title: Transcriptomic profiling of mouse neural stem cells after hypoxia/reoxygenation

city: Shenyang

first: Bo

last: Fang

state: Liaoning

address: NO.155, North Nanjing Street

department: Department of Anesthesiology

institute: The First Hospital of China Medical University

summary: Ischemia-reperfusion injury to the central nervous system (CNS) often causes severe complications. Hypoxia/reoxygenation (H/R) is one of the most common and detrimental internal environmental changes experienced by local cells and is often used to simulate the process of ischemia-reperfusion in vitro. The activation of endogenous neural stem cells (NSCs) is considered a promising therapeutic strategy for nerve repair after injury. However, the specific biological processes and molecular mechanisms of NSC activation remain unclear.

overall_design: RNA-seq was performed on NSCs of control group (n=3) and H/R group (n=3) respectively.

first: Shaoqiong

last: Zhang

first: Yuanyuan

first: Yiting

last: Fan

first: Kaile

last: Cui


title: Expression data from Trigonelline-treated SAMP8 mice Hippocampus

status: Public on Mar 31 2023

city: Tsukuba

first: Farhana

last: Ferdousi

state: Ibaraki

address: Tennodai 1-1-1

country: Japan

institute: University of Tsukuba

summary:
Gene expression profiling reveals neuroprotective and antiinflammatory effects of TG in SAMP8 (aging model ) mice Hippocampus thus helps in acelerating learning and memory restoration process.
by suppressing proinflammatory cytokine related genes and thus accekerate neurotransmitter release in SAMP8 aging model mice hippocampus

overall_design: RNA was extracted using Isogen (Nippon Gene Co. Ltd., Toyama, Japan). The integrity of RNA was quantified using NanoDrop 2000 spectrophotometer (Thermo Scientific, Wilmington, DE, USA). Clariom S assay system (Thermo Fisher, Japan) was used on duplicate RNA samples of each group. In accordance with the user manual, complementary DNA (cDNA) for microarray was generated using the GeneChip WT Plus Reagent kit (Thermo Fisher Science, Japan). Samples were hybridized using Clariom S GeneChip microarray kit (Thermo Fisher Science, Japan). After washing and staining, images were captured, and then CEL data were generated using the GeneChip Scanner 3000 (Thermo Fisher Science, Japan). The raw CEL data were normalized using the transcriptome analysis console (TAC) software ver.4.0.1 following the SST-robust multichip average (SST-RMA) algorithm (Thermo Fisher Scientific, Japan).

first: Aktar

last: Sharmin


title: Nasopharyngeal lymphatic plexus serves as a central hub for drainage of cerebrospinal fluid [Adult]

status: Public on Apr 01 2023

city: Daejeon

first: Myung Jin

last: Yang

country: South Korea

institute: Institute for Basic Science

type: Expression profiling by high throughput sequencing

summary: To investigate the heterogeneity of murine nasopharyngeal LECs, CD31+ PDPN+ LECs from the adult mouse nasopharynx were FACS sorted and single-cell RNA seq was performed

overall_design: NasoPharyngeal LECs (CD31+ PDPN+) were FACS sorted and single-cell libraries were made

first: Gou

middle: Y

last: Koh

first: Myung

middle: J


title: Epigenetic and metabolic reprogramming by HDAC inhibition targets NRF2-active tumors [CUT&Tag]

status: Public on Mar 30 2023

city: New York

first: Dimitris

last: Karagiannis

state: NY

country: USA

institute: Columbia University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: To investigate the NRF2-specific cytotoxic effects of HDAC inhibition, we assessed genomic distribution of histone acetylation modifications and readers in the context of control and NRF2-overexpressing mouse LUAD cells upon HDAC inhibition.

overall_design: CUT&Tag of H3K27ac, H4ac (H4K5ac, H4K8ac, H4K12ac, H4K16ac) and BRD4 in KP1 EV and NRF2 cells treated with DMSO or Romidepsin.

first: Chao

last: Lu


title: Epigenetic and metabolic reprogramming by HDAC inhibition targets NRF2-active tumors [RNA-Seq]

summary: To investigate the NRF2-specific cytotoxic effects of HDAC inhibition, we assessed gene expression in the context of control and NRF2-overexpressing mouse LUAD cells upon HDAC inhibition.

overall_design: Comparative gene expression profiling analysis of RNA-seq data of KP1 EV and NRF2 cells treated with DMSO or Romidepsin. 3 biological replicates per condition are included


title: Epigenetic and metabolic reprogramming by HDAC inhibition targets NRF2-active tumors

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

overall_design: Refer to individual Series


title: Epigenetic and metabolic reprogramming by HDAC inhibition targets NRF2-active tumors [CRISPR Screen]

summary: To identify NRF2-specific dependencies in chromatin regulation, we performed a focused genetic screen mouse LUAD cell lines with or without knock-out of KEAP1.

overall_design: A chromatin-focused CRISPR/Cas9 dropout screen was performed in 2 KP and 2 KPK cell lines and sgRNA enrichment was assessed by deep-sequencing at 0(t0) and 14(t1) population doublings.

first: Warren

last: Wu

first: Francisco

last: Sánchez-Rivera

first: Yadira

middle: M

last: Soto-Feliciano

first: Thales

last: Papagiannakopoulos


title: Unraveling the role of human TSC-specific TFs

status: Public on Mar 22 2023

city: Austin

first: Bum-Kyu

last: Lee

state: TX

address: 2506 Speedway Stop A5000

institute: University of Texas at Austin


title: Unraveling the role of human TSC-specific TFs [RNA-Seq]

summary: Orchestrated actions of tissue-specific enhancers and transcription factors (TFs) govern the development of the placenta which is an essential organ to support the growth of the fetus during pregnancy. However, human trophoblast stem cells (TSCs)-specific enhancers, TFs, and the mechanisms by which TFs modulate placental development are poorly understood. Here we investigated enhancers, super-enhancers (SE), SE-associated genes in human TSC using RNA-seq and ChIP-seq to interrogate the roles of SE-TFs in human TSCs.

overall_design: We investigated the roles of various TSC-specific TFs (FOS, GATA2, MAFK, TEAD4, and TFAP2C) in human trophoblast stem (TS) cells by depleting the TFs using shRNAs. Total RNAs were extracted from the TS cells upon knockdown (KD) of the TFs, and we performed RNA-seq and investigate global gene expression changes upon KD of the TFs.


title: Expression data from colorectal cancer and adjacent normal tissues of human

status: Public on Mar 21 2023

city: Zunyi

first: Handong

last: Huang

state: 贵州

address: 149 Dalian Road

country: China

institute: Affiliated Hospital of Zunyi Medical University

summary:
Dysregulation of RNAs expression is commonly found in cancer and considered  to be involved in tumor pathogenesis.
We used microarrays to detail the global programme of RNA expression in colorectal cancer.

overall_design: Three paired CRC tissues and adjacent normal tissues were collected for RNA extraction and hybridization on Affymetrix microarrays. The global profiling of human RNAs was screened with Clariom D human arrays.

first: Kunming

last: Wen


title: Transcriptional analysis of co-occuring ATRX deficiency and IDH1 mutation in a CT2A glioma model

status: Public on Mar 29 2023

city: Durham

first: David

last: Ashley

state: NC

address: 203 Research Dr, MSRB1

department: Neurosurgery

institute: Duke University

summary: Stimulating the innate immune system has been explored as a therapeutic option for the treatment of gliomas. Inactivating mutations in ATRX, a defining molecular alteration in IDH-mutant astrocytomas, have been implicated in dysfunctional immune signaling. However, little is known about the interplay between ATRX loss and IDH mutation on innate immunity. To explore this biology, we generated ATRX knockout glioma models in the presence and absence of the IDH1R132H mutation. ATRX-deficient glioma cells were sensitive to dsRNA-based innate immune agonism and exhibited impaired lethality and increased T-cell infiltration in vivo. However, the presence of IDH1R132H dampened baseline expression of key innate immune genes and cytokines in a manner restored by genetic and pharmacological IDH1R132H inhibition. IDH1R132H co-expression did not interfere with the ATRX KO-mediated sensitivity to dsRNA. Thus, ATRX loss primes cells for recognition of dsRNA, while IDH1R132H reversibly masks this priming. This work reveals innate immunity as a therapeutic vulnerability of astrocytoma.

overall_design: RNAseq analysis of ATRX-intact or ATRX-deficient CT2A cells with or without IDH1-R132H.

first: Seethalakshmi

last: Hariharan

first: Michelle

middle: L

last: Bowie

first: Kevin

last: Stevenson


title: Comprehensive analysis of the transcriptome-wide m6A methylation in mouse neural stem cells after hypoxia/reoxygenation

first: Bo

last: Fang

summary: Ischemia-reperfusion injury to the central nervous system (CNS) often causes severe complications. Hypoxia/reoxygenation (H/R) is one of the most common and detrimental internal environmental changes experienced by local cells and is often used to simulate the process of ischemia-reperfusion in vitro. The activation of endogenous neural stem cells (NSCs) is considered a promising therapeutic strategy for nerve repair after injury. However, the specific biological processes and molecular mechanisms of NSC activation remain unclear, and the role of N6-methyladenosine (m6A) methylation modification in this process has not been explored.

overall_design: MeRIP-seq was performed on NSCs of control group (n=3) and H/R group (n=3) respectively.

first: Shaoqiong

last: Zhang

first: Yuanyuan

last: Li

first: Yiting

last: Fan

first: Kaile

last: Cui


title: HLA association with active TB

city: La Jolla

first: Cecilia

middle: Sofie

last: Lindestam

state: CA

address: 9420 Athena Circle

department: Sette

institute: La Jolla Institute for Immunology

summary: Several HLA allelic variants have been associated with protection from, or susceptibility to infectious and autoimmune diseases. Here, we examined whether specific HLA alleles would be associated with different Mtb infection outcomes. We found that DQA1*03:01, DPB1*04:02, and DRB4*01:01 were signficantly more frequent in inividuals with active TB (susceptibility alleles). Furthermore, individuals who express any of the three susceptibility alleles were associated with lower magnitude of responses against Mtb antigens. We investigated the gene expression changes induced in PBMCs by Mtb lysate and a peptide pool (MTB300) in individuals with or without expression of the susceptibility alleles.

overall_design: RNAseq of sorted PBMC from cryopreserved PBMC of IGRA+ individuals with or without the susceptibility alleles.

last: Lindestam Arlehamn

first: Leila

last: Chihab


title: Expression data from mRNAs co-precipitated with QKI in SW480 cells

summary:
In CRC cells, lncRNA NONHSAT136151 can bind to protein QKI but does not affect the expression of QKI. The binding of NONHSAT136151 may change the interactino of QKI with its target genes.
We used microarrays to detail the abundance of mRNAs enriched by QKI in NONHSAT136151 silenced group and control group in CRC cells.

overall_design: SW480 cells treated with siLnc (siNONHSAT136151) and siNC (Negative control) were lysed with RIP lysis buffer. Anti-QKI antibody or IgG from rabbit serum were pre-bound to Protein A Magnetic Beads and then incubated with cell lysate at 4°C overnight with rotation. The magnetic bead-antibody-QKI complex was washed and resuspended with RIP wash buffer. RNA was recovered using TRI Reagent and dissolved in RNAse-free water. Subsequently, PrimeViewTM Human Gene Expression Array (Affymetrix Inc.) was utilized to analyze the RNA samples.


title: Unraveling the role of human TSC-specific TFs [ChIP-Seq]

overall_design: ChIP-seq were performed for 6 transcription factors (EP300, FOS, GATA2, MAFK, TEAD4, and TFAP2C) in human trophoblast stem (TS) cells. Input was sequenced for a control.


title: UMSBP2 is chromatin remodeler that functions in regulation of gene expression and suppression of antigenic variation in trypanosomes

city: Jerusalem

first: Inbar

last: Plaschkes

address: The Hebrew University of Jerusalem - Ein Kerem

department: The Faculty of Medicine - Ein Kerem

country: Israel

institute: HUJI


title: Defining CD8+ T cells that provide the proliferative burst after PD-1 therapy

status: Public on Mar 18 2023

city: Suwon-si

first: Se Jin

last: Im

state: Gyeonggi-do

address: 2066, Seobu-ro, Jangan-gu

department: Department of Immunology

institute: Sungkyunkwan University School of Medicine

summary: Chronic viral infections are characterized by a state of CD8 T cell dysfunction termed exhaustion. A better understanding of the mechanisms that regulate CD8 T cell responses during chronic infection is required to improve immunotherapies that restore function in exhausted CD8 T cells. Here we identify a novel population of virus-specific CD8 T cells with a T follicular helper (Tfh)-like signature in mice chronically infected with lymphocytic choriomeningitis virus (LCMV). These Tfh-like CD8 T cells expressed the programmed cell death-1 (PD-1) inhibitory receptor but at the same time also expressed co-stimulatory molecules and had a gene signature that was related to CD8 T cell memory precursor cells and hematopoietic stem cells (HSC). These Tfh-like CD8 T cells acted as stem cells during chronic infection undergoing self-renewal and also differentiating into the terminally exhausted CD8 T cells that were present in both lymphoid and non-lymphoid tissues. The Tfh-like CD8 T cells were found only in lymphoid tissues and resided predominantly in the T cell zones along with naïve CD8 T cells. Interestingly, the proliferative burst after PD-1 blockade came almost exclusively from this Tfh-like CD8 T cell subset. Importantly, the transcription factor TCF1 played a cell intrinsic and essential role in the generation of Tfh-like CD8 T cells. Taken together, our study identifies Tfh-like CD8 T cells as the critical subset for maintaining the pool of virus-specific CD8 T cells during chronic infection and as the cells that proliferate after PD-1 blockade. These findings provide a better understanding of T cell exhaustion and have implications towards optimizing PD-1 directed immunotherapy.

overall_design: 12 samples isolated from CD8 T-cells in naïve mice (5 naive) and B16F10-GP bearing mice (3 PD-1+ Tim-3-, 4 PD-1+ Tim-3+) cells were analyzed

first: SeJin

first: Rafi

last: Ahmed


title: Gene expression profile at single cell level of bone marrow cells in 5TGM1 multiple myeloma mouse model treated with CD24 CAR-T cells

status: Public on Mar 13 2023

city: Little Rock

first: Fumou

last: Sun

state: Arkansas

address: 4301 W. Markham, Slot 508

department: Internal Medicine

institute: University of Arkansas for Medical Sciences

summary: Durable remissions following anti-B cell maturation antigen (BCMA)-specific chimeric antigen receptor (CAR) T-cell treatment of multiple myeloma (MM) are rare. Relapses occur when a small subset of MM tumor-initiating cells (TICs) survive treatment. MM cells expressing CD24 exhibit features of TICs. We developed CD24-CAR-T cells and tested their ability to eliminate MM TICs in vitro and in vivo.

overall_design: We analyzed the immune cell changes in the BM microenvironment of the 5TGM1 mouse model treated with CD24 CAR-T cells using single-cell RNA sequencing (scRNA-seq).

first: Fenghuang

last: Zhan


title: The wheat C2H2 zinc finger protein TaZFP13D modulates the expression of chloroplast-related genes, improves growth and drought stress tolerance.

status: Public on Mar 08 2023

city: Montreal

first: William

last: BOUARD

state: QC

address: 141 Av. du Président-Kennedy

department: sciences biologiques

country: Canada

institute: UQAM

summary: Background  Maintaining global food security in the context of climate changes is an important challenge in the next century. Improving abiotic stress tolerance of major crops, like wheat, can contribute to this goal. Therefore, new genes improving tolerance to abiotic stresses, like drought, are needed to support breeding programs aimed at producing more adapted cultivars. Recently, we screened five wheat Zinc Finger Proteins (TaZFPs) and identified TaZFP13D as a new gene improving water-stress tolerance. However, a more detailed characterization of this gene is required to better evaluate its potential in drought tolerance and to decipher the underlying molecular basis.    Results  We used the Barley Stripe Mosaic Virus to up- or down-regulate TaZFP13D expression in wheat. Overexpression of TaZFP13D under well-watered conditions enhances growth as indicated by improved biomass. Exposing plants to a severe drought stress revealed that TaZFP13D strongly increases survival rate and stress recovery. In addition, TaZFP13D reduces drought-induced oxidative damages, at least in part by improving key antioxidant enzymes activity. Conversely, down-regulation of TaZFP13D decreases drought tolerance and protection against drought-induced oxidative damages. RNA-seq-based transcriptome analysis showed that many genes regulated by TaZFP13D were previously shown to improve drought tolerance, while many others are related to the photosynthetic electron transfer chain and are proposed to improve photosynthesis efficiency and chloroplast protection against ROS damages.    Conclusion  This study highlights the important role of TaZFP13D in wheat drought tolerance, contributes to unravel the complex regulation governed by TaZFPs, and provides a useful marker to select more drought tolerant wheat cultivars.

overall_design: Examination of wheat second leaf transcript profiles modification in 4 wheat plant types under well watered condition and drought condition.

last: Bouard

first: Mario

last: Houde


title: Revisiting chromatin packaging in mouse sperm

status: Public on Mar 10 2023

city: Boston

first: Qiangzong

last: Yin

state: MA

address: 3 Blackfan St, CLS building 440A

department: Medicine

institute: BIDMC/Harvard Medical School

type: Methylation profiling by high throughput sequencing


title: E14 cells knockdown with siRNA or shRNA

city: Singapore

first: Yingying

last: Zeng

state: --- Select a state ---

address: 61 Biopolis Drive

country: Singapore

institute: Institute of Molecular and Cell Biology


title: Revisiting chromatin packaging in mouse sperm [ATAC-Seq]

summary: Mammalian sperm exhibit an unusual and heavily-compacted genomic packaging state. In addition to its role in organizing the compact and hydrodynamic sperm head, it has been proposed that sperm chromatin architecture helps to program gene expression in the early embryo. Scores of genome-wide surveys in sperm have reported patterns of chromatin accessibility, histone localization, histone modification, and chromosome folding. Here, we revisit these studies in light of recent reports that sperm obtained from the mouse epididymis are contaminated with low levels of cell-free chromatin. In the absence of proper sperm lysis we readily recapitulate multiple prominent genome-wide surveys of sperm chromatin, suggesting that these profiles primarily reflect contaminating cell-free chromatin. Removal of cell-free DNA, along with appropriate lysis conditions, are required to reveal a sperm chromatin state distinct from any yet reported. Using ATAC-Seq to explore relatively accessible genomic loci, we identify a landscape of open loci associated with genes expressed during late spermiogenesis. Histone modification and chromosome folding studies also strongly support the hypothesis that prior studies suffer from contamination, but technical challenges associated with reliably preserving the architecture of the compacted sperm head prevent us from confidently assaying true localization patterns for these epigenetic marks. Together, our studies strongly argue that our knowledge of mammalian chromosome packaging remains largely incomplete, and motivate future efforts to more accurately characterize genome organization in mature sperm.

overall_design: Open chromatin profiling in mouse sperm samples that are pre-treated with Dnase or DTT using ATAC-Seq

first: Chih-Hsiang

last: Yang

first: Olga

middle: S

last: Strelkova

first: Yu

first: Sneha

last: Gopalan

first: Liyan

first: Job

last: Dekker

first: Thomas

middle: G

last: Fazzio

first: Xin

middle: Z

first: Johan

last: Gibcus

first: Oliver

last: Rando


title: Transcriptional profiling of diffuse large B-cell lymphoma mouse models

status: Public on Mar 06 2023

city: Pamplona

first: SERGIO

last: ROA

address: Irunlarrea, 1

department: Biochemistry and Genetics

country: Spain

institute: University of Navarra


title: Transcriptional profiling of murine normal germinal center B cells (YFPstopF/+; Cg1Cre/+)

summary: Germinal center (GC) B cells have been presented as the cell-of-origin of diffuse large B-cell lymphoma (DLBCL), and these cells can be functionally targeted with the use of Cgamma1-cre mice (Cg1cre) in wich the expression of Cre recombinase is induced by transcription of the Ig gamma1 constant region gene segment. Here, we aimed to develop and characterize novel immunocompetent multi-lesion mouse models of DLBCL that, by triggering genetic alterations specifically in GC B cells, recapitulate relatively fast the molecular, cellular and tumor microenvironment of aggressive human DLBCL.

overall_design: RNAseq profiling of FACS-sorted reporter positive splenic B cells from DLBCL murine models (B220+GFP+ lymphoma cells) were compared to normal controls (B220+YFP+ GC B cells) during secondary immune response to sheep-red blood cells (SRBC) immunization (i.e. 10 days after second intraperitoneal immunization with SRBC, following a first immunization 20 days before).

first: Sergio

last: Roa

first: Javier

last: Melchor

first: Marcos

last: Lacarte

first: Sara

middle: C

last: Grijalba


title: Transcriptional profiling of DLBCL-like murine pBIC tumors (p53F/F; Blimp1F/F; IKK2castopF/stopF; Cg1Cre/+)


title: Transcription factor interactions explain the context-dependent activity of CRX binding sites

status: Public on Mar 05 2023

city: Saint Louis

first: Michael

middle: Aaron

last: White

state: MO

address: 660 South Euclid Ave

department: Genetics

institute: Washington University in St. Louis School of Medicine

summary: We assessed how the effects of transcription factor binding sites (TFBSs) on the activity of a cis-regulatory sequence (CRS) depend on the local sequence context. We constructed a library of synthetic CRSs composed of TFBSs enriched in mouse photoreceptors and assayed them by massively parallel reporter assay in live mouse retina. We used the resulting data to train neural network-based models that predict CRS activity from sequence.

sample_organism:
Mus musculus
synthetic construct

platform_organism:
Mus musculus
synthetic construct

overall_design: A library of 6600 barcoded reporter gene plasmids were transfected into mouse retinas. Three replicates were performed. We measured barcoded reporter gene activity by RNA-seq, normalized by the DNA-seq reads of the input plasmid pool.

middle: A

first: Kaiser

last: Loell

first: Ryan

last: Friedman


title: Transcriptional characterization of iPSC-derived microglia as a model for therapeutic development in neurodegeneration

status: Public on Feb 28 2023

city: Cambridge

first: Gokul

last: Ramaswami

address: One Kendall Square, 1400 West, 3rd Floor

institute: CAMP4 Therapeutics


title: Gene expression profile in odontoblasts' exosomes was analyzed using a microarray (micro-RNA)

status: Public on Feb 14 2023

city: Guangzhou

first: Xinghong

last: Luo

address: No 366 Jiangnan Avenue South

department: Department of Endodontics

institute: Stomatological Hospital, School of Stomatology, Southern Medical University

type: Non-coding RNA profiling by high throughput sequencing

summary:
To determine whether mTORC1 activity regulates the content of exosomes derived from odontoblasts.
we performed miRNA sequencing on exosomes derived from MDPC23 cells that were treated with shTSC1, rapamycin, or vehicle

overall_design: To identify genes expressed in exosomes, comprehensive gene expression analysis was performed using exosomes from MDPC23 cells, mTORC1-activated MDPC23 cells, and mTORC1-inactivated MDPC23 cells

first: Dandan

last: Ma


title: Transcriptional characterization of iPSC-derived microglia as a model for therapeutic development in neurodegeneration [scRNA-seq]

summary: Microglia are the resident immune cells in the brain that play a key role in driving neuroinflammation. In this study, we performed transcriptional characterization of commercially available human iPSC-derived microglia-like (iMGL) cells by bulk and single cell RNA sequencing.

overall_design: Cells were grown for 4 days in culture. We performed treatment of cells with 2 LXR agonists. Gene expression was profiled using single cell RNA sequencing.

first: Ramaswami

last: Gokul


title: Transcriptional characterization of iPSC-derived microglia as a model for therapeutic development in neurodegeneration [Bulk RNA-seq]

overall_design: Cells were grown for 4 days in culture. We performed treatment of cells with 2 LXR agonists. Gene expression was profiled using bulk RNA sequencing.


title: Gene expression of dissected portions of the chicken embryo gastrula after homochronic and heterochronic grafts of somite progenitors

status: Public on Feb 05 2023

first: Ben

middle: John

last: Steventon

state: Cambridgeshire

address: Downing Street

country: United Kingdom

institute: University of Cambridge

summary: Heterochronic grafts (between different embryonic stages) have been described as having more posterior axis contributions than homochronic (stage-matched) ones. Here, we performed homochronic (HH4 to HH4) and heterochronic (HH8 to HH4) grafts from GFP expressing transgenic donor embryos to wild-type Bovans brown embryos and carried out single cell RNA-sequencing to understand the transcriptomic cell states occupied by homochronic and heterochronic grafts early after grafting.

overall_design: HH8 to HH4 (HH8-HH4) and HH4 to HH4 (HH4-HH4) grafts were performed with GFP donor tissue and wild-type host tissue. Embryos were either dissected 0 hours (30 minutes) or 3 hours after grafting under a fluorescent dissecting scope and the region of the embryo approximately encompassing grafted cells was taken. Approximately 5-10 grafts were pooled per sample and dissociated. The samples included here are HH4-HH4 0 hours, HH4-HH4 3 hours, HH8-HH4 0 hours and HH8-HH4 3 hours. There is an additional replicate of HH4-HH4 0 hours that was collected separately.

first: Lara

last: Busby

first: Benjamin


title: Effect of microtopography-induced nuclear constriction on gene expression in mesenchymal stromal cells in growth and osteogenic differentiation conditions I

status: Public on Feb 04 2023

city: Chicago

first: Priyam

last: Patel

state: IL

address: 750 North Lake Shore Drive, Rubloff 11-146

department: Quantitative Data Science Core

institute: Northwestern University

summary: To investigate the influence of microtopography-induced constriction of cell nuclei on gene expression in human mesenchymal stromal cells (hMSCs)

overall_design: We then performed differential gene expression analysis using data obtained from RNA-seq data for hMSCs cultured on flat and micropillar surfaces.

first: Vadim

last: Backman

first: Vasundhara

last: Agrawal


title: Effect of microtopography-induced nuclear constriction on chromatin accessibility in mesenchymal stromal cells in growth and osteogenic differentiation conditions.

summary: To investigate the influence of microtopography-induced constriction of cell nuclei on chromatin accessibility and gene expression in human mesenchymal stromal cells (hMSCs)

overall_design: We then performed differential gene expression analysis using RNA-seq data & ATAC-Seq datasets for hMSCs cultured on flat and micropillar surfaces.

first: Lucas

last: Carter


title: Stomach-derived human insulin-secreting organoids ameliorate diabetes

status: Public on Jan 10 2023

city: New

first: Sean

last: Houghton

address: 1300 York Ave

institute: Weill Cornell Medicine

summary: Adult stem cells represent an invaluable resource that can be harnessed for therapeutic tissue repair. Gut stem cells are accessible by biopsy and grow indefinitely in culture as organoids or cell lines. Human fetal gut can generate rare insulin-secreting cells. However, the short lifespan of gut cells, amounting to only days in situ, calls into question the feasibility of producing stable and durable gut insulin-secreting cells as a potential engraftable therapeutic. Here, we show that cultured human stomach stem cells can be directed to generate pancreatic islet-like organoids containing long-lived gastric insulin-secreting (GINS) cells that resemble pancreatic b-cells in molecular hallmarks and function. After sequential activation of the inducing factors NGN3 and PDX1-MAFA, gastric stem cells passed through a SOX4High endocrine and a GalaninHigh precursor state before adopting the b-cell fate, at efficiencies exceeding 80%. GINS cells acquired glucose-stimulated insulin secretion 10 days post differentiation and restored glucose homeostasis for over 100 days in diabetic mice after transplantation. This study establishes a promising approach to procuring autologous human insulin producers for diabetes treatment, and further expands the already considerable therapeutic opportunities for gut stem cells.

overall_design:
Single-cell RNA-seq on (1) human gastric stem cells derived from corpus stomach, (2) endocrine progenitors, (3) GINS precursors, (4) corpus GINS organoids, (5) antral  GINS organoids, and (6) corpus GINS cells after transplantation.

Please note that the mixed sample represents:
Human gastric stem cells (hGSCs) derived from corpus stomach
Endocrine progenitors differentiated from corpus hGSCs
GINS precursors differentiated from corpus hGSCs
GINS organoids differentiated from corpus hGSCs

To demultiplex, the CMO IDs for the 10x multiplex are:
Sample1 = CMO01
Sample2 = CMO02
Sample3 = CMO03
Sample4 = CMO04

first: Xiaofeng

last: Huang

first: Wei

last: Gu

first: Jiaoyue

last: Zhang

first: Ying

last: Lan

first: Jonathan

last: Colarusso

first: Qiao

last: Zhou


title: A single-cell time-lapse of mouse prenatal development from gastrula to birth

status: Public on Apr 07 2023

city: Seattle

first: Chengxiang

last: Qiu

state: WA

address: William H. Foege Hall, 3720 15th Ave NE

department: Genome Sciences

institute: University of Washington

summary:
The house mouse, Mus musculus, is an exceptional model system, combining genetic tractability with close homology to human biology. Gestation in mouse development lasts just under three weeks, a period during which its genome orchestrates the astonishing transformation of a single cell zygote into a free-living pup composed of >500 million cells.
Towards a global framework for exploring mammalian development, we applied single cell combinatorial indexing (sci-*) to profile the transcriptional states of 12.4 million nuclei from 83 precisely staged embryos spanning late gastrulation (embryonic day 8 or E8) to birth (postnatal day 0 or P0), with 2-hr temporal resolution during somitogenesis, 6-hr resolution through to birth, and 20-min resolution during the immediately postpartum period. From these data (E8 to P0), we annotate dozens of trajectories and hundreds of cell types, and perform deeper dives into the unfolding of the posterior embryo during somitogenesis, as well as the ontogenesis of the kidney, mesenchyme, retina, and early neurons.
Finally, we leverage the depth and temporal resolution of these whole embryo snapshots, together with other published data, to curate a data-driven pseudotree of mouse development from zygote to pup (E0 to P0). Throughout this pseudotree, we systematically nominate sets of transcription factors (TFs) as candidate drivers of the in vivo differentiation of hundreds of mammalian cell types.
Remarkably, the most dramatic shifts in transcriptional state are observed in a restricted set of cell types in the hours immediately following birth, and presumably underlie the massive changes in physiology that must accompany the successful transition of a placental mammal to extrauterine life.

overall_design: In brief, 12.4 million nuclei from 83 precisely staged embryos spanning late gastrulation (embryonic day 8 or E8) to birth (postnatal day 0 or P0), with 2-hr temporal resolution during somitogenesis, 6-hr resolution through to birth, and 20-min resolution during the immediately postpartum period.

first: Beth

middle: K

last: Martin

first: Ian

last: Welsh

first: Riza

last: Daza

first: Xingfan

first: Eva

last: Nichols

first: Megan

last: Taylor

first: Olivia

last: Fulton

first: Truc-Mai

last: Le

first: Diana

middle: R

last: O'Day

first: Anne

last: Gomes

first: Saskia

last: Ilcisin

first: Sanjay

last: Srivatsan

first: Nobuhiko

last: Hamazaki

first: Xinxian

last: Deng

first: Christine

last: Disteche

first: William

last: Noble

first: Junyue

last: Cao

first: Malte

last: Spielmann

first: Cecilia

middle: B

last: Moens

first: David

last: Kimelman

first: Alexander

middle: F

last: Schier

first: Stephen

last: Murray

first: Cole

last: Trapnell

first: Jay

last: Shendure


title: Effect of microtopography-induced nuclear constriction on gene expression in mesenchymal stromal cells in growth and osteogenic differentiation conditions II

first: Priyam

last: Patel

first: Vadim

last: Backman

first: Vasundhara

last: Agrawal


title: Effect of microtopography-induced nuclear constriction on chromatin accessibility and gene expression in mesenchymal stromal cells in growth and osteogenic differentiation conditions

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

overall_design: Refer to individual Series


title: MAE-seq refines regulatory elements across the genome

status: Public on Jan 06 2023

city: Shenzhen

first: JING

last: LUO

email: luoj17@lzu.edu.cn, luojing9520@163.com

address: No 7,Pengfei Road,Dapeng District

institute: Shenzhen agricultural Genome Research Institute, Chinese Academy of Agricultural Sciences

summary: Proper cell fate determination relies on precise spatial and temporal genome-wide cooperativities among regulatory elements (REs) and their targeted genes. However, the lengths of REs defined by different methods are varied, which indicates sequence redundancy contained and the context of the genome will be unintelligible. To figure this out, we developed a method termed as MAE-seq (Massive Active Enhancers by Sequencing) to experimentally identify functional REs at a 25-bp scale. In this study, more than 626,879 active enhancers are identified in mouse embryonic stem cells. Comparative analysis  indicates most of histone modification datasets could be annotated by MAE-Seq loci. Additionally, 35.03% (219,623) are identified as de novo ones without any epigenetic modification. Validation results show that these 25-bp sequences could act as a functional unit, which shows identical or similar expression patterns as the previously defined larger elements. Additionally, we examined the functions of some novel elements that can up-regulate gene activities. By integrating with Hi-C data, over 55.64% novel elements may have distal association with different targeted genes. As an example, we find Cdh1 gene is interacting with one novel and two known REs in mESCs. And their biological effects are investigated via CRISPR-Cas9. It indicates these distal associations can coordinate Cdh1 gene expression and mESCs proliferation. Therefore, our study provides an experimental approach to refine the REs at 25-bp resolution and it will be a great improvement to unscramble the underlying genome context.

sample_organism:
Homo sapiens
Mus musculus
blank sample

platform_organism:
Homo sapiens
Mus musculus
blank sample

overall_design: Established MAE-seq technology and screened 25bp length functional enhancers in mESCs and HEK293T cells.

first: Yubo

last: Zhang

first: Xiusheng

last: Zhu


title: RiboMeth-seq profiling of ribose methylations in ribosomal RNA of proliferating, quiescent and senescent primary human dermal fibroblasts.

status: Public on Jan 01 2023

city: Heidelberg

first: Martin

last: Kos

address: Im Neuenheimer Feld 328

department: Biochemistry Center (BZH)

country: Germany

institute: University of Heidelberg

summary: The 2’-O-methylation (2’-O-Me) of ribosomal RNA (rRNA) shows plasticity potentially associated with specific cell phenotypes. We used RiboMeth-seq profiling to reveal senescence- and proliferation-specific 2’-O-Me patterns in stress induced premature senescent (SIPS) human dermal fibroblasts.

overall_design: Primary human dermal fibroblasts (HDF) from three healthy donors were kept sub-confluent (= proliferating, P), confluent (=quiescent, Q) or senescence was induced by hydrogen peroxide (=stress-induced premature senescence, SIPS). Duplicates of each cell state from each donor were analyzed by RiboMeth-seq.

first: Guohuan

last: Yang

first: Clemens

last: Heisenberger

first: Isabelle

last: Kos-Braun

first: Norbert

last: Polacek

first: Johannes

last: Grillari

first: Markus

last: Schosserer


title: RNA-sequencing data of mice fed either a control diet or inulin-enriched diet and infected with either Trichuris muris or Citrobacter rodentium

status: Public on Feb 01 2023

city: Frederiksberg C

first: Andrew

last: Williams

address: Dyrlægevej 100

country: Denmark

institute: University of Copenhagen

summary: Mice were fed either a control purified diet, or the same diet with 10% inulin. Mice were then trickle infected with T. muris for 35 days, or given a single infection with C. rodentium for 8 days.

overall_design: RNA was obtained from caecum (T muris) or colon (C rodentium) at necropsy


title: ASPSCR1-TFE3 reprograms transcription by organizing enhancers around hexameric VCP [RNA-Seq, ASPS1_CB5083]

city: Beijing

first: Jinxiu

last: Li

state: Beijing

address: Yuanmingyuan west road 2#

department: College of biological sciences

institute: China Agricutural University

summary: ChIPseq experiments identify that ASPSCR1-TFE3 defines active enhancers across the genome and co-distributes with VCP/p97. RNAseq after knock-down of ASPSCR1-TFE3 or VCP, inhibition of VCP, or overexpression of each in alveolar soft part sarcoma cell lines demonstrates their co-dependence. HiChIP defines chromatin conformations that surround ASPSCR1-TFE3 targets and are lost on VCP knock-down.

overall_design: ASPS cell lines, tumors from ASPS mouse model and tumors from ASPS patients are used for ChIP-seq with antibodies against ASPSCR1, VCP, POLII and various histone modifications. RNAseq in ASPS cell lines after application of siRNA against control, ASPSCR1-TFE3, or VCP, or application of VCP inhibitor CB-5083. H3K27ac-HiChIP in the FU-UR-1 cell line at baseline and after 6 days of siRNA against VCP.

first: Amir

last: Pozner

first: Li

first: Kevin

last: Jones


title: The SRC-family kinase LYN acts as a tumour suppressor gene in an in vivo BRCA1 loss-of-function-associated mammary tumourigenesis model

status: Public on Jan 23 2023

city: Cardiff

first: Matthew

last: Smalley

state: Cardiff

address: Hadyn Ellis Building, Maindy Road

department: School of Biosciences

institute: Cardiff University

summary: To examine the interaction between LYN kinase and BRCA1 loss-of-function in an in vivo mouse mammary tumour model, we have used conditional knockout Brca1 and Lyn alleles targeted to the mammary epithelium, on a p53 heterozygote background. Comparison of tumour cohorts demonstrated that homozygous conditional Lyn cohorts developed tumours significantly faster than the other genotypes. Transcriptomic analysis to identify and compare tumours with the highest and lowest Lyn levels from across the cohorts showed that ‘Lyn high’ tumours had a significantly slower doubling time and were enriched in inflammatory pathways and canonical NfkB signalling. ‘Lyn low’ tumours had a faster doubling time and were enriched in PI3K, WNT and NOTCH pathways. Therefore, these results suggest that, in this model at least, LYN acts as a tumour suppressor in the context of Brca1 loss.

overall_design: RNAseq analysis of mammary tumours from mouse cohorts carrying Brca1 conditional (floxed) alleles on a p53 heterozygous background and either wild type, heterozygous or homozygous for the conditional (floxed) Lyn allele. All cohorts also carried the Blg-CRE transgene, expressed in the . Differentially Expressed Genes (DEGs) were determined in three ways. First, by comparison of BlgCre Brca1 floxed p53 heterozygous Lyn wild type tumours to  BlgCre Brca1 floxed p53 heterozygous Lyn floxed tumours. Second, by determining the thirteen tumours most strongly expressing Lyn ('Lyn high' tumours) and the thirteen tumours with the weakest Lyn expression ('Lyn low' tumours) according to the normalised RNAseq data and comparing DEGs between them. Third, by carrying out an unbiased principal component analysis on all 39 tumours and allowing them to self-sort into (two) distinct groups (PCA group 1+2 and PCA group 3+4) and comparing DEGs between them.

first: Giusy

last: Tornillo


title: ASPSCR1-TFE3 reprograms transcription by organizing enhancers around hexameric VCP [ASPS1 VCP ChIP]

summary: Aberrant transcription in alveolar soft part sarcoma (ASPS) is orchestrated by the fusion oncoprotein, ASPSCR1-TFE3, product of a gene fusion created by a t(X;17) chromosomal translocation. Here, proteomics of proteins co-immunoprecipitating with ASPSCR1-TFE3 revealed strong enrichment of VCP/p97, an AAA+ ATPase with known segregase function. Positive and negative genetic experiments with ASPSCR1-TFE3 and VCP demonstrated that they function co-dependently for cancer cell proliferation, colony formation, enhancer activation, chromatin conformation, and transcription

overall_design: ASPS1 cell line is  used for VCP ChIP-seq


title: ASPSCR1-TFE3 reprograms transcription by organizing enhancers around hexameric VCP [RNA-Seq, 17637_HEK_cdelta]


title: Exclusion of m6A from splice-site-proximal regions by the exon-junction complex dictates m6A topologies and mRNA stability

status: Public on Jan 02 2023

city: Rehovot

first: Anna

last: Uzonyi

address: 234 Herzl street

department: Department of Molecular Genetics

institute: Weizmann Institute of Science

summary: N6-methyladenosine (m6A), a widespread destabilizing mark on mRNA, is non-uniformly distributed across the transcriptome, yet the basis for its selective deposition is unknown. Here, we uncover that m6A deposition is not selective. Instead, m6A distribution is exclusion-based: m6A-consensus harboring sites are methylated by default, unless they are within a window of up to ~200 nt from an exon-intron junction. A simple model which we extensively validate, relying exclusively on presence of m6A motifs and exon-intron architecture allows high accuracy recapitulation of experimentally-measured m6A profiles and of the vast majority of m6A hallmarks. Finally, we provide strong evidence that this exclusion is mediated by the exon-junction complex. Our findings establish a mechanism by which the memory of nuclear RNA splicing is covalently etched on an mRNA in the form of m6A, and determines its cytoplasmic stability, with broad implications on the regulation, function, and evolution of the exon-junction complex and m6A.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design:
RNA sequencing of mESC transfected with a plasmid encoding GFP with a 3' UTR fragment derived from SLC25A3 and subjected to m6A immunoprecipitation. RNA sequencing of HEK293T cells transfected with a massively parallel reporter assay and subjected to m6A immunoprecipitation. RNA sequencing of MCF7 cells transfected with plasmids encoding variants of the mouse Nol12, Coa3 and Calm3 genes and subjected to m6A immunoprecipitation.
RNA sequencing of HEK293T cells transfected with a spliced, long massively parallel reporter assay and subjected to m6A immunoprecipitation. RNA sequencing of MCF7 cells transfected with plasmids encoding variants of the mouse Nol12, Coa3 and Calm3 genes and subjected to m6A immunoprecipitation. RNA sequencing of Mettl3 inhibitor and actD treated HEK293T cells. RNA sequencing of Y14 degron HEK293T cell time point samples with m6A immunoprecipitation.

first: David

last: Dierks

first: Ronit

last: Nir

first: Herve

last: Le hir

first: Boris

last: Slobodin

first: Schraga

last: Schwartz


title: ASPSCR1-TFE3 reprograms transcription by organizing enhancers around hexameric VCP [RNA-Seq, FUUR_CB5083]


title: ASPSCR1-TFE3 reprograms transcription by organizing enhancers around hexameric VCP [Cell_lines_ChIP, FUUR1, FUUR1_VCP]


title: ASPSCR1-TFE3 reprograms transcription by organizing enhancers around hexameric VCP [Cell_lines_ChIP, ASPS1]


title: ASPSCR1-TFE3 reprograms transcription by organizing enhancers around hexameric VCP [hASPS_ChIP, histone_markers]


title: Human iPSC Derived Enamel Organoid Guided by Single Cell Atlas of Human Tooth Development

status: Public on Jan 11 2023

first: Hannele

last: Ruohola-Baker

address: UW Medicine at South Lake Union, 850 Republican Street

department: Department of Biochemistry

summary: Tooth enamel secreted by ameloblasts is the hardest material in the human body, acting as a shield protecting the teeth. However, enamel is gradually damaged or partially lost in over 90% of adults and cannot be regenerated due to a lack of ameloblasts in erupted teeth. Here we use sci-RNA-seq to establish a spatiotemporal single cell atlas for the developing human tooth and identify regulatory mechanisms controlling the differentiation process of human ameloblasts. We reveal key signaling pathways involved between the support cells and ameloblasts during fetal development and recapitulate those findings in a novel human ameloblast in vitro differentiation from iPSCs. We furthermore develop a mineralizing enamel organ-like 3D organoid system. These studies pave the way for future regenerative dentistry and therapies toward genetic diseases affecting enamel formation.

overall_design:
To understand how the early differentiation processes of tooth and salivary gland differ and how the epithelial and mesenchymal cell lineages acquire the odontogenic competence, we analyzed the developmental gene expression profiles of human fetal stages by single cell sequencing approach. Tooth germ and salivary gland samples were collected from five fetal age groups. These age groups represented the following developmental stages for tooth differentiation: the bud stage (9-11gw), the cap stage (12-13gw), the early bell stage (14-16gw), and the late bell stage (17-19gw and 20-22gw). We also collected submandibular salivary glands from three matched timepoints (12-13gw, 14-16gw, 17-19gw) that cover the pseudo-glandular and canalicular stages for salivary gland development. A total of 12 samples were prepared for sci-RNA sequencing that consisted of specific tissue from multiple fetuses. For young fetuses, 9-11gw, dissecting individual tooth germs or salivary glands that were in the bud stage was not feasible due to the large number of cells required to perform sci-RNA-seq protocol, instead whole jaw segments were prepared for sequencing. Ten anterior segments (which span from canine tooth to canine tooth region) were pooled as the anterior jaw sample, and 12 posterior jaw segment pairs were pooled as the posterior jaw sample. For older fetuses from 12-22gw, individual tooth germs and salivary glands were dissected. The numbers of pooled samples varied per stage and tooth type, ranging from 40-66 for anterior teeth (including incisors and canines), and 17-51 for molar teeth, as molar teeth are generally larger in size. The salivary gland pooled samples ranged from 3-7 in the three age groups collected.
We utilized the inferred signaling pathways from the sci-RNA-seq data to develop a novel in vitro differentiation protocol that recapitulated the early stages of human ameloblast development from hiPSCs (iAM differentiation); To analyze the efficiency of the differentiation we performed sci-RNA-seq on the two time points of iPSC derived ameloblast differentiation (day10-OE and day16-Early-ameloblasts) and compared the gene expression data to the fetal tissue gene expression data. Bulk RNA-seq was also performed for day0 and day16 of the differentiation .

first: Ammar

last: Alghadeer

first: Sesha

last: Hanson-Drury

first: Devon

last: Ehnes

first: Yang

middle: T

last: Zhao

first: Anjali

last: Patni

first: Diana

last: O'Day

first: Cailyn

last: Spurrell

first: Aishwarya

last: Gogate

first: Ashish

last: Phal

first: Hai

last: Zhang

first: Arikketh

last: Devi

first: Yuliang

last: Wang

first: Lea

last: Starita

first: Daniel

last: Doherty

first: Ian

last: Glass

first: Jay

last: Shendure

last: Baker

first: Mary

last: Regier

first: Julie

last: Mathieu


title: ASPSCR1-TFE3 reprograms transcription by organizing enhancers around hexameric VCP [RNA-Seq, FUUR1_KD]

first: Jinxiu

last: Li

first: Amir

last: Pozner

first: Li

first: Kevin

last: Jones


title: ASPSCR1-TFE3 reprograms transcription by organizing enhancers around hexameric VCP [hASPS_ChIP, ASPL_VCP_Pol2]

overall_design: ASPS cell lines, tumor from ASPS mouse model and tumor from ASPS patients are used for ASPSCR1, VCP, POLII and various histone modification


title: ASPSCR1-TFE3 reprograms transcription by organizing enhancers around hexameric VCP [mASPS_ChIP, histone_markers]


title: ASPSCR1-TFE3 reprograms transcription by organizing enhancers around hexameric VCP [RNA-Seq, ASPS1_KD]


title: ASPSCR1-TFE3 reprograms transcription by organizing enhancers around hexameric VCP [Cell_lines_ChIP, FUUR1, 17934_FUUR1_KDs_H3K27ac]


title: ASPSCR1-TFE3 reprograms transcription by organizing enhancers around hexameric VCP [Cell_lines_ChIP, FUUR1, FUUR1_ASPL_POLII]


title: ASPSCR1-TFE3 reprograms transcription by organizing enhancers around hexameric VCP [mASPS_ChIP, ASPL_VCP_Pol2]


title: ASPSCR1-TFE3 reprograms transcription by organizing enhancers around hexameric VCP


title: ASPSCR1-TFE3 reprograms transcription by organizing enhancers around hexameric VCP [HiChIP]


title: Ets1 suppresses adipose beiging process via bidirectional regulation of mitochondrial biogenesis and clearance

status: Public on Dec 22 2022

city: Nanjing

first: Kai

address: #818, East Tianyuan Road

institute: Nanjing Medical University

summary: Beige adipocytes accumulates mitochondria and alleviates metabolic disorder via activating energy expenditure. Whether the opposing process of mitochondrial biogenesis and clearance are integrated regulated in beige adipocytes is beyond known. Here we show that DNA binding protein Ets1 suppresses beige adipocyte formation via bidirectional regulation of mitochondrial biogenesis and clearance. The expression level of Ets1 was down-regulated in browning adipocytes, and up-regulated in the subcutaneous fat of obese mice. Adipocyte Ets1 heterozygous knock-in mice showed suppressed beige adipocytes formation under cold stress, while the homozygous knock-in mice are cold intolerance. On the other hand, knocking out Ets1 in adipocytes enhanced energy expenditure and protect the mice from high fat diet induced metabolic disorders. Mechanical assay suggests Ets1 binds to the promoter region of mitochondria complex coding genes and autophagy related genes, transcriptionally suppresses mitochondrial biogenesis and activates its clearance. Our results indicate that Ets1 integrally regulates the balance of mitochondria generation and degradation, hence acts as a pivotal governor of mitochondria content and negatively regulates beige adipocyte formation.

overall_design:
Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for Ets1 in mature adipocytes seperated from iWAT of wild type C57 mice, either after 7 days cold stress or not.
Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for H3k27ac in mature adipocytes seperated from iwat of EA+/+, EC+/+, Flox, and EAKO mice.
Assay for Transposase-Accessible Chromatin with high throughput sequencing (ATAC-seq) for open chromatin in mature adipocytes seperated from iWAT of Flox or EAKO mice.

first: Suyang

last: Wu

first: Chen

last: Qiu

first: Xiao

last: Han


title: Gene expression profiling of knock-out of Rv2869c/Rip1 in M. tuberculosis Erdman and Rv3193c in M. tuberculosis H37Rv

city: College Station

first: Thomas

last: Ioerger

address: 3112 TAMUS

department: Department of Computer Science

institute: Texas A&M University

summary: This RNA-Seq study of gene expression in M. tuberculosis was done as part of the FLUTE project (NIH grant U19-AI107774, Eric Rubin, program director).

overall_design: There a 16 samples organized as a 2x2x2x2 design.  There 2 replicates each for: a knockout of Rv2869c/Rip1 and its parental strain (Erdman), and a knockout of Rv3193c and its parental strain (H37Rv),  each grown in either 7H10-glycerol media or in the presence of phenanthroline (an iron chelator).

first: Christopher

last: Sassetti

first: Samantha

last: Nelson


title: Single cell RNA sequencing reveals distinct T cell populations in immune-related adverse events of checkpoint inhibitors

status: Public on Dec 14 2022

city: New York City

first: Syed

middle: M. Shoiab

last: Bukhari

state: New York

institute: Columbia University

summary: PD-1 is an essential inhibitory receptor in T cells, and antibodies that block its interaction with its ligands can augment anti-tumor immune responses. The clinical potential of these agents is limited by the fact that approximately half of all patients who receive anti-PD-1 treatment subsequently develop immune-related Adverse Events (irAEs). To generate insights into the cellular and molecular changes that occur during anti-PD-1 treatment, and to discover predictive biomarkers of irAEs, we performed single cell RNA sequencing of circulating T cells collected from cancer patients who did and did not develop irAEs following PD-1 blockade. Using the K-nearest-neighbor-based network graph drawing layout, we show the involvement of unique gene expression signatures and subpopulations of T cells. We identified that at baseline, patients with arthritis had significantly less cells with features of CD8 TCM cells, patients with pneumonitis had more CD4 TH2 cells, and patients with thyroiditis had more CD4 TH17 cells, when compared to patients who did not develop irAEs. Moreover, T cell receptor sequencing revealed distinctive clonal expansion, and suggested involvement of organ-specific and potentially pathogenic T cell clones among patients with irAEs. Altogether, these data support the hypothesis that different populations of T cells are associated with different irAEs and that quantification and characterization of these populations of T cells pre-treatment could serve as a toxicity-specific, predictive biomarker.

overall_design: T cells were isolated from PBMCs harvested from cancer patients before and after immunoptherapy.

first: Adam

last: Mor


title: LOX-1 is an N6-methyladenosine-regulated receptor for Helicobacter pylori via binding to the bacterial catalase [RNA-seq]

status: Public on Dec 17 2022

city: Hong Kong

first: Judeng

last: ZENG

address: Room 902, Li Ka Shing Medical Science Building, Prince of Wales Hospital

institute: The Chinese University of Hong Kong

summary: The role of N6-methyladenosine (m6A) modification of host mRNA during bacterial infection is unclear. Here, we show that Helicobacter pylori infection upregulated major m6A “writers” and increased m6A level in gastric epithelial cells. Attenuating m6A increase by hemizygotic deletion of Mettl3 in mice or small interfering RNAs targeting m6A “writers” exacerbated H. pylori colonization. LOX-1 mRNA was identified as a key m6A-regulated target during H. pylori infection. m6A modification destabilized LOX-1 mRNA and reduced LOX-1 protein level. LOX-1 acted as a membrane receptor for H. pylori catalase to mediate the bacterial adhesion. BI-0115, a small-molecule inhibitor of LOX-1, suppressed H. pylori adhesion and colonization. Genetic ablation of Lox-1 also reduced H. pylori colonization in mice. In sum, this study reveals that m6A modification is an auto-protective mechanism against H. pylori infection by downregulating LOX-1 to prevent H. pylori adhesion. LOX-1 could be a druggable target for controlling H. pylori infection.

overall_design: Normal gastric epithelial cells (HFE145) transfected with negative control or WTAP siRNAs were infected with or without H. pylori for 24 hours. Cell samples were divided into four groups, namely siNC, siNC + H. pylori, siWTAP, siWTAP + H. pylori.

first: William

last: Zeng


title: Hyaluronan driven by epithelial aPKC deficiency remodels the microenvironment and creates a therapeutic vulnerability in mesenchymal colorectal cancer IV

status: Public on Dec 16 2022

city: New York

first: Jorge

last: Moscat

state: NY

address: 1188 York Avenue

department: Pathology and Laboratory Medicine

institute: WEILL CORNELL MEDICINE

summary: Mesenchymal colorectal cancer (mCRC) is microsatellite stable (MSS), highly desmoplastic, with CD8+ T cells excluded to the stromal periphery, resistant to immunotherapy, and is driven by low levels of the atypical PKCs (aPKCs). We show here that a salient feature of these tumors is the accumulation of hyaluronan (HA), which along with reduced aPKC levels, predict poor survival. HA promotes epithelial heterogeneity, and the emergence of a fetal metaplastic cell population (TFSC) endowed with invasive cancer features through a network of interactions with activated fibroblasts and components of the immune system. TFSCs are sensitive to HA deposition in vivo and organoids, and their gene expression signature has prognostic value. We demonstrate that in vivo HA degradation with a clinical dose of hyaluronidase impairs mCRC tumorigenesis and enables immune checkpoint blockade therapy by promoting the recruitment of B and CD8+ T cells, including a proportion with resident memory features.

overall_design: Prkcif/fPrkczf/f;Villin-Cre Veh- (n=5) and PEGPH20-treated (n=3) small intestine tumors were profiled

first: Anxo

last: Martinez-Ordoñez

first: Angeles

last: Duran

first: Marc

last: Ruiz-Martinez

first: Tania

last: Cid-Diaz

last: Zhang

first: Qixiu

first: Hiroto

last: Kinoshita

first: Yu

last: Muta

first: Juan

last: Linares

first: Hiroaki

last: Kasashima

first: Mohamed

last: Omar

first: Masakazu

last: Yashiro

last: Pannellini

first: Alessio

last: Pigazzi

first: Giorgio

last: Inghirami

first: Luigi

last: Marchionni

first: Darren

last: Sigal

first: Maria

last: Diaz-Meco


title: LOX-1 is an N6-methyladenosine-regulated receptor for Helicobacter pylori via binding to the bacterial catalase

status: Public on Dec 13 2022

first: Judeng

last: ZENG


title: RNA-seq analysis revealed that the cardiotoxicity caused by herceptin is due to the release of PTX3.

status: Public on Dec 01 2022

city: Hang Zhou

first: Zhifei

last: Xu

address: 866 Yuhangtang Road

institute: Zhejiang University

summary: Herceptin, also known as trastuzumab, is currently approved as a targeted therapy for breast cancer and advanced gastric cancer. However, the clinical application of hercptin was limited  by its severe cardiotoxicity.  We found that  the cardiotoxicity caused by Herceptin is due to the release of PTX3 by vascular endothelial cells, which leads to the decline of cardiac systolic function. This study found the role and mechanism of vascular endothelial cells in indirectly regulating cardiotoxicity, and provided a new idea for the study of clinical drug-induced cardiotoxicity.

overall_design: 3 Vehicle Samples and 3 PTX3 100ng Samples

first: Qiaojun

last: He


title: LOX-1 is an N6-methyladenosine-regulated receptor for Helicobacter pylori via binding to the bacterial catalase [m6A-seq]

status: Public on Dec 11 2022

first: William

last: Wu

last: Zeng


title: Identify and eradicate leukemia stem cells in T-cell acute lymphoblastic leukemia by PD-1 therapy

first: Guo

last: Qiu

state: Guangdong

address: Guangzhou Avenue

institute: Nanfang Hospital, Southern Medical University

summary:
To investigate the characteristics of PD-1+ LSCs in T-ALL, we purified PD-1+ and PD-1– T-ALL cells from the bone marrow (femur and tibia) of T-ALL mice, Pten null T-ALL mice, or PDX recipients.
RNA sequencing was performed to explore the differential gene expression and pathway enrichment of PD-1+ LSCs in T-ALL.

overall_design: Comparative gene expression profiling analysis and gene set enrichment analysis of RNA-seq data for PD-1+ LSCs in murine and human T-ALL.

first: Xi

first: Wenwen

last: Zhang

first: Li

last: Xuan

first: Linjia

last: Jiang

first: Meng

last: Zhao


title: Single cell Seqeuencing of trat pons after stroke [scRNA-seq]

status: Public on Nov 25 2022

first: Yongjun

address: 250, Changgang East Road 250

institute: Guangzhou Medical University

summary: We report the result of scRNA-seq of pontine infarction in rats.

overall_design: Examination of 3 samples in stroke and normal rats

first: Juehua

last: Zhu


title: Distinct and redundant roles for zebrafish her genes during osteoblast differentiation and craniofacial patterning.

status: Public on Dec 12 2022

city: AURORA

first: James

middle: Tucker

last: Nichols

state: CO

department: Craniofacial Biology

institute: University of Colorado - Anschutz Medical Campus

summary: The Notch pathway is a cell-cell communication system which is critical for many developmental processes, including craniofacial development. Notch receptor activation induces expression of several well-known canonical targets including those encoded by the hes and her genes in mammals and zebrafish, respectively. The function of these genes, individually and in combination, during craniofacial development is not well understood. Here, we investigated zebrafish her9 and her6 gene function during craniofacial development. We found that her9 is required for osteoblasts to efficiently mineralize bone, while cartilage is largely unaffected. Strikingly, gene expression studies in her9 mutants indicate that although progenitor cells differentiate into osteoblasts at the appropriate time and place, they fail to efficiently lay down mineralized matrix. This mineralization role of her9 is likely independent of Notch activation. In contrast, her9 also functions redundantly with her6 downstream of Jagged1b-induced Notch activation during dorsoventral craniofacial patterning. These studies disentangle distinct and redundant her gene functions during craniofacial development, including an unexpected, Notch independent, requirement during bone mineralization

overall_design: neural crest cell gene expression profiling of notch pathway related genes in 24 hpf WT D. rerio

first: Amanda

last: Stenzel

first: Abigail

last: Mumme-Monheit

first: Juliana

last: Sucharov

first: Macie

last: Walker

first: Jennyfer

last: Mitchell

first: Bruce

last: Appel


title: Organelle-specific RNA Tagging Probes for Spatially Resolved Profiling of RNA Binding Proteome and Investigation upon Ferroptosis Induction

first: Haofan

last: Sun

address: Grindtorpsvägen 11 7tr Lgh 1803, Grindtorpsvägen 11, 183 32 Täby

institute: National Center for Protein Sciences, Beijing

summary: The key role of RNA-binding proteins (RBPs) in posttranscriptional regulation of gene expression is intimately tied to their subcellular localization. Dysregulated localization may severely disrupt the biological functions of RBPs. To reveal the regulatory mechanisms of RBPs, methods for systematically mapping the subcellular localized RBPs and monitoring their translocations under physiological conditions are in high demand. Herein, a subcellular-specific RNA labeling method was developed for efficient enrichment and deep profiling of nuclear and cytoplasmic RBPs. A total of 1221 nuclear RBPs and 1333 cytoplasmic RBPs were enriched and identified using nuclear/cytoplasm targeting enrichment probes, which represented an increase of 54.4% and 85.7% compared with previous reports. The probes were further applied in the first omics-level investigation of subcellular-specific RBP-RNA interactions upon ferroptosis induction. Interestingly, large-scale RBPs displayed enhanced interaction with RNAs in nucleus but reduced association with RNAs in cytoplasm during ferroptosis process. Among these RBPs with regulated RNA-binding, translation was found as one of the commonly enriched GO functions by different ferroptosis inducers, indicating ferroptosis could disturb protein translation via different pathways. Furthermore, we discovered dozens of nucleoplasmic translocation candidate RBPs upon ferroptosis induction and validated representative ones by immunofluorescence imaging. The enrichment of TCA cycle in the translocation candidate RBPs may provide new insights for investigating their possible roles in ferroptosis induced metabolism dysregulation. The above findings suggest the potential of our enrichment method for high-throughput RBP mapping with organelle-level spatial resolution.

overall_design: Comparative gene expression analysis of RNA-seq data from density gradient centrifugation enriched nuclear RNA, BLTF enriched nuclear RNA, density gradient centrifugation enriched cytoplasmic RNA and BETF enriched cytoplasmic RNA in HeLa cells.


title: Development of a novel aging clock based on chromatin accessibility [ATAC-seq]

city: Lausanne

first: kevin

last: perez

address: rue du Bugnon 27

country: Switzerland

institute: University of Lausanne

summary: The establishment of highly accurate aging clocks based on DNA methylation highlighted the strong link between epigenetic alterations and aging. However, connecting methylation clocks to physiological changes is not straightforward. Transcriptomics and proteomics clocks on the other hand are directly connected to cellular function, yet they do not allow us to understand underlying epigenetic mechanisms. We hypothesize that chromatin accessibility, a readout that integrates many epigenetic mechanisms, may bridge epigenetic changes with their downstream effects in aging. To demonstrate that chromatin accessibility can predict age, we generated chromatin accessibility profiles from peripheral blood mononuclear cells (PBMCs) of 157 human donors, aged 20 to 74 and used them to construct a novel aging clock. Our clock predicted age with a root mean squared error of 7.69 years, a median absolute error of 5.69 years and a correlation of 0.83. Moreover, by comparing our chromatin accessibility data to matched transcriptomic profiles, we show that the genomic sites selected by our clock drive changes in transcription during aging. This chromatin accessibility clock could therefore be used to better understand the mechanisms driving the process of aging and evaluate anti-aging interventions.

overall_design: Chromatin accesibility and transcriptomics profiles from PBMCs of human donors

first: Cheyenne

last: Rechsteiner

first: Francesco

last: Morandini

first: Kevin

last: Perez

first: Alejandro

last: Ocampo


title: mRNA Seqeuencing of MCAO and trat pons after stroke [bulk RNA-seq]

city: Guangzhou

summary: We report the result of mRNA-seq of MCAO and pontine infarction in rats.

overall_design: Examination of 12 samples in stroke and normal rats


title: Trem2 Macrophage Promote Cardiac Repair in Myocardial Infarction via Efferocytosis and Carbohydrate Metabolism

status: Public on Nov 15 2022

city: Boston

first: Ming

last: Zhai

state: Massachusetts

address: Avenue Louis Pasteur

department: Cardiovascular Division, Department of Medicine

institute: Brigham and Women's Hospital

summary: We want to find that the TREM2 mechanism on the Macrophages in the myocardial infarction

overall_design: CCR2+ macrophages within post-MI was specially sorted out by FACS within post-MI and RNA of macrophages was extracted using the TRIzol reagent (15596018, Invitrogen) according to the manufacturer’s instructions. RNA integrity was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara). Then the libraries were constructed using TruSeq Stranded mRNA LT Sample Prep Kit (Illumina, USA) according to the manufacturer’s instructions.

first: Shiyu

last: Gong


title: Synaptopodin regulates denervation-induced plasticity at hippocampal mossy fiber synapses

status: Public on Oct 28 2022

city: Hannover

first: Maximilian

last: Lenz

address: Carl-Neuberg-Straße 1

department: Institute of Neuroanatomy and Cell Biology

institute: Hannover Medical School

summary: Neurological diseases can lead to the denervation of brain regions caused by demyelination, traumatic injury or cell death. Nevertheless, the molecular and structural mechanisms underlying lesion-induced reorganization of denervated brain regions are a matter of ongoing investigation. In order to address this issue, we performed an entorhinal cortex lesion (ECL) in mouse organotypic entorhino-hippocampal tissue cultures of both sexes and studied denervation-induced plasticity of mossy fiber synapses, which connect dentate granule cells (dGCs) with CA3 pyramidal cells (CA3-PCs) and play important roles in spatial learning. Partial denervation caused a strengthening of excitatory neurotransmission in dGCs, in CA3-PCs, and their direct synaptic connections as revealed by paired recordings (GC-to-CA3). These functional changes were accompanied by ultrastructural reorganization of mossy fiber synapses, which regularly contain the plasticity-related protein synaptopodin and the spine apparatus organelle. We demonstrate that the spine apparatus organelle and its integral protein synaptopodin are associated with ribosomes in close proximity to synaptic sites and unravel a synaptopodin-related transcriptome. Notably, synaptopodin-deficient tissue preparations that lack the spine apparatus organelle, failed to express lesion-induced synaptic adjustments. Hence, synaptopodin and the spine apparatus organelle play a crucial role in regulating lesion-induced synaptic plasticity at hippocampal mossy fiber synapses.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for dentate gyrus and CA3 samples from wildtype and synaptopodin deficient cultures. Moreover, synaptopodin-associated transcriptome analysis has been performed.

first: Pia

last: Kruse

first: Gudrun

last: Brandes

first: Hanna

last: Hemeling

first: Zhong

last: Huang

first: Christoph

last: Wrede

first: Jan

last: Hegermann

first: Andreas

last: Vlachos


title: Xijiao Dihuang decoction protects against sepsis-induced cardiac dysfunction

status: Public on Oct 24 2022

city: fuzhou

first: mingrui

last: lin

address: 1 qiuyang

institute: fujian university of traditional chinese medicine

summary: The goals of this study is to identify the differential expressed genes in heart of C57BL/6 mice with or without LPS treatment, and compare the differential expressed genes in the heart of LPS injection C57BL/6 mice after Xijiao Dihuang decoction(XJDHT)  treatment. Briefly, the mice were randomly divided into 3 groups: control, LPS and LPS + XJDHT groups (n=4 for each group). Mice in Control and LPS groups were intraperitoneal injection with saline and 10mg/kg of LPS respectively, and orally administrated with saline; the mice in LPS + XJDHT groups were intraperitoneal injection  with LPS (10 mg/kg) and orally administrated with 50 mg/kg /day of XJDHT for total 3 days.  Then the heart were used to identify differentially expressed genes among different groups.

overall_design: RNA sequencing was performed to compare differential expressed genes in heart of C57BL/6 mice in following 3 groups: control, LPS, LPS + XJDHT (n=4 for each group).

first: Wei

last: Li

first: Zhiqing

last: Shen

first: Mingrui

last: Lin


title: Hypothermic oxygenated machine perfusion promotes mitophagy flux against hypoxia ischemic injury in donation after circulatory death liver

status: Public on Oct 15 2022

city: Hangzhou

first: jia

last: Luo

address: qingchun road

institute: 浙江大学

summary:
HOPE is a dynamic preservation method to attenuate IRI in DCD liver. In a rat model of DCD liver, the protective mechanism of HOPE is probably by promoting mitophagy flux in response to hypoxia-ischemic injury.
We performed gene expression profiling analysis using data obtained from RNA-seq of 4 different groups in DCD liver.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for rat DCD livers  (WI30min, SCS4h,HMP1h and HOPE1h).

first: Jia

first: Jianhu

first: Shusen

last: Zheng


title: Development of a novel aging clock based on chromatin accessibility [RNA-seq]

first: kevin

last: perez

first: Cheyenne

last: Rechsteiner

first: Francesco

last: Morandini

first: Kevin

last: Perez

first: Alejandro

last: Ocampo


title: Development of a novel aging clock based on chromatin accessibility

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

overall_design: Refer to individual Series


title: The effect of serum from children with nephrotic syndrome on transcriptome of human immortalized podocytes cultured in vitro

status: Public on Oct 14 2022

city: Prague

first: Martin

last: Bezdicka

state: Czech Republic

address: V Uvalu 84

department: Department of Pediatrics

country: Czech Republic

institute: Second Faculty of Medicine and Motol University Hospital

summary: Nephrotic syndrome (NS) is an unfavorable disease with heterogeneous causes and variable prognosis. One of the clinically crucial prognostic feature is the response to initial glucocorticoid treatment. Whereas in some children with steroid-sensitive nephrotic syndrome (SSNS) the treatment may induce long-term remission of the disease, steroid-resistant cases (SRNS) are at risk of renal failure requiring renal replacement therapy. The aim of this project was to explore whether sera from children with the two main clinically defined types of NS induce changes in transcriptome of in-vitro cultures of immortalized human podocytes. After 3 days of culture, total RNA was isolated and then library from polyadenylated RNA was prepared and RNA sequencing was performed. Log2 (fold-changes) were calculated to describe differential gene expression. Within the Reactome online tool, Camera methodology was implemented to identify functionally linked gene groups (pathways) that could distinguish the two patient groups. Significant transcriptome differences were found between samples from children with SSNS and SRNS. This may help to reveal the molecular mechanisms of the disease and open up for an effective individualized treatment.

overall_design: SSNS serum samples (n = 9) were obtained at disease manifestation, before the administration of glucocorticoids. SRNS serum samples (n = 4) were obained from patients, who had long-term remission and did not take any immunosuppressive drugs for at least 6 months before blood sampling. Fully differentiated immortalized human podocytes were incubated with 10 % serum samples at 37 °C in 5 % CO2 for 72 hours, in triplicates. The cells were lysed and the RNA was isolated using spin-column method. The RNA libraries were prepared from polyadenylated RNA and sequenced by NextSeq instrument. Sequencing data were processed by STAR program and DESeq2. Pathway analysis was performed by Reactome online software.

first: Ondrej

last: Soucek

last: Cinek


title: Interplay between acetylation and ubiquitination of Isw1 confers multidrug resistance in Cryptococcus neoformans

status: Public on Nov 10 2022

city: shenyang

first: Yang

last: Meng

address: Wenhua street num 11

department: College of Life and Health Sciences

institute: Northeastern University

summary: Cryptococcus neoformans poses a great threat to human communities, given that it quickly becomes resistant to available antifungal drugs. Herein, a conserved chromatin remodeler, Isw1, is shown to function as a master transcriptional modulator of genes responsible for multidrug resistance. It reciprocally controls drug resistance, and cells with disrupted ISW1 demonstrate profound resistance to fluconazole, ketoconazole, 5-fluorocytosine and 5-fluorouracil. Mass spectrometry reveals that Isw1 is both acetylated and ubiquitinated. These two protein posttranslational modifications confer an interplay regulation mechanism that controls Isw1 protein degradation via a ubiquitin-mediated proteasome and, consequently, C. neoformans resistance to drugs. Functional mutagenesis analysis of acetylation and ubiquitination sites reveals that the acetylation status of the lysine 97 residue on Isw1 coordinates its ubiquitination processes at lysines 113 and 441 by modulating the protein interactions between Isw1 and Cdc4, an E3 ligase. Clinical C. neoformans isolates overexpressing the undegradable ISW1 mutant demonstrate impaired drug-resistant phenotypes. Collectively, our studies reveal a sophisticated acetylation-Isw1-ubiquintation regulation axis that controls multidrug resistance in fungal pathogens.

overall_design: Performed paired-end RNA-seq of Cryptococcus neoformans H99s as Control group and isw1∆ strains as in 50ml YPD broth  at OD600=0.8 with 10μg/ml FLC, respectively in biological triplicates.

first: Chen

last: Ding


title: Modelling of pigmentation disorders associated with MITF mutation in Waaredenburg Syndrome revealed an impaired melanogenesis pathway in iPS-derived melanocytes

status: Public on Nov 13 2022

city: Leiden

first: Jiale

last: Chen

address: Einsteinweg 55

country: Netherlands

institute: Leiden University

summary: Waardenburg Syndrome (WS) is a rare genetic disorder that leads to congenital hearing loss and pigmentation defects. MITF is one of its pathogenic genes. While studied extensively in animal models, its pathogenic mechanism still poorly described in humans due to the challenges in accessing embryonic tissues. In recent years, patient-derived human induced pluripotent stem cells(iPSCs) technology offers a promising approach for modeling human melanocyte development and hereditary disease. In this work, we make use of iPSCs derived from one WS patient carrying a heterozygous mutation in MITF gene. Accordingly, we establish a pipeline for profiling iPSCs during differentiation toward the melanocyte, which can be used to characterize the differentiation properties of the MITF+/-  melanocytes. The MITF+/- cell lines showed a reduction in expression of the characteristic melanocyte-related gene expression profile. Analysis of the melanosome maturation process by electron microscopy revealed a lower percentage of mature, fully pigmented melanosomes. Compare with the WT cell lines, The transcriptome analysis reveals widespread gene expression changes at the stage of melanocyte in MITF+/- cell lines, and the differentially expressed genes(DEGs) were enriched with gene ontology (GO) of melanogenesis related pathway. Interesting, ion transport-related genes were also shown significantly difference in MITF+/- induced melanocyte, indicating the mutant MITF may lead to the dysfunction of potassium channels and transporters produced by intermediate cells in cochlear, further causes phenotypes of deafness. Altogether, our study provide valuable insights into how reduced MITF expression in WS patients might resulting in defective melanocyte development and related phenotype base on the patient-derived hiPSC model. The possibility of integrating laboratory data with clinical phenotypes will bring us toward precision medicine approaches in WS in the future.

overall_design: Three stages of triple replicates (three independent inducing from one source of iPSC) from two samples were obtained (iPSC, induced neural crest cell (iNCC) and induced melanocyte from the WT and the patient-specific MITF+/- iPSC) for extracting total RNA for further analysis.

first: Jian

last: Song


title: Hepatic Transcriptomic Responses to Ethinylestradiol in Two Life Stages of Japanese Quail [embryonic day 9 RNA-seq]

status: Public on Oct 01 2022

city: Sainte-Anne-de-bellevue

first: Yeon-Seon

last: Jeon

state: Quebec

address: 21111 Lakeshore

department: Natural Resource Sciences

institute: McGill University

summary: Chemical risk assessment for avian species typically depends on information from toxicity tests performed in adult birds. Early-life stage (ELS) toxicity tests have been proposed as an attractive alternative, but incorporation of these data into existing frameworks will require knowledge about the similarities/differences between ELS and adult responses. The present study uses transcriptomics to assess hepatic gene expression in ELS and adult Japanese quail following exposure to ethinylestradiol (EE2). ELS quail were dosed with 0, 3.33, and 33.3 µg EE2/g egg via air cell injection prior to incubation. Adult quail were fed a single dose of EE2 at 0, 0.5, and 5 mg/kg body weight by gavage. Liver tissue was collected from 5-6 individuals per dose group at mid-incubation for ELS quail, and 4 days after dosing for adult birds. A total of 283 and 111 differentially expressed genes (DEGs) were detected in ELS and adult quail, respectively, 16 of which were shared across life stages. Shared DEGs included estrogenic biomarkers such as vitellogenin genes and Apovitellenin-1. For the dose groups that resulted in the highest number of DEGs (ELS [3.3 µg/g]; adult [5 mg/kg]), 21 and 35 KEGG pathways were enriched, respectively. Ten of these pathways were shared between life stages, including pathways involved with signaling molecules and interaction, and endocrine system. Taken together, our results suggest conserved mechanisms of action following estrogenic exposure across two life stages, with evidence from differentially expressed genes and enriched pathways. This study contributes to the development and evaluation of toxicogenomic and ELS approaches as alternative toxicity testing methods and supports the use of the ELS test for screening estrogenic chemicals.

overall_design: Liver mRNA profile of embryonic day 9 Japanese quail following single exposure to either solvent or ethinylestradiol

first: Doug

last: Crump

first: Emily

last: Boulanger

first: Othman

last: Soufan

first: Bradley

last: Park

first: Niladri

last: Basu

first: Markus

last: Hecker

first: Jeff

last: Xia

first: Jessica

last: Head


title: An NF-κB-responsive long noncoding RNA, PINT, regulates inflammatory gene transcription by scaffolding p65 and EZH2

city: Wuhan

first: RUI

last: Zhou

address: Donghu Road 185

institute: Wuhan University

summary: Long non-coding RNAs (lncRNAs) are central regulators of the inflammatory response and play an important role in inflammatory diseases. PINT has been reported to be involved in tissue development and tumorigenesis. However, potential functions of PINT in the innate immune system are largely unknown. Here, we report a specific role for PINT in activating inflammatory gene transcription. The expression of PINT is primarily dependent on the NF-κB signaling pathway in macrophages and intestinal epithelial cells. Functionally, PINT selectively promotes the expression of inflammatory genes, including TNF-α, in basal and LPS-stimulated cells. Mechanistically, PINT acts as a modular scaffold of p65 and EZH2 to coordinate their localization and specify their binding to the target genes. Further, a high expression of PINT is detected in the intestinal tissue from patients with Inflammatory Bowel Disease (IBD). Together, these findings demonstrate that PINT acts as an activator of inflammatory responses, highlighting the importance of this lncRNA in inflammatory diseases as a potential therapeutic target.

overall_design: RNAseq was performed in human intestinal epithelial SW480 cells with stable knockdown of PINT or EZH2 or wide-type following exposing to PBS or LPS (1 μg/ml) for 4h. Wide-type SW480 exposing to PBS for 4h acted as the control group.

first: Rui

first: Mengling

last: Ye


title: Single-cell Transcriptomics Reveal Different Maturation Stages and Sublineages Commitment of Human Thymic Invariant Natural Killer T Cells

status: Public on Sep 30 2022

city: Stanford

first: Kristina

last: Maas-Bauer

state: California

address: 269 Campus Drive

department: Blood and Marrow Transplantation

institute: Stanford University

summary: Invariant natural killer T (iNKT) cells are a rare but heterogenous T-cell subset with potent cytotoxic and immunomodulatory properties. During thymic development, murine iNKT cells go through different maturation stages and differentiate into distinct sublineages, namely iNKT1, iNKT2, and iNKT17 cells. Recent reports indicate that iNKT2 cells display immature properties and also give rise to other subsets, whereas iNKT1 cells seem to be terminally differentiated. Whether human iNKT cells follow a similar differentiation model is still unknown. To define the maturation stages and to assess the sublineage commitment of human iNKT cells during thymic development, in the present study we performed single-cell RNA sequencing analysis on human iNKT cells isolated from thymocytes. We show that human iNKT cells displayed heterogeneity and our unsupervised analysis identified two clusters: a first cluster expressed an immature profile with high expression of genes that are important for iNKT cell development and proliferation, whereas a second cluster displayed a mature, terminally differentiated profile. Trajectory analysis suggested an ontological relationship between the two clusters. Evaluation of the expression of sublineage-defining gene sets revealed that the first cluster contained mainly cells with an iNKT2 signature, whereas the more differentiated one contained cells that resembled murine iNKT1 cells. Our data point to the existence of different maturation stages of human thymic iNKT cells and provide evidence for sublineage commitment of iNKT cells in the human thymus.

overall_design: 3 samples with iNKT cells from human thymus of children between 5 days and 13 months of age.

first: Swati

last: Acharya

first: Jeanette

last: Baker

first: David

last: Lewis

first: Federico

last: Simonetta

first: Robert

last: Negrin


title: Integrative CUT&Tag/RNA-Seq analysis of histone variant macroH2A1-dependent orchestration of human iPSCs reprogramming

status: Public on Sep 27 2022

city: S. Giovanni Rotondo (FG)

first: Tommaso

last: Mazza

address: Viale Cappuccini, 1

department: Bioinformatics

country: Italy

institute: IRCCS Casa Sollievo della Sofferenza

summary: Human-induced pluripotent stem cells (iPSCs) can be derived from adult stem cells by forced expression of defined transcription factors. This paves the way for autologous iPSC-derived therapies, which, however, are not yet considered safe. Moreover, reprogramming of somatic cells into iPSCs is an inefficient process, in the range of 0.1%–1%. The epigenetic mechanisms implicated in iPSCs reprogramming are not well understood. The substitution of canonical histone H2A with macroH2A1 histone variant exon-spliced isoforms (macroH2A1.1 and macroH2A1.2) appears as an emerging regulator of iPSCs identity. In particular, we have previously shown that overexpression of macroH2A1.1 led to a more efficient iPSCs reprogramming, by not fully defined mechanisms. Cleavage under targets and tagmentation (CUT&Tag) is a recent methodology used for robust epigenomic profiling of a limited amount of cells. Here, we employed human umbilical vein endothelial cells (HUVEC) during their reprogramming into iPSC over-expressing tagged macroH2A1.1 or macroH2A1.2, to perform for the first time an integrative CUT&Tag/RNA-Seq analysis of histone variant macroH2A1-dependent orchestration of iPSCs reprogramming. Our findings reveal a higher and more ubiquitous genome occupancy and number of differentially expressed genes orchestrated by macroH2A1.1 in HUVEC undergoing reprogramming, compared to macroH2A1.2, which involved pervasive functions related to the three embryonic germ layers and increased overlapping with CTCF, FOS, GATA2, and POLR2A transcription factor binding sites. In particular, all predicted macroH2A1.1 activating pathways were related to ectoderm/neural processes. As macroH2A1 isoforms have been previously associated with  pathologies of the nervous system, our findings may provide relevant molecular insights for modeling neurodegenerative diseases using iPSCs.

overall_design:
In vitro study
Here, we employed human umbilical vein endothelial cells (HUVEC) during their reprogramming into iPSC over-expressing tagged macroH2A1.1 or macroH2A1.2, to perform CUT&Tag.

first: Manlio

last: Vinciguerra


title: RNAseq on APAP, APAP+MSC, APAP+HDF at 24h

status: Public on Sep 16 2022

city: Kansas City

last: Umbaugh

email: dumbaug@gmail.com, hjaeschke@kumc.edu

state: KS

address: 3901 Rainbow Blvd

institute: University of Kansas Medical Center

summary: RNAseq of liver homogenate 24h after APAP (300mg/kg) exposure followed by either MSC or HDF at 90 min. MSCs, not HDFs, ameliorate APAP-induced liver injury.

overall_design: mRNA expression profiles of whole liver homogenates in APAP or APAP+MSC or APAP+ HDF. APAP was administered i.p at 300 mg/kg and MSCs or HDFs were administered i.v., 500,000 cells at 90 min post APAP.

first: Hartmut

last: Jaeschke

first: Anup

last: Ramachandran


title: Estrogen-induced cell cycle arrest in patient-derived xenograft (PDX) modal for breast cancer

status: Public on Sep 05 2022

city: Duarte

first: Shiuan

last: Chen

state: CA

address: 1500 E Duarte Rd

department: Cancer Biology-BRI

institute: City of Hope National Medical Center

summary: We performed RNA sequencing analysis to see gene expression changes after estrogen treatment for an aromatase inhibitor-resistant PDX model (named GS3).

overall_design:
Following the treatments that lasted 5 days/10 days/53 days of estradiol (E2) (1mg) or placebo, GS3-PDX tumors were harvested and total RNA was extracted. Each treatment group included two samples.

A second set of samples included the following treatments: placebo, 4 weeks of estradiol (E2) (1 mg), progesterone (10 mg), both estradiol and progesterone and an interval treatement composed of 28 days of E2 (1mg) following by 28 days no treatment followed by another 28 days of E2 (1mg), repeated 3 times.

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

first: Hitomi

last: Mori


title: TBX20 Consolidates Cardiac Reprogramming Factors to Enhance Contractility and Energy Metabolism in Human Induced Cardiomyocytes [CUT&RUN]

status: Public on Sep 14 2022

city: Birmingham

first: Changde

last: Cheng

state: Alabama

address: 1824 6th Ave S, WTI 510G

department: Department of Medicine - Hematology & Oncology

institute: The University of Alabama at Birmingham

summary: Background: Direct cardiac reprogramming of fibroblasts into cardiomyocytes has emerged as one of the promising strategies to remuscularize the injured myocardium. Yet, it is still insufficient to generate functional induced cardiomyocytes (iCMs) from human fibroblasts using conventional reprogramming cocktails, such as our previously published combination consisting of MEF2C, GATA4, TBX5 and microRNA miR-133 (MGT133).   Results: To discover potential missing factors for human direct reprogramming, we performed transcriptomic comparison between human iCMs and functional cardiomyocytes (CMs). We identified T-box transcription factor TBX20 as the top CM gene that is unable to be activated by MGT133. TBX20 is required for normal heart development and cardiac function in adult CMs but its role on cardiac reprogramming remains undefined. Here, we found that transduction of MGT133+TBX20 in human cardiac fibroblasts resulted in enhanced reprogramming featured with significantly activated contractility gene programs and signatures more similar to ventricular CMs. Human iCMs produced with MGT133+TBX20 more frequently demonstrated beating and calcium oscillation in co-culture with pluripotent stem cell derived CMs. More mitochondria and higher mitochondrial respiration were also detected in iCMs after TBX20 overexpression. Mechanistically, comprehensive transcriptomic, chromatin occupancy and epigenomic integration revealed that TBX20 localized to the cis-regulatory enhancers of under-expressed cardiac genes, such as MYBPC3, MYH7 and MYL4, to activate gene expression via strengthening the occupancy and co-occupancy of transcription factors. Furthermore, we identified TBX20-regulated enhancers and confirmed the synergistic effect of MGT and TBX20 on enhancer activation.   Conclusions: TBX20 promotes cardiac cell fate conversion via direct activating cardiac enhancers. Human iCMs generated with TBX20 showed enhanced cardiac function in terms of contractility and mitochondrial respiration.

overall_design: Epigenomic profiling of H3K4me1, H3K27ac and H3K27me3 in human induced cardiomyocytes by CUT&RUN sequencing. Biological duplicates were applied for each group.

first: Yawen

last: Tang

first: Sajesan

last: Aryal

last: Lu

first: Yang


title: TBX20 Consolidates Cardiac Reprogramming Factors to Enhance Contractility and Energy Metabolism in Human Induced Cardiomyocytes


title: The thiolation modification of tRNA is essential for plant immunity

status: Public on Aug 31 2022

first: xueao

last: zheng

state: Not US or Canada

address: Shizishan

institute: Huazhong agricultural university

summary: Plants have evolved sophisticated mechanisms to regulate gene expression to activate immune responses against pathogen infections. However, how the translation system contributes to plant immunity is largely unknown. The evolutionarily conserved thiolation modification of tRNA ensures efficient decoding during translation. Here we show that tRNA thiolation is required for plant immunity in Arabidopsis. The Arabidopsis cgb mutant is hyper-susceptible to the pathogen Pseudomonas syringae. CGB encodes ROL5, a homolog of yeast NCS6 required for tRNA thiolation. ROL5 physically interacts with CTU2, a homolog of yeast NCS2. Mutations in either ROL5 or CTU2 result in loss of tRNA thiolation. Further analyses reveal that tRNA thiolation is required for both transcriptional reprogramming and translational reprogramming during immune responses. The translation efficiency of immune-related proteins reduces when tRNA thiolation is absent. Our study not only uncovers a new biological function of tRNA thiolation but also reveals a new mechanism for plant immunity.

overall_design: We performed the mRNA profiles of  21-day old leaf tissues from tRNA modification mcm5s2U mutant (cgb) and the complementation line (COM) before or after the pathogen infection.

first: Xueao

last: Zheng

first: Chong

last: Wu

first: Shunping

last: Yan


title: Specific PBAF complex (dcPBAF) containing PHF10 lacking DPF maintains transcription in differentiated neurons

status: Public on Aug 30 2022

city: Moscow

first: Natalia

last: Klimenko

address: 34/5 Vavilova Street

country: Russia

institute: Institute of Gene Biology (IGB) of the Russian Academy of Sciences

summary: The PBAF chromatin-remodeling complex is essential for transcription in mammalian cells. We found that PHF10 specific subunit of PBAF lacking C-terminal DPF is expressed in neurons of adult mouse and human brain. We purified the neuronal PBAF of newborn and adult mouse brain using antibodies against PHF10. We found that specific PBAF, designated as dcPBAF, is dominant in mature neurons. dcPBAF is associated with TAF4, TAF5, TAF6, TAF9 subunits of TFIID, does not contain BRD7 and is characterized by the presence of PHF10 isoform lacking N-terminal amino acids and DPF. The dcPBAF binds promoters of actively transcribed housekeeping and neuron specific genes in terminally differentiated neurons of adult mouse. It maintains high transcription level of neuron specific genes in differentiated human neuronal cell. These data indicate some specific features of PBAF mediated chromatin in terminally differentiated mammalian cells.

overall_design: ChIP-seq signal of the PHF10 protein occupancy in cerebellum of P65 (postnatal 56 days) mouse.

first: S

last: Soshnikova

first: N


title: Transcriptional response to vanoxerine in vivo treatments in MC38 colorectal tumors

status: Public on Jul 13 2022

city: Ottawa

first: Yannick

middle: D.

last: Benoit

state: Ontario

address: 451 Smyth road

institute: University of Ottawa

summary: Murine colorectal cancer MC38 cells were injected in the flank of C57BL/6 mice to form tumor grafts over 7 days. Tumor-bearing mice were treated with daily injections of vanoxerine (25mg/kg) or vehichle control (saline) over 10 consecutive days. Tumors were excised and RNA sequencing profiling was performed on both experimental condition.

overall_design: Whole transcriptome profiling

first: Christopher

middle: J

last: Bergin

middle: D


title: Gene expression profile at single cell level of breast cancer patient-derived xenograft models

status: Public on Aug 15 2022

city: San Francisco

first: Juliane

last: Winkler

address: 513 Parnassus Avenue

department: Department of Cell and Tissue Biology

institute: University of California, San Francisco

summary: We profiled the tumor heterogeneity of individual primary tumor of breast cancer using a set of patient derived xenograft models with different metastatic potentials. This data set gives insights into the transcriptional tumor heterogeneity and how these are changing in regard to varying metastatic phenotypes.

overall_design: Live human tumor cells from breast tumor and matched metastatic lung tissues of patient-derived xenograft models were isolated using Fluorescence-activated cell sorting (FACS) based on the human specific CD298 antibody and pooled, captured and processed in microfluidics droplets via 10x Genomics using MULTI-Seq protocol.

first: Angela

last: Pisco

first: Spyros

last: Darmanis

first: Andrei

last: Goga


title: Expression profile analysis of circular RNA in multiple myeloma versus iron-deficiency anemia

status: Public on Jul 22 2022

city: xi'an

first: aili

last: He

address: NO.157 Xiwu Road, Lianhu District

department: Department of Hematology

institute: the Second Affiliated Hospital of Xi'an Jiaotong University

summary: To determine whether circRNAs are involved in multiple myeloma (MM), we analyzed the expression profile of circRNAs and mRNAs in MM.

overall_design: In the study presented here, 5 pairs of MM patients and iron deficiency anemia (IDA) controls were screening by microarray.

first: A

first: Y

last: Feng

last: Shen

first: H

last: Chen

first: X

last: Wang