title: Myeloid cell analysis during a pro-fibrotic ischemia-reperfusion and cardiotoxin muscle injury.

status: Public on Jan 28 2020

city: Ann Arbor

first: Amanda

middle: Katherine

last: Huber

state: MI

address: 1000 Wall Street

department: Computational Medicine and Bioinformatics

country: USA

institute: University of Michigan

summary: Myeloid cells are critical to the development of fibrosis following muscle injury, however, the mechanism of their role in fibrosis formation remains unclear. Here we demonstrate that myeloid cell-derived TGF-β1 signaling is increased in a pro-fibrotic ischemia-reperfusion and cardiotoxin (IR/CTX) muscle injury model. This study analyzes scRNAsequencing from the fibrotic region after a pro-fibrotic ischemia-reperfusion and cardiotoxin muscle injury.

overall_design: We used 10X genomics to perform single cell sequencing of cells from the fibrotic area after a pro-fibrotic ischemia-reperfusion and cardiotoxin muscle injury.

first: Benjamin

last: Levi

first: Simone

last: Marini

first: David

last: Stepien


title: RNA-seq analysis of kdm5 null mutant wing discs

status: Public on Dec 31 2019

city: Bronx

first: Julie

last: Secombe

state: NY

address: 1300 Morris park ave

department: Genetics

institute: Albert Einstein College of Medicine

type: Expression profiling by high throughput sequencing

summary: In order to determine which genes were affected by the complete loss of kdm5, we carried out RNA-seq analysis using wing discs from wildtype and kdm5 140, the new null mutant.  Consistent with the phenotypes observed, transcriptome analyses of kdm5140 mutant wing imaginal discs revealed the dysregulation of a significant number of genes involved in cell cycle progression and DNA repair.

overall_design: 6 samples with wildtype (kdm5 140 rescued by a gKDM5 transgene) in triplicate and kdm5 140 in triplicate

first: Coralie

last: Drelon

first: Helen

middle: M

last: Belalcazar


title: Accelerated evolution of oligodendrocytes in human brain

city: Dallas

first: Genevieve

last: Konopka

state: TX

address: 5323 Harry Hines Blvd.

department: Neuroscience

institute: UT Southwestern Medical Center

summary: Recent discussions of human brain evolution have largely focused on increased neuron numbers and changes in their connectivity and expression.  However, it is increasingly appreciated that oligodendrocytes play important roles in cognitive function and disease. Whether both cell types follow distinctive evolutionary trajectories is not known. We examined the transcriptomes of neurons and oligodendrocytes in the frontal cortex of humans, chimpanzees, and rhesus macaques. We identified human-specific trajectories of gene expression in oligodendrocytes and show that oligodendrocytes have undergone accelerated gene expression evolution in the human lineage. The signature of acceleration is enriched for cell type-specific expression alterations in schizophrenia. These results underscore the importance of oligodendrocytes in human brain evolution.

sample_organism:
Macaca mulatta
Pan troglodytes
Homo sapiens

overall_design: We compared the cell-type specific transcriptome profiling of sorted nuclei from humans to chimpanzees, our closest extant relative, using rhesus macaque as an outgroup. We analyzed genome-wide expression levels in adult human Brodmann area 46 (BA46, 27 individuals), and the homologous regions of chimpanzee (11 individuals), and rhesus macaque (15 individuals). Cell-type specific whole transcriptome data was obtained using fluorescence-activated nuclei sorting (FANS) with antibodies to either NeuN or OLIG2 to isolate neurons (NeuN) or oligodendrocytes (OLIG2) and their precursors, respectively.

first: Stefano

last: Berto

first: Noriyoshi

last: Usui

first: Kazuya

last: Toriumi

first: Connor

last: Douglas


title: Cis- and trans-regulation of alternative splicing by Adenosine Deaminase Acting on the double-stranded RNA (ADAR) proteins

status: Public on Dec 22 2019

city: Singapore

first: Polly Leilei

last: Chen

address: #12-01, MD6, 14 Medical Drive

department: Department of Anatomy

country: Singapore

institute: Cancer Science Institute of Singapore NUS

summary: RNA editing and splicing are the two major processes that dynamically regulate human transcriptome diversity. Despite growing evidence of crosstalk between RNA editing enzymes (mainly ADAR1) and splicing machineries, detailed mechanistic explanations and their biological importance in diseases, such as cancer are still lacking. Herein, we identify approximately a hundred high-confidence splicing events altered by ADAR1 and/or ADAR2, and ADAR1 or ADAR2 protein can regulate cassette exons in both directions. We unravel a binding tendency of ADARs to dsRNAs that involves GA-rich sequences for editing and splicing regulation. ADAR1 edits an intronic splicing silencer, leading to recruitment of SRSF7 and repression of exon inclusion. We also present a mechanism through which ADAR2 binds to dsRNA formed between GA-rich sequences and polypyrimidine (Py)-tract and precludes access of U2AF65 to 3′ splice site. Furthermore, we find these ADARs-regulated splicing changes per se influence tumorigenesis, not merely byproducts of ADARs editing and binding.

overall_design: We constructed strand-specific cDNA libraries of 8 total RNA samples and sequenced the libraries using Illumina Hiseq4000 platform achieving over 200 millions of mappable reads per sample. Then we examined alternative splicing in EC109 cells after depletion or overexpression of ADAR1 or ADAR2.

first: Leilei

first: Sze

middle: J

last: Tang

first: Haoqing

last: Shen

first: Omer

last: An


title: Transition of breast cancer cells from luminal to basal-like phenotype engages a shift from genomic to non-genomic activities of estrogen receptor-alpha activity

city: Rennes

first: Raphaël

last: Métivier

address: Campus de Beaulieu

country: France

institute: CNRS UMR 6290

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Estrogen receptor (ERα) is central in driving the development of hormone-dependent breast cancers. A major challenge in treating these cancers is to understand and struggle endocrine resistance. We have previously shown that the Megakaryoblastic Leukemia 1 (MKL1) protein, a master regulator of actin dynamic and cellular motile functions, directs down-regulation of ERα and hormonal escape of estrogen-responsive breast cancer cell lines. In the present study, we decipher the underlining mechanisms by tracking functional changes in ERα activity. We demonstrate through gene expression microarray analysis that the constitutive activation of MKL1 in ERα-positive MCF7 breast cancer cells induces a transition from a luminal to a basal-like phenotype and suppresses almost all regulations of gene expression by estrogen. Chromatin immunoprecipitation of DNA coupled to high-throughput sequencing (ChIP-Seq) shows a profound reprogramming in ERα cistrome associated with a massive loss of ERα binding sites (ERBSs) generally associated with lower ERα-binding activity. Novel ERBSs appear to be associated with EGF and RAS signaling pathways. ERα dynamic was further impacted by a displacement of its monomer/dimer equilibrium towards its monomer state, associated with a redistribution of the normally nuclear ERα protein to the entire cell volume. We next show that the combination of these remodeled dynamics of ERα alters its interactions with genomic and non-genomic partners. In particular, the formation of ERα/kinase complexes was promoted by the constitutive activation of MKL1. Hence, MKL1-induced transition of ER-positive breast cancer cells from luminal to basal-like phenotype shifts ERα activities from genomic to non-genomic function.

overall_design: Whole-genome analysis of estrogen receptor (ER) binding events in  MCF-7 cells ectopically expressing a dominant form of the MKL1 protein and associated control cells.

first: Tamara

last: Fernandez-Calero

first: Charly

last: Jehanno

first: Denis

last: Habauzit

first: Stephane

last: Avener

first: Frederic

last: Percevault

first: Noureddine

last: Boujrad

first: Pascale

last: Le Goff

first: Monica

last: Marin

last: Michel

first: Gilles

last: Flouriot


title: RNA-Seq from zmknl1 and WT kernels at 14 DAP (day after pollination) with each two independent biological replicates

status: Public on Dec 21 2019

city: Wuhan

first: Handong

last: Su

state: Hubei

address: No.1,Shizishan Street · Hongshan District

country: China

institute: Huazhong Agricultural University

summary: To further understand the basis of the phenotypic defects in the zmknl1 mutant, we performed RNA-Seq from zmknl1 and WT kernels at 14 DAP with each two independent biological replicates. Totally 555 significantly differentially expressed genes (DEGs) were identified according to these RNA-Seq data (q-value <0.05, log2(fold change) >= 1.5), with 317 down- and 238 up-regulated genes.

overall_design: Two independent biological replicates from different ears were used in the study. The cDNA libraries were constructed following Illumina standard protocols and sequenced with Illumina HiSeq 2500 by Berry Genomics Co. Ltd, China. Sequenced reads were trimmed using Trimmomatic (version: 0.36), then mapped to B73 RefGen_v3.31 using hisat2 (version: 2.0.1-beta). Htseq-count was used to count reads of all the annotated genes. Significant DEGs were identified using DESeq2 package as those with threshold (q < 0.05,log2(fold change) > 1.5).

first: Fangpu

last: Han


title: Genome-wide maps of DNA methylation and gene expression for  multiple  regions  within  a  breast tumor [RRBS]

status: Public on Jan 01 2020

city: Harbin

first: Xishan

last: Wang

address: Xue Fu Road 246

institute: The Second Affiliated Hospital of Harbin Medical University

type: Methylation profiling by high throughput sequencing

summary: As the differentiation state of the cells is affected by epigenetic modification regulation, the abnormal epigenetic modification is an important factor leading to the intratumoral heterogeneity. To further understand of the intratumoral epigenetic heterogeneity, we performed Reduced Representation Bisulfite Sequencing and RNA sequencing for multiple regions within a breast tumor and exhibited the epigenetic maps of different regions. We detected intratumoral heterogeneity-related molecular features and further explored the correlation between tumor heterogeneity and tumor hypoxic microenvironment.

overall_design: Our  tumor  samples  were  derived  from  a  patient  with  HER2  breast  invasive  ductal carcinoma  at  stage  II.  The  size  of  tumor  was  45  mm×22  mm  and  the  patient  was without  prior  neoadjuvant  therapy.  For  RNA  and  DNA  libraries  preparation,  the tissues  of  tumor  center,  12  o'clock,  3  o'clock,  6  o'clock  and  9  o'clock  of  tumor periphery as well as adjacent of the tumor were taken for 0.6 mg, respectively. Another case of normal breast tissue was used as a control. Totally, 7 samples were examined by RRBS and RNA sequencing.

first: Yan

last: Zhang

first: Yihan


title: Role of NuRD subunits CHD3 and CHD4 in human melanoma cells (ChIP-seq)

status: Public on Nov 03 2019

city: Illkirch-Graffenstaden

first: Guillaume

last: Davidson

address: 1 Rue Laurent Fries

department: Functional Genomics and Cancer

institute: Institut de Genetique et de biologie moleculaire et cellulaire

summary: The Nuclesome Remodelling and Deacetylation (NuRD) complex is an epigenetic regulator of gene expression comprising two mutually exclusive ATPase subunits CHD3 or CHD4. Here we show that CHD4 silencing in multiple types of cancer cells de-represses expression of the PADI1 (Protein Arginine Deiminase 1) and PADI3 enzymes that convert arginine to citrulline. Increased PADI1 and PADI3 expression enhances citrullination of three arginines of the key glycolytic regulatory enzyme PKM2 (pyruvate kinase) promoting excessive glycolysis, lowered ATP levels and slowed proliferation. PKM2 citrullination lowers its sensitivity to the allosteric inhibitors Tryptophan and Phenylalanine shifting equilibrium towards the allosteric activator Serine, thereby bypassing the normal physiological regulation of glycolysis by low Serine levels. Our results describe a novel pathway linking epigenetic regulation of PADI1 and PAD3 expression by CHD4 to glycolytic flux and the control of cancer cell growth.

overall_design: 2 samples: input control sample and ChIP CHD4 sample

first: Sebastien

last: Coassolo

first: Luc

last: Negroni

first: Giovanni

last: Gambi

first: Sylvain

last: Daujat

first: Christophe

last: Romier

first: Irwin


title: RNA sequencing of splenic B cell populations prevalent in Py-infected mice

status: Public on Nov 01 2019

city: NORTH CHICAGO

first: Rahul

last: Vijay

state: IL

address: 3333 GreenBay Road, BSB 2.450

department: Microbiology and Immunology

institute: Rosalind Franklin University

summary: Purpose: To peform genome wide transcriptomic analyses and compare the expression profile among Plasmablasts, activated B cells and resting B cells obtained form the spleens of Plasmodium yoelli infected mice on day 10

overall_design: 12 C57BL/6 mice obtained from Jackson laboratories were infected with 1 million Plasmodium yoelii paratized RBCs. ON day 10 post infection, spleens were harvested and three different B cell populations ( plasmablasts, activated B cells and resting B cells) were flow sorted, total RNA extracted and sequenced.

first: Noah

last: Butler


title: Role of NuRD subunits CHD3 and CHD4 in human melanoma cells (RNA-seq)

overall_design: Twelve samples: cells treated with siCHD4 compared to cells treated with siControl and cells treated with siCHD3 compared to cells treated with siControl, all conditions are in triplicates.


title: Role of NuRD subunits CHD3 and CHD4 in human melanoma cells

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

overall_design: Refer to individual Series


title: Multiplexed RNA-sequencing of 1M immune cells reveals the cellular, molecular, and genetic correlates of systemic lupus erythematosus

status: Public on Nov 10 2019

city: San Francisco

first: Meena

last: Subramaniam

state: CA

address: 513 Parnassus Ave S-965

institute: UCSF IHG

summary:
Systemic lupus erythematosus (SLE) is an autoimmune disease defined by a broad range of symptoms that disproportionately affects women
Our knowledge of which immune cells mediate the etiology and pathogenesis of the disease remains incomplete
Identifying pathogenic cells using bulk gene expression analysis is confounded by the functional overlap and frequency variation of immune cell types
Here, we used multiplexed single-cell RNA-seq (scRNA-seq) to profile ~1 million peripheral blood mononuclear cells from 134 SLE cases and 58 healthy controls
Cases were marked by a reduction of naive CD4+ T cells, clonal restriction of effector memory CD8+ T cells, and elevated expression of interferon-stimulated genes in classical monocytes
An additional 15 cases experiencing active disease flares displayed increased expansion of effector memory CD8+ T cells and the presence of macrophages not seen in managed disease
Although cell-type-specific expression contributed most to inter-individual expression variability across all cells, cell composition accounted for more variability in genes differentially expressed in cases
We integrated dense genotyping data to map thousands of genetic variants, including SLE-associations, whose effects on expression are modified by cell type or interferon activation
Population-scale scRNA-seq analysis reveals changes in cell composition and state associated with SLE, and when integrated with genetic data, ascribes function to disease-associated and disease-modified variants

overall_design: Multiplexed single cell sequencing of SLE patients and healthy controls

first: Jimmie

last: Ye


title: Quantitative Analysis of Wild Type CBL, CBL 70Z and Y371S 3T3 Stable Cell Transcriptomes

status: Public on Oct 20 2019

city: Glasgow

first: Syed

middle: Feroj

last: Ahmed

state: Bearsden

address: Garscube Estate, Switchback Road

department: Structural Biology

country: United Kingdom

institute: Beatson Institute for Cancer Research

summary: Cbl (Casitas B-lineage lymphoma) is a prominent post-translational regulator of protein tyrosine kinases (PTKs) that targets activated receptors for ubiquitination-mediated degradation. However, mutations within its E3 ubiquitin ligase activity rendering RING domain are often not sufficient to induce transformation. Rather, a conserved residue (Y371) within the linker helix region (LHR) of Cbl has been a mutational hotspot in myeloproliferative diseases. Interestingly, phosphorylation of Y371 is a prerequisite for Cbl’s ability to ubiquitinate PTKs. We have previously shown that Y371 mutations affect the conformation of Cbl that can be related to its transformation potential. We wanted to investigate for any additional advantage that the Cbl-Y371 mutants could gain over their wild-type counterpart so as to explain their oncogenicity. In our current study, we wanted to investigate the transcriptome profiles of cells overexpressing WT CBL or CBL-70Z, a well-characterized oncogenic CBL mutant lacking residues 366-382 and Y371S a prevalent MDS/MPN CBL mutant. We found an interesting inverse correlationship between the transcriptome of cells expressing WT CBL and the mutant CBLs. The results from this study can be linked to the oncogenic abilities of the mutant CBLs.

overall_design: Examination of differences in transcriptome profiles of cells stably expressing WT CBL or mutant CBLs (70Z and Y371S)

middle: F

first: Ann

last: Hedley

first: William

last: Clark

first: Danny

middle: T

last: Huang


title: Gene expression profile of human trabecular meshwork cells with silenced expression of autophagy genes Atg5 and Atg7

status: Public on Oct 01 2019

city: Durham

first: Paloma

middle: B

last: Liton

state: NC

address: DUMC Box 3802

institute: Duke University

summary: In order to investigate the effects of downregulated autophagy in TM cells, we conducted gene expression analysis in human TM cells deficient in autophagy. For this, three independent strains of primary human TM cells were transfected with a cocktail of siRNAs to specifically silence the expression of the autophagy genes Atg5 and Atg7 (siAtg5/7). A scrambled siRNA (siNC) was used as control.

overall_design: siRNA transfection was performed as described previously with minor modifications (Kristine M Porter, Jeyabalan, & Liton, 2014). In brief, primary human TM cells were plated on 24-well plate, with 60-80% confluence, in 0.5 mL of the growth media.  After 24 h, the cells were transfected with either 5 pmol of siRNA against ATG5 (siAtg5, sc-41445) and ATG7 (siAtg7, sc-41447) or 5 pmol of non-targeting siRNA (siNC, sc-37007) using Lipofectamin® RNAiMAX Reagent, according to the manufacturer’s instructions. At 72 h post-transfection, cells were washed with cold PBS and fixed in RNAlater (Qiagen). Total RNA was isolated using RNeasy kit (Qiagen, Valencia, CA), following the manufacturer's protocol, and treated in-column with DNase I. RNA concentration and quality were determined using the Agilent 2100 Bioanalyzer. Total RNA (5 µg) from human TM primary cultures with transient silenced autophagy and controls were independently hybridized to human Clariom D microarrays (ThermoFisher) following the manufacturer's instructions at the Duke Microarray Core Facility. Data analysis was performed using the Partek Flow and Partek Genome Suite statistical analysis software (Partek Incorporated).


title: Different response to oxidative damage of iPS cells and the progenitor fibroblast cells through the lens of the DNA repair system

city: Suita

first: Daisuke

last: Okuzaki

state: Osaka

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

country: Japan

institute: Osaka univ.

summary: In response to DNA damage, cells arrest the cell cycle to repair damage, induce apoptosis when unrepaired, and avoid the accumulation of mutations. Our present analysis showed that oxidative stress causing DNA damage in the same condition resulted in apoptosis in induced pluripotent stem cells (iPSCs), but background levels of apoptosis in progenitor fibroblasts that just suffered cell-cycle arrest. PCA analysis of RNA-seq data and annexin V staining revealed apoptosis in iPSCs recovered within 24 hours. Characteristics as a stem cell obtained by reprogramming have shown that systems have been established that do not leave mutations in daughter cells by quickly induced apoptosis when accurate DNA repair was impossible. The surviving cells' gene expression reverts to approximately the same as that before oxidative damage in 24 hours, although the expression of error-free DNA repair-related genes has not reverted. On the other hand, the expression of error-prone polymerase POLH and REV3 revealed up-regulation. This pattern might cause the possibility of mutation in the genome after oxidative stress.

overall_design: RNA-sequencing analyses were performed in three fibroblast cells and one its-derived induced pluripotent stem cells.

first: Yasuhide

last: Yoshimura


title: Single-cell methylation and accessibility of mouse embryoid body cells, day 3 to day 7. Includes wild type and Tet TKO.

status: Public on Sep 30 2019

city: Cambridge

first: Felix

last: Krueger

address: Granta Park

department: Bioinformatics

institute: Altos Labs

summary:
Formation of the three primary germ layers during gastrulation is an essential step in the establishment of the vertebrate body plan. Recent studies employing single cell RNA-sequencing have identified major transcriptional changes associated with germ layer specification. Global epigenetic reprogramming accompanies these changes, but the role of the epigenome in regulating early cell fate choice remains unresolved, and the coordination between different epigenetic layers is unclear. Here we describe the first single cell triple-omics map of chromatin accessibility, DNA methylation and RNA expression during the exit from pluripotency and the onset of gastrulation in mouse embryos. We find dynamic dependencies between the different molecular layers, with evidence for distinct modes of epigenetic regulation. The initial exit from pluripotency coincides with the establishment of a global repressive epigenetic landscape, followed by the emergence of local lineage-specific epigenetic patterns during gastrulation. Notably, cells committed to mesoderm and endoderm undergo widespread coordinated epigenetic rearrangements, driven by loss of methylation in enhancer marks and a concomitant increase of chromatin accessibility. In striking contrast, the epigenetic landscape of ectodermal cells is already established in the early epiblast. Hence, regulatory elements associated with each germ layer are either epigenetically primed or epigenetically remodelled prior to overt cell fate decisions during gastrulation, providing the molecular logic for a hierarchical emergence of the primary germ layers.

Useful links:
Parsed data: (ftp://ftp.ebi.ac.uk/pub/databases/scnmt_gastrulation)
Github repository: (https://github.com/rargelaguet/scnmt_gastrulation)

overall_design: 192 single cells isolated embryoid bodies from TET KO and matching WT ESCs, processed using scNMT-seq (Clark et al 2018)

first: Ricard

last: Argelaguet

first: Hisham

last: Mohammed

first: Stephen

first: L

middle: C

last: Stapel

first: Christel

first: Chantriolnt-Andreas

last: Kapourani

first: Yunlong

last: Xiang

first: Courtney

last: Hanna

first: Sebastien

last: Smallwood

first: Ximena

last: Ibarra-Soria

first: Florian

last: Buettner

first: Guido

last: Sanguinetti

first: Wei

last: Xie

first: Peter

last: Rugg-Gunn

first: Gavin

last: Kelsey

first: Wendy

last: Dean

first: Jennifer

last: Nichols

first: Oliver

last: Stegle

first: John

last: Marioni

first: Wolf

last: Reik


title: Single-cell methylation and accessibility of mouse embryos E6.5 and E7.5. Second batch.

first: Felix

last: Krueger

overall_design: 1110 single cells isolated from mouse embryos at E4.5, E5.5, E6.5 and E7.5 and processed using scNMT-seq (Clark et al 2018)

first: Ricard

last: Argelaguet

first: Hisham

last: Mohammed

first: Stephen

last: Clark

first: L


title: Genetic interaction analysis of RSA1 deletion strains (GIM screen)

status: Public on Oct 10 2019

city: Paris

first: Cosmin

last: Saveanu

address: 25-28 rue du docteur Roux

department: Genomes and Genetics

institute: Institut Pasteur

summary:
A S. cerevisiae strain with deletion of RSA1 gene was combined with two collections of yeast mutants: one in which non-essential genes were deleted and one in which an long 3' UTR extension has been added to the mRNA of essential genes (GIM method, Decourty et al., 2008). Combined double-mutant deletion cells growth was quantified using barcodes that are specific for each gene mutation. A reference population was obtained by mixing the results of 15 GIM screens DNA prior to barcode amplification and labeling (Decourty et al., in preparation).
The identification of genetic interactions between deletion of RSA1 and deletion of RTT106, a histone chaperone, indicate a potential role of Rtt106 in snoRNP formation.

overall_design: Two independent GIM experiments were analyzed using two Agilent microarrays


title: Single-cell RNA-seq of mouse embryos E6.5 and E7.5. Second batch.

overall_design:
2213 single cells isolated from mouse embryos at E4.5, E5.5, E6.5 and E7.5 and processed using scNMT-seq (Clark et al 2018)

NOTE: the processed data file, embryo_cell_counts_matrix_030719.tsv, contains total 2971 data columns for both GSE121650 (758 cells) and GSE133725 (2213 cells) samples.

last: Stapel

first: Christel

first: Chantriolnt-Andreas

last: Kapourani

first: Yunlong

last: Xiang

first: Courtney

last: Hanna

first: Sebastien

last: Smallwood

first: Ximena


title: Lack of NFATc1 SUMOylation protects from inflammatory diseases

status: Public on Aug 31 2019

city: Würzburg

first: Stefan

last: Klein-Hessling

address: Josef-Schneider-Str. 2

department: Institute of Pathology

country: Germany

institute: University of Würzburg

summary: Post-translational modification with SUMO is known to regulate the activity of transcription factors, but how SUMOylation of individual proteins might influence immunity is mostly unexplored. NFATc1 is a transcription factor of the family of ‘Nuclear Factors of Activated T-cells’ which plays an essential role in antigen receptor-mediated gene regulation. It is expressed in multiple isoforms of which the longer isoforms can be modified by SUMOylation. SUMO modification of NFATc1 represses IL-2 in vitro, but its role in T cell-mediated immune responses in vivo is not clear. To this end, we generated a novel Nfatc1 transgenic mouse with lysine to arginine mutations, which abolish the SUMO modification within NFATc1’s C-terminal domain. Inhibition of NFATc1 SUMOylation ameliorated experimental autoimmune encephalomyelitis as well as graft-versus-host disease. This was due to elevated IL-2 production that promoted Treg expansion and suppressed autoreactive or alloreactive T cells. Mechanistically, increased IL-2 secretion counteracted IL-17 and IFN-γ expression through STAT5 and Blimp-1 induction. Blimp-1 also repressed IL-2 itself and the as well induced survival factor Bcl2A1. Still, lack of NFATc1 sumoylation fine-tunes T-cell responses towards lasting tolerance implying a novel approach to treat inflammatory diseases.

overall_design: CD4+ CD90.1+ T cells from GvHD-induced mice on d4. CD4+ T cells were either of WT (3 samples) or NFATc1/ΔS (3 samples) genotype

first: Matthias

last: Klein

first: Lena

last: Dietz

first: Musga

last: Qureischi

first: Berberich-Siebelt

last: Friederike


title: Expression data from Arabidopsis globular stage embryo regions

status: Public on Aug 06 2019

city: Los Angeles

first: Bob

last: Goldberg

address: 610 Charles E Young Drive East

department: Molecular, Cell and Developmental Biology

institute: University of California, Los Angeles

summary: We collected Arabidopsis globular stage embryo proper and suspensor from 5 or 7-micro paraffin sections using the Lecia LMD6000 system in order to identify the mRNAs present in different embryo regions.

overall_design: Illumina sequencing of transcripts from laser-captured embryo proper and suspensor regions of Arabidopsis globular stage embryo.

first: Robert

first: John

last: Harada

first: Julie

last: Pelletier

first: Min

last: Chen


title: Single-cell RNA-seq of mouse embryoid body cells, day 3 to day 7. Includes wild type and Tet TKO.

first: Felix

last: Krueger

overall_design: 960 single cells isolated embryoid bodies from TET KO and matching WT ESCs, processed using scNMT-seq (Clark et al 2018)

first: Ricard

last: Argelaguet

first: Hisham

last: Mohammed

first: Stephen

first: L

last: Ibarra-Soria

first: Florian

last: Buettner

first: Guido

last: Sanguinetti

first: Wei

last: Xie

first: Peter

last: Rugg-Gunn

first: Gavin

last: Kelsey

first: Wendy

last: Dean

first: Jennifer

last: Nichols

first: Oliver

last: Stegle

last: Marioni

first: Wolf

last: Reik


title: Natural variation in RNA m6A methylation and its relationship with translational status.

status: Public on Sep 16 2019

city: Beijing

first: Yan

last: He

state: Beijing

address: 2 Yuanmingyuan West Road

department: Plant Genetics and Breeding

institute: China Agricultural University

summary: N6-methyladenosine (m6A) is the most abundant modification of eukaryotic messenger RNA. Although m6A has been demonstrated to affect almost all aspects of RNA metabolism, its global contribution to the post-transcriptional balancing of translational efficiency remains elusive in plants. In this study, we performed a parallel analysis of the transcriptome-wide mRNA m6A distribution and polysome profiling in two maize (Zea mays) inbred lines to assess the global correlation of m6A modification with translational status. m6A sites are widely distributed in thousands of protein-coding genes, confined to a consensus motif and primarily enriched in the 3' untranslated regions, and highly coordinated with alternative polyadenylation usage, suggesting a role of m6A modification in regulating alternative polyadenylation site choice. More importantly, we identified that the m6A modification shows multifaceted correlations with the translational status depending on its strength and genic location. Moreover, we observed a substantial intraspecies variation in m6A modification, and this natural variation was shown to be partly driven by gene-specific expression and alternative splicing. Together, these findings provide an invaluable resource for ascertaining transcripts that are subject to m6A modification in maize and pave the way to a better understanding of natural m6A variation in mediating gene expression regulation.

overall_design: m6A-seq, RNA-seq and polysome profiling of 14-day-old B73 and Mo17 seedings were conducted to investigate natural variation in RNA m6A methylation and its correlation with translational status in maize.


title: Identification of Soybean WOX9-like binding sites in soybean seeds during seed development

status: Public on Aug 02 2019

first: Bob

last: Goldberg

summary: To dissect the gene regulatory networks operating during soybean seed development, we identified the binding sites genome-wide for transcription factor in soybean seeds during seed  development using ChIP-seq

overall_design: Identification of soybean WOX9-like binding sites in soybean seeds during seed development. ChIP and total chromatin controls (input) were obtained for two replicates. Samples were sequenced using the Illumina HiSeq2500 platform.

first: Robert

first: Nestor

last: Apuya


status: Public on Sep 17 2019

city: Lakewood

first: Albert

last: Tafur Rangel

state: Colorado

address: 1617 Cole Blvd,

institute: NREL-Universidad de Los Andes-Universidad Popular del Cesar

summary:
Clostridium (Ruminiclostridium) thermocellum is recognized for its ability to ferment cellulosic biomass directly, but it cannot naturally grow on xylose. Recently, C. thermocellum (KJC335) was engineered to utilize xylose through expressing a heterologous xylose catabolizing pathway. Here, we compared KJC335’s transcriptomic responses to xylose versus cellobiose as the primary carbon source and assessed how the bacteria adapted to utilize xylose. Our analyses revealed 417 differentially expressed genes (DEGs) with log2 fold change (FC) > |1| and 106 highly DEGs (log2 FC > |2|). Among the DEGs, two putative sugar transporters, cbpC and cbpD, were up-regulated, suggesting their contribution to xylose transport and assimilation. Moreover, the up-regulation of specific transketolase genes (tktAB) suggests the importance of this enzyme for xylose metabolism. Results also showed remarkable up-regulation of chemotaxis and motility associated genes responding to xylose feeding, as well as widely varying gene expression in those encoding cellulosomal enzymes. For the down-regulated genes, several were categorized in gene ontology terms oxidation-reduction processes, ATP binding and ATPase activity, and integral components of the membrane. This study informs potentially critical, enabling mechanisms to realize the conceptually attractive Next-Generation Consolidated BioProcessing approach where a single species is sufficient for the co-fermentation of cellulose and hemicellulose.
KJC355 unevolved

overall_design: Here, we compared KJC335’s transcriptomic responses to xylose versus cellobiose as the primary carbon source and assessed how the bacteria adapted to utilize xylose. 3 biologically replicates were carried out for xylose and cellobiose growth, respectively.

middle: E

first: Andrés

last: González Barrios

first: Luis

middle: H

last: Reyes

first: Pin-Ching

last: Maness

first: Katherine

last: Chou


title: Transcriptome analysis of C. glutamicum ΔaceE Δpyc versus ΔaceE

status: Public on Jul 31 2019

city: Juelich

first: Tino

last: Polen

state: NRW

address: Wilhelm-Johnen-Str 1

department: IBG-1: Biotechnology

institute: Forschungszentrum Jülich GmbH

summary: The pyruvate dehydrogenase complex (PDHC) catalyzes the oxidative decarboxylation of pyruvate yielding acetyl-CoA and CO2. The PDHC-deficient Corynebacterium glutamicum strain ΔaceE is therefore lacking an important decarboxylation step in central metabolism. Additional inactivation of pyc, encoding pyruvate carboxylase, resulted in a >15 hour lag phase in the presence of glucose, while no growth defect was observed on gluconeogenetic substrates like acetate. Transcriptome analysis as well as an adaptive laboratory evolution experiment of strain ΔaceE Δpyc revealed the reduction of glucose uptake as a key adaptive measure to enhance growth on glucose/acetate mixtures.

platform_organism: Bacillus subtilis subsp. subtilis str. 168

overall_design: For analysis of the transcriptome, C. glutamicum ΔaceE and ΔaceE Δpyc were cultivated in triplicates in 50 ml CGXII containing 154 mM acetate and 222 mM glucose in shake flasks. After reaching exponential phase at an OD600 of around 12-15, the cell suspension was harvested by centrifugation (4256 g, 10 min, 4°C). The resulting pellet was directly frozen in liquid nitrogen and stored at -80°C. RNA preparation, cDNA synthesis as well as microchip hybridization, scanning and data analysis.

first: Aileen

last: Krüger

first: Julia

last: Frunzke


title: Next Generation Sequencing Facilitates Quantitative Analysis of Ventilator-Induced Lung Injury Animal Model and Control Lung Transcriptomes

status: Public on Sep 09 2019

last: Zhang

address: No 2, East Yinghua Road, Chaoyang District, Beijing,  China.

institute: Center for Respiratory Diseases, China-Japan Friendship Hospital, Beijing, China.

summary:
Purpose: Long non-coding RNAs (lncRNAs) have been implicated in the inflammatory response of many diseases; however, their roles in Ventilator-Induced Lung Injury remain unclear. We therefore performed transcriptome profiling of lncRNA and mRNA using RNA-sequencing in lungs collected from mice model of Ventilator-Induced Lung Injury and control groups.
Methods: Gene expression was analyzed through RNA sequencing and quantitative RT-PCR. A comprehensive bioinformatics analysis was used to characterize the expression profiles and relevant biological functions and for multiple comparisons among the controls and the injury models at different time points.
Results:The mRNA transcript profiling, co-expression network analysis, and functional analysis of altered lncRNAs indicated enrichment in the regulation of immune system/inflammation processes, response to stress, and inflammatory pathways.
Conclusions: In summary, our study identified aberrant lncRNA alterations regulated by high-stretch ventilation, and bioinformatics analysis was used to screen the key biological processes and pathways involved in inflammation upon VILI. lncRNA-mediated regulatory patterns might contribute to VILI inflammation.

overall_design: Lung mRNA and lncRNA  profiles of ventilator-Induced Lung Injury mice (time intervals 6 h and 0 h post mechanical ventilation) and control mice were generated by deep sequencing, in triplicate, using Illumina HiSeq 4000.

first: Nannan

first: Yi

first: Lu

last: Wang

first: Jingen

last: Xia

first: Shuntao

last: Liang

first: Zhizhi

first: Xu

last: Huang

first: Min

last: Li

first: Hui

last: Zeng

first: Qingyuan

last: Zhan


title: Next-generation RNA sequencing of FFPE subsections reveals highly conserved stromal reprogramming between canine and human mammary carcinoma

status: Public on Aug 01 2019

city: Zurich

first: Enni

last: Markkanen

address: Winterthurerstr. 260

department: Institute of Veterinary Pharmacology and Toxicology

country: Switzerland

institute: University of Zurich

summary: Cancer-associated stroma (CAS) and matched normal stroma (NS) samples from 15 cases of canine mammary carcinoma (mCA).

overall_design: Spontaneous tumours from patients, formalin-fixed and paraffin embedded. Isolation of stromal areas of interest by LCM, followed by RNA isolation and sequencing.

first: Parisa

last: Amini

first: Sina

last: Nassiri

last: Ettlin

first: Alexandra

last: Malbon


title: Single-cell RNA-seq of mouse embryos E4.5 to E7.5. First batch.

first: Felix

last: Krueger

overall_design:
758 single cells isolated from mouse embryos at E4.5, E5.5, E6.5 and E7.5 and processed using scNMT-seq (Clark et al 2018)

NOTE: The GSE133725 Series supplementary file, embryo_cell_counts_matrix_030719.tsv, contains total 2971 processe data columns for both GSE121650 (758 cells) and GSE133725 (2213 cells) samples.

first: Ricard

last: Argelaguet

first: Hisham

last: Mohammed

first: Stephen

last: Clark

first: L

last: Stapel

first: Christel

first: Chantriolnt-Andreas

last: Kapourani

first: Yunlong

last: Xiang

first: Courtney

last: Hanna

first: Sebastien

last: Smallwood

first: Ximena

last: Ibarra-Soria

first: Florian

last: Buettner

first: Guido

last: Sanguinetti

first: Wei

last: Xie

first: Peter

last: Rugg-Gunn

first: Gavin

last: Kelsey

first: Wendy

last: Dean

first: Jennifer

last: Nichols

first: Oliver

last: Stegle

first: John

last: Marioni

first: Wolf

last: Reik


title: Genome-wide CUT&RUN sequencing of H3K27me3 mark across different stages of T-cell development.

status: Public on Jul 24 2019

city: Seattle

first: Nicholas

last: Pease

state: WA

address: 3720 15th Ave NE

institute: University of Washington

summary: We present CUT&RUN sequencing of H3K27me3 for hematopoietic progenitor cells at the following differentiation stages:  1) cKit+ hematopoietic progenitor cells from bone marrow, 2) monoallelic Bcl11b expressing DN2 progenitors, which have one active and one inactive Bcl11b allele and 3) biallelic Bcl11b expressing DN2 progenitors, which have both Bcl11b alleles active

overall_design: Examination of H3K27me3 in hematopoietic progenitors that have no Bcl11b expression, monoallelic Bcl11b expression, and biallelic Bcl11b expression

first: Phuc

last: Nguyen

middle: A

first: Hao

middle: Y

last: Kueh


title: Comparison of Corynebacterium glutamicum ATCC13032ΔftsR with ATCC13032

status: Public on Jul 12 2019

first: Tino

last: Polen

summary: In summary, we have identified and characterized FtsR as a transcriptional activator of the essential cell division protein FtsZ in C. glutamicum, providing a novel regulatory player in the process of cell division.

overall_design:
To identify genes which are differentially expressed in Corynebacterium glutamicum ATCC13032ΔftsR in comparison to the parent wild type ATCC13032, DNA microarray analyses with these strains were performed. For this purpose RNA was isolated from cells cultivated in CGXII minimal medium with 2% glucose (w/v) and harvested in the exponential growth phase at an OD600 of 6. Three biological replicates were performed.
Please note that ΔftsR corresponds to Δcg1631

first: Kim

last: Kraxner

first: Meike

last: Baumgart

first: Michael

last: Bott


title: Transcriptome Analysis of Fat Deposition in Buffalo at Different Stages

status: Public on Aug 21 2019

city: Xinyang

first: Yun

last: Ma

address: Shihe

institute: Xinyang Normal University

type: Non-coding RNA profiling by high throughput sequencing

summary: Background: Background: In bovines, the development and growth of adipose involves many physiological processes and plays an extremely important role in the quality of beef, however, the regulatory mechanisms underlying the differences in meat quality are largely unknown. Therefore, a buffalo adipose transcriptome analysis was performed to compare gene expression profiles between different growth stages.  Results: Finally, a total of 21,693 mRNAs were obtained, of which 2506 were significantly differentially expressed mRNAs in the two groups, 9494 lncRNAs, a total of 281 lncRNAs and 2506 mRNAs showed significant differential expression patterns and 14990 between the two buffaloes CircRNA, 252 circRNAs were significantly differentially expressed between young and adult buffalo.

overall_design: Six adipose samples from Xinyang buffalo of two developmental states (6Month and 30Month old) were collected from Benniu abattoir, a local slaughterhouse of Xinayang, P.R. China.

first: Jieping

last: Huang


title: Deep Mutagenesis of a Transporter for Uptake of a Non-Native Substrate Identifies Conformationally Dynamic Regions

city: Urbana

first: Erik

last: Procko

address: 601 S Goodwin Ave

department: Biochemistry

institute: University of Illinois

summary: The serotonin transporter, SERT, catalyzes serotonin reuptake at the synapse to terminate neurotransmission via an alternating access mechanism, and SERT inhibitors are the most widely prescribed antidepressants. Here, deep mutagenesis is used to determine the effects of nearly all amino acid substitutions on human SERT surface expression and transport of the fluorescent substrate analogue APP+, identifying many mutations that enhance APP+ import. Comprehensive simulations of the entire ion-coupled import process reveal that while binding of the native substrate, serotonin, reduces free energy barriers between conformational states to promote SERT dynamics, the conformational free energy landscape in the presence of APP+ instead resembles Na+ bound-SERT, with a higher free energy barrier for isomerization to an inward-facing state. The deep mutational scan for SERT-catalyzed import of APP+ finds mutations that promote the necessary conformational changes that would otherwise be facilitated by the native substrate. Indeed, hundreds of gain-of-function mutations for APP+ import are found along the permeation pathway, most notably mutations that favor opening of a solvent-exposed intracellular vestibule. The mutagenesis data support the simulated mechanism in which the neurotransmitter and a symported sodium share a common cytosolic exit pathway to achieve coupling. Furthermore, the mutational landscape for SERT surface trafficking, which likely filters out misfolded sequences, reveals that residues along the permeation pathway are mutationally tolerant, providing plausible evolutionary pathways for changes in transporter properties while maintaining folded structure.

overall_design: Human SERT was encoded by a synthetic codon-optimized gene. The SERT sequence was diversified by overlap-extension PCR to generate two single-site saturation mutagenesis libraries spanning the full length of the gene. The libraries were expressed in human Expi293F cells (a HEK293 derivative) and sorted by FACS for ability to express on the cell surface and the ability to transport a fluorescent neurotransmitter analog, APP+. Enrichment ratios were calculated for all single amino acid substitutions by comparing the frequencies of sequence variants in the sorted cells (from RNA transcripts) with the naive libraries (plasmid DNA). Evolution experiments were duplicated.

first: Heather

last: Young

first: Steven

middle: K

last: Szymanski


title: Comparison of Corynebacterium glutamicum Δsurf1 and wt

status: Public on Jul 11 2019

summary: To identify genes which are differentially expressed in Corynebacterium glutamicum in the cg2460 deletion strain, we performed DNA microarray analyses of C. glutamicum Δcg2460 compared to the WT.

overall_design: RNA was isolated from cells cultivated in CGXII minimal medium with 2% glucose (w/v). The cells were harvested in the exponential growth phase at an OD600 of 5. Four biological replicates were performed.

first: Cedric

last: Davoudi


title: Transcriptional Profile of Glycyrrhiza uralensis Fisch Suspension Cell in Response to Methyl Jasmonate

city: Baotou

first: Yangming

last: Si

state: Inner Mongolia

address: Arding Street No.7

department: School of Life Science and Technology

institute: Inner Mongolia University of Science&Technology

summary: Licorice (Glycyrrhiza uralensis Fisch) flavonoids have many pharmacological effects, as the main chemical component of licorice, its content directly affects the quality of licorice. Methyl jasmine (MeJA) is an important signaling molecule in the secondary metabolic pathway of plants, but the biological mechanisms that stimulating the production of licorice flavonoids and the related changes in transcriptome are still less studied. In this research, the expression of two key enzyme genes: Chalcone synthase (CHS) and Cinnamate 4-hydroxylase (C4H) in the biosynthesis pathway of licorice flavonoids was determined, and it was significantly different after 9 hours of MeJA induction. The transcriptome profiles of licorice cells at 9 hours after MeJA treatment were analyzed to investigate the transcriptional alterations of licorice cell in response to MeJA elicitation by “RNA-seq”. 151, 529 transcripts (200 bp in length) of cDNA from the samples were generated, and 116, 907 unigenes were found. MeJA appeared to stimulate a large number of genes involved in several relevant functional categories, such as carbohydrate metabolism and encoding transcription factors, 11 MYB transcription factors expressed significant differences were screened. This comprehensive description of gene expression information could help elucidate the molecular mechanism of MeJA-mediated biosynthesis of licorice flavonoids and MeJA-regulated network formation.

overall_design: Examination of 3 different Glycyrrhiza uralensis Fisch cells induced by MeJA and 3  different Glycyrrhiza uralensis Fisch cells uninduced by MeJA

first: Yali

last: LI


title: Specificity of enhancer selection by IRF3, IRF5 and IRF9 in dendritic cells

city: Debrecen

first: Lajos

last: Széles

address: Egyetem tér 1.

country: Hungary

institute: University of Debrecen

summary: To discover the key determinants of IRF-specific enhancer selection, we identified and characterized IRF binding regions. Using chromatin immunoprecipitation coupled with deep sequencing (ChIP-seq), we mapped the binding regions of IRF3, IRF5, and IRF9 in murine dendritic cells (DCs) stimulated with TLR3 and TLR9 agonists, as well as IFNβ, respectively. We comprehensively analysed the IRF cistromes to identify characteristic features, including DNA motifs for IRFs and other transcription factors, and chromatin status.

overall_design: CD8-positive dendritic cells were left unstimulated or were treated with 5 μg/ml poly(I:C) HMW or 1 mM class B CpG oligonucleotide 1826 (CpG) or 10U IFN-beta for 90 min.

first: Mária

last: Csumita


title: Transcriptional profiling of the rat retina after optic nerve crush uncovers sustained activation of the complement cascade and Delta-Notch signaling pathways

status: Public on Jul 02 2019

city: Prairie View

first: Dumitru

middle: Andrei

last: Iacobas

address: Ann Preston St

department: Undergraduate Medical Academy

institute: Prairie View A&M University

summary: Glaucoma is a multifactorial neurodegenerative disease, characterized by degeneration of the neurons known as retinal ganglion cells (RGCs). Although distinct in vivo animal models have been used to investigate the mechanisms of both RGC degeneration and reorganization of the retina, there has been little progress in developing efficient strategies for neuroprotection in glaucoma. In the present study, we used transcriptomic profiles of Lister Hooded rats’ retinas 2 weeks after optic nerve crush (ONC) and applied systems biology approaches to better understand the molecular mechanisms by which ONC induced the remodeling of the retinal tissue. We calculated the relative expression variability scored as a statistical measure of the variability of transcript abundance in our datasets and found higher variability after ONC. Also, gene expression stability was used as a score of transcription control and we found a reduction in the number of very stably expressed genes from 336 to 124. Enrichment analysis showed that Complement cascade and Notch signaling pathway were the main affected pathways after ONC. In order to deepen our studies on these two pathways, we performed coordination analysis of genes within each pathway and with the entire transcriptome. ONC increased the number of synergistically coordinated pairs of genes and increased the number of similar profiles. This study goes beyond the regulation of individual gene expression showing striking changes in the control of expression by Complement cascade and Notch signaling functional pathways important for RGC degeneration and remodeling of the retinal tissue two weeks after ONC.

overall_design: One tissue (retina) x one sex (female) x two conditions (ONC = intraorbital optic nerve crush, CTR = control sham operated)

first: P

last: Victorino

first: C

last: Marra

first: D

first: S

last: Spray

first: R

last: Linden

last: Adesse

first: H

last: Petrs-Silva


title: Genome-wide profiling at single-nucleotide resolution of brain cell types in schizophrenia [WGBS]

status: Public on Jun 25 2019

city: Atlanta

first: Soojin

middle: V

last: Yi

state: GA

address: 950 Atlantic Dr

department: School of Biology

institute: Georgia Institute of Technology

summary: We carried out cell-type specific whole genome bisulfite sequencing from BA46 that underwent fluorescence-activated nuclei sorting (FANS).

overall_design: We sampled 61 unique individuals, 29 schizophrenia patients and 32 control, and isolated  NeuN+ and OLIG2+ cells from brain tissue (BA46). We generated 95 WGBS as well as whole-genome sequences of 54 individuals. This series contains only the WGBS data.


title: Genome-wide sequencing of schizophrenia and control individuals [WGS]

summary: We carried out whole genome sequencing of 29 schizophrenia patients and 25 control individuals


title: Gene expression analysis of ER+ and ER- breast cancer cell lines with acquired resistance to palbociclib

status: Public on Jun 20 2019

city: Louisville

first: Eric

middle: Christian

last: Rouchka

state: Kentucky

address: 522 East Gray Street

department: Biochemistry and Molecular Genetics

institute: University of Louisville

summary: While targeted therapies directed against cancer cells have proven effective, their clinical benefit is often limited by acquired resistance. This clinical challenge underscores the importance of uncovering the molecular mechanisms behind resistance in order to develop novel targets and drug combinations that can stop the growth of cancer cells. Two pivotal pathways controlling tumor growth are glucose metabolism and cell cycle. PFKFB3 and CDK4/6 are key regulators of glucose metabolism and cell cycle respectively for which inhibitors have been developed. PFK158 is an inhibitor against PFKFB3 that is currently undergoing phase I clinical trials and has shown to be effective at blocking glucose metabolism in solid tumors. Palbociclib, a novel CDK4/6 inhibitor was recently approved as a first-line approach for the treatment of estrogen receptor (ER) positive breast cancer because of the very promising clinical responses in ER+ breast cancer patients. Unfortunately, the effects of these therapies are short-lasting since cancer cells ultimately develop resistance allowing them to escape treatment. To identify the molecular mechanisms driving resistance to PFK158 or palbociclib, we have generated ER+ MCF7 and ER- MDA-MB231 cells resistant to either PFK158 or palbociclib by continuous exposure to increasing doses of drugs for a period of three months. Our hypothesis is that resistance is driven by activating mutations and/or pathways acquired during the course of treatment. This study is designed to identify specific mutations and/or changes in gene expression responsible for the resistance to PFK158 or palbociclib in ER+ and ER- in vitro. The results of this study will lead to the development of new therapeutic strategies to overcome resistance to PFKFB3 and CDK4/6 inhibitors.

overall_design: Two cell lines (MDA-MB231 and MCF7) with two treatments each: control (parental cell line and palbociclib resistant), with each condition consisting of three biological replicates

first: Yoannis

last: Imbert-Fernandez

first: Xiaohong

last: Li


title: Contribution of differential cell-specific methylation to schizophrenia [RNA-seq]

city: Dallas

first: Genevieve

last: Konopka

address: 5323 Harry Hines Blvd.

department: Neuroscience

institute: UT Southwestern Medical Center

summary: To address the heterogeneity of gene regulation and expression in cell types of a brain region with strong evidence for relevance to schizophrenia, we carried out whole genome methylation and expression analyses using post-mortem brain tissue from BA46 that underwent fluorescence-activated nuclei sorting (FANS). Importantly, we used whole genome bisulfite sequencing (WGBS) for methylation quantification to have an unbiased assessment of epigenetic modifications associated with schizophrenia, and additionally carried out whole genome sequencing (WGS) of the brain samples to account for genetic background differences. We found that a number of schizophrenia GWAS loci overlap with sites of cell-specific differential methylation in schizophrenia brain tissue. Differential methylation is also associated with differential gene expression in a cell-specific manner. Co-expression network analysis can identify groups of genes that are enriched for differentially methylated regions in each cell type, and these groups of co-expressed genes underscore shared molecular pathways that might be at risk in schizophrenia. Together, these data indicate that the integration of multiple levels of data in a cell-specific manner can provide novel biological insights into complex genetic disorders such as schizophrenia.

overall_design: We carried out RNA-sequencing (RNA-seq) of NeuN and OLIG2 positive nuclei from Brodmann area 46 of schizophrenia and matched controls of adult human neocortex.

first: Stefano

last: Berto

first: Noriyoshi

last: Usui

first: Kazuya

last: Toriumi

first: Connor

last: Douglas


title: Mapping cis-regulatory chromatin contacts in neural cells links neuropsychiatric disorder risk variants to target genes [CUT&RUN]

status: Public on Jun 15 2019

city: SAN FRANCISCO

first: Yin

last: Shen

state: CALIFORNIA

address: 513 Parnassus Ave

department: Department of Neurology

institute: UCSF

summary: Mutations in gene regulatory elements have been associated with a wide range of complex neuropsychiatric disorders. However, due to their cell-type specificity and difficulties in characterizing their regulatory targets, the ability to identify causal genetic variants has remained limited. To address these constraints, we perform an integrative analysis of chromatin interactions, open chromatin regions and transcriptomes using promoter capture Hi-C, assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-seq) and RNA sequencing, respectively, in four functionally distinct neural cell types: induced pluripotent stem cell (iPSC)-induced excitatory neurons and lower motor neurons, iPSC-derived hippocampal dentate gyrus-like neurons and primary astrocytes. We identify hundreds of thousands of long-range cis-interactions between promoters and distal promoter-interacting regions, enabling us to link regulatory elements to their target genes and reveal putative processes that are dysregulated in disease. Finally, we validate several promoter-interacting regions by using clustered regularly interspaced short palindromic repeats (CRISPR) techniques in human excitatory neurons, demonstrating that CDK5RAP3, STRAP and DRD2 are transcriptionally regulated by physically linked enhancers.

overall_design: H3K27ac and CTCF CUT&RUN on iPSC-induced excitatory neurons (1 replicates) and iPSC-induced lower motor neurons (2 replicates)

first: Michael

last: Song


title: ECM enriched in developing human spinal cord

status: Public on May 31 2019

city: St Lucia

first: Mohammed

middle: R

last: Shaker

state: QLD

address: Building 75,Cnr College Rd & Cooper Rd,, Brisbane

department: AIBN

country: Australia

institute: The University of Queensland

summary:
NSCs adhesion affinity along the AP axis is under the control of endogenous signalling molecular networks, the Wnt and RA signalling
The caudal spinal cord domain expresses a high amount of ECM genes compare to rostral.

overall_design: Examination of lumbar and cervical human tissues from Gestational age 18.

first: Woong

last: Sun


title: Mapping cis-regulatory chromatin contacts in neural cells links neuropsychiatric disorder risk variants to target genes

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

overall_design: Refer to individual Series


title: RNA-seq analysis of stimulated canine macrophage by Brucella canis

status: Public on Jul 18 2019

city: Seoul

first: Woo Bin

last: Park

address: Gwan-ak ro 1

country: South Korea

institute: Veterinary medicine, Seoul national university

summary: A lot of attempts have been made to understand the immunopathological mechanisms of Brucella canis infection because of the importance of the disease in both public and clinical aspects. However, previous mechanisms are not still revealed. Therefore, in vitro models, which mimic to in vivo infection route using a canine epithelial cell, D17 cell, and a canine macrophage, DH82 cell, was used to solve the clues by analysis of transcriptomes in the cells. In this study, a co-culture model was constructed using the two cells, D17 and DH82 cell lines with trans-well plate. Also, a single cell culture system using DH82 was established. After stimulation of the cells in two different systems with B. canis, gene expressions in the macrophages of the two different system were analyzed by RNA-sequencing.

overall_design: mRNA profiling of canine macrophage-like cell at 2 hours, 12 hours, and 24 hours after stimulation with Brucella canis

first: Woo-Bin

first: Han-Sang

last: Yoo


title: Acceleration of beta cell aging plays a key role in diabetes and senolysis improves metabolic, functional and cellular outcomes

status: Public on May 10 2019

city: Boston

first: Hui

last: Pan

address: 1 Joslin Place

department: Bioinformatics and Biostatistics Core

institute: Joslin Diabetes Center

summary: The risk of type 2 diabetes increases with age. Although changes in function and proliferation of aged beta cells resemble those preceding the development of diabetes, the contribution of beta cell aging and senescence remains unclear. The proportion of aged beta cells increases with animal age but even in young mice, senescent beta cells can be found. We showed that different models of insulin resistance accelerated aging and senescence marker expression in beta cells, BGal, led to loss of function and impaired glucose tolerance. Clearance of p16Ink4a+ cells, using the INK-ATTAC mouse model, ameliorated glucose metabolism, insulin secretion and decreased expression of aging, senescence and SASP genes in pancreatic islets. Senolytic drug ABT263 also improved glucose metabolism and beta cell identity when administered during insulin resistance. Human beta cells from diabetic and non-diabetic donors shared some of the same biology laying the foundation for translation into humans. These novel findings lay the framework to pursue senolysis of beta cells as a preventive and alleviating strategy for T2D.

overall_design: Cells from dispersed islets of 7 month old male C57BL/6J mice were FACS sorted based on acidic beta-galactosidase activity and RNA was extracted using PicoPure Arcturus kit. Gene expression profiling was performed using HiSeq v4 SE50 250 mil reads by Hudson Alpha Institute for Biotechnology (Huntsville, AL).  Reads were aligned to the mouse genome (GRCm38) using Subread and counted with featureCounts.

first: Cristina

last: Aguayo-Mazzucato

first: Susan

last: Bonner-Weir


title: Epigenetic and Transcriptional signatures of Systemic Lupus Erythematosus B cell subsets

status: Public on May 17 2019

first: Chris

last: Scharer

address: 1510 Clifton Rd, Suite 3086A

department: Microbiology and Immunology

institute: Emory University


title: The chromatic loci of H3.3K36M determine the preferential prevalence of K36M mutation at H3.3 in chondroblastomas

status: Public on May 09 2019

city: Hangzhou

first: Dong

last: Fang

state: Zhejiang

address: 866 Yuhangtang Road

department: Life Sciences Institute

institute: Zhejiang University

summary: The histone H3.3K36M mutation, identified in over 90% of chondroblastoma cases, reprograms the H3K36 methylation landscape and gene expression to promote tumorigenesis. However, it’s still unknown how the H3K36M mutation preferentially happens at the histone H3 variant H3.3. Here we report that, H3.3K36M mutation, but not H3.1K36M mutation, promoted increased colony formation and defects in differentiation. The reduction of H3K36 methylation and initiation of new H3K36 methylation sites in chromatin is dependent on the incorporation loci of H3.3K36M and H3.1K36M. Moreover, while both H3.3K36M and H3.1K36M mutation inactivated the enhancers, only H3.3K36M mutation changed the super enhancers associated with genes in general development, depending on the chromatic incorporation loci of H3.3K36M mutant proteins. Together, this study highlights the roles of the chromatic localization of H3.3K36M mutant proteins in the reprograming of epigenome and subsequent induction of tumorigenesis, and sheds light on the molecular mechanisms how H3K36M mutation mainly occurs at histone H3.3 in chondroblastomas.

overall_design: To directly compare the different reprogramming of H3.3K36M and H3.1K36M on the epigenome and gene expression in cells.

first: Yanjun

last: Zhang


title: Comparison of Corynebacterium glutamicum  ATCC 13032 + pEKEx2-malR with ATCC 13032 + pEKEx2

first: Tino

last: Polen

address: Wilhelm-Johnen-Str 1

institute: Forschungszentrum Jülich GmbH

summary: Investigation of the impact of an overexpression of malR (cg3315) on gene expression under standard conditions (CGXII-Glucose)

overall_design: To identify genes which are differentially expressed in Corynebacterium glutamicum ATCC13032 pEKEx2-malR in comparison to the empty vector control ATCC13032 pEKEx2 , DNA microarray analyses with these strains were performed. For this purpose RNA was isolated from cells cultivated in CGXII minimal medium with 2% glucose (w/v) and harvested after 4 hours of incubation. Three biological replicates were performed.

first: Max

last: Hünnefeld

first: Julia

last: Frunzke


title: Multi-dimensional transcriptome analysis of an intact hematopoietic organ for HSPC expansion [Bulk RNA-seq]

status: Public on Apr 23 2019

city: Shanghai

first: Denghui

last: Liu

state: Shanghai

address: ShengLi Building, 320 Yueyang Road

institute: CAS-MPG Partner Institute for Computational Biology (PICB)

summary: To characterize the distinct features of HSPCs and relevant niche cells, we performed RNA-seq with sorted zebrafish HSPCs and niche cells, based on fluorescent protein labeling from distinct regions at six relatively discrete stages.

overall_design: We used double transgenic line Tg (kdrl:mCherry/CD41:GFP) and sorted HSCs, ECs and NCs from embryonic tails at 36 hpf, 52 hpf, 3 dpf and 4 dpf. And we sorted HSPCs and NCs from CD41: GFP kidney marrow at 3 mpf.

first: Yuanyuan

last: Xue


title: Multi-dimensional transcriptome analysis of an intact hematopoietic organ for HSPC expansion [10x]

summary: To investigate the peculiarity of CHT HSPCs, as well as the interaction of CHT niche and HSPCs at higher resolution, we performed scRNA-seq with zebrafish CHT.

overall_design: The 52 hpf transgenic embryos were cut tails for dissecting into single cell suspension with PI staining. The 50 thousand kdrl:mCherry+ cells and 50 thousand CD41:GFP+ cells plus 50 thousands double negative cells were sorted by FACS for 10X genomics.


title: H2A.Z overexpression suppresses senescence and chemosensitivity in pancreatic ductal adenocarcinoma

status: Public on Apr 03 2019

city: Mexico

first: Rosaura

state: Cd. de Mexico

address: Av. Instituto Politécnico Nacional # 2508

department: Biomedicine

country: Mexico

institute: CINVESTAV

summary: Pancreatic ductal adenocarcinoma is one of the most intractable and devastating of all malignant tumors. Epigenetic modifications involving both DNA methylation and histone modification have a relationship between tumor initiation and progression. However, the contribution of histone variants in the PDAC is unknown. Here, we demonstrated that the histone variant H2A.Z is highly expressed in PDAC cell lines and PDAC patients and its overexpression correlated with poor prognosis. We found that the three-histone H2A.Z isoforms (H2A.Z.1, H2A.Z.2.1 and, H2A.Z.2.2), are highly expressed in PDAC cell lines and PDAC patients. Knockdown of three H2A.Z isoforms induces a senescent phenotype, cell cycle arrest in phase G2/M, increased cyclin-dependent kinase inhibitor CDKN2A/p16, SA-β-galactosidase activity and interleukin 8 production in PDAC. Transcriptome analysis of knockdown of the H2A.Z isoforms showed altered gene expression in the fatty acid biosynthesis. As well as in the genes that control the cell cycle and DNA damage repair. Furthermore, H2A.Z isoform deficiency, reduces the tumor size in a mouse xenograft model in vivo, and sensitizes PDAC cells to gemcitabine. These results make H2A.Z a potential candidate as a diagnostic biomarker and therapeutic target for PDAC

overall_design: mRNA profiles of PANC-1 pancreatic cancer cell line (WT) and PZT-2 (KD of three H2A.Z isoforms), using Illumina NextSeq 500

first: P

last: Ávila-López

first: R

last: Hernández-Rivas


title: Multi-dimensional transcriptome analysis of an intact hematopoietic organ for HSPC expansion


title: Expression alterations induced by restoration of AXIN1 expression in SNU449 hepatocellular carcinoma cells

status: Public on Jan 01 2019

city: Rotterdam

first: Ron

last: Smits

address: Wytemaweg 80

country: Netherlands

institute: Erasmus MC

summary: Aberrant activation of Wnt/β-catenin signaling is observed in numerous cancers. In hepatocellular carcinoma activating mutations in CTNNB1 (20-25%) or loss of function mutations in AXIN1 (10%), AXIN2 (2%) and APC (1-2%) are observed. All these mutations lead to aberrant stabilization of β-catenin, which constitutively activates downstream Wnt/β-catenin target genes and triggers a genetic program resulting in tumor formation. However, in relation to AXIN1 mutations some reports have challenged whether these indeed result in tumor growth by enhancing β-catenin signaling (e.g. PMID: 16964294, 29525529). Several alternative pathways have also been linked to AXIN1 (ENSG00000103126), such as TGFβ, SAPK/JNK, p53, YAP/TAZ and c-myc. To identify which one of these or other unknown signaling routes are linked to AXIN1, using CRISPR-Cas9 genome editing, we have successfully repaired the homozygous p.R712* AXIN1 mutation present in the SNU449 hepatocellular carcinoma cell line. Next, using RNA sequencing the RNA expression patterns of 3 independent repaired clones were compared with 3 clones retaining the AXIN1 mutation. Surprisingly, only 5 genes were significantly altered in the repaired clones, among which AXIN2, a well-established β-catenin target gene. Thus, this analysis leads to the surprising observation that a commonly observed mutation in a hepatocellular tumor suppressor gene, is associated with minimal alterations in gene expression, at least in the SNU449 cell line.

overall_design: Comparison of 3 independent repaired SNU449 clones with 3 clones retaining the AXIN1 mutation

first: Pengyu

middle: P

last: Lui

first: Wesley

middle: W

last: van de Geer

first: Harmen

last: van de Werken


title: Gene expression profiles in microglia with or without PGC-1α overexpression

status: Public on Jan 10 2019

city: Tianjin

first: Bin

last: Han

address: 154 Anshan Road, Heping District

institute: Tianjin Medical University General Hospital

summary: PGC-1α overexpression in microglia protects against ischemia-induced brain damage in mice. To investigate the underlying mechanism of PGC-1α, we have employed whole mRNA microarray expression profiling as a discovery platform to identify genes with the potential to change the microglial function. Indeed,  PGC-1α overexpression alters the gene expression profiles of microglia, this suggested that microglial PGC-1α might play an important role after ischemic stroke.

overall_design: Primary microglia were isolated from PGC-1αf/f and mPGC-1α mice using the MojoSortTM mouse P2RY12 selection kit (Biolegend, San Diego, CA, USA) according to the manufacturer’s protocol. Then the samples were processed to perform microarray analysis.

first: Junwei

last: Hao


title: Multi-omics profiling of mouse gastrulation at single cell resolution

status: Public on Sep 30 2019

city: Cambridge

first: Felix

last: Krueger

address: Granta Park

department: Bioinformatics

institute: Altos Labs

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

Useful links:
Parsed data: (ftp://ftp.ebi.ac.uk/pub/databases/scnmt_gastrulation)
Github repository: (https://github.com/rargelaguet/scnmt_gastrulation)


title: Long read sequencing of mouse nucleus accumbens in chronic cocaine treatment

status: Public on Apr 09 2019

city: New York

first: Li

last: Shen

state: NY

address: 1425 Madison Ave

institute: Icahn School of Medicine at Mount Sinai

summary: To better understand the transcriptome of Nucleus Accumbens (NAc) – a key brain reward region – under chronic cocaine treatment, we perform the first Iso-Seq analysis on its mRNAs to determine the full-length transcripts without assembly.

overall_design: Ten 8-10 week old male C57 mice were pooled to generate the RNA for sequencing. Five of the mice were given IP saline injections for 7 days, while the other 5 mice were given 20mg/kg cocaine via IP injection for 7 days. NAc were isolated one hour after the final injection and stored frozen at -80 until RNA extraction. RNA from individual mice was extracted using Qiagen RNeasy Mini kit and pooled prior to library preparation. NAc were isolated from each mouse bilaterally, so a total of 20 NAc punches were used for Iso-Seq long read sequencing.

first: Molly

last: Estill


title: TTseq on TX1072 during time course of DOX induction

city: Paris

first: Aurélie

last: Bousard

address: 26, rue d'Ulm

institute: Institut Curie

summary: During development, changes in gene transcription are accompanied by changes in chromatin modification but the order and causality of events often remain unclear. Here we address this question using X-chromosome inactivation (XCI), which entails chromosome-wide gene silencing and heterochromatin formation. We initiate XCI in female, mouse embryonic stem cells by inducing Xist expression and monitor subsequent changes in transcription and chromatin modification by allele-specific TTseq and ChIPseq respectively. An unprecedented temporal resolution has enabled us to define early alterations in chromatin that are induced upon Xist RNA coating. Xist-induced repression begins with histone deacetylation, which involves the histone deacetylase HDAC3 and occurs before efficient loss of H3K4me3 and H3K4me1 modifications. Polycomb-associated repressive histone marks accumulate rapidly, starting with PRC1-associated H2AK119Ub and followed by PRC2-associated H3K27me3. However, polycomb accumulates initially at large premarked domains, some of which correspond to Xist entry sites, and then spreads into genes. We also show that spreading can only ensue when transcriptional silencing has occurred. These results establish a detailed epigenomic time course for XCI and reveal a hierarchy of events with chromatin playing an important role in transcriptional silencing of the X chromosome.

overall_design: TTseq on TX1072 cell line. TTseq was done at 5 different times of DOX induction (0h, 4h, 8h, 12h, 24h) on TX1072, in replicates.

first: Jan

middle: J

last: Żylicz

first: Kristina

last: Žumer

first: Eusra

last: Mohammad

first: Simão

last: Teixeira da Rocha

first: Björn

last: Schwalb

first: Laurène

last: Syx

first: Patrick

last: Cramer

first: Edith

last: Heard


title: The role of early chromatin changes in X chromosome inactivation


title: Contribution of differential cell-specific methylation to schizophrenia

first: Soojin

last: Yi

address: 950 Atlantic Dr

institute: Georgia Institute of Technology


title: Age-dependent changes in transcription factor FOXO targeting in Drosophila melanogaster

status: Public on Apr 25 2019

city: Ames

first: Allison

last: Birnbaum

email: abirnba1@iastate.edu, abirnba1@uab.edu

state: AL

address: 3247 Pammel Dr

institute: Iowa State University

summary: FOXO transcription factors control numerous pathways involving metabolism, stress response, and longevity. Although direct targets of FOXO have been reported in various long-lived mutants and under stress conditions, no studies have investigated how normal aging impacts the cellular activity of FOXO. In this study, we compared genome wide dFOXO-bound sites in young and aged wild-type flies kept under normal feeding conditions to evaluate the dynamics of FOXO gene targeting during aging.  Our results provide a new insight into FOXO chromatin targeting under a normal aging model and highlight the diverse regulatory mechanisms for FOXO transcriptional activity that are currently less understood.

overall_design: ChIP DNA was prepared from 2-week and 5-week yw;+;+ flies. Two biological replicates were collected for each sample using dFOXO antibody. ChIP-seq libraries were prepared using the standard protocol with indexed adaptors and pooled for sequencing.

first: Hua

last: Bai


title: Non-steoridal Antiinflammtory Drugs' Chronotherapy May Enhance Early Bone Fracture Helaing in Mice

status: Public on Feb 16 2019

city: Montréal

first: Haider

last: Al-Waeli

state: QC

address: #500 2001 McGill College Avenue

department: Dentistry

country: Canada

institute: McGill University

summary: This experiemnt is to identify estimate the differences in genes expression after three days of adminsitration NSAID at different times of the day following bone fracture surgery in comparison to control group

overall_design: Comparison of two experiemntal groups to control group , one group receive NSAID during active phase of the day folowing tibia fracture surgery in mice, the second group received same treatment during resting phase and the control group did not receive any tretament or surgery. Surgery time for both experiemntal groups was performed at the same time of the day in for all mice.

first: F

last: Tamimi

first: B

last: Nicolau


title: Time course of gene expression of peritoneal macrophage from wild-type or LysM-St18flox mice after LPS stimulation

status: Public on Dec 31 2018

city: Tsukuba

first: Yutaro

last: Kumagai

state: Ibaraki

address: Central 5-41, Higashi 1-1-1

department: BRD

institute: AIST

summary: To assess the role of a transcription factor St18 in LPS response, peritoneal macrophage from wild-type or LysM-St18flox mice were stimulated with LPS and gene expressions were compared.

overall_design: Peritoneal macrophages were prepared from wild-type or LysM-St18flox mice and stimulated with LPS for 0 or 3 hours

first: Kenta

last: Maruyama


title: Comparison of target genes from the pregnane X receptor (Pxr) in the liver vs the intestine [colon]

status: Public on Dec 18 2018

city: Toulouse

first: Sandrine

last: Ellero-Simatos

address: 180 chemin de Tournefeuille

institute: INRAe

summary: We performed a transcriptomic comparison of the Pxr-regulated genes in the liver and intestine (ileum and colon) using microarrays in adult wild-type (WT) vs Pxr-/- C57Bl6/J male mice treated with the rodent specific Pxr ligand pregnenolone 16α-carbonitrile (PCN) (100 mg/kg i.p. once daily for 4 days).

overall_design: PCN-induced changes in gene expression was measured 6h after the last PCN treatment. 4 to 6 animals per group were used.

first: Claire

last: Naylies

first: Yannick

last: Lippi


title: Effects of vitamin D on CEBPA binding in THP-1 cells

city: Kuopio

first: Carsten

last: Carlberg

address: Yliopistonranta 1D

department: Institute of Biomedicine

country: Finland

institute: University of Eastern Finland

summary: Three independent repeats of ChIP-seq or ChIPmentation with THP-1 cells after treatment with either 1,25(OH)2D3 (VD) or control (EtOH) using antibody against CEBPA (3 time points).

overall_design: THP-1 cells were treated with vitamin D (1,25(OH)2D3) or solvent (EtOH) for 2h, 8h or 24h before performing ChIP-seq or ChIPmentation with antibody against CEBPA.

first: Sabine

last: Seuter

first: Antonio

last: Neme

first: Veijo

last: Nurminen


title: Effects of vitamin D on histone modification H3K4me3 in THP-1 cells

summary: Three independent repeats of ChIP-seq from THP-1 after 2h and 8h treatment with 1,25D or EtOH (control), using antibody against histone marker H3K4me3.

overall_design: THP-1 cells were treated with vitamin D or solvent (EtOH) for 2h and 8h before performing ChIP with antibodies against H3K4me3 (3 independent repeat experiments).


title: Comparison of target genes from the pregnane X receptor (Pxr) in the liver vs the intestine [ileum]

status: Public on Dec 14 2018


title: Effects of transcription factor CEBPA knockdown on vitamin D target gene regulation in THP-1 cells

summary: Three independent repeats of siRNA knockdown of CEBPA, followed by 24h vitamin D treatment, RNA extraction and RNA-seq.

overall_design: THP-1 cells were transfected for 24h with either negative control siRNA or siRNA against transcription factor gene CEBPA, followed by 24h treatment with vitamin D or solvent (EtOH) before performing RNA extraction and RNA-seq.


title: Comparison of target genes from the pregnane X receptor (Pxr) in the liver vs the intestine

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

overall_design: Refer to individual Series


title: Comparison of target genes from the pregnane X receptor (Pxr) in the liver vs the intestine [liver]


title: The pioneer factor CEBPA modulates vitamin D signaling


title: Nrf2 ChIP-seq data of Nrf2KO, wild-type and Keap1KO esophagus

status: Public on Nov 15 2018

city: Camden

first: Xiaoxin

middle: Luke

last: Chen

state: NJ

address: 403 Haddon Ave

institute: Coriell Institute for Medical Research

summary: To understand how hyperactive NRF2 causes the esophageal phenotype in mice.

overall_design: Nrf2 ChIP-seq of wild-type mice, Keap1KO mice and Nrf2KO mice.

first: Zhaohui

last: Xiong


title: Multi-dimensional transcriptome analysis of an intact hematopoietic organ for HSPC expansion [RNA-seq]

first: Denghui

last: Liu

summary: To decode the complexed mechanism controlling HSC expansion, from the viewpoint of systems biology, we performed spatial transcriptome analysis by dissecting the whole hematopoietic organ, CHT.

overall_design: All the reagents and instruments used in this experiment are RNase-free. The fresh 52 hpf zebrafish tail was embedded in OCT with vertical position and rapid frozen in liquid nitrogen. The cryosection was stained with cresyl violet before laser microdissection. Each sample of sections was acquired using specific LCM platforms. The tail region of 52 hpf zebrafish embryo was cut for cryo-section and six sets of samples (including neuro (N), left muscle (L), right muscle (R), caudal artery (CA), caudal vein (CV) and caudal vein plexus (CVP)) were harvested from each section by Laser Capture Microdissection (LCM).

first: Yuanyuan

last: Xue


title: Heterogeneity of Androgen Receptor Splice Variant-7 (AR-V7) Protein Expression and Response to Therapy in Castration Resistant Prostate Cancer (CRPC)

status: Public on Oct 19 2018

city: Seattle

first: Ilsa

last: Coleman

address: 1100 Fairview Ave N, E2-112

department: Human Biology

institute: Fred Hutchinson Cancer Center

summary: Liquid biopsies have demonstrated that the constitutively active androgen receptor splice variant-7 (AR-V7) associates with reduced response and overall survival (OS) from endocrine therapies in castration resistant prostate cancer (CRPC). However, these studies provide little information pertaining to AR-V7 biology and expression in prostate cancer (PC) tissue. Following generation and validation of a novel AR-V7 antibody for immunohistochemistry (IHC); nuclear AR-V7 protein expression was determined for 358 primary prostate samples (358 patients) and 293 metastatic biopsies (194 patients). Associations with disease progression, nuclear AR full length (AR-FL) expression, response to abiraterone and/or enzalutamide, and gene signatures (from three independent cohorts) was determined.

overall_design: RNA sequencing of metastases from individuals with castration resistant prostate cancer (CRPC) using Illumina HiSeq 2500.

first: Adam

last: Sharp

first: Wei

last: Yuan

first: Cynthia

last: Sprenger

first: David

last: Dolling

first: Daniel

middle: N

last: Rodrigues

first: Joshua

last: Russo

first: Ines

last: Figueiredo

first: Claudia

last: Bertan

first: George

last: Seed

first: Ruth

last: Riisnaes

first: Takuma

last: Uo

first: Antje

last: Neeb

first: Jonathan

last: Welti

first: Colm

last: Morrisey

first: Suzanne

last: Carreira

first: Jun

last: Luo

first: Peter

middle: S

last: Nelson

first: Steven

last: Balk

first: Lawrence

middle: D

last: True

first: Johann

last: de Bono

first: Stephen

last: Plymate


title: Transcriptional analysis of locally advanced rectal cancer pre-therapeutic biopsies and post-therapeutic resections

status: Public on Nov 01 2018

city: Belfast

first: Matthew

last: Alderdice

address: 97 Lisburn Road

department: Centre for Cancer Research and Cell Biology

institute: Queen's University Belfast

summary: Understanding transcriptional changes in locally advanced rectal cancer which are therapy-related and dependent upon tumour regression will drive stratified medicine in the rectal cancer paradigm

overall_design: Total RNA was obtained from 40 matched formalin fixed paraffin embedded (FFPE) LARC biopsy and resections specimens provided by the Northern Ireland Biobank and arrayed using the Illumina HumanHT-12 WG-DASL V4 expression beadchip

first: Manuel

last: Salto-Tellez


title: Comparison of Corynebacterium glutamicum Δcg2699 with WT

status: Public on Aug 28 2018

city: Juelich

first: Tino

last: Polen

address: Wilhelm-Johnen-Str 1

department: IBG-1: Biotechnology

institute: Forschungszentrum Jülich GmbH

summary: To identify genes which are differentially expressed in Corynebacterium glutamicum in the cg2699 deletion strain, we performed DNA microarray analyses of C. glutamicum Δcg2699 compared to the WT.

overall_design: RNA was isolated from cells cultivated in CGXII minimal medium with 2% glucose (w/v). The cells were harvested in the stationary growth phase at an OD600 of 20. Three biological replicates were performed.

first: Xenia

last: Morosow

first: Tina

last: Mack


title: Transcript analysis of CD45+Ter119+CD71+ erythroid-like progenitor cells from tumor-bearing mice

status: Public on Oct 29 2018

city: Chongqing

first: Qingzhu

last: Jia

address: Xinqiao

department: Department of Onoclogy

institute: XinQiao Hospital

summary: We report the application of RNA sequencing technology for high-throughput profiling of transcriptome in mammalian cells. By this method, we report that the CD45+ EPC transcriptome resembled that of MDSCs. Mechanistically, like MDSCs, production of reactive oxygen species is a major mechanism for EPC-mediated immunosuppression.

overall_design: Examination of CD45+Ter119+CD71+ suppressive immune cell types in comparison to 3 cell types, 3 pathological/physiological status.

first: Lintao

last: Zhao

first: Haixia

last: Long

first: Ran

last: He

first: Lilin

last: Ye

first: Qi-Jing

last: Li

first: Bo

last: Zhu


title: Biomarkers for Early Stages of Johne’s Disease Infection and Immunization in Goats

status: Public on Jul 28 2018

city: Madison

first: CHIA-WEI

last: WU

state: WI

address: 1656 Linden Dr

department: Pathobiological Sciences

institute: University of Wisconsin-Madison

summary:
Background:  Mycobacterium avium subsp. paratuberculosis (M. paratuberculosis) is the causative agent of Johne’s disease, a chronic enteric infection of ruminants.  Infection occurs within the first few months of life but remains subclinical for an average of 2-5 years.  Current diagnostics to detect early subclinical infections lack diagnostic sensitivity, which hinders disease control resulting in significant economic losses to the dairy industry worldwide.  The pathophysiology of early infection with M. paratuberculosis is still not well understood and represents a key hurdle towards the development of better diagnostics.
Methods:  The present study employed a large-scale RNA-Sequencing technology to better understand early stages of M. paratuberculosis infection and immunization.  Specifically, gene expression profiles of peripheral blood mononuclear cells (PBMCs) from infected and vaccinated goats were compared to controls.
Results:  The transcriptome of the control goats revealed a large number of genes (N = 226, 1018, 1714, 1133) that were differentially expressed compared to the M. paratuberculosis-infected goats, goats vaccinated with live attenuated or inactivated vaccines, and goats both vaccinated and infected.  Bioinformatics evaluation of the differentially expressed genes indicated the regulation of a large number of genes with immunity and inflammatory functions including IL-18BP, IFN-γ, IL-17A, NOS2, LIPG and IL-22.  Interestingly, a large number of goat genes (N=667) were regulated whether live or inactivated vaccine were used.  Some of the regulated genes (e.g. IL-17A, IFN-g) continued its unique transcriptional profile up to 12 months post-challenge.
Conclusions:  Overall, transcriptome analysis of infected and/or immunized goats identified potential targets for developing early diagnostics for Johne’s disease and a potential approach to differentiate infected from vaccinated animals.  A similar approach could be used to analyze later stages of Johne’s disease or other chronic infections.

overall_design: One-month post-infection trancriptomic analysis (Illumina HiSeq 2000) of goat PBMC from goats that were vaccinated 60 days before experimental infection with Mycobacterium avium subsp. Paratuberculosis. Three to four animals were included in each group.

first: Aubrey

last: Berry

first: Chia-wei

last: Wu

first: Adel

middle: M

last: Talaat


title: Gene expresison studies of lupus and healthy B cell subsets through RNA sequencing

status: Public on Sep 01 2018

city: Atlanta

first: Scott

last: Jenks

state: Georgia

address: 615 Michael St, Whitehead Research Building Rm 255

department: Department of Medicine

institute: Emory University

summary: Dramatic expansions of class switched B cells lacking IgD and CD27 (double negative; DN), are characteristic of Systemic Lupus Erythematous (SLE).  However, their origin, clinical and immunological significance and their relationship to CD27+ memory B cells remain unclear. We demonstrate that SLE DN expansions are dominated by a CXCR5- CD21- subset with a pre-plasma cell phenotype and distinctive transcriptional, and functional properties.  SLE patients with an expansion of CXCR5- DN are predominantly African-American with higher disease activity and anti-Smith/RNP autoantibodies.  CXCR5- DN cells display a distinct transcriptome characterized by differential expression of cytokine receptors, transcription factors, and signaling molecules. DN express high levels of the key INFg effector factor, T-bet  and associated transcription factor Zeb2 and uniquely among B cell subsets, do not express TRAF5, a negative regulator of TLR signaling.   Consistent with this pattern gene expression SLE DN have enhanced responsiveness to TLR7 and can differentiate into autoantibody secreting plasma cells

overall_design: Based on the expression of IgD, CD27, and CXCR5, 4 different B cell subsets were isolated from 3 healthy control donors and 3 SLE patients,  gene expression was compared both between SLE and HCD B cells within each subset and between B cell subsets.

first: Ignacio

last: Sanz

first: Urko

last: Marigorta


title: Comparison of Corynebacterium glutamicum cultivated under copper starvation with copper sufficiency

first: Tino

last: Polen

state: NRW

summary: To identify genes which are differentially expressed in Corynebacterium glutamicum in the absence of copper, we performed DNA microarray analyses of cells cultivated under copper starvation conditions compared to copper sufficiency.

overall_design: RNA was isolated from cells cultivated in CGXII minimal medium with 2% glucose (w/v) with and without the addition of 150 µM BCS and 1 mM ascorbic acid. The cells were harvested in the stationary growth phase at an OD600 of 20. Four biological replicates were performed.

last: Morosov


title: Characterisation of COMPASS activity in ageing yeast

status: Public on Sep 27 2018

first: Felix

last: Krueger

summary: Here we analyse steady mRNA levels in wild type and COMPASS mutants across an ageing timecourse, along with H3K4me3 distribution in ageing wild type

overall_design: Histone (H3) and histone modification (H3K4me3) from Mother Enrichment project (MEP) cells aged for 0, 24 or 48 hours in YPD, and transcriptome (mRNA-Seq) from wildtype, swd1, set1-H1017L, spp1 MEP cells aged for 0, 7.5, 24 or 48 hours in YPD

first: Cristina

last: Cruz

first: Monica

last: Della Rosa

first: Qian

last: Gao

first: Jonathan

last: Houseley


title: Characterisation of COMPASS activity in ageing yeast (no spike-in ChIP-seq experiments)

summary: Here we analyse H3K4me3 distribution in wild type yeast across an ageing timecourse.

overall_design: Histone (H3) and histone modification (H3K4me3) from Mother Enrichment project (MEP) cells aged for 0, 7.5, 24 or 48 hours in YPD. Similar to ChIP-seq data deposited in GSE107744, except no Drosophila spike-ins were included for these samples.


title: The miRNAs and their targets in cucumber shoot apexes in response to temperature and photoperiod environments

status: Public on Jul 31 2018

city: Beijing

first: Xiaohui

last: Zhang

address: Zhong-Guan-Cun South Street 12

institute: Institute of Vegetables and Flowers, Chinese Academy of Agricultural Science

summary: The cucumber is one of the most important vegetables worldwide and is used as a research model for study of phloem transport, sex determination and temperature-photoperiod physiology. The shoot apex is the most important plant tissue in which the cell fate and organ meristems have been determined. In this study, a series of whole-genome small RNA, degradome and transcriptome analyses were performed on cucumber shoot apical tissues treated with high vs. low temperature and a long vs. short photoperiod.

overall_design: small RNAs and mRNAs were pyrosequenced from the shoot apical tissues of cucumber plants grown in four differential temperature-photoperiod treatments (16 h light at 28 °C /8 h dark at 25 °C, HL; 8 h light at 28 °C /16 h dark at 25 °C, HS; 16 h light at 20 °C /8 h dark at 15 °C, LL; 8 h light at 20 °C /16 h dark at 15 °C, LS). The 16 h/8 h and 8-h/16 h of light/dark photoperiods simulated long- and short-day seasons.Three replicates were perfermed on each treatment.

first: Yunsong

last: Lai

first: Wei

first: Xixiang


title: Alkylation-induced gene expression changes in Aag knock-out liver

status: Public on Jun 04 2018

city: Guildford

first: Lisiane

middle: Borges

last: Meira

state: Surrey

address: University of Surrey

department: Clinical and Experimental Medicine

institute: University of Surrey

summary:
We catalogued and quantified the transcripts in livers of wild-type and Aag-deficient mice that had been exposed to the model alkylating agent methyl methanesulfonate (MMS).
Gene expression analysis was performed for samples harvested 6 hours post-MMS treatment.

overall_design: Wild-type and Aag knock-out mice were treated with MMS and livers extracted 6 hours post-treatment.

first: Axel

last: Nohturfft

first: Leona

last: Samson

first: Katherine

last: Pease

first: Jennifer

last: Calvo

first: Rebecca

last: Fry

first: Fugen

last: Li

first: Stuart

last: Levine


title: Effects of vitamin D on histone modifications H3K27ac and H3K4me3 in THP-1 cells

status: Public on Jul 01 2018

first: Carsten

last: Carlberg

summary: Three independent repeats of ChIP-seq from THP-1 after 24h treatment with 1,25D or EtOH (control), using antibodies against histone markers H3K27ac and H3K4me3

overall_design: THP-1 cells were treated with vitamin D or solvent (EtOH) for 24h before performing ChIP with antibodies against H3K27ac and H3K4me3 (3 repeat experiments with each antibody)

first: Veijo

last: Nurminen

first: Sabine

last: Seuter

first: Antonio

last: Neme


title: Pseudotime Ordering of Single Human Beta-Cells Reveals States of Insulin Production and Unfolded Protein Response

status: Public on Jul 11 2018

city: Tarrytown

first: Yurong

last: Xin

address: 777 Old Saw Mill River Road

institute: Regeneron Pharmaceuticals, Inc.

summary: We report the pseudotime ordering of single non-diabetic human beta-cells detected by large-scale RNA sequencing. We identified major states with 1) low UPR and low insulin gene expression, 2) low UPR and high insulin gene expression or 3) high UPR and low insulin gene expression. The latter state was enriched for proliferating cells. Stressed human beta-cells do not dedifferentiate and show little propensity for apoptosis. These data suggest that human beta-cells transition between states with high rates of biosynthesis to fulfill the body’s insulin requirements to maintain normal blood glucose levels and UPR-mediated recovery from ER stress due to high insulin production.

overall_design: Single-cell RNA sequencing of human pancreatic islets

first: Giselle

last: Dominguez Gutierrez

first: Jesper

last: Gromada


title: 100mM ethanol vs. control for 72hr for human esophageal squamous epithelial cells (KYSE510)

status: Public on Mar 15 2018

first: Xiaoxin

last: Chen

summary: Study the influence of ethanol for human esophageal squamous epithelial cells.

overall_design: 100mM ethanol vs. control for 72hr.

first: Zhaohui

last: Xiong

middle: L


title: Bidirectional regulation of adenosine-to-inosine (A-to-I) RNA editing by DEAH box helicase 9 (DHX9) in cancer

status: Public on May 31 2018

city: Singapore

first: Polly Leilei

address: #12-01, MD6, 14 Medical Drive

department: Department of Anatomy

institute: Cancer Science Institute of Singapore NUS

summary: Adenosine-to-inosine (A-to-I) RNA editing entails the enzymatic deamination of adenosines to inosines by adenosine deaminases acting on RNA (ADARs). Dysregulated A-to-I editing has been implicated in various diseases, including cancers. However, the precise factors governing the A-to-I editing and their physiopathological implications remain as a long-standing question. Herein, we unravel that DEAH box helicase 9 (DHX9), at least partially dependent of its helicase activity, functions as a bidirectional regulator of A-to-I editing in cancer cells. Intriguingly, the ADAR substrate specificity determines the opposing effects of DHX9 on editing as DHX9 silencing preferentially represses editing of ADAR1-specific substrates, whereas augments ADAR2-specific substrate editing. Analysis of 11 cancer types from The Cancer Genome Atlas (TCGA) reveals a striking overexpression of DHX9 in tumors. Further, tumorigenicity studies demonstrate a helicase-dependent oncogenic role of DHX9 in cancer development. In sum, DHX9 constitutes a bidirectional regulatory mode in A-to-I editing, which is in part responsible for the dysregulated editome profile in cancer.

overall_design: We constructed strand-specific cDNA libraries of 3 total RNA samples and sequenced the libraries using Illumina Hiseq 4000 platform achieving over 200 millions of mappable reads per sample. Then we examined adenosine-to-inosine (A-to-I) editing sites in EC109 cells after DHX9 depletion.

first: Leilei

first: Huiqi

last: Hong

first: Omer

last: An