title: Murine Model of Familial Hemophagocytic Lymphohistiocytosis Hepatitis is Mediated by IFN-γ in a Predominantly Hepatic-Intrinsic Manner

status: Public on Jun 02 2022

city: Philadelphia

first: Tamir

last: Diamond

state: No

address: 3401 Civic Center Blvd

institute: Children's Hospital of Philadelphia/University of Pennsylvania

summary: Interferon gamma (IFN-γ) is the main cytokine driving Familial Hemophagocytic Lymphohistiocytosis (FHL) organ dysfunction. Hepatocytes are known to have IFN-γ receptor (IFN-γ-R). Blockade of IFN-γ pathway ameliorates FHL hepatitis, in animal models and in humans. However, whether IFN-γ induced hepatitis in FHL is a lymphocyte or liver intrinsic response to the cytokine has yet to be elucidated. We report that IFN-γ-mediated hepatic injury in the murine model of FHL is caused by direct effect on the liver and has a necessary role in recruitment of the inflammatory mediators of injury in FHL: inflammatory monocytes and CD8+ effector memory T lymphocytes (CD8+ CD44hi CD62Llo) (Tem).

overall_design: Fresh mouse liver segments were stored in RNAlater® solution (Thermo Fisher Scientific) at -20°C and thawed for RNA extraction at later date. RNA extraction was performed in livers of 4 mice from the BM IFNgR+/+ and host IFNgR -/- group and 4 mice from the BM IFNgR+/+ and host IFNgR+/+ group using the Qiagen RNeasy Mini Kit protocol from approximately 30mg of homogenized tissue according to manufacturer instructions.

first: Thomas

last: Burn

first: Mailyn

last: Nishiguchi

last: Minichino

first: Julie

last: Chase

first: Niansheng

last: Chu

first: Portia

last: Kreiger

first: Edward

last: Behrens


title: Hippocampus RNA-sequencing of long-term treatment with Q808

status: Public on May 08 2022

city: Changchun

first: Wei

last: Li

state: Jilin

address: No 155 Chuangju Street

country: China

institute: Jilin Provincial Academy of Traditional Chinese Medicine

type: Expression profiling by high throughput sequencing

summary: Antiepileptic drugs (AEDs) are the mainstay treatment in epilepsy and epilepsy treatment usually requires many years and can be lifelong. Thus, evaluating the long-term effect of AEDs is important. Q808 is an innovative antiepileptic chemical under research and development. It exerts effective antiepileptic effect against various epilepsy models. Exploring the gene transcriptomic profile of long-term treatment of Q808 is necessary. In the present study, hippocampus RNA-sequencing was performed to reveal the transcriptome profile of rats after treatment of gavage of Q808 for 28 day.

overall_design: Q808 group is the heallthy rats treatment with Q808 for 28 days

first: Xiang

first: Tianli

last: Chen


title: An embryonic stage 17 single cell atlas from Drosophila melanogaster

status: Public on Jul 22 2022

city: Eugene

first: Austin

last: Seroka

state: Oregon

address: 1440 Franklin Blvd

department: Institute of Neuroscience

country: USA

institute: University of Oregon

summary: A major driver of neural circuit complexity is cellular heterogeneity. We sought to profile all of the neural cell types in the Drosophila embryo at stage 17, a period of rapid synapse and circuit formation in the central nervous system. To do so, we performed whole embryo dissociations of Drosophila embryos followed by single cell RNA sequencing. We then computationally segregated neural cell types based on known gene expression for all neurons (elav) and glia (repo). We hope that this dataset will serve as a community resource for other researchers interested in the molecular determinants of circuit complexity.

overall_design: We dissociated a 50-100 µl pool of surface-sterilized Drosophila embryos (stage 17, 17-18.5 hours after egg laying) in C+G medium using a dounce homogenizer. Cells were then washed and filtered with 40 µm cell strainer. The concentration of viable cells was quantified with Trypan blue using a TC20 automated cell counter. Samples with a minimum viability of 80% were then diluted to 1000 cells/ µl in 1X PBS supplemented with .04% BSA and sequenced using the 10X NextGem v3.1 single cell platform.

first: Sarah

middle: D

last: Ackerman


title: Embryo-scale reverse genetics at single-cell resolution

status: Public on Aug 08 2022

city: Seattle

first: Lauren

last: Saunders

state: WA

address: 3720 15th Ave NE

department: Genome Sciences

institute: University of Washington

summary: The maturation of single cell transcriptomic technologies has facilitated the generation of comprehensive cellular atlases from whole embryos. A majority of this data, however, has been collected from wild type embryos without an appreciation for latent variation present in development. Here we present single cell transcriptomic data from 1812 individually resolved developing zebrafish embryos, encompassing 19 time points, 23 genetic perturbations, and totaling 3.2M cells. The high degree of replication in our study (8 or more embryos per condition) allows us to estimate the variance in cell type abundance organism-wide and to detect perturbation-dependent deviance in cell type composition relative to wild type embryos. Our approach is sensitive to rare cell types, resolving developmental trajectories and genetic dependencies in the cranial ganglia neurons, a cell population that comprises less than 1% of the embryo. Additionally, time-series profiling of individual mutants identified a group of brachyury-independent cells with strikingly similar transcriptomes to notochord sheath cells, leading to new hypotheses about the origins of the skull. We anticipate that standardized collection of high-resolution, organism-scale single cell data from large numbers of individual embryos will enable mapping the genetic dependencies of zebrafish cell types, while also addressing long-standing challenges in developmental genetics, including the cellular and transcriptional plasticity underlying phenotypic diversity across individuals.

overall_design:
Whole zebrafish embryos were collected across multiple timepoints or in response to genetic perturbations with sci-RNA-seq3.

Please note that the following processed data files have been updated on Mar 7, 2023:
zperturb_full_cell_metadata.csv
zperturb_full_gene_metadata.csv
zperturb_full_raw_counts.RDS

first: Cole

last: Trapnell

middle: M

first: Sanjay

middle: R

last: Srivatsan


title: Identification of early neurodegenerative pathways in progressive multiple sclerosis

status: Public on May 12 2022

city: Oxford

first: Lars

last: Fugger

address: The MRC Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, Headley Way

department: Nuffield Department of Clinical Neurosciences

country: United Kingdom

institute: University of Oxford

summary: Progressive multiple sclerosis (MS) is characterized by unrelenting neurodegeneration, which causes cumulative disability and is refractory to current treatments. Drug development to prevent disease progression is an urgent clinical need yet is constrained by an incomplete understanding of its complex pathogenesis. Using spatial transcriptomics and proteomics on fresh-frozen human MS brain tissue, we identified multicellular mechanisms of progressive MS pathogenesis and traced their origin in relation to spatially distributed stages of neurodegeneration. By resolving ligand–receptor interactions in local microenvironments we discovered defunct trophic and anti-inflammatory intercellular communications within areas of early neuronal decline. Proteins associated with neuronal damage in patient samples showed mechanistic concordance with published in vivo knockdown and CNS disease models, supporting their causal role and value as potential therapeutic targets for progressive MS. Our findings provide a new framework for drug development strategies, rooted in an understanding of the complex cellular and signaling dynamics in human diseased tissue, that facilitate this debilitating disease.

overall_design:
Spatial transcriptomics of fresh frozen cortical brain tissue from 32 MS sections and 5 control sections.

NOTE:

The following files were updated (on Aug 23, 2022) to the most recent version that exactly matches the data needed to reproduce the study's findings:

GSE174647_ST_counts.tar.gz
GSE174647_ST_spatial_coord_annotations_spots.csv.gz

The following files have been added to the records (on Nov 24, 2023):

GSE174647_code.tar.gz: This code assists users in working with the data and ensures full reproducibility of our original analysis.
GSE174647_code_accompanying_data.tar.gz: This includes processed data accompanying the code, ensuring that each script can run independently without needing to execute the entire analysis.
GSE174647_tissue_block_identification.pdf: This document offers a detailed explanation of the nomenclature used for identifying each tissue block in the brain, complete with images of reference brain sections for enhanced understanding.

The following files were updated (on Nov 24, 2023) for compatibility with the code:

GSE174647_ST_spatial_coord_annotations_spots.csv.gz
GSE174647_ST_tissue_images.tar.gz

first: Max

last: Kaufmann

first: Anna-Lena

last: Schaupp

first: Rosa

last: Sun

first: Fabian

last: Coscia

first: Calliope

middle: A

last: Dendrou

first: Adrian

last: Cortes

first: Gurman

last: Kaur

first: Hayley

middle: G

last: Evans

first: Annelie

last: Molbrink

first: José

middle: F

last: Navarro

first: Jana

middle: K

last: Sonner

first: Christina

last: Mayer

first: Gabriele

middle: C

last: DeLuca

first: Joakim

last: Lundeberg

first: Paul

last: Matthews

first: Kathrine

middle: E

last: Attfield

first: Manuel

last: Friese

first: Matthias

last: Mann


title: Single-cell RNA sequencing of early, medium, and late glioblastoma flow sorted by CD45

status: Public on Apr 06 2022

city: Boston

first: Jonathan

last: Dreyfuss

state: MA

address: 1 Joslin Pl

department: Bioinformatics & Biostatistics Core

institute: Joslin Diabetes Center

summary: Genetically engineered mouse glioblastoma tumors were flow cytometry sorted into CD45 positive and CD45 negative populations followed by single cell RNA seq.

overall_design:
Three libraries were analyzed. Each library contains multiple samples from 3 tumors.

The Seurat object available at the foot of the SuperSeries GSE195848 record integrates scRNA-seq data from both GSE196175 & GSE175851.

first: Al

last: Charest


title: Multi-omic analysis defines the first microRNA atlas across all small intestinal epithelial lineages and reveals microRNA markers of almost all major cell types

status: Public on Mar 29 2022

city: Ithica

first: Praveen

last: Sethupathy

state: NY

address: Cornell University College of Veterinary Medicine, Box 17

institute: Cornell University

type: Non-coding RNA profiling by high throughput sequencing

summary: MicroRNA-mediated regulation is critical for the proper development and function of the small intestinal epithelium.  However, it is not yet known which microRNAs are expressed in which cell types of the small intestinal epithelium.  To bridge this important knowledge gap, in this study we performed a comprehensive profiling analysis of microRNAs in all major epithelial cell types of the mouse small intestine.  We first used flow cytometry and fluorescence activated cell sorting with multiple different reporter mouse models to isolate intestinal stem cells (ISCs), enterocytes, goblet cells, Paneth cells, enteroendocrine cells (EECs), tuft cells and secretory progenitor cells.  We then subjected these cell populations to small RNA-seq.  We identified highly enriched microRNA markers for every major small intestinal epithelial cell type except goblet cells. Interestingly, one of the secretory progenitor cell enriched microRNAs, miR-672, is deleted in hominin species.  Several of these lineage-enriched microRNAs (LEMs) were observed to be embedded in annotated host genes.  We used chromatin run-on sequencing (ChRO-seq) to determine which of these LEMs are likely co-transcribed with their host genes.  We then employed single cell RNA-sequencing (scRNA-seq) in order to define the cell type specificity of the host genes, and by proxy, the LEMs as well.  Finally, using four additional in vivo models, we validated that miR-375 is highly enriched in secretory progenitor cells that give rise to enteroendocrine and tuft cells and that miR-152 is a Paneth cell-specific microRNA.

overall_design: Small RNAseq of sorted populations of the small intestiinal epithelium cell lineages.

first: Matt

last: Kanke


title: Gene expression profile suggests different mechanisms underlying sporadic and familial mesial temporal lobe epilepsy

status: Public on May 09 2022

city: Campinas

first: Estela

middle: Maria

last: Bruxel

state: São Paulo

address: Tessália Vieira de Camargo, 126

department: Translational Medicine

country: Brazil

institute: UNICAMP

type:
Expression profiling by array
Third-party reanalysis

summary: Most patients with pharmacoresistant mesial temporal lobe epilepsy (MTLE) have hippocampal sclerosis on the postoperative histopathological examination. Although most patients with MTLE do not refer to a family history of the disease, familial forms of MTLE have been reported. We studied surgical specimens from patients with MTLE who had epilepsy surgery for medically intractable seizures. We assessed and compared messenger RNA (mRNA) expression profiles of the tissue lesion found in patients with familial MTLE (n = 3) and sporadic MTLE (n = 5). In addition, we used data from control hippocampi obtained from a public database (n = 7). We obtained expression profiles using the Human Genome U133 Plus 2.0 (Affymetrix) microarray platform. Overall, the molecular profile identified in familial MTLE was distinct from that found in sporadic MTLE. In the tissue of patients with familial MTLE, we found an over-representation of the biological pathways related to protein response, mRNA processing, and synaptic plasticity and function. In sporadic MTLE, the gene expression profile suggests that the inflammatory response is highly activated. We also found enrichment of gene sets involved in inflammatory cytokines and mediators and chemokine receptor pathways in both groups. However, in sporadic MTLE, we also found enrichment of epidermal growth factor signaling, prostaglandin synthesis and regulation, and microglia pathogen phagocytosis pathways. Furthermore, based on the gene expression signatures, we identified different potential compounds to treat patients with familial and sporadic MTLE. To our knowledge, this is the first study assessing the mRNA profile in surgical tissue obtained from patients with familial MTLE and comparing it with sporadic MTLE. Our results clearly show that, despite phenotypic similarities, both forms of MTLE present distinct molecular signatures, thus suggesting different underlying molecular mechanisms that may require distinct therapeutic approaches.

overall_design: We assessed and compared messenger RNA (mRNA) expression profiles of the tissue lesion found in patients with familial MTLE (n = 3) and sporadic MTLE (n = 5). In addition, we used data from control hippocampi obtained from from the GSE11882 dataset (n = 7). We obtained expression profiles using the Human Genome U133 Plus 2.0 (Affymetrix) microarray platform.

first: Claudia

middle: V

last: Maurer-Morelli

first: Jaira

last: de Vasconcellos

first: Iscia

last: Lopes-Cendes


title: Single-cell RNA sequencing of normal, early glioblastoma, and late glioblastoma flow sorted by CD45

summary: Genetically engineered mouse glioblastoma tumors and normal cells at different stages were flow cytometry sorted into CD45 positive and CD45 negative populations followed by single cell RNA seq.

overall_design:
Two replicates of normal, early tumor, and late tumor each flow sorted into CD45 positive and negative.

The Seurat object available at the foot of the SuperSeries GSE195848 record integrates scRNA-seq data from both GSE196175 & GSE175851.


title: Single-Cell RNA sequencing reveals evolution of immune landscape during Glioblastoma progression.

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

overall_design:
Refer to individual Series

The Seurat object available at the foot of this record integrates scRNA-seq data from both GSE196175 & GSE175851.


title: Dynamics of mRNA fate during light stress and recovery: from transcription to stability and translation

status: Public on Jun 10 2022

first: Diep

last: Ganguly

state: PA

address: 433 S University Ave

department: Department of Biology

institute: University of Pennsylvania

summary: The stability of mRNA is an important determinant of its abundance and, consequently, protein production. There has been extensive research on the pathways governing mRNA stability and translation, however, it is unclear the extent to which these processes are modulated by environmental conditions. We previously modelled rapid recovery gene down-regulation (RRGD) following light stress in Arabidopsis thaliana (Arabidopsis) using mathematical calculations to account for transcription in order to predict half-lives and led to the hypothesis of recovery-specific transcript destabilisation. Here, we test this hypothesis by quantifying changes in transcription, mRNA stability, and translation in leaves of mature Arabidopsis undergoing light stress and recovery and investigate processes regulating transcript abundance and fate. Compared to juvenile plants from prior work, here we find that stability is altered for a range of transcripts that encode proteins involved in post-transcriptional processes in mature leaves. We also observe transcript destabilisation during light stress, followed by re-stabilisation upon recovery. Alongside this, we observe fast transcriptional shut-off in recovery that, when paired with transcript destabilisation, promotes rapid down-regulation of stress-induced genes. Translation was dynamic over the course of light stress and recovery, with substantial transcript-specific increases in polysome loading observed during late stress independently of total mRNA abundance. Taken together, we provide evidence for the combinatorial regulation of transcription, mRNA stability, and translation that occurs during light stress and recovery.

overall_design:
PolyA-enriched RNA-sequencing (mRNA-seq) was performed on Arabidopsis leaves infiltrated with cordycepin or mock [buffer only: 1 mM PIPES (pH 6.25), 1 mM sodium citrate, 1 mM KCl, 15 mM sucrose] harvested at 10, 20, 30, and 40 minutes post-infiltration under unstressed (US, 100 uE), high-light (HL, 1000 uE), and recovery conditions (Rec, 1000 ? 100 uE). The transcriptional inhibitor, cordycepin (3'-deoxyadenosine, Sigma-Aldrich), was syringe-infiltrated on the abaxial side of fully-expanded leaves (true leaves 4-6) of 21-day old plants. Individual leaves were infiltrated with 0.1 mL of incubation buffer [1 mM PIPES (pH 6.25), 1 mM sodium citrate, 1 mM KCl, 15 mM sucrose (Seeley et al. 1992)] with 0.6 mM cordycepin, or without (mock), using a 1 mL needleless syringe (Terumo). Excess liquid was removed from the leaf surface and plants were incubated for a minimum of 10 minutes before further treatment and harvesting. Light-stress was induced by increasing the light intensity to 10× growth irradiance (i.e. 1000 ?mol photons m-2 s -1), resulting in a ?hot high-light? treatment that effectively induces oxidative stress (Jung et al. 2013). For recovery, plants were returned to pre-stress light conditions. Each biological replicate was derived from leaves syringe-infiltrated, with either mock or cordycepin treatment, from the same plant at each time point per condition. Infiltrated leaves were excised, at the appropriate time point under each condition, from the base of the petiole and immediately flash-frozen, in a 2 mL safe-lock microcentrifuge tube (Eppendorf), using liquid nitrogen. Changes in polysome- and monosome-bound, and total-mRNAs were also profiled during the course of light stress and recovery. Plants were sampled at 0, 30, and 60 mins of high-light followed by 7.5, 15, and 30 mins of recovery (67.5, 75, 90 mins). Polysome profiling and mRNA-seq was performed in biological triplicate, consisting of multiple whole rosettes (250 mg) from independntly treated plants. Harvested tissue was snap frozen in liquid nitrogen and stored at -80 °C until ready for processing.

[Dec-16-2022] The 'time' information was corrected for GSM6048558-GSM6048627.

first: Aaron

middle: B

last: Smith

first: Marten

last: Moore

first: Barry

middle: J

last: Pogson

first: Peter

last: Crisp


title: Characterization of altered molecular mechanisms in Parkinson’s disease through cell type-resolved multi-omics analyses

status: Public on Mar 05 2023

city: Daejeon

first: Inkyung

last: Jung

address: KAIST, 291 Daehak-ro, Yuseong-gu

department: Biological Sciences

country: South Korea

institute: KAIST

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Parkinson’s disease (PD) is a progressive neurodegenerative disorder. However, cell type-dependent transcriptional regulatory programs responsible for PD pathogenesis remain elusive. Here, we establish transcriptomic and epigenomic landscapes of the substantia nigra (SN) by profiling 113,207 nuclei obtained from healthy controls and PD patients. Our multi-omic data integration provides cell type annotation of 128,724 cis-regulatory elements (cREs), and uncovers cell type-specific dysregulations in cREs with a strong transcriptional influence on genes implicated in PD. The establishment of high-resolution three-dimensional (3D) chromatin contact maps identifies 656 target genes of dysregulated cREs and genetic risk loci, uncovering both potential and known PD risk genes. Notably, these candidate genes exhibit modular gene expression patterns with unique molecular signatures in distinct cell types, highlighting altered molecular mechanisms in dopaminergic neurons and glial cells including oligodendrocytes and microglia. Together, our single-cell transcriptome and epigenome reveal cell type-specific disruption in transcriptional regulations related to PD.

overall_design:
Transcriptomic profiles of post-mortem brain SN tissues of PD and control donors.
Cis-regulatory Profiles for post-mortem brain SN tissues of PD and control donors based on H3K27ac ChIP-seq
3D chromatin contact profiles of post-mortem brain SN tissues for PD and control donors.
Profiling of single-nucleus transcriptome for post-mortem brain SN tissues of PD and control donors.
Profiling of single-nucleus chromatin accessibility for post-mortem brain SN tissues of PD and control donors.

first: Andrew

last: Lee

first: Changyoun

last: Kim

first: Seongwan

last: Park

first: Jaegeon

last: Joo

first: Baekgyu

last: Choi

first: Dongchan

last: Yang

first: Kyoungho

last: Jun

first: Junghyun

last: Eom

first: Seung-Jae

first: Sun-Ju

last: Chung

first: Robert

last: Rissman

first: Jongkyeong

first: Eliezer

last: Masliah


title: Transcriptome analysis on hematopoietic progenitor cell from control and blf-/-;drl 4KO zebrafish embryo by Next Generation Sequencing

status: Public on May 07 2022

city: Nanjing

first: Yuxi

state: Jiangsu

address: Room 402, 12 Xuefu Road, Nanjing University

department: Medical School

institute: Nanjing University

summary: Perturbations in embryonic hematopoiesis may result in illness that ranges from fetal anemia to leukemias. We found hematopoiesis in zebrafish embryo is synergistically regulated by blf and drl cluster genes. In order to determine how loss of blf and drl cluster genes changes the transcriptome landscape, hematopoietic progenitors were collected via FACS by utilizing RFP expression from blf gene trapping allele as lineage tracer and low input RNA-seq was applied.

overall_design: Hematopoietic progenitors from blf+/- and blf-/-;drl 4KO embryos were collected at 20 hpf via FACS by utilizing RFP expression from blf gene trapping allele as lineage tracer. The libraries were constructed with NEBNext® Single Cell/Low Input RNA Library Prep Kit for Illumina (NEB, Cat No.6420) and sequenced on Illumina Novaseq platform.

first: Xue

last: Zhang

first: Xin

last: Lou


title: A genome wide screening for effectors of chromatin accessibility

status: Public on May 01 2022

city: Kanazawa

first: Yusuke

last: Miyanari

address: Kakuma

department: NanoLSI

country: Japan

institute: Kanazawa University

sample_organism:
Homo sapiens
Mus musculus
synthetic construct

overall_design: Refer to individual Series


title: DNA methylation and transcriptomic signatures in patients with peanut- and multi-food allergy (Methylation)

status: Public on Feb 28 2022

city: Parkville

first: Boris

last: Novakovic

state: Victoria

address: Murdoch Children's Research Institute, Royal Children's Hospital, Flemington Road

country: Australia

institute: Murdoch Children's Research Institute

summary: This study profiled the epigenomes and transcriptomes of total nCD4T cell populations from adolescents with peanut-only (single food allergy- SA) and multi-food allergy (MA) at quiescence and following activation with anti-CD3/antiCD28

overall_design: Genome-wide DNA methylation profiles of total nCD4T cell populations isolated using flow cytometry, and cultured in RPMI alone or RPMI+ anti-CD3/CD28 for 72 hours from single-food allergic, multi-food allergic, and non-allergic adolescents.

first: Melanie

last: Neeland

first: Samira

last: Imran

first: Kirsten

last: Perrett

first: Richard

last: Saffery


title: Transcriptome-wide m6A methylome of endometrioid ovarian cancer and ovarian endometriosis

status: Public on Feb 18 2022

city: hangzhou

first: Li

address: banshan east road

institute: zhejiang cancer hospital

type: Methylation profiling by high throughput sequencing

summary: Emerging studies have revealed that N6-methyladenosine modification is involved in the development of various cancers. However, the m6A modification pattern of endometrioid ovarian cancer (EOC) has not been demonstrated. In the present study,  high-throughput sequencing combined with methylated RNA immunoprecipitation (MeRIP-seq) and RNA sequencing were used to obtain the transcriptome-wide m6A modifications of endometrioid ovarian cancer for the first time.

overall_design: Detection of transcriptome-wide m6A modifications of endometrioid ovarian cancer and ovarian endometriosis

first: Aijun

last: Yu

first: Jiejie

last: Chen


title: NPM1c hijacks the active trancription in leukemia development [BRU-Seq]

status: Public on Feb 27 2022

city: Houston

first: Xiaotian

state: TX

address: 6431 Fannin St

department: Biochemistry and Molecular Biology

institute: The University of Texas Health Science Center at Houston

summary: Nucleophosmin (NPM1) is a ubiquitously expressed nucleolar protein with a wide range of functions including ribosome biogenesis, mRNA processing, and maintenance of genomic stability1-4. In acute myeloid leukemia (AML), the terminal exon of NPM1 is often mutated (~30% of adult AMLs), resulting in the change of the nucleolar localization signal into a nuclear export signal and a shift of the protein to the cytoplasm (NPM1c)2,3,5. AMLs carrying this mutation have aberrant expression of the HOXA genes, whose overexpression leads to leukemogenic transformation6-8. Recently, it was shown that depletion or re-localization of the NPM1c protein into the nucleus causes downregulation of the HOXA genes, leading to the speculation that NPM1c directly regulates their transcription9-11. Here, we show that NPM1c binds to a subset of active gene promoters marked with high levels of H3K27ac in NPM1c leukemia cell lines and primary leukemia blasts, including well-known leukemia-driving genes such as posterior HOXA, HOXB, and MEIS1/PBX3 genes as well as novel targets IRX5 and NKX2-3. The binding of NPM1c on chromatin sustains active transcription of key target genes by maintaining high local-concentration of transcriptional complexes, including the Super Elongation Complex (SEC) and Menin/MLL1. NPM1c also maintains the active chromatin landscape by inhibiting the activity of histone deacetylases (HDACs). Depletion of NPM1c causes histone deacetylation and the silencing of key leukemic genes, leading to cell differentiation and growth arrest. The export protein XPO1 plays a key role by tethering NPM1c onto chromatin. The combination of XPO1 inhibitors (e.g., Selinexor and Eltanexor) with the Menin inhibitor MI-3454 has a synergistic effect on inducing differentiation in both NPM1-mutated leukemia cell lines and PDX model. Together, these findings reveal the neomorphic function of NPM1c as transactivator for leukemic gene expression and open up potential avenues for therapeutic intervention.

overall_design: OCI-AML3 NPM1c degron2 cell line treated with DMSO, 25nM Selinexor, 500nM dTag-13 for 12hrs. Nascent RNA was labelled with Br-UTP for 30min. Bru-seq protocol was performed to check the alteration in the nascent transcription. We included the biological duplicates in each treatment group.


title: NKG2D-CAR memory T cells target pediatric T-cell acute lymphoblastic leukemia in vitro and in vivo but fail to eliminate leukemia initiating cells

status: Public on Mar 29 2023

city: Madrid

first: Carlos

last: Rodriguez Antolin

address: Paseo de la Castellana

department: Genetics

country: Spain

institute: Hospital La Paz Institute for Health Research

summary: Refractory/relapsed pediatric acute leukemia are still clinically challenging and new therapeutic strategies are needed. Interactions between Natural Killer Group 2D (NKG2D) receptor, expressed in cytotoxic immune cells, and its ligands (NKG2DL), that are upregulated in leukemic blasts, are important for anti-leukemia immunosurveillance. Nevertheless, leukemia cells may develop immunoescape strategies as NKG2DL shedding and/or downregulation. In this report, we analyzed the anti-leukemia activity of NKG2D chimeric antigen receptor (CAR) redirected memory (CD45RA-) T cells in vitro and in a murine model of T-cell acute lymphoblastic leukemia (T-ALL). We also explored how soluble NKG2DL affected NKG2D-CAR T cells´ cytotoxicity and the impact of NKG2D-CAR T cells on Jurkat cells. In vitro, we found NKG2D-CAR T cells targeted leukemia cells and showed resistance to the immunosuppressive effects exerted by soluble NKG2DL. In vivo, NKG2D-CAR T cells controlled T cell leukemia burden and increased survival of the treated mice but failed to cure the animals. After CAR T cell treatment, Jurkat cells upregulated genes related to proliferation, survival and stemness, and in vivo, they exhibited functional properties of leukemia initiating cells. The data here presented suggest, that, in combination with other therapeutic approaches, NKG2D-CAR T cells could be a novel treatment for pediatric T-ALL.

overall_design: To explore how CAR T cells affected gene expression, Jurkat GFP-luc cells were co-cultured with NKG2D-CAR T cells for 16h, sorted and used to perform transcriptome analysis by RNAseq. Sorted Jurkat-GFP cells that remained after overnight exposition to NKG2D-CAR T cells were washed in PBS and pelleted in RLT lysis buffer supplemented with 1:1000 β-mercaptoethanol. RNA isolation and sequencing was carried out as our group previously reported (Fernández A et al. Cancers, 2021). Reads from RNA-seq were analyzed to quantify genes through the RSEM (Li B et al. Bioinformatics, 2011)  with hg19 as reference for annotation. The differential expression was carried out with edgeR (Robinson MD et al. Bioinformatics, 2009) and the statistical cut-off point was set as FDR < 0.05 and logFC >2. Genes were filtered based on a minimum expression of one Counts Per Million (CPM) in more than one sample. Normalization was performed by the TMM method (trimmed mean of M-values)(Robinson MD et al. Genome Biol, 2010). Functional enrichment of differentially expressed genes was carried out in PFAM (Mistry J. et al, Nucleic Acids Res, 2021), GOTERM_BP_DIRECT (Ashburner M et al. Nat. Genet, 2000) and KEGG REACTOME (Kanehisa M, et al. Protein Sci, 2022)

first: Marta

last: Ibáñez

first: Adrián

last: Fernández

first: Adela

last: Escudero

first: Gloria

last: Esteso

first: Carmen

last: Campos-Silva

first: Miguel

last: Navarro-Aguadero

first: Alejandra

last: Leivas

first: Beatriz

last: Caracuel

last: Rodríguez-Antolín

last: Ortiz

first: Alfonso

last: Navarro-Zapata

last: Mestre-Durán

first: María

last: Balaguer-Pérez

first: Cristina

last: Ferreras

first: Joaquín

last: Martínez

first: Mar

last: Valés-Gómez

first: Antonio

last: Pérez-Martínez

first: Lucía


title: ATF6 is required for the survival of castration-resistant prostate cancer cells

status: Public on Mar 23 2022

city: Wuhan

first: Faming

last: Zhao

state: Hubei

address: Hangkong road 13

department: Tongji Medical College

institute: Huazhong University of Science and Technology

summary: To gain insight into the global ATF6 target gene profile in prostate cancer cells, we performed RNA-seq analysis in DU145 cells upon either ATF6 siRNA-mediated knockdown (siATF6) or Ceapin-A7-mediated ATF6α inhibition.

overall_design: Transcriptomics analysis upon two independent modalities to inhibit ATF6 expression in human DU145 cells

first: Tingting

last: Zhang

first: Xia

last: Sheng


title: Embryo as well as visceral yolk sac gene expression differences elicited by maternal diabetes in pregnancies of the NOD mouse

status: Public on May 04 2022

city: Baton Rouge

first: J. Michael

last: Salbaum

state: LA

address: 6400 Perkins Road

department: Regulation of Gene Expression

institute: Pennington Biomedical Research Center

summary: Maternal diabetes during early pregnancy can cause birth defects, notably of the developing heart and nervous system.  To recognize the gene expression differences that may be the basis for such birth defects, we performed RNA-Seq on mouse embryos of the Non-Obese Diabetic (NOD) strain.  Mice of that strain spontaneously develop type I diabetes.

overall_design: We dissected concepti from diabetic as well as normoglycemic pregnancies at 8.5 days of gestation.  Embryos were prepared by further dissection, somite pairs were counted, and RNA was extracted using the Trizol method.  Furthermore, the visceral yolk sac was also collected, and RNA was extracted with Trizol.  RNA sequencing was performed using the 3’QuantSeq method (Lexogen, Inc.) with the use of Unique Molecular Identifiers.  Alignment to the mouse reference genome was performed using STAR, UMI’s were accounted for using the collapse_UMI_Bam utility, and gene counts were extracted using HTSEQ.

first: J


title: A cell type specific error correction signal in posterior parietal cortex

status: Public on May 11 2023

first: Christopher

last: Harvey

address: 210 Longwood Ave

department: Neurobiology

institute: Harvard Medical School

summary: Neurons in posterior parietal cortex contribute to the execution of goal-directed navigation and other decision-making tasks. Although molecular studies have catalogued over fifty cortical cell types, it remains unknown what distinct functions they serve during goal-directed navigation. Here, we identified a molecularly defined subset of somatostatin (Sst) inhibitory neurons that, in mouse posterior parietal cortex, carry a novel cell type-specific error correction signal for navigation. We obtained repeatable experimental access to these cells using an adeno-associated virus (AAV) in which gene expression is driven by an enhancer that functions specifically in a subset of Sst cells. We found that during goal-directed navigation in a virtual environment, this subset of Sst neurons activates in a synchronous pattern that is distinct from the activity of surrounding neurons, including other Sst neurons. Using in vivo two-photon photostimulation and ex vivo paired patch clamp recordings, we show that nearby cells of this Sst subtype excite each other through gap junctions, revealing a self-excitation circuit motif that contributes to the synchronous activity of this cell type. Remarkably, these cells selectively activate as mice execute course corrections for deviations in their virtual heading during navigation toward a reward location, both for self- and experimentally-induced deviations. We propose that this subtype of Sst neurons provides a self-reinforcing and cell type-specific error-correction signal in posterior parietal cortex that may aid the execution and learning of accurate goal-directed navigation trajectories.

overall_design: Inhibitory neurons of two Gad2-Cre:Sun1-GFP mice were isolated by Fluorescence-activated cell sorting (FACS) according to the presence of GFP signal and analyzed using 10x scATACseq.

first: Jonathan

last: Green

first: Carissa

last: Bruno

first: Lisa

last: Traunmüller

first: Jennifer

last: Ding

first: Siniša

last: Hrvatin

first: Daniel

last: Wilson

first: Thomas

last: Khodadad

last: Samuels

first: Michael

last: Greenberg


title: CUT&Tag for GATA factors, H3K27ac and H3K27me3 in female XEN and TS cells

status: Public on Jan 26 2022

city: Berlin

first: Till

last: Schwämmle

state: Berlin

address: Ihnestrasse 63

department: Otto-Warburg-Laboratory

country: Germany

institute: Max Planck Institute for Molecular Genetics

summary: As the master regulator of X-chromosome inactivation (XCI), the Xist RNA is expressed nearly ubiquitously in female mice. Xist is only absent in the germ line and at the pluripotent state. Xist is generally assumed to be expressed “by default” in females, while being actively repressed in the few tissues where it is silent. Whether activating mechanisms also contribute remained largely unknown. Through a pooled CRISPR screen we identify the GATA family of transcription factors as potent direct activators of Xist. We describe a GATA-responsive regulatory element (RE79), located ~100 kb upstream of the Xist promoter. In cell lines derived from the two extraembryonic lineages, XEN and TS cells, where imprinted Xist expression is maintained, RE79 is bound by different sets of GATA factors expressed in those tissues. Here we use CUT&Tag on GATA factors to profile their involvement at the X inactivation center in XEN and TS cells.

overall_design: CUT&Tag targeting GATA2, GATA3, H3K27ac and H3K27me3  was performed in a female TS cell line. CUT&Tag targeting GATA4, GATA6, H3K27ac and H3K27me3  was performed in a female XEN cell line. The data was collected in replicates.

first: Liat

last: Ravid Lustig

first: Abhishek

middle: S

last: Kumar

first: Gemma

last: Noviello

first: Ilona

last: Dunkel

first: Raha

last: Weigert

first: Guido

last: Pacini

first: Rene

last: Buschow

first: Afrah

last: Ghauri

first: Maximilian

last: Stötzel

first: Alexander

last: Meissner

first: Edda

last: Schulz


title: SHED-derived exosomes ameliorate hyposalivation caused by Sjögren syndrome via Akt/GSK-3β/Slug-mediated ZO-1 expression.

status: Public on Apr 01 2022

city: BeiJing

first: Zhihao

last: Du

address: No.22, Zhongguancun South Avenue, Haidian District

institute: Peking University School and Hospital of Stomatology

summary: SHED-exos can ameliorate Sjögren syndrome-induced hyposalivation through miRNAs mediated Akt/Slug/ZO-1 expression.

overall_design: SHED-exos were administered to the submandibular glands of nonobese diabetic mice, an animal model of  Sjögren syndrome. The saliva flow rate was measured after pilocarpine intraperitoneal injection.Exosomal miRNAs were identified by microarray analysis.Akt/GSK-3β/Slug/ZO-1  expressions were examined by Western blot analysis.


title: A role for the GATA transcription factor family in X-chromosome inactivation as direct potent Xist activators

sample_organism:
Mus musculus
Synthetic plasmid

platform_organism:
Mus musculus
Synthetic plasmid


title: REST targets in the cortex of WT mice and Alzheimer’s disease 3xTg mice

status: Public on Jan 29 2022

first: Jae Joon

last: Choi

address: 77 Avenue Louis Pasteur

summary: We profiled REST targets in WT mice, as well as the Alzheimer’s disease 3xTg mouse model, to gain insight into the regulation of physiological pathways by REST, as well as the altered REST cistrome in Alzheimer’s disease.

overall_design: To gain insight into the regulation of physiological pathways by REST, as well as the altered REST cistrome in Alzheimer?s disease, we used a REST C-terminal antibody to profile the REST binding sites in 11-month-old WT and 3xTg mice. Four biological replicates, each comprised of n=4 frozen cortices from 3xTg mice (females, age 11 months) were processed for ChIP-seq (total n=16 3xTg cortices). Similarly, four biological replicates, each comprised of n=4 pooled frozen cortices from WT mice (females, age 11 months) were processed for ChIP-seq (total n=16 WT cortices). The frozen tissue was sent to Active Motif Services (Carlsbad, CA) to be processed for ChIP-Seq. In brief, the tissue was submersed in PBS + 1% formaldehyde, cut into small pieces and incubated at room temperature for 15 minutes. Fixation was stopped by the addition of 0.125 M glycine (final). The tissue pieces were then treated with a TissueTearer and finally spun down and washed 2x in PBS. Chromatin was isolated by the addition of lysis buffer, followed by disruption with a Dounce homogenizer. Lysates were sonicated and the DNA sheared to an average length of 300-500 bp. Genomic DNA (Input) was prepared by treating aliquots of chromatin with RNase, proteinase K and heat for de-crosslinking, followed by ethanol precipitation. Pellets were resuspended and the resulting DNA was quantified on a NanoDrop spectrophotometer. Extrapolation to the original chromatin volume allowed quantitation of the total chromatin yield. An aliquot of chromatin (25 ug) was precleared with protein A agarose beads (Invitrogen). Genomic DNA regions of interest were isolated using 4 ug of antibody against the C-terminal region of REST (generous gift from Gail Mandel, Vollum Institute). Complexes were washed, eluted from the beads with SDS buffer, and subjected to RNase and proteinase K treatment. Crosslinks were reversed by incubation overnight at 65 C, and ChIP DNA was purified by phenol-chloroform extraction and ethanol precipitation. Illumina sequencing libraries were prepared from the ChIP and Input DNAs by the standard consecutive enzymatic steps of end-polishing, dA-addition, and adaptor ligation. Steps were performed on an automated system (Apollo 342, Wafergen Biosystems/Takara). After a final PCR amplification step, the resulting DNA libraries were quantified and sequenced on Illumina?s NextSeq 500 (75 nt reads, single end).

first: Jaejoon

first: Liviu

last: Aron

first: Bruce

last: Yankner


title: Immune profiles and DNA methylation alterations related to non-muscle-invasive bladder cancer outcomes

status: Public on Feb 01 2022

city: Lebanon

first: Ji-Qing

last: Chen

state: New Hampshire

address: 1 Medical Center Drive, Williamson level 6

department: Epidemiology

institute: Dartmouth College

type: Methylation profiling by genome tiling array

summary: Non-muscle-invasive bladder cancer (NMIBC) patients receive frequent monitoring because ≥ 70% will have recurrent disease. However, screening is invasive, expensive, and associated with significant morbidity making bladder cancer the most expensive cancer to treat per capita. There is an urgent need to expand the understanding of markers related to recurrence and survival outcomes of NMIBC. Our results expand on the knowledge of immune profiles and methylation alteration associated with NMIBC outcomes and represent a first step toward the development of DNA methylation-based biomarkers of tumor recurrence.

overall_design: Bisulphite converted DNA from white blood cells from 603 non-muscle-invasive bladder cancer patients, were hybridized to the Illumina Infinium HumanMethylationEPIC Beadchip v1.0_B4

first: Brock

last: Christensen

first: Lucas

last: Salas

first: Margaret

last: Karagas

first: John

last: Wiencke

first: Devin

last: Koestler

first: Annette

last: Molinaro

first: Angeline

last: Andrew

last: Seigne

first: Karl

middle: T

last: Kelsey


title: ATAC-seq analyses with knockout eHAP cells for effector genes

first: Yusuke

last: Miyanari

summary: A genome-wide screening identified effector genes of chromatin accessibility. To investigate the functional consequences of the loss of each effector gene, we conducted ATAC-seq analysis with eHAP cells knocked out for each effector gene.

overall_design: ATAC-seq with spike-in control

first: Satoko

last: Ishii


title: Scalable, methanol-free manufacturing of the SARS-CoV-2 receptor binding domain in engineered Komagataella phaffii

status: Public on Dec 15 2021

city: Cambridge

first: Charles

middle: Arthur

last: Whittaker

institute: Koch Institute

summary: Prevention of COVID-19 on a global scale will require the continued development of high-volume, low-cost platforms for the manufacturing of vaccines to supply on-going demand. Vaccine candidates based on recombinant protein subunits remain important because they can be manufactured at low costs in existing large-scale production facilities that use microbial hosts like Komagataella phaffii (Pichia pastoris). Here, we report an improved and scalable manufacturing approach for the SARS-CoV-2 spike protein receptor binding domain (RBD); this protein is a key antigen for several reported vaccine candidates. We genetically engineered a manufacturing strain of K. phaffii to obviate the requirement for methanol-induction of the recombinant gene. Methanol-free production improved the secreted titer of the RBD protein by >5x by alleviating protein folding stress. Removal of methanol from the production process enabled scale up to a 1,200 L pre-existing production facility. This engineered strain is now used to produce an RBD-based vaccine antigen that is currently in clinical trials and could be used to produce other variants of RBD as needed for future vaccines.

overall_design: Comparison of 3 replicates of Komagataella phaffii cells grown in 5% MeOH with 3 repliates of cells growing in 4% Sorbitol.

first: Neil

last: Dalvie

first: Andrew

last: Biedermann

first: Sergio

last: Rodriguez-Aponte

first: Christopher

last: Naranjo

first: Harish

last: Rao

first: Meghraj

middle: P

last: Rajurkar

first: Rakesh

last: Lothe

first: Umesh

last: Shaligram

first: Ryan

last: Johnston

first: Laura

last: Crowell

first: Seraphin

last: Castelino

first: Mary

last: Tracey

first: J

last: Love


title: Transcriptomic Analysis of Rat Cerebral Cortex Reveals the Potential Mechanism of Electroacupuncture Opening Blood Brain Barrier

status: Public on Jan 05 2022

city: Hangzhou

first: Congcong

last: Ma

address: No. 548, binwen Road

institute: Zhejiang Chinese Medical University

summary: Therapeutic treatment options for central nervous system (CNS) diseases are greatly limited by the blood-brain barrier (BBB). Electroacupuncture (EA) can be used to induce an increase in BBB permeability on rats, providing a potential approach for the delivery of drugs from the systemic circulation into the brain. However, there remains a large gap in our knowledge regarding the impact of EA on brain gene expression. This work is focused on investigating the transcriptional changes of rat cerebral cortex following EA and expression changes in genes and bioinformatic analysis was performed. Our results provide a valuable resource that will guide mechanism research of EA opening BBB and other ways to mediate drug delivery into the brain.

first: Xianming

last: Lin


title: Algesic activity of the human coronavirus OC43 derived peptide

status: Public on Apr 13 2022

city: La Jolla

first: Andrei

last: Chernov

state: CA

address: 9500 Gilman Dr

department: Anesthesiology

institute: University of California San Diego

summary: The human coronavirus OC43 is responsible for 15-30% of seasonal “common cold” infections with typically mild respiratory symptoms. We demonstrated that the coronavirus OC43 derived small peptide encoded by the viral p65 proteins may exhibit molecular mimicry with the pro-algesic fragment of Myelin Basic Protein (MBP). After intrasciatic injection, the p65-derived peptide induced robust pain hypersensitivity in rats lasting for up to 21 days. Transcriptomic analysis at day 21 revealed extensive spinal up-regulation of pro-nociceptive genes. Strikingly, genome-wide isoform switching due to activation of transcriptional start sites and alternative splicing events has occurred. We hypothesized that the coronavirus-derived peptides can dysregulate MBP function in the PNS/CNS and promote neuropathic chronic pain. Our findings offer paradigm-shifting mechanistic understanding of the viral origin of idiopathic neurological effects including chronic neuropathic pain, a condition currently refractory to therapeutic treatment. This new knowledge will lead to new diagnostic, prognostic, and therapeutic approaches to benefit patients with chronic pain.

overall_design: Compare rat spinal cord transcriptomes after sciatic nerve injections to identify upstream regulators and signaling pathways induced due to molecular mimicry with the coronavirus-derived peptide

first: Veronica

last: Shubayev


title: SETDB1 Fuels the Lung Cancer Phenotype by Modulating Epigenome, 3D Genome Organization, and Chromatin Mechanical Properties

status: Public on Mar 29 2022

city: Amsterdam

first: Mikhail

last: Magnitov

address: Plesmanlaan 121

country: Netherlands

institute: The Netherlands Cancer Institute

summary: Imbalance in the finely orchestrated system of chromatin-modifying enzymes is a hallmark of many pathologies such as cancers, since causing the affection of the epigenome and transcriptional reprogramming. Here, we demonstrate that a loss-of function mutation of the major histone lysine methyltransferases SETDB1 possessing oncogenic activity in lung cancer cells leads to broad changes in the overall architecture and mechanical properties of the nucleus through redistribution of heterochromatin genome-wide, which perturbs chromatin spatial compartmentalization. Together with the enforced activation of the epithelial expression program, cytoskeleton remodeling, reduced proliferation rate, and restricted cellular migration, this leads to the reversed oncogenic potential of lung adenocarcinoma cells. These results emphasize an essential role of chromatin architecture in the determination of oncogenic programs and illustrate a relationship between gene expression, epigenome, 3D genome, and nuclear mechanics.

overall_design: This submission contains RNA-seq, H3K9me3 ChIP-seq, H3K27me3 ChIP-seq, H3K27ac ChIP-seq, H3K4me3 ChIP-seq, CTCF ChIP-seq, and Hi-C experiments on Control (CT) and SETDB1 loss-of-function mutation (KO) A549 cells.

middle: D

first: Vlada

last: Zakharova

first: Slimane

last: Ait-Si-Ali


title: Cell-specific chromatin landscape in human coronary artery resolves regulatory mechanisms of disease risk

status: Public on Dec 14 2021

city: Charlottesville

first: Clint

middle: L

last: Miller

state: VA

department: Center for Public Health Genomics

institute: University of Virginia

summary: Coronary artery disease (CAD) is a complex inflammatory disease involving genetic influences across several cell types. Genome-wide association studies (GWAS) have identified over 170 loci associated with CAD, where the majority of risk variants reside in noncoding DNA sequences impacting cis-regulatory elements (CREs). Here, we applied single-cell ATAC-seq to profile 28,316 cells across coronary artery segments from 41 patients with varying stages of CAD, which revealed 14 distinct cellular clusters. We mapped ~320,000 accessible sites across all cells, identified cell type-specific elements, transcription factors, and prioritized functional CAD risk variants via quantitative trait locus and sequence-based predictive modeling. We identified a number of candidate mechanisms for smooth muscle cell transition states and identified putative binding sites for risk variants. We further employed CRE to gene linkage to nominate disease-associated key driver transcription factors such as PRDM16 and TBX2. This single cell atlas provides a critical step towards interpreting cis-regulatory mechanisms in the vessel wall across the continuum of CAD risk.

overall_design: We profiled genome-wide chromatin accessibility at single cell resolution (scATAC from 10x Genomics) in coronary arteries from 41 patients across a range of atherosclerosis stages.

first: Adam

last: Turner

first: Hu

last: Shengen

first: Chongzhi

last: Zang


title: Single-cell Next Generation Sequencing (scNGS) facilitates analysis of gonadal single cells transcriptomes and revealed germ cell heterogeneity

status: Public on Dec 13 2021

city: Seoul

first: JAE

middle: YONG

last: HAN

address: 1 Gwanak-ro, Gwanak-gu

department: Department of Agricultural Biotechnology

institute: Seoul National University

summary: The unraveling of heterogenous cell populations, — previously masked in bulk transcriptome measurements — are made possible through analysis of single-cell transcriptomics. The goals of this study are to examine single-cell NGS-derived gonadal cell transcriptome profiling and to evaluate heterogeneity of gonadal germ cells in avian species. We performed single-cell RNA sequencing using embryonic gonadal cells of HH stage 28 from male and female zebra finches. We identified 12,489 male transcripts and 10,046 female transcripts. We annotated 9 different cell types from a total of 20 clustered single cells and identified that primordial germ cells, which have been considered as single population, can be distinguishable into three subtypes. The three PGC subtypes were specifically enriched for genes with expression patterns related to germness or pluripotency, suggesting functional differences in PGCs according to the three subtypes. Our study represents the first single-cell RNA seq analysis of gonadal transcriptomes in zebra finch. Our results revealed the first heterogeneity and intrinsic changes of gonadal primordial germ cells, which have hitherto been considered as a single population in avian species. We conclude that single-cell RNA seq based transcriptome analysis would offers new perspectives on avian primordial germ cells.

overall_design: Gonadal cells profiling of male and female zebra finches at single cell level

first: Jae

middle: Y

last: Han

first: Kyung

middle: M

last: Jung


title: CRISPR activation screen to identify X-chromosomal Xist activators in male embryonic stem cells

first: Till

last: Schwämmle

summary: As the master regulator of X-chromosome inactivation (XCI), the Xist RNA is expressed nearly ubiquitously in female mice. Xist is only absent in the germ line and at the pluripotent state. Xist is generally assumed to be expressed “by default” in females, while being actively repressed in the few tissues where it is silent. Whether activating mechanisms also contribute remained largely unknown. Through a pooled CRISPR screen we identify the GATA family of transcription factors as potent direct activators of Xist. We describe a GATA-responsive regulatory element (RE79), located ~100 kb upstream of the Xist promoter. In cell lines derived from the two extraembryonic lineages, XEN and TS cells, where imprinted Xist expression is maintained, RE79 is bound by different sets of GATA factors expressed in those tissues. Here we use a CRISPR activation screen targeting X-chromosomal genes on differentiating XO mouse embryonic stem cells to identify putative Xist activators.

overall_design: A CRISPRa-SunTag screen for Xist was performed in differentiating mESCs (E14-STN) carrying a deletion of the Tsix-promoter to sensitize the male cell line for Xist upregulation. The library contained 8773 gDNAs targeting 757 X-chromosomal genes and 23 autosomal controls, as well as 200 non-targeting guides. After 2 days of differentiation via LIF-withdrawal, the cells were stained for Xist RNA using a FlowFISH protocol and the top 15% bins of Xist-expression was sorted.

first: Liat

last: Ravid Lustig

first: Abhishek

last: Kumar

first: Gemma

last: Noviello

first: Ilona

last: Dunkel

first: Raha

last: Weigert

first: Guido

last: Pacini

first: Rene

last: Buschow

first: Afrah

last: Ghauri

first: Maximilian

last: Stötzel

first: Alexander

last: Meissner

first: Edda

middle: G

last: Schulz


title: The influence of nt-LNA on cell composition and phenotypees in the atherosclerotic lesion.

status: Public on Nov 01 2021

city: Nashville

first: Ryan

last: Allen

state: TN

address: 2220 Pierce Ave

department: Medicine

institute: Vanderbilt University Medical Center

summary: Raw fastq files from paired-end, Illumina-based sequencing on NovaSeq6000

overall_design: Apoe-/- mice were fed a western diet for 4 weeks and administered saline or nt-LNA (30 mg/kg) weekly.  After 4 weeks, aortic arch and thoracic aorta were removed, cleaned of peripheral tissue, minced and digested to achieve a single cell suspension. The single cell suspension was then sorted by FACS to achieve a CD45+/CD3- population of live cells for single-cell 3' RNA Sequencing utilizing the 10X Chromium system.

first: Kasey

last: Vickers

first: Danielle

last: Michell


title: Understanding the role of miRNA-143 (miR-143) in ischemia-induced retinopathy via RNA transcriptome profiling

status: Public on Oct 01 2021

city: Dublin

first: vikrant

last: singh

state: Ireland

address: 31 York Street

country: Ireland

institute: Royal college of Surgeons in Ireland

summary: To investigate molecular network mediated by miR-143, we analyzed the transcriptome profile of retinas isolated from neonatal pups subjected to either normoxia or oxygen-induced retinopathy (OIR) for 14 days (P14) receiving an intravitreal injection of either scrambled miRNAs (control) or miR-143 mimics. Total RNAs were isolated from the retinas and subjected to RNA-Seq. Analysis of RNA-Seq data identified 2064 genes with altered levels between OIR rats and shame rats receiving scrambled RNAs (adjusted p<0.05).

overall_design:
Four groups of samples were analysed:
1) OIR with scrambled RNA (n=3)
2) OIR with miR-143 mimic (n=3)
3) Sham with scrambled RNA (n=3)
4) Sham with miR-143 mimic (n=3)

first: Jiang-Hui

last: Wang

first: Vikrant

last: Singh

first: Alex

middle: W

last: Hewitt

first: Guei-Sheung

last: Liu


title: PD-L1 – PD-1 interactions limit effector Treg cell populations at homeostasis and during infection

status: Public on Oct 24 2021

city: Philadelphia

first: Christopher

last: Hunter

address: 301 S University Ave

department: Pathobiology

institute: University of Pennsylvania

summary: While much is known about the factors that promote diverse Treg cell responses, less is known about mechanisms that constrain Treg cells. Here we demonstrate phenotypic and transcriptional profiling  at homeostasis, which reveals TCR activation promotes a population of Treg cells that display an effector phenotype (eTreg) enriched for production of suppressive proteins such as IL-10 and CTLA-4. However, these eTreg cells express the inhibitory receptor PD-1 and blockade of PD-L1 or loss of PD-1 results in increased eTreg cell activity associated with enhanced homeostatic proliferation and survival. Thus, eTreg cell expression of PD-1 acts as a sensor to rapidly tune the pool of eTreg cells at homeostasis.

overall_design: Three to four biological replicates were analyzed for each of 4 conditions (isotype and antibody treatment; conventional and effector Tregs)

first: Lindsey

last: Shallberg

first: Joseph

last: Perry


title: Expression profiles of long non-coding RNAs in neurogenic bladder of spinal cord injured rats: A transcriptomic analysis

status: Public on Mar 02 2022

city: Beijing

first: Jimeng

last: Ruan

address: No. 45 Changchun Street, Xuanwu District

institute: Xuanwu Hospital Capital Medical University

summary:
Purpose: In this study, the expression profiles of lncRNAs and mRNAs were explored in the bladder tissue of SCI rats using next-generation sequencing.
Methods:Twenty female Wistar rats were randomly divided into SCI 1-3 and normal control (NC) groups. The spinal cord was completely transected at the T9-T10 level to establish the SCI model. Bladder tissues were collected on days 7, 14, and 28 after the operation. The expression profiles of lncRNAs were detected by NGS. Differentially expressed lncRNAs (DELs) were chosen for qRT-PCR verification to validate the RNA sequencing results.
Results: Compared with the NC group, the SCI 1-3 groups had 468, 117, and 408 DELs (fold change (FC) > 2), including 282, 38, and 201 up-regulated and 186, 79, and 207 down-regulated lncRNAs, respectively. Likewise, 6654, 2133, and 5706 mRNAs (FC > 2) were differentially expressed between SCI 1-3 and NC rats, of which 4821, 1195, and 3695 were up-regulated, and 1833, 938, and 2011 were down-regulated, respectively.
Conclusions: The results revealed the expression profiles and possible roles of lncRNAs in SCI rat NB.

overall_design: Twenty female Wistar rats were randomly divided into SCI 1-3 and normal control (NC) groups. The spinal cord was completely transected at the T9-T10 level to establish the SCI model. Bladder tissues were collected on days 7, 14, and 28 after the operation. The expression profiles of lncRNAs were detected by NGS. Differentially expressed lncRNAs (DELs) were chosen for qRT-PCR verification to validate the RNA sequencing results. The results revealed the expression profiles and possible roles of lncRNAs in neurogenic bladder of spinal cord injured rats.

first: Zhenhua

last: Shang


title: H3K27ac ChIP-seq of MCF10A progression series

status: Public on Aug 09 2021

city: Watervliet

first: Ali

middle: Salman

last: Ropri

address: 12 Lakeshore Dr., Apt 1B

department: Biomedical Sciences

institute: SUNY Albany

summary: This study takes an unbiased global analysis of  super-enhancers that are acquired or lost in progression of breast cancer using the MCF10a progression series

overall_design: Using the enhancer mark H3K27ac, we performed ChIP seq to identify enhancers, and subesquently, using ROSE to identify super-enhancers acquired or lost in progression of breast cancer.

first: Jonah

last: Eng


title: Epigenetic changes in mouse neuronal stem cells with histone H3K27M mutations [ChIP-seq]

status: Public on Aug 05 2021

city: Ann Arbor

first: Sriram

last: Venneti

state: MI

address: 3520E MSRB 1, 1150 W. Medical Center Dr.

institute: University of Michigan

summary: H3.3K27M mutations or H3.3 WT were expressed in in neuronal stem cells (Nsc) derived from p16Ink4a/p14Arf knockout (KO) animal. Genomic changes in H3K27me3, H3K27ac and H3K4me3 were assessed between H3.3K27M and H3.3WT cells.

overall_design: H3.3K27M and H3WT cells were subjected to H3K27me3, H3K27ac and H3K4me3 ChiP-Seq and analyzed.

first: S


title: Stress-induced splicing activation of immediate early genes by nuclear speckle reorganization [ANI]

status: Public on Aug 06 2021

city: Göttingen

first: Hsu-Min

last: Sung

state: Niedersachsen

address: Humboldtallee 23

institute: Heart Centre Göttingen

summary: Current models posit that nuclear speckles (NSs) serve as reservoirs of splicing factors and facilitate post-transcriptional processing of mRNA. Here, we discovered that ribotoxic stress leads to a profound reorganization of NSs with enhanced recruitment of factors required for 5' and 3' splice site recognition including the RNA-binding protein TIAR, U1 snRNP proteins and U2-associated factor 65, as well as serine 2 phosphorylated RNA polymerase II. NS reorganization is dependent on the stress-activated p38 mitogen activated protein kinase (MAPK), and goes along with splicing activation of both pre-existing and nascent pre-mRNAs. In particular, ribotoxic stress causes targeted excision of retained introns from pre-mRNAs of immediate early genes (IEGs), whose transcription is induced during the stress response. Importantly, enhanced splicing of the IEGs ZFP36 and FOS is accompanied by re-localization of the corresponding mRNAs to NSs. Our study reveals NSs as a dynamic compartment that is remodeled under stress conditions to promote the excision of retained introns and thereby enhance the expression and processing of IEG mRNAs.

overall_design:
Analysis of alternative splicing changes and differential gene expression in HeLa-TREx cells upon anisomycin-induced ribotoxic stress.
mRNA Half-Life (HL) determination via RNA sequencing
4-thio U labeling combined with sequencing for distinguishing nascent and pre-existing mRNA pool

first: Philipp

last: Boss

first: David

last: Ibberson

first: Uwe

last: Ohler

first: Georg

last: Stoecklin


title: RNAseq of restimulated lung CD8 T cells 21 days post influenza A infection

status: Public on Jul 30 2021

city: Rochester

first: Cameron

last: Baker

address: 601 Elmwood Ave

institute: University of Rochester

summary: We report the RNA sequencing of both non-restimulated and restimulated (using anti CD3/CD28 cross-linking) antigen-experienced (CD44+) mouse lung CD8 T cells 21 days post X31 influenza A infection subsetted by integrin expression of CD49a and CD103. After restimulation, all four subsets (CD49a+CD103+, CD49a+CD103-,CD49a-CD103+, CD49a-CD103-) demonstrate global differences and separate in principle component analysis space, with CD49a+ groups showing elevated transcripts for a number of effector functions. The non-restimulated T cells separate out into CD49a+CD103+/- and CD49a-CD103+/- groups. CD49a serves as a correlate of effector transcripts in mouse lungs to a greater degree than CD103 in both non-restimulated and restimulated conditions.

overall_design: Examination of transcriptome of mouse lung CD8 T cells after influenza infection.

first: Emma

middle: C

last: Reilly

first: Mike

last: Sportiello

last: Topham


title: RNA-seq in TX1072 XO mESCs during differentiation

status: Public on Jan 26 2022

city: Berlin

first: Till

last: Schwämmle

institute: Max Planck Institute for Molecular Genetics

summary: As the master regulator of X-chromosome inactivation (XCI), the Xist RNA is expressed nearly ubiquitously in female mice. Xist is only absent in the germ line and at the pluripotent state. Xist is generally assumed to be expressed “by default” in females, while being actively repressed in the few tissues where it is silent. Whether activating mechanisms also contribute remained largely unknown. Through a pooled CRISPR screen we identify the GATA family of transcription factors as potent direct activators of Xist. We describe a GATA-responsive regulatory element (RE79), located ~100 kb upstream of the Xist promoter. In cell lines derived from the two extraembryonic lineages, XEN and TS cells, where imprinted Xist expression is maintained, RE79 is bound by different sets of GATA factors expressed in those tissues. Here we use RNA-seq on differentiating XO mouse embryonic stem cells as a reference for gene expression during early differentiation.

overall_design: RNA-seq was performed in the TX1072 XO cell line. The data was collected in replicates from cells in 2i+LIF medium (day 0), as well at days 1-4 of differentiation (via 2i+LIF-withdrawal).

first: Liat

last: Ravid Lustig

first: Abhishek

last: Kumar

first: Gemma

last: Noviello

first: Ilona

last: Dunkel

first: Raha

last: Weigert

first: Guido

last: Pacini

first: Rene

last: Buschow

first: Afrah

last: Ghauri

first: Maximilian

last: Stötzel

first: Alexander

last: Meissner

first: Edda

last: Schulz


title: Transcriptome Signature Post Reovirus Treatment In KRAS Mutated Colorectal Cancer

status: Public on May 01 2021

city: Bronx

first: RADHASHREE

last: MAITRA

address: 1300 Morris Park Ave

department: Medicine (Oncology)

institute: Albert Einstein College of Medicine of Yeshiva University

summary: Reovirus propagates with high efficiency in KRAS mutated colorectal cancer (CRC). About 45-50% of CRC patients possess KRAS mutation. Oncolytic reovirus treatment in combination with chemotherapy was tested in patient samples possessing KRAS mutated metastatic CRC. This is the raw data from the peripheral mononuclear cell (PBMC) samples at 4 timepoints (pre treatment, 48 hours, day 8, and day 15).

overall_design: Reovirus was administered as a 60-min intravenous infusion for 5 consecutive days every 28 days, at tissue culture infective dose (TCID50) of 3X1010. Peripheral blood mononuclear cells (PBMC) were isolated from whole blood pre and post reovirus administration at 48hr, Day-8, and Day-15. Clariom_D_Human_Assay was used to determine the overall gene expression compared to pre-reovirus treatment by RNA sequencing.

first: Radhashree

last: Maitra

first: Sanjay

last: Goel

first: Elisha

last: Fogel


title: Single-cell Transcriptome Analysis Reveals an Anomalous Epithelial Variation and Ectopic Inflammatory Response in Chronic Obstructive Pulmonary Disease

status: Public on Jun 29 2021

city: Chuo-ku

first: Yusuke

last: Yamamoto

state: Tokyo

address: 5-1-1, Tsukiji, Chuo-ku

institute: National cancer center research institute

summary: Chronic obstructive pulmonary disease (COPD) is a progressive disease that obstructs the airflow from the lungs, and tobacco smoking is the major cause of COPD. Here, we applied single-cell RNA sequencing to analyze COPD pathogenesis in COPD patients, non-COPD smokers and never-smokers and investigated the disease progression at single-cell resolution. By single-cell transcriptome analysis, COPD was characterized by shifts in the stromal, immune system and epithelial cell compositions. While epithelial components in never-smokers were relatively uniform, the smoker groups presented with extensive heterogeneity in epithelial cells, particularly in the alveolar type II (AT2) lineages. We identified a subpopulation of AT2 epithelial cells that emerged in smokers, such as COPD patients, and specifically expressed a series of chemokines and PD-L1. A trajectory analysis revealed that the inflammatory AT2 cell subpopulation followed a unique differentiation path, and a prediction model of cell-to-cell interactions inferred increased intercellular networks of inflammatory AT2 cells with immune and stromal cell populations. Thus, our analysis reveals a unique cellular differentiation pathway and function underlying the biological and clinical characteristics of COPD pathogenesis.

overall_design: single-cell transcriptome profiling from human lung tissues of 9 COPD, 4 non-COPD smoker, and 3 never-smoker samples.

first: Naoaki

last: Watanabe

first: Jun

last: Nakayama


title: High-throughput RNA Sequencing of THP-1 macrophages treated with or without native LDL for 24h.

first: Ryan

last: Allen

overall_design: Cells treated without (Control; n=3) or with nLDL (Case; n=3)

first: Kasey

last: Vickers


title: Lineage transcription factors ASCL1, NKX2-1, and PROX1 are enriched at super enhancers and co-regulate subtype-specific genes in small cell lung cancer [RNA-seq]

city: Dallas

first: Jane

middle: E

last: Johnson

address: 5323 Harry Hines Blvd

department: Neuroscience

institute: UT Southwestern Medical Center

summary: Heterogeneity between tumors is a major barrier to the treatment of small cell lung cancer (SCLC). Identification of molecular markers to characterize and classify tumors can facilitate the diagnosis and development of targeted therapies. Here, we analyzed genomic regions, called super enhancers (SE), across multiple SCLC cell lines and patient-derived xenograft models, and find SE enrichment is sufficient to classify SCLC models into recently defined SCLC molecular subtypes SCLC-A, SCLC-N, and SCLC-P defined by the transcription factors ASCL1, NEUROD1, and POU2F3, respectively. 3D chromatin structure analysis identified genes associated with the SE that assemble into subtype-specific tumor-signatures with genes functioning in diverse processes. Focusing on the SCLC-A subtype, transcription factors NKX2-1 and PROX1 were identified as ASCL1-interacting proteins. All three factors bind overlapping genomic regions within SEs in SCLC-A cell line models. Nevertheless, combined loss of all three factors suppresses growth of SCLC-A similar to that seen with ASCL1 loss alone, continuing to place ASCL1 as a key dependency factor in a subset of SCLC. Focusing on genes co-regulated by the three transcription factors, two SCLC-A subtype-specific cell surface proteins, SCN3A and KCNB2, were identified. Loss of either channel alone did not disrupt SCLC-A growth in vitro, but they may serve as diagnostic tools in subtyping SCLC.

overall_design: Identification of transcriptional targets that are shared between ASCL1, PROK1 and NKX2.1 (TTF1) in the NCI-H2107 SCLC cell line, by knocking down ASCL1 or ASCL/PROX1/NKX2.1 with siRNAs and RNA-seq.

first: Karine

last: Pozo

first: Rahul

middle: K

last: Kollipara


title: m6A Epitranscriptomic Microarray of primary mouse RPE cells treated with TGF-β2

status: Public on Jun 26 2021

city: Shanghai

first: Yuwei

last: Wang

address: 100 Haining Road

institute: Shanghai General Hospital

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

summary: m6A-mRNA&lncRNA Epitranscriptomic Microarray of primary mouse RPE cells comparing control untreated RPE cells with RPE cells treated with TGF-β2 at a concentration of 10 ng/ml. The goal was to determine the effects of RNA m6a methylation on primary mouse RPE cells undergoing epithelial-mesenchymal transition induced by TGF-β2.

overall_design: Two-condition experiment, TGF-β2-treated RPE cells vs. PBS-treated RPE cells. Biological replicates: 3 replicates for each group.

first: Te

last: Liu

first: Xiaodong

last: Sun


title: Small RNA sequencing of human LDL

summary: Adapter trimmed fastq files, non-redundant identical reads and the results of their alignment using the TIGER pipeline.

overall_design: Total RNA extracted from density-isolated LDL were converted to cDNA using the NextFlex Small RNA Library Kit V3 and sequenced on an Illumina NextSeq500 instrument.


title: Lineage transcription factors ASCL1, NKX2-1, and PROX1 are enriched at super enhancers and co-regulate subtype-specific genes in small cell lung cancer

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

overall_design: Refer to individual Series


title: Wistar rat model of COPD: Cigarette smoking exposure and fine particulate matter (PM2.5) exposure vs. control.

status: Public on Jun 21 2021

city: Fuzhou

first: Qi

last: Lin

state: Fujian

address: No. 1 Xuefu North Road

institute: The School of Public Health,Fujian Medical University

summary: Genome-wide analysis of lncRNA expression profiles in COPD rat model exposed by cigarette smoking (CS) and fine particulate matter (PM2.5). Goal was to explore the differences and similarities lncRNAs expression in rats model of COPD exposed by CS and PM2.5.

overall_design: Three-condition experiment, COPD rat model exposed by CS replicates, COPD rat model exposed by PM2.5 replicates vs. Control. Biological replicates: 3 COPD rat model exposed by CS replicates, 3 COPD rat model exposed by PM2.5 replicates and 3 control replicates.

first: Chao-Feng

last: Zhang

first: Huang-Yuan


title: Portal fibroblasts with mesenchymal stem cell features form a reservoir of proliferative myofibroblasts in liver fibrosis

status: Public on Mar 31 2021

city: PARIS

first: Axelle

last: Cadoret

address: 27 rue de Chaligny

department: UMRS938 CRSA

country: France

institute: INSERM

summary: We performed transcriptomic studies comparing phenotypically defined PMSCs (PDGFRa/CD34/CD9high:CD200low) to HSCs (Vitamin-A fluorescent) of high purity, using bulk RNAseq. We further extended bulk RNAseq analyses of the two cell populations to myofibroblasts derived from both cell types in culture, including an early and late stage of differentiation for PMSC-MFs. Comparative analyses of gene expression indicated that 100 genes in PMSCs and 112 genes in HSCs, i) were overexpressed according to both scRNAseq and bulk RNAseq analyses, and ii) remained differentially expressed in these cells throughout their myofibroblastic differentiation. We selected the most differentially expressed of these genes, to build a multigene expression signature of PMSCs/PMSC-MFs (7 genes) and of HSCs/HSC-MFs (6 genes).

overall_design: mRNA profiles of PMSCs (n=4) and HSCs (n=4), and their derived myofibroblasts in culture, including PMSC-MFs-3d (n=4), PMSC-MFs-7d (n=4) and HSC-MFs-3d (n=4).

first: Justine

last: Guégan

first: Lin

last: Lei

first: Chantal

last: Housset


summary: Portal mesenchymal cells represent a very small amount of cells. They are tightly bound to the bile duct and portal vascular structures, relying on basement membranes. In the present study, we set up a specific procedure to isolate portal mesenchymal cells, for scRNAseq analysis. We identified 16 distinct cell clusters, including fibroblasts (5 clusters), vascular smooth muscle cells (VSCMs, 5 clusters), endothelial cells (4 clusters), HSCs (1 cluster) and mesothelial cells (1 cluster).

overall_design: First, we isolated fragments of the bilio-vascular tree from mouse liver. Next, bilio-vascular fragments were submitted to enzymatic digestion, resulting in a single-cell suspension. The cell suspension was depleted in cells expressing the lineage (Lin) markers of cholangiocytes (EpCAM), endothelial cells (CD31), and hematopoietic cells (CD45 and CD11b) by means of cell sorting. Lin-negative single-cell suspension was processed to generate a scRNAseq cDNA library using the 10x Genomics technology.


title: In vivo transcriptomic responses to thioacetamide exposure in guinea pig liver tissue

status: Public on Mar 25 2021

city: Frederick

first: Mohamed Diwan M.

last: AbdulHameed

address: 2405 Whittier Drive, Suite 200

institute: Biotechnology HPC Software Applications Institute (BHSAI)

summary: In this study we tested the ability to predict organ injury from transcriptomic data in Hartley guinea pigs at early time points after exposure to thioacetamide (9 and 33 hours). We selected thioacetamide, a compound extensively used in animal studies for its ability to cause liver damage.

overall_design: We treated 30 Hartley guinea pigs with saline solution (control), 25 mg/kg (low dose), and 100 mg/kg (high dose) to produce different degrees of injury. RNA samples for gene expression analysis were collected from the liver at 9 and 33 hours. Number of replicates were five.

first: Patric

last: Schyman

first: Richard

last: Printz

first: Venkat

middle: R

last: Pannala

first: Mohamed-Diwan

first: Shanea

last: Estes

first: Chiyo

last: Shiota

first: Kelli

last: Boyd

first: Masakazu

first: Anders

last: Wallqvist


title: Gene expression profiling of Vglut2 neurons in the vestibular nucleus (VN)

status: Public on Feb 27 2021

city: Bellaterra

first: Elisenda

last: Sanz

state: Barcelona

address: M1/113 Facultat de Medicina

department: Institut de Neurociencies

institute: Universitat Autonoma de Barcelona

summary: Vestibular nuclei (VN) are critical for the processing of movement input, and motion-induced activation of VN neurons recapitulates MS-related signs. However, the genetic identity of VN neurons mediating MS-related autonomic and aversive responses remains unknown. Here, we identify diferent markers of glutamatergic vestibular neuronal populations using the RiboTag apparoach.

overall_design: Punches containing the vestibular nuclei (VN) of Vglut2Cre mice injected with the RiboTag viral vector (AAV-DIO-Rpl22·HA) were homogenized and incubated with anti-hemagglutin (HA) antibodies and protein A/G magnetic beads to isolate the polysome-associated mRNAS of VGLUT2 neurons in the VN. To identify differentially expressed transcripts, RNA from the immunoprecipitates was extracted, amplified, labelled and hybridized to MouseRef-8 v2 expression beadchips.

first: Albert

last: Quintana


title: Gene therapy of dominant CRX-Leber congenital amaurosis using patient retinal organoids

status: Public on Feb 17 2021

city: Bethesda

first: Zachary

middle: A

last: Batz

state: MD

address: 6 Center Dr Bldg 6, Rm 303

department: NEI

institute: NIH


first: Axelle


title: Gene therapy of dominant CRX-Leber congenital amaurosis using patient retinal organoids I

summary: Mutations in the cone-rod homeobox (CRX) transcription factor lead to distinct retinopathy phenotypes, including early-onset vision impairment in dominant Leber congenital amaurosis (LCA). Using induced pluripotent stem cells (iPSCs) from a patient with CRX-I138fs mutation, we established an in vitro model of CRX-LCA in retinal organoids that exhibit defective photoreceptor maturation by histology and gene profiling including diminished expression of visual opsins. Gene therapy by delivery of an additional correct CRX allele using an AAV vector partially restored photoreceptor phenotype and expression of phototransduction-related genes as revealed by single cell RNA-sequencing. Retinal organoids derived from iPSCs of a second dominant CRX-LCA patient carrying a K88N mutation revealed loss of opsin expression as a common phenotype, which could also be alleviated by AAV-mediated overexpression of CRX. Our studies provide the proof-of-concept for development of gene therapy for dominant CRX-LCA and other CRX-retinopathies.

overall_design: Profiling gene expression of retinal organoids with and without CRX mutations

first: Kamil

last: Kruczek

first: Zepeng

last: Qu

first: Zhijian

last: Wu

first: Anand

last: Swaroop


title: Suppression of liquid-liquid phase separation by 1,6-hexanediol partially compromises the 3D genome organization in living cells

status: Public on Mar 22 2021

city: Amsterdam

first: Mikhail

last: Magnitov

address: Plesmanlaan 121

institute: The Netherlands Cancer Institute

summary: Liquid-liquid phase separation (LLPS) contributes to the spatial and functional segregation of molecular processes within the cell nucleus. However, the role played by LLPS in chromatin folding in living cells remains unclear. Here, using stochastic optical reconstruction microscopy (STORM) and Hi-C techniques, we studied the effects of 1,6-hexanediol (1,6-HD)- mediated LLPS disruption/modulation on higher-order chromatin organization in living cells. We found that 1,6-HD treatment caused the enlargement of nucleosome clutches and their more uniform distribution in the nuclear space. At a megabase-scale, chromatin underwent moderate but irreversible perturbations that resulted in the partial mixing of A and B compartments. The removal of 1,6-HD from the culture medium did not allow chromatin to acquire initial configurations, and resulted in more compact repressed chromatin than in untreated cells. 1,6-HD treatment also weakened enhancer-promoter interactions and TAD insulation but did not considerably affect CTCF-dependent loops. Our results suggest that 1,6-HD-sensitive LLPS plays a limited role in chromatin spatial organization by constraining its folding patterns and facilitating compartmentalization at different levels.

overall_design: This submission contains the following experiments on untreated (Control and Control_T), 1,6-hexanediol treated (Hex5), Tween-20 treated (Tween), 1,6-hexanediol treated + recovery (Recovery) and Tween-20 treated + recovery (Recovery_T) HeLa cells: 2 biological replicates of Hi-C in Control, Control_T, Hex5, Tween, Recovery and Recovery_T cells, 2 biological replicates of CTCF ChIP-seq in Control, Hex5 and Recovery cells.

first: Sergey

middle: V

last: Razin


title: Chromatin regulatory dynamics of early development and regional specification in a directed differentiation model of the human small intestine

status: Public on Jan 27 2021

city: Ithaca

first: Praveen

last: Sethupathy

state: New York

address: 618 Tower Road, T7006

institute: Cornell University

summary: Assessment of genomewide nascent transcription activity and transcriptomic profiles across different stages of directed differentiation from human pluripotent stem cells (hPSC) into small intesitnal organaoids

overall_design: Global nascent transcirption activity was determined by chromatin run-on sequencing (ChRO-seq) and transcriptomic profile was determined by bulk RNA-seq. The stages of hPSC directed differentiation included human embryonic stem cell (hESC), definitive endoderm (DE), intestinal spheroids representing duodenal region (Duo), intesitnal spheroids representing ileal region (Ile), Duo intestinal organoid, and Ile intesitnal organoid.

first: Yu-Han

last: Hung


title: RNA-seq transcriptome profiling of human pulmonary artery endothelial cells and brain microvascular endothelal cells in response to hypoxia

status: Public on Jan 26 2021

city: Boston

first: Bradley

last: Maron

state: MA

address: 77 Avenue Louis Pasteur

institute: Brigham & Women's Hospital

summary: In this study, we analzyed differences in the effect of hypoxia on the transcriptomic profile of cultured human pulmonary artery endothelial cells (HPAECs) vs. human brain microvascular endothelial cells (HBMVECs). To determine which hypoxia-regulated genes were dependent on hypoxia inducible factor 1-alpha (HIF-1alpha), some cells were transfected with an siRNA against HIF-1alpha prior to treatment with hypoxia. At the completion of the treatment protocol, mRNA was isolated using standard methodology and analyzed further by RNA-seq.

overall_design: Control human pulmonary artery endothelial cells (HPAECs) or human brain microvascular endothelal cells (HBMVECs) from male and female donors were grown under standard tissue culture conditions. Confluent cells (N=3/condition) were treated with normoxia (21% O2) or hypoxia (0.2% O2) for 24 hr. An additional group of HPAECs and HBMVECs were transfected with siRNA-HIF-1A prior to treatment with hypoxia. At the completion of the treatment protocol, mRNA was isolated and subjected to RNA-seq analysis. The Total-RNA samples were quantified using an Agilent 2100 Bioanalyzer instrument, with a  corresponding Agilent Bioanalyzer RNA Nano assay. The resulting RIN (RNA Integrity Number) scoresand concentrations were considered for qualifying samples to proceed. Sequencing was performeed using an Illumina NextSeq 500 instrument, with a High-Output 150-cycle kit to obtain Paired-End 75bp reads. The pool was loaded at 1.9pM, with 5% PhiX spikedmin as a sequencing control.

first: George

last: Alba


title: The mRNA profile from rats ventral prostate submitted to maternal low protein diet

status: Public on Jul 25 2021

city: Botucatu

first: Sérgio

middle: Alexandre Alcantara

last: Santos

state: São Paulo

address: Rua Professor Doutor Antonio 250 Celso Wagner Zanin

department: department of structural and functional biology

institute: UNESP

summary:
Purpose: The goals of this study are to compare NGS-derived ventral prostate transcriptome profiling (RNA-seq) from control and offspring submitted to maternal low protein diet during gestation and lactational period, on postnatal day 21 and 540.
Methods: Ventral Prostate mRNA profiles of 21- and 540-day-old control rats (CTR) and gestational and lactational low protein diet rats (GLLP) were generated by deep sequencing, in triplicate, using Illumina HiSeq-2500.

overall_design: Ventral prostate mRNA profiles of 21- and 540-day-old rat and (CTR) and gestational and lactational low protein diet rats (GLLP).

first: Luis

last: Justulin

first: Ana

last: Camargo

first: Sergio

first: Flávia

middle: B

last: Constatntino

first: Ketlin

middle: T

last: Colombelli


title: RNA sequencing of lung tissue from Angiotensin2/TRV023/losartan treated MCT rats

status: Public on Sep 08 2021

city: Durham

first: Gayathri

last: Viswanathan

state: NC

address: 0150, Carl building, 130 Research Drive

department: Cardiology

institute: Duke University

summary: We report the application of RNA sequencing in lung tissues of MCT rats, that were treated with Angiotensin 2 or TRV023 or Losartan to study their effects on Pulmonary hypertension. We received FPKM data of each gene from each group of MCT rats. The gene expression of the study MCT rats were normalized to control MCT rat. The differentially expressed genes in Angiotensin 2 and TRV023  treated MCT rats, confirmed that like Angiotensin 2, TRV023 is also involved in vascular remodelling and lead to worsening of pulmonary hypertension.

overall_design: MCT rats treated with Angiotensin 2 or TRV023 or Losartan

first: Zhiyuan

last: Ma

first: Sudarshan

last: Rajagopal


title: ChIP seq of CTCF and p53 in MCF10A before and after H-RAS transformation [ChIP-seq]

city: Ramat Gan

first: Ofir

last: Hakim

address: Bar-Ilan University

country: Israel

institute: Bar-Ilan University

summary: Gene transcription is substantially regulated by distant regulatory elements via combinatorial binding of transcription factors. It is more and more recognized that alterations in chromatin state and transcription factor binding in these distant regulatory elements may have key roles in cancer development. Here we focused on the first stages of oncogene induced carcinogenic transformation, and characterized the regulatory network underlying transcriptional reprogramming associated with this process. Using Hi-C data, we couple between differentially expressed genes and their differentially active regulatory elements and reveal two candidate transcription factors, p53 and CTCF, as major determinants of transcriptional reprogramming at early stages of HRas-induced transformation. Strikingly, the malignant transcriptional reprograming is promoted by redistribution of chromatin binding of these factors without major variation in their expression level. Our results demonstrate that alterations in the regulatory landscape have a major role in driving oncogene-induced transcriptional reprogramming.

overall_design: ChIP seq of 2 factors in MCF10A cell type before and after H-RAS transformation

first: Michal

last: Schwartz

first: Avital

middle: S

last: Portugez

first: Bracha

middle: Z

last: Attia

first: Miriam

last: Tannenbaum

first: Olga

last: Loza

first: Aliza

last: Chase

first: Yousef

last: Turman

first: Tommy

last: Kaplan

first: Zaidoun

last: Salah


title: Genomic Retargeting of Tumor Suppressors p53 and CTCF Promotes Oncogenesis


title: Whole transcription profile of responders to anti-TNF drugs in pediatric inflammatory bowel disease

status: Public on Jan 14 2021

city: Madrid

first: Enrique

last: Vazquez de Luis

state: Madrid

address: Melchor Fernandez Almagro, 3

institute: CNIC

summary: Background: In pediatric inflammatory bowel disease (IBD) up to 30% of patients do not respond to anti-TNF therapy. The aim was to identify pharmacogenomic markers that predict early response to anti-TNF drugs in pediatric patients with IBD. Methods: The study population included 29 responders and 9 non-responders to anti-TNF therapy patients aged <18 years with IBD who started treatment with infliximab or adalimumab. Whole gene expression profiles from total RNA isolated from whole-blood samples of 6 responders and 6 non-responders taken before biologic administration and after 2 weeks were analyzed by RNA next-generation sequencing. The expression of 6 selected genes was measured for validation in all of 38 patients recruited using qPCR; Results: Differentially expressed genes in non-responders versus responders to anti-TNF treatment were identified, 32 prior treatment initiation and 44 after 2 weeks (Log2FC (Fold change)>0.6 o <-0.6 and p value < 0.05). After validation, FCGR1A, FCGR1B and GBP1 were overexpressed in non-responders after 2 weeks of anti-TNF treatment (Log2FC 1.05, 1.21 and 1.08, respectively, p value <0.05,); Conclusion: Expression of the FCGR1A, FCGR1B, and GBP1 genes is a pharmacogenomic biomarker of early response to anti-TNF agents in pediatric IBD.

first: Luis

last: López-Fernández

first: Sara

last: Salvador Martín

first: Rebeca

last: Alvarez

last: Vázquez


title: Single cell RNAseq of gammadelta T cells from murine thymus and liver

status: Public on Jan 01 2021

city: Jinan

first: Yuan

last: Hu

state: Shandong

address: 44 Wenhuaxi Rd

institute: Shandong University

summary: Until now, the systematic and comprehensive deciphering of γδ T heterogeneity and the extrathymic developmental pathway of liver γδ T cells remains largely unsolved. In this study, we performed single cell RNA sequencing to comprehensively identify the heterogeneity of γδ T cells from murine liver and thymus. We further revealed the developmental trajectory of γδ T cells and found that liver contains γδ T precursors.

overall_design: 2 samples of  thymic and hepatic γδ T lymphocytes from  C57BL/6J mice

first: Keke

last: Fang

first: Yanan

last: Wang

first: Cai

last: Zhang


title: Next generation sequencing of chicken otocyst with pharmacologically induced loss-of-Wnt signalling

status: Public on Dec 01 2020

city: London

first: Magdalena

last: Zak

address: 332 Grays Inn Road

institute: UCL Ear Institute

summary: Bulk RNA-sequencing of individual E2.5 chicken otocyst incubated in media enriched with Wnt signalling inhibitor IWR-1 or control condition (DMSO) for 24h. Transcripts abundance was mapped to a chicken reference genome using Kallisto package and differentially expressed genes were identify using Sleuth package (genes with p-value < 0.05 were considered as significant). The expression of 1340 genes was significantly changed:733 genes were up-regulated and 607 were down-regulated. Biological Function enrichment analysis (Toppgene online tool) showed that many of these genes were associated with neurogenesis.

overall_design: Identification of genes deregulated in E3 otic explants treated with IRW-1 or DMSO for 24h

last: Żak

first: Nicolas

last: Daudet


title: The Arabidopsis NOT4A E3 ligase promotes PGR3 expression and regulates chloroplast translation

status: Public on Nov 17 2020

city: Birmingham

first: Daniel

middle: J.

last: Gibbs

address: Edgbaston

department: School of Biosciences

institute: University of Birmingham

summary: Chloroplast function requires the coordinated action of nuclear- and chloroplast-derived proteins, including several hundred nuclear-encoded pentatricopeptide repeat (PPR) proteins that regulate plastid mRNA metabolism. Despite their large number and importance, regulatory mechanisms controlling PPR expression are poorly understood. Here we show that the Arabidopsis NOT4A ubiquitin-ligase positively regulates the expression of PROTON GRADIENT REGULATION 3 (PGR3), a PPR protein required for translating several thylakoid-localised photosynthetic components and ribosome subunits within chloroplasts. Loss of NOT4A function leads to a strong depletion of cytochrome b6f and NDH complexes, as well plastid 30S ribosomes, which reduces mRNA translation and negatively impacts photosynthetic capacity, causing pale-yellow and slow-growth phenotypes. Quantitative transcriptome and proteome analyses reveal that PGR3 is misregulated in not4a. We show that the molecular not4a defects mimic those of a pgr3 mutant, and that normal plastid function is restored through transgenic PGR3 expression. Our work identifies NOT4A as crucial for ensuring robust photosynthetic function during development and stress-response, through promoting PGR3 production and chloroplast translation.

overall_design: mRNA profiles of wild-type (Col-0) and not4a mutant Arabidopsis seedlings

middle: J

first: Mark

last: Bailey


title: Microarray on T-Rheb -/- CD4+ and CD8+ cells

city: Baltimore

first: Jonathan

middle: D.

last: Powell

address: 1650 Orleans Street

department: Oncology

institute: Johns Hopkins University

summary:
A microarray was performed on T-Rheb -/- (CD4 cre positive Rheb fl/fl) and Wt C57B6J CD4+ and CD8+ cells.
T-Rheb -/- mice had reduced fasting blood glucose and we were interested to see if there was a difference in the T cells that could mediate our phenotype.

overall_design: Expression profiling was performed on 4 different samples. Gene expression from T-Rheb -/- CD4+ cells were compared to Wt C57B6 CD4+ cells. Gene expression from T-Rheb -/- CD8+ cells were compared to Wt C57B6 CD8+ cells.

first: Adam

last: Waickman

first: Matthew

middle: L

last: Arwood

middle: D


title: Single cell characterization of arrested B-lymphoid differentiation and leukemic cell states in ETV6-RUNX1-positive pediatric leukemia

status: Public on Oct 30 2020

city: Kuopio

first: Merja

last: Heinäniemi

address: Yliopistonranta 1 E

department: School of Medicine

country: Finland

institute: University of Eastern Finland

summary:
Arrested bone marrow (BM) lymphoid cell differentiation underlies the emergence of the most common childhood cancer, acute lymphoblastic leukemia (ALL). Recurrent genetic lesions often directly involve transcription factors (TFs), such as ETV6 and RUNX1 found in the most common ALL translocation. Here, we studied differential gene expression in ETV6-RUNX1 primary ALL samples and the REH cell line using single cell RNA-seq (scRNA-seq).
Submitter declares that the raw data will be deposited in EGA due to patient privacy concerns.
The raw data can be accessed at https://www.ebi.ac.uk/ega/studies/EGAS00001004374

overall_design: Primary patient samples from diagnosis (N=6 BM samples, subtype ETV6-RUNX1, 4000-8000 cells per donor) with day 15 post-treatment sample collected from two cases. Cell line experiment in REH comparing two drugs targeting ETS-factors (TK216 ERG/FLI1 and XRP44X ELK3) at 72 h (N=1, 900-2500 cells per treatment).

first: Juha

last: Mehtonen

first: Susanna

last: Teppo

first: Mari

last: Lahnalampi

first: Aleksi

last: Kokko

first: Riina

last: Kaukonen

first: Laura

last: Oksa

first: Saara

last: Laukkanen

first: Maria

last: Bouvy-Liivrand

first: Tapio

last: Lönnberg

first: Olli

last: Lohi