title: De novo transcriptome sequencing of rough lemon leaves (Citrus jambhiri Lush.) in response to Plenodomus tracheiphilus infection

status: Public on Jan 01 2021

city: Catania

first: Angela Roberta

last: Lo Piero

state: CT

address: Via S. Sofia 98

country: Italy

institute: University of Catania

summary: Mal secco is one of the most severe diseases of citrus, caused by the necrotrophic fungus Plenodomus tracheiphilus that is widespread in different Mediterranean countries. With the main aim of identifying candidate genes involved in the response of citrus plants to “Mal secco”, we performed a de novo transcriptome analysis of rough lemon seedlings subjected to artificial inoculation of P. tracheiphilus in comparison with plants inoculated with water. The analysis of Differential Expressed Genes (DEGs) highlighted a sharp response triggered by the pathogen as a total of 4,986 significant DEGs (2,865 genes up-regulated and 2,121 down-regulated) have been revealed. The analysis of the most significantly enriched KEGG pathways indicated that a crucial role in the plant response to the fungus is played by genes involved in “Plant hormone signal transduction”, “Phenylpropanoid biosynthesis” and “Carbon metabolism”. The main findings of this work are that under fungus challenge, the rough lemon genes involved both in the light harvesting and the photosynthetic electron flow were significantly down-regulated, thus probably inducing a shortage of energy for cellular functions. Moreover, the systemic acquired resistance (SAR) was activated through the induced salicylic acid cascade. Interestingly, RPM1 interacting protein 4, an essential positive regulator of plant defense, and BIR2, which is a negative regulator of basal level of immunity, have been identified thus representing useful targets for molecular breeding.

overall_design: Examination of Citrus jambhiri response to Plenodomus tracheiphilus infection. Six leaf samples coming from six different Citrus jambhiri plants have been analyzed. Three samples come from leaves wounded and inoculated with water, corresponding to three biological replicates of the control thesis. Three samples come from leaves wounded and inoculated with a suspension of Plenodomus tracheiphilus PT10 strain phialoconidia, corresponding to three biological replicates of the treatment thesis.

first: Riccardo

last: Russo

first: Angelo

last: Sicilia

first: Marco

last: Caruso

first: Carmen

last: Arlotta

first: Silvia

last: Di Silvestro

first: Frederick

last: Gmitter Jr

first: Elisabetta

last: Nicolosi

first: Angela

middle: R


title: IMITATION SWITCH is required for normal chromatin structure and gene repression in PRC2 target domains

status: Public on Jan 05 2021

city: Athens

first: Zachary

middle: A

last: Lewis

state: GA

address: 1000 Cedar St. Biosciences Bldg

department: Microbiology

country: USA

institute: University of Georgia

type: Expression profiling by high throughput sequencing

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Polycomb Group (PcG) proteins are part of an epigenetic cell memory system that plays essential roles in multicellular development, stem cell biology, X-chromosome inactivation, and cancer. In animals, plants, and many fungi, Polycomb Repressive Complex 2 (PRC2) catalyzes trimethylation of histone H3 lysine 27 (H3K27me3) to assemble transcriptionally repressed facultative heterochromatin. PRC2 is structurally and functionally conserved in the model fungus Neurospora crassa, and recent work in this organism has generated insights into PRC2 control and function. To identify new components of the facultative heterochromatin pathway, we performed a targeted screen of Neurospora deletion strains lacking individual ATP-dependent chromatin remodeling enzymes. We found the Neurospora homolog of IMITATION SWITCH (ISW) is critical for normal transcriptional repression, nucleosome organization, and establishment of typical histone methylation patterns in facultative heterochromatin domains. We also found that stable interaction between PRC2 and chromatin depends on ISW. A functional ISW ATPase domain is required for gene repression and H3K27 methylation. ISW homologs interact with accessory proteins to form multiple complexes with distinct functions. Using proteomics and molecular approaches, we identified three distinct Neurospora ISW-containing complexes. A triple mutant lacking three ISW-accessory factors and disrupting multiple ISW complexes led to widespread upregulation of PRC2 target genes and altered H3K27 methylation patterns, similar to an ISW-deficient strain. Taken together, our data show that ISW is a key component of the facultative heterochromatin pathway in Neurospora and that distinct ISW complexes perform an apparently overlapping role to regulate chromatin structure and gene repression at PRC2 target domains.

overall_design: RNA-seq, MNAse-seq and ChIP-seq to compare wild type and mutant phenotypes

first: Masayuki

last: Kamei

first: Aileen

last: Ferraro

first: Yael

last: Bar-Peled

first: Abigail

middle: J

last: Ameri


title: An ex vivo physiologic and hyperplastic vessel culture model to study intra-arterial stent therapies

status: Public on May 22 2021

city: New Haven

first: Juan

last: Wang

address: 10 Amistad Street

institute: Yale University

summary: Conventional in vitro methods for biological evaluation of intra-arterial devices such as stents fail to accurately predict cytotoxicity and remodeling events. An ex vivo flow-tunable vascular bioreactor system (VesselBRx), comprising intra- and extra-luminal monitoring capabilities, addresses these limitations. VesselBRx mimics the in vivo physiological, hyperplastic, and cytocompatibility events of absorbable magnesium (Mg)-based stents in ex vivo stent-treated porcine and human coronary arteries, with in-situ and real-time monitoring of local stent degradation effects. Unlike conventional, static cell culture, the VesselBRx perfusion system eliminates unphysiologically high intracellular Mg2+ concentrations and localized O2 consumption resulting from stent degradation. Whereas static stented arteries exhibited only 20.1% cell viability and upregulated apoptosis, necrosis, metallic ion, and hypoxia-related gene signatures, stented arteries in VesselBRx showed almost identical cell viability to in vivo rabbit models (~94.0%). Hyperplastic intimal remodeling developed in unstented arteries subjected to low shear stress, but was inhibited by Mg-based stents in VesselBRx, similarly to in vivo. VesselBRx represents a critical advance from the current static culture standard of testing absorbable vascular implants.

overall_design: Vascular mRNA profiles of native, bioreactor static stented (Stent/Flow-), bioreactor dynamic stented (Stent/Flow++), bioreactor dynamic no-stent (Flow++), and bioreactor dynamic low flow no-stent (Flow+) porcine coronary arteries

first: Jonathan

last: Wu


title: Transcriptomic Signatures of Kidney Injury in Human Renal Biopsy Specimens

status: Public on Dec 22 2020

city: Indianapolis

first: Michael

middle: T

last: Eadon

state: IN

address: 950 W Walnut St

institute: Indiana University

summary: The gene expression signature of the human kidney interstitium is not fully understood. Transcript expression of laser microdissected cortical interstitium (excluding tubules, glomeruli and large vessels) in 9 human reference nephrectomies was compared to 6 human diabetic kidney biopsy specimens. This transcriptomic data revealed novel interstitial markers and enrichment of relevant pathways. Analysis of diabetic interstitium uncovered genes with unchanged as well as down-regulated expression when compared to reference samples. Laser microdissection (LMD) methodology enables collection of transcriptomic data associated with renal interstitium to aid in interpretation of pathophysiology and precision medicine studies.

overall_design: Bulk 20 um thickness specimens from cross-sectional human kidney biopsies or nephrectomies embedded in OCT underwent RNA sequencing. All biopsy subjects had AKI.

first: Ricardo

last: Melo Ferreira

first: Daria

last: Barwinska


title: Investigtion of gene expression regulated by focal adhesion kinase (FAK) in murine squamous cell carcinoma cells.

status: Public on Dec 01 2020

city: Edinburgh

first: Graeme

middle: Richard

last: Grimes

address: Western General Hospital, Crewe Road

department: Human Genetics Unit

country: United Kingdom

institute: University of Edinburgh, The Institute of Genetics and Cancer

summary: RNA-Seq experiment with the aim to identy FAK- and FAK-kinase–dependent gene-sets in a murine squamous cell carcinoma (SCC) model.

overall_design: Three groups, FAK-WT, FAK-null and FAK-kinase dead, with three biological replicates per group.

first: Billie

last: Griffith

first: Bryan

last: Serrels

first: Adam

last: Byron

first: Margaret

middle: C

last: Frame


title: Proteomic Comparison Of DSRCT, Normal Mesenteric Tissues and ES

status: Public on Dec 31 2020

city: Houston

first: Joseph

middle: A.

last: Ludwig

state: Texas

department: Sarcoma Medical Oncology

institute: UT-MD-Anderson Cancer Center

summary: Desmoplastic small round cell tumor (DSRCT) is an aggressive malignancy that occurs predominantly in young adult males and is characterized by abdominopelvic sarcomatosis exhibiting multi-lineage cellular nests of epithelial, muscular, mesenchymal, and neural differentiation admixed with desmoplastic stroma. Prior to the recognition of the disease as a distinct clinical entity, DSRCT was invariably misclassified as poorly differentiated atypical cancer of the testes, ovary, mesentery, or gastrointestinal tract, and the chemotherapies used for those malignancies elicited poor clinical response. As previously reported, a tectonic shift in the treatment of these patients occurred after researchers made two astute observations: 1) DSRCT microscopically resembles other small round “blue cell” sarcoma subtypes (e.g., ES, rhabdomyosarcoma, synovial sarcoma), and 2) DSRCT and ES have the same N-terminal EWSR1 fusion partner. Proteomic analysis using a reverse-phase protein lysate array (RPPA) was used to elucidate biomarkers that distinguish DSRCT from adjacent normal tissue and Ewing sarcoma. This proteomic analysis revealed novel proteins, such as the androgen receptor and Syk, that may be susceptible to drug targeting, as well as oncogenic pathways like Akt-PI3K that are highly expressed in DSRCT.

overall_design: Snap-frozen DSRCT (n=16) or ES (n=6) specimens, and normal-appearing mesenteric tissue (n=8), were collected from core needle biopsies or Complete cytoreductive surgery using clinical protocols approved by MDACC’s Institutional Review Board.  Lysates were created, protein concentrations were determined, and individual protein expression was measured using a well-validated reverse-phase protein array (RPPA) as previously described37,38. Raw log2 intensity values were normalized for global protein expression by median centering across 149 antibodies tested. Individual protein expressions in DSRCT specimens, ES specimens, and mesenteric normal tissue specimens were compared using two-sided unpaired t-tests with the GeneSpring GX software program version 12.6.1-GX (Agilent Technologies). For multiple comparison testing, proteins whose expression levels between specimen types were 2-fold and significantly different (p≤0.05), were subjected to unsupervised hierarchical clustering. The protein lysates from DSRCT and ES  were subjected to RPPA analysis for 149 proteins and phosphoproteins (red, increased signal; green, decreased signal). Unsupervised double-hierarchical clustering using the Pearson correlation distance metric between proteins (rows) and Centroid linkage (a clustering method) separated the 22 samples into two groups by tumor type (columns). Of the 22 proteins, 8 had expression that differed significantly between ES and DSRCT (p≤0.05; fold-change ≥2). Proteomic profiling between DSRCT and normal mesenteric tissue specimens. The protein lysates from DSRCT and normal mesenteric tissue were subjected to RPPA analysis for 149 proteins and phosphoproteins. Unsupervised double-hierarchical clustering using the Pearson correlation distance metric between proteins (rows) and Centroid linkage (a clustering method) separated the 16 samples into two groups (columns). The heat map of all 16 samples showed 20 proteins significantly distinguishing the proteomic profile of DSRCT from that of normal mesenteric tissue (p ≤0.05; fold-change ≥2).

first: Salah-Eddine

last: Lamhamedi-Cherradi

first: Branko

last: Cuglievan

first: Brian

last: Menegaz


title: ZNF416 is a pivotal transcriptional regulator of fibroblast mechano-activation

status: Public on Nov 14 2020

city: Rochester

first: Aditya

last: Bhagwate

state: MN

address: 200 1st Street SW

institute: Mayo Clinic

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: Selinexor, a First-in-Class XPO1 Inhibitor, Is Efficacious and Tolerable in Patients with Myelodysplastic Syndromes Refractory to Hypomethylating Agents

status: Public on Nov 26 2020

city: New York

first: Xiaoli

last: Mi

state: NY

address: 1275 York Ave

department: Human Oncology and Pathogenesis Program

institute: Memorial Sloan Kettering Cancer Center

summary: PURPOSE  The median overall survival (OS) of patients with high-risk myelodysplastic syndromes (MDS) refractory to hypomethylating agents is less than 6 months and there is no standard therapy for such patients. Preclinical studies have shown that inhibition of the nuclear export protein XPO1 causes nuclear accumulation of p53 and disruption of NF-κB signaling, both relevant targets for MDS. We therefore sought to determine the safety, efficacy, and potential molecular correlates of response to selinexor, an oral selective inhibitor of XPO1, in MDS.  PATIENTS AND METHODS   We report the results of a phase 2 clinical trial of selinexor in high-risk MDS patients refractory to hypomethylating agents. The primary endpoint was overall response rate (ORR) and secondary endpoints included safety, response duration, and OS.  RESULTS  In 19 evaluable patients, ORR was 32% (95% CI, 13-57) with an additional 42% (95% CI, 24-71) achieving stable disease (SD). Median OS was 9.6 months (95% CI, 8.5-17.1) with median follow-up of 2.1 years. Grade 3 or 4 adverse events (AEs) in the first 3 patients (thrombocytopenia [n=3] and hyponatremia [n=1]) led to dose reduction to 60mg flat dose twice-weekly for two weeks followed by one week off, resulting in significantly improved tolerability. The most frequent adverse event (AE) thereafter was grade 1 or 2 nausea, anorexia and fatigue. These and other AEs were manageable with supportive care implementation. The presence of an SF3B1 mutation was significantly associated with response to selinexor (p=0.02) and correlative studies suggest splicing alterations were induced by selinexor and affected inflammatory pathways such as NF-κB.   CONCLUSIONS  Selinexor is safe and tolerable in MDS when given at 60mg twice weekly for two weeks with one week off. Responses were enriched in SF3B1 mutated patients.

overall_design: Justin,Taylor

first: Alexander

middle: V

last: Penson

first: Stella

last: Paffenholz

first: Kelsey

last: Alvarez

first: Allison

last: Sigler

first: Stephen

middle: S

last: Chung

first: Raajit

middle: K

last: Rampal

first: Jae

middle: H

last: Park

first: Eytan

middle: M

last: Stein

first: Martin

last: Tallman

first: Filiz

last: Sen

first: Mithat

last: Gönen

first: Omar

last: Abdel-Wahab

first: Virginia

last: Klimek


title: Identification of a Novel PP2A Regulator, WNK1, as Critical For Uterine Function

status: Public on Dec 08 2020

city: RTP

first: Franco

last: Demayo

state: NC

address: 111 TW Alexander Drive

institute: NIEHS

summary: We report the transcriptomic profile of uterine tissues obtained from the control (Wnk1f/f) and Wnk1 cKO (PGRCre/+;Wnk1f/f) mice during pseudopregnancy day 4.5.

overall_design: RNA-seq analyses were conducted on whole uterus during the receptive phase of pseudopregnancy.

first: Ru-pin

last: Chi

first: Tianyuan

last: Wang

first: Chou-Long

last: Huang

first: San-pin

last: Wu

first: Steven

middle: L

last: Young

first: John

last: Lydon

first: Francesco


title: Overexpression of FOXL2 altered uterine structures and functions

status: Public on Nov 06 2020

summary: Pgrcre/+Foxl2LsL/+ mice showed absence of corpus luteum in the ovary, thus the mice were infertile and continuously at diestrus stage with very thin uterus. Multiple uterine defects were observed. The gland number and penetratioin to the stroma were decreased, and the epithelial stratification and the collagen deposition in the stroma were increased. The whole uterus were collected from 12 weeks old control and mutant mice at diestrus stage for RNA-sequencing. In total, 3515 genes were differentially expressed, with 1746 upregulated and 1769 genes downregulated in the mutant mice. Pathways related to extracellular matrix, gland formation, cell proliferation were altered. The muntant mice transcriptomic changes was significantly postively correlated with the human endometriosis transcrptomic changes.

overall_design: The whole uterus were collected from 12 weeks old Pgrcre/+ and Pgrcre/+Foxl2LsL/+ mice mice at diestrus stage for RNA-sequencing.

first: Rong

last: Li

first: Lecong

last: Zhou

first: San-Pin

middle: P

first: Humphry

last: Yao

last: DeMayo


title: High resolution time course transcriptome of Plasmodium falciparum parasite 3D7 strain by RNA-seq

status: Public on Oct 20 2020

city: Singapore

first: Zbynek

last: Bozdech

state: Select if applicable

department: Molecular Genetics&Cell Biology

country: Singapore

institute: Nanyang Technological University

summary: The time course transcriptome of Plasmodium falciparum 3D7 parasite strain was generated by collecting RNA samples every 2 hours during full Intraerythrocytic Developmental Cycle.

overall_design: A total of 24 transcriptomes collected during complete Intraerythrocytic Developmental Cycle and sequenced on Illumina HiSeq4000 platform

first: Grennady

last: Wirjanata

first: Jaishree

last: Tripathi

first: Michal

last: Kucharski

first: Sourav

last: Nayak

first: Lei

last: Zhu


title: Chromatin accessibility dynamics of Chlamydia-infected epithelial cells

status: Public on Oct 28 2020

city: Wurzburg

first: Regan

last: Hayward

address: Josef-Schneider-Straße 2 / D15

country: Germany

institute: Helmholtz Institute for RNA-based Infection Research

summary: We applied Formaldehyde-Assisted Isolation of Regulatory Elements enrichment followed by sequencing (FAIRE-Seq) to generate genome-wide temporal chromatin maps of Chlamydia trachomatis-infected human epithelial cells in vitro over the chlamydial developmental cycle. We detected both conserved and distinct temporal regions of chromatin accessibility associated with C. trachomatis infection. The observed differentially accessible chromatin regions, including several Clusters of Open Regulatory Elements (COREs) and temporally-enriched sets of transcription factors, may help shape the host cell response to infection. These regions and motifs were linked to genomic features and genes associated with immune responses, re-direction of host cell nutrients, intracellular signaling, cell-cell adhesion, extracellular matrix, metabolism and apoptosis. This work will serve as a basis for future functional studies of transcriptional regulation and epigenomic regulatory elements in Chlamydia-infected human cells.

overall_design: Examination of chlamydial infection (Chlamydia trachomatis) on human epithelial cells (HEp2) from four time points using infected and mock infected samples, all in triplicate using FAIRE-Seq

first: James

last: Marsh

first: Mike

last: Humphrys

first: Willa

last: Huston

first: Garry

last: Myers


title: Improved Prediction of Smoking Status via Isoform-Aware RNA-seq Deep Learning Models

city: Boston

first: Peter

last: Castaldi

state: Massachusetts

address: 181 Longwood Ave

institute: Brigham and Women's Hospital

summary: Predictive models based on gene expression are already a part of medical decision making for selected situations such as early breast cancer treatment. Most of these models are based on measures that do not capture critical aspects of gene splicing, butwith RNA sequencing it is possible to capture some of these aspects of alternative splicing and use them to improve clinical predictions. Building on previous models to predict cigarette smoking status, we show that measures of alternative splicing significantly improve the accuracy of these predictive models.

overall_design:
RNA sequencing data were generated from whole blood samples from 2,655 subjects enrolled in the COPDGene Study. Raw read data are submitted to dbGaP.

**RAW DATA will be uploaded to dbGAP**

first: Zifeng

last: Wang


title: SIVagm coevolution leads to altered epigenetic control of CD4 expression [Bisulfite-seq]

status: Public on Oct 07 2020

city: Bethesda

first: Verena

last: Link

address: 4 Memorial Drive

department: NIAID

institute: NIH

type: Methylation profiling by high throughput sequencing

summary: African green monkeys (AGMs) are natural hosts of Simian immunodeficiency virus (SIV) that post-thymically down-regulate CD4 to maintain a large population of CD4-CD8aa+ virus-resistant cells with T-helper functionality. AGMs can become aviremic and seemingly cured of SIV by down-regulating CD4 in all CD4+ T cells in vivo. To understand the mechanisms of this process we performed genome-wide transcriptional analysis on T cells induced to down-regulate CD4 in vitro from AGMs and closely-related Patas monkeys, and T cells that maintain CD4 expression from rhesus macaques. In cells that down-regulated CD4, pathway analysis of genes common to AGM and Patas natural hosts yet unique from divided rhesus CD4+ T cells revealed an atypical regulation of the DNA methylation machinery, which de-repressed CD4 expression when pharmacologically targeted with 5-aza-2 deoxycytidine. This signature was driven largely by the dioxygenase TET3 that became down-regulated with loss of CD4 expression. CpG motifs within the AGM CD4 promoter region became methylated during CD4 downregulation in vitro and were stably imprinted in AGM CD4-CD8aa+ T cells sorted directly ex vivo. These results suggest AGMs employ epigenetic mechanisms to durably silence the CD4 gene. Manipulation of these mechanisms could provide avenues for modulating SIV and human immunodeficiency virus (HIV)-1 entry receptor expression in hosts that become progressively SIV-infected, which could lead to novel therapeutic interventions aimed to reduce HIV viremia in vivo.

overall_design: Examination of CpG methylation frequency of CD4 gene regulatory regions in sorted CD4+, CD4-CD8aa+, and CD4-CD8ab+ AGM T cells.  Cryopreserved splenocytes were flow-sorted directly ex vivo for canonical CD4+ T cells, CD4-CD8aa+ T cells, and classical CD4-CD8ab+ T cells.  The IDs in the "title" column specify African green for "AG" followed by the animal ID and corresponding T cell population sorted.

first: Joseph

last: Mudd


title: Identification of Esg genomic binding sites in Drosophila testes

status: Public on Sep 30 2020

city: London

first: Tony

middle: David

last: Southall

address: South Kensington Campus

department: Life Sciences

institute: Imperial College London

type: Genome binding/occupancy profiling by genome tiling array

summary: Here we use DamID to identify Esg binding sites in Drosophila testes in order to investigate how it maintains somatic cyst stem cells.

overall_design: 3 biological replicates were performed.

middle: D

first: Leanne

last: Jones

first: Andrea

last: Brand


title: Transcriptomic deconvolution of human endometrial cell types

status: Public on Oct 09 2020

city: Coventry

first: Jan

last: Brosens

address: University Hospital Coventry and Warwickshire

department: Warwick Medical School

institute: University of Warwick

summary: The human endometrium is a highly heterogeneous tissue comprising multiple cell-types and cellular states that change in cycle-dependent manner. This tissue heterogeneity is a major drawback when interpreting bulk (whole biopsy) transcriptomic data. To address this hurdle, RNA-seq analysis was performed on four isolated stromal cell populations [SUSD2+ perivascular stromal cells (PVCs), endometrial stromal cells (EnSCs), SUSD2+ clonal cells (MSCs), and clonal transit amplifying cells (TAs)], glandular epithelial cells, uNK cells, and matched whole tissue. Transcriptomic data were obtained for 3 whole endometrial biopsies and 6 matched, purified cell populations.

overall_design: Three independent midluteal biopsies were used to isolate, culture and sequence different endometrial cell types and stromal subsets. Following enzymatic digestion, epithelial cells (EpC) were separated from the stromal and immune cell fraction. Primary EpC were subjected to gland organoid formation and cultured for 10 days. Stromal cells were then subjected to magnetic activated cell sorting (MACS) using the W5C5 antibody that recognises SUSD2, perivascular cell marker. PVC and EnSC were propagated as standard cultures as well as subjected to colony forming unit (CFU) assays.  After overnight incubation, the supernatant of the stromal cell fraction was subjected to MACS to isolate uNK cells using a PE-conjugated anti-human CD56 monoclonal antibody. All samples were frozen and then subjected to RNA extraction and RNA library preparation.  Each library was sequenced on two separate flow cells.

first: Maria

last: Diniz-da-Costa

first: Emma

last: S Lucas

first: Pavle

last: Vrljicak


title: Effect of Smoke Dye Exposure in Zebrafish Embryos

status: Public on Feb 07 2021

city: Vicksburg

first: Natalia

last: Garcia-Reyero

state: MS

address: 3909 Halls Ferry Road

department: Engineer Research and Development Center

institute: U.S. Army Corps of Engineers

summary: Whole transcriptome analysis of dechorinated zebrafish embryos after (static?) exposure to one of five smoke dyes from 6 hours post-fertilization (hpf) to 48 hpf. Smoke dyes tested are Disperse Blue 14, Disperse Red 9, Solvent Red 169, Solvent Violet 47, and Solvent Yellow 33. Results provide insight into the molecular mechanisms of immunological response to the dyes.

overall_design: RNA Seq profiles from 48hpf zebrafish embryos

first: Kimberly

last: To

first: Lisa

last: Truong

first: Robyn

last: Tanguay


title: Comparing transcriptomes of vegetative and reproductive plants of Selaginella nipponica

city: Jishou

first: Gui-Sheng

last: Li

address: 120 Renmin South Street

country: China

institute: Jishou University

summary: Six transcriptomes were generated for vegetative and reproductive plants of the lycophyte Selaginella nipponica, aiming at the molecular basis of the transition between the two growth phases, which is important to clarify the conservation of the SPL regulation in growth phase transition within land plants.

overall_design: Three samples for the vegetative plants and the other three for the reproductive plants


title: Diet-specific circadian transcriptome of Canton-S and Tim01 females.

status: Public on Sep 22 2020

city: MILL VALLEY

first: Brian

last: Hodge

state: CA

address: 338 EDGEWOOD AVE, A

institute: Buck Institute

summary: This study aims to elucidate nutrient dependent changes to the circadian transcriptome of whole flies. In particular, we aim to identify how dietary restriction influence circadian transcriptional output. Circadian analyses were performed to invesitigate diet-dependent changes in the number of circadian transcripts as well as their phases and circadian amplitude.

overall_design: We performed a time-resolved analysis of transcript level expression from whole-fly lysates of adult Canton-S and Tim01 mutant flies reared on nutrient rich (ad libitum, 5% yeast extract) or dietary restriction (0.5% yeast extract) diets. Microarrays were performed every four hours over the course of a day (ZT 0, 4, 8, 12, 16, 20). Prior to collection, flies were reared on AL or DR diets for seven days in a 12:12h light-dark cycle at 25°C.

first: Geoffrey

last: Meyerhof

first: Subhash

last: Katewa

first: Simon

last: Melov

first: Pankaj

last: Kapahi


title: Single Cell RNA Sequencing Reveals Transcriptional Heterogeneity and Stochastic Gene Expression in Plasmodium falciparum Schizonts

status: Public on Jan 09 2021

first: Zbynek

last: Bozdech

address: 60 Nanyang Drive

department: School of Biological Sciences

summary: Genetically identical cells are known to exhibit differential phenotypes in the same environmental conditions. These phenotypic variants are linked to transcriptional stochasticity and have been shown to contribute towards adaptive flexibility of a wide range of unicellular organisms such as yeast and bacteria. Here, we investigated transcriptional heterogeneity and stochastic gene expression in P. falciparum by performing single cell RNA sequencing on blood stage schizonts. Our data reveals significant transcriptional variations in the schizonts stage that appear to reflect several diversification processes including putative developmental “checkpoint”; transcriptomically distinct parasite cells sub-populations; transcriptional switches in variable gene families and a distinct group of highly variable transcripts. Most of these features of transcriptional variability were preserved in isogenic parasite cell populations (albeit with a lesser amplitude) suggesting a role of epigenetic factors in cell-to-cell transcriptional variations in human malaria parasites. Finally, to validate our findings, we applied quantitative qRT-PCR and RNA-FISH approach and confirmed stochastic expression of several genes such as msp1, msp3, msp7, rhopH2 and eba181, some of which represent key candidates for invasion blocking vaccines

overall_design: Examination of stochastic mRNA variations between single parasites in non-isogenic and isogenic lines.

first: Jaishree

last: Tripathi

first: Lei

last: Zhu

first: Sourav

last: Nayak

first: Michal

last: Stoklasa


title: Dynamics and Competition of CRISPR-Cas9 RNP and AAV donors Mediated Genome Editings

status: Public on Dec 14 2020

city: Loma Linda

first: Yawen

last: Fu

address: 11234 Anderson St.

department: Department of Medicine

institute: Loma Linda University

summary: The CRISPR system identified in Streptococcus pyogenes (Sp) has been widely applied in genome editing. In this system, under the direction of gRNA, endonuclease SpCas9 cut both strands of the cognate DNA. These processes may disrupt the open reading frame of the gene and generate a knockout (KO) allele or achieve precise gene knockin (KI). Here we report the dynamics and DNA repair profiles after the delivery of Cas9-guide RNA ribonucleoprotein (RNP) with or without the adeno-associated virus serum type 6 (AAV6) template in four cell types. We show that editing profiles have distinct differences between cell lines. We reveal AAV6-mediated HDR effectively outcompetes MMEJ-mediated longer deletions but not NHEJ-mediated indels. However, a combination of the small molecule compounds M3814 and Trichostatin A (TSA), which potently inhibits predominant NHEJ repairs, leads to an up to a 3-fold increase in HDR efficiency.

overall_design: Illumina sequencing for CRISPR RNP-AAV genome editing on different genes in several cell types.


title: Diet and CLK-dependent expression changes in fly heads

status: Public on Oct 02 2020

summary: This study aims to elucidate how the core circadian transcription factor, CLOCK (Clk), mediates diet-dependent transcriptional changes in fly heads. In particular, we sought to identify how CLK influences gene-level expression changes in fly heads from flies that had been reared on either a high nutrient or low nutrient (dietary restriction) diet.

overall_design: We performed RNA-Seq analyses of heads with inducible, pan-neuronal over-expression of dominant negative CLK protein lacking the basic-helix-loop-helix domain (DNA binding). Flies were heterozygous for the RU486-inducible Elav-GeneSwitch-GAL4 driver as well as a UAS-controlled dominant negative clock allele (CLK-D1). Flies were reared on either a nutrient rich (ad libitum, 5% yeast-extract) or dietary restriction (0.5% yeast-extract) diet with or without the addition of RU486 (200μM) in a 12:12h light-dark cycle at 25°C. mRNA was collected at ZT0 and ZT12 from three independent biological replicates (per genotype/diet) and deep-sequencing was performed (150 PE reads, read depth of 25 million).


title: ZNF416 is a pivotal transcriptional regulator of fibroblast mechano-activation [ChIP-seq]

first: Aditya

last: Bhagwate

summary: Matrix stiffness is a central regulator of fibroblast function. However, the transcriptional mechanisms linking matrix stiffness to changes in fibroblast phenotype are incompletely understood. Here, we evaluated the effect of matrix stiffness on genome-wide chromatin accessibility in freshly-isolated lung fibroblasts using ATAC-seq. We found higher matrix stiffness profoundly increased global chromatin accessibility relative to lower matrix stiffness, and these alterations were in close genomic proximity to known pro-fibrotic gene programs. Motif analysis of these regulated genomic loci identified ZNF416 as a putative mediator of fibroblast stiffness responses. Genome occupancy analysis using ChIP-seq confirmed that ZNF416 occupies a broad range of genes implicated in fibroblast activation and tissue-fibrosis, with relatively little overlap in genomic occupancy with other mechanoresponsive and pro-fibrotic transcriptional regulators. Using loss and gain of function studies we demonstrated that ZNF416 plays a critical role in fibroblast proliferation, extracellular matrix synthesis and contractile function. Together these observations identify ZNF416 as novel mechano-activated transcriptional regulator of fibroblast biology.

overall_design: ChIPseq of ZNF416-FLAG in primary human lung fibroblasts

first: Dakota

last: Jones

first: Daniel

last: Tschumperlin


title: ZNF416 is a pivotal transcriptional regulator of fibroblast mechano-activation [ATAC-seq]

overall_design: ATACseq from freshly-isolated primary mouse lung fibroblasts plated and cultured on soft and stiff matrices


title: Distinct Pathogenic Genes Causing Intellectual Disability and Autism Exhibit a Common Neuronal Network Hyperactivity Phenotype

status: Public on Sep 14 2020

city: Nijmegen

first: Jo Huiqing

last: Zhou

address: Geert Grooteplein 26/28

country: Netherlands

institute: Radboud University

summary: Pathogenic mutations in either one of the epigenetic modifiers EHMT1, MBD5, MLL3, or SMARCB1 have been identified to be causative for Kleefstra syndrome spectrum (KSS), a neurodevelopmental disorder with clinical features of both intellectual disability (ID) and autism spectrum disorder (ASD). To understand how these variants lead to the phenotypic convergence in KSS, we employ a loss-of-function approach to assess neuronal network development at the molecular, single-cell, and network activity level. KSS-gene-deficient neuronal networks all develop into hyperactive networks with altered network organization and excitatory-inhibitory balance. Interestingly, even though transcriptional data reveal distinct regulatory mechanisms, KSS target genes share similar functions in regulating neuronal excitability and synaptic function, several of which are associated with ID and ASD. Our results show that KSS genes mainly converge at the level of neuronal network communication, providing insights into the pathophysiology of KSS and phenotypically congruent disorders.

overall_design: Gene expression analysis in cotrtical neurons in which Kleeftrsa syndome genes have been downregulated

first: Nael

middle: N

last: Kasri

first: Huiqing


title: Validation of AS1 as novel regulator of tumor resistance to immune cell attack

status: Public on Sep 21 2020

city: REGENSBURG

first: Claudia

last: GEBHARD

address: FRANZ-JOSEF-STRAUSS ALLEE 11

institute: UNIVERSITY HOSPITAL REGENSBURG

summary: The experiment was performed to verify wether knockdown of AS1 in combination with TNFa treatment affected the signature of genes involved in tumor cell apoptosis and survival

overall_design: The experiment was conducted with biological replicates. PANC-1 WT cells were reverse transfected either with siCtr1 or with siAS1 s1 (siRNA sequences) in a 6-well plate . Afterwards, the medium was replaced with 1 mL of complete DMEM and 1 mL rHuTNF-α was added at a final concentration of 100 ng/mL.  After 30 min or 4h from stimulation, tumor cells were harvested in trypsin and RNA was isolated using the RNeasy mini kit (Qiagen) according to the manufacturer´s instructions.

first: Antonio

last: Sorrentino

first: Michael

last: Rehli

last: Gebhard


title: PGR-B is responsible for a proliferative gene signature in ovarian neoplasia in PGR-B expressing mice.

status: Public on Sep 10 2020

first: Franco

last: Demayo

summary: Constitutive PGR-B expression in PGR positive cells in the mouse drives ovarian neoplasia. Chronic treatment with RU486 reduced tumor growth in these PGR-B expressing mice. To further identify how PGR-B functions to promote sustained tumor growth, PGRcre/+ PGR-BLsL/+ mice with ovarian tumors were administered a chronic-release pellet of RU486 or placebo for 24 hours. Tissue was harvested and RNA was isolated. After comparative analyses, it was concluded that PGR-B promotes cell cycle regulatory genes and oncogenic signaling pathways.

overall_design: Pgrcre/+PgrBLsL/+ mice with a tumor size between 0.5-1 cm in diameter were treated with either RU486 or placebo for 24 hours. Tumor tissue was collected for microarray analysis.

first: Margeaux

last: Wetendorf

first: Rong

last: Li

first: San-Pin

last: Wu

first: Jian

last: Liu

first: Chad

last: Creighton

first: Tianyuan

last: Wang

first: Kyathanahalli

last: Janardhan

first: Cynthia

last: Wilson

first: Rainer

last: Lanz

first: Bruce

last: Murphy

first: John

last: Lydon

first: Francesco

last: DeMayo


title: PGR-B directly binds to promoters of genes important for cell cycle, proliferation, and tumorigenesis within ovarian neoplasia from PGRcre/+mPGRBLsL/+ mice

summary: Long-term expression of PGR-B in the PGRcre/+mPGRBLsL/+ mice results in ovarian neoplasia as early as 23 weeks of age. Microarray analyses in the ovarian tumors exhibit strong molecular signatures of proliferation and tumorigenesis. In order to identify if PGR-B was directly promoting this tumorigenic agenda, ChIP-Seq was performed on ovarian neoplasia from PGRcre/+mPGRBLsL/+ mice at greater than 7.5 months of age. These data suggest PGR-B directly promotes cell cycle related genes, driving the uncontrolled growth in the ovarian tissue.

overall_design: A total of five ovarian neoplasia samples were obtained from PGRcre/+mPGRBLsL/+ mice over 7.5 months of age. Tissue was flash frozen and submitted to Active Motif for Factor Path chromatin immunoprecipitation and sequencing analysis.


title: PGR-B and ovarian neoplasma

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

overall_design: Refer to individual Series


title: SIVagm coevolutions lead to altered epigenetic control of CD4 expression [RNA-seq]

first: Verena

last: Link

sample_organism:
Erythrocebus patas
Macaca mulatta
Chlorocebus pygerythrus

overall_design: Examination of genes uniquely regulated in natural host CD4 T cells induced to down-regulate CD4 in vitro when compared to progressive host CD4 T cells that maintain CD4 expression upon in vitro stimulation.   Cells were sorted on the basis of divided or non-divided (ie CFSE high/low), CD69 expression and CD4 expression after 5 days of stimulation with SEB.  Upon sample processing, all samples were assigned the abbreviation "JB" (for Jason Brenchley) and randomized 1-54.  The abbreviation "AG" in title column specifies all samples from African green monkeys and number specifies animal ID.  All samples beginning with "R" are for Patas monkeys.  All other animal ID's specify samples from rhesus.

first: Joseph

last: Mudd


title: SIVagm coevolutions lead to altered epigenetic control of CD4 expression

platform_organism:
Erythrocebus patas
Macaca mulatta
Chlorocebus pygerythrus


title: VISTA re-programs macrophage biology through the combined regulation of tolerance and anti-inflammatory pathways

status: Public on Sep 05 2020

city: Lebanon

first: Evelien

last: Schaafsma

state: New Hampshire

address: One Medical Drive

institute: Dartmouth

summary: 1) BMDMs treated with anti-VISTA under tolerizing and immunizing conditions. 2) Time course analysis of anti-VISTA-induced alterations in human monocytes after anti-VISTA treatment. 3) Time course analysis of anti-VISTA-induced alterations in BMDMs after anti-VISTA treatment. 4) Single cell ATAC-seq of BMDMs tolerized in the presence or IgG or anti-VISTA.

overall_design: 1) BMDMs were stimulated with 10 ng/ml LPS and control Ig or anti-VISTA for 15 hours, washed 5 times with 1× PBS, then allowed to rest for 2 hours in LPS-free complete medium. BMDMs were then stimulated with 1 μg/ml LPS for 4 h. For immunization experiments,  the same protocol as the tolerization experiment was followed but the initial LPS stimulation was omitted. 2) Human monocytes treated with IgG or Anti-VISTA (10 mg/ml) for indicated time points. 3) BMDMs treated with IgG or Anti-VISTA (10 mg/ml) for indicated time points. 4) BMDMs were stimulated with 10 ng/ml LPS and control Ig or anti-VISTA for 15 hours, washed 5 times with 1× PBS, then allowed to rest for 2 hours in LPS-free complete medium.

first: Mohamed

last: ElTanbouly

first: Nicole

last: Smits

first: Parth

last: Shah

first: Chao

last: Cheng

first: Christopher

last: Burns

middle: R

last: Blazar

first: Randolph

last: Noelle

first: Rodwell

last: Mabaera


title: Systems-level analysis of peripheral blood gene expression in dementia patients reveals an innate immune response shared across multiple disorders [ad_mci]

status: Public on Nov 13 2020

city: Los Angeles

first: Daniel

last: Nachun

address: 695 Charles E Young Dr S

institute: UCLA

summary: The role of peripheral inflammation in dementia is an important but complex topic. We present here the largest cohort of peripheral blood gene expression data ever assembled from patients with dementia and matching controls.  Importantly, this cohort includes individuals from a diverse set of dementia disorders, including Alzheimer’s Disease (AD), mild cognitive impairment (MCI), and multiple disorders within the frontotemporal dementia (FTD) spectrum.  We found strong transcriptional evidence of an innate immune inflammatory response, mediated by monocytes and neutrophils, in AD, MCI, and two FTD subtypes, PSP and nfvPPA. This transcriptional inflammatory response is enriched for genetic risk for AD, in part because it is also enriched for microglial genes, which have previously been implicated in AD risk. Finally, we show that this transcriptional response is strongly enriched for binding of the transcription factors PU.1 and RELA, which have previously been linked to AD risk and progression.

overall_design: Total RNA obtained from peripheral blood in dementia patients was compared to controls.

first: Giovanni

last: Coppola


title: Gene expression in human embryonic stem cells (hESCs) upon the differentiation to neural lineages by timed delivery of retinoic acid

status: Public on Aug 31 2020

city: Stockholm

first: Johan

last: Ericson

address: Solnavägen 9

department: Cell and Molecular Biology

country: Sweden

institute: Karolinska Instituet

summary: We report gene-expression profiling of hESCs differentiating to neuronal lineages upon the treatment with Retinoic Acid and Smoothened Agonisnt. We study weather RA patterning activity relies on duration of RA exposure and can be used to direct differentiation of hESCs into distinct neuronal cell types.

overall_design: Different time points of hESCs differentiation (day 0, 2, 9, 12, 14, 21): 20 samples resenting 8 conditions in 2 biological replicates.

first: Zhanna

last: Alekseenko


title: Gene expression analysis of serotonin transporter knock-out and wildtype rats during rat postnatal prefrontal cortex development

status: Public on Oct 01 2020

first: Jo Huiqing

last: Zhou

summary: To unravel  the effect of increased extracellular serotonin levels on brain development,  RNA-seq was performed in the medial prefrontal cortex of serotonin transporter knockout and wildtype rats at five time points from early life to adulthood (postnatal day (PND) 8, 14, 21, 35 and 70). Differential expression of protein-coding genes was analyzed and we demonstrate that a lack of functional 5-HTT especially affects gene expression in early postnatal life (PND8).

overall_design: Comparison of gene expression between serotonin transporter wildtype and knockout rats at 5 different developmental time points (postnatal day 8, 14, 21, 35 and 70) in medial prefrontal cortex of Wistar rats. 5 samples per time point per genotype.


title: Impact of differentiation media on Cystic Fibrosis airway epithelial cells

city: Jouy-en-Josas Cedex

first: Vinciane

last: Saint-Criq

address: Centre de recherche Ile-de-France-Jouy-en-Josas, Domaine de Vilvert

country: France

institute: INRAE

summary: In vitro cultures of primary human airway epithelial cells (hAECs) grown at air-liquid interface have become a valuable tool to study airway biology and physiology and for drug discovery in lung diseases such as Cystic Fibrosis (CF). An increasing number of different differentiation media, are now available, making comparison of data between studies difficult. Here we investigated the impact of two common differentiation media on the transcriptome features of CF and non-CF epithelia. RNA-sequencing analysis found 20330 and 19052 transcripts in CF and NCF epithelia, respectively and revealed that 1346 genes were significantly regulated in CF cells compared to 922 in NCF cells.

overall_design: mRNA profiles of 3 CF and 3 non-CF (NCF) airway epithelial cell samples differentiated in 2 different media.

first: Michael

middle: A

last: Gray

first: John

last: Casement

first: Livia

last: Delpiano


title: Time series single cell transcriptomics of cardiac inflammation after myocardial infarction in mice

status: Public on Aug 18 2020

city: Würzburg

first: Antoine-Emmanuel

last: Saliba

summary: We performed time-series single-cell RNA-seq analysis of blood CD11b+ cells and of the inflammatory infiltrate in the heart of C57BL/6J male mice in a model of permanent myocardial infarction.

overall_design: Cardiac CD45+ total leukocytes (datasets F8, F9, F11, F12, G1), cardiac CD11b+ myeloid cells (dataset H10), or blood and cardiac CD11b+ cells (Sample C11_2) were extracted from the blood or heart of mice in the steady state and at various time points after myocardial infarction or sham surgery in a murine model of permanent myocardial ischemia induced by ligation of the left descendant coronary artery, and analyzed by single-cell RNA-sequencing. In the H10 dataset, CD11b+ cells were sampled at 1, 3, and 5 days after infarction, labeled with CITE-Seq and hashtag antibodies and pooled for multiplexed analysis. In Sample C11_2, blood and cardiac CD11b+ cells from control animals and mice at 1 and 3 days after sham or myocardial infarction surgery were labeled with CITE-seq and hashtag antibodies and pooled for multiplexed analysis.

first: Ehsan

last: Vafadarnejad

first: Giuseppe

last: Rizzo

first: Laura

last: Krampert

first: Panagiota

last: Arampatzi

first: Vallery

last: Nugroho

first: Dirk

last: Schulz

first: Melanie

last: Roesch

first: Alma

last: Zernecke

first: Antoine

middle: E

first: Clément

last: Cochain


title: Multiomics profiling during onset of Salmon maturation

status: Public on Aug 28 2020

city: Brisbane

first: Amin

middle: Roushdy

last: Mohamed

state: Queensland

address: 306 Carmody Rd, University of Queensland

department: Agriculture and Food

country: Australia

institute: CSIRO

summary: This SuperSeries is composed of the SubSeries listed below.This contains multi-omics datasets transcriptomic (RNA-Seq), methylomic (WGBS), and epigenomics (ATAC-seq) obtained during onset of sexual maturation in Atlantic salmon. We used gene regulatory networks (GRNs) to integrate results from these multi-omic analyses to identify key regulators of maturation.


title: Immunity to commensal skin fungi promotes psoriasiform skin inflammation

first: Verena

last: Link

summary: Under steady state conditions, the immune system is poised to sense and respond to the microbiota. As such, immunity to the microbiota, including T cell responses, is expected to precede any inflammatory trigger. How this pool of preformed microbiota-specific T cells contributes to tissue pathologies remains unclear. Here, using an experimental model of psoriasis, we show that recall responses to commensal skin fungi can significantly aggravate tissue inflammation. Enhanced pathology caused by fungi pre-exposure depends on Th17 responses and neutrophil extracellular traps and recapitulates features of the transcriptional landscape of human lesional psoriatic skin. Together, our results propose that recall responses directed to skin fungi can directly promote skin inflammation and that exploration of tissue inflammation should be assessed in the context of recall responses to the microbiota.

overall_design: Examination of T cells and whole tissue in control mice versus mice treated with Candida albicans, imiquimod or a combination of Candida albicans and imiquimod with RNA-seq.

first: Charlotte

last: Hurabielle

first: Saeko

last: Nakajima

first: Yasmine

last: Belkaid


title: Induced Expression of VEGFC, ANGPT, and EFNB2 and Their Receptors Characterizes Neovascularization in Proliferative Diabetic Retinopathy

status: Public on Aug 10 2020

city: Wuhan

first: Dong

last: Chen

state: Hubei

address: 388 GaoXin 2nd Road, East Lake Hi-Tech Development Zone

department: Center for Genome Analysis

institute: ABLife, Inc.

summary: Proliferative diabetic retinopathy (PDR) is the advanced stage of diabetic retinopathy (DR), coupling with irregular neovascularization, and is the leading cause of blindness in working-age people; but the molecular mechanism of vascular differentiation in PDR remains poorly characterized. In our study, we obtained the transcriptome profile of neovascular proliferative membrane specimens from patients with PDR via high-throughput sequencing and advanced bioinformatics. Marker genes of neovascularization were validated and distinct gene expression patterns were formed of PDR compared with normal retina. We also discovered gene sets that were co-expressed with vascular endothelial growth factor A (VEGFA), including transcription factors (TFs) that dysregulate VEGFA. In particular, ETS transcription factors family could negatively regulate VEGFA. We also detected a set of genes related to PDR was dramatically changed from pre-mRNA to mature mRNA. In summary, our study firstly presented the profile of neovascular proliferative membrane and identified new marker genes and key regulators of VEGFA, which could contribute the molecular therapy of PDR in the future.

overall_design: Total 30 transcriptome profile of neovascular proliferative membrane specimens from patients with PDR and normal samples.

first: Yi

last: Zhang

first: Yuxin

last: Li


title: Scalable Dual-omic Profiling with Single-nucleus Chromatin Accessibility and mRNA Expression Sequencing 2 (SNARE-seq2)

status: Public on Sep 09 2020

city: La Jolla

first: Kun

address: 9500 Gilman Dr Mailcode: 0412

department: Bioengineering

institute: University of California, San Diego

summary: We perform benchmark experiments using cell lines to develop and assess the performance of a scalable method for generating matched RNA and chromatin accessibility profiles

overall_design: 3T3 cells amd A549 cells were fixed with 1% formaldehyde and cryopreserved in 1x PBS with 10% (vol/vol) DMSO and 0.1% (wt/vol) BSA for three weeks. GM12878 cells were freshly fixed with 1% formaldeyhyde and ran in two separate experiments. GM12878 nuclei were lysed in cell lysis buffer with RNase Inhibitors (10 mM Tris pH 7.4, 10 mM sodium chloride, 3 mM magnesium chloride, 0.1% v/v NP-40, Superase RNase Inhibitors, Enzymatics RNase Inhibitors) then fixed with 1% formaldehyde. Fixed samples were processed with SNARE-seq2 protocol.

first: Nongluk

last: Plongthongkum

first: Dinh

last: Diep


title: Investigation of lncRNA expression signatures in hypoxia-induced HCC cells

status: Public on Aug 01 2020

city: Xi'an

first: Kangsheng

last: Tu

address: 277 Yanta West Road

department: Department of Hepatobiliary Surgery

institute: First Affiliated Hospital of Xi'an Jiaotong University

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

summary: To investigate the differentially expressed lncRNAs between hypoxia-induced Hep3B cells and normoxia cultured Hep3B cells, Arraystar Human LncRNA Microarray V5.0 is employed for the global profiling of human LncRNAs and protein-coding transcripts.

overall_design: The differentially expressed lncRNAs in human Hep3B cells were measured at 48 hours after exposure to normoxia or hypoxia. Three independent repeats were performed for each experiment.

first: Qingguang

last: Liu


title: Comparative transcriptome analysis of the skin reveals the innate immunity difference between wild-type and yellow mutant rainbow trout

status: Public on Jul 09 2020

city: Xining

first: Delin

last: Qi

address: No. 251, Ningda Road

institute: Qinghai university

summary:
Purpose: The goal of this study is to identify the difference of immunity between wild-type and yellow mutant rainbow trout in natural flowing water pond culture environment.
Methods: The transcriptomic profiles of the skin were generated by using the Hiseq™4000 sequencing platform.
Results: A total of 557,976,332 clean reads were yielded from six libraries and then assembled into 38,226 genes. Using P-value of 0.05 as the threshold, 3373 differentially expressed genes (DEGs) were obtained between WR_S and YR_S rainbow trout skin including the members of HSP90, V-ATPases, GST, SUGT1, NLRP3, NOD1, TLR3, IFR3, DHX58, IFIH1, JAK1, JAK2, STAT1 and NAMPT (|log2 fold-change| ranged from 1 to 4). Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis of DEGs were performed. A majority of DEGs were enriched in innate immune-related GO terms and pathways, such as activation of innate immune response, inflammatory response, innate immune response, NAD+ADP-ribosyltransferase activity and NAD biosynthetic process in sub-categories of GO terms, and RIG-I-like receptor signaling pathway, NOD-like receptor signaling pathway, Toll-like receptor signaling pathway, Phagosome, Jak-STAT signaling pathway in KEGG enrichment pathways. Meanwhile, several immune-related metabolic pathways were also identified including metabolism of Xenobiotics by cytochrome P450, Glutathione metabolism, Nicotinate and nicotinamide metabolism. Additionally, 15 DEGs were selected and validated their expression level by qRT-PCR to confirm accuracy of the RNA-seq.
Conclusions: Our study is the first time to clarify the skin innate immunity difference between wild-type and yellow mutant rainbow trout in the natural flowing water pond culture environment. Our results show that the expression of most immune-related genes in the corresponding pathways were up-regulated in WR_S rainbow trout. We presumed that the disease resistance of WR_S rainbow trout might be stronger than YR_S rainbow trout.

overall_design: The transcriptomic profiles of the skin from wild-type and yellow mutant cultured in the natural flowing water pond culture environment were generated by using the Hiseq™4000 sequencing platform

first: Jinqiang

last: Huang

first: Shenji

last: Wu


title: The orchestrated cellular and molecular responses of the kidney to endotoxin define a precise sepsis timeline.

status: Public on Jul 10 2020

city: Indianapolis

first: Michael

middle: T

last: Eadon

address: 950 W Walnut St

institute: Indiana University

summary: Clinical sepsis is a highly dynamic state that progresses at variable rates and has life-threatening consequences. Staging patients along the sepsis timeline requires a thorough knowledge of the evolution of cellular and molecular events at the tissue level. Here, we investigated the kidney, an organ central to the pathophysiology of sepsis. Single cell RNA sequencing and spatial transcriptomics revealed the involvement of various cell populations in injury and repair to be temporally organized and highly orchestrated. We identified key changes in gene expression that altered cellular functions and can explain features of clinical sepsis. These changes converged towards a remarkable global cell-cell communication failure and organ shutdown at a well-defined point in the sepsis timeline. Importantly, this time point was also a transition towards the emergence of recovery pathways. This rigorous spatial and temporal definition of murine sepsis will uncover precise biomarkers and targets that can help stage and treat human sepsis.

overall_design: The 129sv mouse was sacrificed 6 hours after cecal ligation puncture and tissue was placed in an OCT mold and stored at -80 C. A septic mouse kidney was immediately frozen in Optimal Cutting Temperature media (O.C.T.). A 10 μm frozen tissue section was cut and affixed to a Visium Spatial Gene Expression library preparation slide (Catalogue # 1000200, 10X Genomics, Pleasanton, California, USA). The specimen was fixed in methanol and stained with hematoxylin-eosin reagents. Images of hematoxylin-eosin-labeled tissues were collected as mosaics of 10x fields using a Keyence BZ-X810 fluorescence microscope equipped with a Nikon 10X CFI Plan Fluor objective. The tissue was then permeabilized for 12 minutes and RNA was isolated. The cDNA libraries were prepared and then sequenced on an Illumina NovaSeq 6000. Using Seurat 3.1.4, we identified anchors between the integrated single cell object and the spatial transcriptomics datasets and used those to transfer the cluster data from the single cell to the spatial transcriptomics. For each spatial transcriptomics spot, this transfer assigns a score to each single cell cluster. We selected the cluster with the highest score in each spot to represent its single cell associated cluster. Using a Loupe Browser, expression data was visualized overlying the hematoxylin-eosin image.

first: Takashi

last: Hato

first: Ricardo

last: Melo Ferreira

first: Danielle

last: Janosevic


title: Constitutive expression of the progesterone receptor isoforms promotes the hormone-dependent of the ovarian neoplasma

city: RTP

first: Franco

last: Demayo

address: 111 TW Alexander Drive

institute: NIEHS

summary: At 23 weeks old, the PGR-cre induced PGR-B constitute expression promoted the ovarian tumor progression in female mice. The transcriptomice changes can be divided into two subclass, each represented stage I and stage II ovarian tumor we observed in this study. Stage I is the early stage of ovarian tumor with small amount of PGR-B positve cells observed in the ovary but relatively normal ovarian structures. As expected, stage I transcriptome is similar to the Pgrcre/+ ovary but already exhibited 364 differentiated expression genes suggesting the early transformation of PGR-B positive cells to the neoplasma tissues. Stage II contains snumerous large pleomorphic cells, sometimes well circumscribed tumor, and most of these cells are PGR positve, but still maintains some normal ovarian functions. Stage II exibited 3129 differentiated expression genes that are involved in tumorigenesis pathways such as activated PI3K/AKT signaling, altered cell cycle pathways.

overall_design: Pgrcre/+ and Pgrcre/+PgrBLsL/+ mice were sacrificed at diestrus stage around 23 weeks old. The ovaries were collected for microarray analysis

first: Margeaux

last: Wetendorf

first: Rong

first: San-Pin

first: Jian

first: Chad

middle: J

last: Creighton

first: Tianyuan

last: Wang

first: Kyathanahalli

last: Janardhan

first: Cynthia

last: Wilson

first: Rainer

last: Lanz

first: Bruce

last: Murphy

first: John

last: Lydon

first: Francesco

last: DeMayo


title: PGR-B expression in the ovary drives ovarian neoplasia and a tumorigenic transcriptome.

summary: Constitutive PGR-B expression in PGR positive cells in the mouse drives ovarian neoplasia. To compare the differences between the PGR-B expressing ovarian neoplasia tissue and age-matched wildtype ovaries, microarray analysis was performed. It was concluded that PGR-B expression promoted a tumorigenic signature distinctly different from wildtype ovarian tissue.

overall_design: Wildtype and Pgrcre/+PgrBLsL/+ mice were sacrificed at 33 weeks of age. The ovaries were collected for microarray analysis.

last: Li

last: Liu


title: Optimized design of antisense oligomers for targeted rRNA depletion

status: Public on Jun 28 2020

city: Pittsburgh

first: Miler

last: Lee

state: PA

address: 4249 Fifth Ave

department: Biological Sciences

institute: University of Pittsburgh

summary: RNA sequencing (RNA-seq) has become a standard method for quantifying gene expression transcriptome-wide. Due to the extremely high proportion of ribosomal RNA (rRNA) in total RNA, sequencing libraries usually incorporate messenger RNA (mRNA) enrichment. Although polyadenylate (poly(A)) tail selection is widely used, many applications require alternate approaches such as rRNA depletion. Recently, selective rRNA digestion, using RNaseH and antisense DNA oligomers that tile the length of target RNAs, has emerged as an easy, cost-effective alternative to commercial rRNA depletion kits. Here, we present a streamlined RNaseH-mediated rRNA depletion method that uses shorter antisense oligos that only sparsely tile the target RNA, in a digestion reaction of only 5 minutes. We wrote a Web tool, Oligo-ASST, that simplifies oligo design to favor target regions with optimal thermodynamic properties, and additionally allows users to design common oligo pools that can simultaneously target divergent RNAs in their regions of higher sequence similarity. We demonstrate the efficacy of these oligos by building rRNA-depleted sequencing libraries for Xenopus laevis as well as zebrafish, which expresses two distinct versions of the 28S, 18S, 5.8S, and 5S rRNAs during embryogenesis. These libraries efficiently deplete rRNA to <5% of total reads, on par with poly(A) selection, and also reveal expression of many non-adenylated RNA species. Oligo-ASST is freely available at https://mtleelab.pitt.edu/oligo to design antisense oligos for any taxon or to target any abundant RNA for depletion.

sample_organism:
Danio rerio
Xenopus laevis

platform_organism:
Danio rerio
Xenopus laevis

overall_design: RNA-seq with different mRNA enrichment methods

first: Wesley

last: Phelps


title: A cytoskeleton regulator AVIL drives tumorigenesis in glioblastoma

status: Public on Jun 08 2020

city: Charlottesville

first: Zhongqiu

last: Xie

state: VA

address: 345 Crispell Dr,  Charlottesville

department: Pathology

institute: University of Virginia

summary: Total RNA extracted from knockdown or overexpress AVIL  in GBM U87 cells. and RNA-seq after sample quality control.

overall_design: Knockdown or overexpress AVIL in GBM U87 cell samples

first: Hui


title: Hnrnpa21 regulates myogenic fate plasticity

status: Public on Jun 16 2020

city: Boulder

first: Joshua

middle: Riley

last: Wheeler

state: CO

address: 3415 Colorado Ave

department: Biochemistry

institute: University of Colorado

summary: RNA-binding proteins (RBPs) are essential for skeletal muscle regeneration and RBP dysfunction causes muscle degeneration and neuromuscular disease (NMD). How the timing of RBP function governs the complex cell fate decisions during muscle regeneration is poorly understood. Here, single cell analysis of skeletal muscle regeneration reveals the timing of NMD-associated RBPs expression in muscle progenitors, including a massive upregulation of Hnrnpa2b1 (A2b1). A2b1 promotes muscle progenitor plasticity by regulating the splicing of RNAs expressed at specific times during the trajectory of muscle differentiation. Using RBP-RNA engagement scoring and machine learning, we accurately predict NMD-associated RBP functionality in directing myogenesis. Together our analysis reveals how A2b1 regulates myogenic plasticity and provides a broadly applicable single cell methodology for examining how RBPs influence complex cell fate trajectories.

overall_design: RNA-seq in differentiating hnrnpa2b1 KO and WT c2c12 cells

first: Oscar

last: Whitney

first: Bradley

last: Olwin

first: Roy

last: Parker


title: Mechanism of translation inhibition by type II GNAT toxins: AtaT, TacT, and ItaT

status: Public on Jun 17 2020

city: Moscow

first: Dmitry

middle: Vadimovich

last: Bikmetov

state: Moscow

address: Vavilova, 34/5

country: Russia

institute: Center for Precision Genome Editing and Genetic Technologies for Biomedicine, IGB RAS

summary: Type II toxin-antitoxin (TA) systems are two-gene modules widely distributed among prokaryotes. GNAT toxins associated with the DUF1778 antitoxins represent a large family of type II TAs. GNAT toxins inhibit cell growth by disrupting translation via acetylation of aminoacyl-tRNAs. Using ribosome profiling, we investigated the in vivo substrate specificity of three GNAT toxins: AtaT2, TacT3, and ItaT.

sample_organism: Escherichia coli str. K-12 substr. MG1655

overall_design: Ribosome profiling of E. coli BW25113 cells with or without expression of GNAT toxins. Exponentially growing cells transformed with pBAD33 plasmid bearing a toxin gene or an empty pBAD33 vector were collected 15 min after induction.

first: Stepan

middle: V

last: Ovchinnikov

first: Kyle

last: Mangano

first: Nora

last: Vazquez-Laslop

first: Alexander

last: Mankin

first: Konstantin

last: Severinov

first: Svetlana

last: Dubiley


title: Role of long non-coding RNA Gas5 in cocaine action

status: Public on Jun 26 2020

city: Tallahassee

first: Nicholas

middle: James

last: Waddell

state: FL

address: 319 Stadium Dr

institute: Florida State University

summary: Long non-coding RNAs (lncRNAs) are a class of transcribed RNA molecules greater than 200 nucleotides long. Though do not encode proteins, they play functional roles in gene expression regulation. LncRNAs are notably abundant in the brain, however, their neural functions are largely unknown. Here we demonstrate that repeated short- and long-term cocaine administrations all decreased the expression of lncRNA Gas5 in the nucleus accumbens (NAc) of adult male mice. To illustrate the functional role of Gas5, we performed viral mediated overexpression of Gas5 in the NAc and found decreased cocaine-induced conditioned place preference. Furthermore, Gas5 overexpression also led to decreased drug intake, lower motivation, repressed compulsivity to acquire cocaine, and faster extinction of drug during cocaine self-administration. Transcriptome profiling identified numerous Gas5 mediated gene expression changes that are enriched in relevant neural function categories. Interestingly, these Gas5 regulated gene expression changes significantly overlap with chronic cocaine induced transcriptome alterations, which suggests that Gas5 may serve as a main transcription regulator of cocaine response. Our study therefore displays a novel lncRNA based molecular mechanism of cocaine action.

overall_design: Transcriptome profilling of 6 Nucleus Accumbens tissue from mouse brain samples.  3 samples had viral mediated overexpression of Gas5 and 3 control samples received a GFP construct as control, with HSV as the viral vector.

first: Haiyang

last: Xu

first: Amber

last: Brown

first: Xiaochuan

first: Graham

last: Kaplan

first: Javed

last: Chitaman

first: Victoria

last: Stockman

first: Rachel

last: Hedinger

first: Ryan

last: Adams

first: Kristen

last: Abreu

first: Li

last: Shen

first: Rachael

last: Neve

first: Zuoxin

last: Wang

first: Eric

last: Nestler

first: Jian

last: Feng


title: Multitissue transcriptomic profiling during onset of salmon maturation

first: Amin

last: Mohamed

summary: We sequenced mRNA from four biological replicates of each tissue before (T1) and after the onset of maturation (T2, T3, T4). A total of 3.2 billion paired-end reads were mapped against the Atlantic salmon reference genome with 72% mapping efficiency to create an average depth of 50 million reads per library. The number of differentially expressed genes (DEGs) increased with elapsed time following the onset of the long light photoperiod for the two BPG axis tissues (pituitary and ovary). Of these, the ovary underwent the most dramatic remodelling over time with 403, 1,709 and then 3,497 DEGs observed at timepoints T2, T3 and T4 respectively. This increasing trajectory of differential ngene expression, coupled with the elevated GSI following the light stimuli, strongly suggests the experimental approach successfully initiated the onset of maturation. Next, we identified clusters of DEGs in each of the analysed tissues, which describe their physiological roles. The identity of the DEGs, in response to the onset of maturation, revealed the key players involved in the earliest triggers into maturation. Among these, upregulation of genes encoding specififc pituitary hormones such as gonadotropins along with genes encoding transcription factors (such as GATA2) are significant in controlling onset of maturation. In addition, genes encoding pituitary hormone receptors and follicular development were upregulated in ovary.

overall_design: We sequenced mRNA from four biological replicates of four tissues (brain, pituitary gland, ovary and liver) at four timepoints before (T1) and after the onset of maturation (T2, T3, T4).

first: Marina

last: Naval-Sanchez

first: Moira

last: Menzies

first: Bradley

last: Evans

first: Antonio

last: Reverter

first: James

last: Kijas


title: Generation of human bronchial organoids for SARS-CoV-2 research

status: Public on May 26 2020

city: Suita

first: Daisuke

last: Okuzaki

state: Osaka

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

country: Japan

institute: Osaka univ.

summary: Coronavirus disease 2019 (COVID-19) is a disease that causes fatal disorders including severe pneumonia. To develop a therapeutic drug for COVID-19, a model that can reproduce the viral life cycle and can evaluate the drug efficacy of anti-viral drugs is essential. In this study, we established a method to generate human bronchial organoids (hBO) from commercially available cryopreserved primary human bronchial epithelial cells (hBEpC) and examined whether they could be used as a model for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) research. The hBO were found to contain basal, club, ciliated, and goblet cells. Also, angiotensin-converting enzyme 2 (ACE2), which is a receptor for SARS-CoV-2, and transmembrane serine proteinase 2 (TMPRSS2), which is an essential serine protease for priming spike protein of SARS-CoV-2, were highly expressed. After hBO were infected with SARS-CoV-2, remarkable amplification of the viral genome and the expression of spike protein of the virus was confirmed. In addition, cytotoxicity and pyknosis cells were observed due to the virus infection. Furthermore, treatment with camostat, an inhibitor of TMPRSS2, reduced the viral copy number to 2% of the control group. RNA-seq analyses revealed genes whose expression was altered by SARS-CoV-2 infection and camostat treatment. These results suggest that our hBO are acceptable for SARS-CoV-2 infection and replication, but also can be used as a model for COVID-19 drug discovery.

overall_design:
Total RNA was isolated from human bronchial organoids, primary human bronchial epithelial cells, and A549 cell, and then RNA-seq was performed. The human bronchial organoids were infected with SARS-CoV-2 in the presence of absence of camostat. At 5 days after the infection, total RNA was collected and RNA-seq was performed.

**Please note that the processed data *csv files have been updated on June 10, 2020**

first: Toru

last: Okamoto

first: Kazuo

last: Takayama


title: Liver Chromatin accessibility landscapes during onset of salmon maturation

summary: We sequenced 12 ATAC-Seq lbraries from four biological replicates before (T1) and after the onset of maturation (T2, T3, T4) from liver. To characterise changes in chromatin state following long light initiation, we defined differentially accessible regions (DARs) where mapping counts differed significantly between T1 and other time points. This revealed a strong early remodelling in the chromatin state landscape, as most DARs were observed at T2 (n=1501) before decreasing in stepwise fashion at T3 (n=477) and T4. The majority of DARs (n=1036 or 57%) exhibit reduced accessibility at T2 compared with T1 and subsequently remained unchanged at later time points (Fig. 5a; Supplementary Figure S14). Similarly, regions that gained accessibility at T2 (n=696 or 38%) also remained unchanged at later timepoints. This left less than 10% of DARs (n=99) that displayed an oscillating pattern following the onset of the maturation. Together, this revealed the ATAC-seq signatures were predominantly stable chromatin state changes.

overall_design: We sequenced ATAC-seq from four biological replicates of liver at four timepoints before (T1) and after the onset of maturation (T2, T3, T4).


title: Multitissue DNA methylome profiling during onset of salmon maturation

summary: We performed a time course experiment, whereby animals were manipulated with photoperiod before tissues were collected across the time window when animals commence sexual development. We performed whole genome bisulfite sequencing of three salmon tissues (pituitary, ovary and liver) at both the beginning and end of the experiment, to take a first look at the patterns of DNA methylation and examine how they change in response to the onset of an important life history trait. Comparison across timepoints revealed 6,373 differentially methylated regions (DMRs), of which approximately 50% were located within genes (DMGs). The ovary underwent the most profound remodelling, with a strong bias towards increased methylation levels (hyper-methylation). Weak correlation was observed considering all available genes, suggesting methylation may not be the key epigenomic regulator of global expression in the context of our experiment. However, we found a significant overlap between DMGs and differentially expressed genes in the ovary. Taken together, our results suggest chromatin remodelling genes play a role in the commitment of animals to the sexual maturation pathway.

overall_design: We sequenced 12 WGBS libraries of three tissues (pituitary gland, ovary and liver) at two timepoints before (T1) and after the onset of maturation (T4).


status: Public on May 13 2020

city: Shanghai

first: Fangzhou

last: Lou

address: 280 South Chongqing Road

department: Shanghai Institute of Immunology

institute: Shanghai Jiao Tong University School of Medicine

summary: To identify differences between keratinocytes (w/o Pp6) and dermal dendritic cells, epidermal or dermal cell suspensions from C57BL/6 mice or K5. Pp6fl/fl mice were subject to single-cell RNA-seq.

overall_design: Single-cell RNA-seq of mouse epidermal or dermal samples dervied from 10 week-old C57BL/6 mice treated with imiquimod or not, 10 week-old K5. Pp6fl/fl mice without skin lesions, and 18 week-old K5. Pp6fl//fl mice with psoriasis-like skin lesions.

first: Yang

last: Sun


title: NtrBC as a regulator of adaptive lifestyles and virulence

status: Public on Apr 16 2020

city: Vancouver

first: Robert

middle: EW

last: Hancock

state: BC

address: 2259 Lower Mall Research Station

department: Microbiology and Immunology

country: Canada

institute: University of British Columbia

summary: When comparing dNtrB and dNtrC to WT, we identified 790 and 1184 dysregulated genes, respectively. Genes were considered dysregulated if the absolute log2 fold change was greater than 1.5 and an adjusted p value of < 0.05. The large number of commonly DE genes indicated NtrB and C act as a cognate pair. Most notably, there were several dysregulated genes involved in nitrogen and carbon metabolic processes.

overall_design: Examination of two PA14 knockout strains (dNtrB and C) in swarming conditions using RNA-Seq

first: Morgan

last: Alford

first: Arjun

last: Baghela


title: Genome-wide transcriptomics identifies an early preclinical signature of prion infection

status: Public on Jun 12 2020

city: Zurich

first: giancarlo

last: russo

state: Schweiz

address: winterthurerstrasse 190

department: Functional Genomics Center Zurich

country: Switzerland

institute: ETH/University of Zurich

summary: We constructed a searchable genome-wide atlas of mRNA abundance, splicing and editing alterations during the course of disease in prion-inoculated mice.

overall_design: Mice were inoculated with prions or control brain homogenate and were analyzed at different time points during disease progression.

first: Silvia

last: Sorce

first: Mario

last: Nuvolone

first: Giancarlo

last: Russo

first: Claudia

last: Scheckel

first: Adriano

last: Aguzzi


title: DNA Methylation Profiling Reveals Prognostically Significant Groups in Pediatric Adrenocortical Tumors: A Report From the International Pediatric Adrenocortical Tumor Registry

status: Public on May 16 2020

city: Memphis

first: Quynh

last: Tran

state: TN

address: 262 Danny Thomas Place, C4029, Mail Stop 250

institute: St. Jude Children's Research Hospital

type: Methylation profiling by genome tiling array

summary: Pediatric adrenocortical carcinomas (ACCs) are aggressive; the overall survival of pediatric patients with ACCs is 40%-50%. Appropriate staging and histologic classification are crucial as children with incompletely resected tumors or metastatic disease have a dismal prognosis. The clinical course of pediatric adrenocortical tumors (ACTs) is difficult to predict using the current classification schemas, which rely heavily on subjective microscopic and gross macroscopic variables. Recent advances in adult ACT studies have revealed distinct DNA-methylation patterns with prognostic significance that have not been systematically interrogated in the pediatric population.

overall_design: We performed DNA-methylation analyses on 48 newly diagnosed ACTs from the International Pediatric Adrenocortical Tumors Registry (IPACTR) and 12 pediatric adrenal controls to evaluate for distinct methylation groups. Pediatric methylation data were also compared systematically to the adult ACC cohort from The Cancer Genome Atlas (TCGA).

first: Michael

last: Clay

first: Brent

last: Orr


title: A transcriptome-based molecular census of human basal cell carcinoma subtypes at single cell resolution

status: Public on Aug 14 2020

city: Irvine

first: Scott

last: Atwood

state: California

address: 4340 McGaugh Hall, Ring Rd

department: Department of Developmental & Cell Biology

institute: University of California, Irvine

summary: We report the single cell transcriptomes of 4 basal cell carcinoma subtypes and 2 peri-tumor skin samples.

overall_design: Examination of cell heteregeneity in human basal cell carcinoma.

first: Christian

middle: F

last: Guerrero-Juarez

first: Gun

middle: H

last: Lee

first: Qing

last: Nie

first: Kavita

last: Sarin

middle: X


title: Genome-wide RNA analysis of the effects of MASTL silencing in breast cancer cells

status: Public on Apr 14 2020

city: Turku

first: Elisa

last: Närvä

address: Tykistökatu 6

department: Turku Centre for Biotechnology

country: Finland

institute: University of Turku

summary:
The effect of short term (24h and 48h) silencing of MASTL for total transcriptome was studied in human breast cancer cell line (MDA-MB-231).

Microtubule-associated serine/threonine-protein kinase-like (MASTL) is a mitosis-accelerating kinase with emerging roles in cancer progression. However, possible cell cycle–independent mechanisms behind its oncogenicity remain ambiguous. Here, we identify MASTL as an activator of cell contractility and MRTF-A/SRF (myocardin-related transcription factor A/serum response factor) signaling. Depletion of MASTL increased cell spreading while reducing contractile actin stress fibers in normal and breast cancer cells and strongly impairing breast cancer cell motility and invasion. Transcriptome and proteome profiling revealed MASTL-regulated genes implicated in cell movement and actomyosin contraction, including Rho guanine nucleotide exchange factor 2 (GEF-H1, ARHGEF2) and MRTF-A target genes tropomyosin 4.2 (TPM4), vinculin (VCL), and nonmuscle myosin IIB (NM-2B, MYH10). Mechanistically, MASTL associated with MRTF-A and increased its nuclear retention and transcriptional activity. Importantly, MASTL kinase activity was not required for regulation of cell spreading or MRTF-A/SRF transcriptional activity. Taken together, we present a previously unknown kinase-independent role for MASTL as a regulator of cell adhesion, contractility, and MRTF-A/SRF activity.

overall_design: RNA isolated from MDA-MB-231 breast cancer cells after control or MASTL siRNA based silencing for 24 or 48 hours

first: Laura

last: Elo

first: Johanna

last: Ivaska


title: The histone variant macroH2A1 regulates key genes for myogenic cell fusion in a splice-isoform dependent manner

status: Public on Apr 03 2020

city: Badalona

first: Roberto

last: Malinverni

state: Barcelona

address: Josep Carreras Building, Ctra de Can Ruti,

country: Spain

institute: Josep Carreras Leukaemia Research Institute

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

overall_design: Refer to individual Series


title: RNA expression in WT and Dot1L KO CD8 T cell subsets

status: Public on Jul 29 2020

city: Amsterdam

first: Fred

last: van Leeuwen

address: Plesmanlaan 121

department: Gene Regulation

institute: Netherlands Cancer Institute

summary: We studied the role of the histone methyltransferase DOT1L in T cell development and differentiation. Here we generated RNA-seq data from sorted CD8 subpopulations from WT (Lcre+/-) and Dot1L KO (Lcre+/-;Dot1Lfl/fl) mice. This data was to define tissue specific expression signatures and it was compared with H3K79me2 ChIP-seq data from the same subsets.

overall_design: RNA-seq in sorted CD8 T cell populations from WT and Dot1L KO mice.

first: Teun

last: van den Brand

first: Eliza

middle: M

last: Kwesi-Maliepaard


title: The histone variant macroH2A1 regulates key genes for myogenic cell fusion in a splice-isoform dependent manner [ChIP-Seq]

summary: MacroH2A histone variants have functions in differentiation, somatic cell reprogramming and cancer. However, at the present it is not clear how macroH2As affect gene regulation to exert these functions. Here, we have addressed the question of whether the two splice isoforms of macroH2A1 differentially regulate genes in a physiological context. We have focused on myotube formation that is a key process in embryonic myogenesis and highly relevant for muscle regeneration after acute or chronic injury. We have parted from the initial observation that loss of total macroH2A1 led to a change in the morphology of myotubes differentiated ex vivo that was indicative of reduced fusion. Individual perturbation of the two isoforms in myotubes forming in vitro from myogenic C2C12 cells showed an opposing phenotype with macroH2A1.1 enhancing and macroH2A1.2 reducing fusion. Transcriptomic analysis allowed us to associate this phenotype with the differential regulation of a subset of fusion-related genes encoding components of the extracellular matrix and cell surface receptors for adhesion. In conclusion, we describe for the first time splice isoform-specific phenotypes for the histone variant macroH2A1 in a physiologic process and provide evidence for a novel, yet unknown underlying molecular mechanism of gene regulation independent of PARP1.

overall_design: ChIP-seq examination of macroH2A1.1 histone variant on C2C12 cell line

first: Sarah

last: Hurtado-Bagès

first: Melanija

middle: P

last: Marjanovic

first: Vanesa

last: Valero

first: David

last: Corujo

first: Anne-Claire

last: Lavigne

first: Kerstin

last: Bystricky

first: Marcus

last: Buschbeck


title: The histone variant macroH2A1 regulates key genes for myogenic cell fusion in a splice-isoform dependent manner [RNA-Seq]

overall_design: Myoblast expression profile after 4 days of myotube diffentation of WT vs si mH2A1.1 and mH2A1.2


title: Bulk RNA sequencing from patient bone marrow samples

status: Public on Jul 02 2020

city: St. Louis

first: Nathan

last: Singh

state: MO

institute: Washington University School of Medicine

summary: Analyzed sequencing data from bone marrow samples taken from patients enrolled on ENSIGN or ELIANA clinical trials prior to infusion of CART19.

overall_design:
Pre-treatment bone marrow samples were processed and underwent bulk RNAsequencing. Data presented are normalized read counts.  Disease response: CR=complete response, NR=no response

>>>Submitter states that raw data are unavailable due to patient privacy concerns<<<<

first: Elene

last: Orlando


title: Molecular characterization of the microenvironment in CLL-like monoclonal B cell lymphocytosis and early stage chronic lymphocytic leukemia

status: Public on Mar 29 2020

city: Barcelona

first: Magdalena

last: Arnal Segura

address: Carrer de Natzaret 113

institute: Vall d'Hebron Institute of Oncology

summary: Several studies have demonstrated an impaired function of the microenvironment in chronic lymphocytic leukemia (CLL), contributing to immune evasion of tumor cells and disease progression. However, in CLL-like monoclonal B cell lymphocytosis (MBL) studies are scarce. Herein, a comprehensive characterization of the microenvironment in 59 MBL, 56 early stage CLL and 31 healthy controls was conducted. Gene expression arrays and qRT-PCR were performed on RNA from CD4+ peripheral blood cells; serum cytokines were measured by immunoassays and proteomic studies; and flow cytometry was applied to evaluate peripheral blood cytotoxic, Th1, exhausted and effector CD4+ T cells, besides monocytic CD14, CD4 and HLA-DR expression. MBL and early stage CLL showed a similar upregulation of cytotoxic and Th1-related genes, expanded perforin+ and CXCR3+ CD4+ T cells as well as PD1+ CD4+ T cells compared to controls. However, a strong inflammatory response was only identified in MBL: enhanced phagocytosis, pattern recognition receptors, IL8, HMGB1, TREM1 and acute response signaling pathways, along with increased levels of proinflammatory cytokines (remarkably IL8, IFN? and TNF?). Of note, this inflammatory drive was decreased in early stage CLL: diminished proinflammatory cytokines including IFN?, decreased IL8 signaling pathway and lower monocytic HLA-DR expression compared to MBL. Besides, this inflammation was especially reduced in IGHV mutated CLL, involving a decrease of the proinflammatory HMGB1 signaling pathway. These novel findings reveal a different pathophysiology between MBL and CLL, paving the way for the development of pre-emptive immunotherapies with optimal benefits at MBL and early stage CLL, before intense immune exhaustion.

overall_design: 36 samples: CLL (n=14); CTRL (n=9); MBL (n=13)

first: Gonzalo

middle: B

last: Ares

first: Anna

last: Metge

first: Blanca

last: Solà


title: The effects of gul1 deletion on the transcriptome of Trichoderma reesei

status: Public on Mar 19 2020

city: Qingdao

first: Guodong

last: Liu

state: Shandong

address: Binhai Road 72

department: State Key Laboratory of Microbial Technology

institute: Shandong University

summary: The morphology of filamentous fungi has a close relationship with the production of many products (e.g. industrial enzymes).  In this study, we deleted gul1, which encodes a putative RNA-binding protein, in cellulolytic fungus Trichoderma reesei. The mutant showed different morphologies both on agar plates and in liquid cultures compared with its parent. RNA-seq study showed that the expression levels of genes in many biological processes were affected by gul1 deletion.

overall_design: A total of 6 samples were analyzed, which include biological triplicates. The reference strain QPP was considered as a control.

first: Qinqin

last: Zhao

first: Liwei

last: Gao


title: Single Cell Transcriptomics Reveals Dysregulated Cellular and Molecular Networks in a Fragile X Syndrome Model

city: Worcester

first: Elisa

last: Donnard

state: MA

address: 368 Plantation St

department: Bioinformatics and Integrative Biology

institute: University of Massachusetts Medical School

summary: Despite advances in understanding the pathophysiology of Fragile X syndrome (FXS), its molecular bases are still poorly understood. We performed single cell RNA-seq from the cortex of both Fmr1-knock out (Fmr1-KO) and wild type (WT) FVB animals at postnatal day 5. After stringent filtering, we obtained 18,393 cells for which we detected an average of 1,778 genes and 3,988 transcripts. We identified a total of 18 distinct populations, these include vascular cells (endothelial cells and pericytes), fibroblasts, ependymal cells, different neuron subtypes and glial cells. Our findings present new insights into the cell type specific consequences of FXS. We found that FXS results in a highly cell type specific effect and it is strongest among different neuronal types. We detected a downregulation of mRNAs bound by FMRP and this effect is prominent in neurons. Metabolic pathways including translation are significantly upregulated across all cell types with the notable exception of excitatory neurons. These effects point to a potential difference in the activity of mTOR pathways, and together with other dysregulated pathways suggest an excitatory-inhibitory imbalance in the FXS cortex which is exacerbated by astrocytes. Our data demonstrate the cell-type specific complexity of FXS and provide a resource for interrogating the biological basis of this disorder.

overall_design: Wild type (WT; FVB.129P2-Pde6b+ Tyrc-ch/AntJ; JAX stock 004828) and Fmr1 knockout (Fmr1-KO; FVB.129P2-Pde6b+ Tyrc-ch Fmr1tm1Cgr/J; JAX stock 004624) mice at postnatal day 5 (P5) of both sexes were used. The cortex of three mice per genotype were used for single-cell collection independently using the InDrop system. Collected cells for each mouse were aliquoted and libraries were built independently for the aliquots containing an average of 1200 cells.

first: Manuel

last: Garber


title: Single Cell Transcriptomics  identifies Focal Segmental Glomerulosclerosis Remission  Endothelial Biomarker

status: Public on Mar 03 2020

city: Ann Arbor

first: Rajasree

last: Menon

state: Michigan

address: 4544E, MSRB2, Catherine Street, University of Michigan

department: Department of Computational  Medicine and Bioinformatics

institute: University of Michigan

summary: Intrinsic nephron cell types and tissue resident immune cells were recovered from renal biopsy specimens using a scRNAseq protocol for the Kidney Precision Medicine Project (KPMP), designed for deployment in a multicenter research network. Combined processing of 24 samples including 16 tumor-nephrectomy, 5 surveillance and 3 pre-perfusion biopsies using the scRNAseq protocol yielded 22,268 cells (4690 from surveillance biopsies, 16,491 from tumor-nephrectomies and 2834 cells from pre-perfusion biopsies) .

overall_design:
scRNA-seq: Using multiple sources of healthy kidney tissue samples, we generated 22,268 single cell profiles. Unbiased clustering resulted in 31 distinct cell clusters that were successfully linked to intrinsic kidney and immune cell types using specific cell markers. In silico assignment of the three endothelial cell clusters to distinct vascular beds were confirmed by in situ hybridization. Transcripts defining the glomerular endothelial cluster (GEC) were evaluated in biopsies from patients with ten different glomerular diseases in the NEPTUNE and ERCB studies.  Focal segmental glomerulosclerosis (FSGS) samples were associated with higher GEC scores.
bulk RNA-seq: Transcripts defining the glomerular endothelial cluster (GEC) were evaluated in biopsies from patients with FSGS glomerular diseases in the NEPTUNE  cohort studies.
***The submitters are not legally permitted to submit the raw data to GEO or a restricted-access database such as dbGaP or EGA. Therefore, raw data is not provided ****

first: Matthias

last: Kretzler


title: Expression data from BMDM

status: Public on Mar 05 2020

city: Burlington

first: SABIKUNNAHAR

last: SABIKUNNAHAR

state: Vermont

address: 318 Rowell, 106 Carrigan Dr

department: Biomedical and Health Sciences

institute: The University of Vermont

summary:
sex-specific role of p38-MAPK in EAE is regulated by estrogen receptor alpha;

Biological sex is a critical factor in regulating immune function. A striking example of this is the higher prevalence of autoimmune diseases such as multiple sclerosis (MS) and lupus in females compared to males. While many studies have implicated the role of sex hormones such as estrogens and androgens in these sex differences, surprisingly little is known about other molecular pathways that underlie sex differences or interact with sex hormones. We have previously shown that conditional ablation of p38α MAP kinase signaling in myeloid cells (p38αCKO) was protective in a mouse model of MS, experimental autoimmune encephalomyelitis (EAE), in female but not male mice. This sex difference was dependent on the presence of sex hormones, leading us to hypothesize that the pathogenic function of p38α in EAE depends on estrogen signaling via one of the two nuclear estrogen receptors, encoded by Esr1 and Esr2. To test this hypothesis, we performed experiments with p38αCKO macrophages, which demonstrated that the effects of estradiol and p38α were independent of one another in vitro. Since many sex hormone effects are lost in vitro, we generated p38αCKO mice lacking either Esr1 or Esr2, and evaluated their EAE susceptibility in vivo. Myeloid-specific deletion of Esr1 abrogated protection in p38αCKO females, although global deletion of Esr1 and Esr2 did not. Moreover, global or myeloid-specific disruption of Esr1 unexpectedly promoted protection from EAE in p38αCKO males. Mechanistically, Esr1 deletion resulted in partial reprogramming of p38α-dependent transcriptional modules in male macrophages, in particular those regulated by TGFβ, BRD4, and SMARCA4. These results demonstrate that estrogen signaling in myeloid cells plays an important sex-specific role in programming their dependence on specific intracellular signaling pathways in the context of autoimmune disease pathogenesis, suggesting potential avenues for sex-specific therapeutics or combinatorial approaches for the treatment of such diseases.

overall_design:
We used microarray to compare the gene expression in three different groups of mice-  WT (p38 W and DO W), p38-Conditional knockout (p38 KO) and p38-ESR1-double KO (DO KO)
All our WT and KOs are in C57BL/6 background. P38α and ESR1 were floxed and LysM-cre was used to create the KOs
We collected BMDMs from these three different groups of mice and stimulated them with LPS (100ng/ml) for 4 hours. Then, RNA was extracted and samples were undergone Affymatrix microarray (Clariom S mouse Assays)

first: Sabikunnahar

last: Sabikunnahar

first: Mahalia

last: McGill

first: Dimitry

last: Krementsov


title: Transcriptional alterations in BPH

status: Public on Mar 18 2020

city: New York

first: Deli

state: New York

address: 1300 York Ave

institute: Weill Cornell Medicine

summary: We identified a BPH transcriptional signature that included 392 significantly differential expressed genes between BPH and control samples, and  validated this BPH transcriptional signature using two independent study cohorts. By performing integrative analysis using transcriptional and methylation profiling, we identified two distinct BPH subtypes, supporting robust biologically distinct subgroups across different data types. To validate these BPH subtypes, we tested our signature via k-means clustering in two independent cohorts, and identified nearly identical subgroups. To nominate potential subtype specific therapeutic options, we utilized a Connectivity Map analysis, and found 50% of nominated compounds in one subgroup were related to inhibition of mTOR signaling.

overall_design: Identification of BPH and subgroup transcriptional signatures

first: Christopher

last: Barbieri


title: Keratinocyte-intrinisic MHCII expression controls Microbiota-specific Th1 cell responses

city: Bethesda

first: Verena

last: Link

address: 4 Memorial Drive

department: NIAID

institute: NIH

summary: The crosstalk between the microbiota and the immune system plays a fundamental role in the control of host physiology. However, the tissue-specific factors controlling this dialogue remain poorly understood. Here we demonstrate that T cell responses to commensal colonization are associated with the development of organized clusters within the skin epithelium. These organized lymphocyte clusters are surrounded by specialized keratinocytes expressing a discrete program associated with antigen presentation and anti-microbial defense. Notably, IL-22-mediated keratinocyte-intrinsic MHC class II expression was required for the selective accumulation of commensal-induced IFN- but not IL-17A-producing CD4+ T cells within the skin. Together, this work uncovers an unexpected role for keratinocyte-mediated antigen presentation in the licensing of homeostatic type 1 responses to the microbiota, findings that have important implications in our understanding of the unique rules governing the dialogue between the host and its microbiota.

overall_design: Keratinocytes were FACsorted from the epidermis of ear pinnae of C57BL/6 mice from naïve mice or day 14 post topical association with S. epidermidis NIHLM087. CD49f+Sca-1+ Keratinocytes were sorted as CD45-CD31-CD34- cells and further separated based on their expression of MHCII.

first: Samira

last: Tamoutounour


title: The long non-coding RNA LUCAT1 is a negative feedback regulator of the Interferon Response in humans

status: Public on Feb 19 2020

first: Katherine

last: Fitzgerald

state: Massachusetts

address: 364 Plantation Street

department: Medicine

institute: Umass Chan Medical