title: Transcriptional activity and epigenetic regulation of transposable elements in the symbiotic fungus Rhizophagus irregularis

status: Public on Sep 16 2021

city: Cambridge

first: Charles

last: Bradshaw

address: Tennis Court Road

department: Gurdon Institute

institute: University of Cambridge

summary: We report polyA+ mRNA profiles in a developmental assay where R. irregularis spores were exposed to either medium containing rice root-derived exudates or a mock nutrient medium. We report small RNA repertoires produced from R. irregularis spores using two different isolation techniques. We report the application of single-molecule-based DNA sequencing for profiling of CG methylation in untreated R. irregularis. spores.

overall_design: Examination of mRNA profiles in mock and exudate-treated spores at three time points: a 0h untreated time point, 24h and 48h post treatment. RNAseq reads were generated by deep sequencing, in quadruplicate, using paired-end 150bp Illumina sequencing. Small RNA profiles were produced by oxidation (NaIO4 treatment) and Argonaute isolation (Lexogen TraPR column treatments), and compared to untreated controls.

first: Alexandra

last: Dallaire

first: Bethan

last: Manley

first: Sebastian

last: Schornack


title: Postnatal SETD1B is essential for learning and the regulation of neuronal plasticity genes

city: Gottingen

first: Andre

last: Fischer

state: NS

address: Von Sieboldstr 3a

department: Epigenetic Mechanisms in Dementia

country: Germany

institute: German Center for Neurodegenerative Diseases (DZNE)

type: Genome binding/occupancy profiling by high throughput sequencing

type: Expression profiling by high throughput sequencing

summary: We have analyzed changes in histone 3 lysine 4 methylation (H3K4me3 and H3K4me1), histone acetylation (H3K9ac and H3K27ac) and gene expression resulting from Setd1b knockdown in adult hippocampal CA neurons in mice. We implemented Cre/loxP-mediated conditional knockout strategy in order to knockdown this histone methyltransferase in excitatory forebrain neurons in adult mice.

overall_design: Examination of H3K4me3, H3K4me1, H3K9ac and H3K27ac levels, and gene expression in hippocampal CA neurons of adult Setd1b cKO mice.

first: Cemil

last: Kerimoglu

first: M Sadman

last: Sakib


title: Transcriptome analysis of novel CPT-CEF-treated HT29 colon cancer cells to evaluate drug cytotoxicity

status: Public on Sep 15 2021

city: Chennai

first: Suresh

middle: Kumar

last: Subbiah

address: 173, Agaram Main Rd, Selaiyur, Chennai, Tamil Nadu 600073, India

country: India

institute: Bharath university

summary:
Purpose: To identify differentially expressed genes in HT29 colon cancer cells after treatment with a novel formulation of camptothecin with β-cyclodextrin-EDTA-Fe3O4 nanoparticle-conjugated nanocarriers (CPT-CEF)
Methods:Treated HT29 cell lines with CPT-CEF, isolated total RNA from HT29 colon cancer cells, and prepared library for RNA sequencing. Carried out comparative transcriptomic studies between treated and untreated cells to find out which gene functions were dysregulated by CPT-CEF.
Results: The study yielded 247 DEGs ((FDR<0.05, FC>2.0) that were affected by CPT-CEF treatment in the HT29 colon cancer cells. The results obtained from cell cycle analysis, mitochondrial depolarization assay and acridium orange/propidium iodide double staining showed potential of CPT-CEF in cancer cell inhibition.
Conclusion: Our study successfully identified DEGs in the CPT-CEF treated HT29 colon cancer cells that pointed to inhibition of cancer progression. To further affirm, animal studies are needed.

overall_design: Comparative transcriptomic studies between β-cyclodextrin-EDTA-Fe3O4 nanoparticles treated and untreated HT29 cells

middle: K

first: Pooi

middle: L

last: Mok


title: Transcriptome-wide maps of m6A RNA methylation marks in murine liver

city: Columbus

first: Kalpana

last: Ghoshal

state: Ohio

address: 1645 Neil Ave

department: Pathology

country: USA

institute: The Ohio State University

summary: N6-methyladenosine (m6A), the most prevalent modification of mRNAs at the (G/A)(m6A)C motif installed by METTL3 that plays critical role in regulation of gene expression. METTL3 is essential for embryonic development, and its dysregulation is linked to various diseases including metabolic disorders and cancer.  Here, we provide insight into this by generating Mettl3fl/fl; Alb-Cre (M3LKO) mice carrying a hepatocyte-specific deletion of Mettl3.  RNA-seq and MeRIP-seq analyses of mRNA identified significant dysregulation of metabolic genes in M3LKO mice.

overall_design: Enrichment of m6A methylated RNA in 4 murine WT and METTL3 knockout livers, and transcriptome-wide sequencing of polyadenylated RNA in 6 and 8 WT and METTL3 KO livers, respectively.

first: Cho-Hao

last: Lin

first: Hui-Lung

last: Sun

first: Juan

middle: M

last: Barajas


title: RNA Sequencing analysis of primary HCASMC genetic expression following MK2i-NP treatment.

city: Nashville

first: John

middle: William

last: Tierney

state: TN

address: 5824 Stevenson Center

department: Biomedical Engineering

institute: Vanderbilt University

summary: Primary HCASMCs that were untreated or underwent MK2i-NP treatment were compared based on genetic expression of ECM, inflammatory, and phenotype-specific genes.

overall_design: HCASMCs were cultured in 20% serum to induce phenotype switch. Treated cells were treated with MK2i-NPs for 2 hours at each passage. RNA was harvested at passage 5 when cells were ~80% confluent.

middle: W

first: Craig

last: Duvall


title: HIF-1 Dependent Genes in ER-negative PyMT Mammary Tumor Cells

status: Public on Sep 10 2021

city: Memphis

first: Daniel

middle: Lee

last: Johnson

state: Tennessee

address: 71 S Manassas

department: Molecular Informatics Core

institute: UTHSC

summary: PyMT cells (HIF-1 wild type, WT and HIF-1 knockout, KO) were compared for differential gene expression at normoxia or after exposure to hypoxia, 0.5% oxygen for 6h

overall_design: n=3 HIF-1 WT grown at normoxia, n=3 HIF-1 WT grown at hypoxia, n=3 HIF-1 KO grown at normoxia, n=3 HIF-1 KO grown at hypoxia cultured in DMEM/F12 supplemented with 2% FBS

first: Tiffany

middle: N

last: Seagroves


title: Gene expression in commercial human cerebral microvascular endothelial cells (hCMECs) line knock out or not for RNF213

status: Public on Sep 08 2021

city: Québec

first: Gaëtan

last: Le-Bel

state: Quebec

address: Local H2-00, Hôpital du Saint-Sacrement,1050 Chemin Sainte-Foy

country: Canada

institute: CUO-Recherche

summary: To study the role of RNF213, we generated RNF213-deficient human cerebral microvascular endothelial cells by the CRISPR-Cas9 double nickase method and showed that RNF213 may be an important regulator of the blood-brain barrier permeability and homeostasis

overall_design: One commercial line of hCMECs at passage 33 cultivated in proliferation or at confluency and transfected or not (wild type) with Cas9 without guide RNA (transfection control) or with ZNF213 specific guide RNA (knock-out ZNF213)

first: Vincent

last: Roy

first: Jay

last: Ross

first: Rémy

last: Pépin

first: Sergio

last: Cortez Ghio

first: Alyssa

last: Brodeur

first: Lydia

last: Touzel Deschênes

last: Phillips

first: Geneviève

last: Milot

first: Patrick

last: Dion

first: Sylvain

last: Guérin

first: Lucie

last: Germain

first: François

last: Berthod

last: Auger

first: Guy

last: Rouleau

first: Nicolas

last: Dupré

last: Gros-Louis


title: Gene expression in the hippocampal DG in WT and Cav3.1KO mice

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: 10-1 tebiro 6-chome

country: Japan

institute: Toray Industries,Inc.

summary: Low-threshold voltage gated T-type calcium channels are characterized by unique electrophysiological features with the fast inactivation and slow deactivation kinetics. Previous reports suggest that T-type calcium channels may be involved in the adult hippocampal neurogenesis, however, function of T-type calcium channels in newly generated cells is still uncertain. We demonstrated that Cav3.1 is predominantly localized in the NPCs in mouse SGZ, and that deletion of Cav3.1 attenuates proliferation and survival in 5-bromo-2'-deoxyuridine (BrdU)-labeled new born cells in the hippocampal DG. To reveal mechanism underlying impaired adult hippocampal neurogenesis in Cav3.1 KO mice, gene expression in the hippocampal DG is compared between WT and Cav3.1 KO mice. We here defined several altered genes related with cell apoptosis, proliferation and neuronal differentiation in Cav3.1 KO mice.

overall_design: After decapitation of animals, brain tissue from hippocampal DG region was dissected and stored at −80 °C until assay. We assayed 4 brain slices of WT and Cav3.1 KO mice, respectively.

first: Yasushi

last: Yabuki

first: Norifumi

last: Shioda

first: Kohji

last: Fukunaga


title: Multiomic analysis reveals decidual-specific transcriptional programing of MAIT cells

status: Public on Sep 07 2021

city: Madison

first: Aleksandar

middle: K.

last: Stanic

state: WI

address: 202 S. Park St., Meriter Atrium B

department: Obstetrics and Gynecology

institute: University of Wisconsin - Madison

summary:
Problem: Mucosal-Associated Invariant T (MAIT) cells have been recently identified at the maternal-fetal interface. However, transcriptional programming of decidual MAIT cells in pregnancy remains poorly understood.
Method of Study: We employed a multiomic approach to address this question. Mononuclear cells from the decidua basalis and parietalis, and control PBMCs, were analyzed via flow cytometry to investigate MAIT cells in the decidua and assess their transcription factor expression. In a separate study, both decidual and matched peripheral MAIT cells were analyzed using Cellular Indexing of Transcriptomes and Epitopes by Sequencing (CITE-seq) coupled with gene expression analysis. Lastly, decidual MAIT cells were stimulated with E. coli and expression of MR1 by antigen presenting cells was measured to evaluate decidual MAIT cell function.
Results: First, we identified MAIT cells in both the decidua basalis and parietalis. CITE-seq, coupled with scRNAseq gene expression analysis, highlighted transcriptional programming differences between decidual and matched peripheral MAIT cells at a single cell resolution. Transcription factor expression analysis further highlighted transcriptional differences between decidual MAIT cells and non-matched peripheral MAIT cells. Functionally, MAIT cells are skewed towards IFNg and TNFa production upon stimulation, with E. coli leading to IFNg production. Lastly, we demonstrate that MR1, the antigen presenting molecule restricting MAIT cells, is expressed by decidual APCs.
Conclusion: MAIT cells are present in the decidua basalis and obtain a unique gene expression profile. The presence of MR1 on APCs coupled with in vitro activation by E. coli suggests that MAIT cells might be involved in tissue-repair mechanisms at the maternal-fetal interface.

overall_design: CD3+ T cells were obtained from matched decidua basalis and peripheral blood samples from three individuals and submitted for single cell RNA and antibody capture sequencing. Unsupervised clustering analysis identified a cluster that was determined to be MAIT cells based on the surface protein expression of CD161 and TCR-Va7.2.

first: Jessica

last: Vazquez

first: Melina

last: Chavarria

first: Deborah

last: Chasman

first: Rene

last: Welch Schwartz

first: Chanel

middle: T

last: Tyler

first: Gladys

last: Lopez

first: Rachel

middle: C

last: Fisher

first: Irene

last: Ong


title: Low-input bulk RNA sequencing of thymic, mediastinal adipose tissue, and aortic arch CD4+CD8+ (DP) cells

status: Public on Sep 28 2021

city: La Jolla

first: Vasantika

last: Suryawanshi

state: CALIFORNIA

address: 9420 Athena Circle

institute: La Jolla Institute of Immunology

summary:
Purpose: To establish if and how mediastinal and adipose tissue and aortic arch CD4+CD8+TCRb- cells (DPs) would differ from thymic DPs, we sorted DPs from all three regions by flow cytometry and subjected the cells to a low-input deep transcriptional profiling assay.
Methods: Thymi, mediastinal adipose tissue, and aortic arches of five female, 8-week-old C57BL/6J mice were collected and pooled. Aortic arches and mediastinal adipose tissue were digested as previously described (PMID: 14597735) and single cell suspensions were generated from all three tissues. Four pools were generated per tissue. 400 viable CD4+CD8b+TCRb- cells were sorted into 8ul low-input lysis buffer containing RNaseH inhibitor, dNTPs, and 0.1% Triton X-100 in replicates. Material of 200 cells was reverse transcribed and amplified. Illumina libraries were prepared and sequenced.
Results: A total of 2147 genes were differentially regulated between the different DP populations. Extrathymic DPs had 858 genes upregulated and 1284 genes downregulated compared to thymic DPs. 94 genes were commonly regulated in the two extrathymic DP subsets, whereas 23 genes were uniquely expressed in MAT DPs, 31 different genes were exclusively expressed in aortic arch DPs.
Conclusion: Our study is the first to identify and provide deep transcriptional analysis two extra-thymic DP populations in mice.

overall_design: Bulk transcriptomes of CD4+CD8+TCR- DPs residin in the thymus, medastinal adipose tissue, and aortic arch of female, 8-week-old C57BL/6J mice.

first: Holger

last: Winkels

first: Yanal

last: Ghosheh

first: Klaus

last: Ley


title: RNA-seq analysis of zip-1(jy13) mutants (ERT590) following 0.5 h and 4 h BTZ treatment

status: Public on Sep 05 2021

first: Emily

last: Troemel

state: California

address: 4202 Bonner Hall, 9500 Gilman #0349

department: Cell and Developmental Biology

institute: University of California, San Diego

summary: Comparison of gene expression in wild-type and zip-1(jy13) mutant animals following bortezomib or DMSO (control) treatment. We report that induction of some genes upon bortezomib treatment is zip-1 dependent.

overall_design: Synchronized populations of N2 and zip-1(jy13) animals that were grown at 20°C for 48 h were treated with DMSO or bortezomib (BTZ) for 0.5 h or 4 h. Total RNA was isolated. 3 experimental replicates were performed.

first: Vladimir

last: Lažetić

first: Fengting

last: Wu

first: Lianne

middle: B

last: Cohen

first: Kirthi

last: Reddy

first: Ya-Ting

last: Chang

first: Spencer

middle: S

last: Gang

first: Gira

last: Bhabha

middle: R


title: Single cell atlas for mammals, reptiles and birds

status: Public on Sep 04 2021

city: shenzhen

first: CNSA

last: CNGB

address: BGI

country: China

institute: BGI

summary: The availability of viral entry factors is a prerequisite for the cross-species transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Large-scale single-cell screening on animal cells is a powerful tool to reveal the expression patterns of viral entry genes for different hosts. But such exploration for SARS-CoV-2 remained limited. Here, we presented the broadest pan-species single-nucleus RNA sequencing study to date, covering 11 representative species in pets (cat, dog, hamster, lizard), livestock (goat, rabbit), poultry (duck, pigeon) and wildlife (pangolin, tiger, deer), from which we investigated the co-expression of ACE2 and TMPRSS2. Notably, the proportion of SARS-CoV-2 putative target cells in cat was found considerably higher than that of other species investigated in this study, highlighting the necessity to carefully evaluate the role of cats during SARS-CoV-2 circulation. Furthermore, cross-species analysis of comparative lung cell atlas in mammals, reptiles and birds revealed core developmental programs, critical connectomes and conserved regulatory circuits among evolutionarily distant species. Additionally, we developed a user-friendly and freely accessible online platform named PANDORA for researchers to fully exploit the pan-species single cell atlas. Overall, our work provides a compendium of gene expression profiles for non-model animals, which could be employed to identify potential SARS-CoV-2 target cells and narrow down putative zoonotic reservoirs. Alternatively, our resources could also be utilized to illuminate the cellular and molecular mechanisms underlying animal tissue evolution.

sample_organism:
Anas platyrhynchos
Columba livia
Canis lupus familiaris
Felis catus
Capra aegagrus
Manis javanica
Oryctolagus cuniculus
Mesocricetus auratus
Anolis carolinensis
Cervus nippon taiouanus
Panthera tigris altaica

overall_design: To investigate the expression of SARS-CoV-2 receptors ACE2 and TMPRSS2 from 11 representative species in pets (cat, dog, hamster, lizard), livestock (goat, rabbit), poultry (duck, pigeon) and wildlife (pangolin, tiger, deer).

first: Dongshegn

last: Chen


title: Embryonic small RNA and RNA profiles of Parhyale hawaiensis

status: Public on Sep 06 2021

city: Mancheste

first: Llilians

last: Calvo

address: Oxford Rd

country: United Kingdom

institute: University of Manchester

type: Non-coding RNA profiling by high throughput sequencing

summary: Next generation sequencing analysis of small RNA-seq and RNA-seq of successive time intervals during P. hawaiensis embryogenesis

overall_design: Total RNA was extracted from staged embryos and small RNAs and RNAs were separated into two fractions using the SPLIT RNA extraction kit from Lexogen. Small RNA or stranded polyA-RNA libraries were generated according to the manufacturer's instructions (Lexogen and Illumina kits respectively).

first: Maria

last: Birgaoanu

first: Tom

last: Pettini

first: Matthew

last: Ronshaugen

first: Sam

last: Griffiths-Jones


title: Extracellular vesicles induce aggressive phenotype of luminal breast cancer cells by PKM2 phosphorylation

status: Public on Sep 09 2021

city: Seoul

first: Seo Young

last: Kang

address: Magokdong-ro 2-gil, Gangseo-gu

country: South Korea

institute: Ewha Womans University College of Medicine

summary: We report that EVs originated from cancer cells can modulate glucose metabolism in the recipient cancer cells and induce cell proliferation and aggressive phenotype. Two breast cancer cell lines with different levels of glycolytic activity, MDA-MB-231 of a claudin low-type breast cancer cell and MCF7 of luminal type breast cancer cell, were selected and co-cultured, as the originating and recipient cells using indirect co-culture system such as transwell system or microfluidic system. Proteomic profiling of the co-cultured MCF7 cells revealed proliferation and dedifferentiation of the MCF7 cells following co-culture with the MDA-MB-231 cells. Transcriptomic analysis demonstrated that glycolysis increased in the co-cultured MCF7 cells, and the component analysis of glycolysis-related genes revealed that the second-most component after cytoplasm was extracellular exosomes. In addition, 36 significant KEGG pathways were identified in a total of 856 proteins identified by proteomin analysis of MDA-MB-231-induced EVs. Among these pathways were the main pathways (glycolysis/gluconeogenesis, pyruvate metabolism, and PI3K-Akt signaling pathways) that could explain the metabolic modulation of MCF7 cells. In our work, we indirectly show that it is MDA-MB-231-derived EVs that play an important role in this phenomenon. Our study highlights the potential effects of aggressive cancer cells on other surrounding cancer cells through EVs.

overall_design: Glucose metabolism changes in MCF7 cells after co-culture with MDA-MB-231 cells

first: Seo

middle: Y

first: Eun

middle: J

last: Lee

first: Yoori

last: Choi

first: Do

last: Hwang

first: Dong


title: RNAseq analysis of genes differentially expressed in C. elegans exposed to the mold Penicillium brevicompactum

city: New York

first: Sean

last: Wallace

state: NY

address: 1230 York Avenue Box 46

department: Laboratory of Developmental Genetics

institute: The Rockefeller University

summary: We report genes that are differentially expressed in wild type and nhr-45 mutant C. elegans that were grown in the presence or absence of the mold Penicillium brevicopactum

overall_design: sequencing of mRNA obtained from young adult C. elegans (approximately 48 hours from L1 arrest at 20 degrees C)

first: Shai

last: Shaham


title: Identification and drug-induced reversion of molecular signatures of Alzheimer´s disease onset and progression in AppNL-G-F, AppNL-F and 3xTg-AD mouse models (RNA-seq: WT/NLGF)

status: Public on Sep 03 2021

city: Sabadell

first: Antoni

last: Berenguer-LLergo

state: Barcelona

address: Parc del Taulí, 1

department: A8G2 Group - Rheumatology Service

country: Spain

institute: Parc Taulí Research and Innovation Institute (I3PT)

summary: Alzheimer's disease (AD) is the most common form of dementia. Over fifty years of intense research have revealed many key elements of the biology of this neurodegenerative disorder. However, our understanding of the molecular bases of the disease is still incomplete, and the available medical treatments for AD are mainly symptomatic and hardly effective. Indeed, the robustness of biological systems have revealed that the modulation of a single target is unlikely to yield the desired outcome, and we should move from gene-centric to   systemic therapeutic strategies. Here, we present the complete characterization of three murine models of AD at different stages of the disease (i.e. onset, progression and advanced). To identify genotype-to-phenotype relationships, we combine the cognitive assessment of these mice with histological analyses and a full transcriptional and protein quantification profiling from hippocampus. Comparison between the gene and protein expression trends observed in AD progression and physiological ageing exposed certain commonalities, such as the upregulation of microglial and inflammation markers. However, although there is an accelerated ageing in AD models, there are other factors specifically associated with A_ pathology. Despite the clear correlation between mRNA and protein levels of the dysregulated genes, we discovered a few proteins whose abundance increases with AD progression, while the corresponding transcript levels remain stable. Indeed, we show that at least two of these proteins, namely lfit3 and Syt11, co-localize with A_ plaques in the brain. Finally, we derive specific A_-related molecular AD signatures, and we look for drugs able to globally revert them. We found two NSAIDs (dexketoprofen and etodolac) and two anti-hypertensives (penbutolol and bendroflumethiazide) that overturn the cognitive impairment in AD mice   while reducing A_ plaques in the hippocampus and partially restoring the physiological levels of AD signature   genes to wild-type levels.

overall_design: We analyzed the gene expression changes in the hippocampus of 6 months old AppNL-G-F mice treated with Etodolac (50 mg/kg), dexketoprofen (15 mg/kg), fenoprofen (50 mg/kg) and bendroflumethiazide (20 mg/kg) and the corresponding controls (vehicle-treated AppNL-G-F and Appwt/wt mice). We analyzed four mice per condition.

first: Eduardo

last: Pauls

first: Sergi

last: Bayod

first: Lidia

last: Mateo

first: Miquel

last: Duran-Frigola

first: Teresa

last: Juan-Blanco

first: Víctor

last: Alcalde

first: Patrick

last: Aloy


title: Identification and drug-induced reversion of molecular signatures of Alzheimer´s disease onset and progression in AppNL-G-F, AppNL-F and 3xTg-AD mouse models (RNA-seq: WT/3xTg)

overall_design: We analyzed the gene expression changes in the hippocampus of and 3-, 8- and 15-months 3xTg-AD mice and their corresponding controls (C57BL6/129SvJ mice). We analyzed four mice per condition.


title: Identification and drug-induced reversion of molecular signatures of Alzheimer´s disease onset and progression in AppNL-G-F, AppNL-F and 3xTg-AD mouse models (RNA-seq: WT/NLF/NLGF)

overall_design: We analyzed the gene expression changes in the hippocampus of 3-, 9- and 18-months AppNL-F mice; 3-, 6- and 9-months AppNL-G-F mice; and their corresponding controls  (Appwt/wt mice). We analyzed four mice per condition.


title: CHD5 inhibits metastasis of neuroblastoma

status: Public on Sep 11 2021

city: Ulm

first: Christian

last: Beltinger

address: Eythstr. 24

department: Dept. of Pediatrics and Adolescent Medicine

institute: University Medical Center Ulm

summary: CHD5, a tumor suppressor at 1p36, is frequently lost or silenced in poor prognosis neuroblastoma (NB) and many adult cancers. The role of CHD5 in metastasis is unknown. We confirm that low expression of CHD5 is associated with stage 4 NB. Forced expression of CHD5 in NB cell lines with 1p loss inhibited key aspects of the metastatic cascade in vitro: anchorage-independent growth, migration and invasion. In vivo, formation of bone marrow and liver metastases developing from intravenously injected NB cells was delayed and decreased by forced CHD5 expression. Genome-wide mRNA sequencing revealed reduction of genes and gene sets associated with metastasis when CHD5 was overexpressed. Known metastasis-suppressing genes preferentially up-regulated in CHD5-overexpressing NB cells included PLCL1. In patient NB, low expression of PLCL1 was associated with metastatic disease and poor survival. Knock-down of PLCL1 and of p53 in IMR5 NB cells overexpressing CHD5 reversed CHD5-induced inhibition of invasion and migration in vitro. In summary, CHD5 is a metastasis suppressor in NB.

overall_design: Comparison of gene expression from control cells and CHD5 overexpressing neuroblastoma cells

first: C

first: A

last: Laut


title: Next Generation Sequencing Facilitates Quantitative Analysis of metformin on adipogenesis Transcriptomes

status: Public on Sep 02 2021

city: Nanjing，Zhenjiang

first: Zhicong

last: Zhao

state: Jiangsu province

address: 163 Xianlin Avenue，438 Jiefang Road

institute: School of life sciences, Nanjing university, Affiliated Hospital of Jiangsu University

summary: We reported the application of transcriptome sequencing in high-throughput analysis of metformin intervention in adipogenesis. By obtaining differentially expressed genes from transcriptome, we constructed the mRNA expression profile in mouse embryonic fibroblast adipose differentiation model. We found that metformin can effectively distinguish expressed, ready to express or stably inhibited genes in the process of adipose differentiation, which reflects the cell state and lineage potential. Using an optimized data analysis workflow, we identified 5362 different expression adipogenesis responsive genes and 2539 metformin responsive genes. This study provided a framework for the application of comprehensive transcriptome analysis to the network regulation mechanism of metformin inhibiting preadipocyte differentiation

overall_design: Examination of metformin on adipose differentiation of 3T3-L1 preadipocytes

first: Guoyue

last: Yuan


title: Identification and drug-induced reversion of molecular signatures of Alzheimer’s disease onset and progression in AppNL-G-F, AppNL-F, and 3xTg-AD mouse models

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

overall_design: Refer to individual Series


title: Intestinal lipid metabolism regulates absorption and surface of gut epithelium

city: Genève

first: Jordi

last: Altirriba

address: Rue Michel-Servet 1

department: Dpts de Médecine Interne et de Physiologie cellulaire et Métabolisme

country: Switzerland

institute: Centre Médical Universitaire de Genève

summary: Intestinal surface changes in size and function in response to environmental conditions, but what propels these alterations and what are the metabolic consequences is not clear. Here we show that in mice gut surface enlarges by increasing food amount rather than caloric intake, contributing to an increased absorptive function, and that it can be reversed by reducing daily food amount. Genetic- and environment-induced gut enlargement due to overeating is principally supported by upregulation of the intestinal lipid metabolism and transport. Intestinal knock-out, and pharmacological inhibition of PPARα supress intestinal crypt formation and shorten villi in the small intestine of mice and in human intestinal biopsies, respectively, and diminish post-prandial triglyceride transport and nutrient uptake. PPARα inhibition limits lipid absorption and restricts lipid droplet growth and PLIN2 levels, critical for the droplet formation. This improves lipid metabolism, reduces body adiposity and liver steatosis, suggesting an alternative target for treating obesity.

overall_design: Examination of 2 different histone modifications in Neural progenitor cells.

first: Ozren

last: Stojanović

first: Dorothée

last: Rigo

first: Martina

last: Spiljar

first: Salvatore

last: Fabbiano

first: Nicola

last: Zamboni

first: Pierre

last: Maechler

first: Françoise

last: Rohner-Jeanrenaud

first: Mirko

last: Trajkovski


title: Transcriptome profiling of Candidatus Liberibacter asiaticus in citrus and psyllids

status: Public on Sep 01 2021

city: Norwich

first: Wenbo

last: Ma

address: Norwich Research Park

institute: The Sainsbury Laboratory

summary: Candidatus Liberibacter asiaticus (Las) is an emergent bacterial pathogen associated with the devastating citrus Huanglongbing (HLB), also known as the greening disease. Vectored by the Asian Citrus Psyllid (Diaphorina citri), Las colonizes the phloem tissue of citrus. So far, efforts of cultivating Las in vitro have not been successful and dual-transcriptome analyses could only detect ~100 Las genes due to the low abundance of bacterial RNA in infected citrus/psyllid tissues. Therefore, the biology of this pathogen is poorly understood. Here, we established a procedure to enrich Las RNA for transcriptome analysis in order to obtain insights into the interactions of Las with its two hosts. We were able to confidently determine the expression profiles of >400 Las genes, including 106 that were differentially expressed between citrus and psyllids. Genes related to transcription/translation and defense were found to be upregulated in citrus; whereas genes upregulated in psyllids are involved in metabolic pathways related to tricarboxylic acid (TCA) cycle. Genes encoding the succinate dehydrogenase and NADH quinone oxidoreductase complexes, as well as the flagellar system are also expressed to higher levels in psyllids. We also analyzed the relative expression levels of Sec-delivered effectors, which are considered key virulence factors of Las. This work advances our understanding of the HLB biology and offers novel insight into the HLB pathogenesis.

sample_organism:
Citrus x paradisi
Diaphorina citri
Citrus macrophylla

overall_design: Samples collected from midribs on HLB-infected citrus (grapefruit and macrophylla) and Asian Citrus Psyllid (ACP) insects. RNA samples underwent various pre-enrichment and post-enrichment treatments for CLas transcripts

first: Amelia

middle: H

last: Lovelace

first: Agustina

last: De Francesco


title: Potassium channel-driven bioelectric signaling affects the metastatic potential of triple negative breast cancer

city: Medford

first: Samantha

last: Payne

state: MA

address: 200 College Ave

institute: Tufts University

summary: Our data demonstrate that altering the RMP of triple-negative breast cancer (TNBC) cells by manipulating potassium channels increases in vitro invasion, tumor growth, and metastasis, inducing changes in gene expression associated with cell adhesion. We describe a novel mechanism for RMP-mediated cell migration involving cadherin-11 and the MAPK pathway. Importantly, we identify a new treatment strategy for metastatic TNBC by repurposing FDA-approved potassium channel blockers. Our results provide an understanding of a mechanism by which the bioelectricity regulates cancer cell invasion and metastasis that can advance the development of a potential new class of TNBC therapeutics.

overall_design: Examination of genetic changes in MDA-MB-231 human breast cancer cell line with overexpression of two different potassium ion channels, Kir2.1 and Kv1.5


title: Therapeutic delivery of transcription factor HNF4A mRNA attenuates liver fibrosis

city: Muenster

first: Marcos

middle: J.

last: Araúzo-Bravo

address: Rogentstrasse

institute: Max Planck Institute for Molecular Biomedicine

summary: The mRNA-based therapeutics such as COVID-19 vaccines are rapidly progressing into the clinic with a tremendous potential of benefiting millions of people worldwide. Therapeutic targeting of injuries that require transient restoration of proteins by mRNA delivery is an attractive aspect, however until recently, it has remained poorly explored. In this study, we examined for the first time therapeutic utility of mRNA delivery in liver fibrosis and cirrhosis, which contributes to millions of deaths, annually. Here, demonstrated the therapeutic efficacy of the human transcription factor hepatic nuclear factor alpha (HNF4A) encoding mRNA in murine chronically injured liver leading to fibrosis and cirrhosis. We investigated restoration of hepatocyte functions by HNF4A mRNA transfection in vitro, and analyzed the attenuation of liver fibrosis and cirrhosis in multiple mouse models, by delivering hepatocyte-targeted biodegradable lipid nanoparticles (LNP) encapsulating HNF4A mRNA. To identify potential mechanism, we performed microarray-based gene expression profiling, single cell RNA sequencing, and chromatin immunoprecipitation. We used primary liver cells and human liver buds for further functional validation. Expression of HNF4A encoding mRNA led to restoration of metabolic activity of fibrotic primary murine and human hepatocytes in vitro. Repeated in vivo delivery of HNF4A mRNA encapsulated-LNP induced a robust inhibition of fibrogenesis in four independent mouse models of hepatotoxin- and cholestasis-induced liver fibrosis. Mechanistically, we discovered that paraoxonase 1 is a direct target of HNF4A and it contributes to HNF4A-mediated attenuation of liver fibrosis via modulation of liver macrophages and hepatic stellate cells. Collectively, our findings provide the first direct preclinical evidence of the applicability of HNF4A mRNA therapeutics for the treatment of fibrosis in the liver.

overall_design: Single cell RNA-seq analysis of control and HNF4A treated mice. The Control data is split in 12 fastq files. The HNF4A data is split into 12 fastq files.

first: Taihua

last: Yang

first: Marion

last: Poenisch

first: Zhen

last: Dai

first: Qingluan

last: Hu

first: Rajendra

last: Khanal

first: Ruomeng

last: Li

first: Guangqi

last: Song

first: Qinggong

first: Qunyan

last: Yao

first: Xizhong

last: Shen

first: Richard

last: Taubert

first: Bastian

last: Engel

first: Elmar

last: Jaeckel

first: Christine

last: Falk

first: Axel

last: Schambach

first: Daniela

last: Gerovska

first: Michael

middle: P

last: Manns

first: Nigel

last: Horscroft

first: Asha

last: Balakrishnan

first: Tobias

last: Cantz

first: Frédéric

last: Chevessier

last: Ott

first: Amar

middle: D

last: Sharma


title: 5-hydroxymethylcytosine is required for terminal differentiation of Purkinje neurons

city: NYC

first: Elitsa

last: Stoyanova

address: 1230 York Ave

department: Molecular Biology

institute: Rockefeller University

type: Methylation profiling by high throughput sequencing

summary: Principal neurons in the mammalian brain exit cell cycle and execute a complex and prolonged differentiation program that continues into early adult life. Although high levels of 5-hydroxymethylcytosine (5hmC) accumulate in neurons, it is not known whether 5hmC can serve as an intermediate in DNA demethylation in postmitotic neurons. Here we report high resolution mapping of DNA methylation and hydroxymethylation, chromatin accessibility, and activating and repressive histone marks in developing postmitotic Purkinje cells (PCs).  Our data reveal new relationships between PC transcriptional and epigenetic programs, and identify a class of late expressed genes that lose both 5mC and 5hmC during terminal differentiation. Deletion of the 5hmC writers Tet1, Tet2, and Tet3 from postmitotic Purkinje cells prevents loss of 5mC and 5hmC in regulatory domains and gene bodies and hinders transcriptional and epigenetic developmental transitions, resulting in hyper-excitability and increased susceptibility to excitotoxic drugs. Our data demonstrate that Tet-mediated active DNA demethylation occurs in vivo, and that acquisition of the precise molecular and electrophysiological properties of adult PCs requires continued oxidation of 5mC to 5hmC during the final phases of differentiation.

overall_design: RNA-Seq, ATAC-Seq, ChIP-Seq, OxBS-Seq, BS-Seq

first: Micheal

last: Riad

first: Anjana

last: Rao

first: Nathaniel

last: Heintz


title: Total RNA-seq from Drosophila melanogaster.

city: Nanjing

first: Yan

last: Zeng

address: No.1, Weigang

institute: Nanjing Agricultural University

summary: High-throughput sequencing was used to study mRNA and miRNA distribution in Drosophila melanogaster.

overall_design: Total RNA was isolated from the adult fruit fly. mRNA-seq and miRNA-seq analysis were performed.


title: Differential transcriptional responses of murine alveolar macrophages to elongated mineral particles of asbestiform and non-asbestiform varieties

city: Morgantown

first: Timur

middle: Oskarovich

last: Khaliullin

state: WV

address: 1000 Frederick Lane

department: HELD

institute: NIOSH

summary: Occupational exposures to asbestiform elongated mineral particles (EMPs) may lead to diffuse fibrosis, lung cancer, malignant mesothelioma and autoimmune diseases. Cleavage fragments (CF) are chemically identical to asbestiform varieties of parent mineral, but there is no consensus on whether to treat them as asbestos from toxicological and regulatory standpoints. Alveolar macrophages (AM) are the first-responders to inhaled particulates, participating in clearance, and activating the other resident and recruited immunocompetent cells, which has an impact on the long-term outcomes. In the current study we addressed the question of how asbestiform vs. non-asbestiform EMPs affect AM responses. Max Planck Institute (MPI) cells, a non-transformed mouse line that has AM phenotype and genotype, were treated with surface area-equivalent concentrations of respirable asbestiform and non-asbestiform riebeckite/tremolite EMPs for 24h. Detectable changes in macrophage gene expression happen within 6-24 hours post-stimuli (Schneider et al., 2019), thus we performed the next generation RNA sequencing of the MPI cells 24 hours post exposure to surface area-equivalent doses of riebeckite and tremolite EMPs to see if AM immediate transcriptional reprogramming patterns are intrinsic for different minerals and/or crystallization habit.

overall_design: Global RNA expression profiles of the Max Planck Institute (MPI) cells 24 hours after treatment mith various elongated mineral particles (n=3 per treament type), were compared with expression profiles of untreated cells (n=3).

middle: O

first: Vadim

last: Zhernovkov

first: Naveena

last: Yanamala

first: Anna

middle: A

last: Shvedova


title: Transcription factors Bcl11a and Bcl11b are Required for the production and differentiation of cortical projection neurons

status: Public on Aug 31 2021

city: shanghai

first: heng

last: du

address: 131 Dong'an Road

department: Institutes of Brain Science

institute: Fudan University

summary:
Purpose:To assess changes in gene expression profiles of single cell from the wild type littermate controls cortices in E13.5, E15.5 and P0, and conditional knockout Bcl11a (and Bcl11b) at cortical projection neurons in the mouse cortices of the same ages.
Methods: E13.5, E15.5 and P0 control and mutant cortices were carefully dissected under a clean environment. Then total RNA was isolated using an RNeasy Mini Kit (QIAGEN) according to the manufacturer’s protocol, quantified using NanoDrop ND-2000, and checked for RNA integrity using Agilent 2100 bioanalyzer. RNA-seq libraries were prepared according to the Illumina TruSeq protocol.
Results: An average of 15 million reads per sample were obtained.

overall_design: RNA-seq: three mice cortical samples in each genotype at each age, totally three ages each with three different genotypes

first: Heng

last: Du

first: Ziwu

last: Wang

first: Rongliang

last: Guo

first: Lin

last: Yang

first: Guoping

last: Liu

first: Zhuangzhi

last: Zhang

first: Zhejun

last: Xu

first: Yu

last: Tian

first: Zhengang

first: Xiaosu

last: Li

first: Bin

last: Chen


title: Gene expression of murine DCs from bone marrow and spleen

city: Amsterdam

first: Martijn

last: Nolte

state: Noord-Holland

address: Plesmanlaan 125

department: Molecular Hematology

country: Netherlands

institute: Sanquin Bloedvoorziening

summary: Next to driving hematopoiesis, the bone marrow (BM) also serves as a secondary lymphoid organ, as it can drive T cell priming by resident dendritic cells (DC). When analyzing these DCs in murine BM, we uncovered that they are localized around sinusoids, can (cross)-present antigens, become activated upon intravenous LPS-injection, and for the majority belong to the cDC2 subtype which is associated with Th2/Th17 immunity. Gene-expression profiling revealed that BM-resident DCs are enriched for several c-type lectins, including Dectin-1, which can bind beta-glucans expressed on fungi and yeast. Indeed, DCs in BM were much more efficient in phagocytosis of both yeast-derived zymosan-particles and Aspergillus than their splenic counterparts, which was highly dependent on Dectin-1. DCs in human BM could also phagocytose zymosan, which was dependent on β1-integrins. Moreover, zymosan-stimulated BM-resident DCs enhanced the differentiation of hematopoietic stem and progenitor cells towards neutrophils, while also boosting the maintenance of these progenitors. Our findings signify an important role for BM DCs as translators between infection and hematopoiesis, in particular in anti-fungal immunity. The ability of BM-resident DCs to boost granulopoiesis is relevant from a clinical perspective, and contributes to our understanding of the increased susceptibility for fungal infections following BM damage.

overall_design: mRNA profiles of sort-purified dendritic cells from spleen or bone marrow from wildtype, healthy, adult mice.

first: Marieke

last: Goedhart


title: Determining the effects of hepatic As3mt overexpression on the response to arsenic in the liver of zebrafish larvae

city: Abu Dhabi

first: Kirsten

last: Sadler Edepli

state: Abu Dhabi

department: Biology

country: United Arab Emirates

institute: New York University Abu Dhabi

summary: This study was carried out to compare changes in gene expression in 120 hpf livers that overexpress as3mt in hepatocytes between after 24-hour exposure to 1.0 and 1.5 mM iAs. Tg(fabp10a:As3mt) untreated = CL 1 AS3MT 0; Tg(fabp10a:As3mt) iAs treated = CL 1 AS3MT 1 or CL 1 AS3MT 1.5.

overall_design: The samples in this series include only livers from 120 hpf zebrafish larvae that over express as3mt in hepatocytes with and without exposure to 1 and 1.5 mM of inoragnic arsenic (iAs) from 96 - 120 hpf. This study was carried out by comparing RNA extracted from 120 hpf zebrafish livers from six groups: untreated or 24-hour exposure to 1 mM or 1.5 mM iAs in CAAX-EGFP positive larvae and CAAX-EGFP positive and as3mt overexpressing larvae. To generate these samples, (tg:(fab10a:as3mt, cry:dsRed) were outcrossed to tg(fabp10a:CAAX-EGFP) and the larvae that only had the CAAX-EGFP expression in the liver and cry:dsRed in the eye were collected.  RNA from 12 livers per group collected from 5 clutches (biological replicates) per group were extracted using Trizol/Chlorofom, PolyA selected and sequenced on Illumina NextSeq550.

first: Patrice

last: Delaney

first: Anjana

last: Ramdas Nair

last: Sadler

first: Chi


title: RNA-seqencing datasets for three different vernalization time course of radish

city: Anseong

first: Dong Hwan

last: Kim

state: Gyeonggi

address: 4726 Seodong-daero, Daedeok-myeon

department: Department of Plant science and Technology

institute: Chung-Ang University

summary: We report here NGS RNA-seqencing datasets for htree different vernalization time course of radish cultivar, "Taebaek".

overall_design: Three different cold treatment (NV, V40, AV) to radish whole plants and leaf and root tissues were collected as samples: NV; 4 weeks old (non-cold treated), V; 28 days cold treated; AV; 28 days cold treated, then followed by 14 days warm temperature

first: Dong


title: Heterocellular OSM-OSMR signalling drives pancreatic cancer growth and metastasis through functional fibroblast reprogramming

status: Public on Aug 30 2021

city: MANCHESTER

first: Alexander

last: Kononov

address: Oglesby Building, 555 Wilmslow Rd,

institute: Cancer Research UK Manchester Institute

summary: Pancreatic ductal adenocarcinoma (PDA) is a lethal malignancy characterised by a pathological fibroinflammatory microenvironment. Dichotomous tumour-promoting and -restrictive roles have been ascribed to the tumour microenvironment, however the effects of individual stromal subsets remains incompletely characterised. Here, we describe how heterocellular OSM-OSMR signalling instructs fibroblast reprogramming, tumour growth and metastasis. Macrophage-secreted OSM stimulates inflammatory gene expression in cancer-associated fibroblasts (CAFs), which in turn induce a pro-tumorigenic environment and engage tumour cell survival and migratory signalling pathways. Tumour cells implanted in Osm-deficient (Osm-/-) mice display an epithelial-dominated morphology, reduced tumour growth and did not metastasise. Moreover, the tumour microenvironment of Osm-/- animals exhibit increased abundance of αSMApos myofibroblasts and a shift in myeloid and T cell phenotypes, consistent with a more immunogenic environment. Taken together, these data demonstrate how OSM-OSMR signalling coordinates heterocellular interactions to drive a pro-tumorigenic environment in PDA.

overall_design: RNAsequencing of pancreatic stellate cells from mono-culture and isolated from co-culture with tumour cells or tumour cells and macrophages. 4 biological replicates for each culture condition

first: Brian

last: Lee

first: Christopher

last: Below

first: Adrian

last: Blanco-Gomez

first: Felix

last: Heider

first: Jingshu

first: Colin

last: Hutton

first: Xiaohong

first: Tamara

last: Scheidt

first: Kenneth

last: Beattie

first: Claus

last: Jørgensen


title: Aberrant chromatin landscape upon loss of the H3.3 chaperone Daxx leads to Pu.1-mediated neutrophilia and inflammation

city: Bonn

first: Paolo

last: Salomoni

address: Sigmund-Freud-Str. 27

institute: DZNE e.V.


title: Assessing the global distribution of histone modifications in KBM-7 cells

status: Public on Aug 27 2021

city: Cambridge

first: Iva

last: Tchasovnikarova

address: Tennis Court Road

department: The Gurdon Institute

institute: University of Cambridge

summary: The goal of the experiment was to determine the distrubtion of histone modifications in KBM-7 cells.

overall_design: Examination of 9 different histone modifications (H3K27ac, H3K9ac, H3K4me1, H3K4me2, H3K4me3, H3K79me2, H3K36me3, H4K16ac and H3K27me3) across the genome of KBM-7 cells using ChIP-seq

first: Robert

middle: E

last: Kingston


title: Circulating circRNA signature in pregnancies with gestational diabetes mellitus

city: Ningbo

first: Jin

last: Xu

address: 818 Fenghua Road

institute: Ningbo University

summary:
Circular RNA can regulate blood glucose levels by targeting mRNA expression, but the role of circRNA in GDM is still unknown. Therefore, a joint microarray analysis of circRNAs and their targeting mRNAs using the peripheral blood of GDM patients and healthy pregnant women was carried out for the first time.
In our study, high-throughput microarray sequencing technique was used to analyze the expression profile of circRNA and transcripts mRNA in the peripheral blood of GDM patients, in order to comprehensively evaluate the role of circRNAs targets and their parents genes in the signal pathways related to the pathogenesis of GDM.  Some of the discovered circRNAs and their linear transcript mRNAs related to T cell receptor signaling pathway were further verified in larger samples by droplet digital PCR(ddPCR) and quantitative real-time PCR(qRT-PCR), respectively. The verification results confirmed the initial microarray results.

overall_design: CircRNA transcriptional spectrums of peripheral blood mononuclear cells between the GDM patients and the healthy controls were obtained through gene microarray technology.

first: Yanming

last: Chen


title: Aberrant chromatin landscape upon loss of the H3.3 chaperone Daxx leads to Pu.1-mediated neutrophilia and inflammation [CUT&Tag]

summary: Defective silencing of retroviral elements has been linked to inflamm-aging, cancer and auto-immune diseases. However, the underlying mechanisms are only partially understood. Here, we implicate the histone H3.3 chaperone Daxx, a retrotransposable element (RTE) repressor inactivated in myeloid leukemia and other neoplasms, in protection from inflammatory disease. Loss of Daxx has profound effects on chromatin landscapes and histone marks of hematopoietic progenitors, leading to engagement of a Pu.1-dependent transcriptional program for myelopoiesis at the expense of B-cell differentiation. This causes neutrophilia and inflammation, predisposing mice to development of an autoinflammatory skin disease. These molecular and phenotypic perturbations are in part reverted in animals lacking both Pu.1 and Daxx. However, hematopoietic progenitors in these mice also show unique chromatin and transcriptome alterations, suggesting synergistic interaction between the two pathways. Overall, our findings implicate RTE silencing in hematopoiesis and reveal a potential functional relationship between the H3.3 loading machinery and the pioneer transcription factor Pu.1.

overall_design: Examination of gene expression profiles, chromatin accessibility and epigenetic changes in hematopoietic stem/progenitor cells comparing wild-type and Daxx knock-out cells.

first: Julia

last: Gerber

first: Jenny

last: Russ

first: Vijay

last: Chandrasekar

first: Nina

last: Offermann

first: Hang-Mao

first: Sarah

last: Spear

first: Nicola

last: Guzzi

first: Simona

last: Maida

first: Sundararaghavan

last: Pattabiraman

first: Ruoyu

last: Zhang

first: Amir

last: Kayvanjoo

first: Preeta

last: Datta

first: Jagath

last: Kasturiarachchi

first: Teresa

last: Sposito

first: Natalia

last: Izotova

first: Kristian

last: Händler

first: Peter

last: Adams

last: Marafioti

first: Tariq

last: Enver

first: Jörg

last: Wenzel

first: Marc

last: Beyer

first: Elvira

last: Mass

first: Cristian

last: Bellodi

first: Joachim

middle: L

last: Schultze

first: Melania

last: Capasso

first: Rachael

last: Nimmo


title: RNA sequencing data of CT26-shppp2r1a and CT26-scr samples

status: Public on Aug 26 2021

city: Taichung

first: Yu-Ting

last: Yen

address: No.91, Hsueh-Shih Road

department: Graduate Institute of Biomedical Sciences

country: Taiwan

institute: China Medical University

summary: Goal: Microsatellite-instable (MSI) tumors are one of the few cancers that respond to immune checkpoint blockade (ICB); however, the mechanism of MSI status development is unclear. Here, we report that protein phosphatase 2A (PP2A) deletion or inactivation converted cold microsatellite-stable (MSS) into MSI tumors. Objectives: Using RNA sequencing data of three CT26-shppp2r1a data and a CT26-scr data, we demonstrate that these intestinal tumors display differential core driver pathways.

first: Shih-Chieh

last: Hung

first: May

last: Chien


title: Stromal androgen and hedgehog signaling regulates stem cell niches in pubertal prostate development

city: Duarte

first: Zijie

last: Sun

state: CA

address: 1500 E. Duarte Rd.

department: Cancer Biology

institute: City of Hope

summary: Androgen-signaling is essential for prostate development. However, how androgen action facilitates prostatic stem/progenitor initiated pubertal prostatic growth remains unclear. Here, we demonstrate that androgens regulate Shh-signaling to control the cellular niche in prostatic epithelial development.  Selective deletion of androgen receptor (AR) in stromal Shh-responsive cells significantly impedes pubertal prostatic epithelial morphogenesis and growth. Dysregulation of developmental signaling networks revealed in both prostatic stromal and epithelial cells of AR-deficient mice. Specifically, deletion of AR yielded increased Gli1 expression in prostatic stromal cells, elevated Shh expression in adjacent epithelial cells and stark inhibition of prostate cell growth. Trajectory analysis revealed AR deletion induces abnormal differentiation patterns of prostatic epithelia. Recombination of prostatic epithelial cells with AR-deficient stromal Gli1-expressing cells fails to develop normal prostatic epithelia. These data demonstrate the decisive role of stromal AR in interacting with Shh-signaling in the cellular niche to control pubertal prostatic morphogenesis and growth.

overall_design:
Two sequencing datasets were analyzed each containing tissue from 2 mice

Please note that the processed data has been updated on Jan 4, 2022.

first: Joseph

last: Aldahl


title: Genetic variants and cell-specific signatures in PBMCs of pre transplant recipients

status: Public on Aug 29 2021

city: New York

first: Zeguo

address: 1468 Madison Avenue

institute: Ichan School of Medicine at Mount Sinai

summary: Long-term survival of the renal allograft is a challenge. A single cell sequencing analysis is a powerful approach to identify genetic/genomic risk for development of long-term graft loss at single cell level. In this study, we compared single cell RNA sequencing profiles of pre-transplant PBMC samples from 4 transplant patients (2 patients with graft loss within 3 years vs 2 patients without graft loss) with simultaneous genome-wide genotype data for common variants to idenitfy the immune cell subtypes and transcriptomic signatures associated with long-term graft loss. These transcriptomic data  also  integrates with genetic data in an effort to identify genes that mediate the risk  for graft survival in a cell-type specific context.

overall_design: 4 PBMC samples: two with graft loss within 3 years and the other two without graft loss

first: Jia

last: Fu

first: Madhav

last: Menon

first: Zhongyang

last: Zhang


title: Aberrant chromatin landscape upon loss of the H3.3 chaperone Daxx leads to Pu.1-mediated neutrophilia and inflammation [ATAC-Seq]

first: Paolo

last: Salomoni

summary: The lymphoid and myeloid lineages are in equilibrium during steady-state hematopoiesis. Tilting hematopoiesis towards innate immunity has been linked to inflammation and may predispose to myeloproliferative disease. Although epigenetic players have been implicated in the control of hematopoiesis and pathogenesis of blood neoplasms, the role of chromatin-based mechanisms in regulating the lymphoid/myeloid balance remains only partially understood. Here, we show that loss of the H3.3 chaperone Daxx causes myeloid skewing, neutrophilia and pyoderma gangrenosum-like lesions, a human skin disease of unknown etiology. Daxx deficiency leads to chromatin opening at intergenic regions, including TERRA target sites, deregulation of repeat elements and activation of anti-viral defense pathways. Finally, the other main H3.3 chaperone, Hira, is dispensable for normal hematopoiesis but supports expansion of Daxx-deficient neutrophils. These results define a role for Daxx in proper selection of lymphoid versus myeloid lineages, linked to control of repeat elements and anti-inflammatory responses.

overall_design: Examination of gene expression profiles and chromatin accessibility in hematopoietic stem/progenitor cells comparing wild-type and Daxx knock-out cells.

first: Julia

last: Hofmann

first: Jenny

last: Russ

first: Sarah

last: Spear

first: Nicola

last: Guzzi

first: Vijay

last: Chandrasekar

first: Natalia

last: Izotova

first: Simona

last: Maida

first: Kristian

last: Händler

first: Peter

last: Adams

first: Teresa

last: Marafioti

first: Tariq

first: Racheal


title: Epigenetic landscape of Mammalian Brain M1 by Single Nucleus Methylation Sequencing [MM_M1_2]

status: Public on Oct 06 2021

city: La Jolla

first: Joseph

last: Ecker

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

institute: HHMI-Salk-Institute

summary: Illustrating the cellular architecture of the mammalian brain is critical to understanding its diverse functions and complex animal behaviors. Single nucleus methylation sequencing was applied to M1 regions of human and mouse brains. we identified distinct cell clusters and formed them in a hierarchical taxonomy. These clusters include known primary brain cell types and possible sub-types. We use these data to identify the epigenomic characteristics and to define specific regulatory elements for each cell cluster.

overall_design: Apply snmC-seq2 to brain M1 regions to identify epigenomic landcape of the adult human and marmoset brains

first: Wei

last: Tian

first: Hanqing

last: Liu

first: Chongyuan

last: Luo

first: Anna

last: Bartlett

first: Fenna

middle: M

last: Krienen

first: Rebecca

last: Hodge

first: Jacinta

last: Lucero

last: Nery

first: Angeline

last: Rivkin

first: Andrew

last: Aldridge

first: Rosa

last: Castanon

first: Huaming

last: Chen

first: Sheng-Yong

last: Niu

first: M

last: Behrens

first: Guoping

last: Feng

first: Ed

last: Lein


title: Aberrant chromatin landscape upon loss of the H3.3 chaperone Daxx leads to Pu.1-mediated neutrophilia and inflammation [RNA-Seq]

first: Paolo

last: Salomoni

first: Julia

last: Hofmann

first: Jenny

last: Russ

first: Sarah

last: Spear

first: Nicola

last: Guzzi

first: Vijay

last: Chandrasekar

first: Natalia

last: Izotova

first: Simona

last: Maida

first: Kristian

last: Händler

first: Peter

last: Adams

first: Teresa

last: Marafioti

first: Tariq

last: Enver

first: Jörg

last: Wenzel

first: Marc

last: Beyer

first: Cristian

last: Bellodi

first: Joachim

last: Schultze

first: Melania

last: Capasso

first: Racheal

last: Nimmo


title: Amniotic Fluid primary human keratinocyte culture

status: Public on Aug 25 2021

city: Linköping

first: Johan

last: Junker

state: Östergötland

address: KEF 09

department: Clinical and Experimental Medcine

country: Sweden

institute: Linköping University

summary:
Fetal wounds repair by regeneration rather than wound healing and the environment is dominated by amniotic fluid. We are looking at early transcriptional regulation of keratinocytes cultured in amniotic fluid in vitro.
Keratinocytes were isolated and expanded to passage three after which they were starved in DMEM for 12h then cultured for 24h in human amniotic fluid (50%), fcs (50%) or DMEM alone for another 24h. N=2, pooled replicates per CEL-file.

overall_design: Two cultures per group, three groups (AmnioticFluid - AF; Fetal calf serum - FCS; DMEM); duplicates were pooled after cell pelleting and RNA isolation and run on one chip per group.

first: Erika

last: Nyman

first: Elvira

last: Lindholm

first: Jonathan

last: Rakar

first: Gunnar

last: Kratz


title: Binding and Transcriptional profile of Halobacterium salinarum histone

city: Durham

first: Amy

last: Schmid

state: NC

address: 3242 French Family Science Center

institute: Duke University

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

overall_design: Refer to individual Series


title: Gut microbiota influences the expression of microRNA and their target mRNA in murine colonic lamina propria mononuclear cells [miRNA]

city: Kamakura

first: Satoshi

last: Kondo

address: 10-1 tebiro 6-chome

institute: Toray Industries,Inc.

summary: Microarray analyses were carried out to compare expression profile of microRNA and mRNA in colonic lamina propria mononuclear cells between germ-free and SPF mice. Germ-free mice showed higher levels of some microRNAs and lower expression of target mRNAs, suggesting that microRNAs mediate gut microbiota regulation of gut immunity.

overall_design: MicroRNAs and mRNAs in the mononuclear cells isolated from colon lamina propria of germ-free and SPF mice were analyzed by microarray.

first: Kei

last: Sonoyama


title: Gut microbiota influences the expression of microRNA and their target mRNA in murine colonic lamina propria mononuclear cells [mRNA]


title: Binding profile of Halobacterium salinarum histone [ChIP-Seq]

summary: Unlike the characterised histone proteins of a number of methanogenic and themophilic archaea, previous research indicated that HpyA, the sole histone encoded in the model halophile Halobacterium salinarum, is not involved in DNA packaging. Instead, it was found to have widespread but subtle effects on gene expression, and affect cell morphology. Here we report that HpyA is important for growth in reduced salinity and regulates gene expression of ion uptake and nucleotide metabolism pathways in a salt-dependent manner. Analysis of the genome-wide binding pattern of HpyA reveals that its binding is dependent on external salt concentration as well as growth phase. Combining the transcriptomic and ChIP-Seq data suggests a role for HpyA as a regulator of the expression of ion uptake genes as well as a co-regulator of other genes of diverse functions in a salt-dependent manner. In this GEO series , we use ChIP-Seq to study the genome-wide binding of HpyA-HA in optimal (4.2M NaCl) and reduced (3.4M) in exponential and stationary phase, using HA-tag-allone strains as a control

overall_design: Examination of HpyA binding sites in the halophilic archaeon Halobacterium salinarum in mid-logarithmic and stationary phases of growth, in optimal (4.2M NaCl) and reduced (3.4M NaCl) salt concentrations.

first: Saaz

last: Sakrikar


title: Gut microbiota influences the expression of microRNA and their target mRNA in murine colonic lamina propria mononuclear cells

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


title: Effects of Mettl3 and Alkbh5 knockdown on total RNA

city: Nashville

first: James

middle: G.

last: Patton

state: TN

address: 2325 Stevenson Center

department: Department of Biological Sciences

institute: Vanderbilt University

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

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

first: Jessica

last: Abner

first: Xiao

last: Liu

first: Qi

middle: G


title: Neoadjuvant T-DM1/pertuzumab and paclitaxel/trastuzumab/pertuzumab for HER2-positive breast cancer in the adaptively randomized I-SPY2 trial.

status: Public on Aug 24 2021

city: Novato

first: Christina

last: Yau

address: 8001 Redwood Blvd

institute: Buck Institute of Age Research

summary: Ado-trastuzumab emtansine plus pertuzumab (T-DM1/P) and paclitaxel plus trastuzumab and pertuzumab (THP) are two of the experimental regiments evaluated in I-SPY 2, a neoadjuvant platform trial for high risk, early stage breast cancer.   In pre-defined analyses we assessed 10 biomarkers at the pre-treatment timepoint in the HER2, ER/PR, and proliferation pathways to test their association with pCR (complete pathologic response).

overall_design: Fresh-frozen pre-treatment breast cancer tumors (n=127: 52 TDM1/P arm, 44 THP arm, 31 TH control arm) from the neoadjuvant ISPY2 trial for high risk, early-stage breast cancer were assayed using GPL16233 (n=22) or GPL20078 (n=105) expression arrays; and these data were combined into a single gene-level dataset after batch-adjusting using ComBat.    The sample characteristics and their values represent:  HER2: the status of the HER2 gene.  1 = positive; 0 = negative.  HR: the status of hormone (estrogen and progesterone) receptors  1 = positive; 0 = negative.  pCR: the status of a pathological complete response (pCR)  1 = complete response; 0 = failed complete response  MP: MammaPrint status  0 = MammaPrint high 1 (MP1); 1 = MammaPrint (ultra) high 2 (MP2)  Arm: arm of the trial per patient - 'T-DM1/P arm', 'THP arm', or 'TH Control'.      Originally, a ComBat batch correction process was applied to the raw data on a larger group of patients (~900), which we cannot release.  Linear adjustment factors from this group were derived so they can be applied to this smaller group of 127 patients.  The ISPY2_LinearFit_forCombiningExp<GPLXXXXX> files contain linear adjustments to go from raw to batch corrected data.    For fully normalized and batch corrected data on the gene level, please use ISPY2ResID_THP_TDM1P_Ctr_ExpDat_GeneLevel_n127.txt, provided in the supplementary files.  For biomarkers/signatures used in the manuscript, please see supplemental data file in the manuscript.

first: Denise

last: Wolf

first: Laura

last: van ‘t Veer


title: Ribosome Profiling with CNOT1 depletion

status: Public on Aug 23 2021

city: Glasgow

first: Sarah

middle: Louise

last: Gillen

address: Beatson Institute, Garscube Estate, Switchback Road, Bearsden

institute: Beatson Institute for Cancer Research

summary: Ribosome profiling in HEK293 cells with and without the depletion of CNOT1. This allows the determination of translational efficiency and nucleotide resolution of ribosome occupancy.

overall_design:
Ribosome profiling for HEK293 cells treated with either control of CNOT1-targeting siRNA for 48hrs, conducted for three biological replicates. Ribo-zero treated total RNA samples are also included.
The control ribosome profiling data has also previously been used in Wilczynska et al. eIF4A2 drives repression of translation at initiation by Ccr4-Not through purine-rich motifs in the 5'UTR. Genome Biol 2019 Dec 2;20(1):262. PMID: 31791371 (GSE134517)


title: Single-cell analysis of human primary prostate cancer reveals the heterogeneity of tumor-associated epithelial cell states

city: San Francisco

first: Hanbing

last: Song

address: 513 Parnassus Ave

institute: UCSF

summary:
Methods: To characterize the prostate cancer tumor microenvironment, we performed single-cell RNA-sequencing on prostate biopsies, prostatectomy specimens, and patient-derived organoids from localized prostate cancer patients.
Results: We identify a population of tumor-associated club cells that could be associated with prostate carcinogenesis and uncover heterogeneous cellular states in prostate epithelial cells marked by high androgen signaling states that are enriched in prostate cancer. ERG- tumor cells, compared to ERG+ cells, demonstrate shared heterogeneity with surrounding luminal epithelial cells and appear to give rise to common tumor microenvironment responses. Finally, we show that prostate epithelial organoids recapitulate tumor-associated epithelial cell states and are enriched with distinct cell types and states from their parent tissues.
Conclusions:Our results provide diagnostically relevant insights and advance our understanding of the cellular states associated with prostate carcinogenesis.

overall_design: Single-cell RNA sequencing based on Seq-Well S^3 protocol of 6 prostate biopsies from 3 different patients, 4 radical prostatectomies with tumor-only samples from 4 patients, and 4 radical prostatectomies with matched normal samples from 4 patients. Organoids derived from radical prostatectomy paired tumor and normal tissue samples.

first: Hannah

middle: N

last: Weinstein

first: Paul

last: Allegakoen

first: Marc

last: Wadsworth II

first: Jamie

last: Xie

first: Heiko

last: Yang

first: Franklin

middle: W

last: Huang


title: How does the skin respond to genotoxic stress: The programmed gene expression change in C57BL/6 mice after ultraviolet radiation damage

status: Public on Aug 21 2021

city: xiamen

first: Qingxiang

last: Gao

address: Xiang'an south way

institute: Xiamen University

summary: Ultraviolet (UV) radiation is a major source of skin damage. It is important to define the programmed gene expression change after UV exposure, particularly in the C57BL/6 lab mice model. Here we systematically analyze the acute gene expression change in mouse skin after UV exposure.

overall_design: The back fur of C57BL/6 mice was depilated, and a mixed UV light source was used to irradiate the skin. Full thickness skin samples were collected at 0, 0.5h, 2h, 6h, 12h, and 24h. Total RNAs were extracted and subjected to RNA sequencing analysis.

first: Zhicao

last: Yue


title: Transcriptional profile of Halobacterium salinarum histone [RNA-seq]

first: Amy

last: Schmid

summary: Unlike the characterised histone proteins of a number of methanogenic and themophilic archaea, previous research indicated that HpyA, the sole histone encoded in the model halophile Halobacterium salinarum, is not involved in DNA packaging. Instead, it was found to have widespread but subtle effects on gene expression, and affect cell morphology. Here we report that HpyA is important for growth in reduced salinity and regulates gene expression of ion uptake and nucleotide metabolism pathways in a salt-dependent manner. Analysis of the genome-wide binding pattern of HpyA reveals that its binding is dependent on external salt concentration as well as growth phase. Combining the transcriptomic and ChIP-Seq data suggests a role for HpyA as a regulator of the expression of ion uptake genes as well as a co-regulator of other genes of diverse functions in a salt-dependent manner. In this GEO series , we use RNA-Seq to study the transcriptonal effect of HpyA in optimal (4.2M NaCl) and reduced (3.4M) during exponential growth phase.

overall_design: Examination of HpyA transcriptionall profile in the halophilic archaeon Halobacterium salinarum in mid-logarithmic phase of growth, in optimal (4.2M NaCl) and reduced (3.4M NaCl) salt concentrations, comparing Δura3 ("WT") and ΔhpyA ("KO") strains

first: Saaz

last: Sakrikar


title: The evolution of gene spatiotemporal expression in six brassica species during embryogenesis

status: Public on Aug 22 2021

city: Saskatoon

first: Daoquan

last: Xiang

state: SK

address: 110 Gymnasium Place

department: Aquatic and Crop Resource Development

institute: National Research Council of Canada

summary: We present an atlas of global gene expression covering embryo and seed coat development in B. rapa, B. nigra, B. oleracea, B. juncea, B. napus and B. carinata, providing insights into the evolution of gene expression in embryogenesis and seed development of brassica species.

sample_organism:
Brassica juncea
Brassica napus
Brassica nigra
Brassica rapa
Brassica oleracea
Brassica carinata

overall_design: We investigate the dynamics and evolution of gene expression throughout seven stages of embryonic development in embryo and seed coat across six brassica species, two replicates for each stage.

first: Peng

first: Raju

last: Datla


title: Proximal jejunum of ob/ob mice compared to C57BL6/J

status: Public on Aug 20 2021

city: Genève

first: Ozren

last: Stojanovic

address: 1, rue Michèl-Servet

department: Faculté de Médecine, Dept. PHYM

institute: University of Geneva

summary: Intestinal surface changes in size and function, but what propels these alterations and what are their metabolic consequences is unknown. Here we show that the food amount is a major positive determinant of the gut surface area contributing to an increased absorptive function, reversible by reducing daily food. While several upregulated intestinal energetic pathways are dispensable, the intestinal lipid metabolism is instead necessary for the genetic and environment overeating–induced increase of the gut absorptive capacity. In presence of dietary lipids, intestinal PPARα knock-out or its pharmacological antagonism suppress intestinal crypt expansion and shorten villi in mice and in human intestinal biopsies, diminishing the post-prandial triglyceride transport and nutrient uptake. Intestinal PPARα ablation limits systemic lipid absorption and restricts lipid droplet expansion and PLIN2 levels, critical for droplet formation. This improves the lipid metabolism, and reduces body adiposity and liver steatosis, suggesting an alternative target for treating obesity.

overall_design: 3 samples per group, each sample is a pool of two jejunua


title: Ganitumab and Metformin plus Standard Neoadjuvant Therapy in Stage 2/3 Breast Cancer: Results from the I-SPY2 Adaptively Randomized Platform Trial

first: Denise

last: Wolf

address: 2340 Sutter st

institute: University of California, San Francisco

summary: Ganitumab and Metformin was one of the experimental regiments evaluated in I-SPY 2, a neoadjuvant platform trial for high risk, early stage breast cancer.   Based on the hypotheses that pre-treatment IGF-1R axis signaling at the expression level may predict response to Ganitumab and Metformin, in pre-defined analyses we assessed 11 genes involved in IGF1R pathway signaling, the IGFBP5/IGFBP4 ratio, and two IGFR expression signatures to test their association with pCR (complete pathologic response).

overall_design: Fresh-frozen pre-treatment breast cancer tumors (n=233: 106 Ganitumab arm, 127 control arm) from the neoadjuvant ISPY2 trial for high risk, early-stage breast cancer were assayed using GPL16233 (n=70) or GPL20078 (n=163) expression arrays; and these data were combined into a single gene-level dataset after batch-adjusting using ComBat.    The sample characteristics and their values represent:  HER2: the status of the HER2 gene.  1 = positive; 0 = negative.  HR: the status of hormone (estrogen and progesterone) receptors  1 = positive; 0 = negative.  pCR: the status of a pathological complete response (pCR)  1 = complete response; 0 = failed complete response  MP: MammaPrint status  0 = MammaPrint high 1 (MP1); 1 = MammaPrint (ultra) high 2 (MP2)  Arm: arm of the trial per patient - 'Ganitumab arm' or 'Control arm'.      Originally, a ComBat batch correction process was applied to the raw data on a larger group of patients (~900), which we cannot release.  Linear adjustment factors from this group were derived so they can be applied to this smaller group of 233 patients.  The ISPY2_LinearFit_forCombiningExp<GPLXXXXX> files contain linear adjustments to go from raw to batch corrected data.    For fully normalized and batch corrected data on the gene level, please use ISPY2ResID_AgilentGeneExp_GanitumabPlusCtr_FrshFrzn_meanCol_geneLevel_n233.txt, provided in the supplementary files.  For biomarkers, including 11 genes involved in IGF1R pathway signaling, the IGFBP5/IGFBP4 ratio, and two IGFR expression signatures (as used in the publication), please use ISPY2ResID_Ganitumab_biomarkers_20210607.csv, provided in the supplementary files.

first: Christina

last: Yau

first: Laura


title: YAP/TAZ and ATF4 collaboratively drive resistance to Sorafenib therapy in hepatocellular carcinoma by preventing ferroptosis

city: Basel

first: Ravi Kiran Reddy

last: KALATHUR

state: Basel

address: Mattenstrasse 28

department: Departement Biomedizin

institute: University of Basel

summary: Understanding the mechanisms underlying evasive resistance in cancer is an unmet medical need to improve the efficacy of current therapies. In this study, a combination of shRNA-mediated synthetic lethality screening and transcriptomic analysis revealed the transcription factors YAP/TAZ as key drivers of Sorafenib resistance in hepatocellular carcinoma (HCC) by repressing Sorafenib-induced ferroptosis. Mechanistically, in a TEAD-dependent manner YAP/TAZ induce the expression of SLC7A11, a key transporter maintaining intracellular glutathione homeostasis, thus enabling HCC cells to overcome Sorafenib-induced ferroptosis. At the same time, YAP/TAZ sustain the protein stability, nuclear localization and transcriptional activity of ATF4 which in turn cooperates to induce SLC7A11 expression. Our study uncovered a critical role of YAP/TAZ in the repression of ferroptosis and thus in the establishment of Sorafenib resistance in HCC, highlighting YAP/TAZ-based rewiring strategies as potential approaches to overcome HCC therapy resistance.

overall_design: RNA-Seq of siCtrl, siYAP/TAZ, siATF4 with DMSO or Sorafneib treatment in HLE cell line

first: Ruize

first: Fengyuan

last: Tang

first: Ravi

middle: K

last: Kalathur

first: Gerhard

last: Christofori


title: EMT-related lncRNA expression profiles in keloid

status: Public on Aug 18 2021

city: Hangzhou

first: Xi

last: Chu

address: 261 Huansha Road

institute: Hangzhou First People's Hospital

summary: To identify differentially expressed EMT-related lncRNAs between keloid and adjacent normal skin specimens

overall_design: EMT-specific microarray analysis was performed to identify differentially expressed lncRNAs and mRNAs by 3 pairs of keloid and adjacent normal skin specimens

first: Zhixiong

last: Chen

first: Jinghong

last: Xu


title: Sustained experimental activation of FGF8/ERK in the developing chicken spinal cord reproducibly models early events in ERK-mediated tumorigenesis

status: Public on Aug 17 2021

city: Marseille

first: Marie-Claire

last: DELFINI

address: Campus de Luminy

country: France

institute: IBDM / CNRS

summary: Most human cancers demonstrate activated MAPK/ERK pathway signaling as a key tumor initiation step, but the immediate steps of further oncogenic progression are poorly understood due to a lack of appropriate models. Spinal cord differentiation follows caudal elongation in vertebrate embryos; both processes are regulated by a FGF8 gradient highest in neuromesodermal progenitors (NMP), where kinase effectors ERK1/2 maintain an undifferentiated state. FGF8/ERK signal attenuation is necessary for NMPs to progress to differentiation. We show that sustained ERK1/2 activity, using a constitutively active form of the kinase MEK1 (MEK1ca) in the chicken embryo, reproducibly provokes neopasia in the developing spinal cord. Transcriptomic data show that neoplasia not only relies on the maintenance of NMP gene expression, and the inhibition of genes expressed in the differentiating spinal cord, but also on a profound change in the transcriptional signature of the spinal cord cells leading to a complete loss of cell-type identity. MEK1ca expression in the developing spinal cord of the chicken embryo is therefore a tractable in vivo model to identify the critical factors fostering malignancy in ERK-induced tumorigenesis.

overall_design: Neural tube in ovo electroporations were performed at HH11. Two pCIG controls and two pCIG-MEK1ca experiments were performed. GFP-expressing cells were FACS-isolated and total polyA RNA sequenced.

first: Axelle

last: Wilmerding

first: Lauranne

last: Bouteille

first: Nathalie

last: Caruso

first: Ghislain

last: Bidaut

first: Heather

middle: C

last: Etchevers

first: Yacine

last: Graba

last: Delfini


title: Single cell RNA sequencing of skin T cells from patient with mycosis fungoides

city: Lausanne

first: Yun-Tsan

last: Chang

address: Avenue de Beaumont 29

department: Dermatology

institute: CHUV

summary: Capture and processing of single skin T cells from patient with mycosis fungoides was performed using the Fluidigm C1 Autoprep system. Cells were loaded at a concentration of 2,000 cells/μL onto C1 integrated fluidic circuits (IFC) chips for 5-10 μm cells. All C1 capture sites were microscopically inspected to determine the sites containing only a single cell. Empty sites and those with multiple cells were excluded from further analysis. ERCC (External RNA Controls Consortium) spike-in RNAs were added and served as a control. SMARTer Ultra Low RNA Kit (Clontech) was used for reverse transcription and cDNA preamplification. The cDNA products from each cell were then used to prepare Illumina sequencing libraries and then sequenced on Illumina HiSeq2500 using single-end 100-base reads. Gene expression was quantified using Kallisto and then normalized to TPM values

overall_design: single-cell RNA-seq investigation of a cutaneous T-cell lymphoma

first: Desislava

last: Ignatova

first: Christina

last: Fassnacht

first: Emmanuella

last: Guenova

first: Wolfram

last: Hoetzenecker

first: Steve

last: Pascolo


title: Comparative analysis among different species reveals that androgen receptor is a core transcriptional factor regulating the chicken follicular selection and ovulation [RNA-Seq 2]

status: Public on Aug 16 2021

city: Wuhan

first: Ying

last: Huang

state: Hubei

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

institute: Huazhong Agricutural University

summary: The differences in reproductive processes at the molecular level between viviparous and oviparous animals are evident, and the site in the ovary that synthesizes sex hormones (androgens and oestrogens) and the trends for enriching sex hormones during follicle development in chickens are different from those in mammals, suggesting that the effect of sex hormones on follicle development in chickens is probably different from that in viviparous animals. To explore the specific role of androgen receptors (ARs) on chicken follicular development, we matched the correspondence of follicular development stages among chickens, humans, cows and identified chicken-specific genes related to follicle development (GAL-SPGs) by comparing follicle development-related genes and their biological functions among species (chickens, humans, and cows). A comparison of the core transcription factor regulatory network of granulosa cells (or ovaries) based on super enhancers among species (chicken, human, and mouse) revealed that AR is a core transcriptional regulator specific to chickens. In vivo experiments showed that inhibition of AR significantly reduced the number of syf (selected stage follicles) in chickens and decreased the expression of GAL-SPGs in F5 follicles, while in vitro experiments showed that inhibition of AR expression in chicken granulosa cells (GCs) significantly down-regulated the expression levels of GAL-SPGs, indicating that AR could regulate follicle selection through chicken-specific genes related to follicle development. A comparison among species (77 vertebrates) of the conserved genomic regions, where chicken super-enhancers are located, revealed that the chicken AR super-enhancer region is conserved in birds, suggesting that the role of AR in follicle selection may be widespread in birds. In summary, we found that AR can regulate follicle selection through chicken-specific genes related to follicle development, which also emphasizes the important role of AR in follicle selection in chickens and provides a new perspective for understanding the unique process of follicle development in chickens.

overall_design: RNA extracted from primary granulosa cells transfected with AR-specific siRNA (treat) and nonsense siRNA (control) were sent to Novogene Co., Ltd. (Beijing, China) for library construction, and sequencing. All samples performed paired-end 150 bp sequencing on the Illumina Nova platform.

first: Yanzhang

last: Gong


title: Identification of LIN-29 target genes

status: Public on Aug 10 2021

city: Bethesda

first: Sijung

last: Yun

state: Maryland

address: 8908 Ewing Drive

institute: NIH/JHU

summary: To further explore the regulatory network coordinated by LIN-29, and to possibly uncover potential new roles for this transcription factor, we searched for its downstream target genes at the genomic level. To do this, we chose not to modify LIN-29 expression via loss-of-function mutations in upstream heterochronic pathway components, but rather to temporally misexpress LIN-29 directly and examine changes in development and in gene expression.

overall_design: We carried out early overexpression of LIN-29 by heat-shock inducing hs::lin-29 and hs::control strains in early L3 stage larva, and assessed gene expression by RNA-seq.

first: Patricia

last: Abete-Luzi

first: Tetsunari

last: Fukushige

first: Michael

last: Krause

first: David

last: Eisenmann


title: Single-cell RNA-seq of bone marrow cells from aplastic anemia patient and healthy donor

status: Public on Aug 15 2021

city: Hangzhou/Zhejiang Province

first: Liming

last: Yin

state: Zhejiang Province

address: 548 Binwen Road

department: Institute of hematology

institute: Zhejiang Chinese Medical University

summary: BM samples were collected from two adult healthy donors and two AA patients at the first hospital affiliated from Zhejiang Chinese University. Mononuclear cells (MNCs) were isolated using Ficoll-Hypaque gradient separation. CD34+ cells were purified from MNCs with the human anti-CD34 MicroBeads Isolation kit according to the manufactures specifications. Isolated cell was the purification of CD34+ cell. Then, MNCs mixed with CD34+ cells at 4:1 ratio and were analyzed by 10×Genomics.

overall_design: a large-scale single-cell transcriptomic sequencing of 20,000 bone marrow cells from two adult healthy donors and two AA patients

first: Tonglin

last: Hu

first: Yanna

last: Zhao

first: Xaioling

last: Yu

first: Ruilan

last: Gao


title: Long-term perturbation of the blood transcriptome months after SARS-CoV-2 infection.

city: Adelaide

first: Feargal

middle: J

last: Ryan

state: Adelaide

address: North Terrace

country: Australia

institute: SAHMRI

summary: Blood collected from recovered COVID-19 patients at 12, 16 and 24 weeks post infection was found to retain a signature of active infection which was associated with severity of disease

overall_design: Total RNA sequenced from healthy controls, and from recovered COVID-19 patients at 12, 16 and 24 weeks post infection

last: Lynn

first: Miriam

first: Branka

last: Grubor-Bauk


title: FOXD3 acts as a repressor of repeat elements in a heterochromatin-mediated pathway

status: Public on Aug 05 2021

city: Pune

first: Deepika

last: Puri

state: Maharashtra

address: Ganeshkhind road

institute: National Centre for Cell Science

summary: Repeat element transcription plays a vital role in early embryonic development. Upregulation of repeats such as MERVL characterises the 2 cell-like population in a mouse embryonic stem cell culture. Repeat element sequences contain binding sites for numerous transcription factors. We identify a the forkhead domain transcription factor FOXD3 as a regulator of repeat element transcription. FOXD3 binds to and recruits the histone methyl transferase Suv39h1 to MERVL and major satellite repeats in mouse embryonic stem cells, consequentially repressing the transcription of these repeats by establishment of the H3K9me3 heterochromatin modification. Notably, depletion of Foxd3 leads to the de-pression of MERVL and major satellite repeats and in turn the activation of a subset of genes expressed in the 2 cell state, shifting the balance between the stem cell and 2 cell-like population in culture. Thus FOXD3 acts as a negative regulator of repeat transcription, ascribing a novel function to this transcription factor.

overall_design: Total RNA Seq analysis of Foxd3 conditional KO mouse ES cells without and with tamoxifen induced depletion of Foxd3


title: Effect of lactational high fat diet on offspring liver RNA expression

status: Public on Aug 14 2021

city: Ann Arbor

first: Dave

last: Bridges

state: MI

address: 1415 Washington Heights

department: Nutritional Sciences

institute: University of Michigan

summary:
The goal was to study the long term metabolic programming effects of exposure of offspring to a dam eating 60% high fat diet during the lactation period only.
We previously showed that offspring from dams given lactational high fat diet (HFD) are predisposed to obesity, glucose intolerance and inflammation. The purpose of these studies was to understand the programming implications of lactational HFD on offspring metabolic liver disease risk. Dams were fed a 60% lard-based HFD from the day of delivery through the 21 day lactation period. Starting at weaning offspring were fed normal fat diet until 3 months of age at which point a subset were challenged with an additional HFD stressor. Lactational HFD fed male offspring developed hepatic insulin resistance. Postweaning HFD challenge led male offspring progressing to NAFLD with more severe outcomes in the lactational HFD challenged offspring.

overall_design: We analyzed 4 adult male offspring livers from each group (HFD-PN and control PN). PN=postnatal

first: Brigid

last: Gregg


title: SPaRTAN, a computational framework for linking cell-surface receptors to transcriptional regulators

city: Pittsburgh

first: Hatice

middle: Ulku

last: Osmanbeyoglu

state: Pennsylvania

address: 5607 Baum Blvd

department: Biomedical Informatics

institute: University of Pittsburgh

summary: The identity and functions of specialized cell types are dependent on the complex interplay between signaling and transcriptional networks. Recently single-cell technologies such as CITE-seq have been developed that enable simultaneous quantitative analysis of cell-surface receptor expression with transcriptional states. To date, these datasets have not been used to systematically develop cell-context-specific maps of the interface between signaling and transcriptional regulators orchestrating cellular identity and function. We present SPaRTAN (Single-cell Proteomic and RNA based Transcription factor Activity Network), a computational method to link cell-surface receptors to transcription factors (TFs) by exploiting cellular indexing of transcriptomes and epitopes by sequencing (CITE-seq) datasets with cis-regulatory information. SPaRTAN is applied to immune cell types in the blood to predict the coupling of signaling receptors with cell context-specific TFs. The predictions are validated by prior knowledge and flow cytometry analyses. SPaRTAN is then used to predict the signaling coupled TF states of tumor infiltrating CD8+ T cells in malignant peritoneal and pleural mesotheliomas. SPaRTAN greatly enhances the utility of CITE-seq datasets to uncover TF and cell-surface receptor relationships in diverse cellular states.

overall_design: Human malignant mesotheliomas were profiled using CITE-seq

middle: U

first: Ashwin

last: Somasundaram

first: Zengbiao

last: Qi

first: Xiaojun

last: Ma


title: Global transcriptomic analysis of  Drosophila Hinfp mutant and wild-type gut to understand their role in genome stability

city: Worcester

first: Y.

middle: Tony

last: Ip

state: Massachusetts

address: 373 Plantation Street, Ste 109

department: Molcular Medicine

institute: University of Massachusetts Medical School

summary: Drosophila hinfp mutant is lethal. They are unble to ecolose from the pupal case and died.  To investigate the molecular function of Hinfp in Drosophila gut, we isolated RNA from mutant and wild type adult pharate gut and performed RNA-seq analysis. The comparison of mutant and control samples revealed significantly changed expression of over more than thousand Drosophila genes. Among the down regulated genes were many Histone genes. Further validation of RNA-seq data of Histone genes divulged that His1 is significantly down-regulated lead to genome instability through de-repression of menay of the retrotransposon. We also rescued the all phenotypes by overexpression of UAS-Hinfp and UAS-His1 gene.

overall_design: Fifty midguts with malpighian tubules were dissected from 5-6 days old control and 8-9 days old mutants and rescue male adults pharate and adult cultured at 25°C. The genotypes of the flies were, Y/FRT19A; +/+; +/+, Y/Hinfp2; +/+; +/+ and Y/Hinfp2; +/+; tub-Gal4/UAS-Hinfp-HA, Y/Hinfp2; +/+; tub-Gal4/UAS-His1-HA. Total RNA was extracted by Tri- reagent (Sigma, USA) according to the instructions, followed by DNAas I (catalog no. 79254; Qiagen) and purified with RNA-easy kit (Qiagen (catalog no. 74104; Qiagen)). RNA was quantified at by absorbance at 260 nm using a ND-1000 spectrophotometer (Nanodrop Technology, USA) and quality was assessed using a Bioanalyzer 2100 (Agilent Technology, USA) from UMMS molecular Biology core. All RNA-seq procedures start from quality, library construction using ribo-depletion kit to sequencing were carried out according to Company protocol (BGI, Hong Kong). The pair-end reads of 100 bp were done on the BGISEQ-500 platform for the following data analysis study.

first: Niraj

last: Nirala

first: Rui

last: Li

first: Lihua

last: Zhu

first: Y

middle: T


title: RNA sequencing of DDX23 knockdown by siRNA in ovarian cancer cells

status: Public on Jul 31 2021

city: Jinan

first: Chen

last: Zhao

state: China

address: 107 Wenhua Xi Road

department: Department of Obstetrics and Gynecology

institute: Qilu Hospital, Shandong University

summary: DDX23 belongs to DEAD-box family of RNA helicases and plays crucial roles in spliceosome formation and pre-mRNA splicing.  In this study, DDX23 was first identified as a key DEAD-box RNA helicase in ovarian cancer, and its overexpressed was associated with poor clinical outcomes. High expression of DDX23 was involved in the malignant proliferation and aggressiveness of ovarian cancer.

overall_design: The assay was performed on three biological triplicates as well as three experimental triplictes of DDX23 knockdown and control ovarian cancer cells.


title: Fetus-derived IGF2 matches placental development to fetal demand II [RNA-seq]

city: Cambridge

first: Brian

middle: Yee Hong

last: Lam

address: Box 289 Addenbookes Hospital, Hills Road

department: Metabolic Research Laboratories

institute: University of Cambridge

summary: We used transcriptome analysis to identify genes transcriptionally disregulated in feto-placental endothelial cells from mutants with conditional deletion of Igf2 gene driven by the Tek-cre.

overall_design: RNA-seq in FACS-sorted feto-placental endothelial cells isolated from E16 Igf2ECKO mutants (n=4) and littermate controls (n=4)

first: Ionel

last: Sandovici

middle: Y

first: Miguel

last: Constancia


title: Epigenetic silencing of UBXN8 contributes to leukemogenesis of t(8;21) acute myeloid leukemia

city: Shenzhen

first: De

middle: sheng

last: Gong

state: Guangdong

address: Xueyuan AVE 1098, Nanshan District

department: Department of Hematology and Oncology, International Cancer Center

institute: Shenzhen University General Hospital

summary: The formation of the AML1-ETO fusion protein, resulting from the t(8;21) translocation, is considered to be among the t(8;21) acute myeloid leukemia (AML) initiating events. However, the mechanisms of the oncogenic activity of AML1-ETO remains unclear. In this study, we found that AML1-ETO triggers the heterochromatic silencing of UBXN8 by recognizing the AML1 binding sites and recruiting chromatin remodeling enzymes to the UBXN8 promoter region. Decitabine, a specific inhibitor of DNA methylation, upregulated the expression of UBXN8 in AML1-ETO+ AML cell lines. Overexpression of UBXN8 inhibited the proliferation and colony-forming ability and promoted cell cycle arrest in t(8;21) AML cell lines. Enhancement of UBXN8 level can significantly inhibit the tumor proliferation of AML1-ETO+ cells in vivo. Thus, our results indicated that epigenetic silencing of UBXN8 via its promoter region methylation mediated by the AML1-ETO fusion protein contributes to the leukemogenesis of t(8;21)AML. These results demonstrated the feasibility and effectiveness of the pharmacological disruption of AML1-ETO/HDACs/DNMTs complex and that the UBXN8 targeting maybe an potential therapeutic strategy for t(8;21)AML.

overall_design: The SKNO-1, SKNO1-siAE cell lines were maintained in RPMI 1640 medium supplemented with 10% fetal calf serum (Hyclone, Logan, UT, USA), penicillin (107 U/L) and streptomycin (10 mg/L) at 37°C in a 5% CO2 atmosphere. SKNO-1 cells infected with the pRRLcPPT.hPGK, a lentiviral vector encoding the previously described 12siAGF1 oligonucleotides, which were designed against the AML1-ETO mRNA fusion site, allowing the silencing of AML1-ETO in SKNO-1 cells12, 13 to produce the SKNO1-siAE cell lines.

first: Erna

last: Yang

first: Wei

last: Guan

first: Yonghui

first: Li

last: Yu


title: Analysis of transcriptomic changes with a special focus on processing sites in Synechocystis sp. PCC 6803 thermo-sensitive RNase E mutants before and after a 1 h heat shock

status: Public on Jul 30 2021

city: Freiburg

first: Ute

middle: A.

last: Hoffmann

address: Schänzlestr. 1

department: Institute of Biology III

institute: University of Freiburg

summary: We compared transcriptomic changes, 5'-triphosphorylated (TSS) and 5'-monophosphorylated (PSS) RNA ends of a thermo-sensitive and a wild-typic RNase E mutant strain of the cyanobacterium Synechocystis sp. PCC6803 (rne(Ts) and rne(WT)) before and after a heat shock. Analysis of changing 5'-monophosphorylated ends revealed RNase E depedent processing sites on a transcriptome-wide level.

overall_design: Triplicates of RNA samples of  strains rne(WT) and rne(Ts) grown at 30°C with and without heat treatment (39°C) were analysed

middle: A

first: Florian

last: Heyl

first: Said

last: Rogh

first: Thomas

last: Wallner

first: Rolf

last: Backofen

first: Wolfgang

middle: R

last: Hess

first: Claudia

last: Steglich

first: Annegret

last: Wilde