title: Gene-expression profiling of osseous and non-osseous DLBCL with the NanoString nCounter technology

city: Leiden

first: Ruben

last: de Groen

address: Albinusdreef 2

department: Hematology

country: Netherlands

institute: Leiden University Medical Center

summary:
Primary bone diffuse large B-cell lymphoma (PB-DLBCL) is a rare extranodal lymphoma subtype. This retrospective study elucidates the currently unknown genetic background of a large clinically well-annotated cohort of DLBCL with osseous localizations (O-DLBCL), including PB-DLBCL. 103 O-DLBCL patients were included and compared with 63 (extra)nodal non-osseous (NO)-DLBCLs with germinal center B-cell phenotype (NO-DLBCL-GCB). Cell-of-origin (COO) was determined by immunohistochemistry and gene-expression-profiling (GEP) using (extended)-NanoString/Lymph2Cx. Mutational profiles were identified with targeted next-generation deep-sequencing, including 52 B-cell lymphoma-relevant genes. O-DLBCLs, including 34 PB-DLBCL, were predominantly classified as GCB-phenotype based on immunohistochemistry (74%) and NanoString analysis (88%). Unsupervised hierarchical clustering of an extended-NanoString/Lymph2Cx demonstrated significantly different GEP-clusters for PB-DLBCL as opposed to NO-DLBCL-GCB (P<0.001). Expression levels of 23 genes of two different targeted GEP-panels, indicated a centrocyte–like phenotype for PB-DLBCL, whereas NO-DLBCL-GCB showed a centroblast-like constitution. PB-DLBCL had significantly more frequent mutations in four GCB-associated genes, i.e. B2M, EZH2, IRF8, and TNFRSF14, compared to NO-DLBCL-GCB (P=0.031, P=0.010, P=0.047, and P=0.003). PB-DLBCL with its corresponding specific mutational profile were significantly associated with a superior overall survival compared to equivalent Ann Arbor limited-stage I/II NO-DLBCL-GCB (P=0.011). This study is the first to demonstrate that PB-DLBCL is characterized by a GCB-phenotype, with a centrocyte-like GEP-pattern and a GCB-associated mutational profile (both involved in immune surveillance) and a favorable prognosis. These novel biology-associated features provide evidence that PB-DLBCL represents a distinct extranodal DLBCL entity and its specific mutational landscape holds potential for targeted therapies (e.g. EZH2-inhibitors).
The NanoString analsyis consisted out of 219 probes for Lymph2Cx classifier (COO), MYC-activity GEP score, CNV-associated GEP signature, consensus clustering, and immune-ratio signature. This custome probeset was used to differentiate GEPs between osseous and non-osseos DLBCL of the GCB-phenotype.

overall_design: In total, 25 primary bone DLBCL (one osseous localization with or without locoregional lymphodenopathy), 6 polyostotic-DLBCL (multiple osseous localizations), 11 Disseminated-DLBCL (Osseous and non-osseous localizations), 20 non-osseous DLBCL with GCB-phenotype (extranodal, nodal, or mixed) were collected for RNA isolation and consecutively analysis with the NanoString nCounter system and the custom probeset.

first: R

middle: L

first: J

middle: P

last: Vermaat


title: Transcriptional organization and regulation of the Pseudomonas putida flagellar system

status: Public on May 05 2021

city: Sevilla

first: Fernando

last: Govantes

state: Sevilla

address: Carretera de Utrera, Km. 1

department: Biología Molecular e Ingeniería Bioquímica

country: Spain

institute: Centro Andaluz de Biología del Desarrollo, Universidad Pablo de Olavide

type: Expression profiling by high throughput sequencing

summary: The entire set of flagellar structural components and flagellar-specific transcriptional regulators, as well as much of the core chemotaxis machinery, is encoded into a >70 kbp cluster in Pseudomonas putida KT2440 genome. We have performed RNA-seq of the wild-type strain in order to identify operon boundaries and promoters location in this cluster.

overall_design: 3 biological replicates of wild-type P. putida KT2440 were grown to stationary phase (OD600=2) in Luria-Bertani (LB) broth at 30ºC and 180 rpm shaking.

first: Marta

last: Pulido-Sánchez

first: Aroa

last: López-Sánchez


title: RNA-seq after DDX41 knockdown in U2OS cells

status: Public on May 04 2021

city: Mainz

first: Petra

last: Beli

address: Ackermannweg 4

country: Germany

institute: Institute of Molecular Biology (IMB)

summary:
Purpose: Investigating transcriptome changes after depletion of DDX41.
Methods: mRNA profiles after DDX41 knockdown compared to control knockdown were generated in 5 biological replicates. Samples were mapped using STAR (v2.7) against hg38 with the Gencode annotation. Reads per gene were counted using featureCounts (v.1.6). The differential expression analysis was performed using Bioconductor (v2.46)/DESeq2 (v1.26). Genes were deemed sign. diff. regulated with an FDR below 1%
Results: We were able to map 32,705 transcripts. Reactome pathway analysis revealed members of the NOTCH and TGFß family to be significantly upregulated when comparing a control knockdown to DDX41 knockdown. In addition, genes in chromatin organization were upregulated.

overall_design: mRNA profiles 48 hours after a control knockdown or DDX41 knockdown in U2OS cells

first: Thorsten

last: Mosler

first: Andrea

last: Voigt

first: Nastasja

last: Kreim


title: RNA-seq analysis of subcutaneus inguinal adipose tissue from Tmem120a fat specific knockout mice (females)

status: Public on Jun 10 2021

city: Edinburgh

first: Shaun

middle: Michael

last: Webb

address: 2.21 Swann Building, Kings Buildings

department: Wellcome Trust Centre for Cell Biology

country: United Kingdom

institute: University of Edinburgh

summary: Tmem120a was shown to be important for adipocytes differentiation. Here we analyze gene expression in suncutaneous adipose tissue form Tmem120a fat-specific knockout mouse on high fat vs low fat diet.

overall_design: Wild type and kncokout female mice were subjected to low fat and high fat diet for 15 weeks. Tissues were collected at the age of 6 months and RNA extracted.

first: Eric

middle: C

last: Schirmer

first: Rafal

last: Czapiewski


title: MapR in U2OS and HCT116 cells and RNA-seq in U2OS

type: Genome binding/occupancy profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: SuperSeries Acute depletion of CTCF directly affects MYC regulation through loss of enhancer–promoter looping

status: Public on May 17 2021

city: Memphis

first: Chunliang

last: Li

state: TN

address: 262 Danny Thomas Place

country: USA

institute: St.Jude Children's Research Hospital


title: Transcriptome of LBR-null mouse kidneys

status: Public on Jun 01 2021

city: Bar Harbor

first: Samuel

last: Beck

state: Maine

address: 159 Old Bar Harbor Rd

department: Davis Center for Regenerative Biology and Medicine

institute: MDI Biological Laboratory

summary: We tested overall gene expression change upon chromatin architecture disruption. RNA-seq was performed using nuclear architecture-disrupted mice carrying a loss-of-function mutation in LBR (Lbric-J/ic-J; LBR-null mice).  LBR is an INM protein that tethers heterochromatin to the nuclear envelope whose level is decreased in various aging contexts.

overall_design: Heterozygous LBR-null mice were recovered from cryopreservation at The Jackson Laboratory (C57BL/6J-Lbric-J/J; stock number 000529). After the breeding and genotyping, three homozygous LBR-null mice (Lbric-J/ic-J) and one WT littermate were sacrificed at age of 4 weeks. When they were sacrificed, the right kidneys of mice were flash-frozen, then pulverized and aliquoted for RNA extraction. The LBR-null kidneys were lysed and homogenized in TRI Reagent (R2050, Zymo Research). Trizol RNA miniprep plus kit (R2070, Zymo Research) was used to isolate total RNA. Library preparation with poly(A) selection and 150 bp paired-end sequencing on an Illumina HiSeq were performed by Genewiz (South Plainfield, NJ).

first: Jun-Yeong

last: Lee

first: Ian

last: Davis


title: ATAC-seq of mice liver upon different diet treatment

status: Public on May 27 2021

city: Los Angeles

first: Zhengyi

last: Zhang

address: Westwood

institute: UCLA

summary: ATAC-seq was performed using mice liver from chow diet, western diet or high fat diet treatment.

overall_design: Male mice were given chow diet, western diet or high fat diet treatment for 4 weeks. ATAC-seq was performed using 75000 nuclei isolated from liver.

first: David

middle: A

last: Salisbury

first: Tamer

last: Sallam


title: Cdk5 drives formation of heterogeneous pancreatic neuroendocrine tumors.

city: Birmingham

first: Nilesh

last: Kumar

state: Alabama

address: 1331 14th Ave S Apt 10

department: Biology

institute: University of Alabama at Birmingham

summary: Pancreatic neuroendocrine tumors (PanNETs) are a heterogeneous population of neoplasms that arise from hormone-secreting islet cells of the pancreas and have increased markedly in incidence over the past four decades. Non-functional PanNETs, which occur more frequently than hormone-secreting tumors, are often not diagnosed until later stages of tumor development and have poorer prognoses. Development of successful therapeutics for PanNETs has been slow, partially due to a lack of diverse animal models for pre-clinical testing. Here, we report development of an inducible, conditional mouse model of PanNETs by using a bitransgenic system for regulated expression of the aberrant activator of Cdk5, p25, specifically in b-islet cells. This model produces a heterogeneous population of PanNETs that includes a subgroup of well-differentiated, non-functional tumors. The utility of this model is enhanced by ability to form tumor-derived allografts. Production of these tumors demonstrates the causative potential of aberrantly active Cdk5 for generation of PanNETs. Further, we show that human PanNETs express Cdk5 pathway components, are dependent on Cdk5 for growth, and share genetic and transcriptional overlap with the INS-p25OE model. This new model of PanNETs will facilitate molecular delineation of Cdk5-dependent PanNETs and the development of new targeted therapeutics.

overall_design: All animal work was performed in accordance with the Animal Welfare Act and the Guide for the Care and Use of Laboratory Animals under UTSW and UAB Institutional Animal Care and Use Committee approved protocols. Bi-transgenic Ins-p25OE animals were generated from crossing of the tetOp-p25GFP strain (The Jackson Laboratory stock # 005706) with the Ins2-rtTA strain (The Jackson Laboratory stock # 008250). Breeders and pups were maintained in the absence of doxycycline to allow for normal development of offspring prior to transgene induction. Upon weaning, at 3-4 weeks of age, offspring were administered 1 mg/L doxycycline via drinking water to induce transgene expression in bi-transgenic animals. Bi-transgenic animals were co-housed with transgene negative littermates. Transgene negative littermates were used as normal controls. All mice were maintained in the C57BL/6 background. Animals were euthanized by CO2 administration and cardiac perfusion.

first: Angela

middle: M

last: Carter

first: Rahul

last: Telange

first: Hayden

last: Bickerton

first: Ronadip

last: Banerjee

first: M

middle: S

last: Mukhtar

first: James

last: Bibb


title: Differentially expressed genes (DEGs) in oviducts of Yun7 and its giant egg mutant Yun7Ge of silkworm, Bombyx mori

status: Public on May 01 2021

city: Ankang

first: Anli

last: Chen

address: Yucai Road

country: China

institute: The Key Sericultural Laboratory of Shaanxi

summary: Yun7Ge (Yun7Ge is represented by Ge in the high-throughput sequencing results) is a giant egg mutant found in the silkworm variety Yun7 (Yun7 is represented by Se in the high-throughput sequencing results). The amount of laid eggs and the hatching rate of Yun7Ge are reduced, which is not conducive to the reproduction. The target gene controlling giant egg trait is located on the Z chromosome (chromosome 1) was determined through genetic analysis. To find mutant gene and explore the relationship between mutant gene and giant egg trait, the differentially expressed genes (DEGs) in the oviducts of Yun7 and Yun7Ge were analyzed by high-throughput sequencing, and two replicates were set for each sample. ∣log 2∣>1, the value of FPKM>100 and the genes were up-regulated or down-regulated in giant eggs of the two replicates as the standard for screening DEGs. A total of 65 DEGs were screened. Among these DEGs, 7 genes were up-regulated and 58 genes were down-regulated in giant eggs. These DEGs were classified according to the chromosome where the genes are located. The results showed that there was only one DEG (PHYHD1) on chromosome Z, and it was almost not expressed in giant eggs. Interestingly, there were 35 DEGs on chromosome 2, including 25 chorion genes, and these 25 genes are all down-regulated. After knocking out the PHYHD1 using CRISPR/Cas9, the chorion genes were significantly down-regulated. These results indicate that the silencing of PHYHD1 leads to the down-regulation of many chorion protein genes, which may be the direct cause of giant eggs.

first: Qiongyan

first: Pengfei

last: Liao

first: Min

last: Liu


title: Genome-wide expression changes in response to the treatment of anti-CD93 in mouse tumor endothelial cells

city: Aurora

first: Yi

last: Sun

state: CO

department: Surgery

institute: UC Denver

summary: We isolated ECs from anti-CD93 antibody treated or control KPC tumor and performed RNA-seq to investigate genome-wide expression changes in response to the treatment of anti-CD93. Many of the genes affected by anti-CD93 were functionally related to cell adhesion, angiogenesis or vasculature development. Gene ontology analysis further confirmed that the transcriptomic changes by anti-CD93 were mainly related to biological pathways of angiogenesis, cell adhesion, or vasculature development.

overall_design: Total RNA was extracted and purified using QIAGEN RNeasy Mini Kit (Cat.74104) from tumor endothelial cells, which were isolated by FACS sorting (CD31+CD45- population) from established subcutaneous KPC tumor after 48 hours of antibody treatment. The mRNA libraries were constructed using Takara SMARTer Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian (Cat. 634411). 150bp paired-end RNA sequencing was performed on Illumina NovaSEQ 6000 platform and the RNA-seq data were generated by the Genomics and Microarray Shared Resource at UCCC.

first: Yuwen

last: Zhu


title: The RNA binding protein MEX3A controls G1/S transition via regulating RB/E2F pathway in clear cell renal cell carcinoma

status: Public on May 25 2021

city: guangzhou

first: yuntan

last: qiu

state: guangdong

address: 107 Yanjiang West Road, Guangzhou City, Guangdong Province

department: Research Center of Medicine

institute: Sun Yat-Sen Memorial Hospital


title: Aromatic dimer dehydrogenases from Novosphingobium aromaticivorans reduce aromatic diketones

status: Public on May 22 2021

city: Madison

first: Alexandra

last: Linz

state: Wisconsin

address: 1552 University Ave

institute: University of Wisconsin-Madison

summary: Aromatic diketones are a major product of formic acid lignin depolymerization. Novosphingobium aromaticivorans can degrade these diketones, but the enzymes used in this process were unknown. We used RNA-Seq to identify aromatic dimer dehydrogenases as potential candidates for the initial reduction of the aromatic G-diketone, then verified this using in vitro enzyme assays.

sample_organism: Novosphingobium aromaticivorans DSM 12444

overall_design: Comparison of G-type aromatic compounds (vanillic acid, vanillin, and ferulic acid), protocatechuic acid, G-diketone, and GP-1 (a reduced intermediate) to a glucose control. All conditions contain equimolar amounts of glucose and the selected aromatic substrates.

first: Yanjun

last: Ma

first: Jose

last: Perez

first: Kevin

last: Myers

first: Wayne

last: Kontur

first: Daniel

middle: R

last: Noguera

first: Timothy

middle: J

last: Donohue


title: Clostridioides difficile strain dependent and independent adaptations to a microaerobic environment

status: Public on May 21 2021

city: Tampa

first: Andy

last: Weiss

state: Florida

address: 4202 East Fowler Avenue, ISA2015

department: Department of Cell Biology, Microbiology and Molecular Biology

institute: University of South Florida

summary: Clostridioides difficile (formerly Clostridium difficile) colonizes the gastrointestinal tract following disruption of the microbiota and can initiate a spectrum of clinical manifestations ranging from asymptomatic to life-threatening colitis. Following antibiotic treatment, luminal oxygen concentrations increase, exposing gut microbes to potentially toxic reactive oxygen species (ROS). Though typically regarded as a strict anaerobe, C. difficile can grow at low oxygen concentrations. How the bacterium adapts to a microaerobic environment and whether those responses to oxygen are conserved amongst strains is not entirely understood. Here, two C. difficile strains (630 and CD196) were cultured in 1.5% oxygen and the transcriptional response was evaluated via RNA-sequencing. During growth in a microaerobic environment, several genes predicted to protect against oxidative stress were upregulated, including ruberythrins and rubredoxins. Genes involved in metal homeostasis were positively correlated with increasing oxygen levels and were also amongst the most differentially transcribed. These included ferrous iron transporters (feo), a zinc transporter (zupT), and predicted siderophore transporters. To directly compare the transcriptional landscape between C. difficile strains, a ‘consensus-genome’ was generated. On the basis of the identified conserved genes, basal transcriptional differences as well as variations in the response to oxygen were evaluated. While several responses were similar between the strains, there were significant differences in the abundance of transcripts for amino acid and carbohydrate metabolism. Furthermore, homologous metal homeostasis genes were similarly transcribed, but the intracellular metal concentrations significantly varied both in an oxygen-dependent and independent manner. Overall, these results indicate that C. difficile adapts to grow in a low oxygen environment through transcriptional changes, though the specific strategy employed varies between strains.

overall_design: Two strains of Clostridioides difficile were grown anaerobically or in microaerobic environment. RNA was isolated from each of the strains and conditions in triplicate and RNA sequencing performed. Transcriptomes and changes in expression patterns were compared across each samples using CLC genomics workbench.

first: Christopher

last: Lopez

first: William

middle: N

last: Beavers

first: Jhoana

last: Rodriguez

first: Eric

last: Skaar


title: RNA profiling of  mouse spinal cord ependymal stem cells in vivo and in vitro in different conditions

status: Public on Apr 28 2021

city: MOntpellier

first: jean-philippe

last: hugnot

state: languedoc

address: IGF INSERM UM 141 rue de la cardonille

country: France

institute: inserm inm u1191

summary:
After spinal cord injury,  ependymal cells considered as stem cells activate, proliferate and differentiate mainly into glial cells.  To understand this further at the molecular level, we performed RNA profiling of these cells in situ using laser-dissection and also when they are cultured as neurospheres in  different conditions (growth, differentiation, dedifferentiation)
Abstract: Numerous vertebrates, including Human, maintain a pool of immature cells in the ependymal region of the adult spinal cord. During injury, these ependymal cells, considered as multipotent stem cells, rapidly activate, proliferate and generate neurons and glial cells in lower vertebrates or mainly glial cells in mammals. The mechanisms underlying this activation are ill-defined and we intended to fill this gap by performing RNA profiling of mouse ependymal region after lesion. Bioinformatics and immunofluorescence identified activation of STAT3 and ERK/MAPK signaling in ependymal cells after injury. This was also accompanied by downregulation of cilia-associated genes and FoxJ1, a central transcription factor of ciliogenesis. Six genes were upregulated more than 20 fold, namely Crym, Ecm1, Ifi202b, Nupr1, Osmr, Rbp1, Thbs2 whereas only one, Acta1 was downregulated to this extent. We explored further the role and regulation in ependymal cells of Osmr, the receptor for oncostatin (OSM). This inflammatory cytokine is specifically expressed by microglia cells and we observed interactions between these cells and ependymal cells in vivo. Using culture of ependymal cells in neurospheres, we found that several cytokines induced OSMR, OSM being the most potent. OSMR is also upregulated by co-culture with OSM-expressing microglial cells. Treatment of spinal cord neural stem cells with OSM decreased their proliferation, upregulate p-Stat3 and reduced their differentiation into oligodendrocyte-lineage Olig1+ cells. These results suggest an important role for microglia-derived oncostatin in the activation and fate of spinal cord ependymal cell.

overall_design: We extracted RNA from laser-microdissected ependymal cells in the normal mouse spinal cord and after 3 days post  injury (needle insertion). We also extracted RNA from neurospheres derived from the ependymal region and placed in media with and without FGF2 and EGF. RNA profilings were performed using affymetrix microarrays

first: Jean-Philippe

last: Hugnot


title: The effect of Mtb aggregation on monocyte-derived macrophage transcription profiles

status: Public on Apr 30 2021

city: Durban

first: Alex

last: Sigal

state: KwaZulu-Natal

address: 719 Umbilo Road, level 5 K-RITH tower building, Nelson R. Mandela Medical School, Umbilo

country: South Africa

institute: Africa Health Research Institute

summary: Mycobacterium tuberculosis (Mtb) bacilli readily aggregate. We previously reported that Mtb aggregates lead to phagocyte death and subsequent efficient replication in the dead infected cells. Here we examined the transcriptional response of human monocyte derived macrophages to phagocytosis of aggregated Mtb relative to phagocytosis of non-aggregated single or multiple bacilli. Infection with aggregated Mtb led to an early upregulation of pro-inflammatory associated genes and enhanced TNF-alpha signaling via the NFkappaB pathway. These pathways were significantly more highly upregulated relative to infection with single or multiple non-aggregated bacilli per cell.

overall_design: We infected monocyte derived macrophages with single, multiple non-aggregated and multiple aggregated Mtb bacilli (3 repeats for each of 4 infection conditions from 5 donors). Total number of samples  =  60, including 15 uninfected controls.

first: Hylton

middle: E

last: Rodel

first: Isabella

last: Ferreira

first: Carly

middle: G

last: Ziegler

middle: K

last: Shalek


title: Developing RT-LAMP Assays for Detection of SARS-CoV-2 in Saliva

status: Public on Apr 22 2021

city: Chicago

first: Xiaowei

last: Wang

state: IL

address: 909 S Wolcott Ave, Rm 5137

institute: University of Illinois at Chicago

summary: Reverse transcription loop-mediated isothermal amplification (RT-LAMP) is a fast and convenient method to amplify and identify the transcripts of a targeted pathogen. We combined bioinformatic and experimental analyses to improve the RT-LAMP assay performance for COVID-19 diagnosis. First, we developed an improved algorithm to design LAMP primers targeting the nucleocapsid (N), membrane (M), and spike (S) genes of SARS-CoV-2. Next, we rigorously validated these new assays for their efficacy and specificity. Further, we demonstrated that multiplexed RT-LAMP assays could directly detect as low as a few copies of SARS-CoV-2 RNA in saliva, without the need of RNA isolation. Importantly, further testing using saliva samples from COVID-19 patients indicated that the new RT-LAMP assays were in total agreement in sensitivity and specificity with standard RT-qPCR. In summary, our new LAMP primer design algorithm along with the validated assays provide a fast and reliable method for the diagnosis of COVID-19 cases.

sample_organism:
Homo sapiens
synthetic construct

platform_organism:
Homo sapiens
synthetic construct

overall_design: Validated RT-LAMP assays could directly detect SARS-CoV-2 RNA in saliva

first: Xin

last: Huang

first: Gongyu

last: Tang


title: Influence of dual-species coaggregation on transcriptional changes of Streptococcus gordonii and Fusobacterium nucleatum subsp. polymorphum

status: Public on May 20 2021

city: Guangzhou

first: Tingjun

last: Liu

address: 56 Lingyuanxi Road

department: Hospital of Stomatology, Guanghua School of Stomatology

institute: Sun Yat-sen University

summary: Interspecies coaggregation promotes transcriptional changes of oral bacteria, contributing to the development of structurally balanced biofilms as well as oral diseases such as periodontitis. Streptococcus gordonii (S. gordonii) is an early colonizer of the oral cavity, and Fusobacterium nucleatum (F. nucleatum) may act as a bridge adhering to both early and late oral colonizers. These two species were commonly detected in healthy and periodontitis-diseased oral sites and could interact with immune cells such as macrophages. However, little research explored how intergeneric coaggregation affected transcriptional changes in S. gordonii and F. nucleatum subsp. polymorphum and how these gene changes might affect both species’ pathogenicity. The present study investigated transcriptional changes of both species in response to dual-species physical association using dual RNA-seq. Results indicated that after 30-min dual-species coaggregation, 148 genes were significantly up-regulated, and 124 genes were significantly down-regulated in S. gordonii. A total of 154 genes were significantly down-regulated, and 10 genes were significantly up-regulated in F. nucleatum subsp. polymorphum. A majority of up-regulated S. gordonii genes were involved in the biosynthesis and export of cell-wall proteins and the pathway of carbohydrate metabolism, and a group of down-regulated S. gordonii genes were associated with fatty acid biosynthesis and peptidoglycan biosynthesis. The transcriptome profiles indicated that the interspecies coaggregation led to a reduced level of DNA repair and lipopolysaccharides virulence in F. nucleatum subsp. polymorphum. The present study revealed that dual-species coaggregation induced a wide array of gene changes in S. gordonii and F. nucleatum subsp. polymorphum, enhancing S. gordonii’s adherence ability and attenuating F. nucleatum subsp. polymorphum's ability to produce LPS.

overall_design: Comparisons between transcriptional profiles of coaggregated S. gordonii (Group CAB) and mono-culture S. gordonii (Group Sg) were made to explore coaggregation-induced DEGs in S. gordonii DL1. Comparisons were also made between coaggregated F. nucleatum subsp. polymorphum (Group CAB) and mono-culture F. nucleatum subsp. polymorphum (Group Fnp) to investigate coaggregation-induced DEGs in F. nucleatum subsp. polymorphum.   Note: Streptococcus gordonii DL1 and Streptococcus gordonii str. Challis substr. CH1 represent the same organism.

first: Lihong

last: Guo


title: Multi-functional barcoding enables high resolution study of clonal dynamics (RNA-seq)

status: Public on Apr 18 2021

city: Austin

first: Amy

last: Brock

state: TX

address: 107 West Dean Keeton St.

institute: University of Texas at Austin

summary: The remarkable evolutionary capacity of cancer poses major challenges to current therapeutic efforts, and results from the vast clonal heterogeneity and ability of individual cancer cells to adapt to diverse selective pressures. More complete mechanistic understanding of the basis of therapeutic resistance has been limited by difficulties in coupling information regarding genetic and epigenetic alterations present within individual cells to their respective transcriptomic and functional outputs. To this end, we developed a novel high-complexity expressed barcode system, ClonMapper, that integrates DNA barcoding with single-cell RNA-sequencing and clonal isolation to characterize thousands of clones within a mixed cancer cell population. In applying this system to the chronic lymphocytic leukemia cell line HG3 in the setting of resistance to fludarabine-based chemotherapy, we discover pretreatment sub-populations with distinct expression profiles (i.e. upregulated Wnt, Notch and CXCR4 signaling) that not only confer distinct treatment survivorship trajectories, but also provide the basis for long-term clonal equilibrium between co-existing clones in the absence of treatment. Characterization of individual clones comprising these sub-populations revealed remarkable genetic heterogeneity and the persistence of unique transcriptomic signatures throughout treatment exposure. These data reveal the diverse clonal characteristics and therapeutic responses of a heterogeneous cancer cell population and highlight the unprecedented resolution that can be achieved using ClonMapper.

overall_design: Bulk RNA-seq of FACS-sorted subpopulations of HG3 cell line

first: Catherine

last: Gutierrez

first: Aziz

last: Al’Khafaji

last: Brenner

first: Kaitlyn

last: Johnson

first: Ziao

last: Lin

first: Russell

last: Durrett

first: Shuqiang

last: Li

first: Salma

last: Parvin

first: Satyen

last: Gohil

first: Binyamin

last: Knisbacher

first: Wandi

last: Zhang

first: Kenneth

last: Livak

first: Donna

last: Neuberg

first: Anthony

last: Letai

first: Gad

last: Getz

last: Wu


title: Multi-functional barcoding enables high resolution study of clonal dynamics

last: Brock


title: Multi-functional barcoding enables high resolution study of clonal dynamics (ATAC-seq)

overall_design: Bulk ATAC-seq of FACS-sorted subpopulations of HG3 cell line

last: Gutierrez

first: Eric


title: CD95 expression in triple negative breast cancer blocks induction of an inflammatory state through differential regulation of NF-κB Signaling

status: Public on Apr 17 2021

city: Limoges

first: Justine

last: Pollet

address: 2, avenue Martin Luther King

institute: CBRS

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: CD95 expression in triple negative breast cancer blocks induction of an inflammatory state through differential regulation of NF-κB Signaling [MDA-MB-231]

summary: CD95L is expressed by tumor-infiltrating lymphocytes to eliminate CD95-expressing tumor cells and thereby CD95 loss by tumor cells is often considered as a consequence of an immunoediting process. Nonetheless CD95 expression is maintained in most triple negative breast cancers (TNBCs), and we recently reported that CD95 loss in TNBC cells triggers the induction of a pro-inflammatory program promoting the recruitment of cytotoxic NK and CD8+ T-cells and impairing tumor growth. Using a comprehensive proteomic approach, we have identified two yet unknown CD95 interaction partners, Kip1 ubiquitination-promoting complex protein 2 (KPC2) and p65. KPC2 contributes to the partial degradation of p105 (NFκB1) and the subsequent generation of p50 homodimers, which transcriptionally represses pro-inflammatory NF-κB-driven gene expression. Mechanistically, KPC2 directly interacts with the C-terminal region of CD95 and links the receptor to RelA (p65) and KPC1, the catalytic subunit of the KPC complex that acts as E3 ubiquitin-protein ligase promoting the partial degradation of p105 into p50. Loss of CD95 in TNBC cells releases KPC2, limiting the formation of the NF-κB inhibitory homodimer complex (p50/p50), promoting NF-κB activation and the production of pro-inflammatory cytokines including CSF1, CSF2, CXCL1 and IL1 members, known to promote recruitment and differentiation of certain adaptive and innate immune effector cells.

overall_design: Total RNAs of 2 CD95-ko (CRISPR/Cas9) TNBC MDA-MB-231 clones and their wild type counterpart were isolated and compared.

first: Jean-Philippe

last: Guégan

first: Christophe

last: Ginestier

first: Emmanuelle

last: Charafe-Jauffret

first: Marcus

last: Peter

first: Patrick

last: Legembre


title: CD95 expression in triple negative breast cancer blocks induction of an inflammatory state through differential regulation of NF-κB Signaling [4T1]

overall_design: 2 CD95-ko (CRISPR/Cas9) TNBC cell lines 4T1 cells and 2 wild type cell lines


title: Next Generation Sequencing Facilitates Quantitative Analysis of  epididymal adipose tissue transcriptomes from mice fed either a control-diet or aWestern-diet for one or five successive generations

status: Public on Apr 15 2021

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

institute: IPMC/CNRS

summary:
Purpose: Successive paternal generations of unhealthy diet induce a fat mass increase. The goal of this study is to compare  epididymal adipose tissue transcriptome profiling (RNA-seq) of mice fed either a control-Diet or a High-Fat-Diet for One or Five successive generations.  The aim of the study is to identify differentially expressed  RNA in epididymal adipose tissue of obese males which might be involved in the exacerbation of  induced by the maintenance of High Fat Diet feeding for 5 successive generations.
Methods: Epididymal adipose tissue mRNA profiles of 18-months-old mice fed either a control-Diet or a Western-Diet for One or Five successive generations were generated by deep sequencing, in triplicate, using Illumina GAIIx. The sequence reads that passed quality filters were quantitavely analyzed. Reads abundance was evaluated for each gene followed by annotation versus mouse GTF by using the featureCounts function.The R package Edger was used in order to normalize the reads and to identify differentially expressed (DE) genes.
Results:  RNA-seq data revealed a specific enrichment in gene related to metabolic syndrome traits in male mice obtained after successive paternal generations of Western-Diet.

overall_design: RNA transcriptomes of epididymal adipose tissue from C57BL6/J mice fed either a control (CD) or Western-diet (WD) for one or five successive generations  were generated by deep sequencing, in triplicate, using Illumina NextSeq 500.

first: Valérie

last: Grandjean

first: Fabrizio

last: Serra

first: Pascal

last: Barbry


title: MicroRNAs as Regulators of Aging Processes in the Cochlear Lateral Wall of the Mouse Inner Ear (mRNA data set)

status: Public on Apr 14 2021

city: Charleston

first: Jeremy

last: Barth

state: SC

address: 173 Ashley Ave, BSB 627

institute: MUSC

summary: Age-related hearing loss (presbycusis) affects more than one-third of Americans over the age of 60, with its prevalence and severity increasing with age. Pathological alterations to the cochlear lateral wall (CLW) disrupting the maintenance of the endocochlear potential (EP) are a major cause of (metabolic) presbycusis. Although molecular mediators of CLW degeneration are largely unknown, several cellular events, including oxidative stress, apoptosis, and inhibition of proliferation, are known to contribute to this dysfunction. Here we have analyzed mRNA and microRNA expression in CLW of young and old mice to profile transcriptional changes that occur as a function of aging. Our results reinforce prior findings about molecular processes and pathways affected by aging and implicate microRNAs that may be involved in influencing these changes.

overall_design: CBA/CaJ young adult (1-3 months) and aged (1.5 years) mice were used in this study. Mice were euthanized and CLWs were micro-dissected from the inner ear. All sample types were prepared in experimental triplicate (n=3).

first: Hainan

last: Lang


title: MicroRNAs as Regulators of Aging Processes in the Cochlear Lateral Wall of the Mouse Inner Ear (microRNA data set)


title: Microglia protect memories formed during sleep deprivation

status: Public on May 12 2021

city: San Francisco

first: Nicholas

last: Gentry

state: California

institute: UCSF

summary: Purpose: To determine the specific effects of 6 hours sleep deprivation after a learning event on the transcriptomes of microglia. Sleep deprivation can generate inflammatory responses in the neuronal environment. In turn, this inflammation increases sleep drive, leading to a rebound in sleep duration. Microglia, a type of support cell found exclusively in the brain, have previously been found to release of inflammatory signals and exhibit altered characteristics in response to sleep deprivation. Together, this suggests microglia may be partially responsible for the brain’s response to sleep deprivation through their inflammatory activity. In this study, we fully and selectively ablated microglia from the mouse brain and assessed resulting sleep, circadian, and sleep deprivation phenotypes. We find microglia are dispensable for both homeostatic sleep and circadian function and the sleep rebound response to sleep deprivation. However, we uncover a phenomenon by which microglia appear to be essential for the protection of synapses and associated memories formed during a period of sleep deprivation, further expanding the list of known functions for microglia in synaptic modulation.

overall_design: Mice were fear conditioned and then sleep deprived for 6 hours for sample extraction. Control mice were fear conditioned and allowed to sleep for 6 hours following training. All samples were extracted from hippocampal dissections using a microglia-specific ribotag IP pulldown method. Mouse line: P2RY12CreER x Rpl22HA RiboTag. Two biological replicates were pooled for each technical replicate to ensure enough sample for sequencing.

middle: W


title: Bone Marrow Endothelial Cell Response to anti-NRP1 infusion

status: Public on Apr 12 2021

first: John

last: Chute

state: CA

address: 615 Charles E Young Drive South OHRC 545

institute: University of California, Los Angeles (UCLA)

summary: Control and Irradiated C57BL/6J mice were treated with the radiomitigator anti-NRP1.   Bone marrow endothelial cells were FACs sorted and analyzed for expression changes at 72 hours.

overall_design: Four treatment groups:  Non-irradiated control, Non-irradiated; anti-NRP1 treatment, Irradiated control, Irradiated + anti-NRP1 treatment

first: Heather

last: Himburg


title: MicroRNAs as Regulators of Aging Processes in the Cochlear Lateral Wall of the Mouse Inner Ear

type:
Expression profiling by array
Non-coding RNA profiling by array

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

platform_organism:
Mus musculus
synthetic construct

overall_design: Refer to individual Series


title: Endometrial luminal epithelium transcriptome during early diestrus defines pregnancy outcome in cattle

status: Public on Apr 07 2021

first: Francisco

last: Peñagaricano

address: 1675 Observatory Drive

department: Animal and Dairy Sciences

summary: Prior to implantation, embryonic development occurs in the confinement of the reproductive tract lumen. The endometrial epithelia determines the uterine luminal composition and, consequently, the molecular milieu available to the pre-implantation embryo. This cow RNA-seq study was especially designed to (i) evaluate the impact that progesterone concentration has on the transcriptome of luminal epithelial cells, and (ii) evaluate the impact that endometrial gene expression has on pregnancy outcome. Luminal epithelial cells were collected using a cytology brush three days prior to embryo transfer, so that the molecular evaluation and the pregnancy outcome, measured 30 days after estrus, pertained to the same reproductive cycle.

overall_design: Forty three multiparous Angus x Brahman cows were enrolled in two rounds (block = 1 or 2) of estrus synchronization for embryo transfer. Estrus was synchronized with (i) the insertion of an intravaginal P4-releasing device and an i.m. injection of GnRH analogue, (ii) seven days later, the P4 device was removed and the animals were treated i.m. with PGF2alpha analogue and fitted with an estrus detection patch, and (iii) three days after P4 device removal, all cows received a dose of GnRH analogue; this was considered experimental day 0. Only cows detected in estrus were used in this study. On D4, cows were subjected to collection of uterine luminal samples for RNA-sequencing using a cytology brush. Also on D4, a blood sample was collected to measure progesterone concentration. On D7, cows received a single in vitro-produced embryo. Finally, pregnancy (yes = 1; no = 0) was evaluated around D30.

first: Mario

last: Binelli


title: Stress ball morphogenesis: how the lizard builds its lung

status: Public on Apr 03 2021

city: Princeton

first: Michael

middle: A.

last: Palmer

state: New Jersey

address: 25 William Street

department: Chemical and Biological Engineering

institute: Princeton University

summary: Lung function is closely coupled to its structural anatomy, which varies greatly across vertebrates. Although architecturally simple, a complex pattern of airflow is thought to be achieved in the lizard lung due to its cavernous central lumen and honeycomb-shaped wall. We find that the wall of the lizard lung is generated from an initially smooth epithelial sheet, which is pushed through holes in a hexagonal smooth muscle meshwork by forces from fluid pressure, similar to a stress ball. By combining next-generation sequencing with timelapse imaging, we reveal that the hexagonal smooth muscle geometry self-assembles in response to circumferential and axial stresses downstream of pressure. A quantitative computational model predicts the pressure-driven changes in epithelial topology, which we replicate using a 3D-printed engineered tissue model of optogenetically-driven smooth muscle contraction. These results reveal the physical principles used to sculpt the unusual architecture of the lizard lung, which could be exploited as a novel strategy to engineer tissues.

overall_design: Lungs were dissected from anole embryos at embryonic day 5 and 6 and dissociated in dispase. Cells were processed in the 10x Genomics Chromium system. The tissues we isolated contain all expected cell types of embryonic lungs, including mesenchymal cells at each stage of differentiation into smooth muscle.

first: Celeste

last: Nelson


title: A novel vitronectin peptide facilitates differentiation of oligodendrocytes from human embryonic stem cells (Synthetic ECM for oligodendrocyte differentiation)

status: Public on May 05 2021

city: Seongbuk-gu

first: Gyu-Bum

last: Yeon

state: Seoul

address: 145, Anam-ro

department: Department of Biodtechnology

country: South Korea

institute: Korea University

summary: Differentiation of oligodendrocytes (ODs) presents a challenge in regenerative medicine due to their role in various neurological diseases associated with dysmyelination and demyelination. Here, we designed a peptide derived from vitronectin (VN) using in silico docking simulation and examined its use as a synthetic substrate to support the differentiation of ODs derived from human embryonic stem cells.

overall_design: 8 samples

first: Won

last: Park

first: Dae-Sung

last: Kim


title: Expression analysis of miRNA involved in radioresistance of oral squamous cell carcinoma.

status: Public on Apr 02 2021

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: 10-1 tebiro 6-chome

country: Japan

institute: Toray Industries,Inc.

summary: Oral squamous cell carcinoma (OSCC) is not significant improved in prognosis despite advancement in treatments. The presence of treatment resistant OSCC is responsible for stagnation in the survival rate. The inter-cellular communications between tumor cells is one of the molecular mechanisms involved in the acquisition of treatment resistance of OSCC. Extracellular vesicles (EVs) and encapsulated miRNAs are important mediators of the inter-cellular communication. We searched for miRNAs involved in radioresistance of OSCC, in order to elucidate the mechanism of acquisition of radioresistance

overall_design: We picked up serum samples from 3 patients who responded to chemoradiotherapy and 4 patients who did not respond to chemoradiotherapy. Also, we extracted EVs from cell cultures of clinically relevant radioresistant (CRR) OSCC cells and non-radiatioresistant OSCC cells (cell-EVs). Then, the expression profile of miRNA in serum samples and cell-EVs was analyzed.

first: Keisuke

last: Yamana

first: Ryoji

last: Yoshida


title: RNA Sequencing of human liver hepatocellular carcinoma cell line HepG2 transcriptomes

status: Public on Apr 01 2021

city: Beijing

first: Hui

last: Yang

address: 7 Panjiayuan Nanli, Room314

department: Department of Toxicology

institute: China National Center for Food Safety Risk Assessment (CFSA)

summary: HepG2 cells were treated with MEHP with/without M1/M2 macrophages for 24h. Then cells were collected and applied to RNA-sequencing. We found that MEHP significantly affected metabolic pathways of HepG2 and co-culturing with M2 macrophages weaked or reversed these effects.

overall_design: mRNA profiles of 4 differentially treated HepG2 cells  were examined by Illumina novaseq 6000.

first: Miao

last: Xu


title: Genome wide mapping of native R-loops using a targeted nuclease approach in U2OS cells after DDX41 siRNA knockdown or ActinomycinD treatment (MapR)

status: Public on May 04 2021

city: Mainz

first: Petra

last: Beli

address: Ackermannweg 4

institute: Institute of Molecular Biology (IMB)

summary:
Purpose: Investigation of genome-wide changes in R-loop levels after knockdown of DDX41 U2OS cells in comparison to a control knockdown.
Method: Concanavalin A-coated beads were activated in Binding Buffer (20 mM Hepes-KOH pH 7.9, 10 mM KCl, 1mM CaCl2, 1 mM MnCl2). 5*105 U2OS cells were washed twice with Wash Buffer (Hepes-NaOH pH7.5, 150 mM NaCl, 0.5 mM Spermidine, 1 mM protease inhibitor) at room temperature and afterwards immobilized on the activated beads in 50 µl Wash Buffer containing 0.05% Digitonin. Either pA-MNase or RHΔ-MNase were added to the cells overnight at 4°C on a rotating wheel. After three washes with Wash Buffer containing 0.05% Digitonin, samples resuspended in 100 µl Dig-Wash-Buffer were equilibrated on ice. Activity of the MNase was triggered by adding 2mM CaCl2 to the samples for 30 minutes. 2x Stop Buffer (68 µl 5M NaCl, 40 µl 0.5 M EDTA, 20 µl 0.2 M EGTA, 10 µl 5% digitonin, 5 µl 10mg/ml RnaseA, 20 pg/ml spike-in Drosophila DNA (Active Motif)) was mixed with the samples to stop the reaction. Chromatin fragments were released by incubating the samples for 20 minutes at 37°C and centrifugation at 16.000×g for 10 minutes at 4°C. Supernatants were incubated at 70°C in the presence of 0.1% SDS and 5 µg proteinase K. Before library preparation, the DNA was recovered by phenol-chloroform extraction
Results: We were able to map R-loop dynamics genome-wide in U2OS cells in biological triplicates. MapR signal was significantly increased around the transcription start site in the absence of DDX41 and decreased after treatment with ActinomycinD.

overall_design: R-loop mapping using MapR after either 6h ActinomycinD treatment with 4 µM or 48h knockdown with a control siRNA or a DDX41 siRNA

first: Thorsten

last: Mosler

first: Francesca

last: Conte

first: Nastasja

last: Kreim


title: RNA resequencing of liver in macrophage-specific-Pparg knockout mice model

summary: Wild type and macrophage-specific-Pparg knockout C57 mice were gavaged with CMC or DEHP for 28 or 90continuous days. At the end of the experiment, livers were harvested for RNA-seq. Data analysis revealed that DEHP induced remarkable changes of lipid metabolic genes in liver, and that loss of Pparg in hepatic macrophages significantly abrogated the elevation of gene overexpression associated with fatty acid metabolism.

overall_design: Liver mRNA profiles of mice models were generated by sequencing, using Illumina Hiseq.

first: Yongning

last: Li


title: Cisplatin-inducible death receptor 5 antisense long non-coding RNA modulates cell cycle and proliferation in HeLa cells

city: Izmir

first: Bünyamin

last: Akgül

state: Urla

address: Gulbahce Campus

department: Molecular Biology and Genetics

country: Turkey

institute: Izmir Institute of Technology

summary: We have performed a transcriptomics study in which we first transfected LNA GapmeRs against DR5-AS lncRNA to silence it in HeLa cells. Total RNA was isolated from control as well as transfected cells and silencing was confirmed by qPCR. Total RNAs were subjected to deep-sequencing to identify differentially expressed mRNAs. We then took advantage of bioinformatic tools to identify which pathways are affected by DR5-AS knock-down.

overall_design: Total RNA was isolated from negative control (Negative GapmeR) and DR5-AS GapmeR treated HeLa cells in triplicate to perform deep-sequencing. Negative GapmeR was used as control and denoted as 160701_SND393_B_L002_GDU-31, 160701_SND393_B_L002_GDU-32 and 160701_SND393_B_L002_GDU-33

first: Dilek

last: Gurer

first: Ipek

last: Erdogan

first: Ulvi

last: Ahmadov

first: Osama

last: Sweef

first: Bunyamin

last: Akgul


title: RNA resequencing of liver in liver-specific-Pparg knockout mice model

summary: Two groups of liver-specific-Pparg knockout C57 mice were gavaged with CMC or DEHP for 28 continuous days. At the end of the experiment, livers were harvested for RNA-seq, we found that metabolism related genes were significantly changed by DEHP in paralell with the PPAR signaling pathway.


title: Podocalyxin governs the barrier function of human endometrial epithelium and critically regulates receptivity for embryo implantation

city: Adelaide

first: James

last: Breen

state: SA

address: 108 North Terrace (Ground Floor)

department: John Curtin School of Medical Research

country: Australia

institute: Australian National University

summary: Embryo implantation is a key step in establishing pregnancy and a major limiting factor in IVF. Implantation requires the endometrium, the inner lining of the uterus, to transform from a non-receptive to a receptive state, to allow embryos to attach to the surface and enter into the tissue. However, the fundamental mechanisms governing receptivity are not well understood. Here we show that transmembrane protein podocalyxin is a major and clinically significant factor regulating human endometrial receptivity. Podocalyxin is expressed in all endometrial epithelial cells in the non-receptive state but is selectively down-regulated in the luminal epithelium at receptivity. We present evidence that podocalyxin critically governs the barrier function of the endometrial epithelium, likely as an intrinsic protective mechanism, rendering it non-receptive to an embryo. In addition, podocalyxin suppresses genes promoting receptivity (eg LIF, CSF1) but stimulates those inhibiting implantation (eg WNT7A, LEFTY2). Down-regulation of podocalyxin in the luminal epithelium, likely mediated by progesterone, selectively converts the endometrial surface to a more adhesive state that facilitates embryo attachment and penetration. Furthermore, inadequate down-regulation of podocalyxin in the endometrial luminal epithelium is associated with poorer implantation rates in IVF. We thus propose that podocalyxin promotes the barrier function of human endometrial epithelial cells and critically regulates receptivity for embryo implantation.

overall_design: RNA-seq (control vs PCX-overexpression) 4 replicates per group

first: Sarah

last: Paule

first: Sophea

last: Heng

first: Nirukshi

last: Samarajeewa

first: Ying

first: Yao

last: Wang

first: Andrew

middle: I

last: Webb

first: Steve

last: Young

first: Bruce

last: Lessey

first: Mary

last: Hull

first: Hilde

last: Van de Velde

first: Maxine

last: Scelwyn

first: Beverley

last: Vollenhoven

first: Luk

last: Rombauts

first: Guiying

last: Nie


title: Gene expression profiling of trout muscle during flesh quality recovery following spawning

status: Public on Mar 29 2021

city: Rennes

first: Aurelie

last: LE CAM

address: Campus de Beaulieu

department: PHASE

institute: INRA

summary: Sexual maturation causes loss of fish muscle mass and deterioration of fillet quality attributes that prevent market purpose. We recently showed that fillet yield and flesh quality are recovered in female trout after spawning. To gain insights into the molecular mechanisms regulating flesh quality recovery we conducted a time-course analysis of large-scale gene expression in trout muscle from spawning to 33 weeks post-spawning. Using an Agilent-based microarray plate-form, we identified about 5500 unique genes that were differentially expressed during the post-spawning period. These genes segregated into four major clusters with distinct temporal expression profile and functional categories. A first cluster containing around 2000 genes down-regulated after 4 weeks after spawning was enriched in genes linked to mitochondrial ATP synthesis, fatty acid catabolism and proteolysis. A second cluster comprising about 1200 genes with early and transient induction between 2 to 8 weeks post-spawning was enriched in genes involved in RNA processing, translation, ribosome biogenesis and protein folding. A third cluster containing about 700 genes up-regulated from 4 weeks post-spawning onwards was enriched in genes encoding ribosomal subunits or regulating translation and cell cycle. At last a fourth cluster which contained about 1000 genes with late up-regulation from 13 weeks post- spawning onwards, was dominated by genes encoding myofibrillar proteins and matricial components and genes involved in glycolysis. On the whole our study indicates that muscle tissue restoration and flesh quality recovery occurring after spawning is mainly associated with anaerobic ATP production, muscle fibre hypertrophic growth, fatty acid metabolism and extracellular matrix remodelling. The generation of the first database of genes associated with post-spawning muscle recovery will allow future mechanistic studies and facilitate identification of genetic markers for fish muscle yield and quality traits.

overall_design: Trout muscle at different post-spawning (PS) timepoints (PS0, PS2, PS4, PS8, PS13, PS16, PS24, and PS33) as well as muscle of control (immature) trout (C0 and C33) were considered for RNA extraction and transcriptome analysis.

first: Y

middle: D

last: Ahongo

first: A

last: Le Cam

first: J

last: Montfort

last: Bugeon

first: F

last: Lefevre

first: P

middle: Y

last: Rescan


title: Gene expression profile of mouse intestinal epithelial cells during homeostasis and villus atrophy at single-cell resolution

status: Public on Mar 27 2021

city: Cleveland

first: Thaddeus

last: Stappenbeck

state: OH

address: 9500 Euclid Ave

department: Inflammation and Immunity

institute: Lerner Research Institute

summary: The epithelium that lines small intestinal villi is critically important for nutrient absorption, defense against pathogens, and mucosal homeostasis. Atrophy or blunting of the villi as a result of epithelial damage is commonly observed in celiac disease, viral gastroenteritis, and various other pathologies. Whereas adaptive responses during epithelial stem cell injury are increasingly well understood, how epithelial tissues, and particularly the intestine, cope with drastic loss of differentiated cells remains unclear. Using an acute model of viral gastroenteritis induced by poly(I:C), we aimed to dissect the cellular adaptations that follow severe intestinal villus injury.

overall_design: Single-cell transcriptional profiling of intestinal epithelial cells was performed using the 10x Genomics platform on two separate sets of samples: (1) wild-type mice during homeostasis and villus atrophy, two replicates each; (2) Yap WT and Yap KO mice during villus atrophy, two replicates each. The villus atrophy samples from the first set were taken just from the damaged region of the gut, whereas the villus atrophy samples from the second set were taken from both the damaged and distal non-damaged region of the gut.

first: Takahiro

last: Ohara

first: Marco

last: Colonna


title: Genome-wide chromosomal associationof Upf1 is linked toPol II transcriptionin Schizosaccharomyces pombe

status: Public on Mar 24 2021

city: Edgebaston

first: Saverio

last: Brogna

state: West midlands

address: School of Biosciences, University of Birmingham

department: School of Biosciences

institute: University of Birmingham

type: Genome binding/occupancy profiling by genome tiling array


title: Genome-wide chromosomal associationof Upf1 is linked toPol II transcriptionin Schizosaccharomyces pombe [ChIP-chip]

summary: Although the RNA helicase Upf1 has hitherto been examined mostly in relation to its cytoplasmic role in nonsense mediated mRNA decay (NMD), here we report high-throughput ChIP data indicating genome-wide association of Upf1 with active genes in Schizosaccharomyces pombe. This association is RNase sensitive and it correlates with Pol II transcription and mRNA expression levels. Changes in Pol II occupancy were detected at only some genes in a Upf1-deficient (upf1strain, however there is an increased Ser2 Pol II signal at all highly transcribed genes examined by ChIP-qPCR. Furthermore, upf1cells are hypersensitive to  the transcription elongation inhibitor 6-azauracil and display Pol II abnormalities suggestive of hyperphosphorylation. A significant proportion of the genes associated with Upf1 in wild-type conditions are also mis-regulated in upf1. These data predict that via association with the nascent transcript Upf1 might influence Pol II phosphorylation and transcription as well as mRNA processing of multiple genes.

overall_design: In total 4 samples; 2 input control files and 2 immunoprecipitation files

first: David

last: Edwards

first: Sandip

last: De


title: Multi-functional barcoding enables high resolution study of clonal dynamics [multiplexed HG3 ClonMapper recalls]

first: Amy

last: Brock

summary: The remarkable evolutionary capacity of cancer poses major challenges to current therapeutic efforts, and results from the vast clonal heterogeneity and ability of individual cancer cells to adapt to diverse selective pressures. More complete mechanistic understanding of the basis of therapeutic resistance has been limited by difficulties in coupling information regarding genetic and epigenetic alterations present within individual cells to their respective transcriptomic and functional outputs. To this end, we developed a novel high-complexity expressed barcode system, ClonMapper, that integrates DNA barcoding with single-cell RNA-sequencing and clonal isolation to characterize thousands of clones within a mixed cancer cell population. In applying this system to the chronic lymphocytic leukemia cell line HG3 in the setting of resistance to fludarabine-based chemotherapy, we discover pretreatment sub-populations with distinct expression profiles (i.e. upregulated Wnt, Notch and CXCR4 signaling) that not only confer distinct treatment survivorship trajectories, but also provide the basis for long-term clonal equilibrium between co-existing clones in the absence of treatment. Characterization of individual clones comprising these sub-populations revealed remarkable genetic heterogeneity and the persistence of unique transcriptomic signatures throughout treatment exposure. These data reveal the diverse clonal characteristics and therapeutic responses of a heterogeneous cancer cell population and highlight the unprecedented resolution that can be achieved using ClonMapper.

overall_design: Single cell RNA-seq of multiplexed HG3 ClonMapper recalls

first: Catherine

last: Gutierrez

first: Aziz

last: Al’Khafaji

first: Eric

last: Brenner

first: Kaitlyn

last: Johnson

first: Ziao

last: Lin

first: Russell

last: Durrett

first: Shuqiang

last: Li

first: Salma

last: Parvin

first: Satyen

last: Gohil

first: Binyamin

last: Knisbacher

first: Wandi

last: Zhang

first: Kenneth

last: Livak

first: Donna

last: Neuberg

first: Anthony

last: Letai

first: Gad

last: Getz

last: Wu


title: Genome-wide chromosomal associationof Upf1 is linked toPol II transcriptionin Schizosaccharomyces pombe [ChIP-Seq]

first: Saverio

last: Brogna

overall_design: 5 samples, 1 control and 4 immunopricipitation samples

first: David

last: Edwards

first: Jianming

last: Wang


title: Gene expression profile of mouse intestinal epithelial cells during homeostasis and villus atrophy

status: Public on Mar 09 2021

first: Thaddeus

last: Stappenbeck

overall_design: Transcriptional profiling of laser-capture microdissected (LCM) epithelial cells from homeostatic and atrophic villi was performed by microarray, each with four replicates.

first: Takahiro

last: Ohara


title: CRISPR Knockout screens for the identification of X-linked genes that drive sex differences in mouse embryonic stem cells

status: Public on Mar 16 2021

city: Berlin

first: Oriana

last: Genolet

address: Ihnestrasse 63

department: OWL Schulz

institute: Max Planck Institute for Molecular Genetics

summary: Dosage imbalance for X-chromosomal genes contributes to sex differences, in particular during early development, when both X chromosomes are active in females. X-encoded inhibitors of the differentiation-promoting MAP kinase (MAPK) signalling pathway slow down development, increase levels of naive pluripotency factors, and decrease MAPK target gene expression. Through a hierarchical CRISPR screening approach in murine embryonic stem cells(mESC) we have comprehensively identified X-linked genes that modulate MAPK signalling, pluripotency factor expression, and differentiation.

overall_design: 1. Primary knockout screen for the identification of genes that modulate MAPK target genes expression using an sgRNA library targeting all X-linked genes (SRE-Elk screen, GeCKOx sgRNA library). 2. Secondary knockout screens on top hits from the primary screen (GeCKOxs sgRNA library) for the identification of genes modulating pluripotency  factor expression (Nanog screen), differentiation kinetics (Esrrb screen) and Mek phosphorylation (pMek screen).

first: Edda

last: Schulz


title: Multi-functional barcoding enables high resolution study of clonal dynamics (scRNA-seq)

status: Public on Apr 18 2021

first: Amy

last: Brock

address: 107 West Dean Keeton St.

institute: University of Texas at Austin

overall_design: Single cell RNA-seq of HG3 cell line with chemotherapy treatment

first: Catherine

last: Gutierrez

first: Aziz

last: Al’Khafaji

first: Eric

last: Brenner

first: Kaitlyn

last: Johnson

first: Ziao

last: Lin

first: Russell

last: Durrett

last: Li


title: Single-cell RNA sequencing reveals B cells-related molecular biomarkers for Alzheimer's Disease

status: Public on Mar 10 2021

city: Chengdu

first: Tinghua

state: China

address: 17, Section 3 South Renmin Road, Institute of Neurological Disease, Department o

institute: Sichuan University

summary:
In the current study, differentially expressed cells subpopulations in PBMCs and differentially expressed genes in B cells were identified with 4 AD patients and 2 controls by single-cell sequencing analysis. Some correlations were found among the Clinical Dementia Rating (CDR) score of AD patients, the number variation of B cells and the expression changes of marker genes as the disease developed. The indispensable function of B cell in AD progression was further validated using AD mice. Our results obtained proof-of-concept identification of possible pathogenic cell types and molecular biomarkers underlying AD, concealing the feasibility of predicting disease biomarkers in certain special types of cells rather than in the overall blood and an AD diagnostic or early warning kit based on this single-cell RNA sequencing is urgently needed.
Here, a single-cell RNA sequencing analysis of PBMCs from 4 AD patients (2 at early stage, 2 at late stage) and 2 normal controls was performed to explore the differential cell subpopulations in PBMCs of AD patients. A significant decrease of B cells in the blood of AD patients was detected and its reduction was closely correlated with the Clinical Dementia Rating (CDR) score of AD patients. Functional experiments were performed in AD mice to verify the role of B cell in AD progression, and the results demonstrated B cell depletion markedly aggravated the cognitive function and augmented the Aβ burden in AD mice. Importantly, 18 genes were found to be specifically up-regulated and 7 genes down-regulated in B cell as the disease proceeded, among which several exhibited close correlation with AD.

overall_design: Single-cell RNA sequencing analysis of PBMCs from 4 AD patients (2 at early stage, 2 at late stage) and 2 normal controls was performed to explore the differential cell subpopulations in PBMCs of AD patients.

first: Liu-Lin

last: Xiong

first: Ruo-Lan

last: Du

first: Lu-Lu

last: Xue

first: Rui-Ze

last: Niu

first: Li

last: Chen

first: Jie

first: Qiao

last: Hu

first: Ya-Xin

last: Tan

first: Chang-Yin

last: Yu

first: Jia

last: Liu

first: Ting-Hua


title: The genetic basis of sex differences in murine embryonic stem cells

first: Oriana

last: Genolet

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

overall_design: Refer to individual Series


status: Public on Mar 01 2021

city: Hørsholm

first: Jens Christian

last: Nielsen

address: Hørsholm Kongevej

country: Denmark

institute: Gubra

summary:
Therapeutic PYY/GLP-1 receptor co-agonism in obese-diabetic mice synergistically activates discrete hypothalamic and brainstem neuronal circuitries for weight reduction, increased insulin sensitization, recovery of pancreatic ß-cell function and diabetes remission.
GLP1-R agonism (IP118) and PYY-2R agonism (PY115) in combination yield surprising synergistic effects on energy homeostasis in mammals.  To better understand the genesis of these effects, RNAseq profiling was performed on key brain regions following an acute dose of IP118+PY115.

overall_design: Gene expression profiles of brain regions in mice four hours following IP injection of a single acute systemic administration of IP118/PY115 or vehicle

first: Brandon

middle: B

last: Boland

first: Jens

first: Christopher

last: Rhodes

first: Joseph

last: Grimsby


title: Gene expression profiles of larval zebrafish under homeostatic conditions, after induced epithelial cell loss, and during tissue repair.

city: Houston

first: George

last: Eisenhoffer

address: 1515 Holcombe Blvd., Unit 1010

department: Genetics

institute: The University of Texas MD Anderson Cancer Center

summary: Formation and maintenance of an epithelial barrier is essential for defense against fungal invasion and other noxious stimuli and is fundamental to the survival of all animals. As part of homeostatic repair mechanisms, mucosal tissues eliminate damaged epithelial cells while trying to preserve barrier function. Compromised epithelial integrity following trauma is a common mode of infection, and therefore, enhancing mucosal repair may help to mitigate opportunistic invasion. However, the technical challenges to efficiently manipulate and monitor mucosal injury in vivo has thus far prevented a detailed characterization and therapeutic exploitation of key epithelial repair mechanisms. Here we establish a high-throughput mucosal injury and repair model by inducible loss of epithelial cells in larval zebrafish. Transcriptional profiling identified a significant upregulation of the epidermal growth factor receptor ligand epigen (EPGN) upon tissue damage, and we found treatment with recombinant human EPGN suppressed epithelial cell loss to maintain barrier integrity in the face of damage. This study provides key insights into the mechanisms regulating epithelial cell loss during mucosal injury and identifies key pathways associated with rapid restoration of barrier function and epithelial tissue integrity.

overall_design: Examine gene expression in larval zebrafish under homeostatic conditions, after induced epithelial cell loss, and during repair of the tissue to restore barrier integrity. The experiment was performed in triplicate for each condition.

middle: T

first: Oscar

last: Ruiz


title: Neutralizing antibodies against SARS-CoV-2 require intact Fc effector functions and monocytes  for optimal therapeutic activity

city: St. Louis

first: Jinsheng

state: MO

address: 660 S. Euclid Ave.

institute: Washington University School of Medicine

summary: SARS-CoV-2 has spread globally and caused the COVID-19 pandemic. Although passively delivered neutralizing antibodies against SARS-CoV-2 are in clinical trials, their mechanism of action in vivo is incompletely understood. Here, we define correlates of protection of neutralizing human monoclonal antibodies (mAbs) in SARS-CoV-2-infected mice. Whereas Fc effector functions are fully dispensable when mAbs are administered as prophylaxis, they are required for optimal protection as therapy. When given after infection, intact but not LALA-PG loss of Fc effector function variant mAbs reduce SARS-CoV-2 burden and lung disease in mice and hamsters. Fc engagement of neutralizing antibodies mitigates inflammation and improves respiratory mechanics, and transcriptional profiling suggests these phenotypes are associated with diminished innate immune signaling and enhanced tissue repair. Immune cell depletions establish that neutralizing mAbs require monocytes for therapeutic efficacy. Our study demonstrates that therapeutic neutralizing mAbs require Fc effector functions to reduce SARS-CoV-2 infection and modulate protective immune responses.

overall_design: RNA sequencing analysis was performed with the lung homogenates of naive K18-hACE2 mice or mice infected with SARS-CoV-2 infection at 8 dpi. At 1 (D+1) or 2 (D+2) dpi, mice were given a single 200 ug dose of COV2-2050 or COV2-2050 LALA-PG via an intraperitoneal injection. Note: data for 4 of 6 naive samples were uploaded previously under GSE154104 and labeled as D0 group.

first: Emma

last: Winkler

first: Pavlo

last: Gilchuk

first: Adam

middle: L

last: Bailey

first: Rita

first: James

last: Case

first: Robert

middle: H

last: Carnahan

first: Tamarand

last: Darling

first: Adrianus

middle: C

last: Boon

first: Matthias

last: Mack

first: Richard

last: Head

first: Theodore

last: Ross

last: Crowe Jr

first: Michael

last: Diamond


title: CUT&Tag on H3K4me3, H3K27ac, H3K4me1, H3K9me3, H3K27me3, H3K36me3 and H2AK119ub in TX1072 XXΔXic and XO mESCs during differentiation

status: Public on Mar 04 2021

first: Till

last: Schwämmle

state: Berlin

department: Otto-Warburg-Laboratory

summary: Developmental genes are controlled by complex cis-regulatory landscapes that integrate multiple signals to ensure the correct spatio-temporal expression pattern. To investigate the underlying regulatory principles, we use the Xist locus as a model, which encodes the master regulator of X-chromosome inactivation. Xist is upregulated at the primed pluripotent state in a female-specific manner, thus integrating developmental cues and X-dosage information. It remains poorly understood how these signals are decoded by the ~800kb genomic region that controls Xist. While a series of repressive cis-regulatory elements have been identified, the distal enhancers that activate Xist transcription remain largely unknown. Here we use CUT&Tag on several histone modifications to profile the chromatin landscape of the X inactivation center at the onset of random X-chromosome inactivation using an endogenous cell model of the inactive (TX 1072 XXΔXic) and active (TX 1072 XO) X chromosome.

overall_design: CUT&Tag targeting H3K4me3, H3K27ac, H3K4me1, H3K9me3, H3K27me3, H3K36me3 and H2AK119ub was performed in the TX1072 XXΔXic (XX line carrying a heterozygous deletion of the Xic: chrX:103182701-103955531 on the B6 allele) and TX1072 XO (X chromosome from Cast background) cell lines. The data was collected in replicates from cells in 2i+LIF medium (day 0), as well at day 2 and day 4 of differentiation (via 2i+LIF-withdrawal).

first: Rutger

last: Gjaltema

first: Pauline

last: Kautz

last: Robson

last: Schöpflin

first: Liat

last: Ravid

first: Lennart

last: Brandenburg

first: Ilona

last: Dunkel

first: Carolina

last: Vechiatto

first: Evgenia

last: Ntini

first: Verena

last: Mutzel

first: Vera

last: Schmiedel

first: Annalisa

last: Marsico

first: Stefan

last: Mundlos

first: Edda

last: Schulz


title: The CLASSY family controls tissue-specific DNA methylation patterns in Arabidopsis [ChIP-seq]

city: La Jolla

first: Julie

middle: Ann

last: Law

address: 10010 North Torrey Pines Rd

department: PLANT MOLECULAR AND CELLULAR BIOLOGY LABORATORY

institute: The Salk Institute for Biological Studies

summary: DNA methylation alters the epigenetic landscape of the genome, plays critical roles in regulating gene expression, and ensures transposon silencing. As evidenced by the numerous defects associated with aberrant DNA methylation landscapes, establishing proper tissue-specific methylation patterns is critical. Yet, how such differences arise remains a largely open question in both plants and animals. Here we demonstrate that four CLASSY proteins (CLSY1-4), which are differentially expressed during plant development, play major roles in controlling tissue-specific DNA methylation patterns. Depending on the tissue, the genetic requirements for specific CLSYs differ significantly and on a global scale, certain clsy mutants are sufficient to largely shift the epigenetic landscape between tissues. Together, these findings not only reveal substantial epigenetic diversity between tissues, but assign these changes to specific CLSY proteins, revealing how locus-specific targeting combined with tissue-specific expression enables the CLSYs to generate epigenetic diversity during plant development.

overall_design: 3 ChIP-seq libraries were sequenced.

first: Ming

last: Zhou

middle: A


title: RNA sequencing of Dusp9 and Klhl13 mutants in 1.8 female mouse embryonic stem cells (mESCs)

first: Oriana

last: Genolet

summary: Dosage imbalance for X-chromosomal genes contributes to sex differences, in particular during early development, when both X chromosomes are active in females. X-encoded inhibitors of the differentiation-promoting MAP kinase (MAPK) signalling pathway slow down development, increase levels of naive pluripotency factors, and decrease MAPK target gene expression. Through a hierarchical CRISPR screening approach in murine embryonic stem cells(mESC) we have comprehensively identified X-linked genes that modulate MAPK signalling, pluripotency factor expression, and differentiation. Here, we carried out transcriptional profiling of the two top hits, Dusp9 and Klhl13, and observe that Klhl13 contributes more to the X-dosage induced transcriptome changes than Dusp9, and that a combined effect of both can explain about 50% of the observed sex differences.

overall_design: RNA-seq of 1.8 wild type cells together with Dusp9 and Klhl13 mutant cell lines


title: Hepatic miR20b promotes nonalcholic fatty liver diseases by targeting PPARα

city: Eonyang-eup, Ulju-gun

first: Sounkou

last: Kim

state: Ulsan

department: Department of Biological Science

institute: Ulsan National Institute of Science and Technology

summary: Nuclear receptors (NRs) play a crucial role in non-alcoholic fatty liver disease (NAFLD) and have been widely studied(Tran et al. 2018). However, the underlying mechanisms of NR regulation remain largely unclear. Here, we show that miR-20b plays a key role in modulating PPARα, a master regulator of nutrient metabolism and energy homeostasis in the pathogenesis of fatty liver(Wahli et al. 1995; Dongiovanni and Valenti 2013). Using network analysis and RNA-seq to determine the correlation between NRs and microRNA in NAFLD patients, we revealed that miR-20b directly targets PPARα. The expression of miR-20b was remarkably upregulated in free fatty acid (FA)-treated hepatocytes and the livers of both obesity-induced mice and NAFLD patients. Overexpression of miR-20b dramatically increased hepatic lipid accumulation and plasma triglyceride levels. Furthermore, miR-20b significantly reduced fatty acid oxidation and mitochondrial biogenesis by directly targeting PPARα. Fenofibrate, a specific agonist of PPARα, lost its ability to ameliorate hepatic steatosis in miR-20b-introduced mice. Finally, inhibition of miR-20b dramatically increased FA oxidation and uptake, resulting in improved insulin sensitivity and a decrease in NAFLD progression. Taken together, these results demonstrate that the novel miR-20b directly targets PPARα, plays a significant role in hepatic lipid metabolism, and presents an opportunity for the development of novel therapeutics for NAFLD.

overall_design: Analysis of differential expression (DE) caused by over expression (mimic) of hsa-miR-20b

first: Yo Han

last: Lee

first: Hyun-Jun

last: Jang


title: RNA sequencing of 1.8 female mouse embryonic stem cells (mESCs) and XO subclones.

overall_design: RNA-seq of 1.8 wild type cells together with their XO subclones

first: Zeba

last: Sultana


title: Investigation of miRNAs from PBMC in Kangal type Akkaraman sheep with small RNA-seq

status: Public on Mar 11 2021

city: Konya

first: gonca

last: sonmez

address: Akademi Mah

institute: selcuk university

summary:
Purpose: Aim of this study was to determine the miRNAs associated with average daily gain in Kangal Akkaraman lambs. Depending on the average daily gain, two groups were formed as low average daily gain (LDG) and high average daily gain (HDG).
Methods: Peripheral blood mononuclear cells (pbmc) were separated from blood samples obtained from lambs and RNA was isolated with TRI Reagent (Sigma). Isolated total RNAs from LDG (n = 17) and HDG (n = 21) groups were pooled. miRNA libraries (LDG and HDG groups) were prepared with NEBNext® Multiplex Small RNA Library Prep Set for Illumina® (NEB, USA.) and sequenced with Illumina Novaseq. Readings were mapped with the Bowtie program using the Oar_v3.1 sheep reference genome. Differential expression analysis of the two groups was performed using the DESeq R package (1.8.3).
Results: Using an optimized data analysis workflow, we mapped about 18 million sequence reads in HDG and 21 million sequence reads n LDG samples to the ovis aries genome (oar_v3.1). In total, 129 known miRNAs were identified, 134 novel miRNAs were predicted, and 40 differentially expressed miRNAs were found between the groups.
Conclusions: Our study represents the first detailed analysis of Kangal type Akkaraman sheep PBMC miRNAs with RNA-seq technology. The obtained sequence reads would provide data for futher breeding studies related to average daily gain in Kangal Akkraman sheep.

overall_design: Examination of PBMC miRNA expression in low average daily gain and high average daily gain Kangal Akkaraman lambs.

first: Gonca

last: Sonmez

first: Seref

last: Inal


title: The CLASSY family controls tissue-specific DNA methylation patterns in Arabidopsis [RNA-seq]

overall_design: 84 RNA-seq libraries were sequenced.


title: Comparative analysis among different species reveals that the androgen receptor regulates chicken follicle selection through species-specific genes related to follicle development

status: Public on Feb 28 2021

city: Wuhan

first: Ying

last: Huang

state: Hubei

address: No.1,Shizishan Street · Hongshan District · Wuhan · Hubei Province

institute: Huazhong Agricutural University


title: The CLASSY family controls tissue-specific DNA methylation patterns in Arabidopsis

type: Methylation profiling by high throughput sequencing

type: Non-coding RNA profiling by high throughput sequencing


title: The CLASSY family controls tissue-specific DNA methylation patterns in Arabidopsis [BiSulfite-seq]

overall_design: 36 methylC-seq libraries were sequenced.


title: Comparative analysis among different species reveals that androgen receptor is a core transcriptional factor regulating the chicken follicular selection and ovulation [RNA-Seq]

summary: The differences of reproductive processes at molecular levels between the viviparous and oviparous animals are still unclear, and in the oviparous animal, the locations to synthetize sex hormones and also the trends to enrich sex hormones during follicle development are different from that of viviparous animals. To explore the commonalities (key factors for follicular development) and individualities (factors that cause differences among species) in the follicular development of viviparous and oviparous animals, we compared the similarities and differences in follicle development between viviparous and oviparous animals in terms of transcriptome and super-enhancer-based transcriptional regulation, using humans, bovines, and mice as representatives of viviparous animals and chickens, for oviparous animals. It was found that follicle development in molecular terms tended to be more conservative between viviparous and oviparous animals. Estrogen receptors and androgen receptors occupied central positions in the transcriptional regulatory networks of viviparous and oviparous animals respectively, which may be related with differences in the synthesis and secretion of sex hormones between oviparous and viviparous animals. The role of androgen receptors in chicken follicle development was verified through cell level and field experiments. Our study would facilitate to extend existing results of follicle development in viviparous animals to oviparous animals, and our results emphasized the importance of the androgen receptor in chicken follicle development. Comparative analysis among different species in follicle development will help us to gain insight on the mechanisms of follicle development.

overall_design: Tissues in three follicle development stages (syf 6mm, F5, F1) from granulosa cell layer and theca cell layer from hens (3 biological replicates) of blank (NC), 15 mg bicalutamide (bic 15 mg), and 100 mg mestanolone (mes 100 mg) were sent to Novogene Co., Ltd. (Beijing, China) for RNA extraction, library construction, and sequencing. All samples performed paired-end 150 bp sequencing on the Illumina Nova platform.

first: Yanzhang

last: Gong


title: Comparative analysis among different species reveals that androgen receptor is a core transcriptional factor regulating the chicken follicular selection and ovulation [ChIP-Seq]

overall_design: Examination of histone modification H3K27ac (Abcam, ab4729) in granulosa cells in prehierarchical and preovulatory follicles of chickens.


status: Public on Feb 25 2021

city: Iruma-gun

first: Toshiaki

last: Miyazaki

state: Saitama

address: 38 Morohongo, Moroyama-machi

department: Social Medicine

institute: Saitama Medical University

summary: Among the examined genes, none of genes associated with high frequency microsatellite instability (MSI-H) in the panel was mutated (MLH1, MSH2, POLE). In addition, clustering analyses based on RNA-seq data indicated that expression profiles of the spheroids were more similar to colon cancer cells in the CMS-2 and CMS-3 category than those in the MSI-H-related CMS-1. These data suggested that all the examined spheroids were associated with microsatellite stable (MSS) phenotype.

overall_design: Expression profiles of the spheroids derived from colon cancer patients was measured.


title: Alternative Developmental and Transcriptomic Responses to Host Plant Water Stress in a Butterfly metapopulation

city: University of Helsinki

first: Aapo

last: Kahilainen

address: P.O. Box 65

department: Research Centre for Ecological Change

country: Finland

institute: University of Helsinki

summary: Predicting how climate change affects biotic interactions and their evolution poses a challenge. Plant-insect herbivore interactions are particularly sensitive to climate change, as climate-induced changes in plant quality cascade into the performance of insect herbivores. Whereas the immediate survival of herbivore individuals depends on plastic responses to climate change induced nutritional stress, long-term population persistence via evolutionary adaptation requires genetic variation for these responses. In order to assess the prospects for population persistence under climate change, it is therefore crucial to characterise response mechanisms to climate change induced stressors, and quantify their variability in natural populations. Here, we test developmental and transcriptomic responses to water limitation induced host plant quality change in a Glanville fritillary butterfly (Melitaea cinxia) metapopulation. We combine nuclear magnetic resonance spectroscopy on the plant metabolome, larval developmental assays and an RNA seq analysis of the larval transcriptome. We observed that responses to feeding on water limited plants, in which amino acids and aromatic compounds are enriched, showed marked intrapopulation variation, with individuals of some families performing better on control and others on water limited plants. The transcriptomic responses were concordant with the developmental responses: Families exhibiting opposite developmental responses also produced opposite transcriptomic responses, e.g. in growth associated intracellular signalling. The opposite developmental and transcriptomic responses are associated with between families differences in organic compound catabolism and storage protein production. The results reveal heritable intrapopulation variability in plasticity, suggesting potential for evolutionary responses to drought-induced changes in host plant quality in the Finnish M. cinxia metapopulation.

overall_design: We fed Melitaea cinxia pre-diapause larvae representing various genetic backgrounds with control watered and water limited Plantago lanceolata and examined their developmental and transcriptomic responses to host plant water limitation.

first: Vicencio

last: Oostra

first: Panu

last: Somervuo

first: Guillaume

last: Minard

first: Marjo

last: Saastamoinen


title: Expression analysis of human stage Ta and stage T1 bladder tumours

status: Public on Feb 22 2021

city: Leeds

first: Margaret

last: Knowles

state: West Yorkshire

address: Becket Street

department: LICAP

institute: University of Leeds

summary:
Expression data derived from this analysis was used for transcriptional subtyping and to compare expression features of genomic subgroups
In this dataset, we include the expression data obtained from  113 stage Ta and 104 stage T1 bladder tumours

overall_design: 217 bladder tumour samples were analysed on the Affymetrix HTA 2.0 platform

first: Carolyn

last: Hurst


title: RNA-seq analysis of uveal melanoma cells and biopsy samples treated with FR900359

status: Public on Feb 15 2021

city: Saint Louis

first: Michael

last: Onken

address: 660 S. Euclid Ave

department: Biochemistry & Molecular Biophysics

summary: Uveal melanoma cell lines and short-term cultures of human uveal melanoma cells from biopsy samples were treated with 100 nM FR900359 or vehicle. RNA-seq was performed.

overall_design: Cell line samples were collected from two independent experiments for each. Human biopsy samples were divided immediately after collection and cultured in medium containing vehicle or FR900359.

first: Kendall

middle: J

last: Blumer


title: Genome wide mapping of DNA lesions by Repair Assisted Damage Detection sequencing – RADD-Seq

status: Public on Feb 17 2021

city: Tel Aviv

first: Yuval

last: Ebenstein

state: HaMerkaz (Central)

address: Ramat Aviv

country: Israel

institute: Tel Aviv University

summary: This method, termed Repair Assisted Damage Detection sequencing (RADD-seq), uses repair enzymes to excise the DNA lesions leaving a single-strand gap. The damage sites are then repaired in-vitro with biotinylated nucleotides, followed by DNA fragmentation, immunoprecipitation and sequencing. Reads are mapped back to the reference genome, indicating the locations of damage sites.

overall_design: RADD-seq analysis of damage and repaired samples, as well as an input DNA sample; Final concentration of 50 mM KBrO3 was added to culture medium for one hour. Cells were washed with PBS twice, and genomic DNA was immediately extracted (for damage samples). Alternatively,  cell medium was replaced, and cells were allowed to repair for one hour at 37 °C with 5% CO2 before DNA extraction (for repaired samples). Cells were allowed to grow up to a week post KBrO3 treatment, to validate their viability.

first: Noa

last: Gilat

first: Dena

last: Fridman

first: Hila

last: Sharim

first: Sapir

last: Margalit

first: Natalie

middle: R

last: Gassman

first: Yael

last: Michaeli


title: Single-cell RNAseq analysis of mesenchymal cells in the periodontal space of the murine molar

first: Noriaki

last: Ono

state: Texas

department: School of Dentistry

institute: University of Texas Health Science Center at Houston

summary: A single cell transcriptional profile of mesenchymal cells in the periodontal space of the murine molar marked by 2.3kb Col1a1-GFP or PTHrP-creER-lineage marked cells at postnatal day 25 (P25)

overall_design: GFP+, tdTomato+ and GFP+tdTomato+ cells were FACS-isolated from postnatal day 25 (P25) periodontal space of Col1a1(2.3kb)-GFP; PTHrP-creER; R26R-tdTomato mice (tamoxifen at P3). 15,000 cells were loaded onto 10X Genomic Chromium Single Cell Expression Solution version 3 platform. cDNA was sequenced by Illumina HiSeq 4000


title: A positive feedback circuit between mTORC1 signaling and cathelicidin promotes skin inflammation in rosacea [mouse]

status: Public on Feb 08 2021

city: Changsha

first: Zhili

last: Deng

address: Xiangya Hospital, Central South University, Xiangya Road, Changsha, Hunan 410008, China.

department: Department of Dermatology

summary: The goal of this study is to figure out the role of mTORC1 signaling in the pathogenesis of rosacea by comparing rosacea mouse model skin lesion transcriptome profiling (RNA-seq) to that of control mouse skin treated with or without rapamycin.

overall_design: Examination of transcriptome profiling via RNA-seq in skin from LL37 or control mice treated with or without rapamycin.

first: Ji

last: Li


title: Effects of Mettl3 and Alkbh5 knockdown on small RNA export into EVs

status: Public on Feb 12 2021

city: Nashville

first: James

middle: G.

last: Patton

state: TN

address: 2325 Stevenson Center

department: Department of Biological Sciences

institute: Vanderbilt University

summary: Understanding the functional role of RNA modifications and to what extent they might regulate mature miRNA function and their secretion in extracellular vesicles (EVs) is unknown.  Analysis of RNA content across a variety of EVs has shown differential miRNA enrichment when compared to parental cell expression patterns.  Whether this is due to differential stability, specific regulation of miRNA export, or other mechanisms is unclear.  Here, we tested whether RNA base modifications and recognition of those modifications might underlie differential miRNA export into EVs derived from KRAS mutant cell lines.  We found that decreased levels of Mettl3, a writer of N6-methyladenosine (m6A) modification, altered extracellular transfer of miRNAs containing consensus sequences for m6A.  Further, EVs prepared from cells expressing shRNAs against Mettl3 were incapable of conferring colony growth in 3D to wild type KRAS cells.  Our data indicate that m6A modification plays an important role in miRNA export to EVs.

overall_design: RNAseq analysis of parental and knockdown cellular and EV RNA samples. There were 18 total samples, 9 cellular and 9 EV.

first: Jessica

last: Abner

first: Xiao

last: Liu

first: Qi


title: Distal and proximal cis-regulatory elements sense X-dosage and developmental state at the Xist locus

first: Till

last: Schwämmle

summary: Developmental genes such as Xist, the master regulator of X-chromosome inactivation (XCI), are controlled by complex cis-regulatory landscapes, which decode multiple signals to establish specific spatio-temporal expression patterns. Xist integrates information on X-chromosomal dosage and developmental stage to trigger XCI at the primed pluripotent state in females only. Through a pooled CRISPR interference screen in differentiating mouse embryonic stem cells, we identify functional enhancer elements of Xist during the onset of random XCI. By quantifying how enhancer activity is modulated by X-dosage and differentiation, we find that X-dosage controls the promoter-proximal region in a binary switch-like manner. By contrast, differentiation cues activate a series of distal elements and bring them into closer spatial proximity of the Xist promoter. The strongest distal element is part of an enhancer cluster ~200 kb upstream of the Xist gene which is associated with a previously unannotated Xist-enhancing regulatory transcript, we named Xert. Developmental cues and X-dosage are thus decoded by distinct regulatory regions, which cooperate to ensure female-specific Xist upregulation at the correct developmental time. Our study is the first step to disentangle how multiple, functionally distinct regulatory regions interact to generate complex expression patterns in mammals.

sample_organism:
Mus musculus
synthetic construct

overall_design: Refer to individual Series


title: LAMP2 Cardiomyopathy: The Consequences of Impaired Autophagy in the Mouse Heart

status: Public on Feb 14 2021

city: Boston

first: Joshua

middle: M

last: Gorham

state: MA

address: 77 Ave Louis Pasteur, NRB 256

institute: Harvard Medical School

summary: Bulk RNAseq analyses of wild type and Lamp 2 deficient mice, which model Danon disease.

overall_design: PolyA mRNA was isolated from the cardiac left ventricle of mutant and wildtype mice and analyzed by RNAseq.

first: Ronny

last: Alcalai

first: Michael

last: Arad

first: J

middle: G

last: Seidman


title: The involvement of Mycobacterium type III-A CRISPR-Cas system in oxidative stress and intracellular fitness

status: Public on Feb 05 2021

city: Guang zhou

first: siyuan

last: feng

address: 74 zhongshan 2nd road

institute: Sun Yat-Sen University

summary: Previous studies suggest that type I and type II CRISPR-Cas systems were employed to evade host immunity by targeting interference of bacteria’s own genes. Although Mycobacterium bovis (M. bovis) and Mycobacterium tuberculosis (M. tuberculosis) possess integrated type III-A CRISPR-Cas system, its role in mycobacteria remains obscure. Here, we observed that seven cas genes (csm2~6, cas10, cas6) were significantly upregulated under oxidative stress treatment. To explore the function of type III-A CRSIRP-Cas system, Total CRISPR system (TCR) mutant strain was generated in M. bovis Bacille Calmette-Guérin (BCG). Deletion of TCR results in increased sensitivity in response to H2O2 and reduced cell envelope integrity. By using RNA-Seq, 590 differential expression genes were found in mutant for TCR, of which 220 genes were upregulated and 370 genes were downregulated, indicating an important role of TCR in controlling gene expression in mycobacteria. Consistently, disrupting TCR results in poor intracellular survival in vivo and in vitro. Moreover, we showed for the first time that TCR contributed to the regulation of regulatory T cell population, supporting a role of TCR in modulating host immunity. These observations demonstrate that type III-A CRISPR-Cas system as an important factor for intracellular survival and host immunoregulation in mycobacteria, may be a potential target for therapy.

sample_organism: Mycobacterium tuberculosis variant bovis

overall_design: For RNA-seq: Examination of 2 strains (Wild type VS ΔTCR).

first: Siyuan

last: Feng


title: Enhancers predominantly control transcription initiation [mNET-seq]

status: Public on Feb 03 2021

city: Oxford

first: Martin

middle: Stephen Charles

last: Larke

state: Oxfordshire

address: Headley Way

department: MRC Weatherall Institute of Molecular Medicine

institute: University of Oxford

summary: Gene transcription occurs via a cycle of linked events including initiation, promoter proximal pausing and elongation of RNA polymerase II (Pol 2).  A key question is how do transcriptional enhancers influence these events to control gene expression? Here we have used a new approach to quantify transcriptional initiation and pausing in-vivo, while simultaneously identifying transcription start sites (TSSs) and pause-sites (TPSs). When analysed in parallel with nascent RNA-seq, these data show that differential gene expression is achieved predominantly via changes in transcription initiation rather than Pol 2 pausing or elongation. Using genetically engineered mouse models deleted for specific enhancers we show that these elements control gene expression via Pol 2 recruitment and/or initiation rather than via promoter proximal pause release. Using genome-wide analysis we show that enhancers, in general, control gene expression at the stage of Pol 2 recruitment and initiation rather than via pausing.

overall_design:
To characterise nascent RNA engaged with Pol2 we performed mNET-seq on K562 cells, primary mouse erythroid cells from wildtype or HS2HS3, R1R2 lines.

HS2HS3 genotype: HS2 and HS3 enhancers of beta globin are homozygously deleted in combination
R1R2 genotype: A compound homozygous deletion of the R1 and R2 (a.k.a -26 and -31) transcriptional enhancers of the alpha globin gene (first reported in Hay et al 2016, Nature Genetics).

first: Takayuki

last: Nojima

first: Robert

last: Beagrie

first: Sue

last: Butler

first: Jacqueline

last: Sharpe

last: Sloane-Stanley

first: Jim

last: Hughes

first: Douglas

last: Higgs