title: Single-Cell RNA-Seq and Patient-Specific iPSCs Reveal Endocardial Abnormalities in Hypoplastic Left Heart Syndrome

status: Public on Aug 17 2020

city: Stanford

first: Lei

last: Tian

address: 1215 Welch Rd

institute: Stanford's Postdoctoral Scholar programs

summary: Hypoplastic left heart syndrome (HLHS) is one of the most devastating forms of congenital heart defects. Previous studies have only focused on intrinsic defects in the myocardium. However, this does not sufficiently explain the abnormal development of the cardiac valve, septum, and vasculature, which are known to originate from the endocardium. Here, using single-cell RNA profiling, induced pluripotent stem cells, and fetal heart tissue with an underdeveloped left ventricle, we identified a developmentally impaired endocardial cell population in HLHS. The intrinsic endocardial deficits contributed to abnormal endothelial to mesenchymal transition, NOTCH signaling, and extracellular matrix organization, all of which are key factors in valve formation. Consequentially, endocardial abnormalities conferred reduced proliferation and maturation of cardiomyocytes through a disrupted fibronectin-integrin interaction. Several known HLHS de novo mutations all contributed to the abnormal endocardial gene expression through the alteration of promoter/enhancer activities. These mechanistic discoveries provide an alternative angle for early intervention and heart regeneration in HLHS.

overall_design: This is the first study providing evidence that a developmentally impaired endocardium can contribute to the ventricular and valvular hypoplasia in hypoplastic left heart syndrome (HLHS), which may provide a novel therapeutic target for early intervention and heart regeneration for this condition.

first: Yifei

last: Miao

first: Mingxia

last: Gu


title: ChIP-Seq data from IMR90 Control and IMR90 HRAS-G12V using an H3K79me3 antibody

status: Public on Aug 21 2020

city: Pittsburgh

first: Katherine

last: Aird

state: PA

address: 5051 Centre Ave.

country: USA

institute: University of Pittsburgh School of Medicine

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Oncogene-induced senescent cells display a robust change in their epigenome and have increased transcription and secretion of numerous pro-inflammatory cytokines and chemokines termed the senescence-associated secretory phenotype (SASP). Therefore, understanding how and if the epigenome is involved in regulating the transcription of the SASP is critical to understanding how to restrain the harmful effects of the SASP. The active histone marks H3K79me2 and H3K79me3 and their methyltransferase DOT1L are increased during oncogene-induced senescence.  Whether H3K79 methylation and DOT1L expression are involved in the transcriptional regulation of the SASP is unknown.

overall_design: ChIP Seq using an H3K79me3 antibody on IMR90 control and IMR90 HRASG12V (RAS) cells were generated by using the NovaSeq 6000 Sequencing System  (Illumina)

first: Kelly

middle: E

last: Leon

first: Raquel

last: Buj

first: Elizabeth

last: Lesko

first: Erika

middle: S

last: Dahl

first: Chi-Wei

last: Chen

first: Yuka

last: Imamura

first: Andrew

middle: V

last: Kossenkov

first: Ryan

middle: P

last: Hobbs

middle: M


title: Gene expression data from IMR90 Control, IMR90 HRAS-G12V, IMR90 HRAS-G12V+shDOT1L, IMR90 DOT1L Overexpression

type: Expression profiling by high throughput sequencing

overall_design: mRNA profiles of IMR90 control (CT), IMR90 HRASG12V (RAS),  IMR90 HRASG12V + knockdown of DOT1L (KD), IMR90 DOT1L overexpression (OE)  were generated by deep sequencing, in triplicate, using  NovaSeq 6000 Sequencing System  (Illumina)


title: Gene expression patterns in septic and non-septic shock postsurgical patients

status: Public on Aug 16 2020

city: Valladolid

first: Pedro

last: Martinez-Paz

state: Valladolid

address: C/ Ramón y Cajal 7

country: Spain

institute: Faculty of Medicine

summary: Nowadays, there is no gold standard of sepsis diagnosis, thus there is a challenge to differentiate between shock septic and non-septic shock following a surgery, since patients with both conditions show similar signs and symptoms. In this sense, to get a quick and accurate diagnosis of septic shock is required to allow an immediate and specific treatment for this condition. In this work, we have evaluated the expression profile by microarray analysis from post-surgical septic shock and non-septic shock patients with the aim of proposing a candidate set genes as gold standard to help in distinguishing both conditions.

overall_design: Microarray analysis was performed to compare the gene expression profiles from septic shock and non-septic shock and identify the differentially expressed genes. After, a set of six upregulated genes were evaluated by real time PCR as a validation platform to verify the potential of these genes to differentiate both conditions.

last: Martínez-Paz

first: Eduardo

last: Tamayo

first: Emilio

last: García-Morán


title: Lymphatic endothelial cells contribute to blood vessel formation in tumours

status: Public on Sep 05 2020

city: Leuven

first: Florian

last: Rambow

address: Herestraat 49 box 912

country: Belgium

institute: VIB

summary: Using multicolor lineage tracing, in vivo time-lapse imaging and single cell transcriptional profiling in a mouse glioma model, we identify tumour blood endothelial cells carrying a Csf1r lineage trace. These Csf1r lineage endothelial cells (CLECs) form up to 10% of the tumour vasculature and express endothelial cell markers as well as a unique set of genes that can also be found in single cell transcriptome data of tumour endothelium from various human tumours.

sample_organism:
Mus musculus
blank sample

platform_organism:
Mus musculus
blank sample

overall_design: The transcriptomes of 768 single cells were sequenced (scRNAseq) after FACS sorting.


title: Transcriptomic changes in sapx tapx, pgr5, and triple mutants under high-light stress

status: Public on Aug 26 2020

city: Matsue

first: Takanori

last: Maruta

address: 1060 Nishikawatsu

country: Japan

institute: Shimane University

summary: We focused on Arabidopsis chloroplast ascorbate peroxidases (sAPX and tAPX) and proton gradient regulation 5 (PGR5) and used pgr5 single mutant, sapx tapx double mutant, and sapx tapx pgr5 triple mutant for RNA-seq analysis.

overall_design: Transcriptome change in the Arabidopsis mutants under high light stress conditions.

first: Takahiro

last: Ishikawa

first: Takaya

last: Okayasu


title: Identification of ISG20 as the nuclease involved in interferon-induced decline of hepatitis B virus cccDNA

status: Public on Jul 22 2020

city: Munich

first: Kristian

last: Unger

address: Marchioninistr. 15

department: Department of radiation oncology

country: Germany

institute: LMU University Hospital

summary: Hepatitis B virus (HBV) persists by depositing a covalently closed circular DNA (cccDNA) in the nucleus that cannot be targeted by available antivirals. Cytokine treatments can purge cccDNA from the nucleus of infected cells by APOBEC3-mediated deamination. cccDNA levels in HBV-infected cells were not reduced by overexpression of APOBEC3A alone, but only after simultaneous addition of interferon. This indicated the need of an additional, interferon-induced factor (ISG). Microarray analysis identified ISG20 as the only nuclease located to the nucleus induced by type I and II interferons. ISG20 was confirmed to be expressed in acute, self-limiting but not in chronic hepatitis B in human livers. ISG20 knockdown abolished the interferon-induced loss of cccDNA, and co-expression of ISG20 and APOBEC3A was sufficient to diminish cccDNA without further treatment. To conclude, nucleolar ISG20 was identified as the nuclease contributing to interferon-induced purging of HBV cccDNA, opening new avenues for antiviral targeting.

overall_design: Transcriptional profiles of HBV infected HepaRG cells expressing A3A in presence of Interferon Alpha were compared with HepaRG cells expressing A3A without Interferon Alpha.


title: Tanshinone I inhibit normal and malignant hematopoiesis by repressing EZH2 activity

status: Public on Aug 04 2020

city: Hang Zhou

first: Tao

last: cheng

state: Zhe Jiang

address: 886 Yuhangtang Road

department: Institute of genetics

country: China

institute: Zhejiang University

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

sample_organism:
Danio rerio
Homo sapiens

platform_organism:
Danio rerio
Homo sapiens

overall_design: Refer to individual Series


title: Tanshinone I inhibit normal and malignant hematopoiesis by repressing EZH2 activity [zebrafish]

summary:
Purpose: To explore the mechanism of how Tan I inhibits malignant hematopoiesis at the gene expression level
Methods: 72 hpf Tg(c-mybhyper: GFP) zebrafish embryos treated with DMSO or Tan I 60 μM were collected for RNA sequencing
Results: We found that 1882 genes were differentially expressed between DMSO and Tan I treatment in c-mybhyper fish embryos (p value <=0.05, |log2 fold change| >= 0.25)
Conclusions: We identified MMP9 and ABCG2 as two possible downstream genes of Tan I’s effects on EZH2

last: Cheng

first: Ying

last: Huang

first: Shan-He

last: Yu


title: Tanshinone I inhibit normal and malignant hematopoiesis by repressing EZH2 activity [human]

summary:
Purpose: To explore the mechanism of how Tan I inhibits malignant hematopoiesis at the gene expression level
Methods: NB4 cells treated with DMSO or Tan I 10 μM were collected for RNA sequencing
Results: We found that 376 genes were differentially expressed between DMSO and Tan I treatment in the NB4 cells (p value <=0.05, |log2 fold change| >= 0.25)
Conclusions: We identified MMP9 and ABCG2 as two possible downstream genes of Tan I’s effects on EZH2


title: Timing of tumor initation predicts medulloblastoma heterogeneity, stem cell composition and probability of relapse [array]

status: Public on Aug 01 2020

city: chapel hill

first: Seth

last: Weir

address: 115 mason farm rd

institute: UNC Chapel Hill

summary: Patients with medulloblastoma are typically treated with a narrow range of therapies, but may experience widely divergent outcomes; 80-90% become long-term survivors while 20% develop incurable recurrence. Transcriptomic profiling has identified four subgroups with different recurrence risks, but outcomes remain variable for individual patients within each subgroup. To gain new insight into why patients with similar-appearing tumors have variable outcomes, we examined how the timing of tumor initiation effects medulloblastomas triggered by a single, common driver mutation. We genetically-engineered mice to express an oncogenic Smo allele starting early in development in the broad lineage of neural stem cells, or later, in the more committed lineage of cerebellar granule neuron progenitors. Both groups developed medulloblastomas and no other tumors. We compared medulloblastoma progression, response to therapy, gene expression profile and cellular heterogeneity, determined by single cell transcriptomic analysis (scRNA-seq). The average transcriptomic profiles of the tumors were similar. However, stem cell-triggered medulloblastomas progressed faster, contained more OLIG2-expressing tumor stem cells, and consistently showed radioresistance. In contrast, progenitor-triggered MBs progressed slower, lost stem cell character over time and were radiosensitive.  Progenitor-triggered medulloblastomas also contained more diverse stromal populations, including tumor-associated macrophages, indicating that the timing of oncogenesis affected the subsequent interactions between the tumor and microenvironment. Our findings show that developmental events in tumorigenesis may be impossible to infer from transcriptomic profile, but while remaining cryptic can nevertheless influence tumor composition and the outcome of therapy. Precise understanding of medulloblastoma pathogenesis and prognosis requires supplementing transcriptomic data with biomarkers of cellular heterogeneity.

overall_design:
Expression microarray comparison between SHH-driven medulloblastomas that form in 2 different genotypes of mice, using Affymetrix expression arrays.
We performed an expression microarray analysis of medulloblastomas that form in transgenic mice. This bulk transcriptomic analysis is complemented by a scRNA-seq analysis. We compare tumors that form in Gfap-Cre/SmoM2 (G-Smo) mice to umors that form in Math1-Cre/SmoM2 (M-Smo) mice. In both genotypes, tumors are driven by the same mutant, oncogenic allele of Smo. In G-Smo mice, SmoM2 is expressed starting from neural stem cells early brain development and continuing in most cells of the brain. In M-Smo mice, SmoM2 is expressed starting in committed neural progenitors later in development, and continuing in a subset of neurons. Both genotypes develop medulloblastoma and no othe tumor type. All mice were raised to P15 after which tumors were dissected and processed for transcriptomic anlaysis.

first: Jennifer

last: Ocasio

first: Timothy

middle: R

last: Gershon


title: Sexual dimorphism in the immune system becomes evident in the perinatal period in the four core genotypes mouse

city: Cleveland

first: Kuan-Hui

middle: Ethan

last: Chen

state: MS

address: 1003 W Sunflower Rd

institute: Delta State University

summary: We conclude an existence of a previously unrecognized role for estradiol in the regulation of cell development in the neonatal thymus and an organizational role for perinatal testosterone in the development of immune sexual dimorphism

overall_design: To determine the effect of testosterone surge and estradiol during the perinatal period, day 7 thymic epithelium/stroma was collected. RNA was extracted from the thymic epithelium/stroma of four core genotype mouse and then subjected to microarray analysis using probe sets present on an Affymetrix mouse GeneChip 1.0 ST array.

first: Kuan-hui

first: Mrinal

last: Ghosh

first: Riva

last: Dill-Garlow

first: Lisa

last: Ma

first: Tomohiro

last: Yonezawa

first: Yuichiro

last: Itoh

first: Lorena

last: Rivera

first: Kelly

last: Radecki

first: Quiming

last: Wu

first: Arthur

last: Arnold

first: H

middle: K

last: Muller

first: Ameae

last: Walker


title: Investigating the role of IL-2 in shaping the epigenome in T cells [DNAse-seq]

status: Public on Sep 14 2020

city: Birmingham

first: Csilla

last: Varnai

address: Haworth Building

department: Institute of Cancer and Genomic Sciences

country: United Kingdom

institute: University of Birmingham

summary: During T cell activation hundreds of genes are primed for efficient activation. Here we show that IL-2 signaling is required to maintain open chromatin at gene regulatory elements which are associated with alternate pathways of T cell differetiation.IL-2 actiavtes binding of AP-1 and STAT5 at sites that can subsequently bind other STAT and lineage dietermining proteins, depending on what other factors exist in their enviroment.

overall_design: DNase-seq samples were generated in duplicate for T-blast cells cultured in IL-2 or IL-7 with and without activation with PMA and calcium ionophore and in T-blast cells cultured for 16 hours in the absence of IL-2 or IL-7 (IL-2nil or IL-7nil) with and without activation with PMA and calcium ionophore. DNAse-seq samples were also generated from T-blast cells cultured with control DMSO or Ruxolitinib.

first: Sarah

middle: L

last: Bevington

first: Peter

last: Keane


title: Investigating the role of IL-2 in shaping the epigenome in T cells [ChIP-seq]

overall_design: ChIP-seq samples detecting binding of STAT5 and JUND in T-blast cells cultured with and without IL-2


title: Genomewide transcriptional analysis of growth hormone-treated human podocytes

status: Public on Aug 28 2020

city: Hyderabad

first: Anil

middle: Kumar

last: Pasupulati

state: Telangana

address: CRRAO road Gachibowli

department: Department of Biochemistry

country: India

institute: University of Hyderabad

summary: The growth hormone plays a significant role in normal renal function and overactive growth hormone signaling has been implicated in proteinuria in diabetes. Earlier studies from our group have shown that the glomerular podocytes, which play an essential role in renal filtration, express the growth hormone receptor, suggesting the direct action of growth hormone on these cells. Nevertheless, the precise mechanism and the downstream pathways that are induced by the excess growth hormone in these podocytes leading to diabetic nephropathy are not clearly established. To compressively understand the growth hormone’s effect on podocytes at transcript level we performed RNA-Sequencing. Conditionally immortalized human podocytes were employed in this study.

overall_design: Human podocytes in duplicates were treated with (500 ng/ml) or without growth hormone for 30 min and total RNA was isolated. Both by running on an agarose gel and using the bioanalyzer confirmed the quality of RNA.  High-quality RNA libraries were constructed using mRNA templates, random hexamers, oligo-dT primers, and Illumina second strand synthesis buffer. RNA sequencing was performed on Illumina 2500 Hi-Seq devise by pair-end reads at Nucleome Informatics Facility, Hyderabad, India.

first: Dhanunjay

last: Mukhi

first: Rajkishor

last: Nishad

first: Srinivas

last: Kethavath


title: ChIP-seq analysis of SNAIL transcription factor binding sites in RH30 rhabdomyosarcoma cells

status: Public on Jul 15 2020

city: Krakow

first: Klaudia

last: Skrzypek

address: Wielicka 265

department: Department of Transplantation

country: Poland

institute: Jagiellonian University Medical College

summary: ChIP-seq analysis of SNAIL binding sites in RH30 cells was performed to discover novel SNAIL binding sites in rhabdmyosarcoma cells.

overall_design: ChIP was performed using SimpleChip Enzymatic Chromatin IP Kit (Cell Signaling Technology) according to the manufacturer’s protocol. For ChIP assays 10 µg of goat antibody against SNAIL (R&D Systems, cat. AB-108-C), . After immunoprecipitation, the DNA was isolated using spin columns from the kit. Subsequently, ChIP-Seq analysis of the immunoprecipitated sample and input sample was performed using the Intelliseq sp. z o. o. (Cracow, Poland) company service in cooperation with Novogene Co., Lt d (Cambridge, UK) using Illumina high-throughput sequencer.

first: Marcin

last: Majka


title: Extracellular vesicles containing miR-146a-5p activate hepatocytic progenitor cells in regenerating retrorsin-treated rat livers

status: Public on Jul 09 2020

city: Sapporo

first: Norihisa

last: Ichinohe

state: Hokkaido

address: South-1, West-17, Chuo-ku,

department: Department of Tissue Development and Regeneration

institute: Sapporo Medical University School of Medicine

summary: We found that the transplantation of bone marrow mesenchymal cells (BM-MCs) transiently increased the liver mass by expanding resident small hepatocy-like progenitor cells (SHPCs). We used microarrays to detail the gene expression of SHPCs clusters with and without BM-MCs transplantation.

overall_design: SHPCs clusters were selected by micro-dissected from Ret/PH livers for RNA extraction and hybridization on Agilent microarrays.

first: N

first: T

last: Mitaka


title: RNAseq of transfected protoplasts of  Populus trichocarpa

status: Public on Jul 11 2020

city: Harbin

first: Baoguang

last: Liu

state: Heilongjiang Province

address: No.51 Hexing Road

department: forestry

institute: northeast forestry university

summary: PtrHSFB3-1 and PtrMYB092 are xylem specific genes in xylem of P. trichocarpa, and their expression levels are down regulated most significantly in tension wood. These two transcription factors were transiently overexpressed in stem differentiating xylem (SDX) of P. trichocarpa , and transcriptomic sequencing was performed to identify the regulatory effects of the two transcription factors on wood formation related genes.

overall_design: We incubated SDX protoplast of P. trichocarpa transfected with GFP, PtrHSFB3-1 and PtrMYB092  genes for 12h to insight into the regulation of these two genes on wood formation related genes

first: V

last: Chiang


title: Transcription-dependent domain-scale 3D genome organization in dinoflagellates

status: Public on Jul 08 2020

first: Georgi

middle: Kolev

last: Marinov

state: California

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

department: Genetics

institute: STANFORD UNIVERSITY

summary: Dinoflagellate chromosomes represent a unique evolutionary experiment, as they exist in a permanently condensed, liquid crystalline state, are not packaged by histones, and contain genes organized into polycistronic arrays, with minimal transcriptional regulation. We analyze the 3D genome of {Breviolum minutum}, and find large topological domains without chromatin loops, demarcated by convergent gene array boundaries (``dinoTADs’’). Transcriptional inhibition degrades dinoTADs, implicating transcription-induced supercoiling as the primary topological force in dinoflagellates.

overall_design: Hi-C libraries associated with the project

first: Alexandro

last: Trevino

first: Tingting

last: Xiang

first: Anshul

last: Kundaje

first: Arthur

last: Grossman

first: William

middle: J

last: Greenleaf


title: A prion accelerates proliferation at the expense of lifespan

city: Eugene

first: David

last: Garcia

state: OR

address: 1318 Franklin Blvd.,, Room 273 Onyx Bridge

department: Biology

institute: University of Oregon, Institute of Molecular Biology

summary: Organisms often commit to one of two strategies: living fast and dying young or living slow and dying old. In fluctuating environments, however, switching between these two strategies could be advantageous. Lifespan is often inversely correlated with cell size and proliferation, which are both limited by protein synthesis. Here we report that a highly conserved RNA-modifying enzyme, the pseudouridine synthase Pus4/TruB, can act as a prion, endowing yeast with greater proliferation rates at the cost of a shortened lifespan. Cells harboring the prion can grow larger and exhibit altered protein synthesis. This epigenetic state, [BIG+] (better in growth), allows cells to heritably yet reversibly alter their translational program, leading to the differential expression of hundreds of proteins, including many that regulate proliferation and aging. Our data reveal a functional role for aggregation of RNA-modifying enzymes in driving heritable epigenetic states that transform cell growth and survival.

overall_design:
RNA-sequencing of naive (non-prion) and prion-containing, or [BIG+], budding yeast cells

A related dataset that includes spike-in controls is available at GSE176577.

first: Edgar

middle: A

last: Campbell

first: Christopher

last: Jakobson

first: Mitsuhiro

last: Tsuchiya

first: Acadia

last: DiNardo

first: Matt

last: Kaeberlein

first: Daniel

middle: F

last: Jarosz


title: RNAseq of motor neurons and neurons with differential vulnerability isolated from a mouse model of spinal muscular atrophy using laser capture microdissection

city: Stockholm

first: Eva

last: Hedlund

address: Svante Arrhenius v. 16C

department: Department of Biochemistry and Biophysics

country: Sweden

institute: Stockholm University

summary: Motor neurons are selectively vulnerable in spinal muscular atrophy (SMA). However, some brainstem motor neuron groups, including oculomotor and trochlear, which innervate the muscles around the eyes, are for unknown reasons spared. Here, we investigate the transcriptional dynamics in discrete neuronal populations in health and SMA to identify mechanisms of vulnerability and resistance. Such mechanisms could reveal targets for future gene therapy studies aimed towards preserving vulnerable motor neurons.

overall_design: We used laser capture microdissection to isolate discrete neurons from the ‘delta7’ mouse model of SMA (Smn-/-/SMN2+/+/SMN∆7+/+) and littermate controls (Smn+/+/SMN2+/+/SMN∆7+/+) (Jax Stock No 005025). We analyzed a total of 168 samples with 3-7 biological replicates per condition. We included 6 neuronal groups with differential vulnerability in this disease and investigated 3 time points throughout disease progression including a pre-, early and late symptomatic stage (postnatal days 2, 5 and 10).

first: Susanne

last: Nichterwitz

first: Helena

last: Storvall

first: Rickard

last: Sandberg


title: The effect of SNAIL transcription factor on microRNA transcriptome in rhabdomyosarcoma

first: Klaudia

last: Skrzypek

type: Non-coding RNA profiling by high throughput sequencing

summary: The main goal of the project was to analyze the effect of SNAIL transcription factor on microRNA expression profile in rhabdomyosarcoma (RMS) cells using the next generation sequencing. Differential expression of microRNAs between three groups was compared in RH30 alveolar RMS cells: WT (WT), shCTRL (modified with control shRNA vector) and shSNAIL (modified with shRNA against SNAIL).  Different groups were compared to investigate the effect of SNAIL silencing on microRNA up- or downregulation.

overall_design: Total RNA from three different cell types (RH30 WT, shCTRL, shSNAIL) was isolated at three independent time points (three independent experiments) and microRNA expression profile was analyzed by the next generation seqeuncing at Exiqon Services, Denmark.

first: Marcin

last: Majka


title: Genome-wide association study of body weights in Hu sheep

status: Public on Jun 18 2020

city: Ningbo

first: cao

last: yuhao

state: Zhejiang Province

address: 818 Fenghua Road, Jiangbei District, Ningbo City, Zhejiang Province

institute: Medical School of Ningbo University

type:
Genome variation profiling by SNP array
SNP genotyping by SNP array

summary: Body weight (BW) is a critical economic trait for meat production in sheep. The current study aimed to perform a genome-wide association study (GWAS) to detect significant single-nucleotide polymorphisms (SNPs) that are associated with BW in Hu sheep.

overall_design: The 240 Hu sheep selected for the study were from the parent (G1) and progeny (G2) of Hu sheep nucleus herd Culture Department in Huzhou Taihu Lake Culture Cooperative. BW measurements, including birth weight, weaning weight, 6-month weight, and yearling weight, were taken in a quiet, relaxed state in the two nucleus herds of Hu sheep. Genotyping of individual SNPs was performed using the Ovine SNP50BeadChip

first: Yuhao

last: Cao

first: Xuemei

last: Song


title: Long-read Nanopore sequencing of mouse neural stem cells

city: PARKVILLE

first: Xueyi

last: Dong

state: VIC

address: 1G ROYAL PARADE

country: Australia

institute: Walter and Eliza Hall Institute of Medical Research

summary:
Purpose: The aim of this study is to identify genes that are under the transcriptional control of the epigenetic modifier Smchd1 in mouse neural stem cells.
We profiled the transcriptomes of mouse neural stem cells from samples that were either wild-type or contained a null mutation in the epigenetic regulator Smchd1 using Oxford Nanopore Technologies (ONT) direct cDNA sequencing protocol and a PromethION sequencer.

overall_design: Total RNA was extracted and polyA RNA purified from each cell line for transcriptome analysis by Nanopore direct cDNA sequencing.

first: Quentin

last: Gouil

first: Marnie

last: Blewitt


title: RNAseq of bending treated  Populus trichocarpa

status: Public on Jul 05 2020

first: Baoguang

last: Liu

institute: Northest forestry university

summary: We treated 6 month Populus trichocarpa by bending for 0, 3, and 7 days to see effects of bending treatment on wood formation at transcript level

first: V

last: Chiang


title: Expression data from mouse MLL/AF10(OM-LZ) myeloid leukemia cells harboring wild-type KRAS, KRAS-G12C, wild-type PTPN11, PTPN11-G503A, without or with Hoxa11

status: Public on Jul 01 2020

city: TauYau

first: Yun-Shien

last: Lee

state: Taiwan

address: TauYau

department: Dept. Biotechnology

country: Taiwan

institute: Ming Chuan Univ

summary:
Cooperation of MLL/AF10 with RAS pathway mutations accelerated myeloid leukemia development. The detail molecular mechanism is analyzed by identification of the differentially expressed genes between MLL/AF10 cells harboring wild-type and mutant RAS pathway genes and by with or without Hoxa11.
We used cDNA microarray to compare transcriptomes between mouse MLL/AF10 myeloid leukemia cells harboring wild-type KRAS and harboring KRAS-G12C (AKw1G and AK3G), or between MLL/AF10 cells harboring wild-type PTPN11 and harboring PTPN11-G503A (APw-1 and APm-1), or between MLL/AF10 cells without and with Hoxa11 (12G-V and 12G-H11).

overall_design: RNAs were prepared from the in vitro cultured cells, RNA was amplified and hybridized to the Affymetrix Mouse Transcriptome Array 1.0 (MTA-1_0) chips.

first: Jen

last: Fu


title: Generation of mature compact ventricular cardiomyocytes from human pluripotent stem cells

status: Public on Jun 17 2020

city: Toronto

first: Gordon

last: Keller

state: Ontario

address: 101 College St

department: Medicine

country: Canada

institute: McEwen Stem Cell Institute

summary: Here we established a differentiation strategy  that promotes the specification, proliferation and maturation of a compact cardiomyocyte population from hPSCs. The cardiomyocytes generated under these conditions display the hallmark phenotypic characteristics of post-natal cardiomyocytes.

overall_design: Examination of heterogeneity and global transcriptome between immature and mature VCMs

first: Shunsuke

last: Funakoshi

first: Ian

last: Fernandes

first: Stephanie

last: Protze

first: Jeehoon


title: Single-cell RNA-seq of bone marrow-derived stromal cells from 5 Diversity Outbred mice

status: Public on Jun 20 2020

city: Charlottesville

first: Basel

last: Al-Barghouthi

state: VA

institute: University of Virginia

summary: Genome-wide association studies (GWASs) for osteoporotic traits have identified over 1000 associations; however, their impact has been limited by the difficulties of causal gene identification and a strict focus on bone mineral density (BMD). Here, we used Diversity Outbred (DO) mice to directly address these limitations by performing the first systems genetics analysis of over 50 complex skeletal phenotypes. We applied a network approach to cortical bone RNA-seq data to discover 46 genes likely to be causal for human BMD GWAS associations, including the novel genes SERTAD4 and GLT8D2. We also performed GWAS in the DO for a wide-range of bone traits and identify Qsox1 as a novel gene influencing cortical bone accrual and bone strength. Our results provide a new perspective on the genetics of osteoporosis and highlight the ability of the mouse to inform human genetics.

overall_design: Here, we performed single-cell RNA-seq on pooled polyA-selected total RNA from bone marrow-derived stromal cells, cultured from the femoral bone marrow of 5 Diversity Outbred mice (1 male, 4 females). These data allowed us to profile the expression of novel bone-related genes in osteoblasts and bone marrow-derived stromal cells.

first: Larry

last: Mesner

first: Gina

last: Calabrese

first: Daniel

last: Brooks

first: Steven

last: Tommasini

first: Mary

last: Bouxsein

first: Mark

last: Horowitz

first: Clifford

last: Rosen

first: Kevin

last: Nguyen

first: Samuel

last: Haddox

first: Emily

last: Farber

first: Suna

last: Onengut-Gumuscu

last: Pomp

first: Charles


title: RNAseq analysis of blood-meal induced gene-expression changes in Aedes aegypti ovaries

status: Public on Jun 11 2020

city: Slingerlands

first: Dilip

last: Nag

state: NY

address: 5668 State Farm Road

department: Division of Infectious Diseases

institute: Griffin Laboratory, Wadsworth Center, New York State Department of Health

summary: We report here RNAseq analysis of the comparison of gene expression between sugar fed and blood fed Aedes aegypti ovaries, to understand blood meal induced changes in gene expression.

overall_design: Ovary samples were collected on Day 3, 10, and 20 post blood meal

first: Laura

last: Kramer


title: In-vivo inhibition of Fgfr2b signalling in embryonic mouse lungs

status: Public on Jun 23 2020

city: Giessen

first: Jochen

last: Wilhelm

state: Hessen

address: Aulweg 132

department: Institute for Lung Health

institute: Justus-Liebig University Giessen

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

overall_design: Refer to individual Series


title: Transcriptome analysis of apoplastic reactive oxygen species signaling in Arabidopsis thaliana accessions with varying ozone sensitivity.

city: Örebro

first: Luis

last: Morales

address: Fakultetsgatan 1

department: School of Science and Technology

institute: Örebro University

summary: Ozone (O3) is a phytotoxic air pollutant that enters the plant through stomata and activates cell death programs leading to development of lesions in sensitive plant species. Exposure to O3 provokes the formation of reactive oxygen species (ROS) in the apoplast of plant cells. Imbalanced ROS homeostasis has deleterious toxic effects on DNA, proteins, lipids, and carbohydrates. However, ROS are not merely damaging molecules, as they also initiate signaling events that help plants acclimate to stress. Like under most abiotic and biotic stresses, apoplastic ROS signaling triggered by O3 induces massive changes in gene expression, enzyme activities and metabolic profiles. Thus, O3 is a very useful tool to study general mechanisms of ROS signaling and regulation of gene expression. Here we used a combination of transcriptome analysis and cell death assays to identify molecular mechanism initiated by apoplastic ROS signaling involved in the regulation of defense signaling and cell death in Arabidopsis thaliana.

overall_design: Transcriptome profiling of ozone response in three Arabidopsis accessions with different ozone sensitivity (Col-0, Shahdara and Cvi-0) to identify molecular mechanisms triggered by apoplastic ROS signaling. Raw sequencing data for Col-0 was previously submitted (GSE65740) and re-analyzed in the current study.

middle: O

first: Johanna

last: Leppälä

first: Omid

last: Safronov

first: Mikael

last: Brosché


title: The transcription factor Hhex cooperates with the corepressor Tle3 to promote memory B cell development

status: Public on Jun 29 2020

city: San Francisco

first: Brian

last: Laidlaw

state: CA

address: 513 Parnassus Avenue, HSE 1001

institute: University of California, San Francisco

summary: Memory B cells (MBCs) are essential for long-lived humoral immunity. However, the transcription factors (TFs) involved in MBC differentiation are poorly defined. Here, by single cell RNAseq analysis, we identified a population of germinal center (GC) B cells in the process of differentiating into MBCs. Using an inducible Crispr/Cas9 screening approach we identified the hematopoietically-expressed homeobox gene Hhex as a transcription factor regulating MBC differentiation. The co-repressor Tle3 was also identified in the screen and was found to interact with Hhex to promote MBC development. Bcl6 directly repressed Hhex in GC B cells. Reciprocally, Hhex-deficient MBCs exhibited derepressed Bcl6 and reduced expression of Bcl6-repressed Bcl2. Overexpression of Bcl2 was able to rescue MBC differentiation in Hhex-deficient cells. We also identified Ski as an Hhex-induced transcription factor involved in MBC differentiation. These findings establish an important role for Hhex-Tle3 in regulating the transcriptional circuitry governing MBC differentiation.

overall_design: Bulk-seq includes 5 samples- 2 groups (Het, 2 replicates; KO 3 replicates) and 1 scRNA-seq Sample of LCMV infected mice.

first: Lihui

last: Duan

first: Ying

last: Xu

first: Sara

last: Vazquez

first: Jason

middle: G

last: Cyster


title: Signaling state and abundance of circulating immune cell subpopulations determine cancer response to immunotherapy

status: Public on Jun 09 2020

city: Houston

first: Jeffrey

last: Chang

address: 6431 Fannin St

institute: University of Texas

summary: We profiled 70,781 peripheral immune cells taken before, during, and after treatment with chemotherapy and immunotherapy of patients with advanced gastrointestinal cancers using single cell RNA sequencing. Prior to therapy, responders had a higher relative abundance of undifferentiated (naïve) CD4+ T cells, while non-responders had more differentiated CD4+  and CD8+ effector memory (EM) cells.  Further, the EM cells present in responders were exhausted, suggesting prior recognition of tumor. Upon anti-PD-1 treatment, T cells of responders showed a shift towards increased differentiation and a higher relative abundance of cytotoxic CD8+ T cells than non-responders, with both populations and monocytes showing striking activation of interferon and MHC processing pathways. In addition to T cells, responders were enriched in classical monocytes prior to therapy, with a predominance of high TNF-α and growth factor activity associated with inhibition of NF-κB. The number and signaling activation states of T cells and classical monocytes, as well as their evolution soon after the initiation of therapy, may be predictive markers of immunotherapy response.

overall_design: Examination of GI patient PBMC single cell profiles at mutliple time points using the 10X platform

first: Andrea

last: Bild

first: Lance

last: Pflieger


title: Long-read Nanopore sequencing of synthetic "sequin" controls

first: Xueyi

last: Dong

summary:
Purpose: To generate a reference long-read transcriptomic data set for use in developing new analysis pipelines and comparing their performance with existing methods.
Synthetic “sequin” RNA standards (Hardwick et al. 2016) were sequenced using the Oxford Nanopore Technologies (ONT) GridION platform.

overall_design: Technical replicates of each sequin mix were generated.

first: Yair

last: David Joseph Prawer

first: Ric

last: De Paoli-Iseppi

first: Michael

last: Clark

first: Matthew

last: Ritchie


title: Stat3-Bdnf-TrkB axis promotes alveolar regeneration [scRNA-seq]

status: Public on Jun 01 2020

city: Philadelphia

first: G

middle: Scott

last: Worthen

state: PA

address: 3615 Civic Center Blvd

department: Pediatrics

institute: Children's Hospital of Philadelphia

summary: Regenerating new alveolar epithelium is essential for recovery from many lung diseases. This multi-cellular regenerative process occurs when type II alveolar pneumocytes (AT2), with support from mesenchymal niche cells, proliferate to generate more AT2 cells and transdifferentiate in type I pneumocytes. To elucidate how coordinated events between AT2 cells and mesenchyme restore alveolar epithelium we used unbiased genome-wide analysis of chromatin accessibility and gene expression in both cell types following acute lung injury. We observed that chromatin acessability in AT2 cells changes signficantly following acute lung injury. Newly accessible chromatin reveals new STAT3 binding motifs adjacent to genes that regulate essential regenerative pathways in AT2 cells. Restoration of alveolar structures following both sterile and infectious lung injuries was inhibited when STAT3 signaling was lost in AT2 cells. Single-cell transcriptome analysis of regenerating AT2 cells identified brain neurotrophic factor (Bdnf) as the sole STAT3 target gene whose chromatin becomes newly accessible in a regenerating population of AT2 cells. BDNF increased alveolar organoid size and forming efficiency in murine and human models. The receptor for BDNF, TrkB, is uniquely? expressed on mesenchymal alveolar niche cells (MANC). Exposure of BDNF to TrkB increases expression of fibroblast growth factor 7 (Fgf7), an essential regenerative cytokine, in MANCs. Blocking Bdnf signaling with a TrkB receptor antagonist abrogated murine and human alveolar organoid formation. Finally, a small molecule TrkB agonist improved functional and histological outcomes in vivo following sterile and infectious lung injuries. Collectively, these data highlight the biological and therapeutic importance of the Stat3-Bdnf-TrkB axis in orchestrating alveolar epithelial regeneration

overall_design: One control mouse and one 24 hr injured mouse. At2 cells isolated by flow, and single cells captured using 10x platform.

first: Andrew

last: Paris


title: Systems genetic analysis in Diversity Outbred mice informs human bone mineral density GWAS and identifies Qsox1 as a novel determinant of bone strength

first: Basel

last: Al-Barghouthi

overall_design: Here, we sequenced total RNA from 192 Diversity Outbred marrow-depleted left femurs.

first: Larry

last: Mesner

first: Gina

last: Calabrese

first: Daniel

last: Brooks

first: Steven

last: Tommasini

first: Mary

last: Bouxsein

first: Mark

last: Horowitz

first: Clifford

last: Rosen

first: Kevin

last: Nguyen

first: Samuel

last: Haddox

first: Emily

last: Farber

first: Suna

last: Onengut-Gumuscu

last: Pomp

first: Charles


title: RNA-sequencing of Panc-1 cells with ABCG2 over-expression

city: Huntsville

first: Sara

last: Cooper

state: AL

address: 601 Genome Wau

institute: HudsonAlpha Institute

summary: The goal of this study was to determine whether the selected sgRNAs increases expression of ABCG2 and whether there are other significant off-target effects

overall_design: Four samples. Two non-targeting controls and two independent guides targeting ABCG2 over-expression


title: A molecular map of lymph node blood vascular endothelium at single cell resolution

status: Public on May 15 2020

city: Palo Alto

last: Brulois

address: 3801 Miranda Ave

institute: Stanford University

summary: Blood vascular endothelial cells (BECs) control the immune response by regulating immune cell recruitment, metabolite exchange and blood flow in lymphoid tissues. However, the diversity of BEC and their origins during immune angiogenesis remain poorly understood. Here we profile transcriptomes of BEC from mouse peripheral lymph nodes and map key phenotypes to the vasculature. Our analysis identifies multiple novel subsets including a venous population whose gene signature predicts an unexpectedly selective role in myeloid cell (vs lymphocyte) recruitment to the medulla, confirmed by 2 photon videomicroscopy.   We define five phenotypes of capillary lining BEC including a capillary resident regenerative population (CRP) that displays stem cell and migratory gene signatures and contributes to homeostatic BEC turnover and to vascular neogenesis after immunization. Trajectory analyses reveal retention of developmental programs along a progression of cellular phenotypes from CRP to mature venous and arterial BEC subsets. Overall, our single cell atlas provides a molecular blueprint of the lymph node blood vasculature and defines subset specialization for immune cell recruitment and vascular homeostasis.

overall_design: We performed droplet-based single cell RNA sequencing (scRNAseq, 10x Chromium v2) of FACS sorted BEC (CD31+ PDPN - CD45 -) from resting PLN of adult mice. Four cohorts were analyzed, including a group of male and female Balb/c (PLN1) processed together and resolved in silico, an additional group of female Balb/c mice (PLN2), and one of female mice of mixed background (PLN3).

first: Eugene

middle: C

last: Butcher


title: Stat3-Bdnf-TrkB axis promotes alveolar regeneration [ATAC-seq]

first: G

last: Worthen

overall_design: 3 replicates each of control and injured murine AT2 cells isolated from lungs

middle: S

last: Paris


title: Myeloid regulation signature persists after virus clearance in mild human primary dengue serotype 2 infection

status: Public on Jun 12 2020

city: Burlington

first: Korin

last: Eckstrom

state: VT

address: 89 Beaumont Ave

institute: University of Vermont

summary: Healthy flavivirus-naive volunteers (n=11) were infected with the live attenuated dengue serotype 2 challenge virus (rDEN2delta30) as the control arm of a dengue vaccine challenge trial. Whole blood RNA was collected in Paxgene tubes for expression profiling prior to infection (day 0), and on days 8, and 28 after rDEN2delta30 infection. Whole blood RNA was depleted of globin-and rRNA transcripts and equal amounts of depleted RNAs were used to generate libraries for SE 100 RNA sequencing per sample on by Illumina. To generate technical replicates, each library was run in different flow cells/lanes and aggregated to an average of approximately 26 million reads total per sample with <1% variation in counts across lanes in a given sample. Comparisons of gene expression in count-normalized samples were focused on analysis of grouping data by timepoint as well as by examining consensus intra-subject timepoint-associated gene expression changes after rDEN2delta30 infection, focusing on pairwise comparisons (Day 8 vs Day 0, Day 28 vs Day 8, and Day 28 vs,. Day 0).

overall_design: Whole blood transcriptomics of patients on days 0, 8, and 28 after rDEN2delta30 challenge.

first: John

last: Hanley

first: Julie

last: Dragon

first: Dorothy

last: Dickson

first: Nicholas

last: Selig

first: Scott

last: Tighe

middle: V

last: Scarpino

first: Stephen

last: Whitehead

first: Anna

last: Durbin

first: Kristen

last: Pierce

first: Beth

middle: D

last: Kirkpatrick

first: Donna

last: Rizzo

first: Seth

last: Frietze

first: Sean

last: Diehl


title: IL-23 promotes a coordinated B-cell germinal center program for class-switch recombination to IgG2b in BXD2 mice

status: Public on May 14 2020

city: Birmingham

first: Min

last: Gao

address: 1900 University Blvd, THT Building Suite #130G

institute: University of Alabama at Birmingham

summary: IL-23 promotes autoimmune disease including Th17 CD4 T-cell development and autoantibody (autoAb) production.  Here, we show that a deficiency of the p19 component of IL-23 in autoimmune BXD2 (BXD2-p19−/−) mice leads to an imbalance of the follicular T-helper cell program with a shift from Tfh-IL-17 to Tfh-IFN-ɣ.  Although the germinal center (GC) size and number of GC B cells remained the same, BXD2-p19−/− mice exhibited a lower class-switch recombination (CSR) program in the GC B cells, leading to a lower serum levels of IgG2b.  Single cell transcriptomics analysis revealed that while GC B cell expression of Ifngr1 and Il21r genes exhibited a synchronized expression pattern with plasma cell program genes, Il17ra exhibited a synchronized expression pattern with pre-plasmablast GC program genes.  Down-regulation of Ighg2b in BXD2-p19−/− GC B cells was associated with decreased expression of CSR-related base excision repair genes that were otherwise predominantly expressed by Il17ra+ cells compared to Ifngr1+ GC B cells in BXD2 mice.  Together, these results suggest that although IL-23 is dispensable for GC formation, it is essential for development of the Tfh-IL17 Tfh subpopulation, which drives CSR-related base excision repair genes during the pre-plasmablast GC stage of development.

overall_design: We carried out single cell RNAseq and single-cell V(D)J seq for GC B cells derived from the spleens of BXD2 mice and IL-23-deficient BXD2 (BXD2-p19-/-)mice

first: Huixian

last: Hong

first: Shanrun

last: Liu

first: Hui-Chen

last: Hsu

last: Mountz


title: miR-200c induction in Met-1 mammary carcionma cells

status: Public on May 28 2020

city: Aurora

first: Michelle

middle: M

last: Williams

state: CO

department: Pathology

institute: University of Colorado Anschutz Medical Campus

summary: We performed RNA-seqeuncing analysis on mouse Met-1 cells that express miR-200c in a doxycycline (DOX)-inducible manner from the miR-200c-TripZ system.

overall_design: Six samples. Two groups in biological triplicate. Met-1-pTripZ-200c cells, plated in triplicate, were cultured in DOX for 48 hours. Control cells were treated with vehicle (diH2O).

first: Kenneth

last: Jones

first: Jessica

last: Chirstenson

first: Kathleen

middle: I

last: O'Neill

first: Sabrina

last: Hafeez

first: Claire

last: Ihle

first: Nicole

last: Sploelstra

first: Jill

middle: E

last: Slansky

first: Jennifer

last: Richer


title: Stat3-Bdnf-TrkB axis promotes alveolar regeneration

first: G

last: Worthen


title: ConnecTF: A platform to integrate validated transcription factor-target interactions to build and refine gene regulatory networks

status: Public on Jun 13 2020

city: Urbana

first: Matthew

middle: D.

last: Brooks

state: Illinois

address: 1201 W Gregory Drive

department: GCPRU

institute: USDA

summary: The direct targets of 16 TFs were identified using the TARGET system. Arabidopsis plants were grown on 1/2X MS media and after 10 days protoplasts were generated from root tissue, Cells were transfected with a vector containing the GR-TF fusion and incubated overnight. Each experiment also included a GR-only empty vector control. In the morning, samples were pre-treated with cycloheximide for 20 minutes, before TF entry into the nucleus was induced with dexamethasone. 3 hours after dex treatment samples were FACS sorted into RNA extraction buffer and RNA-seq libraries were generated. Transcriptional response to each TF compared to empty vector was assayed.

overall_design: Genome-wide direct regulated targets of 16 TFs were determined by comparison to an empty vector control. Vectors were expressed in protoplasts isolated from root tissue, samples were done in triplicate, and sequenced using the Illumina NextSeq platform.

first: Gloria

last: Coruzzi


title: Stability of Aire-upregulated and Aire-neutral transcripts in medullary thymic epithelial cells

status: Public on May 05 2020

city: Nantes

first: Matthieu

last: Giraud

address: 30 bd Jean Monnet

department: CRTI

country: France

institute: INSERM _ Université de Nantes

summary: Aire-upregulated transcripts exhibit higher stability than the transcripts neutral to Aire's action in mTEChi

overall_design: Total RNA isolated by Trizol extraction from MHC-II high or low mTECs (from pooled thymi of B6 mice) was used to generate poly-A-selected transcriptome libraries using the non-directionnal TruSeq V3 RNA Sample Prep Kit (without additional pre-amplification) for WT and Aire-KO mTEChi, as well as for mTEChi used as the reference timepoint (ActinoD 0h) or for mTEChi and lo from the same mice. Paired-end sequencing (2x100bp) was performed for these samples. 1h30, 3h, 6h and 12h-ActinoD-treated mTEChi libraries were generated using the Smarter Ultra Low Input RNA kit (Clontech) combined to the Nextera library preparation kit (Illumina). Single-end sequencing was performed for these ActinoD-treated samples. Sequencing was performed on the Illumina HiSeq2000 machine.

first: Clotilde

last: Guyon


title: shRNA screen of factors involved in Aire-sensitive gene expression on their 3'UTR lengthening

summary: CLP1 controls the expression of Aire-sensitive genes with proximal pAs and their shortening in HEK293 cells

overall_design: Specific knockdown of CLP1, HNRNPL, DDX5, DDX17, PARP1, PRKDC, SUPT16H, PABPC1, CPSF6 and the control LacZ gene in HEK293 cells

first: Nada

last: Jmari


title: RNAseq profiling of Ctr and CLP1 knockdown HEK293 cells

summary: CLP1 promotes 3’UTR shortening and higher expression at Aire-sensitive genes in HEK293 cells

overall_design: Specific knockdown of CLP1 and the control LacZ gene in HEK293 cells maintained in complemented DMEM high glucose medium, was performed by infection with lentivirus-expressing shRNAs. shRNA2 (sh2) and shRNA3 (sh3) were cloned into the lentivirus vector pLKO with an expression driven by the ubiquitously active U6 promoter. Total RNA isolated by Trizol extraction was used to generate poly-A-selected transcriptome libraries using the non-directionnal TruSeq V3 RNA Sample Prep Kit (without additional pre-amplification) following the manufacturer's protocols. Single-end (50 bp) sequencing was performed using the Illumina HiSeq2000 machine.


title: Differential DNA Methylation in Somatic and Sperm cells of Hatchery versus Wild (Natural-Origin) Steelhead Trout Populations

status: Public on May 24 2020

city: Pullman

first: Michael

middle: K

last: Skinner

state: WA

address: Abelson 507

department: SBS

institute: WSU

type: Methylation profiling by high throughput sequencing

summary: The study was designed to investigate the impacts of hatchery spawning and rearing on steelhead trout (Oncorhynchus mykiss) versus the wild fish on a molecular level. Additionally, epigenetic differences between feeding practices that allow slow growth and fast growth hatchery trout were investigated.  The sperm and RBC DNA both had a large number of DMRs when comparing the hatchery versus wild steelhead trout populations. Interestingly, the DMRs were cell type specific with negligible overlap. Slow growth compared to fast growth steelhead also had a larger number of DMRs in the RBC samples. Observations demonstrate a major epigenetic programming difference between the hatchery and wild fish populations, but negligible genetic differences. Therefore, hatchery conditions and growth rate can alter the epigenetic developmental programming of the steelhead trout, which may correlate to the phenotypic variations observed.

overall_design: The sperm and red blood cells (RBC) from adult male slow growth hatchery steelhead, fast-growth hatchery steelhead, and wild (natural-origin) steelhead were collected for DNA preparation to investigate potential alterations in differential DNA methylation regions (DMRs). An MeDIP-seq procedure was used to identify the DMR.

first: Eric

last: Nilsson

first: Ingrid

last: Sadler-Riggleman

first: Daniel

last: Beck


title: Expression data from cochlea isolated from Meis2 mutant and wild-type mice at E15

status: Public on May 06 2020

city: Valladolid

first: Thomas

last: Schimmang

address: Sanz y Fores 3

institute: CSIC

summary:
The aim of this study consists in detecting genes regulated by Meis2 in the murine cochlea
In this data set we present 256 genes differentially regulated by Meis2 in the murine cochlea. These data serve as a platform for verifying their differential regulation by Meis2 via RNA in situ hybridisation or qPCR

overall_design: 4 Total samples were analyzed. A pairwise comparison between two wild-type and 2 Meis2 mutants samples was conducted. Genes with a FDR<0.05 are presented.Briefly, the robust microarray analysis (RMA) algorithm was used for background correction, intra- and inter-microarray normalization, and expression signal calculation. Once the absolute expression signal for each gene (i.e., the signal value for each probe set) was calculated in each microarray, a method [called significance analysis of microarray (SAM)] was applied to calculate significant differential expression and find the gene probe sets that characterized the highly metastatic samples. The method uses permutations to provide robust statistical inference of the most significant genes and provides P valuesadjusted to multiple testing using false discovery rate (FDR).

first: Carlos

middle: P

last: Sanchez


title: 4-hydroxy-2-nonenal (4-HNE) induced transcriptional changes in Listeria monocytogenes

status: Public on May 10 2020

city: Seattle

first: Hannah

last: Tabakh

address: 750 Republican St Bldg F

department: Microbioloby

institute: University of Washington

summary: Pathogens must counteract a wide array of antimicrobial responses, including the reactive oxygen species (ROS) burst. ROS mediated oxidation of host membrane poly-unsaturated fatty acids (PUFAs) leads to the production of the toxic alpha-beta carbonyl 4-hydroxy-2-nonenal (4-HNE). 4-HNE has been studied extensively in the context of sterile inflammation but understanding of its role during bacterial infection remains limited. In this work we found that 4-HNE is generated during bacterial infection and that the intracellular pathogen Listeria monocytogenes induces a specific set of genes in response to 4-HNE exposure.

overall_design: L. monocytogenes grown to mid-log (0.4-0.8 OD) in tryptic soy broth at 37C, then a bolus of 640 micromolar 4-HNE or vehicle (ethanol) was added. Bacteria were exposed to 4-HNE for 20 minutes at 37C after which they were quenched with methanol and RNA was extracted for transcriptional analysis.

first: Joshua

last: Woodward


title: Single cell RNA-seq of microglia isolated from different brain regions of WT and 5xFAD mice.

status: Public on May 25 2020

city: Freiburg

first: Ori

last: Staszewski

address: Breisacher Str. 64

department: Institute of Neuropathology

institute: University Medical Center Freiburg

summary: Single cell RNA-seq data were obtained from FACS sorted microglia isolated from different brain regions of 30 weeks old WT and 5xFAD mice to find commonly expressed genes in all clusters.

overall_design: single microglia were sequenced with 3-4 replicate mice per condition. The different brain regions were obtained from the same mice.

first: Marco

last: Prinz

first: Roman

last: Sankowski

first: Takahiro

last: Masuda

first: Lukas

last: Amann


title: Clp1 knockdown lentigenic mouse generation

summary: Clp1 promotes 3’UTR shortening and higher levels of Aire-upregulated transcripts in mTEChi

overall_design: Three shRNAs against Clp1 were cloned into a cluster of micro RNAs construct. This construct was transferred to a lentiviral backbone, downstream of the doxycycline inducible promoter TRE3G and upstream of the ZsGreen protein. A second construct expressing the TetOn3G transactivator under the control of the EF1 promoter was generated. A single ultra-high purified and concentrated lentivector (2.2x109 TU/mL) containing both constructs was generated and purified by both Tangential Flow Filtration and Chromatography. Fertilized oocytes (B6) were microinjected under the zona pellucida with the lentivirus suspension. Transduced oocytes were reimplanted into pseudopregnant females. Newborns were selected for integration of both constructs by PCR with primers matching the ZsGreen or TetOn3G sequences. At 3 weeks of age, mice were treated with doxycycline food pellets (2 g/kg) for two weeks and then sacrificed for mTEChi isolation. One generated pup, with integration of both plasmids. exhibited, after doxycycline treatment, a 60% reduction of Clp1 mRNA levels in GFP+ (Clp1 knockdown) versus GFP- (Ctr) mTEChi taken from the same mouse. Total RNA isolated by Trizol extraction to generate poly-A-selected transcriptome libraries using the Smarter Ultra Low Input RNA kit (Clontech) combined to the Nextera library preparation kit (Illumina). Single-end sequencing was performed on the Illumina NextSeq 500 machine.


title: Clinical and biological implications of target occupancy in chronic lymphocytic leukemia treated with acalabrutinib

status: Public on Apr 07 2020

city: Bethesda

first: Mehdi

last: Pirooznia

state: MD

address: 12 SOUTH DR

institute: National Institutes of Health

summary: Inhibition of the B-cell receptor pathway, and specifically of Bruton tyrosine kinase (BTK), is a leading therapeutic strategy in chronic lymphocytic leukemia (CLL). Target occupancy has been measured as a pharmacodynamic parameter in clinical studies of covalent BTK inhibitors. However, the kinetics of BTK turnover, which determines occupancy, and the relationship between occupancy, pathway inhibition and clinical outcomes remains undefined. This randomized phase 2 study investigated the safety, efficacy, and pharmacodynamics of a selective BTK inhibitor acalabrutinib at 100 mg twice daily or 200 mg once daily in 48 patients with relapsed/refractory or high-risk treatment naïve CLL. Acalabrutinib was well tolerated and yielded an overall response rate (ORR) of partial response or better of 95.8% (95% CI 78.9%, 99.9%) and an estimated progression-free survival (PFS) rate at 24 months of 91.5% (95% CI 70.0%, 97.8%) with twice daily dosing and an ORR of 79.2% (95% CI 57.9%, 92.9%) and an estimated PFS rate at 24 months of 87.2% (95% CI 57.2%, 96.7%) with once daily dosing. BTK resynthesis was faster in CLL than in healthy volunteers. Twice daily dosing maintained higher BTK occupancy and achieved more potent pathway inhibition compared to once daily dosing. Additional follow-up is required to address the impact of dosing schedule and BTK occupancy on long-term clinical outcomes.

overall_design:
RNA sequencing of CD19+ peripheral blood mononuclear cells and lymph node core biopsies before and during treatment with acalabrutinib
ACP = acalabrutinib
BID = twice daily
QD = once daily
D3/4/5 = day 3/4/5 of treatment
C1/6 = after cycle 1/6 of treatment

first: Clare

last: Sun

first: Ellen

last: Kendall

first: Adrian

last: Wiestner


title: WT and Aire-KO mouse MEChi RNAseq profiling

first: Matthieu

last: Giraud

summary: Aire-sensitive genes exhibit short 3'UTR transcript isoform preference in WT and Aire-KO mTEChi

overall_design: ~100ng of total RNA isolated by Trizol extraction from MHC-II high mTECs (pool of 4 mice) was used to generate poly-A-selected transcriptome libraries using the non-directionnal TruSeq V3 RNA Sample Prep Kit (without additional pre-amplification) following the manufacturer's protocols.  Enrichment of DNA fragment with adapter molecules on both ends was done using 15 cycles of PCR amplification using the Illumina PCR mix and primer cocktail. Paired-end (2 × 100 bp) sequencing was performed using the Illumina HiSeq2000 machine.

first: Clotilde

last: Guyon


title: Regulatory function of Pja2 mediated by the P2rx3/P2rx7 axis in mouse hippocampal neuronal cells

status: Public on Apr 25 2020

city: Hefei

first: Kan

last: He

state: Anhui

address: 111 Jiulong Road

department: School of life sciences

institute: Anhui University

summary:
A member of the growing family of mammalian RING E3-ubiquitin ligases praja2 (Pja2) was reported to function not only in several types of cancer but also in the neurological diseases and disorders.
As a result, the expression of App, Mapt and Gsap could be inhibited by Pja2 overexpression and activated by the knockdown of Pja2. RNA sequencing (RNA-seq) was then used to evaluate and quantify the transcriptomes in response to the overexpression of Pja2 in mouse hippocampal neuronal HT-22 cells.

overall_design: Inducible Pja2 in HT-22 cells were the treated samples and uninduced cells were used as controls. Experiments were performed in duplicate. Gene expression profiling analyses by high throughput sequencing were performed on mRNA samples isolated from the sense Pja2 in HT-22 cells (Pja2/+) and the wildtype cells.

first: Mengting

last: Gong


title: Expression data from WT and Klf3 KO BMDMs treated with LPS

status: Public on Mar 24 2020

city: UNSW Sydney

first: Kate

last: Quinlan

state: NSW

address: Room 3102, Level 3, Biosciences South Building (E26)

department: School of Biotechnology and Biomolecular Sciences

institute: UNSW Sydney

summary: Gene expression in bone marrow-derived macrophages (BMDMs) from WT and mice lacking the transcriptional repressor Kruppel-like factor 3 (KLF3). We cultured BMDMs from bone marrow for 7-10 days then treated cells with 100 ng/mL lipopolysaccharide (LPS) or vehicle (PBS) for 0 h or 8 h, followed by RNA extraction. We aimed to investigate deregulated genes and pathways in macrophages lacking KLF3, during the inflammatory response to endotoxin (LPS).

overall_design: Bone marrow from 10-14 week-old male mice was flushed and cultured in DMEM-F12 (containing 10% serum and 1% antibiotics) and conditioned medium harvested from L929 cells (containing M-CSF) in a 80:20 ratio. After 7-10 days, adherent macrophages (BMDMs) were confluent and treated with 100 ng/mL LPS or vehicle (PBS), with samples harvested at 0 h (no treatment) or 8 h for RNA extraction. RNA was extracted from isolated cells using a Qiagen RNeasy Mini Kit then subjected to quality control using an Agilent 2100 Bioanalyzer. An Affymetrix 3’ IVT Kit was used prior to microarrays which were performed on an Affymetrix GeneChip HT MG-430PM Array Plate.

first: Merlin

last: Crossley

first: Alexander

last: Knights


title: RNAseq profiling of Aire and Ctr-transfected HEK293 cells

summary: Aire-sensitive genes exhibit short 3'UTR transcript isoform preference in Aire and Ctr-transfected HEK293 cells

overall_design: HEK293 cells were transfected with the pCMV-Aire-Flag plasmid (or the control empty plasmid) using the TransIT-293 transfection reagent (Mirus) for 48 hours. CLP1 knockdown was performed by lentivirus infection of CLP1-specific shRNAs (sh2 and sh3). Total RNA isolated by Trizol extraction was used to generate poly-A-selected transcriptome libraries using the non-directionnal TruSeq V3 RNA Sample Prep Kit (without additional pre-amplification) following the manufacturer's protocols. Single-end (50 bp) sequencing was performed using the Illumina HiSeq2000 machine. Single-end (75bp) reads generated by the Illumina NextSeq 500 machine (lentivirus infected samples) were truncated to 50 bp.

first: Nada

last: Jmari

first: Francine

last: Padonou


title: Transcriptional Idenetity of Itch-activated Central Amygdala Neurons

status: Public on Apr 23 2020

city: St Louis

first: Vijay

last: Samineni

state: MO

address: 4940 Parkview Place, Room 5539 Department of Anesthesiology

institute: Washington university St. louis

summary: We performed RNA-seq to identify transcriptional profiles of itch-activated CeA neurons. To do this, we crossed FosTRAP mice to the Cre-dependent tdTomato flox-stop reporter line as described above.  We then injected chloroquine into the nape of the neck, paired with injection of 4-OHT to FosTRAP expression of tdTomato in itch-activated neurons. The CeA was harvested, the cells dissociated and sorted by FACS, and tdTomato+ cells were compared to TdTomato- cells.

overall_design: Facs CeA TdTomato+ve and tdTomato _ve neurons after TRAPping these neurons to chloroquine stimuli.


title: PRRX1 deficiency induces mesenchymal-epithelial transition through PITX2/miR-200-dependent SLUG/CTNNB1 regulation in hepatocellular carcinoma

status: Public on Apr 18 2020

city: Nanjing

first: Weibo

last: Chen

state: Jiangsu

address: No. 321 Zhongshan Road

department: Department of Hepatobiliary Surgery

institute: Affiliated Drum Tower Hospital of Nanjing University Medical School

summary:
Metastasis is a major obstacle to better prognosis in patients with hepatocellular carcinoma (HCC). Mesenchymal-epithelial transition (MET) is the driving force for metastatic colonization in which E-cadherin reexpression is a critical procedure. It has been reported that the loss of paired-related homeobox transcription factor 1 (PRRX1) is required for cancer cell metastasis in vivo. However, the role of PRRX1 in MET and how its downregulation triggers E-cadherin reexpression are unknown. In this study, we performed a systematic, mechanistic study regarding the role of PRRX1 in MET of HCC. We observed PRRX1 downregulation in HCC tissues which correlated with early metastasis and short overall survival time. Overexpression of PRRX1 induced EMT, but did not promote metastasis formation, while knockdown of PRRX1 promoted metastasis and colonization of circulating HCC cells as shown in in situ liver tumor model and colonization model. PRRX1 protein levels reversely correlated with E-cadherin levels in HCC cell lines. PRRX1 knockdown promoted E-cadherin reexpression and cell proliferation, inhibited cell invasion and migration.
The microarray results showed that PRRX1 deficiency regulated extracellular matrix (ECM) interaction, focal adhesion, TGF-β signaling and cancer pathways. PRRX1 knockdown upregulated PITX2 (paired like homeodomain 2) and inhibited CTNNB1 (catenin beta 1) and SLUG. Silencing of PITX2 reversed CTNNB1 and SLUG inhibition and E-cadherin reexpression. PITX2 upregulation increased miR-200a and miR-200b/429, which further inhibited the transcription of CTNNB1 and SLUG, respectively, thus abrogating the inhibitory effect on E-cadherin. In conclusion, our data showed that the downregulation of PRRX1 induced E-cadherin reexpression through PITX2/miR-200a/CTNNB1 and PITX2/miR-200b/429/SLUG pathway, making PRRX1 a novel prognostic factor for HCC.

overall_design: The clinical relevance of PRRX1 was examined by western blotting of HCC cells and immunohistochemistry staining of HCC microarray slides. The prognostic effect of PRRX1 was analyzed by univariate and multivariate analysis. Functional assays, such as the transwell assay, wound healing assay, colony formation assay, xenografts, circulating tumor cell colonization assay and western blotting were used to determine the biological role of PRRX1 in HCC. Thereafter, microarray and related experiments were performed to investigate the possible mechanisms. The interaction between paired-like homeodomain transcription factor 2 (PITX2) and snail family zinc finger 2 (SLUG)/CTNNB1 was verified after PITX2 siRNA transfection. The interaction between SLUG/ catenin beta 1 (CTNNB1) and microRNAs was verified by microRNA mimic/inhibitor transfection and luciferase assay.

first: Chunping

last: Jiang


title: Overexpression of the selective autophagy receptor AtNBR1

status: Public on Apr 20 2020

city: Warsaw

first: Agnieszka

last: Sirko

address: Pawinskiego 5A

institute: Institute of Biochemistry and Biophysics

summary:
Cargo receptors are well established elements of the selective autophagy in all eukaryotes. The NBR1-like family of such receptors is evolutionarily conserved, however plants have only one member of the family, which is a functional and structural hybrid of its two animal counterparts, p62 (SQSTM1) and NBR1.
Examination of plants overexpressing NBR1 indicates that they are oversensitive to TOR inhibitors and have more autophagosomes than the parental lines. The observed changes in shoots suggested induction of ABA signalling pathway, what was further corroborated by the germination tests and the assay of ABA level. The transcriptome changes in roots, such as lower level of snoRNA and some tRNAs, suggested inhibition of ribosome biogenesis, what is supported by identification of RPS6, an important component of TOR-dependent translational control, as a novel partner of NBR1.

Grant number: 2014/15/B/NZ3/04854
Grant funding source: National Science Centre (Poland)
Grantee Name: Agnieszka Sirko
Grant title: Upstream regulators and cellular targets of the selective autophagy cargo receptor AtNBR1 in different phases of sulfur deficiency in plants.

overall_design: Arabidopsis plants, 33 days old, were harvested and total RNA were separately isolated from shoots and roots. We looked for effects of the NBR1 gene overexpression in the OX.7.5 line compared to the the wild type plants (Col-0). These effects were investigated in roots and shoots separately under conditions of both nutritional sufficiency and sulfur limitation. Totally, 24 samples of RNA were prepared.

first: Milagros

last: Rodríguez

first: Leszek

last: Tarnowski

first: Anna

last: Fogtman

first: Jerzy

last: Brzywczy


title: Total RNA-sequencing Detects Transcriptomic Differences in Mouse Preosteoblast Response to Bulk Nanostructured Titanium.

status: Public on Apr 09 2020

city: Socorro

first: Rebecca

last: Reiss

state: NM

address: 801 Leroy Place

department: Biology

institute: New Mexico Institute of Mining and Technology

summary:
Rational:  Titanium is the most widely used alloy family in dental and orthopedic implants due to its natural ability to integrate into bone, but cytotoxic alloying elements are required in titanium for its mechanical properties to match the functionality of natural bone in high-load bearing applications. Recent advances in nanostructuring, such as Continuous Equal Channel Angular Pressing (C-ECAP), reduce the grain size and increase the strength of pure grades of titanium, thereby eliminating the need for cytotoxic elements and increasing cytocompatibilty as measured by traditional cell biology techniques. Transcriptomic profiling of cells grown on conventional coarse grain (CG) versus nanostructured ultrafine grain (UG) surfaces can simultaneously enhance our understanding of genomics and biomaterials, facilitating the development of a new generation of implantable materials.
Objective: We initiated this pilot project to develop a workflow for transcriptional profiling of both protein coding and non-coding RNAs (ncRNAs) in cells grown on Ti discs that are characterized for grain size, 12.1 μm for CG Ti and 0.28 μm for UG Ti.
Methods: Two Ti substrates were designed for cell growth in 24-well culture dishes, CG and UG. Mouse pre-osteoblasts were cultured on Ti disc for 72 hours.  Cells were harvested and total-RNA extracted.  Ribosomal RNA subtraction was performed prior to Illumina sequencing library construction.  Single-end 50 base pairs reads were subjected to Illumina quality control and the resulting reads were mapped to the mouse genome and annotations with Genomic Short-read Nucleotide Alignment Program (GSNAP) and HTseq-count.  Read count files were normalized and statistically analyzed with empirical analysis of digital gene expression data in R (EdgeR) and filtered for low expression levels using Zipf’s Power Law. Transcripts with adequate coverage and significant expression differences were subjected to GO Biological Process term enrichment and network analyses with the Cytoscape App ClueGO.
Results: Gene expression differences with an FDR≤0.05 are limited to six genes, five of which are likely ncRNAs.  Of the 432 transcripts with significant differences at p≤0.05 117 form an interconnected network of genes and 12 GO biological processes (P(adj) ≤ 0.05). Biological processes that connect to predominately upregulated genes include cell division, mRNA metabolic processes, chromatin modification and protein localization to the cytoskeleton, while downregulated processes include regulation of apoptosis, of p38MAK cascade, and response to molecules of bacterial origin.
Conclusions:  After 72 hours, the transcriptional profile of cells on UG Ti confirms more rapid cell division than on CG. These results demonstrate that informative transcriptional profiling of cells growing on substrates that differ only in their crystallographic structure can be accomplished by a workflow that includes standard cell biology techniques, transcriptomic profiling, data mining, and network analyses.

overall_design:
Sterile Ti discs, 13.5 mm in diameter, polished to a 2 nm average surface roughness (Ra), were arrayed in a non-tissue culture treated 24-well cell culture plate using a block design, with 12 CG and 12 UG disks.  Wells were re-fed after 24 hours and after 72 hours Ti discs were transferred to new plates for standard cell harvesting protocols.  The cells from four wells were consolidated into one sample resulting in three biological replicates for each sample. Consolidated samples were stored at -80°C in RNAlater and all subsequent steps were identical for all samples.  Samples on CG were used as the control for UG-CG comparisons.

This project was partially supported by grants from the National Center for Research Resources (5P20RR016480-12) and the National Institute of General Medical Sciences (8 P20 GM103451-12) from the National Institutes of Health.

first: Terry

last: Lowe

first: Johnny

last: Sena

first: Patrick

last: Illescas

first: Casey

last: Davis

first: Melanie

last: Connick


title: Genome-wide identification and characterization of long non-coding RNAs conferring resistance to Colletotrichum gloeosporioides in walnut (Juglans regia)

status: Public on Mar 18 2020

city: Taian

first: shan

last: feng

address: Daizong Avenue

department: Forestry College

institute: Shandong Agricultural University

summary: Walnut anthracnose caused by Colletotrichum gloeosporioides (Penz.) Penz. and Sacc. is a major disease affecting walnut production in China. Although the long non-coding RNAs (lncRNAs) are important for plant disease resistance , the molecular mechanisms underlying resistance to C. gloeosporioides in walnut remain poorly understood.The anthracnose-resistant F26 fruits from the B26 clone and the anthracnose susceptible F423 fruits from the 4-23 clone of walnut were used as the test materials. Specifically, we performed a comparative transcriptome analysis of F26 fruit bracts and F423 to identify differentially expressed LncRNAs (DELs) at five time-points (tissues at 0 hpi, pathological tissues at 24 hpi, 48 hpi, 72 hpi, and distal uninoculated tissues at 120 hpi). Compared with F423, a total of 14525 DELs were identified, including 10645 upregulated lncRNAs and 3846 downregulated lncRNAs in F26. The number of upregulated lncRNAs in F26 compared to in F423 was significantly higher at the early stages of C. gloeosporioides infection. A total of 5 modules related to disease resistance were screened by WGCNA and the target genes of lncRNAs were obtained. Bioinformatic analysis showed that the target genes of upregulated lncRNAs were enriched in immune-related processes during the infection of C. gloeosporioides , such as activation of innate immune response, defense response to bacterium, incompatible interaction and immune system process, and enriched in plant hormone signal transduction, phenylpropanoid biosynthesis and other pathways. And 124 known target genes for 96 hub lncRNAs were predicted, including 10 known resistance genes. The expression of 5 lncRNAs and 5 target genes was confirmed by qPCR, which was consistent with the RNA-seq data.The results of this study provide the basis for future functional characterizations of lncRNAs regarding the C. gloeosporioides resistance of walnut fruit bracts.

overall_design: The expression profiles of lncRNAs during the infection of walnut by Colletotrichum gloeosporioides

first: Shan

last: Feng

first: Hongcheng

last: Fang

first: Xia

last: Liu

first: Yuhui

last: Dong

first: Ke

middle: Q

last: Yang


title: Transcriptome and N6-methyladenosine RNA methylome analyses in aortic dissection and normal human aorta

status: Public on Mar 17 2020

city: guangzhou

first: xianwu

last: zhou

address: No. 106, Zhongshan Second Road, Yuexiu District, Guangzhou

institute: Guangdong Provincial People's Hospital

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

overall_design: Refer to individual Series


title: N6-methyladenosine RNA methylome analyses in aortic dissection and normal human aorta

summary: To identify the m6A methylome in the aorta of patients with acute aortic dissection. MeRIP-seq and RNA-seq experiments of aortic media tissue samples obtained from AD patients and controls were conducted. Compared with control group, the upmethylated coding genes of AD were primarily enriched in the processes associated with extracellular fibril organization, while the genes with downmethylation were enriched in the processes associated with cell death regulation. Furthermore, many differentially methylated m6A sites (DMMSs) coding proteins were mainly annotated during the extracellular matrix and inflammatory responses.

first: Xianwu

last: Zhou

first: Tucheng

last: Sun


title: TET1-mediated DNA hydroxy-methylation regulates adult remyelination

status: Public on Mar 14 2020

city: New York

first: Sarah

last: Moyon

address: 85 St Nicholas Terrace

department: Neuroscience

institute: CUNY ASRC

summary: Adult myelination is essential for brain function and response to injury, but the molecular mechanisms remain elusive. Here we identify DNA hydroxy-methylation, an epigenetic mark catalyzed by Ten-Eleven translocation (TET) enzymes, as necessary for adult myelin repair. While DNA hydroxy-methylation and high levels of TET1 were detected in young adult mice during myelin regeneration after demyelination, this process was defective in old mice. Constitutive or inducible lineage-specific ablation of Tet1 (but not of Tet2) recapitulated the age-related decline of DNA hydroxy-methylation and inefficient remyelination. Genome-wide hydroxy-methylation and transcriptomic analysis identified solute carrier gene families as TET1 targets. Lower transcripts for these genes in Tet1 mutants and old mice were associated with swelling at the neuroglial interface, a phenotype detected also in zebrafish Slc12a2b mutants. We conclude that TET1-mediated DNA hydroxy-methylation is necessary for adult myelination after injury, by modulating the levels of the solute carrier SLC12A2 at the axo-myelin interface.

overall_design: mRNA profiles of oligodendroglial-enriched samples from P60 control (Olig1+/+;Tet1fl/fl) and Tet1 mutants (Olig1cre/+;Tet1fl/fl), from either unlesioned spinal cord or 4-day-post-lysolecithin-injection lesions. Samples generated by RNA-sequencing, in triplicate, using Illumina HiSeq 4000.

first: Frawley

last: Rebecca

first: Katy

last: Cole

first: Boguslawa

last: Sadowski

first: Dennis

last: Huang

first: Yong-Hui

last: Jiang

first: David

last: Lyons

first: Wiebke

last: Moebius

first: Patrizia

last: Casaccia


title: Transcriptome analyses in aortic dissection and normal human aorta

overall_design: To identify the m6A methylome in the aorta of patients with acute aortic dissection.


title: Small-molecule inhibition of Lats kinases promotes Yap-dependent proliferation in postmitotic mammalian tissues

status: Public on Apr 13 2020

city: Los Angeles

first: Ksenia

last: Gnedeva

address: 1501 San Pablo St

department: USC Caruso Department of Otolaryngology – Head and Neck Surgery

institute: USC

summary: We report on the gene expression changes associated with Lats1/2 inhibition in supporting cells of the vestibular inner ear sensory epithelium

overall_design: Examination of gene expression (RNA-seq) in one cell type in two culture conditions


title: Effects of STOX1 expression variants on trophoblastic cell lines

status: Public on Apr 05 2020

city: Paris

first: Daniel

last: Vaiman

address: 24 rue du Faubourg St Jacques

department: Genetics and Development

institute: INSERM

summary: The STOX1 transcription factor has been involved in a complex human disease of pregnancy, preeclampsia, in human families, and mouse models. However, its mode of action is still largely unknown. Overexpression of either the long (STOX1A) or the short (STOX1B) isoform was obtained in the BeWo villous trophoblast model, a cell line able to fuse in syncytiotrophoblast following induction by forskolin treatment. The effects at the transcriptional level are evaluated in every condition.

overall_design: Microarray Affymetrix Clariom S


title: Genomic repeats coordinate macroscopic gene function and expression

status: Public on Mar 10 2020

city: Rochester

first: jinlong

last: lu

address: 213 Hutchinson Hall

institute: University of Rochester

summary: Despite abundant distribution of repetitive elements, the roles they have been coopted in mammalian genomes are insufficiently characterized. Here we reveal a pervasive role for genic repeat in shaping macroscopic gene function and expression in both human and mouse. Specifically, genes enriched in SINE, L1 and simple repeat produce proteins with functions in distinct categories. To maintain/regulate the homeostatic expression of gene with diversified functions, SINE and L1 are targeted by different classes of transcriptional regulators and also show a nonrandom genomic and nuclear distribution, with B1 in the nuclear interior and L1 in the nuclear and nucleolar peripheries. Abnormal expression of L1-enriched gene compromise proliferation of embryonic stem cells. Moreover, L1 transcripts tend to bind L1-enriched genes, transacting L1 DNA information and mainly function as transcriptional repressors. These results demonstrate that genomic repeats have subtly shaped the function of host-gene they embedded in, and provide a paradigm shift in understanding function of genomic “parasites” in their host-genome.

overall_design: ChIRP-seq of L1 and Malat1 RNA

first: Xiaohua

last: Shen

first: Yafei

last: Yin

first: Yuyang

last: Lu


title: Sites on TAPBPR that scaffold assembly of a MHC-I H chain with beta2m are important for TAPBPR chaperone activity

city: Urbana

first: Erik

last: Procko

state: IL

address: 601 S Goodwin Ave

department: Biochemistry

institute: University of Illinois

summary: TAP-binding protein-related (TAPBPR) facilitates the processing of nascent class I MHC (MHC-I) by (1, chaperone function) acting as a chaperone for misfolded or partially folded MHC-I substrates in the cell and (2, editing function) by catalyzing exchange of low affinity for high affinity antigenic peptides in the MHC-I peptide-binding groove. In cells in which the principal MHC-I-specific chaperone and TAPBPR homologue tapasin has been knocked out, the processing and surface trafficking of the human MHC-I allele HLA-A2 is substantially reduced. Over-expression of TAPBPR can partially replace tapasin and rescue HLA-A2 surface expression. Using this assay as the basis for a fluorescence-based selection, TAPBPR was deep mutationally scanned at 92 positions in the core, at the interface with MHC-I, and on the ‘backside’ distal from where MHC-I binds. Critical regions of TAPBPR for rescue of HLA-A2 processing map to sites that contact the underside of the MHC-I alpha-2 domain and residues that contact the junction between beta-2 microglobulin and alpha-3 domains. Key sites on TAPBPR for chaperone activity therefore scaffold assembly of the MHC-I H chain with beta-2 microglobulin.

overall_design: A chimeric fusion was constructed between the extracellular domains of human TAPBPR and the transmembrane and cytosolic regions of tapasin. The chimera, called TAPBPR-CT, has higher activity for functional replacement of tapasin than wild type TAPBPR, possibly because of recruitment to the TAP1/2 transporter mediated by the tapasin C-terminal tail. A library was constructed in TAPBPR-CT in which 92 positions were diversified with degenerate NNK codons. The library was transfected in to tapasin-knock out Expi293F cells after 1500-fold dilution with a carrier plasmid; this ensures most cells express no more than a single sequence variant and there is a tight connection between genotype and phenotype. Illumina sequencing data to validate the introduction of indel mutations in exon 2 of the tapasin gene is in GEO Series Acc. No. GSE126206. Cells expressing the TAPBPR-CT library were stained for surface HLA-A2 with R-phycoerythrin-conjugated anti-HLA-A2 clone BB7.2, and the 0.5% of cells with the highest fluorescence were collected by FACS. Following Illumina sequencing, the frequencies of mutations from transcripts in the sorted cells were compared to their respective frequencies in the naive plasmid library. The calculated enrichment ratios are a proxy for relative activity of the TAPBPR sequence variants.

first: Christine

last: Devlin


title: Genome information processing by the INO80 chromatin remodeler positions nucleosomes

status: Public on Apr 30 2020

city: Göttingen

first: Elisa

last: Oberbeckmann

address: Justus-von-Liebig Weg 11

department: Molecular Biology

institute: University Medical Center Göttingen

summary: The mechanistics by which ATP-dependent chromatin remodelers process (epi)genetic information to generate hallmark features of chromatin are fundamental for genome regulation. Here, we advance whole-genome reconstitutions into a fully definable, recombinant approach for probing how remodelers determine nucleosome positioning. Using wild type and structure-guided mutant versions of the Saccharomyces cerevisiae 15-subunit INO80 remodeler, we show that INO80-intrinsic nucleosome positioning relies on direct DNA shape read-out. This requires especially the interplay between the INO80 nuclear actin and core modules, to a lesser extent the HMG-box Nhp10 module and not histone modifications/variants or the Rvb1/2 AAA+-ATPase activity. Extrinsically, nucleosome positioning is guided by the barrier Reb1 via Ino80 ATPase activity modulation or by mere DNA double strand breaks. Taken together, we present a defined and unbiased approach to understand remodeler-mediated nucleosome positioning and delineate how INO80 processes genomic information into nucleosome positioning.

overall_design: We used our genome-wide in vitro reconstitution system (Krietenstein et al. 2016, Cell) to investigate the effect of histone modification, type and tails on nucleosome positioning by the recombinantly purified S. cerevisiae remodeler INO80.

first: Nils

last: Krietenstein

first: Vanessa

last: Niebauer

first: Kevin

last: Schall

first: Manuela

last: Moldt

first: Tobias

last: Straub

first: Karl-Peter

last: Hopfner

first: Philipp

last: Korber

first: Sebastian

last: Eustermann


title: Identification of EGL-43 target genes in C. elegans L3 larvae.

status: Public on Mar 09 2020

city: Cambridge

first: Julie

last: Ahringer

address: Tennis Court Road

department: The Gurdon Institute

institute: University of Cambridge

summary: The C. elegans homolog of the Evi1 proto-oncogene, egl-43, coordinates G1 cell cycle arrest with pro-invasive gene expression during anchor cell invasion by regulating the expression of fos-1, and lin-12.

overall_design: ChIP-seq was used to profile EGL-43::GFP binding sites in  C. elegans L3 larvae.

first: Przemyslaw

last: Stempor


title: Lgr5+ telocytes are a signaling hub at the intestinal villus tip

status: Public on Feb 05 2020

city: Rehovot

first: Keren

last: Bahar-Halpern

address: Herzl St 234

country: Israel

institute: Weizmann Institute

summary: We molecularly characterized thousands of intestinal cells including epithelial, masenchymal and immune cells using scRNAseq. This enable us to uncover the important role of villus tip telocytes as master regulators of the epithelial spatial expression programs along the villus axis

overall_design: mRNA profiles from single cells, EDTA isolated jejunum epithelial cells and LCM samples extracted from mouse jejunum were sequenced in several batches in an Illumina NextSeq.

middle: B

last: Halpern

first: Hassan

last: Massalha

first: Andreas

last: Moor

first: Rachel

last: Zwick

first: David

last: Azofeifa

first: Milena

last: Rozenberg

first: Lydia

last: Farack

first: Adi

last: Egozi

first: Dan

last: Miller

first: Inna

last: Averbukh

first: Yotam

last: Harnik

first: Noa

middle: W

last: Corem

first: Frederic

middle: J

last: de Sauvage

first: Ido

last: Amit

first: Ophir

last: Klein

first: Michal

last: Carmel

first: Shalev

last: Itzkovitz


title: Characterization of Arabidopsis thaliana promoter bidirectionality and antisense RNAs by depletion of nuclear RNA decay pathways

status: Public on Feb 17 2020

city: Copenhagen

first: Axel

last: Thieffry

state: Hovedstaden

address: Lersø Parkallé 42-44

department: R&D

country: Denmark

institute: BioPhero-FMC


title: Ruler elements in chromatin remodelers set nucleosome array spacing and phasing

status: Public on Feb 10 2020

first: Elisa

last: Oberbeckmann

summary: Arrays of regularly spaced nucleosomes dominate chromatin and are often phased, i.e., aligned at reference sites like active promoters. How distances between nucleosomes and distances between phasing sites and nucleosomes are determined remained unclear, specifically, the role of ATP dependent chromatin remodelers in it. Here, we used a genome-wide reconstitution system to probe how yeast remodelers generate phased nucleosome arrays. We find that remodelers bear a structural element named the ‘ruler’ that sets nucleosome spacing, in the order Chd1 < ISW1a < ISW2 < INO80. Structure-based mutagenesis confirmed the functional significance of the ruler element in INO80. Differences in the ruler elements of different remodelers explain the observed nucleosome array features. More generally, we propose that remodelers use their rulers to regulate the direction of nucleosome sliding in response to nucleosome density and environment, leading to nucleosome positioning relative to other nucleosomes, DNA bound factors or DNA sequence elements.

sample_organism:
Escherichia coli
Schizosaccharomyces pombe
Saccharomyces cerevisiae

overall_design: We used our genome-wide in vitro reconstitution system (Krietenstein et al. 2016, Cell) to investigate the effect of varying nucleosome densities, different barriers (Reb1 and DNA double strand breaks) and underlying DNA sequences from different genomes (S. cerevisiae, S. pombe and E. coli) on all S. cerevisiae remodelers with spacing activity (INO80, ISW2, ISW1a and Chd1). Additionally, we used structural-guided INO80 mutans to find insights into INO80s' spacing mechanism.

first: Vanessa

last: Niebauer

first: Shinya

last: Watanabe

first: Lucas

last: Farnung

first: Manuela

last: Moldt

first: Andrea

last: Schmid

first: Patrick

last: Cramer

first: Craig

middle: L

last: Peterson

first: Sebastian

last: Eustermann

first: Karl-Peter

last: Hopfner

first: Philipp

last: Korber


title: Discovery and characterization of a novel p-hydroxybenzoate-m-hydroxylase, protocatechuate 3,4 ring-cleavage dioxygenase and hydroxyquinol 1,2 ring-cleavage dioxygenase from Aspergillus niger

status: Public on Feb 26 2020

city: Utrecht

first: Ronald

last: de Vries

address: Uppsalalaan 8

department: fungal physiology

country: Netherlands

institute: Centre of fungal biodiversity

summary: The aim of this study was to find candidate genes in A. niger involved in the degradation of benzoic acid.

overall_design: Transcriptome data on aromatic compounds was used to find candidate genes encoding benzoic acid metabolic enzymes

first: Ronnie

last: Lubbers

first: Adiphol

last: Dilokpimol

first: Mao

last: Peng

first: Jaap

last: Visser

first: Kristiina

last: Hildén


title: Multiple myeloma

status: Public on Jan 24 2020

city: New Delhi

first: Ritu

last: Gupta

state: Delhi

address: Dr. B.R.A.IRCH, Ansari Nagar

department: Laboratory Oncology

institute: All India Institute of Medical Sciences, New Delhi

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


title: Single-cell analysis of childhood leukemia reveals a link between developmental states and ribosomal protein expression as a source of intra-individual heterogeneity

status: Public on Jan 30 2020

city: Montreal

first: Guillaume

last: Bourque

state: QC

address: 740 Dr penfield

department: Human Genetics

institute: Mcgill university

summary: Assessing intra-individual transcriptional heterogeneity in cALL patients using single cell RNA-seq

overall_design: 10X Genomics 3’ single cell RNA-seq: Pre-B t(12;21) [ETV6-RUNX1] acute lymphoblastic leukemia, Pre-B High hyper diploid [HHD] acute lymphoblastic leukemia, Pre-T acute lymphoblastic leukemia, Healthy pediatric bone marrow mononuclear cells. Annotations.tsv contains sample, cell cycle phase, tSNE/UMAP coordinates, and assigned cell type.

first: Maxime

last: Caron

first: Pascal

last: St-Onge

first: Thomas

last: Sontag

first: Yu

last: Wang

first: Chantal

last: Richer

first: Ioannis

last: Ragoussis

first: Daniel

last: Sinnett


title: miRNA expression signatures in multiple myeloma

summary: In the present study, miRNome profiling was carried out to investigate the microRNA expression patterns of multiple myeloma patients and to assess the pathogenetic role of differentially expressed miRNAs by correlating their expression pattern with the expression of their target genes.

overall_design: MiRNA expression profiling was carried out in 44 myeloma samples and 4 controls (Pooled from 10 Hodgkin's disease samples).

first: Nitin

last: Mathur

first: Lata

last: Rani

first: Amit

last: Katiyar

first: Punit

last: Kaur

first: Lalit

last: Kumar

first: Atul

last: Sharma


title: Gene expression signatures in multiple myeloma

summary: In the present study, the gene expression profiling was carried out to identify the gene targets affected by miRNAs deregulated in multiple myeloma. A gene expression signature was generated for 45  patients of multiple myeloma as compared to controls (Pooled from 10 Hodgkin's disease samples).

overall_design: Gene expression profiling was carried out in 45 myeloma samples and 3 controls (Pooled from 10 Hodgkin's disease samples).


title: Polycomb-mediated repression of EphrinA5 promotes growth and invasion of glioblastoma

status: Public on Feb 01 2020

city: London

first: Silvia

last: Marino

address: 4, Newark St

institute: Queen Mary University of London

summary: Glioblastoma (GBM) is the most common and most aggressive intrinsic brain tumour in adults. Integrated transcriptomic and epigenomic analyses of glioblastoma initiating cells (GIC) in a mouse model uncovered a novel epigenetic regulation of EfnA5. In this model, Bmi1 enhances H3K27me3 at the EfnA5 locus and reinforces repression of selected target genes in a cellular context dependent fashion. EfnA5 mediate Bmi1-dependent proliferation and invasion in vitro and tumour formation in an allograft model. Importantly, we show that this novel Polycomb feed-forward loop is also active in human GIC and we provide preclinical evidence of druggability of EFNA5 in GBM xenografts overexpressing BMI1.

overall_design:
H3K27me3-ChIPSeq: 1 Control NSC, 1 Bmi1over NSC, 1 GIC.
RNASeq: 2 replicas of control NSC, 2 replicas of Bmi1over NSC, 2 replicas of GIC.

first: Barbara

last: Ricci

middle: O

last: Millner

first: Nicola

last: Pomella

first: Xinyu

last: Zhang

first: Loredana

last: Guglielmi

first: Sara

last: Badodi

first: Dario

last: Ceric

first: Carolina

last: Gemma

first: Erica

last: Cognolato

first: Ying

first: Sebastian

last: Brandner

first: Micheal

middle: R

last: Barnes