title: Senescent melanocytes driven by glycolytic changes are characterized by melanosome transfer dysfunction.

first: Jin Cheol

last: Kim

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

overall_design: Refer to individual Series


title: Gene expression profile at single cell level of human cerebral cortical organoids with and without LIF treatment

status: Public on Mar 23 2023

city: San Francisco

first: Li

last: Wang

state: CA

address: 35 medical center way RMB-932E

department: Regeneration Medicine

country: USA

institute: University of California - San Francisco

type: Expression profiling by high throughput sequencing

summary: Proper regulation of the proliferation and differentiation of radial glia (RG), the neural stem cells of the developing cortex, is fundamental for brain growth and organization. In humans, a specialized RG subtype, the outer radial glia (oRG), are abundant and give rise to diverse neuronal and glial progeny. However, the mechanisms regulating oRG development and differentiation are not fully understood. Here we investigated the regulation of oRG expansion and lineage potential by perturbing Leukemia Inhibitory Factor (LIF) signaling in the developing human cortex and in human pluripotent stem cell (PSC)-derived cortical organoids. LIF receptors are specifically expressed in oRG cells during neurogenesis, and, consistent with the previously described role of this cytokine as an activator of stem cell self-renewal, LIF treatment increased the number of oRG cells. Surprisingly, LIF treatment also increased the production of inhibitory interneurons (INs) in the cortex. Comparative transcriptomic analysis suggested that these INs resemble INs produced in the caudal ganglionic eminence (CGE). To test if oRG cells are the progenitors of these CGE-like INs, we isolated oRG cells from primary developing cortex and cultured them for several weeks with and without LIF treatment. We found that CGE-like INs were produced by oRG cells, and their abundance is increased by LIF treatment. Together, these observations suggest that LIF signaling regulates oRG lineage potential and capacity to generate CGE-like INs.

overall_design: We cultured cerebral cortical organoisds with and without LIF treatment for up to 15 weeks. For short-term treatment, LIF was added between weeks 6-8 in the treatment group, and organoids were harvested at weeks 8, 10, and 15 for single-cell RNA sequencing. For long-term treatment, LIF was added between weeks 5-15 in the treatment group, and organoids were harvested at weeks 8, 10, and 15 for single-cell RNA sequencing.

first: Madeline

middle: G

last: Andrews

first: Clara

last: Siebert

first: Aparna

last: Bhaduri


title: Transcriptomic expression profiling by high throughput sequencing for human induced pluripotent stem cells (iPSCs) derived neural stem cells with Ethidium Bromide (EtBr) exposure

city: Bergen

first: Kristina Xiao

last: Liang

state: Hordaland

address: Jonas Lies vei 87, P. O. Box 7804

country: Norway

institute: University of Bergen

summary: The pupose of this study is to explore the transcriptome profiling changes of the neural stem cells differentiated from POLG patient iPSCs during EtBr treatment

overall_design:
Examination of mRNA profile in iPSC-derived neural stem cells
**RAW data not provided due to patient privacy concerns**

first: Cecilie

middle: K

last: Kristiansen

first: Kristina

middle: X


title: 4E-BP1-dependent translation in nociceptors controls mechanical hypersensitivity via TRIM32/type I interferon signaling

status: Public on Mar 27 2023

city: Montreal

first: Arkady

last: Khoutorsky

address: McIntyre Medical Building, Room 1208

department: Department of Anesthesia and Faculty of Dentistry

country: Canada

institute: McGill University

summary: Activation of the mechanistic target of rapamycin complex 1 (mTORC1) contributes to the development of chronic pain. However, the specific mechanisms by which mTORC1 causes hypersensitivity remain elusive. The eukaryotic initiation factor 4E-binding protein 1 (4E-BP1) is a key mTORC1 downstream effector that represses translation initiation. Here we show that nociceptor-specific deletion of 4E-BP1, mimicking activation of mTORC1-dependent translation, is sufficient to cause mechanical hypersensitivity.

overall_design: Using the translating ribosome affinity purification in nociceptors lacking 4E-BP1, we identified a pronounced translational upregulation of TRIM32, an E3 ubiquitin ligase that promotes interferon signalling. Downregulation of TRIM32 in nociceptors or blocking type I interferon signaling reversed the mechanical hypersensitivity in mice lacking 4E-BP1. Furthermore, nociceptor-specific ablation of TRIM32 alleviated mechanical hypersensitivity caused by tissue inflammation. These results show that mTORC1 in nociceptors promotes hypersensitivity via 4E-BP1-dependent upregulation of TRIM32/interferon signaling and identify TRIM32 as a new therapeutic target in inflammatory pain.


title: Identifying the origin and mechanisms of pathological angiogenesis in neuroinflammatory diseases

status: Public on Mar 14 2023

city: New York

first: Vilas

last: Menon

state: NY

department: Neurology

institute: Columbia University Medical Center

summary: Multiple sclerosis (MS) is a chronic demyelinating disease of the central nervous system (CNS). Studies in human MS and its animal model experimental autoimmune encephalomyelitis (EAE) have shown that new abnormal vessels develop in demyelinating plaques through pathological neo-angiogenesis, which exacerbates MS/EAE pathology by contributing to the leakage of serum components and infiltration of immune cells into the CNS. However, the cellular origin and the signaling pathways underlying this pathology remain poorly understood. Here, using single-cell RNA sequencing and validation with in situ hybridization and immunofluorescence, we discovered that neo-angiogenesis is initiated specifically by venous endothelial cells during EAE. Moreover, we identified VEGF-A signaling as the primary driver of neo-angiogenesis in EAE, as treatment with the VEGF-A blocking antibody, bevacizumab, ameliorated the EAE pathology by reducing neo-angiogenesis in vivo. Our findings may lead to the development of novel therapeutics designed to reduce neo-angiogenesis and improve long-term neurological deficits in MS.

overall_design: MOG35-55 EAE was induced in 10–12-week-old TCF/LEF1::H2B::eGFP female Wnt reporter mice in the C57BL/6J background and spinal cords were collected at acute peak (score = 2-4; 16-17 d.p.i.) and early chronic (score ≤ 1; 28-29 d.p.i.) phases of the disease. Age-matched healthy and CFA-immunized mice served as controls. To test whether VEGF-A is necessary to induce neo-angiogenesis in vivo in EAE, EAE-induced wild-type C57BL/6J mice were treated with either the humanized, anti-VEGF-A monoclonal antibody (mAb), bevacizumab, or IgG control antibody. Following single cell dissociation of the spinal cord, endothelial cells were labeled with CD31-APC antibody and FACS for single cell RNA sequencing analysis.

first: Sanjid

last: Shahriar

first: Dritan

last: Agalliu


title: The arginine methyltransferase PRMT1 establishes transcriptomic homeostasis essential for spermatogonial differentiation and male fertility

status: Public on Mar 31 2023

city: Hefei

first: Caoling

last: Xu

state: Anhui

address: 96 Jinzhai Road

department: Department of Life Sciences and Medicine

country: China

institute: University of Science and Technology of China

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Protein arginine methyltransferase 1 (Prmt1) is known as the major Type-I protein arginine methyltransferase that deposits asymmetrical dimethylarginine (ADMA) in both histone and non-histone substrates. Nonetheless, how Prmt1 and its downstream signalling through substrate methylation function in the male germline development remains poorly understood. In this study, we discovered that Prmt1 is predominantly present in the spermatogonial population during mouse spermatogenesis. Using three Cre-mediated conditional Prmt1 knockout mouse lines, we observed that Prmt1 is essential for the maintenance of spermatogonial cells and Prmt1-deposited ADMA marks coordinate an inherent homeostasis among three types of substrate methylation. In conjunction with high-throughput Cut&Tag and modified mini-bulk Smart-seq2 analyses, we unveiled that Prmt1-mediated H4R3me2a mark enriched in the promoter region, together with other histone arginine methylations, drives a global transcriptomic landscape that maintains the regular gene expression and alternative splicing. Collectively, we provide the genetic evidence showing the essential role of Prmt1-deposited arginine methylation in the establishment of transcriptional homeostasis, and shed light on the methylarginine signalling pathway in orchestrating spermatogonial development in the mammalian germline.

overall_design: We used WT and Prmt1 conditional knockout samples for all the experiments through tamoxifen injection for 3 days. For WT CUT&Tag we used C57BL/6J

first: Muhammad

last: Azhar

first: Jianqiang

last: Bao


title: LINC01133 can induce acquired resistance to ferroptosis in pancreatic cancer by enhancing the mRNA stability of FSP1 through forming the LINC01133-FUS-FSP1 complex [circRNA]

status: Public on Mar 10 2023

city: hongkong

first: Yangchao

last: Chen

state: State...

address: Lo Kwee-Seong Integrated Biomedical Sciences Bld , hongkong

department: School of Biomedical Science

country: Hong Kong

institute: Chinese University of Hongkong

type: Non-coding RNA profiling by high throughput sequencing

summary: To explore the critical non-coding RNAs in the regulation of ferroptosis,  we treated panc-1 with cystine depletion.We then performed gene expression profiling analysis using data obtained from RNA-seq of panc-1 cultured normally and panc-1 treated with cystine depletion for 24h in triplicate.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for panc-1 cultured normally and panc-1 treated with cystine depletion for 24h in triplicate

first: Shaowen


title: LINC01133 can induce acquired resistance to ferroptosis in pancreatic cancer by enhancing the mRNA stability of FSP1 through forming the LINC01133-FUS-FSP1 complex [lncRNA]


title: LINC01133 can induce acquired resistance to ferroptosis in pancreatic cancer by enhancing the mRNA stability of FSP1 through forming the LINC01133-FUS-FSP1 complex


title: LINC01133 can induce acquired resistance to ferroptosis in pancreatic cancer by enhancing the mRNA stability of FSP1 through forming the LINC01133-FUS-FSP1 complex [miRNA-seq]


title: FIGNL1 AAA+ ATPase remodels RAD51 and DMC1 filaments in meiotic DNA replication and recombination

city: Suita

first: Masaru

last: Ito

state: Osaka

address: Yamadaoka 3-2

country: Japan

institute: Osaka University

summary: The formation of RAD51/DMC1 filaments on single-stranded (ss)DNAs, which is essential for homology search and strand exchange in DNA double-strand break (DSB) repair and for the protection of stalled DNA replication forks, is tightly regulated in time and space. FIGNL1 AAA+++ ATPase plays positive and negative roles in the RAD51-mediated recombination in human cells. However, the role of FIGNL1 in gametogenesis remains unsolved. Here, we characterized a germ-line-specific conditional knockout (cKO) mouse of FIGNL1. The Fignl1 cKO male mice showed defective chromosome synapsis and impaired meiotic DSB repair with the accumulation of RAD51/DMC1 on chromosomes in mid-meiotic prophase I, supporting a role of FIGNL1 in a post-assembly stage of RAD51/DMC1 filaments. Fignl1 cKO spermatocytes accumulate RAD51 and DMC1 ensembles on chromosomes not only in early meiotic prophase I but also in meiotic S-phase. These RAD51/DMC1 assemblies are independent of meiotic DSB formation. Finally, we showed that purified FIGNL1 dismantles RAD51 filament on double-stranded (ds)DNA as well as ssDNA. These results suggest a critical role of FIGNL1 to limit the uncontrolled assembly of RAD51 and DMC1 on native dsDNAs during the meiotic S-phase and meiotic prophase I.

overall_design: Chromatin immunoprecipitation followed by single-stranded DNA sequencing (ChIP-SSDS) for RAD51 in control and Fignl1 cKO mouse testes

first: Asako

last: Furukohri

first: Kenichiro

last: Matsuzaki

first: Yurika

last: Fujita

first: Atsushi

last: Toyoda

first: Akira

last: Shinohara


title: Screen for the lncRNAs that are specificly upregulated in fetal liver by microarry analysis

status: Public on Mar 15 2023

city: Shanghai

first: Yiqing

last: Zhu

address: No.800 Xiangyin

institute: Naval Medical University

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

summary: To identify oncofetal lncRNAs that are specificly upregulated in fetal liver, we analyzed the expression profiles of lncRNAs in human fetal livers (3 samples) and adult livers (3 samples) using microarray assays.

overall_design: 6 samples are analyzed, and 3 replicates are include

first: Fang

last: Wang

first: Bang

last: Xiao

first: Meng

last: Liu


title: RNA sequencing of peripheral blood mononuclear cells isolated from Korean patients with asthma

status: Public on Mar 08 2023

city: Seoul

first: Ji Eun

last: Lim

address: 26, Kyungheedae-ro, Dongdaemun-gu

department: Department of Biochemistry and Molecular Biology, School of Medicine

country: South Korea

institute: Kyung Hee University

summary: More than 200 asthma-associated genetic variants have been identified in genome-wide association studies (GWASs). Expression quantitative trait loci (eQTL) data resources can help identify causal genes of the GWAS signals, but it can be difficult to find an eQTL that reflects the disease state because most eQTL data are obtained from normal healthy subjects. We performed a blood eQTL analysis using transcriptomic and genotypic data from 436 Korean asthma patients. To identify asthma-related genes, we carried out colocalization and Summary-based Mendelian Randomization (SMR) analysis using the results of asthma GWASs and eQTL data. In addition, we compared the results of disease eQTL data and asthma-related genes with two normal blood eQTL data from Genotype-Tissue Expression (GTEx) project and a Japanese study. We identified 342,054 cis-eQTL and 2,931 eGenes from asthmatic eQTL analysis. We compared the disease eQTL results with GTEx and a Japanese study and found that 63.2 % of the 2,931 eGenes overlapped with the GTEx eGenes and 38.5 % with the Japanese eGenes. Following the integrated analysis of the asthmatic eQTL data with asthma GWASs, using colocalization and SMR methods, we identified 13 asthma-related genes specific to the Korean asthmatic eQTL data. We provided Korean asthmatic cis-eQTL data and identified asthma-related genes by integrating them with GWAS data. In addition, we suggested these asthma-related genes as therapeutic targets for asthma. We envisage that our findings will contribute to understanding the etiological mechanisms of asthma and provide novel therapeutic targets.

overall_design: RNA-seq of peripheral blood mononuclear cells from 436 patients with asthma

first: Dong

middle: J

last: Kim

first: Ji

middle: E

first: Hae-Un

last: Jung

first: Ju

middle: Y

last: Chung

first: Eun

last: Baek

first: Hyein

first: Shin

last: Kwon

first: Han

first: Ji-One

last: Kang

first: Kyungtaek

last: Park

first: Sungho

last: Won

first: Tae-Bum

first: Bermseok

last: Oh


title: Transcriptomic alterations in HEK293 cells under short-term and long-term exposure to citrinin

status: Public on Mar 01 2023

city: Taipei

first: Jui-Feng

last: Tsai

address: No. 1, Sec. 1, Ren'Ai Rd,

department: Graduate Institute of Toxicology

country: Taiwan

institute: National Taiwan University

summary: Mycotoxin citrinin (CTN) is a secondary metabolite of fungi, becoming a contaminant widely found in foods, feeds, and fermented health supplements. CTN is known to disrupt microtubule and chromosome arrangement at high dose (50 - 150 μM), but the toxicological effect of CTN long-term exposure has not been clearly studied. To investigate the molecular mechanisms of genotoxic, clastogenic, and carcinogenic effects of CTN, RNA-seq was performed on HEK293 cells  exposed to chronic 20 μM CTN treatment (3 days for short-term and 30 days for long-term). The transcriptomic profile may reveal some underlying mechanisms regarding chronic carcinogenic potential of CTN, providing information for risk assessment of CTN-contaminated grains and its commercial food products.

overall_design: RNA-seq analysis was performed for CTN-exposed samples. HEK293 cells were treated with 20 μM CTN for 3 days (short-term, ST) and 30 days (long-term, LT). Colony formation assay was performed at day 30 and the colonies formed were picked up for RNA-seq analysis. HEK293 cells treated with vehicle for 30 days were served as control (CTRL). Biological duplicates were performed for each sample.

first: Ting-Shuan

last: Wu

first: Biing-Hui


title: 'Effect of markerless deletion of PA14_16550 from P. aeruginosa PA14 biofilm colonies on M6301-glycerol agar for 3 d at 25C

city: Stillwater

first: Matthew

last: Cabeen

state: Oklahoma

address: 307 Life Science East

department: Microbiology and Molecular Genetics

institute: Oklahoma State University

summary: To determine the transcriptomic effect when PA14_16550, which encodes a TetR-type DNA-binding protein, is absent from cells. Deletion of this gene results in lower exopolysaccharide levels (a biofilm defect). Here, we compared PA14 deleted for amrZ (which has a moderately hyper-biofilm phenotype) and cells deleted for both amrZ and 16550. We also analyzed wild-type PA14 cells.

overall_design: Total RNA was extracted from mechanically dispersed colonies grown on M6301-1% agar for 3 d at 25C. Transcriptomes were compared among PA14, PA14 delta-amrZ, and PA14 delta-amrZ delta-16550.

first: Amal

middle: H

last: Yahya

middle: T

first: Somalisa

last: Pan


title: RNA stability controlled by m6A methylation provides X to autosome compensation in mammals [RNA-seq]

status: Public on Feb 14 2023

city: Würzburg

first: Julian

last: Konig

address: Am Hubland

country: Germany

institute: Würzburg University

summary: In therian mammals, X-chromosomal genes are expressed only from a single active X chromosome, both in males (XY) as well as females (XX). To compensate for this reduction in dosage compared to the evolutionary ancestral state on two autosomes, it has been proposed that genes from the active X chromosome exhibit dosage compensation (“Ohno’s hypothesis”). However, the existence and mechanism of X-to-autosome dosage compensation are still under debate. Here, we show that dosage compensation is achieved via differential N6-methyladenosine (m6A) RNA modification. X-chromosomal transcripts are reduced in m6A modifications and more stable compared to the autosomal counterparts. Acute depletion of m6A using a small molecule inhibitor differentially affects autosomal and X-chromosomal transcripts across sexes, cell types, tissues and species, resulting in perturbed dosage compensation. We propose that higher stability of X-chromosomal transcripts is directed by lower levels of m6A, indicating that mammalian dosage compensation occurs via epitranscriptomic RNA regulation.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design:
RNAseq experiments were performed on polyA RNA with 4 biological replicates per condition. For female mESC clones, RNAseq experiments were performed on individual clones in one replicate per condition.

Please note that the 'HEK293T cells, DMSO, rep1' sample records have been added on Nov 16, 2023.

first: Cornelia

last: Rücklé

first: Nadine

last: Körtel

first: Felicia

middle: M

last: Basilicata

first: Anke

last: Busch

first: Kathi

last: Zarnack

first: Claudia

last: Valsecchi

last: König


title: Genome-wide chromatin profiles of PBRM1 [ChIP-Seq]

status: Public on Feb 13 2023

city: Singapore

first: Xiaosai

last: Yao

address: 60 Biopolis Street, Genome, #02-01

country: Singapore

institute: Genome Institute of Singapore

summary: PBRM1 encodes an accessory subunit of the PBAF subclass of the SWI/SNF chromatin remodeler and the inactivation of PBRM1 is the second most frequent mutational event in kidney cancer. However, the impact of PBRM1 loss on chromatin remodeling, especially pertaining to kidney tumorigenesis, has not been well examined. Here we show that in VHL-deficient renal tumors, PBRM1 deficiency results in aberrant PBAF complexes that localize to de novo genomic loci and activate the pro-tumorigenic NF-?B pathway. PBRM1-deficient PBAF complexes, despite retaining the association between SMARCA4 and ARID2, have loosely tethered BRD7 and redistribute from promoter proximal regions to distal enhancers containing NF-?B motifs. Subsequently, PBRM1-deficient cells display heightened NF-?B activity in multiple models and clinical samples. The ATPase function of SMARCA4 maintains chromatin occupancy of both pre-existing and newly acquired RELA specific to PBRM1 loss, and activates downstream target gene expression. Proteasome inhibitor bortezomib reverses NF-?B activation by reducing RELA occupancy and delays growth of PBRM1-deficient tumors. In conclusion, PBRM1 safeguards the chromatin by repressing aberrant liberation of pro-tumorigenic NF-?B target genes by residual PBRM1-deficient PBAF complexes.

overall_design: Comparison of chromatin changes with and without PBRM1

first: Bin

last: Teh


title: Nicotinamide enhances natural killer cell function and yields remissions in patients with non-Hodgkin lymphoma

status: Public on Jan 13 2023

city: Minneapolis

first: Ralph

last: White

state: MN

address: 420 Delaware Street SE

institute: University of Minnesota

summary: Natural killer (NK) cells are innate cytotoxic lymphocytes that play an important role in surveillance and elimination of cancer. Allogeneic NK cell adoptive transfer has shown the potential to induce remissions in relapsed/refractory acute myeloid leukemia (AML) and lymphomas, but strategies to enhance NK cell survival and function are needed to improve clinical efficacy. Here, preclinical data is presented demonstrating that NK cells cultured ex vivo with IL-15 and nicotinamide (NAM) exhibited significant and stable induction of CD62L, a lymphocyte adhesion molecule important for lymph node homing. High frequencies of CD62L were associated with elevated levels of the transcription factor forkhead box O1 (FOXO1), and NAM promoted the stability of FOXO1 by preventing ubiquitin-mediated proteasomal degradation. NK cells cultured with NAM exhibited metabolic changes associated with elevated glucose flux through the tricarboxylic acid cycle and protection against oxidative stress. Importantly, NK cells incubated with NAM displayed enhanced cytotoxicity and inflammatory cytokine production in vitro and were maintained at high levels xenogeneic adoptive transfer experiments. We report results from a first-in-human phase 1 clinical trial testing adoptive transfer of NK cells expanded ex vivo with IL-15 and NAM (GDA-201) combined with monoclonal antibodies in patients with relapsed or refractory non-Hodgkin lymphoma (NHL) and myeloma (NCT03019666). Cellular therapy with GDA-201 and rituximab was well-tolerated and yielded an overall response rate of 74% in 19 patients with advanced NHL. Thirteen patients had a complete response, and 1 patient had a partial response. GDA-201 cells were detected for up to 14 days in blood, bone marrow, and tumor tissues and maintained a favorable metabolic profile. The safety and efficacy of GDA-201 justify further development as a cancer therapy.

overall_design: Peripheral blood was collected for the clinical trial testing NAM-expanded NK cells. From 3 donors, NK cells were sorted from apheresis products before ex vivo expansion. NK cells were also sorted from cells expanded with IL-15 and NAM prior to adoptive transfer. From 3 patients, donor and host NK cells were sorted using antibodies against HLA to distinguish doner and host. All cells were analyzed by single cell RNA-seq.

first: Frank

last: Cichocki

first: Abderrahman

last: Day


title: Combination of transcriptomic, proteomic and degradomic profiling reveals common and distinct patterns of pathogen-induced cell death in maize

status: Public on Jan 09 2023

city: Cologne

first: Gunther

last: Doehlemann

address: Zuelpicher Str. 47a

institute: University of Cologne

summary: Regulated cell death (RCD) is crucial for plant development, as well as in decision-making in plant-microbe interactions. Previous studies revealed components of the molecular network controlling RCD, including different proteases. However, the identity, the proteolytic network as well as molecular components involved in the initiation and execution of distinct plant RCD processes, still remain largely elusive. In this study, we analyzed the transcriptome, proteome, and N-terminome of Zea mays leaves treated with the Xanthomonas effector avrRxo1, the mycotoxin Fumonisin B1 (FB1), or the phytohormone salicylic acid (SA) to dissect plant cellular processes related to cell death and plant immunity. We found highly distinct and time-dependent biological processes being activated on transcriptional and proteome levels in response to avrRxo1, FB1, and SA. Correlation analysis of the transcriptome and proteome identified general, as well as trigger-specific markers for cell death in Zea mays. We found that proteases, particularly papain-like cysteine proteases, are specifically regulated during RCD. Collectively, this study characterizes distinct RCD responses in Z. mays and provides a framework for the mechanistic exploration of components involved in the initiation and execution of cell death.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for maize leaves treated with Xanthomonas oryzae pv oryzae PXO99A bacteria carrying pHMI (control for avrRxo1/D193T), pHMI-avrRxo1, or the inactive mutated version pHMI-avrRxo1-D193T, 1% DMSO (control for FB1/SA), the toxin Fumonisin B1 (FB1) as well as salicylic acid (SA). Three biological replicates were generated.

first: Sina

last: Barghahn

first: Georgios

last: Saridis

first: Melissa

last: Mantz

first: Ute

last: Meyer

first: Jaqueline

last: Mellueh

first: Johana

middle: C

last: Misas Villamil

first: Pitter

middle: F

last: Huesgen


title: Genome-wide DNA methylation dynamics in carbon tetrachloride-induced   mice liver fibrosis

status: Public on Jan 11 2023

city: Xinxiang

first: Deming

last: Li

state: Henan

address: 46# East of Construction Road

department: College of Life Science

institute: Henan Normal University

type: Methylation profiling by high throughput sequencing

summary: Liver fibrosis was found to be existed in all kinds of chronic liver diseases. Many studies suggested that DNA methylation was related with the pathogenesis of liver fibrosis. The aim of this study was to quantitatively detect DNA methylation changes in the whole genome in fibrotic liver tissues. Carbon tetrachloride (CCl4) was used to induce male mice liver fibrosis by intraperitoneal injection for 4 weeks. A genome-wide methylome analysis was performed using 850K BeadChips assays. The methylation status of 27 CpG dinucleotides located in 3 genes was detected by pyrosequencing to confirm chips data accuracy, and their mRNA expressions were examined by RT-qPCR methods. A total of 130,068 differentially methylated sites (DMS, 58,474 hypermethylated and 71,594 hypomethylated) between fibrotic liver tissues and control mice liver tissues were identified by the 850k BeadChips array. They distribute in each chromosome. Recognition of apoptotic cell, Notch and p38MAPK et al activities were significantly enriched in the Gene Ontology (GO) analyses. Cholesterol metabolism, bile secretion and more biosynthesis and metabolism pathway were enriched in KEGG pathway analyses. Many classical pathways of fibrogenesis and liver activity, as well as more biosynthetic and metabolic pathways, were found to be related to methylation changes. Our result facilitates future research for clinical application.

overall_design: Genome-wide DNA methylation profiles of the liver tissues from 9 liver fiber mice and 9 normal mice.

first: Xiaoshu

last: Guo

first: Guoying

last: Yu


title: Genome-wide chromatin profiles of PBRM1

status: Public on Feb 11 2023

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

overall_design: Refer to individual Series


title: Serum response factor reduces gene expression noise and confers cell state stability

status: Public on Jan 01 2023

city: New Haven

first: Shangqin

state: CT

address: 10 Amistad ST

department: Cell Biology

institute: Yale University


title: HepG2 HepAD38 TP53BP2-knockdown

city: Beijing

first: Guan

last: Guiwen

state: Beijing

address: 38 Xueyuan Road, Haidian District

institute: Peking University


title: HepG2 TP53BP2-knockdown

summary: HepG2 TP53BP2-knockdown

overall_design: HepG2 TP53BP2-knockdown

first: Zhang

last: Ting

first: Ning

last: Jing

first: Chen

last: Xiangmei

first: Lu

last: Fengmin


title: RNA-sequencing data of liver tissue of intrauterine growth restricted (IUGR) piglets with or without supplementary energy treatment

city: Frederiksberg C

first: Andrew

last: Williams

address: Dyrlægevej 100

country: Denmark

institute: University of Copenhagen

overall_design:
Piglets identified as IUGR or normal at birth received an energy boosting supplement and then were euthanized 72 hours later.
RNA was obtained from liver tissue following euthanasia

middle: R


title: Cultured Neural Progenitors from Nasal Turbinate as a Cellular Model of Neurodevelopmental Component of Schizophrenia Etiology

status: Public on Dec 05 2022

city: Brooklyn

first: Oleg

middle: V

last: Evgrafov

state: New York

address: 450 Clarkson Ave

institute: SUNY Downstate Health Sciences University

summary: We previously created cell lines with neural progenitor characteristic deriverd from superior or middle turbinated of patients with schizophrenia and control groups. We used single-cell RNA sequencing(scRNA-seq) to study the gene expression of schizophrenia

overall_design: Single cell 3' RNAseq of middle turbinate biopsy samples from 1 patient with schizophrenia and 1 sample from control group and neural progenitor/mesenchymal cell cultures derived from biopsies of from 1 patient with schizophrenia and 1 sample from control group using the 10X Genomics Chromium platform and sequenced on Illumina NovaSeq6000.

first: Victoria

middle: S

last: Tung


title: Profiling Mouse Brown and White Adipocytes to Identify Metabolically Relevant small ORFs and Functional Microproteins [Ribo-seq]

status: Public on Dec 13 2022

city: San Diego

first: April

middle: Elizabeth

state: California

address: 10010 N Torrey Pines Rd

department: IGC

institute: Salk Institute for Biological Studies

summary: The absence of thousands of recently annotated small open reading frame (smORF)-encoded peptides and small proteins (microproteins) from databases has precluded their analysis in metabolism and metabolic disease. Given the outsized importance of small proteins and peptides in metabolism—insulin, leptin, amylin, glucagon, and glucagon-like peptide-1  (GLP-1)—microproteins are a potentially rich source of uncharacterized metabolic regulators. Here, we annotate smORFs in primary differentiated brown, white, and beige mouse adipose cells. Ribosome profiling (Ribo-Seq) detected a total of 3,877 unannotated smORFs. Analysis of RNA-Seq datasets revealed diet-regulated smORF expression in adipose tissues, and validated the adipose translation of the feeding-neuron marker gene Gm8773. Gm8773 encodes the mouse homolog of FAM237B, a neurosecretory protein that stimulates food intake and promotes weight gain in chickens. Testing of recombinant mFAM237B produced similar orexigenic activity in mice further supporting a role for FAM237B a metabolic regulator and part of the brain-adipose axis. Furthermore, we showed that data independent acquisition mass spectrometry (DIA-MS) proteomics can provide a sensitive, flexible, and quantitative platform for identifying microproteins by mass spectrometry. Using this system led to the detection of 58 microproteins from cell culture and an additional 25 from mouse serum. The proteomics data established the anti-inflammatory microprotein AW112010 as a circulating factor, and found that serum levels of a microprotein translated from a FRS2 uORF is elevated in older obese mice. Together, the data highlight the value of this database in examining understudied smORFs and microproteins in metabolic research and identifying additional regulators of metabolism.

overall_design: total RNA and polyA RNA extracted for deep paired-end transcriptome profiling

first: Thomas

last: Martinez

first: Maxim

middle: N

last: Shokhirev

first: Alan

last: Saghatelian

first: Christopher

middle: A

last: Barnes


title: Profiling Mouse Brown and White Adipocytes to Identify Metabolically Relevant small ORFs and Functional Microproteins


title: Profiling Mouse Brown and White Adipocytes to Identify Metabolically Relevant small ORFs and Functional Microproteins [RNA-seq]


title: Lab evolution, transcriptomics, and modeling reveal mechanisms of paraquat tolerance

status: Public on Dec 19 2022

city: La Jolla

first: Kevin

last: Rychel

address: 9500 Gilman Dr

department: Bioengineering

institute: University of California San Diego

summary: We use adaptive laboratory evolution to generate strains which tolerate high levels of the redox cycling compound paraquat, which produces reactive oxygen species (ROS). We combine resequencing, iModulon analysis of the transcripome, and metabolic models to elucidate six interacting stress tolerance mechanisms: 1) modification of transport, 2) activation of ROS stress responses, 3) use of ROS-sensitive iron regulation, 4) motility, 5) broad transcriptional reallocation toward growth, and 6) metabolic rewiring to decrease NADH production. This work thus reveals the genome-scale systems biology of ROS tolerance.

sample_organism: Escherichia coli str. K-12 substr. MG1655

overall_design: Tolerization adaptive laboratory evolution (ALE) to increase paraquat. We started with GLU4 (0_0), a strain of E. coli MG1655 which was media-adapted using ALE in LaCroix et al. 2015 (doi: 10.1128/AEM.02246-14). We then evolved it with increasing PQ concentrations over 33 days in triplicate, generating strains 1_0, 2_0, and 3_0. Following that, 11 more strains were generated using a second gerenation of ALE for up to 55 days in a hierarchy, with 1_1, 1_2, ... descending from 1_0; 2_1, 2_2, ... descending from 2_0, and so on. Data from 0_0, 1_0, and 2_0 are available at GEO accession number GSE134256. See http://aledb.org/stats/?ale_experiment_id=1540 for the sets of mutations for all strains. Each evolved strain was cultured in M9 minimal media with 0.4% w/v glucose to an OD of 0.025 then exposed to 0, 250, or 750 uM paraquat for 20 minutes prior to RNA collection. These samples were also included in PRECISE-1K, a dataset which can be explored on iModulonDB.org.

first: Justin

last: Tan

first: Bernhard

last: Palsson


title: ChIP-seq analysis of LHX2 in hES-RPE cells

status: Public on Nov 21 2022

city: Tel Aviv

first: Mai

last: Eshel

address: Klatzkin 35

department: Human Molecular Genetics and Biochemistry

country: Israel

institute: Tel Aviv University

summary: LHX2 binding sites were profiled in RPE cells generated from human embryonic stem cells (hES-RPE)

overall_design: LHX2 binding profile was generated in hES-RPE cells

first: Rani

last: Elkon

first: Ruth

last: Ashery-Padan


title: RNA-seq analysis of hES-RPE cells in 14d from LHX2 KD and control - non-specific shRNA

summary: RNA-seq analysis was applied in duplicates to hES-RPE cells in 14d: LHX2-KD and control - non-specific shRNA

overall_design: Transcriptome analysis of hES-RPE cells, in duplicates, from hES-RPE cells in 14d: LHX2-KD and control - non-specific shRNA


title: Regeneration signatures of TGFB1-treated mouse intestinal organoids and Ki67 positive primary cells sorted from mice after irradiation

status: Public on Feb 08 2023

city: Nanjing

first: Lei

last: Chen

address: No.2 Sipailou

institute: Southeast University

summary: The adult gut epithelium has a remarkable ability to recover from damage, a process that involves a temporary transition to a fetal-like state during regeneration. To achieve the goal of cellular therapies to restore and/or replace defective gastrointestinal epithelia, it is important to discover the natural components of the regenerative process. We employed a combination of –omics approaches, mouse genetic models, and murine and human organoids to characterize a role for TGFB in recovery from irradiation. In organoid culture conditions, TGFB1-treatment was necessary and sufficient to induce a transcriptomic shift to the fetal-like/regenerative state.

overall_design: Bulk RNA-seq, scRNA-seq and ATAC-seq were employed to profile vehicle and TGFB1-treated organoids. scRNA-seq was also employed to profile Ki67-RFP positive cells isolated from Mki67tm1.1Cle/J mice after 56 hours post-irradiation and their non-IR littermate control.

first: Michael

middle: P

last: Verzi


title: Effect of insulin on West Nile virus (WNV) infection in Drosophila S2 cells.

status: Public on Nov 01 2022

city: Pullman

middle: G.

last: Goodman

state: WASHINGTON

address: 100 Dairy Rd., BLS 202

department: School of Molecular Biosciences

institute: Washington State University

summary:
Cells were treated +/- 1.7uM bovine insulin then mock- or WNV-infected for 8 h.
We then performed gene expression profiling analysis using data obtained from RNA-seq.

overall_design:
Comparative gene expression profiling analysis of RNA-seq data for S2 cells +/- insulin +/- WNV infection.
Gene expression was normalized to S2 cells not receiving insulin nor WNV.

first: Chasity

last: Trammell


title: Molecular Logic of Synaptic Diversity Between Drosophila Tonic and Phasic Motoneurons

city: Cambridge

first: Charles

middle: Arthur

last: Whittaker

state: MA

institute: Koch Institute

summary: Although neuronal subtypes often display unique synaptic organization and function, the underlying transcriptional differences necessary to establish these features is poorly understood. To identify molecular pathways that establish synaptic diversity, single neuron PatchSeq RNA profiling was performed on Drosophila tonic and phasic glutamatergic motoneurons. Tonic motoneurons form weaker facilitating synapses onto single muscles, while phasic motoneurons form stronger depressing synapses onto multiple muscles. Super-resolution microscopy and in vivo imaging demonstrated synaptic active zones in phasic motoneurons are more compact and display enhanced Ca2+ influx compared to their tonic counterparts. Genetic analysis identified unique synaptic properties that mapped onto gene expression differences in several cellular pathways, including distinct signaling ligands, post-translational modifications and intracellular Ca2+ buffers. These findings provide insights into how unique transcriptomes can drive functional and morphological differences between two closely related neuronal subgroups.

overall_design: PatchSeq RNA profiling of 105 1B motor neurons, 101 1S motor neurons, 17 M1 muscle cells and 26 M4 muscle cells.

first: Suresh

middle: K

last: Jetti

first: Andrés

middle: B

last: Crane

first: Yulia

last: Akbergenova

first: Nicole

last: Aponte-Santiago

first: Karen

middle: L

last: Cunningham

first: J

last: Littleton


title: HepAD38 TP53BP2-knockdown

first: Guan

last: Guiwen

summary: HepAD38 TP53BP2-knockdown

overall_design: HepAD38 TP53BP2-knockdown

first: Zhang

last: Ting

first: Ning

last: Jing

first: Chen

last: Xiangmei

first: Lu

last: Fengmin


title: Effect of overexpression of TRPM8 on gene expression of tumor pericytes

status: Public on Oct 31 2022

city: Guang Zhou

first: Qun

last: Miao

address: Huangpu avenue

institute: Jinan University

summary: RNA-sequencing for 6 samples

overall_design: Performed gene-expression profiling using data obtained from RNA-seq from 2 differentially treated cells

first: Dongmei

last: Zhang

first: Minfeng

first: Xiaobo

last: Li


title: Single cell-resolved study of advanced murine MASH reveals a homeostatic pericyte signaling module

status: Public on Feb 01 2023

city: Odense M

first: Kim

last: Ravnskjaer

address: Campusvej 55

department: Biochemistry and Molecular Biology

institute: University of Southern Denmark

summary: Non-alcoholic steatohepatitis (NASH) is associated with hepatic steatosis, intralobular inflammation, and fibrosis. The degree of hepatic fibrosis, mainly caused by excessive production of extracellular matrix proteins, is the sole predictor of liver-related and overall mortality in NASH patients. The hepatic stellate cells (HSCs) are causally implicated in fibrogenesis during NASH development but as sinusoidal pericytes also vital for vascular homeostasis of the healthy liver. Using single-cell RNA-sequencing we have analyzed whole liver plasticity and interrogated the transition of HSCs from pericytes in the healthy liver to collagen-producing cells in a diet-induced murine model of advanced NASH. We show how postprandial cues are sensed and integrated by HSCs promoting their phenotypic stabilization and, through paracrine mediators, sinusoidal health. While dominant under healthy conditions the basis for this multimodal signaling through stellate cell-specific Gs protein-coupled receptors and the bile-acid receptor NR1H4/FXR deteriorates in activated HSCs of the NASH liver. Expression of key signaling components were validated in situ in human and murine liver tissue supporting the translatability of our findings and pharmacological relevance in treatment of chronic liver diseases as NASH.

overall_design: Comparative bulk RNA-seq analysis of eight 52 weeks western diet-treated mice and nine 52 weeks chow diet-treated mice

first: Sofie

last: Bendixen

first: Peter

last: Sørensen

first: Mike

last: Terkelsen

first: Daniel

last: Hansen

first: Kamilla

middle: H

last: Hejn

first: Frederik

last: Bjerre

first: Annemette

last: Thulesen

first: Niels

middle: G

last: Eriksen

first: Phillip

last: Hallenborg

first: Trine

last: Dam

last: Larsen

first: Charlotte

middle: W

last: Wernberg

first: Janusa

last: Vijayathurai

first: Emma

last: Scott

first: Ann-Britt

last: Marcher

first: Sönke

last: Detlefsen

first: Lars

last: Groentved

first: Henrik

last: Dimke

first: Mette

last: Lauridsen

first: Aleksander

last: Krag

first: Blagoy

last: Blagoev


title: Next generation sequencing of chicken otocyst with gain- and loss-of-Notch signalling activity

status: Public on Dec 01 2022

city: London

first: Magdalena

last: Zak

address: 332 Grays Inn Road

country: United Kingdom

institute: UCL Ear Institute

summary:
Bulk RNA-sequencing of individual chicken otocysts, in which Notch activity was either stimulated or blocked. To stimulate Notch activity, the E2 otic placodes were in ovo transfected with a construct overexpressing Notch1 Intracellular domain (NICD1) or a control plasmid expressing mRFP1 and collected 6h or 24h later. To pharmacologically block Notch activity, E2.5 chicken otocysts were incubated in media enriched with γ-secretase
Inhibitor or control condition (DMSO) for 6h or 24h. Transcripts abundance was mapped to a chicken reference genome using Kallisto package.

overall_design: Identification of genes deregulated in the otocyst in response to the manipulation of Notch signaling activity

last: Żak

first: Nicolas

last: Daudet


title: Epigenetic and transcriptional landscapes during cerebral cortex development in a microcephaly mouse model

city: Shenzhen

first: Cao

last: Qiang

address: No. 66 Gongchang Road, Guangming District, Shenzhen

department: School of Medicine

institute: Sun Yat-sen University

summary: The cerebral cortex is a pivotal structure that is integral to advanced brain functions within the mammalian central nervous system. Patterns of DNA methylation and hydroxymethylation play important roles in regulating cerebral cortex development. However, it remains unclear whether abnormal cerebral cortex development, such as microcephaly, could rescale the epigenetic landscape, potentially contributing to dysregulated gene expression during brain development. In this study, we characterize and compare the DNA methylome/hydroxymethylome and transcriptome profiles of the cerebral cortex across several developmental stages in wild-type (WT) mice and Mcph1 knockout (Mcph1-del) mice with severe microcephaly. Intriguingly, we discover a global reduction of 5'- hydroxymethylcytosine (5hmC) level, primarily in TET1-binding regions, in Mcph1-del mice compared to WT mice during juvenile and adult stages. Notably, genes exhibiting diminished 5hmC levels and concurrently decreased expression are essential for neurodevelopment and brain functions. Additionally, genes displaying a delayed accumulation of 5hmC in Mcph1-del mice are significantly associated with the establishment and maintenance of the nervous system during the adult stage. These findings reveal that aberrant cerebral cortex development in early stages can profoundly alter the epigenetic regulation program, which provides new insights into the molecular mechanisms underpinning diseases related to cerebral cortex development.


title: Angiogenic potential of skeletal muscle derived extracellular vesicles differs between oxidative and glycolytic muscle

status: Public on Oct 26 2022

city: Pittsburgh

first: Chris

last: Kargl

state: Pennsylvania

address: 4200 Fifth Avenue

institute: University of Pittsburgh

summary: Skeletal muscle fibers regulate surrounding endothelial cells (EC) via secretion of numerous angiogenic factors, including extracellular vesicles (SkM-EV). Muscle fibers are broadly classified as oxidative (OXI) or glycolytic (GLY) depending on their metabolic characteristics. OXI fibers secrete more pro-angiogenic factors and have greater capillary densities than GLY fibers. OXI muscle secretes more EV than GLY, however it is unknown whether muscle metabolic characteristics regulate EV contents and signaling potential. Extracellular vesicles were isolated from primarily oxidative or glycolytic muscle tissue in mice. MicroRNA (miR) sequencing was done to determine SkM-EV miR contents and cultured endothelial cells were treated with OXI- and GLY-EV to investigate angiogenic signaling potential. There were considerable differences in miR contents between OXI- and GLY-EV and pathway analysis identified that OXI-EV miR were predicted to positively regulate multiple endothelial-specific pathways including nitric oxide (NO) and vascular endothelial growth factor (VEGF) pathways, compared to GLY-EV miRs. OXI-EV improved EC migration (+19%) and tube formation (length: +20%; # of tubes +35%) compared to GLY-EV. These benefits may have been NO pathway mediated, as OXI-EV increased phosphorylation of endothelial nitric oxide synthase (eNOS) and treatment of ECs with the NOS inhibitor L-NAME abolished differences in migration and tube formation between OXI- and GLY-EV. This is the first report to show widespread differences in miR contents between SkM-EV isolated from metabolically different muscle tissue and the first to demonstrate that oxidative muscle tissue secretes EV with greater angiogenic signaling potential than glycolytic muscle tissue.

overall_design: 8 total samples were sequenced. Small RNA was isolated from skeletal muscle derived extracellular vesicles oxidative (n=4) and glycolytic (n=4) muscle from mice. Oxidative muscle consisted of the soleus and red portions of the gastrocnemius. Glycolytic muscle consisted of the whole quadriceps.

first: Tim

last: Gavin

first: Monica

last: Hubal


title: Expression data from acute lymphoblastic leukemia cell lines

status: Public on Nov 24 2022

city: Tampa

first: Rafael

last: Renatino Canevarolo

state: FL

address: 12902 USF Magnolia Dr

department: Cancer Physiology

institute: H Lee Moffitt Cancer Center & Research Institute

summary: We used microarrays to detail the constitutive global programme of gene expression of a series of acute lymphoblastic leukemia (ALL) cell lines. 6 B-cell precursor ALL and 7 T-cell ALL cell lines were investigated.

overall_design: Cell lines (10 × 10e7) were cultured in RPMI-1640 medium, 10% fetal bovine serum (FBS), and penicillin/streptomycin at 37°C and 5% CO2 for 30 hours

first: Andre

last: Bortolini Silveira

first: Jose

last: Yunes


title: Novel Therapeutic Strategies Exploiting Unique Properties of Neuroendocrine Tumors

city: New York

first: Luigi

last: Scotto

address: 650 West 168th Street, P&S 8-460

department: Medicine

institute: Columbia University Medical Center

summary: We perform expression analysis on a panel of neuroendocrine cell lines.

overall_design: Gene expression profiles of neuroendocrine cells

first: Susan

middle: E

last: Bates

first: Maryam

last: Safari


title: Epigenetic and transcriptional landscapes during cerebral cortex development in a microcephaly mouse model [RNA-seq]

overall_design: Expression profiling by high throughput sequencing

first: Qing

last: Yang

first: Qiang

last: Cao

first: Yue

last: Yu

first: Xianxin

last: Lai

first: Jiahao

last: Feng

first: Xinjie

last: Li

first: Zhongwei

last: Zhou

first: Xin


title: Functional T cells are capable of supernumerary cell division and longevity

status: Public on Nov 17 2022

city: Minneapolis

first: David

last: Masopust

address: 2101 6th St SE

department: Microbiology and Immunology

institute: University of Minnesota

overall_design: Refer to individual Series


title: Single-Nucleus RNA Sequencing of Developing and Mature Superior Colliculus Identifies Neuronal Diversity and Candidate Mediators of Circuit Assembly

status: Public on Apr 12 2023

city: Miami

first: James

last: Choi

address: 1095 NW 14th Terrace

institute: University of Miami Miller School of Medicine

summary: The superior colliculus (SC) is a sensorimotor structure in the midbrain that integrates inputs from multiple sensory modalities to initiate motor commands. It undergoes well-characterized steps of circuit assembly during development, rendering the mouse SC a popular model to study establishment and refinement of neural connectivity. Here we performed single nucleus RNA-sequencing analysis of the mouse SC isolated at various developmental time points. Our study provides a transcriptomic landscape of the cell-types that comprise the SC across murine development with particular emphasis on neuronal heterogeneity. We used these data to identify Pax7 as a marker for an anatomically homogeneous population of GABAergic neurons. Lastly, we report a repertoire of genes differentially expressed across the different postnatal ages, many of which are known for regulating axon guidance and synapse formation. Our data provide a valuable resource for interrogating the mechanisms of circuit development, and identifying markers for manipulating specific neuronal populations and circuits in the SC.

overall_design: Superior colliculus was microdissected from embryonic day 19 (E10), post-natal day 4 (P4), P8, or P21 C57BL/6J mice. Tissue was pooled from multiple animals and homogenized inRNAase-free lysis buffer (0.32 M sucrose, 3 mM CaCl2, 3 mM MgAc2, 0.1 mM EDTA, 10 mM Tris-HCl,1 mM DTT, 0.1% Triton X-100 in DEPC-treated water) using glass dounce homogenizer on ice. The homogenate was loaded into a polycarbonate ultracentrifuge tube containing sucrose solution (1.8 M sucrose, 3 mM MgAc2, 1 mM DTT, 10 mM Tris-HCl in DEPC-treated water) in the bottom and centrifuged at 107,000 g for 2.5 hours at 4°C. Supernatant was aspirated, and the nuclei containing pellet was incubated in RNAse-free 1x PBS, 0.04% BSA, 0.2 U/µl RNAse Inhibitor on ice before resuspending the pellet. The nuclear suspension was filtered twice through a 30 µm cell strainer RNAase-free. Single nucleus suspension was processed and sequenced using 10X Genomics 3’ v3 snRNA-seq platform with a target capture of 2000 nuclei per sample. Libraries were sequenced on NovaSeq SP 100 (200,000 reads/nucleus). After sequencing, Illumina output was processed using CellRanger v3.0.2. Base call files for each sample were demultiplexed. A pre-mRNA reference was generated with cellranger mkref using the mm10 mouse genome. Each sample was aligned to the custom mm10 mouse reference genome using CellRanger.

first: Ana

middle: C

last: Ayupe

first: Felipe

last: Beckedorff

first: Robyn

last: McCartan

first: Konstatin

last: Levay

first: Kevin

last: Park


title: Epigenetic and transcriptional landscapes during cerebral cortex development in a microcephaly mouse model [RRBS/oxRRBS]

first: Cao

last: Qiang


title: The Aryl Hydrocarbon Receptor Regulates Th17/Th22 Effector Functions and HIV Replication/Outgrowth in Human CD4+ T-cells

city: Montréal

first: Jean-Philippe

last: Goulet

state: Québec

address: C.P. 6128, succursale Centre-ville

institute: Université de Montréal

summary: Aryl Hydrocarbon Receptor Regulates Th17/Th22 Effector Functions and HIV Replication/Outgrowth in Human CD4+ T-cells. 6 patients (HIV + ART) Memory CD4+ T-cells  and 2 conditions (DMSO andCH223191).

overall_design: 6 patients (HIV + ART) Memory CD4+ T-cells , 2 conditions: DMSO. CH223191

first: Debashree

last: Chatterjee

first: Yuwei

last: Zhang

first: Tomas

last: Salinas

first: Dominique

last: Yoka

first: Huicheng

last: Chen

first: Yasmine

last: Smail

first: Brendan

last: Bell

first: Jean-Pierre

last: Routy

first: Petronela

last: Ancuta


title: RAW macrophages: Control vs. LPS treated or Immunobiotic treated

status: Public on Oct 22 2022

city: San Miguel de Tucuman

first: Leonardo

last: Albarracin

address: Chacabuco 145

country: Argentina

institute: CERELA

summary: The ability of Lactiplantibacillus plantarum LOC1 and LOC3, originally isolated from fresh tea leaves, to modulate the response of murine macrophages to the activation of Toll-like receptor 4 (TLR4) by the stimulation with lipopolysaccharide (LPS) was evaluated.

overall_design: RAW macrophages were stimulated with LOC1 or LOC3 strains for 12 hours.  Untreated macrophages were used as control. The three groups were then challenged with LPS. Microarray analysis was performed in macrophages 3 hours after the stimulation with the TLR4 agonist. Groups: unchallenged RAW macrophages, RAW macrophages + LPS, RAW macrophages + LOC1 + LPS, RAW macrophages + LOC3 + LPS. One replicate for each group.

first: Masahiko

last: Suzuki

first: Yuji

last: Tsujikawa

first: Iwao

last: Sakane

first: Julio

last: Villena

first: Haruki

last: Kitazawa

first: Kohtaro

last: Fukuyama


title: Effect of POLDIP2 knockout in ARPE-19 cells

status: Public on Oct 01 2022

city: East Melbourne

first: Raymond

middle: CB

last: Wong

state: VIC

address: 32 Gisborne St

country: Australia

institute: Centre for Eye Research Australia

summary:
To study the function of AMD-associated gene POLDIP2 in retinal pigment epithelial (RPE) cells, we used CRISPR/Cas to knockout POLDIP2 in the human RPE cell line ARPE19.
We then performed RNA-seq to profile the transcriptome of wildtype ARPE19 and POLDIP2 knockout.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for wildtype ARPE19 and POLDIP2 knockout.


title: Efficient combinatorial targeting of RNA transcripts in single cells with Cas13 RNA Perturb-seq

status: Public on Sep 29 2022

first: Hans-Hermann

last: Wessels

address: 101 Avenue of the Americas

institute: New York Genome Center

summary: Pooled CRISPR screens coupled with single-cell RNA-sequencing have enabled systematic interrogation of gene function and regulatory networks. Here, we introduce Cas13 RNA Perturb-seq (CaRPool-seq) which leverages the RNA-targeting CRISPR/Cas13d system and enables efficient combinatorial perturbations alongside multimodal single-cell profiling. CaRPool-seq encodes multiple perturbations on a cleavable array which is associated with a detectable barcode sequence, allowing for the simultaneous targeting of multiple genes. We compared CaRPool-seq to existing Cas9-based methods, highlighting its unique strength to efficiently profile combinatorially perturbed cells. Finally, we apply CaRPool-seq to perform multiplexed combinatorial perturbations of myeloid differentiation regulators in an acute myeloid leukemia (AML) model system and identify extensive interactions between different chromatin regulators that can enhance or suppress AML differentiation phenotypes.

overall_design: We developed CaRPool-seq for efficient combinatorial targeting of multiple targets in single-cells. We performed pooled combinatorial CRISPR Cas13d screen with scRNA sequencing to understand genetic interactions in an acute myeloid leukemia cell model.

first: Alejandro

last: Méndez-Mancilla

first: Yuhan

last: Hao

first: Efthymia

last: Papalexi

first: William

middle: M

last: Mauck III

first: Lu

last: Lu

first: John

last: Morris

first: Eleni

last: Mimitou

first: Neville

last: Sanjana

first: Rahul

last: Satija


title: Gene expression of antigen presenting cells in tumor and spleen of mice receiving either a self-assembling nanoparticle vaccine or an adenovirus vaccination by different routes.

status: Public on Oct 07 2022

city: Bethesda

first: Robert

last: Seder

state: MD

address: 40 Convent Dr

department: VRC

institute: NIAID, NIH

summary: Intravenous vaccination with different vaccines modulates the cells in the tumor microenvironemt. We sought to characterize the effects of vaccination by different routes at single cell resolution to determine what key changes are associated with the improved efficacy we observe when vaccines are given systemically as opposed to locally.

overall_design: Mice were vaccinated 1 day prior to sacrifice. Tumors and spleens were collected, Live CD45+ CD11b+ CD11c+ cells were sorted by FACS and then loaded into the 10X chromium controller.

first: Faezzah

last: Baharom

first: Ramiro

last: Ramirez-Valdez

first: Ahad

last: Khalilnezhad


title: Nascent transcription upon interferon-α2 stimulation on human and rhesus macaque lymphoblastoid cell lines

status: Public on Oct 02 2022

city: Boulder

first: Robin

middle: D.

last: Dowell

state: CO

address: 596 UCB

department: Molecular, Cellular and Developmental Biology

institute: University of Colorado Boulder

summary: Changes in gene transcription regulation are necessary for species to respond to changes in their environment. In particular, host-pathogen dynamics have been observed to entail rapid evolution of genes involved in the host innate immune system. Cytokines such as type I interferon alpha and beta trigger an antiviral cellular state controlled by members of the transcription factor families STAT and IRF. However, it remains poorly understood how gene transcription regulation has been rewired through evolutionary time to achieve species-specific interferon-controlled changes in gene expression. We generated nascent transcription (PRO-seq) datasets to determine the initial transcriptional response on lymphoblastoid cell lines derived from homo sapiens and macaca mulatta upon stimulation with interferon alpha2 to assess species-specific changes in gene regulation.

sample_organism:
Macaca mulatta
Homo sapiens

platform_organism:
Macaca mulatta
Homo sapiens

overall_design: We used lymphoblastoid cell lines derived from two individuals (one male and one female) from homo sapiens and from macaca mulatta; a single replicate per individual, and therefore two samples per species per treatment. PRO-seq datasets were obtained from each individual cell line treated for 1 hour with either BSA (negative control), homo sapiens IFN alpha2, or rhesus macaque IFN alpha2.

first: Daniel

last: Ramirez

middle: D


title: DIAPH1-MFN2 interaction regulates mitochondria-sarcoplasmic reticulum contact and modulates ischemic/hypoxic stress

status: Public on Sep 28 2022

first: Raveena

last: Vakil

state: NY

address: 435 E 30th St

department: Diabetes Research Program

institute: NYU Langone Health

summary: Inter-organelle contact and communication between mitochondria (Mito) and endoplasmic reticulum (ER), also known as sarcoplasmic reticulum (SR) in cardiomyocytes (CM), play vital roles in the maintenance of Mito and SR properties and cellular homeostasis. Here, we tested the hypothesis that the formin, Diaphanous-1 (DIAPH1), which regulates actin dynamics and signal transduction, contributes to these processes. Mice bearing CM-specific deletion of Diaph1 displayed reduced injury and superior functional recovery after the induction of cardiac ischemia and reperfusion (I/R). Studies in DIAPH1-silenced human induced pluripotent stem cell-derived CMs (HiPSC-CMs) and murine hearts devoid of CM-Diaph1 revealed that DIAPH1 interacts directly with Mitofusin-2 (MFN2) to regulate Mito-SR contact, Mito turnover, mitophagy, and oxidative stress. Ischemic murine hearts and human heart biopsies revealed more robust DIAPH1-MFN2 interaction vs. that observed in non-ischemic hearts. Solution structure studies affirm this interaction and reveal strong pH-dependent interaction between the Diaphanous Inhibitory Domain (DID) and the cytosolic GTPase domain of MFN2. In HiPSC-CMs, introduction of synthetic linkers, which reduce the Mito-SR distance, mitigated the cardioprotective benefits of Diaph1 deletion. Finally, DIAPH1 binding to the cytoplasmic domain of receptor for advanced glycation endproduct (RAGE) supports signal transduction and contributes to I/R injury in the heart; in HiPSC-CMs, small molecule antagonism of RAGE-DIAPH1 reduced DIAPH1-MFN2 interaction and increased Mito-SR distance. This work establishes fundamental roles for DIAPH1-MFN2 interaction in the regulation of Mito-SR contact networks that control responses to ischemic stress. Targeting pathways that regulate DIAPH1-MFN2 may facilitate recovery from cardiac ischemic injury.

overall_design: Two by two factorial experiment with DIAPH1 knockdown, scramble control, DIAPH1 knockdown under hypoxia, and scramble control under hypoxia. Four biological replicates per experimental group. All samples were pooled for Illumina sequencing in a single lane, and the resulting pool was run twice on different days, creating technical replicates for all samples.

first: Gautham

last: Yepuri

first: Lisa

first: Sergei

middle: V

last: Reverdatto

first: Gregory

last: Theophall

first: Nosirudeen

last: Quadri

first: Syed

middle: N

last: Hasan

first: Lei

last: Bu

first: Devi

last: Thiagarajan

last: Wilson

first: Raquel

last: Díez

first: Paul

middle: F

last: Gugger

first: Kaamashri

last: Mangar

first: Navneet

last: Narula

first: Stuart

last: Katz

first: Boyan

last: Zhou

first: Huilin

last: Li

first: Aleksandr

last: Stotland

first: Roberta

last: Gottlieb

first: Ann

last: Schmidt

first: Alexander

last: Shekhtman

first: Ravichandran

last: Ramasamy


title: CEG1 DEPLETION REVEALS MECHANISMS GOVERNING DEGRADATION OF NON-CAPPED RNAs

status: Public on Sep 25 2022

city: Birmingham

first: Onofrio

last: Zanin

address: School of Biosciences, University of Birmingham, Edgbaston

institute: University of Birmingham

summary: All eukaryotic mRNAs contain a 7-methylguanosine (m7G) cap which serves as a platform that recruits proteins to support essential biological functions such as mRNA processing, nuclear export and cap-dependent translation. Although the caping is one of the first steps of transcription and uncapped mRNA is not functional, the fate and turnover of uncapped transcripts have not been studied extensively. Here, we employed fast nuclear depletion of the capping enzymes in yeast Saccharomyces cerevisiae to uncover the turnover of transcripts that failed to be capped. We found that the degradation of non-capped mRNA is mainly performed by Xrn1, the exonuclease which is predominantly localized in the cytoplasm, and the fate of such transcripts is determined principally by the abundance of their synthesis. Nuclear depletion of the capping enzymes increased the levels of poorly expressed mRNAs and non-coding RNAs and did not affect the distribution of RNA Polymerase II on chromatin. Overall, our data indicate that mRNAs that failed to be capped are not directed to any specific quality-control pathway and are stochastically degraded.

first: Daniel

last: Hebenstreit

first: Pawel

last: Grzechnik


title: Transcriptomic alterations of thallium-exposed zebrafish embryos

status: Public on Sep 21 2022

city: Taipei

first: Jui-Feng

last: Tsai

address: No. 1, Sec. 1, Ren'Ai Rd,

institute: National Taiwan University

summary: Thallium (Tl) is a trace metal element used in the electronics, semiconductor and electro-optical industries. With the development of high-tech industries, thallium severely pollutes the aquatic environment. The purpose of this study was to evaluate the cardiotoxicity and developmental toxicity of Tl by using vertebrate model zebrafish embryos. RNA-seq was performed on wild type zebrafish embryos exposed to 0, 200, and 800 ppb Tl from 6 to 48 hpf. The transcriptomic profile revealed molecular understanding regarding the cardiovascular and developmental toxicity of Tl,  providing valuable information for risk assessment of the emerging contaminant thallium.

overall_design: RNA-seq analysis was performed for Tl-exposed samples. Wild type zebrafish embryos were treated with Tl 0 ppb, 200 ppb, and 800 ppb from 6 hpf to 48 hpf.

first: Yung

last: Chang

first: Ying-Tzu

last: Huang

first: Biing-Hui

last: Liu


title: Investigate Drl and Blf genome-wide occupancy in zebrafish hematopoietic progenitors with CUT&Tag

status: Public on Sep 01 2022

city: Nanjing

first: Yuxi

last: Yang

state: Jiangsu

address: Room 402, 12 Xuefu Road, Nanjing University

department: Medical School

institute: Nanjing University

summary: Perturbations in embryonic hematopoiesis may result in illness ranges from fetal anemia to leukemias. We found hematopoiesis in zebrafish embryo are synergistically regulated by blf and drl cluster genes. To investigate the blf and drl cluster regulatory network and mechanism of action, we used CUT&Tag technology to investigate their genome-wide occupancy in haematopoietic progenitors.

overall_design: To recapitulate the physiological binding profile, mRNA coding Drl-FLAG and Blf-FLAG were injected into blf-/-; drl 4KO embryos respectively and haematopoietic progenitors were purified by using RFP as lineage tracer at 20 hpf.

first: Xue

last: Zhang

first: Xin

last: Lou


title: Molecular and cellular changes underlying evolutionary specializations of primate dorsolateral prefrontal cortex II

status: Public on Aug 25 2022

city: New haven

first: Nenad

last: Sestan

address: 333 Cedar street

department: Neuroscience

institute: Yale University

summary: The granular dorsolateral prefrontal cortex (dlPFC) is an evolutionary specialization of primates that is centrally involved in cognition. Here, we assessed over 600,000 single-nucleus transcriptomes from human, chimpanzee, macaque, and marmoset dlPFC. While major subclasses of transcriptomically-defined cell subtypes are conserved, we detected several subtypes only in some species and substantial species-specific molecular differences across homologous neuronal, glial and non-neural subtypes. The latter are exemplified by human-specific switching between translation of the neuropeptide somatostatin (SST) and tyrosine hydroxylase (TH), the rate-limiting enzyme in dopamine production, in certain interneurons, and also by expression of the neuropsychiatric risk gene FOXP2, which is human-specific in microglia and primate-specific in layer-4 granular neurons. We generated a comprehensive transcriptomic and cellular survey of dlPFC evolution in anthropoid primates.

overall_design: Single nucleus Multiome sequencing (ATAC-seq and RNA-seq) of the adult human dorsolateral prefrontal cortex

first: Shaojie

last: Ma

first: Mario

last: Skarica

first: Matthew

last: Girgenti

first: Stephen

last: Strittmatter

first: Andre

last: Sousa


title: Integrative Multi‑omics Analysis Reveals Candidate Biomarkers for Oral Squamous Cell Carcinoma

status: Public on Oct 31 2022

city: Hengyang

first: Zhengqing

last: Wan

address: 28 West Changsheng Road

institute: University of South China

summary: We analyzed differentially expressed genes (DEGs) associated with OSCC using RNA sequencing technology. Methylation‑regulated and differentially expressed genes (MeDEGs) of OSCC were further identified via an integrative approach by examining methylomic datasets together with our own transcriptomic data. Protein‑protein interaction (PPI) networks of MeDEGs were constructed and highly connected hub MeDEGs were identified from these PPI networks. A total of 56 upregulated MeDEGs and 170 downregulated MeDEGs were identified in OSCC. Eleven hub genes with high degree of connectivity were picked out from the protein‑protein interaction (PPI) networks constructed by those MeDEGs.

overall_design: RNA profiles of 17 paired samples of OSCC and NAT

first: Danling

last: Wang


title: Comparative analysis of genome-wide transcriptional responses to continuous heat stress in Pleurotus tuoliensis

status: Public on Oct 25 2022

city: Tianjin

first: Long

last: Chen

address: 17km Jinjing Rd

institute: Tianjin Academy of Agricultural Sciences

summary:
The whole-genome gene expression profiling was performed by RNA-Seq after 96 h HS treatment of P. tuoliensis mycelia. Divergent mycelial growth rates were observed under the HS with different intensities, which facilitated comparative analyses combining both physiological and transcriptomic data.
The goal aimed to acquire a deeper insight into the genome-wide gene expression patterns during the response to HS in mushrooms.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for Pleurotus tuoliensis mycelia under multi-level heat stresses

first: Ying

last: Luo

first: Jiazheng

last: Li

first: Zhijun

first: Di

last: Wu


title: A tissue-engineered model of the blood-tumor barrier during metastatic breast cancer

status: Public on Oct 11 2022

city: Baltimore

first: Peter

last: Searson

address: 3400 North Charles Street

institute: Johns Hopkins University

summary: We report changes in gene expression of iPSC-derived brain microvascular endothelial cells (iBMECs) within 3D tissue-engineered microvessels co-cultured with metastatic breast cancer spheroids and macrophages.

overall_design: 9 total samples; n=3 for iBMEC microvessels with surrounding cancer spheroids, cancer spheroid and macrophage co-culture, and their corresponding control (no cancer or macrophages).

first: Raleigh

last: Linville

first: Tracy

last: Chung


title: Metastasis-repressive CircRNA MASCOT Regulates Distribution of the Splicing Factor hnRNP M

status: Public on Sep 10 2022

city: Chengdu

first: Wenrong

last: Liu

address: No. 17, Block 3, Southern Renmin Road

institute: West China Hospital, Sichuan University

summary: Alternative splicing (AS) diversifies the transcriptome complexity and is usually hijacked by cancer cells. Here, we identified heterogeneous nuclear ribonucleoprotein M (hnRNP M) as an indispensable contributor to EMT-related AS reprogramming, whose sub-nuclear distribution of hnRNP M is altered in metastatic tumors. Upon TGFβ stimulation, hnRNP M trends to disassociate with a circRNA called MASCOT (hnRNP M-ASsociated Circular RNA Of TGFβ) that demonstrated an impressive inhibitory effect on EMT process and tumor metastasis. Mechanistically, the anti-metastatic effect of MASCOT is attributed to not only its competition with U2 RNA splicing factors to recruit hnRNP M in the nucleoplasm, but also the anchorage of hnRNP M with nucleolin into the nucleolus to cause a temporospatial separation of hnRNP M from spliceosome. Moreover, the correlation between MASCOT expression and hnRNP M sub-nuclear localization was validated in clinical specimens. Our study deciphers the regulatory codes controlling AS networks and highlights MASCOT as a promising therapeutic to treat metastasis.

overall_design: Guo et al. revealed a dynamic sub-nuclear distribution of hnRNP M mediated by the circRNA called MASCOT which functions as a scaffold to fasten hnRNP M with nucleolin to prevent hnRNP M from being recruited by spliceosomes and thus suppresses the EMT-related alternative splicing events and tumor metastasis.

first: Jiawei

last: Guo

first: Ke

first: Yue

last: Ming

first: Yitong

last: Pan

first: Qingbin

first: Shuang

first: Fuyan

last: Xu

first: Jian

last: Cheng

first: Yu

first: Jin

first: Chengdi

first: Heng

first: Guowei

last: Che

first: Lunzhi

last: Dai

first: Weimin

first: Yong

last: Peng


title: Synovial fibroblasts assume distinct functional identities and secrete R‑spondin 2 to drive osteoarthritis

city: Ann Arbor

first: Tristan

last: Maerz

state: MI

address: 109 Zina Pitcher Place, Office 2017

institute: University of Michigan

summary: Synovium is acutely affected following joint trauma and contributes to post-traumatic osteoarthritis (PTOA) progression. Little is known about discrete cell types and molecular mechanisms in PTOA synovium. We aimed to describe synovial cell populations and their dynamics in PTOA. Single-cell RNA-seq profiling of synovium revealed fibroblasts (comprised of various functional subsets), macrophages, endothelial cells and pericytes to be the predominanent synovial cell types, along with rarer populations including T cells, Schwann cells and mast cells. Cell types undergo profound changes in abundance and gene expression following joint injury.

overall_design: Single-cell RNA-sequencing of murine knee synovium. Mice were subjected to non-invasive anterior cruciate ligament rupture (ACLR) to induce post-traumatic osteoarthritis. Synovium were harvested from one male and one female mouse (pooled) for the following three conditions: Sham (no injury), 7d post-ACLR, 28d post-ACLR. Two biological replicates were performed for each condition for a total of six samples (with each sample comprised of one male, one female).

first: Alexander

last: Knights

first: Easton

last: Farrell


title: Single cell transcriptome analysis of aortic valves from hyperlipidemic and control mice

status: Public on Aug 22 2022

city: Seoul

first: Jae-Hoon

last: Choi

address: 222 Wangsimniro, Seongdong Gu

department: Department of Life Science

institute: Hanyang University

summary: We performed single cell RNA sequencing (scRNA-seq) for 6,574 cells from the aortic valves of C57BL/6J (wild type), Ldlr-/-, and Apoe-/- mice. The extensive single cell profiles depicted hyperlipidemia-associated cellular dynamics in aortic valves.

overall_design: Single-cell mRNA profiles of wild type (WT), Apoe-/-, and Ldlr-/- mice


title: Adipose-enriched peri-tumoral stroma, in contrast to myofibroblast-enriched stroma, prognosticates poorer survival in breast cancers.

city: Singapore

first: Kanaga

last: Sabapathy

state: --None--

address: 11 Hospital Crescent

department: Division of Cellular & Molecular Research

institute: National Cancer Centre Singapore

summary: Breast cancers display a high degree of diversity between and within tumors due to variations in both tumor cells and non-malignant cells of the tumor microenvironment (TME). While most studies on the TME have focused on stroma located within the tumor mass, few studies have examined the peri-tumoral microenvironment, which extends beyond the tumor margins and includes the surrounding, benign-appearing tissues. Here, we examined the heterogeneity in tumors and peri-tumoral stroma from 10 ER+PR+HER2- invasive breast carcinomas, through multi-region transcriptomic profiling.     Tumor samples were obtained from the center, superior, inferior, medial, and lateral (C, S, Inf, M, L) regions of each tumor. Peritumoral samples were obtained from four radial directions corresponding to the regions the tumor samples were collected from (S, Inf, M, L) and from three zones of increasing distances from the tumor margins (Zone 1: 1-3 cm, Zone 2: 3-5 cm, Zone 3: 5-7 cm). To represent the normal breast transcriptomic state, 5 non-directional samples were each obtained from 3 non-tumor bearing breasts (NTB) - 1 patient had undergone cosmetic reduction mammoplasty and 2 patients were germline BRCA2-mutation carriers who had undergone risk-reducing mammoplasties. Total RNA was isolated and microarray was performed using the human Clariom™ S Assay (ThermoFisher Scientific). In total, 144 transcriptomic profiles (47 Tumor, 82 peri-tumoral stroma, 15 NTB) were analyzed.     Heterogeneity was observed both within and between the tumor samples, highlighting that unlike the histological classification, an individual tumor is often comprised of several molecular sub-types.  Similarly, the peri-tumoral stroma was also heterogeneous, albeit independent of the tumor heterogeneity.  Four distinct stromal clusters were noted, which differed in their molecular pathways and cell type composition. Among these, the adipose-enriched stroma that had inflammatory cancer-associated fibroblasts and innate immune cells was significantly associated with poorer overall survival, in contrast to the myofibroblast-enriched stroma.  These data together suggest that the peri-tumoral heterogeneity may be an important determinant of the evolution and treatment of breast cancers.

overall_design:
Microarray analysis was performed on 144 samples (47 breast Tumor, 82 peri-tumoral stroma, 15 non-tumor bearing breast samples) using [Clariom_S_Human] Affymetrix Clariom S Assay, Human (GPL23159).

UPDATE: [06-22-2023] The patient IDs for Samples GSM6500282-GSM6500289 were changed from "BC9" to "BC8" to correspond with the patient IDs used in the associated publication. Only the Sample titles and patient ID characteristics were changed.

first: Hannah

middle: S

last: Lau


title: Small RNA-seq profiling of a directed differentiation model that programs human embryonic stem cells toward the small intestinal lineage

status: Public on Jul 27 2022

city: Ithaca

first: Praveen

last: Sethupathy

address: 618 Tower Road, T7006

institute: Cornell University

summary: Small RNA-seq profiling of a directed differentiation organoid model revealed changing microRNA landscapes of early human small intestinal development

overall_design: Small RNA-seq was performed for the following stages of directed differentiation: human embryonic stem cell (hESC), definitive endoderm (DE), duodenal (Duo) spheroid, ileal (Ile) spheroid, Duo organoid and Ile organoid.

first: Yu-Han

last: Hung


title: Dual RNA-seq of Trichophyton mentagrophytes complex

status: Public on Aug 19 2022

city: Beijing

first: Yubo

last: Ma

address: Xicheng street

institute: peking university first hospital

summary: We report the application of dual RNA-sequencing technology for high-throughput profiling of histone modifications in HaCat cells and Trichophyton mentagrophytes complex.For co-culture assays, a ratio of 2.5×105 cells/mL of keratinocytes to 2.5×105 conidia/mL of T. mentagrophytes, T. interdigitale, and T. tonsurans solution were used (MOI=1). The experiment was carried out for 24 h in a humidified incubator maintained at 37 ºC . We  used dual RNA-seq to study the different host immune responses against the T. mentagrophytes complex and we  the transcriptional profiles of differentially expressed genes in dermatophytes.

sample_organism:
Homo sapiens
Trichophyton tonsurans
Trichophyton interdigitale
Trichophyton mentagrophytes

overall_design: examine the response of HaCat cell co-culture with T.mentagrophytes complex for 24 hours.

first: Xiaowen

last: Wang

first: Ruoyu

last: Li


title: Single-cell RNA-seq profiling of small intestinal epithelium from whole body miR-375 knockout mice (baseline)

summary: MicroRNAs (miRNAs) are important post-transcriptional gene regulators in organ development. To explore candidate roles for miRNAs in prenatal SI lineage specification in humans, we used a multi-omic analysis strategy in a directed differentiation model that programs human pluripotent stem cells toward the SI lineage. We leveraged small RNA-seq to define the changing miRNA landscape, and integrated chromatin run-on sequencing (ChRO-seq) and RNA-seq to define genes subject to significant post-transcriptional regulation across the different stages of differentiation. Our analyses showed that the elevation of miR-182 and reduction of miR-375 are key events during SI lineage specification. We demonstrated that loss of miR-182 leads to an increase in the foregut marker SOX2. We also used single-cell analyses in murine adult intestinal crypts to support a life-long role for miR-375 in the regulation of Zfp36l2. We also uncovered opposing roles of SMAD4 and WNT signaling in regulating miR-375 expression during SI lineage specification. Beyond the mechanisms highlighted in this study, we also present a web-based application for exploration of post-transcriptional regulation and miRNA-mediated control in the context of early human SI development.

overall_design: To validate candidate miR-375 target genes that are identified through multi-omics analyses, we performed single-cell RNA-seq of small intestinal epithelium (isolated crypts from the jejunal segment) from wildtype and whole body miR-375 knockout mice. Be noted that the single-cell RNA-seq data of wildtype mice has been published through GSE178826.

first: Yu


title: TBX20 Consolidates Cardiac Reprogramming Factors to Enhance Contractility and Energy Metabolism in Human Induced Cardiomyocytes [CUT&Tag]

status: Public on Sep 14 2022

first: Changde

state: Alabama

address: 1824 6th Ave S, WTI 510G

department: Department of Medicine - Hematology & Oncology

institute: The University of Alabama at Birmingham

summary: Background: Direct cardiac reprogramming of fibroblasts into cardiomyocytes has emerged as one of the promising strategies to remuscularize the injured myocardium. Yet, it is still insufficient to generate functional induced cardiomyocytes (iCMs) from human fibroblasts using conventional reprogramming cocktails, such as our previously published combination consisting of MEF2C, GATA4, TBX5 and microRNA miR-133 (MGT133).   Results: To discover potential missing factors for human direct reprogramming, we performed transcriptomic comparison between human iCMs and functional cardiomyocytes (CMs). We identified T-box transcription factor TBX20 as the top CM gene that is unable to be activated by MGT133. TBX20 is required for normal heart development and cardiac function in adult CMs but its role on cardiac reprogramming remains undefined. Here, we found that transduction of MGT133+TBX20 in human cardiac fibroblasts resulted in enhanced reprogramming featured with significantly activated contractility gene programs and signatures more similar to ventricular CMs. Human iCMs produced with MGT133+TBX20 more frequently demonstrated beating and calcium oscillation in co-culture with pluripotent stem cell derived CMs. More mitochondria and higher mitochondrial respiration were also detected in iCMs after TBX20 overexpression. Mechanistically, comprehensive transcriptomic, chromatin occupancy and epigenomic integration revealed that TBX20 localized to the cis-regulatory enhancers of under-expressed cardiac genes, such as MYBPC3, MYH7 and MYL4, to activate gene expression via strengthening the occupancy and co-occupancy of transcription factors. Furthermore, we identified TBX20-regulated enhancers and confirmed the synergistic effect of MGT and TBX20 on enhancer activation.   Conclusions: TBX20 promotes cardiac cell fate conversion via direct activating cardiac enhancers. Human iCMs generated with TBX20 showed enhanced cardiac function in terms of contractility and mitochondrial respiration.

overall_design: Profiling of genome-wide binding of MEF2C, GATA4, TBX5 and TBX20 in human induced cardiomyocytes by CUT&Tag sequencing.

first: Yawen

last: Tang

first: Sajesan

last: Aryal

first: Rui

last: Lu

first: Yang

last: Zhou


title: Divergent clonal differentiation trajectories of T cell exhaustion (scATAC-seq)

status: Public on Jul 25 2022

city: Stanford

first: Ansuman

middle: T

last: Satpathy

state: CA

address: 300 Pasteur Drive

department: Pathology

institute: Stanford University

summary: T cells activated by chronic antigen exposure in the setting of viral infections or cancer can adopt an exhausted T cell (TEx) state, characterized by reduced effector function and proliferative capacity, and the upregulation of inhibitory receptors. Here, we generate a single-cell multi-omic atlas of T cell exhaustion in chronic viral infection that redefines the phenotypic diversity and molecular regulation of TEx states. Longitudinal analysis of the T cell response identifies an early effector phenotype that is epigenetically primed for TEx differentiation. However, clonal T cell trajectories defined using paired single-cell RNA and T cell receptor (scRNA/TCR-seq) sequencing reveal divergent differentiation trajectories among clones that recognize shared antigens, resulting in TEx- or effector memory-biased clone behaviors. Multi-organ clonal analysis reveals that T cell clone behaviors are sensitive to the tissue environment, and the liver niche preclude the development of effector memory phenotypes and induce exaggerated exhaustion. Finally, we show that divergent clonal trajectories are driven by differences in TCR affinity, and that high-affinity T cell clones preferentially adopt the divergent fate, while low-affinity clones adopt effector memory fates that are deleted in high antigen niches. These findings reveal heterogeneity in clonal T cell responses to chronic antigen and link TCR signal strength and epigenetic programming to TEx cell fates and persistence, which may be manipulated for cancer immunotherapy.

overall_design: T cells from 8 and 21 dpi with LCMV-c13 or LCMV-Armstrong were sorted to obtain either gp-33 positive or negative CD8+ T cells. Sorted cells were subjected to single cell ATAC sequencing on the droplet based 10X Genomics platform.

first: Bence

last: Daniel

first: Kathryn

last: Yost

first: Katalin

last: Sandor

last: Xia

first: Kamir

middle: J

last: Hiam-Galvez

first: Stefanie

last: Meier

first: Julia

middle: A

last: Belk

first: Yanyan

last: Qi

first: Howard

middle: Y

last: Chang

first: Takeshi

last: Egawa


title: Divergent clonal differentiation trajectories of T cell exhaustion (scRNA-seq)

summary: T cells activated by chronic antigen exposure in the setting of viral infections or cancer can adopt an exhausted T cell (Tex) state, characterized by reduced effector function and proliferative capacity, and the upregulation of inhibitory receptors. However, whether all antigen-specific T cell clones follow the same molecular and cellular Tex differentiation trajectory remains unclear. Here, we generate a single-cell multi-omic atlas of T cell exhaustion that redefines the phenotypic diversity and molecular regulation of Tex phenotypes. Longitudinal analysis during chronic viral infection identifies an early effector phenotype that is epigenetically primed for Tex differentiation and two late-stage Tex cell states with either a terminal exhaustion or a killer cell lectin-like receptor (KLR)-expressing cytotoxic gene signature. We define clonal trajectories of antigen-specific T cells using paired single-cell RNA and T cell receptor sequencing and reveal distinct differentiation trajectories resulting in terminal Tex-biased, KLR Tex-biased, or divergent clones that differentiate into both phenotypes. Comparison of Tex phenotypes among shared T cell clones that traffic to multiple organs reveals that clonal differentiation trajectories are maintained across tissues. Finally, we show that differences in clonal differentiation trajectory are driven by TCR signaling avidity, whereby high-avidity T cell clones preferentially adopt a terminal Tex fate, while low-avidity clones adopt an effector-like KLR Tex fate. These findings reveal clonal heterogeneity in the T cell response to chronic antigen and genomic programs that underlie Tex fates and persistence.

overall_design: T cells from 5, 8, or 21 dpi with LCMV-c13 or LCMV-Armstrong were sorted to obtain either gp-33 positive or negative CD8+ T cells. Sorted cells were subjected to single cell RNA and TCR sequencing on the droplet based 10X Genomics platform.

first: Sunnie

last: Hsiung

first: Mollie

last: Black

first: Colin

last: Raposo

first: Quanming

last: Shi

middle: L

first: Josephine

middle: R

last: Giles

first: E

last: Wherry


title: Methylation analysis of white blood cells DNA samples from healthy males

status: Public on Jul 07 2022

city: Bergen

first: Oleksii

last: Nikolaienko

state: Vestland

address: Jonas Lies veg 87

department: Department of Clinical Science

institute: University of Bergen

summary: The objective of this study was to compare the sensitivities of next-generation sequencing and tiling array in detection of low-frequency, mosaic DNA methylation

overall_design: 8 genomic DNA samples were analysed, no replicates or controls were included in the analysis

first: Stian

last: Knappskog


title: Experimental evolution reveals the genetic basis and systems biology of superoxide stress tolerance

city: La Jolla

first: Wun Kiat Justin

last: Tan

address: 9500 Gilman Drive #0412, PFBH 414

institute: UCSD

summary: E. coli frequently encounters oxidative stress both in its natural environment or in industrial biotechnology. Elucidating the mechanisms behind tolerance to oxidative stress would be beneficial for understanding pathogenesis as well as improving production strain fitness. We make use of adaptive laboratory evolution to develop two strains of E. coli which exhibit 500% increased tolerance to paraquat stress compared to wild type. Evolved strains tolerate oxidative stress by reduction of flux through TCA, dyregulation of iron-uptake genes, and up-regulation of cell motility or iron-sulfur cluster repair genes.

overall_design:
Tolerization adaptive laboratory evolution to increase tolerance to paraquat. Transcriptomics was performed on 2 end point strains and WT with and without addition of paraquat. Ribosome profiling was performed on WT, 1 end point strain and a mid-point strain to investigate read-through of a non-sense mutation in aceE
PQ1 and PQ2 are end-point strains from an adaptive laboratory evolution (ALE) which took place over 33 days and a total of 8x10^11 cumulative cell divisions (CCD). GLU4 is the wild type strain which comes from LaCroix et. al. 2015 (doi: 10.1128/AEM.02246-14 ). The MP strain was isolated from the midpoint of the evolution of PQ2 at 6x10^11 CCD. Genome mutations for these strains will be available at ALEdb (Phaneuf et. al. 2019 - https://doi.org/10.1093/nar/gky983)

first: Justin

first: Bernhard

middle: O

last: Palsson


title: Amplicon-based bisulfite sequencing of promoter regions for selected tumour supressor genes in DNA from white blood cells.

summary: We report the higher sensitivity of NGS-based methylation analysis compared to the array-based techniques for the detection of low-frequency, mosaic, monoallelic methylation. This study describes a computational framework for the analysis of methylation sequencing data.

overall_design: DNA methylation analysis in male white blood cell samples using bisulfite sequencing and tiling array.


title: Methylation analysis of promoter regions for selected tumour suppressor genes in DNA from white blood cells.

status: Public on Jul 03 2022

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

overall_design: Refer to individual Series


title: De novo fatty acid synthesis in invariant NKT cells is critical for the development of airway hyperresponsiveness

status: Public on Jun 15 2022

first: Jaemoon

last: Koh

address: Daehak-ro

department: Department of Pathology

institute: Seoul National University Hospital

summary: Allergic responses in airway against house dust mites (HDMs) depend on lipid metabolism. However, whether the state of lipid metabolism in iNKT cells serves as a critical mechanism to impact development of allergic asthma remains elusive. Here, we showed that acetyl-CoA-Carboxylase 1 (ACC1), a key enzyme for fatty acid synthesis, was highly expressed in iNKT cells from asthmatic lungs. In ovalbumin (OVA)- and HDM-induced allergic asthma models, Cd4-CreAcc1fl/fl mice exhibited impaired homeostasis of iNKT cells and failed to develop AHR. ACC1-deficient iNKT cells reduced intracellular lipid concentration and expression of fatty acid binding proteins (FABPs) and peroxisome proliferator-activated receptor-gamma (PPAR-γ), whereas these cells were increased in glycolytic capacity. Moreover, ACC1-FABP-PPAR-γ axis regulated cell death of ACC1-deficient iNKT cells. Adoptive transfer of wild type (WT) iNKT cells restored AHR in Jɑ18 knockout mice in OVA or HDM-induced asthma models, whereas that of ACC1-deficient iNKT cells did not, indicating that fatty acid synthesis in iNKT cells is one of main contributors to the development of AHR. Our finding demonstrate fatty acid metabolism in iNKT cells is critical contributor for the development of AHR and airway inflammation in asthma.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for iNKT cells from ACC1f/f (WT) mice and ACC1f/fCD4cre (KO) mice

first: Yeon

last: Woo


title: Small RNA sequencing of lipoproteins (HDL) obtained from germ-free mice and facility matched specific-pathogen free mice.

status: Public on Jun 29 2022

city: Nashville

first: Ryan

last: Allen

state: TN

address: 2220 Pierce Ave

institute: Vanderbilt University Medical Center

summary: Plasma was harvested from two cohorts of facility-matched germ free (GF) and specific-pathogen free (SPF) mice at the National Gnotobiotic Rodent Resource Center (NGRRC; North Carolina, USA). Plasma was then fractionated by size-exclusion chromatography using three tandem Superdex200 increase columns (Cytiva). Fractions corresponding with HDL were then pooled and concentrated prior to RNA isolation. Small RNA libraries were generated from total RNA using NextFlex V3 Small RNA Seq-kit (Perkin Elmer) according to manufacturer’s instructions. Equimolar amounts of each library were then pooled and sequenced on the NextSeq500 platform (Illumina). Individual libraries were then demultiplexed and analyzed with the TIGER analytical pipeline.

overall_design: GF (Case) vs SPF (Control)

first: Danielle

last: Michell

first: Kasey

last: Vickers


title: Transcriptomic alterations in response to citrinin in human neuronal cells SH-SY5Y

status: Public on Aug 24 2022

first: Jui-Feng

last: Tsai

address: No. 1, Sec. 1, Ren'Ai Rd,

department: Graduate Institute of Toxicology

institute: National Taiwan University

summary: Mycotoxin citrinin (CTN) is a contaminant widely found in foods, feeds, and fermented health supplements. To investigate the potential neurotoxic effect of CTN, RNA-seq was performed on human neuroblastoma cells SH-SY5Y exposed to 0, 10, and 20 μM CTN for 72 h. The transcriptomic profile revealed novel underlying mechanisms of CTN neurotoxicity, providing useful information for risk assessment of consuming CTN-contaminated grains and its commercial food products.

overall_design: RNA-seq analysis was performed for CTN-exposed samples. Human neuroblastoma cells SH-SY5Y were treated with vehicle (CTN0), 10 μM CTN (CTN10), and 20 μM CTN (CTN20) for 72 h. Three replicates were performed for each sample.

first: Biing-Hui

last: Liu


title: Single cell TCR-RNAseq of thymocyte populations

status: Public on May 31 2022

city: Minneapolis

first: Rebecca

last: LaRue

state: MN

address: 117 Pleasant St SE

department: Department of Lab medicine and Pathology

institute: University of Minnesota

summary: A single cell TCR-RNAseq data set comprised of CD4+CD8+ and CD4+ thymocytes and CD25+ Treg progenitors (TRP), Foxp3lo TRP, de novo developing Tregs and recirculating mature Tregs.

overall_design: Pooled thymocytes from 8 female mice (7-12 weeks of age) TCliB+ x TCRa+/- x Foxp3-GFP mice were sorted into 6 populations (CD4+CD8+, CD4+, CD25+ TRP, Foxp3lo TRP, CD73- Treg and CD73+ Treg), each labelled with a specific hashtag. All cells were sorted based on expression of TCR Vα2 on the cell surface to reduce TCR diversity.

first: David

last: Owen

first: Michael

last: Farrar


title: Nucleosome sliding by the Chd1 chromatin remodeler relies on the integrity of the DNA duplex

status: Public on May 12 2022

first: Taekjip

last: Ha

state: Maryland

address: 3400 N. Charles Street

summary: The experiments are done with three libraries by introducing base-pair perturbations on Widom 601: (1) poly(dA:dT) tract library (2) mismatch library (3) insertion library. And additional two more  libraries based on native yeast genomic sequences: (4) Park97 mismatch library (5) Park97 insertion library.  And we measured the nucleosome positioining in the base-pair resolution for before and after sliding by Chd1 chromatin remodeler.

first: Sangwoo

last: Park

first: Giovanni

middle: B

last: Brandani

first: Gregory

last: Bowman


title: ChIP-seq analysis of OTX2 in hES-RPE cells

status: Public on Nov 21 2022

city: Tel Aviv

first: Mai

last: Eshel

address: Klatzkin 35

department: Human Molecular Genetics and Biochemistry

institute: Tel Aviv University

summary: OTX2 binding sites were profiled in RPE cells generated from human embryonic stem cells (hES-RPE)

overall_design: OTX2 binding profile was generated in hES-RPE cells

first: Rani

last: Elkon

first: Ruth

last: Ashery-Padan


title: LDL delivery of microbial small RNAs drives atherosclerosis through macrophage TLR8

status: Public on Jun 25 2022