title: RNA Seq of TFH cells in Th1 vaccine regimen

status: Public on Dec 10 2019

city: Pittsburgh

first: Smita lab

last: Lab

state: PA

address: 3550 Terrace Street

department: Pathology

country: USA

institute: University of Pittsburgh

summary: Generating durable humoral immunity through vaccination depends upon effective interaction of follicular helper T cells (Tfh) with germinal center (GC) B cells. Th1 polarization of Tfh cells is an important process shaping the success of Tfh-GC B cell interactions by influencing co-stimulatory and cytokine-dependent Tfh help to B cells. However, the question remains whether adjuvant-dependent modulation of Tfh cells enhances HIV-1 vaccine-induced anti-Envelope (Env) antibody responses. We investigated whether an HIV-1 vaccine platform designed to increase the number of Th1-polarized Tfh cells enhances the magnitude and quality of anti-Env antibodies. Utilizing a novel interferon-induced protein (IP)-10-adjuvanted HIV-1 DNA prime, followed by an MPLA+QS-21-adjuvanted Env protein boost in macaques (DIP-10 PALFQ), we observed higher anti-Env serum IgG titers with greater cross-clade reactivity, specificity to V1V2, and effector functions when compared to macaques primed with DNA lacking IP-10 and boosted with MPLA+alum-adjuvanted Env protein (DPALFA) The DIP-10 PALFQ vaccine regimen elicited higher anti-Env IgG1 and lower IgG4 antibodies in serum, showing for the first time that adjuvants can dramatically impact the IgG subclass profile in macaques. The DIP-10 PALFQ regimen also increased vaginal and rectal IgA antibodies to a greater extent. Within lymph nodes, we observed augmented GC B cell responses and promotion of Th1 gene expression profiles in GC Tfh cells. The frequency of GC Tfh cells correlated with both the magnitude and avidity of anti-Env serum IgG. Together, these data suggest that adjuvant-induced stimulation of Th1-Tfh cells is an effective strategy for enhancing the magnitude and quality of anti-Env antibody response.

overall_design:
We report enrichment of Th1 transcriptional profiles in TFH cells following vaccination with DIP-10PALFQ
Comparision of transciptome profiles across CD4 subsets

first: Smita

last: Iyer


title: Gene expression profile of liver obtained from liver-specific LPIAT1 KO (LKO) mice on chow or high fat diet (HFD).

status: Public on Dec 13 2019

city: Hongo, Bunkyo-ku

first: Yuta

last: Shimanaka

state: Tokyo

department: Graduate School of Pharmaceutical Sciences

country: Japan

institute: University of Tokyo

summary: To investigate gene expression changes induced by LPIAT1 depletion, Lpiat1F/F and LKO mice were fed high fat diet (HFD) or chow for 18 weeks from 6 weels old and microarray gene profiling were performed. Categorization of the differentially expressed genes between HFD-fed Lpiat1f/f and LKO mice, in relation to their functions in biological pathways, revealed an enrichment of genes involved in inflammation and fibrosis

overall_design: 4 samples

first: Yuki

last: Tanaka

first: Hiroyuki

last: Arai

first: Nozomu

last: Kono


title: CD94-CD56dim, CD94+CD56dim and CD94+CD56hi natural killer (NK) cell chromatin histone modification assay

city: Worcester

first: Alan

middle: G

last: Derr

state: Massachusetts

address: 55 Lake Ave North

department: Program in Bioinformatics and Integrative Biology

institute: University of Massachusetts Medical School

summary: CUT and RUN  was performed for 3 NK populations and found CD94+CD56hi NK cells exhibit unique H3K4me1, H3K4me4 enriched region, we also identified TCF7 binding region in CD94+CD56hi NK cells.

overall_design:
CD94-CD56dim, CD94+CD56dim and CD94+CD56hi NK cells were sorted then subject to CUT and RUN using antibodies against rabbit IgG, H3K4me1, H3K4me3, H3K27ac, H3K27me3, TCF7

A note on the file naming convention:
 - "sample1" or "sample2" represents 2 different donors;
 - "minus" represents CD94-CD56dim NK cells, "plus" represents CD94+CD56dim NK cells, "plusplus" represents  CD94+CD56hi NK cells.
 - The last digit "0-5" represents different antibodies used in CUT&RUN:
     "0" represents Rabbit anti-human IgG
     "1" represents anti-H3K4me1
     "2" represents anti-H3K27ac
     "3" represents anti-H3K4me3
     "4" represents anti-TCF7
     "5" represents anti-H3K27me3

Example: GSM3473668 "cut and run sample1 minus0" in GEO data set means Rabbit anti-human IgG CUT&RUN for CD94-CD56dim NK cells from donor 1.

first: Yetao

last: Wang

first: Lawrence

last: Lifshitz

first: Pranitha

last: Vangala

first: Alper

last: Kucukural

first: Patrick

last: McDonel

first: Manuel

last: Garber

first: Jeremy

last: Luban


title: microRNA expression during tooth development

status: Public on Dec 07 2019

city: Sendai

first: Takashi

last: Nakamura

address: 4-1 Seiryomachi, Aobaku

institute: Tohoku University Graduate School of Dentistrey

summary: We investigated expression profiles of miRNAs in developing first molars at E16, P1, and P3.

overall_design: Small RNA samples prepared from developing molars were examined by means of Genopal®-MICH07 DNA chips.

first: Satoshi


title: Transcriptomic analysis of cyst germination in Rhodospirillum centenum

city: Bloomington

first: Nandhini

last: Ashok

state: INDIANA

address: 212 south hawthorne drive

department: Biology

institute: Indiana University Bloomington

type: Expression profiling by high throughput sequencing

summary: We extracted and sequenced the RNA during different stages of an 8 hour cyst germination in Rhodospirillum centenum. It has aided in defining the chronology of molecular events during dormant cell germination in this model Gram-negative, cyst-forming organism.

overall_design: Cysts of Rhodospirillum centenum were induced to germinate in nutrient rich CENS medium. RNA extracted from 0hr, 0.5hr, 1hr, 1.5hr, 2hr, 2.5hr, 3hr, 4hr, 5hr, 6hr, 7hr and 8hours after induction of germination. RNA sequenced and each time point compared to 0hr to define pathways and processes (time-wise) that get up/downregulated during germination. Done in triplicates

first: Carl

middle: E

last: Bauer


title: Diacetyl determines plant-bacteria relation via phosphate-dependent modulation of plant immunity

status: Public on Dec 03 2019

city: Shanghai

first: Huiming

last: Zhang

address: No. 3888 Chenhua Road

country: China

institute: Shanghai Center for Plant Stress Biology, and CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences

summary: Plants establish mutualistic association with beneficial microbes while deploy the immune system to defend against pathogens. Little is known about the interplay between mutualism and immunity and about the mediator molecules. Here we show that plants respond differently to a bacterial volatile compound through integral modulation of the immune system and the phosphate starvation response (PSR) system, resulting in either mutualism or immunity. We found that the same exposure of a recognized plant growth-promoting rhizobacterium unexpectedly causes either beneficial or deleterious effects to plants. The beneficial-to-deleterious transition is dependent on plant nutrition of phosphorus (P) and is mediated by diacetyl (DA), a bacterial volatile compound. In P-sufficient plants, DA partially suppresses plant production of reactive oxygen species (ROS) and enhances symbiont colonization without compromising disease resistance. In P-deficient plants, DA elevates phytohormone-mediated immunity and consequently causes plant hypersensitivity to P deficiency. Therefore, DA affects the types of relation between plants and certain rhizobacteria in a way that depends on plant PSR system and phytohormone-mediated immunity.

overall_design: RNA-Seq of 6 samples, each has 2 replicates. The first four samples are for GMVs treatment, HMZ008_0.05 denotes, plants grown on nutrient deficient medium (1/20th strength MS medium) and samples HMZ008_0.5, refer to plant grown on 1/2 MS medium. C= mock samples and T= samples treated with GMVs. Last two samples are plants grown on 1/2 strength MS medium analysed for effect of diacetyl on platnt transcriptome, HMZ014_CK=mock and HMZ014_Dione= plants treated with 200µM Diacetyl.

first: Rafael

middle: J

last: Morcillo

first: Sunil

middle: K

last: Singh

first: Danxia

last: He

first: Guo

last: An

first: Kai

last: Tang

first: Jian-Kang

last: Zhu


title: Spatial genome re-organization between fetal and adult hematopoietic stem cells

status: Public on Dec 16 2019

city: PHILADELPHIA

last: Tan

address: 3501 CIVIC CENTER BLVD.

institute: Children's Hospital of Philadelphia

type: Genome binding/occupancy profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Massively multiplex chemical transcriptomics at single cell resolution

status: Public on Dec 05 2019

city: New York

first: José

middle: L

last: McFaline-Figueroa

email: jm5200@columbia.edu, joselmc@uw.edu

state: NY

department: Biomedical Engineering

institute: Columbia University

summary: Single-cell RNA-seq libraries were generated using two and three level single-cell combinatorial indexing RNA sequencing (sci-RNA-seq) of untreated or small molecule inhibitor exposed HEK293T, NIH3T3, A549, MCF7 and K562 cells. Different cells and different treatment were hashed and pooled prior to sci-RNA-seq using a nuclear barcoding strategy. This nuclear barcoding strategy relies on fixation of barcode containing well-specific oligos that are specific to a given cell type, replicate or treatment condition.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

first: S

last: Srivatsan

first: J

first: V

last: Ramani

first: L

last: Saunders

last: Cao

last: Packer

first: H

middle: A

last: Pliner

first: D

last: Jackson

first: R

middle: M

last: Daza

last: Christiansen

first: F

last: Steemers

last: Shendure

first: C

last: Trapnell


title: Sphingosine 1-phosphate receptor signaling establishes AP-1 transcriptional factor  gradients and permits retinal endothelial specialization

city: Boston

first: Eric

last: Engelbrecht

state: MA

address: 1 Blackfan Street

department: Vascular Biology Program

institute: Boston Children's Hospital

summary: Transcriptional mechanisms that drive angiogenesis and organotypic endothelial specialization are poorly understood. Here, we show that retinal endothelial sphingosine 1-phosphate receptors (S1PRs), which restrain vascular endothelial growth factor (VEGF)-induced angiogenesis, spatially restrict expression of JunB, a member of the activator protein 1 (AP-1) family of transcription factors. Mechanistically, VEGF induces JunB expression at the sprouting vascular front while S1PR-dependent VE-cadherin assembly suppresses JunB expression in the nascent vascular network, thus creating a gradient of this transcription factor. Endothelial-specific JunB knockout mice showed diminished expression of neurovascular guidance genes and attenuated retinal vascular network progression. In addition, endothelial S1PR signaling is required for normal expression of ß-catenin-dependent genes such as TCF/LEF1 and ZIC3 transcription factors, transporters and junctional proteins. These results show that S1PR signaling restricts JunB function to the expanding vascular front, thus creating an AP-1 transcriptional factor gradient and enables organotypic endothelial specialization of the vascular network.

overall_design: Individual biological replicates represents retinas from 4-6 P6 pups pooled for FACS isolation of retinal endothelial cells for each experiment (ATAC-seq and RNA-seq). N=5 for RNAseq, N=3 for ATAC-seq.

first: Keisuke

last: Yanagida

first: Timothy

last: Hla


title: The MADS-box transcription factor PHERES1 controls imprinting in the endosperm by binding to domesticated transposons

city: Uppsala

first: Juan

middle: C

last: Santos-González

state: Uppsala

address: Almas Allé 5

department: Department of Plant Biology and Forest Genetics

country: Sweden

institute: SLU

summary: MADS-box transcription factors (TFs) are ubiquitous in eukaryotic organisms and play major roles during plant development. Nevertheless, their function in seed development remains largely unknown. Here we show that the imprinted Arabidopsis thaliana MADS-box TF PHERES1 (PHE1) is a master regulator of paternally expressed imprinted genes, as well as of non-imprinted key regulators of endosperm development. PHE1 binding sites show distinct epigenetic modifications on maternal and paternal alleles, correlating with parental-specific transcriptional activity. Importantly, we show that the CArG-box-like DNA-binding motifs bound by PHE1 have been distributed by RC/Helitron transposable elements. Our data provide an example of molecular domestication of these elements, which by distributing PHE1 binding sites throughout the genome, have facilitated the recruitment of crucial endosperm regulators into a single transcriptional network.

overall_design: PHE1::PHE1-GFP ChIPs were performed on 2DAP siliques of plants expressing a PHE1::PHE1-GFP construct. Two biological replicates were used. Analysis of H3K27m3 modifications in Ler x Col-osd1 endosperm in Arabidopsis include two replicates for each cross. RNA-seq  experiments were performed on 6DAP seeds derived from the indicated crosses. Two biological replicates for each cross were used.

first: Rita

last: Batista

first: Jordi

last: Moreno-Romero

first: Yichun

last: Qiu

first: Joram

last: van Boven

first: Duarte

middle: D

last: Figueiredo

first: Claudia

last: Köhler


title: Genome-wide gene expression profiles of primary prostate cancer

status: Public on Dec 06 2019

city: Seattle

first: Janet

middle: L.

last: Stanford

state: WA

address: 1100 Fairview Ave. N.

institute: Fred Hutchinson cancer research center

summary: Prognostic biomarkers are useful to screen patients with clinically localized prostate cancer (PCa) who are at high risk of metastatic progression. The tumor transcriptome can be used to evaluate the aggressiveness of PCa and predict adverse patient outcomes. Genomewide gene expression levels were measured in primary tumor samples of 503 patients in a population‐based cohort.

overall_design: Formalin‐fixed, paraffin‐embedded (FFPE) PCa tumor tissue blocks were obtained from radical prostatectomy samples and used to make H&E‐stained slides, which were reviewed by a PCa pathologist to confirm the presence of and the location of prostate adenocarcinoma. For each patient, two 1‐mm tumor tissue cores were taken from the areas enriched with ≥ 75% tumor cells from the dominant lesion. The RNeasy® FFPE Kit (Qiagen Inc., Valencia, CA, USA) was used to isolate the RNA from tissue cores, and the samples were quantified with RiboGreen, aliquoted (200 ng per patient) onto 96‐well plates, and shipped to Illumina for gene expression profiling. Tumor RNA samples from patients with various outcomes were randomly distributed across the plates and laboratory personnel were blinded to this information.


title: Tristetraprolin targets Nos2 expression in the colonic epithelium

status: Public on Dec 04 2019

city: Hershey

first: Yuka

last: Imamura Kawasawa

address: 500 University Dr.

department: College of Medicine, Pharmacology

institute: Penn State University

summary: Tristetraprolin (TTP), encoded by the Zfp36 gene, is a zinc-finger protein that regulates RNA stability primarily through association with 3’ untranslated regions (3’UTRs) of target mRNAs. While TTP is expressed abundantly in the intestines, its function in intestinal epithelial cells (IECs) is unknown. Here we used a cre-lox system to remove Zfp36 in the mouse epithelium to uncover a role for TTP in IECs and to identify target genes in these cells. While TTP was largely dispensable for establishment and maintenance of the colonic epithelium, we found an expansion of the proliferative zone and an increase in goblet cell numbers in the colon crypts of Zfp36ΔIEC mice. Furthermore, through RNA-sequencing of transcripts isolated from the colons of Zfp36fl/fl and Zfp36ΔIEC mice, we found that expression of inducible nitric oxide synthase (iNos or Nos2) was elevated in TTP-knockout IECs. We demonstrate that TTP interacts with AU-rich elements in the Nos2 3’UTR and suppresses Nos2 expression. In comparison to control Zfp36fl/fl mice, Zfp36ΔIEC mice were less susceptible to dextran sodium sulfate (DSS)-induced acute colitis. Together, these results demonstrate that TTP targets Nos2 expression in IECs and aggravates acute colitis.

overall_design: Colonic mRNA profiles of 6- to 8- week old Zfp36fl/fl and Zfp36ΔIEC mice were generated by deep sequencing, in triplicate.

first: Melanie

last: Eshelman

middle: I

last: Kawasawa

first: Gregory

middle: S

last: Yochum


title: Insights from long non-coding RNAs profiling of beta cells undergoing high glucose/palmitate -induced glucolipotoxicity

status: Public on Dec 01 2019

city: WUhu

first: Xiang

last: Kong

address: zheshanxi road NO 2

department: Central Laboratory of Yijishan Hospital

institute: The First Aflliated Hospital of Wannan Medical College

summary: RNA-Seq  was performed to compare the control INS-1 cells (rat beta cell line)with the high glucose/palmitate-treated INS-1 cells. According to the expression profiling data, 264 significantly dysregulated lncRNAs were identified with a set filter (fold-change ≥2.0, p < 0.05) in the HG/PA-treated INS-1 cells: 153 were up-regulated, while 111 were down-regulated.

overall_design: Identify the lncRNAs that are differentially expressed in high glucose/palmitate-treated INS-1 beta cells by RNA sequencing

first: L

middle: V

last: Kun


title: Virus-induced immune response during pregnancy

city: Maastricht

first: Christof

last: Seiler

address: Bouillonstraat 8-10

department: Department of Data Science and Knowledge Engineering

country: Netherlands

institute: Maastricht University

summary: We evaluated transcriptional profiles in peripheral blood mononuclear cells (PBMCs) from 54 pregnant women in Kenya, 19 of whom delivered preterm.

overall_design: To characterize immune function in these women, we either left PBMCs unstimulated or stimulated the PBMCs in vitro with the A/California/2009(pH1N1) strain of influenza to understand the virus-induced immune response.

first: Nicholas

last: Bayless

first: Rosemary

last: Vergara

first: Catherine

last: Blish


title: Differences in serum proteins in traditional Chinese medicine constitutional population: analysis and verification

status: Public on Nov 22 2019

city: Guangzhou

first: Huihua

last: Zhang

address: 601, west Huangpu avenue, Tianhe district

department: Biomedicine Institute & Cell Biology Department

institute: Jinan University

summary: Using high-throughput antibody microarray, through cross-sectional sample detection and verification of samples that had undergone physical changes over time, it was found that people with balanced constitution and dampness constitution in Chinese medicine showed differences in serum protein expression. The differences were expressed as the level changes of 19 proteins such as Dectin-2, Siglec-7, AIF and TACI. The research results provided the basis for the scientific expression of traditional Chinese medicine (TCM) constitution.

overall_design: We prospectively enrolled two cohorts into for our study. The first cohort included 4 balanced constitution (BC) individuals transformed to dampness constitution (DC), another 3 DC individuals transformed to BC.  The second cohort contained 38 DC individuals and 37 BC individuals with no diagnosed diseases. Whole blood was collected in vacutainer serum tubes, and then 1000 serum proteins were analyzed simultaneously using an antibody-based array. We identified and verified 19 different serum proteins by high-throughput antibody microarray technology in BC and DC group, as well as serum profiles with constitution changes at different time points. Meanwhile, these differential proteins were closely related to clinical information such as human lifestyle and characteristics by established SVM model, sensitivity and specificity screening. We found that the main functions of these differential proteins were mainly focused on the immunity and inflammation by functional analysis, which might be the biological basis for the differences between BC and DC group.

first: Ruo-Pan

last: Huang

first: Zhimin

last: Yang


title: Transgenic mice expressing tunable levels of DUX4 develop characteristic facioscapulohumeral muscular dystrophy-like pathophysiology ranging in severity

first: Guo-Liang

last: Chew

address: 1100 Fairview Ave N

department: Basic Sciences and Public Health Sciences

institute: Fred Hutchinson Cancer Research Center

summary: All types of facioscapulohumeral muscular dystrophy (FSHD) are caused by the aberrant myogenic activation of the somatically silent DUX4 gene, which initiates a cascade of cellular events ultimately leading to FSHD pathophysiology.  Therefore, FSHD is a dominant gain-of-function disease that is amenable to modeling by DUX4 overexpression.  However, there is large variability in the patient population.  Typically, progressive skeletal muscle weakness becomes noticeable in the second or third decade of life, yet there are many genetically FSHD individuals who develop symptoms much later in life or remain relatively asymptomatic throughout their lives.  Conversely, in rare cases, FSHD may present clinically prior to 5-10 yrs of age, ultimately manifesting as a very severe early onset form of the disease.  Thus, there is a need to control the timing and severity of pathology in FSHD-like models.  Methods: We have recently described a line of conditional DUX4 transgenic mice, FLExDUX4, that develop a myopathy upon induction of human DUX4-fl expression in skeletal muscle.  Here, we use the FLExDUX4 mouse crossed with the skeletal muscle-specific and tamoxifen inducible line ACTA1-MerCreMer to generate a highly versatile bi-transgenic mouse model with chronic, low-level DUX4-fl expression and mild pathology, that can be induced to develop more severe FSHD-like pathology in a dose-dependent response to tamoxifen.  We identified conditions to reproducibly generate models exhibiting mild, moderate, or severe DUX4-dependent pathophysiology, and characterized their progression.  Results:  We assayed DUX4-fl mRNA and protein levels, fitness, strength, global gene expression, histopathology, and immune response, all of which are consistent with an FSHD-like myopathic phenotype.  Importantly, we identified sex-specific and muscle-specific differences that should be considered when using these models for preclinical studies.  Conclusions:  The ACTA1-MCM;FLExDUX4 bi-transgenic mouse model expresses a chronic low level of DUX4-fl and has mild pathology and detectable muscle weakness.  The onset and progression of moderate to severe pathology can be controlled via tamoxifen injection to provide consistent and readily screenable phenotypes for assessing therapies targeting DUX4-fl mRNA and protein.  Thus, these FSHD-like mouse models can be used to study a range of DUX4-fl expression and pathology dependent upon investigator need, through controlled mosaic expression of DUX4.

overall_design: Gene expression profiling of dissected muscle from mouse models of FSHD by high throughput sequencing of mRNA

first: Takako

last: Jones

first: Pamela

last: Barraza-Flores

first: Spencer

last: Schreier

first: Monique

last: Ramirez

first: Ryan

last: Wuebbles

first: Dean

last: Burkin

first: Robert

last: Bradley

first: Peter


title: Staging Alzheimer’s disease in brains and retinas of APP/PSEN1 mice by transcriptional profiling

status: Public on Nov 25 2019

city: Farmington

first: Asli

last: Uyar

state: CT

address: 10 Discovery Dr

department: Computational Sciences

institute: The Jackson Laboratory

summary: Alzheimer’s disease (AD) is a common form of dementia characterized by amyloid plaque deposition, TAU pathology, neuroinflammation and neurodegeneration. Mouse models recapitulate some key features of AD. For instance, the B6.APP/PS1 model (carrying human transgenes for mutant forms of APP and PSEN1) shows plaque deposition and associated neuroinflammatory responses involving both astrocytes and microglia beginning around 6 months of age. However, in our colony, TAU pathology, significant neurodegeneration and cognitive decline are not apparent in this model even at older ages. Therefore, this model is ideal for studying neuroinflammatory responses to amyloid deposition. Here, RNA sequencing of brain and retinal tissue, generalized linear modeling (GLM), functional annotation followed by validation by immunofluorescence (IF) was performed in B6.APP/PS1 mice to determine the earliest molecular changes prior to and around the onset of plaque deposition (2-6 months of age).

overall_design: Brain transcriptomes of 2, 4, 5 and 6-month old, and retina transcriptomes from 2 and 6-month old wild type (WT) and APP/PS1 female mice from C57BL/6J (B6) were generated.

first: Sumana

middle: R

last: Chintapaludi

first: Harriet

last: Jackson

first: Casey

last: Acklin

first: Xulong

last: Wang

first: Michael

last: Sasner

first: Gregory

middle: W

last: Carter

first: Gareth

last: Howell


title: Next Generation Sequencing Facilitates Quantitative Analysis of Yeast Cells Treated with and without Proanthocyanidins

status: Public on Nov 27 2019

city: Qingdao

first: Hongwei

last: Zhao

address: No.53 Zhengzhou Rd., Qingdao, China

institute: Qingdao University of Science and Technology

summary: Proanthocyanidins (PAs) could pose significant enhancement on the metabolism and fermentation efficiency of Saccharomyces cerevisiae yeast cells, which has been elucidated from metabolic level and cell phenotype in our previous work. The goals of this study are to compare the  transcriptome profiling (RNA-seq) of yeast cells treated with and without PAs to explore the possible global protection mechanism. After treated with 0 g/L, 0.1g/L, 1.0 g/L PAs, the total RNA of Saccharomyces cerevisiae strain AWRI R2 was extracted and sequenced at  Illumina HiSeq sequencing platform. The analysis yielded a total of 524025062 clean sequencing reads. The clean reads were processed for the following bioinformatics analysis.

overall_design: Saccharomyces cerevisiae strain AWRI R2 was cultivated in model synthetic medium (MSM) supplemented with 0 g/L, 0.1g/L, 1.0 g/L PAs  (marked as group A, group B and group C, respectively). The total RNA was extracted and sequencing library was prepared after quantity and quality evaluation. Illumina HiSeq sequencing platform was employed for the library sequencing at GENEWIZ (Suzhou, China). The sequencing data were processed in the following bioinformatics analysis after reads filtration.

first: Jingyuan

last: Li


title: Transcriptome analysis after IAA paste application on pin1 mutant inflorescence meristems

city: Mohali

first: Hasthi

last: Ram

address: Sector 81

department: Agriculture biotechnology

country: India

institute: NABI (National Agri-Food Biotechnology Institute)

summary: pin1 mutnat doesn't produce any floral organs, which can be rescued by exogenous application of IAA paste. Here we applied exogenous IAA paste and collected meristem tissue after different time points (30 min, 4hr, 12hr, 16hr). As a control we applied mock paste. Around 10 meristems were dissected under dissecting scope for each biological replicate. Some known IAA inducible genes were checked for their upregulation in extracted RNA, and there after the RNA was sequenced.

overall_design: 4 time points were used and 3-4 biological replicates were used for each time point.

first: Hathi

first: Sudeep

last: Sahadevan

first: Marcus

last: Heisler


title: Time course analysis of large-scale gene expression in incised muscle using correspondence analysis

status: Public on Nov 19 2019

city: Nagoya

first: Tetsuya

last: Horita

state: Aichi

address: 1 Kawasumi Mizuho-cho Mizuho-ward

department: Department of Forensic Medicine

institute: Nagoya City University Graduate School of Medical Sciences

summary: The time course of wound healing or the estimation of wound age is one of the most important research subjects in forensic pathology. In this study, we obtained microarray data of incision injury samples of mouse skeletal muscle at 3 different time points post-injury (6, 12, and 24 h). To visualize the time course fluctuation in gene expression on a plot, and to examine large-scale data using various analytical methods, correspondence analysis (CA) was carried out on microarray data that was converted to a matrix (data type is fold change (FC) values) consisting of data of each time point (columns) by each gene (rows) as variables. Genes were successfully clustered based on the magnitude relationship of FC values of 3 time series with a CA plot, which effectively visualizes the data of time course experiments.

overall_design: Pathogen-free 8-week-old male BALB/c mice were divided into 4 groups (control, 6, 12, and 24 h after injury: n=4 each). After nasal anesthesia of mice with isoflurane, the skin on the dorsal side of the left hind limb was shaved, and about a 1-cm incision was made on the skin using sterile straight stainless-steel scissors. Then, a 5 mm incision was made in the biceps femoris muscle, and then the skin incision was closed using a silk suture. At 6, 12, and 24 h after injury, a 3-mm thick injured muscle tissue sample (about 30 mg) with the injury in the center was excised. As a control sample, biceps femoris muscle was collected from an uninjured mouse that was euthanized without making the injury.

first: Mohammed

middle: H

last: Gaballah

first: Yasuhiro

last: Aoki


title: RNA-seq of Moraxella catarrhalis CCRI-195ME ModM3 ON and ModM3 OFF phase variants

status: Public on Nov 15 2019

city: Gold Coast

first: Kate

last: Seib

state: QLD

address: Parklands Drive

department: Institute for Glycomics

country: Australia

institute: Griffith University

summary: Moraxella catarrhalis contains an N6-adenine DNA-methyltransferase (ModM3), that is subject to phase variable expression (random ON/OFF switching). Phase-variable switching of DNA methyltransferase activity results in the presence or absence of methylation at a specific target sequence, leading to co-ordinated, epigenetically-regulated switching of expression of multiple genes across the genome. The suite of genes thus regulated are known as a phasevarion (phase-variable regulon). Phase variation of modM is mediated at the translational level by a 5′-(CAAC)n-3′ tetranucleotide repeat tract present within its open reading frame (ORF). Analysis of the genomes of 51 M. catarrhalis strains identified six modM alleles (modM1-6) that vary in their target recognition domains. The modM3 allele is also overrepresented in middle ear isolates of M. catarrhalis from children with OM. Here we characterise the genes regulated in the ModM3 phasevarion and show that phase variation of the M.catarrhalis CCRI-195ME  ModM3 epigenetically regulates the expression of a phasevarion containing multiple genes that are potentially important in the progression of otitis media.

overall_design: Direct comparison of biological triplicates of modM3 ON and modM3 OFF variants

first: Luke

last: Blakeway

first: Aimee

last: Tan

first: Joseph

last: Jurcisek

first: Lauren

middle: O

last: Bakaletz

first: John

last: Atack

first: Ian

last: Peak


title: MicroRNA-431 promotes metastasis of pancreatic neuroendocrine tumors by targeting DAB2IP, a RasGAP tumor suppressor

status: Public on Nov 21 2019

first: Nancy

last: Du

state: New York

address: 1300 York Ave

institute: Weill Cornell Medicine

summary: Analysis of  pathways regulated by miR-431 at the mRNA expression levels in pancreatic neuroendocrine tumor cells

overall_design: Total RNA was extracted from actively growing mouse pancreatic neuroendocrine tumor cell line (N134) overexpressing GFP-miR-LacZ (control) and GFP-miR-431.

first: Yi-Chieh Nancy

first: Soyoung

last: Choi

first: Tuo

last: Zhang

first: Jenny

middle: Z

last: Xiang


title: Gene expression of human chord blood hematopoietic progenitor cells and induced hemato-endothelial progenitor cells derived from human iPSC

status: Public on Nov 13 2019

city: Hannover

first: Adrian

last: Schwarzer

address: Carl-Neuberg-Str. 1

department: Experimental Hematology

country: Germany

institute: Hannover Medical School

summary: Induced pluripotent stem cells (iPSC) offer a promising platform to model early embryonic developmental processes, to create disease models and proof-of-concept experiments for regenerative medicine. However, generation of iPSC derived hemato-endothelial and hematopoietic progenitor cells for these applications is challenging due to variable and limited cell numbers, which necessitates enormous up-scaling or development of demanding protocols. Here, we unravel the function of key transcriptional regulators SCL, LMO2, GATA2, ETV2 (SLGE) on early hemato-endothelial specification and establish a fully inducible and stepwise hemato-endothelial forward programming system, based on SLGE regulated overexpression. Regulated induction of SLGE in stable SLGE-iPSC lines drives very efficient generation of large numbers of hemato-endothelial progenitor cells (HEP) (CD144+/CD73-), which generate hematopoietic progenitor cells (CD45+/CD34+/CD38-/CD45RA-/CD90+/CD49f+) through a gradual process of endothelial-to-hematopoietic transition (EHT).

overall_design: A human fibroblast-derived iPSC line (H2E6C) was engineered to conditionally (doxycyclin-induction) express the transcription factors  SCL (S), LMO2 (L), GATA2 (G) and ETV2 (E). On day 0, Phase I (hemato-endothelial programming; "SLGE-HEP") was started with a change to differentiation medium and an initial mesodermal priming boost by adding a GSK3 inhibitor (CHIR990221). After mesodermal priming, expression of SGLE was initiated by addition of Dox on day 1. Cells were differentiated towards the hemato-endothelial lineage via SLGE-expression and a mixture of supportive cytokines (SCF, TPO, IL-3, FGF2, VEGF). Phase II (generation of hematopoietic progenitor cells; "SLGE-HPC") was started on day 7 by Dox-withdrawal and cultivation of dissociated SLGE-HEP in STEMdiff APEL 2 medium supplemented SCF, TPO, Flt3L, IL-3 and FGF2. RNA-Seq was performed from iPS, day1, day 2, day 7 SLGE-HEP and compared to day 11 SLGE-HPC and human umbilical cord blood (CB)  hematopoietic stem cells sorted for CD45+/CD34+/CD38-/CD45RA-/CD90high/CD49fhigh expressing cells.

first: Lucas

last: Lange


title: Single-cell and spatial transcriptomics reveal somitogenesis in gastruloids

city: Utrecht

first: Anna

last: Alemany

state: Utrecht

address: Uppsalalaan 8

institute: Hubrecht Institue

summary: Gastruloids are three-dimensional aggregates of embryonic stem cells (ESCs) that display key features of mammalian post-implantation development, including germ layer specification and axial organization.  Gastruloids have mostly been characterized with microscopy-based approaches, limiting the number of genes that can be explored. It is therefore unclear to what extent gene expression in gastruloids reflects in vivo embryonic expression. Using both single-cell RNA-seq (scRNA-seq) and spatial transcriptomics we systematically compared cell types and spatial expression patterns between mouse gastruloids and mouse embryos.

overall_design:
RNA sequencing data from tissue sections isolated from mouse gastruloids (tomo-seq and scRNA-seq)

For mGst-Lfng-* samples, each processed data was generated from both run1 and run2 samples, and is linked to the corresponding run1 sample records.

first: Susanne

last: van den Brink

first: Vincent

last: van Batenburg

first: Naomi

last: Moris

first: Marloes

last: Blotenburg

first: Judith

last: Vivié

first: Peter

last: Baillie-Johnson

first: Jennifer

last: Nichols

first: Katharina

middle: F

last: Sonnen

first: Alfonso

last: Martinez-Arias

first: Alexander

last: van Oudenaarden


title: DNA methylation dynamics underlie metamorphic gene regulation programs in Xenopus tadpole brain [RNA-seq]

status: Public on Nov 08 2019

city: Ann Arbor

first: Robert

middle: J

last: Denver

state: Michigan

address: 1105 North University Ave

department: MCDB

institute: University of Michigan

summary: Changes in gene expression in the preoptic area/hypothalamus/thalamus of Xenopus tropicalis tadpoles were analyzed using RNAseq at four stages of metamorphosis.

overall_design: The middle brain region containing preoptic area/hypothalamus/thalamus was microdissected from Xenopus tropicalis tadpoles at four stages of metamorphosis: Nieuwkoop-Faber (NF) stage 50 (pre-metamorphosis), NF56 (pro-metamorphosis), NF62 (metamorphic climax), and NF66 (completion of metamorphosis). We isolated genomic DNA from tadpole brain to generate 3 biological replicates per developmental stage, isolated total RNA, generated libraries and did deep sequencing.

first: Christopher

last: Sifuentes

first: Yasuhiro

last: Kyono

first: Samhitha

last: Raj

first: Nicolas

last: Buisine

first: Laurent

last: Sachs


title: FIGLA, LHX8 and SOHLH1 transcription factor networks regulate mouse oocyte growth and differentiation

status: Public on Nov 06 2019

city: Bethesda

first: Chen-Yu

last: Liu

state: MD

address: 9000, Rockville Pike, Bldg 50, Rm. 3346

institute: NIDDK

summary: Germ-cell transcription factors control gene networks that regulate primordial follicle formation and oocyte differentiation during early, postnatal mouse oogenesis. Taking advantage of gene-edited mice lacking transcription factors expressed in female germ cells, we analyzed global gene expression profiles in perinatal ovaries from wildtype, FiglaNull, Lhx8Null and SohlhNull mice. Figla deficiency dysregulates expression of meiosis-related genes (e.g., Sycp3, Rad51 and Msy2) and a variety of genes (e.g., Nobox, Lhx8, Taf4b, Sohlh1, Sohlh2 and Gdf9) associated with oocyte growth and differentiation. The absence of FIGLA significantly impedes meiotic progression, causes DNA damage and results in oocyte apoptosis. Moreover, we find that FIGLA and other transcriptional regulators (e.g., NOBOX, LHX8, SOHLH1 and SOHLH2) are co-expressed in the same subset of germ cells in perinatal ovaries and Figla ablation dramatically disrupts KIT, NOBOX, LHX8, SOHLH1 and SOHLH2 expression. In addition, not only do FIGLA, SOHLH1 and LHX8 cross-regulate each other, they also cooperate by direct interaction with each during early oocyte development and share downstream gene targets. Thus, our findings substantiate a major role for FIGLA, LHX8 and SOHLH1 as multifunctional regulators of networks necessary for oocyte maintenance and differentiation during early folliculogenesis.

overall_design: RNA-seq was performed using embryonic day 18.5 (E18.5) or postnatal day 0 (P0) ovaires between control and Figla knockout mice in order to identify the differentially expressed genes. RNA-seq was performed using P0 ovaires between control and Lhx8 knockout mice in order to identify the differentially expressed genes.

first: Zhengpin

last: Wang

first: Jurrien

last: Dean


title: CpG dinucleotides introduced into gag can inhibit HIV-1 gene expression by modulating pre-mRNA splicing

status: Public on Nov 07 2019

city: London

first: Reiner

last: Schulz

address: 8th floor Guy's Tower

department: Medical & Molecular Genetics

country: United Kingdom

institute: King's College London

summary: Progressively longer regions of the gag gene sequence in HIV-1 were codon-optimized, which introduced 11, 18 or 26 CpGs (CM22-165: codon-optimized gag from nucleotide 22 to 165, adding 11 CpGs; CM22-261: 18 CpGs; CM22-378: 26 CpGs).

overall_design: Two independent transfections of HeLa cells with plasmids encoding HIV-1 provirus were performed for each of the codon-optimized HIV-1 versions as well as the un-optimized, wildtype version of HIV-1.

first: Chad

last: Swanson

first: Stuart

last: Neil

first: Harry

last: Wilson

first: Andrew

middle: E

last: Firth

first: Rupert

last: Hugh-White

first: Irati

last: Antzin-Anduetza

first: Mattia

last: Ficarelli

first: Helin

last: Sertkaya


title: CRISPRa-mediated Kcna1 upregulation decreases neuronal excitability and suppresses seizures in a rodent model of temporal lobe epilepsy

city: Milano

first: Luca

last: Massimino

state: MI

address: Via Olgettina, 58

department: Gastroenterology

country: Italy

institute: Ospedale San Raffaele

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

overall_design: Refer to individual Series


title: Proteomic and transcriptional profiling of rat amygdala following social play

status: Public on Nov 04 2019

city: Louisv

first: Juw

middle: Won

last: Park

state: KY

address: 213 Duthie Center

department: CECS

institute: University of Louisville

summary: Social play is a frequently studied behavior and it is the most characteristic form of social interaction observed in adolescent rats. Social play is necessary for adolescents to develop proper cognitive, emotional, and social competency. Deficits in social play have been observed in several neurodegenerative disorders such as autism, schizophrenia, and attention deficit hyperactivity disorder. However, the information available on neural substrates and the mechanism involved in social play is still limited. This study characterized social play by proteomic and transcriptional profiling studies. Social play was performed on male Sprague Dawley rats on postnatal day 38 and protein and gene expression in the amygdala was determined following behavioral testing. The proteomic analysis led to the identification of 170 differentially expressed proteins (p≤0.05) with 67 upregulated and 103 downregulated proteins. The transcriptomic analysis led to the identification of 188 genes (adjusted p≤0.05) with 55 upregulated and 133 downregulated genes. Based on both protein and gene expression data, DAVID analysis revealed that social play altered neurotransmitter signaling including GABAergic and glutamatergic signaling and G-protein coupled receptor (GPCR) signaling. These data suggest that the synaptic levels of GABA and glutamate increased during play. Ingenuity Pathway Analysis (IPA) confirmed these alterations. IPA also revealed that differentially expressed genes/proteins in our data had significant over representation of  additional neurotransmitter signaling systems, including the opioid, serotonin, and dopamine systems, suggesting that play alters the systems involved in the regulation of reward. In addition, corticotropin-releasing hormone signaling was altered indicating that an increased level of stress occurs during play. Our data suggest that increased inhibitory GPCR signaling in these neurotransmitter pathways occurs following social play as a physiological response to regulate the induced level of reward and stress and to maintain the excitatory-inhibitory balance in the neurotransmitter systems.

overall_design: Social play was performed on male Sprague Dawley rats on postnatal day 38 and gene expression in the amygdala was determined following behavioral testing. Total RNA was isolated from amygdala using a Qiagen miRNA easy micro kit (Germantown, MD) which is specialized for isolation of RNA from lipid rich tissue. The RNA quality was verified by NanoDrop. Each RNA sample containing 1 µg of RNA was used for poly A selected RNA-seq library preparation using the NEB Ultra-Directional RNA Library Prep Kit for Illumina, Cat# E7420. Each library was barcoded using NEBNext Multiplex Oligos for Illumina (Cat# E6609) based on the manufacturer's protocols. From total of 24 RNA-Seq libraries, 8 individual RNA-Seq libraries were equimolar pooling into one pooled library sample and sequenced with 1 lane of paired-end 100bp (2x100) using Illumina HiSeq4000 sequencer. Total of 3 lanes were subjected to sequencer.

first: Russell

last: Carr

first: Mohammed

last: Sayed


title: FMRP recruits AGO2, modulating access to miRNA recognition elements in G-Quadruplexes through association with Mov10.

city: Urbana

first: Phillip

middle: James

last: Kenny

state: IL

address: 407 S. Goodwin

institute: University of Illinois, Urbana-Champaign

summary: FMRP modulates AGO's association with microRNA Recognition elements.

overall_design: The analysis includes 2 samples. One sample was an AGO2 eCLIP of WT mouse brain.  One sample was an AGO2 eCLIP of FMR1 ko mouse brain

first: Stephanie

last: Ceman


title: Developmental ROS targets histone methylation to individualize stress resistance and lifespan

first: Bioinformatics

last: Core

address: BRCF Bioinformatics Core, 2800 Plymouth Rd

summary: We report the differences in gene expression between N2jrIs2[Prpl-17::Grx1-roGFP2] worms sorted based on their Grx1-roGFP2 into more oxidized or more reduced subpopulations (i.e. redox states between 2 and 3 standard deviations above (oxidized subpopulation) or below (reduced subpopulation) the mean population). We used fluorescence microscopy to confirm that the redox states of individuals sorted into oxidized and reduced subpopulations are indeed significantly different

overall_design: Total RNA from 4 biological replicates of worms (~10,000 individuals for each biological replicate) was used

first: Ursula

last: Jakob

first: Daphne

last: Bazoupolu

first: Rebecca

last: Tagett


title: Histone ChIP-Seq of neuroblastoma cell lines

status: Public on Nov 03 2019

city: Philadelphia

first: Jo Lynne

last: Rokita

state: PA

address: 3501 Civic Center Blvd

institute: Children's Hospital of Philadelphia

overall_design: Here, we provide H3K27Ac, H3K27me3, H3K4me1, and H3K4me3 ChIP-Seq for ten neuroblastoma cell lines.

first: J

middle: L

first: Kristen

last: Upton

first: John

middle: M

last: Maris


title: ATAC-Seq of neuroblastoma cell lines.

summary: ATAC-Seq of neuroblastoma cell lines.

overall_design: ATAC-Seq of 14 neuroblastoma cell lines.

first: Jo


title: RNA sequencing analysis of liver after overexpressing of hepatic miR-378

status: Public on Nov 02 2019

city: shanghai

first: chao

last: sun

state: shanghai

address: 320 Yueyang Road, Xuhui District, Shanghai, China

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

summary: An improved mechanistic understanding of the thyroid hormone (TH) action on bile acid (BA) synthetic pathway, the major route for cholesterol elimination, will facilitate the identification of novel therapeutic targets for hypercholesterolemia. Here, we show that hepatic miR-378 is positively regulated by TH. Transient overexpression of miR-378 in the liver of mice reduces the serum cholesterol levels, which is accompanied with an upregulation of key enzymes involved in the intrahepatic conversion of cholesterol to BAs. Importantly, transgenic mice with liver-specific and moderate overexpression of miR-378 also display a decrease in serum cholesterol levels accompanied with an enhanced BA synthesis and are resistant to diet-induced hypercholesterolemia. In contrast, mice lacking miR-378 exhibit an elevation of serum cholesterol levels accompanied with an impaired BA synthesis. Mechanistic studies reveal that hepatic miR-378 regulates BA synthesis and cholesterol homeostasis through its direct target gene MAFG, which is a transcriptional repressor of BA synthetic genes. We also show that miR-378 serves as an essential component in either incoherent or coherent feed-forward loop to confer robust and precise controls on BA synthesis in response to TH signalling. Together, we identify a previously undescribed miR-378-mediated mechanism underlying the cholesterol-lowering effect of TH. Our findings not only add a new dimension to our understanding the regulation of BA synthesis by TH, but also provide new therapeutic regimens to manage serum cholesterol levels.

overall_design: There are two groups, Ad-Ctrl and Ad-378, and three sample per group.

first: Chao

last: Sun

first: Wei

last: Liu


title: Molecular events controlling cessation of trunk neural crest migration and onset of differentiation

city: Northridge

first: Maria Elena

last: de Bellard

state: CA

address: 18111 Nordhoff St

department: Biology

institute: California State University Northridge

summary:
Neural crest cells migrate extensively in vertebrate embryos to populate diverse derivatives including ganglia of the peripheral nervous system.
Little is known about the molecular mechanisms that tell migrating trunk neural crest cells to settle at selected sites in the embryo by ceasing migration and initiating differentiation programs.

overall_design: Our study is the first to demonstrate that macrophage migration inhibitory factor (MIF), is a potent chemoattractant for tNCC that may regulate the process that leads migrating tNCC to coalesce into DRG.

first: Vivian

last: M. Lee

first: Sergio

last: Hernandez

first: Belle

last: Giang

first: Chris

last: Chabot

first: Jazmir

first: Maria


title: Global H-NS counter-silencing by LuxR activates quorum sensing gene expression [RNA-seq]

status: Public on Nov 01 2019

city: Bloomington

first: Julia

middle: C

last: van Kessel

state: IN

address: 1001 E 3rd Street

institute: Indiana University

summary: Bacteria coordinate cellular behaviors using a cell-cell communication system termed quorum sensing. In Vibrio harveyi, the master quorum sensing transcriptional factor LuxR directly regulates >100 genes in response to changes in population density. Here, we show that LuxR derepresses quorum sensing loci by competing with H-NS, a global transcriptional repressor that oligomerizes on DNA to form filaments and bridges. We first identified H-NS as a repressor of bioluminescence gene expression, for which LuxR is a required activator. In an hns deletion strain, LuxR is no longer necessary for transcription activation of the bioluminescence genes, suggesting that the primary role of LuxR is to displace H-NS to derepress gene expression. Using RNA-seq and ChIP-seq, we determined that H-NS and LuxR co-regulate and co-occupy 28 promoters driving expression of 63 genes across the genome. ChIP-PCR assays show that as autoinducer concentration increases, LuxR protein accumulates at co-occupied promoters while H-NS protein disperses. LuxR is sufficient to evict H-NS from promoter DNA in vitro, which is dependent on LuxR DNA binding activity. From these findings, we propose a model in which LuxR serves as a counter-silencer at H-NS-repressed quorum sensing loci by disrupting H-NS nucleoprotein complexes that block transcription.

overall_design: RNA-seq of cultures grown to OD600=1.0

first: Ryan

last: Chaparian

first: Minh

last: Tran

first: Laura

last: Conrad

first: Douglas

middle: B

last: Rusch


title: MYCN and MYC ChIP-Seq profiling in neuroblastoma cell lines

first: Jo Lynne

summary: MYCN and MYC profiling in neuroblastoma cell lines

overall_design: Here, we provide MYCN ChIP-Seq for three neuroblastoma MYCN-amplified and one non-amplified (negative control) cell lines and MYC ChIP-Seq for one MYCN-amplified and three non-amplified cell lines.

first: Kristen

first: Khushbu

last: Patel

first: John


title: Global H-NS counter-silencing by LuxR activates quorum sensing gene expression

overall_design: ChIP-seq of FLAG-tagged proteins collected from Vibrio campbellii cultures grown to an OD600 of 1.0.


title: Epigenomic profiling of neuroblastoma cell lines

last: Rokita

summary:
Understanding the aberrant transcriptional landscape of neuroblastoma is necessary to provide insight to the underlying influences of the initiation, progression and persistence of this developmental cancer. Here, we present chromatin immunoprecipitation sequencing (ChIP-Seq) data for the oncogenic transcription factors, MYCN and MYC, as well as regulatory histone marks H3K4me1, H3K4me3, H3K27Ac, and H3K27me3 in ten commonly used human neuroblastoma-derived cell line models. In addition, for all of the profiled cell lines we provide ATAC-Seq as a measure of open chromatin. We validate specificity of global MYCN occupancy in MYCN amplified cell lines and functional redundancy of MYC occupancy in MYCN non-amplified cell lines. Finally, we show with H3K27Ac ChIP-Seq that these cell lines retain expression of key neuroblastoma super-enhancers (SE). We anticipate this dataset, coupled with available transcriptomic profiling on the same cell lines, will enable the discovery of novel gene regulatory mechanisms in neuroblastoma.

This SuperSeries is composed of the SubSeries listed below.


title: RNA-Seq and GRO-seq on MCF7 cells induced with sgRNA vectors targeting CTCF binding elements

city: Tel Aviv

first: Ran

last: Elkon

address: Ramat Aviv

department: Human Genetics

country: Israel

institute: Tel Aviv University


title: Regional Analysis of The Brain Transcriptome In Mice Bred For High And Low Methamphetamine Consumption

city: Portland

first: Priscila

last: Darakjian

state: OR

address: 3181 SW Sam Jackson Park Road, L470

department: Behavioral Neuroscience

institute: Oregon Health and Science University

summary: Transcriptome profiling can broadly characterize drug effects and risk for addiction in the absence of drug exposure. Modern large-scale molecular methods, including RNA-sequencing (RNA-Seq), have been extensively applied to alcohol-related disease traits, but rarely to risk for methamphetamine (MA) addiction. We used RNA-Seq data from selectively bred mice with high or low risk for voluntary MA intake to construct coexpression and cosplicing networks for differential risk. Three brain reward circuitry regions, the nucleus accumbens (NAc), prefrontal cortex (PFC) and ventral midbrain (VMB), were explored. With respect to differential gene expression and wiring, the VMB was more strongly affected than either the PFC or NAc. Coexpression network connectivity was higher in the low line than the high line in the VMB, oppositely affected in the NAc, and little impacted in the PFC. Gene modules protected from the effects of selection may help to eliminate certain mechanisms from significant involvement in risk for MA intake. One such module was enriched in genes with dopamine-associated annotations. Overall, the data suggest that mitochondrial function and glutamate-mediated synaptic plasticity have key roles in the outcomes of selective breeding for high versus low levels of MA intake.

overall_design: We used mass selection procedures to generate the third replicate set of the MA high and low drinking lines. The originating population for these lines was a B6D2F2 (F2) cross, and methods were precisely as described for the replicate 1 and 2 lines. The founding population of 120 F2 mice (60 per sex; 53-56 days of age on the initial day of testing) was tested in a 2-bottle choice examination of water vs. MA intake. Brain tissue was obtained from experimentally naïve, non-MA exposed replicate 3 high and low line mice from second or later litters of generation S5.

first: Robert

last: Hitzemann

first: Ovidiu

middle: D

last: Iancu

first: Cheryl

last: Reed

first: Harue

last: Baba

first: Denesa

last: Lockwood

first: Tamara

last: Phillips


title: RNA-seq on MCF7 cells induced with sgRNA vectors targeting CTCF binding elements

summary: We performed a CRISPR-based functional genetic screen targeting CTCF binding elements (CBEs) located in the vicinity of ERα-bound enhancers. The screen identified four functional CBEs whose targeting resulted in a marked negative effect on the proliferation of MCF-7 cells (ERα-positive cells) but no significant effect on MDA-MB-231 (ERα-negative cells) cells. We then carried out RNA-seq analysis on MCF-7 cells induced with sgRNA vectors targeting these four CBEs: sgRNA_1118, sgRNA_1659, sgRNA_680 and sgRNA_810, as well as non-targeting sgRNA as control.

overall_design: RNA-seq in MCF7 cells induced with sgRNA vectors targeting four CTCF bidning elements identified by a functional screen as well non-targeting sgRNA control vector.

first: Gozde

last: Korkmaz

first: Reuven

last: Agami

first: Rani


title: GRO-seq on MCF7 cells induced with sgRNA vectors targeting CTCF binding elements

summary: We performed a CRISPR-based functional genetic screen targeting CTCF binding elements (CBEs) located in the vicinity of ERα-bound enhancers. The screen identified four functional CBEs whose targeting resulted in a marked negative effect on the proliferation of MCF-7 cells (ERα-positive cells) but no significant effect on MDA-MB-231 (ERα-negative cells) cells. Here, we carried out GRO-seq analysis on MCF-7 cells induced with an sgRNA vector targeting one of the hits detected by the screen: sgRNA_1118, as well as non-targeting sgRNA and sg1830 as control.

overall_design: GRO-seq in MCF7 cells induced with a sgRNA vector (sg1118) targeting a CTCF bidning element identified by a functional screen as well non-targeting sgRNA and sg1830 control vectors.


title: RNA sequencing data describing transcriptional changes in aorta of ApoE-/- mice after alpha 7 nicotinic acetylcholine receptor (α7nAChR) stimulation.

status: Public on Oct 29 2019

city: Gothenburg

first: Maria

last: Johansson

address: Medicinaregatan 11

department: Physiology

institute: University of Gothenburg

summary: This manuscript is a companion paper to Ulleryd M.U.  et al (1). Data shown here include RNA sequencing data from whole aorta of ApoE-/- mice treated with the alpha 7 nicotinic acetylcholine receptor (α7nAChR) agonist AZ6983 for 8 weeks using subcutaneously implanted osmotic minipumps.  1. Ulleryd MA, Mjornstedt F, Panagaki D, Yang LJ, Engevall K, Gutierrez S, et al. Stimulation of alpha 7 nicotinic acetylcholine receptor (α7nAChR) inhibits atherosclerosis via immunomodulatory effects on myeloid cells Re-submitted. 2019.

overall_design: ApoE-/- mice were treated with alpha 7 nicotinic acetylcholine receptor (α7nAChR) agonist AZ6983 or vehicle for 8 weeks using subcutaneously implanted osmotic minipumps. RNA from whole aorta were extracted and used for RNA sequencing analysis. n=6 per group.

first: Marcus

middle: A

last: Ulleryd

first: Filip

last: Mjörnstedt

first: Dimitra

last: Panagaki

first: Li

last: Yang

first: Kajsa

last: Engevall

first: Saray

last: Gutierrez

first: Yixin

last: Wang

first: Li-ming

last: Gan

first: Holger

last: Nilsson

first: Erik

last: Michaelsson


title: Genetic variability in response to Amyloid beta deposition influences Alzheimer's disease risk

status: Public on Oct 31 2019

first: Dervis

last: Salih

address: Gower St

department: Dementia Research Institute

institute: University College London

summary: The purpose of this project was to compare whole genome expression in 5 transgenic mice that show either amyloid plaques or tangle pathology to the expression in wild-type control mice at different stages of disease progression (2, 4, 8 or 18 months of age). Mouse genes with expression correlating to pathology were then compared to human genes showing DNA variation in human population associated with dementia (from GWAS).

overall_design: Five transgenic lines: TAS10-mice, TPM-mice, HET-TASTPM-mice, HO-TASTPM-mice and Tau-mice. Control line: C57Bl/6J wild-type mice. Four ages: 2, 4, 8 and 18 months.

first: Sevinc

last: Bayram

first: Sebastian

last: Guelfi

first: Regina

last: Reynolds

first: Maryam

last: Shoai

first: Mina

last: Ryten

first: Jonathan

last: Brenton

first: David

last: Zhang

first: Mar

last: Matarin

first: Juan

last: Botia

first: Runil

last: Shah

first: Keeley

last: Brookes

first: Tamar

last: Guetta-Baranes

first: Kevin

last: Morgan

first: Eftychia

last: Bellou

first: Damian

last: Cummings

first: Valentina

last: Escott-Price

first: John

last: Hardy


title: Intestinal response to prenatal inflammation

status: Public on Oct 25 2019

city: Copenhagen

first: Xiaoyu

last: Pan

address: Dyrlægevej 68

country: Denmark

institute: University of Copenhagen

summary: Chorioamnionitis (CA), resulting from intra-amniotic inflammation, is a frequent cause of preterm birth and exposes the immature intestine to bacterial toxins and/or inflammatory mediators before birth via fetal swallowing. This may affect intestinal immune development, interacting with the effects of enteral feeding and gut microbiota colonization just after birth. Using preterm pigs as model for preterm infants, we hypothesized that prenatal exposure to gram-negative endotoxin influences postnatal bacterial colonization and gut immune development. Pig fetuses were given intra-amniotic lipopolysaccharide (LPS) 3 d before preterm delivery by cesarean section, and were compared with litter-mate controls (CON) at birth and after 5 d of formula feeding and spontaneous bacterial colonization. Amniotic fluid was collected for analysis of leukocyte counts and cytokines, and the distal small intestine was analyzed for endotoxin level, morphology and immune cell counts. Intestinal gene expression and microbiota were analyzed by transcriptomics and metagenomics, respectively. At birth, LPS-exposed pigs showed higher intestinal endotoxin, neutrophil/macrophage density and shorter villi. About 1.0% of intestinal genes were affected at birth and DMBT1, a regulator of mucosal immune defense, was identified as the hub gene in the co-expression network. Genes related to innate immune response (TLR2, LBP, CD14, C3, SFTPD), neutrophil chemotaxis (C5AR1, CSF3R, CCL5) and antigen processing (MHC II, CD4) were also affected and expression levels correlated with intestinal neutrophil/macrophage density and amniotic fluid cytokine levels. On day 5, LPS and CON pigs showed similar necrotizing enterocolitis (NEC) lesions, endotoxin levels, morphology, immune cell counts, gene expressions and microbiota (except for difference in some low-abundant species). Our results show that CA markedly affects intestinal genes at preterm birth, including genes related to immune cell infiltration. However, a few days later, following the physiological adaptations to preterm birth, CA had limited effects on intestinal structure, function, gene expression, bacterial colonization and NEC sensitivity. We conclude that short-term, prenatal intra-amniotic inflammation is unlikely to exert marked effects on intestinal immune development in preterm neonates beyond the immediate neonatal period.

overall_design: A total of 40 pig fetuses were given intra-amniotic lipopolysaccharide (LPS, n=20) 3 d before preterm delivery by cesarean section, and were compared with litter-mate controls (CON, n=20). For each group, half of the animals were randomly selected to be euthanized at birth, and the other half were raised until postnatal day 5.

first: Du

first: Duc

middle: N

last: Nguyen

first: Wei

last: Wei

first: Xinxin

last: Yu

first: Fei

last: Gao

first: Per

middle: T

last: Sangild


title: CD47 blockade augmentation of Trastuzumab antitumor efficacy dependent upon antibody-dependent-cellular-phagocytosis

city: Durham

first: Zachary

middle: Conrad

last: Hartman

state: NC

address: Research Drive MSRB rm 414

department: Surgery

institute: Duke University

summary: Analysis of HER2 breast tumor immune infiltrates in mice treated with murine Trastuzumab and CD47 checkpoint blockade therapy

overall_design: Single Cell RNA Seq (scRNAseq) was performed on endogenous HER2-driven breast cancer in transgenic mice. The goal of this experiment is to compare effects of different antibody therapy combinations on tumor macrophages transcriptome

first: Li-Chung

last: Tsao

first: Pankaj

last: Agarwal

first: Erika

last: Crosby

first: Herbert

middle: K

last: Lyerly


title: NOTCH/HES5 signaling exhibits distinct roles in MYC- and AKT-driven liver carcinogenesis

city: Mannheim

first: Carolina

last: Delatorre

address: Theodor-Kutzer-Ufer 1-3

institute: University Heidelberg

summary: Notch signaling plays a pivotal role in liver development and aberrant Notch signaling may lead to hepatocellular (HCC) or cholangiocellular carcinoma (CCA) development. Using whole exome sequencing of 54 human HCC samples, we discovered 19 somatic missense mutations in 15 different Notch pathway genes affecting 24.6% (14 of 57) of patients. Prediction of functional impact of these Notch pathway mutations revealed HES5-R31G to have high relevance.

overall_design: We used Hep3B cells infected with pTRIPZ expressing HES5 wildtype or HES5-R31G. Protein expression was induced with doxycycline (Dox).

first: Stephanie

last: Roessler


title: DNA methylation dynamics underlie metamorphic gene regulation programs in Xenopus tadpole brain

status: Public on Oct 23 2019

first: Robert

last: Denver

address: 1105 North University Ave

institute: University of Michigan

type: Methylation profiling by high throughput sequencing

summary: Changes in DNA methylation in the preoptic area/hypothalamus/thalamus of Xenopus tropicalis tadpoles were analyzed using Methylated DNA Capture sequencing (MethlCap-seq) at four stages of metamorphosis.

overall_design: The middle brain region containing preoptic area/hypothalamus/thalamus was microdissected from Xenopus tropicalis tadpoles at four stages of metamorphosis: Nieuwkoop-Faber (NF) stage 50 (pre-metamorphosis), NF56 (pro-metamorphosis), NF62 (metamorphic climax), and NF66 (completion of metamorphosis). We isolated genomic DNA from tadpole brain to generate 3 biological replicates per developmental stage, conducted Methylated DNA Capture using the Diogenode kit, generated libraries and did deep sequencing.

first: Christopher

last: Sifuentes

first: Yasuhiro

last: Kyono

first: Samhitha

last: Raj

first: Nicolas

last: Buisine

first: Laurent

last: Sachs


title: In vitro culture of cynomolgus monkey embryos beyond gastrulation

city: Beijing

first: Xiangxiang

last: Jiang

state: Beijing

address: 1 Beichen West Road, Chaoyang District

institute: Institute of Zoology, Chinese Academy of Sciences

summary: Gastrulation is a milestone event of embryonic development, during which germ layers are specified and reassigned into the body plan. Due to the inaccessibility in vivo at this stage and the ethical limitations, gastrulation currently remains a mystery in primates. Here, we report the establishment of an in vitro system to culture cynomolgus monkey embryos after up to 20 days to develop beyond the initiation of gastrulation. The histology, immunostaining and single cell sequencing results showed that the in vitro cultured embryos largely recapitulated the key events of early post-implantation development, and initiated gastrulation in primates. Considering the high similarities between monkeys and humans, this system will provide a unique platform for the investigations of human early post-implantation development at physiological, pathological and environmental conditions.

overall_design: Embryonic mRNAs profile of cynomolgus embryos cultured in vitro for 12, 13, 17 days were generated by single cell RNA sequencing. Day 12, 1 embryo; day 13, 2 embryos; day 17 2 embryos.

first: Jiang

last: Xiangxiang

first: Zhai

last: Jinglei

first: Ma

last: Huaixiao

first: Wang

last: Hongmei

first: Li

last: Lei


title: RNA-sequencing in Mouse Embryonic Fibroblasts exposed to different Intensities of Hyperosmotic Stress

status: Public on Oct 11 2019

city: Cleveland

first: Maria

last: Hatzoglou

state: OH

address: 10900 Euclid Ave

department: Genetics and Genome Science

institute: Case Western Reserve University

summary: The inability of cells to adapt to increased environmental tonicity can lead to inflammatory gene expression and pathogenesis. The Rel family of transcription factors TonEBP and NF-κB p65 play critical roles in the switch from osmoadaptive homeostasis to inflammation, respectively. Here we identified a marker of the termination of adaptation and initiation of inflammation. We found that high stress inhibits protein interactions essential for the increased expression of TonEBP-dependent osmoprotective genes. This resulted in enhanced formation of TonEBP/NF-κB p65 complexes and enhanced proinflammatory gene expression.

overall_design: MEFs were treated with control, 500 mOsm, or 600 mOsm sucrose in triplicate and analyzed via RNA-seq

first: Kenneth

last: Farabaugh


title: Expression data from  TCQA-treated mice skin

status: Public on Oct 10 2019

city: Tsukuba,

first: Meriem

last: Bejaoui

state: Ibaraki

address: 1 Chome-1-1 Tennodai

institute: University of Tsukuba

summary:
Gene expression profiling reveals a potential role of TCQA in the upregulation of hair pigmentation in mice hair shaft
Skin was isolated from mice dorsal part treated with MilliQ and TCQA; Microarray gene expression profiling was conducted.

overall_design: RNA was extracted using Isogen (Nippon Gene Co. Ltd., Toyama, Japan). The integrity of RNA was quantified using NanoDrop 2000 spectrophotometer (Thermo Scientific, Wilmington, DE, USA). RNA samples were prepared for gene expression profiling analysis with GeneChip® 3' Expression Arrays using 3' IVT PLUS Reagent Kit (Affymetrix Inc., Santa Clara, CA, USA). Two hundred and fifty ng of total RNA from each sample was used to generate amplified and biotinylated complementary RNA (cRNA) from poly (A) RNA in a total RNA sample according to the user manual. IVT Incubation time was 16 hour. GeneAtlas® Hybridization, Wash and Stain Kit was used for hybridizing 3' IVT Array Strips according to the user manual . Mouse genome array strips  were hybridized for 16 hours in a 45oC incubator, washed and stained and finally imaging was done with the GeneAtlas Fluidics and Imaging Station.


title: Transcriptomic changes during cell wall biogenesis and modifications during xylogenesis in stems and pioneer roots of Populus trichocarpa

status: Public on Oct 14 2019

city: Poznan

first: Katarzyna

last: Marzec-Schmidt

address: Umultowska 89

department: General Botany

country: Poland

institute: Adam Mickiewicz University

summary: We studied the changes that occur in gene transcription and the biosynthesis of cell-wall-related compounds during xylogenesis in Populus trichocarpa pioneer roots and stems. Transcriptional profiling was conducted with the use of microarrays to identify genes involved in xylem formation. Pioneer roots were examined in segments corresponding to their developmental stage: apical meristem (PR1), primary development (PR2), and secondary development (PR3). Comparative segments were used to analyze xylogenesis in stems: apical meristem with primary development (PS1), secondary development (PS2), and isolated secondary xylem (PS3). Results indicated that only approximately 10% of the genes that were identified to be differentially expressed during xylogenesis were common to both pioneer roots and stems. Despite the dissimilarity in gene expression, however, many fundamental mechanisms were similar, e.g. the pattern of expression of genes involved in the biosynthesis of cell wall proteins, polysaccharides and lignins. While hemicellulose degradation was typical for stems, possibly due to the intensive level of cell wall lignification.  Our study is the first to conduct a comprehensive analysis, at the structural and molecular level, of xylogenesis, and clearly reveals the great complexity of molecular mechanisms underlying cell wall formation and modification during xylogenesis.

overall_design: All experiments were performed on seed-grown Populus trichocarpa (Torr. & Gray) growing in rhizotrons filled with natural soil with shoots extending from the top into the air. Waterlogging was avoided by installing a drainage hole in the bottom of each rhizotron that permitted soil aeration and drainage of excess water. At sampling, pioneer roots were divided into the following segments corresponding to their developmental stage: 0-2cm – root tips with apical meristem (PR1); 4-6cm – primary development (PR2); and 13-16cm – secondary development (PR3). Similarly, stems were also sampled based on developmental stages: 0-2cm – apical meristem with primary development (PS1); 20-25cm – secondary development (PS2) and 40-45cm – isolated secondary xylem (PS3). ). Root tips were treated as a negative control for the process of xylogenesis, while isolated secondary xylem served as a positive control. Total RNA was extracted from three biological replicates of each developmental stage of roots and stems using an RNeasy Plant Mini kit (Qiagen, USA). RNA quantity and quality were assessed using a NanoDrop1000 (Thermo Fisher Scientific Inc., USA). cRNA synthesis and microarray hybridization to an Affymetrix GeneChip Poplar Genome Array (A-AFFY-131) were performed according to the provided Affymetrix protocol.

first: Agnieszka

last: Bagniewska-Zadworna


title: Runx2 regulates cranial suture closure by regulating hedgehog, Fgf, Wnt, and Pthlh signaling pathway genes in suture mesenchymal cells

status: Public on Oct 09 2019

city: Nagasaki

first: Toshihisa

last: Komori

address: 1-7-1 Sakamoto

department: Cell Biology

institute: Nagasaki University

summary: CCD, which is characterized by hypoplastic clavicles, open fontanelles, supernumerary teeth, and short stature, are caused by heterozygous mutation of RUNX2. However, the reason why the suture closure is severely impaired in CCD patients remains to be clarified. The closure of posterior frontal (PF) and sagittal sutures was completely interrupted in Runx2+/– mice, and the proliferation of the suture mesenchymal cells was reduced compared with that in wild-type mice. To reveal the molecular mechanism, the differentially expressed genes between wild-type and Runx2+/– PF sutures were identified by microarray and real-time RT-PCR analyses. The expression of hedgehog, Fgf, Wnt, Pthlh signaling pathway genes, including Gli1, Ptch1, Ihh, Fgfr1-3, Tcf7, Wnt10b, Wnt1, and Pth1r,  was reduced in PF sutures of Runx2+/– mice. These findings indicated that more than half dosage of Runx2 is required for the proliferation of suture mesenchymal cells, their commitment into osteoblast-lineage cells, and the induction of the hedgehog, Fgf, Wnt, and Pthlh signaling pathway gene expression in the sutures.

overall_design: We extracted mRNAs from the PF sutures of wild-type mice at P5 and P7 and Runx2+/– mice at P7 and compared them by microarray.

first: Xin

last: Qin

first: Qing


title: Adipose derived stem cells (ASCs) methylation differences between Crohn Disease and No-Crohn individuals

status: Public on Oct 03 2019

city: Tarragona

first: Carolina

last: Serena

state: Tarragona

address: C/Dr. Mallafre Guasch, 4

department: Research Unit

country: Spain

institute: Health Institute Pere Virgili

summary: Pathological expansion of adipose tissue (AT) is supported by adipocyte precursors, termed adipose-derived stem cells (ASCs). Elucidation of mechanisms underlying ASC function may lead to therapeutic interventions to use in cell therapy treatments on Crohn’s disease patients. Using epigenome-wide association studies, we explored the impact of Crohn’s disease on the methylation signature of human ASCs

overall_design: Genomic DNA was extracted from cells using the NucleoSpin® Tissue Kit (Macherery-Nagal GmbH). DNA methylation profiles were generated on the Infinitum Human-EPIC Methylation850K BeadChip (Illumina). The BeadChip was developed to assay more than 850,000 CpG sites and selected CpG loci in parallel. DNA methylation data were processed using GenomeStudio software (Illumina) by applying the default settings.

first: Miriam

last: Ejarque

first: Alfonso

last: Saera

first: Joan

last: Vendrell

first: Sonia

last: Fernández-Veledo


title: Nivolumab treatment for relapsed/refractory Epstein-Barr virus-associated hemophagocytic lymphohistocytosis in adults

status: Public on Oct 07 2019

city: Chengdu, Cihna

first: Xaingyu

last: Pan

state: Sichuan

address: No.17 Renming road section3

department: State Key Laboratory of Biotherapy, West China Hospital, Sihcuan University.

institute: Sichuan University

summary: Single cell RNA sequencing (scRNA-seq) was performed with peripheral blood cells before (Day 0, T0), during nivolumab treatment (Day 7, T1; Day 21, T2), and when plasma EBV turned negative (Day 76, T3) in 1 patient (patient 7). scRNA-seq libraries were generated following the recommended protocol of the 3’ scRNA-seq 10X genomics platform and using v2 chemistry, and sequenced data was collected by illumina NovaSeq 6000 sequencing.

overall_design: Single cell RNA sequencing (scRNA-seq) in 4 stages

first: Pengpeng

last: Liu

first: Xiangyu

first: Chong

last: Chen

first: Ting

last: Niu

first: Xiao

last: Shuai

first: Jian

last: Wang

first: Xuelan


title: Single-cell RNA-seq of sorted CD8+ T cells from B16 melanoma tumors

city: Epalinges

first: Santiago

last: Carmona

address: Ch. des Boveresses 155

country: Switzerland

institute: UNIL

summary: CD8 T cells are the main effectors of the adaptive immune response against intracellular pathogens and cancer. Chronic antigen stimulation and inflammation lead to CD8 T cell differentiation and function that differ from those generated during acute infections. A comprehensive definition of the heterogeneity existing within both tumor-specific and total CD8 tumor-infiltrating T cells remains to be clearly established. To investigate this heterogeneity at the transcriptomic level, we performed paired single-cell RNA and TCR sequencing of >3500 CD8 T cells infiltrating B16 murine melanoma tumors, including cells of known tumor-specificity.

overall_design: Tumor-infiltrating CD8 T cells from B16.F10 melanoma tumor bearing C57BL/6 (CD45.1 locally bred, n=4) and PMEL (n=3) (Jackson Laboratory, Cat#005023) mice were sorted by flow cytometry 15 days post-tumor engraftment. Paired transciptomic profiles and TCR sequences were obtained at single-cell resolution using 10X Genomics Chromium technology.

first: David

last: Gfeller

first: Imran

last: Siddiqui

first: Werner

last: Held


title: Simultaneous measurement of DNA repair activities and mRNA abundance in single cells

status: Public on Oct 02 2019

city: Aurora

first: Jay

middle: R.

last: Hesselberth

state: CO

department: Biochemistry and Molecular Gentetics

institute: University of Colorado School of Medicine

summary: New methods that measure the static abundance of DNA, RNA, and proteins in single cells are rapidly transforming biology. But these methods do not provide insight into dynamic cellular activities, precluding a complete understanding of cellular heterogeneity. We developed a method to measure enzymatic activities in single cells and used it to simultaneously measure DNA repair enzyme activities and mRNA expression. By including polyadenylated DNA hairpin substrates with defined lesions in a single-cell mRNA sequencing experiment, we measured repair activities by capturing repair intermediates and products catalyzed by activities in single cells.

sample_organism:
Homo sapiens
synthetic construct

platform_organism:
Homo sapiens
synthetic construct

overall_design: Single cell mRNA sequencing libraries and matching DNA repair activity libraries from the 10X genomics platform.

first: Amanda

last: Richer

first: Kent

last: Riemondy

middle: R


title: Gene expression data from lymphoblastoid cell lines from African American participants in the GENOA study

status: Public on Oct 17 2019

city: Ann Arbor

first: Lulu

last: Shang

state: Michigan

address: 1415 Washington Heights

department: Biostatistics

summary: African-American individuals of the GENOA cohort

overall_design: Participants in this study are drawn from the GENOA study, a population-based study from Jackson, Mississippi.

first: Sharon

last: Kardia

first: Jennifer

last: Smith

first: Steven

last: Turner


title: Transcriptome analysis of adductor muscle with VPS29 RNAi in QN Orange scallops

city: Qingdao

first: JunLin

last: Song

address: Changcheng Road

institute: JunLin Song

summary: QN Orange scallops is new strain with carotenoid deposition in orange adductor muscle, which provided suitable model for studying carotenoid accumulation. The present study was conducted to further understand the role of VPS29 in carotenoids deposition process via RNA interference (RNAi) of VPS29. Transcriptomic analysis revealed 534 differentially expressed genes (DEGs) between the groups without and with RNAi, among which were 288 upregulated and 246 were downregulated. Among these DGEs, genes related to carotenoids biosynthesis decrease in the expression of low-density lipoprotein receptor domain class (LDLR), cytochrome P450 (CYP 450), Niemann Pick C1-like 1 (NPC1L1) and ATP binding cassette transporter (ABC transporter) were identified. These results indicated that VPS29 played a vital role on carotenoids deposition by regulating other genes.

overall_design: Total mRNA profiles of the control group without VPS29 RNAi and the experimental group with VPS29 RNAi were generated by deep sequencing, in triplicate.

first: Junlin


title: Genetic compensation in a stable slc25a46 mutant zebrafish

status: Public on Oct 04 2019

city: Miami

first: Matt

last: Danzi

state: FL

address: 1095 NW 14th Terrace, Lois Pope LIFE Center 4-26

institute: University of Miami

summary: A phenomenon of genetic compensation is commonly observed when an organism with a disease-bearing mutation does not show phenotypic penetrance due to compensatory gene expression changes. Reports have spread showing the absence of disease phenotypes in stable knockout models, but not in transient knockdown models. As such, these incidents present a challenge for the disease modeling field, although a deeper understanding of genetic compensation may also hold the key for novel therapeutic interventions. In our study we created a knockout model of slc25a46 gene, which is a recently discovered important player in mitochondrial dynamics and deleterious mutations in which are known to cause peripheral neuropathy, optic atrophy and cerebellar ataxia. We report a case of genetic compensation in the fourth generation (F4) of slc25a46 knockout zebrafish mutant, in contrast to a penetrant disease phenotype in the first generation (F0) slc25a46 mosaic mutant (crispant), generated with CRISPR/Cas-9 technology. We show that F0 crispant phenotype is specific and rescuable. By performing mRNA sequencing, we define significant changes in slc25a46 F4 mutant’s gene expression profile, which are nearly not present in F0 crispants. We find that among the top candidates for the phenotypic compensation anxa6 gene stands out as a functionally relevant player in mitochondrial dynamics. We also find that our genetic compensation case does not arise from previously identified mechanisms driven by mutant mRNA decay. Our study serves as an important contribution to the understanding of phenomenon of genetic compensation and presents novel insights on Slc25a46 function. Furthermore, our study provides the evidence for the efficiency of F0 CRISPR screens for disease candidate genes, which may advance the field of functional genetics.

overall_design: RNA-sequencing epxeriment of three groups with four biological replicates per group

first: Elena

last: Buglo

first: Stephan

last: Zuchner

first: Julia

last: Dallman


title: Next-generation sequencing of Drosophila melanogaster transcriptome upon removal of unique exons encoding Sgg-PA and Sgg-PB (major shaggy isoforms)

city: Cambridge

first: Steve

last: Russell

address: Downing Street

department: Genetics

institute: University of Cambridge

summary: Purpose: The goals of this study are to compare the embryonic transcriptome of embryos lacking major shaggy transcript isoforms to determine the impact of particular proteoforms on gene expression and identify affected pathways.

overall_design: Examination of transcriptome changes upon knockout of 2 major shaggy isoforms of Drosophila melanogaster.

first: Dagmara

last: Korona

first: Bettina

last: Fischer


title: A novel lncRNA lncRNA-AK096729 promotes colorectal carcinogenesis and glucose metabolism by stabilizing and specifying the transcription modification pattern of c-Myc

status: Public on Oct 01 2019

city: Shanghai

first: Haoyan

last: Chen

state: Shanghai

address: 145 Shandong Road

institute: Renji Hospital

summary: To elucidate whether  lncRNA-AK096729 plays a role in  colorectal cancer tumorigenesis, a RNA-seq analysis was performed to compare the gene expression profiles of  lncRNA-AF339830 siRNA and control siRNA transfectants.

overall_design: RNA-seq was performed in SW480  colorectal cancer cells after lncRNA-AK096729 knock down

first: Bao

last: Yujie


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

status: Public on Sep 24 2019

city: Santiago de Compostela

first: Diego

last: Robledo

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

institute: University of Santiago de Compostela

summary: We have previously shown that GABA ainhibits caspase activation and promote axon regeneration in descending neurons of the sea lamprey brainstem after a complete spinal cord injury. Here, we repeated this treatment and performed Illumina RNA sequencing studies in the brainstems of control and GABA treated animals.

overall_design: RNA-Seq of 3 control and 3 GABA-treated samples of lamprey brainstem 9 days post spinal cord injury. BioProject PRJNA561093. SRA SRP218749.


title: Transcriptional silencers in Drosophila serve a dual role as transcriptional enhancers in alternate cellular contexts

status: Public on Sep 25 2019

city: Boston

first: Stephen

last: Gisselbrecht

state: MA

address: 77 Avenue Louis Pasteur, Rm 468

department: Division of Genetics, Department of Medicine

institute: Brigham and Women's Hospital

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

overall_design: Refer to individual Series


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

summary: We have previously shown that baclofen treatments inhibit caspase activation and promote axon regeneration in descending neurons of the sea lamprey brainstem after a complete spinal cord injury. Here, we repeated this treatment and performed Illumina RNA sequencing studies in the brainstems of control and baclofen treated animals.

overall_design: RNA-Seq of 5 control and 5 baclofen-treated samples of lamprey brainstem 29 days post spinal cord injury. BioProject PRJNA561123. SRA SRP219534.


title: Global transcriptomic analysis of murine ovarian surface epithelial (MOSE) cells with PAX8 overexpression

city: Chicago

first: Matthew

middle: J.

last: Schipma

state: IL

address: 750 N. Lake Shore Drive

department: Biochemistry and Molecular Genetics

institute: Northwestern University

summary: To identify the role of PAX8 in transformation of the ovarian surface epithelium (OSE).

overall_design: Three experimental samples (MOSE-PAX8) and three reference samples (MOSE-NEO) were obtained for RNA sequencing analysis.

first: Laura

last: Hardy

first: Melissa

last: Pergande

first: Karina

last: Esparza

first: Kimberly

last: Heath

first: Hayat

last: Onyuksel

first: Stephanie

last: Cologna

first: Joanne

last: Burdette


title: RNA-seq analysis of citrus leaf samples of treated and untreated trees infected with Liberibacter asiaticus

status: Public on Sep 20 2019

city: Gainesville

first: Leandro

middle: Octavio

last: Balzano

address: 1275 Center Drive

department: Pathology, Immunology, and Laboratory Medicine

institute: University of Florida

summary: We evaluated the effect on citrus trees of two newly-identified molecules, benzbromarone and tolfenamic acid, used as antimicrobials in commercial groves of sweet orange (Citrus sinensis). We delivered the molecules by trunk injection and evaluated safety and efficacy parameters by performing  RNAseq of the citrus host responses.

overall_design: Examination of  two different molecules over L. asiaticus host transcriptome

first: Cécile

last: Pereira

first: Ana

last: Conesa

first: Danilo

last: da Silva

first: Christopher

last: Gardner


title: Capsulized fecal microbiota transportation ameliorates post-weaning diarrhea through modulating the gut microbiota in piglets

status: Public on Sep 17 2019

city: Chengdu

first: Wenjie

last: Tang

address: NO.211 HuiMing road district, wenjiang

institute: Sichuan Agricultural University

summary: Early-weaning-induced stress causes diarrhea, thereby reduces growth performance of piglets. Gut bacterial dysbiosis emerges as a leading cause of post-weaning diarrhea. The present study was aimed to investigate the effect of capsulized fecal microbiota transportation (FMT) on gut bacterial community, immune response and gut barrier function of weaned piglets. Thirty-two were randomly divided into two groups fed with basal diet for 21 days. Recipient group was inoculated orally with capsulized fecal microbiota of health Tibetan pig daily morning during whole period of trial, while control group was given orally empty capsule. The results showed that the F/G ratio, diarrhea ratio, diarrhea index, and histological damage score of recipient piglets were significantly decreased. FMT treatment also significantly increased the colon length of piglets. Furthermore, the relative abundances of Firmicutes, Euryarchaeota, Tenericutes, Lactobacillus, Methanobrevibacter and Sarcina in colon of recipient piglets were increased, and the relative abundances of Campylobacter, Proteobacteria, and Melainabacteria were significantly decreased compared with control group.

overall_design: Piglets were randomly allotted to two groups (n = 16 per group) matched for body weight and litter origin as follows: Group FMT received capsulized fecal microbiota for 21 days (full-trial period); control group received empty capsule for 21 days; the same diet was used for all groups throughout the process.

first: wenjie


title: Transcriptome sequencing of purified dermal adipocytes harvested from P21, P25, P29, P35 and P49 mice

status: Public on Sep 16 2019

city: Wuhan

first: Zhuzhen

last: Zhang

state: Hubei

address: 6015Shengke Building, College of life sciences, 299 Bayi Road, Wuchang

department: Biochemistry

institute: Wuhan University

summary:
Purpose: The goals of this study are to compare the transcription changes of dermal adipocytes during hair cycling.
Methods: Transcriptome of purified dermal adipocytes were generated by deep sequencing, using Illumina Novaseq 6000 sequencing system.

overall_design: Dorsal skin were harvested at different time points, and then digested the skin to get pure mature dermal adipocytes. RNA are extracted from the tissues for whole transcriptome RNA-seq.

first: Philipp

middle: E

last: Scherer


title: Transcriptomic comparison of ST556 WT and rr11  mutants  of Streptococcus pneumoniae ST556 under different condition

status: Public on Sep 14 2019

city: Beijing

first: Juanjuan

last: Wang

address: Haidian Strict

department: Medical department

institute: Tsinghua University

summary: The opaque and transparent colonies frequency of rr11 mutants has been changed siginificantly compared with that of WT. The molecular mechanism of the regulation of RR11 on phase variation will help understand the penumococcal adaptation since RR11 belongs to a typical Two-component system. But the regulon of RR11 hasn't been identified until now.  The RNA sequcing will help identify the regulons of RR11 in ST556.

overall_design: Pairwise comparison of ST556 WT with TH9063 (∆rr11) knockout and TH11425 (rr11D53A) mutant of Streptococcus pneumoniae ST556 (RNA-seq), repectively, analyzing the effect of rr11 deletion and inactivation on the pneuomococal transcriptome. It was performed with deep sequencing, using an Illumina Hiseq_X-TEN sequencer with 150 nt paired-end reads.


title: Neurogenomic insights into paternal care and its relation to territorial aggression

status: Public on Sep 15 2019

city: Urbana

first: Alison

last: Bell

state: Illinois

address: Justin Smith Morrill Hall, 505 S Goodwin Ave #393

department: Animal Biology

institute: University of Illinois at Urbana Champaign

summary: Motherhood is characterized by dramatic changes in brain and behavior, but less is known about fatherhood. Here we report that male sticklebacks – a small fish in which fathers provide care – experience dramatic changes in neurogenomic state as they become fathers. Some genes are unique to different stages of paternal care, some genes are shared across stages, and some genes are added to the previously acquired neurogenomic state. Comparative genomic analysis suggests that some of these neurogenomic dynamics resemble changes associated with pregnancy and reproduction in mammalian mothers. Moreover, gene regulatory analysis identified transcription factors that are regulated in opposite directions in response to a territorial challenge versus during paternal care. Altogether these results show that some of the molecular mechanisms of parental care might be deeply conserved and might not be sex-specific, and suggest that tradeoffs between opposing social behaviors are managed at the gene regulatory level.

overall_design: In order to track transcriptional dynamics associated with becoming a father, we sampled males for brain gene expression profiling at five different points during the reproductive cycle (n=5 males per time point): nest, eggs, early hatching, middle hatching and late hatching (control: reproductively mature males with no nests). Males in the nest condition had a nest but had not yet mated. Males in the eggs condition were sampled four days after their eggs were fertilized. Because males in the eggs condition were sampled four days after mating, the transcriptomic effects of mating are likely to have attenuated by the time males were sampled at this stage. Hatching takes place over the course of the fifth day after fertilization, and a previous study found that brain activation as assessed by Egr-1 expression was highest while male sticklebacks were caring for fry as compared to males with nests or eggs. In order to capture males’ response to the new social stimulus of their fry, we focused on three time points on the day of hatching which capture the start of the hatching process (9am), when approximately half of the clutch is hatched (1pm) and when all of the eggs have hatched (5pm). Males in the nest, eggs and early hatching conditions were sampled at 9am, males in the mid-hatching condition were sampled at 1pm and males in the late hatching condition were sampled at 5pm. Males in these conditions were compared to reproductively mature circadian-matched control males that did not have a nest (n=5 males per control group). Wild-caught females from the same population were used as mothers. Males were quickly netted and sacrificed by decapitation within seconds. All methods were approved by the IACUC of the University of Illinois at Urbana-Champaign (#15077).

first: Syed Abbas

last: Bukhari


title: Loss-of-function of the long non-coding RNA A830019P07Rik in mice does not affect insulin expression and secretion

city: Lausanne

first: Jennifer

middle: Yihong

last: Tan

address: Rue du Bugnon 27

department: Department of Computational Biology

institute: University of Lausanne

summary: Long non-coding RNAs (lncRNAs) contribute to diverse cellular functions and the dysregulation of their expression or function can contribute to diseases, including diabetes. The contributions of lncRNAs to β-cell development, function and survival has been extensively studied in vitro. However, very little is currently known on the in vivo roles of lncRNAs in the regulation of glucose and insulin homeostasis. Here we investigated the impact of loss-of-function in mice of the lncRNA A830019P07Rik, hereafter P07Rik, which was previously reported to be associated with reduced plasma insulin levels. Compared with wild-type littermates, male and female P07Rik mutant mice did not show any defect in glycaemia and plasma insulin levels in both fed and fasted state. Furthermore, P07Rik mutant mice displayed similar glucose and insulin levels in response to an intra-peritoneal glucose tolerance test. Ex vivo, islets from mutant P07Rik released similar amount of insulin in response to increased glucose concentration as wildtype littermates. In contrast with previous reports, our characterization of P07Rik mouse mutants revealed that loss of function of this lncRNA does not affect glucose and insulin homeostasis in mice.

overall_design: RNAseq of mouse islet in P07Rik KO and WT mice

first: Claudiane

last: Guay

first: Baroj

last: Abdulkarim

middle: Y

first: Gilles

last: Dubuis

first: Sabine

last: Rütti

first: Christian

last: Widmann

first: Romano

last: Regazzi

last: Marques


title: Identification of FUBP1 as a long tail driver and widespread regulator of tumor suppressor and oncogene alternative splicing

status: Public on Sep 12 2019

first: Jessica

middle: Sarah

last: Elman

address: 150 Harrison Ave

department: DMCB

institute: Tufts University

summary: Comprehensive sequencing approaches have allowed for the identification of the most frequent contributors to cancer, known as drivers. They have also revealed a class of mutations in understudied, infrequently altered genes, referred to as “long tail” (LT) drivers. A key challenge has been to find clinically relevant LT drivers and understand how they cooperate to drive disease. Here, we identified Far Upstream Binding Protein 1 (FUBP1) as a LT driver using an in vivo CRISPR screen. FUBP1 cooperates with other tumor suppressor genes to transform mammary epithelial cells by disrupting cellular differentiation and tissue architecture. Mechanistically, FUBP1 participates in regulating m6A RNA methylation, and its loss leads to global changes in RNA splicing and widespread expression of aberrant driver isoforms. These findings suggest that somatic alteration of a single gene involved in RNA splicing and m6A methylation can produce the necessary panoply of contributors for neoplastic transformation.

overall_design: Examination of gene expression profile of normal mammary epithelial cells with loss of FUBP1

middle: S

first: Charlotte

last: Kuperwasser