title: Three-component mixed cell lines RNA-seq experiment

city: Houston

first: Wenyi

state: TX

address: Unit 1410 1400 Pressler

institute: The University of Texas MD Anderson Cancer Center

summary: To generate this dataset in RNA-seq, we performed a mixing experiment, in which we mixed mRNAs from three cell lines: lung adenocarcinoma in humans (H1092), cancer-associated fibroblasts (CAFs) and tumor infiltrating lymphocytes (TIL), at different proportions to generate 32 samples, including 9 samples that correspond to three repeats of a pure cell line sample for three cell lines. The RNA amount of each tissue in the mixture samples was calculated on the basis of real RNA concentrations tested in the biologist’s lab. This dataset was generated in house and then used to generate the count table that counts the number of reads mapped to each exon for all the samples. This count data will be pre-processed by total count normalization and genes that contained zero counts are removed.

overall_design: We run the RNA samples at 8-plex/lane at the Illumina sequencing core. We fit 4 sequencing lanes for 32 samples total at 76bp PE, and prepare 2 lanes for each sample.

first: Zeya

first: Shaolong

last: Cao


title: Effect of Influenza virus infection on lncRNA expression in A549 cells

status: Public on Oct 12 2018

city: Stillwater

first: CHAOQUN

last: HUANG

state: OK

address: 264 McElroy Hall

department: Physiological Sciences

country: USA

institute: Oklahoma State University

type: Expression profiling by high throughput sequencing

type: Non-coding RNA profiling by high throughput sequencing

summary: Long non-coding RNAs (lncRNAs) are a new arm of gene regulatory mechanism as discovered by sequencing techniques and follow-up functional studies. There are only few studies on lncRNAs as related to gene expression regulation and anti-viral activity during influenza virus infection. We sought to identify and characterize lncRNAs involved in influenza virus replication. In the current study, we identified dys-regulated lncRNAs in influenza virus-infected human lung epithelial A549 cells using RNA sequencing in A549 cells.

overall_design: RNA sequencing of A549 cells with Influenza virus and MOCK infection.

first: Chaoqun

last: Huang

first: Lin

last: Liu

first: Sunil

last: More


title: Rbfox1 mediates cell-type specific splicing in cortical interneurons

city: New York City

first: Alireza

last: Khodadadi-Jamayran

state: NY

address: 550 1st Ave, MSB 304

department: Division of Advanced Research Technologies (DART)

institute: New York University, NYU Langone Medical Center

summary: Cortical interneurons display a remarkable diversity in their morphology, physiological properties and connectivity. Elucidating the molecular determinants underlying this heterogeneity is essential for understanding interneuron development and function. We discovered that alternative splicing differentially regulates the integration of somatostatin- and parvalbumin-expressing interneurons into nascent cortical circuits through the cell-type specific tailoring of mRNAs. Specifically, we identified a role for the activity-dependent splicing regulator Rbfox1 in the development of cortical interneuron subtype specific efferent connectivity. Our work demonstrates that Rbfox1 mediates largely non-overlapping alternative splicing programs within two distinct but related classes of interneurons.

overall_design: RNA-seq of FACS sorted PV+ and SST+ cortical interneuronals at P8 of wt and conditional Rbfox1 Kos

first: Brie

last: Wamsley

first: Xavier

middle: H

last: Jaglin

first: Gord

last: Fishell


title: Dissection of uniparental reproduction barriers in mice using haploid embryonic stem cells [RNA-Seq]

city: Beijing

first: Qi

last: Zhou

address: Datun Road, Chaoyang District

country: China

institute: Institute of Zoology,CAS

type: Methylation profiling by high throughput sequencing

summary: Uniparental reproduction is widespread among lower vertebrates, but not in mammals. Researchers have produced bimaternal mice with a deletion of the H19 imprinted region. However, the mechanism of a single deletion in an immature oocyte sufficient to cross uniparental barriers is unknown. We found bimaternal-derived mice to be defective in multiple aspects. More importantly, bipaternal reproduction has not been achieved in mammals. Thus, the barrier of uniparental reproduction in mammals has not been elucidated. We identified a DNA hypomethylation status in haploid embryonic stem cells similar to that in primordial germ cells, with which bimaternal and bipaternal mice can be obtained by injection of haploid ES cells with genetic modifications. The phenotypic analyses of derived mice support the genetic conflict theory of genomic imprinting. Taken together, our results highlight the factors necessary for crossing uniparental reproduction barriers in mammals.

overall_design: mRNA profiles of different type mouse embryos, brains and ESCs were generated by RNA sequencing using Illumina HiSeq 2500. The differentially methylated regions (DMRs) modified haploid ESCs were used to produce the embryos, including KO2 (knocking out H19-DMR and IG-DMR), KO3 (knocking out H19-DMR, IG-DMR, and Rasgrf1-DMR) as well as KO7 (knocking out Nespas-DMR, Grb10-DMR, Igf2r-DMR, Snrpn-DMR, Kcnq1-DMR, Peg3-DMR and Gnas-DMR) samples.

first: Zhi-Kun

last: Li

first: Le-Yun

last: Wang

first: Li-Bin

first: Gui-Hai

last: Feng

first: Xue-Wei

last: Yuan

first: Wei

first: Bao-Yang

last: Hu


title: SHP2 Drives Adaptive Resistance to ERK Signaling Inhibition in Molecularly Defined Subsets of ERK-dependent Tumors

city: Oakland

first: Ravi

last: Sachidanandam

state: CA

address: 2945 Webster St

institute: Girihlet Inc.

summary: We performed RNA sequencing analysis using NextSeq500 to identify drivers that mediate feedback RAS activation in BRAF(V600E) cells that are SHP2 independent.

overall_design: mRNA expression of three BRAF (V600E) cancer cells was examined before and after treatment with vemurafenib (RAF inhibitor) using NextSeq500


title: Variants in PUS7 cause intellectual disability with speech delay, microcephaly, short stature, and aggressive behavior

status: Public on Oct 13 2018

city: Rehovot

first: Schraga

last: Schwartz

state: Choose a State or Province

address: Herzl 234, Department of Molecular Genetics

country: Israel

institute: WEIZMANN INSTITUTE OF SCIENCE

summary: We describe six patients from three families with three homozygous protein truncating variants in PUS7: c.89_90del, p.(Thr30Lysfs20*); c.1348C>T, p.(Arg450*); and a deletion of the penultimate exon 15. All patients have intellectual disability with speech delay, short stature, microcephaly, and aggressive behavior. PUS7 encodes the RNA-independent pseudouridylate synthase 7. Pseudouridylation is the most abundant post-transcriptional modification in RNA, which is primarily thought to stabilize secondary structures of RNA. We show that the disease-related variants lead to abolishment of PUS7 activity on both tRNA and mRNA substrates. Moreover, Pus7 knockout in Drosophila melanogaster results in a number of behavioral defects, including increased activity with slower walking speed and disorientation supporting that neurological defects are caused by PUS7 variants. Our findings demonstrate that RNA pseudouridylation by PUS7 is essential for proper neuronal development and function.

overall_design: Mapping of pseudouridylation in WT versus pus7 mutants in drosophila samples.


title: SUMOylation of ROR-gt inhibit IL-17 expression and inflamatiion

city: Dallas

first: Uthra

last: Balaji

state: Texas

address: 3434 Live Oak St

department: Biostatistics Core

institute: Baylor Scott & White Research Institute

summary: RNA sequencing of ROR-gt-/- mouse-derived T cells reconstituted with either WT-ROR-gt or mutant (SUMOylation-defective ROR-gt)

overall_design: transcriptomic profiles of 4 WT and 4 mutant mice were analyzed using high-throughput RNA-sequencing data

first: Venuprasad

last: Poojary


title: Dissection of uniparental reproduction barriers in mice using haploid embryonic stem cells [RRBS]

overall_design: Reduced representation bisulfite sequencing (RRBS) for a global DNA methylation analysis of wild type (WT) or the differentially methylated region knocking out (DMR-KO) haploid ESCs androgenetic haploid ESCs (ahESC), parthenogenetic haploid ESCs (phESCs), diploid ESCs, embryos and brain tissue. Compared to wild type (WT) embryo, which was produced by normal zygote deriving  from normal sperm and oocyte, the bimaternal (BM) embryo was produced through injecting a phESC into an MII oocyte and the bipaternal (BP) embryo was produced through injecting injecting an ahESC and a sperm into an enucleated oocyte.


title: Genome-wide CRISPR-Cas9 interrogation of splicing networks reveals a mechanism for recognition of autism-misregulated neuronal microexons

city: Toronto

first: Ulrich

last: Braunschweig

state: Ontario

address: 160 College Street

department: Donnelly Centre

country: Canada

institute: University of Toronto

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

sample_organism:
Mus musculus
synthetic construct

platform_organism:
Mus musculus
synthetic construct

overall_design: Refer to individual Series


title: Transcriptomic but not genomic variability confers phenotype of breast cancer stem cells

city: Dalian

first: Meng ying

last: Tong

state: Liaoning

address: Longtou Street

institute: Dalian Medical University

summary:
Background: Breast cancer stem cells (BCSCs) are considered responsible for cancer relapse and drug-resistance. Understanding the identity of BCSCs may open new avenues in breast cancer therapy. Although several discoveries have been made on BCSCs characterization, the factors critical to BCSCs is largely unclear. This study was aimed to determine whether genomic mutation contributes to the acquisition of cancer stem-like phenotype, and to investigate the genetic and transcriptional features of BCSCs.
Methods: We detected the potential mutation hotspot regions by using whole genome sequencing on parental cancer cells and derived serial-generation spheroids in increasing order of BCSC frequency, and then performed target deep DNA sequencing in the level of bulk-cell and single-cell. To identify the transcriptional program associated with BCSCs, bulk-cell and single-cell RNA sequencing were performed.
Results: By analyzing whole genome sequencing of bulk cells, potential BCSCs associated mutation hotspot regions were detected. Validation by target deep sequencing, in both bulk-cell and single-cell levels, revealed no genetic changes specifically associated with BCSC phenotype. Moreover, single-cell RNA sequencing showed that cancer cells display profound transcriptional variability at the single-cell level that predicts BCSC features. Notably, this transcriptomic variability is enriched in transcription of a number of genes, revealed as BCSC markers. Individuals with breast cancer in a high-risk recurrence group exhibited higher expression of these transcriptomic variabilities, highlighting their clinical significance.
Conclusions: Transcriptional variability, not genetic mutations, distinguish BCSCs from non-BCSCs. The identified BCSCs markers can become novel targets for BCSCs.

overall_design: To identify the transcriptional program associated with BCSCs, bulk-cell and single-cell RNA sequencing was performed on both spheroids and cells that cannot give rise to spheroid.

first: Quentin

last: Liu

first: Ziqian

last: Deng


title: Genome wide RNA-seq of wild-type  iBMDMs upon HSV-1 infection.

status: Public on Oct 11 2018

first: Shengde

address: 38 Xueyuan Rd , Haidian District

institute: Peking University Health Science Center

summary: Genome wide RNA-Seq screen was did to detect gene expression. We used  immortalized bone-marrow-derived macrophages cells that were uninfected or infected with HSV-1 for 6 hours to detect the expression levels of genes, and  we found that interferon stimulated genes were increased and some of genes that inhibit interferon production were decreased in HSV-1 infected iBMDMs, compared to wild-type iBMDMs. we choose some genes that are unknown about their functions on antiviral  innate immunity, and adress how they participate in antiviral  innate immunity.

overall_design: Wild-type iBMDM were infected with HSV-1 for 6 hours, and then  genome wide RNA-Seq screen to detect the expression of genes.

first: Fuping

last: You


title: Genome-wide CRISPR-Cas9 interrogation of splicing networks reveals a mechanism for recognition of autism-misregulated neuronal microexons [RNA-seq]

summary: Alternative splicing has critical roles in diverse cellular, developmental and pathological processes. However, the full repertoires of factors that control individual splicing events are not known. We describe a CRISPR-based screening strategy for the systematic identification of genes that control 3-27 nt microexons with functions in nervous system development and that are commonly disrupted in autism. Besides known regulators including nSR100/Srrm4, Rbfox and Ptbp1, approximately 200 additional genes impact microexon splicing. These genes are enriched in genetic links to autism. Two of the screen hits, Srsf11 and Rnps1, preferentially regulate Srrm4-dependent microexons relative to other exons. These factors form mutually stabilizing interactions with Srrm4 that bridge upstream intronic enhancer elements and exonic sequences to activate microexon splicing. Our study thus presents a system for the genome-wide definition of splicing regulatory networks and further reveals a mechanism for the recognition of microexons with critical roles in nervous system development and disorders.

overall_design: RNA-Seq of N2A cells upon RNAi-mediated knockdown of Rnps1, Srrm3 and Srrm4, Srsf11, Rbfox2, or control non-targeting knockdown, in two replicates.

first: Thomas

last: Gonatopoulos-Pournatzis

first: Mingkun

last: Wu

first: Jonathan

last: Roth

first: Hong

last: Han

first: Andrew

last: Best

first: Bushra

last: Raj

first: Michael

last: Aregger

first: Dave

last: O'Hanlon

middle: D

last: Ellis

first: John

middle: A

last: Calarco

first: Jason

last: Moffat

first: Anne-Claude

last: Gingras

first: Benjamin

middle: J

last: Blencowe


title: Quantifying post-transcriptional regulation in the development of Drosophila melanogaster

city: Mainz

first: Sergi

last: Sayols

address: Ackermannweg 4

country: Germany

institute: Institute of Molecular Biology, Mainz


title: Advantages of single nucleus over single cell RNA-seq in adult kidney

city: St. Louis

first: Haojia

state: Missouri

address: 600 S Euclid Ave

department: Renal Division/Internal Medicine

institute: Washington University in St. Louis

summary: A key limitation in single cell genomics is generating a high-quality single cell suspension that contains rare or difficult to dissociate cell types and is free of RNA degradation or transcriptional stress responses. Samples with unpredictable availability or that must be collected at several timepoints present additional challenges. Using adult mouse kidney, we compared single-cell RNA sequencing (scRNA-seq) data generated using DropSeq with snRNA-seq data generated from nuclei using sNuc-DropSeq, DroNc-seq and 10X Chromium. We validated snRNA-seq on fibrotic kidney from day 14 unilateral ureteral obstruction (UUO).

overall_design: Dropseq, sNucDropseq, DroNcSeq and 10X Chromium were used to profile mouse healthy and fibrotic kidneys

last: Humphreys


title: Next Generation Sequencing of human SMA and healthy control Motor Neurons

city: Bosisio Parini

first: Uberto

last: Pozzoli

state: LC

address: Via Don L. Monza, 20

department: Neurobiology, Computational Biology and Pharmacology

country: Italy

institute: Scientific Institute IRCCS E.Medea

summary: Spinal muscular atrophy (SMA) is a motor neuron (MN) disorder caused by mutations in SMN1. The reasons of MNs selective vulnerability linked to SMN reduction remain unclear. To address this question, we performed deep RNA sequencing on SMA human MNs to detect specific altered splicing/expressed genes and to identify the presence of a common sequence motif in these genes. Many deregulated genes, such as Neurexin and Synaptotagmin families, are implicated in critical MN-function like axonogenesis and synapses. Motif-enrichment analyses of differentially expressed/spliced genes, including Neurexin2 (NRXN2), revealed a common Motif, Motif-7, which is target of SYNCRIP protein. Interestingly, SYNCRIP interacts only with full-length SMN, binding and modulating several MN transcripts, including SMN itself. SYNCRIP overexpression rescued SMA-MNs, due to the consequent increase of SMN and their down-stream target NRXN2, through a positive loop mechanism. SMN/SYNCRIP complex through motif-7 might account for selective MN degeneration and represent a potential therapeutic target.

overall_design: total RNA collected from control iPSC and patient iPSC derived spinal motor neurons

first: Stefania

last: Corti


title: A novel Cpa3-Cre; miR-9∆fl/∆fl mouse reveals a functional role for miR-9 in promoting a mast cell invasive phenotype via upregulation of CMA1

city: Columbus

first: Joelle

middle: Marie

last: Fenger

state: Ohio

address: 601 Vernon L Tharp Street, OSU Veterinary Medical Center

department: Veterinary Clinical Sciences

institute: The Ohio State University

summary: The purpose of this study was to investigate the biologic consequences of miR-9 overexpression in normal mast cells and interrogate the mechanisms by which mir-9 enhances invasion.  We generated a transgenic mouse line carrying a floxed-STOP-miR-9 transgene (miR-9∆fl/∆fl) and crossed it with Cpa3-Cre transgenic mice in which Cre recombinase expression is restricted largely to mast cells and basophils, by the carboxypeptidase A3 (Cpa3) promoter. RNA-seq revealed a unique transcriptional profile associated with miR-9 overexpression in BMCMCs, notably up-regulation of mast cell-restricted proteases CMA1 and MCP6 involved in extracellular matrix remodeling. Targeting of the transcriptional corepressor SIN3A by miR-9 enhanced CMA1 expression, indicating a novel regulatory pathway through which miR-9 upregulates CMA1 expression, thereby promoting an invasive phenotype.  These data support a role for miR-9 in mast cell invasive properties and provide a mechanism through which dysregulation of miR-9 in mast cells may contribute to pathologic conditions involving mast cell-mediated tissue remodeling.

overall_design: Bone marrow-cultured mast cells (BMCMCs) were generated from age- and sex-matched Cpa3-Cre and Cpa3-Cre;miR-9∆fl/∆fl mice.  RNA-seq was performed at the OSUCCC Genomics Shared Resource using the Illumina HiSEq-2500 instrument at a depth of ∼70 million paired-end, 50bp long, strand-specific reads per sample.  Statistical analysis relative to mRNA expression data was performed using DESeq2 Software.  Differential gene expression was determined by one-way ANOVA and p-values of <0.0001 were considered statistically significant.

middle: M


title: Role of SOX4 in mouse embryonic neural stem cells (NSCs)

city: Utrecht

first: Paul

last: Coffer

address: Uppsalalaan 6

department: Regenerative Medicine Center

country: Netherlands

institute: UMC Utrecht

type: Genome binding/occupancy profiling by high throughput sequencing


title: Tri-mannose grafting of chitosan nanocarriers remodels the macrophage response to bacterial infection

city: Paris

first: Juan Manuel

last: Coya

address: 25-28 Rue du Dr Roux

country: France

institute: Institut Pasteur

summary:
Background: Infectious diseases are still a leading cause of death and, with the emergence of drug resistance, pose a great threat to human health. New drugs and strategies are thus urgently needed to improve treatment efficacy and limit drug-associated side effects. Nanotechnology-based drug delivery systems are promising approaches, offering hope in the fight against drug resistant bacteria. However, how nanocarriers influence the response of innate immune cells to bacterial infection is mostly unknown.
Results: Here, we used Mycobacterium tuberculosis as a model of bacterial infection to examine the impact of mannose functionalization of chitosan nanocarriers (CS-NCs) on the human macrophage response. Both ungrafted and grafted CS-NCs were similarly internalized by macrophages, via an actin cytoskeleton-dependent process. Although tri-mannose ligands did not modify the capacity of CS-NCs to escape lysosomal degradation, they profoundly remodeled the response of M. tuberculosis-infected macrophages. mRNA sequencing showed nearly 900 genes to be differentially expressed due to tri-mannose grafting. Unexpectedly, the set of modulated genes was enriched for pathways involved in cell metabolism, particularly oxidative phosphorylation and sugar metabolism.
Conclusions: The ability to modulate cell metabolism by grafting ligands at the surface of nanoparticles may thus be a promising strategy to reprogram immune cells and improve the efficacy of encapsulated drugs.

overall_design: Evaluation of host response to chitosan nanocarriers funtionalized or not with trimannose in infected and uninfected macrophages.

first: Juan

first: Ludovic

last: Tailleux


title: Genome-wide CRISPR-Cas9 interrogation of splicing networks reveals a mechanism for recognition of autism-misregulated neuronal microexons [CLIP-seq]

first: Ulrich

last: Braunschweig

overall_design: iCLIP-seq of Rnps1, Srsf11, or GFP in N2A cells, as well as Srrm4 and GFP in in-vitro differentiated neurons.

first: Thomas

last: Gonatopoulos-Pournatzis

first: Mingkun

last: Wu

first: Jonathan

last: Roth

first: Hong

last: Han

first: Andrew

last: Best


title: Dissection of uniparental reproduction barriers in mice using haploid embryonic stem cells

first: Qi

last: Zhou


title: Stable knockdown of PLAGL2 in hepatocellular carcinoma cells

city: Nanjing

first: Hu

last: Weiwei

address: No. 639, long Mian Road, Jiangning District, Nanjing

institute: China Pharmaceutical University

summary: Pleomorphic adenoma gene like-2 (PLAGL2), along with PLAG1 and PLAGL1, belong to PLAGL gene family of zinc-finger transcription factors, PLAG proteins are highly homologous, and with the structures of the seven C2H2 zinc finger domain on the N-terminal. PLAG proteins recognize similar GC rich consensus DNA-binding sequences, that these family members function as regulators of transcription target genes and pathways. PLAGL2 has been shown to have both oncogenic and tumor suppressor activities, PLAGL2 is mainly consided as a transcription factor, other functions which may contribute to its oncogenic potential are not clear. So it is meaningful to study the role of PLAGL2 in different diseases. To our knowledge, there is no report about the PLAGL2 in the development process of HCC.

overall_design: mRNA profile of Hepatocarcinoma cell line HCC-LM3 with shctrl and shPLAGL2 were generated by deep sequencing

first: Yong

last: Yang

first: Weiwei

last: Hu


title: Species and Cell-Type Properties of Classically Defined Human and Rodent Neurons and Glia [Mouse ATAC-Seq]

city: New York

first: Xiao

last: Xu

address: 1230 York Ave

department: Laboratory of Molecular Biology

institute: The Rockefeller University

summary: Determination of the molecular properties of genetically targeted cell types has led to fundamental insights into mouse brain function and dysfunction. Here, we report an efficient strategy for precise exploration of gene expression events in specific cell types in a broad range of species. We demonstrate that classically defined, homologous neuronal and glial cell types differ between rodent and human by the expression of hundreds of orthologous, cell specific genes. Confirmation that these genes are differentially active was obtained using epigenetic mapping, quantitative PCR, and immunofluorescence localization. Studies of sixteen human postmortem brains revealed cell-specific molecular responses to aging, and the induction of a shared, robust response to an unknown external event experienced by three donors. Our data establish a comprehensive approach for analysis of unique molecular events associated with specific circuits and cell types in a wide variety of human conditions.

overall_design: RNA purified from nuclei or cytoplasm from mouse, rat, or human cerebellum. ATAC-seq was also performed using cerebellar nuclei from the three species.

first: X

first: E

middle: I

last: Stoyanova

first: A

last: Lemiesz

first: J

last: Xing

first: D

middle: C

last: Mash

first: N

last: Heintz


title: Genome-wide CRISPR-Cas9 interrogation of splicing networks reveals a mechanism for recognition of autism-misregulated neuronal microexons [CRISPR screen]

first: Ulrich

overall_design: sgRNA sequencing in N2A cells expressing a fluorescent splicing reporter and infected with a CRISPR loss-of-function library, unsorted cells or sorted based on reporter

first: Bushra

last: Raj

first: Michael

last: Aregger

first: Dave

last: O'Hanlon

last: Ellis

first: John

last: Calarco

first: Jason

last: Moffat

first: Anne-Claude

last: Gingras

first: Benjamin

last: Blencowe


title: A cell atlas of mouse lung development reveals a signaling role for lung basophils in alveolar macrophage maturation

first: Ido

last: Amit

address: 234 Herzl st.

department: Immunology

institute: Weizmann Institute of Science

summary:
Lung development and function arises from the interactions between diverse cell types and lineages. Using single cell RNA-seq we characterize the cellular composition of the lung during development and identify vast dynamics in both the composition of cells and their molecular characteristics. Analyzing 818 ligand-receptor interaction pairs within and between cell lineages, we identify broadly interacting cells, including AT2, ILC and basophils. Using IL33-receptor knockout mice and in vitro experiments, we show that basophils establish a lung-specific function imprinted by IL-33 and GM-CSF, characterized by unique signaling of cytokines and growth factors important for stromal, epithelial and myeloid cell fates.
Antibody depletion strategies, diphtheria toxin–mediated selective depletion of basophils, and co-culture studies, show that lung resident basophils are important regulators of alveolar macrophage development and function. Together, our study demonstrates how whole tissue cell interaction analysis on the single cell level can broaden our understanding of cellular networks in health and disease.

overall_design:
Transcriptional profiling of single cells from the different  timepoints of lung development, generated from deep sequencing of tens of thousands of cells, sequenced in several batches on illumina Nextseq500
metadata.txt: Meta data file associating each single cell with its amplification batch and index sorting readouts

first: Merav

last: Cohen

first: Amir

last: Giladi

first: Anna-Dorothea

last: Gorki


title: Thyroid hormone signaling specifies cone subtypes in human retinal organoids

city: Baltimore

first: Robert

last: Johnston

state: MD

address: 3400 N Charles St, Mudd Hall Room 314

department: Biology

institute: Johns Hopkins University

summary: The mechanisms underlying specification of neuronal subtypes within the human nervous system are largely unknown. The blue/S, green/M and red/L cones of the retina enable high-acuity daytime and color vision. To determine the mechanism controlling S vs. L/M fates, we studied the differentiation of human retinal organoids. Organoids and retinas have similar distributions, expression profiles, and morphologies of cone subtypes. S cones are specified first, followed by L/M cones, and thyroid hormone signaling controls this temporal switch. Dynamic expression of thyroid hormone-degrading and activating proteins within the retina ensures low signaling early to specify S cones and high signaling late to produce L/M cones. This work establishes organoids as a model for determining mechanisms of human development with promising utility for therapeutics and vision repair.

overall_design: EP1 iPSC-derived organoids were analyzed at time points ranging from day 10 to day 250 of differentiation. We took samples at day 10 (n=3), day 20 (n=2), day 35 (n=3), day 69 (n=3), day 111 (n=3), day 128 (n=3), day 158 (n=2), day 173 (n=3), day 181 (n=3), day 200 (n=3), and day 250 7 (n=3). RNA from individual organoids was extracted using the Zymo Direct-zol RNA Microprep Kit (Zymo Research) according to manufacturer’s instructions. Individual libraries were prepared for each sample using the Illumina TruSeq stranded mRNA kit and sequenced on an Illumina NextSeq 500 with single 200 bp reads.

first: Kiara

last: Eldred

first: Sarah

middle: E

last: Hadyniak

first: Katarzyna

last: Hussey

first: Boris

last: Brenerman

first: Ping-Wu

last: Zhang

first: Xitiz

last: Chamling

first: Valentin

last: Sluch

first: Derek

middle: S

last: Welsbie

first: Samer

last: Hattar

first: James

last: Taylor

first: Karl

last: Wahlin

first: Donald

last: Zack

last: Johnston Jr


title: Comprehensive analysis of chromatin signature and transcriptome in nephron progenitor cells

city: North Hills

first: Masaki

last: Nishikawa

address: 16111 Plummer st

institute: UCLA / VA

summary: Examination of 2 different histone modifications in 3 cell types, and RNA sequence of 2 cell types.

first: Shunsuke

last: Yuri

first: Norimoto

last: Yanagawa


title: Argonaute2 attenuates active transcription by limiting RNA Polymerase II elongation in Drosophila melanogaster [ChIPseq-triptolide]

city: Bethesda

first: Cameron

last: Palmer

address: 50 South Drive

department: National Institute of Diabetes and Digestive and Kidney Diseases

institute: National Institutes of Health

summary: Increasing lines of evidence support that Argonaute2 (AGO2) harbors several nuclear functions in metazoa. In particular, Drosophila AGO2 modulates transcription of developmentally regulated genes; however, the molecular mechanisms behind AGO2 recruitment into chromatin and its function in transcription have not been deeply explored. In this study, we show that Drosophila AGO2 chromatin association depends on active transcription. In order to gain insight into how AGO2 controls transcription, we performed differential ChIP-seq analysis for RNA Polymerase II (Pol II) upon depletion of AGO2. Interestingly, we find specific accumulation of the elongating but not initiating form of Pol II after AGO2 knockdown, suggesting that AGO2 impairs transcription elongation. Finally, AGO2 also affects Negative Elongation Factor (NELF) chromatin association but not the Cyclin Dependent Kinase 9 (CDK9). Altogether, these results provide key insights into the molecular role of AGO2 in attenuating elongation of certain actively transcribed genes.

overall_design: ChIP-seq of AGO2 in Drosophila melanogaster Kc167 cells in mock treatment and triptolide (transcription inhibitor) treatment. Two replicates per condition, with paired inputs.

first: Ezequiel

last: Nazer

first: Elissa

middle: P

last: Lei


title: Argonaute2 attenuates active transcription by limiting RNA Polymerase II elongation in Drosophila melanogaster [ChIPseq-PolII-S5]

summary: Increasing lines of evidence support that Argonaute2 (AGO2) harbors several nuclear functions in metazoa. In particular, Drosophila AGO2 modulates transcription of developmentally regulated genes; however, the molecular mechanisms behind AGO2 recruitment into chromatin and its function in transcription have not been deeply explored. In this study, we show that Drosophila AGO2 chromatin association depends on active transcription. In order to gain insight into how AGO2 controls transcription, we performed differential ChIP-seq analysis for RNA Polymerase II (Pol II) upon depletion of AGO2. Interestingly, we find specific accumulation of the elongating but not initiating form of Pol II after AGO2 knockdown, suggesting that AGO2 impairs transcription elongation. Finally, AGO2 also affects Negative Elongation Factor (CDK9) chromatin association but not the Cyclin Dependent Kinase 9 (CDK9). Altogether, these results provide key insights into the molecular role of AGO2 in attenuating elongation of certain actively transcribed genes.

overall_design: ChIP-seq of RNA PolII S5 (serine 5 phosphorylated) in Drosophila melanogaster Kc167 cells in mock treatment, Ago2 knockdown, and LaminB knockdown. Two replicates per condition, with paired inputs.


title: Argonaute2 attenuates active transcription by limiting RNA Polymerase II elongation in Drosophila melanogaster [ChRIPseq-AGO2]

overall_design: ChRIP-seq of AGO2 in Drosophila melanogaster Kc167 cells. Three input replicates and two IP replicates (one removed as PCA outlier).


title: Argonaute2 attenuates active transcription by limiting RNA Polymerase II elongation in Drosophila melanogaster

overall_design: Refer to individual Series


city: Cork

first: Patrick

last: O' Connor

address: Western Gateway building

country: Ireland

institute: UCC

summary: Snapshot of translation in mammalian cells that are depleted of polyamines or replete with polyamines. Hek293T cells treated with DFMO or Spermidine.

overall_design: DFMO vs. Spermidine treatment

first: Ivaylo

last: Ivanov

first: Byung-Sik

last: Shin

first: Gary

last: Loughran

first: Sara

middle: K

last: Young-Baird

first: Ioanna

last: Tzani

first: Chune

last: Cao

first: John

middle: F

last: Atkins

first: Thomas

last: Dever


title: Argonaute2 attenuates active transcription by limiting RNA Polymerase II elongation in Drosophila melanogaster [ChIPseq-PolII-8WG16]

overall_design: ChIP-seq of RNA PolII 8WG16 (hypophosphorylated CTD) in Drosophila melanogaster Kc167 cells in mock treatment, Ago2 knockdown, and LaminB knockdown. Two replicates per condition, with paired inputs.


title: Argonaute2 attenuates active transcription by limiting RNA Polymerase II elongation in Drosophila melanogaster [ChIPseq-NELFE]

overall_design: ChIP-seq of NELF-E in Drosophila melanogaster Kc167 cells in mock treatment and Ago2 knockdown. Two replicates per condition, with paired inputs.


title: RNA and miRNA sequencing of an IGF1R transgenic mouse model of lung cancer

city: Guelph

first: Roger

last: Moorehead

address: 50 Stone Rd E

department: Biomedical Sciences

institute: University of Guelph

summary: RNA and miRNA sequencing of lung tumors induced by transgenic overexpression of the type-I insulin like growth factor receptor was carried out to examine the molecular changes associated with lung tumorigenesis and explore potential similarities with a collection of mouse lung cancer models and human non-small cell lung cancer.

overall_design: 4 tumor samples from SPC-IGF1R mice and 4 normal lung samples from non-transgenic (wild type) mice were used for RNA and miRNA sequencing for a total of 16 samples

first: Rob

last: Jones


title: Setd5 haploinsufficiency alters neuronal network connectivity and leads to autistic-like behaviors in mice

status: Public on Oct 10 2018

city: La Jolla

first: Jason

middle: Samuel

last: Seidman

address: 9500 Gilman Drive, Mail code 0651

department: Cellular and Molecular Medicine

institute: University of California San Diego

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


title: RNA-seq of bone marrow tissue of wild type and Elf4 deficient mice after Plasmodium yoelii 17XNL infection

city: Beijing

first: Zeming

last: Zhang

address: 38 Xueyuan Rd , Haidian District,Beijing,China

institute: Institude of Systems Biomedicine

summary: We infected wild type and Elf4 deficient mice with Plasmodium yoelii 17XNL, a non-lethal species, to investigate and compare anti-Plasmodium response of two groups of mice.

overall_design: 10-week old wild type and Elf4 deficient mice were intraperitoneally injected with 1x10^5 Plasmodium infected red blood cells as experiment group. Bone marrow tissues from uninfected mice (Day0) and mice infected for 2 days (Day2) were collected and used to carry out RNA-seq experiment.

first: Dandan

last: Wang

first: Fuping

last: You


title: Comparative analysis of WT and ZEB1 KO cells in different stages during differentiation

first: Xiangxiang

last: Jiang

state: Beijing

address: 1 Beichen West Road, Chaoyang District

institute: Institute of Zoology, Chinese Academy of Sciences

summary: We performed RNA-Seq and identified the differnetially expressed gene information among WT and ZEB1 KO cells

overall_design: mRNA profiles between 2 cell types during differentiation

first: Hongmei

first: Yuan

first: Long

last: Yan


title: Epigenetic reprogramming of melanoma cells by vitamin C treatment

city: Provo

first: David

middle: Wayne

last: Sant

state: UT

address: 1712 South East Bay Blvd, Building 5 Suite 300

department: Biomedical Informatics

institute: Noorda College of Osteopathic Medic

summary: In this study we show that ascorbate (vitamin C) shifts the  transcriptome of melanoma cells, and decreases malignant phenotypes.

overall_design: Examination of transcriptome in vitamin C treated  or control A2058 melanoma cells

first: Gaofeng

middle: W

first: Chris

last: Gustafson


title: RNA-seq of spleen tissue of wild type and Elf4 deficient mice after Plasmodium yoelii 17XNL infection

overall_design: 10-week old wild type and Elf4 deficient mice were intraperitoneally injected with 1x10^5 Plasmodium infected red blood cells as experiment group. Spleen from uninfected mice (Day0) and mice infected for 2 days (Day2) were collected and used to carry out subsequent RNA-seq experiment.


title: Maintenance of nucleolar homeostasis by PC2 alleviates senescence and osteoarthritis

first: Zunpeng

last: Liu

address: Beichen West Road

department: Institute of Zoology, Chinese Academy of Sciences

institute: State Key Laboratory of Stem Cell and Reproductive Biology

summary: Polycomb 2 protein (PC2), a component of polycomb repressive complex 1 (PRC1), plays important roles in the maintenance of cell identity and organ development through epigenetic silencing. However, whether PC2 regulates the homeostasis of human stem cells remains unclear. Here, we demonstrate that PC2 counteracts human mesenchymal stem cell (hMSC) aging via the maintenance of nucleolar homeostasis. PC2 protein is decreased in aged hMSCs, and targeted PC2 knockout in young hMSCs results in destabilized nucleolar heterochromatin, increased ribosome biogenesis and protein translation, and accelerated cellular senescence. PC2 maintains nucleolar homeostasis by recruiting nucleolar protein fibrillarin and heterochromatin organization associated protein KAP1 at nucleolar rDNA, limiting the excessive expression of rRNAs. Importantly, overexpression of PC2 alleviates physiological hMSC aging and attenuates the development of posttraumatic osteoarthritis in mice. Taken together, our findings reveal a novel role of PC2 in counteracting senescence by maintaining nucleolar homeostasis, providing a potential therapeutic target for aging-associated disorders.

overall_design: Transcriptome analysis of knee joints tissues upon the treatment of lentiviruses expressing Luc, PC2 in anterior cruciate ligament transection (ACLT) induced osteoarthritis (OA) mouse model.

first: Guanghui


title: Setd5 haploinsufficiency alters neuronal network connectivity and leads to autistic-like behaviors in mice [bulk RNA]

summary: SETD5, a gene linked to intellectual disability (ID) and autism spectrum disorder (ASD), is a member of the SET-domain family and encodes a putative histone methyltransferase (HMT). To date, the mechanism by which SETD5 haploinsufficiency causes ASD/ID remains an unanswered question. Setd5 is the highly conserved mouse homolog, and although the Setd5 null mouse is embryonic lethal, the heterozygote is viable. Morphological tracing and multi electrode array was used on cultured cortical neurons. MRI was conducted of adult mouse brains and immunohistochemistry of juvenile mouse brains. RNA-Seq was used to investigate gene expression in the developing cortex. Behavioral assays were conducted on adult mice. Setd5+/- cortical neurons displayed significantly reduced synaptic density and neuritic outgrowth in vitro, with corresponding decreases in network activity and synchrony by electrophysiology. A specific subpopulation of fetal Setd5+/- cortical neurons showed altered gene expression of neurodevelopment-related genes. Setd5+/- animals manifested several autism-like behaviors, including hyperactivity, cognitive deficit, and altered social interactions. Anatomical differences were observed in Setd5+/- adult brains, accompanied by a deficit of deep-layer cortical neurons in the developing brain. Our data converge on a picture of abnormal neurodevelopment driven by Setd5 haploinsufficiency, consistent with a highly penetrant risk factor.

overall_design: Bulk RNA-Seq of CD24+ CD45- neuronal cells  isolated from E18.5 WT or SetD5 +/- mouse fetuses.

first: Alysson

middle: R

last: Muotri


title: RNA-seq analysis of tissues from PKCepsilon defiient mice

city: Sydney

first: Carsten

last: Schmitz-Peiffer

state: NSW

address: 384 Victoria St, Darlinghurst

department: Diabetes and Obesity Division

country: Australia

institute: Garvan Institute of Medical Research

summary: Comparison of RNA expression in liver and gonadal fat from female adipose-specific protein kinase C epsilon knockout mice and littermate controls, fed a high fat diet

overall_design: 5  mice per group were fed a high fat diet for 1 week, fasted for 6 hours and sacrificed, after which tissues were removed for RNA isolation


title: Chromatin Remodeler RSC2 Modulates Binding of the Transcriptional Activator Ace1p and Improves the Transcription of CUP1 by Fast Cycles of Remodeling

first: Razvan

middle: V.

last: Chereji

state: Maryland

address: 6 Center Drive, Room 2A14

department: NICHD

summary: Little is known about how dynamic binding of Transcription Factors (TF) is coordinated with chromatin remodeling. Using Single Molecule Tracking (SMT) we show that a chromatin remodeler (RSC2 complex) speeds up the search process of the TF Ace1p for its Response Elements (RE) in CUP1 promoter, ensuring a homogeneous response of the cell population to heavy metal stress. By SMT and MNase-seq, RSC2 binds to activated promoter transiently indicating that preinitiation at CUP1 is dependent on short repetitive remodeling events. Using smFISH, we demonstrate that RSC2 improves the search by increasing (a) the fraction of accessible RE, and (b) the molecular 'on' rate of the TF. Thus 'on' rates of binding can play a key role in gene regulation.

overall_design: Nucleosome occupancy was determined for the following four conditions: (1) Rsc2+ (No Auxin), no Cu activation, (2) Rsc2+ (No Auxin), with Cu activation, (3) Rsc2- (With Auxin), no Cu activation, (4) Rsc2- (With Auxin), with Cu activation.

first: Peter

last: Eriksson

middle: V

last: Clark

first: Gunjan

last: Mehta

first: Tatiana

last: Karpova


title: Setd5 haploinsufficiency alters neuronal network connectivity and leads to autistic-like behaviors in mice [single cell]

first: Jason

overall_design: Single cell RNA-Seq of CD24+ CD45- neuronal cells  isolated from E18.5 WT or SetD5 +/- mouse fetuses.


title: Brain RNA-seq: Esomeprazole/stress interactions.

city: Aurora

first: Richard

middle: A

last: Radcliffe

state: CO

address: 12850 E Montview Blvd., Room V20-3124

department: Pharmaceutical Sciences

institute: University of Colorado Anschutz Medical Campus

summary:
Purpose: The goals of this study were to evaluate the effects of acid suppression on the brain transcriptomer in a murine model of stress. In addition, the effects of the proton pump inhibitor (PPI), esomeprazole, on the brain transcriptome were evaluted in the presence or absence of stress.
Methods: Male C57BL/6 mice were subjected to three days of stress by hypothermic immobilization or control environment for three hours daily and either esomeprazole 2 mg/kg or saline by intraperitoneal injection daily. Standard RNA-seq methods were employed to assess mRNA expression in the hippocampus and frontal cortex.
Results: There was no effect of stress or esomeprazole on the frontal cortex transcriptome. Stress had no impact on the hippocampus transcriptome, but the addition of esomeprazole induced differential expression of 124 genes, many of which are involved in cognitive and behavior pathways.
Conclusions: Further studies are needed to evaluate the associations between microbiota, host gene expression, the abundance of CNS neurocognitive modulators, and their impact on cognition and behavior.

overall_design: mRNA from hippocampus and frontal cortex was profiled using Illumina HiSeq 2000 (2x151).  Tissue was generated from 4 groups of 6 male C57BL/6 mice: 1) control environment plus vehicle; 2) control environment plus esomeprazole (2 mg/kg); 3) stress environment plus vehicle; 4) stress environment plus esomeprazole (2 mg/kg).

first: Robert

last: MacLaren

first: Edward

middle: T

last: Van Matre

first: Daniel

middle: N

last: Frank


title: The effect of the Rocaglate on the macrophage gene expression

city: Boston

first: Marina

last: Kasaikina

state: MA

address: 450 Brookline avenue SM944

department: Cancer Biology

institute: Dana Farber Cancer Institute

summary: We report the analysis of the differential genes in mouse macrophages treated with the 100 nM of the Rocaglate vs untreated macrophages.

overall_design: Mouse macrophages were treated with 100nM Rocaglate or DMSO for 6h. After that cells were collected and gene expression was assessed by RNA-Seq.

first: Igor

last: Kramnik

first: Alexander

last: Gimelbrant

first: Sujoy

last: Chatterjee

first: Bidisha

last: Bhattacharya


title: The signaling axis atypical protein kinase C l/i-Satb2 mediates leukemic transformation of B-cell progenitors

city: Cincinnati

first: Ramesh

middle: Chandra

last: Nayak

address: 3333 Burnet Ave

department: Experimental Hematology and Cancer Biology

institute: Cincinnati Children's Hospital Medical Center

summary: Oncogene driven transformation of leukemic progenitors results in B-acute lymphoblastic leukemia. Genetic deletions at specific hotspots are driven by recombination of epigenetically repressed loci and cause B cell transformation, and epigenetically regulated transcriptional plasticity has been proposed as a mechanism of differentiation arrest and resistance to therapy. The upstream signals driving epigenetic silencing have not been elucidated. BCR-ABL leukemias are initiated by leukemic stem cells/progenitors, and their modeling in vivo represents an opportunity for the identification of the epigenetic progress contributing to lineage leukemogenesis. We have found that primary human and murine BCR-ABL+ leukemic progenitors have increased activation of Cdc42 and the downstream atypical protein kinase C (aPKC). While the isoform aPKCz behaves as a leukemic suppressor, aPKCl/i is critically required for oncogenic progenitor proliferation, survival, and B cell differentiation arrest, but not for normal B cell lineage differentiation. We found that in vitro and in vivo B cell transformation by BCR-ABL requires the downregulation of key genes in the B-cell differentiation program through an aPKCl/i-dependent Etv5/Satb2 chromatin repressive signaling complex. Thus genetic or pharmacological targeting of aPKC impairs human oncogenic addicted leukemias in vitro and in vivo. Therefore, the aPKCl/i-SATB2 signaling cascade is required for leukemic BCR-ABL+ B-cell progenitor transformation and is amenable to non-BCR-ABL kinase inhibition.

overall_design: RNA seq analyse to identify  the gene expression changes associated with the deficiency of atypical protein kinase C (aPKC) in p210-BCR-ABL+ leukemic B- cell progenitors.   In 3 independent experiments, 50,000 leukemic B cell precursors were isolated from WT and aPKC  deficient chimeric secondary recipient mice at 2 months post transplantation. Total RNA was isolated using QIAGEN RNAeasy minikit.

first: Shailaja

last: Hegde

first: Mark

middle: J

last: Althoff

first: Ashley

middle: H

last: Wellendorf

first: Fatima

last: Mohmoud

first: John

last: Perentesis

first: Damien

last: Reynaud

first: Yi

last: Zheng

first: Maria

last: Diaz-Meco

first: Jorge

last: Moscat

first: Jose

last: Cancelas


title: NuRD-interacting protein ZFP296 regulates genome-wide NuRD localization and differentiation of mouse embryonic stem cells

city: Zürich

first: Ino

last: Karemaker

address: Winterthurerstrasse 190

country: Switzerland

institute: University of Zurich

overall_design: Refer to individual Series


title: NuRD-interacting protein ZFP296 regulates genome-wide NuRD localization and differentiation of mouse embryonic stem cells (ChIP-seq)

summary: The Nucleosome Remodeling and Deacetylase (NuRD) complex plays an important role in gene expression regulation, stem cell self-renewal, and lineage commitment. Yet little is known about the dynamics of NuRD during cellular differentiation. Here, we study these dynamics using genome-wide profiling and quantitative interaction proteomics in mouse embryonic stem cells (ESCs) and neural progenitor cells (NPCs). The genomic targets of NuRD are highly dynamic during differentiation, with most binding occurring at cell-type specific promoters and enhancers. We identify ZFP296 as a novel, ESC-specific NuRD interactor that also interacts with the SIN3A complex. ChIP-sequencing in Zfp296 knockout (KO) ESCs reveals decreased NuRD binding both genome-wide and at ZFP296 binding sites, although this has little effect on the transcriptome. Nevertheless, Zfp296 KO ESCs exhibit delayed induction of lineage-specific markers upon differentiation to embryoid bodies. In summary, we identify an ESC-specific NuRD interacting protein which regulates genome-wide NuRD binding and cellular differentiation.

overall_design: ChIP-seq samples for H3K4me1, H3K4me3, H3K27ac, H3K27me3, MBD3, CHD4, and corresponding inputs from wildtype ESCs and NPCs. ChIP-seq for GFP-ZFP296 and SIN3A in wildtype ESCs. ChIP-seq with spike-in for MBD3, CHD4, SIN3A, H3K27ac, and corresponding inputs in wildtype and Zfp296 KO ESCs.

middle: D

first: Susan

middle: L

last: Kloet


title: IGF2BP1 promotes SRF-dependent transcription in cancer in a m6A- and miRNA-dependent manner [miRNA-seq]

city: Halle

first: Markus

last: Glaß

address: Kurt-Mothes-Str. 3a

department: Institute of Molecular Medicine

institute: Martin Luther University Halle-Wittenberg

summary: The oncofetal mRNA-binding protein IGF2BP1 and the transcriptional regulator SRF modulate gene expression in cancer. In cancer cells, we demonstrate that IGF2BP1 promotes the expression of SRF in a conserved and N6-methyladenosine (m6A) dependent manner by impairing the miRNA-directed decay of the SRF mRNA. This results in enhanced SRF-dependent transcriptional activity and promotes tumor cell growth and invasion. At the post-transcriptional level, IGF2BP1 sustains the expression of various SRF-target genes. The majority of these SRF/IGF2BP1-enhanced genes, including PDLIM7 and FOXK1, shows conserved upregulation with SRF and IGF2BP1 synthesis in cancer. PDLIM7 and FOXK1 promote tumor cell growth and were reported to enhance cell invasion. Consistently, 35 SRF/IGF2BP1-dependent genes showing conserved association with SRF and IGF2BP1 expression indicate a poor overall survival probability in ovarian, liver and lung cancer. In conclusion, these findings identify the SRF/IGF2BP1-, miRNome- and m6A-dependent control of gene expression as a conserved oncogenic driver network in cancer.

overall_design: small RNA-Seq of four cancer derived cell lines. Two replicates per condition.

first: Simon

last: Müller

first: Anurag

last: Singh

first: Jacob

last: Haase

first: Nadine

last: Bley

first: Tommy

last: Fuchs

first: Marcell

last: Lederer

first: Andreas

last: Dahl

first: Huilin

last: Huang

first: Jianjun

last: Chen

first: Guido

last: Posern

first: Stefan

last: Hüttelmaier


title: HJURP antagonizes CENP-A mislocalization driven by the H3.3 chaperones HIRA and DAXX

first: David

last: Sturgill

state: MARYLAND

address: Building 41, Rm B622

department: NCI

institute: NIH

summary: The centromere specific histone H3 variant CENP-A/CENH3 specifies where the kinetochore is formed in most eukaryotes. Despite tight regulation of CENP-A levels in normal cells, overexpression of CENP-A is a feature shared by various types of solid tumors and results in its mislocalization to non-centromeric DNA. How CENP-A is assembled ectopically and the consequences of this mislocalization remain topics of high interest. Here, we report that in human colon cancer cells, the H3.3 chaperones HIRA and DAXX promote ectopic CENP-A deposition. Moreover, the correct balance between levels of the centromeric chaperone HJURP and CENP-A is essential to preclude ectopic assembly by H3.3 chaperones. In addition, we find that ectopic localization can recruit kinetochore components, and correlates with mitotic defects and DNA damage in G1 phase. Finally, CENP-A occupancy at the 8q24 locus is also correlated with amplification and overexpression of the MYC gene within that locus. Overall, these data provide insights into the causes and consequences of histone variant mislocalization in human cancer cells.

overall_design: CENP-A ChIP-Seq in SW480 cells

first: Jon

last: Nye

first: Rajbir

last: Athwal

first: Yamini

last: Dalal


title: IGF2BP1 promotes SRF-dependent transcription in cancer in a m6A- and miRNA-dependent manner


title: A novel population of Hopx-dependent human-like basal radial glial cells in the developing mouse neocortex

city: Leipzig

first: Gray

last: Camp

address: Deutscher Pl. 6

department: Evolutionary Genetics

institute: Max Planck Institute for Evolutionary Anthropology

summary: A specific subpopulation of neural progenitor cells, the basal radial glia cells (bRGCs) of the outer subventricular zone (OSVZ), are thought to have a key role in the evolutionary expansion of mammalian neocortex. In the developing lissencephalic mouse neocortex, bRGCs exist at low abundance and show significant molecular differences from bRGCs in developing gyrencephalic species. Here, we demonstrate that developing mouse medial neocortex, in contrast to the canonically studied lateral neocortex, exhibits an OSVZ and an abundance of bRGCs similar to that in developing gyrencephalic neocortex. Unlike bRGCs in developing mouse lateral neocortex, the bRGCs in medial neocortex exhibit human bRGC-like gene expression, including expression of Hopx, a human bRGC marker. Disruption of Hopx expression in mouse embryonic medial neocortex and forced Hopx expression in mouse embryonic lateral neocortex demonstrate that Hopx is required and sufficient, respectively, for a bRGC abundance as found in developing gyrencephalic neocortex. Taken together, our data identify a novel bRGC subpopulation in developing mouse medial neocortex that is highly related to bRGCs of developing gyrencephalic neocortex.

overall_design: 221 single-cell transcriptomes from microdissected medial neocortex of E18.5 mouse embryos (two independent analyses using a pool of 8 neocortices each).

first: J

middle: G

first: Barbara

last: Treutlein


title: PDGFRβ Cells Rapidly Relay Inflammatory Signal from the Circulatory System to Neurons via Chemokine CCL2

city: Shanghai

first: Xiang

last: Yu

address: 320 Yue Yang Road

institute: Institute of Neuroscience, Chinese Academy of Sciences

summary: Identify the cell type that responses to LPS in the brain during the acute phase of infection

overall_design: Three independent sets of experiments were carried out. In each experiment, P14 mice were i.p. injected with saline (SA, control) or 10 mg/kg LPS, and sacrificed two hours later.

first: Lihui

last: Duan


title: Ex-vivo Human Hematopoietic Stem Cell Expansion Requires Coordination of Cellular Reprogramming with Mitochondrial Remodeling and P53 Activation[10x]

city: New York

first: Yongchao

last: Ge

state: NY

address: One Gustave L Levy Place #1137

department: Neurology

institute: Icahn School of Medicine at Mount Sinai

summary: Ex-vivo culture conditions used to expand the numbers of hematopoietic stem cells (HSCs) present within an umbilical cord blood (UCB) unit create cellular stresses leading to loss or at best maintenance of the primitive HSCs. Recently, we have shown that treatment with a histone deacetylase inhibitor, valproic acid (VPA), increases substantially the numbers of transplantable HSCs from UCB-CD34+ cells. In this report, we demonstrate that VPA treatment orchestrates cellular mechanisms that drive UCB-CD34+ cells into a primitive state in which they acquire and retain phenotypic, transcriptomic and primitive mitochondrial profiles, all of which characterize long-term HSCs. Remarkably, our data link the acquisition of the HSC phenotype to the remodeling of the mitochondrial network and p53 activation and establish both as critical regulators of ROS and therefore of HSC fate. VPA treatment leads to restructured mitochondria with reduced mass, membrane potential and ROS levels. p53 activity is critical for the activation of antioxidant defense mechanisms, which rely on magnesium superoxide dismutase (MnSOD) activity. Failure to activate the p53-MnSOD axis compromises both the acquisition and the maintenance of the HSC phenotype. These studies indicate that suppression of ROS through the coordination of p53 activity and mitochondrial remodeling determines the fate of ex-vivo expanded human HSCs

overall_design: Examination of transcriptome on a single cell level of Cord blood isolated CD34+ culture in stemline media + cytokine + Valproic acid at 2 different days of culture.

first: Luena

last: Papa

first: Mansour

last: Djedaini

last: ge

first: Robert

last: Sebra

first: Stuart

last: Sealfon

first: Ronald

last: Hoffman


title: NuRD-interacting protein ZFP296 regulates genome-wide NuRD localization and differentiation of mouse embryonic stem cells (RNA-seq)

first: Ino

last: Karemaker

overall_design: RNA-seq samples of wildtype R1 ESCs and Zfp296 CRISPR KO clone 2 R1 ESCs

first: Susan

last: Kloet


title: Profiling the wild type (WT) and Rb mutant Drosophila eye disc using Drop-seq (single cell RNA-seq)

city: Chicago

first: Majd

middle: Maher

last: Ariss

state: IL

address: 900 S Ashland Ave rm. 2356

department: Biochemistry and Molecular Genetics

institute: University of Illinois at Chicago

summary: We characterized the Drosophila third instar eye disc using single cell RNA-seq and labelled the multiple cell populations. The results identified a novel transcriptional switch in photoreceptors relating to axonal projections. We then performed single cell RNA-seq on rbf (Rb) mutants and compared the results to the WT cell populations. This identified a specific cell population only in the Rb mutant tissue. This cell population has an upregulation of HIF1A and glycolitic genes such as Aldolase and Lactate dehydrogenase. As a result these cells produce lactate and undergo apoptosis. We also show this process to be directly regulated by E2F/Dp. The paper uncovers a novel metabolic aspect of Rb/E2F dependent apoptosis.

overall_design: examining WT and Rb mutants third instar eye disc using single cell RNA-seq

middle: M

first: Maxim

last: Frolov

first: Abul

middle: B

last: Islam


title: IGF2BP1 promotes SRF-dependent transcription in cancer in a m6A- and miRNA-dependent manner [Huh-7]

first: Markus

last: Glaß

overall_design: total RNA-Seq of Huh-7 cells transfected with either control siRNAs (siC) or siRNAs directed against IGF2BP1.

first: Simon

last: Müller

first: Anurag

last: Singh

first: Jacob

last: Haase

first: Nadine

last: Bley

first: Tommy

last: Fuchs

first: Marcell

last: Lederer

first: Andreas

last: Dahl

first: Huilin

last: Huang

first: Jianjun

last: Chen

first: Guido

last: Posern

first: Stefan

last: Hüttelmaier


title: RNA-seq to determine PRC2 targets in the aging Drosophila brain.

city: Pittsburgh

first: Jason

last: Kennerdell

state: PA

address: 100 Technology Drive

department: Aging Institute

institute: University of Pittsburgh

summary: Aging is a prominent risk factor for neurodegenerative disease, therefore defining mechanisms critical for healthy brain aging should lead to insight into genes that modulate susceptibility to disease.  To define such genes, we have pursued analysis of miR-34 mutants in Drosophila. The miR-34 mutant brain displays a gene profile of accelerated aging, and miR-34 upregulation is a potent suppressor of polyglutamine-induced neurodegeneration. We investigated targets of miR-34 to define those important for its functions in mitigating degeneration and impacting health of the brain with age. These studies show that miR-34 targets for silencing two components of polycomb repressive complex 2 (PRC2)—Pcl and Su(z)12—in the brain with age. PRC2 is a histone methyltransferase that confers the repressive H3K27me3 mark, suggesting that a critical role of miR-34 is to modulate the function of PRC2 to silence key genes in the brain with age. Remarkably, gene expression profiling of the brains of hypomorphic mutants in Enhancer of zeste (E(z)), the enzymatic methyltransferase component of PRC2, revealed a younger brain transcriptome profile and identified the small heat shock proteins as key modulated genes. These findings indicate that PRC2 epigenetic mechanisms impact the susceptibility of the brain to degenerative disease with age, and highlight the role of small heat shock proteins to protect the brain from age-associated decline and disease.

overall_design: The design involves three factors: genotype, age, and cultivation temperature. Genotype can be either w[1118] (wild-type control) or w[1118]; E(z)[61] / E(z)[731] (E(z) hypomorphic mutant). Samples have an age of either 3d (3 days) or 20d (20 days). Animals are cultivated at either 25 degrees Celsius or 29 degrees Celsius. Samples are derived from Drosophila brain. We evaluate changes in gene expression with age.  We also evaluate changes in gene expression in animals with hypomorphic mutations in E(z), with blocking on temperature.

first: Nancy

last: Bonini


title: Ichthyosis molecular fingerprinting shows profound Th17-skewing and a unique barrier genomic signature

first: Emma

last: Guttman

state: New York

address: 1425 Madison Ave

institute: Icahn School of Medicine at Mt. SInai

summary: The purpose of this study was to analyze the genomic signatures and profiles of skin from  ichthyosis (various subtypes) vs. healthy patients. The analysis strategy was to study differentially expressed genes common to the ichthyosis shared phenotype, as well as individual ichthyosis subtypes, and compare and contrast to the genomic profiles of atopic dermatitis and psoriasis.

overall_design: Skin biopsy samples from 21 patients with ichthyosis (3 Netherton, 7 lamellar ichthyosis/LI, 6 congenital ichthyosiform erythroderma/CIE, 5 epidermolytic ichthyosis/EI) and 14 healthy controls were collected and analyzed by gene microarray

first: E

last: Guttman-Yassky

first: A

last: Paller


title: HiSeq analysis of human gene expression profile following infection with highly pathogenic avian influenza A virus (H5N1; A/Chicken/Vietnam/0008/04)

status: Public on Oct 09 2018

city: East Geelong

first: Siying

last: Ye

state: VIC

address: AAHL CSIRO, 5 Portarlington Road

institute: Deakin University

summary: Current prophylactic and therapeutic strategies targeting human influenza viruses include vaccines and antivirals. Given variable rates of vaccine efficacy and antiviral resistance, alternative strategies are urgently required to improve disease outcomes. Here we describe the use of HiSeq deep sequencing to analyze host gene expression in primary human alveolar epithelial type II (ATII) cells infected with highly pathogenic avian influenza H5N1 virus. We employed primary human ATII cells isolated from normal human lung tissue donated by patients that underwent lung resection. Human host gene expression following HPAI H5N1 virus (A/Chicken/Vietnam/0008/04) infection of primary ATII cells was analyzed using Illumina HiSeq deep sequencing.

overall_design: Human non-tumor lung tissue samples were donated by three anonymous patients undergoing lung resection at Geelong Hospital, Barwon Health, Australia. The research protocols and human ethics were approved by the Human Ethics Committees of Deakin University, Barwon Health and the Commonwealth Scientific and Industrial Research Organisation (CSIRO). An informed consent was obtained from all tissue donors. All research were performed in accordance with the guidelines stated in the National Statement on Ethical Conduct in Human Research (2007). The sampling of normal lung tissue was confirmed by the Victorian Cancer Biobank, Australia.

first: Chris

last: Cowled

first: Cheng-Hon

last: Yap

first: John

last: Stambas


title: Adult Connective Tissue-Resident Mast Cells Originate from Late Erythro-Myeloid Progenitors

city: Hangzhou

first: ZHI

middle: QING

last: LI

address: 866 Yuhangtang Road

institute: Zhejiang University School of Medicine

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


title: Combined Experimental and System-Level Analyses Reveal the Complex Regulatory Network of miR-124 during Human Neurogenesis [ZNF787]

city: Dresden

first: Volker

last: Busskamp

state: Saxony

address: Fetscherstraße 105

department: CMCB

institute: Technische Universität Dresden

summary: Non-coding RNAs regulate many biological processes including neurogenesis. The brain-enriched miR-124 is assigned as a key player of neuronal differentiation via its complex, but little understood, regulation of thousands of annotated targets. To systematically chart its regulatory functions, we used CRISPR/Cas9 gene editing to disrupt all six miR-124 alleles in human stem cells. Upon neuronal induction, miR-124-depleted cells underwent neurogenesis and became functional neurons, albeit with altered morphology and neurotransmitter specification. By RNA-induced-silencing-complex precipitation, we found that other miRNA species were upregulated in miR-124 depleted neurons. Furthermore, we identified 98 miR-124 targets of which some directly led to decreased viability. We performed advanced transcription-factor-network analysis and revealed indirect miR-124 effects on apoptosis and neuronal subtype differentiation. Our data emphasizes the need for combined experimental- and systems-level analyses to comprehensively disentangle and reveal miRNA functions, including their involvement in the neurogenesis of diverse neuronal cell types found in the human brain.

overall_design: RNA profile of neuronal Neurogenin-1 and 2-triggered differentiation from human iPSCs (wildtype, ∆miR-124 and wildtype with ZNF787 overexpression), 4 days post induction.

first: Lisa

middle: K

last: Kutsche

first: Mathias

last: Lesche


title: Bisulfite-free, nano-scale analysis of 5-hydroxymethylcytosine at single base resolution

first: Bo

last: He

address: Yiheyuan Road 5th.

department: School of Life Science

institute: Peking University

summary: High-resolution detection of genome-wide 5-hydroxymethylcytosine (5hmC) sites of small-scale samples represents a continuous challenge. Here, we present CATCH-seq, a bisulfite-free, base-resolution method for the genome-wide detection of 5hmC. CATCH-seq is based on selective 5hmC oxidation, labeling and subsequent C-to-T transition during PCR. Applications of CATCH-seq to nano-scale DNA samples reveal previously underappreciated non-CG 5hmCs in the hESC genome and base-resolution hydroxymethylome in human cell-free DNA.

overall_design: We developed a method named "CATCH-Seq" , a bisulfite-free, base-resolution method for the genome-wide detection of 5hmC. Our method is based on: (1) selective oxidation of 5hmC to 5fC ; (2) subsequent labeling of the newly generated 5fC; and (3) 5fC labeling adduct caused C-to-T transition during DNA amplification.We then applied CATCH-seq to 100 ng, 50 ng and 10 ng genomic DNA isolated from hESCs, respectively. To further demonstrate the utility of CATCH-seq in analyzing precious clinical samples, we next applied this approach to sequence the hydroxymethylome of cell-free DNA (cfDNA).

first: Hu

last: Zeng

last: Xia

first: Chengqi

last: Yi


title: Active translatome profiling with RiboLace in MCF7 cells

city: Povo

first: Toma

last: Tebaldi

state: Trento

address: via Sommarive n. 9

department: Centre for Integrative Biology

institute: University of Trento

summary:
We developed RiboLace, a novel method based on a new puromycin-containing molecule, for the isolation of active ribosomes and associate RNAs by means of an antibody-free and tag-free pull-down approach. RiboLace is fast, it works with very low input material and can be easily and rapidly used to obtain a transcriptome-wide snapshot of active translation from eukaryotic in vitro and in vivo systems.
Keywords: translation, RiboLace, polysome profiling, RNA-seq, POL-seq, active translation

overall_design: We performed RiboLace sequencing, polysomal RNA sequencing (POL-seq), total RNA sequencing (RNA-seq) and sequencing of the pull-down with mP-beads. Experiments were performed in duplicate on MCF7 cells in three conditions: control, serum starved (12h), serum starved and EGF treated (12h+4h).

first: Massimiliano

last: Clamer

first: Gabriella

last: Viero


title: Single-cell transcriptome dynamics in stabilized pituitary gonadotrope cells [mini_dropseq]

first: Yongchao

last: Ge

summary: Studying dynamic transcripts in single cells (SC) requires large numbers of timed samples. We report an easy to use protocol to stabilize RNA in intact SCs without perturbing transcriptional patterns, and demonstrate its applicability for SC transcriptome assays with cells and tissue. We identify a gene-specific hierarchical pattern of all-or-none transcript induction elicited by different concentrations of pulsatile hormone stimuli in pituitary gonadotropes.

overall_design: SC Mini Drop-seq experiments were performed on two samples from dissociated human cortical tissue: one is neocortex from a glioblastoma multiforme (GBM, tumor), the other is normal neocortex adjacent to the tumor.

first: Frederique

last: Ruf-Zamojski

first: Venugopalan

last: Nair

first: Michel

last: Zamojski

first: Hanna

last: Pincas

first: Chirine

last: Toufaily

first: Jessica

last: Tome-Garcia

first: Marlon

last: Stoeckius

first: William

last: Stephenson

first: Daniel

last: Bernard

first: Nadedja

last: Tsankova

first: Boris

last: Hartmann

first: Miguel

last: Fribourg

first: Peter

last: Smibert

first: Harold

last: Swerdlow

first: Judith

last: Turgeon

first: Stuart

middle: C

last: Sealfon


title: Single-cell transcriptome dynamics in stabilized pituitary gonadotrope cells [bulk_lbt2]

first: Yongchao

last: Ge

overall_design: Bulk RNA-seq was performed on three samples of fresh LβT2 cells (reference samples) and three samples of LβT2 cells stabilized with RNA-Best: all were treated with GnRH (2 nM GnRH for 40 min).


title: Pomalidomide inhibits PD-L1 induction to promote anti-tumor immunity

status: Public on Oct 08 2018

first: Yuwen

last: Zhu

address: 12800 E 19th Avenue

department: Surgery

institute: University of Colorado Anschutz Medical Campus

summary: We examined genome-wide how pomalidomide affects IFN-gamma-induced PD-L1 expression in human melanoma cell line.

overall_design: RNA-Seq of SK-MEL-624 cells treated with or without IFN-gamma as well as pomalidomide.. Total RNA was extracted using RNAqueous® Micro Kit (Invitrogen, Waltham MA) as the manufacturer instruction. RNA library preparation and sequencing were conducted by the Genomics and Microarray Core at University of Colorado Cancer Center. The 151bp single-end fastq files generated from Illumina HiSeq 4000 platform were aligned to the UCSC human hg19 reference genome using the STAR 2.4.0 RNA-seq aligner.


title: Argonaute2 attenuates active transcription by limiting RNA Polymerase II elongation in Drosophila melanogaster [ChIPseq-PolII-S2]

city: Bethesda

first: Cameron

last: Palmer

address: 50 South Drive

department: National Institute of Diabetes and Digestive and Kidney Diseases

institute: National Institutes of Health

summary: Increasing lines of evidence support that Argonaute2 (AGO2) harbors several nuclear functions in metazoa. In particular, Drosophila AGO2 modulates transcription of developmentally regulated genes; however, the molecular mechanisms behind AGO2 recruitment into chromatin and its function in transcription have not been deeply explored. In this study, we show that Drosophila AGO2 chromatin association depends on active transcription. In order to gain insight into how AGO2 controls transcription, we performed differential ChIP-seq analysis for RNA Polymerase II (Pol II) upon depletion of AGO2. Interestingly, we find specific accumulation of the elongating but not initiating form of Pol II after AGO2 knockdown, suggesting that AGO2 impairs transcription elongation. Finally, AGO2 also affects Negative Elongation Factor (CDK9) chromatin association but not the Cyclin Dependent Kinase 9 (CDK9). Altogether, these results provide key insights into the molecular role of AGO2 in attenuating elongation of certain actively transcribed genes.

overall_design: ChIP-seq of RNA PolII S2 (serine 2 phosphorylated) in Drosophila melanogaster Kc167 cells in mock treatment, Ago2 knockdown, and LaminB knockdown. Two replicates per condition, with paired inputs.

first: Ezequiel

last: Nazer

first: Elissa

middle: P

last: Lei


title: Combined Experimental and System-Level Analyses Reveal the Complex Regulatory Network of miR-124 during Human Neurogenesis [d7+d14]

first: Volker

last: Busskamp

overall_design: RNA profile of neuronal Neurogenin-1 and 2-triggered differentiation from human iPSCs (wildtype and ∆miR-124) at 7 and 14 days post induction.

first: Lisa

last: Kutsche

first: Deisy

last: Gysi

first: Mathias

last: Lesche

first: Andreas

last: Dahl


title: Combined Experimental and System-Level Analyses Reveal the Complex Regulatory Network of miR-124 during Human Neurogenesis [Timecourse RNA-Seq]

overall_design: RNA profile for timecourse of neuronal Neurogenin-1 and 2-triggered differentiation from human iPSCs (wildtype and ∆miR-124).


title: Single-cell transcriptome dynamics in stabilized pituitary gonadotrope cells [10x]

overall_design: GEM Drop-seq was performed on two samples of LβT2 cells preserved with RNA-Best: one sample was treated with vehicle (Control), the other with 2nM GnRH for 40 min.

first: Frederique

last: Ruf-Zamojski

first: Venugopalan

last: Nair

first: Michel

last: Zamojski

first: Hanna

last: Pincas

first: Chirine

last: Toufaily

first: Jessica

last: Tome-Garcia

first: Marlon

last: Stoeckius

first: William

last: Stephenson

first: Daniel

last: Bernard

first: Nadedja

last: Tsankova


title: Single-cell transcriptome dynamics in stabilized pituitary gonadotrope cells [bulk_pituitary]

first: Yongchao

last: Ge

overall_design: Bulk RNA-seq was performed on two primary mouse pituitary cell samples, one stored in RNA-Best, the other in RNAlater (reference sample).

first: Boris

last: Hartmann

first: Miguel

last: Fribourg

first: Peter

last: Smibert

first: Harold

last: Swerdlow

first: Judith

last: Turgeon

first: Stuart

last: Sealfon


title: Kdm3a in mouse promotes pressure overload induced cardiac hypertrophy [RNA-seq]

city: Dalals

first: zhi-ping

last: liu

state: TX

address: 6000 Harry Hines Blvd

department: internal medicine

institute: ut southwestern

summary: Heart disease and failure is a leading cause of mortality worldwide. Left ventricular hypertrophy (LVH) and myocardial fibrosis are major risk factors for cardiovascular morbidity and mortality and the development of heart failure. Pathological LVH induced by sustained pressure-overload engages transcriptional programs including reactivation of canonical fetal genes and those inducing fibrosis. Histone lysine demethylases (KDMs) are emerging potent regulators of transcriptional reprogramming in cancer, though their potential role in abnormal growth and fibrosis in heart disease remains little understood. Here, we investigated gain and loss of function of an H3K9me2 specific demethylase, Kdm3a, in myocytes and in vivo, and show it promotes LVH and myocardial fibrosis in response to pressure-overload. Cardiomyocyte KDM3A activates the transcription of tissue-inhibitor of MMP type 1 (Timp1) with pro-fibrotic activity.  By contrast, a pan-KDM inhibitor, JIB-04, suppresses TAC-induced LVH and fibrosis. JIB-04 inhibits KDM3A and suppresses the transcription of fibrotic genes that overlap with genes downregulated in Kdm3a-KO mice versus WT controls. Our study provides genetic and biochemical evidence for a pro-hypertrophic function of KDM3A and proof-of principle for pharmacological targeting of KDMs as an effective strategy to counter LVH and pathological fibrosis.

overall_design: There are four samples in this project: sham+veh, sham+JIB-04, TAC+Veh, TAC+JIB-04. Sham+Veh is used as a control to show the normal gene expression profile in mouse heart tissue. Sham+JIB-04 is used to show the change of gene expression caused by JIB-04 under baseline condition. TAC+Veh results show the gene expression change caused by pressure overload. TAC+JIB-04 results show the gene expressional change caused by JIB-04 under pressure overload condition.

first: Qing-jun

last: Zhang

first: Zhi-ping

last: Liu


title: Combined Experimental and System-Level Analyses Reveal the Complex Regulatory Network of miR-124 during Human Neurogenesis [AGO2-RIP-Seq]

first: Volker

last: Busskamp

overall_design: RNA interacting protein immunoprecipitation with AGO2 for miRNA enrichment from neuronal Neurogenin-1 and 2-triggered differentiation from human iPSCs (wildtype and ∆miR-124) and subsequent sequencing.

first: Lisa

last: Kutsche

first: Joerg

last: Fallmann

first: Mathias

last: Lesche

first: Andreas

last: Dahl


title: Combined Experimental and System-Level Analyses Reveal the Complex Regulatory Network of miR-124 during Human Neurogenesis.

overall_design: Refer to individual Series


title: Single-cell transcriptome dynamics in stabilized pituitary gonadotrope cells

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: Combined Experimental and System-Level Analyses Reveal the Complex Regulatory Network of miR-124 during Human Neurogenesis [AGO2-RIP-Seq -miRNAs]

overall_design: RNA interacting protein immunoprecipitation with AGO2 for miR-124 target enrichment from neuronal Neurogenin-1 and 2-triggered differentiation from human iPSCs (wildtype and ∆miR-124) and subsequent sequencing.


title: Nondestructive, base-resolution sequencing of 5-hydroxymethylcytosine using a DNA deaminase

city: Philadelphia

first: Hao

last: Wu

address: 415 Curie Boulevard

department: Genetics

institute: University of Pennsylvania

summary: Here we present APOBEC-coupled epigenetic sequencing (ACE-seq), a bisulfite-free method for localizing 5-hydroxymethylcytosine (5hmC) at single-base resolution with low DNA input. The method builds on the observation that AID/APOBEC family DNA deaminase enzymes can potently discriminate between cytosine modification states and exploits the non-destructive nature of enzymatic, rather than chemical, deamination. ACE-seq yielded high-confidence 5hmC profiles with at least 1,000-fold less DNA input than conventional methods. Applying ACE-seq to generate a base-resolution map of 5hmC in tissue-derived cortical excitatory neurons, we found that 5hmC was almost entirely confined to CG dinucleotides. The whole-genome map permitted cytosine, 5-methylcytosine (5mC) and 5hmC to be parsed and revealed genomic features that diverged from global patterns, including enhancers and imprinting control regions with high and low 5hmC/5mC ratios, respectively. Enzymatic deamination overcomes many challenges posed by bisulfite-based methods, thus expanding the scope of epigenome profiling to include scarce samples and opening new lines of inquiry regarding the role of cytosine modifications in genome biology.

overall_design: Whole-genome ACE-seq analysis of WT or Tet1-3 KO mouse embryonic stem cells as well as adult mouse cortical excitatory neurons

first: Emily

last: Schutsky

first: Rahul

last: Kohli


title: YAP and MRTF-A, transcriptional co-activators of RhoA- mediated gene expression, are critical for glioblastoma tumorigenicity

city: SAN DIEGO

first: Olivia

last: Yu

state: California

address: 9420 Athena Cir, La Jolla

institute: LJI

summary: The role of YAP (Yes associated protein 1 gene) and MRTF-A (Megakaryoblastic Leukemia gene, MLK1), two transcriptional co-activators regulated downstream of GPCRs (G-protein coupled receptor) and RhoA, in growth of glioblastoma cells and in vivo GBM tumor development was explored using human glioblastoma cell lines  (1321N1) and tumor initiating cells derived from patient derived xenografts (PDX)PDX (GSC-23) cells. Knockdown of these co-activators in PDX cells using shRNA significantly attenuated in vitro proliferation and stemness assessed by limiting dilution and neurosphere formation. Orthotopic xenografts of the MRTF-A and YAP knockdown PDX cells formed significantly smaller tumors with lower morbidity than wild-type cells. In vitro studies of cellular responses to the GPCR agonist sphingosine 1-phosphate (S1P) demonstrated that YAP was required for glioblastoma cell invasion and migration, whereas MRTF-A, was required for cell adhesion. S1P- stimulated proliferation was abolished by knockout of either YAP or MRTF-A. Gene expression analysis by RNA-sequencing of S1P- treated 1321N1 cells in which MRTF-A and or YAP were deleted knockout cells identified 44 genes that were induced through RhoA and highly dependent on YAP, MRTF-A, or both. Knockdown of F3 (tissue factor; TF), a target gene regulated selectively through YAP, when knocked down blocked 1321N1 cell invasion and migration, whereas knockdown of HBEGF (Hheparin binding EGF-like growth factor) (HBEGF), a gene selectively induced through MRTF-A, prevented cell adhesion in response to S1P. Proliferation was sensitive to knockdown of several target genes dually regulated through both YAP and MRTF-A (CCN1 and MYC) or of those regulated by either factor. Expression of these same genes was decreased in tumors from PDX cells lacking YAP or MRTF-A, indicating that these transcriptional pathways are regulated in the in vivo GBM tumor environment and suggesting that their activation through GPCRs and RhoA contributes to growth and maintenance of human GBM.

overall_design: 18 samples analyzed in biological triplicates, control samples are wild-type, untreated (WT_Untreated)

first: Joan

last: Heller Brown

first: Anjana

last: Rao

first: Shigeki

last: Miyamoto

first: Jason

last: Greenbaum


title: TimeSignature: A Universal Method for Robust Detection of Circadian State from Gene Expression

first: Marta

last: Iwanaszko

address: 303 E. Superior Street, Simpson Querrey 7th Floor,

institute: Northwestern University Feinberg School of Medicine

summary:
Profiles of circadian gene expression in whole blood from 11 healthy adult subjects.
Abstract: Circadian clocks play a key role in regulating a vast array of biological processes, with significant implications for human health. Accurate assessment of physiological time using transcriptional biomarkers found in human blood can significantly improve diagnosis of circadian disorders and optimize the delivery time of therapeutic treatments. To be useful, such a test must be accurate, minimally burden some to the patient, and readily generalizable to new data. A major obstacle in development of gene expression biomarker tests is the diversity of measurement platforms and the inherent variability of the data, often resulting in predictors that perform well in the original datasets but cannot be universally applied to new samples collected in other settings. Here we introduce TimeSignature, a new algorithm that robustly infers circadian time from gene expression. We demonstrate its application in data from three independent studies using Pdistinct microarrays, and further validate it against a new set of samples profiled by RNA-Seq. Our results show that TimeSignature is more accurate and efficient than competing methods, estimating circadian time to within 2h for the majority of samples. Importantly, we demonstrate that once trained on data from a single study, the resulting predictor can be universally applied to yield highly accurate results in new data from other studies independent of differences in study population, patient protocol, or assay platform without renormalizing the data or retraining. This feature is unique amongst expression–based predictors, and addresses a major challenge in the development of generalizable, clinically–useful tests.

overall_design: Whole blood transcriptional profiles of 11 individuals with intermediate circadian phenotype, were generated by RNA sequencing, using Illumina NextGen 500. Whole blood was collected every 2hr over 28hr (15 time points), yelding total of 165 samples, of which 153 passed the QA and underwent further analysis.

first: Ravi

last: Allada

first: Rosemary

last: Braun

first: Phyllis

last: Zee

first: William

last: Kath

first: Elzbieta

last: Kula-Eversole

first: Sabra

last: Abbott

first: Kathryn

last: Reid


title: Active ribosome profiling  with RiboLace and standard ribosome profiling in HEK-293 cells

first: Toma

last: Tebaldi

summary:
We developed RiboLace, a novel method based on a new puromycin-containing molecule, for the isolation of active ribosomes by means of an antibody-free and tag-free pull-down approach. RiboLace is fast, it works with very low input material and can be easily and rapidly used to enhance Ribo-Seq, obtaining  a global snapshot on active ribosome footprints at single nucleotide resolution from  eukaryotic in vitro and in vivo systems.
Keywords: ribosome profiling, translation, RiboLace, Ribo-Seq, active translation

overall_design: We performed active ribosome profiling with RiboLace and standard ribosome profiling in HEK-293 cells. Experiments were performed in biological duplicate.

first: Massimiliano

last: Clamer

first: Paola

last: Bernabò

first: Fabio

last: Lauria

first: Gabriella

last: Viero


title: Mediator is essential for small nuclear and nucleolar RNA transcription in yeast

city: Bloomington

first: Gabriel

middle: E

last: Zentner

state: IN

address: 915 E 3rd St

department: Biology

institute: Indiana University

summary: Eukaryotic RNA polymerase II (RNAPII) transcribes mRNA genes and non-protein coding RNAs (ncRNAs) including small nuclear and nucleolar RNAs (sn/snoRNAs). In metazoans, RNAPII transcription of sn/snoRNAs is facilitated by a number of specialized complexes, but no such complexes have been discovered in yeast. It has been proposed that yeast sn/snoRNA promoters use the same factors as mRNA promoters, but the extent to which regulators of mRNA genes function at yeast sn/snoRNA genes is unclear. Here, we investigated a potential role for the Mediator complex, essential for mRNA gene transcription, in the transcription of sn/snoRNA genes. We found that the Mediator maps to most sn/snoRNA gene regulatory regions and that rapid depletion of the essential structural subunit Med14 strongly reduces RNAPII and TFIIB occupancy as well as nascent transcription of sn/snoRNA genes. Deletion of Med3 and Med15, subunits of the activator-interacting Mediator tail module, does not affect Mediator recruitment to or RNAPII and TFIIB occupancy of sn/snoRNA genes. Our analyses suggest that Mediator promotes PIC formation and transcription at sn/snoRNA genes, expanding the role of this critical regulator beyond its known functions in mRNA gene transcription and demonstrating further mechanistic similarity between the transcription of mRNA and sn/snoRNA genes.

overall_design: ChEC-seq was used to map Mediator binding to the genome and TFIIB ChIP-seq was used to monitor the effect of auxin degron-mediated destabilization of Mediator on pre-initiation complex formation.

last: Tourigny

first: Moustafa

last: Saleh


title: Mapping multi-layered regulation in response to environmental stress

first: Shuvadeep

last: Maity

address: 12 waverly place

department: Center for Genomics and Systems Biology

institute: New york University

summary: We have mapped transcript and protein concentrations in cervical cancer cells responding to treatment with tunicamycin over an eight hour time course. We complement this dataset with RNA footprints of ribosomes and non-ribosomal proteins to determine changes in translation and trans-factor binding. The goals of this study are to unveil the time dependent complexity of the signaling pathways at the level of transcription and  translation during different stress conditions like stress of the endoplasmic reticulum and oxidative stress.

overall_design: Hela cells were subjected to ER stress or oxidative stress. Transcript, ribosome footprint and protein occupency profiles were generated for different time points (0, 1 , 4 , and 8 hours) by deep sequencing, in triplicate, using Illumina Illumina HiSeq 2500.

first: Christine

last: Vogel


title: RNASeq Analysis of Gene Expression in Naïve and Regulatory CD4+ T cells from Wild Type and YAP-deficient mice

city: Dalian

first: Jinsong

last: Yan

address: 9 west section, Lvshun south road, Dalian, Liaoning Province, China

department: Institute of Cancer Stem Cell

institute: Dalian Medical University

summary: Regulatory T cells (Tregs) are critical for maintaining self-tolerance and immune homeostasis, but their suppressive function can impede effective anti-tumor immune responses. Foxp3 is a transcription factor expressed in Tregs that is required for their function. The pathways and microenvironmental cues governing Foxp3 expression and Treg function are not completely understood. We found that Yes-associated protein (YAP), a co-activator of the Hippo pathway, is highly expressed in Tregs and bolsters Foxp3 expression and Treg function in vitro and in vivo. To assess how YAP influences patterns of gene expression in Tregs, naïve CD4+ T cells and Tregs were isolated from wild type mice and CD4+ T cell lineage-restricted YAP knockout mice (YAPflox/flox, CD4-Cre+). Gene expression by naïve CD4+ T cells and their resting and stimulated Treg counterparts was analyzed by RNASeq. Our findings reveal that YAP ablation undermines expression of multiple genes involved in the TGFβ/SMAD signaling pathway in Tregs including Activin. These findings suggest that YAP potentiates activity along a pro-Treg signaling axis.

overall_design: The gene expression patterns in naïve T cells and nTregs from Wild type and  YAP cKO (YAP flox/flox,CD4-Cre+) mice were assessed and compared using RNASeq. Sequencing was performed using a Illumina Hiseq2000.

first: Fan

last: Pan

first: Zhiguang

last: Li

first: Xuehong

last: Zhang


title: Single-cell transcriptome dynamics in stabilized pituitary gonadotrope cells [smartseq_pituitary]

first: Yongchao

last: Ge

address: One Gustave L Levy Place #1137

institute: Icahn School of Medicine at Mount Sinai

overall_design: SC RNA-seq was performed on primary mouse pituitary cell cultures following stabilization in RNA-Best and IFC-SC isolation. A total of 56 SCs were analyzed.

first: Frederique

last: Ruf-Zamojski

first: Venugopalan

last: Nair

first: Michel

last: Zamojski

first: Hanna

last: Pincas

first: Chirine

last: Toufaily

first: Jessica

last: Tome-Garcia

first: Marlon

last: Stoeckius

first: William

last: Stephenson

first: Daniel

last: Bernard

first: Nadedja

last: Tsankova

first: Boris

last: Hartmann

first: Miguel

last: Fribourg

first: Peter

last: Smibert

first: Harold

last: Swerdlow

first: Judith

last: Turgeon

first: Stuart

last: Sealfon


title: MYC interacts with the G9a histone methyltransferase to drive transcriptional repression and tumorigenesis

city: Toronto

first: Yu-Jia

last: Shiah

state: Ontario

address: MaRS Centre 661 University Avenue Suite 510

department: Informatics and Bio-computing

institute: Ontario Institute for Cancer Research

summary: MYC is an oncogenic driver that regulates transcriptional activation and repression, yet molecular mechanisms of MYC transformation remain unclear. We demonstrate that MYC interacts with the G9a H3K9-methyltransferase complex to control transcriptional repression. Inhibiting G9a hinders MYC chromatin binding at MYC-repressed genes and de-represses gene expression to antagonize cellular transformation. By identifying the MYC Box II region as essential for MYC-G9a interaction, a long-standing missing link between MYC transformation and gene repression is unveiled. In breast cancer, anti-proliferative sensitivity to G9a pharmacological inhibition associates with MYC sensitivity and the basal subtype. Inhibiting G9a in vivo suppresses MYC-dependent basal breast tumor growth. Our findings reveal G9a as an epigenetic regulator of MYC-mediated transcriptional repression and a therapeutic vulnerability in MYC-driven cancers.

overall_design: Transcriptome-wide analysis comparing the effect of G9a knockdown (using two independent shRNAs) versus scramble control (shSCR) in MCF10A breast epithelial cells transformed with ectopic PI3KH1047R and MYC (MCF10A.PM). Three biological replicates for each shRNA condition was performed.

last: Tu

first: Paul

last: Boutros

first: Linda

middle: Z

last: Penn


title: TDP-43 modulates translation of specific mRNAs linked to neurodegenerative disease

city: Hamburg

first: Giorgio

last: Gonnella

address: Bundesstrasse 43

department: Zentrum für Bioinformatik

institute: Universität Hamburg

summary: We generated total mRNA libraries and ribosome footprint libraries from motor neuron-like cells (MN1) and primary cortical neurons expressing GFPor pure wild type cells as control, human TDP-43 wild type and mutant proteins to identify translational targets of human TDP-43 mutant protein

overall_design: We used two replicates for MN1 cells and three replicates for primary neurons from which total mRNA and ribosome footprint libraries were generated. The libraries were multiplexed sequenced on an Illumina HiSeq2500 SR 50 base run.

first: Nagammal

last: Neelagandan

first: Stefan

last: Dang

first: Malik

last: Alawi

first: Daniela

last: Indenbirken

first: Adam

last: Grundhoff

last: Kurtz

first: Kent

last: Duncan


title: Subtype diversification and synaptic specificity of stem cell-derived spinal interneurons

status: Public on Oct 07 2018

first: Phuong

middle: Thi

last: Hoang

address: 630 West 168th St

department: Pathology

institute: Columbia University Medical Center

summary: Neuronal diversification is a fundamental step in the construction of functional neural circuits, yet how neurons generated from single progenitor domains acquire diverse subtype identities remains poorly understood. Here, we developed a stem cell-based system to model subtype diversification of V1 interneurons, a class of spinal neurons comprising four clades, each containing dozens of molecularly distinct neuronal subtypes. We demonstrate that V1 subtype diversity is not hard-wired and can be modified by extrinsic signals. Inhibition of Notch and activation of retinoid signaling results in a switch to MafA clade identity and enriches differentiation of Renshaw cells, a specialized MafA subtype that mediates recurrent inhibition of spinal motor neurons. We show that in vitro-generated Renshaw cells migrate into appropriate spinal laminae upon transplantation and form subtype-specific synapses with motor neurons. Our results demonstrate that stem cell-derived neuronal subtypes can be used to investigate mechanisms underlying neuronal subtype specification and circuit assembly.

overall_design: Total RNA profiles during differentiation of mouse ES cell-derived V1 and dI4 spinal interneurons by deep sequencing

middle: T

first: Joshua

middle: I

last: Chalif

first: Jay

last: Bikoff

first: George

last: Mentis

first: Thomas

last: Jessell

first: Hynek

last: Wichterle


title: Small and large RNA sequencing of mouse livers during development and after miR-122 exicision

city: Seattle

last: Valdmanis

state: WA

address: 1705 NE Pacific St, HSB J-309

department: Medicine

institute: University of Washington

summary: miR-122 is a highly-expressed liver microRNA that is activated perinatally and aids in regulating cholesterol metabolism and promoting terminal differentiation of hepatocytes.  Disrupting expression of miR-122 can re-activate embryo-expressed adult-silenced genes, ultimately leading to the development of hepatocellular carcinoma (HCC).   We interrogated the liver transcriptome at various time points after genomic excision of miR-122 to determine the cellular consequences leading to oncogenesis.  Loss of miR-122 led to specific and progressive increases in expression of imprinted clusters of microRNAs and mRNA transcripts at the Igf2 and Dlk1-Dio3 loci that could be curbed by re-introduction of exogenous miR-122.  mRNA targets of other abundant hepatic microRNAs became functionally repressed leading to widespread hepatic transcriptional de-regulation.   Together, this reveals a transcriptomic framework for the hepatic response to loss of miR-122 and the outcome on other microRNAs and their cognate gene targets.

overall_design: RNA sequencing of 14 liver samples of mice with LoxP sites surrounding mature miR-122.  Triplicate of uninjected mice and mice harvested 21, and 45 days after receiving AAV-Cre and one mouse each 100 or 200 days after Cre.  Triplicate liver samples of additional germline miR-122 knockout mice.  Small RNA sequencing of the same liver samples along with additional time points after Cre removal of miR-122.  Small RNA sequencing of livers of wildtype 129Sv/J mice at various stages of embryo and post-natal development.

middle: N

first: Mark

middle: A

last: Kay