title: Transcriptomic profile of single-cell sorted monocytes, T cells and CD3+CD14+ cells from one subject infected with latent tuberculosis

status: Public on Jul 08 2021

city: La Jolla

first: Bjoern

last: Peters

state: California

address: 9420 Athena Cir

institute: La Jolla Institute for Immunology

summary: We set out to detect a transcriptional signature in CD4 T cells of individuals at risk of progression to active tuberculosis. We indeed found such a signature which surprisingly could be tracked to a cell population expressing both T cell (CD3) and monocyte (CD14) markers. To identify the nature of the CD3+CD14+ population, we determined the transciptomic profile of single cells CD3-CD14+ Monocytes (n=21), CD3+D14- T cells (n=22), CD3+CD14+ cells in the Monocyte gate (Mgate) (n=22) and CD3+CD14+ cells in the lymphocyte gate (Lgate) (n=20) from one subject infected with latent tuberculosis by RNA sequencing. PCA on all genes showed that CD3+CD14+ cells represent an intermediate population between Monocytes and T cells, with CD3+CD14+ L gate cells closer to T cells compared to CD3+CD14+ Mgate cells.

overall_design: Single cell RNA-sequencing of sorted singlets monocytes (CD14+CD3-), singlets T cells (CD14-CD3+), CD3+CD14+ cells (Lgate or Mgate) from one subject infected with latent tuberculosis.

first: Julie

last: Burel

first: Mikhail

last: Pozmanoy

first: Gregory

last: Seumois

first: Pandurangan

last: Vijayanand

first: Alessandro

last: Sette


title: Glucocorticoid action in the hippocampus revealed by integrated genome-wide ChIP and RNA analysis [ChIP-seq]

status: Public on Jul 10 2021

city: Bristol

first: Johannes

last: Reul

address: Dorothy Hodgkin Building, Whitson Street

department: Bristol Medical School

country: United Kingdom

institute: University of Bristol

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Glucocorticoid hormones (GCs) play a critical role in physiological regulation and behavioural adaptation through mineralocorticoid (MR)- and glucocorticoid receptor (GR)-mediated actions in the hippocampus. We conducted genome-wide MR and GR ChIP-Seq studies on rat hippocampus to elucidate MR- and GR-regulated genes under physiological conditions like acute stress and circadian variation. Rat hippocampus tissue was collected under early morning baseline conditions, at 30 min after the start of a 15-min forced swim session (acute stress), or under late afternoon baseline conditions. We identified many genomic loci in which MR and/or GR binds following acute stress or due the circadian rise in GC secretion.

overall_design:
Examination of the binding of two transcription factors to the rat hippocampus genome under early morning baseline conditions, following an acute stressor or under late afternoon baseline conditions

Please note that each peak file was generated with the corresponding ChIP and input samples, and is linked to the corresponding ChIP-seq sample records.

first: K

middle: R

last: Mifsud

first: C

middle: L

last: Kennedy

first: J

middle: M

first: Silvia

last: Salatino


title: Bioplatforms Australia: Antibiotic Resistant Sepsis Pathogens Framework Initiative - Escherichia coli MS14386

status: Public on Jul 01 2021

city: Sydney

last: Bioplatforms Australia

state: NSW

address: Level 4, Building 4WW, Research Park Drive, Macquarie University

country: Australia

institute: Bioplatforms Australia

type: Expression profiling by high throughput sequencing

summary: The Antibiotic Resistant Sepsis Pathogens Framework Initiative aims to develop a framework dataset of 5 sepsis pathogens (5 strains each) using an integrated application of genomic, transcriptomic, metabolomic and proteomic  technologies. The pathogens included in this initiative are: Escherichia coli, Klebsiella pneumoniae complex, Staphylococcus aureus, Streptococcus pyogenes, and Streptococcus pneumoniae. This submission pertains to strains MS14386.

overall_design:
12 samples, 2 conditions, 6 biological replicates per condition.
contributor: Bioplatforms Australia Antibiotic Resistant Sepsis Pathogens Framework Initiative


title: Bioplatforms Australia: Antibiotic Resistant Sepsis Pathogens Framework Initiative - Escherichia coli B36

summary: The Antibiotic Resistant Sepsis Pathogens Framework Initiative aims to develop a framework dataset of 5 sepsis pathogens (5 strains each) using an integrated application of genomic, transcriptomic, metabolomic and proteomic  technologies. The pathogens included in this initiative are: Escherichia coli, Klebsiella pneumoniae complex, Staphylococcus aureus, Streptococcus pyogenes, and Streptococcus pneumoniae. This submission pertains to strain B36.


title: Bioplatforms Australia: Antibiotic Resistant Sepsis Pathogens Framework Initiative - Escherichia coli MS14384

summary: The Antibiotic Resistant Sepsis Pathogens Framework Initiative aims to develop a framework dataset of 5 sepsis pathogens (5 strains each) using an integrated application of genomic, transcriptomic, metabolomic and proteomic  technologies. The pathogens included in this initiative are: Escherichia coli, Klebsiella pneumoniae complex, Staphylococcus aureus, Streptococcus pyogenes, and Streptococcus pneumoniae. This submission pertains to strain MS14384.


title: Bioplatforms Australia: Antibiotic Resistant Sepsis Pathogens Framework Initiative - Escherichia coli MS14387

summary: The Antibiotic Resistant Sepsis Pathogens Framework Initiative aims to develop a framework dataset of 5 sepsis pathogens (5 strains each) using an integrated application of genomic, transcriptomic, metabolomic and proteomic  technologies. The pathogens included in this initiative are: Escherichia coli, Klebsiella pneumoniae complex, Staphylococcus aureus, Streptococcus pyogenes, and Streptococcus pneumoniae. This submission pertains to strain MS14387.


status: Public on Sep 01 2021

city: Baltimore

first: Chulan

last: Kwon

state: MD

address: 720 Rutland Ave, Ross 954

department: Medicine, Cardiology, Heart & Vascular Institute, Institute for Cell Engineering, and Cellular and Molecular Medicine

country: USA

institute: Johns Hopkins University

summary: bluk RNA-seq of human dermal fibroblasts reprogrammed into cardiomyocytes with the addition of siAJSZ

overall_design: HDFs overexpressing Mef2c, Gata4, and Tbx5 were treated with siATF7IP, siJUNB, siSP7, and siZNF207

first: Sean

middle: A

last: Murphy

first: Alexandre

last: Colas


title: Bioplatforms Australia: Antibiotic Resistant Sepsis Pathogens Framework Initiative - Klebsiella pneumoniae KPC2

summary: The Antibiotic Resistant Sepsis Pathogens Framework Initiative aims to develop a framework dataset of 5 sepsis pathogens (5 strains each) using an integrated application of genomic, transcriptomic, metabolomic and proteomic  technologies. The pathogens included in this initiative are: Escherichia coli, Klebsiella pneumoniae complex, Staphylococcus aureus, Streptococcus pyogenes, and Streptococcus pneumoniae. This submission pertains to strain KPC2.


title: Bioplatforms Australia: Antibiotic Resistant Sepsis Pathogens Framework Initiative - Klebsiella pneumoniae AJ218

summary: The Antibiotic Resistant Sepsis Pathogens Framework Initiative aims to develop a framework dataset of 5 sepsis pathogens (5 strains each) using an integrated application of genomic, transcriptomic, metabolomic and proteomic  technologies. The pathogens included in this initiative are: Escherichia coli, Klebsiella pneumoniae complex, Staphylococcus aureus, Streptococcus pyogenes, and Streptococcus pneumoniae. This submission pertains to strain AJ218.


title: Bioplatforms Australia: Antibiotic Resistant Sepsis Pathogens Framework Initiative - Klebsiella variicola 03-311-0071

summary: The Antibiotic Resistant Sepsis Pathogens Framework Initiative aims to develop a framework dataset of 5 sepsis pathogens (5 strains each) using an integrated application of genomic, transcriptomic, metabolomic and proteomic  technologies. The pathogens included in this initiative are: Escherichia coli, Klebsiella pneumoniae complex, Staphylococcus aureus, Streptococcus pyogenes, and Streptococcus pneumoniae. This submission pertains to strain 03-311-0071.


title: Bioplatforms Australia: Antibiotic Resistant Sepsis Pathogens Framework Initiative - Klebsiella variicola AJ055

summary: The Antibiotic Resistant Sepsis Pathogens Framework Initiative aims to develop a framework dataset of 5 sepsis pathogens (5 strains each) using an integrated application of genomic, transcriptomic, metabolomic and proteomic  technologies. The pathogens included in this initiative are: Escherichia coli, Klebsiella pneumoniae complex, Staphylococcus aureus, Streptococcus pyogenes, and Streptococcus pneumoniae. This submission pertains to strain AJ055.


title: Bioplatforms Australia: Antibiotic Resistant Sepsis Pathogens Framework Initiative - Staphylococcus aureus BPH2760

summary: The Antibiotic Resistant Sepsis Pathogens Framework Initiative aims to develop a framework dataset of 5 sepsis pathogens (5 strains each) using an integrated application of genomic, transcriptomic, metabolomic and proteomic  technologies. The pathogens included in this initiative are: Escherichia coli, Klebsiella pneumoniae complex, Staphylococcus aureus, Streptococcus pyogenes, and Streptococcus pneumoniae. This submission pertains to strain BPH2760.


title: Bioplatforms Australia: Antibiotic Resistant Sepsis Pathogens Framework Initiative - Staphylococcus aureus BPH2819

summary: The Antibiotic Resistant Sepsis Pathogens Framework Initiative aims to develop a framework dataset of 5 sepsis pathogens (5 strains each) using an integrated application of genomic, transcriptomic, metabolomic and proteomic  technologies. The pathogens included in this initiative are: Escherichia coli, Klebsiella pneumoniae complex, Staphylococcus aureus, Streptococcus pyogenes, and Streptococcus pneumoniae. This submission pertains to strain BPH2819.


title: Macrophage and MDA-MB-231 coculture and mitochondrial transfer

status: Public on Aug 06 2021

city: Salt Lake City

first: Minna

last: Roh-Johnson

state: UT

address: 15 N Medical Drive, 5200J Emma Eccles Jones Medical Research Building

department: Biochemistry

institute: University of Utah

summary: The goals of this study were to determine the effects of lateral transfer of mitochondria on recipient cell biology. We therefore collected cancer cells with and without macrophage mitochondria, and macrophages with and without cancer cell mitochondria, and analyzed transcriptomes by single-cell RNA-sequencing. Through our analysis, we found that cancer cells that received macrophage mitochondria have an enrichment of transcripts associated with cell cycle progression compared to cancer cells without macrophage mitochondria. We further validated these findings with wet lab experiments using cell proliferation markers.

overall_design: MDA-MB-231 cells cultured with Human blood monocyte derived macrophages. n=1 blood donor; 2 technical replicates per conditions.

first: Daniel

last: Greiner


title: Bioplatforms Australia: Antibiotic Resistant Sepsis Pathogens Framework Initiative - Staphylococcus aureus BPH2900

summary: The Antibiotic Resistant Sepsis Pathogens Framework Initiative aims to develop a framework dataset of 5 sepsis pathogens (5 strains each) using an integrated application of genomic, transcriptomic, metabolomic and proteomic  technologies. The pathogens included in this initiative are: Escherichia coli, Klebsiella pneumoniae complex, Staphylococcus aureus, Streptococcus pyogenes, and Streptococcus pneumoniae. This submission pertains to strain BPH2900.

overall_design:
11 samples, 2 conditions, 5-6 biological replicates per condition.
contributor: Bioplatforms Australia Antibiotic Resistant Sepsis Pathogens Framework Initiative


title: Bioplatforms Australia: Antibiotic Resistant Sepsis Pathogens Framework Initiative - Staphylococcus aureus BPH2986

summary: The Antibiotic Resistant Sepsis Pathogens Framework Initiative aims to develop a framework dataset of 5 sepsis pathogens (5 strains each) using an integrated application of genomic, transcriptomic, metabolomic and proteomic  technologies. The pathogens included in this initiative are: Escherichia coli, Klebsiella pneumoniae complex, Staphylococcus aureus, Streptococcus pyogenes, and Streptococcus pneumoniae. This submission pertains to strain BPH2986.


title: Bioplatforms Australia: Antibiotic Resistant Sepsis Pathogens Framework Initiative - Streptococcus pyogenes 5448

summary: The Antibiotic Resistant Sepsis Pathogens Framework Initiative aims to develop a framework dataset of 5 sepsis pathogens (5 strains each) using an integrated application of genomic, transcriptomic, metabolomic and proteomic  technologies. The pathogens included in this initiative are: Escherichia coli, Klebsiella pneumoniae complex, Staphylococcus aureus, Streptococcus pyogenes, and Streptococcus pneumoniae. This submission pertains to strain 5448.


title: Bioplatforms Australia: Antibiotic Resistant Sepsis Pathogens Framework Initiative - Streptococcus pyogenes HKU419

summary: The Antibiotic Resistant Sepsis Pathogens Framework Initiative aims to develop a framework dataset of 5 sepsis pathogens (5 strains each) using an integrated application of genomic, transcriptomic, metabolomic and proteomic  technologies. The pathogens included in this initiative are: Escherichia coli, Klebsiella pneumoniae complex, Staphylococcus aureus, Streptococcus pyogenes, and Streptococcus pneumoniae. This submission pertains to strain HKU419.


title: Bioplatforms Australia: Antibiotic Resistant Sepsis Pathogens Framework Initiative - Streptococcus pyogenes PS006

summary: The Antibiotic Resistant Sepsis Pathogens Framework Initiative aims to develop a framework dataset of 5 sepsis pathogens (5 strains each) using an integrated application of genomic, transcriptomic, metabolomic and proteomic  technologies. The pathogens included in this initiative are: Escherichia coli, Klebsiella pneumoniae complex, Staphylococcus aureus, Streptococcus pyogenes, and Streptococcus pneumoniae. This submission pertains to strain PS006.


title: Quantitative Analysis of Erythroblast Transcriptomes in Control and NUP-17d Treatment Groups

status: Public on Jun 09 2021

city: Chicago

first: Xu

last: Han

state: Illinois

address: 303 E Chicago Avenue, Ward 3-240

department: Pathology

institute: Northwestern University

summary: NUP-17d (17d) is an effective inhibitor of Plek2 protein. NUP-17d treatment inhibits erythroblast proliferation, differentiation and enucleation in a dose-dependent manner via directly binding to Plek2 protein. To reveal the detailed involving mechanism of NUP-17d treatment, we performed RNA sequencing to analyze the gene expression profiles change in erythroblasts which were treated with NUP-17d or DMSO (NC) for 48 hours in the EPO induction culture system.

overall_design: mRNA profiles of erythroblasts treated with NUP-17d or DMSO (NC) for 48 hours in the EPO induction culture system were generated by deep sequencing, in triplicate, using DNBseq SE50 RNA-Seq.

first: Peng

last: Ji


title: 4T1 Exsporosi

status: Public on Jun 21 2021

city: Bethesda

first: Li

last: Yang

state: Maryland

address: 37 Convent Dr.

department: NCI

institute: NIH

summary: We performed RNA-seq on a 3D culture system with 4T1 cells that naturally produce exsporosi, and a 2D culture system where exsporosi were added.

overall_design: RNA-seq of 2D and 3D culture systems with exsporosi or apoptotic debris

first: Justin

last: Gray

first: Woo

middle: Y

last: Park


title: Nanostring Expression profile of Fibrous Dysplasia/McCune-Albright Syndrome bone biopsies varies according to their histological appearance

status: Public on Jun 07 2021

city: ROMA

first: domenico

last: raimondo

state: RM

address: Viale Regina Elena 324

department: Molecular Medicine

country: Italy

institute: Sapienza University of Rome

type:
Expression profiling by array
Other

summary:
Identifying the molecular networks that underlie FD lesions and histological variants thereof is key to understand the pathogenesis of the disease, to refine current diagnostic approaches and to develop efficacious therapies. In this study, we used the NanoString nCounter Analysis System to investigate the gene signature of a series of archival FFDPE FD lesions and to establish a correlation between the molecular and histopathological profiles of the tissue specimens.
We analyzed the gene expression profile of a series of human FFDPE  bone biopsies from 1 to 9 years by employing Nanostring technology. The analysis of the differentially regulated genes led to segregation of samples into two groups, which were well characterized by different histological appearance.

overall_design: The expression level from 770 genes were determined by NanoString technology on a small series of formalin-fixed, decalcified and paraffin-embedded (FFDPE) FD biopsies. Moreover a detailed histological review was performed  in order to associate samples with pathological sub-groups.

first: Agnese

last: Persichetti

first: Edoardo

last: Milanetti

first: Biagio

last: Palmisano

first: Annamaria

last: Di Filippo

first: Emanuela

last: Spica

first: Samantha

last: Donsante

first: Ilenia

last: Coletta

first: Ernesto

last: Ippolito

last: Corsi

first: Mara

last: Riminucci

first: Domenico

last: Raimondo


title: Bioplatforms Australia: Antibiotic Resistant Sepsis Pathogens Framework Initiative - Streptococcus pyogenes SP444

last: Bioplatforms Australia

summary: The Antibiotic Resistant Sepsis Pathogens Framework Initiative aims to develop a framework dataset of 5 sepsis pathogens (5 strains each) using an integrated application of genomic, transcriptomic, metabolomic and proteomic  technologies. The pathogens included in this initiative are: Escherichia coli, Klebsiella pneumoniae complex, Staphylococcus aureus, Streptococcus pyogenes, and Streptococcus pneumoniae. This submission pertains to strain SP444.


title: Single-cell Transcriptomic Analysis Reveals Disparate Effector Differentiation Pathways in Human Treg Compartment [Treg_HD]

status: Public on May 27 2021

city: TianJin

first: Changlu

last: Xu

state: TianJin

address: 288 Nanjing Rd, Heping

department: State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology & Blood Diseases Hospital

country: China

institute: Chinese Academy of Medical Sciences & Peking Union Medical College

summary: Human FOXP3+ regulatory T (Treg) cells are central to immune tolerance. However, their heterogeneity and differentiation remain incompletely understood. Here we use single-cell RNA and T cell receptor sequencing to resolve Treg cells from healthy individuals and patients with or without acute graft-versus-host disease (aGVHD) who undergo stem cell transplantation. These analyses, combined with functional assays, separate Treg cells into naïve/activated/effector stages, and resolve the HLA-DRhi, LIMS1hi, highly suppressive FOXP3hi, and highly proliferative MKI67hi effector subsets. Trajectory analysis assembles Treg subsets into two differentiation paths (I/II) with distinctive phenotypic/functional programs, ending with the FOXP3hi and MKI67hi subsets, respectively. Transcription factors FOXP3 and SUB1 contribute to some Path I and Path II phenotypes, respectively. These FOXP3hi and MKI67hi subsets and two differentiation pathways are conserved in transplanted patients, despite having functional/migratory impairments under aGVHD. The findings expand the understanding of Treg cell heterogeneity and differentiation and provide a single-cell atlas for the dissection of Treg complexity in health and disease.

overall_design: Here, we performed droplet-based scRNA-seq of human FOXP3+ regulatory T (Treg) cells to construct a molecular landscape and dissecting the heterogeneity of Treg cells from healthy donors and transplanted patients with or without acute graft-versus-host disease (aGVHD).

first: Yuechen

last: Luo

first: Bing

last: Wang

first: Qing

last: Niu

first: Xiuhua

last: Su

first: Mingzhe

last: Han

first: Erlie

last: Jiang

first: Lihong

last: Shi

first: Xiaoming

last: Feng


title: Characterization of human erythropoiesis using ex vivo differentiation of CD34 HSC (ATAC-seq)

status: Public on May 28 2021

city: Headington

first: Damien

last: Downes

state: Oxfordshire

address: John Radcliffe Hospital

department: MRC Weatherall Institute of Medicine

institute: The University of Oxford

summary: Genome Wides Association Studies (GWAS) have identified tens of thousands of associations between human genetic variation and common disease. Despite the abundance of GWAS associations, functional identification and characterization of causative variants and effector genes remains a challenging prospect. Human erythropoiesis provides a highly tractable model system for the development of tools for GWAS analysis. We have developed a three-phase protocol for differentiation of peripheral CD34+ Haematopoietic Stem Cells (HSC) into mature enucleating erythrocytes. This protocol has been characterized for it’s the changes observed morphologically, immunologically (by FACS) and epigenetically (by ATAC-seq, ChIP-seq, and RNA-seq). We have used this protocol to study the effects of common GWAS variants affecting red blood cell traits, and more severe mutations causing  Type-1 Congenital Dyserythropoietic Anemia (CDA-I).

overall_design: To characterise the epigenetic landscape and identify nucleosome depleted regions during erythropoiesis, ATAC-seq was carried out at days 7, 10, 11, 13 and 17 of HSC differentiation. CD34+ HSC were differentiated from three separate donors on multiple occasions with technical replicates (rep1 and rep2) performed for the first differentiation.

middle: J

first: Caroline

last: Scott

first: Matthew

last: Gosden

first: Lea

last: Nussbaum

first: Jelena

last: Telenius

first: Jim

last: Hughes


title: Single cell transcriptomic analysis of developing fetal cortex in in-vivo fetal alcohol exposure mouse model.

status: Public on Apr 07 2021

city: Bryan

first: Rajesh

last: Miranda

address: 8447 Riverside Parkway

institute: Texas A&M University

summary: We performed single-cell RNA sequencing on murine dorsal telencephalon isolated at gestational day (GD) 14.5, 48 hours after dams are exposed to ethanol or control air in a vapour chamber for 1 hour.

overall_design: Pregnant C57Bl6/J mice served as controls or were exposed to ethanol vapor on gestational day (GD) 12.5. On GD14.5, fetal dorsal telencephalon, excluding ganglionic eminences, cortical hem and overlying meningeal tissue, was micro-dissected. A total of 12 samples (6 male and 6 female samples), originating from 6 pregnant dams, 3 alcohol-treated (alcohol dose ranged from 210-260 mg/dL ) and 3 control.

first: Nihal

last: Salem

first: Amanda

middle: H

last: Mahnke

first: Andrew

middle: E

last: Hillhouse

first: Kranti

last: Konganti

middle: C


title: In vivo tissue-specific chromatin profiling in Drosophila melanogaster using GFP-tagged nuclei

status: Public on May 23 2021

city: West Lafayette

first: Vikki

last: Weake

state: Indiana

address: 175 S University St

institute: Purdue University

summary: We report the application of different chromatin profiling techniques applied to cell-type specific nuclei obtained with a nuclei immuno-enrichment protocol described in this manuscript, referred as NEI protocol. By optimizing these methods, we generated genome-wide datasets associated with the nuclear RNA transcriptome, chromatin accessibility, and distribution of histone H3 and two H3 two lysine tri-methylation marks, H3K4me3 and H3K36me3 respectively. This study provides a framework for the application of different aspects of chromatin biology using nuclei derived from specific cell types in Drosophila. Further, it demonstrates the low input requirements necessary for these chromatin studies.

overall_design: Photoreceptor neuron-specific profiling of nuclear transcriptome by RNA-seq, chromatin accessibility by Omni-ATAC and histone modification distribution by ChIP-seq and CUT&Tag

first: Juan

middle: P

last: Jauregui-Lozano


title: A deep learning approach to identify new gene targets of a novel therapeutic for human splicing disorders

status: Public on Mar 29 2021

city: Boston

first: Susan

last: Slaugenhaupt

state: MA

address: 185 Cambridge St

department: Center for Genomic Medicine

institute: Massachusetts General Hospital

summary: Pre-mRNA splicing is a key control point in human gene expression. Disturbances in splicing due to mutation or aberrant splicing regulatory networks lead to dysregulated protein expression and contribute to a substantial fraction of human disease. Several classes of active and selective splicing modulator compounds (SMCs) have been recently identified and establish that pre-mRNA splicing represents a viable target for therapy. This also raises the intriguing possibility that SMCs may have broad capabilities to ameliorate aberrant splicing across multiple human disorders. We describe herein the identification of BPN-15477, a novel SMC that restores correct splicing of exon 20 in the Elongator complex protein 1 (ELP1) gene carrying the major IVS20+6T>C mutation responsible for familial dysautonomia.   Given that BPN-15477 corrects splicing and increases full-length ELP1 protein in vivo, we developed a machine learning approach to evaluate the therapeutic potential of BPN-15477 to correct splicing in other human genetic diseases. Using transcriptome sequencing from compound-treated fibroblast cells, we identified treatment responsive sequence signatures, the majority of which center at the 5' splice site of exons whose inclusion or exclusion is modulated by SMC treatment. We then leveraged this model to identify 155 human disease genes that harbor ClinVar mutations predicted to alter pre-mRNA splicing as potential targets for BPN-15477 treatment. Using in vitro splicing assays, we validated representative predictions by demonstrating successful correction of splicing defects caused by mutations in the genes responsible for cystic fibrosis (CFTR), cholesterol ester storage disease (LIPA), Lynch syndrome (MLH1) and familial frontotemporal dementia (MAPT). Importantly, we also validated these predictions in two disease relevant cellular models for LIPA and CFTR, confirming that treatment increases functional protein and confirming the clinical potential for our model predictions. Our study shows that deep learning techniques can identify a complex set of sequence signatures and predict response to pharmacological modulation, strongly supporting the use of in silico approaches to expand the therapeutic potential of drugs that modulate splicing.

overall_design: Both placebo and BPN-15477 treatment were applied on six human WT fibroblast lines. Paired-end RNASeq were applied to generate twelve libraries.

first: Dadi

last: Gao

first: Elisabetta

last: Morini

first: Monica

last: Salani


title: RNA seq profile of adult newborn neurons

status: Public on Apr 01 2021

city: Tuebingen

first: Olga

last: Garaschuk

state: BW

address: Keplerstraße 15

department: Neurophysiology Department

country: Germany

institute: University of Tuebingen

summary: The integration of adult-born neurons in the existent neural circuitry is known to be activity-dependent. To decipher the underlying mechanisms, we genetically manipulated excitability of adult-born cells (via cell-specific overexpression of either Kv1.2 or Kir2.1 K+ channels). Longitudinal in vivo Ca2+ imaging and transcriptome analyses revealed that endogenous but not sensory-driven activity governs migration, morphogenesis, survival, and functional integration of adult-born juxtaglomerular neurons in the mouse olfactory bulb. The proper development of these cells required fluctuations of cytosolic Ca2+ levels, phosphorylation of CREB, and pCREB-mediated gene expression. Attenuating Ca2+ fluctuations via K+ channel overexpression strongly downregulated genes involved in neuronal migration, differentiation, and morphogenesis and upregulated the apoptosis-related genes, thus locking adult-born cells in the vulnerable and immature state. Together, the data identify signaling pathways connecting the endogenous intermittent neuronal activity/Ca2+ fluctuations as well as proper Kv1.2/Kir2.1 K+ channel function to migration, maturation, and survival of adult-born neurons.

overall_design: we used 12 male 3 months-old mice and split them into three groups, namely control NBNs, Kv1.2-overexpressing NBNs, and Kir2.1-overexpressing NBNs. The 4 mice in each group were further divided into two subgroups to have 2 biological replicates in each group. For each sample, NBNs from two mice were pooled together. In total, we analyzed 6 samples.


title: Bioplatforms Australia: Antibiotic Resistant Sepsis Pathogens Framework Initiative - Klebsiella variicola AJ292

last: Bioplatforms Australia

summary: The Antibiotic Resistant Sepsis Pathogens Framework Initiative aims to develop a framework dataset of 5 sepsis pathogens (5 strains each) using an integrated application of genomic, transcriptomic, metabolomic and proteomic  technologies. The pathogens included in this initiative are: Escherichia coli, Klebsiella pneumoniae complex, Staphylococcus aureus, Streptococcus pyogenes, and Streptococcus pneumoniae. This submission pertains to strain AJ292.


title: Bioplatforms Australia: Antibiotic Resistant Sepsis Pathogens Framework Initiative - Klebsiella variicola 04153260899A

summary: The Antibiotic Resistant Sepsis Pathogens Framework Initiative aims to develop a framework dataset of 5 sepsis pathogens (5 strains each) using an integrated application of genomic, transcriptomic, metabolomic and proteomic  technologies. The pathogens included in this initiative are: Escherichia coli, Klebsiella pneumoniae complex, Staphylococcus aureus, Streptococcus pyogenes, and Streptococcus pneumoniae. This submission pertains to strain 04153260899A.


title: SOX2 Reprograms the Esophageal Squamous Carcinoma Epigenome and Induces Endogenous Retroviral Elements and dsRNA, Thereby Promoting ADAR1 Dependence

status: Public on Mar 17 2021

first: Yingtian

last: Xie

address: 450 BROOKLINE AVE

institute: DANA FARBER CANCER INSTITUTE INC

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: SOX2 Reprograms the Esophageal Squamous Carcinoma Epigenome and Induces Endogenous Retroviral Elements and dsRNA, Thereby Promoting ADAR1 Dependence [RNA-Seq]

summary: We analyzed ChIP-seq, chromatin accessibility and RNA-seq across mouse esophageal squamous organoids and human esophageal squamous cell cancer

overall_design: RNAseq analysis of esophageal squamous organoids and cancer cell lines

first: Henry

last: Long

first: Zhong

last: Wu


title: Distinct dynamics and functions of H2AK119ub and H3K27me3 in mouse preimplantation  embryos (STAR-ChIP)

status: Public on Mar 15 2021

city: Doha

first: Mohamed Nadhir

last: Djekidel

state: Doha

address: Gharafa

department: Translational Medicine Department

country: Qatar

institute: Sidra Medicine

summary: Polycomb repressive complexes 1 and 2 (PRC1/2) maintain transcriptional silencing of developmental genes largely by catalyzing mono-ubiquitination of histone H2A at lysine 119 (H2AK119ub1) and trimethylation of histone H3 at lysine 27 (H3K27me3), respectively. How Polycomb domains are reprogrammed during mammalian preimplantation development remains largely unclear. Here we show that, although H2AK119ub1 and H3K27me3 are highly colocalized in gametes, they undergo differential reprogramming dynamics following fertilization. H3K27me3 maintains thousands of maternally biased domains up to the blastocyst stage, whereas maternally biased H2AK119ub1 distribution in zygotes is largely equalized at the two-cell stage. Notably, while maternal PRC2 depletion has a limited effect on global H2AK119ub1 in early embryos, it disrupts allelic H2AK119ub1 at H3K27me3 imprinting loci including Xist. By contrast, acute H2AK119ub1 depletion in zygotes does not affect H3K27me3 imprinting maintenance, at least by the four-cell stage. Importantly, loss of H2AK119ub1, but not H3K27me3, causes premature activation of developmental genes during zygotic genome activation (ZGA) and subsequent embryonic arrest. Thus, our study reveals distinct dynamics and functions of H3K27me3 and H2AK119ub1 in mouse preimplantation embryos.

overall_design:
H2Aub in sperm were profiled using STAR-ChIp in two biological replicates
H3K27me3 in sperm were profiled using STAR-ChIp

first: Zhiyuan

last: Chen

first: Mohamed

middle: N

first: Yi

last: Zhang


title: Distinct dynamics and functions of H2AK119ub and H3K27me3 in mouse preimplantation embryos


title: Bioplatforms Australia: Antibiotic Resistant Sepsis Pathogens Framework Initiative

sample_organism:
Escherichia coli
Klebsiella pneumoniae
Staphylococcus aureus
Streptococcus pneumoniae
Streptococcus pyogenes
Klebsiella variicola


title: Bioplatforms Australia: Antibiotic Resistant Sepsis Pathogens Framework Initiative - Staphylococcus aureus BPH2947

summary: The Antibiotic Resistant Sepsis Pathogens Framework Initiative aims to develop a framework dataset of 5 sepsis pathogens (5 strains each) using an integrated application of genomic, transcriptomic, metabolomic and proteomic  technologies. The pathogens included in this initiative are: Escherichia coli, Klebsiella pneumoniae complex, Staphylococcus aureus, Streptococcus pyogenes, and Streptococcus pneumoniae. This submission pertains to strain BPH2947.


status: Public on Feb 22 2021

city: Durham

first: Joshua

middle: Aaron

last: Granek

state: NC

address: Box 3568, 213 Research Drive

department: Department of Biostatistics and Bioinformatics

institute: Duke University School of Medicine

summary:
Mar1 deletion and RNA enrichment in Cryptococcus neoformans: pilot data for a high-throughput sequencing course.

The goal of this project was to generate pilot data in preparation for a summer course on high-throughput sequencing where participants prepared their own RNA-Seq libraries and analyzed the resulting data. This pilot experiment addressed two questions:
1. Does this experimental system (Cryptococcus neoformans H99 wildtype and mar1 deletion mutant grown in YPD and tissue culture media) provide a good dataset for course participants to analyze.

2. Which rRNA depletion method is best to use in the wetlab component of the course.

This data was generated in preparation for the intensive summer course on high-throughput sequencing, funded by NIH grant 5R25EB023928-03 "A hands-on, integrative next-generation sequencing course: design, experiment, and analysis".

overall_design: This project generated 63 libraries from 24 different samples. Samples from 6 biological replicates were generated for each treatment x genotype. The two treatments conditions were growth in YPD and tissue culture media. The two genotypes were H99 wildtype and mar1 deletion mutant. Two libraries were made from each RNA sample using different methods for rRNA depletion: poly(A) isolation and Ribo-Zero. For 3 of the samples libraries were also made from unenriched RNA and RNA enriched using the RNase H method. For these 3 samples unenriched, RNase H, and poly(A) enriched libraries were prepared and sequenced in 2019 and unenriched, poly(A), and Ribo-Zero libraries were prepared and sequenced in 2018. All other libraries were prepared and sequenced in 2018.

first: Calla

last: Telzrow

first: Paul

last: Zwack

first: Shannon

last: Righi

first: Fred

middle: S

last: Dietrich

first: Cliburn

last: Chan

first: Kouros

last: Owzar

first: J

last: Alspaugh


title: IRF8 is an AML-specific Susceptibility Factor that Regulates Signaling Pathways and Proliferation of AML Cells

status: Public on Feb 12 2021

city: Marburg

first: Robert

last: Liefke

state: Hessen

address: Hans-Meerwein-Str. 2

department: Institute of Molecular Biology and Tumor Research (IMT)

institute: Philipps University of Marburg

summary: Personalized treatment of acute myeloid leukemia (AML) that target individual aberrations strongly improved the survival of AML patients. However, AML is still one of the most lethal cancer diseases of the 21st century, demonstrating the need to find novel drug targets and to explore alternative treatment strategies. Upon investigation of public perturbation data, we identified the transcription factor IRF8 as a novel AML-specific susceptibility gene in humans. IRF8 is upregulated in a subset of AML cells and its deletion leads to impaired proliferation in those cells. Consistently, high IRF8 expression is associated with poorer patients’ prognoses. Combining gene expression changes upon IRF8 deletion and the genome-wide localization of IRF8 in the AML cell line MV4-11, we demon-strate that IRF8 directly regulates key signaling molecules, such as the kinases SRC and FAK, the transcription factors RUNX1 and IRF5, and the cell cycle regulator Cyclin D1. IRF8 loss impairs AML-driving signaling pathways, including the WNT, Chemokine, and VEGF signaling pathways. Additionally, many members of the focal adhesion pathway showed reduced expression, providing a putative link between high IRF8 expression and poor prognosis. Thus, this study suggests that IRF8 could serve as a biomarker and potential molecular target in a subset of human AMLs.

overall_design: ChIP-Seq of IRF8 in Control and IRF8 KO cells. RNA-Seq of Control and IRF8 KO cells in 4 replicates. All experiments were performed in the human AML cell line MV4-11.

first: Franziska

last: Liss

first: Andrea

last: Nist


title: Bioplatforms Australia: Antibiotic Resistant Sepsis Pathogens Framework Initiative - Streptococcus pyogenes PS003

last: Bioplatforms Australia

summary: The Antibiotic Resistant Sepsis Pathogens Framework Initiative aims to develop a framework dataset of 5 sepsis pathogens (5 strains each) using an integrated application of genomic, transcriptomic, metabolomic and proteomic  technologies. The pathogens included in this initiative are: Escherichia coli, Klebsiella pneumoniae complex, Staphylococcus aureus, Streptococcus pyogenes, and Streptococcus pneumoniae. This submission pertains to strain PS003.

overall_design:
12 samples, 2 conditions, 6 biological replicates per condition.
contributor: Bioplatforms Australia Antibiotic Resistant Sepsis Pathogens Framework Initiative


title: Genomic imbalance determines positive and negative modulation of gene expression in diploid maize

status: Public on Feb 02 2021

city: Hangzhou

first: Xiaowen

last: Shi

state: Zhejiang

address: 866 Yuhangtang Road NongshenghuanA443

department: College of Agriculture and Biotechnology

institute: Zhejiang University

summary: We examined the impact of both increased and decreased dosage of fifteen distal and one interstitial chromosomal regions via RNA-seq of maize mature leaf tissue to reveal new aspects of genomic imbalance. The results indicate that significant changes in gene expression in aneuploids occur both on the varied chromosome (cis) and the remainder of the genome (trans), with a wider spread of modulation compared with the whole-ploidy series of haploid to tetraploid. In general, cis genes in aneuploids range from a gene-dosage effect to dosage compensation, whereas for trans genes the most common effect is an inverse correlation in that expression is modulated towards the opposite direction of the varied chromosomal dosage, although positive modulations also occur. Furthermore, this analysis revealed the existence of increased and decreased effects in which expression of many genes under genome imbalance are modulated towards the same direction regardless of increased or decreased chromosomal dosage, which is predicted from kinetic considerations of multicomponent molecular interactions. The findings provide novel insights into understanding mechanistic aspects of gene regulation.

overall_design: Global gene expression analysis of aneuploidy and whole-ploidy series compared with diploid control.

first: James

last: Birchler


title: Distinct dynamics and functions of H2AK119ub and H3K27me3 in mouse preimplantation embryos (CUT&RUN)

first: Mohamed Nadhir

last: Djekidel

overall_design: To determine H2Aub reprogramming dynamics, H2Aub was profiled using CUT&RUN in mouse germinal vesicle (GV) (2 rep) and metaphase II (MII) oocytes (2 rep), zygotes (2 rep), 2-cell (3 rep), 4-cell (2 rep), morula (2 rep), inner cell mass (ICM) (1 rep) from blastocysts, and epiblast (2 rep) from embryonic day 6.5 (E6.5) embryos. STAR-ChIP was used to profile H2Aub in sperm. To assess how loss of H3K27me3 may affect H2Aub, H2Aub CUT&RUN was performed in Eed KO oocytes (2 rep) and Eed maternal KO 4-cell (2 rep) and morula embryos (2 rep). To determine how loss of H2Aub affects H3K27me3, H3K27me3 CUT&RUN was performed in H2Aub-depleted 4-cell embryos (2 rep for control, 2 rep for depletion). CUT&RUN was also performed to conirm that H2Aub was depleted in 4-cell embryos (1 rep for control and 1 rep for depletion).


title: Transcriptome deviation in early neuronal stage of MBD5-Associated Neurodevelopmental Disorder (MAND)

status: Public on Nov 30 2020

city: Columbia

first: Toshihiko

last: Ezashi

state: MO

address: 240a CS Bond Life Sciences Center

department: Animal Sciences

institute: University of Missouri-Columbia

summary:
Purpose: MBD5-Associated Neurodevelopmental Disorder (MAND) is an Autism Spectrum Disorder (ASD) disorder characterized by intellectual disability, motor delay, severe speech impairment and autism-like behavioral problems. The role of MBD5 in neurodevelopmental function remains largely undefined. In this study, we explored the neurodevelopmental phenotype of 2q23.1 deletion syndrome through creating neuronal progenitor stem cells (NPC) derived from 2q23.1 patients and conducting RNA-seq to identify the contributory altered gene and to expand our knowledge about gene network differences and possible interactions between the related disease pathways and ASD.
Methods: Primary skin fibroblasts from three MAND patients and four control cases were converted into induced pluripotent stem cell (iPSC) lines by transient transfections of episomal plasmids.  Directed differentiation of these iPSC to NPC was accomplished with monolayer culture protocol for two weeks.
Results: The RNA-seq analysis identified 498 genome-wide significant (q < 0.05) differentially expressed gene in the patients derived NPC lines as a consequence of reduced MBD5 dosage.  25 ASD associated genes were included in the differentially expressed gene list. On the top of the list, FOXG1 expression is significantly (P < 0.0001) increased  in the patient derived NPC samples. The differentially expressed gene list was highly overlapped with the SFARI autism gene set, identifying biological processes that are implicating neurological phenotype and ASD such as central nervous system development, neuron differentiation, and regulation of neurogenesis.  The findings of the transcriptome deviation in early neuronal stage of MAND can provide potential connection to the overlapping neurocognitive and neuropsychiatric phenotypes associated with growing risk factors, such as other chromatin modifiers and epigenetic factors that link to ASD.  Such in vitro models can nurture hypotheses toward therapeutic interventions.

overall_design: Three NPC mRNA profiles of MAND were compared with those of four control NPC by RNA sequencing with Illumina HiSeq 2500.

first: Sureni

middle: V

last: Mullegama

first: Sarah

last: Elsea


title: High-content single-cell combinatorial indexing

city: Portland

first: Ryan

last: Mulqueen

state: OR

address: 3181 SW Sam Jackson Park Rd

department: Molecular and Medical Genetics

institute: Oregon Health and Science

summary: We describe a new generalizable library generation chemistry with increased efficiency that is  amendable to tagmentation-based split-pool barcoding strategies, such as single-cell combinatorial indexing (sci). Symmetrical strand sci (‘s3’) uses a novel uracil-based adapter switching approach that provides an improved rate of conversion of source DNA into viable sequencing library fragments following tagmentation. We apply this chemistry to assay chromatin accessibility (s3-ATAC) to profile human cortical and mouse whole brain tissues, with mouse datasets demonstrating a 6-to-13-fold improvement in usable reads obtained per cell when compared to other available methods performed on the same sample type. We also demonstrate the generalizability of s3 by applying it to single-cell whole genome sequencing (s3-WGS), and whole genome plus chromatin conformation (s3-GCC), for structural variant calling in a patient-derived cancer cell line model. Using the high-coverage profiles produced by the s3 technologies we characterized preserved clonal structure and identified a putative subclone-specific translocation.

overall_design:
s3-ATAC was performed on two samples, a flash-frozen mouse whole brain and a flash-frozen human cortex sample. Library generation was performed as a barnyard with an equimolar mix of human and mouse nuclei at various steps. Cross-species nuclei were mixed either prior to tagmentation, after tagmentation, or kept isolated. See Fig2a in our manuscript or metadata files for more details.

For s3-WGS and s3-GCC data, was performed on patient derived cell lines (PDCLs) and GM12878. Processed files are supplied. s3-WGS data is supplied as a read count per bin (s3-GCC read count data is included) as well as a bed format of read alignment location. s3-GCC data is supplied as a pairix format file with distal contacts information.

first: Dmitry

last: Pokholok

first: Brendan

last: O'Connell

first: Casey

last: Thornton

first: Fan

last: Zhang

first: Brian

last: O’Roak

first: Jason

last: Link

first: Galip

middle: G

last: Yardimci

first: Rosalie

last: Sears

first: Frank

last: Steemers

first: Andrew

last: Adey


title: Altered oligodendroglia and astroglia in chronic traumatic encephalopathy

status: Public on May 24 2021

first: Kevin

middle: Blake

last: Chancellor

address: 77 Avenue Louis Pasteur

department: Genetics

institute: Harvard Medical School

summary: Chronic traumatic encephalopathy (CTE) is a progressive tauopathy found in contact sport athletes, military veterans, and others exposed to repetitive head injury. Brain white matter atrophy and axonal loss have been reported in CTE but have yet to be well characterized on a molecular or cellular level. Here, we present RNA sequencing profiles of cell nuclei from postmortem dorsolateral frontal white matter from eight individuals with neuropathologically confirmed CTE and eight age- and sex-matched controls. Analyzing these profiles using unbiased clustering approaches, we identified eighteen transcriptomically distinct cell groups (clusters), reflecting cell types and/or cell states, of which a subset showed differences between CTE and control tissue. Independent in situ methods applied on tissue sections adjacent to that used in the single-nucleus RNA-seq work yielded similar findings. Oligodendrocytes were found to be most severely affected in the CTE white matter samples; they appeared diminished in number and altered in the relative proportions across subtype clusters. Further, the CTE-enriched oligodendrocyte population showed greater abundance of transcripts relevant to iron metabolism and cellular stress response. CTE tissue also demonstrated excessive iron accumulation histologically. Astrocyte alterations were more nuanced; total astrocyte number was indistinguishable between CTE and control samples, but transcripts associated with neuroinflammation were elevated in the CTE astrocyte groups as compared to controls. These results demonstrate specific molecular and cellular differences in CTE-associated oligodendrocytes and astrocytes and may provide a starting point for the development of diagnostics and therapeutic interventions.

overall_design: Single-nucleus RNA sequencing comparative transcriptomic analysis of human subjects diagnosed neuropathologically with mid-state chronic traumatic encephalopathy (CTE) and age- and post-mortem (PMI)-matched controls.

middle: B

first: Benjamin

last: Okaty

first: Susan

last: Dymecki


title: Spatial transcriptomics unveils ZBTB11 as a regulator of cardiomyocyte degeneration in cardiomyopathy

status: Public on May 22 2021

city: Utrecht

first: Abel

last: Vertesy

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute

summary:
Aims
Arrhythmogenic cardiomyopathy (ACM) is an inherited cardiac disorder that is characterized by progressive fibro-fatty replacement of the myocardium, arrhythmias, and sudden death. While myocardial degeneration and fibro-fatty replacement occurs in specific locations, the underlying molecular changes remain poorly characterized. Here we aim to delineate local changes in gene expression to help identify new genes or pathways that are relevant for specific remodelling processes occurring during ACM.

Methods and Results
Using Tomo-Seq, a genome-wide transcriptional profiling with high spatial resolution, we created a transmural epicardial to endocardial gene expression atlas of an explanted ACM heart to gain molecular insights into disease-driving processes. This enabled us to link gene expression profiles to the different regional remodelling responses and allowed us to identify genes that are potentially relevant for disease progression. In doing we revealed BTB (broad-complex, tramtrack, bric-à-brac) domain containing 11 (ZBTB11) to be specifically enriched at sites of active fibrofatty replacement of myocardium. Immunohistochemistry indicated ZBTB11 to be enriched in cardiomyocytes flanking fibrofatty areas, which could be confirmed in multiple cardiomyopathy patients. Forced overexpression of ZBTB11 in iPS-derived cardiomyocytes showed ZBTB11 to function as a potent inducer of cardiomyocyte atrophy.

Conclusion
By combining spatial transcriptomics with classical histological approaches we identified gene expression changes underlying local remodelling responses in ACM. In doing so we found ZBTB11 to function as a relevant driver of cardiomyocyte atrophy. These data show the power of Tomo-Seq to unveil new molecular mechanisms and indicate ZBTB11 as a potential new target for cardiomyopathy.

overall_design: The dataset contains the following experiments: 1. Spatial transcriptomics by RNA-tomography (TomoSeq) on 20um sections on diseased heart. After isolation, we cryosectioned samples, extracted RNA from the individual sections, and amplified and barcoded mRNA using the CEL-seq protocol as in (Junker 2014, PMID: 25417113). Libraries were sequenced on Illumina NextSeq 500 using 75p paired end sequencing. 2. Bulk RNA-seq processed by the CEL-seq protocol. IPS derived cardiomyocytes were transduced with AAV-ZBTB11, AAV-GFP, or not transduced. 7 days after transduction, cells were harvested and RNA-Seq was performed. RNA-Seq on nontransduced control, AAV-GFP transduced and AAV-ZBTB11 transduced iPS derived cardiomyocytes.

first: Grégory

last: Lacraz

first: Ábel

last: Vértesy

first: Cornelis

last: J. Boogerd

first: Ilaria

last: Perini

first: Hesther

last: de Ruiter

first: Andreas

last: Brodehl

first: Petra

last: van der Kraak

first: Mauro

last: Giacca

first: Manon

last: Huibers

first: Nicolaas

last: de Jonge

first: Jan Philip

last: Junker

first: Aryan

last: Vink

first: Eva

last: van Rooij


title: The RNA m6A reader YTHDF2 controls NK cell anti-tumor and anti-viral immunity

status: Public on May 08 2021

city: duarte

first: Shoubao

last: Ma

state: California

address: 1500 East Duarte Road

institute: City of Hope

summary: N6-methyladenosine (m6A) is the most prevalent post-transcriptional modification on RNA. NK cells are the predominant innate lymphoid cells that mediate anti-viral and anti-tumor immunity. However, whether and how m6A modifications affect NK cell immunity remains unknown. Here, we discover that YTHDF2, a well-known m6A reader, is upregulated in NK cells upon activation by cytokines, tumors, and cytomegalovirus infection. Ythdf2 deficiency in NK cells impairs NK cell anti-tumor and anti-viral activity in vivo. YTHDF2 maintains NK cell homeostasis and terminal maturation, correlating with modulating NK cell trafficking and regulating Eomes, respectively. YTHDF2 promotes NK cell effector function and is required for IL-15-mediated NK cell survival and proliferation by forming a STAT5-YTHDF2 positive feedback loop. Transcriptome-wide screening identifies Tardbp to be involved in cell proliferation or survival as a YTHDF2-binding target in NK cells. Collectively, we elucidate the biological roles of m6A modifications in NK cells and highlight a new direction to harness NK cell anti-tumor immunity.

overall_design: Purified splenic NK cells from Ythdf2 WT and Ythdf2 ∆NK  mice were expanded by IL-2 (1000 U/ml) in vitro for 7 days. RNA was extrated and m6A MeRIP sequencing was performed to detect the m6A modification alterations in two groups. YTHDF2 RNA immunoprecipitation sequencing was performed to map the target transcripts bound by YTHDF2 in NK cells.

first: Jianhua

last: Yu


title: Epigenome analysis of 65 CID cases

status: Public on May 01 2021

city: Cambridge

first: Eguzkine

last: Ochoa

address: Addenbrookes Hospital

department: Medical Genetics

institute: University of Cambidge

type: Methylation profiling by genome tiling array

summary: Genome wide DNA methylation profiling of 65 congenital imprinting disorder samples, 45 BWS and 22 SRS. The Illumina Infinium HumanMethylation450 BeadChips was used to obtain DNA methylation profiles across approximately 485,000 CpGs in blood samples.

overall_design: Bisulphite converted DNA from the 65 CID samples (43 BWS and 22 SR) were hybridized to the Illumina Infinium HumanMethylation450 BeadChips

first: Eamonn

middle: R

last: Maher


title: A novel cell culture system modeling the SARS-CoV-2 life cycle

status: Public on Dec 03 2020

city: Beijing

first: Jingrui

last: Li

address: Yuanmingyuan West Road No.2

institute: China Agricultural Universtiy

summary: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causes the global pandemic of COVID-19, and no effective antiviral agents and vaccines are available. SARS-CoV-2 is classified as a biosafety level-3 (BLS-3) agent, impeding the basic research into its biology and the development of effective antivirals. Here, we described a safe cell culture system for production of transcription and replication-competent, biologically contained SARS-CoV-2 virus like particles (trVLP) that express a reporter gene (GFP) replacing viral nucleocapsid gene, which is required for viral genome packaging and virion assembly (SARS-CoV-2-GFP/N trVLP). The complete viral life cycle can be exclusively achieved and confined in the cells expressing SARS-CoV or SARS-CoV-2 N proteins in trans, but not MERS-CoV N. Additionally, genetic recombination of N supplied in trans into viral genome was not detected, as evidenced by sequence analysis after one-month serial passages in N-expressing Caco-2 cells. Moreover, Intein-mediated protein trans-splicing approach was utilized to split the viral N gene into two independent vectors, and the ligated viral N protein could function in trans to recapitulate entire viral life cycle, further securing the biosafety of this cell culture model. To prove the suitability of this system in antivirals discovery, we developed a 96-well format high throughput screening to identify salinomycin, monensin sodium and lycorine chloride exhibiting potent antiviral activities against SARS-CoV-2 infection. Collectively, we propose that this cell culture system based on Intein-N genetic complementation to produce SARS-CoV-2 trVLP provides a safe means to dissect the virus life cycle, and thus accelerate our understanding of virus biology, as well as for more applied uses such as the screening and development of novel antivirals, and thus represent powerful tools for SARS-CoV-2 study.

overall_design: Caco-2 cells infected with SARS-CoV-2 GFP delN P1 or P10 virus are used for RNA-seq

first: Qiang

last: Ding

first: Xiaohui

last: Ju


title: SOX2 Reprograms the Esophageal Squamous Carcinoma Epigenome and Induces Endogenous Retroviral Elements and dsRNA, Thereby Promoting ADAR1 Dependence [ChIP-Seq, ATAC-Seq]

first: Yingtian

last: Xie

overall_design: ChIPseq and ATACseq analysis of esophageal squamous organoids and cancer cell lines

first: Henry

last: Long

first: Zhong

last: Wu

first: Xiaoyang

last: Zhang


title: Persistent Epigenetic Reprogramming of Sweet Taste by Diet

status: Public on Nov 11 2020

city: Ann Arbor

first: Monica

last: Dus

state: Michigan

address: 1105 N University, 4224

institute: University of Michigan

summary: We report the application of ribosomal profiling based RNA sequencing technology for high-throughput profiling of the Gr5a cells of male Drosophila melanogaster adults. By expressing the UAS-Rpl3-3XFLAG transgene using the Gr5a-GAL4 driver.

overall_design: 2-3 replicates from both the Gr5a and input fraction per dietary condition is obtained using the illumna NextSeq-500 platform. The dietary conditions include control diet, sugar diet 3 days, sugar diet 7 days and sugar diet to control diet 14 days.

first: Anoumid

last: Vaziri


title: High-throughput sequencing and analysis of gene modification regulated by epigenetics modification in adult and old intracerebral hemorrhage rats.

city: wuhan

first: dong

last: chen

state: Hubei

address: GaoXin 2nd Road

institute: ablife

overall_design: Refer to individual Series


summary: We report the application of targeted DNA Adenine Methyltransferase identification DNA sequencing technology for high-throughput profiling of Pcl occupancy in the Gr5a cells of male Drosophila melanogaster adults. By expressing the UAS-LT3-Dam::Pcl and UAS-LT3-Dam transgene using the Gr5a-GAL4;tubulinGAL80ts driver.

overall_design: 3 replicates from the Gr5a cells  per dietary condition per genotype is obtained using the illumna NextSeq-500 platform


title: Predominantly inverse modulation of gene expression in genomically unbalanced disomic haploid maize

first: James

last: Birchler

address: 310 Tucker Hall

summary: The phenotypic consequences of the addition or subtraction of part of a chromosome is more severe than changing the dosage of the whole genome. By crossing diploid trisomies to a haploid inducer, we identified seventeen distal segmental haploid disomies that cover ~80% of the maize genome. Disomic haploids provide a level of genomic imbalance that is not ordinarily achievable in multicellular eukaryotes, allowing the impact to be stronger and more easily studied. Transcriptome size estimates revealed that a few disomies inversely modulate most of the transcriptome. Based on RNA sequencing, the expression levels of genes located on the varied chromosome arms (cis) in disomies ranged from being proportional to chromosomal dosage (dosage effect) to showing dosage compensation with no expression change with dosage. For genes not located on the varied chromosome arm (trans), an obvious trans-acting effect can be observed, with the majority showing a decreased modulation (inverse effect). The extent of dosage compensation of varied cis genes correlates with the extent of trans inverse effects across the 17 genomic regions studied. The results also have implications for the role of stoichiometry in gene expression, the control of quantitative traits, and the evolution of dosage-sensitive genes.

overall_design: Gene expression analysis of disomies and the haploid control

first: Hua

last: Yang


title: Synovial fibroblasts from obese hip osteoarthritis patients exhibit distinct single-cell subsets characterised by pathological inflammatory functions

status: Public on Oct 31 2020

city: Bath

first: Mark

middle: Andrew

last: Lindsay

address: Claverton Down

department: Pharmacy and Pharmacology

institute: University of Bath

summary: Inflammation of synovial tissue (synovitis) is a hallmark of osteoarthritis (OA) pathogenesis and is pronounced in obese individuals. The aim of this study was therefore to perform scRNA-seq analysis of synovial fibroblast from hip OA patients who were either obese or normal-weight to identify specific fibroblast subsets that exhibit disease-associated inflammatory functions. :  scRNA-seq identified eight OA synovial fibroblast clusters, with distinct differences between obese and normal-weight patients.  Fibroblast clusters in obese OA patients highly expressed gene signatures related to immune cell regulation, fibrosis and inflammatory signalling, including Chitinase3-like 1 (CHI3L1), CXCL12, osteonectin (SPARC), SMOC2 and Galectin-1 (LGALS1). Pseudotemporal expression dynamics demonstrated a transition in the expression of the transcriptional regulator MYC and Inhibin A in normal-weight clusters, and the expression of FOS and CHI3L1 in obese fibroblast clusters. Analysis of fibroblast conditioned media showed that obese OA fibroblasts secreted significantly greater amounts of CHI3L1, whilst normal-weight fibroblasts secreted greater amounts of Inhibin.

overall_design: Synovial joint tissue was obtained from n=4 obese hip OA patients (BMI >30) and n=4 normal-weight hip OA patients (BMI 18.5-24.9) who were undergoing elective joint replacement surgery. Synovial fibroblasts were isolated, and subjected to scRNA-seq, using Chromium 10X and analysed using Seurat and Monocle software.

first: Susanne

last: Wijesinghe

first: Amel

last: Badoume

first: Dominika

last: Nanus

first: Edward

middle: T

last: Davis

first: Simon

middle: W

last: Jones


title: Prostate cancer cell-intrinsic interferon signaling regulates dormancy and metastatic outgrowth in bone

status: Public on Oct 01 2020

city: Melbourne

first: Katie

middle: Louise

last: Owen

state: VIC

address: 305 Grattan Street

department: Research

institute: Peter MacCallum Cancer Centre

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


title: Single cell RNA sequencing of dormant and proliferating prostate cancer cells from murine bone metastases

summary: Using the immunocompetent bone-metastatic RM1 murine model of prostate cancer, the transriptomes of proliferating (PKH26-) eCFP+/luc2+ RM1 single cells (referred to as RM1536) were compared  to dormant (PKH26+) RM1536 single cells dervied from bioluminescence imaging-verified bone metastases in mice at ~d16 post-intracardiac injection of PKH26 labelled RM1536 cells

overall_design:
Following intracardiac injection of PKH26-labeled RM1 cells expressing cerulean (eCFP) and luciferase (luc2; identified as RM1536) into C57BL/6 mice, dormant (occurring at a rate of ~2-6 in 3x10e7 bone marrow cells in ~1 in 8 tumor-bearing mice) and proliferating single RM1 cells were FACS-isolated from bone metastases ~16 days post-injection. Single cell RNA-seq of 28 dormant (PKH+) and 32 proliferating (PKH-) cells was performed and BASiCS normalisation employed. Pre- and post-normalization of all samples revealed no significant batch effects and potential technical noise was corrected after normalization. Confirmation of RM1 markers (eCFP and luc2) demonstrated the authenticity of more than 83% of single tumor cells from bone.
Of 2410 differentially expressed genes in dormant cells, 1609 were identified by BASiCs as having no residual over-dispersion within dormant and proliferating groups, validating the absence of spurious signals in mean gene expression shifts.
Stratification of DEGs enriched in dormant cells compared to proliferating cells isolated from the same hosts (counts appear under the file name 4_mice_of_interest, indicating dormant and proliferating cells derived from the same host, with 4 independent hosts included in analysis ) confirmed that differential gene expression did not result from unequal representation of dormant cells derived from a single mouse and proliferating cell from a separate host. Rather they encompass unbiased population-level changes evident across multiple tumor-bearing animals.
Dormant (PKH+) and proliferating (PKH-) RM1 cells were isolated from 8 independent animals at different time-points of metastasis ~16 days post-intracardiac injection across independent experiments.

middle: L

first: Belinda

last: Parker

first: Dainel

last: Roden

first: Weng

last: Khoo

first: Linden

middle: J

last: Gearing

first: Alexander

last: Swarbrick


title: Next generation sequencing of parental RM cells and RM1 cells derived bone and lung metastases for preliminary assessment of differential tumor cell gene expression in bone

summary: Using the immunocompetent bone-metastatic murine model of prostate cancer, the transcriptomes of proliferating (PKH26-) eCFP+/luc2+ RM1 cells (referred to as RM1536) were compared to FACS-isolated, proliferating (PKH26-) RM1536 cells derived from matched bone and lung metastases for preliminary assessment of gene alterations that may specifically occur in bone.

overall_design: mRNA profiles of unlabelled RM1 cells (n = 2), eCFP+/luc2+ RM1 (RM1536; n = 2), proliferating (PKH-) bone-derived RM1536 (n = 1) and proliferating (PKH-) lung-derived RM1536 (n = 1) from the same animal at D16 post-intracardiac injection of PKH26-labelled tumor cells were compared following read generation using the Illumina HiSeq2500 platform.

first: Marek

last: Cmero

first: Chris

last: Hovens


title: Distinct dynamics and functions of H2AK119ub and H3K27me3 in mouse preimplantation embryos (RNA-Seq)

first: Mohamed Nadhir

last: Djekidel

summary: Polycomb repressive complexes 1 and 2 (PRC1/2) maintain transcriptional silencing of developmental genes largely by catalyzing mono-ubiquitination of histone H2A at lysine 119 (H2AK119ub1) and trimethylation of histone H3 at lysine 27 (H3K27me3), respectively. How Polycomb domains are reprogrammed during mammalian preimplantation development remains largely unclear. Here we show that, although H2AK119ub1 and H3K27me3 are highly colocalized in gametes, they undergo differential reprogramming dynamics following fertilization. H3K27me3 maintains thousands of maternally biased domains up to the blastocyst stage, whereas maternally biased H2AK119ub1 distribution in zygotes is largely equalized at the two-cell stage. Notably, while maternal PRC2 depletion has a limited effect on global H2AK119ub1 in early embryos, it disrupts allelic H2AK119ub1 at H3K27me3 imprinting loci including Xist. By contrast, acute H2AK119ub1 depletion in zygotes does not affect H3K27me3 imprinting maintenance, at least by the four-cell stage. Importantly, loss of H2AK119ub1, but not H3K27me3, causes premature activation of developmental genes during zygotic genome activation (ZGA) and subsequent embryonic arrest. Thus, our study reveals distinct dynamics and functions of H3K27me3 and H2AK119ub1 in mouse preimplantation embryos.

overall_design:
RNA-seq was performed in H3K27me3 depleted 2-cell (2 rep for control and 2 rep for depletion) and H2Aub-depleted 2-cell (2 rep for control and 2 rep for depletion) and 4-cell embryos (2 rep for control and 2 rep for depletion) to determine how loss of H3K27me3 or H2Aub affects transcriptome.

RNA-seq was performed in H3K27me3 depleted 4-cell (2 rep for control and 2 rep for depletion) and Eed maternal knockout 4-cell (2 rep for control and 2 rep for maternal KO). RNA-seq was also performed for MII oocyctes and 2-cell embryos (2 rep for each stage)

first: Zhiyuan

last: Chen

first: Mohamed

first: Yi

last: Zhang


title: Massively parallel characterization of CYP2C9 variant enzyme activity and abundance

status: Public on Mar 13 2021

city: Seattle

first: Clara

last: Amorosi

state: Washington

address: 3720 15th Ave. NE

department: Genome Sciences

institute: University of Washington

summary: CYP2C9 encodes a cytochrome P450 enzyme responsible for metabolizing up to 15% of small molecule drugs, and CYP2C9 variants can alter the safety and efficacy of these therapeutics. In particular, the anti-coagulant warfarin is prescribed to over 15 million people annually and polymorphisms in CYP2C9 can affect patient response leading to an increased risk of hemorrhage. We developed Click-seq, a pooled yeast-based activity assay to test thousands of variants. Using Click-seq, we measured the activity of 6,142 missense variants expressed in yeast. We also measured the steady-state cellular abundance of 6,370 missense variants expressed in a human cell line using Variant Abundance by Massively Parallel sequencing (VAMP-seq). These data revealed that almost two-thirds of CYP2C9 variants showed decreased activity, and that protein abundance accounted for half of the variation in CYP2C9 function. We also measured activity scores for 319 previously unannotated human variants, many of which may have clinical relevance.

sample_organism:
Escherichia coli
Saccharomyces cerevisiae
Homo sapiens

overall_design: Barcoded single amino acid variant libraries of CYP2C9 variants were generated for yeast and human expression. A humanized yeast strain was transformed with the yeast codon-optimized CYP2C9 library, labeled with activity-based protein profiling, sorted for activity, and plasmid DNA extracted. Barcodes were amplified and counted with Illumina sequencing. The eGFP-tagged CYP2C9 library was recombined into HEK293T cells previously engineered to contain a Bxb1 recombination site at the AAVS1 locus. Upon sorting cells for APC or eGFP expression, genomic DNA was extracted. Barcodes were amplified and counted with Illumina sequencing. For both libraries, barcodes were associated back to the corresponding CYP2C9 variant by comparison with a barcode-variant map previously created by sequencing the variant library plasmids using PacBio sequencing.

first: Maitreya

last: Dunham

first: Douglas

middle: M

last: Fowler


title: Non-CG methylation and multiple epigenetic layers associate child abuse with immune and small GTPase dysregulation

status: Public on Sep 22 2020

city: Strasbourg

first: Pierre-Eric

last: Lutz

address: 8 allée du général Rouvillois

country: France

institute: Institut des Neurosciences Cellulaires et Intégratives, INCI CNRS UPR3212

type: Methylation profiling by high throughput sequencing

summary: Early-life adversity (ELA) is a major predictor of psychopathology, and is thought to increase lifetime risk by epigenetically regulating the genome. Here, focusing on the lateral amygdala, a major brain site for emotional homeostasis, we described molecular cross-talk among multiple epigenetic mechanisms, including 6 histone marks, DNA methylation and the transcriptome, in subjects with a history of ELA and controls. We first uncovered, in the healthy brain, previously unknown interactions among epigenetic layers, in particular related to non-CG methylation in the CAC context. We then showed that ELA associates with methylomic changes that are as frequent in the CAC as in the canonical CG context, while these two forms of plasticity occur in sharply distinct genomic regions, features, and chromatin states. Combining these multiple data indicated that immune-related and small GTPase signaling pathways are most consistently impaired in the amygdala of ELA individuals. Overall, this work provides new insights into epigenetic brain regulation as a function of early-life experience.

overall_design: Examination of gene expression, DNA methylation and 6 histone marks in human brain tissue samples from the lateral amygdala, and comparison to gene expression data generated in another brain region, the anterior cingulate cortex (data first reported in Lutz, Tanti et al, The American Journal Of Psychiatry 2017, 174:12)

first: Marc-Aurèle

last: Chay

first: Gustavo

last: Turecki

first: Jean-François

last: Théroux


title: Transcriptional Profile of Brain Endothelial Cells in Response to Perturbations of Glutamatergic Neural Acticity

status: Public on Aug 24 2020

city: La Jolla

first: Robert

last: Pulido

state: CA

address: 9500 Gilman Ave, BSB 3095

institute: UC San Diego

summary: Bulk RNA sequencing of Brain Endothelial Cells from brain regions that underwent 3 hours of DREADDs-mediated glutamatergic activation or silencing compared to respective littermate controls or volitional whisker-mediated barrel cortex activation compared to no whisker controls.

overall_design: Glutamatergic DREADDs mice and littermate controls that did not express DREADDs were injected with CNO to either activate or silence glutamatergic neural activity, then 3 hours later, cortices and hippocampi were dissected out, dissociated into a single cell suspension, live stained for CD31 and non-endothelial markers, CD31+ cells were enriched using FACS sorting, sequenced and compared to littermate controls. Gene expression profiles of 4 biological samples for each of the two DREADDs mice were sequenced and compared to their respesctive littermate controls. For the whisker experiments, wildtype mice explored a novelly enriched environment in the dark using their whiskers through voltional behavior, and then their barrel cortices were pooled together and the same brain enodthelial enrichment protocol was used. Gene expression profiles of 3 biological samples consisting of 5 pairs of barrel cortices were generated per group and compared to 3 biological samples consisting of 5 pairs of barrel cortices from wildtype mice without whiskers in an empty cage.

first: Richard

last: Daneman


title: CD62L expression level determines the cell fate of myeloid progenitors in mice and humans

status: Public on Feb 04 2021

city: Shinjuku-ku

first: Yusuke

last: Ito

state: Tokyo

address: 35 Shinanomachi

department: Division of Tumor Immunology

country: Japan

institute: Keio University

summary: Through gene expression analysis of CMPs and GMPs at single cell levels, we identified CD62L as a marker to reveal the heterogeneity of CMPs and GMPs. We confirmed that the CD62L-low CMPs represent ‘bona fide’ CMPs, whereas CD62L-high CMPs are mostly restricted to GMP potentials both in mice and humans. In addition, we identified CD62L-neg GMPs as the most immature subsets in GMPs and Ly6c+CD62L-low and Ly6c+CD62L-high GMPs are skewed to neutrophil and monocyte differentiation, respectively. We performed gene expression profiling of CD62L-low CMPs, CD62L-high CMPs, CD62L-neg GMPs, CD62L-low GMPs, CD62L-high GMPs, bulk CMPs, and bulk GMPs.

overall_design: Gene expression profiling of CD62L-low CMPs, CD62L-high CMPs, CD62L-neg GMPs, CD62L-low GMPs, CD62L-high GMPs, bulk CMPs, and bulk GMPs


title: Effect of BET bromodomain inhibitor and/or mTOR inhibitor on transcriptome of small cell lung cancer patient-derived xenograft LX95 tumors

status: Public on Sep 01 2020

city: Bethesda

first: Haobin

state: MD

address: Building 10-CRC, Room 3-5848

department: NCI/CCR

institute: NIH

summary: We report mTOR inhibitor (mTORi) is synergistic with BET inhibitor (BETi) in controlling tumor growth and inducing apoptosis in small cell lung cancer (SCLC) patient-derived xenograft (PDX) models. In this study, we studied impact of different treatment on whole-genome mRNA transcriptome in SCLC PDX tumors. Four different treatments (vehicle control, NHWD870 [BETi; 1.5mg/kg], everolimus [mTORi; 2mg/kg], and the combo [NHWD870 1mg/kg and everolimus 1.5mg/kg] were administered daily for one week in a small cell lung cancer PDX LX-95 model. Tumor cells were isolated from PDX tumors using a magnetic-activated cell sorting method to enrich human tumor cells and total RNA was extracted using the RNeasy Mini Kit (Qiagen).  mRNA libraries were constructed and pair-ended sequenced using Illumina high-throughput sequencing technology. The length of sequence reads was 150 bp.The samples have 12 to 129 million pass filter reads with more than 90% of bases above the quality score of Q30. We found BET inhibitor increases expression of RPS6KA2, a gene that mediates crosstalk between MAPK and mTOR pathway.

overall_design: mRNA profiles of the LX95 small cell lung cancer PDX after one-week treatment of BET inhibitor and/or mTOR inhibitor

first: V

middle: K

last: Hughitt


title: Stem cell-derived neutrophil-primed progenitors prevent lethal infection

status: Public on Aug 22 2020

summary: We show that engineered neutrophil-primed progenitors derived from human induced pluripotent stem cells (NeuPs-XL) can produce functional neutrophil-like cells (NeuCs-XL) that can act promptly in vivo against lethal bacterial infections at a clinically applicable scale. We performed global gene expression profiling of NeuPs-XL and NeuCs-XL with or without LPS stimulation.

first: Masashi

last: Miyauchi

first: Fumio

last: Nakahara

first: Toshiya

last: Hino

first: Fumi

last: Nakamura

first: Yuki

last: Iwasaki

first: Taiki

last: Kawagoshi

first: Junji

last: Koya

first: Akihide

last: Yoshimi

first: Shunya

last: Arai

last: Kagoya

first: Mineo

last: Kurokawa


title: Role of the White Collar photoreceptor WcoA on the F. fujikuroi transcriptome

status: Public on Jan 15 2021

first: Javier

last: Avalos

address: Av. Reina Mercedes sn

country: Spain

institute: University of Seville

summary: The proteins of the White Collar 1 family (WC) constitute a major class of flavin photoreceptors, widely distributed in fungi, that work in cooperation with a WC 2 protein forming a regulatory complex. The WC complex was investigated in great detail in Neurospora crassa, a model fungus in photobiology studies, where it controls all its major photoresponses. The fungus Fusarium fujikuroi, a model system in the production of secondary metabolites, contains a single WC-1 gene called wcoA. The best-known light response in this fungus is the photoinduction of the synthesis of carotenoids, whose pathway has been investigated in great detail. Loss of WcoA in F. fujikuroi results in a drastic reduction in the mRNA levels of the carotenoid genes, and a diversity of morphological and metabolic changes, including alterations in the synthesis of several secondary metabolites, suggesting a complex regulatory role. To investigate the function of WcoA, the transcriptome of F. fujikuroi was analyzed in the dark and after 15-, 60- or 240-min illumination in a wild strain and in a formerly investigated wcoA insertional mutant. Using a threshold of 4-fold change in transcript levels, 298 genes were activated and 160 were repressed in the wild strain under at least one of the light exposures. Different response patterns were observed among them, with genes exhibiting either fast, intermediate and slow photoinduction, or intermediate or slow repression. All the fast and intermediate photoresponses, and most of the slow ones, were lost in the wcoA mutant. However, the wcoA mutation altered the expression of a much larger number of genes irrespective of illumination, reaching at least 16% of the annotated genes in this fungus. Such genes include many related to secondary metabolism, as well as others related to photobiology and other cellular functions, including the production of hydrophobins. As judged by the massive transcriptomic changes exhibited by the wcoA mutant in the dark, the results point to WcoA as a master regulatory protein in F. fujikuroi, in addition to a central function as the photoreceptor responsible for most of the transcriptional responses to light in this fungus.

overall_design: To check the role of the WcoA protein, we compared the transcriptomes of the wild strain and a wcoA mutant incubated in the dark or illuminated for 15 min, 60 min or 240 min. Data were obtained from three independent biological replicates for each condition

middle: P

last: Medina

first: Gabriel

last: Gutiérrez

first: M

middle: C

last: Limón


title: Expression data from gastric cancer organoids

status: Public on Jul 10 2020

city: hiroshima

first: Shoichi

last: Ukai

address: minami-ku kasumi 1-2-3

institute: Hiroshima University

summary:
To understand the molecular basis of the acquisition of 5-FU resistance in gastric cancer stem cells, we established 5-FU-resistant gastric cancer organoids.
We used microarrays to detail the global program of gene expression underlying 5-FU resistance and maintenance of stem cell properties in gastric cancer.

overall_design: To scrutinise the mechanism involved in the acquisition of 5-FU resistance in GC stem cells, we established 3 GCOs from surgically resected specimens. We then tried to establish GCOs with acquired resistance to 5-FU by continuous and stepwise escalation of 5-FU in the culture media. Normal gastric organoid are employed as controls.

first: Naoya

last: Sakamoto


title: Loss of Tdp-43 disrupts the axonal transcriptome of motoneurons accompanied by impaired axonal translation and mitochondria function

status: Public on Jul 27 2020

city: Würzburg

first: Silke

last: Appenzeller

address: Schweinfurter Str. 28

institute: University Wuerzburg

summary: Protein inclusions containing the RNA-binding protein TDP-43 are a pathological hallmark of amyotrophic lateral sclerosis and other neurodegenerative disorders. The loss of TDP-43 function that is associated with these inclusions affects post-transcriptional processing of RNAs in multiple ways including pre-mRNA splicing, nucleocytoplasmic transport, modulation of mRNA stability and translation. In contrast, less is known about the role of TDP-43 in axonal RNA metabolism in motoneurons. Here we show that depletion of Tdp-43 in primary motoneurons affects axon growth. This defect is accompanied by subcellular transcriptome alterations in the axonal and somatodendritic compartment. The axonal localization of transcripts encoding components of the cytoskeleton, the translational machinery and transcripts involved in mitochondrial energy metabolism were particularly affected by loss of Tdp-43. Accordingly, we observed reduced protein synthesis and disturbed mitochondrial functions in axons of Tdp-43-depleted motoneurons. Treatment with nicotinamide rescued the axon growth defect associated with loss of Tdp-43. These results show that Tdp-43 depletion in motoneurons affects several pathways integral to axon health indicating that loss of TDP-43 function could thus make a major contribution to axonal pathomechanisms in ALS.

overall_design: Total number of samples is 20. Gene expression data from axonal compartment of cultured control motoneurons, somatodendritic compartment of cultured control motoneurons, axonal compartment of cultured Tdp-43 knockdown motoneurons, and somatodendritic compartment of cultured Tdp-43 knockdown motoneurons.

first: Michael

last: Briese

first: Lena

last: Saal-Bauernschubert

first: Patrick

last: Lüningschrör

first: Mehri

last: Moradi

first: Benjamin

last: Dombert

first: Verena

last: Surrey

first: Chunchu

last: Deng

first: Sibylle

last: Jablonka

last: Sendtner


title: TFEB-induced 5hmC and 5mC changes in AML cells [oxRRBS-seq]

status: Public on Jun 12 2020

city: Tampa

first: Chia-Ho

last: Cheng

address: 12902 USF Magnolia Drive

institute: Moffitt Cancer Center

summary: We report reduced representation oxidation bisulfite-sequencing data after TFEBS211A overexpression in HL60 cell line.

overall_design: HL60 cells lines were transduced with either pRRL-EV-puro or pRRL-TFEBS211A-puro which inducibly overexpress TFEBS211A in doxycycline dependent manner. Then, reduced representation oxidation BS-seq was performed comparing TFEBS211A expressing cells vs. three other control groups. All samples were prepared as triplicate (biologically independent experiments).

first: John

last: Cleveland

first: Seongseok

last: Yun


title: Persistent Epigenetic Reprogramming of Sweet Taste by Diet

first: Monica

last: Dus

summary: We report the application of ribosomal profiling based RNA sequencing technology for high-throughput profiling of the Gr5a cells of male Drosophila melanogaster adults. By expressing the UAS-Rpl3-3XFLAG transgene using the Gr5a-GAL4 driver on Pclc429 mutant flies.

overall_design: 3 replicates from the Gr5a cells  per dietary condition is obtained using the illumna NextSeq-500 platform

first: Anoumid

last: Vaziri


title: TFEB-induced gene expression changes in AML cells [RNA-seq]

summary: We report gene expression changes after TFEBS211A overexpression in HL60 cell line.

overall_design: HL60 cells lines were transduced with either pRRL-EV-puro or pRRL-TFEBS211A-puro which inducibly overexpress TFEBS211A in doxycycline dependent manner. Then, RNA-seq was performed comparing TFEBS211A expressing cells vs. three other control groups. All samples were prepared as triplicate (biologically independent experiments).


title: TFEB-induced gene expression, 5hmC and 5mC changes in AML cells

overall_design: Refer to individual Series


title: Absence of Plekhg5 Results in Myelin Infoldings Corresponding to an Impaired Schwann Cell Autophagy, and a Reduced T-Cell Infiltration Into Peripheral Nerves

summary: Inflammation and dysregulation of the immune system are hallmarks of several neurodegenerative diseases. An activated immune response is considered to be the cause of myelin breakdown in demyelinating disorders. In the peripheral nervous system (PNS), myelin can be degraded in an autophagy-dependent manner directly by Schwann cells or by macrophages, which are modulated by T-lymphocytes. Here, we show that the NF-κB activator Pleckstrin homology containing family member 5 (Plekhg5) is involved in the regulation of both Schwann cell autophagy and recruitment of T-lymphocytes in peripheral nerves during motoneuron disease. Plekhg5-deficient mice show defective axon/Schwann cell units characterized by myelin infoldings in peripheral nerves. Even at late stages, Plekhg5-deficient mice do not show any signs of demyelination and inflammation. Using RNAseq, we identified a transcriptional signature for an impaired immune response in sciatic nerves, which manifested in a reduced number of CD4+ and CD8+ T-cells. These findings identify Plekhg5 as a promising target to impede myelin breakdown in demyelinating PNS disorders.

overall_design: Total number of samples is 6

first: Carsten

last: Slotta

first: Peter

last: Heimann

first: Ulrich

last: Weikert

first: Bita

last: Massih

first: Christian

last: Kaltschmidt

first: Barbara


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


title: A novel mouse model of hepatocellular carcinoma mediated by hepatitis B virus-specific CD8+ T cells

status: Public on Apr 29 2020

city: Hefei

first: Xiaolei

last: Hao

state: Anhui

address: huangshan Road 443

institute: Institute of Immunology, USTC


title: Developmental trajectory of pre-hematopoietic stem cell formation from endothelium

status: Public on Apr 27 2020

city: San Francisco

first: Qin

last: Zhu

address: 600 Minnesota Street

institute: UCSF


title: RNA-Sequencing analysis of Meox1 siRNA knockdown in p53 and PTEN deficient triple negative breast cancer in vitro cell lines of BT-549 and MDA-MB-468

status: Public on May 26 2020

first: Duxin

last: Sun

state: MI

address: 1600 Huron Parkway

summary: The goal for this experiment was to analyze how knockdown of homeobox transcription factor Meox1 altered functional and mechanist biology of p53 and PTEN deficient triple negative breast cancer in vitro cell lines of claudin-low BT-549 and basal-like MDA-MB-468.

overall_design: Two different subtypes of triple negative breast cancer with p53 and PTEN deficiencies were utilized, claudin-low BT-549 and basal-like MDA-MB-468. For knocking down Meox1, siRNA transfection experiment was conducted with Negative Control siRNA and Meox1 siRNA, two biological replicates using Negative Control siRNA and Meox1 siRNA for each cell line were conducted. For RNA Seqeuncing, two technical replicates for each biological replicate were sequenced, making a total of 16 samples for sequencing.

first: Mari

last: Gasparyan


title: A multimodal treatment of carbon ions irradiation, miRNA-34 and mTOR inhibitor specifically control high-grade chondrosarcoma cancer stem cells

status: Public on Oct 15 2020

city: Fontenay-aux-Roses

first: Guillaume

last: Vares

institute: IRSN

summary: High-grade chondrosarcomas are chemo- and radio-resistant cartilage-forming tumors of bone that often relapse and metastase. Thus, new therapeutic strategies are urgently needed. Here we show that high-grade chondrosarcoma cells contain a population of radioresistant cancer stem cells that can be targeted by a combination of carbon-ion therapy, miR-34 mimic administration and/or rapamycin treatment that triggers FOXO3 and miR-34 over-expression. mTOR inhibition by rapamycin triggered FOXO3 and miR-34, leading to KLF4 repression. Our results show that particle therapy combined with molecular treatments effectively controls cancer stem cells and may overcome treatment resistance of high-grade chondrosarcoma.

overall_design: Transcriptional response of CH-2879 cells to carbon-ion irradiation

first: Vidhula

last: Ahire

first: Shigeaki

last: Sunada

first: EunHo

last: Kim

first: Sei

last: Sai

first: Francois

last: Chevalier

first: Paul-Henri

last: Romeo

first: Tadashi

last: Yamamoto

first: Tetsuo

last: Nakajima

first: Yannick

last: Saintigny


title: Whole Transcriptome analysis for porcine alveolar macrophage infected by African Swine Fever Virus

status: Public on Oct 20 2020

first: Jingrui

last: Li

address: Yuanmingyuan West Road No.2

institute: China Agricultural Universtiy

type: Non-coding RNA profiling by high throughput sequencing

summary: African swine fever virus (ASFV) is one of the most devastating swine pathogens characterized by nearly 100% mortality in naive herds and was recently emerged the in China. In this study, we generated the expression profile of porcine alveolar macrophages (PAMs) infected with a high pathogenic ASFV (Pig/Heilongjiang/2018 (Pig/HLJ/18) ASFV). Our data indicated that ASFV infection lead to a strong inhibition of host immunity but promote chemokine-mediated signaling pathway and neutrophil chemotaxis. Moreover, ASFV infection can modulate the host miRNA involved regulation network, leading to a significant increase of host metabolism related genes and acceleration of virus replication. Furthermore, ASFV-derived viral small RNAs (vsRNAs) can target some host immune response related genes. In conclusion, our transcriptome-wide data provide some insights into the regulatory mechanism during ASFV infection.

overall_design: MicroRNA and mRNA profiles of porcine alveolar macrophages (PAMs) at different time-points post ASFV infection. MicroRNA and mRNA datasets were generated by deep sequencing, in triplicate, using Illumina Nextseq CN500 and Hiseq Xten platforms, respectively.

first: Qiang

last: Ding

first: Xiaohui

last: Ju

first: Yuchen


title: HDAC3 IS AN EPIGENETIC INHIBITOR OF THE CYTOTOXICITY PROGRAM IN CD8 T CELLS [ChIP-seq]

status: Public on Apr 22 2020

city: Boston

first: Yingtian

last: Xie

state: MA

address: 450 BROOKLINE AVE

institute: DANA FARBER CANCER INSTITUTE INC

summary: Cytotoxic T cells play a key role in adaptive immunity by killing infected or cancerous cells. While the transcriptional control of CD8 T cell differentiation and effector function following T cell activation has been extensively studied, little is known about epigenetic regulation of these processes. Here we show that the histone deacetylase HDAC3 inhibits CD8 T cell cytotoxicity early during activation and is required for persistence of activated CD8 T cells following resolution of an acute infection. Mechanistically, HDAC3 inhibits gene programs associated with cytotoxicity and effector differentiation of CD8 T cells including genes encoding essential cytotoxicity proteins and key transcription factors. These data identify HDAC3 as an epigenetic regulator of the CD8 T cell cytotoxicity program.

overall_design: CD8 T cells were magnetically isolated from OT-I transgenic mice and activated by co-culture with irradiated, OVA peptide-pulsed bone marrow-derived dendritic cells. For drug/no drug treatment experiments, the same source material was used for both experiments. For KO vs WT experiments, we used cells collected from KO and WT littermates as the source material, respectively.

first: Rong

middle: E

last: Tay

first: Paloma

last: Cejas


title: HDAC3 IS AN EPIGENETIC INHIBITOR OF THE CYTOTOXICITY PROGRAM IN CD8 T CELLS [RNA-seq]

overall_design: CD8 T cells were magnetically isolated from OT-I transgenic mice and activated by co-culture with irradiated, OVA peptide-pulsed bone marrow-derived dendritic cells. We performed three replicates per experimental condition. For drug/no drug treatment experiments, the same source material was used for both experiments. For KO vs WT experiments, we used cells collected from KO and WT littermates as the source material, respectively.


title: HDAC3 IS AN EPIGENETIC INHIBITOR OF THE CYTOTOXICITY PROGRAM IN CD8 T CELLS


title: Differential gene expression analysis of MYCN-amplified neuroblastoma cells after THZ1 and TKI combination therapy.

status: Public on Mar 20 2020

city: Sydney

first: matthew

middle: kwok kei

last: wong

state: New South Wales

address: Lowy cancer centre, University of New South Wales

department: histone modification group

institute: Children's Cancer Institute

summary:
The CDK7 inhibitor THZ1 has been shown to suppress MYCN gene transcription but not cause significant cell death as a  single agent.
The tyrosine kinase inhibitors (TKIs) ponatinib and lapatinib were found to exert synergistic anti-cancer effects in combination with the CDK7 inhibitor THZ1, on MYCN amplified neuroblastoma cell lines.

overall_design: We performed Affymetrix Human Gene 2.0 ST microarray experiments in BE2C neuroblastoma cells after 6hrs treatment with either vehicle control, 32nM THZ1, 250nM ponatinib, 1000nM lapatinib, THZ1 + ponatinib or THZ1 + lapatinib. Differential expression analysis (drug treatment - vehicle control) was analysed for each drug treatment.

first: Tao

last: Liu

first: Andrew

last: Tee

first: Matthew

last: Wong

first: Nicolas

last: Ho


title: An airway protection program revealed by sweeping genetic control of vagal afferents

status: Public on Apr 05 2020

first: Sara

last: Prescott

state: Massachusetts

address: 240 Longwood Avenue

institute: Harvard Medical School

summary: Sensory neurons evoke a suite of defensive reflexes to ensure airway integrity. Dysfunction of laryngeal neurons is life-threatening, causing pulmonary aspiration, dysphagia, and choking, yet relevant sensory pathways remain poorly understood. Here, we discover rare throat-innervating neurons (~100 neurons/mouse) that guard the airways against assault. We used genetic tools that broadly cover a vagal/glossopharyngeal sensory neuron atlas to map, ablate, and control specific afferent populations. Optogenetic activation of vagal P2RY1 neurons evokes a coordinated airway defense program- apnea, vocal fold adduction, swallowing, and expiratory reflexes. Selective ablation of vagal P2RY1 neurons eliminates protective responses to laryngeal water and acid challenge. Anatomical mapping revealed numerous terminal morphologies in the larynx, with P2RY1 neurons forming corpuscular endings that appose laryngeal taste buds. Epithelial cells are primary airway sentinels that communicate with second-order P2RY1 neurons through ATP. These findings provide mechanistic insights into airway defense, and a general molecular/genetic roadmap for internal organ sensation by the vagus nerve.

overall_design: Single-neuron sequencing of murine vagal sensory ganglia

first: Stephen

last: Liberles

first: Ben

last: Umans

first: Erika

last: Williams

first: Rachael

last: Brust


title: EHMT1 gene truncation in HEK293 cells recapitulates Kleefstra Syndrome disease phenotype

status: Public on Sep 04 2020

city: North Coogee

first: Denise

last: Anderson

state: WA

address: 71 Caledonia Loop

institute: INSiGENe Pty Ltd

summary: Haploinsufficiency of the Euchromatin histone methyltransferase 1 (EHMT1) gene leads to Kleefstra Syndrome, a rare disease characterised by moderate to severe developmental delay/intellectual disability, childhood hypotonia and distinct facial features, comprising microcephaly. This study examines the genetic variant EHMT1_Ter (p.[Tyr1148=];[Tyr1148Leufs*9]) in HEK293 cells.

overall_design:
Comparison of HEK293  EHMT1_Ter cells and EHMT1_WT cells by NGS analytics after CRISPR editing
RNAseq and CLLAG (Cap dependent Linker Ligation Analysis of Gene expression)

first: Vanessa

middle: S

last: Fear


title: PRMT1 regulates B cell fate after positive selection in the germinal center

status: Public on Mar 27 2020

city: bethesda

first: Seolkyoung

last: Jung

address: 10 Center Dr

department: NIAMS

summary: RNAseq on B cells from HSC to GC B cell in mouse

overall_design: B cells from HSC to GC B cell

first: Ludivine

last: Litzler

first: Adrien

last: Sprumont

first: Astrid

last: Zahn

last: Methot

first: Anne-Marie

last: Patenaude

first: Stephane

last: Richard

first: Javier

last: Noja

first: Claudia

last: Kleinman

first: Kiersten

last: Dionne

first: Silvana

last: Ferreira

first: michael

last: Slattery

first: Steven

last: Hebert

first: Nisha

last: Kabir

first: P Ganesh

last: Subramani