title: Decreasing Mutant ATXN1 Nuclear Localization Improves a Spectrum of SCA1-Like Phenotypes and Brain Region Transcriptomic Profiles

city: Minneapolis

first: Christine

middle: M.

last: Henzler

address: 117 Pleasant St SE

institute: University of Minnesota, Twin Cities (Minneapolis, MN, US)

summary: Spinocerebellar ataxia type 1 (SCA1) is a dominant trinucleotide repeat neurodegenerative disease characterized by motor dysfunction, cognitive impairment, and premature death. Degeneration of cerebellar Purkinje cells is a frequent and prominent pathological feature of SCA1. We previously showed that transport of ATXN1 to Purkinje cell nuclei is required for pathology, where mutant ATXN1 alters transcription. To examine the role of ATXN1 nuclear localization broadly in SCA1-like disease pathogenesis, CRISPR-Cas9 was used to develop a mouse with an amino acid alteration (K772T) in the nuclear localization sequence of the expanded ATXN1 protein. Characterization of these mice indicates proper nuclear localization of mutant ATXN1 contributes to many disease-like phenotypes including motor dysfunction, cognitive deficits, and premature lethality. RNA sequencing analysis of genes with expression corrected to WT levels in Atxn1175QK772T/2Q mice indicates that transcriptomic aspects of SCA1 pathogenesis differ between the cerebellum, brainstem, cerebral cortex, hippocampus, and striatum.

overall_design: Genetic expression profile comparison (RNA sequencing) of WT, Atxn1175QK772T/2Q, and Atxn1175Q/2Q mouse cerebellum, brainstem, cortex, hippocampus, and striatum at 10 weeks of age and cerebellum, medulla, cortex, hippocampus, and striatum at 26 weeks of age. N=4 mice per genotype at each age.

first: Hillary

last: Handler

first: Harry

middle: T

last: Orr


title: Effect of conditioned media from Aeromonas caviae on the transcriptomic changes of the porcine isolates of Pasteurella multocida

status: Public on Dec 01 2022

city: Bangkok

first: Teerasak

last: E-kobon

address: 50 Ngam Wong Wan Rd, Lad Yao, Chatuchak

department: Department of Genetics

country: Thailand

institute: Kasetsart University

type: Expression profiling by high throughput sequencing

summary: To investigate the interaction between two porcine isolates of P. multocida (PM2 for type D and PM7 for type A) with Aeromonas caviae by co-culturing P. multocida in the conditioned media prepared from A. caviae

overall_design: Comparative gene expression profiling analysis of RNA-seq data for P. multocida (PM2 and PM7) growth in reference and conditioned media

first: Nonzee

last: Hanchanachai

first: Pramote

last: Chumnanpuen


title: CNV analysis of 233 individuals of European ancestry and 6 individuals of non-European ancestry with cleft lip and/or cleft palate

city: Iowa City

first: J.

middle: Robert

last: Manak

state: Iowa

address: 455 Biology Building, 129 East Jefferson Street

department: Biology and Pediatrics

country: USA

institute: The University of Iowa

type: Genome variation profiling by genome tiling array

summary: Cleft lip with or without cleft palate (CL/P) is a common birth defect with a complex, heterogeneous etiology. It is well-established that both common and rare sequence variants contribute to the formation of CL/P, however, the contribution of copy number variants (CNVs) to cleft formation remains relatively understudied. To fill this knowledge gap, we conducted a large-scale comparative analysis of genome-wide CNV profiles of 869 individuals from the Philippines and 233 individuals of European ancestry with CL/P with three primary goals: first, to evaluate whether differences in CNV number, amount of genomic content, or amount of coding genomic content existed within clefting subtypes; second, to assess whether CNVs in our cohort overlapped with known Mendelian clefting loci; and third, to identify unestablished Mendelian clefting genes. Significant differences in CNVs across cleft types or in individuals with non-syndromic versus syndromic clefts were not observed, however, several CNVs in our cohort overlapped with known syndromic and non-syndromic Mendelian clefting loci. Moreover, employing a filtering strategy relying on population genetics data that rare variants are on the whole more deleterious than common variants, we identify several CNV-associated gene losses likely driving non-syndromic clefting phenotypes. By prioritizing genes deleted at a rare frequency across multiple individuals with clefts yet enriched in our case cohort compared to controls, we identify COBLL1, RIC1, and ARHGEF38 as clefting genes. CRISPR/Cas9 mutagenesis of these genes in Xenopus laevis and Danio rerio yielded craniofacial dysmorphologies, including clefts analogous to those seen in human clefting disorders.

overall_design: array-based Comparative Genomic Hybridization (aCGH) of 233 probands of European ancestry and 6 probands of unknown ancestry with cleft lip and/or cleft palate assessed for rare deletions

first: J

middle: R

first: Lisa

middle: A

last: Lansdon


title: Mettl3 regulates late-stage retinogenesis and mouse retina m6A epitranscriptome

status: Public on Dec 02 2022

city: Guangzhou

first: SHUYI

last: CHEN

state: Guangdong

address: 54 S. Xianlie Rd

department: State Key Laboratory of Ophthalmology

country: China

institute: Zhongshan Ophthalmic Center, SYSU

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

overall_design: Refer to individual Series


title: Effect of PPARG modulators on gene expression in HT-1197 cells.

city: Boston

first: Andrew

last: Cherniack

state: Mass

address: 450 Brookline Ave

department: Molecular Oncology

institute: Dana Farber Cancer Institute

summary: To investigate gene expression changes in a bladder cancer cell line with RXRA p.S427F hotspot mutation after 24 hour treatment with PPARG agonist, rosiglitzone, and PPARG inverse-agonists; T0070907, SR10221, and BAY-4931

overall_design: Comparative gene expression profiling analysis of RNA-seq data for HT-1197 cells after 24 hour treatment with PPARG modulators. Samples in biological triplicates.

first: Jonathan

last: Goldstein

middle: D


title: Phase II Clinical and Immune Correlate Study of Adjuvant Nivolumab plus Ipilimumab for High-Risk Resected Melanoma

city: Aurora

first: Ann

last: Strange

state: CO

address: 12801 E. 17th Ave, 8th floor

department: Division of Medical Oncology

institute: CU Anschutz

summary:
Background: Adjuvant therapy for high-risk resected melanoma with PD-1 blockade results in median relapse-free survival (RFS) of 5 years. The addition of low dose ipilimumab (IPI) to a regimen of nivolumab (NIVO) in Checkmate-915, did not result in increased RFS. A pilot phase II adjuvant study of either standard or low dose IPI with NIVO was conducted at two centers to evaluate RFS with correlative studies.
Methods: Patients (pts) with resected stages IIIB/IIIC/IV melanoma received either IPI 3mg/kg and NIVO 1mg/kg (cohort 4) or IPI 1mg/kg and NIVO 3mg/kg (cohorts 5 and 6) induction therapy every three weeks for 12 weeks, followed by maintenance NIVO. Peripheral blood samples at baseline and on-treatment were assessed by flow cytometry for potential biomarkers. Peripheral CD8+ T-cells were assessed by RNA-Seq.
Results: High rates of grade 3-4 adverse events precluded completion of induction therapy in 50%, 35% and 7% of patients in cohorts 4, 5 and 6 respectively. At a median of 63.9 months of follow up, 16/56 pts (29%) relapsed. For all patients, at five-years, RFS was 71% (95% CI: 60, 84), and overall survival was 94% (95% CI: 88, 100). Expansion of CD3+CD4+CD38+CD127-GARP- T-cells, an on-treatment increase in CD39 expression in CD8+ T-cells, and T-cell expression of phosphorylated STAT2 and STAT5 were associated with relapse.
Conclusions: Adjuvant IPI/NIVO at the induction doses used resulted in excellent relapse-free survival, albeit with a high rate of grade 3-4 adverse events. Biomarker analyses highlight an association of ectoenzyme-expressing T-cells and STAT signaling pathways with relapse.

overall_design: Comparative gene expression profiling analysis of CD8+ T-cells RNA-seq data from patient PBMC samples

first: Nikhil

middle: I

last: Khushalani

first: Zeynep

last: Eroglu

first: Youngchul

last: Kim

first: Biwei

last: Cao

first: Judith

last: Goldberg

first: Melinda

last: Vassallo

first: Robert

last: Ferguson

first: Kelsey

last: Monson

first: Tomas

last: Kirchhoff

first: Paulo

last: Burke

first: Emily

last: Monk

first: Carol

last: Amato

first: Geoffrey

last: Gibney

first: Ragini

last: Kudchadkar

first: Joseph

last: Markowitz

middle: S

last: Brohl

first: Anna

last: Pavlick

first: Allison

last: Richards

first: David

last: Woods

first: Jeffrey

last: Weber


title: The expression of apoptosis related genes in HK-2 cells overexpressing PPM1K was determined by RNA-seq analysis

city: Urumqi

first: Li

last: Zhang

address: the First Affiliated Hospital of Xinjiang Medical University, Urumqi,China

institute: Nephrology center of the First Affiliated Hospital of Xinjiang Medical University

summary:
To investigate the role of PPM1K in chronic kidney disease, we overexpressed PPM1K in human kidney-2 cells (HK-2).
We then performed gene expression profiling analysis using data obtained from RNA-seq of 12 different cells.

overall_design: Comparative gene expression profiling of RNA sequence data of human kidney-2 cells (HK-2) overexpressing PPM1K.

first: Wenjun

last: Yang

first: Chen

last: Lu


title: CNV analysis of 869 individuals from the Philippines with cleft lip and/or cleft palate

first: J.

last: Manak

overall_design: array-based Comparative Genomic Hybridization (aCGH) of 869 probands from the Philippines with cleft lip and/or cleft palate assessed for rare deletions

first: J

first: Lisa

last: Lansdon


title: neonatal and adult mouse retina m6A epitranscriptome [meRIP-seq]

first: SHUYI

last: CHEN

type: Methylation profiling by high throughput sequencing

summary: m6A epitranscriptome of  newborn and adult mouse retina was sequenced using MeRIP-seq

overall_design: C57BL/6J mouse retinas were collected into TRIzol, and processed for MeRIP-seq

first: Shuyi

last: Chen


title: GLP is critical for oogenesis exhibiting a G9A-independent role in transcriptional repression

city: Cambridge

first: Felix

last: Krueger

address: Granta Park

department: Bioinformatics

country: United Kingdom

institute: Altos Labs

type: Genome binding/occupancy profiling by high throughput sequencing

summary: GLP (EHMT1) functions as an H3K9me1 and H3K9me2 methyltransferase through its reportedly obligatory dimerization with G9A (EHMT2). Here, we investigated the role of GLP in oocyte and embryo development in comparison to G9A using oocyte-specific conditional knockout mouse models (G9a cKO, Glp cKO, G9a-Glp cDKO). Loss of GLP in oogenesis severely impairs oocyte maturation, fertilization and embryo development, resulting in lethality before embryonic day E12.5. In contrast, loss of G9A has a milder effect with a proportion of embryos producing viable offspring. The Glp cKO also showed loss of G9A protein and, hence, was phenotypically very similar to the G9a-Glp cDKO. H3K9me2 was equally depleted in all cKO genotypes, whereas H3K9me1 was decreased only in Glp cKO and G9a-Glp cDKO oocytes. Furthermore, the transcriptome, DNA methylome and proteome were markedly more affected in G9a-Glp cDKO than G9a cKO oocytes, demonstrating that in the absence of GLP there are widespread epigenetic and gene expression changes in the oocyte independent of H3K9me2. Gene dysregulation with coupled changes in DNA methylation suggest localised loss of chromatin repression, resulting in upregulated protein expression. Together, our findings demonstrate that GLP can function independently of G9A in the oocyte and is required for oocyte developmental competence.

overall_design: low input RNA-seq, BS-seq (PBAT) and H3K9me2 ChIP-seq (ULI-nChIP) of mouse oocytes (100-200 per sample) libraries were prepared. At least 3 samples per genotype. Genotypes used: Control, G9a cKO and G9a-Glp cDKO

first: Hannah

last: Demond

first: Courtney

middle: W

last: Hanna

first: Juan

last: Castillo-Fernandez

first: Fatima

last: Santos

first: Evangelia

middle: K

last: Papachristou

first: Anne

last: Segonds-Pichon

first: Kamal

last: Kishore

first: Clive

last: D'Santos

first: Gavin

last: Kelsey


title: A Role for IFITM3 in Regulating Fibrinogen Endocytosis and Platelet Reactivity in Non-Viral Sepsis

city: Salt Lake City

first: Robert

last: Campbell

state: UT

institute: University of Utah

summary: Platelets and megakaryocytes are critical players in immune responses. Recent reports suggest infection and inflammation alter the megakaryocyte and platelet transcriptome to induce altered platelet reactivity. We examined if non-viral sepsis induces differential platelet gene expression and reactivity. Non-viral sepsis significantly upregulated IFITM3, an interferon responsive gene that restricts viral replication

overall_design: 6 healthy donors and 6 non-viral sepsis patients

first: Matthew

last: Rondina


title: THERMO-SENSITIVE BARREN PANICLE (TAP) is required for rice panicle and spikelet development at high temperature

city: Shanghai

first: Jin

last: Shi

address: 800 Dongchuan Rd

department: Life Science and technology Department

institute: Shanghai Jiaotong University

summary: We then performed gene expression profiling analysis using data obtained from RNA-seq of 2 genotype (tap mutant and wild type) at two time points and two temperatures.

overall_design: Comparative gene expression profiling analysis of RNA-seq data tap mutant and wild type with 2mm and 3mm inflorescence under high temperature and low termperature

first: Peng

last: Zhang

first: Wanqi

last: Liang


title: Myoblast differentiation is associated with and benefits from increased autophagy

city: Blacksburg

first: Honglin

last: Jiang

state: VA

address: Litton Reaves Hall

department: School of Animal Sciences

institute: Virginia Tech

summary: The goal of this study was to identify potentially novel mechanisms that mediate myoblast differentiation using the C2C12 cell as a myoblast model. The study started with an RNA-seq analysis to identify genes differentially expressed during myoblast differentiation. This analysis and subsequent functional analysis resulted in the identification of autophagy as one of the upregulated biological processes in differentiating myoblasts.

overall_design: RNA-seq libraries were prepared from 5 samples of undifferentiated C2C12 cells and 5 samples of differentiating C2C12 cells. RNA-seq libraries were sequenced and sequencing reads mapped and analyzed.


title: Altered expression profile of multiple tissues after immune checkpoint blockade treatment

city: Houston

first: Chunru

last: Lin

state: TX

address: 1515 Holcombe Boulevard

department: Department of Molecular and Cellular Oncology

institute: The University of Texas MD Anderson Cancer Center

summary: We report the expression alteration of kidney, lung, liver, heart, skeletal muscle and tumor with high dosage of immune checkpoint blockade (ICB) or IgG treatment in C57BL/6 mice bearing MC38 tumor. We find several differentially expressed genes after ICB treatment in different tissues as compared with IgG control group.  This study provides a basis for the ICB induced toxicity.

overall_design: Age and sex matched C57BL/6 wild-type mice bearing MC38 tumor were treated with high-dosage of anti-PD1 and anti-CTLA4 antibodies or IgG control. Major organs including kidney, lung, liver, heart and skeletal muscles and tumor tissues were collected and RNA was isolated. The mRNA expression profiling of mice with ICB or IgG treatment were measured using bulk RNAseq.

first: Ying

last: Jing


title: RNA-seq analysis of the mouse brain reveals inflammatory genes associated with early artesunate treatment of experimental cerebral malaria

first: Ziyi

last: Pan

address: NO.12, Airport Road, Baiyun District

institute: Guangzhou University of Chinese Medicine

summary:
Purpose:This study aimed to investigate the transcriptome-wide response of experimental cerebral malaria (ECM) and artesunate treated mice brain on 6 days post-infection.
Methods: C57BL/6 mice were infected with Plasmodium berghei ANKA to construct a murine ECM in MB and AB group. AB group treated with artesunate (30mg/kg), while CB group treated with PBS for 4 days. Mice brain was tested by RNA-seq.
Results: Gene ontology and KEGG pathway analyses of differentially expressed genes (DEGs) were performed. quantitative reverse transcription polymerase chain reaction (qPCR) verify DEGs such as Il6, Il1b, Il10, Tnf, Ifng, Il21, Icam1, which were up-regulated in MB vs. CB, while down-regulated in AB vs. MB.
Conclusions:Our study revealed a transcriptome-wide profile in ECM and artesunate treated mice brain, and help to explore the underlying mechanism, as well as the further development of therapeutic strategies for clinical cerebral malaria.

overall_design: Cerebral mRNA profiles of 6 weeks old mice with ECM and ECM mice treated with artesunate


title: The m6A methyltransferase METTL3 participate in the attenuated effect of BPA on learning and memory in rat

city: Hefei

first: Danyang

last: Li

address: No. 193 Tunxi Road

institute: Hefei university of technology

summary: Bisphenol A (BPA), a widely used endocrine disruptor, has been implicated in cognitive impairment via epigenetic machinery. N6-methyladenosine (m6A) has recently emerged as a new epigenetic factor that negatively influencing cognition, but the role of m6A in BPA induced cognitive deficits has not been explored yet.Here, m6A sequencing in total RNA of neurons after BPA exposure was performed and compare.

overall_design: Primary neurons were cultured and exposed to BPA with 1mM for 48h on DIV 12-14. Total RNA was extracted using RNA isolater Total RNA Extraction Reagent (R401-01, Vazyme, China) according to the manufacturer’s instructions. m6A RNA-Seq service was provided by Cloudseq Biotech Inc. (Shanghai, China).

first: Shu

last: Ai

first: Huili

last: Wang


title: Sustained Activation of Non-canonical NF-kB Signalling Drives Glycolytic Reprogramming in Doxorubicin-resistant DLBCL

city: Singapore

first: chenchen

last: peng

address: 60 Nanyang Dr, Singapore 637551

department: SBS

country: Singapore

institute: NTU

summary: The transcriptomic profiles of two resistant (HT and OCI-LY3) and two sensitive (SUDHL5 and OCI-LY19) DLBCL cell lines before and after doxorubicin treatment were analysed by RNA-seq. To further investigate the molecular basis underlying the development of doxorubicin resistance, acquired doxorubicin-resistant cells (OCI-LY19R) were generated by periodically treating the parental doxorubicin-sensitive OCI-LY19 cells (OCI-LY19S) with increasing doses of doxorubicin over a prolonged period till its IC50 exceeded 200 nM. RNA-seq analysis was then performed using OCI-LY19R and OCI-LY19S cell lines to examine the transcriptomic changes following acquisition of doxorubicin resistance.

overall_design: HT, OCI-LY3, SUDHL5 and OCI-LY19 cell lines with or without 0.2 uM doxorubicin exposure for 24h were harvested for RNA-seq analysis. Parental doxorubicin-sensitive cells (OCI-LY19S) and acquired doxorubicin-resistant cells (OCI-LY19R) were also harvested for RNA-seq analysis. Each sample was obtained from three independent experiments.

first: Chenchen

last: Peng

first: Yinghui


title: Mettl3 regulates late-stage retinogenesis

status: Public on Dec 03 2022

first: SHUYI

last: CHEN

summary: To study the function of Mettl3 during retinal development, we used Six3-Cre and Mettl3floxed mice to conditionally knock out Mettl3 from retinal progenitor cells. The mutant mice show defects in late-stage retinogenesis and structural and physiological homeostasis of the retina.

overall_design: Retinas of postnatal day 7 Six3-Cre+; Mettl3floxed/floxed mice (4 samples), as well as retinas of their littermate control mice (4 samples), were collected into TRIZol, and processed for RNA-seq.

first: Shuyi

last: Chen


title: S63845 resistance mechnism

city: Tampa

first: Jianguo

last: Tao

state: Florida

address: 12902 Magnolia Dr

institute: Moffitt Cancer Center

summary: MCL-1 plays a central role in B-cell lymphoma progression and drug resistance. Pharmacologically targeting MCL-1, therefore, represents an attractive strategy to combat these lymphomas. S63845, a MCL1 inhibitor, was shown to have high response rates in mantle cell lymphoma (MCL) and burkitt lymphoma.

overall_design: RNA sequencing to profile expression in paired parental and S63845 resistant  lymphoma cell lines

first: Xiaohong

last: Zhao

first: Michelle

middle: Y

first: Jing

last: Gao


title: Active DNA demethylation promotes cell fate specification and the DNA damage response

first: Wei

last: Wu

state: Shanghai

address: 320 yueyang road

department: Center for Excellence in Molecular Cell Science

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: Genome-wide analysis of copy number variation in humans with cleft lip and/or cleft palate identifies COBLL1, RIC1, and ARHGEF38 as clefting genes

first: J.

last: Manak


title: Active DNA demethylation promotes cell fate specification and the DNA damage response [SEAL]

institute: Center for Excellence in Molecular Cell Science

summary: Neurons harbor high levels of endogenous single strand DNA breaks (SSBs) that are targeted to neuronal enhancers and correlate with marks of DNA demethylation. To determine the source of SSBs at neuronal enhancers, we depleted the thymidine DNA glycosylase TDG, which excises TET-mediated oxidized methylcytidines 5fC and 5caC, to produce unmodified C. In differentiating neurons, induced degradation of TDG led to the disappearance of SSBs, demonstrating the existence of ongoing TET‑mediated oxidation. Using an independent model of macrophage differentiation from reprogrammed pre-B cells, we demonstrate that TET/TDG-mediated active demethylation may be a general mechanism underlying post-mitotic lineage specification. We find that macrophage differentiation prefers short patch base excision repair (SP-BER) to fill-in single nucleotide gaps, whereas neurons also frequently utilize the long-patch (LP-BER) sub-pathway. By measuring the distribution of SSBs relative to sites of oxidized cytosine, we observed that stretches of 2-30 bases are synthesized distal from the methylated CpG site during repair. Disrupting gap-filling using anti-neoplastic nucleoside analogs resulted in continuous DNA damage/repair events at enhancers each resolving within 1-2 hours, but ultimately triggering neuronal cell death. This DNA damage response and toxicity was dependent on TDG activity. Thus, TET-mediated active DNA demethylation promotes endogenous DNA damage at regulatory elements, a process which normally contributes to cell identity but can also provoke neurotoxicity following anti-cancer treatments.

overall_design: We developed the oxditative end sequencing (oxEND-seq) to detect 5fC/5caC sites in postmotitic neurons and macrophages. Combined with ChIP-seqs, SEAL-seq, END-seq,  S1-END-seq, and RNA-seq, we were able to study the active DNA demethylation and its roles in cell fate determination. Meanwhile, we used anti-neoplastic nucleoside analogs to measure the DNA damage/repair events at enhancers and the relationship with TET/TDG activity.

first: Dongpeng

first: Elsa

last: Callen

first: Raphael

last: Pavani

first: Nicholas

last: Zolnerowitch

first: Srikanth

last: Kodali

first: Dali

last: Zong

first: Nancy

last: Wong

first: Santiago

last: Noriega

first: William

middle: J

last: Nathan

first: Gabriel

last: Matos-Rodrigues

first: Raj

last: Chari

first: Michael

last: Kruhlak

first: Ferenc

last: Livak

last: Ward

first: Keith

last: Caldecott

first: Bruno

last: Di Stefano

first: André

last: Nussenzweig


title: Active DNA demethylation promotes cell fate specification and the DNA damage response [RNA-Seq]

first: Wei

last: Wu

last: Wang


title: Active DNA demethylation promotes cell fate specification and the DNA damage response [END-Seq]

overall_design: We developed the oxditative end sequencing (oxEND-seq) to detect 5fC/5caC sites in postmotitic neuron cells and macrophages. Combined with ChIP-seqs, SEAL-seq, END-seq,  S1-END-seq, and RNA-seq, we were able to study the active DNA demethylation and its roles in cell fate determination. Meanwhile, we used anti-neoplastic nucleoside analogs to measure the DNA damage/repair events at enhancers and the relationship with TET/TDG activity.

first: Dongpeng

last: Callen

last: Pavani


title: Active DNA demethylation promotes cell fate specification and the DNA damage response [PB-Seq]

first: Sarah

middle: E

last: Hill

first: Jacob

last: Paiano

first: Elsa

first: Kenta

last: Shinoda

first: Niek

last: van Wietmarschen

first: Jennifer

middle: M

last: Colón-Mercado

first: Raffaella

last: de Pace

first: Han-Yu

last: Shih

first: Steve

last: Coon

first: Maia

last: Parsadanian

first: Hana

last: Hanzlikova

first: Solji

last: Park

first: Seol

last: Jung

first: Peter

last: McHugh

first: Andres

last: Canela

first: Chongyi

last: Chen

first: Rafael

last: Casellas


title: Arabidopsis histone variant H3.3 establishes a proper chromatin regulatory landscape essential for post-embryonic development [ChIP-Seq]

city: Beijing

first: Zhang

last: Huairen

address: No. 1 West Beichen Road

institute: Institute of Genetics and Developmental Biology, Chinese Academy of Sciences

summary:
The acquisition of germination and post-embryonic developmental ability during seed maturation is vital for seed vigor, an important trait for plant propagation and crop production. How seed vigor is established in seeds is still poorly understood. Here, we report the crucial function of Arabidopsis histone variant H3.3 in chromatin structure regulation that endows seeds with post-embryonic developmental potentials. H3.3 is not essential for seed formation, but the loss of H3.3 results in severely impaired germination and post-embryonic development. H3.3 exhibits a seed-specific 5’ gene end distribution, which facilities chromatin opening in seeds. During germination, this H3.3-established chromatin accessibility is essential for proper gene transcriptional regulation. Moreover, H3.3 is constantly loaded at the 3’ gene end and restricts chromatin accessibility to prevent cryptic transcription and protect gene body DNA methylation. Our results suggest a fundamental role of H3.3 in initiating chromatin opening at regulatory regions in seed to license the embryonic to post-embryonic transition.
Transcriptome, chromatin accessibility, H3.3 and H2A.Z enrichment, and DNA methylation were examined in Col or h3.3ko mutant

overall_design: Danhua,Jiang

first: Huairen

last: Zhang

first: Jingyun

last: Lu


title: Arabidopsis histone variant H3.3 establishes a proper chromatin regulatory landscape essential for post-embryonic development [Bisulfite-seq]

summary: The acquisition of germination and post-embryonic developmental ability during seed maturation is vital for seed vigor, an important trait for plant propagation and crop production. How seed vigor is established in seeds is still poorly understood. Here, we report the crucial function of Arabidopsis histone variant H3.3 in chromatin structure regulation that endows seeds with post-embryonic developmental potentials. H3.3 is not essential for seed formation, but the loss of H3.3 results in severely impaired germination and post-embryonic development. H3.3 exhibits a seed-specific 5’ gene end distribution, which facilities chromatin opening in seeds. During germination, this H3.3-established chromatin accessibility is essential for proper gene transcriptional regulation. Moreover, H3.3 is constantly loaded at the 3’ gene end and restricts chromatin accessibility to prevent cryptic transcription and protect gene body DNA methylation. Our results suggest a fundamental role of H3.3 in initiating chromatin opening at regulatory regions in seed to license the embryonic to post-embryonic transition.

overall_design: Transcriptome, chromatin accessibility, H3.3 and H2A.Z enrichment, and DNA methylation were examined in Col or h3.3ko mutant

first: Danhua

last: Jiang


title: Arabidopsis histone variant H3.3 establishes a proper chromatin regulatory landscape essential for post-embryonic development [RNA-Seq]


title: Arabidopsis histone variant H3.3 establishes a proper chromatin regulatory landscape essential for post-embryonic development [ATAC-seq (h3.3ko)]


title: Active DNA demethylation promotes cell fate specification and the DNA damage response [SAR-Seq]

first: Wei

last: Wu

overall_design: We developed the oxditative end sequencing (oxEND-seq) to detect 5fC/5caC sites in postmotitic neurons and macrophages. Combined with ChIP-seqs, SEAL-seq, END-seq,  S1-END-seq, and RNA-seq, we were able to study the active DNA demethylation and its roles in cell fate determination. Meanwhile, we also applyed anti-neoplastic nucleoside analogs to measure the DNA damage/repair events at enhancers and the relationship with TET/TDG activity.

first: Dongpeng

last: Wang

first: Elsa

last: Callen

first: Raphael

last: Pavani

first: Nicholas

last: Zolnerowitch

first: Srikanth

last: Kodali

first: Dali

last: Zong

first: Nancy

last: Wong

first: Santiago

last: Noriega

first: William

last: Nathan

first: Gabriel

last: Matos-Rodrigues

first: Raj

last: Chari

first: Michael

last: Kruhlak

first: Ferenc

last: Livak

last: Ward

first: Keith

last: Caldecott

first: Bruno

last: Di Stefano

first: André

last: Nussenzweig


title: Transcription elongator SPT6L regulates the occupancies of the SWI2/SNF2 chromatin remodelers SYD/BRM and nucleosomes at transcription start sites in Arabidopsis

first: Chen

last: Chen

address: 723 Xinke Rd.

institute: South China Botanical Garden, Chinese Academy of Science

summary: Chromatin remodelers have been thought to be crucial in creating an accessible chromatin environment before transcription activation. However, it is still unclear how chromatin remodelers recognize and bind to the active regions. In this study, we found that chromatin remodelers SPLAYED (SYD) and BRAHMA (BRM) interact and co-occupy with the Suppressor of Ty6-like (SPT6L), a core subunit of the transcription machinery, at thousands of the transcription start sites (TSS). The association of SYD and BRM to chromatin is dramatically reduced in spt6l and can be Chromatin remodelers have been thought to be crucial in creating an accessible chromatin environment before transcription activation. However, it is still unclear how chromatin remodelers recognize and bind to the active regions. In this study, we found that chromatin remodelers SPLAYED (SYD) and BRAHMA (BRM) interact and co-occupy with Suppressor of Ty6-like (SPT6L), a core subunit of the transcription machinery, at thousands of the transcription start sites (TSS). The association of SYD and BRM to chromatin is dramatically reduced in spt6l and can be restored mainly by SPT6LΔtSH2, which binds to TSS in a RNA polymerase II (Pol II)-independent manner. Furthermore, SPT6L and SYD/BRM are involved in regulating the nucleosome and Pol II occupancy around TSS. The presence of SPT6L is sufficient to restore the association of the chromatin remodeler SYD to chromatin and maintain normal nucleosome occupancy. Our findings suggest that the two chromatin remodelers can form protein complexes with the core subunit of the transcription machinery and regulate nucleosome occupancy in the early transcription stage.

overall_design:
Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for Pol II, SPT6L, SYD, and BRM in Arabidposis.MNase-seq for WT, SPT6L, and SPT6LdetlaSH2
10-day old seedlings were used for ChIP-seq and Mnase-seq assays.

first: Jie

last: Shu

first: Ning

last: Ding

first: Jun

last: Liu

first: Yuhai

last: Cui


title: Arabidopsis histone variant H3.3 establishes a proper chromatin regulatory landscape essential for post-embryonic development [Strand-specific RNA-seq]

first: Zhang

last: Huairen

first: Danhua

last: Jiang

first: Huairen

last: Zhang

first: Jingyun

last: Lu


title: Distinct and opposite effects of leukemogenic Idh and Tet2 mutations in hematopoietic stem and progenitor cells (RNA-Seq)

city: New York

first: Cem

last: Meydan

state: New York

address: 1305 York

department: Physiology & Biophysics

institute: Weill Cornell Medical College

summary: Mutations in IDH1, IDH2, and TET2 are recurrently observed in myeloid neoplasms and may influence prognosis. IDH1 and IDH2 encode isocitrate dehydrogenase isoforms, which normally catalyze the conversion of isocitrate to α-ketoglutarate (α-KG).  Oncogenic IDH1/2 mutations confer neomorphic activity, leading to the production of D-2-hydroxyglutarate (D-2-HG), a potent inhibitor of α-KG-dependent enzymes which include TET methylcytosine dioxygenases. Given their mutual exclusivity in myeloid neoplasms, IDH1, IDH2, and TET2 mutations are thought to converge on a common oncogenic mechanism. Contrary to this expectation, we observed that they have non-overlapping, and even opposite, effects on hematopoietic stem and progenitor cells in genetically engineered mice. Epigenetic and single-cell transcriptomic analyses revealed that Idh2R172K and Tet2 loss-of-function have divergent consequences on the expression and activity of key hematopoietic and leukemogenic regulators. Notably, chromatin accessibility and transcriptional dysregulation in Idh2R172K cells were partially disconnected from DNA methylation alterations. These results highlight unanticipated divergent effects of IDH1/2 and TET2 mutations, providing support for the optimization of genotype-specific therapies in myeloid neoplasms.

overall_design: Lin-cKit+Sca1+ cells from 3-4 month old +/+; Vav-Cre (control), Idh1LSL-R132H/+;Vav-Cre, Idh2LSL-R140Q/+;Vav-Cre, Idh2LSL-R172K/+;Vav-Cre, and Tet2-/- mice were analyzed. For each genotype,  4 pools of 2 mice each (each forming a biological replicate), were analyzed.

first: Jerome

last: Fortin

first: Ming-Feng

last: Chiang

first: Jonathan

last: Foox

first: Parameswaran

last: Ramachandran

first: Ari

last: Melnick

first: Christopher

last: Mason

first: Tak

last: Mak


title: Membrane fraction RNA-seq of active and dormant (ovoid) M. smegmatis

city: Moscow

first: Artem

last: Grigorov

address: Ulitsa Miklukho-Maklaya, 16/10

department: Genomics and Postgenomic Technologies

country: Russia

institute: Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry

summary: A study was conducted to analyse the membrane fraction transcriptome of active and dormant (ovoid) M. smegmatis cells.

overall_design: Comparative gene expression profiling analysis of RNA-seq data from active and dormant (ovoid) M. smegmatis bacterial cultures.

first: Mikhail

last: Zamakhaev

first: Julia

last: Bespyatykh

first: Tatyana

last: Azhikina

first: Anna

last: Goncharenko

last: Shumkov


title: Evaluation of splicing alterations in mice treated with RECTAS.

city: Higashi-Osaka

first: Kei

last: IIDA

state: Osaka

address: Kowakae 3-4-1

country: Japan

institute: Kindai University

summary: Aberrant pre-mRNA splicing events in tumor cells generate tumor-specific splice junctions, translating potential neoantigens. RNA-seq was performed to examine whether a small molecule compound RECTAS affect splice patterns followed by neoantigen repertoire in mouse colon, lung, and liver tissues.

overall_design: C67BL/6N mice of 7-weeks old were per os administered with 100 mg/kg body weight RECTAS in 0.5% carboxymethyl cellurose (CMC) or 0.5% CMC only, twice with 4 h interval. Individual tissue were collected for RNA extraction in total 8 h after the first administration. Extracted RNAs were applied for RNA-Seq.

first: Shingo

last: Matsushima

first: Masahiko

last: Ajiro

last: Iida

first: Kenji

last: Chamoto

first: Tasuku

last: Honjo

first: Masatoshi

last: Hagiwara


title: Gene expression and radiation response of two different types of neuroblastoma cell lines

city: Chicago

first: Matthew

middle: J.

last: Schipma

state: IL

address: 750 N. Lake Shore Drive

department: Biochemistry and Molecular Genetics

institute: Northwestern University

summary: Clonogenic assays were used to establish radiation responses for SK-N-AS, S-type and SK-N-DZ, N-type cell lines; cells were then irradiated at doses that cause 90% cell killing based on clonogenic assay and their RNA was isolated one hour post-irradiation. In addition, cells were transfected with pre-miRNA constructs that led to overexpression of micro-RNAs hsa-miR-34a and hsa-miR-1228. Statistically significant differences were detected for expression of several thousands of genes when the two cell lines were compared with each other. In comparison, radiation led only to minor, less than two-fold gene expression differences. Overexpression of micro-RNAs in either cell line did not change this outcome.

overall_design: Neuroblastoma cell line SK-N-AS was irradiated with 6Gy dose of X-rays 20-24h after transfection, cell line SK-N-DZ was processed the same way but the radiation dose was 4Gy. Gene expression at 1h after radiation was evaluated.

first: Gayle

last: Woloschak

first: Jelena

last: Popovic

first: Carissa

last: Ritner

first: Aushra

last: Abouzeid

first: Tatjana

last: Paunesku


title: Distinct and opposite effects of leukemogenic Idh and Tet2 mutations in hematopoietic stem and progenitor cells (ATAC-Seq)

first: Cem

last: Meydan

first: Jerome

last: Fortin

first: Ming-Feng

last: Chiang

first: Jonathan

last: Foox

first: Parameswaran

last: Ramachandran

first: Ari

last: Melnick

first: Christopher

last: Mason

first: Tak

last: Mak


title: Distinct and opposite effects of leukemogenic Idh and Tet2 mutations in hematopoietic stem and progenitor cells

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

overall_design: Refer to individual Series


title: Arabidopsis histone variant H3.3 establishes a proper chromatin regulatory landscape essential for post-embryonic development [ATAC-seq (h2a.z)]

first: Zhang

last: Huairen

first: Danhua

last: Jiang

first: Huairen

last: Zhang

first: Jingyun

last: Lu


title: 5-Fluorouridine restores functional full-length p53 in TP53 nonsense mutant human tumor cells (RNA-Seq)

city: Utrecht

first: Sebastiaan

last: van Heesch

address: Heidelberglaan 25

country: Netherlands

institute: Princess Maxima Center

summary: The tumor suppressor gene TP53 is mutated in approximately half of all human tumors. Of those, around 10% are nonsense mutations that produce truncated and inactive p53 protein. Induction of translational readthrough is a promising approach for rescuing full-length p53 and thereby eliminate tumor cells with nonsense mutant TP53. To find novel nonsense mutant TP53 readthrough-inducing compounds with a tolerable toxicity profile, we performed an in silico screening of data at the National Cancer Institute database and identified 5-Fluorouracil (5-FU). We show here that 5-FU induces full-length p53 in human tumor cells carrying R213X nonsense mutant TP53 and that this activity is mediated by its metabolite 5-Fluorouridine (FUr). Ribo-seq analysis validated induction of translational readthrough by FUr. We also show that FUr is incorporated into RNA where it potentially allows base pairing of Arg tRNA at the R213X UGA premature termination codon. Full-length p53 rescued by FUr is transcriptionally active and triggers p53-dependent cell death. Moreover, treatment with 5-FU or FUr restores full-length p53 expression in TP53 R213X mutant human tumor xenografts in vivo. Our results suggest that induction of readthrough by 5-FU/FUr could contribute to therapeutic efficacy in patients with TP53 nonsense mutant tumors.

overall_design: mRNA-seq analysis of readthrough in three conditions (Untreated, FUr, G418) in empty vector and R213X vector. Four replicates per group.

first: Mireia

last: Palomar-Siles

first: Angelos

last: Heldin

first: Meiqiongzi

first: Charlotte

last: Strandgren

first: Viktor

last: Yurevych

first: Jip

last: van Dinter

first: Sem

last: Engels

first: Damon

last: Hofman

first: Susanne

last: Öhlin

first: Birthe

last: Meineke

first: Vladimir

middle: N

last: Bykov

first: Klas

middle: G

last: Wiman


title: 5-Fluorouridine restores functional full-length p53 in TP53 nonsense mutant human tumor cells


title: Arabidopsis histone variant H3.3 establishes a proper chromatin regulatory landscape essential for post-embryonic development

first: Zhang


title: Distinct and opposite effects of leukemogenic Idh and Tet2 mutations in hematopoietic stem and progenitor cells (BS-seq)

first: Cem

last: Meydan

first: Jerome

last: Fortin

first: Ming-Feng

last: Chiang

first: Jonathan

last: Foox

first: Parameswaran

last: Ramachandran

first: Ari

last: Melnick

first: Christopher

last: Mason

first: Tak

last: Mak


title: Pharmacological inhibition of the MAPK pathway ameliorates RIT1M90I-driven cardiac tissue hypertrophy.

city: San Francisco

first: Antonio

last: Cuevas-Navarro

state: CA

department: HDFCCC

institute: UCSF

summary: To investigate whether MEK1/2 inhibition attenuates MAPK signaling in RIT1 M90I mice and ameliorates cardiac tissue overgrowth, we treated a cohort of 4-week-old mice harboring a germline Rit1M90I variant with the allosteric MEK1/2 inhibitor trametinib (MEKi).

overall_design: Comparative gene expression profiling analysis of RNA-seq data for heart tissue isolated from Rit1 M90I/+ mice treated with Trametinib (1mg/kg, q.d) or vehicle control for 20 weeks starting at 4 weeks of age.

first: Pau

last: Castel

first: Frank

last: McCormick


title: RNA-seq analysis revealed that lapatinib-induced keratinocyte apoptosis is related to mitochondrial dysfunction and DNA damage

city: Hang Zhou

first: Zhifei

last: Xu

address: 866 Yuhangtang Road

institute: Zhejiang University

summary: Lapatinib, a widely used dual EGFR and ERBB2 inhibitor, have been seriously limited due to skin rash, one of its most common adverse effects caused by EGFR inhibitors in clinical. Here, we found that lapatinib could induce mitochondrial dysfunction, lead to DNA damage and finally cause apoptosis of keratinocytes according to the RNA-sequencing clues. Mechanistically, downregulated expression of DNA repair protein HMGB1 played a critical role in these toxic reaction processes. We found that saikosaponin A could significantly rescue the reduced HMGB1 transcription, which could alleviate lapatinib-induced DNA damage, inhibit keratinocyte apoptosis and further prevent the cutaneous toxicity in mice caused by lapatinib.

overall_design: 3 Control Samples and 3 Lapatinib-treated Samples

first: Qiaojun

last: He


title: SGOL1-AS1 enhances cell survival in Acute Myeloid Leukemia by maintaining pro-inflammatory signaling

city: Aldereley Park

first: Georges

last: Lacaud

address: University of Manchester

institute: Cancer Research UK Manchester Institute

summary: To investigate the effect of SGOL1-AS1 loss on gene expression in THP-1 cells, Cells were transfected with a Non Targeting ASO, or an ASO targeting SGOL1-AS1. RNA was taken at 5 days post transfection

overall_design: RNAseq performed on Nontargeting transfected (n=2) or SGOL1-AS1 targeting transfect (n=2) THP-1 cells

first: Ewan

last: Selkirk


title: Activation of gp130 signaling in T-cells drives TH17-mediated multi-organ autoimmunity [WT vs Stat3c]

city: Berlin

first: Francis

last: Baumgartner

address: Hindenburgdamm 30

country: Germany

institute: Charité University Medicine Berlin

summary:
Purpose: Recently discovered activating Interleukin-6 receptor subunit beta (IL6ST, encoding glycoprotein 130 (gp130)) mutations, as well as germline Signal transducer and activator of transcription 3 (STAT3) gain-of-function mutations are associated with multi-organ autoimmunity, severe morbidity, and adverse prognosis, resulting in an unmet medical need.
Methods: To dissect crucial cellular subsets and disease biology involved in activated gp130 signaling, in this study we constitutively activated the gp130/JAK/STAT3 axis by means of a transgene, L-gp130, specifically targeted to T-cells.
Results: Activating gp130 signaling in vivo resulted in fatal early-onset multi-organ autoimmunity, resembling numerous clinical features of human STAT3 gain-of-function disease. On a cellular level, strong T-cell activation and effector differentiation, accompanied by TH17 expansion and interferon-gamma production was observed. Transcriptome profiling of murine CD4+ and CD8+ T-cells of Lgp and Stat3C mice revealed commonly dysregulated genes and a gene signature that allowed for discrimination between STAT3 gain-of-function patients and healthy controls. In summary, we demonstrate that hyperactive gp130/STAT3 signaling leads to TH17-driven autoimmunity, phenotypically resembling human STAT3 gain-of-function disease.
Conclusions: Hyperactive gp130/STAT3 signaling leads to strong TH17-mediated autoimmunity phenotypically resembling human STAT3 gain-of-function disease and identify TH17-cells as a key cellular subset for initiation and maintenance of autoimmunity

overall_design: Comparing the transcriptome of in vitro differentiated pathogenic Th17 cells from Stat3C loxP-STOP-loxP /flCD4Cre and Stim1fl/flStat3CSTOPfl/flCD4Cre mice

first: U

last: Kaufmann

first: S

last: Feske

first: F

last: Bamopoulos


title: Transcriptional response to bacterial and viral pathogens in patients with acute febrile illness

city: Stanford

first: Stephen

last: Popper

department: Division of Infectious Diseases, Dept. of Medicine

institute: Stanford University

summary: Non-specific clinical presentation and lack of sensitive acute-phase diagnostic reagents hinder early recognitiion and manangement of  systemic infections. To identify pathogen-specific features of the acute host response to infection we examined genome-wide patterns of whole blood gene expression in febrile patients with well-defined bacterial and viral infections (n=49), as well as health controls (n=12)


title: 5-Fluorouridine restores functional full-length p53 in TP53 nonsense mutant human tumor cells (Ribo-Seq)

first: Sebastiaan

last: van Heesch

overall_design: Ribo-seq analysis of readthrough in three conditions (Untreated, FUr, G418) in empty vector and R213X vector. Four replicates per group.

first: Mireia

last: Palomar-Siles

first: Angelos

last: Heldin

first: Meiqiongzi

last: Zhang

first: Charlotte

last: Strandgren

first: Viktor

last: Yurevych

first: Jip

last: van Dinter

first: Sem

last: Engels

first: Damon

last: Hofman

first: Susanne

last: Öhlin

first: Birthe

last: Meineke

first: Vladimir

last: Bykov

first: Klas

last: Wiman


title: Next Generation Sequencing Facilitates Quantitative Analysis of si-nc and si-SRSF11 LOVO Transcriptomes

city: xuzhou

first: Yao-Jie

last: Pan

address: 209 Tong Shan Road, Xuzhou, Jiangsu, P. R. China

institute: xuzhou medical university

summary:
Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare the  difference of mRNA between si-nc and si-SRSF11 in LOVO cell line
Methods: LOVO mRNA profiles of si-nc and si-SRSF11 were generated by deep sequencing, in triplicate, using Illumina Novaseq . The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks. qRT–PCR validation was performed using TaqMan and SYBR Green assays. Sample collection and preparation RNA quantification and qualification 1RNA degradation and contamination was monitored on 1% agarose gels.  2RNA purity was checked using the NanoPhotometer spectrophotometer (IMPLEN, CA, USA) .  3RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA).  Library preparation for Transcriptome sequencing  A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.  Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase(RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 250~300 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 μl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 min followed by 5 min at 95 °C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system. Clustering and sequencing (Genchem Experimental Department)  The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina Novaseq platform and 150 bp paired-end reads were generated.  Data Analysis  Quality control  Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.  Reads mapping to the reference genome  Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.  Novel transcripts prediction  The mapped reads of each sample were assembled by StringTie (v1.3.3b) (Mihaela Pertea.et al. 2015) in a reference-based approach. StringTie uses a novel network flow algorithm as well as an optional de novo assembly step to assemble and quantitate fulllength transcripts representing multiple splice variants for each gene locus.   Quantification of gene expression level  featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is  currently the most commonly used method for estimating gene expression levels.  Differential expression analysis  (For DESeq2 with biological replicates) Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.16.1). DESeq2 provide statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate . Genes with an adjusted P-value <0.05 found by DESeq2 were assigned as differentially expressed.  (For edgeR without biological replicates) Prior to differential gene expression analysis, for each sequenced library, the read counts were adjusted by edgeR program package through one scaling normalized factor. Differential expression analysis of two conditions was performed using the edgeR R package (3.18.1). The P values were adjusted using the Benjamini & Hochberg method. Corrected P-value of 0.05 and absolute foldchange of 2 were set as the threshold for significantly differential expression.   GO and KEGG enrichment analysis of differentially expressed genes  Gene Ontology (GO) enrichment analysis of differentially expressed genes was implemented by the clusterProfiler R package, in which gene length bias wascorrected. GO terms with corrected Pvalue less than 0.05 were considered significantly enriched by differential expressed genes.  KEGG is a database resource for understanding high-level functions and utilities of the biological system, such as the cell, the organism and the ecosystem, from molecular-level information, especially large-scale molecular datasets generated by genome sequencing and other high-through put experimental technologies (http://www.genome.jp/kegg/). We used clusterProfiler R package to test the statistical enrichment of differential expression genes in KEGG pathways.  SNP analysis  GATK2 (v3.7) software was used to perform SNP calling. Raw vcf files were filtered with GATK standard filter method and other parameters (cluster:3; WindowSize:35; QD < 2.0 o; FS > 30.0; DP < 10 and SnpEff software was used to annotation for the Variablesite.  AS analysis  Alternative Splicing is an important mechanism for regulate the expression of genes and the variable of protein. rMATS(3.2.5) software was used to analysis the AS event.  PPI analysis of differentially expressed genes  PPI analysis of differentially expressed genes was based on the STRING database, which known and predicted Protein-Protein Interactions.  Weighted correlation network analysis  WGCNA (Weighted correlation network analysis) is a systematic biological method used to describe the gene association modes among different samples. it can be used to identify gene sets that are highly synergistic changed, and identify candidate biomarkers or therapeutic targets based on the coherence of gene sets and the correlation between gene sets and phenotypes. The R package WGCNA is a set of functions used to calculate various weighted association analysis, which can be used for network construction, gene screening, gene cluster identification, topological feature calculation, data simulation and visualization. WGCNA is suitable for multi- sample data. Generally, more than 15 samples are required. One input file is sample information, that is, a matrix describing the traits of the sample: the traits used for association analysis must be numeric; If it is a regional or categorical variable, it needs to be converted to a 0-1 matrix. The other is gene expression data. For transcriptome sequencing ,FPKM can be used as gene expression data.

overall_design: LOVO cell mRNA profiles after si-nc or si-SRSF11 treatment

first: Dong-Sheng

last: Pei


title: Expression of RIT1 M90I in primary cardiomyocytes

first: Antonio

last: Cuevas-Navarro

summary: To investigate the impact of mutant RIT1 expression in cardiac cells, we isolated neonatal cardiomyocytes from mice harbouring an engineered Rit1 locus with Cre recombinase-inducible expression of the pathogenic variant Rit1M90I. Upon isolation, cardiomyocytes were treated with adenoviruses encoding for Cre recombinase to induce expression of the Rit1M90I variant.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for primary cardiomyocytes expressing WT RIT1 or RIT1 (M90I).

first: Richard

last: Van

first: Pau

last: Castel

first: Frank

last: McCormick


title: MAFB promotes the malignant phenotypes by IGFBP6 in esophageal squamous cell carcinomas

city: beijing

first: shaobo

last: zhang

address: 北京市朝阳区潘家园南里17号

institute: 北京协和医学院

summary: Purpose: Next Generation sequencing (NGS) has revolutionized system-based cellular pathway analysis. The purpose of this study was to conduct RNA-SEQ analysis after knocking down the gene MAFB in human esophageal squamous cell carcinoma cell line KYSE450 to observe the expression changes of the transcriptome genes

overall_design: Retinal mRNA profiles of KYSE450  and MAFB knockdown KYSE450

first: tongyang

last: gong

first: yabing


title: ChrRNA-seq, ATAC-seq and Chrm6A-seq of ESCs and differentiated cardiomyocytes with or without METTL3

city: Hangzhou

first: Yuanhui

last: Mao

state: Zhejiang

address: 1369 West Wenyi Road

summary: Transcriptional programming plays a key role in determining the cell state. Timely reconfiguration of chromatin structure and attenuation of pluripotent genes are required for efficient embryonic stem cell (ESC) differentiation. Here, we identify METTL3, a core N6-methyladenosine (m6A) catalyzing enzyme, as a crucial modulator of dynamic transcription and chromatin accessibility upon ESC-derived cardiac differentiation. Genome-wide analysis of chromatin-associated RNAs revealed that depletion of METTL3 failed to dramatically attenuate the transcription of pluripotent genes, as well as activate nascent cardiomyocyte-specific transcripts upon differentiation. Consistently, ATAC-seq analysis showed that loss of METTL3 markedly attenuated the dynamic alteration of chromatin accessibility at both promoters and gene bodies, resulting in reduced sensitivity of ESC chromatin structure to cardiac differentiation signal. Furthermore, using chromatin-associated m6A sequencing, we found that nuclear m6A underwent a dramatic increase upon differentiation, which correlates with the decrease of chromatin accessibility. Collectively, our findings reveal that METTL3 and nuclear m6A epitranscriptome couples with chromatin state to ensure transcriptional regulation of cell fate transition.

first: Shu-Bing

last: Qian

first: Xiao-Min

last: Liu


title: Intracellular Calcium links Milk Stasis to Lysosome Dependent Cell Death during Early Mammary Gland Involution

city: Seoul

first: Jungmin

last: Choi

state: Seoul

address: 73, Goryeodae-ro, Seongbuk-gu

department: Department of Biomedical Sciences

country: South Korea

institute: Korea University College of Medicine

summary: Involution of the mammary gland after lactation is a dramatic example of coordinated cell death. Weaning results in the distension of the alveolar structures by the accumulation of milk, which, in turn, activates STAT3 and initiates a caspase-independent but lysosome-dependent cell death (LDCD) pathway.  Although the importance of STAT3 and LDCD in early mammary involution is well established, it has not been entirely clear how milk stasis activates STAT3.  In this report, we demonstrate that protein levels of the PMCA2 calcium pump are significantly downregulated within 2-4 hours of experimental milk stasis. Reductions in PMCA2 expression correlate with an increase in cytoplasmic calcium in vivo as measured by multiphoton intravital imaging of GcAMP6f fluorescence. These events occur concomitant with the appearance of nuclear pSTAT3 expression and prior to significant activation of LIF, IL6 and TGFb3 production or LDCD. Interestingly, we observed the activation of TFEB led by activation of TGFb signaling and deactivation of mTOR signaling in the involution of mammary gland. Finally, we demonstrate that increased intracellular calcium activates STAT3 by degrading SOCS3 mediated by TGFb signaling.  In summary, these data suggest that intracellular calcium serves as an important biochemical signal linking milk stasis to STAT3 activation, increased lysosome biogenesis, and lysosome-mediated cell death.

overall_design: mRNA profile in control, high calcium (10mM calcium with ionomycin) and TGFb3 treated MCF10A cells

first: Jaekwang

last: Jeong

first: John

last: Wysolmerski


title: Role of epithelial to mesenchymal transition (EMT) in promoting a trailblazer state

city: Washington

first: Garrett

middle: Thomas

last: Graham

state: DC

address: 3970 Reservoir Rd NW

department: Oncology

institute: Georgetown University Medical Center

summary: We report the role of EMT in promtoing a trailblazer state in C3-TAg tumors. We extracted whole RNA for sequencing from C3-TAg tumors (invasive) and tumor derived noninvasive clonal cell lines. Data was aligned to GRCm38.

overall_design: Examination of RNA-seq of 4 C3-TAg derived tumor organoids and three C3-TAg derived non-invasive cell lines in duplicates

first: Sharon

last: Camacho

first: Apsra

last: Nasir

first: Gray

last: Pearson


title: The amino acid sensor GCN2 controls red blood cell life cycle and iron metabolism through regulation of tissue resident macrophages

first: Soroush

last: Tahmasebi

address: 909 S Wolcott Ave

department: Department of Pharmacology and Regenerative Medicine

institute: University of Illinois at Chicago

summary:
GCN2 (General Control Nonderepressible 2) is a serine/threonine-protein kinase that controls mRNA translation in response to amino acid availability. Here we show that production and clearance of erythrocytes are controlled by GCN2. Our data highlight the importance of tissue-resident macrophages as the primary cell type mediating this effect. During different stress conditions, such as hemolysis, amino acid deficiency or hypoxia, GCN2 knockout (GCN2-/-) mice displayed resistance to anemia as compared to wild-type (GCN2+/+) mice. GCN2-/- liver macrophages display defective erythrophagocytosis and lysosome maturation. Molecular analysis of GCN2-/- cells indicates that the ATF4-NRF2 pathway is a critical downstream mediator of GCN2 in regulating RBC clearance and iron recycling.
We performed NRF2 (Nfe2l2) ChIP-seq experiments in both WT and GCN2 KO MEFs with or without leucine deprivation.

overall_design: WT and GCN2 KO MEFs were cultured in DMEM with or without Leucine for 24h prior to crosslinking and NRF2 ChIPs.

first: Catherine

last: Dufour

first: Eloi

last: Mercier

first: Guillaume

last: Bourque

first: Vincent

last: Giguère


title: Gene expression profile of control and enzalutamide-resistant C4-2 PCa cell line

city: Rochester

first: LIGUO

last: WANG

state: MN

address: 200 1st St SW

department: Division of Computational Biology

institute: Mayo Clinic

summary: We report the expression profile of genes in control and enzalutamide drug-resistant (C4-2-ENZ) C4-2 cells. The C4-2-ENZ cells were treated with enzalutmaide for at least 1 months. C4-2-CON serves as a control. Total RNA was extracted for RNA-seq.

overall_design: 2 replicates of C4-2-CON and C4-2-ENZ were used in each group

first: Huang

last: Haojie

first: Wang

last: Liguo

first: Zhao

last: Yu


title: Fusobacterium nucleatum promotes colorectal carcinogenesis via an m6A dependent pathway

city: Shanghai

first: Haoyan

last: Chen

address: 145 Shandong Road

institute: Renji Hospital

summary: Previous reports have indicated that RNA m6A modification plays an important role in colorectal carcinogenesis. We hypothesized that F. nucleatum promoted colorectal carcinogenesis dependent on RNA m6A alterations. To test this hypothesis, we conducted a RNA-seq analysis in HT29 cells cocultured with F. nucleatum and medium control.

overall_design: RNA-seq was performed in HT29 cells cocultured with F. nucleatum and medium control

first: Gao

last: Yaqi


title: Gene expression of Vero E6 cells with antivirals treatment

city: Shenzhen

first: Yan

address: 1068 Xueyuan Ave

institute: Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences

summary: In addition to directly inhibiting viral proteins, some antiviral drugs inhibit virus replication through regulation of host gene expression. Here we test whether antiviral activity of antivirals is independent of modulating gene expression in infected host cells.

overall_design: Transcriptional profiling was employed to test whether antivirals inhibit viral replication through the modulation of host gene expression in Vero E6 cells.

last: Wang

first: Jinwen

last: Zhang


title: Role of TGFB and EGFR signaling in inducing a trailblazer state

first: Garrett

last: Graham

summary: We report the role of TGFI and EGFR signaling in inducing a trailblazer state in C3-TAg tumor derived organoid line. We extracted whole RNA for sequencing from C3-TAg organoids treated with a combination of growth factors and receptor inhibitor. Data was aligned to GRCm38.

overall_design: Examination of RNA-seq of C3-TAg derived 1339-org line organoids treated with different growth factors and receptor inhibitors (TGFI1, TGFI1+Erlotinib, EGF, EGF+A83-01) in duplicate

middle: T

first: Alec

last: McIntosh


title: Lin-CD34+ cord-blood cells

city: Hamilton

first: Ava

last: Keyvani Chahi

state: ON

address: 1280 Main Street West

country: Canada

institute: McMaster University

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

overall_design: Refer to individual Series


title: RNA-seq of Lin-CD34+ cord-blood cells overexpressing PLAG1-S or firefly Luciferase [OE]

summary: To characterize transcriptional changes associated with gain of the transcription factor PLAG1-S that could contribute to transient ex vivo expansion of human cord-blood (CB) derived HSC we performed RNA-seq of 2 pools of Lin-CD34+ CB cells 72 hours following lentiviral introduction of ectopic PLAG1-S or firefly Luciferase (control).

overall_design: Lin-CD34+ samples from 2 biologically distinct pools of CB were transduced to overexpress PLAG1-S or firefly Luciferase (control), and 72 hours following viral introduction transduction marker positive cells were FACS-isolated for bulk RNA-seq.

last: KeyvaniChahi

first: Muluken

last: Belew

first: Kristin

last: Hope


title: Identification of splice-neoepitopes in mouse cancer cell lines treated with RECTAS

city: Higashi-Osaka

first: Kei

last: IIDA

institute: Kindai University

summary: Aberrant pre-mRNA splicing events in tumor cells generate tumor-specific splice junctions, translating potential neoantigens. RNA-seq was performed to examine whether a small molecule compound RECTAS affected splice patterns followed by neoantigen repertoire in mouse cancer cell lines.

overall_design: Mouse cancer cell lines were treated with RECTAS (10 μM) or 0.1% DMSO. Six hours after treatment, total RNA was extracted from mouse cancer cell lines. Extracted RNAs were applied for RNA-Seq.

first: Shingo

last: Matsushima

first: Masahiko

last: Ajiro

last: Iida

first: Kenji

last: Chamoto

first: Tasuku

last: Honjo

first: Masatoshi

last: Hagiwara


title: Gene expression profiling of tumor-associated macrophages and in-vitro-polarized macrophages

city: London

first: JONATHAN

last: CARON

state: Greater London

address: New Hunt's House, Newcomen St

department: Cancer Studies

institute: KING'S COLLEGE LONDON

summary: The aim of this study was to decipher gene expression of tumor-associated macrophage in the 4T1 mouse model of breast cancer and of in-vitro-polarized macrophages.

overall_design: For in-vitro-polarized macrophages, Ly6C+ monocytes were isolated from splenocytes of 4T1-bearing mice using Miltenyi magnetic beads, seeded in a 6-wells plate at 1 million cells per wells in RPMI 10% FCS, penicillin/streptomycin, 50ng/ml M-CSF and cultured for 72h. M0 basal macrophages were cultured with no extra-cytokine, while we added LPS+IFN for M1, IL4 for M2 and IL6 for M6 (all at 50ng/mL). F4/80+ TAMs were isolated from enzyme-digested 4T1 tumors using Miltenyi magnetic beads, and lysed directly in Ambion's PureLink RNA Mini Kit lysis buffer.

first: J

last: Arnold

last: Caron


title: RNA-seq of Lin-CD34+ cord-blood cells expressing shRNA against PLAG1 or control [KD]

summary: To characterize transcriptional changes associated with loss of the transcription factor PLAG1-S that could contribute to PLAG1 essentiality in long-term human HSC we performed RNA-seq of 2 pools of Lin-CD34+ cord-blood derived hematopoietic stem and progenitor cells 72 hours following lentiviral introduction of shRNA against PLAG1 or non-targeting control.

overall_design: Lin-CD34+ samples from 2 biologically distinct pools of CB were transduced to express shPLAG1 or shControl, and 72 hours following viral introduction transduction marker positive cells were FACS-isolated for bulk RNA-seq.


title: REVEILLE5 buffers the activity of CIRCADIAN CLOCK ASSOCIATED1 to modulate thermoresponsive hypocotyl growth in Arabidopsis [ChIP-seq]

city: hangzhou

first: wei

last: li

address: Yuhangtang Road 866 ,Zijingang Campus, Zhejiang University

institute: zhejiang univeisity

summary: To further understand how RVE5 controls thermo-responses, we generated RVE5-MYC overexpression plants with the CaMV 35S promoter. Using these RVE5-MYC overexpression plants grown at 29°C, we performed Chromatin Immunoprecipitation-Sequencing (ChIP-Seq).

overall_design: 14-day-old seedlings of RVE5-MYC overexpression plants grown at 22°C were treated at 29°C for 12 hours and sampled at ZT 12 hr for ChIP-Seq. ChIP-Seq was performed with an Illumina NovaSeq 6000. 4 samples: 1 input, 3 CHIP_RVE5-MYC.

first: Wei

last: Li

first: Jian

middle: X

last: Liu


title: REVEILLE5 buffers the activity of CIRCADIAN CLOCK ASSOCIATED1 to modulate thermoresponsive hypocotyl growth in Arabidopsis [RNA-seq]

summary: To understand how RVE5 regulates thermomorphogenic gene expression, we carried out an RNA-Seq analysis of WT and rve5-2 T-DNA mutant (GK_225C06) treated at 22°C and 29°C.

overall_design: 12 samples, five-day-old seedlings of WT and rve5-2 grown at 22°C were treated at 22°C or 29°C for 12 hours and sampled with three replicates at ZT 12 hr for RNA-Seq analysis in accordance with the standard Illumina protocol.


title: Chk1 inhiitors decrease the expressions of STAT3 downstream target genes in multiple myeloma cells

city: Richmond

first: Liang

last: Zhou

state: Virginia

address: 401 college street

department: Internal Medicine

institute: Virginia Commonwealth University

summary:
Study #1: U266 cells were treated with 100 nM PF477736 for 4 hr.
Study #2: U266 cells were treated with 100 nM PF477736 for 16 hr.
Study #3: KAS/6-1 cells were treated with 50 nM PF477736 or 300 nM CEP3891 for 2 hr.

overall_design: RT-PCR profiling of multiple myeloma cells

first: Kanika

last: Sharma

first: Yu

last: Zhang


title: AUTS2 forms a novel complex to recruit CUL4 E3 for BMP inhibition and neural differnetiation

city: Hershey

first: Zhonghua

last: Gao

state: PA

address: 500 University Drive

department: Department of Biochemistry and Molecular Biology

institute: Penn State University College of Medicine

summary: Neurodevelopmental disorders (NDD) present a great challenge for medicine due to their complicated etiology and diverse genetic lesions. Although many risk genes have been identified, we know little about their mechanistic impact on NDD pathogenesis, including that of a prominent risk factor, Autism Susceptibility Candidate 2 (AUTS2). Disruptions of AUTS2 have been frequently observed in NDD patients, but it remains unclear how AUTS2 controls the neurodevelopmental program. Our studies investigated the role of AUTS2 in neuronal differentiation and discovered that AUTS2, together with WDR68 and SKI, form a novel protein complex (AWS) specifically in neuronal progenitors and promotes neuronal differentiation through inhibiting BMP signaling. Genomic and biochemical analyses demonstrated that the AWS complex achieves this effect through the recruitment of the CUL4 E3 ubiquitin ligase complex to mediate poly-ubiquitination and subsequent proteasomal degradation of phosphorylated SMAD1/5/9. Using primary cortical neurons from Auts2 deficient mice, we also observed aberrant BMP signaling and dysregulated expression of neuronal genes, indicating that the AWS-CUL4-BMP axis plays a role in regulating neuronal lineage specification in vivo. Our findings uncover a sophisticated cellular signaling network, mobilized by a prominent NDD risk factor, presenting multiple potential therapeutic targets for NDD.

overall_design: Examination of the function of Auts2 in neuronal differentiation using WT and Auts2-/- mESC and the identification of the importance of Auts2-Ski-Wdr68 complex in differentiation.

first: Zhuangzhuang

last: Geng


title: HNF4a acts as upstream functional regulator of intestinal Wnt3 and Paneth cell fate [RNA-seq]

city: Sherbrooke

first: Francois

last: Boudreau

state: QC

address: 3201 Jean-Mignault

department: Immunology and Cell Biology

institute: Université de Sherbrooke

summary: Maturation of Paneth cells depends on canonical Wnt signaling, but few transcriptional regulators have been identified to this end. We showed that HNF4a plays a non-redundant and crucial role in supporting the growth and survival of small intestinal epithelial cultures when cultured ex vivo as organoids. Transcriptomic analyses revealed an autosomal function of HNF4a in Wnt3 transcriptional regulation and Paneth cell differentiation. We showed that Wnt3a supplementation reversed cell death and transcriptional changes caused by the deletion of Hnf4a in jejunal organoids.

overall_design: mRNA profiles of DMSO-treated (Control) and 4OHT-treated (Hnf4a-depleted) jejunal organoids at day 2 and 4 (4 replicates/condition)

first: Christine

last: Jones

first: Mariano

last: Avino


title: Sequencing 5-formyluracil in genome DNA at single-base resolution

city: wuhan

last: yang

address: No.299 Bayi Road

institute: wuhan university

summary: Albeit with low content, in genome DNA, the 5-formyluracil has been an important modification. The 5-formyluracil was found to be widely distributed amongst living bodies (prokaryotes and mammalian cells). Capable of binding to proteins to prevent the gene expressions, the 5-formyluracil could also induce mismatch in the DNA. In certain cancerous tissues, the content of 5-formyluracil was found to be higher than the normal tissues adjacent to the tumor. Nonetheless, the lack of a higher resolution mapping technique, has been hampering the studies of 5-formyluracil. Hence, we adopted the single-base resolution analysis method to profile 5-formyluracil at the genome scale. We analyzed the distribution of 5-formyluracil in the genome. This technique enabled us to have a better understanding of 5-formyluracil.

overall_design: The Azi-BIAN not only selectively labelled and enriched the 5-formyluracil in the genome DNA, rather also influenced the electro-density. Our results established that the azi-BIAN labelled 5-formyluracil could mismatch with guanine under pH 8.8 and match with adenine under pH 7.2, without any interference of the other canonical nucleobases.  We used azi-BIAN to enrich the 5-formyluracil in the genome DNA of  the human thyroid carcinoma cells. In the preperation of library, we used two different pH. In pH 7.2, the 5-formyluracil sites was read as thymine (e.g., Cal62_output_nonmismatch1 and Cal62_output_nonmismatch2), and the 5-formyluracil sites was read as cytosine (e.g., Cal62_output_mismatch1 and Cal62_output_mismatch2) in pH 8.8. By comparison the inputs (e.g., Cal62_input1 and Cal62_input2) and outputs (e.g., Cal62_output_nonmismatch1, Cal62_output_nonmismatch2, Cal62_output_mismatch1 and Cal62_output_mismatch2), we got the the 5-formyluracil peaks in the human thyroid carcinoma cells. Therefore, in the 5-formyluracil peaks, we got the 5-formyluracil sites by comparison the mutations in two libraries in the human thyroid carcinoma cells.

first: W

last: Yang

first: S

last: Han

first: X

first: Y

last: Wang


title: circRNA expression and characterization in multiple sclerosis patients and controls

city: Pieve Emanuele

first: Elvezia

middle: Maria

last: Paraboschi

address: via Rita Levi Montalcini 4

country: Italy

institute: Humanitas University

type: Non-coding RNA profiling by high throughput sequencing

summary: Circular RNAs (circRNAs) are a class of non-coding RNAs increasingly emerging as crucial actors in the pathogenesis and progression of human diseases, including autoimmune and neurological disorders as multiple sclerosis (MS). We performed RNA-seq experiments on circRNA-enriched samples, derived from peripheral blood mononuclear cells of 10 MS patients and 10 matched controls. We detected 5,663 circRNAs, and expression analysis revealed 166 differentially expressed circRNAs in MS patients.

overall_design: circularRNA profile from 10 MS patients and 10 controls in peripheral blood mononuclear cells

first: Giulia

last: Cardamone

last: Soldà

first: Stefano

last: Duga

first: Rosanna

last: Asselta


title: miRNA profiling of mouse motor neuron during development

city: Hsinchu

first: Joye

last: Li

address: 1001 University Road

country: Taiwan

institute: National Chiao Tung University

summary: We profiled miRNAs from embryonic stem cells to motor neurons derived via RA (retinoic acid) and distinguished different developmental stages by days. Those developmental stages are ESC, Day2, Day3, Day4, and both motor neuron and interneuron with day7. We also provide the fractionated nuclear and cytoplasm miRNA profiling with motor neuron and interneuron respectivey.

overall_design: MiRNA profiling from total RNAs extracted from mouse motor neuron and interneuron during development. The reference BioProject accession is PRJNA615782 with 17 sequence data (SRAs).

first: Jun-An

last: Chen

first: Jui-Hung

last: Hung


title: profiling of histone modifications in SARS-CoV-2 infected cells

city: Philadelphia

first: Karl

middle: Michael

last: Glastad

address: 3400 Civic Center Blvd, Bldg 421

department: CDB

institute: University of Pennsylvania

summary:
Purpose: The goal of this study is to understand the response and pathology of the epigenome upon infection with SARS-CoV-2 in lung and heart tissues
Methods: AT2 and induced cardiomyocytes were infected (MOI 4) with SARS-CoV-2 or Mock infection control for 48 hours followed by chromatin immunoprecipitation and sequencing.
Results: global differences in hPTMs were observed upon infection related to SARS-CoV-2 histone mimicry
Conclusions: SARS-CoV-2 sucks

overall_design: ChIP-seq profiling of hPTMs in AT2 and iCM cells upon infection

first: Shelley

last: Berger


title: Role of TGFi1 in epithelial to mesenchymal transition (EMT)

first: Garrett

last: Graham

summary: We report the role of TGFi1 in promoting EMT in C3-TAg tumor derived organoid line. We extracted whole RNA for sequencing from C3-TAg derived org-line organoids treated with TGFi1 for different time points. Data was aligned to GRCm38.

overall_design: Examination of RNA-seq of C3-TAg derived 1339-org line organoids treated with TGFi1 for 0 (Control), 2 , 7 and 22 days in duplicate

first: Sharon

last: Camacho

first: Apsra

last: Nasir

first: Alec

last: McIntosh

first: Gray

last: Pearson


title: Transcriptional profile of bone marrow-derived macrophages from Cd28 KO mice

city: Madrid

first: Miguel

middle: A

last: Vega

address: Ramiro de Maeztu 9

country: Spain

institute: CIB (CSIC)

summary: Analysis of the transcriptome of bone marrow-derived macrophages from Cd28 KO mice.   Methods:  C57BL/6J (WT) and Cd28 KO (B6.129S2-Cd28tm1Mak/J) mice were used. Bone marrow-derived macrophages were obtained by flushing the femurs of 6- to 10-wk-old C57BL/6, and Cd28 KO mice, and culturing cells during 7 days in DMEM supplemented with 10% FCS and 50 mM 2-ME, containing human M-CSF (25 ng/ml), with cytokine addition every 2 days.

overall_design: mRNA profiles of bone marrow-derived macrophages from Cd28 KO and wild type

first: Amaya

last: Puig Kroger

first: José

last: Rojo

first: Angel

middle: L

last: Corbí


title: Single-cell RNA-seq of the tendon enthesis cells

city: New York

first: Fei

last: Fang

address: 650 W 168th Street, Blacking Building 1408

department: Orthopedic Surgery

institute: Columbia University

summary: Our studies used scRNA-seq analysis to get a full map of transcriptional profiles of enthesis cells and also a seprate Gli1-lineage enthesis stem cells. By harvesting enthesis cells from different development stages for scRNA-seq analysis, we revealed enthesis cell heterogeneity and identified six cell sub-populations using scRNA-seq. We infered cell differentiation trajectories for enthesis stem cells differentiating into mineralizing chondrocytes. A gene regulatory network analysis combined fluorescent in situ hybridization were then used to identify a number of transcription factors coordinating tenogenesis, chondrogenesis, and osteogenesis to form an enthesis with spatially graded mineralization.To further define the enthesis stem cell population, enthesis Gli1-lineage cells were isolated and their transcriptomes were characterized at single cell resolution. These specific Gli1-responsive cells had a linear trajectory and a capacity of chondrogenesis and osteogenesis. The full characterization of transcriptional landscape of tendon enthesis stem cells demonstrates a promising therapeutic strategies using this cell source for enthesis regeneration.

overall_design: mRNA profiles of of tendon enthesis at P11, P18, and P56 old wild type (WT); mRNA profiles of Gli1-lineage cells at P7, P11, P14, P18, P21, P28, and P42

first: Stavros

last: Thomopoulos


title: REVEILLE5 buffers the activity of CIRCADIAN CLOCK ASSOCIATED1 to modulate thermoresponsive hypocotyl growth in Arabidopsis

first: wei

last: li

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

overall_design: Refer to individual Series


title: Drug screening in Drosophila for repurposing in neuropsychiatry

city: New Delhi

first: Manoj

middle: Ramesh

last: Teltumbade

state: Delhi

address: Mathura Road, Near Sukhdev Vihar, bus depo

country: India

institute: Institute of Genomics and Integrative Biology

summary:
The study analyses the effect of multiple drugs on transcriptomic profile of Drosophila melanogaster.
At the end of treatment, the head tissues were collected and homogenized in trizol for RNA extraction. The transcriptomic profiling was done using Affymetrix Drosophila Genome 2.0 array.

overall_design: 3-4 days old adult unmated male flies were treated with single or combination of drug for one week. The total RNA was isolated from adult head part.

first: Abhay

last: Sharma


title: CUT&RUN of PLAG1-S global chromatin occupancy in Lin-CD34+ cord-blood cells [Cut & Run]

first: Ava

last: Keyvani Chahi

summary: To characterize genome-wide chromatin occupancy of the transcription factor PLAG1-S that could contribute to transient ex vivo expansion of human cord-blood (CB) derived HSC we performed CUT&RUN. 3 pools of Lin-CD34+ CB cells transduced to overexpress 3xFLAG-PLAG1-S were used for anti-FLAG or anti-IgG control enrichment of specific PLAG1-S DNA binding sites.

overall_design: Lin-CD34+ samples from 3 biologically distinct pools of CB were transduced to overexpress PLAG1-S, and 72 hours following viral introduction transduction marker positive cells were FACS-isolated for CUT&RUN and high-throughput sequencing.

last: KeyvaniChahi

first: Gabriela

last: Krivdova

first: Sajid

last: Marhon

first: Daniel

middle: D

last: DeCarvalho

first: Kristin

last: Hope


title: Muscle injury prepares stem cells for terminal myocyte differentiation through changes in gene expression and long-term changes in DNA methylation

city: Jerusalem

first: Tal

last: Michaeli

address: Ein Kerem Campus

country: Israel

institute: The Hebrew University


title: Targeted RNA-Seq analysis of the gene expression changes in the livers of female mice treated with the perfluorinated alkyl substance PFESA-BP2 (Nafion byproduct 2)

city: Research Triangle Park

first: Christopher

last: Corton

state: NC

address: 109 TW Alexander Dr.

institute: US-EPA

summary: The perfluorinated alkyl substance PFESA-BP2 (1,1,2,2-tetrafluoro-2-[1,1,1,2,3,3-hexafluoro-3-(1,1,2,2-tetrafluoroethoxy)propan-2-yl]oxyethane-1-sulfonic acid; also known as nafion BP2) has been detected in the blood of people living in the North Carolina Cape Fear River basin downstream of an industrial manufacturing facility. Given that almost nothing is known about the potential toxicity of PFESA-BP2 and safe exposure levels have not yet been determined, we performed a benchmark dose analysis of phenotypic and genomic effects. Female mice were exposed to PFESA-BP2 at 0, 0.03, 0.3, 3, and 6 mg/kg-day each day for 7 days by oral gavage. Transcript profiling showed that PFESA-BP2 activates a number of transcription factors linked to liver toxicity including constitutive activated/androstane receptor, pregnane X receptor, and Nrf2, but unlike other long-chain PFAS, there was only weak activation of peroxisome proliferator-activated receptor α. Steatosis was coincident with activation of sterol response element binding proteins as well as increases in the expression of the very low density lipoprotein receptor.

overall_design: Balb-C female mice at 10-12 weeks of age were dosed by gavage for 7 consecutive days using 20-gauge stainless steel feeding needles. Doses of 0, 0.03, 0.3, 3.0, and 6.0 mg/kg-day were administered once daily in the afternoon. Control animals were administered an equal volume of deionized water. Four biological replicates consisting of individual animals were included in each dose group. RNA was isolated from liver tissues and gene expression was determined using Illumina NexSeq 500 system.

first: J

middle: C


title: Elevated Extra-cellular Matrix Signaling in Adipose Mesothelial Cells is Linked to Insulin Resistance in Obesity

city: Dallas

first: Olga

last: Gupta

state: TX

address: 5323 Harry Hines Blvd

institute: UTSW

summary:
Visceral adipose tissue fibrosis is linked to metabolic dysfunction in obesity;  however, critical cell types that trigger and contribute to fibrosis in this depot are not completely understood.
Whether adipose mesothelial cells (AMCs) play a role in pathologic obesity has been unclear.

overall_design: Whole-genome expression profiling was conducted on AMCs isolated from a cohort of patients with varying degrees of metabolic disease undergoing bariatric surgery.  Computational analysis of gene expression profiles was used to identify differentially expressed gene and gene signatures.


title: RNA-Seq data of tumors and paired adjacent tissues from 15 HCC patients

city: Shanghai

first: Xi

last: Chen

address: 8th Panshan Road

institute: Second Military Medical University

summary: Hepatitis B virus (HBV) mutations promote the occurrence of hepatocellular carcinoma (HCC). However, their association with postoperative prognosis remains obscure. Here, we aimed to characterize the evolution of HBV in different sources and identify viral mutation pattern that facilitates postoperative prognosis of HCC.

overall_design: RNA-seq of matched adjacent normal and tumor samples from HCC patients

first: Jianhua

last: Yin

first: Guangwen

last: Cao


title: Identification of Bacillus anthracis genes differentially expressed in human serum

city: Chicago

first: Hyunwoo

last: Lee

address: 900 S. Ashland Ave., MBRB #3020

department: Center for Biomolecular Sciences

institute: University of Illinois at Chicago

summary: Bacillus anthracis causes anthrax infections in mammals. Large-scale mortality resulting from the intentional release of B. anthracis spores represents a potential bioterrorism threat. Inhalational anthrax almost invariably proceeds to fatal systemic infection, characterized by massive bacteremia. A better understanding of host-pathogen interactions is urgently needed for effective treatment of this lethal disease. However, virulence mechanisms used by B. anthracis to survive and multiply in human blood are not completely understood. Identification of genes that are differentially expressed during the growth of B. anthracis in human serum can elucidate how this pathogen successfully colonizes the bloodstream. We compared the transcriptional profile of B. anthracis growing in heat-inactivated human serum to that in LB medium. Genes involved in the biosynthesis of purines, certain amino acids and riboflavin and lipid metabolism, genes encoding ABC transporters, respiratory enzymes and several genes with hypothetical function were identified as being upregulated during growth in serum.

overall_design: Direct comparison of experimental (human serum) RNA samples to control (LB) RNA samples in a two-color hybridization. Four independent experimental samples were compared against four indepdent control samples with dye-swapping.

first: Shalaka

last: Samant


title: Transfection experiment with the plasmid containing pri-mir-124 in HEK293 cells

first: Haiyang

last: Hu

address: 320 Yueyang Road

institute: PICB

summary: The microRNAome is comprised of annotated canonical miRNAs (anomiR) and a variety of recently identified microRNA isoforms (isomiR). While anomiR is well-studied in the last two decades, the functionality of most isomiRs is largely illusive. Here, we conducted both computional and experimental assays to estimate the functionality of isomiRs expressed in brains.

overall_design: Total RNA after transfecting with the plasmid containing pri-mir-124  and empty plasmid  were isolated and sequenced by deep sequencing using Illumina HiSeq 4000

last: HU

first: Juanjuan

last: Zhu

first: Mingju

last: Lyu


title: Isolated of dermal papilla cells from follicular unit extraction

city: Guangzhou

first: Yuxin

address: Nanfang Dadao Street, Baiyun district

institute: Nanfang Hospital of Southern Medical University

summary: Hair follicles were originally obtained in the form of intact hair follicles from human scalp during microscopic hair transplant procedures of Follicular Unit Extraction (FUE). Dermal papilla cells were freshly isolated or traditionally isolated and cultured in basic medium supplied with 10% FBS. Freshly-isolated DPCs and cultured DPCs were sequenced using third generations of sequencing.

overall_design: DPCs were isolated from human dermal papilla and cultured.Total RNAs of DPC-fresh, DPC-P0 and DPC-P3 were extracted and used for mRNA sequencing.

first: Lijuan

last: Du

first: Junfei

last: Huang


title: Targeted RNA-Seq analysis of the gene expression changes in the livers of male and female mice treated with the perfluorinated alkyl substance PFESA-BP2 (Nafion byproduct 2)


title: cDC1 derived IL27 regulates the transcriptional profile of SI-LP Th subsets

status: Public on Nov 30 2022

city: Lyngby

first: Fredrik

last: Junghus

address: DTU Building 202

department: Experimental and Translational Immunology

country: Denmark

institute: Technical University of Denmark

summary: To assess the broader impact of cDC1 derived IL-27 on the properties of SI-LP CD4+ T cells, these cells were sorted from Xcr1-cre.p28fl/fl mice and p28fl/fl controls (4 mice/group) and subjected to single cell RNA sequencing (scRNA-seq).

overall_design: Single cell RNA sequencing of CD4 T cells isolated from mouse small-instestine lamina propria, in p28fl/fl controls (wild-type) and Xcr1-cre.p28fl/f mice

first: Fatemeh

last: Ahmadi

first: Christian

last: Ashworth

first: Amanda

last: Lappalainen

first: Urs

last: Mörbe

first: Knut

last: Kotarsky

first: William

middle: W

last: Agace


title: Targeted RNA-Seq analysis of the livers of male mice treated with the perfluorinated alkyl substance PFESA-BP2 (Nafion byproduct 2)

first: Christopher

last: Corton

summary: The perfluorinated alkyl substance PFESA-BP2 (1,1,2,2-tetrafluoro-2-[1,1,1,2,3,3-hexafluoro-3-(1,1,2,2-tetrafluoroethoxy)propan-2-yl]oxyethane-1-sulfonic acid; also known as nafion BP2) has been detected in the blood of people living in the North Carolina Cape Fear River basin downstream of an industrial manufacturing facility. Given that almost nothing is known about the potential toxicity of PFESA-BP2 and safe exposure levels have not yet been determined, we performed a benchmark dose analysis of phenotypic and genomic effects. Male mice were exposed to PFESA-BP2 at 0, 0.03, 0.3, 3, and 6 mg/kg-day each day for 7 days by oral gavage. Transcript profiling showed that PFESA-BP2 activates a number of transcription factors linked to liver toxicity including constitutive activated/androstane receptor, pregnane X receptor, and Nrf2, but unlike other long-chain PFAS, there was only weak activation of peroxisome proliferator-activated receptor α. Steatosis was coincident with activation of sterol response element binding proteins as well as increases in the expression of the very low density lipoprotein receptor.

overall_design: Balb-C male mice at 10-12 weeks of age were dosed by gavage for 7 consecutive days using 20-gauge stainless steel feeding needles. Doses of 0, 0.03, 0.3, 3.0, and 6.0 mg/kg-day were administered once daily in the afternoon. Control animals were administered an equal volume of deionized water. Four biological replicates consisting of individual animals were included in each dose group. RNA was isolated and gene expression was determined using the mouse TempO-Seq targeted RNA-Seq platform (BioSpyder, Inc; Carlsbad CA).

first: J


title: RNA surveillance controls 3D genome structure via stable cohesin chromosome interaction

city: Daejeon

first: Yoonjung

last: Choi

address: 291 Daehak-ro, Yuseong-gu

institute: KAIST

summary: The 3D architecture that the genome is folded into is regulated by CTCF, which determines domain borders, and cohesin, which generates interactions within domains. However, organisms lacking CTCF have been reported to still have cohesin-mediated 3D structures with strong borders. How this can be achieved and precisely regulated are yet unknown. Using in situ Hi-C, we found that 3’-end RNA processing factors coupled with proper transcription termination are a cis-acting determinant that regulates the localization and dynamics of cohesin on the chromosome arms. Loss of RNA processing factors, including nuclear exosome and Pfs2, destabilizes cohesin from the 3'-ends of convergent genes and results in decreased cohesin-mediated domain boundaries. We observed the co-localization between Rad21 and a wide range of 3'end RNA processing/termination factors. Further, deletion of Rrp6 leads to cohesin redistribution to facultative heterochromatin, resulting in improper domain boundaries. Importantly, we observed that knockdown of Rrp6Exosc10 caused a defect in cohesin binding and loss of local topologically associating domains (TADs) interactions in mouse embryonic stem cells. Based on these findings, we propose a novel function of the RNA surveillance pathway in 3D genome organization via cohesin complex, which provides the molecular basis underlying the dynamics of cohesin function.

sample_organism:
Schizosaccharomyces pombe
Saccharomyces cerevisiae

overall_design:
For ChIP-seq experiment (S. pombe): Genome-wide distributions of Rad21, Psc3, Rrp6 and RNAPII ser2p in wild-type and S. pombe exosome mutants.
For RNA-seq experiment: Strand-specific mRNA-Seq of wild type and S. pombe exosome mutants.

first: Yujin

last: Chun

first: Taemook

last: Kim

first: Sungwook

last: Han

first: Daeyoup


title: Raw RNA-seq data of small intestine tissue from control and Lats1/2 knock out mice

city: Worcester

first: Junhao

last: Mao

state: MA

address: 55 N Lake Ave

department: MCCB

institute: UMass Medical School

overall_design: At day 8 postnatal , control (Lats1/2f/f without Cre)  and VilCre;Lats1/2 knock out mice were sacrifieced and small intestien tissue was colletct to extract the total RNA for RNA-seq

first: Lihua

first: Qi

last: Li

first: Rui


title: Impact of ATP-citrate lyase catalytic activity and serine 455 phosphorylation on histone acetylation and inflammatory responses in human monocytic cells

city: Frankfurt

first: Dmitry

last: Namgaladze

address: Theodor Stern Kai 7

institute: Goethe University Frankfurt

summary: ATP-citrate lyase (ACLY) is a key enzyme provoking metabolic and epigenetic gene regulation. Molecularly, these functions are exerted by the provision of acetyl-coenzyme A, which is then used as a substrate for de novo lipogenesis or as an acetyl-group donor in acetylation reactions. It has been demonstrated that ACLY activity can be positively regulated via phosphorylation at serine 455 by Akt and protein kinase A. Nonetheless, the impact of phosphorylation on ACLY function in human myeloid cells is poorly understood. In this study we reconstituted ACLY knockout human monocytic THP-1 cells with a wild type ACLY as well as catalytically inactive H760A, and phosphorylation-deficient S455A mutants. Using these cell lines, we determined the impact of ACLY activity and phosphorylation on histone acetylation and pro-inflammatory gene expression in response to lipopolysaccharide (LPS). Our results show that ACLY serine 455 phosphorylation does not influence the proper enzymatic function of ACLY, since both, wild type ACLY and phosphorylation-deficient mutant, exhibited increased cell growth and histone acetylation as compared to cells with a loss of ACLY activity. Transcriptome analysis revealed enhanced expression of pro-inflammatory and interferon response genes in ACLY knockout and H760A THP-1 cells under unstimulated or LPS-treated conditions. At the same time, S455A ACLY-expressing cells showed a phenotype very similar to wild type cells. Contrary to ACLY knockout, pharmacological inhibition of ACLY in THP-1 cells or in primary human macrophages does not enhance LPS-triggered pro-inflammatory gene expression. Our data thus suggest that ACLY retains functionality in the absence of Akt/PKA-mediated phosphorylation in human myeloid cells. Furthermore, loss of ACLY activity may elicit long-term adaptive mechanisms, increasing inflammatory responses.

overall_design: RNA-Seq of human THP-1 cell lines with a knockout of ATP citrate lyase (ACLY) reconstituted with a wild type, H760A or S455A mutant ACLY under control or lipopolysaccharide-stimulated (100 ng/ml, 3h) conditions (n=4).

first: Monica

last: Dominguez


title: Histone-acetyl Epigenome Regulates TGF-β Pathway-associated Chemoresistance

first: Haoyan

last: Chen

state: Shanghai

address: 145 Shandong Road

institute: Renji Hospital

summary: Chip-seq analysis was performed to probe the epigenome related to TGF-β signaling pathway in  colorectal cancer

overall_design: Chip-seq was performed on SW480  colorectal cancer cells

first: Xianlong

last: Tian