title: Human Regulatory T cells from Umbilical Cord Blood Display Increased Repertoire Diversity and Lineage Stability Relative to Adult Peripheral Blood

status: Public on Mar 31 2020

city: Gainesville

first: Todd

last: Brusko

state: FL

address: 1275 Center Drive

institute: University of Florida

summary: Single-cell RNA and TCR sequencing data from sorted Tregs in umbilical cord blood and adult peripheral blood, both pre- and post-expansion.

overall_design: Single-cell profiles of Tregs (gene expression and VDJ) from umbilical cord blood and adult peripheral blood were compared both pre- and post-expansion.

first: Keshav

last: Motwani

first: Leeana

last: Peters

first: William

last: Vliegen

first: Ahmed

middle: G

last: El-sayed

first: Howard

middle: R

last: Seay

first: M

last: Lopez

first: Henry

last: Baker

first: Amanda

middle: L

last: Posgai

first: Maigan

first: Daniel

last: Perry

first: Rhonda

last: Bacher

first: Joseph

last: Larkin

last: Haller


title: Genome-wide survey of adjacent gene rearrangements in breast cancer identifies triple-negative specific BCL2L14-ETV6 fusions

status: Public on Mar 28 2020

city: Pittsburgh

first: Xiaosong

last: Wang

state: Pennsylvania

address: 5150 Centre Ave

department: Pathology

country: USA

institute: University of Pittsburgh

type: Expression profiling by high throughput sequencing

summary:
Purpose: We investigated the function of overexpressed BCL2L14-ETV6 fusion variants in triple-negative breast cancer using high-throughput mRNA sequencing (RNA-Seq) analysis in BT20 human basal-like breast cancer cell line.
Methods: The BCL2L14-ETV6 fusion variants or wildtype ETV6 cDNA containing the full-length ORFs were subcloned into the lentiviral pLenti7.3 vector, and later transduced into the BT20 cell line.  BT20 cells were cultured in EMEM (ATCC) with 10 % fetal bovine serum (Hyclone). Total RNA was extracted from cells in individual confluent 10 cm dish, using the standard procedure of Qiagen RNeasy kit. The NovaSeq 6000 library for DNA sequencing was prepared using TruSeq Stranded mRNA Library Prep Kit (Illumina) following the protocol provided by the manufacturer. The final libraries were normalized by quantification with LightCycler 480 II (Roche Applied Science, Indianapolis, IN, USA) and qualification with Bioanalyzer (Agilent, Palo Alto, CA, USA). The final loading concentration was adjusted to 10 pM following the NovaSeq 6000 loading protocol. The NovaSeq 6000 S2 Reagent Kit (Illumina) was used for paired-end reads (2×150 bp) sequencing reactions. Sequencing data was given as raw data with a Phred Q30 score of 80 or better.
Results: Confirming the overexpression of BCL2L14-ETV6 fusion variants, the reads that match to partial of BCL2L14 and ETV6 mRNA transcripts were 32~256 fold higher in the stable BT20 cell lines expressing BCL2L14-ETV6 fusion, compared to the cells the express the vector control. We found some key genes in cell migration and invasion are up-regulated in these stable BT20 cells compared with the cells the express the vector control and the wildtype ETV6.
Conclusions: BCL2L14-ETV6 fusions endow enhanced cell migration and invasion in breast cancer.

overall_design: We generated the stable BT20 cell models by transduction of the lentivirus containing either the pLenti7.3 vector control expresssing the lacZ gene, wildtype ETV6 cDNA, or three BCL2L14-ETV6 fusion variants E2E3 (BCL2L14-Exon2_ETV6-Exon3), E4E3 (BCL2L14-Exon4_ETV6-Exon3) and E4E2 (BCL2L14-Exon4_ETV6-Exon2). Each group was triplicated in the RNAseq expriments.

first: Yiheng

last: Hu

first: Sanghoon

last: Lee

first: Suet Kee

last: Loo


title: Novel Role of JAC1 in Influencing Photosynthesis, Stomatal Conductance, and Photooxidative Stress Signalling Pathway in Arabidopsis thaliana

status: Public on Mar 26 2020

city: Gent

first: Patrick

last: Willems

address: Technologiepark 927

department: PSB

country: Belgium

institute: Ghent University

summary: Regulation of light absorption under variable light conditions is essential to optimize photosynthetic and acclimatory processes in plants. Light energy absorbed in excess has a damaging effect on chloroplasts and can lead to cell death. Therefore, plants have evolved protective mechanisms against excess excitation energy that include chloroplast accumulation and avoidance responses. One of the proteins involved in facilitating chloroplast movements in Arabidopsis thaliana is the J domain-containing protein required for chloroplast accumulation response 1 (JAC1). The function of JAC1 relates to the chloroplast actin filaments appearance and disappearance. So far, the role of JAC1 was studied mainly in terms of chloroplasts photorelocation. Here, we demonstrate that the function of JAC1 is more complex, since it influences the composition of photosynthetic pigments, the efficiency of photosynthesis, and the CO2 uptake rate. JAC1 has positive effect on water use efficiency (WUE) by reducing stomatal aperture and water vapor conductance. Importantly, we show that the stomatal aperture regulation is genetically coupled with JAC1 activity. In addition, our data demonstrate that JAC1 is involved in the fine-tuning of H2O2 foliar levels, antioxidant enzymes activities and cell death after UV-C photooxidative stress. This work uncovers a novel function for JAC1 in affecting photosynthesis, CO2 uptake, and photooxidative stress responses.

overall_design: Two genotypes (wild-type, jac1) x two conditions (non-treated and UV-treated)

first: Weronika

last: Czarnocka

first: Frank

last: Van Breusegem

first: Stanislaw

last: Karpinski


title: Proteosomal degradation of NSD2 by BRCA1 promotes leukemia cell differentiation

status: Public on Mar 25 2020

city: seoul

first: JinWoo

last: Park

state: Soul-t'ukpyolsi

address: Department of life science, college of nature science

country: South Korea

institute: Chung-Ang Univ

summary:
Inhibiton of NSD2 by shRNA induces K562 differentiation via increasing erythroid specfic lineage factors
The human myelogenous leukemic cell line, K562 undergoes erythroid differentiation by exposure to hemin. Here, we uncovered NSD2 as an innate erythroid differentiation-related factor through the genome-wide CRISPR library screening and explored the regulatory role of NSD2 during myeloid leukemia cell differentiation. We found that NSD2 stability was disrupted by poly-ubiquitination in differentiated K562 cells. Proteomic analysis revealed interaction between NSD2 and an E3 ubiquitin ligase, BRCA1 which ubiquitylates NSD K292 residue. Depletion of BRCA1 stabilized NSD2 protein and suppressed K562 cell differentiation. Furthermore, BRCA1 protein level was decreased in bone marrow tumor, while NSD2 level was elevated. Surprisingly, among BRCA1 mutation(s) discovered in lymphoma patients, BRCA1 K1183R prevented its translocation into the nucleus and did not reduce NSD2 protein level in hemin-treated K562 cells and eventually disrupted cell differentiation. Our results indicated that regulation of NSD2 stability by BRCA1-mediated ubiquitination as a potential therapeutic target process in multiple myeloma.

overall_design: Differential expression analysis of K562 cells which are generated with shNSD2 or shNC lentivirus

first: Jin

middle: W

first: Sangboem

last: Seo


title: Macrophage-derived extracellular vesicles regulate concanavalin A-induced hepatitis by suppressing macrophage cytokine production.

status: Public on Mar 20 2020

city: Nagoya

first: Reo

last: Kawata

address: 65 Tsurumai-cho, Showa-ku, Nagoya, Japan

department: Drug Safety Sciences

country: Japan

institute: Nagoya university

type: Non-coding RNA profiling by high throughput sequencing

summary: Acute liver failure is a clinical syndrome of severe hepatic dysfunction. Immune cells play an important role in the failure. In recent years, the immunoregulatory function of extracellular vesicles (EVs) has been reported; therefore, it is inferred that EVs have some role in an immune mediated liver injury. In this study, we investigated the immunoregulatory function of EVs in a concanavalin A (Con A)-induced liver injury. The mouse model was prepared by a single intravenous administration of 15 mg/kg Con A, in which there was a significant increase in serum EVs number. In in vitro study, the secreted EVs number was also significantly increased in Con A-treated RAW264.7, a mouse macrophage cell line, but not Hepa1-6, a mouse hepatoma cell line. In in vitro EVs treatment study, the EVs from Con A-treated mice serum and Con A-treated RAW264.7 suppressed the inflammatory cytokines production in Con A-stimulated RAW264.7. miRNA sequencing analysis showed that mmu-miR-122-5p and mmu-miR-148a-3p were commonly increased in these EVs and the EVs-treated cells. The enriched pathways in the miRNAs predicted target genes included the inflammatory response pathways. mRNA levels of the target genes in the pathways (mitogen-activated protein kinase, Phosphoinositide 3-kinase/Akt and Rho/Rho associated coiled-coil containing protein kinase pathways) were decreased in the EVs-treated cells. In in vivo RNA interference study, knock down of liver RAB27A, an EVs secretion regulator, significantly exacerbated the Con A-induced liver injury. These data suggest that macrophage-derived EVs play an important role in a Con A-induced liver injury through the immunoregulation.

overall_design: miRNA profiles in RAW264.7 cells and extracellular vesicles from mouse serum or RAW264.7 culture supernatant were analyzed with MiSeq system (Illumina).

first: R

first: S

last: Oda

first: T

last: Yokoi


title: Gene signatures of rifampin, rifabutin an rifapentine anti-tuberculosis drugs in human primary hepatocytes.

city: Omaha

first: SHETTY RAVI

last: DYAVAR

state: NE

address: 4040 EMILE ST

department: Pharmacy Practice and Science

institute: University of Nebraska Medical Center

summary: We report the application of  next generation sequencing technology for high-throughput profiling of total RNA to determine the expression of all genes expressed in human primary hepatocytes derived from three healthy (drug/tobacco/alcohol free) volunteers in response to anti-tuberculosis antibiotics, including, rifampin, rifabutin and rifapentine through comparison with gene profiles of vehicle (methanol) treated and untreated cells. We determined the response of over 22,000 genes expressed in human primary hepatocytes following rifampin, rifabutin and rifapentine treatment for 72h. We found that several drug metabolizing enzymes, including cytochrome P450 3A4 and drug transporters are differentially expressed in human primary hepatocytes in response to rifamycin antibiotics.  We utilized the information generated with differential gene expression study to determine  interaction of rifamyicn antibiotics with antiviral, antibacterial, antifungal agents and other drugs used to treat several ailments in tuberculosis patients. This study provides a comprehensive profiles of genes expressed in response to rifamycin antibiotics towards characterization of their drug interactions with the drugs that are combined to treat various viral, bacterial, fungal and other diseases, including cancer.

overall_design: Profiling the genes expressed in human primary hepatocytes in response to rifampin, rifabutin and rifapentine anti-tuberculosis antibiotics.

first: Shetty


title: Arabidopsis thaliana embryos: wild type vs cuc1 cuc2 double mutant

status: Public on Mar 19 2020

city: Kumamoto

first: Mitsuhiro

last: Aida

address: 2-39-1 Kurokami, Chuo-ku

institute: Kumamoto University

summary: Transcriptional profiling of Arabidopsis embryos comparing cuc1-1 cuc2-1 mutant (test) and wild type Ler (reference). Goal was to screen genes regulated by CUC1 and CUC2 transcription factors, which are required for shoot meristem formation and cotyledon separation.

overall_design: Two-condition experiment, wild type (Ler) vs. cuc1 cuc2 double mutant embryos. No biological replicates. Technical replicates: 2 (Dye swap).

first: Yuka

last: Tsubakimoto


title: Systems analysis of insulin and IGF1 receptors networks in breast cancer cells identifies commonalities and divergences in expression patterns

status: Public on Mar 18 2020

city: Tel Aviv

first: Metsada

last: Pasmanik-Chor

address: Ramat Aviv

department: Biology

country: Israel

institute: Tel Aviv University

summary:
Commonalities and dissimilarities between the IGF1R and INSR pathways
Insulin and insulin-like growth factor-1 (IGF1), acting respectively via the insulin (INSR) and IGF1 (IGF1R) receptors, play key developmental and metabolic roles throughout life. In addition, both signaling pathways fulfill important roles in cancer initiation and progression. The inherent complexity of the INSR/IGF1R pathways, along with the well documented cross-talk between insulin-like ligands and receptors, translated into a disappointingly slow pace in the development of INSR/IGF1R-directed therapies in oncology. The present study was aimed at identifying mechanistic differences between INSR and IGF1R using a recently developed bioinformatics tool, the Biological Network Simulator (BioNSi). This application allows to import and merge multiple pathways and interaction information from the KEGG database into a single network representation. The BioNsi network simulation tool allowed us to exploit the availability of gene expression data derived from breast cancer cell lines with specific disruptions of the INSR or IGF1R genes in order to investigate potential differences in protein expression that might be linked to biological attributes of the specific receptor networks. Modeling-generated information was corroborated by experimental and biological assays. Our simulation analysis identified a number of commonalities and, most importantly, dissimilarities between the IGF1R and INSR pathways that were experimentally validated and that might help explain the basis for the biological differences between these networks.

overall_design: MCF7 cells expression as baseline for a network simulation study

first: Rive

last: Sarfstein

first: Adva

last: Yeheskel

first: Tali

last: Sinai-Livne

first: Haim

last: Werner


title: RNA-seq Reveals Differences in Expressed Tumor Mutation Burden in Colorectal and Endometrial Cancer With and Without Defective DNA Mismatch Repair

status: Public on Mar 13 2020

city: Rochester

first: Asha

last: Nair

address: 200 1ST ST SW

institute: Mayo Clinic

summary: Tumor mutation burden (TMB) is an evolving biomarker for predicting response to immune checkpoint inhibitors (ICI’s). The goal of this study was to evaluate the use of RNA-seq for determining TMB in patients with defective DNA MMR (dMMR) due to MMR mutations or MLH1 promoter hypermethylation (HM) and tumors without dMMR.  We included tumors and paired normal tissue from 58 patients for TMB analysis using RNA-seq.  Forty-six tumors were MSI-H (29 with a DNA MMR germline mutation and 17 with MLH1 promoter HM) and 12 were MSS.  TMB was measured using the expressed somatic nucleotide variants (eTMB). We developed a method that leverages mutational signatures to remove FFPE derived artifact from total eTMB and thereby accurately measure the eTMB. There was a significant difference in the eTMB observed between MSI-H and MSS cases; MSI-H cases had a median of 27.3 mutations/Mb compared to 6.7 mutations/Mb for MSS cases (p=3.5e-9). Among tumors with dMMR the tumors with DNA MMR mutations had a significantly higher eTMB (p=0.037) than tumors with MLH1 promoter HM: a median of 28.1 mutations/Mb vs. a median of 17.5 mutations/Mb. Furthermore, through multivariate analysis we found that MSI status, tissue type (endometrial or colorectal) and patient ages are significantly associated with eTMB. These results demonstrate that RNA-seq analysis can be used to measure eTMB in FFPE tumor specimens. Further studies are needed to determine how eTMB as determined by RNA-seq compares to TMB as determined by DNA-based NGS assays

overall_design: RNA-seq was perfomed on 91 tumors, with 19 MSS, 19 MSI-H cases due to HM and the remaining 53 were putative Lynch Syndrome cases. For 85 out of the 91 tumors, RNA-seq was performed adjacent normal tissue

first: Kevin

last: Halling

first: Margaret

last: Diguardo


title: Microbes modulate sympathetic neurons via a gut-brain circuit

city: New York

first: Paul

middle: Andrew

last: Muller

state: NY

address: 1230 York Avenue

institute: The Rockefeller University

summary: Gut-brain connections monitor the intestinal tissue and its microbial and dietary content1, regulating both intestinal physiological functions such as nutrient absorption and motility2,3, and brain–wired feeding behaviour2. It is therefore plausible that circuits exist to detect gut microbes and relay this information to central nervous system (CNS) areas that, in turn, regulate gut physiology4. We characterized the influence of the microbiota on enteric–associated neurons (EAN) by combining gnotobiotic mouse models with transcriptomics, circuit–tracing methods, and functional manipulation. We found that the gut microbiome modulates gut–extrinsic sympathetic neurons; while microbiota depletion led to increased cFos expression, colonization of germ-free mice with short-chain fatty acid–producing bacteria suppressed cFos expression in the gut sympathetic ganglia. Chemogenetic manipulations, translational profiling, and anterograde tracing identified a subset of distal intestine-projecting vagal neurons positioned to play an afferent role in microbiota–mediated modulation of gut sympathetic neurons. Retrograde polysynaptic neuronal tracing from the intestinal wall identified brainstem sensory nuclei activated during microbial depletion, as well as efferent sympathetic premotor glutamatergic neurons that regulate gastrointestinal transit. These results reveal microbiota–dependent control of gut extrinsic sympathetic activation through a gut-brain circuit.

overall_design:
Actively translated mRNA profiles from immunoprecipitated ribosome-bound mRNA from the nodose ganglion,  dorsal root ganglion, and celiac superior mesentetic of Snap25:RiboTag specific pathogen free or germ free mice were prepared by deep sequencing on an Illumina NextSeq.
Actively translated mRNA profiles from immunoprecipitated ribosome-bound  mRNA from the nodose ganglion of SNS:RiboTag, Nav1.8:RiboTag, and Advillin:RiboTag mice were prepared by deep sequencing on an Illumina NextSeq
16S RNA profiles, from cecal samples of C57BL6/J mice given streptomycin or PBS, were prepared for deep sequencing on an Illumina MiSeq.

middle: A

first: Marc

last: Schneeberger

first: Fanny

last: Matheis

first: Putianqi

last: Wang

first: Zachary

middle: J

last: Kerner

first: Anoj

last: Ilanges

first: Kyle

last: Pellegrino

first: Josefina

last: del Marmol

first: Tiago

last: Bruno Rezende de Castro

first: Matthew

last: Perkins

first: Wenfei

last: Han

first: Ivan

last: de Araujo

first: Daniel

last: Mucida


title: Epigenetic and transcriptional changes in aging mouse rod photoreceptors [CUT&RUN]

status: Public on Mar 10 2020

city: Bethesda

last: Batz

state: MD

address: 6 Center Dr Bldg 6, Rm 303

department: NEI

institute: NIH

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Aging-associated functional decline and disease susceptibility are believed to be mediated, at least in part, through alterations in the epigenome. To explore epigenetic changes that might influence visual function with advanced age, we performed whole genome bisulfite sequencing of purified mouse rod photoreceptors at four different ages and identified 2054 genomic regions that gain or lose DNA methylation. Differentially methylated regions (DMRs) clustered at chromosomal hotspots, especially on Chromosome 10 that included a longevity interactome.  DMRs were preferentially detected at an early stage of aging in long neuronal genes and in rod-specific regulatory regions containing open chromatin domains and H3K27 acetylation. Integration of methylome to age-related transcriptome changes, chromatin signatures and first order protein-protein interactions uncovered an enrichment of DMRs in pathways associated with aging, longevity, synaptic function, and energy homeostasis. In concordance, we detected reduced mitochondrial maximum reserve capacity with retinal age in ex vivo assays. Our study reveals age-dependent genomic and chromatin features susceptible to DNA methylation changes in rod photoreceptors and identifies associations with established and cell type-specific pathways altered in aging.

overall_design: Flow-sorted rod photoreceptors from 3M male mice (H3K27ac: n = 4, H3K27me3: n = 6) were cryopreserved in a solution of HBSS containing 10% DMSO and slowly frozen using a Mr.FrostyTM container (Invitrogen, CA, USA). CUT&RUN was performed as previously described (Skene and Henikoff 2017) using 200-300,000 cells per experiment.

first: X

last: Corso-Díaz

first: C

last: Jaeger

first: M

last: Brooks

first: J

last: Gentry

first: R

last: Rebernick

first: F

last: van Asten

first: K

last: Kooragayala

first: L

last: Gieser

first: A

middle: K

last: Mondal

first: T

last: Cogliati

last: Swaroop


title: Clinical significance of recurrent copy number abnormalities revealed by SNP array in childhood T-cell acute lymphoblastic leukemia

status: Public on Mar 24 2020

city: Lublin

first: Monika

last: Szelest

address: ul. Antoniego Gębali 6

department: Laboratory of Genetic Diagnostics

country: Poland

institute: Medical University of Lublin

summary: T-cell acute lymphoblastic leukemia (T-ALL) is a genetically highly heterogeneous disease, and numerous genetic aberrations in the leukemic genome are responsible for the biological and clinical differences among particular ALL subtypes. However, there is limited knowledge about the association of whole genome copy number abnormalities (CNAs) in childhood T-cell ALL with the course of leukemia and outcome. The aim of study was identification the pattern of whole genome CNAs in 86 newly diagnosed childhood T-ALL using a high-density single-nucleotide polymorphism (SNP) array.A series of bone marrow aspirates from 86 children with newly diagnosed T-ALL were analysed prior to any oncological treatment.

overall_design: The researched material was the genomic DNA extracted from bone marrow samples using the QIAamp DNA Blood Mini Kit (Qiagen, Hilden, Germany). The median leukemic cell count in collected bone marrow at diagnosis assessed by flow-cytometry was 82.43% (range 30–100). The concentration and quality of isolates were determined by spectrophotometry (NanoDrop 8000, Thermo Fisher Scientific, Waltham, United States). The microarray analyses were performed with the use of a CytoScan HD array (2 670 000 markers, including 750 000 single-nucleotide polymorphism (SNP) and 1 900 000 nonpolymorphic copy number variant (CNV) markers) (Applied Biosystems part of Thermo Fisher Scientific, Waltham, United States). All laboratory procedures were carried out according to the manufacturers' protocols.In total, 250 ng of the genomic DNA was analyzed in accordance with the manufacturers' protocols. The study was based on an analysis of scanned data files that was generated with the Chromosome Analysis Suite v 3.3 (ChAS, Thermo Fisher Scientific, Waltham, MA). Furthermore, the copy numbers of altered regions (CNAs) were calculated, and the data were normalized to a reference model (Thermo Fisher Scientific) of baseline reference intensities, NA 33 (hg19/CRCh37). The copy number states (CNS) and their breakpoints were determined with the use of the hidden Markov model (HMM) software package. The threshold levels of log2 ratio ≥0.5 and ≤0.5 were used for the categorization of the altered chromosomal regions as CNV gains and losses, respectively. The identification of normal diploid markers in the cancer samples constituted an essential part of the algorithm, which was particularly significant in highly sample-induced aberrations. Furthermore, unaltered diploid markers were used for the calibration of signals, resulting in a log2 ratio of 0 (e.g., copy number 2). The algorithm also indicated that the identified unaltered diploid markers could correspond with CN=4. In such a case, the log2 ratio was readjusted, and the chromosomal ploidy of 4 was reported. The obtained data were analyzed based on two different criteria: genome-wide CNVs and leukemia-associated region/gene-specific CNAs (leukemia genes_all_20150505; Fullerton Overlap Map_hg19). The minimal number of probes was applied to determine the CNAs were 50 probes for duplication (gain) and 25 probes for deletion (loss). Copy number-neutral loss of heterozygosity is reported when greater than 3000 kbp in length. To further identify the genes involved in the CNVs, two databases were applied: the UCSC database (http://genome.ucsc.edu) and Ensemble (http://www.ensembl.org). For microarray results copy number polymorphisms were excluded based on comparison with the Database of Genomic Variants (http://projects. tcag.ca/variation/)

last: Lejman

last: Włodarczyk

last: Pastorczak


title: Epigenetic and transcriptional changes in aging mouse rod photoreceptors [WGBS]

first: Zachary

type: Methylation profiling by high throughput sequencing

overall_design: WGBS was performed on two to three biological replicates of mouse rod photoreceptors at each of four time points (3M, 12M, 18M, and 24M)

first: AK


title: Intergrative analysis of proteome and transcriptome dynamics during Bacillus subtilis spore revival

status: Public on Mar 04 2020

city: Amsterdam

first: Bhagyashree

last: Swarge

state: North Holland

address: Science park 908

country: Netherlands

institute: Swammerdam institute of life sciences, University of Amsterdam

summary: To gain insight into spore germination and outgrowth, the transcriptome changes during Bacillus subtilis spore conversion to vegetative cells were analyzed. The transcriptome analysis also allowed us to trace the different functional groups of genes expressed during this conversion. . Our analysis identified 34 abundant mRNA transcripts in the dormant spores, at least 31 of which were rapidly degraded after the phase transition and observed 3152 differentially expressed genes during spore germination and outgrowth.

overall_design: The RNA was isolated from spores harvested at t = - 30 min for dormant spores, during heat activation t = - 15 min and after heat activation and adding germinants at t= 0, and during germination and outgrowth at t = 30, 60, 90, 180 and 330 min. All the samples except t = 15 and 150 were analysed in triplicates.

first: Martijs

last: Jonker


title: YerA41, a Yersinia ruckeri bacteriophage: determination of non-sequencable bacteriophage genome and investigation of bacterial response to infection.

city: Helsinki

first: Päivi

last: Saavalainen

address: Haartmaninkatu 8

department: TRIMM

country: Finland

institute: University of Helsinki

summary: YerA41 is a myoviridae bacteriophage that was originally isolated due its ability to infect Yersinia ruckeri bacteria, the causative agent of enteric redmouth disease of salmonid fish. Several attempts to determine its genomic DNA sequence using traditional and next generation sequencing technologies failed, indicating that the phage genome is modified such way that it is an unsuitable template for PCR amplification and sequencing. To determine the YerA41 genome sequence we isolated RNA from phage-infected Y. ruckeri cells at different time points post-infection, and sequenced it. The host-genome specific reads were substracted and de novo assembly was performed on the unaligned reads.

overall_design: Total RNA from phage-infected Y. ruckeri cells was isolated at different time points post-infection and sequenced. The host-genome specific reads were substracted and de novo assembly was performed on the unaligned reads.

first: Katarzyna

last: Leskinen

first: Maria

last: Pajunen

first: Darren

last: Smith

first: Mikael

last: Skurnik


title: Epigenetic and transcriptional changes in aging mouse rod photoreceptors [RNA-seq]

last: Batz

overall_design: Total RNA from FACS-purified rod photoreceptors was extracted using TRIzol® (Invitrogen, Carlsbad, CA), treated with DNase and cleaned up using the MagMAX mirVana Total RNA Isolation Kit (Applied Biosystems, Foster City, CA) following the manufacturer’s instructions. Libraries were constructed with SMARTer Stranded Total RNA-Seq Kit v2 – Pico Input Mammalian (Takara Bio USA, Mountain View, CA) with 4 ng of RNA and 13 PCR cycles library amplification. Paired-end reads of 125 base pairs were obtained using the HiSeq 2500 platform (Illumina, San Diego, CA). Four biological replicates from each of the four studied time points (3M, 12M, 18M, and 24M) were sequenced.

first: X

last: Corso-Díaz

first: C

last: Jaeger

first: M

last: Brooks

first: J

last: Gentry

last: Rebernick

last: van Asten


title: TWIST1 direct targets during embryonic stem cell differentiation

status: Public on Mar 12 2020

city: WESTMEAD

first: PIERRE

last: OSTEIL

state: NSW

address: 214 Hawkesbury Road

department: Embryology

country: Australia

institute: CMRI

summary: Twist1 encodes a basic helix-loop-helix (bHLH) transcription factor and is a key regulator of craniofacial development. Mutations of TWIST1 gene in human are associated with Saethre-Chotzen syndrome (SCS), a developmental disorder characterized by facial and skull malformations, which are phenocopied by Twist1-null heterozygous mice. Mechanisms that dictate the tissue-specificity of Twist1 in regulating distinct transcriptional targets in different craniofacial cell types remain to be determined. Our work using mass-spectrometry and co-expression analysis in cell lines and embryonic head tissues has revealed that the most prevalent forms of TWIST1 were homodimers and heterodimers with E-proteins (TCF3,TCF4 and TCF12). RNA-seq analysis of embryoid bodies expressing tethered TWIST-E-protein dimers, and ChIP-seq profiling of TWIST1 genome-wide binding sites revealed  mechanisms of TWIST1 functional regulation. This study highlighted the pleiotropic roles of TWIST1 dimers in development and revealed a potential molecular mechanism underpinning Twist1-related developmental defects of craniofacial tissues.

overall_design: Refer to individual Series


title: Mycobacterium tuberculosis produces small noncoding RNAs that support mycobacterial survival in infected cells

status: Public on Mar 03 2020

city: Dallas

first: Igor

middle: M

last: Dozmorov

state: TX

address: 5323 Harry Hines Blvd

department: Immunology

institute: UT Southwestern Medical Center

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

sample_organism:
Mycobacterium tuberculosis
Homo sapiens

platform_organism:
Mycobacterium tuberculosis
Homo sapiens


title: Differences between colonial cells of Phaeocystis globosa from two Strains (GX and ST)

status: Public on Mar 01 2020

city: Guangzhou

first: dayong

last: liang

state: Guangdong

address: 604, Huangpu Avenue West, Tianhe District

country: China

institute: Jinan University

summary:
purpose:The large-scale reproduction of Phaeocystis globosa has caused serious damage to the marine ecosystem in the coastal waters of China. The outbreak of algae blooms depends on the competitive advantage of their heteromorphic life history: colonial formation is beneficial to resist zooplankton predation, and the single isolated cells can absorb nutrients rapidly.
methods:For RNA exaction, the biomass was resuspended in 2 mL RNA extraction buffer (1:1 mix of aqua-phenol and buffer L [0.5% SDS, 10 mM EDTA, 0.2 M sodium acetate (pH 5), and 1:100 β-mercaptoethanol)] and then incubated with DNase I (Takara, Japan) for 30 min at 37 °C to remove genomic DNA. RNA quality analysis, library construction, sequencing, data filtering and mapping were performed by the Novogene Bioinformatics Technology Co., Ltd. (Beijing, China).
results:Three biological replicates from GX-C and ST-C were ensured statistical comparability and reliability of data. Raw data ranged from 25, 608,632 to 35,516,726 reads per sample. After producing more than 24 million clean reads, removing low-quality sequences and adapter sequences. Additionally, 4386 genes were differentially expressed at statistically significant levels, which included 2268 up-regulated genes and 2118 down-regulated genes. Genes with significant differential expression were involved in several pathways, including starch and sucrose, phagosome, inositol phosphate metabolism, fatty acid degradation.
conclusions: In summary, we can find that colonial cells have stronger carbon fixation capacity. It is not used to synthesize fatty acids as reserves of energy, but to secrete EPS. The reduction of fatty acid makes P. globosa become “low-quality food” and the formation of colony from EPS reduces the chance of being ingestion by zooplankton.

overall_design: mRNA profiles of 10 days GX-C  and ST-C were generated by deep sequencing, in triplicate, using Illumina NovaSeq.

first: Dayong

last: Liang

first: Xiaodong

last: Wang

first: Yan

first: Yiping

last: Huo

first: Shaoshan

last: Li


title: Epigenetic and transcriptional changes in aging mouse rod photoreceptors

first: Zachary


title: Yap RNAseq

city: Baltimore

first: Liam

last: Chung

state: Maryland

address: 400 N Broadway FL5001

department: Oncology

institute: Johns Hopkins University

summary: Bulk YapKO RNAseq

overall_design: Bulk RNA seq on WT and YapKO cells extracted from spleen and lymph node

first: Andriana

last: Lebid


title: Mycobacterium tuberculosis produces small noncoding RNAs that support mycobacterial survival in infected cells [RNA-seq]

summary: The purpose of this study was to identify the role of sncRNA-1 using a gain of function approach. It was overexpressed in 3 clones and Total RNA was sequenced in 3 clones that had either the ctl vector or the sncRNA-1 vector. Differentially expressed genes were analyzed.

overall_design: Examination of all bacterial genes in 2 groups

first: Nicolai

last: van Oers

first: Fatma

last: Coskun


title: Topoisomerases modulate the timing of meiotic DNA breakage and chromosome morphogenesis in Saccharomyces cerevisiae

status: Public on Mar 06 2020

first: Andreas

last: Hochwagen

address: 1009 Silver Center 100 Washington Square East

institute: New York University

summary: During meiotic prophase, concurrent transcription, recombination, and chromosome synapsis place substantial topological strain on chromosomal DNA, but the role of topoisomerases in this context remains poorly defined. Here, we analyzed the roles topoisomerases I and II (Top1 and Top2) during meiotic prophase in Saccharomyces cerevisiae. We show that both topoisomerases accumulate primarily in promoter-containing intergenic regions of actively transcribing genes, including many meiotic double-strand break (DSB) hotspots. Despite the comparable binding patterns, top1 and top2 mutations have different effects on meiotic recombination. TOP1 disruption delays DSB induction and shortens the window of DSB accumulation by an unknown mechanism. By contrast, temperature-sensitive top2-1 mutants exhibit a marked delay in meiotic chromosome remodeling and elevated DSB signals on synapsed chromosomes. The problems in chromosome remodeling were linked to altered Top2 binding patterns rather than a loss of Top2 catalytic activity and stemmed from a defect in recruiting the chromosome remodeler Pch2/TRIP13 to synapsed chromosomes. No chromosomal defects were observed in the absence of TOP1. Our results imply independent roles for topoisomerases I and II in modulating meiotic chromosome structure and recombination.

overall_design: ChIP-seq analysis of Top1 and Top2, Mnase-seq, and RNA-seq in S. cerevisiae in meiosis. Each bedgraph file is the combined results from two biological replicates (each with a paired Input and ChIP sample).

first: Jonna

last: Heldrich

first: Luis

last: Vale Silva


title: PKI overexpression in HEK293 cells

first: Ramiro

last: Iglesias-Bartolome

address: 37 Convent Drive

department: LCMB

institute: NIH/NCI

summary: RNA sequencing (RNAseq) of unstimulated cells transiently expressing PKI1-24 or inPKI1-24 as a control.

overall_design: HEK293 cells where transduced in triplicate with plasmids expressing for GFP fusion proteins for PKI1-24 (PKI) or inPKI1-24 (inPKI) as a control and RNA was harvested after 48hs.

first: James

last: Hoy


title: Molecular characterization of ovarian serous cystadenomas and fibromas [Copy number]

city: East Melbourne

first: Kylie

last: Gorringe

state: Victoria

address: St Andrew's Pl

department: Research Division

institute: Peter MacCallum Cancer Centre

type:
Genome variation profiling by SNP array
SNP genotyping by SNP array

summary: This study aimed to characterize the molecular changes in benign serous ovarian tumors (cystadenomas and cystadenofibromas) in comparison to pure fibromas.

overall_design:
8 pure fibromas, 19 benign serous tumors and 3 normal ovaries. Integration of genomic copy number analysis (Affymetrix SNP6.0 arrays and Affymetrix OncoScan), exome sequencing (NimbleGen Roche v1 and 2) and expression analysis (Affymetrix Gene 1.0 ST).
SNP6 dataset: Normalized data and raw data are provided.
OncoScan dataset: Normalized data is provided. Raw data is retained by Affymetrix.

first: Ian

last: Campbell

first: Sally

last: Hunter


title: Molecular characterization of ovarian serous cystadenomas and fibromas

type:
Genome variation profiling by SNP array
SNP genotyping by SNP array
Expression profiling by array


title: Conversion of fibroblasts to functional Leydig like cells using defined small molecules

status: Public on Feb 26 2020

first: Chengxing

last: Zhou

address: Jinan University

summary: we report that fibroblasts can be efficiently and directly reprogrammed into Leydig-like cells by exposing to a combination of small molecules, Forskolin, 20α-hydroxycholesterol, luteinizing hormone (LH), and SB431542. The chemical compounds induced Leydig-like cells (CiLCs) expressed steroidogenic genes, had a global gene expression profile similar to that of Leydig cell, and acquired androgen synthesis capabilities.

overall_design: A total of 6 samples（2 CiLCs, 2 MEFs, 2 LCs） were tested using the BGISEQ platform for this project to prove that the CiLC resemble Leydig cell in genome-wide gene expression profile.

last: Yang


title: U1A iCLIP-seq (individual-nucleotide resolution UV crosslinking and immunoprecipitation coupled with RNA sequencing) analysis in HeLa cells

status: Public on Feb 28 2020

city: guangzhou

first: chengguo

last: yao

address: No. 74 zhongshan 2rd road

department: school of medicine

institute: sysu

summary: To better understand the mechanism of U1A functions in human cells, we performed U1A iCLIP-seq analysis in HeLa cells. iCLIP-seq is a previously well-established protocol that is believed to detect protein-RNA interaction at individual-nucleotide resolution. Indeed, successful completion of U1A iCLIP-seq has helped us to illuminate more detailed mechanism through which U1 snRNP prevents mRNA PCPA (premature cleavage and polyadenylation)

overall_design: HeLa cells were grown in 10 cm cell dishes, protein-RNA were crosslinked by UV light exposure. U1A-RNA were immunoprecipitated by anti-U1A antibody (santa cruz : sc-101149). Immunoprecipitated RNAs were further purified and prepared for RNA-seq library construction. For detailed protocol, please check the published protocol (Methods. 2014 Feb; 65(3): 274–287.)

first: Yanhui

last: Deng

first: Junjie

last: Shi

first: Yi

last: Ran

first: Andy

middle: P

last: Xiang

first: Chengguo

last: Yao


title: Mycobacterium tuberculosis produces small noncoding RNAs that support mycobacterial survival in infected cells [miRNA discovery screen]

status: Public on Feb 24 2020

first: Igor

last: Dozmorov

summary: The purpose of this study was to identify Mtb- and hsa-encoded miRNAs produced in infected macrophages. RNA from 9 THP-1 samples (3 were uninfected, 3 were infected with Mtb H37Rv for 3 days and 3 were infected with Mtb H37Rv for 6 days) was sequenced and miRNAs were detected.

overall_design: Examination of miRNAs in 3 groups

first: Nicolai

last: van Oers

last: Coskun


title: Molecular characterization of ovarian serous cystadenomas and fibromas [Expression]

overall_design:
8 pure fibromas, 19 benign serous tumors and 3 normal ovaries. Integration of genomic copy number analysis (Affymetrix SNP6.0 arrays and Affymetrix OncoScan), exome sequencing (NimbleGen Roche v1 and 2) and expression analysis (Affymetrix Gene 1.0 ST).
Expression dataset comprises: 8 pure fibromas, 15 benign serous tumors and 3 normal ovaries.


title: Maternal recognition of pregnancy in the horse: are microRNAs the secret messengers?

city: Gent

first: Laurentijn

last: Tilleman

address: Ottergemsesteenweg 460

institute: Ghent University


title: Maternal recognition of pregnancy in the horse: are microRNAs the secret messengers? [miRNA-seq]

summary: The signal for maternal recognition of pregnancy (MRP) has still not been identified in the horse. Endometrial biopsies, uterine fluid, embryonic tissues and yolk sac fluid were collected 13 days after ovulation during pregnant and control cycles from the same mares. Micro-RNA-Sequencing was performed on all collected samples and mRNA-Sequencing was conducted on the same endometrial and embryonic tissue samples

overall_design: miRNA-seq

first: Katrien

last: Smits

first: Yannick

last: Gansemans

first: Filip

last: Van Nieuwerburgh

first: Margot

last: Van De Velde

first: Ilse

last: Gerits

first: Cyriel

last: Ververs

first: Kim

last: Roels

first: Jan

last: Govaere

first: Luc

last: Peelman

first: Dieter

last: Deforce

first: Ann

last: Van Soom


title: Maternal recognition of pregnancy in the horse: are microRNAs the secret messengers? [RNA-seq]

overall_design: RNA-seq


title: Transcriptome profiling following knockdown of NAA50 in Arabidopsis

status: Public on Feb 20 2020

city: Bloomington

first: Roger

last: Innes

state: IN

address: Myers Hall 302

institute: Indiana University

summary: We utilized RNA-seq to identify transcriptome changes following knockdown of the Arabidopsis N-terminal acetyltransferase NAA50. Transgenic Arabidopsis plants carrying a dexamethasone-inducible amiRNA were used to study the effects of NAA50 knockdown. Significant changes occurred in the transcriptomes of NAA50 knockdown plants at 12 and 24 hours after dexamethasone treatment. These changes demonstrate that loss of NAA50 results in a reduction in signaling related to plant growth and development, as well as an increase in the expression of stress- and defense-related pathways.

overall_design: Transcriptome changes following knockdown of NAA50 were observed. A dexamethosone-inducible amiRNA targetting Arabidopsis NAA50 was utilized to achieve NAA50 knockdown. A transgenic line containing a dexamethasone-inducble scrambled amiRNA was used as a negative control. Four-week-old plants were treated with dexamethasone and RNA was collected 0, 12, and 24 hours later. RNA was collected from rosettes.

first: Matthew

last: Neubauer


title: Integrating Next Generation Sequencing with Morphology Improves Prognostic and Biologic Classification of Spitz Neoplasms

city: Chicago

first: Pedram

last: Gerami

state: Illinois

address: 420 E Superior St

institute: Northwestern University

type: Genome variation profiling by high throughput sequencing


title: p53-bound enhancer elements require locally acting transcription factors

city: Albany

first: Morgan

last: Sammons

address: 1400 Washington Ave, Life Sciences 2075

department: Biological Sciences

institute: University at Albany - SUNY

summary: Using a massively parallel reporter assay (MPRA), we examined the effect of local sequence context on p53-dependent enhancer activity.

overall_design: 296 putative p53-bound enhancer elements were selected from the hg19 genome assembly and were systematically randomized in 20bp sections from the 5' end. This allowed the investigation into the requirement for local sequence context and transcription factor motifs in the activity of p53 at enhancers.

first: Allison

middle: N

last: Catizone


title: Genome-Wide Association Study Towards Genomic Predictive Power for High Production and Quality of Milk in American Alpine Goats

status: Public on Feb 19 2020

city: Langston

first: Yonathan

last: Tilahun

state: OK

address: 100 Success Dr.

department: Extension

institute: Langston University

summary:
Alpine goat phenotypes for quality components have been routinely recorded for many years and deposited in the Council on Dairy Cattle Breeding (CDCB) repository. The data collected were used to conduct an exploratory genome-wide association study (GWAS) from 72 female Alpine goats originating from locations throughout the U.S. Genotypes were identified with the Illumina Goat 50K single nucleotide polymorphisms (SNP) Beadchip. The analysis used a polygenic model where the dropping criteria was the Call Rate ≥ 0.95. The initial dataset was composed of ~ 60,000 rows of SNPs, 21 columns of phenotypic traits and composed of 53,384 scaffolds containing other informative data points used for genomic predictive power. Phenotypic association with the 50KBeadchip revealed 26,074 reads of candidate genes. These candidate genes segregated as separate novel SNPs and were identified as statistically significant regions for genome and chromosome level trait associations. Candidate genes associated differently for each of the following phenotypic traits: test day milk yield (13,469 candidate genes), test day protein yield (25,690 candidate genes), test day fat yield (25,690 candidate genes), percentage protein (25,690 candidate genes), percentage fat (25,690 candidate genes), and percentage lactose content (25,690 candidate genes). The outcome of this study supports elucidation of novel genes that are important for livestock species in association to key phenotypic traits. Validation towards the development of marker-based selection that provide precision breeding methods will thereby increase breeding value.
Specific aims:
1) Improve on contributions to the phenotype repository, the Council on Dairy Cattle Breeding (CDCB) for milk quality traits that are economically important for goat production while developing a corresponding DNA repository for each of the animals with significant genotype-phenotype associations.
2) Develop genomic prediction tools and provide data for a better database for tools to predict phenotypic traits by initially using the high density Goat50KSNP BeadChip for the selection of more specific SNPs associated with select signatures (genes) for phenotypic traits in American Alpine goats.
3) To establish whether a low number of goat subjects (< 300 goats) will provide statistically significant (p < 0.05) predictive capabilities for desired breeding traits in American Alpine dairy goats.

overall_design: There were 72 female Alpine goats originating from locations throughout the U.S. Genotypes that were identified with the Illumina Goat 50K single nucleotide polymorphisms (SNP) Beadchip. Phenotypic association with the 50KBeadchip revealed 26,074 reads of candidate genes. These candidate genes segregated as separate novel SNPs and were identified as statistically significant regions for genome and chromosome level trait associations. Candidate genes associated differently for each of the following phenotypic traits: test day milk yield (13,469 candidate genes), test day protein yield (25,690 candidate genes), test day fat yield (25,690 candidate genes), percentage protein (25,690 candidate genes), percentage fat (25,690 candidate genes), and percentage lactose content (25,690 candidate genes).

first: Terry

last: Gipson

first: Fisher

last: Davis

first: Talia

last: Alexander

first: Khalil

last: Muhammed

first: Malcolm

last: McCallum

first: Peter

last: Hoyt


title: An atlas of cell types in the mammalian epididymis and vas deferens [single-cell RNA-Seq]

city: Worcester

first: Elisa

last: Donnard

state: MA

address: 368 Plantation St

department: Bioinformatics and Integrative Biology

institute: University of Massachusetts Medical School

summary: The epididymis is comprised of multiple segments/compartments that, in addition to concentrating sperm and preventing their premature activation, play key roles in remodeling the protein, lipid, and RNA composition of maturing sperm. In order to understand the complex roles for the epididymis in reproductive biology, we generated a single cell atlas of gene expression from the murine epididymis and vas deferens using droplet-based (10X Chromium) single cell RNA-Seq. Following single-cell RNA-Seq, quality control, and removal of reads attributable to contaminating cell-free RNA we were able to profiled the expression of 16878 genes in 8,880 individual cells with an average of 3110 (median = 1965) unique molecular identifiers (UMIs) per cell from across the epididymis and the vas deferens. We recovered all the key cell types of the epididymal epithelium, including principal cells, clear cells, and basal cells, along with its associated support cells that include fibroblasts, smooth muscle, macrophages and other immune cells. Our data confirm and extend prior studies of segment-restricted gene expression programs, and reveal that these region-specific programs are largely driven by principal cells. In addition to the extensive region-specific specialization of principal cells, we find evidence for functionally-specialized subpopulations of stromal cells, and, most notably, two distinct populations of clear cells. Furthermore, we find several novel cell subpopulations, most notably including an Amylin-positive clear cell subtype, and predict intercellular signaling networks between the various cell types. Together, these data provide an atlas of cell composition across the epididymis, and a wealth of molecular hypotheses for future efforts in reproductive physiology.

overall_design: Sperm-depleted single cell suspensions were obtained from eight epididymides from four 10-12 weeks old FVB mice. The organ was cut into four segments that roughly corresponded to caput, corpus, cauda, and vas deferens. Single-cell RNA sequencing libraries were prepared using Chromium Single Cell 3’ Reagent Kit V2 (10X Genomics).

first: Vera

last: Rinaldi

first: Oliver

last: Rando


title: Two component system RspA1A2-dependent regulation of carbon metabolism in Streptomyces albus

status: Public on Feb 17 2020

city: Shanghai

first: Kuipu

last: Zhang

address: 130  Meilong Rd.

department: State  Key  Laboratory  of  Bioreactor  Engineering

institute: East  China  University  of  Science and Technology

summary: The diﬀerences between the ΔrspA1 mutant and the original strain A30 transcriptomes were analyzed at 30h in ferentaion cultures complemented with 75mM glutamate when the conditions preceding the diﬀerences observed in glucose consumption rate,pH and cell dry weight.

overall_design: RNA samples from ΔrspA1 and the parental strain A30 were sequenced  in duplicate at 30h when cultured in fermentation medium


title: High glucose levels increase influenza-associated damage to the pulmonary epithelial-endothelial barrier

status: Public on Feb 14 2020

city: Brisbane

first: Kyle

last: Upton

state: Qld

address: Cooper Road

department: SCMB

institute: University of Queensland

summary: Here, the effects of high glucose levels on influenza severity were investigated using an in vitro model of the pulmonary epithelial-endothelial barrier. We show that compared to low glucose levels, high glucose conditions prior to influenza A virus infection increased virus-induced barrier damage. Increased barrier damage was not associated with increased cell death nor increased virus replication, but rather an increased pro-inflammatory response in endothelial cells and the subsequent damage of the epithelial junctional complex.

overall_design: Human epithelial cells and human pulmonary microvascular endothelial cells were grown in a transwell system. Endothelial cells were exposed to either normoglycemic (7mM glucose) or hyperglycaemic conditions (12mM glucose). Cells were then infected with Influenza A Virus (or mock infection protocol for control) before performing RNA-Seq analysis.

first: Kirsty

last: Short


title: Deregulated overexpression of the high affinity Cu transporter COPT1 alters iron homeostasis in Arabidopsis

status: Public on Feb 04 2020

city: Valencia

first: Francisco

last: Vera-Sirera

address: Ingeniero Fausto Elio, s/n

country: Spain

institute: IBMCP (UPV-CSIC)

summary: The present work describes the effects on iron homeostasis when copper transport was deregulated in Arabidopsis thaliana by overexpressing copper transporters (COPTOE). A genome-wide analysis conducted on COPT1OE plants, highlighted that iron homeostasis gene expression was affected, both under copper deficiency and excess.  Among the inhibited genes were those encoding the iron uptake machinery and their transcriptional regulators. Subsequently, COPTOE seedlings contained less iron and were more sensitive than controls to iron deficiency. These results emphasized the importance of appropriate spatiotemporal copper uptake for iron homeostasis under copper deficiency. The deregulation of copper-I uptake difficulted the transcriptional activation of the subgroup Ib of basic helix-loop-helix (bHLH-Ib) factors. Oppositely, copper excess inhibited the expression of the master regulator FIT but activate bHLH-Ib expression in COPTOE plants, in both cases leading to the lack of an adequate iron uptake response. As copper increased in the media, iron-III was accumulated in roots, accounting for a defective iron mobilization to the aerial parts, and this effect was exacerbated in COPTOE plants. Thus, iron-III overloading in roots inhibited local iron deficiency responses, aimed to metal uptake from soil, leading to a general lower iron content in the COPTOE seedlings. The understanding of the role of copper uptake in iron metabolism could be applied for increasing crops resistance to iron deficiency

overall_design: At least three biological replicates of Arabidopsis seedlings were generated for 2 genotypes, Col-0 and COPT1 overexpressor line (COPT1 OE); and 2 growth condictions; first one with a cupper deficient medium (Cu Def, 0 μM CuSO4) and a second one with a cupper excess medium (Cu Exc, 10 μM CuSO4). For each growth condition, COPT1 OE versus Col-0 samples were compared;  in each comparasion at least three biological replicates were made, two replicas were labeled with Cy5 for the COPT1 OE and Cy3 for the Col-0  sample, while the other replicas were reversed-labeled.

first: Ana

last: Perea-García

first: Amparo

last: Andrés-Bordería

first: Miguel

last: Pérez-Amador

first: Sergi

last: Puig

first: Lola

last: Peñarrubia


title: RNA sequencing of adult cardiomyocyte cyclin C deletion

status: Public on Feb 08 2020

city: Iowa City

first: Chad

last: Grueter

state: Iowa

address: 285 Newton Rd, 4332 PBDB, 285 Newton Rd

institute: University of Iowa

summary: The goal of this study was to identify differentially expressed genes in hearts with cardiomyoycte deletion of cyclin c compared to cyclin c floxed controls.

overall_design: RNA from three, six week old male hearts from cyclin C fl/fl and cyclin C fl/fl; aMHC cre was isolated. The University of Iowa Institute of Human Genetics, Genomics Division, generated polyA-enriched stranded RNA libraries followed by RNAseq using the Illumina HiSeq platform. Raw sequence reads were analyzed with BaseSpace (www.illumina.com) by aligning reads to the Mus musculus mm10 genome using the TopHat Alignment app. Transcripts were assembled and significant differentially expressed genes were determined with the Cufflinks Assembly and DE app using a false discovery rate <0.05.

middle: E


title: DNA methylation profiling of proliferating and differentiating keratinocytes

city: Nijmegen

first: Jos

last: Smits

state: Gelderland

address: Rene Descartesdreef 1

department: Dermatology

institute: Radboudumc

type: Methylation profiling by genome tiling array

summary: The epidermal compartment of the skin is regenerated constantly by proliferation of epidermal keratinocytes. Differentiation of a subset of these keratinocytes allows the epidermis to retain its barrier properties. Regulation of keratinocyte fate – whether to remain proliferative or terminally differentiate – is complex and not fully understood. The objective of our study was to assess if DNA methylation changes contribute to the regulation of keratinocyte fate. We employed genome-wide MethylationEPIC beadchip array measuring approximately 850,000 probes combined with RNA sequencing of in vitro cultured nondifferentiated and terminally differentiated adult human primary keratinocytes. We did not observe a correlation between methylation status and transcriptome changes and only two differentially methylated probes were detected, of which one was located in the TRIM29 gene. TRIM29 knockdown resulted in significantly lower expression levels of terminal differentiation genes as a group, although differences for individual genes were considered minor (<2 fold). From these results we conclude that it is unlikely that DNA methylation has a main regulatory role in terminal keratinocyte differentiation regulation in vitro.

overall_design: Primary keratinocytes of 5 different skin cell donors were cultured and DNA was harvested during proliferation and after terminal differentiation.

first: René

last: Dirks

first: Jieqiong

last: Qu

first: Ellen

middle: H

last: van den Bogaard


title: Men1 and Daxx loss in a mouse model of chronic pancreatitis

status: Public on Feb 13 2020

city: Houston

first: Yuan

last: Qi

address: 1400 Pressler St

department: Bioinformatics & Computational Biology

institute: University of Texas M.D. Anderson Cancer Center

summary: Gene expression was evaluated by RNA-seq of mouse pancreas 5 days following chronic caerulein-induced pancreatitis. Four different genotypes were evluated: i) wild-type, ii) Men1fl/flPdx1-CreTg, iii) Daxxfl/flPdx1-CreTg iv) Daxxfl/flMen1fl/flPdx1-CreTg.

overall_design: 4 independent biological replicates for each genotype were sequenced (16 samples total)

first: Amanda

last: Wasylishen

first: Guillermina

last: Lozano

first: Xiaoping

last: Su


title: Expression of formate-THF ligase has a deep impact on primary metabolism of Synechocystis sp. PCC 6803

status: Public on Jan 17 2020

city: Freiburg

first: Wolfgang

middle: R.

last: Hess

state: Baden-Würtemberg

address: Schänzlestrasse 1

department: Institute of Biology III

country: Germany

institute: University of Freiburg

summary: The introduction of alternative CO2-fixing pathways such as formate synthesis and assimilation may improve the efficiency of biological carbon fixation that appears to be limited by the enzymatic properties of ribulose 1,5-bisphosphate carboxylase/oxygenase (RubisCO). Here we aimed to establish a formate assimilation pathway in the model cyanobacterium Synechocystis sp. PCC 6803. The formate-tetrahydrofolate ligase (FTL) from Methylobacterium extorquens AM1 was expressed in Synechocystis to enable formate assimilation and reduce the loss of fixed carbon in the photorespiratory pathway. Transgenic strains accumulated serine and 3-phosphoglycerate, and consumed more 2-phosphoglycolate and glycine, which seemed to reflect the efficient utilization of formate. However, labelling experiments showed that the serine accumulation was not due to the expected incorporation of formate. DNA-microarray experiments were performed to analyze possible transcriptome changes due to ftl expression. Marked changes in expression of genes encoding proteins associated with serine biosynthesis and enzymes involved in nitrogen and C1 metabolism revealed that ftl expression had a regulatory impact on these metabolic routes. Our results indicate that the expression of new pathways could have a severe impact on the cellular regulatory network, which hampers the establishment of newly designed pathways.

overall_design: Synechocstis PCC 6803 WT cells and cells expressing formyl-THF ligase (FTL) from Methylobacterium extorquens AM1 were studied in the presence of absence of 10 mM sodium formate for 3 days under constant illumination and air bubbling. Samples were taken in biological replicates.

first: Shanshan

last: Song

first: Stefan

last: Timm

first: Steffen

last: Linder

first: Viktoria

last: Reimann

first: Martin

last: Hagemann

first: Eva-Maria

last: Brouwer


title: The transcriptional fingerprint of satellite glial cells changes over time following peripheral nerve injury

status: Public on Jan 22 2020

city: London

first: Sara

middle: Elgaard

last: Jager

address: Hodgkin Building, Guy's Campus

country: United Kingdom

institute: King's College London

summary:
Website for easy exploration of the data: https://rna-seq-browser.herokuapp.com/#

For the first time, we here characterize the transcriptional signature of satellite glial cells (SGCs) in a nerve injury-paradigm by isolating SGCs from mouse dorsal root ganglia (DRGs) after peripheral nerve injury followed by next generation RNA sequencing (RNA-seq).
We found that SGCs regulate their gene expression differently at 3 days and 14 days after peripheral nerve injury suggesting that they change their function over time. At both time points, we found downregulation of several genes linked to cholesterol. After 14 days we further detect regulation of genes linked to the immune system (MHC protein complex and leukocyte migration).
The SGC RNA-seq data is accompanied by RNA-seq of purified nociceptors from injured (partial sciatic nerve ligation) or sham (ipsi after sham operation or contra after partial sciatic nerve ligation) L3-L5 DRGs.

overall_design:
RNA was purified from naïve SGCs, naïve DRGs, SGCs 3 and 14 days after sciatic nerve ligation, SGCs 3 and 14 days after sham operation, nociceptors 8 days after partial sciatic nerve ligation and nociceptors 8 days after sham operation. The RNA was sequences with next generation sequencing (RNA-seq).
The gene expression was compared in the following ways: naive SGCs vs naive DRG; SGCs 3 days after injury vs SGCs 3 days after sham; SGCs 14 days after injury vs SGCs 14 days after sham; nociceptors 8 days after injury vs nociceptors 8 days after sham.

first: Franziska

last: Denk

first: Stephen

last: McMahon

first: Christian

middle: B

last: Vægter


title: Exploration of small RNA biomarkers for testicular injury in the serum exosomes of rats

status: Public on Jan 16 2020

city: Nagoya

first: Reo

last: Kawata

address: 65 Tsurumai-cho, Showa-ku, Nagoya, Japan

department: Drug Safety Sciences

institute: Nagoya university

summary: Testicular injury is often observed in drug development. Serum hormones are usually used as non-invasive biomarkers for testicular injury; however, their sensitivity is low. Therefore, it is difficult to monitor testicular injury in pre-clinical and clinical drug developments. In recent years, molecules in body fluid exosomes are attracting attention as disease biomarkers such as cancer. In this study, small RNAs in serum exosomes were analyzed for identifying non-invasive biomarkers of testicular injury in rats, which are mainly used in a pre-clinical drug development. Testicular injury models in rats were prepared by a single oral administration of 2000 mg/kg ethylene glycol monomethyl ether in which spermatocytes degeneration and sertoli cells vacuolation were observed, or 400 mg/kg carbendazim in which sertoli cells vacuolation and seminiferous tubules dilation were observed. Serum exosome small RNA-seq was performed in these models. The analysis identified 3 small RNAs that fluctuated in common between the models, and miR-423-5p and miR-128-3p were selected as candidate markers. For qPCR validation of the candidates, testicular injury models were further prepared by a single oral administration of 60 mg/kg 1,3-dinitrobenzene or 500 mg/kg nitrofurazone in which spermatocytes degeneration and sertoli cells vacuolation were observed. In qPCR analysis, the selected two miRNAs in exosomes were upregulated in the all models except for 1,3-dinitrobenzene model in which severe hemolysis was observed. On the other hand, the miRNAs in serum did not significantly change in the any models. In conclusion, we identified miR-423-5p and miR-128-3p in serum exosome as non-invasive biomarkers for testicular injury in rats.

overall_design: Serum exosome small RNA profiles in rats with testicular injury were analyzed with MiSeq system (Illumina)

first: R

first: T

last: Kagawa

first: S

last: Oda

last: Yokoi


title: Comprehensive analysis of mRNA and lncRNA transcriptomes reveals the differentially hypoxic response of preadipocytes during adipogenesis

status: Public on Jan 18 2020

city: Chengdu

first: Mingzhou

last: Li

address: huimin road No.211

institute: sichuan agricultural university

summary: Local hypoxia is recently reported to be occur in white adipose tissue (WAT) microenvironment at obesity. Adipocyte have own life cycle that reflect in different stages of adipogenesis in WAT niche. Long noncoding RNAs (lncRNAs) play an important role in cellular response to hypoxia. However, the different hypoxic responses of preadipocytes during adipogenesis and the potential role of lncRNAs in this process remain to be elucidated. Here we evaluated the different hypoxic responses of primary hamster preadipocytes during adipogenesis and analyzed the expression of mRNAs and lncRNAs from same Ribo-Zero RNA-seq libraries. Hypoxia induced HIF-1α protein during adipogenesis and caused the divergent changes of cell phenotypes. A total of 10,318 mRNAs were identified to be expressed in twenty libraries (five timepoints), and 149, 326, 365, 1099, 2504 differentially expressed mRNAs (DE mRNAs) were detected in D0, D1, D3, D7 and D11, respectively (hypoxia vs normoxia). Functional enrichment analysis revealed the shared and specific hypoxia response pathways in different stages of adipogenesis. Hypoxia differentially modulates the expression profile of adipose-associated genes, including adipokines, lipogenesis, lipolysis, hyperplasia, hypertrophy, inflammatory and extracellular matrix (ECM). We also identified 4,296 lncRNAs that were substantially expressed and detected 1,431 DE lncRNAs in five timepoints. Afterward, 2, 3, 5, 13 and 50 DE mRNAs in D0, D1, D3, D7 and D11, respectively, were highly correlated and loci-nearby with DE lncRNAs, and were mainly involved in cell cycle, vesicle-mediated transport and mitochondrion organization. We also identified twenty-eight one-to-one lncRNA-mRNA pairs that might be closely related to adipocyte function, such as ENSCGRT00015041780-Hilpda, TU2105-Cdsn, TU17588-Ltbp3. These lncRNAs may represent the crucial regulation axis in cellular response to hypoxia during adipogenesis. Altogether, this study dissected the effects of hypoxia in the cell during adipogenesis, and uncovered novel regulator potentially associated with obesity and may provide a new view for interpretation and treatment of obesity.

overall_design: Primary preadipocyte in iWAT were isolated and cultured from the from 6-week-old hamsters (Cricetulus griseus). Differentiation of preadipocytes was performed by classic cocktail methods. Cells grown to 100% confluence (D0) were induced using differentiation medium (DM) containing CM, 1 M dexamethasone, 10g/ml insulin and 0.5 mM IBMX (Sigma). Two days after the induction, medium was replaced to the maintenance medium (MM) containing CM and 10 g/ml insulin (Sigma). For hypoxia treatment, cells at five differentiation timepoints (D-1, D0, D2, D6, D10) received hypoxia treatment for 24 h in a modular incubator chamber with 5% CO2, 1% O2 and 95% N2 (MIC-101, Billups-Rothenberg, Del Mar, CA). Corresponding medium in different groups were pre-equilibrated to hypoxia for at least 4 h before use. Cells in the normoxia-matched group were placed in conventional conditions (5% CO2 and 95% air) and served as the control. A total of twenty cell samples (hypoxia vs normoxia, 5 timepoints, 2 replicates) were collected and stored at -80°C until required for RNA extraction, sequencing and transcriptome analysis.

first: Jinwei

last: Zhang

first: Xiankun

last: Zhou

first: Jideng

last: Ma

first: Surong

last: Shuai


title: Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and CANT1 Overexpression Retinoblastoma  Transcriptomes

status: Public on Feb 05 2020

city: shanghai

first: Hongyan

last: Ni

address: 639 zhizaoju Road

institute: Ninth People’s Hospital, Shanghai JiaoTong University School of Medicine

summary:
PURPOSE: Retinoblastoma (RB) is the most common malignant intraocular tumor of childhood. Recent studies have shown that long non-coding RNAs (lncRNAs), which are longer than 200 bp and without protein-coding ability, are key regulators of tumorigenesis. However, the role of lncRNAs in retinoblastoma remains to be elucidated.
METHODS: LncRNA CASC15-New-Transcript 1 (CANT1) expression was determined by real-time PCR in RB cells. Tumor characteristics in CANT1-overexpressing RB cells were determined through CCK8 cell viability assay, soft agar assay and mouse xenograft experiment. RNA transcriptome-sequencing was performed to find downstream target genes of CANT1. CANT1's interactions with phosphoinositide 3-kinase gamma (PI3Kγ) were studied through chromatin oligonucleotide precipitation (ChOP) and chromatin immunoprecipitation (ChIP) assays.
RESULTS: In this study, we found that the expression of lncRNA CANT1 was significantly downregulated in RB. Notably, CANT1 overexpression significantly inhibited RB growth both in vitro and in vivo. Furthermore, lncRNA CANT1, which was mainly located in the nucleus, occupied the promoter of PI3Kγ and blocked histone methyltransferase hSET1 from binding to the PI3Kγ promoter, thus abolishing hSET1-mediated histone H3K4 trimethylation of the PI3Kγ promoter and inhibiting PI3Kγ expression. Furthermore, we found that silencing PI3Kγ either by CANT1 overexpression or by PI3Kγ siRNA, reduced the activity of PI3K/Akt signaling and suppressed RB tumorigenesis.
CONCLUSIONS: LncRNA CANT1 acts as a suppressor of RB progression by blocking gene-specific histone methyltransferase recruitment. These findings outline a new CANT1 modulation mechanism and provide an alternative option for RB treatment.

overall_design: mRNA profiles of wild type (WT) and lncRNA CANT1 overexpressing retinoblastoma cells  were generated by deep sequencing, using  Ion Torrent PGM.

first: Peiwei

last: Chai


title: A blood miRNA signature associates with sporadic Creutzfeldt-Jakob disease diagnosis

status: Public on Jan 13 2020

first: Simon

last: Mead

address: 33 Cleveland St

department: MRC Prion Unit at UCL

institute: University College London

summary: Sporadic Creutzfeldt-Jakob disease (sCJD) presents as a rapidly progressive dementia which is usually fatal within six months. No clinical blood tests are currently available for diagnosis or disease monitoring. Here, we profiled blood microRNA (miRNA) expression in sCJD. Small RNA-sequencing of 57 sCJD patients and 48 healthy controls revealed differential expression of hsa-let-7i-5p, hsa-miR-16-5p, hsa-miR-93-5p and hsa-miR-106b-3p. Downregulation of hsa-let-7i-5p, hsa-miR-16-5p and hsa-miR-93-5p replicated in an independent cohort using quantitative PCR, with concomitant upregulation of four of their mRNA targets. Absence of correlation in cross-sectional analysis with clinical phenotypes paralleled the lack of association between rate of decline in miRNA expression and rate of disease progression in a longitudinal cohort of 50 samples from 21 sCJD patients. Finally, the miRNA signature showed a high level of accuracy in discriminating sCJD from Alzheimer’s disease (AD). These findings highlight novel molecular alterations in the periphery in sCJD which can provide information about differential diagnosis and improve mechanistic understanding of human prion diseases.

overall_design: Case-control study generating microRNA profiles in patients with sCJD and healthy control individuals by small RNA sequencing.

first: Penny

last: Norsworthy

first: Andrew

last: Thompson

first: Tze

last: Mok

first: Ross

last: Paterson

first: Jonathan

last: Schott

first: John

last: Collinge

first: Emmanuelle

last: Viré

first: Fernando

last: Guntoro

first: Luke

middle: C

last: Dabin

first: Akin

last: Nihat


title: In vivo high-throughput screening of novel adeno-associated viral capsids identifies variants for transduction of adult neural stem cells within the subventricular zone

city: Heidelberg

first: Ana

last: Martin-Villalba

address: Im Neuenheimer Feld 280

department: Molecular Neurobiology

institute: German Cancer Research Center

summary:
The adult mammalian brain entails a reservoir of neural stem cells (NSCs) generating glial cells and neurons. However, NSCs become increasingly quiescent with age, which hampers their regenerative capacity. New means are therefore required to genetically modify adult NSCs for re-enabling endogenous brain repair. Recombinant adeno-associated viruses (AAVs) are ideal gene therapy vectors due to an excellent safety profile and high transduction efficiency. We thus conducted a high-throughput screening of 157 intraventricularly injected barcoded AAV variants profiled by transcriptome sequencing. Transcriptome analysis identified two synthetic capsids, AAV9_A2 and AAV1_P5 transducing active and quiescent NSCs. Further optimization of AAV1_P5 by judicious selection of promoter and dose of injected viral genomes enabled targeting of 57% of the NSC compartment. Importantly, transduced NSC readily produced neurons. The present study identifies AAV variants with a high specificity and transduction efficiency of adult NSCs thereby paving the way for preclinical testing of regenerative gene therapy.
We identified a synthetic Adeno-associated virus (AAV) capsid, AAV1_P5, that transduces active and quiescent neural stem cells (NSCs). In order to fully characterize the identity of AAV1_P5-transduced cells, as well as potential changes arising by the AAV-transduction itself, we profiled these cells and untransduced ones from the same mouse by single cell RNA sequencing. To this end, three months-old eYFP-reporter mice were injected with 109 vg/mouse AAV1_P5 harboring the CMV_Cre construct. Transduction induces expression of eYFP. 37 days post injection, we isolated cells from the v-SVZ and other brain regions. More precisely, we isolated labeled cells of the ventricular-subventricular zone and the striatum, rostral migratory stream (RMS) and olfactory bulb, here referred to as rest of the brain (RoB). To capture the remaining unlabeled cells of the NSC-lineage in the v-SVZ, we also isolated GLAST+ v-SVZ cells. Two samples of two pooled mice each were subjected to single cell RNA sequencing.

overall_design:
identification of AAV variants with a high specificity and transduction efficiency of adult NSCs

Single cell RNA sequencing of eYFP-reporter brain cells transduced with the synthetic adeno-associated virus capsid AAV1_P5

first: Sascha

last: Dehler

first: Lukas

last: Kremer

first: Thomas

last: Stiehl

first: Jonas

last: Weinmann

first: Heike

last: Abendroth

first: Alexander

last: Laure

first: Anna

last: Marciniak-Czochra

first: Dirk

last: Grimm


title: Post-sepsis immunosuppression depends on NKT cell regulation of mTOR/IFN-gamma in NK cells

status: Public on Jan 21 2020

city: Boston

first: Edy

middle: Yong

last: Kim

address: 60 Fenwood Rd

institute: Brigham and Women’s Hospital

summary: We show a new immunosuppressive function for NKT cells, and the NKT cell-mTOR axis may be a therapeutic target to prevent post-sepsis immunosuppression

overall_design: We examined the innate immune response to sepsis and identified a mechanism that predicted susceptibility to secondary infection

middle: Y

first: Hadas

last: Ner-Gaon

first: Aidan

last: Cullen

first: Jingyu

last: Guo

first: Jiyoung

last: Choi

first: Tomoyoshi

last: Tamura

first: Tal

last: Shay

first: Michael

last: Brenner


title: Over-expression of a transcription factor mEmBP-1a increases rice photosynthesis, biomass and yield by regulating the expression of multiple key photosynthesis genes

status: Public on Jan 08 2020

first: Faming

last: Chen

address: 320 Yue Yang Road

department: CAS-MPG Partner Institute for Computational Biology

institute: Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences

summary: Improvement in the photosynthetic efficiency is a major approach to improve crop yield potential. So far, most of the demonstrated cases of photosynthesis improvement was achieved through manipulation of one or a few photosynthesis related genes. Present study found that over-expression of one maize transcription factor, mEmBP-1 gene, led to simultaneously increased expression of nearly all genes in photosynthesis pathway, including genes encoding chlorophyll a and  b-binding proteins (Lhca and Lhcb), photosystem II (PsbR3 and PsbW) and PS I reaction center subunits (PsaK and PsaN), genes encoding for chloroplast ATP synthase subunit and electron transport reaction (Fd1 and PC), and also major genes in the Calvin Benson Bassham cycle, Rubisco, GAPDH, FBA, TK and PRK. This increased photosynthesis gene expression resulted in increased leaf chlorophyll pigment, photosynthetic rate, quantum yields, biomass growth and grain yield both in the greenhouse and also in natural field conditions. Using DNA-Protein binding experiment, we found that mEmBP-1a protein can directly bind to the promoter regions of photosynthesis genes, suggesting that the direct binding of mEmBP-1a to the G-box domain of photosynthetic genes upregulates expression of these genes. Hence, this study shows that mEmBP-1a is a major regulator of photosynthesis.

overall_design: For RNA-sequencing (RNA-seq) analysis, we collected the top second leaves of mEmBP-OE-4 line and WT at early heading stage at about 10:00 a.m. from field grown plants. Four replications of mEmBP-OE-4 line (mEmBP-OE-4_rep1-4) and WT (WT_rep1-4) were collected, respectively. RNA was extracted using the PureLink RNA Mini Kit following manufacturer’s protocol (Life Technologies Corporation). RNA libraries were prepared for sequencing based on standard Illumina protocols and sequenced using Ilumina X Ten platform in paired-end 150 mode.

first: Shahnaz

last: Perveen

first: Xinguang

last: Zhu


title: RNA-seq, ChIP-seq, and ATAC-seq analyses of mTECs

status: Public on Feb 07 2020

city: bunkyo

first: Yoshihiko

last: Tomofuji

state: Tokyo

address: hongo 7-3-1

department: Immunology

institute: University of Tokyo

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

overall_design: Refer to individual Series


title: Profiles of IL-4 stimulated mouse peritoneal macrophages

status: Public on Jan 04 2020

city: Saint Louis

first: Mei San

last: Tang

state: MO

address: 660 S Euclid, Campus Box 8118

department: Pathology & Immunology

institute: Washington University in St Louis


title: Differential expression profiling of human milk derived exosomal MicroRNAs in HIV-1 infected Women from Nigeria

city: Toronto

first: Muhammad

middle: Atif

last: Zahoor

state: Ontario

address: 101 College St.

country: Canada

institute: University Health Network

summary: Despite the use of current antiretroviral therapy (ART) in HIV-1 infected mothers, approximately 5% of new HIV-1 infections still occur in breastfed infants annually. Human Milk (HM) exosomes are highly enriched in maternal microRNAs (miRNAs) and after ingestion and subsequent absorption play an important role in neonatal innate and adaptive immunity. Although, HM exosomes derived from healthy donors are known to inhibit HIV-1 transmission; the effect of HIV-1 on HM exosomal miRNA signatures remains unknown. In the present study, for the first time HM derived exosomal miRNA profiles were determined in HIV-1 infected women.

overall_design: HM exosomes were purified from uninfected control and HIV-1 infected mothers (n=36), processed for RNA extraction and subjected to miRNA expression profiling by NanoString technology. The data were analyzed, and targets were predicted.

first: Xiao-Dan

last: Yao

first: Bethany

last: Henrick

first: Chris

last: Verschoor

first: Alash'le

last: Abimiku

first: Sophia

last: Osawe

first: Kenneth

middle: L

last: Rosenthal


title: STAT3 Signaling Pathway in Keloid Pathogenesis Implicated by Preliminary Transcriptome and ATAC Analyses

status: Public on Jan 11 2020

city: Los Angeles

first: Randall

middle: B.

last: Widelitz

state: California

address: 2011 Zonal Ave HMR 305

department: Department of Pathology

institute: University of Southern California

summary: Keloids are wounding-induced fibroproliferative human tumor–like skin scars of complex genetic makeup and poorly defined pathogenesis. Fibroblasts are the principal mediator of fibroproliferative disorders. To reveal dynamic epigenetic and transcriptome changes of keloid fibroblasts, a vertical study from RNA-seq and ATAC-seq analyses followed by in vivo confirmation of candidate molecule expression and subsequent functional testing was carried out using an early passage, freshly isolated keloid fibroblast cell strain and its paired normal control. These keloid fibroblasts produce keloid-like scars in a plasma clot-based skin equivalent humanized keloid animal model. RNA-seq analysis reveals that Hepatic fibrosis is the most significant pathway followed by Wnt–b-catenin signaling, TGF-b signaling, regulation of the EMT pathway, the STAT3 pathway, and adherens junction signaling. ATAC-seq analysis shows that STAT3 signaling is the most active pathway in keloid fibroblasts, followed by Wnt signaling (Wnt5) and regulation of the EMT pathway. Immunohistochemistry confirms that activated STAT3, (Tyr705 phospho-STAT3) and/or b-catenin are upregulated in dermal fibroblasts of keloid clinical specimens and mature keloid skin equivalent implants from the humanized mouse model compared to the normal control. The effect of STAT3 signaling on keloid fibroblast collagen expression was further tested in plasma clot-based skin equivalents using Cucurbitacin I, a selective JAK2/STAT3 inhibitor. A non-linear dose response of Cucurbitacin I was observed in collagen type I expression indicating a likely role of STAT3 signaling pathway in keloid pathogenesis. This work also demonstrates the utility of the recently established humanized keloid mouse model in exploring the mechanism of keloid formation.

overall_design: Control and keloid samples, each in duplicate

first: Yun-Shain

last: Lee

first: Ya-Chen

last: Liang

first: Ping

last: Wu

first: David

last: Kulber

first: Kylie

last: Tanabe

first: Cheng-Ming

last: Chuong

first: Tai-Lan

last: Tuan


title: Accessible chromatin profiles of IL-4 stimulated mouse peritoneal macrophages derived from different cellular lineages

summary: Interleukin-4 (IL-4) activates macrophages to adopt a distinct phenotype important for tissue repair and helminth infection, but the molecular basis of chromatin remodeling in response to IL-4 stimulation is not understood. We find that IL-4 activation of terminally differentiated macrophages in mice is accompanied by cell-type-specific chromatin remodeling in regions enriched with binding motifs of the pioneer transcription factor PU.1. Mutation studies based on natural genetic variation between C57BL/6 and BALB/c mouse strains demonstrate that accessibility of these IL-4 induced regions can be regulated through differences in DNA shape, without disruption of pioneer factor motifs. We propose a model whereby DNA shape features of stimulation-dependent genomic elements contribute to differences in the accessible chromatin landscape of alternatively activated macrophages on different genetic backgrounds.

overall_design: We FACS-sorted resting and IL-4 stimulated mouse peritoneal macrophages of F4/80hi CD206- (tissue resident) and F4/80int CD206+ (monocyte-derived) phenotypes for accessible chromatin profiling by ATAC-Seq.

first: P'ng

last: Loke


title: Genome-wide Expression Profiling and Pathway Analysis in Cyclic Stretched Human Trabecular Meshwork Cells

status: Public on Feb 01 2020

city: Augusta

first: Yutao

last: Liu

state: GA

address: 1120 15th Street

department: Cell Biology and Anatomy

institute: Medical College of Georgia

summary: To identify differentially expressed miRNAs in human trabecular meshwork (HTM) cells in response to cyclic mechanical stretch

overall_design: This study profiled the miRNA expression of 6 HTM cell lines in the presence and absence of 15% mechanical stretch (1 cycle/s) for 24 hours

first: Michelle

middle: D

last: Drewry


title: Intrauterine infusion of pathogenic bacteria persistently the transcriptome of oocytes.

status: Public on Jan 01 2020

city: GAINESVILLE

first: FAHONG

last: YU

state: FL

address: 2033 Mowry Rd

department: ICBR

institute: UNIVERSITY OF FLORIDA

summary: To better understand the impact of infection on oocyte quality we employed global transcriptomics of oocytes collected from heifers after receiving intrauterine infusion of pathogenic Escherichia coli and Trueperella pyogenes. We hypothesized that oocyte transcriptome would be altered in response to intrauterine infection. A total of 452 differentially expressed genes were identified in oocytes collected from heifers 4 days after bacteria infusion compared to vehicle infusion, while 539 differentially expressed genes were identified in oocytes collected from heifers 60 days after bacteria infusion. Only 42 genes were differentially expressed in bacteria infused heifers at both day 4 and day 60. Interferon, HMGB1, ILK, IL-6 and TGF-beta signaling pathways were downregulated in oocytes collected at day 4 from bacteria infused heifers, while interferon, ILK and IL-6 signaling were upregulated in oocytes collected at day 60 from bacteria infused heifers. These data suggest that bacterial infusion alters the oocyte transcriptome differently at day 4 and day 60, suggesting different follicle stages are susceptible to damage. Characterizing the long-term impacts of uterine infection on oocyte transcriptome aids in our understanding of how infection causes infertility in dairy cattle.

overall_design: To understand the effect of uterine disease on the oocyte, we induced clinical endometritis in virgin heifers by intrauterine infusion of pathogenic E. coli and T. pyogenes. Oocytes were collected by transvaginal guided ultrasound at day 4 and day 60 post infection and subjected to global transcriptome analysis. We hypothesized that oocyte transcriptome would be altered in response to intrauterine infection. These data will enable us to better understand the consequence of uterine infection on the oocyte, and potential mechanisms by which infection reduces fertility in cattle.

first: R

last: Piersanti

first: J

last: Block

first: Z

middle: X

last: Ma

first: K

last: Jeong

last: Santos

first: F

last: Yu

first: I

last: Sheldon

middle: J

last: Bromfield


title: Novel inducible filamentous sliding motility identified in pathogenic Bacillus cereus group species

city: Vancouver

first: Martha

state: British Columbia

address: 2350 Health Sciences Mall

department: Microbiology and Immunology

institute: University of British Columbia

summary: We isolated an atmospheric contaminant, subsequently identified as a new strain of Bacillus mobilis, which showed a novel, robust, inducible filamentous sliding motility and completely colonized a bacterial culture plate in less than 48 h under some conditions. This flagella-independent sliding motility was characterized by long filamentous cells at the expanding edge, and was induced when cells were inoculated onto lawns of metabolically inactive Campylobacter jejuni cells, heat killed bacterial biomass, and milk or blood dried onto agar plates. Phosphatidylcholine (PC), bacterial membrane components, and sterile human fecal extracts were sufficient to induce filamentous expansion. Screening of eight other Bacillus spp. (five from the B. cereus group and three other Bacillus spp.) showed that filamentous motility was conserved amongst B. cereus group species to varying degrees. RNAseq of filamentously expanding cells collected from PC and milk lawn plates in comparison to rod-shaped cells from control plates revealed that genes related to metabolism, ion and amino acid transport were differently regulated, genes controlling sporulation were reduced, and some virulence genes (e.g., hblA/B/C/D and plcR) were increased. We hypothesize that the robust and conserved nature of filamentous motility in pathogenic B. cereus group species can enhance bacterial colonization during host colonization.

overall_design: Growth of B. mobilis ML-A2C4 on three different agar plate conditions were tested at n=3 biological replicates each for a total of 9 samples. The growth conditions are 1) control: growth on control MH 1.5% agar plates, 2) milk: growth on MH 1.5% agar plates covered with an adsorbed milk layer prepared by drying 1.5 mL of 10% smilk milk powder solution onto the surface of the plate, and 3) PC: growth on MH 1.5% agar plates that were spread plated with 0.5mL of a 2% phosphatidylcholine (PC) in 50% EtOH.

middle: M

first: Shannon

last: Coleman

first: Lauren

last: Wilkinson

first: Maren

last: Smith

first: Thomas

last: Hoang

first: Manjari

last: Mukherjee

first: Steven

last: Huynh

first: Craig

middle: T

last: Parker

first: Jasna

last: Kovac

first: Robert

last: Hancock

first: Erin

last: Gaynor


title: Transcriptional profiles of IL-4 stimulated mouse peritoneal macrophages derived from different cellular lineages and of different genetics backgrounds

first: Mei San

last: Tang

overall_design: We FACS-sorted IL-4 stimulated mouse peritoneal macrophages of F4/80hi CD206- (tissue resident) and F4/80int CD206+ (monocyte-derived) phenotypes for transcriptional profiling by CEL-Seq2 (Hashimshony et al, Genome Biology 2016).

first: P'ng

last: Loke


title: RNA Seq Analysis of mouse primary hepatocytes treated with Neurotropin

city: Shanghai

first: Qinglan

last: Wang

address: 1200 Cailun Road

institute: Shanghai University of Traditional Chinese Medicine

summary: Purpose:The goals of this study are to find the genes regulated by Neurotropin (NTP)

overall_design: Primary hepatocytes were pretreated with NTP for 1 h, followed by treatment with 200 uM palmitate (PA) or 12 uM linoleate (LA) for an additional 24 h.

first: Ekihiro

last: Seki


title: Gene expression analyses of GI eosinophils and macrophages from naive colons and intra-tumor

city: Tel Aviv

first: Hadar

last: Reichman

address: 30 Haim Levanon

department: Microbiology & Immunology

institute: Tel Aviv University

summary: RNA-seq was performed on eosinophlis/macrophages isolated from colons of naive or tumor bearing C57/BL6 mice.

overall_design: RNA-seq analysis of eosinophils and macrophages from naive colons and tumors

first: Ariel

last: Munitz


title: Ozone exposure differentially changed global gene expression at brainstem and hypothalamus in healthy (SHAM) and adrenalectomized rats

status: Public on Dec 31 2019

city: RTP

first: John

middle: S.

last: House

state: NC

address: 111 TW Alexander Drive

department: Biostatistics & Computational Biology Branch

institute: National Instititute of Environmental Health Sciences

summary: Ozone exposure in SHAM rats resulted in increases and decreases in expression of hundreds of genes in brainstem and hypothalamus relative to air-exposed SHAM rats (303 and 568 genes, respectively). Adrenalectomy in air-exposed rats resulted in few significant transcriptional differences in the brainstem and hypothalamus (~20 genes per tissue).  Differentially expressed genes from ozone exposure were enriched for pathways involving hedgehog signaling, responses to alpha-interferon, hypoxia, and  mTORC1, among others. Gene changes in both brain areas were analogous to those altered by corticosteroids and L-dopa, suggesting a role for endogenous glucocorticoids and catecholamines. AD completely prevented this ozone-induced transcriptional response. These findings show that short-term ozone inhalation promotes a shift in brainstem and hypothalamic gene expression that is dependent on the presence of circulating adrenal-derived stress hormones.

overall_design: Adult SHAM and adrenalectomized rats were exposed  to filtered air or ozone (0.8 ppm, whole-body) for 4hr (~0700 - 1100 AM). Immediately after, hypothalamus and brainstem were collected and frozen.Later, RNA was extracted and sequenced.

first: Andres

middle: R

last: Henriquez

middle: S

first: Samantha

last: Snow

first: Colette

middle: N

last: Miller

first: Mette

last: Schladweiler

first: Anna

last: Fisher

first: Hongzu

last: Ren

first: Matthew

last: Valdez

first: Prasada

last: Kodavanti

first: Urmila

middle: P


title: Involvement of in vitro TNF receptor signaling in normal and neoplastic breast epithelial cell fusion with human mesenchymal stroma/stem cells (MSC)

city: Hannover

first: Ralf

last: Hass

state: Germany

address: Carl-Neuberg-Str. 1

department: Gynecology

institute: Hannover Medical School

summary: Co-cultures of MSC with neoplastic MCF10A cells demonstrated hybrid cell formation between 0.3% and about 2% of the populations within 72h

overall_design: In total, 4 different total RNA samples were subjected to microarray analysis according to a single-color design.

first: Catharina

last: Melzer


title: Gastrointestinal tissue-specific chromatin accessibility and gene expression during development (ChIP-seq)

city: TORONTO

first: Haiyang

last: Guo

address: 101 College Street, 11-601D, TMDT, 11-601D, TMDT

department: Princess Margaret Cancer Centre

institute: UNIV HEALTH NETWORK

summary: We used H3K27ac ChIP-Seq to profiling epigenomic changes during the embryonic development of gastrointestinal  tract.

overall_design: H3K27ac ChIP-Seq of mouse embryonic tissues

first: Roshane

last: Francis

first: Musa

last: Ahmed

first: Theodora

last: Yung

first: Peter

middle: B

last: Dirks

first: Housheng

middle: H

last: He

first: Tae-Hee

last: Kim


title: Genome-wide synthetic lethal CRISPR screen identifies FIS1 as a genetic interactor of ALS-linked C9ORF72

status: Public on Dec 23 2019

city: Stanford

first: Julien

last: Couthouis

state: CA

address: 279 Campus Dr

department: Genetics

institute: Stanford University

summary: Mutations in the C9ORF72 gene are the most common cause of amyotrophic lateral sclerosis (ALS). Both toxic gain of function and loss of function pathogenic mechanisms have been proposed. Accruing evidence from mouse knockout studies point to a role for C9ORF72 as a regulator of immune function. To provide further insight into its cellular function, we performed a genome-wide synthetic lethal CRISPR screen in human myeloid cells lacking C9ORF72. We discovered a strong synthetic lethal genetic interaction between C9ORF72 and FIS1, which encodes a mitochondrial membrane protein involved in mitochondrial fission and mitophagy. Mass spectrometry experiments revealed that in C9ORF72 knockout cells, FIS1 strongly bound to a class of immune regulators that activate the receptor for advanced glycation end (RAGE) products and trigger inflammatory cascades. These findings present a novel genetic interactor for C9ORF72 and suggest a compensatory role for FIS1 in suppressing inflammatory signaling in the absence of C9ORF72.

overall_design:
RNA-seq: RNA was extracted from undifferentiated and PMA-treated control and C9KO U937 cells using the PureLink RNA Mini Kit (Life Technologies) according to the manufacturer’s protocol, with on-column PureLink DNase treatment. Total RNA concentration and quality control was determined using the RNA 6000 Nano assay kit (Agilent) on the Agilent 2100 Bioanalyzer System for all samples. mRNA libraries were prepared for Illumina paired-end sequencing using the Agilent SureSelect Strand Specific RNA-Seq Library Preparation kit on the Agilent Bravo Automated Liquid Handling Platform. Libraries were sequenced on an Illumina HiSeq 4000 sequencer. Alignment of RNA-sequencing reads to the transcriptome was performed using STAR with ENCODE standard options, read counts were generated using rsem, and differential expression analysis was performed in R using DESeq2 package (Love et al., 2014). All bioinformatics analyses were performed on Sherlock, a Stanford HPC cluster.
CRISPR screen: The lentiviral genome-wide sgRNA library was produced and infected separately into control and C9KO U937 cells stably expressing EF1a-Cas9-Blast as previously described (Haney et al., 2018). Control and C9KO infected populations were maintained in separate spinner flasks. Briefly, ~300 million control cells and ~300 million C9KO cells were infected with the 10 guide/gene genome-wide sgRNA library at a MOI < 1. Infected cells underwent puromycin selection (1ug/mL) for 5 days. Puromycin was then removed and cells were resuspended in normal growth media without puromycin. After selection, sgRNA infection was measured by flow cytometry confirming that > 90% of cells were mCherry+. Sufficient sgRNA library representation at the starting point of the screen was confirmed by Illumina sequencing after selection. Cells were maintained for 10 days at 1000× coverage (~1000 cells containing each sgRNA) at a concentration of 500,000 cells/mL, after which ~450 million control and ~450 million C9KO cells were removed for 50nM PMA differentiation in three 15cm plates as described above. At the end of the 5 day differentiation, genomic DNA was extracted for all screen populations separately according to the protocol included with QIAGEN Blood Maxi Kit. sgRNA sequences were amplified and prepared for deep-sequencing by two sequential PCR reactions as described previously (Morgens et al., 2016). Final PCR products were sequenced using an Illumina NextSeq.

first: Noori

last: Chai

first: Michael

last: Haney

first: David

middle: W

last: Morgens

first: Kathryn

last: Wu

middle: C

last: Bassik

first: Aaron

last: Gitler


title: AGO HITS-CLIP Reveals Distinct Patterns of miRNA Regulation of Visceral and Brown Adipose Tissue Identity

status: Public on Dec 28 2019

city: New York

first: Sean

last: O'Connor

state: NY

address: 1230 York Ave

department: Laboratory of Molecular Metabolism

institute: Rockefeller University

summary: Wildtype mouse adipose tissue was dissected and subjected to Ago-CLIP sequencing to identify Ago:RNA regulatory sites and RNA sequencing. Adipose tissue from a separate cohort of mice was used for small RNA sequencing.

overall_design: Ago-CLIP sequencing mRNA sequencing analysis for two types of wildtype mouse adipose tissue and miRNA sequencing analysis for six types of wildtype mouse adipose tissue.