
Analysis of PCNA levels at stalled Saccharomyces cerevisiae replication forks upon Replication Factor C (RFC) Removal
Analysis of nascent DNA incorporation at progressing Saccharomyces cerevisiae replication forks upon Rfc1 depletion

overall_design: Affymetrix Saccharomyces cerevisiae 1.0R tiling arrays were used to analyse 1.)  Global chromosomal PCNA distribution in WT, ctf18∆, elg1∆, ctf18∆elg1∆ cells treated with hydroxyurea (HU).  2.)  Nascent DNA incorporation in WT and Rfc1 depleted cells undergoing S phase.

first: Hon

middle: W

first: Céline

last: Bouchoux

first: Mélanie

last: Panarotto

first: Yasutaka

last: Kakui

first: Harshil

last: Patel

first: Frank

last: Uhlmann


title: Division of Labor between PCNA Loaders in DNA Replication and Sister Chromatid Cohesion Establishment [BrdU-IP-ssSeq, ChIP-ssSeq and eSPAN analysis]

summary: Strand Specific PCNA loading by Ctf18-RFC and Rfc1-RFC at Saccharomyces cerevisiae replication forks

overall_design: BrdU-IP-ssSeq, ChIP-ssSeq and eSPAN analysis of RFC large subunits and PCNA


title: Modeling cancer-associated mutations reveals an integrated role for the Pol epsilon catalytic core in replisome assembly and DNA synthesis

city: New York

first: Xiaolan

last: Zhao

state: NY

address: 1275 York Avenue

institute: Memorial Sloan Kettering Cancer Center

type: Genome variation profiling by high throughput sequencing

summary: DNA polymerase epsilon (Pol epsilon) plays multiple roles in genome duplication and its catalytic subunit POLE suppresses tumorigenesis in humans. Despite its importance, we have limited understanding of Pol epsilon functional mechanisms and how its loss-of-function affects the evolution of cancer genomes. To address this issue, we used the budding yeast ortholog Pol2 to model cancer-associated POLE mutations that affect an uncharacterized yet highly conserved Pol2/POLE family-specific region. Analysis of pol2 mutants revealed an unexpected role for this region in the incorporation of Pol epsilon into the pre-loading complex during replisome assembly. Cellular and reconstitution experiments further identified a separate role for this region in promoting Pol epsilon polymerase activity. Unlike previously reported POLE mutations leading to hypermutation in cancer cells, the examined pol2 variants increase gross chromosomal rearrangements but not mutation rates. Our findings thus suggest that the Pol epsilon catalytic core integrates replisome assembly and DNA polymerization functions and that POLE tumor suppressive roles likely extend beyond limiting replication errors.

overall_design: Two sets of samples at are included: 1) set 1 contains 3 reference samples, collected at G1, and 30 min, 40 min post G1 release; 2) set 2 contains 3 mutant samples, collected at the same time point as the reference. Whole genome sequencing (Illumina HiSeq) was used to access the copy number change and origin firing in these samples.

first: Xiangzhou

last: Meng

first: Tuo

last: Zhang

first: Jenny

last: Xiang


title: Unique Properties of a Subset of Human Pluripotent Stem Cells With High Capacity for Self-Renewal [scRNA-Seq]

city: St. Lucia

first: Othmar

last: Korn

state: Queensland

address: University of Queensland

country: Australia

institute: Australian Institute for Bioengineering and Nanotechnology

first: Kevin

last: Lau

first: Elizabeth

middle: A

last: Mason

first: Joshua

last: Kie

first: David

last: De Souza

first: Joachim

last: Kloehn

first: Dedriea

last: Tull

first: Malcolm

last: McConville

first: Andrew

last: Keniry

first: Tamara

last: Beck

first: Marnie

middle: E

last: Blewitt

first: Matthew

last: Ritchie

first: Shalin

last: Naik

first: Daniela

last: Zalcenstein

first: Shian

last: Su

first: Irene

middle: G

last: Romero

first: Catrina

last: Spruce

first: Christopher

middle: L

last: Baker

first: Tracy

last: McGarr

first: Christine

last: Wells

first: Martin

last: Pera


title: A deletion in Eml1 leads to bilateral subcortical heterotopia in the tish rat

status: Public on Mar 28 2020

city: Charlottesville

first: Pankaj

last: Kumar

state: VA

address: JPA, 1312A Pinn Hall

department: Bioinformatics Core

country: USA

institute: University of Virginia

summary: Malformations of cortical development (MCD) are present in up to 40% of children with pharmacoresistant epilepsy. Although epilepsy surgery can be successful in a subset of children, not all forms of MCD are operable. Understanding the genetic and neurobiological mechanisms underlying MCD and MCD-related epilepsy are necessary for the development of novel anti-epilepsy drugs. The tish (telencephalic internal structural heterotopia) rat is a unique model of MCD and spontaneous seizures, but the underlying genetic mutation has been, heretofore, unknown. DNA and RNA-sequencing revealed that a deletion encompassing a previously unannotated exon markedly diminished EML1 transcript and protein abundance in the tish brain. Developmental electrographic characterization of the tish rat demonstrated spontaneous spike-wave discharge (SWD) bursts beginning as early as postnatal day (P) 17. A dihybrid cross demonstrated that the mutantEml1 allele segregates with the observed dysplastic cortex and SWD bursts in monogenic autosomal recessive frequencies. Our data link the development of the bilateral, heterotopic dysplastic cortex of the tish rat to a mutation in Eml1 and provide a novel rat model of MCD.

overall_design: Examination of gene expression in TISH vs. SD rats

first: Denise

last: Grosenbaugh

first: Suchitra

last: Joshi

first: Mark

last: Fitzgerald

first: Kevin

middle: S

last: Lee

first: Pravin

last: Wagley

first: Alexander

last: Koeppel

first: Stephen

middle: D

last: Turner

first: Michael

middle: J

last: McConnell

first: Howard

last: Goodkin


title: Unique Properties of a Subset of Human Pluripotent Stem Cells With High Capacity for Self-Renewal

first: Othmar

last: Korn

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

overall_design: Refer to individual Series


title: RNASeq of PD-1loCTLA-4lo versus PD-1hiCTLA-4hi CD8 tumor-infiltrating lymphocytes from human melanoma

city: San Francisco

first: Kelly

middle: Maria

last: Mahuron

state: CA

address: 513 Parnassus Avenue, HSW 1201B

institute: UCSF

summary: The aim of the study is to analyze and compare the transcriptional profiles of PD-1loCTLA-4lo versus PD-1hiCTLA-4hi CD8 tumor-infiltrating lymphocytes from human melanoma

overall_design: PD-1loCTLA-4lo and PD-1hiCTLA-4hi CD8 tumor-infiltrating lymphocytes from 5 samples of human melanoma were sort-purified and RNA-sequenced

middle: M

first: Joshua

last: Moreau

last: Rosenblum


title: Temporal changes in the corpus luteum during early pregnancy

city: University Park

first: Camilla

middle: H. K.

last: Hughes

state: PA

address: 439 Shortlidge Rd

department: Animal Science

institute: Penn State University

platform_organism:
Homo sapiens
Bos taurus


title: Division of Labor Between PCNA Loaders in DNA Replication and Sister Chromatid Cohesion Establishment

first: Hon Wing

last: Liu


title: Temporal changes in miRNA abundance in the corpus luteum during early pregnancy

summary: Although rescue of the corpus luteum is required for pregnancy, luteal function during maternal recognition of pregnancy remains largely unexplored.  CL were collected from pregnant cattle on days 14, 17, 20, and 23, to encompass the maternal recognition of pregnancy period. Nanostring technology was used to profile miRNA. A total of 27 miRNA changed. MiRNA that increased were predicted to inhibit phosphatidylinositol signaling, while those that decreased may be negative regulators of steroidogenesis. Overall, these data indicate that there are changes in the CL of pregnancy that are important for continued luteal function.

overall_design: Corpora lutea were collected from pregnant cattle. Upon observation of estrus, cattle were bred naturally and then bred by artificial insemination 12 hours later, to maximize chances of pregnancy establishment. CL were collected on days 14, 17, 20, and 23 after breeding (n=4/group confirmed pregnant; those not confirmed pregnant were not used). RNA were profiled by next generation sequencing and miRNA were profiled using nanostring technology.

first: E

last: Inskeep

first: Joy

last: Pate


title: Diurnal patterns of gene expression in the dorsal vagal complex and the central nucleus of the amygdala

status: Public on Mar 27 2020

city: Glassboro

first: Mary

last: Staehle

state: NJ

address: 201 Mullica Hill Road

department: Biomedical Engineering

institute: Rowan University

summary:
Genes that establish the circadian clock have differential expression with respect to solar time in central and peripheral tissues. Here, we find circadian-time-induced differential expression in a large number of genes not associated with circadian rhythms in two brain regions lacking overt circadian function: the dorsal vagal complex (DVC) and the central nucleus of the amygdala (CeA). These regions primarily engage in autonomic, homeostatic, and emotional regulation. However, we find striking diurnal shifts in gene expression in these regions of male Sprague Dawley rats with no obvious patterns that could be attributed to function or region.  These findings have implications for the design of gene expression studies as well as for the potential effects of xenobiotics on these regions that regulate autonomic and emotional states.
Micropunches of dorsal vagal complex (DVC) and central nucleus of the amygdala (CeA) were collected from male, Sprague Dawley rats at three different times of the day.  Animals were not experimentally different in any way except for the time of sacrifice and collction.  Gene expression of 145 genes were measured with Fluidigm's Biomark 96.96 platform.

overall_design: High-throughput qRT-PCR profiling of 145 genes using Fluidigm's 96.96 array.  Bilateral samples from a single animal were considered as one sample.  There was no inter-animal pooling of samples.  Samples were collected at ZT3, 5, and 9 (where ZT0 is lights on in the facility).

first: Sean

last: O'Sullivan

first: Rajanikanth

last: Vadigepalli

first: Kate

last: Kernan

first: Gregory

last: Gonye

first: Babatunde

last: Ogunnaike

first: James

last: Scwhaber


title: Unique Properties of a Subset of Human Pluripotent Stem Cells With High Capacity for Self-Renewal [RNA-Seq]

overall_design: hESC were FACS sorted using a panel of CD9, GCTM2 and EPCAM expression. The total population was surveyed for hESC cultured under defined conditions of matrigel and mTESR1 with and without the treatment of protein kinase c inhibitors. The triple-high sub-population of cells represents those hESC cultured under defined conditions expressing the highest level of markers.

first: Kevin

middle: X

last: Lau

first: Elizabeth

last: Mason

last: Kie

first: David

middle: P

last: De Souza

first: Joachim

last: Kloehn

first: Dedriea

last: Tull

first: Malcolm

last: McConville

first: Andrew

last: Keniry

first: Tamara

last: Beck

first: Marnie

last: Blewitt

first: Matthew

last: Ritchie

first: Shalin

last: Naik

first: Daniela

last: Zalcenstein

first: Shian

last: Su

first: Irene

last: Romero

first: Catrina

last: Spruce

first: Christopher

last: Baker

first: Tracy

last: McGarr

first: Christine

last: Wells

first: Martin

last: Pera


title: Temporal changes in mRNA abundance in the corpus luteum during early pregnancy

first: Camilla

last: Hughes

summary: Although rescue of the corpus luteum is required for pregnancy, luteal function during maternal recognition of pregnancy remains largely unexplored.  CL were collected from pregnant cattle on days 14, 17, 20, and 23, to encompass the maternal recognition of pregnancy period. Next Generation Sequencing was used to profile mRNA abundance during this time, while tandem mass spectrometry and Nanostring technology were used to profile proteins and miRNA, respectively. A total of 1157 mRNA were differentially abundant. mRNA that increased were regulators of interferon signaling and DNA repair, while those that decreased were associated with luteolytic processes, such as calcium signaling and matrix metallopeptidase (MMP) signaling, indicating inhibition of these processes. mRNA that were maximally abundant on day 20 were primarily associated with immune processes.  Overall, these data indicate that there are changes in the CL of pregnancy that are important for continued luteal function.

overall_design: Corpora lutea were collected from pregnant cattle. Upon observation of estrus, cattle were bred naturally and then bred by artificial insemination 12 hours later, to maximize chances of pregnancy establishment. CL were collected on days 14, 17, 20, and 23 after breeding (n=4/group confirmed pregnant; those not confirmed pregnant were not used). RNA were profiled by next generation sequencing.

middle: H

first: E

last: Inskeep

first: Joy

last: Pate


title: Nuclease-mediated depletion biases in ribosome footprint profiling libraries

city: Baltimore

first: Boris

last: Zinshteyn

state: Maryland

address: 725 N Wolfe St, PCTB 714

department: Molecular Biology and Genetics

institute: Johns Hopkins University School of Medicine

summary: Ribosome footprint profiling is a high throughput sequencing based technique that provides detailed and global views of translation in living cells. An essential part of this technology is removal of unwanted, normally abundant, ribosomal RNA sequences in order to save on sequencing costs. The most effective commercial solution (Ribo-Zero) has been discontinued and a number of new, experimentally distinct commercial applications have emerged on the market. Here we evaluated several commercially available alternatives designed for RNA-seq of human samples and find them unsuitable for ribosome footprint profiling. We instead recommend the use of custom-designed biotinylated oligos, which were widely used in early ribosome profiling studies. Importantly, we warn that depletion solutions based on targeted nuclease cleavage significantly perturb the high-resolution information that can be derived from the data, and thus do not recommend their use for any applications that require precise determination of the ends of RNA fragments.

overall_design: Ribosome profiling libraries were genereated in several cell lines using different rRNA depletion techniques

first: Jamie

last: Wangen

first: Boyang

last: Hua

first: Rachel

last: Green


title: Effect of sesaminol on C2C12 cells on myogenesis pathway

city: Bengaluru

first: Sona

last: Rajakumari

state: Karnataka

address: CV Raman Road

country: India

institute: Indian Institute of Science

summary: Adipocytes are key players in maintaining energy homeostasis and are classified into two different categories: white and brown adipocyte. While white adipocytes store energy as triacylglycerols in lipid droplets, brown adipocytes combust excess chemical energy and release in the form of heat through uncoupled respiration. This characteristic phenomenon of brown fat attracts researchers and pharmacological industries to view brown fat as one of the potential therapeutic targets for obesity and associated metabolic disease. In the current study, we investigated the effect of a small molecule, sesaminol (SML) on brown fat activity and found that SML induces thermogenic program in primary white adipocytes as well as chow diet fed mice. In particular, SML treatment to mice elevated mitochondrial complex proteins and the rate oxygen consumption in brown and white fat. Administration of SML to high fat diet (HFD) challenged mice decreased weight gain, adiposity and cholesterol levels along with an increase of brown fat gene program in brown and white fat. Mechanistically, SML repressed the myogenic gene program in C2C12 myoblasts and increased all mitochondrial marker genes as appeared in brown adipose cells. Together, our results demonstrate that SML stimulates brown adipose function and protects mice against diet induced weight gain.

overall_design: Transcriptome analysis of C2C12 cells treated with or without sesaminol (SML) was performed (n=2). Our study showed that majority of genes that promote myogenesis were down regulated on SML treatment.


title: p-Ezrin (Thr567) regulates Hippo pathway and Yap in liver

city: Pittsburgh

first: George

middle: K.

last: Michalopoulos

state: Pennsylvania

address: 200 Lothrop Street

institute: University of Pittsburgh

summary:
It has been shown that up regulation activity of CD81(TAPA-1, the portal of entry of Hepatitis C virus) by agonistic antibody results in phosphorylation of Ezrin. We have previously shown that in liver, Ezrin phosphorylation occurs via Syk kinase, causing suppression of hippo intensity, therefore increases sequential Yap activity. The opposite occurs when Glypican-3 (GPC3) or E2 protein of HCV bind to CD81. Mice over-expressing GPC3 in hepatocytes have decreased p-Ezrin(Thr567) and Yap, increased Hippo activity and suppressed liver regeneration. The role of Ezrin in these processes has been speculated, but not proven. We now provide dynamic picture of Ezrin regulates Hippo pathway and Yap. Forced expression of plasmids expressing mutant Ezrin (T567D) (which mimics p-Ezrin(Thr567)) suppressed Hippo activity and activated Yap signaling. And this mutant Ezrin drive more cell proliferation to cell division through up regulated Yap activity in vitro and in vivo.  CD81 loses expression, while p-Ezrin(Thr567) increases in JM1 and JM2 hepatocellular carcinoma (HCC) cells. Administration with compound NSC668394, a characterized p-Ezrin(Thr567) antagonist, caused significant decrease in HCC cell proliferation. We additionally present evidence that pEzrin(T567) is also controlled by EGFR and MET.   Conclusions: Ezrin phosphorylation, mediated by CD81 associated Syk kinase, is directly involved in regulation of Hippo pathway, Yap levels and growth rates of normal and neoplastic hepatocytes. The finding has mechanistic and potentially therapeutic applications in understanding and regulating growth of hepatocytes and HCC and HCV pathogenesis.
We used microarrays to detail the global programme of gene expression in GFP positive hepatocytes of FVB mice adminstration with EzrinT567D plasmids

overall_design: Six- to eight-week-old wild-type FVB/N mice (Charles River, Wilmington, MA) were used. For hydrodynamic tail vein injection, PT3EF5α EzrinT567D (10μg) and pCMV/SB (0.8μg) were diluted into 2ml 0.9% NaCl solution, sterile filtered with 0.2μm filters, and then injected into mouse lateral tail vein within 5–7 seconds. Isolation of primary hepatocytes from liver was performed according to the two-step collagenase digestion 1 week after plasmids injection. All fluorescence-activated cell sorting (FACS) analyses were performed with a FACS Aria II-SORP (BD Biosciences, San Jose, CA) equipped with a 130-μm nozzle and running DiVa software version 8.0.2 (BD Biosciences). FACS plots were generated with FlowJo software version 9.9.6 (TreeStar, Ashland, OR). Microarray analysis was performed on RNAs isolated from the GFP - (i.e. EzrinT567D negative) and GFP + (i.e. EzrinT567D positive)  group from isolated hepatocytes for study, using the GeneChip® Mouse Genome 430 2.0 Array Set 430 (Affymetrix, Santa Clara, CA).

first: Yuhua

last: Xue


title: Developmental regulation of Canonical and small ORF translation from mRNAs

city: Seville

first: Juan

middle: Pablo

last: Couso

address: Carretera de Utrera, Km 1

country: Spain

institute: Centro Andaluz de Biologia del Desarrollo

summary: We present a genome-wide assessment of the translation of small open reading frames (smORF) in Drosophila melanogaster mRNAs, using ribosomal profiling of polysomal fractions in three contiguous temporal windows, which encopass all of embryogenesis. We also performed the same protocol using S2 cells. In this way, mRNAs bound by multiple ribosomes can be isolated and distinguished from mRNAs bound by sporadic, putatively non-productive single ribosomes or ribosomal subunits.

overall_design: Ribosomal profiling of polysomal fractions (Poly-Ribo-Seq) in Drosophila melanogasterembryos to assess translation of small ORFs

first: Pedro

last: Patraquim

first: Muhammad

last: Mumtaz

first: José

middle: I

last: Pueyo

first: Julie

last: Aspden


title: mRNAs and miRNAs for Women's Healthy Eating and Living (WHEL) Study

city: La Jolla

first: Loki

last: Natarajan

address: 3855 Health Sciences DR

institute: University of California, San Diego

summary:
The nCounter miRGE™ assay was used to quantify transcript expression with a custom codeset containing probes for 123 endogenous mRNAs and 25 miRNAs to assess the association of genomic markers with long-term breast cancer survival.
A total of 1,253 FFPE primary breast cancer samples with high-quality reads were obtained.

overall_design:
We interrogated mRNAs and miRNAs using the Nanostring nCounter miRGE platform with a custom codeset, aiming to investigate if the PAM50 research model could be improved by addition of other mRNAs and miRNAs implicated in oncogenesis using the WHEL breast cancer cohort with >15 years of follow-up and archived tumor specimens.
Refer to https://library.ucsd.edu/dc/object/bb2493244b

first: Sherri

last: Davies

first: Tammi

last: Vickery

first: Minya

last: Pu


title: TDP-43 dysfunction restricts dendritic complexity by inhibiting CREB activation and altering gene expression

status: Public on Mar 26 2020

city: Waltham

first: WEIJIN

last: XU

state: MASSACHUSETTS

address: 415 SOUTH STREET

institute: Brandeis University/HHMI

summary: Identified TDP-43 targets in rat cortical neurons, many related to the CREB pathway

sample_organism:
Homo sapiens
Mus musculus
Rattus norvegicus

overall_design: First application of TRIBE in mammalian system, used human ADAR2 catalytic domain for the experiment. Expression of TRIBE construct via lentiviral trasduction in rat cortical neurons

first: Josiah

last: Herzog

first: Weijin

last: Xu

first: Michael

last: Rosbash

first: Suzanne

last: Paradis


title: Reorganized 3D genome structures support transcriptional regulation in mouse spermatogenesis

city: Hefei

first: xiaoyuan

last: song

address: Huangshan Road

institute: University of Science & Technology of China

summary: Three-dimensional chromatin structures undergo dynamic reorganization during mammalian spermatogenesis; however, their impacts on gene regulation remain unclear. Here, we focused on understanding the structure-function regulation of meiotic chromosomes by Hi-C and other omics techniques in mouse spermatogenesis across five sequential stages. Beyond confirming recent reports regarding changes in compartmentalization and reorganization of topologically associating domains (TADs), we further demonstrated that chromatin loops are present prior to and after, but not at, the pachytene stage. By integrating Hi-C and RNA-Seq data, we showed that the switching of A/B compartments between spermatogenic stages is tightly associated with meiosis-specific mRNAs and piRNAs expression. Moreover, our ATAC-Seq data indicated that chromatin accessibility per se is not responsible for the TAD and loop diminishment at pachytene. Additionally, our ChIP-Seq data demonstrated that CTCF and cohesin remain bound at TAD boundary regions throughout meiosis, suggesting that dynamic reorganization of TADs does not require CTCF and cohesin clearance.

overall_design: Primitive type A spermatogonia (PriSG-A), type A spermatogonia (SG-A), pachytene spermatocytes (pacSC), and round spermatids (rST) were isolated from C57BL/6 mice and are used to conduct Hi-C experiment, ATAC-seq and native ChIP-seq experiments.

first: Zhengyu

last: Luo

first: Xiaorong

last: Wang

first: Xiaoyuan

last: Song

first: Fei

last: Sun


title: RNA sequencing of chemotherapy-resistant muscle-invasive urothelial bladder cancer

city: Seoul

first: Woosung

last: Chung

state: State...

address: Samsung Medical Center

country: South Korea

institute: Samsung Genome Institute

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: Gene expression profile of c-MYC driven mouse liver tumours, compared with Normal livers from control mice

first: Mariia

last: Yuneva

address: 1, Midland Road

summary:
Liver tumours are induced by overexpresion of human c-MYC (LAP-tTA/tet-o-MYC)
Using Affymetrix microarrays we compared gene expression of both tissues

overall_design: The Affymetrix GeneChip Mouse Gene 1.0 ST arrays were used to define gene expression profiles in Livers and MYC driven tumours

first: Xin

last: Chen