title: Epigenetic methylation chip analysis of childhood PFA ependymoma patient samples [EPIC Methylation]

summary: DNA methylation analysis was perfomed using Infinium EPIC Methylation BeadChip platform on 65 PFA ependymoma patient samples. Resulting .idat files were then uploaded to the molecularneuropathology.org classifier to obtain molecular subgroup and copy number variance. Idat files were batch normalized and background corrected using default settings of the R package ChAMP to obtain GpG methylation beta values for analysis of differentially methylated GpG regions.

overall_design: Bisulphite converted DNA from the 65 samples were hybridised to the Illumina Infinium EPIC Methylation Beadchip


title: RNAseq analysis of M. roreri expression in different conditions

status: Public on Jun 01 2023

city: Verona

first: Andrea

last: Minio

address: Via dell'Artigliere 8

department: Applied Biotechnologies

country: Italy

institute: Università di Verona

type: Expression profiling by high throughput sequencing

summary: The basidiomycete Moniliophthora roreri causes frosty pod rot of cacao (Theobroma cacao) in the Western hemisphere. M. roreri is considered asexual and haploid throughout its hemibiotrophic lifecycle. To understand the processes driving genome modification, using long-read sequencing technology we sequenced and assembled five high quality M. roreri genomes out of a collection of ninety-nine isolates collected throughout the pathogen's range. We obtained chromosome-scale assemblies composed of eleven scaffolds. We used short-read technology to sequence the genomes of twenty-two similarly chosen isolates. Alignments among the five reference assemblies revealed inversions and segmental translocations and duplications between and within scaffolds. Isolates at the front of the pathogens’ expanding range tend to share lineage-specific structural variants, as confirmed by short-read sequencing. We identified, for the first time, three new mating type A locus alleles (five in total) and one new potential mating type B locus allele (three in total). Currently only two mating type combinations, A1B1 and A2B2, are known to exist outside of Colombia. A systematic survey of the M. roreri transcriptome across twenty-two isolates identified an expanded candidate effector pool and provided evidence that effector candidate genes unique to the Moniliophthoras have been selected for preferential expression during the biotrophic phase of disease. Notably, M. roreri isolates in Costa Rica carry a chromosome segment duplication that has doubled the associated gene complement and includes secreted proteins and candidate effectors. Clonal propagation of the haploid M. roreri genome has allowed lineages with unique genome structures and compositions to dominate as it expands its range, displaying a significant founder effect.

first: Shahin

middle: S

last: Ali

first: Rosa

last: Figueroa-Balderas

first: Stephen

middle: P

last: Cohen

first: Denny

last: Carriel

first: Dahyana

last: Britto

first: Conrad

last: Stack

first: Indrani

middle: K

last: Baruah

first: Jean-Philippe

last: Marelli

first: Dario

last: Cantu

first: Bryan

middle: A

last: Bailey


title: RNAseq analysis of M. perniciosa expression in different conditions


title: Identification of key genes and signaling pathways in microtia by the analysis of transcriptomics

city: Beijing

first: Qiao-li

last: Shang

state: Beijing

address: 33 Badachu Road, Shijingshan District

country: China

institute: Plastic Surgery Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College

summary: Microtia is a complex congenital defect which is one of the most common birth defects in the world. Depending on the degree of deformity, microtia can be divided into many types. However, it is not clear whether the different degrees of microtia share the same underlying mechanism. The present study detected transcriptomic profiles of auricular cartilage tissues in 6 patients with mild and severe malformation and 3 control auricular cartilage tissues by RNA-seq technology. Relative mRNA abundances were compared and evaluated for their function and putative involvemen.t in microtia. A total of 1058, 1648 and 1150 differentially expressed genes respectively in the group of MIC-Ⅱ-vs-NOR, MIC-Ⅲ-vs-NOR and MIC-Ⅲ-vs-MIC-Ⅱwere identified. Bioinformatics analysis demonstrated that some of these genes showed potential associations with microtia. In the MIC-Ⅱ microtia, the changed biological processes mainly enriched in mitosis. And in the MIC-Ⅲ microtia, the changed biological processes not only enriched in mitosis but also in migration. The key genes, IL-6 and COMP, and key signaling pathway, PI3K-AKT signaling pathway, were found to be dysregulated, which could contribute to microtia. The present study was a report on the transcriptomic analysis of microtia using the auricular samples from different degrees of microtia. Additional studies are required to clarify the roles of potential key genes in microtia.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for normal auricular cartilage (NOR) , mild deformity microtia (MIC-Ⅱ) and severe deformity microtia (MIC-Ⅲ)

first: Leren

last: He


title: Condition-specific 3’ mRNA isoform half-lives and stability elements in yeast

city: Boston

first: Zarmik

last: Moqtaderi

state: MA

address: 240 Longwood Avenue C2-355

department: BCMP

country: USA

institute: Harvard Medical School

summary: Alternative polyadenylation generates numerous 3’ mRNA isoforms that can differ in their stability, structure, and function.  These isoforms can be used to map mRNA stabilizing and destabilizing elements within 3’ untranslated regions (3’UTRs).  Here, we examine how environmental conditions affect 3’ mRNA isoform turnover and structure in yeast cells on a transcriptome scale.  Isoform stability broadly increases when cells grow more slowly, with relative half-lives of most isoforms being well correlated across multiple conditions.  Surprisingly, dimethyl sulfate probing reveals that individual 3’ isoforms have similar structures across different conditions, in contrast to the extensive structural differences that can exist between closely related isoforms in an individual condition. Unexpectedly, most mRNA stabilizing and destabilizing elements function only in a single growth condition.  The genes associated with some classes of condition-specific stability elements are enriched for different functional categories, suggesting that regulated mRNA stability might contribute to adaptation to different growth environments. Condition-specific stability elements do not result in corresponding condition-specific changes in steady-state mRNA isoform levels.  This observation is consistent with a compensatory mechanism between polyadenylation and stability, and it suggests that condition-specific mRNA stability elements might largely reflect condition-specific regulation of mRNA 3’ end formation.

overall_design: Using the DREADS method, we determined DMS reactivity profiles of individual mRNA 3' isoforms genome-wide in four different growth conditions: YPD (previously deposited in GEO as GSE95788), YPGal, YPD + sorbitol, and minimal medium.

first: Joseph

middle: V

last: Geisberg

first: Kevin

last: Struhl


title: Single-cell transcriptomic profiling of healthy and dystrophic muscle macrophage

city: Irvine

first: S.

middle: Armando

last: Villalta

state: California

address: 843 Health Sciences Rd

institute: University of California Irvine

summary: The monocytic/macrophage system is essential for skeletal muscle homeostasis, but its dysregulation contributes to the pathogenesis of muscle degenerative disorders. Despite our increasing knowledge of the role of macrophages in degenerative disease, it still remains unclear how macrophages contribute to muscle fibrosis. Here, we used single-cell transcriptomics to determine the molecular attributes of dystrophic and healthy muscle macrophages.

overall_design: Muscle macrophages were isolated from healthy and dystrophic muscle by FACS to generate single-cell libraries with the 10X Genomics platform, which were then sequenced on Illumina instruments

first: S

first: Jyoti

last: Jaiswal

first: Melissa

middle: J

last: Spencer


title: Genome-wide association mapping and transcriptomic analysis reveal key drought-responding genes in barley seedlings

city: hangzhou

first: xiong

last: jiangyan

address: sandun street

institute: zhejiang University

summary: RNA-seq was carried out on the leaves of BCS8 and BCS24 after 7 days of drought treatment in order to better understand the molecular pathways underlying drought tolerance and to find the relevant candidate genes.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for barley BCS8 and BCS24 under drought treatment.

first: Jiangyan

last: Xiong

first: Danyi

last: Chen

first: Yeke

first: Dezhi

last: Wu

first: Guoping

last: Zhang


title: Bulk RNAseq of HDLECs [ctl vs ITGB3 siRNA]

city: Guangzhou

first: lei

last: zeng

address: No. 74, Zhongshan 2nd Road, Yuexiu District

institute: SUN YAT-SEN UNIVERSITY

summary: Bulk RNAseq was performed using control or ITGB3 siRNA treated human dermal lymphatic endothelial cells (HDLECs)

overall_design: Treated cells were detached and lysed. Total RNAs were extracted and then subjected to RNAseq analysis

first: Feng

first: Xinyu

last: Gu


title: Gene expression changes between control and C1orf112-knockout (KO) human multiple myeloma (MM) cell lines

city: Nagoya

first: Akinobu

last: Ota

state: Aichi

address: 1-1 Yazakokarimata

department: Food and Nutritional Environment

country: Japan

institute: Kinjo Gakuin University

summary: To examine the effect of C1orf112 disruption on the gene expression changes in MM cells , we generated C1orf112-KO cells with KMS-11, OPM-2, and ANBL-6 cells. The control and C1orf112-KO MM cells were incubated for 48 h in the typical cell culture medium.

overall_design: MM cells were maintained in RPMI 1640 supplemented with 10% FBS at 37 ℃ in 5% CO2 humidified atmosphere.

first: Ichiro

last: Hanamura

first: Sivasundaram

last: Karnan


title: Cell-type specific vulnerability to Alzheimer’s neurodegeneration in a subcortical limbic circuit node

city: Pittsburgh

first: Hansruedi

last: Mathys

address: 3501 5th Avenue

institute: University of Pittsburgh

summary: We used single cell RNA sequencing (scRNA-seq) to analyze subtypes of mammillary body neurons from WT mouse and from 5XFAD and WT littermates.

overall_design: Mammillary body neurons were isolated from the mouse using Miltenyi cell dissociation kit and prepared for 10X Chromium Controller  (10X Genomics) according to the manuscaturer's instructions.

first: Tsai

last: LH


title: Transcriptomic Profiling and Pathway Analysis of Mesenchymal Stem Cells following Low Dose-Rate Radiation Exposure

city: Bethesda

first: Anthony

middle: Robert

last: Soltis

state: MD

address: 4301 Jones Bridge Road

department: Anatomy, Physiology and Genetics

institute: Uniformed Services University

summary: Using total RNAseq, we examined gene expression differences in MSC exposed to 0.66 cGy/h for 1 and 2 weeks, for a total of 1 and 2 Gy radiation.

overall_design: Comparison of gene expression in non-irradiated cells with that of cells irradiated at 0.66 cGy/h to reach 1 Gy or 2 Gy gamma-radiation.

first: Regina

middle: M

last: Day

first: Clifton

middle: L

last: Dalgard

middle: R

first: John

middle: E

last: Slaven


title: Recruitment of stem-like T cells and resistance to exhaustion support CD4 T cell responses in autoimmunity (scCITE-Seq).

city: Salt Lake City

first: Maria

last: Bettini

address: University of Utah

institute: University of Utah

summary: Recent findings suggest that undifferentiated, stem-like, antigen specific T cells serve as an important long-term reservoir for autoimmune CD8 T cell responses. However, it is still unclear whether CD4 T cells exhibit a similar differentiation trajectory culminating in terminal differentiation, acquisition of an exhausted phenotype, and loss of stemness and function. We analyzed islet infiltrating T cells by scRNAseq and flow cytometry and found that while CD4 T cells in autoimmune diabetes share many features of exhaustion with CD8 T cells, expression patterns of inhibitory receptors are distinct in autoimmune T cells compared to T cells in chronic LCMV infection.

overall_design: scCITE-Seq

first: Denise

last: Allard

first: Arielle

last: Raugh

first: Bryant

last: Perkins

first: Nouf

last: Aljobaily

first: Elizabeth

last: Kolawole

first: Baoyu

last: Liu

first: Tessa

last: Galland

first: Yi

last: Jing

first: Zac

last: Stephens

first: Brian

last: Evavold

first: Scott

last: Hale

first: Matthew


title: Clonal propagation of Moniliophthora roreri and the emergence of unique lineages with distinct genomes during range expansion

first: Andrea

last: Minio

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

sample_organism:
Moniliophthora perniciosa
Moniliophthora roreri

overall_design: Refer to individual Series


title: Environmentally Induced Sperm RNAs Transmit Cancer Susceptibility to Offspring in a Mouse Model [RNA-seq II]

city: Washington

first: Sonia

last: de Assis

state: DC

address: 3970 Reservoir Rd. NW, New Research Building E408

department: Oncology

institute: Georgetown University

summary: DNA sequence accounts for the majority of disease heritability, including cancer. Yet, not all familial cancer cases can be explained by genetic factors. It is becoming clear that environmentally induced epigenetic inheritance occurs and that the progeny’s traits can be shaped by parental environmental experiences. In humans, epidemiological studies have implicated environmental toxicants, such as the pesticide DDT, in intergenerational cancer development, including breast and childhood tumors. Here, we show that the female progeny of males exposed to DDT in the pre-conception period have higher susceptibility to developing aggressive tumors in mouse models of breast cancer. Sperm of DDT-exposed males exhibited distinct patterns of small non-coding RNAs, with an increase in miRNAs and a specific surge in miRNA-10b levels. Remarkably, embryonic injection of the entire sperm RNA load of DDT-exposed males, or synthetic miRNA-10b, recapitulated the tumor phenotypes observed in DDT offspring. Mechanistically, miR-10b injection altered the transcriptional profile in early embryos with enrichment of genes associated with cell differentiation, tissue and immune system development. In adult DDT-derived progeny, transcriptional and protein analysis of mammary tumors revealed alterations in stromal and in immune system compartments. Our findings reveal a causal role for sperm RNAs in environmentally induced inheritance of cancer predisposition and, if confirmed in humans, this could help partially explain some of the “missing heritability” of breast, and other, malignancies.

overall_design: c57bl/6 mouse zygotes injected with synthetic miRNA-10b or controls were cultured and harvested at the blastocyst stage (E3.5) and used for RNA-seq analysis.

middle: D

last: McCoy


title: Recruitment of stem-like T cells and resistance to exhaustion support CD4 T cell responses in autoimmunity (scRNA-Seq).

summary: Recent findings suggest that undifferentiated, stem-like, antigen specific T cells serve as an important long-term reservoir for autoimmune CD8 T cell responses. However, it is still unclear whether CD4 T cells exhibit a similar differentiation trajectory culminating in terminal differentiation, acquisition of an exhausted phenotype, and loss of stemness and function. We analyzed islet infiltrating T cells in 8- and 16-week old NOD mice by scRNAseq and flow cytometry and found that while CD4 T cells in autoimmune diabetes share many features of exhaustion with CD8 T cells, expression patterns of inhibitory receptors are distinct in autoimmune T cells compared to T cells in chronic LCMV infection.

overall_design: We performed scRNAseq on T cells isolated from pancreatic islets of 8-week-old and 16-week-old NOD females to compare their transcriptome profile.


title: Single cell RNA trajectory analysis reveals a CD9 positive cell state to contribute to exit from stem cell-like and embryonic diapause states and transit to drug resistant states

city: Portland

first: Xi

last: Li

state: Oregon

address: 2730 SW Moody Ave

institute: Oregon Health & Science University

summary: Bromo- and extra-terminal domain (BET) inhibitors (BETi) have been shown to decrease tumor growth in preclinical models and clinical trials. However, toxicity and rapid emergence of resistance have limited their clinical implementation. To identify state changes underlying acquisition of resistance to the JQ1 BETi, we reanalyzed single-cell RNAseq data from JQ1 sensitive and resistant SUM149 and SUM159 triple negative breast cancer cell lines. Parental and JQ1-resistant SUM149 and SUM159 exhibited a stem cell-like and embryonic diapause (SCLED) cell state as well as a transitional cell state between the SCLED state existing both treatment naïve and treated cells, and a number of JQ1 resistant cell states. A transitional cell state transcriptional signature but not a SCLED state transcriptional signature predicted worsened outcomes in basal-like breast cancer patients suggesting that transit from the SCLED state to drug resistant states contributes to patient outcomes. Entry of SUM149 and SUM159 into the transitional cell state was characterized by elevated expression of the CD9 tetraspanin. Knockdown or inhibition of CD9 sensitized cells to multiple targeted and cytotoxic drugs in vitro. Importantly, CD9 knockdown or blockade sensitized SUM149 to JQ1 in vivo by trapping cells in the SCLED state and limiting transit to resistant cell states. Thus, CD9 appears to be critical for transition from a SCLED state into treatment resistant cell states and warrants exploration as a therapeutic target in basal-like breast cancer.

overall_design: scRNA-seq by 10x genomics of shCD9 or shCON SUM149 tumors growing in NSG mouse after 30 days of 25mg/kg/day JQ1 treatment.

first: Grodon

middle: B

last: Mills


title: Environmentally Induced Sperm RNAs Transmit Cancer Susceptibility to Offspring in a Mouse Model [non-coding RNA-Seq]

first: Lu

last: Jin

address: 3970 Reservoir Rd NW

type: Non-coding RNA profiling by high throughput sequencing

summary: While mature sperm is transcriptionally inactive, recent studies show that, following testicular its exit, the mammalian sperm acquires a load of small non-coding RNAs during transit in the epididymis, the last stage of sperm maturation. Importantly, this non-coding RNA load is sensitive to environmental insults.

overall_design: To determine the impact of DDT exposure on the mouse sperm RNA content and to establish whether regulation of miRNAs and in sperm was, in fact, induced by DDT exposure, we treated DDT-exposed mice with phenobarbital (PB), a drug known to promote hepatic enzymes activation and accelerate DDT metabolism and excretion in humans and animals. Then, we performed RNA-seq analysis to profile small RNAs.

first: Raquel

last: Santana da Cruz


title: Environmentally Induced Sperm RNAs Transmit Cancer Susceptibility to Offspring in a Mouse Model


title: Environmentally Induced Sperm RNAs Transmit Cancer Susceptibility to Offspring in a Mouse Model [RNA-seq]

summary: Our study revealed that miRNAs constituted the main small RNA subtype altered by DDT exposure, with a specific DDT-induced surge in sperm miRNA-10b. This miRNA, along with other members of the miRNA-10 family, plays a critical role in embryonic development  and cell differentiation through the regulation of Homeobox (Hox)  and other genes. Interestingly, studies examining different paternal environmental exposures including obesity and malnutrition report a upregulation of miRNA-10b and other members of the miR-10 family in sperm. It has also been reported that both sperm miRNA-10a and miRNA-10b are conserved across species including humans. These miRNAs are acquired by sperm cells during epididymal transit in mice, suggesting that alterations in this family could potentially act as a “sensor” of paternal environments.

overall_design: To further validate the functional importance of miRNA-10b to phenotypes observed in DDT offspring, we injected synthetic miR-10b (or control scramble-miR or vehicle solution) into normal mouse zygotes. Injected embryos were then transferred into surrogate dams to generate the miR-10b and CO offspring


title: Reprogramming of rhythmic liver metabolism by intestine clock

first: Min

last: Chen

state: Guangdong

address: No. 232, East Waihuan Street/Road

institute: Guangzhou university of Chinese medicine

summary: To assess potential impact of intestine clock on the rhythmicity of peripheral tissues (liver, kidney and WAT), mice with Bmal1 specifically deleted in the intestine (Bmal1-iKO mice, showing loss of clock function in the intestine) were generated. We collected liver, kidney and WAT samples from Bmal1-iKO and control (Bmal1-flox) mice every 4 hours throughout a light/dark cycle, and subsequently performed transcriptomic analyses.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for Bmal1-iKO and Bmal1-flox mice.

first: Baojian

last: Wu

first: Yanke

last: Lin


title: TWIST1 ChIP-seq analysis of human mesenchymal stem cells

city: Jupiter

first: Christopher

middle: Lee

last: Haga

state: Florida

address: 130 Scripps Way, BldgA261A

department: Molecular Medicine

institute: UF Scripps Biomedical Research

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Mesenchymal stem/stromal cells (MSCs) function as skeletal progenitors in bone marrow and regulate hematopoiesis and hemodynamic processes via secretion of paracrine acting factors. Although TWIST1 plays important roles in mesoderm formation and skull and vascular development, its role in MSCs is poorly defined.   Therefore, we conducted ChIP-seq analysis to identify genes potentially regulated by TWIST1.

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) of TWIST1 binding sites in human mesenchymal stem cells.

first: Cori

middle: N

last: Booker

first: Donald

middle: G

last: Phinney


title: The AT-hook is an evolutionarily conserved auto-regulatory domain of SWI/SNF required for cell lineage priming [MNase-seq]

city: Houston

first: Junwoo

last: Lee

state: Texas

address: 2120 El Paseo Street, Apt.603

department: Epigenetics and Molecular Carcinogenesis

institute: MD Anderson Cancer Center

summary: The SWI/SNF ATP-dependent chromatin remodeler is a master regulator of the epigenome, controlling pluripotency and differentiation. Towards the C-terminus of the catalytic subunit of SWI/SNF is a motif called the AT-hook that is evolutionary conserved. The AT-hook is present in many chromatin modifiers and generally thought to help anchor them to DNA. We observe however that the AT-hook regulates the intrinsic DNA-stimulated ATPase activity aside from promoting SWI/SNF recruitment to DNA or nucleosomes by increasing the reaction velocity a factor of 13 with no accompanying change in substrate affinity (KM). The changes in ATP hydrolysis causes an equivalent change in nucleosome movement, confirming they are tightly coupled. The catalytic subunit’s AT-hook is required in vivo for SWI/SNF remodeling activity in yeast and mouse embryonic stem cells. The AT-hook in SWI/SNF is required for transcription regulation and activation of stage-specific enhancers critical in cell lineage priming. Similarly, growth assays suggest the AT-hook is required in yeast SWI/SNF for activation of genes involved in amino acid biosynthesis and metabolizing ethanol. Our findings highlight the importance of studying SWI/SNF attenuation versus eliminating the catalytic subunit or completely shutting down its enzymatic activity.

overall_design: Mnase-seq of WT, dAT, dSnAC, CD, and dSnf2

first: Yuan-chi

first: Yue

last: Lu

first: Solomon

last: Hailu


title: Cell-specific vulnerability to metabolic failure: the crucial role of parvalbumin expressing neurons in Creatine Transporter Deficiency

city: irvine

first: Siwei

state: CA

address: 66304 Verano Road South

department: Computer Science

institute: University of California, Irvine

summary: Mutations in the X-linked solute carrier family 6-member (Slc6a8) gene, encoding the protein responsible for cellular creatine (Cr) uptake, cause Creatine Transporter Deficiency (CTD), an X-linked neurometabolic disorder presenting with cognitive dysfunction, autistic-like features, and epilepsy. The pathological determinants of CTD are still poorly understood and this lack of knowledge might hinder the development of therapeutic strategies. Here, we show that Cr deficiency perturbs gene expression in excitatory neurons, inhibitory cells and oligodendrocytes, inducing a remodeling of circuit excitability and synaptic wiring, while no effects are present in astrocytes and endothelial cells. We also describe specific alterations of high-energy demanding, Parvalbumin-expressing (PV+) interneurons, exhibiting a reduction in cellular and synaptic density, and a hypofunctional phenotype, affecting initiation, kinetics and frequency of action potentials. Mice lacking Slc6a8 only in PV+ neurons recapitulate numerous CTD features, such as cognitive deterioration, impaired cortical processing and hyperexcitability of brain circuits, demonstrating that Cr deficit in PV+ cells is sufficient to determine the CTD neurological endophenotype. Moreover, a pharmacological treatment targeted to restore the efficiency of PV+ synapses induces a significant improvement of cortical activity in Slc6a8 knock-out animals. Altogether, these data establish that Slc6a8 is critical for the normal function of PV+ interneurons and that a subtle dysfunction of these cells is critical for the disease pathogenesis, suggesting a novel therapeutic venue for CTD.

overall_design: Case-control design, with 4 biological replicates for KO animals and 3 biological replicates for WT controls

first: Elsa

last: Ghirardini

first: Giulia

last: Sagona

first: Angel

last: Marquez-Galera

first: Francesco

last: Calugi

first: Carmen

last: Navarron

last: Cacciante

first: Federica

last: Di Vetta

first: Lorenzo

last: Dadà

first: Raffaele

last: Mazziotti

first: Leonardo

last: Lupori

first: Elena

last: Putignano

first: Pierre

last: Baldi

first: Jose

last: Lopez-Atalaya

first: Tommaso

last: Pizzorusso

first: Laura

last: Baroncelli


title: Counting and correcting errors within unique molecular identifiers to generate absolute numbers of sequencing molecules [scRNA-Seq]

city: Oxford

first: Adam

last: Cribbs

address: Windmill Road

department: NDORMS

country: United Kingdom

institute: University of Oxford

summary: Unique Molecular Identifiers (UMIs) are random oligonucleotide barcodes sequences? that are critical for the removal of PCR amplification biases within both bulk and single-cell sequencing experiments. However, the impact that PCR and sequencing errors have on the accuracy of generating absolute counts of RNA molecules is underappreciated. We demonstrate that PCR errors and not sequencing errors are the main source of inaccuracy in sequencing data and that the use of UMIs synthesized with homotrimeric nucleoside building blocks provides a solution to pinpoint and remove errors, allowing absolute counting of sequenced molecules.

overall_design: In order to evaluate the accuracy of our homotrimer barcode assignment we captured mixed mouse and human cells (at ratio of 50:50 for 10X or 20:80 for drop-seq) and then performed single-cell RNA sequencing.


title: Single-cell gene expression profile of adult cochlea in NIHL vs. VPA-NIHL

first: Volkan

last: Ergin

address: 243 Charles St.

department: Otolaryngology, Harvard Medical School

institute: Massachusetts Eye and Ear

summary: Hearing functions through the mechanical transduction of inner ear sensory cells, hair cells, and their connections to the auditory neurons, which convert the stimuli into electrical signals to be detected by the brain. Noise-induced hearing loss (NIHL)  caused by exposure to excessively sounds cannot be medically corrected. Strategies to overcome the apparently irreversible noise-induced hearing loss (NIHL) in mammals become paramount for hearing treatment. The drug has been reported in attenuating inflammation in different species. Here, we tested the effect of the drug in acoustic trauma. We carried out single-cell RNA sequencing to examine the gene expression profiles comparing Drug group with Untreated group in response to the acoustic trauma.

overall_design: In experimental group, we treated WT C57bl/6j adult cochlear with the drug (90mg/ml) followed by noise exposure before dissecting sensory epithelium to create cDNA libraries subjected to 10X Genomics pipeline barcoding, library preparation, and sequencing. The untreated contralateral ears from the same mice were treated as control group (Noise-only; NIHL). Gene expression profiles of cochlea pretreated with Drug before noise exposure were compared with untreated, noise-exposed cochleae. NIHL (Noise-only; n=5) vs. Drug-NIHL (n=5).

first: Yizhou

last: Quan

first: Zheng-Yi

last: Chen


title: Single cell gene expression profile of adult cochlear in NIHL vs. ISL1-NIHL

summary: Exposure to excessive noise levels is considered one of the main etiologies of acquired hearing loss. Noise-induced hearing loss (NIHL) affects a large number of people during the productive years of life, and imposes a large impact on quality of life and a high socioeconomic burden. Here, we tested the effect of the ISL1 in NIHL. We used an inbred mouse strain (CBA/CaJ) and carried out single-cell RNA sequencing to examine the gene expression profiles comparing (AAV-ISL1) with (NIHL-only).

overall_design: In experimental group, we treated WT CBA/CaJ adult cochlear with the ISL1 (AAV titration: 10e12 GC/ml) followed by noise exposure, before dissecting sensory epithelium to create cDNA libraries subjected to 10X Genomics pipeline barcoding, library preparation, and sequencing. The untreated contralateral ears from the same mice were treated as control group. Gene expression profiles of cochlea AAV-treated v.s. untreated were compared (NIHL-only,  n=5; AAV-ISL1 n=5).

first: Wan

last: Du


title: Single cell gene expression profile of adult cochlear explants over the course of hair cell regeneration stimulated by chemical reprogramming [CocktailVehicleAtoh1]

summary: Strategies to overcome irreversible cochlear hair cell (HC) damage and loss are of vital importance to develop a treatment for hearing loss. HC regeneration in adult cochlea relies on a two-phase process: 1) Reprogramming mature cochlear (SCs) to regain the properties of their younger selves; 2) Activating Atoh1, a gene responsible for HC fate-determining, in the reprogrammed adult SCs for HC regeneration. We have shown that, by transient co-activation of Myc and NICD (Notch1 intracellular domain), the adult mouse cochlea can be successfully reprogrammed to a relatively younger stage and regain progenitor capacity, with the regeneration of HCs following Atoh1 overexpression in vitro and in vivo. We identified a combination (the cocktail) of drug-like molecules composing of small molecules and siRNAs to activate the pathways of Myc, Notch1, Wnt and cAMP. To identify molecules to reprogram mature cochlear SCs and HC regeneration, we utilized single-cell RNA sequencing and uncovered the pathways and their target genes underlying chemical-mediated reprogramming. We used an in-house adult cochlea explant culture system and carried out single-cell RNA sequencing to examine the gene expression profiles of cochlear explants, in response to chemical-induced reprogramming. We compared gene expression profiles between Vehicle/ad.Atoh1 activation vs. Cocktail (chemical reprogramming)/ad.Atoh1 activation.

overall_design: In chemical reprogramming group, we treated whole adult WT C57BL/6J cochlear explants with VPA (1.5 mM), LiCl (8mM), FSK (20μM), siFIR (0.02 μM), and siMxi1 (0.02 μM) for 4 days, followed by 2 weeks ad.Atoh1 overexpression, before dissecting sensory epithelium to create cDNA libraries subjected to 10X Genomics pipeline barcoding, library preparation, and sequencing. In control group, we treated whole adult WT C57bl/6j cochlear explants with sterile water with 0.1%DMSO in vitro for four days, followed by 2 weeks ad.Atoh1 overexpression, before dissecting sensory epithelium to create cDNA libraries. Vehicle (sterile water containing 0.1% DMSO)_ad.Atoh1, n=5; Cocktail (chemical reprogramming)_ad.Atoh1 group, n=5.


title: Analysis of different mouse CD8+T cell subset gene signatures in presence and absence of IL-17 signaling during LCMV CL13 infection

first: Lawrence

middle: P.

last: Kane

state: PA

address: 5051 Centre Ave.

department: Immunology

summary: WT mice were infected with LCMV CL-13, and 100ug/ml anti-IL-17A or isotype control antibody (BioxCell) was administered on Day 0, 3 and 6. On day 12 post-infection, live CD8+ T cells were FACS-sorted from spleen according to PD-1, Tim3 and CD44 expression directly into SmartSeq low-input RNA kit lysis buffer

overall_design: 100 ug/day. Three injections of IL-17 on day 0, 3 and 6. Same we used in our NI paper.

first: Saikat

last: Majumder

first: Mandy

last: McGeachy

first: Hridesh

last: Banerjee


title: ATM suppresses c-Myc overexpression in the mammary epithelium in response to estrogen

city: Kyoto

first: Rifat

middle: Ara

last: Najnin

state: Kyoto

address: Yoshida Konoe, Sakyo-ku

department: Radiation Genetics

institute: Kyoto University

summary: ATM gene mutation carriers are predisposed to estrogen receptor (ER)-positive breast cancer (BC). ATM prevents BC oncogenesis by activating p53 in every cell; however, much remains unknown about tissue-specific oncogenesis following ATM loss. Here, we report that ATM controls the early transcriptional response to estrogens. This response depends on topoisomerase II (TOP2), which generates TOP2-DNA double-strand break (DSB) complexes and rejoins the breaks. When TOP2-mediated ligation fails, ATM facilitates DSB repair. Following estrogen exposure, TOP2-dependent DSBs arise at the c-MYC enhancer in human BC cells, and their defective repair changes the activation profile of enhancers and induces the overexpression of many genes including the c-MYC oncogene. CRISPR/Cas9 cleavage at the enhancer also causes c-MYC overexpression, indicating that this DSB causes c-MYC overexpression. Estrogen treatment induced c-Myc protein overexpression in mammary epithelial cells of ATM-deficient mice. In conclusion, ATM suppresses the c-Myc-driven proliferative effects of estrogens, possibly explaining such tissue-specific oncogenesis.

overall_design: Comparative gene expression profiling analysis of NET-CAGE data for MCF-7 cells.

first: Md

last: Mahmud

last: Rahman

first: Shunichi

last: Takeda

first: Hiroyuki

last: Sasanuma

first: Hisashi

last: Tanaka

first: Yasuhiro

last: Murakawa

first: Naoto

last: Shimizu

first: Salma

last: Akter

first: Masatoshi

last: Takagi

first: Takuro

last: Sunada

first: Shusuke

last: Akamatsu

first: Gang

last: He

first: Junji

last: Itou

first: Masakazu

last: Toi

first: Mary

last: Miyaji

first: Kimiko

last: Tsutsui

first: Scott

last: Keeney

first: Shintaro

last: Yamada


title: Single cell gene expression profile of adult cochlear explants over the course of hair cell regeneration stimulated by Atoh1 activation [DoxVehicleAtoh1]

first: Volkan

last: Ergin

summary: Strategies to overcome irreversible cochlear hair cell (HC) damage and loss are of vital importance to develop a treatment for hearing loss. HC regeneration in adult cochlea relies on a two-phase process: 1) Reprogramming mature cochlear (SCs) to regain the properties of their younger selves; 2) Activating Atoh1, a gene responsible for HC fate-determining, in the reprogrammed adult SCs for HC regeneration. We have shown that, by transient co-activation of Myc and NICD (Notch1 intracellular domain), the adult mouse cochlea can be successfully reprogrammed to a relatively younger stage and regain progenitor capacity, with the regeneration of HCs following Atoh1 overexpression in vitro and in vivo. To identify molecules to reprogram mature cochlear SCs and HC regeneration, we utilized single-cell RNA sequencing and uncovered the pathways and their target genes underlying MYC/NICD-mediated reprogramming. We used an in-house adult cochlea explant culture system and carried out single-cell RNA sequencing to examine the gene expression profiles of cochlear explants from a transgenic mouse model, rtTa/tet-Myc/-tet-NICD, in response to Dox-induced MYC/NICD co-activation. We compared gene expression profiles between Atoh1 activation vs. MYC/NICD/Atoh1 co-activation.

overall_design: In MYC/NICD activation group, we treated whole adult cochlear explants (rtTa/tet-Myc/-tet-NICD) with Dox in vitro for four days followed by 2 weeks ad.Atoh1 overexpression before dissecting sensory epithelium to create cDNA libraries subjected to 10X Genomics pipeline barcoding, library preparation, and sequencing. In control group, we treated whole adult cochlear explants (rtTa/tet-Myc/-tet-NICD) with sterile water in vitro for four days, followed by 2 weeks ad.Atoh1 overexpression, before dissecting sensory epithelium to create cDNA libraries. Dox plus adAtoh1 (n=5) and Vechicle (sterile water) plus ad.Atoh1 (n=5).

first: Yizhou

last: Quan

first: Zheng-Yi

last: Chen


title: The N6-methyladenosine METTL3 Regulates Tumorigenesis and Glycolysis by Mediating m6A Methylation of the Tumor Suppressor LATS1 in Breast Cancer

first: Youqin

last: Xu

address: No.1023 North Shatai Road

institute: Southern Medical University

summary: Background: Post-transcriptional modification of tumor-associated factors plays a pivotal role in breast cancer progression. However, the underlying mechanism remains unknown. Modifications to m6A are dynamic and reversible in cancer cells and have been found to impact tumor initiation and progression through various mechanisms. In this study, we explored the regulatory mechanism of m6A methylation in the Hippo pathway, a key pathway involved in cell proliferation and metabolism.  Methods: First, a combination of MeRIP-seq, RNA-seq and metabolomics-seq was utilized to reveal the map of m6A modifications in breast cancer tissues and cells. Secondly, we identified the relationship between m6A proteins and LATS1 in m6A regulation in breast cancer cells by performing RNA pull-down assays, RIP-qPCR, MeRIP-qPCR, and RNA stability analysis. The expression and biological functions of METTL3 and YTHDF2 were confirmed in breast cancer cell lines in vitro and in vivo. Furthermore, we investigated the phosphorylation levels and localization of YAP/TAZ to reveal that the activity of the Hippo pathway could be affected by m6A regulation of LATS1 in breast cancer cells.  Results: We demonstrated that m6A regulation plays an important role in proliferation and glycolytic metabolism in breast cancer through the Hippo pathway factor, LATS1. METTL3 was identified as the m6A writer, with YTHDF2 as the reader protein of LATS1 mRNA, which plays a positive role in promoting both tumorigenesis and glycolysis in breast cancer. High levels of m6A modification were induced by METTL3 in LATS1 mRNA. YTHDF2 identified m6A sites in LATS1 mRNA and reduced its stability. Knockout of the protein expression of METTL3 or YTHDF2 increased the expression of LATS1 mRNA and suppressed breast cancer tumorigenesis by activating YAP/TAZ in the Hippo pathway.  Conclusions: In summary, we discovered that the METTL3-LATS1-YTHDF2 pathway plays an important role in the progression of breast cancer by activating YAP/TAZ in the Hippo pathway.

overall_design: MeRIP-seq was conducted in two paired breast duct cancer tissues and adjacent normal breast tissues.

first: Mu

last: Song

first: Minfeng

last: Liu

first: Qiang

last: Zuo


title: Inhibition of mitochondrial transcription by the neurotoxin MPP+

city: Stockholm

first: Alexander

last: Pfab

state: Stockholms län [SE-01]

address: Svante Arrhenius väg 20B

department: MBW

country: Sweden

institute: Stockholm University

summary: The neurotoxin MPP+ triggers cell death of dopamine neurons and induces Parkinson’s disease symptoms in mice and men, but the immediate transcriptional response to this neurotoxin has not been studied. We therefore treated human SH-SY5Y cells with a low dose (0.1 mM) of MPP+ and measured the effect on nascent transcription by precision run-on sequencing (PRO-seq). We found that transcription of the mitochondrial genome was significantly reduced already after 30 min, whereas nuclear gene transcription was unaffected. Inhibition of respiratory complex I by MPP+ led to reduced ATP production, that may explain the diminished activity of mitochondrial RNA polymerase. Our results show that MPP+ has a direct effect on mitochondrial function and transcription, and that other gene expression or epigenetic changes induced by this neurotoxin are secondary effects that reflect a cellular adaptation program.

overall_design: Analysis of nascent transcription by precision run-on sequencing (PRO-seq) in SH-SY5Y cells treated with 0.1 mM MPP+  for 0.5h and 24h and non-treated control cells in 2 replicates each.

first: Sergey

last: Belikov

first: Mattias

last: Mannervik


title: Molecular subtypes of head and neck cancer – Prognostic impact and correlations with morphological characteristics

city: Berlin

first: Raik

last: Otto

state: Berlin

address: Rudower Chaussee 25

department: Computer Sciences

country: Germany

institute: Humboldt-Universität zu Berlin

summary: Aim Treatment options for patients with recurrent or metastatic head and neck squamous cell carcinoma (R/M-HNSCC) are limited. Therefore, prognostic and predictive biomarkers for the application of personalized therapies are urgently needed.

overall_design: To this end, we designed, applied and evaluated a NanoString gene panel which revealed the subtype in R/M-HNSCC in order to identify potential treatment-relevant conditions and correlations with histomorphological characteristics.  Material and Methods 130 formalin-fixed, paraffin-embedded samples from 95 treated CeFCiD trial patients with R/M-HNSCC were sequenced and analyzed. A customized NanoString panel composed of 231 genes was utilized to determine molecular subtypes and gene expression levels of potential predictive genes. For 67 patients, clinical data and H&E stained slides were available for additional comprehensive histomorphological analyses (e.g., histotype, grading, tumor cell budding (TCB), nuclear size, stroma content).   Results 114 out of 130 (88%) samples passed quality control and we could successfully determine their molecular subtype in 103 of 114 (90%) cases. Gene expression levels of AREG were significantly higher for the basal and classical subtype compared to the mesenchymal subtype. Cases assigned to the classical subtype showed superior progression-free and overall survival rates compared to non-classical subtypes. Additionally, among histomorphological parameters high TCB was associated with poor outcomes.  Conclusion The highly compact NanoString panel was able to determine the molecular subtype of R/M-HNSCC. The implications of molecular subtypes on prognosis and therapy prediction might aid in treatment planning of R/M-HNSCC patients. The prognostic significance of the histomorphological parameters TCB could be confirmed.

first: Fabian

last: Stögebauer

first: Korinna

last: Jöhrens

first: Ingeborg

last: Tinhofer-Keilholz

first: Ulrich

last: Keilholz

last: Keller

first: Ulf

last: Leser

first: Wilko

last: Wichert

first: Melanie

last: Boxberg

first: Konrad

last: Klinghammer


title: Multi-omic colon organoid analysis highlight MSH4 as a marker of Lynch syndrome and microsatellite instability [RNA-sequencing]

city: Charlottesville

first: Matthew

last: Devall

state: Virginia

address: 1335 Lee Street

institute: University of Virginia

summary: Approximately 15% of colorectal cancer (CRC) patients present with high levels of microsatellite instability (MSI-H), which is driven by defective mismatch repair (dMMR). While about 20% of MSI-H tumors are associated with the hereditary condition, Lynch syndrome (LS), the majority develop through non-hereditary mechanisms. In recent years, the molecular processes underpinning tumor development in LS patients has been debated, with the longstanding view that dMMR is a secondary process in CRC development of LS patients being questioned. Here, we performed the first multi-omic analysis of normal colon organoids developed from LS and healthy patients to address questions regarding the development of dMMR in LS colon epithelial cells from cancer-free individuals.

overall_design: RNA-sequencing protocols were performed on healthy and lynch syndrome colon organoids derived from right colon at the time of colonoscopy.

first: Mourad

middle: W

last: Ali

first: Stephen

last: Eaton

first: Dan

last: Weisenberger

first: Steven

last: Powell

first: Li

last: Li

first: Graham

last: Casey


title: Multi-omic colon organoid analysis highlight MSH4 as a marker of Lynch syndrome and microsatellite instability

type: Methylation profiling by genome tiling array

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

overall_design: Refer to individual Series


title: Identification of host regulators of Mycobacterium tuberculosis phenotypic states uncovers a role for the MMGT1-GPR156-lipid droplet axis in the induction of persistence [CRISPRscreen]

city: Cambridge

first: Haroon

last: Kalam

address: 415 main st.

department: IDMP

institute: Broad Institute of MIT and Harvard University

summary: The ability of Mycobacterium tuberculosis (Mtb) to establish latency directly impacts disease and response to treatment but the host’s influence on this switch remains elusive. Using a novel Mtb reporter strain to separate macrophages infected with replicating or latent Mtb, we performed transcriptomics and genome-wide CRISPR screens. After validating the recovery of known susceptibility loci from TB GWAS as modifiers of active replication, we identified multiple pathways and novel modulators of latency. We validated multiple controllers of latency and mechanistically characterized the transporter MMGT1. MMGT1-deficient macrophages upregulated lipid metabolism genes and accumulated lipid droplets during infection. Critically, targeting triacylglycerol synthesis reduced both droplet formation and Mtb latency. We identified GPR156, an orphan GPCR as a key inducer of droplet accumulation in ΔMMGT1 cells. Altogether, our work uncovers the role of MMGT1-GPR156-lipid droplets in the induction of Mtb latency, suggesting that host-directed therapies could be used to modulate Mtb phenotypes during infection.

overall_design: Genome wide CRISPR screen by high throughput sequencing of THP1 with active Mtb or THP1 with latent Mtb

first: Chih-Hung

last: Chou


title: Identification of host regulators of Mycobacterium tuberculosis phenotypic states uncovers a role for the MMGT1-GPR156-lipid droplet axis in the induction of persistence [AR_SNR_RNAseq]

overall_design: Transcriptome profiling (RNA-seq) by high throughput sequencing of THP1 with active Mtb or THP1 with latent Mtb


title: The NAMPT inhibitor FK866 increases metformin sensitivity in pancreatic cancer cells

city: Montreal

first: Thulaj

last: Meharwade

state: QC

address: 110 Pine Ave W,

department: Division of Systems Biology

country: Canada

institute: Montreal Clinical Research Institute

summary: Pancreatic cancer (pancreatic ductal adenocarcinoma: PDAC) is one of the most aggressive neoplastic diseases. Metformin use was associated with reduced pancreatic cancer incidence or better survival in diabetics. Metformin has been shown to inhibit PDAC cells survival and growth in vitro and in vivo. However, clinical trials using metformin failed to decrease pancreatic cancer progression in patients, raising important questions about molecular mechanisms that protect tumor cells from the antineoplastic activities of metformin. We confirm that metformin acts through inhibition of mitochondrial complex I, decreasing the NAD+/NADH ratio and that NAD+/NADH homeostasis determines metformin sensitivity in several cancer cell lines. Metabolites that can restore the NAD+/NADH ratio turned PDAC cells resistant to metformin. In addition,  metformin treatment of PDAC cell lines induced a compensatory NAMPT expression increasing the pool of cellular NAD+. The NAMPT inhibitor FK866 sensitized PDAC cells to the antiproliferative effects of metformin in vitro and decreased cellular NAD+ pool. Intriguingly, FK866 combined with  metformin increased survival in mice bearing KP4 cells xenografts but not in mice with PANC1 xenografts. Transcriptome analysis revealed that the drug combination reactivated genes in the p53 pathway and oxidative stress providing new insights about the mechanisms leading to cancer cell death.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for KP4 cells treated with either DMSO, Metformin, FK866 and Metformin+FK866.

first: Gerardo

last: Ferbeyre


title: Identification of host regulators of Mycobacterium tuberculosis phenotypic states uncovers a role for the MMGT1-GPR156-lipid droplet axis in the induction of persistence [THP1_MMGT1_RNAseq]

overall_design: Transcriptome profiling (RNA-seq) by high throughput sequencing of uninfected THP1, Mtb infected THP1, uninfected ΔMMGT1 and Mtb infected ΔMMGT1 macrophage


title: LSD1 inhibition disrupts super-enhancer activities in CRPC [scRNA-seq]

city: Boston

first: Changmeng

last: Cai

address: 100 William T Morrissey Blvd

institute: University of Massachusetts Boston

summary: Our studies revealed a novel oncogenic function of LSD1 in driving PCa progression by activating MYC signaling and mediating CRPC SEs activities, cotargeting LSD1 and BRD4 achieved significant synergistic effects in repressing CRPC tumor growth

overall_design: single-cell RNA-seq

first: Mingyu

last: Liu

first: Wanting

last: Han

first: Shuai

last: Gao


title: Identification of host regulators of Mycobacterium tuberculosis phenotypic states uncovers a role for the MMGT1-GPR156-lipid droplet axis in the induction of persistence


title: Effect of PPARg on the transcriptome of regulatory T cells (Tregs)

first: CBDM

last: Lab

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

institute: Harvard Medical School

summary: To investigate the role of PPARg in Tregs, we established conditional knockout mice that lack PPARg specifically in Tregs (Ppargf/f Foxp3-Cre mice).

overall_design: We then performed RNA-Seq analysis on Tregs from the spleen and skin of 2-week-old Pparg+/+ Foxp3-Cre and Ppargf/f Foxp3-Cre mice.

first: Chaoran

first: Diane

last: Mathis


title: LSD1 inhibition disrupts super-enhancer activities in CRPC [ChIP-seq]

overall_design: BRD4 ChIP-Seq were performed in LNCaP cells cultured in 5% CSS. All ChIP-seq samples contain replications.

first: Dong


title: The AT-hook is an evolutionarily conserved auto-regulatory domain of SWI/SNF required for cell lineage priming [ATAC-seq]

first: Junwoo

last: Lee

summary: The SWI/SNF ATP-dependent chromatin remodeler is a master regulator of the epigenome, controlling pluripotency and differentiation. Towards the C-terminus of the catalytic subunit of SWI/SNF is a motif called the AT-hook that is evolutionary conserved. The AT-hook is present in many chromatin modifiers and generally thought to help anchor them to DNA. We observe however that the AT-hook regulates the intrinsic DNA-stimulated ATPase activity aside from promoting SWI/SNF recruitment to DNA or nucleosomes by increasing the reaction velocity a factor of 13 with no accompanying change in substrate affinity (KM). The changes in ATP hydrolysis causes an equivalent change in nucleosome movement, confirming they are tightly coupled. The catalytic subunit’s AT-hook is required in vivo for SWI/SNF remodeling activity in yeast and mouse embryonic stem cells. The AT-hook in SWI/SNF is required for transcription regulation and activation of stage-specific enhancers critical in cell lineage priming. Similarly, growth assays suggest the AT-hook is required in yeast SWI/SNF for activation of genes involved in amino acid biosynthesis and metabolizing ethanol. Our findings highlight the importance of studying SWI/SNF attenuation versus eliminating the catalytic subunit or completely shutting down its enzymatic activity.

overall_design: Biological duplicates of wild type (WT) and two AT hook domain deletion mutants (dAT1, dAT2) in naïve and primed condition were sequenced by 50bp PE HiSeq3000.

first: Kyle

last: Feola

first: Dhurjhoti

last: Saha

first: Yue

last: Lu

first: Bin


title: The AT-hook is an evolutionarily conserved auto-regulatory domain of SWI/SNF required for cell lineage priming

sample_organism:
Saccharomyces cerevisiae
Mus musculus

platform_organism:
Saccharomyces cerevisiae
Mus musculus


title: The MeRIP-seq and RNA-Seq of SiHa and H8 cells

city: Shenzhen

first: sheng

last: zhong

address: The Xinhu Road 1333

institute: The Sourthern Medical University

type: Methylation profiling by high throughput sequencing

summary: To investigate the different gens expression and RNA methylation degree in the cervical immortalized cervical cells and cervical cancer cells，

overall_design: We then performed gene expression profiling analysis using data obtained from MeRIP-seq of 2 different cells.

first: Xia

last: Guo

first: Xiaona

last: Chen


title: Clockwork orange-mediated control of sugar responsive transcription

city: Helsinki

first: Krista

last: Kokki

address: Viikinkaari 9, Biocenter 1, Institute of Biotechnology P.O.Box. 56

department: Department of Biosciences (Genetics)

country: Finland

institute: University of Helsinki

sample_organism:
Drosophila melanogaster
Mus musculus

platform_organism:
Drosophila melanogaster
Mus musculus


title: The AT-hook is an evolutionarily conserved auto-regulatory domain of SWI/SNF required for cell lineage priming [ChIP-seq]

overall_design: Immunoprecipitated samples (Brg1/SMARCA4, H3K4me1, H3K4me3 and H3K27ac) and mock control samples (IgG) were prepared for biological duplicates of wild type (WT) and two AT hook domain deletion mutants (dAT1, dAT2) in naïve and primed conditions. These samples were sequenced by 75bp paired-end or 50bp signle reads, Illumina HiSeq3000.

first: Abhinav

middle: K

last: Jain


title: The AT-hook is an evolutionarily conserved auto-regulatory domain of SWI/SNF required for cell lineage priming [PRO-seq]

overall_design: Biological duplicates of wild type (WT) and two AT hook domain deletion mutants (dAT1, dAT2) in naïve condition, and quadraplicates of WT and triplicates of dATs in primed condition were sequenced by 75bp SE Nextseq 500.

first: Yuan-chi

last: Lin


title: LSD1 inhibition disrupts super-enhancer activities in CRPC [RNA-seq]

first: Changmeng

overall_design: CRPC xenograft models were treated with LSD1 inhibitor and BET inhibitor alone or in combination (LSD1 inhibitor with lower dosage). All RNA-seq samples contain replications.

first: Mingyu

first: Muqing

last: Li

first: Wanting


title: Clockwork orange-mediated control of sugar responsive transcription [time series]

summary: Feeding on high sugar diet reprograms metabolism, partially mediated through a gene regulatory network controlled by intracellular sugar sensor Mondo/ChREBP-Mlx. Sugar-induced gene expression changes include activation of genes encoding enzymes of glycolysis, pentose phosphate pathways, and de novo lipogenesis, collectively driving the flux of sugar-derived carbon into triacylglycerides. These sugar-induced metabolic changes are likely to trigger compensatory responses to avoid depletion of necessary metabolites, but they remain poorly characterized. Through a global temporal clustering analysis of sugar-induced gene expression in Drosophila we identify new gene expression programs controlled by sugar feeding. These include rapid and transient downregulation of ribosome biogenesis genes, known targets of transcription factor Myc. Through in silico motif predictions and experimental validation, we identify transcriptional repressor Clockwork orange (CWO) as a mediator of this response. CWO expression is directly activated by Mondo-Mlx and it counteracts Myc through repression of its expression as well as through binding to overlapping regulatory regions of ribosome biogenesis genes. Loss of CWO function leads to depletion of UDP-GlcNAc pools and impaired viability on high sugar diet. Analysis of CWO orthologs, BHLHE40 and BHLHE41, in mouse hepatocytes revealed a conserved role for BHLHE41 in repressing ribosome biogenesis genes. Collectively, our data uncover a gene regulatory circuit balancing the activities of lipid and protein biosynthesis to maintain homeostasis during high sugar feeding.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for high and low sugar in Drosophila larvae.

first: Ville

last: Hietakangas


title: Clockwork orange-mediated control of sugar responsive transcription [cwo mutant]

overall_design: Comparative gene expression profiling analysis of RNA-seq data for Cwo mutant in Drosophila larvae in high and low sugar conditions.


title: Loss of function mutation in progressive ankylosis (Ank) gene causes aberrant mineralization and acquisition of osteoblast-like-phenotype by annulus fibrosus cells in the intervertebral disc

city: Philadelphia

first: Makarand

middle: V.

last: Risbud

address: 1025 Walnut Street, Suite 501 College Bldg.

department: Department of Orthopaedic Surgery

institute: Thomas Jefferson University

summary:
Transcriptomic analysis of nucleus pulposus (NP) and annulus fibrosus (AF) tissues from intervertebral discs of 3-month-old mice with loss of function mutation of Ank gene.
Regulator of extracellular inorganic pyrophosphate, Ank is essential for preventing ectopic mineralization in the extracellular matrices, maintaining the health of the intervertebral disc of mice. We examined the transcriptomic profiles of nucleus pulposus and annulus fibrosus cells in control and Ank mutant mice using microarrays.

overall_design: Tissues from the nucleus pulposus (NP) and annulus fibrosus (AF) were harvested from the intervertebral discs of five wild-type (WT) and five Ank mutant mice (ank/ank) of 13-week-old of age. NP and AF tissues were separately pooled from lumbar and caudal discs in each animal for RNA extraction and hybridization using Affymetrix microarrays.

first: Takashi

last: Ohnishi

middle: V


title: Clockwork orange-mediated control of sugar responsive transcription [ChIP-seq]

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for ChREBP and Dec1 in mice fed a standard diet.


title: Next Generation Sequencing of hormone receptor-positive and triple negative primary breast cancer tumors

city: Montréal

first: Claude

last: Perreault

state: Québec

address: 2950, Chemin de Polytechnique

institute: Institute for Research in Immunology and Cancer

summary: In order to identify relevant targets for cancer immunotherapy in breast cancer, we characterized the immunopeptidome of 26 primary breast cancer samples with a proteogenomic approach relying on RNA-seq and mass spectrometry (MS). We were able to describe the landscape of MHC-I associated peptides presented by breast cancer tumors. Furthermore, bioinformatic analysis allowed us to identify tumor-specific and tumor associated antigens, which can be used for the development of anti-cancer vaccines or as targets for engineered T-cells.

overall_design: mRNA sequencing was performed on hormone receptor-positive (n=14) or triple negative (n=12) primary breast cancer tumors.

first: Eralda

last: Kina


title: Evaluating Cancer Subtypes and Enhancer Dynamics During the Acquisition of Drug Resistance by Nascent RNA-Sequencing

first: Andrew

middle: Ryan

last: Field

state: MA

address: 25 Shattuck St

department: Biological Chemistry and Molecular Pharmacology

summary: Precision Run-On Sequencing (PRO-seq) was performed on triple negative breast cancer (TNBC) cell lines and drug resistant cell lines to determine the epigenetic factors that contribute to TNBC subtypes and drug resistance.

overall_design: PRO-seq libraries were generated from 11 TNBC cell lines and 8 drug resistant derivatives.

first: Seth

last: Goldman

first: Laura

last: Stevens

first: Bojana

last: Jovanovic

first: Kornelia

last: Polyak

first: Karen

last: Adelman


title: Bulk RNA sequencing of wildtype and ABCA3 mutant human iPSC-derived mutant containing the ABCA3:GFP fusion reporter

first: Pushpinder

last: Bawa

state: Massachusetts

address: 670 Albany St

department: Boston University Medical Campus

institute: Center for Regenerative Medicine

summary: We performed transcriptomic profiling of induced pluripotent stem cell (iPSC)-derived iAEC2s containing wildtype, E690K homozygous ABCA3 mutantion, and W308R homozygous ABCA3 mutation.  We first performed CRISPR-Cas9 gene editing on a wildtype human iPSC line (BU3) to engineer a GFP reporter bi-allelically targeted at the stop codon of the endigenous ABCA3 locus, thus generating an ABCA3:GFP fusion reporter line (as previous published iin Sun. et al, 2021). Next we utilized CRISPR-Cas9 gene-mutagenesis to introduce two homozygous ABCA3 mutations (E690K and W308R), resulting in two, new ABCA3 mutant iPSC lines containg the ABCA3:GFP fusion reporter, totally a total of 3 ABCA3:GFP fusion iPSC lines (wildtype, E690K-AG, W308R-AG). Following triplicate distal lung directed differentiations of all 3 ABCA3:GFP fusion iPSC lines we sorted the ABCA3:GFP positive iAEC2s on day 43 for transcriptomic analyses.

overall_design: Global transcriptomic profiling of human iPSC-derived iAEC2s containing mutant or wildtype ABCA3:GFP fusion reporter. Three total samples include: wildtype ABCA3 (WT), E690K mutant ABCA3 (E690K-AG), and W308R mutant ABCA3 (W308R-AG). ABCA3:GFP positive, live cells were on day 43 of human distal lung differentiation. Each sample have three biological replicates separated at day 0 (n=3). Prior to sorting for this bulk RNAseq run, the cells were previously sorted on day 15 using CD47hi/CD26low and on day 30 using CPM to enrich for NKX2-1.

first: Yuliang

last: Sun

first: Carlos

last: Villacorta-Martin

first: Darrell

last: Kotton


title: RNA sequencing of E13.5 mouse Foxd1Cre;Ptch1(flox/-) whole kidneys

city: Toronto

first: Norman

last: Rosenblum

address: 686 Bay Street

institute: The Hospital for Sick Children

summary: Transcriptional profiling to identify genes differentially regulated by stromal specific Ptch1-deficiency during embryonic kidney development. Ptch1 was specifically deleted from stromal progenitors using Foxd1-driven Cre recombinase

overall_design: Whole paired kidneys were collected from 3 Foxd1Cre;Ptch1 (flox/-) mice and control littermates (Ptch1 flox/+) at E13.5, followed by RNA extraction and next generation RNA sequencing.

first: Robert

last: D'Cruz


title: Expression data from human kidney organoids treated with the Hedgehog agonist SAG

summary:
The kidney, similar to non-renal tissue, is adversely affected by increased Hedgehog signaling. We treated human kidney organoids with the Hedgehog activator SAG in order to study the effects of constitutive active Hedghog signaling on human kidney development.
We used microarrays to identify gene expression changes in human kidney tissue following Hedgehog activation.

overall_design: Induced pluripotent stem cells were differentiated for 7 days to intermediate mesoderm cells. At the stage of cellular aggregation, kidney organoids were treated with either DMSO (control) or 120 nM SAG. RNA was collected from kidney organoid tissue after 18 days of treatment (at day 25).


title: Population ATAC-seq of in vitro polarized ATAC CD4 T cells

first: Pratiksha

middle: I

last: Thakore

address: 415 Main St

institute: Broad Institute

summary: To understand the molecular programs driving Th17 heterogeneity and ATAC CD4 T cell fate, we profiled in vitro polarized non-pathogenic Th17, pathogenic Th17, Th1, and Treg cells using ATAC-seq.

overall_design: We profiled in vitro polarized and in vivo mouse primary ATAC CD4 T cells in the following independent experiments: 1) non-pathogenic and pathogenic Th17 cells harvested polarized from naive ATAC CD4 T cells isolated from Il17-eGFP reporter mice, sorted for GFP+ and all cells (ATAC Il17eGFP); 2) non-pathogenic Th17, pathogenic Th17, Th1, and Treg cells harvested after 72h polarization from naive mouse ATAC CD4 T cells (ATAC CD4_diff); 3)  non-pathogenic Th17, pathogenic Th17, and Th1 harvested at ATAC Time points ranging from 0 to 48 hr after polarization from naive mouse ATAC CD4 T cells (ATAC Time_course); 4) Il17-expressing Th17 cells from the draining lymph node and central nervous system of mice at the peak of experimental autoimmune encephalomyelitis response (ATAC EAE); 5) non-pathogenic Th17, pathogenic Th17, and Th1 cells with ATAC Bach2 CRISPR KO vs controls; 6) Th17 cells with ATAC Bach2 overexpression vs controls

first: Alexandra

last: Schnell

first: Maryann

last: Zhao

first: Elena

last: Christian

first: Vasundhara

last: Singh

first: Orit

last: Rozenblatt-Rosen

first: Aviv

last: Regev

first: Vijay

last: Kuchroo


title: Bulk RNA sequencing of ABCA3 mutant, and gene-corrected patient iPSC-derived  iAEC2s

summary: We performed transcriptomic profiling of patient  induced pluripotent stem cell (iPSC)-derived iAEC2s containing E690K and W308R ABCA3 mutations  as well as their syngeneic, gene-corrected iAEC2s (total of four iPSC-derived iAEC2 lines).  We first reprogrammed iPSCs from 2 patients with two homozyguos ABCA3 mutations (E690K and W308R ABCA3 mutations). Next we utilized TALENs gene-editing technique previously published in Jacob et al. (2017) to monoallelically target the endogenous SFTPC locus with the tdTomato reporter, allowing for sorting and isolation of SFTPCtdTomato positive iAEC2s. Finally, we used CRISPR-Cas9 footprint-free gene-correction to generate syngeneic patient iPSCs which were dfferentiated into  the corresponding iAEC2s for syngeneic comparisons. Following tripplicate  differentiations of all 4 patient iPSC lines, we sorted the SFTPCtdTomato+ iAEC2s on day 43-44 of differentiation for transcriptomic analyses.

overall_design: Global transcriptomic profiling of patient iPSC-derived iAEC2s containing homozygous ABCA3 mutations and their corresponding gene-corrected iAEC2s. Total of 4 patient iPSC-derived iAEC2s were differentiated in biological triplicate (n=3) separated from day 0 of directed differentiation: homozygous E690K mutant (E690K) line; gene-corrected E690  line (cE690);W308R  mutant (W308R) line; gene-corrrected W308  line (cW308). Upon directed diifferentiation following protocol previously published by our lab (Jacob et al., 2017, 2019), SFTPCtdTomato+ iAEC2s were sorted onday 43-44 of differentiation for transcriptomic analyses.


title: Comprehensive effects of GmVP2-overexpression on plant growth, P-remobilization and rhizosphere microbial community

city: Guangzhou

first: baoxing

last: xie

address: Tianhe

institute: South China Agricultural University

summary: Increased root H+ secretion is known as a strategy of plant adaption to low phosphorus (P) stress by enhancing mobilization of sparingly soluble P-sources. However, it remains fragmentarywhether enhanced H+ exudation could reconstruct the plant rhizosphere microbial community under low P stress. The present study found that P deficiency led to enhanced H+ exudation from soybean (Glycine max) roots. Three out of all eleven soybean H+-pyrophosphatases (GmVP) geneswere up-regulated by Pi starvation in soybean roots. Among them, GmVP2 showed the highest expression level under low P conditions. Transient expression of a GmVP2-green fluorescent protein chimera in tobacco (Nicotiana tabacum) leaves, and functional characterization of GmVP2 in transgenic soybean hairy roots demonstrated that GmVP2 encoded a plasma membrane transporter that mediated H+ exudation. Meanwhile, GmVP2-overexpression in Arabidopsis thaliana resulted in enhanced root H+ exudation, promoted plant growth, and improved sparingly soluble Ca-P utilization. Overexpression of GmVP2 also changed the rhizospheric microbial community structures, as reflected by a preferential accumulation of acidobacteria in the rhizosphere soils. These results suggested that GmVP2 mediated Pi-starvation responsive H+ exudation,which is not only involved in plant growth and mobilization of sparingly soluble P-sources, but also affects microbial community structures in soils.

overall_design: To investigate the effects of GmVP2 overexpression on Arabidopsis growth,wild-type (WT, Columbia-0) and transgenic seeds (OX3) were cultivated in solid MS containing 1250 μM (+P) and 6.25 μM (-P) for 10 d.

first: Cuiyue

last: Liang

first: Jiang

last: Tian

first: Baoxing

last: Xie

first: Qianqian

last: Chen


title: Gene expression profiling of human brain microvascular endothelial cells with Nox4 overexpression

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

institute: Toray Industries,Inc.

summary: The objective of the present study is to investigate the effect of Nox4 overexpression on human brain endothelial cells. Comparative gene expression analysis was performed using cultured human brain microvascular endothelial cells with adenovirus-mediated LacZ or Nox4 overexpression. Gene expression was analyzed using 3D-Gene® Human 25k oligonucleotide microarrays and computational gene expression analysis tools. Nox4 overexpression resulted in significant changes in numerous genes related with (1) signaling pathways mediated by cytokines and chemokines, (2) stress responses, such as NFB activation, and (3) leukocyte chemotaxis and migration.

overall_design: Total RNAs were extracted from human brain microvascular endothelial cells with adenovirus-mediated LacZ or Nox4 overexpression (5 MOI or 10MOI) using the RNeasy mini kit with the RNase-free DNase set and subjected to microarray analysis.

first: Koichi

last: Arimura

first: Yoji

last: Yoshikawa

first: Kuniyuki

last: Nakamura

first: Tetsuro

last: Ago


title: Identifying transcription factor-DNA interactions using machine learning

city: Athens

first: Robert

middle: J

last: Schmitz

state: GA

address: B416 Davison Life Sciences

department: Genetics

institute: University of Georgia

summary: We focused on building models that incorporated transcription factor (TF)-DNA interaction data for 12 members of the Auxin Response Factor (ARF) family from soybean as assessed by DNA Affinity Purification and sequencing (DAP-seq).

overall_design: We produced DAP-seq data for the 12 members of maize ARF using soybean genomic DNA as input.


title: RNA-seq profiling of tissue from deer mouse embryo tails

first: Evan

last: Kingsley

summary: We used RNA-seq to compare transcriptional profiles from the embryonic tails from E12.5–E15.5 Peromyscus maniculatus. Samples are from two ecotypes, forest (P.m.nubiterrae) and prairie (P.m.bairdii) with different numbers of caudal vertebrae.

sample_organism:
Peromyscus maniculatus bairdii
Peromyscus maniculatus nubiterrae

overall_design: Embryonic tail RNA expression profiles from E12.5–E15.5 P. m. nubiterrae (n = 18) and P. m. bairdii (n = 17)

middle: P


title: RNA-seq of arsenite-induced stress granule transcriptomes in control and Mettl3- and m6A-depleted mouse embryonic fibroblasts (MEFs)

city: New York

first: Ryan

last: Ries

state: NY

address: 1300 York Avenue

institute: Weill Cornell Medical College

summary: N6-methyladenosine (m6A) is the most abundant nucleotide modification found on mRNA.  m6A has been previously shown to facilitate recruitment of mRNAs to stress granules due to interactions between m6A and the YTHDF proteins.  Although protein-RNA interactions are known to contribute to the recruitment of mRNAs to stress granules, the predominant driver of mRNA recruitment to stress granules is thought to be RNA-RNA interactions between long RNAs.  Here, we show that m6A contributes significantly to the length-dependent effect of mRNA enrichment in stress granules and that upon depletion of METTL3, the enzyme responsible for adding m6A to nascent transcripts, the nature of the stress granule transcriptome is fundamentally altered by greatly reducing the propensity of long mRNAs to enter stress granules.  This reveals that not only does m6A enhance the phase separation of mRNAs, but that it is a driving force underpinning length-dependent enrichment of mRNAs in stress granules.

overall_design: RNA-seq was performed on control and METTL3- and m6A-depleted E13.5 mouse embryonic fibroblasts.   Total mRNA samples were harvested under standard conditions.  Stress granule-enriched mRNA fractions were isolated following arsenite stress (500 uM, 30 min) and stress granule enrichment via centrifugation. Each condition has two biological replicates.

first: Brian

middle: F

last: Pickering

first: Hui Xian

last: Poh

first: Samie

last: Jaffrey


title: RNA-seq profiling of tissue from hybrid deer mouse embryo tails

summary: We used RNA-seq to estimate allelic expression bias in the embryonic tails of E12.5 and E14.5 Peromyscus maniculatus nubiterrae x bairdii. Samples are from F1 hybrids between forest (P.m.nubiterrae) and prairie (P.m.bairdii) with different numbers of caudal vertebrae.

sample_organism: Peromyscus maniculatus nubiterrae x Peromyscus maniculatus bairdii

overall_design: Embryonic tail RNA expression profiles from E12.5 (n = 4) and E14.5 (n = 4) P. m. nubiterrae x bairdii hybrids


title: Whole blood DNA methylation arrays of individuals with psoriatic arthritis, psoriasis vulgaris, and healthy control subjects

city: Changsha

first: Min

last: Deng

state: Hunan

address: Renmin Middle Road 139

department: Dermatology

institute: the Second Xiangya Hospital of Central South University

summary: Genome-wide DNA methylation was analyzed to screen for differentially methylated CpG sites in the discovery phase to explore the role of DNA methylation CpG markers in the diagnosis of psoriatic arthritis patients.

overall_design: DNA methylation array was used to screen for differentially methylated CpG sites in 25 patients with psoriatic arthritis, 20 patients with psoriasis vulgaris, and 19 healthy controls.

first: Qianjin

last: Lu

first: Ming

last: Zhao

first: Yuwen

last: Su


title: Nitrate reduction by Geobacter sulfurreducens and the catalytic role of palladium on the reduction pathway

city: Mexico

first: Leticia

last: Vega

state: Mexico

address: Circuito Ext s/n

country: Mexico

institute: Universidad Nacional Autonoma de Mexico

summary: Geobacter sulfurreducens is a widely explored microorganism recognized by its metabolic versatility able to reduce a number of external electron acceptors. In the present study the capacity of this strain to reduce nitrate was evaluated along with its transcriptomic profile under nitrate-reducing conditions and the catalytic role of Pd nanoparticles on the reductive pathway. Results demonstrated that G. sulfurreducens was able to reduce nitrate and important kinetic differences related to the time response were found among the electron donors used (acetate and hydrogen). When using acetate, a delay response on nitrate reduction of 4 days and reduction of 94% of nitrate was achieved, while nitrite was not detected, and all the nitrogen was recovered as ammonium (79.6 ± 5.7 %). The use of hydrogen as electron donor increased 2-fold the maximum rate of nitrate reduction, leading to 93% reduction of nitrate during the first 20 h with recovery of 45% as ammonium, while nitrite was not detected. In addition, transcriptome profiling analysis of G. sulfurreducens under nitrate-reducing conditions using hydrogen or acetate as an electron donor at 2 and 6 days reveals that a core of 146 genes (69 upregulated and 77 downregulated) are differentially expressed in all conditions. Genes related to nitrogen metabolism, such as nrfA and nrfH, gdhA, and amtB, were upregulated in the incubations and RT-qPCR data confirmed upregulations of these genes. Experiments performed with biologically synthesized Pd (Bio-Pd) + G. sulfurreducens cells demonstrated synergistic input of Bio-Pd and the metabolic capacity of G. sulfurreducens. These results expand the metabolic versatility of G. sulfurreducens, which may have important implications in nitrogen cycling in natural environments and engineered systems.

overall_design: Transcriptomic profiling analysis of Geobacter sulfurreducens under nitrate-reducing conditions. We used cultures with acetate-nitrate or hydrogen-nitrate (as a donor-acceptor electron) for 2 (48 hours) and 6 (144 hours) days of incubation. As a control was used cells of Geobacter sulfurreducens growing in NBAF medium.

first: Aurora

last: Pat-Espadas

first: Alberto

last: Hernández-Eligio

last: Vega-Alvarado

first: Katy

last: Júarez

first: Francisco

last: Cervantes


title: Single Cell RNAseq and VDJ sequence of ACE2 reactive and non-reactive B-cells isolated from COVID-19 patients peripheral blood

city: Baltimore

first: Srinivasan

last: Yegnasubramanian

state: MD

address: 1661 Orleans St

institute: Johns Hopkins SOM

summary: Flow cytometry sorted B-cells reactive to ACE2 peptides isolated from peripheral blood of COVID-19 patients compared with non-reactive B-cells using pooled hashtag barcoding and 10x genomics 5'DGE kit and VDJ recombination of B-cells

overall_design: B-cells isolated from 7 COVID-19 patient's peripheral blood were seperated into ACE2 reactive and non-reactive population using ACE2 peptides. Each of these patient's B-cells were labelled with Hashtag oligo linked to antibody, which allowed to barcode each patient with unique DNA oligo sequence. Then ACE2 reactive B cells from 7 patients were pooled together and loaded on 10x Genomics Chip G using 5'DGE kit to interogate single cell 5DGE (Digital gene expression) and VDJ sequence in B-cells. Similarly, ACE2 non-reactive cells were pooled together.

first: Antony

last: Rosen

first: Ajay

last: Vaghasia

first: Livia

last: Casciola-Rosen


title: Controlled release of exosomes by AMPK/SREBPs pathway

city: Shanghai

first: Zhan

last: Ding

address: FengLin 300

institute: CAS Center for Excellence in Molecular Plant Science

summary: Exosome-like extracellular vesicles (EVs) are very important vesicles for intercellular signal transmission. Although host factors involving exosome-like EV production and release has been reported, the cellular signaling pathway regulating EV production is largely unknown. Here we performed a kinase inhibitor library screening to identify pathways controlling EV’s production. We found a kinase inhibitor, APY0201, which significantly increased EV secretion through upregulation of intracellular sterol synthesis and the volume of intracellular multivesicular bodies (MVBs). APY0201 specifically caused the decrease of AMP-activated protein kinase (AMPK) phosphorylation and activation of sterol regulatory element-binding protein (SREBP1), a pivotal transcription factor of sterol synthesis gene expression. In addition, both AMPK agonist and SREBP inhibitor deteriorate augmented EV production induced by APY0201. Ectopic expression of AMPK and SREBP1 corroborated that AMPK and SREBP1 are two major host factors governing the production of exosome-like EVs. Taken together, we identified that APY0201 is a novel kinase inhibitor targeting AMPK-SREBP1 pathway which is important for EV biogenesis and release. Our findings might pave the way to achievable finely upregulated EV production.

overall_design: RNA-seq of 8 cell samples, including 2 DMSO controls. Each sample had 2 biological replicates.

first: Wen

middle: X

last: Bian

first: Gang

last: Long


title: Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and KRAS mutated lung oraganoids Transcriptomes

first: Jun

last: Liu

state: Guangdong

address: No.2 Lujing Road

department: Dermatology Hospital

institute: Southern Medical University

summary:
Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare lung organoids transcriptome profiling (RNA-seq) between wild type and KRAS mutation
Methods:  mRNA profiles of wild-type (WT) and KRAS mutated organoids were generated by deep sequencing, in triplicate, using Illumina HiSeq. 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.

overall_design: lung organoids mRNA profiles of wild type (WT) and KRAS mutation

first: Jianqi

last: Feng

first: Zhili

last: Rong


title: Investigation of mettl4 mediated alterative splicing variation

city: Bad Nauheim

first: Lei

last: Gu

state: MASSACHUSETTS

address: parkstreet 1

institute: Max Planck Institute for heart and lung research

summary: We compare mettl4 KO and WT samples from different species to understand how mettl4 affects the alterative splicing

sample_organism:
Schizosaccharomyces pombe
Drosophila melanogaster
Danio rerio
Homo sapiens
Mus musculus

overall_design: mRNA profiles of mettl4 KO and WT


title: Cerebrospinal fluid cell-free DNA methylomes subtyping pediatric medulloblastoma

city: Houston

first: Jia

last: Li

state: Texas

address: 2121 W HOLCOMBE BLVD

department: CEDP

institute: Guangzhou Medical University

summary: Medulloblastoma (MB) is an embryonal tumor of the cerebellum and a highly malignant childhood brain tumor. Cell-free circulating tumor DNA (ctDNA) from the cerebrospinal fluid (CSF) of patients with brain tumors faithfully represent genomic alterations of brain tumors. Distinct epigenetic signatures among subgroups of MB allow us to detect epigenetic alterations in CSF to aid classify and guide therapy of MB tumors. Here, we evaluate DNA methylation of ctDNA derived from small amount of CSF (200 µL) and matched tumor DNA from four subtypes of MB patients. We find highly concordance of DNA methylation between CSF ctDNA and tumor DNA in a subtype manner. Our results show that CSF ctNDA methylation can be a minimal invasive precisely method to assess epigenetic alterations of MB in a subtype manner, which is complementary to current diagnoses of MB tumors.

overall_design: We collected CSF  samples from four subtypes of pediatric MB patients; We performed WGBS for these samples

first: Yun

last: Huang

first: Xiaonan


title: RNA-seq analysis of ASCL1-induced neuronal differentiation in WT and MED25 knockout Glioblastoma Stem Cells

first: Graham

last: MacLeod

state: ON

address: 144 College Street

department: Pharmaceutical Sciences

institute: University of Toronto

summary: Glioblastoma stem cells were infected with lentivirus expressing a control (gRNA-AAVS1) or MED25 targeting gRNA to assess the role of MED25 in the stem cell compartment of Glioblastoma stem cells. Cells were the subjected to doxycycline-induced ASCL1 overexpression (+DOX) to induced neuronal differentiation.

overall_design: 3 biological replicates each for gRNA-AAVS1 -DOX, gRNA-AAVS1 +DOX, gRNA-MED25 -DOX, gRNA-MED25 +DOX

first: Moloud

last: Ahmadi

first: Andy

last: Yang

first: Stephane

last: Angers


title: Whole transcriptome expression profiles in Ti particles induced inflammatory response

city: Jinan

first: yonghui

last: jiang

address: #44 Wenhuaxi Road

institute: Shandong University

summary: We performed a high throughput RNA sequencing to evaluate the expression profiles of messenger RNAs (mRNAs) and non-coding RNAs (lncRNAs, miRNAs, and circRNAs) in Titanium (Ti) particles induced inflammatory responses using RAW264.7 cells.

overall_design: Examination of mRNA and ncRNA profiles in  Ti induced RAW264.7 cells.

first: Yonghui

last: Jiang

first: Huanzhi

last: Ma

first: Qin

last: Zhang

first: Wei


title: Role of iron in gene regulation in Prevotella intermedia

city: Richmond

first: Janina

last: Lewis

state: VA

address: 521 North 11th Street

department: Philips Institute of OCMB

institute: Virginia Commonwealth University

overall_design: Prevotella intermedia OMA14 strain grown in iron replete conditions was used to compare to P. intermedia OMA14 grown under iron deplete conditions.  The strain was obtained from Dr. Mariko Naito, DNA Res. 2016 Feb;23(1):11-9.

last: Gui


title: Genome-wide binding profile of Smad3 and Smad7 in mouse Ch12 cell line (ChIP-Seq)

city: Bethesda

first: Yongbing

last: Zhao

state: Maryland

address: 10 Center Drive RooM 13C101A

department: NIAMS

institute: National Institutes of Health

summary: Mammalian genome encodes approximately 1,700 transcription factors (TFs), 1,300 out of which have sequence specific binding motifs. Transcription in mammalian cells is regulated by the recruitment of TFs to specific cis-regulatory elements. In spite of consistent efforts on the function of individual TF, the question still remains how TFs bind to DNA and form enhancer. Here, we try to solve this problem by investigating the relationship between TF binding pattern and chromatin accessibility (ATAC-Seq). We first systematically acquired ATAC-Seq dataset as well as matched RNA-Seq dataset from different mouse primary tissues. A comprehensive TF binding map was built for each tissue/cell type by genomic approaches.

overall_design: We analyzed genome-wide binding profile of Smad3 and Smad7 in mouse Ch12 cell line.

first: Andrea

last: Conte

first: Supriya

last: Vartak

first: Rafael

last: Casellas


title: Genome-wide binding profile of Smad3 and Smad7 in mouse Ch12 cell line (RNA-Seq)


title: Expression data from WT and Zak-deficient naïve CD4+ T cells stimulated with anti-CD3 and anti-CD28 for 0, 6 or 48 hours

city: Shang Hai

first: Yan

last: Wang

address: Yue yang Road 320

institute: Chinese Academy of Science

summary: We conducted gene expression profile analysis by using wild-type and Zak-deficient naive CD4+ T cells. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis revealed the most prominent biological processes altered in naive CD4+ T cells  stimulated with α-CD3/28 for 6 hours were associated with AKT signaling and autoimmune disease.

overall_design: Genome-wide expression profiling of WT and Zak-deficient naïve CD4+ T cells stimulated with α-CD3/28 for 0, 6 or 48 hours were generated by RNA-sequencing analysis

first: Yichuan

last: Xiao


title: Expression data of peripheral CD4+ T cells from young(6-8-week-old) and old(11-month-old) mice

summary: We conducted gene expression profile analysis by using peripheral CD4+ T cells from young and old mice.Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis revealed the most prominent biological processes altered in peripheral CD4+ T cells from young and old mice were associated with cytoplasmic DNA-sensing, AKT signaling and autoimmune disease.

overall_design: Genome-wide expression profiling of peripheral CD4+ T cells from young and old mice that were stimulated with α-CD3/28 for 6 hours were generated by RNA-sequencing analysis


title: Analysis of microarray data of lesional and unaffected skin from morphea patients

city: Dallas

first: Jane

last: Zhu

address: 5323 Harry Hines Blvd

institute: University of Texas Southwestern Medical Center

overall_design: Total RNA was isolated, ampliifed, quality checked, and labeled by the UT Southwestern Microarray Core Facility using the TotalPrep RNA amplification kit.

first: Heidi

last: Jacobe


title: Expression data from PyMT P11-KO or P11-WT mammary tumours

city: Halifax

first: Paola

last: Marcato

state: Nova Scotia

address: 5850 College Street

department: Pathology

institute: Dalhousie University

summary:
S100A10 (p11) is a plasminogen receptor that regulatess cellular plasmin generation by cancer cells. In the current study we used the MMTV-PyMT mouse breast cancer model to investigate the role of p11 in oncogenesis. Genetic deletion of p11 resulted in significantly decreased tumor onset, growth rate and spontaneous pulmonary metastatic burden in the PyMT/p11-KO mice. This phenotype was accompanied by substantial reduction in Ki67 positivity, macrophage infiltration and decreased vascular density in the primary tumors, and appearance of invasive carcinoma and pulmonary metastasis. Surprisingly, immunohistochemical analysis of wild-type MMTV-PyMT mice failed to detect p11 expression in the tumors or metastatic tumor cells and loss of p11 did not decrease plasmin generation in the PyMT tumors and cells.  Furthermore, tumor cells expressing p11 displayed dramatically reduced lung metastasis when injected into p11-depleted mice, further strengthening the stromal role of p11. Transcriptome analysis of the p11-depleted tumors showed marked reduction in genes involved in breast cancer development, progression, and inflammation such as AREG, MUC1 and S100A8. The PyMT/p11-KO tumors displayed remarkable increase in inflammatory cytokines such as IL-6, IL-10 and IFN-γ. Gene expression profiling and immunohistochemistry primary breast cancer samples showed that p11 mRNA and protein was significantly higher in tumors compared to normal mammary tissue. The mRNA expression was significantly associated with poor patient prognosis and significantly elevated in high grade, triple negative tumors and tumors with high proliferative index.
We used microarray to detail the global programme of gene expression underlying reduced growth/establishment of P11-KO PyMT tumours.

overall_design: Spontaneous mammary tumours from PyMT P11-KO or P11-WT mice were excised from 12 week old mice. Individual tumours were homogenized for RNA extraction and hybridization on Affymetrix microarray.

first: Alamelu

last: Bharadwaj

first: Margaret

middle: L

last: Dahn


title: Host-viral infection maps at single-cell resolution reveal signatures of severe COVID-19 patients

city: Shenzhen

first: Zheng

address: No. 29, Bulan Road

institute: Shenzhen 3rd People's Hospital

summary: Viruses are a constant threat to global health as shown by the current COVID-19 pandemic. Currently, lack of data underlying the biology of the interaction of the human host with SARS-CoV-2 virus is limiting effective therapeutic intervention. We introduce Viral-Track, a computational method that globally scans unmapped scRNA-seq data for the presence of viral RNA, enabling transcriptional cell sorting of infected versus bystander cells. We demonstrate the ability of Viral-Track to detect various viruses from multiple models of infection. Applying Viral-Track to Bronchoalveloar Lavage samples from severe and mild COVID-19 patients reveals a dramatic impact of the SARS-CoV-2 virus on the immune system of severe patients as compared to mild cases. The SARS-CoV-2 infection is mainly restricted to epithelial and macrophage subsets. In addition, Viral-Track detects in one of the severe patients an unexpected co-infection of the human MetaPneumoVirus, present mainly in monocytes and strongly dampening their type-I IFN-signaling.

overall_design: single cell RNA-seq of hepatitis-B positive liver and male severe covid19 positive lung.

first: Pierre

last: Bost

first: Amir

last: Giladi

first: Yang

last: Liu

first: Yanis

last: Bendjelal

first: Gang

last: Xu

first: Eyal

last: David

first: Ronnie

last: Blecher-Gonen

first: Merav

last: Cohen

first: Chiara

last: Medaglia

first: Hanjie

last: Li

first: Shuye

first: Benno

last: Schwikowski

first: Ido

last: Amit


title: Elucidating the role of Zuo1 protein on the translational control of gene expression in Saccharomyces cerevisiae

city: Ann Arbor

first: mehmet

last: tardu

state: MI

address: 930 N University Ave

department: Chemistry

institute: University of Michigan

summary: The ribosome associated complex (RAC) is a ribosome bound protein chaperone complex reported to surveil the translation of proteins with positively charged regions. It has been posited that RAC might be able to directly regulate translation by coupling co-translational folding with the peptide-elongation cycle. To identify the targets of RAC in cells and test the hypothesis that the complex modulates translation, we performed ribosome profiling on wild- type yeast cells and cells lacking a key component of the RAC that binds near the ribosome active site (zuo1Δ). Ribosome profiling is a sequencing-based technique that allows us to take a nucleotide resolution snapshot of where every ribosome sits on every mRNA in a cell at a given point in time. This powerful approach can provide information about the contributions of individual proteins to the translational landscape of a cell. We identified >300 targets for the RAC, and unexpectedly observed that the ribosome frameshifts on ~10% of these targets in zuo1Δ cells. The maintenance of ribosome reading frame is essential for cell health because frameshifts can result in the production of non-functional truncated and extended protein products. These studies have the potential to uncover RAC as a critical determinant of translational fidelity in eukaryotic cells.

overall_design: mRNA-seq and Ribosome profiling of exponentially growing (OD600 = 0.6) Saccharomyces cerevisiae cells were performed by deep sequencing , in two biological replicates, using Illumina HiSeq-4000 platform.

first: Mehmet

last: Tardu

first: Kristin

middle: S

last: Koutmou


title: Evaluation of the potential of non-starch soluble polysaccharides from 3 algae to modulate the immune response and metabolic state in the intestine

city: Lelystad

first: Marcel

last: Hulst

state: Flevoland

address: Edelhertweg 15

department: Livestock research

country: Netherlands

institute: Animal Sciences Group

summary: Non-starch soluble polysaccharides (NSPs) produced by yeasts are used in animal nutrition to improve health and performance. However, the magnitude of the effect may be dependent upon the quantity and the composition of the polysaccharides. As seaweeds are attractive sources of NSPs, this study was set up to evaluate their potential to improve intestinal health. The effect of NSP extracts prepared from Saccharomyces cerevisiae containing β-glucan and mannan (PSY1, positive control) or a mixture of mannanoligosaccharides (PSY2, positive control), micro algae containing β-glucan (PSA1), brown macro algae containing fucoidan and laminarin (PSA2), and green macro algae containing ulvan (PSA3) on intestinal porcine epithelial cells J2 (IPEC-J2) was studied in the presence and absence of the enterotoxigenic bacterium Escherichia coli k99 strain (ETEC) as an in vitro challenge. The E.coli-k99 strain with adhesion factor F41 (41/32) was isolated from a mastitis-infected udder. In addition, a mixed extract prepared from vegatal orgin supplemented with phenolic compounds from vegetal origin, zinc and selenium (9631), and ZnO were tested to compare responses to NSP extracts. Gene expression was measured in IPEC-J2 cells after 2 and 6 hours of incubation using “whole genome” porcine microarrays (submission as a conference paper at the SEAGRICULTURE 2017 6th International Seaweed Conference).

overall_design:
IPEC-J2 cells were grown in 2 cm2 wells for 7 days at 37 ºC and 5% CO2 using 1:1 DMEM/Ham’s F10 1:1 medium supplemented with 5% FCS without antibiotics. For all tests, confluent monolayers were washed twice with medium without FCS (hereafter denoted as medium) and incubated for 1 hour with this medium. Hereafter, the medium was discarded and an extract dissolved/suspended in medium was added. Different concentrations of extracts and ZnO (concentrations are specified in the source name column) were used for incubation of IPEC-J2 monolayers for a period of 2 and 6 hours in the absence and presence of ETEC. All incubations were tested in duplicate and for each type of additive duplicate control wells containing no additive (only culture medium) were incubated for 2 and 6 hours. After incubation total RNA was extracted. RNA's extracted from replicates were pooled (biological replicates) and this pool was hybridized in duplicate (technical replicates).
IPEC-J2 enterocyte cell line derived from the jejunum of piglets, host-feed interaction

middle: M

first: Arjan

last: Hoekman

first: Marinus

last: van Krimpen

first: Alexandre

last: Budan


title: Plasmodium falciparum intraerythrocytic stage transcription time course for NF54 and isogenic mutant line with altered K13 expression II.

city: Notre Dame

first: Michael

middle: T

last: Ferdig

state: IN

address: 100 Galvin Life Sciences Center

department: Biological Sciences

institute: University of Notre Dame

summary: Plasmodium falciparum intraerythrocytic stage transcription four hour time course for NF54 and PB58 (an isogenic line with a piggyBac transposon in the promotor of K13 that alters K13 expression)

overall_design: The parasite strains NF54 and PB58  (the K13 mutant) were maintained in identical standard culture conditions and synchronized by 3 rounds of sorbitol synchronization. A four hour time-course was collected at 2, 6, 10, 14, 18, 22, 26, 30, 34, 38, 42, and 46 hours post invasion (hpi) with triplicate samples at 6, 26 and 38 hpi.

first: Katrina

middle: A

last: Button-Simons


title: Affymetrix SNP array data for an INAD patient

status: Public on May 31 2023

city: Huzhou

first: yongxue

last: lv

address: No. 2 East Street

institute: Huzhou Maternity & Child Health Care Hospital

summary:
Infantile neuroaxonal dystrophy (INAD) is an ultra-rare early-onset autosomal recessive neurodegenerative disorder due to PLA2G6 variants.
Copy number analysis of SNP arrays was performed on one INAD patient sample.

overall_design: Affymetrix SNP arrays were performed according to the manufacturer's directions on DNA extracted from the patient's peripheral blood sample.

first: Yongxue

last: Lv

first: Fengfeng

last: Qi