title: Modeling human telencephalic development and autism-associated SHANK3 deficiency using organoids generated from single neural rosettes [bulk RNA-seq1]

city: Salt Lake City

first: Yueqi

last: Wang

state: Utah

address: 20 South 2030 East

country: USA

institute: University of Utah

summary: Human telencephalon is an evolutionary advanced brain structure associated with many uniquely human behaviors and disorders. However, cell lineages and molecular pathways implicated in human telencephalic development remains largely unknown. We generated human telencephalic organoids from stem cell-derived single neural rosettes (SNRs) and investigated telencephalic development under normal and pathological conditions. SNR-derived organoids contained pallial and subpallial neural progenitors (NPs), excitatory and inhibitory neurons, as well as macroglial and periendothelial cells, and demonstrated predictable organization and cytoarchitecture. We comprehensively characterized the properties of neurons in SNR-derived organoids and identified transcriptional programs associated with the specification of+B50:B51 excitatory and inhibitory lineages from a common pool of NPs early in telencephalic development. We also demonstrated that neurons in organoids with a hemizygous deletion of an autism- and intellectual disability associated gene SHANK3 exhibit intrinsic and excitatory synaptic deficits associated with impaired expression of clustered protocadherins. Collectively, this study  validates SNR-derived organoids as a reliable new model for studying human telencephalic development and identifies novel molecular pathways disrupted by SHANK3 hemizygosity in human telencephalic tissue.

overall_design: Comparative gene expression profiling analysis of bulk RNA-seq data for ESC(H9, EYQ)- and iPSC (7349.3, GM)-derived 5-months-old telencephalic organoids.

first: Simone

last: Chiola

first: Guang

last: Yang

first: Chad

last: Russell

first: Celeste

last: Armstrong

first: Yuanyuan

last: Wu

first: Jay

last: Spampanato

first: Paisley

last: Tarboton

first: H

middle: M

last: Arif Ullah

first: Nicolas

last: Edgar

first: Amelia

last: Chang

first: David

last: Harmin

first: Vittoria

last: Dickinson Bocchi

first: Elena

last: Vezzoli

first: Dario

last: Besusso

first: Jun

last: Cui

last: Cattaneo

first: Jan

last: Kubanek

first: Aleksandr

last: Shcheglovitov


title: The trophectoderm acts as a niche for the inner cell mass through IL-6 signaling [reprogramming_embryo]

status: Public on Aug 11 2022

city: Barcelona

first: Gregoire

last: Stik

state: select a state

address: 88 Dr Aiguader

country: Spain

institute: CRG

type: Expression profiling by high throughput sequencing

summary: IL-6 has been shown to be required for somatic cell reprogramming into induced pluripotent stem cells (iPSCs). However, how the cytokine is regulated and if it plays a role during embryo development remains unknown. Here we describe that IL-6 is strictly necessary for C/EBPa-enhanced reprogramming of B cells into iPSCs but not for B cell to macrophage transdifferentiation. C/EBPa induces the expression of both Il6 and Il6ra genes in B cells and in PSCs. During preimplantation embryo development C/EBPa is expressed in blastocysts where it is required for the maintenance of Il6. The expression of Cebpa is enriched in trophectoderm together with Il6 whereas the receptor gene Il6ra is predominantly expressed in the inner cell mass (ICM), in both mouse and humans. Blastocysts secrete IL-6 and neutralization of the cytokine delays the morula to blastocyst transition. Our study indicates that the trophectoderm acts as a niche for the ICM through the secretion of C/EBPa-regulated IL-6, facilitating efficient blastocyst development.

overall_design: (1) Study of gene expression changes from mRNA of WT and Il6 K.O. B cells during their reprogramming into iPSCs. (2) Gene expression changes from mRNA of Cebpa morulas and blastocysts derived from heterozygous Cebpa crosses.

first: Marcos

last: Plana-Carmona

first: Romain

last: Bulteau

first: Carolina

last: Segura-Morales

first: Noelia

last: Alcázar

first: Chris

middle: D

last: . Wyatt

first: Antonios

last: Klonizakis

first: Luisa

last: de Andrés-Aguayo

first: Maxime

last: Gasnier

first: Tian

middle: V

last: Tian

first: Guillem

middle: T

last: Garcia

first: Maria

last: Vila-Casadesús

last: Plachta

first: Manuel

last: Serrano

first: Mirko

last: Francesconi

first: Thomas

last: Graf


title: The trophectoderm acts as a niche for the inner cell mass through IL-6 signaling [ESCs_TSCs]

overall_design: (1) Study of gene expression changes from mRNA of mouse embryonic stem cells (ESCs) after the overexpression of the transcription factor C/EBPa. (2) Gene expression profile of mouse trophoblast stem cells (TSCs).

last: Wyatt

first: Nicolas


title: RNA-Seq transcriptomic analysis reveals gene expression profiles of acetic acid bacteria under high-acidity submerged industrial fermentation process

city: Wuhan

first: Haoran

last: Yang

address: Shizishan Street No.1, Hongshan Distric

country: China

institute: Huazhong Agricultural University

summary: In this study, we performed an RNA-Seq transcriptomic analysis concerning acetic acid bacteria’s acid resistance mechanisms during a continuous and periodical industrial submerged vinegar fermentation process, where the acetic acid concentration fluctuates between ~8% and ~12%

overall_design: Samples were directly taken from the initial (CK), mid and final stages of the same period of the on-going fermentation.

first: Yating

last: He

first: Jing

last: Liao

first: Xin

last: Li

first: Junhong

last: Zhang

first: Wolfgang

last: Liebl

first: Fusheng

last: Chen


title: mRNA changes in dyf-1(mn335)compared to wildtype N2

status: Public on Aug 12 2022

city: Cologne

first: Thorsten

last: Hoppe

state: NRW

address: Joseph-Stelzmann-Str. 26

department: Institut für Genetik

country: Germany

institute: Universität zu Köln

summary: In order to assess mRNA changes in dyf-1(mn335) compared to wildtype (N2) we performed a Microarray analysis with 4 biological replicates at day 1 of adulthood.

overall_design: Synchronized day 1 C. elegans were collected for RNA extraction and subsequent hybridization on an Affymetrix microarray.

first: Fabian

last: Finger


title: Specific transcriptional programs differentiate ICOS and CD28 co-stimulatory signals in human naïve CD4 + T cells

city: Novara

first: Francesco

last: Favero

state: NO

address: Corso Trieste 15/A

department: Translational Medicine - CAAD (Center for Translational Research on Autoimmune and Allergic Diseases)

country: Italy

institute: University of Eastern Piedmont

summary: a global transcriptome profiling was performed by RNA-seq on naïve CD4+ T cells upon ICOS or CD28 co-stimulation and bioinformatically was revealed a set of pathways specifically associated to each costimulatory molecule.

overall_design: exploitation of the RNA-Seq technology to compare gene transcription induced in naive Th cells by co-stimulation of either ICOS or CD28

first: Danny

last: Incarnato

first: Salvatore

last: Oliviero

first: Silvia

last: Zucchelli

first: Umberto

last: Dianzani

first: Davide

last: Corà


title: Microenvironment Impacts the Molecular Architecture and Interactivity of Resident Cells in Marmoset Brain

city: Bethesda

first: Daniel

middle: S

last: Reich

state: Maryland

address: 10 Center Drive Bldg 10 Rm 5C103

department: NINDS

institute: NIH

summary: We sought to define and compare the diversity of cells across many brain areas, including various white matter (WM) regions, the volume and complexity of which is limited in mouse brain. We employed magnetic resonance (MR) image-guided sampling and snRNA-seq to survey the transcriptome at cellular resolution. Tissue types included WM (frontal, parietal, temporal), corpus callosum (anterior, posterior), optic tract, cerebral cortex (frontal, parietal, temporal, occipital, cingulate), caudate, hippocampus, lateral geniculate nucleus, cerebellum, thalamus, midbrain, pons, and cervical spinal cord. We profiled nuclei from confined regions (cylinders of tissue 2 mm in diameter and 3 mm in height, ~10 μL), which can be consistently located and repeated based on MR images from animal to animal. We analyze and discuss the global landscape of neural cell types across brain regions, comparing compositional differences of subpopulations of glia in GM and WM, modeling intercellular communication in each milieu, and cataloging their contributions to neurological disorders.

overall_design: Central nervous system marmoset cell atlas was generated from 2 healthy, 5.5-year-old common marmosets (Callithrix jacchus), one female (CJH01) and one male (CJR02). Most single nucleus libraries (38) were prepared using 10x Genomics Chromium Single Cell 3’ Library & Gel Bead Kit v3, 4 libraries were done in v2 chemistry following the manufacture’s protocol (total 42 samples). Briefly, nuclei suspensions were prepared as described above and diluted with resuspension buffer to achieve the desired concentration, and then loaded into Chromium Controller to generate Gelbeads in Emulsion (GEMs). For both cDNA amplification and library sample index PCR, 12 cycles were used. Most libraries were sequenced on Illumina Novaseq S2, but some used Illumina Miseq, Hiseq 2500, or Hiseq 4000, according to manufacturer’s protocol; see Figure S2 and Table S1 for details.

first: Jing-Ping

last: Lin

first: Hannah

last: Kelly

first: Yeajin

last: Song

first: Riki

last: Kawaguchi

middle: H

last: Geschwind

first: Steven

last: Jacobson


title: Effect of depletion of CD38 on gene expression in LPS/IFNg-stimulated primary mouse astrocytes

city: Tel Aviv

first: Lior

last: Mayo

state: Israel

address: Britannia Bldg. Room 204, Tel Aviv univeristy

country: Israel

institute: Tel Aviv Unoversity

summary: To investigate the role of CD38 activity on astrocyte pro-inflmmatory activation

overall_design: Comparative gene expression profiling analysis of RNA-seq data for WT or CD38KO astrocytes activated for 6 h with LPS/IFNγ or left untreated (Con).

first: Tom

last: Meyer

first: Dor

last: Shimon


title: The Hippo pathway links adipocyte plasticity to adipose tissue fibrosis

city: Beijing

first: Hongyu

last: Shen

address: Wang Kezhen Building, No.5 Yiheyuan Road

institute: Peking University

summary: Fibrosis disrupts adipose tissue (AT) homeostasis in response to chronic caloric excess, exacerbating metabolic dysfunction. The molecular mechanisms linking adipocyte plasticity to AT fibrosis are largely unknown. Here we show that the Hippo pathway is coupled with TGFbeta signaling to orchestrate a functional adipocyte-to-myofibroblast transition in AT fibrosis. We found that Lats1/2-knockout adipocytes could dedifferentiate into DPP4+ progenitor cells and convert to DPP4- myofibroblasts upon TGFbeta stimulation. Macrophages recruited by CCL2 served as a major cell source of TGFbeta. YAP and TAZ, the Hippo downstream effectors, enhanced SMAD2 stability to promote fibrotic responses. Importantly, inhibition of YAP/TAZ activity in obese mice markedly relieved AT fibrosis and improved metabolic homeostasis. Together, our findings identify the Hippo pathway as a molecular switch in the initiation and development of AT fibrosis, implying it as a therapeutic target.

overall_design: RNA sequencing of adipocytes from the constitutive Lats1/2 adipocyte knockout mouse model (Lats1f/fLats2f/fAdipoqCre) and control littermates ((Lats1f/fLats2f/f). Adipocytes isolated from subcutaneous white adipose tissue of four P7 male mice were pooled as a sample.

first: Xun

last: Huang

first: Yiheng

last: Zhao

first: Yifu

last: Qiu


title: MicroRNA Expression Profiling of Lumbar Spinal Cord in a Rat Model of Bone Cancer Pain

status: Public on Aug 10 2022

city: Changsha

first: Xinran

last: Hou

state: Hunan

address: Xiangya Road 87

institute: Central South University

type: Non-coding RNA profiling by high throughput sequencing

summary: Bone cancer pain (BCP), in which the majority is caused by metastasis from other cancer sites, is the most common type of chronic cancer pain. Bone cancer pain is developed accompanied by changes of numerous genes expression, from peripheral to central nervous system, which may account for this dysfunctional nociceptive perception. Although the pivotal role of lncRNA in neuropathic pain are well acknowledged, the involvement of lncRNA in bone cancer pain development are remain to be clarified. Thus, in the present study we performed transcriptome sequencing to explore changes in expression profiles of lncRNA and mRNA to provide a landscape of dysregulated miRNA in spinal cord of bone cancer pain.

overall_design: On the fourteenth day after tumor inoculation, total RNA was extracted from the ipsilateral side of spinal cord of bone-cancer-pained and sham-operated Wistar rats, in triplicates, and high throughput sequencing of ncRNA and mRNA was performed by  Illumina NovaSeq 6000.

first: Jian

last: Wang

first: Zhuofeng

last: Ding

first: Zongbin


title: Transcriptional data from yeast treated with 10 mg/ml of neomycin sulfate for 4h

status: Public on Aug 09 2022

city: MADRID

first: Teresa

last: Fernandez-Acero

address: PLAZA DE RAMÓN Y CAJAL S/N

department: Departamento de Microbiología II

institute: Facultad de Farmacia UCM

summary: We studied the transcriptional profile in yeast cells in response to treatment with 10mg/ml of neomycin sulfate for 4 h.

platform_organism:
Schizosaccharomyces pombe
Saccharomyces cerevisiae

overall_design: Three biological replicates of samples of yeast cells were untreated or treated with 10mg/ml of neomycin sulfate and subjected to a microarray experiment.


title: Transcriptome-wide identification of STING agonist programed B cells

city: Chapel Hill

first: John

last: Wrobel

state: NC

address: 120 Mason Farm Rd

department: Department of Biochemistry and Biophysics

institute: University of North Carolina

summary: We employed RNA-seq to study the transcriptomic change in B lymphocytes in response to STING agonist. Transcriptomic analysis of wild type and TMEM173–/– B cells stimulated with STING agonist revealed that the inflammatory response pathway enriched in 3'3'-cGAMP treated WT B cells but lacking in Tmem173-/-B cells comprised of a cluster containing inhibitory regulators, provoking STING signal to evade immune surveillance by inducing an immunosuppressive B cell population.

overall_design: The primary B cells were isolated from WT, Tmem173-/- mice, and then treated with 3'3'-cGAMP for 12 hours. The total RNA was extracted and applied to RNA-Seq analysis.

first: Sirui

last: Li

middle: A

first: Xianming

last: Tan

first: Jenny

middle: P

last: Ting


title: Defining specific cell states of MPTP-induced Parkinson's disease by single-nucleus RNA sequencing

city: 上海市

first: Junjie

last: Ma

address: 上海市徐汇区岳阳路320号

institute: SINH

summary: Parkinson’s disease (PD), a neurodegenerative disease with the impairment of movement execution that is related to age, genetic and environmental factors. 1-methyl-4-phenyl-1,2,3,6-tetrahydropyri-dine (MPTP) is a neurotoxin widely used to induce PD models, but the effect of MPTP on cell-gene of PD has not been fully elucidated. By single-nucleus RNA sequencing, we uncovered the PD-specific cells and revealed remarkable changes in their cellular states, including astrocytosis, endothelial cells absence, as well as a cluster of PD-exclusive medium spiny neuron cells. Furthermore, trajectory analysis of astrocyte and endothelial cells populations predicted candidate target gene sets that might be associated with PD. Notably, the detailed regulatory roles of astrocyte-specific transcription factors Dbx2 and Sox13 in PD were first revealed in our work. Finally, we characterized the cell-cell communications of PD-specific cells and found that the overall communication strength was enhanced in PD compared with matched control, especially the signaling pathways of NRXN and NEGR. Our work provides comprehensive overview on the changes of cellular states of the MPTP-induced mouse brain.

overall_design: we performed snRNA-seq on the mixed samples of cerebral cortex, hippocampus, striatum and cerebellum from MPTP-PD and CN mice, and obtained 19,531 high-quality nuclei.

first: Yunxia

last: Guo


title: Transcriptomic profiles of muscular dystrophy with myositis (mdm) in extensor digitorum longus, psoas, and soleus muscles from mice

status: Public on Aug 08 2022

city: Lowell

first: Matthew

last: Gage

state: Massachusetts

address: 265 Riverside St

department: Chemistry

institute: University of Massachusetts Lowell

summary: Titinopathies are inherited muscular diseases triggered by genetic mutations in the titin gene. Muscular dystrophy with myositis (mdm) is one such disease caused by a deletion in the N2A-PEVK region of titin, one of the most active binding sites in titin, and mice with this deletion develop progressive muscle degeneration. The range of phenotypic differences observed in mdm mice extends well beyond impacts on titin, making it clear that deletion of this region initiates a cascade of additional transcriptomic changes. Previous research has focused on correlating phenotypic differences with muscle function in mdm mice. These studies have provided understanding of the downstream physiological effects resulting from the deletion but only provide insights on processes that can be physiologically observed and measured. We used differential gene expression (DGE) to compare the transcriptomes of extensor digitorum longus (EDL), psoas and soleus muscles from wild-type and mdm mice to develop a deeper understand of these tissue-specific responses.

overall_design: Comparative study of transcriptomes of slow-twitch Soleus and fast-twitch TA muscle tissues.

first: Pabodha

last: Hettige

first: Uzma

last: Tahir

first: Kiisa

middle: C

last: Nishikawa


title: Transcriptome profiling of colon biopsies from pre-clinical models of colitis

city: London

first: Nick

last: Powell

address: Du Cane Road

department: Department of Metabolism, Digestion and Reproduction

country: United Kingdom

institute: Imperial College London

summary: We carried out genome-wide expression profiling of colon biopsies from innate, adaptive and chemically-induced models of colitis and corresponding control mice to investigate their similarities and differences at the molecular level.

overall_design: Comparative analysis of transcriptomic profiles from colonic biopsies of mice with colitis induced by DSS, DNBS, T-cell transfer, anti-CD40 antibodies, IL-10 deficiency or T-bet-/- × RAG2-/- deficiency.

first: Jon

last: Lo

first: Domenico

last: Cozzetto


title: Study of new molecular mechanism for Th9 differentiation

first: Keji

last: Zhao

state: MD

address: Building 10 Room 7B06A

department: National Heart, Lung, and Blood Institute

institute: national Institute of Health

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Th9 cells are differentiated from naïve CD4+ T cells by T cell receptor (TCR) stimulation in the presence of the cytokines transforming growth factor-beta (TGF-b) and IL-4, but the molecular mechanisms by which signaling via these two cytokines control Il9 gene expression remain incompletely understood. We show here opposing functions of albumin site D-binding protein (DBP) and E2F8, an atypical member of the E2F family member of transcription factors , in controlling Th9 cell differentiation. Specifically, TGF-b and IL-4 signaling induced phosphorylation of the Serine 213 site in the linker region of the Smad3 protein (pSmad3L-Ser213)  via the activation of phosphorylated MAPK p38 (p-p38). pSmad3L-Ser213, but not the phosphorylation of the C-terminal of SMAD3 (pSmad3C), was necessary and sufficient for Il9 gene transcription. We identified DBP and E2F8 as a potential activator and repressor, respectively, for Il9 gene transcription by analyzing the global chromatin accessibility and transcriptomes and discovered that pSmad3L-Ser213 was required for the increase in DBP expression but decreased E2F8 expressions during Th9 cell differentiation. We found that while DBP and E2F8 directly bound to the promoters of Il9 gene, DBP enhanced, but E2F8 suppressed, Il9 gene transcription in CD4+ T cells in response to TGF-b and IL-4 signaling, as revealed by functional gene loss- and gain-of-function studies. Notably, the Dbp-deficient and E2f8-deficient Th9 cells promoted and suppressed tumor growth, respectively, in experimental tumor models of melanoma and fibrosarcoma in mice. Importantly, DBP and E2F8 also exhibited opposing roles in regulating human TH9 differentiation in vitro. Thus, we have revealed a previously unrecognized molecular mechanism of Smad3 linker region-mediated opposing functions of DBP and E2F8 in Th9 differentiation.

first: Sang-A

last: Park

first: Yun-Ji

last: Lim

first: Wai

middle: L

last: Ku

first: Dunfang

last: Zhang

first: Kairong

last: Cui

first: WanJun

last: Chen


title: Fusion genes in EGFR mutant lung cancer

city: Boston

first: Elizabeth

last: Cohen

state: MA

address: 450 Brookline Ave

institute: Dana-Farber Cancer Institute

summary: The clinical significance of gene fusions detected by DNA-based next generation sequencing remains unclear as resistance mechanisms to EGFR tyrosine kinase inhibitors (TKIs) in EGFR mutant non-small cell lung cancer (NSCLC). Through comprehensive evaluation of potential drug resistance-imparting fusion oncogenes in EGFR mutant lung cancers, we selected candidate samples to be further validated by confirmatory assay. Here, we performed RNA sequencing as an unbiased genome-wide method to identify novel oncogenic fusions. In 11 samples from 10 patients, 3 different fusion callers consistently detected only the DLG1-BRAF fusion in sample 6. None of other putative fusions detected by DNA-based hybrid capture sequencing were validated.We concluded that only a subset of putative fusion was validated by RNA-seq.

overall_design: Examination of mRNA expresion and fusion genes in lung adenocarinoma tisuues

first: Yoshihisa

last: Kobayashi

middle: F

first: Michael

middle: Y

last: Tolstorukov

first: Pasi

last: Jänne


title: A combination of plasma membrane sterol biosynthesis and autophagy is required for shade-induced hypocotyl elongation

city: Lausanne

first: Leonore

last: Wigger

address: Amphipôle Building

country: Switzerland

institute: Swiss Institute of Bioinformatics

summary: We hypothesized a convergence of transcriptome profiles in hypocotyls of low blue light (LB) or low red/far red light (LRFR) treated seedlings as both conditions trigger hypocotyl cell elongation. To test this hypothesis, we did a transcriptome analysis in of 5d-old long-day (LD)-grown Col-0 (wild type, WT), pif457, and yuc2589 seedlings treated for 3 hours with LB, LRFR or remaining in the same light condition (WL). We used dissected cotyledons and hypocotyls to characterize the LB and LRFR response in both organs and determine their dependency on PIFs and YUC-mediated auxin biosynthesis.

overall_design: Total mRNA profiles of 5 day old Arabidopsis cotyledons and hypocotyls from three genotypes: Col-0 (WT), pif457, yuc2589, and smt2-1, which were subjected to three light conditions: white light (WL), low blue (LB) and low red/far red (LRFR).

first: Yetkin

last: Ince

first: Sylvain

last: Pradervand

first: Christian

last: Fankhauser


title: Ribosome profiling of WT E14, Dgcr8_KO, Dorsha_KO, Dicer_KO and Ago1&2_Double_KO mouse embryonic stem cells

city: Zurich

first: Constance

last: Ciaudo

state: Zurich

address: Otto-Stern-Weg 7, HPL G.31

department: D-BIOL

institute: ETH Zurich

summary: miRNAs are short regulatory single stranded RNA sequences that upon complementary binding to mRNAs lead to the inhibition or degradation of their targets. This regulatory mechanisms has been shown to play crucial roles throughout the whole life cycle of animals and plants as well as in disease. While a plethora of methods exist to predict targets of miRNA, which suggest that up to 80% of the genome is miRNA regulated, it has recently been reported that many of these predictions are false positives, cell type specific or represent non-functional binding. In order to identify the subset of real functional miRNAs and their targets, we established miRNA pathway mutants in mouse embryonic stem cells (mESC), allowing the dissection of canonical and non-canonical functions of pathway members. Additional data integration of downstream regulatory layers (CLIP-seq, ribosome profiling and MS) enabled us to follow and track down real functional miRNA-gene interactions, which reduced the miRNA  genome regulation to approximately 1%.

overall_design:
Purpose: The goals of this study was to obtain the ribosome binding profile of WT and RNAi mutant mESCs.
Ribosome profiling of different RNAi mutant mouse embryonic stem cells (E14) were generated by deep sequencing, in duplicate, using Illumina HiSeq2500.


title: Transcriptomics analysis of C. elegans intestines

status: Public on Aug 07 2022

city: Hangzhou

first: Caiyong

state: Zhejiang

address: 866 Yuhangtang Road

institute: Zhejiang University

summary: To identify new heme responsive genes, we performed transcriptomics analysis on the intestines isolated from worms that were cultured at different concentrations of heme. Results of SMART-seq and gene expression profiling showed that 578 genes were differentially expressed at different heme concentrations.

overall_design: Adult worms that had been cultured with 2, 20, or 400 μM heme were paralyzed and dissected. Intestines from three adult worms were combined into one sample. The mRNA profiles were analyzed by SMARTseq, in triplicate, using Illumina NovaSeq 6000 platform.


title: scRNAseq of lungs from APOE knock-in mice with COVID-19

city: Berlin

first: Benjamin

middle: N

last: Ostendorf

address: Augustenburger Platz 1

institute: Charité University Medicine

summary: We performed single cell RNA-sequencing of lungs from APOE knock-in mice in the absence of infection or four days post infection with SARS-CoV-2 MA10. Infected mice showed major remodeling of the cellular composition with expansion of myeloid cells and relative depletion of epithelial cells. In infected mice, APOE2 mice showed enrichment of pathways implicated in immune activation, consistent with immunologic misfiring.

overall_design:
scRNAseq of lungs from APOE knock-in mice with or without COVID-19. Libraries were prepared with the whole transcriptome 100K kit from Parse Biosciences, which involves barcoding and then pooling cells from all samples prior to generation of eight sublibraries. Because of the design of the kit, sequencing reads of all samples are distributed across all eight sublibraries. For further details see attached `README.txt` file.
Samples: ctrl_01_E2, ctrl_02_E2, ctrl_03_E2, ctrl_04_E3, ctrl_05_E3, ctrl_06_E3, ctrl_07_E4, ctrl_08_E4, ctrl_09_E4, inf_01_E2, inf_02_E2, inf_03_E3, inf_04_E3, inf_05_E4, inf_06_E4, inf_07_E4, inf_08_E2, inf_09_E2, inf_10_E2, inf_11_E3, inf_12_E3, inf_13_E4, inf_15_E4, inf_16_E4, inf_17_E2, inf_18_E3, inf_19_E4, inf_20_E4, inf_23_E3


title: Next Generation Sequencing Facilitates Quantitative Analysis of Mock/ZIKV infected Guinea Pig Lung Transcriptomes

first: Rui-Ting

last: Li

state: Beijing

address: No.20 Dongda Street, Fengtai District

department: State Key Laboratory of Pathogen and Biosecurity

institute: Beijing Institute of Microbiology and Epidemiology

summary: Whether Zika virus (ZIKV) could be transmitted via aerosol routes remains unknown. In this study, we demonstrated that aerosolized ZIKV is fully infectious in vitro and in vivo.Transcriptome analysis further revealed that genes expression related to viral process, biological regulation and immune system response were significantly changed.

overall_design: Guinea pigs before or after infection (1,3 or 7 dpi)  were used for RNA-seq.

first: Hong-Ying

last: Qiu


title: RNA-seq of homogenized lungs of APOE knock-in mice during COVID-19 II

summary: Here we analyze the transcriptional profiles of homogenized lungs resected from APOE2, APOE3, and APOE4 knock-in mice on day 4 post infection with SARS-CoV-2 MA10. This experiment validated a prior RNA-seq experiment revealing blunted adaptive immunity in APOE2 and APOE4 mice during COVID-19 progression.

overall_design: Weighted gene co-expression network analysis and pathway analysis of RNA-sequencing data.


title: RNA-seq of homogenized lungs of APOE knock-in mice during COVID-19

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

overall_design: Refer to individual Series


title: DNA-RNA IP sequencing for R-loops in XPO4 Knockout NIH/3T3 cell

city: Hefei

first: Ge

last: Shan

state: Anhui

address: 443 Huangshan Road

department: School of Life Sciences

institute: University of Science and Technology of China

summary: Numerous RNAs are exported from the nucleus, abnormalities of which lead to cellular complications and diseases. We report the identification of Exportin 4 (XPO4) as a conserved circular RNA (circRNA) exportin. Cellular insufficiency of XPO4 causes nuclear circRNA accumulation, circRNA:DNA (ciR-loop) formation, linear RNA:DNA (liR-loop) buildup, and DNA damage. These results provide insights into the mechanism and biomedical links of circRNA nuclear export.

overall_design: Examination of R-loops level in NIH/3T3 cells.


title: RNA-seq of homogenized lungs of APOE knock-in mice during COVID-19 I

summary: Here we analyze the transcriptional profiles of homogenized lungs resected from APOE2, APOE3, and APOE4 knock-in mice in the absence of infection (day 0) and on days 2 and 4 post infection with SARS-CoV-2 MA10. Weighted gene co-expression analysis identified gene modules enriched for genes implicated in T and B cell activation to be downregulated in APOE2 and APOE4 mice during COVID-19 progression.


title: Comparison of single-nucleus and single-cell transcriptomes in hepatocellular carcinoma tissue

city: Qingdao

first: Hai

middle: Xia

last: Qu

state: China

address: No. 5, Donghai Zhong Road

institute: Qingdao Municipal Hospital

summary: In the present study, scRNA-seq(single-cell RNA sequencing) was compared with snRNA-seq(single-nucleus RNA sequencing) in tumor tissue obtained from patients with HCC, using the 10X Genomics Chromium platform.

overall_design: Tumor tissue samples obtained from a 65-year-old male patient with HCC who underwent curative resection were used to explore scRNA-seq and snRNA-seq.

first: Haixia

first: Lin

last: Xu


title: Host Acid Signal Controls Salmonella Flagella Biogenesis through CadC-YdiV Axis

status: Public on Aug 06 2022

city: Jinan

first: wei

middle: wei

last: wang

address: No. 6699 Qingdao Road, Huaiyin District, Jinan City, Shandong Province

institute: Shandong First Medical University & Shandong Academy of Medical Sciences

summary: Upon entering host cells, Salmonella quickly turn off flagella biogenesis to avoid recognition by the host immune system. However, it is not clear which host signal(s) Salmonella senses to initiate flagellum control.During the infection of a host,acid pH acts as an important environmental factor to triggers some genes expression. To investigate the effect of environmental acid signaling on the regulation of Salmonella flagella synthesis, we cultivated Salmonella typhimurium ATCC 14028s to an OD600 of 0.4, and then continued to culture for 2 h at pH 7.0 or pH 5.0. We then performed gene expression profiling analysis using data obtained from RNA-seq of cultured cells at different pH condition.

sample_organism: Salmonella enterica subsp. enterica serovar Typhimurium

overall_design: Comparative gene expression profiling analysis of RNA-seq data for  Salmonella typhimurium ATCC 14028s under differnent pH condition (pH 7.0 or pH 5.0),and each set has 3 repetitions .

first: Weiwei

last: Wang

first: Bingqing

first: Yingying

last: Yue

first: Min

last: Zhang

first: Nannan

last: Song

first: Haihong

last: Jia

first: Yuanji

last: Dai

first: Fengyu

first: Cuiling


title: Transcriptome sequence of cucumber seeding under cold stress

city: Shenyang

first: Xiaoyu

last: Duan

address: Dongling street 120

institute: Shenyang Agricultrual University

summary: Purpose: the goals of this study are to identify the GST gene and to analyse their function under cold stress

overall_design: The transcriptome sequence of cucumber seedings under cold stress were generated by deep sequencing with three repeats using Illumina. The sequence reads that passed filters were mapped to cucumber genome (http://cucurbitgenomics.org/organism/18) using HISAT2 software. The differently expressed genes were identify by |log2(FoldChange)| > 0 & p < 0.05, and qRT–PCR validation was performed using SYBR Green assays

first: Xuejing

last: Yu

first: Yidan

first: Wei

last: Fu

first: Ruifang

last: Cao

first: Lu

last: Yang

first: Xueling

last: Ye


title: The TRESLIN-MTBP complex couples completion of DNA replication with S/G2 transition

city: Copenhagen N

first: Mads

last: Lerdrup

address: Blegdamsvej 3C

department: Department of Cellular and Molecular Medicine

country: Denmark

institute: University of Copenhagen

summary: It has been proposed that ATR kinase senses the completion of DNA replication to initiate the S/G2 transition. In contrast to this model, we show here that the TRESLIN-MTBP complex prevents a premature entry into G2 from early S-phase independently of ATR/CHK1 kinases. TRESLIN-MTBP acts transiently at pre-replication complexes (preRCs) to initiate origin firing and is released after the subsequent recruitment of CDC45. This dynamic behavior of TRESLIN-MTBP implements a monitoring system that checks the activation of replication forks and senses the rate of origin firing to prevent the entry into G2. This system detects the decline in the number of origins of replication that naturally occurs in very late S, which is the signature that cells use to determine the completion of DNA replication and permit the S/G2 transition. Our work introduces TRESLIN-MTBP as a key player in cell cycle control independent of canonical checkpoints.

overall_design: Asynchronous HeLa cells transfected with control or TRESLIN siRNA for 24 or 48 hours are analyzed. Three biological replicates per condition were collected and analyzed.

first: Gijs

last: Zonderland

first: Riccardo

last: Vanzo

first: Sampath

last: Amitash

first: Elena

last: Martín-Doncel

first: Fabian

last: Coscia

first: Andreas

last: Mund

first: Jan

last: Benada

first: Dominik

last: Boos

first: Luis

last: Toledo


title: Effect of restraint stress on gene expression in peripheral blood cells of mice

first: Hao

last: He

state: Shandong

address: No.6699, Qingdao Road, Huaiyin District

institute: Shandong First Medical University

summary: Psychological stress could affect the immune system and then regulate the disease process. It is generally believed that chronic stress is harmful to health, while acute stress is conducive to life survival. At present, most studies focused on the effects of chronic stress on diseases and immune cells. How acute stress affects the immune system remains poorly understood. In this study, female C57BL/6 mice received restraint stress or no stress for 6 hours. RNA was harvested from peripheral blood and transcriptome sequencing was performed.

overall_design: Mice received restraint stress or no stress for 6 hours, and then RNA was extract from peripheral blood for transcriptome sequencing.

first: Lanjing

last: Tang

first: Li

last: Kang


title: Methylation study of rapamycin treatment during development in mice

status: Public on Aug 05 2022

city: Los Angeles

first: Steve

last: Horvath

state: CA

address: 695 Charles E. Young Drive South, Box 708822

department: Human Genetics

institute: University of California, Los Angeles

type: Methylation profiling by genome tiling array

summary: An Infinium microarray platform (HorvathMammalMethylChip320) was used to generate DNA methylation data from n=48 liver samples from mice. Treatment: encapsulated rapamycin treated or control mice

platform_organism:
Macaca mulatta
Homo sapiens
Mus musculus
Rattus

overall_design: n=48 samples. Liver samples from UMHET3 mice. Mice were fed chow containing 42 ppm of eudragit-encapsulated rapamycin (eRapa) or the corresponding amount of encapsulating material as a control (Eudragit).

first: Vadim

last: Gladyshev


title: Microarray gene expression data from MCF-7 and LetR cells

city: Odense M

first: Carla

last: Alves

address: Fioniavej 36, 2. sal

institute: SDU

summary: Resistance to aromatase inhibitor (AI) treatment and combined CDK4/6 inhibitor (CDK4/6i) and endocrine therapy (ET) are crucial clinical challenges in treating estrogen receptor-positive (ER+) breast cancer. Understanding the resistance mechanisms and identifying reliable predictive biomarkers and novel treatment combinations to overcome resistance are urgently needed. Herein, we show that upregulation of CDK6, p-CDK2, and/or cyclin E1 is associated with adaptation and resistance to AI-monotherapy and combined CDK4/6i and ET in ER+ advanced breast cancer. Importantly, co-targeting CDK2 and CDK4/6 with ET synergistically impairs cellular growth, induces cell cycle arrest and apoptosis, and delays progression in AI-resistant and combined CDK4/6i and fulvestrant-resistant cell models and in an AI-resistant autocrine breast tumor in a postmenopausal xenograft model. Analysis of CDK6, p-CDK2, and/or cyclin E1 expression as a combined biomarker in metastatic lesions of ER+ advanced breast cancer patients treated with AI-monotherapy or combined CDK4/6i and ET revealed a correlation between high biomarker expression and shorter progression-free survival (PFS), and the biomarker combination was an independent prognostic factor in both patients cohorts. Our study supports the clinical development of therapeutic strategies co-targeting ER, CDK4/6 and CDK2 following progression on AI-monotherapy or combined CDK4/6i and ET to improve survival of patients exhibiting high tumor levels of CDK6, p-CDK2, and/or cyclin E1.

overall_design: Total RNA from 3 biological replicates of MCF7, LetR1 and LetR3 cells was extracted and arrayed separately in Human Transcriptome Array 2.0 (HTA, Affymetrix).


title: Exon skipping in genes encoding lineage-defining myogenic transcription factors in rhabdomyosarcoma

city: Dallas

first: Lei

last: Guo

state: TX

address: 5323 Harry Hines Blvd

department: Department of Population and Data Sciences

institute: University of Texas Southwestern Medical Center

summary: Rhabdomyocarcoma (RMS) contains myoblast-like cells that fail in terminal differentiation. To explore the potential defects in differentiation, we studied mRNA splicing variants in genes encoding transcription factors critical for skeletal muscle differentiation with RNA-Seq data from RMS specimens and cell lines. We identified novel exon 2 skipping form of MYOD1 and MYF5. Further study on MYODΔEx2 protein showed that it failed to robustly induce muscle-specific genes but its ectopic expression conferred a selective advantage in cultured fibroblasts and an RMS xenograft. Therefore, alternative splicing can represent a mechanism to alter the function of these two transcription factors in RMS.

overall_design: Bulk RNA-Seq was carried out with 6 RMS cell lines and human skeletal muscle myoblasts (HSMM).

first: Stephen

middle: X

last: Skapek


title: Development and validation of novel inflammatory response-related gene signature to predict prostate cancer recurrence and response to immune checkpoint therapy

status: Public on Aug 04 2022

city: Foshan

first: Yong

last: Luo

state: Guangdong

address: 78 Weiguo Road

department: Department of Urology

institute: The Second People’s Hospital of Foshan, Affiliated Foshan Hospital of Southern Medical University

summary: The aim of this study is to construct an inflammatory response-related genes (IRRGs) signature to monitor biochemical recurrence (BCR) and treatment effects in prostate cancer patients (PCa)

overall_design: We applied RNA-seq to screen out the differentially expressed genes (DEGs) between the benign prostate cell line and the PCa cell line, including 4 of BPH-1, 4 of DU145, and 4 of PC3

first: Xiaopeng

last: Liu

first: Jingbo

last: Lin

first: Weide

last: Zhong

first: Qingbiao

last: Chen


title: Characterization of genomic and chromatin landscape of RPE-1 WT cells

status: Public on Aug 03 2022

city: Amsterdam

first: Anoek

last: Friskes

address: Plesmanlaan 121

country: Netherlands

institute: Netherlands Cancer Institute

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for histone variants H3K9me3/H3K27Ac/H2A.Z/H3K36me3/H4K4me1/H3K4me3/H3K27me3 in RPE-1 WT cells

first: Anna

last: Gonzalez Manjon

first: Tesa

last: Severson

first: René

last: Medema


title: Effects of temperature on transcriptome and energy metabolism of porcine myoblasts

city: Dummerstorf

first: Siriluck

last: Ponsuksili

address: Wilhelm-stahl-allee 2

institute: FBN

summary: 47,880 probe-sets were screened

overall_design:
RNAs of porcine myoblasts were hybridized to Affymetrix Porcine Snowball Array.
MIXED procedure in SAS (Version 9.4, SAS Institute Inc.). The pool (pool 5 or pool 20), temperature (35°, 37°, 39° or 41 °C) and the interaction of temperature and pool were used as fixed factors.

first: Klaus

last: Wimmers


title: Gene expression data of mRNA from liver sample of F2 population based German Landrace (DL) and Pietrain (Pi) pig breeds

summary: 47,880 probe-sets were screened, in the first part of this study pig embryos at 63 days post conception (dpc)

overall_design: RNAs of liver from  F2 at 63 dpc were hybridized to Affymetrix Porcine Snowball Array.


title: Methylation study of whole blood from elderly participants with human umbilical cord blood plasma treatment

summary: An Infinium microarray platform (GPL23976, Illumina Infinium HumanMethylation850 BeadChip) was used to generate DNA methylation data from human whole blood samples. Treatment: human umbilical cord plasma concentrate injection

overall_design: n=36 samples. For this safety study, 18 elderly participants were treated with human umbilical cord plasma concentrate injection weekly (1 ml intramuscular) over a 10-week period. Blood was drawn before and after the treatment.

first: James

last: Clement


title: NAT10 modulates fatty acid metabolism of palmitate driven MCF7 in ac4C dependent manner

city: Jeddah

first: Mohammad

middle: Imran

last: Khan

state: Makkah

address: King Abdullah Road

department: Biochemistry

country: Saudi Arabia

institute: King Abdulaziz University

summary: We show that non-toxic exogenous palmitate uptake in MCF7 cells promotes NAT10 expression and NAT10-dependent ac4C RNA modification. It was previously reported that NAT10 modulates the addition of ac4C on RNA transcripts in normal and cancer conditions. However, no study report the impact of NAT10 in palmitate driven cells. Here we performed RNA immunoprecipitation sequencing (RIP-seq) in palmitate loaded MCF7 knockdown with NAT10 siRNA. Based on the pathways and enrichment landscape identified. We found that ac4C peaks of fatty acid metabolic genes including ELOVL6, ACSL1, ACSL3, ACSL4, ACADSB and ACAT1 were significantly decreased upon knockdown with NAT10 siRNA.  Overall, our results revealed the impact of NAT10 as a regulator of fatty acid metabolism in ac4C-dependent manner

overall_design: Exogenous palmitate uptake coupled with knockdown using NAT10 siRNA followed by RNA precipitation using ac4C antibody

first: Dalhat

last: Hassan

first: Khan

last: Mohammad Imran


title: RNA-seq in mouse WT and ABAT cKO T cells

status: Public on Aug 02 2022

city: columbus

first: Ruoning

last: Wang

state: OH

address: 700 Children's Drive

institute: Nationwide children's hospital

summary:
Purpose: To gain more mechanistic insights into the effects of ABAT deletion on T cells, we performed RNAseq in activated CD4 WT and ABAT cKO TH0 cells.
Methods: Total RNA was isolated according to the RNeasy Mini Kit (Qiagen) and treated with DNase I. RNA quality was assessed using the Agilent 2100 Bioanalyzer and RNA Nano Chip kit (Agilent Technologies, CA). RNA-seq libraries were generated using TruSeq Stranded Total RNA with Ribo-Zero Globin Complete kit (Illumina, CA). Approximately 60–80 million paired-end 150 bp reads were generated per sample using Illumina HiSeq 4000 platform
Results: RNA-seq revealed an decreased pro-inflammatory gene signature in ABAT cKO T cells after activation
Conclusions: Inhibition of ABAT suppresses TH17 but enhances iTreg cell differentiation

overall_design: mRNA profiles of activated WT and ABAT cKO T cells were generated by deep sequencing

first: Siwen

last: Kang


title: Identification of in vivo roles of ErbB4-JMa and its direct nuclear signaling using a novel isoform-specific knock out mouse

city: Ann Arbor

first: Gabriel

last: Corfas

state: MI

address: 1150 West Medical Center Dr.

department: Otolaryngology

institute: University of Michgian

summary: Like all receptor tyrosine kinases (RTKs), ErbB4 signals through a canonical signaling involving phosphorylation cascades. However, ErbB4 can also signal through a non-canonical mechanism whereby the intracellular domain is released into the cytoplasm by regulated intermembrane proteolysis (RIP) and translocates to the nucleus where it regulates transcription. These different signaling mechanisms depend on the generation of alternative spliced isoforms, a RIP cleavable ErbB4-JMa and an uncleavable ErbB4-JMb. Non-canonical signaling by ErbB4-JMa has been implicated in the regulation of brain, heart, mammary gland, lung, and immune cell development. However, most studies on non-canonical ErbB4 signaling have been performed in vitro due to the lack of an adequate mouse model. We created an ErbB4-JMa specific knock out mouse and demonstrate that RIP-dependent, non-canonical signaling by ErbB4-JMa is required for the regulation of GFAP expression during cortical development. We also show that ErbB4-JMa signaling is not required for the development of the heart, mammary glands, sensory ganglia. Furthermore, we identify genes whose expression during cortical development is regulated by ErbB4, and show that the expression of two of them, CRYM and DBi, depend on ErbB4-JMa. Thus, we provide the first animal model to study the roles of non-canonical RTK in vivo.

overall_design: mRNA profiles of wild-type (WT) and ErbB4 KO E15.5 cortex (n = 4 of each genotype)

first: Robert

last: Doherty

first: Brenna

last: MacLeod

first: Megan

middle: M

last: Nelson

first: Mostafa

last: Ibrahim

first: Beatriz

last: Borges

first: Nada

middle: W

last: Jaradat

first: Matthew

last: Finneran

first: Roman

middle: J

last: Giger


title: Toxicity Testing in the 21st Century: An Integrated Approach to Genetic Safety Testing using the TGx-DDI Genomic Biomarker and High-Throughput CometChip® [NanoString]

city: Ottawa

last: Meier

state: Ontario

address: 251 Sir Frederick Banting Driveway

department: Health Canada

country: Canada

institute: Government of Canada

summary: The TGx-DDI is a transcriptomic biomarker used to predict the DNA damage-inducing (DDI) capability of chemicals by providing mechanistic information to aid in the interpretation of positive genotoxicity data. The biomarker was developed within the Health and Environmental Sciences Institute (HESI) and measures transcriptional changes in a set of primarily p53-responsive genes. We investigated three antibiotic drugs, nitrofurantoin (NIT), novobiocin sodium salt (NOV) and metronidazole (MTZ), with a long history of clinical use in human and/or veterinary applications. While all three drugs are considered safe, there is some evidence of chromosome damage with NIT and NOV. We conducted high-throughput CometChip and TGx-DDI assays to evaluate the drugs in a parallel test strategy to explore their toxicity using these newer mechanism-based tests. An extended concentration-response analysis was conducted in human TK6 cells (from 0 to 1 mM). The alkaline CometChip assay was used to measure DNA damage, while TGx-DDI was applied using TempO-Seq and NanoString technologies (in two different laboratories) to confirm reproducibility of the results. The CometChip was negative for all three drugs except at overtly cytotoxic concentrations, which were eliminated from the gene expression analysis. NIT and MTZ were classified as non-DDI by TGx-DDI at all concentrations tested. NOV classified as DDI at the highest concentrations tested. NOV is bacterial DNA-gyrase inhibitor that also acts as a topoisomerase II inhibitor at high concentrations. The TGx-DDI classification results were identical across laboratories/technologies. This case study demonstrates the utility of TGx-DDI to de-risk NIT and NOV, and the reproducibility of the biomarker.

overall_design: Examination of the complementarity of two high-throughput genotoxicity tests, the CometChip® assay to assess DNA damage and TGx-DDI biomarker analysis for chemical classification using nCounter® and TempO-Seq® gene expression technologies, following exposure to three case study drugs in human TK6 cells. Furthermore, the reproducibility of the TGx-DDI biomarker was examined.

first: Julie

middle: K

last: Buick

first: Andrea

last: Rowan-Carroll

first: Rémi

last: Gagné

first: Andrew

last: Williams

first: Renxiang

last: Chen

first: Heng-Hong

last: Li

first: Albert

last: Fornace Jr.

first: Christy

last: Chao

first: Bevin

last: Engelward

first: Roland

last: Frötschl

first: Heidrun

last: Ellinger-Ziegelbauer

first: Syril

middle: D

last: Pettit

first: Jiri

last: Aubrecht

first: Carole

last: Yauk


title: Toxicity Testing in the 21st Century: An Integrated Approach to Genetic Safety Testing using the TGx-DDI Genomic Biomarker and High-Throughput CometChip®

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

overall_design: Refer to individual Series


title: Toxicity Testing in the 21st Century: An Integrated Approach to Genetic Safety Testing using the TGx-DDI Genomic Biomarker and High-Throughput CometChip® [Sequencing]


city: Warszawa

first: Cecilia

middle: Lanny

last: Winata

address: Ks. Trojdena 4

country: Poland

institute: International Institute of Molecular and Cell Biology in Warsaw

summary: Adar-mediated A-to-I editing is required for establishment of embryonic body axes in zebrafish. To assess the effect of Adar KD and OE, uninjected wild-type and embryos injected with 1 ng of adar MO or 50 pg of adar mRNA were kept until desired developmental stage: 128-cell or 50% epiboly. Two replicates of 20 pooled embryos from each time point were isolated for RNA extraction. For the analysis at 12 hpf, a separate batch of uninjected control, as well as Adar KD and OE samples were generated in three replicates.

overall_design: Parental DNA was extracted from one individual male and female fishes from tail-fin clipping, together with RNA from their offspring at 16-cell, 3.5 hpf, and 5.3 hpf stages. For each time-point, at least 20 embryos were pooled for RNA extraction. To assess the effect of Adar KD and OE, uninjected wild-type and embryos injected with 1 ng of adar MO or 50 pg of adar mRNA were kept until desired developmental stage: 128-cell or 50% epiboly. Two replicates of 20 pooled embryos from each time point were isolated for RNA extraction. For the analysis at 12 hpf, a separate batch of uninjected control, as well as Adar KD and OE samples were generated in three replicates. Total RNA was extracted using TRIzol LS (Thermo Fisher Scientific, USA) and cleaned up on the Qiagen Rneasy Mini column (Qiagen, USA). Quality control of extracted RNA was performed using the 2200 TapeStation system from Agilent Technologies (USA). To avoid the bias caused by cytoplasmic polyadenylation during early embryonic stages, total RNA was rRNA-depleted using Ribo-Zero Magnetic Gold Kit (Human, Mouse, Rat; Epicenter).  cDNA synthesis for Next-Generation Sequencing (NGS) was performed by SMARTer Stranded RNA-seq kit  (Clontech Laboratories, USA) as recommended by the manufacturer. Paired-end sequencing (2 × 75 bp reads) was performed with NextSeq 500 (Illumina, USA).

first: Matthias

last: Bochtler

first: Leszek

last: Pryszcz


title: Hedgehog signaling activates a mammalian heterochronic gene regulatory network controlling differentiation timing across lineages

city: Chicago

first: Ivan

last: Moskowitz

state: IL

address: 900 East 57th Street, KCBD Room 5102

institute: Univeristy of Chicago


title: Global Profiling of Histone Modifications in Plasmodium falciparum using CUT&RUN.

status: Public on Aug 01 2022

city: New York

first: Bjorn

middle: FC

last: Kafsack

state: NY

address: 1300 York Avenue

department: Microbiology & Immunology

institute: Weill Cornell Medicine

overall_design:
CUT&RUN

This series includes re-analysis of SRR4444647, SRR4444639, SRR5935737, SRR5935738, SRR065659 and SRR065664.

first: Riward

middle: A

last: Campelo Morillo

first: Chantal

middle: T

last: Harris

first: Kit

last: Kennedy

first: Björn


title: Placental DNA methylation as mediators of assisted reproduction and parental metabolic risk on offspring phenotype: a multiethnic cohort study

city: Singapore

first: Jonathan

middle: Yinhao

last: Huang

state: « choose one »

address: 30 Medical Drive

country: Singapore

institute: Singapore Institute for Clinical Sciences

summary: Alterations in genomic imprinting are posited as a mechanism for effects of assisted reproduction technologies (ART) and in vitro fertilization (IVF) on long term offspring phenotype. Our previous work has investigated the role of fetal cord tissue DNA methylation in mediating these relationships (Huang, et al. 2021. DOI: 10.1038/s41467-021-25899-4). To study the extent to which fetal-derived placental DNA methylation may mediate these relationships, we conducted a nested cohort study within the Growing Up in Singapore Towards healthy Outcomes (GUSTO) prospective parent-offspring study. We assayed DNA methylation in 408 bulk placental tissue samples arising from 200 placenta obtained at the time of live singleton birth. We oversampled on the basis of conceptions via IVF (ART group) and spontaneous conceptions amongst couples where the father had one or more cardiometabolic risk factors (advanced age, obesity, hypertension, or diabetes history; SC_HIGHRISK group). We then took a random sample of all other spontaneous conceptions (SC_RANDOM). For each of 200 placentas, one sample each was taken from the fetal-facing and maternal facing side of the (fetal-derived) placenta. An additional 8 technical replicated were assayed resulted in the 408 total samples. After QC and elimination of replicates, DNA methylation data were available from 196 unique fetal-facing and 195 maternal-facing placental bulk tissue samples. These repeated measures were used to reduce residual technical and unmeasured confounding biases in downstream analyses.

overall_design: Following delivery of placenta, bulk tissue samples were sampled from across the respective aspects of the placenta, washed, aliquoted, and immediately frozen at -80 C by standard protocols. Samples were later crushed, thawed, extracted, and assayed according to protocols outlined below. Overall, samples arose from N = 200 placenta distributed as: 68 ART group; 43 SC_HIGHRISK group; 89 SC_RANDOM group. After QC, DNA methylation data were available for 66 ART; 42 SC_HIGHRISK; and 88 SC_RANDOM subjects. Principle components analyses showed no strong associations between DNA methylation and technical covariates with the exception of placental side. Cell types were imputed from a single-cell reference using the planet R package.

first: Ai

middle: L

last: Teh


title: Increasing cell size remodels the proteome and promotes senescence

city: Stanford

first: Georgi

middle: Kolev

last: Marinov

state: California

address: 279 Campus Drive West, Beckman Center, B-257A/259

department: Genetics

institute: STANFORD UNIVERSITY

summary: Cell size is tightly controlled in healthy tissues, but it is unclear how deviations in cell size affect cell physiology. To address this, we measured how the proteome changes with cell size. Protein concentration changes are widespread and predicted by subcellular localization, size-dependent mRNA concentrations, and protein turnover. As proliferating cells grow larger, concentration changes associated with cellular senescence are increasingly pronounced, suggesting that large size may be a cause rather than just a consequence of cell senescence. Consistent with this hypothesis, larger cells are prone to replicative, DNA damage-, and CDK4/6i-induced senescence. Size-dependent changes to the proteome, including those associated with senescence, are not observed when an increase in cell size is accompanied by an increase in ploidy. Together, our findings show how cell size could impact many aspects of cell physiology through remodeling the proteome and provide a rationale for cell size control and polyploidization.

sample_organism:
Drosophila melanogaster
Homo sapiens

platform_organism:
Drosophila melanogaster
Homo sapiens

overall_design: Primary human lung fibroblasts (HLF) were arrested in G1 with the Cdk4/6 inhibitor Palbociclib and sorted by FACS into different 4 bins according to their size: bin1 = smallest and bin4 = largest. "Pre-sort" cells were also collected before sorting and "sort-all" cells were run through the FACs procedure without separating according to cell size. For each sample, 200,000 HLF cells were mixed with 100,000 D. melanogaster S2 cells as a spike-in and RNA was extracted for RNA-seq. Two biological replicates with two technical replicates each were performed for each condition.

first: Michael

middle: C

last: Lanz

first: Evgeny

last: Zatulovskiy

first: Matthew

middle: P

last: Swaffer

first: Lichao

last: Zhang

first: Ilayda

last: Ilerten

first: Shuyuan

first: Dong

middle: S

last: You

first: Patrick

last: McAlpine

first: Josh

middle: E

last: Elias

first: Jan

last: Skotheim


title: Single cell atlas identifies lipid-processing and immunomodulatory endothelial cells in healthy and malignant breast

city: Vienna

first: Laura

middle: de

last: Rooij

address: Lazarettgasse 14

country: Austria

institute: CeMM

summary: Since a detailed inventory of endothelial cell (EC) heterogeneity in breast cancer (BC) is lacking, we perform single cell RNA-sequencing of 26,515 cells (including 8,433 ECs) from 9 BC patients and compare them to published EC taxonomies from lung tumors. Angiogenic ECs are phenotypically similar, while other EC subtypes are different. Predictive interactome analysis reveals known but also previously unreported receptor-ligand interactions between ECs and immune cells, suggesting an involvement of breast EC subtypes in immune responses. We also identify a capillary EC subtype (LIPEC (Lipid Processing EC)), which expresses genes involved in lipid processing that are regulated by PPAR-gamma and is more abundant in peri-tumoral breast tissue. Retrospective analysis of 4,648 BC patients reveals that treatment with metformin (an indirect PPAR-gamma agonist) provides long-lasting clinical benefit and is positively associated with LIPEC abundance. Our findings warrant further exploration of this LIPEC/PPAR-gamma link for BC treatment.

overall_design: single-cell RNA-seq of human breast cancer patient-derived endothelial cells (CD31+CD102+; EC-enriched dataset) and whole stroma (Viability Dye-; non-EC-enriched dataset)

first: Vincent

last: Geldhof

last: de Rooij

first: Liliana

last: Sokol

first: Jacob

last: Amersfoort

first: Maxim

last: De Schepper

first: Katerina

last: Rohlenova

first: Griet

last: Hoste

first: Adriaan

last: Vanderstichele

first: Anne-Marie

last: Delsupehe

first: Edoardo

last: Isnaldi

first: Naima

last: Dai

first: Federico

last: Taverna

first: Shawez

last: Khan

first: Anh-Co

last: Truong

first: Laure-Anne

last: Teuwen

first: François

last: Richard

first: Lucas

last: Treps

first: Ann

last: Smeets

first: Ines

last: Nevelsteen

first: Birgit

last: Weynand

first: Stefan

last: Vinckier

first: Luc

last: Schoonjans

first: Joanna

last: Kalucka

first: Christine

last: Desmedt

last: Neven

first: Massimiliano

last: Mazzone

first: Giuseppe

last: Floris

first: Kevin

last: Punie

first: Mieke

last: Dewerchin

first: Guy

last: Eelen

first: Hans

last: Wildiers

first: Xuri

last: Li

first: Yonglun

last: Luo

first: Peter

last: Carmeliet


title: Circulating monocytes associated with anti-PD-1 resistance in human biliary cancer induce T cell paralysis [CITE-seq]

city: San Francisco

first: Bridget

last: Keenan

address: 505 PARNASSUS AVE

institute: University of California San Francisco

summary: Suppressive myeloid cells can contribute to immunotherapy resistance, but their role in response to checkpoint inhibition (CPI) in anti-PD-1 refractory cancers, such as biliary tract cancer (BTC), is largely unknown. We use multiplexed single-cell transcriptomic and epitope sequencing to profile greater than 200,000 peripheral blood mononuclear cells from advanced BTC patients (n=9) and matched healthy donors (n=8). Following anti-PD-1 treatment, CD14+ monocytes expressing high levels of immunosuppressive cytokines and chemotactic molecules (CD14CTX) increase in the circulation of patients with BTC tumors that are CPI-resistant. CD14CTX can directly suppress CD4+ T cells and induce SOCS3 expression in CD4+ T cells rendering them functionally unresponsive. The CD14CTX gene signature associates with worse survival in patients with BTC as well as in other anti-PD-1 refractory cancers. These results demonstrate that monocytes arising after anti-PD-1 treatment can induce T cell paralysis as a distinct mode of tumor-mediated immunosuppression leading to CPI resistance.

overall_design:
Blood samples from patients with biliary tract cancer (BTC) and healthy donors were processed using ficoll; after centrifugation, the peripheral blood mononuclear cell (PBMC) layer was isolated and cryopreserved in cell media with human serum and DMSO. Previously frozen PBMCs were thawed using media containing RPMI, heat-inactivated sterile filtered human serum, penicillin-streptomycin, non-essential amino acids, sodium pyruvate, and L-glutamine. Samples were then incubated for DNAse I before washing and counting. 1 x10>6 cells from 16 unique samples were combined and stained with one pooled cocktail containing 99 AbSeq antibody-oligonucleotide conjugates (BD Biosciences) per standard protocols (Olvera JG et al., 2018), following pre-incubation with TruStain FcX (Fc Receptor Blocking Solution). Samples from different individuals and timepoints were randomly mixed across experiments to minimize batch and confounding effects. Droplet-based single cell RNA sequencing (scRNAseq) was performed using the 10x Genomics Chromium Single Cell 3ʹ Reagent Kits v3, according to manufacturer instructions.

>>>Submitter states:  Raw data not included where identifiable.<<<

first: Elizabeth

last: McCarthy

first: Arielle

last: Ilano

first: Hai

last: Yang

first: Li

last: Zhang

first: Kathryn

last: Allaire

first: Zenghua

last: Fan

first: Tony

first: David

last: Lee

first: Yang

last: Sun

first: Alexander

last: Cheung

first: Diamond

last: Luong

first: Hewitt

last: Chang

first: Brandon

last: Chen

first: Jaqueline

last: Marquez

first: Brenna

last: Sheldon

first: Robin

last: Kelley

first: Chun

last: Ye

first: Lawrence

last: Fong


title: P450 oxidoreductase (POR) Regulates Barrier Maturation by Mediating Retinoic Acid Metabolism in a Model of the Human BBB

city: Jerusalem

first: Inbar

last: Plaschkes

address: The Hebrew University of Jerusalem - Ein Kerem

department: The Faculty of Medicine - Ein Kerem

institute: HUJI

summary: The blood-brain barrier (BBB) is a multicellular neurovascular unit (NVU) that allows the selective passage of necessary molecules into the central nervous system (CNS), while limiting the entry of neurotoxins and most drugs. A crosstalk with pericytes and neural cells mediates the acquisition of specialized properties, such as the formation of tight junctions (TJs), in brain microvascular endothelial cells (BMECs). TJs limit the paracellular passage of solutes, thereby regulating CNS homeostasis. However, the mechanisms by which NVU cells communicate to mediate TJ formation remains a mystery. Retinoic acid (RA), a key signaling molecule during vertebrate embryonic development, is commonly used to enhance functional barrier properties in in vitro BBB models. However, its physiological relevance and affected pathways are not fully understood.

overall_design: induced pluripotent stem (iPS)-derived brain microvascular endothelial-like cells, from healthy controls, POR-deficient patients and POR mutated lines . Each line was differentiated with 0, 0.25, 1, 10 uM of all-trans retinoic acd (RA), in triplicates . These triplicates include 2 technical duplicates and an one additional biological replicate.

first: Gad

last: Vatine


title: Generation of functional rat spermatozoa in sterile mice utilizing blastocyst complementation with pluripotent stem cells [scRNAseq_rat]

city: Schwerzenbach

first: Ori

last: Bar-Nur

state: Zurich

address: Schorenstrasse 16

department: Health Sciences and Technology

institute: ETH Zurich

summary: Pluripotent stem cells (PSCs) provide a powerful tool to produce transgenic animals for biomedical research. However, impaired PSC contribution to chimerism and most notably to the germline oftentimes impedes production of genetically modified animals, rendering techniques that expediate PSC contribution to the germline highly desirable. Blastocyst complementation denotes a technique which purposes to generate organs, tissues or cells in animal chimeras following microinjection of PSCs into genetically compromised blastocyst-stage embryos. Here, we report on successful blastocyst complementation of the male germline in adult chimeras via microinjection of mouse or rat PSCs into mouse blastocysts mutated for Tsc22d3, an essential gene for spermatozoa production. Microinjection of mouse embryonic stem cells (ESCs) or induced pluripotent stem cells (iPSCs) into Tsc22d3-KnockOut (KO) blastocyst-stage embryos gave rise to intraspecies chimeras embodying functional spermatozoa, which were solely derived from the microinjected PSCs. Furthermore, microinjection of rat ESCs into Tsc22d3-KO mouse embryos gave rise to viable mouse-rat chimeras that exhibited extensive contribution of rat cells to various tissues and organs. Notably, multiple mouse-rat chimeras showed contribution of rat ESCs to the male germline, solely harboring rat spermatids and spermatozoa that were rat ESC-derived and could fertilize rat oocytes. Collectively, this study reports on a method for exclusive germ cell production of one species in another via blastocyst complementation with PSCs. Implications of this study may extend to development of transgenic rat gametes in sterile mice and could further assist efforts to generate germ cells from endangered animal species.

overall_design: Samples were isolated from an adult mouse-rat chimera testis (host: goGermline, Ozgene. Donor: DAC8 rat ESCs) via the protocol published by Valli et al, Fertility and Sterility, 2014

first: Joel

last: Zvick

first: Adhideb

last: Ghosh


title: Generation of functional rat spermatozoa in sterile mice utilizing blastocyst complementation with pluripotent stem cells [scRNAseq_chimera]

summary: Pluripotent stem cells (PSCs) provide a powerful tool to produce transgenic animals for biomedical research. However, impaired PSC contribution to chimerism and most notably the germline oftentimes impedes production of genetically modified animals, rendering techniques that expediate PSC contribution to the germline highly desirable. Blastocyst complementation denotes a technique which purposes to generate organs, tissues or cells in animal chimeras via microinjection of PSCs into genetically compromised blastocyst-stage embryos. Here we report on successful blastocyst complementation of the male germline in adult chimeras following microinjection of mouse or rat PSCs into mouse blastocysts mutated for Tsc22d3, an essential gene for spermatozoa production. Microinjection of mouse embryonic stem cells (ESCs) or induced pluripotent stem cells (iPSCs) into Tsc22d3-KnockOut (KO) blastocyst-stage embryos gave rise to intraspecies chimeras embodying functional spermatozoa, which were solely derived from microinjected PSCs. Furthermore, microinjection of rat ESCs into Tsc22d3-KO mouse embryos gave rise to viable mouse-rat chimeras that exhibited extensive contribution of rat cells to various organs. Notably, multiple mouse-rat chimeras showed contribution of rat ESCs to the male germline, solely harboring rat spermatids and spermatozoa that were rat ESC-derived and could fertilize rat oocytes. Collectively, this study reports a method for exclusive production of functional germ cells of one species in another via blastocyst complementation with PSCs. Implications of this study extend to development of transgenic rats via sterile mice, and may further assist efforts to generate xenogeneic gametes from endangered animal species.

sample_organism:
Mus musculus
Rattus norvegicus

platform_organism:
Mus musculus
Rattus norvegicus

first: Falko

last: Noé


title: RNA Seq analysis of WT vs rv3249c mutant

city: Portland

first: Georgiana

last: Purdy

state: OR

address: 3181 SW Sam Jackson Park Rd

department: Molecular Microbiology and Immunology

institute: Oregon Health & Science University

summary: We report the characterization of an Mtb transcriptional regulator Rv3249c (AlkX). Combined, our results define the primary role of AlkX as a transcriptional repressor of the alkBrubAB operon and suggests the operon contributes to intracellular survival of the pathogen and potential persistence phenotypes.

overall_design: RNAseq analysis of was performed on the wild-type H37Rv and mutant strains of M. tuberculosis grown planktonically


title: Circulating monocytes associated with anti-PD-1 resistance in human biliary cancer induce T cell paralysis [scRNA-seq]

first: Bridget

last: Keenan

overall_design: Tumor samples were collected from patients with biliary tract cancer undergoing surgical resection. Samples were digested in media and live cell isolation was performed. scRNAseq of tumor samples was completed on fresh material with 10x 5’ version 1 kits. All sequencing was performed on an Illumina NovaSeq S4 sequencer with paired end 200 base pair read length and 25,000 reads per droplet.

first: Elizabeth

last: McCarthy

first: Arielle

last: Ilano

first: Hai

last: Yang

first: Li

last: Zhang

first: Kathryn

last: Allaire

first: Zenghua

last: Fan

first: Tony

last: Li

first: David

last: Lee

first: Yang

last: Sun


title: Transcriptomics effects of IFNb and IFNg stimulation on murine cancer cell lines

city: Cambridge

first: Peter

last: Du

state: MA

address: 415 Main St

institute: Broad Institute

summary: To measure the transcriptomic changes in response to IFNb and IFNg stimulation, we collected RNAseq of various cell lines that were stimulated or unstimulated by interferon for 48 hours

overall_design: We performed RNAseq of eight murine cancer cell lines after 48 hours of in vitro IFNb or IFNg stimulation

first: Juan

last: Dubrot

first: Sarah Kate

last: Lane-Reticker

first: Kathleen

middle: B

last: Yates

first: Robert

last: Manguso


title: EWS/FLI mediated reprogramming of 3D chromatin promotes an altered transcriptional state in Ewing sarcoma (Hi-C)

status: Public on Aug 15 2022

city: Columbus

first: Iftekhar

middle: Ahmed

last: Showpnil

address: 700 Childrens Drive

department: CCCBD

institute: Nationwide Children's Hospital

summary: Ewing sarcoma is a prototypical fusion transcription factor-associated pediatric cancer that expresses EWS/FLI or highly related fusions. EWS/FLI dysregulates transcription to induce and maintain sarcomagenesis, but the mechanisms utilized are not fully understood. We therefore sought to define the global effects of EWS/FLI on chromatin conformation and transcription in Ewing sarcoma.  We found that EWS/FLI (and EWS/ERG) genomic localization is largely conserved across multiple patient-derived Ewing sarcoma cell lines. EWS/FLI binding is primarily associated with compartment activation, establishment of topologically-associated domain (TAD) boundaries, enhancer-promoter looping that involve both intra- and inter-TAD interactions, and gene activation.  Importantly, local chromatin features provide the basis for transcriptional heterogeneity in regulation of direct EWS/FLI target genes across different Ewing sarcoma cell lines.  These data demonstrate a key role of EWS/FLI in mediating genome-wide changes in chromatin configuration and support the notion that fusion transcription factors serve as master regulators through three-dimensional reprogramming of chromatin.

overall_design: in situ Hi-C of A673 Ewing sarcoma cells transduced with shRNA targeting EWS/FLI or Luciferase followed by rescue of EWS/FLI expression with a 3X-FLAG tagged EWS/FLI cDNA construct or empty vector

first: Stephen

last: Lessnick


title: Single cell transcriptomics of the tumor immune microenvironment from checkpoint blockade-treated KPC tumors

summary: Single cell transcriptomes of CD45+ cells from KPC tumor subcutaneous allografts, either treated with PD-1+CTLA-4 checkpoint blockade or treatment-naïve.

overall_design: We isolated CD45+ cells from KPC tumors and performed 10X single-cell sequencing. KPC tumors were either treated with PD-1+CTLA-4 combination checkpoint blockade on days 6 and 9 post tumor challenge or treatment-naïve. Four tumors per experimental group were collected and sequenced.

first: Emily

last: Kessler


title: Transcriptome of a Synthetic Microbial Community

city: Athens

first: He

last: Fu

state: GA

address: 120 Cedar St

department: Microbiology

institute: University of Georgia

summary: To explore the ecological basis for multiple bacteria species coexistence, we set up three bacteria (Ruegeria pomeroyi DSS-3, Vibrio hepatarius HF70, and Thalassospira sp. HF15), either in monoculture or in co-cultures (in all combinations) for a 8 day growth-dilution cycles. At ~15h of day 4 (P4) and day 8 (P8) of growth-dilution cycles, we examined transcriptomic responses  of these bacteria. Differential gene expressions were used to generate hypothesis about ecological and physiological responses of one in the presence of another/other bacteria.

sample_organism:
Vibrio hepatarius
Ruegeria pomeroyi DSS-3
Thalassospira sp. HF15

overall_design:
mRNA profile of three bacteria under different conditions
Please note that mono-culture samples of three bacterial species were pooled together for RNA-seq library prep and sequencing run.

first: Mary

last: Moran

first: Christa

last: Smith


title: The Genomic Architecture of Pregnancy-Associated Plasticity in the Maternal Mouse Hippocampus

city: Boston

first: Brian

last: Kalish

address: 220 Longwood Ave

department: Neurobiology

institute: Boston Children's Hospital

summary: We performed single nucleus RNA-seq and single nucleus ATAC-seq from the mouse hippocampus before, during, and after pregnancy.

overall_design: Single cell RNA-seq and ATAC seq from female hippocampus under three conditions: 8 week old virgin female mice, embryonic day 18 (E18) pregnant female mice, and P21 (post-partum) female mice


title: Comparative expression analysis of the Arabidopsis smax1 smxl2 under dehydration conditions

city: Changchun

first: Weiqiang

address: No. 4888 Shengbei Street

department: Center for Sustainable Resource Science

institute: Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences

summary: To understand the role of SMAX1 and SMXL2 in water stress response, we have carried out comparative expression analysis of the smax1 smxl2 mutant and WT plants under dehydration and well-watered (control) conditions. Aligent's whole Arabidopsis Gene Expression Microarray (G2519F-021169, V4, 4x44K) was used.

overall_design: Two-week-old WT and smax1 smxl2 mutant plants were transferred from GM plates to soil and grown for 10 additional day. The aerial parts of 24-d-old plants were detached and exposed to dehydration on KimTowel papers for 0 (well-watered, control), 2 and 4 h. All rosette leaves of independent 24-d-old plants were collected. Total RNA was prepared and used for the microarray hybridization. Three independent biological replicates were used for each plant sample.

first: Yasuko

last: Watanabe

first: Maho

last: Tanaka

first: Motoaki

last: Seki

first: Lam‑Son

last: Tran


title: Small RNAs deep sequencing from Tomato-Orobanche interaction

city: Kermanshah

first: Hooman

last: Salari

address: Emam khomaini hyw.

department: Production Engineering and Plant Genetics

country: Iran

institute: Razi University

summary: High-throughput sequencing of small RNAs derived from different tissues of Orobanche plants.

first: Zahra

last: Zangishei


title: Huntington disease mice exhibit a TCF7L2-responsive suppression of both homeostatic and compensatory remyelination

city: Rochester

first: John

last: Mariani

address: 601 Elmwood Avenue

department: Neurology

institute: University of Rochester

summary: PDGFRA-EGFP+ striaal cells were isolated for bulk RNA-sequencing from R6/2 (6wk and 12wk) and zQ175 (12wk and 1yr) HD mice and littermate controls.

overall_design: RNA was extracted from FACS isolated PDGFRA-EGFP+ striatal cells of R6/2 (6wk and 12wk) and zQ175 (12wk and 1yr) HD mice and littermate controls using Qiagen Rneasy Plus Mini kits.  Libraries were generated using the TruSeq RNA v2 kit and sequenced on an Illumina HiSeq 2500 (Paired-end 125 bp).

middle: N

first: Abdellatif

last: Benraiss

first: Steven

last: Goldman


title: Circulating monocytes associated with anti-PD-1 resistance in human biliary cancer induce T cell paralysis

first: Bridget

last: Keenan

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

overall_design: Refer to individual Series


title: Dominant role of DNA methylation over H3K9me3 in ERV silencing during embryonic endoderm development [ChIP-Suv39]

city: Planegg-Martinsried

first: Gunnar

last: Schotta

address: Grosshaderner Strasse 9

department: Biomedical Center

institute: LMU Munich

summary: Silencing of endogenous retroviruses (ERVs) is largely mediated by repressive chromatin modifications, such as H3K9me3 and DNA methylation. Their impact on ERV silencing differs in various cell types and, no systematic analyses on the interdependence between H3K9me3 and DNA methylation have been performed in differentiated cells. Here we show that deletion of the H3K9me3 HMTase Setdb1 in mouse embryonic endoderm results in ERV de-repression in only a subset of endoderm cells. We found that de-repression is restricted to visceral endoderm descendants and does not occur in definitive endoderm cells. Deletion of Setdb1 in visceral endoderm progenitors resulted in loss of H3K9me3 and reduced DNA methylation of IAPEz, consistent with up-regulation of this ERV family. In definitive endoderm cells, loss of Setdb1 did not affect H3K9me3 nor DNA methylation, suggesting Setdb1-independent pathways for maintaining these modifications. Importantly, Dnmt1 ko resulted in ERV de-repression in both visceral and definitive endoderm cells, while H3K9me3 was unaltered. Thus, our data suggest a dominant role of DNA methylation over H3K9me3 in ERV silencing in endoderm cells. Our findings suggest, that H3K9me3 is not sufficient for ERV silencing, but rather critical for maintaining high DNA methylation.

overall_design: H3K9me3 ChIP-seq of ES/XEN/DE cells

first: Zeyang

last: Wang

first: Rui

last: Fan

first: Filippo

last: Cernilogar


title: Eukaryotic initiation factor 5A2 regulates expression of antiviral genes

first: Amy

middle: Si-Ying

last: Lee

address: 450 Brookline Ave SM520

department: Cancer Immunology and Virology

institute: DFCI

summary: Using ribosome profiling and RNA-Sequencing, we reveal that eIF5A2 is functionally distinct from eIF5A1 and does not regulate transcript-specific or global protein synthesis. Instead, eIF5A2 knockout leads to decreased intrinsic antiviral gene expression.

overall_design: SW480 cells were grown in complete media for a day before harvesting.

first: Dorian

last: Farache


title: Dominant role of DNA methylation over H3K9me3 in ERV silencing during embryonic endoderm development [ChIP-Seq]


title: Generation of functional rat spermatozoa in sterile mice utilizing blastocyst complementation with pluripotent stem cells [bulk RNA-seq]

first: Ori

last: Bar-Nur

overall_design: Sample 1 ordered from RRRC line 464, confirmed rat embryonic stem cell. Sample 2-4 biological replicates, rat tail tip fibroblasts

first: Joel

last: Zvick

first: Adhideb

last: Ghosh


title: Dominant role of DNA methylation over H3K9me3 in ERV silencing during embryonic endoderm development [RNA-Seq]

overall_design: RNA-seq of Embryo/ES/XEN/DE cells


title: Dominant role of DNA methylation over H3K9me3 in ERV silencing during embryonic endoderm development [ChIP-Dnmt]

first: Alexander

last: Nuber

first: Silvia

last: Schirge

first: Iva

last: Dzhilyanova

first: Tobias

last: Anton

first: Heinrich

last: Leonhardt

first: Heiko

last: Lickert


title: MYC controls a double-stranded RNA-dependent autocrine pathway that links nuclear mRNA splicing to pro-inflammatory signaling in pancreatic carcinoma

city: Wuerzburg

first: Martin

last: Eilers

address: Am Hubland

department: Chair for Biochemistry and Molecular Biology

institute: University of Wuerzburg

summary: The oncogene MYC supresses TBK1 activity in a KRAS/mutant p53-driven pancreas carcinoma model and thereby interferes with the signaling that follows recognition of dsRNA species by the pattern recoginition receptor TLR3, allowing the tumor cells to evade recognition by the immune system.

overall_design: 4SU-seq and RNA-seq experiments to determine nascent RNA synthesis and global gene expression after MYC knockdown, after TBK1 knockout, after MycWT or MycVD overexpression and after overexpression of an IKBa mutant in a pancreatic carcinoma model system (KPC) in vitro and in vivo.

first: Bastian

last: Krenz

first: Anneli

last: Gebhardt

first: Carsten

last: Ade

first: Abdallah

last: Gaballa

first: Florian

last: Röhrig

first: Emilia

last: Vendelova

first: Apoorva

last: Baluapuri

first: Ursula

first: Peter

last: Gallant

first: Luana

last: D'Artista

first: Armin

last: Wiegering

first: Georg

last: Gasteiger

first: Matthias

last: Rosenfeldt

first: Lars

last: Zender

first: Elmar

last: Wolf


title: Dominant role of DNA methylation over H3K9me3 in ERV silencing during embryonic endoderm development [RNA-Seq Suv39]

first: Gunnar

last: Schotta

first: Zeyang

last: Wang

first: Rui

last: Fan

first: Filippo

last: Cernilogar


title: Ex Utero Development of Post-Gastrulation Synthetic-Embryos Generated Solely from Mouse Naïve Pluripotent Stem Cells [scRNA-seq]

status: Public on Jul 31 2022

city: Rehovot

first: Noa

last: Novershtern

address: Weizmann Institute

department: Molecular Genetics

institute: Weizmann Institute of Science

summary: Different types of in vitro expanded stem cells can contribute to embryonic or extra-embryonic compartments after microinjection into blastocysts. However, whether stem cells could give rise to advanced gastrulating whole embryo-like structures with both embryonic and extra-embryonic compartments, without relying on a micro-injected host embryo, remains to be achieved. Thus far, in vitro aggregated stem cells have failed to generate post-gastrulation embryos ex utero or in utero, which partially resulted from the lack of methods for prolonged expansion of embryos until advanced developmental stages ex utero. Here we adapt recently optimized platform and conditions for ex utero growth of natural embryos, to generate complete mouse synthetic embryos, with both embryonic and extra-embryonic compartments, and by starting solely from naïve ESCs. The latter is achieved following co-aggregating non-transduced naïve ESCs, with Cdx2- and Gata4- transiently pulsed naïve ESCs, to promote their trophoblast and primitive endoderm lineage induction, respectively. The obtained synthetic embryos adequately advance in this platform through developmental milestones and accomplish gastrulation and develop organs progenitors within normally developed extra-embryonic compartments. Our findings highlight the plastic developmental potential of the naïve pluripotent state to functionally self-organize and reconstitute the entire early mammalian embryo.

overall_design: Five scRNA-seq 10X Genomics samples of synthetic embryos, generated with iCdx2 cells, induced for 3 or 10 days, or with established TSC cells. The embryos were developed ex-utero. In addition, six 10X Genomics samples of mouse E8.5 natural embryos, developed in-utero.

first: Shadi

last: Tarazi

first: Alejandro

last: Aguilera-Castejon

first: Jacob

middle: H

last: Hanna


title: FBXO42 facilitates Notch signaling activation and global chromatin relaxation by promoting K63-linked polyubiquitination of RBPJ

city: HangZhou

first: Hua

last: Jiang

state: Zhejiang

address: Hangzhou, Zhejiang province, China

institute: Westlake University

summary: Dysregulation of the Notch-RBPJ signaling pathway has been found associated with various human diseases including cancers; however, precisely how this key signaling pathway is fine-tuned via its interactors and modifications is still largely unknown. In this study, using a proteomic approach, we identified FBXO42 as a novel RBPJ interactor. FBXO42 promotes RBPJ polyubiquitination on lysine (K) 175 via K63 linkage, which enhances the association of RBPJ with chromatin remodeling complexes and induces a global chromatin relaxation. Genetically depleting FBXO42 or pharmacologically targeting its E3 ligase activity attenuates the Notch signaling-related leukemia development in vivo. Taken together, our findings not only revealed FBXO42 as a critical regulator of the Notch pathway by modulating RBPJ-dependent global chromatin landscape changes, but also provide insights into the therapeutic intervention of the Notch pathway for leukemia treatment.

overall_design: DNA binding capacity of transcription factor RBPJ was analyzed by Cut&tag-seq and chromatin status was analyzed by ATAC-seq.

first: Weixiang

last: Bian

first: Yue

last: Sui

first: Xu

last: Li


title: Differentially expressed genes after siRNA transfection in human cancer cell line

city: Kagoshima city

first: Ryutaro

last: Yasudome

state: Kagoshima

address: 8-35-1 Sakuragaoka

department: Digestive Surgery, Breast and Thyroid Surgery

country: Japan

institute: Kagoshima University

summary: To identify differentially expressed genes by siRNAs transfection in human colon cancer cell line, HCT116  was subjected to Agilent whole genome microarrays.

overall_design: HCT116 was treated with siRNA(siKRT80)

first: R

first: N

last: Seki


title: Ca2+ channels couple spiking to mitochondrial metabolism in substantia nigra dopaminergic neurons

city: Chicago

first: Enrico

last: Zampese

address: 303 E Superior st

department: Neuroscience

country: USA

institute: Northwestern University

summary: How do neurons match generation of adenosine triphosphate (ATP) by mitochondria to the bioenergetic demands of regenerative activity? Although the subject of speculation, this coupling is still poorly understood, particularly in neurons that are tonically active. To help fill this gap, pacemaking substantia nigra dopaminergic neurons were studied using a combination of optical, electrophysiological and molecular approaches. In these neurons, spike-activated calcium (Ca2+) entry through Cav1 channels triggered Ca2+ release from the endoplasmic reticulum, which stimulated mitochondrial OXPHOS through two complementary Ca2+-dependent mechanisms: one mediated by the mitochondrial uniporter and another by the malate-aspartate shuttle. Disrupting either mechanism impaired the ability of dopaminergic neurons to sustain spike activity. While this feedforward control helps dopaminergic neurons meet the bioenergetic demands associated with sustained spiking, it also is responsible for their elevated oxidant stress and possibly to their decline with aging and disease.

overall_design: Comparative gene expression profiling analysis of RNA-seq data of MCU-KO and wildtype substantia nigra dopaminergic neurons selectively pulled-down with the RiboTag approach

first: David

last: Wokosin

first: Patricia

last: Gonzalez Rodriguez

first: Jaime

last: Guzman

first: Tatiana

last: Tkatch

first: Jyothisri

last: Kondapalli

first: William

last: Surmeier

first: Karis

last: D'Alessandro

first: Diego

last: De Stefani

first: Rosario

last: Rizzuto

first: Masamitsu

last: Iino

first: Jeffery

middle: D

last: Molkentin

first: Navdeep

last: Chandel

first: Paul

last: Schumacker

first: D

middle: J


title: Programming of the hepatic lipid metabolism via a parental high carbohydrate low protein diet in rainbow trout

city: Saint-Pée-sur-Nivelle

first: Thérèse

last: Callet

country: France

institute: INRA

summary: In rainbow trout (Oncorhynchus mykiss), the effect of a paternal and a maternal high carbohydrate-low protein diet was assessed on progeny at long term. To this purpose, two-year old male and female rainbow trout were fed either a control diet or a high carbohydrate/low protein diet for an entire reproductive cycle for females and for 5  months for males. Crossed-fertilizations were carried out in order to obtain 4 groups of offspring. Offspring were fed with a commercial diet until they reached a market size and were then challenged with a complete plant-based diet for 3 months. After the challenge, hepatic transcriptomes were analysed to detect any effect of the parental diet on offspring metabolism.

overall_design: Two-year old male and female rainbow trout were fed either a control diet (NC, 63.89% protein and 0% carbohydrates) or a high carbohydrate/low protein diet (HC/LP, 42.96% protein and 35.30% carbohydrates) for an entire reproductive cycle for females and for 5 months for males. During the spawning period, spawns from NC and HC/LP females were cross-fertilized with milts from males from each experimental condition. Thus, offspring from 4 different conditions were obtained: NN (offspring from both males and females fed the control NC diet); HN (offspring from only females fed the HC/LP diet and males fed the control NC diet); NH (offspring from only males fed the HC/LP diet and females fed the NC diet); and HH (offspring from both parents fed the HC/LP diet). Offspring were reared into 9 tanks (n=3/condition) in a  flow-though rearing system supplied with natural spring water at 17°C. Since their first feeding,  fish were fed ad libitum with a commercial diet (T3-P Omega, Skretting, France). After 6 months, juveniles were fed during a 3-month trial a complete plant-based diet. At the end of the challenge, liver were sampled in offspring (n=6 per confition).

first: T

first: L

last: Marandel


title: Effect of SRSF1 splicing factor knockdown in the physiology and function of cytotoxic CD8 T lymphocytes and a potential molecular mechanism in viral immunopathogenesis

first: Sean

last: Lawler

address: 75 Francis St

institute: Brigham and Women's Hospital

summary:
Cytotoxic CD8 T cells are crucial for the host antigen-specific immune response to viral pathogens. Here we report the identification of an essential role for the serine/arginine-rich splicing factor (SRSF) 1 in CD8 T cell homeostasis and function
Transcriptomics analyses of Srsf1-deficient T cells reveal that SRSF1 controls cell cycle, MAP kinase signaling and IFN signaling pathways.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for Srsf1.flox dLck.cre spleen total T cells of B6 mice after LCMV infection for 8 days.

first: Vaishali

middle: M

last: Moulton

first: Zachary

last: Herbert


title: Role of m6A in cold stress response

city: Stillwater

first: Ramanjulu

last: Sunkar

state: OK

address: 359 Noble Research Center

department: Department of Biochemistry and Molecular Biology

institute: Oklahoma State University

summary: Post transcriptional regulation of mRNA under environental stress in plants

overall_design: 3 replicates m6A-IP Cold treated 20 day old seedlings, 3 replicates m6A-IP Control 20 day old seedlings, 3 replicates mRNA seq Cold treated 20 day old seedlings, 3 replicates mRNAseq Control 20 day old seedlings, 2 replicates polysomal seq Cold treated 20 day old seedlings, 2 replicates polysomal seq Control 20 day old seedlings

first: Bishwas

last: Sharma

first: Ganesan

last: Govindan

first: Yongfang

last: Li

first: Christopher

last: Armstrong

first: Brian

last: Gregory


title: Impact of knockdown of the lncRNA 3930402G23Rik on gene expression profile of mouse liver in response to activation of PPARA by WY-14643.

first: David

middle: J.

last: Waxman

address: 5 Cummington Mall

department: Department of Biology and Bioinformatics Program

institute: Boston University

summary: Gene expression in livers of wild type adult male mice and in lncRNA 3930402G23Rik ("G23Rik") knockdown adult male mouse liver was assayed by RNA-seq, as part of a study of liver transcriptomic changes in response to activation of PPARA by WY-14,643, published in Molecular and Cellular Endocrinology (2022). These studies found that G23Rik-null mice were more susceptible to hepatic lipid accumulation in response to acute fasting. Histological analysis further revealed a pronounced buildup of lipid droplets and a significant increase in neutral triglycerides and lipids as indicated by enhanced oil red O staining of liver sections. Hepatic cholesterol, non-esterified fatty acid, and triglyceride levels were significantly elevated in G23Rik-null mice and associated with induction of the lipid-metabolism related gene Cd36. These findings provide evidence for a lncRNA dependent mechanism by which PPARA attenuates hepatic lipid accumulation in response to metabolic stress through lncRNA G23Rik induction.

overall_design: Twelve independent pools, comprised of RNA isolated from n=3-5 individual mouse livers per pool, were prepared and used for RNA-seq. Three pools were untreated, wild-type male mouse livers; three pools were WY-14,643-treated wild-type male mouse livers; three pools were untreated, lncRNA 3930402G23Rik-knockout male mouse livers; and three pools were WY-14,643-treated, lncRNA 3930402G23Rik-knockout mouse livers. Wy-14,643 treatment was given via the diet, at 0.1% for 48 hr.

first: Chad

last: Brocker

first: Tomoki

last: Yagai

first: Donghwan

last: Kim

first: Kritika

last: Karri

first: Frank

last: Gonzalez


title: Expression of CD94 and CD96 on CD8+ T cells early after allogeneic stem cell transplantation is predictive of subsequent disease relapse and survival

city: Birmingham

first: Paul

last: Moss

state: West Midlands

address: Vincent Drive

department: Immunology and Immunotherapy

institute: University of Birmingham

summary: Allogeneic stem cell transplantation is used widely in the treatment of hematopoietic malignancy. However relapse of malignant disease is the primary cause of treatment failure and reflects loss of the immunological graft versus leukaemia effect. We studied the transcriptional and phenotypic profile of CD8+ T cells in the first month following transplantation and related this to risk of subsequent relapse. Single cell transcriptional profiling identified 5 discrete CD8+ T cell clusters. High levels of T cell activation and acquisition of a regulatory transcriptome were apparent in patients who went on to suffer disease relapse. A relapse-associated gene signature of 39 genes was then assessed in a confirmation cohort of 34 patients. High level expression of the inhibitory receptor CD94/NKG2A on CD8+ T cells within the first month was associated with 4.8 fold increased risk of relapse and 2.7 fold reduction in survival over the subsequent 4 years. Furthermore, reduced expression of the activatory molecule CD96 was associated with 2.2 fold increased risk of relapse and 1.9 fold reduction in survival. This work identifies CD94 and CD96 as potential targets for CD8-directed immunotherapy in the very early phase following allogeneic transplantation with the potential to reduce long term relapse rates and improve patient survival.

sample_organism:
Homo sapiens
Mus musculus
blank sample

platform_organism:
Homo sapiens
Mus musculus
blank sample

overall_design: RNA profiles of single peripheral CD4 and CD8 T cells at 2 weeks following allogeneic stem cell transplant

first: Kriti

last: Verma

first: Wayne

last: Croft

first: Hayden

last: Pearce

first: Jianmin

last: Zu

first: Christine

last: Stephens

first: Jane

last: Nunnick

first: Francesca

middle: A

last: Kinsella

first: Ram

last: Malladi