title: Transcription landscape of adipose tissue changes in response to telomerase knockout in mesenchymal progenitors

status: Public on Sep 11 2020

city: Houston

first: Yulin

last: Dai

state: TX

address: 7000 fannin, suite 600

department: School of Biomedical Informatics

institute: University of Texas health science center at Houston

summary: We generated mice with telomerase (TERT) gene knock-out (KO) that undergo premature telomere shortening in adipose stromal cells expressing Pdgfra or Pdgfrb. Stromal vascular cells were isolated from inguinal adipose tissue of Pdgfra-Cre; TERT fl/fl mice (Sample name A_SAT), Pdgfrb-Cre; TERT fl/fl mice (Sample name KO_SAT), and of control TERT WT mice (Sample name PBS_SAT).

overall_design: scRNAseq analysis of subcutaneous adipose tissue stromal vascular cells was performed.

first: Mikhail

last: Kolonin

first: Zhanguo

last: Gao

first: Alexes

last: Daquinag


title: Defining Essential Enhancer for Pluripotent stem cells using Features Oriented CRISPR-Cas9 Screen (RNA-Seq 2)

status: Public on Sep 13 2020

city: Singapore

first: Chadi

last: El Farran

address: 61 Biopolis Drive

country: Singapore

institute: Institute of Molecular and Cell Biology

type: Expression profiling by high throughput sequencing

summary: Cis Regulatory Elements (CREs) regulate the expression of the genes in their genomic neighborhoods and influence cellular processes such as cell-fate maintenance and differentiation. To date, there remain major gaps in the functional characterization of CREs and the identification of its target genes in the cellular native environment. In this study, we performed a Features Oriented CRISPR Utilized Systematic (FOCUS) screen of Oct4-bound CREs using CRISPR/Cas9 to identify functional CREs important for pluripotency maintenance in mouse ES cells.

overall_design: RNA profiling of CRE KO mESCs(10 CREs) and NT KO mESCs(2 NTs)

first: H

middle: F

last: Wang

first: T

last: Warrier

first: C

middle: A

last: Li

first: Y

middle: H

last: Loh


title: Multi-contact 3C data reveal that the human genome is largely unentangled

status: Public on Sep 12 2020

city: Worcester

first: Bastiaan

last: Dekker

state: Massachusetts

address: 368 Plantation street

department: Systems Biology

country: USA

institute: University of Massachusetts Medical School

summary: Setup Pacbio sequencing in combination with 3C

overall_design: DpnII MC-3C on Asynchronious cells

first: Filipe

last: Tavares-Cadete

first: Davood

last: Norouzi

first: Yu

last: Liu

first: Job


title: Regulation of neuronal commitment in mouse embryonic stem cells by the Reno/Bahcc1 locus

city: Rehovot

first: Igor

last: Ulitsky

address: Hertzl St.

country: Israel

institute: Weizmann Institute of Science

type: Genome binding/occupancy profiling by high throughput sequencing

overall_design: RNA-seq and ATAC-seq of ES cells, NPCs, and neurons

first: Hadas

last: Hezroni


title: Defining Essential Enhancer for Pluripotent stem cells using Features Oriented CRISPR-Cas9 Screen

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

overall_design: Refer to individual Series


title: circZNF827 nucleates a transcription inhibitory complex to balance neuronal differentiation

city: Aarhus C

first: Thomas

middle: B

last: Hansen

state: State...

address: C.F. Moellers Alle 3, build 1130

country: Denmark

institute: MBG, Aarhus University

summary: Here, we have mapped high-confidence circRNA inventories of mouse embryonic stem cells, neuronal progenitor cells and in differentiated glutamatergic neurons and identify hundreds of differentially expressed circRNAs. By screening a panel of candidate circRNAs  for a potential function in neuronal differentiation, we found that knockdown of circZNF827 significantly induces expression of key neuronal markers while slowing cell proliferation, suggesting that this molecule normally negatively regulates neuronal differentiation.

overall_design: RNAseq of total and RNAseR treated RNA from neuronal differentiation of mESCs

first: Christian

middle: K

last: Damgaard

first: Anne

last: Hollesen


title: Molecular signatures of immune cells and neuroblasts in the aged brain

city: Beijing

first: Wei-Na

last: Jin

state: Beijing

address: NO.119, Southwest of the Fourth Ring Road, Fengtai District

department: China National Clinical Research Center for Neurological Diseases

country: China

institute: Beijing Tiantan Hospital, Capital Medical University

summary: Normal aging is accompanied by escalating systemic inflammation. To comprehensively characterize the impact of aging on immune cells in the brain and periphery, we harvested immune cells from mouse spleen and brain tissues. Single cell sequencing was performed to compare the genetic signatures in these isolated immune cell subsets from spleen and brain tissues in young and aged mice. Our results demonstrate increased accumulations of immune cells such as natural killer (NK) cells in the aged brain as compared to the young brain. In addition, NK cells in the aged brain display augmented proliferation activity and cytotoxicity.  RNA-sequencing of neuroblasts isolated from the aged brain revealed that aging induces dysregulated expression of genes related to DNA damage response and upregulation of senescence signatures.

overall_design: The 6 samples were divided into two groups to extract total RNA ,construct mRNA Library  and use quantitative real-time PCR

first: Kaibin

last: Shi

first: Wenyan

last: He

first: Jun-Hong

last: Sun

first: Luc

last: Van Kaer

first: Fu-Dong

first: Qiang


title: Defining Essential Enhancer for Pluripotent stem cells using Features Oriented CRISPR-Cas9 Screen (4C-Seq)

first: Chadi

last: El Farran

overall_design: 4C-seq of 5 CREs in mESCs and MEF

first: H

last: Wang

first: T

last: Warrier

first: C

first: Y


title: MARCH1 regulates anti-malarial immunity through interferon signaling and T cell activation

city: Bethesda

first: Timothy

middle: G

last: Myers

state: MD

address: 50 South Drive, Room 5509

department: Research Technologies Branch

institute: National Institute of Allergy and Infectious Diseases

summary: Malaria infection induces complex and diverse immune responses, including impairment of dendritic cell (DC) function and immune suppression that may contribute to the low vaccination antibody titers to some antigens in endemic populations. To elucidate the mechanisms underlying host-parasite interaction, we performed a genetic screen during early Plasmodium yoelii infection and identified a large number of interacting host and parasite genes/loci after trans-species expression quantitative trait loci (Ts-eQTL) analysis. We next investigated a host E3 ubiquitin ligase gene (march1) that was clustered with interferon stimulated genes. March1 can inhibit MAVS/STING induced IFN-I signaling and reverse inhibition of viral replication mediated by MAVS in vitro. However, in malaria-infected hosts, deficiency of march1 activates IFN signaling inhibitors such as SOCS1, SOCS3, and TRIM24, leading to reduced early (24h) serum IFN-I levels. Increased CD86+ DC populations and elevated levels of IFN-? and IL-10 produced by T cells day 4 post infection protect infected march1-/- mice. Malaria lysate stimulate MACRH1 expression, which reduces CD86+ DC cells and impairs T cell activation. This study reveals previous unknown functions of MARCH1 in innate response to malaria infections and provides potential avenues for activating anti-malaria immunity and enhancing vaccine efficacy.

overall_design: Whole spleen RNA from mice (strain C57BL/6, sourced from two different suppliers, or March1 Knockout) infected with malaria strains YM, N67, or N67C, harvested 24 hrs or 4 days post infection.

first: Jian

last: Wu

first: Lu

last: Xia

first: Xiangyu

last: Yao

first: Xiao

last: Yu

first: Keyla

last: Tumas

first: Wenxiang

first: Yang

last: Cheng

first: Yu-chih

last: Peng

first: Chen

last: Qi

first: Silvia

last: Bolland

first: Sonja

middle: M

last: Best

first: Channe

last: Gowda

first: Ruili

last: Huang

first: Carole

last: Long

first: Rongfu

first: Xin-zhuan

last: Su


title: RNA-Seq expression profiling of clonal populations from the OCI-C5x patient-derived ovarian clear cell carcinoma cell line

city: Boston

first: Joan

middle: S.

last: Brugge

state: MA

address: 240 Longwood Avenue

department: Department of Cell Biology

institute: Harvard Medical School

summary: Intratumoral heterogeneity is well-recognized but its impact on tumor progression is unclear. Here, we derived unbiased clonal populations from OCI-C5x, a patient-derived ovarian clear cell carcinoma cell line, and assessed their tumorigenicity and tracked their fate during tumor progression. Results provide insight into intratumoral heterogeneity of clear cell carcinoma transcriptomes.

overall_design: RNA-Seq was performed on the OCI-C5x clear cell carcinoma line and 11 derived clones.

first: Suha

last: Naffar-Abu Amara

first: Laura

last: Selfors

middle: S


first: Wei-Na

last: Jin

overall_design: The 4 samples were divided into two groups to sort single cell and construct single cell Library

first: Kaibin

last: Shi

first: Wenyan

last: He

first: Jun-Hong

last: Sun

first: Luc

last: Van Kaer

first: Fu-Dong

first: Qiang

last: Liu


title: Non-canonical Wnt/PCP signalling regulates intestinal stem cell lineage priming towards enteroendocrine and Paneth cell fates

city: Neuherberg

first: Johannes

last: Beckers

address: Ingolstaedter Landstr. 1

department: Institute of Experimental Genetics

country: Germany

institute: Helmholtz Zentrum Muenchen


title: Identification of differential gene expression in blood vessels from patients with uremia (data set 2)

city: Roskilde

first: Vibe

last: Skov

address: Koegevej 7-13

department: Hematology

institute: Roskilde Hospital

overall_design: To use as non-renal vasculature, mammary arteries samples from 5 patients undergoing by-pass operations with elevated plasma creatine (above 140 µM) were compared with 5 age and gender matched individuals with no known renal disease.

first: Skov

last: Vibe


title: IL-4 Receptor a Subunit Deficiency Alleviates Murine Intestinal Inflammation In Vivo through the Enhancement of Intestinal Mucosal Barrier Function

status: Public on Sep 10 2020

city: Toyama

first: Shusaku

last: Hayashi

address: 2630 Sugitani

country: Japan

institute: University of Toyama

summary: In the present study we investigate the role of IL-4 receptor a subunit in intestinal inflammation using DSS-induced colitis model. Our finding suggest that IL-4Ra deficiency enhances intestinal mucosal barrier function through the upregulation of NOX1-dependent ROS production, thereby suppressing the development of intestinal inflammation.

overall_design: Gene expression profile in the colon tissue of WT and IL-4Ra-/- treated with 3% DSS or water as a control for 7 days. Mice colon were analyzed on day 7 after DSS treatment. mRNA samples was pooled from 3-6 mice of each group (WT Normal, WT Colitis and KO Colitis)

first: Ai

last: Hertati

first: Yudai

last: Ogawa

first: Takeshi

last: Yamamoto

first: Makoto

last: Kadowaki


title: Identification of differential gene expression in blood vessels from patients with uremia


title: Identification of differential gene expression in blood vessels from patients with uremia (data set 1)

overall_design: We used microarrays to assess gene expression profiling of 15 uremic patients undergoing renal transplantation and 19 renal artery samples from donors undergoing renal nephrextomy.


title: The NKL-code for innate lymphoid cells reveals deregulated expression of NKL homeobox genes HHEX and HLX in ALCL [II]

city: Braunschweig

first: Claudia

last: Pommerenke

address: Inhoffenstraße 7B

institute: Leibniz Institute DSMZ

summary: NKL homeobox genes encode developmental transcription factors regulating basic processes in cell differentiation. According to their physiological expression pattern in early hematopoiesis and B-cell development, particular members of this homeobox gene subclass constitute an NKL-code. These B-cell specific genes generate a regulatory network and their deregulation is implicated in B-cell lymphomagenesis. Epstein-Barr virus (EBV) infects B-cells and influences the activity of signalling pathways including JAK/STAT and several genes encoding developmental regulators. Therefore, EBV-infection impacts the pathogenesis and the outcome of B-cell malignancies including Hodgkin lymphoma and diffuse large B-cell lymphoma (DLBCL). Here, we isolated EBV-positive and EBV-negative subclones from the DLBCL derived cell line DOHH-2. These subclones served as model to investigate the role of EBV in deregulation of the B-cell specific NKL-code members HHEX, HLX, MSX1 and NKX6-3. We showed that the EBV-encoded factors LMP1 and LMP2A activated the expression of HLX via STAT3. HLX in turn repressed NKX6-3, SPIB and IL4R which normally mediate plasma cell differentiation. In addition, HLX repressed pro-apoptotic factor BCL2L11/BIM supporting cell survival. Thus, EBV aberrantly activated HLX thereby disturbing both B-cell differentiation and apoptosis in DLBCL. The results of our study contribute to better understand the pathogenic role of EBV in B-cell malignancies.

overall_design: siRNA-mediated knockdown of NKL homeobox gene HLX in ALCL cell line SU-DHL-1

first: S

last: Nagel

first: C


title: The NKL-code for innate lymphoid cells reveals deregulated expression of NKL homeobox genes HHEX and HLX in ALCL [I]

overall_design: forced expression of NKL homeobox gene HHEX in ALCL cell line SU-DHL-1


title: Distinct oligodendrocyte populations have spatial preference and different responses to spinal cord injury

city: Stockholm

first: Eneritz

last: Agirre

address: Solnavägen 9

department: MBB

country: Sweden

institute: Karolinska Institutet

summary: In this study, we unveil that transcriptionally distinct oligodendrocyte populations have spatial preference and differential response to spinal cord injury. We also assess by different methods, including single-cell RNA sequencing, that the developmental origin of oligodendrocyte progenitors does not determine their specification into mature olgodendrocyte populations.

overall_design: We pooled the corpus callosum from two adult (P60) Emx1::Cre-Sox10::Cre-GFP-STOP-TdTom mice from which we took two samples (GFP+ and TdTom+ oligodendrocytes) to address the influence of the oligodendrocyte developmental origin in their subpopulation identity in adulthood. The corpus callosum of P60 Emx1::Cre-Sox10::Cre-LoxP-GFP-STOP-TdTom was sectioned at the microtome and microdissected from two mice. The injury site, rostral and caudal wallerian degeneration regions or control spinal cord of three months Sox10::Cre-GFP mice were microdissected from eight injured and five laminectomy mice.

first: Elisa

last: Floriddia

first: Tania

last: Lourenco

first: Shupei

last: Zhang

first: David

last: van Bruggen

first: Markus

last: Hilscher

first: Petra

last: Kukanja

first: João

middle: P

last: Gonçalves dos Santos

first: Müge

last: Altınkök

first: Chika

last: Yokota

first: Enric

last: Llorens-Bobadilla

first: Sarah

last: Mulinyawe

first: Mário

last: Grãos

first: Lu

middle: o

first: Jonas

last: Frisén

first: Mats

last: Nilsson

first: Gonçalo

last: Castelo-Branco


title: Next Generation Sequencing Analysis of Human Glioblastoma Transcriptomes And Quantitative Analysis of PDGFRA Positive/Negative Human Glioma Cells Transcriptomes

city: Zhejiang

first: Chong

last: Liu

address: NO.866 of Yuhang Tong Road

institute: Medical College of Zhejiang University

summary: We report the high-throughput profiling of thirteen human glioblastoma and four pairs of panned(pdgfra+) and supernatant(pdgfra-) human glioma cells. The subtypes and the different expression genes(DEGs) was identified integrated genomic analysis:single sample GSEA and DESeq.We obtained the enrichment gene pathway by using Gene Ontology Enrichment analysis-Functional classification viewed in pie chart.We find that the features of Proneural were enriched generaly when comparing the four pairs of the panned(pdgfra+) and supernatant(pdgfra-) human glioma cells.

overall_design: Seven Glioblastoma tissue and four pairs of panned(pdgfra+) and supernatant(pdgfra-) human glioma cells were generated by deep sequencing, using Illumina Hiseq X_Ten.

last: liu


title: Next generation sequencing of CD11b+ cells from female and male Wildtype and Cystatin C knockout mice with experimental allergic encephalomyelitis (EAE)

status: Public on Sep 09 2020

city: Calgary

first: Shalina

last: Ousman

state: Alberta

address: 3330 Hospital Drive NW

country: Canada

institute: University of Calgary

summary:
Rationale: Towards clarifying the role of the cysteine protease inhibitor, Cystatin C (CysC), whose expression is augmented in the brains of multiple sclerosis (MS) patients and C57BL/6J mice with experimental allergic encephalomyelitis (EAE - a model of MS), we discovered that CysC plays a detrimental function in MOG35-55-induced EAE, but only in female animals. Female CysC null mice displayed significantly lower clinical signs of disease compared to wildtype (WT) littermates that was associated with reduced interleukin-6 production and lower expression of key proteins (CD80, CD86, MHC II, LC3A/B) involved in antigen processing, presentation and co-stimulation in antigen presenting cells (APCs), specifically CD11b+ cells. To delineate if these antigen presenting markers in CD11b+ cells as well as unidentified others were expressed differentially between the two genotypes and sexes, we performed Next Generation Sequencing on total RNA from CD11b+ cells from female and male Wildtype and Cystatin C knockout mice with experimental allergic encephalomyelitis (EAE) at 7 days post-immunization.
Methods: CD11b+ cells were isolated by positive selection (Miltenyi Biotec) from day 7 EAE female and male WT and CysC-/- spleens and RNA retrieved with an RNeasy Mini Kit (Qiagen). Samples with an RNA integrity number greater than 8 were subjected to Deep Sequencing and each sample is from an individual mouse. All samples were subjected to reverse transcription and Multiple Displacement Amplification with REPLI-g SensiPhi DNA Polymerase and oligo-dT primers as per the QIAGEN REPLI-g Single Cell RNA Library preparation kit and the manufacturer's protocol. Libraries were prepared using the QIAGEN GeneRead Adaptor I Set A 12-plex index adapters as per the REPLI-g single cell RNA library prep kit's protocol and subjected to on-board cluster formation and sequencing on an Illumina NextSeq 500 sequencer with a high-output v2 75 cycle sequencing kit as per the standard Illumina protocols. After sequencing, the bcl data was converted to fastq data files using the Illumina BCL2FASTQ utility. Alignment was performed using bwa 0.7.12 in ÒmemÓ alignment mode against mm10 reference genome with default parameters. Output was imported into Ingenuity Pathway Analysis software for physiological function analysis.
Results: Our RNASeq data revealed that LC3B and CD80 in female EAE CysC null cells were overwhelming present in immune modulation functional pathways that were decreased (negative z-score) compared to the male cohort.
Conclusions: These findings imply that CysC plays a role in promoting an appropriate molecular response needed for the maturation or antigen processing, loading and presentation by antigen presenting cells in female mice during EAE.

overall_design: Spleen-derived CD11b+ cells from day 7 EAE wildtype (WT) and Cystatin C knockout female and male mice

first: Vahid

last: Hoghooghi

first: Paul

last: Gordon


title: Creld1-deficient CD4+ T cells under homeostatic condition and CD3/CD28 stimulation

city: Bonn

first: Joachim

last: Schultze

state: NRW

address: Carl-Troll-Strasse 31

department: Genomics and Immunoregulation

institute: LIMES (Life and Medical Sciences Center Genomics and Immunoregulation)

summary: Transciptome profiling of sorted naive CD4+ T cells from control or Creld1 conditional KO mice (CD4-Cre) both directly ex vivo and with or without stimulation with anti-CD3/anti-CD28 antibodies to study the impact of Creld1 on T cell biology

overall_design: Conventional naïve CD4+ T cells from either Creld1 conditional knockout (CD4-Cre) or control mice as well as from eight-hour ex vivo cultures with or without T cell receptor stimulation by anti-CD3/anti-CD28 (n=3 /  group)

first: L

last: Bonaguro

first: J

last: Schulte-Schrepping

first: T

last: Ulas

first: K

last: Haendler

middle: L

first: A

middle: C

last: Aschenbrenner


title: H1 linker histones regulate the balance of repressive and active chromatin domains via localized genomic compaction [ChIP-seq]

city: Bronx

first: Boris

last: Bartholdy

state: NY

address: 1300 Morris Park Ave

department: Cell Biology

institute: Albert Einstein College of Medicine

summary: H1 linker histones are the most abundant chromatin binding proteins. Their association with chromatin determines the spacing between nucleosomes and enables arrays of nucleosomes to fold into more compact chromatin structures. Mammals express multiple H1 proteins and are able to compensate for the loss of one or even two members by increasing synthesis of other members to maintain a constant H1 to nucleosome stoichiometry. To study the role of H1 in mammalian development, we generated a conditional triple H1 knockout (H1cTKO) mouse strain that enables depletion of H1 in specific cell types. Here, we report on the effects of depleting H1 in adult hematopoietic cells. Deletion of the genes encoding three widely expressed H1 subtypes (H1c, H1d, and H1e) has particularly profound effects on B- and T- lymphocyte development. H1 depletion leads to de-repression of T-cell activation genes, and a shift in T-cells towards effector functions, a process that mimics normal T-cell activation. Comparison of chromatin structure in normal and H1-depleted CD8+ T-cells revealed that H1 binding produces localized chromatin compaction within spatially defined chromatin domains containing above average levels of H1. Reduction of H1 stoichiometry in these regions leads to decreases in H3K27 methylation and increases in H3K36 methylation. In vitro, H1 promotes PRC2-mediated H3K27 methylation and inhibits NSD2-mediated H3K36 methylation. Mechanistically, H1 mediates these opposite effects by promoting physical compaction of the chromatin substrate. These findings identify H1 as a critical regulator of the epigenetic landscape in mammalian cells.

overall_design: CD8+ splenic T cells from wildtype and cTKO animals were isolated by flow cytometry, and ChIP-seq using anti-H3K27me3 and anti-H3K36me2 antibodies was performed

first: Sean

middle: E

last: Healton

first: Cary

middle: N

last: Weiss

first: Michael

last: Willcockson

first: Arthur

middle: I

last: Skoultchi


title: H1 linker histones regulate the balance of repressive and active chromatin domains via localized genomic compaction [CUT&Tag]

middle: Alton

state: New York

address: 1300 Morris Park Ave, Chanin 402

overall_design: CD8+ splenic T cells were isolated from adult C57BL/6 WT or H1 cTKO mice.  CD8+ splenic T cells were stimulated ex vivo for 3 days using IL2 and CD3e/CD28 co-stimulatory beads. CUT&Tag was performed with the indicated antibody. 2 independent replicates were used for IGG and 4 independent replicates were used for H1 and H3 antibodies. H1 and H3 CUT&Tag was performed before and after ex vivo stimulation.


title: Creld1 deficient CD4+ T cells from 1-year-old animals under homeostatic

summary: Transcriptomic profile of Creld1 deficient naïve CD4+ T cells and control 1-year-old mice. Sorted naïve CD4+ T cells were analysed to underling the transcriptomic impact Creld1 deficiency in the aging of the lymphoid compartment

overall_design: Analysis  the RNA expression of naïve CD4+ T cells from control or Creld1cKO mice aged 1 year


title: Early emergence of T central memory precursors programs clonal dominance during chronic viral infection [bulkRNAseq]

city: Munich

first: Jonas

last: Mir

address: Trogerstraße 30

department: Institut für medizinische Mikrobiologie, Immunologie und Hygiene

institute: Technische Universität München

summary: Chronic infection with cytomegalovirus (CMV) leads to long-term maintenance of extraordinarily large CMV-specific T cell populations. The magnitude of this so-called ‘memory inflation’ is thought to be mainly determined by the availability of antigenic stimuli during the chronic phase of infection. However, by mapping the long-term development of CD8+ T cell families derived from single naive precursors, we find that T cell fate decisions, taken during the acute phase of murine CMV infection, can alter the level of memory inflation by more than 1000-fold. Counterintuitively, a T cell family’s capacity for memory inflation is not determined by its initial clonal expansion. Instead, those rare T cell families that strongly dominate the chronic phase of infection show an early transcriptomic signature akin to that of established T central memory cells. Accordingly, a T cell family’s long-term dominance is best predicted by its early content of T central memory precursors, which later serve as a stem cell-like source for the antigen-driven maintenance of memory inflation.

overall_design: Of sixteen single cell derived OT-1 T cell families 100 progeny cells were sorted from spleen at day 8 post infection with MCMV-ie2-SIINFEKL. BulkRNA-Seq was performed for each of the populations.

first: Veit

middle: R

last: Buchholz

first: Simon

last: Grassmann

first: Lorenz

last: Mihatsch

first: Atefeh

last: Kazeroonian

first: Roza

last: Rahimi

first: Sophie

last: Flommersfeld

first: Kilian

last: Schober

first: Inge

last: Hensel

first: Justin

last: Leube

first: Ludwig

middle: O

last: Pachmayr

last: Kretschmer

first: Qin

last: Zhang

first: Adrien

last: Jolly

first: Zeeshan

last: Chaudhry

first: Matthias

last: Schiemann

first: Luka

last: Cicin-Sain

first: Thomas

last: Höfer

first: Dirk

last: Busch

last: Flossdorf


title: Single cell analysis in the adult bone marrow vascular niche after Vegfc deletion

status: Public on Sep 08 2020

city: Nanjing

first: Shentong

last: Fang

address: Longmian Avenue

institute: China Pharmaceutical University

summary: To analyze the role of endothelial derived VEGF-C in the adult bone marrow vascular niche

overall_design: We isolated ECs and LepR+ cells and analyzed in total 3 samples, aiming with all the samples at 3000-5000 cells.

first: Kari

last: Alitalo


title: H1 linker histones regulate the balance of repressive and active chromatin domains via localized genomic compaction [ATAC-seq]

first: Boris

last: Bartholdy

overall_design: CD4+ or CD8+ splenic T cells, as well as peripheral blood B cells were isolated from adult C57BL/6 WT or H1 cTKO mice, with 2 independent replicates for most samples and 4 for CD4+ T cells.

first: Sean

last: Healton

first: Cary

last: Weiss

first: Michael

middle: A

last: Willcockson

first: Arthur

last: Skoultchi


title: MYC Promotes Bone Marrow Stem Cell Dysfunction in Fanconi Anemia

city: Helsinki

first: Kaiyang

state: Finland

address: Biomedicum Helsinki 1, Haartmaninkatu 8

department: Faculty of Medicine

country: Finland

institute: University of Helsinki

summary: We profiled primary HSPCs from Fanconi anemia (FA) patients for single cell transcriptome (scRNA-seq) to identify additional determinants of HSPC impairment leading to the bone marrow failure,. Trajectory analysis revealed that early hematopoietic differentiation potential is preserved in FA HSPCs. As expected, p53 and TGFβ pathway genes were overexpressed in HSPCs from FA patients. The oncogene MYC was also identified as one of the top over-expressed genes in FA HSPCs. Interestingly, we observed co-existence of “High-TP53” expressing HSPCs and HighMYC expressing HSPCs in FA bone marrow. Inhibition of MYC expression by the BET bromodomain inhibitor (+)-JQ1 reduced the clonogenic potential of primary HSPCs from FA patients but rescued the physiological/genotoxic stress in HSPCs from FA mice. The “High-MYC” expressing HSPCs exhibited a significant downregulation of cell adhesion genes, such as CXCR4. Consistently, HSPCs in FA patients showed a defect in adhesion to their bone marrow niche resulting in egression from the bone marrow into peripheral blood. We speculate that MYC overexpression impairs HSPC function and contributes to exhaustion of HSPCs in FA bone marrow.

overall_design: Expression profiles of single cells from seven Fanconi Anemia patients and five healthy donors.

first: Alfredo

last: Rodríguez

first: Alan

middle: D

last: D’Andrea


title: Creld1-deficient CD4+ T cells

first: Joachim

last: Schultze

overall_design: Refer to individual Series


title: Early emergence of T central memory precursors programs clonal dominance during chronic viral infection

first: Jonas

last: Mir


title: Co-option of neutrophil fates by tissue environments

city: Milano

first: Eleonora

last: Lusito

address: Via Olgettina 60

country: Italy

institute: Ospedale San Raffaele

summary: Classically considered short-lived, purely defensive leukocytes, neutrophils are unique in their fast and moldable response to stimulation. This plastic behavior may underlie variable and even antagonistic functions during inflammation or cancer, yet the full spectrum of neutrophil properties as they enter healthy tissues remains unexplored. Using a new model to track neutrophil fates, we found short but variable lifetimes across multiple tissues. Through analysis of the receptor, transcriptional and chromatin accessibility landscapes, we identify varying neutrophil states and assign non-canonical functions, including vascular repair and hematopoietic homeostasis.

overall_design: scRNASeq data were generated from different tissues, namely Bone Marrow (BM), peripheral blood (PB), Lung and Spleen in biological quadruplicate from healthy WT mice using the 10X Chromium platform

first: Ivan

last: Ballesteros

first: Andrea

last: Rubio-Ponce

first: Marco

last: Genua


title: Clonal Evolution of Acute Myeloid Leukemia Revealed by High-Throughput Single-Cell Genomics

city: Houston

first: FENG

last: WANG

address: 1881 East Road

institute: UT MD Anderson Cancer Center

type:
Genome variation profiling by SNP array
SNP genotyping by SNP array

summary: Clonal diversity contributes to treatment resistance and cancer recurrence. Precise delineation of clonal substructure is essential to understand the resistance mechanism, however, bulk DNA sequencing cannot accurately resolve the complex clonal architectures. Here we report the single-cell DNA sequencing of 123 acute myeloid leukemia (AML) patients and provide cell-level evidence of co-occurrence and mutual exclusivity among driver mutations. Reconstruction of tumor phylogeny uncovers linear and branching clonal evolution patterns, with the latter involving functional convergence. Single-cell DNA sequencing of xenotransplanted samples reveales clonal diversity in leukemia initiating cell populations. Simultaneous single-cell profiling of mutations and cell surface proteins provides cellular genotype-phenotype associations. Analysis of longitudinal samples visualizes the behavior of each individual clone in response to therapy, illustrating the underlying evolutionary process of therapeutic resistance and disease recurrence. Together, these data portray clonal diversity, architecture, and evolution of AML, and highlight their clinical relevance in the era of precision medicine.

overall_design: Genomic DNA from 40 samples in which scDNA-seq data showed at least 5% of homozygously mutated clones were analyzed.

first: Kiyomi

last: Morita

first: Feng

last: Wang

first: Katharina

last: Jahn

first: Tianyuan

last: Hu

first: Tomoyuki

last: Tanaka

first: Yuya

last: Sasaki

first: Jack

last: Kuipers

first: Sanam

last: Loghavi

first: Sa

first: Yuanqing

last: Yan

first: Ken

last: Furudate

first: Jairo

last: Matthews

first: Latasha

last: Little

first: Curtis

last: Gumbs

first: Jianhua

last: Zhang

first: Xingzhi

last: Song

first: Erika

last: Thompson

first: Keyur

last: Patel

first: Carlos

last: Bueso-Ramos

first: Courtney

last: DiNardo

first: Farhad

last: Ravandi

first: Elias

last: Jabbour

last: Andreeff

first: Jorge

last: Cortes

first: Kapil

last: Bhalla

first: Guillermo

last: Garcia-Manero

first: Hagop

last: Kantarjian

first: Marina

last: Konopleva

first: Daisuke

last: Nakada

first: Nicholas

last: Navin

first: Niko

last: Beerenwinkel

first: P

last: Futreal

first: Koichi

last: Takahashi


title: H1 linker histones regulate the balance of repressive and active chromatin domains via localized genomic compaction [RNA-seq]

first: Boris

last: Bartholdy

overall_design: 5x10^5 B, and CD4+ and CD8+ T cells were sorted to Trizol by FACS. RNA seq libraries were prepared from polyA-enriched RNA by Genewiz.

first: Sean

last: Healton

first: Cary

last: Weiss

first: Michael

last: Willcockson

first: Arthur

last: Skoultchi


title: Single-cell RNAseq profiling of mouse invariant NKT thymocytes

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

country: France

institute: IPMC/CNRS

summary: Total invariant Natural Killer T cells were purified from mouse thymi (pool of 4 mice) of Fhl2+/+ or Fhl2-/- mice (5 week-old)

first: Virginie

last: Magnone

first: Thomas

last: Baranek

first: Christophe

last: Paget


title: Metformin Alters Skeletal Muscle Transcriptome Adaptations to Resistance Training in Older Adults

city: North Chicago

first: Ameya

last: Kulkarni

state: Illinois

address: 1 N Waukegan Road

department: Genomics Research Center

institute: AbbVie

summary: Evidence from clinical trials and observational studies suggests that both progressive resistance training (PRT) and metformin delay a variety of age-related morbidities. Previously, we completed a clinical trial testing the effects of 14 weeks of PRT + metformin (metPRT) compared to PRT with placebo (plaPRT) on muscle hypertrophy in older adults. We found that metformin blunted PRT-induced muscle hypertrophic response. To understand potential mechanisms underlying the inhibitory effect of metformin on PRT, we analyzed the muscle transcriptome in 23 metPRT and 24 plaPRT participants. PRT significantly increased expression of genes involved in extracellular matrix remodeling pathways, and downregulated RNA processing pathways in both groups, however, metformin blunted the number of differentially expressed genes within these pathways compared to plaPRT. Pathway analysis showed that genes unique to metPRT modulated aging-relevant pathways, such as cellular senescence and autophagy. Differentially expressed genes from baseline biopsies in older adults compared to resting muscle from young volunteers were reduced following PRT in plaPRT and were further reduced in metPRT. We suggest that although metformin may blunt pathways induced by PRT to promote muscle hypertrophy, adjunctive metformin during PRT may have beneficial effects on aging-associated pathways in muscle from older adults.

overall_design: The Metformin to Augment Strength Training Effective Response in Seniors (MASTERS) Trial (ClinicalTrials.gov identifier: NCT02308228) is a randomized, controlled, double blind trial comparing the effects of metformin versus placebo during a 14-week progressive resistance training (PRT) intervention in healthy men and women ≥ 65 years of age. Participants were recruited at University of Kentucky and University of Alabama at Birmingham, UAB. The detailed study design and participant characteristics have been published previously (PMID: 28441958 and PMID: 31557380).  Total RNA was isolated from baseline muscle biopsies in 37 plaPRT and 28 metPRT participants and from 16-week post-training muscle biopsies from 26 plaPRT and 24 metPRT participants. Of these, 24 plaPRT and 23 metPRT participants had biopsies at both timepoints. Additionally, total RNA was isolated from muscle biopsies in 21 young healthy donors.  RNA content, integrity and purity were determined with a Nanodrop 2000 spectrophotometer and the 2100 Bioanalyzer. A minimum RNA Integrity Number (RIN) of 6.5 was set for all samples.

first: Bailey

last: Peck

first: R

last: Walton

first: Philip

last: Kern

first: Jessica

last: Mar

first: Samuel

middle: T

last: Windham

first: Marcas

last: Bamman

first: Nir

last: Barzilai

first: Charlotte

last: Peterson


title: Vitamin C regulates Schwann cell myelination by promoting DNA demethylation of pro-myelinating genes

city: Provo

first: David

middle: Wayne

last: Sant

state: UT

address: 1712 South East Bay Blvd, Building 5 Suite 300

department: Biomedical Informatics

institute: Noorda College of Osteopathic Medic

type: Methylation profiling by high throughput sequencing

summary: In this study we show that vitamin C promotes demethylation of DNA and regulates the expression of genes involved in Schwann cell development and function.

overall_design: Primary rat Schwann cells cultured until passage 3 treated or not with Vitamin C.

first: Tyler

last: Huff

first: Gaofeng

last: Wang


title: Alpha Ketoglutarate Prevents Age-related Osteoporosis via Regulating Histone Methylations

city: Chengdu

first: Quan

last: Yuan

state: Sichuan

address: 14 Third section, Renmin Nan Road

institute: West China Hospital of Stomatology, Sichuan University

summary: The aim of this study is to investigate the effect of aKG treatment on the self-renewal and  lineage specification of mouse bone marrow derived mesenchymal stem/stromal cells (mBMSCs). The sequence reads were mapped to mouse genome (build mm10) using TopHat followed by Cufflinks. Expression of key genes was validated by SYBR Green RT-qPCR assays.

overall_design: mRNA profiles of aKG-treated mBMSCs and contorl cells were generated by deep sequencing, in duplicate.

first: Yuan

first: Peng

last: Deng

first: Weimin

last: Lin


title: ATAC-seq of tissue resident neutrophils

city: Oxford

first: Irina

last: Udalova

state: Oxfordshire

address: The Kennedy Institute of Rheumatology, Roosevelt Drive, Headington

department: NDORMS

country: United Kingdom

institute: Kennedy Institute

summary: Neutrophils residing in bone marrow, blood, lung, and spleen were sorted and subjected to ATAC-seq to investigate tissue heterogeneity

overall_design: samples: bone marrow, blood, lung, spleen. 2 biological replicates

first: Iván

last: Ballesteros Martín

first: Erinke

last: Van Grinsven

first: Tariq

last: Khoyratty


title: Single cell analysis in the adult bone marrow

first: Shentong

last: Fang

summary: To analyze the role of VEGF-C in the adult bone marrow, we analyzed the bone marrow stromal fraction on LepR+ cells and endothelial cells to further dissect the source of VEGF-C in the adult bone marrow.

overall_design: We analyzed in total 2 samples, aiming with all the samples at 2000-3000 cells.

first: Kari

last: Alitalo


title: Longitudinal characterization of transcriptomic, functional, and morphological features in human iPSC-derived neurons and their application to investigate translational progranulin disease biology

status: Public on Sep 07 2020

city: La Jolla

first: Andreas

last: Zembrzycki

state: CA

address: 10901 N Torrey Pines Rd

institute: Sanford Burnham Prebys Medical Discovery Institute

summary: The disease biology of frontotemporal lobe dementia (FTD) is complex and not fully understood, with limited translational value appreciated from animal models to date. Human cellular systems that can recapitulate phenotypic features of disease offer promise as translational tools to not only increase our understanding of disease processes but also increase the probability of success of translating novel treatment options to patients. However not all researchers may necessarily have access to well characterized induced pluripotent stem cell (iPSC)-derived human neurons. We therefore sought to comprehensively profile phenotypic features over time in one commercially-available IPSC-derived human neuron cell line. This included systems-level assessments of neurite outgrowth dynamics, neuronal network function and genome-wide gene expression. By investigating progranulin biology as an example we then demonstrated utility of these cells as a tool to investigate human disease biology. For example, by using siRNA-mediated knockdown of the progranulin (GRN) gene, we demonstrated establishment of an isogenic human cellular model to facilitate translational FTD research. We reproduced findings from rodent neurons by demonstrating that recombinant progranulin (rPGRN) mediated neuroprotection. Contrary to previous rodent data, in our human cellular models, growth factor treatment showed no consistent sensitivity to modulate neurite outgrowth dynamics. Our study further provides first evidence that rRPGRN modulated neuronal firing and synchrony in human neurons. Taken together, our datasets are a valuable systems-level resource demonstrating the utility of the tested commercially-available human iPSC neurons for investigating basic human neurobiology, translational neuroscience, and drug discovery applications in neurodegenerative and other CNS diseases.

overall_design: RNA-Seq on iCell® GlutaNeurons following 3 siRNA treatments (Untreated, Non-targeting, or Progranulin targeting) taken at 5 timepoints (7, 10, 14, 17, and 21 days in vitro). Four independent experiments were performed. A total of 60 samples are included in the analysis.

last: Hauser


title: MLL4 establishes enhancer-associated condensates to counterbalance Polycomb-mediated nuclear mechanical stress in Kabuki Syndrome [3'UTR RNA-seq]

city: Trento

first: CIBIO

last: Zippo

state: Not Applicable

address: via sommarive 9

department: Cellular, Computation and Integrative Biology (CIBIO)

institute: University of Trento

summary: The genetic elements required to tune gene expression are partitioned in active and repressive nuclear condensates. These chromatin compartments include enhancer-associated clusters whose dynamic establishment and functioning depends on multivalent interactions occurring among transcription factors, cofactors and basal transcriptional machinery. However how chromatin modifiers contribute to the assembly of enhancer-associated condensates have not been addressed. We herein defined the non-catalytic function of MLL4 in driving the formation active nuclear condensates and its interplay with Polycomb compartment in determining the nuclear architecture. By interrogating the role of haploinsufficiency of KMT2D in Kabuki Syndrome, we found that MLL4 guides the assembly of enhancer-associated condensates through liquid-liquid phase separation. The loss-of-function of MLL4 impaired the correct chromatin compartmentalization of Polycomb proteins, altering nuclear architecture. By releasing the nuclear mechanical stress through the inhibition of the mechano-sensor ATR, we re-established the mechano-signaling of MSCs and their commitments towards chondrocytes. This study supports the notion that MLL4 contributes to the functional partitioning of chromatin, which is required to determine the structure and the mechanical properties of the nucleus.

overall_design:
We address the impact of ATR inhibiton on gene expression in wildtype and MLL4 (Q4092X/wt) heterozygous hTERT-immortalized human mesenchymal stem cells (iMSCs).
Two different cell types, wildtype and MLL4 (Q4092X/wt) heterozygous iMSCs, were treated with an ATR inhibitor for 8 hours and 24 hours or left untreated, respectively. 3'UTR RNA-seq was performed to analyse gene expression changes due to the inhibitor treatment.

first: Sven

last: Beyes

first: Alessio


title: H1 linker histones regulate the balance of repressive and active chromatin domains via localized genomic compaction [Hi-C]

first: Boris

last: Bartholdy

overall_design: CD8+ splenic T cells were isolated from adult C57BL/6 WT or H1 cTKO mice, with 2 independent replicates.

first: Sean

last: Healton

first: Cary

last: Weiss

first: Michael

last: Willcockson

first: Arthur

last: Skoultchi


title: pan-Kinase degrader response time course

city: Boston

first: Eric

last: Fischer

address: 450 Brookline Ave

department: Cancer Biology

institute: Dana-Farber Cancer Institute

summary: Targeted protein degradation (TPD) refers to the use of small molecules to induce ubiquitin-dependent degradation of proteins. These degrader molecules are of great interest in drug development as they can address previously inaccessible targets. However, degrader discovery and optimization remains an inefficient and empirical process due to a lack of understanding of the key molecular events required to successfully induce target degradation.  Here we used a time-course experiment to assess the transcriptional response to rapid pan-Kinase degradation.

overall_design: We analyzed a total of 24 samples of MOLT4 cells that include 4 replicates for each of a matched DMSO control, and SK-3-91 pan-kinase degrader treatments at 1 hour, 4 hours, and 8 hours.

first: Katherine

last: Donovan

first: Jonathan

middle: W

last: Bushman


title: H1 linker histones regulate the balance of repressive and active chromatin domains via localized genomic compaction

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


title: Redefining the Clostridioides difficile σB regulon: σB activates genes involved in detoxifying radicals that can result from the exposure to antimicrobials and hydrogen peroxide

city: Braunschweig

first: Rebekka

last: Biedendieck

address: Rebenring 56

department: Institute of Microbiology

institute: Technische Universtität Braunschweig

summary: In Gram-positive organisms the general stress response is regulated by the alternative sigma factor sigma B (σB). In C. difficile this sigma factor has been implicated in protection against stressors such as reactive oxygen species and antimicrobial compounds. Here, we show that an anti-σB antibody can be used to demonstrate overexpression of σB in C. difficile and that this overexpression is tolerated for short periods of time, despite its toxicity. Toxicity associated with σB-overexpression leads to loss of the plasmid used for anhydrotetracycline-induced σB expression. By uncoupling σB from its native regulatory network, we refined the previously proposed σB regulon and confirmed a direct role for σB in the induction of selected genes using in vitro run-off transcription reactions. Finally, using a plate-based luciferase reporter assay we demonstrated that different antibiotics and hydrogen peroxide induce genes positively regulated by σB in a manner dependent on this sigma factor. Together, our work suggests that lethal exposure to antibiotics may result in the formation of toxic radicals that lead to σB-dependent gene activation.

overall_design: Clostridioides difficile 630∆erm∆sigB (Clostron mutant) containing either Ptet-slucopt (control) or Ptet-sigB was grown until OD≈0.3 (exponential phase) and induced for one hour with 100 ng/ul anhydrotetracyclin (ATc). Biological quadruplicates were used for RNA isolation and the DNA array

first: Ilse

middle: M

last: Boekhoud

first: Annika-Marisa

last: Michel

first: Mareike

last: Berges

first: Wiep

middle: K

last: Smits

first: Jeroen

last: Corver

first: Dieter

last: Jahn


title: A Steroid Receptor Coactivator Stimulator (MCB-613) Prevents Adverse Remodeling After Myocardial Infarction

status: Public on Sep 06 2020

first: Jong

middle: H

last: Kim

state: TX

address: One Baylor Plaza

institute: Baylor College of Medicine

overall_design: We used single cell sequencing to profile the effect of MCB-613 treatment on cardiac interstitual cells at 24 hours and 12 weeks after myocardial infarction. Two hearts were collected and sequenced separately for each time point and experimental condition (Control and Drug treated)

first: Lisa

last: Key Mullany

first: James

middle: F

last: Martin

first: Bert

last: O'Malley


title: Gene expression profiling of miR-128 overexpression in Primary Mouse Vascular Smooth Muscle Cells (VSMCs)

city: Rozzano

first: Simone

last: Serio

state: Milano

address: Via Alessandro Manzoni, 56

department: Cardiovascular Medicine

institute: Humanitas Research Hospital

summary: MicroRNAs (miRNAs) are small non-coding RNAs that modulate gene expression by negatively regulating translation of target genes. miRNAs involvement in vascular smooth muscle cell (VSMC) biology has been deeply investigated, nevertheless the role of miR-128 in such context has not been yet explored. We aimed to evaluate whether this miR-128 might modulate VSMC phenotype similarly to what was previously observed for other type of contractile cells, such as cardiomyocytes (CM) and skeletal muscle cells. To this end, we compared the expression profiles of miR-128 overexpression in Primary mouse VSMCs  and control groups (treated with scrambled miRNA). The expression profiles were defined by Illumina arrays.

overall_design: Profiling of the transcriptome of miR-128 overexpression in Primary mouse VSMCs. Two biological replicates were profiled for each group.

first: Floriana

last: Farina

first: Elia

last: Leonardo


title: Diversification of posterior Hox patterning by graded ability to engage inaccessible chromatin [RNA-seq]

city: University Park

first: Shaun

last: Mahony

state: PA

address: 404 South Frear Bldg

department: Biochemistry & Molecular Biology

institute: Penn State University

summary: While Hox genes encode for similar transcription factors (TFs), they induce different fates across body axes. We sought to understand how Hox TF genomic binding preferences relate to their patterning activities during neuronal differentiation. To generate the required neuronal diversity for locomotor activity, Hox TFs specify spinal motor neuron and interneuron subtypes along the rostro-caudal axis. Our data revelated that Hoxc6 and Hoxc8 of the central group induce limb-innervating fates by binding to the same sites. On the other hand, the posterior group Hox genes assign different positional identities: Hoxc9 (thoracic), Hoxc10 (limb-innervating) and Hox13 (axial elongation termination) by binding to distinct sites with the same primary motif. We find that their genomic binding distributions are explained by differential abilities to bind to previously inaccessible chromatin. Thus, the vertebrate posterior Hox expansion and its associated patterning diversification is the product of their differential abilities to associate with less accessible chromatin.

overall_design:
RNA-Seq was used to investigate global gene expression prior to and upon Hox TF induction during ESC-to-MN differentiation
Please note that each processed data file was generated from all replicates and is linked to the corresponding rep1 sample records.

first: Milica

last: Bulajić

first: Divyanshi

last: Srivastava

first: Jeremy

middle: S

last: Dasen

first: Hynek

last: Wichterle

first: Esteban

last: Mazzoni


title: Early emergence of T central memory precursors programs clonal dominance during chronic viral infection [scRNAseq]

status: Public on Sep 05 2020

first: Jonas

last: Mir

address: Trogerstraße 30

institute: Technische Universität München

summary: Chronic infection with cytomegalovirus (CMV) leads to long-term maintenance of extraordinarily large CMV-specific T cell populations. The magnitude of this so-called ‘memory inflation’ is thought to be mainly determined by the availability of antigenic stimuli during the chronic phase of infection. However, by mapping the long-term development of CD8+ T cell families derived from single naive precursors, we find that T cell fate decisions, taken during the acute phase of murine CMV infection, can alter the level of memory inflation by more than 1000-fold. Counterintuitively, a T cell family’s capacity for memory inflation is not determined by its initial clonal expansion. Instead, those rare T cell families that strongly dominate the chronic phase of infection show an early transcriptomic signature akin to that of established T central memory cells. Accordingly, a T cell family’s long-term dominance is best predicted by its early content of T central memory precursors, which later serve as a stem cell-like source for the antigen-driven maintenance of memory inflation.

overall_design: one mRNA profile of CD8 positive OT-1 T cells during MCMV-ie2-SIINFEK infection (day 60 p.i.) from the spleen

first: Veit

last: Buchholz

first: Simon

last: Grassmann

first: Lorenz

last: Mihatsch

first: Atefeh

last: Kazeroonian

first: Roza

last: Rahimi

first: Sophie

last: Flommersfeld

first: Kilian

last: Schober

first: Inge

last: Hensel

first: Justin

last: Leube

first: Ludwig

last: Pachmayr

last: Kretschmer

first: Qin

last: Zhang

first: Adrien

last: Jolly

first: Zeeshan

last: Chaudhry

first: Matthias

last: Schiemann

first: Luca

last: Cicin-Sain

first: Thomas

last: Höfer

first: Dirk

last: Busch

first: Michael

last: Flossdorf


title: FSH-regulated gene expression in mouse granulosa cells as revealed by ChIP- and RNA- Sequencing

city: Sainte-Anne-de-Bellevue

first: Raj

last: Duggavathi

state: Quebec

address: 21111 Rue Lakeshore

department: Animal Science

institute: McGill University

summary: Follicle stimulating hormone (FSH) regulates ovarian follicular development through a specific gene expression program. We analyzed FSH-regulated transcriptome and histone modification in granulosa cells during follicular development. We used super-stimulated immature mice and collected granulosa cells prior to and 48h after stimulation with equine chorionic gonadotropin (eCG). We profiled the transcriptome using RNA-sequencing (N=3/time-point) and genome wide trimethylation of lysine 4 of histone H3 (H3K4me3; an active transcription marker) using chromatin immunoprecipitation and sequencing (ChIP-Seq; N=2/time-point). Across the mouse genome 14,583 genes had an associated H3K4me3 peak and 63-66% of these peaks were observed within < 1kb promoter region. There were 72 genes with differential H3K4me3 modification at 48h-eCG (absolute log fold change >1; FDR<0.05) relative to 0h-eCG.  Transcriptome data analysis showed 1463 differentially expressed genes at 48h-eCG (absolute log fold change > 1; FDR<0.05). Among the 20 genes with differential expression and altered H3K4me3 modification, Lhcgr had higher H3K4me3 abundance and expression, while Nrip2 had lower H3K4me3 abundance and expression. Using ChIP-qPCR, we showed that FSH regulated expression of Lhcgr, Cyp19a1, Nppc and Nrip2 through regulation of H3K4me3 at their respective promoters. Transcript isoform analysis using Kallisto-Sleuth tool revealed 875 differentially expressed transcripts at 48h-eCG (b>1; FDR<0.05). Pathway analysis of RNA-seq data demonstrated that TGFB signaling and steroidogenic pathways were regulated at 48h-eCG. Thus, FSH regulates gene expression in granulosa cells through multiple mechanisms namely altered H3K4me3 modification and inducing specific transcripts. These data form the basis for further studies investigating how these specific mechanisms regulate granulosa cell functions.

overall_design:
Two biological replicates were analyzed for each of 2 conditions (0h and 48h eCG) using H3K4me3 antibody in ChIP-Seq.
For RNA-Seq, three biological replicates were analyzed for each of 2 conditions (0h and 48h eCG)

first: Ejimedo

last: Madogwe

first: Deepak

last: Tanwar

first: Milena

last: Taibi

first: Yasmin

last: Schuermann

first: Audrey

last: St-Yves


title: Diversification of posterior Hox patterning by graded ability to engage inaccessible chromatin

first: Shaun

last: Mahony

overall_design: Refer to individual Series


title: Polygenic architecture informs potential vulnerability to drug-induced liver injury

city: Tokyo

first: Masaru

last: Koido

address: 4-6-1, Shirokanedai, Minato-ku

institute: Institute of Medical Science, The University of Tokyo

summary: Drug-Induced-Liver-Injury (DILI) is a leading cause of termination in drug development programs and removal of drugs from the market because of inability to identify potential patients prior to clinical testing. Here, we approached a polygenic risk score (PRS) based strategy by aggregating effects of numerous genome-wide loci identified from previous large-scale genome-wide association studies (GWAS). The PRS predicted the susceptibility to DILI in patients in a clinical trial, and in multi-donor derived primary hepatocytes and stem cell-derived organoids. Pathway analysis highlighted processes previously implicated in DILI, including unfolded protein responses and oxidative stress alleviated by a potent antioxidant. Furthermore, hepatocytic transcriptomic signatures related to polygenic score identified potential drugs with clinical DILI evidence through in silico 941 compound screening. This genetic-, cellular-, organoid- and human-scale evidence underscored the polygenic architectures underlying DILI vulnerability at the level of hepatocytes, thus facilitating future mechanistic studies. Moreover, the proposed “polygenicity-in-a-dish” strategy potentially will contribute to prospective designs of safer, more efficient, and robust clinical trials.

overall_design: Basal expression levels of Primary Human Hepatocytes (PHH) and Human Liver Organoids (HLO); Effect of Cyclosporin A (CsA) and Lithocholic Acid (LCA) on transcriptome.

first: Takanori

last: Takebe

first: Eri

last: Kawakami


title: Gene expression responses to ABA and to osmotic stress in the bon123 triple mutant

status: Public on Sep 04 2020

city: Shanghai

first: Yang

last: Zhao

state: Shanghai

address: 300 Fenglin RD

institute: Shanghai Center for Plant Stress Biology, and CAS Center of Excellence in Molecular Plant Sciences, Chinese Academy of Sciences

summary: Hyperosmotic stress caused by drought and salinity is a significant environmental threat that limits plant growth and agricultural productivity. Osmotic stress induces diverse responses in plants including Ca2+ signaling, accumulation of the stress hormone abscisic acid (ABA), reprogramming of gene expression, and altering growth. Despite intensive investigation, no global regulators of all of these responses have been identified. Here, we show that the Ca2+-responsive phospholipid binding BONZAI (BON) proteins are critical for all of these osmotic stress responses. A Ca2+-imaging-based forward genetic screen identified a loss-of-function bon1 mutant with a reduced cytosolic Ca2+ signal in response to hyperosmotic stress. The loss-of-function mutants of the BON1 gene family, bon1bon2bon3, are impaired in the induction of gene expression and ABA accumulation in response to osmotic stress. In addition, the bon mutants are hypersensitive to osmotic stress in growth inhibition. BON genes have been shown to negatively regulate plant immune responses mediated by intracellular immune receptor NLR genes including SNC1. We found that the defects of the bon mutants in osmotic stress responses were suppressed by mutations in the NLR gene SNC1 or the immunity regulator PAD4. Our findings indicate that NLR signaling represses osmotic stress responses and that BON proteins suppress NLR signaling to enable global osmotic stress responses in plants.

overall_design: Wild type and bon123t mutant seedlings were grown vertically for 9 days before treatment. These seedlings were mock treated, or treated with 100 µM ABA or 300 mM mannitol for 24 hours on 1/2 MS medium.  The transcriptome were analyzed by deep sequencing, in triplicate, using Illumina HiSeq 2500.

first: Kong

last: Chen

first: Jinghui

last: Gao

first: Shujing

last: Sun


title: Diversification of posterior Hox patterning by graded ability to engage inaccessible chromatin [ATAC-seq]

overall_design:
ATAC-Seq was used to identify accessible chromatin prior to and upon Hox TF induction during ESC-to-MN differentiation
Please note that each processed data file was generated from both replicates and is linked to the corresponding rep1 sample records.

first: Milica

last: Bulajić

first: Divyanshi

last: Srivastava

first: Jeremy

last: Dasen

first: Hynek

last: Wichterle

first: Esteban

last: Mazzoni


title: ERG-mediated coregulator complex formation maintains androgen receptor signaling in prostate cancer [Bulk RNA-seq]

first: Neel

last: Shah

state: MA

summary: We report the effects of ERG on prostate tumorigenesis, ERG-mediated oncogene addiction, and downstream AR signaling pathways. We determined that ERG facilitates AR-signaling and mediates transformation of prostate cells by maintaining coregulator complex formation at AR-bound sites across the genome.

overall_design: We measured changes in multiple chromatin, transcription factor binding, and transcriptomic profiles from genetic alterations of Pten and ERG murine prostate organoids

first: Myles

last: Brown

first: Nikolas

last: Kesten


title: ERG-mediated coregulator complex formation maintains androgen receptor signaling in prostate cancer [single cell RNA-seq]


title: Bulk transcriptional profiling of murine lung epithelial cells after expression of oncogenic KRAS

first: Aaron

middle: L.

last: Moye

address: 1 Blackfan Circle

department: Stem Cell Program

institute: Boston Children's Hospital

summary: The goal of this study was to define the transcriptional changes that follow oncogenic KRAS-G12D expression in aveolar type 2 (AT2) cells. We induced KRAS-G12D expression in AT2 cells in vitro and studied transcriptional changes using bulk RNA-Sequencing seven days after plating.

overall_design: Alveolar type 2 (AT2) cells were sorted using FACS (CD31-/CD45-/EPCAM+/SCA1-) from lungs of mixed and pooled male and female uninduced KRAS-LSL-G12D;LSL-YFP (KY) or KRAS-LSL-G12D; p53FL/FL; LSL-YFP (KPY) mice. AT2 cells were then not induced (NI control), or infected with Cre expressing (CRE), or empty (EMP control) adenovirus and plated in 3D organoid co-culture. Seven days after plating, multiple wells (>10) were pooled,  single cell suspensions were made from the organoid cultures, and epithelial cells were FACS sorted using EPCAM. This experiment was repeated 4 times for 3-4 biological samples per condition.

first: Antonella

last: Dost

first: Carla

last: Kim


title: ERG-mediated coregulator complex formation maintains androgen receptor signaling in prostate cancer


title: ERG-mediated coregulator complex formation maintains androgen receptor signaling in prostate cancer [H3K27ac ChIP]


title: ERG-mediated coregulator complex formation maintains androgen receptor signaling in prostate cancer [AR ChIP]


title: ERG-mediated coregulator complex formation maintains androgen receptor signaling in prostate cancer [ATAC]


title: ERG-mediated coregulator complex formation maintains androgen receptor signaling in prostate cancer [ERG ChIP]


title: Single cell transcriptional profiling of distal epithelial cells during early-stage KRAS-driven lung adenocarcinoma in mice

summary: The purpose of this study was to understand the transcriptional changes that occur during early stage lung adenocarcinoma in mouse models using single cell RNA Seq

overall_design: Examination of distal lung epithelial cells 7 weeks after induction of KRAS-G12D using an AD5-CMV-Cre vector.

middle: L


title: ERG-mediated coregulator complex formation maintains androgen receptor signaling in prostate cancer [PolII ChIP]


title: Molecular signatures of immune cells and neuroblasts in the aged brain

city: Beijing

first: Wei-Na

last: Jin

state: Beijing

address: NO.119, Southwest of the Fourth Ring Road, Fengtai District

department: China National Clinical Research Center for Neurological Diseases

institute: Beijing Tiantan Hospital, Capital Medical University


title: Expression data from human pancreatic ductal adenocarcinomas by stroma types

status: Public on Sep 03 2020

city: Shinjuku

first: Yohei

last: Masugi

state: Tokyo

address: 35 Shinanomachi

department: Pathology

institute: Keio University School of Medicine

summary:
Pancreatic cancer is characterized by abundant desmoplastic stroma.  Despite numerous theoretical and experimental efforts, therapeutic approaches targeting pancreatic cancer stroma have been largely unsuccessful, highlighting the need for more comprehensive assessment of inter- and intratumoral stromal heterogeneity in a large series of clinical tumors.  Quantitative computation of FAP-dominant fibroblasts, ACTA2-dominant fibroblasts, and intratumoral collagen in whole-tissue sections from 215 treatment-naïve pancreatic cancers allowed us to identify three distinct stroma types (FAP-dominant fibroblast-rich stroma [F-stroma], ACTA2-dominant fibroblast-rich stroma [A-stroma], and collgen-rich stroma [C-stroma]), which were differentially associated with patient outcomes, molecular characteristics and the immunosuppressive tumor microenvironment.
We explored differentially expressed genes between three distinct stroma types (F-stroma, A-stroma, and C-stroma) using frozen samples from 20 patients with pancreatic cancer.

overall_design: Frozen specimens from 20 PDAC patients were obtained from the biobank of Keio University School of Medicine (Tokyo, Japan).  These frozen tissues were sampled from surgical specimens under the supervision of pathologists and were stored at –80°C.

first: Yurina

last: Ogawa

first: Tokiya

last: Abe

first: Ken

last: Yamazaki

first: Akihisa

last: Ueno

first: Yoko

last: Fujii-Nishimura

first: Shutaro

last: Hori

first: Hiroshi

last: Yagi

first: Yuta

first: Minoru

last: Kitago

first: Michiie

last: Sakamoto


title: SOX9 promotes stress-responsive transcription of VGF nerve growth factor inducible gene in renal tubular epithelial cells

city: Columbus

first: NavjotSingh

last: Pabla

state: OH

address: 496 w 12th ave

department: Pharmaceutics and Pharmacology

institute: Ohio State University

summary: Acute kidney injury (AKI) is a common clinical condition associated with diverse etiologies and abrupt loss of renal function. In patients with sepsis, rhabdomyolysis, cancer, as well as cardiovascular disorders, the underlying disease or associated therapeutic interventions can cause hypoxic, cytotoxic, and inflammatory insults to renal tubular epithelial cells (RTECs) resulting in the onset of AKI. To uncover stress-responsive disease-modifying genes, here we have carried out renal transcriptome profiling in three distinct murine models of AKI. We find that Vgf nerve growth factor inducible gene upregulation is a common transcriptional stress response in RTECs to ischemia, cisplatin, and rhabdomyolysis-associated renal injury. The Vgf gene encodes a secretory peptide precursor protein that has critical neuro-endocrine functions; however, its role in the kidneys remains unknown. Our functional studies show that RTEC-specific Vgf gene ablation exacerbates ischemia, cisplatin, and rhabdomyolysis-associated AKI in vivo and cisplatin-induced RTEC cell death in vitro. Importantly, addback experiments showed that aggravation of cisplatin-induced renal injury caused by Vgf gene ablation is partly reversed by TLQP-21, a Vgf-derived peptide. Finally, in vitro and in vivo mechanistic studies showed that injury-induced Vgf upregulation in RTECs is driven by the transcriptional regulator Sox9. These findings identify Vgf as an essential stress-responsive gene and reveal a crucial molecular target of the Sox9 regulated transcriptional program that controls epithelial cell fate during AKI.

overall_design: We isolated renal tissues from control (mock and vehicle, n=8), IRI (24 hours, n=4), rhabdomyolysis (24 hours, n=4), and cisplatin (72 hours, n=4) treated mice and then performed RNA sequencing (4-8 biological replicates).

first: Navjot

first: Ji

middle: Y


title: Derivation of endometrial gland organoids from term placenta

city: Buffalo

first: Vincent

middle: J.

last: Lynch

state: NY

address: 551 Cooke Hall

department: Department of Biological Sciences

institute: University at Buffalo, SUNY

summary: A limitation of current methods for the generation of endometrial gland organoids is their reliance on decidua isolated from endometrial biopsies or elective abortion. Here we report the establishment of endometrial gland organoids from decidua isolated from term placental membranes. These organoids express typical markers of glandular epithelia such as E-cadherin, Laminin and Cytokeratin 7, and can be propagated in cell culture through multiple passages. Additionally, we identified potential survival factors for the co-culture of organoids and endometrial stromal fibroblasts. These modifications facilitate the generation of patient-specific endometrial gland organoids with known pregnancy outcomes.

overall_design: RNA-Seq to determine gene expression profiles of: unprocessed endometrial gland elements (collected from decidua digest), growing organoids derived from those gland elements and endometrial stromal fibroblasts isolated from the same samples and established as primary cell cultures.

first: M

last: Marinic

first: V

middle: J


title: Gene expression changes following cytokinin treatment in hy5 Arabidopsis thaliana seedlings

city: Chapel Hill

first: Charles

last: Hodgens

state: North Carolina (NC)

address: 250 Bell Tower Drive

department: GMB

institute: UNC Chapel Hill

summary: Wild type (Columbia-0) and hy5 loss of function mutants were treated with benzyl adenine (a synthetic cytokinin analog) for 1 hour and then mRNA was extracted for an RNA-seq differential expression experiment.

overall_design: Two replicates were sequenced for each combination of genotype and treatment of wild-type, hy5, control-treated, and cytokinin-treated

first: Joseph

last: Kieber


title: Single cell transcriptional profiling of murine lung epithelial cells after expression of oncogenic KRAS

first: Aaron

last: Moye

summary: The goal of this study was to define the transcriptional changes that follow oncogenic KRAS-G12D expression in aveolar type 2 (AT2) cells. We induced KRAS-G12D expression in AT2 cells in vitro and studied transcriptional changes using scRNA-Sequencing seven days after plating.

overall_design: Alveolar type 2 (AT2) cells were sorted using FACS (CD31-/CD45-/EPCAM+/SCA1-) from lungs of mixed and pooled male and female uninduced KRAS-LSL-G12D;LSL-YFP (KY) mice. AT2 cells were then infected with Cre expressing or empty (control) adenovirus and plated in 3D organoid co-culture. Seven days after plating, multiple wells (>10) were pooled,  single cell suspensions were made from the organoid cultures, and epithelial cells were FACS sorted using EPCAM. EPCAM+ cells were encapsulated and processed using the 10x genomics platform.

first: Antonella

last: Dost

first: Carla

last: Kim


title: RNA-seq Analysis of Differential Gene Expression in Obese Compared with Non-Obese Breast Cancer Patients

city: Jeddah

first: Mohammed

middle: Abdullah

last: Hassan

state: Jeddah

address: King Abdulaziz University

department: Department of Biochemistry

country: Saudi Arabia

institute: King Abdulaziz University

summary: Breast cancer (BC), the most common malignant tumor type, ranked top in incidence with high prevalence and mortality among females worldwide. Obesity poses a serious public health issue worldwide, it consider as one of BC risk factors. Obesity has profound effects on cancer cell transcriptome that can affect the outcome of cancer therapy. The information regarding the potential effects of obesity on BC transcriptome to identify novel transcripts biomarker and pathways related to disease progression are still elusive. Therefore, the RNA-seq analysis was performed to investigate the whole blood differential epressed genes profile in the blood liquid biopsy of obese compared with non-obese BC patients to provide a better understanding of the biological status and shed new insights into potential molecular mechanisms interaction and biomarkers in the relationship between obesity and BC.

overall_design: Total RNA was isolated from whole blood of obese and non-obese BC patients for gene expression profile analysis by RNA high throughput sequencing using NextSeq500 system.   The differentially expressed genes between obese compared with non-obese BC patients were identified.

first: Kaltoom

last: Al-Sakkaf

first: Ashraf

last: Dallol

first: Jaudah

last: Al-Maghrabi

first: Alia

last: Aldahlawi

first: Sawsan

last: Ashoor

first: Jiannis

last: Ragoussis

first: Wei

last: Wu

first: Abdulrahman

last: Al-Malki

first: Hani

last: Choudhry


title: Cooperation between Caenorhabditis elegans COMPASS and condensin in germline chromatin organization

city: Lyon

first: Marion

last: Herbette

address: 46 allée d'Italie

department: Laboratoire de Biologie et Modélisation de la Cellule

institute: ENS de Lyon

summary: Deposition of histone H3 lysine 4 (H3K4) methylation at promoter regions by the SET1/COMPASS complex is associated with context-dependent effects on gene expression.  Transcription-independent functions have also been attributed to this highly conserved complex, but whether these contribute to higher-order chromosome organization has not been explored. Using a quantitative FRET (Förster resonance energy transfer)-based fluorescence lifetime imaging microscopy (FLIM) approach to assay nanometer scale chromatin compaction in live animals, we reveal an unexpected role for SET1/COMPASS in structuring meiotic chromosomes in the germline of C. elegans. Inactivation of SET-2, the C. elegans homologue of the catalytic subunit SET1, strongly enhanced chromosome organization defects and loss of fertility resulting from partial depletion of condensin-II.  Loss of CFP-1, the chromatin targeting subunit of COMPASS, similarly affected germline chromatin compaction measured by FLIM-FRET and enhanced condensin-II knock-down phenotypes. Defects in chromosome morphology following conditional inactivation of topoisomerase II, another structural component of chromosomes, were also aggravated in the absence of set-2. Our results are consistent with a role of SET1/COMPASS in shaping meiotic chromosomes in the C. elegans germline, and have important implications for how chromatin-modifying complexes and histone modifications may cooperate with non histone-proteins to achieve proper chromosome organization, not only in meiosis, but also in mitosis.

overall_design: Expression profilling in germline tissue of  C.elegans strains have been anayzed in 3 biological replicates of wild-type strain (WT) (used as a control) and mutant strain set-2(bn129)

first: Francesca

last: PALLADINO

first: Robert

last: FEIL

first: David

last: Llères

first: Aymeric

last: Bailly

first: Valérie

last: Robert

first: Loïc

last: Gely

last: HERBETTE


title: Ethanol stress in yeast

status: Public on Sep 17 2020

city: New York

first: Jamie

last: Yang

address: 1150 St. Nicholas Avenue

institute: Columbia University

type: Genome variation profiling by high throughput sequencing

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


title: Intestine-to-germline transmission of epigenetic information transgenerationally ensures systemic stress resistance in C. elegans

city: Kyoto

first: Eisuke

last: Nishida

address: Kitashirakawa, Sakyo-ku

department: Department of Cell and Developmental Biology

institute: Graduate School of Biostudies, Kyoto University

summary:
Epigenetic states are metastable and changed throughout life, and their changes play a major role in the regulation of organismal homeostasis, including stress resistance. However, the mechanisms coordinating epigenetic states and systemic stress resistance across tissues remain largely unknown. Here, we identify the intestine-to-germline communication of epigenetic states, which enhances stress resistance transgenerationally in C. elegans. We firstly show that the alteration in epigenetic states by deficiency of the histone H3K4me3 modifier ASH-2 in the intestine or germline increases organismal oxidative stress resistance, which is abrogated by knockdown of the H3K4 demethylase RBR-2 in the same tissue. Remarkably, the increase in stress resistance induced by ASH-2 deficiency in the intestine is abrogated by RBR-2 knockdown in the germline, suggesting the existence of inter-tissue transmission of epigenetic information from intestine to germline. Simultaneously, this intestine-to-germline communication in the parental generation transgenerationally provides the increase in stress resistance of the descendants for over two generations. Further analyses reveal that the inter-tissue communication requires the insulin/IGF-1 signaling effector DAF-16/FOXO in the intestine and is mediated, at least in part, by transcriptional regulation of F08F1.3, one of the intestinal ASH-2 target genes. These results unveil the novel intestine-to-germline communication of epigenetic information that provides the transgenerational regulation of organismal stress resistance.
To further investigate the molecular mechanisms underlying intestine-to-germline communication, we sought the gene expression changes in the intestine ash-2 knockdown worms.

overall_design: Total RNA was isolated using TRIzol reagent (Invitrogen) in N2, VP303, NR350, TU3401 worms under Control RNAi and ash-2 RNAi conditions. Other procedures were performed according to Ambion WT cDNA Expression Kit protocols. RNA degradation and cRNA elongation were verified with an Agilent 2100 Bioanalyzer. The fragmented cRNA was hybridized using GeneChip C. elegans Gene 1.0 ST Array (Affymetrix) at 45℃ for 16 h. Hybridized arrays scanned using an Affymetrix GeneChip Scanner. Scanned chip images were analyzed with Affymetrix GeneChip Command Console version 2.0 (AGCC) and processed using default settings. The Affymetrix output (CEL files) were imported into the GeneSpring GX 11.0.2 (Agilent Technologies) microarray analysis software for the presentation of the expression profiles.

first: Masanori

last: Nono

first: Saya

last: Kishimoto

first: Masaharu

last: Uno


title: An Xist-dependent protein assembly mediates Xist localization and gene silencing

city: Los Angeles

first: Kathrin

last: Plath

address: 615 Charles E. Young Drive South

department: Biological Chemistry

institute: UCLA

summary: Nuclear compartments play diverse roles in regulating gene expression, yet the molecular forces and components driving compartment formation are not well understood. Studying how the lncRNA Xist establishes the inactive-X-chromosome (Xi)-compartment, we found that the Xist RNA-binding-proteins PTBP1, MATR3, TDP43, and CELF1 form a condensate to create an Xi-domain that can be sustained in the absence of Xist. The E-repeat-sequence of Xist serves a multivalent binding-platform for these proteins. Without the E-repeat, Xist initially coats the X-chromosome during XCI onset but subsequently disperses across the nucleus with loss of gene silencing. Recruitment of PTBP1, MATR3, TDP-43 or CELF1 to E-Xist rescues these phenotypes, and requires both self-association of MATR3 and TDP-43 and a heterotypic PTBP1-MATR3-interaction. Together, our data reveal that Xist sequesters itself within the Xi-territory and perpetuates gene silencing by seeding a protein-condensate. Our findings uncover an unanticipated mechanism for epigenetic memory and elucidate the interplay between RNA and RNA-binding-proteins in creating compartments for gene regulation.

overall_design: We examined the localization of RNA binding proteins PTBP1, MATR3 and CELF1 on Xist RNA by CLIP-seq and the localization of PTBP1 on DNA by ChIP-seq in male ESCs in which the Xist promoter is replaced by a doxycycline inducible one. We also examined Xist occupancy over the X-chromosome using RAP (RNA-affinity purification) in cells expressing Xist cDNA transgenes (under dox control) engineered to include (or not) the Xist E-repeat region.

first: Amy

last: Pandya-Jones

first: Yolanda

last: Markaki

first: Jacques

last: Serizay

first: Tsotne

last: Chitiashvilli

first: Walter

last: Mancia

first: Andrey

last: Damianov

first: Costantinos

last: Chronis

first: Bernadett

last: Papp

first: Chun-Kan

last: Chen

first: Robin

last: McKee

first: Xiao-Jun

last: Wang

first: Anthony

last: Chau

first: Shan

last: Sabri

first: Heinrich

last: Leonhardt

first: Sika

last: Zheng

first: Mitchell

last: Guttman

first: Douglas

last: Black


title: Transcriptome profiling to determine molecular mechanisms of acquired EGFR TKI resistance

city: Houston

first: Lixia

last: Diao

address: 1400 Pressler Steet

department: Bioinfomatics and Computational Biology

institute: University of Texa MD Anderson

summary: The goal of this study was to compare the transcriptome (RNA-seq) of EGFR TKI sensitive NSCLC cells with that of cells with acquired resistance to erlotinib.  HCC827 and HCC4006 cells were continuously cultured in erlotinib until erlotinib resistant (ER) variants emerged.  All ER variants were negative for T790M. RNA from parental and ER cells was isolated for transcriptomic profiling.  RNA-seq analysis reveals that EGFR TKI resistance is associated with a mesenchymal gene expression signature.

overall_design: RNA-seq on total RNA from EGFR mutant NSCLC cells with or without erlotinib resistance

first: John

last: Heymach


title: Gene expression changes in hiPS-derived cardiomyocytes under R-2HG exposure and doxorubicin treatment

status: Public on Sep 02 2020

city: Halle

first: Razif

last: Gabdoulline

state: Sachsen-Anhalt

address: Ernst-Grube-Straße 40

department: Innere Medizin IV Haematologie und Onkologie

institute: Universitätsklinikum Halle

summary: RNA sequencing and immunostaining in hiPS-derived cardiomyocytes indicated that the oncometabolite R-2HG exacerbated doxorubicin mediated cardiotoxicity.

overall_design: To validate whether R-2HG increases myocardial vulnerability to anthracyclines, we exposed human induced pluripotent stem cell (hiPS)-derived cardiomyocytes to 1μM doxorubicin (DOX) with or without the addition of R2-HG.

first: Badder

last: Kattih

first: Michael

last: Heuser


title: Subtypes of Gbx2+ amacrine cells in mouse retina

city: Portland

first: Patrick

middle: C

last: Kerstein

state: OR

address: 3232 SW Research Drive

department: Vollum Institute

institute: Oregon Heath and Science University

summary: The goal of this project was to determine the differential expression of mRNA between two subtypes of Gbx2+ amacrine cells. These data will aid in distinguishing these two related, but distinct, amacrine cell subtypes by providing unique gene markers and physiological pathways.

overall_design: Two amacrine cell subtypes were labeled in mouse retina with fluorescent tags, tdtomato and GFP using Gbx2-CreERT2-IRES-EGFP; Ai9 transgenic mice. Mice retinae from P6-7 mice were dissected and Tdtomato labeled amacrine cells were purified by flow cytometry. Tdtomato-labeled amacrine cells were separated into two groups, GFP-negative (Cell type 1) and GFP-positive (Cell type 2), by flow cytometry. 4 biological replicates, originating from 3 different mouse litters, were collected. RNA was extracted from 750-2500 sorted cells. One GFP and one Tdtomato cell type sample will be collected from each animal. There was at least  1 male and 1 female sample used in this study.

first: Kevin

last: Wright


title: Methylation and gene expression microarray of human gingival epithelial cells stimulated with arecoline

city: Ishikari-Tobetsu

first: Durga

last: Paudel

state: Hokkaido

address: Kanazawa

institute: Health Sciences University of Hokkaido

type: Methylation profiling by genome tiling array

overall_design: Refer to individual Series


title: Hypoxia-mediated regulation of histone demethylases affects angiogenesis associated functions in endothelial cells

city: Kuopio

first: Oscar Hsin-Fu

last: Liu

state: Finland

address: P.O.Box 1627 (Neulaniementie 2)

department: Department of Biotechnology and Molecular Medicine

institute: University of Eastern Finland

summary:
Purpose: Jumonji-containing (jmjC) family of proteins are involved in epigenetic gene regulation through histone specific lysine demethylation. Previous studies have demonstrated that the expression of several members of this family is induced by hypoxia. However, the mechanisms by which lysine specific demethylases (KDMs) are regulated under hypoxia and how they affect angiogenesis, the primary method to restore blood oxygen, remains unknown. In this study, we characterized regulation of KDMs using a combination of nascent and mature mRNA profiling. Furthermore, we aimed to identify KDMs that play a role in mediating the VEGF-mediated angiogenic response in endothelial cells.
Results: We demonstrated that majority of KDMs were induced by hypoxia and this effect is more prominent upon constitutive activation of HIF2α compared to HIF1α. Half of the changes in mRNAs levels were attributed to transcriptional regulation as evidenced by similar changes at the level of nascent mRNAs, whereas half was likely due to post-transcriptional mechanisms affecting mature mRNA levels.  Hypoxia induced genome-wide redistribution of H3K27me3 at 2000 transcriptionally active loci in human umbilical vein endothelial cells (HUVECs). Among these, we further verified the induction of VEGF-A by demethylation of the locus by KDM4B and KDM6B in response to hypoxia. Accordingly, knockdown of KDM4B and KDM6B led to decreased proliferation and tube formation of HUVECs.
Conclusions: Hypoxia leads to both transcriptional and post-transcriptional induction of KDMs and wide redistribution of H3K27me3 at active chromatin regions. Main mediator of angiogenesis, VEGFA, is regulated by KDM4B- and KDM6B- mediated demethylation in HUVECs with functional implications for cell proliferation and tube formation. These findings provide novel insights into the regulation of KDMs by hypoxia and the epigenetic regulation of angiogenesis.

overall_design: Examination of KDM expressions profiling and H3K27me3 modification near angiogenesis-related genes by KDMs in human umbilical vein endothelial cell (HUVEC).

first: Oscar

first: Minna

middle: U

last: Kaikkonen


title: KDM5A and PHF2 positively control expression of pro-metastatic genes repressed by EWS/Fli1, and promote growth and metastatic properties in Ewing Sarcoma

city: Aurora

first: Andrew

last: Goodspeed

state: CO

address: 12801 E 17th Ave, Mail Stop 8303

institute: University of Colorado Anschutz Medical Campus

summary: The goal of this study was to understand the role of the chromatin factors KDM5A and PHF2 in Ewing Sarcoma progression.

overall_design: RNA-seq was used to define the effects of KDM5A and PHF2 depletion on gene expression in the patient-derived Ewing Sarcoma cell line A673.

first: Paul

last: Jedlicka

first: Tyler

last: McCann

first: Janet

last: Parrish

first: Joseph

last: Hsieh

first: Marybeth

last: Secher

first: Lays

last: Sobral

first: Chelsea

last: Self

first: Kenneth

last: Jones

first: James

last: Costello


title: A single cell approach to map cellular subsets involved in Systemic Lupus Erythematosus (SLE) heterogeneity

city: Farmington

first: William

last: Flynn

state: CT

address: 10 Discovery Drive

institute: The Jackson Laboratory

summary: In this study, we analyzed the transcriptomes of ~276k single PBMCs from 33 childhood SLE (cSLE) and 11 healthy matched donors (cHD). Our findings were validated in an independent cohort including 8 adult SLE (aSLE) patients and 6 matched controls (aHD; ~132k PBMCs).

overall_design:
cSLE dataset included 33 cSLE (cSLE1 to cSLE33). 11 cHD controles (cHD1 to cHD11) aSLE dataset included 8 aSLE (aSLE1 to aSLE8) and 6 aHD controles (aHD1 to aHD6). Clinical information to be found in supplementary table 1.

**The raw data have been deposited in dbGaP (Study accession: phs002048.v1.p1) due to patient privacy concerns.**

first: Djamel

last: Nehar-Belaid

first: Jacques

last: Banchereau

first: Virginia

last: Pascual

last: Robson


title: Methylation array of arecoline treated human gingival epithelial cells

first: Durga

last: Paudel

summary: Identify the methylation level of  genes in epithelial cells stimulated with arecoline, a main component of betel quid.

overall_design:
Human gingival epithelial progenitors were cultured and treated with a 3-day alternating regimen with/without 50 μg/ml arecoline for 1 month
Please note that experiments were performed technically as dual channel (eg, Cy3 and Cy5-labeled samples hybridized to the same array) but the results were processed as though they are single channel (Cy3 and Cy5 signals are calculated; Cy3/Cy5 ratios are not calculated), and thus the 'Raw data.txt' file contains raw data for both Sample 1 (Control) and Sample 2 (Arecoline).

first: Yoshihiro

last: Abiko

first: Osamu

last: Uehara


title: Gene expression analysis of arecoline treated human gingival epithelial cells

summary: To identify the presence of a novel gene in epithelial cells stimulated with arecoline, a main component of betel quid.

overall_design: Human gingival epithelial progenitors were cultured and treated with a 3-day alternating regimen with/without 50 μg/ml arecoline for 1 month


title: m6A-sequencing

city: Shanghai

first: Ding

last: Yu

address: Number 953 Jianchuan Road

institute: Newcore biotechnology

summary: M6A-sequencing for 12 samples

overall_design: Examing 3 conditions, each with 4 replicates

first: Jianxiao

last: Shen

first: Wanpeng

last: Wang

first: Xinghua

last: Shao

first: Zhaohui

last: Ni


title: Data sets of microglia isolated from C57BL/6 WT mice and animals harboring microglial IL10Ra and TNF mutations, at steady state or after peripheral LPS challenge (RNAseq) and WT microglia with and without peripheral LPS challenge (ATACseq)

city: Rehovot

first: Jung-Seok

last: Kim

address: 234 Herzl street

department: Immunology

institute: Weizmann Institute of Science

summary: To define the microglia response to septicemia, C57BL/6 WT mice and animals harboring microglial IL10Ra and TNF mutations were challenged with LPS and microglia were sorted for RNAseq analysis (WT, mutants) aor ATACseq (WT).

overall_design: RNAseq and ATACseq were performed on microglia isolated by flow cytometry according the CD45 and CD11b expression from C57BL/6 WT mice, either untreated or at indicated times after peripheral LPS challenge

first: Anat

last: Shemer

first: Steffen

last: Jung


title: RNA associating with PIWI proteins in Bombyx mori BmN4 cells

city: Tokyo

first: Mikiko

last: Siomi

address: Faculty of Science Bldg.3, Rm126, 2-11-16 Yayoi, Bunkyo-ku

institute: The University of Tokyo

type: Non-coding RNA profiling by high throughput sequencing

summary: RNAs associating with PIWI proteins were Immunoisolated from BmN4 cells. Sequence libraries were generated with NEBNext Small RNA Library Prep Set for Illumina(NEB). Libraries were sequenced using Illumina MiSeq (single-end, 51 cycles).

overall_design: Small RNA sequences of RNAs associating with PIWI proteins expressed in BmN4 cell were performed with miSeq

first: Kazumichi

last: Nishida

first: Kazuhiro

last: Sakakibara


title: RNA-seq of Arabidopsis wild-type (WT)-expressing aequorin and card1 mutants (WT-expressing aequorin background) in response to DMBQ.

city: Yokohama

first: Anuphon

last: Laohavisit

state: Kanagawa

address: 1-7-22 Suehiro-cho

institute: RIKEN


title: RNAseq of Arabidopsis wild-type (WT)-expressing aequorin, card1-1 mutant (WT-expressing aequorin background), card1-2 mutant (WT-expressing aequorin background) in response to 10 minute DMBQ or DMSO treatment

summary: Our study suggested that DMBQ induces several transcripts, which are absent in card1 mutants

overall_design: Transcript profiles of 7-day old seedlings WT-expressing aequorin, card1-1, and card1-2 were generated by sequencing, in quadruplicate, using Illumina HiSeq4000

first: Ken

last: Shirasu


title: Analysis of off target generated by CRISPR/Cas9 in DM1 mutant haploid embryonic stem cells

first: Qing

last: Li

address: 320 Yueyang Road

department: institute of biochemistry and cell biology

institute: Chinese Academy of Science

summary: The androgenetic embryonic stem cells we generated carrying several genes mutations could be injected into the oocyte and produce the semi-cloned mice. Those semi-cloned mice could mimic several DM1-associated phenotypes. We try to identify if any off-target exist in those cells inducing by CRISPR/Cas9.

overall_design: Examination of off target position in two cell lines.

first: Jinsong

first: Qi

last: Yin


title: The effects of perfluorooctanoate on high fat diet induced non-alcoholic fatty liver disease in mice

city: Bloomington

first: Xilin

state: Indiana

address: 2719 E 10th street Rm230

institute: Indiana University

summary: We reported the hepatic gene expression profiling in mice treated by perfluorooctanoate (PFOA) and high fat diet (HFD). Chronic HFD treatment was associated with gene expression changes in cholesterol biosynthetic process, lipid metabolic process, extracellular matrix, and inflammatory response pathways. Many chemokine related genes including Ccl2, Ccr2, Ccl3l3, Cx3cl1, Cx3cr1, Cxcl14, and toll-like receptor (TLR) related genes including Tlr2, Tlr7, Tlr8, Tlr13 were all significant upregulated comparing vehicle-treated HFD-fed mice to control diet (CD)-fed mice, suggesting their roles in the development of steatohepatitis. PFOA induced gene expression changes in PPAR signaling, fatty acid degradation, biosynthesis of unsaturated fatty acids, and chemical carcinogenesis pathways regardless of diet. However, we showed preexisting fatty liver enhanced the lipid clearance effect of PFOA compared to that in a normal liver. At last, chronic exposure to HFD and PFOA was found to interact on genes related to PPAR signaling, chemical carcinogenesis, and ABC transporter pathways.

overall_design: Two groups of mice were fed with either a control or high-fat diet for 16 weeks to induce normal or steatotic livers, respectively. Subsequently, mice from each diet group were treated with PFOA or vehicle for another 8 weeks. Each mouse was considered a biological replicate. A total of 4 groups with 4 mice in each group were used.

first: Zemin

first: Ram

last: Podicheti

first: James

middle: E

last: Klaunig


title: RNAseq of Arabidopsis wild-type (WT)-expressing aequorin and card1-2 mutant (WT-expressing aequorin background) in response to DMBQ or DMSO treatment at 0 hr, 0.5 hr, 1 hr and 6 hr

summary: Our study suggested that DMBQ induces several transcripts, which are regulated by CARD1

overall_design: Transcript profiles of 7-day old seedlings WT-expressing aequorin and card1-2 were generated by sequencing, in triplicate, using Illumina NextSeq500


title: Pioglitazone induces extensive PPARg-dependent hepatic expression of nuclear-mitochondrial genes

city: St. Louis

first: Paul

last: Cliften

address: 4320 Forest Park Parkway

department: Genetics

institute: Washington University

summary: We report the results of RXR ChIP-Seq on 2 month old wildtype and liver specific PPARg knockout mice, fed control-diet or high fat-diet supplemented with Pio or vehicle for 12 weeks

overall_design: Examination of the effect of Pioglitazone and high fat diet on liver RXR-DNA binding patterns

first: David

middle: A

last: Rudnick


title: Comparative transcriptional profiling of motor neuron disorder-associated genes in various human cell culture models

status: Public on Sep 01 2020

city: Tuebingen

first: Ludger

last: Schöls

address: Hoppe-Seyler-Strasse 3

department: Department of Neurology and Hertie Institute for Clinical Brain Research

institute: University of Tübingen

summary: Disease modelling requires appropriate cellular models that best mimic the underlying pathophysiology. Human origin and an adequate expression of the disease protein are pre-requisites that support information from a model to be meaningful. In this study we investigated expression profiles of (i) PBMCs and (ii) fibroblasts as patient derived cells as well as (iii) lymphoblasts and (iv) induced pluripotent stem cells (iPSC) as immortalized sources and (v) iPSC-derived cortical neurons to assess its aptitude to model motor neuron diseases (MNDs) including hereditary spastic paraplegia (HSP), amyotrophic lateral sclerosis (ALS) and spinal muscular atrophy (SMA). We generated all five cell lines from two healthy donors and performed RNA sequencing to display expression patterns in MND-related genes. For the ten most common HSP genotypes we proved gene expression by qPCR. Depending on the specific MND gene we found largely different expression patterns. Out of 168 MND-related genes, 50 had their highest expression in iPSC-derived cortical neurons, 41 were most strongly expressed in fibroblasts, 26 in lymphoblasts, 22 in iPSCs and 14 in PBMCs. 15 MND-related genes were not detectable in any of the analyzed cell types. This study provides comprehensive information on expression of genes associated with a large spectrum of MNDs. Expression profiles can be used to inform on appropriate cell models for genotype specific motor neuron research.

overall_design: In total, 10 samples are analyzed, distributed over five different cell types with duplicates for each type.

first: Stefan

last: Hauser

first: Stefanie

last: Schuster

first: Elena

last: Heuten

first: Philip

last: Höflinger

first: Jakob

last: Admard

first: Yvonne

last: Schelling

first: Ana

last: Velic

first: Boris

last: Macek

first: Stephan

last: Ossowski


title: pan-cancer single cell RNA-seq analysis of cell lines

first: Itay

last: Tirosh

address: Herzl 234

institute: WEIZMANN INSTITUTE OF SCIENCE

summary: To understand the diversity of expression states in cancer cell lines, we profiled 198 cancer cell lines by single-cell RNA-seq with 10X chromium.

overall_design: Nine pools, each containing multiple cell lines, were profiled by 10x chromium. The cells in each pool were assigned to the corresponding cell line based on similarity in gene expression and in SNP profiles.

first: Alissa

last: Greenwald

first: Gabriela

last: Kinker