title: A single-cell map of maternal and zygotic mRNA dynamics during cell-type specification in zebrafish embryos [SLAM-seq]

summary: During early embryogenesis, embryos undergo a massive degradation of maternally inherited mRNAs and produce new zygotic transcripts. This maternal-to-zygotic transition requires a tight interplay of mRNA transcription and degradation, but distinguishing their unique contributions remains a challenge. Here, we dissect gene regulation during the zebrafish maternal-to-zygotic transition by combining single-cell RNA-sequencing with RNA metabolic labeling and nucleotide conversion within zebrafish embryos. We decompose single-cell transcriptomes into their new (zygotic) and old (maternal) mRNA components, and elicit critical information on gene regulation as it unfolds over both time and space. We show that most cell-type restricted expression arises by zygotic transcription, but distinguish a specific role for maternal transcripts in defining germ-cell and enveloping-layer identity, two earliest specified cell identities. We recover the underlying replacement between maternal and zygotic copies of embryonic genes with a relatively constant overall mRNA level, and associate a fast replacement with genes that has a restricted zygotic expression in either cell-type or time. Our study provides a valuable resource to investigate maternal and zygotic transcriptomes and reveals post-transcriptional events that control gene regulation during early embryogenesis.

overall_design: SLAM-seq, zebrafish embryos, 1hpf and 6hpf, 2 technical replicates

first: Lior

last: Fishman

first: Gal

last: Nechooshtan

first: Florian

last: Erhardt

first: Aviv

last: Regev

first: Jeff

last: Farrel


title: The initiation and maintenance of CHH methylation and its effects on gene expression are unique in maize

status: Public on May 10 2023

city: Oxford

first: Beibei

last: Liu

state: OH

address: Heather Ln. Apt.5

department: Biology Department

country: USA

institute: Miami university (Ohio)

type: Expression profiling by high throughput sequencing

type: Non-coding RNA profiling by high throughput sequencing

type: Methylation profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: A single-cell map of maternal and zygotic mRNA dynamics during cell-type specification in zebrafish embryos [scSLAM-seq]

status: Public on May 11 2023

city: Jerusalem

first: Michal

last: Rabani

address: Hebrew University, Edmond J. Safra Campus, Silberman building

country: Israel

institute: Hebrew University of Jerusalem

overall_design: single cell, SLAM-seq, 3 developmental stages, with treated and untreated samples, and biological replicates


title: A novel kinase inhibitor for b-catenin mutant hepatocellular carcinoma [Cut&Run]

status: Public on May 03 2023

city: New York

first: Julia

middle: Nanyi

last: Zhao

state: NY

address: 1470 Madison Ave

department: Oncological Sciences

institute: Icahn School of Medicine at Mount Sinai

type: Genome binding/occupancy profiling by high throughput sequencing

summary: We screened HCC organoids to identify a CTNNB1-mutant HCC selective small molecule (WNTinib), with MOA depending on reactivation of cytoplasmic EZH2, leading to its nuclear translocation and selective transcriptional block of WNT targets

overall_design: Comparative Cut and Run analysis of H3K27me3-binding sites for MYC-CTNNB1 organoids +/- WNTinib vs MYC-Tp53 organoids +/- WNTinib, at 2 timepoints (+DMSO)

first: Alex

last: Rialdi

middle: N

first: Austin

last: Meadows

first: Xuedi

last: Wang


title: A novel kinase inhibitor for b-catenin mutant hepatocellular carcinoma II


title: Ribosomal frameshifting at normal codon repeats recodes functional chimeric proteins in human.

status: Public on May 01 2023

city: KunMing

first: Lu

last: Zhang

state: YunNan

address: WuJiaYing Street

country: China

institute: YunNan University


title: Ribosomal frameshifting at normal codon repeats recodes functional chimeric proteins in human[ChIP-seq]

summary: Ribosomal frameshifting refers to the process that ribosomes slip into +1 or -1 reading frame, thus produce chimeric trans-frame proteins. In viruses and bacteria, programmed ribosomal frameshifting can produce essential trans-frame proteins for viral replication or regulation of other biological processes. In humans, however, functional trans-frame protein derived from ribosomal frameshifting is scarcely documented. Combining multiple assays, we show that short codon repeats could act as cis-acting elements that stimulate ribosomal frameshifting in humans, abbreviated as CRFS hereafter. Using proteomic analyses, we identified many putative CRFS events from 32 normal human tissues supported by trans-frame peptides positioned at codon repeats. Finally, we show a CRFS-derived trans-frame protein (HDAC1-FS) functions by antagonizing the activities of HDAC1, thus affecting cell migration and apoptosis. These data suggest a novel type of translational recoding associated with codon repeats,which may expand the coding capacity of mRNA and diversify the regulation in human.

overall_design: ChIP-seq for the histone modifications H3K9ac to understand FS

first: GuiPing

last: Ren

first: ZhanBiao

last: Li


title: Multiomic profiling of in vitro models of endothelial-to-mesenchymal transition reveals endothelial cell subtype is a major determinant of fidelity to observed states in atherosclerosis

city: Tucson

first: Casey

last: Romanoski

state: AZ

address: 1230 N Cherry Ave

institute: U. Arizona

summary: Endothelial-to-mesenchymal transition (EndMT) is an example of endothelial cell (EC) heterogeneity which is commonly modeled in vitro to better understand driving mechanisms of disease proceses, including atherosclerosis. We used multi-modal single nucleus RNA sequencing (snRNA-seq) and ATAC sequencing (snATAC-seq) to analyze the diversity of ECs in vitro, divergent EC responses to known EndMT perturbations, and the ability of in vitro EC known EndMT models to recapitulate the in vivo 'omic profiles of cells observed in atherosclerosis.

overall_design:
ECs were treated with and without known EndMT-promoting perturbations and subject to 10x Genomics snRNA-seq and snATAC-seq.
Please note that processed data files generated from both scRNA-seq and ATAC-seq raw data are linked to the corresponding *RNA sample records.

first: Maria

middle: L

last: Adelus

first: Jiacheng

last: Ding

first: Binh

middle: T

last: Tran

middle: C

last: Conklin

first: Anna

middle: K

last: Golebiewski

first: Lindsey

last: Stolze

first: Michael

middle: B

last: Whalen

first: Darren

middle: A

last: Cusanovich

middle: E


title: Ribosomal frameshifting at normal codon repeats recodes functional chimeric proteins in human [RNA-seq]

summary: Ribosomal frameshifting refers to the process that ribosomes slip into +1 or -1 reading frame, thus produce chimeric trans-frame proteins. In viruses and bacteria, programmed ribosomal frameshifting can produce essential trans-frame proteins for viral replication or regulation of other biological processes. In humans, however, functional trans-frame protein derived from ribosomal frameshifting is scarcely documented. Combining multiple assays, we show that short codon repeats could act as cis-acting elements that stimulate ribosomal frameshifting in humans, abbreviated as CRFS hereafter. Using proteomic analyses, we identified many putative CRFS events from 32 normal human tissues supported by trans-frame peptides positioned at codon repeats. Finally, we show a CRFS-derived trans-frame protein (HDAC1-FS) functions by antagonizing the activities of HDAC1, thus affecting cell migration and apoptosis. These data suggest a novel type of translational recoding associated with codon repeats, which may expand the coding capacity of mRNA and diversify the regulation in human.

overall_design: Comparative gene expression profiling analysis of RNA-seq data


title: A novel kinase inhibitor for b-catenin mutant hepatocellular carcinoma [RNA-seq]

summary:
We screened HCC organoids to identify a CTNNB1-mutant HCC selective small molecule (WNTinib), with MOA depending on reactivation of cytoplasmic EZH2, leading to its nuclear translocation and selective transcriptional block of WNT targets
We then performed gene expression profiling analysis using data obtained from RNA-seq of 2 genetically different organoids at 3 time points.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for MYC-CTNNB1 organoids +/- WNTinib vs MYC-Tp53 organoids +/- WNTinib (DMSO as controls)

first: Kevin

last: Mohammed


title: Single cell RNA sequencing on PyMT mammary gland primary tumor and lung metastases

status: Public on Apr 29 2023

city: Bronx

first: Rachel

last: Hazan

address: 1300 Morris Park Avenue

department: Pathology

institute: Albert Einstein College of Medicine

summary: Using scRNA-seq of the PyMT/GPx2 KD versus the PyMT control tumor model, we identified an overlap in cell clustering involving six luminal-like clusters and one basal/mesenchymal-like cluster (cluster 3). Similarly, scRNA-seq of lung metastases derived from the GPx2 KD tumor unraveled several luminal-like clusters and one mesenchymal-like cluster (M-cluster) which was highly homologous to primary tumor cluster 3.

overall_design: PyMT-GPx2 KD tumor cells were GFP-labeled in vitro and then injected into mammary fat pad of mice for incubating 45 days. We then harvested GPx2 KD primary tumor and lungs and generated single cell suspension by FACS sorting from GPx2 KD, and paired lung metastases. 10X Genomics was used to make cDNA library. We then sequenced the samples with Illumina high throughput sequencing.

first: Zuen

first: Jessica

last: Mar

first: Atefeh

last: Taherian Fard

first: Malindrie

last: Dharmaratn

first: Ameya

last: Kulkarni


title: Transcriptomic profiling of human pancreatic cell lines hPNE/hTert stably over-expressing DNMTs compared to GFP-hPNE/hTert over-expressing control cells after lentiviral transduction

status: Public on Apr 20 2023

city: Toulouse

first: jerome

last: torrisani

address: 2 avenue Hubert Curien

country: France

institute: inserm

summary:
The overexpression of DNA methyltransferases (DNMTs) is a common hallmark of numerous cancers. These aberrant changes in DNA methylation profiles are correlated to the overexpression of DNMTs.
Although this association is clearly demonstrated, the causal role of DNMT overexpression in pancreatic cancer has not been clearly established.
Consequently, we decided to determine whether DNMT overexpression induces diffrent methylation patterns in non-cancerous pancreatic cells.

overall_design: Four-condition experiment. DNMT1-hPNE/hTert, DNMT3A-hPNE/hTert, DNMT3B-hPNE/hTert vs GFP-hPNE/hTert Control stable cell lines. Biological replicates: 4 DNMTs-hPNE/Tert replicates, 3 GFP-hPNE/hTert replicates.

first: Jerome

last: Torrisani

first: Lucrece

last: Dagnon

first: Pascal

middle: G

last: Martin

first: Yannick

last: Lippi


title: Role of Dppa3 during primordial germ cell development II

status: Public on Apr 27 2023

city: Fukuoka

first: Wan Kin

last: Au Yeung

address: 3-1-1 Maidashi, Higashi-ku

department: Medical Institute of Bioregulation

country: Japan

institute: Kyushu University

summary: We performed whole-genome bisulfite sequencing of Dppa3 knockout fully grown oocytes (FGOs).

overall_design: Isolation of FGOs from control and Dppa3 knockout mice for genome-wide analysis

first: Keisuke

last: Toriyama

first: Hiroyuki

last: Sasaki


title: Gastrulation-stage gene expression in Nipbl+/- mouse embryos foreshadows the development of syndromic birth defects

status: Public on May 07 2023

city: Irvine

first: Anne

last: Calof

state: CA

address: Biological Sciences III, 519 Ring Rd

department: Developmental & Cell Biology

institute: University of California, Irvine

summary: In animal models, Nipbl-deficiency phenocopies gene expression changes and birth defects seen in Cornelia de Lange Syndrome (CdLS), the most common cause of which is Nipbl-haploinsufficiency. Previous studies in Nipbl+/- mice identified aberrant gene expression and heart defects as early as cardiac crescent (CC) stage. Here, we performed single-cell RNA-sequencing on wildtype (WT) and Nipbl+/- mouse embryos at CC- and earlier (gastrulation) stages. Nipbl+/- embryos had fewer mesoderm cells than WT and altered proportions of mesodermal cell subpopulations. These findings were associated with an underexpression of genes implicated in driving specific mesodermal lineages. Nipbl+/- embryos also misexpressed developmentally-critical genes, including the transcription factor, Nanog, and genes governing left-right and anterior-posterior patterning. These events of cell misallocation and transcriptional dysregulation foreshadowed defects in tissue composition and patterning that arise later in Nipbl+/- mice, offering insights into early developmental contributions to birth defects in CdLS.

overall_design:
We performed single cell RNA sequencing (10X Genomics Chromium) on 2 pairs of E7.4 early bud wildtype mouse embryos, 5 pairs of E7.5 late bud Nipbl Flox/+ (which express Nipbl at wildtype levels) embryos, 6 pairs of E7.5 late bud Nipbl FIN/+ (which express Nipbl at Nipbl +/- levels) embryos, 2 pairs of E7.6 early head fold wild type embryos, 8 E7.75 cardiac crescent Nipbl Flox/+ embryos, and 8 E7.75 cardiac crescent Nipbl FIN/+ embryos.

Update: [09-22-2023] GSM4586367 (LB_FLOX_2) was removed because the sample  contained cells of mixed genotype.
Update: [10-17-2023] Additional samples, and processed data generated from multiple/merged samples (as detailed in the readme.txt) have been included.

first: Stephenson

last: Chea

first: Arthur

middle: D

last: Lander


title: Role of Dppa3 during primordial germ cell development I

summary: We performed whole-genome bisulfite sequencing and RNA-seq analysis of Stella knockout primordial germ cells (PGCs).

overall_design: Isolation of GFP-positive PGCs from control and Stella knockout PGCs for genome-wide analysis


title: Aberrant activation of canonical Notch1 signaling in the mouse prostate drives epithelialcell proliferation and induces prostatic hyperplasiaby increasing androgen receptor sensitivity

status: Public on Apr 11 2023

city: Guangzhou

first: Ren-Wei

last: Su

state: Guangdong

address: 483 Wushan Road

department: Histology and Embryology

institute: South China Agricultural University

summary: To investigate the regulatory role of Notch1 signaling pathway in mouse prostate growth and development, we constructed mice with prostate-specific overactivation of Notch1 intracellular domain N1ICD, in which Notch1 signaling was overactivated in prostate epithelial cells. We then analyzed gene expression profiles in the prostates of overexpressed and normal Notch1 mice.

overall_design: Comparative analysis of gene expression profiles of RNA-SEQ data from two types of mouse anterior prostatic cells.

first: Renwei


title: Molecular characterization stratifies VQ myeloma cells into two clusters with distinct risk signatures and drug responses [Repertoire-Seq]

status: Public on Apr 04 2023

city: Milwaukee

first: Demin

last: Wang

state: WI

address: 8727 West Watertown Plank Road

institute: Versiti Blood Research Institute

summary: Multiple myeloma (MM) is a cancer of malignant plasma cells in the bone marrow and extramedullary sites. We previously characterized a VQ model for human high-risk MM. Different VQ lines display distinct disease phenotypes and survivals, suggesting significant intra-model variation. Here, we use whole exome sequencing and copy number variation (CNV) analysis coupled with RNA-Seq to stratify VQ lines into corresponding clusters: Group A cells had monosomy chr5 and overexpressed genes and pathways associated with sensitivity to bortezomib (Btz) treatment in human MM patients. By contrast, Group B VQ cells carried recurrent amplification (Amp) of chromosome (chr) 3 and displayed high-risk MM features, including downregulation of Fam46c, upregulation of cancer growth pathways associated with functional high-risk MM, and expression of Amp1q and high-risk UMAS-70 and EMC-92 gene signatures. Consistently, in sharp contrast to Group A VQ cells that showed short-term response to Btz, Group B VQ cells were de novo resistant to Btz in vivo. Our study highlights Group B VQ lines as highly representative of the human MM subset with ultrahigh risk.

overall_design: high-throughput sequencing analysis of BCR repertoire on four primary VQ donor lines (VQ-D1, D2, D4, and D5), as well as two cell lines derived from VQ-D2 recipient mice (4935 and 4938)

first: Evan

last: Flietner

first: Mei

last: Yu

first: Govinda

last: Poudel

first: Anthony

middle: J

last: Veltri

first: Yun

last: Zhou

first: Adhithi

last: Rajagopalan

first: Yubin

last: Feng

first: Terra

last: Lasho

first: Zhi

last: Wen

first: Yuqian

last: Sun

first: Mrinal

middle: M

last: Patnaik

first: Natalie

middle: S

last: Callander

first: Fotis

last: Asimakopoulos

first: Jing

last: Zhang


title: Molecular characterization stratifies VQ myeloma cells into two clusters with distinct risk signatures and drug responses [RNA-Seq]

overall_design: RNA-Seq libraries of MM cells isolated from BM, spleen, LN, liver from multiple recipient mice that received transplantation of VQ-D1, VQ-D2, VQ-D4, VQ-D5, or t-VK12653 donor cells.


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

status: Public on Apr 10 2023

first: Jian-Hua

last: Yang

address: No. 135, Xingang Xi Road

department: School of Life Sciences

institute: Sun Yat-sen University

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

overall_design: Total or subcellular RNA were ligated to small RNA-seq adapors, 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

first: Anrui

first: Di

last: Wu

first: Jie

first: Ping

first: Chang

first: Qiao

last: Lin

first: Xiaoqin

first: Qiaojuan

last: Huang

first: Hui

first: Lianghu

last: Qu

first: Jianhua


title: Molecular characterization stratifies VQ myeloma cells into two clusters with distinct risk signatures and drug responses

first: Demin

last: Wang


title: TRAIL receptor associates with phosphatase SHP-1 and enables suppressing T-cell receptor signaling via inactivating Lck

status: Public on Apr 06 2023

city: Taipei

first: I-Tsu

last: Chyuan

state: Outside of the US

address: No. 280, Sec. 4, Renai Rd.

department: Internal Medicine

country: Taiwan

institute: Cathay General Hospital

summary: We utilized whole-transcriptome RNA sequencing (RNA-seq) in TRAIL-treated activated T cells to identify the gene expression signatures and the possible regulatory pathways associated with TRAIL-R signaling on T-cell activation.

overall_design: CD4+ T cells were isolated from murine spleens using negative selection kits, EasySep™ Mouse CD4+ T Cell Isolation Kit (StemCell Technologies), and were cultured in RPMI-1640 medium (Invitrogen) containing 10% fetal calf serum (Invitrogen) plus penicillin (10 units/ml) and streptomycin (10 µg/ml) (Invitrogen). The CD4+ T cells were stimulated with anti-CD3 (3 µg/ml) and anti-CD28 (2 µg/ml) antibodies (BioLegend) in the presence or absence of TRAIL (10 µg/ml)(GenScript) for 24 hours. Total RNA extraction was performed using TRIzol (Invitrogen) following the manufacturer's protocol. RNA libraries for RNA-seq were prepared using Agilent SureSelect XT HS2 mRNA Library Prep Kit following manufacturer's protocols.

first: Ping-Ning

last: Hsu


title: T cell immunotherapies trigger neutrophil activation to eliminate tumor antigen escape variants [bulk RNA-seq]

status: Public on Mar 30 2023

first: Levi Mark

middle: Bala

last: Mangarin

address: 413 E 69th St

department: Meyer Cancer Center

institute: Weill Cornell Medical Center

summary: RNAseq data set of Ly6g+ FACS sorted mouse tumors

overall_design: Bulk RNAseq of mice across treatment conditions

first: Daniel

last: Hirschhorn

first: Levi

first: David

last: Redmond

first: Taha

last: Merghoub


title: A comprehensive map of early T cell development at single-cell resolution

status: Public on Apr 03 2023

city: Fitzroy

first: Mark

last: Chong

state: Victoria

address: 9 Princes Street

country: Australia

institute: St Vincent's Institute of Medical Research

summary: To achieve a more precise understanding of early T cell development, single-cell RNA-sequencing (scRNA-seq) was employed to re-assemble de novo a model of the early stages in T cell development based on the transcriptional profiles of individual cells. >20,000 CD4-CD8- double negative (DN) and gammadelta thymocytes were analysed using Chromium 10x scRNA-seq over three runs. This revealed a comprehensive map of early T cell development at single-cell resolution.

overall_design: Single-cell RNA-sequencing of DN and gammadelta thymocytes from mouse thymus.

first: Xin


title: T cell immunotherapies trigger neutrophil activation to eliminate tumor antigen escape variants

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

overall_design: Refer to individual Series


title: T cell immunotherapies trigger neutrophil activation to eliminate tumor antigen escape variants [scRNA-Seq]

summary: scRNAseq data set of CD11b sorted B16;B7H1 mixed mouse tumors treated with IgG or aOX40

overall_design: Single cell transcriptome and hashtaging of 5 mice per condition


title: Single-cell RNA-sequencing from stroma in a mouse submandibular salivary gland 14 days after ligation or mock surgery

status: Public on Mar 29 2023

city: Albany

first: Melinda

last: Larsen

address: 1400 Washington Ave., LSRB 10

department: Dept. of Biological Science

institute: University at Albany, SUNY

summary: The submandibular salivary gland stroma makes up only a small portion of the total salivary gland and the stromal response to salivary gland injury has been understudied. We used single-cell RNA-sequencing (scRNAseq) to analyze which cell types are present in both control and ligated samples, how the cell type abundance is altered following injury, and how the transcriptome of those cells is being altered. This will allow us to examine which cell types are important contributors to fibrosis induced by salivary gland ductal ligation injury.

overall_design: Submandibular salivary glands were dissociated into single cells followed by two rounds of magnetic activated cell sorting (MACs) to deplete for epithelial cells expressing EpCAM and red blood cells expressing Ter119. The samples then went through one round of dead cell removal using Miltenyi dead cell removal kit.

first: Amber

last: Altrieth

first: Joey

last: Tavarez

first: Nicholas

last: Moskwa

first: Deirdre

last: Nelson


title: A realistic mixture of Persistent Organic Pollutants affects zebrafish embryogenesis and behavior

status: Public on Mar 31 2023

city: Liège

first: Marc

last: Muller

address: B34 Sart Tilman

department: Life Sciences

country: Belgium

institute: Université de Liège

summary: A realistic mixture of Persistant Organic Pollutants (POPs), as found in the blood of a Scandinivian population, was used at realistic concentrations to evaluate developmental, behavioral, and gene expression modifications in zebrafish larvae.

overall_design: Zebrafish embryos were treated with an artificial mixture of POPs, designed using data from blood serum contaminations in a Scandinavian population, at 0, 75x, or 125x the concentration found in the blood serum.

first: Gustavo

last: Guerrero-Limon

first: Dinh

last: Thanh


title: Dynamics of Chromatin Accessibility during Hematopoietic Stem Cell Differentiation into Lineage-Committed Progeny

city: Santa Cruz

first: Camilla

last: Forsberg

state: California

address: 1156 High Street

institute: Institute for the Biology of Stem Cells, University of California Santa Cruz

summary: Epigenetic mechanisms regulate the multilineage differentiation capacity of hematopoietic stem cells (HSCs) into a variety of blood and immune cells. Our recent work revealed evidence of multilineage gene priming in HSCs, where open cis-regulatory elements (CREs) exclusively shared between HSCs and unipotent lineage cells were enriched for DNA binding motifs of known lineage-specific transcription factors. To test the hypothesis that HSC-primed lineage-specific CREs remain accessible throughout differentiation, we used ATAC-seq to map the temporal dynamics of chromatin remodeling during blood cell differentiation. We observed epigenetic-driven clustering of oligopotent and unipotent progenitors into distinct erythromyeloid and lymphoid branches, with multipotent HSCs and MPPs associating with the erythromyeloid lineage. We mapped the dynamics of lineage-primed CREs throughout hematopoiesis and identified both unique and shared CREs as potential lineage reinforcement mechanisms at fate branch points in hematopoiesis. These findings provide insight into the regulation of stem cell multipotency and lineage commitment throughout hematopoiesis and serve as a resource to test functional drivers of hematopoietic lineage fate.

overall_design: ATAC-seq of Hematopoietic Progenitors, 7 cell types

first: Eric

middle: W

last: Martin

first: Alessandra

last: Rodriguez y Baena

first: Roman

last: Reggiardo

first: Jana

last: Krietsch

middle: H

last: Kim

first: E


title: Whole blood transcriptional profiling of pulmonary functional sequelae in ARDS- secondary to SARS-CoV-2 infection

status: Public on Mar 28 2023

city: Lleida

first: David

last: de Gonzalo-Calvo

state: Lleida

address: Rovira Roure 80

country: Spain

institute: IRBLleida

summary:
Up to 80% of patients surviving acute respiratory distress syndrome (ARDS) secondary to SARS-CoV-2 infection present persistent anomalies in pulmonary function after hospital discharge. There is a limited understanding of the mechanistic pathways linked to post-acute pulmonary sequelae.
Our main goal was to identify the molecular underpinnings associated with severe lung diffusion involvement in survivors of SARS-CoV-2-induced ARDS.
Survivors attended to a complete pulmonary evaluation 3 months after hospital discharge. RNA sequencing (RNA-seq) was performed using Illumina technology in whole-blood samples from 50 patients with moderate to severe diffusion impairment (DLCO<60%) and age- and sex-matched individuals with mild-normal lung function (DLCO≥60%). A transcriptomic signature for optimal classification was constructed using random forest. Transcriptomic data were analyzed for biological pathway enrichment, cellular deconvolution, cell/tissue-specific gene expression and candidate drugs.
RNA-seq identified 1357 differentially expressed transcripts. A model composed of 14 mRNAs allowed the optimal discrimination of survivors with severe diffusion impairment (AUC=0.979). Hallmarks of lung sequelae involved cell death signaling, cytoskeleton reorganization, cell growth and differentiation and the immune response. Resting natural killer (NK) cells were the most important immune cell subtype for the prediction of severe diffusion impairment. Components of the signature correlated with neutrophil, lymphocyte and monocyte counts. A variable expression profile of the transcripts was observed in lung cell subtypes and bodily tissues. One upregulated gene, TUBB4A, constitutes a target for FDA-approved drugs.
This work defines the transcriptional programme associated with post-acute pulmonary sequelae and provides novel insights for targeted interventions and biomarker development.

overall_design: Comparative gene expression profiling analysis of RNAseq data from whole blood from survivors of COVID-19-driven ARDS with moderate-to-severe functional pulmonary sequelae (DLCO<60% of predicted; group of study) and with mild or absence of functional pulmonary sequelae (DLCO≥60% of predicted; control group).

first: María

last: García-Hidalgo

first: Rafael

last: Peláez

first: Ignacio

last: Larráyoz


title: Effect of norepinephrine and/or propranolol on fallopian tube epithelial cells in ultra-low attachment conditions

status: Public on Mar 27 2023

city: Philadelphia

first: Hunter

last: Reavis

state: PA

address: 421 Curie Blvd

institute: University of Pennsylvania

summary: To investigate the role of norepinephrine on 3D spheroid formation and survival in early high-grade serous ovarian cancer, we cultured immortalized human fallopian tube epithelial cell lines in ultra-low attachment conditions in the presence or absence of norepinephrine and/or propranolol over 2 different timepoints.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for FT237 and FT246 cultured under ultra-low attachment conditions for 4 or 24 hours, -/+ norepinephrine and/or propranolol

first: Renata

last: Pellegrino Da Silva

first: Jamie

last: Moon

first: Priyanka

last: Rawat

first: Dave

last: Hoon

first: Ronny

last: Drapkin


title: scRNA-seq profiling of tumor microenvironment in glioblastoma patient-derived orthotopic xenogratfs (PDOXs)

status: Public on Mar 07 2023

city: Esch-sur-Alzette

first: Kamil

last: Grzyb

email: kamilgen@gmail.com, kamil.grzyb@uni.lu

address: 2, avenue de l'Université

country: Luxembourg

institute: University of Luxembourg - LCSB

summary: Single-cell RNA-sequencing was performed on the tumor microenvironment of the glioblastomas isolated from PDOX models (Golebiewska et al., Acta Neuropathologica, 2020; Oudin et al., STAR Protocols 2021). Sample names correspond to PDOX models. Normal mouse brain was used as a contol. One PDOX model was treated with temolozomide (P3TMZ).

overall_design: Glioblastoma tumors were derived by intracranial implantation of patient-derived organoids in the brain of nude mice. A total of 9 glioblastoma tumor models and one normal brain (Nude-brain) were processed for scRNA-seq.  P3 PDOX model was collected from untreated and temozolomide-treated mice (P3 vvs P3TMZ). DROP-seq was performed on the mouse cells corresponding to the the tumor microenvironment in PDOXs.

first: Yahaya

last: Yabo

first: Alexander

last: Skupin

first: Alessandro

last: Michelucci

first: Anna

last: Golebiewska


title: Simultaneous single-cell analysis of 5mC and 5hmC with SIMPLE-seq

status: Public on Feb 28 2023

city: New York

first: Dongsheng

last: Bai

address: 101 Avenue of the Americas

institute: New York Genome Center

summary: We used a new technology, named SIMPLE-seq, to perform simultaneous profiling of 5mC and 5hmC on mESCs and PBMCs at single-cell,single molecule level.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: We develop SIMPLE-seq for simultaneously profiling the genome-wide true methylome and hydroxymethylome quantitatively, in highly scalable single-cell manner. SIMPLE-seq measures both true 5mC and 5hmC on the same DNA molecule from one cell. To demonstrate the utility of SIMPLE-seq, we measured single-cell methylome and hydroxymethylome in mouse embryonic stem cells (mESC) and human peripheral blood mononuclear cells.

first: Chenxu

last: Zhu


title: DNA methylation profiling for molecular classification of adult diffuse lower‑grade gliomas

status: Public on Feb 27 2023

city: Gothenburg

first: Helena

last: Carén

address: Medicinaregatan 1F

country: Sweden

institute: University of Gothenburg

type: Methylation profiling by genome tiling array

summary: DNA methylation profiling has become a powerful tool for neuro-oncology diagnostics. We investigated the value of using DNA methylation profiling to achieve molecular diagnosis in adult primary diffuse lower-grade gliomas according to WHO 2016 classification system of central nervous system tumors. We further evaluated the use of methylation profiling for improved molecular characterization of the tumors and identify prognostic differences beyond histological grade and molecular markers (IDH mutation and 1p/19q codeletion status).

overall_design: We investigated genome-wide DNA methylation profiles of 106 IDH-mutant gliomas using the Infinium MethylationEPIC BeadChip (Illumina, San Diego, USA) according to the manufacturer's instructions.

first: Sandra

last: Ferreyra Vega

first: Asgeir

last: Jakola


title: Comprehensive mutagenesis of AAV2 rep

city: Boston

first: Nina

last: Jain

state: Massachusetts

address: CLSB 5FL 528/6c, Center for Life Sciences, 3 Blackfan Circle

department: Wyss Institute

institute: Harvard University

summary: Recombinant adeno-associated viruses (rAAVs) are the predominant gene therapy vector. Several rAAV vectored therapies have achieved regulatory approval, but production of sufficient rAAV quantities remains difficult. The AAV Rep proteins, which are essential for genome replication and packaging, represent a promising engineering target for improvement of rAAV production but remain underexplored. To gain a comprehensive understanding of the Rep proteins and their mutational landscape, we assayed the effects of all 39,297 possible single codon mutations to the AAV2 rep gene on AAV2 production. Most beneficial variants are not observed in nature, indicating that improved production may require synthetic mutations. Additionally, the effects of AAV2 rep mutations were largely consistent across capsid serotypes, suggesting that production benefits are capsid independent. Our results provide a detailed sequence-to-function map that enhances our understanding of Rep protein function and lays the groundwork for Rep engineering and enhancement of large scale gene therapy production.

overall_design: Two plasmid libraries, WT AAV2 and pCMV-Rep78/68, containing all possible single codon mutations to the AAV2 rep gene were cloned. The WT AAV2 library also expresses the AAV2 cap gene while the pCMV-Rep78/68 library only expresses the rep gene. The library formats also differ in the promoter used to drive rep expression: p5 in the WT AAV2 library and CMV in the pCMV-Rep78/68 library. Variants in each library contain unique 20 bp barcodes at the 3' end of rep/cap and ITRs to enable packaging of rep variant sequences into AAV capsids. The plasmid libraries were transfected into HEK293T cells to produce AAV2 capsids. Viral particles were purified and barcodes were amplified and sequenced from both the plasmid and viral pools. The pCMV-Rep78/68 library was also used to investigate the effect of rep mutations on AAV5 and AAV9 capsid production. All transfections were conducted in duplicate.

first: Pierce

last: Ogden

first: George

last: Church


title: Expression data from mice bladder with MB49-induced cancer treated with alpha1-oleate alone or in combination Epirubicin or Mitomycin C, short-term effects

status: Public on Feb 25 2023

city: Lund

first: Ines

last: Ambite

address: Klinikgatan 28

department: Laboratory Medicine

institute: Lund University

summary: Bladder cancer is common and one of the most costly cancer forms, due to a lack of curative therapies. Recently, clinical safety and efficacy of the alpha1-oleate complex was demonstrated in a placebo-controlled study of non-muscle invasive bladder cancer. This study investigated if long-term therapeutic efficacy is improved by repeated treatment cycles and by combining alpha1-oleate with low-dose chemotherapy. Rapidly growing bladder tumors were treated by intravesical instillation of alpha1-oleate, Epirubicin or Mitomycin C alone or in combination. One treatment cycle arrested tumor growth, with a protective effect lasting at least four weeks in mice receiving 8.5 mM of alpha1-oleate alone or 1.7 mM of alpha-oleate combined with Epirubicin or Mitomycin C. Repeated treatment cycles extended protection, defined by a lack of bladder pathology and a virtual absence of bladder cancer-specific gene expression. Synergy with Epirubicin was detected at the lower alpha1-oleate concentration and alpha1-oleate was shown to enhance the uptake and nuclear translocation of Epirubicin, by tumor cells. Effects at the chromatin level affecting cell proliferation were further suggested by reduced BrdU incorporation. In addition, alpha1-oleate triggered DNA fragmentation, defined by the TUNEL assay. The results suggest that bladder cancer development may be prevented long-term in the murine model, by alpha1-oleate alone or in combination with low-dose Epirubicin. In addition, the combination of alpha1-oleate and Epirubicin reduced the size of established tumors. Exploring these potent preventive and therapeutic effects will be of immediate interest in patients with bladder cancer.

overall_design: Bladder cancer was induced in C57BL/6J female mice by intravesical instillation of MB49 (RRID:CVCL7076) mouse bladder carcinoma cells (2 × 10^5 cells in 50 μl cell media) in empty bladders preconditioned by intravesical instillation of 100 μl of poly-L-lysine solution (0.1 mg/ml, 30 minutes). Mice were randomly assigned to the different treatment groups and subjected to 100 μl instillations with alpha1-oleate (1.7 mM or 8.5 mM) or chemotherapeutic drugs (MMC 25 μg, Epirubicin 25 μg), alone or in combination on days 3, 5, 7, 9 and 11. Sham treated mice received PBS and healthy mice bladders were used as control. The catheter was left in place for about one minute and the time to voiding was 2 - 3 hours. Bladder samples were collected on day 12 day or day 28 days (follow-up, 4 weeks). Isolated RNA was subjected to Affymetrix whole genome transcriptomic analysis.

first: Hien

last: Tran

first: Murphy

last: Wan

first: Catharina

last: Svanborg


title: Expression data from mice bladder with MB49-induced cancer treated with alpha1-oleate alone or in combination Epirubicin or Mitomycin C, long-term effects

overall_design: Bladder cancer was induced in C57BL/6J female mice by intravesical instillation of MB49 (RRID:CVCL7076) mouse bladder carcinoma cells (2 × 10^5 cells in 50 μl cell media) in empty bladders preconditioned by intravesical instillation of 100 μl of poly-L-lysine solution (0.1 mg/ml, 30 minutes). Mice were randomly assigned to the different treatment groups and subjected to 100 μl instillations with alpha1-oleate (8.5 mM) alone or in combination with chemotherapeutic drugs (MMC 25 μg, Epirubicin 25 μg). Other mice were subjected to 2 or 3 treatment rounds (5 consecutive treatments, 1 every other day), starting on days 3, 28 and 56. Bladder samples were then collected on days 56 (8 weeks, 2 treatment rounds) and 84 (12 weeks, 3 treatment rounds), respectively. Sham treated mice received PBS and healthy mice bladders were used as control. The catheter was left in place for about one minute and the time to voiding was 2 - 3 hours. Isolated RNA was subjected to Affymetrix whole genome transcriptomic analysis.


title: Expression data from mice bladder with MB49-induced cancer treated with alpha1-oleate alone or in combination Epirubicin or Mitomycin C


title: Transcriptome characterization of embryogenesis at a single cell resolution [C. elegans]

status: Public on Mar 22 2023

city: Vienna

first: Alison

last: Cole

address: Djerassiplatz 1

department: Neurosciences and Developmental Biology

country: Austria

institute: University of Vienna

summary: By collecting and processing individual embryonic cells from sequentially older embryos we have generated the first single cell transcriptome dataset describing embryogenesis from the fertilizaed zygote through to the  penultimate cell division for most founder cell lines.

overall_design: Embryos from approximately the first 450 minutes of embryonic development were collected. Individual embryos were dissociated manually and single cells were collected for processing. Each cell was barcoded, and samples were multiplexed into a single sequencing library for each embryo processed.

first: Tamar

last: Hashimshony

first: Itai

last: Yanai


title: MacroH2A histone variants modulate enhancer activity to repress oncogenic programs and cellular reprogramming

status: Public on Feb 21 2023

city: Rochester

first: Alexandre

last: Gaspar-Maia

state: MN

address: 200 First street SW

institute: Mayo Clinic

summary: In this study, we have identified a unique type of enhancer element that is bound by the histone variant macroH2A and devoid of the active histone mark H3K27ac through a comprehensive analysis performed using the cis-regulatory elements as recently described in ENCODE 3. To lay the ground for a better understanding of this new enhancer biology, we have surveyed the epigenetic landscape of four cell types (three normal and a cancer cell line) and incorporated the signal of several histone modifications and histone variants to classify enhancer elements, particularly, inactive ones. We validated our novel classification with gene expression signatures and defined a class of inactive enhancers enriched for macroH2a histone variants, which we termed ‘macro-Bound Enhancers’.

overall_design: To determine the relationship between enhancer activity and macroH2A enrichment, we profiled the epigenomes (using ChIP-seq and ATAC-seq) of several cell lines. We also performed single cell profiling in a estrogen responsive breast cancer cell line with and without macroH2A2

first: Wazim

last: Ismail

first: Dan

last: Hasson

first: Stephanie

last: Safgren

first: Tamas

last: Ordog

first: Emily

last: Bernstein


title: Fetal liver macrophages contribute to the hematopoietic stem cell niche by controlling granulopoiesi

status: Public on Feb 17 2023

city: Bonn

first: Amir Hossein

last: Kayvanjoo

address: Carl-Troll-Straße 31

country: Germany

institute: LIMES Institute


title: Gene expression profile at single cell level of various immune cell populations from the whole lung of treated and untreated mice.

status: Public on Feb 13 2023

city: Columbia

first: Bryan

last: Holloman

state: SC

address: 6311 Garners Ferry Rd

institute: University of South Carolina

summary: LPS induces a variety of changes to the lung immune cell landscape, this is also true with the treatment of Indole-3-Carbinol (I3C). We used single cell RNA sequencing (scRNA-seq) to analyze the diversity of immune cells in the lung.

overall_design: Acute lung injury was induced via intranasal introduction of LPS and subsequent treatment with I3C after 48 hours lungs were euthanized, single cell suspensions of the lung were collected, and analyzed using scRNAseq.

first: Holloman

last: Bryan Latrell

first: Cannon

last: Alkeiver

first: Wilson

last: Kiesha M

first: Nagarkatti

last: Prakash N

last: Mitzi


title: Fetal liver macrophages contribute to the hematopoietic stem cell niche by controlling granulopoiesi [bulkRNA-seq]

summary: Investigating the effect of macrophages on the function of LT-HSC and hematopoiesis during embryogenesis in the fetal liver

overall_design: Comparative gene expression profiling analysis of RNA-seq data of LT-HSCs between Tnfrsf11aCre/+; Spi1f/f and Spi1f/f

first: Amir

first: Iva

last: Splichalova

first: David

last: Bejarano

first: Hao

last: Huang

first: Katharina

last: Mauel

first: Nikola

last: Makdissi

last: Heider

first: Nora

middle: R

last: Balzer

first: Collins

last: Osei-Sarpong

first: Kevin

last: Bassler

first: Joachim

last: Schultze

first: Stefan

last: Uderhardt

first: Eva

last: Kiermaier

first: Marc

last: Beyer

first: Andreas

last: Schlitzer


title: Expression profile of primary murine astrocyte-enriched cultures (AEC) exposed to oxygen-glucose deprivation

status: Public on Feb 11 2023

city: setagaya-ku

first: Kengo

last: Moriyama

state: Tokyo

address: 2-1-6 kamikitazawa

institute: Tokyo metropolitan institute of medical science

summary: Microarray analysis was used to identify genes that fluctuated by oxygen-glucose deprivation of mouse astrocytes.  Astrocyte-enriched cultures were generated from mixed glial cultures of mice and compared to control samples with 15 hours of oxygen-glucose deprivation. The results showed that 173 genes were upregulated with Fold change >10, P < 0.05. Both Nr4a1 and Nr4a3, which is an orphan nuclear receptor subfamily and known as an immediate early gene, were upregulated.

overall_design: Oxygen-glucose deprivation (OGD) induced gene experession in mouse astrocyte enriched culture cells was measured at 15h exposure of OGD. One experiments were performed using different samples for the experiment.

first: Yasumasa

last: Nishito

first: Hiroshi

last: Sakuma


title: Differential gene expression in spt-2 mutant worms.

status: Public on Feb 09 2023

city: Cambridge

first: Francesco Nicola

last: Carelli

address: Henry Wellcome Building of Cancer and Developmental Biology,  Tennis Court Road

country: United Kingdom

institute: University of Cambridge

summary: The SPT-2 histone chaperone is involved in the maintenance of chromatin structure during transcription. Here, we performed mRNA-seq to compare gene expression profiles of spt-2 mutant worms. We compare two full spt-2 gene knock-out worm strains (KO-A and KO-B), or a strain expressing an spt-2 allele with reduced binding to histones (M627A), to wild type N2 worms.

overall_design: We performed mRNA-seq comparing RNA extracted from spt-2 mutant worms to WT control; worms were collected as synchronised adults. The experiment was performed in triplicate. We first compared WT to spt-2 KO worms (Batch 1) and then WT to spt-2 M627A worms (Batch 2).

first: Giulia

last: Saredi

first: Francesco

middle: N

first: Julie

last: Ahringer

first: John

last: Rouse


title: Identification of GFP-SPT-2 binding sites in the Caenorhabditis elegans genome

summary: We aimed at investigating whether the newly identified C. elegans SPT2 histone chaperone controls chromatin structure. We decided to profile SPT-2 binding sites to identify its genomic targets and we performed GFP ChIP-seq on a C. elegans strain expressing  endogenously GFP-tagged SPT-2, using WT N2 untagged worms as control for binding specificity.

overall_design: We performed GFP ChIP-seq on synchronised adult worms expressing endogenously GFP-tagged SPT-2, or WT N2 untagged controls. Two independent replicates of the experiment were performed.

first: Alex

last: Appert


title: Single-cell and Bulk Transcriptomics of the Human Submandibular Gland Reveals Conserved Factors and Pathways [Bulk RNA-seq]

status: Public on Feb 08 2023

city: Buffalo

first: Rose-Anne

last: Romano

address: Main Cir

institute: SUNY University at Buffalo

summary: We performed bulk RNA-sequencing analysis of human submandibular gland samples and then compared to expression of multiple human tissues in order to identify a salivary gland gene signature.

overall_design: Bulk RNA-sequencing was performed on 15 human submandibular gland samples. DEG analyses were performed in order to identify genes enriched in the SMG.

first: Erich

last: Horeth

first: Satrajit

last: Sinha


title: Acute versus long-term exercise adaptation of adipose tissue and skeletal muscle in humans: A matched transcriptomics approach after 8-week training-intervention

status: Public on Feb 01 2023

city: Neuherberg

first: Johannes

last: Beckers

address: Ingolstaedter Landstr. 1

department: Institute of Experimental Genetics

institute: Helmholtz Zentrum Muenchen

summary:
The participants performed an 8-week supervised aerobic endurance exercise intervention program. Biopsies of both adipose tissue and skeletal muscle were collected at associated timepoints and a matched analysis was performed.

This SuperSeries is composed of the SubSeries listed below.

overall_design:
We performed gene expression microarray analysis in human adipose and muscle tissue biopsies from subjects before and after acute exercise as well as before and after training interventions.

Refer to individual Series


title: Single-cell and Bulk Transcriptomics of the Human Submandibular Gland Reveals Conserved Factors and Pathways [scRNA-seq]

summary: Single-Cell RNA-seq Analysis of Human Submandibular Glands

overall_design: 1 male and 1 female human submandibular glands underwent single-cell RNA-sequencing Analysis


title: Methylation Analysis of ALK-positive pediatric Anaplastic Large Cell Lymphom

status: Public on Jan 02 2023

city: Memphis

first: Timothy

middle: Isham

last: Shaw

state: TN

address: 262 Danny Thomas Pl

department: Computational Biology

institute: St Jude Children's Research Hospital

summary: Anaplastic large cell lymphoma (ALCL) is a peripheral T-cell lymphoma that accounts for 10–15% of all childhood lymphomas. Despite the observation that more than 90% of the cases show ALK-rearrangement resulting in aberrant ALK kinase expression, there is significant clinical, morphologic, and biological heterogeneity. To gain insight into the molecular heterogeneity within ALK-positive ALCL, we analyzed 46 ALK-positive ALCL samples by whole-exome sequencing, RNA-sequencing, and DNA methylation array analysis. Gene expression and methylation profiling consistently subclassified ALK-positive ALCL cases into two groups differentiated by ALK expression level. The ALK-low group showed enrichment pathways of the immune response and cytokine signaling and were more heavily hypermethylated than the ALK high group, which was characterized by enriched pathways of cell growth, proliferation, metabolic pathways, and large copy number change. Taken together, these findings suggest that there is molecular heterogeneity within pediatric ALK+ALCL, predicting distinct biological mechanisms that may be utilized as prognostic markers.

overall_design: Methylation Analysis of 41 primary samples ALK-positive pediatric ALCL

first: Vasiliki

last: Leventaki


title: spt-2 in C. elegans.

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

sample_organism:
Caenorhabditis elegans
Homo sapiens

platform_organism:
Caenorhabditis elegans
Homo sapiens

overall_design: Refer to individual Series


title: A multi-omics atlas of the human retina at single-cell resolution

status: Public on Mar 14 2023

city: Palo Alto

first: Lattice

last: Data Coordination

address: 3165 Porter Drive

department: Genetics

institute: Stanford University

summary: Cell types in the human retina are highly heterogeneous with their abundance varies by several orders of magnitude. To decipher the complexity of gene expression and regulation of the human retinal cell types, we generated a multi-omics single-cell atlas of the adult human retina, including over 250K nuclei for single-nuclei RNA-seq and 150K nuclei for single-nuclei ATAC-seq. Over 60 cell subtypes have been identified based on their transcriptomic profiles, reaching a sensitivity of 0.01%. Integrative analysis of this single-cell multi-omics dataset identified gene regulatory elements across the genome for each cell subtype. In addition, when combined with other data modalities, such as eQTL, potential causal variants can be identified through fine mapping. Taken together, this new dataset represents the most comprehensive single-cell multi-omics profiling for the human retina that enables in-depth molecular characterization of most cell subtypes.

overall_design: snRNA-seq and snATAC-seq of peripheral region of retina tissue, fovea centralis tissue, macula lutea proper tissue, macula lutea tissue from 25 human donors. For the macular/foveal region, we directly profiled nuclei without enrichment. In contrast, for the retinal peripheral region, nuclei are fractioned based on the NeuN staining.

first: Rui

last: Chen

first: Margaret

last: DeAngelis

first: Qingnan

last: Liang

first: Xuesen

last: Cheng

first: Jun

last: Wang

first: Jin

last: Li


title: Investigating how the SPT-2 histone chaperone affects chromatin structure in C. elegans.

first: Francesco Nicola

last: Carelli

summary: Histone chaperones play essential roles in the regulation of chromatin structure. Here, we investigated how the SPT-2 histone chaperone controls chromatin structure and accessibility in C. elegans. To achieve this, we performed ATAC-seq comparing WT N2 worms to spt-2 KO or spt-2 histone binding mutant (spt-2 M627A) worms.

overall_design: We performed ATAC-seq on synchronised adult worms of the indicated genotypes, and two independent replicates of the experiment were performed.

first: Giulia

last: Saredi

first: Francesco


title: Variation of the Intestinal Microbiome during the life course of the Intra-Uterine Growth Restricted Rat Offspring Exposed to a High Fat and Fructose Diet

status: Public on Jan 11 2023

city: los angeles

first: Shubhamoy

last: Ghosh

address: 650 Charles E Young  Dr East

department: Pediatrics

institute: University of California Los Angeles

summary: We reported the variation in the  gut microbiome diversity under the influence of Intrauterine Growth restriction or Exposure to High Fat High fructose diet followed by Intrauterine growth restriction.

overall_design: We compared four experimental rat groups: 1) Ad lib fed regular chow diet pre- and postnatally (CON),   2-3) IUGR induced by maternal caloric restriction prenatally followed postnatally (PN) by either 2) the control diet (IUGR/RC) or   3) High-Fat-high-fructose (IUGR/HFhf) diet, and lastly 4) HFhf ad lib pre- and postnatally (HFhf).   Fecal samples were collected from dams and male and female rat offspring at postnatal day 2, 21, adult at  day 180d, and subjected to microbiome analysis by 16S-based rRNA sequencing.

first: Liesbeth

last: Maggiotto

first: Bo-Chul

last: Shin

first: Jonathan

last: Jacobs

first: Sherin

last: Devaskar


title: Epitranscriptomic regulation of cortical neural stem cell maintenance via Mettl8-dependent mitochondrial tRNA m3C modification

status: Public on Jan 12 2023

city: Philadelphia

first: Feng

last: Zhang

address: 415 Curie Boulevard

department: Department of Neuroscience and Mahoney Institute for Neurosciences

institute: Perelman School for Medicine, University of Pennsylvania

summary:
Increasing evidence implicates critical roles of various epitranscriptomic RNA modifications in different biological processes. Methyltransferase METTL8 installs 3-methylcytosine modification of mitochondrial tRNAs in vitro, however, its role in intact biological systems is completely unknown. Here we show that Mettl8 is localized in the mitochondria and installs m3C in mitochondrial tRNASer(UCN)/Thr in mouse embryonic cortical neural stem cells.
At molecular and cellular levels, Mettl8 deletion in cortical neural stem cells leads to reduced mitochondrial protein translation and attenuated respiration activity. At the functional level, conditional Mettl8 deletion in mice results in impaired embryonic cortical neural stem cell maintenance in vivo, which can be rescued by pharmacologically enhancing mitochondrial functions. Similarly, METTL8 regulates mitochondrial protein expression and neural stem cell maintenance in human forebrain cortical organoids. Together, our study reveals a conserved epitranscriptomic mechanism of Mettl8 and mitochondrial tRNA m3C modification in maintaining embryonic cortical neural stem cells in mice and humans.

overall_design: Comparative gene expression profiling analysis of RNA-seq data and genome-wide Mettl8-dependent m3C modification profiling for wild-type (WT) and Mettl8-conditional-knockout (cKO) mouse neural progenitor cells (NPCs) cultured in vitro.

first: Kijun

last: Yoon

first: Daniel

middle: Y

first: Nam-Shik

last: Kim

first: Guo-li

last: Ming

first: Hongjun

last: Song


title: Global and cell type-specific immunological hallmarks of severe dengue progression

status: Public on Jan 16 2023

city: Kensington

first: Yike

last: Xie

state: NSW

address: Lowy 2, Cnr High and Botany St

institute: UNSW Sydney

summary: Dengue virus (DENV) causes widespread mosquito-borne infection. While most symptomatic patients experience mild disease, a fraction progresses to severe dengue (SD)--a life-threatening condition whose pathogenesis remains largely unknown. We integrated virus-inclusive single cell RNA-Seq 2 (viscRNA-Seq 2) with functional assays to determine the immunological hallmarks of SD progression in children’s blood. We show that beyond myeloid cells, in natural infection, B cells harbor replicating DENV capable of infecting permissive cells. Alterations in cell abundance, gene and protein expression and secretion, and cell-cell communications suggesting increased migration and inflammation in SD progressors, yet concurrent: i) impaired interferon responses and antigen presentation, in part DENV-modulated, by antigen presenting cells (APCs) in face of intact uptake; ii) activation, regulation, and exhaustion of effector responses, enhanced IFNγ-responses, and appearance of HLA-DR-expressing NK cells possibly compensating for APCs impairments. These observations reveal the target cells of DENV in human blood and provide insight into SD pathogenesis beyond antibody-mediated enhancement.

overall_design: PBMCs derived from 20 DENV-infected children and 4 healthy controls were isolated by magnetic separation and analyzed via a optimized viscRNA-Seq 2 approach

first: Zhiyuan

last: Yao

first: Luca

last: Ghita

first: Veronica

last: Duran

first: Halise

last: Busra Cagirici

first: Ilham

last: Osman

first: Olga

middle: L

last: Agudelo Rojas

first: Ana

last: Sanz

first: Malaya

last: Kumar Sahoo

first: Makeda

last: Robinson

first: Rosa

last: Gelvez

first: Nathalia

last: Bueno

first: Benjamin

last: Pinsky

first: Jose

last: Montoya

first: Maria

middle: I

last: Estupiñan Cardenas

first: Stephen

last: Quake

first: Luis

last: Villar Centeno

first: Elsa

last: Rojas Garrido

first: Fernando

last: Rosso

first: Shirit

last: Einav

first: Fabio

last: Zanini


title: Single-cell and Bulk Transcriptomics of the Human Submandibular Gland Reveals Conserved Factors and Pathways

first: Rose-Anne

last: Romano

state: NY


title: scRNAseq + scV(D)J of cerebrospinal fluid samples across age

status: Public on Dec 12 2022

city: Chicago

first: David

last: Gate

state: IL

address: 303 E Chicago Ave, Chicago, IL 60611

department: Neurology

institute: Northwestern University

summary: Cerebrospinal fluid (CSF) contains a tightly regulated, specialized immune system. Yet, little is known about how aging influences CSF immunity in cognitively typical versus cognitively impaired individuals. Here, we performed single cell RNA sequencing (scRNAseq) on CSF collected from 45 cognitively typical subjects ranging from 54-82 years old. We then assessed age-related transcriptomic changes using several bioinformatic approaches, including linear and local polynomial regression. We reveal pronounced changes to several CSF immune cell types that occur around age 75, including alterations to clonally expanded T cells and activated monocytes. We then compared CSF immune systems from cognitively typical subjects to 14 subjects with mild cognitive impairment or Alzheimer’s disease. Our results indicate disparate age-related CSF immune system perturbations in cognitively impaired subjects. These results highlight the potential to utilize CSF immune changes to identify age-related neuroinflammation in cognitively impaired individuals.

overall_design: Examination of immune changes in the CSF due to aging and MCI/AD

first: Natalie

last: Piehl


title: Comparative expression analysis of wild-type and OsC3'H1-knockout rice plant by RNA sequencing

status: Public on Dec 31 2022

city: Tsuruoka

first: Yuri

last: Takeda-Kimura

state: Yamagata

address: 1-23 Wakabamachi

department: Faculty of Agriculture

institute: Yamagata University

summary: Knockout of a gene encoding p-coumaroyl ester 3-hydroxylase (OsC3'H1) leads to increase p-hydroxyphenyl (H) lignin aromatic composition in rice. We compared the global gene expression profiles of wild-type and OsC3'H1-knockout mutants by RNA sequencing to examine the possible effects of OsC3'H1 disruption on gene expression. We subsequently applied the up- and down-regulated gene sets to gene ontology term enrichment analysis. The results demonstrated that biotic stress-related gene expressions were elevated and, in contrast, photosynthesis-repated gene expression were depressed in the mutant compared with wild-type plants.

overall_design: Gene expression of aerial parts from wild-type and OsC3'H1-knockout rice plants was measured. Three biological replicates were prepared for each genotype.

last: Takeda

first: Yuki

last: Tobimatsu

first: Shiro

last: Suzuki

first: Tatuya

last: Mori

first: Masahiro

last: Sakamoto

first: Kazuki

last: Saito

first: Ryo

last: Nakabayashi

first: Toshiaki

last: Umezawa


title: RNA co-immunoprecipitation with 3xFLAG::Hfq in Caulobacter crescentus

city: Jena

first: Kathrin

last: Fröhlich

state: Thuringia

address: Winzerlaer Straße 2

department: Fakultät für Biowissenschaften, Bacterial RNA Biology

institute: Friedrich-Schiller-Universität Jena

summary: In this study we used RNA co-immunoprecipitation followed by RNA-sequencing to identify Hfq-binding RNAs in C. crescentus.

overall_design: C. crescentus wild-type and 3xFLAG::hfq strains were cultivated in PYE medium to OD660 of 1.0. Cells were subjected to RNA co-immunoprecipitation and RNA was isolated. The experiment was performed with two independent biological replicates.


title: YAMAT-seq of mature tRNA pools in the bacterium Pseudomonas fluorescens SBW25 and derivatives.

status: Public on Dec 02 2022

city: Ploen

first: Jenna

last: Gallie

address: August-Thienemann Strasse 2

institute: Max Planck Institute for Evolutionary Biology

summary: Mature tRNA pools were measured using an adaptation of YAMAT-seq (Shigematsu et al., 2017; doi:10.1093/nar/gkx005 ) and further described in (Ayan et al., 2020; doi:10.7554/eLife.57947) in eight strains dervied from the model bacterium, Pseudomonas fluorescens SBW25. The aim of the experiment was to determine the effect on the mature tRNA pool of (i) removing multi-copy tRNA genes by genetic engineering, and (ii) duplicating tRNA genes during a subsequent, compensatory evolution experiment. We found that (i) results in a reduction in some tRNA isotypes in the mature tRNA pool, and (ii) results in an increase in a compensatory increase in their expression.

overall_design: Three replicates of eight strains: SBW25 (wildtype), rWT (reconstructed wildtype, engineering control), W1-1 (wildtype control from evolution experiment), DEGEG (deletion mutant missing a four-gene tRNA locus: gluTTC-glyGCC-gluTTC-glyGCC), DglyGCC (deletion mutant missing one glyGCC gene), M1-1 (evolved from DEGEG; contains ~1 Mb duplication fragment encompassing 7 tRNA genes), M3-1 (evolved from DEGEG; contains ~0.49 Mb duplication fragment encompassing 1 tRNA gene:glyGCC), M5-1 (evolved from DEGEG; contains ~1 Mb duplication fragment encompassing 7 tRNA genes, plus a non-synonymous point mutation in rplC).

first: WingYui

last: Ngan


title: The effect of trisomic chromosomes on spatial genome organization and global transcription in embryonic stem cells

city: Beijing

first: Mengfan

last: Li

address: No.5 Yiheyuan Road

institute: Peking University

summary: Aneuploidy frequently occurs in cancer and developmental diseases such as Down syndrome, with its functional consequences implicated in dosage effects on gene expression and global perturbation of stress response and cell proliferation pathways. However, how aneuploidy affects spatial genome organization remains less understood. In this study, we addressed this question by utilizing the previously established isogenic wild-type (WT) and trisomic mouse embryonic stem cells (mESCs). We employed a combination of Hi-C, RNA-seq, chromosome painting and nascent RNA imaging technologies to compare the spatial genome structures and gene transcription among these cells. We found that trisomy has little effect on spatial genome organization at the level of A/B compartment or topologically associating domain (TAD). Inter-chromosomal interactions are associated with chromosome regions with high gene density, active histone modifications and high transcription levels, which are confirmed by imaging. Imaging also revealed contracted chromosome volume and weakened transcriptional activity for trisomic chromosomes, suggesting potential implications for the transcriptional output of these chromosomes. Our data resources and findings may contribute to a better understanding of the consequences of aneuploidy from the angle of spatial genome organization.

overall_design: Analysis of 3D genome architecture and gene expression data for WT mESC and trisomic mESCs with an extra copy of chromosome 6, 8, 11 and 15, respectively (named Ts6, Ts8, Ts11, Ts15). There are 3 replicates for each Hi-C sample (except for Ts15 with 2 Hi-C replicates), and 3 replicates for each RNA-seq sample.


title: Single-cell Sequencing Highlights Heterogeneity and Malignant Progression in Actinic Keratosis and Cutaneous Squamous Cell Carcinoma

city: Shenzhen

first: Yutong

last: He

state: Guangdong

address: GongChangLu 66

institute: sun yat-sen university

summary: Cutaneous squamous cell carcinoma (cSCC) is the second most frequent of the keratinocyte-derived malignancies with actinic keratosis (AK) as a precancerous lesion. To comprehensively delineate the underlying mechanisms for the whole progression from normal skin to AK to invasive cSCC, we performed single-cell RNA-seq (scRNA-seq) to acquire the transcriptomes of 138,982 cells from 13 samples of six patients including AK, squamous cell carcinoma in situ (SCCIS), cSCC and their normal tissues, covering comprehensive clinical courses of cSCC. We identified diverse cell types, including important subtypes with different gene expression profiles and functions in major keratinocytes. In SCCIS, we discovered the malignant subtypes of basal cells with differential proliferative and migration potential. Differentially expressed genes (DEG) analysis screened out multiple key driver genes including transcription factors (TFs) along AK to cSCC progression. Immunohistochemistry (IHC) / immunofluorescence (IF) experiments and single-cell ATAC sequencing (scATAC-seq) data verified the expression changes of these genes. The functional experiments confirmed the important roles of these genes in regulating cell proliferation, apoptosis, migration and invasion in cSCC tumor. Furthermore, we comprehensively described the tumor microenvironment (TME) landscape and potential keratinocyte-TME crosstalk in cSCC providing theoretical basis for immunotherapy. Together, our findings provide a valuable resource for deciphering the progression from AK to cSCC and identifying potential targets for anticancer treatment of cSCC.

overall_design: single-cell RNA-seq profiles of 13 samples from 6 patients presenting for surgical resection using the 10X Genomics Chromium platform. All these samples included 3 AK samples, 1 SCCIS tumor samples, 3 cSCC tumor samples (low-risk and high-risk) and patient-matched 6 normal skin samples without any treatment

first: Yu-Tong

first: Ya-Zhou

last: Sun

first: Dan-Dan

last: Zou

first: Xin-Jie


title: Gene expression analysis of mouse Kras-mutant lung adenocarcinoma cells and cancer stem cells

status: Public on Nov 30 2022

city: Houston

first: Humam

last: Kadara

state: TX

address: 2130 W. Holcombe Blvd

institute: University of Texas MD Anderson Cancer Center

summary: Mechanisms underlying cancer stemness in Kras-mutant lung adenocarcinoma (KM-LUAD) are poorly understood. We previously found that mice with knockout of Gprc5a develop LUADs with somatic Kras mutations. We also previously derived Gprc5a-/- KM-LUAD cells (MDA-F471 cells) from a mouse exposed to the tobacco-specific carcinogen NNK. We also derived cancer stem cells (CSCs; grown and cultured as spheres in 3D cultures) from MDA-F471 cells. To better understand the biology of these CSCs, we compared the transcriptomes of MDA-F471 cells and their CSC counterparts by bulk RNA-sequencing.

overall_design: CSCs were grown in spheres using sphere formation assays. Total RNA were isolated form three biological replicates of each of MDA-F471 cells and CSCs and analyzed by bulk RNA-sequencing using the NovaSeq6000 platform from Illumina.

first: Reem

last: Daouk


title: Different expression of non-alcoholic fatty liver disease in rats induced by high-fat diet

status: Public on Jan 09 2023

city: Nanning

first: xing

last: lin

address: Shuangyong Road

institute: Guangxi medical university

summary: This study aimed to investigate the effect and underlying mechanism of Didymin on lipid metabolic disturbance in rats with non-alcoholic fatty liver disease (NAFLD). Rats were administrated with a high-fat diet (HFD) for 8 weeks to induce NAFLD, followed by  different dose Didymin treatment for further 8 weeks.

overall_design: Rats were randomly devided into four groups, including normal group, model group (high-fat diets for 8 weeks) and different dose Didymin groups

first: Bin

last: Fang

first: Rou

last: Mo

first: Xing

last: Lin

first: Renbin

last: Huang

first: Quanfang


title: Axon guidance signal ensures neurite growth pace while sensitizing repulsive cues through induction of a dual function facilitator

city: Seoul

first: Jung-Woong

last: Kim

address: 84 Heuksuk-ro Dongjak-ku

department: Life Science

country: South Korea

institute: Chung-Ang University

summary:
Purpose: profiling the differential transcripts usage in wild type and Plxnd1 knockout condition of brain
Methods: transcriptome analysis by the RNA-seq through the mRNA pull-down
Results: We performed RNA-seq analysis from neonatal mouse striatum and found that the repulsive Semaphorin 3E (Sema3E)-Plexin-D1 guidance signaling transcriptionally upregulates Mtss1 in striatonigral projecting neurons of basal ganglia circuitry
Conclusions: our findings demonstrate a molecular mechanism in which repulsive guidance cues activate an autoregulatory program enabling growing axons to perform both avoiding repellants and continuing axonal extension in the navigation to their target

overall_design: Profiling the differential transcripts usage in wild type and Plxnd1 knockout condition of brain

first: Won-Jong

last: Oh


title: Establish the male meiocyte-specific epigenomic landscape

status: Public on Nov 23 2022

city: Wuhan

first: feng

last: zhao

state: Hubei

address: No. 1, Shizishan Street, Hongshan District

institute: Huazhong Agricultural University

summary: Histone modification maps of H3K4me3 and H3K27me3 of meiocytes were obtained by microlibrary and high-throughput sequencing by extracting meiocytes from rice varieties Azucena and IR64. And the DNA methylation results of meiocytes and flag-leaf of Azucena and IR64 were obtained. By collating this data, the male meiocyte-specific epigenomic landscape is constructed

sample_organism:
Oryza sativa Indica Group
Oryza sativa Japonica Group

overall_design: By micromanipulation technology, the meiocytes of Azucena and IR64 were obtained, respectively. Libraries were constructed by CUT&Tag technology to obtain histone modification data. DNA methylation libraries were constructed by scBS-seq technology. In addition, flag-leaf's DNA methylated library is constructed by directly extracting whole genome DNA

first: Feng

last: Zhao

first: Bo

last: Zhu


title: Aberrant miR-29 is a predictive feature of severe phenotypes in pediatric Crohn’s disease

status: Public on Dec 23 2022

city: Ithaca

first: Praveen

last: Sethupathy

email: as3999@cornell.edu, pr46@cornell.edu

address: T7 006D Veterinary Research Tower, Box 17

department: Department of Biomedical Sciences

institute: Cornell University

summary: Crohn's disease (CD) is a chronic inflammatory gut disorder.  Molecular mechanisms underlying the clinical heterogeneity of CD remain poorly understood.  MicroRNAs (miRNAs) are important regulators of gut physiology and several have been implicated in the pathogenesis of adult CD.  However, there is a dearth of large-scale miRNA studies for pediatric CD.  We hypothesized that specific miRNAs uniquely mark pediatric CD.  We performed small RNA-sequencing of patient-matched non-inflamed colon and ileum biopsies from treatment-naïve pediatric patients with CD (n=169) and a control cohort (n=108).  Comprehensive miRNA analysis revealed 58 miRNAs altered in pediatric CD.  Notably, multinomial logistic regression analysis revealed that index levels of ileal miR-29 are strongly predictive of severe inflammation and stricturing.  Transcriptomic analyses of transgenic mice overexpressing miR-29 show a significant reduction of the tight junction protein gene Pmp22 and classic Paneth cell markers.  The dramatic loss of Paneth cells was confirmed by histologic assays.  Moreover, we also found that pediatric CD patients with elevated miR-29 exhibit significantly lower Paneth cell counts, increased inflammation scores, and reduced levels of PMP22.  These findings strongly indicate that miR-29 up-regulation is a distinguishing feature of pediatric CD, highly predictive of severe phenotypes, and associated with inflammation and Paneth cell loss.

overall_design: We performed small RNA-sequencing of patient-matched non-inflamed colon and ileum biopsies from treatment-naïve pediatric patients with CD and a control cohort. We also performed RNA-sequencing of transgenic mice overexpressing miR-29 with doxycycline and without doxycycline.

first: Alexandria

last: Shumway

first: Michael

last: Shanahan


title: To be updated

first: Kathrin

last: Fröhlich

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

overall_design: Refer to individual Series


title: Target identification for R0199

summary: In this study we determined the target spectrum of C. crescentus sRNA R0199 via pulse-expression followed by RNA-sequencing.

overall_design: Transcriptome profiles of C. crescentus strain carrying either pBVMCS-6 (empty vector control) or pKF482 (pBVMCS-6 with R0199). The bacteria were grown to OD660=0.8, expression of R0199 was induced by addition of 0.5 mM vanillate, and RNA-samples were collected 15 minutes after induction. Three independent biological replicates for each condition were analyzed.


title: The role of Egr1 and FosB in the 6 hour injury response

status: Public on Nov 16 2022

city: Newark

first: Melinda

middle: K.

last: Duncan

state: DE

address: 327 Wolf Hall

department: Biological Sciences

institute: University of Delaware

summary: This trancriptome analysis reports genes that are differentially expressed in wildtype (WT) lens epithelial cells (LEC) between 6 hours and zero hours after injury, and  between Egr1 (E1) or FosB (FB) null LEC and wildtype LEC at zero hours (0H) and at 6 hours (6H) after injury.

overall_design: For each genotype (Wildtype, Egr1 Null, and FosB Null), injury experiments were conducted in mice according to the following procedure. The fiber cell mass was surgically removed from the lens of one eye via an anterior incision, leaving the lens capsule and associated LEC inside the eye.  Six hours later the procedure was repeated on the second eye, the mouse was sacrifieced and both lens capsules were harvested.  Each biological sequencing replicate consisted of 5 capsules from one interval as described above. Three biological replicates were sequenced for each interval and genotype.     FosB null LEC were generated by conditional deletion (cKO) of these genes in the lens from floxed alleles using cre recombinase under the control of a lens-specific promoter (mlr10cre).    Egr1 Null LEC were harvested from Egr1 null mice that were homozygous for a systemic Egr1 knockout generated by the insertion of a neo cassette into exon 2 causing an early stop codon and a truncated Egr1.    All mice used in this study were between three and five months age.  Samples were sequenced in September of 2021.

first: Novo

last: SG

first: Faranda

last: AP

first: Duncan

last: MK


title: The six-hour injury response in lens epithelial cells

summary: This trancriptome analysis reports genes that are differentially expressed in wildtype (WT) lens epithelial cells (LEC) between 6 hours and zero hours after injury.

overall_design: Injury experiments were conducted in mice according to the following procedure. The fiber cell mass was surgically removed from the lens of one eye via an anterior incision, leaving the lens capsule and associated LEC inside the eye.  Six hours later the procedure was repeated on the second eye, the mouse was sacrifieced and both lens capsules were harvested.  Each biological sequencing replicate consisted of 5 capsules from one interval as described above. Three biological replicates were sequenced for each interval. All mice used in this study were 2 months old. Samples were sequenced in september of 2018.

first: Shihan

last: MH


title: Candida albicans: control vs. alpha1-antitrypsin (AAT) treatment

status: Public on Jan 01 2023

first: Mark

middle: S.

last: Gresnigt

address: Beutenebergstraße 11a

department: Adaptive Pathogenicity Mechanisms

institute: Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute

summary: Transcriptional profiling of Candida albicans SC5314 comparing C. albicans grown in RPMI1640  or in RPMI1640 with 100ug/ml AAT. Goal was to determine the effects of AAT on global C. albicans gene expression.

overall_design: Two-condition experiment, C. albicans vs. AAT-treated C. albicans. Biological replicates: 4 control replicates, 4 treated replicates.


title: Osteocytes regulate skeletal senescence during development

status: Public on Nov 21 2022

city: Shanghai

first: Junjie

last: Gao

address: 600 Yishan Road

institute: Shanghai Sixth People’s Hospital Affiliated to Shanghai Jiao Tong University School of Medicine

summary: To understand the mechanism underlying the bone phenotype in osteocytes ablation mice.

overall_design: RNA sequencing was performed on cortical bones from DTAhet and WT mice.Selected osteogenesis related gene ontology (GO) analysis was performed.

first: Peng

last: Ding

first: Youshui

first: Chuan


title: pre-mRNA splicing in C. elegans

status: Public on Nov 02 2022

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

address: 259, Apoorva 4th cross,80 feet Road,RMV 2ND STAGE

country: India

institute: Genotypic Technology

summary: To study pre-mRNA splicing function of the ubiquitin-like protein Hub1/UBL-5 in Caenorhabditis elegans. We have employed splicing-sensitive microarray expression profiling to examine the changes in pre-mRNA splicing. We collected wild-type and ubl-5 knock out worms at L3 stage and isolated total RNA. Which was reverse transcribed to double-stranded cDNA and cRNA was generated by in vitro transcription. The labeled cRNA samples were fragmented at 60°C and hybridized on to an Agilent Gene Expression Microarray. The data showed accumulation of intron- and outron containing transcripts in ubl-5 knockout worms in comparison to wild-type worms

overall_design: Agilent Custom  C.elegans 8x60k one color Gene Expression Array designed  by Genotypic Technology Private Limited.  (AMADID: 84944)

first: Kiran

middle: K

last: Kolathur

first: Pallavi

last: Sharma

first: Nagesh

last: Kadam

first: Kavita

last: Babu

first: Shravan

last: Mishra


title: Chromatin Accessibility Profiling of Osteoclasts Precursor Cells

status: Public on Nov 01 2022

first: Kibyeong

last: Kim

address: 50-1, Yonsei-ro, Seodaemun-gu

institute: Yonsei University

summary: To understand the pathogenic mechanisms of bone erosion in rheumatoid arthritis (RA), we investigated osteoclast-specific epigenetic programs, RANKL-responsive super-enhancers (SEs) and SE-associated enhancer RNAs (SE-eRNAs) in human osteoclasts.

overall_design: ATAC-seq

first: Seyeon

last: Bae

first: Kyung-Hyun

last: Park-Min

first: SungHo

last: Park


title: Investigation of Genomic RNA Polymerase II-Rich Locations in Osteoclast Precursor Cells

overall_design: ChIP-seq, RNA polymerase II, control and RANKL


title: The soil microbiome reduces Striga infection in sorghum by modulation of host-derived signaling molecules and root development

status: Public on Oct 31 2022

city: Davis

first: Dorota

last: Kawa

state: CA

address: 451 Health Science Dr

institute: University of California DAvis

summary: Sorghum bicolor is one of the most important cereal crops in the world, predominantly grown in sub‑Saharan Africa by smallholder farmers. Despite its outstanding resilience to abiotic stresses, approximately 20% of sorghum yield is annually lost on the African continent due to infestation with the parasitic weed Striga hermonthica. Existing Striga management strategies to decrease Striga infestation often show low efficiency and are not easily integrated into current agricultural practices. Microbial-based solutions may prove an effective, low-cost mode for reducing Striga parasitism in sub-Saharan Africa. Here, we demonstrate that the microbiome component of a field soil suppresses Striga infection of sorghum. Potential mechanisms underlying the soil microbiome’s influence on the host plant include root endodermal suberization and aerenchyma formation. Moreover, we observed a depletion of haustorium inducing factors, compounds essential for Striga to establish the host-parasite association, in root exudates collected from sorghum grown in the presence of the soil microbiome as compared to sterile conditions. We further identified individual microbial taxa associated with reduced Striga infection via changes in root cellular anatomy and differentiation as well as in exudate composition. Our study identifies a suite of traits that can be harnessed by individual microbial isolates or their consortia to induce Striga resistance. Combining microbes that elicit Striga resistance directly (affecting the parasite) via repression of haustorium formation with those that act indirectly (affecting the host), by reducing of Striga penetration through root tissue, can broaden the effectiveness of microbe-induced protection from Striga.

overall_design: Root transcriptome profiling of sorghum variety Shanqui Red control and infected with Striga hermonthica in the natural and sterlie soil. Three to four biological replicates and three technical replicates for each RNA sample.

first: Siobhan

last: Brady


title: RNA-seq of AD and VaD  model animals

status: Public on Oct 25 2022

first: Zhuo

last: Wang

address: No. 169, Donghu Road, Wuchang District, Wuhan, Hubei

institute: Zhongnan Hospital of Wuhan University

summary: Changes in survival-death related signaling molecules in AD and VaD model animals.

sample_organism:
Mus musculus
Rattus norvegicus

platform_organism:
Mus musculus
Rattus norvegicus

overall_design:
We then performed gene expression profiling analysis using data obtained from RNA-seq of 3xTg-AD wild type mouse, 3xTg-AD mouse, Sham rat and 2VO rat.
Comparative gene expression profiling analysis of RNA-seq data for 3xTg-AD wild type mouse, 3xTg-AD mouse, Sham rat and 2VO rat.

first: Zhipeng

last: Xu

first: Yi

last: Luo

first: Sisi

last: Peng

first: Hao

last: Song

first: Tian

last: Li

first: Jiaxin

last: Zheng

last: Liu

first: Shenjia

last: Wu

first: Junxia

last: Zhang

first: Lei

first: Yuan

last: Hu

first: Jiapei

last: Dai

first: Junjian


title: The efficacy of chemotherapy is limited by intratumoral senescent cells that persist through the upregulation of PD-L2

status: Public on Oct 19 2022

city: Barcelona

first: Camille

last: Stephan Otto Attolini

state: Select a State or Province

address: Baldiri Reixac 10

department: Biostatistics and bioinformatics Unit

institute: IRB Barcelona

summary: Anti-cancer therapies often result in a subset of surviving cancer cells that undergo therapy induced senescence (TIS). Senescent cancer cells strongly modify the intratumoral microenvironment favoring immunosuppression and, thereby, tumor growth. An emerging strategy to optimise current therapies is to combine them with treatments that eliminate senescent cells. To this end, we undertook an unbiased proteomics approach to identify surface markers contributing to senescent cells immune evasion. Through this approach, we discovered that the immune checkpoint inhibitor PD-L2, but not PD-L1, is upregulated across multiple senescent human and murine cells. Importantly, blockade of PD-L2 strongly synergises with genotoxic chemotherapy, causing remission of solid tumors in mice. We show that PD-L2 inhibition prevents the persistence of chemotherapy-induced senescent cells, which exert cell-extrinsic immunomodulatory actions. In particular, upon chemotherapy, tumors deficient in PD-L2 fail to produce cytokines of the CXCL family, do not recruit myeloid-derived suppressor cells (MDSCs) and are eliminated in a CD8 T cell-dependent manner. We conclude that blockade of PD-L2 improves chemotherapy efficacy by reducing the intratumoral burden of senescent cells and their associated recruitment of immunosuppressive cells. These findings provide a novel strategy to exploit vulnerabilities arising in tumor cells as a result of therapy-induced damage and cellular senescence

overall_design: Panc02 murine pancreatic adenocarcinoma cells, WT or PD-L2-KO, were treated (n = 4) with doxorubicin to induce senescence, and gene expressión was analyzed by RNAseq.

first: Selim

last: Chaib

first: Freddy

last: Monteiro

first: José

last: Pons

first: Jose

middle: A

last: Lopez-Dominguez

first: Lidia

last: Mateo

last: Stephan-Otto Attolini

first: Manuel

last: Serrano


title: Epigenetic and Transcriptomic Profiling in Developing Osteoclasts

first: Kibyeong

last: Kim


title: Circadian clock controls rhythms in ketogenesis by interfering with PPARa transcriptional network

status: Public on Aug 31 2022

city: Cleveland

first: Roman

last: Kondratov

state: Ohio

address: 2121 Euclid Ave

department: Department of Biological Geological and Environmental Sciences

institute: Cleveland State University

type: Genome variation profiling by high throughput sequencing

summary: Ketone bodies, intermediates in energy metabolism and signaling, have attracted significant attention due to their role in health and disease. We performed around the clock study on ketone bodies and ketogenesis with mice on different diets. We found that caloric restriction, a dietary intervention that improves metabolism and longevity, induced high amplitude circadian rhythms in blood βOHB. The blood βOHB rhythms resulted from rhythmic ketogenesis in the liver controlled by the interaction between the circadian clock and PPAR transcriptional networks. This interaction results in transcriptional reprogramming of in beta-oxidation and ketogenesis enzymes. The reprogramming is impaired in circadian clock mutant mice. The circadian clock gated ketogenesis contributes to the diet impact on health and longevity.

overall_design: RNA-seq analysis of liver transcriptome of mice on calorie restriction (CR) diet versus ad libitum (AL) fed mice.

first: Volha

last: Mezhnina

first: Oghogho

middle: P

last: Ebeigbe

first: Nikkhil

last: Velingkaar

first: Allan

last: Poe

first: Yana

last: Sandlers


title: Transcriptomic comparison of a second-generation AKT degrader to the catalytic AKT inhibitor GDC0068 in breast cancer cells [PRO-seq]

status: Public on Oct 15 2022

city: Dundee

first: Ralitsa

middle: Radostinova

last: Madsen

address: Dow Street

department: Medical Research Council Protein Phosphorylation and Ubiquitylation Unit

institute: School of Life Sciences, University of Dundee

summary: We report the development of a second-generation AKT degrader INY-05-040, which outperformed catalytic AKT inhibition both with respect to biochemical and cellular suppression of AKT/mTORC1-driven phenotypes in diverse breast cancer cell lines. Using multi-omic profiling and causal network integration, we demonstrate that the enhanced efficacy of INY-05-040 relies in part on potent downstream activation of stress mitogen activated protein kinase (MAPK) signaling. Systematic measurements of growth inhibition across 288 cancer cell lines confirmed the substantial improvement in potency for INY-05-040 compared to the first-generation AKT degrader (INY-03-041) and catalytic AKT inhibition with GDC-0068. Subsequent integration of breast cancer cell line-specific data with publicly available transcriptomic, proteomic and reverse phase protein array (RPPA) measurements revealed that decreased sensitivity to INY-05-040 correlates with a high baseline activation of inflammatory/stress signaling pathways. Collectively, our data uncover a unique mechanism of breast cancer cell line sensitivity to AKT degradation, further suggesting that the efficacy of catalytic AKT inhibition may be enhanced by activation of stress MAPKs in breast cancer cells with low baseline activity of these components.

overall_design: We performed comparative precision nuclear run-on sequencing sequencing (PROseq) in ER+ T47D breast cancer cells, exposed to the catalytic AKT inhibitor GDC0068 or the second-generation AKT degrader INY-05-040 for 5 h. To limit the confounding effect of differential potency, we determined the doses of INY-05-040 (100 nM) and GDC-0068 (500 nM) that would result in comparable suppression of downstream signaling. Treatment with DMSO was used as control. The data are from two independent experiments, performed in growth factor-complete medium.

first: Alex

last: Toker

first: Emily

last: Erickson

first: Karen

last: Adelman

first: Seth

last: Goldman


title: scNanoATAC-seq: Long-read Single-cell ATAC-seq by Oxford Nanopore Technologies Sequencing [DATASet2: bulkATAC-seq]

status: Public on Sep 07 2022

first: Fuchou

last: Tang

state: Beijing

address: No.5 Yiheyuan Road, Haidian District

institute: Biomedical Pioneering Innovation Center, Peking University

summary: We present scNanoATAC-seq (Single-cell Assay for Transposase Accessible Chromatin by Oxford Nanopore Technologies Sequencing), an effective method for simultaneous detection of chromatin accessibility and genetic variation. Long fragments (about 4-5Kb) of single-cell ATAC-seq library were enriched and sequenced by Oxford Nanopore Technologies platform. Ends of long ATAC-seq fragments are regarded as chromatin accessibility signal in downstream analysis.

overall_design: Short-read bulk ATAC-seq was performed on following cell lines: GM12878, HEK293T, HFF1, K562 and mESC.

first: Yuqiong

last: Hu

first: Zhenhuan

last: Jiang

first: Kexuan

last: Chen


title: Single nuclei RNAseq of rat area nucleus accumbens after morphine exposure

status: Public on Sep 20 2022

city: Philadelphia

first: Benjamin

middle: C.

last: Reiner

state: PA

address: 125 S 31st St

institute: University of Pennsylvania

summary: We performed single-nuclei RNAseq of Brown Norway rat nucleus accumbens after a single injection of morphine or after morhpine self-administration

overall_design: We performed the 10x Genomics 3' gene expression assay (v3.1) on nuclei isolated from frozen Brown Norway (BN) rat nucleus accumbens brain punches. A cohort of male BN rats received an experimenter delivered dose of morphine (10.0 mg/kg, ip) or saline (n=5 each) and were sacrificed two hours after injection. A second cohort of male BN rats underwent volitional IV morphine self-administration (1.0mg/kg/infusion) for three hours daily for 10 days, along with their saline yoked controls (n=6 each), and animals were sacrificed two hours after their final self-administration session. Brains were removed and snap-frozen in dry ice-cold isopentane. Brains were coronally sectioned and the nucleus accumbens core and shell was removed by micro-punch bilaterally, and the punches were stored at -80°C until further processing. Nuclei were isolated by differential centrifugation and microfluidically captured using the 10x Genomics Chromium controller. Sequencing libraries were constructed and sequenced on an Illumina NovaSeq 6000.

middle: C

first: Richard

last: Crist

first: Wade

last: Berrettini

first: Heath

last: Schmidt


title: Sirtuin 3 is a common target of non-steroidal anti-inflammatory drugs to induce gastric cancer cell death and gastric mucosal injury II.

status: Public on Nov 14 2022

city: Kolkata

first: Uday

last: Bandyopadhyay

state: WB

address: EN 80, Salt Lake, College More, EN Block, Sector V, Kolkata,

department: Division of Molecular Medicine

institute: Bose Institute

summary: Nonsteroidal anti-inflammatory drugs (NSAIDs), the quintessential medicines to treat pain and inflammatory conditions, induce cell death in human cancer cells, as repurposed anticancer agents, and in normal gastric mucosa, as a major side effect. The subcellular target/s of NSAIDs that leads to the cell death remained elusive so far. Here, by venturing transcriptomics followed by functional validation, we, for the first time, identified mitochondrial deacetylase Sirtuin 3 (Sirt3) as a non-canonical target of NSAIDs whose depletion induced the hyperacetylation of mitochondrial proteome, OGG1 depletion, mtDNA damage, electron transport chain defect associated mitochondrial dysfunction and finally cell death. Silencing of Sirt3 in AGS cells (a human gastric adenocarcinoma cell line) significantly aggravated NSAID-induced cytopathology. Whereas, honokiol mediated induction of Sirt3 corrected the NSAID-induced transcriptome alteration and gastropathy in rodent model. Together, the results identify Sirt3 as a common target used by NSAIDs to induce gastric carcinoma cell death and gastric mucosal injury.

overall_design: AGS cells were plated and allowed to grow over-night. Cells were treated with 0.5 mM indomethacin for 24 hrs. Then the cells were harvested and used for transcriptome analysis and protein expression profiling to capture the subtle effects on cellular metabolism.


title: Analysis of Immune and Prognostic-Related lncRNA PRKCQ-AS1 for Predicting Prognosis and Regulating Effect in Sepsis

status: Public on Nov 11 2022

city: zhongshan

first: yongyan

last: pei

address: Long life water, wuguishan street, zhongshan city

department: School of Pharmaceutical and Chemical Engineering

institute: Guangdong Pharmaceutical University

summary: Sepsis is a common systemic inflammatory response syndrome caused by infection. It has high mortality and great harm. Long non-coding RNA (lncRNA) has been reported to play a regulatory role in a variety of diseases and is a potential prognostic marker and therapeutic target. However, there are few data on the regulatory effect of lncRNA on sepsis. Therefore, we used transcriptome sequencing and series methods to screen and analyze lncRNAs with potential for prognostic markers in sepsis.we collected 4 sepsis patients whole blood samples and 4 healthy controls whole blood samples for transcriptome sequencing. After quality filtering of the raw sequencing data, we obtained a total of 125.581 Gb Clean Data, the average data amount of each sample was 15.698 Gb, the percentage of Q30 bases was over 93.89%, and the GC content was between 47.53% and 57.54%. Subsequently, we used HISAT2 to align the Clean Data of each sample with the human GRCH38 genome, and the alignment rate was between 96.355% and 97.986%. Through statistics, we found that the obtained lncRNAs were divided into 10 types (figure 1A), among which antisense (36.05%) and lincRNA (33.76%) were the main types.

overall_design: LncRNA and mRNA profiles of 4 sepsis patients whole blood samples and 4 healthy controls whole blood samples

first: Xian

last: Ding

first: Wenqi

last: Liang

first: hongjuan

last: xia

first: Yuee

last: Liu

first: Shuxiong

first: xinyu

first: Xiaoli

last: Zhu

first: Yongyan

last: Pei

first: Dewen

last: Zhang


title: STAT3 couples activated tyrosine kinase signaling to the oncogenic core transcriptional regulatory circuitry of anaplastic large cell lymphoma [ChIP-seq]

status: Public on Aug 26 2022

city: Memphis

first: Brian

middle: J

last: Abraham

state: TN

address: 262 Danny Thomas Blvd

institute: St. Jude Children's Research Hospital

summary: Anaplastic large cell lymphoma (ALCL) is an aggressive, CD30+ T-cell lymphoma of children and adults. ALK fusion transcripts or mutations in the JAK-STAT pathway are observed in most ALCL tumors, but the mechanisms underlying tumorigenesis are not fully understood. Here we show that dysregulated STAT3, together with a core transcriptional regulatory circuit consisting of BATF3–IRF4–IKZF1, co-occupies gene enhancers to establish an oncogenic transcription program and maintain the malignant state of ALCL. Critical downstream targets of this network in ALCL cells include the proto-oncogene MYC, which requires active STAT3 to facilitate high levels of MYC transcription. The activity of this auto-regulatory transcription loop is reinforced by MYC binding to the enhancer regions associated with STAT3 and each of the core regulatory transcription factors. These findings provide new insights for understanding how dysregulated signaling pathways hijack cell-type-specific transcriptional machinery to drive tumorigenesis and create therapeutic vulnerabilities in genetically defined tumors.

overall_design: ChIP-Seq against transcription regulators in ALCL cell lines.

first: Nicole

last: Prutsch

first: Shuning

last: He

first: Alla

last: Berezovskaya

first: Adam

middle: D

last: Durbin

first: Neekesh

last: Dharia

first: Kelsey

last: Maher

first: Jamie

last: Matthews

first: Lucy

last: Hare

first: Suzanne

last: Tumer

first: Kimberly

last: Stegmaier

first: Lukas

last: Kenner

first: Olaf

last: Merkel

last: Young

first: A

middle: T

last: Look

first: Mark

last: Zimmerman


title: STAT3 couples activated tyrosine kinase signaling to the oncogenic core transcriptional regulatory circuitry of anaplastic large cell lymphoma [CUT&RUN-seq]

overall_design: CUT&RUN-sequencing against transcription regulators in ALCL cell lines.

first: Richard

middle: W