title: Age-associated suppression of exploratory activity during sickness is linked to meningeal lymphatic dysfunction and microglia activation [aged]

first: Jonathan

last: Kipnis

summary: The objective of this study is to assess the contribution of meningeal lymphatic vessels to microglia response to peripheral inflammation.  Aged mice (over 2 years old) were selected as a physiologically and clinically relevant model for lymphatic dysfunction because previous reporting demonstrates meningeal lymphatic function declines with age. We sequence CD11b+ cells sorted from whole brain of aged mice two hours following 1μg IL-1β or saline vehicle intraperitoneal injection.  To facilitate comparison and integration with adult mouse and experimental lymphatic ablation data, identical methods were employed.

overall_design: Mice were maintained under specific pathogen-free conditions, with controlled temperature and humidity, on 12 h light:dark cycles, and ad libitum access to food and water.  Experiments were all performed during light cycle.  Male C57BL/6J mice over 2 years old were injected i.p. with either 1μg IL-1β or saline vehicle (5 mice per group, 2 groups +/-IL-1β).  Two hours later, mice were euthanized by lethal dose of anesthetic (Euthasol) and perfused with cold PBS.  One whole hemisphere of brain was collected from each mouse and biological replicates were pooled.  Brain tissue was dissociated in 5mL Hank’s buffering saline solution with DNaseI (50U/mL) and papain (4U/mL) at 37ºC for 45 minutes.  Cell suspension was then passed through a 70um strainer and CD11b+ cells were magnetically sorted using CD11b MicroBeads, human and mouse (Miltenyi) as per manufacturer’s instructions using AutoMACS (Miltenyi) and 2000 cells per condition were targeted for sequencing.

first: Dylan

last: Goldman


title: Exploiting Synergistic Effect of Controlled Co-Delivery Medicine for Soft Tissue Transplantation using Double System of Bio-Multifunctional Hydrogel

status: Public on Jun 09 2022

city: changchun

first: Jingyan

last: Ren

state: chaoyang

address: hanseng

country: China

institute: The first hospital of Jilin University

type: Expression profiling by high throughput sequencing

summary: Autologous skin flap transplantation is a common method to repair complex soft tissue defects caused by cancer, trauma, and congenital malformations, among other conditions; however, limited blood supply range and post-transplantation ischemia-reperfusion injury (IRI) can cause distal necrosis of the flap and loss of long-term function, severely limiting the indications for this type of surgery. Here, development of a bio-multifunctional hydrogel for programmatic co-delivery medicine, DCDM, that meets the blood supply requirements of skin flap transplantation and can deliver two types of gas molecules, CO and NO, in a timely manner and with a concentration gradient during surgery, is described. DCDM maintains the immediate opening of blood flow channels in transplanted tissue and effective blood perfusion throughout the perioperative period, activating perfusion of the hemodynamic donor site. These results demonstrate that DCDM promotes distal vascularization and long-term functional reconstruction of transplanted tissues by inhibiting inflammatory damage and accelerating blood vessel formation. The findings presented here are applicable to the extended fields of large soft tissue defect repair and transplant of various organs.

overall_design: RNA integrity was assessed using an RNA Nano 6000 Assay Kit for the Bioanalyzer 2100 system (Agilent Technologies, CA, USA). Total RNA was used as input material for RNA sample preparation. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer (5×). First strand cDNA was synthesized using random hexamer primers and M-MuLV Reverse Transcriptase, then RNaseH used to degrade the RNA. Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and dNTPs. Remaining overhangs were converted into blunt ends using exonuclease/polymerase activities. After adenylation of the 3' termini of DNA fragments, adaptors with hairpin loop structures were ligated to prepare for hybridization. To preferentially select cDNA fragments of 370–420 bp in length, library fragments were purified using the AMPure XP system (Beckman Coulter, Beverly, USA). Then, PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers, and Index (X) Primer. Finally, PCR products were purified using the AMPure XP system, and library quality assessed on the Agilent Bioanalyzer 2100 system. Clustering of index-coded samples was performed using a cBot Cluster Generation System with a TruSeq PE Cluster Kit v3-cBot-HS (Illumina), according to the manufacturer’s instructions. After cluster generation, prepared libraries were sequenced on an Illumina Novaseq platform to generate 150 bp paired-end reads. The data obtained were subjected to quality control, reads mapped to the reference genome, novel transcripts predicted, gene expression levels quantified, differential expression analysis quantified, as well as GO and KEGG enrichment analysis, Gene Set Enrichment Analysis, single nucleotide polymorphism analysis, alternative splicing analysis, and protein-protein interaction analysis of differentially expressed genes, including weighted correlation network analysis.

first: Xiaoduo

last: Tang

first: Junhu

last: Zhang

first: Laijin

last: Lu


title: Gene expression profile at single cell level of fibroblasts from untreated (UT) and imiquimod (IMQ)-induced mouse skin.

status: Public on Jun 01 2022

city: Shanghai

first: Xiaojie

last: Cai

address: 650 Xinsongjiang Road, Fangsong Street, Songjiang District

department: Precision Research Center for Refractory Diseases

institute: Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine

summary: We used single-cell RNA sequencing (scRNA-seq) to analyze the heterogeneity of dermal fibroblasts in homeostasis and skin inflammation.

overall_design: Dermal fibroblasts of the UT/IMQ-induced PdgfraDreER-tdTomato mice were isolated by Fluorescence-activated cell sorting (FACS) according to the presence or absence of tdTomato signal and analyzed using scRNA-seq.


title: A palmitate-rich metastatic niche enables metastasis growth via p65 acetylation [ChIP-seq]

city: Leuven

first: Juan

last: Fernández-García

address: Campus Gasthuisberg, O&N4, Herestraat 49, box 912

department: VIB-KU Leuven Center for Cancer Biology

country: Belgium

institute: VIB/KU Leuven

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Cancer cells outgrowing in distant organs of metastasis rewire their metabolism to fuel on the available nutrients. While this is often considered an adaptive pressure limiting metastasis formation, some nutrients available at the metastatic site naturally or through changes in organ physiology may inherently promote metastatic growth. We find that the lung, a frequent site of metastasis, is a lipid-rich environment. Moreover, we observe that pathological conditions such as pre-metastatic niche formation and obesity further increase the availability of the fatty acid palmitate in the lung. We find that targeting palmitate processing inhibits spheroid growth in vitro and metastasis formation in lean and obese mice. Mechanistically, we discover that breast cancer cells use palmitate to synthesize acetyl-CoA in a carnitine palmitoyltransferase 1a (CPT1a)-dependent manner. Lysine acetyltransferase 2a (KAT2a), whose expression is promoted by palmitate availability, relies on the available acetyl-CoA to acetylate the NF-B subunit p65. This favors nuclear location of p65 and activates a pro-metastatic transcriptional program. Accordingly, deletion of KAT2a phenocopies CPT1a silencing in vitro as well as in vivo and patients with breast cancer show co-expression of both proteins in metastases across palmitate-rich metastatic sites. In conclusion, we find that palmitate-rich environments foster metastasis growth by increasing p65 acetylation resulting in elevated NF-B signaling.

overall_design: ChIPmentation sequencing with H3K9ac antibody

first: Patricia

last: Altea-Manzano

first: Sofie

last: Demeyer

first: Sarah

middle: M

last: Fendt


title: Insulin secretion deficits in a Prader-Willi syndrome β-cell model are associated with a concerted downregulation of multiple endoplasmic reticulum chaperones

city: Pittsburgh

first: Erik

last: Koppes

state: PA

address: 204 Craft Ave

department: MWRI

country: USA

institute: University of Pittsburgh

type: Non-coding RNA profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Transcriptomic Profiling Reveals Discrete Poststroke Dementia Neuronal and Gliovascular Signatures

city: SHEFFIELD

first: Rachel

last: Waller

state: South Yorkshire

address: SITraN, 385A Glossop Road

department: Neuroscience

country: United Kingdom

institute: The University of Sheffield

summary:
Around 25% of stroke survivors over 65 years old develop progressive cognitive decline more than 3 months post-stroke, with features of vascular dementia. Poststroke dementia (PSD) is associated with pathology in frontal brain regions, in particular dorsal lateral prefrontal cortex (DLPFC) neurons and white matter, remote from the infarct, implicating damage to anterior cognitive circuits (ACC) involved in impaired executive function. We hypothesised that PSD results from progressive neuronal damage in the DLPFC and that this is associated with alterations in the gliovascular unit (GVU) of frontal white matter. We aimed to identify the cellular and molecular basis of PSD by investigating the transcriptomic profile of the neurons and white matter GVU cells previously implicated in pathology.
Laser capture microdissected neurons, astrocytes and endothelial cells were obtained from the Cognitive Function After Stroke (COGFAST) cohort.  Gene expression was assessed using microarrays and pathways analysis to compare changes in PSD with controls and with poststroke non-dementia (PSND). Laser captured microdissected neurons were obtained from the bilateral carotid artery stenosis (BCAS) model and equivalent SHAM animals

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Control (n=10), PSD (n=10) and Post-stroke non dementia (PSND) (n=10) human subjects. Sham Group (n=5) and Bilateral carotid artery stenosis (BCAS) gorup (n=5)

first: Yoshiki

last: Hase

first: Julie

middle: E

last: Simpson

first: Paul

middle: R

last: Heath

first: Matthew

last: Wyles

first: Rajesh

last: Kalaria

first: Stephen

middle: B

last: Wharton


title: hapln1 defines an epicardial cell subpopulation that establishes cardiogenic hotspots during heart morphogenesis and regeneration

status: Public on Jun 17 2022

city: ATLANTA

first: Jinhu

last: Wang

state: Georgia

address: 101 WOODRUFF CIRCLE WMB 2304

institute: Emory University

summary: The epicardium, a thin mesothelial tissue layer that encompasses the heart, is a dynamic structure that is essential for cardiac regeneration in species with elevated regenerative capacity like zebrafish. To dissect epicardial cell states and associated pro-regenerative functions, we performed single-cell RNA-sequencing and identified 7 epicardial cell clusters in adult zebrafish, with 3 of these clusters enhanced during regeneration. ECM components encoded by hapln1 paralogs label an enriched epicardial cell type that accumulates and encloses dedifferentiated and proliferating cardiomyocytes during regeneration. Genetic inactivation of hapln1b, or induced genetic depletion of hapln1a-expressing cells, disrupted cardiomyocyte proliferation and heart regeneration.  hapln1a+ cells first emerge at the juvenile stage, when they associate with and are required for cardiogenic foci that direct growth of the juvenile heart. Our findings identify a subset of epicardial cells that emerges in post-embryonic animals and sponsors regions of active cardiomyogenesis during heart growth and regeneration

overall_design: Single cell RNA sequencing of FACS isolated eppicaridal cells  (tcf21:nucEGFP) from uninjured and regenerating hearts

first: Jisheng

last: Sun

first: Elizabeth

middle: A

last: Peterson

first: Annabel

middle: Z

first: Kieko

last: Smith

first: Kenneth

middle: D

last: Poss


title: Insulin secretion deficits in a Prader-Willi syndrome β-cell model are associated with a concerted downregulation of multiple endoplasmic reticulum chaperones [RNA-seq]

summary: A Prader-willi syndrome (PWS) model of β-cell dysfunction

overall_design: Total RNA expression analysis of 3 control and 3 PWS clonal genome-edited INS1 lines

first: Robert

last: Nicholls


title: Single-cell RNA-seq of mouse epidermal or dermal samples in mouse psoriasiform skin

status: Public on Jun 14 2022

first: Fangzhou

last: Lou

address: 280 South Chongqing Road

department: Shanghai Institute of Immunology

institute: Shanghai Jiao Tong University School of Medicine

summary: Epidermal or dermal cell suspensions from imiquimod-induced C57BL/6 mice were subject to single-cell RNA-seq.

overall_design: Epidermal or dermal live cells were isolated separately by Fluorescence-activated cell sorting (FACS) from 10 week-old C57BL/6 mouse skin treated with imiquimod and analyzed using scRNA-seq.

first: Yang


title: Insulin secretion deficits in a Prader-Willi syndrome β-cell model are associated with a concerted downregulation of multiple endoplasmic reticulum chaperones [ncRNA-Seq]

first: Erik

overall_design: small (<200bp) ncRNA expression analysis of 3 control and 3 PWS clonal genome-edited INS1 lines


title: A palmitate-rich metastatic niche enables metastasis growth via p65 acetylation [RNA-Seq]

first: Juan

last: Fernández-García

overall_design: mRNA profiles of 3D and 2D cultured 4T1 breast cancer cells in the presence or absence of palmitate

first: Patricia

last: Altea-Manzano

first: Sofie

last: Demeyer

first: Sarah


title: Comparative interactome analysis of the PRE DNA-binding factors: purification of the Combgap, Zeste, Psq, and Adf1 associated proteins

status: Public on Jun 10 2022

city: Moscow

first: Marina

middle: Yu.

last: Mazina

address: Vavilova, 34/5

country: Russia

institute: Institute of Gene Biology RAS

summary: To gain an insight into the PRE DNA-binding protein regulatory network, here, using immunoaffinity purification coupled to the high throughput mass spectrometry, we isolated factors associated with the Combgap, Psq, Zeste and Adf1 PRE DNA-binding proteins. We show that Combgap and Zeste are more tightly associated with the Polycomb repressive complex 1 (PRC1), while Psq interacts strongly with the TrxG proteins, including the BAP SWI/SNF complex. The Adf1 interactome contained Mediator subunits as the top interactors. In addition, Combgap efficiently interacted with AGO2, NELF, and TFIID. Combgap, Psq, and Adf1 have architectural proteins in their networks. We further investigated the existence of direct interactions between different PRE DNA-binding proteins and demonstrated that Combgap-Adf1, Psq-Dsp1, and Pho-Spps can interact in the yeast two-hybrid assay. Overall, our data suggest that Combgap, Psq, Zeste and Adf1 are associated with the protein complexes implicated in different regulatory activities and indicate their potential multifunctional role in the regulation of transcription.

overall_design: ChIP-seq of Combgap, Zeste, Psq, and Adf1 in S2 cells

middle: Y

first: Darya

last: Chetverina

first: Maxim

last: Erokhin

first: Nadezhda

last: Vorobyeva


title: Body temperature variation controls pre-mRNA processing and transcription of anti-viral genes

status: Public on May 31 2022

city: Berlin

first: Marco

last: Preussner

address: Takustrasse 6

country: Germany

institute: FU berlin

summary: Anti-viral innate immunity represents the first line of defense against invading viruses and is key to control viral infections, including the pandemic SARS-CoV-2. Body temperature is an omnipresent variable but was so far neglected when addressing host defense mechanisms and susceptibility to SARS-CoV-2 infection. Here we show that increasing temperature in a 1.5°C window, between 36.5°C and 38°C, strongly increases anti-viral immunity. We show that alternative splicing coupled to nonsense-mediated decay decreases STAT2 expression in colder conditions and suggest that increased STAT2 expression at elevated temperature induces the expression of diverse anti-viral genes. This cascade is activated in a remarkably narrow temperature range below febrile temperature, which reflects individual, circadian and age-dependent body temperature variation. Accordingly, decreased body temperature with ageing correlates with reduced expression of anti-viral genes in older individuals. Using cell culture and in vivo models, we show that higher body temperature indeed reduces SARS-CoV-2 replication, which likely impacts on the different vulnerability of children versus seniors towards severe SARS-CoV-2 infection. Altogether, our data reveal a molecular mechanism, from temperature sensing and pre-mRNA processing to an in vivo phenotype connecting body temperature variation with SARS-CoV-2 replication, thus providing a new paradigm for the regulation of anti-viral innate immunity.

overall_design: Raw264.7. Cells were incubated for 12h at 34°C, 37°C or 38°C

first: Florian

last: Heyd


title: Variant Polycomb complexes in Drosophila consistent with ancient functional diversity

status: Public on Apr 29 2022

city: Boston

first: Mitzi

last: Kuroda

state: Massachusetts (MA)

address: 77 Ave Louis Pasteur NRB 168

department: Division of Genetics

institute: Brigham and Women’s Hospital

summary: Polycomb group (PcG) mutants were first identified in Drosophila based on their failure to maintain proper Hox gene repression during development.  The proteins encoded by the corresponding fly genes mainly assemble into one of two discrete Polycomb Repressive Complexes: PRC1 or PRC2.  However, biochemical analyses in mammals have revealed alternative forms of PRC2, and multiple distinct types of non-canonical or variant PRC1.  Through a series of proteomic analyses, we identify analogous PRC2 and variant PRC1 complexes in Drosophila, as well as a broader repertoire of interactions implicated in early development.  Our data provide strong support for the ancient diversity of PcG complexes, and a framework for future analysis in a longstanding and versatile genetic system.

overall_design: Genome binding/occupancy profiling by high throughput sequencing of BioTAP-Jarid2 and BioTAP-Pcl from 12-24 hr  embyos

first: H

last: Kang

first: M

middle: I


title: ChIP-Seq analysis of day 6 male and female gametocytes of the malaria parasite Plasmodium falciparum

status: Public on May 07 2022

city: Erlangen

first: Michaela

last: Petter

address: Wassertrumstr. 3-5

department: Mirkobiologisches Institut

institute: Univeritätsklinikum Erlangen

summary: Plasmodium falciparum parasites alternate between two different obligate hosts during their life cycle: humans and Anopheles mosquitoes. During the blood stage in the human host they proliferate asexually inside erythrocytes. A small proportion of parasites develops into male and female gametocytes, which enter the sexual part of the life cycle once taken up by a mosquito. The production of male and female gametocytes is therefore critical for malaria transmission. It has been shown that epigenetic processes play a role in this differentiation processes, however, the exact mechanisms remain unknown. To gain insight into these processes, we separated male and female gametocytes, based on the female specific expression of an endogenously GFP-tagged ABCG2 gene, using flow cytometry (male parasites as GFP low, female parasites as GFP high population). We subsequently performed ChIP-Seq for several histone variants and modifications (H2A.Z, H2A.Zac, H2B.Z, H3K4me3, H3R17me2, H3K27ac, H3K9me3) on day 6 of gametocytogenesis. Our study reveals a global remodelling of the chromatin landscape in gametocytes compared to asexual parasites, as well as sex specific differences.

overall_design: ChIP-Seq analysis of chromatin moditications and variants H2A.Z, H2A.Zac, H2B.Z, H3K4me3, H3R17me2, H3K27ac, H3K9me3 in immature male and female gametocytes

first: Michael

middle: F

last: Duffy

first: Shamista

last: Selvarajah

first: Jingyi

last: Tang

first: Myriam

last: Jeninga

first: Alexander

middle: G

last: Maier


title: A mRNA motif mediates TGF-β1 upregulation of NEU3 translation in human lung fibroblasts

status: Public on Apr 28 2022

city: College Station

first: Richard

middle: H

last: Gomer

state: TX

address: 301 Old Main Drive

department: Biology

institute: Texas A&M University

summary: To elucidate how TGF-β1 regulates translation, we treated human lung fibroblasts (HLF) with TGF-β1 and used RNA-seq to determine the effect of TGF-β1 on total RNAs, and mRNA polysome/monosome ratios.

overall_design: 4 human lung fibroblast (HLF) cell lines were treated with or without TGF-β1, and total RNAs or mRNAs in monosome and polysome fractions were extracted and used for RNA-seq. Total RNA levels and Polysome/Monosome mRNA ratios were compared between control and TGF-β1 treated samples.

first: Wensheng

last: Chen


title: Priming a vascular-selective cytokine response permits CD8+ T-cell entry into tumors

status: Public on May 02 2022

city: Charlottesville

first: Pankaj

last: Kumar

state: VA

address: JPA, 1312A Pinn Hall

department: Bioinformatics Core

institute: University of Virginia

summary: Targeting DNA methyltransferase 1 (DNMT1) has immunomodulatory and anti-neoplastic activity, especially when paired with cancer immunotherapies. Here we explored the immunoregulatory functions of DNMT1 in the tumor vasculature. Dnmt1 deletion in endothelial cells (ECs) impairs tumor growth and metastatic seeding while priming expression of cytokine-driven cell adhesion molecules and chemokines important for CD8+ T-cell trafficking across the vasculature; consequently, the efficacy of immune checkpoint blockade (ICB) is enhanced. Tumor ECs reduced in IFNg response genes are enriched in cell cycle effectors, including Dnmt1, indicating mitotic ECs suppress anti-tumor immune responses. Targeting Dnmt1 in ECs reduces proliferation and augments adhesion and diapedesis of CD8+ T-cells, suggesting Dnmt1 programs immunologically anergic tumor vasculature. Our study is in good accord with preclinical observations that pharmacologically disrupting DNMT1 enhances the activity of ICB, but suggests an epigenetic pathway presumed to be targeted in cancer cells, is also operative in the tumor vasculature.

overall_design: Overall design: "Tumor associated endothelial cells or mammary gland endothelial cells were isolated (from pooled orthotopically implanted E0771 mammary tumors or normal mammary glands) using FACS for CD45-/CD31+ populations."

first: Dae-Joong

last: Kim

first: Andrew

middle: C

last: Dudley


title: Gene dysregulation in acute HIV-1 infection – early transcriptomic analysis reveals the crucial biological functions affected

status: Public on May 30 2022

city: Crawley

first: Erica

middle: Louise

last: Parker

state: WA

address: 35 Stirling Highway

country: Australia

institute: University of Western Australia

summary: Transcriptomic analyses from early human immunodeficiency virus (HIV) infection have the potential to reveal how HIV causes widespread and lasting damage to biological functions, especially in the immune system. Previous studies have been hampered by difficulties in obtaining early specimens. We studied 29 HIV infected subjects 1 month from presentation and 46 contemporaneous uninfected controls. We used RNA-seq to examine circulating immune cells to describe in detail the profound gene dysregulation observed in early HIV infection. Correlations were sought between viral load and differential gene expression, and biological implications were examined. The most profoundly upregulated biological functions related to cell cycle regulation, DNA repair and replication, microtubule and spindle organization, and immune activation and response. Our findings provide insight into the pathogenic mechanisms of early HIV-induced immune damage, information important for timely interventions to prevent clinical progression, inhibit reservoir seeding, and enable vaccine development.

overall_design: Cohort study; this sub-analysis comparing acute HIV infection to uninfected controls

first: Melinda

last: Judge

first: Lucia

last: Pastor

first: Laura

last: de la Fuente-Soro

first: Chenjerai

last: Jairoce

first: Kim

last: Carter

first: Denise

last: Anderson

first: Inácio

last: Mandomando

first: Holly

last: Clifford

last: Naniche

first: Peter

middle: N

last: Le Souëf


title: RNA-seq and ChIP-seq of OsLEC1

status: Public on Apr 23 2022

city: Hangzhou

first: Fu

last: Guo

address: Yuhangtang Road 866

institute: Zhejiang University


title: Functional analysis of ANGPTL8 in clear cell renal cell carcinoma

status: Public on May 25 2022

city: Kitakyushu

first: Takuo

last: Matsukawa

address: 1-1 Iseigaoka, Yahatanishi-ku, Kitakyushu, Fukuoka

country: Japan

institute: University of Occupational and Environmental Health

summary: To investigate the function of ANGPTL8 in clear cell renal cell carcinoma, Caki-1 cells overexpressing ANGPTL8 and ANGPTL8 knockout were established.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for Caki-1 cells and its  ANGPTL8 overexpressing/ANGPTL8 knockout.

first: Doi

last: Tomomitsu

first: Endo

last: Motoyoshi


title: The Epstein-Barr virus hijacks BRD7 to conquer c-Myc-mediated viral latency maintenance via chromatin remodeling

status: Public on May 14 2022

city: Changsha

first: Shen

last: Li

address: 110 Xiangya Road

department: School of Basic Medical Science

institute: Central South University

summary:
The Epstein-Barr virus (EBV) switches between latent and lytic phases in hosts that are important in developing related diseases. However, the underlying mechanism of how the viral latent-lytic switch is controlled and how EBV itself mediates this regulation remains largely unknown. This study identified the upregulated histone acetyl reader bromodomain-containing protein 7 (BRD7) during EBV latent infection. Based on the ChIP-sequencing of endogenous BRD7 in Burkitt lymphoma cells, we found that EBV drove BRD7 to regulate cellular and viral genomic loci, including the transcriptional activation of c-Myc, a recently reported regulator of EBV latency. Additionally, EBV-mediated BRD7 signals enriched around the FUSE site in chromosome 8, and the enhancer LOC108348026 in the lgH locus, which might activate the c-Myc alleles. Mechanically, EBV-encoded nuclear antigen 1 (EBNA1) bound and recruited BRD7 to colocalize at promotor regions of the related genes, thus serving as cofactors for the maintenance of viral latency. Moreover, the disruption of BRD7 decreased the c-Myc expression, induced the BZLF1 expression, and reactivated the lytic cycle. Our findings reveal the unique role of BRD7 hijacked by EBV in maintaining the viral latency state via chromatin remodeling. The study paved the way for understanding the new molecular mechanism of EBV-induced chromatin remodeling and latent-lytic switch regulation, providing novel therapeutic candidate targets for EBV persistent infection.
With establishing persistent infection in most human hosts, EBV is usually at a latent infection state. How the viral latency is maintained in cells remains largely unknown. c-Myc was recently reported to act as a controller of the lytic switch, while whether and how EBV regulates it remains to be explored. Here, we identified that BRD7 is involved in controlling EBV latency. We found that EBV-mediated BRD7 was enriched in both the normal promoter regions and the translocation alleles of c-Myc, and the disruption of BRD7 decreased c-Myc expression to reactivate the lytic cycle. We also demonstrated that EBV-encoded EBNA1 bound to and regulated BRD7. Therefore, we reveal a novel mechanism by which EBV can regulate its infection state by hijacking host BRD7 to target c-Myc. Our findings will help future therapeutic intervention strategies of EBV infection and pathogenesis.

overall_design: To further study the influence on the BRD7 in chromatin remodeling by EBV, a ChIP-seq assay was performed on the EBV positive and EBV negative Akata cell lines.

first: Li

last: Yang

first: Wenxing

last: Yue

first: Jianhong

last: Lu


title: Next Generation Sequencing of Wild Type and Oslec1-1 Transcriptomes

summary: Acquiring the OsLEC1 regulated genes network by comparing the differentially expressed genes.

overall_design: mRNA profiles of 7-DAP and 25-DAP embryos of wild type (NIP) and Oslec1-1

first: Hongwu

last: Bian

first: Peijing

last: Zhang

first: Yan

last: Wu


title: satmut_utils: a simulation and variant calling package for multiplexed assays of variant effect

status: Public on Apr 22 2022

city: Austin

first: Can

last: Cenik

address: Moffett Molecular Biology Building 2.122 2500 Speedway

department: Molecular Biosciences

institute: The University of Texas at Austin

summary: We use stable expression of a cystathionine-beta synthase (CBS) variant library in HEK293T cells to identify CBS coding sequence variants that alter mRNA abundance

sample_organism:
Homo sapiens
unidentified plasmid

platform_organism:
Homo sapiens
unidentified plasmid

overall_design: Amplicon and rapid amplification of cDNA ends (RACE)-like targeted library preparation chemistries were used to assay variant abundance in total RNA and gDNA by Next-Generation Sequencing

first: Ian

last: Hoskins

first: Song

last: Sun

first: Atina

last: Cote

first: Frederick

last: Roth


title: Next Generation Sequencing analysis of BCR-induced gene expression in adult and neonatal splenic B cells

status: Public on Apr 20 2022

city: Silver Spring

first: Jiro

last: Sakai

state: Maryland

address: 10903 New Hampshire Avenue

institute: US Food and Drug Administration

summary: Newborns are unable to reach the adult-level humoral immune response partly due to the potent immunoregulatory role of IL-10. IL-10 expression is controlled by various transcription factors including nuclear factor-κB (NF-κB), signal transducer and activator of transcription 3 (STAT3), and GATA binding protein 3 (GATA3) depending on the upstream signaling pathways and cell types. In B cells, IL-10 production has been shown to be activated by B cell receptor (BCR) engagement, CD40 ligand, TLR agonists, IL-1β and IL-6. We have shown increased IL-10 production by BCR-stimulated neonatal B cells compared to adult counterparts. To gain insight into the underlying mechanisms of enhanced IL-10 production in BCR-stimulated neonatal B cells, we performed RNA sequencing and Gene Set Enrichment Analysis for adult and neonatal B cells following BCR engagement. To identify signaling pathways uniquely activated by neonatal BCR, we compared adult and neonatal B cell data using hallmark gene sets from the Molecular Signatures database (MSigDB) C5 gene ontology (GO) collection. Pathways enriched in neonatal B cells included cytokine receptor signaling pathways leading to Signal Transducer And Activator Of Transcription (STAT) protein activation. We also conducted GSEA using the MSigDB C3 transcription factor targets (TFT) hallmark gene collection to identify transcription factors uniquely activated in neonatal B cells. This analysis revealed that target gene sets for STAT3, STAT5A and STAT5B were highly enriched in neonatal B cells, suggesting that these STAT proteins were activated in neonatal B cells after BCR engagement.

overall_design: Total RNA obtained from isolated adult and neonatal splenic CD19+CD43- B cells subjected to 0 or 7 hours ex vivo anti-IgM. 18 samples containing triplicated 6 conditions.

first: Mustafa

last: Akkoyunlu

first: Wells

middle: W

first: Chao-Kai

last: Chou


title: Induced expression of PD-L1 in spermatogonial stem cells by self-renewal division allows allogeneic offspring production [Sequencing]

status: Public on Apr 11 2022

city: Kyoto

first: Satoshi

last: Watanabe

state: Kyoto

address: 53, Kawahara-cho, Shogoin, Sakyo

department: Graduate School of Medicine

institute: Kyoto University

summary: Testis immune privilege is thought to be mediated by somatic cells. However, it is not strong enough to protect allogeneic spermatogonial stem cells (SSCs) transplanted into the seminiferous tubules. Here we report successful production of allogeneic offspring by inducing PD-L1 in SSCs. Activation of self-renewal division induced PD-L1 and B7-H3 expression in cultured SSCs, which produced sperm after allogeneic transplantation. While B7-H3 depletion did not influence colonization, PD-L1 depletion prevented donor-derived spermatogenesis. PD-L1 expression was induced by BCL6B via reactive oxygen species (ROS) generation, suggesting that self-renewal stimulation confers immune privilege by ROS. In contrast, reduced ROS or Mapk14 deficiency downregulated PD-L1 expression. Allogeneic offspring were produced by SSC transplantation into congenitally infertile mice and busulfan-treated wild-type mice. Therefore, SSCs can escape rejection when their self-renewal division is stimulated.

overall_design: Analysis of expression profiles during establishment (0weeks, 1weeks, 2weeks, 3weeks, established cultured SSCs) of cultured spermatogonial stem cells, in duplicate, using illumina NextSeq 500.

first: Mito

last: Kanatsu-Shinohara

first: Takuya

last: Yamamoto

first: Takashi

last: Shinohara


title: Induced expression of PD-L1 in spermatogonial stem cells by self-renewal division allows allogeneic offspring production [microarray]

overall_design: Analysis of expression level change during establishment (0weeks, 1weeks, 2weeks, 3weeks, established cultured SSCs) of cultured spermatogonial stem cells


title: T cell AHR activity tunes the Gut Microenvironment to Sustain Autoimmunity [sephouse_feces]

status: Public on Apr 10 2022

first: Alban

last: Gaultier

address: 409 Lane Rd

summary: The contribution of the environment and, in particular, the gut flora to multiple sclerosis (MS) etiology is well documented but not well understood. The aryl hydrocarbon receptor (AHR) binds numerous molecules present in the environment and is a therapeutic target for MS: however, its precise function in T lymphocytes, the orchestrators of MS, has not been described. Here, we show that CD4 specific Ahr knockout drives recovery in an animal model of MS driven by a decrease in T cell fitness. At the mechanistic level, we show that the absence of AHR changes the gut microenvironment composition to generate metabolites, such as bile salts and short chain fatty acids, that impact T cell viability.  Our study demonstrates a newly emerging role for AHR in mediating the interdependence between T lymphocytes and the microbiota while identifying new potential molecular targets for the treatment of MS and other autoimmune diseases.

overall_design: Microbiome comparative analysis via 16S sequencing of feces of separatly housed Cd4creAhrfl/fl and Ahrfl/fl mice.

first: Andrea

last: Merchak

first: Hannah

middle: J

last: Cahill

first: Lucille

last: Brown

first: Ryan

middle: M

first: Courtney

last: Rivet-Noor

first: Rebecca

last: Beiter

first: Erica

last: Slogar

first: Deniz

last: Olgun


title: Single-cell transcriptome profiling of the trigeminal ganglion of mice under normal and inflammatory pain conditions

status: Public on May 24 2022

city: Guangzhou

first: li

middle: hao

last: yuan

address: International Biotech Island

institute: Forevergen Biosciences Co.,Ltd

summary: Orofacial inflammation could lead to transcriptional alterations in the trigeminal ganglion (TG). In this study, we performed single-cell RNA-sequencing (scRNA-seq) analysis of mouse TG to identify all cell types and profile transcriptomic alterations of TG cells under inflammatory conditions. A total of 7 types of cells including endothelial cells, fibroblasts, glial cells, granulocytes, lymphocytes, monocyte-macrophages and several subtypes of neurons were identified. In addition, we performed annotation of neuronal subtypes and differential gene expression analysis among TG neurons, identifying several differential genes involved in pain modulation such as Scn10a, Zbtb20 and Runx1. Collectively, our study revealed the heterogeneity of TG cells and diverse neuronal transcriptomic responses to orofacial inflammation, which aids in the development of novel therapeutics for orofacial inflammatory pain.

overall_design: 2 samples, 5-8 weeks mouse under control and inflammatory pain conditions respectively

first: Qing

last: Liu

first: Lijia

last: Mai

first: Shengyan

last: Yang

first: Shilin

last: Jia

first: Hongwen

last: He

first: Wenguo

last: Fan

first: Fang

last: Huang


title: T cell AHR activity tunes the Gut Microenvironment to Sustain Autoimmunity [sephouse_cecum]

first: Alban

overall_design: Microbiome comparative analysis via 16S sequencing of cecum contents of separatly housed Cd4creAhrfl/fl and Ahrfl/fl mice.

middle: R


title: T cell AHR activity tunes the Gut Microenvironment to Sustain Autoimmunity [cohouse_feces]

overall_design: Microbiome comparative analysis via 16S sequencing of feces of cohoused Cd4creAhrfl/fl and Ahrfl/fl mice.

first: Andrea


title: Loss of Mitochondrial Fatty Acid Beta-Oxidation Protein Short Chain Enoyl-CoA Hydratase Disrupts Oxidative Phosphorylation Protein Complex Stability and Function

city: Melbourne

first: Mark

last: Ziemann

state: VIC

address: 85 Commercial Rd

department: Bioinformatics Working Group

institute: Burnet Institute

summary: Short chain enoyl-CoA hydratase 1 (ECHS1) is involved in the second step of mitochondrial fatty acid β-oxidation (FAO), catalysing the hydration of short chain enoyl-CoA esters to short chain 3-hyroxyl-CoA esters. Genetic deficiency in ECHS1 (ECHS1D) is associated with a specific subset of Leigh Syndrome, a disease typically caused by defects in oxidative phosphorylation (OXPHOS). Here, we examined the molecular pathogenesis of ECHS1D using a CRISPR/Cas9 edited human cell ‘knockout’ model and fibroblasts from ECHS1D patients. Transcriptome analysis of ECHS1 ‘knockout’ cells showed reductions in key mitochondrial pathways, including the TCA cycle, receptor mediated mitophagy and nucleotide biosynthesis. Subsequent proteomic analyses confirmed these reductions and revealed additional defects in mitochondrial oxidoreductase activity and fatty acid β-oxidation. Functional analysis of ECHS1 ‘knockout’ cells showed reduced mitochondrial oxygen consumption rates when metabolising glucose or OXPHOS complex I-linked substrates, as well as decreased complex I and complex IV enzyme activities. ECHS1 ‘knockout’ cells also exhibited decreased OXPHOS protein complex steady-state levels (complex I, complex III2, complex IV, complex V and supercomplexes CIII2/CIV and CI/CIII2/CIV). Patient fibroblasts exhibit varied reduction of mature OXPHOS complex steady-state levels, with defects detected in CIII2, CIV, CV and the CI/CIII2/CIV supercomplex. Overall, these findings highlight the contribution of defective OXPHOS function, in particular complex I deficiency, to the molecular pathogenesis of ECHS1D.

overall_design: Here, we used CRISPR/Cas9 gene editing to  ‘knockout’ the ECHS1 gene in 143BTK- osteosarcoma cells. Control and knock-out cells underwent RNA sequencing with four replicates.

first: Harrison

last: Burgin

first: Alice

last: Sharpe

first: Shuai

last: Nie

first: James

last: Pitt

first: Akira

last: Ohtake

first: Kei

last: Murayama

first: Matthew

last: McKenzie


title: Postnatal day 6 cerebellum of Ts65Dn and TcMAC21 Down syndrome mouse models

status: Public on May 16 2022

city: Worcester

first: Summer

middle: B

last: Thyme

state: MA

address: 55 N Lake Ave

institute: UMass Chan

summary: Dysregulation of Sonic hedgehog (SHH) signaling may contribute to multiple Down syndrome-associated phenotypes, including cerebellar hypoplasia, congenital heart defects, craniofacial and skeletal dysmorphologies, and Hirschsprung disease. Granule cell precursors isolated from the developing cerebellum of Ts65Dn mice are less responsive to the mitogenic effects of SHH than euploid cells, and a single postnatal dose of the SHH pathway agonist SAG rescues cerebellar morphology and performance on learning and memory tasks in Ts65Dn mice. SAG treatment also normalizes expression levels of OLIG2 in neural progenitor cells derived from human trisomy 21 iPSCs. However, despite evidence that activating SHH signaling rescues Down syndrome-associated phenotypes, chromosome 21 does not encode any canonical components of the SHH pathway. Here, we screened 163 chromosome 21 cDNAs in a series of SHH-responsive cell lines to identify chromosome 21 genes that modulate SHH signaling and confirmed overexpression of trisomic candidate genes using RNA-seq in Ts65Dn and TcMAC21 cerebellum. Our study indicates that some chromosome 21 genes, including DYRK1A, activate SHH signaling while others, such as HMGN1 and MIS18A, inhibit SHH signaling. Moreover, overexpression of genes involved in chromatin structure and mitosis, but not genes previously implicated in ciliogenesis, regulate the SHH pathway. Our data suggest that cerebellar hypoplasia and other phenotypes related to aberrant SHH signaling arise from the net effect of trisomy for multiple chromosome 21 genes rather than the overexpression of a single trisomic gene. Identifying which chromosome 21 genes modulate SHH signaling may also suggest new therapeutic avenues for ameliorating Down syndrome phenotypes.

overall_design: Comparative gene expression profiling analysis for 4 Ts65Dn cerebella, 4 Ts65Dn euploid littermate cerebella, 4 TcMAC21 cerebella, and 4 TcMAC21 euploid littermate cerebella

first: Anna

last: Moyer

first: Yicong

last: Li

first: Liliana

last: Florea

first: Roger

last: Reeves


title: CHIP-seq for TCF21 overexpressing tumor pericytes

status: Public on Apr 06 2022

city: ChangSha

first: Ke

last: Gong

address: 139 Renmin Middle road

department: cardiovascular surgery

institute: The Second Xiangya Hospital of Central South University

summary: This study aims to investigate genes regulated by TCF21.

overall_design: Tumor pericytes with TCF21-overexpressing were acquired for CHIP-seq

first: Xiaobo

first: Jinghua

last: Pan

first: Tongzheng

last: Liu

first: Minfeng

last: Chen

first: Wencai

last: Ye

first: Dongmei

last: Zhang


title: Nitrate or urea responsive microarray in a pair of contrsting rice genotypes

city: New Delhi

first: Nandula

last: Raghuram

state: Delhi

address: Block A

department: USBT

country: India

institute: GGSIP University

summary:
To find out the genotype specific differentially expressed genes in response to N source
Two contrasting Indica rice genotypes namely, Nidhi and Panvel 1 were used. Arnon Hoagland medium with either nitrate or urea were used as fertilizer sources. Two N doses, normal (15 mM of N) was used as control while low (1.5mM of N) was used as test.

overall_design: 12 rice samples for two contrasting genotypes were analyzed for dual colour gene expression analysis.  3 biological replicates were used for this analysis. For this purpose whole tissue (shoot and root)of 21 old days grown plants in nutrient depleted soil, fertilized with normal (15mM) or low (1.5mM) nitrate or urea were used.

first: Narendra

last: Sharma


title: RNA-seq and CHIP-seq for TCF21 overexpressing tumor pericytes

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

overall_design: Refer to individual Series


title: Gene Expression data from HuR-RIP-microarray from human PDAC, Mia PaCa-2 cell line

city: Philadelphia

first: Aditi

last: Jain

address: 1015 Walnut Street

department: Surgery

institute: Thomas Jefferson University

summary: RNA binding protein, Human Antigen R (HuR/ELAVL1), regulates mRNA stability of key species involved in pancreatic ductal adenocarcinoma (PDAC) cell survival under conditions of chemotherapeutic stress, hypoxia, low glucose environment. We used RNA immunoprecipitation-microarray or RNP-IP from cytoplasmic extracts of PDAC cell lines exposed to chemotherpaeutic stress (olaparib and gemcitabine) to evaluate whole transcriptome gene expression profile associated with HuR and find novel trargtes associated with DNA repair functions of HuR.

overall_design: Cells were treated with chemotherapeutic stressors for 16 hours and cytoplamic HuR was immunoprecipitated using RNP-IP protocol and RNA extracted. Bound RNA were microarrayed using human Clariom D whole transcriptome assays.

first: Jonathan

last: Brody

last: McCoy

first: Sankar

last: Addya

first: Samantha

middle: Z

last: Brown

first: Carl

last: Pelz

first: Rosalie

last: Sears

first: Charles

last: Yeo


title: Developmental pyrethroid exposure and age influence phenotypes in a Chd8 haploinsufficient autism mouse model

status: Public on Apr 01 2022

city: Boston

first: Jeremy

last: Simon

address: 450 Brookline Ave

department: Department of Data Science

institute: Dana-Farber Cancer Institute

summary: Hundreds of genes have been associated with autism spectrum disorder (ASD), including loss-of-function mutations in chromodomain helicase DNA binding protein 8 (Chd8). Environmental factors also are implicated in autism risk and have the potential to exacerbate phenotypes in genetically sensitized backgrounds. Here we investigate transcriptional and behavioral phenotypes in a Chd8 haploinsufficient (Chd8V986*/+) mouse line exposed to the pesticide deltamethrin (DM) from conception to postnatal day 22. Vehicle-exposed Chd8V986*/+ mice displayed ASD-associated phenotypes, including anxiety-like behavior and altered sociability, replicating a previous study with this mouse line. A core set of genes was altered in Chd8V986*/+ mice at multiple ages, including Usp11, Wars2, Crlf2, and Eglf6, and proximity ligation data indicated direct binding of CHD8 to the 5’ region of these genes. Moreover, a neurodegenerative transcriptional phenotype was apparent in 12 and 18 month old Chd8V986*/+ mice. Following DM exposure, the mutant mice displayed an exacerbated phenotype in the elevated plus maze, and genes associated with vascular endothelial cells were downregulated in the cerebral cortex of older Chd8V986*/+ animals. Our study reveals a gene x environment interaction with a Chd8 haploinsufficient mouse line and points to the importance of investigating phenotypes in ASD animal models across the lifespan.

overall_design: RNA-seq of WT and Chd8V986 het mouse cortex, comparing deltamethrin exposure vs oil control at P5 and 12 months. Additional RNA-seq of WT and Chd8V986 het mouse cortex at 18 months

first: Jessica

middle: A

last: Jimenez

first: Mark

last: Zylka


status: Public on Mar 30 2022

city: Ribeirão Preto

first: Guilherme

middle: Da Silva

last: Rodrigues

address: Avenida Bandeirantes, 3900

country: Brazil

institute: Universidade de São Paulo

type: Methylation profiling by genome tiling array

summary: Background: Pre-diabetes condition precedes the Diabetes Mellitus (DM) disease and is a critical period for hyperglycemia treatment, especially for menopausal women, considering all metabolic alterations due to hormonal changes. Recently, the literature has demonstrated the role of physical exercise in epigenetic reprogramming to modulate the gene expression patterns of metabolic conditions, such as hyperglycemia, preventing DM development. In the present study, we hypothesized that physical exercise training could modify the epigenetic patterns of women with poor glycemic control. Methods: 48 post-menopause women aged 60.3±4.5 years were divided according to the fasting blood glucose levels into two groups: Prediabetes Group, PG (n=24) and Normal Glucose Group, NGG (n=24). All participants performed 14 weeks of physical exercise three times a week. The Infinium Methylation EPIC BeadChip measured the participants’ Different Methylated Regions (DMRs). Results: Before the intervention, the PG group had 12 DMRs compared to NGG. After the intervention, five DMRs remained different. Interestingly, when comparing the PG group before and after training, 118 DMRs were found. The enrichment analysis revealed that the genes were related to different biological functions such as energy metabolism, cell differentiation, and tumor suppression. Conclusion: Physical exercise is a relevant alternative in treating hyperglycemia and preventing DM in post-menopause women with poor glycemic control.

overall_design:
MethylationBrazil Assay
Fourteen-weeks combined exercise epigenetically modulated 118 genes of menopausal women with prediabetes

last: da Silva Rodrigues


title: Mapping the developing human cardiac endothelium at single cell resolution identifies MECOM as a regulator of arteriovenous identity.

status: Public on Mar 02 2022

city: Edinburgh

first: Ian

last: McCracken

address: 47 Little France Crescent

department: Centre for Cardiovascular Science

institute: University of Edinburgh

summary: Aims: Coronary vasculature formation is a critical event during cardiac development, essential for heart function throughout perinatal and adult life. However, current understanding of coronary vascular development has largely been derived from transgenic mouse models. The aim of this study was to characterise the transcriptome of the human fetal cardiac endothelium using single-cell RNA sequencing (scRNA-seq) to provide critical new insights into the cellular heterogeneity and transcriptional dynamics that underpin endothelial specification within the vasculature of the developing heart.  Methods and Results: We acquired scRNA-seq data of over 10,000 fetal cardiac endothelial cells (EC), revealing divergent EC subtypes including endocardial, capillary, venous, arterial, and lymphatic populations. Gene regulatory network analyses predicted roles for SMAD1 and MECOM in determining the identity of capillary and arterial populations, respectively. Trajectory inference analysis suggested an endocardial contribution to the coronary vasculature and subsequent arterialisation of capillary endothelium accompanied by increasing MECOM expression. Comparative analysis of equivalent data from murine cardiac development demonstrated that transcriptional signatures defining endothelial subpopulations are largely conserved between human and mouse. Furthermore, we revealed that knockdown of MECOM in human embryonic stem cell-derived EC (hESC-EC) resulted in an increase in venous EC marker expression, validating our prediction of its role in arterial EC identity. Conclusions: scRNA-seq of the human fetal cardiac endothelium identified distinct EC populations. A predicted endocardial contribution to the developing coronary vasculature was identified, as well as subsequent arterial specification of capillary EC. Loss of MECOM in hESC-EC increased venous EC marker expression, suggesting a role in maintaining arterial EC identity.

overall_design: Characterisation of the human fetal cardiac endothelium by single cell RNA sequencing.

first: Ross

last: Dobie

first: Matthew

last: Bennett

first: Rainha

last: Passi

first: Abdelaziz

last: Beqqali

first: Neil

last: Henderson

first: Joanne

last: Mountford

first: Paul

last: Riley

first: Chris

middle: P

last: Ponting

first: Nicola

last: Smart

first: Mairi

last: Brittan

first: Andrew

last: Baker


title: Integrated microRNA and secretome analysis of human endometrial organoid reveal the miR-3194-5p/Aquaporin/S100A9 module in regulating trophoblast functions

status: Public on Mar 15 2022

city: Hong Kong

first: Jianlin

last: Li

address: L 7-08, Department of Obstetrics and Gynecology  Laboratory block, 21th Sassoon Road, Hong Kong

country: Hong Kong

institute: The University of Hong Kong

summary: We adopted the endometrial organoid model to simulate the hormonal conditions in the menstrual cycle and early gestation. We then established the first secretome profiles and miRNA atlas of these endometrial organoid in relation to their hormonal changes. We demonstrated for the first time that the miR-3194-5p/S100A9 axis is a key regulator of trophoblast invasion during early pregnancy.

overall_design: Study the effect of organoid secretion in proliferative phase, secretary phase and early pregnancy phase conditions on the functions on EVCTs in vitro.

first: Yang

last: Dong

first: Cheuk-Lun

last: Lee

first: Philip

last: Chiu


title: Inhibitory input directs astrocyte morphogenesis through glial GABABR

status: Public on Mar 16 2022

city: Houston

first: Yi-Ting

last: Cheng

address: 1 Baylor Plaza

institute: Baylor College of Medicine


title: T cell AHR activity tunes the Gut Microenvironment to Sustain Autoimmunity.

city: Charlottesville

first: Alban

last: Gaultier

institute: University of Virginia


title: Inhibitory input directs astrocyte morphogenesis through glial GABABR [scRNA-Seq]

summary: The goal of the study is to profile molecular signature of different cell populations between Gabbr1 control and Gabbr1 cKO animals.

overall_design: We performed scRNA-seq on P28 cortical astrocytes from Gabbr1 control and cKO animals.

first: Benjamin

last: Deneen


title: Inhibitory input directs astrocyte morphogenesis through glial GABABR [bulk RNA-Seq]

summary: The goal of the study is to profile (1) molecular signature of astrocytes in different developmental stages across different brain regions, (2) differential gene expression between Gabbr1 control and Gabbr1 cKO animals.

overall_design: We performed RNA-seq on (1) P1, P7, and P14 astrocytes from olfactory bulb, cortex, and hippocampus, (2) P28 cortical astrocytes from Gabbr1 control and cKO animals.


title: KLF2 and KLF4 in heart and lung endothelial cell transcriptional dynamics

status: Public on Feb 03 2022

city: Cleveland

first: Mukesh

last: Jain

state: OH

address: 2103 Cornell Rd

institute: Case Western Reserve University


title: Microarray miRNA expression analysis of white and brown adipose tissue depots from mice exposed to cold or room temperature

status: Public on Feb 06 2022

city: Bellaterra

first: Jordi

last: Rodo

state: Barcelona

address: Carrer de la Vall Moronta, edifici H

country: Spain

institute: CBATEG, UAB

summary: In the last decades, adipose tissue has been defined to play a central role in the control of energy balance. Furthermore, the proven endocrine and thermogenic functions of adipocytes have renewed interest in the study of this tissue, as the activation of non-shivering thermogenesis may hold great potential for the future treatment of obesity and T2D. Cold exposure has defined to activate this process.    Here, the miRNA transcriptomic response of epididymal and inguinal white adipose depots (eWAT and iWAT, respectively) as well as that of the interscapular brown adipose depot (iBAT) of C57Bl/6 mice either exposed to 22ºC or 4ºC for the period of 4 days were examined.    This in-detail study of the adaptation of each depot to cold exposure has allowed unraveling depot-specific regulatory molecular mechanisms.

overall_design: A total number of 8 mice were divided in two cohorts of 4 mice. The first group was housed at room temperature and the second group at cold exposure. Then, iBAT, iWAT and eWAT samples were collected from each mice. Total samples 24.

first: Miguel

last: Garcia

first: Fatima

last: Bosch


title: Induced expression of PD-L1 in spermatogonial stem cells by self-renewal division allows allogeneic offspring production

first: Satoshi

last: Watanabe


title: RNA-seq for TCF21 overexpressing tumor pericytes

first: Ke

last: Gong

summary: This study aims to investigate genes regulated by TCF21

overall_design: TCF21 was overexpressed in tumor pericytes derived from non-metastatic CRC patients, and then tumor pericytes transfected with vector or TCF21-overexpressing plasmid were analyzed by RNA-seq.

first: Xiaobo

first: Jinghua

last: Pan

first: Tongzheng

last: Liu

first: Minfeng

last: Chen

first: Wencai

last: Ye

first: Dongmei

last: Zhang


title: KLF2 and KLF4 in heart and lung endothelial cell transcriptional dynamics [ChIP-seq]

summary: We report bulk RNA-sequencing, ChIP-seq, and ATAC-seq of endothelial cells harvested from heart and lung of multiple mouse strains investigating the role of KLF2 and KLF4 in endothelial transcription

overall_design: Endothelial cells (ECs) were isolated from heart or lungs using flow cytometry (see below) and sujected to multiple sequencing modalities.

first: David

last: Sweet

middle: K

first: Vinesh

last: Vinayachandran

first: Roshan

last: Padmanabhan


title: KLF2 and KLF4 in heart and lung endothelial cell transcriptional dynamics [RNA-seq]


title: Enamel organ mRNA expression in the limiited bedding and nesting (LBN) mouse model

status: Public on Apr 05 2022

city: San Francisco

first: Dawud

last: abduweli uyghurturk

state: California

address: 513 Parnassus Ave.

institute: UCSF

summary: In a systemic effort to survive environmental stress, organ systems fluctuate and adapt to overcome external pressures. The evolutionary drive back towards homeostasis, makes it difficult to determine if an organism experienced a toxic exposure to stress, especially in early prenatal and neonatal periods of development. Previous studies indicate that primary human teeth may provide historical records of experiences related to stressors during that early time window. To assess the molecular effects of early life adversity on enamel formation, we used a limited bedding and nesting (LBN) mouse model of early life adversity (ELA), to assess changes in enamel organ gene expression and enamel mineralization. Enamel of postnatal day 12 (P12) weight-matched ELA mice was more mineralized as compared control enamel. RNAseq showed 724 genes significantly upregulated in ELA enamel organs as compared to controls, and 574 significantly downregulated genes (DESeq2 p-value <= 0.05). Transcripts expressing the enamel matrix proteins amelogenin (Amelx) and enamelin (Enam) were among the top 4 most differentially expressed genes. The most significantly enriched GO and Reactome pathway was Extracellular Matrix Organization, while the most significantly enriched KEGG Pathways were Butanoate metabolism and Synthesis and Degradation of Ketone Bodies. qPCR analysis of weight-matched ELA and control enamel organs confirmed that expression of the ameloblast-specific proteins Amelx and Enam were highly upregulated in ELA mice. When evaluating molecular mechanisms for amelogenin upregulation, we found significantly increased expression of Dlx3, while transcripts for clock genes Per1 and Nrd1, which have also positively associated with amelogenin expression, were downregulated. These findings suggest that the developing enamel organs are sensitive to the pressures of early life adversity and produce structural biomarkers in tooth enamel mineral to reflect these changes. Together these results support the possibility that tooth enamel may contain biomarkers of cellular effects associated with systemic early life adversity.

overall_design: Compare gene expression in enamel organs from an early life adversity mouse model as compared to controls

first: Pamela

last: Den Besten


title: Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and IRX5-overexpression hMSCs Transcriptomes

status: Public on Jan 31 2022

first: Tian

last: Tian

address: 3615 Civic Center Blvd

department: Center of Applied Genomics

institute: Children's Hospital of Philadelphia

summary: We aimed to clarify the influence of IRX5 overexpression on the transcripts of human bone marrow-derived mesenchymal stem cells (hMSCs). We overexpressed IRX5 in hMSCs by Lentivirus. RNA of CTRL and IRX5-overexpressing hMSCs were generated by deep sequencing, in triplicate, using Illumina NovaSeq 6000. The Sample read counts were summarized by StringTie2 with the GENCODE V32 annotation file. Differential expression analysis was determined based on read counts by using DESeq2. As a results, we found that adipogenesis-associated genes were up-regulated in the Plvx/IRX5 group; whereas glycolysis-associated genes were down-regulated compared to control hMSCs.

overall_design: Examination of CTRL hMSCs group and IRX5-overexpression hMSCs group.Every group has 3 biological repetition.

first: Bulin

last: Jiang

first: Fangfang

last: Song


title: Microbiota-derived pentanoate promotes differentiation of regulatory T cells via enhancing iron uptake in the intestine [Treg_in_vivo]

city: Xihu District, Hangzhou

first: Xing

last: Chang

state: Zhejiang

address: No.18 Shilongshan Road Cloud Town

department: School of Life Sciences

institute: Westlake University

summary: Iron deficiencies are the most common non-enteric syndromes observed in patients with inflammatory bowel diseases (IBD), yet little is known how iron deficiencies impact immune tolerance in the intestine. The goal of this study is to illuminate role of iron in colonic Treg homeostasis regulation.

overall_design: mRNA profiles in WT and Tfrc fl/fl Foxp3 YFP-IRES-Cre mice Treg cells

first: Lizhen

last: Zhu

first: Geng

last: Li


title: Microarray gene expression analysis of white and brown adipose tissue depots from mice exposed to cold or room temperature.

first: Jordi

last: Rodo

summary: In the last decades, adipose tissue has been defined to play a central role in the control of energy balance. Furthermore, the proven endocrine and thermogenic functions of adipocytes have renewed interest in the study of this tissue, as the activation of non-shivering thermogenesis may hold great potential for the future treatment of obesity and T2D. Cold exposure has defined to activate this process.  Here, the transcriptomic response of epididymal and inguinal white adipose depots (eWAT and iWAT, respectively) as well as that of the interscapular brown adipose depot (iBAT) of C57Bl/6 mice either exposed to 22ºC or 4ºC for the period of 4 days were examined.  This in-detail study of the adaptation of each depot to cold exposure has allowed unraveling depot-specific regulatory molecular mechanisms.

first: Miguel

last: Garcia

first: Fatima

last: Bosch


title: USP18 is an essential regulator of muscle cell differentiation and maturation

status: Public on Mar 23 2022

city: Leiden

first: Hailiang

last: Mei

address: Einthovenweg 20

department: Sequencing Analysis Support Core

country: Netherlands

institute: Leiden University Medical Center

summary: USP18 is an interferon type 1 (IFN-1) induced gene that negatively regulates the IFN-1 signalling pathway, which plays a role in many immune related pathologies. Dermatomyositis (DM) is characterised by excessive IFN-1 immune response and muscle degeneration. We found USP18 to be expressed in DM myofibers suggesting a role in muscle cell biology. USP18 depletion induced muscle cell differentiation under nutrient-rich conditions independent of IFN-1 signalling. Downregulation of cell cycle gene network and sarcomeric protein networks, and dysregulation of myogenic (co-)transcription regulators were found in USP18-depleted differentiated cells. Sarcomeric integrity of USP18-depleted cells deteriorated during muscle cell maturation. Our results revealed USP18 as a critical regulator at the intersection between proliferation and differentiation as well as during the maturation of muscle cells. We suggest that a USP18 IFN-1-independent pathway may contribute to muscle regeneration in muscle pathologies.

overall_design: Control versus USP18 KD in nutriet-rich or starving conditions (N=4). All samples were analysed in biological triplets.

first: Cyriel

middle: S

last: Olie

first: Vered

last: Raz


title: A Single-copy Knock In Translating Ribosome ImmunoPrecipitation (SKI TRIP) tool kit for tissue specific profiling of actively translated mRNAs in C. elegans.

city: BOSTON

first: Laura

middle: Elisabeth

last: Wester

state: Massachusetts

address: 677 Huntington Ave

institute: Harvard T.H. Chan School of Public

summary: Translating Ribosome Affinity Purification (TRAP) methods have emerged as a powerful approach to profile actively translated transcripts in specific cell and tissue types.  Epitope tagged ribosomal subunits are expressed in defined cell populations and used to pull down ribosomes and their associated mRNAs, providing a snapshot of cell type-specific translation occurring in that space and time. Current TRAP toolkits available to the C. elegans community have been built using multi-copy arrays, randomly integrated in the genome.  Here we introduce a Single-copy Knock In Translating Ribosome ImmunoPrecipitation (SKI TRIP) tool kit, a collection of C. elegans strains engineered by CRISPR in which tissue specific expression of FLAG tagged ribosomal subunit protein RPL-22 is driven by cassettes present in single copy from defined sites in the genome. In depth characterization of the SKI TRIP strains and methodology shows that 3xFLAG tagged RPL-22 expressed from its endogenous locus or within defined cell types incorporates into actively translating ribosomes and can be used to efficiently and cleanly pull-down cell type specific transcripts without impacting overall mRNA translation or fitness of the animal. We propose SKI TRIP use for the study of processes that are acutely sensitive to changes in translation, such as aging.

overall_design:
RNAseq from C. elegans after Polysome Profiling (total RNA and polysome profiling RNA in triplicates per strain) from WT (polysome profiling RNA of all polysomes) and strains MSD470=ubiquitous (1x polysome profiling RNA of all polysomes (PP); 1x polysome profiling RNA of 60S, 80S and polysomal ribosomes (PP2))
RNAseq from C. elegans after SKI TRIP (IP) experiments (total RNA and IPed RNA in triplicates per strain) from strains MSD470=UBI, WBM1364=soma, WBM1471=neuroB, MSD473=neuroA, WBM1339=muscle, WBM1471=intestine

middle: E

first: Anne

last: Lanjuin

first: Emanuel

last: Bruckisch

first: Maria

last: Perez Matos

first: Caroline

last: Heintz

first: Martin

last: Denzel

first: William

last: Mair


title: Transcriptome analysis of human blastocysts with different levels of chromosomal mosaicism after preimplantation genetic testing.

city: Valencia

first: Angel

last: Martin

address: Avenida Fernando Abril Martorell, 106 – Edificio Biopolo. Torre A, Planta 1

department: Research

institute: IVI Foundation-HRI La Fe

summary: An inner cell mass biopsy and the remaining trophectoderm were separately collected from 14 blastocysts with preimplantation genetic testing result into RNAse-free PCR tubes containing 2 µl of 10X reaction buffer (SMART-Seq v4 Ultra-Low Input RNA kit for Sequencing, Takara Bio, USA). cDNA was obtained from mRNA with 3′SMART-Seq CDS primer II (Takara Bio, USA) and PCR-amplified (17 cycles) from 10 pg of RNA. Amplified cDNA was purified using AMPure XP magnetic beads (Illumina, USA). After confirming cDNA integrity on a 2100 Bioanalyzer (Agilent Technologies, USA), 1 ng of cDNA per sample were fragmented, and libraries were constructed using NexteraXT DNA sample preparation (Illumina, USA). Samples were quantified using Qubit dsDNA Quantitation Assay (Thermo Fisher Scientific, USA), and 3 samples were excluded due to poor cDNA quality. An RNA pool was generated with 25 samples using equal concentration (5 nM) of RNA per sample. Sequencing was performed in duplicate in a single run using an Illumina NovaSeq 6000 S1 platform (Illumina, USA) with a 200-nucleotide read length in a paired-end design (100-bp fragments). FastQC was used for checking the quality of the raw sequence data. Fragments that did not meet quality requirements were trimmed using Trimmomatic. Alignment and quantification were performed using the Salmon algorithm (reference genome GRCh38). Raw counts were directly used for differential gene expression analysis.

overall_design: Prospective cohort study comparing the global gene expression profiles of inner cell mass and trophectoderm samples from blastocysts classified as euploid, low-level mosaic and high-level mosaic after preimplantation genetic testing.

first: María

last: De los Santos

first: Ángel

last: Martín


title: Microbiota-derived pentanoate promotes differentiation of regulatory T cells via enhancing iron uptake in the intestine.

first: Xing

last: Chang

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

overall_design: Refer to individual Series


title: Microbiota-derived pentanoate promotes differentiation of regulatory T cells via enhancing iron uptake in the intestine [FeSO4_treated_Treg]

overall_design: mRNA profiles in iTreg cells treated with FeSO4 or Mock

first: Lizhen

last: Zhu

first: Geng

last: Li


title: Identification of fatty acid amide hydrolase as a metastasis suppressor in breast cancer

status: Public on Mar 09 2022

city: Madrid

first: Eduardo

last: Pérez-Gómez

state: Madrid

address: José Antonio Novais 12

department: Biochemistry and Molecular Biologý

institute: Universidad Complutense de Madrid)

summary: Clinical management of breast cancer (BC) metastasis remains an unmet need as it accounts for 90% of BC-associated mortality. Although the luminal subtype, which represents >70% of BC cases, is generally associated with a favorable outcome, it is susceptible to metastatic relapse as late as 15 years after treatment discontinuation. Seeking therapeutic approaches as well as screening tools to properly identify those patients with a higher risk of recurrence is therefore essential. Here, we report that the lipid-degrading enzyme fatty acid amide hydrolase (FAAH) is a predictor of long-term survival in patients with luminal BC, and that it blocks tumor progression and lung metastasis in cell and mouse models of BC. Together, our findings highlight the potential of FAAH as a biomarker with prognostic value in luminal BC and as a therapeutic target in metastatic disease.

overall_design: mRNA profile of the three T-47D-derived cell lines (parental, FAAH KO and rescue)

first: Isabel

last: Tundidor


title: Expression data of hippocampal CA3 from Adora1 knockout and wild type mice

status: Public on Jan 20 2022

city: Xiangyang

first: lanting

last: zhou

address: No.296, Longzhong Road, Xiangyang City, Hubei Province

institute: Hubei university of arts and science

summary:
Purpose: The goals of this study are to analyze the mRNAs expression in hippocampal CA3 after Adora1 knockout by High-throughput sequencing.
Methods: The brain was dissected and followed by 20 μm cryosection onto 20 glass slides. The hippocampus CA3 was isolated from brain slides by using laser capture microdissection. Then the samples were stored on dry ice until RNA extraction by Trizol. The RNAseq was conducted by using Illumina HiSeq2000 platform.
Results: By performing RNA sequencing on RNAs isolated from the hippocampus CA3 neurons of AKO and C57 mice at 3-month-old. We found that 51 mRNAs were upregulated, whereas 77 mRNAs were downregulated in AKO mice.
Conclusion:We deciphered the underlying neuroprotective mechanisms of A1R knockdown in AD mouse models. By employing the RNA-seq technique, we compared the alterations in gene expression in the hippocampus between AKO and wild-type mice.

overall_design: Adora1 knockout mice (n=3; AKO mice) were compared to wild type mice (n=3). All mice are C57BL/6 background.

first: Lan-Ting

last: Zhou

first: Dan

last: Liu

first: He-Zhou

last: Huang

first: Ling-Qiang


title: A global analysis on the differential regulation of RNA binding proteins (RBPs) by TNF–α as potential modulators of metabolic syndromes

status: Public on Jan 21 2022

city: Zuarinagar, near MES College, Vasco

middle: maria

last: Talukdar

state: Goa

address: BITS Pilani K.K Birla Goa Campus

department: Department of Biological Sciences

institute: BITS PILANI K.K BIRLA GOA CAMPUS

summary:
Purpose:Metabolic syndrome (MetS) is associated with a group of conditions including diabetes, obesity, insulin resistance etc. The goal of our study is to identify the differentially regulated genes under metabolic syndromes induced by TNF-α.
Methods:A Homosapines Reference based Transcriptome sequencing is performed to understand the genes that are diffrerentially regulated under metabolic synromes with TNF-α as upstream. The HEK293 cells were treated with TNF alpha at 10ng/ml for 6hrs to induce the metabolic disturbances mimicking the metabolic syndromes and untreated HEK 293 cells were considered as control. For the Control set (31 million reads) and TNF-α treated (34 million reads) samples was obtained through the Illumina NextSeq 500 platform and comprised of paired end reads of 76 bp (2X76). FastQC software was used to check the quality of the NextSeq 500 paired end reads and were further processed by in-house script for adapter removal and low quality bases trimming. Tophat-2.02  and Cufflinks-2.1.14 tools were used for the analysis. A two fold change and p-value <0.05 cut-off was used to report the differentially expressed genes (DEGs). Owing to the absence of replicates, no FDR correction was used.For each gene a RPKM (Reads per kilo base per million mapped reads) value was calculated for each gene. Apart from the RPKM value, p-value and a fold change value was also calculated for control and treated samples. The genes were validated using qPCR using using Brilliant Ш Ultra-Fast SYBR green qPCR Master Mix in AriaMx PCR System (Agilent Technologies).
Results: Around 6056 and 5495 transcripts were shown as up and down regulated respectively using a twofold change cut-off. On excluding the transcripts with no gene names,   the numbers of up and down regulated transcripts were found out to be 4444 (3551 genes) and 4365 (3418 genes) respectively.Among which 1218 genes are unique, and highly significant(based on p-value cut-off) and  transcriptionally regulated genes by TNF-α, among which about 15% are RBPs; identified by the EuRBPDB data base. Among these transcriptionally regulated genes, we have identified 204 MetS genes by IPA analysis, more than 10% of which are identified as RBPs.
Conclusion: Transcriptional regulation of the MetS genes by TNF-α, which   also act as RBPs predicts the existence of feed-forward loops and interconnected pathways, which may influence the onset of MetS at the molecular level.

overall_design: Reference based transcriptome analysis was performed to understand how TNF alpha regulate genes under metabolic syndromes.

first: Indrani

first: Jiss

last: Louis


title: Effect of the janus kinase inhibitor ruxolitinib on gene expression of chronic lymphocytic leukemia cells in vivo

status: Public on Mar 05 2022

city: Toronto

first: YU XUAN

last: LUO

state: ON

address: 2075 Bayview Avenue

department: Biological sciences

country: Canada

institute: Sunnybrook research institute

summary: Symptomatic previously untreated chronic lymphocytic leukemia patients were treated with the janus kinase (JAK)-inhibitor ruxolitinib (clinicaltrials.gov, number NCT02015208). CLL cells from 6 of the patients were purified prior to commencing ruxolitinib and again 4 or 8 weeks after treatment and analyzed by RNAseq. Ruxolitinib induced a stereotyped response in all patients consisting of a rapid decrease in palpable lymphadenopathy accompanied by increased lymphocytosis and blood lactate dehydrogenase. This response was associated with evidence of inhibited JAK-signaling in CLL cells but activation of other oncogenic pathways.

overall_design: Gene expression in circulating CLL cells before and 4-8 weeks after treatment with ruxolitinib were compared by RNAseq.

first: David

last: Spaner

first: Daniel

last: Harari


title: Comparative RNA sequencing identifies superior cytocidal mechanisms of imatinib over rapamycin in Pulmonary Lymphangioleiomyomatosis (LAM) Tumor Cells

status: Public on Jan 15 2022

city: New York

first: Uchenna

last: Unachukwu

state: New York

address: 630 West 168th Street, P&S 7-430

department: Anesthesiology

institute: Columbia University Medical Center

summary: We report results of RNA sequencing analysis of serum starved pulmonary LAM tumor cells comparatively treated for 24hrs at 37C and 5% CO2 with rapamycin (0.05uM and 1uM) and tyrosine kinase inhibitor (TKI) imatinib (1uM, 5uM, and 10uM). Experiments were done in duplicates per drug concentration. This study was performed to investigate the biological mechanisms underlying superior cytocidal capabilities of the TKI over FDA-approved rapamycin by inhibiting receptor tyrosine kinases on mesenchymal tumorigenic cells in Tuberous Sclerosis and Lymphangioleiomyomatosis (LAM) diseases. Total RNA isolates (RIN>8.0) were sequenced on an illumina Novaseq6000 platform at 100 base pairs to a depth of 20 milllion paired end reads. Real-Time Analysis was used for base callling converted to fastq format with bcl2fastq2. Pseudoalignment of RNA-seq reads to a kallisto index was created from human reference genome NCBI/GRCh38.p13. Differential expression was resolved using Sleuth in R and signaling pathway analysis was performed using Ingenuity Pathway Analysis (IPA). Results reveal differential inactivation of the Cell Cycle: G2/M DNA Damage Checkpoint Regulation SIgnaling Pathway only in pulmonary LAM tumor cells treated with 10uM imatinib concentration.We further determined that increasing imatinib conentrations from 1uM to 10uM induced endoplasmic reticulum inositol triphosphate receptor (IP3R) subtype switching from type I to type III typically associated with differential ER calcium efflux and apoptosis.

overall_design: Comparing total RNA profiles of pulmonary LAM tumor cells treated with Rapamycin vs. Imatinib

first: Jeanine

last: D'Armiento


title: Predicting sepsis severity at first clinical presentation: the role of endotypes and mechanistic signatures

status: Public on Jan 10 2022

city: Vancouver

first: Robert

middle: EW

last: Hancock

state: BC

address: 2259 Lower Mall Research Station

department: Microbiology and Immunology

institute: University of British Columbia

summary: Identifying at first clinical presentation gene expression signatures that predict subsequent severity will allow clinicians to identify the most at risk groups of patients, and also enable appropriate antibiotic use. Accordingly, we characterized the blood immune profiles of patients with early/pre-sepsis to identify signatures reflecting disease severity, organ dysfunction, mortality, and specific endotypes/mechanisms.

overall_design: Whole blood RNA-seq and clinical data was collected from 348 patients from four emergency rooms and one intensive care unit.

first: Arjun

last: Baghela


title: Comparative RNA sequencing identifies superior cytocidal mechanisms of imatinib over rapamycin in UMB1949 renal angiomyolipoma cells

summary: We report results of RNA sequencing analysis of serum starved UMB1949 renal angiomyolipoma (AML) cells comparatively treated for 24hrs at 37C and 5% CO2 with rapamycin (0.05uM and 1uM) and tyrosine kinase inhibitor (TKI) imatinib (1uM and 10uM). Experiments were done in triplicates per drug concentration. This study was performed to investigate the biological mechanisms underlying superior cytocidal capabilities of the TKI over FDA-approved rapamycin by inhibiting receptor tyrosine kinases on mesenchymal tumorigenic cells in Tuberous Sclerosis and Lymphangioleiomyomatosis (LAM) diseases. Total RNA isolates (RIN>8.0) were sequenced on an illumina Novaseq6000 platform at 100 base pairs to a depth of 30 milllion single end reads. Real-Time Analysis was used for base callling converted to fastq format with bcl2fastq2. Pseudoalignment of RNA-seq reads to a kallisto index was created from human reference genome NCBI/GRCh38.p13. Reads were also mapped to this reference genome using STAR (2.5.2b) and featureCounts (v1.5.0-p3) for results comparison. Differential expression was resolved using Sleuth and DESeq2 in R and signaling pathway analysis was performed using Ingenuity Pathway Analysis (IPA). Results reveal differential inactivation of the GPVI pathway and key cell survival and viability genes only in renal AML cells treated with imatinib conentrations.We further determined that this TKI differentially induced ER calcium efflux that disrupted mitochondrial permeability leading to increased cytosolic cytochrome C, caspase 3 activation and apoptosis.

overall_design: Comparing total RNA profiles of renal angiomyolipoma cells treated with Rapamycin vs. Imatinib


title: KLF2 and KLF4 in heart and lung endothelial cell transcriptional dynamics [ATAC-seq]

first: Mukesh

last: Jain

last: Sweet

first: Vinesh

last: Vinayachandran

first: Roshan

last: Padmanabhan


title: RNA-Seq of E. coli DY330 in different growth phases

status: Public on Jan 01 2022

city: Seattle

first: Dmitry

last: Sutormin

address: 401 Terry Ave N

institute: Institute for Systems Biology

summary: To quantify the transcription level of genes for Escherichia coli DY330 in different growth phases a series of RNA-Seq experiments was performed.

overall_design: Total RNA was extracted and sequenced from E. coli DY330 culture growing in LB medium at different time-points after starter culture inoculation: 2 h after the starter inoculation (OD600~0.6, exponential phase culture); 6 h after the starter inoculation (OD600~6, exponential-to-stationary phase transition culture); 14 h after the starter inoculation (OD600~10, stationary phase culture). For each condition 3 biological replicates were processed and sequenced.


title: Regulation of Chromatin Looping by CTCF and Cohesin

status: Public on Dec 31 2021

city: Berkeley

first: Xavier

last: Darzacq

state: CA

address: 475D Li Ka Shing Center

department: Molecular and Cell Biology

institute: University of California, Berkeley

summary: As part of a study to understand the dynamics of chromatin looping and its regulation by CTCF and cohesin, we have determined the genome-wide binding profiles of CTCF and cohesin (Smc1a subunit) in a genome-edited mouse Embryonic Stem Cell (mESC) line referred to as clone C65. We have also performed 3D genome mapping using Micro-C in another genome-edited mESC line referred to as clone C36.

overall_design: We performed Micro-C in the mESC clone C36 (5 replicates) and ChIP-seq in the mESC clone C65 (input, normal rabbit IgG, rabbit anti-CTCF and rabbit anti-Smc1a antibodies, single replicates).

first: Ander

last: Hansen

first: Tsung-Han

last: Hsieh

first: Claudia

last: Cattoglio

first: Michele

last: Gabriele

first: Asmita

last: Jha

first: Hugo

last: Brandao

first: Leonid

last: Mirny

first: Simon

last: Grosse-Holz

first: Christoph

last: Zechner

first: Gina

last: Dailey


title: Regulation of alternative splicing by C9ORF78, a novel BRR2 interactor II

city: Berlin

first: Marco

last: Preussner

address: Takustrasse 6

institute: FU berlin

summary: The RNA helicase BRR2 (SNRNP200) is one of the key remodeling factors of the spliceosome. Here we show its direct interaction with C9ORF78, a poorly characterized protein predicted to be largely intrinsically disordered. We present cryo-EM structures showing how C9ORF78 and the spliceosomal B-complex protein FBP21 wrap around the C-terminal helicase cassette of BRR2 and that binding of the two proteins is mutually exclusive. C9ORF78 associates with the spliceosome, as we confirm via proteomics and RNA UV-crosslinking. An siRNA mediated C9ORF78 knockdown reveals changes in alternative splicing of specific target pre-mRNAs, which in part depend on its interaction with BRR2. In particular, C9ORF78 regulates a substantial number of alternative 3’ splice sites, which might be facilitated through an additional interaction with human PRP22 (DHX8).

overall_design: HEK293T cells were transfected either with empty vector, C9ORF78WT or C9ORF78mut and 2h lather either with a CTRL siRNA ( empty vector C) or an siRNA targeting C9orf78 (empty vector S, C9ORF78WT W or C9ORF78mut M); 72h after transfection RNA was extracted and analyzed by RNA-Seq.

first: Florian

last: Heyd

first: Alexandra

last: Bergfort

first: Markus

middle: C

last: Wahl


title: Genetic and genomic analysis of chronic nicotine treatment and withdrawal in the mouse

status: Public on Jan 03 2022

city: Richmond

first: Michael

last: Miles

state: VA

department: Pharmacology and Toxicology

institute: Virginia Commonwealth Univ.

summary: C57BL/6J and DBA/2J mice were delivered (-)-Nicotine hydrogen tartrate [(-)-1-methyl-2-(3- pyridyl) pyrrolidine (þ)-bitartrate] in 0.9% sodium chloride solution by osmotic minipump for 14 days. Mice in the chronic cohort were delivered nicotine up to moment of sacrifice. Mice in the withdrawal cohort had the minipumps surgically removed 24 hours before sacrifice. Nucleus accumbens tissue was dissected and snap frozen in liquid nitrogen. RNA was then extracted and hybridized to Affymetrix Mouse Transcriptome 1.0 arrays for transcriptome quantification.

overall_design: Affymetrix MTA 1.0 arrays were used to determine the transcriptomic effect of chronic nicotine delivered by minipump, or nicotine withdrawal, in the nucleus accumbens of C57BL/6J or DBA/2J mice.

first: Maren

middle: L

last: Smith

first: Kristin

last: Mignogna

first: Jo

last: Harenza

middle: F

first: M

middle: I

last: Damaj


title: Delayed processing of blood samples may impair the accuracy of mRNA-based biomarkers

status: Public on Dec 30 2021

city: Blacksburg

first: Fernando

middle: H

last: Biase

address: 175 West Campus Drive

department: School of Animal Sciences

institute: Virginia Tech

summary: Background: The transcriptome of peripheral white blood cells (PWBCs) contains valuable physiological information, thus making them a prime biological sample for investigating mRNA-based biomarkers. However, prolonged storage of whole blood samples can alter gene transcript abundance in PWBCs, compromising the results of biomarker discovery. Here, we designed an experiment to interrogate the impacts of delayed processing of whole blood samples on gene transcript abundance in PWBCs. We hypothesized that storing blood samples for 24 hours at 4°C would cause RNA degradation resulting in altered transcriptome profiles.  Results: We produced RNA-sequencing data for 30 samples collected from five estrus synchronized heifers (Bos taurus). We quantified transcript abundance for 12,414 protein-coding genes in PWBCs. Analysis of parameters of RNA quality revealed no statistically significant differences (P>0.05) between samples collected from the jugular vein and coccygeal vein, as well as among samples processed after 1, 3, 6, or 8 hours. However, samples processed after 24 hours of storage had a significantly lower RNA integrity number value (P=0.03) in comparison to those processed after one hour of storage. Next, we analyzed RNA-sequencing data between samples using those processed after one hour of storage as the baseline for comparison. Interestingly, evaluation of 3’/5’ bias revealed no statistically significant differences between genes with lower transcript abundance in samples stored for 24 hours relative to one hour. In addition, sequencing coverage of transcripts was similar between samples from the 24 hours and one-hour groups. We identified four and 515 genes with differential transcript abundance in samples processed after storage for eight and 24 hours, respectively, relative to samples processed after one hour.  Conclusions: The PWBCs respond to prolonged cold storage by increasing genes related to active chromatin compaction which in turn reduces gene transcription. This alteration in transcriptome profiles can impair accuracy of mRNA-based biomarkers. Therefore, blood samples collected for mRNA-based biomarker discovery should be refrigerated immediately and processed within six hours post sampling.

overall_design: Blood samples were collected via the jugular (n=5) and coccygeal (n=1) veins from beef heifers (n=5) who were enrolled in an estrus sychronization protocol. Samples were then stored for either 1, 3, 6, 8, or 24 hours prior to processing at 4°C to simulate transportation time. All samples collected from the coccygeal vein were processed  1 hour after collection.

first: Chace

last: Wilson


title: Hydropriming: the plant endophyte Pseudomonas argenenensis SA190 induces drought tolerance in plants via reprograming aquaporin expression and water use efficiency

city: Jeddah

first: Sabiha

last: Parween

address: Thuwal

department: Hirt lab

country: Saudi Arabia

institute: KAUST

summary: The objective of the study was to understand the mechanism of the interaction between Arabidopsis thaliana and SA190 under drought stress.

overall_design: Col-0 plants were either mock or with the bacteria SA190 under 1/2 MS or PEG

first: Khairiah

middle: M

last: Alwutayd

first: Anamika

last: Rawat

first: Arsheed

last: Sheikh

first: Ihsanullah

last: Daur

first: Mohamed

last: Ewis

first: Marilia

last: Almeida-Trapp

first: Alaguraj

last: Veluchamy

last: Karampelias

first: Rewaa

last: Jalal

first: Maged

last: Saad

first: Heribert

last: Hirt


title: Microbiota-derived pentanoate promotes differentiation of regulatory T cells via enhancing iron uptake in the intestine [scRNAseq_Treg]

first: Xing

last: Chang

summary: Iron deficiencies are the most common non-enteric syndromes observed in patients with inflammatory bowel diseases (IBD), yet little is known how iron deficiencies impact immune tolerance in the intestine. The goal of this study is to illuminate role of iron in colonic Treg homeostasis regulation.

overall_design: To investigate which subsets of Treg cells were strictly dependent on TfR1-mediated iron uptake, we conducted single-cell RNA seq (scRNA seq) analysis of total Treg cells (CD25+CD4+) isolated from heterozygous Tfrc fl/fl Foxp3 YFP-IRES-Cre mice ,TfR1-deficient cells (YFP+) and WT (YFP-) cells were separated in silico based on detection of the YFP-IRES-CRE transcript.

first: Lizhen

last: Zhu

first: Geng

last: Li


title: Antigen-Multimers: Specific, Sensitive, Precise, and Multifunctional High-Avidity CAR-Staining Reagents

status: Public on Dec 15 2021

city: Chicago

first: Jun

last: Huang

state: IL

address: Eckhardt, 5640 S Ellis Ave

department: Institute for Molecular Engineering

institute: University of Chicago

summary: Antigen-multimers are high-avidity CAR-staining reagents. We reported the specificity of antigen-multimers in distinguishing CAR-T from non-CAR-T cells from patient biospecimens by performing paired single-cell RNA- and TCR-sequencing on sorted CAR-T patient samples.

overall_design: Peripheral blood mononuclear cells from a patient with diffuse large B-cell lymphoma and treated with axicabtagene ciloleucel was taken at day 21 post-infusion. The sample was stained with anti-CD3 antibodies and CD19-tetramers (for CAR detection) for sorting. 12,000 sorted endogenous CD3+Tet- ("Endo-T") and 7,853 sorted therapeutic CD3+Tet+ ("CAR-T") cells were separately partitioned into droplets for single-cell paired RNA-seq and TCR-seq profiling.

first: Justin

last: Kline

first: Guoshuai

last: Cao

first: Yifei

last: Hu


title: A genetic program boosts mitochondrial function to power macrophage tissue invasion

city: Klosterneuburg

first: Daria

last: Siekhaus

address: Am Campus 1

department: Bertalanffy Building

country: Austria

institute: IST Austria

summary: This SuperSeries is composed of the SubSeries listed below. This includes RNA seq data on macrophages FACs sorted from wt or atos- (aka CG9005)- embryos (4 replicates); RNA seq of total RNA (input) from wt S2 cells or those treated with RNAi against porthos; andRNA seq of RNA obtained from the polysome fraction of wt S2 cells or those treated with RNAi against porthos. (3 replicates for each)

overall_design: Refer to individual Series


title: Genome-wide analysis of differentially expressed profiles of miRNAs, mRNAs, lncRNAs and circRNAs in F. nucleatum infection

status: Public on Dec 13 2021

city: Chengdu

first: Jieyu

last: Zhou

address: No. 14, section 3, Renmin South Road

department: Department of Periodontics

institute: West China Hospital of Stomatology, Sichuan University

summary: F. nucleatum is an opportunistic pathogen that usually colonize in oral cavity, thereby closely associated with the development of periodontitis.However, the immune regulation mechanism of F. nucleatum to macrophage’s function in disease progress has not been clearly elucidated.Long non-coding RNA (lncRNA) and circular RNA (circRNA) were discovered to play an important role in regulating occurrence and progression of many diseases and identified as effective biomarkers for diagnosis and prognosis of several diseases. In the present study, the expression profiles of mRNA, lncRNA and circRNA associated with F. nucleatum infection were investigated for the first time. The results revealed that the expressions of 375 mRNAs, 64 lncRNAs, and 180 circRNAs were altered during F. nucleatum infection. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) biological pathway analysis showed that the target genes were mainly involved in the MAPK signaling pathway, Toll-like receptor signaling pathway, NF-kappa B signaling pathway and apoptosis. Conclusions: The present study firstly provides the expression profiles of mRNAs, lncRNAs and circRNAs during F. nucleatum infection, and describes a novel perspective on the potential roles of lncRNAs and circRNAs underlying the pathogenesis mechanism of F. nucleatum infection.

overall_design: 3 control and 3 infected  macrophages were analyzed

first: Lin

last: Liu

first: Peiyao

last: Wu

first: Lei

last: Zhao

first: Yafei


title: Spatially resolved transcriptomics of high-grade serous ovarian carcinoma

status: Public on Dec 02 2021

city: Houston

first: Anil

middle: K.

last: Sood

address: 1515 Holcombe Blvd

institute: MD Anderson Cancer Center

summary: Bulk and single-cell RNA sequencing do not provide full characterization of tissue spatial diversity in cancer samples, and currently available in situ techniques (multiplex immunohistochemistry, imaging mass cytometry) allow for only limited analysis of a small number of targets. The current study represents the first comprehensive approach to spatial transcriptomics of high-grade serous ovarian carcinoma using intact tumor tissue. We selected a small cohort of patients with highly annotated high-grade serous ovarian carcinoma, categorized them by response to neoadjuvant chemotherapy (poor or excellent), and analyzed pre-treatment tumor tissue specimens. Our study uncovered extensive differences in tumor composition between the poor responders and excellent responders to chemotherapy, related to cell cluster organization and localization. This in-depth characterization of high-grade serous ovarian carcinoma tumor tissue from poor and excellent responders showed that spatial interactions between cell clusters may influence chemo-responsiveness more than cluster composition alone.

overall_design: High-grade serous ovarian carcinoma biopsy samples from 12 female patients were collected under a protocol approved by the Institutional Review Board of The University of Texas MD Anderson Cancer Center, and all patients provided written informed consent. The fresh frozen tumor tissues were obtained from the MD Anderson Gynecologic Tumor Bank. Patients underwent a standardized therapeutic approach following chemotherapy and surgery protocols established in the Department of Gynecology Oncology & Reproductive Medicine at MD Anderson. We selected six patients with poor response to NACT with carboplatin and paclitaxel and six patients with excellent response to NACT. The definition of poor response was stable or progressive disease after three to four cycles according to radiologic evaluation and/or suboptimal interval cytoreduction after NACT according to the Response Evaluation Criteria in Solid Tumors (RECIST 1.1). Excellent responders were those with complete response or only microscopic disease left at the time of interval surgery and/or pathologic analysis after interval surgery. We did not include replicates.

first: Elaine

last: Stur

first: Sara

last: Corvigno

first: Mingchu

last: Xu

first: Ken

last: Chen

first: Yukun

last: Tan

first: Sanghoon

last: lee

first: Jinsong

first: Emily

last: Ricoo

first: Daniel

last: Krushaar

first: Patricia

last: Castro

first: Jianhua

last: Zhang


title: Age-related changes in blood and spleen-derived immune cells in long and short lived mice strains

status: Public on Dec 01 2021

city: Farmington

first: Duygu

last: Ucar

state: Connecticut

address: 10 Discovery Drive

institute: The Jackson Laboratory

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


title: Spatiotemporal transcriptional atlas of lung adenocarcinoma from adenocarcinoma in situ to invasive carcinoma [ST]

status: Public on Nov 30 2021

city: Xi'an

first: Yue

last: Fan

address: Yanta West Road No.76

institute: Xi'an Jiaotong University

summary: To illuminate the evolutionary trajectory of LUAD from AIS to IAC, high-throughput scRNA-seq and ST data were generated and integrated to create a large-scale, single-cell spatiotemporal atlas of LUAD. We compiled a multi-omics atlas of the early-stage LUAD invasion process that reflects the heterogeneity of cancer cells, the competitive polyclonal origin of LUAD, signalling interactions between cancer cells and the TME, and the pseudo-chronological nature of LUAD invasion. The spatial distribution characteristics of LUAD cells revealed the spatial heterogeneity of LUAD and the mechanism of spatial immune escape in LUAD, which provides strong evidence supporting clinical diagnosis and surgical intervention at the single-cell level. The seurat object of ST data are available on https://drive.google.com/drive/folders/1dkGF4kKMbHSm04DKHg6P_y_iTD1pXCH8?usp=sharing.

overall_design: Nine resected samples (TD1-9, three each from AIS, MIA and IAC cases) from nine treatment-naïve patients were collected for droplet-based scRNA-seq. In parallel, six paired samples were subjected to ST

first: Tao

last: Jiang

first: Shiquan

last: Sun

first: Jianfei

last: Zhu