title: Single cell transcriptomics of fetal kidney and Wilms tumor nephrogenic progenitors

city: Los Angeles

first: Stefano

last: Da Sacco

state: CA

address: 4650 Sunset Blvd MS#35

institute: Children's Hospital Los Angeles

summary:
Purpose: Bulk transcriptomics analysis of Wilms tumor SIX2+CITED1+ cells to compare and identify unique nephron progenitor transcriptome profiling (RNA-seq) signature between unfavorable and favorable Wilms Tumors and against human fetal kidney
Methods: Wilms tumor and human fetal kidney samples were collected and transported on ice at 4°C in RPMI-1640 and a single cell suspensions were prepared following mechanical and enzymatic dissociation as previously publication. Enzymatic dissociation was performed with 125 U/ml collagenase I in RPMI-1640 at 37 °C for 35 min. The digested cells were then passed through a 100-μm cell strainer and a 40-μm cell strainer with washes of 1x PBS. The cell suspension was than centrifuged at 1500 rpm for 5 min and erythrocytes were eliminated using a red blood cell lysis kit.  WT SIX2+CITED1+ cells were isolated using SIX2-Cy5 and CITED1-Cy3 Smartflare RNA probes following manufacturer’s instructions and previous publication. Briefly, cells were incubated over night at 37 °C with both RNA probes diluted at 1:20 in PBS and 25ul/ml in RPMI-1640 supplemented with 5% FBS, and 0.2% antimicrobial agent Primocin. After 16-18 h, cells were dissociation using TrypLE 1x for 5 min, cells were centrifuged at 1500 rpm for 5 min and prepared for FACS. Freshly isolated SIX2+CITED1+ cells from a 16 WGA hFK, freshly isolated SIX2+CITED1+ cells from WT8 (favorable stage II Wilms’ Tumor), freshly digested xenograft derived from cultured SIX2+CITED1+ cells (Passage 6) isolated from WT8, freshly digested xenograft generated from freshly isolated SIX2+CITED1+ cells from WT8, and total cell population of WT8. Approximately 3,000 cells were captured on a 10x Chromium device using a 10X V2 Single Cell 3′ Solution kit.  All protocols were performed following manufacturer's instructions. Final library concentrations were determined using a Qubit high Sensitivity DNA assay Kit. Final sequencing libraries were analyzed on a Sequencing: HiSeq 4000, 2x150bp PE, and ~625M total reads/lane (QuickBiology) to determine the library size;  Approximately, 300 million reads per sample were sequenced
Results: Transcriptomics analysis of Wilms Tumor SIX2+CITED1+ cells in comparison to human fetal kidneys confirmed the nephrogenic signature of hFK-SIX2+CITED1+ and WT-SIX2+CITED1+ cells but highlighted differences in expression of pluripotency and self renewal-related genes.Trajectory inference analysis generated from sc-RNAseq data of SIX2+CITED1+ cells and cells dissociated from total WT (from where the SIX2+CITED1+ cells were isolated), suggests that SIX2+CITED1+ cells are the root cells that give rise to all the tumor cell types.
Conclusion: Our study represents the first single cell transcriptomic characterization of Wilms Tumor cancer stem cells (SIX2+CITED1+) against human fetal kidney SIX2+CITED1+ cells and against the total tumor and xenografts from cultured and fresh isolated SIX2+CITED1+ WT cells. Identifying that WT SIX2+CITED1+ cells arise early in nephrogenesis and have an expression pattern favoring proliferation over differentiation that overlaps considerably with the expression pattern of both the tumor of origin and with the expression pattern of WT they generate after grafting.

overall_design: Single cell transcriptomics of SIX2+CITED1+ cells from hFK and WT against total WT and xenografts generated from cultured and freshly isolated SIX2+CITED1+ cells.

last: Perin

first: Astgik

last: Petrosyan


title: Genome-wide binding of FOXD3 in mouse ESCs

status: Public on Apr 30 2023

city: San Francisco

first: Robert

last: Blelloch

address: 35 Medical Center Way

department: Urology

country: USA

institute: UCSF

type: Genome binding/occupancy profiling by high throughput sequencing

summary: We performed streptavidin pulldown sequencing of endogenously and exogenously Avi-tagged FOXD3 to determine genome-wide binding pattern of this transcription factor in asynchronous or cell cycle synchronized naive mouse ESCs.

overall_design: Endogenously Avi-tagged FOXD3 was compared to non-BirA expressing cells and exogeneously Avi-tagged FOXD3 was compared to non-induced cells.

first: Deniz

last: Gökbuget


title: Expression data of freshly isolated and sorted HSC populations from murine fetal liver or adult bone marrow [array]

city: Hannover

first: Dorit

last: Borchert

address: Carl-Neuberg-Str. 1

department: Pediatric Hematology and Oncology

country: Germany

institute: Hannover Medical School

summary:
We isolated murine fetal liver and murine adult bone marrow and FACS sorted LT-HSCs, ST-HSCs and MPPs.
We used global expression analysis by microarray to compare regulated genesets in different HSC populations in fetal and adult.

overall_design: We isolated murine fetal liver (from e13.5 embryos) and murine adult bone marrow, FACS sorted LT-HSCs, ST-HSCs and MPPs based on LSK Cd150 and Cd48 staining and isolated total RNA for expression analysis by microarray.

first: Dirk

last: Heckl


title: Transcriptional profiling of Treg cells obtained from lymph nodes of Foxp3GFP-Fth∆/∆ and control Foxp3GFP-Fth∆/∆ mice

city: Msida

first: Brendon

last: Scicluna

address: Msida campus

country: Malta

institute: University of Malta

type: Expression profiling by high throughput sequencing

summary: To gain further mechanistic insight on how ferritin H chain (FTH) impacts TREG cell lineage maintenance.

overall_design: We compared the gene expression profiles of (CD4+GFP+) TREG cells isolated from lymph nodes of Foxp3GFP-Fth∆/∆ (n=5) to control Foxp3GFP-Fth∆/∆ mice (n=5). Mice were bred and maintained under specific pathogen-free (SPF) conditions at the Instituto Gulbenkian de Ciência (IGC). Experimental protocols were approved by the Ethics Committee of the IGC, the “Órgão Responsável pelo Bem-estar dos Animais (ORBEA)” and the Portuguese National Entity (Direcção Geral de Alimentação e Veterinária). Experimental procedures were performed according to the Portuguese (Portaria n° 1005/92, Decreto-Lei n° 113/2013) and European (Directive 2010/63/EU) legislations, concerning housing, husbandry and animal welfare.

middle: P

first: Miguel

last: Soares


title: Oncofetal gene reactivation drives EZH2-mutant myeloid leukemia pathogenesis

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

overall_design: Refer to individual Series


title: Expression data from murine BM Tx transduced with BRSST gRNA +/- sgEzh2 [array]

summary:
Mice transplanted with BRSST (Bcor, Runx1, Sh2b3, Stag2, Tet2) sgRNAs in addition to the sgEzh2 develop myeloid leukemia with a significantly earlier onset compared to missing sgLuc.
We used global expression analysis by microarray to determine regulated gene programs after addition of the Ezh2 sgRNA.

overall_design: LSK cells expressing SpCas9 were transduced with the sgRNA combination and transplanted into irradiated C57Bl/6J mice. BM was harvested after development of a leukemia or after 6 month and used for RNA extraction.


title: Expression data from canine alveolar macrophages

city: Nanjing

first: Maoda

last: Pang

address: NO.1 Zhongling Street

country: China

institute: Nanjing Agricultural University

summary:
MicroRNAs (miRNAs), a class of noncoding RNAs measuring 18 to 23 nucleotides (nt) that play important regulatory roles in host-virus interactions. Avian-origin H3N2 canine influenza virus (CIV) has emerged as the most prevalent subtype among dogs in Asia since 2007. To evaluate the roles of host miRNAs in H3N2 CIV infection, here, miRNA profiles obtained from primary canine bronchiolar epithelial cells (CBECs) and canine alveolar macrophages (CAMCs) were compared between infected and mock-infected cells with the H3N2 CIV JS/10. It was found that cfa-miR-125b, cfa-miR-151 and cfa-miR-423a expressions were significantly decreased in CIV-infected canine primary cells. Bioinformatics prediction indicated that 5’ seed regions of three miRNAs are partially complementary to the mRNAs of nucleoprotein (NP) and non-structural protein 1 (NS1) of JS/10. As determined by virus titration, quantitative real-time PCR (qRT-PCR) and western blotting, overexpression of cfa-miR-125b and cfa-miR-151 inhibited CIV infection, whereas overexpression or inhibition of cfa-miR-423a inhibited this infection. These results indicated that CIV replication could be regulated by miRNAs from host cells infected with CIV. Our findings support the notion that cellular miRNAs can inhibit virus infection, help to elucidate the resistance of host cells to viral infection and to clarify the pathogenesis of H3N2 CIV.
We used microarrays to detail the global programme of gene expression of primary canine alveolar macrophages (CAMCs) compared between infected and mock-infected cells with the H3N2 canine influenza virus (CIV) JS/10.

overall_design: Total RNA was extracted from 1×10e6 cells of primary CAMCs infected and mock-infected with JS/10 for 24 h using TRIzol reagent. RNA samples were spectroscopically verified for purity, quality of the intact RNA without genomic DNA contamination was assessed using an Agilent 2100 Bioanalyzer. For infected and mock-infected CAMCs, an Affymetrix miRNA4.0 canine microRNA Microarray Kit (8×15 K) was used to profile the microRNA transcripts on the Affymetrix Technologies microRNA Platform. The probe in microarray chip is specifically designed for known canine miRNA sequences.

first: Xing

last: Xie

first: Yongjie

last: Liu


title: Genome-wide gene expression analysis of triple negative breast cancer tissue and matched normal tissue

city: Seoul

first: Jong Hoon

last: Park

address: Cheongpa-ro 47-gil 100, Yongsan-gu,

country: South Korea

institute: Sookmyung Women's university

summary: To identify specifically gene expression level in only TNBC subtype, we analyed mRNA microarray in 3 TNBC samples and matched normal samples.

overall_design: 3 TNBC vs. 3 normal breast tissue samples

first: Jong

middle: H

first: Ye

middle: S

last: Kim

first: Woosung

last: Cheong

first: Hyun

middle: K

last: Kong


title: Mouse ear tissue at 7 days post immunization

status: Public on Apr 29 2023

city: Silver Spring

first: Sreenivas

last: Gannavaram

state: MD

address: 10903 New Hampshire Ave

department: DETTD

institute: US FDA

summary:
Gene expression analysis using NanoString nCounter immunology panel for profiling among naïve controls and immunized treatment samples.
We explored the interplay between type-I IFNs and the development of host protective Th1 immunity in mice immunized with LmCen-/- parasites and challenged with L. donovani parasites and show that downregulation of IRF7 mediated production of IFN-α/β is critical for the induction of protective immunity.

overall_design: In this study, using transcriptomics, we present differential gene exression to evaluate early immune response conditions upon immunization.

first: Telly

last: Sepahpour

first: Derek

middle: D

last: Ireland


title: Mouse ear tissue at 21 days post immunization

summary:
Gene expression analysis using nCounter immunology panel for profiling among naïve controls and immunized treatment samples.
We explored the interplay between type-I IFNs and the development of host protective Th1 immunity in mice immunized with LmCen-/- parasites and challenged with L. donovani parasites and show that downregulation of IRF7 mediated production of IFN-α/β is critical for the induction of protective immunity.


title: Genome-wide maps of chromatin state from secondary murine BM Tx transduced with BRSST gRNA +/- sgEzh2 [ChIP-seq]

summary: To decipher the role of Ezh2 mutations in leukemia we transplanted mice secondarily with BRSST (Bcor, Runx1, Sh2b3, Stag2, Tet2) sgRNAs with or without sgEzh2 to observe development of myeloid leukemia. Whole BM was used for ChIP-Seq analysis of histone modifications.

overall_design: Examination of H3K27me3 and H3K4me3 in whole BM of transplanted, leukemic mice.


title: Effects of RELA and RELB in spheroid and adherent ovarian cancer

status: Public on Apr 28 2023

city: BETHESDA

first: Christina

last: Annunziata

state: Maryland (MD)

address: 10 center drive, Building 10, room 12N226

institute: National Cancer Institute

type: Non-coding RNA profiling by high throughput sequencing

summary: Purpose: To understand the role of NF-kB signaling in tumor-initiating cell (TIC) and non-TIC populations in ovarian cancer. Methods: OV90 cells with inducible shRNA against RelA and RelB, and a non-targeting shRNA control were induced by doxycycline treatment and were grown in adherent (non-TIC) or spheroid (TIC) conditions. Total RNA was extracted from each condtion and RNAseq was performed and analysed for differential gene expression between the conditions.

overall_design: Comparison of OV90 cells grown in adherent or spheroid conditions, and the effect of silencing RelA or RelB in each condition.

first: Carrie

last: House

middle: M

first: Nathan

last: Wong

first: Yongmei

last: Zhao


title: Mouse ear tissue


title: RNA-seq of AMFR mutant human in vitro differentiated neural stem cells

city: Rotterdam

first: Tahsin Stefan

last: Barakat

state: South Holland

address: Dr. Molewaterplein 40

department: Clinical Genetics

country: Netherlands

institute: The Erasmus University Medical Center

summary: We report transcriptome analysis of human in vitro differentiated neural stem cells (derived from H9 human embryonic stem cells), comparing wild type and AMFR homozygous knock-out mutant cells. To model a novel genetic disorder caused by bi-allelic loss-of-function variants in AMFR and to study the effects on the global transcriptome caused by the absence of AMFR, we generated knock-out mutant cells, by CRISPR-Cas9 genome editing, targetting exon 4. This resulted in frame shift mutations with absence of full length AMFR confirmed by Western blotting. Knockout mutant and wild type cells were then compared to determine differentially expressed genes.

overall_design: For the RNA-seq experiments, two independent wild type cultures, three independent clones harboring the  homozygous AMFR mutation were used. All cell lines were cultured in two technical replicates, and sequenced at passage 5 of NSC differentiation.

first: Tahsin


title: Mouse ear tissue at 2 days post immunization


title: An ERK-dependent molecular switch antagonizes fibrosis and promotes regeneration in spiny mice (Acomys)

city: Utrecht

first: Antonio

last: Tomasso

address: Uppsalalaan 8

institute: Hubrecht Institute

summary: Although most mammals heal injured tissues and organs with scarring, spiny mice (Acomys) naturally regenerate skin and complex musculoskeletal tissues. Currently, the core signaling pathways driving mammalian tissue regeneration are poorly characterized. Here, we show that, while immediate ERK activation is a shared feature of scarring (Mus) and regenerating (Acomys) injuries, ERK activity is only sustained at high levels during complex tissue regeneration. Following ERK inhibition, ear punch regeneration in Acomys shifted towards fibrotic repair. Using scRNA-seq, we identified ERK-responsive cell types. Loss- and gain-of-function experiments prompted us to uncover FGF and ErbB signaling as upstream ERK regulators of regeneration. Strikingly, the ectopic activation of ERK in scar-prone injuries induced a pro-regenerative response, including cell proliferation, extracellular matrix remodeling and hair follicle neogenesis. Our data detail an important distinction in ERK activity between regenerating and poorly regenerating adult mammals and open avenues to redirect fibrotic repair towards regenerative healing.

overall_design: The pERK inhibitor and relative DMSO control were injected from D12 to D15.

first: Tim

last: Koopmans

first: Philip

last: Lijnzaad

first: Kerstin

last: Bartscherer

first: Ashley

middle: W

last: Seifert


title: An ERK-dependent molecular switch antagonizes fibrosis and promotes  regeneration in spiny mice (Acomys)

city: UTRECHT

first: PHILIP

last: LIJNZAAD

state: Utrecht

address: HEIDELBERGLAAN 25

department: Single Cell Facility

institute: Princess Maxima Center for Pediatric Oncology

summary: Although most mammals heal injured tissues and organs with scarring, spiny mice (Acomys) naturally regenerate skin and complex musculoskeletal tissues. Currently, the core signaling pathways driving mammalian tissue regeneration are poorly characterized. Here, we show that, while immediate ERK activation is a shared feature of scarring (Mus) and regenerating (Acomys) injuries, ERK activity is only sustained during complex tissue regeneration. Following ERK inhibition, regeneration in Acomys shifted towards a fibrotic repair. Using scRNA-seq, we uncovered that MAPK/ERK signaling acts in a cell type specific manner to direct regenerative healing. Loss- and gain-of-function experiments prompted us to identify FGF and ErbB signaling as upstream ERK regulators of regeneration. By ectopically activating ERK in Mus injuries, a pro- regenerative response was induced, including cell proliferation, extracellular matrix remodeling and hair follicle neogenesis. Our data provide new insights into why some mammals regenerate better than others and open avenues to redirect fibrotic repair towards regenerative healing.

sample_organism:
Acomys cahirinus
Mus musculus

platform_organism:
Acomys cahirinus
Mus musculus

overall_design: pERK, FGFR and ErbB2 inhibitors were injected from D12 to D15, similarly to DMSO control;  micro-beads soaked with either PBS, recombinant FGF-2/NRG-1 were implanted locally at D10.


title: Age-associated DNA methylation changes in Xenopus frogs, and Targeted bisulfite sequencing to profile age-associated DNA methylation changes in Xenopus frogs

city: Parma

first: Marco

last: Morselli

state: Parma

address: Parco Area delle Scienze, 23/A

country: Italy

institute: University of Parma

type: Methylation profiling by high throughput sequencing


title: Targeted bisulfite sequencing to profile age-associated DNA methylation changes in Xenopus frogs

summary: Here we present clear patterns of age-associated changes in DNA methylation in the aquatic vertebrate species Xenopus tropicalis. We selected approximately 3500 sites highly correlated with age from WGBS data from 9 frogs of 3 different age groups (young, approx. 1 year old; mature, approx. 5 years old; old, approx. 9 years old - GSE221656) and designed probes for the development of cost effective targeted bisulfite sequencing (TBSeq) assay. Here, we present the TBSeq assay in sixteen different frogs as a pilot experiment to validate our previous findings.

overall_design: We have previously generated whole genome bisulfite sequencing (WGBS) profiles in nine Xenopus tropicalis samples representing young, mature and old adults to study how DNA methylation relates to aging in frogs (GSE221656). Here, we performed a pilot Targeted Bisulfite Sequencing (TBSeq) experiment to confirm the results in a different cohort.

first: Ronan

last: Bennett

first: Nikko

middle: I

last: Shaidani

first: Marko

last: Horb

first: Leonid

last: Peshkin

first: Matteo

last: Pellegrini


title: Age-associated DNA methylation changes in Xenopus frogs

summary: Here we present clear patterns of age-associated changes in DNA methylation in the aquatic vetebrate species Xenopus tropicalis. We generated nine whole-genome bisulfite sequencing (WGBS) datasets from three distinct age groups (young, approx. 1 year old; mature, approx. 5 years old; old, approx. 9 years old) to characterize the gene- and chromosome-scale changes.

overall_design: We have generated whole genome bisulfite sequencing (WGBS) profiles in nine Xenopus tropicalis samples representing young, mature and old adults to study how DNA methylation relates to aging in frogs.

first: Nikko-Ideen


title: RNA-seq of mutant delta POX03070 and delta PoxCxrA after transfer from glucose medium to Avicel medium for 24 hours

city: Nanning

first: Di

last: Tian

address: DaXue east road

institute: College of Life Science and Technology,GuangXi university

summary: To explore the effect of  POX03070 on transcription levels of plant-biomass-degrading enzyme-encoding genes in Penicillium oxalicum,and the interaction between POX03070 and PoxCxrA in transcriptional level.

overall_design: Mutant delta POX03070, delta PoxCxrA and the parental strain delta ku70 with three replicates for each strain

first: Li-Xiang

last: Mo

first: Shuai


title: A multiple super-enhancer region establishes inter-TAD interactions and controls Hoxa function in cranial neural crest [Hi-C]

city: Basel

first: Filippo

middle: M.

last: RIJLI

address: Maulbeerstrasse 66

country: Switzerland

institute: Friedrich Miescher Institute for Biomedical Research

summary: Enhancer-promoter interactions preferentially occur within boundary-insulated topologically associating domains (TADs), limiting inter-TAD interactions. Enhancer clusters in linear proximity, termed super-enhancers (SEs), ensure high target gene expression levels. Little is known about SE topological regulatory impact during craniofacial development. Here, we identified 2232 genome-wide putative SEs in mouse cranial neural crest cells (CNCCs), 147 of which target genes establishing CNCC positional identity during face formation. In second pharyngeal arch (PA2) CNCCs, a multiple SE-containing region, partitioned into Hoxa Inter-TAD Regulatory Element 1 and 2 (HIRE1 and HIRE2), establishes long-range inter-TAD interactions selectively with Hoxa2, that is required for external and middle ear structures. HIRE2 deletion in a Hoxa2 haploinsufficient background results in microtia. HIRE1 deletion phenocopies the full homeotic Hoxa2 knockout phenotype and induces PA3 and PA4 CNCC abnormalities correlating with Hoxa2 and Hoxa3 transcriptional downregulation. Thus, SEs can overcome TAD insulation and regulate anterior Hoxa gene collinear expression in a CNCC subpopulation-specific manner during craniofacial development.

overall_design:
Hi-C analysis of the 3D chromatin structure in Md, PA2 and the Pinna at developmental stages E10.5, E12.5 and E14.5
Hi-C analysis of the 3D chromatin structure in mESCs

first: Sandra

last: Keßler

first: Maryline

last: Minoux

first: Onkar

last: Joshi

first: Yousra

last: Ben Zouari

first: Sebastien

last: Ducret

first: Fiona

last: Ross

first: Nathalie

last: Vilain

first: Adwait

last: Salvi

first: Joachim

last: Wolff

first: Hubertus

last: Kohler

first: Michael

last: Stadler

last: Rijli


title: NSC-derived exosomes enhance therapeutic effects of NSC transplantation on cerebral ischemia in mice

status: Public on Apr 26 2023

city: wuhan

first: Meng

last: Cai

state: hubei

address: Building 5, Precision Medicine Industrial Base, East Lake New Technology Development Zone

institute: iregene

summary: Transplantation of neural stem cells (NSCs) has been proved to promote functional rehabilitation of brain lesions including ischemic stroke. However, the therapeutic effects of NSC transplantation is limited by the low survival and differentiation rates of NSCs due to the harsh environment in the brain after ischemic stroke. Here, we employed NSCs derived from human induced pluripotent stem cells (iPSCs) together with exosomes extracted from NSCs to treat cerebral ischemia induced by middle cerebral artery occlusion/reperfusion (MCAO/R) in mice. The results showed that NSC-derived exosomes significantly reduced the inflammatory response, alleviated oxidative stress after NSC transplantation, and facilitated NSCs differentiation in vivo. The combination of NSCs with exosomes ameliorated the injury of brain tissue including cerebral infarct, neuronal death and glial scarring, and promoted the motor function recovery. To explore the underlying mechanisms, we analyzed the miRNA profiles of NSC-derived exosomes and the potential downstream genes. Our study provided the rationale for the clinical application of NSC-derived exosomes as a supportive adjuvant for NSC transplantation after stroke.

overall_design: Eighty-eight MCAO/R mice were randomly divided into 4 groups at 7 days post operation, and twelve mice with low body weight (less than 15g) were excluded. Mice were anesthetized and placed in a mouse stereoscopic apparatus (RWD, China). The skull was drilled to make a burr hole above the lateral ventricle (AP+0, ML-1, DV-2.25 mm) for NSCs and exosomes injection. NSCs were genetically labeled with tdTomato for cell tracking. The five groups were treated as follows: Model (MCAO/R mice treated with 5 μL PBS), Exo (MCAO/R mice treated with 10 μg exosomes in 5 μL PBS), NSC (MCAO/R mice treated with 5×105 NSCs in 5 μL PBS), NSC+Exo (MCAO/R mice treated with 5×105 NSCs combine with 10 μg exosomes in 5 μL PBS) and Sham (fifteen mice with sham operation not treated). We did not perform high-throughput sequencing of all samples that participated in animal experiments.

first: Jun

last: Wei

first: Weibing

last: Mao

first: Ruolin

last: Zhang


title: Transcriptomic and Metabolomic Studies Reveal That Toll-like Receptor 2 Has a Role in Glucose-Related Metabolism in Unchallenged Zebrafish Larvae (Danio rerio)

status: Public on Apr 27 2023

city: Leiden

first: Herman

middle: Pieter

last: Spaink

address: Einsteinweg 55

department: Institute of Biology

institute: Leiden University

summary:
Toll-like receptors (TLRs) have been implicated in the regulation of various metabolism pathways, in addition to their function in innate immunity. Here, we investigate the metabolic function of TLR2 in a larval zebrafish system. We studied larvae from a tlr2 mutant and the wild type sibling controls in an unchallenged normal developmental condition using transcriptomic and metabolomic analyses methods. RNAseq was used to evaluate transcriptomic differences between the tlr2 mutant and wild-type control zebrafish larvae and found a signature set of 149 genes to be significantly altered in gene expression. The expression level of several genes was confirmed by qPCR analyses. Gene set enrichment analysis (GSEA) revealed differential enrichment of genes between the two genotypes related to valine, leucine, and isoleucine degradation and glycolysis and gluconeogenesis. Using 1H nuclear magnetic resonance (NMR) metabolomics, we found that glucose and various metabolites related with glucose metabolism were present at higher levels in the tlr2 mutant. Furthermore, we confirmed that the glucose level is higher in tlr2 mutants by using a fluorometric assay. Therefore, we have shown that TLR2, in addition to its function in immunity, has a function in controlling metabolism during vertebrate development. The functions are associated with transcriptional regulation of various enzymes involved in glucose metabolism that could explain the different levels of glucose, lactate, succinate, and malate in larvae of a tlr2 mutant.
RNAseq was used to evaluate transcriptomic differences between the tlr2 mutant and wild-type control zebrafish larvae and found a signature set of 149 genes to be significantly altered in gene expression

overall_design: Zebrafish larvae at 5 dpf from line tlr2 mutant and wild-type control were collected for RNAseq

first: Wanbin

last: Hu


title: Spatiotemporal multi-omics decoding of the developing human spinal cord I

status: Public on Apr 25 2023

city: Solna

first: Paulo

last: Czarnewski

address: Tomtebodavägen 23b

country: Sweden

institute: KTH

summary: The human spinal cord contains diverse cell types, governed by a series of spatiotemporal events for tissue assembly and functions. However, the regulation of cell fate specification in the human developing spinal cord remains largely unknown.  By performing single-cell and spatial multi-omics methods, we integrated the datasets and created a comprehensive human developmental atlas of the first trimester spinal cord. Unexpectedly, we discovered unique events in human spinal cord development, including early loss of active neural stem cells, simultaneous occurrence of neurogenesis and gliogenesis, and distinct spatiotemporal genetic regulations of fate choices. We also identified distinct regulations of cancer stem cells in ependymomas from our atlas. Thus, we demonstrate spatiotemporal genetic regulation of human spinal cord development and its potential to understand novel disease mechanisms.

overall_design:
The human embryos and fetuses were transported immediately from the clinics to the dissection lab in Hibernation medium (Gibco A13706-01). After staging, spinal cords were removed from the intact tissue in ice cold saline (Fresenius Kabi, B306443/01). W5-7 spinal cords were kept as one piece, and W8-12 spinal cords were dissected into cervical, thoracic, and lumbar regions. Spinal cords were then kept in ice cold hibrination medium or snap frozen in OCT for scRNA-seq immediately, or cryosectioning in the future respectively.
--------------------------
Authors state "However, raw reads from our cohort are considered sensitive and protected by GDPR regulations, and will therefore be uploaded to Swedish federated EGA."

first: Xiaofei

last: Li

first: Erik

last: Sundström


title: β-catenin programs a tissue-specific epigenetic vulnerability in aggressive adrenocortical carcinoma (ChIP-seq)

city: Ann Arbor

first: Antonio

middle: Marcondes

last: Lerario

state: MI

address: 109 Zina Pitcher Place, 1528 BSRB

department: MEND

institute: University of Michigan

summary: Adrenocortical carcinoma (ACC) is a rare cancer in which tissue-specific differentiation is paradoxically associated with dismal outcomes. The differentiated ACC subtype CIMP-high is prevalent, incurable, and routinely fatal. CIMP-high ACC possess abnormal DNA methylation and frequent β-catenin activating mutations. Here, we demonstrate that this differentiated state is maintained by a balance between nuclear, tissue-specific β-catenin-containing complexes and the ACC epigenome. On chromatin, β-catenin binds master adrenal transcription factor SF1 and hijacks the adrenocortical super-enhancer landscape to maintain differentiation. Off chromatin, β-catenin binds histone methyltransferase EZH2, which is redistributed by the CIMP-high DNA methylation signature. SF1/β-catenin and EZH2/β-catenin complexes exist in normal adrenals and are selected for through all phases of ACC evolution. EZH2 inhibition in CIMP-high ACC favors EZH2/β-catenin assembly and purges SF1/β-catenin from chromatin, erasing differentiation and restraining cancer growth in vitro and in vivo. Our studies illustrate how tissue-specific programs shape oncogene selection, surreptitiously encoding targetable therapeutic vulnerabilities.

sample_organism:
Drosophila melanogaster
Homo sapiens

platform_organism:
Drosophila melanogaster
Homo sapiens

overall_design: Human ACC cell line NCI-H295R was treated with vehicle DMSO (baseline) or EZH2 inhibitor EPZ-6438 (EZH2i) to evaluate the impact of EZH2 inhibition on the ACC epigenome. At endpoint, cells were harvested for ChIP-seq using antibodies against the following epitopes: H3K27ac, H3K27me3, EZH2, β-catenin, steroidogenic factor 1 (SF1). We used Drosophila melanogaster chromatin as a spike-in control to enable quantitative comparisons across ChIP-seq samples.

first: Dipika

middle: R

last: Mohan

first: Gary

last: Hammer


title: β-catenin programs a tissue-specific epigenetic vulnerability in aggressive adrenocortical carcinoma (RNA-seq)

overall_design:
Human ACC cell line NCI-H295R was treated with vehicle DMSO (baseline), Forskolin (FSK), EZH2 inhibitor EPZ-6438 (EZH2i), or CBP inhibitor PRI-724 (CBPi) to evaluate the impact on the ACC transcriptome by RNA-seq. Libraries are named as follows:

s_138221	NCI-H295R, baseline
s_138222	NCI-H295R, baseline
s_138223	NCI-H295R, baseline
s_138224	NCI-H295R, EZH2i
s_138225	NCI-H295R, EZH2i
s_138226	NCI-H295R, EZH2i
s_138227	NCI-H295R, CBPi
s_138228	NCI-H295R, CBPi
s_138229	NCI-H295R, CBPi
s_138230	NCI-H295R, FSK
s_138231	NCI-H295R, FSK
s_138232	NCI-H295R, FSK


title: β-catenin programs a tissue-specific epigenetic vulnerability in aggressive adrenocortical carcinoma (DNA methylation array)

overall_design: Human ACC cell line NCI-H295R was treated with vehicle DMSO (baseline) or EZH2 inhibitor EPZ-6438 (EZH2i) to evaluate the impact of EZH2 inhibition on the ACC epigenome. At endpoint, cells were harvested for DNA methylation array profiling by Illumina EPIC array. Alternatively, human adrenal glands were microdissected for zona fasciculata (ZF), zona reticularis (ZR), or fetal zone (FZ). After microdissection, DNA was extracted and submitted for methylation profiling by Illumina EPIC array. Donors for ZF and ZR samples are identified by number at the end of title (e.g. Donor 1 provided ZF1 and ZR1, Donor 3 provided ZF3 and ZR3 and so on). Fetal zone samples came from independent donors.

first: Juilee

last: Rege

first: William

middle: E

last: Rainey


title: β-catenin programs a tissue-specific epigenetic vulnerability in aggressive adrenocortical carcinoma (ATAC-seq)

overall_design:
Human ACC cell line NCI-H295R was treated with vehicle DMSO (baseline), Forskolin (FSK), EZH2 inhibitor EPZ-6438 (EZH2i), or CBP inhibitor PRI-724 (CBPi) to evaluate the impact on the ACC epigenome by ATAC-seq. Libraries are named as follows:

27-CLP-3	NCI-H295R, baseline
27-CLP-4	NCI-H295R, baseline
27-CLP-5	NCI-H295R, EZH2i
27-CLP-6	NCI-H295R, EZH2i
27-CLP-7	NCI-H295R, CBPi
27-CLP-8	NCI-H295R, CBPi
27-CLP-9	NCI-H295R, FSK
27-CLP-10	NCI-H295R, FSK

first: Christopher

last: LaPensee


title: Dissecting molecular pathways of neuropathology of PHTS by transcriptomics and proteomics

city: Hong Kong

first: Andrew

last: Chan

address: Room 407, 4/F, Lo Kwee-Seong Integrated Biomedical Sciences Building,, Area 39, The Chinese University of Hong Kong

department: School of Biomedical Science

country: Hong Kong

institute: The Chinese University of Hong Kong

summary:
PTEN Harmatoma Tumor Syndrome is a collection of clinical diagnosis with patients harbouring germline mutation in the PTEN gene. Most affected individuals have extreme macrocephaly and autism spectrum disorders were diagnosed in ~10% of the patients.  However, the underpinning molecular mechanisms are not fully defined. The aim of this study is to compare the transcriptomic profiles of somatosensory cortices from Pten+/- and wild-type littermates (C57Bl6/J) of female and male at P30 and P42, primary neural cells, neuroprogenitor cells (NPCs), cortical astrocytes (PCA) and cortical neurons (PCN) from C57Bl6/J mice, with wild-type (WT as control for Pten+/- or CTRL as control for Nes-KO), heterozygous (Pten+/-)and complete knockout of Pten (Nes-KO). The study included performing RNA sequencing of these tissues and neural cells and integrating the data with human autism candidate genes (SFARI), and enrichment with GWAS genes for neurological diseases and traits.
Methods: RNA sequencing of the somatosensory cortices and primary neural cells: Somatosensory cortices are cut from female and male mice at P30 and P42. NPCs are from E12.5 embryons. PCNs are from E15.5 embryos. PCAs are from P0 or P2 pups. Samples were lysed in TRIzol and RNA was extracted with chloroform/isopropanol and ethanol. Poly-A eniched RNA was used for library contruction.
Results: We identified widespread signature genes in different samples, with enhanced immune response and oligodendrocyte development in somatosensory cortex,  suppressed immediate early response genes in Pten+/- neurons, upregulated cilium components in astrocyte and downregulated inhibitory neurons in Pten knockout neural cells through RNA sequencing, which further enriched in GWAS genes of schizophrenia.
Conclusion: Our study represents the first detailed comprehensive RNA-sequencing of somatosensory cortex and individual types of neural cells of transgenic mice with Pten heterozygous and homozygous knockout. The result suggested Pten effects on dysregulated immune response, immediately early response, cilium function and  interneurons development which would direct further molecular studies on neuropathologenic mechanisms for PHTS.

overall_design:
All individual groups of somatosensory cortex and cell types with their control were from littermates, each genotype has 3 biological replicates, except Pten+/- group of P30M (which has 2 samples).
P30F (WT vs Pten+/-): 3x WT and 3x Pten(+/-), sequenced on Hiseq Xten platform with paired-end read at 150bp and 20M bp reads per sample.
P30M (WT vs Pten+/-): 3x WT and 2x Pten(+/-), sequenced on Hiseq Xten platform with paired-end read at 150bp and 20M bp reads per sample.
P42F (WT vs Pten+/-): 3x WT and 3x Pten(+/-), sequenced on Hiseq Xten platform with paired-end read at 150bp and 20M bp reads per sample.
P42M (WT vs Pten+/-): 3x WT and 3x Pten(+/-), sequenced on Hiseq Xten platform with paired-end read at 150bp and 20M bp reads per sample.
NPC (WT vs Pten+/-): 3x WT and 3x Pten(+/-), sequenced on Hiseq2500 platform with single read at 50bp and 20M bp reads per sample.
PCA (WT vs Pten+/-): 3x WT and 3x Pten(+/-), sequenced on Hiseq4000 platform with paired-end read at 150bp and 20M bp reads per sample.
PCN at DIV14 (WT vs Pten+/-): 3x WT and 3x Pten(+/-), sequenced on Hiseq4000 platform with paired-end read at 150bp and 20M bp reads per sample.
NPC (CTRL vs Nes-KO): 3x CTRL and 3x Nes-KO, sequenced on Hiseq4000 platform with paired-end read at 150bp and 13.3M bp reads per sample.
PCA (CTRL vs Nes-KO): 3x CTRL and 3x Nes-KO, sequenced on Hiseq2500 platform with paired-end read at 150bp and 20M bp reads per sample.
PCN at DIV14 (CTRL vs Nes-KO): 3x CTRL and 3x Nes-KO, sequenced on Hiseq2500 platform with paired-end read at 150bp and 20M bp reads per sample.

first: Stanley

last: Cheung

first: Jacinda

last: Kwok

first: Penelope

last: Or

first: Chi

last: Wong

first: Bo

last: Feng

first: Kwong

last: Choy

first: Raymond

middle: C

last: Chang

first: J

last: Burbach

first: Alfred

last: Cheng


title: An optimized approach for multiplexing single-cell ATAC-seq using oligonucleotide conjugated antibodies

city: College Station

first: Masako

last: Suzuki

state: TX

address: 498 Olsen Blvd, Norman E. Borlaug Building 202C

department: Nutrition

institute: Texas A&M University

overall_design: Bulk ATAC-seq was performed on mouse hematopoietic progenitor cell, HPC7.

first: Betelehem

last: Bera

first: Deyou

last: Zheng

first: Bernice

last: Morrow

first: John

last: Greally


title: Analyses to examine the effect of the iron chelator deferoxamine on 3T3-L1 pre-adipocyte cells

status: Public on Apr 23 2023

city: Maebashi

first: Tetsuro

last: Komatsu

address: 3-39-15 Showa-machi

country: Japan

institute: Gunma University

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

overall_design: Refer to individual Series


title: Cortical glia in SOD1(G93A) mice are subtly affected by ALS-like pathology

status: Public on Apr 21 2023

city: Vestec

first: Zuzana

last: Matusova

address: Prumyslova 595

department: Laboratory of Glial Biology and Omics Technologies

country: Czech Republic

institute: Institute of Biotechnology of the Czech Academy of Sciences

summary: The role of glia in amyotrophic lateral sclerosis (ALS) is undeniable. Their disease-related activity has been extensively studied in the spinal cord, but only partly in the brain. We present herein a comprehensive study of glia in the motor cortex of SOD1(G93A) mice – a widely used model of ALS. Using single-cell RNA sequencing (scRNA-seq) and immunohistochemistry, we inspected astrocytes, microglia and oligodendrocytes, in four stages of the disease, respecting the factor of sex. We report insignificant motor neuron loss in the cortex, and likewise, minimal changes of glia throughout the disease progression and regardless of sex. Pseudobulk and single-cell analyses revealed subtle disease-related transcriptional alterations at the end-stage in microglia and oligodendrocytes, which were supported by immunohistochemistry. Therefore, our data conclusively prove that the SOD1(G93A) mouse motor cortex does not recapitulate the disease in patients, and we recommend the use of a different model for future studies of the cortical ALS pathology.

overall_design:
Cerebral cortex of control (CTRL) and SOD1(G93A) mutant mice (SOD1) was isolated at four time points (1, 2, 3 and 4 months of age). Two males and two females were pooled per condition for preparation of cell suspension. The cell suspension was enriched for astrocytes, microglia and oligodendrocytes using FACS and was analysed by scRNA-seq (10X Genomics platform).
Please note that transgenic mice expressing high levels of human SOD1(G93A) (JAX Strain: 004435 C57BL/6J-Tg (SOD1*G93A)1Gur/J) and their non-carrier littermates are used in the study.

first: Tereza

last: Filipi

first: Pavel

last: Abaffy

first: Ondrej

last: Vanatko

first: Jana

last: Tureckova

first: Sarka

last: Benesova

first: Monika

last: Kubiskova

first: Denisa

last: Kirdajova

first: Jakub

last: Zahumensky

first: Lukas

last: Valihrach

first: Miroslava

last: Anderova


title: Whole genome bisulfite sequencing analysis to examine the effect of the iron chelator deferoxamine on DNA methylation levels in 3T3-L1 pre-adipocyte cells

summary: Adipocyte differentiation has been shown to require iron, but the underlying mechanism remains elusive. Ferrous iron ion is known to function as a co-factor for alpha-ketoglutarate-dependent dioxygenases, including demethylases for histones, DNA, and RNA. Previously we reported several alpha-ketoglutarate-dependent histone demethylases as critical epigenetic regulators during adipogenesis. These lines of evidence led us to hypothesize that iron orchestrates epigenetic/epitranscriptional regulations during adipogenesis by controlling demethylation activities. In this study, we conducted genome-wide analysis on methylation landscapes of histones, DNA, and RNA in differentiation of 3T3-L1 pre-adipocytes. Using the iron chelator deferoxamine, we demonstrate here how dynamically methylation levels of histones, DNA, and RNA are regulated by iron during adipogenesis.

overall_design: 3T3-L1 cells were induced for adipogenesis using the differentiation cocktail (insulin, DEX, and IBMX). In the first 2 days of differentiation, cells were cultured in the absence or presence of the iron chelator deferoxamine. Genomic DNA samples were prepared on Days 0, 2, and 8. For each time point, samples were prepared as triplicate (n=3). WGBS library was prepared using the tPBAT protocol (Miura et al. 2019 Nucleic Acids Res) and analyzed on an Illumina HiSeq X Ten platform.

first: Takeshi

last: Inagaki

first: Fumihito

last: Miura

first: Takashi

last: Ito


title: FOXD2-dependent genome-wide maps in HCT116 cells [RNA-seq]

status: Public on Apr 20 2023

city: Seoul

first: Tae-Young

last: Roh

state: --- Select One ---

address: 52 Ewhayeodae-gil, Seodaemun-gu

department: Life Sciences

institute: Ewha Womans University

summary: This study provides transcription, histone modifications, chromatin accessibility, and enhancer-promoter interactions in HCT116 upon FOXD2 expression. We identified the functional role of FOXD2 by analyzing mutli-omics data.

overall_design: RNA-Seq and ATAC-Seq were performed to survey transcriptional dynamics in HCT116 with FOXD2 presences. MNase ChIP-seq, HiChIP-seq of H3K4me3, H3K27ac, and H3K4me1 upon FOXD2 over expression to speculate enhancer-promoter interactions.

first: Hyo-Min

last: Kim

first: Byunghee

last: Kang


title: RNA-seq analysis to examine the effect of the iron chelator deferoxamine on gene expression profile in 3T3-L1 pre-adipocyte cells

first: Tetsuro

last: Komatsu

overall_design: 3T3-L1 cells were induced for adipogenesis using the differentiation cocktail (insulin, DEX, and IBMX). In the first 2 days of differentiation, cells were cultured in the absence or presence of the iron chelator deferoxamine. Total RNA was extracted on Days 0, 1, 2, 4, and 8, and for each time point RNA samples were prepared as duplicate (n=2). Column-purified RNA samples were subjected to library preparation using KAPA Stranded mRNA-seq Kit. RNA-seq run was done on an Illumina NextSeq 500 platform.

first: Reika

last: Kawabata


title: FOXD2-dependent genome-wide maps in HCT116 cells [ChIP-seq]


title: ChIP-seq analysis to examine the effect of the iron chelator deferoxamine on histone methylation levels in 3T3-L1 pre-adipocyte cells

overall_design: 3T3-L1 cells were induced for adipogenesis using the differentiation cocktail (insulin, DEX, and IBMX). In the first 2 days of differentiation, cells were cultured in the absence or presence of the iron chelator deferoxamine. ChIP samples for H3K4me3, H3K9me2, H3K9me3, and H3K27me3 were prepared on Days 0, 2, and 8. For each time point, samples were prepared as duplicate (n=2). ChIP-seq library was prepared using ThruPLEX DNA-Seq Kit and analyzed on an Illumina NextSeq 500 platform.


title: FOXD2-dependent genome-wide maps in HCT116 cells [ATAC-seq]


title: Generation of transcriptional regulatory network of Lgr5+ small and large intestinal stem cells from mouse [scRNA-seq]

summary: The goal of this study is to survey transcriptional machinery in intestinal stem cells from small and large intestine of mice. We established intestinal stem cell specific gene-regulatroy network to understand regional identity.

overall_design: Small intestine (2-3cm from pylorous and 2-3cm from cecum) and large intestine (cecum to rectum) of mice aged 6-12 weeks were extracted, and opened horizontally and washed with cold PBS buffer. Small intestinal stem cell (Lgr5-EGFP+/CD24-) and large intestinal stem cell (Lgr5-EGFP+) were obtained from enriched intestinal crypts by FACS analysis. Sorted cells were directly applied to single cell partitioning and barcoding of Chromium Controller.


title: FOXD2-dependent genome-wide maps in HCT116 cells


title: The PRAK-NRF2 axis promotes the differentiation of Th17 cells by mediating the redox homeostasis and glycolysis

status: Public on Apr 19 2023

city: Beijing

first: ziheng

last: zhao

address: 38 Xueyuan Road, Haidian District

institute: Peking university

summary:
To investigate the  function of PRAK in the regulation of Th17 differentiation, we polarized wild type and PRAK-KO naïve CD4+ T cells into Th17 cells for 72h in vitro.
We then collected two types of polarized Th17 cells  and performed gene expression profiling analysis using data obtained from RNA-seq.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for wild type and PRAK knock out Th17 cells.

first: Ziheng

last: Zhao

first: Yan

last: Wang

first: Wei


title: Crol contributes to PRE-mediated repression and Polycomb group proteins recruitment in Drosophila (ChIP-seq)

city: Bethesda

first: Mingan

last: Sun

state: Maryland

address: Building 6B, 6 Center Drive

department: Eunice Kennedy Shriver National Institute of Child Health and Human Development

institute: National Institute of Health

summary: The Polycomb group (PcG) proteins are fundamental epigenetic regulators that control the repressive state of target genes in multicellular organisms. One of the open questions is defining the mechanisms of PcG recruitment to chromatin. In Drosophila, the crucial role in PcG recruitment is thought to belong to DNA-binding proteins associated with Polycomb response elements (PREs). However, current data suggests that not all PRE-binding factors have been identified. Here, we report the identification of the transcription factor Crooked legs (Crol) as a novel PcG recruiter. Crol is a C2H2-type Zinc Finger protein that directly binds to poly(G)-rich DNA sequences. Mutation of Crol binding sites as well as crol CRISPR/Cas9 knockout diminish the repressive activity of PREs in transgenes. Like other PRE-DNA binding proteins, Crol co-localizes with PcG proteins inside and outside of H2K27me3 domains.  Crol knockout impairs the recruitment of the PRC1 subunit Polyhomeotic and the PRE-binding protein Combgap at a subset of sites. The decreased binding of PcG proteins is accompanied by dysregulated transcription of target genes. Overall, our study identified Crol as a new important player in PcG recruitment and epigenetic regulation.

overall_design: We generated ChIP-Seq and RNA-Seq data in this study. ChIP-Seq data are for Crol, Cbp, Fsl, H3K27ac, H3K27me3, Psq, Trx, E(z), Pc and Ph in 3rd instar whole larvae and/or 3rd instar larval imaginal discs and brains. For some proteins, matched ChIP-Seq data for wild-type and Crol-KO Drosophila are both generated. RNA-Seq data are for wild-type and Crol-KO 3rd instar whole larvae.

first: Maksim

last: Erokhin

first: Lesley

last: Brown

first: Dmitry

last: Lomaev

first: Nadezhda

last: Vorobyeva

first: Liangliang

last: Zhang

first: Lika

middle: V

last: Fab

first: Marina

last: Yu Mazina

first: Ivan

last: Kulakovskiy

first: Rustam

last: Ziganshin

first: Paul

last: Schedl

first: Pavel

last: Georgiev

first: Ming-an

first: Judith

middle: A

last: Kassis

first: Darya

last: Chetverina


title: Crol contributes to PRE-mediated repression and Polycomb group proteins recruitment in Drosophila


title: FOXD2-dependent genome-wide maps in HCT116 cells [HiChIP-seq]

first: Tae-Young

last: Roh

first: Hyo-Min

last: Kim

first: Byunghee

last: Kang


title: Crol contributes to PRE-mediated repression and Polycomb group proteins recruitment in Drosophila (RNA-seq)

first: Mingan

last: Sun

first: Maksim


title: Single-cell RNA-sequencing reveals an intratumor heterogeneity in pancreatic adenocarcinoma [ATAC-seq]

city: Kumamoto city

first: Masaya

last: Yamazaki

address: 1-1-1, Honjyo, Chuo-ku

institute: Kumamoto university

summary: We examined the intratumor heterogeneity in S2-VP10 xenograft by single-cell RNA-sequencing. We found a hierarchical tumor progression originating from ROR1high cells with a partial EMT gene signature. We also found that ROR1high cells have the strong capacity as tumor-initiating cells to support tumorigenecity, chemoresistance, and metastasis. CUT&RUN and ATAC-sequencing revealed that ROR1 gene expression is regulated through YAP-BRD4 axis. Together, these data uncover a role for ROR1high cells in tumor progression, suggesting that ablating ROR1high tumor-initiating cells may be the alternative therapeutic strategy in pancreatic adenocarcinoma.

overall_design: Examination of chromatin accessibility using ATAC-sequencing in S2-VP10 cells and sorted cells from S2-VP10 xenograft.


title: Single-cell RNA-sequencing reveals an intratumor heterogeneity in pancreatic adenocarcinoma [CUT&RUN]

overall_design: Examination of 3 diffierent histone modifications using CUT&RUN in S2-VP10 cells and sorted cells from S2-VP10 xenograft.


title: Depleting CD103+ resident memory T cells in vivo reveals immunostimulatory functions in oral mucosa

status: Public on Apr 18 2023

city: Minneapolis

first: James

middle: Michael

last: Stolley

state: MN

address: 2101 6th St. SE

department: Microbiology and Immunology

institute: University of Minnesota

summary: The oral mucosa is a frontline for microbial exposure and juxtaposes several unique tissues and mechanical structures. Based on parabiotic surgery of mice receiving systemic viral infections or co-housing with microbially diverse pet shop mice, we report that the oral mucosa harbors CD8+ CD103+ resident memory T cells (TRM), which locally survey tissues without recirculating. Oral antigen reencounter during the effector phase of immune responses potentiated TRM establishment within tongue, gums, palate, and cheek. Upon reactivation, oral TRM triggered changes in somatosensory and innate immune gene expression. We developed in vivo methods for depleting CD103+ TRM while sparing CD103neg TRM and recirculating cells. This revealed that CD103+ TRM were responsible for inducing local gene expression changes. Oral TRM putatively protected against local viral infection. This study provides methods for generating, assessing, and in vivo depleting oral TRM, documents their distribution throughout the oral mucosa, and provides evidence that TRM confer protection and trigger responses in oral physiology and innate immunity.

overall_design: mRNA profiles of buccal mucosa from WT or CD103KO mice in which mice were left untreated, sham swabbed, or orally swabbed with T cell reactivating peptides

first: J

first: Milcah

last: Scott

first: David

last: Masopust


title: Single cell RNA-seq data for iPSC differentiation into Syndetome

city: Los Angeles

first: Wensen

last: Jiang

address: 127 S San Vicente Blvd

department: Board of Governors Regenerative Medicine Institute

institute: Cedars-Sinai Medical Center

summary: We developed a protocol to differentiate iPSC into iPSC-derived Tenocytes (Syndetome)

overall_design: We collected cells at each stage for scRNA-seq, then optimze Syndetome with WNT inhibitor and sent for scRNA-seq, then applied to 83i cells and sent for scRNA-seq

first: Angela

last: Papalamprou

first: Victoria

last: Yu

first: Dmitriy

last: Sheyn


title: Single-cell RNA-sequencing reveals an intratumor heterogeneity in pancreatic adenocarcinoma [RNA-seq]

overall_design: Examination of RNA-sequencing in  (1) ROR1high and ROR1low cells sorted from S2-VP10 xenograft, PDO#1 xenograft, and (2) siRNA against ROR1 transfected PANC-1 cells.


title: Differential expression analysis of a Chrysanthemum mutant with an increased percentage of disc florets.

city: Wageningen

first: Annemarie

last: Castricum

state: Gelderland

address: Droevendaalsesteeg 4

department: Bioscience

institute: Wageningen university and research

summary: Expression was measured for variety 2 (V2) and mutant 2 (M2) to find differences in expression that could contribute to the increase in the percentage of disc florets.

overall_design: 4 stages of development were measured with biological triplicates and for each stage, differential expression was determined between the variety and its corresponding mutant.

first: Marian

last: Bemer

first: Richard

last: Immink

first: Gerco

last: Angenent


title: Single-cell RNA-sequencing reveals an intratumor heterogeneity in pancreatic adenocarcinoma [scRNA-seq]

overall_design: Examination of single-cell RNA sequencing using 10X genomics chromium in S2-VP10 xenograft.


title: Single-cell RNA-sequencing reveals an intratumor heterogeneity in pancreatic adenocarcinoma


title: Differential expression analysis of two Chrysanthemum mutants with an increased percentage of disc florets.

summary: Expression was measured for variety 1 (V1) and mutant 1 (M1) to find differences in expression that could contribute to the increase in the percentage of disc florets.


title: Quantitative Transcriptomes Analysis of Wild Type and ompR mutant of K. pneumoniae ATCC43816 .

first: Lijun

last: Wang

state: Beijing Shi

address: Shuangqing Road 30#

department: Department of Basic Medical Science

institute: Tsinghua University

summary: Purpose: This study aims to compare the transcriptome profiling (RNA-seq) of ompR mutant to that of WT and to evaluate the transcrptional regulation of OmpR in K. pneumoniae.

overall_design: mRNA profiles of  K. pneumoniae ATCC43816 wild-type (WT) and ompR knockout mutant were generated by deep sequencing, in duplicate, using Illumina Illumina NovaSeq 6000. The sequence reads that passed quality filters were analyzed at the transcript isoform level with RSEM using the Expectation Maximization (EM) algorithm. TPM method is used to calculated expression level.


title: Dissection of melanocyte stem cell transcriptomes during melanocyte regeneration in adult zebrafish

city: Worcester

first: William

middle: T

last: Frantz

state: MA

address: 368 Plantation Street

department: Molecular Medicine

institute: UMass Medical School

summary: To elucidate mechanisms governing McSC self-renewal and differentiation we analyzed individual transcriptomes from thousands of melanocyte lineage cells during the regeneration process. We identified transcriptional signatures for McSCs, deciphered transcriptional changes and intermediate cell states during regeneration, and analyzed cell-cell signaling changes to discover mechanisms governing melanocyte regeneration.

overall_design: scRNAseq profiling of melanocyte stem cells isolated from WT adult zebrafish skin during melanocyte regeneration

first: Sharanya

last: Iyengar

last: Neiswender

first: Alyssa

last: Cousineau

first: Rene

last: Maehr

first: Craig

middle: J

last: Ceol


title: Single cell RNA sequencing of DHT treated human male Islet cells

status: Public on Apr 17 2023

city: New Orleans

first: Franck

last: Mauvais-Jarvis

state: LA

address: 1430 Tulane Avenue Lab# 2301

department: Department of Medicine - Section of Endocrinology and Metabolism

institute: Tulane University

summary: We analyzed DHT’s effects on the human islet cell transcriptome using single-cell RNA sequencing. We identified the four main endocrine cell subtypes, α, β, δ, pancreatic polypeptide (PPY) cells, as well as ductal, acinar, endothelial, and immune cells by unbiased graph-based clustering. Resulting data was used to evaluate differentially expressed genes across these cell clusters.

overall_design: Human islets (750 IEQ per condition) were treated with either 10nM DHT or EtOH overnight in a humidified incubator containing 4% CO2 at 37°C. Islet cells were then dispersed using TrypLE (Thermofischer), and immediately evaluated for viability (89.88±1.77%) by Cellometer Automated Cell Counter (Nexcelom Bioscience) prior to single cell RNAseq library preparation. For 10x single cell RNAseq library preparation, 5000 individual live cells per sample were targeted by using 10x Single Cell 3’ RNAseq technology provided by 10x Genomics (10X Genomics Inc). Briefly, viable single cell suspensions were partitioned into nanoliter-scale Gel Beads-In-EMulsion (GEMs). Full-length barcoded cDNAs were then generated and amplified by PCR to obtain sufficient mass for library construction. Following enzymatic fragmentation, end-repair, A-tailing, and adaptor ligation, single cell 3’ libraries comprising standard Illumina P5 and P7 paired-end constructs were generated. Library quality controls were performed by using Agilent High Sensitive DNA kit with Agilent 2100 Bioanalyzer (Agilent) and quantified by Qubit 2.0 fluorometer (ThermoFisher). Pooled libraries at a final concentration of 750pM were sequenced with paired end single index configuration by Illumina NextSeq 2000 (Illumina).

first: Mirza Muhammad

middle: F

last: Qadir


title: Adult male prairie vole nucleus accumbens RNAseq dataset for "Prolonged partner separation erodes nucleus accumbens transcriptional signatures of pair bonding in male prairie voles."

city: Boulder

first: Julie

last: Sadino

state: CO

address: 1945 Colorado Ave

department: MCDB

institute: University of Colorado Boulder

summary: This dataset contains RNA sequencing results from  adult male prairie voles that were in either opposite-sex or same-sex pairs that were subsequently either separated from or remained paired with their partner for either 48 hours or 4 weeks prior to collecting nucleus accumbens tissue. The goal of this experiment was to determine the nucleus accumbens transcriptional response specific to separation from an opposite-sex partner. RNA sequencing was done on polyA enriched transcripts using Illumina single-end sequencing. Samples from 3 groups were from a Ribo-seq protocol using a virally delievered, vole optimized Translating Ribosome Affinity Purification construct (Heiman et al., 2008). These samples contain files for both the input fraction and the pulldown fraction (denoted with a _P suffix).

overall_design: This experiment contains 8 groups with 5-9 biological samples per group. Samples were hand dissected adult male prairie vole nucleus accumbens brain tisame-sexue according to Heiman et al., 2014. Half of the groups were males in opposite-sex pairs (experimental groups) while the other half were males in same-sex pairs (naive, control groups). Within each pairing type, animals were cohoused for 2 weeks then they were either separated or remained paired for either 48 hours or 4 weeks prior to tissue collection to assess the transcriptional trajectory of partner loss. RNA integrity and library quality was assessed by TapeStation and only samples with a RIN above 7.3 were prepared into libraries. Library preparation was via the KAPA mRNA HyperPrep kit with polyA enrichment for 1X75 RNA sequencing using Illumina NextSeq V2 for a total read depth of ~20M reads/sample. Samples that were part of the vTRAP groups have both input and pulldown files.

first: Zoe

last: Donaldson


title: human iPSC-neurons and human cortex

city: Philadelphia

first: Jennine

last: Dawicki-McKenna

state: PA

address: 700 CRB, 415 Curie Blvd

department: Physiology

institute: University of Pennsylvania

overall_design: Refer to individual Series


title: OpcA and PorB are novel bactericidal antigens of the 4CMenB vaccine in mice and humans

status: Public on Apr 15 2023

city: Siena

first: Erika

last: Bartolini

state: Italy

address: Via Fiorentina 1

department: AIMB

institute: GSK Vaccines

summary: In this study, we describe the development and use of an ad hoc protein microarray to study the immune response induced by the OMV component of 4CMenB vaccine in infant sera before and after vaccination

overall_design: A panel of recombinant meningococcal proteins were printed randomly in replicates on a non-commercial protein microarray. With the expection of NadA, GNA2091-fHbp and NHBA-GNA1030 (that are tagless), all the proteins were expressed as FLAG- and His-tagged fusions. Recombinant antigens were expressed in E. coli and then purified either from the cytoplasmic fraction as soluble proteins or resolubilized from the inclusions bodies as insoluble forms. Controls consisted of 8 serial 2-fold dilutions of human IgG, proteins expressed and purified from E. coli following the same expression and purification protocol, but originating from different pathogens other than MenB and PBS + 40% glycerol spots. Sera were profiled for anti-Human IgG specific analysis of reactivity to the spotted proteins.

first: Viola

last: Viviani


title: Topologically Associating Domain Boundaries are Required for Normal Genome Function

city: Berkeley

first: Sudha

last: Rajderkar

state: CA

address: 1 Cyclotron Rd

institute: Lawrence Berkeley National Laboratory

summary: Large-scale reaarangements and/or disruption of the three dimensional organization of the mammalian genome has been shown to cause develomental phenotypes. However, the functional requirement of TAD boundaries alone in development and disease remains an outstanding question in the field. Here, we show that TAD boundaries are required for the functional integrity of the genome in vivo. Using systematic genome-wide selection criteria and CRISPR/Cas9 editing, we deleted eight individual TAD boundaries ranging between 11-80 kb in size and investigated the in vivo consequences comprehensively by assessing survival, chromatin interaction data, gene expression and detailed phenotypic characterization. A majority of boundary deletions resulted in altered chromatin interactions, and/or multiple boundary deletions causing reduced embryonic survival or other developmental phenotypes. Our results elucidate the functional requirement of TAD boundary integrity in development and suggest that TAD bondary deletion may be sufficient to cause developmental phenotypes.

overall_design: For chromosome conformation capture (HiC), liver tissue from TAD boundary mutant and wild type control mice, at age p56, was collected, processed and analyzed for HiC per standard protocols. RNA-seq was performed using standard protocols on the indicated tissue from E11.5 embryos, homozygous as well as wild type controls, for each of the TAD boundary deletion lines.

first: Yiwen

last: Zhu

first: Rong

last: Hu

first: Bin

last: Li

first: Yanxiao

last: Zhang

first: Len

last: Pennacchio


title: Restoring bone marrow niche function rejuvenates aged hematopoietic stem cells by reactivating the DNA Damage Response [5]

status: Public on Apr 14 2023

city: New York

first: David

last: Redmond

state: New York

address: 1300 York Avenue

institute: Weill Cornell Medicine

summary: The bone marrow (BM) niche comprised of BM endothelial cells (BMECs) and LepR+ mesenchymal stromal cells (MSCs), plays a critical role in preserving the fitness of hematopoietic stem cells (HSCs). Aging is associated with defects in the BM niche that impair their ability to support HSC activity. However, mechanisms underlying age-related defects in the BM niche remain poorly understood. In this study, we identify BM niche derived Netrin-1 (NTN1) as a critical regulator of BM niche cell fitness during aging. Conditional deletion of NTN-1 specifically within BM MSCs or BMECs of young mice resulted in premature aging phenotypes within the BM niche including increased vascular leakiness, hypoxia, DNA damage and adiposity. On the other hand, supplementation of aged mice with NTN1 resulted in restoration of these hallmark niche defects and a rejuvenation of HSC activity. Mechanistically, we identify NTN1 as a critical regulator of DNA Damage Response (DDR) within BM niche cells and HSCs. In this experiment, RNA Seq analysis was performed on BM MSCs and BMECs following conditional deletion of NTN1 within BMECs or MSCs to characterize transcriptional alterations within BM niche cells resulting from a deficiency of niche derived NTN1.

overall_design: Comparative gene expression profiling analysis of BM niche cells (BM MSCs and BMECs) following recombinant NTN1 treatment in aged (18 month old) mice.

first: Pradeep

last: Ramalingam

first: Michael

last: Poulos

first: Jason

last: Butler


title: Restoring bone marrow niche function rejuvenates aged hematopoietic stem cells by reactivating the DNA Damage Response [3]

summary: The bone marrow (BM) niche comprised of BM endothelial cells (BMECs) and LepR+ mesenchymal stromal cells (MSCs), plays a critical role in preserving the fitness of hematopoietic stem cells (HSCs). Aging is associated with defects in the BM niche that impair their ability to support HSC activity. However, mechanisms underlying age-related defects in the BM niche remain poorly understood. In this study, we identify BM niche derived Netrin-1 (NTN1) as a critical regulator of BM niche cell fitness during aging. Conditional deletion of NTN-1 specifically within BM MSCs or BMECs of young mice resulted in premature aging phenotypes within the BM niche including increased vascular leakiness, hypoxia, DNA damage and adiposity. On the other hand, supplementation of aged mice with NTN1 resulted in restoration of these hallmark niche defects and a rejuvenation of HSC activity. Mechanistically, we identify NTN1 as a critical regulator of DNA Damage Response (DDR) within BM niche cells and HSCs. In this experiment, RNA Seq analysis was performed on BMECs derived from young (3 month old) and aged (18 month old) mice to characterize transcriptional alterations within BMECs during aging.

overall_design: Comparative gene expression profiling analysis of BMECs derived from young (3 month old) and aged (18 month old) mice


title: SCUBE2 mediates bone metastasis of luminal breast cancer by modulating immune-suppressive osteoblastic niches

city: Shanghai

first: Guohong

address: No.320, Yueyang Roda, Xuhui disteict

department: Shanghai Institute of Nutrition and Health

institute: Chinese Academy of Sciences

summary: Estrogen receptor (ER)-positive luminal breast cancer is a subtype with generally lower risk of metastasis to most distant organs. However, bone recurrence occurs preferentially in luminal cancer. The mechanisms of the subtype-specific organotropism remain elusive. Here we show that an ER-regulated secretory protein SCUBE2 contributes to bone tropism of luminal breast cancer. Single-cell RNA sequencing analysis reveals osteoblastic enrichment by SCUBE2 in early bone-metastatic niches. SCUBE2 facilitates release of tumor membrane-anchored SHH to activate Hedgehog signaling in mesenchymal stem cells, thus promoting osteoblast differentiation. Osteoblasts deposit collagens to suppress NK cells via the inhibitory LAIR1 signaling and promote tumor colonization. SCUBE2 expression and secretion are associated with osteoblast differentiation and bone metastasis in human tumors. Targeting Hedgehog by Sonidegib and targeting SCUBE2 with a neutralizing antibody both effectively suppress bone metastasis in multiple metastasis models. Overall, our findings provides an explanation for bone preference in luminal breast cancer and new approaches for metastasis treatment.

overall_design: mRNA profiles of murine mesenchymal stem cell (MSC) and MSC-derived osteoblasts treated with conditioned media of control or SCUBE2-deficient MCF7

first: Qiuyao

last: Wu


title: Restoring bone marrow niche function rejuvenates aged hematopoietic stem cells by reactivating the DNA Damage Response

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


title: MAPT expression is mediated by long-range interactions with cis-regulatory elements [RNA_timecourse]

status: Public on Apr 12 2023

city: Huntsville

first: J.

middle: Nicholas

last: Cochran

state: AL

address: 601 Genome Way

institute: HudsonAlpha Institute for Biotechnology

summary: Tau is encoded by MAPT and abnormal aggregates of tau are a hallmark of a group of neurodegenerative diseases called tauopathies. MAPT is lowly expressed in neural progenitor cells (NPCs), but it is more highly expressed in oligodendrocytes, astrocytes, and neurons that derive from NPCs. This expression switch at differentiation suggests that MAPT expression is controlled by transcription factors and cis-regulatory elements specific to these differentiated cell types, including neurons.

overall_design: We performed HiC and three-dimensional chromatin conformation capture (Capture-C), single-nucleus multiomics (RNA-seq and ATAC-seq), bulk ATAC-seq, and ChIP-seq for H3K27Ac and CTCF in neurons differentiated from human iPSC cultures. From these methods, we nominated candidate cis-regulatory elements (cCREs) for MAPT in human NPCs, NPCs differentiated to neurons, and pure inhibitory or excitatory neuron cultures. We then functionally assessed nominated regions using luciferase assays and CRISPR dCas9-KRAB inhibition experiments to assess the effect of nominated regions on MAPT expression.

first: Brianne

middle: B

last: Rogers

first: Ashlyn

middle: G

last: Anderson

first: J

middle: N


title: Effect of Caspase1 deletion on oxygen-induced retinopathy in C57BL/6 mice

city: Detroit

first: Nikhlesh

middle: Kumar

last: Singh

state: Michigan

address: 6135 Woodward Avenue, #3414 IBio, #3414 IBio

institute: Wayne State University School of Medicine

summary: To investigate the expression profile of genes involved in oxygen-induced retinopathy (OIR) and the effect of caspase1 deletion on those genes in retina.

overall_design: C57BL/6 and Caspase1 mice were exposed to normoxia and 3 day hypoxia (3 day post OIR) and then eyes were enucleated and retinas isolated. The RNA was isolated from retina and then gene expression profiling was performed using 3 prime RNA sequencing.

first: Shivantika

last: Bisen


title: Dependency of NELF-E-SLUG-KAT2B epigenetic axis in breast cancer carcinogenesis

city: Singapore

first: Zhenhua

last: hu

state: singapore

address: 31 Biopolis drive

country: Singapore

institute: IMCB, A*STAR

summary: Cancer cells undergo transcriptional reprogramming to drive tumorigenesis and caner progression. Here, we identified the transcriptional complex, NELF (Negative elongation factor), as an important regulator of this process. Using cancer cell lines and patient-derived tumor organoids, we demonstrated that loss of NELF inhibits breast cancer. Specifically, we found that epithelial-mesenchymal transition (EMT) and stemness-associated genes are downregulated in NELF-depleted breast cancer cells. Afterwards, we pinpointed that SLUG, a key EMT transcription factor, was a top hit of NELF interactome during EMT progression. Furthermore, ChIP-seq analysis revealed that loss of NELF led to impaired SLUG binding on chromatin. Through integrative transcriptomic and genomic analyses, we identified the histone acetyltransferase, KAT2B, as a key functional target of NELF-E-SLUG. Genetic and pharmacological inactivation of KAT2B ameliorate expression of critical EMT marker genes, phenocopying NELF ablation. Elevated NELF-E and KAT2B expressions are associated with poorer prognosis in breast cancer patients, highlighting the clinical relevance of our findings. Taken together, we uncovered a crucial role of the NELF-E-KAT2B epigenetic axis in breast cancer carcinogenesis.

overall_design: RNA-seq of CRISPR/CAS9-mediated NELF-E KO MCF7, BT549 and SUM159 cell lines and their parental wildtype lines, NELF-E/scrambled shRNA transduced MCF7ras+SS cells and KAT2B/scrambled siRNA transfected MCF7ras+SS cells with the induction of Doxycycline or DMSO vehicle, Doxycycline-induced MCF7ras+SS cells treated with Garcinol (GA) or DMSO vehicle. ChIP-seq of NELF-E, RNAP II, SLUG and KAT2B in corresponding MCF7ras+SS cells.

first: Jieqiong

first: Wee-Wei

last: Tee


title: MAPT expression is mediated by long-range interactions with cis-regulatory elements [RNA-seq]


title: MAPT expression is mediated by long-range interactions with cis-regulatory elements [HiC and Capture-C]


title: Astrocytes' Radiation Response

city: Koeln

first: Christine

middle: Elisabeth

last: Hellweg

state: Nordrhein-Westfalen

address: Linder Hoehe

department: r, IInstitute of Aerospace Medicine

institute: German Aerospace Center

summary:
Gene expression of X-irradiated primary murine astrocytes

Roggan MD, Kronenberg J, Wollert E, Hoffmann S, Nisar H, Konda B, Diegeler S, Liemersdorf C and Hellweg CE (2023) Unraveling astrocyte behavior in the space brain: Radiation response of primary astrocytes. Front. Public Health 11:1063250.

overall_design: The aim of this project was to study the radiation-induced changes in murine astrocytes on the gene expression level. For this purpose, the cells were irradiated with different doses of X-rays (0 Gy, 0.1 Gy, 2 Gy) and RNA was extracted at two different time points (6 h, 24 h) after irradiation. We determined the kinetics of gene expression changes for a low dose (0.1 Gy) and a moderate dose (2 Gy) and the dose-effect relationship for two timepoints (6 h, 24 h).

first: Marie

middle: D

last: Roggan

first: Jessica

last: Kronenberg


title: ARTICLE OPEN OpcA and PorB are novel bactericidal antigens of the 4CMenB vaccine in mice and humans

first: Erika

last: Bartolini

summary: In this study, we describe the development and use of an ad hoc protein microarray to study the immune response induced by the OMV component of 4CMenB vaccine in mouse sera before and after immunization.

overall_design: A panel of 26 recombinant E. coli Outer Membrane Vesicles (hereafter called GMMA) expressing meningococcal antigens, two GMMA empty, OMV from NZ98/254 and the major recombinant proteins of 4CMenB (NadA, GNA2091-fHbp and NHBA-GNA1030) were printed randomly in replicates on a non-commercial protein microarray. With the expection of NadA, GNA2091-fHbp and NHBA-GNA1030, all the proteins expressed in E.coli GMMA were e FLAG- and His-tagged fusions. Recombinant GMMA were obtained from the supernatant of a late-exponential growth of E. coli. The supernatants were subjected to high-speed centrifugation and the pellets containing the GMMA were washed with PBS. Controls consisted of 8 serial 2-fold dilutions of mouse IgG and PBS + 40% glycerol spots. Sera were profiled for anti-Mouse IgG specific analysis of reactivity to the spotted proteins.

first: Viola

last: Viviani


sample_organism:
Homo sapiens
Mus musculus


title: DEF cells infected with NDV

status: Public on Apr 11 2023

city: Guangzhou

first: Lei

last: Fan

state: Guangdong

address: 483 Wushan Road,

institute: South China Agricultural University

summary: The NDV GM strain was used to infect DEF cells with 1moi, while an uninfected group was set up as a control. Changes in transcript levels of different genes after NDV infection of duck cells were identified by high-throughput sequencing. It is hoped to reveal the unique antiviral mechanism of waterfowl in resisting NDV infection.

overall_design: The control groups were DN-1, DN-2, and DN-3, while the experimental groups were DK-1, DK-2, and DK-3. NDV was used in the experimental group infected at 1 MOI, and samples were collected at 9 h post infection along with the control group for sequencing.

first: Bin

last: Xiang

first: Jinlian

last: Ren

first: Yiyi

last: Chen


title: Total RNA-seq in the modulo mutant reveals broad changes to the transcriptome.

status: Public on Apr 10 2023

city: Cambridge

first: Jun

middle: I

last: Park

address: 455 Main St

institute: Whitehead Institute

summary: Modulo mutant has been known to cause male infertility, although the reason has remained unknown. This study aimed to utilize RNA-seq data as part of an investigation into the mechanism of infertility.

overall_design: Three biological replicates of wt and mutant samples, each split into 3 different lanes.

first: George

middle: W

last: Bell

first: Yukiko

middle: M

last: Yamashita


title: Identification of signature genes of Dilated cardiomyopathy Using Integrated bioinformatics analysis

city: Shijiazhuang

first: Zhimin

last: Wu

address: Zhongshan East Road

department: Department of phamarcy

institute: Hebei Medical University

summary: Dilated cardiomyopathy (DCM) is characterized by left ventricular or biventricular enlargement with systolic dysfunction. To date, the underlying molecular mechanisms of dilated cardiomyopathy pathogenesis have not been fully elucidated, although some insights have been presented. In this study, we combined public database resources and a doxorubicin-induced DCM mouse model to explore the significant genes of DCM in full depth. We first retrieved six DCM-related microarray datasets from the GEO database using several keywords. Then we used the "LIMMA" (linear model for microarray data) R package to filter each microarray for differentially expressed genes (DEGs). Robust rank aggregation (RRA), an extremely robust rank aggregation method based on sequential statistics, was then used to integrate the results of the six microarray datasets to filter out the reliable differential genes. To further improve the reliability of our results, we established a doxorubicin-induced DCM model in C57BL/6N mice, using the "DESeq2" software package to identify DEGs in the sequencing data. We cross-validated the results of RRA analysis with those of animal experiments by taking intersections and identified three key differential genes (including Bex1, RGCC and VSIG4) associated with DCM as well as many important biological processes (extracellular matrix organization, extracellular structural organization, sulphur compound binding, and extracellular matrix structural components) and a signalling pathway (HIF-1 signalling pathway).

overall_design: Six male C57BL/6N mice were randomly divided into two groups, three in the control group and three in the DCM group. Doxorubicin was injected intraperitoneally to establish the model of dilated cardiomyopathy and controls were given equal amounts of saline. After determining the success of the model, heart tissues were collected and sequenced on MGISEQ-T7 to obtain 150bp paired-end reads.

first: Xu

last: Wang


title: N6-Methyladenosine modification of mRNA regulates the transition from 2D to 3D growth in the moss Physcomitrium patens

city: Coyoacan

first: V Miguel

last: Palomar

state: Mexico City

address: Circuito Exterior SN

department: Biochemistry

country: Mexico

institute: School of Chemistry, UNAM


title: Restoring bone marrow niche function rejuvenates aged hematopoietic stem cells by reactivating the DNA Damage Response [4]

first: David

last: Redmond

summary: The bone marrow (BM) niche comprised of BM endothelial cells (BMECs) and LepR+ mesenchymal stromal cells (MSCs), plays a critical role in preserving the fitness of hematopoietic stem cells (HSCs). Aging is associated with defects in the BM niche that impair their ability to support HSC activity. However, mechanisms underlying age-related defects in the BM niche remain poorly understood. In this study, we identify BM niche derived Netrin-1 (NTN1) as a critical regulator of BM niche cell fitness during aging. Conditional deletion of NTN-1 specifically within BM MSCs or BMECs of young mice resulted in premature aging phenotypes within the BM niche including increased vascular leakiness, hypoxia, DNA damage and adiposity. On the other hand, supplementation of aged mice with NTN1 resulted in restoration of these hallmark niche defects and a rejuvenation of HSC activity. Mechanistically, we identify NTN1 as a critical regulator of DNA Damage Response (DDR) within BM niche cells and HSCs. In this experiment, RNA Seq analysis was performed on HSCs derived from young mice (3 month old), PBS treated aged mice (18 month old), and NTN1 treated aged mice (18 month old), to characterize transcriptional alterations within HSCs during aging, and following NTN1 treatment of aged mice.

overall_design: Comparative gene expression profiling analysis of HSCs derived from young mice (3 month old), PBS treated aged mice (18 month old), and NTN1 treated aged mice (18 month old).

first: Pradeep

last: Ramalingam

first: Michael

last: Poulos

first: Jason

last: Butler


title: Restoring bone marrow niche function rejuvenates aged hematopoietic stem cells by reactivating the DNA Damage Response [2]

summary: The bone marrow (BM) niche comprised of BM endothelial cells (BMECs) and LepR+ mesenchymal stromal cells (MSCs), plays a critical role in preserving the fitness of hematopoietic stem cells (HSCs). Aging is associated with defects in the BM niche that impair their ability to support HSC activity. However, mechanisms underlying age-related defects in the BM niche remain poorly understood. In this study, we identify BM niche derived Netrin-1 (NTN1) as a critical regulator of BM niche cell fitness during aging. Conditional deletion of NTN-1 specifically within BM MSCs or BMECs of young mice resulted in premature aging phenotypes within the BM niche including increased vascular leakiness, hypoxia, DNA damage and adiposity. On the other hand, supplementation of aged mice with NTN1 resulted in restoration of these hallmark niche defects and a rejuvenation of HSC activity. Mechanistically, we identify NTN1 as a critical regulator of DNA Damage Response (DDR) within BM niche cells and HSCs. In this experiment, RNA Seq analysis was performed on BM MSCs derived from young (3 month old) and aged (18 month old) mice to characterize transcriptional alterations within BM MSCs during aging.

overall_design: Comparative gene expression profiling analysis of BM MSCs derived from young (3 month old) and aged (18 month old) mice.


title: MAPT expression is mediatedd by long-range interactions with cis-regulatory elements.

first: J.

last: Cochran

overall_design: We performed HiC, chromatin conformation capture (Capture-C), single-nucleus multiomics (RNA-seq+ATAC-seq), bulk ATAC-seq, and ChIP-seq for H3K27Ac and CTCF in NPCs and neurons differentiated from human iPSC cultures. We nominated candidate cis-regulatory elements (cCREs) for MAPT in human NPCs, differentiated neurons, and pure cultures of inhibitory and excitatory neurons. We then assayed these cCREs using luciferase assays and CRISPR interference (CRISPRi) experiments to measure their effects on MAPT expression. Finally, we integrated cCRE annotations into an analysis of genetic variation in AD cases and controls.


title: PTBP2 eCLIP from human iPSC-neurons and human cortex (Brodmann area 4) [CLIP-seq]

status: Public on Apr 13 2023

first: Jennine

last: Dawicki-McKenna

summary: To determine direct targets of PTBP2-dependent alternative splicing, we performed CLIP-seq analysis of PTBP2 binding in both human cortical tissue and human neurons derived from induced-pluripotent stem cells (iPSC-neurons), and we combine this with splicing analysis following PTBP2 depletion in iPSC-neurons.

overall_design: We performed enhanced cross-linking immunoprecipitation (eCLIP) of PTBP2 in human cortex (Brodmann area 4) and human iPSC-neurons.

first: Alex

last: Felix

first: Elisa

last: Waxman

first: Congsheng

last: Cheng

first: Defne

last: Amado

first: Paul

last: Ranum

first: Alexey

last: Bogush

first: Lea

last: Dungan

first: Elizabeth

last: Heller

first: Deborah

middle: L

last: French

first: Beverly

last: Davidson

first: Benjamin

last: Prosser


title: RIP-PEN-seq for 15.5K in HEK293T cells

first: Jian-Hua

last: Yang

address: No. 135, Xingang Xi Road

department: School of Life Sciences

institute: Sun Yat-sen University

summary: Here, we developed a RNA ImmunoPrecipitation coupled with sequencing of Paired-Ends of NcRNAs (RIP-PEN-seq) method to identify the full-length sequences of ncRNAs bound by 15.5K protein and discover a novel class of backward K-turn RNAs.

overall_design: Analysis of 15.5K binding RNAs in HEK293T cells.

first: Bin

last: Li

first: Shurong

last: Liu

first: Wujian

last: Zheng

first: Peng

last: Yu

first: Anrui

first: Di

last: Wu

first: Jie

last: Zhou

first: Ping

last: Zhang

first: Chang

first: Qiao

last: Lin

first: Xiaoqin

first: Qiaojuan

last: Huang

first: Hui

first: Lianghu

last: Qu

first: Jianhua


title: sub-PEN-seq for identifying novel non-coding RNAs and their expression in cultured cells II

summary: Small RNAs between 20-500nt were least explored. Here we used RNase H-based rRNA depletion and a serial of strategies to developed sub-PEN-seq method for identifying novel non-coding RNAs in Subcellular RNAs.

overall_design: Subcellular RNA were ligated to  RNA adaptors, followed by rRNA and snRNA depletion. After reverse transcription and library amplification, inserts between 20-500bp were size selected and subjected to Illumina sequencing.


title: RIP-PEN-seq for 15.5K in Hepa1-6 cells

overall_design: Analysis of 15.5K binding ncRNAs in Hepa1-6 cells.


title: CLASH for 15.5K and FBL proteins in HEK293T cells

summary: We performed CLASH for 15.5K and FBL in HEK293T cells which overexpressed 15.5K and FBL, respectively.

overall_design: triplicates


title: Gene expression and intron retention analysis of bktRNA1-depleted human cells

summary: Backwark kink-turn RNA 1 (bktRNA1) is a novel post-transcriptional regulator with a role in RNA modification. Here, we show that human bktRNA1 interacts with 15.5K and FBL and guides 2’-O-methylation in the 8th of U12 snRNA. Given that U12 plays crucial role in minor intron splicin, we knockouted bktRNA1 in HCT116 cells and examined the effects of the modification on minor splicing by transcriptome analyses. Our work defines a novel functional interaction bwtween bktRNA1 and RNA processing and highlighs that a single modification alteration may contribute to global impairment of the splicing machinery.

overall_design: We analysed RNA from wild-type HCT116 (WT) cells and four bktRNA1-deficient (KO-1, KO-2, KO-3 and KO-4) clones. For each condition, mRNA-seq analysis was conducted in triplicate from three independent expriments. We compare KO-1 vs WT, KO-2 vs WT, KO-3 vs WT and KO-4 vs WT.


title: Transcriptomic Alterations in Diabetic Aortic Endothelial Cells Following Low-Dose Radiation Exposure

status: Public on Apr 07 2023

city: Cheonan

first: Keunsoo

last: Kang

state: Chungnam

address: Dandae-ro 119

department: Microbiology

institute: Dankook University

summary: Low-dose radiation refers to exposure to ionizing radiation at levels that are generally considered safe and not expected to cause immediate health effects. However, the effects of low-dose radiation are still not fully understood and research in this area is ongoing. In this study, we investigated changes in gene expression in diabetic human aortic endothelial cells (T2D-HAECs) derived from type 2 diabetes patients. To this end, we used RNA-seq to profile the transcriptomes of cells exposed to varying doses of low-dose radiation (0.1Gy, 0.5Gy, and 2.0Gy) and compared them to a control group with no radiation exposure. Differentially expressed genes and enriched pathways were identified using the DESeq2 and gene set enrichment analysis (GSEA) methods, respectively. The data generated in this study are publicly available through the gene expression omnibus (GEO) database. This study provides a valuable resource for studying the effects of low-dose radiation on T2D-HAECs and can contribute to a better understanding of the potential human health risks associated with low-dose radiation exposure.

overall_design: Transcriptomic profiling analysis of diabetic human aortic endothelial cells (T2D-HAECs) and human aortic endothelial cells (HAECs) exposed to various low-dose radiation levels (0, 0.1Gy, 0.5Gy, and 2.0Gy).

first: Hae-June

last: Lee

first: Yeonghoon

last: Son

first: Kwang

last: Kim

first: Jihye

last: Park


title: Adaptive regulation of stopover refueling during bird migration: insights from whole blood transcriptomics

city: Ioannina

first: Anastasios

last: Bounas

address: University Campus

department: Department of Biological Applications and Technology

country: Greece

institute: University of Ioannina

summary: We used transcriptomic information from the whole blood of migrating Garden warblers (Sylvia borin) to identify key regulatory pathways related to adaptations for migration. Birds were temporarily caged during stopover and then sampled twice at different refuelling states (lean vs fat), reflecting different migratory stages (stopover arrival vs departure) after the crossing of an extended ecological barrier.

overall_design: Ten migrating Garden warblers were captured during spring migration and then housed in individual cages in natural conditions for five days. Blood samples were collected from each bird twice, on the first and fifth day (shortly before migratory birds were released).

first: Chrysoula

last: Komini

first: Artemis

last: Talioura

first: Elisavet-Aspasia

last: Toli

first: Konstantinos

last: Sotiropoulos

first: Christos

last: Barboutis


title: MAPT expression is mediated by long-range interactions with cis-regulatory elements [ATAC-seq]

first: J.

last: Cochran

summary: Tau is encoded by MAPT and abnormal aggregates of tau are a hallmark of a group of neurodegenerative diseases called tauopathies. MAPT is lowly expressed in neural progenitor cells (NPCs), but it is more highly expressed in oligodendrocytes, astrocytes, and neurons that derive from NPCs. This expression switch at differentiation suggests that MAPT expression is controlled by transcription factors and cis-regulatory elements specific to these differentiated cell types, including neurons.

overall_design: We performed HiC and three-dimensional chromatin conformation capture (Capture-C), single-nucleus multiomics (RNA-seq and ATAC-seq), bulk ATAC-seq, and ChIP-seq for H3K27Ac and CTCF in neurons differentiated from human iPSC cultures. From these methods, we nominated candidate cis-regulatory elements (cCREs) for MAPT in human NPCs, NPCs differentiated to neurons, and pure inhibitory or excitatory neuron cultures. We then functionally assessed nominated regions using luciferase assays and CRISPR dCas9-KRAB inhibition experiments to assess the effect of nominated regions on MAPT expression.

first: Brianne

last: Rogers

first: Ashlyn

last: Anderson

first: J


title: Restoring bone marrow niche function rejuvenates aged hematopoietic stem cells by reactivating the DNA Damage Response [1]

first: David

last: Redmond

summary: The bone marrow (BM) niche comprised of BM endothelial cells (BMECs) and LepR+ mesenchymal stromal cells (MSCs), plays a critical role in preserving the fitness of hematopoietic stem cells (HSCs). Aging is associated with defects in the BM niche that impair their ability to support HSC activity. However, mechanisms underlying age-related defects in the BM niche remain poorly understood. In this study, we identify BM niche derived Netrin-1 (NTN1) as a critical regulator of BM niche cell fitness during aging. Conditional deletion of NTN-1 specifically within BM MSCs or BMECs of young mice resulted in premature aging phenotypes within the BM niche including increased vascular leakiness, hypoxia, DNA damage and adiposity. On the other hand, supplementation of aged mice with NTN1 resulted in restoration of these hallmark niche defects and a rejuvenation of HSC activity. Mechanistically, we identify NTN1 as a critical regulator of DNA Damage Response (DDR) within BM niche cells and HSCs. In this experiment, RNA Seq analysis was performed on BM MSCs and BMECs following conditional deletion of NTN1 within BMECs or MSCs to characterize transcriptional alterations within BM niche cells resulting from a deficiency of niche derived NTN1.

overall_design: Comparative gene expression profiling analysis of BM niche cells (BM MSCs and BMECs) following deletion of NTN1 in LepR+ MSCs (LepR_NTN1KO) or BMECs (CDH5_NTN1KO) of young (4-6 month old) mice.

first: Pradeep

last: Ramalingam

first: Michael

last: Poulos

first: Jason

last: Butler


title: RNA-DNA interactome of a prokaryotic cell uncovered by proximity ligation

city: Moscow

first: Grigory

last: Evko

address: Vavilova str., 34/5

country: Russia

institute: Institute of Gene Biology of the Russian Academy of Sciences

summary: We used one of the RNA-DNA proximity ligation approaches, RedC, for the analysis of an RNA-DNA interactome of microbial cells. We assess the distribution of main RNA types — mRNA, tRNA and rRNA — along the genomes of E.coli, B.subtilis, and thermophilic archaea T. adornatum.

sample_organism:
Escherichia coli
Bacillus subtilis
Thermofilum adornatum

overall_design: The RedC experimental protocol for mapping RNA-DNA interactions is based on formaldehyde fixation of RNA-protein-DNA complexes in vivo followed by ligation of RNA and DNA fragments present in one nucleoprotein complex via a biotinylated bridge adapter with a subsequent identification of ligated fragments using a paired end sequencing

first: Alexey

last: Gavrilov

middle: S

first: Alexander

middle: V

last: Tyakht


title: PEN-seq for identifying non-coding RNAs and their expression in 15.5K-knockdown HEK293T cells

first: Jian-Hua

last: Yang

summary: 15.5K is a RNA binding protein involved in the Minor Spliceosome. Here, we used shRNAs to knock down 15.5K in HEK293T cells to analysis the function of 15.5K in ncRNA expression.

overall_design: Total RNA from negative control HEK293T (shNC) cells and two 15.5K-knockdown  (sh15.5K-1 and sh15.5K-2) cells  were ligated to RNA adaptors, followed by rRNA and snRNA depletion. After reverse transcription and library amplification, inserts between 20-500bp were size selected and subjected to Illumina sequencing.

first: Bin

last: Li

first: Shurong

last: Liu

first: Wujian

last: Zheng

first: Peng

last: Yu

first: Anrui

first: Di

last: Wu

first: Jie

last: Zhou

first: Ping

last: Zhang

first: Chang

first: Qiao

last: Lin

first: Xiaoqin

first: Qiaojuan

last: Huang

first: Hui

first: Lianghu

last: Qu

first: Jianhua


title: The small iridoid compound genipin prevents alpha-synuclein aggregation and toxicity by affecting endocytosis, metabolism and lipid storage

status: Public on Apr 06 2023

city: Lisbon

first: Rita

last: Rosado-Ramos

address: Lisbon

country: Portugal

institute: Nova Medical School

summary: Parkinson’s Disease (PD) is a common neurodegenerative disorder affecting millions of people worldwide for which there are only symptomatic therapies. Small molecules able to target key pathological processes in PD have emerged as interesting options for modifying disease progression. We have previously shown that a (poly)phenol-enriched fraction (PEF) of Corema album L. leaf extract modulates central events in PD pathogenesis, namely α-synuclein (αSyn) toxicity, aggregation and clearance. PEF was now subjected to a bio-guided fractionation with the aim of identifying the critical bioactive compound. We identified genipin, an iridoid, which relieves αSyn toxicity and aggregation. Furthermore, genipin promotes metabolic alterations and modulates lipid storage and endocytosis. Importantly, genipin was able to prevent the motor deficits caused by the expression of αSyn-GFP in a Drosophila melanogaster  model of PD. These findings open new avenues for the exploitation of genipin for PD therapeutics.

overall_design: Yeast cells, either controls or disease model were incubated with genipin, a protective compound, and the transcriptomics were assessed.

first: Gonçalo

last: Poças

first: Daniela

last: Marques

first: Alexandre

last: Foito

first: David

last: Sevillano

first: Mafalda

last: Lopes-da-Silva

first: Luís

last: Gonçalves

first: Regina

last: Menezes

first: Marcel

last: Ottens

first: Derek

last: Stewart

first: Alain

last: Ibáñez de Opakua

first: Markus

last: Zweckstetter

first: Miguel

middle: C

last: Seabra

first: César

last: Mendes

first: Tiago

last: Fleming Outeiro

first: Pedro

last: Domingos

first: Cláudia

last: Nunes dos Santos


title: RIP-PEN-SHAPE-MaP for 15.5K-interacted RNAs

first: Jian-Hua

last: Yang

summary: RNA secondary structure is crucial for RNA mentalism, including transcription, splicing, translation, RNA-binding protein interaction as well as turnover. The kink-turn (K-turn) structure motif is is an RNA three-dimensional (3D) structure that exists in all three primary phylogenetic domains and plays vital roles in RNA metabolism. In order to investigate the K-turn secondary structure in vivo, we combined SHAPE-Map and our RIP-PEN-seq to profile the RNA structure of 15.5K-interacted RNAs.

overall_design: The 15.5K-interacted RNAs were first isolated by 15.5K-specific antibody and followed by on-beads modification with SHAPE reagent NAI-N3 or DMSO (negative control). After RNA isolation and DNase I-treatment, the 15.5K-interacted RNAs were ligated to 3’ and 5’ randomized RNA adaptors. Then the ligated products were subjected to rRNA, snRNA and some high-abundance snoRNA depletion utilizing an RNase H-based strategy. Following the reverse transcription under SHAPE-MaP conditions, the libraries were amplified with Illumina small RNA indexed PCR primers.

first: Bin

last: Li

first: Anrui

last: Liu

first: Lianghu

last: Qu

first: Jianhua