title: Principles of Meiotic Chromosome Assembly

first: Geoffrey

last: Fudenberg

address: 1650 Owens

department: Data Science and Biotechnology

institute: Gladstone Institutes

summary: During meiotic prophase, chromosomes organise into a series of chromatin loops emanating from   a proteinaceous axis, but the mechanisms of assembly remain unclear. Here we elucidate how   this elaborate three-dimensional chromosome organisation is underpinned by genomic sequence in Saccharomyces cerevisiae. Entering meiosis, strong cohesin-dependent grid-like Hi-C   interaction patterns emerge, reminiscent of mammalian interphase organisation, but with distinct regulation. Meiotic patterns agree with simulations of loop extrusion limited by barriers, yet are   patterned by convergent transcription rather than binding of the mammalian interphase factor,   CTCF, which is absent in S. cerevisiae—thereby both challenging and extending current paradigms of local chromosome organisation. While grid-like interactions emerge independently   of meiotic chromosome synapsis, synapsis itself generates additional compaction that matures differentially according to telomere proximity and chromosome size. Collectively, our results   elucidate fundamental principles of chromosome assembly and demonstrate the essential role of cohesin within this evolutionarily conserved process.

overall_design: This submission contains the following Hi-C experiments: meiotic timecourse samples of wt (0h, 2h, 3h, 4h, 5h, 6h, 8h) main figure; meiotic timecourse samples of wt (2h, 3h, 4h, 6h) supplementary figure; 2 biological replicates of the following genotypes grown for 8h in sporulation media, accumulating in pachytene: ndt80-d; rec8-d ndt80-d; zip1-d ndt80-d; 1 replicate of hop1-d ndt80-d. 2 biological replicates of wt diploid cells grown exponentially and arrested in G2/M by addition of the spindel poison nocodazole.

first: Stephanie

last: Schalbetter

first: Jonathan

last: Baxter

first: Katherine

last: Pollard

first: Matthew

last: Neale


title: Hypoxic transcriptomic signature of A549 cells (Agilent microarrays)

status: Public on Sep 04 2019

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

country: France

institute: IPMC/CNRS

summary: To assess the transcriptomic response of the LUAD cell line A549 to hypoxia, cells were exposed to 1% (Hx) or 21% O2 (Nx) during 24 hours. Two independent experiments were carried out.

overall_design: 4 samples in duplicates: Nx versus Hx

first: R

last: Rezzonico

first: N

last: Nottet

first: B

last: Mari

first: P

last: Barbry

first: K


title: Planarians recruit piRNAs for mRNA turnover in adult stem cells

city: Bayreuth

first: Claus

last: Kuhn

address: Universitätsstr. 30

department: BIOmac Research Center, NW I

country: Germany

institute: University of Bayreuth

type: Expression profiling by high throughput sequencing

type: Non-coding RNA profiling by high throughput sequencing

type: Genome binding/occupancy profiling by high throughput sequencing

summary: PIWI proteins utilize small RNAs called piRNAs to silence transposable elements, thereby protecting germline integrity. In planarian flatworms, PIWI proteins are essential for regeneration, which requires adult stem cells termed neoblasts. Here, we characterize planarian piRNAs and examine the roles of PIWI proteins in neoblast biology. We find that the planarian PIWI proteins SMEDWI-2 and SMEDWI-3 cooperate to degrade active transposons via the ping-pong cycle. Unexpectedly, we discover that SMEDWI-3 plays an additional role in planarian mRNA surveillance. While SMEDWI-3 degrades numerous neoblast mRNAs in a homotypic ping-pong cycle, it is also guided to another subset of neoblast mRNAs by antisense piRNAs and binds these without degrading them. Mechanistically, the distinct activities of SMEDWI-3 are primarily dictated by the degree of complementarity between target mRNAs and antisense piRNAs. Planarian PIWI proteins thus act as both nucleases and RNA-binding proteins, enabling planarians to repurpose piRNAs for critical roles in neoblast mRNA turnover.

overall_design:
RNA-Seq, small RNA-Seq and Degradome-Seq libraries were prepared in triplicates. CLASH-Seq and HITS-CLIP have in total 9 replicates of separately prepared and sequenced libraries from up and down CLIP signal band. RNAi knockdown of smedwi-2 and smedwi-3 were carried out by feeding worms with dsRNA. As a control planarians were fed with dsRNA of unc-22 (C. elegans). For SHAPE-map total RNA was treated with 20 mM of 1M7 in DMSO or neat DMSO (as a negative contol). CHIP-Seq libraries were prepared in duplicates. Each replicate of CHIP-Seq libraries was sequenced on four lanes (four FASTQ files per sample).

Please note that the CLASH_and_CLIP_counts.txt.gz contains 9  (weighted counts from merged and jointly processed) data columns generated from the following sample raw data as described below:
hitsclip1 - GSM3704066 and GSM3704067
hitsclip2 - GSM3460485 and GSM3460488
hitsclip3 - GSM3460486 and GSM3460489
clash 1-6 - GSM3704054 to GSM3704065

first: Iana

middle: V

last: Kim

first: Elizabeth

middle: M

last: Duncan

first: Eric

last: Ross

first: Vladyslava

last: Gorbovytska

middle: H

last: Nowotarski

first: Sarah

middle: A

last: Elliott

first: Alejandro

middle: S

last: Alvarado

middle: D


title: Impact of NLUCAT1 deletion on A549 cells in normoxic and hypoxic conditions

summary: Three independent parental or NLUCAT1 CRISPR/Cas9-deleted A549 clones were cultured in normoxia (Nx) or exposed to hypoxia (Hx) at 1% O2 for 24 hours.

overall_design: Experiments were performed in a one color design, corresponding to 4 conditions performed in triplicates (WT A549 Nx, n = 3 clones; WT A549 Hx, n = 3 clones; DEL A549 Nx, n = 3 clones, DEL A549 Hx, n = 3 clones) for a total of 12 samples.


title: Transcriptome profiling of 57 LUAD samples and 11 peritumoral normal lung tissues

summary: RNA was extracted from 57 LUAD patients hospitalized from 2004 to 2010 at the Pasteur Hospital (Departments of Pulmonary Medicine, and Thoracic Surgery, CHU de Nice, France) and 11 normal lung tissue specimens taken from areas at standard distance (3 cm) from the same cohort of patients.The diagnosis of LUAD patients was based on examination of all tumor specimens using the 7th pTNM classification and on the last histological classification of NSCLC. Written informed consent was obtained from participants after explaining the nature of the study, which was approved by the research ethics board of the Nice University hospital and was performed according to the guidelines of the Declaration of Helsinki. The main clinical and pathological data are summarized.  Enrollment of patients in our study was conditioned by stringent criteria such as obtained signed consent, availability of resected surgical specimens, good quality RNA and time of follow-up for surviving patients (min 40 months for surviving patients).

overall_design: 68 independent samples: 57 LUAD (T) and 11 Healthy lungs (N).

last: Pottier


title: Distinct imprinting signatures and biased differentiation of human androgenetic and parthenogenetic embryonic stem cells [RNA-Seq I]

status: Public on Sep 05 2019

city: Jerusalem

first: Ido

last: Sagi

address: Givat Ram

department: Genetics

country: Israel

institute: The Hebrew University of Jerusalem

summary: Genomic imprinting is an epigenetic mechanism that results in parent-of-origin monoallelic expression of specific genes, which precludes uniparental development and underlies various diseases. Here, we explored molecular and developmental aspects of imprinting in humans by generating exclusively paternal human androgenetic embryonic stem cells (aESCs) and comparing them with exclusively maternal parthenogenetic ESCs (pESCs) and bi-parental ESCs, establishing a pluripotent cell system of distinct parental backgrounds. Analyzing the transcriptomes and methylomes of human aESCs, pESCs, and bi-parental ESCs enabled the characterization of regulatory relations at known imprinted regions and uncovered imprinted gene candidates within and outside known imprinted regions. Investigating the consequences of uniparental differentiation, we showed the known paternal-genome preference for placental contribution, revealed a similar bias toward liver differentiation, and implicated the involvement of the imprinted gene IGF2 in this process. Our results demonstrate the utility of parent-specific human ESCs for dissecting the role of imprinting in human development and disease.

overall_design: RNA sequencing analysis was performed on undifferentiated human pESC line pES6 and bi-parental ESC line NYSCF2.

first: Nissim

last: Benvenisty

first: Dieter

last: Egli


title: Synaptic dysfunction in human neurons with Autism associated deletions in PTCHD1-AS

status: Public on Sep 03 2019

city: Toronto

first: Stephen

middle: W

last: Scherer

state: Ontario

address: 686 Bay Street

department: Genetics and Genomic Biology

country: Canada

institute: The Hospital for Sick Children

summary: The Xp22.11 locus that encompasses PTCHD1, DDX53, and the long noncoding RNA (lncRNA) PTCHD1-AS is frequently disrupted in males with autism spectrum disorder (ASD), but the functional consequences of these genetic risk factors for ASD are unknown. : iPSC-derived neurons from the ASD subjects exhibited reduced miniature excitatory post-synaptic current (mEPSC) frequency and NMDA receptor hypofunction. We found that 35 ASD-associated deletions mapping to the PTCHD1 locus disrupt exons of PTCHD1-AS. We also report a novel ASD-associated deletion of PTCHD1-AS exon 3, and we show exon 3 loss alters PTCHD1-AS splicing without affecting expression of the neighboring PTCHD1 coding gene. Finally, targeted disruption of PTCHD1-AS exon 3 recapitulated diminished mEPSC frequency, supporting a role for the lncRNA in the etiology of ASD. Our genetic findings provide strong evidence that PTCHD1-AS deletions are risk factors for ASD, and human iPSC-derived neurons implicate these deletions in the neurophysiology of excitatory synapses and in ASD-associated synaptic impairment.

overall_design: To evaluate the functional consequences of PTCHD1 locus deletions, we generated induced pluripotent stem cells (iPSCs) from unaffected controls and two ASD subjects with microdeletions affecting PTCHD1-AS/PTCHD1or PTCHD1-AS/DDX53. Function of iPSC-derived cortical neurons was assessed using molecular approaches and electrophysiology. We also compiled novel and known genetic variants of the PTCHD1 locus to explore the roles of PTCHD1 and PTCHD1-AS in genetic risk for ASD and other neurodevelopmental disorders. Finally, genome editing was used to explore the functional consequences of deleting a single conserved exon of PTCHD1-AS.

first: Muhammad

last: Faheem


title: Immediate and deferred epigenomic signatures of in vivo neuronal activation in mouse hippocampus

city: Sant Joan d'Alacant

first: Angel

last: Barco

state: Alicante

address: Av. Santiago Ramón y Cajal

country: Spain

institute: Instituto de Neurociencias (UMH-CSIC)

summary: Activity-driven transcription plays an important role in many brain processes, including those underlying memory and epilepsy. Here, we combine genetic tagging of nuclei and ribosomes with RNA-seq, ChIP-seq, ATAC-seq and Hi-C to investigate transcriptional and chromatin changes occurring in mouse hippocampal excitatory neurons at different timepoints after synchronous activation during seizure and sparse activation by novel context exploration. The transcriptional burst is associated with an increase in chromatin accessibility of activity-regulated genes and enhancers, de novo binding of activity-regulated transcription factors, augmented promoter-enhancer interactions, and the formation of gene loops that bring together the TSS and TTS of induced genes and may sustain the fast re-loading of RNAPII complexes. Some chromatin occupancy changes and interactions, particularly those driven by AP1, remain long after neuronal activation and could underlie the changes in neuronal responsiveness and circuit connectivity observed in these neuroplasticity paradigms, perhaps thereby contributing to metaplasticity in the adult brain.

overall_design: nuRNA-seq, riboRNA-seq, ATAC-seq, ChIP-seq and HiC in mouse adult hippocampal excitatory neurons

first: Jordi

last: Fernandez-Albert

first: Maria

middle: T

last: López-Cascales

middle: L

last: Barco Guerrero


title: Dynamic incorporation of histone H3 variants into chromatin is essential for acquisition of aggressive traits and metastatic colonization [ATAC-seq]

city: NEW YORK

first: John

last: Blenis

state: NY

address: 413 E 69TH ST FL 13

country: USA

institute: Weill Cornell Medicine

summary: Metastasis is the leading cause of cancer mortality. Chromatin remodeling is crucial for metastasis formation, laying the ground for the cellular reprogramming necessary to drive metastasis. However, little is known about the nature of this remodeling and its regulation. Here, we show that metastasis-inducing pathways regulate histone chaperones to reduce canonical histone incorporation into chromatin, triggering deposition of H3.3 variant at the promoters of poor-prognosis genes and metastasis-inducing transcription factors. This specific incorporation of H3.3 into chromatin is both necessary and sufficient for the induction of aggressive traits that allow for metastasis formation. Together, our data clearly show histone variant H3.3 as a major regulator of cell fate during tumorigenesis, and histone chaperones as valuable therapeutic targets for invasive carcinomas.

overall_design: Examination of changes in chromatin accesibility in MCF10A cells expressing ERK2 D319N by ATAC-seq .

first: Ana

middle: P

last: Gomes

first: Didem

last: Ilter


title: Impaired adult hippocampal neurogenesis in a mouse model of familial hypercholesterolemia: a role for the LDL receptor and cholesterol metabolism in adult neural precursor cells (LDLR Knockdown)

city: Dresden

first: Gerd

last: Kempermann

state: Saxony

address: Tatzberg 41

institute: German Center for Neurodegenerative Diseases (DZNE)

summary: In familial hypercholesterolemia (FH), mutations in the low-density lipoprotein (LDL) receptor (LDLr) gene result in increased plasma LDL cholesterol. Clinical and preclinical studies revealed an association between FH and hippocampus-related memory and mood impairment. We here asked whether hippocampal pathology in FH might be a consequence of compromised adult hippocampal neurogenesis. We evaluated hippocampus-dependent behaviour and neurogenesis in adult C57BL/6JRj and LDLr-/- mice. Behavioural tests revealed that adult LDLr-/- mice showed reduced performance in a dentate gyrus (DG)-dependent metric change task. This phenotype was accompanied by a reduction in cell proliferation and adult neurogenesis in the DG of LDLr-/- mice, suggesting a potential direct impact of LDLr mutation on NPC. We thus investigated the effects of elevated cholesterol and the function of LDLr in neural precursor cells (NPC) isolated from adult C57BL/6JRj mice in vitro. Exposure of NPC to LDL as well as LDLr gene knockdown reduced proliferation and disrupted transcriptional activity of genes involved in endogenous cholesterol synthesis and metabolism. The LDL treatment also induced an increase in intracellular lipid storage. Functional analysis of differentially expressed genes revealed parallel modulation of distinct regulatory networks upon LDL treatment and LDLr knockdown. Together, these results suggest that high LDL levels and a loss of LDLr function, which are characteristic to individuals with FH, might contribute to a disease-related impairment in adult hippocampal neurogenesis and, consequently, cognitive functions.

overall_design: Adult mouse hippocampal progenitor cells propagated in vitro were transfected with siRNAs targeting mouse LDLR or control siRNAs for 48 h prior RNA extraction. Three independent replicates from different passages were performed.

first: Daiane

last: Engel

first: Anna

middle: N

last: Grzyb

first: Jade

last: de Oliveira

first: Alexandra

last: Pötzsch

first: Tara

last: Walker

first: Patricia

last: Brocardo

first: Andreza

last: de Bem


title: Molecular determinants for enzalutamide-induced transcription in prostate cancer

city: Durham

first: Zhong

last: Chen

state: NC

address: 905 S. LaSalle Street

department: Pathology

institute: Duke University

summary: Enzalutamide, a second-generation androgen receptor (AR) antagonist, has demonstrated clinical benefit in men with prostate cancer. However, it only provides a temporary response and modest increase in survival, indicating a rapid evolution of resistance. Previous studies suggest  that enzalutamide may function as a partial transcriptional agonist, but the underlying mechanisms for enzalutamide-induced transcription remain poorly understood. Here, we show that enzalutamide stimulates expression of a novel subset of genes distinct from androgen-responsive genes. Treatment of prostate cancer cells with enzalutamide enhances recruitment of pioneer factor GATA2, AR, Mediator subunits MED1 and MED14, and RNA Pol II to regulatory elements of enzalutamide-responsive genes. Mechanistically, GATA2 functions in directing AR, Mediator and Pol II loading to enzalutamide-responsive gene loci.  Importantly, the GATA2 inhibitor K7174 inhibits enzalutamide-induced transcription by decreasing binding of the GATA2/AR/Mediator/Pol II transcriptional complex, contributing to sensitization of prostate cancer cells to enzalutamide treatment. Our findings provide mechanistic insight into the future combination of GATA2 inhibitors and enzalutamide for improved AR-targeted therapy.

overall_design:
mRNA profiles of LNCaP cells treated with vehicle, DHT and Enzalutamide were generated by deep sequencing, in duplicate, using Illumina HiSeq2500

mRNA profiles of LNCaP cells (sicontrol or siGATA2) treated with vehicle and Enzalutamide were generated by deep sequencing, in triplicate, using Illumina HiSeq4000

first: Fuwen

last: Yuan

first: Qianben

last: Wang


title: Dynamic incorporation of histone H3 variants into chromatin is essential for acquisition of aggressive traits and metastatic colonization

summary: Carcinomas can acquire metastatic potential by undergoing a cellular program referred to as epithelial-to-mesenchymal transition (EMT). During EMT, the genome undergoes major epigenetic changes required for the expression of genes that promote cell motility, invasiveness, and survival under stress. While recent data point to a crucial role of chromatin remodeling in this process, little is known about the nature of this remodeling and the signals that trigger it. Here we show that metastasis-inducing pathways regulate histone chaperones to reduce canonical histone incorporation into chromatin. This triggers deposition of H3.3 to the promoters of EMT-inducing transcription factors and poor prognosis genes, a phenomenon that is sufficient and necessary for the induction of EMT and metastasis. Together, we have discovered histone H3.3 variant as a major regulator of cell fate during tumorigenesis and histone chaperones as valuable therapeutic targets for metastatic disease.

overall_design: Examination of chromatin enrichment of histone H3 variants in a highly metastatic cell line.


title: RNA-Seq of Metastatic Clone versus Non-Metastatic Clone in Sarcoma

first: Yuning

middle: Jackie

last: Tang

department: Program in Developmental Biology

institute: Hospital for Sick Children

summary: We report that metastasis in an autochthonous mouse model of sarcoma is driven by a single clone in the primary tumor.  We performed RNA-seq comparing the gene expression profiles of the metastatic clones (MC) to matched non-metastatic clones (non-MC) from the same tumor for multiple tumors.  RNA from lung metastases (Lung-Met) of matched tumors are sequenced as well.

overall_design: RNA-seq profiling of distinct sarcoma tumor clones and lung metastases

middle: J

first: Benjamin

last: Alman

first: David

last: Kirsch


title: The NOTCH-FOXM1 Axis Plays a Key Role in Mitochondrial Biogenesis in the Induction of Human Stem Cell Memory-like CAR-T Cells

city: Tokyo

first: Taisuke

last: Kondo

department: Medicine

country: Japan

institute: Keio University

summary: Recent studies have shown that stem cell memory T (TSCM) cell-like properties are important for the successful adoptive immune therapy by the chimeric antigen receptor-engineered-T (CAR-T) cells. We previously reported that both human and murine activated T cells are converted into stem cell memory-like T (iTSCM) cells by co-culture with stromal OP9 cells expressing the NOTCH-ligand. However, the mechanism of NOTCH-mediated iTSCM reprogramming remains to be elucidated. Here, we report that the NOTCH/OP9 system efficiently converts conventional human CAR-T cells into TSCM-like CAR-T, “CAR-iTSCM” cells, and that the mitochondrial metabolic reprogramming plays a key role in this conversion. The NOTCH signals promote mitochondrial biogenesis and fatty acid synthesis during iTSCM formation, which are essential for the properties of iTSCM cells. We identified fork head box M1 (FOXM1) as a downstream target of NOTCH, which is responsible for these metabolic changes and the subsequent iTSCM differentiation. Like NOTCH-induced CAR-iTSCM cells, FOXM1-induced CAR-iTSCM cells possess superior antitumor potential compared to conventional CAR-T cells. We propose that the NOTCH- or FOXM1-driven CAR-iTSCM formation is an effective strategy for improving cancer immunotherapy.

overall_design: We activated CD8+ T cells by aCD3/28 dynabeads for 7 days. After TCR stimulation, to activate Notch signaling, activated T cells were co-cultured with OP9-hDLL1 cells. NICD- or FOXM1ΔN-transduced T cells were cultured in OP9-hDLL1 conditioned medium.

first: Makoto

last: Ando

first: Akihiko

last: Yoshimura


title: Arabidopsis PP6 phosphatases dephosphorylate PIF proteins to repress photomorphogenesis.

city: Wuhan

first: xiaodan

last: yu

state: Hubei Province

address: No.1,Shizishan Street · Hongshan District

department: College of Life Science and Technology

country: China

institute: Huazhong Agricultural University

summary: Light-induced phosphorylation is necessary and essential for the degradation of phytochrome-interacting factors (PIFs), the central repressors of photomorphogenesis. Although the kinases responsible for PIF phosphorylation have been extensively studied, the phosphatases underlying PIF dephosphorylation are largely unknown. Here, we real that mutation of FyPP1 and FyPP3, two catalytic subunits of PP6 phosphatases, promoted photomorphogenesis of seedlings in the dark. PP6 and PIFs functioned synergistically to repress photomorphogenesis. FyPP1 and FyPP3 directly interacted with and dephosphorylated PIF3 and PIF4. The light-induced degradation of PIF4 and the PIF transcriptional activities were dependent on PP6 activity. These data demonstrate that PP6 phosphatases repress photomorphogenesis through regulation of PIF phosphorylation, protein stability and transcriptional activity.

overall_design: RNA-seq to arabidopsis thaliana seedlings of Col,f1f3 and pifq, grown in the dark and at 22°C for 4 days. Each sample has 2 biological replicates.

first: Xiaodan

last: Yu


title: Single-Cell RNA-Seq of Myocardial Infarction in Mouse

status: Public on Sep 02 2019

city: Cincinnati

first: Nathan

last: Salomonis

state: OH

address: 3333 Burnet Avenue

department: Biomedical Informatics

institute: Cincinnati Children's Hospital

summary: We applied single-cell transcriptomics to identify cellular and molecular heterogeneity in distinct heart cell populations in myocardial infarction versus sham surgery mice.

overall_design: Myocardial infarction of wild-type mice was performed to identify discrete cell populations within the injured heart by scRNA-Seq (DropSeq).

first: Inigo

last: Valiente

first: Burns

last: Blaxall

first: Stephanie

last: Kidder

first: Fei

last: Sun


title: WGBS analysis of Landrance and Wuzhishan miniature pig

city: Guangzhou

first: Delin

last: Mo

address: Xingang Road

institute: Sun Yat-sen University

type: Methylation profiling by high throughput sequencing

summary: Here, we performed the first whole-genome bisulfite sequencing (WGBS) of longissimus dorsi muscle (LDM) from Landrace (LR) and Wuzhishan (WZS) miniature pig during early embryonic stages (18, 21 and 28 dpc (days post coitum)).

overall_design: Examination of LDM tissue from LR and WZS in 18,21,28 dpc using pooled library construction

first: Xumeng

last: Zhang


title: Hematopoietic stem cells in perisinusoidal niches are protected from ageing

city: Ulm

first: Johannes

last: Pospiech

address: Albert-Einstein Allee 11

institute: Ulm University

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

overall_design: Refer to individual Series


title: Hematopoietic stem cells in perisinusoidal niches are protected from ageing [aged, GFP-label retaining HSCs]

summary:
With ageing, intrinsic hematopoietic stem cell (HSC) activity decreases, resulting in impaired tissue homeostasis, reduced engraftment following transplantation and increased susceptibility to diseases. However, whether ageing affects also the HSC niche impairing the capacity to support HSC function is still largely unknown.
Here, by using in-vivo long-term label retention assays we demonstrate that aged labelling retaining (LR) HSCs, which are in the old mice the most quiescent HSC subpopulation with the highest regenerative capacity and cellular polarity, reside predominantly in perisinusoidal niches. Furthermore, we demonstrate that sinusoidal niches and perisinusoidal Nes-GFPlow cells are uniquely preserved in shape, morphology and number upon ageing. Finally, we show that myeloablative chemotherapy can selectively disrupt aged sinusoidal niches, which is linked to hematopoietic failure and decreased survival of aged mice.  Overall, our data characterize for the first time the functional alterations of the aged HSC niche and unveil that perisinusoidal niches are uniquely preserved and protect HSCs from ageing.

overall_design: Single-cell RNA-Seq dataset of aged, GFP-label retaining HSCs. 37 aLR-HSCs and 28 anLR-HSCs were isolated in 4 biological repeats (total of 65 cells). All libraries were manually prepared using Illumina’s Nextera XT DNA Library preparation kit.

first: Rebekah

last: Karns


title: Single-Cell Analysis of Human Mononuclear Phagocytes Reveals Subset-Defining Markers and Identifies Circulating Inflammatory Dendritic Cells

city: Singapore

first: Vipin

last: Narang

address: Immunos #04-01, 8A Biomedical Grove, Singapore-138648

country: Singapore

institute: Singapore Immunology Network (SIgN)


title: Hematopoietic stem cells in perisinusoidal niches are protected from ageing [young and aged BM CD45-CD31+ endothelial cells]

summary:
With ageing, intrinsic hematopoietic stem cell (HSC) activity decreases, resulting in impaired tissue homeostasis, reduced engraftment following transplantation and increased susceptibility to diseases. However, whether ageing affects also the HSC niche impairing the capacity to support HSC function is still largely unknown.
Here, by using in-vivo long-term label retention assays we demonstrate that aged labelling retaining (LR) HSCs, which are in the old mice the most quiescent HSC subpopulation with the highest regenerative capacity and cellular polarity, reside predominantly in perisinusoidal niches. Furthermore, we demonstrate that sinusoidal niches and perisinusoidal Nes-GFPlow cells are uniquely preserved in shape, morphology and number upon ageing. Finally, we show that myeloablative chemotherapy can selectively disrupt aged sinusoidal niches, which is linked to hematopoietic failure and decreased survival of aged mice.
Overall, our data characterize for the first time the functional alterations of the aged HSC niche and unveil that perisinusoidal niches are uniquely preserved and protect HSCs from ageing.

overall_design: Single-cell RNA-Seq dataset of young and aged BM CD45-CD31+ endothelial cells. A total of five libraries was generated in three biological replicates (three libraries from young animals, two libraries from aged animals). All libraries were prepared using the 10X Genomics Chromium Single Cell 3’ Solution platform.


title: Long-term maintenance of functional primary human hepatocytes using small molecules

status: Public on Sep 01 2019

city: Philadelphia

first: Takeshi

last: Katsuda

state: PA

address: 421 Curie Blvd, BRB II/III Rm531

department: Perelman School of Medicine

institute: University of Pennsylvania

summary: Primary human hepatocytes (PHHs) were cultured with or without a cocktail of four small molecules, Y-27632, PD0325901, A83-01 and CHIR99021 (termed YPAC), and their transcriptomes after a long-trm culture were compared.

overall_design: Cryopreserved PHHs were cultured as a monolayer with or without YPAC for 40 days.

first: Takahiro

last: Ochiya


title: RNA-seq of circulating inflammatory human cDC2 dendritic cells

summary: Distinct subsets of circulating human cDC2 dendritic cells were sorted based on CD5, CD163 and CD14 expression, including a subset of inflammatory CD5-CD163+CD14+ cells related to DC3s which were expanded in systemic lupus eryhtematosus (SLE) patients and correlated with disease activity.

overall_design: Four distinct subsets of circulating human cDC2 dendritic cells, CD5+, CD5-CD163-, CD5-CD163+CD14-, CD5-CD163+CD14+, were FACS sorted from PBMCs obtained from healthy donors and donors with autoimmune disease.

first: Florent

last: Ginhoux

first: Charles-Antoine

last: Dutertre


title: RNAseq of Notch signaling responsive and unresponsive thymus DN1a/b cells

first: Juan Carlos

last: Zuniga-Pflucker

address: 2075 Bayview Avenue

department: Immunology

institute: University of Toronto

summary: We report the gene expression profile of thymus DN1a/b cells that are either responsive to Notch signals, or unresponsive to Notch signals due to absence of expression of RBPJ, a key mediator of the Notch signaling pathway.

overall_design: Thymus DN1a/b cells were FACS sorted from control mice (always maintained expression of RBPJ), RBPJ uninduced mice (lacked expression of RBPJ), and RBPJ induced mice (initially lacked expression of RBPJ but made to induce expression of RBPJ through doxycycline treatment).

first: Edward

last: Chen

first: Patrycja

middle: K

last: Thompson

first: Juan

middle: C


title: Whole exome and transcriptome sequencing of murine tumor models

city: Chapel Hill

first: Benjamin

middle: Garrett

last: Vincent

address: Lineberger Comprehensive Cancer Center, CB# 7295 125 Mason Farm Rd. Room 5230E Marsico Hall

department: Department of Microbiology and Immunology UNC-Chapel Hill Immunology Division of Hematology/Oncology

institute: University of North Carolina at Chapel Hill

summary: These data were used for prediction of neoantigens and minor histocompatibility mismatch antigens, which were subsequently used for design of a machine-learning algorithm for tumor-specific antigen (TSA) immunogenicity prediction.  TSA vaccines are a growing area of study for cancer immunotherapy, but identification of clinically relevant targets remains a challenge. The study associated with these data provides the first description of a computational method for direct prediction of TSA immunogenicity trained entirely from validated TSA immunogenicity scores. This tool has allowed us to 1) predict for clinically efficacious TSA targets, 2) identify genomic correlates of TSA immunogenicity, and 3) demonstrate evidence of alternative out-of-frame TSAs which can promote anti-tumor immunity.

overall_design:
Examination of whole exome and transcriptome patterns in 6 murine tumor models, as well as whole exome patterns in respective wild-type cells.

Quantified processed data are not available for the RNA-seq data because gene expression data were not generated or considered for the analysis.

first: Christof

last: Smith

first: Shengjie

last: Chai

first: Amber

middle: R

last: Washington

first: Samuel

last: Lee

first: Elisa

last: Landoni

first: Kevin

last: Field

first: Jason

last: Garness

first: Lisa

last: Bixby

first: Sara

last: Selitsky

first: Joel

last: Parker

first: Barbara

last: Savoldo

first: Jonathan

last: Serody

middle: G


title: Transcriptome analysis of reticulated platelets reveals a prothrombotic profile

city: Munich

first: Gianluca

last: Santamaria

state: Germany

address: Ismaninger Strasse 22

department: Department of Medicine I

institute: Klinikum rechts der Isar – Technical University Munich


title: Genetic screen of the yeast environmental stress response dynamics uncovers a succession of regulatory phases

first: Nir

last: Friedman

institute: The Hebrew University of Jerusalem

summary: Cells respond to environmental fluctuations by regulating multiple transcriptional programs. This response can be studied by measuring the effect of environmental changes on the transcriptome or the proteome of the cell at the end of the response. However, the dynamics of the response reflect working of the regulatory mechanisms in action. Here we utilized a fluorescent stress reporter gene to track the dynamics of protein production in yeast responding to environmental stress. The response is modulated by changes in both the duration and rate of transcription. We probed the underlying molecular pathways controlling these two dimensions using a library of ~1600 single and double mutant strains. Dissection of the effects of these mutants and the interactions between them identified distinct modulators of response duration and response rate. Using a combination of mRNA-seq and live-cell microscopy we uncover mechanisms by which Msn2/4, Mck1, Msn5, and the cAMP/PKA pathway modulate the response of a large module of stress-induced genes in two discrete regulatory phases. Our results and analysis show that transcriptional stress response is regulated by multiple mechanisms that overlap in time and cellular location.

overall_design: The dataset includes 144 3'RNA-Seq samples. 18 mutant strains that were measured in 8 timepoints after exposure to 0.4M KCl.


title: RNA-seq of Notch signaling responsive

first: Juan Carlos

last: Zuniga-Pflucker


title: SOX2 epidermal overexpression promotes cutaneous wound healing via activation of EGFR/MEK/ERK signaling mediated by EGFR ligands

city: Bethesda

first: Maria

middle: Irene

last: Morasso

state: Maryland

address: Bldg 50

institute: NIAMS NIH

summary: We perfomed RNA-seq and wound healing analysis to identify the mechanism how SOX2 promote wound healing. We showed that induction of SOX2 in skin keratinocytes accelerates cutaneous wound healing by promoting keratinocyte migration and proliferation, and enhancement of angiogenesis via the upregulation of EGFR ligands.

overall_design: Whole skin mRNA profiles in the unwounded (Day0) or wounded (Day4) state from Vehicle or Tamoxifen treated mice were examined in triplicate or quadruplicate.

middle: I

first: Stephen

last: Brooks

first: Akihiko

last: Uchiyama


title: Transcriptome analysis of reticulated platelets reveals a prothrombotic profile [miRNA-Seq]

summary:
To compare immature and mature platelet transcriptome
Methods: reticulated or immature platelets(RPs) were defined as the platelets with the highest thiazole orange staining intensity (15% highest, RNAhigh) according to previous experiences and mature platelets were defined as the platelet with the 30% lowest thiazole orange staining intensity (RNAlow) and sorted (supplemental Figure S1D).
RPs have a prothrombotic transcriptomic profile

overall_design: Platelets RNA was acquired frome healthy donors. And analyzed using using NextSeq-500

first: Dario

last: Bongiovanni


title: Single-Cell Chromatin Analysis of Mammary Gland Development Reveals Cell-State Transcriptional Regulators and Lineage Relationships

city: San Diego

first: Chi-Yeh

last: Chung

state: CA

address: 10770 Science Center Drive

institute: Pfizer Inc.

summary: We perfromed single-nucleus ATAC-seq (snATAC-seq) on normal mammary epithelial cells

overall_design: snATAC-seq was performed on freshly sorted cell nuclei as detailed in the Methods section of the manuscript

first: Geoffrey

last: Wahl

first: Christopher

last: Dravis


title: Follicular regulatory T cells control humoral and allergic immunity by restraining early B cell responses

city: Boston

first: Peter

last: Sage

address: 221 Longwood Ave

department: Medicine/Renal

institute: Brigham and Women's Hospital

overall_design: Examination of Tfh and Tfr cells from OVA or HDM challenged mice.  Mice were challenged with 4-Hydroxy-3-nitrophenylacetyl hapten-ovalbumin subcutaneously or house dust mite antigen intranasally.  Lymph nodes were harvested and Tconventional, Tfh or Tfr cells were sorted for RNAseq transcriptional analysis.


title: PGRMC2 is an Intracellular Heme Chaperone Critical for Adipocyte Function

city: La Jolla

first: Nasun

last: Hah

address: 10010 North Torrey Pines Rd

department: Next Generation Sequencing

institute: The Salk Institute

summary: We describe a role for the poorly annotated protein PGRMC2 in retrograde transport of heme from mitochondria to the nucleus.  In absence of PGRMC2, less signaling heme reaches the nucleus, with a consequent alteration of heme-sensitive transcriptional programs that ultimately engenders severe mitochondrial dysfunction in brown adipocytes.  These mitochondrial defects compromise, not only the primary function of BAT, to activate thermogenesis and preserve body temperature, but also its contribution to maintain systemic glucose and lipid homeostasis.

overall_design: PolyA+ RNAseq profilling of Brown Adipose Tissue (BAT) isolated from wild-type and PGRMC2 adipose tissue knockout mice housed at 30°C

first: Andrea

last: Galmozzi

first: Enrique

last: Saez


title: Affymetrix SNP array data for dic(1;7)(q10;p10) in Myelodysplastic Syndromes (MDS)

city: Perugia

first: Cristina

last: Mecucci

address: Piazzale Menghini n.9

department: Department of Medicine, Hematology and Bone Marrow Transplantation Unit

country: Italy

institute: University of Perugia

summary:
The unbalanced translocation t(1;7)(q10;p10), generating 1q trisomy and  7q monosomy, is due to centromere-centromere juxtaposition. This dicentric chromosome is a recurrent change in myelodysplastic syndromes (MDS), with half the cases arising after chemo/radio-therapy. To date, given the absence of genes within the centromeric regions, no specific molecular events have been identified in this cytogenetic subgroup.
We first identified a comprehensive genetic and epigenetic landscape of MDS with dic(1;7)(q10;p10) and compared it to normal controls and other therapy-related Myeloid Neoplasms (t-MNs).
RNA-seq showed a unique downregulated signature in dic(1;7) cases, affecting more than  80% of differentially expressed genes. As revealed by pathway and gene ontology analyses, downregulation of ATP-binding cassette (ABC) transporters and of genes related to lipid metabolism, and upregulation of p53 signaling were the most relevant biological features of dicentric-positive MDS.
Despite 1q trisomy, more than 50% of 1q deregulated genes were downregulated. This partial gene dosage effect was clarified by epigenetic analysis, which highlighted the presence of a specific hypermethylated pattern on 1q. Furthermore, in a supervised analysis, hypermethylation in all dicentrics clustered at intronic enhancers and was enriched for Krüppel-like transcription factors binding sites. Low expression levels of enhancer putative target genes accounted for more than 30% of the downregulated signature.
Our findings demonstrate that alteration of centromeric DNA in dic(1;7) cases imposes a specific transcriptional program, driven by a unique epigenomic signature.

overall_design: Copy number analysis of Affymetrix 100K and 500K SNP arrays was performed for 5 dic(1;7)(q10;p10) MDS cases

middle: E

last: Figueroa

last: Barba

first: Valentina

last: Pierini

first: Anair

last: Lema Fernandez


title: Changes in genetic transcription patterns in Jurkat cells treated with Tamoxifen

city: Colima

first: Ivan

last: Delgado-Enciso

state: Colima

address: Av Universidad 333

department: School of Medicine

country: Mexico

institute: Universidad de Colima

summary: In this research, we use DNA microarray analysis to clarify the gene expression responses in Jurkat cells after Tamoxifen treatment. Jurkat cells are a dexamethasone-resistant cell line derived from a T-cell Acute Lymphoblastic Leukaemia  sample in relapse

overall_design: Analysis used Jurkat as control samples for comparison to the experimental sample: Jurkat cells treated with 7.5 µM Tamoxifen for 24 hours. Jurkat cells (control), compared to Jurkat cells treated with 7.5 µM Tamoxifen. One replicate array.

first: Lilana

last: Torres-Lopez

first: Paola

last: Maycotte

first: Andromeda

last: Liñan-Rico

first: Liliana

first: Luis

last: Donis-Maturano

first: Carmen

last: Meza-Robles

first: Clemente

last: Vasquez-Jiménez

first: Oxana

last: Dobrovinskaya


title: Expression Analysis of dic(1;7)(q10;p10) in Myelodysplastic Syndromes (MDS) compared to control cohort and therapy-related Myeloid Neoplasms (t-MN)

overall_design: mRNA profiles of 5 dic(1;7)(q10;p10) cases, 4 controls (bone marrow samples from non-neoplastic cytopenias, normal bone marrow morphology and normal karyotype), and 5 therapy-related Myeloid Neoplasms (t-MNs) cases.

first: Maria


title: Multiplex Enhanced Reduced Representation Bisulfite Sequencing (mERRBS) Analysis of dic(1;7)(q10;p10) in Myelodysplastic Syndromes (MDS) compared to control cohort and therapy-related Myeloid Neoplasms (t-MN)

overall_design: mERRBS profiles of 5 dic(1;7)(q10;p10) cases,4 controls (bone marrow samples from non-neoplastic cytopenias, normal bone marrow morphology and normal karyotype), and 3 therapy-related Myeloid Neoplasms (t-MNs) cases.


title: Single-Cell Genomics of Transverse Aortic Constriction in Mouse

first: Nathan

last: Salomonis

summary: We applied single-cell transcriptomics to identify cellular heterogeneity in distinct heart cell populations in addition to their transcriptomic differences.

overall_design: Transverse aortic constriction (TAC) of wild-type mice was performed to identify discrete cell populations within the injured heart by scRNA-Seq (DropSeq). Over 20,000 cells were loaded into droplets prior to cDNA generation and high-throughput sequencing.

first: Inigo

last: Valiente

first: Burns

last: Blaxall

first: Stephanie

last: Kidder

first: Fei

last: Sun


title: A Distinct Epigenetic Program Underlies the 1;7 Translocation in Myelodysplastic Syndromes (MDS)

first: Cristina

last: Mecucci

overall_design: Refer to individual Series


title: The RNA-seq analyses of transcriptional changes responsing to manganese depletion in Drosophila

status: Public on Aug 31 2019

first: Yanhui

last: Hu

state: MA

address: 77 Avenue Louis Pasteur

institute: Harvard Medical School

summary:
Purpose: identifying genes responding to manganese depletion in Drosophila through whole transcriptome RNA-seq analyses
Methods: 10 females and 10 males of wild type of the Oregon R-C genotype, were mated and allowed to lay eggs for five days on two variants of chemical diet (no manganese added or 5 ppm manganese). Parents were removed and recently-eclosed females were transferred to fresh medium, respectively, for another five days. 10 midguts were dissected in PBS and homogenized in TRIzol (Invitrogen). RNA extraction and purification was performed using the Direct-zol RNAMicroPrepkit (Zymo Research) method.  two biological replicates were used for each dietary treatment group. The RNA was eluted with sterile water and each RNA solution was divided into two aliquots, one of which was freshly used to obtain an RNA Integrity Number (RIN) evaluation at the Harvard Medical School Biopolymers Facility. For samples with RIN > 6.7 and no RNA degradation, the other aliquot stored at -80°C was submitted for sequencing.
Results: we identified differentially expressed genes responding to to manganese depletion in Drosophila.

overall_design: Samples of two chemical diets (no manganese or 5 ppm manganese added) with replicates were sequenced and analyzed for differentially expressed genes responsing to manganese depletion.

first: Johana

last: Vásquez-Procopio

first: Fangge

last: Li

last: Mohr

first: Norbert

last: Perrimon

first: Fanis

last: Missirlis


title: The role of PHF19 in promoting H3K27me3 deposition in multiple myeloma (RNA-Seq)

first: Greg

last: Wang

address: 3 Genome Court

department: Duke Department of Pharmacology and Cancer Biology  and Duke Cancer Institute

institute: Duke University School of Medicine, and Department of Biochemistry and Biophysics, UNC at Chapel Hill (adjunct)

summary: Dysregulation of Polycomb Repressive Complex 2 (PRC2) promotes oncogenesis partly through its enzymatic function for inducing tri-methylation of histone H3 lysine 27 (H3K27me3). However, it remains to be determined how PRC2 activity is regulated in normal and diseased settings. We here report a PRC2-associated cofactor, PHD finger protein 19 (PHF19, also known as Polycomb-like 3), as a crucial mediator of tumorigenicity in multiple myeloma (MM). Overexpression and/or genomic amplification of PHF19 is found associated with malignant progression of MM and plasma cell leukemia, correlating to worse treatment outcomes. Using various MM models, we demonstrated a critical requirement of PHF19 for tumor growth in vitro and in vivo. Mechanistically, PHF19-mediated oncogenic effect relies on its PRC2-interacting and chromatin-binding functions. ChIP-Seq profiling showed a critical role for PHF19 in maintaining the H3K27me3 landscape. PHF19 depletion led to loss of broad H3K27me3 domains possibly due to impaired H3K27me3 spreading from CpG islands, which is reminiscent to the reported effect of an ‘onco’-histone mutation, H3K27-to-methionine (H3K27M). RNA-Seq-based transcriptome profiling in MM lines also demonstrated a requirement of PHF19 for optimal silencing of PRC2 targets, which include cell cycle inhibitors and interferon-JAK-STAT signaling genes critically involved in tumor suppression.

overall_design: Examination of transcriptome profiles in the MM.1S cells with stable expression of either empty vector (shEV) or shPHF19 for knockdown of PHF19  (PHF19-KD), as well as  PHF19-KD cells  rescued with shRNA-resistant PHF19 (KD_Rescued)


title: scRNAseq of Notch signaling responsive and unresponsive bone marrow lymphoid-primed multipotent progenitors (BM LMPPs)

city: Toronto

first: Juan Carlos

last: Zuniga-Pflucker

summary: We report the gene expression profile of single cell BM LMPPs that are either responsive to Notch signals, or unresponsive to Notch signals due to absence of expression of RBPJ, a key mediator of the Notch signaling pathway.

overall_design: BM LMPPs were FACS sorted from control mice (always maintained expression of RBPJ), RBPJ uninduced mice (lacked expression of RBPJ), and RBPJ induced mice (initially lacked expression of RBPJ but made to induce expression of RBPJ through doxycycline treatment).

first: Edward

last: Chen

first: Patrycja

last: Thompson

first: Juan


title: The role of PHF19 in promoting H3K27me3 deposition in multiple myeloma

city: Durham

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


title: The role of PHF19 in promoting H3K27me3 deposition in multiple myeloma (ChIP-seq)

summary: We here report a PRC2-associated cofactor, PHD finger protein 19 (PHF19, also known as Polycomb-like 3), as a crucial mediator of tumorigenicity in multiple myeloma (MM). Using various MM models, we demonstrated a critical requirement of PHF19 for tumor growth in vitro and in vivo. Mechanistically, PHF19-mediated oncogenic effect relies on its PRC2-interacting and chromatin-binding functions. ChIP-Seq profiling showed a critical role for PHF19 in maintaining the H3K27me3 landscape. PHF19 depletion led to loss of broad H3K27me3 domains possibly due to impaired H3K27me3 spreading from CpG islands

overall_design: Examination of the genome-wide binding of H3K27me3 in the L-363 multiple myeloma cell line before and after knockdown of PHF19

first: Zhihong

last: Ren

first: John

last: Ahn


title: Single-cell transcriptomic analysis of 96hour AEL wild type wing imaginal discs

city: Hong Kong

first: Yan

last: Yan

address: Clear Water Bay

department: LIFS

institute: HKUST

summary:
Genotype: FRT82B
Method: Staged wild type wing imaginal discs were dissected and transferred to DPBS. The wing imaginal discs were dissociated in 0.25% Trypsin-EDTA solution at 37 ℃ for 10 min. Cells were then washed in DPBS and passed through 35μm filter before library preparation. Construction of 10x single cell libraries and sequencing on Illumina Hiseq platform were performed by Novogene.

overall_design: 10X  based single-cell mRNA profiles of wild type wing imaginal discs

first: Lina

last: Zhang

first: Wang

last: Ying

first: Mingxi

last: Deng


title: Isolation, characterization and safety evaluation of human skin-derived precursors from adherent monolayer culture system

city: Chengdu

first: Ru

last: Dai

state: Sichuan

address: No.37 Guo Xue Xiang

department: Dermatology

institute: West China hospital

summary: FBs were distinctive from tSKPs in spite of sharing several characteristics in certain properties

overall_design: To distinguish tSKPs from FBs, we compared their transcriptomes.

first: Dai

last: Ru

first: Li


title: IL4 improves white matter repair after stroke

city: Pittsburgh

first: Jun

address: 200 Lothrop Street

department: Neurology

institute: University of Pittsburgh

summary: The repair of white matter damage is of paramount importance for functional recovery after brain injuries.We report that interleukin-4 (IL-4) promotes oligodendrocyte regeneration and remyelination. IL-4 receptor expression was detected in a variety of glial cells after ischemic brain injury, including oligodendrocyte lineage cells. IL-4 deficiency in knockout mice resulted in greater deterioration of white matter over 14 days after stroke. Consistent with these findings, intranasal delivery of IL-4 nanoparticles after stroke improved white matter integrity and attenuated long-term sensorimotor and cognitive deficits in wild-type mice, as revealed by histological immunostaining, electron microscopy, diffusion tensor imaging, and electrophysiology. The selective effect of IL-4 on remyelination was verified in an ex vivo organotypic model of demyelination. By leveraging primary oligodendrocyte progenitor cells (OPCs), microglia-depleted mice, and conditional OPC-specific PPARγ knockout mice, we discovered a direct salutary effect of IL-4 on oligodendrocyte differentiation that was mediated by the PPARγ axis. Our findings reveal a new regenerative role of IL-4 in the CNS, which lies beyond its known immunoregulatory functions on microglia/macrophages or peripheral lymphocytes. Therefore, intranasal IL-4 delivery may represent a novel therapeutic strategy to improve white matter integrity in stroke and other brain injuries.

overall_design: Rat primary OPC cultures were isolated with the differential attachment method and treated with PBS or IL-4 (20 ng/mL) for 3 days. Total RNA was extracted from PBS (n=4) or IL-4 (n=4) treated OPCs for microarray analysis.

first: Xiaoming

last: Hu


title: Microtubule Motor KIF3A Regulates Pulmonary Innate Defenses to Aspergillus and Influenza A Virus

city: Cincinnati

middle: M.

last: Snowball

address: 3333 Burnet Ave

department: Pulmonary Research

institute: Cincinnati Childrens Hospital

summary: Susceptibility to respiratory infection, decreased barrier function, impaired epithelial regeneration and enhanced inflammation are likely to contribute to the association between the KIF3A gene and asthma pathogenesis.

overall_design: Kif3a deficient mice were chronicle or acutely exposed to aspergillus extract and then loss of Kif3a was assessed by Epcam sorted RNA Seq

first: Premkumar

middle: V

last: Giridhar

first: Jeffrey

middle: A

last: Whitsett


title: Assessing the remarkable morphological diversity and transcriptomic basis of leaf shape in Ipomoea batatas (sweetpotato)

city: Ann Arbor

first: Sonal

last: Gupta

state: Michigan

address: 1121 Maiden Lane, Apt 106

department: Ecology and Evolutionary Biology

summary: Leaf shape is a spectacularly diverse trait that influences various aspects of plant physiology, and is even correlated with crop yield and quality in multiple species. However, only a few genetic dissections of leaf shape have been accomplished at a species-wide level. Here, we perform an initial characterization of leaf shape variation in Ipomoea batatas, the sweetpotato, at multiple scales of analysis. We use a transcriptomic survey to identify gene expression changes associated with two commonly studied leaf shape traits--circularity and aspect ratio using 19 individuals (accession) of sweetpotato. We comprehensively describe the remarkable morphological diversity in leaf shape in sweetpotato, and identify 147 differentially regulated genes associated with circularity and aspect ratio, providing an initial set of hypotheses regarding the genetic basis of leaf shape in this species.

overall_design: To obtain an initial set of candidate genes responsible for leaf shape traits (circularity and aspect ratio), total mRNA was extracted from 19 individuals (unique accessions) of sweetpotato. These plants were grown in the greenhouse to reduce gene expression variation due to environmental noise. Accessions displaying very high and low lobedness, and likewise accessions exhibiting high/low aspect ratio were chosen. Eleven individuals were used to assess variation in circularity (six entire (PI566613, PI585054, PI585108, PI592993, PI595868, PI612701), five lobed (PI573318, PI585061, PI585067, PI599387, PI634379)) and 9 individuals were chosen to assess variation in aspect ratio (five high AR (PI208886, PI344123, PI566617, PI566638, PI585061), four low AR (PI318848, PI531122, PI564154, PI599392)); one accession (PI585061) was common for circularity and AR. RNA was extracted from three to five leaves that were in P3-P5 stage of growth, from multiple branches of each individual accession, and combined replicate leaves per individual to increase the coverage of the transcriptome.

first: David

middle: M

last: Rosenthal

last: Stinchcombe

first: Regina

middle: S

last: Baucom


title: Identification of NOTCH3 unique target genes

city: Winnipeg

first: Afshin

last: Raouf

state: Manitoba

address: 471 Apotex centre, 750 McDermot Avenue

institute: University of Manitoba

summary:
Notch signaling is an evolutionarily conserved signaling pathway.NOTCH3 signaling has been shown to potentially paly an important role in luminal cell fate commitment in human breast tissue by regulating unique target genes
We overexpressed the intracellular domain of NOTCH1 (N1ICD) and NOTCH3  (N3ICD) receptor in nonmalignant human breast cell line, 184-hTerts

overall_design: 184-hTert cells were lentivirally transduced with either empty vector control, N1ICD or N3ICD. RNA was isolated for affymetrix microarray analysis

first: Vasudeva

last: Bhat

first: Victoria

last: Lee-Wing

first: Pingzhao


title: Culture condition modifications to improve pluripotency in porcine pluripotent stem cells

city: Columbia

first: Toshihiko

last: Ezashi

state: MO

address: 240a CS Bond Life Sciences Center

department: Animal Sciences

institute: University of Missouri-Columbia

summary: Understanding essential signaling network requirements and adjustment the culture conditions for porcine pluripotent stem cells (pPSC) that allow its full potential are necessary. Here we compared culture conditions of various cytokine and kinase inhibitor combinations by deriving porcine induced pluripotent stem cells (piPSC) and porcine embryonic stem cell (pESC)-like cells.  We modified the naïve-type human PSC condition by replacing TGFB1 with TGFB inhibitor and developed a so-called FL6i condition, consisting of FGF2, LIF, p38i, JNKi, TGFBi, GSK3i, MEKi, and BMPi. In such conditions, the primed type lentiviral reprogrammed piPSC (Lv-piPSC) was converted into naïve-like state demonstrating increased expression of endogenous pluripotent genes.  By using the FL6i condition, new piPSC lines were generated with non-integrative episomal plasmids (Epi-piPSC). While concurrently generated piPSC in condition with FGF2 and LIF only, and without inhibitors lost the pluripotency within a couple passages of the culture, piPSC in FL6i were successfully established stable lines (> 45 passages) with pluripotent phenotypes. The Epi-piPSC-FL6i lines expressed higher endogenous pPOU5F1, and pSOX2 expressions than Lv-piPSC, however, variable transgene expressions were detected with consistent presence of POU5F1. The teratomas generated from Epi-piPSC-FL6i that developed fully differentiated teratomas while those from Lv-piPSC lines and Epi-piPSC derived in a different condition were limited in differentiation range, suggesting the beneficial role of the FL6i condition supporting elevated pluripotent phenotypes. FL6i conditions were also able to maintain the embryo derived cells with dome-shaped phenotype and extended the culture period that cells showed undifferentiated phenotype than the ones cultured with FGF2 alone. But neither conditions established stable pESC lines. RNAseq analysis with the piPSC and pESC-like cells revealed elevated expressions of early differentiation markers in the lines derived without inhibitors. The pathway analysis suggested that the activation of TGFB and BMP signaling pathways may be responsible for losing pluripotent state in porcine cells.

overall_design: RNAseq results from the piPSC and pESC-like cells were compared to evaluate impacts of the culture conditions of various cytokine and kinase inhibitor combinations onto the gene expressions in the cells lines derived in the respective conditions.

first: Ye

last: Yuan

first: Jinkyu

last: Park

first: R

last: Roberts


title: Molecular characterisation of muscle and spinal cord tissues from young, old and old exercised C57BL/6 wild type male mice

city: Basel

first: Sophie

last: Brachat

address: Novartis Campus

department: Muskuloskeletal

country: Switzerland

institute: Novartis Institutes For Biomedical Research

summary: To investigate the effect of exercise in several tissues, mice had free access to the wheel for two months, starting at the age of 16 to 18 months. Age-matched and younger sedentary controls were included. Running wheels were removed from the cages at least 4 days before necropsy, to eliminate acute effects of exercise. At the end of the trial, RNA was isolated from spinal cord, gastrocnemius and quadriceps muscle to perform bulk transcriptome (RNAseq) analysis. Despite many genes were differentially expressed in skeletal muscle samples following exercise, only few individual genes resulted changed by exercise in spinal cord.

overall_design: mRNA profiling of whole spinal cord, quadriceps and gastrocnemius muscles of young (10 months), mid-aged (18 months) sedentary and exercised wild type male mice

first: Elisa

last: Giorgetti

first: Marc

last: Altofer

first: Ulrike

last: Naumann

first: Mark

last: Nash


title: RNA-Seq of patient derived osteosarcoma xenograft samples

first: Rachel

last: Flynn

address: 72 East Concord Street, K-712D

department: Department of Pharmacology

institute: Boston University School of Medicine

summary: Observing the gene expression of  ATRX, DAXX, H3F3A, SMARCAL1, SLX4IP and TERT in 7 patient derived osteosarcoma xenograft samples (Houghton et al., 2007) which are using the Alternative Lengthening of Telomere (ALT) pathway.

overall_design:
7 patient derived osteosarcoma xenograft samples sequenced in triplicate, totaling 21 sequencing samples
39 other samples have been uploaded earlier in GSE118488.
Total:  60 samples.

middle: L

first: Emily

last: Mason-Osann

first: Adam

last: Labadorf

first: Anqi

last: Dai


title: DUX4-induced histone variants H3.X and H3.Y mark DUX4 target genes for expression

city: Seattle

first: Stephen

last: Tapscott

state: WASHINGTON

address: 1100 Fairview N. Ave

department: Human Biology

institute: Fred Hutch Cancer Research Center


title: DUX4-induced histone variants H3.X and H3.Y mark DUX4 target genes for expression (RNA-seq)

summary: We determined the effects of short pulses of DUX4 expression on genome-wide transcription, mimicking the embryonic expression of this gene, using a DUX4-inducible cell culture model of FSHD (MB135iDUX4). We found that a second pulse of DUX4 has a synergistic effect and shows greater induction of DUX4 targets. Knockdown of DUX4-induced histone variants H3.X and H3.Y has no effect on DUX4 targets with a single pulse of DUX4 but eliminates the superinduction seen with a second pulse, showing that these histones are required for this increase in expression.

overall_design: transcriptional profile of MB135iDUX4 myoblasts after 1 or 2 pulses of DUX4 with either histone H3.X/Y  or control knockdown, or without DUX4 induction, in triplicate

first: Rebecca

last: Resnick

first: Chao-Jen

last: Wong

first: Peter

last: Skene

first: Sandra

last: Hake

first: Steven

last: Henikoff

first: Silvere

last: van der Maarel


title: Predator-prey interactions between bacteria and the nematode Caenorhabditis elegans via interkingdom signaling molecule indole

city: Gyeongsan-Si

first: Jintae

last: Lee

state: Gyeongsangbuk-Do

address: 214-1 Daedong

department: Chemical engineering

country: South Korea

institute: Yeungnam University

summary: Indole is an intercellular and interkingdom signaling molecule, which is widespread in diverse ecological niches. Caenorhabditis elegans is a bacterivorous nematode living in soil and compost environments and a useful model host for the study of host-microbe interactions. While various bacteria and some plants produce a large quantity of extracellular indole, little is known about the effects of indole, its derivatives, and indole-producing bacteria on behaviors in C. elegans and animals. Here, we show that C. elegans senses and moves toward indole and indole-producing bacteria, such as Escherichia coli, Shigella boydii, Providencia stuartii, and Klebsiella oxytoca, while avoids non-indole producing pathogenic bacteria. It was also found that indole-producing bacteria and non-indole-producing bacteria exert divergent effects on egg-laying behavior of C. elegans via indole. In addition, various indole derivatives also modulate chemotaxis, egg-laying behavior, and survival of C. elegans. In contrast, indole at a high concentration to kill C. elegans that has the ability to detoxify indole via oxidation and glucosylation, indicating predator-prey interactions via a double-edged molecule indole. Transcriptional analysis showed that indole markedly up-regulated gene expression of cytochrome P450 family, UDP-glucuronosyltransferase, glutathione S-transferase, which explained well the modification of indole in C. elegans, while down-regulated expression of collagen genes and F-box genes. Our findings suggest that indole and its derivatives are important interkingdom signaling molecules in bacteria-nematode interactions.

overall_design: Four-condition experiment, None vs. 0.1, 0.5, 1.0 mM treated cells. Biological replicates: 1 control replicates, 1 transfected replicates.

first: Jin-Hyung

first: Yong-guy

last: Kim

first: Min Su


title: Functional DNA methylation signatures for genomic loci that confer an increased risk for autism spectrum disorder: 16p11.2 deletions and CHD8 variants

first: Rosanna

last: Weksberg

state: Ontario

address: 555 University Ave.

department: Genetics and Genome Biology

institute: The Hospital for Sick Children

type: Methylation profiling by genome tiling array

summary: Autism spectrum disorder (ASD) is a common and etiologically heterogeneous neurodevelopmental disorder. Although many genetic causes have been identified (>200 ASD-risk genes), no single gene mutation accounts for >1% of all ASD cases. A role for epigenetic mechanisms in ASD etiology is supported by the fact that many ASD-risk genes function as epigenetic regulators and evidence that epigenetic dysregulation can interrupt normal brain development. To investigate the epigenome in patients with ASD, genome-wide DNA methylation (DNAm) was assessed using the Illumina Infinium HumanMethylation450K array in blood from individuals with ASD of heterogeneous, undefined etiology (n=52) and individuals with 16p11.2 deletions (16p11.2del, n=9) or pathogenic variants in the chromatin modifier CHD8 (CHD8+/-, n=7), two of the most common genomic variants conferring increased risk for ASD. DNAm patterns did not clearly distinguish heterogeneous ASD cases from controls. However, the homogeneous genetically-defined 16p11.2del and CHD8+/- subgroups each exhibited unique DNAm signatures that distinguished 16p11.2del or CHD8+/- individuals from both heterogeneous ASD and control groups with high sensitivity and specificity. These signatures also classified additional 16p11.2del (n=9) and CHD8 (n=9) variants as pathogenic or benign. Our findings that DNAm alterations in each signature targets unique genes in biological pathways relevant to neural development support their functional relevance. Furthermore, genes identified in our CHD8+/- DNAm signature in blood overlapped differentially expressed genes in CHD8+/- human-induced pluripotent cell-derived neurons and cerebral organoids from independent studies. Our study constitutes a novel approach for ASD molecular classification that elucidates the vital cross-talk between genetics and epigenetics in the etiology of ASD.

overall_design: Bisulphite converted DNA samples were hybridized to the Illumina Infinium Human Methylation450 Beadchip.

first: Michelle

middle: T

last: Siu

first: Sanaa

last: Choufani

first: Andrei

last: Turinsky


title: Short and long-term effects of CDK4/6 inhibition on early stage breast cancer

status: Public on Aug 30 2019

city: Washington

first: Garrett

middle: Thomas

last: Graham

state: DC

address: 3970 Reservoir Rd NW

department: Oncology

institute: Georgetown University Medical Center

summary: CDK4/6 inhibitors are used in the treatment of advanced estrogen receptor (ER)(+) breast cancer (BC). Their efficacy in ER(-) and early stage BC is currently under investigation. Here, we show that palbociclib, a CDK4/6 inhibitor, can inhibit both progression of ductal carcinoma in situ (DCIS) and growth of invasive disease in both an ER(-) basal BC model (MCFDCIS) and an ER(+) luminal model (MCF7 intraductal injection). In MCFDCIS cells palbociclib repressed cell cycle gene expression, inhibited proliferation, induced senescence and normalized tumorspheres formed in Matrigel whilst the formation of acini by normal mammary epithelial cells (MCF10A) was not affected. Palbociclib treatment of mice with MCFDCIS tumors inhibited their malignant progression and reduced proliferation of invasive lesions. Transcriptomic analysis of the tumor and stromal cell compartments showed that cell cycle and senescence genes, and MUC16, an ovarian cancer biomarker gene, were repressed during treatment. Knockdown of MUC16 in MCFDCIS cells inhibited proliferation of invasive lesions but not progression of DCIS. After cessation of palbociclib treatment genes associated with differentiation, e.g. p63, inflammation, IFNγ response and antigen processing and presentation remained suppressed in the tumor and surrounding stroma. We conclude that palbociclib can prevent progression of DCIS and is anti-proliferative in ER(-) invasive disease mediated in part via MUC16. Lasting effects of CDK4/6 inhibition after drug withdrawal on differentiation and the immune response could impact the approach to treatment of early stage ER(-) breast cancer.

overall_design: 3 Tumor Replicates/group. 4 Groups - 2wk Palbociclib, 2wk Vehicle, 2wk Palbociclib + Recovery and 2wk Vehicle + Recovery. Vehicle treated tumors were used as baseline for comparisons and interrogation of drug effects.

first: William

middle: B

last: Kietzman

first: Virginie

last: Ory

first: Ghada

last: Sharif

first: Max

middle: H

last: Kushner

first: Gregory

last: Gallanis

first: Bhaskar

last: Kallakury

first: Anton

last: Wellstein

first: Anna

last: Riegel


title: Tumour exosomal CEMIP protein promotes cancer cell colonization in brain metastasis

city: New York

first: Lyden

middle: C

last: David

state: NY

address: 413 East 69th Street, Room BB1228

department: Cell and Developmental Biology

institute: Weill Cornell Medicine

summary: Development of effective therapies against brain metastasis is currently hindered by limitations in our understanding of the molecular mechanisms driving it. Here we define the contributions of tumour-secreted exosomes to brain metastatic colonization and demonstrate that pre-conditioning the brain microenvironment with exosomes from brain metastatic cells enhances cancer cell outgrowth. Proteomic analysis identified cell migration-inducing and hyaluronan-binding protein (CEMIP) as elevated in exosomes from brain metastatic, but not lung or bone metastatic cells. CEMIP depletion in tumour cells impaired brain metastasis, disrupting invasion and tumour cell association with the brain vasculature, phenotypes rescued by pre-conditioning the brain microenvironment with CEMIP+ exosomes. Moreover, uptake of CEMIP+ exosomes by brain endothelial and microglial cells induced endothelial cell branching and inflammation in the perivascular niche by upregulating Ptgs2, Tnf, and Ccl/Cxcl cytokines, known to promote brain vascular remodeling and metastasis. CEMIP was elevated in tumour tissues and exosomes from patients with brain metastasis and predicted brain metastasis progression and patient survival. Collectively, our findings suggest that targeting of exosomal CEMIP could constitute a future avenue for the prevention and treatment of brain metastasis.

overall_design: 24 samples, 3 replicates each, 4 different conditions (Wildtype, PBS, Knock-out 1, and knock-out 2)

first: Goncalo

last: Rodrigues

first: David

last: Lyden


title: Genetic Ancestry and Natural Selection Drive Population Differences in Immune Responses to Pathogens

status: Public on Aug 29 2019

city: Chicago

first: Luis

last: Barreiro

state: Illinois

address: 900 E 57th Street

department: Genetics Section

institute: University of Chicago

summary: Individuals from different populations vary considerably in their susceptibility to immune-related diseases. To understand how genetic variation and natural selection contribute to these differences, we tested for the effects of African versus European ancestry on the transcriptional response of primary macrophages to live bacterial pathogens. A total of 9.3% of macrophage-expressed genes show ancestry-associated differences in the gene regulatory response to infection, and African ancestry specifically predicts a stronger inflammatory response and reduced intracellular bacterial growth. A large proportion of these differences are under genetic control: for 804 genes, more than 75% of ancestry effects on the immune response can be explained by a single cis- or trans-acting expression quantitative trait locus (eQTL). Finally, we show that genetic effects on the immune response are strongly enriched for recent, population-specific signatures of adaptation. Together, our results demonstrate how historical selective events continue to shape human phenotypic diversity today, including for traits that are key to controlling infection.

overall_design:
We include here ATAC-Seq datasets with two replicates for each of three conditions: macrophages which are non-infected (i), infected with S. typhimurium (ii), and infected with L. monocytogenes (iii), at 12 hours post infection.
We also include the QTL lists obtained from the analysis.


title: Influenza Vaccination Primes Human Myeloid Cell Cytokine Secretion and Natural Killer Cell Function

city: London

first: Harry

last: Pickering

state: Greater London

address: LSHTM, Keppel Street

country: United Kingdom

institute: London School of Hygiene and Tropical Medicine

summary: 51 healthy adults were vaccinated with seasonal influenza vaccine and PBMC were collected before and up to 30 days after vaccination and myloid and lymphoid (NK) cell function in response to restimulation with IL-15 alone virus was assessed.

overall_design: PBMC were cultured with IL-15 alone (low dose; 0.75ng/ml) overnight and then separated in to NK cell enriched and depleted fractions and RNA was extracted for RNA trascriptional analysis.

first: Helen

last: Wagstaffe

first: Joanna

last: Houghton

first: Jason

middle: P

last: Mooney

first: Asia-Sophia

last: Wolf

first: Natalie

last: Prevatt

first: Ron

last: Behrens

first: Martin

middle: J

last: Holland

first: Eleanor

last: Riley

last: Goodier


title: Irf6 wildtype and knock out ATAC-seq

city: South San Francisco

first: Rohit

last: Reja

address: 1 DNA Way

institute: Genentech

summary: The integrity of the mammalian epidermis is essential for organism survival, and it depends on a balance of proliferation and differentiation in the resident stem cell population. The kinase Ripk4 and the transcription factor Irf6 are mutated in severe developmental syndromes in humans, and mice lacking these genes display epidermal hyperproliferation and soft tissue fusions, resulting in neonatal lethality. However, the mechanism by which these genes control epidermal differentiation in vivo is unknown. By generating various mouse knock-out and knock-in strains we demonstrate that in vivo the role of Ripk4 in development is dependent on its kinase activity, Ripk4 and Irf6 function cell autonomously in the epidermis,Ripk4 and Irf6 lie on a linear pathway and phosphorylation of Irf6 on Serine413 and Serine424 is essential to prime it for activation. This priming then allows Ripk4 to phosphorylate Irf6 on Serine90, which ensures Irf6 activation. We then use RNA-seq, ChIP-seq and ATAC-seq analysis to define the global transcriptional targets of Irf6 in epidermal differentiation. Collectively, our results explain how Ripk4 activates Irf6, and how this pathway ensures epidermal differentiation and a functional barrier. This is crucial for understanding the etiology of developmental syndromes that are characterized by orofacial, skin and genital abnormalities.

overall_design: ATAC-seq was performed on the following genotypes in two replicates: Irf6 wildtype and Irf6 knock out.

first: N

last: Oberbeck

first: R


title: RNAseq E16.5 mouse skin Irf6 KO vs WT

overall_design: RNA was extracted from kinase dead skin of E16.5 mouse embryos for the following genotypes - wildtype (WT), Irf6 knockout (Irf6KO).


title: HMGA2-driven gene expression in human colorectal DLD-1 cells.

city: New Taipei City

first: Pei-Ming

last: Yang

address: No. 301, Yuantong Rd., Zhonghe Dist.

department: Graduate Institute of Cancer Biology and Drug Discovery

country: Taiwan

institute: Taipei Medical University

summary: Gene expression analysis of stable HMGA2-overexpressing DLD-1 cells (DLD-1-HMGA2) and its control cells (DLD-1-Vector).

overall_design: Stable HMGA2-overexpressing DLD-1 (DLD-1-HMGA2) and the corresponding vector-overexpressing (DLD-1-Vector) cell lines were established by transfecting tGFP-tagged pCMV6-HMGA2 and pCMV6-AC-GFP plasmids, respectively, and then stable clones were selected with 1 mg/mL G418. Stable cells were maintained in medium containing 0.5 mg/mL G418. Total RNA from untreated cells were prepared form microarray analysis.


title: Ketogenic diet activates protective γδ T cell responses against influenza virus infection

city: New Haven

first: Emily

last: Goldberg

state: CT

address: 310 Cedar Street

institute: Yale

summary: Influenza A virus (IAV) infection-associated morbidity and mortality are a key global healthcare concern, necessitating the identification of novel therapies capable of reducing the severity of IAV infections. In this study, we show that the consumption of a low-carbohydrate, high-fat ketogenic diet (KD) protects mice from lethal IAV infection and disease. KD feeding resulted in an expansion of γδ T cells in the lung that improved barrier functions, thereby enhancing anti-viral resistance. Expansion of these protective γδ T cells required metabolic adaptation to a ketogenic diet, as neither feeding mice a high-fat high-carbohydrate diet nor providing chemical ketone body substrate that bypasses hepatic ketogenesis protected against infection. Therefore, KD mediated immune-metabolic integration represents a viable avenue towards preventing or alleviating influenza disease.

overall_design: We profiled IAV-infected whole lung tissue and gdT cells sorted from infected lungs 3 days post-infection.

first: Ryan

middle: D

last: Molony

first: Eriko

last: Kudo

first: Sviatoslav

last: Sidorov

first: Yong

last: Kong

first: Vishwa

last: Dixit

first: Akiko

last: Iwasaki


title: RNAseq E15.5 mouse skin WT, Irf6 KO, Ripk4 KD, and Irf6 S413A.S424A knockin

overall_design: RNA was extracted from kinase dead skin of E15.5 mouse embryos for the following genotypes - wildtype (WT), Irf6 knockout (Irf6KO), Ripk4 knockout (Ripk4KD), and Irf6 S413A.S424A knockin (Irf6.S413A.S424A).


title: Ripk4-Irf6 signaling axis ensures differentiation and barrier function

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

overall_design: Refer to individual Series


title: Irf6 wildtype and knock out ChIP-seq

overall_design: ChIP-seq of 3 histone modifications (H3K4me3, H3K27ac, H3K27me3)was performed on the following genotypes in two replicates: Irf6 wildtype and Irf6 knock out. We had one pooled input sample as control.


title: N6-Methyladenosine Modification Controls Circular RNA Immunity.

city: Stanford

first: Howard

last: Chang

address: 269 Campus Drive

institute: Stanford University School of Medicine

summary: Identification of m6A modification sites on circRNAs in Hela cells.

overall_design: 3 replicates from HeLa cells expressing either circRNAs generated by endogenous splicing or autocatalytic splicing mechanisms.

first: James

last: Broughton

first: Ye

middle: G

last: Chen

middle: Y


title: Transcriptome characterization of embryogenesis at a single cell resolution [Acrobeloides nanus]

city: Vienna

first: Alison

last: Cole

address: Djerassiplatz 1

department: Neurosciences and Developmental Biology

country: Austria

institute: University of Vienna

summary: By collecting and processing individual embryonic cells from sequentially older embryos we have generated the first comparative single cell transcriptome dataset describing embryogenesis.

overall_design: Embryos from approximately the first 450 minutes of embryonic development were collected. Individual embryos were dissociated manually and single cells or small chuncks of cells were collected for processing. Each sample was barcoded, and samples were multiplexed into sequencing libraries.

first: Itai

last: Yanai


title: Characterisation of young, old and old repopulating microglia in spinal cord and brain of C57BL/6 wild type male mice

first: Sophie

last: Brachat

summary: To address whether, after depletion by Csf1r inhibition, microglia repopulating the CNS revert to a “younger” phenotype, we treated a group of 23 months old mice with the Csf1r inhibitor for 5 days and let microglia repopulate the central nervous system for 7 days. Young (3 months old) and old (23 months old) mice were included as controls. After the repopulation time, whole spinal cord samples and Fluorescence Activated Sorting (FACS)-sorted microglia cells from brain tissue were collected to perform bulk transcriptome (RNAseq) analysis. Analysis of whole spinal cord suggested that repopulating microglia tend to re-acquire its original aged phenotype. Gene expression in FACS-sorted microglia was then analyzed to better characterize its intrinsic phenotype after repopulation. In contrast to the whole spinal cord samples, old and old-treated replicates separated in Principal Component Analysis, suggesting that repopulating microglia displayed a different phenotype compared to old microglia.

overall_design: NGS based mRNA profiling of whole spinal cord and FACS-sorted microglia of young (3 months), old and old repopulating (23 months) samples. 8 replicates per group were used.

first: Elisa

last: Giorgetti

first: Marc

last: Altofer

first: Ulrike

last: Naumann

first: Mark

last: Nash


title: Expression profiling analysis of  fungus Penicillium oxalicum wild type strain and its Podot1 deletion strain.

city: Jinan

first: Yanan

last: Li

address: Shanda south road 27

institute: Shandong University

summary: The goals of this study are to compare different gene expressions for Penicillium oxalicum wild type strain (WT), and Podot1 knockout strain (ΔPodot1) in different carbon sources. The deletion of Podot1 downregulated genes involved in the septin complex, extracellular region, and interspecies interaction between organisms when strains were cultivated with 2% glucose as carbon sources, and downregulated genes involved in cellulase activity, cellulose binding, glucosidase activity, and polysaccharide catabolic process when strains were cultivated with 1% microcrystalline cellulose and 1% wheat bran as carbon sources. We find the extracellular region was downregulated under both different carbon sources in ΔPodot1. This study provides the information that PoDot1 function are required in mycelial development and hydrolase activity of P. oxalicum.

overall_design: Examination of differential gene expressions by digital gene expression tag profiling in Penicillium oxalicum wild type strain and Podot1 knockout mutant strains in 24h in modifeid Mendal’s medium with 2% glucose or 1% cellulose and 1% wheat bran as carbon sources.Three replicates were included for each samples.

first: Yuqi

last: Qin


title: TNF-a induced gene expression in epithelial cell lines

status: Public on Aug 28 2019

city: Spring House

first: Matthew

last: Loza

state: PA

address: 1400 McKean Rd

department: Immunology - Biomarkers

institute: Janssen R&D, LLC

summary: TNF-a is elevated in a variety of inflammatory disease involving epithelial tissues.  To better understand the the impact of TNF-a on epithelial biology, 3 epithelial cell lines were cultured with and without TNFa and the transcriptomes compared using were profiled using Affymetrix GeneChip® HG-U133+2 array or HG-U133+PM arrays.

overall_design: Three epithelial cell lines (A549, HT-29, 293) and K562 (mylegenous leukemia) cell line were cultured in 6 replicates for 4 hrs with and without TNF-a and transcriptomes were assessed using Affymetrix GeneChip HT HG-U133+ PM 96 array plates. A list of genes from TNF-stimulated cultured primary human keratinocytes were also obtained for the experiment (original historical dataset not available). Data from K562 were not included in the summary gene set for TNF stimulation.


title: Single-cell transcriptomic analysis of the scrib mutant wing imaginal discs

status: Public on Aug 27 2019

city: Hong Kong

first: Yan

last: Yan

address: Clear Water Bay

department: LIFS

institute: HKUST

summary:
Investigation of intratumor heterogeneity  in the scrib¹ mutant wing imaginal discs.
Method: Staged scrib¹ wing imaginal discs were dissected and transferred to DPBS. The wing imaginal discs were dissociated in 0.25% Trypsin-EDTA solution at 37 ℃ for 10 min. Cells were then washed in DPBS and passed through 35μm filter before library preparation. Construction of 10x single cell libraries and sequencing on Illumina platform were performed by Novogene.

overall_design: 10X  based single-cell mRNA profiles of 4, 5, 8, 14-day scrib mutant wing imaginal discs from prolonged larval stages.

first: Lina

last: Zhang

first: Wang

last: Ying

first: Mingxi

last: Deng


title: CSF-1 induced gene expression in human whole blood

summary: CSF-1 is a key regulator of the macrophage lineage.  Macrophages are key mediators of inflammation, cancer, and homeostasis and in some cases differentiate from infiltrating blood monocytes.   To better understand the the impact of CSF-1 on blood monocytes, transcriptomic changes in ex vivo cultured human whole blood were measured 4 and 24 hrs after addition of CSF-1 and compared to blood cultured without adding CSF-1.  The expression of more than 50 genes was induced with geometric means >2-fold relative to unstimulated control conditions (p<0.05) at either 4 or 24 hrs.

overall_design: Blood from 3 healthy donors was cultured ex vivo with and without supplementation with 50 ng/ml CSF-1 and total RNA was isolated at 4 and 24 hrs and submitted to microarray analysis using GeneChip HT HG-U133+ PM 96 array plates.


title: K5 capsule and lipopolysaccharide are important in resistance to T4 phage attack in probiotic E. coli strain Nissle 1917

city: Würzburg

first: Richa

last: Bharti

state: Bavaria

address: Josef-Schneider-Straße 2 / Bau D15

department: IMIB,Core Unit Systemmedizin

institute: University of Wuerzburg

summary: Rapidly growing antibiotic resistance among gastrointestinal pathogens, and the ability of antibiotics to induce the virulence of these pathogens makes it increasingly difficult to rely on antibiotics to treat gastrointestinal infections. The probiotic E. coli strain Nissle 1917 (EcN) is the active component of the pharmaceutical preparation Mutaflor® and has been successfully used in the treatment of gastrointestinal disorders. Gut bacteriophages are dominant players in maintaining the microbial homeostasis in the gut, however, their interaction with incoming probiotic bacteria remains to be at conception. The presence of bacteriophages in the gut makes it inevitable for any probiotic bacteria to be phage resistant, in order to survive and successfully colonize the gut. This study addresses the phage resistance of EcN, specifically against lytic T4 phage infection. From various experiments we could show that i) EcN is resistant towards T4 phage infection, ii) EcN’s K5 polysaccharide capsule plays a crucial role in T4 phage resistance and iii) EcN’s lipopolysaccharide (LPS) inactivates T4 phages and notably, treatment with the antibiotic polymyxin B which neutralizes the LPS destroyed the phage inactivation ability of isolated LPS from EcN. Our results further indicate that N-acetylglucosamine at the distal end of O6 antigen in EcN’s LPS could be the interacting partner with T4 phages.  From our findings, we have reported for the first time, the role of EcN’s K5 capsule and LPS in its defense against T4 phages. In addition, by inactivating the T4 phages, EcN also protects E. coli K-12 strains from phage infection in tri-culture experiments. The combination of the identified properties is not found in other tested commensal E. coli strains. Furthermore, our research highlights phage resistance as an additional safety feature of EcN, a clinically successful probiotic E. coli strain.

overall_design: EcN culture (1e8 CFUs/ml) and 100 µl of a phage extract (~1e8 pfus/ml) were added to final volume of 1 ml LB medium in a 24 well plate. The plates were incubated in a static manner for 2 h of time at 37 °C.

first: Manonmani

last: Soundararajan

first: Tobias

last: Oelschlaeger


title: DUX4-induced histone variants H3.X and H3.Y mark DUX4 target genes for expression (CUT&RUN)

first: Stephen

last: Tapscott

summary: We determined the effects of short pulses of DUX4 expression on genome-wide transcription, mimicking the embryonic expression of this gene, using a DUX4-inducible cell culture model of FSHD (MB135iDUX4). We found that a second pulse of DUX4 has a synergistic effect and shows greater induction of DUX4 targets. Knockdown of DUX4-induced histone variants H3.X and H3.Y has no effect on DUX4 targets with a single pulse of DUX4 but eliminates the superinduction seen with a second pulse, showing that these histones are required for this increase in expression.

overall_design: genome-wide incorporation of histone variants H3.X and H3.Y in MB135iDUX4 myoblasts with overnight DUX4 induction, in triplicate, as well as IgG control

first: Rebecca

last: Resnick

first: Chao-Jen

last: Wong

first: Peter

last: Skene

first: Sandra

last: Hake

first: Steven

last: Henikoff

first: Silvere

last: van der Maarel


title: the CDP-Etn pathway accelerates mesenchymal-to-epithelial transition in somatic cell reprogramming

status: Public on Aug 25 2019

city: guangzhou

first: Yi

last: Wu

state: guangdong

address: Kaiyuan road 190

institute: guangzhou institutes of biomedicine and health

summary: Metabolic reprogramming has emerged as key regulators of cell fate decisions. Whereas the glucose and amino acid metabolism have been extensively documented, the roles of lipid metabolism in pluripotency remain largely unexplored. Here, we report that the CDP-Ethanolamine (CDP-Etn) pathway for phosphatidylethanolamine synthesis is required for somatic cell reprogramming at the early stage. Mechanistically, the CDP-Etn pathway inhibits NF-κB signaling and mesenchymal genes in a Pebp1 dependent manner, resulting in accelerated mesenchymal-to-epithelial transition and enhanced reprogramming. In addition, we show that phospholipids are critical for the growth of mESC though without effects on pluripotency. Our study reveals an unforeseen connection between phospholipids, cell migration and pluripotency and highlights the importance of phospholipids in cell fate transitions.

overall_design: We inhibited the CDP-Etn pathway by shRNAs (shEtnk1/2 or shPcyt2) or Etn deprivation in MEFs undergoing reprogramming and performed RNA-seq. We also knocked down Pebp1 using shPebp1 with or without Etn and performed RNA-seq to determine whether Etn functions in a Pebp1-dependent manner.

first: Keshi

last: Chen

first: Xingguo

last: Liu


title: Transcriptional characterization of intestinal ILC3 lacking BMAL1

first: Gregory

last: Putzel

address: 430 East 29th Street

department: Microbiology

institute: NYU Langone Health

summary: Small intestinal group 3 innate lymphoid cells (ILC3) from ILC3-conditional BMAL1 knock out mice or littermate control mice were sort-purified for transcriptional analysis

overall_design: ILC3 were sort-purified by flow cytometry from small intestinal lamina propria of 7-9 weeks old BMAL1 conditional KO mice and littermate control. Sorted cells were used to prepare RNA-seq libraries by using the Clontech SMARTer Ultra Low Input RNA Kit V4 (Clontech Laboratories).

first: Fei

last: Teng

middle: F

last: Sonnenberg


title: Cap analysis gene expression (CAGE) of Aspergillus luchuensis mut. kawachii control and laeA disruptant strains

status: Public on Aug 15 2019

city: Kagoshima

first: Taiki

last: Futagami

address: Korimoto 1-21-24

department: Department of Agriculture

institute: Kagoshima University

summary: LaeA, a putative methyltransferase, is a global regulator for metabolic and development process in filamentous fungi. We characterized the laeA homologous genes in the white koji fungus, Aspergillus luchuensis mut. kawachii (A. kawachii) to examine their role in citric acid production. The ΔlaeA strain showed a significant reduction in the citric acid productivity. The cap-analysis gene expression (CAGE) revealed the laeA is required for the gene expression of a putative citrate exporter encoding cexA, which has a critical role for the citric acid production. The deficient citric acid productivity of the ΔlaeA strain was remedied by overexpression of cexA to a comparative level to that of the cexA overexpressing ΔcexA strain. In addition, chromatin immunoprecipitation coupled with quantitative PCR (ChIP-qPCR) analysis indicated that LaeA regulates gene expression of the citrate exporter encoding cexA gene via histone H3K4 and histone H3K9 methylation levels. These results indicate that LaeA is involved in the citric acid production through epigenetic regulation of cexA in A. kawachii.

overall_design: CAGE profiles of Aspergillus luchuensis mut. kawachii control and laeA disruptant strains were investigated by Illumina NextSeq 500.

first: Chihiro

last: Kadooka


title: A miR-23~27~24 regulon that controls follicular helper T cell differentiation

status: Public on Aug 21 2019

city: La Jolla

first: Li-Fan

last: Lu

state: CA

address: 9500 Gilman Dr., NSB 5314

department: Biological Sciences

institute: University of California, San Diego

summary: Follicular helper T (Tfh) cells are essential for generating protective humoral immunity. To date, microRNAs (miRNAs) have emerged as important players in regulating Tfh cell biology. Here, we show that loss of miR-23~27~24 clusters in T cells resulted in elevated Tfh cell frequencies upon different immune challenges whereas overexpression of this miRNA family led to reduced Tfh cell responses. Mechanistically, miR-23~27~24 clusters coordinately control Tfh cells through targeting a network of genes that are crucial for Tfh cell biology. Among them, thymocyte selection-associated HMG-box protein (TOX) was identified as a central transcription regulator in Tfh cell development. TOX is highly up-regulated in both mouse and human Tfh cells in a BCL6-dependent manner. In turn, TOX promotes the expression of multiple molecules that play critical roles in Tfh cell differentiation and function. Collectively, our study on miR-23~27~24-mediated control of humoral immunity reveals a TOX-driven regulatory circuit in orchestrating Tfh cell responses.

overall_design: CD44-CD4+ naive T cells (Tn), CD44+PSGL1hiCXCR5-CD4+ T cells (Th1), CD44+PSGL1intCXCR5+CD4+ T cells (Tfh) and CD44+PSGL1loCXCR5+CD4+ T cells (GC-Tfh) isolated from LCMV-infected mice with T cell-specific deletion of both miR-23~27~24 clusters or WT littermates

first: Cheng-Jang

first: Sunglim

last: Cho

first: Hsi-Yuan

last: Huang

first: Chun-Hao

first: Jasmin

last: Russ

first: Leilani

middle: O

last: Cruz

first: Flavia

last: da Cunha

first: Mei-Chi

first: Ling-Li

last: Lin

first: Lindsey

last: Warner

first: Daniel

last: Utzschneider

first: Sara

last: Quon

first: Niels

last: Saraiva Camara

first: Li-Chen

first: Ming-Ling

last: Kuo


title: Spatial Transcriptomics of Human Cardiac Tissue

city: Lund

first: Olof

last: Gidlof

address: Solvegatan 19

country: Sweden

institute: Lund University

summary: Transplanted (healthy) and explanted human heart tissue sections (affected by different heart failure etiologies) were investigated for gene expression differences by using the Spatial Transcriptomics technology.

overall_design: Spatial transcriptomics analysis of biopsies from normal and hypertrophic, dilated and ischemic cardiomyopathy patients.

last: Gidlöf

first: Gustav

last: Smith


title: The Molecular Landscape of ETMR at Diagnosis and Relapse [methylation]

status: Public on Aug 26 2019

city: Heidelberg

first: Marcel

last: Kool

address: Im Neuenheimer Feld 280

department: Pediatric Neurooncology

institute: German Cancer Research Center DKFZ

summary: ETMRs are aggressive pediatric embryonal brain tumors with universally dismal outcome. We collected 193 ETMR samples and an additional 23 matched relapses to investigate the genomic landscape of this distinct entity. We found that patients having tumors without C19MC amplification, the proposed driver, frequently harbor DICER1 germline mutations or other miRNA-related aberrations such as somatic miR-17-92 miRNA cluster amplifications. Despite these distinct genetic aberrations, no molecular subgrouping was observed. Whole-genome sequencing revealed an overall low recurrence of SNVs, but prevalent R-loop-associated chromosomal instability, of which we show that this can be induced by loss of DICER1 function. Comparing primary tumors and matched relapses revealed a strong conservation of SVs but low conservation of SNVs. Moreover, many newly acquired SNVs are associated to a new cisplatin treatment related mutational signature. Finally, we show that targeting R-loops with topoisomerase and PARP inhibitors might be an effective treatment strategy for this deadly disease.

overall_design: 193 unique samples and 23 matched recurrences were profiled using either Illumina 450K arrays or EPIC arrays and both copy numbers and methylation clustering was investigated.

first: Sander

last: Lambo


title: Gene expression from ErbB2-driven mamamry tumors (MMTV-NIC model) with beta 1 integrin KO, beta 3 integrin KO or beta 1/beta 3 double KO

status: Public on Aug 23 2019

city: Montreal

first: Tung

last: Bui

state: Quebec

address: 1160 Pine Ave. W, R507

department: Biochemistry

institute: McGill University

summary:
In this study, we used conditional knockout and gene expression approaches to understand global molecular and transciptional changes due to ablation of each integrin subunit.
Affymetrix MoGene-2_0-st-v1 gene chip

overall_design: Beta 1 integrin and/or beta 3 integrin were specifically deleted in the mammary epithelium of MMTV-NIC mice. Total RNA was collected from end-burden tumors (flash frozen) and subjected to microarray gene expression. Data acquisition was performed by Quebec Genome Inovative Centre, McGill University.