title: ATF4 regulates MYB to increase g-globin in response to loss of β-globin

first: Jacob

last: Lab

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

overall_design: Refer to individual Series


title: A single cell transcriptome atlas of myeloid blood cell lineages in Drosophila [bulk RNA-seq]

status: Public on Jul 25 2020

city: Seoul

first: Jin-Wu

last: Nam

address: Seongdong-Gu Hangdang-dong

department: Department of Life Science

country: South Korea

institute: Hanyang University

type: Expression profiling by high throughput sequencing

summary: The Drosophila lymph gland (LG) is the larval hematopoietic organ comprised of multipotent prohemocytes and mature hemocytes and has been a valuable model for understanding mechanisms underlying the hematopoiesis and immune responses. There are three types of mature hemocytes in the lymph gland; plasmatocytes, lamellocytes, and crystal cells, all of which are analogous to myeloid-lineage blood cells. To date, the Drosophila hematopoietic system has been primarily defined by classical genetic methods that may limit the promise of its advantage as a model. In this study, we used single-cell RNA sequencing method to comprehensively profile the heterogeneity of developing myeloid hemocytes in the wild-type lymph gland and their transitions upon active immunity caused by wasp infestation. Moreover, we compared hemocytes originated from the embryonic and the lymph gland hematopoiesis and unraveled genetic and cellular diversity of two different ancestries. Finally, hemocytes of the Drosophila lymph gland and human immune cells are contrasted at a transcriptome level, highlighting evolutionary conservations of myeloid cells across species. Overall, our single-cell RNA seq analyses disclose the development of myeloid hemocytes at a single-cell level and provide comparative insights into two different lineages of hemocytes in Drosophila and perspectives on the evolution of myeloid cells, serving as an ample resource for revealing essentials of the hematopoiesis.

overall_design: Single-cell RNA-sequencing of Drosophila larvae LGs under normal or wasp infested states using Drop-seq

first: Sang-Ho

last: Yoon

first: Bumsik

last: Cho

first: Jiwon

last: Shim


title: A single cell transcriptome atlas of myeloid blood cell lineages in Drosophila


title: Analysis of mRNA expression in CHAPIR overexpressed heart

status: Public on Jul 24 2020

city: Qingdao

first: Kun

last: Wang

state: Shandong

address: 308 Ningxia Road

country: China

institute: Qingdao University

summary: To elucidate the molecular mechanism by which cardiac-hypertrophy-associated piRNA (CHAPIR) regulates gene expression, RNA-seq was performed on control or CHAPIR-overexpressing mice heart. Based on RNA-seq data, 720 differentially expressed genes were shown in CHAPIR-overexpressing heart relative to NC control, including 519 upregulated and 201 downregulated genes.

overall_design: Total RNAs were extracted from CHAPIR mimic or mimic-negative control (NC) overexpressed heart. Then, high throughput RNA sequencing was performed to identify differences in the gene expression profile.

first: Xiang-Qian

last: Gao

first: Yu-Hui

last: Zhang

first: Fang

last: Liu

first: Murugavel

last: Ponnusamy


title: Conserved interferon-gamma signaling and decreased immune exclusion programs in responses to immune checkpoint blockade therapy

city: Los Angeles

first: Antoni

last: Ribas

state: CA

address: 9-954 Factor Bldg

department: Medicine, HemOnc Division

country: USA

institute: University of California, Los Angeles

summary:
Purpose:  We treated melanoma cell lines with IFNG to assess which ones would be resistant or responsive to T-cell attack.
Methods:  We treated the melanoma cell lines with IFNG and then sequenced them at 6 hours to assess changes the transcriptome.
Results:  Unless the cell lines had JAK1 or JAK2 KO, they responded very consistently with human melanocytes (normals), revealing a consistent signature for IFNG response in melanoma.
Conclusions:  IFNG signaling is conserved in melanoma cell lines, and there are genes that go down in IFNG that allow immune infiltration to make immune blockade response possible.

overall_design: Melanoma cell line mRNA profiles befor and after 6 hours of treatment with interferon gamma.

first: Grasso

last: Catherine

first: Ribas

last: Antoni


title: Analysis of m6A methylome in CHAPIR overexpressed heart [MeRIP]

summary: To elucidate the molecular mechanism by which cardiac-hypertrophy-associated piRNA (CHAPIR) regulates m6A modification, we performed m6A methylated RNA immunoprecipitation sequencing (MeRIP-seq) in control or CHAPIR-overexpressing mice heart. The sequential analysis of m6A peaks showed that RGACH motif was highly enriched within m6A sites in heart and that is aligning with the classical consensus sequence of mammals ‘RGACH’, where ‘R’ indicates purine (A/G) and ‘H’ indicates non-guanine base (A/C/U). In CHAPIR treated heart, m6A mostly occurred in mRNAs (89.5%) and only about 10.5% were identified in non-coding RNAs. The majority of mRNAs contain one or two m6A peaks (89.2%) and 10.8% mRNA contain >2 m6A peaks . M6A peaks were predominantly distributed in coding sequences (CDSs), 3’ untranslated regions (3’UTRs) and near stop codon.

overall_design:
Total RNAs were extracted from CHAPIR mimic or mimic-negative control (NC) overexpressed heart. MeRIP was performed to enrich m6A methylated mRNAs using anti-N6-methyadenosine (m6A) antibody. We used commercial kit (KAPA Stranded mRNA-seq Kit) for RNA-seq library preparation of both m6A enriched RNAs and input mRNAs. Then, high throughput RNA sequencing was performed to identify differences in the gene expression profile.
Please note that each processed data was generated from both IP and input samples, and is linked to the corresponding IP sample records.


title: Differentially Expressed piRNAs in TAC-induced mouse cardiac hypertrophy

summary: To systematically investigate the potential role of piRNA(s) and for the identification of specific piRNA(s) dysregulated in cardiac hypertrophy, we examined the global expression profile of piRNAs in left ventricle samples obtained 4 weeks after TAC surgery in adult mice.

overall_design: Left ventricle hypertrophy was induced in C57BL/6 mice by transverse aortic constriction (TAC). 4 weeks later, one TAC mouse and one sham operation mouse were used for piRNA microarray analysis.


title: Microparticles globally reprogram the metabolism of Streptomyces albus

city: Bielefeld

first: Christian

last: Ruckert-Reed

address: Sequenz 1

department: Medical School OWL

country: Germany

institute: Bielefeld University

summary: Streptomyces sp. are a rich source for natural products with recognized industrial value, explaining the high interest to improve and streamline production in these microbes. Here, we studied the production of pamamycins, macrodiolide homologues with a high activity against multi-resistant pathogenic microbes, using recombinant S. albus J1074/R2. Talc particles of micrometer size added to submerged cultures of the recombinant strain tripled pamamycin production up to 50 mg L-1. Furthermore, they strongly affected morphology, reduced the size of cell pellets, formed by the filamentous microbe during the process, up to six-fold, and shifted the pamamycin spectrum to larger derivatives. Integrated analysis of transcriptome and metabolome of particle-enhanced and control cultures provided detailed insights into the underlying molecular changes. The microparticles affected the expression of 3341 genes (56%), revealing a global and fundamental impact on metabolism. Morphology-associated genes, encoding major regulators such as SsgA, RelA, EshA, Factor C, as well as chaplins and rodlins, were found massively upregulated, indicating that the particles caused a substantially accelerated morphogenesis. In line, the pamamycin cluster was strongly upregulated (up to log2 10-fold). Furthermore, the microparticles perturbed genes encoding for central catabolism and CoA-ester metabolism, which were mainly activated. The altered expression resulted in changes in the availability of intracellular CoA-esters, the building blocks of pamamycin. Notably, the ratio between methylmalonyl CoA and malonyl-CoA was increased four-fold. Both metabolites compete for incorporation into pamamycin so that the altered availability explained the pronounced preference for larger derivatives in the microparticle-enhanced process. Our findings are straightforward to further develop pamamycins into antituberculosis leads. The novel insights into the behavior of S. albus in response to talc appears of general relevance to further explore and upgrade the concept of microparticle enhanced cultivation, widely used for filamentous microbes.

overall_design: Whole transcriptomes of a pamamycin production strain derived from two time points and two treatments (+/- talc microparticles) using 3 biological replicates each.

first: Martin

last: Kuhl

first: Lars

last: Glaeser

first: Yuriy

last: Rebets

last: Rueckert

first: Namrata

last: Sarkar

first: Thomas

last: Hartsch

first: Jörn

last: Kalinowski

first: Andriy

last: Luzhetskyy

first: Christoph

last: Wittmann


title: Division of labor between YAP and TAZ in non-small cell lung cancer

city: Rehovot

first: Moshe

last: Oren

address: 234 Herzl

country: Israel

institute: Weizmann Institute of Science

type: Genome binding/occupancy profiling by high throughput sequencing


title: Division of labor between YAP and TAZ in non-small cell lung cancer [RNA]

summary: The paralogous transcriptional cofactors Yes-associated protein (YAP) and transcriptional co-activator with PDZ-binding motif (TAZ, also called WWTR1), the main downstream effectors of the Hippo signal transduction pathway, are emerging as pivotal determinants of malignancy in lung cancer. Traditionally, studies have tended to consider YAP and TAZ as functionally redundant transcriptional cofactors, with similar biological impact. However, there is growing evidence that each of them also possesses distinct attributes. We sought to systematically characterize the division of labor between YAP and TAZ in non-small cell lung cancer (NSCLC), the most common histological subtype of lung cancer. We showed that the two paralogs orchestrate non-overlapping transcription programs in this cancer type.

overall_design: To compare YAP and TAZ impact on the transcriptome of lung cancer-derived cells, we performed RNA-sequencing (RNA-seq) analysis following siRNA-mediated transient knockdown of either YAP or TAZ. Human NSCLC-derived H1299and A549 cells were transiently transfected with siRNA SMARTpools targeting either YAP (siYAP) or TAZ (siTAZ) or with control siRNA; RNA was extracted 48 hours later and subjected to RNA-seq analysis.

first: Michal

last: Shreberk-Shaked

first: Bareket

last: Dassa

first: Sanju

last: Sinha

first: Silvia

last: Di Agostino

first: Ido

last: Azuri

first: Saptaparna

last: Mukherjee

first: Yael

last: Aylon

first: Giovanni

last: Blandino

first: Eytan

last: Ruppin


title: Division of labor between YAP and TAZ in non-small cell lung cancer [ChIP]

overall_design: To compare YAP and TAZ chromatin binding in lung cancer-derived cells, we performed ChIP-sequencing (ChIP-seq) analysis with either anti-YAP or anti-TAZ antibodies.


title: Meningeal gd T cells regulate anxiety like behaviors via Il17a signaling on Neurons (PFC neurons)

city: Saint Louis

first: Jonathan

last: Kipnis

state: MO

address: 4515 McKinley Ave

department: Pathology and Immunology

institute: Washington University in Saint Louis

summary: Interleukin 17a (IL-17a) is a cytokine that has been highly conserved during evolution of the vertebrate immune system and widely studied in contexts of infection and autoimmunity. Recent studies in mouse models of maternal immune activation suggest that IL-17a is also linked to behavioral changes reminiscent of those seen under pathological conditions such as autism spectrum disorders (ASD)1 and in aggregation behavior in Caenorhabditis elegans2, raising the intriguing possibility that this cytokine might have evolved for the homeostatic regulation of neuronal activity. Here, by in-depth cellular and molecular characterization of a unique population of meningeal-resident gd17 T cells, we characterized the nearest central nervous system (CNS)-associated source of IL-17a under homeostasis. Meningeal gd T cell-derived IL-17a was associated with anxiety-like behaviors in mice, which partially depended on T-cell receptor engagement and commensal microbiota. IL-17a receptor was highly expressed in glutamatergic neurons under steady state and its genetic deletion decreased anxiety-like behavior in mice by shaping the transcriptional landscape and synaptic transmission of neurons in the medial prefrontal cortex (mPFC). From an evolutionary perspective, these findings suggest that IL-17a production by tissue-resident meningeal gd17 T cells may represent an evolutionary bridge between conserved anti-pathogen molecules and avoidance/survival behavioral traits in vertebrates.

overall_design: 3 nuclei samples of 4 mice pooled after elevated plus maze task from SynCre:Il17rafl/fl, SynCre, and Il17ra fl/fl mice.

first: Kalil

last: Alves de Lima

first: Justin

last: Rustenhoven

first: Sandro

last: Da Mesquita

first: Morgan

last: Wall

first: Andrea

middle: F

last: Salvador

first: Igor

last: Smirnov

first: Guilherme

middle: C

last: Martelossi

first: Tornike

last: Mamuladze

first: Wendy

last: Baker

first: Zach

last: Papadopoulos

first: Maria

middle: B

last: Lopes

first: William Sam

last: Cao

first: Xinmin Simon

last: Xie

first: Jasmin

last: Herz


title: Meningeal gd T cells regulate anxiety like behaviors via Il17a signaling on Neurons (DG neurons)

overall_design: Two samples, engram (GFP+) and nonengram (GFP-), of neuronal nuclei isolated from the Dentate Gyrus of WT (C57BL6) mice with 3 mice pooled per sample .


title: TP53 c.1000G>C; p.G334R is an Ashkenazi Jewish predominant mutation associated with a low penetrance Li-Fraumeni Syndrome

city: Philadelphia

first: Priyankara

middle: J

last: Wickramasinghe

state: PA

address: 3601 Spruce Street

department: Bioinformatics

institute: The Wistar Institute

summary: Multiple family members with cancer or individuals with multiple primary cancers are indicative of potential genetic etiology1.  Germline mutations in TP53 cause a rare high penetrance cancer syndrome, Li Fraumeni Syndrome (LFS)2.  We identified a TP53 tetramerization domain (TD) missense mutation c.1000G>C;p.G334R, in a family with LFS-associated cancers.  Twenty-one additional probands were identified, and available tumors showed biallelic somatic inactivation of TP53.  The majority of families were of Ashkenazi Jewish descent, and the TP53 c.1000G>C allele was found on a commonly inherited haplotype.  While classical p53 target gene activation was maintained in p.G334R mutant cell lines treated with Nutlin-3a, a subset of p53 target genes, including PCLO, PLTP, PLXNB3 and LCN15, showed defective transactivation.  Structural analysis demonstrated thermal instability of the mutant TD, and the G334R mutant protein showed increased preponderance of mutant conformation protein.  TP53 c.1000G>C;p.G334R is a rare AJ-predominant mutation associated with low penetrance Li-Fraumeni Syndrome

overall_design: RNA-seq analysis of LCL cells with p.G334 and p.R334 p53 variants in response to nutlin treatment

first: Kara

last: Maxwell

first: Maureen

last: Murphy

first: Jacquelyn

last: Powers


title: Structure-seq2 probing of RNA structure upon amino acid starvation reveals both known and novel RNA switches in Bacillus subtilis

city: University Park

first: Laura

last: Ritchey

address: 203 Althouse Lab

department: Chemistry

institute: Pennsylvania State University

summary: Here we use Structure-seq2 to probe the in vivo RNA structurome of B. subtilis grown in the presence and absence of amino acids.  We show that the change in global RNA structurome is inversely proportional to the change in abundance upon amino acid starvation and that this trend is pronounced in the stringent response and codY regulons. We also use this data to characterize known and novel RNA switches.

overall_design: Structure-seq2 libraries prepared from RNA extracted from B. subtilis (20 mL cultures) grown to mid-esponential phase in the presence of all amino acids as well as in the absence of all amino acids except glutamine. These were done without and with 50 mM dimethyl sulfate (DMS) added prior to RNA extraction. Three biological replicates were prepared for +/- amino acids and +/- DMS for a total of 12 individual samples. These were labeled with unique Illumina TruSeq barcodes and were sequenced by HiSeq 2500.

middle: E

first: David

last: Tack

first: Helen

last: Yakhnin

first: Elizabeth

middle: A

last: Jolley

first: Sarah

middle: M

last: Assmann

first: Philip

last: Bevilacqua

first: Paul

last: Babitzke


title: Meningeal gd T cells regulate anxiety like behaviors via Il17a signaling on Neurons

first: Jonathan

last: Kipnis


summary: By characterizing the meningeal compartment of naive mice, here we explored a unique population of tissue-resident gd T cells, which we found to be the major source of IL-17A in the steady state meninges. gd T cells rapidly harbor meninges at perinatal stages and actively make IL-17A. Their IL-17A production was TCR-dependent but it occurred independent of commensal microbiota. The absence of meningeal gd T cells was related with risk-taking behavior in mice, which was dependent on the IL-17A signaling directly in the prefrontal cortex neurons. Our results demonstrate that tissue-resident meningeal gd T cell-derived IL-17A may represent an evolutionary bridge between anti-pathogen response and avoidance behavioral traits in vertebrates.

overall_design: Each sample for meningeal gd T cells (Adults; n = 1 and Pups; n = 1) was obtained by pooling 15 animals. For splenic gd T cells (Adults; n = 1 and Pups; n = 1), it was pooled 5 mice.

first: Kalil

last: Alves de Lima

first: Justin

last: Rustenhoven

first: Sandro

last: Da Mesquita

first: Morgan

last: Wall

first: Andrea

last: Salvador

first: Igor

last: Smirnov

first: Guilherme

last: Martelossi

first: Tornike

last: Mamuladze

first: Wendy

last: Baker

first: Zach

last: Papadopoulos

last: Lopez


title: Peptide gene sequences of substrate phage for different proteases

status: Public on Jul 23 2020

city: San Francisco

first: Jim

last: Wells

department: Pharmaceutical Chemistry

institute: ucsf

summary: We present a method that employs two genetically encoded substrate phage display libraries coupled with next generation sequencing (SPD-NGS) that allows up to 10,000-fold deeper sequence coverage of the typical 6 to 8 residue protease cleavage sites compared to state-of-the-art synthetic peptide libraries or proteomics. We applied SPD-NGS to two classes of proteases, the intracellular caspases 2, 3, 6, 7 and 8, and the ectodomains of the membrane sheddases, ADAMs 10 and 17. The first library (Lib 10AA) was used to determine substrate cleavage motifs. Lib 10AA contains a highly diverse randomized 10-mer substrate peptide sequences (10^9 unique members) that was displayed mono-valently on filamentous phage and bound to magnetic beads via an N-terminal biotin. The protease was allowed to cleave the SPD beads, and the released phage subjected to up to three total rounds of positive selection followed by next generation sequencing (NGS). This allowed us to identify from 10^4 to 10^5 unique cleavage sites over a broad dynamic range of NGS counts (ranging from 3-5000), and produced consensus and optimal cleavage motifs based positional sequencing scoring matrices and state-of the-art machine learning algorithm that closely matched synthetic peptide data. A second SPD-NGS library (Lib hP) was constructed that allowed us to identify candidate human proteome sequences.  Lib hP displayed virtually the entire human proteome tiled in contiguous 49AA sequences with 25AA overlaps (nearly 1 million members). After three rounds of positive selection we identified up to 10^4 natural linear cut sites depending on the protease and captured most of the examples previously identified by proteomics (ranging from 30 to 1000) and predicted 10 to 100-fold more.

overall_design: To perform a SPD-NGS screening, 1 mL of biotinylated substrate phage library was incubated with 100 µL magnetic StreptAvidin (SA) beads for 30 min and after that, the SA beads were then stringently washed with PBS buffer supplemented with 0.05% Tween20 and 0.2% BSA to get rid of any free phage. After the SA beads were treated with protease of interest, released phage in supernatant were collected and propagated as protease-sensitive pool, and those bound on the beads can also be propagated as protease-resistant pool after released by non-specific proteases like trypsin. After three rounds of selection, phage polymerase chain reaction (PCR) was conducted, followed by NGS to identify sensitive substrate sequences in each pool. We tested 7 proteases and generated 21 x 2 datasets  (3 rounds of selection for each protease).

first: Jie

last: Zhou

first: Shantao

last: Li

first: Kevin

middle: K

last: Leung

first: Brian

last: O’Donovan

first: James

middle: Y

last: Zou

first: Joseph

middle: L

last: DeRisi


title: Evaluation of the role of Fbxw7 in interferon-gamma (Ifng) signaling in tumor cells

city: Boston

first: Rizwan

last: Haq

state: MA

address: 450 Brookline Avenue

department: Medical Oncology

institute: Dana-Farber Cancer Institute

summary: RNA-sequencing followed by gene set enrichment analysis was used to identify pathways enriched or depleted in Fbxw7-deficient cells. We found that virus sensing, as well as type I and II IFN signaling pathways, were among the most significantly downregulated gene sets in Fbxw7-deficient cells compared with controls. These results establish Fbxw7 as a regulator of the dsRNA sensing and IFN signaling pathways.

overall_design: Fbxw7-deficient and control melanoma cells were treated with Ifng (10ng/mL) for 24h. Total RNA was extracted and  submitted to the Molecular Biology Core Facility at Dana-Farber Cancer Institute for sequencing.

first: Cecile

last: Gstalder


title: A single cell transcriptome atlas of myeloid blood cell lineages in Drosophila [scRNA-seq]

first: Jin-Wu

last: Nam

overall_design: Single-cell RNA-sequencing of Drosophila larvae LGs or circulating hemocytes under normal or wasp infested states using Drop-seq

first: Sang-Ho

last: Yoon

first: Bumsik

last: Cho

first: Sooyoung

last: Oh

first: Seok

last: Moon

first: Jiwon

last: Shim


title: Analysis of miRNA expression in mouse heart after myocardial infarction

city: Honolulu

first: Allison

middle: Lesher

last: Williams

state: HI - Hawaii

address: 651 Ilalo St BSB 311

institute: University of Hawaii

type: Non-coding RNA profiling by high throughput sequencing

summary: MicroRNAs (miRNAs) are an important component of post-transcriptional regulation of gene expression. We hypothesized that early changes in miRNAs may be important for responses to cardiac injury. The goal of this study was to use high throughput sequencing to determine which miRNAs are altered in the initial response to ischemia after myocardial infarction.

overall_design: After ligation of the left anterior descending (LAD) artery in mice, ischemic heart tissue was isolated at 1 day and 3 days post-injury. Tissue was flash frozen and pulverized before RNA extraction. Sham-operated animals (no ligation of artery) were used as controls for each time point. Two mice were used for each condition as biological replicates.

first: Vedbar

middle: S

last: Khadka

first: Ralph

middle: V

last: Shohet


title: Host immune response against the emerging fungal pathogen Candida auris: transcriptional and functional insights

city: Nijmegen

first: Mariolina

last: Bruno

address: Geert Grooteplein Zuid 10

department: Experimental Internal Medicine

country: Netherlands

institute: Radboudumc

summary: Candida auris is amongst the most important emerging fungal pathogens, yet mechanistic insights in its immune recognition and control are lacking. Here, we integrate transcriptional and functional immune cell profiling to uncover innate anti-C. auris defense mechanisms. C. auris induces a specific transcriptome in human mononuclear cells, a stronger cytokine response compared to C. albicans, but a lower macrophage lysis capacity. C. auris-induced innate immune activation is mediated through recognition of C-type lectin receptors, mainly elicited by structurally unique C. auris mannoproteins. In in-vivo experimental models of disseminated candidiasis, C. auris was less virulent than C. albicans. Collectively, these results demonstrate that C. auris is a strong inducer of innate host defense and identify possible targets for adjuvant immunotherapy.

overall_design:
RNAsequencing profiles of PBMCs stimulated for 4h and 24h with live C. albicans and C. auris and their cell wall components

Treatment definitions:

RPMI: media control
calb_live : PBMCs stimulated with C. albicans live
calb_man: PBMCs stimulated with C. albicans-purified mannan
calb_bg: PBMCs stimulated with C. albicans-purified beta glucan
caur_KTClive: PBMCs stimulated with C. auris live
caur_KTCman: PBMCs stimulated with C. auris-purified mannan
caur_KTCbg: PBMCs stimulated with C. auris-purified beta glucan

first: Simone

last: Kersten

first: Alexander

last: Hoischen

first: Mihai

last: Netea


title: RNA-seq of human and mouse brain microvessels isolated by laser capture microdissection and matched whole brain samples

city: La Jolla

first: Benjamin

middle: D

last: Gastfriend

address: 9500 Gilman Dr

institute: University of California, San Diego

summary: Brain microvessels form the blood-brain barrier, and are dysfunctional in several neurological disorders. Brain microvessels are formed by brain microvascular endothelial cells (BMECs) and pericytes, and the molecular constituents of these cell types remain incompletely characterized, especially in humans. To improve molecular knowledge of these cell types and identify species differences in gene expression, we performed RNA-sequencing on brain microvessels isolated from human and mouse tissue samples using laser capture microdissection. We also performed RNA-sequencing of matched whole brain samples to identify genes with microvessel-enriched expression.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: A total of 12 samples were analyzed: 6 mouse samples and 6 human samples. For each species, there are 3 biological replicates of brain microvessels isolated by laser capture microdissection, and 3 matched whole brain controls.

first: Hannah

middle: W

last: Song

first: Koji

last: Foreman

first: John

last: Kuo

first: Sean

middle: P

last: Palecek

first: Eric

last: Shusta


title: Limited proliferation capacity of aorta intima resident macrophages requires monocyte recruitment for atherosclerotic plaque progression

status: Public on Jul 22 2020

city: St. Louis

first: Maxim

last: Artyomov

state: Missouri

address: 425 S Euclid Ave

department: Pathology & Immunology

institute: WASHINGTON UNIVERSITY IN ST LOUIS

summary: Atherosclerosis is modulated by immune cells. Understanding the diversity and heterogeneity in the aorta in steady state, as well as during different stages of disease will help to determine mechanisms promoting disease progression. To characterize the immune cells, we performed single cell RNA sequencing of aortic CD45+ leukocytes from C57BL/6 (WT) on chow diet and early disease Ldlr-/- mice fed high fat diet (HFD) for 21-days. The single cell RNA-seq analyses revealed the heterogeneity of aortic macrophages in steady state and early atherosclerotic disease.

overall_design: Single cell RNA sequencing of aortic CD45+ cells from nascent (n=10, C57BL/6 8-weeks age) and early atherosclerotic Ldlr-/- mice (n=10, HFD 21-days), using Illumina HiSeq4000.

first: Jesse

first: Konstantin

last: Zaitsev

first: Ki-Wook

last: Kim

first: Stoyan

last: Ivanov

first: Brian

last: Saunders

first: Patricia

middle: R

last: Schrank

first: Kyeondae

first: Andrew

last: Elvington

first: Seung

middle: H

first: Christopher

middle: G

last: Tucker

first: Mary

last: Wohltmann

middle: T

last: Fife

first: Slava

last: Epelman

middle: N

first: Kory

last: Lavine

first: Bernd

last: Zinselmeyer

first: Jae-Hoon

last: Choi

first: Gwendalyn

last: Randolph


title: Transcriptional reprogramming of distinct peripheral sensory neuron subtypes after axonal injury

first: Will

last: Renthal

address: 60 Fenwood Rd.

institute: Brigham and Women's Hospital

summary: Primary somatosensory neurons specialize in transmitting distinct types of sensory information through differences in cell size, myelination, and the expression of various receptors and ion channels, which together define their transcriptional and functional identity. By profiling sensory ganglia at single-cell resolution, we find that the different somatosensory neuronal subtypes undergo a similar transcriptional response to peripheral nerve injury that both promotes axonal regeneration and suppresses cell identity. This transcriptional reprogramming, which is not observed in non-neuronal cells from sensory ganglia, resolves over a similar time course as target reinnervation and is associated with the restoration of original cell identity. Injury-induced transcriptional reprogramming requires ATF3, a transcription factor which is induced rapidly after injury and necessary for axonal regeneration and functional recovery. Our findings suggest that the transcription factors induced early after peripheral sensory neuron injury promote their transcriptional and functional metamorphosis, analogous to their known roles in reprogramming cell fate.

overall_design: Single-nucleus RNA sequencing was performed on dorsal root ganglia from male and female C57/Bl6 mice or Atf3 conditional KO mice after models of nerve injury.

first: William

first: Lite

last: Yang

first: Ivan

last: Tochitsky

first: Clifford

last: Woolf


title: Gene expression profiles of primary LN3 T-ALL cells and wild-type T-lineage cells from the thymus and spleen

city: Austin

first: Lauren

last: Ehrlich

state: TX

address: 2506 Speedway A5000

department: Molecular Biosciences

institute: The University of Texas at Austin

summary: T cell acute lymphoblastic leukemia (T-ALL) develops spontaneously in the thymus of LN3 mice and infiltrates secondary organs, including spleen. We found leukemia-associated myeloid cells from the spleens of overtly sick LN3 mice significantly support survival of splenic T-ALL cells, but not tumor-free splenic CD8+ T cells, in vitro. To determine gene signatures induced in T-ALL cells by tumor-supportive myeloid cells, but not induced in wild-type T cells, we transcriptionally profiled primary LN3 T-ALL cells from leukemic mice and T-lineage cells from tumor-free mice, isolated from thymuses and spleens, via RNA-sequencing.

overall_design: Thymic and splenic T-ALL cells were isolated from mechanically dissociated thymuses and spleens, respectively, of overtly sick LN3 mice. For controls, total thymocytes and splenocytes were purified from mechanically dissociated thymuses and spleens, respectively, from C57BL/6J tumor-free mice, and CD8+ T cells (purity 85-95%) were then isolated from the splenocytes using a negative enrichment kit for isolating mouse CD8 T cells. Total RNA was isolated using the RNeasy Mini Kit and RNA quality and concentration were assessed on an Agilent Bioanalyzer 2100 using the Eukaryote Total RNA Pico/Nano assay. mRNA was enriched from total RNA using the Poly(A)Purist Mag kit and RNA libraries were prepared using the NEBNext Ultra II Directional RNA Library Prep kit for Illumina. 2 x 150 bp paired-end sequencing was run on Illumina HiSeq 4000, with an average of 29.7 million read-pairs per sample.

first: Aram

last: Lyu

first: Todd

last: Triplett

first: Seo

last: Nam

first: Zicheng

last: Hu

first: Dhivya

last: Arasappan

first: Wesley

last: Godfrey

first: Rachel

last: Ames

first: Adviti

last: Sarang

first: Hilary

middle: J

last: Selden

first: Chang-Han

last: Lee

first: George

last: Georgiou

first: Terzah

last: Horton

middle: I


title: Role of the histone demethylase Kdm6b/Jmjd3 in somatic cell reprogramming [ATAC-Seq]

city: Shenzhen

first: Andrew

last: Hutchins

address: 1088 Xueyuan Rd

institute: Southern University of Science and Technology

summary: Somatic cells can be reprogrammed to pluripotent stem cells through the addition of just four transcription factors, OCT4, SOX2, KLF4 and c-MYC (OSKM). Although OSKM initiates reprogramming it is clear that extensive epigenetic remodeling is required to complete reprogramming. Critically, OSKM do not directly activate gene expression but instead recruit co-activators and co-repressors that remodel the local chromatin and in some way make the cells permissive for reprogramming. Consequently understanding how epigenetic co-repressors and co-activators are involved in reprogramming is a critical step in understanding the reprogramming process in detail. In this study we explored the role of the lysine-specific demethylase Kdm6b/Jmjd3 and its role in the reprogramming of somatic cells to pluripotent cells.

overall_design: ChIP-seq data consists of either input chromatin (MEF cells) or anti-H3K27me3 precipitated chromatin. Experiments were performed at three time points (MEFS, Day 5 and 10 of reprogramming cells) and in two MEF lines, one with Jmjd3wildtype and another with Jmjd3 Knockout. Additionally, either FLAG or Jmjd3 was overexpressed. The Jmjd3 knockout mice were a kind gift from Dr. Takashi Satoh (Takashi et al., 2010 Nat. Immunol.). ATAC-seq data was performed according to Buenrostro et al., 2015, on MEFs, ESCs, and Day 5 and day 10 OSKM-reprogramming cells

first: Baoming

last: Qin

first: Huang

last: Yinghua


title: Transcriptome of nkx2.2a(+), olig2(+), dbx1b(+) cells from 14hpf zebrafish embryo

first: Tony

middle: Yu-Chen

last: Tsai

address: 200 Longwood Avenue, WAB 536

department: Systems Biology

institute: Harvard Medical School

summary: cDNA extracted from FACS-sorted GFP positive cells taken from trunk region of 14hpf zebrafish embryo with transgenic reporter TgBAC(nkx2.2a:memGFP), TgBAC(olig2:GFP), or TgBAC(dbx1b:GFP)

overall_design: transcriptome of nkx2.2a(+), olig2(+), dbx1b(+) cells from 14hpf zebrafish embryo

first: Carl-Philipp

last: Heisenberg

first: Sean

last: Megason


title: Analysis of transposable element expression in mouse ESCs with and without Ncor1, and a time course RNA-seq of mouse ESC differentiation to EpiLCs

summary: Mouse embryonic stem cells (ESCs) were differentiated to Epiblast-like cells (EpiLCs) according to the protocol in Hayashi et al., 2011. Samples were taken at 0, 12, 24, 36 and 48 hours. Wildtype and Ncor2 knockout ESCs were also sequenced to measure gene expression.

overall_design: The data was sequenced to a depth suitable for the analyiss of transposable elements. All samples have at least 10 million paired-end sequence tags, and each read is 150 bp in length

first: Li

last: Sun

first: Qiang

last: Zhuang


title: CHD7 regulates osteogenic differentiation of human dental follicle cells via PTH1R signaling

city: ChengDu,SiChuan

first: Caojie

last: Liu

address: No.14,3Rd Section Of Ren Min Nan Rd.

institute: West China Hospital of Stomatology, Sichuan University

summary: Chromodomain helicase DNA-binding protein 7 (CHD7) is an ATP-dependent chromatin remodeling enzyme, functioning as chromatin reader to conduct epigenetic modification. Its effect on osteogenic differentiation of human dental follicle cells (hDFCs) remains unclear. Here we show CHD7 expression increases with osteogenic differentiation. knockdown of CHD7 impairs the osteogenic ability of hDFCs, characterized by reduced alkaline phosphatase activity and mineralization, and decreased expression of osteogenesis-related genes. Conversely, CHD7 overexpression enhances the osteogenic differentiation of hDFCs.   Mechanically, RNA-seq analyses revealed the down-regulated enrichment of PTH (parathyroid hormone)/PTH1R (parathyroid hormone receptor-1) signaling pathway after CHD7 knockdown. We found the expression of PTH1R positively correlates with CHD7. Importantly, overexpression of PTH1R in CHD7-knockdown hDFCs partially rescued the impaired osteogenic differentiation. Our research demonstrates that CHD7 regulates the osteogenic differentiation of hDFCs by regulating the transcription of PTH1R.

overall_design: 6 samples were analyzed.

first: Qiwen

last: Li

first: Qingyue

last: Xiao

first: Ping

last: Gong

first: Ning

last: Kang


title: Comparative gene expression analysis of splenic T cells derived from rapamycin and PBS-treated mice

city: Ulm

first: Jasmin

last: Scheurer

address: Eythstraße 24

institute: Dept of Pediatrics and Adolsecent medicine

summary:
The macrolide rapamycin is known for its immunosuppressive properties since it inhibits mTOR (mammalian target of rapamycin), which activity affects differentiation and functions of various innate and adaptive immune cells involved in graft-versus-host disease development. Since rapamycin procures immunosuppressive effects on the immune response, rapamycin is an attractive candidate for graft-versus-host disease prevention after allogeneic bone marrow transplantation
We used an MHC class I and II mismatched parent into F1 bone marrow transplantation mouse model to elucidate the mechanisms of rapamycin on T cells in the context of graft-versus-host disease prevention. To define the impact of rapamycin therapy on T cells gene expression profile, we performed mircoarray analysis and compared gene expression profiles of sorted splenic T cells from rapamycin and PBS treated mice

overall_design: Splenic T cells were isolated 10 days after bone marrow transplantation for RNA extraction and hybridization on a affymetrix microarray. We analyzed 3 mice each group.

first: Gudrun

last: Strauss

first: Karlheinz

last: Holzmann


title: mRNA-sequencing for MM.1S cells that were treated with pomalidomide or were expressing shRNA against ARID2 or Aiolos.

city: Yokohama

first: Yuki

last: Yamaguchi

address: Nagatsutacho 4259

department: School of Life Science and Technology

country: Japan

institute: Tokyo Institute of Technology

summary: To dissect the roles of  ARID2 and Aiolos in pomalidomide-induced transcriptional changes, we performed mRNA-sequencing of MM.1S cells expressing shRNA against ARID2 or Aiolos and compared them with MM.1S cells that were treated with pomalidomide for 24, 48, or 72 hours.

overall_design: We performed mRNA-sequencing for MM.1S cells that were treated with 1 µM pomalidomide for 0, 24, 48, or 72 hours or were expressing shRNA against ARID2 or Aiolos for 72 hours (7 conditions with 3 biological replicates). Sequencing was done on the NovaSeq 6000 system (Illumina).

first: Junichi

last: Yamamoto


title: Age-related transcriptional profiling of phagocytic cells isolated from murine epididymal white adipose tissue

city: Buffalo

first: Brandon

last: Hall

state: NY

address: 640 Ellicott Street, Ste. 444

institute: Everon Biosciences, Inc.

summary: Age-related changes in macrophages are thought to underlie deleterious changes in adipose tissue during aging. RNAseq analysis of phagocyte-enriched and -depleted stromal vascular fractions of perigonadal white adipose tissue from young and aged mice revealed age-related differences in gene expression towards identification of adipose tissue macrophage-specific regulation.

overall_design: The stromal vascular fractions (SVF) of pooled epididymal white adipose tissue (eWAT) were isolated from young (10-week old; n=12) and old (80-week old; n=6) C57BL/6 mice and incubated with a suspension of superparamagnetic nanoparticles (~150-nm EasySep™ Magnetic Particles; StemCell Technologies). Subsequently, cells that phagocytized these particles were separated from non-phagocytic cells by performing magnetic-activated cell isolation, yielding macropahge-enriched phagocytic fraction and resultant phagocyte-depleted sub-populations. These fractions were used for RNAseq analysis.

first: Andrei

last: Gudkov

middle: M


title: Translation initiation site profiling reveals widespread synthesis of non-AUG-initiated protein isoforms in yeast

city: Berkeley

first: Gloria

last: Brar

address: 626 Barker Hall

department: MCB

institute: UC Berkeley

summary: Genomic analyses in budding yeast have helped to define the foundational principles of eukaryotic gene expression, but have systematically excluded specific classes of potential coding regions, including those with non-AUG start codons. Without methods to define coding regions empirically, the prevalence of these non-canonical coding regions has been impossible to assess. Here, we applied an experimental approach to globally annotate translation initiation sites in yeast and identified a class of 149 genes that encode N-terminally extended alternate protein isoforms that result from translation initiation at non-AUG codons upstream of the annotated AUG start codon. These alternate isoforms are produced in concert with canonical isoforms and are translated with a high degree of specificity, resulting from initiation at only a small subset of possible start codons in 5’ leader regions. Their translation is enriched during meiosis, and is induced by low eIF5A levels, which are observed in this context. These findings reveal widespread production of non-canonical protein isoforms and, more generally, show unexpected complexity to the rules by which the budding yeast genome is decoded.

overall_design: We performed ribosome profiling following pre-treatment of budding yeast cells with 3 micromolar of the translation initiation inhibitor, lactimidomycin (LTM).

first: Amy

last: Eisenberg

first: Ina

last: Hollerer

middle: A


title: Role of the histone demethylase Kdm6b/Jmjd3 in somatic cell reprogramming [ChIP-Seq]

first: Andrew

last: Hutchins

overall_design: ChIP-seq data consists of either input chromatin (MEF cells) or anti-H3K27me3/H3K27ac precipitated chromatin, anti-KLF4 ChIP-seq or anti-FLAG ChIP-seq against a FLAG-JMJD3. Experiments were performed at three time points (MEFS, Day 5 and 10 of reprogramming cells) and in two MEF lines, one with Jmjd3 Wildtype and another with Jmjd3 Knockout. Additionally, either FLAG or Jmjd3 was overexpressed. The Jmjd3 knockout mice were a kind gift from Dr. Takashi Satoh (Takashi et al., 2010 Nat. Immunol.)

first: Baoming

last: Qin

first: Huang

last: Yinghua


title: Role of the histone demethylase Kdm6b/Jmjd3 in somatic cell reprogramming

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

overall_design: Refer to individual Series


title: meRIP-seq and RNA-seq on proliferating and differentiating cultured C2C12 cells

status: Public on Jul 21 2020

city: Birmingham

first: Anna

middle: E

last: Thalacker-Merc er

state: Alabama

address: 1720 University Blvd

institute: University of Alabama at Birmingham

summary: To determine differences in the m6A-modified transcriptional profile of cultured proliferating and differentiating myoblasts.

overall_design: The m6A profile of C2C12 myoblasts during proliferation (n=2) and that had been in differentiation media for 3 days (n=2) were compared.

last: Thalacker-Mercer

last: Gheller

first: Jamie

last: Blum

first: Ern

last: Fong

first: Olga

last: Malysheva

first: Benjamin

last: Cosgrove


title: Comparative gene expression analysis of ex vivo isolated myeloid-derived suppressor cells (MDSCs) derived from rapamycin and PBS-treated mice

first: Jasmin

last: Scheurer

summary:
The macrolide rapamycin is known for its immunosuppressive properties since it inhibits mTOR (mammalian target of rapamycin), which activity affects differentiation and functions of various innate and adaptive immune cells involved in graft-versus-host disease development. Since rapamycin procures immunosuppressive effects on the immune response, rapamycin is an attractive candidate for graft-versus-host disease prevention after allogeneic bone marrow transplantation. Recently, an activating effect of rapamycin on the function of myeloid-derived suppressor cells (MDSCs), a subset of immune suppressive cells of myeloid origin was reported. However, the effect of rapamycin treatment on MDSCs induction and function in the management of graft-versus-host disease is largely unknown.
We used an MHC class I and II mismatched parent into F1 bone marrow transplantation mouse model to elucidate the mechanisms of rapamycin on MDSCs in the context of graft-versus-host disease prevention. To define the impact of rapamycin therapy on MDSCs gene expression profile, we performed mircoarray analysis and compared gene expression profiles of ex vivo isolated MDSCs from rapamycin and PBS treated mice

overall_design: Splenic MDSCs were isolated 10 days after bone marrow transplantation for RNA extraction and hybridization on a affymetrix microarray. We analyzed 3 mice each group.

first: Gudrun

last: Strauss

last: Holzmann


title: Transcriptomic analysis of intestinal mucosa reveals covert condition in celiac patients on gluten free diet

city: Tampere

first: Mikko

last: Oittinen

address: Arvo Ylpön katu 34

department: Tampere Center for Child Health Research

country: Finland

institute: Tampere University

summary: Background & Aims: Traditional celiac disease diagnostics based on histomorphometric evaluations are liable to misinterpretations due to the common technical flaws e.g. wrong orientation of the biopsy and subjective errors are relatively common e.g. interobserver errors.  We envisioned that there is a need for molecular histomorphometric tool that obviates these error sources yielding an objective ratio instead. Gene expression determine the state of a tissue, so the changes in expression may be associated with the severity of lesions during CD and can be used to classify it. Methods: 15 CD patients, who have been at least one year on gluten-free diet, were enrolled.  All participants were biopsied before and after the gluten challenge (10 weeks, 4 grams of gluten daily). 6 healthy non-CD individuals were included as controls. Biopsies were taken on PAXgene biological fixative and embedded in paraffin and Vh/Cd ratio was assessed. RNA was extracted from the same sections and subjected to genome-wide 3’RNA-sequencing. Sequencing data was used to determine differentially expressed genes and regression model, that successfully describes the mucosal damage, was created and tested in independent material. Results: 167 differentially expressed genes were identified in healthy vs. treated CD comparisons with 117 genes downregulated and 50 genes upregulated. 415 differentially expressed genes were identified in Post gluten challenge to Treated CD comparisons with 195 genes downregulated and 220 genes upregulated. 119 genes whose expression highly correlates to Vh/Cd ratio (Spearman’s rank correlation coefficient, |rho|>0.7) were identified. Gene ontology analyses show that genes involved in cellular response to cytokines, including interferons, were over-represented. Stepwise regression allowed us computationally cut down the number of genes, that describe Vh/Cd ratio changes, to 7 and IELs number to 5. Created models describe 98.9% of  observed Vh/Cd and 97.5% of IELs number variabilities; there is a strong correlation between the model’s predicted and observed ratios. Conclusions: Adoption of molecular histomorphometry, with our selected set of target genes, is quantitative and reliable way of estimating gluten-induced mucosal injury and inflammation. By including this technology one can overcome the typical shortcomings common in celiac disease diagnostics based on traditional histomorphometry analyses alone. Likewise, molecular histomorphometry is a promising instrument when incorporated in clinical trials where assessing drug efficacy on mucosal health is paramount. In addition, despite deemed healthy, based on traditional histomorphometric analyses, celiac patients on gluten free diet have significantly distinctive molecular histomorphometric pattern when compared to healthy controls.

overall_design: 15 coeliac disease patient biopsies before and after a gluten challenge were gathered. Additionally 6 healthy non-coeliac disease control samples were included.

first: Valeriia

last: Dotsenko

first: Juha

last: Taavela

first: Alina

last: Popp

first: Jani

last: Sarin

first: Francisco

last: Leon

first: Jorma

last: Isola

first: Markku

last: Mäki

first: Keijo

last: Viiri


title: Microglia promote glioblastoma growth via mTOR-mediated immunosuppressive conditioning of the tumor microenvironment.

city: London

first: Silvia

last: Marino

address: 4, Newark St

country: United Kingdom

institute: Queen Mary University of London

summary: Tumor-associated microglia and macrophages (TAM) are the most numerous non-neoplastic populations in the tumor microenvironment of glioblastoma (GBM), the most common malignant brain tumor in adulthood. The mTOR pathway, an important regulator of cell survival and proliferation, is known to be upregulated in GBM, but little is known about a potential role of this pathway in TAM. Here, we show that GBM-initiating cells (GIC) induce mTOR signalling in TAM-Microglia (TAM-MG) but not TAM-Macrophages (TAM-BMDM) in in vitro and in vivo GBM mouse models. mTOR-dependent regulation of STAT3 and NF-ĸB activity promotes an immunosuppressed phenotype in TAM-MG which hinders effector T cell proliferation and immune reactivity, thereby contributing to tumor immune evasion and promoting tumor growth in a mouse model. The translational value of these results is demonstrated in whole transcriptome datasets of human GBM and in a novel in vitro model whereby IPSC-derived microglia-like cells are conditioned by syngeneic patient-derived GIC. These results raise the possibility that tumor cells might not be the primary target of mTOR inhibition, and TAM-MG should be considered instead.

overall_design:
Intracranial injections of GL261 cells in Cx3cr1-cre;Rheb1-loxp mice 3 weeks post-tamoxifen injections. GL261 cells were injected at a concentration of 2x10e4 cells/5µl in PBS at 6 weeks of age. samples were collected  3 weeks post tumor initiation. Mouse models have been previously reported (Bowman et al., 2016, Yona, Kim et al., 2013, Zou, Zhou et al., 2011)
TAM-MG were sorted by gating on single live CD11b+ CD45low cells.

first: Anaelle

last: Dumas

first: Nicola

last: Pomella

first: Gabriel

last: Rosser

first: Loredana

last: Guglielmi

first: Claire

last: Vinel

first: Thomas

middle: O

last: Millner

first: Jeremy

last: Rees

first: Natasha

last: Aley

first: Denise

last: Sheer

first: Jun

last: Wei

first: Anantha

last: Marisetty

first: Amy

middle: B

last: Heimberger

first: Robert

middle: L

last: Bowman

first: Sebastian

last: Brandner

first: Johanna

last: Joyce


title: Effect of cpc-1 deletion in Neurospora crassa on transcriptome under different culture conditions

city: Dallas

first: xueliang

last: lyu

state: Texas

address: 6001 Forest Park Road

department: Physiology

institute: UT Southwestern Medical Center

summary: The high throughput mRNA-seq technology was used to measure the effect of cpc-1 deletion on transcriptome change of Neurospora crassa grown under different culture conditions using standard Illumina protocols.

overall_design: The transcription profiles of wild-type (WT) strain FGSC4200 and cpc-1 deletion mutant (cpc-1∆) of Neurospora crassa were generated by deep sequencing using Illumina sequencing platform. The WT and cpc-1∆ strains were cultured in 2% glucose medium (1 × Vogel’s, 2% glucose), 0.1% glucose medium (1 × Vogel’s, 0.1% glucose and 0.17% arginine) or 2% glucose medium with 5 mM 3-AT.  A 5’ epitope-tagged versions of cpc-1(WT) ORF under the control of the ccg-1 promoter and the ccg-1 5’ untranslated region (5’ UTR) was expressed in cpc-1∆ strain. This strain (cpc-1KO+cpc-1(WT)) was cultured in 2% glucose medium with 5 mM 3-AT.

first: Xueliang

last: Lyu

first: Yi

last: Liu


title: Transcriptome-wide gene expression analysis of prostate cancer (PCa) needle biopsies

city: Leipzig

first: Kristin

last: Reiche

address: Perlickstr. 1

institute: Fraunhofer Institute for Cell Therapy and Immunology

summary:
We assessed transcriptome-wide gene expression in needle biopsies of PCa patients prior to radical prostatectomy (RP) by next-generation sequencing (HiSeq 2500). We applied Cox proportional hazard models to the cohorts from different platforms and specimen types and combined the evidence from these by fixed effect meta-analysis to identify genes predictive for time to DoD (death of disease). Genes were combined by a weighted median approach into a prognostic score.
Tumor cell content and GS from the biopsy cores were evaluated by pathologists. If applicable, the hospital provided tissue sections from the biopsy with the highest tumor cell content. If multiple biopsy cores were used for analysis, the average tumor cell content of all the samplings (typically 2 o 3 cores) was calculated. The primary clinical endpoint of the cohort was death of disease (DoD).

overall_design:
Total RNA of FFPE needle biopsies of 16 PCa patients was assessed for gene expression profiling by strand-specific total RNASeq.
------------------------------------------------
Raw data not submitted to GEO due to patient privacy issues

first: Gustavo

last: Baretton

first: Sophie

last: Bartsch

first: Catharina

last: Bertram

first: Conny

last: Blumert

first: Tilo

last: Buschmann

first: Sabina

last: Christ

first: Kati

last: Erdmann

first: Maik

last: Friedrich

first: Michael

last: Froehner

first: Susanne

last: Fuessel

first: Joerg

last: Hackermueller

first: Friedemann

last: Horn

first: Markus

last: Kreuz

first: Dennis

last: Loeffler

last: Muders

first: Dominik

last: Otto

first: Sven-Holger

last: Puppel

last: Rade

first: Stephan

last: Schreiber

last: Specht

first: Marieta

last: Toma

first: Karolin

last: Wiedemann

first: Manfred

last: Wirth


title: Dioxin Disrupts Dynamic DNA Methylation Patterns in Genes that Govern Cardiomyocyte Maturation [RNA-seq]

city: Cincinnati

first: Mario

last: Medvedovic

state: OH

address: 3223 Eden Av. ML 56

department: Department of Environmental Health

institute: University of Cincinnati

summary: To test the hypothesis that the disruption caused by TCDD in cardiomyocytes results from changes in DNA methylation and gene expression patterns, we established a stable mouse embryonic stem cell line expressing a puromycin resistance selectable marker under the control of the cardiomyocyte-specific Nkx2.5 promoter. Differentiation of these cells in the presence of puromycin induces the expression of a large suite of cardiomyocyte specific markers. To assess the consequences of TCDD treatment on gene expression and DNA methylation in these cardiomyocytes, we subjected them to transcriptome and methylome analyses in the presence of TCDD. Unlike control cardiomyocytes maintained in vehicle, the TCDD-treated cardiomyocytes showed extensive gene expression changes, with a significant correlation between differential RNA expression and DNA methylation in 122 genes, many of which are key elements of pathways that regulate cardiovascular development and function. Our findings provide an important clue towards the elucidation of the complex interactions between genetic and epigenetic mechanisms, and environmental factors that may contribute to CHD incidence.

overall_design: To analyze gene expression and DNA methylation changes across time, we compared  Nkx2-5- positive cells treated with vehicle (control) with a) untreated ES cells, and b) Nkx2-5- positive cells treated with 5 nM TCDD for 24, 72, and 96 hours.

first: Matthew

last: de Gannes

first: Chia-I

last: Ko

first: Xiang

last: Zhang

first: Jacek

last: Biesiada

first: Liang

last: Niu

first: Sheryl

last: Koch

first: Jack

last: Rubinstein

first: Alvaro

last: Puga


title: mRNA-seq of worms and the mitochondrial unfolded protein response (UPRmt)

status: Public on Jul 19 2020

city: Beijing

first: Liwa

last: Shao

address: No.5 Yiheyuan Road Haidian District

institute: Peking University

summary: To cope with a challenging and unpredictable environment, living systems have evolved several organelle-specific stress responses, e.g. the cytosolic heat shock response (HSR), the endoplasmic reticulum unfolded protein response (UPRER) and the mitochondrial unfolded protein response (UPRmt). UPRmt monitors mitochondrial function and homeostasis in general. However, the mechanism of UPRmt remains largely unexplored. Here we identified that histone deacetylase HDA-1 is associated with homeobox domain-containing protein DVE-1 in UPRmt activation in Caenorhabditis elegans. Knocking down ATP synthase subunit atp-2 generates mitochondrial stress and induces UPRmt. After analyzing the mRNA profiles of worms on L4440 RNAi, hda-1 RNAi or dve-1 RNAi and untreated or treated with atp-2 RNAi, we found that 283 hda-1_dependent genes and 218 dve-1_dependent genes were upregulated in response to atp-2 RNAi.

overall_design: mRNA profiles of worms were generated by deep sequencing, in duplicate, using Illumina HiSeq2500. Worms on L4440 RNAi, hda-1 RNAi or dve-1 RNAi were untreated or treated with atp-2 RNAi

first: Li-Wa

first: Qi

last: Peng

first: Yumei

last: Li


title: SPT6-driven error-free DNA repair safeguards genomic stability of glioblastoma cancer stem-like cells

status: Public on Jul 17 2020

city: Copenhagen

first: Kristoffer

last: Vitting-Seerup

address: Ole maaloesvej 5

department: Department of Biology

country: Denmark

institute: University of Copenhangen, Denmark

summary: Knockdown of SUPT6H (aka Spt6) using siRNA against Spt6 compared to treatement with scrambled CTRL siRNA in patient derived glioblastoma cell line

overall_design: siSpt6 vs scrambled CTRL siRNA


title: DVE-1_ChIP-seq and HDA-1_ChIP-seq of worms

summary: Mitochondria are important organelles, but their function is often challenged by toxic products of metabolism as well as by pathogen attack. The mitochondrial unfolded protein response (UPRmt) monitors mitochondrial function in general: it is responsible for buffering the mitochondrial protein folding environment, and controlling mitochondria-nuclear balance of the electron transport chain (ETC) components. Besides, UPRmt plays essential roles in aging and lifespan. Here we found that knocking down histone deacetylase hda-1 robustly attenuated UPRmt and lifespan extension. We identified HDA-1 as a required factor for UPRmt activation and HDA-1 is associated with the homeobox domain-containing protein DVE-1.So, we performed ChIP-seq of worms to find DNA regions on which HDA-1 and DVE-1 bound, and if their binding depend on each other.

overall_design:
hda-1p::hda-1::gfp worms and dve-1p::dve-1::gfp worms were used for HDA-1-ChIP and DVE-1-ChIP. Worms on L4440 RNAi, hda-1 RNAi or dve-1 RNAi  were untreated or treated with atp-2 RNAi. ChIP-seq data were generated by deep sequencing, using Illumina HiSeqXten.
HDA-1_input/ChIP (dve-1); HG-D.repOverlap.finalPeak.bed3
HDA-1_input/ChIP (dve-1+atp-2); HG-DA.repOverlap.finalPeak.bed3
DVE-1_input/ChIP (hda-1); DG-H.repOverlap.finalPeak.bed3
DVE-1_input/ChIP (hda-1+atp-2); DG-HA.repOverlap.finalPeak.bed3


title: Gene expression profiles in Agpat3 KO liver

city: Shinjyuku-ku Tokyo

first: Daisuke

last: Hishikawa

address: Toyama 1-21-1

institute: NCGM

summary: To further understand the effect of DHA-containing phospholipid deficiency on hepatic metabolism, we have compared hepatic gene expression profiles between WT and Agpat3 KO mice

overall_design: Livers from four male mice from each genotype were used for analysis

first: Yoshiko

last: Iizuka


title: Mechanism suppressing transcription of the globin genes in Danio rerio nonerythroid cells

city: Moscow

first: Natalia

last: Klimenko

address: 34/5 Vavilova Street

country: Russia

institute: Institute of Gene Biology (IGB) of the Russian Academy of Sciences

summary: In genomes of modern fish and amphibia α- and β- globin genes are grouped at a single locus that may resemble the ancestral one and is syntenic to α-globin locus of modern warm-blooded vertebrates. In Danio rerio, the major locus of α/β globin genes comprises two subclusters, one of them harboring genes expressed in adult and the other – genes expressed in embryonic and larval erythrocytes. The results of our previous study suggested that the adult subcluster of this locus has evolved into α-globin gene domain of vertebrate animals. Here we studied how adult and embryo-larval genes of Danio rerio major globin gene locus are repressed in fibroblasts. The results obtained suggest that that at least some of the globin genes present within the adult subcluster are repressed by Polycomb similarly to human α-globin genes. Furthermore, within two α/β gene pairs repression of α-type and β-type genes appears to be mediated by different mechanisms as increasing the level of histone acetylation can activate transcription of only β-type genes.

overall_design:
Target-enriched ChIP-Seq for H3K27me3, H3panac and H4panac in Danio rerio fibroblasts with and without TSA treatment (the libraries are enriched with the sequences of a/b-globin gene locus and flanking areas).

Each sample in this series represents two replicates. The raw data for the replicates are represented as two independent SRR.

first: O

last: Iarovaia


title: Dioxin Disrupts Dynamic DNA Methylation Patterns in Genes that Govern Cardiomyocyte Maturation

first: Mario

last: Medvedovic

type: Methylation profiling by high throughput sequencing


title: Integrated single-cell analysis reveals coupled molecular gradient and functional subnetworks in the thalamic reticular nucleus

city: Cambridge

first: Joshua

last: Levin

address: 75 Ames St

department: Stanley Center

institute: Broad Institute

summary: The thalamic reticular nucleus (TRN), the major source of thalamic inhibition, is known to regulate thalamocortical interactions critical for sensory processing, attention and cognition. TRN dysfunction has been linked to sensory abnormality, attention deficit and sleep disturbance across multiple neurodevelopmental disorders. Currently, little is known about the organizational principles underlying its divergent functions. We performed an integrative study linking single-cell molecular and electrophysiological features of the mouse TRN to connectivity and systems-level function. We found that TRN cellular heterogeneity is characterized by a transcriptomic gradient of two negatively correlated gene expression profiles, each containing hundreds of genes. Neurons in the extremes of this transcriptomic gradient express mutually exclusive markers, exhibit core/shell-like anatomical structure and have distinct electrophysiological properties. The two TRN subpopulations make differential connections to the functionally distinct first-order and higher order thalamic nuclei to form molecularly defined TRN-thalamus subnetworks. Selective perturbation of the two subnetworks in vivo revealed their differential role in regulating sleep. Taken together, our study provides a comprehensive atlas for TRN neurons at the single-cell resolution, and links molecularly defined subnetworks to the functional organization of the thalamo-cortical circuits.

overall_design: The project involved 8 plates of TRN nuclei with NeuN selection, 9 plates of TRN nuclei without NeuN selection, 4 plates of TRN-adjacent (Thalamus and Globus Pallidus) nuclei, 7 plates hippocampus Pvalb+ nuclei, 2 plates somatosensory cortex Pvalb+ nuclei, 1 plate striatium Pvalb+ nuclei, 3 plates M2 cortex Pvalb+ nuclei, and 3 batches of Patch-seq samples. We used 96-well plates to collect and process nuclei for Smart-seq2 library construction.

middle: Z

first: Sean

middle: K

last: Simmons

first: Zhanyan

last: Fu

first: Yinqing

first: Violeta

last: Lopez

first: Xian

last: Adiconis

first: Guoping

last: Feng


title: RNA-seq analysis of PRMT5 targeted  genes in  Tu686 cells

status: Public on Jul 16 2020

city: Meizhou

last: Wang

address: Meisong Road

institute: Jiaying University

summary: RNA-seq was performed to identify transcriptional targets of PRMT5 in Tu686 cells treated with shPRMT5 or shNC.PRMT5 was abnormally upregulated in high-grade laryngeal carcinoma tissues. The expression of PRMT5 was positively correlated with tumor stages, lymphatic metastasis and poor outcome.. Western blotting and immunofluorescence analyses observed that PRMT5 expression significantly downregulation of E-cadherin and upregulationg of N-cadherin, Snail and MMP9 in laryngeal carcinoma cells. All these changes were further confirmed by RNA-seq analysis of biological process and cellular component.

overall_design: Examination of 2 different shPRMT5 in Tu686 cells

first: Xuekui

last: Liu


title: 5hmC RNA role in mouse Embryonic stem cell differentiation to Embryonic bodies [TetRIP-seq]

city: Gosselies

first: Martin

last: Bizet

address: Rue Adrienne Bolland, 8

country: Belgium

institute: Université Libre de Bruxelles

summary: Tet-enzyme-mediated 5-hydroxymethylation of cytosine in DNA plays a crucial role in mouse embryonic stem cells (ESCs). In RNA also, 5-hydroxymethylcytosine (5hmC) has recently been evidenced, but its physiological roles are still largely unknown. Here we show the contribution and function of this mark in mouse ESCs and differentiating embryoid bodies. Transcriptome-wide mapping in ESCs revealed hundreds of messenger RNAs marked by 5hmC at sites characterized by a defined unique consensus sequence and particular features. During differentiation a large number of transcripts, including many encoding key pluripotency-related factors (such as Eed and Jarid2), showed decreased cytosine hydroxymethylation. Using Tet-knockout ESCs, we found Tet enzymes to be partly responsible for deposition of 5hmC in mRNA. A transcriptome-wide search further revealed mRNA targets to which Tet1 and Tet2 bind, at sites showing a topology similar to that of 5hmC sites. Tet-mediated RNA hydroxymethylation was found to reduce the stability of crucial pluripotency-promoting transcripts. We propose that RNA cytosine 5-hydroxymethylation by Tets is a mark of transcriptome flexibility, inextricably linked to the balance between pluripotency and lineage commitment.

overall_design: Identification  of mRNAs bound by Tet1 (2 samples), Tet2 (4 samples), and RNA-binding-domain-tuncated Tet2 (Tet2dRBD) (4samples) in wild type mouse embryonic stem cell using RNA immunoprecipitation and Input controls

first: Jie

last: Lan

first: Nicholas

last: Rajan

first: Audrey

last: Penning

first: Nitesh

last: Singh

first: Diana

last: Guallar

first: Emilie

last: Calonne

first: Andrea

last: Li Greci

first: Elise

last: Bonvin

first: Rachel

last: Deplus

first: Phillip

last: Hsu

first: Sigrid

last: Nachtergaele

first: Chengjie

last: Ma

first: Renhua

last: Song

first: Alejandro

last: Fuentes-Iglesias

first: Bouchra

last: Hassabi

first: Pascale

last: Putmans

first: Frédérique

last: Mies

first: Gerben

last: Menschaert

first: Justin

last: Jong-Leong Wong

first: Jianlong

first: Miguel

last: Fidalgo

first: Bifeng

last: Yuan

first: François

last: Fuks


title: RNA-Seq of MADM induced UPDs of Chr. 7, 11, 12 (QuantSeq)

city: Klosterneuburg

first: Florian

last: Pauler

address: Am Campus 1

country: Austria

institute: Institute of Science and Technology Austria (IST Austria)

summary: In mammalian genomes a subset of genes is regulated by genomic imprinting resulting in silencing of one parental allele. Imprinting is essential for cerebral cortex development but prevalence and functional impact in individual cells is unclear. Here we determined allelic expression in cortical cell types and established a quantitative platform to interrogate imprinting in single cells. We created cells with uniparental disomy (UPD) containing either two copies of the maternal or paternal chromosome hence imprinted genes will be twofold overexpressed or not expressed. By genetic labeling of UPD we determined cellular phenotypes and transcriptional responses to deregulated imprinted gene expression at unprecedented single cell resolution. We discovered an unexpected degree of cell type specificity and a novel function of imprinting in the regulation of cortical astrocyte survival. More generally our results suggest functional relevance of imprinted gene expression in glial astrocyte lineage and thus for generating cortical cell type diversity.

overall_design: Overview of transcriptome changes upon sparse MADM UPD of Chr.7, Chr.11, Chr.12 in multiple cell types of the brain using QuantSeq 3’mRNA library preparation kit (Lexogen)

first: Susanne

last: Laukoter

first: Simon

last: Hippenmeyer


title: RNA-Seq of B6/CAST crosses in major forebrain cell types (single cell)

overall_design: Quantification of imprinted gene expression in single cells


title: 5hmC RNA role in mouse Embryonic stem cell differentiation to Embryonic bodies [hMeRIP-seq]

first: Martin

last: Bizet

overall_design: 5hmC RNA marks identification in wild type mouse embryonic stem cell (WT ESC), Tet1,2,3 triple knock-out mouse embryonic stell cell (TKO ESC) and wild type embryonic bodies (WT EB) in triplicates and Tet2 and Tet2 delta-RBD knock-in (KI) embryonic stem cell in duplicates using 5hmC RNA immunoprecipitation and Input controls

first: Jie

last: Lan

first: Nicholas

last: Rajan

first: Audrey

last: Penning

first: Nitesh

last: Singh

first: Diana

last: Guallar

first: Emilie

last: Calonne

first: Andrea

last: Li Greci

first: Elise

last: Bonvin

first: Rachel

last: Deplus

first: Phillip

last: Wang


title: Single cell RNA-Seq of Emx1 positive cells in MADM induced UPD of Chr. 7

overall_design: Quantification of  transcriptome changes upon sparse MADM UPD of Chr.7 in single cells


title: Involvement of circulating factors in the transmission of paternal experiences through the germline

status: Public on Jul 14 2020

city: Zürich

first: Deepak

last: Tanwar

state: ZH

address: Winterthurerstrasse 190

country: Switzerland

institute: ETH Zürich

summary: Using a mouse model of paternal exposure to traumatic stress, we identify circulating factors involving peroxisome proliferator-activated receptor (PPAR) pathways in the effects of exposure to the germline. Chronic injection of serum from trauma-exposed males into controls recapitulates metabolic phenotypes in the offspring. Pharmacological PPAR activation in vivo reproduces metabolic dysfunctions in the offspring and grand-offspring of injected males, and affects the sperm transcriptome in fathers and sons. In germ-like cells in vitro, both serum and PPAR agonist induce PPAR activation. Together, these results highlight the role of circulating factors as potential communication vectors between the periphery and the germline.

overall_design: 3-month old mice were injected i.p. with either tesaglitazar solution at 10 µg per kg body weight or vehicle control twice per week for 4 weeks. Tesaglitazar (Sigma Aldrich) was solubilized in DMSO at 10 µg per µl and resuspended in sterile 0.9% saline. Vehicle consisted of equivalent DMSO in 0.9% sterile saline. Sperm was collected 24h and 46 days after the last injection. For MSUS, litters were exposed to unpredictable maternal separation combined with unpredictable maternal stress (MSUS) during the first 14 days after birth (Franklin et al., 2010), and serum was collected from 3 months old MSUS and CTRL mice.

first: Gretchen

last: van Steenwyk

first: Katharina

last: Gapp

first: Pierre-Luc

last: Germain

first: Eric

last: Miska

first: Isabelle

last: Mansuy


title: Transcriptome-wide gene expression analysis of prostate cancer (PCa) tissue specimen II

first: Kristin

last: Reiche

summary:
We assessed transcriptome-wide gene expression in tissue specimens of PCa patients who underwent radical prostatectomy (RP) by next-generation sequencing (HiSeq 2500). We applied Cox proportional hazard models to the cohorts from different platforms and specimen types and combined the evidence from these by fixed effect meta-analysis to identify genes predictive for time to DoD (death of disease). Genes were combined by a weighted median approach into a prognostic score.
We stratified PCa patients according to seven clinical risk groups based on Gleason Score (GS), the presence of regional lymph node metastases (pN) and the occurrence of death of disease (DoD): (i) very low  risk (group V: GS<7, pN0), (ii) low risk (group L: GS=7, pN0), (iii) medium risk (group M: GS<=7, pN1), (iv) high risk survivors without lymph node infiltration (group H-s: GS>7, pN0), (v) high risk non-survivors without lymph node infiltration (group H-d: GS>7, pN0, DoD), (vi) high risk survivors with lymph node infiltration (group H+s: GS>7, pN1), (vii) high risk non-survivors with lymph node infiltration (group H+d: GS>7, pN1, DoD). For high risk groups adjacent tumor-free prostate tissue samples were obtained (groups H+sf, H-sf, H+df, H+df).
Information on the course of the disease, survival of the patients and the cause of death were obtained from the general practitioners or treating urologists or from records of the regional tumor registry. Clinicopathological parameters were obtained by routine histopathological examination of the surgical specimens. Serum levels of the prostate-specific antigen (PSA) were determined preoperatively (Abbott, Wiesbaden, Germany).

overall_design:
Total RNA of RP-derived FFPE specimen of 13 PCa patients was assessed for gene expression profiling by strand-specific total RNASeq.
Raw data not submitted to GEO due to patient privacy issues

first: Gustavo

last: Baretton

first: Sophie

last: Bartsch

first: Catharina

last: Bertram

first: Conny

last: Blumert

first: Tilo

last: Buschmann

first: Sabina

last: Christ

first: Kati

last: Erdmann

first: Maik

last: Friedrich

first: Michael

last: Froehner

first: Susanne

last: Fuessel

first: Joerg

last: Hackermueller

first: Friedemann

last: Horn

first: Markus

last: Kreuz

first: Dennis

last: Loeffler

last: Muders

first: Dominik

last: Otto

first: Sven-Holger

last: Puppel

last: Rade

first: Stephan

last: Schreiber

last: Specht

first: Marieta

last: Toma

first: Karolin

last: Wiedemann

first: Manfred

last: Wirth


title: Deconstructing Stepwise Fate Conversion of Human Fibroblasts to Neurons by MicroRNAs: Subseries 7 [Figure 4, RNA-seq]

city: Saint Louis

first: Kitra

last: Cates

address: 4523 Clayton Ave, MCD SCI 361

department: Developmental Biology

institute: Washington University in St. Louis

summary: Cell-fate conversion generally presumes the activity of reprogramming effectors to both introduce fate programs of the target cell type and erase the identity of starting cell population. Here, we reveal novel insights into the activity of microRNAs, miR-9/9* and miR-124 (miR-9/9*-124) as reprogramming agents that orchestrate direct conversion of human fibroblasts by first eradicating fibroblast identity and promoting uniform transition to a neuronal state in sequence. Among the direct target genes of miR-9/9*-124, we identify KLF-family transcription factors whose repression is critical for erasing fibroblast fate. The subsequent upregulation of a small nuclear RNA, RN7SK induces accessibilities of chromatin regions and neuronal gene activation, pushing the reprogramming cells to a neuronal state. Our study defines deterministic components in the reprogramming cascade by microRNAs.

overall_design: De-identified healthy human adult dermal fibroblasts were transduced with lentivirus to express the brain enriched microRNAs, miR-9/9* and miR-124 or non-specific miRNA (miR-NS) control as previously established (Yoo et al., Nature 2011; Richner et al., Nat. Prot. 2015; Abernathy, Kim, and McCoy et al., 2017). Total RNA from reprogrammed neurons and controls was collected, then prepared for analysis as described in the Protocol.

first: Yangjian

last: Liu

first: Bo

last: Zhang

first: Shaopeng

first: Paul

last: Gontarz

first: Woo

last: Kim

first: Andrew

middle: S

last: Yoo


title: The change of mRNA stability upon T cell activation

city: Washington DC

first: Weiqun

last: Peng

state: Washington DC

address: 800 22nd St NW

department: Physics

institute: George Washington University

summary: T cell activation is a well-established model for studying cellular responses to exogenous stimulation. In this study, we performed BruChase-Seq to experimentally monitor the expression dynamics of nascent transcripts in resting and activated CD4+ T cells, and applied computational modeling to investigate the impact of IR on the kinetics of mRNA degradation. As expected, intron retained transcripts are considerably less stable than spliced transcripts. In addition, the decrease in the steady-state IR level in activated CD4+ T cells are in part due to increased splicing efficiency and further stabilization of spliced transcripts. We propose that coordination between splicing regulation and mRNA stability may provide a novel paradigm to achieve spatiotemporal control of gene expression during T cell activation. We also found the mRNA stability change is not due to the 3’UTR-isoform choice but may be regulated by the RBP for example the LARP4 is the most significant binding protein in 3’ UTR of the β1-decreased genes. Furthermore, the mRNAs of the activated CD4+ T cells in LARP4 Knock-out (KO) mice showed the decreased stability and comparable transcriptional level for some genes including the NFkB1 and PSMD7 when comparing to the wild-type (WT) mice, resulting in the down-regulation of these genes. Finally, the LARP4 KO down-regulated NFkB1 target genes such as IL2 and IFNG upon CD4+ T cell activation, which is critical for the T cell proliferation and function.

overall_design: To investigate the involvement of mRNA stability in CD4+ T cell activation, we employed BruChase-Seq, a high-throughput sequencing method for monitoring RNA degradation rate by pulse-chase labelling of nascent transcripts.  Resting and activated human primary CD4+ T cells were pulse labelled with Bromouridine (BrU) for 1 h. Cells were harvested 30 min or 2 h after switching back to culture medium that contains regular uridine. Labelled transcripts were immunoprecipitated by anti-BrU antibody and then fragmented. The resulting RNA fragments were subsequently analyzed by RNA-Seq.

first: Jun

last: Zhu


title: Epigenome wide Association and Stochastic Epigenetic Mutation analysis on cord blood of preterm birth.

status: Public on Jul 20 2020

city: Cusano Milanino

first: Luciano

last: Calzari

state: MI

address: Via Zucchi 18

country: Italy

institute: IRCCS Istituto Auxologico Italiano

summary: Preterm birth (PTB) can be defined as the endpoint of a complex process that could be influenced by maternal and environmental factors. Epigenetics recently emerged as an interesting field of investigation since it represents an important mechanism of regulation. This study evaluates epigenetic impact of preterm birth on DNA methylation. Genome-wide DNAm was measured using the Illumina 450K array in cord blood samples obtained from 72 full term and 18 preterm newborns. Lymphocyte composition was calculated based on specific epigenetic markers that are present on the 450k array. Differential methylation analysis was performed both at site and region level, moreover Stochastic Epigenetic Mutations (SEMs) were also evaluated. The study showed significant differences in blood cell composition between the two groups. Moreover, after multiple testing correction, statistically significant differences in DNA methylation levels emerged between the two groups both at site and region levels. Results obtained have been compared to those obtained by previous EWAS and a list of genes have been found to be consistent. The SEMs analysis revealed that the burden of SEMs resulted significantly higher in the preterm group. In conclusion, PTB resulted associated to specific epigenetic signatures that involve immune system. Moreover, SEMs analysis revealed an increased epigenetic drift at birth in the preterm group.

overall_design: Genome-wide DNA methylation analysis of a cohort of 18 preterm newborns (cord blood) using Illumina Human Methylation 450K Beadchip.

first: Michele

last: Vignali

first: Davide

last: Gentilini


title: BIC1 acts as a transcriptional coactivator to promote brassinosteroid signaling and plant 14 1 growth

first: zongju

last: Yang

address: 12 Zhongguancun South Street

institute: Chinese Academy of Agriculture Science

summary: The BRASSINAZOLE-RESISTANT 1 (BZR1) transcription factor family plays an essential role in plant brassinosteroid (BR) signaling, but the signaling mechanism through which BZR1 and its homologs cooperate with certain coactivators to facilitate transcription of target genes remains incompletely understood. In this study, we used an efficient protein interaction screening system to identify blue-light inhibitor of cryptochromes 1 (BIC1) as a new BZR1-interacting protein in Arabidopsis thaliana. We show that BIC1 positively regulates BR signaling and acts as a transcriptional coactivator for BZR1-dependent activation of BR-responsive genes. Simultaneously, BIC1 interacts with the transcription factor PIF4 to synergistically and interdependently activate expression of downstream genes including PIF4 itself, and to promote plant growth. Chromatin immunoprecipitation assays demonstrate that BIC1 and BZR1/PIF4 interdependently associate with the promoters of common target genes. In addition, we show that the interaction between BIC1 and BZR1 is evolutionally conserved in the model monocot plant Triticum aestivum (bread wheat). Together, our results reveal mechanistic details of BR signaling mediated by a transcriptional activation module BIC1/BZR1/PIF4 and thus provide new insights into the molecular mechanisms underlying the integration of BR and light signaling in plants.

overall_design: Wild type Col-0 and BIC1-YFP seedlings grown under long-day conditions chamber for 10 days and were collected. Three replicates were prepared for each sample. RNA was extracted using an ethanol precipitation protocol and Trizol (Invitrogen) reagent. Libraries were constructed and further sequenced on Illumina HiSeq. 2000 platform (Illumina Inc., USA) with three independent biological replications for each sample. After screening and trimming, clean reads were mapped to the Arabidopsis thaliana genome (TAIR10, www.arabidopsis.org). Cufflinks methods were used for determination of expression values. Genes with estimated absolute fold changes ≥ 0.5 were identified as reliable DEGs.

first: Zongju

first: Jiaqiang

last: Sun


title: Transcriptional profiling and immunophenotyping show sustained activation of blood monocytes in subpatent Plasmodium falciparum infection.

city: Smithfield

first: Matt

last: Field

address: 14-88 Macgregor Road

country: Australia

institute: James Cook University

summary:
Objectives: Malaria, caused by Plasmodium infection, remains a major global health problem. Monocytes are integral to the immune response yet, their transcriptional and functional responses in primary Plasmodium falciparum infection and in clinical malaria are poorly understood.
Methods: The transcriptional and functional profile of monocytes were examined in controlled human malaria infection with P. falciparum blood-stages and in children and adults with acute malaria. Monocyte gene expression and functional phenotypes were examined by RNA-sequencing and flow cytometry at peak-infection and compared to pre-infection or at convalescence in acute malaria.
Results: In subpatent primary infection, the monocyte transcriptional profile was dominated by an interferon (IFN) molecular signature. Pathways enriched included type I IFN signalling, innate immune response, cytokine-mediated signalling. Monocytes increased TNF and IL-12 production upon in vitro toll-like receptor stimulation, and increased IL-10 production upon in vitro parasite restimulation. Longitudinal phenotypic analyses revealed sustained significant changes in the composition of monocytes following infection, with increased CD14+CD16- and decreased CD14-CD16+ subsets. In acute malaria, monocyte CD64/FcγRI expression was significantly increased in children and adults, while HLA-DR remained stable. Although children and adults showed a similar pattern of differentially expressed genes, the number and magnitude of gene expression change was greater in children.
Conclusions: Monocyte activation during subpatent malaria is driven by an IFN molecular signature with robust activation of genes enriched in pathogen detection, phagocytosis, antimicrobial activity and antigen presentation. The greater magnitude of transcriptional changes in children with acute malaria suggest monocyte phenotypes may change with age or exposure.

overall_design: Examination of paired isolated monocytes in two different human malaria cohorts; CHMI (before and peak-infection) and clinical malaria (acute infection vs convalescence)

first: Jessica

middle: R

last: Loughland

first: Gabriela

last: Minigo

first: Michelle

last: Boyle


title: RNA-Seq of enriched astrocytes with MADM induced UPD of Chr. 7 (SMARTer)

first: Florian

last: Pauler

overall_design: Detailed analysis of transcriptome changes in pure astrocyte populations with MADM UPD of Chr.7

first: Susanne

last: Laukoter

first: Simon

last: Hippenmeyer


title: RNA-Seq of B6/CAST crosses in major forebrain cell types (bulk)

overall_design: Quantification of imprinted expression of 5 different cell types in the mouse neocortex


title: RNA-Seq of MADM induced UPD of Chr. 7 (SMARTer)

overall_design: Detailed analysis of transcriptome changes upon sparse MADM UPD of Chr.7


title: 5hmC RNA role in mouse Embryonic stem cell differentiation to Embryonic bodies [RNA-seq]

first: Martin

last: Bizet

overall_design: Transcriptome of wild type mouse embryonic stem cells (3 samples), amanitin-treated 0h (2 samples), amanitin-treated 4h (2 samples) and Tet1,2,3 triple knock-out mouse embryonic stell cell amanitin-treated 0h (2 samples) and amanitin-treated 4h (2 samples)

first: Jie

last: Lan

first: Nicholas

last: Rajan

first: Audrey

last: Penning

first: Nitesh

last: Singh

first: Diana

last: Guallar

first: Emilie

last: Calonne

first: Andrea

last: Li Greci

first: Elise

last: Bonvin

first: Rachel

last: Deplus

first: Phillip

last: Hsu

first: Sigrid

last: Nachtergaele

first: Chengjie

last: Ma

first: Renhua

last: Song

first: Alejandro

last: Fuentes-Iglesias

first: Bouchra

last: Hassabi

first: Pascale

last: Putmans

first: Frédérique

last: Mies

first: Gerben

last: Menschaert

first: Justin

last: Jong-Leong Wong

first: Jianlong

last: Wang

first: Miguel

last: Fidalgo

first: Bifeng

last: Yuan

first: François

last: Fuks


title: ChIP-Seq for FOXA1 in LNCaP cell line with GSK treatment and VEH control

city: Boston

first: Changmeng

last: Cai

state: Massachusetts

address: 100 William T. Morrissey Blvd.

institute: University of Massachusetts Boston

summary: We show in prostate cancer cells that LSD1 co-localizes with FOXA1 and active enhancer markers, and that LSD1 inhibition globally disrupts FOXA1 chromatin binding.

overall_design: ChIP-Seq of FOXA2 was performed in LNCaP cells treated with vehicle or  GSK2879552

first: Shuai

last: Gao

first: Dong

last: Han

first: Sujun

last: Chen

first: Housheng

middle: H

last: He


title: ATAC-Seq in LNCaP cell line with GSK treatment and VEH control

overall_design: ATAC-Seq analysis was performed in LNCaP cells treated with vehicle or  GSK2879552


title: 5hmC RNA role in mouse Embryonic stem cell differentiation to Embryonic bodies

first: Martin

last: Bizet

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

overall_design: Refer to individual Series


title: Identification of Differential Tumor Subtypes of T1 Bladder Cancer

status: Public on Jul 13 2020

city: Chicago

first: Joshua

middle: James

last: Meeks

state: IL

address: 676 N. St Clair St

department: Urology

institute: Northwestern University

summary: Stage T1 bladder cancers have the highest progression and recurrence rates of all non-muscle invasive bladder tumors. T1 tumors are heterogeneous; while most T1 patients are treated with BCG, many will progress and die from bladder cancer, and particularly aggressive tumors could be treated by early cystectomy. To better understand the molecular heterogeneity of T1 cancers, we performed transcriptome profiling and unsupervised clustering, identifying five consensus subtypes of T1 tumors treated with reTUR, induction and maintenance BCG. The T1-LumGU subtype was associated with CIS (6/13, 46% of all CIS), had high E2F1 and EZH2 expression, and enriched E2F target and G2M checkpoint Hallmarks. T1-Inflam was inflamed and infiltrated with immune cells. While most T1 tumors were classified as luminal papillary, the T1-TLum subtype had the highest median Luminal Papillary score and FGFR3 expression, no recurrence events, and the fewest copy number gains. T1-Myc and T1-Early subtypes had the most recurrences (14/30 within 24 months), highest median MYC expression, and, when combined, had significantly worse recurrence-free survival than the other three subtypes. T1-Early had 5 (38%) recurrences within the first 6 months of BCG, and repressed IFN-alpha and IFN-gamma Hallmarks and inflammation. We developed a single-patient T1 classifier and validated our subtype biology in a second cohort of T1 tumors. Future research will be necessary to validate the proposed T1 subtypes and to determine if therapies can be individualized for each subtype.

overall_design: Identify and characterize unsupervised expression subtypes in RNA-seq data, validate a single-sample subtype classifier in a second cohort.

first: A

middle: G

last: Robertson

first: Clarice

last: Groeneveld

first: Brian

last: Jordan

first: Xiquo

last: Lin

first: Kimberly

last: McLaughlin

first: Arighno

last: Das

first: Leigh

last: Fall

first: Damiano

last: Fantini

first: Timothy

last: Taxter

first: Lauren

last: Mogil

first: Sia

middle: V

last: Lindskrog

first: Lars

last: Dyrskjøt

first: David

last: McConkey

first: Robert

last: Svatek

first: Aurélien

last: De Reynies

first: Mauro

last: Castro


title: Single cell and bulk RNA-Seq of B6/CAST crosses as well as MADM induced UPDs in major forebrain cell-types

first: Florian

last: Pauler


title: Pharmacophore hybridization and nanoscale assembly to discover new self-delivering lysosomotropic chemical entities for cancer therapy

city: Sacramento

first: Zhao

last: Ma

state: California

address: 2700 Stockton Blvd, 2301

department: Biochemistry and Molecular Medicine

institute: University of California, Davis

summary: Cancer lysosome is a potential target for cancer therapy. We designed and prepared a type of single-drug nanoparticles. These nanoparticles can specifically accumulate in lysosomes when entering cancer cells and are dissociated into small molecules. The small molecules not only act as lysosomotropic detergents to induce lysosomal membrane permeabilization directly, but also act as lysosomomotropic alkalizers to inhibit autophagy. In the meanwhile, these nanoparticles also show a strong proton-sponging effect and induce lysosomal dysfunction. As a result, the nanoparticles exhibit good antiproliferative activity in vitro. These single-drug nanoparticles also demonstrate excellent pharmacokinetic and toxicological profiles and dramatic antitumour efficacy in vivo. In addition, they are able to encapsulate and deliver additional drugs to tumour sites and are thus promising agents for autophagy inhibition-based combination therapy. Given their transdisciplinary advantages, these nanoparticles have enormous potential to improve cancer therapy.

overall_design: There are 15 samples totally that were analyzed in this study. MIA PaCa-2 cells were treated for 24 h with Vehicle control, Lys05 (5 μM), BAQ12 (5 μM), BAQ13 (5 μM) or 12O (5 μM). The total RNA were exacted and collected for RNA-seq analysis

first: Yuanpei

last: Li

first: Ryan

last: Davis

first: Stephenie

last: Liu


title: Deconstructing Stepwise Fate Conversion of Human Fibroblasts to Neurons by MicroRNAs: Subseries 6 [Figure 4, HITS-CLIP]

first: Kitra

last: Cates

overall_design: De-identified healthy human adult dermal fibroblasts were transduced with lentivirus to express the brain enriched microRNAs, miR-9/9* and miR-124 or non-specific miRNA (miR-NS) control as previously established (Yoo et al., Nature 2011; Richner et al., Nat. Prot. 2015; Abernathy, Kim, and McCoy et al., 2017). Argonaute target transcripts from reprogrammed neurons and controls was collected, then prepared for analysis as described in the Protocol.

first: Yangjian

first: Bo

last: Zhang

first: Shaopeng

first: Paul

last: Gontarz

first: Woo

last: Kim

first: Andrew

last: Yoo


title: RNA sequencing of seeds from Mthsfa9 Tnt1 insertion mutants

status: Public on Jul 12 2020

city: Beaucouze

first: Julia

last: Buitink

address: 42 rue Georges Morel

department: BAP

country: France

institute: INRAE

summary: HSFA9 (Medtr4g126070) is a seed-specific heat shock transcription factor that is upregulated during the later stages of seed maturation. To identify genes that are regulated by this transcription factor in the model legume Medicago truncatula, Tnt1 insertion mutants were identified and RNA sequencing was performed on mature seeds from two hsfa9 mutants and the wild type seeds.

overall_design: Three replicates of 50 seeds harvested from different plants were sequenced for two Tnt1 insertion mutants, NF10440 (hsfa9-1) and NF13157 (Mthsfa9-2) in the R108 background and the wildtype R108.

last: Zinsmeister

last: Lalanne


title: B cells sorted from VHL floxed MB1- Cre

first: John

middle: Robert

last: Ferdinand

address: Department of Medicine

institute: University of Cambridge

summary: ProB-PreB, immature and mature B cells were sorted from the bone marrow of mice and the RNA subsequently sequenced. The mice were all Mb1-Cre +/- and either Vhl flox/flox or VHL flox/WT

overall_design: 3 different cell types from the bone marrow of 2 genotypes of mice

first: Natalie

last: Burrows

first: Vijesh

middle: J

last: Bhute

first: Laura

last: Bergamaschi

first: Girolamo

last: Giudice

first: Evangelia

last: Petsalaki

first: Menna

last: Clatworthy

first: Patrick

last: Maxwell


title: Next-Generation Sequencing Analysis of ChIP

city: Geneva

first: Sylvain

last: LEMEILLE

address: 1 rue Michel-Servet

department: Department of Pathology and Immunology

institute: University of Geneva Medical School

summary:
Purpose: This study was carried out to determine RFX1 or RFX2 or RFX3 binding sites in nuclei of multiciliated ependymal cells.
Methods: DNA was extracted from ependymal cell cultures. ChIP-sequencing was used to determine the binding sites of RFX1 , RFX2 or RFX3.

overall_design: For each RFX, binding sites were determined by deep sequencing using DNA from 2 independent ChIP replicas.

first: Marie

last: Paschaki

last: Lemeille

first: Dominique

last: Baas

first: Laurette

last: Morlé

first: Jean

last: Duteyrat

first: Emmanuèle

last: Barras

first: Fabien

last: Soulavie

first: Julie

last: Jerber

first: Joëlle

last: Thomas

first: Yong

first: Michael

last: Holtzman

first: Walter

last: Reith

first: Bénédicte

last: Durand


title: Single cell transcriptional profile of third instar larval wing discs in Drosophila using drop-seq (single cell RNA-seq)

first: Elizaveta

last: Benevolenskaya

address: 900 S. Ashland Ave.

department: Biochemistry and Molecular Genetics

institute: University of Illinois at Chicago

summary: Our study focuses on understanding the early transcriptional changes taking place during the divergence of the adult muscle precursors that give rise to indirect flight muscles and direct flight muscles in Drosophila. We analyzed the heterogenous cell population of the adult muscle precursors by scRNA-seq and build an integrated single-cell reference atlas. We addressed the differences among muscle-type and different cell state during myoblast differentiation. Also, our dataset includes the transcriptional profile of the epithelial cells localized in the presumptive hinge and notum of third instar larval wing discs. In addition we studied the functional relevance of Amalgam in flight muscle development by depleting Ama expression specifically in the adult muscle precursors. We determined the transcriptional changes and perturbations in AMP cell identity upon Ama knockdown.

overall_design:
Drop-seq on the single cell suspension from third instar larval wing discs (hinge and notum, pouch was manually removed during dissection). A total of eight wild type samples were processed, including two wild types lines. In addition three replicates were included to study muscle-specific depletion of Amalgam
Single cell RNA-seq was performed using Drop-seq platform

first: Maria

middle: P

last: Zappia

first: Maxim

last: Frolov

first: Abul

last: Islam

first: Majd

last: Ariss