title: Profiling of Histone H3 Trimethylation at Lysine 36 (H3K36me3) in mouse embryonic stem cells: Setd2 knockdown and control cells

first: Jianjun

last: Chen

summary: Setd2 is the specific methyltransferase of H3K36me3. To obtain Setd2-dependent landscape of H3K36me3 in mouse genome, we used mouse embryonic stem cells (mESCs) model with doxycycline (Dox)-induced Setd2 knockdown, and performed ChIP sequencing in mESCs with or without Dox treatment.

overall_design: ChIP-seq in mESCs with or without Dox-induced Setd2 knockdown.

first: Huilin

last: Huang

first: Hengyou

last: Weng

first: Keren

last: Zhou

first: Boxuan

last: Zhao

first: Tong

last: Wu

first: Chuan

last: He

first: Jianhua

last: Yang


title: Profiling of N6-methyladenosine in mouse embryonic stem  cells: Setd2 knockdown and control cells

status: Public on Feb 21 2019

city: Monrovia

state: CA

department: Systems Biology

country: USA

institute: Beckman Research Institute of City of Hope

type: Methylation profiling by high throughput sequencing

summary: Setd2 is the specific methyltransferase of H3K36me3. To understand the global effect of H3K36me3 on m6A modification, we used mouse embryonic stem cells (mESCs) model with doxycycline (Dox)-induced Setd2 knockdown, and performed m6A-IP followed by sequencing in mESCs with or without Dox treatment. We found that depletion of H3K36me3 by Setd2 silencing globally reduced  m6A in mouse transcriptome.

overall_design: m6A-seq in mESCs with or without Dox-induced Setd2 knockdown.


title: Human prostate cancer cell lines treated with BET Bromodomain inhibitor JQ1

status: Public on Feb 20 2019

city: New York

first: Wendy

last: Mao

state: NY

department: Center for Translational Immunology

institute: Columbia University

type: Expression profiling by high throughput sequencing

summary: RNA-Sequencing data for DU145 and PC3 cell lines treated with two concentrations of JQ1 in combination with IFN-y to determine effects of BET Bromodomain inhibition on prostate cancer cell lines

overall_design: RNA-Sequencing of DU145 and PC3 cell lines treated with JQ1 in varying doses and IFN-y, in triplicate

first: Mao

last: Wendy


title: Transcriptomic analysis of the effect of histone H4 K31R mutation in U2OS cells

city: rochester

first: Zhenkun

last: Lou

state: mn

address: 200 1st street sw

institute: mayo clinic

summary: To explore the genome-wide gene expression changes induced by the K31R mutation in the histone H4 protein, we performed RNA-sequencing analysis in U2OS cells expressing either wildtype H4 or K31R mutant H4. We found that the lysine (K) to arginine (R) mutation mainly affected oxidative phosphorylation, mtiochondria dysfunction and et al, but not DNA damage signaling pathways.

overall_design: Total RNAs were extracted from 3 wild-type (WT) H4 and 3 K31R mutant H4 expressing U2OS cells and profiled by RNA-sequencing.

first: Bo

last: Qin

first: Yu

last: Jia

first: Nowsheen

last: Somaira

first: Wang

last: Minghui

first: Tu

last: Xinyi

first: Liu

last: Tongzheng

first: Li

last: Honglin


title: MicroRNAs from saliva of anopheline mosquitoes mimic human endogenous miRNAs and may contribute to vector-host-pathogen interactions

status: Public on Feb 22 2019

city: Rome

first: Bruno

last: Arca

address: P.le Aldo Moro 5

department: Public Health and Infectious Diseases

country: Italy

institute: Sapienza University

type: Non-coding RNA profiling by high throughput sequencing

summary: During blood feeding haematophagous arthropods inject into their hosts a cocktail of salivary proteins whose main role is to counteract host haemostasis, inflammation and immunity. However, animal body fluids are known to also carry miRNAs. To get insights into saliva and salivary gland miRNA repertoires of the African malaria vector Anopheles coluzzii we used small RNA-Seq and identified 214 miRNAs, including tissue-enriched, sex-biased and putative novel anopheline miRNAs. Noteworthy, miRNAs were asymmetrically distributed between saliva and salivary glands, suggesting that selected miRNAs may be preferentially directed toward mosquito saliva. The evolutionary conservation of a subset of saliva miRNAs in Anopheles and Aedes mosquitoes, and in the tick Ixodes ricinus, supports the idea of a non-random occurrence pointing to their possible physiological role in blood feeding by arthropods. Strikingly, eleven of the most abundant An. coluzzi saliva miRNAs mimicked human miRNAs. Prediction analysis and search for experimentally validated targets indicated that miRNAs from An. coluzzii saliva may act on host mRNAs involved in immune and inflammatory responses. Overall, this study raises the intriguing hypothesis that miRNAs injected into vertebrates with vector saliva may contribute to host manipulation with possible implication for vector-host interaction and pathogen transmission.

overall_design: Small RNAs from Anopheles coluzzii saliva and salivary glands were analyzed by RNAseq. Adult males and females mosquitoes were used as reference samples. All samples were in triplicates with the exception of saliva (five replicates).

first: Alessio

last: Colantoni


title: Single cell analysis of diverse pathogen responses defines a molecular roadmap for generating antigen-specific immunity

status: Public on Feb 19 2019

city: Rehovot

first: Ido

last: Amit

address: 234 Herzl st.

department: Immunology

country: Israel

institute: Weizmann Institute of Science

summary: The immune system generates pathogen-tailored responses. The precise innate immune cell types and pathways that direct robust adaptive immune responses have not been fully characterized. By using fluorescent pathogens combined with massively parallel single cell RNA-seq, we comprehensively characterized the initial 48 hours of the innate immune response to diverse pathogens. We found that across all pathogens tested, most of the lymph node cell types and states showed little pathogen-specificity. In contrast, the rare antigen-positive cells displayed pathogen-specific transcriptional programs as early as 24 hours after immunization. In addition, mycobacteria activated a specific NK driven IFNγ response. Depletion of NK cells and IFNγ showed that IFNγ initiated a monocyte specific signaling cascade, leading to production of major chemokines and cytokines that promote Th1 development. Our systems immunology approach sheds light on early events in innate immune responses and may help further development of safe and efficient vaccines.

overall_design: Transcriptional profiling of single cells from pathogen-injected mouse auricular lymph nodes, generated from deep sequencing of thousands of cells, sequenced in several batches on illumina Nextseq500. For all experiments, innate immune lymph node cells were sorted accordng to the markers indicated in  Samples' Characteristics "selection marker" field into 384-well MARS-seq2.0 cell capture plates. Sorting of antigen-carrying cells (Ag+) was based on the AF488-fluorescence of the pathogens injected. Different pathogens and time points were used, as indicated in the Samples' Characteristics "infection" and "time points" fields.

first: Ronnie

last: Blecher-Gonen

first: Pierre

last: Bost

first: Kerry

middle: L

last: Hilligan

first: Eyal

last: David

first: Tomer

middle: M

last: Salam

first: Elsa

last: Roussel

first: Lisa

last: Connor

first: Johannes

middle: U

last: Mayer

first: Keren

middle: B

last: Halpern

first: Beáta

last: Tóth

first: Shalev

last: Itzkovitz

first: Benno

last: Schwikowski

first: Franca

last: Ronchese


title: Neuronal Development And The Onset Of Electrical Activity In The Human Enteric Nervous System

city: Rotterdam

first: Erwin

last: Brosens

state: - If in U.S, Select a State -

address: Dr molewaterplein 50

department: Clinical genetics

country: Netherlands

institute: ErasmusMC

summary:
Objective: To assess the development of neuronal subtypes and the emergence of evoked electrical activity within the developing human ENS.
Methods: Human foetal gut samples were obtaining via the MRC-Wellcome Trust Human Developmental Biology Resource (UK). Characterisation of the developing ENS was performed by immunohistochemistry, calcium imaging, RNAseq and qRT-PCR
Results: Human foetal colon samples displayed robust Tuj1 immunohistochemistry by embryonic week (EW) 12 with a dense neuronal network at the level of the myenteric plexus. At EW12 expression of excitatory neurotransmitter markers (VAChT and Sub P) was observed. By contrast, inhibitory neurotransmitter markers (nNOS and VIP) were not observed until EW14. Co-labeling with synaptic markers (SYN1/SNAP-25) demonstrated the development of synaptic contacts by EW12. However, electrical train stimulation (40V,2s,20Hz of 300?s electrical pulses) did not evoke activity within the myenteric plexus of EW12 foetal gut (n=0/3). Similarly, the majority of EW14 gut tissues assessed (80%), demonstrated no response to electrical stimulation (n=4/5). Interestingly, at EW16 Tuj1+ expression, in the myenteric plexus, was observed within discrete ganglia and was combined with the emergence of calcium transients (F/F0=1.273±0.024;n=3), upon electrical stimulation (n=3/3), which were abolished after the addition of 1uM TTX (n=3/3). RNAseq and qRT-PCR analysis between EW12-16 revealed increases in expression in genes involved in neurotransmission and action potential generation including SCN9A and KCNQ3.
Conclusion: Here we demonstrate the temporal development of human enteric neuronal subtypes from EW12-14 and the subsequent emergence of coordinated electrical activity within the human foetal ENS at approximately EW16.

overall_design: total RNA was isolated from three human embryonic colon samples. Three technical replicates/timepoint were sequenced.

first: Conor

middle: J

last: McCann

first: Maria

last: Alves

first: Dipa

last: Natarajan

first: Silvia

last: Perin

first: Robert

last: Hofstra

first: Alan

last: Burns

first: Nikhil

last: Thapar


title: Histone H3 Trimethylation at Lysine 36 (H3K36me3) Guides m6A RNA Modification

first: Jianjun

last: Chen

type: Genome binding/occupancy profiling by high throughput sequencing

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: Active ribosome profiling in SETD2 or METTL14 knockdown HepG2 cells

summary: SETD2 is the specific methyltransferase of H3K36me3, while METTL14 is a critical subunit of the m6A methyltransferase complex. To evaluate the effect of SETD2 and METTL14 on translation, we conducted robosome profiling in SETD2 and METTL14 knockdown and control HepG2 cells. Our RNA ribosome profiling revealed that depletion of SETD2 and METTL14 resulted in a global reduction in RNA translation and the changes of translation efficiency were correlated between SETD2 and METTL14 knockdown cells.

overall_design: We performed active ribosome profiling in HepG2 cells with stably expressed SETD2, METTL14 or control shRNA.

first: Huilin

last: Huang

first: Hengyou

last: Weng

last: Zhou

first: Tong

last: Wu

first: Chuan

last: He

first: Jianhua

last: Yang


title: PAR-CLIP-seq of HA-METTL14 in HepG2 cells

summary: The METTL3-METTL14 heterodimer is the core component of the N6-methyltransferase complex (MTC) that catalyzes methylation of adenosine residues at the N(6) position of RNA. As the non-catalytic subunit of MTC, METTL14 functions as the RNA-binding scaffold that recognizes the RNA substrate. To identify METTL14 binding sites in the transcriptome, we overexpressed HA-tagged METTL14 in HepG2 cells and performed PAR-CLIP (Photoactivatable Ribonucleoside-Enhanced Crosslinking and Immunoprecipitation) using HA antibody. Subsequent deep sequencing identified 5,961 METTL14 binding sites, in which the GGAC motif was enriched.

overall_design: PAR-CLIP using HA antibody in HepG2 cells with HA-METTL14 overexpression

first: Keren


title: Characterization of the dynamics of lamin A and lamin B LADs in HepG2 cells: impact of cyclosporin A

city: Oslo

first: Philippe

last: Collas

address: PO Box 1112 Blindern

department: Institute of Basic Medical Sciences

country: Norway

institute: University of Oslo

summary:
Purpose: to qualify and quantify the rearrangement of interactions of nuclear lamins A/C and B with the genome, in relation to nuclearradial  repositioning of loci and changes in gene expression, in HepG2 cells exposed to cyclosporin A. .To compare HepG2 cell line transcriptome profiling (RNA-seq) with radially positioning of the chromatin anchored at the nuclear periphery before and after CsA treatment.
Methods: To this end, we mapped lamin A and lamin B lamina-associated domains (LADs) by  chromatin immunoprecipitation-sequencing (ChIP-seq) of lamin A/C (antibody sc7292x, Santa Cruz Biotechnology) and lamin B1 (antibody ab16048, Abcam), respectively. HepG2 cells were either cultured under proliferative conditions (controls) or exposed for 3 days to 10 uM cyclosporin A. We also assesed the transcriptome by RNA-seq under each condition in duplicate cultures.
Results: CsA elicits accumulation of pre-lamin A in HepG2 cells, raising the hypothesis of a global rearrangement of lamin-chromatin interactions. We show here the existence of overlapping and distinct lamin A and B lamina-associated domains (which we refer to as A- and B-LADs, respectively). Whereas B-LADs largely remain constitutive, CsA elicits the formation of facultative A-LADs. Re-localization of A-LADs occur mainly on preexisting B-LADs. However, LAD rearrangement does not correlate with systematic changes in gene expression within LADs. We find a reorganization of A- and B-LADs after CsA treatment, entailing distinct contributions of A- and B- type lamins. to genome organization. Indeed, classification of lamin A LADs and lamin B LADs into properties of ‘A-only’, ‘B-only’ and ‘A-B’ LADs show an overall  loss of A-only LADs after CsA treatment. A- only and B-only LADs are highly dynamic with A-B LADs being more stable.The rearrangement of lamin association after CsA treatment correlates with repositioning of loci in the nuclear space with, notably, a loss of lamin B associated with a re-localization of loci towards the nuclear center and conversely, a gain of lamin B linked to a repositioning of loci towards the nuclear periphery. Predictions on radial repositioning of LADs, and of loci within, from 3D structural models of the genome were supported by fluorescence in situ hybridization (FISH) analyses.
Conclusions: We show that, while they amply co-localize on well-conserved LADs, lamins A and B also interact with distinct genomic regions that can interchange (switch) between lamin A and B upon CsA treatment. We unveil distinct lamin A and B interactions with chromatin, suggesting complementary contributions to genome conformation. Our data suggest that  and lamins A and B may differentially modulate genome organization.

overall_design: Lamin A/C and lamin B1 ChIP-seq analysis, and RNA-seq analysis, of the hepatocarcinoma HepG2 cell line under 2 different treatment conditions: control (Ctl) and cells treated with 10 µM Cyclosporin A (CsA) for 72 h. For ChIp-seq, ChIP DNA was purified by phenolchloroform extraction and ethanol precipitation, before Illumina library preparation at our sequencing facility on an Illumina HiSeq2500. For RNA-seq, total RNA was isolated from 2 replicates of control and CsA-treated cells using the RNeasy Mini Kit (Qiagen). DNase treatment was done with RQ1 RNase-Free DNase (M101, Promega) and libraries were prepared and sequenced on an Illumina HiSeq2500.

first: Frida

last: Forsberg

first: Annaël

last: Brunet

first: Tharvesh

last: Liyakat Ali


title: RNA-seq analysis of AKTi MK2206 resistant BT474 and T47D cells

city: Lexington

first: Binhua

middle: P

state: KY

address: 789 South Limestone

department: Markey Cancer Center/Biochemistry

institute: University of Kentucky School of Medicine

summary: BRD4 assembles transcriptional machinery at gene super-enhancer regions and governs the expression of genes that are critical for cancer progression. However, it remains unclear whether BRD4-mediated gene transcription is required for tumor cells to develop drug resistance. Our data show that prolonged treatment of luminal breast cancer cells with AKT inhibitors induces FOXO3a de-phosphorylation, nuclear translocation, and disrupts its association with SIRT6, eventually leading to FOXO3a acetylation as well as BRD4 recognition. Acetylated FOXO3a recognizes the BD2 domain of BRD4, recruits the BRD4/RNAPII complex to the CDK6 gene promoter and induces its transcription. Pharmacological inhibition of either BRD4/FOXO3a association or CDK6 significantly overcomes the resistance of luminal breast cancer cells to AKT inhibitors in vitro and in vivo. Our study reports the involvement of BRD4/FOXO3a/CDK6 axis in AKTi resistance and provides potential therapeutic strategies for treating resistant breast cancer.

overall_design: Total RNA was extracted from MK2206 resistant cells for RNA sequencing. Parental cells without MK2206 resistance were used as controls.

first: Jian

last: Shi


title: ChIP-seq of HA-METTL14 in HepG2 cells

summary: The METTL3-METTL14 heterodimer is the core component of the N6-methyltransferase complex (MTC) that catalyzes methylation of adenosine residues at the N(6) position of RNA. As the non-catalytic subunit of the MTC, METTL14 functions as the RNA-binding scaffold that recognizes the RNA substrate. We found METTL14 could  interacte with chromatin through recognition of H3K36me3. ChIP-seq with HA-tagged METTL14 using an HA antibody identified 300 peaks in HepG2 cells, among which 53% peaks were located in the gene body and only 3% peaks were located in the promoter. The binding sites of METTL14 on chromatin correlate with that of H3K36me3.To investigat whether this interaction is Pol II dependent, we treated cells with a Pol II inhibitor 5,6-Dichlorobenzimidazole 1-β-D-ribofuranoside (DRB) for a short time. Interestingly, we found the interaction of METTL14 with chromatin in gene body region was not affected by DRB treatment .

overall_design: ChIP-seq using HA antibody in HepG2 cells with HA-METTL14 overexpression


title: Destabilization of AETFC through C/EBPalpha-mediated repression of LYL1 contributes to t(8;21) leukemic cell differentiation

city: Shanghai

first: Chun-hui

last: Xu

state: Shanghai

address: 197 Ruijin Road II

department: State Key Laboratory of Medical Genomics

country: China

institute: Shanghai Institute of Hematology, Rui Jin Hospital, Shanghai Jiao Tong University School of Medicine

summary: In t(8;21) leukemic cells, the leukemogenic fusion protein AML1-ETO is stabilized and functions through the AML1-ETO-containing transcription factor complex (AETFC). Destabilization of AETFC thus provides a strategy to target AML1-ETO. In this study, we found that AETFC can be destabilized by a specific mechanism involving a direct repression of the core component LYL1 by C/EBPalpha at transcriptional level. We performed a ChIP-seq analysis of the genome-wide occupancy of C/EBPalpha and identifeid a -1 kb C/EBPalpha-binding site in the LYL1 locus that mediate this repression. As LYL1 acts as a linker between the AML1-ETO-E and LMO2-LDB1 parts of AETFC, depletion of LYL1 causes a destabilization of AETFC, which increases susceptibility of the leukemic cells to differentiation. Our results have provided a novel mechanism by which C/EBPalpha can directly destabilize AETFC, and have identified LYL1 as a new therapeutic target for treatment of t(8;21) leukemia.

overall_design: Since the expression of C/EBPalpha in the AML1-ETO-expressing Kasumi-1 cells is very low, we overexpressed an HA-tagged C/EBPalpha in the cells and performed the ChIP-seq with an anti-HA antibody. We also performed RNA-seq analysis of the C/EBPalpha-overexpressing Kasumi-1 cells and the control cells transduced with the MIGR1 vector.

first: Meng-Meng

last: Zhang

last: Liu

first: Yuan-Liang

first: Bowen

last: Rong

first: Chun-Hui

first: Fei

last: Lan

first: Qiu-Hua

first: Xiao-Jian

last: Sun


title: Identification of the AVRa7,AVRa9, AVRa10 and AVRa22 effector genes from barley powdery mildew fungus (Bgh) association analysis between transcript polymorphisms and AVRa phenotypes from 27 Bgh isolates.

city: Cologne

first: Takaki

last: Maekawa

address: Carl-von-Linne Weg 10

country: Germany

institute: Max-Planck Institute for Plant Breeding Research

summary: Disease resistance is mediated by specific recognition of pathogen avriulence effectors (AVR) by nucleotide-binding leucine-rich repeat (NLR) receptors. The barley (Hordeum vulgare) mildew locus A (mla) resistance gene homolog 1 (RGH1) encoded NLRs (MLAs) confer isolate-specific resistance to the widespread mildew fungus Blumeria graminis forma specialis hordei (Bgh). In barley, MLA has been subject to extensive functional diversification, resulting in allelic resistance specificities, each recognizing a cognate Bgh AVRa. The by genetic association isolated AVRa1 and AVRa13 effectors belong to the candidate secreted effector protein (CSEP)   gene family (Lu et al., 2016). To unravel the complex mechanisms underlying MLA functional diversification in barley and wheat, isolation of numerous Bgh AVRa genes and recognition of their gene products by MLA is necessary. Our here deployed higher resolution genetic association approach identified the Bgh avirulence gene candidate loci AVRa7, AVRa9, AVRa22 and AVRa10 by associating of transcript polymorphisms and AVRa phenotypes from a collection of 27 Bgh isolates. We collected 10 Bgh isolates from a local Bgh population in Cologne in addition to our previous collection of 17 Bgh isolates (Lu et al., 2016).

overall_design: Detached leaves of the barely cultivar Pallas or Manchuria were infected with previously sequenced Bgh isolates CC52 and CC88 (Lu et al. 2016, PNAS) as well as 10 new Bgh isolates collected locally in Cologne in 2016 and 2017. For each isolate, samples were collected at 18 and 48 hours post inoculation (hpi), and RNA extracted as described below, resulting in a total of 32 RNA-seq samples that were analyzed.

first: Isabel

last: Saur

first: Saskia

last: Bauer

first: Barbara

last: Kracher

first: Paul

last: Schulze-Lefert


title: Genome-wide DNA Methylation Comparison between Live Human Brain and Peripheral Tissues within Individuals

city: Iowa City

first: Gen

last: Shinozaki

state: IA

address: University of Iowa Hospitals and Clinics, 200 Hawkins Dr

department: Psychiatry

institute: University of Iowa

type: Methylation profiling by genome tiling array

summary: Differential DNA methylation (DNAm) in the brain is associated with many psychiatric diseases, but access to brain tissues is essentially limited to post-mortem samples. The use of surrogate tissues has become common in identifying methylation changes associated with psychiatric disease. In this study, we determined the extent to which peripheral tissues can be used as surrogates for DNAm in the brain. Blood, saliva, buccal, and live brain tissue samples from 27 medically intractable epilepsy patients undergoing brain resection were collected. Genome-wide methylation was assessed with the Infinium HumanMethylation450 (n=12) and HumanMethylationEPIC BeadChip arrays (n=21). For each CpG and each gene, levels of brain-peripheral tissue correlation varied widely. This indicates that to determine the most useful surrogate tissue for representing brain DNAm, the patterns specific to the genomic region of interest must be considered. To assist in that objective, we have developed a website, IMAGE-CpG, that allows researchers to interrogate DNAm levels and degree of cross-tissue correlation in user-defined locations across the genome.

overall_design: Genome-wide methylation was assessed with the Infinium HumanMethylation450 and HumanMethylationEPIC BeadChip arrays. The 450K dataset includes 12 subjects with brain, blood, and saliva samples. The EPIC dataset includes 21 subjects with brain, blood, buccal, and saliva samples. Additionally, fluorescence activated cell sorting (FACS) was performed to separate cells positive for a neuronal marker, resulting in five neuronal positive samples (brain_pos) and twelve neuronal negative ones (brain_neg) with sufficient DNA quantity for analysis with the EPIC array.

first: Patricia

middle: R

last: Braun


title: Loss of TET3-mediated 5hmC promotes the Neurodegeneration of Alzheimer’s disease

city: Edison

first: Jiali

last: Li

state: middlesex

address: 65 James ST

department: Neuroscience Intitute

institute: HMH JFK Medical Center

summary: Alzheimer's disease (AD) was attributed to alterations in multiple epigenetic systems including DNA methylation and demethylation patterns. DNA 5-hydroxymethylcytosin (5hmC), an epigenetic hallmark, plays importantly regulatory role in many biological processes. However, the 5hmC-mediated epigenetic underpinnings of AD neurodegeneration remain poorly understood. Here we report that selective loss of 5hmC is substantially presented in human AD and 3xTg-AD mouse neocortical and hippocampal neurons. Quantitative genome-wide analysis of hMeDIP-seq reveals that neuron-specific shift in decreased 5hmC enrichment in regions of promoter, intergenic and gene body of mRNA and lncRNA genes was found in3xTg-AD mice. We further identified that TET3, an enzyme that converts 5-methylcytosine (5mC) to 5hmC, responded to Beta amyloid neuronal toxicity and was mainly responsible for loss of 5hmC in AD brain. Overexpression of human TET3 catalytic domain (hTET3CD) significantly improves the neuroinflammation, neuropathological progression and cognitive deficits in 3xTg-AD mice. These findings implicate as a potential hallmark, TET3-mediated 5hmC epigenetic dysregulation is involved in driving AD neurodegeneration.

overall_design: There are four groups, wild type and 3xTg-AD mouse cortical neurons; wild type and 3xTg-AD mouse cortical astrocytes. For each group, genomic DNA samples were immunoprecipitated with anti-5hmC (n=3). There were also three replicates of input control for each group.

first: Lianwei


title: The dynamic transcriptional landscape of mammalian organogenesis at single cell resolution

city: Seattle

first: Junyue

last: Cao

state: WA

address: Foege Building S-210, 3720 15th Ave NE

department: Department of Genome Sciences

institute: University of Washington

summary: During mammalian organogenesis, the cells of the three germ layers transform into an embryo that includes most major internal and external organs. The key regulators of developmental defects can be studied during this crucial period, but conventional approaches lack the throughput and resolution to obtain a global view of the molecular states and trajectories of a rapidly diversifying and expanding number of cell types. Here we set out to investigate the transcriptional dynamics of mouse development during organogenesis at single cell resolution. With an improved single cell combinatorial indexing-based protocol (‘sci-RNA-seq3’), we profiled over 2 million cells derived from 61 mouse embryos staged between 9.5 and 13.5 days of gestation (E9.5 to E13.5; 10 to 15 replicates per timepoint). We identify hundreds of expanding, contracting and transient cell types, many of which are only detected because of the depth of cellular coverage obtained here, and define the corresponding sets of cell type-specific marker genes, several of which we validate by whole mount in situ hybridization. We explore the dynamics of proliferation and gene expression within cell types over time, including focused analyses of the apical ectodermal ridge, limb mesenchyme and skeletal muscle. With a new algorithm (Monocle 3), we identify the major single cell developmental trajectories of mouse organogenesis, and within these discover examples of distinct paths to the same endpoint, i.e. branching and convergence. These data comprise a foundational resource for mammalian developmental biology, and are made available in a way that will facilitate their ongoing annotation by the research community.

first: Malte

last: Spielmann

first: Xiaojie

last: Qiu

first: Daniel

last: Ibrahim

first: Xingfan

last: Huang

first: Andrew

last: Hill

first: Fan

first: Stefan

last: Mundlos

first: Lena

last: Christiansen

first: Frank

last: Steemers

first: Cole

last: Trapnell

first: Jay

last: Shendure


title: Profiling of Histone H3 Trimethylation at Lysine 36 (H3K36me3) in HepG2 cells: SETD2 knockdown and control cells

first: Jianjun

last: Chen

summary: SETD2 is the specific methyltransferase of H3K36me3. To obtain SETD2-dependent landscape of H3K36me3 in human genome, we performed ChIP sequencing in SETD2 silenced and control HepG2 cells.

overall_design: ChIP-seq in HepG2 cells with stably expressed SETD2 or non-specific control shRNAs.

first: Huilin

first: Hengyou

last: Weng

first: Keren

last: Zhou

first: Boxuan

last: Zhao

first: Tong

last: Wu

first: Chuan

last: He

first: Jianhua

last: Yang


title: Gene expression signatures of SATB2-defficient vs wild-type adult neocortex

city: Innsbruck

first: Galina

last: Apostolova

address: Innrain 66

department: Institute for Neuroscience

country: Austria

institute: Medical University Innsbruck

summary: During CNS development, the nuclear protein SATB2 is expressed in superficial cortical layers and determines projection neuron identity. In the adult CNS, SATB2 is expressed in pyramidal neurons of all cortical layers and is a regulator of synaptic plasticity and long-term memory. Common variation in SATB2 locus confers risk of schizophrenia whereas rare, de novo structural and single nucleotide variants cause severe intellectual disability and absent or limited speech. To which extent symptoms in SATB2-related human pathologies depend on developmental or adult functions of the protein remains to be established. To characterize differences in SATB2 molecular function in developing vs adult neocortex, we compared SATB2 protein interactomes and SATB2-driven gene expression programs at the two ontogenetic stages by co-IP mass spectrometry and RNAseq analyses, respectively. Our results demonstrated that 1) SATB2 interacts with different protein networks at the two ontogenetic stages, with a switch from transcriptional repression towards organization of chromatin structure and 2) SATB2 determines differential transcriptional programs in neonatal vs adult cortex.

overall_design: Analysis of neocortex transcriptomes of adult (3 month old) SATB2-deficient (Satb2flx/flx::Camk2a-Cre ) vs floxed mice

first: Georg

last: Dechant


title: FTO controls reversible m6Am RNA methylation during snRNA biogenesis

status: Public on Feb 18 2019

city: Heidelberg

first: Jan

last: Mauer

state: BW

address: Im Neuenheimer Feld, 583

institute: BioMed X Innovation Center

summary: Small nuclear RNAs (snRNAs) are core spliceosome components and mediate pre-mRNA splicing. Here we show that snRNAs contain a regulated and reversible nucleotide modification causing them to exist as two different methyl isoforms, m 1 and m 2 , reflecting the methylation state of the adenosine adjacent to the snRNA cap. We find that snRNA biogenesis involves the formation of an initial m 1 isoform with a single-methylated adenosine (2′-O-methyladenosine, Am), which is then converted to a dimethylated m 2 isoform (N 6 ,2′-O-dimethyladenosine, m 6 Am). The relative m 1 and m 2 isoform levels are determined by the RNA demethylase FTO, which selectively demethylates the m 2 isoform. We show FTO is inhibited by the oncometabolite d-2-hydroxyglutarate, resulting in increased m 2 -snRNA levels. Furthermore, cells that exhibit high m 2 -snRNA levels show altered patterns of alternative splicing. Together, these data reveal that FTO controls a previously unknown central step of snRNA processing involving reversible methylation, and suggest that epitranscriptomic information in snRNA may influence mRNA splicing.

overall_design: miCLIP was performed with total RNA from wild-type and Fto knockout mouse liver

first: Samie

last: Jaffrey


title: The Hippo Pathway Prevents YAP/TAZ–Driven Hypertranscription and Controls Neural Progenitor Number

city: Memphis

first: David

last: Finkelstein

state: TN

address: 332 N. Lauderdale St.

department: Computational Biology

institute: St Jude Children's Research Hospital


title: Profiling of N6-methyladenosine in HepG2 cells: SETD2, METTL3, METTL14 or WTAP knockdown and control cells

summary: SETD2 is the specific methyltransferase of H3K36me3, while METTL3, METTL14 and WTAP are the components of m6A methyltransferase complex. To understand the global effect of H3K36me3 on m6A modification, we compared the m6A profiling in SETD2 and METTL3, METTL14 or WTAP knockdown HepG2 cells, and found depletion of H3K36me3 by SETD2 silencing globally reduced m6A in human transcriptome. What’s more, most of the SETD2-dependent hypomethylation sites also responded to knockdown of METTL3, METTL14, or WTAP.

overall_design: m6A-seq in HepG2 cells with stable-y expressed SETD2, METTL3, METTL14, WTAP or non-specific control shRNAs.

last: Huang


title: RNA-seq of B2, B1 and B2toB1 cells

status: Public on Feb 15 2019

city: Berlin

first: Robin

last: Graf

address: Robert Rössle Str. 10

department: Immune Regulation and Cancer

institute: Max Delbrueck Center for Molecular Medicine

summary: RNA-seq of splenic follicular B2 cells, peritoneal 5C5 B1 cells and peritoneal B2toB1 cells 30 days post transfer

overall_design: Comparison of transcriptome profile of B2 cells (n=3), B1 cells (n=3) and B2B1 cells (n=3)

first: Klaus

last: Rajewsky


title: The Hippo Pathway Prevents YAP/TAZ–Driven Hypertranscription and Controls Neural Progenitor Number [RNA-seq]

summary: The Hippo pathway controls the activity of YAP/TAZ transcriptional coactivators through a kinase cascade. Despite the critical role of this pathway in tissue growth and tumorigenesis, it is not fully understood how YAP/TAZ–mediated transcription drives proliferation. By analyzing the effects of inactivating LATS1/2 kinases, the direct upstream inhibitors of YAP/TAZ, on mouse brain development and applying cell-number–normalized transcriptome analysis, we discovered that YAP/TAZ activation causes a global increase in transcription activity, known as hypertranscription, and upregulates many genes associated with increased biosynthetic capacity and proliferation. In contrast, conventional read-depth–normalized RNA-sequencing analysis failed to detect the scope of the transcriptome shift and missed most relevant gene ontologies. Hypertranscription in neural progenitors inhibits differentiation and triggers DNA replication stress, DNA damage, and p53 activation, resulting in massive apoptosis. Our findings reveal the remarkable impact of YAP/TAZ activation on global transcription activity and have important implications for understanding YAP/TAZ function.

overall_design: Cell-number-normalized RNA-seq comparing E12.5 WT and Lats1/2;Nestin-Cre dKO mouse telencephalons

first: Alfonso

last: Lavado

first: Ram

last: Kumar

first: Beisi

last: Xu

first: Yiping

last: Fan

first: Geoffrey

last: Neale

first: Xinwei

last: Cao


title: Genome-Wide Detection of CNVs and Their Association with Complex Traits in Holsteins

status: Public on Feb 16 2019

city: Beltsville

first: George

middle: E

last: Liu

address: 10300 Baltimore Avenue

institute: USDA

type: Genome variation profiling by genome tiling array

summary: Copy number variation (CNV) is an important type of genetic variation contributing to phenotypic differences among mammals. Up to now, GWAS analysis using CNV called by array CGH is lacking  in livestock like Holstein cattle. The objectives of this work are to identify CNVs using high-density aCGH data and explore functional CNVs which are associated with complex traits by GWAS method in Holstein cattle. In this study, we reported a systematic CNV association analysis of CNVs and 39 complex production traits in Holsteins.  This research identified 1043 CNV regions (CNVRs) by array CGH data in 47 Holstein bulls. Using a genome-wide association analysis (GWAS) approach, we identified 79 significant CNVRs associated with at least one complex traits after false discovery rate (FDR) correction. Notably, 24 CNVRs were markedly related to daughter pregnancy rate (DPR). This study observed the pleiotropy phenomenon of 39 CNV loci which can simultaneously regulate at least 2 complex traits. In summary, the significant CNVs identified in this research could be utilized additional molecular markers for genetic improvement programs in Holsteins.

overall_design: Whole genome high-denstiy CGH arrays manufactured by NimbleGen containing 2,166,464 oligonucleotide probes were designed and fabricated on a single slide to provide an evenly distributed coverage on cattle UMD3.1 with an average interval of ~1.2 kb between probes. A total of 48 samples were analyzed. 47 of them were male Holsteins for test samples. Six of them have been uploaded in previous work. Their GSE numbers are GSM1537659, GSM1537660, GSM1537661, GSM1537662, GSM1537663, GSM1537664 in Platform GPL11314. Herein, we uploaded other 41 test samples (semen-BTHO-7~semen-BTHO-47) and one reference sample (L1 Dominette 01449, a Hereford cow of European descent and named its result as DTTRACE).

first: Mei

first: Eyal

last: Seroussi


title: Single-cell RNA sequecing of E13.5 mouse cerebella

city: Farmington

first: James

middle: YH

last: Li

state: CT

address: 263 Farmington Ave

department: Genetics and Genome Sciences

institute: UCHC

summary: In this study we performed single-cell sequencing of E13.5 mouse cerebella, revealing different newly generated neurons and their associated molecular features.

overall_design: Design: Single-cell suspensions were prepared using Accumax digestion followed by manual trituration using a Pasteur pipette. Cells were processed with the 10X Genomics Chromium Single Cell Kit Version 1


title: The Hippo Pathway Prevents YAP/TAZ–Driven Hypertranscription and Controls Neural Progenitor Number [ChIP-seq]

overall_design: H3K4me3 ChIP-seq comparing E12.5 control (no Cre) and Lats1/2;Nestin-Cre dKO mouse brains


title: Cell lineage-specific genome-wide DNA methylation analysis of patients with paediatric-onset systemic lupus erythematosus

city: Hong Kong

first: Brian

last: Chung

state: Hong Kong

address: 102 Pokfulam Road

department: Paediatrics and Adolescent Medicine

country: Hong Kong

institute: The University of Hong Kong

summary:
Background: Patients with paediatric-onset systemic lupus erythematosus (SLE) often present with more severe clinical courses than adult-onset patients. Although genome-wide DNA methylation (DNAm) profiling has been performed in adult-onset SLE patients, parallel data on paediatric-onset SLE are not available. Therefore, we undertook a genome-wide DNAm study in paediatric-onset SLE patients across multiple blood cell lineages.
Methods: The DNAm profiles of four purified immune cell lineages were compared in 16 Chinese patients with paediatric-onset SLE and 13 healthy controls using the Illumina HumanMethylationEPIC BeadChip. The DNAm dataset consisted of 145 samples, including data from CD4+ T cells, CD8+ T cells, B cells, neutrophils and whole blood.
Results: Genome-wide DNAm analysis revealed considerable variation in DNAm levels across samples, and as expected, clustering occurred by cell type rather than disease status. Comparison of DNAm in whole blood and within each independent cell lineage identified a consistent pattern of loss of DNAm at 21 CpG sites overlapping 15 genes, which represented a robust, disease-specific DNAm signature for paediatric-onset SLE in our cohort. This DNAm signature shows considerable overlap with that identified in our adult-onset SLE patient cohort, predominantly showing a loss of DNAm and enrichment in genes involved in type I interferon signalling in SLE, regardless of the age of onset. In addition, cell lineage-specific changes, involving both loss and gain of DNAm, were observed in both novel genes and genes with well-described roles in SLE pathogenesis.
Conclusion: The SLE-specific DNAm signature has the potential to develop into a diagnostic biomarker for SLE, which is particularly important for paediatric-onset patients, as diagnosing SLE in children can be challenging. This study also highlights the importance of studying DNAm changes in different immune cell lineages rather than only whole blood, since cell type-specific DNAm changes facilitated the elucidation of the cell type-specific molecular pathophysiology of SLE.

overall_design: DNA was extracted from whole blood and four purified lineages (CD4+ T cells, CD8+ T cells, CD19+ B cells and CD16+ neutrohils) from each participant. The DNA methylation data of 16 SLE was compared with 13 ethnic-matched healthy controls. All the patients are self-reported to be Chinese and all met the criteria of the American College of Rheumatology for SLE diagnosis. Genomic DNA was bisulfite converted and DNA methylation was measured by Illumina MethylationEPIC BeadChip.

first: Kit

middle: S

last: Yeung

first: Tsz

last: Lee

first: Mo

middle: Y

last: Mok

first: Chun

last: YuMak

first: Wanling

last: Yang

last: Chong

first: Pui

middle: W

first: Hok

middle: K

last: Ho

first: Sanaa

last: Choufani

first: Chak

last: Lau

first: Yu

first: Rosanna

last: Weksberg

first: Hon


title: Epigenetic changes in amygdala and cortex of fear-conditioned and ErbB4 Knock-out mice

city: Cold Spring Harbor

first: Jesse

last: Gillis

address: 1 Bungtown Rd

institute: Cold Spring Harbor Laboratory

summary: Chromatin accessibility provides an important window into the regulation of gene expression. Recently, the Assay of Transposase Accessible Chromatin with sequencing (ATAC-seq) was developed to profile genome-wide chromatin accessibility. Here we applied a read-downsampling approach to call robust ATAC-seq peaks in order to profile the regions of differential chromatin accessibility of central amygdala and cortex between different experimental conditions; fear-conditioned vs. control mice and ErbB4 knock-out vs. wild-type mice.

overall_design: Amygdala and cortex of 18 mouse samples under two experimental conditions 1) fear-conditioned and control and 2)ErbB4 knockout in SOM+ cells and wildtype

first: Jayon

last: Lihm

first: Sandra

last: Ahrens

first: Sara

last: Ballouz

first: Hayan

first: Megan

last: Crow

first: Jessica

last: Tollkuhn

first: Shane

last: McCarthy

first: Bo

first: W

last: McCombie


title: Expression data from anisomycin- and imiquimod-induced dermatitis

city: Kyoto

first: Kenji

last: Sakurai

address: 54 Shogoin Kawara-cho, Sakyo

department: Dermatology

country: Japan

institute: Kyoto University

summary:
We provide a new psoriasis mouse model which is induced by p38 activation in skin. We compared the individual transcriptomic proﬁles of anisomycin and imiquimod-induced dermatitis.
We used microarrays to compare the gene expression pattern between anisomycin- and imiquimod- induced dermatitis.

overall_design: Total RNAs prepared from the ears of mice treated with anisomycin and IMQ for 5 consecutive days (n = 3) were subjected to the microarray analysis. An amplified sense-strand DNA product was synthesized with the Ambion WT Expression Kit (Life Technologies, Carlsbad, CA), was fragmented and labelled by the WT Terminal Labelling and Controls Kit (Affymetrix, Santa Clara, CA) and was hybridized to a Mouse Gene 1.0 ST Array (Affymetrix).

first: Soken

last: Tsuchiya

last: Garcet


title: UTX and 53BP1 co-regulate genetic programs for neural differentiation of human embryonic stem cells

first: Beisi

last: Xu

state: Tennessee

address: 262 Danny Thomas Pl

department: Center for Applied Bioinformatics

institute: St Jude Children's Research Hosipital

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

overall_design: Refer to individual Series


title: Effect of mutant TRP53 proteins on nutlin-3a treated mouse lymphoma cell lines (RNA-seq)

city: Parkville

first: Gordon

last: Smyth

state: Vic

address: 1G Royal Pde

department: Bioinformatics

country: Australia

institute: Walter and Eliza Hall Institute of Medical Research

summary: Mutations in TRP53, prevalent in human cancers, reportedly drive tumorigenesis through dominant-negative-effects (DNE) over wt TRP53 and neomorphic gain-of-function (GOF) effects. We show that five TRP53 mutants do not accelerate lymphomagenesis on a TRP53-deficient background but strongly synergize with c-MYC over-expression. RNA-seq analysis revealed that mutant TRP53 does not globally repress wt TRP53 function but exerts a DNE with disproportionate impact on subsets of wt TRP53 target genes, particularly those involved in DNA repair, proliferation and metabolism. This reveals that the mutant TRP53 DNE drives tumorigenesis by modulating wt TRP53 function in a manner that is advantageous for neoplastic transformation.

overall_design: Each of 5 mutant human TRP53 proteins, and a negative control, was expressed in 3 mouse lymphoma cell lines, both before and after activation of WT TRP53 with nutlin-3a.


title: Attenuated chromatin compartmentalization in meiosis and its maturation in sperm development

city: Cincinnati

first: Satoshi

middle: H

last: Namekawa

state: Ohio

address: Cincinnati Children's Hospital Medical Center

department: Division of Reproductive Sciences

type:
Other
Third-party reanalysis

summary: Germ cells manifest a unique gene expression program and regain totipotency in the zygote. Here, we perform Hi-C analysis to examine 3D chromatin organization in male germ cells during spermatogenesis. We show that the highly compartmentalized 3D chromatin organization characteristic of interphase nuclei is attenuated in meiotic prophase. Meiotic prophase is predominated by short-range intrachromosomal interactions that represent a condensed form akin to that of mitotic chromosomes. However, unlike mitotic chromosomes, meiotic chromosomes display weak genomic compartmentalization, weak topologically associating domains, and localized point interactions in prophase. In postmeiotic round spermatids, genomic compartmentalization increases and gives rise to the strong compartmentalization seen in mature sperm. The X chromosome lacks domain organization during meiotic sex-chromosome inactivation. We propose that male meiosis occurs amid global reprogramming of 3D chromatin organization and that strengthening of chromatin compartmentalization takes place in spermiogenesis to prepare the next generation of life.

overall_design: Examination of meiotic pachytene spermatocytes (PS; 2 biological replicates) and postmeiotic round spermatids (RS; 2 biological replicates) via Hi-C, performed alongside third-party reanalyses of the following published reference datasets: sperm (PMID 28178516, GSE79230; 2 biological replicates) and embryonic stem cells (ESC; PMID 24185094, GSE48592; 2 biological replicates), non-synchronized human foreskin fibroblasts (HFF1 non-synchronized; PMID 24200812, ArrayExpress E-MTAB-1948; 1 biological sample), synchronized prometaphase mitosis human foreskin fibroblasts (HFF1 mitosis; PMID 24200812, ArrayExpress E-MTAB-1948; 1 biological sample), and metaphase meiosis II oocytes (MII oocytes; PMID 28703188, GSE82185; 2 biological replicates).

first: Kris

middle: G

last: Alavattam

first: So

last: Maezawa

first: Akihiko

last: Sakashita

first: Haia

last: Khoury

first: Artem

last: Barski

first: Noam

last: Kaplan


title: Critical role of the fibroblast growth factor signalling pathway in Ewing's sarcoma octamer binding transcription factor 4 mediated cell proliferation and tumorigenesis

status: Public on Feb 14 2019

city: SEOUL

first: JUNG

middle: HOON

last: KIM

state: MAPOGU

address: SOGANG R 1206

department: LIF SCIENCE

country: South Korea

institute: SOGANG UNIV

summary: Fibroblast growth factor signalling pathway mediated by EWS-OCT-4 is important for proliferation and tumorigenesis

overall_design: we used Niwa-GFP stable cell line as control group, and Niwa EWS-OCT4A-GFP stable cell line as an experimental group.  All experiments are triplicated.

first: HYO

last: Kim

last: Shim

first: JUNGWOON

last: Lee

first: AH


title: Species-specific maturation profiles of human, chimpanzee and bonobo neural cells

city: La Jolla

first: Fred

last: Gage

state: CA

address: 10010 N Torrey Pines Rd

institute: The Salk Institute for Biological Studies

summary: Understanding the evolutionary mechanisms underlying expansion and reorganization of the human brain is essential to comprehend the emergence of the cognitive abilities typical of our species. Comparative analyses of neuronal phenotypes in closely related species (Homo sapiens; human, Pan troglodytes; chimpanzees and Pan paniscus; bonobos) can shed light onto neuronal changes occurring during evolution, the timing of their appearance and the role of evolutionary mechanisms favoring a particular type of cortical organization in humans. The availability of post-mortem brains of endangered primates is limited and often does not represent important species-specific developmental hallmarks. We used induced pluripotent stem cell (iPSC) technology to model neural progenitor cell migration in Homo and Pan and early development of cortical pyramidal neurons in humans and chimpanzees after following cells grafted in vivo. We present results suggesting differential migration patterns in human neural progenitor cells compared to those of chimpanzees and bonobos in vitro and in vivo. Additionally, we reveal morphometric and functional differences that are suggestive of heterochronic changes in developing human neurons compared to chimpanzees. This report provides a comprehensive analysis of comparative neural development in closely related hominids. The strategy proposed here lays the groundwork for further comparative analysis between human and non-human primates and opens new avenues for understanding the differences in the neural underpinnings of cognition and neurological disease susceptibility between species.

sample_organism:
Pan paniscus
Pan troglodytes
Homo sapiens

overall_design: RNA-sequencing from human, chimpanzee, and bonobo iPS-derived neural progenitor cells

first: Sara

last: Linker

first: Maria

middle: C

last: Marchetto


title: Mouse Embryonic Stem Cells Resist c-Jun induced Differentiation in Suspension

city: Guangzhou

first: dongwei

last: Li

state: Guangdong province

address: 190 Kai Yuan Avenue, Science Park

department: South China Institute for Stem Cell Biology and Regenerative Medicine

institute: Guangzhou Institutes of Biomedicine and Health,Chinese Academy of Sciences

summary: The oncogene c-Jun plays a key role in development and cancer. Yet, its role in cell fate decision remains poorly understood at the molecular level. Here we report that c-Jun confers different fate decisions upon mouse embryonic stem cells (mESCs) in adhesion vs suspension. We developed a Tet-on system for temporal induction of c-Jun expression by Doxycycline treatment in mESCs. We show that mESCs carrying the inducible c-Jun TetOn remain pluripotent and grow slowly in suspension with induction of c-Jun, while undergoing differentiation with normal proliferative potentials in adherence upon c-Jun induction. Apparently, c-Jun pushes mESCs in suspension into cell cycle arrest at G1/S, through the induction of Cdkn1a/b and Cdkn2/a/b/c. Despite cell cycle arrest, they can re-enter cell cycle upon plating on adhesive surface and grow into typical mESC colonies albeit at lower efficiency.  These results demonstrate that mESCs respond to c-Jun differently in suspension or adherence. Our results suggest that cells in suspension may be more resistant to differentiation than in adherence.

overall_design: TRE-ESCs cells  were cultured in N2B27+2i+LIF medium in low adsorption petri dish with or without dox

first: Dongwei


title: UTX and 53BP1 co-regulate genetic programs for neural differentiation of human embryonic stem cells [ChIP-seq]

first: Beisi

last: Xu

summary: UTX is a histone H3 lysine 27 demethylase required for development. However, the mechanisms underlying developmental gene regulation by UTX are unclear. Here, we discovered a molecular interaction between UTX and 53BP1 that regulates gene expression in a human neurogenesis model. Human 53BP1 contains a UTX-binding site that diverges from its mouse homolog by 41%, and our data suggest that the UTX-53BP1 interaction is conserved in primates but not rodents. ChIP-Seq revealed that the genome-wide targets of UTX and 53BP1 overlap by 84%. We used CRISPR-Cas9 to generate mutations of 53BP1 and UTX in human embryonic stem cells, and found that both 53BP1 and UTX are required to promote the expression of hundreds of neurogenic genes during neural differentiation. Further, 53BP1 is required for human neural progenitor differentiation into neurons. Our findings suggest that the UTX-53BP1 interaction controls gene expression important for neural differentiation in humans.

overall_design: Examination of 2 transcription factors as 53BP1 and UTX binding sites in hESC and hNPC, H3K27me3 and H3K27ac in WT and 53BP1 KO cells. Intergrated analysis with transcriptome.


title: Comparative transcriptomics of sympatric species of coral reef fishes (genus: Haemulon)

city: Buffalo

first: Moises

middle: A

last: Bernal

state: NY

address: 109 Cooke Hall

department: Biological Sciences

institute: SUNY Buffalo

summary: Three sympatric species of Caribbean grunts (H. flavolineatum, H. carbonarium and H. macrostomum) were collected while SCUBA diving. RNA was extracted from livers, and the transcriptomes were assembled and annotated to investigate positive selection (Pairwise dN/dS) and patterns of gene expression between the three species.

sample_organism:
Haemulon flavolineatum
Haemulon carbonarium
Haemulon macrostomum

overall_design: Samples were collected in the wild in a period of two days

first: Moisés


title: RNA sequencing of denervated white and brown adipose tissue of obese mice

city: Oxford

first: Haifei

last: Shi

state: OH

address: 501 E. High Street

department: Biology

institute: Miami University

summary: We report differential expressed genes in white and brown adipose tissues with surgical denervation procedure in male mice fed with a high-fat diet.

overall_design: Methods: Male C57BL/6J mice at age of 6 weeks - 10 weeks fed either a high-fat rodent diet.  These adipose tissues were surgically denervated. mRNA profiles were generated by deep sequencing, in triplicates, using Illumina NextSeq500 sequencing system.  The sequence reads that passed quality filters were analyzed at the gene level with DESeq2.

first: Qi

last: Zhu

first: Mengyang

first: Jingyi

last: Cao

first: Lin

last: Liu

first: Benjamin

last: Hinkel

first: Bradley

last: Glazier

first: Chun

last: Liang


title: RNA sequencing of denervated white and brown adipose tissue of lean mice

summary: We report differential expressed genes in white and brown adipose tissues with surgical denervation procedure in male mice fed with a low-fat diet.

overall_design: Methods: Male C57BL/6J mice at age of 6 weeks - 10 weeks fed either a standard low-fat rodent diet.  These adipose tissues were surgically denervated. mRNA profiles were generated by deep sequencing, in triplicates, using Illumina NextSeq500 sequencing system.  The sequence reads that passed quality filters were analyzed at the gene level with DESeq2.


title: Deletion of myeloid IRS2 enhances adipose tissue sympathetic nerve function and limits obesity

city: London

first: Sanjay

middle: Padmakar

last: Khadayate

address: Du Cane Road

country: United Kingdom

institute: MRC London Institute of Medical Sciences

summary:
Aim:  We generated mice lacking Irs2 which mediates signaling pathways from insulin and IL-4 specifically in lyzM Cre expressing cells. We  isolated BMDM from control and Irs2LyzM-/-  mice and compared their differential gene expression under veihicle, IL-4 and LPS treatment by performing mRNA sequencing studies.
Methods: BMDM from control and Irs2LyzM-/-  mice were treated for 24 hours with vehicle,  IL-4 (10 ng/ml) or LPS (100 ng/ml). RNA integrity was confirmed and concentration measured using a Bioanalyzer. cDNA libraries were created from up to 5 μg total RNA. There were three (Irs2LyzM-/-) and four (control) biological replicates for each group and each biological replicate was divided into eight technical replicates and sequenced on individual lanes on the Illumina HiSeq 2000 (100 bp paired-end read length) at the Sanger Institute. Raw reads from the sequenced RNAseq libraries were mapped with Tophat splice junction aligner (Kim, Pertea et al. 2013), version 2.0.8 against Ensembl mouse genome reference sequence assembly (mm9) and transcript annotations. All parameters were set to default except inner distance between mate pairs (r = 130). Gene-based read counts were then obtained using the HTSeq count module (version 0.5.4p3). Differential expression analysis was performed on the counts data using the DESeq2 Bioconductor package (version 1.16.1). The GSEA  preranked tool from GSEA version 2.2.4 was used forGeneset enrichment analysis. Gene ontology enrichment analysis was also performed using the topGo Bioconductor package  separately for up and down-regulated genes in the comparisons analysed ( A. Alexa, J. Rahnenfuhrer, topGO: Enrichment Analysis for Gene Ontology. R package version 2.24.0 (2016)).
Results: The mRNA seq. results reveal  an anti- inflammatory transcriptional profile  in LPS-treated Irs2LyzM-/-  BMDM  compared to control BMDM. Deletion of Irs2 in BMDM under all conditions (vehicle, IL-4 and LPS) manifest alteratons in genes involved in scavenging catecholamines and supporting increased sympathetic innervation.

overall_design: BMDM were isolated from 10 week- old control and Irs2LyzM-/- male mice. RNA was isolated and cDNA libraries were prepared using the standard illumina library preparation protocol.

first: Dominic

last: Withers

first: Marie

middle: T

last: Rached


title: Single-Dose CRISPR/Cas9 Therapy Extends Lifespan of Mice with Hutchinson-Gilford Progeria Syndrome

city: Freiburg im Breisgau

first: Galina

last: Erikson

address: Stübeweg 51

institute: Max Planck Institute of Immunobiology and Epigenetics

summary:
Hutchinson-Gilford Progeria Syndrome (HGPS) is a rare lethal genetic disorder characterized with symptoms reminiscent of accelerated aging.  The major underlying genetic cause is a substitution mutation in the gene coding for lamin A, causing the production of a toxic isoform called progerin.  Here we show the RNA sequencing analyses performed on primary mouse fibroblasts of different genotypes (in terms of Progeria; Cas9 background) treated with Cas9 guide RNAs targeting Lmna/Progerin.
The mouse genetic background in (1) Pro/Pro;Cas9/+: homozygous for Progeria and heterozygous for transgenic Cas9
The mouse genetic background in (2) Pro/+; +/+: heterozygous for Progeria and no transgenic Cas9 (wild type)
The mouse genetic background in (3) +/+;Cas9/+: no Progeria (wild type) and heterozygous for transgenic Cas9

overall_design: Gene expression analyses of (1) Pro/Pro;Cas9/+ (2) Pro/+; +/+ (3) +/+;Cas9/+ primary mouse fibroblasts treated with a mock gRNA or Lmna target gRNA1, or Lmna target gRNA2.  Each treatment was performed on fibroblast cells isolated from 2 different mice (2 biological replicates).  The gRNAs were delivered into the cells by Lentiviral vectors that carried the mCherry gene as a reporter; no selection or sorting was performed post-treatment, however each sample was more than 80% mCherry-positive based on fluorescence microscopy.  mock gRNA (a gRNA with no match on the genome) treatment was used as a negative control.  Likewise, no transgenic Cas9 background (Pro/+; +/+) was used as another negative control.

first: Ergin

last: Beyret

first: Hsin-Kai

last: Liao

first: Yunpeng

last: Fu

first: Mako

last: Yamamoto

first: Reyna

last: Hernandez-Benitez

first: Pradeep

last: Reddy

first: Juan

last: Izpisua Belmonte


title: UTX and 53BP1 co-regulate genetic programs for neural differentiation of human embryonic stem cells [mouse RNA-seq]

first: Beisi

last: Xu

overall_design: Examination of 2 transcription factors as 53BP1 and UTX binding sites in hESC and hNPC, H3K79me2, H3K27me3 and H3K27ac in WT and 53BP1 KO cells. Intergrated analysis with transcriptome.


title: Transcriptome of  draining lymph nodes from the mice immunized with RABV

city: Wuhan

first: Zhaochen

last: Luo

state: Hubei

address: No.1 Shi-zi-shan Street

institute: Huazhong Agricultural University

summary: Here we show the transcriptome of lymph nodes draining from RABV vaccinated B6 mice and TLR7 KO mice. These differential transcripts will provide a reference for studies focus on the relationship between TLR7-denpendent signaling and humoral immunity.

overall_design: B6 mice were vaccinated with RABV and RNA from draining lymph nodes were collected at 7 day p.i.

first: Ling

last: Zhao


title: Modeling spinocerebellar ataxias 2 and 3 with iPSCs reveals a major role of glutamate in disease pathology

city: Taipei

first: Ching-Yu

last: Chuang

address: 128 Academia Road, Section 2, Nankang

department: Genomics Research Center

country: Taiwan

institute: Academia Sinica

summary: Spinocerebellar ataxias 2 and 3 (SCA2 and SCA3) are dominantly inherited neurodegenerative diseases caused by expansion of polyglutamine-encoding CAG repeats in the affected genes. The etiology of these disorders is known to involve widespread loss of neuronal cells in the cerebellum, however, the mechanisms that contribute to cell death are still elusive. Here we established SCA2 and SCA3 induced pluripotent stem cells (iPSCs) and demonstrated that SCA-associated pathological features can be recapitulated in SCA-iPSC-derived neurons. Importantly, our results also revealed that glutamate stimulation promotes the development of disease-related phenotypes in SCA-iPSC-derived neurons, including altered composition of glutamatergic receptors, destabilized intracellular calcium, and eventual cell death. Furthermore, anti-glutamate drugs and calcium stabilizer treatment protected the SCA-iPSC-derived neurons and reduced cell death. Collectively, our study demonstrates that the SCA-iPSC-derived neurons can recapitulate SCA-associated pathological features, providing a valuable tool to explore SCA pathogenic mechanisms and screen drugs to identify potential SCA therapeutics.

overall_design: Control-iPSC derived neurons from 3 non-SCA normal individuls , SCA2-iPSC -derived nurons from 2 patients (each patient pick 2 iPSC lines),  SCA3-iPSC -derived nurons from 2 patients (each patient pick 2 iPSC lines)

first: Ching-yu


title: YAP Partially Reprograms Chromatin Accessibility to Directly Induce Adult Cardiogenesis in Vivo

city: Cambridge

first: Matthew

last: Hill

state: MA

address: 75 Aimes Street

institute: Broad Institute of MIT and Harvard

summary: Specialized adult somatic cells, such as cardiomyocytes (CMs), are highly differentiated with poor renewal capacity, an integral reason underlying organ failure in disease and aging. Among the least renewable cells in the human body, CMs renew approximately 1% annually. Consistent with poor CM turnover, heart failure is the leading cause of death. Here, we show that an active version of the Hippo pathway effector YAP, termed YAP5SA, partially reprograms adult mouse CMs to a more fetal and proliferative state. One week after induction, 19% of CMs that enter S-phase do so twice, CM number increases by 40%, and YAP5SA lineage CMs couple to pre-existing CMs. Genomic studies showed that YAP5SA increases chromatin accessibility and expression of fetal genes, partially reprogramming long-lived somatic cells in vivo to a primitive, fetal-like, and proliferative state.

overall_design: We isolated cardiomyocyte nuclei from control and YAP5SA animals and performed nuclear RNA-seq (nucRNA-seq), ATAC-seq, and 4C-seq.

first: Tanner

middle: O

last: Monroe

first: James

middle: F

last: Martin


title: Gene expression and chromatin organization changes in lamin A/C haploinsufficient human induced pluripotent stem cell-derived cardiomyocytes

status: Public on Feb 13 2019

city: Seattle

first: Alessandro

last: Bertero

address: 850 Republican St

department: Institute for Stem Cell and Regenerative Medicine

institute: University of Washington


title: Gene Level Expression Profiling in human tongue squamous carcinoma cell line (SAS): gene expression profile in SAS cells transfected with scrambled control or C6orf141 mimic

city: Kaohsiung

first: Sung-Chou

last: Li

state: Kaohsiung

address: No.386, Dazhong 1st Rd

department: Department of Medical Education and Research

institute: Kaohsiung Veterans General Hospital

summary:
Transcriptome analysis of RNA samples from cells
The RNA samples from four plates were subject to sample preparation and microarray experiment.

overall_design:
We analyzed 2 scrambled control RNA samples and 2 C6orf141 overexpression RNA samples
contributor: Kaohsiung Chang Gung Memorial Hospital, Taiwan


title: Chaetocin Mediated Changes in Gene Expression Profile of GBM Cells

city: Istanbul

first: Tugba

last: Bagci-Onder

state: Sariyer

address: Koc University School of Medicine

department: School of Medicine

country: Turkey

institute: Koc University

summary: Chaetocin treatment significantly modulated expression profile of GBM cells such that 373 genes were up and 478 genes were down regulated significantly (FDR<0.05). Genes involved in DNA damage response, reactive oxygen species pathway and cell cycle regulation as well as epithelial to mesenchymal transition are significantly modified by Chaetocin, which render GBM cells much more prone to apoptosis.

overall_design: Examination of Chaetocin's effect on gene expression profile of U87MG cells. 2 sets of samples were prepared for Chaetocin treated (50 nM, 24h) and untreated (control)  conditions.

first: Tuğba

first: Ezgi

last: Özyerli-Göknar

first: Fırat

last: Uyulur


title: Gene expression and chromatin organization changes in lamin A/C haploinsufficient human induced pluripotent stem cell-derived cardiomyocytes [Hi-C]

state: WA

summary: Pathogenic mutations in A-type nuclear lamins may dysregulate gene expression due to changes in chromatin organization into active (A) and inactive (B) compartments. To test this, we performed genome-wide chromosome conformation analyses (Hi-C) and transcriptome profiling (RNA-seq) in human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CM) with a haploinsufficient mutation for Lamin A/C that causes cardiac laminopathy. Mutant hiPSC-CM have marked electrophysiological, contractile, and gene expression alterations. While large-scale changes in chromatin topology are evident, differences in chromatin compartmentalization are limited to a few hotspots. These regions normally transition from A to B during cardiogenesis, but remain in A in mutant hiPSC-CM. Non-cardiac genes located within such aberrant domains are ectopically expressed, including the neuronal P/Q-type calcium channel CACNA1A. Pharmacological inhibition of the resulting currents partially mitigates elongation of field potential duration in mutant hiPSC-CM. On the other hand, A/B compartment changes do not explain most gene expression alterations observed in mutant hiPSC-CM, putting in perspective the role of chromatin organization dysregulation in cardiac laminopathy.

overall_design: Hi-C analyses of human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CM) with a heterozygous R225X mutation (mutant), and hiPSC-CM from two isogenic control lines where such mutation was reverted to the wild-type allele using CRISPR/Cas9 (corrected); two biological replicates from independent differentiations per cell line.

first: Charles

last: Murry


title: UVB irradiation effect on mouse lens epithelium

city: Kahoku-gun

first: Yasuo

last: Yoshitomi

state: Ishikawa

address: 1-1 Daigaku, Uchinada-machi

department: Biochemistry

institute: Kanazawa Medical University

summary: Analysis of gene expression in mouse lens epithelium with or without UVB-irradiation in mouse eye lens. Results provide insight into a role for the respons to UVB-irradiation in lens epithelial cells.

overall_design: Gene expression profiling of mouse lens epithelium with or without UVB-irradiation in in vivo.

first: Y

first: H

last: Osada

last: Yonekura


title: Using RNA sequencing to examine age-dependent skeletal muscle transcriptome response to bed rest-induced atrophy, and age independent disuse-induced insulin resistance

city: Salt Lake City

first: Micah

middle: J

last: Drummond

state: Utah

address: 520 Wakara Way

department: Physical Therapy and Athletic Training

institute: The University of Utah

summary: Short-term bed rest is used to simulate muscle disuse in humans.  In our previous reports, we found that 5d of bed rest induced a ~4% loss of skeletal muscle mass in OLD (60-79 y) but not YOUNG (18-28 y) subjects. Identifying muscle transcriptional events in response to bed rest and age-related differences will help identify therapeutic targets to offset muscle loss in vulnerable older adult populations.  Skeletal muscle dysregulation during bed rest in the old may be driven by alterations in molecules related to fibrosis, inflammation, and cell adhesion. This information may aide in the development of mechanistic-based therapies to combat muscle atrophy during short-term disuse.  Short-term muscle disuse is also characterized by skeletal muscle insulin resistance, though this response is divergent across subjects. The mechanisms regulating inactivity-induced insulin resistance between populations that are more or less susceptible to disuse-induced insulin resistance are not known, and delineated by age. High Susceptibility participants were uniquely characterized with muscle gene responses described by a decrease in pathways responsible for lipid uptake and oxidation, decreased capacity for triglyceride export (APOB), increased lipogenesis (i.e., PFKFB3, FASN), and increased amino acid export (SLC43A1).

overall_design: RNA was isolated and sequenced from muscle biopsies obtained from the vastus lateralis of YOUNG (N=9) and OLD (N=18) men and women before and after five days of bed rest. Sequencing libraries (18 pM) were chemically denatured and applied to an Illumina TruSeq v3 single read flowcell using an Illumina cBot.  Hybridized molecules were clonally amplified and annealed to sequencing primers with reagents from an Illumina TruSeq SR Cluster Kit v3-cBot-HS (GD-401-3001).   Following transfer of the flowcell to an Illumina HiSeq 2500 instrument (HCS v2.0.12 and RTA v1.17.21.3), a 50 cycle single read sequence run was performed using TruSeq SBS v3 sequencing reagents (FC-401-3002). The design formula was constructed by following the section on group-specific condition effects, individuals nested within groups in the DESeq2 vignette.   The design included age + age:nested + age:time to test for differences in bed rest in old subjects, young subjects and the interaction, in this case if bed rest effects are different between the two age groups (where age is young or old, nested is patient number nested by age and time is pre- or post-bed rest).  A similar design was used to determine susceptibility to disuse-induced insulin resistance, where “susceptibility” took the place of “age”.

first: Ziad

last: Mahmassani

first: Paul

last: Reidy

first: Alec

middle: I

last: McKenzie

first: Chris

last: Stubben

first: Michael

last: Howard


title: Allele imbalance in Reps1 and Adpgk

city: Chiyoda

first: Ranmaru

last: Shimoda

state: Tokyo

address: 3F Yayoi Bldg., 3-7-4 Iwamotocho

institute: Rhelixa, Inc.

summary: Effective anti-cancer immunity is associated with the presence of T cells directed at potentially immunogenic tumor neoantigens arising from tumor-specific mutation. We confirmed the expression of reported MC38 neoantigens (Nature 515: 572, 2014). MC38 cells in our laboratory had the same point mutation at amino acid position 299 in Adpgk (ASMTN[R/M]ELM), but did not have a point mutation at amino acid position 42 in Reps1 (AQL[P/A]NDVVL). The allele frequency of mutated Adpgk (ASMTNMELM) was 30%.

overall_design:
Total RNASeq reads covering the variant position for 2 genes corresponding to the previously reported neoepitope peptides.

Only bam files were generated to compare the allele imbalance among samples and made available as SRA records.

last: Uemura

first: R

last: Zhang


title: Type I Interferon Delivery by iPSC-Derived Myeloid Cells Elicits Antitumor Immunity  via XCR1+ Dendritic Cells

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

overall_design: Refer to individual Series


title: Local administration of IFN-α-iPSC-pMCs alters gene expression profiles in tumor microenvironment.

summary: Local administration of IFN-α-producing proliferating myeloid cells (IFN-α-iPSC-pMCs) inhibited the tumor growth not only at the treatment site (right) but also at the distant site (left). We identified genes with log fold expression change ≥ 1 or ≤ −1 in untreated versus IFN-α-iPSC-pMC-treated tumors and iPSC-pMC-treated versus IFN-α-iPSC-pMC-treated tumors for treatment or distant site, respectively. Of the overlapping genes differentially expressed in IFN-α-iPSC-pMC-treated mice, 301/671 distant site and 460/928 treated site genes were ISGs, of which 95.3% and 94.7%, respectively, were type I IFN-related. By gene ontology, the up-regulated ISG signatures were enriched for “T cell-mediated immune responses”, “cytolysis”, and “migration of immune cells” associated genes. Collectively, Local administration of IFN-α-iPSC-pMCs alters the tumor microenvironment and propagates molecular signature associated with type I IFN.

overall_design: Gene expression profiles of treated tumor (right) and distant tumor (left)


title: Gene expression and chromatin organization changes in lamin A/C haploinsufficient human induced pluripotent stem cell-derived cardiomyocytes [RNA-seq]

first: Alessandro

last: Bertero

overall_design: RNA-seq analyses of human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CM) with a heterozygous R225X mutation (mutant), and hiPSC-CM from two isogenic control lines where such  mutation was reverted to the wild-type allele using CRISPR/Cas9 (corrected); three biological replicates from independent differentiations per cell line.

middle: E


title: IFN-α-producing proliferating myeloid cells reveal type I IFN-stimulating gene signature

summary: We previously established a method to generate myeloid lineage cells with proliferation capacity from induced pluripotent stem cells (iPSCs) (Zhang R. Cancer Immunol Res. 3: 668, 2015). In this study, we generated the IFN-α-producing cells by genetic engineering of mouse iPSC-derived myeloid cells (iPSC-pMCs). Gene expression profiling of IFN-α-producing iPSC-pMCs (IFN-α-iPSC-pMCs) revealed a distinct interferon-stimulated gene (ISG) signature: of 613 differentially expressed genes (versus iPSC-pMC), 345 genes were ISGs of which > 70 % were type I IFN-related. Gene ontology analysis showed that the up-regulated gene signature was enriched for transcripts associate with immune responses, cellular responses to type I IFN, and defense responses to virus.

overall_design: Gene expression profiles of iPSC-pMCs, IFN-α-transuduced iPSC-pMCs, and IFN-α-treated iPSC-pMCs.


title: UTX and 53BP1 co-regulate genetic programs for neural differentiation of human embryonic stem cells [RNA-seq]

city: Memphis

first: Beisi

last: Xu

address: 262 Danny Thomas Pl

institute: St Jude Children's Research Hosipital

summary: UTX is a histone H3 lysine 27 demethylase required for development. However, the mechanisms underlying developmental gene regulation by UTX are unclear. Here, we discovered a molecular interaction between UTX and 53BP1 that regulates gene expression in a human neurogenesis model. Human 53BP1 contains a UTX-binding site that diverges from its mouse homolog by 41%, and our data suggest that the UTX-53BP1 interaction is conserved in primates but not rodents. ChIP-Seq revealed that the genome-wide targets of UTX and 53BP1 overlap by 84%. We used CRISPR-Cas9 to generate mutations of 53BP1 and UTX in human embryonic stem cells, and found that both 53BP1 and UTX are required to promote the expression of hundreds of neurogenic genes during neural differentiation. Further, 53BP1 is required for human neural progenitor differentiation into neurons. Our findings suggest that the UTX-53BP1 interaction controls gene expression important for neural differentiation in humans.

overall_design: Examination of 2 transcription factors as 53BP1 and UTX binding sites in hESC and hNPC, H3K27me3 and H3K27ac in WT and 53BP1 KO cells. Intergrated analysis with transcriptome.


title: Virus-specific memory T cells populate tumors and can be repurposed for tumor immunotherapy

city: Minneapolis

first: Sathi

last: Wijeyesinghe

state: MN

institute: University of Minnesota

summary: Improvements in cancer immunotherapy are needed. The immunosuppressive tumor microenvironment limits the success of current immunotherapies. The host retains memory T cells specific for previous infections throughout the entire body that are capable of executing potent and immediate immunostimulatory functions. Here we show that virus-specific memory T cells extend their surveillance to mouse and human tumors. Reactivating these antiviral T cells can arrest growth of checkpoint blockade-resistant and poorly immunogenic tumors in mice after injecting adjuvant-free non-replicating viral peptides into tumors. Peptide mimics a viral reinfection event to memory CD8+ T cells, triggering antigen presentation and cytotoxic pathways within the tumor, activating dendritic cells and natural killer cells, and recruiting the adaptive immune sytem. Viral peptide treatment of ex vivo human tumors recapitulates immune activation gene expression profiles in mice. Lastly, peptide therapy renders resistant mouse tumors susceptible to PD-L1 blockade. Thus, re-stimulating known antiviral immunity may provide a unique therapeutic approach for cancer immunotherapy.

overall_design:
For B16 mouse tumor studies, B16 tumors in OT-1 chimeras were treated with relevant or irrelevant viral peptide. 9 hours after peptide delivery, B16 tumors were harvested from 3 mice per group. RNA was isolated from tumor homogenate for sequencing.
For Braf/Pten tumor studies, murine melanoma tumors in OT-1 chimeras were isolated, sliced into thin sections, and incubated with relevant or irrelevant peptide ex vivo. RNA was isolated from tumor culture homogenate for sequencing.
For human tumor samples, tumors were sliced into thin sections, and incubated with relevant or irrelevant viral peptides ex vivo. RNA was isolated from tumor culture homogenate for sequencing.

first: Pamela

last: Rosato

first: David

last: Masopust


title: Nr4a transcription factors limit CAR-T cell function in solid tumors

city: Denver

first: James

last: Scott-Browne

state: Colorado

address: 1400 Jackson St, K806

institute: National Jewish Health


title: Nr4a transcription factors limit CAR-T cell function in solid tumors [RNA-Seq]

summary: Chromatin accessibility with ATAC-seq and gene expression with RNA-seq for CD8 T cells expressing chimeric antigen receptors in solid tumors or after in vitro culture.

overall_design: RNA-Seq: 47 samples

first: Joyce

last: Chen

first: Isaac

last: Lopez-Moyado


title: Single cell data of microglia and perivascular macrophages identified from a single cell RNAseq analysis of mouse brain tissue.

city: Freiburg

first: Ori

last: Staszewski

address: Breisacher Str. 64

department: Institute of Neuropathology

institute: University Medical Center Freiburg

summary: Single cell sequencing of microglia and perivascular macrophages was performed on brain tissue from different brain regions to obtain single cell expression profiles dependent on celltype and regional location.

overall_design: 425 cells from mouse (CD-1) brains at different postnatal ages as well as embryonic day E11.5-E18.5.

first: Takahiro

last: Masuda

first: Amit

last: Zeisel

first: Sten

last: Linnarsson

first: Marco

last: Prinz


title: Expression data from fibrin-stimulated macrophages treated with 5B8 antibody or IgG2b control

city: San Francisco

first: Katerina

last: Akassoglou

address: 1650 Owens St

institute: Gladstone Institutes

summary: Activation of innate immunity and deposition of blood-derived fibrin in the central nervous system (CNS) occur in autoimmune and neurodegenerative diseases, including multiple sclerosis (MS) and Alzheimer’s disease (AD). However, mechanisms linking blood-brain barrier (BBB) disruption with neurodegeneration are poorly understood, and exploration of fibrin as a therapeutic target has been limited by its beneficial clotting functions. Here we report the generation of monoclonal antibody 5B8 targeted against the cryptic fibrin epitope γ377-395 to selectively inhibit fibrin-induced inflammation. 5B8 suppressed fibrin-induced proinflammatory gene expression, nicotinamide adenine dinucleotide phosphate (NADPH) oxidase activation, and oxidative stress. In animal models of MS and AD, 5B8 entered the CNS and bound to parenchymal fibrin, and its therapeutic administration reduced innate immune activation and neurodegeneration without interfering with clotting. Thus, fibrin-targeting immunotherapy inhibits autoimmune- and amyloid-driven neurotoxicity and may have clinical benefit without globally suppressing innate immunity or interfering with coagulation in diverse neurological diseases.

overall_design: Mouse macrophages were stimulated for 6 hr with fibrin in the presence of  5B8 or isotype control IgG2b and subjected for RNA extraction and hybridization on Affymatrix microarrays. Data are from three independent biological replicates.

first: Jae

last: Ryu


title: Nr4a transcription factors limit CAR-T cell function in solid tumors [ATAC-Seq]

overall_design: ATAC-seq: 70 new samples and 21 re-analyzed samples from GSE88987


title: Expression data from mice neonatal pancreas (P1, same litter as control and Elastase-Cre mediated Pdx1cKO)

city: kyoto

first: yoshiya

last: kawaguchi

address: 53, shogoin kawaharachou, sakyo

institute: kyoto university

summary:
During embryogenesis, exocrine and endocrine pancreatic tissues are formed in distinct regions within the branched ductal structure in mice. We previously reported that exocrine-specific inactivation of Pdx1, an indispensable gene for pancreatogenesis, by Elastase-Cre caused not only hypoplastic exocrine formation but also substantial endocrine defects resulting in diabetic phenotype, indicating the existence of exocrine-driven factor(s) that regulate proper endocrine development.
We obtained pancreata from control and mutant mice at P1 and subjected to microarray analysis.

overall_design: To obtain Pdx1-conditional knock-out mice, Pdx1loxP mice and Elastase-Cre transgenic mice were interbred. Pancreata were dissected from postneonatal day 1 and immediately submerged in RNAlater (Ambion, Inc., Austin, TX) and subjected to microarray analysis.

first: Koji

last: Hirata

first: Takuya

last: Yamamoto

first: Yoshiya

last: Kawaguchi


title: Next Generation Sequencing Facilitates Quantitative Analysis of ischemic postconditioning (IPO) to attenuate hepatic ischemia-reperfusion injury in mice

city: Changsha

first: Pengpeng

last: Zhang

state: Hunan

address: No.138 Tongzipo Road

institute: The Third Xiangya Hospital of Central South University

summary: This is the first study to investigate mRNA expression profiling in regard to hepatic I/R and IPO by next-generation RNA-Seq. Our results may provide an experimental basis for elucidating the underlying mechanism of IPO and reveal candidate biomarkers with which to assess hepatic I/R injury

overall_design: liver mRNA profiles of sham, I/R and IPO mice were generated by next-generation  sequencing, in triplicate, using Illumina HiSeq 4000.

first: Qifa

last: Ye


title: Simultaneous quantification of antibody-RNA conjugates and the transcriptome by single cell RNA-sequencing

city: Nijmegen

first: Jan

middle: Patrick

last: Gerlach

address: Geert Grooteplein Zuid 28

department: Molecular Developmental Biology

institute: Radboud Institute for Molecular Life Sciences

summary: Undifferentiated and differentiated Keratinocytes (AG1478 treated) were stained with antibody-RNA conjugates (targeting EGFR and ITGA6) to measure protein-based differentiation changes in conjunction with single-cell transcriptomics.

overall_design: Two 384 wells plates for untreated and two 384 wells plates for AG1478 treated cells were processed for single cell transcriptomics.

middle: P

first: Klaas

last: Mulder


title: Simultaneous quantification of antibody-RNA conjugates and the transcriptome from fixed cells by RAID

summary: Undifferentiated and differentiated Keratinocytes (AG1478 treated) were stained with antibody-RNA conjugates to measure protein-based diffrentiation changes in conjunction with single-cell transcriptomics. The cells were crosslinked and stained according to the RAID procedure to allow intracellular immunostaining. Antibodies used in this experiment are (TGM1, NOTCH1, KLK6, JAG1, phospho-RPS6, phospho-FAK).

overall_design: Three 384 wells plates for untreated and Three 384 wells plates for AG1478 treated cells were processed for single cell transcriptomics


title: RAID allows multiplexed quantification of intracellular (phospho-)proteins and transcriptomes from fixed single cells


title: Single cell RNA-seq data of microglia cells from normal mouse brain at three ages (embryonic, 3 weeks and 16 weeks)

summary: Single cell RNA-seq data was obtained from FACS sorted microglia from different brain regions of normal embryonic, 3 weeks and 16 weeks old CD1 mice in order to elucidate microglia heterogeneity in a regional and time specific manner.

overall_design: 2688 cells total were sequenced with 3-4 replicate mice per region and age. For normal tissue multiple different brain regions from the same mice were obtained.


title: Comparison of single-cell transcriptomics quality between unfixed cells and cells that were fixed and mock stained according to the RAID procedure

summary: Cell fixation, permeabilization and antibody staining of could have adverse effects on the quality of single cell transcriptomics data. To assess the effects of the RAID procedure, which includes such steps, we performed a direct comparison of single cell transcriptomics by CELseq2 using unfixed and RAID-processed cells.  Quality measures (gene complexity, gene detection rate, average gene expression) were performed using 40000 samples UMI counts per cell.

overall_design: Single cells were sorted in 96, wells plates. Per condition (unfixed or RAID) three sets (A,B,C) of 48 cells were processed with the CELseq2 protocol.


title: Next Generation Sequencing Facilitates Quantitative Analysis of Ramos and Rituximab-resistant Ramos cell Transcriptomes

city: Shanghai

first: Jianfeng

last: Chen

state: Shanghai

address: 270 Dong'an Road

institute: Fudan University Shanghai Cancer Center

summary: The goal of this study is to screen the differential genes between Ramos and Rituximab-resistant Ramos cells, then analyze the significant pathways.

overall_design: The total RNA of each group was pooled from 3 different passages separately. RNA-seq was performed using the proton sequencing process.

first: Weiguo

last: Hu


title: Nonalcoholic fatty liver, but not nonalcoholic steatohepatitis is a protective factor to tetrachloroethylene-associated kidney effects in male C57BL/6J mice

city: College Station

first: Ivan

last: Rusyn

address: Department of Veterinary Integrative Biosciences  College of Vet Medicine & Biomedical Sciences  4458 TAMU Texas A&M University

institute: Texas A&M University

summary: Purpose: We investigated the tetrachloroethylene associated changes in kidney transcriptomes among healthy mice, nonalcoholic fatty liver disease mice, and nonalcoholic steatohepatitis mice.

overall_design: Male C57BL/6J mice were fed a low-fat diet (4% fat), high-fat diet (31% fat), or methionine/choline/folate deficient diet. Following an 8-week diet, mice were administered either a single dose of tetrachloroethylene (PERC, 300 mg/kg/d in 5% Alkamuls-EL620 in saline, 5 mL/kg) and euthanized at 24 hours post dose, or five consecutive daily doses of PERC or vehicle (n=8/diet/treatment) and euthanized at 4hours post dose. The harvested kidneys were subjected to mRNA sequencing using Illumina Hiseq 2500. Jac-NASH-063 was excluded from analysis because it did not have a good yield.


title: Distinct Pathological Signatures in Human Cellular Models of Myotonic Dystrophy Subtypes

status: Public on Feb 12 2019

city: Chicago

first: Anthony

middle: Martin

last: Gacita

state: IL

address: 303 E Superior St. Lurie 7-240

department: Center for Genetic Medicine

institute: Northwestern Univeristy Feinberg School of Medicine

summary: Myotonic dystrophy (DM) is the most common autosomal dominant muscular dystrophy and encompasses both skeletal muscle and cardiac complications.  Myotonic dystrophy is nucleotide repeat expansion disorder in which type 1 (DM1) is due to a trinucleotide repeat expansion on chromosome 19 and type 2 (DM2) arises from a tetranucleotide repeat expansion on chromosome 3.  Developing representative models of myotonic dystrophy in animals has been challenging due to instability of nucleotide repeat expansions, especially for DM2 which is characterized by nucleotide repeat expansions often greater than 5000 copies.  To investigate mechanisms of human DM, we generated cellular models of DM1 and DM2.  We used regulated MyoD expression to reprogram urine-derived cells into myotubes.  In this cell model, we found impaired dystrophin expression, MBNL foci, and aberrant splicing in DM1 but not in DM2 cells.  We generated induced pluripotent stem cells (iPSC) from healthy controls, DM1 and DM2 subjects and differentiated these into cardiomyocytes.  DM1 and DM2 cells displayed an increase in RNA foci concomitant with cellular differentiation.  IPSC-derived cardiomyocytes from DM1 but not DM2 had aberrant splicing and MBNL sequestration.  High resolution imaging revealed tight association between MBNL clusters and RNA FISH foci in DM1.  Ca2+ transients differed between DM1 and DM2 IPSC-derived cardiomyocytes and from healthy control cells.  RNA-sequencing from DM1 and DM2 iPSC-derived cardiomyocytes both altered gene expression as well as distinct splicing patterns as differential between DM1 and DM2.  Together these data support that DM1 and DM2, despite some shared clinical and molecular features, have distinct pathological signatures.

overall_design: 2 Control, 2 Myotonic Dystrophy Type 1, and 2 Myotonic Dystrophy type 2 IPSC-cardiomyocytes were analyzed.

middle: M


title: Macrophage phenotype in anti-PD-L1 treated MC38 tumors

city: South San Francisco

first: Dorothee

last: Nickles

state: CA

address: 1 DNA Way

institute: Genentech

summary:
Checkpoint inhibitors like anti-PD1/PD-L1 have demonstrated significant therapeutic efficacy in a subset of patients partly through reinvigoration of CD8 T cells. However, their impact on myeloid cells remains largely unknown. Here we report that anti-PD-L1 treatment favorably impacts the phenotype and function of tumor macrophages by polarizing the macrophage compartment towards a more pro-inflammatory phenotype. This phenotype was characterized by a decrease in Arginase-I (ARG1) expression and an increase in iNOS, MHCII, and CD40 expression. Whole-transcriptome profiling further confirmed extensive polarization of both tumor monocytes and macrophages from a suppressive to a pro-inflammatory, immuno-stimulatory phenotype. This polarization was driven mainly through IFNγ and was associated with enhanced T cell activity. Transfer of monocytes into anti-PD-L1-treated tumor-bearing mice led to macrophage differentiation into a more pro-inflammatory phenotype, with an increase in CD8 T cells expressing granzyme B and an increase in the CD8/Treg ratio compared to control-treated mice. While in responsive tumor models anti-PD-L1 treatment remodeled the macrophage compartment with beneficial effects on T cells, both macrophage reprogramming and depletion were needed to maximize anti-PD-L1 responses in a tumor immune contexture with high macrophage burden. Our results demonstrate that anti-PD-L1 treatment can favorably remodel the macrophage compartment in responsive tumor models towards a more pro-inflammatory phenotype, mainly through increased IFNγ levels. They also suggest that directly targeting these cells with reprogramming and depleting agents may further augment the breadth and depth of response to anti-PD-L1 treatment in less responsive or more macrophage-dense tumor microenvironments.

The "SAMPLE_ID" sample characteristic is a sample identifier internal to Genentech.
The ID of this project in Genentech's ExpressionPlot database is NGS1772.

overall_design: RNA isolated from sorted macrophages and monocytes from control or anti-PD-L1 treated MC38 tumors 7 days after treatment initiation.

first: Rafael

last: Cubas


title: High-resolution analysis of chromatin structure by Mnase-SSP

first: Vijay

last: Ramani

state: California

department: Biochemistry & Biophysics

institute: UCSF

summary: Proof-of-concept for Mnase-SSP: a variant of Mnase-seq. Mnase-SSP dramatically increases the representation of short fragments of nucleolytically-digested DNA, enabling simultaneous analysis of transcription factor binding and nucleosome occupancy using the same assay. We used MNase-SSP to demarcate chromatin architecture at murine promoters and at transcription factor binding sites in murine embryonic stem cells. Are results reveal heterogeneity in the binding mode of C2H2 zinc fingers like Ctcf and Rest, demonstrating that Mnase-SSP, and SSP in general, as a flexible platform for profiling nucleolytically digested DNA for MNase-seq, MNase-ChIP, or CUT&RUN with reduced bias.

overall_design:
Nuclei are purified, treated with varying amounts of micrococcal nuclease, and then DNA fragments are purified. DNA is melted, ligated to a 3' single-strand adapter, and then subjected to second-strand synthesis, adaptor ligation, and PCR.

Please note that these libraries are non-traditional in the sense that the library prep is very different from standard Illumina protocols, and so the raw fastqs have been subjected to non-standard adaptor trimming + read filtration (in addition to read deduplication), generating BAM files as only processed data.


title: Gene expression analysis of WT and Stat1-/- CD4+ T cells pre and post transfer into Rag1-/- mice

city: Boston

first: Scott

last: Snapper

address: 300 Longwood Avenue, Enders 670

department: GI/Nutrition

institute: Boston Children's Hospital

summary: To understand the basis behind the defective survival/expansion of Stat1-/- CD4+ T cells in Rag1-/- mice, we analyzed the gene expression of WT and Stat1-/- CD4+ T cells pre- and post-transfer into these mice by RNAseq.

overall_design: WT (C57BL/6) or Stat1-/- CD4+ T cells (3 donor mice/group) were MACS sorted by negative selection. Some of the T cells from each mouse was used for RNAseq (Pre-transfer, WT=1, KO=2). The remaining T cells were injected into Rag1-/- mice (5 mice/group) and FACS sorted from the spleens and lymph nodes (CD45+ CD3ε+ CD4+) 7 days later. In the post-transfer setting, the T cells from the 5 mice of each group were split into 3 biological replicates each containing 1-2 mice (denoted as WT or KO).

first: Yu Hui

last: Kang

first: Amlan

last: Biswas

first: Michael

last: Field

middle: B


title: Human colon organoids reveal distinct physiologic and oncogenic Wnt responses

status: Public on Feb 11 2019

city: Frankfurt

first: Henner

middle: F.

last: Farin

address: Paul-Ehrlich-Str. 42-44

department: Institute for Tumor Biology and Experimental Therapy

institute: DKTK/Georg-Speyer-Haus

summary: Constitutive Wnt activation upon loss of Adenoma polyposis coli (APC) acts as main driver of colorectal cancers (CRC). Targeting Wnt signaling has proven difficult because the pathway is crucial for homeostasis and stem cell renewal. To distinguish oncogenic from physiologic Wnt activity, we have performed comprehensive transcriptome and proteome profiling in human colon organoids. Culture in the presence or absence of exogenous ligand allowed us to discriminate receptor-mediated signaling from the effects of CRISPR/Cas9 induced APC loss. We could catalogue two non-overlapping molecular signatures that were stable at distinct levels of stimulation. Newly identified markers for normal colon stem/progenitor cells and adenomas were validated by immunohistochemistry and flow cytometry. We found that oncogenic Wnt signals are associated with good prognosis in tumors of the consensus molecular subtype 2 (CMS2). In contrast, receptor-mediated signaling was linked to CMS4 tumors and poor prognosis. Together, our data represent a valuable resource for biomarkers that allow more precise stratification of Wnt responses in CRC.

overall_design: Culturing normal and CRISPR/Cas9 engineered APC mutant isogenic organoid lines in the presence or absence of Wnt-stimulation, followed by transcriptome and proteome profiling allowed for the stratification of physiologic and oncogenic Wnt responses.

first: Birgitta

last: Michels

first: Mohammed

last: Mosa

first: Britta

last: Grebbin

first: Diego

last: Yepes

first: Tahmineh

last: Darvishi

first: Johannes

last: Hausmann

first: Henning

last: Urlaub

first: Stefan

last: Zeuzem

first: Hans

last: Kvasnicka

first: T

last: Oellerich


title: Expression data from cortical tissue of 5XFAD mice treated with 5B8 antibody or IgG control

first: Katerina

last: Akassoglou

overall_design: Cortical tissue was isolated from brains of 5XFAD mice following two months of i.p. injection every other day with 5B8 antibody or control IgG antibody beginning at 3 months of age. RNA was extracted and subsequently processed for hybridization on Affymetrix microarrays. Gene expression data were adjusted for background and normalized using RMA.

first: Jae

middle: K

last: Ryu