title: thCHART of roX2 lncRNA [DNA]

summary: Understanding the targeting and spreading patterns of lncRNAs on chromatin requires a technique that can detect both high intensity binding sites and reveal genome-wide spreading patterns with high confidence. We developed an improved hybridization capture protocol to determine lncRNA localization using biotinylated LNA-containing oligonucleotides that hybridize to the target RNA and enhance capture specificity by including a protecting oligonucleotide that competitively displaces contaminating species, leading to highly specific RNA capture. This approach revealed the spreading pattern of roX2, a lncRNA involved in dosage compensation in D. melanogaster, how this pattern relates to chromatin features, and how spreading of roX2 changes upon cellular stress.  Upon heat shock, roX2 displays reduced spreading on X chromosome and surprising relocalization to sites on autosomes, revealing how this improved hybridization capture approach can reveal previously uncharacterized changes in the targeting and spreading of lncRNAs on chromatin.

sample_organism:
Drosophila melanogaster
Mus musculus

platform_organism:
Drosophila melanogaster
Mus musculus


title: Histone Modifications and Chromatin Accessibility in Endothelial Cells under Shear Stress (ATAC-seq)

status: Public on Mar 11 2020

city: La Jolla

first: John

last: Shyy

state: California

address: 9500 Gilman Dr., BRF2 Rm 1217 Bay LL

department: Medicine

country: USA

institute: University of California, San Diego

type: Genome binding/occupancy profiling by high throughput sequencing

summary: This data set reveals the changes of histone modifications and chromatin accessibility in human umbilical vein endothelial cells (HUVECs) under atheroprotective pulsatile shear (PS), atheroprone oscillatory shear (OS), or with KLF4 overexpression. Using ChIP-Seq, we defined the H3K27ac and H3K4me1 enrichment under PS and OS conditions. Using ATAC-seq, we identified the chromatin accessibility under KLF4 overexpression.

overall_design: ECs were infected with adenovirus-KLF4 or the empty vehicle (Ad-null) for 24 hr. Chromosome accessibility were evaluated with ATAC-seq. Two biological replicates were collected for each condition.

first: Ming

last: He

first: Tse-Shun

last: Huang

first: Shuai

last: Li

first: Hsiao-Chin

last: Hong

first: Zhen

last: Chen

first: Marcy

last: Martin

first: Hsi-Yuan

first: Jian

last: Kang

first: Hsien-Da

first: Shu

last: Chien

middle: J


title: Effect of chronic uremia on the transcriptional profile of the calcified aorta analyzed by RNA sequencing.

status: Public on Mar 10 2020

city: Copenhagen N

first: Jakob

middle: Lewin

last: Rukov

address: Ole Maaløes Vej 5

country: Denmark

institute: University of Copenhagen

type: Expression profiling by high throughput sequencing

summary: 1. We used RNA-seq to examine vascular tissue (aorta) transcriptomes from chronic kidney disease rat model (uremic) developing vascular calcifications, compared with controls. Uremic calcified aortas have extensive changes in the transcriptional profile. Among the 10,153 genes with an expression level of >1 reads/kilobase transcript/million mapped reads, 2,663 genes were differentially expressed with 47% upregulated genes and 53% downregulated genes in uremic rats. Significantly deregulated genes were enriched for ontologies related to the extracellular matrix, response to wounding, organic substance, and ossification. The individually affected genes were of relevance to osteogenic transformation, tissue calcification, and Wnt modulation.      2. We demonstrated extensive changes in the transcriptional profile of the uremic calcified aorta, which were consistent with a shift in phenotype from vascular tissue toward an osteochondrocytic transcriptome profile.      3. Moreover, neither the normal vasculature nor calcified uremic vasculature expresses Klotho.

overall_design: Uremia was induced by 5/6 nephrectomy. Induction of vascular calcification requires reduced kidney function and also a high-phosphate diet in addition to vitamin D. After 8 wk of uremia, rats were treated with vitamin D, alfacalcidol 30 ng three times weekly and euthanized after 6 wk of vitamin D treatment and a total of 14 wk of uremia (uremic). An extra control group of normal rats given vitamin D was added (control+D) to examine the specific effect of vitamin D in our model. Control group (control) was left untreated until euthanization after 14 wk.

middle: L


title: L-methionine counteracts cocaine-conditioned place preference in mice through Glutamatergic plasticity pathways

city: BeiJing

first: Wang

last: Yan

address: 16# LinCui Road

country: China

institute: Institute of Psychology

type: Non-coding RNA profiling by high throughput sequencing

summary: Drug-induced alterations in gene expression play an important role in the development of addictive behavior. Methionine has been proven to inhibit addictive behaviors of cocaine dependence. However, the mechanisms underlying how methionine use corresponds to drug-induced behaviors still remain unclear. We performed mRNA and miRNA high-throughput sequencing of the prefrontal cortex in a mouse model of cocaine CPP combined with L-methionine in order to identify L-methionine target miRNAs and genes that participate in the cocaine conditioned place preference (CPP). We found that the L-methionine inhibits cocaine CPP. Sequencing data analysis showed that L-methionine down-regulates genes enriched in the Glutamatergic Synapse pathways and significantly reversed the cocaine-induced expression changes of the substance dependence pathways (Morphine addiction and Nicotine addiction) and the neurotransmitter synapse pathways (Glutamatergic Synapse, Cholinergic Synapse and GABAergic Synapse). Furthermore, the Glutamatergic synapse was either overlapped between DEGs with DEGs-miRNA induced by cocaine CPP, or with the MET effects on cocaine CPP.  Nineteen targeted genes were investigated and five were identified (Gria4, Grid1, Grik4, Grik5 and Grin3a) to belong to iGluR family. Interestingly, there were several miRNAs that had the same sequence which targets the iGluR family: Mmu-miR-30e-50p and mmu-miR-380-5p share UUGAC motif and targets Grik4; mmu-miR-6940-3p and mmu-miR-212-5p both share UGGCU motif which targets Gria4 and Grid1 respectively. Thus, we demonstrated the efficacy of L-methionine in counteracting the effects of cocaine CPP and identified specific genes of synaptic plasticity pathways, especially the Glutamatergic synapse pathway, which is modulated by L-methionine in response to cocaine dependence.

overall_design: PFC region of cocaine-conditioned place preference mice and methionine treated cocaine-conditioned place preference mice were performed mRNA and miRNA sequenceing

first: Yan

last: Wang

first: Mei

last: Zhao


title: Heterochromatic islands in euchromatin are in spatial contacts with the hierarchically organized heterochromatin domain

city: Irvine

first: Grace

middle: Yuh Chwen

last: Lee

state: CA

address: UCI

institute: University of California, Irvine

summary: We study the 3D conformation of euchromatic regions enriched with suppressive H3K9me2 epigenetic marks

overall_design: We performed ChIP-seq targeting H3K9me2 at 16-18hr Drosophila melanogaster embryos. Five genotypes were assayed and each genotype has two replicates of IP. IP samples, along with their corresponding INPUT, were sequenced with Illumina Hiseq4000

first: Yuh

middle: C

first: David

last: Acevedo

first: Gary

middle: H

last: Karpen


title: Differential Expression and Quantitative Analysis of H. congolense DSM 11287 Transcriptome in Biofilms

status: Public on Mar 20 2020

city: Annandale

first: Aaron

middle: Alexander

last: Jones

state: NJ

address: 1545 Route 22 East

institute: ExxonMobil Research and Engineering

summary: Purpose: Evaluation of differential expression using Illumina HiSeq 2500 analysis of RNA of pure cultures of H. congolense grown in biofilms on various surfaces to assess the impact of surface type on transcriptome.

overall_design: We evaluate differential expression of transcriptomes in biofilms grown in a single once-flow-through biofilm bioreactor.

middle: A

first: Zarath

middle: M

last: Summers

first: Joshua

middle: T

last: Claypool

first: Giovanni

last: Pilloni

first: Antonio

last: Paiva


title: Uncovering Modifier Genes of X-linked Alport Syndrome Using a Novel Multi-parent Mouse Model

city: Bar Harbor

first: Ron

last: Korstanje

state: ME

address: 600 Main St

institute: The Jackson Laboratory

summary: RNAseq of mouse kidney RNA from Col4a5 muntant mice crossed with diversity ourbred mice to find modifier genes of Alport disease.

overall_design: 192 kidney RNA samples one male and one female sibiligh pair carring col4a5 mutation  from each DO male used in a col5a4x DO cross

first: Yuka

last: Takemon

first: Valerie

last: Wright

first: Bernard

last: Davenport

first: Daniel

last: Gatti

first: Susan

last: Sheehan

first: Holly

middle: S

last: Savage

first: Rachel

last: Lennon


title: Expression data from wild type and Sox17 heterozygous mutant uteri in early pregnancy

city: Tokyo

first: Masami

last: Kanai-Azuma

address: 1-5-45 Yushima, Bunkyo-ku

country: Japan

institute: Tokyo Medical and Dental University

summary:
SOX17 activity in the uterine epithelium is essential for the implantation of mouse embryos. Previously, we demonstrated that female Sox17-heterozygous mutant mice are subfertile, and two active copies of Sox17 are required for the proper implantation of mouse embryos.
To understand which implantation step is most sensitive to the Sox17 gene dosage, we comprehensively investigated the RNA transcriptomes of Sox17-heterozygous mutant mice.

overall_design: Total RNA prepared from the uterine epithelium of wild-type and Sox17GFP/+ female mice was used for microarray analysis with a GeneChip® 3' IVT PLUS Reagent Kit (Affymetrix, CA, USA)

first: Hayakawa

last: Kana

first: Miura

last: Kento

first: Hirate

last: Yoshikazu

first: Kanai

last: Yoshiakira

first: Kanai-Azuma

last: Masami


title: Genome-wide mapping of m6A sites in cells expressing normal- versus slow-elongating RNA polymerase II (RNAPII)

city: Tel Aviv

first: Ran

last: Elkon

address: Ramat Aviv

department: Human Genetics

country: Israel

institute: Tel Aviv University

summary: We report enhanced deposition of m6A in cells expressing slow-elongated version of RNAPII

overall_design: Cells (HEK293) expressing the alpha-amanitin mutants of RNAPII were subjected to MeRIP-seq protocol (Dominissini et al., 2013).

first: Boris

last: Slobodin

first: Ruiqi

last: Han


title: Tailoring a global iron regulon to a uropathogen

city: Madison

first: Kevin

last: Myers

state: WI

address: 5127 WEI, 1552 University Ave

department: Great Lakes Bioenergy Research Center

institute: University of Wisconsin - Madison

summary: Pathogenicity islands and plasmids encode genes for pathogenesis of various Escherichia coli pathotypes.Although there is a basic understanding of the contribution of these virulence factors to disease, less is known about variation in regulatory networks in determining disease phenotypes. Here we dissected aregulatory network directed by the conserved iron homeostasis regulator, Ferric Uptake Regulator (Fur), inuropathogenic E. coli strain CFT073. Comparing anaerobic genome-scale Fur DNA binding, with Fur dependent transcript expression and protein levels of the uropathogen to that of commensal E. coli K-12 strain MG1655, showed that the Fur regulon of the core genome is conserved but also includes genes within the pathogenicity/genetic islands. Unexpectedly, regulons indicative of amino acid limitation and the general stress response were also indirectly activated in the uropathogen fur mutant, suggesting that induction of the Fur regulon increases amino acid demand. Using RpoS levels as a proxy, addition of amino acids mitigated the stress. In addition, iron chelation increased RpoS to the same levels as in the fur mutant. The increased amino acid demand of the fur mutant or iron chelated cells was exacerbated by aerobic conditions, which could be partly explained by the O2-dependent synthesis of the siderophore aerobactin, encoded within a pathogenicity island. Taken together, this data suggest in the iron-poor environment of the urinary tract, amino acid availability could play a role in the proliferation of this uropathogen, particularly if there is sufficient O2 to produce aerobactin.

overall_design: Four RNA-seq samples each with three biological replicates were analyzed (WT, deltaFur, deltaRhyB, deltaFur_deltaRhyB). Two biological replicate ChIP-seq samples for Fur chromosomal occupancy along with two deltaFur ChIP-seq control biolocial replicates and two CHIP-sq input biological replicates.

first: Rajdeep

last: Banerjee

first: Erin

last: Weisenhorn

last: Schwartz

first: Jeremy

middle: D

last: Glasner

first: Nicole

last: Perna

first: Joshua

last: Coon

first: Rodney

last: Welch

first: Patricia

last: Kiley


title: A Novel Progesterone Biosensor Derived from Microbial Screening [RNA-seq]

city: Boston

first: James

last: Galagan

state: MA

address: 44 Cummington Mall

department: Biomedical Engineering

institute: Boston University

summary: Mining of gene clusters responsive to hormones

overall_design: Performed RNA-Seq on P. simplex using RNA purified from P. simplex with and without hormones at specified timepoints. Sequencing was performed on an Illumina NextSeq500 using 75bp single end reads.

first: Chloé

last: Grazon

first: R

last: Baer

first: Uros

last: Kuzmanovic

first: Thuy

last: Nguyan

first: Mingfu

last: Chen

first: Marjon

last: Zamani

first: Margaret

last: Chern

last: Aquino

first: Xiaoman

last: Zhang

first: Sebastien

last: Lecommandoux

first: Andy

last: Fan

first: Mario

last: Cabodi

first: Catherine

last: Klapperich

first: Mark

middle: W

last: Grinstaff

first: Allison

last: Dennis


title: Epigenome-Wide Association Study in multiple system atrophy (MSA)

city: Odense

first: Rasmus

last: Rydbirk

address: Fioniavej 34

department: Functional Genomics and Biochemistry

institute: University of Southern Danmark

type: Methylation profiling by genome tiling array

summary: Genome-wide methylation profiling of DNA extracted from the prefrontal cortex of post-mortem MSA patients (n=41) or normal, healthy controls (CTRLs; n=37). The Illumina Infinium MethylationEPIC BeadChip was used, investigating app. 850,000 CpG sites throughout the genome

overall_design: Bisulphite (BS) or oxidative bisulphite (oxBS) converted DNA from 78 samples (41 MSA, 37 CTRL) were hybridized to the Illumina Infinium MethylationEPIC BeadChip.

first: Tomasz

last: Brudek

first: Bente

last: Pakkenberg

first: Jorg

last: Tost

first: Susana

last: Aznar


title: Harnessing enhanced nucleotide chemistry and toehold nanotechnology to reveal lncRNA spreading on chromatin

city: West Haven

first: Matthew

last: Simon

state: CT

address: 600 West Campus Dr. MIC312

department: Molecular Biophysics & Biochemistry

institute: Yale University Chemical Biology Instiute

summary:
Understanding the targeting and spreading patterns of lncRNAs on chromatin requires a technique that can detect both high intensity binding sites and reveal genome-wide spreading patterns with high confidence. We developed an improved hybridization capture protocol to determine lncRNA localization using biotinylated LNA-containing oligonucleotides that hybridize to the target RNA and enhance capture specificity by including a protecting oligonucleotide that competitively displaces contaminating species, leading to highly specific RNA capture. This approach revealed the spreading pattern of roX2, a lncRNA involved in dosage compensation in D. melanogaster, how this pattern relates to chromatin features, and how spreading of roX2 changes upon cellular stress.  Upon heat shock, roX2 displays reduced spreading on X chromosome and surprising relocalization to sites on autosomes, revealing how this improved hybridization capture approach can reveal previously uncharacterized changes in the targeting and spreading of lncRNAs on chromatin.

This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series

first: Martin

last: Machyna

first: Lea

last: Kiefer


title: GCN2 drives macrophage and MDSC function and immunosuppression in the tumor microenvironment

city: Braunschweig

first: Andreas

last: Kloetgen

state: NI

address: Inhoffenstr 7

department: Department for Computational Biology of Infection Research

country: Germany

institute: Helmholtz Centre for Infection Research

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: A Novel Progesterone Biosensor Derived from Microbial Screening [ChIP-seq]

first: James

last: Galagan

summary: Determination of target binding sites of a novel allosteric transcription factor,  SRTF1

overall_design: Performed in vitro ChIP-Seq on P. simplex using genomic DNA and purified tagged SRTF1 protein. Sequencing was performed on an Illumina NextSeq500 using 75bp single end reads.

first: Chloé

last: Grazon

first: R

last: Baer

first: Uros

last: Kuzmanovic

first: Thuy

last: Nguyan

first: Mingfu

last: Chen

first: Marjon

last: Zamani

first: Margaret

last: Chern

first: Patricia

last: Aquino


title: GCN2 drives macrophage and MDSC function and immunosuppression in the tumor microenvironment [ChIP-Seq]

summary: The purpose of our study was to examine the role of GCN2 in the function of immunosuppressive cells such as tumor associated macrophages and MDSCs. We show that a myeloid lineage specific deletion of GCN2 results in a shift towards a more proinflammatory phenotype of tumor associated macrophages and MDSCs, thereby promoting anti-tumor immunity.

overall_design: We determined the expression pattern of tumor associated macrophages and MDSCs, impact of ATF4 and GCN2 silencing in M0, M1 and M2 polarized macrophages as well as ATF4 binding sites in M0 or M2 polarized bone marrow derived macrophages using RNA-Seq, scRNA-Seq and ChIP-Seq.

first: Marie

last: Halaby

first: Kebria

last: Hezaveh

first: Tracy

last: McGaha


title: Mouse limb and respiratory muscle show distinct cachexia profiles in response to human pancreatic tumors

first: Boston University

last: Microarray and Sequencing Resource

address: 72 East Concord Street, E631

department: Microarray and Sequencing Resource


title: Single-cell RNA-sequencing of full thickness mouse skin during anagen and telogen

city: Huddinge

first: Simon

last: Joost

address: Blickagången 16

department: BioNut

country: Sweden

institute: Karolinska Institutet

summary: Despite the recent application of single-cell RNA-sequencing to aspects of mouse skin biology, the full cellular heterogeneity of the mouse skin (including both epidermis and skin stroma) and its relationship with the hair cycle is still uncharted. In order to systematically compare the cellular composition of mouse skin during rest and hair growth, we created single-cell RNA-sequencing libraries from full thickness mouse skin cell suspensions sampled during anagen (5w) and telogen (9w).

overall_design: Full thickness skin cell suspensions (including both epidermal and stromal cells) were isolated from the dorsal skin of female wildtype C57bl/6 mice during anagen (5w, n = 3) and telogen (9w, n = 3). Single-cell cDNA libraries were created using the Chromium Single Cell 3’ kit (version1, 10X Genomics) and sequenced on an Illumina HiSeq2500 (main dataset). Note that one 9w replicate was removed from the analysis retroactively. For cluster validation, a second dataset (validation dataset) was created using the Chromium Single Cell 3’ kit (version3, 10X Genomics) and sequenced on an Illumina NovaSeq 6000. Note that cells for validation - 9w - replicate 2 and validation - 9w -replicate 3 were isolated from the same animal.

first: Rickard

last: Sandberg

first: Maria

last: Kasper


title: Overexpression of the non-muscle RBFOX2 isoform triggers cardiac conduction defects in myotonic dystrophy

city: Urbana

first: Sushant

last: Bangru

state: Illinois

address: 600 S Mathews Avenue

department: Biochemistry

institute: University of Illinois, Urbana-Champaign

summary: Myotonic dystrophy type 1 (DM1) is a multisystemic genetic disorder caused by a  CTG trinucleotide repeat expansion in the 3′ untranslated region of DMPK gene. Heart  dysfunctions occur in nearly 80% of DM1 patients and are the second leading cause of  disease-related deaths, yet, the underlying mechanisms remain unclear. Herein, we  report that upregulation of a non-muscle splice isoform of RNA binding protein RBFOX2  in DM1 heart tissue—due to altered splicing factor and microRNA activities—induces  the characteristic cardiac conduction defects detected in DM1 individuals. Mice  engineered to express the non-muscle RBFOX2 isoform in heart via tetracycline-  inducible transgenesis, or CRISPR/Cas9 targeted genome editing, reproduced DM1-  related cardiac-conduction delay and spontaneous episodes of arrhythmia.  Furthermore, by integrating RNA binding with cardiac transcriptome datasets of DM1  patients, and mice expressing the non-muscle RBFOX2 isoform, we identified a core  network of RBFOX2-driven splicing defects in sodium, potassium, and calcium  channels that can alter their rate of ion diffusion and electrophysiological properties.  Thus, our results uncover a trans-dominant role for an aberrantly expressed RBFOX2  isoform in DM1 cardiac pathogenesis.

overall_design: The two set of mice, namely MHC and Rbfox2 OE were fed doxycycline containing diet for a period of 3 days, and at this point the mice were sacrificed and from harvested hearts, cardiomyocytes were isolated using the langendorff perfusion method. RNA was isolated from the cardiomyocytes using Qiagen kit, and sequenced on the Illumina HiSeq4000 platform after polyA RNA selection and library prep.

first: Chaitali

last: Misra

first: Auinash

last: Kalsotra


title: Transcriptional profiling of the peri-pulmonary vein region of the adult mouse left atrium and corresponding Tbx5-dependence

city: Cincinnati

first: Jeffrey

last: Steimle

email: jeffrey.steimle@cchmc.org, jeffrey.steimle@bcm.edu, jsteimle@uchicago.edu, jsteimle@alumni.nd.edu

state: OH

address: 240 Albert Sabin Way

department: Molecular Cardiovascular Biology

institute: Cincinnati Children's Medical Hospital Center

summary: The left atrium consists of three major parts: the peri-pulmonary vein portion, the appendage, and the vestibule. Previous transcriptional profiling of the adult left atrium and identification of the Tbx5-dependent transcriptome has focused on the atrial appendage (Nadadur et al 2016, Science Translational Medicine). In that study, Tbx5 was shown to regulate a gene regulatory network of atrial identity in the appendage and in its absence results in atrial fibrillation. In order to investigate the regional differences in the transcriptome of the left atrium, the left atrial appendage and the peri-pulmonary vein portion from adult mice were compared by RNA-sequencing. Additionally, as Tbx5 is major regulator of atrial identity, the peri-pulmonary vein portion of the atria was likewise examined following removal of Tbx5 using an adult specific conditional knockout of Tbx5.

overall_design: Mice harboring the ROSA26 tamoxifen-inducible cre recombinase transgene, Gt(ROSA)26Sortm1(cre/ERT2)Tyj (R26creERT2), were bred with mice harboring the Tbx5tm1Jse allele (Tbx5flox) to generate Tbx5 conditional mutants, R26creERT2/creERT2; Tbx5flox/flox, and controls, R26creERT2/creERT2; Tbx5+/+. Tamoxifen was administered by intraperitoneal injection on three consecutive days in mice 6 weeks of age and tissue samples were harvested 1 week after treatment as previously reported (Nadadur et al 2016 Science Translational Medicine). Transcriptional profiling was performed on the peri-pulmonary vein region of the left atrium. Total RNA was extracted from four controls and 6 conditional mutants. Following rRNA removal, libraries were prepared using the Illumina TruSeq RNA Sample prep kit v2. Samples were pooled in equimolar ratios and sequenced on the Illumina HiSeq4000 platform. Library preparation and sequencing was performed by the Genomics Core Facility at the University of Chicago. The peri-pulmonary vein samples were compared with the previously published corresponding left atrial appendage samples (Nadadur et al 2016 Science Translational Medicine). Both the peri-pulmonary vein and left atrial appendage samples were analyzed in parallel. Reads were aligned to the GRCm38/mm10 build of the Mus musculus genome (retrieved from UCSC May 23, 2012) using TopHat2. Reads were filtered to remove poorly aligned, duplicated, and unmapped reads using BamTools. Post-alignment, post-filtered reads were assigned to transcripts using StringTie. Downstream analysis performed using R. Differential expression testing was performed using edgeR  and limma.

first: Brigitte

last: Laforest

first: Rangarajan

last: Nadadur

first: Ivan

middle: P

last: Moskowitz


title: Hepatic transcriptomics reveals that lipogenesis is a key signaling pathway in isocitrate dehydrogenase 2 deficient mice

city: Fayetteville

first: Jeong Hoon

last: Pan

state: Arkansas

address: 987 W. Maple St.

institute: University of Arkansas

summary: The present study was conducted to capture signatures of isocitrate dehydrogenase 2 deficient (Idh2-/-) mice liver transcriptome using mRNA sequencing technique which provides information to discover new transcripts and to quantify transcript levels. Using this mRNA sequencing results, bioinformatic analyses will be performed to further identify key biological functions of Idh2 influencing disease-related signaling pathways.

overall_design: Hepatic mRNA profiles of wild type (WT) and Idh2-/- mice were generated by deep sequencing, in triplicate, using Illumina HiSeq 2500.

first: Jae

middle: K

last: Kim

first: Byungwhi

last: Kong


title: Functional Characterization and Expression Analyses Show Differential Roles of Maternal and Zygotic Dgcr8 in Early Embryonic Development

status: Public on Mar 09 2020

city: Hong Kong

first: Christopher H.K.

last: Cheng

address: Rm604,39 zone, CUHK, Shatin

institute: The Chinese University of Hong Kong


title: Mouse limb and respiratory muscle show distinct cachexia profiles in response to human pancreatic tumors II

summary: Background: Cancer cachexia is a life-threatening metabolic syndrome that causes significant loss of skeletal muscle mass and significantly increases mortality in cancer patients. Currently, there is an urgent need for better understanding of the molecular pathophysiology of this disease, so that effective therapies can be developed. Almost all pre-clinical studies evaluating skeletal muscle’s response to cancer have focused on one or two pre-clinical models, and almost all have focused specifically on limb muscles. In the current study, we reveal key differences in the histology and transcriptomic signatures of a limb muscle and a respiratory muscle in orthotopic pancreatic cancer patient-derived xenograft (PDX) mice.  Methods: To create the four cohorts of PDX mice evaluated in this study, tumors resected from four pancreatic ductal adenocarcinoma (PDAC) patients were portioned and attached to the pancreas of immunodeficient NSG mice.  Results: Body weight, muscle mass, and fat mass were significantly decreased in each PDX line. Histological assessment of cryosections taken from the tibialis anterior (TA) and diaphragm (DIA) revealed differential effects of tumor-burden on their morphology. Subsequent genome-wide microarray analysis on TA and DIA revealed key differences between their transcriptomes in response to cancer as well. Indeed, upregulated genes in the diaphragm were enriched for extracellular matrix (ECM) protein-encoding genes and genes related to the inflammatory response, and downregulated genes were enriched for mitochondria related protein-encoding genes. Conversely, the TA showed upregulation of canonical atrophy-associated pathways such as ubiquitin-mediated protein degradation and apoptosis and enrichment of downregulated genes encoding ECM proteins.  Conclusions: These data suggest that distinct biological processes account for wasting in different skeletal muscles in response to the same tumor burden. Further investigation into these differences will be critical for the future development of effective clinical strategies to counter cancer cachexia.

overall_design: Four cohorts of PDX mice were evaluated in this study: tumors resected from four pancreatic ductal adenocarcinoma (PDAC) patients were portioned and attached to the pancreas of immunodeficient NSG mice which developed cachexia in response to tumor growth (sham mice underwent surgery with no tumor implantation). RNA was extracted from the tibialis anterior (TA) and diaphragm (DIA) of sham and PDAC-PDX mice. Subsequent microarray analysis was performed with multiple samples from both muscles of mice from each of the four cohorts.

first: Rachel

last: Nosacka

first: Andrew

last: Judge


title: Mouse limb and respiratory muscle show distinct cachexia profiles in response to human pancreatic tumors I

first: Boston University

last: Microarray and Sequencing Resource

overall_design: PDAC-PDX (Cohort 1) mice were evaluated in this study: tumor resected from a pancreatic ductal adenocarcinoma (PDAC) patient was portioned and attached to the pancreas of immunodeficient NSG mice which developed cachexia in response to tumor growth (sham mice underwent surgery with no tumor implantation). RNA was extracted from the tibialis anterior (TA), diaphragm (DIA) and abdominal muscle (ABD) of sham and PDAC-PDX mice. The ABD muscle was collected as a 1cm x 1cm square cut from the abdominal wall within the right lumbar and umbilical region thus including part of the internal and external obliques and transverse and rectus abdominus.  Subsequent microarray analysis was performed with 3 samples of each muscle.


title: NELF regulates a promoter-proximal step distinct from RNA Pol II pause-release

city: Chicago

first: Ali

last: Shilatifard

state: IL

address: 320 E Superior St

department: Department of Biochemistry and Molecular Genetics

institute: Northwestern University Feinberg School of Medicine

summary: RNA polymerase II (Pol II) is generally paused at promoter-proximal regions in most metazoans, and based on in vitro studies, this function has been attributed to the negative elongation factor (NELF). Here, we show that upon rapid depletion of NELF, Pol II fails to be released into gene bodies, stopping instead around the +1 nucleosomal dyad-associated region. The transition to the 2nd pause region is independent of positive transcription elongation factor P-TEFb. During the heat shock response, Pol II is rapidly released from pausing at heat shock induced genes, while most genes are paused and transcriptionally downregulated during the heat shock response. We find that both aspects of the heat shock response remain intact upon NELF loss. We find that NELF depletion results in global loss of cap-binding complex from chromatin without global reduction of nascent transcript 5’ cap stability. Thus, our studies implicate NELF functioning in early elongation complexes distinct from Pol II pause-release.

overall_design: Examination of NELF functions in human cells using the auxin-inducible degron system and high-throughput sequencing (PRO-seq, ChIP-seq, PRO-cap).

first: Yuki

last: Aoi

first: Edwin

middle: R

last: Smith


title: Identification of miR-181a target mRNAs by RIP-CHIP during terminal differentiation of DC-SIGN+ mo-DCs

first: Bernett

last: Lee

address: 8A Biomedical Grove #03-06 Immunos

country: Singapore

institute: Singapore Immunology Network

summary: DC-SIGN+ monocyte-derived dendritic cells (mo-DCs) play important roles in bacterial infections and inflammatory diseases, but the factors regulating their differentiation and proinflammatory status remain poorly defined. Here, we identify a micro-RNA, miR-181a, and a molecular mechanism that simultaneously regulate the acquisition of DC-SIGN+ expression and the activation state of DC-SIGN+ mo-DCs. Specifically, we show that miR-181a promotes DC-SIGN expression during terminal mo-DC differentiation and limits its sensitivity and responsiveness to TLR triggering and CD40 ligation. Mechanistically, miR-181a sustains ERK-MAPK signaling in mo-DCs, thereby enabling the maintenance of high levels of DC-SIGN and a high activation threshold. Low miR-181a levels during mo-DC differentiation, induced by inflammatory signals, do not support the high phospho-ERK signal transduction required for DC-SIGNhi mo-DCs and lead to development of proinflammatory DC-SIGNlo/- mo-DCs. Collectively, our study demonstrates that high DC-SIGN expression levels and a high activation threshold in mo-DCs are linked and simultaneously maintained by miR-181a.

overall_design: RIP-CHIP (RNA-Binding Protein Immunoprecipitation-Microarray (Chip) Profiling) was performed to identify miR-181a specific target genes and delineate the Ago-2 dependent miRNA-targetome during terminal differentiation of DC-SIGN+ mo-DCs. Here, CD14+ monocyte intermediates (designated progenitor cell-derived monocytes, or moPs) arising in cultures of cord blood CD34+ progenitor cells were transduced with miR-181a KD or scramble control vectors, and supplemented with GM-CSF and IL-4 for 24 hours; then Ago-2-dependent miRNAs and their associated target mRNAs were pulled down, isolated, and analyzed on Affymetrix microarray chips.

first: Clarice

middle: X

last: Lim

first: Olivia

last: Geiger

first: Christina

last: Passegger

first: Michaela

last: Beitzinger

first: Johann

last: Romberger

first: Anika

last: Stracke

first: Christoph

last: Högenauer

first: Anton

last: Stift

first: Heribert

last: Stoiber

first: Michael

last: Poidinger

first: Armin

last: Zebisch

first: Gunter

last: Meister

first: Adam

last: Williams

first: Richard

last: Flavell

first: Jorge

last: Henao-Mejia

first: Herbert

last: Strobl


title: RNA sequencing of primary acute lymphoblastic leukemia xenograft brains with and without treatment with chimeric antigen receptor T (CAR-T) cell therapy

city: Rochester

first: Saad

last: Kenderian

state: MN

address: 200 First Street SW

department: Hematology Research

institute: Mayo Clinic

summary: NSG mice were IP injected with 30mg/kg busulfan. The following day, mice received 1,000,000-3,000,000 primary blasts derived from the peripheral blood of patients with ALL. Mice were monitored for engraftment for ~10-13 weeks via tail vein bleeding for engraftment. Some mice received high dose CAR-T cell therapy and an isotype control antibody treatment. RNA was isolated using miRNeasy Micro kit (Qiagen, Gaithersburg, MD, USA) and treated with RNase-Free DNase Set (Qiagen, Gaithersburg, MD, USA). RNA-seq analyses of brain sections harvested from mice treated with CAR-T cells showed significant upregulation of genes regulating the T cell receptor, cytokine receptors, T cell immune activation, T cell trafficking, and T cell and myeloid cell differentiation. Xenografts treated with CAR-T cell therapy developed neurotoxicity.

overall_design: RNA sequencing was performed on brain tissue of NSG primary acute lymphoblastic leukemia (ALL) xenografts with and without CAR-T cell treatment using three biological replicates for each condition

first: Rosalie

last: Sterner

first: Michelle

last: Cox


title: Transcriptome analysis of Chx10-Cre Rb1/p107 and Chx10-Cre Rb1/p107/Hells P21 retinae

city: Irvine

first: Claudia

last: Benavente

address: 839 Medical Sciences Ct, Sprague Hall 108

institute: University of California, Irvine

summary: We used novel genetically engineered mouse models to investigate the role of HELLS during tumorigenesis. Loss of HELLS drastically decreased the incidence of retinoblastoma, delayed tumor progression, and increased overall survival. Retinae from Rb1/p107 DKO and Rb1/p107/Hells TKO mice at postnatal day 21 were analyzed for gene expression using RNA-seq.

overall_design: Retinal mRNA profiles of 21-day-old Chx10-Cre Rb1/p107 and Chx10-Cre Rb1/p107/Hells mice were generated by deep sequencing, in triplicate, using Illumina HiSeq 4000.

first: Jie

last: Wu


title: Chromatin remodeling protein HELLS is critical for retinoblastoma tumor initiation and progression


title: Identification and characterization analysis of the microRNA in human cerebral microvesscular endothelial cells response to methphatamine using a deep sequencing approach

city: Nanjing

first: Li

last: Yang

state: Jiangsu

address: Dingjiaqiao 87

department: Pharmacology

institute: Southeast University

summary: Disruption of the cerebrovascular integrity is involved in the context of drug abuse. Our study provides a potential new therapeutic strategy to cerebrovascular damage in the context of drug abuse.

overall_design: MicroRNAs were involved in a number of CNS pathologies, including brain tumors, neurodegeneration and MS. Moreover, miRNAs are envisioned as therapeutic strategies to treat neurovascular-dependent brain diseases since a certain number of miRNAs have been implicated in the regulation of BBB function under normal and inflammatory conditions.Therefore, miRNA profiling was performed to identify the specific miRNA in the regulation of endothelial cell function in of HBMECs treated with Meth. MiR-30d-5p was characterized because its down-regulation was validated in HBMECs treated with Meth or LPS.


title: Compensatory upregulation of X-inactivation escape genes in Xq deletion

city: Rio de Janeiro

first: Cíntia

middle: Barros

last: Santos-Rebouças

state: RIO DE JANEIRO

address: Rua São Francisco Xavier, 524 - PHLC - sala 501F - Maracanã

department: Department of Genetics

country: Brazil

institute: State University of Rio de Janeiro

summary: We report on genetic and functional data from an asymptomatic female with a large deletion on the X-chromosome. Blood RNA samples from individual II.3 and an age and sex-matched control were  analyzed by RNA-Seq in Illumina platform. Total RNA was purified using poly-T oligo-attached magnetic beads with rRNA removal. The resulting directional RNA-Seq NEB libraries were sequenced in paired-end format. Image analysis and per-cycle base calling were performed with Illumina Real-Time Analysis software (RTA1.9). Conversion to FastQ read format was obtained by CASAVA-1.8 and sequenced reads were quality-checked with FastQC. Sequence adaptors were removed with cutadapt v1.2.1, and reads were aligned to the human reference genome (GRCh37/hg19) with STAR. BAM files were visualized by using the Integrative Genomics Viewer. The quantification of reads were obtained by HTSeq v0.6.1. Transcriptome-wide analysis in individual II.3 uncovered 1,026 differentially blood-expressed genes, as compared with the matched control sample. From the 598 RefSeq genes mapping within the X-chromosome deletion, 241 genes were expressed on blood. From these, 117 transcripts have more than ten counts in at least in one of the samples (individual II.3 or control). Only three genes within the deletion (GPR112, SLC6A8 and, FUNDC2) showed statically significant adjusted p-values and |log2(FoldChange)|.Our data suggest that a protective gene-by-gene mechanism occurs at the transcriptional level in the active X chromosome to counterbalance detrimental effects of large Xq deletions.

overall_design: Examination of blood samples of an assymptomatic patient with Xq deletion and a female control, by Illumina HiSeq (Genone Biotechnologies - Rio de Janeiro - Brazil)

first: C

middle: B

last: Piergiorge


title: MicroRNA expression profiles in pigeon(Columba livia) skeletal muscle satellite cells during differentiation

city: Chengdu

first: Xun

last: Wang

state: China

address: Huimin road 211#, Wenjiang district

institute: Sichuan agricultural university

summary: A comparative profile of miRNAs in pre- and post-differentiated pigeon SMSCs (SMSC-1d and SMSC-5d) was performed by using high-throughput sequencing. We identified known porcine miRNAs, novel miRNAs, and miRNAs that are conserved in other birds and mammals. Our findings demonstrated that miRNAs are extensively involved in the differentiation of SMSCs in pigeons, and provide a valuable resource for the pigeon breeding.

overall_design: we investigated miRNA expression profiles from pigeon skeletal muscle satellite cells during differentiation by using high-throughput sequencing technology.

first: Siyuan

last: Feng


title: Functional Characterization and Expression Analyses Show Differential Roles of Maternal and Zygotic Dgcr8 in Early Embryonic Development [miRNA-seq]

first: Christopher H.K.

last: Cheng

overall_design: Methods: Embronic miRNA expression of 4.5 hours post fertilization wild-type (WT) and maternal zygotic mutant (MZdgcr8) zebrafish were generated by deep sequencing, in triplicate.

first: Christopher

first: Ou

last: Sha

first: Zeyao

last: Zhu


title: Functional omics analyses reveal only minor effects of microRNAs on human somatic stem cell differentiation

first: Andreas

last: Kloetgen

overall_design: Refer to individual Series


title: Expression data from advanced non-small cell lung cancer

city: Guangzhou

first: Shangbiao

last: Li

address: Department of Radiation Oncology, Zhujiang Hospital, Southern Medical University, 253 Industrial Avenue, Guangzhou, China

department: Department of Radiation Oncology

institute: Southern Medical University

summary:
We used microarrays to detail the differentially expressed miRNA before and after down-regulation of miR-744 in lung cancer cell lines by genome-wide expression microarray
To gain insights into the molecular mechanism of miR-744 in the promotion of malignant phenotype of lung cancer cells, we analyzed the mRNAs differentially expressed before and after miR-744 down-regulation.

overall_design: Lung cancer cells were transfected with antagomir-744 (IN1, IN2, IN3) or antagomir-NC(NC1, NC2, NC3) for RNA extraction and hybridization on Affymetrix microarrays by using genome-wide expression profile chip.

first: Xiaoxia


title: Transcriptome analysis of Chx10-Cre Rb1/p107 and Chx10-Cre Rb1/p107/Hells tumors

summary: We used novel genetically engineered mouse models to investigate the role of HELLS during tumorigenesis. Loss of HELLS drastically decreased the incidence of retinoblastoma, delayed tumor progression, and increased overall survival. Tumors from Rb1/p107 DKO and Rb1/p107/Hells TKO mice were analyzed for gene expression using RNA-seq.

overall_design: Tumor mRNA profiles of from Chx10-Cre Rb1/p107 and Chx10-Cre Rb1/p107/Hells mice were generated by deep sequencing, in triplicate, using Illumina 4000.

first: Jingtian

first: Zocchi

last: Loredana


title: miR-302 is a temporal regulator of neural crest development

city: Houston

first: Rachel

last: Keuls

state: TX

address: One Baylor Plaza, Alkek N1020

institute: Baylor College of Medicine

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

sample_organism:
Gallus gallus
Mus musculus

platform_organism:
Gallus gallus
Mus musculus


title: Comprehensive analysis of transcriptomic changes in cutaneous squamous cell carcinoma

city: Stockholm

first: Kunal

last: Das Mahaptra

state: Select Option

address: PO BOX 23109

summary:
Purpose: We report the coding and non-coding transcriptomic changes in primary cutaneous squamous cell carcinoma
Methods: 4 mm punch biopsies were collected from 7 unmatched healthy and 9 cSCC patients and snap frozen. The library preparation was done using Illumina TruSeq® Stranded Total RNA (with Ribo-Zero Gold) preparation kit. 100 ng of total RNA was depleted of rRNAs using ribo-zero gold magnetic bead based capture-probe system (Illumina Inc.). The remaining RNA was subsequently purified (RNAcleanXP, Beckman Coulter) and fragmented using enzymatic fragmentation. Then first strand synthesis and second strand synthesis were performed and the double stranded cDNA was purified (AMPure XP, Beckman Coulter). The cDNA was end repaired, 3’ adenylated and Illumina sequencing adaptors ligated onto the fragments ends, and the library was purified (AMPure XP). The stranded libraries were amplified with PCR and purified (AMPure XP). The libraries size distribution was validated and quality inspected on a Bioanalyzer. Sequencing was performed on NextSeq 500 instrument using v2 reagent kits according to the manufacturer instructions (Illumina Inc.).
Results: On average 49.8 million 100 base pair (bp) paired-end reads were obtained from each sample and genome mapping was on average 55% for all samples. Altered expression of 5,352 protein-coding genes, 908 lncRNAs and 55 circular RNAs was identified.
Conclusions: Here, we report the coding and non-coding transcriptomic changes from cSCC samples, along with identification of skin specific transcripts and novel deregulated circRNAs.

overall_design: Whole transcriptome profile of 9 cSCC and 7 unmatched healthy controls

last: Das Mahapatra

first: Andor

last: Pivarcsi

first: Lorenzo

last: Pasquali

first: Jonas

last: nørskov Søndergaard

first: Enikö

last: Sonkoly


title: Next Generation Sequencing Facilitates Quantitative Analysis of normal and YTHDF2 Overexpressing SMMC7721 cells in normoxia and hypoxia condition

status: Public on Mar 17 2020

city: Shanghai

first: Zhenjun

last: Zhao

state: Shanghai

address: 1630 Dongfang Road, Puundong New District, Shanghai, China

institute: Renji Hospital, Shanghai Jiao Tong University, School of Medicine

summary: Dynamic N6-methyladenosine (m6A) modification was previously identified as a ubiquitous post-transcriptional regulation that affected mRNA homeostasis. However, the m6A-related epitranscriptomic alterations and functions remain elusive in human diseases such as cancer. Here we show that hypoxia restrains the ‘reader’ protein YTH domain family 2 (YTHDF2), to stabilize the methylated oncogene mRNAs in inflammation-associated liver cancer. YTHDF2 silenced in human cancer cells or depleted in mouse hepatocytes evoked pro-inflammatory responses and accelerated tumor growth and metastatic progression. Under hypoxia, YTHDF2 processed the decay of m6A-containing interleukin 11 (IL11) and serpin family E member 2 (SERPINE2) mRNAs, which were responsible for the inflammation-mediated malignancy. Reciprocally, YTHDF2 transcription succumbed to hypoxia-inducible factor-2α (HIF-2α). Administration of a HIF-2α antagonist (PT2385) restored YTHDF2-programed epigenetic machinery and repressed liver cancer. Hence, our findings provide a new insight into the mechanism by which hypoxia adapts m6A-mRNA editing to promote cancer.

overall_design: Normal and YTHDF2 overexpressing SMMC7721 cells were cultured in normoxia and hypoxia conditions. mRNA profiles of all four cells were generated by deep sequencing with Illumina HiSeq X

first: Jiajie

last: Hou


title: Functional omics analyses reveal only minor effects of microRNAs on human somatic stem cell differentiation [mRNA-Seq]

address: Inhoffenstr 7

summary: Functional analysis of transcriptome (mRNA and microRNA) and proteome formation during treatment of cord-blood derived stem cell lines (USSC) with retinoic acid-containing XXL-medium to estimate the impact of microRNAs on final proteome.

overall_design: NGS analysis (mRNA and microRNAs) and proteome of native and XXL-treated USSC. Bioinformatic target prediction analysis of regulated microRNAs in comparison to regulated proteome. Transfection of USSC with regulated microRNAs, followed by XXL treatment and subsequent proteome anlysis to estimate the contribution of microRNAs to proteome shaping in USSC upon XXL-treatment.

first: Jessica

last: Schira-Heinen

first: Hans-Ingo

last: Trompeter


title: Functional omics analyses reveal only minor effects of microRNAs on human somatic stem cell differentiation [miRNA-Seq]


title: miR-302 is a temporal regulator of neural crest development [Mouse miRNA-seq]

summary: We analyzed wildtype and miR-302 knockout embryos at E7.5 and sorted neural crest using Wnt1-Cre at E8.5 and Sox9 at E9.5 to capture miRNA differences during neural crest development

overall_design: Wildtype and miR-302 knockout embryos were analyzed at each timepoint E7.5, E8.5, and E9.5

first: Ronald

middle: J

last: Parchem


title: Functional Characterization and Expression Analyses Show Differential Roles of Maternal and Zygotic Dgcr8 in Early Embryonic Development [RNA-seq]

first: Christopher H.K.

last: Cheng

overall_design: Methods: Embronic mRNA profiles of 4.5 hours post fertilization wild-type (WT) and maternal zygotic mutant (MZdgcr8) zebrafish were generated by deep sequencing, in triplicate.

first: Christopher

first: Ou

last: Sha

first: Zeyao


title: Gene expression profiling of B cell lymphoma in dogs reveals dichotomous metabolic signatures distinguished by oxidative phosphorylation

city: Philadelphia

first: Ying

last: Wu

state: Pennsylvania

address: 3900 Spruce Street

institute: University of Pennsylvania

summary: We analyzed the transcriptomic profile of neoplastic CD5-CD21+ B cells isolated ex vivo from the enlarged lymph node of dogs with B cell lymphoma

overall_design: Transcriptomic profiles of neoplastic CD5-CD21+ B cells isolated ex vivo from 11 dogs with B cell lymphoma were generated by RNA-seq, using Illumina HiSeq 4000 System.

first: Oliver

last: Garden


title: A Novel Progesterone Biosensor Derived from Microbial Screening

city: Boston

first: James

last: Galagan

address: 44 Cummington Mall

institute: Boston University


title: Cellular origin, tumour progression and pathogenic mechanisms of cutaneous neurofibromas revealed by mice with Nf1 knockout in boundary cap cells

city: PARIS

first: Stephane

last: Le Crom

address: 46 rue Ulm

department: Genomic Core Facility

country: France

institute: IBENS

summary: Patients carrying an inactive NF1 allele develop tumours of Schwann cell origin called neurofibromas (NFs). Genetically engineered mouse models have significantly enriched our understanding of plexiform forms of NFs (pNFs). However, this has not been the case for cutaneous neurofibromas (cNFs), observed in all NF1 patients, as no previous model recapitulates their development. Here, we show that conditional Nf1 inactivation in Prss56-positive boundary cap cells leads to bona fide pNFs and cNFs. This work identifies subepidermal glia as a likely candidate for the cellular origin of cNFs, and provides insights on disease mechanisms, revealing a long, multistep pathological process in which inflammation play pivotal role. This new mouse model is an important asset for future clinical and therapeutic investigations of NF1-associated neurofibromas.

overall_design: Comparaison between injured (14 days post-injury) versus uninjured skin isolated from Nf1-KO and control mice

first: Katarzyna

last: Radomska

first: Fanny

last: Coulpier

first: Aurelie

last: Gresset

first: Alain

last: Schmitt

first: Amal

last: Debbiche

first: Sophie

last: Lemoine

first: Pierre

last: Wolkenstein

first: Jean-Michel

last: Vallat

first: Patrick

last: Charnay

first: Piotr

last: Topilko


title: microRNA expression in rat hippocampus up to 1 year after fluid percussion brain injury

city: Galveston

first: Helen

middle: Lee

last: Hellmich

address: 601 Harborside Dr. Bldg.21 Rm 3.202H

department: Anesthesiology

institute: University of Texas Medical Branch

summary:
Purpose: The goal of this study is to investigate the expression of microRNAs up to 1 year after fluid percussion TBI
Methods: miRNA-Seq analysis of microRNA expression in the hippocampus of TBI and sham surgery rats

overall_design: miRNA-seq profiling of hippocampal microRNAs in TBI and sham surgery rats

first: Harris

last: Weisz

first: Debbie

last: Boone

first: Steven

middle: G

last: Widen

middle: L


title: miR-302 is a temporal regulator of neural crest development [Mouse RNA-seq]

first: Rachel

last: Keuls

summary: We analyzed wildtype and miR-302 knockout embryos at E7.5 and sorted neural crest using Wnt1-Cre at E8.5 and Sox9 at E9.5 to capture transcriptomic differences during neural crest development

first: Ronald

last: Parchem


title: microRNA expression in human traumatic brain injury biofluids

summary:
Purpose: The goal of this study is to investigate the expression of microRNAs in TBI biofluids compared to uninjured controls
Methods: miRNA-Seq analysis of microRNA expression TBI and uninjured control biofluids

overall_design: miRNAseq analysis of biofluids obtained from acute and chronic human TBI and uninjured controls


title: Whole gene expression analysis in offspring liver

city: Tsukuba

first: Keisuke

last: Yoshida

state: Ibaraki

address: 3-1-1 Koyadai,

institute: RIKEN

summary:
Increasing evidence indicates that paternal dietary conditions influence the metabolic disorders of offspring. Previous studies suggested the involvement of epigenetic regulation for such phenomena, but the mechanism remains elusive. To reveal the molecular function of  stress-dependent epigenetic regulator ATF7 in paternal inheritance of dietry effect on offpring phenotype, we analyzed ATF7-binding profiles in testicular germ cells by ChIP-seq, DNA methylation profiles in sperm by TGBS, small RNA expression profiles in HRCS by RNA-seq, and whole expression profiles in offspring liver by expression array analysis, using wild-type and ATF7 heterozygous mutant mice fed with control diet or low-protein diet.
We performed expression array analysis to identidy genes which expressions are affected by paternal diet and ATF7 mutation.

overall_design: This series contains six sets of exression array data; WT_CD, WT_LPD, ATF7+/–_CD, ATF7+/–_LPD, ATF7+/+_CD and ATF7+/+_LPD. For all data set, we prepared eight CEL files generated by eight biological-independent experiments.

first: Maekawa

last: Toshio

first: Shunsuke

last: Ishii


title: TBX1-FGF11 as a novel axis governing limb development

city: Montpellier

first: Said

last: Assou

address: 80, av. Augustin Fliche

department: Institute for Regenerative Medecine and Biotherapy

institute: University Hospital of Montpellier, Inserm

summary:
Although intensively studied, the gene networks regulating limb development is still incomplete. Indeed, efforts to decipher the genetic and transcriptional control of limb formation rely mainly on transcriptome approaches obtained from embryos collected 0.5 or 1 day apart from E9.5 to E13.5. This approach identified gene networks tightly regulated during limb morphogenesis as well as novel genes possibly involved in these networks. However, given the complexity and speed of the underlying molecular processes at these stages, relying on time points 1 or even 0.5 day apart limits our ability to capture regulatory changes taking place at a faster pace, and to identify the factors on which they depend.
To obtain a comprehensive view of the limb developmental progression at the molecular level, we used the roller system to culture E10.5 and E12.5 mouse embryos over a 6h time window and performed a microarray analysis (Affymetrix GeneChip® Mouse Exon 1.0 ST Arrays) on the collected samples

overall_design: The forelimbs of E10.5 from non-cultured mouse embryos and the forelimbs from E10.5 and E12.5 mouse embryos cultured for 1, 3 or 6 hours were collected for RNA extraction and hybridization on Affymetrix GeneChip® Mouse Exon 1.0 ST Arrays according to Affymetrix recommendations.

first: Gautier

last: Tejedor

first: Béryl

last: Laplace-Builhé

first: Patricia

last: Luz-Crawford

first: Audrey

last: Barthelaix

first: Karima

last: Kissa

first: Christian

last: Jorgensen

first: Jérôme

last: Collignon

first: Paul

last: Chuchana

first: Farida

last: Djouad


title: miR-302 is a temporal regulator of neural crest development [Chicken miRNA-seq]

summary: expression of miR-302 was analyzed in chicken embryos using small RNA-seq to verify an increase or decrease in exppression when miR-302 was overexpressed or knocked down

overall_design: cells in which miR-302 was either overexpressed or knocked down were also GFP positive and FACS sorted. Expression of miR-302 from the GFP positive cells was compared to that of the GFP negative cells


title: Gene expression in the murine liver, effect of hepatic expression of Niemann-Pick C1-like 1 protein.

city: Tokyo

first: Yu

last: Toyoda

address: 7-3-1 Hongo, Bunkyo-ku

department: Department of Pharmacy

institute: The University of Tokyo Hospital

summary: To characterize basal differences in hepatic gene-expression patterns, we performed a microarray analysis using wild-type and L1-Tg mice fed a control fat diet (CE-2: CLEA Japan, Inc., Tokyo, Japan) for two weeks.

overall_design: RNA samples were taken from the livers of mice, and then subjected to a microarray analysis. Comparisons among groups were made by one-color method with normalized data from Cy3 channels for data analysis.

first: Tappei

last: Takada

first: Masakazu

last: Umezawa

first: Ken

last: Takeda

first: Hiroshi

last: Suzuki


title: RNA-Seq analysis of genes differentially regulated in naïve Cd4 T cells from wide-type and PIK3CD GOF mice

city: Chongqing

first: Xiaodong

last: Zhao

state: Chongqing

address: No.136, Zhongshan 2nd Rd, Yuzhong District

institute: Chongqing Medical University

summary:
Objective:mRNA sequencing of sorted naive CD4+ T cells from the spleens of PIK3CD GOF mice and WT littermate mice.
Methods:Naive CD4+ T cells were negatively isolated ex vivo(Stemcell Technologies).Total RNA from isolated naive CD4+ T cells was extracted using RNeasy Plus Mini Kit (Qiagen, GmBH, Germany) according to the manufacture’s instruction and checked for RNA integrity by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, US). Qualified total RNA was further purified by RNeasy micro kit (QIAGEN) and RNase-Free DNase Set (QIAGEN). Paired-end libraries were constructed using the TruSeq® RNA Sample Preparation Kit (Illumina, USA) according to the manufacturer’s instructions. The products are purified, enriched, quantified by Qubit® 2.0 Fluorometer (Life Technologies, USA) and validated by Agilent 2100 bioanalyzer to confirm insert size and calculate the mole concentration. Cluster was generated using cBot with the library diluted to 10 pM and then were sequenced on the Illumina HiSeq 2500 (Illumina, USA). The library construction and sequencing was performed at Shanghai Biotechnology Corporation (Shanghai, China).
Results:Compared to the expression profiles for the WT cells, those for the mutant TNaive showed 2,307 genes with differential expression, of which 1,749 were upregulated and 558 were downregulated. Gene ontology analysis showed that PIK3CD GOF TNaive upregulated the expression of genes encoding molecules involved in the cell cycle and mitosis, including E2f1, E2f2, cyclin A2, cyclin B2, Cdk1, Hells and Nuf2, all of which might synergistically promote entry into the cycling phase. In addition, the genes encoding T cell activation, cytokines and cytokines receptors, chemokines and chemokine receptors, transcription factors, and metabolic regulators were differentially regulated in PIK3CD GOF mice compared to WT mice. Kyoto Encyclopedia of Genes and Genomes analysis showed that the altered genes in TNaive from PIK3CD GOF mice displayed significant enrichment of several sets associated with infection, inflammation and autoimmune disease
Conlusion:PIK3CD GOF results in a loss of quiescence-associated gene expression patterns in naive T cells by collectively coupling the cell cycle, nutrient metabolism, cell trafficking and signal transduction.

overall_design: naïve CD4 T cells of WT and PIK3CD GOF mice （8 week, male, n=3-4 mice per group）were nagetively isolated, and the total RNA was extracted by RNeasy Plus Mini Kitand checked for RNA integrity. The Qualified total RNA was further purified by RNeasy micro kit and RNase-Free DNase Set. Paired-end libraries were constructed using the TruSeq® RNA Sample Preparation Kit.Purified libraries were quantified by Qubit® 2.0 Fluorometer and validated to confirm insert size and calculate the mole concentration. Cluster was generated using cBot with the library diluted to 10 pM and then were sequenced on the Illumina HiSeq 2500 by Shanghai Biotechnology Corporation(Shanghai, China).

first: Yanjun

last: Jia


title: LATS kinase-mediated selective disruption of CTCF genomic binding

city: Gainesville

first: Jianrong

last: Lu

state: FL

address: 2033 Mowry RD

department: Biochemistry and Molecular Biology

institute: University of Florida

summary: We identified CTCF as a substrate of the LATS kinases. Under cellular stress conditions that activated LATS, CTCF was phosphorylated in a LATS-dependent manner and lost DNA-binding activity. LATS signaling target genes resided in CTCF-mediated insulated neighborhoods and depended on such chromatin organization to sustain their expression. Genome-wide CTCF DNA-binding profiling revealed that metabolic stress reduced CTCF occupancy specifically at a small subset of CTCF-binding sites that encompassed many LATS target genes and were most significantly associated with LATS signaling. Dissociation of CTCF from LATS target genes disrupted corresponding CTCF-mediated chromatin domains and downregulated LATS target gene expression.

overall_design: CTCF ChIP-seq  for WT and Glucose free medium treatment in MCF7 breast cancer cells

first: Huacheng

last: Luo


title: Molecular function of stress-dependent epigenetic regulator ATF7 in paternal inheritance of dietary effect on offspring phenotype

first: Keisuke

last: Yoshida

type: Methylation profiling by high throughput sequencing

overall_design: Refer to individual Series


title: The Anxiolytic Drug FGIN-1-27 Ameliorates Autoimmunity by Metabolic Reprogramming of Pathogenic Th17 Cells

city: Bethesda

first: Stefan

last: Muljo

state: MD

address: 10 CENTER DR RM 11N306

institute: NIH/NIAID

summary: CD4 T cells were treated with DMSO (control) or FGIN-1-27 under Th17 polarizing conditions and RNA sequencing was done to look at differentially expressed transcripts

overall_design: Purified CD4 T cells were treated with DMSO or FGIN-1-27 under Th17 polarizing conditions

first: Bryan

last: Chim

first: Anju

last: Singh


title: Transcriptomic Profiling of Human and Mouse Kidneys

city: Baltimore

first: Theresa

last: Hodges

address: 801 W. Baltimore Street

department: Institute for Genome Sciences

institute: University of Maryland Baltimore

summary: RNA-seq of human and mouse kidneys reveals both known and uncharacterized alternative transcripts derived from genes that are critical for sodium reabsorption and blood pressure regulation.

overall_design: Total RNA was extracted from four replicates of human kidney, 2 replicates of mouse kidney cortex & 2 replicates of mouse kidney medulla (WT mice, 8-10 weeks old)

first: Carlo

last: Mercado

first: Yen-Pei

middle: C

last: Chang


title: In vivo delivery of CRISPR/Cas9 nanocomplexes in post-mitotic neurons for Alzheimer’s disease therapy

city: Bukgu

first: Jihwan

last: Park

state: Gwangju

address: 123 Cheomdangwagi-ro

country: South Korea

institute: GWANGJU INSTITUTE OF SCIENCE /TECHNOLOGY

summary: The clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 system has emerged as a powerful technique for correcting genetic disease-causing mutations. However, in vivo gene editing using CRISPR/Cas9 remains a major challenge currently limiting its therapeutic application for disease correction. In the present study, we developed novel Cas9/gRNA nanocomplexes that lead to efficient in vivo gene targeting of neurons in the brain. We demonstrate the in vivo efficacy of Cas9-nanocomplexes as therapeutic agents for Alzheimer’s disease (AD) by targeting the BACE1 gene. Remarkably, in vivo BACE1 targeting by using Cas9-nanocomplexes results in decreased Aβ42 production and improvement of cognitive decline in an AD mouse model. These results suggest that Cas9-nanocomplexes represent an effective in vivo gene editing platform in the brain, and that this strategy may be applicable to the treatment of a broad range of neurological diseases.

overall_design: HEK 293T cell was used for human control and CRISPR/Cas9 nanocomplex (Nano) treated samples. Mouse brain was used for control and CRISPR/Cas9 nanocomplex (Nano) treated samples. For human samples, PCR amplicons of 4 target sites were pooled and sequenced (total 2 samples). For mouse samples, PCR amplicons of 4 target sites were sequenced separately (total 8 samples).

first: Hanseul

first: Jungju

last: Oh

first: Yujung

first: Soonbong

last: Baek

first: Hongwon

last: Kim

first: Hwan

last: Chio

first: Junsang

last: Yoo

first: Minhyung

last: Lee

first: Christopher

last: Lengner

first: Jongpil


title: Transportation stress suppress reproductive performance in female mice and relevant genes detection

status: Public on Mar 07 2020

city: Jinan

first: Jiajia

last: Liu

state: Shandong

address: No 336, West Road of Nan Xinzhuang,

institute: University of Jinan

summary:
Animals in transport are exposed to both psychological and physical stressors, which affect performance and health. The objectives of this study were to investigate whether and how the transportation stress effect on female reproduction in mice, and detect differentially expressed genes association with stress response and reproductive capacity utilizing gene expression profiles.
After transported mice by car to and from laboratory for a total period of 10 h, nearly 1000 km distance, measurements were carried out to explore effects of transportation stress on reproductive traits including puberty, estrous cycle, follicular number within ovaries, fertility and superovulation quality. Early life stress suffered mice before puberty promoted puberty onset, altered estrous cycle length and reduced large antral follicle number. Pubertal and adult mice exposure to transportation stress induced their pregnancy rate decline. Furthermore, adult stressed mice showed an obvious reduction in fertility with less litter size and litter weight in birth, which may cause reduced ovulation oocytes identified by superovulation. Assuming ovulated oocytes number as reproductive parameter, genes differently expressed between mice with extremely high and extremely low oocytes were compared within control and stress group separately.

overall_design: Affymetrix GeneChip® Mouse Gene 2.0 ST Arrays (PN: 902118) were used for transcriptome analysis to investigate gene expression difference between control and stressed mice for superovulation potential. Ten pairs of 6 weeks old female BABL/c mice with same parents were chosen in this experiment. Each pair of littermates were distributed into control and stress groups randomly and fed until 9 weeks old before performing superovulation. Mice were killed to number the oocytes in oviduct and separated hypothalamus (H), pituitary gland (P) and ovary (O) from each animal. The tissues were placed in a micro-centrifuge tube, flash-frozen in liquid nitrogen and stored at - 80℃ until further experiment. Each kind of tissue in both control and stress groups were divided into three sets according to mice ovulated oocytes number. The highest (h) stood for tissue from mouse with highest oocytes, the lowest (l) meant tissue from mouse with lowest oocytes and the pool (m) set were mixed samples from another 8 mice in each group.

first: Zia-ur

last: Rehman

first: Qing

first: Liguo

last: Yang


title: Endothelial CXCL12 regulates neovascularization during tissue repair and tumor progression

city: Stanford

first: Michael

last: Januszyk

state: CA

address: 257 Campus Dr

department: Surgery

institute: Stanford University

summary: Tissue repair and tumor progression are linked by their reliance on the response to ischemia. Coordinated interplay between resident and circulating cells, governed by a myriad of factors, is critical for new blood vessel formation and tissue survival in both. The vascular endothelium exhibits paracrine activity and provides an interface for the recruitment of circulating cells, which in turn influence the neovascularization and extra-vascular tissue growth. CXC chemokine ligand 12 (CXCL12; stromal cell-derived factor 1 [SDF-1]) has been implicated in tumor biology and neovascularization, but its specific role and mechanism of action remain poorly understood. We have previously demonstrated that CXCL12 expression is hypoxia responsive and occurs in vascular endothelium. Here we use a conditional CXCL12 knockout mouse to show that endothelial-specific deletion of CXCL12 (eKO) reduces the survival of ischemic tissue, which alters both tissue repair and tumor progression. The loss of vascular endothelial CXCL12 disrupts endothelial – fibroblast crosstalk necessary for stromal growth and vascularization. Using single-cell gene expression analysis in combination with a parabiosis model, eKO is found to impair the recruitment of a specific population of non-inflammatory circulating cells defined by genes regulating cell survival and neovascularization. These findings indicate an essential role of endothelial CXCL12 expression during the adult neovascular response in tissue injury and tumor progression, paving the way for future therapeutic interventions.

overall_design: Wild Type and endothelial CXCL12 KO (eKO) recipient mice were parabiosed to GFP positive donor mice and cross-circulation was confirmed. Excisional wounds were created on the dorsum of eKO recipient mice. To better characterize the progenitor cells differentially recruited to eKO and control recipient mice, microfluidic technology was applied to perform a massively parallel single cell transcriptional analysis (SCA)

first: Zeshaan

last: Maan

first: Janos

last: Barrera


title: Effect of 1-MCP and ozone post-harvest treatments on the transcriptional profiling of Granny Smith apple peel (Malus x domestica Borkh) after cold storage.

city: Beaucouzé

first: Mathilde

last: ORSEL

address: 42, rue Georges Morel

institute: IRHS

summary: Granny Smith apples (Malus x domestica Borkh) grown in commercial orchards were harvested at physiological mature stage and maintained 6 months in cold storage with or without 1-MCP post-harvest treatment, and with or without enriched ozone atmosphere.

overall_design: The experimental design includs 8 samples in 4 comparisons with respectively 1-MCP, O3, 1-MCP+O3 treated fruits versus control fruits, and 1-MCP+O3 treated fruits versus O3 treated fruits, all after 6 months of cold storage. Each comparisons included two sampling repetitions with dye swich for each treatment or control fruits. Each sample included peel from 7 fruits.

first: Evangelos

last: Karagiannis

first: Maryline

last: Cournol

first: Sandrine

last: Balzergue

first: Muriel

last: Bahut

first: Sandra

last: Pelletier

last: Orsel

first: Athanassios

last: Molassiotis


title: Gene expression profiling of mouse osteotropic lung cancer cells

city: Tainan

first: Kuan-Chung

last: Hsiao

address: 367 shengli road

country: Taiwan

institute: NHRI

summary: Analysis of gene expression profiling in osteotropic Lewis Lung carcinoma cells. The osteotropic lung cancer cell sublines were established throuth in vivo selection. The gene expression profiling of parental and osteotropic sublines was identified through microarray analysis.

overall_design: Total RNA was extracted with QIAGEN Rneasy mini kit and the cDNA was synthesized with SuperScript™ III First-Strand Synthesis SuperMix kit

first: Ko-Jiunn


title: Protein arginine methylation in Trypanosomes

city: Buffalo

first: Laurie

last: Read

state: NY

address: 955 Main St

department: Microbiology and Immunology

institute: Jacobs School of Medicine and Biomedical Sciences

summary: We report on mRNA expression changes in Trypanosoma brucei with Zinc finger protein ZFP3 variants R68/71F, R68/71K, and an RNAi knockdown. Abundance of mRNA transcripts was determined with short read RNA-Seq after variant expression or RNAi knockdown induction with doxycycline. Differentially expressed transcripts were identified across all conditions.

overall_design: Doxycycline inducible case-control design across 4 conditions (WT, R68/71F, R68/71K, RNAi), 2 replicates each.

first: Daniel

last: McSkimming


title: Small RNA expression analysis in histone replacement-completed sperm

first: Keisuke

last: Yoshida

summary: Increasing evidence indicates that paternal dietary conditions influence the metabolic disorders of offspring. Previous studies suggested the involvement of epigenetic regulation for such phenomena, but the mechanism remains elusive. To reveal the molecular function of  stress-dependent epigenetic regulator ATF7 in paternal inheritance of dietry effect on offpring phenotype, we analyzed ATF7-binding profiles in testicular germ cells by ChIP-seq, DNA methylation profiles in sperm by TGBS, small RNA expression profiles in HRCS by RNA-seq,and whole expression profiles in offspring liver by expression array analysis, using wild-type and ATF7 heterozygous mutant mice fed with control diet or low-protein diet.

overall_design: Quantification of small RNA expression in histone replacement-completed sperm (HRCS) collected from four groups of mice; WT_CD, WT_LPD, ATF7+/-_CD and ATF7+/-_LPD.

first: Muratani

last: Masafumi

first: Shin-ichiro

last: Fujita

first: Maekawa

last: Toshio

first: Shunsuke

last: Ishii


title: The unstable lncRNA OLE negatively regulates its sense-overlapping neighbor UNE15 and osmotic tolerance of Arabidopsis

city: Beijing

first: Jingrui

last: Li

state: Beijing

address: Medicine Building

institute: Tsinghua University

summary: To explore the PRC2-associated RNA in Arabidopsis on a genome-wide scale, we designed a high-throughput sequencing followed by PRC2 RNA-IP. We used the transgenic plants to purify the Myc-tagged CLF protein, the homologs of EZH2 (the methyltransferase of PRC2 complex) in mammal.

overall_design: The CLF-RNA complex was co-immunoprecipitated from the 3-week-old plants. The RNAs were de-crosslinked from CLF and purified by TRIzol reagent. Then, RNA-seq libraries were constructed and sequenced by using Illumina platforms.

first: Bi

last: Lian


title: Genome-wide mapping of ATF7 in total testicular germ cells

overall_design: Identification of ATF7 binding sites in total testicular germ cells (TGCs) collected from four groups of mice; WT_CD, WT_LPD, ATF7+/-_CD and ATF7+/-_LPD.


title: Effect of a single dose and chronic exposure to celecoxib or rofecoxib on the transcriptome of mouse aorta

city: Philadelphia

first: Gregory

middle: Robert

last: Grant

state: PA

address: 3400 Civic Center Blvd.

department: Genetics

institute: University of Pennsylvania

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


title: Celecoxib, Rofecoxib Gavage Treated Mice, Aorta RNA-Seq

overall_design: RNA-Seq. A total of 15 samples, mouse aorta. Mice were treated with 100 uL of celecoxib (30 mg/Kg), rofecoxib (10 mg/Kg), or vehicle (PEG-400) by gavage and were sacrified 6hrs later. Five biological replicates for each of the three conditions.

first: Emanuela

last: Ricciotti

first: Dimitra

last: Sarantopoulou

first: Eun-Ji

last: Kim

first: Tilo

last: Grosser

first: Garret

last: FitzGerald


title: Celecoxib, Rofecoxib Chronically Treated Mice, Aorta RNA-Seq

overall_design: RNA-Seq 24 samples, mouse aorta. Treated with Celecoxib (100 mg/kg/day), Rofecoxib (50 mg/kg/day), or normal chow for three weeks. Eight biological replicates for each of the three conditions.


title: Comparison of transcriptome profiles between  bulls and steers in the longissimus dorsi muscle of Korean cattle

city: Seoul-si

first: Sang Weon

state: Seoul-si

address: 1, Gwanak-ro, Gwanak-gu, Seoul-si

department: College of Agriculture and Life Science

institute: Seoul National University

summary:
Purpose: The goals of this study are to determine effects of castration on gene expression in longissimus dorsi muscle by comparing transcriptome profiles and to search candidate genes related with beef quality like flavor, tenderness, juiciness and fat deposition
Methods: longissimus dorsi muscle mRNA profiles of 3 bulls and 3 steers of Korean cattles were generated by RNA sequencing using Illumina NextSeq 500.  After quality checking, Tophat2 software was used for read mapping, and EdgeR was used to identify differentially expressed genes (DEGs) between bulls and steers. Gene ontology pathway analysis on DEGs was conducted  with DAVID tool for categorization of DEGs.
Results: Using an optimized data analysis workflow, we mapped about 58 million sequence reads per sample to the bovine genome (build UMD3.1) and identified 18,027 expressed genes in the longissimus dorsi muscle of bulls and steers with TopHat2 workflow. RNA-seq data confirmed 1,146 differentially expressed genes (adjusted p-value, FDR <0.05).
Conclusions: We comparatively analyzed the transcriptome profile from longissimus dorsi muscle of bulls and steers of Korean cattles using NGS and identified DEGs between bulls and steers. The functional annotation analysis of DEGs found that transcriptome profile difference in longissimus dorsi muscle by castration.

overall_design: longissimus dorsi muscle mRNA profiles of bulls and steers were generated by RNA sequencing using Illumina NextSeq 500.

first: Myunggi

last: Baik


title: Genome-wide maps of chromatin state in liver cells.

status: Public on Mar 08 2020

city: Wuhan

first: Shu

state: Hubei

address: Donghu Road 185

department: Department of Immunology

institute: liver

summary: We report the application of single-molecule-based sequencing technology for high-throughput profiling of histone modifications in mammalian cells. By obtaining over four billion bases of sequence from chromatin immunoprecipitated DNA, we generated genome-wide chromatin-state maps of mouse liver cells. We find that lysine 4 trimethylation effectively discriminates genes that are expressed, poised for expression, or stably repressed, and therefore reflect cell state and lineage potential. Lysine 9 and 27 trimethylation marks primary coding and non-coding transcripts, have no differents in gene annotation. Trimethylation of lysine 4 is detected has different expresssion at mir124 site front of lnc-RNA(10835)Far. Finally, we show that chromatin state can be read in an allele-specific manner by using single nucleotide polymorphisms. This study provides a framework for the application of comprehensive chromatin profiling towards characterization of diverse mammalian cell populations.

overall_design: Examination of 3 different histone modifications in C57 and ficolinA ko mouse liver cells .

first: Shanbo

last: Tang

first: Qiaoyun

last: Long

first: Chuan

last: Gao


title: Microglial transcriptome of Maternal Immune Activation model at different developmental Stages and after microglia repopulation

status: Public on Mar 06 2020

city: Boston

first: Tsuneya

last: Ikezu

state: MA

address: 72 East Concord St

department: BUSM - Department of Pharmacology and Experimental Therapeutics

institute: Boston University School of Medicine

summary: To determine the transcriptomic changes underlying the MIA microglia phenotype and their reversal by PLX, we performed RNA-sequencing of magnetic CD11B beads-isolated microglia from the whole brain in Saline and MIA male and female offspring at E17, P7, P20, and P60, as well as from MG-REP male and female offspring at P60. Microglial transcriptome reveals novel MIA and repopulation modules and overlap of MIA microglial genes with ASD gene network. 14,225 microglial genes from RNA-seq data revealed distinct transcriptional signatures of immature microglia (IM module, 4681 transcripts, enriched in E17 and P7 Saline), MIA immature microglia (MIA-IM module, 2816 transcripts, enriched in E17 and P7 MIA), Juvenile microglia (JM module, 2318 transcripts, enriched in P20 Saline and MIA), Adult microglia (AM module, 3276 transcripts, enriched in P60 Saline + CTRL, P60 MIA + CTRL and P60 MIA + MG-REP), and repopulated adult microglia (REP-AM module, 1,134 transcripts, enriched in P60 Saline + MG-REP)

overall_design: CD11b+ Microglia mRNA transcriptome profiling using RNA-seq Illumina HiSeq2000 across different development periods consisting of  E17, P7, P20, and P60 from saline and MIA treated mothers. At P60, mice from saline and MIA treated mothers were treated with control or CSF1R inhibitor PLX5622 (MG-REP group)

first: Seiko

first: Maya

middle: E

last: Woodbury

first: Hana

last: Yeh

first: Jean Christophe

last: Delpech


title: Stimulation of LTβR on human fibroblasts

city: La Jolla

first: Richard

last: Virgen-Slane

address: 10901 North Torrey Pines Rd

department: Infectious and Inflammatory Diseases Center

institute: Sanford Burnham Prebys Medical Discovery Institute

summary: LTβR signaling is crucial for immune development, homeostasis, and inflammation. To identify new factors that influence the quality of LTβR function, we combined transcriptomics with WGCNA.

overall_design: Normal human dermal fibroblasts were stimulated with agonistic goat anti-human LTBR antibody for 0, 2, 6, or 20 hours.

first: Carl

middle: F

last: Ware


title: Differentially RNA expressions of brain metastases from lung adenocarcinoma and paired paracancerous tissue

city: Tianjin

first: chunyang

last: jiang

address: 190 Jieyuan Road, Hongqiao District, Tianjin

institute: Tianjin Union Medical Center

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

summary:
This study aims to find the specific lncRNA molecule relating BMs from LADC in situ tumor to BM tumor tissue using gene chip technology and, combined with biological information database, through the competitive endogenous RNA (ceRNA) mechanism for microRNA (miRNA) related to specific lncRNA, to verify the possible target genes and therefore to explore the role and mechanism of specific lncRNA in BMs from LADC. By detecting the gene expression profiles of lncRNA and mRNA in cancer tissues of five cases of LADC and the paired paracancerous tissue samples, it was found that there were a large number of differentially expressed lncRNAs and mRNAs in LADC tissues and paracancerous tissues. By detecting the gene expression profiles of lncRNA and mRNA in three cases of BMs from LADC and matched paracancerous tissues, it was found that there were significant differences in the expression of lncRNAs and mRNAs between BM tumors of LADC and paracancerous tissues. These findings will provide a scientific basis for the early diagnosis and targeted therapy of BMs from LADC for application in further studies.
Differential expression of lncRNAs and mRNAs in cancer tissues of three cases of BMs from LADC and the paired paracancerous tissue samples, it was found that there were a large number of differentially expressed lncRNAs and mRNAs in BMs tissues and paracancerous tissues.

overall_design:
Three cases of BMs from LADC and the paired paracancerous tissue samples

Please note that experiments were performed technically as dual channel (eg, Cy3 and Cy5-labeled samples hybridized to the same array) but processed as single channel (Cy3 and Cy5 signals are calculated; Cy3/Cy5 ratios are not calculated).  Each raw data file is linked to the corresponding 151483C_N* sample records.

first: Chunyang

last: Jiang


title: RNA expression of lung adenocarcinoma and paired paracancerous tissue

overall_design: Refer to individual Series


title: Next-generation sequencing reveals differential responses to acute versus long-term exposures to graphene oxide in human lung BEAS-2B cells

city: Stockholm

first: Sourav

middle: Prasanna

last: Mukherjee

address: IMM, Karolinska Institutet

institute: KI

summary: Numerous studies have addressed the biological impact of graphene-based materials including graphene oxide (GO), yet few have focused on long-term effects. Here, we utilized RNA-sequencing to unearth responses of human lung cells to GO. To this end, the BEAS-2B cell line derived from normal human bronchial epithelium was subjected to repeated, low-dose exposures of GO (1 µg/mL or 5 µg/mL) for 28 days, or to the equivalent, cumulative amount of GO for 48 h. Then, samples were analyzed by using the NovaSeq™ 6000 sequencing system followed by pathway analysis and gene ontology enrichment analysis of the differentially expressed genes. Significant differences were seen between the low-dose, long-term exposures and the high-dose, short-term exposures. Hence, exposure to GO for 48 h resulted in mitochondrial dysfunction. In contrast, exposure to GO for 28 days was characterized by engagement of apoptosis pathways with downregulation of genes belonging to the inhibitor of apoptosis protein (IAP) family. Validation experiments confirmed that long-term exposure to GO affected the apoptosis threshold in lung cells, accompanied by a loss of IAPs. These studies have revealed the sensitivity of RNA-sequencing approaches and showed that acute exposure to GO is not a good predictor of the long-term effects of GO.

overall_design: The BEAS-2B cell line was originally derived from normal human bronchial epithelium obtained at autopsy, and the cells are normally maintained in serum-free, bronchial epithelial cell growth medium supplemented with specific growth factors, as detailed in the experimental section. Using these cells, we performed acute versus long-term exposures to equivalent doses of GO. Hence, we exposed BEAS-2B cells to 1 µg/mL or 5 µg/mL twice per week for up to 4 weeks (in other words, a total dose of 8 µg/mL and 40 µg/mL, respectively). In addition, we exposed the cells to the same, cumulative dose (8 µg/mL and 40 µg/mL) for 48 h. Cells were also exposed to a high dose (80 µg/mL) for 48 h, for comparison. Cells were harvested at 48 h and at 1 week and 4 weeks, respectively, and total cell RNA samples were extracted and RNA-sequencing were performed using NovaSeq™ 6000 sequencing system .

first: Bengt

last: Fadeel

first: Jun

last: Wang


title: Myosin Heavy Chain-embryonic is a crucial regulator of skeletal muscle development and differentiation.

city: Faridabad

first: Sam

last: Mathew

state: Haryana

address: NCR Biotech Science Cluster, 3rd Milestone, Faridabad-Gurgaon Expressway,

department: Developmental Genetics

country: India

institute: Regional Centre for Biotechnology

summary: mRNA from 4 different muscles from control and Myosin heavy chain-embryonic knockout neonate mice were sequenced.

overall_design:
Identify differentially expressed mRNAs upon developmental loss of Myosin heavy chain-embryonic in 4 different neonatal muscles. 6 replicates were sequenced for
control and Myosin heavy chain embryonic knockouts, each for the quadriceps, tibilalis anterior, gastrocnemius and diaphragm muscles

first: Megha

last: Agarwal

first: Akashi

last: Sharma

first: Pankaj

last: Kumar

first: Amit

first: Anushree

last: Bharadwaj

first: Masum

last: Saini

first: Gabrielle

last: Kardon


title: Hyper-activated Wnt-β-catenin signaling in the absence of sFRP1 and sFRP5 represses Mash2 expression derailing normal spongiotrophoblast differentiation

city: Xiamen

first: Wenbo

last: Deng

state: Fujian

address: Xiang'an Road

department: School of Medicine

institute: Xiamen University


title: The preceding root system drives the rhizosphere microbiome

city: Urrbrae

first: YI

last: ZHOU

address: Waite Campus

country: Australia

institute: The University of Adelaide

summary:
Background: The soil environment is responsible for sustaining most terrestrial plant life on earth, yet we know surprisingly little about the important functions carried out by diverse microbial communities in soil. Soil microbes that inhabit the channels of decaying root systems, the detritusphere, are likely to be essential for plant growth and health, as these channels are the preferred locations of new root growth. Understanding the microbial metagenome of the detritusphere and how it responds to agricultural management such as crop rotations and soil tillage will be vital for improving global food production.
Methods: The rhizosphere soils of wheat and chickpea growing under + and - decaying root were collected for metagenomics sequencing. A gene catalogue was established by de novo assembling metagenomic sequencing. Genes abundance was compared between bulk soil and rhizosphere soils under different treatments.
Conclusions: The study describes the diversity and functional capacity of a high-quality soil microbial metagenome. The results demonstrate the contribution of the microbiome from decaying root in determining the metagenome of developing root systems, which is fundamental to plant growth, since roots preferentially inhabit previous root channels. Modifications in root microbial function through soil management, can ultimately govern plant health, productivity and food security.

overall_design: Totally 18 samples were analysed, including the rhizosphere soils of wheat and chickpea growing under + and - decaying root, soils attached on the decaying root, and bulk soil with three replicates.

first: Yi

last: Zhou

first: Matthew

last: Denton


title: Tcf ChIP_Seq analysis in cultured differentiated TSC cells at the presence of DMSO or CHIRGene expression in the placenta of WT and Ctnnb1 overexpression mice

summary: Wnt signaling are essential for the maintenance and differentiation of stem/progenitor cells, including trophoblast stem cells during placental development. Hyper-activation of Wnt signaling has been shown to relate with human trophoblast diseases. However, litter is known about the impact and underlying mechanisms of excessive Wnt signaling during placental trophoblast development. In the present work, we found that Sfrp1,5 double mutant mouse exhibited disturbed trophoblast differentiation in the placental ectoplacental cone (EPC), where the precursors of secondary trophoblast giant cells (TGCs) and trophoblast cells in the spongiotrophoblast layer are located. Employing mouse models expressing a trunked β-catenin with exon 3 deletion globally and trophoblast-specifically, combining cultured trophoblast stem cells, we found that hyper-activation of canonical Wnt pathway exhausted the trophoblast precursor cells in the EPC, resulting in the overabundance of giant cells at the expense of spongiotrophoblast cells. Further examination uncovered that hyper-activation of canonical Wnt pathway disturbed trophoblast differentiation in the EPC via repressing Mash2 expression. Collectively, our findings demonstrate that appropriate canonical Wnt-β-catenin pathway is essential for EPC trophoblast differentiation during placental development. Our work also has high clinical relevance, since abnormal Wnt signaling are often associated with trophoblast-related diseases.

overall_design: To detect the direct target genes of Ctnnb1 in differentiated TSC cells, differentiated TSC cells at the presence of CHIR are collected and subjected to ChIP-Seq. After aligned to mouse mm10 by HISAT2, peaks are called by MACS2. Our results show that Ctnnb1 the key regulator for placentation by repressing Ascl2 expression as indicated by the presence of significant enrichment of TCF4 at the distal region of Aslc2. This specific enrichment was confirmed by ChIP-qPCR. Additionlly, there are also some other direct genes of Ctnnb1, indicating the essential role of Ctnnb1. This ChIP-Seq data provides fundamental information for our further physiological study of Ctnnb1.


title: Human Monocyte Heterogeneity as Revealed by High-Dimensional Mass Cytometry

first: Huy

middle: Q

last: Dinh

address: 9420 Athena Circle

department: Division of Inflammation Biology

institute: La Jolla Institute

summary: We used the high dimensionality of mass cytometry together with the FlowSOM clustering algorithm to accurately identify and define monocyte subsets in blood of healthy human subjects and those with coronary artery disease (CAD). To study the behavior and functionality of the newly defined monocyte subsets, we performed RNA sequencing, transwell migration, and efferocytosis assays. Here, we identify 8 human monocyte subsets based on their surface marker phenotype. We found that 3 of these subsets fall within the CD16+ nonclassical monocyte population and 4 subsets belong to the CD14+ classical monocytes, illustrating significant monocyte heterogeneity in humans. As nonclassical monocytes are important in modulating atherosclerosis in mice, we studied the functions of our 3 newly identified nonclassical monocytes in subjects with CAD. We found a marked expansion of a Slan+CXCR6+ nonclassical monocyte subset in CAD subjects, which was positively correlated with CAD severity. This nonclassical subset can migrate towards CXCL16 and shows an increased efferocytosis capacity, indicating it may play an atheroprotective role.

overall_design: Expression profiling by high throughput sequencing for sorted monocyte cells in human blood from healthy individuals

first: Anouk

middle: A

last: Hamers

first: Catherine

last: Hedrick


title: Gene expression in the placenta of WT and Ctnnb1 overexpression mice

overall_design:
To detect the gene profiles in WT and Ctnnb1 over expression placentas, placenta are collected and subjected to RNA-Seq. After aligned to mouse mm10 by HISAT2, RPKM value was calculated by Edger. Our results show that Ctnnb1 the key regulator for placentation by repressing Ascl2 expression. The expression of Ascl2 was further confirmed by qPCR and ChIP-qPCR. In lieu of Ctnnb1, there are also some other genes differentially expressed after Ctnnb1 overexpression, indicating the essential role of Ctnnb1. This RNA-Seq data provides fundamental information for our further physiological study of Ctnnb1.
Total RNAs in whole placenta from two independent mouse were extracted by TRIzol and purified by ploy-A before subjected to RNA-Seq by HiSeq2500. The expression of level of each gene is normalized to RPKM.


title: Differentially RNA expression of lung adenocarcinoma and paired paracancerous tissue

first: chunyang

last: jiang

summary:
This study aims to find the specific lncRNA molecule relating BMs from LADC in situ tumor to BM tumor tissue using gene chip technology and, combined with biological information database, through the competitive endogenous RNA (ceRNA) mechanism for microRNA (miRNA) related to specific lncRNA, to verify the possible target genes and therefore to explore the role and mechanism of specific lncRNA in BMs from LADC. By detecting the gene expression profiles of lncRNA and mRNA in cancer tissues of five cases of LADC and the paired paracancerous tissue samples, it was found that there were a large number of differentially expressed lncRNAs and mRNAs in LADC tissues and paracancerous tissues. By detecting the gene expression profiles of lncRNA and mRNA in three cases of BMs from LADC and matched paracancerous tissues, it was found that there were significant differences in the expression of lncRNAs and mRNAs between BM tumors of LADC and paracancerous tissues. These findings will provide a scientific basis for the early diagnosis and targeted therapy of BMs from LADC for application in further studies.
Differential expression of lncRNAs and mRNAs in cancer tissues of five cases of LADC and the paired paracancerous tissue samples, it was found that there were a large number of differentially expressed lncRNAs and mRNAs in LADC tissues and paracancerous tissues.

first: Chunyang

last: Jiang


title: Kentucky assay: Indole/ionone

city: Lexington

first: Timothy

middle: S

last: McClintock

state: Kentucky

address: 508 Medical Science Buildi

department: Physiology

institute: University of kentucky

summary:
Mice have 1,100 odorant receptors.  Nearly all are orphan receptors.  The pattern of receptor responses to odorants is the input that allows the brain to detect and discriminate odors
The Kentucky assay measures the function of each of the 1,100 odorant receptors and 14 TAARs  in vivo.

overall_design: FACS samples from S100a5-tauGFP mice (in groups of 3) simultaneously exposed to clean air (vehicle) or odorant were subjected to microarray analysis using Clariom S arrays

first: William

last: Titlow


title: Kentucky assay: Citrus accord, 100%


title: Kentucky assay: Citrus accord, 5%

overall_design: FACS samples from S100a5-tauGFP mice (in groups of 3) simultaneously exposed to clean air (vehicle) or odorant were subjected to microarray analysis using Mouse Gene 1.0 ST arrays


title: Kentucky assay: Indole


title: A Cas12a ortholog with stringent PAM recognition followed by low off-target editing rates for genome editing

first: chen

last: peng

address: College of Life Sciences, Wuhan University

department: College of Life Sciences

institute: Wuhan University

summary: Our study shows that CeCas12a nuclease is active in human cells and the stringency of PAM recognition could be an important factor shaping off-target editing in gene editing. Thus, CeCas12a provides a promising candidate with distinctive characteristics for research and therapeutic applications

sample_organism:
Homo sapiens
synthetic construct

platform_organism:
Homo sapiens
synthetic construct

overall_design: we identify a novel Cas12a nuclease CeCas12a from Coprococcus eutactus, which is a programmable nuclease with genome editing efficiencies comparable to AsCas12a and LbCas12a in human cells. Moreover, CeCas12a is revealed to be more stringent for PAM recognition in vitro and in vivo followed by very low off-target editing rates in cells. Notably, CeCas12a renders less off-target edits located at C-containing PAM at multiple sites compared to LbCas12a and AsCas12a, as assessed by targeted sequencing methods

first: Lei

last: Yin

first: Peng

last: Chen