title: circRNA expression in C2C12 myoblasts and myotubes

city: Guangzhou

first: Rui

last: Chen

address: 466 Xin Gang Zhong Road

department: Guangdong Traditional Medical and Sports Injury Rehabilitation Research Institute

institute: Guangdong Second Provincial General Hospital

summary: To determine the circRNA expression profile in C2C12 myoblasts and myotubes, we used mouse circRNA microarray from Arraystar to examine the expression of circRNAs in C2C12 myoblasts and myotubes.

overall_design: Cells from cell line C2C12 were distributed into two experimental groups: myoblast group and myotube group, then perform circRNAs chips by Arraystar mouse circRNAs chip. Three independent experiments were performed at each group.

first: Yanling

last: She

first: Ting

last: Jiang


title: Non-cell Autonomous Regionalization of Sertoli Valve Epithelia in the Terminal Segment of the Seminiferous Tubules of Mouse Testes

status: Public on Mar 19 2021

city: Yayoi, Bunkyo-ku

first: Yoshiakira

last: Kanai

state: Tokyo

country: Japan

institute: The University of Tokyo

type: Expression profiling by high throughput sequencing

summary: In mammalian testes, undifferentiated spermatogonia undergo meiotic differentiation in high retinoic acid (RA) signaling states, while their undifferentiated states are maintained by fibroblast growth factors (FGFs) and glial cell line-derived neurotrophic factor (GDNF), the major niche factors for spermatogonial stem/progenitor cells, in the basal compartment of the convoluted seminiferous tubules (STs). In the valve-like terminal end of the STs adjacent to the rete testis (RT), the Sertoli valve (SV) epithelia constitutively lack most spermatogenesis activity due in part to high GDNF expression, leading to the SV-specific enrichment of undifferentiated spermatogonia; however, the molecular and cellular characteristics of the SV epithelia are unclear. By performing a Sertoli cell ablation/replacement experiment using a mouse diphtheria toxin receptor-mediated system, we show here that the SV epithelia are non-cell autonomously specified, together with having high AKT phosphorylation, in the Sertoli cells located adjacent to the RT epithelia. RNA analyses revealed constitutively high expression of Cyp26a1, which encodes an RA-degrading enzyme, in the SV region, together with high expression of Fgf9 in the adjacent RT. Exogenous in vivo RA treatment induced meiotic differentiation of the spermatogonia located within the SV region, leading to disruption of the SV structure by the ectopic appearance of adluminal meiotic germ cells in some severely affected STs. We therefore propose that the regionalization and inactive spermatogenesis of SV epithelia are mediated in part by low RA signaling, together with high FGF9 signals in the terminal end of the STs.

overall_design: SV fragments mRNA profiles from 7-week-old W/Wv mouse testes were generated using Illumina 2500.

first: Kasane

last: Imura-Kishi

first: Aya

last: Uchida


title: Non-muscle myosin heavy chain 9 maintains intestinal homeostasis by preventing epithelium necroptosis and colitis adenoma formation

status: Public on Mar 20 2021

city: Beijing

first: shan

last: wang

address: Tsinghua university medical building c244

country: China

institute: Tsinghua university

summary: Non-muscle myosin IIA plays an important role in cell adhesion, cell migration and tissue architecture. We previously showed that low activity of the heavy chain of non-muscle myosin II Myh9 is beneficial to Lgr5+ intestinal stem cell maintenance. However, the function of Myh9 in adult mouse intestinal epithelium is largely unclear. In this study, we used the inducible Villin-creERT2 knockout approach to delete Myh9 in adult mouse intestinal epithelium and observed that homozygous deletion of Myh9 causes colitis-like morphologic changes in intestine, leads to a high sensitivity to dextran sulfate sodium and promotes the colitis related adenomas formation in colon. Myh9 deletion disturbs cell junctions and impairs intestinal lumen barrier integrity, promoting the necroptosis of epithelial cells. Consistently, these changes can be partially rescued by Ripk3 knockout. Our results indicate that Myh9 is required for the maintenance of intestinal epithelium integrity and the prevention of cell necroptosis.

overall_design: Intestinal mRNA profiles of wild type (WT) and Myh9-/- mice

first: Shan

last: Wang

first: Siqi

last: Li

first: Yehua

first: Quanlong

first: Xingtong

first: Jing-Dong

last: Han

first: Yuan

last: Liu

first: Ye-Guang


title: QSER1 Protects DNA Methylation Valleys from De Novo Methylation

first: Heng

last: Pan

address: 49 North Garden Rd., Haidian District

institute: Peking University Third Hospital

type: Genome binding/occupancy profiling by high throughput sequencing

type: Methylation profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Divergent roles of astrocytic versus neuronal EAAT2 deficiency on cognition and overlap with aging and Alzheimer’s molecular signatures

status: Public on Mar 18 2021

city: New York

first: Aarthi

last: Ramakrishnan

state: New York

address: 1425 Madison Avenue

department: Neuroscience

country: USA

institute: Icahn School of Medicine at Mount Sinai

summary: The excitatory amino acid transporter 2 (EAAT2) is the major glutamate transporter in the brain expressed predominantly in astrocytes and at low levels in neurons and axonal terminals. EAAT2 expression is reduced in aging and sporadic Alzheimer’s disease (AD) patients’ brains. The role EAAT2 plays in cognitive aging and its associated mechanisms remains largely unknown. Here, we show that conditional deletion of astrocytic and neuronal EAAT2 results in age-related cognitive deficits. Astrocytic, but not neuronal EAAT2, deletion leads to early deficits in short-term memory and in spatial reference learning and long-term memory. Neuronal EAAT2 loss results in late-onset spatial reference long-term memory deficit. Neuronal EAAT2 deletion leads to dysregulation of the kynurenine pathway, and astrocytic EAAT2 deficiency results in dysfunction of innate and adaptive immune pathways, which correlate with cognitive decline. Astrocytic EAAT2 deficiency also shows transcriptomic overlaps with human aging and AD. Overall, the present study shows that in addition to the widely recognized astrocytic EAAT2, neuronal EAAT2 plays a role in hippocampus-dependent memory. Furthermore, the gene expression profiles associated with astrocytic and neuronal EAAT2 deletion are substantially different, with the former associated with inflammation and synaptic function similar to changes observed in human AD and gene expression changes associated with inflammation similar to the aging human brain.

overall_design: 6 mice across 4 groups (gfapCre+ EAAT2Δ/+; gfap-Cre− EAAT2+/+; syn-Cre+ EAAT2−/−; syn-Cre− EAAT2+/+) were sequenced to study differential expression b/w conditions

first: Abhijeet

last: Sharma

first: Syed

middle: F

last: Kazim

first: Chloe

middle: S

last: Larson

first: Ana

middle: C

last: Pereira


title: Characterizing the properties of bisulfite sequencing data: maximizing power and sensitivity to identify differences in DNA methylation [Array]

city: Exeter

first: Emma

last: Walker

address: RILD Barrack Rd

country: United Kingdom

institute: University of Exeter

type: Methylation profiling by genome tiling array

summary:
Background The combination of sodium bisulfite treatment with highly-parallel sequencing is a common method for quantifying DNA methylation across the genome. The power to detect between-group differences in DNA methylation using bisulfite-sequencing approaches is influenced by both experimental (e.g. read depth, missing data and sample size) and biological (e.g. mean level of DNA methylation and difference between groups) parameters. There is, however, no consensus about the optimal thresholds for filtering bisulfite sequencing data with implications for the reproducibility of findings in epigenetic epidemiology.
Results We used a large reduced representation bisulfite sequencing (RRBS) dataset to assess the distribution of read depth across DNA methylation sites and the extent of missing data. To investigate how various study variables influence power to identify DNA methylation differences between groups, we developed a framework for simulating bisulfite sequencing data. As expected, sequencing read depth, group size, and the magnitude of DNA methylation difference between groups all impacted upon statistical power. The influence on power was not dependent on one specific parameter, but reflected the combination of study-specific variables. As a resource to the community, we have developed a tool, POWEREDBiSeq, which utilizes our simulation framework to predict study-specific power for the identification of DNAm differences between groups, taking into account user-defined read depth filtering parameters and the minimum sample size per group.
Conclusions Our data-driven approach highlights the importance of filtering bisulfite-sequencing data by minimum read depth and illustrates how the choice of threshold is influenced by the specific study design and the expected differences between groups being compared. The POWEREDBiSeq tool can help users identify the level of data filtering needed to optimize power and aims to improve the reproducibility of bisulfite sequencing studies.

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus

overall_design:
DNA was collected from mouse entorhinal cortex samples and methylation levels quantified using both array and RRBS technology. Array data was measured using the HorvathMammalMethylChip40 Methylation Beadchip on the Illumina platform.
Randomly assigned groups 1 and 2 are used for power calculations and are not meaningful biological groups in the paper that this data is associated with.

first: Dorothea

last: Seiler Vellame

first: Isabel

last: Castanho


title: RNA Sequencing of WT, RAG2-KO, and RAG2-KO TCRbeta-Transduced CD4+CD8+ T-Cells Derived From Human Embryonic Stem Cells

city: Toronto

first: Juan Carlos

last: Zuniga-Pflucker

state: Ontario

address: 2075 Bayview Avenue

department: Immunology

country: Canada

institute: University of Toronto

summary: T-cell development is predicated on the successful rearrangement of the T-cell receptor (TCR) gene loci, which encode for antigen-specific receptors that enable an immune response. Recombination Activating Gene (RAG) 2 is required for TCR gene rearrangements, which occur during specific stages of T-cell development. Here, we differentiated human pluripotent stem cells with a CRISPR/Cas9-directed deletion of the RAG2 gene (RAG2-KO) to elucidate the requirement for the TCRb chain in mediating b-selection during human T-cell development in vitro. In stark contrast to what is seen in mice, human RAG2-KO T-lineage progenitors progressed to the CD4+CD8+ double-positive (DP) stage in the absence of TCRb rearrangements. Nevertheless, RAG2-KO DPs retrovirally-transduced to ectopically express a rearranged TCRb chain showed increased survival and proliferation as compared to control-transduced RAG2-KO DPs. Furthermore, transcriptomic analysis showed that TCRb-transduced and control-transduced RAG2-KO DPs differed in gene pathways related to survival and proliferation. Our results provide new insights as to the distinct requirement for the TCRb chain during human T-cell development.

overall_design: Cells were collected at OP9-DL4-7FS co-culture day 24-28 and stained with fluorochrome-labelled monoclonal antibodies to CD45, CD7 (eBioscience), CD5, CD4, CD8 (BD Biosciences), DAPI, and sorted into CD4+CD8+ DP populations using FACSVantage Diva or FACSAria cell sorters (BD Biosciences). Total RNA was extracted from the sorted cell populations using TRIzol. Purified RNA were subjected to RNA sequencing using Illumina Novaseq 6000. Library preparation was done using Illumina TruSeq Strandard Total RNA Sample Preparation kit. Sequencing was done using 100-cycle paired read protocol and multiplexing to obtain ~40 million reads/sample. Samples were aligned to GRCh38 using HISAT2. Read counts were calculated using HTSeq. Differential gene expression analysis was done using edgeR package and R program.

first: Edward

middle: L

last: Chen

first: Patrick

middle: M

last: Brauer

first: Elisa

last: Martinez

first: Xiaotian

last: Huang

first: Ning

last: Yu

first: Yang

first: Juan

last: Zúñiga-Pflücker


title: Analysis of hiPSC-derived microglia compared to other cell types

city: La Jolla

first: Dorit

last: Trudler

state: CA

address: 11119 N Torrey Pines Rd. Suite 125

institute: The Scripps Research Institute

summary: We performed RNA-seq analysis to compare hiPSC-derived microglia with hiPSCs, NPCs and human fetal microglia. We analyzed additional RNA-seq data from published human brain microglial cells and other monocytic cells to offer further support for the identity of our hiMG.

overall_design: comparison of gene expression of hiMG after 21 days of differentiation with other cell types.

first: Stuart

middle: A

last: Lipton

first: Rajesh

last: Ambasudhan


title: The role of Niemann-Pick type C2 in zebrafish embryonic development

city: Bethesda

first: Ryan

last: Dale

state: MD

address: Rm 10D39, 10 Center Drive

department: National Institute of Child Health and Human Development

institute: National Institutes of Health

summary: Niemann-Pick disease type C (NPC) is a rare fatal neurodegenerative lysosomal storage disease caused by mutations of either NPC1 or NPC2.  NPC2 is a soluble lysosomal protein that in coordination with NPC1 is responsible for the efflux of unesterified cholesterol from the lysosome.  Mutations of both genes cause a similar cellular pathology, that includes the accumulation of unesterified cholesterol and other lipids in the late endosome/lysosome, while reducing cholesterol bioavailability. Here we describe a npc2 null zebrafish model generated by CRISPR/Cas9 gene targeting.  Zygotic npc2m/m zebrafish from the intercross of npc2+/m individuals showed significant unesterified cholesterol accumulation at larval stages, and a reduction in body size in adulthood.  Additionally, zygotic npc2m/m adults exhibited motor and balance defects shortly before a premature death.  These findings mimic defects found in human and mice, however the phenotype at embryonic stages were milder than expected.  To address the possible dose protection effects of npc2 mRNA present in the oocyte at the time of fertilization we intercrossed npc2m/m zebrafish to generate Maternal-zygotic (MZ) npc2m/m embryos. MZnpc2m/m zebrafish exhibited significant developmental defects including absent otolith, abnormal head/brain development, curved/twisted body axis, no circulating blood cells, and died by 72 hpf.   These developmental defects have not previously been reported in connection with either NPC2 or NPC1.  RNA-seq analysis conducted on 30 hpf npc2+/m and MZnpc2m/m embryos revealed a significant reduction in notch3 expression as well as reduction in other downstream genes in the signally pathway such as hey1 and her12 that could be partially rescued by microinjection of a plasmid containing the constitutively active notch3 ICD at the 1-cell stage, suggesting that impaired Notch3 signaling likely underlies some aspects of the developmental defects observed in MZnpc2m/m zebrafish.

overall_design: RNA-seq of homozygous and heterozygous npc2 mutant zebrafish compared to WT; 3 replicates for each genotype

first: Wei-Chia

last: Tseng

first: Forbes

last: Porter


title: Gene expression profiling of monocyte in response to Pf-iRBC stimulation from Pf-PCR negative Malian children and adults during dry season.

city: Rockville

first: Rajan

last: Guha

address: 5625 Fishers Lane,Room No:4N07

institute: NIAID/NIH

summary: In malaria-naïve individuals, P. falciparum (Pf) infection results in numerous Pf-infected red blood cells (iRBCs) that trigger systemic inflammation and fever. Conversely, repeatedly infected individuals in endemic areas are often asymptomatic and have low levels of iRBCs, even children who have yet to acquire reliably protective antibodies. The molecular mechanisms underlying these clinical observations are unclear. PBMCs collected from Malian children before the malaria season responded to iRBCs by producing pyrogenic, pro-inflammatory mediators such as IL-1β, IL-6 and TNF. However, following febrile malaria there was a marked shift in the response to iRBCs with the same children's PBMCs producing lower levels of those cytokines. These data suggest that malaria-induced epigenetic reprogramming of innate immune cells may play a role in immunity to malaria. Accordingly, age-stratified analysis of monocytes collected before the malaria season showed an inverse relationship between age and pro-inflammatory cytokine production capacity.

overall_design: Total 24 monocytes samples were analyzed. Eight monocyte samples from Pf-iRBC stimulated Malian Children were compared with eight monocyte from Pf-iRBC stimulated Malian adults. Four unstimulated monocyte samples from Malian children and four from Malian adults were used as internal control, these unstimulated samples were independent of Pf-iRBC stimulated experimental monocyte sample.

first: Peter

last: Crompton

first: Judith

last: Zaugg

first: Anna

last: Mathioudaki


title: LRIG1 is a gatekeeper to exit from quiescence in adult neural stem cells

city: Edinburgh

first: Ben

last: Southgate

address: Little France Dr

institute: University of Edinburgh

summary: Adult neural stem cells (NSCs) must tightly regulate quiescence and proliferation. Single cell analysis has suggested a continuum of cell states as NSCs exit quiescence. Here we capture and characterize in vitro primed quiescent NSCs and identify LRIG1 as an important regulator. We show that BMP-4 signaling induces a dormant non-cycling quiescent state (d-qNSCs), whereas combined BMP-4/FGF-2 signalling induces a distinct primed quiescent state poised for cell cycle re-entry. Primed quiescent NSCs (p-qNSCs) are defined by high levels of LRIG1 and CD9, as well as an interferon response signature, and can efficiently engraft into the adult subventricular zone (SVZ) niche. Genetic disruption of Lrig1 in vivo within the SVZ NSCs leads an enhanced proliferation. Mechanistically, LRIG1 primes quiescent NSCs for cell cycle re-entry and EGFR responsiveness by enabling EGFR protein levels to increase but limiting signaling activation. LRIG1 is therefore an important functional regulator of NSC exit from quiescence.

overall_design: We used 2 independent adult neural stem cells lines.  They were derived from the SVZ (Subventricular zone) of young WT adult mice (6-8 weeks old). ANS4 (A4) and Bl6. The cells were used at passage less than 10 and were plated at low density for 3 days. We used 2 biological replicas per condition in each line. NSCs were treated in EGF/FGF, BMP4 (B) and BMP4+FGF2 (BF) for 3 days and after RNA was extracted using Quiagen kit.

first: Maria

last: Marqués-Torrejón

first: Benjamin

first: Steven

last: Pollard


title: Single-cell mRNA profiling reveals changes in solute carrier expression and a metabolic switch during zebrafish pronephros development

city: Freiburg im Breisgau

first: Toma

middle: Antonov

last: Yakulov

address: Hugstetter Str. 55

department: Department of Medicine

country: Germany

institute: University Freiburg Medical Center

summary: Developing organisms need to adapt to environmental variations as well as to rapid changes in substrate availability and energy demands imposed by fast-growing tissues and organs. Little is known about the adjustments that kidneys undergo in response to these challenges. We performed single-cell RNA sequencing of zebrafish pronephric duct cells to understand how the developing kidney responds to changes in filtered substrates and intrinsic energy requirements.

overall_design: Single cell RNA sequencing was performed on pronephric cells from 1, 2 and 3-day old zebrafish larvae.

last: Sagar

first: Maximilian

last: Schoels

first: Gerd

last: Walz


title: Characterization of estrogen, progesterone and the endocrine-disrupting chemical-induced mouse mammary gland reorganization via single-cell RNA-sequencing

city: Duarte

first: wei

last: chen

address: 1500 E Duarte Rd

department: Cancer Biology-BRI

institute: City of Hope National Medical Center

summary: The mammary epithlium goes through the drastic reorganization during development, pregnancy, and menopause as well as by external hormones and its mimicry, which risks the gland for the specific type of breast cancer. Using a surgical menopausal (ovariectomized) mouse model, we assessed how mammary gland tissue was affected by 17β-estradiol (E2), progesterone (P4) and polybrominated diphenyl ethers (PBDEs). Then, we integrated the transcriptomes of 50K mouse and 24K human mammary epithelial cells from five different datasets and four individuals obtained by single-cell RNA sequencing (scRNAseq). The results indicated a putative trajectory originating from the embryonic mammary stem cells and differentiating into the three different epithelial lineage (Basal, Luminal alveolar, and Luminal hormone sensing) that were presumably sustained by unipotent progenitors in the postnatal glands. The identified lineage-specific gene sets inferred cells of origin of breast cancer using The Cancer Genome Atlas data and scRNAseq of human breast cancer. The comprehensive mammary cell atlas presented novel insights into the impact of the internal and external stimulati on the mammary epithelium in an unprecedented resolution.

overall_design: Female BALB/cj mice were ovariectomized 20 weeks before treatment. They were treated with 5 different conditions for 1 week; 1)Vehicle, 2) E2, 3) E2 and PBDEs, 4) E2 and P4, and 5) E2, P4 and PBDEs, .  The 4th mammary glands were harvested and single-cell RNA sequencing was performed.

first: Chen

last: Shiuan

first: Noriko

last: Kanaya

first: Kohei

last: Saeki


title: Methyl capture sequencing (Truseq Epic from Illumina) of H1 WT, H1 QSER1 KO, H1 TET1 KO, H1 DNMT3B KO, H1 QSER1 KOpm (passaged matched with DKOs), H1 QSER1/TET1 DKO, and H1 QSER1/DNMT3B DKO hESCs

first: Heng

last: Pan

summary: DNA methylation is essential to mammalian development, and dysregulation can cause serious pathological conditions. Key enzymes responsible for deposition and removal of DNA methylation are known, but how they cooperate to tightly regulate the methylation landscape remains a central question. Utilizing a knockin DNA methylation reporter, we performed a genome-wide CRISPR/Cas screen in human embryonic stem cells to discover DNA methylation regulators. The top screen hit was an uncharacterized gene QSER1, which proved to be a key guardian of bivalent promoters and poised enhancers of developmental genes, especially those residing in DNA methylation valleys (or canyons). We further demonstrate cooperation of QSER1 and TET1 through genetic and biochemical interactions to inhibit DNMT3-mediated de novo methylation and safeguard developmental programs.

overall_design: For methyl capture sequencing, genomic DNA was isolated using the DNeasy Blood & Tissue Kit (Qiagen, 69504) following manufacturer’s guidelines. Two replicates were done for each genotype.

first: Pan

last: Heng

first: Dixon

last: Gary


title: High throughput screening identifies SOX2 as a Super Pioneer Factor that inhibits DNA methylation maintenance at its binding sites

city: Geneva

first: victor

last: YTHIER

state: Geneva

address: Rue Michel-Servet,1

department: GEDEV

country: Switzerland

institute: University of Geneva

summary:
Access of mammalian transcription factors (TFs) to regulatory regions, an essential event for transcription regulation, is hindered by chromatin compaction involving nucleosome wrapping, repressive histone modifications and DNA methylation. Moreover, methylation of TF binding sites (TBSs) affects TF binding affinity to these sites. Remarkably, a special class of TFs called pioneer transcription factors (PFs) can access nucleosomal DNA, leading to nucleosome remodelling and chromatin opening. However, whether PFs can bind to methylated sites and induce DNA demethylation is largely unknown.
Here, we set up a highly parallelized approach to investigate PF ability to bind methylated DNA and induce demethylation. Our results indicate that the interdependence between DNA methylation and TF binding is more complex than previously thought, even within a select group of TFs that have a strong pioneering activity; while most PFs do not induce changes in DNA methylation at their binding sites, we identified PFs that can protect DNA from methylation and PFs that can induce DNA demethylation at methylated binding sites. We called the latter “super pioneer transcription factors” (SPFs), as they are seemingly able to overcome several types of repressive epigenetic marks. Importantly, while most SPFs induce TET-dependent active DNA demethylation, SOX2 binding leads to passive demethylation by inhibition of the maintenance methyltransferase DNMT1 during replication. This important finding suggests a novel mechanism allowing TFs to interfere with the epigenetic memory during DNA replication.

overall_design: RNA-seq – Bisulfite-Seq – AmpBis-Seq - Sanger

first: Ludovica

last: Vanzan

first: Hadrien

last: Soldati

first: Victor

last: Ythier

first: Santosh

last: Anand

first: Nicole

last: Francis

first: Simon

last: Braun

first: Rabih

last: Murr


title: Transcriptome changes in differentiating primary brite adipocytes 24 hours after knockdown of long noncoding RNA Ctcflos

city: Freising

first: Tobias

last: Fromme

address: Gregor-Mendel-Str. 2

department: Molecular Nutritional Medicine

institute: Technical University of Munich

summary: We analyzed coding and noncoding transcript abundance in primary differentiating brite adipocytes derived from murine inguinal white adipose tissue, 24 hours in response to lncRNA Ctcflos knockdown at day 1 of differentiation

overall_design: We prepared primary preadipocytes from stromal-vascular fraction of murine inguinal white adipose tissue of 129SvEv mice, induced them at sub-confluence for 2 days and differentiated them for 1 day in the presence of rosiglitazone to induce browning. Cells were reverse transfected with lncRNA Ctcflos-targeting or non-targeting control LNA Gapmer Antisense oligonucleotides [50nM] and harvested either 24 hours post transfection. We deep sequenced total RNA and determined transcript abundance.

first: Andrea

last: Bast-Habersbrunner

first: Yongguo

last: Li

first: Fromme

last: Tobias

first: Martin

last: Klingenspor


title: RNA Sequencing analyses of control and HuD KO (Elavl4 null) mouse cortical transcriptomes

status: Public on Mar 17 2021

city: Albuquerque

first: Nora

last: Perrone-Bizzozero

state: NM

address: 1 University of New Mexico MSC08 4740

department: Neurosciences

institute: University of New Mexico

summary:
Purpose: The goal of this study was to analyse RNA-seq data to determine the effect of deletion of the RNA-binding protein HuD in transcriptiome-wide alternative splicing and polyadenylation in the neocortex of adult HuD KO vs. wild type littermates (controls)
Methods: Cortical mRNA profiles of adult HuD KO (Elavl4 -/-) mice and Control mice were generated by RNA sequencing, in triplicate, using Illumina NovaSeq 6000 platform. The quality of raw RNA-sequencing reads was evaluated using FastQC software (version 0.11.5) and adapters were removed using the Cutadapt (version 1.15) and Trimmomatic (version 0.38) software. Alternative splicing was evaluated using rMATS software (version 4.0.2)  and BAM files were converted to BedGraph before examining alternative polyadenylation using DaPars software (version 0.9.1)
Methods (cont.): RNA-seq data was aligned to the M musculus genome (UCSC browser, mm10) using STAR (version 2.7.3a), and MultiQC (version 1.8) was used to perform a final quality check on STAR alignment files. If alignments were found to be the same read length and have >80% reads mapped to a unique location, the data was considered good quality and alternative splicing and polyadenylation analyses were performed. Sequence reads per sample were aligned to the mouse genome (build mm10).
Results: HuD KO affected alternative splicing of 310 genes, including 17 validated HuD targets such as Cbx3, Cspp1, Snap25 and Gria2.  In addition, deletion of HuD affected polyadenylation of 53 genes, with the majority of significantly altered mRNAs shifting towards usage of the proximal polyadenylation signal (PAS), resulting in shorter 3’ untranslated regions (3’ UTRs).
Conclusions: HuD KO had a greater effect on alternative splicing than polyadenylation, with many of the affected genes implicated in several neuronal functions and neuropsychiatric disorders.

overall_design: We used three biological replicates per genotype: 3 Elavll4-/- ( HuD KO) and 3 wild type (controls)

middle: I


title: mRNA expression profiling of DNA damage-induced senescent cells

city: Seoul

first: Jaejin

last: Kim

address: Gwanak-ro 1

country: South Korea

institute: Seoul National University

summary: To identify differentially expressed genes during cellular senescence, we performed transcriptional profiling with RNA sequencing (RNA-seq) before and after senescence induction using a stress-induced senescence model (bleomycin-induced senescence).

overall_design: IMR90 cells were treated with bleomycin (10 ug/ml for 24 h) to induce senescence, and total RNAs from normal (-bleomycin) and senescent (+bleomycin, 10 days after exposure to bleomycin) IMR90 cells were isolated using the acidic phenol extraction method. One microgram of high-quality RNA samples (RIN > 7.0) was used to construct RNA-seq libraries using the TruSeq Stranded mRNA LT Sample Prep Kit (Illumina). RNA-seq was performed on an Illumina NovaSeq 6000 sequencer.

first: Yeonghyeon

last: Lee

first: Misung

first: Chanhee

last: Kang


title: KDM6B-dependent chromatin remodelling underpins effective virus-specific CD8+ T cell differentiation (RNA-Seq timecourse)

city: Clayton

first: Monash

middle: Bioinformatics

last: Platform

state: VIC

address: Wellington Road

country: Australia

institute: Monash Bioinformatics Platform

summary: We report on the dynamic regulation of H3K27me3 demethylation during early T cell activation

overall_design: Examination of gene expression across 4 time points within 1 cell type

first: Stephen

last: Turner


title: KDM6B-dependent chromatin remodelling underpins effective virus-specific CD8+ T cell differentiation (RNA-Seq K6B)

overall_design: Examination of gene expression across 2 time points within 1 cell type isolated from 2 different strains of mice


title: Bulk RNA seq of sorted C. elegans neurons

city: New Haven

first: Marc

last: Hammarlund

state: Connecticut

address: 295 Congress Ave

department: Genetics

institute: Yale University

summary: Bulk RNA seq of FACS isolated C. elegans neurons, with pan-neuronal reference, and sorted viable cell reference samples. Collected for comparison to single cell sequencing data

overall_design: Cell type specific C. elegans neuronal samples were obtained via FACS for comparison to each other, and to pan-neuronal and all cell references. Sample names describe the cell type targeted (ASG, AVE, AWA, etc…), Rab3 indicates samples targeted with a Pan-Neuronal Marker for direct comparison to each individual cell type. Ref samples were obtained by dissociating and FACS isolation using only stains to sepatate living and dead cells and thus represents an "all cell" reference.

first: Alec

last: Barrett

first: Rebecca

last: McWhirter

first: Seth

middle: R

last: Taylor

first: Alexis

last: Weinreb

first: David

last: Miller III


title: KDM6B-dependent chromatin remodelling underpins effective virus-specific CD8+ T cell differentiation

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

overall_design: Refer to individual Series


title: KDM6B-dependent chromatin remodelling underpins effective virus-specific CD8+ T cell differentiation (ATAC-Seq)

overall_design: Examination of chromatin accessibility across 3 time points within 1 cell type


title: Exosomes Facilitate Therapeutic Targeting of STAT3 in Liver Fibrosis

city: Houston

first: Raghu

last: Kalluri

address: 1881 East road

department: Cancer Biology

institute: MD Anderson Cancer Center

summary: Hepatic fibrosis is a wound healing process which results in excessive accumulation of extracellular matrix (ECM) in response to chronic hepatic injury. To determine the impact of iExosomes treatment on target cells gene expression, we extracted total RNA was  from livers using TRIzol and purified according to manufacturer instructions. RNA integrity was determined using RNA 6000 Nano Assay by the MDACC Sequencing and ncRNA Program core. Liver RNA sequencing was performed using Illumina TrueSeq stranded mRNA seq MDACC Sequencing and ncRNA Program core. Genome mapping was performed using TopHat software. We found that siSTAT3 iExosomes treatment increased the expression of 1918 genes and decreased expression of 2460 genes, whereas STAT3 mASO iExosomes treatment increased the expression of 2140 genes and decreased expression of 2021 genes. Our results indicate STAT3 is an important ECM deposition relevant-gene for future clinical treatment.

overall_design: Hepatic mRNA profiles of mice from  siCntrl iExos, siSTAT3 iExos, mASO STAT3 iExos, mASO Scrbl iExos groups

first: Min

last: Tang

first: Bingrui

first: Valerie

last: LeBleu


title: Elevated Extracellular cGMP Produced after Exposure to Enterotoxigenic Escherichia coli (ETEC) Heat-Stable Toxin (ST) Induces Epithelial IL-33 Release and Alters Intestinal Immunity

city: New Orleans

first: Jay

last: Kolls

state: LA

address: 1430 Tulane Ave

department: Medicine

institute: Tulane University

type: Non-coding RNA profiling by high throughput sequencing

summary: The purpose of our study was to examine the effect of enterotoxigenic E. coli (ETEC) heat-stable toxin (ST) on global T84 gene expression at selected time points following intoxication, with the goal of understanding the functional effects of ST on host epithelium. RNASeq analysis relvealed that ST alters inflammatory gene expression, including the IL-1 family member IL33, which is induced downstream of cGMP.

overall_design: We studied the effects of ETEC ST on T84 gene expression. We treated T84 cells with ST and collected three replicates each after 3 hr, 6 hr, and 24 hr post-intoxication. Treatment groups (in triplicate) were compared to untreated T84 cells (in triplicate).

first: Natalya

last: Motyka

first: Sydney

last: Stewart

first: Ian

middle: E

last: Hollifield

first: Thomas

last: Kyllo

first: Joshua

last: Mansfield

first: Elizabeth

middle: B

last: Norton

first: John

middle: D

last: Clements

first: Jacob

middle: P

last: Bitoun


title: 5-hydroxymethylcytosine (5hmC) profiling of H1 WT hESCs

city: Beijing

first: Heng

last: Pan

address: 49 North Garden Rd., Haidian District

institute: Peking University Third Hospital

summary: DNA methylation is essential to mammalian development, and aberrant regulation can lead to disease. The enzymes responsible for deposition and removal of DNA methylation have been identified, but how tightly regulated DNA methylation patterns are achieved globally remains a central question. To discover regulators of DNA methylation in human Embryonic Stem Cells (hESCs), we engineered a DNA methylation reporter line and performed a genome-wide CRISPR/Cas screen. Through our screen, we identified the functionally uncharacterized gene QSER1, which proved to be essential for protection from DNA hypermethylation at bivalent promoters and poised enhancers of developmental genes, especially those residing in DNA Methylation Valleys (DMVs). Further mechanistic enquiry revealed that QSER1 protein depends on TET1 for efficient recruitment to DNA, and QSER1 occupancy inhibits the binding of DNMT3B. Our discovery of QSER1 is a major advance in understanding TET-dependent protection from DNA hypermethylation and provides mechanistic insight into how epigenetic factors can cooperate to target locus-specific regulation.

overall_design: For 5hmC profiling (5hmC-Seal), genomic DNA was isolated from H1 WT hESCs using the DNeasy Blood & Tissue Kit (Qiagen, 69504) following manufacturer’s guidelines. Two replicates were performed for each sample.

first: Pan

last: Heng

first: Dixon

last: Gary

first: Rivas

last: Marco


title: ChIP-seq of QSER1-FLAG, TET1-V5, DNMT3A, DNMT3B, EZH2, BCOR, H3K4me3, H3K27me3, H3K36me2, H3K36me3, H3K27ac, and H3K4me1.

overall_design: ChIP-seq was performed for QSER1-FLAG (H1 WT and H1 TET1 KO hESCs), TET1-V5 (H1 WT and H1 QSER1 KO hESCs), DNMT3A (H1 WT, H1 QSER1 KO, H1 TET1 KO, and H1 QSER1/TET1 DKO hESCs), DNMT3B (H1 WT, H1 QSER1 KO, H1 TET1 KO, and H1 QSER1/TET1 DKO hESCs), EZH2 (H1 WT and H1 QSER1 KO hESCs), BCOR (H1 WT and H1 QSER1 KO hESCs), H3K4me3 (H1 WT and H1 QSER1 KO hESCs), H3K27me3 (H1 WT and H1 QSER1 KO hESCs), H3K36me2 (H1 WT and H1 QSER1 KO hESCs), H3K36me3 (H1 WT and H1 QSER1 KO hESCs), H3K27ac (HUES8 WT hESCs), and H3K4me1 (HUES8 WT hESCs).


title: KDM6B-dependent chromatin remodelling underpins effective virus-specific CD8+ T cell differentiation (ChIP-Seq)

first: Monash

last: Platform

overall_design: Examination of 1 histone modification across 4 time points within 1 cell type

first: Stephen

last: Turner


title: Transcriptomic analysis of acquired resistance to a novel trimethoprim-based photoswitchable antibiotic in Escherichia coli CS1562

city: Groningen

first: Anne

middle: de

last: Jong

address: Nijenborgh 7

department: Molecular Genetics

country: Netherlands

institute: university of Groningen

summary: Effect of three different antimicrobial compounds, trimethoprim(TMP), cis-tetra-ortho-chloroazobenzene-trimethoprim (TCATa) and trans-tetra-ortho-chloroazobenzene-trimethoprim (TCATd) , on the resistance development and transcriptome of the E. coli strain CS1562. In addition, acontrol sample was taken along of the propagated parent strain (CS1562) without the addition of any compounds.

overall_design: 4 samples; no replicates

first: Anna

last: Lauxen

first: Piermichele

last: Kobauri

first: Nicole

last: Galenkamp

first: Giovanni

last: Maglia

first: Wiktor

last: Szymanski

first: Ben

last: Feringa

first: Oscar

last: Kuipers


title: RNA quantitative sequencing in TGF-beta treated  PDCD5 knockdown C22 cells

first: Ho-Geun

last: Yoon

address: 50-1 Yonsei-ro, Seodaemun-gu

institute: Yonsei University College of Medicine

summary: The role of bronchial epithelial club (clara) cell in lung fibrosis is unclear. We found programmed cell death 5 (PDCD5) expression is elevated in lung fibrosis. To investigate the molecular mechanism by which PDCD5 mediates lung fibrosis in club cell, mouse C22 cells were analyzed by RNA-sequencing with or without Pdcd5 knockdown after TGF-beta treatment.

overall_design: Mouse lung epithelial clara cell line C22 mRNA profile after PDCD5 knockdown with or without 20ng/ml TGF-beta1 treatement for 24 hours, in triplicate

first: Soo-Yeon

last: Park


title: Quantitative Analysis of Endothelial Transcriptomes after Irradiation

first: Yoon-Jin

last: Lee

address: Nowon GU

institute: Korea Institute of Radiological & Medical Sciences

summary: Transcriptional profiling of HUVECs with or without irradiation.

overall_design: mRNA profiles of endothelial cells with or without irradiation were generated by deep sequencing using Illumina HiSeq X10. HUVEC cells were collected before and 5 and 72 hrs post-irradiation. Three biological replicates for each condition were sequenced.

first: Seo-Hyun

last: Choi


title: Characterization of transcriptional analysis of LKB1 mutant lung nodules

city: Chapel Hill

first: Charles

middle: M.

last: Perou

state: NC

address: 12-044 Lineberger Comprehensive Cancer Center CB# 7295

department: Professor of Genetics, and Pathology & Laboratory Medicine; Lineberger Comprehensive Cancer Center

institute: University of North Carolina at Chapel Hill

summary: Inactivating mutations in LKB1/STK11 are present in ~20% of non-small cell lung cancers (NSCLC) and portend poor response to anti-PD-1 immunotherapy in patients and genetically engineered mouse model (GEMMs). Here, we sought to uncover the basis for immunotherapy resistance of these tumors and to define strategies that overcome this barrier. Whereas high tumor mutational burden (TMB) often correlates with response to anti-PD1 treatment, we found that LKB1-deficient NSCLCs from non-smokers and GEMMs exhibited striking elevations in nonsynonymous mutations compared to LKB1 wildtype tumors. Correspondingly, LKB1 mutant NSCLC cell lines showed defects in both replication dependent and independent double-strand DNA break (DSB) repair, which were reversed upon LKB1 re-expression.

overall_design: Examine mRNA level of KP and KP GEMM lung tumor nodules for target gene expression and GSEA pathway analysis.

first: Kwok-Kin

last: Wong


title: Transcriptome RNA Sequencing Data Set of Differential Gene Expression in Escherichia Coli BW25113 SlyA Wild Type and Mutant Strains

status: Public on Mar 16 2021

city: dover

first: Derrick

last: Scott

state: Delaware

address: 1200 n dupont hwy

institute: Delaware State University

summary: Escherichia coli laboratory strains remain instrumental to the discovery and development of biomarkers as drugs and diagnostic analytes in the post genomic era. The transcriptional regulator SlyA is a member of the multiple antibiotic resistance regulator family of transcription factors, which is associated with bacterial responses to host-derived oxidative stress, antibiotics resistance and virulence, and homologues exist in other Enterobacteriaceae. Here, we announce a transcriptome RNA sequencing data set detailing global gene expression in the wild type E. coli BW25113 and the slyA mutant. Results reveal heterogeneous functionality of SlyA that may vary between pathovars of E. coli. but which require further annotations of differentially expressed tRNAs

overall_design: Examination of Gene expresison profiles of SlyA mutant and WT strains of Escherichia Coli BW25113

first: Olabisi

last: Ojo

first: Babatunde

last: Odetoyin

first: Bamidele

last: Iwalokun

last: Grove


title: Recognition of cellular RNAs by the S9.6 antibody creates pervasive artifacts when imaging RNA:DNA hybrids

city: Davis

first: Frederic

last: Chedin

address: 1 Shields Avenue

department: MCB

institute: UC Davis

summary: We showed that the majority of the signal observed in S9.6 immunofluorescence microscopy images of fixed human cells arises from RNA, not RNA:DNA hybrids. S9.6 staining is quantitatively unchanged by pre-treatment with the human RNA:DNA hybrid-specific nuclease, RNase H1, despite experimental verification that the enzyme was active in situ. S9.6 staining was, however, significantly sensitive to pre-treatments with RNase T1, and in some cases RNase III, two ribonucleases that specifically degrade single-stranded and double-stranded RNA, respectively. In contrast, genome-wide maps obtained by high-throughput DNA sequencing after S9.6-mediated DNA:RNA Immunoprecipitation (DRIP) are RNase H1-sensitive and RNase T1- and RNase III-insensitive. Altogether, these data demonstrate that the S9.6 antibody, though capable of recognizing RNA:DNA hybrids in situ and in vitro, suffers from a lack of specificity that precludes reliable imaging of RNA:DNA hybrids and renders associated imaging data inconclusive in the absence of controls for its promiscuous recognition of cellular RNAs.

overall_design: Characterization of RNA:DNA hybrid structures in NTERA-2 D1 (NT2) cells using sDRIP-seq on samples treated with RNase H1, RNase III, and/or RNase T1.

first: John

last: Smolka

first: Lionel

last: Sanz

first: Stella

last: Hartono


title: Extended archaeal histone-based chromatin structure regulates global gene expression in Thermococcus kodakarensis

city: Fort Collins

first: Thomas

last: Santangelo

address: 1062 Campus Delivery

institute: Colorado State University

summary: Using the model organism Thermococcus kodakarensis, we genetically alter the chromatin landscape and quantify the resultant changes in gene expression, including unanticipated and significant impacts on provirus transcription. Global transcriptome changes resultant from varying chromatin landscapes reveal the regulatory importance of higher-order histone-based chromatin architectures in regulating gene expression.

overall_design: Examination of 3 variant chromatin structures on gene expression

first: Travis

middle: J

last: Sanders

first: Fahad

last: Ullah

first: Alexandra

last: Gehring

first: Brett

middle: W

last: Burkhart

first: Robert

last: Vickerman

first: Sudili

last: Fernando

first: Andrew

last: Gardner

first: Asa

last: Ben-Hur


title: Mechanism of circADD2 as ceRNA in Childhood Acute lymphoblastic leukemia

city: Nanjing

first: Ting

middle: Yu

last: Zhu

address: No. 72 Guangzhou Road

institute: Children's Hospital of Nanjing Medical University

summary: In the present study, we found that circADD2 was down-regulated in ALL tissues and cell lines. Overexpression of circADD2 inhibited cell proliferation and promoted apoptosis both in vitro and in vivo. Additionally, we found that miR-149-5p may increase the expression of the target gene AKT2 through the mechanism of RNAa, and the level of AKT2 can be reversed by circADD2. Briefly, circADD2 could directly sponge miR-149-5p to downregulate AKT2 expression.

overall_design: circADD2 was selected by microarray assay and confirmed by qRT-PCR; in vitro effects of circADD2 were determined by CCK8 and flow cytometry; while mice subcutaneous tumor model was designed for in vivo analysis. RNA immunoprecipitation and dual-luciferase assay were applied for mechanistic study. Protein levels were examined by Western blot assay.

first: Yongjun

last: Fang

first: Yao

last: Xue

first: Yuting


title: Itaconate as an adjunct therapy to treat ocular bacterial infection

city: Detroit

first: Ashok

last: Kumar

state: MI

address: 4717 St. Antoine

department: Department of Ophthalmology, Visual, and Anatomical Sciences

institute: Wayne State University School of Medicine

summary: The eye is highly susceptible to inflammation-mediated tissue damage evoked during bacterial infection. We observed the itaconate as one of the highly induced metabolites in mouse retina and activated macrophages, yet its functional significance remains unknown in ocular infections.

overall_design: In the current study, we assessed the transcriptomic changes due to 4- Octyl itaconate treatment in mouse bone marrow-derived macrophages (BMDMs). Briefly, BMDMs were plated in 65 mm Petri-dishes (4x106) for in-vitro experiments and placed in a 5% CO2 37°C incubator overnight. BMDMs were either untreated or pre-treated (2 h) with 4-Octyl itaconate (125 µM) and left uninfected or infected with S. aureus RN6390 strain (multiplicity of infection (MOI) 10:1), for 8 h. RNA was isolated using the RNeasy Mini Kit (Qiagen) and processed as per manufacturer’s instructions for the paired-end RNA sequencing using Illumina platform.

first: Sukhvinder

last: Singh

first: Pawan

last: Kumar Singh

first: Alokkumar

last: Jha

first: Shailendra

last: Giri


title: The T cell-DC CD40L-CD40 axis, but not platelet CD40L, drives atherosclerosis

city: Amsterdam

first: Esther

last: Lutgens

address: Meibergdreef 15

department: Medical Biochemistry

institute: Amsterdam UMC, location AMC

summary: Atherosclerosis, the underlying vascular cause of cardiovascular disease, has a strong inflammatory component. The co-stimulatory CD40-CD40 ligand (CD40L) signaling axis is a pivotal regulator of immune responses in atherosclerosis. However, therapeutic long-term inhibition of CD40L will severely compromise the immune system making it a non-viable treatment option. To circumvent this issue, cell-specific inhibition may present a better approach to target the CD40-CD40L axis. Therefore, we generated T cell and platelet-specific knockout mice for CD40L and apolipoprotein E, which were aged for 28 weeks to study their effects on immune status and atherosclerosis. Here, we show that T cell specific deficiency in CD40L signaling reduced plaque progression through hampered Th1 polarization as well as reduced antigen-dependent proliferation and oxLDL IgM production. DC-specific CD40 deficient mice displayed a similar phenotype. Platelet-specific CD40L deficiency, however, failed to decrease atherosclerosis, but ameliorated atherothrombosis. Together, our results illuminate the divergent cell-specific mechanisms of CD40-CD40L signaling in atherosclerosis, which may lead to advances in targeted therapies.

overall_design: Comparison of gene expression in CD4+ T cells from wild-type mice and CD4+ T cell-specific CD40L-deficient mice

first: Michael

last: Lacy

first: Norbert

last: Gerdes

first: Christina

last: Bürger

first: Maiwand

last: Ahmadsei

first: Holger

last: Winkels

first: Katrin

last: Nitz

first: Claudia

last: van Tiel

first: Tom

middle: T

last: Seijkens

first: Pascal

last: Kusters

first: Koen

middle: H

last: Prange

first: Ela

last: Karshovka

first: Sigrid

last: Reim

first: Marijke

last: Kuipers

first: Myrthe

last: Reiche

first: Remco

last: Megens

first: Johan

last: Heemskerk

first: Christian

last: Weber

first: Dorothee

last: Atzler


title: Characterization of tumor mutational burden in LKB1 mutant lung tumors

city: New York

first: Igor

last: Dolgalev

address: 550 1st Ave

institute: NYU Grossman School of Medicine

overall_design: Examine mRNA of KP and KL GEMM lung tumor nodules derived cell lines for mutational burden analysis.

first: Jiehui

last: Deng

first: Kwok

middle: K

last: Wong


title: Uncovering the dosage-dependent roles of Arid1a in gastric tumorigenesis for combinatorial drug therapy [scRNA-Seq]

city: TORONTO

first: Haiyang

last: Guo

address: 101 College Street, 11-601D, TMDT, 11-601D, TMDT

department: Princess Margaret Cancer Centre

institute: UNIV HEALTH NETWORK

summary: Gastric cancer (GC) is one of the most common deadly cancers in the world. Although patient genomic data have identified ARID1A, a key chromatin remodeling complex subunit, as the second most frequently mutated gene after TP53, its in vivo role and relationship to TP53 in gastric tumorigenesis remains unclear. Establishing a novel mouse model that reflects the ARID1A heterozygous mutations found in the majority of human GC cases, we demonstrated that Arid1a heterozygosity facilitates tumor progression through a global loss of enhancers and subsequent suppression of the p53 and apoptosis pathways. Moreover, our mouse genetic and single cell analyses demonstrated that the homozygous deletion of Arid1a confers a competitive disadvantage through the activation of the p53 pathway, highlighting its distinct dosage dependent roles. Utilizing this unique vulnerability of Arid1a mutated GC cells, our combinatorial treatment with an epigenetic inhibitor and a p53 agonist selectively inhibited Arid1a heterozygous tumor growth, providing a novel therapeutic option for GC.

overall_design: scRNA-Seq of mouse stomach glands

first: Adrian

last: Kwan Loe

first: Roshane

last: Francis

first: Jieun

last: Seo

first: Ji-Eun

last: Kim

first: Shaheed

last: Hakim

first: Jungeun

first: Housheng

last: He

first: Tae-Hee


title: Uncovering the dosage-dependent roles of Arid1a in gastric tumorigenesis for combinatorial drug therapy

overall_design: Refer to individual Series


title: RNA-Seq analysis on the liver of mice treated with high-fat diet and liraglutide

city: Toronto

first: Tianru

last: Jin

address: 101 college street

institute: University Health Network

summary: GLP-1 based diabetes drugs are effective to reduce hepatic lipid accumulation beyong glycemic control. As GLP-1 receptor (GLP-1R) is not expressed in hepatocytes, the mechanism behind the beneficial effects of GLP-1 based drugs on the liver remained elusive. Several studies have shown that the expression of hepatic fibroblast growth factor 21 (FGF21) can be stimulated by GLP-1-based drugs. Therefore, the present study aimed to assess such stimulation in mice and in mouse primary hepatocytes, determine whether hepatic FGF21 mediates functions of the GLP-1R agonist liraglutide, and to explore the potential mechanisms of liraglutide regulating the expression of FGF21. In high-fat diet induced obese mice, we observed hepatic and plasma FGF21 elevation, improved glucose disposal, and reduced plasma triglyceride levels by liraglutide treatment. Moreover, RNA-sequencing on the liver suggested that Fgf21 was the most upregulated gene after liraglutide treatment. In liver-specific FGF21 knock-out mice on high-fat and high-fructose diet, the body-weight gain attenuation and lipid homeostatic effects of liraglutide was lost or significantly reduced. These studies implied that hepatic FGF21 was the critical mediator of liraglutide-induced metabolic improvement.

overall_design: RNA was isolated from liver of mice treated with high-fat diet for 4 weeks and then subcutaneously injected with liraglutide at 300 μg/kg body weight for 3 days.

first: Dinghui

last: Liu

first: Juan

last: Pang

first: Weijuan

last: Shao


title: Transcriptional profiles of yolk sac upon HNF4A loss in mice by RNA-seq

status: Public on Mar 15 2021

city: Piscataway

first: Michael

last: Verzi

state: NJ

address: 145 Bevier Road

institute: Rutgers, the State University of New Jersey

summary: Knockout of HNF4A in yolk sac resulted in decreased expression levels of brush border genes and increased expression levels of stress fiber genes.

overall_design: Transcriptional profiling was employed to identify HNF4A-dependent gene expression in the mouse yolk sac

first: Lei

last: Chen


title: Autism-linked Cullin3 germline haploinsufficiency severely impacts mouse brain development and cortical neurogenesis through RhoA signaling

city: La Jolla

first: Lilia

middle: M

last: Iakoucheva

state: California

address: 9500 Gilman Drive, MC0603

department: Psychiatry

institute: University of California San Diego

summary: E3-ubiquitin ligase Cullin3 (Cul3) is a high confidence risk gene for Neurodevelopmental Disorders such as Autism Spectrum Disorder (ASD) and Developmental Delay (DD). This study identifies the impact of the ASD-associated de novo Cul3-mutation on brain anatomy, behavior, molecular, cellular, and circuit-level mechanisms during early neocortical development. We report that Cul3 mutant mice have microcephaly and severe brain structure defects. This mouse model exhibits social and cognitive deficits and hyperactivity behavior. Spatiotemporal transcriptomic and proteomic profiling of Cul3 mouse brain implicates neurogenesis and cytoskeletal defects as key drivers of Cul3 functional effect. We show that Cul3 is critical for neuron growth and development. Cultured cortical neurons from the mutant mice have reduced dendritic length, actin cytosketon defects, reduced network activity, and increased cell death. At the molecular level, we implicate upregulation of small GTPase RhoA, involved in regulation of cytoskeletal dynamics, and neurite outgrowth as one of the pathways impacted by the de novo Cul3 mutations in ASD. Treatment with small molecule RhoA inhibitor Rhosin rescues dendrite length phenotype and implicates RhoA pathway in ASD.

overall_design: Bulk RNA-seq of 108 samples containing Cul3+/- heterozygous and WT mice were performed at different developmental time periods- embryonic(E17.5), Postnatal (P7) and adult (4-6 weeks)

first: Megha

last: Amar

first: Alysson

last: Muotri


title: Uncovering the dosage-dependent roles of Arid1a in gastric tumorigenesis for combinatorial drug therapy [RNA-Seq]

first: Haiyang

overall_design: RNA-Seq of mouse stomach glands

first: Adrian


title: Discovery of tumor specific antigens in acute myeloid leukemia.

city: Montréal

first: Claude

last: Perreault

state: Québec

address: 2950, Chemin de Polytechnique

institute: Institute for Research in Immunology and Cancer

summary: We performed RNA-Seq and mass spectrometry (MS) on the immunopeptidome of 19 human primary AML samples and discovered a set of 58 tumor specific antigens (TSA) that could serve to design an anti-AML immunotherapy.

overall_design: Four proteogenomic approaches were used to create cancer-specific MS databases. Peptide identifications were made on the samples used for RNA-Seq and database construction. Various bioinformatic approaches were then performed to establish the TSA nature of the peptides identified by MS. Data reported here are paired-end stranded RNA-sequencing (R1 map on reverse strand and R2 on forward strand) of the 19 AML samples at a coverage >120M reads / sample. MS data are freely available on PRIDE (PXD018542 and 10.6019/PXD018542).

first: G

last: Ehx

first: C


title: RNA-seq of sorted pancreatic endocrine progenitor cells

city: Aurora

first: Alexandra

last: Theis

state: Colorado

address: 1775 Aurora Ct, Room 4202A

department: Barbara Davis Center

institute: University of Colorado Anschutz Medical Campus

summary: Pancreatic endocrine cells arise from a NGN3+ population during pancreas organogenesis. To gain a more thorough understanding of this progenitor pool, we used a reporter mouse - NGN3-EGFP - and sorted EGFP+ cells from e15.5 pancreata of control animals. The data generated from this experiment will allow us to visualize gene expression levels in endocrine progenitors during normal development and can be used to compare against mutant animal gene expression.

overall_design: RNA-seq of NGN3-EGFP cells sorted from e15.5 embryos (n=2)

first: Lori

last: Sussel


title: Transcriptional profiles of kidney upon HNF4A loss in mice by RNA-seq

summary: Adult-onset knockout of HNF4A resulted in decreased expression levels of brush border genes. We find a robust shift in the transcriptome away from proximal tubule transcripts and towards distal tubule transcripts in the kidney upon HNF4A loss.

overall_design: Transcriptional profiling was employed to identify HNF4A-dependent gene expression in the mouse kidney

first: Rohit

last: Aita


title: Gene expression profile in cerebral ischemia-reperfusion injury of rat model

city: Chang Chun

first: Xuan

state: Jilin

address: Xinmin Street

department: The First Hospital of Jilin University

institute: Jilin university

summary: To reveal the alterations of mRNA profile in cerebral ischemia-reperfusion injury in rat. The SD rats were used to established the middle cerebral artery occlusion and reperfusion (MCAO/R) model. RNA-seq were performed to identify differences in gene expression.

overall_design: Examination of MCAO/R and Sham rat brain samples（n=3）

first: Luo

last: Qi

first: Chen

last: Xuan


title: Six melanoma cancer cell lines transcriptomics (metastatic and primary)

status: Public on Mar 14 2021

city: West Haven

first: Wenxue

last: Li

state: CT     Connecticut

address: 300 Heffernernan Dr Bldg A42,, Bldg 840, Room ABC 367

institute: Yale University

summary: We report the six metastatic (RPMI-7951,SK-MEL-3,SH-4) and primary (A375,G-361,SK-MEL-1) melanoma cancer cells transcriptomics.

overall_design: Supply a high-throughput and high quality multi-omics (transcriptomics, proteomics, phosphoproteomics) data resource for metastatic and primary melanoma cancer cells

first: Erli

last: Gao

first: Chongde

last: Wu

first: Yansheng


title: RNA-sequencing of livers in wt and sirt6-tg mice

city: Ramat-Gan

first: Ilana

last: Lebenthal-Loinger

address: Bar-Ilan University

department: The Mina & Everard Goodman Faculty of Life Sciences

country: Israel

institute: Bar-Ilan University

summary: Whole body SIRT6 overexpression (SIRT6-tg) extends lifespan. Here we examine the effect of SIRT6 overexpression on liver mRNA profile

overall_design: Liver mRNA profiles of 5-7 months old wild type (WT) and SIRT6-transgenic (SIRT6-tg) male and female C57BL/6JOlaHsd mice

first: Haim

middle: Y

last: Cohen


title: Precision radiotherapy: Reduction in radiation for oropharyngeal cancer - the 30 ROC trial

first: Xin

last: Pei

state: NY

address: 417 E 68th St,Mortimer B. Zuckerman Research Center

department: Radiation Oncology

institute: Memorial Sloan Kettering Cancer Center

summary: These are the RNAseq data in the publication. The detailed information can be obtained from the supplementary tables in the paper.

overall_design: This is a phase-I clinical trial to investigate whether functional imaging could identify patients who could be safely de-escalated to 30Gy of radiotherapy

first: Nadeem

last: Riaz

first: Eric

last: Sherman

first: Rachna

last: Shah

first: Nancy

last: Lee


title: DNA molecular combing-based replication fork directionality profiling

city: PARIS

first: Benoit

last: Le Tallec

address: 46 rue d'Ulm

country: France

institute: IBENS

summary: The replication strategy of metazoan genomes is still unclear, mainly because definitive maps of replication origins are missing. High-throughput methods are based on population average and thus may exclusively identify efficient initiation sites, whereas ineffective origins go undetected. Single-molecule analyses of specific loci can detect both common and rare initiation events along the targeted regions. However, these usually concentrate on positioning individual events, which only gives an overview of the replication dynamics. Here, we computed the replication fork directionality (RFD) profiles of two large genes in different transcriptional states in chicken DT40 cells, namely untranscribed and transcribed DMD and CCSER1 expressed at WT levels or overexpressed, by aggregating hundreds of oriented replication tracks detected on individual DNA fibres stretched by molecular combing. These profiles reconstituted RFD domains composed of zones of initiation flanking a zone of termination originally observed in mammalian genomes and were highly consistent with independent population-averaging profiles generated by Okazaki fragment sequencing (OK-seq). Importantly, we demonstrate that inefficient origins do not manifest as detectable RFD shifts, explaining why dispersed initiation has remained invisible to population-based assays. Our method can both generate quantitative profiles and identify discrete events, thereby constituting a comprehensive approach to study metazoan genome replication.

overall_design: OK-seq (Okazaki fragment sequencing) profiles of selected loci in chicken DT40 cells

first: Marion

last: Blin

first: Laurent

last: Lacroix

first: Natalia

last: Petryk

first: Yan

last: Jaszczyszyn

first: Chun-Long

last: Chen

first: Olivier

last: Hyrien

first: Benoît


title: Spear-ATAC: Pooled, droplet-based, single-cell chromatin accessibility CRISPR screens

city: STANFORD

first: Jeffrey

middle: Michael

last: Granja

state: CA

address: 279 Campus Drive W

institute: Stanford University

summary: Spear-ATAC is a modified droplet-based single-cell ATAC-seq (scATAC-seq) protocol that enables simultaneous read-out of chromatin accessibility profiles and integrated sgRNA spacer sequences from thousands of individual cells at once. Spear-ATAC profiling of 104,592 cells representing 414 sgRNA knock-down populations across three experiments revealed the temporal dynamics of epigenetic responses to regulatory perturbations in cancer cells and the associations between transcription factor binding profiles, demonstrating a high-throughput method for perturbing and evaluating dynamic single-cell epigenetic states.

first: Sarah

last: Pierce


title: Uncovering the dosage-dependent roles of Arid1a in gastric tumorigenesis for combinatorial drug therapy [ChIP-Seq]

first: Haiyang

last: Guo

state: Ontario

overall_design: ChIP-Seq of mouse stomach glands

first: Adrian

last: Kwan Loe

first: Roshane

last: Francis

first: Jieun

last: Seo

first: Ji-Eun

last: Kim

first: Shaheed

last: Hakim

first: Jungeun

first: Housheng

last: He

first: Tae-Hee


title: MPP8 is essential for sustaining self-renewal of ground-state pluripotent stem cells

first: Iris

last: Mueller

state: New York

address: 430 East 67th Street

institute: MSKCC

summary: Deciphering the mechanisms that control the pluripotent ground state is key for understanding embryonic development. Nonetheless, the epigenetic regulation of ground-state mouse embryonic stem cells (mESCs) is not fully understood. Here, we identify the epigentic protein MPP8 as being essential for ground-state pluripotency. Its depletion leads to cell cycle arrest and spontaneous differentiation. MPP8 has been suggested to repress LINE1 elements by recruiting the human silencing hub (HUSH) complex to H3K9me3-rich regions. Unexpectedly, we find that LINE1 elements are efficiently repressed by MPP8 lacking the chromodomain, while the unannotated C-terminus is essential for its function. Moreover, we show that SETDB1 recruits MPP8 to its genomic target loci, whereas transcriptional repression of LINE1 elements is maintained without retaining H3K9me3 levels. Taken together our findings demonstrate that MPP8 protects the DNA-hypomethylated pluripotent ground state through its association with the HUSH core complex, however, independently of detectable chromatin binding and maintenance of H3K9me3.

overall_design: MPP8, FLAG and H3K9me3 chromatin immunoprecipitation profiles (ChIP-seq) analyzed in mouse embryonic stem cells which have been engineered to homozygously express MPP8 carrying a C-terminal miniAID (mAID) tag from the endogenous Mphosph8 locus as well as the E3 ligase OsTIR1 exogenously (Mpp8mAID; OsTIR1 cells). Cells were left untreated or treated with auxin (IAA) for indicated time points to remove endogenous MPP8.   MPP8, FLAG and H3K9me3 chromatin immunoprecipitation profiles (ChIP-seq) analyzed in the Mpp8mAID; OsTIR1 background additionally expressing FLAG-tagged MPP8 fragments, Mpp8wt, Mpp8112-858 and MPP81-729, respectively (wt corresponds to the full length protein sequence, Npart corresponds to amino acid 1-729, Cpart correspond to amino acid 112-858). Cells were left untreated or treated with auxin (IAA) for indicated time points to remove endogenous MPP8. FLAG ChIPSeq analysis in cells engineered to homozygously express MPP8, TASOR and PPHLN1 carrying a C-terminal FLAG2 tag at the endogenous Mphosph8, Tasor and Pphln1 loci, respectively, or untagged parental control.  RNA-seq analysis in Mpp8mAID; OsTIR1 cells, and cells additionally expressing FLAG-tagged MPP8 fragments, Mpp8wt, Mpp8112-858 and MPP81-729, respectively. Cells were left untreated or treated with auxin (IAA) for indicated time points to remove endogenous MPP8.

last: Müller

first: Ann

middle: S

last: Moroni

first: Daria

last: Shlyueva

first: Sudeep

last: Sahadevan

first: Erwin

last: Schoof

first: Aliaksandra

last: Radzisheuskaya

first: Jonas

last: Højfeldt

first: Tülin

last: Tatar

first: Richard

last: Koche

first: Chang

last: Huang

first: Kristian

last: Helin


title: Arabidopsis MED8 functions in oxidative stress

city: Gent

first: Patrick

last: Willems

address: Technologiepark 927

department: PSB

country: Belgium

institute: Ghent University

summary: In this work, we describe a TDNA insertion mutant for Mediator complex subunit 8 (MED8) that regulates the oxidative stress responses. Wild-type Col-0 and med8 seedlings were growth under control condition or oxidative stress (induced by methyl viologen treatment) and were subjected to RNA-seq profiling. Total mRNA fractions were isolated and subjected to signle-end deep sequencing (approx.30M reads/sample) to reveal differential expression between genotypes and conditions.

overall_design: 2 genotypes (Col-0 and med8), 2 conditions (control and stress) X  3 replicates = 18 samples

first: Amna

last: Mhamdi

first: Huaming

first: Frank

last: Van Breusegem


title: Expression data for post-bifurcation internal carotid atheroma

status: Public on Mar 13 2021

city: Pittsburgh

first: ROBERT

middle: MAX

last: FRIEDLANDER

state: PA

address: Suite B-400, 200 Lothrop Street

department: Neurological Surgery

institute: University of Pittsburgh Medical Center

summary:
There are regional differences in plaque morphology and mechanistic differences between areas upstream and downstream of the lipid core.
Transcript expression profiles were determined for post-bifurcation carotid plaques to identify genes differentially expressed between symptomatic and asymptomatic patients.

overall_design: Carotid plaques were collected from 9 symptomatic patients and 9 asymptomatic patients undergoing carotid endarterectomy (CEA). Symptomatic patients underwent CEA up to 184 days from one or more ipsilateral ischemic cerebral or retinal symptoms, in accord with the clinical definition of a symptomatic carotid stenosis covering up to 6 months after the onset of neurological symptoms. Patients were classified as symptomatic if they suffered a transient ischemic attack, transient monocular blindness ipsilateral to the study artery, or minor or non-disabling ipsilateral stroke. Otherwise, patients were classified as asymptomatic. Asymptomatic and symptomatic patients presented with significant carotid stenosis (60%-100%).

first: Ellen

last: Caparosa

first: Andrew

last: Sedgewick

first: Georgios

last: Zenonos

first: Yin

last: Zhao

first: Diane

middle: L

last: Carlisle

first: Lucia

last: Stefaneanu

first: Brian

last: Jankowitz

first: Paul

last: Gardner

first: Yue-Fang

last: Chang

first: William

middle: R

last: Lariviere

middle: A

last: Laframboise

first: Panayiotis

middle: V

last: Benos

first: Robert

last: Friedlander


title: Comparison of the whole transcriptomes between ALS-mutant and Healthy control motor neurons

city: ULM

first: Alberto

last: Catanese

address: Albert-Einstein-Allee 11

institute: Ulm University

summary: We performed total RNA sequencing to analyze and compare the whole transcriptomes of hiPSC-derived motor neurons obtained from ALS patients harboring mutations in the C9orf72 (2 patients) and FUS (2 patients) genes, and from control hiPSC lines. The Healthy control cells were obtained from 1 healthy individual, and by correcting the pathogenic mutation within C9orf72 gene with Crispr technology

overall_design: Whole transcriptome analysis of 35 days old motor neurons

first: Tobias

last: Böckers


title: Clonally focused public and private T cells in resected brain tissue from surgeries to treat children with intractble seizures.

status: Public on Mar 12 2021

city: Los Angeles

first: Geoffrey

last: Owens

address: 300 Stein Plaza Ste 562

department: Neurosurgery

institute: UCLA

summary: As part of a study of the involvement of adaptive immunity in pediatric patients who undergo surgery to treat their drug resistant seizures, brain-infiltrating leukocytes were isolated from epileptogenic brain tissue from a tuberous sclerosis complex patient. Combined single cell gene expression and T cell receptor sequencing of these leukocytes revealed that the two predominant T cell clonotypes in the resected tuber were CD8 effector T cells, indicating that they are very likely to be pathologically relevant.

overall_design: Single cell RNA sequencing to determine the phenotypes and T cell receptors expressed by brain-infiltrating T cells in a surgery case of tuberous sclerosis complex.

middle: C


title: Cross-Platform Validation of Neurotransmitter Release Impairments in Schizophrenia Patient-Derived NRXN1-Mutant Neurons

city: Cincinnati

first: Bruce

last: Aronow

state: OH

address: 240 Albert Sabin Way

department: Biomedical Informatics, Developmental Biology

institute: Cincinnati Children's Hospital Medical Center

summary: Heterozygous NRXN1 deletions constitute the most prevalent currently known single-gene mutation associated with schizophrenia, and predispose to multiple other neurodevelopmental disorders. Previous studies showed that engineered heterozygous NRXN1 deletions impaired neurotransmitter release in human neurons, suggesting a synaptic pathophysiological mechanism. Utilizing this observation for drug discovery, however, requires confidence in its robustness and validity. Here, we describe a multi-center effort to test the generality of this pivotal observation, using independent analyses at two laboratories of patient-derived and newly engineered human neurons with heterozygous NRXN1 deletions. We show that in neurons that were trans-differentiated from induced pluripotent stem cells derived from three NRXN1-deletion patients, the same impairment in neurotransmitter release was observed as in engineered NRXN1-deficient neurons. This impairment manifested as a decrease in spontaneous synaptic events and in evoked synaptic responses, and an alteration in synaptic paired-pulse depression. Nrxn1-deficient mouse neurons generated from embryonic stem cells by the same method as human neurons did not exhibit impaired neurotransmitter release, suggesting a human-specific phenotype. NRXN1 deletions produced a reproducible increase in the levels of CASK, an intracellular NRXN1-binding protein, and were associated with characteristic gene expression changes. Thus, heterozygous NRXN1 deletions robustly impair synaptic function in human neurons regardless of genetic background, enabling future drug discovery efforts.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Using four-weeks old, relatively mature human neurons generated from the three pairs of patient-derived NRXN1del and control iPS cells, we performed bulk RNA-sequencing analysis of total RNA from three independent culture batches. We also performed bulk RNAseq analyses on triplicate cultures of  isogenic pairs of human neurons without or with the heterozygous NRXN1 deletion that were trans-differentiated from a de novo engineered iPS cell line carrying a conditional NRXN1del allele and compared this to 3 unrelated wild-type iPS cell lines (in duplicate). In total, we performed differential gene expression analyses on 30 samples (9 controls vs. 9 schizophrenia-NRXN1 mutants, 3 controls vs. 3 engineered NRXN1 mutants, and 6 wild-type iPS cell samples) in triplicates or duplicates (replicates refer to independent cultures performed at different time points).  As a result of the co-culturing scheme of human neurons with mouse glia, the RNAseq data on neurons were composed of a mixture of human neuronal and mouse glia transcriptomes. A key step in processing of the RNAseq data was to deconvolve the two transcriptomes and to normalize the relative abundance of each mRNA from each species to the total number of mRNAs from that species only. As described in the Methods, the Kallisto program was able to unambiguously assign each paired 150 base-pair sequence to mouse and human reference transcriptomes. The mouse:human mRNA ratios differed between cultures of neurons trans-differentiated from various iPS cell lines. To control for these differences, we adjusted each sample’s species-specific mRNA abundance based on Transcripts per Million (TPM) for each gene, summed these for each gene, and then carried out per-sample quantile normalization steps for each sample. This approach provided a reproducible abundance measure for each gene in each sample. The resulting values were used to form a log2(TPM+1) gene-by-sample matrix that was used for differential gene expression analyses using LIMMA.

first: ChangHui

last: Pak

first: Jinzhao

last: Wang

first: Xianglong

last: Zhang

first: Pingping

last: Qu

first: Tamas

last: Danko

first: Alexis

last: Mittelpunkt

first: Alexander

middle: E

last: Urban

first: Zhiping

middle: P

last: Pang

first: Kang

last: Jin

first: Philip

last: Dexheimer

first: Eric

last: Bardes

first: Douglas

middle: F

last: Levinson

first: Marius

last: Wernig

first: Thomas

last: Südhof


title: MicroRNA expression data for post-bifurcation internal carotid atheroma

first: ROBERT

last: FRIEDLANDER

summary:
There are regional differences in plaque morphology and protein expression.
MicroRNA expression profiles were determined for post-bifurcation carotid plaques to identify gene regulation mechanisms differentially expressed between symptomatic and asymptomatic patients.

first: Ellen

last: Caparosa

first: Andrew

middle: J

last: Sedgewick

first: Georgios

last: Zenonos

first: Yin

last: Zhao

first: Diane

last: Carlisle

first: Lucia

last: Stefaneanu

first: Brian

last: Jankowitz

first: Paul

last: Gardner

first: Yue-Fang

last: Chang

first: William

last: Lariviere

last: Laframboise

first: Panayiotis

last: Benos

first: Robert

last: Friedlander


title: RNA-seq of Control and PRMT5-/- JHH-7 Cell Transcriptomes

city: Shanghai

first: Cen

last: Xie

address: 501 Haike Road

institute: Shanghai Institute of Materia Medica

summary:
Purpose: The goals of this study are to use RNA-seq-derived JHH-7 cell transcriptome profiling  for differentially expressed genes after PRMT5 knockdown.
Methods: mRNA profiles of control and PRMT5 knockdown JHH-7 cells were generated by RNA-seq, using Illumina Novaseq 6000.The sequence reads that passed quality filters were analyzed at the transcript isoform level with TopHat2  or HISAT2. The gene expression quantification was performed using RSEM tool and generated raw count for all genes individually. qRT–PCR validation was performed using SYBR Green assays.
Results: On average, we generated >200 million paired end reads for each sample, with more than 95% of the reads passed the QC.

overall_design: mRNA profiles of control and PRMT5-/- JHH-7 cells

first: Yuqing

last: Gao


title: Transcriptomic analyses of embryonic pancreata from pancreas-specific Groucho mutants

first: Alexandra

last: Theis

summary: A large number of studies have identified and characterized the many transcription factors and cofactors that regulate pancreas organogenesis.  Groucho-related genes/Transducin-like Enhancer of Split (Grgs/TLEs) are one such family of cofactors that act as transcriptional co-repressors and are critical for many developmental processes. Several essential pancreatic transcription factors are capable of interacting with GRGs; however, the role of GRG-mediated transcriptional repression in pancreas development is only partially characterized. In this study, we used phenotypic and transcriptomic analyses to determine that GRG3 is essential for β cell development, and in the absence of Grg3 there is compensatory upregulation of Grg4. In Grg3/4 double mutants, mice have severe dysregulation of the pancreas gene program with ectopic expression of liver genes and Foxa1, a master regulator of the liver program. Neurod1, an essential β cell transcription factor and predicted target of Foxa1, becomes downregulated in Grg3/4 mutants, resulting in a loss of β cell proliferation, hyperglycemia, and early lethality. These findings uncover a novel function of GRG-mediated repression in pancreas development.

overall_design: e18.5 pancreas RNA-seq from Pdx1:Cre, Pdx1:Cre; Grg and Pdx1:Cre; Grg3/4 embryos (n=3 for each genotype)

first: Lori

last: Sussel


title: Histone H3K27 acetylation at CTCF sites mediates cell type-specific chromatin interactions between them.

city: Busan

first: AeRi

last: Kim

address: 2, Busandaehak-ro 63beon-gil, Geumjeong-gu

institute: Pusan national university

summary: We found that CTCF sites was acetylated at H3K27 and this modification was decreased by histone acetyltransferases and depletion of GATA-1.

overall_design: CTCF and H3K27ac ChIP-seq was performed in control, CBP/p300 knockdown and GATA-1 knockdown cells


title: Establishment of an induced pluripotent stem cell line from a female domestic ferret (Mustela putorius furo) with an X chromosome instability

city: Shinjuku

first: Sho

last: Yoshimatsu

state: Tokyo

address: 35 Shinanomachi

department: Physiology

institute: Keio University School of Medicine

summary: The domestic ferret (ferret; Mustela putorius furo) is an important animal model for neuroscience and preclinical/veterinary medicine owing to its susceptibility to avian influenza and corona viruses. Nevertheless, there is a lack of in vitro ferret models, since immortal cell lines including induced pluripotent stem cells (iPSCs) of ferrets have been scarce. In this study, we established an induced pluripotent stem cell line from skin fibroblasts of a neonatal female ferret using a previously validated method in multiple mammalian species. The established line, fiPS-1, showed standard characteristics of pluripotency, but it showed an X chromosome instability characterized by the high emergence rate of aneuploid 39X cells from the original 40XX euploid cells.

overall_design: RNA seq of ferret iPSCs

first: Hideyuki

last: Okano


title: Influence of RD2 on gene expression in serotype M1 and M49 GAS isolates

city: Reno

last: Sumby

state: NV

address: 1554 N. Virginia St.

department: Microbiology & Immunology

institute: University of Nevada

summary: We used RNA-Seq to assess how the presence/absence of the RD2 pathogenicity island influences global gene expression in the parental serotype M1 GAS isolate MGAS2221 and the parental serotype M49 isolate NZ131

overall_design: The parental isolates (MGAS2221 and PGAS812 [also known as NZ131]) and derivatives containing the RD2 pathogenicity island (PGAS885 and PGAS890, respectively) were compared.  Each strain was grown in triplicate in THY broth (37 degrees centigrade in 5% CO2) to the exponential phase of growth (O.D.600 of 0.5).  Samples were taken and processed for RNA isolation.

first: Roshika

last: Roshika


title: Single-nucleotide-level mapping of DNA regulatory elements that control fetal hemoglobin expression (HiCHIP)

city: Memphis

first: Yong

last: Cheng

state: Tennessee

address: 262 Danny Thomas Place

department: Department of Hematology

institute: St. Jude Children’s Research Hospital

summary: gRNA screening for HbF+ and HbF- samples were performed to identify candidate cis-regulatory elements.

overall_design: CRISPR pooled gRNA screening, RNA-seq, ChIP-seq, ATAC-seq and HiCHIP were performed

first: Li

first: Yichao

last: Li


title: miRNA-independent function of long noncoding pri-miRNA loci

city: San Francisco

first: David

last: Wu

address: 35 Medical Center Way

institute: UCSF

summary: Among the large, diverse set of mammalian long noncoding RNAs (lncRNAs), long noncoding primary microRNAs (lnc-pri-miRNAs) are those that host miRNAs. Whether lnc-pri-miRNA loci have important biological function independent of their cognate miRNAs is poorly understood. From a genome-scale lncRNA screen, lnc-pri-miRNA loci were enriched for function in cell proliferation, and in glioblastoma (i.e., GBM) cells with DGCR8 or DROSHA knockdown, lnc-pri-miRNA screen hits still regulated cell growth. To molecularly dissect the function of a lnc-pri-miRNA locus, we studied LOC646329 (also known as MIR29HG), which hosts the miR-29a/b1 cluster. In GBM cells, LOC646329 knockdown reduced miR-29a/b1 levels, and these cells exhibited decreased growth. However, genetic deletion of the miR-29a/b1 cluster (LOC646329-miR29Δ) did not decrease cell growth, while knockdown of LOC646329-miR29Δ transcripts reduced cell proliferation. The miR-29a/b1-independent activity of LOC646329 corresponded to enhancer-like activation of a neighboring oncogene (MKLN1), regulating cell propagation. The LOC646329 locus interacts with the MKLN1 promoter, and antisense oligonucleotide knockdown of the lncRNA disrupts these interactions and reduces the enhancer-like activity. More broadly, analysis of genome-wide data from multiple human cell types showed that lnc-pri-miRNA loci are significantly enriched for DNA looping interactions with gene promoters as well as genomic and epigenetic characteristics of transcriptional enhancers. Functional studies of additional lnc-pri-miRNA loci demonstrated cognate miRNA-independent enhancer-like activity. Together, these data demonstrate that lnc-pri-miRNA loci can regulate cell biology via both miRNA-dependent and miRNA-independent mechanisms.

overall_design: Analysis of transcriptome following knockdown of LOC646329 in different genotypes

first: Daniel

last: He

last: Lim


title: Identifcation of Meis2 target genes in the otic cell line VOT-E36 via ChIP analysis

city: Madrid

first: Enrique

last: Vazquez de Luis

state: Madrid

address: Melchor Fernandez Almagro, 3

country: Spain

institute: CNIC

summary: Meis genes have been shown to control essential processes during development of the central and peripheral nervous system. Here we have defined the roles of the Meis2 gene during vertebrate inner ear induction and the formation of the cochlea. Meis2 is expressed in several tissues required for inner ear induction and in non-sensory tissue of the cochlear duct. Global inactivation of Meis2 in the mouse leads to a severely reduced size of the otic vesicle. Tissue-specific knock outs of Meis2 reveal that its expression in the hindbrain is essential for inner ear induction. Inactivation of Meis2 in the inner ear itself leads to an aberrant coiling of the cochlear duct. By analyzing transcriptomes obtained from Meis2 mutants and ChIPseq analysis of an otic cell line we define candidate target genes for Meis2 which may be directly or indirectly involved in cochlear morphogenesis. Taken together, these data show that Meis2 is essential for inner ear formation and provide an entry point to unveil the network underlying proper coiling of the cochlear duct.

overall_design: ChIPSeq was used to determine Meis2 genome occupancy in the VOT-E36 cell line which is derived from the ventral part of the otic vesicle at embryonic day 10.5

first: Thomas

last: Schimmang

first: María

middle: B

last: Durán Alonso

last: Vázquez


title: Histone H3K27 acetylation at CTCF sites mediates cell type-specific chromatin interactions between them

summary: We found that H3K27ac at CTCF sites was decreased around the β-globin locus by loss of GATA-1 binding.

overall_design: H3K27ac ChIP-seq was performed in control and HS3∆∆GA cells


title: DNA Methylation Potential Energy Landscape Analysis of Pediatric Pre-B cell Acute Lymphoblastic Leukemia (ALL) and Normal B cells and precursors

city: Baltimore

first: Michael

last: Koldobskiy

state: MD

address: 855 N. Wolfe St.

department: Center for Epigenetics

institute: Johns Hopkins University

summary: Acute lymphoblastic leukemia (ALL) is the most common cancer in children. We applied WGBS and the informME analysis pipeline to investigate the role of DNA methylation stochasticity in pre-B cell ALL.

overall_design: WGBS was carried out on pediatric pre-B cell acute lymphoblastic leukemia primary samples, cell lines, and normal umbilical cord blood CD19+ cells.  The informME analytic pipeline was applied to these data as well as to existing WGBS data for normal B cell precursors. Single-cell RNA-seq of ETV6-RUNX1 pre-B acute lymphoblastic leukemia primary patient samples and normal umbilical cord blood derived CD19+ cells. RNA-seq of ETV6-RUNX1 pre-B acute lymphoblastic leukemia primary patient samples and normal umbilical cord blood derived CD19+ cells. Raw data for the PreB2-1 and -2 samples is available elsewhere (EGA download, previously released data).

first: Andrew

last: Feinberg


title: ChAP-seq analysis to identify GoxR binding sites

status: Public on Mar 11 2021

city: Jülich

first: Angela

last: Kranz

state: NRW

address: Wilhelm-Johnen-Strasse

department: IBG-1: Biotechnology

institute: Forschungszentrum Jülich GmbH

summary: Gene expression in the obligatory aerobic acetic acid bacterium Gluconobacter oxydans was shown to respond to oxygen limitation, but the regulators involved are unknown. In this study, we analyzed the function of a transcriptional regulator named GoxR, which belongs to the FNR family. Here, we applied ChAP-seq analysis with a strep-tagged GoxR version to identify binding sites of this regulator in the genome of G. oxydans.

overall_design: For ChAP-seq the strain G. oxydans 621H::goxR-strep was constructed. This strain was cultivated aerobically. After harvesting of the cells, the pellet was treated with formaldehyde to perform cross-linking between bound proteins and the DNA. Afterwards, DNA bound to Strep-tagged GoxR was purified and submitted to sequencing.

last: Bott


title: Selenite induces cell cycle arrest and apoptosis through ROS-dependent inhibition of the AKT/mTOR pathway in thyroid cancer

city: Guangzhou

first: Zhen

state: China

address: 58 Zhongshan Er Road, Guangzhou

institute: The First Affiliated Hospital of Sun Yat-Sen University

summary: We conducted a comprehensive RNA-seq analysis of early transcriptomic changes in KHM-5M to decipher the underlying mechanism of sodium selenite.

overall_design: Thyroid cancer cells(KHM-5M) were treated with PBS (negative control) or sodium selenite respectively. Cells were harvested and Total RNA was extracted using Trizol reagent and purified by Oligo(dT)-attached magnetic beads. the single end 50 bases reads were generated on BGIseq500 platform (BGI-Shenzhen, China). The sequencing data was filtered with SOAPnuke, stored in FASTQ format, and mapped to HISAT2 (v2.0.4). The expression level was calculated by RSEM (v1.2.12).

first: Shubin

last: Hong

first: Haipeng

last: Xiao


title: Adaptive cell invasion maintains organ homeostasis

city: Kansas City

first: Tatjana

last: Piotrowski

state: MO

address: 1000 East 50th Street

institute: Stowers Institute for Medical Research

summary: Mammalian inner ear and fish lateral line sensory hair cells depend on fluid motion to transduce environmental signals and elicit a response. In mammals, actively maintained ionic homeostasis of the cochlear and vestibular fluid (endolymph) is essential for hair cell function and numerous mammalian hearing and vestibular disorders arise from disrupted endolymph ion homeostasis. Lateral line hair cells, however, are openly exposed to the aqueous environment with fluctuating ionic composition. How sensory transduction in the lateral line is maintained during environmental changes of ionic composition is not fully understood. Using lineage labeling, in vivo time lapse imaging and scRNA-seq, we discovered highly motile skin-derived cells that invade mature mechanosensory organs of the zebrafish lateral line and differentiate into Neuromast-associated (Nm) ionocytes. Furthermore, the invasive behavior is adaptive as it is triggered by drastic fluctuations in environmental stimuli. Our findings challenge the notion of an entirely placodally-derived lateral line and identify Nm ionocytes as likely regulators of mechanosensory hair cell function possibly by modulating the ionic microenvironment. The discovery of lateral line ionocytes provides an experimentally accessible in vivo system to study cell invasion and migration, as well as the physiological adaptation of vertebrate organs to changing environmental conditions.

overall_design: Single cell RNA sequecing on FACS sorted cells from the zebrafish line cldnb:EGFP in 5df embryos

first: Julia

last: Peloggia


title: Classical and variant Merkel cell carcinoma cell lines display different degrees of epithelial-mesenchymal transition [mRNA]

city: Essen

first: Jan

last: Gravemeyer

address: Universitätstraße 1

institute: DKZF

summary: variant MCC cell lines show higher expression levels of the EMT-related genes, similar to that of SCC cell lines but opposite to classcial MCC cell lines

overall_design: This study compared the expression of mRNA in variant and classical MCC cell lines. Additionally, miRNA expression of cancer associated genes and differences in DNA methylation were investigated.

first: Jürgen

last: Becker


title: Transcript-specific determinants of pre-mRNA splicing revealed through in vivo kinetic analyses of the 1st and 2nd chemical steps

city: Ithaca

first: Jeffrey

last: Pleiss

address: 453 Biotech

institute: Cornell University

summary: Understanding how the spliceosome processes its composite of substrates through the two chemical steps required for mRNA production will be essential to deciphering splicing regulation and mis-regulation. Here we measure the in vivo rates of these steps across the genome by coupling metabolic RNA labeling, targeted sequencing, and first order kinetic modeling. We reveal a wide variety of rates by which introns are removed, that splice site sequences are primary determinants of first step rates, and that the second step is generally faster than the first. We show that ribosomal protein genes (RPGs) are spliced faster than non-RPGs at each step, and that RPGs share evolutionarily conserved cis-features which facilitate their splicing. A genetic variant defective at the first step shows the expected defect in the first step, but an unexpected change in the second step which suggests how co-transcriptional splicing functions as an important determinant of splicing rates.

overall_design: MPE-seq libraries for ten time points in two conditions in triplicate

last: Gildea

first: Zachary

middle: W

last: Dwyer


title: Classical and variant Merkel cell carcinoma cell lines display different degrees of epithelial-mesenchymal transition [methylation]

summary: variant MCC cell lines show differential methylation for EMT related genes and microRNAs in comparison to classcial MCC cell lines

overall_design: This study compared the DNA methylation patterns variant and classical MCC cell lines. Additionally, mRNA expression of cancer associated genes and microRNA expression were investigated.


title: Formaldehyde-responsive proteins, TtmR and EfgA, reveal a tradeoff between formaldehyde resistance and efficient transition to methylotrophy in Methylorubrum extorquens

city: Saint Paul

first: Jannell

middle: V.

last: Bazurto

state: MINNESOTA

address: 1500 Gortner Ave

department: Plant and Microbial Biology

institute: University of Minnesota

summary: In order for bacteria to thrive, they must be well-adapted to their environmental niche, which may involve specialized metabolism, timely adaptation to shifting environments, and/or the ability to mitigate numerous stressors. These attributes are highly dependent on cellular machinery that can sense both the external and intracellular environment. Methylorubrum extorquens is an extensively studied facultative methylotroph, an organism that can use single-carbon compounds as their sole source of carbon and energy. In methylotrophic metabolism, carbon flows through formaldehyde as a central metabolite; thus, formaldehyde is both an obligate metabolite and a metabolic stressor. Via the one-carbon dissimilation pathway, free formaldehyde is rapidly incorporated by formaldehyde activating enzyme (Fae), which is constitutively expressed at high levels. In the presence of elevated formaldehyde levels, a recently identified formaldehyde-sensing protein, EfgA, induces growth arrest. Herein, we describe TtmR, a formaldehyde-responsive transcription factor that, like EfgA, modulates formaldehyde resistance. It is a member of the MarR family of transcription factors and impacts the expression of 75 genes distributed throughout the genome, many of which are themselves transcription factors and/or involved in stress response, including efgA. Notably, when M. extorquens is adapting its metabolic network during the transition to methylotrophy, efgA and ttmR mutants experience an imbalance in formaldehyde production and a notable growth delay. Although methylotrophy necessitates that M. extorquens maintain a relatively high level of formaldehyde tolerance, this work reveals a tradeoff between formaldehyde resistance and the efficient transition to methylotrophic growth and suggests that TtmR and EfgA play a pivotal role in maintaining this balance.

overall_design: RNASeq analysis of wild-type and ttmR mutant of Methylorubrum extorquens PA1 during growth on methanol.

first: Eric

last: Bruger

first: Jessica

last: Lee

first: Leah

last: Lambert

first: Christopher

last: Marx


title: Single-nucleotide-level mapping of DNA regulatory elements that control fetal hemoglobin expression (gRNA screening)

first: Yong

last: Cheng

overall_design: CRISPR pooled gRNA screening, RNA-seq, ChIP-seq and ATAC-seq were performed

first: Li

first: Yichao

last: Li


title: Ultra-high throughput single-cell RNA sequencing by combinatorial fluidic indexing

city: Vienna

first: Christoph

last: Bock

address: Lazarettgasse 14

country: Austria

institute: CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences

summary: Cell atlas projects and high-throughput perturbation screens require single-cell sequencing at a scale that is challenging with current technology. To enable cost-effective single-cell sequencing for millions of individual cells, we developed “single-cell combinatorial fluidic indexing” (scifi). The scifi-RNA-seq assay combines one-step combinatorial pre-indexing of entire transcriptomes inside permeabilized cells with subsequent single-cell RNA-seq using microfluidics. Pre-indexing allows us to load multiple cells per droplet and bioinformatically demultiplex their individual expression profiles. Thereby, scifi-RNA-seq massively increases the throughput of droplet-based single-cell RNA-seq, and it provides a straightforward way of multiplexing thousands of samples in a single experiment. Compared to multi-round combinatorial indexing, scifi-RNA-seq provides an easier, faster, and more efficient workflow. In contrast to cell hashing methods, which flag and discard droplets containing more than one cell, scifi-RNA-seq resolves and retains individual transcriptomes from overloaded droplets.

overall_design: We benchmarked scifi-RNA-seq on various human and mouse cell lines, validated it for primary human T cells, and applied our method in a highly multiplexed CRISPR screen with single-cell transcriptome readout of T cell receptor activation.

first: Paul

last: Datlinger

first: André

last: Rendeiro

first: Thorina

last: Boenke

first: Martin

last: Senekowitsch

first: Thomas

last: Krausgruber

first: Daniele

last: Barreca


title: Classical and variant Merkel cell carcinoma cell lines display different degrees of epithelial-mesenchymal transition [miRNA]

first: Jan

last: Gravemeyer

summary: variant MCC cell lines show lower expression levels of the EMT-related microRNAs miR-200c-141 and miR-183-96-182 in contrast to classcial MCC cell lines

overall_design: This study compared the expression of microRNAs in variant and classical MCC cell lines. Additionally, mRNA expression of cancer associated genes and differences in DNA methylation were investigated.

first: Jürgen

last: Becker