title: Transcription Factor GATA2 Promotes Chromatin Remodeling at the Super-Enhancers of the Key Mast Cell Identity Genes and Primes Enhancers to Respond to Antigenic Stimulation [ChIP-seq]

summary: Mast cells are critical effectors in causing allergic inflammation and in protecting against certain parasitic infections. We previously demonstrated that transcription factors GATA2 and MITF are the mast cell lineage-determining factors (LDTFs). However, it is unclear whether these LDTFs play a role in regulating chromatin accessibility at the enhancer regions. In this study, we demonstrate that GATA2 promotes chromatin accessibility at the super-enhancers of mast cell identity genes and primes both the typical and super-enhancers at the genes that respond to antigenic stimulation. We found that the number and densities of GATA2, but not MITF, -bound sites at the super-enhancers were several folds higher than that at the typical enhancers. Our study reveals that GATA2 promotes robust gene transcription to maintain mast cell identity and respond to antigenic stimulation simply by binding to a larger number of GATA2 binding sites available at the super-enhancers of the key mast cell genes.

overall_design:
Histone modifications in unstimulated or stimulated WT and Gata2 KO BMMCs, in duplicate, using Illumina NovaSEQ6000 platform

GATA2 binding in unstimulated or stimulated WT BMMCs, in duplicate, using Illumina NovaSEQ6000 platform

first: Yapeng

last: Li


title: Transcription Factor GATA2 Promotes Chromatin Remodeling at the Super-Enhancers of the Key Mast Cell Identity Genes and Primes Enhancers to Respond to Antigenic Stimulation [ATAC-seq]

status: Public on Nov 25 2020

city: Denver

first: Hua

last: Huang

state: CO

address: 1400 Jackson St

department: Biomedical Research

country: USA

institute: National Jewish Health

type: Genome binding/occupancy profiling by high throughput sequencing

overall_design: Omni-ATAC-seq in unstimulated or stimulated WT and Gata2 KO BMMCs, in duplicate, using Illumina NovaSEQ6000 platform.


title: Study of ribosome dynamics of rpl3[W255C] and its interactions with ribosome-associated chaperones

city: Solna

first: Vicent

last: Pelechano

address: Nobels väg 16

department: MTC

country: Sweden

institute: ScilifeLab - Karolinska Institutet

type: Expression profiling by high throughput sequencing

summary: Proteostasis is a fundamental network of cellular pathways that ensures the optimal concentration and composition of correctly folded proteins within cells in normal and stress conditions. Among key components of this network are the molecular chaperones, which mediate protein folding but also act as modulators of protein synthesis. We have reported on a functional link between translation and de novo folding of proteins in the yeast Saccharomyces cerevisiae by uncovering a specific synthetic-lethal interaction between apparent unrelated mutant variants, the uL3[W255C] variant of the ribosomal protein uL3 and the null mutants of Zuo1 and Ssz1. Zuo1 and Ssz1 are components of the chaperone system named as ribosome-associated complex. Here, we performed a genome-wide analysis of ribosome dynamics by 5PSeq (Pelechano et al. 2015 PMID 26046441) in strains harbouring either wild-type uL3 or mutant uL3[W255C] in the presence or absence of Zuo1 or Ssz1. This method allows the study of ribosome dynamics, by sequencing 5’ phosphorylated mRNA co-translational degradation intermediates. Our results indicate that the rpl3[W255C] mutant is slightly impaired in translation elongation, defect that is significantly enhanced when combined with the deprivation of either Zuo1 or Ssz1.

overall_design: We performed 2 biologically independent 5PSeq experiments.

first: Olga

last: Rodríguez-Galán

first: Juan

middle: J

last: García-Gómez

first: Iván

middle: V

last: Rosado

first: Wu

last: Wei

first: Lars

middle: M

last: Steinmetz

first: Dieter

last: Kressler

first: Jesús

last: de la Cruz


title: Transcription Factor GATA2 Promotes Chromatin Remodeling at the Super-Enhancers of the Key Mast Cell Identity Genes and Primes Enhancers to Respond to Antigenic Stimulation [RNA-seq]

overall_design: mRNA profiles of unstimulated or stimulated WT and Gata2 KO BMMCs were generated by deep sequencing, in triplicate or duplicate, using Illumina NovaSEQ6000 platform.


title: RiboMeth-seq data from Pyrococcus furiosus

status: Public on Nov 24 2020

city: Copenhagen

first: Nicolai

last: Krogh

address: Blegdamsvej 3B

department: Department of Cellular and Molecular Medicine

country: Denmark

institute: University of Copenhagen

summary: Semiconductor sequencing of alkaline degraded total RNA from Pyrococcus furiosus annotated for ”The 23S ribosomal RNA from Pyrococcus furiosus is circularly permuted” published in Frontiers in Microbiology”

overall_design: P. furiosus RNA was degraded at denaturing conditions into small fragments, long enough to be mapped by sequence alignment to the reference genome (20-40 nucleotides). The fragments were ligated to RNA oligos using a tRNA ligase that was mutated to remove its kinase activity, reverse transcribed and the cDNA used as input for Ion semiconductor sequencing. The first and last nucleotides of the inserts were recorded using the full sequence for mapping and the read-ends plotted against the sequence. 2'-O-Methylated RNA positions are protected from cleavage, and read ends from such positions are therefore underrepresented compared to the surrounding positions.

first: Ulf

last: Birkedal

first: Henrik

last: Nielsen


title: RNAseq analysis of peripheral blood and synovial fluid neutrophils from rheumatoid arthritis patients

city: Liverpool

first: Helen

middle: Louise

last: Wright

address: 6 West Derby Street

department: Institute of Life Course and Medical Sciences

country: United Kingdom

institute: University of Liverpool

summary: We report changes in gene expression that take place in human neutrophils following migration from peripheral blood to synovial joints in patients with rheumatoid arthritis

overall_design: Neutrophils (purity >97%) were isolated from paired peripheral blood and synovial fluid (SF) from n=3 patients with severe rheumatoid arthritis. RNA was isolated using Trizol and sequenced on the Illumina HiSeq 2000 platform.

middle: L

first: Max

last: Lyon

first: Elinor

middle: A

last: Chapman

first: Robert

last: Moots

first: Steven

middle: W

last: Edwards


title: Circadian Cryptochrome 1 (CRY1) Rhythmically Modulates the DNA Damage Response [RNA-seq]

city: Philadelphia

first: Ayesha

last: Shafi

state: PA

address: 233 South 10th Street, 1032 BLSB

institute: Thomas Jefferson University

summary: These studies identify a novel node of AR-regulated DNA repair through CRY1 directly regulating HR-mediated DNA repair to enhance cancer progression and discern a potential avenue to be targeted in late stage disease to improve patient outcome.

overall_design: Transcriptional alterations upon CRY1 loss were assessed in hormone proficient conditions through RNA-Seq of C4-2 shCON and C4-2 shCRY1 prostate cancer cells

first: Karen

middle: E

last: Knudsen


title: RNA extracted from the left ventricle of 3 different mouse heart disease models, wild type, mdx, and mdx sln+/- hearts

city: Newark

first: Gopal

middle: J.

last: Babu

state: New Jersey

address: 185 South Orange Ave

institute: Rutgers NJMS

summary: We report that ablation of one SLN allele positively affects mouse mdx DMD heart failure model mice by several metrics including intracellular calcium handling.

overall_design: 3 mouse populations in a C57 genetic background, a wild type control population, an mdx heart failure model, and an mdx sln +/- . # samples of each population were sacked at 6 months old and RNA was extracted from the left ventricle and sequenced using paired-end sequencing in order to determine molecular pathways associated with cardiac pathology.

first: Satvik

last: Mareedu


title: T-cells' gene expression after high-dose melphalan

status: Public on Nov 23 2020

city: Bochum

first: Thomas

last: Mika

address: Universitätsstr. 150

country: Germany

institute: Ruhr-University Bochum

summary: T-cells' transduction efficacy by lentiviral transduction is diminished after high-dose melphalan. To investigate transcriptional changes regarding genes inhibiting viral entry, reverse transcription, nuclear transport and viral genome integration, we performed microarray transcription analysis.

overall_design: Peripheral blood mononuclear cells of patients, who were treated with high-dose melphalan and autologous stem-cell transplantation, were isolated from peripheral blood via density centrifugation and subsequently activated by CD3/28-nanomatrix (Human TransAct, Miltenyi Biotech) and Interleukin-2. After 3 days, T-cells were isolated by cell-sorting (MoFlow Astrios, Beckman Coulter), and whole-RNA was extracted by Qiagen RNEasy Kit.

first: M

last: Becker

first: T


title: Whole transcriptome sequencing of peripheral blood mononuclear cells from patients with COVID-19

city: Kunming

first: Yong-Gang

last: Yao

state: Yunnan

address: 32 Jiaochang Donglu

department: Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province

country: China

institute: Kunming Institute of Zoology

type: Non-coding RNA profiling by high throughput sequencing

summary: Understanding the process of immune remodeling and regulation in SARS-CoV-2 infected patients from hospitalization to rehabilitation is crucial for therapy of patients with COVID-19. Here, we performed a longitudinal whole-transcriptome RNA sequencing on peripheral blood mononuclear cell (PBMC) samples of 18 patients with mild, moderate or severe COVID-19 symptoms during the treatment, convalescence and rehabilitation stages. After identifying the differentially expressed mRNAs, miRNAs and lncRNAs between different clinical stages or different clinical types and predicting the target genes of non-coding RNAs, we analyzed the functional and regulatory networks of their interactions. The type I interferon response was found to be significantly down-regulated after the patient rehabilitation, and the humoral immunity declined rapidly from the convalescence stage. Robust T-cell activation and differentiation at the whole transcriptome level constituted the main events during the recovery process of COVID-19. The formation of this T cell immune memory had the characteristics of multi-directional and multi-level regulation, and presented a higher early differentiation in mild patients. These findings uncovered the dynamic pattern of immune responses and indicated the key role of T cell immunity in the formation of immune protection against COVID-19.

overall_design: Peripheral blood mononuclear cells (PBMC) from 18 patients with COVID-19 were collected and subjected to total RNA extraction. rRNA-depleted library and small RNA library were constructed for each sample to capture the expression of mRNA, lncRNA, and miRNA. In a total of 18 patients with COVID-19, there were 6, 7, and 5 patients with mild, moderate, and severe symptoms, respectively. PBMC samples were collected at the treatment stage, convalescence stage, and rehabilitation stage for each sample.

first: Yong

middle: T

last: Zheng

first: Hong

middle: Y

first: Min

last: Xu


title: Circadian Cryptochrome 1 (CRY1) Rhythmically Modulates the DNA Damage Response

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

overall_design: Refer to individual Series


title: Circadian Cryptochrome 1 (CRY1) Rhythmically Modulates the DNA Damage Response [ChIP-seq]

overall_design: CRY1 occupancy was assessed in hormone proficient conditions through ChIP-Seq in C4-2 prostate cancer cells


title: Dual RNA 3’ end processing of H2A.X messenger RNA maintains DNA damage repair throughout the cell cycle

city: Oxford

first: Esther

last: Griesbach

address: South Parks Road

department: Sir William Dunn School of Pathology

institute: University of Oxford

summary: Replication-dependent (RD) histone mRNA are the only non-polyadenylated protein coding transcripts in humans. However, a subset of RD histone genes also expresses polyadenylated mRNA upon terminal differentiation to maintain histone proteins. We now show that even in cycling cells, RD histone genes express some poly(A) mRNA. The H2AFX gene, encoding the DNA damage signalling histone variant H2A.X, expresses both an S-phase-specific SL mRNA ending in the typical stem-loop (SL) structure and substantial amounts of an extended poly(A) mRNA. We show, by the selective removal of either mRNA isoform, that the S-phase-specific H2A.X SL mRNA can generate sufficient histone for deposition onto DNA damage responsive (DDR) chromatin in some cell types. In contrast, when cells have evolved to make predominantly H2A.X poly(A) mRNA they then require de novo H2A.X for efficient DDR. This highlights the importance of differential H2AFX mRNA 3’ end processing for the maintenance of effective DDR

overall_design: To characterise histone mRNA transcription profiles across the cell cycle, HeLa cells were synchronised in S or G1 phases using either aphidicolin or nocodazole, respectively. arrested cells were then subjected to nuclear and cytoplasmic fractionation, followed by protein and RNA isolation. Nuclear and cytoplasmic mRNA was then subjected to poly(A)+ selection, followed by ribosomal RNA depletion of the poly(A)- mRNA. Both poly(A)+ and poly(A)- mRNA were used for RNA-seq library preparation and then subjected to Illumina sequencing.

first: Margarita

last: Schlackow

first: William

middle: F

last: Marzluff

first: Nicholas

last: Proudfoot


title: MicroRNA profiling of cisplatin-resistant and cisplatin-sensitive ovarian cancer cells

status: Public on Nov 20 2020

city: San Juan

first: Pablo

last: Vivas-Mejía

state: PR

address: Medical Sciences Campus

department: Cancer Medicine

country: Puerto Rico

institute: University of Puerto Rico Cancer Center

summary: Platinum resistance is a major drawback in the treatment of ovarian cancer. Evidence suggests that microRNAs are key players in the initiation, progression, and drug resistance of cancer cells. However, the precise miRNAs dysregulated and contributing to platinum resistance in ovarian cancer cells have not been fully elucidated. Here, we conducted a miRNA expression profiling of cisplatin-sensitive (A2780) and cisplatin-resistant (CP20 and CIS) ovarian cancer cells to identify potential miRNAs involved in platinum resistance.

overall_design: Total RNA from ovarian cancer cells was isolated using the mirVana total RNA extraction kit. RNA was biotin-labeled and subjected to Affymetrix GeneChip miRNA 2.0 Arrays.

first: Vivas-Mejía

last: PE


title: Transcriptional, behavioural and biochemical profiling in the 3xTg-AD mouse model reveals a specific signature of amyloid deposition and functional decline in Alzheimer’s disease

status: Public on Nov 21 2020

city: Cardiff

first: Jimena

last: Monzón-Sandoval

address: Maindy Road

institute: UK Dementia Research Institute at Cardiff University

summary: Alzheimer’s disease (AD)-related degenerative decline is associated to the presence of amyloid beta (Aβ) plaque lesions and neuro fibrillary tangles (NFT). However, the precise molecular mechanisms linking Aβ deposition and neurological decline are still unclear. Here we combine genome-wide transcriptional profiling of the insular cortex of 3xTg-AD mice and control littermates from early through to late adulthood (2-14 months of age), with behavioural and biochemical profiling in the same animals to identify transcriptional determinants of functional decline specifically associated to build-up of Aβ deposits. Differential expression analysis revealed differentially expressed genes (DEGs) in the cortex long before observed onset of behavioural symptoms in this model. Using  behavioural and biochemical data derived from the same mice and samples, we found that down but not up-regulated DEGs show a stronger average association with learning performance than random background genes in control not seen in AD mice. Conversely, these same genes were found to have a stronger association with Aβ deposition than background genes in AD but not in control mice, thereby identifying these genes as potential intermediaries between abnormal Aβ/NFT deposition and functional decline. Using a complementary approach, gene ontology analysis revealed a highly significant enrichment of learning and memory, associative, memory and cognitive functions only among down-regulated, but not up-regulated, DEGs. Our results demonstrate wider transcriptional changes triggered by the abnormal deposition of Aβ/NFT occurring well before behavioural decline and identify a distinct set of genes specifically associated to abnormal Aβ protein deposition and cognitive decline.

overall_design: Bulk RNAseq time course of the insular cortex of WT and 3xTg-AD mice. A total of 30 samples, including 3 mice per genotype group (WT and 3xTg-AD) at 5 different time points (2, 7, 8, 11 and 14 months old).

first: Wencheng

last: Yin

first: Navei

last: Cerda-Hernandez

first: Atahualpa

last: Castillo-Morales

first: Mayra

last: Ruiz-Tejada-Segura

first: Perla

last: Moreno-Castilla

first: Rodrigo

last: Pérez-Ortega

first: Federico

last: Bermudez-Rattoni

first: Araxi

last: Urrutia

first: Humberto

last: Gutierrez


title: RNA-Seq for transcriptome analysis of germinal center B cells upon GSK3 inhibition

status: Public on Nov 22 2020

city: Chuncheon

first: Seung Goo

last: Kang

address: 1, Kangwondaehak-gil

department: Biomedical Convergence

country: South Korea

institute: Kangwon National University

summary: To compare transcriptional changes of germinal center B cells upon GSK3 inhibition, induced GC B cells were treated with GSK3 inhibitor, CHIR99021. 407 differentially expressing genes were identified

overall_design: Comparing mRNA expression profiles between  DMSO treated control induced GC B cells and  CHIR99021 treated induced GC B cells in biological triplicate

first: Seung

middle: G

first: Sun

middle: S

last: Choi


title: Comparative transcriptome, metabolome and ionome analysis of two contrasting common bean genotypes in saline conditions

city: Istanbul

first: Harun

last: Niron

address: North Campus Kuzey Park Building, Teras Lab Bebek

department: Molecular Biology and Genetics

country: Turkey

institute: Bogazici University

summary:
Background: Soil salinity is a major abiotic stress factor that limit agricultural productivity worldwide, and this problem is expected to grow in the future. Common bean (Phaseolus vulgaris L.) is an important protein source in developing countries is highly susceptible to salt stress. To understand the underlying mechanism of salt stress responses, transcriptomics, metabolomics, and ion content analysis were utilized for response comparison of salt-tolerant and salt-susceptible common bean genotypes in saline conditions.
Results: Transcriptome analysis has revealed that the tolerant genotype had increased photosynthesis in saline conditions while the susceptible genotype acted in a contrasting way. The chlorophyll content measurements have backed up this result with increase in tolerant and decrease in susceptible genotype. Transcriptome also displayed a more active carbon and amino acid metabolism for the tolerant genotype as well. Analysis of primary metabolites with GC-MS demonstrated the boosted carbohydrate metabolism in the tolerant genotype with increased sugar content as well as better amino-acid metabolism with the accumulation of glutamate and asparagine and hinted a lowered photorespiration level for the tolerant one. Accumulation of lysine, valine, and isoleucine in the roots of the susceptible genotype suggested a halted stress response pathway. According to ion content comparison, the tolerant genotype managed to block accumulation of Na+ in the leaves while accumulating significantly less Na+ in the roots compared to susceptible genotype. K+ levels increased in the leaves of both genotype and the roots of the susceptible one but dropped in the roots of the tolerant genotype. Additionally, Zn+2 and Mn+2 levels were also dropped in the tolerant roots, while Mo+2 levels were significantly higher in all tissues in both control and saline conditions for tolerant genotype.
Conclusion:The results of the presented study have demonstrated the differences in contrasting genotypes and thus provide valuable information on the pivotal molecular mechanisms underlying salt tolerance mainly in common bean, but for all crops.

overall_design: Comparison of mRNA profiles of leaf and root tissues of two common bean genotypes in salt stress and control conditions

first: Muge

last: Turet


title: Antagonistic inflammatory phenotypes dictate tumor fate and response to immune checkpoint blockade (scRNA-seq dataset: SZ11)

city: Manchester

first: Santiago

last: Zelenay

state: UK

address: Alderley Park

institute: CRUK Manchester Institute

summary: In this study we searched for primary regulators of cancer-inhibitory inflammation using murine tumors of immune-dependent progressive or regressive fates linked to antagonistic inflammatory tumor microenvironments

overall_design: RNA profile of total leukocytes sorted on day 4 from Ptgs-deficient tumors or Ptgs-deficient tumors injected in NK-cell depleted C57BL/6 mice

first: Eduardo

last: Bonavita

first: Christian

middle: P

last: Bromley


title: Two miRNAs are sufficient for C. elegans embryogenesis

city: Vienna

first: Jingkui

last: Wang

address: Campus-Vienna-Biocenter 1

country: Austria

institute: Research Institute of Molecular Pathology (IMP)

summary: The Microprocessor, composed of Drosha and Pasha/DGCR8, is necessary for the biogenesis of canonical microRNAs (miRNAs), and required for animal embryogenesis. However, the cause for this requirement is largely unknown. The Microprocessor may be required to produce one or few essential miRNAs, or alternatively, many individually non-essential miRNAs. Additionally, Drosha and Pasha/DGCR8 may be required for processing non-miRNA substrates. To distinguish between these possibilities, we developed a system in C. elegans to stringently deplete embryos from the Microprocessor and miRNAs. We show that the early embryonic arrest upon loss of the Microprocessor is rescued by the addition of two individual miRNAs from the miR-35 and miR-51 families, resulting in morphologically normal larvae. Thus, just two canonical miRNAs are sufficient for morphogenesis and organogenesis in C. elegans, and indicate that miRNA processing explains the essential requirement for the Microprocessor during embryogenesis.

sample_organism:
Arabidopsis thaliana
Caenorhabditis elegans

overall_design: 22 small RNA libraries from C. elegans embryos / L1 larvae, as well as Arabidopsis total RNA for control purposes. Spike in oligos have been added [design based on (Lutzmayer et al., 2017, Sci Rep)] and used for absolute quantification of mature miRNA levels

first: Philipp

last: Dexheimer

first: Luisa

last: Cochella


title: Antagonistic inflammatory phenotypes dictate tumor fate and response to immune checkpoint blockade


title: Antagonistic inflammatory phenotypes dictate tumor fate and response to immune checkpoint blockade (RNA-seq dataset: SZ8)

overall_design: RNA profile of tumor associated macrophages (TAMs) sorted from Ptgs-competent or -deficient tumors implanted in C57BL/6 mice


title: Antagonistic inflammatory phenotypes dictate tumor fate and response to immune checkpoint blockade (RNA-seq dataset: SZ3)

overall_design: RNA profile of bulk Ptgs+/+ and Ptgs-/- tumors four days post implantation in wild type mice or Ptgs-/- tumors from NK-cell depleted mice.


title: Difference between day and night temperatures affects stem elongation in tomato (Solanum lycopersicum) seedlings via regulation of gibberellin and auxin synthesis

status: Public on Nov 18 2020

city: yokohama

first: Kinuka

last: Ohtaka

address: 1-7-22, suehiro-cho

country: Japan

institute: RIKEN

summary: Temperature is a critical environmental factor governing plant growth and development. The difference between day temperature (DT) and night temperature (NT), abbreviated as DIF, influences plant architecture. Subjecting plants to artificial DIF treatments is an effective strategy in ornamental horticulture. For example, negative DIF (when DT – NT < 0) generally inhibits stem elongation, resulting in dwarf plants. However, the mechanisms underlying stem growth regulation by DIF remains to be completely elucidated. In this study, we aimed to analyze the growth, transcriptome, and phytohormone profiles of tomato (Solanum lycopersicum) seedlings grown under different DIF treatments. Under positive DIF (when DT – NT > 0), in contrast to the control temperature (25°C/20°C, DT/NT), high temperature (30°C/25°C) increased stem length and thickness, as well as the number of xylem vessels. Conversely, compared with the positive high temperature DIF treatment (30°C/25°C), under negative DIF treatment (25°C/30°C) stem elongation was inhibited, but stem thickness and the number of xylem vessels were not affected. The negative DIF treatment decreased the expression of gibberellin (GA)-, auxin-, and cell wall-related genes in the epicotyl, as well as the concentrations of GAs and indole-3-acetic acid (IAA). The expression of these genes and concentrations of these hormones increased under high temperature compared to those under the control temperature positive DIF. Our results suggest that stem length in tomato seedlings is controlled by changes in GA and IAA biosynthesis in response to varying day and night temperatures.

overall_design: Changes in expression of S. lycopersicum genes were investigated at 7 days in 30°C/25°C (+DIF) versus 25°C/30°C (-DIF). This experiment was performed at same time using different three samples for each temperature conditions.

first: Akiko

last: Yoshida

first: Yusuke

last: Kakei

first: Kosuke

last: Fukui

first: Mikiko

last: Kojima

first: Yumiko

last: Takebayashi

first: Kanako

last: Yano

first: Shunsu

last: KeImanishi

first: Hitoshi

last: Sakakibara


title: N-Quinoline Benzenesulfonamide Derivatives Exert Potent Anti-Lymphoma effect by Targeting NF-κB

city: New York

first: Matko

last: Kalac

state: New York

address: 1 Gustave L Levy Place

department: Tisch Cancer Institute

institute: Ichan School of Medicine at Mount Sinai

summary: We perform expression analysis on lymphoma cell line OCI-Ly10 treated with a novel NF-kB translocation inhibitor CU-O75

overall_design:
Gene expression profiles pre- and post-treatment with CU-O75 in OCI-Ly10 cell line

>>>Submitter states that raw data are not available due to patient privacy concerns<<<

first: Kalac

last: Matko

first: Bansal

last: Mukesh


title: The effect of MCM3 gene knockdown on gene expression profile of tamoxifen-resistant breast cancer cell lines

status: Public on Nov 17 2020

city: Odense

first: Henrik

last: Ditzel

state: Denmark

address: J.B. Winsløwsvej 25

institute: University of Southern Denmark

summary:
MCM3 is one of several genes whose expression profile is markedly altered in tamoxifen-resistant breast cancer cell lines. We observed that increased MCM3 expression is associated with tamoxifen resistance. Knockdown of MCM3 resulted in increased susceptibility of tamoxifen-resistant breast cancer cell lines. Moreover, MCM3 expression is significantly associated with clinical outcome of endocrine treated receptor positive breast cancer. To understand the effect of MCM3 on the mechanism of endocrine resistance, we performed gene expression array on tamoxifen-resistant breast cancer cell lines. Here we show that MCM3 knockdown affects the expression of hundreds of genes.
Resistance to endocrine therapy in estrogen receptor-positive (ER+) breast cancer is a major clinical problem with poorly understood mechanisms. There is an unmet need for prognostic and predictive biomarkers to allow appropriate therapeutic targeting. We evaluated the mechanism by which minichromosome maintenance protein 3 (MCM3) influences endocrine resistance and its predictive/prognostic potential in ER+ breast cancer. We discovered that ER+ breast cancer cells survive tamoxifen and letrozole treatments through upregulation of minichromosome maintenance proteins (MCMs), including MCM3, which are key molecules in cell cycle and DNA replication. Lowering MCM3 expression in endocrine-resistant cells restored drug sensitivity and altered phosphorylation of cell cycle regulators, including p53(Ser315,33), CHK1(Ser317) and cdc25b(Ser323), suggesting that the interaction of MCM3 with cell cycle proteins is an important mechanism of overcoming replicative stress and anti-proliferative effects of endocrine treatments. Evaluation of MCM3 levels in primary tumors from four independent cohorts of breast cancer patients receiving adjuvant tamoxifen mono-therapy or no adjuvant treatment, including the Stockholm tamoxifen (STO-3) trial, showed MCM3 to be an independent prognostic adding information beyond Ki67. In addition, MCM3 was shown to be a predictive marker of response to endocrine treatment. Our study reveals a coordinated signaling network centered around MCM3 that limits response to endocrine therapy in ER+ breast cancer and identifies MCM3 as a clinically useful prognostic and predictive biomarker that allows personalized treatment of ER+ breast cancer patients.

overall_design: The experiment involved three tamoxifen-resistant and 1 tamoxifen-sensitive MCF7 cell lines. MCM3 gene knockdown was performed by transfecting cells with gene specific siRNA and control siRNA. The effect of MCM3 gene knockdown on global gene expression profile was assessed by performing gene array using HG-U133_Plus_2 Affymetrix array platform.

first: Sanne

last: Løkkegaard

first: Daniel

last: Elias

first: Martin

last: Bennetzen

first: Anne-Vibeke

last: Lænkholm

last: Bak

first: Morten

last: Gjerstorff

first: Lene

last: Johansen

first: Henriette

last: Vever

first: Christina

last: Bjerre

first: Tove

last: Kirkegaard

first: Bo

last: Nordenskjold

first: Tommy

last: Formander

first: Olle

last: Stål

first: Linda

last: Lindström

first: Laura

last: Esserman

first: Anne

last: Lykkesfeldt

first: Jens

last: Andersen

first: Rikke

last: Leth-Larsen


title: Profiling the blood compartment of Hematopoietic Stem Cell Transplant patients during Human Cytomegalovirus reactivation

city: Rehovot

first: Noam

last: Stern-Ginossar

address: 234 herzel

department: Molecular Genetics

country: Israel

institute: Weizmann Institute

summary: Human cytomegalovirus (HCMV) reactivation is a leading infectious cause of morbidity and mortality in hematopoietic stem cell transplantation (HSCT) patients. HCMV reactivation is characterized by detection of viral DNA in the blood (DNAemia), however, the role of the blood compartment during HCMV reactivation is not well characterized. Using powerful molecular tools, we characterized HCMV infection in Peripheral Blood Mononuclear Cells (PBMCs) during DNAemia in HCMV reactivating HSCT patients. Surprisingly we found that all PBMC populations harbored extremely low levels of viral DNA and extremely low levels of viral transcripts. Remarkably, the viral transcripts detected in these samples were mainly immediate early genes indicating that these cells do not go through a full productive cycle. Analysis of the cellular transcriptome revealed characteristic transcriptional changes in high DNAemic samples implying the development of HCMV-specific T cells and inhibition of regulatory T cell function. Overall, our data indicate that DNAemia in HCMV reactivating HSCT patients is associated with distinct immune signatures but is not necessarily accompanied by substantial infection of PBMCs, and that PBMCs are not productively infected. These findings are important for understanding the role of the blood compartment in progression and control of HCMV during reactivation.

overall_design: MARS-Seq bulk protocol was used for PBMC from HSCT recipients with HSCT reactivation and for monocytes infected with HCMV ex-vivo

first: Biana

last: Bernstein

first: Aharon

last: Nachshon

first: Miri

last: Shnayder

first: Lauren

last: Stern

first: Selmir

last: Avdic

first: Emily

last: Blyth

first: David

last: Gottlieb

first: Allison

last: Abendroth

first: Barry

last: Slobedman

first: Michal

last: Schwartz


title: Comprehensive profiling of gene expression in the cerebral cortex and striatum of BTBRTF/ArtRbrc mice compared to C57BL/6J mice

status: Public on Nov 19 2020

city: Noda

first: Shota

last: Mizuno

state: Chiba

address: 2641 Yamazaki

department: Department of Applied Biological Science

institute: Tokyo University of Science

summary: Mouse line BTBR T+ Iptr3tf/J (hereafter referred as to BTBR/J) is a congenic mouse strain that shows lower sociability compared to the C57BL/6J mouse strain (hereafter referred to as B6) and thus is often utilized as a model for autism spectrum disorder (ASD). In this study, we utilized another subline, BTBRTF/ArtRbrc (RIKEN BioResource Research Center; RBRC, Tsukuba, Japan; RBRC ID: 01206, hereafter referred to as BTBR/R), and analyzed the associated brain transcriptome compared to B6 mice using microarray analysis. We focused on the cerebral cortex and the striatum, both of which are thought to be brain circuits associated with ASD symptoms. Our results identified the transcriptome profiling in BTBR/R mice compared to B6 mice, which could contribute to the understanding of ASD molecular pathology as well as the differences in sociality observed between BTBR/J mice and B6 mice.

overall_design: The BTBR/R and B6 mice were housed in the animal facility on 12-h light and dark cycle from 8 a.m. to 8 p.m. The brain tissue samples (cerebral cortex and striatum) from mice of each strain were dissected out (Male; 4–6 months of age; N = 4 per experimental group).

first: Teiichi

last: Furuichi


title: Transcriptional responses of Tanreqing treated Pseudomonas aeruginosa cells

city: Beijing

first: Qing

last: Wei

address: NO.1 Beichen West Road, Chaoyang District

institute: Institute of Microbiology, Chinese Academy of Sciences

summary: Analysis of Pseudomonas aeruginosa PAO1 (ATCC 15692) treated by Tanreqing. PAO1 cells are evaluated with RNA-seq to understand the genes affected by this antibacterial agent. Our results provide new vision on the mode of action by Tanreqing.

overall_design: We used three PAO1 replicates and three Tanreqing (TRQ)-treated PAO1 replicates to compare the differential gene expression under two growth conditions: exponential phase (EXP) and stationary phase (STA).

first: Yi

last: Wang


title: Flanking sequence preference modulates de novo DNA methylation in the mouse genome

status: Public on Nov 16 2020

city: Utrecht

first: Tuncay

last: Baubec

address: Padualaan 8

department: Department of Biology

country: Netherlands

institute: Utrecht University

type: Methylation profiling by high throughput sequencing

summary: Mammalian de novo DNA methyltransferases (DNMT) are responsible for the establishment of cell-type-specific DNA methylation in healthy and diseased tissues. Through genome-wide analysis of de novo methylation activity in murine stem cells we uncover that DNMT3A prefers to methylate CpGs followed by cytosines or thymines, while DNMT3B predominantly methylates CpGs followed by guanines or adenines. These signatures are further observed at non-CpG sites, resembling methylation context observed in specialised cell types, including neurons and oocytes. We further show that these preferences result from structural differences in the catalytic domains of the two de novo DNMTs and are not a consequence of differential recruitment to the genome. Molecular dynamics simulations suggest that, in case of human DNMT3A, the preference is due to favourable polar interactions between the flexible Arg836 side chain and the guanine that base-pairs with the cytosine following the CpG. By exchanging arginine to a lysine, the corresponding sidechain in DNMT3B, the sequence preference is reversed, confirming the requirement for arginine at this position. This context-dependent de novo DNA methylation by DNMT3A and DNMT3B, provides additional insights into the complex regulation of methylation patterns.

overall_design: Whole-genome bisulfite sequencing for Dnmt1,3a,3b-triple-KO ES cells expressing DNMT3A, DNMT3B and mutant DNMT3A


title: long non coding RNA expression in post myocardial infarction 3 days and 14 days

status: Public on Nov 14 2020

city: Hang Zhou

first: Feng

last: Zhang

state: Zhejiang

address: Kaixuan road number 258

institute: Zhejiang University

summary: To explore the key lncRNAs involved in regulating essential pathophysiological processes of the adult heart, we performed microarray-based transcriptome profiling on mouse hearts 3 days and 14 days after myocardial infarction (MI) or sham surgery. Microarray analysis revealed a total of 7,339 differentially expressed transcripts in MI 3 days hearts compared to sham controls (FC≥2, p<0.05). Kyoto Encyclopedia of Genes and Genomes (KEGG) or Gene Ontology (GO) pathway analyses revealed that oxidative phosphorylation, ECM-receptor interaction, cell proliferation, and inflammatory responses were among the top dysregulated genes in MI hearts. Interestingly, 209 lncRNAs are upregulated and 543 lncRNAs are downregulated in MI 3 days hearts (FC≥2, p<0.05). Among these lncRNA transcripts, we found that 8 lncRNAs are mostly upregulated and 6 lncRNAs mostly downregulated (FC≥2, p<0.05), whereas the expression level of the AK048087 transcript was increased by 25 fold and lncRNA AK034241 appears to be the most downregulated lncRNA.

overall_design: 10 mice were subjected to permanent occlusion of the anterior interventricular artery while 5 mice were subjected to the identical surgical procedure without coronary ligation. 3days and 14 days after the permanent occlusion, mice were sacrificed and the border zone of ventricles of heart were harvested for RNA isolation. Total RNAs were labelled and hybridised on Agilent Mouse SurePrint G3 Array. One sample per array.

first: Xuyang

last: Fu

first: Masaharu

last: Kataoka

first: Da-zhi

first: Jinghai

last: Chen


title: Tnfaip2/Exoc3 driven lipid metabolism is essential for stem cell differentiation & organ homeostasis [Mus musculus, 2]

city: Jena

first: Philipp

last: Koch

address: Beutenbergstraße 11

department: Core Facility Life Science Computing

institute: Leibniz Institute on Aging - Fritz Lipmann Institute

summary: Lipid metabolism is recognized as a key process for stem cell maintenance and differentiation but genetic factors that instruct stem cell function by influencing lipid metabolism remain to be delineated. Here we identify Tnfaip2 as an inhibitor of reprogramming of mouse fibroblasts into induced pluripotent stem cells. Tnfaip2 knockout embryonic stem cells (ESCs) exhibit differentiation failure and knockdown of the planarian orthologue, Smed-exoc3, abrogates in vivo differentiation of somatic stem cells, tissue homeostasis, and regeneration. Tnfaip2 deficient ESCs fail to induce synthesis of cellular triacylglycerol (TAG) and lipid droplets (LD) coinciding with reduced expression of Vimentin (Vim) – a known inducer of LD formation. Knockdown of Vim and Tnfaip2 act epistatically in enhancing cellular reprogramming of mouse fibroblasts. Similarly, planarians devoid of Smed-exoc3 displayed acute loss of TAGs. Supplementation of palmitic acid (PA) and palmitoyl-L-carnitine (a mitochondrial carrier of PA) restores the differentiation capacity of Tnfaip2 deficient ESCs as well as stem cell differentiation and organ maintenance in Smed-exoc3-depleted planarians. Together, these results identify a novel pathway, which is essential for stem cell differentiation and organ maintenance by instructing lipid metabolism.

overall_design: Delineation of transcriptome profile following 3 days of in vitro differentiation of WT and Tnfaip2-/- mouse embryoid bodies (EBs) that were grown either in the presence or absence ofpalmitic acid (PA) and palmitoyl-L-carnitine (PC).

first: Sarmistha

last: Deb

first: Marco

last: Groth


title: Tnfaip2/Exoc3 driven lipid metabolism is essential for stem cell differentiation & organ homeostasis [Mus musculus, 1]

overall_design: Delineation of transcriptome profile following 3 days of in vitro differentiation of WT and Tnfaip2-/- mouse embryoid bodies (EBs).


title: lncRNA Cfast knockdown in cardiac fibroblasts

status: Public on Nov 13 2020

summary: Cardiac fibrosis occurs in most cardiac diseases, which reduces cardiac muscle compliance, impairs both systolic and diastolic heart function and, ultimately, leads to heart failure. Using unbiased transcriptome profiling in a mouse model of myocardial infarction, we identified a cardiac-fibroblast enriched lncRNA (AK048087) named cardiac fibroblast-associated transcript (Cfast), which is significantly elevated after myocardial infarction. Here, we show that silencing Cfast expression by lentiviral shRNAs resulted in suppression of fibrosis-related gene expression and transdifferentiation of myofibroblasts into cardiac fibroblasts. We performed the RNA-seq profiling in both lentivirus Cfast knockdown and lentivirus scramble group in cardiac fibroblasts. Finally, the transcriptome analysis indicates that genes related to cell differentiation, cell migration, extracellular matrix organization downregulated in Cfast knockdown group.

overall_design: Examination of mRNA profiles in cardiac fibroblast treated by lentivirus Cfast knockdown and scramble


title: Tnfaip2/Exoc3 driven lipid metabolism is essential for stem cell differentiation & organ homeostasis

status: Public on Nov 15 2020

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

sample_organism:
Mus musculus
Schmidtea mediterranea

platform_organism:
Mus musculus
Schmidtea mediterranea

overall_design: Refer to individual Series


title: Tnfaip2/Exoc3 driven lipid metabolism is essential for stem cell differentiation & organ homeostasis [Schmidtea mediterranea]

overall_design: Delineation of transcriptome profile of gfp (control) and Smed-exoc3 depleted planarian X1 population that constitutes pluripotent stem cells called neoblasts


title: Validation of human microRNA target pathways enables evaluation of target prediction tools [miRNA]

city: Homburg

first: Lena

last: Krammes

address: Kirrbergerstraße

department: Institute for Human Genetics

institute: Saarland University

summary: MicroRNAs are regulators of gene expression. A wide-spread, yet not validated, assumption is that the targetome of miRNAs is non-randomly distributed across the transcriptome but that targets share functional  pathways.  We  developed  a  computational  and  experimental  strategy  termed  high-throughput miRNA interaction reporter assay (HiTmIR) to facilitate the validation of target pathways. First, targets and target pathways are predicted and prioritized by computational means to increase the specificity and positive predictive value. Second, the novel webtool MIRTAH facilitates guided designs of reporter assay constructs at scale. Third, automated and standardized reporter assays are performed. We evaluated HiTmIR using miR-34a-5p, for which TNF- and TGFB-signaling, and Parkinson’s Disease (PD)-related categories were identified and repeated the pipeline for miR-7-5p. HiTmIR validated 58.9% of the target genes for miR-34a-5p and 46.7% for miR-7-5p. We confirmed the targeting by measuring the endogenous protein levels of targets in a neuronal cell model. The standardized  positive  and  negative  targets  are  collected  in  the  new  miRATBase  database, representing a resource for training, or benchmarking new target predictors. Applied to 88 target predictors with different confidence scores, TargetScan 7.2 and miRanda outperformed other tools. Our experiments demonstrate the efficiency of HiTmIR and provide evidence for an orchestrated miRNA-gene targeting.

overall_design: LUHMES cells were differentiated towards dopaminergic neurons and treated with the neurotoxin MPP+ to induce Parkinson's Disease phenotype. Alterations in miRNome as well as transcriptome were monitored by microarray in four independet experiments.

first: Fabian

last: Kern

first: Karin

last: Danz

first: Caroline

last: Diener

first: Tim

last: Kehl

first: Oliver

last: Küchler

first: Tobias

last: Fehlmann

first: Mustafa

last: Kahraman

first: Stefanie

last: Rheinheimer

first: Ernesto

last: Aparicio

first: Sylvia

last: Wagner

first: Nicole

last: Ludwig

first: Christina

last: Backes

first: Hans-Peter

last: Lenhof

first: Hagen

last: von Briesen

first: Martin

last: Hart

first: Andreas

last: Keller

first: Eckart

last: Meese


title: Validation of human microRNA target pathways enables evaluation of target prediction tools [mRNA]

first: Lena

last: Krammes

overall_design: LUHMES cells were differentiated towards dopaminergic neurons and treated with the neurotoxin MPP+ to induce PD phenotype. Alterations in miRNome as well as transcriptome were measured by microarray in four independet experiments.

first: Fabian

last: Kern


title: Co-location of chromatin loop anchors with the gene transcription machinery in maize.

status: Public on Nov 12 2020

city: Johnston

first: John

middle: Anthony

last: Crow

state: Iowa

address: 7000 NW 62nd Ave

department: Applied Science and Technology

institute: Corteva Agriscience

summary: We report the use of ultra-high Hi-C sequencing to characterize TAD-like domains and chromatin loops in maize, along with their co-location characteristics with open chromatin (ATAC-Seq) peaks and gene expreesion (mRNA-Seq) data generated from the same tissue samples.

overall_design: Examination of two distinct B73 leaf v04 biological replicates

first: Stephane

last: Deschamps

first: Nadia

last: Chaidir

first: Brooke

last: Peterson-Burch

first: Sunil

last: Kumar

first: Haining

last: Lin

first: Gina

last: Zastrow-Hayes

first: Gregory

middle: D

last: May


title: Global transcriptomic changes in P. falciparum NF54 gametocytes treated with the histone demethylase inhibitor ML324

city: Pretoria

first: LynMarie

last: Birkholtz

state: Gauteng

address: c/o Lunnon Road and Heroldt Street, Hatifeld

department: Biochemistry

country: South Africa

institute: University of Pretoria

summary: Global transcriptomic profiling of ML324 treated and untreated control gametocytes to determine the downstream effects of histone methyltransferase inhibition on gametocyte development

overall_design: Gene expression profiling with  microarrays (Agilent Technologies, USA, (Painter, H. J. Methods in Molecular Biology 923: 213-219, doi:10.1007/978-1-62703-26-7_14 (2013)) was performed to determine the global transcriptomic changes in P. falciparum gametocytes arising from treatment with ML324.  P. falciparum NF54 gametocytes were induced by culturing parasites in glucose-deficient media with a concurrent drop in haematocrit as described previously (Reader, J. et al. Malaria Journal 14, 213, doi:10.1186/s12936-015-0718-z (2015)). Gametocytes (1-3% gametocytaemia, 4% haematocrit) were treated with ML324 (5 µM) and sampled 24 h thereafter using 0.01% (w/v) saponin. RNA was extracted and cDNA synthesised and dye-coupled with Cy5 as previously described (Painter, H. J. Methods in Molecular Biology 923: 213-219, doi:10.1007/978-1-62703-26-7_14 (2013)). The ML324 treated and paired untreated sample were hybridised to arrays with an equal quantity of Cy3-labeled reference pool cDNA that consisted of a 3D7 mixed asexual parasite population and the  untreated and treated gametocyte samples. Slides were scanned with an Agilent G2600D scanner using methods previously described (Painter, H. J. Methods in Molecular Biology 923: 213-219, doi:10.1007/978-1-62703-26-7_14 (2013)).

first: Janette

last: Reader

first: Mariëtte

last: van der Watt

first: Dale

last: Taylor

first: Claire

last: Le Manach

first: Nisha

last: Mittal

first: Sabine

last: Ottilie

first: Anjo

last: Theron

first: Natalie

last: Spillman

first: Ann

last: Cowell

first: Jessica

last: Connacher

first: Phanankosi

last: Moyo

first: Erica

last: Erlank

first: Luisa

last: Nardini

first: Nelius

last: Venter

first: Sonja

last: Lauterbach

first: Belinda

last: Bezuidenhout

first: Andre

last: Horatscheck

first: Ashleigh

last: van Heerden

first: Daniel

last: Opperman

first: Lindsey

last: Orchard

first: Manuel

last: Llinás

last: Goldberg

first: Grant

last: Boyle

first: David

last: Calvo

first: Dalu

last: Mancama

first: Theresa

last: Coetzer

first: Elizabeth

last: Winzeler

first: James

last: Duffy

first: Lizette

last: Koekemoer

last: Basarab

first: Kelly

last: Chibale

first: Lyn-Marié


title: Differential glia activation in early epileptogenesis - insights from cell-specific analysis of DNA methylation and gene expression in the contralateral hippocampus

city: Oslo

first: Magnus

middle: D.

last: Vigeland

address: Kirkeveien 166

department: Medical Genetics

country: Norway

institute: University of Oslo

summary: Morphological changes in mesial Temporal Lobe Epilepsy with Hippocampal Sclerosis (mTLE-HS) are well characterized. Yet it remains elusive whether these are a consequence of seizures or originate from a hitherto unknown underlying pathology. We recently published data on changes in gene expression (GE) and DNA methylation (DNAm) in the ipsilateral hippocampus (ILH), using the intracortical kainate mouse model of mTLE-HS. In order to explore the effects of epileptic activity alone and also to further disentangle what triggers morphological alterations, we investigated glial and neuronal changes in GE and DNAm in the contralateral hippocampus (CLH). The intracortical kainic acid mouse model of mTLE-HS was used to elicit status epilepticus. Hippocampi contralateral to injection site from 8 kainate injected (KA) and 8 sham (SH) mice were extracted, and shock frozen at 24 hours post injection. Glial- and neuronal nuclei were sorted by flow cytometry. Alterations in GE and DNAm were assessed using reduced representation bisulfite sequencing (RRBS) and RNA sequencing (RNAseq). The R package edgeR was used for statistical analysis. The CLH featured substantial, mostly cell-specific changes in both GE and DNAm in glia and neurons. While changes in GE overlapped to a great degree between CLH and ILH, alterations in DNAm did not. In the CLH we found a significantly lower number of glial genes up- and downregulated compared to previous results from the ILH. Furthermore, several genes and pathways potentially involved in anti-epileptogenic effects were upregulated in the CLH. By comparing GE data from the CLH to previous results from the ILH (featuring hippocampal sclerosis), we derive potential upstream targets for epileptogenesis, including glial Cox2 and Cxcl10. Despite the absence of morphological changes, the CLH displays substantial changes in GE and DNAm. We find that GE changes related to potential anti-epileptogenic effects seem to dominate compared to pro-epileptogenic effects in the CLH and speculate whether this imbalance contributes to prevent morphological alterations like neuronal death and reactive gliosis.

overall_design: DNA methylation (RRBS) and gene expression (mRNA-seq) changes in neurons and glia; Left hippocampi of mice exposed to a right sided suprahippocampal kainate injection (number of mice=8, number of samples=3) compared to left hippocampi of mice exposed to a right sided suprahippocampal NaCl injection (number of mice=8, number of samples=3) at 24 hrs past injection.

first: Toni

middle: C

last: Berger

first: Hanne

last: Hjorthaug

first: Cecilie

last: Nome

first: Erik

last: Taubøll

first: Kaja

middle: K

last: Selmer

first: Kjell

last: Heuser


title: Single-cell transcriptome profiling of the vaginal wall in women with severe anterior vaginal prolapse

first: Bao-Fa

last: Sun

address: Da-Tun Road

institute: Beijing Institute of Genomics (BIG) of Chinese Academy of Sciences (CAS)


title: scRNA-seq analysis of vaginal wall tissue in pelvic organ prolapse and control sample

summary: Anterior vaginal prolapse, as the most common form of POP, severely affect women’s physical and mental health. However, the cellular profiles of vaginal wall and molecular mechanism in pathological process of POP remain unclear. Here, we built the first single-cell transcriptomic atlas of prolapsed vaginal wall. We further revealed prolapse induced aberrant gene expression and transcriptional regulatory networks in cell-type specific manner in POP. Besides extracellular matrix dysregulation, dysfunction of immune cells and immune response were involved with prolapse occur. Computational prediction demonstrated that the abnormal cell-cell communication patterns present among fibroblasts, smooth muscle cells and macrophages in POP, with interplay in extracellular matrix remodeling and regulation of immune reaction. Taken together, our work provides the ﬁrst comprehensive single-cell transcriptomic atlas for deciphering gene expression landscapes of heterogeneous cell types in prolapsed anterior vaginal wall, broadens our understanding of cell identities and cell-type-speciﬁc gene changes in POP and demonstrated the vital role of enhanced interplay between non-immune cells and immune cells in prolapsed vaginal wall.

first: Ya-Qian

last: Li

first: Qing-Yang

last: Zhang

first: Yun-Gui

last: Yang

first: Lan

last: Zhu


title: Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and Otud1-/- distal colonic tumor Transcriptomes

city: beijing

first: Tongtong

last: Liu

address: Peking University Health Science Center, 38 Xueyuan Road, Haidian District, Beijing

institute: Peking University

summary: Conclusion: Otud1-/- mice are more sensitive to azoxymethane(AOM)-Dextran sulfate (DSS) induced colon tumorigenesis

overall_design: 6 weeks WT and Otud1-/- C57BL/6 male mice were Intraperitoneal injection AOM at the day 0, followed by 3 cycles of 4 days 1.5% DSS and 14 days water. At day 81, Then distal tumor-filled colon was taken out and the RNA is extracted by Trizol method, followed by eukaryotic RNA-seq and associated analysis

first: Fuping

last: You


title: Combination treatment with metformin and tacrolimus improves systemic immune cellular homeostasis by modulating Treg and Th17 imbalance

status: Public on Nov 11 2020

city: Seoul

first: Mi-La

last: Cho

address: 222,Banpo-daero, Seocho-gu

institute: The Catholic University of Korea

summary: Recycling and supply of plasma membrane (PM), referred to as PM turnover, are essential for maintaining integrity of neurons undergoing continuous dynamic morphological changes. Yet, the link of PM turnover to neuronal pathophysiology remains largely elusive. Here we showed that a subset of toxic polyglutamine proteins markedly compromised local targeting-recycling of PM components, reflecting a unique feature of early neuropathies. Such disruption of PM turnover in dendrites was ascribed primarily to alterations in dendritic endosomes and Golgi outposts accounting for local PM recycling and supply, respectively. Genome-wide mRNA-sequencing analysis identified CREB3L1/CrebA-COPII pathway to be responsible for the disruption of PM turnover. Indeed, CrebA overexpression reversed PM turnover impairment caused by these toxic proteins through restoring COPII pathway. Thus we demonstrate how PM turnover is linked to aberration of neuronal integrity in pathological conditions as well as its near-complete restoration through genetic engineering of CREB3L1/CrebA-COPII pathway.

overall_design: mRNA expression profiles of spleen CD4+ cells by Illumina NovaSeq 6000.

first: M

middle: J

last: Park


title: Single nuclei RNA-sequencing of adult human hearts

city: Lund

first: Olof

last: Gidlof

address: Solvegatan 19

institute: Lund University

summary: We report single nuclei RNA-sequencing data from two frozen left ventricular biopsies from a patient with dilated cardiomyopathy, providing a perspective on the cell types of the adult human failing heart.

overall_design: Droplet-based single nuclei RNA-sequencing of PCM1+ and PCM1- nuclei from adult left ventricular tissue

last: Gidlöf

first: Gustav

last: Smith


title: CDK1-formin signal confers microvillar effacement by an attaching and effacing (A/E) pathogen

city: Tainan

first: Cheng-Rung

last: Huang

address: University Road

country: Taiwan

institute: National Cheng Kung University

summary: Enterohemorrhagic Escherichia coli (EHEC) induces the attachment and effacement of intestinal microvilli. While the molecular mechanisms contributed to the attachment of EHEC have been thoroughly studied, the underlying mechanisms for the effacement of intestinal microvilli induced by EHEC remained elusive.  By focus RNAi screening and genetic analysis in C. elegans and further reconfirmed in human Caco-2 intestinal epithelial cells, we demonstrate that the CDK1-formin signal axis is required for this EHEC-induced microvillar effacement in vitro and in vivo.

overall_design: The mRNA profiles of N2 wild type C. elegans of during pathogen EDL933 and non-pathogen OP50 6 hours treatment were generated by deep sequencing, using Illumina HiSeq 2000.

first: Bang-Yu


title: Comparison of the transcriptome across cardiac cell types and cellular compartments

status: Public on Nov 10 2020

summary: The aim of the project was to compare the cytoplasmic and nuclear transcriptome of cardiac cells to that of human cardiac bulk tissue and nuclei isolated from cardiac tissue

overall_design: Whole transcriptome array analysis was performed on total, nuclear and cytoplasmic RNA from cultured human cardiac cells and human cardiac biopsies


title: Targeting mitochondrial metabolism for detection and treatment of doxorubicin-induced heart failure

city: Oxford

first: Eshita

last: Sharma

state: Oxfordshire

address: Roosevelt Drive, Headington

department: Bioinformatics

institute: Wellcome Trust Centre for Human Genetics

summary: We conducted RNAseq using mRNA extracted from rat hearts to elucidate the effect of doxorubicin chemotherapy on the heart. Rats were 250g at the start of the treatment protocol. Tissues were collected post five weekly intravenous injections of either sterile saline or 3mg/kg/week doxorubicin. Hearts were excised under deep isoflurane anaesthesia and rapidly frozen with liquid-nitrogen cooled Wallenberger tongs. Total mRNA was extracted with a Qiagen RNeasy fibrous tissue mini kit. Gene set enrichement analysis (GSEA) shows that unlike previously reported, oxidative stress is not involved in the cardiac pathology of our model (reduced cardiac function and atrophy). However, gene sets responsible for mRNA processing, ribosomes and protein synthesis and processing are decreased in doxorubicin-treated rat hearts compared to saline control hearts.

overall_design: 16 RNASeq samples across 2 conditions:  saline control (n=10) and high DOX (n=6)

first: Kerstin

last: Timm

first: Damian

last: Tyler

first: John

last: Broxholme


title: Cardiac fibroblast proliferation rates and collagen expression mature early in life and do not change with advancing age [RNA-Seq]

city: Vienna

first: Anela

last: Tosevska

address: Waehringer Guertel 18-20

department: Division of Rheumatology

institute: Medical Univrsity of Vienna

summary: RNA sequencing from mouse hearts or PDGFR⍺ cardiac fibroblasts along time of aging.

overall_design: Examination of mouse heart cell expression changes after myocardial Infarction

first: Rimao

last: Wu

first: Feiyang

last: Ma

first: Colin

last: Farrell

first: Matteo

last: Pellegrini

first: Arjun

last: Deb


title: m6A profiling of early, adolescent, aged and Alzheimer brains

city: Atlanta

first: Andrew

last: Shafik

address: 615 Michael Street

department: Human Genetics

institute: Emory University

summary: m6A-seq was performed on 4 brain regions (cortex, cerebellum, hypothalmus and hippocampus) of 2 week, 4 week, 6 week, 26 week and 52 week old BL6 mice. m6A profiling was also performed on human adolescent and old brain tissue (region BA9). m6A-seq was also performed on WT and 5xFAD mice (Alzheimer).

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: RNA was extracted from the brain tissues in biologcial duplicates. m6A-seq was completed on these samples using a m6A-antibody coupled with NGS. RNA-seq of the same samples are also included to serve as a background for m6A peak calling.

first: Peng

last: Jin


title: Validation of human microRNA target pathways enables evaluation of target prediction tools

first: Lena

last: Krammes

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


title: A single day of TGF-β1 exposure activates chondrogenic and hypertrophic differentiation pathways in bone marrow-derived stromal cells (BMSC)

city: Bethesda

first: Kathryn

last: Futrega

state: MD

address: 30 Convent Ave

department: NIDCR

institute: NIH

summary: We profile the change in gene expression of BMSC and ACh in chondrogenic differentiation cultures when exposed to TGF-β1 for variable durations (0, 1, 3, 7, or 21 days) over a 21 day micro-pellet culture. For BMSC differentiation cultures, as little as 1-day of TGF-β1 exposure resultsedin similar gene expression on day 21 as in BMSC cultures that were exposed to TGF-β1 for 3, 7, or 21 days of the total culture period. In contrast, ACh chondrogenic cultures do not respond to TGF-β1 in a similar fashion, and gene expression differences are observed with the early withdrawl of TGF-β1. When comparing the global gene expression of BMSC and ACh cultures, the gene expression of these cell types diverged, rather then converged over time, despite being cultured under the same conditions.

overall_design:
Purpose: To determine the duration of TGF-β1 exposure required to initiate chondrogenic differentiation of bone marrow-derived stromal cells (BMSC), also known as "mesenchymal stem cells (MSC)".
Method: Micro-pellet cultures were established in custom-made microwell plates (Microwell-mesh plates), such that each pellet was derived from 5,000 cells each. Three BMSC and two ACh donors were analysed. We analyzed cultures before induction (day 0) and harvested on day 1, 3, 7, and 21 from chonrogenic cultures continuously exposed to TGF-β1. Additionally, for one BMSC and one ACh donor, we analyzed micro-pellets cultured until day 21, with exposure to TGF-β1 for only the first 1, 3, or 7 days of the total 21-day culture.
Results: For BMSC chondrogenic differentiation cultures, regardless of the TGF-β1 exposure time (1, 3, 7, or 21 days), all the cultures converged on a similar gene expression profile by day 21. Despite the phenotypic appearance of cartilage-like tissue in BMSC differentiation cultures, based on gene expression, these cells diverged from that of ACh cultures over the same culture conditions and durations.
Conclusion: We found that a single day of TGF-β1 exposure was sufficient to trigger BMSC chondrogenic differentiation and tissue formation, similar to 21 days of TGF-β1 exposure.  Despite cessation of exogenous TGF-β1 exposure following 24 hours, intrinsic programming mediated further chondrogenic and hypertrophic BMSC differentiation.

first: Pamela

last: Robey

first: Travis

last: Klein

first: Ross

last: Crawford

first: Michael

middle: R

last: Doran


title: Single Cell Transcriptomic Analysis of Human Pluripotent Stem Cell Chondrogenesis [bulk RNA-seq]

status: Public on Nov 09 2020

city: St. Louis, MO 63110

first: Farshid

last: Guilak

state: MO

address: Campus Box 8233, Couch Research Bldg, Room 3121

department: Orthopaedic Surgery

institute: Washington University in Saint Louis

summary: It has been notoriously challenging for researchers in the fields of stem cell biology and regenerative medicine to robustly generate uniform populations of differentiated cells from human induced pluripotent stem cells (hiPSCs). In particular, the process of iPSC chondrogenesis has been difficult to reproduce among different laboratories.  While several differentiation protocols are being developed, few, if any, yield homogenous hiPSC-derived chondrocytes without any off-target contaminating cells. To improve homogeneity of hiPSC chondrogenesis, we have developed the first application of single-cell RNA sequencing to systemically deconstruct each differentiation step and delineate molecular mechanisms underlying lineage commitment of hiPSCs toward chondrocytes. We identified that MITF as well as several specific canonical and non-canonical WNTs are hub genes of gene regulatory networks governing the off-target differentiation into neural cells and melanocytes during hiPSC chondrogenesis. By inhibiting these off-target molecules, we significantly enhanced chondrogenic lineage commitment of hiPSCs without cell sorting. Using sequencing data of day 28 (pellet time point) as an example, the percentage of chondrocytes within the pellet was improved from 59.63% (standard protocol) to 87.92% (optimized protocol; note: the other 12.07% belong to mesenchymal cells). Importantly, none of the off-target neural cells and melanocytes were detected, suggesting 100% removal of off-target differentiation by the optimized method. Our optimized protocol was validated by 3 unique hiPSC lines and 3 unique hMSC lines, indicating the protocol can be broadly applied to multiple cell lines. Moreover, therapeutic efficacy of hiPSC-derived chondrocytes was further validated in vivo by subcutaneous implantation and osteochondral defect repair in immunodeficient mice.  In addition to the 11 consecutive time points from mesodermal to chondrogenic differentiation stages that were sequenced by bulk RNA-seq, we also sequenced 14 chondrogenic time points at single cell resolution. We believe that our bioinformatic analyses including gene regulatory networks, multicellular signaling models, as well as the large amount of data reported here will provide invaluable resources to investigate cell fate decision during human cartilage development.

overall_design: Bulk RNA sequencing of the samples from various time points over the course of mesodermal and chondrogenic differentiation of human induced pluripotent stem cells. Three unique hiPSC lines (i.e., BJFF, ATCC, and STAN) were sequenced in the current study.

first: Chia-Lung

first: Amanda

last: Dicks


title: Drosophila PDGF/VEGF signaling from muscles to hepatocyte-like cells protects against obesity

city: Boston

first: Yifang

last: Liu

state: MA

address: 77 Avenue Louis Pasteur, NRB 336

institute: Harvard Medical School

summary: PDGF/VEGF ligands regulate a plethora of biological processes in multicellular organisms via autocrine, paracrine and endocrine mechanisms. Here, we investigated organ-specific roles of Drosophila PDGF/VEGF-like factors (Pvfs). We combine genetic approaches and single-nuclei sequencing to demonstrate that muscle-derived Pvf1 signals to the Drosophila hepatocyte-like cells/oenocytes to suppress lipid synthesis by activating the Pi3K/Akt1/mTOR signaling cascade in the oenocytes. Additionally, we show that this signaling axis regulates the rapid expansion of adipose tissue lipid stores observed in newly eclosed flies. Flies emerge after pupation with limited adipose tissue lipid stores and lipid levels are progressively restored via lipid synthesis. We find that pvf1 expression in the adult muscle increase rapidly during this stage and that muscle-to-oenocyte Pvf1 signaling inhibits restoration of adipose tissue lipid stores as the process reaches completion. Our findings provide the first evidence in a metazoan of a PDGF/VEGF ligand acting as a myokine that regulates systemic lipid homeostasis by activating mTOR in hepatocyte-like cells.

overall_design: 10x single-nuclei RNA-sequencing of adult Drosophila Abdominal cuticle which consists of oenocytes, adipose tissue, and muscle

first: Arpan

last: Ghosh

first: Sudhir

last: Tattikota

first: Aram

last: Comjean

first: Yanhui

last: Hu

first: Victor

last: Barrera

first: Shannan

middle: H

last: Sui

first: Norbert

last: Perrimon


title: ChIP-seq of CREPT in intestinal crypts

status: Public on Nov 08 2020

city: Beijing

first: Liu

last: Yang

address: Qinghuayuan street

institute: Tsinghua University

summary: CREPT was demonstrated as a key regulator of intestinal stem cells.  To figure out the role of CREPT on transcription level, a ChIP-seq experiment was performed to identify the CREPT down-stream genes in intestinal crypt cells.

overall_design: Whole sheared DNA of intestinal crypt cells were sequenced as input, and CREPT antibody pulled-down DNA sequnces were refered to input to obtain the Peak distribution.

first: Zhijie

last: Chang


title: Gene expression profiles of irradiated WT and CREPT deleted intestinal epithelium

summary: Intestinal stem cells (ISCs) residing in the crypts are critical for the continual self-renewal and rapid recovery of intestinal epithelium. The regulatory mechanism of ISCs is not fully understood. Here we report that CREPT, a recently identified tumor-promoting gene, is preferably expressed in the crypts, where the ISCs reside, but not in the villi. The Lgr5+ ISCs have much higher CREPT protein level than Lgr5- cells. To explore the function of CREPTduring regeneration, we isolated irradiated WT and CREPT deleted intestines (Vil-CREPTKO) to perform Next generation sequencing.

overall_design: To verify the role of CREPT in intestine, we knock out CREPT in intestinal epithelium by introducing villin-cre into CREPT flox/flox mice. We applied X-ray irradiation and allowed the regeneration of intestinal villus and crypts. Total RNAs were extracted from irradiated intestines, and sequenced by BGISEQ-500.


title: Gene expression profiles of WT and CREPT deleted Lgr5+ intestinal stem cells

summary: Intestinal stem cells (ISCs) residing in the crypts are critical for the continual self-renewal and rapid recovery of intestinal epithelium. The regulatory mechanism of ISCs is not fully understood. Here we report that CREPT, a recently identified tumor-promoting gene, is preferably expressed in the crypts, where the ISCs reside, but not in the villi. The Lgr5+ ISCs have much higher CREPT protein level than Lgr5- cells. To explore the function of CREPT in ISCs, we isolated WT and CREPT deleted Lgr5+ ISCs (Lgr5-CREPTKO) to perform Next generation sequencing.

overall_design: To verify the role of CREPT in Lgr5+ ISCs, we knock out CREPT in Lgr5-GFP+ cells by intraperitoneal injection of Tamoxifen into mice, and sorted the Lgr5-GFPhigh cells from disaggregated WT and Lgr5-CREPTKO intestines. Total RNAs were extracted from sorted cells, and sequenced by BGISEQ-500.


title: Transcriptomics analysis of gene expression in pelvic organ prolapse and control sample

first: Bao-Fa

last: Sun

overall_design: Examination of gene expressive levels in pelvic organ prolapse and control sample

first: Ya-Qian

last: Li

first: Qing-Yang

last: Zhang

first: Yun-Gui

first: Lan

last: Zhu


title: Gene expression profiles of WT and Vil-CREPTKO intestinal cyrpts

summary: Intestinal stem cells (ISCs) residing in the crypts are critical for the continual self-renewal and rapid recovery of intestinal epithelium. The regulatory mechanism of ISCs is not fully understood. Here we report that CREPT, a recently identified tumor-promoting gene, is preferably expressed in the crypts, where the ISCs reside, but not in the villi. To explore the function of CREPT in ISCs, we isolated crypts to perform Next generation sequencing.

overall_design: To verify the role of CREPT in intestine, we knock out CREPT in intestinal epithelium by introducing villin-cre into CREPT flox/flox mice. Crypts were disaggregated from intestinal epithelium of WT and Vil-CREPTKO mice. Total RNAs were extracted from crypts, and sequenced by Illumina XTEN


title: Chromatin topology and the timing of enhancer function at the HoxD locus [4C-seq]

city: Geneva

first: Eddie

last: Rodríguez-Carballo

address: 4, Boulevard d'Yvoy

department: Department of Genetics and Evolution

country: Switzerland

institute: Université de Genève

summary: In tetrapods, the HoxD gene cluster is critical for proper limb formation. In the emerging limb buds, different sub-groups of Hoxd genes respond first to a proximal regulatory signal, then to a distal signal that organizes digits. These two regulations emanate from the two TADs flanking HoxD, both containing a range of appropriate enhancer sequences. The telomeric TAD (T-DOM) contains several regulatory elements controlling Hoxd genes, initially in a temporal manner and then in the proximal presumptive forearm. T-DOM is divided into two sub-TADs separated by a CTCF-rich boundary defining two regulatory modules with most limb enhancers concentrated in the more distant module. In order to understand the importance of this regulatory topology to elicit a precise Hoxd gene transcription in time and space, we both deleted or inverted this sub-TAD boundary and eliminated the CTCF binding sites. These perturbations caused a time delay in gene activation, which was subsequently resumed. We then inverted the entire T-DOM to change the respective position of the two sub-TADs, which concomitantly introduced a TAD boundary between HoxD and the inverted T-DOM. This re-arrangement had a stronger impact on the early expression and flattened the Hoxd mRNAs levels. The latter effect was rescued by re-granting access to the enhancers upon deletion of the ectopic boundary. These results highlight the importance of regulatory topologies in the temporal control of gene expression. We also show that, along with time, the affinity of enhancers to find their natural target genes can overcome the presence of both a strong TAD border, and an unfavourable orientation of CTCF sites.

overall_design: 4C-seq analysis of several viewpoints inside ther HoxD gene cluster and on the telomeric gene desert in developing mouse limb tissues.

first: Lucille

last: Lopez-Delisle

first: Denis

last: Duboule


title: Single Cell Transcriptomic Analysis of Human Pluripotent Stem Cell Chondrogenesis [scRNA-seq]

first: Farshid

last: Guilak

country: USA

overall_design: single cell RNA sequencing of the samples from various time points over the course of mesodermal and chondrogenic differentiation of human induced pluripotent stem cells

first: Chia-Lung

last: Wu

first: Amanda

last: Dicks


title: RNA microarray analysis of human placenta in normal pregnancy and preeclampsia

status: Public on Nov 06 2020

city: Shanghai

first: Lu

last: Gao

address: 800 Xiangyin Rd.

department: Physiology

institute: Second Military Medical University

summary: To investigate the differentially expressed lncRNAs and mRNAs in human placenta between normal pregnancy and preeclampsia, we performed the human LncRNA microarray analysis of 8 samples from clinical patients.

overall_design: Thirty preeclampsia patients (mean age of 33.20±0.46 years) and thirty control patients (mean age of 32.60±0.47 years) who received a caesarean section were included in this study. Preeclampsia was clinically diagnosed before caesarean. The main criteria for PE diagnosis were: SBP ≥ 140 or DBP ≥ 90 on two occasions at least 4 h apart; and proteinuria >0.3 g/24h. The control pregnancy was defined as: no medical complications and proteinuria, maternal blood pressure < 140/90 mm Hg. Of the thirty pairs of placenta samples, four pairs were randomly selected for lncRNA and mRNA microarray analysis, and the other samples were used for the following verification.

first: Wen


title: Potential importance of early focal radiotherapy following gross total resection for long-term survival in children with embryonal tumors with multilayered rosettes (ETMR)

first: Johannes

last: Gojo

address: Währinger Gürtel 18-20

department: Department of Pediatrics and Adolescent Medicine

institute: Medical University of Vienna

summary: We have generated DNA methylation profiles of 9 ETMR cases treated at the Medical University of Vienna

overall_design: 9 ETMR tumor tissue samples were profiled on IlluminaHumanMethylationEPIC arrays

first: Marcel

last: Kool


title: Transcriptomic analyses during oocyte growth

city: Illkirch

first: Stephane

last: VINCENT

address: 1 rue Laurent Fries

department: Development and Stem Cells

country: France

institute: IGBMC

summary: Our aim is to characterize the role of the TBP2 protein during the growth of the oocyte. To that aim, we analyzed by RNA-seq the transcriptome of primary oocytes from wild type and Tbp2 null ovaries at the primary (post natal day 7) and secondary follicular stage (post natal day 14).

overall_design: RNA-seq of primary oocytes at  primary follicle or secondary follicle stage from wild type or Tbp2 mutant mice.

last: Vincent


title: VAL1 and 2 recruit SWN to targets

city: guangzhou

first: Liang

middle: Bing

last: Yuan

state: Guangdong

address: No. 135, Xingang Xi Road, Guangzhou, 510275, P. R. China

department: Life of Science

institute: Sun Yat-Sen University

summary: VAL1 and 2 recruit SWN to targets

overall_design: 14-day-old seedling of pSWN:SWN-GFP swn and pSWN:SWN-GFP swn val1 val2 ChIP-seq

first: Liang-bing

first: Chen-long


title: Co-stimulation with opposing macrophage polarization cues leads to orthogonal secretion programs in individual cells

city: New Haven

first: Miller-Jensen

last: Lab

state: CT

address: 55 Prospect Street

department: Biomedical Engineering

institute: Yale University

summary: Macrophages are innate immune cells that contribute to fighting infections, tissue repair, and maintaining tissue homeostasis. To enable such functional diversity, macrophages resolve potentially conflicting cues in the microenvironment via mechanisms that remain unclear. Here, we use single-cell RNA sequencing to explore how individual macrophages respond when co-stimulated with the inflammatory stimuli, LPS+IFN-γ, and the resolving cytokine, IL-4. We find that co-stimulated macrophages display a distinct global transcriptional program. However, variable negative cross-regulation between some LPS+IFN-γ- and IL-4-specific genes results in significant cell-to-cell heterogeneity in transcription. Interestingly, negative cross-regulation leads to mutually exclusive expression of the T-cell-polarizing cytokines Il6 and Il12b versus the IL-4-associated factors Arg1 and Chil3 in single co-stimulated macrophages, and single-cell secretion measurements show that these specialized functions are maintained for at least 48 hours. Overall, our study suggests that increasing functional diversity in the population is one strategy macrophages use to respond to conflicting environmental cues.

overall_design: Bone marrow-derived macrophages were analyzed  by single-cell RNAseq (10X) after stimulation with media alone (control), LPS+IFNg, IL-4, or a combination of both.

first: Andrés

last: Muñoz-Rojas

first: Kathryn

last: Miller-Jensen


title: Chromatin topology and the timing of enhancer function at the HoxD locus [RNA-seq]

first: Eddie

summary: The HoxD gene cluster is critical for proper limb formation in tetrapods. In the emerging limb buds, different sub-groups of Hoxd genes respond first to a proximal regulatory signal, then to a distal signal that organizes digits. These two regulations are exclusive from one another and emanate separately from two TADs flanking HoxD, both containing a range of appropriate enhancer sequences. The telomeric TAD (T-DOM) contains several enhancers active in presumptive forearm cells and is divided into two sub-TADs separated by a CTCF-rich boundary, which defines two regulatory sub-modules. To understand the importance of this particular regulatory topology to control Hoxd gene transcription in time and space, we either deleted or inverted this sub-TAD boundary, eliminated the CTCF binding sites or inverted the entire T-DOM to exchange the respective positions of the two sub-TADs. The effects of such perturbations on the transcriptional regulation of Hoxd genes illustrates the requirement of this regulatory topology for the precise timing of gene activation. However, the spatial distribution of transcripts is eventually resumed, showing that the presence of enhancers sequences, rather than either their exact topology or a particular chromatin architecture, is the key factor. We also show that the affinity of enhancers to find their natural target genes can overcome the presence of both a strong TAD border and an unfavourable orientation of CTCF sites.

overall_design: RNA-seq analysis of wild-type and mutant (del(CS38-40)) in forelimb buds from E9.5 mouse embryos.


title: Single Cell Transcriptomic Analysis of Human Pluripotent Stem Cell Chondrogenesis

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

overall_design: Refer to individual Series


title: Genome-wide investigation of the dynamic changes of epigenome modifications after DNA methylation editing [ChIP-Seq]

city: Stuttgart

first: Albert

last: Jeltsch

address: Allmandring 31

department: Institute of Biochemistry and Technical Biochemistry

institute: University Stuttgart

summary: The aim of this study was to investigate the stability of DNA methylation, the dynamics of different histone modifications and the changes in expression after genome-wide introduction of DNA methylation in promotor CpG islands. Therefore, the catalytic domain of DNMT3A was fused to a zinc finger protein and expressed for three days to globally introduce de novo DNA methylation and subsequently,  the changes in the epigenome were monitored for up to eleven days.

overall_design: A stable HEK293 cell line was constructed with the catalytic domain of DNMT3A fused to a zinc finger (ZnF-3AC) which is under the control of a doxycycline (dox)-inducible promoter. GFP is co-expressed via an IRES and serves as a reporter. Cells were either harvested before dox treatment ("no dox") or grown under dox conditions for three days ("3d dox"). GFP-positive cells were enriched by FACS after 3d dox and a fraction of these cells was re-seeded on a 6-Well-plate without supplementation of dox. Five and eight days after dox removal ("5d / 8d / 11d off"), cells were harvested and a fraction of cells was re-seeded again. After eleven days of dox removal ("11d off"), cells were harvested and the experiment was stopped.

first: Julian

last: Broche

first: Goran

last: Kungulovski

first: Pavel

last: Bashtrykov

first: Philipp

last: Rathert


title: Distinct whole blood transcriptome profile of children with metabolic healthy overweight/obesity compared to metabolic unhealthy overweight/obesity

status: Public on Nov 05 2020

city: Irvine

first: ABEL

last: PLAZA FLORIDO

state: California

address: 101 Academy, Suite 150 Irvine

department: Department of Pediatrics, UC Irvine School of Medicine

institute: Pediatric Exercise and Genomics Research Center (PERC)

summary:
Background and aims: Youth populations with overweight/obesity (OW/OB) exhibit heterogeneity in cardiometabolic health phenotypes (e.g. fasting glucose, serum triglycerides, etc.). The underling mechanisms for those differences are still unclear. This study aimed to analyze the whole blood transcriptome profile (RNA-seq) of children with metabolic healthy overweight/obesity (MHO) and metabolic unhealthy overweight/obesity (MUO) phenotypes.
Methods: 27 children with OW/OB (10.14 ± 1.3 years, 59% boys) from the ActiveBrains project were included. MHO was defined as having none of the following criteria for metabolic syndrome: elevated fasting glucose, high serum triglycerides, low high-density lipoprotein cholesterol, and high systolic or diastolic blood pressure, while MUO was defined as presenting one or more of these criteria. Inflammatory markers interleukin-1β (IL-1β), IL-6, tumor necrosis factor-α (TNF-α), epidermal growth factor (EGF) and, vascular endothelial growth factor A (VEGF) were additionally determined. Total-blood RNA was analyzed by 5’-end RNA sequencing. Two different bioinformatics approaches were performed: 1) Differential gene expression analyses using Limma R/Bioconductor software package (analyses adjusted by sex and maturational status) and 2) weighted gene coexpression network analyses (WGCNA).
Results: Children with MHO had lower values of pro-inflammatory cytokines TNF-α and IL-6 compared to MUO (p < 0.05). 40 genes were differentially expressed (FDR < 0.05) in children with MHO compared to MUO. WGCNA analysis identified 23 gene coexpression modules (i.e. clusters of genes) with low preservation (Zsummary < 2) in children with MHO compared to MUO. Differential and WGCNA gene expression patterns identified 32 genes linked to metabolism, mitochondrial and immune functions.
Conclusions: Whole blood transcriptome analysis revealed a distinct pattern of gene expression in children with MHO compared to MUO children. The identified gene expression patterns related to metabolism, mitochondrial and immune functions can promote a better understanding of cardiovascular disease prognosis in individuals with MHO.

overall_design:
Total whole blood mRNA profiles of 27 children with overweight/obesity were analyzed by 5’-end RNA sequencing.
The maturational status of the participants was reflected by peak height velocity (PHV) using age and height in validated algorithms (Moore et al. 2015; PMID: 25423445). Maturity offset was calculated by subtracting the PHV age from the chronological age. All files (data and scripts) will be publicly available from the Open Science Framework (https://osf.io/xt8v4/), after the publication of the manuscript.

>>>Raw data are not available due to patient privacy concerns<<<

first: Abel

last: Plaza-Florido

first: Signe

last: Altmäe

first: Francisco

last: Esteban

first: Cristina

last: Cadenas-Sanchez

first: Concepción

middle: M

last: Aguilera

first: Elisabet

last: Einarsdottir

first: Shintaro

last: Katayama

first: Kaarel

last: Krjutškov

first: Juha

last: Kere

first: Frank

last: Zaldivar

first: Shlomit

last: Radom-Aizik

middle: B

last: Ortega Porcel


title: Single-cell transcriptome profiling of an adult human cell atlas of 15 major organs

city: Guangzhou

first: Jin-Xin

last: Bei

address: 651 Dongfeng Road East, Yuexiu District, Guanzhou, P.R. China

institute: Sun Yat-sen University Cancer Center

summary:
Background: As core units of organ tissues, cells of various types play their harmonious rhythms to maintain the homeostasis of the human body. It is essential to identify the characteristics of cells in human organs and their regulatory networks for understanding the biological mechanisms related to health and disease. However, a systematic and comprehensive single-cell transcriptional profile across multiple organs of a normal human adult is missing.
Results: We perform single-cell transcriptomes of 84,363 cells derived from 15 tissue organs of one adult donor and generate an adult human cell atlas. The adult human cell atlas depicts 252 subtypes of cells, including major cell types such as T, B, myeloid, epithelial, and stromal cells, as well as novel COCH+ fibroblasts and FibSmo cells, each of which is distinguished by multiple marker genes and transcriptional profiles. These collectively contribute to the heterogeneity of major human organs. Moreover, T cell and B cell receptor repertoire comparisons and trajectory analyses reveal direct clonal sharing of T and B cells with various developmental states among different tissues. Furthermore, novel cell markers, transcription factors and ligand-receptor pairs are identified with potential functional regulations in maintaining the homeostasis of human cells among tissues.
Conclusions: The adult human cell atlas reveals the inter- and intra-organ heterogeneity of cell characteristics and provides a useful resource in uncovering key events during the development of human diseases in the context of the heterogeneity of cells and organs.

overall_design:
We performed single-cell transcriptomes of 84,363 cells derived from 15 tissue organs of one adult donor and generated an adult human cell atlas (AHCA).

Keywords: Human cell atlas, Single-cell RNA sequencing, TCR, BCR, Transcriptome

first: Shuai

last: He

first: Lin

last: Wang

first: Yang

last: Liu

first: Yi

middle: Q

last: Li

first: Hai

middle: T

last: Chen

first: Jing

last: Xu

first: Wan

last: Peng

first: Guo

middle: W

last: Lin

first: Pan

last: Wei

first: Bo

first: Xiao

last: Xia

first: Dan

first: Jin

middle: X

first: Zhi

last: Guo


title: Genome-wide analysis of chromatin states of Ectocarpus sporophytes and gametophytes, 2020

city: Roscoff

first: J. Mark

last: Cock

address: Place Georges Teissier

institute: Station Biologique de Roscoff


title: Host cholesterol modulates the generation and enrichment of persisters during Mycobacterium tuberculosis infection

city: Singapore

first: Kaibo

last: Duan

address: 8A Biomedical Grove, Immunos Building, Level 4

country: Singapore

institute: Singapore Immunology Network

summary: A worldwide increase in the frequency of multidrug-resistant and extensively-drug-resistant cases of tuberculosis is mainly due to the therapeutic noncompliance associated with a lengthy treatment regimen. This protracted regimen is attributed to a supposedly nonreplicating and metabolically inert subset of the Mycobacterium tuberculosis (Mtb) population, called ‘persisters’. We have earlier reported that the utilization of host cholesterol is essential for Mtb persistence. However, the mechanism underlying stochastic generation and enrichment of persisters is not fully known. In this study, we showed that cholesterol-induced activation of ribonuclease toxin (VapC12) inhibits translation by targeting proT tRNA and is critical for the generation of persisters in a heterogeneous Mtb population.  A vapC12-null mutant strain (ΔvapC12) failed to persist and showed hypervirulence in a guinea pig model of tuberculosis. We identify a novel strategy through which cholesterol-specific activation of a toxin–antitoxin (TA) module in Mtb leads to the persister formation during infection. Our study provides an opportunity for targeting persisters, a new paradigm facilitating tuberculosis drug development.

overall_design: Examination of the effect of glycerol and cholesterol on Wild type Mtb (H37Rv) and mutant Mtb strain (vapC12 mutant) during rifampicin treatment

first: Sakshi

last: Talwar

first: Amit

last: Pandey

last: Singhal


title: 4-1BB Co-stimulation Further Enhances Anti-PD-1-Mediated Reinvigoration of Exhausted CD39+ CD8 T Cells from Primary and Metastatic sites of Epithelial Ovarian Cancers

status: Public on Nov 04 2020

city: Daejeon

first: Galam

last: Leem

address: 291 Daehakro Yusunggu

institute: KAIST

overall_design: Compare gene expression patterns between CD137 expressing PD-1high CD39+ CD8 T cells and CD137 non-expressing PD-1high CD39+ CD8 T cells. Control cells were PD-1+ CD39- CD8 T cells.

first: Su-Hyung

last: Park


title: A temporally resolved transcriptome for developing “Keller” explants of the Xenopus laevis dorsal marginal zone

city: Seattle

first: Anneke

middle: Dixie

last: Kakebeen

state: WA

address: 5611 9th Ave NW

institute: University of Washington

summary: Explanted tissues from vertebrate embryos reliably develop in culture and have provided essential paradigms for understanding embryogenesis, from early embryological investigations of induction, to the extensive study of Xenopus animal caps, to the current studies of mammalian gastruloids. Cultured explants of the Xenopus dorsal marginal zone (“Keller” explants) serve as a central paradigm for studies of convergent extension cell movements, yet we know little about the global patterns of gene expression in these explants. In an effort to more thoroughly develop this important model system, we provide here a time-resolved bulk transcriptome for developing Keller explants.

overall_design: RNA-Seq analysis of a timecourse of dorsal marginal zone explants from Xenopus embryos from stage 11 to stage 18.

last: Kakebeenm

first: Robert

last: Huebner

first: Asako

last: Shindo

first: Kujin

last: Kwon

first: Taejoon

first: Andrea

last: Wills

first: John

last: Wallingford


title: Next generation sequencing of the transcriptome of NPC cell line C666_1 under various drug treatments.

city: London

first: Matt

last: Lechner

state: Please Select

address: 72 Huntley Street

country: United Kingdom

institute: UCL

summary: The NPC cell line C666_1 is known to be infected with Epstein Barr virus (EBV), and to have high expression of SSTR2A.  The cell line was treated with PENN221 (an SSTR2A targeted drug conjugate) , Belinostat (a histone deacetylase inhibitor), DMSO (negative control) or left untreated (negative control). Both PENN221 and Belinstat resulted in increased cell death of the cell line. Treated samples were sequenced at 24h and 72h post treatment.

overall_design: mRNA profiles of untreated and PEN221, Belinostat or DMSO treated NPC cell line C666_1 at 24h and 72h post treatment.

first: Christopher

last: Steele

first: Volker

last: Schartinger


title: Chromatin occupancy assessment an AML cell line treated with vehicle control, BETi, MDM2i, or a drug combination (BRD4-bound profiles)

city: La Jolla

first: Xue

last: Lei

state: CA

address: 10901 N Torrey Pines Rd

institute: SBP medical discovery institute

summary:
BRD4 chromatin occupancy changes in human OCI-AML3 cells treated with DMSO (vehicle control), the BET inhibitor CPI-203, the MDM2 inhibitor Nutlin-3a, or a combination of both drugs, were compared.
Method: Genomic DNA from the OCI-AML3 cell line treated for 24 hrs with either DMSO, CPI-203, Nutlin-3a or a combination of both drugs was extracted, BRD4-bound chromatin was immunoprecipitated, then DNA was sequenced with an Illumina NextSeq 500 sequencer. Sequence reads passing the quality control filters were aligned using Bowtie2 and then analysed with SICER.

overall_design: BRD4-bound chromatin profiles from drug-treated human OCI-AML3 cells were generated, in duplicate, using an Illumina NextSeq 500 sequencer.

first: Ashley

last: Newcombe

first: Peter

last: Adams

first: Kathryn

last: Gilroy


title: Chromatin occupancy assessment an AML cell line treated with vehicle control, BETi, MDM2i, or a drug combination (p53-bound profiles)

summary:
p53 chromatin occupancy changes in human OCI-AML3 cells treated with DMSO (vehicle control), the BET inhibitor CPI-203, the MDM2 inhibitor Nutlin-3a, or a combination of both drugs, were compared.
Method: Genomic DNA from the OCI-AML3 cell line treated for 24 hrs with either DMSO, CPI-203, Nutlin-3a or a combination of both drugs was extracted, p53-bound chromatin was immunoprecipitated, then DNA was sequenced with an Illumina NextSeq 500 sequencer. Sequence reads passing the quality control filters were aligned using Bowtie2 and then analysed with MACS.

overall_design: p53-bound chromatin profiles from drug-treated human OCI-AML3 cells were generated, in quadruplicate, using an Illumina NextSeq 500 sequencer.

first: Anne-Louise

last: Latif


title: Acute effects of beta2-adrenergic receptor activation on macrophage transcriptome

status: Public on Nov 03 2020

city: Molndal

first: Kasparas

last: Petkevicius

address: Pepparedsleden 1

department: CVRM Metabolism

country: Sweden

institute: AstraZeneca

summary: The study was designed to investigate the acute effects of B2AR receptor activation on global gene expression changes in bone marrow-derived macrophages. Fenoterol was chosen as B2AR agonist, but our earlier experiments using B2AR antagonists and B2AR knockout cells indicated that norepinephrine signal predominantly via B2AR in macrophages.

overall_design: Bone marrow cells were isolated from 4 mice and differentiated to macrophages in vitro. Cells from each mouse were either untreated (control) or treated with beta2-adrenergic receptor agonist fenoterol for 1 or 4 hours, in the presence of BMDM culture medium. Cells were then lysed and total RNA was isolated for sequencing.

first: Antonio

last: Vidal-Puig


title: Analysis of IFN-I responses of human CD1c+ DC and monocytes by CITE-sequencing

status: Public on Nov 01 2020

city: Toronto

first: Melanie

last: Girard

address: 1 King's College Circle

department: Immunology

country: Canada

institute: University of Toronto

summary: Using CITE-sequencing, cell-type specific responses to type-I interferon stimulation were analysed across human CD1c+ dendritic cell and monocyte subsets, showing that IFN-β drives the maturation of DC3 and the acquisition of a unique costimulatory profile characterized by high GITRL expression.

overall_design: PBMC from three distinct human donors were cultured for 18h with or without recombinant human IFN-β. Cells were then enriched for CD1c+ dendritic cells and monocytes, labeled with TotalSeq-A antibodies and partitioned using the 10X platform. The list of Total-seq A antibodies and their oligo tag sequence is available as a supplementary file.

first: Jaclyn

last: Law

first: Maria

middle: I

last: Edilova

first: Tania

last: Watts


title: RNA-seq of WT, val1, val2, and val1 val2 14-day-old seedling in Arabidopsis

first: Liang

last: Yuan

country: China

summary: 14-day-old seedling of WT, val1, val2, and val1val2 were performed RNA-seq to analyzed their differential expression genes in Arabidopsis.

overall_design: 12 samples from wild-type, val1, val2 and val1 val2 14-d-old seedlings with three biological replicates.

first: Chen

middle: L

last: Li