title: Identification of microRNA expression patterns in human myofibroblasts with/without the JQ-1 treatment and/or TGF-b

summary: Idiopathic pulmonary fibrosis (IPF) is a chronic lung disease that normal parenchyma is progressively replaced by fibrotic foci comprised of myofibroblasts, active differentiated fibroblasts. IPF has an overall poor prognosis with median survival ranging from 2.5 to 3.5 years. The underlying disease mechanisms in IPF are largely unknown, and there is still no effective drug that prolongs survival of patients with IPF.  It has been known that JQ-1, a BET bromodomain inhibitor, prevents TGF-β-mediated fibroblast to myofibroblast differentiation. Moreover, JQ-1 modulates miRNAs expression in various types of cancer cell. In this study, to gain understanding of the relationship between miRNAs expression and the effect of JQ-1 on the dedifferentiation of established myofibroblast, we investigated miRNA profiles in human myofibroblasts with/without the JQ-1 treatment and/or TGF- using miRNA microarray assay.

overall_design: In this miRNA microarray experiment, we used human myofibroblasts. To determine JQ-1-responsive miRNAs in myofibroblasts, total 4 samples were derived from the absence or presence of JQ-1 or TGF-treatment.


title: Identification of the lymphangioleiomyomatosis cell and its uterine origin

status: Public on Jul 11 2020

city: Cincinnati

first: Yan

last: Xu

state: OH

address: 3333 Burnet Ave

country: USA

institute: Cincinnati Children's Hospital Medical Center

type: Expression profiling by high throughput sequencing

summary: Lymphangioleiomyomatosis (LAM) is a metastasizing neoplasm of reproductive age women which causes cystic lung remodeling and progressive respiratory failure. While LAM lesions are known to contain abnormal smooth muscle-like cells which harbor mTOR activating mutations in TSC1 or TSC2, the tissue origins of the mutant “LAM cells” that invade the lung remain unclear. By employing single cell and single nuclear RNA sequencing on explanted LAM lungs, we identified a unique population of cells and associated signature genes and gene networks which  were readily distinguished from those of endogenous lung cells. These unique LAMCORE cells shared closest transcriptomic similarity to normal uterus and share transcriptomic features with neural crest, as identified in uterine LAM lesions by single nuclear RNA-seq. Immunofluorescence microscopy demonstrated the expression of LAMCORE cell signature genes within LAM lesions in both lung and uterus. Serum aptamer proteomics and ELISA identified biomarkers consistent with the signature genes expressed and predicted to be secreted by LAMCORE cells. Single cell transcriptomics strongly supports a uterine neural crest origin of LAMCORE cells; providing insights into disease pathogenesis and informing future treatment strategies for LAM.

overall_design: scRNA-seq and snRNA-seq was performed using the 10x Chromium platform on four lung explants from LAM patients undergoing lung transplantation. We also performed scRNA-seq on a renal AML resected from a patient with a sporadic AML (S-AML), and snRNA-seq on uterine tissue obtained at hysterectomy from an S-LAM patient. As controls, we conducted scRNA-seq on a 31 years old female explanted lung, brain dead, beating-heart, organ donor and snRNA-seq on one normal uterine tissue at hysterectomy from a  29 years old female patient with cervical cancer, and obtained scRNA-seq data of six additional female donor lungs from Gene Expression Omnibus (GSE122960) and scRNA-seq data from normal mouse uterus (GSE118180). qRT-PCR, immunofluorescence and immunochemical stains to validate the spatial relationships of LAM cells and LAMCORE signature genes.Serum aptamer proteomics and ELISA assays screening were used for validation of secretome predictions.

first: M

last: Guo

first: Y

first: F

middle: X

last: McCormack

first: J

last: Whitsett

first: Jane

last: Yu

first: A

middle: K

last: Perl

first: K

middle: A

last: Wikenheiser-Brokamp

first: S

middle: S

last: Potter


title: Gene expression in HDAC8 and HDAC9 silencing keratinocyte

city: La Jolla

first: Richard

middle: L

last: Gallo

state: California

address: 9500 Gilman Drive

department: Dermatology

institute: University of California San Diego

summary: In this study, we analyzed inflammatory response to Poly:IC under HDAC8 or HDAC9 silencing keratinocyte and performed pathway analysis by RNA-seq.

overall_design: Gene expressions were analyzed in HDAC8 or HDAC9 silencing keratinocyte after Poly:IC stimulation

first: Yu

last: Sawada


title: Small RNA Species and microRNA Profiles are Altered in Severe Asthma Nanovesicles from Broncho Alveolar Lavage and Associate with Impaired Lung Function and Inflammation

city: Southampton

first: Ana

last: Garcia

address: Tremona Road

country: United Kingdom

institute: University of Southampton

type: Non-coding RNA profiling by high throughput sequencing

summary: In this study, we particularly focused on microRNA cargo of nanovesicles in bronchoalveolar lavage of severe asthmatic patients when compared to healthy controls. We extracted nanovesicle RNA using a serial filtration method. RNA content was analyzed with small RNA sequencing and mapped to pathways affected using WebGestalt 2017 Software. We report that severe asthma patients have deficient loading of microRNAs into their airway luminal nanovesicles and an altered profile of small RNA nanovesicle content (i.e., ribosomal RNA and broken transcripts, etc.).

overall_design: Small RNA sequencing comparing RNA content of nanovesicles from severe asthmatic patients and healthy controls.

last: Fancisco-Garcia

first: Eva

middle: M

last: Garrido-Martin

first: Hitasha

last: Rupani

first: Laurie

middle: C

last: Lau

first: Rocio

middle: T

last: Martinez-Nunez

first: Peter

middle: H

last: Howarth

first: Tilman

last: Sanchez-Elsner


title: RT-PCR analysis of HSV-1 infected mouse astrocytes and microglia

city: Chicago

last: Longnecker

state: IL

address: 303 E Chicago Ave

department: Microbiology and Immunology

institute: Northwestern University Feinberg School of Medicine

summary: Primary mouse microglia and astrocytes were isolated from 6-8 week old C57BL/6J mice and infected with HSV-1 KOS at an MOI of 5 for 12 hours.

overall_design: RT-PCR gene expression profiling of pro-inflammatory genes using the RT2 PCR Profiler Array

first: Cooper

last: Hayes


title: Transcriptome analysis of banana (Musa acuminata) in response to low-nitrogen stress

city: Haikou

first: Guo

last: Panyang

address: Renmin road NO.58

country: China

institute: Hainan University

summary: Nitrogen (N) is an abundant and essential macronutrient for plants growth and development processes, especially for the huge banana trees with high biomass. In this paper, we studied the response of banana resists to low N stress ueing Illumina RNA-Seq technology, and analyzed the DEGs associated with the absorption, transport, and ulitilize of nitrogen.

overall_design: Using low-nitrogen culture solution (low nitrogen group, LN) treated banana plants, constracted with the normal group adopted Hoagland complete culture solution (control group, CK). In the natural conduction of Hainan province, Banana plants were fixed with clean sands and put into growth chamber with a temperature 28-35°C. The normal group (CK) and treated group (LN) materials were collected separately after 60 days treatment. Each group of plants were divided into an aboveground part (leaves and pseudo-stems) and an underground part (roots),resulting in four different types of sample: normal -nitrogen leaves (CL), normal - nitrogen roots (CR),low - nitrogen leaves (NL) and low - nitrogen roots (NR). Part of these plant tissues were frozen in liquid nitrogen immediately and kept at -80 °C refrigerator for storage.

first: Rui

last: He

first: Pan-Yang

last: Guo

first: Min

last: Xu

first: Yun

last: Peng

first: Yang

last: Liu

first: Can-Bin

last: Zeng

first: Hua

last: Tang


title: Legionella pneumophila infection rewires the Acanthamoeba castellanii transcriptome, highlighting a class of sirtuin genes

city: Melbourne

first: Shivani

last: Pasricha

address: 792 Elizabeth Street

country: Australia

institute: Peter Doherty Institute

summary: Through RNA-sequencing we  compared A. castellanii infected with wild type L. pneumophila to A. castellanii infected with an isogenic dotA mutant strain, which is unable to replicate intracellularly. We identified clear morphological and transcriptional changes in A. castellanii over the course of infection. Genes differentially expressed during infection fell into fundamental biological processes, such as small GTPase signalling, cytoskeleton dynamics, metabolism and cell proliferation. Members of the Sirtuin family of class III histone deacetylases were upregulated by A. castellanii throughout wild type L. pneumophila infection. sir6f expression was important for A. castellanii proliferation during infection and L. pneumophila replication

overall_design: RNA-sequencing analysis on A. castellanii trophozoites left uninfected or infected with wild type L. pneumophila or the isogenic DdotA mutant for 3 h, 8 h (early infection), 16 h (mid infection) or 24 h (late infection).

first: Pengfei

last: Li

first: Dane

last: Vassiliadis

first: Sze

middle: Y

last: Ong

first: Vicki

last: Bennett-Wood

first: Chihiro

last: Sugimoto

first: Junya

last: Yamagishi

first: Elizabeth

last: Hartland


title: Mutant Kras co-opts a progenitor-derived enhancer network to initiate pancreatic tumorigenesis [RNA-seq]

city: Beijing

first: Yi

address: 30 Shuangqing Rd, Haidian Qu, Beijing Shi, China

institute: Tsinghua university

summary: Oncogenes are highly specific in the cells they can transform, although the molecular basis for this is poorly understood. Inflammation often promotes tumorigenesis, and in the pancreas it promotes cellular plasticity and accelerates Kras-driven neoplasia. We demonstrate that plasticity is coupled to the emergence of transient progenitor cells that are readily transformed by KrasG12D. The progenitor state is linked to coordinate upregulation of proliferation genes through chromatin opening at nearby lineage-specific enhancers. Mutant Kras taps into this program by co-opting the normally transient enhancer elements, making them permanent and Kras-dependent in cancer. Mechanistically, co-option occurs through cooperation of Kras-driven transcription factors with the existing landscape of pancreatic lineage transcription factors, which are recruited to play a central role in driving the mutant Kras-dependent transcriptional program. These observations suggest that proliferation is controlled by tissue-specific enhancer networks that are tapped into by oncogenes, helping explain the lineage specificity of cancer drivers.

overall_design:
Examination of transcriptome of
[1] mCherry-positive cells on day0,day,day7 after CAE injection.
[2] eGFP-positive cells from pancreas after knocking out Kras,Junb,Fosl1,Klf5,Foxa2,Rosa.injection and the PDA.
[3] mCherry-positive cells from Tamoxifen induced KrasG12D on day7 after CAE injection and the PDA.

first: Charles

middle: J

last: David

first: Yong


title: Immediate transcriptional responses to heat shock of plant leaf

city: Guangzhou

first: Zhicheng

last: Dong

state: Guangdong

address: 230 Wai Huan Xi Road,Guangzhou Higher Education Mega Center

department: School of Life Sciences

institute: Guangzhou University

summary: Ambient temperature is one of the most important environment factors that direct all organisms for morphogenesis, metabolisms and growth. Plants have evolved efficient mechanisms adapting temperature fluctuation such as heat stress response (HSR). Although transcriptional regulatory network of plant HSR has been established, little is known on the genome-wide transcriptional changes within first several minutes upon heat shock (HS). To precisely measure the very first wave of transcriptional response to HS, we investigated the nascent RNA and mature mRNA from plant leaf tissue exposure to 5-min HS treatment using global run-on sequencing (GRO-seq) and RNA sequencing (RNA-seq) methods. We found that only a small group of genes were both up- or down-regulated at nascent RNA and mRNA levels. Primed plants that already exposed to a mild heat stress induced a more drastic transcriptomic alteration than naïve plants which had not experienced a heat stress. Group A1 HEAT SHOCK TRANSCRIPTION FACTORs (HsfA1s) are the major transcription factors in charge of the very early transcriptional HSR. Within 5-minute HS, we also observed that: 1) Engaged RNA polymerase II (Pol II) was accumulated downstream of transcription start sites; 2) 5' pause-release is a rate limiting step for induction of some heat shock protein genes; 3) A good number of genes switched transcription modes; 4) Pervasive read-through was induced at terminators. Plants' HSR is transcriptionally very quick. GRO-seq is sensitive and robust to detect quick response to HS. Heat stress memory takes place at multiple steps of transcription cycles such as Pol II recruitment, 5' pausing, elongation and termination.

overall_design: Transcriptional profiling by GRO-seq and RNA-seq

first: Jiafu

last: Zhu


title: PAX6D instructs neural retinal specification from human embryonic stem cell-derived neuroectoderm

city: Nanjing

first: Yunlong

last: Tao

state: Jiangsu

address: 163 Xianlin Road

department: School of life sciences

institute: Nanjing University

type: Genome binding/occupancy profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Mutant Kras co-opts a progenitor-derived enhancer network to initiate pancreatic tumorigenesis [ATAC-seq]

last: He

overall_design:
Examination of chromatin accessiblity of
[1] mCherry-positive cells on day0,day,day7 after CAE injection.
[2] eGFP-positive cells from pancreas after knocking out Kras,Junb,Fosl1,Klf5,Foxa2,Rosa.
[3] mCherry-positive cells from Tamoxifen induced KrasG12D on day7 after CAE injection and the PDA.


title: Mutant Kras co-opts a progenitor-derived enhancer network to initiate pancreatic tumorigenesis [ChIP-seq]

overall_design:
Examination of
[1] 2 different histone modifications and 4 different transcription factors in PDA cell line.
[2] H3K27ac histone modifications in two different types of PDA cell line by using MEK inhibitors or AKT inhibitor treatment.
[3] Klf5 and Foxa2 in PDA cell line by Junb and Fosl1 overexpression .


title: Mutant Kras co-opts a progenitor-derived enhancer network to initiate pancreatic tumorigenesis

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: Gene expression in retinal cells from wildtype H9 human embryonic stem cells, PAX6 KO and PAX6D KO cell lines

summary: PAX6 is essential for eye and forebrain development but how PAX6 instructs retinal versus neuroectoderm specification remains unknown. We found that the paired-less PAX6, PAX6D, is uniquely expressed in retinal cells during human eye development and along human embryonic stem cell (hESC) differentiation to retinal cells. HESCs with deletion of PAX6D failed to enter retinal differentiation. Induced expression of PAX6D but not PAX6A under the PAX6-null background restored the retinal differentiation capacity. ChIP-Seq, confirmed by functional assays, revealed a set of retinal genes and neural genes that are targets of PAX6D, including WNT8B. Inhibition of WNTs restored the retinal differentiation capacity of neuroepithelia with PAX6D knockout whereas activation of WNTs blocks retinal differentiation even when PAX6D is induced. Thus, PAX6D specifies neuroepithelia to retinal cells, partly via regulation of WNTs.

overall_design:
We used RNA-Seq to identify differentially expressed genes in PAX6 KO cells and PAX6D KO cells during retinal differentiation
day 20 retinal cells from each cell lines, 3 biological repicates.

first: Su-chun

last: Zhang


title: ChIP-Seq analysis of PAX6A and PAX6D target genes

overall_design:
we used ES cell lines with either PAX6A flag-tagged or PAX6D flag-tagged  and identify the differential target genes for PAX6D and PAX6A by ChIP-Seq
day 10 neuroepithelial cells from each cell lines, DOX used to turn on respective isoform gene expression, 2 biological repicates.


title: Transcriptome analysis of CHEK1 overexpression (AC or HC)  VS control (A or H) and CHEK1 knockdown (AK_D or HK_D) VS control (AK or HK) in Mutiple Myeloma.

first: Rong

middle: Fang

last: Wei

address: 138 Xianlin Road

institute: Nanjing Unveristy of Chinese Medicine

summary: Transcriptome sequencing was used to analyze changes in related signaling pathways and gene expression in Mutiple Myeloma cells when CHEK1 was overexptressed or knocked down.

overall_design: Examination of  eight cell types

first: Rongfang

first: Wang

last: Wang


title: Epigenetic enhancer changes during oncogenic transformation [RNA-seq]

city: London

first: Paola

last: Scaffidi

address: 1 Midland Road

institute: Francis Crick Institute

summary: Identification of differential enhancers active during oncogenic transformation, using RNA-seq with FAIRE-seq and ChIP-seq for H3K4me1 and H3K27ac.

overall_design: RNA-seq analysis of biological replicates from SSEA1+ in vitro transformed human skin fibroblasts.

first: M

last: Burney

first: P


title: miRNA sequencing

status: Public on Jul 10 2020

city: kunming

first: Zhenhuan

last: Ma

address: 176 Qingnian Road，650021，Kunming，China

institute: The Second People's Hospital of Yunnan Province

summary: Through the high-throughput sequencing platform illumina Hiseq4000, explore the molecular mechanism of miRNA molecules in the development of gastric cancer

overall_design: examination of miRNA in two group cell


title: Expression data from neonatal heart after apex resection

city: Chongqing

first: Chunyu

last: Zeng

state: Chongqing

address: 10 Changjiangzhilu Road

institute: Third Military Medical University

summary:
Apical resection in 1-day-old mice results in complete regenerated heart and normal cardiac function, which is characterized by significant cardiomyocyte proliferation with minimal fibrosis.
Local damage on hearts of 1-day-old mice can amplify cardiomyocyte proliferation located in the whole ventricle rather than limited damage area. This response provides a reasonable screening model to identify novel genes involved in endogenous cardiac regeneration

overall_design: Sham and AR ventricles were prepared by removing apex of sham or scar of AR hearts to highlight differences in proliferation rather than fibrosis for RNA extraction and hybridization on Affymetrix microarrays. Through a mouse model of neonatal apex resection,we sought to looking for novel lncRNAs affecting cardiomyocyte proliferation

first: Wenbin

last: Fu

first: Wei

middle: E


title: Single Cell RNA Sequencing Identifies an Early Monocyte Gene Signature in Acute Respiratory Distress Syndrome

city: Pittsburgh

first: Anuradha

last: Ray

state: PA

address: 3459 Fifth Ave, MUH 628 NW

department: Medicine/Pulmonary

institute: University of Pittsburgh

summary: The acute respiratory distress syndrome (ARDS) results from overwhelming pulmonary inflammation. We used single cell RNA sequencing to probe ARDS at a higher resolution for  insights into ARDS pathogenesis. Peripheral blood mononuclear cells of patients with pneumonia and sepsis with early ARDS were compared to that of sepsis patients who did not develop ARDS. Monocyte clusters from ARDS patients revealed multiple distinguishing characteristics in comparison to monocytes from patients without ARDS including down-regulation of SOCS3 expression accompanied by a pro-inflammatory signature with up-regulation of multiple type I IFN-induced genes, especially in CD16+ cells. These data show that monocytes of ARDS patients up-regulate expression of genes not just restricted to those associated with inflammation. Together, our findings identify molecules that are likely involved in ARDS pathogenesis that may inform biomarker and therapeutic development.

overall_design: 7 Frozen PBMC samples, 4 with sepsis only, 3 with sepsis and ARDS

first: Prabir

first: Jie

last: Chen

first: Brian

middle: R

last: Rosborough


title: The Role of Satb1 in Shaping the Repertoire of T Cell Receptor Genes

first: Hao

last: bingtao

address: ShataiNan Road, Baiyun District, Guangzhou, Guangdong Province

institute: Southern Medical University

summary: To explore the role of Satb1 in rearrangement and repertoire of TCR genes, we used Satb1contional knockout micwhich the Satb1 gene was deleted in long term hematopoietic stem cells. We applied 5ʹRACE (rapid amplification of cDNA ends) PCR technique to generate deep sequencing libraries of Tcrd, Tcrg, Tcrb, and Tcra cDNA by using a single set of primers for each TCR gene. We obtained millions of TCR sequences and unraveled the complexity of T-cell diversity. Our experimental evidence demonstrates that Satb1 has substantial influences on the TCR repertoire.

overall_design: TCR repertoire profiles of 4-12 weeks old wild type (WT) and Satb1cKO mice were generated by deep sequencing, in trplicate, using Illumina Hiseq

first: Delong

last: Feng

first: Zhaoqiang

last: Li


title: Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and lncRNA-DRR-/- Heart Transcriptomes

summary: To understand the mechanism of lncRNA-DRR induced effect on cardiomyocyte proliferation, high-throughput transcriptome sequencing was performed on hearts of WT and lncRNA-DRR−/− mice 2w  after myocardial infarction, and gene enrichment analysis revealed that cell cycle process and cellular response to DNA damage were up-regulated in hearts of lncRNA-DRR−/− mice

overall_design: Heart mRNA profiles of  wild type (WT) and lncRNA-DRR-/- mice 2w after myocardial infarction


title: Transcriptional profiling of germinal center B cells and isotype switched memory B cells (scRNA-Seq)

city: Tucson

first: Deepta

last: Bhattacharya

state: Arizona

address: 1656 E. Mabel Street, MRB 217

department: Department of Immunobiology

institute: University of Arizona

summary: Germinal center B cells were analyzed for memroy B cell gene signature to identify a memory B cell precursor population.  Sorted isotype-switched memory B cells were used to confirm the identified memroy B cell precursor population

overall_design: Antigen specific germinal center B cells (CD19+GL7+IgD-EphrinB1+WNV WT DIII tetramer+) and polyclonal memory B cells (CD19+IgD-IgM-CD80+CCR6+) were sorted from 30 pooled 8-12 week old C57BL/6 mice that were vaccinated with Innovator WNV vaccine 7 days prior.

first: Rachel

last: Wong


title: RNA-seq of HCC1428 LTED breast cancer cell line post ligand treatment

city: Cambridge

first: Joon Sang

last: Lee

state: MA

address: 270 Albany Street

department: Oncology

institute: Sanofi

summary: Global gene expression analysis of HCC1428-LTED (long term estrogen deprived) breast cancer cell lines was evaluated after overnight treatment with 6 selective estrogen receptor degarders (SERDs).  Two gene expression signatures were identified.  GDC-0810 and AZD9496 have a similar gene expression profile which is distinct from fulvestrant. SAR439859 gene expression signature clusters closely with fulvestrant.  Replacing the carboxylic side chain of GDC-0810 and AZD9496 with a basic side chain of SAR439859 to make novel SERDs, GDC-SAR and AZD-SAR, respectively, shifts the gene expression signature to more closely align to that of fulvestrant. The effect of SERDs on gene expression can be used to further differentiate classes of SERDs.

overall_design: RNAseq of HCC1428 breast cancer cell line with 6 different estrogen receptor degraders at two concentrations in duplicate.

first: Maysoun

last: Shomali

first: Monsif

last: Bouaboula

first: Hui

last: Cao

first: Jack

last: Pollard


title: Transcriptomic analysis of day 1 (D1) differentiating WT and HDAC11-deficient mouse myoblasts

city: Badalona

first: Lauro

last: Sumoy

state: Barcelona

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

department: High Content Genomics and Bioinformatics

country: Spain

institute: IGTP

summary: To get insight into the transcriptomic changes caused by HDAC11 loss at early myogenic differentiation, we performed RNA sequencing (RNA-Seq) in 24 h differentiated primary myoblasts from WT and HDAC11-deficient mice. Satellite cell-derived primary myoblasts were obtained after FACS isolation of skeletal muscle cells by growing them at low confluence in proliferation medium. To induce myoblast differentiation, cells were plated at high confluence and changed to differentiation media. Gene Ontology (GO) analysis of the genes upregulated in HDAC11 KO differentiating myoblasts revealed a statistically significant enrichment of cell cycle-related processes while the downregulated genes in HDAC11 KO differentiating myoblasts were enriched in “muscle system process” and “muscle contraction” GO categories.

overall_design: This is an mRNA sequencing study which addressed the effect of loss of Hdac11 gene on gene expression. A total of six samples were inlcuded in the study: Three biological replicates derived from Hdac11 knock out mice and three derived from wild type mice. The polyA+ RNA fraction was sequenced using Illumina technology and differential expression was assessed by comparing normalized sequencing read count levels between the two conditions.

first: Yaiza

last: Núñez-Álvarez

first: Erica

last: Hurtado-Caballero

first: Mar

last: Muñoz

first: Gabriel

last: Rech

first: Ignacio

last: García-Tuñon

first: Alberto

last: Pendás

first: Miguel

last: Peinado

first: Mònica

last: Suelves


title: dAKAP1 signaling complexes coordinate local synthesis at the mitochondrial surface

city: Seattle

first: John

last: Scott

state: Washington

address: 1959 NE Pacific Street, HSB K316

department: Pharmacology

institute: University of Washington

summary: We find that the KH domain of dAKAP1 binds mRNAs encoding proteins required for mitochondrial metabolism

overall_design: total RNA was incubated with purified protein of dAKAP1 KH and Tudor domains (KHT) followed by immunoprecipitation for protein tag; 4-5 replicates were performed for input RNA, KHT, and negative controls

first: Scott

last: John


title: Molecular structures and mechanisms of DNA break processing in mouse meiosis

city: New York

first: Shintaro

last: Yamada

state: New York

address: 1275 York Avenue

department: MOLECULAR BIOLOGY PROGRAM

institute: MEMORIAL SLOAN-KETTERING CANCER CENTER

summary: Exonucleolytic resection is a critical step in repair of DNA double-strand breaks (DSBs) via homologous recombination, but resection mechanisms are not well understood, particularly in mammalian meiosis. Here, we use a genome-wide, nucleotide-resolution analysis to define the molecular structure of resected DSBs in mouse spermatocytes. Resection tracts averaged 1100 nucleotides on each side of a DSB, but with a broad distribution and substantial fine-scale heterogeneity at individual hotspots. Surprisingly, eliminating the nuclease activity of EXO1 only modestly decreased resection lengths, thus EXO1 is not the major 5′→3′ exonuclease in mouse meiosis. In contrast, the DSB-responsive kinase ATM proved to be a key regulator of both the initiation and extension of resection. In wild type, apparent intermolecular recombination intermediates clustered near to but offset from DSB positions, consistent with joint molecules with incompletely invaded 3′ ends. Finally, we provide evidence for PRDM9-dependent chromatin remodeling leading to increased accessibility at recombination sites. Our findings give insight into the mechanisms of DSB processing and repair in meiotic chromatin.

overall_design: Detection of double-strand break end resection and changes in local chromatin structure at recombination sites in mouse meiosis

first: Yamada

last: Shintaro

last: Keeney


title: Soy protein nanofiber scaffolds for uniform maturation of hiPSC-derived retinal pigment epithelium

city: Bethesda

first: Matthew

last: Brooks

state: MD

address: 6 Center Dr Bldg 6, Rm 303

department: NEI

institute: NIH

summary: Retinal pigment epithelial cells differentiated from human induced pluripotent stem cells (hiPSCs), called iRPE, are being explored as a cell-based therapy for the treatment of retinal degenerative diseases, especially age-related macular degeneration (AMD). The success of RPE implantation is believed to be linked to the use of biomimetic scaffolds that simulate Bruch’s membrane and aid in its maturation and integration. Current practices widely utilize fibrous scaffolds from synthetic polymers, such as polycaprolactone (PCL), rather than from natural biomaterials. Here, we tested the hypothesis that naturally derived fibrous scaffolds, with their unique translational potential, can provide favorable conditions permissive for the maturation of iRPE in vitro. We show that the culture of iRPE on natural, soy protein-derived nanofibrous scaffolds match the results of similar cells cultured on synthetic PCL nanofibrous scaffolds. The mechanical properties of soy scaffolds better emulate the native Bruch’s membrane, which would likely limit the foreign body reaction triggered by mismatch of host and biomaterial strength. Additionally, soy scaffolds exhibit unique biochemistry that improves biocompatibility and have tunable crosslinking to control degradation rates. Comparative transcriptome analysis demonstrates that iRPE maturation on nanofibrous scaffolds, either natural or synthetic, yielded more consistent outcomes than on other non-fibrous substrates. Taken together, our studies suggest that the maturation of cultured RPE for subsequent clinical applications will benefit from the use of nanofibrous scaffolds derived from natural proteins.

overall_design: Human iPSC derived retinal pigment epithelium (RPE) were diffentiated on laminin-coated chamber slides, Transwell™ only, electrospun soy scaffolds or polycaprolactone (PCL) scaffolds. Differentiation experiments were performed in triplicate and RNA harvested for RNA-seq library construction.

first: Michael

last: Phelan

first: Kamil

last: Kruczek

last: Wilson

first: Anand

last: Swaroop

first: Peter

middle: I

last: Lelkes

first: Tiansen

last: Li


title: Dysregulation of microRNA expression in diabetic skin

city: Milan

first: Fabio

last: Martelli

address: via morandi 30

country: Italy

institute: IRCCS-Policlinico San Donato

summary: Clinical skin manifestations are common in diabetes; however, molecular mechanisms underlying such defects are largely unknown. Several findings indicate a role for microRNA (miRNA) in skin homeostasis. We investigated whether miRNA expression is altered in the skin of a Type 1 mouse model of diabetes.  For this purpose, miRNA profiling by microarray analysis was performed on RNA extracted from the skin of diabetic mice and non-diabetic controls.   >400 different miRNA species were identified, differential expression-analysis revealed miRNA dysregulation in diabetic skin. Interestingly, among the 30 most significantly modulated genes, 27 were downregulated and 3 were upregulated in diabetic mice. Pathway analysis using Tarbase showed an enrichment of signature-miRNA target genes in pathways with roles in skin homeostasis, such as TGF-β and Wnt.

overall_design: Total RNAs from the back skin of streptozotocin-induced diabetic mice (a model of type I diabetes) and non-diabetic controls were extracted and miRNA profiling by microarray analysis was performed.

first: Enke

last: Baldini

first: Erika

last: Testa

first: Emanuela

last: De Domenico

first: Francesca

last: Cianfarani

first: Christine

last: Voellenkle

first: Salvatore

last: Ulisse

first: Teresa

last: Odorisio


title: 10X genomic single cell RNA-seq of WT and p47phox-KI lungs with acute lung injury

city: New Haven

first: Rihao

last: Qu

state: CT

address: 300 George Street

institute: BBS Program, Yale University

summary: We performed single cell RNA sequencing of CD45-negative cells sorted from WT and p47phox-KI lungs with ALI to characterize the impacts of the loss of p47phox phosphorylation in blood cells on pulmonary endothelial and epithelial cells. We found many genes are pertinent to enhancement of pulmonary vasculature integrity, maintain alveolar roles, promote ATII cell proliferation and lower oxidative stress state in p47phox-KI lungs.

overall_design: Compare gene expression in single cell level between WT and p47phox-KI lungs

first: Dan

last: Wu

first: Qianying

last: Yuan


title: Whole Transcriptome Sequencing (mRNA-seq) of cultured pulmonary primary endothelial cells treated with or without H2O2

summary: ROS once released from myeloid cells is quickly converted into H2O2 in lungs.  We performed RNAseq of cultured pulmonary primary endothelial cells treated with or without H2O2.  Pathway enrichment analysis revealed that some of the signaling pathways that are altered by H2O2 are related to AKT signaling. AKT signaling has a protective role in a murine model of ALI by preventing capillary leakage.  Moreover, H2O2 stimulates AKT activation in endothelial cells to strengthen vessel barrier integrity

overall_design: mRNA profiles of cultured pulmonary primary endothelial cells treated with or without H2O2, in triplicate, using Illumina.


title: Investigation of transcriptional response upon loss of RanBP3

first: Alexei

last: Arnaoutov

address: 49 Convent Dr, Bldg 49 Room 5A10

department: PCRM

institute: NICHD

summary: Transcriptional changes were assessed using RNA-Seq after depleting RanBP3 or RCC1 protein.

overall_design: We degraded the RanBP3 or RCC1 using the Auxin-based degron system and look at transcriptional changes.

first: H

last: Lee

first: K

last: Yau

first: A

first: M

last: Dasso


title: Myeloid ROS remodels pulmonary microenvironment to protect lungs from acute lung injury

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

overall_design: Refer to individual Series


title: Collapse of the hepatic gene regulatory network in the absence of FoxA factors

city: Philadelphia

first: Klaus

last: Kaestner

address: University of Pennsylvania, 12-126 Smilow Center for Translational Research, 3400 Civic Center Boulevard

department: Department of Genetics and Institute for Diabetes Obesity and Metabolism, Perelman School of Medicine

institute: University of Pennsylvania

summary: FoxA transcription factors are critical for liver development through their pioneering activity, which initiates a highly complex network thought to become resistant to the loss of any individual hepatic transcription factor via mutual redundancy. To investigate the dispensability of FoxA factors for this regulatory network, we ablated all FoxA genes in the adult liver. Remarkably, loss of FoxA caused a rapid and massive reduction in the expression of key liver genes back to the low levels of the fetal prehepatic endoderm stage, leading to necrosis and lethality within days. Mechanistically, we found FoxA proteins to be required for maintaining chromatin activity, nucleosome positioning and binding by other hepatic transcription factors. Thus, the hepatic gene regulatory network is dependent on the FoxA proteins throughout life.

overall_design: We depleted all three FoxA genes in 8 week-old mice by injecting adeno-associated virus 8 (AAV8) carrying the gene for Cre recombinase under the control of the hepatocyte-specific thyroid-binding globulin (Tbg) promoter to adult FoxA1L/L/FoxA2 L/L/FoxA3-/- mice and validated FoxA depletion (FoxA triple null). As controls we injected the same transgenes with AAV expressing GFP. FoxA triple nulls were compared also to FoxA1/A2 lox animals, FoxA1/A2 cre alfp and to hepatoblast and new-born RNA-seq data. In addition, RNA-seq was also performed on HNF4a null livers depleted in adult livers.

first: Yitzhak

last: Reizel

first: Ashleigh

last: Morgan


title: 4sU-seq of EV vs PRL3 expressing melanoma cells

city: Edinburgh

first: Jeanette

middle: Astorga

last: Johansson

state: Scotland

address: Western General Hospital, Crewe Road

department: IGMM

institute: Edinburgh University

summary: We report the use of 4sU-seq to determine the role of PRL3 in transcriptional processivity in human melanoma cells overexpressing either PRL3 or empty vector control. Genome-wide analysis of read coverage across length of equalised genes revealed a distinct accumulation of transcripts towards the 5’ end in PRL3 overexpressing cells. Furthermore, we identify the genes that were enriched with 5’ transcripts in the PRL3 expressing cells by comparing the intronic read counts (normalized for length) at the 5’ and 3’ end of the gene and termed this metric the transcriptional processivity ratio (TPR).  Comparing the TPRs for each gene between control cells and cells expressing PRL3, we found 1745 genes that were enriched for transcripts at the 5’ end and 40 genes that were enriched at the 3’ end in the PRL3 expressing melanoma cells compared with controls. Over 62% of the genes with altered TPRs showed a significantly altered change in total RNA differential expression analysis between PRL3 cells and control cells. These data illustrate a function for PRL3 in the regulation of transcriptional processivity that is enough to substantially alter steady-state mRNA levels.

overall_design: 4sU labelled nascent RNA was profiled in stably transfected A375 human melanoma cells overexpressing PRL and empty vector (EV), in triplicates, using Illumina HiSeq 4000.

first: Philippe

last: Gautier

first: Rob

last: Illingworth

first: E

last: Patton


title: RNA sequencing analysis of ex vivo expanded CD27+CD70- and CD27-CD70+ human regulatory T cells

city: Oxford

first: Rebeca

middle: Casilda

last: Arroyo Hornero

state: Not applicable

address: John Radcliffe Hospital, Headington

department: NDS

institute: University of Oxford

summary: Our study shows that after extended stimulation of human CD4+CD25+CD127- Tregs in vitro, a stable cell subset that downregulates CD27 and upregulates CD70 develops. Expanded CD27+CD70- Tregs display a gene profile which closely relates to the previously described “Treg gene signature”, whereas CD27-CD70+ Tregs express some genes associated with Treg gene signature and some genes overexpressed in conventional T cells.

overall_design: Comparison of the transcriptome profile of CD27+CD70- and CD27-CD70+ human regulatory T cells isolated from healthy individuals and after having been in vitro-expanded for 4 weeks using polyclonal stimulation

first: Joanna

last: Hester


title: Comprehensive analysis of the whole coding and noncoding RNA transcriptome expression profiles and construction of the circRNA-lncRNA co-regulated ceRNA network in laryngeal squamous cell carcinoma [miRNA]

city: haerbin

first: Ming

last: Liu

address: No. 246 xuefu road, nangang district

institute: The Second Affiliated Hospital, Harbin Medical University

summary:
We explored the whole expression profiles of transcriptome included miRNA, circRNA, lncRNA and mRNA in 5 pairs of LSCC and matched non-LSCC tissues by microarray
The LSCC-related competing endogenous RNA (ceRNA) networks were constructed based on these microarray data.

overall_design: We simultaneously detected the expression profiles of the whole transcriptome, including miRNA, circRNA and lncRNA+mRNA, in five paired laryngeal squamous cell carcinoma (LSCC)and matched non-carcinoma tissues by microarrays. The lncRNA-miRNA-mRNA and circRNA-miRNA-mRNA ceRNA network were constructed using both physical interactions and expression correlations. When cirRNAs in the circRNA-miRNA-mRNA ceRNET and lncRNAs in the lncRNA-miRNA-mRNA ceRNET shared the same miRNA-mRNA interactions, these pairs were retained to construct the circRNA-lncRNA co-regulated ceRNA network. Nine modules were further  identified in the network

first: Rui

last: Zhao


title: Investigation of transcriptional response upon loss of individual Y-complex nucleoporins

summary: Transcriptional changes were assessed using RNA-Seq after depleting Nup160, Nup133, Nup96, Nup85 and Nup107

overall_design: Using the Auxin-based degron, we degraded the Y-complex nucleoporins. This was followed by RNA-Seq to look at transcriptional changes.

first: S

last: Regmi


title: Comprehensive analysis of the whole coding and noncoding RNA transcriptome expression profiles and construction of the circRNA-lncRNA co-regulated ceRNA network in laryngeal squamous cell carcinoma [lncRNA-mRNA]

type:
Expression profiling by array
Non-coding RNA profiling by array


title: Estrogen-related receptor agonism reverses mitochondrial dysfunction and inflammation in the aging kidney

status: Public on Jul 09 2020

city: haifa

first: Moshe

last: Levi

state: Washington, DC

address: 37th and O Streets NW

department: Department of Biochemistry and Molecular & Cellular Biology at Georgetown University Medical Center

institute: Georgetown University

summary: Background: A gradual decline in renal function occurs even in healthy aging individuals. In addition to aging per se, concurrent metabolic syndrome and hypertension, which are common in the aging population, can induce mitochondrial dysfunction and inflammation, which collectively contribute to age-related kidney dysfunction and disease. Here we studied the role of the nuclear hormone receptors, the estrogen related receptors (ERRs) in regulation of age-related mitochondrial dysfunction and inflammation.  Methods: ERRs were decreased in aging human and mouse kidneys and were preserved in aging mice with lifelong caloric restriction (CR). Pan-ERR agonist was used to treat 21-month-old mice for 8-weeks.    Results: Remarkably, only an 8-week treatment with the pan-ERR agonist reversed the age-related increases in albuminuria and podocyte loss, mitochondrial dysfunction and inflammatory cytokines, including the cGAS-STING and STAT3 signaling pathways. A 3-week treatment of 21-month-old mice with a STING inhibitor reversed the increases in inflammatory cytokines and the senescence marker p21 but also unexpectedly reversed the age-related decreases in PGC-1α, ERRα, mitochondrial complexes and MCAD expression.   Conclusions: Our studies identified ERRs as important modulators of age-related mitochondrial dysfunction and inflammation.

first: Xiaoxin

middle: X

last: Wang

first: Avi

last: Titievsky


title: Comprehensive analysis of the whole coding and noncoding RNA transcriptome expression profiles and construction of the circRNA-lncRNA co-regulated ceRNA network in laryngeal squamous cell carcinoma

type:
Non-coding RNA profiling by array
Expression profiling by array

platform_organism:
Homo sapiens
synthetic construct


title: Comprehensive analysis of the whole coding and noncoding RNA transcriptome expression profiles and construction of the circRNA-lncRNA co-regulated ceRNA network in laryngeal squamous cell carcinoma [circRNA]


title: HIF1α is an essential regulator of steroidogenesis in the adrenal gland

city: Dresden

first: Ben

last: Wielockx

address: Fetscherstr. 74

country: Germany

institute: Institut für Klinische Chemie und Laboratoriumsmedizin

summary: Hormones produced by the adrenal cortex are absolutely essential for numerous processes in living animals. Our research group investigated to what extend the central regulators of deprived oxygen, hypoxia inducible factors (HIFs), contribute to this steroidogenesis. For this, we developed a set of new transgenic mouse lines displaying modified HIF1α and HIF2α levels in cortical cells and revealed that HIF1α exclusively regulates the transcription of a majority of enzymes responsible for the production of glucocorticoids and mineralocorticoids as well as a consequent inflection of cytokines in circulation. These novel tools will be helpful to understand how sustained and chronic changes in adrenocortical hormones can impact during health and disease.

overall_design: FACS sorted cortical cells from transgenic mice (n=3) versus WT controls (n=3) of different genders

first: Deepika

last: Watts

first: Anupam

last: Sinha


title: RNA-Seq analysis was performed with total RNA isolated from WT and mutant endosperms at 12 DAP

city: Taian

first: yiming

last: Wei

address: Daizong Street, 61

institute: Shandong Agricultural University

summary: We performed a molecular characterization of the maize small kernel mutant with endosperm developmental deficiency phenotypes.To elucidate how SMK8 affects kernel development, we performed RNA sequencing (RNA-seq), and the results  revealed numerous differentially expressed genes related to storage proteins and starch biosynthesis and biosynthesis of amino acids.

overall_design: Three biological repeats of the Endosperm tissue from smk8-ref (14_M1, 14_M2, 14_M3) and WT (14_WT1, 14_WT2, 14_WT3) at 12 DAP were used for RNA sequencing

first: Yi

first: Xiang


title: Single-Cell Transcriptional profiling of regenerated radiation proctitis by colonoids transplantation.

city: Seongnam-si

first: Joohyun

last: Jee

state: Gyeonggi-Do

address: 712 CHA Bio Complex, 335 Pangyo-Ro, Sampyeong-Dong, Bundang-Gu

department: Department of Microbiology

country: South Korea

institute: CHA University

summary: Single-cell RNA-seq has colon epithelial cell analysis of colonoids transplanted colon tissue.  The goals of this study are to colonoid engrafted tissue transcriptome profiling (RNA-seq) to define theraputic effect in radiation colitis mice.

overall_design: colon epithelium scRNA-Seq

first: Jongman

last: Yoo


title: Next Generation Sequencing  explore the relationship between apolipoprotein AV (APOAV) overexpression and insulin resistance in hepatocytes.

city: Changsha

first: wang

last: zhao

address: No.139 Middle Renmin Road, Changsha, Hunan

department: Department of Cardiovascular Medicine, The Second Xiangya Hospital

institute: Central South University

summary: We sought to explore the relationship between apolipoprotein AV (APOAV) overexpression and insulin resistance in hepatocytes. The insulin-resistant HepG2 cell model was constructed and then APOAV overexpressed HepG2 cells (B-M) were induced by infecting with recombinant adenovirus vector. Microarray data were developed from B-M samples compared with negative controls (A-con) and the microarray data were analyzed by bioinformatic methods.  APOAV overexpression induced 313 up-regulated genes and 563 down-regulated ones in B-M sample. The differentially expressed genes (DEGs) were significantly classified in Fat digestion and absorption pathway. Protein-protein interaction network was constructed and AGTR1 (angiotensin II receptor type 1) and P2RY2 (purinergic receptor P2Y, G-protein coupled 2) were found to be the significant nodes closely related with G-protein related signaling. Additionally, overexpression of APOAV could change the expression of Glut4 and release insulin resistance of hepatic cells. Thus, APOAV overexpression may prevent the insulin resistance in liver cells by mediating the genes such as AGTR1 and P2RY2.

overall_design: mRNA profiles of B-M(APOAV overexpressed HepG2 cells) samples and negative controls (A-con) were generated by deep sequencing, in triplicate, using Illumina HiSeq4000.

first: Wang


title: Circadian transcriptome of intestinal ILC2 and ILC3

city: Parkville

first: Alexandra

last: Garnham

state: Victoria

address: 1G Royal Parade

institute: Walter and Eliza Hall Institute of Medical Research

summary: Identification of cycling genes in intestinal ILC2 and ILC3 cells

overall_design: These data comprise samples of female mouse intestinal ILC2 and ILC3 cells taken over time at 4, 10, 16 and 23 hours. For each time point and cell type combination there are 1-2 biological replicates per group.

first: Cyril

last: Seillet

first: Gabrielle

last: Belz


title: Patient-derived HK-374 glioblastoma cells treated with radiation and ONC201

status: Public on Jul 08 2020

city: Los Angeles

first: Frank

last: Pajonk

state: CA

address: 10833 Le Conte Ave

institute: UC Los Angeles

summary: RNASeq results for HK-374 treated with DMSO, radiation, ONC201 or radiation plus ONC201

overall_design: Cells were irradiated with 0 or 4 Gy and treated with solvent or ONC201 at 2.5µM


title: Combining mathematical and statistical modeling to simulate time course bulk and single cell gene expression data in cancer with CancerInSilico

city: Baltimore

first: Elana

middle: Judith

last: Fertig

address: 670 W. Baltimore Street, 3rd floor

department: Institute for Genome Sciences

institute: University of Maryland, Baltimore

summary: We develop an R/Bioconductor package CancerInSilico to simulate bulk and single cell transcriptional data from a known ground truth obtained from mathematical models of cellular systems. This package contains a general R infrastructure for cell-based mathematical model, implemented for an off-lattice, cell-center Monte Carlo mathematical model. We also adapt this model to simulate the impact of growth suppression by targeted therapeutics in cancer and benchmark simulations against bulk in vitro experimental data. Sensitivity to parameters is evaluated and used to predict the relative impact of variation in cellular growth parameters and cell types on tumor heterogeneity in therapeutic response.

overall_design: Time course Illumina microarray data for the BxPC-3 cell line treated with cetuximab (10µg/ml) and negative controls.

first: Yong

last: Tang


title: Testicular transcriptome in crossbred and Zebu cattle

city: Bangalore

first: Arumugam

last: Kumaresan

state: Karnataka

address: Hosur Road

department: Veterinary Gynaecology and Obstetrics

country: India

institute: National Dairy Research Institute

summary: To understand the etiology behind higher incidence of infertility in crossbred bulls, we performed transcriptomic analysis of testicular samples derived from crossbred males and compared with testicular transcriptomic profile of Zebu cattle

overall_design: Microarray Gene expression Study : Agilent Bos Taurus 8x60k Microarray: AMADID: 29411

first: A


title: Expression profiling of viologen hebicides in a mouse hepatocyte model

city: Hillsboro

first: Brendan

middle: D

last: Stamper

state: OR

department: Pharmacy

institute: Pacific University

summary: Paraquat and diquat are viologen herbicides used in commercial agriculture and for residential outdoor weed control. They are related structurally, each containing multiple aromatic rings and two quaternary ammonium cations.  Paraquat is one of the most widely used herbicides in the world; however, due to recent toxicity studies and its association with Parkinson’s disease, it is now available only to commercially licensed users in the United States.  In contrast, diquat has not been associated with Parkinson’s disease and is available for both commercial and residential applications in the United States. In general, the proposed mechanism by which toxicity occurs following exposure to either herbicide is similar.  Both are readily converted to free radicals via the superoxide anion radical and react with molecular oxygen to generate additional redox products that promote oxidative stress and potentially cell death. Diquat is generally considered a safer alternative to paraquat based on its lower incidence of poisoning reports; however, recent work in our lab suggests diquat is significantly more hepatotoxic than paraquat.  Studies reporting direct comparisons of paraquat and diquat, especially regarding their potential impact on liver injury, are definitely lacking.  The goal of this project is to address this knowledge gap by exposing an in vitro hepatocellular model (TGF-alpha transgenic mouse hepatocytes; TAMH) with each viologen herbicide to further elucidate toxicologic mechanisms and outcomes.  The microarray data identified MAPK as an important contributor to diquat-induced toxicity and offers a new generalized approach for broader gene expression-level investigations.

overall_design: 9 arrays, 3 experimental groups, 9hr DQ, 9hr PQ, 9hr Control

first: Ngoc

middle: U

last: Nguyen


title: Epigenetic footprint of hepatoblastoma defines a novel integrative molecular classification with clinical implications [Infinium MethylationEPIC]

city: Badalona

first: Carolina

last: Armengol

address: Crta Can Ruti; cami de les escoles, S/N

institute: Germans Trias i Pujol Health Research Institute

type: Methylation profiling by genome tiling array

summary: Hepatoblastoma (HB) is the predominant pediatric liver cancer with limited therapeutic options for patients with aggressive tumors. Nevertheless, it is a rare disease. Here, we performed a high-throughput molecular study of 32 patients with HB and major findings were validated in additional 80 cases. We unveiled an epigenetic footprint including downregulation of RNA-editing, hyperediting of the tumor suppressor BLCAP,14q32 DLK1-DIO3 locus overexpression, DNA hypomethylation and CpG island hypermethylation. Based on these findings, we defined an integrative molecular classification of HB that improve current clinical stratification, and identified CHKA as a therapeutic target for the poor prognostic subclass.

overall_design: 49 samples from 28 patients with Hepatoblastoma and 5 fetal liver samples

first: Juan

last: Carrillo-Reixach

first: Laura

last: Torrens

first: Marina

last: Simon-Coma

last: Royo

first: Montserrat

last: Domingo-Sàbat

first: Jordi

last: Abril-Fornaguera

first: Nicholas

last: Akers

first: Margarita

last: Sala

first: Sonia

last: Ragull

first: Magdalena

last: Arnal

first: Núria

last: Villalmanzo

first: Stefano

last: Cairo

first: Alberto

last: Villanueva

first: Roland

last: Kappler

first: Marta

last: Garrido

last: Guerra

first: Constantino

last: Sábado

first: Gabriela

last: Guillén

first: Mar

last: Mallo

first: David

last: Piñeyro

first: María

last: Vázquez-Vitali

first: Olga

last: Kuchuk

first: María Elena

last: Mateos

first: Gema

last: Ramírez

first: Manuel

last: López-Santamaría

first: Yasmina

last: Mozo

first: Aroa

last: Soriano

first: Michael

last: Grotzer

first: Sophie

last: Branchereau

first: Nagore

last: García de Andoin

first: Blanca

last: López-Ibor

first: Ricardo

last: López-Almaraz

first: José Antonio

last: Salinas

first: Bárbara

last: Torres

first: Francisco

last: Hernández

first: José Javier

last: Uriz

first: Monique

last: Fabre

first: Julià

last: Blanco

first: Claudia

last: Paris

first: Lara

last: Nonell

first: Piotr

last: Czauderna

first: Bruce

last: Morland

first: Daniela

last: Sia

first: Bojan

last: Losic

first: Marie Annick

last: Buendia

first: Maria Rosa

last: Sarrias

first: Josep Maria


title: Determine differences in gene expression between OPSCC cell lines with different sensitivity to IR

city: CARDIFF

first: Peter

last: Giles

address: Heath Park

institute: Cardiff University

summary: mRNA sequencing was performed on 10 oropharyngeal cancer cell lines (5 HPV-positive and 5 HPV-negative cell lines) for this project. Two cell lines (CU-OP-17 and CU-OP-20) were newly derived from HPV-negative and HPV-positive tonsil cancers, respectively (described in " Sensitivity of human papillomavirus-positive and -negative oropharyngeal cancer cell lines to ionizing irradiation" by Holzhauser et al.   This study was performed with the goal to identify differences in gene expression between irradiated and non-irradiated cell line samples. Additionally, the aim was to identify possible changes in genes, involved in DNA repair or DNA damage response of the HPV-positive and HPV-negative cell lines.  The data published showed an increase of HPV integration sites after irradiation. Additionally, all HPV-positive cell lines in this study showed expression of HPV encoded genes. However, no direct correlation of changes or expression of DNA repair genes was identified.

overall_design: Identification of differences in gene expression by mRNA sequencing between non-irradiated and irradiated (2Gy) HPV-positive and HPV-negative OPSCC cell lines. Cells were grown under standard cell culture condition, mRNA was extracted and sequencing perfomed with 75bp PE (sequencing readlength)- TruSeq stranded total RNA with ribo-zero GOLD

first: Stefan

last: Holzhauser

first: Ned

last: Powell

first: Stephen

last: Man


title: Modelling and rescue of RP2 Retinitis Pigmentosa using iPSC Derived Retinal Organoids

city: London

first: Michael

last: Cheetham

address: 11-43 Bath Street

institute: University College London

summary: Mutations in RP2 lead to a severe form of X-linked retinitis pigmentosa (XLRP). RP2 functions  as a GTPase activating protein (GAP) for the small GTPase ARL3, which is essential for cilia  function and for photoreceptor development and maintenance. The mechanisms of RP2  associated retinal degeneration in humans are poorly understood, and genetically engineered  animal models of RP2 XLRP present with differing retinal phenotypes and slow degeneration  suggesting potential species differences. Here, we developed CRISPR gene edited isogenic  RP2 knock-out (RP2 KO) induced pluripotent stem cells (iPSC) and RP2 patient derived iPSC  to produce 3D retinal organoids as a human retinal disease model. The isogenic RP2 KO retinal  organoids and two unrelated RP2 patient iPSC lines produced retinal organoids with a defined  photoreceptor cell layer (ONL) containing rod and cone photoreceptors. Strikingly the RP2  KO and RP2 patient derived organoids showed a thinning of the ONL by 180 days (D180) of  culture, which was associated with a spike in cell death in the ONL at D150 of differentiation.  RNA sequencing confirmed induction of cell death pathways in the RP2 null organoids at this  stage. Photoreceptor cell death and ONL thinning was attributed to cells undergoing terminal  rod cell differentiation characterized by reduced RHO expression and fewer rhodopsin  immunoreactive photoreceptors. Gene augmentation with a human RP2 transgene in an  AAV2/5 vector efficiently transduced RP2 KO organoids and led to high levels of RP2  expression in both rods and cones. Importantly, the viral transduction significantly increased  ONL thickness and restored rhodopsin expression, suggesting rescue of the RP2 degeneration  phenotype. These data show that 3D retinal organoids can be used to model molecular defects  associated with inherited retinal disease, photoreceptor cell death and also to test potential  therapies targeted to prevent photoreceptor degeneration.

overall_design: Retinal mRNA profiles of 150-days old retinal organoids from a control line in triplicate, an isogenic RP2-KO CRISPRed cell line in duplicate and a patient carring the R120X mutation in RP2 were generated by sequencing using Illumina technology.

first: Amelia

last: Lane

first: Katarina

last: Jovanovic

first: Ciara

last: Shortall

first: Daniele

last: Ottaviani

first: Anna

last: Brugulat  Panes

first: Rosellina

last: Guarascio

first: Nele

last: Schwarz

first: Matthew

last: Hayes

first: Arpad

last: Palfi

first: Naomi

last: Chadderton

first: G

last: Farrar

first: Alison

last: Hardcastle


title: scRNA-seq of murine effector CD8 T cells in response to local vaccination

city: Amsterdam

first: Lianne

last: Kok

address: Plesmanlaan 121

country: Netherlands

institute: Netherlands Cancer Institute

summary: Mice received barcode-labelled OT-I T cells and were challenged with a DNA vaccine, encoding the OVA peptide,  which was applied locally on the skin of the hind legs. 12 days after vaccination, we performed single cell RNA sequencing on circulating effector CD8+ T cells (isolated from blood). We detected cells which transcriptionally resemble mature tissue resident memory T cells.

overall_design: Blood samples were collected from 3 vaccinated recipient mice, barcode-labelled OT-I T cells were isolated by FACS, after which cells were processed for scRNA-seq was preformed (10X Chromium 3' kit), and sequenced on NextSeq

first: Feline

last: Dijkgraaf

first: Kaspar

last: Bresser

first: Ton

last: Schumacher


title: miRNA-seq in H661 cells

city: BOSTON

first: Li

last: Chai

address: 77 AVENUE LOUIS PASTEUR, NRB652-4A

institute: BRIGHAM AND WOMENS HOSPITAL

summary: We identified Entinostat can decrease SALL4 expression via post-transcriptional regulation which miRNAs might be involved. In order to discover the potential miRNAs that regulated by Entinostat and also target SALL4, we did miRNA-seq in H661 cells after 8 hours of DMSO or Entinostat treatment.

overall_design: miRNA-seq in H661 cells after DMSO or Entinostat treatment

first: Junyu

last: Yang

first: Yue

last: Wu


title: Oral squamous cell carcinoma may originate from bone marrow-derived stem cells

city: Toon

first: Koh-ichi

last: Nakashiro

state: Ehime

address: 454 Shitsukawa

department: Oral and Maxillofacial Surgery

country: Japan

institute: Ehime University Graduate School of Medicine

summary:
In this study, sex chromosome analysis was performed in patients with oral squamous cell carcinoma (OSCC) that developed after hematopoietic stem cell transplantation from the opposite gender to examine whether OSCC originates from bone marrow (BM) stem cells. Gene expression patterns in patients with possible BM stem cell-derived OSCC were compared with those in patients with normally developed OSCC.
We used microarray analysis to examine whether OSCC with a possible BM origin shows specific pattern of the gene expression.

overall_design: We compared the gene expression profiles of BM stem cell-derived OSCC and normal OSCC tissues.

first: Tomonori

last: Hasegawa


title: TLR4 signaling and macrophage inflammatory responses are dampened by GIV/Girdin

city: San Diego

first: Pradipta

last: Ghosh

address: 9500 Gilman Dr

department: Cellular and Molecular Medicine

institute: University of California San Diego

summary: Sensing of pathogens by Toll-like receptor 4 (TLR4) induces an inflammatory response; controlled responses confer immunity but uncontrolled responses cause harm. Here we define how a multi-modular scaffold, GIV (a.k.a Girdin) titrates such inflammatory response in macrophages. Upon challenge with microbe-derived lipopolysaccharides (LPS, a ligand for TLR4), macrophages with GIV mount a more tolerant (hypo-reactive) transcriptional response and suppress pro-inflammatory cytokines and signaling pathways (i.e., NFkB and CREB) downstream of TLR4 compared to their GIV-depleted counterparts.

overall_design: Two biological replicates (using two different shRNAs) were analyzed for RAW macrophages simulated with LPS for 5hrs.


title: Absence of central tolerance in Aire-deficient mice synergizes with immune-checkpoint inhibition to enhance antitumor responses [bulk RNA-seq]

city: Tarrytown

first: Asiel

middle: Arturo

last: Benitez

address: 777 Old Saw Mill River Rd, 92-516A

department: Immunology & Inflammation

institute: Regeneron Pharmaceuticals, Inc

summary: Therapeutic targeting of immune checkpoint pathways, that are exploited by tumors to evade the immune system, can result in increased overall survival for some patients with specific types of cancers.  The endogenous antitumor response is limited in part by the absence of tumor-reactive T cells, an inevitable consequence of thymic central tolerance mechanisms ensuring their deletion to protect against autoimmunity.   In this study, we show that compared to wild-type mice, tumor rejection induced by immune checkpoint blockade is significantly enhanced in Aire-deficient mice, the epitome of central tolerance breakdown.  The observed synergy in tumor rejection extended to different tumor models and was accompanied by increased numbers of activated T cells expressing high levels of genes such as Gzma, Gzmb, Perforin, Cxcr3, and tumors contained high levels of the chemokines Cxcl9 and Cxcl10 compared to wild-type mice.  Furthermore, there was an enrichment of T cells expressing markers associated with the potent anti-tumor tissue-resident memory T cells expressing Cd103.  Consistent with Aire’s central role in T cells repertoire selection, single cell TCR sequencing unveiled the expansion of several clones with high tumor reactivity.  Together, these results show that a break in central tolerance in combination with immune checkpoint blockade can potently enhance anti-tumor immunity and serve as a model system to unmask novel anti-tumor therapies.

overall_design:
Tumor (B16F10) bearing Aire+/+ and Aire-/- mice were treated with anti-CTLA4 or control antibodies and harvested on Day 23 and bulk-RNAseq was performed (Samples GSM4592014-GSM4592033).

Tumor (MC38) bearing Aire+/+ and Aire-/- mice were treated with anti-PD1 or control antibodies and tumors, spleens and lymph nodes were harvested on Day 23 and bulk-RNAseq was performed (Samples GSM4591941-GSM4592013).

middle: A

first: Sara

last: Khalil-Aguero

first: Anjali

last: Nandakumar

first: Namita

last: Gupta

first: Wendy

last: Zhang

first: Gurinder

middle: S

last: Atwal

first: Andrew

last: Murphy

last: Sleeman

first: Sokol

last: Haxhinasto


title: Absence of central tolerance in Aire-deficient mice synergizes with immune-checkpoint inhibition to enhance antitumor responses

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

overall_design:
Tumor (B16F10) bearing Aire+/+ and Aire-/- mice were treated with anti-CTLA4 or control antibodies and harvested on Day 23 and bulk-RNAseq was performed (Samples GSM4592014-GSM4592033).

Tumor (MC38) bearing Aire+/+ and Aire-/- mice were treated with anti-PD1 or control antibodies and tumors, spleens and lymph nodes were harvested on Day 23 and bulk-RNAseq was performed (Samples GSM4591941-GSM4592013).

Tumor bearing Aire+/+ and Aire-/- mice were treated with anti-PD1 or control antibodies and tumors, spleens were harvested on Day 19. scRNAseq was performed on CD45+ splenic or intra-tumoral cells. scRNAseq was also performed on splenic CD8+ T cells and CD8+ TILs. (Samples GSM4592034-GSM4592049).


title: Liver-specific ceramide reduction alleviates steatosis and insulin resistance in alcohol-fed mice

city: Philadelphia

first: Gary

state: PA

address: 915 Biomedical Research Building, 421 Curie Blvd

department: Department of Medicine, Division of Gastroenterology

institute: University of Pennsylvania

summary: Alcohol’s impairment of both hepatic lipid metabolism and insulin resistance (IR) are key drivers of alcoholic steatosis, the initial stage of alcoholic liver disease (ALD).  Pharmacologic reduction of lipotoxic ceramide prevents alcoholic steatosis and glucose intolerance in mice, but potential off-target effects limit its strategic utility.  Here, we employed a hepatic-specific acid-ceramidase (ASAH) overexpression model to reduce hepatic ceramides in a Lieber-DeCarli model of experimental alcoholic steatosis. We examined effects of alcohol on hepatic lipid metabolism, body composition, energy homeostasis and insulin sensitivity as measured by hyperinsulinemic-euglycemic clamp.  Our results demonstrate that hepatic ceramide reduction ameliorates the effects of alcohol on hepatic lipid droplet accumulation by promoting VLDL secretion and lipophagy, the latter of which involves ceramide cross-talk between the lysosomal and lipid droplet compartments.  We additionally demonstrate that hepatic ceramide reduction prevents alcohol’s inhibition of hepatic insulin signaling. These effects on the liver are associated with a reduction in oxidative stress markers and are relevant to humans, as we observe peri-lipid droplet ASAH expression in human ALD.  Together, our results suggest a potential role for hepatic ceramide inhibition in preventing ALD.

overall_design: Liver RNA from mice fed an alcohol diet mice was analyzed by RNAseq (N=4/group).  Hepatic ceramides were reduced by inducing  the transgene ASAH1, a ceramidase, in a liver-specific, dox-inducible fashion.   To assess the optimal control for transgene induction, we performed RNAseq to compare strategies varying either genetics (transgene- or transgene+ fed Etoh-dox) or diet (transgene+ mice fed an Etoh or Etoh-dox diet).

first: Jason

middle: M

last: Correnti

first: Chelsea

last: Lin

first: Jascha

last: Brettschneider

first: Amy

last: Kuriakose

first: Sookyoung

last: Jeon

first: Eleonora

last: Scorletti

first: Amanke

last: Oranu

first: Dru

last: McIver-Jenkins

first: Isabelle

last: Kaneza

first: Delfin

last: Buyco

first: Yedidya

last: Saiman

first: Emma

last: Furth

first: William

middle: L

last: Holland

first: Rotonya

last: Carr


title: Absence of central tolerance in Aire-deficient mice synergizes with immune-checkpoint inhibition to enhance antitumor responses [scRNA-seq]

first: Asiel

last: Benitez

overall_design: Tumor bearing Aire+/+ and Aire-/- mice were treated with anti-PD1 or control antibodies and tumors, spleens were harvested on Day 19. scRNAseq was performed on CD45+ splenic or intra-tumoral cells. scRNAseq was also performed on splenic CD8+ T cells and CD8+ TILs.

first: Sara

last: Khalil-Aguero

first: Anjali

last: Nandakumar

first: Namita

last: Gupta

first: Wendy

last: Zhang

first: Gurinder

last: Atwal

first: Andrew

last: Murphy

first: Matthew


title: Hepatocyte-Specific TAK1 Deficiency Drives RIPK1 Kinase-dependent Inflammation to Promote Liver Fibrosis and Hepatocellular Carcinoma

city: shanghai

first: jing

last: zhao

address: Qiuyue Road

institute: IRCBC

summary: Transforming growth factor beta-activated kinase1 (TAK1) encoded by the gene MAP3K7 regulates multiple important downstream effectors involved in immune response, cell death and carcinogenesis. Hepatocyte-specific deletion of TAK1 in Tak1_Hep mice promotes liver fibrosis and hepatocellular carcinoma (HCC) formation. Here, we report that genetic inactivation of RIPK1 kinase using kinase dead knock-in D138N mutation in Tak1_Hep mice inhibits the expression of liver tumor biomarkers, liver fibrosis and HCC formation. Inhibition of RIPK1, however, has no or minimum effect on hepatocyte loss and compensatory proliferation, which are the recognized factors important for liver fibrosis and HCC development. Using single cell RNA-seq, we discover that inhibition of RIPK1 strongly suppresses inflammation induced by hepatocyte-specific loss of TAK1. Activation of RIPK1 promotes the transcription of key proinflammatory cytokines, such as CCL2, and CCR2+ macrophage infiltration. Our study demonstrates the role and mechanism of RIPK1 kinase in promoting inflammation, both cell-autonomously and cell-non-autonomously, in the development of liver fibrosis and HCC, independent of cell death and compensatory proliferation. We suggest the possibility of inhibiting RIPK1 kinase as a therapeutic strategy for reducing liver fibrosis and HCC development by inhibiting inflammation.

overall_design: Examination of transcriptional change in different cell types between WT and double mutants

first: Shuixia

last: Tan

first: Jing

last: Zhao

last: Liu

first: Junying

last: Yuan


title: Gene expression profiling of mouse uterine stromal cells isolated on day 5 of pregnancy

city: Urbana

first: Indrani

middle: C

last: Bagchi

state: IL

address: 2001 S Lincoln

department: Comparative Biosciences

institute: Univ of Illinois at Urbana Champaign

summary:
Our study revealed that hypoxia inducible factor 2 alpha, Hif2 alpha, is a downstream target of estrogen signaling in mouse uterine stroma at the time of implantation. Further, conditional deletion of Hif2 alpha in mouse uterus leads to infertility due to impaired epithelial remodeling at the time of implantation.
To identify the downstream targets of Hif2 alpha in the uterus, we performed gene expression profiling of uterine stromal cells isolated from Hif2 alpha-intact and -null mice on day 5 of pregnancy, overlapping the window of implantation. The microarray results revealed altered expression of mRNAs corresponding to factors involved in protein trafficking in uterine stroma of Hif2 alpha-ablated mice. These factors mediate crosstalk between uterine storma and epithelial cells to promote epithelial remodeling and implantation. Thus, Hif2 alpha regulates embryo implantation by controlled trafficking of secretory granules during early pregnancy.

overall_design: Mouse uterine stromal cells were isolated from control and conditional knockout mice on day 5 of pregnancy. The stromal cells from 3 animals/genotype were pooled and total RNA was isolated and then hybridized to high density affymetrix microarrays according to the Affymetrix protocol (Mouse Genome 430A 2.0 Array)

first: Arpita

last: Bhurke

first: Athilakshmi

last: Kannan


title: Metabolic Regulation of the Epigenome Drives Lethal Infantile Ependymoma

city: Toronto

first: Paul

last: Guilhamon

state: ON

address: 686 Bay Street

country: Canada

institute: SickKids

summary: Posterior fossa type A (PFA) ependymomas are a lethal glial malignancy of the hindbrain found in babies and toddlers. Lacking any highly recurrent somatic mutations, PFAs have been proposed as a largely epigenetically driven tumor type. An almost complete lack of model systems has inhibited discovery of novel PFA therapies. Both in vitro and in vivo, the PFA hypoxic microenvironment controls the availability of specific metabolites to diminish histone methylation, and to increase both histone demethylation and acetylation at H3K27. PFA ependymoma initiates from a cell lineage in the first trimester of human development where there is a known hypoxic microenvironment. Unique to PFA cells, transient exposure to ambient oxygen results in irreversible cellular toxicity. PFA tumors exhibit a low basal level of H3K27me3, and paradoxically inhibition of H3K27 methylation shows significant and specific activity against PFA. Targeting metabolism and/or the epigenome presents a unique opportunity for rational therapy for infants with PFA ependymoma.

overall_design: Bisulphite converted DNA from each sample was hybridised to the Illumina Infinium EPIC Human Methylation BeadChip.

first: K

last: Michealraj

first: Sachin

last: Kumar

first: Leo

middle: J

last: Kim

first: Stephen

last: Mack

first: Sameer

last: Agnihotri

first: Jeremy

middle: N

last: Rich

first: Micheal

last: Taylor


title: RNA Seqeuncing of Adult Tissue after Maternal Diet Manipulation

city: Potsdam

first: Rachel

last: Lippert

address: Arthur-Scheunert-Allee 114-116

institute: German Institte of Human Nutrition

summary: We report differnces to gene expression in the Dorsal Striatum, Ventral Striatum, Ventral Tegmental Area and Substantia Nigra in adult offspring as a consequence of Maternal HFD exposure during lactation.

overall_design: 5 control and 6 CH animals in each gender. Mice were rapidly decapitated. Substantia nigra (SN), ventral tegmental area (VTA), dorsal Striatum (CPu) and ventral striatum (NuAcc) were cut with brain matrix and collected and frozen on dry ice and and stored in -80 freezers. All the samples were subjected to an RNA extraction protocol (see details in protocol part) and RNA concentrations were measured by Qbit machine. Those samples were deep mRNA sequenced for further analysis.

first: Jens

last: Brüning


title: Microenvironmental Th9- and Th17-lymphocytes induce epithelial-mesenchymal transition in lung cancer cells, thereby promoting metastatic spreading

city: bad nauheim

first: Stefan

last: Günther

address: ludwigtr. 43

institute: MPI for heart and lung research

summary: Analysis of gene expression profile of cancer cells after T lymphocyte-cancer cell co-culture

overall_design: LLC1 cells were sorted for RNAsequencing analysis after direct co-culture with specific T cell subsets Th0, Th9 and Th17

first: Ylia

last: Salazar

first: Rajkumar

last: Savai


title: The DGCR8-UGU interaction in microRNA biogenesis

city: Hong Kong

first: Duc

middle: Trung

last: Nguyen

address: Clear Water Bay

department: Life Science

country: Hong Kong

institute: The Hong Kong University of Science and Technology

summary: Human Microprocessor is a trimeric complex composed of the RNase III enzyme, DROSHA, and a dimer of DGCR8 (its cofactor). Microprocessor initiates the biogenesis of microRNA by processing primary microRNAs (pri-miRNAs), during which, its cleavage efficiency and accuracy are enhanced because DGCR8 interacts with the apical UGU motif of pri-miRNAs. However, the mechanism of DGCR8-UGU interaction and influence of this interaction on the expression of cellular miRNA are still elusive. In this study, we demonstrated that the Rhed domain (i.e., the RNA-binding heme domain, amino acids 285-478) of DGCR8 is sufficient to recognize and interact with UGU. In addition, we identified three amino acid residues in Rhed (amino acids 361-363), which are critical for the UGU interaction, and we showed that these residues are essential for the Microprocessor complex to accurately and efficiently process pri-miRNAs in vitro. Furthermore, we found that within the DGCR8 dimer, the UGU-binding site from just one monomer is capable of discriminating between UGU- and non-UGU-containing pri-miRNAs. Finally, we showed that these amino acids are more important for the expression of UGU miRNAs than non-UGU miRNAs in human cells. This study improves our understanding of the substrate-recognizing mechanism of DGCR8, and implicates the roles of this recognition in differentiating miRNA expression in human cells.

overall_design: DGCR8-KO cells were transfected with pCK empty, pCK-DGCR8 WT or pCK-DGCR8 mut1 plasmid. Small RNA sequencing libraries of the transfected DGCR8-KO cells were generated using the TruSeq Small RNA Library Prep kit. The experiment was repeated three times.

first: Tuan

first: Thi

last: Dang

first: Shaohua

last: Li

first: Thuy

first: Trung


title: Replication Stress in Hair-Follicle-Stem-Cell Leads to IFI16-STING dependent inflammation in Hidradenitis Suppurativa

city: Créteil

first: cecile

last: lefebvre

address: 51 Avenue du Marechal De Lattre de Tassigny

country: France

institute: INSERM U955_VRI

summary: Hidradenitis suppurativa (HS) is a chronic, relapsing, inflammatory skin disease. We characterized hair follicle stem cells isolated from HS and healthy (HD) patients and more precisely the Outer Root Sheath Cells (ORS). We show that transcriptomic analyses of hair follicles from HS (n=6) and HD (n=5) revealed an interferon signature and an alteration of cell cycle pathways

overall_design: HS (n=6) and HD (n=5)

first: C

last: Lefebvre

first: P

last: Tisserand

first: H

last: Hocini


title: RNAseq analysis of CC strains after influenza A virus infection identifies genetic control of the host response

city: Münster

first: Klaus

last: Schughart

address: Von-Esmarch-Str 56

department: Virology

institute: University Münster

summary:
Gene expression changes in the lung was studied by RNAseq in different CC mouse strains infected with influenza A virus.
Results: Strong differences between the genetically CC mouse strains can be observed in the activation of host defense genes. These differences can be related to genetic variants in the genome of the CC strains. Furthermore, different strains exhibit variant susceptibility to infections (body weight loss and survival). These differences can be correlated to differences in gene expression profiles.

overall_design: Female mice from 11 CC mouse strains were infected with mouse-adapted H3N2 virus and lungs were harvested at day3, 5 nd 8 after infection. Total RNA was isolated and mRNA was sequenced.


title: Genome-wide mapping of binding of HDAC1/HDAC2 and H3K9/14Ac modification in control and Tet2/Tet3-deficient B cells

city: Fukuoka

first: SHINYA

last: TANAKA

address: 3-1-1, maidashi, Higashi-ku

institute: Kyushu University

summary: We report the genome-wide accumulation of HDAC1, HDAC2 and H3K9/14Ac in B cells. We found that the binding of HDAC1 and HDAC2 was observed mainly on proximal promoters, suggesting a redundant role of these HDACs in transcriptional regulation. This study  provides a basis for the comprehensive understanding of Tet2/Tet3-HDACs-mediated B cell regulation.

overall_design: Examination of global binding of HDAC1/HDAC2 and H3K9/14Ac modification in control and Tet2/Tet3-deficient B cells

first: Shinya

last: Tanaka


title: Analysis of long noncoding RNAs in macrophages

city: Chiba

first: Ichiro

last: Manabe

address: 1-8-1 Inohana, Chuo

institute: Chiba University

overall_design: Refer to individual Series


title: Genome-wide mapping of gene expression in control and Tet2/Tet3-deficient B cell subsets

summary: We report the global gene expression in Tet2/Tet3-sufficient and -deficient B cell subsets. We found an alteration of multiple gene expressions in the absence of Tet2 and Tet3 in B cells. This study  provides a basis for the comprehensive understanding of Tet function in B cells.

overall_design: Examination of global gene expression in control and Tet2/Tet3-deficient B cell subsets

first: Wataru

last: Ise


title: FoxO1 Binding in Cardiac Hypertrophy

first: Jessica

last: Pfleger

address: 3500 North Broad Street

institute: Temple University

summary: Anti-FoxO1 chromatin immunoprecipitation-high throughput sequencing (ChIP-Seq) was performed on mouse heart tissue following 7 days vehicle treatment/sham-operation, isoproterenol injection (subcutaneous, 3mg/kg/day), or transverse aortic constriction (TAC). Pool of 3 hearts per condition.

overall_design: Mice were subjected to vehicle treatment/sham operation, isoproterenol treatment (subcutaneous, 3 mg/kg/day) or transverse aortic constriction (TAC) (n=3, pool per condition). Hearts were dissected, snap frozen,  and sent to Active Motif for anti-FoxO1 ChIP-Seq.

first: Walter

last: Koch


title: Transcriptomic analysis of CD34+ progenior cells from normal bone marrow controls and chronic phase chronic myeloid leukemia

city: Singapore

first: Jia

address: 8 College Road

country: Singapore

institute: Duke-NUS

summary: Using RNA-sequencing, we report the differences in gene expression between healthy bone marrow and chronic phase CML progenitor cells

overall_design: CD34+ cells which had been isolated from human peripheral blood, harvested for RNA following a 96 h culture in Stempro media supplemented with human cytokines

first: Joanna

middle: R

last: Sinnakannu

first: Li

last: Jia


title: Genome-wide analysis of methylated DNA in control and Tet2/Tet3-deficient B cells

type: Methylation profiling by high throughput sequencing

summary: We report the global DNA methylation status in B cells. We found that DNA demethylation occurred around gene promoters and Tet-dependent demethylation sites at the genome-wide manner. This study  provides a basis for the comprehensive understanding of role of Tet2 and Tet3 in DNA demethylation-dependent regulation of transcription in B cells.

overall_design: Examination of global DNA methylation status in control and Tet2/Tet3-deficient B cells

first: Fumihito

last: Miura


title: Analysis of lncRNAs in macrophages

summary: We identified long noncoding RNAs (lncRNAs) expressed in macrophages and characterized one lncRNA, designated lncFAO. To analyze the function of lncFAO, effects of knockdown and knockout of lncFAO were analyzed by RNA-seq.

overall_design: [1] RNA-seq profiling of effects of the knockdown and deletion of lncFAO. [2] RNA-seq profiling of time-course effects of deletion of lncFAO.

first: Yukiteru

last: Nakayama


title: Transcriptome sequencing of the developing internode and ligular region of maize mutant Sdw3

city: Beijing

first: Hongchao

address: No.2 Yuanmingyuan West Road

department: Crop Genetics and Breeding

institute: China Agricultural University

summary: The reduced plant height and enlarged leaf angle of Sdw3 are mainly attributed to a reduction in longitudinal cell elongation in the internode and an increase in the auricle. To investigate the transcriptome changes during internode and auricle development in Sdw3 versus N18, we performed RNA sequencing analysis.

overall_design: Examination the differentially expressed genes in the developing internode and ligular region between Sdw3 and N18

last: Hongchao


title: ChIP-seq profiling of macropahge response to LPS

summary: To analyze epigenetic profiles of lncRAN loci, we perfomed ChIP-seq of H3K4me3 and PU.1 in bone marrow-derived macrophages.

overall_design: ChIP-seq profiling of LPS response in  histone modifications in macrophages.


title: RNA sequencing of wildtype and PHOSPHO1 knockout brown fat

city: Cambridge

first: Nai-Jia

last: Huang

state: MA

address: 455 Main Street

institute: Whitehead Institute

summary: We report the RNA expression of the mature brown fat from 6 week old wild type (WT) and PHOSPHO1 knockout (KO) mice. Mature brown fat was isolated from brown adipose tissue after collagenase digestion.  Increased expression of mitochondrial genes is found in KO brown fat.

overall_design: Examine gene expression of two type of cells (WT and KO). Each sample is from 3 mice and each type of cells has triplicates (WT1-3 and KO1-3).

first: Mengxi

last: Jiang

first: Harvey

last: Lodish


title: Transcriptomic analysis of SRSF1 overexpression and imatinib treatment in K562 CML cell lines

last: Li

summary: Using RNA-sequencing, we report the effects of overexpressing the proto-oncogene SRSF1 in K562 cells on gene expression and alternative splicing. We found that overexpressing SRSF1 antagonized the gene expression changes brought about by imatinib treatment.

overall_design: K562 cells stably expressing either the empty vector or SRSF1 gene. Treated with 0.5uM imatinib for 48 h.


title: The role of fibronectin in the post natal lens

city: Newark

first: Melinda

middle: K.

last: Duncan

state: DE

address: 327 Wolf Hall

department: Biological Sciences

institute: University of Delaware

summary: This trancriptome analysis reports genes that are differentially expressed upon deletion of the fibronectin gene from the lens during late embryonic development.

overall_design: Lenses were isolated from two month Wild Type (WT) and Fibronectin Conditional Knockout mice (FNcKO) by microdissection (2 lenses/sample, three biological replicates/genotype) and total RNA was isolated. cDNA libraries were constructed using SMARTer Stranded Total RNA-Seq - Pico Input Mammalian, and sequenced using an Illumina NextSeq 500 (DNA Link USA, Inc) in an attempt to undestand the role of fibronectin in the post natal lens.

first: Mahbubul

middle: H

last: Shihan

middle: K


title: Designing of Lactococcus lactis platform for isobutanol production using multiple rounds of adaptive laboratory evolution

city: NewDelhi

first: Krishna

middle: Jyoti

last: Mukherjee

state: Delhi

address: Behind administration building

department: SBT

institute: JNU

summary: This work was primarily focused on removing the main bottleneck for isobutanol production which is the toxicity of isobutanol towards its host and the major reason for its low-level production. Recently, there have been many reports where people have tried various strategies including continuous in-situ product removal from the bioreactor which led to a significant increase in the final product titers. Clearly, it is the intrinsic tolerance levels of the host which decides the end product titers. Importantly, if the host microbe can originally tolerate higher concentrations of toxin (here isobutanol) then it is likely to have a better potential for further improvement of tolerance levels. In our work, we tried to enhance the isobutanol tolerance of wild type NZ9000 using continuous culture. We used the principle of adaptive laboratory evolution to enhance the natural tolerance ability (0.8% isobutanol) of the wild type strain. The strain was cultivated for more than 60 days (>250 generations), while increasing the selection pressure (here isobutanol) gradually in the feed. This finally led to the strain that showed exceptionally higher tolerance (4%) for isobutanol. Transcriptomic analysis also showed fluctuations in gene expression levels from a wide range of categories, precluding any attempt to reverse engineer this phenotype.

overall_design: Analysing the transcriptome of wild type (WT) and 4% isobutanol tolerant strain grown in absence of isobutanol (4B0) or in presence of 4% isobutanol (4B4). One biological replicate of wild type (WTD) was also included in the analysis.

first: Jaya

last: Gupta

first: Sagar

last: Thapa

first: Madhulika

last: Verma

first: K


title: RNA-sequencing on sorted tumor-associated macrophages from vehicle or JHU083 pro-drug of 6-Diazo-5-oxo-L-norleucine (glutamine antagonist) treated 4T1 (breast cancer) tumor bearing mice

city: Baltimore

first: Jonathan

middle: D.

last: Powell

state: MD

address: 1650 Orleans Street

department: Oncology

institute: Johns Hopkins University

summary: RNA-sequencing was performed on sorted tumor-associated macrophages (CD45+7AAD-CD11b+F4/80+CD8-Ly6C-Ly6G-) from 4T1 tumor (murine breast cancer) bearig mice with or without JHU083, pro-drug of 6-Diazo-5-oxo-L-norleucine (glutamine antagonist) treatment for expression profiling

overall_design: Expression profiling by high throughput sequencing (Illumina NextSeq 500/550  V2 - PE 150 Cycle) on sorted tumor associated macrophages

first: Maureen

last: Horton

first: Minhee

last: Oh


title: Lamina Associated Domains in MEFs depleted of specific lamin isotypes

status: Public on Jul 07 2020

first: Karen

last: Reddy

address: 855 North Wolfe Street

department: Center for Epigenetics/Biological Chemistry

summary:
Purpose: To compare the effects on Lamina Associated Domains (LADs) of shRNA treatment against lamin isotypes.
Results:  Using an optimized data analysis workflow (LADetector, available at https://github.com/thereddylab/LADetector), We found near identical sequences within the genome-wide maps indicating that ensemble methods are not effective for measuring random perturbations - perturbations that vary from cell to cell.

overall_design: LAD profiles, of MEFs, corresponding to LmnB1 at the nuclear periphery were generated following the DamID protocol (L.Guelen et al, Nature 2008), library randomization and sequencing preparation using the NEBNext Ultra DNA library prep kit for Illumina (NEB, E7370S) and sequenced on the Illumina HiSeq 2500.

first: Xianrong

last: Wong


title: Macrophage response to extracellular ADP stimulation

city: Shanghai

first: Xiaoyu

last: Zhang

address: 500 Dongchuan Road

department: School of Life Sciences

institute: East China Normal University

summary: The gene expression analysis of bone marrow-derived macrophages (BMDM) treated with 100uM ADP was employed. Extracellular ADP is a danger signal that induces immune responses. Results provide insight into macrophage functions altered in ADP stimulation.

overall_design: Extracellular ADP induced gene expression in BMDMs was measured at 6 hours after exposure to dose of 100uM ADP. Three independent experiments were performed at each time using different donors for each experiment.

first: Bing

last: Du


title: ChIP-seq for two forms of Gcr1, during exponential phase and diauxic shift

city: seoul

first: seungwoo

last: cha

address: 1 Gwanak-ro, Gwanak-gu

department: School of Chemical and Biological Engineering

institute: Seoul National University

summary: Gcr1, the most important transcription factor for glycolytic genes in Saccharomyces cerevisiae, was recently revealed to have two isoforms, Gcr1(U) and Gcr1(S), produced from unspliced and spliced transcripts, respectively. We generated strains expressing only Gcr1(U) or Gcr1(S) form using the CRISPR/Cas9 system, and added a TAP tag protein to the Gcr1(U) and Gcr1(S), using HIS3MX6 marker system. We conducted ChIP-seq for both strains during the glycolytic phase or after the diauxic shift.

overall_design: The data contains the result of ChIP-seq for TAP-tagged Gcr1 transcription factor of S. cerevisiae, which is known to have two forms in accordance with the intron processing (Gcr1(U) and Gcr1(S)).  Duplicated ChIP-seq sampling was conducted at two time points; during exponential phase (6 hr after incubation) and after diauxic shift (12 hr after incubation), for Gcr1(U)-TAP and Gcr1(S)-TAP each.

first: Ji-Sook

last: Hahn

first: Seungwoo

last: Cha

first: Chang

middle: P

last: Hong


title: ChIP-seq and RNA-seq for two forms of Gcr1, during exponential phase and diauxic shift

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


title: RNA-seq for two forms of Gcr1, during exponential phase and diauxic shift

summary: Gcr1, the most important transcription factor for glycolytic genes in Saccharomyces cerevisiae, was recently revealed to have two isoforms, Gcr1(U) and Gcr1(S), produced from unspliced and spliced transcripts, respectively. We generated strains expressing only Gcr1(U) or Gcr1(S) form using the CRISPR/Cas9 system, and performed RNA-seq for the two strains. Since Gcr1 works as a glycolytic gene transcription factor, we extracted whole RNA at the exponential phase (6 hrs after incubation) and the diauxic shift (12 hrs after incubation).

overall_design: The data contains the result of RNA-seq Gcr1 transcription factor of S. cerevisiae, which is known to have two forms in accordance with the intron processing (Gcr1(U) and Gcr1(S)).  Duplicated RNA-seq sampling was conducted at two time points; during exponential phase (6 hr after incubation) and after diauxic shift (12 hr after incubation), for Gcr1(U) and Gcr1(S) each.


title: Single cell transcriptomic analysis of KLB expressing cells in the hypothalamus

city: Iowa City

first: Kyle

middle: Harrington

last: Flippo

state: IA

address: 169 Newton Road, 3320 PBDB

department: Neuroscience and Pharmacology

institute: University of Iowa

summary: Using a custom primer set for cDNA library construction we performed single cell RNA sequencing on FACs sorted tdTomato positive cells from single cell suspensions prepared from the hypothalamus of mice expressing cre-recombinase under the endogenus KLB promoter that were crossed with tdTomato reporter mice (Ai14). We then performed unbiased clustering analysis on 1,904 cells using the single cell transcriptomes to identify 12 different cell types which express KLB in the hypothalamus including neuronal and non-neuronal cell types. This information was then used to delete KLB in specific cell populations to determine the direct target of FGF21 in the brain responsible for suppression of sucrose preference.

first: Matthew

last: Potthoff

first: Sharon

middle: O

last: Jensen-Cody


title: Expression analysis of WT or Card14E138A ears 5 days and 1 month after injecton of tamoxifen

city: London

first: Steve

last: Ley

address: Pond Street

department: Institute of Immunity & Inflammation

institute: University College London

summary: The inducible nature of our knock-in mouse strain allowed us to determine the immediate effects of dysregulated CARD14 signalling and compare them to the long term effects of its expression. CARD14E138A-induced skin inflammation and systemic disease were independent of adaptive immune cells, substantially reduced by antibody blocking of TNF and induced by CARD14E138A signaling only in keratinocytes.

overall_design: To investigate how psoriasis-associated mutations in CARD14 induce psoriasis, we have generated a Card14LSL-E138A knock-in mouse that allows conditional expression of Card14E138A from the endogenous mouse Card14 locus via tamoxifen activation of CreERT2. The highly penetrant CARD14E138A psoriasis-associated mutation was first identified in a child suffering from GPP and induces CARD14 to constitutively activate NF-kB. The new Card14LSL-E138A strain allowed the immediate and chronic effects of CARD14E138A signaling to be studied, as well as the cell types involved.

first: Joan

last: Manils

first: Stefan

last: Boeing

first: Louise

last: Webb