title: Transcriptional profiling of pancreatic acinar to ductal metaplasia using laser capture microdissection

city: Duarte

first: Juan

last: Du

state: CA

address: 1500 E. Duarte Rd

institute: Beckman Research Institute, City of Hope

summary: Pancreatic ductal adenocarcinoma (PDAC) is a deadly disease when diagnosed at a late stage, however patient survivorship significantly increases when the disease is detect prior to metastasis. To study the earliest events leading to PDAC initiation, we developed a genetically engineered mouse model of PDAC utilizing a tamoxifen-inducible Cre Recombinase knocked into the transcription factor Ptf1a locus to induce expression of oncogenic KrasG12D and Trp53R270H alleles in adult pancreatic acinar cells. Mice of the genotype KrasLSL-G12D/+; Trp53LSL-R270H/+; Ptf1aCreERTM/+ (KPT) developed PDAC following tamoxifen injection while control Cre recombinase negative KrasLSL-G12D/+; Trp53LSL-R270H/+; (KP) mice injected with tamoxifen did not develop PDAC. Acinar cells comprising the pancreata of tamoxifen treated KPT mice we observed to undergo acinar to ductal metaplasia (ADM), and formed precancerous lesions. We used laser capture microdissection (LCM) and RNA sequencing to generate, to our knowledge, the first transcriptional profile of an enriched population of metaplastic acinar cells in situ. Comparing the transcriptional profile of metaplastic acinar cells with the transcriptional profile of healthy pancreatic tissue identified differentially expressed genes associated with ADM. Ingenuity pathway analysis revealed transcriptional regulators and canonical signaling pathways involved in ADM. LCM was used to generate a transactional profile of cancer cells isolated from pancreatic tumors, and differential gene expression analysis revealed a subset of genes which are overexpressed in both ADM and PDAC relative to healthy pancreas. Further analysis of genes expressed in both pancreatic cancer precursor ADM lesions and invasive PDAC may lead to the identification of novel biomarkers of PDAC.

overall_design: Total RNA was extracted from metaplastic epithelial cells isolated using LCM from the pancreata of 3 unique tamoxifen treated KPT mice. Total RNA was extracted from cancer epithelium which was isolated from PDAC tumors using LCM. Tumors were resected from 3 unique tamoxifen treated KPT mice. Healthy pancreatic control total RNA was extracted from the pancreata of 3 unique tamoxifen treated KP mice. cDNA libraries were prepared from extracted RNA using the Kapa RNA HyperPrep kit with RiboEase (Kapa Biosystems), following the manufacturer’s protocol. Sequencing was performed using the Illumina HiSeq 2500 platform using the HiSeq SBS V4 Kit. Real-time analysis (RTA) software version 2.2.38 was used to process the resulting sequencing images and perform base calling.

first: Benjamin

middle: L

last: Johnson

first: Don

middle: J

last: Diamond

first: Du

last: Juan

first: Guo

last: Chao

first: Wang

last: Jinhui

first: Wu

last: Xiwei


title: CsIND regulates vascular formation and resistance to biotic and abiotic stresses in cucumber (Cucumis sativus L.)

status: Public on Sep 02 2019

city: Shanghai

first: Hailing

last: Zi

address: Chenhua road3888

country: China

institute: Shanghai center for plant stress biology

type: Expression profiling by high throughput sequencing

summary: The plant vascular system is essential for the enlarged plant stature and successful colonizzation the land by delivering resources throughout the plants and providing mechanical support. Despite several regulators of vascular patterning have been reported, how vascular system mediates stress resistance remain largely unknown. Here we identified a CsIND transcription factor that is specifically expressed in the xylem and phloem tissues in cucumber. Knock down of CsIND by RNAi lead to dwarf plants with enlarged or disorganized vascular systems in all aerial organs. The content of both auxin and jasmonic acid were increased in the CsIND-RNAi lines. Transcriptome profiling by RNA-Seq hints CsIND-regulated gene networks for defense response and vascular development. Biochemical analyses verified that CsIND directly binds to well-known vascular regulators including CsCCR1, CsMYB116, CsYAB5, CsBP and CsAUX, and physically interacts with dorsiventral patterning genes CsKAN2 and CsYAB5. Further, CsIND-RNAi plants displayed significantly enhanced tolerance to nitrogen dificency and resistance to cucumber downy mildew. Therefore, CsIND regulates vascular formation and resistance to biotic and abiotic stresses in cucumber, through the combinarory interactions with well-known vascular regulaors and hormone metabolism and signaling pathways.

overall_design:
Leaf veins and fruits four days before anthesis of WT and CsIND-RNAi transgenic cucumber plants were collected for RNA-seq analysis. Two biological replicates were performed for each tissue sample.

Please note that [1] the identifiers in the processed data file are searchable at: http://www.icugi.org/cgi-bin/ICuGI/genome/home.cgi?ver=2&organism=cucumber&cultivar=Chinese-long
[2] the 'M' is changed to 'G', and the isoform information has been deleted. For example, the 'Csa3G002400' corresponds to 'Csa3M002400.1' in the website.

first: Shuangshuang

last: Yan

first: Kang

last: Ning

first: Lian

last: Ding

first: Hongyan

last: Zheng

first: Zhihua

last: Cheng

first: Zhongyi

last: Wang

first: Qingyang

last: Lv

first: Jianyu

last: Zhao

first: Gen

last: Che

first: Wensheng

first: Li

last: Jiang

first: Hongyin

first: Xiaofeng

last: Liu

first: Zijing

last: Chen

first: Junjun

last: Shen

first: Ran

last: Gu

last: Qian

first: Renyi

first: Laixin

last: Luo

first: Xuexian

last: Li

first: Xiaolan

last: Zhang


title: Virus- and interferon alpha-induced smallRNA-Seq transcriptomes of cells from the microbat Myotis daubentonii

status: Public on Sep 05 2019

city: Jena

first: Martin

last: Hölzer

state: Thuringia

address: Leutragraben 1

department: Faculty of Mathematics and Informatics

country: Germany

institute: University of Jena

type: Non-coding RNA profiling by high throughput sequencing

summary: These small RNA-Seq data set was generated to study the virus- and interferon alpha-induced immune response of M. daubentonii (microbat) kidney cells with a focus on small RNAs, especially miRNAs. For the virus challenge, a RVFV clone (Clone-13) was used.

overall_design: Total RNA from control (mock), interferon-alpha (IFN) or Rift Valley fever virus Clone 13 (Clone13) infected cells were isolated at two time points (6h, 24h) post treatment/infection. The quality and integrity of the RNA was controled by a Agilent 2100 Bioanalyzer followed by deep sequencing. For each total RNA sample small RNA libraries were prepared utilizing the Illumina TruSeq smallRNA Kit (hereafter sRNA). Overall, 18 sRNA libraries were sequenced on one HiSeq 2500 lanes with 51 cycles resulting in ~10-20 million strand-specific single-end reads per sample. The complete experiment was performed in three independent, biological replicates. As no reference genome for M. daubentonii was available when conducting this study, we used the genome of the closely related microbat species M. lucifugus as a reference for mapping and quantification.

first: Andreas

last: Schoen

first: Julia

last: Wulle

first: Marcel A

last: Müller

first: Christian

last: Drosten

first: Manja

last: Marz

first: Friedemann

last: Weber


title: Human Eosinophils Express a Distinct Gene Expression Program in Response to IL-3 Compared to Common Beta-Chain Cytokines IL-5 and GM-CSF

status: Public on Sep 06 2019

city: San Diego

first: Pandurangan

last: Vijayanand

state: California

address: 9420 Athena Circle

department: Vaccine Discovery

country: USA

institute: La Jolla Institute for Immunology

summary:
Background: Despite recent advances in asthma management with anti-IL-5 therapies, many patients with eosinophilic asthma remain poorly controlled. IL-3 shares a common beta subunit receptor with both IL-5 and GM-CSF, but through alpha subunit-specific properties, uniquely influences eosinophil biology and may serve as a potential therapeutic target.

Objective: We aimed to globally characterize the transcriptomic profiles of GM-CSF, IL-3, and IL-5 stimulation and identify differences in gene expression using advanced statistical modeling.

Methods: Human eosinophils were isolated from the peripheral blood of healthy volunteers and stimulated with either GM-CSF, IL-3 or IL-5 for 48 hours. RNA was then extracted and bulk sequencing performed. DESeq analysis identified differentially expressed genes and weighted gene co-expression network analysis independently defined modules of genes that are highly co-expressed.

Results: IL-3 stimulation yielded the most numbers of differentially expressed genes that were also highly co-expressed. GM-CSF and IL-5 stimulation demonstrated redundancy in eosinophil gene expression.

Conclusion: IL-3 produces a distinct eosinophil gene expression program among the beta-chain receptor cytokines.

overall_design: A total of 28 samples were analyzed (7 eosinophil donors, with each eosinophil collection split and independently subjected to 4 conditions - unstimulated, GM-CSF stimulated, IL-3 stimulated, IL-5 stimuated). RNA-Seq data was mapped against the hg38 reference using TopHat [15] (v1.4.1., --librarytype fr-secondstrand -C) and the RefSeq gene annotation downloaded from the UCSC Genome Browser site.

first: Ryan

middle: K

last: Nelson

first: Howard

last: Brickner

first: Bharat

last: Panwar

first: Ciro

last: Ramirez-Suastegui

first: Laura

middle: C

last: Alexander

first: Grégory

last: Seumois

first: Praveen

last: Akuthota


title: RNA-Sequencing data of coxsackievirus type B3(CVB3) infected human neural progenitor stem cell(hNPC)

status: Public on Sep 03 2019

city: Seoul

first: Ok Sarah

last: Shin

address: 148, Gurodongro, Gurogu

country: South Korea

institute: Korea Univ.

summary: RNA profiles of hNPC infected with CVB3 were generated by Quant-Seq

overall_design: Investigation of host immune response to CVB3 infection by time point

first: Ok

middle: S

first: Soo-Jin

last: Oh


title: RNA sequencing analysis of the sea lamprey brainstem after spinal cord injury and GABA or baclofen treatments

status: Public on Sep 24 2019

city: Santiago de Compostela

first: Diego

last: Robledo

address: Rúa Lope Gómez de Marzoa s/n CIBUS building

department: Genetics

country: Spain

institute: University of Santiago de Compostela

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

overall_design: Refer to individual Series


title: Next Generation Sequencing of Wild Type and RXRa-/- peritoneal cavity macrophages

status: Public on Sep 01 2019

city: New York

first: Maria

last: Casanova Acebes

state: New York

address: 1470 Madison Ave

department: Oncological Sciences

institute: Mount Sinai School of Medicine

summary: The goal of this study is to compare the transcriptome profile (RNA-seq) of peritoneal cavity macrophages of RXRa-deficient and WT mice to identify genes which are controlled by the expression of the TF RXRa

overall_design: PC F480+MHCIINEG CD102+ macrophages of 8 weeks old wild type (WT) and RXRa-/- mice were generated by ULI (ultra-low input) sequencing in duplicates, using Illumina NextSeq-500 system.

last: Casanova-Acebes


title: Transcriptomic analysis of the Csr system in Erwinia amylovora

status: Public on Aug 21 2019

city: Urbana

first: Frank

last: Zhao

state: IL

address: 1201 W. Gregory Dr.

department: Crop Sciences

institute: University of Illinois

summary: This RNA-seq analysis examined the global effect of CsrA and its non-coding small RNA (ncsRNA) csrB in E. amylovora under the T3SS-inducing condition. The csrA mutant showed differential expression of more than 20% genes in the genome, which include significant down-regulation of T3SS genes and those required for cell growth and viability. On the other hand, the csrB mutant exhibited significant up-regulation of most major virulence genes, suggesting antagonistic effect of csrB on CsrA targets.

overall_design: Differential gene expression of the csrA and csrB mutants versus wild type grown in the T3SS-inducing condition for 6 hours

first: Jae

middle: H

last: Lee

first: Tiyakhon

last: Chatnaparat

first: Youfu


title: Chromatin profiles of chromosomally integrated human herpesvirus-6A [MNase-seq]

status: Public on Aug 15 2019

city: Burlington

first: Seth

last: Frietze

state: VT

address: 149 Beaumont Avenue

department: Biomedical and Health Sciences

institute: University of Vermont

type: Genome binding/occupancy profiling by high throughput sequencing

summary: We report the regulatory chromatin of the chromosomally integrated HHV6 genome. Using MNase-seq titration analysis, we find that the integrated virus in both patient and experimental infections that the HHV6 genome is tightly compacted with limited accessibility.

sample_organism:
Homo sapiens
Human betaherpesvirus 6A

platform_organism:
Homo sapiens
Human betaherpesvirus 6A

overall_design: Examination of chromatin accessibility by MNase-seq along the HHV6 genome using patient samples or experimental infections.


title: Chromatin profiles of chromosomally integrated human herpesvirus-6A [RNA-seq]

summary: We report the gene expression of HHV6 infected cells using RNA-seq and small RNA-seq. We find that the integrated virus is transcriptionally inactive.

overall_design: Examination of gene expression of HHV6 genes in patient cells or experimental infections.


title: Three congruent human Schwann cell models of CMT1A reveal a converged phenotype

first: Macrogen

last: Inc.

address: 12F, World Meridian Venture Center #254 Beotkkot-ro, Geumcheon-gu

institute: Macrogen Inc.

summary: Three CMT1A patient Schwann cell populations which were derived from hESC, hiPSC, or direct converted hiNC share the disease relevant phenotypes. From comparing deep sequencing results of these populations, potential therapeutic targets were newly identified.

overall_design:
Schwann cells from CMT1A hESC, hiPSC, or hfibroblast were analyzed for RNA sequencing followed by gene ontology analysis. We were able to purify discrete Schwann cell populations at Schwann cell precursor or neural crest stages by using Schwann cell surface marker and FACS sorting.
We differentiated human Schwann cell precursors from hESCs (H9 or PGD CMT1A hESCs) and hiPSCs (healthy donor 00024, 02623, and CMT1A disease line 05148, 05165) by using 2i protocol, and WNT was activated for iNC differentiation.

first: Yong

last: Kim

first: Gabsang


title: Green Tea Polyphenol EGCG Attenuates MDSCs-mediated Immunosuppression through Canonical and Non-Canonical Pathways in a 4T1 Murine Breast Cancer Model

status: Public on Aug 11 2019

city: Hangzhou

first: Ping

last: Xu

state: Zhejiang

address: 866 Yuhangtang Rd

department: Department of Tea Science

institute: Zhejiang University

summary: This study is set out to identify EGCG transcriptional targets in 4T1 breast cancer mediated myeloid-derived suppressor cells (MDSCs) in vitro. MDSCs were sorted from the spleens of 4T1-bearing mice and cultured with EGCG for 6h. RNA was extracted from either the Control group or EGCG group and for RNA-sequence.

overall_design: Transcriptomic profiling of control and EGCG-treated MDSCs was performed.

first: Le

last: Ying

first: Feng

last: Yan


title: Virus- and interferon alpha-induced transcriptomes of cells from the microbat Myotis daubentonii

first: Martin

last: Hölzer

summary: These RNA-Seq data set was generated to study the virus- and interferon alpha-induced immune response of M. daubentonii (microbat) kidney cells. For the virus challenge, a RVFV clone (Clone-13) was used.

overall_design: Total RNA from control (mock), interferon-alpha (IFN) or Rift Valley fever virus Clone 13 (Clone13) infected cells were isolated at two time points (6h, 24h) post treatment/infection. The quality and integrity of the RNA was controled by a Agilent 2100 Bioanalyzer followed by deep sequencing. For each total RNA sample cDNA libraries were prepared utilizing the Illumina Ribo-Zero rRNA Removal Kit for human/mouse/rat (hereafter rRNA-). Importantly, no polyA selection was applied. Overall, 18 rRNA- libraries were sequenced on six HiSeq 2500 lanes with 51 cycles resulting in 60-70 million strand-specific single-end reads per sample. The complete experiment was performed in three independent, biological replicates. As no reference genome for M. daubentonii was available when conducting this study, we used the genome of the closely related microbat species M. lucifugus as a reference for mapping and quantification.

first: Andreas

last: Schoen

first: Julia

last: Wulle

first: Marcel A

last: Müller

first: Christian

last: Drosten

first: Manja

last: Marz

first: Friedemann

last: Weber


title: Chromatin profiles of chromosomally integrated human herpesvirus-6A


title: Chromatin profiles of chromosomally integrated human herpesvirus-6A [ChIP-seq]

summary: We report the regulatory chromatin of the chromosomally integrated HHV6 genome. Using  ChIP-seq analysis, we find that the integrated virus is transcriptionally inactive and is enriched with distinct patterns of posttranslational histone modifications and TRF1/2.

overall_design: Examination of histone modifications and transcription factors along the HHV6 genome using patient samples or experimental infections.


title: Molecular and anatomical organization of the dorsal raphe nucleus

status: Public on Aug 06 2019

city: Boston

first: Kee Wui

last: Huang

state: MA

address: 200 Longwood Ave, WAB 347

department: Neurobiology

institute: Harvard Medical School

summary: The dorsal raphe nucleus (DRN) is an important source of neuromodulators and has been implicated in a wide variety of behavioral and neurological disorders. The DRN is subdivided into distinct anatomical subregions comprised of multiple cell types, and its complex cellular organization has impeded efforts to investigate the distinct circuit and behavioral functions of its subdomains. Here we used single-cell RNA sequencing, in situ hybridization, anatomical tracing, and spatial correlation analysis to map the transcriptional and spatial profiles of cells from the mouse DRN. Our analysis of 39,411 single-cell transcriptomes revealed at least 18 distinct neuron subtypes and 5 serotonergic neuron subtypes with distinct molecular and anatomical properties, including a serotonergic neuron subtype that preferentially innervates the basal ganglia. Our study lays out the molecular organization of distinct serotonergic and non-serotonergic subsystems, and will facilitate the design of strategies for further dissection the DRN and its diverse functions.

overall_design: Single cell RNA sequencing of live dissociated cells (unsorted) from mouse brain tissue containing the dorsal raphe nucleus using the inDrops v3 platform.

first: Kee

first: Bernardo

last: Sabatini


title: Exploring genetic interaction manifolds constructed from rich phenotypes

status: Public on Aug 08 2019

city: San Francisco

first: Thomas

last: Norman

address: Biochemistry Box 2542, 1700 4th St QB3 Rm 404

department: CMP

institute: University of California, San Francisco

summary: Rich phenotyping using single-cell RNA sequencing reveals principles and mechanisms of genetic interactions.

overall_design: Single-cell, pooled CRISPR screening experiment comparing the transcriptional effects of overexpressing genes alone or in combination

middle: M

first: Max

middle: A

last: Horlbeck

first: Luke

last: Gilbert

first: Jonathan

last: Weissman


title: Therapeutic efficacy of dimethyl fumarate in relapsing-remitting multiple sclerosis is linked with monocytic oxidative responses [Affymetrix]

status: Public on Jul 31 2019

city: Stockholm

first: Ewoud

last: Ewing

address: CMM L8:05, Karolinska University Hospital

department: Clinical Neuroscience

country: Sweden

institute: Karolinska Institutet

summary: Dimethyl fumarate (DMF) is a first-line-treatment for relapsing-remitting multiple sclerosis (RRMS). The redox master regulator Nrf2, essential in redox balance, is a target of DMF, but the precise therapeutic mechanisms remain elusive. Here we show impact of DMF on circulating monocytes and T cells in a prospective longitudinal RRMS patient cohort. DMF increased the level of oxidized isoprostanes in peripheral blood. Other observed changes, including methylome and transcriptome profiles, occur in monocytes prior to T cells. Importantly, monocyte counts and monocytic ROS increase following DMF and distinguish patients with beneficial treatment-response from non-responders. A single nucleotide polymorphism in the ROS-generating NOX3 gene is associated with beneficial DMF treatment-response and suggestively associated with increased ROS generation.  Our data implicate monocyte-derived oxidative processes in autoimmune diseases and their treatment, and identify NOX3 genetic variant, monocyte counts and redox state as parameters potentially useful to inform clinical decisions on DMF therapy of RRMS.

overall_design: 14 multiple sclerosis patients at baseline or after 6 months after DMF treatment. Extracted Celltypes are CD4+ Tcells from the same patients.

first: Karl

last: Carlström


title: Therapeutic efficacy of dimethyl fumarate in relapsing-remitting multiple sclerosis is linked with monocytic oxidative responses [Illumina]

type: Methylation profiling by genome tiling array

overall_design: 19 multiple sclerosis patients at baseline or after 3 or 6 months after DMF treatment. Extracted Celltypes are CD4+ Tcells and CD14+ Monocytes from the same patients.


title: Concentration-dependent recruitment of mammalian odorant receptors

city: Durham

first: Hiroaki

last: Matsunami

state: NC

address: 264 CARL Building

department: Molecular Genetics & Microbiology

institute: Duke University

summary: A fundamental challenge in studying principles of organization used by the olfactory system to encode odor concentration information has been to identify comprehensive sets of activated odorant receptors (ORs) across a broad concentration range inside freely behaving animals. In mammals, this has recently become feasible with high-throughput sequencing-based methods that identify populations of activated ORs in vivo. In this study, we characterized the mouse OR repertoires activated by the two odorants, acetophenone and 2,5-dihydro-2,4,5-trimethylthiazoline, from 0.01% to 100% (v/v) as starting concentrations using phosphorylated ribosomal protein S6 capture followed by RNA-Seq. We found Olfr923 to be one of the most sensitive ORs that is enriched by acetophenone. Using a mouse line that genetically labels Olfr923-positive axons, we provided evidence that acetophenone activates the Olfr923 glomeruli in the olfactory bulb. Through molecular dynamics stimulations, we identified amino acid residues in the Olfr923 binding cavity that facilitates acetophenone binding. This study sheds light on the active process by which unique OR repertoires may collectively facilitate the discrimination of odorant concentrations.

overall_design: pS6-IP RNA-Seq in odor stimulated vs control mice olfactory epithelium

first: Xiaoyang

last: Hu


title: RNA Sequencing Facilitates Quantitative Analysis of Transcriptomes of H1 derived cells and H1 after MSX2-knockout derived cells at Day8 after human early hematopoietic differentiation .

status: Public on Aug 01 2019

city: Tianjin

first: Jiaxi

last: Zhou

state: Tianjin

address: 288# Nanjing Road, He ping district

institute: PUMC

summary:
Purpose: The goals of this study are to verify MSX2 knock is suffice to promote hematopoiesis during human early hematopoietic differentiation through comparing the transcriptome profilings in WT samples and MSX2-knockout samples collected at day 8 after hematopoietic differentiation.
Method: mRNA profiles of hESC samples collected at day 8 after hematopoiesis differentiation were generated by deep sequencing using Illumina GAIIx. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks. qRT–PCR validation was performed using TaqMan and SYBR Green assays
Conclusions: MSX2 knock is suffice to promote hematopoiesis during early hematopoietic differentiation of H1 cells.

first: Hongtao

last: Wang


title: RNA PolyRNA Polymerase II CTD phosphatase Rtr1 prevents premature transcription termination

status: Public on Jul 30 2019

city: Indianapolis

first: Yunlong

last: Liu

state: IN

address: 410 West 10th Street

department: Medical and Molecular Genetics

institute: Indiana University School of Medicine

summary: RNA Seq and ChIP-exo experiments related to this project

overall_design: Four RNA-Seq biological replicates each for deletion mutant (RTR1, RRP6, RTR1 RRP6) and reference cells (WT)

first: Melanie

last: Fox

first: Jose

middle: F

last: Victorinio

first: Whitney

middle: R

last: Smith-Kinnaman

first: Sarah

last: Peck Justice

first: Hongyu

last: Gao

first: Asha

last: Boyd

first: Megan

last: Zimmerly

first: Rachel

last: Chan

first: Gerald

middle: O

last: Hunter

first: Amber

last: Mosley


title: Landscape of innate immune system transcriptome and acute T-cell mediated rejection of human kidney allografts

status: Public on Jul 26 2019

first: Akanksha

last: Verma

address: 1300, York Avenue

department: Department of Physiology and Biophysics

institute: Weill Cornell Medical College

summary: Acute rejection of human allografts has been viewed mostly through the lens of adaptive immunity, and the intragraft landscape of innate immunity genes has not been characterized in an unbiased fashion. We did RNA sequencing of 34 kidney allograft biopsy specimens from 34 adult recipients; 16 were categorized as Banff acute T-cell mediated rejection (TCMR) and 18 as normal. Computational analysis of intragraft mRNA transcriptome identified significantly higher abundance of mRNA for pattern recognition receptors in TCMR compared to normal biopsies, as well as increased expression of mRNAs for cytokines, chemokines, interferons, and caspases. Intragraft levels of calcineurin mRNA were higher in TCMR biopsies suggesting under immunosuppression compared to normal biopsies. Cell-type enrichment analysis revealed higher abundance of dendritic cells and macrophages in TCMR biopsies. Damage associated molecular patterns, the endogenous ligands for pattern recognition receptors, as well markers of DNA damage were higher in TCMR. mRNA expression patterns supported increased calcium flux and indices of endoplasmic, cellular oxidative, and mitochondrial stress were higher in TCMR. Expression of mRNAs in major metabolic pathways were decreased in TCMR. Our global and unbiased transcriptome profiling identified heightened expression of innate immune system genes during an episode of TCMR in human kidney allografts.

overall_design: We studied 34 adult kidney transplant recipients, a subset of kidney allograft recipients transplanted and followed at our center. Biopsies were done under ultrasound guidance and were read and reported independently by two renal pathologists at our center (S.S and S.V.S), based on the Banff 2017 update of the Banff ‘97 classification of allograft pathology (64, 65). Biopsy tissue sections were stained with hematoxylin and eosin, periodic acid–Schiff, and Masson trichrome, as well as for polyomavirus, and for complement factor 4 degradation product d (C4d). Each patient provided a single biopsy sample for this study.

first: Franco

middle: B

last: Mueller

first: Olivier

last: Elemento

first: Manikkam

last: Suthanthiran

first: Thangamani

last: Muthukumar


title: Cannabinoid exposure in rat adolescence reprograms the initial behavioral, molecular, and epigenetic response to cocaine

status: Public on Jul 27 2019

first: Philippe

last: Melas

address: 1051 Riverside Drive

institute: Columbia University

summary: This dataset includes ATAC-Seq and RNA-seq data from rat prefrontal cortex and/or nucleus accumbens (postnatal date, PND 61), as part of characterizing how the rat brain responds to its first encounter with cocaine (PND 60) with or without preexposure to the synthetic cannabinoid WIN 55,212-2 (WIN) during adolescence (PND 42-52). WIN was administered twice daily during the latter eleven consecutive days (2 mg/kg, 3 days; 4 mg/kg, 4 days; 8 mg/kg, 4 days) and, following a week of WIN abstinence, animals were IP challenged with cocaine (10 mg/kg). Brain dissections were performed 24 hours after the cocaine IP challenge.

overall_design: ATACseq in PFC in 4 treatments. RNAseq in PFC and Nacc

first: Denise

last: Kandel


title: Therapeutic efficacy of dimethyl fumarate in relapsing-remitting multiple sclerosis is linked with monocytic oxidative responses

first: Ewoud

last: Ewing

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

overall_design: Refer to individual Series


title: Runx/CBFβ transcription factor complexes regulate Ccl5 expression through two novel enhancers to enhance tumor immunity [dataset 3]

status: Public on Jul 12 2019

city: Kyoto

first: Wooseok

last: Seo

address: Yoshida-Konoe-cho, Sakyo-ku

country: Japan

institute: Kyoto University Graduate School of Medicine

summary: CCL5 (also known as RANTES) was originally known to be important to recruit memory T cells to infected sites, but it received much attention as an inhibitor to HIV’s entry into T lymphocytes of AIDS patients. Recently, it has been reported to be necessary to sustain Trm (Tissue-resident memory) T cells at local tissues as well as to play roles in manipulating tumor microenvironment by both host immunity and cancer cells. Nonetheless, little is known how Ccl5 expression is regulated, thus making it quite difficult for therapeutic intervention. Our study reveals that Runx/CBFβ transcription factor complexes antagonizes Ccl5 expression through two novel transcriptional enhancers. The proximal enhancer is required for the homeostatic expression of Ccl5 during the steady state, meanwhile the distal enhancer is necessary for the expression Ccl5 during the activated stage. We employed enChIP-seq to identify the distal enhancer located 1.35 Mb away from the promoter. This long distance interaction requires the help from Satb1, a global chromatin organizer. Our study reveals that the reduced amounts of Ccl5 by the deletion of the proximal enhancer results in an enhancement of metastasis in B16-F10 melanoma model. On the other hand, a Runx3-mutant mouse line in which Ccl5 expression is increased showed the opposite outcome, suggesting a novel inverse correlation between host Ccl5 levels and metastasis rate.

overall_design: Identification of RNAs differentially expressed by the absence of Ccl5-PE (proximal enhancer) from lung and spleen NK cells by RNA-seq.

first: Kanako

last: Shimizu

first: Satoshi

last: Kojo

first: Okeke

last: Arinze

first: Terumi

last: Kowhi-Shigematsu

first: Shin-Ichiro

last: Fujii

first: Ichiro

last: Taniuchi


title: Transcriptome analysis by RNA-Seq of spp381-ts mutant

status: Public on Jul 05 2019

city: Seville

first: Andrés

last: Aguilera

address: Av. Américo Vespucio 24

department: Genome BIology

institute: CABIMER, Universidad de Sevilla

summary: THO/TREX is a conserved complex with a role in messenger ribonucleoprotein biogenesis that links gene expression and genome instability. Here we show that human THO interacts with MFAP1, a spliceosome-associated factor. Interestingly, MFAP1 depletion impairs cell proliferation and genome integrity, increasing γH2AX foci and DNA breaks. This phenotype is not dependent either on transcription or RNA-DNA hybrids. Mutations in the yeast orthologous gene SPP381, also confer a similar transcription-independent genome instability supporting a conserved role. MFAP1 depletion has a wide effect on splicing and gene expression in human cells, determined by transcriptome analyses, that affects a number of DNA damage response (DDR) genes, which supports an indirect role of MFAP1 on genome integrity. Our work defines a novel functional interaction between THO and RNA processing and argues that splicing factors may contribute to genome integrity indirectly by regulating the expression of DDR genes rather than by a direct role.

overall_design: Analysis of gene expression in the Saccharomyces cerevisiae mutant spp381-ts under 1h of restrictive temperature.

first: Rosa

last: Luna

first: Irene

last: Salas-Armenteros

first: Mónica

last: Pérez-Alegre

first: Eloísa

last: Andújar

first: Sonia

middle: I

last: Barroso

first: Ana

middle: G

last: Rondon


title: Using RNA Seq to identify a CF habitat specific transcriptional profile

status: Public on Jul 04 2019

city: Hanover

first: Susanne

last: Häußler

address: Feodor-Lynen-Str. 7

department: Molecular Bacteriology

institute: Twincore

summary:
Purpose: The goal of this study was to use RNA Seq to explore whether and to what extent genetic heterogeneity would shape the transcriptional profile in the environment of the CF lung

Methods : mRNA profiles were generated for Pseudomonas aerugionsa samples derived from explanted lung tissue or pure cultures isolated from the same lung regions by deep sequencing. To enrich the bacterial RNA MicrobeEnrich Kit (Ambion) was used. The removal of ribosomal RNA was performed using the Ribo-Zero Bacteria Kit (Illumina) and cDNA libraries were generated with the ScriptSeq v2 Kit (Illumina) . The samples were sequenced in single end mode on an Illumina HiSeq 2500 device and mRNA reads were trimmed and mapped to the PAO1 NC_002516 reference genome from NCBI using Stampy pipeline with defaut settings.

overall_design: mRNA profiles either from Pseudomonas aeruginosa containing explanted lung tissue from a single patient from various regions of the lung or pure P. aeruginosa liquid cultures grown in LB at 37C from the same lung regions as the ex vivo samples were generated and deep sequenced using Illumina HiSeq 2500.

first: Adrian

last: Kordes

first: Matthias

last: Preuße

first: Sven

middle: D

last: Willger


title: Transcriptomics analysis of gene expression in wildtype and NSUN2 knockdown T24 cell

status: Public on Jul 02 2019

city: Beijing

first: Bao-Fa

last: Sun

address: Da-Tun Road

institute: Beijing Institute of Genomics (BIG) of Chinese Academy of Sciences (CAS)

summary: Total RNA was isolated using TRIzol® Reagent (Ambion). The RNA concentration and quality were determined with NanoDrop, Qubit and agarose gel analysis. The Dynabeads® mRNA Purification Kit (Ambion) was used to enrich the mRNAs, which were used as templates for RNA-Seq library construction. RNA-Seq libraries was directly constructed by using KAPA mRNA Stranded mRNA-Seq Kit (KAPA) according to the manufacturer’s instructions. The libraries were sequenced on the Illumina HiSeq X-Ten platform at Novogene (Tianjin, CA) with paired-end 150 bp read length. The different genes expression between the control and NSUN2 knockdown cell were detected.

overall_design: Examination of gene expressive levels in wildtype and NSUN2 knockdown T24 cell

first: Xin

last: Chen

first: Ang

last: Li

first: Baofa

first: Dan

last: Xie

first: Yuigui

last: Yang


title: Identification of PRDM15 Cistrome in Emu-Myc Lymphoma cells

first: Julia

middle: Nanyi

last: Zhao

state: NY

address: 1470 Madison Ave

institute: Icahn School of Medicine at Mount Sinai

summary: Genome-wide binding targets of PRDM15 were identified in Emu-Myc Lymphomas

overall_design: ChiP-Seq analysis was performed to identify PRDM15 binding sites in Emu-Myc Lymphomas

first: Diana

last: Low

first: Slim

last: Mzoughi


title: A Cancer rainbow mouse for visualizing the functional genomics of field cancerization

status: Public on Jul 15 2019

first: Joshua

last: Snyder

state: North Carolina

address: 203 Research Dr

department: Surgery

summary: Comparison of mouse intestinal crypt epithelial cells isolated from wild-type or ROBO-Crainbow small intestine.

overall_design: Single-cell RNA-seq (scRNAseq) was performed on WT and ROBO-Crainbow mouse intestinal crypt cells. The goal of the experiment was to compare the stem cell lineage in normal and precancerous intestine (ROBO Crainbow).

first: Peter

last: Boone

first: Lauren

last: Rochelle

first: Veronica

last: Lubkov

first: Wendy

last: Roberts

first: P

last: Nicholls

first: Cheryl

last: Bock

first: Mei

last: Flowers

first: Richard

last: von Furstenberg

first: Barry

last: Stripp

first: Pankaj

last: Agarwal

first: Alexander

last: Borowsky

first: Robert

last: Cardiff

first: Larry

last: Barak

first: Marc

last: Caron

first: H

last: Lyerly


title: RNA-BisSeq for YBX1 RIP in normal T24 cell

first: Bao-Fa

last: Sun

type: Methylation profiling by high throughput sequencing

summary: Flag-YBX1 overexpressed T24 cells pellets were resuspended with 2 volume of lysis buffer (150 mM KCl, 10 mM HEPES pH 7.6, 2 mM EDTA, 0.5% NP-40, 0.5 mM DTT, 1:100 protease inhibitor cocktail, 400 U/ml RNase inhibitor), and incubated at 4 °C for 30 min with rotation. Then the lysate was centrifuged at 15 000 g for 20 min. Before incubating the lysate with Flag beads, 100ul were taken as input. The anti-Flag M2 magnetic beads (Sigma, 10 μl per mg lysate) were washed with NT2 buffer (200 mM NaCl, 50 mM HEPES pH 7.6, 2 mM EDTA, 0.05% NP-40, 0.5 mM DTT, 200 U/ml RNase inhibitor) four times. Cell lysate was mixed with M2 beads and incubated at 4 °C for 4 h with rotation. The beads were washed two times with 1 ml ice-cold NT2 buffer. Then the beads were subject to Micrococal nuclease (NEB) digestion (1:1 000 000 dilution) for 8 min at 37 °C. The beads were cooled on ice immediately for 5 min and washed two times with 1 ml ice-cold 1× PNK+EGTA buffer (50 mM Tris-HCl pH 7.5, 20 mM EDTA, 0.05% NP-40, 200 U/ml RNase inhibitor) and two times with 1 ml ice-cold 1× PK buffer (50 mM NaCl, 100 mM Tris-HCl pH 7.5, 10 mM EDTA, 0.2% SDS, 200 U/ml RNase inhibitor). Then the beads were digested with 200 μl pre-heated (20 min at 50 °C) Proteinase K and RNAs were extracted with an equal volume of Acid-Phenol: Chloroform, pH 4.5 (Ambion). The RNAs were subjected to rRNA removal and Bisseq. The libraries were sequenced on the Illumina HiSeq X-Ten platform at Novogene (Tianjin, CA) with paired-end 150 bp read length.The m5C sites were called using meRanCall from meRanTK (FDR < 0.01).

overall_design: Examination of m5C sites in YBX1 binding targets.

first: Xin

last: Chen

first: Ang

last: Li

first: Baofa

first: Dan

last: Xie

first: Yuigui

last: Yang


title: Transcriptomics analysis of gene expression in human urothelial carcinoma of the bladder (UCB) and adjacent normal tissues.

summary: 36 cases of UCB and 29 adjacent normal bladder tissues (22 pairs) were derived from patients diagnosed with UCB and received radial cystectomy at Sun Yat-sen University Cancer Center (SYSUCC, Guangzhou, China). Total RNA was isolated using TRIzol® Reagent (Ambion). The RNA concentration and quality were determined with NanoDrop, Qubit and agarose gel analysis. The Dynabeads® mRNA Purification Kit (Ambion) was used to enrich the mRNAs, which were used as templates for RNA-Seq library construction. RNA-Seq libraries was directly constructed by using KAPA mRNA Stranded mRNA-Seq Kit (KAPA) according to the manufacturer’s instructions. The libraries were sequenced on the Illumina HiSeq X-Ten platform at Novogene (Tianjin, CA) with paired-end 150 bp read length. The different genes expression between the UCB and adjacent normal tissues were detected. Several genes related to cancer pathways were dysregulated.

overall_design: Examination of gene expressive change in human urothelial carcinoma of the bladder (UCB)


title: m5C Promotes Pathogenesis of the Bladder Cancer Through Stabilizing mRNAs


title: PARCLIP analysis of YBX1, ELAVL1 and ALYREF to detect their binding targets

summary: The PAR-CLIP sample was separated by SDS-PAGE, RNA were recovered from the gel by D-tubeTM Dialyzer Midi(Millipore).The mixture were digested by 4 μg/μl proteinase K (Roche, 03115828001) and precipitated in ethanol with the help of glycogen (Thermo, R0551). RNAs in ethanol were used for the small RNA library construction (NEB, E7300L). Finally, the library was sequenced on the Illumina HiSeq X-Ten platform with paired-end 150 bp (PE150) kits. Only the forward reads were used in the data analysis and uploaded. Bowtie was applied to map sequencing reads against hg19 genome with up to two mismatches allowed. PARalyzer software was used to define proteins binding clusters.

overall_design: Examination of YBX1, ELAVL1 and ALYREF binding targets


title: RNA m5C analysis in wildtype and NSUN2 knockdown T24 cell

summary: RNA fragmentation and bisulfite conversion were performed. In brief, 200 ng of mRNAs along with 1 ng in vitro transcribed mouse dihydrofolate reductase (Dhfr) spike-in RNA were used. The bisulfite treated samples were desalted with Nanoseq with 3K omega 500/pk centrifugal devices (PALL). Sequencing was performed on an Illumina HiSeq X-Ten sequencing system. The m5C sites were called using meRanCall from meRanTK (FDR < 0.01). The differential m5C sites were detected

overall_design: Examination of m5C changes in NSUN2 knockdown samples


title: Investigation of transcriptional changes in cells expressing different levels of MeCP2

status: Public on Jun 27 2019

city: Edinburgh

first: Shaun

middle: Michael

last: Webb

address: 2.21 Swann Building, Kings Buildings

department: Wellcome Trust Centre for Cell Biology

country: United Kingdom

institute: University of Edinburgh

summary: MeCP2 is transcriptional regulator, however the mechanism is not fully understood. This study uses various levels of MeCP2 in human neurons to discover mechanism of MeCP2 action. The transcriptional data are used to correlate with methylation status of genes.

overall_design: LUHMES-derived neurons have been modified to express seven levels of MeCP2 and RNA-seq was performed for all the cell lines.

first: Justyna

last: Cholewa-Waclaw

first: Kashyap

last: Chhatbar


title: Young and Old C57BL/6N Mouse HSC RNA Sequencing

status: Public on Jul 01 2019

first: Paul

middle: Vincent

last: Dellorusso

address: 701 West 168th Street, 724 Hammer Health Sciences Center

department: Genetics and Development

institute: Columbia University Irving Medical Center

summary: RNA sequencing of hematopoietic stem cells isolated from young (8-12 week) and old (24-27 month) BL6 mice.

overall_design: 3 biological replicates per age group were processed for low-input RNA library preparation and 50bp read length single-end sequencing.

first: Evgenia

last: Verovskaya

first: Theodore

last: Ho

first: Emmanuelle

last: Passegué


title: Study of MeCP2 occupancy and biniding localization in the genome

summary: MeCP2 ChIP-seq was performed to study localisation of MeCP2 in the genome and to confirm binding to mCG.

overall_design: MeCP2 ChIP-seq was performed on LUHMES-derived neurons including: controls, MeCP2 KO and OE.


title: Study of MeCP2 binding and accessibity of chromatin in absence and presence of MeCP2 using ATAC-seq

summary: ATAC-seq was performed to study changes in chromatin openness in the MeCP2 knock-outs and overexpressions. Additionally data was used to visualise the foorprint of MeCP2 bound to chromatin in vivo.

overall_design: ATAC-seq was performed on LUHMES-derived neurons including: controls, MeCP2 KO and OE.


title: Study of DNA methylation pattern in single basepair resolution in the human dopaminergic neurons

summary: Whole genome bisulfite sequencing was done in order to visualise the sides of DNA methylation in human genome.

overall_design: Whole genome bisulfite sequencing was performed using three different techniques TAB-seq, ox-BS and WGBS on WT LUHMES derived neurons at day 9.


title: ERα-CtBP-mediated repression of Homologous-recombination repair in ovarian cancer improves chemo-sensitivity

status: Public on Jun 26 2019

city: Houston

first: Tianpeng

last: Gu

address: Cambridge steet

institute: Baylor College of Medicine


title: Study of MeCP2 in LUHMES-derived neurons


title: GATA2 promotes hematopoietic development and represses cardiac differentiation of human mesoderm

status: Public on Jul 09 2019

city: Badalona

first: Elisabetta

last: Mereu

address: Ctra de Can Ruti, Camí de les Escoles, s/n

institute: Josep Carreras Leukemia Research Institute

summary: In vertebrates, GATA2 is a master regulator of hematopoiesis and is expressed throughout embryo development and in adult life. Although the essential role of GATA2 for the onset of mouse hematopoiesis is well established, its involvement during early human hematopoietic development is not clear. By combining time-controlled overexpression of GATA2 with genetic knockout experiments, we found that GATA2, at the mesoderm specification stage, promotes the generation of hemogenic progenitors and their further differentiation to hematopoietic progenitor cells, while negatively regulating cardiac differentiation. Surprisingly, genome-wide transcriptional and chromatin immunoprecipitation analysis showed that GATA2 bound preferentially to regulatory regions, and repressed the expression of cardiac development-related genes. By contrast, genes important for hematopoietic differentiation were upregulated by GATA2 in a mostly indirect manner. Collectively, our data reveal a hitherto unrecognized role of GATA2 as a direct repressor of cardiac fates, and highlight the importance of coordinating the specification and repression of alternative cell fates.

overall_design: Single cells RNA-seq (scRNA-seq) analysis of mesodermal and hemogenic progenitors derived from human iPS with and without GATA2 gene overexpression.

first: Alessandra

last: Giorgetti

first: Holger

last: Heyn


title: ERα-CtBP-mediated repression of Homologous-recombination repair in ovarian cancer improves chemo-sensitivity [ChIP-seq]

summary: Deficiency in homologous recombination repair (HRR) is frequently associated with hormone-responsive cancers. Epithelial ovarian cancer (EOC) is a typical hormone-related tumor, with defects of HRR in up to half of cases. However, whether there are molecular connections between estrogen signaling and HRR deficiency in EOC remains unknown. Here we report an inverse correlation between estrogen signaling and HRR activity in EOC. Genome-wide mapping of ERα reveals ERα co-bindings with co-repressor CtBP, especially on many HRR gene loci, in EOC cells but not in breast cancer cells. Consistently, depleting ERα in EOC cells up-regulates HRR activity and HRR gene expression. Importantly, estrogen signaling enhances the sensitivity of ovarian cancer cells to chemotherapy agents in vitro and in vivo. Large-scale analyses further indicate that estrogen replacement and ERα expression are associated with favorable survival of EOC patients. These findings characterize a novel role of ERα in mediating the molecular connection between hormone and HRR in EOC, and suggest that estrogen signaling may improve the treatment outcome of EOC patients.

overall_design: ChIPSeq of SKOV3 cells. Samples including Input, anti-CtBP, anti-ERα and anti-CtBP treated with Fulverstrant.

first: Dapeng

last: Hao

first: Jianlin

last: Wang

first: Li-Jun

last: Di


title: RNA m5C analysis in human urothelial carcinoma of the bladder (UCB) and adjacent normal tissues.

first: Bao-Fa

last: Sun

summary: 36 cases of UCB and 29 adjacent normal bladder tissues (22 pairs) were derived from patients diagnosed with UCB and received radial cystectomy at Sun Yat-sen University Cancer Center (SYSUCC, Guangzhou, China).Total RNA was isolated using TRIzol® Reagent (Ambion). The RNA concentration and quality were determined with NanoDrop, Qubit and agarose gel analysis. The Dynabeads® mRNA Purification Kit (Ambion) was used to enrich the mRNAs, which were used as templates for RNA-BisSeq library construction. For RNA-BisSeq, bisulfite-treated mRNAs were first subjected to reverse transcription with ACT hexamers and Superscript II Reverse Transcriptase (Invitrogen), and the following processes were carried out with KAPA mRNA Stranded mRNA-Seq Kit (KAPA) according to the manufacturer’s instructions. The libraries were sequenced on the Illumina HiSeq X-Ten platform at Novogene (Tianjin, CA) with paired-end 150 bp read length. The m5C sites were called using meRanCall from meRanTK (FDR < 0.01). The differential m5C sites were detected and the hypermethylated m5C in UCB samples correlates with oncogene mRNA overexpression in UCBs.

overall_design: Examination of RNA m5C changes in UCB patients

first: Xin

last: Chen

first: Ang

last: Li

first: Baofa


title: Ssr4-regulated genes in Beauveria bassiana

status: Public on Jun 06 2019

first: wei

last: shao

state: zhejiang

address: Zijingang Campus of Zhejiang University,Yuhangtang Road No.866

institute: zhejiang university

summary: Ssr4 was experimentally proven to be required for radial growth, aerial conidation, insect infection and virulence-related cellular events in the insect mycopathogen Beauveria bassiana.  For in-depth insight into the essential role of Ssr4 in the insect mycopathogen, transcriptomic analysis was carried out via high throughput sequencing (RNA-Seq), resulting in nearly one fourth of the whole genome differentially expressed in the Dssr4 mutant versus wild-type strain.

overall_design: Total RNAs obtained from three cultures (replicates) of the Dssr4 mutant were compared with those of the wild-type (WT) cultures grown on SDAY plates (Glucose 4%, Peptone 1%, and Yeast extract 1% plus 1.5% Agar).

first: Ming-Guang

last: Feng

first: Wei

last: Shao


title: Networks of enhancers and microRNAs drive variation in cell states

status: Public on Jun 14 2019

city: Cambridge

first: Salil

last: Garg

state: Massachusetts

department: Biology

institute: Koch Institute for Integrative Cancer Research

summary: We measure gene expression changes in three naturally arising states of embryonic stem cells.  These states exhibit intrinsic heterogeneity through varying at activity at subsets of enhancers.  Variation at enhancers drives variation in protein coding genes and microRNAs, the latter of which further contribute to cell state variation across the population of ESC.

overall_design: Examination of gene expression in three ESC states defined by Nanog and Sox2 levels in three replicates

first: Meenakshi

last: Chakraborty


title: Identification of genes with enriched expression in early developing mouse cone photoreceptors

city: New York

first: Mark

middle: Monroe

last: Emerson

address: 160 Convent Ave

institute: The City College of New York

summary: A LHX4 transgenic reporter line with high specificity for developing mouse cone photoreceptors was identified and used to purify early stage cone photoreceptors for profiling by single cell RNA sequencing.

overall_design: Collection of FACS-sorted LHX4::GFP+ E14.5 early cones and LHX4::GFP- retinal cells for further analysis.

first: Diego

last: Buenaventura

first: Adrianne

last: Corseri


title: ERα-CtBP-mediated repression of Homologous-recombination repair in ovarian cancer improves chemo-sensitivity [RNA-seq]

first: Tianpeng

last: Gu

overall_design: RNAseq of SKOV3 cells (Control, ERα overexpression and CtBP overexpression)

first: Yuan

last: Meng


title: Investigation of mRNA expression pattern by over-expression of two CEBPB transcription factor isoforms

city: Jena

first: Marco

last: Groth

address: Beutenbergstraße 11

department: Core Facility - Next Generation Sequencing

institute: Leibniz Institute on Aging - FLI

summary: The RNA binding protein Lin28b is highly expressed during embryogenesis but its expression declines in adult tissues, and aberrant expression of Lin28b is associated with tumour development and maintenance. Lin28b regulates the translation of several glycolytic and mitochondrial enzymes in order to enhance cellular metabolism and energy production. Lin28b is repressed by let-7 family microRNAs in a reciprocal negative regulatory circuitry where Lin28b suppresses maturation of let-7. This circuitry obtains input from master regulators such as MYC that transcriptionally upregulates Lin28b, which is required for let-7 suppression and proliferation. Not much is known of how this circuitry is regulated through transcription of the let-7 microRNAs. Here we show that the transcription factor C/EBPbeta-LIP induces aerobic glycolysis and mitochondrial respiration reminiscent to cancer cell metabolism. By integrating transcriptome, proteome and metabolic flux analysis, we reveal that this LIP-induced metabolic reprogramming is dependent on Lin28b and that LIP enhances Lin28b expression through transcriptional repression of the let-7 microRNA family. Transgenic mice overexpressing LIP have reduced levels of let-7 in bone marrow, skin and spleen, which is associated with induction of Lin28b and hyperplasia. This study establishes LIP as a regulator of the let-7/Lin28b regulatory circuitry and we hypothesize that the LIP-controlled let-7/Lin28b regulation is involved in the de-regulation of tissue homeostasis and tumourigenesis.

overall_design: Total samples: 9 (3 samples CEBPB-LIP overexpression; 3 samples CEBPB-LAP overexpression; 3 samples empty vector control CEBPB k/o).

first: Tobias

last: Ackermann

first: Cornelis

last: Calkhoven


title: APA usage in vaporized cannabis plant matter (CPM) exposure rats

status: Public on Jun 05 2019

city: pullman

first: Shuwen

last: Zhang

state: WASHINGTON

address: 1815 Ferdinand’s Lane

institute: Washington State University

summary: Role of alternative polyadenylation (APA) in rat brain after vaporized cannabis plant matter (CPM) exposure remains largely undetermined. Our WTTS-seq approach to capture 3'-end of RNAs clearly revealed alternative polyadenylation events responsible for dominantly down-regulates APA expression on Glutamatergic Transcripts in rats after CPM Exposure.

overall_design: Total RNA samples obtained from the mediobasal hypothalamus of CPM exposure (MJ) rats and control rats were used to construct WTTS-seq libraries. Eight WTTS-seq libraries including four MJ rats and four control rats were involved in this submission.

first: Pique

last: Choi

first: Yangzi

first: Meagan

middle: J

last: Stotts

first: Jennifer

last: Michal

first: Jon

last: Davis

first: Zhihua

last: Jiang


title: Next Generation Sequencing identifies lymph node lymphatic endothelial cell genes regulated by RANKL

status: Public on Jun 01 2019

city: Strasbourg

first: Christopher

middle: G.

last: Mueller

address: 2 Allée Gaspard Monge

department: IBMC

country: France

institute: CNRS

summary:
Purpose: The objective was to identify genes regulted by RANK signalling in lymph node lymphatic endothelial cells
Method: Lymphatic endothelial cells were FACS sorted from peripheral lymph nodes of mice deficient for stromal RANKL (Ccl19 Cre Rankl flox/flox) versus littermate controls (Rankl flox/flox) and processed for bulk RNA sequencing
Results: Upregulated and downregulated genes were identified

overall_design: Lymphatic cell mRNA profiles of 8 week old littermate (Rankl flox/flox) and stromal RANKL-conditional knock out (Ccl19 Cre Rankl flox/flox) mice were generated by deep sequencing.  The sequence reads that passed quality filters and key genes were validated by  qRT-PCR using TaqMan and SYBR Green assays on lymphatic cells isolated from Prox-1 Cre Rank flox/flox mice.


title: Inactivation of Bap1 Cooperates with Losses of Nf2 and Cdkn2a to Drive the Development of Pleural Malignant Mesothelioma in Conditional Mouse Models

status: Public on May 30 2019

city: Philadelphia

first: yinfei

last: tan

state: PA

address: 333 cottman ave

department: Genomic Core

institute: Fox Chase Cancer Center

summary: Mutations/deletions of BAP1, CDKN2A, and NF2 are the most frequent genetic lesions in human MM. We introduced various combinations of these deletions in the pleura of conditional knockout (CKO) mice, focusing on the contribution of Bap1 loss.

overall_design: RNA-seq analysis of MMs from triple-CKO vs. double KO mice revealed enrichment of genes transcriptionally regulated by the polycomb repressive complex 2 (PRC2) and others previously implicated in known Bap1-related cellular processes.

first: Anna

last: Kukuyan

first: Joseph

last: Testa


title: Drug combination of 17-AAG and Belinostat on MDA-MB-231 breast cancer cells

status: Public on May 17 2019

city: Shanghai

first: Cheng

last: Luo

state: Shanghai

address: No. 555 Zuchongzhi Road

institute: Shanghai Institute of Materia Medica

summary: Breast cancer is the most common cancer that threatens women's health. While the strategy of drug combination can help to reduce adverse effects and to overcome the resistance of clinical treatment of single drug. In this work, we report the synergetic effect between a HSP90 inhibitor 17-AAG and a HDAC inhibitor Belinostat, on the triple-negative breast cancer MDA-MB-231 cells. The RNA-Seq data analysis showed that the most over-represented KEGG pathways in the combination group came from migration or invasion related genes, which were not observed in the differentially expressed genes after the treatment of 17-AAG or Belinostat alone.

overall_design: The RNA-Seq data was collected for MDA-MB-231 cells after the treatment of 17-AAG, Belinostat, and the Combination of 17-AAG with Belinostat

first: Yu

last: Zuo

first: Heng

last: Xu

first: Hao


title: Transcriptome analysis of Arabidopsis thaliana photoreceptor mutants impaired in UV and blue light signaling

status: Public on May 29 2019

city: Örebro

first: Luis

last: Morales

address: Fakultetsgatan 1

department: School of Science and Technology

institute: Örebro University

summary: Plants use sunlight as a source of energy for photosynthesis but also as an important environmental cue to regulate growth, development and light acclimation. Wavelengths in the UV-B (280-315 nm) and UV-A/blue (315-500 nm) regions of the spectrum are perceived by UV RESISTANCE LOCUS 8 (UVR8) and cryptochromes (CRY1 and CRY2), respectively. Despite recent advances in our understanding of how these photoreceptors promote photomorphogenesis, very little is known about the molecular mechanisms regulated by UVR8 and CRYs in sunlight exposed plants. Here, a factorial experiment was designed to assess the roles of UVR8 and CRYs in regulating transcriptome wide changes, hormone accumulation, and growth competence of Arabidopsis thaliana plants exposed to solar UV-B, UV-A, and blue radiation.

overall_design: Transcriptome profiling of solar UV and blue responses in Arabidopsis wild-type Ler and photoreceptor mutants (uvr8-2 and cry1cry2) to assess the roles of UVR8 and cryptochromes in the regulation of gene expression in sunlight.

first: Neha

last: Rai

first: Pedro

last: Aphalo

first: Mikael

last: Brosché


title: Regulation of gene expression by MgrA in Staphylococcus aureus USA300 strain LAC

status: Public on May 07 2019

city: Aurora

first: Alexander

last: Horswill

state: CO

department: Immunology and Microbiology

institute: University of Colorado Anschutz Medical Campus

summary: MgrA is a global regulator of gene expression in Staphylococcus aureus. Here we use RNA-sequencing to compare gene expression in a wild-type USA300 strain and an isogenic mgrA mutant.

sample_organism: Staphylococcus aureus subsp. aureus USA300

overall_design: Illumina RNA-sequencing of S. aureus USA300 LAC and LAC ΔmgrA in triplicate.

first: Heidi

last: Crosby


title: Dupilumab progressively improves systemic and cutaneous abnormalities in patients with atopic dermatitis

status: Public on May 02 2019

first: Mayte

last: Suarez-Farinas

address: 1425 Madison Ave, L2-70C, Box 1077,

institute: Mount SinaiSchool of Medicine

summary: Background: Dupilumab is an IL-4 receptor a mAb inhibiting signaling of IL-4 and IL-13, key drivers of type 2-driven inflammation, as demonstrated by its efficacy in patients with atopic/allergic diseases. Objective: This placebo-controlled, double-blind trial (NCT01979016) evaluated the efficacy, safety, and effects of dupilumab on molecular/cellular lesional and nonlesional skin phenotypes and systemic type 2 biomarkers of patients with moderate-to-severe atopic dermatitis (AD). Methods: Skin biopsy specimens and blood were evaluated from 54 patients randomized 1:1 to weekly subcutaneous doses of 200 mg of dupilumab or placebo for 16 weeks.                             Results: Dupilumab (vs placebo) significantly improved clinical signs and symptoms of AD, was well tolerated, and progressively shifted the lesional transcriptome toward a nonlesional phenotype (weeks 4-16). Mean improvements in a meta-analysis-derived AD transcriptome (genes differentially expressed between lesional and nonlesional skin) were 68.8% and 110.8% with dupilumab and 210.5% and 55.0% with placebo (weeks 4 and 16, respectively; P < .001). Dupilumab significantly reduced expression of genes involved in type 2 inflammation (IL13, IL31, CCL17, CCL18, and CCL26), epidermal hyperplasia (keratin 16 [K16] and MKi67), T cells, dendritic cells (ICOS, CD11c, and CTLA4), and Th17/Th22 activity (IL17A, IL-22, and S100As) and concurrently increased expression of epidermal differentiation, barrier, and lipid metabolism genes (filaggrin [FLG], loricrin [LOR], claudins, and ELOVL3). Dupilumab reduced lesional epidermal thickness versus placebo (week 4, P 5 .001; week 16, P 5 .0002). Improvements in clinical and histologic measures correlated significantly with modulation of gene expression. Dupilumab also significantly suppressed type 2 serum biomarkers, including CCL17, CCL18, periostin, and total and allergen- specific IgEs. Conclusion: Dupilumab-mediated inhibition of IL-4/IL-13 signaling through IL-4 receptor a blockade significantly and progressively improved disease activity, suppressed cellular/ molecular cutaneous markers of inflammation and systemic measures of type 2 inflammation, and reversed AD-associated epidermal abnormalities. (J Allergy Clin Immunol 2019;143:155-72.)

overall_design: Skin biopsies from lesional and non-lesional skin were evaluated from 52 patients randomized 1:1 to weekly subcutaneous doses of 200 mg of dupilumab or placebo for 16 weeks.

first: E

last: Guttman-Yassky

first: R

last: Bissonnette

first: B

last: Ungar

first: M

last: Suárez-Fariñas

last: Ardeleanu

first: H

last: Esaki

last: Suprun

first: Y

last: Estrada

first: X

last: Peng

first: J

last: Silverberg

first: A

last: Menter

last: Krueger

last: Zhang

first: U

last: Chaudhry

last: Swanson

first: N

last: Graham

first: G

last: Pirozzi

last: Yancopoulos

first: D

last: Hamilton


title: MeRIP-seq for host response to Flaviviridae infection

status: Public on May 09 2019

city: Zurich

last: McIntyre

address: Winterthurerstrasse 190

department: Molecular Life Sciences

country: Switzerland

institute: University of Zurich

summary: The modification N6-methyladenosine (m6A) affects rates of translation and degradation of mRNA transcripts. We analyzed m6A across the transcriptome following infection by dengue virus (DENV), Zika virus (ZIKV), West Nile virus (WNV), and hepatitis C virus (HCV) using MeRIP-seq. We used the uninfected replicates, among which we would expect little biological variation in methylation, as negative controls to validate statistical methods for the detection of m6A changes in MeRIP-seq data. Applying validated statistical methods, we found that innate immune response to Flaviviridae viruses alters m6A modification of specific cellular transcripts compared to uninfected controls. Finally, we find that these changes in m6A can in turn affect splicing or translation of genes relevant to infection.

overall_design: 3 replicates for each virus (DENV, HCV, WNV, and ZIKV) were generated, with IP (anti-m6A antibody, NEB) and input samples for each. RNA was extracted from Huh7 cells at 48 hours post infection. Uninfected samples were sequenced for comparison, with 3 replicates per lab of incubation (mockL - matched to WNV, and mockH - matched to DENV, HCV, and ZIKV) and two time points, early (mocks at 16 or 24 hours) and late (mocks and viruses at 48 hours).

first: Alexa

first: Nandan

middle: S

last: Gokhale

first: Helen

last: Lazear

first: Christopher

middle: L

last: Holley

middle: E

last: Mason

first: Stacy

last: Horner


title: Cooperation between Constitutive and Inducible Chemokines Enables T-cell Engraftment and Immune Attack in Solid Tumors

city: Lausanne

first: Mauro

last: Delorenzi

address: Génopode Building, Quartier Sorge

institute: Swiss Institute of Bioinformatics

summary: We investigated the role of chemokines in regulating T-cell accumulation in solid tumors. CCL5 and CXCL9 overexpression was associated with CD8+ T-cell infiltration in common solid tumors. T-cell infiltration required tumor cell-derived CCL5 and was amplified by IFN-dependent, myeloid cell-secreted CXCL9. Accordingly, CCL5-CXCL9 co-expression revealed immunoreactive tumors with prolonged survival and response to checkpoint blockade. Loss of CCL5 expression in human tumors was associated with epigenetic silencing through DNA methylation. Reduction of CCL5 expression caused TIL desertification whereas forced CCL5 expression prevented Cxcl9 and TIL loss and attenuated tumor growth in mice through IFN. The cooperation between tumor-derived CCL5 and IFN-inducible CXCR3 ligands secreted by myeloid cells is key for orchestrating T-cell infiltration in immunoreactive and immunoresponsive tumors.

overall_design: RNA isolated from tumor tissues of early (3weeks ) and late (6weeks) ID8 tumors was subjected to trasncriptomic analysis by using theNanostring Gene Expression CodeSet profiling of 561 immunology-related mouse genes (GLP19964).

first: Denarda

last: Dangaj

first: George

last: Coukos


title: Spinal cord injury

status: Public on May 04 2019

city: Louisville

first: Eric

middle: Christian

last: Rouchka

state: Kentucky

address: 522 East Gray Street

department: Biochemistry and Molecular Genetics

institute: University of Louisville

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

overall_design: Refer to individual Series


title: MeRIP-seq for heat shock in B-cell lymphoma cells

summary: We ran MeRIP-seq on RNA from heat shocked (43 C for 1 hr) and untreated cells to compare to previous reports as part of an evaluation of MeRIP-seq reproducibility.

overall_design: 3 replicates of heat shocked and 3 replicates of control OCI-Ly1 diffuse B-cell lymphoma cells

first: Leandro

last: Cerchietti

middle: M


title: Runx/CBFβ transcription factor complexes regulate Ccl5 expression through two novel enhancers to enhance tumor immunity [dataset 2]

status: Public on May 01 2019

city: Kyoto

first: Wooseok

last: Seo

address: Yoshida-Konoe-cho, Sakyo-ku

institute: Kyoto University Graduate School of Medicine

summary: CCL5 (also known as RANTES) was originally known to be important to recruit memory T cells to infected sites, but it received much attention as an inhibitor to HIV’s entry into T lymphocytes of AIDS patients. Recently, it has been reported to be necessary to sustain Trm (Tissue-resident memory) T cells at local tissues as well as to play roles in manipulating tumor microenvironment by both host immunity and cancer cells. Nonetheless, little is known how Ccl5 expression is regulated, thus making it quite difficult for therapeutic intervention. Our study reveals that Runx/CBFβ transcription factor complexes antagonizes Ccl5 expression through two novel transcriptional enhancers. The proximal enhancer is required for the homeostatic expression of Ccl5 during the steady state, meanwhile the distal enhancer is necessary for the expression Ccl5 during the activated stage. We employed enChIP-seq to identify the distal enhancer located 1.35 Mb away from the promoter. This long distance interaction requires the help from Satb1, a global chromatin organizer. Our study reveals that the reduced amounts of Ccl5 by the deletion of the proximal enhancer results in an enhancement of metastasis in B16-F10 melanoma model. On the other hand, a Runx3-mutant mouse line in which Ccl5 expression is increased showed the opposite outcome, suggesting a novel inverse correlation between host Ccl5 levels and metastasis rate.

overall_design: Identification of DNA regions associated with CBFb on CD4+ and CD8+ T cells by ChIP-seq.

first: Kanako

last: Shimizu

first: Satoshi

last: Kojo

first: Okeke

last: Arinze

first: Terumi

last: Kowhi-Shigematsu

first: Shin-Ichiro

last: Fujii

first: Ichiro

last: Taniuchi


title: Single cell RNAseq of human TCRVdelta 1 and TCRVdelta 2 gammadelta T lymphocytes purified from healthy adults blood

city: Toulouse

first: Jean Jacques

last: FOURNIE

address: 2 av Hubert Curien

department: oncology

institute: INSERM

summary: γδ T lymphocytes represent ~1% of human PBMC and even more cells in most tissues of vertebrates. Although they have important anticancer functions, most current scRNA-Seq studies do not identify γδ T lymphocytes since their transcriptomes at the single cell level are unknown. Here we show that high resolution clustering of large scRNA-Seq data sets and a combination of gene signatures allow the specific detection of human γδ T lymphocytes and identification of their TCRVδ1 and TCRVδ2 subsets in large data sets from complex cell mixtures. In t-SNE plots from blood and tumor samples, the few γδ T lymphocytes appear collectively embedded between cytotoxic CD8 T and NK cells. Their TCRVδ1 and TCRVδ2 subsets form close yet distinct sub-clusters respectively neighbouring NK and CD8 T cells owing to expression of shared and distinct cytotoxic maturation genes. Similar pseudo-time maturation trajectories of TCRVδ1 and TCRVδ2 γδ T lymphocytes were discovered, unveiling in both subsets an unattended pool of TEMRA cells with preserved proliferative capacity, a finding confirmed by in vitro proliferation assays. Overall, the single cell transcriptomes of thousands of individual gd T lymphocytes from different CMV+ and CMV- donors reflect cytotoxic maturation stages driven by the immunological history of donors. This landmark study establishes the rationale for identification, subtyping and deep characterization of human γδ T lymphocytes in further scRNA-Seq studies of complex tissues in physiological and disease conditions.

overall_design: 6 samples of purified human gd T cells from 3 donors (CMV+ and CMV-). Cell-sorted TCRVdelta1 and TCRVdelta2 T lymphocytes from each donor PBMC.

first: Jean-Jacques

last: Fournié


title: Runx/CBFβ transcription factor complexes regulate Ccl5 expression through two novel enhancers to enhance tumor immunity


title: Activity-induced changes in the liver transcriptome after chronic spinal cord injury

status: Public on Apr 29 2019

summary: Spinal cord injury (SCI) is a devastating clinical condition resulting in significant disabilities for affected individuals. Apart from local injury within the spinal cord, SCI patients develop a myriad of complications characterized by multi-organ dysfunction. Disorders, such as lung injury, cardiovascular disease, liver damage, kidney and urinary tract dysfunction, alterations in gut microbiome, neuropathic pain, depression and altered immune responses are common in SCI patients. Such whole body, systemic responses hinder the functional recovery and can be life-threatening in SCI population. Investigations of organ specific gene expression analyses can provide a better understanding of the injury response and identify molecular targets. Consequently, this can be used to develop treatment for SCI, promoting functional recovery and overall quality of life.

overall_design: The effect of post-SCI activity on the liver transcriptome was explored with two different approaches. In the first approach, liver tissue was harvested from three groups of rats housed in cages of varying size at 11.5 weeks post-SCI. The experimental groups consisted of 1) T2 contusion injury in large cages, 2) T2 contusion injury in tiny cages, and 3) uninjured controls in standard cages.  In the second approach, liver tissue was harvested from five groups of rats at 11.5 weeks post SCI. Experimental groups consisted of 1) T2 contusion injury 2) T2 contusion injury followed by swimming (SWIM), 3) T2 contusion injury followed by shallow water walking (SWW), 4) T2 transection injury, and 5) uninjured contols. In the second approach, all rats were housed in tiny cages. Each experimental group consists of 4-5 replicates.

first: Julia

middle: H

last: Chariker

first: Sujata

last: Ohri

first: Cynthia

last: Gomes

first: Fiona

last: Brabazon

first: Kathryn

middle: A

last: Harmon

first: David

last: Magnuson

first: Michal

last: Hetman

first: Jeffrey

middle: C

last: Petruska

first: Scott

middle: R

last: Whittemore


title: Pro-inflammatory cytokine blockade attenuates myeloid expansion in a murine model of rheumatoid arthritis

first: Eric

last: Pietras

address: 12700 E. 19th Avenue, Research Complex 2 Room 10014

department: Medicine

summary: This study identifies molecular changes in hematopoietic stem cells (HSC) isolated from mice with chronic autoimmune arthritis induced using the collagen-induced arthritis (CIA) model.

overall_design: RNA-sequencing of pooled murine hematopoietic stem cells (LSK/Flk2-/CD48-CD150+) on arthritis day 21. 3 biological replicates per condition (Control and CIA).

first: Giovanny

last: Hernandez

first: Taylor

last: Mills

first: Jennifer

last: Rabe

first: James

last: Chavez

first: Susan

last: Kuldanek

first: Gregory

last: Kirkpatrick

first: Leila

last: Noetzli

first: Widian

last: Jubair

first: Michelle

last: Zanche

first: Jason

last: Myers

first: Brett

last: Stevens

first: Courtney

last: Fleenor

first: Biniam

last: Adane

first: Charles

last: Dinarello

first: John

last: Ashton

first: Craig

middle: T

last: Jordan

first: Jorge

last: Di Paola

last: Hagman

first: V

last: Holers

first: Kristine

last: Kuhn


title: Generation of  induced keratinocyte stem cells from human urine cells by defined transcription factors

status: Public on Apr 11 2019

city: Seoul

first: Seungkwon

last: You

address: Anam-dong Sungbuk-go

institute: Korea University

summary: Analysis of induced keratinocyte stem cells from male/female urine cells (MiKSC/FiKSC) by defined transcription factors vs. foreskin derived primary human neonatal epidermal keratinocytes (pKC) and male/female urine cells (MUC/FUC). Results provide insight into molecular similarities between induced keratinocyte stem cells and human foreskin derived primary human neonatal epidermal keratinocytes.

overall_design: RNA profiles of induced keratinocyte stem cells from male urine cells,  induced keratinocyte stem cells from female urine cells, male urine cells, female urine cells and primary human neonatal epidermal keraitnocytes were generated by RNA sequencing, in duplicate

first: Jie

last: Zheng


title: Comprehensive gene expression analysis of TNF-alpha-stimulated human umbilical vein endothelial cells (HUVECs)

city: Tokyo

first: Yoshiki

last: Higashijima

address: 1-5-45 Yushima, Bunkyo

department: Medical Research Institute

institute: Tokyo Medical and Dental University

summary: Lysine 9 di-methylation and lysine 27 tri-methylation of histone H3 (H3K9me2 and H3K27me3) are mostly linked to gene repression. However, functions of repressive histone methylation dynamics during inflammatory responses remain poorly understood. Here, we show that lysine demethylase 7A (KDM7A) and 6A (UTX) are rapidly transported to nuclear factor kappa-B (NF-κB) related elements in human endothelial cells in response to tumor necrosis factor (TNF)-α. KDM7A and UTX demethylate H3K9me2 and H3K27me3, respectively, and cooperatively activate NF-κB dependent inflammatory genes. Furthermore, using both in situ Hi-C and other 3C based technology, loops between super enhancers (SEs) are newly formed following TNF-α-stimuli at NF-κB-dependent inflammatory loci where KDM7A- and UTX-recruitment coincide. Collectively, these findings suggest that erasing of repressive histone marks by KDM7A and UTX within NF-κB-related elements might functionally associate with formation of SE-SE three-dimensional interactions and could be a cue signal during inflammatory responses in human endothelial cells.

overall_design: Total 29 samples were derived from [1] HUVECs in the absence or presence of TNF-alpha (0, 4, and 24 hrs) to determine TNF-alpha-responsive genes during inflammation, [2] si control, siKDM7A, siUTX, or siKDM7A+siUTX transfected HUVECs under TNF-alpha-stimuli (4 hrs) to understand molecular function of KDM7A and UTX during inflammation.

first: Yasuharu

last: Kanki


title: miRNA expression data through TNF-alpha-signaling in human umblical vein endothelial cells (HUVECs)

overall_design: Total 4 samples were derived from HUVECs in the absence or presence of TNF-alpha (4 and 24 hrs) to determine TNF-alpha-responsive miRNAs during inflammation.

last: Higashijia

first: Tsuyoshi

last: Inoue


title: The role of (p)ppGpp in the heat shock response in B. subtilis

status: Public on Apr 15 2019

city: Braunschweig

first: Michael

last: Beckstette

state: Lower Saxony

address: Inhoffenstrase 7

department: Molecular Infection Biology

institute: Helmholtz Centre for Infection Research

summary: Bacterial and eukaryotic cells survive an otherwise lethal heat shock once they are primed by a mild pre-heat shock. Using B. subtilis as a model organism, we investigated transcriptional changes during thermotolerance development at 37 °C, 48 °C, 53 °C and 48/53 °C and observed a comprehensive upregulation of genes of the general and heat shock response and the downregulation of many translation-related genes. In addition, strains lacking (p)ppGpp (ppGpp0) or with elevated (p)ppGpp levels (ΔrelA) were analyzed at 37 °C and 48 °C, revealing broad and pleiotropic transcripional changes mediated by (p)ppGpp in the ΔrelA mutant. In addition, our data suggests a contribution of the (p)ppGpp-mediated stringent response in the heat-mediated transcripional down-regulation of ribosomal genes and additional processes.

overall_design:
RNA of heat shocked B subtilis wild type, (p)ppGpp0 and ΔrelA strains
Please note that the *NoPP samples are special 5' enriched/depleted libraries which were used for TSS and promotor analysis and therefore, no processed (count or RPKM) data was generated.

first: Heinrich

last: Schäfer

first: Aaron

last: Nuss

first: Petra

last: Dersch

first: Kürşad

last: Turgay


title: Hi-C analysis in TNF-alpha-stimulated human umblical vein endothelial cells (HUVECs)

overall_design: Total 4 Hi-C samples include [1] no treatment (replicate 1 and 2) [2] TNF-alpha 1 hr (replicate 1 and 2).

first: Shuichi

last: Tsutsumi

first: Verena

last: Link

first: Yohei

last: Abe

first: Christopher

middle: K

last: Glass


title: Vast differences in organ-specific rhythms of transcription in field-grown sugarcane

status: Public on Apr 10 2019

city: Sao Paulo

first: Carlos

last: Hotta

state: SP

address: Av. Lineu Prestes, 748

department: Biochemistry

country: Brazil

institute: University of Sao Paulo

summary: Sugarcane (Saccharum hybrid, SP80-3280) was grown in the field in Araras (Brazil) for 9 months. Leaves +1 (F1), internodes 1&2 (I1), and internodes 5 (I5) were harvested every 2 h for 26 h, starting 2h before dawn.

overall_design: Samples were collected from 2h before dawn (00) of one day to 2 h after dawn of the next day (26). Leaves +1 (F1), internodes 1&2 (I1), and internodes 5 (I5) were harvested. Samples were taken every 2 h were labelled accordingly. Two biological replicates of each time point were made, with a dye swap with the reference. The reference used was an equimolar solution of all samples.

first: L

middle: B

last: Dantas

first: O

middle: N

last: de Lima

first: Y

last: Nishiyama Jr

first: S

last: Carneiro

first: M

middle: G

last: Souza

first: T


title: Chromatin Interaction Analysis by Paired-End Tag Sequencing (ChIA-PET) analysis in TNF-alpha-stimulated human umblical vein endothelial cells (HUVECs)

first: Yoshiki

last: Higashijima

overall_design: Total 3 ChIA-PET samples include [1] no treatment [2] TNF-alpha 30 min [3] TNF-alpha 60 min

first: Yasuharu

last: Kanki

first: Takahide

last: Kohro

first: Yijun

last: Ruan

first: Youichiro

last: Wada


title: Transcriptome-wide binding profile of RNA-binding protein HuR and its inhibitor in MDA-MB-231 cells

status: Public on Apr 09 2019

city: Lawrence

first: Liang

last: Xu

state: KS

address: 1567 Irving Hill Rd 3177 ISB

institute: University of Kansas


title: Genome-wide distribution of histone modification enzymes (KDM7A and UTX), histone modification (H3K9me2, H3K27me3, H3K4me3, H3K27ac), and transcription factor (p65) in TNF-alpha-stimulated human umbilical vein endothelial cell (HUVECs)

overall_design: Total 51 ChIP-seq samples include [1] input for each experiment, [2] histone modification enzyme (KDM7A and UTX) ChIP samples, [3] repressive histone marks (H3K9me2, H3K9me3, H3K27me3) ChIP samples, [4] active histone marks (H3K4me3 and H3K27ac), [5] transcription factor (p65).


title: Transcriptome-wide binding profile of RNA-binding protein HuR in MDA-MB-231 cells

status: Public on Apr 05 2019

summary: The purpose of this study is to generate RNA binding profile of RNA-binding protein HuR in human breast cancer cell line MDA-MB-231 cells by ribonucleoprotein immunoprecipitation sequencing (RIP-deq). RNA immunoprecipitated by mouse anti-HuR antibody or mouse IgG was collected for library prepareation and deep sequencing, in duplicate, using Illumina Hiseq 2500 system.  About 30 million sequence reads per sample were mapped to the human genome (build hg38), the corresponding peaks were then detected and annotated. Finally, the RIP peaks that correspond to significant transcript abundance change were identified and compiled.

overall_design: RNA binding profile of RNA-binding protein HuR in MDA-MB-231 cells was generated by RIP-seq, in duplicate, using Illumina Hiseq 2500 system.

first: Xiaoqing

last: Wu


title: Transcriptional responses to glutaminyl tRNA synthetase Gln4p depletion in Saccharomyces cerevisiae

status: Public on Apr 01 2019

city: Aberdeen

first: Ian

last: Stansfield

address: Foresterhill

department: Institute of Medical Sciences

institute: University of Aberdeen

summary: A tet-off strain of Saccharomyces cerevisiae was constructed in which the GLN4 glutamine tRNA synthetase gene was placed under control of a doxycycline-regulated promoter. The transcriptional responses to Gln4p tRNA synthetase depletion were assessed by growth of the strain in the presence, or absence, of doxycycline (1 µg/ml). A control, wild-type strain was similarly treated with doxycycline or left untreated as a reference. Each strain/condition RNA isolation was performed using triplicate independent biological samples A, B and C.

overall_design: Total RNA samples were extracted from control, or GLN4 tet-off yeast growing in the presence or absence of doxycycline, and the RNA subjected to Illumina RNA-seq.

first: Matthew

last: McFarland


title: Transcriptome of dorsal root ganglia caudal to a spinal cord injury with modulated behavioral activity

first: Eric

last: Rouchka

summary: Spinal cord injury (SCI) is a devastating clinical condition resulting in significant disabilities for affected individuals. Apart from local injury within the spinal cord, SCI patients develop a myriad of complications characterized by multi-organ dysfunction. Some of the dysfunctions are directly related to the disrupted integrity of sensory afferents from DRGs, which signal to both the spinal cord and peripheral organs. Some classes of DRG neurons undergo axonal sprouting both peripherally and centrally after spinal cord injury. Such physiological and anatomical re-organization of afferent axons after SCI contributes to both adaptive and maladaptive plasticity, which may be modulated by activity/exercise. In this study, we collected comprehensive gene expression data in whole dorsal root ganglia (DRGs) throughout the levels below the injury comparing the effects of SCI with and without activity/exercise.

overall_design: Rats were subjected to a single level laminectomy at T2 vertebrae before receiving a complete transection injury or moderately-severe contusion injury (25 g-cm SCI) at the T2 spinal cord level using the NYU Impactor (W.Young, Rutgers University, Newark, NJ). After four days of recovery, all animals were housed two per cage in tiny cage (7.5” x 8.5” x 8”) as opposed to standard cage (22” x 12.5” x 8”) to restrict their motion for the duration of the study. The subjects were then randomized in to one of four groups: 1) Contusion SCI + swimming (SWIM), 2) Contusion SCI + shallow water walking (SWW), 3) Contusion SCI, un-exercised, 4) Complete Transection, un-exercised and 5) un-injured and un-exercised control group. Swimming and shallow water walking as exercise intervention, began 2.5 weeks post injury in T2 contused group and was conducted 5 days a week for 10 weeks. Animals were sacrificed at 13.5 weeks post-injury for contusion SCI+Exercise, at 11.5 weeks post-injury for contusion SCI alone, and 8.5 weeks post-injury for transection SCI. DRGs from T11-L4 levels were retrieved from both sides of the spinal column of each animal and total RNA was extracted for Illumina NextSeq RNA sequencing.

first: Julia

last: Chariker

first: Cynthia

last: Gomes

first: Fiona

last: Brabazon

first: Kathryn

last: Harmon

first: Sujata

last: Ohri

first: David

last: Magnuson

first: Scott

last: Whittemore

first: Jeffrey

last: Petruska


title: Runx/CBFβ transcription factor complexes regulate Ccl5 expression through two novel enhancers to enhance tumor immunity [dataset 1]

status: Public on Apr 25 2019

first: Wooseok

last: Seo

summary: CCL5 (also known as RANTES) was originally known to be important to recruit memory T cells to infected sites, but it received much attention as an inhibitor to HIV’s entry into T lymphocytes of AIDS patients. Recently, it has been reported to be necessary to sustain Trm (Tissue-resident memory) T cells at local tissues as well as to play roles in manuplating tumor microenvironment by both host immunity and cancer cells. Nonetheless, little is known how Ccl5 expression is regulated, thus making it quite difficult for therapeutic intervention. Our study reveals that Runx/CBFβ transcription factor complexes antagonizes Ccl5 epxression through two novel transcriptional enhancers. The proximal enhancer is required for the homeostatic expression of Ccl5 during the steady state, meanwhile the distal enhancer is necessary for the expression Ccl5 during the activated stage. We employed enChIP-seq to identify the distal enhancer located 1.35 Mb away from the promoter. This long distance interaction requires the help from Satb1, a global chromatin organizer. Our study reveals that the redeced amounts of Ccl5 by the deletion of the proximal enhancer results in an enhancement of metastasis in B16-F10 melanoma model. On the other hand, a Runx3-mutant mouse line in which Ccl5 expression is increased showed the opposite outcome, suggesting a novel inverse correlation between host Ccl5 levels and metastasis rate.

overall_design: Identification of DNA regions interacting with the mouse Ccl5 promoter from in vitro activated (day 5) CD8+ T cells by enChIP-seq

first: Kanako

last: Shimizu

first: Satoshi

last: Kojo

first: Okeke

last: Arinze

first: Terumi

last: Kowhi-Shigematsu

first: Shin-Ichiro

last: Fujii

first: Ichiro

last: Taniuchi


title: An intramolecular salt bridge linking TDP43’s RNA recognition motifs dictates RNA binding, protein stability and TDP43-dependent neurodegeneration

status: Public on Mar 22 2019

city: Ann Arbor

first: Bioinformatics

last: Core

state: MI

address: BRCF Bioinformatics Core, 2800 Plymouth Rd

institute: University of Michigan

summary: The majority of individuals with amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD) exhibit neuronal cytoplasmic inclusions rich in the RNA binding protein TDP43. Even so, the relationship between TDP43’s RNA binding properties and neurodegeneration remain obscure. Here we show that engineered mutations disrupting a salt bridge between TDP43’s RNA recognition motifs interfere with nucleic acid binding and eliminate recognition of native TDP43 substrates. The accumulation of WT TDP43, but not RNA binding-deficient variants, disproportionately affected the abundance and splicing of encoding ribosome and oxidative phosphorylation components.

overall_design: TDP43 variants harboring mutations affecting RNA binding were transfected into human embryonic kidney  (HEK293T)  cells and subjected to RNA-seq to identify transcripts selectively affected by WT TDP43.

first: Sami

last: Barmada

first: Brittany

last: Flores

first: Rich

last: McEachin


title: Neuronal deletion of Gtf2i, associated with Williams syndrome, causes behavioural and myelin alterations rescuable by a remyelinating drug [human]

status: Public on Mar 26 2019

city: Tel Aviv

first: Boaz

last: Barak

address: 122 Sharett Bldg

country: Israel

institute: Tel Aviv University

summary: Williams syndrome (WS), caused by a heterozygous microdeletion in 7q11.23, is a neurodevelopmental disorder characterized by hypersociability and neurocognitive abnormalities. Of the deleted genes, general transcription factor II-i (Gtf2i) has been linked to hypersociability in WS, though the underlying mechanisms are poorly understood. We show that selective deletion of Gtf2i in forebrain excitatory neurons caused neuroanatomical defects, fine motor deficits, increased sociability and anxiety. Unexpectedly, 70% of the genes with significantly decreased mRNA levels in the mutant mouse cortex are involved in myelination, and mutant mice had reduced mature oligodendrocyte cell numbers, reduced myelin thickness and impaired axonal conductivity. Restoring myelination properties with clemastine or increasing axonal conductivity rescued the behavioural deficits. Frontal cortex from WS patients similarly showed reduced myelin thickness, mature oligodendrocyte cell numbers and mRNA levels of myelination-related genes. Our study provides molecular and cellular evidence for myelination deficits in WS linked to neuronal deletion of Gtf2i.

overall_design: Frontal cortex (BA9) human tissue samples.

first: Guoping

last: Feng


title: Gene expression signatures of Naïve vs Revertant CD8 T cells from human cord blood

status: Public on Mar 27 2019

city: Birmingham

first: Paul

last: Moss

state: West Midlands

address: Vincent Drive

department: Immunology and Immunotherapy

institute: University of Birmingham

summary: We have employed whole genome microarray expression profiling as a discovery platform to identify genes with the potential to distinguish between naive CD8+ T cells (TN) and the same cells which, after activation and incubation with homeostatic cytokines, had reverted to a naive-like phenotype (TNrev). Three umbilical cord blood samples were used to enrich TN and to produce the respective TNrev. Successive ATAC-Seq analysis showed correlation between degree of chromatin accessibility and gene expression  profile for both TN and TNrev cells.

overall_design: Gene expression profile was measured in TN cells from 3 human cord blood samples and in the same cells after activation with anti CD3 for 6 days, followed by incubation with IL-7 25 ng/ml for further 13 days.

first: G

last: Frumento

first: W

last: Croft

first: S

last: Kissane


title: CHROMATIN LANDSCAPES REVEAL DEVELOPMENTALLY ENCODED TRANSCRIPTIONAL STATES THAT DEFINE GLIOBLASTOMA [HumanMethylation850 BeadChip]

status: Public on Mar 18 2019

city: Houston

first: Stephen

middle: Mack

last: Christopher

state: TX

address: 1102 Bates Avenue C1030.02

department: Pediatrics

institute: Baylor College of Medicine

summary: Glioblastoma is an incurable brain cancer characterized by high genetic and pathological heterogeneity. Here we mapped active chromatin landscapes with gene expression, whole-exomes, copy number profiles, and DNA methylomes across 44 glioblastoma stem cell (GSCs) models, 50 primary glioblastomas, and 10 neural stem cells (NSCs) with the goal of identifying essential super enhancer (SE)-associated genes and the core transcription factors that establish them and glioblastoma identity. Glioblastomas segregate with two dominant enhancer profiles that coopt unique developmental transcription factor regulatory programs to enforce tumor identity. From group specific enhancer profiles, we inferred core transcription factors that define subgroup identity. These transcription factors show higher activity in glioblastomas versus normal neural stem cells, are associated with poor clinical outcomes, and are required for glioblastoma growth in vitro and in vivo. Given challenges with genetically-defined targeted therapies for glioblastoma, we propose targeting underlying transcriptional identity may serve as an important therapeutic strategy.

overall_design:
Bisulphite converted DNA from 90 glioblastoma primary tumors, neural stem cells, and glioblastoma stem cell models were hybridised to the Illumina EPIC 850K Human Methylation Beadchip arrays. Arrays were processed according to manufacturers recommended protocols.
For primary GBM samples, we have 50 GBM samples in total, 46 of which have H3k27ac ChIPseq data, 45 of which have RNAseq data, and 39 of which have methylation data (GBM74 has replicate data).

For glioblastoma stem cell samples, we have 44 GSC samples in total, 43 of which have H3k27ac ChIPseq data, 44 of which have RNAseq data, and 41 of which have methylation data.

For neural stem cell samples, we have 10 NSC samples in total, 9 of which have H3k27ac ChIPseq data, 9 of which have RNAseq data, and 9 of which have methylation data.

last: Mack

first: Irtisha

last: Singh

first: Xiuxing

last: Wang

first: Rachel

last: Hirsch

first: Charles

middle: Y

last: Lin

first: Jeremy

last: Rich


title: CHROMATIN LANDSCAPES REVEAL DEVELOPMENTALLY ENCODED TRANSCRIPTIONAL STATES THAT DEFINE GLIOBLASTOMA

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

overall_design: Refer to individual Series


title: Gene expression data of naïve and activated ILC2s isolated from female and male mouse lungs

status: Public on Mar 13 2019

city: Vancouver

first: Laura

last: Mathae

state: British Columbia

address: 675 W.10th Ave

country: Canada

institute: British Columbia Cancer Research Centre

summary: Epidemiological studies have shown sex differences in prevalence of non-allergic asthma. Recent reports demonstrated negative effects of androgen signaling on group 2 innate lymphoid cells (ILC2s), explaining a potential mechanism behind sex bias in asthma prevalence. To further understand the difference in ILC2s based on sex, we have investigated the effects of sex and age on the number and function of lung ILC2s, and epithelium derived cytokines. Naive male and female mice of any ages tested did not differ in the number of ILC2s in the lung. Upon IL-33 injection, lung ILC2s in post puberty female mice responded more vigorously than male counterpart. Purified female lung ILC2s more rapidly produced cytokines than male mouse ILC2s. Gene expression profiles of naïve male and female ILC2s differed in 4% of the genes, and gene set enrichment analysis showed that female ILC2s are enriched for gene signatures of memory T cells. Epithelium-derived cytokines including IL-33 were more highly expressed in post puberty naïve female mouse lungs than male mouse lungs. However, the differences in responsiveness of male and female ILC2s were not affected in IL-33-deficient mice. Therefore, female ILC2s are more readily activated than male ILC2s, likely due to their similarity to memory T cells as suggested by the gene expression profiles.

overall_design: ILC2s were isolated from female and male lungs of naïve and IL-33 treated mice one day after three consecutive intranasal injections. RNA was extracted from three samples per group and analyzed for gene expression.

last: Mathä

first: Hanjoo

last: Shim

first: Catherine

last: Steer

first: Yi Han

last: Yin

first: Itziar

last: Martinez-Gonzalez

first: Fumio

last: Takei


title: CHROMATIN LANDSCAPES REVEAL DEVELOPMENTALLY ENCODED TRANSCRIPTIONAL STATES THAT DEFINE GLIOBLASTOMA [RNA-Seq]

overall_design:
Dataset consists of total RNA isolated from either glioblastoma primary tissue or gliblastoma stem cell models and an analysis of gene expression signatures.

For primary GBM samples, we have 50 GBM samples in total, 46 of which have H3k27ac ChIPseq data, 45 of which have RNAseq data, and 39 of which have methylation data (GBM74 has replicate data).

For glioblastoma stem cell samples, we have 44 GSC samples in total, 43 of which have H3k27ac ChIPseq data, 44 of which have RNAseq data, and 41 of which have methylation data.

For neural stem cell samples, we have 10 NSC samples in total, 9 of which have H3k27ac ChIPseq data, 9 of which have RNAseq data, and 9 of which have methylation data.