title: RNA-sequencing shows the changes on transcriptomes after deletion of Setd2 in VHL deficient mice.

status: Public on Oct 19 2022

first: ChangWei

address: No. 1954 Huashan Road, Xuhui District

institute: Shanghai Jiaotong University

summary: To explore the possible role of SETD2 in renal fibrosis formation, we generated VHL-KO and VHL-KO; SETD2-KO mice with a transgenic Ksp1.3/Cre mouse line. To get an insight into the mechanism of how SETD2 deletion promotes renal fibrogenesis in the absence of VHL, we performed RNA-seq using the renal tubules isolated from VHL-KO and VHL -KO; SETD2-KO mice

overall_design: Renal primary tubular epithelial cells mRNA profiles of three VHL -KO mice, three VHL -KO; SETD2-KO mice were generated by deep sequencing, in triplicate.

first: C

first: L


title: Characterization of human pluripotent stem cell differentiation by single-cell dual-omics analyses

status: Public on Oct 28 2022

city: Hangzhou

first: Xiaoping

last: Han

state: Zhejiang

address: Yuhangtang Road 866

department: Center for Stem Cell and Regenerative Medicine

country: China

institute: Zhejiang University School of Medicine

type: Expression profiling by high throughput sequencing

type: Genome binding/occupancy profiling by high throughput sequencing

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: Transcriptome-wide profiling and quantification of N6-methyladenosine by enzyme-assisted adenosine deamination [site_specific_quantification]

status: Public on Oct 24 2022

city: Chicago

first: Shun

last: Liu

state: IL

address: 929 E. 57th. Street

department: Chemistry

country: USA

institute: University of Chicago

summary: We report evolved TadA-assisted N6-methyladenosine sequencing (eTAM-seq), an enzyme-assisted sequencing technology for quantitative, base-resolution profiling of m6A. eTAM-seq functions by global adenosine deamination, enabling detection of m6A as persistent A. We demonstrate adenosine-to-inosine (I) conversion rates up to 99% using a hyperactive TadA variant. With eTAM-seq, we profile and quantify m6A in the whole transcriptomes of HeLa cells and mouse embryonic stem cells (mESCs), with simultaneous deconvolution of the transcriptome and epitranscriptome. Further, we showcase deep sequencing-free, site-specific m6A quantification with as few as 10 cells, an input demand that is at least 4 orders of magnitude lower than existing methods. Collectively, eTAM-seq enables sensitive detection and faithful quantification of m6A with limited RNA input, representing a novel solution to deciphering the epitranscriptome.

overall_design: Two gene (ACTB and EIF2A) transcripts from serial diluted samples. Two gene (ACTB and EIF2A) transcripts from limited total RNA samples. 16 gene transcripts with in vio or in vitro transcription. Four gene transcripts with in vio transcription.

first: Yulan

last: Xiao

first: Ruiqi

last: Ge

first: Yuan

last: Wu

first: Chuan

last: He

first: Mengjie

last: Chen

first: Weixin

last: Tang


title: Transcriptome-wide profiling and quantification of N6-methyladenosine by enzyme-assisted adenosine deamination [probes_assay]

sample_organism:
Escherichia coli
synthetic construct

platform_organism:
Escherichia coli
synthetic construct

overall_design: Two synthetic RNA probes with and without TadA8.20 treatment. One E. coli tRNA with or without WTTadA or TadA8.20 treatment.


title: NRAS hydrodynamic tail vein injection

status: Public on Oct 21 2022

city: Regensburg

first: Alexander

last: Scheiter

state: Bavaria

address: Franz-Josef-Strauss Allee 11

department: Institute of Pathology

country: Germany

institute: University of Regensburg

summary: comparison of liver tumors, surrounding liver tissue and empty vector (EV) injected control mouse livers

overall_design: 4x Tumor (T), 4x surrounding tissue with preneoplasias (NT), 4x empty vector (EV) injected liver


title: Transcriptome-wide profiling and quantification of N6-methyladenosine by enzyme-assisted adenosine deamination

sample_organism:
Escherichia coli
Homo sapiens
Mus musculus
synthetic construct


title: Transcriptome analysis after METTL14 overexpression in ocular melanoma cells

status: Public on Oct 12 2022

city: Shanghai

first: AI

last: ZHUANG

address: 639 Zhizaoju Road

department: Ophthalmology

institute: Shanghai Ninth People's Hospital, Shanghai JiaoTong University School of Medicine

summary: In order to study the mechanism of METTL14 and the development of ocular melanoma, we established a model of overexpression of METTL14 in ocular melanoma. The results showed that the expression of FAT4 was increased after METTL14 overexpression. In order to reveal the interaction between METTL14 and FAT4 and to further explore the relationship between the expression level of METTL14 and the survival time of ocular melanoma patients provides new ideas for the treatment of malignant tumors.

overall_design: METTL14 overexpression in ocular melanoma cells affects its biological function.

first: A

last: Zhuang

first: X

last: Fan


title: Characterization of human pluripotent stem cell differentiation by single-cell dual-omics analyses (scATAC-seq)

summary: In vivo differentiation of human pluripotent stem cells (hPSCs) has unique advantages such as multilineage differentiation, angiogenesis, and close cell‒cell interactions. To systematically investigate the multilineage differentiation mechanisms of hPSCs, we constructed the in vivo hPSC differentiation landscape containing 239,670 cells using teratoma models. We inferred 18 cell differentiation trajectories and characterized common and specific gene regulation patterns during hPSC differentiation at both transcriptional and epigenetic levels. The results of developing single cell Basic Local Alignment Search Tool (dscBLAST), our self-developed tool for cell identification and developmental stage speculation, further confirmed the differentiated cell identity and suggested that cells in the teratoma are largely at immature developmental stages. Overall, our study offers new insights into stem cell fate decisions and embryonic development; dscBLAST shows favorable cell identification performance, providing both developmental and adult cells with a powerful tool for cell annotation and stage speculation.

overall_design: To construct the landscape of teratoma,18 teratomas were used for single-cell RNA sequencing (scRNA-seq) based on Microwell-seq. Among them, six were generated from H9 embryonic stem cells (ESCs), and 12 were from H1 ESCs. To conduct joint analysis of dual-omics data, additional three teratomas from H9 ESCs were utilized for scRNA-seq and scATAC-seq simultaneously. For each teratoma sample, there are human-derived cells differentiated from ESCs and mouse-derived cells infiltrating from the thigh muscles of NOD/SCID mice, where the ESCs were injected.

first: Guoji

last: Guo

first: Daiyuan

first: Yuting

last: Fu

first: Xinru

last: Wang

first: Xueyi


title: Effect of overexpressing of hepatitis B protein x (HBx) on the expression of circular RNAs (circRNAs) in HepG2 cells

status: Public on Oct 18 2022

first: Jian

last: Yu

address: 225 Changhai Road

institute: Eastern Hepatobiliary Surgery Hospital

type: Non-coding RNA profiling by high throughput sequencing

overall_design: CircRNA-sequencing in HBx-overexpressing (HBx-oe) and NC (negative control) HepG2 cells. Three biological replicates for each group.


title: Transcriptome-wide profiling and quantification of N6-methyladenosine by enzyme-assisted adenosine deamination [eTAM-seq]

first: Shun

overall_design: Nine HeLa wild type (3 FTO-, 3 FTO+ and 3 IVT),  six mESC wild type (2 FTO-, 2 FTO+ and 2 IVT),  two mESC Mettl3 cko ctrl (1 FTO- and 1 FTO+) and two mESC Mettl3 cko (1 FTO- and 1 FTO+)  polyA samples were collected for high-throughput sequencing.


title: Effect of depletion of TRIM25 and inhibition of p300 on gene expression in breast cancer cells

status: Public on Oct 11 2022

city: Eggenstein-Leopoldshafen

first: Christine

last: Blattner

address: Hermann-von-Helmholtz-Platz 1

department: IBCS-BIP

institute: KIT

summary: To analyze the effect of TRIM25 on gene expression, TRIM25 was knocked out in MCF7 cells. To understand a possible contribution of p300 on this gene regulation, p300 was inhibited. RNA seq was performed to see changes in the whole transcriptome

overall_design: TRIM25 was targeted by CRISPR/Cas9 or p300 was inhibited by treatment with CCS1477 for 20 h in MCF7 cells. Total RNA was prepared and sequenced


title: Megakaryocyte and erythroblast DNA in plasma and platelets

city: Jerusalem

first: Joshua

last: Moss

address: Faculty of Medicine, The Hebrew University of Jerusalem, Ein Kerem

department: Developmental Biology and Cancer Research

country: Israel

institute: Hebrew University of Jerusalem

type: Methylation profiling by high throughput sequencing

summary: Circulating nucleic acids are present in plasma and are derived from a range of cell types, mainly cells of hematopoietic origin, enabling their use as biomarkers for diseases involving these cell types. Using cell type-specific methylation markers, we determined that megakaryocytes are major contributors to cfDNA (~26%), while erythroblasts contribute 1-4% of cfDNA in healthy individuals. Additionally, we identified megakaryocyte-derived DNA within platelets, providing non-invasive access to the megakaryocyte genome and epigenome. Analysis of cfDNA in women who have received male platelet transfusions indicates that megakaryocyte-derived cfDNA does not originate from platelets but is rather released directly from megakaryocytes. The concentration of megakaryocyte-derived cfDNA is elevated in individuals with pathologies involving increased platelet production (Essential Thrombocythemia, Idiopathic Thrombocytopenic Purpura) and decreased by bone marrow suppression (due to chemotherapy), while erythrocyte progenitor cfDNA is elevated in patients with Thalassemia. Megakaryocyte- and erythroblast-specific DNA methylation patterns may serve as novel biomarkers for pathologies involving increased or decreased thrombopoiesis and erythropoiesis.

overall_design:
Whole Genome Bisulfite Sequencing (WGBS) of DNA extracted from platelets

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

first: Yuval

last: Dor

first: Ruth

last: Shemer


title: Lamin A/C-dependent chromatin architecture safeguards naïve pluripotency to prevent aberrant cardiovascular cell fate and function [RNA-seq_ Lmna KD at CM]

city: Mannheim

first: Gergana

last: Dobreva

state: Baden Württemberg

address: Ludolf-Krehl-Str. 7-11

department: Cardiovascular Genomics and Epigenomics

institute: Medical Faculty Mannheim/University of Heidelberg

summary: Tight control of cell fate choices is crucial for normal development. Here we show that lamin A/C plays a key role in chromatin organization in embryonic stem cells (ESCs), which safeguards naïve pluripotency and ensures proper cell fate choices during cardiogenesis. We find major changes in chromatin compaction and localization of cardiac genes already in Lmna−/−ESCs resulting in precocious activation of a transcriptional program promoting cardiomyocyte versus endothelial cell fate, accompanied by premature cardiomyocyte differentiation, cell cycle withdrawal, and abnormal contractility. Gata4 is activated by lamin A/C loss and Gata4 silencing or haploinsufficiency rescues the aberrant cardiovascular cell fate choices induced by lamin A/C deficiency. Importantly, we observe divergent functions of lamin A/C in naïve pluripotent stem cells and cardiomyocytes, which has distinct contributions to the transcriptional alterations of patients with LMNA-associated cardiomyopathy. Thus, disruption of lamin A/C-dependent chromatin architecture in ESCs is a primary event in LMNA loss-of-function cardiomyopathy.

overall_design: Wild type E14 Tg(Nkx2-5-EmGFP)  mESCs were differentiated by  directed differentiation method. CMs  were stably transfected with control (pLKO) and Lmna shRNA at day8 and collected at day10 for RNA-seq.

first: Yinuo

first: Julio

last: Cordero

first: Adel

last: Elsherbiny

first: Linda

last: Kessler


title: DUSP4 silencing

status: Public on Nov 06 2022

first: Alexander

summary: siRNA mediated DUSP4 silencing in a cell line derived from a) AKT/NRAS double injected hepatocellular carcinoma in a mouse by hydrodynamic injection => AKT/NRAS and b) these cell lines with Cre knockout for AKT => AKT/NRAS Cre

overall_design: 3x siRNA and 3 x SCR both in AKT/NRAS and AKT/NRAS/Cre


title: Lamin A/C-dependent chromatin architecture safeguards naïve pluripotency to prevent aberrant cardiovascular cell fate and function [ATAC-seq_CM]

overall_design: Conrol and Lmna KO E14 Tg(Nkx2-5-EmGFP)  mESCs were differentiated by hanging drop method.Day10 CMs were  FACS-sorted by Nkx2-5+ GFP expression and performed ATAC-seq.


title: Lamin A/C-dependent chromatin architecture safeguards naïve pluripotency to prevent aberrant cardiovascular cell fate and function [HiC-seq_ESC]

overall_design: Conrol and Lmna KO E14 Tg(Nkx2-5-EmGFP)  mESCs  were maintained on mitomycin treated mouse embryonic fibroblasts (MEF) in DMEM high glucose  supplemented with 15% fetal bovine serum, 2 mM L-glutamine, 0.1 mM 2-mercaptoethanol, 0.1 mM non-essential amino acids, 1 mM sodium pyruvate, 4.5 mg/ml D-glucose, 1% penicillin-streptomycin and 1000 U/ml leukemia inhibitory factor and collected for Hi-C.


title: Generation of human chambered cardiac organoids from pluripotent stem cells for improved modelling of cardiovascular diseases

status: Public on Oct 10 2022

city: Singapore

first: Boon Seng

last: SOH

address: 61 Biopolis Drive, Proteos

department: Institute of Molecular and Cell Biology (IMCB)

country: Singapore

institute: A*STAR

summary: hPSC-CM has been used to model cardiac-related disease phenotypes. However, hPSC-CMs constrains their potential in cell-based therapy, disease modeling and drug discovery. Engineered heart tissues (EHT) or scaffold generated structures are unable to recapitulate the cardiovascular systems sufficiently to improve clinical reliance. Hence in this study, we demonstrate the

overall_design: Utilizing human embryonic stem cells, chambered cardiac organoids (CCOs) were generated. Single cell RNA sequencing was performed on day8, day14 and day 21 of the CCOs differentiation. RNA-sequencing confirmed the presence of various cell types, such as smooth muscle cells, endothelial cells, cardiomyocytes and cardiac fibroblasts. We also demonstrated the utility of CCOs in modelling cardiac related disease, cardiac hypertrophy (CH). CH was modelled using endothelin-1, a known inducer of CH and its associated phenotypes. CCOs demonstrated capability of modelling functional dysregulation such as ejection fraction, thickening of cardiac chamber and arrythmic tendencies.

first: Beatrice

middle: X

last: Ho

first: Jeremy

middle: K

last: Pang

first: Qian

middle: H

last: Phua

first: Lee

middle: C

last: Liew

first: Boon

middle: M

last: Poh

first: Ying

last: Chen

first: Yuin-Han

last: Loh

first: Omer

last: An

first: Henry

last: Yang

first: Veerabrahma

middle: P

last: Seshachalam

first: Judice

middle: L

last: Koh

first: Woon-Khiong

last: Chan

first: Shi-Yan

last: Ng

first: Boon-Seng

last: Soh


title: Lamin A/C-dependent chromatin architecture safeguards naïve pluripotency to prevent aberrant cardiovascular cell fate and function[RNA-seq_CM]

first: Gergana

last: Dobreva

overall_design: Conrol and Lmna KO E14 Tg(Nkx2-5-EmGFP)  mESCs were differentiated by hanging drop method.Day10 CMs were  FACS-sorted by Nkx2-5+ GFP expression and performed RNA-seq.

first: Yinuo

last: Wang

first: Julio

last: Cordero

first: Adel

last: Elsherbiny

first: Linda


title: Interleukin-17 drives sex-dependent weight loss and changes in feeding behaviour during Trypanosoma brucei infection

status: Public on Oct 08 2022

city: Manchester

first: Matthew

middle: Christopher

last: Sinton

state: Greater Manchester

address: Core Technology Facility

department: Division of Immunology, Immunity to Infection and Respiratory Medicine

country: United Kingdom

institute: University of Manchester

summary: African trypanosomes, the causative agents of Human and Animal African trypanosomiasis or sleeping sickness, reside in tissue niches proposed to be important for disease outcome and transmission. Here, we demonstrate that parasites in the inguinal white adipose tissue (iWAT) niche induce sexually dimorphic physiological and immunological responses. Following chronic Trypanosoma brucei infection, male mice experience weight loss, reduced adipose tissue mass and altered tissue function, as well as changes in feeding behaviour, whereas females do not. We identified that interleukin-17 (IL-17), a cytokine that we show is elevated in sleeping sickness patients, orchestrates a sex-specific response to T. brucei infection in experimental infections. Deletion of murine IL-17a/f abolishes infection-associated weight loss, alters feeding behaviour, and limits adipose tissue wasting in male mice only. We propose that these effects might be triggered locally in adipocytes via engagement of IL-17 with its cognate receptor leading to lipolysis and tissue wasting, and/or systemically, via IL-17 signalling in the hypothalamus, potentially suggesting that IL-17 signalling coordinates brain-adipose tissue communication during sleeping sickness. Our findings also suggest a key sex-dependent role for the IL-17 isoforms IL-17A and IL-17F in regulating adipose tissue and energy balance during infection. Altogether, the results presented here open new directions to understand energy balance and brain-adipose tissue communication during chronic infection.

overall_design: Male and female wild type C57BL/6 mice were infected with Trypanosoma brucei brucei Antat1.1E for a period of 25 days. We infected 4 mice per group, and we included 4 naïve males and 4 naïve females. At the end of the infection, mice were perfused, and the inguinal white adipose tissue (iWAT) was dissected and snap frozen on dry ice. RNA was purified from whole iWAT, using a standard a Qiagen RNEasy Kit, with a Trizol step

first: Alex

last: Girard

first: John

last: Ogunsola

first: Praveena

last: Chandrasegaran

first: Paul

last: Capewell

first: Georgia

last: Perona-Wright

first: Dieudonné

last: Ngoyi

first: Nono

last: Kuispond

first: Bruno

last: Bucheton

first: Mamadou

last: Camara

first: Shingo

last: Kajimura

first: Cecile

last: Benezech

first: Annette

last: MacLeod

first: Juan

middle: F

last: Quintana


title: Transcriptome analysis after treating with LBH589 in ocular melanoma cells

status: Public on Oct 02 2022

first: AI

last: ZHUANG

summary: In order to study the mechanism of histone acetylation affecting development of ocular melanoma, we treated ocular melanoma cells with histone deacetylatase inhibitor LBH589. The results showed that the METTL14 was increased after LBH589 treatment. The study aims to reveal the interaction between histone acetylation and m6A modification, and to further explore the relationship between the expression level of METTL14 and the survival time of ocular melanoma patients, hopefully providing new ideas for the treatment of malignant tumors.

overall_design: Histone acetylation in ocular melanoma cells affects its biological function.

first: A

last: Zhuang

first: P

last: Chai

first: X

last: Fan


title: Lamin A/C-dependent chromatin architecture safeguards naïve pluripotency to prevent aberrant cardiovascular cell fate and function[RNA-seq_D10 EBs]

first: Gergana

last: Dobreva

overall_design: Conrol and Lmna KO E14 Tg(Nkx2-5-EmGFP)  mESCs were differentiated by hanging drop method. RNA-seq was performed from d10 EBs.

first: Yinuo

last: Wang

first: Julio

last: Cordero

first: Adel

last: Elsherbiny

first: Linda

last: Kessler


title: Identify and characterize the polyploidization process of primary human proximal tubular cells (hPTC)

status: Public on Oct 01 2022

city: Firenze

first: Roberto

last: Semeraro

address: Viale Pieraccini, 6

department: Medicina Sperimentale e Clinica

country: Italy

institute: Università degli studi di Firenze

summary: We generated single-cell RNA sequencing (scRNAseq) datasets of primary cultures of  human proximal tubular cells at different passages which we have found to contain a polyploid fraction. Within hPTC clusters, we found genes previously associated with different phases of endoreplication-mediated polyploidy and established that YAP1 controls the polyploidization process of hPTC. These observations were verified by treating hPTC with verteporfin (a YAP1 inhibitor), YAP1 silencing and by quantifying  the expression of YAP1 downstream targets in sorted polyploid hPTC

overall_design: Analyze the polyploidization process of primary human proximal tubular cells (hPTC)

first: Letizia

last: De Chiara

first: Elena

last: Lazzeri

first: Paola

last: Romagnani


title: Analyze the mechanism of polyploidization of proximal tubular cells (PTC) in the unilateral ischemia reperfusion injury model of acute kidney injury (AKI) in mice

summary: We found that PTC undergo polyploidization immediately after AKI induced by ischemia. To identify the mechanism controlling polyploidization of PTC, we generated single-cell RNA sequencing (scRNAseq) datasets from healthy mouse kidneys, 2 and 30 days after ischemia reperfusion injury.  We found that polyploid PTC become hypertrophic and undergo polyploidization in a YAP1-related manner. In particular, YAP1 controls polyploidization of PTC via E2f7, E2f8 and Akt1. We confirmed these findings by knocking-down those genes in vitro.

overall_design: Identify and characterize the mechanism controlling the polyploidization process of PTC after Acute Kidney Injury


title: Histone acetylation modification analysis in uveal melanoma cells and normal melanocytes

summary: In order to study the histone modification differences in uveal melanoma cells and normal melanocytes.

overall_design: Examination of histone acetylation modifications in 2 cell types.


title: The chromatin landscape of the euryarchaeon Haloferax volcanii

city: Stanford

first: Georgi

middle: Kolev

last: Marinov

state: California

address: 279 Campus Drive West, Beckman Center, B-257A/259

department: Genetics

institute: STANFORD UNIVERSITY

summary: Archaea, together with Bacteria, represent the two main divisions of life on Earth, with many of the defining characteristics of the more complex eukaryotes tracing their origin to evolutionary innovations first made in their archaeal ancestors. One of the most notable such features is nucleosomal chromatin, although archaeal histones and chromatin differ significantly from those of eukaryotes. Despite increased interest in archaeal histones in recent years, the properties of archaeal chromatin have been little studied using genomic tools. Here, we adapt the ATAC-seq assay to the archaeal context and use it to map the accessible landscape of the genome of the euryarchaeote Haloferax volcanii. We integrate the resulting datasets with genome-wide maps of active transcription and single-stranded DNA (ssDNA), and find that while H. volcanii promoters exist in a preferentially accessible state, modulation of transcriptional activity is not associated with changes in promoter accessibility, unlike the typical situation in eukaryotes. Applying orthogonal single-molecule footprinting methods, we quantify the absolute levels of physical protection of H. volcanii, and find that archaeal nucleosomal chromatin is at its baseline comparably to slightly more open than that of eukaryotes. We also evaluate the degree of coordination of transcription within archaeal operons and make the unexpected observation that some CRISPR arrays are associated with highly prevalent ssDNA structures. These results provide a foundation for the future functional studies of archaeal chromatin.

overall_design: KAS, ATAC-seq, NOME-seq, dSMF

first: S

middle: T

last: Bagdatli

first: Tong

last: Wu

first: Chuan

last: He

first: Anshul

last: Kundaje

first: William

middle: J

last: Greenleaf


title: A Novel MIP-1 Expressing Macrophage Subtype in Bronchoalveolar Lavage Fluid from Healthy Volunteers

status: Public on Sep 30 2022

first: Deborah

middle: R

last: Winter

address: 240 E. Huron Street, M300

institute: Northwestern University

summary: We perform single-cell RNA-seq on Bronchoalvaolar Lavage (BAL) fluid from 4 healthy volunteers.

overall_design:
single-cell RNA-seq of BAL fluid.
** The submitter declare that  the raw data files will be submitted to dbGap due to patient privacy issue***


title: Impact of bacterial mono-colonization on intestinal and splenic CD4 T cells responses

status: Public on Sep 27 2022

city: Boston

first: CBDM

last: Lab

state: MA

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

institute: Harvard Medical School

summary: Intestinal T cells responses are strongly influenced by microbes. In this study we aimed to adress how different microbes and what microbial factors  influce intestinal T cells  differentiation and subsequent clonal expansion. Paticularly we choose Clostridium ramosum (Cr) as a strong induced of a subest of intestinal Tregs (Rorc+),  a medium inducer or Rorc+ Tregs an T1h7  Escherichia coli Nissle (EcN) and a strain that did not impact either o those cell (Pm). In addition,  to study the impact of  Escherichia coli Nissle (EcN) ploysaccharide K5 capsule on intestinal  T cells  activation, we used a EcN strain lacking the K5 capsule (kfiCD). At day 21 post-monocolonization we isolated CD4 T cells from monocolonized mice in both intestinal Lamina Propria and spleen and performed single cells RNA and TCR seq.

overall_design: Germ-free mice were monocolonized by oral gavage for 2 weeks with the indicated microbes: C. ramosum (CR), P.magnus (PM), E.coli Nissle (EcN) and EcN mutant kifCD (kif).  To assess the transcriptional inductions in colonic and splenic CD4 T cells, we flow-cytometrically sorted CD4 T cells (DAPI- CD19- CD4+ TCRβ+) or for somesamples CD4 (DAPI- CD19- CD4+ TCRβ+ CD44+)  from Germ-free mice (GF), CR, PM, EcN wild-type (EcN) and EcN kfiCD (kif) mutant at day 14 post-monocolonization and single cell RNA and TCR seq.

first: Martina

last: Sassone-Corsi

first: Deepshika

last: Ramanan

first: Diane

last: Mathis

first: Christophe

last: Benoist


title: SnoRNA antagonizes IL-15-mediated lipolysis and promotes obesity

status: Public on Sep 18 2022

city: Houston

first: Haoqiang

last: Ying

state: Texas

address: 1515 Holcombe Blvd

institute: M. D. Anderson Cancer Center

summary: Obesity has long been considered one of the most important risk factors for a number of cancer types, including breast cancer and remains one the more severe disease concerns. However, the functional importance of noncoding RNA elements remains elusive. Here, we report the upregulation of SNORD46 in obesity serum. The expression status of SNORD46 is correlated with donor’s body mass index (BMI). The expression of SNORD46 in adipocytes was regulated in a CEBP-beta-dependent manner. Mechanically, adipocyte-expressed SNORD46 bound with interleukin-15 (IL-15) in serum, by which Snord46 G11A mutant exhibited enhanced interaction with IL-15. A knockin mouse strain harboring a Snord46 G11A mutation (referred as Snord46mut/mut mice) exhibited obesity and obesity associated complexities compared to wild type or heterozygous littermates. The SNORD46-IL-15 interaction blocked IL-15-dependent non-canonical signaling events, which contained the tyrosine-protein kinase Fer-dependent phosphorylation of platelet glycoprotein 4 (CD36) and monoglyceride lipase (MGLL). Consequently, the obesity-expressed SNORD46 suppressed the IL-15 triggered, Fer-dependent phosphorylation of CD36 and MGLL, leading to inhibited lipase of adipocytes. SNORD46 locked nucleic acids (LNAs) effectively conquered the inhibitory effect of SNORD46 and exhibited anti-obesity effects. Hence, our findings demonstrated the functional importance of snoRNAs in obesity and the efficacy of snoRNA LNAs for antagonizing obesity.

overall_design: The CD3-CD56+ NK cells were negatively selected from the peripheral blood mononuclear cells of normal weight donors and obese donors. Then total RNA was profiled after being isolated using QIAzol Lysis Reagent.

first: Yaohua

last: Zhang

first: Zilong

last: Zhao

first: Lisa

middle: A

last: Huang

first: Yuan

last: Liu

first: Chengcao

last: Sun

first: Yajuan

last: Li

first: Zhao

first: Youqiong

last: Ye

first: Tina

last: Nguyen

first: Jun

last: Yao

first: Nikhil

last: Garlapati

first: Andrew

first: Sergey

middle: D

last: Egranov

first: David

last: Hawke

first: Abigail

last: Caudle

first: Asygual

last: Sahin

first: Bora

last: Lim

first: Laura

last: Beretta

first: George

last: Calin

first: Dihua

last: Yu

first: Mien-chie

last: Hung

first: Michael

last: Curran

first: Boyi

last: Gan

first: Leng

last: Han

first: Chunru

last: Lin

first: Liuqing

last: Yang


title: Analysis of gene expression changes in fetal erythroid cells obtained from mice with Csnk2b gene conditional deletion in the hematopoietic system.

city: Verona

first: Nicola

last: Vitulo

state: Verona

address: Ca' Vignal 1, Strada Le Grazie 15

department: Department Biotechnology

institute: University of Verona

summary: Protein Kinase CK2 is a pleiotropic and constitutively expressed enzyme (phosphotransferase) usually present as a tetrameric complex of two catalytic alpha and two regulatory beta subunits. Alpha and beta proteins can also work independently from the holoenzyme exerting different functions on other protein targets. It is well known the CK2 role in promoting cell survival and proliferation and in sustaining the growth of many hematological malignances. However, its physiological role in hematopoiesis, in particular in erythropoiesis is still unknown. Our analysis was focused on the hematopoietic functions of the beta subunit through the generation of conditional KO mice for Csnk2b gene in the hematopoietic system. Our purpose was to asses if CK2b plays a role in the development of erythroid cells. To this aim, we performed a mRNA sequencing analysis of erythroid TER119+ cells purified from control (Csnk2b+/+) and KO (Csnk2b-/-) embryos and here we report a complete list of the genes resulted to be differentially expressed.

overall_design: Csnk2b conditional KO mice were generated using the Cre/loxp system where the Cre recombinase is under the control of the pan-hematopoietic Vav1 promoter. Since the KO phenotype was lethal, we shifted the analysis during gestation. We examined the mRNA profiles of TER119+ erythroid cells purified from the livers of control (n=3) and KO embryos (n=2). Samples were collected at 14.5 days post conception.

last: Quotti Tubi

first: Sara

last: Canovas Nunes

first: Elisa

last: Mandato

first: Marco

last: Pizzi

first: Elena

last: Doriguzzi Breatta

first: Sabrina

last: Manni

first: Anna

last: Fregnani

first: Mitja

last: Nabergoj

first: Odile

last: Filhol

first: Brigitte

last: Boldyreff

first: Gianpietro

last: Semenzato

first: Carmela

last: Gurrieri

first: Francesco

last: Piazza


title: Aqp1 overexpression may enhance glioma tumorigenesis by interacting with the transcriptional regulation networks of Foxo4, Maz, and E2F families

status: Public on Sep 19 2022

city: Haikou City

first: Jianqiang

last: Chen

state: Hainan Province

address: 43 People's Avenue, Meilan District, Haikou City, Hainan Province

institute: Haikou People 's Hospital

summary: Gliomas is the most common and aggressive primary brain tumor. The C6 glioma cell line has been widely used for decades as experimental model system for the study of glioblastoma growth and invasion. Recently, aquaporin-1 (Aqp1) is reported to facilitate cell migration and potentially involved in tumor progression. Here we overexpressed Aqp1 in C6 cells to examine its potential role in glioblastoma. We found overexpression of Aqp1 in C6 cells significantly increased cell viability and cell migration. The upregulated genes were enriched for cell mobility and glioblastoma. Transcriptional factor binding analysis indicates the upregulated genes were regulated by FOXO4, MAZ, and E2F TF families, which are known factors involved in cell cycle control and cancer progression. Our study suggests Aqp1 is potentially involved in gliomas formation by interacting with the transcriptional regulation networks of FOXO4, MAZ, and E2F TF families.

overall_design: three treatment (overexpress Aqp1 in C6 cells) vs. three control (no overexpression in C6 cells)

first: Guan

last: Ying

first: Chen

last: Die

first: Zhan

last: Yuefu

last: Jianqiang


title: Effect of HAPLN1-PTR1 on RPMI8226 multiple myeloma cells

status: Public on Sep 06 2022

city: Madison

first: Hae Yeun

last: Chang

state: WI

address: 1111 Highland ave., WIMR II

institute: UW-Madison

summary: To investigate the role of HAPLN1 in multiple myeloma, we treated RPMI8226 multiple myeloma cells with recombinant HAPLN1-PTR1. We then performed gene expression profiling analysis using data obtained from RNA-seq.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for RPMI8226 multiple myeloma cells treated with 100 nM GST (control) or GST-PTR1 (experimental group) for 6 h.

first: Mailee

last: Huynh

first: Shigeki

last: Miyamoto


title: Circulating CircRNA expression profiling of  Graves' disease

status: Public on Sep 01 2022

city: zhenjiang

first: xiangmei

last: ding

address: No. 8 of Power Road

institute: The Affiliated People’s Hospital of Jiangsu University

summary: NGS was performed to detect human circRNAs.  We found many upregulated and downregulated circRNAs in GD patients. Through high-throughput sequencing technology, 23215 upregulated and 13715 down-regulated circRNAs were detected between gd patient group and the healthy control group. Of the 218 circRNAs with significant difference, 359 were up-regulated and 309 were down-regulated.

overall_design: Circulating circRNA profiles of five Graves' disease patients and five healthy volunteers were generated by deep sequencing,using Illumina HiSeq 4000

first: Yingzhao

last: Liu

first: Huiyong

last: Peng

first: Si

last: Xiong

first: Xiangmei

last: Ding

first: Xuehua

last: Wang


title: Lysosomal Dynamics Orchestrate Neurogenesis [Polysome-seq]

status: Public on Aug 31 2022

city: Beijing

first: Jianwei

last: Jiao

state: Beijing

address: 1 Beichen West Road

department: State Key Laboratory of Reproductive Biology

institute: Institute of Zoology, Chinese Academy of Sciences

summary: Lysosomes are cellular recycling stations and metabolic signaling hubs. Whether lysosome dynamics regulate mammalian brain development is unknown. We found that radial glia cells possess a large number of endolysosomes and that asymmetric inheritance of lysosomes in daughters of radial glia cells can predict fate and cell cycle length. To determine the translation control by the mTORC1, we performed polysome profiling of mRNAs associated with >3 ribosomes for neural progenitor cells that treated with DMSO or Torin1 for 2 hours.

overall_design: Polysome profiling was performed for mouse E13.5 neural progenitor cells that were cultured overnight and treated with DMSO or Torin1 for 2 hours.

first: Wenzheng

last: Zou

first: Yuqing

last: Lv

first: Ling

last: Sun

first: Shukui

last: Zhang


title: Lysosomal Dynamics Orchestrate Neurogenesis [RIP-Seq]

summary: Lysosomes are cellular recycling stations and metabolic signaling hubs. Whether lysosome dynamics regulate mammalian brain development is unknown. We found that radial glia cells possess a large number of endolysosomes and that asymmetric inheritance of lysosomes in daughters of radial glia cells can predict fate and cell cycle length. To determine the lysosomal regulation of translation initiation by mTORC1/eIF4E axis, we performed RNA immunoprecipitation sequencing (RIP-seq) with antibody against eIF4E in E13.5 neocortex.

overall_design: RIP-seq was performed for cytoplasmic mRNA in mouse E13.5 brain neocortex with eIF4E antibody (MBL, RN001P) or control immunoglobulin G (Bioss, bs0295P).


title: Lysosomal Dynamics Orchestrate Neurogenesis

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

overall_design: Refer to individual Series


title: Diffuse Alveolar Damage Patterns Reflect the Immunological and Molecular Heterogeneity in Fatal COVID-19

city: São Paulo

first: Jhonatas

middle: Sirino

last: Monteiro

state: São Paulo

address: 748 Professor Lineu Prestes Ave.

department: Deparment of Biochemistry, Institute of Chemistry

country: Brazil

institute: University of São Paulo

summary: To date, few studies analyzed the nature of the temporal and spatial cell arrangement during the complex immune/inflammatory/molecular and structural cell alterations that take place in the lungs in severe COVID-19. Such information is crucial to better envision the disease complexity. To this end, we have applied a platform for multiplex imaging complemented with assessment of SARS-CoV-2, bacterial/fungi identification and cytokine/transcriptomic profiling in 18 lungs of deceased patients from Sao Paulo.

overall_design: Comparative gene expression profile of lung samples of deceased COVID-19 patients. There are 12 biological replicates for COVID-19 patients and 4 biological replicates for control group. Each biological replicate has 4 technical replicates.

first: Jonas

middle: S

last: Erjefält

first: Natália

last: Costa

first: Jimmie

last: Jönsson

first: Olga

last: Cozzolino

first: Katia

last: Dantas

first: Carl-Magnus

last: Clausson

first: Premkumar

last: Siddhuraj

first: Caroline

last: Lindö

first: Suzete

last: Lombardi

first: Alfredo

last: Júnior

first: Leila

last: Antonangelo

last: Faria

first: Amaro

middle: N

last: Neto

first: Renata

first: João

last: Pinho

first: Michele

last: Gomes-Gouvêa

first: Roberta

middle: V

last: Pereira

last: Setubal

first: Ellen

last: Oliveira

last: Sanden

first: Luiz

last: Silva

first: Paulo

last: Saldiva

first: Marisa

last: Dolhnikoff

first: Thais

last: Mauad


title: Single-nucleus RNA sequencing of OCTN2-defective engineered heart tissues and isogenic control

status: Public on Aug 22 2022

city: Hamburg

first: Arne

last: Hansen

address: Martinistraße 52

department: Institute of Experimental Pharmacology and Toxicology

institute: University Medical Center Hamburg-Eppendorf

summary: Primary carnitine deficiency (PCD) is an autosomal recessive disorder caused by mutations in the gene SLC22A5, encoding for the plasmalemmal carnitine transporter OCTN2. PCD patients suffer from muscular weakness and dilated cardiomyopathy (DCM). However, currently available PCD models were unable to distinguish causative from secondary pathomechanisms. To further understand the contribution of cellular subclusters to the PCD disease phenotype we analyzed engineered heart tissues from OCTN2-defective genotype in comparison to isogenic control using single-nucleus RNA sequencing.

overall_design:
Two OCTN2-defective human induced pluripotent stem cell lines were generated from a healthy control line, carrying a full OCTN2-knockout and a homozygous OCTN2 (N32S) loss of function mutation. Cardiomyocytes were differentiated and the engineered heart tissue (EHT) technology served as a three-dimensional disease model. EHTs were cultured for 14 days and subsequently analyzed by single-nucleus RNA sequencing.

**RAW data not provided due to GDPR regulations of this cell line**

first: Henrike

last: Maatz

first: Sabine

last: Schmidt

first: Giannino

last: Patone


title: Diurnal small RNA expression and post-transcriptional regulation in young and old Drosophila melanogaster heads

city: Corvallis

first: Rosalyn

middle: M.

last: Fey

state: OR

address: 1500 SW Jefferson Way

institute: Oregon State University

summary: MicroRNAs are a class of small (~22nt) endogenous RNAs that regulate target transcript expression post-transcriptionally. Previous studies characterized age-related changes in diurnal transcript expression but it is not understood how these changes are regulated, and whether they may be attributed in part to changes in microRNA expression or activity with age. Diurnal small RNA expression changes with age were not previously studied. To interrogate changes in small RNA expression with age, we collected young (5 day) and old (55 day) Drosophila melanogaster around-the-clock and performed deep sequencing on size-selected RNA from whole heads. We find several microRNAs with changes in rhythmicity after aging, and we investigate microRNAs which are differentially expressed with age. We find that predicted targets of differentially expressed microRNAs have RNA-binding and transcription factor activity. We use a previously published method to identify mRNA transcripts which show evidence of microRNA targeting that is altered after aging, and find several that are involved in muscle development and maintenance. Finally, we identify novel microRNAs using the random-forest-based method miRWoods, which surprisingly also discovered transfer RNA-derived fragments.

overall_design: RNA-sequencing and analysis of small RNA from Drosophila melanogaster heads, collected every 4 hours over 24 hours

first: Eileen

last: Chow

first: Barbara

middle: O

last: Gvakharia

first: Jadwiga

last: Giebultowicz

first: David

last: Hendrix


title: Hotspots of single-strand DNA "breakome" are enriched at transcriptional start sites of genes

status: Public on Aug 18 2022

city: Xiamen

first: Huifen

last: Cao

email: hfcao_bnu@163.com, hfcao@hqu.edu.cn

state: Fujian

address: 668 Jimei Road

department: School of Biomedical Sciences

institute: Huaqiao University

summary: Single strand breaks (SSBs) represent one of the most common types of DNA damage yet not much is known about the genome landscapes of this type of DNA lesions in mammalian cells. Here, we found that SSBs are more likely to occur in certain positions of the human genome — SSB hotspots — in different cells of the same cell type and in different cell types.  We hypothesize that the hotspots are likely to represent biologically relevant breaks. And, we found that the hotspots had a prominent tendency to be enriched in the immediate vicinity of transcriptional start sites (TSSs). We show that these hotspots are not likely to represent technical artifacts, or be caused by common mechanisms previously found to cause DNA cleavage at promoters, such as apoptotic DNA fragmentation or topoisomerase type II (TOP2) activity. Therefore, such TSS-associated hotspots could potentially be generated using a novel mechanism, that could involve preferential cleavage at cytosines, and their existence is consistent with recent studies suggesting a complex relationship between DNA damage and regulation of gene expression.

first: Philipp

last: Kapranov


status: Public on Aug 19 2022

city: Daegu

first: Hyo-Gyoung

last: Kang

address: Hoguk-ro, Buk-gu

department: Cell and Matrix Research Institute, School of Medicine

country: South Korea

institute: Kyungpook National University

summary: We hypothesized that functional polymorphisms in NEUROD1 target genes may also affect the clinical outcomes of patients with SCLC, as NEUROD1 plays a crucial role in SCLC carcinogenesis. To test this hypothesis, we performed ChIP-seq of NeuroD1 and H3K4me3 in SCLC cells.  Then we evaluated the association between putative functional polymorphisms in NEUROD1 target genes and the chemotherapy response and survival outcomes of patients with SCLC.

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for NeuroD1 and H3K4me3 in SCLC cells.

first: Hyo

middle: G

first: Jae

middle: Y

last: Park

first: Seung

last: Yoo


title: Skeletal-Muscle Glutamate-Ammonia Ligase as Potential Biomarker of Preclinical Prion Diseases

city: Zurich

first: Davide

last: Caredio

state: Switzerland

department: Institute of Neuropathology

country: Switzerland

institute: University Hospital of Zurich

summary: We provide here a comprehensive transcriptional profiling of murine blood, spleen and skeletal muscle and brain on eight different time points after intracerebral prion inoculation. Our findings provide a detailed time course of extra-neural, transcriptional changes during prion disease which we presume to be of immediate relevance for biomarker development. Data analysis scripts can be found on https://github.com/marusakod/RML_extraneural_organs.

overall_design: Six-week-old (main and validaition cohort) C57BL/6 mice were inoculated in the right hemisphere . For prion inoculations, 30 μl of RML6 (passage 6 of Rocky Mountain Laboratory strain mouse-adapted scrapie prions) at a 10−2 dilution of a 10% homogenate, containing 9.02 log LD50 of infectious units per ml in 10% homogenate. Control inoculations were performed using 30 μl of non-infectious brain homogenate (NBH) from CD-1 mice at the same dilution. Each timepoint and treatment group (n = 44 different treatment groups) entails at least 3 and up to 6 animals, except for brains from NBH-inoculated animals at 20 weeks post inoculation (n = 2).

first: Adriano

last: Aguzzi

first: Karl

last: Frontzek

first: Maruša

last: Koderman


title: Single cell multi-omics profiling of H3-K27M DMG

status: Public on Aug 09 2022

first: Li

last: Jiang

address: 360 Longwood Ave

department: Pediatric Oncology

institute: Dana Farber Cancer Institute

summary: Multi-omics profiling of H3-K27M DMGs across different age groups and locations, using fresh single whole cell RNA-seq, scATACseq, spatial in situ sequencing, and WES/targeted exome sequencing.

overall_design: Single cell transcriptomic profiling of 45 H3-K27M DMGs. Co-analysis of single cell accessible chromatin (scATAC-seq) profiles in 8 tumors. For RNA-seq data, unnormalized counts are packaged in GSE184357_DMG_raw_counts.tar.gz. The rest are normalized TPM values. The raw fastq data can be requested from EGA with accession number EGAD00001011339 (RNA-seq) and EGAD00001010170 (ATAC-seq).

first: Mariella

last: Filbin


title: Effect of cholic acid on gene expression of crypts isolated from DSS-induced colitic mice

status: Public on Aug 05 2022

city: Shanghai

first: Tingying

last: Jiao

state: Shanghai

address: 501 Haike Road, Pudong New Area

institute: SIMM

summary:
To investigate the exact mechanism of CA has on DSS-induced colitis
We then performed gene expression profiling analysis using data obtained from RNA-seq of 8 samples from 2 groups

overall_design: Comparative gene expression profiling analysis of RNA-seq data for colitic crypts and cholic acid-treated colitic crypts

last: Chen


title: Quiescent ovarian cancer cells, in response to chemotherapy, secrete follistatin to induce chemotherapy resistance in surrounding cells.

status: Public on Aug 10 2022

city: Pittsburgh

first: Santiago

last: Panesso

state: PA

address: 204 Craft Ave B330

department: Obstetrics and Gynecology

institute: Magee Womens Research Institute

summary:
We sought to identify mechanism of NFATC4 quiescence-driven chemoresistance.
RNA-Seq identified upregulation of follistatin (FST) in quiescent OvCa cells.

overall_design: Comparative gene expression profiling analysis of HEY1 and SKOV3 cell lines expressing the IcNFATC4 or ILUC constructs were treated for 24, 48 and 96h with 100 ng/mL doxycyclin

last: Panesso-Gomez

first: Ronald

last: Buckanovich

first: Alexander

last: Cole


title: H3K27me3 CUT&Tag - Jmjd3-scKO, Utx-scKO, Tdt-Ctrl, IgG-His

status: Public on Aug 04 2022

first: Jeffrey

last: Dilworth

state: Wisconsin

address: 1111 Highland Ave

institute: University of Wisconsin

summary: Stem cells reside in specialized niches that play a critical role in modulating their fate. Supporting cells in the niche instruct fate changes to the stem cells through epigenetic enzymes that transduce cell signaling to modify gene expression. Recent studies showed that the innate immune response to muscle injury alters the muscle stem cell (MuSC) niche, it remains unknown how MuSC adapt to the modified milieu to mediate muscle repair. Here we show that the epigenetic enzyme JMJD3 coordinates MuSC adaptation to the regenerative niche in a non-cell autonomous manner where it modifies their extracellular matrix to integrate signaling that stimulates exit of quiescence. Genomics and transcriptomics approaches identified the hyaluronic acid (HA) synthesis enzyme Has2 as a key JMJD3 target gene that allows MuSCs to integrate signals from the regenerative niche. Overall, we identified a specific role for JMJD3 in regulating the expression of genes that allow MuSCs to adapt to the modified niche of regenerating muscle. We aim to determine the differential occupancy of histone H3 lysine 4 trimethyl mark muscle satellite stem cells isolated from JMJD3scKO, UTXscKO and Wild-type mice.

overall_design: CUT&Tag was performed on muscle satellite cells isolated from hindlimb muscles at 30 hrs post cardiotoxin injury.

first: Kiran

last: Nakka

first: F


title: H3K4me3 CUT&Tag - Jmjd3-scKO, Utx-scKO, Tdt-Ctrl, IgG-His


title: Jmjd3-Lab UTX-Lab CUT&Tag


title: Single-cell RNA-seq - Jmj KO, Utx KO, Tdt.Control

summary: Stem cells reside in specialized niches that play a critical role in modulating their fate. It remains unknown how MuSC adapt to the modified milieu to mediate muscle repair. Here, we show that the epigenetic enzyme JMJD3 coordinates MuSC adaptation to the regenerative niche in a non-cell autonomous manner where it modifies their extracellular matrix to integrate signaling that stimulates exit of quiescence. Genomics and transcriptomics approaches identified the hyaluronic acid (HA) synthesis enzyme Has2 as a key JMJD3 target gene that allows MuSCs to integrate signals from the regenerative niche.

overall_design: Single-cell RNA-Seq was performed on muscle satellite cells prepared from indicated mouse strains. Muscle satellite cells were isolated by FACS at 40 h post Cardiotoxin injury.


title: Bulk RNA-Seq in JMJD3scKO, UTXscKO and Wild-type satellite cells

overall_design: RNA-Seq was performed on muscle satellite cells prepared from indicated mouse strains in duplicates. Muscle satellite cells were isolated by FACS at 30 h post Cardiotoxin injury.


title: RNA-seq identifies IL15-induced adipogenesis and fatty acid metabolism pathways in human adipocytes

status: Public on Aug 03 2022

city: Indianapolis

first: Yuan

last: Liu

state: IN

address: 410 W. 10th Street

institute: Indiana University

summary: IL15 has been suggested to reduce WAT mass in obese mice models. However, the underlying molecular mechanism is largely unknown. We determined the gene expression profile of human adipocytes treated with vehicle or IL15. Adipocytes isolated from healthy donors exhibited reduced expression of gene signatures related to adipogenesis and fatty Acid metabolism upon IL15 stimulation, which is consistent with the previous notion that IL15 exhibits an anti-obesity effect. Taken together, our findings suggested that SNORD46 physically interact with IL15 and acts as a natural IL15 antagonist in the serum of donors with obesity to hinder the anti-obese effect of IL15.

overall_design: Comparative gene expression profiling in adipocytes from 6 human donors treated ex-vivo with IL15 or vehicle.

first: Yaohua

last: Zhang

first: Liuqing

last: Yang


title: Antisense oligonucleotides targeting the miR-29b binding site in the GRN mRNA increase progranulin translation

status: Public on Aug 01 2022

city: St. Louis

first: Andrew

middle: D.

last: Nguyen

state: MO

address: 1402 S Grand Blvd, Doisy Hall, R205

department: Internal Medicine

institute: Saint Louis University

summary: Heterozygous GRN (progranulin) mutations cause frontotemporal dementia (FTD) due to haploinsufficiency, and increasing progranulin levels is a major therapeutic goal. Several microRNAs, including miR-29b, negatively regulate progranulin protein levels. Antisense oligonucleotides (ASOs) are emerging as a promising therapeutic modality for neurological diseases, but strategies for increasing target protein levels are limited. Here, we tested the efficacy of ASOs as enhancers of progranulin expression by sterically blocking the miR-29b binding site in the 3' UTR of the human GRN mRNA. We found 16 ASOs that increase progranulin protein in a dose-dependent manner in neuroglioma cells. A subset of these ASOs also increased progranulin protein in iPSC-derived neurons and in a humanized GRN mouse model. In FRET-based assays, the ASOs effectively competed miR-29b from binding to the GRN 3' UTR RNA. The ASOs increased levels of newly synthesized progranulin protein by increasing its translation, as revealed by polysome profiling. Together, our results demonstrate that ASOs can be used to effectively increase target protein levels by partially blocking miR binding sites. This ASO strategy may be therapeutically feasible for progranulin-deficient FTD as well as other conditions of haploinsufficiency.

overall_design: miR profiling of human H4 neuroglioma cells and HMC3 microglia cells

first: Michelle

last: Pherson

first: Monica

last: Pavlack


title: RNA-Seq and CUT&Tag of satellite stem cells


title: Retinoic acid receptor activity is required for the maintenance of type 1 innate lymphoid cells

status: Public on Jul 31 2022

city: Kyoto

first: Koichi

last: Ikuta

state: Kyoto

address: 53 Shogoin-Kawaharamacho, Sakyo-ku

department: Department of Virus Research

country: Japan

institute: Institute for Frontier Life and Medical Sciences, Kyoto University

summary: This study examines the role of retinoic acid receptor (RAR) activity in type 1 innate lymphoid cells (ILC1s) by using Rosa26-RARα403 mice, that enable Cre-mediated inhibition of RAR activity in a dominant negative manner.

overall_design: Transcriptional profiling of ILC1s and NK cells sorted from control mice or Ncr1-Cre Rosa26-RARα403 mice

first: Takuma

last: Asahi


title: Altered costimulatory signaling and hypoxia support chromatin landscapes that limit the functional potential of exhausted T cells in cancer

first: B. Rhodes

last: Ford

address: 4401 Penn Ave.

department: Department of Pediatrics

institute: University of Pittsburgh


title: Altered costimulatory signaling and hypoxia support chromatin landscapes that limit the functional potential of exhausted T cells in cancer [RNA-seq]

summary: Increases in terminally exhausted T cells in the tumor are associated with poor responses to immunotherapy, yet the mechanisms that promote progression to terminal exhaustion remain undefined. To understand the effect of epigenetic changes in subsets of tumor-infiltrating CD8+ T cells, we performed RNA-seq to understand changes in gene expression. CD8 T cells were sorted from the murine  B16 melanoma tumor using PD1 and Tim3 expression to define four subsets: PD1lo, PD1mid, PD1hi, and PD1hiTim3+. Additional control samples include paired CD44+ cells from the tumor-draining lymph node of tumor bearing mice, and OT-I effector CD8 T cells isolated from Vaccinia-ova infection. CD8 TIL PD1hi Tim3+ from B16 tumors treated with IgG control, anti-PD1 or anti-41BB agonist immunotherapies were also isolated for RNAseq.

overall_design: Three individual biological replicates of each sorted population: dLN CD8+ CD44+; TIL CD8+ PD1lo; TIL CD8+ PD1mid; TIL CD8+ PD1hi; TIL CD8+ PD1hi Tim3+; OT-I CD8+ effector from d10 Vaccinia-Ova infection; TIL CD8+ PD1hi Tim3+ IgG control treated; TIL CD8+ PD1hi Tim3+ anti-PD1 treated; TIL CD8+ PD1hi Tim3+ anti-4-1BB treated

first: B

first: Natalie

last: Rittenhouse

first: Nicole

middle: E

last: Scharping

first: Paolo

last: Vignali

first: Greg

middle: M

last: Delgoffe

first: Amanda

middle: C

last: Poholek


title: Succinyl-CoA synthetase deficiency in mouse forebrain results in hyper-succinylation with perturbed neuronal transcriptional regulation and metabolism (ATAC-Seq)

status: Public on Jul 27 2022

first: Brett

middle: Harrison

last: Graham

address: 975 West Walnut Street, IB 252C

department: Medical & Molecular Genetics

institute: Indiana University School of Medicine

summary: Lysine-succinylation is a subtype of protein acylation associated with metabolic regulation of succinyl-CoA in the TCA cycle. Deficiency of succinyl-CoA synthetase (SCS), the TCA-cycle enzyme catalyzing the reversible conversion of succinyl-CoA to succinate, leads to mitochondrial encephalomyopathy in humans and embryonic lethality in mice. This report presents a conditional forebrain-specific knock-out (KO0 mouse model of Sucla2, the gene encoding the ATP-specific beta isoform of SCS, resulting in postnatal deficiency of the entire SCS complex. Results demonstrate that the accumulation of succinyl-CoA in the absence of SCS leads to hyper-succinylation within the cerebral cortex of adult mice. With previous research identifying succinylation marks on histones, and with proteomic evidence of histone lysine-succinylation within the presented model, global chromatin accessibility was surveyed in Sucla2 mutant and control mice via ATAC-sequencing. Data show wide-scale alterations in chromatin landscape and global gene expression. Computational analysis of combined chromatin-accessibility and gene expression data reveal perturbation of neuronal transcriptional regulatory networks in the mutant forebrain, suggesting SCS-related changes in the protein succinylome and chromatin accessibility play a significant role in the neuronal pathogenesis of SCS-deficiency.

overall_design: Assessment of global chromatin accessibiliy and bulk mRNA-sequencing in murine cortex with enriched protein succinylation resulting from loss of Kreb's Cycle enzyme succinyl-CoA synthetase

first: Makayla

last: Anderson

middle: H


title: Succinyl-CoA synthetase deficiency in mouse forebrain results in hyper-succinylation with perturbed neuronal transcriptional regulation and metabolism

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

overall_design: Refer to individual Series


title: Cancer specific microbiome revealed by cell-free RNA reads in patients' plasma

status: Public on Jul 12 2022

first: Zhi

middle: John

last: Lu

address: Shuangqing Road

department: School of Life Sciences

institute: Tsinghua University

summary: We sequenced cell-free RNA (cfRNA) for five cancer types (colorectal cancer, stomach cancer, liver cancer, lung cancer and esophageal cancer) and healthy individuals in 230 plasma samples collected from 6 clinical centers in China.  Cancer related signaling pathway and microbial genus were identified. Cancer detection and specific classification were achieved through combining both host and microbial cfRNA reads.

first: Shanwen

last: Chen

first: Yunfan

last: Jin

first: Siqi

last: Wang

first: Shaozhen

last: Xing


title: Succinyl-CoA synthetase deficiency in mouse forebrain results in hyper-succinylation with perturbed neuronal transcriptional regulation and metabolism (RNA-Seq)


title: The intestinal microbiota reprograms intestinal lipid metabolism through long non-coding RNA Snhg9

status: Public on Jul 15 2022

city: Hangzhou

first: Yuhao

state: Zhejiang

address: No.268 Kaixuan Road

institute: Zhejiang University

summary: The intestinal microbiota is a key regulator of mammalian lipid absorption, metabolism, and storage. Here we show that the microbiota reprograms intestinal lipid metabolism in mice by repressing the expression of long non-coding RNA (lncRNA) Snhg9 in small intestinal epithelial cells. Snhg9 suppressed the activity of the transcription factor peroxisome proliferator–activated receptor γ (PPARγ) – a central regulator of lipid metabolism – by dissociating the PPARγ inhibitor Sirtuin 1 from cell cycle and apoptosis protein 2 (CCAR2). Forced expression of Snhg9 in the intestinal epithelium of conventional mice lowered dietary lipid absorption, reduced body fat, and protected against diet-induced obesity. The microbiota repressed Snhg9 expression through an immune cell signaling relay encompassing myeloid cells and innate lymphoid cells. Our findings thus identify an unanticipated role for a lncRNA in microbial control of host metabolism.

overall_design: 1. RNAseq analysis of laser captured epithelial cell transcripts in conventionally raised SPF mice and germ-free mice. 2. RNAseq analysis of ileal transcripts in villin-Snhg9 transgenic mice and wild-type mice. 3. 16s sequencing analysis of fecal bacterial composition in villin-Snhg9 transgenic mice and wild-type mice before and after switching from chow diet to high-fat diet.

first: Zheng

last: Kuang

first: Yun

last: Li

first: Zehan

last: Hu

first: Brian

last: Hassell

first: Kelly

last: Ruhn

first: Cassie

middle: L

last: Behrendt

first: Lora

last: Hooper


title: Melanoma Brain Metastasis Atlas [SlideSeq]

status: Public on Jul 06 2022

city: New York

first: Jana

last: Biermann

state: New York

address: 622 W168th Street

institute: Columbia University

summary: We performed single-cell/nuclei RNA-sequencing (sc/snRNA-seq) of 22 treatment-naïve melanoma brain metastases (MBM; 5 samples using scRNA-seq and 17 snRNA-seq) from 21 patients and 10 treatment-naïve peripheral (extracranial) metastases (ECM; all snRNA-seq) from 10 patients. We performed matched spatial sequencing using SlideSeq2 (n=16) on 11 snRNA-seq samples.

overall_design:
Single-cell/nuclei RNA sequencing of 22 treatment-naïve melanoma brain metastses (MBM) and 10 treatment-naïve peripheral (extracranial) metastases (ECM) with matched spatial sequencing using SlideSeqV2 (n=16) of 11 snRNA-seq samples.
>>>Submitter states: Due to patient privacy concerns the raw data will be submitted to dbGAP.<<<

first: Benjamin

last: Izar

first: Johannes

last: Melms


title: An ex vivo model of Toxoplasma recrudescence reveals host-dependent pluripotency of Toxoplasma bradyzoites.

status: Public on Jul 23 2022

city: TAMPA

first: David

middle: Dongpyo

last: Hong

state: FL

address: 3720 SPECTRUM BLVD. #325

institute: UNIVERSITY OF SOUTH FLORIDA

summary: Toxoplasma has been a useful parasite model for decades because it is relatively easy to genetically modify and culture, however, attempts to generate and study the recrudescence of tissue cysts have come up short with lab-adapted strains generating low numbers of tissue cysts in vivo.  Here we have established a new model of Toxoplasma recrudescence using bradyzoites from an unadapted Type II ME49 strain (ME49EW) isolated from murine brain tissue.  Ex vivo bradyzoite infection of fibroblasts and astrocytes produced sequential tachyzoite growth stages; a fast-growing stage was followed by formation of a slower-growing stage.  In astrocytes, but not in fibroblasts, bradyzoites also initiated a second recrudescent pathway involving bradyzoite to bradyzoite replication.  Intraperitoneal infections of mice with either bradyzoites or the fast-growing tachyzoite stage efficiently disseminated to brain tissue leading to high numbers of tissue cysts, while infections with the slow-growing tachyzoite stage were largely retained in the peritoneum.  Poor infection and cyst formation of slow-growing tachyzoites was reversible by serial tissue cyst passage, while the poor tissue cyst formation of lab-adapted tachyzoites was not reversible by these approaches.  To distinguish strain developmental competency, we identified Toxoplasma genes highly expressed in ME49EW in vivo tissue cysts and developed a qPCR approach that differentiates immature from mature bradyzoites.  In summary, the results presented describe a new ex vivo bradyzoite recrudescence model that fully captures the growth and developmental processes during toxoplasmosis reactivation in vivo opening the door to the further study of these important features of the Toxoplasma intermediate life cycle.

overall_design: ME49 type II strain and ME49EW cyst

middle: D

first: Amber

last: Goerner

first: Michael

last: W White


title: Genomewide effects of regular caffeine intake on hippocampal metabolism and learning-dependent transcription [Cut & Tag]

status: Public on Jun 22 2022

city: Lille

last: Blum

state: Cedex

address: 1 place de Verdun

department: Lille Neurosience & Cognition

country: France

institute: Inserm

summary: Caffeine is the most widely consumed psychoactive substance worldwide. Strikingly, molecular pathways engaged by its regular consumption remain unclear. We herein addressed the mechanisms associated with habitual (chronic) caffeine consumption in the mouse hippocampus using untargeted orthogonal-omics techniques. Our results revealed that chronic caffeine exerts concerted pleiotropic effects in the hippocampus, at the epigenomic, proteomic and metabolomic levels, lowered metabolic-related processes in bulk tissue, while inducing neuronal-specific epigenetic changes at synaptic transmission/neuronal activity-related genes. Altogether, these findings suggest that regular intake of caffeine improves the signal-to-noise ratio during information encoding in learning in part through a re-setting of metabolic genes helping to bolster the salience of information processing in neuronal circuits.

overall_design: Cut & tag


title: Genomewide effects of regular caffeine intake on hippocampal metabolism and learning-dependent transcription


title: Melanoma Brain Metastasis Atlas


title: Genomewide effects of regular caffeine intake on hippocampal metabolism and learning-dependent transcription [RNA-Seq]

summary: Caffeine is the most widely consumed psychoactive substance worldwide. Strikingly, molecular pathways engaged by its regular consumption remain unclear. We herein addressed the mechanisms associated with habitual (chronic) caffeine consumption in the mouse hippocampus using untargeted orthogonal-omics techniques. Our results revealed that caffeine exerts concerted pleiotropic effects in the hippocampus, at the epigenomic, proteomic and metabolomic levels, aimed at lowering metabolic-related processes while re-setting learning-associated transcriptome associated with neuronal activity. These processes involve BDNF, CREB and adenosine A2A receptors-related mechanisms. Altogether, these findings suggest that regular intake of caffeine improves the signal-to-noise ratio during information encoding in learning and bolsters the salience of information encoding in brain circuits.

overall_design: Two-three month-old mice were randomly assigned to the two following experimental groups: water (control group) and caffeine. The caffeine solution was kept in dark bottles thus protected from light and changed weekly. Treatment started at eight to nine weeks of age and lasted for two weeks. The chronic caffeine treatment in mice has been set in order to mimic the usual dose range of caffeine consumption in Humans. The selected caffeine dose of 0.3 g/L p.o., administered through drinking water at 0.3 g/L, has been previously shown to provide a significant benefit in neurodegenerative contexts (Arendash et al., 2006; Arendash et al., 2009; Laurent et al., 2014).


title: B Cell-Like Neutrophil Found in Peripheral Blood of Melanoma Patients

status: Public on Jun 30 2022

city: La Jolla

first: Huy

middle: Q

last: Dinh

state: CA

address: 9420 Athena Circle

department: Division of Inflammation Biology

institute: La Jolla Institute

summary: An expansion of neutrophils often marks cancer. To date, neutrophils are assumed to be a relatively homogenous population, but recent studies describe both pro- and anti-tumor functions in neutrophils. This suggests there is more heterogeneity in neutrophils than previously appreciated. To better understand and target neutrophil functions in cancer, we must dissect neutrophil heterogeneity and how it changes from health to disease. To this end, we employed single-cell transcriptome technology to profile immature neutrophils from bone marrow of healthy individuals. Intriguingly, we identified a new neutrophil subset that expresses several B cell markers, including CD79a/b, components of the B cell receptors and PAX5, a lineage-specific transcriptional factor. We termed this population the BNeut. Using flow cytometry, we found that BNeuts are confined to the bone marrow of healthy individuals but expand into the blood of melanoma patients at an early stage, suggesting BNeuts might be a biomarker for disease. Additionally, we find BNeuts in the mouse models of different cancer types, including breast and lung carcinoma. The BNeut appears and functions more similar to a neutrophil than a B cell. BNeuts possess a neutrophil-like transcriptional profile, large cytoplasm with segmented nucleus, and produce ROS and NETs. Using imaging, we show that the BNeuts are single cells co-expressing both CD66b and CD79b, and lack the B cell surface marker CD19. To understand why neutrophils might use a B cell program, we explored different B cell functions including antigen presentation, a function that is usually absent from neutrophils. We show BNeuts are excellent at phagocytosis, including uptake of tumor cells. Further, BNeuts have increased expression of antigen presentation-related genes compared to other neutrophils and can modulate CD4+ T cell responses. Together, we have identified a novel neutrophil subset expressing B cell markers that is preferentially expanded in the blood of melanoma patients and poised to control T cell responses during disease.

overall_design: Expression profiling by high throughput sequencing for sorted neutrophils cells in human bone marrow and melanoma blood

first: Melissa

middle: A

last: Meyer

first: Catherine

last: Hedrick


title: Electrical stimulation with a conductive ITO glass promotes neurite outgrowth and its putative mechanisms of action for direct and alternating current in primary cortical neurons

city: Tianjin

first: Mi

last: Zhou

address: Anshan street 168th

institute: Tianjin Medical University

summary: In this study, we investigated the effects of DCS and ACS on rat primary cortical neurons. Our goal was to probe the optimal stimulation parameters and underlying mechanism of ES on the primary cortical neurons.

overall_design: We then performed gene expression profiling analysis using data obtained from RNA-seq of 3 different groups at same time points.

first: Hao

last: Zhong

first: Zeyu

last: Jia

first: Guangzhi

last: Ning


title: Genomewide effects of regular caffeine intake on hippocampal metabolism and learning-dependent transcription [ChIP-Seq]


title: Developmental and evolutionary comparative analysis of a HoxD regulatory landscape in mammals and birds

status: Public on Jun 20 2022

city: Geneva

first: Aurelie

last: Hintermann

address: 30 quai Ernest-Ansermet

department: Genetics and Evolution

institute: University of Geneva

sample_organism:
Gallus gallus
Mus musculus

platform_organism:
Gallus gallus
Mus musculus


title: Fibroblasts-derived from Pluripotent Cells Harboring a Single Allele Knockout in Two Pluripotency Genes Exhibit DNA Methylation Abnormalities and Reprogramming Defects

status: Public on Jun 16 2022

city: Cambridge

first: Albert

middle: W

last: Cheng

state: MA

address: Room 453, 9 Cambridge Center

institute: Whitehead Institute

summary: Gene expression comparison between various pluripotent stem cell lines (as indicated below) that grew under 2i/Lif or S/Lif conditions

overall_design: ESCs (V6.5), secondary iPSCs system with one allele of Nanog KO (NGFP2N+/-) or with additional KO in one allele in Sall4 (NGFP2N+/-; S+/-), Esrrb (NGFP2N+/-; E+/-) or Utf1 (NGFP2N+/-; U+/-) were grown under 2i/Lif or S/Lif conditions and subjected to RNA sequencing.

first: Rudolf

last: Jaenich

first: Yosef

last: Buganim


title: AOM/DSS colorectal cancer mouse epigenetic landscape and transcriptome profile in the progression of colites to tumor.

status: Public on Jun 14 2022

city: Wuhan

first: Min

last: Wu

state: Hubei

address: Room 5005, Life Science College, Wuhan University

department: College of Life Science and Technology of Huazhong Agricultural University

institute: Wuhan universioty


title: Developmental and evolutionary comparative analysis of a HoxD regulatory landscape in mammals and birds [ChIP-seq]

summary: Modifications in gene regulation during development are considered to be a driving force in the evolution of organisms. Part of these changes involve rapidly evolving cis-regulatory elements (CREs), which interact with their target genes through higher-order 3D chromatin structures. How such 3D architectures and variations in CREs contribute to transcriptional evolvability nevertheless remains elusive. During vertebrate evolution, Hox genes were redeployed in different organs in a class-specific manner, while maintaining the same basic function in organizing the primary body axis. Since a large part of the relevant enhancers are located in a conserved regulatory landscape, this gene cluster represents an interesting paradigm to study the emergence of regulatory innovations. In this work, we analyzed Hoxd gene regulation in both murine vibrissae and chicken feather primordia, two mammalian- and avian-specific skin appendages which express different subsets of Hoxd genes, and compared their regulatory modalities with the regulations at work during the elongation of the posterior trunk, a mechanism highly conserved in amniotes. We show that in the former two structures, distinct subsets of Hoxd genes are contacted by different lineage-specific enhancers, likely as a result of using an ancestral chromatin topology as an evolutionary playground, whereas the regulations implemented in the mouse and chicken embryonic trunk partially rely on conserved CREs. Nevertheless, a high proportion of these non-coding sequences active in the trunk appear to have functionally diverged between the two species, suggesting that transcriptional robustness is maintained despite a considerable divergence in CREs’ sequence, an observation supported by a genome-wide comparative approach.

overall_design: ChIP-seq analysis of CTCF in mouse and chicken embryonic posterior trunks. ChIP-seq analysis of H3K27ac in mouse and chicken posterior trunk, skin and brain samples.

first: Aurélie

first: Isabel

last: Guerreiro

first: Christopher

last: Bolt

first: Lucille

last: Lopez-Delisle

first: Sandra

last: Gitto

first: Denis

last: Duboule

first: Leonardo

last: Beccari


title: AOM/DSS colorectal cancer mouse transcriptome profile across 5 time point in the progression of colites to tumor [RNA-seq]

summary: Azoxymethane (AOM) and dextran sulfate sodium (DSS) mice, as a classic model for the study of colorectal cancer, can completely simulate the inflammatory cancer transformation in the development of colorectal cancer.Although people have been trying to reveal the key mechanism of colorectal cancer transformation. But the current understanding of it is still not enough. In this study, we injected mice with AOM and then periodically treated them with DSS. The mice were made to develop tumors in the colon finally. In this process, we sampled the intestinal tissues of the mice at different time points, respectively, at the 0th week, 2nd week, 4th week, 7th week and 10th week after AOM injection. to describe the gene exprression profile across all time point, we get the RNA-seq data for all samples.

overall_design: RNA-seq samples of AOM/DSS mouse colon across 5 time point (week-0, week-2, week4, week-7, week-10)

last: wu

first: Zhen-xia

last: Chen

first: Lin

first: Zhi-Hui

last: Luo

first: Chen

last: Zhao

first: Qing-Lan

last: Li

first: Ying-jie

last: Geng

first: Lian-Yun


title: RNA-seq of sorted KPC Sf3b1-K700E murine PDAC cells

status: Public on Jun 07 2022

first: Patrik

last: Simmler

address: Otto-Stern-Weg 7

institute: ETH Zurich

summary: We established a mouse model of KrasG12D, Trp53-/- and Sf3b1-K700E murine pancreatic cancer to elucidate the impact of the SF3B1 mutation found in human PDAC on the KPC mouse model.

overall_design: Cancer cells were isolated using EpCam-based FACS sorting (3 KPC, 4 KPC-SF3B1-K700E). Isolated cells were subjected to RNA-sequencing.


title: AHR ChIP-seq in primary human hepatocytes treated with TCDD

status: Public on Jun 09 2022

city: East Lansing

first: Sudin

last: Bhattacharya

state: MI

address: 775 Woodlot Dr

department: Biomedical Engineering

institute: Michigan State University

summary: ChIP-seq was done on cryopreserved primary human hepatocyte with vehicle control - 0.1% dimethylsulfide (DMSO), or 1nM 2,3,7,8 tetrachlorodibezno-p-dioxin (TCDD) agonist treatment to identify AHR binding regions throughout the genome. We identified 1,984 binding peaks when comparing TCDD vs. vehicle control

overall_design: Primary human hepatocytes were treated with vehicle control (DMOS) or 1 nM TCDD for 24 hours before cells were collected for ChIP-seq. Sequencing was carried out on Illumina HiSeq 2000

first: Edward

last: LeCluyse

first: Melvin

last: Andersen

first: David

last: Filipovic


title: Nicotinamide promotes formation of retinal organoids from human pluripotent stem cells via enhanced neural cell fate commitment

city: Bethesda

first: Zachary

last: Batz

state: MD

address: 6 Center Dr Bldg 6, Rm 303

department: NEI

institute: NIH

summary: Retinal organoids (ROs) derived from human pluripotent stem cells (hPSCs) recapitulate key features of human retinogenesis and thus provide a promising platform to study the mechanisms of retinal development and disease in a human context and to evaluate therapies. Although multiple differentiation protocols are currently in use, hPSCs exhibit tremendous variability in differentiation efficiency, with some cell lines consistently yielding few or even no ROs thus limiting their utility in research. To improve the efficiency and robustness of RO generation, we set out to identify factors  that promote neural retina differentiation from hPSCs. We report here that nicotinamide (NAM) treatment at the early stage of differentiation significantly improved RO yield across 8 hPSC lines from different donors. Importantly, NAM treatment enabled efficient production of ROs from cell lines that would otherwise fail to generate meaningful number of ROs. Further analyses revealed that NAM treatment promotes neural commitment of hPSCs at the expense of non-neural ectodermal cell fate, which in turn increases eye field commitment and RO generation. This effect is mediated, at least in part, through inhibition of BMP signaling. Thus, our modified protocol with a simple NAM treatment improves the yield of ROs in all lines tested, and importantly greatly benefits to cell lines that previously proved to be intractable in retinal differentiation. Our data should facilitate the broader use of human ROs for disease modeling applications requiring the use of multiple cell lines or a larger scale of cell source such as therapy screening.

overall_design: Retinal organoids were generated two human induced pluripotent stem cell lines with and without nicotinamide supplementation. Total RNA was extracted at two time points (D4 and D7) using RNAeasy Plus Mini kit (Qiagen, Germantown, MD). Quality of isolated RNAs was assessed using Bioanalyszer RNA 6000 nano assays and only high-quality RNAs (RIN > 8) were used for construction of mRNA sequencing library. 100ng of total RNA were used to construct the strand-specific libraries using TruSeq RNA Sample Prep Kit-v2 (Illumina, San Diego, CA). Libraries were sequenced on two lanes of an Illumina HiSeq 2500 in paired-end mode (125 bp read length). Reads passing the Illumina chastity filter were demultiplexed then trimmed to remove low quality bases and adapters using Trimmomatic v0.36. Next, reads were aligned to the human transcriptome (GRCH38.p13, Ensembl 98) and quantified to the transcript-level using Kallisto v0.45.0.

first: Florian

last: Regent

first: Ryan

last: Kelley

first: Linn

last: Gieser

first: Anand

last: Swaroop

first: Holly

first: Tiansen


title: Single-cell transcriptomic analysis of craniogenesis in control and SOXC-mutant mice

status: Public on Jun 08 2022

city: Philadelphia

first: Véronique

last: Lefebvre

state: Pennsylvania

address: 3615 Civic Center Boulevard, ARC 912

department: Division of Orthopaedic Surgery

institute: The Children's Hospital of Philadelphia Research Institute

summary: SOXC genes (i.e., Sox4, Sox11 and Sox12) are important members of the SOX transcription factor family. They are involved in several developmental processes, including skeleton formation. However, their role in intramembranous ossification and, particularly, in skull development has not beed investigated yet. Here, we employed single-cell RNA-seq technology to better understand the roles of the SOXC genes in craniogenesis and how their inactivation could affect this process. We identified the expression of the SOXC genes in several cranial populations, including osteodermal and meningeal progenitors. Removal of the SOXC genes in the cranial mesenchyme with a Prx1Cre transgene showed changes in the proportions of progenitor clusters and deriving populations (dermal, hypodermal, periosteal, suture and bone cells). Mutant progenitors showed the downregulation of genes involved in cytoskeleton organization, cell adhesion and migration, cell proliferation and steorl biosynthesis. As a result, SOXC-mutant fetuses have underdeveloped bones, sutures, dermis and hypodermis, particularly in the apical regions.

overall_design:
10X Genomics single-cell RNA-sequencing profiling of cranial tissues from control and SOXC-mutant embryos at different developmental stages (i.e., E11.5, E12.5, 13.5, E15.5 and E17.5). For the E17.5 stage the dermis and hypodermis were removed and only cranial bones were used.

[UPDATE] 12-22-2023: The titles and characteristics of Samples GSM5324644-GSM5324647 were corrected. The associated raw data and processed data did not change.

first: Marco

last: Angelozzi


title: AOM/DSS colorectal cancer mouse epigenetic landscape in the progression of colites to tumor [ChIP-seq]

first: Min

last: Wu

summary: Azoxymethane (AOM) and dextran sulfate sodium (DSS) mice, as a classic model for the study of colorectal cancer, can completely simulate the inflammatory cancer transformation in the development of colorectal cancer.Although people have been trying to reveal the key mechanism of colorectal cancer transformation. But the current understanding of it is still not enough. In this study, we injected mice with AOM and then periodically treated them with DSS. The mice were made to develop tumors in the colon finally. In this process, we sampled the intestinal tissues of the mice at different time points, respectively, at the 0th week, 2nd week, 4th week, 7th week and 10th week after AOM injection. In order to fully describe the epigenetic pattern of colorectal cancer in AOM/DSS mice, especially the dynamic changes in the process of inflammatory cancer transformation. we generated the histone modification profile of 5 markers, including H3K27Ac (active enhancer), H3K4me1 (enhancer), H3K4me3 (promoter), H3K9me3 (heterochromatin) and H3K27me3 (multicomb suppression) across 5 time points (week-0, week-2, week-4, week-7, week-10). Genome-wide epigenetic analysis found that during the tumorigenesis process, enhancer chromatin state region increased. And functionally related to apoptosis and mitochondrial function. When detecting the dynamic changes of the signal intensity of H3K27ac, it was found that the enhanced enhancer signal-related genes were enriched in the inflammatory factor NFKB signaling pathway. It shows that in the process of inflammatory cancer transformation, H3K27ac are involved in inflammation and cell apoptosis, and play an important role in inflammatory cancer transformation.

overall_design: ChIP-seq samples of 5 different marks (H3K27ac, H3K4me1, H3K4me3, H3K27me3, H3K9me3) across 5 time point (week-0, week-2, week4, week-7, week-10)

last: wu

first: Zhen-xia

last: Chen

first: Lin

first: Zhi-Hui

first: Chen

first: Qing-Lan


title: WTAP regulates gene expression by binding to the promoters in primary hepatocytes.

status: Public on Jun 02 2022

city: Harbin

first: Zheng

state: Heilongjiang

address: 92 Xidazhijie  Harbin Institute of Technology

institute: Harbin Institute of Technology

summary: We demostrated that WTAP regulates gene expression by binding to the promoters in hepatocytes.

overall_design: To screen DNA targets of WTAP, primary hepatocytes were isolated and infected with Ad-Flag-WTAP adenovirus overnight. We performed chromatin immunoprecipitation assay using anti-Flag.

first: Xinzhi

last: Li


title: m6ARIP-Seq of liver in Wtapflox/flox and hepatocyte-specific Wtap knockout (HKO) mice

summary:
Purpose: Through mRNA m6A-profiling, we aim to characterize the mRNA m6A changes in the liver obtained from Wtapflox/flox and Wtap-HKO mice.
Methods: Total RNA was extracted using Tripure Isolation Reagent (Roche, Mannheim, Germany) from liver of Wtap flox/flox and Wtap-HKO mice at 8 weeks old. Each sample (300 μg total RNA) was pooled from 5 mice for each group. Two independent biological replicates for each group were used for m6ARIP-seq. Poly(A)+ RNA was purified using Dynabeads™ mRNA Purification Kit (Invitrogen) following the manufacturer’s instructions. Fragmented mRNA was incubated with m6A antibody (Synaptic System, 202003) for immunoprecipitation. Then, immunoprecipitated mRNAs or Input was used for library construction with NEBNext ultra RNA library prepare kit for Illumina (New England Biolabs).The library preparations were sequenced on an Illumina Novaseq 6000 platform with a paired-end read length of 150 bp according to the standard protocols. The m6A peaks were detected by exomePeak R package (version 2.16.0). The motif search was detected by HOMER(version 4.9.1).
Conclusion: The mRNA m6A profiles in the liver of Wtapflox/flox and Wtap-HKO mice were characterized.

overall_design: To map the changes of mRNA m6A modification caused by hepatic deletion of Wtap, MeRIP-seq was performed in liver obtained from Wtapflox/flox and Wtap-HKO mice.


title: Assay for transposase-accessible chromatin-sequencing (ATAC-seq) of liver samples in Wtapflox/flox and hepatocyte-specific Wtap knockout (Wtap-HKO) mice

summary:
Purpose: The goal of this study is to determine whether hepatic deletion of Wtapaffects chromatin accessibility.
Methods: Each liver sample was pooled from three Wtap-HKO and Wtapflox/flox mice, respectively. Three independent biological replicates of each group were used for ATAC-seq. Nuclei was extracted from liver samples, and the nuclei pellet was resuspended in the Tn5 transposase reaction mix. The transposition reaction was incubated at 37°C for 30 min. Equimolar Adapter1 and Adatper 2 were added after transposition, PCR was then performed to amplify the library. After the PCR reaction, libraries were purified with the AMPure beads and library quality was assessed with Qubit. The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumina) according to the manufactuer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina NovaSeq 6000 platform and 150 bp paired-end reads were generated. ATAC-seq analysis was performed using a standard protocol.
Results: The hepatic chromatin accessibility in Wtapflox/flox and Wtap-HKO mice were characterized.

overall_design: To assess chromatin accessibility in the liver casued by hepatic deletion of Wtap, ATAC-seq analysis of liver samples in Wtapflox/flox and hepatocyte-specific Wtap knockout (Wtap-HKO) mice was performed.


title: RNA-seq analysis of mRNA profiles in the livers of Wtapflox/flox and hepatocyte-specific Wtap knockout (HKO) mice

summary:
Purpose: The goal of this study is to compare transcriptome profilings of liver from Wtapflox/flox and hepatocyte-specific Wtap knockout (HKO) mice.
Methods: Total RNA was extracted using Tripure Isolation Reagent (Roche, Mannheim, Germany) from livers of Wtap flox/flox and Wtap-HKO mice at 8 weeks old. mRNA profiles were generated by deep sequencing using an Illumina Novaseq platform. Paired-end clean reads were aligned to the mouse reference genome(Ensemble_GRCm38.p6) with TopHat (version 2.0.12), and the aligned reads were used to quantify mRNA expression by using HTSeq-count (version 0.6.1).
Conclusion: Our study represents the first detailed analysis of hepatic mRNA profiles in Wtapflox/flox and Wtap-HKO mice at 8 weeks old, generated by RNA-seq technology. Our results showed that 3486 genes were downregulated, and 3706 genes were upregulated. Gene ontology (GO) analysis showed that downregulated genes were associated with small molecule catabolic process, fatty acid metabolic process, amino acid metabolic process, steroid metabolic process, cholesterol metabolic process, xenobiotic metabolic process, fatty acid beta-oxidation, alcohol metabolic process, and glucose metabolic process, whereas the upregulated genes were associated with wound healing, leukocyte migration, chemotaxis, and positive regulation of cytokine production.

overall_design: The hepatic mRNA profiles of Wtap-HKO and Wtapflox/flox mice (n=3 for each group) were generated by deep sequencing using Illumina Novaseq platform.


title: Microarray gene expression analysis in 1-month-old mice comparing lens epithelial cells, lens superficial cortical cells, and lens deep cortical cells

status: Public on Jun 03 2022

city: Newark

first: Melinda

last: Duncan

state: DE

address: 105 The Green

department: Biological Sciences

institute: University of Delaware

summary: Microarray analysis comparing the gene expression of three tissues laser-microdissected from 1-month-old lenses in mice. The original study aimed to discover additional genes that belong to a distinct subset caled late fiber genes which are expressed in cells bordering the organelle-free-zone (OFZ) of the lens.

overall_design: Cells were harvested from three layers of the lens by laser-microdissection. RNA was isolated from each layer in order to conduct microarray analysis.

first: Alicia

last: De Maria

first: Steven

last: Bassnett

first: Anthony

middle: J

last: Pompetti


title: mRNA expression data from human umbilical vein endothelial cells treated with PRELP conditioned media

status: Public on Jun 01 2022

city: London

first: Alex

last: Leung

state: London

address: 11-43 Bath Street

institute: UCL Institute Of Ophthalmology

summary: PRELP conditioned media was generated by induction of PRELP-tet-inducible system in HEK293T cells over 48 h. Conditioned media was applied to HUVECs for 24 h before RNA was extracted and expression profile analysis performed

overall_design: Comparison of human umbilical vein endothelial cells treated with control and PRELP 293T conditioned media for 24 hours in replicates of five

first: Hongorzul

last: Davaapil

first: Ken

last: Asada

first: Nadia

last: Bonnin

first: Vasiliki

last: Papadaki

first: Jack

last: Hopkins

first: Hirofumi

last: Kosuge

first: Takumi

last: Tashima

first: Makoto

last: Nakakido

first: Ryohei

last: Sekido

first: Kohei

last: Tsumoto

first: Ryuji

last: Hamamoto

first: Mandeep

last: Sagoo

first: Shin-Ichi

last: Ohnuma


title: HUVEC treated with PRELP conditioned media; meninges of PRELP knockout mouse

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

overall_design: Refer to individual Series


title: mRNA expression profiling analysis obtained from meninges of PRELP knockout mouse

summary: PRELP knockout animals constructed on C57BL/6 mouse strain and meninges RNA extracted from 22-25 week-old mice for expression profiling analysis

overall_design: Comparison of meninges mRNA expression profile between control and PRELP knockout mice


title: Characterizing the Tumor Immune Microenvironment of Syngeneic Mouse Models of Ovarian Cancer to Predict Response to PD-L1 blockade

city: Ottawa

first: David

last: Cook

state: ON

address: 501 Smyth Rd

department: Cancer Therapeutics Program

country: Canada

institute: Ottawa Hospital Research Institute

summary: Epithelial ovarian cancer (EOC) is the most lethal gynecologic cancer with an imperative need for new treatments. Immunotherapy has had marked success in some cancer types; however, clinical trials studying the efficacy of immune checkpoint inhibitors for the treatment of EOC provided benefit in <15% of patients. EOC is a particularly complex cancer since it develops from various tissues in the reproductive tract and metastasizes into the peritoneal cavity where it is able to colonize almost all organs, creating different tumor microenvironments (TME) containing a variety of immune profiles. In this study, we assessed the immune composition of different murine syngeneic models of EOC from different cellular origins (ovarian and fallopian tube epithelium) and harboring known mutations relevant to human disease, including TP53 mutation, PTEN suppression, and constitutive KRAS activation. We determined immunogenicity of multiple tumor models in vivo, the T and myeloid profile of orthotopic tumors and the immune composition of ascites, by flow cytometry, IHC and single cell RNA-sequencing. Our findings allowed us to predict which models might respond best to PD-L1 blockage, according to key characteristics such as tumor immunogenicity, MHC status, and T cell infiltration. Together these data highlight the heterogeneity found in murine EOC, as in human disease, identified features that might predict immune checkpoint inhibitor efficacy, and revealed crucial information about differences between murine models in the TME composition vs. ascites fluid. These data provide a solid foundation for selecting models in future testing of immunotherapies according to the immune composition and tumor characteristics.

overall_design: scRNA-seq profiles of primary orthotopic STOSE and ID8 mouse tumors

first: Galaxia

last: Rodriguez

first: Kristianne

last: Galpin

middle: P

first: Barbara

last: Vanderhyden


title: Lactate  receptor GPR81 drives breast cancer growth and invasiveness through regulation of ECM properties and Notch ligand DLL4

status: Public on May 23 2022

city: Copenhagen

first: Jiayi

last: Yao

state: Copenhangen

address: Ole Maaløes Vej 5

country: Denmark

institute: University of Copenhagen

summary: The lactate receptor GPR81 contributes to cancer development, yet the mechanisms remain unclear. Here, we show that GPR81 is upregulated in human cancers and further upregulated by extracellular lactate and three-dimensional growth of breast cancer spheroids. GPR81 knockdown (KD) increased spheroid necrosis and reduced invasion and in vivo tumor growth. GPR81 KD altered GO terms relating to extracellular matrix (ECM) and cell adhesion, including upregulation of Protocadherin-7 (PCDH7), which exhibited a striking, clustered expression in spheroids. Single cell analysis revealed that PCDH7 was inversely related with Ki-67 and co-clustered with other GPR81 KD-upregulated genes including Ephrin-type-A receptor-7 (EPHA7). The matricellular protein SPARC and the Notch ligand Delta-like-4 (DLL4), were downregulated upon GPR81 KD, and their KD elicited spheroid necrosis (DLL4) and inhibited invasion. We conclude that GPR81 supports breast cancer aggressiveness at least in part via SPARC and DLL4. Our findings substantiate GPR81 as a promising target in breast cancer treatment.

overall_design: MCF-7 cells stably expressing the empty pLKO.1 vector or GPR81 shRNA in pLKO.1, respectively, were grown in DMEM with either 5 mM glucose or 20 mM lactate for 72 h before being subjected to RNA sequencing (BGI).

first: Kathrine

last: Lundoe

first: Oksana

last: Dmytriyeva

first: Louise

last: Spoehr

first: Eliana

middle: G

last: Alves

first: Laia

last: Blasco

first: Mette

last: Traulsen

first: Muthulakshmi

last: Ponniah

first: Marc

last: Severin

first: Albin

last: Sandelin

first: Marie

last: Kveiborg

first: Thue

last: Schwartz

first: Stine

middle: F

last: Pedersen


title: Candida albicans exhibits distinct cytoprotective responses to anti-fungal drugs

status: Public on May 29 2022

first: Michael

last: Hallett

state: Ontario

address: 1151 Richmond St

department: Biochemistry

institute: Western University

summary: We transcriptionally profiled thousands of C. albicans untreated and drug-treated cells at early and late timepoints by modifieying a single cell platform for fungal setting. Our DROP-seq set up was able to capture transcriptional signals in ~20K C. albicans . We were able to show cell-cell heterogeneity in seemingly isogenic populations of C. albicans untreated cells that coupled with cell cycle checkpoints. We also observed that individuals treating with different anti-fungals were partitioned into 20  subpopulations. The data shows a bifurcation into two major responses, term 𝛂 and 𝛃 responses, two days post-treatment. A transition from 𝛂 response  to 𝛃 response was observed at day 3 which stay consistent to day 6. Bulk DNA sequencing does not show genomic abberation to be related to either 𝛂 or 𝛃 responses and the resistance does not change from day two to day six in diffusion disk assay. This can be an evidence of selection for cells that are able to mount an efficient tolerance response to anti-fungals early post treatment.Targeting 𝛃 cells, or genes and pathways that support the 𝛂 to 𝛃 transition are interesting avenues to block drug tolerance.

overall_design: Transcription profiling of C.albicans before and after drug treatment with single cell approches.

first: Vanessa

last: Dumeaux

first: Samira

last: Massahi


title: AMPK activator-treated human cardiac spheres have enhanced maturation and enable pathological modeling

status: Public on May 27 2022

city: ATLANTA

first: Dong

last: Li

state: GEORGIA

address: 2015 UPPERGATE DR

department: Pediatrics

institute: Emory University

summary:
To investigate the functions of AMPK activation on maturation of hiPSC derived cardiomyocytes, we treated 3D hiPSC derived cardiomyocytes with AMPK activator EX229 at 10 µM for 7 days.
Transcriptomic analyse was performed to identify molecular actions of AMPK activation.

overall_design: RNA-sequencing analysis was performed to compare global gene expression profiles of hiPSC derived cardiomyocytes treated with AMPK activator EX229 at 10 µM (E10)  vs. DMSO treatment (DMSO) vs. left ventricle tissue samples (LV).

first: Lawrence

last: Armand

first: Hyun

last: Hwang

first: Chunhui

last: Xu