title: Chromatin state in RA or LE540-treated human CD4+ T cells

first: Fumihiro

last: Fujiki

summary: Retinoic Acid (RA)-treated T cells show effector-like properties such as down-regulation of CD62L, weak proliferation, low survival in vitro/in vivo. In contrast, LE540 (RAR antagonist)-treated T cells show memory-like properties. In this study, using ChIP-seq, we investigated change of chromatin state induced by RAR signaling in T cells. We found that RAR signaling comprehensively induces repressive chromatin states and deletes the memory T cell profile.

overall_design: Examination of 2 different histone modifications in 3 cell types.


title: Genome-wide maping the chromatin status of 5637 cells following infection with Uropathogenic E.coli

status: Public on Dec 31 2021

city: Giessen

first: Marek

last: Bartkuhn

state: Hessen

address: Aulweg 132

department: Biomedical Informatics and Systems Medicine

country: Germany

institute: Justus-Liebig-University Giessen

type: Genome binding/occupancy profiling by high throughput sequencing

summary: We report the application of H3 Lysine9 acetylation (H3K9ac) immunoprecipitation coupled next generation sequencing (ChIP-seq) in human bladder epithelial cells 5637 following treatment with Urophathogenic Escherichia coli strain 536 (UPEC) or the mutant with deletion of both α-hemolysin (hlyA) genes in the UPEC 536 strain (hlyA double mutant = UPEC 536 HDM) or UPEC supplemented with acetate. We found dramatic depletion of H3K9ac peaks was observed in UPEC infected cells, which was partially rescued by supplementation of acetate. In contrast, H3K9ac peaks of untreated cells are comparable with HDM treated cells. A total 21834 merged peak regions were identified in untreated control, whilst UPEC infection significantly decreased the signal across the merged peak regions, which was rescued partially by adding acetate. Deacetylation and its rescue by addition of acetate were observed in a global manner and affected the vast majority of H3K9ac sites throughout the genome. This observation holds true for different classes of cis-regulatory elements. Analysis of average binding across all human transcriptional start sites analysis further revealed that UPEC treatment also decrease H3K9ac signals at promoter regions, and can be rescue by supplementation of acetate. Moreover H3K9ac signal is also correlated with gene expression pattern. This study established that UPEC infection could epigenetically manipulate the host cell gene expression.

overall_design: Examination of H3K9ac in 5637 cells treate with UPEC, HDM or UPEC + acetate

first: Sudhanshu

last: Bhushan

first: Zhengguo

last: Zhang


title: Based RNA-Seq to research hydrogen production of Chlamydomonas reinhardtii strain CC-849

city: Beijing

first: Zhenzhen

last: Yang

address: Building 104,Beichen West Road No.1,Chaoyang District

country: China

institute: Beijing Institute of Genomics,CAS

type: Expression profiling by high throughput sequencing

summary: Chlamydomonas reinhardtii strain CC849 is seclected to sequence its transcriptome at different times under normal and stress conditions.Before we conducted RNA-sequencing at 0h (start point) and other seven timepoints(24hour, 48hour, 72hour, 96hour, 120hour, 168hour, 192hour) under normal and stress condition, respectively. These data are contained in GSE100763. Now, we add the RNA-seq data at 4hour, 12hour under normal and stress condition, respectively.

overall_design: In order to find hub genes and important pathways by comparing gene expression with hydrogen production of chlamydomonas reinhardtii CC849 at different time under normal and stress conditions

first: Shuangxiu

last: Wu


title: A Congenital Anemia Dissociates the Pleiotropic Functions of Master Transcription Factor GATA1 [G1E_RNAseq]

city: New York

first: Caleb

last: Lareau

state: New York

address: 417 E 68th St, Zuckerman - ZRC 1132

country: USA

institute: Memorial Sloan Kettering

summary: Master regulators, such as the hematopoietic transcription factor GATA1, have numerous roles in lineage commitment and differentiation. While human GATA1 mutations result in several blood diseases, all characterized mutations act relatively early to impair hematopoietic differentiation. Here, we describe a distinct form of hemolytic anemia involving impaired terminal erythropoiesis with a reduced lifespan of circulating red blood cells. We show that this unique blood disorder results from mutations in a poorly characterized and intrinsically disordered C-terminal region of GATA1.

overall_design: Murine G1E cells were transduced with the HMD lentiviral vector encoding human wildtype GATA1 or point mutants p.R307C or p.R307H

first: Leif

last: Ludwig

first: Vijay

last: Sankaran


title: A Congenital Anemia Dissociates the Pleiotropic Functions of Master Transcription Factor GATA1 [Patient scRNA-seq]

summary: Master regulators, such as the hematopoietic transcription factor (TF) GATA1, play an essential role in orchestrating lineage commitment and differentiation1. However, the precise mechanisms by which such TFs regulate transcription through interactions with specific cis-regulatory elements remain incompletely understood2,3. Here, we characterize a distinct form of congenital hemolytic anemia caused by missense mutations in an intrinsically disordered region of GATA1, with a poorly understood role in transcriptional regulation. Through integrative functional approaches, we demonstrate that these mutations perturb GATA1 transcriptional activity by partially impairing nuclear localization and selectively altering precise chromatin occupancy by GATA1. These alterations in chromatin occupancy and concordant accessibility changes alter faithful gene expression, with failure to both effectively silence and activate select genes necessary for effective red cell production. We demonstrate how disease-causing mutations can reveal regulatory mechanisms that enable the faithful genomic targeting of master TFs during cellular differentiation.

overall_design: In vitro cultured human bone marrow mononuclear cells from a patient carrying the GATA1 p.R307C mutation and healthy controls cells were sorted and forwarded to 10x scRNA-seq


title: Gene expression of mouse small intestinal 3D organoid myofibroblast-epithelium co-culture

city: München

first: Michael

last: Quante

address: Ismaninger Str 22

department: II Medizinische Klinik

institute: Technische Universität München

summary: The gene expression of mouse wt small intestinal epithelium and myofibroblast,3D organoids, both in monoculture and in co-culture, as well as small interstinal adenoma organoids from the Apc+/1638N mouse model, were measured by Affymetrix Mouse Gene 2.1 ST Array.

overall_design:
Mice were sacrifced at 8-10 weeks
Gene expression of the following mouse small intestinal cells were analyzed
a. wt epithelium  cells in monoculture (n=2)
b. wt epithelium  cells in co-culture (n=2)
c. Apc+/1638N adenoma  cells  (n=4 mice, 6 samples)
d. wt fibroblasts in monoculture (n=3)
e. wt fibroblasts in co-culture (n=3)

first: Agnieszka

last: Pastula

first: Klaus-Peter

last: Janssen

first: Katja

last: Steiger

first: Julia

last: Slotta-Huspenina

first: Richard

middle: A

last: Friedman

first: Stefanie

middle: M

last: Hauck

first: Mauricio

last: Ruiz

first: Maximilian

last: Fottner

first: Ursula

last: Ehmer

first: Roland

last: Schmid

first: Timothy

middle: C

last: Wang


title: Analysis of mouse monozygotic twin blastocysts produced in two different culture media

city: Muenster

first: Michele

last: Boiani

address: Roentgenstrasse 20

institute: Max Planck Institute Muenster

summary: Following fertilization in mammals, it is generally accepted that totipotent cells are exclusive to the zygote and to each of the two blastomeres originating from the first mitotic division. We counter that this classic view needs to be revised, because we have presented compelling evidence the sister blastomeres are both totipotent in only a subset of 2-cell stage mouse embryos (PMID 28811525). Building on our previous findings, we here ask the question if the differences between sister blastomeres can be modulated experimentally. To this end, we separate the sister blastomeres, yielding monozygotic twins. We culture these twins in two different media (GM501 vs. Sage 1 step), to see if the mRNA ratios of twin blastocysts lie more far apart from each other when culture took place in different media as compared to culture in the same medium (GSE90674). Transcriptome analysis followed by intra-pair mRNA ratio analysis revealed differences between the blastocysts of the same monozygotic pair. Some of the differences were sensitive to the choice of culture conditions, while other differences were insensitive.

overall_design: After in vivo zygote production and short (2 hours) culture in KSOM(aa) medium, 2-cell embryos were split, and the individual blastomeres were cultured in parallel in GM501 vs. Sage 1 step medium. Resultant monozygotic twins were sampled at the blastocyst stage, respecting the original pair associations (e.g. blastocyst '1a' and blastocyst '1b' both derived from same 2-cell embryo number '1'). Samples were subjected to Affymetrix microarray analysis, performed by Anika Witten c/o Institut fuer Humangenetik, Universitaetsklinikum Muenster.

first: Verena

last: Nordhoff


title: Comparative transcriptomic analysis of Central Neurocytoma-derived tumor spheres as compared to its differentiated cells and fetal SVZ-derived neural stem cells.

city: Seoul

first: Sun Ha

last: Paek

address: 101 Daehak-ro,  Jongno-gu

department: Neurosurgery

country: South Korea

institute: Seoul National University

summary: We obtained tissues of Central neurocytomas (CNs) from surgeries of patients, and then we performed primary cultures of CN tissues. Tumor spheres of CN were isolated from the differentiated CN cells. Fetal subventricular zone tissues (this sample was derived from inevitable abortion because of fatal defects) were primary cultured as well.  Going forward, we compared the RNA of the pools via microarray to identify markers of tumor stem cells of Central Neurocytomas (CNs) as compared to its differentiated cells and fetal subventricular zone (SVZ)-derived neural stem cells (NSCs) to be able to characterize its origin of CN. Interestingly, CN-tumor spheres have characteristics of Transit amplifying Type C cells and Radial glial cells (RGCs). Moreover CN-tumor spheres expressed well known cancer stem cells markers of glioblastomas.

overall_design: Use of human CN tumor samples (N=3) for primary cultures in this study was approved by the Institutional Review Board (IRB) of Seoul National University Hospital (IRB approval C-0710-040-223). Attributing to its benign characteristics of CN, only one sample among those three was able to make robust number of tumor spheres were made from one sample after primary culture. Other sample also made tumor spheres, but the amount of RNA was not optimal for the microarray. We compared CN-differentiated cells (N=1) and CN-derived tumor spheres (N=1) to defined specific genes, expressed on CN-tumor spheres. Gene expression of CN-tumor spheres were also compared with Fetal SVZ-derived NSCs to detect overlapped and differential expression. For a comparative study between samples, expression data was standardized using z-score transformation. For a normal control we used “GSM469410” from the public GEO database (http://www.ncbi.nlm.nih.gov/geo/).

first: Hye Young

last: Shin

first: Kiyoung

last: Lee


title: RNA-seq profiling of murine Tet-off MLL-AF9; NRAS acute myeloid leukemia at different timepoints upon doxycycline-induced MLL-AF9 down-regulation.

city: Parkville

first: Alexandra

last: Garnham

state: Victoria

address: 1G Royal Parade

country: Australia

institute: Walter and Eliza Hall Institute of Medical Research

summary: Using an acute myeloid leukemia (AML) mouse model driven by tet-regulated MLL-AF9 (fusion between the gene MLL1 (KMT2A/MLL) and MLLT3 (AF9)) co-expressed with oncogenic NRASG12D (Tet-off MLL-AF9), we investigated the effect of modulating the expression of the MLL-AF9 fusion oncogene on the transcriptome and proteome of established murine AML. Treatment in vitro or in vivo of these Tet-off MLL-AF9 AMLs with doxycycline (DOX) results in the efficient down-regulation of the expression of the driver oncogene MLL-AF9. RNA sequencing analysis was performed on primary Tet-Off MLL-AF9 AML cells obtained from the spleen of leukemic animals and cultured in vitro for either 2 or 4 days in the presence of doxycycline (1μg/ml) (DOX= down-regulation of MLL-AF9) or left untreated (UT).

overall_design: Primary murine acute myeloid leukemias (Tet-off MLL-AF9 AML) driven by the doxycycline-reversible (Tet-OFF) expression of the oncogenic fusion protein MLL-AF9 linked to dsRED reporter, in association with oncogenic NRASG12D (Tet-off MLL-AF9) were generated by reconstituting lethally irradiated congenic mice with foetal liver cells co-transduced with a Tet-Off-MLL-AF9-dsRED retroviral vector and a second vector co-expressing NRASG12D together with the Tet-Off responsive transcriptional activator. Four primary Tet-Off MLL-AF9 leukemias obtained from the spleen of terminally sick animals were cultured in vitro in the presence of doxycycline (1μg/ml) or left untreated. The RNA was collected at day 2 and 4 after the start of the doxycycline treatment. Total RNA extraction was performed using Trizol reagent (Invitrogen) according to the manufacturer’s instructions. RNA-seq libraries were prepared from 400 ng of total RNA using the Illumina Truseq V2 RNA-seq kit. Paired-end 50bp RNA-seq short reads were generated using HiSeq2500. 4 biological replicates (UT vs DOX) are provided for each of the 2 timepoints.

first: Jarrod

middle: J

last: Sandow

first: Margherita

last: Ghisi

first: Paul

middle: G

last: Ekert

first: Ricky

middle: W

last: Johnstone

first: Gordon

middle: K

last: Smyth

middle: L

first: Waruni

last: Abeysekera


title: Transcriptional responses analysis of the inflorescence meristems in Jatropha curcas following gibberellin treatment

first: Wenkai

last: Hui

state: Beijing

address: Qinghua East Street

institute: Beingjing Forestry University

summary: Our results showed that 951 differentially expressed genes (DEGs) were obtained to response to gibberellin treatment. The 6-h time point was an important phase in the response to exogenous gibberellin. Furthermore, the plant endogenous gibberellin, auxin, ethylene, abscisic acid, and brassinolide signaling transduction pathways were repressed after exogenous GA3 treatment. However, the DEGs (JcAHP1, JcHK3, and JcMYC2, JcMYC4) which were respectively associated with cytokinin and jasmonic acid signaling were up-regulation for 24-h time point following GA3 treatment. In addition, the floral meristem determinacy genes (JcLFY and JcSOC1) and floral organ identity genes (JcAP3, JcPI, and JcSEP1-3) were significantly up-regulated, but their negative factor (JcSVP) was down-regulated after GA3 treatment.

overall_design: Five different samples after exogenous GA3 treatment.

first: Xiaoyang

last: Chen


title: Transcriptional profiling of putative half ABC transporter gene orf19.3120 knockout cells in Candida albicans

city: New Delhi

first: Nitesh

middle: Kumar

last: Khandelwal

state: Delhi

address: Near Munirka

department: School of Life Sciences

country: India

institute: Jawaharlal Nehru University

summary: Inventory of ABC transporters of Candida albicans shows presence of large no of ABC transporters in its genome.The large no of such protein presence suggested that these proteins may involve in various functions.To know involvement of PM ABC  transporter orf19.3120 in different physiological roles transcriptional profiling have been peformed and compared between WT(SC5314) Candida albicans cells vs  orf19.3120 knockout cells after 6hrs growth of culture.The assay as peformed in biological duplicate sample.

overall_design: Agilent one-color experiment,Organism: Candida albicans  ,Custom Agilent Candida albicans 8x15k Microarray Gene expression  (AMADID: 026377) designed by Genotypic Technology Private Limited  , Labeling kit: Agilent Quick-Amp labeling Kit (p/n5190-0442)

first: Rajendra

last: Prasad


title: Expression data from mdx mice at 5 day, 2 weeks, 3 weeks, and 6 weeks

city: Binghamton

first: Kanneboyina

last: Nagaraju

state: NY

address: PO Box 6000

department: Pharmaceutical Sciences

institute: Binghamton University-SUNY

summary: We used microarrays to identify molecular pathways that define different disease stages and contribute to disease progression in the mdx mouse

overall_design: Quadricep muscle was dissected out of BL10 and mdx mice at four different time points for RNA extraction and hybridization on Affymetrix microarrays. We sought to obtain a gene expression profile of mdx mouse skeletal muscle during different disease stages.

first: Jessica

middle: F

last: Boehler

first: James

middle: S

last: Novak

first: Zuyi

last: Wang

first: Joe

middle: N

last: Kornegay

first: Peter

middle: P

last: Nghiem

first: Rashmi

last: Rawat

first: Yi-Wen

first: Eric

last: Hoffman


title: Full-length transcriptome of Glycyrrhiza uralensis Fisch. in under four treatment

status: Public on Dec 30 2021

city: Yinchuan

first: Xiang

last: Xiao

state: Ningxia

address: Shengli Street

institute: Ningxia Medical University

summary:
Purpose: The goal of this study are to reveal the internal mechanism of Bacillus cereus G2 increased Glycyrrhiza uralensis Fisch. seedlings salt-tolerance by RNA-Seq.
Methods: mRNA profiles of Glycyrrhiza uralensis Fisch. Seedling in four treatment: control treatment, G2 treatment, salt treatment, salt and G2 treatment.
Results: We mapped about 3 million sequence reads per sample to the G. uralensis transcriptome. A total of 35,831 genes in all samples of G. uralensis were identified and quantified by transcriptions, among which 3608 DEGs were identified. There are 1589, 623, 469 and 927 DEGs in S vs CK, CK+B vs CK, S+B vs S and S+B vs CK+B comparisons, respectively. Validation of expression levels for 12 randomly selected DEG candidates was carried out by quantitative real-time PCR (qRT-PCR). The results showed high congruence between RNA-Seq and qRT-PCR results (coefficient of determination R2 =0.9088) indicating the reliability of RNA-Seq quantification of gene expression.
Conclusions: Our study help to better understand the underlying molecular mechanisms of G2 improve the salt tolerance of G. uralensis.

overall_design: Full-length transcriptome analysis of Glycyrrhiza uralensis Fisch. seedling under control or salt treatment with or without Bacillus cereus G2.

first: Xinhui

last: Zhang

first: Qiuli

first: Xin

last: Ma

first: Duoyong

last: Lang

first: Zhenggang

last: Guo


title: The neural cell adhesion molecule NrCAM regulates development of hypothalamic tanycytes

status: Public on Dec 29 2021

city: Baltimore

first: Dong Won

middle: Thomas

last: Kim

state: Maryland

address: 733 N.Broadway, MRB building (Rm 332)

department: Neuroscience

institute: Johns Hopkins University

summary: Purpose: highthroughput sequencing (scRNA-Seq) to study hypothalamic tanycytes and astrocytes with NrCAM KO

overall_design: scRNA-Seq on dissected hypothalamus in wildtype and NrCAM KO

first: Alex

last: Moore

first: Kavitha

last: Chinnaiya

first: Dong

first: Sarah

last: Brown

first: Ian

last: Stewart

last: Robins

first: Georgina

last: Dowsett

first: Charlotte

last: Muir

first: Marco

last: Travaglio

first: Jo

middle: E

last: Lewis

first: Fran

last: Ebling

first: Seth

last: Blackshaw

first: Andrew

last: Furley

first: Marysia

last: Placzek


title: Ataxin-2 is essential for cytoskeletal dynamics and neurodevelopment in Drosophila

city: Chicago

first: Matthew

middle: J.

last: Schipma

state: IL

address: 750 N. Lake Shore Drive

department: Biochemistry and Molecular Genetics

institute: Northwestern University

summary: Using RNAseq we report differentially expressed genes after knockdown of Ataxin-2 in Drosophila S2 lysate and Drosophila 3rd instar larvae brain

overall_design: 3 repeats of control vs Ataxin-2 dsRNA treated cultured Drosophila S2 cells. 3 repeats of control vs Ataxin-2 shRNA expressing dissected 3rd instar larvae brains.

first: Urko

last: del Castillo

first: Rosalind

last: Norkett

first: Vladimir

middle: I

last: Gelfand


title: An adipose lncRAP2 - Igf2bp2 complex enhances adipogenesis and energy expenditure by stabilizing target mRNAs.

city: Cambridge

first: Juan

middle: R

last: Alvarez-Dominguez

state: MA

address: 7 Divinity Ave

department: Stem Cell and Regenerative Biology

institute: Harvard University

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

overall_design: Refer to individual Series


title: Single cell ATAC-seq of the developing human retina and stem cell-derived retinal organoids shows changing epigenomic landscapes during cell fate acquisition.

city: SEATTLE

first: THOMAS

middle: A

last: REH

state: WA

address: 1959 NE PACIFIC STREET

department: BIOLOGICAL STRUCTURE

institute: UNIVERSITY OF WASHINGTON

summary: Single cell genomic analyses provide a new perspective on the development of complex tissues, like the vertebrate neural retina. We previously used single cell transcriptomic analysis to characterize human fetal retinal development and assessed the degree to which retinal organoids recapitulate normal fetal development. In this study we extend the transcriptomic analyses of fetal human retina to incorporate single nuclear scATAC-seq, a powerful new method to characterize potential gene regulatory networks through the changes in accessible chromatin that accompany cell state changes. The combination of scATAC-seq and sc-RNA-seq can be used to study the process of neurogenesis in the developing fetal human retina at unprecedented resolution. We identify the key transcription factors relevant to specific fates and the order of the transcription factor cascades that define each of the major retinal cell types. These transcriptomic and epigenomic features are largely recapitulated in retinal organoids; however, there are differences in Notch signaling and amacrine cell gene regulation, which are not as robust in organoids. The datasets we generated constitute an excellent resource for the continued improvement of retinal organoid technology, and have the potential to inform and accelerate regenerative medicine approaches to retinal disease.

overall_design: Initially, we performed scATAC-seq on freshly dissociated human fetal retina and stem cell-derived retinal organoids. We collected 12 fetal retinal samples as follows: two eyes from fetal week 8 (FW8), three eyes from FW11 and five eyes from FW13 samples. To see the developmental changes within a sample, we separated the central and peripheral retina at FW13. We also processed 5 samples of retinal organoids at equivalent ages of the fetal retina (FW8 and FW11). We sequenced a total of 82,648 cells, with 6,309 average median fragments per cell. After sequencing, we used CellRanger ATAC1.2.0 to align the reads and carry out initial stages of data processing. Peaks were called with MACS2 and further analyzed using Signac/Seurat (Hao et al., 2021), Chromvar (Schep et al., 2017) and Monocle  (Cao et al., 2019; Trapnell et al., 2014).

first: Connor

last: Finkbeiner

first: Isabel

last: Ortuño-Lizarán

first: Akshayalakshmi

last: Sridhar

first: Marcus

last: Hooper

first: Sidnee

last: Petter

first: Thomas

last: Reh


title: RNA-seq of coronavirus infected and treated mouse lungs

city: Vienna

first: Manuel

last: Salzmann

address: Lazarettgasse 14

department: Department of Medicine II, Division of Cardiology

country: Austria

institute: Medical University of Vienna

summary: An infection with SARS-CoV-2 can be symptomatic or asymptomatic depending on the respective activation of the immune system. We used the bacterial extract Broncho Vaxom (BV) to preactivate the immune system before a coronavirus infection using the murine coronavirus MHV A59 in a mouse model. The activation of the immune system led to a reduction in viral load and protected lung tissue from enhanced cell apoptosis. Using RNA sequencing we were able to demonstrate that lung tissue from mice receiving BV resembled an intermediate state between infected and healthy tissue. On a cellular level, treatment with BV enhanced alveolar and interstitial macrophages in the lung. We were able to phenocopy the effect of BV by transplanting naïve lung macrophages into recipient mice thereby enhancing the local cellular amount before infection. We conclude that recruitment and preactivation of the innate immune system by the bacterial extract BV is beneficial during a coronavirus infection.

overall_design: RNA-seq of middle, right lobe of 5 healthy mice, 5 infected control mice at day 4, and 5 infected and treated mice at day 4

first: Sophia

last: Derdak

first: Philipp

last: Hohensinner


title: Single cell transcriptomic and chromatin profiles suggest Layer Vb is the only layer with shared excitatory cell types in the medial and lateral entorhinal cortex

status: Public on Dec 28 2021

city: Trondheim

first: Stefan

last: Blankvoort

address: Olav Kyrresgt 9

department: Kavli Institute for systems Neuroscience

country: Norway

institute: NTNU

summary: All brain functionality arises from the activity in neural circuits in different anatomical regions. These regions contain different circuits comprising unique cell types. An integral part to understanding neural circuits is a full census of the constituent parts, i.e., the neural cell types. This census can be based on different characteristics. Previously combinations of morphology and physiology, gene expression, and chromatin accessibility have been used in various cortical and subcortical regions. This has given an extensive yet incomplete overview of neural cell types. However, these techniques have not been applied to all brain regions. Here we apply single cell analysis of accessible chromatin on two similar but different cortical regions, the medial and the lateral entorhinal cortices. Even though these two regions are anatomically similar, their intrinsic and extrinsic connectivity are different. In 4136 cells we identify 20 different clusters representing different cell types. As expected, excitatory cells show regionally specific clusters, whereas inhibitory neurons are shared between regions. We find that several deep layer excitatory neuronal cell types as defined by chromatin profile are also shared between the two different regions. Integration with a larger scRNA-seq dataset maintains this shared characteristic for cells in Layer Vb. Interestingly, this Layer contains three clusters, two specific to either subregion and one shared between the two. These clusters can be putatively associated with particular functional and anatomical cell types found in this layer. This information is a step forwards into elucidating the cell types within the entorhinal circuit and by extension its functional underpinnings.

overall_design: Two tissue samples (bilateral LEC and MEC) in duplicate from two wild type C57Bl6 mice (P56).

first: Lene

middle: C

last: Olsen

first: Clifford

last: Kentros


title: Diurnal 3D genome organization remodeling orchestrates rhythmic gene expression in rice [DAP-seq]

status: Public on Dec 24 2021

city: Wuhan

first: Baibai

last: Gao

address: 1 Shizishan Street, Hongshan District

institute: National Key Laboratory of Crop Genetic Improvement

summary: Genome-wide rhythmic occupancy of RNA polymerase II (RNAPII) is highly coordinated with rhythmic genes expression. Rhythmic RNAPII binding dynamically modulates diurnal 3D genome architecture remodeling with 91% of the chromatin interactions were altered. The rhythmic genes cluster at the 8:00 (AM) circadian phase form spatial interacting clusters in turn assist coordinated rhythmic gene expression, while non-rhythmic genes tend to tether together and contribute to expression at 20:00 (PM) circadian window. Target genes and associated cis-binding motifs of transcription factors enrichment points to the existence of subnuclear organization hub enriched around the TFs. RNAPII-associated chromatin interaction domains (CIDs) are under circadian control, and static CIDs with common node genes but changed connecting genes along the circadian cycle, reveal they may function as distinct clock components in the interconnected circuits between morning and evening. Core circadian clock genes related chromatin connectivity networks reveal a compact and highly connected chromatin architecture serving to coordinate gene expression in the morning, whereas a scattered, loose chromatin architecture coordinates PM gene expression. Our findings uncover novel diurnal fundamental genome folding principles in plants, and reveal the distinct higher-order chromosome organization that is crucial for coordinating diurnal dynamics of transcriptional regulation.

overall_design: Here, we generated genome-wide occupancy of RNA polymerase II (RNAPII) by ChIP-seq, whole-transcriptome by RNA-seq, and chromatin accessibility by FAIRE-seq throughout the six-time course. We also performed RNAPII long-read ChIA-PET from the same tissues used for ChIP-seq, RNA-seq, and FAIRE-seq at 8:00 and 20:00. Together, we constructed comprehensive high-resolution dynamic chromatin architecture, and disected its effects on diurnal gene expression.

first: Li

last: Deng


title: RNA sequencing of G-MDSC in peripheral blood of normal mice, tumor-bearing mice for 2 and 3 weeks

city: changchun

first: yingying

last: sun

state: jilin

address: 5268 Renmin Street

department: school of life science

institute: northeast normal university

summary: Purpose:  The effect of tumor conditions on the immunosuppressive function of G-MDSC with tumor progression

overall_design: RNA of G-MDSC in peripheral blood of normal mice, tumor-bearing mice for 2 and 3 weeks were generated by deep sequencing, using Illumina HiSeq 2500 instrument

first: Xianlu

last: Zeng

first: Yingying

last: Sun


title: MUTYH Actively Contributes to Microglial Activation and Impaired Neurogenesis in the Pathogenesis of Alzheimer’s Disease

status: Public on Dec 23 2021

city: Fukuoka

first: Yusaku

last: Nakabeppu

state: Fukuoka

address: 3-1-1 Maidashi Higashi-ku

department: Department of Immunobiology and Neuroscience

country: Japan

institute: Medical Institute of Bioregulation, Kyushu University

summary: Oxidative stress is a major risk factor for Alzheimer’s disease (AD), which is characterized by brain atrophy, amyloid plaques, neurofibrillary tangles, and loss of neurons. 8-Oxoguanine, a major oxidatively generated nucleobase highly accumulated in the AD brain, is known to cause neurodegeneration. In mammalian cells, several enzymes play essential roles in minimizing the 8-oxoguanine accumulation in DNA. MUTYH with adenine DNA glycosylase activity excises adenine inserted opposite 8-oxoguanine in DNA. MUTYH is reported to actively contribute to the neurodegenerative process in Parkinson and Huntington diseases and some mouse models of neurodegenerative diseases by accelerating neuronal dysfunction and microgliosis under oxidative conditions; however, whether or not MUTYH is involved in AD pathogenesis remains unclear. In the present study, we examined the contribution of MUTYH to the AD pathogenesis. Using postmortem human brains, we showed that various types of MUTYH transcripts and proteins are expressed in most hippocampal neurons and glia in both non-AD and AD brains. We further introduced MUTYH deficiency into AppNL-G-F/NL-G-F knock-in AD model mice, which produce humanized toxic amyloid-β without the overexpression of APP protein, and investigated the effects of MUTYH deficiency on the behavior, pathology, gene expression, and neurogenesis. MUTYH deficiency improved memory impairment in AppNL-G-F/NL-G-F mice, accompanied by reduced microgliosis. Gene expression profiling strongly suggested that MUTYH is involved in the microglial response pathways under AD pathology and contributes to the phagocytic activity of disease-associated microglia. We also found that MUTYH deficiency ameliorates impaired neurogenesis in the hippocampus, thus improving memory impairment. In conclusion, we propose that MUTYH, which is expressed in the hippocampus of AD patients as well as non-AD subjects, actively contributes to memory impairment by inducing microgliosis with poor neurogenesis in the preclinical AD phase and that MUTYH is a novel therapeutic target for AD, as its deficiency is highly beneficial for ameliorating AD pathogenesis.

overall_design: Six month-old female App[NL-G-F/NL-G-F]•Mutyh-/- mice harboring deficiency in Mutyh gene besides three pathogenic App-knock-in mutations, that promote aggressive amyloidosis by increasing total Abeta production (Swedish mutation KM670/671NL) and increasing the Abeta42 aggregation (Arctic mutation E693G) and increasing the Abeta42/Abeta40 ratio (Iberian mutation I716F) under the control of the endogenous App promoter  were used for hippocampal gene expression profiling with the Affymetrix Genechip Mouse Gene 2.0 ST Array. Array data was processed by Affymetrix Transcriptome Analysis Console (TAC) software 4.0. GEO accession number for App[NL-G-F/NL-G-F] and wild type control data was re-used from GSE157161.

first: Nona

last: Abolhassani

first: Yuri

last: Mizuno


title: Generation of induced nephron progenitor-like cells from human urine-derived cells

first: WEIWEI

last: GAO

address: Anam-ro

institute: Korea University

summary: Analysis of induced nephron progenitor cells from female/male urine cells (iNPC-F/INPC-M) by defined transcription factors vs. ESC derived nephron progenitor cell (ESC-NPC_H9/ESC-NPC_BG01) and female/male urine cells (UC-F/UC-M). Results provide insight into molecular similarities between induced nephron progenitor cells and human ESC derived nephron progenitor cell

overall_design: RNA profiles of UC-F, UC-M, iNPC-F, iNPC-M, ESC-NPC_H9 and ESC-NPC_BG01  were generated by RNA sequencing

first: Wei-Wei

first: Seungkwon

last: You


title: Translesion DNA synthesis-driven mutagenesis in very early embryogenesis of fast cleaving embryos

city: Montpellier

first: Domenico

last: Maiorano

address: 141, rue de la cardonille

country: France

institute: CNRS

type: Genome variation profiling by high throughput sequencing

summary: During very early embryogenesis of fast cleaving embryos DNA synthesis is short and surveillance mechanisms preserving genome integrity are inefficient implying the possible generation of mutations. To explore this possibility, we have analyzed mutagenesis in Xenopus laevis and Drosophila melanogaster embryos. We report the occurrence of a nucleus-to-cytoplasmic ratio-sensitive high mutation rate in Xenopus. We also show that mutagenesis is dependent upon the master regulator of translesion DNA synthesis (TLS) Rad18 and alleviated by the mismatch repair system. Unexpectedly, using separation of function mutants, we observed a homology-directed repair contribution of Rad18 in reducing the mutation load. While in Drosophila no Rad18 orthologs could be identified, genetic invalidation of TLS in the pre-blastoderm embryo resulted in reduction of both the hatching rate and Single Nucleotide Variations on specific chromosome regions in adult flies. Altogether these findings indicate that in the very early Xenopus and Drosophila embryos TLS strongly contributes to the high mutation rate. This may constitute a previously unforeseen source of genetic diversity contributing to the polymorphisms of each individual with implications for genome evolution and species adaptation.

overall_design: Mutagenesis analysis during very early Xenopus and Drosophila embryogenesis

first: Elena

last: Lo Furno

first: Isabelle

last: Busseau

first: Claudio

last: Lorenzi

first: Cima

last: Saghira

first: Stephan

last: Zuchner


title: Integrative analysis of altered genes expressed in human Alzheimer’s disease brain (RNA-Seq)

summary: We had previously performed comparative gene expression profiling of human postmortem Alzheimer’s disease (AD) brains donated for the Hisayama study. The hippocampi from AD brains showed the most significant alteration in gene expression profile [PMID: 23595620]. In the present study, in order to identify molecular pathological alterations in AD hippocampus, we applied human transcriptome array and RNA-sequencing to the same samples and reanalyzed the gene array data, and performed integrative analysis of all 3 methods. We also applied gene array to hippocampus of 6-month-old AppNL-G-F/NL-G-F knock-in AD model mice as a preclinical AD stage model, and at last we performed the interspecies comparison. Functional annotation clustering with the results of all 3 or at least 2 methods in human, showed synapse, cell junction, calmodulin binding, ion transport and glycoproteins as the top affected terms. In hippocampi of AppNL-G-F/NL-G-F mice which exhibit significant amyloidosis but not neuronal degeneration, we found that expression of genes categorized in signaling specially signaling peptides with disulfide bond or glycoproteins, together with the innate immune response and lysosome of cells are upregulated. Comparing the extended human data with mouse data, we found and confirmed by qRT-PCR, 2 common up-regulated genes, Clec7a and C4b, which induce innate immune response and synapse elimination. We also found and confirmed by qRT-PCR, 2 common down-regulated genes, one is Slc17a6, which can affect synaptic transmission of glutamate, and second one is Rxfp1, which is involved in gene transcription. Amyloid-𝛽 accumulation is the major hallmark of AD at 6 month-old AppNL-G-F/NL-G-F  mice, therefore our data suggests that amyloid-𝛽 accumulation induces innate immune response, synapse elimination, besides it can decreases glutamate transmission, and affect gene transcription in early stage of hippocampal AD brain, prior to neuronal degeneration.

overall_design: We analyzed postmortem human hippocampus brains from 8 AD and 10 non-AD subjects using Illumina TruSeq stranded mRNA LT Sample Prep kit. Sequences were obtained by using HiSeq1500. One AD and one non-AD sample applied two independent times to sequencer in order to obtain more reads.


title: Diurnal 3D genome organization remodeling orchestrates rhythmic gene expression in rice [RNA-Seq]

first: Baibai

summary: Genome-wide rhythmic modulation of RNAPII occupancy and histone acetylation modifications are highly coordinated with rhythmic gene expression, and dynamically modulates diurnal 3D genome architecture remodeling. The rhythmic genes at AM circadian phase and target genes of transcription factors (TFs) are enriched within limited spatial clusters, which forming subnuclear organization hubs to coordinate looping gene expression. Core circadian clock genes related chromatin connectivity networks suggested they co-localized within the same ?transcriptional factory? and define a distinct nuclear landscape and circadian outputs in the AM and PM. Our findings uncover novel diurnal fundamental genome folding principles in plants, and reveal a distinct higher-order chromosome organization that is crucial for coordinating diurnal dynamics of transcriptional regulation.

overall_design: Here, we generated genome-wide occupancy of RNA polymerase II (RNAPII) and histone modifications (H3K4me3, H3K9me2, H3K27ac, H3K27me3, H3K4me1 and H3K9ac) by ChIP-seq, whole-transcriptome by RNA-seq, chromatin accessibility by FAIRE-seq and DNA methylation by Bisulfite-seq throughout the six-time course. We also performed RNAPII long-read ChIA-PET from the same tissues used for ChIP-seq, RNA-seq, FAIRE-seq and Bissulfite-seq at 8:00 and 20:00. Together, we constructed comprehensive high-resolution dynamic chromatin architecture, and disected its effects on diurnal gene expression.


title: Diurnal 3D genome organization remodeling orchestrates rhythmic gene expression in rice [FAIRE-seq]

first: Li


title: RNA-seq profiling of foetal-derived Langerhans cells from wildtype and Suz12 knockout mice

status: Public on Dec 22 2021

first: Gordon

last: Smyth

state: Vic

address: 1G Royal Pde

department: Bioinformatics

summary: Macrophages are at the forefront of immune responses and their transcriptional programs are modified by their tissue environment and in response to immunological challenge. Post-translational modifications of histones, such as histone H3 lysine 27 tri-methylation (H3K27me3) by the polycomb repressive complex 2 (PRC2), are tightly associated with epigenetic regulation of gene expression. To explore whether H3K27me3 is involved in either the establishment or function of the mononuclear phagocyte system, we selectively deleted the SUZ12 gene in one-week old mice, a core component of PRC2.

overall_design: SMART-Seq RNA libraries were generated from 5000 purified Langerhans cells from the skin of one week old wild mice (2 biological replicates) or Suz12cKO (3 biological replicates). Samples were sequenced with an Illumina NextSeq 500 sequencing system, producing between 22-34 million paired-end 75 bp reads per sample.

first: Pedro

last: Baldoni


title: Transcriptome Analysis of mRNA and miRNA in Adherent Intestinal Cells of Atlantic Salmon, Salmo salar

city: Bodø

first: Jorge

last: Fernandes

address: Universitetsalleen 11

department: Faculty of Biosciences and Aquaculture

institute: Nord University

type: Non-coding RNA profiling by high throughput sequencing

summary: Head kidney (HK) and distal intestine (DI) from Atlantic salmon (average 550g) were collected. Immune cells from DI and HK were extracted and grown at 12°C in Leibovitz’s L-15 Medium (L-15). The isolated DI or HK leukocytes were allowed to adhere on a petri dish with 2 mL L-15+ for 2 days at 12°C. After removing the supernatant containing non-adherent cells, the adherent cells on petri dish were detached by washing three times with 1.5 mL ice-cold PBS supplemented with 5 mM EDTA. The cells were centrifuged (500 × g, 5 min, 4°C) and re-suspended with 2 mL L-15+. Total RNA was extracted from adherent cells from HK or DI (< 500,000 cells). To understand the miRNA expression profiles of adherent intestinal cells (AICs) and to compare them with those of adherent head kidney cells (AKCs), twelve libraries (6 for AIC and 6 for AKC) were prepared. Small RNA-sequencing revealed 37 differentially expressed miRNAs; 20 were up-regulated and 17 were down-regulated. Of them, 12 miRNAs in AIC were found to be involved in regulating macrophage functions.

overall_design: Twelve samples were prepared including 6 from distal intestine and 6 from head kidney.

first: Youngjin

last: Park

first: Qirui

last: Zhang

first: Geert

last: Wiegertjes

middle: M

first: Viswanath

last: Kiron


title: Autoinflammatory keratinization disease with hepatitis and autism reveals roles for JAK1 kinase hyperactivity in autoinflammation.

city: Nagoya

first: Takuya

last: Takeichi

address: 65 Tsurumai-cho, Showa-ku

institute: Nagoya University Graduate of School

summary: Clinical observations reinforced by analysis of a knock-in mouse model confirm the crucial role of JAK1 in regulating physiological inflammatory processes. The present findings expand the phenotypic spectrum resulted from JAK1 hyperactivation and further underscore how gain-of-function JAK1 mutations contribute to multisystem autoinflammation.

overall_design: RNA sequencing was performed using extracted RNA from the brain, liver, and skin of newborn Jak1 knock in (KI) mice (Jak1H595D/+;I596I/+;Y597Y/+) and wild type (WT) mice . We performed a gene set enrichment analysis using the hallmark gene set database.

first: John

middle: Y

last: Lee

first: Yusuke

last: Okuno

first: Masashi

last: Akiyama


title: RNA-seq profiling of bone marrow-derived alveolar macrophages from wildtype and Suz12 knockout mice

institute: Walter and Eliza Hall Institute of Medical Research

summary: Macrophages are at the forefront of immune responses and their transcriptional programs are modified by their tissue environment and in response to immunological challenge. Post-translational modifications of histones, such as histone H3 lysine 27 tri-methylation (H3K27me3) by the polycomb repressive complex 2 (PRC2), are tightly associated with epigenetic regulation of gene expression. To explore whether H3K27me3 is involved in either the establishment or function of the mononuclear phagocyte system, we selectively deleted the SUZ12 gene in mice, a core component of PRC2. SUZ12 ablation induced a rapid loss of the alveolar macrophage networks under both steady state and inflammatory conditions. Ablation of SUZ12 abrogated the proliferation of these cells required for their self-renewal.

overall_design: C57BL/6-Ly5.1 mice were lethally irradiated and reconstituted with either a ratio of 90% wt Ly5.2: 10% wt Ly5.1, or 90% Suz12 cKO Ly5.2: 10% wt ly5.1. TruSeq RNA libraries were generated from alveolar macrophages selected by flow cytometry from wild type mice (4 biological replicates) or Suz12cKO (3 biological replicates) lung. Samples were sequenced with an Illumina NextSeq 500 sequencing system, producing between 14-20 million single-end 85 bp reads per sample.


title: Single cell RNA-seq analysis of novel splenic DC

city: Seoul

first: Chae Gyu

address: 50 Yonsei-ro, Seadaemun-gu

institute: YONSEI UNIVERSITY

summary: To understand the cellular diversity within CD11b+ splenocytes between control and GM-CSF-treated mice, we performed the CITE-seq in control and GM-CSF treated mice.

overall_design: FACS sorted CD11b+ splenocytes were loaded into the Chromium system (10x Genomics, Pleasanton, CA, USA) targeting 7,000 cells per sample. The cDNA libraries for mRNA were generated using Chromium Single Cell 3' v3 Reagent Kits according to the manufacturer’s instruction. Following the CITE-seq protocol, ADT PCR additive primers were added to cDNA PCR and the ADT libraries were generated separately from the mRNAs.

first: Chae-Gyu

first: Seul-Hye

last: Ryu

first: Hye-Hyeon

last: Eum

first: Hae-Ock


title: INO80 requires a polycomb subunit to regulate the establishment of poised chromatin in murine spermatocytes [RNA-seq]

status: Public on Dec 21 2021

city: Chapel Hill

first: Prabuddha

last: Chakraborty

state: NC

address: 120 Mason Farm Road5023 B, Genetic Medicine Building, CB#7264

department: Genetics

institute: University of North Carolina at Chapel Hill

summary: INO80 is the catalytic subunit of the multi-subunit INO80-chromatin remodeling complex that has been implicated in DNA replication, repair, and transcription regulation. Ino80-deficiency in murine spermatocytes (Ino80cKO) results in pachytene arrest of spermatocytes, due to incomplete synapsis and aberrant DNA double-strand break repair (DSBR) that leads to apoptosis. We explored the mechanism by which INO80 mediates meiotic progression. RNA-seq on Ino80cKO spermatocytes revealed major changes in transcription, indicating that an aberrant transcription program arises upon INO80 depletion. In Ino80WTspermatocytes, genome-wide analysis showed that INO80-binding sites were mostly promoter proximal and necessary for the regulation of spermatogenic gene expression, primarily of premeiotic and meiotic genes. Further, most of the genes poised for activity, as well as those genes that are active, shared INO80 binding. In Ino80cKO spermatocytes, most poised genes demonstrated de-repression due to reduced H3K27me3 enrichment, and in turn showed increased expression levels. INO80 interacts with the core PRC2 complex member SUZ12 and promotes its recruitment. Further, INO80 mediates H2A.Z incorporation at the poised promoters, which was reduced in Ino80cKO spermatocytes. Taken together, INO80 is emerging as a major regulator of the meiotic transcription program by mediating poised chromatin establishment through SUZ12 binding.

overall_design: RNA-seq was performed on spermatogenic cells obtained from Ino80WT and Ino80cKO (testis specific Ino80-deletion generated with Stra8-Cre) testes.

first: Terry

last: Magnuson


title: The transcription factor Hepatocyte Nuclear Factor 4A acts in the intestine to promote white adipose tissue energy storage

city: Sherbrooke

first: Francois

last: Boudreau

state: QC

address: 3201 Jean-Mignault

department: Immunology and Cell Biology

country: Canada

institute: Université de Sherbrooke

summary: HNF4A is a transcription factor that controls metabolic features of several endodermal epithelia.  Using an intestinal conditional mouse model, here we demonstrate that HNF4A is not required for intestinal lipid metabolism per se, but unexpectedly influences whole body energy expenditure under diet-induced obesity (DIO). Deletion of intestinal HNF4A causes mice to become DIO-resistant with preference for fat as an energy substrate and energetic changes in association with white adipose tissue (WAT) beiging. Intestinal HNF4A is crucial for fat-induced release of glucose-dependent insulinotropic polypeptide (GIP), while reintroduction of a stabilized GIP analog rescues the DIO-resistance phenotype of the mutant mice. Our study provides evidence that intestinal HNF4A plays a non-redundant role in whole body lipid homeostasis and points to a novel non-cell-autonomous regulatory circuit for body fat management.

overall_design: mRNA profiles of eWAT and iWAT from control mice injected with saline or GIP analog (3 replicates/condition)

first: Romain

last: Girard

first: Sarah

last: Tremblay


title: Novel splenic DC

first: Seul Hye

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

institute: Yonsei University

summary: To understand the cellular diversity within splenocytes between control and GM-CSF-treated mice

overall_design: Global mRNA sequencing of DC subsets and CD115+ populations in spleen from control mice and GM-CSF-treated mice

first: Chae

middle: G

first: Seul

middle: H


title: Diurnal 3D genome organization remodeling orchestrates rhythmic gene expression in rice [ChIA-PET]

first: Baibai

last: Gao

first: Li

last: Deng


title: Loss-of-function ROX1 mutations suppress the fluconazole susceptibility of upc2A∆ mutation in Candida glabrata, implicating additional positive regulators of ergosterol biosynthesis

status: Public on Dec 20 2021

city: Iowa City

first: Damian

middle: J

last: Krysan

state: IA

address: 25 South Grand, 2040 ML

department: Division of Pediatrics & Infectious Disease

institute: University of Iowa Hospitals and Clinics

summary: Two of the major classes of antifungal drugs in clinical use target ergosterol biosynthesis. Despite its importance, our understanding of the transcriptional regulation of ergosterol biosynthesis genes in pathogenic fungi is essentially limited to the role of hypoxia and sterol-stress induced transcription factors such as Upc2 and Upc2A as well as homologs of Sterol Response Element Binding (SREB) factors. To identify additional regulators of ergosterol biosynthesis in Candida glabrata, an important human fungal pathogen with reduced susceptibility to ergosterol biosynthesis inhibitors relative to other Candida spp., we used a serial passaging strategy to isolate suppressors of the fluconazole hypersusceptibility of a upc2A∆ deletion mutant. This led to the identification of loss of function mutants in two genes: ROX1, the homolog of a hypoxia gene transcriptional suppressor in Saccharomyces cerevisiae, and CST6, a transcription factor that is involved in the regulation of carbon dioxide response in C. glabrata.  Here, we describe a detailed analysis of the genetic interaction of ROX1 and UPC2A. In the presence of fluconazole, loss of Rox1 function restores ERG11 expression to the upc2A∆ mutant and inhibits the expression of ERG3 and ERG6, leading to increased levels or ergosterol and decreased levels of the toxic sterol, 14α methyl-ergosta-8,24(28)-dien-3β, 6α-diol, relative to upc2A∆. Our observations establish that Rox1 is a negative regulator of ERG gene biosynthesis and indicate that a least one additional positive transcriptional regulator of ERG gene biosynthesis must be present in C. glabrata.

overall_design: C. glabrata mRNA expression of upc2A∆, rox1∆, and upc2a∆ rox1∆ were compared against WT in both YPD medium and YPD plus fluconazole media. Within each comparison, wild-type cells represent baseline expression and each strain has three biological replicates.

first: Tomye

middle: L

last: Ollinger

first: Bao

last: Vu

first: Daniel

last: Murane

first: Josie

last: Parker

first: Lucia

last: Simonicova

first: Laura

last: Doorley

first: Mark

last: Stamnes

first: Steven

last: Kelley

first: P

middle: D

last: Rogers

first: W

last: Moye-Rowley


title: INO80 requires a polycomb subunit to regulate the establishment of poised chromatin in murine spermatocytes [CUT&RUN]

first: Prabuddha

last: Chakraborty

overall_design: CUT&RUN was performed for H3K27me3 and SUZ12 on spermatogenic cells obtained from Ino80WT and Ino80cKO (testis specific Ino80-deletion generated with Stra8-Cre) testes.

first: Terry

last: Magnuson


title: INO80 requires a polycomb subunit to regulate the establishment of poised chromatin in murine spermatocytes [ATAC-seq]

overall_design: ATAC-seq was performed on spermatogenic cells obtained from Ino80WT and Ino80cKO (testis specific Ino80-deletion generated with Stra8-Cre) testes.


title: INO80 requires a polycomb subunit to regulate the establishment of poised chromatin in murine spermatocytes [ChIP-seq]

overall_design: INO80 ChIPs were performed on spermatogenic cells isolated from Ino80WT mouse testis on P18. H2A.Z ChIPs were performed on spermatogenic cells obtained from Ino80WT and Ino80cKO (testis specific Ino80-deletion generated with Stra8-Cre) testes.


title: INO80 requires a polycomb subunit to regulate the establishment of poised chromatin in murine spermatocytes

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

overall_design: Refer to individual Series


title: Single-cell chromatin accessibility and lipid profiling reveals SCD1-dependent metabolic shift in adipocytes induced by bariatric surgery

city: Ithaca

first: Paul

middle: D.

last: Soloway

address: T4 018 Veterinary Research Tower

department: Biomedical Sciences

institute: Cornell University

summary: We applied single-cell ATAC sequencing and lipid profiling to inguinal and epididymal adipose depots from mice that received sham surgery or vertical sleeve gastrectomy (VSG). We observed depot-specific cellular composition and chromatin accessibility patterns that were altered by VSG. Specifically, accessibility at Scd1, a fatty acid desaturase, was substantially reduced after VSG in mature adipocytes of inguinal but not epididymal depots. This was accompanied by reduced accumulation of SCD1-produced unsaturated fatty acids. Given these findings and reports that reductions in Scd1 attenuate obesity and insulin resistance our results suggest VSG exerts its beneficial effects through an inguinal depot-specific reduction of SCD1 activity.

overall_design:
single-cell chromatin accessibility (ATAC-seq) of inguinal and epididymal adipose depots from mice 2.5 months after a sham surgery or verical sleeve gastrectomy.
Please note that the raw fastq.gz files were generated by Illumina pipeline software v2.18, then decomplexed to integrate the barcodes from index1 and index2 reads into the read names of the R1 and R2 files using snATAC decomplex by the Ren lab (https://github.com/r3fang/snATAC). the barcode metadata that lists the barcodes associated with each sample in a file called barcode_metadata.txt.

first: Blaine

last: Harlan

first: Hui

last: Park

first: Roman

last: Spektor

first: Bethany

last: Cummings

first: J

middle: T

last: Brenna


title: Transcriptomic analysis of Aspergillus flavus in response to the solvent Dimethyl Sulfoxide

city: Toulouse

first: Yannick

last: Lippi

address: 180 chemin de tournefeuille

department: GeT-TRiX facility

institute: INRAE

summary: Dimethyl sulfoxide (DSMO) is a simple molecule widely used because of its great solvating ability. Beyond its physico-chemical properties, it is also biologically active, including on fungal species. Aspergillus flavus is a saprophytic and famous pathogenic fungus able to produce Aflatoxin B1 (AFB1), a potent carcinogenic mycotoxin which may contaminate many food crops. The aim of this study was to characterize the effect of DMSO on A. flavus transcriptome profile using high-throughput RNA-sequencing assay.

overall_design: Six replicated fungal mycelium cultures were grown in three conditions (CTRL, DMSO Dose 1, DMSO Dose 2) to generate 18 samples in total which were extracted and processed to perform a RNAseq study.

last: Costes

first: Claire

last: Naylies

first: Clemence

last: Genthon

first: Olivier

last: Puel

first: Jean-Denis

last: Bailly


title: Pan-AMPK activator O304 prevents gene expression changes and re-mobilization of histone marks in islets of diet-induced obese mice

city: Pamplona

first: Ana

middle: Rosa

last: López-Pérez

address: Calle Irunlarrea, 3

country: Spain

institute: Navarrabiomed - Fundacion Migues Servet


title: HPVE6-USP46 Mediated Cdt2 Stabilization Reduces Set8   Mediated H4K20-Methylation to Induce Gene Expression Changes

city: Birmingham

first: Anindya

last: Dutta

state: AL

address: 720 20th Street South, Kaul 230

institute: University of Alabama at Birmingham

summary: Cervical cancer is one of the most common cancers in women. More than 95% of the cervical cancers are caused by the human papilloma viruses. Earlier we had identified a protein target, USP46 that can be inhibited to block the cancer growth. We found that the viral E6 and human USP46 complex increases the levels of Cdt2 in cervical cancers. In this paper we compared real cervical tumors with matched normal tissue from same patients and found that the effects of E6 mediated USP46 activation are indeed reflected as increased levels of Cdt2 and decreased levels of Set8 protein in the real tumors. We also found that the HPV protein E6 alone can stimulate the enzymatic activity of human USP46. By doing this it activates several cellular pathways that are required for the growth of cancers. One such pathway is the EGFR pathway that is normally upregulated in cervical cancers. We find that E6-USP46 contributes to the activation of EGFR by inducing epigenetic changes on the DNA by degrading the Set8 protein. These findings illuminate the role of viral E6 protein in inducing cancers and substantiate the candidature of USP46 as a drug target for HPV induced cancers.

overall_design: HeLa cells were transfected with control siRNAs or HPV-E6 siRNA or HPV-E6 and Set8 siRNAs. Cells were collected 48 h after siRNA transfection and RNA was extracted using the Qiagen RNA extraction kit. RNA samples were sent to Beijing Novogene Co., Ltd. (Beijing, China ) for library preparation and next generation RNA sequencing. More than 50 million paired end reads were obtained for each sample. Three experimental replicates were prepared for each sample and RNA integrity numbers (RIN) derived from a Bioanalyzer were used to ascertain the quality of RNA.

first: Shashi

last: Kiran

first: Briana

last: Wilson

first: Shekhar

last: Saha

first: Julia

last: Graff


title: Pan-AMPK activator O304 prevents gene expression changes and re-mobilization of histone marks in islets of diet-induced obese mice (RNA-Seq)

summary: AMP-activated protein kinase (AMPK) have an important role in cellular energy homeostasis and has  emerged as a promising target for treatment of Type 2 Diabetes (T2D) due to its beneficial effects on  insulin sensitivity and glucose homeostasis. O304 is a pan-AMPK activator that has been shown to  improve glucose homeostasis in both mouse models of diabetes and in human T2D subjects. Here,  we describe the genome-wide transcriptional profile and chromatin landscape of pancreatic islets  following O304 treatment of mice fed high-fat diet (HFD). O304 largely prevented genome-wide gene  expression changes associated with HFD feeding in CBA mice and these changes were associated  with remodelling of active and repressive chromatin marks. In particular, the increased expression  of the β-cell stress marker Aldh1a3 in islets from HFD mice is completely abrogated following O304  treatment, which is accompanied by loss of active chromatin marks in the promoter as well as distant  non-coding regions upstream of the Aldh1a3 gene. Moreover, O304 treatment restored dysfunctional  glucose homeostasis as well as expression of key markers associated with β-cell function in mice  with already established obesity. Our findings provide preclinical evidence that O304 is a promising  therapeutic compound not only for T2D remission but also for restoration of β-cell function following  remission of T2D diabetes.

overall_design: Analysis of gene expression and two histone modifications in mice fed with RD, HFD and HFD-O304. For RNA-seq 7 replicates per condition and for ChIP-seq 2 replicates per condition.

first: Stefan

last: Norlin

first: Pär

last: Steneberg

first: Silvia

last: Remeseiro

first: Helena

last: Edlund

first: Andreas

last: Hörnblad


title: Pan-AMPK activator O304 prevents gene expression changes and re-mobilization of histone marks in islets of diet-induced obese mice (ChIP-Seq)


title: Transcriptomics and network analysis highlight potential pathways in the pathogenesis of pterygium

status: Public on Dec 18 2021

city: Campinas

first: Juliana

middle: Albano de

last: Guimarães

state: SP

address: Tessália Vieira de Camargo, 126, Cidade Universitária

department: Ophthalmology

country: Brazil

institute: School of Medical Sciences of University of Campinas

summary: Differential expression comparing active pterygium with atrophic pterygium using data generated from the Brazilian cohort identified differentially expressed genes between the two forms of presentation of this condition

overall_design: Samples from nine patients were collected during surgery after photo documentation and clinical characterization of pterygia. Gene expression experiments were performed using Human Clariom D Assay gene chip. Differential gene expression analysis between active and atrophic pterygia was performed using limma package after adjusting variables by age.

last: de Guimarães

first: Bidossessi

middle: W

last: Hounpke

first: Bruna

last: Duarte

last: Boso

first: Marina

last: Viturino

first: Letícia

last: de Carvalho Baptista

first: Mônica

middle: B

last: de Melo

first: Monica

last: Alves


title: Differential gene expression analysis identified determinants of cell fate plasticity during radiation-induced regeneration in Drosophila

status: Public on Dec 19 2021

city: Aurora

first: Andrew

last: Goodspeed

state: CO

address: 12801 E 17th Ave, Mail Stop 8303

institute: University of Colorado Anschutz Medical Campus

summary: We used here a combination of lineage tracing, FACS and genome-wide RNAseq to identify two key changes that accompany hinge-to-pouch fate change: (1) repression of hinge determinants and (2) upregulation of ribosome biogenesis.

overall_design: We performed a genome-wide analysis of gene expression changes during regeneration of the Drosophila larval wing disc. By dissociating the discs into single cells and using Fluorescence-Activated Cell Sorting we monitored the hinge versus the rest of the disc, to identify genes that are differentially expressed in the two cell populations during regeneration and fate change.

first: Michelle

last: Ledru

first: Caitlin

last: Clark

first: Jeremy

last: Brown

first: Shilpi

last: Verghese

first: Sarah

last: Ferrara

first: Tin

last: Su


title: Engagement of ICOS in tissues promotes establishment of CD8+ tissue-resident memory T cells

city: Minneapolis

first: Todd

middle: P

last: Knutson

state: MN

address: 117 Pleasant St SE

department: Minnesota Supercomputing Institute

institute: University of Minnesota

summary: Recirculating and tissue-resident memory CD8+ T cells provide distinct modes of immune protection, yet the signals that dictate differentiation of these populations are ill-defined. In particular, the interactions within tissues that promote generation of resident memory T cells (TRM) are unclear. Here, we show that the inducible costimulatory molecule ICOS, well known to regulate differentiation of CD4+ T cell populations, is required for CD8+ TRM but not recirculating memory subsets. Furthermore, ICOS engagement during CD8+ T cell recruitment to non-lymphoid tissues is critical for efficient TRM establishment: ICOS/ICOS-L interactions are dispensable throughout CD8+ T cell priming and for TRM maintenance, while ICOS-L expression by radioresistant cells is key for optimal TRM generation. This role for ICOS depends on its ability to signal through PI3K. Together, our data illustrate that specific local costimulatory cues promote production of tissue-resident populations, with potential implication for therapeutic manipulation.

overall_design:
CD8+ P14 T cells from WT or Icos knockout (KO) mice were mixed, co-adoptively transferred into recipient mice, and the mice were infected with LCMV the following day. CD8+ T cells were isolated from recipient mouse spleen, small intestine intraepithelial lymphocytes (SI-IEL), and kidney in two different cohorts (i.e. day 5 or day 32 post infection). Cellular indexing of transcriptomes and epitopes by sequencing (CITE-seq) single cell RNA sequencing (scRNA-seq) analysis was completed. Cells were stained with antibody-oligo derived tags (ADTs) against CD45.2 and ICOS to identify cells derived from WT and Icos KO mice, and three hashtag oligos (HTOs) to identify cells derived from different tissues. For each timepoint, cells from different tissues were mixed at equal proportion and captured in the same library using the 10x Genomics Chromium Single Cell 3' (ver. 3.1) reagent kits, generating three independent gene expression (GEX) and feature barcode (ADT and HTO) sequencing libraries.
The metadata.txt (representing 14 samples) contains each sample information and additional details.

first: Changwei

last: Peng

first: Matthew

last: Huggins

first: Kelsey

last: Wanhainen

first: Hanbin

last: Lu

first: Hristo

last: Georgiev

first: Kristen

last: Mittelsteadt

first: Nicholas

middle: N

last: Jarjour

first: Haiguang

last: Wang

first: Kristin

last: Hogquist

first: Daniel

last: Campbell

first: Henrique

last: Borges da Silva

first: Stephen

last: Jameson


title: RNA-seq profiling of foetal-derived alveolar macrophages from wildtype and Suz12 knockout mice

city: Parkville

first: Gordon

middle: K

last: Smyth

summary: Macrophages are at the forefront of immune responses, and their transcriptional programs are modified by their tissue environment and in response to immunological challenge. Post-translational modifications of histones, such as histone H3 lysine 27 tri-methylation (H3K27me3) by the polycomb repressive complex 2 (PRC2), are tightly associated with epigenetic regulation of gene expression. To explore whether H3K27me3 is involved in either the establishment or function of the mononuclear phagocyte system, we selectively deleted the SUZ12 gene in one-week old mice, a core component of PRC2. SUZ12 ablation induced a rapid loss of the alveolar macrophage networks under both steady state and inflammatory conditions. Ablation of SUZ12 abrogated the proliferation of these cells required for their self-renewal.

overall_design: TruSeq RNA libraries were generated from FACS purified alveolar macrophages from one week old wild type (4 biological replicates) or Suz12cKO (5 biological replicates) lung. Samples were sequenced with an Illumina NextSeq 500 sequencing system, producing between 19-56 million single-end 85 bp reads per sample.

first: Pedro

last: Baldoni


title: Apolipoprotein E derived from CD11c+ cells ameliorates atherosclerosis

city: Eggenfelden

first: Christian

middle: Albert

last: Gleissner

address: Simonsöder Allee 20

department: Cardiology

institute: Rottal-Inn Kliniken KU

summary: ApoE-/- and Bl6 mice were fed normal chow of high fat diet. CD11c+ cells were isolated from mouse spleens. and mRNA expression was quantified using gene arrays.

overall_design: ApE-/- and Bl6 with or without high fat diet (n=3 per group).


title: Heat Shock Factor 1 (HSF1) regulates ESR1 action in breast cancer

city: Bergen

first: Tomasz

last: Stokowy

address: Nygardsgaten 5

department: IT Division

institute: University of Bergen

summary: Heat shock factor 1 (HSF1) is a key regulator of transcriptional responses to proteotoxic stress. It has been recently linked to signaling of estrogen via ESR1. To study the cooperation of HSF1 and ESR1 in the transcriptional response to estrogen, we established estrogen receptor (ER)-positive breast cancer cell lines with reduced HSF1 levels using specific shRNA or CRISPR/Cas9 approach. HSF1 deficiency led to the inhibition of the mitogenic effect of estrogen in MCF7 and T47D cells. RNA-seq analyses revealed that the stimulatory effect of E2 on the transcriptome was smaller in HSF1-deficient MCF7 cells. This could partially result from the higher basal expression of E2-dependent genes in these cells as a consequence of the enhanced binding of unliganded ESR1 to chromatin, which was revealed by ChIP-seq analyses. Thus, we postulate that some fraction of ESR1 could be released from the inhibitory complex with HSP90 and gain transcriptional competence without E2-stimulation.

overall_design: MCF7 cells with different status of HSF1 (HSF1+/+ and HSF1-/-) were untreated or treated with 10 nM E2 for 4 hour. Then total RNA was isolated from each sample using the Direct-ZolTM RNA MiniPrep Kit (Zymo Research), digested with DNase I (Worthington Biochemical Corporation) and next-generation sequenced using the Illumina protocol. For each experimental point, three independent biological repeats were done including RNA isolation and sequencing.

first: Natalia

last: Vydra

first: Patryk

last: Janus

first: Wieslawa

last: Widlak


title: Integratome analysis of adipose tissues reveals abnormal epigenetic regulation of adipogenesis, inflammation, and insulin signaling in obese individuals with type 2 diabetes

city: Hong Kong

first: Nana

last: Jin

address: CUHK, Sha tin, NT

country: Hong Kong

institute: CUHK

summary: Type 2 diabetes (T2D) is associated with cardiovascular-renal complications and premature death. Although most patients with T2D are obese, not all obese individuals develop T2D. Thus, an understanding of the mechanistic relationships between obesity and T2D is crucial. In this study, using subcutaneous (SAT) and visceral adipose tissues (VAT) from obese individuals with or without T2D collected during metabolic surgery, integration of the transcriptomes and methylomes of VAT and SAT with publicly available tissue-specific regulatory networks, we discovered the close relation between T2D and inflammatory response in both SAT and VAT in obese individuals, although less differences were observed respectively in transcriptome or methylome. Specifically, a HOX gene family-enriched functional epigenetic sub-network in T2D-SAT, as well as a novel such sub-network was discovered, which involved multiple genes implicated in activation of obesity-induced inflammatory response. Our integrated approach of using biosamples, multi-omic data and public databases to understand complex diseases for discovery of novel biology, including biomarkers and drug targets, can be applied to diseases other than T2D and obesity.

overall_design: 40 methylation samples from 24 individuals were sequenced, including SAT from 10 T2D and 9 control individuals and VAT from 10 T2D and 11 control individuals.

first: Heung-Man

last: Lee

first: Allen

middle: C

last: Yu

first: Jing-Woei

last: Li

first: Alice

last: Kong

first: Candice

last: Lam

first: Simon

last: Wong

first: Enders

last: Ng

first: Ronald

last: Ma

first: Juliana

last: Chan

first: Ting-Fung


title: RNA-seq time course analysis of in vitro differentiated antibody-secreting cells

status: Public on Dec 17 2021

city: Atlanta

first: Chris

last: Scharer

state: GA

address: 1510 Clifton Rd, Suite 3086A

department: Microbiology and Immunology

institute: Emory University

summary: We examined the transcriptional changes that occur as Antibody Secreting Cells (ASC) differentiate and mature using an in vitro culture system. ASC were profiled directly post isolation and at time points weekly out to 48 days in culture. These data reveal how the long-lived ASC transcriptome matures over time.

overall_design: Comparison of human blood ASC transcriptomes over different time points from in vitro cultures.

first: Christopher

first: Frances

middle: E


title: Single Cell Analysis Unveils the Role of the Tumor Immune Microenvironment and Notch Signaling in Dormant Minimal Residual Disease

city: Guangzhou

first: Yuchen

last: Yang

state: Guangdong

address: Xingangxi Road 135

institute: Sun Yat-sen University

summary: Understanding the complex ecosystem that promotes dormant cell survival and elucidating those factors that eventually overcome growth constraints and result in proliferation may provide new insights and help identify novel strategies to prolong dormancy and prevent recurrence. To dissect the molecular pathways and the microenvironments involved in regulation of tumor dormancy, we utilized a novel immunocompetent transgenic model to study residual disease, dormancy, and relapse. We discovered a significant reorganization of cancer cell structures, stroma, and immune cells with cancer cells showing dormant cell signatures. Single-cell RNA sequencing uncovered remodeling of myeloid and lymphoid compartments. Additionally, the Jagged-1/Notch signaling pathway was shown to regulate many aspects of tumorigenesis including stem cell development, epithelial-mesenchymal transition, and immune cell homeostasis during dormancy. An anti-Jagged-1 inhibitory antibody prolonged dormancy and delayed tumor recurrence due to the pleotropic effects of inhibiting the Jagged-1/Notch signaling pathway both in the tumor cells and the microenvironment.

overall_design: Single-cell RNA-seq profiles of tumors from 4 stages: Primary, dormant, long-term dormant, and recurrent, and 2 treatment arms (control and anti-Jagged-1) were generated by deep sequencing using 10x Genomics Chromium System.

first: Mahnaz

last: Janghorban

first: Xiang

last: Zhang

first: Jeffrey

middle: M

last: Rosen


title: Hierarchical interactions between chromatin remodeling transcription factors define the epigenetic landscape of antiviral T cells [scATAC]

city: Shanghai

first: Yi

last: Zhong

address: 227 South Chongqing Rd.

institute: SJTU

summary: T cell activation induces rapid proliferative expansion and the acquisitions of specialized effector functions that enable protection against invading pathogens.  While a multitude of transcription factors (TFs) have been implicated in the regulation of T cell activation, it remains largely unclear how their functions are organized and integrated at the genomic level. Here, we leveraged naturally occurring TF binding site polymorphisms in wild derived inbred mice to identify the most critical “heavy lifters” that shape the epigenetic landscape of naïve and activated antiviral CD4 and CD8 T cells. We found that representative members of Ets, Runx, and TCF/Lef families occupied the vast majority of accessible chromatin regions and that interactions between them were associated with distinct epigenetic responses to T cell activation. We define prevalent genomic functions of Ets1, Runx1, and TCF1 as “housekeeper”, “universal amplifier”, and “placeholder”, respectively. Interestingly, regulatory elements associated with some of the most strongly induced and well-characterized immune response genes showed a non-canonical pattern of TF recruitment.

overall_design: The project studied the single cell chromatin accessibility of CD8/CD4 T cell in response to virial infection. CD4 and CD8 T cells were sorted from pooled splenocytes of 3 LCMV Armstrong infected (B6/Cast) F1 mice on day 7 post infection.

first: Sarah

last: Walker

first: Yuri

last: Pritykin

first: Christina

middle: S

last: Leslie

first: Alexander

last: Rudensky

first: Joris

last: van der Veeken


title: Identification of DNA methylation biomarkers for prediction of response to neoadjuvant chemotherapy in triple-negative breast cancer [EPIC Array]

city: Sydney

first: Braydon

last: Meyer

state: NSW

address: 384 Victoria St, Darlinghurst

department: Genetics and Epigenetics

institute: Garvan Institute of Medical Research

summary: Response to neoadjuvant chemotherapy (NAC) in triple-negative breast cancer is linked to long-term patient survival. However, response to NAC is highly variable and cannot reliably be predicted by clinical or other current methods. This study aims to address this problem by utilising the stable, yet dynamic marker known as DNA methylation. By defining the methylation differences at diagnosis in patients that achieve a pathological complete remission against those that do not respond, we can identify a marker that can potentially predict chemotherapy response and help further personalise the chemotherapy decision making in the clinic.

overall_design: DNA methylation microarrays were used in primary triple-negative breast cancer samples to discriminate patient response to neoadjuvant chemotherapy within the SETUP cohort.

first: B

first: R

last: Pidsley


title: RNA-Seq analysis of human blood and bone marrow naïve B cell subsets

summary: To compare the transcriptome of human naïve B cells from the blood or bone marrow we sorted each population from a diverse healthy cohort and performed RNA-seq

overall_design: Comparison of human naïve B cell transcriptomes from the blood or bone marrow

last: Lee


title: RNA-Seq analysis of human blood and bone marrow antibody secreting cell subsets

summary: Antibody secreting cells (ASC) circulate after vaccination and infection and migrate to the bone marrow (BM) where a subset known as long-lived plasma cells (LLPC) persist and secrete antibodies for a lifetime. The mechanisms of how circulating ASC become LLPC is not well elucidated. Here, we show that human early-minted blood ASCs have distinct morphology, transcriptomes, and epigenetics compared to human BM LLPC. Compared to blood ASC, BM LLPC have decreased nucleus/cytoplasm ratio but increased endoplasmic reticulum and numbers of mitochondria. Additionally, LLPC acquire transcriptional and epigenetic differences in multiple cellular pathways that include apoptosis. Upregulation of the anti-apoptotic genes MCL1, BCL2, BCL-XL while simultaneously downregulation of pro-apoptotic genes HRK1, CASP3, and CASP8 occurs in LLPC. Consistent with the decrease in gene expression, pro-apoptotic gene loci are less accessible in LLPC. In contrast, anti-apoptotic gene expression is increased but is not always accompanied by changes in accessibility. Importantly, we show that early-minted blood ASCs undergo morphological and transcriptional changes that make these cells resemble ex vivo BM ASCs, suggesting that the BM microniche at least in part promotes LLPC maturation. Overall, our study demonstrates that early-minted blood ASC in the BM microniche must undergo morphological, transcriptional, and epigenetic changes to mature into apoptotic-resistant LLPC.

overall_design: Comparison of human blood and BM ASC transcriptomes


title: Analysis of Chinese sheep preimplantation embryo development and block by single-cell DNA methylome sequencing

status: Public on Dec 15 2021

city: Zhengzhou

first: zijing

last: zhang

state: Henan

address: NO:116 road

department: Institute of Animal Husbandry and Veterinary Scienc

institute: Henan Academy of Agricultural Sciences

type: Methylation profiling by high throughput sequencing

summary: The early stages of mammalian embryonic development involve the participation and cooperation of numerous complex processes, including nutritional, genetic, and epigenetic mechanisms. However, in embryos cultured in vitro, a developmental block occurs that affects embryo development and the efficiency of culture. Although the block period is reported to involve the transcriptional repression of maternal genes and transcriptional activation of zygotic genes, how epigenetic factors regulate developmental block is still unclear. In this study, we systematically analyzed whole-genome methylation levels during five stages of sheep oocyte and preimplantation embryo development using SC-WGBS technology. Then, we examined several million CpG sites in individual cells at each evaluated developmental stage to identify the methylation changes that take place during the development of sheep preimplantation embryos. Our results showed that two strong waves of methylation changes occurred, namely, demethylation at the 8- to 16-cell stage and methylation at the 16- to 32-cell stage. Analysis of DNA methylation patterns in different functional regions revealed a stable hypermethylation status in 3'UTRs and gene bodies; however, significant differences were observed in intergenic and promoter regions at different developmental stages. Changes in methylation at different stages of preimplantation embryo development were also compared to investigate the molecular mechanisms involved in sheep embryo development at the methylation level. In conclusion, we report a detailed analysis of the DNA methylation dynamics during the development of sheep preimplantation embryos. Our results provide an explanation for the complex regulatory mechanisms underlying the embryo developmental block based on changes in DNA methylation levels.

overall_design: We systematically analyzed whole-genome methylation levels during five stages of sheep oocyte and preimplantation embryo development using SC-WGBS technology.

first: Zijing

first: Jiawei

last: Xu

first: Shijie

last: Lyv

first: Eryao

last: Wang


title: single cell RNA sequencing of spleen mesenchymal reticular cells

city: Melbourne

first: Scott

last: Mueller

state: Victoria

address: 792 Elizabeth street

institute: The University of Melbourne

summary: We report the single cell transcriptome of mouse splenic mesenchymal reticular cells obtained from Ccl19-cre x R26R-EYFP mice on a C57BL/6 background.

overall_design: Spleen CD45- CD31- Ter119- cells that expressed at least one of the markers CD157, PDPN and EYFP were flow cytometrically sorted and encapsulated into emulsion droplets using a Chromium Controller (10x Genomics) and libraries prepared. scRNA-seq libraries were constructed using Chromium Single Cell 3' v3 Reagent Kit according to the manufacturer’s protocol. Cells were examined under a microscope and counted with a hemocytometer before loading. Libraries were run on the HiSeq2500 for 100 bp paired end Illumina sequencing.


title: Transcriptomics reveals the cytotoxicity of PM2.5 to mouse spermatocyte-derived GC-2spd cells

status: Public on Dec 16 2021

city: Chongqing

first: Fuquan

last: Shi

address: 30 Gaotanyan Street

institute: Army Medical University

summary: We have found that PM2.5 exposure can induce spermatocyte damage and inhibit GC-2spd cell proliferation in vivo and vitro studies. Transcriptomics was performed to explore the potential mechanism of PM2.5-induced reproductive toxicity. With RNA-sequencing technique, the differentially expressed genes induced by PM2.5 exposure were mainly enriched in the metabolism of xenobiotics by cytochrome P450 pathway, and Cyp1a1 was the most significantly changed gene.

overall_design: mRNA profiles of PM2.5-treated and untreated in GC-2spd cells. Each group includes three replicates.

first: Lin

last: Ao

first: Jia

last: Cao


title: Differential Expression Profiles and Potential Intergenerational Functions of tRNA-Derived Small RNAs in Mice After Cadmium Exposure

city: wuhan

first: ping

last: su

state: hubei

address: qiaokou district hankong road 13

department: Institute of Reproductive Health, Tongji Medical College

institute: huazhong university of science and technology

summary: Cadmium (Cd) is a toxic heavy metal and ubiquitous environmental endocrine disruptor. Previous studies on Cd-induced damage to male fertility mainly focus on the structure and function of testis, and semen quality. Nevertheless, to date, no studies have investigated the effects of Cd exposure on sperm epigenetic inheritance and intergenerational inheritance. In our study, we systematically revealed the changes in sperm tRNA-derived small RNAs (tsRNA) profiles and found that 14 tsRNAs (9 up-regulated and 5 down-regulated) were significantly altered after Cd exposure. Bioinformatics of tsRNA-mRNA-pathway interactions revealed that the altered biological functions mainly were related to ion transmembrane transport, lipid metabolism and cell membrane system.  In addition, we focused on two stages of early embryo development and selected two organs to study the impact of these changes on cell membrane system, especially mitochondrion and lysosome, two typical membrane-enclosed organelles. Surprisingly, we found that the content of mitochondrion was significantly decreased in 2-cell stage, whereas remarkably increased in the morula stage. The contents of mitochondrion and lysosome were significantly increased in the testes of 6-days offspring and livers of adult offspring, whereas remarkably decreased in the testes of adult offspring. This provides a possible basis to further explore the effects of paternal Cd exposure on offspring health.

overall_design: The sperm small non-coding RNAs in cadmium-exposed group and control group were analyzed by Illumina NextSeq 500 Sequencing.

first: Ling

last: Zeng

first: Jinzhao

last: Zhou

first: Yanwei

last: Zhang

first: Xiaofei

first: Mei

first: Ping

last: Su


title: Single-cell delineation of lineage and genetic identity in the mouse brain

city: Martinsried

first: Christian

last: Mayer

address: Am Klopferspitz 18

institute: Max Planck Institute of Neurobiology.

summary: We used massively parallel tagging of progenitors to track clonal relationships and transcriptomic signatures during murine forebrain development. We found several examples of clonal divergence and convergence in both neurons and glia, and examined the processes that led to clonal divergence of GABAergic neurons. Immediately after exiting the cell-cycle, GABAergic neurons originating from the same mitotic progenitor diverged into different trajectories, suggesting that differentiation into subtypes is initiated as a lineage-dependent processes at the progenitor cell level.

overall_design: Transcriptomic and barcode-lineage tracing of developing mouse forebrain cell subtypes

first: Rachel

last: Bandler

first: Ilaria

last: Vitali

first: Ryan

last: Delgado


title: Spreading-dependent or independentSir2-mediated gene silencing in budding yeast

city: Chuncheon-si, Gangwon-do

first: soojin

last: yeom

address: 1 Kangwondaehak-gil

institute: Kangwon National University

summary:
purpose: investigation the global insights into Sir2-dependent gene silencing on all silent chromatin regions in budding yeast
Method: RNA-sequencing
Results: the Sir2 binding domain length caused by Sir2 spreading from the chromosomal end is different in each telomere in budding yeast. Expression of most subtelomeric genes increased in the ∆sir2 strain. Some Sir2-regulated subtelomeric genes were positioned within the telomeric Sir2-binding domain, while the others were outside the Sir2-binding domain. In addition, Sir2 was bound to the mating-type loci and rDNA region, and gene expression increased in the ∆sir2 strain.
Conclusion: that S. cerevisiae has two modes of Sir2-mediated gene silencing: One is dependent on chromatin binding and spreading of Sir2, and the other is independent of spreading of Sir2

overall_design: RNA-sequencing and Sir2 ChIP-sequencing was analyzed in FM391 and dsir2 strain

first: Jung-Shin

last: Lee

first: Soojin

last: Yeom

first: Junsoo

last: Oh


title: MAL2 mediates the formation of stable HER2 signaling complexes within lipid raft-rich membrane protrusions in breast cancer cells.

city: Seoul

first: Jungmin

last: Choi

state: Seoul

address: 73, Goryeodae-ro, Seongbuk-gu

department: Department of Biomedical Sciences

institute: Korea University College of Medicine

summary: The lipid raft resident protein, MAL2, has been implicated as contributing to the pathogenesis of several malignancies, including breast cancer, but the underlying mechanism for its effects on tumorigenesis is unknown. Here, we show that MAL2-mediated lipid raft formation leads to HER2 plasma membrane retention and enhanced HER2 signaling in breast cancer cells. We employed proximity ligation assays (PLA) to define physical interactions between HER2 and MAL2 in lipid rafts and super-resolution structured illumination microscopy (SR-SIM imaging) to determine the structural organization of the HER2/Ezrin/NHERF1/PMCA2 protein complex. Formation of this protein complex maintains low intracellular calcium concentrations in the vicinity of the plasma membrane. Importantly, we also observed enhanced HER2-MAL2 protein interactions in lipid rafts in trastuzumab-resistant breast cancer cells. Our findings suggest that MAL2 is crucial for lipid raft formation, HER2 signaling and HER2 membrane stability in breast cancer cells, suggesting MAL2 as a potential therapeutic target.

overall_design: Two replicates from SKBR3 cells.

first: Jaekwang

last: Jeong

first: Jaehun

last: Shin

first: John

last: Wysolmerski


title: Mycobacterium tuberculosis transcriptional response to Pyrazinoic acid

city: Seattle

first: Eliza

last: Peterson

state: WA

address: 401 Terry Ave N

institute: Institute for Systems Biology

summary: The ability of Mycobacterium tuberculosis (Mtb) to adopt heterogeneous physiological states, underlies it’s success in evading the immune system and tolerating antibiotic killing. Drug tolerant phenotypes are a major reason why the tuberculosis (TB) mortality rate is so high, with over 1.8 million deaths annually. To develop new TB therapeutics that better treat the infection (faster and more completely), a systems-level approach is needed to reveal the complexity of network-based adaptations of Mtb. Here, we report the transcriptional response of Mtb to the drug Pyrazinoic acid . We performed transcriptomic sequencing (RNA-seq) on Mtb bacilli at 4, 24, 72 h following exposure to the drug.

overall_design: Cultures of Mycobacterium tuberculosis were grown in 7H9 media supplemented with ADC, 0.2% glycerol and 0.05% tyloxapol in a 37 degrees C  incubator with shaking until mid log phase. Frozen 1 mL stocks of Mtb cells were added to 7H9-rich media and grown until the culture reached an OD600 of ~0.4-0.8. The cells were then diluted to OD600 of 0.05 and added to 7H9-rich media containing Pyrazinoic acid  at the predetermined amounts (0 or 3100 μg/mL,  as indicated in each sample title). Samples were collected at 4 h, 24 h, and 72 h from three biological replicates. The sequence reads that passed quality filters were aligned with Bowtie2 and processed using the R package DuffyNGS.

middle: J

first: Nitin

last: Baliga


title: Persistent Coxsackievirus B1 infection results in extensive changes in the transcriptome of a pancreatic cell line

city: Turku

first: Riitta

last: Lahesmaa

address: Tykistökatu 6 A

country: Finland

institute: Turku Bioscience Centre, University of Turku

summary: Enteroviruses, particularly the group B Coxsackieviruses have been associated with the development of type 1 diabetes. Several CVB serotypes can establish chronic infection in human cells in vivo and in vitro. However, the mechanisms of leading to enterovirus persistency and, possibly, bell-cell autoimmunity are not fully understood. We established a carrier-state persistent infection model in human pancreatic ductal-like cell line PANC-1 using two distinct CVB1 strains and profiled infection-induced changes in cellular transcriptome. In the current study we observed clear changes in the gene expression of factors associated with the pancreatic microenvironment, the secretory pathway and lysosomal biogenesis during persistent CVB1 infections. Moreover, we gained deeper insights into immune-related genes which differed clearly between the two persistent infections. Overall our study reveals extensive transcriptional responses in persistently CVB1 infected pancreatic cell line with strong opposite but also common changes between the two strains.

overall_design: Carrier-state persistent infection in human pancreatic ductal-like cell line PANC-1 cells using two distinct CVB1 strains (ATCC and 10796, 3 replicates in each) was established and compared to non-infected controls (3 replicates) for infection-induced changes in cellular transcriptome.

first: Tanja

last: Buchacher

first: Anni

last: Honkimaa

first: Tommi

last: Välikangas

first: Niina

last: Lietzén

first: Karoliina

last: Hirvonen

first: Jutta

last: Laiho

first: Amir-Babak

last: Sioofy-Khojine

first: Eeva-Liisa

last: Eskelinen

first: Heikki

last: Hyöty

first: Laura

middle: L

last: Elo


title: Mycobacterium tuberculosis transcriptional response to Rifampicin

summary: The ability of Mycobacterium tuberculosis (Mtb) to adopt heterogeneous physiological states, underlies it’s success in evading the immune system and tolerating antibiotic killing. Drug tolerant phenotypes are a major reason why the tuberculosis (TB) mortality rate is so high, with over 1.8 million deaths annually. To develop new TB therapeutics that better treat the infection (faster and more completely), a systems-level approach is needed to reveal the complexity of network-based adaptations of Mtb. Here, we report the transcriptional response of Mtb to the drug Rifampicin. We performed transcriptomic sequencing (RNA-seq) on Mtb bacilli at 4, 24, 72 h following exposure to the drug.

overall_design: Cultures of Mycobacterium tuberculosis were grown in 7H9 media supplemented with ADC, 0.2% glycerol and 0.05% tyloxapol in a 37 degrees C  incubator with shaking until mid log phase. Frozen 1 mL stocks of Mtb cells were added to 7H9-rich media and grown until the culture reached an OD600 of ~0.4-0.8. The cells were then diluted to OD600 of 0.05 and added to 7H9-rich media containing Rifampicin at the predetermined amounts (0, 0.008, 0.02 μg/mL,  as indicated in each sample title). Samples were collected at 4 h, 24 h, and 72 h from three biological replicates. The sequence reads that passed quality filters were aligned with Bowtie2 and processed using the R package DuffyNGS.


title: Mycobacterium tuberculosis transcriptional response to Bedaquiline

summary: The ability of Mycobacterium tuberculosis (Mtb) to adopt heterogeneous physiological states, underlies it’s success in evading the immune system and tolerating antibiotic killing. Drug tolerant phenotypes are a major reason why the tuberculosis (TB) mortality rate is so high, with over 1.8 million deaths annually. To develop new TB therapeutics that better treat the infection (faster and more completely), a systems-level approach is needed to reveal the complexity of network-based adaptations of Mtb. Here, we report the transcriptional response of Mtb to the drug Bedaquiline. We performed transcriptomic sequencing (RNA-seq) on Mtb bacilli at 4, 24, 72 h following exposure to the drug.

overall_design: Cultures of Mycobacterium tuberculosis were grown in 7H9 media supplemented with ADC, 0.2% glycerol and 0.05% tyloxapol in a 37 degrees C  incubator with shaking until mid log phase. Frozen 1 mL stocks of Mtb cells were added to 7H9-rich media and grown until the culture reached an OD600 of ~0.4-0.8. The cells were then diluted to OD600 of 0.05 and added to 7H9-rich media containing Bedaquiline at the predetermined amounts (0, 5.75, 11.5 μg/mL,  as indicated in each sample title). Samples were collected at 4 h, 24 h, and 72 h from three biological replicates. The sequence reads that passed quality filters were aligned with Bowtie2 and processed using the R package DuffyNGS.


title: Mycobacterium tuberculosis transcriptional response to Moxifloxacin

summary: The ability of Mycobacterium tuberculosis (Mtb) to adopt heterogeneous physiological states, underlies it’s success in evading the immune system and tolerating antibiotic killing. Drug tolerant phenotypes are a major reason why the tuberculosis (TB) mortality rate is so high, with over 1.8 million deaths annually. To develop new TB therapeutics that better treat the infection (faster and more completely), a systems-level approach is needed to reveal the complexity of network-based adaptations of Mtb. Here, we report the transcriptional response of Mtb to the drug Moxifloxacin. We performed transcriptomic sequencing (RNA-seq) on Mtb bacilli at 4, 24, 72 h following exposure to the drug.

overall_design: Cultures of Mycobacterium tuberculosis were grown in 7H9 media supplemented with ADC, 0.2% glycerol and 0.05% tyloxapol in a 37 degrees C  incubator with shaking until mid log phase. Frozen 1 mL stocks of Mtb cells were added to 7H9-rich media and grown until the culture reached an OD600 of ~0.4-0.8. The cells were then diluted to OD600 of 0.05 and added to 7H9-rich media containing Moxifloxacin at the predetermined amounts (0, 0.12, 0.3 μg/mL,  as indicated in each sample title). Samples were collected at 4 h, 24 h, and 72 h from three biological replicates. The sequence reads that passed quality filters were aligned with Bowtie2 and processed using the R package DuffyNGS.