title: Cardiac ReductomiRs: Identification of Novel Nrf2-Dependent microRNAs as Post-Transcriptional Regulators of Myocardial Gene Expression [mRNA]

first: Mark

last: Pepin

summary:
Background: Although modern advances in the treatment of heart disease have reduced mortality rates, long-term medical management is often associated with a progressive loss of function that manifests as heart failure. Nuclear factor, erythroid 2 like 2 (Nfe2l2, a.k.a. Nrf2) is a transcriptional regulator that provides the ischemic heart with transient cytoprotection following acute myocardial insult; however, its sustained activation paradoxically causes reductive stress, an emerging pathological phenomenon characterized by excessive antioxidant function and proteotoxic remodeling. Yet, the molecular mechanism by which chronic reductive stress produces heart failure remains elusive.
Methods: Cardiac-specific constitutively active Nrf2 transgenic (caNrf2-Tg) mice expressing the transgene at low (TgL) and high (TgH) levels were employed in integrative mRNA and small RNA (miRNA) sequencing.
Results and Conclusion: Here, we reveal several Nrf2 dose-responsive miRNA loci harboring putative upstream antioxidant response elements (AREs). Intriguingly, Nrf2-mediated miRNA responses were distinctly enriched for post-transcriptional regulation of cardiac-specific mRNAs. Altogether, these data reveal Nrf2 as a potent regulator of cardiac miRNA expression and provide novel candidates for future mechanistic investigation into the relationship between myocardial redox status and pathophysiology.

overall_design: RNA Sequencing analysis of left ventricle samples.

first: Rajasekaran

middle: N

last: Soorappan

middle: E

first: Justin

middle: M

last: Quiles


title: INO80 complex assembly is antagonized by PRC2.

status: Public on Apr 01 2020

city: Chapel Hill

first: Jesse

last: Raab

address: 120 Mason Farm Rd

department: Genetics

country: USA

institute: University of North Carolina Chapel Hill

type: Genome binding/occupancy profiling by high throughput sequencing

type: Expression profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Expression analysis of INO80 complex in HepG2 liver cancer cells [RNA-seq]

summary: We carried out two sets of experiments to understand how the INO80 complex affected gene expression. Expression analysis following depletion  of INO80 with two siRNAs to determine INO80 dependent transcription programs. In addition siMCRS1 or siNTG expression analysis with and without treatment with EZH2 inhibitor (EPZ-6438) was performed to determine what genes in HepG2 cells are de-repressed by EZH2 inhibition, and test the hypothesis that changes at INO80 autonomous sites would depdend on expression of other INO80 subunits (MCRS1). We found that de-repression caused by EZH2 inhbition was blunted when cells were treated with an siRNA targeting MCRS1 and that this was especially pronounced at a set of INO80 target genes.

overall_design: HepG2 cells were treated with siRNA against INO80, MCRS1, or with 1uM EPZ-6438 H3K27me3 inhibitor and subjected to RNAseq.


title: Cocaine Induces Differential Circular RNAs Expression in Striatum

city: Chengdu

first: Xiaobo

last: Cen

state: Sichuan

address: #28 Gaopeng Street, High Technological Development Zone

department: State Key Lab of Biotherapy

country: China

institute: West China Hospital of Sichuan University

summary: Circular RNA (circRNA) has recently emerged as a novel type of endogenous non-coding RNA. It plays natural microRNA sponge effect that represses the activity of corresponding miRNAs by binding with them, thus regulating gene expression. Recent studies demonstrate that circRNAs are significantly enriched in the brain and a disproportionate fraction of them is derived from host genes that code for synaptic proteins. In addition, studies have shown that microRNAs are involved in synaptic plasticity, memory formation and cocaine addiction. However, the role of circRNAs in cocaine reward is largely unknown. This study aimed to identify the expression profile of circRNAs in the striatum of mice after cocaine self-administration by using circRNA microarray analysis.

overall_design: circRNAs expression profile in the striatum from three mice after cocaine self-administration and three after saline-administration.

first: Hailei

last: Long


title: Cardiac ReductomiRs: Identification of Novel Nrf2-Dependent microRNAs as Post-Transcriptional Regulators of Myocardial Gene Expression [miRNA]

city: Stanford

middle: Emile

state: CA

address: 870 Quarry Road

department: Cardiovascular Medicine

institute: Stanford University

type: Non-coding RNA profiling by high throughput sequencing

overall_design: microRNA sequencing analysis of left ventricle samples.


title: Single cell analyses of Amyloid-beta42 and Interleukin-4 on neural stem cell plasticity IV

city: New York

first: Caghan

last: Kizil

state: NY

institute: Columbia University Irving Medical Center

summary: Neural stem cells (NSCs) constitute the reservoir for new cells and might be harnessed for stem cell-based regenerative therapies. Zebrafish has remarkable ability to regenerate its brain by inducing NSC plasticity upon Alzheimer’s pathology. We recently identified that NSCs enhance their proliferation and neurogenic outcome in an Amyloid-beta42-based (Aβ42) experimental Alzheimer’s disease model in zebrafish brain and Interleukin-4 (IL4) is a critical molecule for inducing NSC proliferation in AD conditions. However, the mechanisms by which Aβ42 and IL4 affect NSCs remained unknown. Using single cell transcriptomics, we determined distinct subtypes of NSCs and neurons in adult zebrafish brain, identified differentially expressed genes after Aβ42 and IL4 treatments, analyzed the gene ontology and pathways that are affected by Aβ42 and IL4, and investigated how cell-cell communication is altered through secreted molecules and their receptors. Our results constitute the most extensive resource in the Alzheimer’s disease model of adult zebrafish brain, are likely to provide unique insights into how Aβ42/IL4 affects NSC plasticity and yield in novel drug targets for mobilizing neural stem cells for endogenous neuro-regeneration.

overall_design: Single cell analyses of zebrafish telencephalon by 10X Genomics

first: Mehmet

middle: I

last: Cosacak


title: Gene expression profiling of control or TFEB knock out HeLa cell under Wnt3a-CM treatment condition

status: Public on Mar 31 2020

city: Seoul

first: Eek-hoon

last: Jho

address: 163 Seoulsiripdae-ro, Dongdaemoon-gu

department: Department of Life Science

country: South Korea

institute: University of Seoul

summary: HeLa cells under control or TFEB knock down condition were treated with L-CM of Wnt3a-CM and then were extracted by TRIZOL.

first: Soyoung

last: Kim


title: Genomic occupancy of the INO80 complex [ChIP-seq]

summary: We mapped 4 subunits of the INO80 complex using ChIP-seq in HepG2 and Huh7 liver cancer cell lines. We found a subclass of sites occupied by the INO80 ATPase subunit, but not by any accessory subunits that we call 'Autonomous' INO80 sites. These sites are present in both HepG2 and Huh7 cells and are characterized by repressed chromatin. Relief of reprissive histone modifications thorugh EZH2 inhbiition led to the increase in H3K27ac at INO80 targets.

overall_design:
ChIP-seq was performed for INO80 subunits in two cell lines and H3K27ac was mapped in one cell line by ChIP-seq following inhibition of H3K27me3 activity using EPZ-6438. Each experiment was performed twice, and cells were processed for ChIP as previously described (Raab et al 2015), followed by high throughput sequencing.

Please note that the YY1_HepG2 processed data was generated from the ENCODE  Accession ENCFF000PSE and ENCFF000PSD with the same pipeline as all the other data (and thus, no GEO sample records were created, and the re-processed data files are included as Series supplementary files).

The author's note: The experiments are quantitative ChIP-seq using drosophila chromatin (Active Motif #53083). We spike this chromatin into each IP, and then use the amount of drosophila chromatin in each sample for calculating the appropriate normalizations between samples. For each experiment there is a bam file corresponding to the sample aligned against hg19 (for the experiment we care about) and against dm3 (for normalizing between sample; GSM2564091-98)

middle: R

first: Terry

last: Magnuson


title: Effect of INO80 loss on open chromatin in HepG2 cells [ATAC-seq]

summary: Loss of INO80 from INO80 canonical bound regions decreases open chromatin. Loss of INO80 did not affect chromatin accessibility at autonomous sites.

overall_design: Two indepdent siRNAs targeting INO80 were used to deplete HepG2 cells followed by ATAC-seq library preparation as described in Buenrostro et al. 2013). Data were generated from three independent siRNA transductions.


title: Transcriptome analysis of bone marrow cells of Evi1-overexpressing leukemia mouse

city: Tokyo

first: Hideaki

last: Mizuno

address: HongoSanchome 7-3-1

country: Japan

institute: Unviersity of Tokyo

summary:
Puropose: To detemine transcriptome profile of Evi1-overexpressing leukemia cells by RNA sequencing
Method: RNA samples were isolated from GFP+Lin-c-kit+ mouse bone marrow cells

overall_design: mRNA profiles of GFP+ Lin- c-kit+ bone marrow cells isolated from mice transplanted with mouse bone marrow cells transduced with Evi1-GFP or GFP at 4 weeks or 6 months after transplantation were generated by deep sequencing, in duplicate, using Illumina HiSeq 2000 sequencer.

first: J

last: Koya

first: H


title: Circular RNA hsa_circ_0000848 promotes trophoblast cell migration and invasion and inhibits cell apoptosis by sponging hsa-miR-6768-5p

city: Shenzhen

first: Jiansheng

last: Xie

address: Medical genetic center, Shenzhen Maternity and Child Healthcare Hospital, Southern Medical University, Shenzhen 518000, Guangdong province, China

summary: To investigate the expression profiles of circRNAs in the placental tissues from pregnant women with  fetal growth restriction (FGR), Arraystar Human circRNA Array V2 analysis was performed. Six samples (three samples each from FGR group and healthy controls group) were used in the microarray screening. 13532 circRNAs were identified in the placental tissues from FGR and normal groups, and only 244 circRNAs were found to be more differentially expressed in the placental tissues of the FGR group than in normal placenta (fold-change > 1.5, p < 0.05). Among them, 100 and 144 circRNAs were up- and down-regulated, respectively. To verify circRNA expression in the FGR placenta, we chose hsa_circ_0007738, hsa_circ_0071271, and hsa_circ_0000848, which have the greatest expression differences between FGR and normal groups, for further analysis. Hsa_circ_0000848 expression level was significantly lower in FGR placental tissues than in the normal placenta tissues, whereas hsa_circ_0007738 and hsa_circ_0071271 expression levels did not change significantly. Further, we found that hsa_circ_0000848  promoted trophoblast cell migration and invasion, and inhibited cell apoptosis via sponging miR-6768-5p.

overall_design: Firstly, microarray analysis was performed to investigate the expression profiles of circRNAs in the placental tissues from pregnant women with  fetal growth restriction. Furthermore, we investigated the function and regulatory mechanism of hsa_circ_0000848 in HTR-8 cells, a human extravillous trophoblast (EVT) cell line, to study trophoblast functions including cell fusion, migration, and invasion.

first: Hui

last: Wang

first: Jian-sheng


title: Parallel PRC2/cPRC1 and vPRC1 pathways silence lineage-specific genes and maintain self-renewal in mouse embryonic stem cells

status: Public on Apr 02 2020

city: Vienna

first: Thomas

middle: Rainer

last: Burkard

address: Dr. Bohrgasse 7

country: Austria

institute: IMBA

summary: The transcriptional repressors Polycomb Repressive Complex 1 (PRC1) and PRC2 are required to maintain cell fate during embryonic development. PRC1 and PRC2 catalyse distinct histone modifications, establishing repressive chromatin at shared targets. Loss of PRC1, but not PRC2, from mouse embryonic stem cells (mESCs) triggers exit from pluripotency. How PRC2 and PRC1, which consists of distinct “variant PRC1” (vPRC1) and “canonical PRC1” (cPRC1) complexes, cooperate to silence genes and support mESC self-renewal is unclear. Here, we report that independent pathways composed of vPRC1 and cPRC1/PRC2 repress shared target genes. Individual loss of vPRC1, cPRC1, or PRC2 disrupts only one pathway and does not impair mESC pluripotency. However, loss of both pathways leads to mESC differentiation and activation of a subset of poised target genes co-occupied by relatively high levels of PRC1/PRC2. Thus, parallel pathways explains the differential requirements for PRC1 and PRC2, and provides robust silencing of poised, lineage-specific genes.

overall_design: 198 samples in total: 102 ChIP-Seq (80x2 replicates each , 1x3 replicates Input, 1x3 replicates Cbx7 in Eed-null), 96 RNA-Seq (32x3 replicates each)

first: Jorge

middle: A

last: Zepeda-Martinez

first: Carina

last: Pribitzer

first: Jingkui

first: Oliver

last: Bell


title: Organism-specific depletion of highly abundant RNA species from bacterial total RNA

city: Braunschweig

first: Florian

last: Engelhardt

address: Inhoffenstraße 7

department: Molecular Bacteriology

country: Germany

institute: Helmholtz Centre for Infection Research

summary: We assess the mRNA-enrichment performance of a custom-made non-mRNA depletion protocol in comparison to a commercially available mRNA-enrichment kit (Ribo-off, Vazyme). Whereas most available kits focus only on removal of rRNA, our method also targets the transfer-messenger RNA (tmRNA). tmRNA was shown to consume up to 25% of the reads in RNA-sequencing data of Pseudomonas aeruginosa.  Our established depletion technique is based on the targeting of overly abundant RNA species (16S and23S rRNA, tmRNA) in total RNA preparations of Pseudomonas aeruginosa PA14 by hybridization with organism-specific DNA probes and subsequent degradation by RNase H treatment. While introducing no systematic bias into the gene expression profile we were able to increase the mRNA read share of the total reads in the samples treated with our mRNA-enrichment protocol to 93% - 99%. Therefore, our custom-made depletion technique outcompeted the commercially available reference kit (72% mRNA share) and represents a cost-efficient mRNA-enrichment method for high-throughput next-generation sequencing.

overall_design: Total RNA preparations from Pseudomonas aeruginosa PA14 harvested in exponential or stationary growth phase were treated with a custom-made mRNA enrichment protocol or a reference depletion kit (Ribo-off, Vazyme). Experiment was performed in two biological and two technical replicates.

first: Engelhardt

last: Florian

first: Tomasch

last: Jürgen

first: Häussler

last: Susanne


title: Transcriptome analysis in siNC and siSMO medulloblastoma cells

city: Zhoukou

first: Li

last: Guoyin

address: Wenchang street

department: College of Life Science and Agronomy

institute: Zhoukou Normal University

summary:
Purpose: Medulloblastoma (MB) is the most common malignant brain tumor in children. About 30% MB isreleated to the abnormally activation of the Hedgehog signaling pathway. Smoothened(SMO) is a G protein-coupled receptor that interacts with the patched protein(PTCH) to transduce the hedgehog's proteins signal.This study analyzed the differential expression gene and obtained GO(Gene Ontology) terms and KEGG of these genes after SMO knockdown in Daoy medulloblastoma cells by transcriptome profiling (RNA-seq) .This study aims to provide the basis for subsequent study on medulloblastoma's driven genes.
Methods: Cultured Daoy medulloblastoma cells were transfected with 50nM SMO small interference RNA(siRNA) or negtive control siRNA using Lipofectamine 2000 for 48 hours, and transfection efficiency was analyzed by reverse transcription polymerase chain reaction (qRT–PCR) and Western Blot. Then the transriptome profiles of siNC and siSMO cell were sequenced with high-throughput sequencing technology.
Results: Using a standardized data analysis workflow, we mapped about 45 million sequence reads per sample. With comparative analysis of transcriptome of siNC and siSMO samples that each repeated three times, 216 differentially expressed genes (DEGs) were found, including 79 up-regulated and 137 down-regulated genes.Genes with q≤0.05 and |log2_ratio|≥1 are identified as DEGs. The ratio that sequence data mapping into reference genome is above 97%. Gene sequences were aligned to public datases such as GO,  KEGG(kyoto Encyclopedia of Genes and Genomes) and STRING (Protein-Protein Interaction Networks Functional Enrichment Analysis). 47 genes were matched to GO database. 158 genes were up regulate in 114 pathways and 306 genes were down regulate in 179 pathways in KEGG database.
Conclusions: In cancer research, cancer cell lines are important for examining and manipulating molecular and cellular process. DAOY cell line is grouped in the TP53 mutant SHH subgroup MB.Our study represents the first detailed analysis of SMO transcriptomes in Daoy medulloblastoma cells, with biologic replicates, generated by RNA-seq technology. We conclude that knockdown of SMO could participate in transcriptional regulation of many genes and lead to changes in many signaling pathways, witch provises important basis for further investigation of molecular mechanism in SHH subtype MS.

overall_design: Total mRNA profiles of siNC and siSMO in Daoy medulloblastoma cells were generated by deep sequencing, in triplicate, using Illumina platform.

first: Lintao

last: Jia

first: Shan

first: Guoyin

last: Li


title: The histone variant H2A.Z is required to establish normal patterns of H3K27 methylation in Neurospora crassa

city: Athens

first: Zachary

last: Lewis

state: GA

address: 1000 Cedar St. Biosciences Bldg

department: Microbiology

institute: University of Georgia

summary: H2A.Z regulates H3K27 methylation via eed expression

overall_design: Mycelial cultures collected at 12, 18, 24 hours. Cells lysed and subjected to RNA extraction or chromatin immunoprecipitation. 54 total samples, replicates vary by sample.

first: Abigail

middle: J

last: Courtney

first: Masayuki

last: Kamei

first: Aileen

last: Ferraro

first: Kexin

last: Gai

first: Qun

last: He

first: Shinji

last: Honda


title: Affymetrix  CytoScan array data for leukemia cell lines TK6 and WIL2-NS

city: Ibaraki

first: Fumio

last: Kasai

state: Osaka

address: Saito-Asagi 7-6-8

department: JCRB Cell Bank

institute: National Institute of Biomedical Innovation

summary: Genome reference profiles of TK6 and WIL2-NS cell lines

overall_design: Affymetrix CytoScan™ HD Arrays were performed according to the manufacturer's directions on DNA extracted from cell lines.


title: Investigating chromatin accessibility differences in stem cells and inflammatory cells in heterotopic ossification using ATAC-Seq

city: Ann Arbor

first: Bioinformatics

last: Core

state: MI

address: BRCF Bioinformatics Core, 2800 Plymouth Rd

institute: University of Michigan

summary: Mice were injured and their response in Mesenchymal Stem Cells (MSC) were studied over a period of seven days. The injury site was either non-immobilized or immobilized. The aim of the project is to study how immobilization affects stemness and inflammatory cell response after injury by investigating chromatin accessibility differences using ATAC-Seq.

overall_design:
ATAC-Seq libraries were prepared at the UM Epigenomics Core by using the Omni-ATAC protocol for cells as described in Corces et al., 2017 without modifications.
ATAC-Seq analysis was carried out on all these samples.

first: Karthik

last: Padmanabhan

first: Amanda

last: Huber

first: Benjamin

last: Levi


title: Single-cell transcriptomic analysis of adult mouse pituitary reveals sexual dimorphism and physiologic demand-induced cellular plasticity

city: Philadelphia

first: Peng

last: Hu

state: PA

address: 415 Curie Blvd, 545 CRB

institute: University of Pennsylvanian

summary: The anterior pituitary gland drives a set of highly conserved physiologic processes in mammalian species. These hormonally controlled processes are central to somatic growth, pubertal transformation, fertility, lactation, and metabolism. Current models, largely based on candidate gene based immuno-histochemical and mRNA analyses, suggest that each of the seven hormones synthesized by the pituitary is produced by a specific and exclusive cell-lineage. However, emerging evidence suggests more complex relationship between hormone specificity and cell plasticity. Here we have applied massively parallel single-cell RNA sequencing (scRNA-seq), in conjunction with complementary imaging-based single-cell analyses of mRNAs and proteins, to systematically map both cell-type diversity and functional state heterogeneity in adult male and female mouse pituitaries at single-cell resolution and in the context of major physiologic demands. These quantitative single-cell analyses reveal sex-specific cell-type composition under normal pituitary homeostasis, identify an array of cells associated with complex complements of hormone-enrichment, and undercover non-hormone producing interstitial and supporting cell-types. Interestingly, we also identified a Pou1f1-expressing cell population that is characterized by a unique multi-hormone gene expression profile. In response to two well-defined physiologic stresses, dynamic shifts in cellular diversity and transcriptome profiles were observed for major hormone producing and the putative multi-hormone cells. These studies reveal unanticipated cellular complexity and plasticity in adult pituitary, and provide a rich resource for further validating and expanding our molecular understanding of pituitary gene expression programs and hormone production.

overall_design: Single-cell RNA sequencing analysis of adult mouse pituitary under different well-defined physiologic stresses

first: Yugong

last: Ho

first: Michael

middle: T

last: Peel

first: Sixing

last: Chen

first: Pablo

middle: G

last: Camara

first: Douglas

last: Epstein

first: Hao

last: Wu

first: Stephen

last: Liebhaber


title: FMRP Control of Ribosome Translocation Promotes Chromatin Modifications and Alternative Splicing of Neuronal Genes Linked to Autism

city: Worcester

first: Sneha

last: Shah

state: Massachusetts

address: 373 Biotech II, Suite 204, Plantation Street

department: Molecular Medicine

institute: UMASS CHAN MEDICAL SCHOOL


title: Impact of ex-vivo sample handling on DNA methylation profiles in human cord blood and neonatal dried blood spots

city: Toronto

last: Matthews

state: Ontario

address: 1 King's College Circle

country: Canada

institute: University of Toronto

type: Methylation profiling by high throughput sequencing

summary: Typical conditions prior to sample storage associated with cord blood samples obtained from clinical investigations were examined using reduced representation bisulfite sequencing.

overall_design: Whole cord blood to whole cord blood comparison at 0hr, 4hr, and 24hr after collection (n=3 matched samples per time point, total n of 9). Whole cord blood to dried blood spot comparison at 0hr for whole blood and 4hr after collection (n=3 matched samples per time point, total n of 6). Dried blood spot to dried blood spot comparison at 4hr, 24hr and 7days after collection (=3 matched samples per time point, total n of 9).

first: A

last: Sasaki

first: S


title: FMRP Control of Ribosome Translocation Promotes Chromatin Modifications and Alternative Splicing of Neuronal Genes Linked to Autism (H3K36me3 ChIP-seq)

summary: Silencing of FMR1 and loss of its gene product FMRP results in Fragile X Syndrome. FMRP binds brain mRNAs and inhibits polypeptide elongation. Using ribosome profiling of the hippocampus, we find that ribosome footprint levels in Fmr1-deficient tissue mostly reflect changes in RNA abundance. Profiling over a time course of ribosome runoff in wildtype tissue reveals a wide range of ribosome translocation rates; on many mRNAs, the ribosomes are stalled. Sucrose gradient ultracentrifugation of hippocampal slices after ribosome runoff reveals that FMRP co-sediments with stalled ribosomes; and its loss results in decline of ribosome stalling on specific mRNAs. One such mRNA encodes SETD2, a lysine methyltransferase that catalyzes H3K36me3. ChIP-Seq demonstrates that loss of FMRP alters the deployment of this epigenetic mark on chromatin. H3K36me3 is associated with alternative pre-RNA processing, which we find occurs in an FMRP-dependent manner on transcripts linked to neural function and autism spectrum disorders.

overall_design: H3K36me3 ChIP-seq was performed for hippocampus tissue from P35 C57BL/6N wild-type or Fmr1 KO male mice littermates. 4 animals (one hippocampi each) per genotype were used to generate 2 biological replicates per genotype (hippocampi from 2 animals was pooled per sample)

first: Gemma

last: Molinaro

first: Botao

last: Liu

first: Ruijia

last: Wang

first: Kimberly

first: Joel

middle: D

last: Richter


title: FMRP Control of Ribosome Translocation Promotes Chromatin Modifications and Alternative Splicing of Neuronal Genes Linked to Autism (Hrt timecourse ribosome profiling)

overall_design: Ribosome profiling of Transverse hippocampal or hippocampal-cortical brain slices treated with homoharringtonine for 0,5,10,30 or 60 minutes respectively, were acutely prepared from P28-35 C57BL/6N wild-type or Fmr1 KO male mice littermates using Illumina Nextseq.

last: Huber


title: FMRP Control of Ribosome Translocation Promotes Chromatin Modifications and Alternative Splicing of Neuronal Genes Linked to Autism (Steady-state ribosome profiling)

overall_design: Ribosome profiling of Transverse hippocampal or hippocampal-cortical brain slices  were acutely prepared from P28-35 C57BL/6N wild-type or Fmr1 KO male mice littermates using Illumina Nextseq.


title: Quiescence specific β-catenin transcriptional networks in myogenic cells

city: SAN ANTONIO

first: PRETHISH

last: SREENIVAS

state: TX

address: 8403 Floyd Curl Dr

department: GCCRI

institute: UTHSCSA

summary:
Wnt/β-catenin signaling is active during cellular quiescence in muscle myoblasts. Exposure of quiescent myoblasts to Wnt3a led to deregulation of genes associated with both myogenic differentiation and proliferation. Genome-wide analysis Ctnnb1 by ChIP-chip revealed quiescence-specific enrichment on genes of multiple functional classes. The major class of genes bound by Ctnnb1were Wnt pathway genes and all occupied promoters were highly enriched for TCF DNA binding motifs. Cross-comparison of ChIP-Chip with transcriptome data revealed both transcriptional activation as well as repression in Ctnnb1 occupied genes. Inhibition of Ctnnb1-mediated transactivation using shRNA and pharmacological agents led to de-regulation of the quiescence-associated transcriptional profile. Ctnnb1 binding is associated with repression of myogenic genes and cell cycle progression factors while maintaining differential response by these genes to Wnt signaling during quiescence.
Microarray analysis of Wnt3A treated G0 myoblasts compared to untreated G0 cells

overall_design: Myogenic Cell were synchronized in G0 by resuspending them in semi-solid media and treated with purified Wnt3A for 48 hours and harvested for RNA isolation

first: Prethish

last: Sreenivas

first: Ajoy

last: Aloysius

first: Hardik

last: Gala


title: FMRP Control of Ribosome Translocation Promotes Chromatin Modifications and Alternative Splicing of Neuronal Genes Linked to Autism (Polysome RNA-seq)


title: Comparison among samples subjected to a novel in vitro tissue culture system, VISUAL-CC

city: Kobe

first: Yuki

last: Kondo

address: 1-1 Rokkodai-cho, Nada-ku

department: Graduate School of Science

institute: Kobe University

summary:
We established a novel in vitro tissue culture system (named VISUAL-CC), in which phloem companion cell (CC) differentiation can be induced with Arabidopsis thaliana cotyledons. To compare gene expression profiles between VISUAL and VISUAL-CC, we conducted GeneChip analysis using two different in vitro cultures.
CC-S means a sample that strongly induces CC differentiation. CC-M means a sample that moderately induces CC differentiation. V means a VISUAL sample, that does not induce CC differentiation at all.

overall_design: Arabidopsis cotyledons cultured with the CC-induction medium were sampled at 96 hours after the induction.

first: Yukiko

last: Sugisawa


title: Plasma miRNome analysis from retinoblastoma patients reveals the size of the circulating miRNome, a tumor signature and new normalizers candidates.

city: Mexico City

first: Diana

middle: Emilce

last: Alvarez Suarez

state: Mexico

address: Av cuautemoc 330

department: Unidad de Investigacion Medica Enf. Infecciosas

country: Mexico

institute: hospital de pediatria CMNSXXI

summary: In This work we analyzed the mirnome in plasma and corresponding extracellular vesicles (EVs) from 12 patients affected by retinoblastoma (Rb) a childhood intraocular malignant tumor, as well as from 12 healthy aged matched controls. Using hierarchical clustering with the detection score microarrays provide for each miRNA and we identified a plasma signature of 19 miRNAs in all Rb cases that were able to discriminate both cases from controls.

overall_design: mirnomic profiles from plasma and Extra cellular Vesicles from 12 retinoblastoma patients and 12 age matched healthy controles were analyzed

first: Blanca

last: Castro-Magdonel

first: Manuela

last: Orjuela

last: Alvarez-Suarez

first: Javier

last: Camacho

first: Lourdes

last: Cabrera-Muñoz

first: Stanislaw

last: Sadowinski-Pine

first: Noé

last: Durán-Figueroa

first: María

last: de Jesús Orozco-Romero

first: Adriana

last: Hernández-Angeles

first: Daphne

last: García-Vega

first: Yolanda

last: Vázquez

first: M

middle: V

last: Ponce-Castañeda


title: characterization of organoid culture

city: Kamakura

first: Satoshi

state: Kanagawa

address: 10-1 tebiro 6-chome

institute: Toray Industries,Inc.

summary: Squamocolumnar junction (SCJ) of the uterine cervix is a target of human papilloma virus (HPV) infection and thereby a putative cell-of-origin for uterine cervical cancer. However at present, in vitro models that accurately phenocopy its homeostasis is lacking. In this study, we aimed at establishing organoids of SCJ cells and identifying its characteristics. Samples were collected from the uterine cervix of 4 cases who underwent hysterectomy at our department, and processed to initiate organoid culture. Organoids were obtained from 3 samples among them, and they were analyzed both histologically and by transcriptome analysis.

overall_design:
In this study, expression profiles of organoid cultures from uterine cervix were compared with those of three cell lines
Cervical tissues were obtained from patients who underwent hysterectomy without any malignant findings on their uterus. In 3 cases, these tissues were propagated and maintained by organoid culture. Total RNA samples were extracted from these passaged samples. In comparison, RNA samples were isolated from 3 cell lines, Ect1/E6E7, End1/E6E7 and Normal immortal human keratinocytes (NIKS), which were obtained from ATCC and cultured as previously described. All of these RNA samples were subjected to TORAY 3D-gene analysis using the 3D-Gene Human Oligo chip 25K.

first: Akira

last: Kawata

first: Ayumi

last: Taguchi


title: Genowide analysis of H2Aub level upon glucose deprivation

city: Irvine

first: Jiejun

last: Shi

address: 5270 California Ave

department: School of Medicine

institute: University of California Irvine

summary: The role of H2A monoubiquitination  at K119 in regulating gene expression and cellular function upon glucose deprivation is unknown. Here, we conducted ChIP-seq for UMRC6 cells cultured with or without glucose  for 8 hours using primary antibody against H2Aub. Genes with deregulated H2Aub level under glucose starvation condition were particular of interest.

overall_design: ChIP-seq of H2AK119ub was applied in UMC6 cells

first: Yilei

last: Zhang

first: Boyi

last: Gan


title: Transcriptional response of Bacillus anthracis to targocil and role of EdsRS in regulating this response

city: Nashville

first: Clare

last: Laut

state: TN

address: 1161 21st Avenue South  Medical Center North  RM# A5104

institute: Vanderbilt University

summary: Bacillus anthracis is a spore-forming bacterium that causes devastating infections and has been used as a bioterror agent. This pathogen can survive hostile environments through the signaling activity of two-component systems, which couple environmental sensing with transcriptional activation to initiate a coordinated response to stress. In this work, we describe the identification of a two-component system, EdsRS, which mediates the B. anthracis response to the antimicrobial compound targocil. Targocil is a cell envelope-targeting compound that is toxic to B. anthracis at high concentrations. Exposure to targocil causes damage to the cellular barrier and activates EdsRS to induce expression of a previously uncharacterized cardiolipin synthase, which we have named ClsT. Both EdsRS and ClsT are required for protection against targocil-dependent damage. Induction of clsT by EdsRS during targocil treatment results in an increase in cardiolipin levels, which protects B. anthracis from envelope damage. Together, these results reveal a two-component system signaling response to an envelope-targeting antimicrobial induces production of a phospholipid associated with stabilization of the membrane. Cardiolipin is then used to repair envelope damage and promote B. anthracis viability.

overall_design: Transcriptional profiling of B. anthracis strains with genetic deletions of edsRS in the presence and absence of targocil

middle: L

first: Eric

middle: P

last: Skaar


title: Expression data of CD44 variant-positive and -negative cells derived from gastric cancer JSC153 cells

city: Tokyo

first: Tetsuo

last: Mashima

address: Koto-ku, Ariake 3-8-31

department: Cancer Chemotherapy Center

institute: Japanese Foundation for Cancer Research

summary: Cancer stem cells are subpopulation of cancer cells with highly tumorigenic and drug-resistant potential and are believed to contribute to the early phases of drug resistance. In gastric cancer, a population of cancer cells expressing splicing variants of a cell surface transmembrane glycoprotein, CD44, (CD44v), particularly CD44v9 containing variant exons 8–10, was shown to possess cancer stem cell properties. We sorted CD44v9-positive and -negative cells from patient-derived gastric cancer JSC15-3 cells and examined gene expression profile of the cells (JSC153CD44v9Plus, JSC153CD44v9Minus).

overall_design: We established patient-derived gastric cancer JSC15-3 cells, sorted CD44v9-positive and -negative cells by flow cytometry, and then obtained gene expression data (JSC153CD44v9Plus, JSC153CD44v9Minus).

first: Risa

last: Iwasaki

first: Naomi

first: Ryuhei

last: Kawakami

first: Koshi

last: Kumagai

first: Hiroyuki

last: Seimiya


title: Expression data from liver of Balb/c and Balb/cBy mice

city: ChengDu

first: Yulong

last: Chen

address: No.1,Keyuan Fourth Road

institute: Molecular medicine researh center

summary:
Free fatty acid β oxidation and akt signal pathway processes were up-regulated in liver of Balb/cBy mice after 12 week HFD-fed, which can conrtibute to up-regulate free fatty acid β oxidation and improved insulin signal transduction
We used microarrays to detail the global genes expression underlying free fatty acid β oxidation, unfolded protein response and akt signal pathway, and then identified up-regulated and down-regulated genes during there processes.

overall_design: Eight week-old Balb/c and Balb/cBy mice were housed in conventional animal facility with 12 week HFD-fed. Total RNA extraction from liver of Balb/c and Balb/cBy mice, and then hybridization on Affymetrix microarray.

first: Zhiguang

last: Su


title: RNA Sequencing Analysis of human glioblastoma derived cells and xenograft derived primary cells

city: New York

first: Daochun

last: Sun

state: New York

department: Cancer Biology and Genetics

institute: Memorial Sloan Kettering Cancer Center

summary: RNA sequencing was performed on cultured human glioblastoma cells from patient directly or from the patient derived xenografts

first: Z

last: Wang

first: D

first: L

middle: F

last: Parada


title: JunB plays a crucial role in the development of regulatory T cells by regulating interleukin-2 signaling

first: Takaharu

last: Katagiri

address: 5-21-16 Omori-Nishi,Ota-ku

department: Biochemistry

institute: Toho University School of Medicine

summary: The AP-1 transcription factor JunB is crucial for multiple biological processes, such as placental development and bone homeostasis. We recently reported that JunB plays an essential role in development of Th17 cells, and thus Junb-deficient mice are resistant to experimental autoimmune encephalomyelitis. However, the role of JunB in CD4+ T cells under other inflammatory disease conditions is unknown. Here we show that mice lacking JunB in CD4+ T cells (Junbfl/flCd4-Cre mice) were more susceptible to dextran sulfate sodium (DSS)-induced colitis, a disease model induced by innate immune cells. While the Th17-associated genes Il17a and Il22 are shown to be protective against DSS-induced colitis, their expression was not impaired in the colon of Junbfl/flCd4-Cre mice. In addition to the defect in Th17 development, the colon of Junbfl/flCd4-Cre mice exhibited reduction in regulatory T (Treg) cells. Junb-deficient CD4+ T cells needed high concentration of IL-2 for differentiating into Treg cells in vitro because of their hyporesponsiveness to IL-2. Mechanistically, JunB directly up-regulated expression of CD25, the α−chain of high affinity IL-2 receptor, thereby increasing a sensitivity to IL-2 under Treg-inducing conditions. We uncover a crucial role for JunB in development of Treg cells and defense against an epithelial cell damage-induced colitis.

overall_design: To further characterize the exacerbation of DSS-induced colitis in Junbfl/flCd4-Cre mice, we performed genome-wide transcriptome analysis using total RNA prepared from the colon after DSS administration.

first: Soh

last: Yamazaki

first: Hiroyasu

last: Nakano


title: Specialized cell state and spatial compartments within the germinal center dark zone

city: Chicago

first: Mark

last: Maienschein-Cline

state: IL

address: 900 S Ashland Ave, Rm 1058, M/C 937

department: Research Resources Center

institute: University of Illinois at Chicago

summary: Within germinal centers (GCs), complex and highly orchestrated molecular programs must balance proliferation, somatic hypermutation (SHM), class switch recombination (CSR) and selection to both provide effective humoral immunity and to protect against genomic instability and neoplastic transformation. In contrast to this complexity, GC B cells are canonically divided into two principal populations, dark zone (DZ) and light zone (LZ) cells. We now demonstrate that following selection in the LZ, B cells migrate to microniches within the canonical DZ that are sites of ongoing cell division. These proliferating DZ (DZp) cells then transit into the larger DZ to become differentiating DZ (DZd) cells before re-entering the LZ. Multidimensional analysis revealed distinct molecular programs in each population commensurate with observed compartmentization of non-compatable functions. These data provide a new three cell zone model that both orders critical GC functions and reveals essential molecular programs of humoral adaptive immunity.

overall_design: 32 samples from mouse: 10 ATAC-Seq samples; 9 ChIP-Seq (ChIP-Tagmentation-Sequencing [ChIP-Tag-Seq]) samples, including GCB cell input; 10 bulk RNA-Seq samples; and 3 Drop-Seq captures for single cell RNA-Seq.

first: Domenick

last: Kennedy

first: Michael

middle: K

last: Okoreeh

first: Junting

last: Ai

first: Margaret

last: Veselits

first: Kaitlin

middle: C

last: McLean

first: Yogesh

last: Dhugana

first: Hong

first: Junmin

last: Peng

first: Hongbo

last: Chi

first: Malay

last: Mandal

first: Marcus

last: Clark


title: The hippocampus in sham or 5/6Nx mice

city: fukuoka

first: naoya

last: matsunaga

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

institute: kyushu university

summary: The gene expression in hippocampus in  sham or 5/6Nx mice was measured.

overall_design: Differential gene expression  between sham mice and 5/6Nx mice was measured on the hippocampus at 8 weeks after operation.

first: Naoya

last: Matsunaga

first: Atsushi

last: Doi

first: Kaori

last: Yasuda


title: Semen sampling as a non-invasive surrogate for prostate health screening

city: Burley-in-Wharfedale

first: David

middle: Edwin

last: Iles

state: West Yorkshire

address: 50 Hall Drive

country: United Kingdom

institute: Omics Ltd.

summary:
We looked for the presence of prostatic cells and RNAs (cellular and acellular) of prostatic origin in the ejaculate semen from fertile and sterilized men and from men with prostate cancer, to ascertain the suitability  of ejaculate semen for studying and monitoring prostate health.
Methods. For prostatic cells, semen from fertile and sterile men and men with prostate cancer were subjected to density gradient centrifugation on a 60% cushion of Suprasperm™ and fractions containing somatic cells were washed and cytospun onto coated slides prior to fixation and immunocytochemistry with antibodies recognizing prostatic markers. Small RNAs were isolated from liquefied semen clarified of all cellular and other insoluble material by high-speed ultra-centrifugation. Sequencing libraries were prepared from fractions isolated by PAGE, corresponding to small non-coding (snc) RNAs in the 18-23 nt and 30-35 nt size ranges. Libraries were interrogated by next generation sequencing and analysed to generate lists of differentially expressed RNAs associated with cancer and sterility.
Results.  Cells positive for cytokeratin 18, PSMA, NKX3.1 and CD24 were observed in most ejaculate samples by indirect immunocytochemistry as either discrete cellular entities or within clumps of cell containing material (DAPI+; antigen positive and negative) and cytoplasmic fragments (DAP–; antigen positive and negative). RNA from populations of cells enriched by differential density gradient centrifugation supported their immunocytochemical designation as prostatic cells.   Small RNAs (18 - 43 nt) from seminal plasma were highly heterogeneous although tRNAs and 5SRNAs were the dominant forms. A degree of overlap between the respective differential expression profiles of small RNAs from sterile and cancer samples, suggested a common feature, perhaps indicating an inflammatory response.
Conclusion. This study supports a wider appraisal of ejaculate semen for studying and monitoring prostate health.

overall_design: Size-fractionated RNAs isolated from liquefied semen clarified by high-speed ultra-centrifugation of all cellular and other insoluble material, were used for the preparation of libraries using a NEBNext® Multiplex Small RNA Library Prep Set for Illumina® kit. Samples (5 non-vasectomized, 5 vasectomized and 4 prostate cancer) were sequenced on an Illumina NextSeq 500 sequencer.

first: Gisela

last: Lorente

first: Panos

last: Ntostis

first: Norman

last: Maitland

first: Lourdes

last: Mengual

first: Mirela

last: Musquera

first: Asif

last: Muneer

first: Rafael

last: Oliva

last: Miller


title: Enhanced cardiac repair by human telomerase reverse transcriptase over-expression in human cardiac mesenchymal stem cells

city: Darlinghurst

first: Andrian

last: Yang

state: NSW

address: 405 Liverpool Street

country: Australia

institute: Victor Chang Cardiac Research Institute

summary: RNA-seq profiling of gene expression of human telomerase reverse transcriptase (hTERT)-expressing human cardiac mesenchymal stem cells.

overall_design: mRNA profiles of non-transduced (NT), empty vector (EV) or hTERT-transduced human cardiac mesenchymal stem cells from young, adult and diseased samples were generated by deep sequencing on Illumina HiSeq 2500 using the Illumina TruSeq Stranded mRNA sample preparation kit Set A (Illumina, CA, USA). Four different patient samples per group.

first: Thi

middle: Y

last: Le

first: Joshua

middle: W

last: Ho

first: James

last: Chong


title: Chromatin landscape of Leishmania major

city: St. Louis

first: Stephen

last: Beverley

state: MO

address: 660 S. Euclid, Campus Box 8230

department: Molecular Microbiology

institute: Washington University School of Medicine

summary: We sought to identify nuclease-hypersensitive sites and to quantify nucleosome positions in an effort to identify cis-regulatory elements in the protozoan parasite Leishmania major.  Using micrococcal nuclease digestion of chromatin (MNAse-seq), we report that few nuclease hypersensitive sites are present within the presumed regions of RNA polymerase II-mediated transcription initiation, and that similar numbers of nuclease hypersensitive sites were found in control datasets.  However, utilizing an independent approach (FAIRE), we observe that a heterogeneous population of nuclease hypersensitive sites are present in and around these regions, and that nucleosomes within these regions are susceptible to MNAse overdigestion.

overall_design: Micrococcal nuclease digestion of chromatin (MNAse-seq), formaldehyde-assisted isolation of regulatory elements (FAIRE)

middle: M

first: Britta

last: Anderson


title: Identification of a novel fungal PRC2 accessory subunit

status: Public on Mar 30 2020

city: Eugene

first: Eric

last: Selker

state: Oregon

address: 1370 Franklin Blvd.

department: Biology

institute: University of Oregon

summary: Here we utilize a forward genetics approach in Neurospora crassa to identify novel effectors of Polycomb repression. We recovered two mutant alleles of a gene (NCU04278), which we determined encodes a PRC2 accessory subunit (PAS). PAS is not essential for all H3K27 methylation, but rather its absence leads to losses of H3K27 methylation concentrated near chromosome ends.

overall_design:
ChIP-seq: We perform H3K27me2/3 ChIP-seq on biological replicates of ∆pas and ∆npf strains. We compared H3K27 methylation levels to previously published wild type data (Bicocca et al. 2018, GSE118495)
RNA-seq: We performed polyA-RNAseq on biological replicates of ∆pas and wild type strains and compared gene expression levels to previously published data sets from wild type and ∆set-7 strains (Klocko et al. 2016, GSE82222).

first: Kevin

last: McNaught

first: Elizabeth

last: Wiles

middle: U


title: A common molecular basis to the convergent evolution of the selfing syndrome in Capsella.

city: Uppsala

first: Adrien

last: Sicard

address: Almas Allé 5

department: Uppsala BioCenter

country: Sweden

institute: Swedish University of Agricultural Sciences

summary: Whether, and to what extent, phenotypic evolution follows predictable genetic paths, remains an important question in evolutionary biology. Convergent evolution of similar characters provides a unique opportunity to address this question. The transition to selfing and the associated changes in flower morphology are among the most prominent examples of repeated evolution in plants. Yet, to date no studies have directly compared the extent of similarities between convergent adaptations to selfing. In this study, we take advantage of the independent transitions to self-fertilization in the genus Capsella to test the existence of genetic and developmental constraints imposed on flower evolution in the context of the selfing syndrome. While C. rubella and C. orientalis have emerged independently, both have evolved almost identical flower characters. Not only the evolutionary outcome is identical but, in both cases, the same developmental strategies underlie the convergent reduction of flower size. This has been associated with convergent evolution of gene-expression changes. The transcriptomic changes common to both selfing lineages are enriched in genes with low-network connectivity and with organ-specific expression patterns. Comparative genetic mapping also indicates that, at least in the case of petal size evolution, these similarities are largely caused by mutations at the same loci. Together, these results suggest that the limited availability of low-pleiotropy paths predetermine closely related species to similar evolutionary outcomes.

sample_organism:
Capsella rubella
Capsella grandiflora
Capsella orientalis

overall_design: Gene expression at three developmental stages for three Capsella species.

first: Natalia

last: Woźniak

first: Christian

last: Kappel

first: Cindy

last: Marona

first: Lothar

last: Altschmied

first: Barbara

last: Neuffer


title: Custom DNA microarrays reveal diverse binding preferences of proteins and small molecules to thousands of G-quadruplexes [design 3]

status: Public on Mar 27 2020

city: Bethesda

first: Desiree

last: Tillo

state: MD

address: 41 Center Dr, Room D310

institute: NIH/NCI

summary: Single-stranded DNA (ssDNA) containing guanine repeats can form G-quadruplex (G4) structures.  While cellular proteins and small molecules can bind G4s, it has been difficult to broadly assess their sequence specificity.  Here, we use custom DNA microarrays to examine the binding specificities of proteins, small molecules, and antibodies across ~15,000 G4 structures.  Molecules used include fluorescently labeled pyridostatin (Cy5-PDS, a small molecule), BG4 (Cy5-BG4, a G4-specific antibody), and eight proteins (GST-tagged nucleolin, IGF2, CNBP, FANCJ, PIF1, BLM, DHX36, and WRN).  Cy5-PDS and Cy5-BG4 selectively bind sequences known to form G4s, confirming their formation on the microarrays.  Cy5-PDS binding decreased when G4 formation was inhibited using lithium or when ssDNA features on the microarray were made double-stranded.  Similar conditions inhibited the binding of all other molecules except for CNBP and PIF1.  We report that proteins have different G4 binding preferences suggesting unique cellular functions.  Finally, competition experiments are used to assess the binding of an unlabeled small molecule, revealing the structural features in the G4 required to achieve selectivity.  These data demonstrate that the microarray platform can be used to assess the binding preferences of molecules to G4s on a broad scale, helping to understand the properties that govern molecular recognition.

sample_organism:
Homo sapiens
Bos taurus
synthetic construct

overall_design: Binding microarray experiments were performed for G-quadruplex (G4) DNA interacting proteins (nucleolin, IGF2, CNBP), helicases (BLM, FANCJ, DHX36, PIF1, WRN), the anti-G4 antibody BG4, and the small molecules pyridostatin (PDS), TmPyP4, and DC-34.  Briefly, the binding experiments involved incubating GST-tagged proteins or Cy5-conjugated molecules (BG4, PDS) to 180K feature Agilent microarrays pre-incubated with 100mM potassium chloride (KCl) in order to determine their binding preferences to G4-forming sequences.


title: Expression data from liver of Balb/c(WT) and Balb/cBy mice(KD)

first: Yulong

last: Chen

summary:
Free fatty acid beta oxidation and Akt signal pathway process were up-regulated in liver of Balb/cBy mice after 12 week HFD-fed, which can conrtibute to up-regulate free fatty acid beta oxidation and improve insulin signal transduction
We used microarrays to detail the global  gene expression underlying free fatty acid beta oxidation, unfolded protein response and Akt signal pathway,  and then identified  up-regulated and down-regulated genes during there process.

overall_design: Eight week-old Balb/c and Balb/cBy mice were housed in conventional animal facility with 12 week HFD-fed. total RNA extraction from liver of Balb/c and Balb/cBy mice, and then hybridization on Affymetrix microarray.

first: Zhiguang

last: Su


title: Custom DNA microarrays reveal diverse binding preferences of proteins and small molecules to thousands of G-quadruplexes

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

overall_design: Refer to individual Series


title: A chondrocyte-specific Indian hedgehog enhancer activated in both skeletal development and postnatal cartilage degeneration [ChIP-seq]

first: Shinsuke

last: Ohba

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

department: Division of Clinical Biotechnology, Center for Disease Biology and Integrative Medicine

institute: The University of Tokyo

summary: Sox6-DNA interaction was profiled in the same chondrocyte population as used for our Sox9 ChIP-seq analysis (GSE69109). First, we classified Sox6 peaks into TSS-associated Class I and distally located Class II as in our previous study. Class II targets were strongly associated with genes related to skeletal tissues, whereas Class I targets were related to general cellular processes, not chondrocyte-specific activities. When we investigated the overlap of the Sox6 ChIP-seq peaks with Sox9 ChIP-seq peaks identified in our previous study, the majority of Sox9 peaks overlapped with Sox6 peaks in both Class I and Class II regions, which is in line with previous findings that Sox9 and Sox6 co-engage in gene expression for the chondrocyte program.

overall_design:
Sox6 ChIP-seq in mouse primary rib chondrocytes.
Sox9 ChIP-seq in mouse primary rib chondrocytes:  Third-party re-analysis of Samples GSM1692996 and GSM1693004.  Peak calling of Sox9 was performed as for Sox6.  Processed data file Cho_Sox9.2s.FDR1.peaks.bed.gz linked below as a supplementary file.

first: A

last: Yamakawa

first: H

last: Hojo

first: S


title: Gene Expression Analysis of Nestin-creERT2, or NG2-creERTM driven P53f/f; Nf1f/+; Ptenf/+ mouse GBM

first: Daochun

last: Sun

summary: We have developed spontaneous genetically engineered GBM mouse models from two distinct cells of origin: subventricular zone neural stem cells (SVZ; Nestin-creERT2) and oligodendrocyte lineage progenitor cells (OPC; NG2-creERTM). These tumors are biologically separable and are reflective of their lineage of origin.

overall_design: Seven Nestin-creERT2 driven (Type 1) and Seven NG2-creERTM driven (Type 2) primary mouse tumors with consistant histology features were characterized by mRNA profiling in two different batches.

first: Z

last: Wang

first: D

first: L

last: Parada


title: Comparative transcriptomic analysis of global gene expression mediated by (p)ppGpp reveals common regulatory networks in Pseudomonas syringae

status: Public on Mar 23 2020

city: Urbana

first: Frank

last: Zhao

address: 1201 W. Gregory Dr.

department: Crop Sciences

institute: University of Illinois

summary: This RNA-seq analysis examined the global effect of (p)ppGpp in P. syringae under the T3SS-inducing condition. The (p)ppGpp mutant showed differential expression of more than 30% genes in the genome, which include significant down-regulation of T3SS genes and those required for cell growth and viability.

overall_design: Differential gene expression of the (p)ppGpp mutants versus wild type grown in the T3SS-inducing condition for 3 hours

first: Jun

last: Liu

first: Menghao

last: Yu

first: Youfu


title: Identification of a DC1 immuno-regulatory module that limits antitumor CD8+ T cell immunity in lung cancer lesions.

status: Public on Mar 26 2020

city: NEW YORK

first: Miriam

last: Merad

address: 1470 Madison Ave, Room 5-301

department: Oncological Sciences

institute: ICAHN SCHOOL OF MEDICINE AT MOUNT SINAI

summary: While conventional dendritic cells (DC)1 and DC2 are found in tumors, DC1 were shown to control tumor response to checkpoint blockade in preclinical models and are associated with better overall survival in cancer patients, reflecting their specialized ability to prime CD8+ T cell responses. Paradoxically, DC1 can also be found in tumors that resist checkpoint blockade, suggesting that, like many tumor infiltrating T cells, DC1 functionality may be altered in tumors.  To address this question, we performed scRNAseq analyses to characterize DC gene architecture in mouse non-small cell lung cancer (NSCLC) lesions. To understand the relationship of the resulting transcriptional signatures with antigen uptake and migration, we profiled lung DCs in CCR7-/- mice, or DCs that had taken up (i) GFP from GFP-expressing tumors that had been seeded in the lung, and (ii) fluorescent microbeads that had been applied intranasally.

overall_design: CITEseq of DCs from the lungs of wild-type tumor-naïve, tumor-bearing, or CCR7-/- mice. Bulk RNAseq of cDC1 sorted from the lungs of mice bearing GFP-expressing tumors based on GFP antigen uptake, or from the lungs of mice that were subjected to intranasal application of fluorescent microbeads and sorted based on bead uptake.

last: Maier

first: Andrew

last: Leader

first: Steven

first: Navpreet

last: Tung

first: Christie

last: Chang

first: Jessica

last: LeBerichel

first: Aleksey

last: Chudnovskiy

first: Shrisha

last: Maskey

first: Laura

last: Walker

first: John

last: Finnigan

first: Margaret

middle: E

last: Kirkling

first: Boris

last: Reizis

first: Sourav

last: Ghosh

first: Natalie

middle: R

last: D'Amore

first: Nina

last: Bhardwaj

first: Carla

last: Rothlin

first: Andrea

last: Wolf

first: Raja

last: Flores

first: Thomas

last: Marron

first: Adeeb

middle: H

last: Rahman

first: Ephraim

last: Kenigsberg

first: Brian

last: Brown


title: Macrophage's response to TNF alpha blocker etanercept and Aspergillus fumigatus infection.

status: Public on Mar 25 2020

city: Jena

first: Bastian

last: Seelbinder

address: Adolf-Reichwein-Straße 23

department: Systems Biology and Bioinformatics

institute: Hans-Knoell-Institute Jena

summary: Macrophages from 3 healthy donors were generated and stimulated with A. fumigatus germ tubes (MOI 0,5). Furthermore, macrophages were stimulated also with drug etanercept (TNF alpha blocker). After 6 hours of incubation, macrophages were harvested and RNA was extracted using Qiagene RNeasy mini kit. Extracted RNA samples were sent for RNA-seq to IMGM in Munich and RNA-seq analysis was performed at HKI in Jena.

overall_design: Examination of Macrophage‘s response to TNF alpha blocker etanercept and/or Aspergillus fumigatus infection.

first: Michael

last: Weber

first: Tamara

last: Zoran

first: Jürgen

last: Löffler

first: Jörg

last: Linde


title: The stringent response regulator (p)ppGpp mediates virulence gene expression and survival in Erwinia amylovora

first: Frank

last: Zhao

summary: This RNA-seq analysis mainly examined the global effect of stringent resonse in E. amylovora under the T3SS-inducing condition. The (p)ppGpp mutant showed differential expression of more than 30% genes in the genome, which include significant down-regulation of T3SS genes and gene related to motiliey. On the other hand, genes involved in  amino acid biosynthesis, translation, SOS response, DNA replication, chromosome segregation, as well as nucleotide metabolism, fatty acid and lipid biosynthesis were significantly up-regulated in (p)ppGpp mutant. These findings sugested that (p)ppGpp mediate the balance between virulence and survival.

overall_design: Differential gene expression of the (p)ppGpp mutants versus wild type grown in the T3SS-inducing condition for 3 hours; Differential gene expression of WT under 6 hours versus 3 hours T3SS-inducing condition.

first: Ho-Wen

last: Yang

first: Menghao

last: Yu

first: Jae

last: Lee

first: Youfu


title: Elucidating the role of glycogen debranching enzyme AGL in bladder carcinogenesis by generation and characterization of knockout mice

city: Los Angeles

first: Dan

last: Theodorescu

state: CA

address: 8700 Beverly Blvd., Davis Building, Rm 3057

institute: Cedars Sinai Medical Center

summary: Amylo-alpha-1-6-glucosidase-4-alpha-glucanotransferase (AGL) is an enzyme primarily responsible for glycogen debranching. Inactivating germline mutations lead to glycogen storage disease III (GSDIII). AGL was found to be a tumor suppressor in xenograft models of bladder cancer (BC) and low levels of expression in BC were associated with poor patient prognosis. However, the impact of AGL levels in normal tissues on susceptibility to carcinogenesis is unknown. We address this gap by developing a full body/germline AGL knock-out (AGL-FBKO) that recapitulates biochemical and histological features of GSDIII. AGL-FBKO mice exposed to N-Butyl-N-(4-hydroxybutyl) nitrosamine (BBN) had higher BC incidence at several time points following exposure, compared to wild type littermates (AGL-FBWT). To determine if this increased BC prevalence was due to decreased expression of AGL in the urothelium, we derived a urothelium specific conditional AGL knock-out (AGL-cKO) mouse driven by a Uroplakin II-Cre/loxP system. BBN experiments with these mice revealed AGL-cKO had higher BC incidence than mice without AGL knock-out (AGL-cWT). RNA-sequencing revealed that tumors from AGL-FBKO had 19 differentially expressed genes compared to AGL-FBWT mice. An “AGL Loss” gene signature was developed and found to successfully stratify normal and tumor samples in two BC patient datasets. These results support the role of AGL as a tumor suppressor. Our work suggests that evaluating AGL expression levels, or AGL KO gene signature scores, in normal urothelium may serve as a predictor for increased risk of BC development in individuals with carcinogenic exposures, such as smoking.

overall_design: RNA-seq of BBN induced tumors in AGL-FBWT and AGL-FBKO mice

first: Joseph

last: Sottnik


title: RNAseq profiling of skin samples from wild type and RIPK1E-KO mice

city: Cologne

first: Manolis

last: Pasparakis

state: NRW

address: Joseph Stelzmann Strasse, 26

department: Institute for Genetics

institute: University of Cologne

summary: Keratinocyte-specific RIPK1 deficiency causes skin inflammation due to ZBP1-induced necroptosis. RNA-Seq analysis of the skin from wild type and RIK1E-KO mice was performed to examine how RIPK1 deficiency affects the expression of mRNAs as well as endogenous retroelement-derived transcripts.

overall_design: RNAseq was performed in RNA from either epidermal or total skin samples from wildtype and RIK1E-KO mice that were untreated or treated with reverse transcriptase inhibitors.

first: Snehlata

last: Kumari

first: Huipeng

last: Jiao

first: Laurens

last: Wachsmuth

first: George

last: Kassiotis


title: Positive auto-feedback regulation of Ptf1a transcription generates the levels of PTF1A required to specify dorsal spinal cord inhibitory neurons

city: Dallas

first: Jane

last: Johnson

address: 5323 Harry Hines Blvd

department: Neuroscience

institute: UT Southwestern Medical Center

summary: Peripheral somatosensory input is modulated in the dorsal spinal cord by a network of excitatory and inhibitory interneurons. PTF1A is a transcription factor essential in dorsal neural progenitors for specification of these inhibitory neurons. Thus, mechanisms regulating Ptf1a expression are key for generating neuronal circuits underlying somatosensory behaviors. Mutations targeted to distinct cis-regulatory elements for Ptf1a in mice, tested the in vivo contribution of each element individually and in combination. Mutations in an auto-regulatory enhancer resulted in reduced levels of PTF1A, and reduced numbers of specific dorsal spinal cord inhibitory neurons, particularly those expressing Pdyn and Gal.

overall_design: Nuclei were isolated from postnatal day 25 cervical spinal cords from mice (MUT) heterozygous for a null allele of Ptf1a (Ptf1aCre) and heterozygous for a Ptf1a enhancer mutation AR-DNT1 (Ptf1aCre/AR-DNT1;Ai14).  Controls were  Ptf1aCRE/+;Ai14.  The Ai14 is a tdTomato reporter of Cre activity. 2 animals per genotype were combined for each snRNA-seq sample. Note: the tdTomato transcripts from Ai14 were not detected.


title: Mammalian mediator structure and conformation regulation by the Tail module

city: bethesda

first: Seolkyoung

last: Jung

address: 10 Center Dr

department: NIAMS

institute: NIH

summary: The Mediator complex plays an essential and multi-faceted role in regulation of RNA  polymerase II transcription in all eukaryotes. Structural analysis of yeast Mediator  provided an understanding of the conserved core of the complex and its interaction  with RNA polymerase II, but failed to reveal how Mediator might enable a response to  interaction with transcription factors (TFs). Here we present an atomic model of  mammalian (Mus musculus) Mediator, derived from a 4.0 Å resolution cryo-EM map of  the complex. The mammalian Mediator structure reveals how the previously  unresolved Tail module, which includes a number of metazoan specific subunits,  modulates Mediator conformation and interactions. The structure also suggests how a  bi-partite organization of TF-interacting subunits can be exploited to enable a Mediator  mechanism that combines conformational control of molecular interactions and  enhancement of transcription through phase separation and enhancer-specific  recruitment

overall_design: ChIP-seq in mouse CH12 cell line

first: Haiyan

first: Natalie

last: Young

first: Jens

last: Kalchschmidt

first: Jenna

last: Lieberman

first: Supriya

last: Vartak

first: Laila

last: Khattabi

first: Rafael

last: Casellas

first: Francisco

middle: J

last: Asturias


title: Custom DNA microarrays reveal diverse binding preferences of proteins and small molecules to thousands of G-quadruplexes [design 2]

first: Desiree

last: Tillo

overall_design: Binding microarray experiments were performed for G-quadruplex (G4) DNA interacting proteins (nucleolin, IGF2, CNBP) and the small molecule pyridostatin (PDS).  Briefly, the binding experiments involved incubating GST-tagged proteins or Cy5-conjugated molecules (PDS) to 180K Agilent microarrays pre-incubated with 100mM potassium chloride (KCl) in order to determine their binding preferences to G4-forming sequences.


title: Custom DNA microarrays reveal diverse binding preferences of proteins and small molecules to thousands of G-quadruplexes [design 1]

overall_design: Binding microarray experiments were performed for G-quadruplex (G4) DNA interacting proteins and helicases (nucleolin, IGF2, CNBP,BLM,FANCJ), the anti-G4 antibody BG4, and the small molecule pyridostatin (PDS).  Briefly, the binding experiments involved incubating GST-tagged proteins or Cy5-conjugated molecules (BG4, PDS) to 180K feature Agilent microarrays pre-incubated with 100mM potassium chloride (KCl) in order to determine their binding preferences to G4-forming sequences.


title: Protein ISGylation regulated gene expression in mouse mammary epithelial cells

city: La Jolla

first: Junbao

last: Fan

address: 3855, Health Sciences Drive

department: Moores Cancer Center

institute: University of California, San Diego

summary:
Purpose: The goals of this study are to use RNA-seq to identify genes whose expression are regulated by protein ISGylation in a genome-wide scale
Methods: mRNA profiles of PyVmT/Uba7 KO + Control and PyVmT/Uba7 KO+UBE1L mammary epithelial cells (MECs) were generated by deep-sequecing in duplicates, using Illumina HiSeq4000.
Results: Using an optimized data analysis workflow, we mapped about 25 million sequence reads per sample to the mouse genome (M16 genome annotation). 259 genes are identified as differentially expressed transcripts from RNA-seq analysis of PyVmT/Uba7 KO + empty vector vs PyVmT/Uba7 KO + UBE1L MECs treated by LPS (100ng/mL) for 6 hours after IFN (1000 U/mL) priming for 24 hours.
Conclusions: protein ISGylation facilitated expression of a group genes, which are regulated by STAT1/STAT2 containing complexes.

overall_design: mRNA profiles of PyVmT/Uba7 KO + Control and PyVmT/Uba7 KO+UBE1L MECs were generated by deep sequencing in duplicates using Illumina HiSeq400

first: Dong-Er

last: Zhang

first: Jun-bao


title: Dual RNA-Seq characterization of host and pathogen gene expression in liver cells infected with Crimean-Congo Hemorrhagic Fever Virus

city: Quebec

first: Gary

last: Kobinger

state: Quebec

address: 2705 blvd Laurier

institute: Universite de Laval

summary: Crimean-Congo hemorrhagic fever virus (CCHFV) is a tick-borne virus that can cause a hemorrhagic fever in humans, with a case fatality rate of up to 50%. Cases of CCHFV have been reported in Africa, Asia, and southern Europe; and recently, due to the expanding range of its vector, autochthonous cases have been reported in Spain. Although it was discovered over 70 years ago, our understanding of the pathogenesis of this virus remains limited.   We used RNA-Seq in two human liver cell lines (HepG2 and Huh7) infected with CCHFV (strain Ib 10200), to examine kinetic changes in host expression and viral replication simultaneously at 24 and 72 hours post infection. Through this, numerous host pathways were identified that were modulated by the virus including: antiviral response and endothelial cell leakage. Notably, DDX60, a cytosolic component of the RIG-I signalling pathway and OAS2 were both shown to be dysregulated. Interestingly, the PTPRR gene was induced in Huh7 cells. This has been associated with the TLR9 signalling cascade, and polymorphisms in the TLR9 gene have been associated with poor outcomes in patients. Additionally, we whole-genome sequenced CCHFV to assess viral diversity over time, and its relationship to the host response.  As a result, we have demonstrated that through next-generation mRNA deep-sequencing it is possible to not only examine mRNA gene expression, but also to examine viral evolution. This demonstrates a proof-of-principle that specimens can be analyzed to identify both the virus, and host biomarkers that may have implications for prognosis.

overall_design: Triplicate samples of two different cell lines (HepG2 and Huh7) were infected with CCHFV or kept as control. RNA was isolated on days 1 and 3.

first: Kozak

middle: A

last: Robert

first: Fraser

middle: S

last: Russell

first: Mia

last: Biondi

first: Anna

last: Majer

first: Patrick

last: Stapleton

first: Chantal

last: Urfano

first: Giorgi

last: Babuadze

first: Kym

last: Antonation

first: Lisa

last: Fernando

first: Sarah

last: Medina

first: Stephanie

last: Booth

first: Brandon

middle: N

last: Lillie


title: Super-resolution imaging reveals disrupted higher-order heterochromatin organization at early-stage carcinogenesis on pathological tissue

status: Public on Mar 19 2020

city: Pittsburgh

last: Hainer

state: PA

address: 4249 Fifth Ave

department: Department of Biological Sciecnes

institute: University of Pittsburgh

summary: Abnormal chromatin structure is one of the hallmarks in cancer and has long been used for cancer diagnosis, but the observed aberrant chromatin structures characteristic of cancer cells is limited to microscale features, largely due to due to the diffraction-limited resolution of conventional light microscopy. Recent advances in super-resolution microscopy overcome the technical limitations of conventional light microscopy and enable the in-situ visualization of the higher-order chromatin structure down to ~30 nm. Here we present PathSTORM, a variant of stochastic optical reconstruction microscopy (STORM) optimized for super-resolution imaging of densely packed higher-order chromatin organization at different epigenomic states on pathological tissue. We then apply this tool to characterize the structural alteration of higher-order heterochromatin, enriched with H3K9me3 and satellite repeats, at various stages of carcinogenesis in mouse models and human tissue specimens. PathSTORM reveals that a significant disruption of higher-order heterochromatin structure occurs in early carcinogenesis when tissue still appears histologically normal and becomes progressively severe during neoplastic progression. The disrupted higher-order heterochromatin structure also appears to be a common feature that reflects the evolution of carcinogenesis independent of molecular pathways in multiple tumor types. Taken together, PathSTORM can serve as a powerful tool to visualize higher-order chromatin structure in the spatial context of tissue architecture on pathological tissue. Our findings provide new insights on the role of higher-order heterochromatin structure in carcinogenesis, especially at the early stage, and have the potential for improving cancer diagnosis, risk stratification and facilitating the development and evaluation of new preventive strategies.

overall_design:
To identify the specific genomic regions affected by the disrupted heterochromatin structure, using CUT&RUN, we profiled native (no crosslinking) chromatin structure of intestinal epithelial cells brushed from normal mouse intestine of wild-type and age-matched ApcMin/+mice at 5-6 weeks, which is in early carcinogenesis when tissue still appears histologically normal.
CUT&RUN is a genome-scale protein localization technique that utilizes an enzyme-tethering strategy and serves as an alternative to chromatin immunoprecipitation (ChIP) to investigate the chromatin landscape and genome-wide occupancy of DNA-bound proteins. Briefly, a recombinant protein A-micrococcal nuclease (MNase) fusion bound to a primary antibody is tethered to the genomic regions occupied by the protein of interest, and followed by MNase-mediated cleavage of DNA and release of the targeted protein-DNA complexes to solution. The released DNA fragments are extracted and used for library construction and sequencing.
We profiled the occupancy of H3K9me3 and H3K4me3, as well as a control lacking a primary antibody (but still including the proteinA-MNase to control for nonspecific fragment digestion and release) referred to as 'no antibody'.

first: Hongqiang

last: Ma

first: Hongbin

first: Wei

last: Jiang

first: Shimei

last: Zhao

first: Jianquan

last: Xu

first: Chenxi

last: Gao

first: Eun-Ryeong

last: Hahm

first: Ming

last: Sun

first: Reet

last: Pai

first: Donna

middle: B

last: Stolz

first: Shivendra

last: Singh

first: Randall

last: Brand

first: Douglas

last: Hartman

first: Jing

last: Hu

first: Yang

last: Liu


title: F508del homozygous cystic fibrosis patients and healthy controls [RNA-seq]

city: Montpellier

first: Albertina

last: DE SARIO

address: 641, av du doyen Gaston Giraud

department: PhyMedExp

country: France

institute: INSERM 1046-CNRS 9214-Univ Montpellier

summary: To identify genes relevant for cystic fibrosis pathophysiology, we profiled blood samples in CF patients and healthy controls using RNA-seq. Weighted Gene Co-expression Network Analysis of a transcriptomic dataset allowed us to identify 28 co-expressed modules that correlated with clinical traits of interest in cystic fibrosis.

overall_design: 33 cystic fibrosis patients and 16 healthy controls

last: De Sario

first: Fanny

last: Pineau

first: Davide

last: Caimmi

first: Milena

last: Magahaes

first: Enora

last: Fremy

first: Abdillah

last: Mohamed

first: Laurent

last: Mely

first: Sylvie

last: Leroy

first: Marlène

last: Murris

first: Mireille

last: Claustres

first: Raphaël

last: Chiron


title: Dnmt3a associates with promoters and enhancers to protect epidermal stem cells from cancer [MeDIP-seq]

city: Barcelona

first: Lorenzo

last: Rinaldi

state: Spain

address: Carrer Reixac Baldiri 10

department: Oncology

country: Spain

institute: IRB

summary: The de novo DNA methyltransferase Dnmt3a is mutated in human acute myeloid leukemia, and suppresses tumorigenesis in murine models of leukemia and lung cancer. Conversely, deregulation of the other de novo DNA methyltransferase, Dnmt3b, predominantly promotes tumorigenesis. However, the molecular mechanisms underlying the roles of Dnmt3a and Dnmt3b in cancer remain poorly understood. Using conditional knockout mice, here we show that Dnmt3a -- but not Dnmt3b -- strongly protects epidermal stem cells from carcinogen-induced tumor initiation, without affecting the progression of benign lesions to aggressive carcinomas. Only upon combined deletion of Dnmt3a and Dnmt3b, squamous cell carcinomas acquired a more aggressive fate and even became metastatic, indicating that Dnmt3b is tumor-suppressive, rather than pro-tumorigenic, in epidermal neoplasia. Mechanistically, Dnmt3a promotes the expression of epidermal differentiation genes by interacting with their enhancers, and inhibits the expression of lipid metabolism and cell proliferation genes by directly methylating their promoters. Altogether, we demonstrate that Dnmt3a, but not Dnmt3b, is critical for suppressing epidermal tumor initiation, while both enzymes prevent tumor progression.

overall_design: The study was performed to analyse the differentially methylated regions between skin tumors derived from mouse epidermis of wild type and Dnmt3a-deficient animals.

first: Alexandra

last: Avgustinova

first: Debayan

last: Datta

first: Guiomar

last: Solanas

first: Neus

last: Prats

first: Salvador

last: Aznar Benitah


title: Single cell ATAC-seq of cardiomyocytes from neonatal mouse hearts after injury

status: Public on Mar 18 2020

city: New York

first: Zhaoning

last: Wang

address: 701 West 168th Street Hammer 14 - 1410

department: Genetics and Development

institute: Columbia University

summary: The adult mammalian heart is incapable of regeneration following injury. In contrast, the neonatal mouse heart has a transient ability to regenerate, however the molecular mechanism that mediates this regenerative response is not fully understood. Here, by single-nucleus RNA sequencing we map the transcriptome landscape of cardiomyocytes in neonatal mouse hearts at healthy, regenerative, and remodeling conditions. We show that an immature cardiomyocyte population enters cell-cycle in response to injury. Absence of this cardiomyocyte population overtime is associated with the loss of the ability of the heart to regenerate. We show a defined injury response in these cardiomyocytes, including activation of transcription factors NFYa and NFE2L1, which play proliferative and protective roles, respectively. We further show that overexpression of these two factors in vivo promotes heart regeneration. Thus, these findings refined our understanding of cellular basis of neonatal heart regeneration and reveal dynamic transcriptome landscape of cardiomyocytes in response to injury.

overall_design: We surgically induced myocardial infarction in mouse hearts at postnatal day 1. At 3d post surgery, ventricle samples below the surgery plane were collected for nuclei extraction. Cardiomyocyte nuclei were enriched using PCM1 immunostaining and FACS sorting, and subjected to single cell ATAC-seq.

first: Miao

last: Cui

first: Wei

last: Tan

first: Eric

last: Olson


title: Investigation of heat stress response by RNA-Seq in Arabidopsis

city: Beijing

first: Linhua

last: Sun

state: Beijing

address: No.5 Yiheyuan Road Haidian District

institute: Peking University

summary: To investigate genome-wide Arabidopsis TE release, we sequenced the wild-type Col-0 transcriptome under Control, Heat and Recovery conditions

overall_design: RNA-Seq in Control, Heat, and Recovery.

first: Weiqiang

last: Qian


title: Glucocorticoid resistance in pediatric leukemia is associated with altered splicing profiles and vulnerability to spliceosome modulation

status: Public on Mar 24 2020

city: Amsterdam

first: Rocco

last: Sciarrillo

state: North Holland

address: De Boelelaan 1117

department: Hematology

country: Netherlands

institute: Amsterdam UMC

summary: The aim of the current study is to characterize the global alternative splicing profiles associated with ex vivo GC resistance in pediatric acute lymphoblastic leukemia (ALL). Specifically, we investigated differential splicing profiles in 38 primary childhood ALL samples by using RNA sequencing. Finally, we tested whether GC-resistant cell lines can be sensitized to GC treatment by using the SF3B modulator Pladienolide-B.

overall_design: RNA-sequencing of primary pediatric ALL samples which display different levels of ex-vivo glucocorticoid resistance. RNA-sequencing of leukemia cell lines treated with the spliceosome small-molecule modulator Pladienolide-B.

first: Anna

last: Wojtuszkiewicz

first: Costa

last: Bachas


title: In vivo atlas of RNA secondary structures recognized by ADARs

city: Guangzhou

first: Rui

last: Zhang

address: No. 135, Xingang Xi Road

institute: Sun Yat-sen University

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

overall_design: Refer to individual Series


title: Transcriptomic and metabolomic analyses reveal mechanisms of adaptation to salinity in which carbon and nitrogen metabolism is altered in sugar beet roots

city: Changchun

first: Lei

last: Liu

address: 4888 Shengbei Street

institute: Northeast Institute of Geography and Agroecology, CAS

summary: Here, we first systematically identified and characterized responsive mRNAs expressed in roots of sugar beet at a genome-wide scale, focusing on salt-responsive mRNAs.

overall_design: Four-week-old seedlings were treated with Hoagland solution, containing 300 mM mixed neutral-salt solution (NaCl and Na2SO4, at a 2:1 molar ratio, 300 mmol L-1 Na+) for 1 day (control and treatment designated as CK_1 and S_1) and 7 days (control and treatment designated as CK_7 and S_7). Roots from the same position of seedlings at different treatments were collected, and three biological replicates were sampled.

first: Caifeng

last: Li


title: Excessive β-catenin in excitatory neurons results in reduced social and increased repetitive behaviors and altered expression of multiple genes linked to human autism

status: Public on Mar 17 2020

city: BOSTON

first: Michele

last: Jacob

state: Massachusetts

address: 136 Harrison Ave, Neuroscience Arnold 305A

institute: Tufts University

summary: Multiple human autism risk genes are predicted to converge on the β‐catenin (β‐cat)/Wnt pathway. However, direct tests to link β‐cat up‐ or down‐regulation with autism are largely lacking, and the associated pathophysiological changes are poorly defined. Here we identify excessive β‐cat as a risk factor that causes expression changes in several genes relevant to human autism. Our studies utilize mouse lines with β‐cat dysregulation in forebrain excitatory neurons, identified as cell types with convergent expression of autism‐linked genes in both human and mouse brains. We show that mice expressing excessive β‐cat display behavioral and molecular changes, including decreased social interest, increased repetitive behaviors, reduced parvalbumin and altered expression levels of additional genes identified as potential risk factors for human autism. These behavioral and molecular phenotypes are averted by reducing β‐cat in neurons predisposed by gene mutations to express elevated β‐cat. Using next-generation sequencing of the prefrontal cortex, we identify dysregulated genes that are shared between mouse lines with excessive β‐cat and autism‐like behaviors, but not mouse lines with reduced β‐cat and normal social behavior.  Our findings provide critical new insights into β‐cat, Wnt pathway dysregulation in the brain causing behavioral phenotypes relevant to the disease and the molecular etiology which includes several human autism risk genes.

overall_design: Examination of gene changes in the prefrontal cortex of different mouse models with excessive or reduced beta-catenin levels

first: Jonathan

last: Alexander


title: AmpliSeq Transcriptome profiling of human B cells from EBV-infected and FK506-treated humanized mice.

city: Zurich

first: Christian

last: Münz

address: Winterthurerstrasse 190

department: Institute of Experimental Immunology

country: Switzerland

institute: University Of Zurich

summary: to investigate the effects of FK506 on the course of EBV infection in vivo

overall_design: we reconstituted NOD-scid IL2Rγc−/− HLA-A2 transgenic mice with CD34+ hematopoietic progenitor cells (HPC) from HLA-A2+ human fetal livers.  Upon assessment of human immune cell reconstitution in the peripheral blood at three to four-months after HPC injection, mice were infected with EBV (strain B95-8) or mock-infected with PBS. Three weeks post-infection (p.i.), animals were either treated with subcutaneous (s.c.) injections of FK506 (Tacrolimus) every second day or left untreated for a further two weeks.

first: Nicole

last: Caduff

first: Donal

last: McHugh

first: Michael

last: Prummer

first: Laurent

last: Hoffmann

first: Friedrich

last: Raulf

first: Tina

last: Rubic-Schneider

first: Elisabetta

last: Traggiai

last: Kammüller


title: Transcriptome profiling of Arabidopsis tac1 and lazy1 mutant shoot tips under normal and gravistimulated conditions

status: Public on Mar 21 2020

city: East Lansing

first: Courtney

last: Hollender

state: MI

address: 1066 Bogue St

department: Dept. of Horticulture

institute: Michigan State University

summary: This data is was generated in connection with a study on the  'Opposing influences of TAC1 and LAZY1 on Lateral Shoot Orientation in Arabidopsis'. RNA was extracted from individual shoot tips from wild type (Columbia; Col), tac1, and lazy1 plants that experienced either 0 or 45 minutes of gravistimulation by 90-degree reorientation. The summary of the entire project is as follows: TAC1 and LAZY1 are members of a gene family that regulates lateral shoot orientation in plants. TAC1 promotes outward orientations in response to light, while LAZY1 promotes upward shoot orientations in response to gravity via altered auxin transport. We performed genetic, molecular, and biochemical assays to investigate possible interactions between these genes. In Arabidopsis they were expressed in similar tissues and double mutants revealed the wide-angled lazy1 branch phenotype, indicating it is epistatic to the tac1 shoot phenotype. Surprisingly, the lack of TAC1 did not influence gravitropic shoot curvature responses. Combined, these results suggest TAC1 might negatively regulate LAZY1 to promote outward shoot orientations. However, additional results revealed that TAC1- and LAZY1 influence on shoot orientation is more complex than a simple direct negative regulatory pathway. Transcriptomes of Arabidopsis tac1 and lazy1 mutants compared to wild type under normal and gravistimulated conditions revealed few overlapping differentially expressed genes. Overexpression of each gene did not result in major branch angle differences. Shoot tip hormone levels were similar between tac1, lazy1, and Col, apart from exceptionally elevated levels of salicylic acid in lazy1. The data presented here provide a foundation for future study of TAC1 and LAZY1 regulation of shoot architecture.

overall_design: Arabidopsis plants containing only a single inflorescence shoot, with a height of ~15-18 cm, and no more than 3 lateral shoots (each no larger than ~1 cm) were used for expression profiling. Prior to collection, plants were left for at least 12 hours in a dark chamber with wooden stakes to support primary shoots to ensure they would be vertical at the time of collection. Primary shoot tips from upright (t0) plants and plants after 45 minutes of gravistimulation in the dark by a 90° reorientation (t45 plants) were collected on the same day. The t0 collections were at ~10 AM and t45 collections were at ~10:45 AM (having been reoriented at ~10 AM). From all plants, the upper most ~1 cm of primary shoot apical tissue (minus any leaves, flowers, or opening buds) was harvested and immediately frozen in liquid nitrogen. Total RNA was extracted from apical tissues using the Qiagen Plant Mini RNeasy kit (Germantown, MD) including a DNAse treatment with Invitrogen Turbo DNA-free (Carlsbad, CA). Approximately 2 ug of total RNA for each sample was sent to the Cornell Weill Medical Genomics Resources Core Facility (New York, NY, USA) where RNA TruSeq 50 bp unpaired barcoded libraries were prepared for each and sequenced with nine libraries per lane on an Illumina HiSeq 2000.

first: Chris

last: Dardick


title: Dual functionality of the TasA amyloid protein in Bacillus physiology and fitness on the phylloplane

status: Public on Mar 22 2020

city: Malaga

first: Jesus

last: Camara-Almiron

address: Calle Severo Ochoa, 34

institute: University of Malaga

summary: We report the application of a high-throughput technique, RNA-seq, to study the transcriptomic response of a Bacillus subtilis mutant for the tasA gene growing in biofilm-inducing solid medium (MSgg).

sample_organism: Bacillus subtilis subsp. subtilis NCIB 3610 = ATCC 6051 = DSM 10

overall_design: B. subtilis NCIB 3610 tasA mutant and WT mRNA profiles comparing their growth in solid MSgg medium at 24 and 48 h of growth to complement the data obtained at 72 h of growth.

first: Jesús

last: Cámara-Almirón

first: Diego

last: Romero


title: CD14+ IMC treated TGF-beta

city: San Francisco

first: Mary Helen

last: Barcellos-Hoff

address: 2340 Sutter Street

department: Radiation Oncology

institute: UCSF

summary: CD14+ human immature myeloid cells were treated with TGF-beta for increased periods of time to study the effects of TGF-beta in regulating the myeloid cell lineage and functions.

overall_design: CD14+ human immature myeloid cells freshly isolated from healthy volunteer donor PBMC were treated with or without TGF-beta for increased periods of time

first: M

first: A

last: Gonzalez-Junca

first: R

last: Roy


title: Gene expression of primary chondrocytes obtained from Hif1afl/fl mice transduced with adenovirus expressing GFP or Cre

city: TOKYO

first: Taku

last: Saito

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

department: Orthopaedic Surgery, Faculty of Medicine

institute: The University of Tokyo

summary: To identify gene expression profiles when Hif1a is deleted in chondrocytes

overall_design: Primary chondrocytes were isolated from Hif1afl/fl mice, and transduced with adenovirus expressing GFP or Cre.


title: The novel microRNAs hsa-miR-nov7 and hsa-miR-nov3 are over-expressed in locally advanced breast cancer

city: Bergen

first: Stian

last: Knappskog

department: Department of Clinical Sciences

country: Norway

institute: University of Bergen

summary: We analyzed small RNA massive parallel sequencing data from 50 locally advanced breast cancers aiming to identify novel breast cancer related microRNAs. We successfully predicted 10 novel miRNAs, out of which 2 (hsa-miR-nov3 and hsa-miR-nov7) were recurrent. Applying high sensitivity qPCR, we detected these two microRNAs in 206 and 214 out of 223 patients in the study from which the initial cohort of 50 samples were drawn. We found hsa-miR-nov3 and hsa-miR-nov7 both to be overexpressed in tumor versus normal breast tissue in a separate set of 13 patients from whom both tumor tissue and normal tissue were available. We observed hsa-miR-nov3 to be expressed at higher levels in ER-positive compared to  ER-negative tumors. Further stratifications revealed particularly low levels in the her2-like and basal-like cancers compared to other subtypes.

overall_design: Analysis to identify novel miRNAs expressed in locally advanced breast cancer.

first: Deepak

last: Poduval

first: Zuzana

last: Sichmanova

first: Anne

last: Straume

first: Per

last: Lønning

last: Knappskogg


title: Different Egyptian rousette interferon omega proteins elicit an overlapping but not identical transcriptional response in bat cells.

status: Public on Mar 16 2020

city: Boston

first: Stephanie

middle: Sarah

last: Pavlovich

address: 700 Albany St, W508D

department: Microbiology

institute: Boston University School of Medicine

summary: Abstract from accompanying publication: "Bats host a number of viruses that cause severe disease in humans without experiencing overt symptoms of disease themselves. While the mechanisms underlying this ability to avoid sickness are not known, deep sequencing studies of bat genomes have uncovered genetic adaptations that may have functional importance in the antiviral response of these animals. Egyptian rousette bats (Rousettus aegyptiacus) are the natural reservoir hosts of Marburg virus (MARV). In contrast to humans, these bats do not become sick when infected with MARV. A striking difference to the human genome is that Egyptian rousettes have an expanded repertoire of IFNW genes. To probe the biological implications of this expansion, we synthesized IFN-ω4 and IFN-ω9 proteins and tested their antiviral activity in Egyptian rousette cells. Both IFN-ω4 and IFN-ω9 showed antiviral activity against RNA viruses, including MARV, with IFN-ω9 being more efficient than IFN-ω4. Using RNA-Seq, we examined the transcriptional response induced by each protein. Although the sets of genes induced by the two IFNs were largely overlapping, IFN-ω9 induced a more rapid and intense response than did IFN-ω4. About 13% of genes induced by IFN-ω treatment are not found in the Interferome or other ISG databases, indicating that they may be uniquely IFN-responsive in this bat."

overall_design: mRNA trancriptional profiles of bat cells pretreated with bat interferons, media, universal interferon, or an unrelated protein for 4 or 8 hours at three different concentrations, in triplicate, sequenced on Illumina HiSeq 2500

first: Adam

last: Hume

first: Feng

last: Feng

first: Elke

last: Mühlberger

first: Thomas

last: Kepler


title: Multiplex secretome engineering enhances recombinant protein production and purity

city: San Diego

first: Nathan

middle: E.

last: Lewis

address: 9500 Gilman Dr.

department: Pediatrics

institute: University of California, San Diego

summary: Host cell proteins (HCPs) are process-related impurities generated during biotherapeutic protein production. HCPs can be problematic if they pose a significant metabolic demand, degrade product quality, or contaminate the final product. Here, we present an effort to create a “clean” Chinese hamster ovary (CHO) cell by disrupting multiple genes to eliminate HCPs. Using a model of CHO cell protein secretion, we predicted the elimination of unnecessary HCPs could have a non-negligible impact on protein production. We analyzed the total HCP content of 6-protein, 11-protein, and 14-protein knockout clones and characterized their growth in shake flasks and bioreactors. These cell lines exhibited a substantial reduction in total HCP content (40%-70%). We also observed higher productivity and improved growth characteristics, in specific clones. With the reduced HCP content, protein A and ion exchange chromatography more efficiently purified a monoclonal antibody (mAb) produced in these cells during a three-step purification process. Thus, substantial improvements can be made in protein titer and purity through large-scale HCP deletion, providing an avenue to increased quality and affordability of high-value biopharmaceuticals.

overall_design: CHO-S cells were subjected to 4 cycles of CRISPR/Cas9-mediated multiplex gene disruption to produce 6-protein (BGN, TIMP1, LGALS3BP, NID1.1, NID1.2, and CTSD), 11-protein (BGN, TIMP1, LGALS3BP, NID1.1, NID1.2, CTSD, Aga, Erp29, Gpr56, Tinagl1, and Lgmn), and 14 protein (BGN, TIMP1, LGALS3BP, NID1.1, NID1.2, CTSD, Aga, Erp29, Gpr56, Tinagl1, Lgmn, Yeats2, Sparc, and Lpl) knockout strains.  WT CHO-S and knockout cell lines (6x, 11x, and 14x) were transacted with a plasmid encoding the Rituximab antibody and the zeocin selection gene using Freestyle MAX reagent.  The WT CHO-S, 6xKO and 11xKO strains were subjected to RNA-Seq  at 3 different time points (4 days, 6 days, and 8 days). Library preparation was performed with Illumina’s TruSeq Stranded mRNA Library Prep Kit High Throughput (Catalog ID: RS-122-2103).


title: Memory of cell divisions directs the continuous process of primitive hematopoietic lineage commitment

status: Public on Mar 14 2020

first: Kateri

last: Moore

address: One Gustave L. Levy Place, Box 1496

department: Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai

institute: Icahn School of Medicine at Mount Sinai

summary: Hematopoietic stem cells (HSCs) exist in a dormant state, and progressively lose regenerative potency as they undergo successive divisions. Why this functional decline occurs and how this information is encoded is unclear. To better understand how this information is stored, we performed RNA sequencing on HSC populations differing only in their divisional history. Comparative analysis revealed that genes upregulated with divisions are enriched for lineage commitment factors, and are regulated by cell cycle-associated transcription factors, indicating that proliferation itself drives primitive hematopoietic lineage priming. In contrast, downregulated genes are associated with an HSC signature and are targeted by the Polycomb Repressive Complex 2 (PRC2). We find that Ezh2 targets HSC signature genes for repression, and a divisional history-dependent switch from Ezh1 to Ezh2 underlies HSC decline with progressive divisions. Thus cell divisions drive lineage priming and Ezh2 accumulation, which represses HSC signature genes and consolidates information on divisional history into memory.

overall_design: RNAseq of HSC populations distinguished by H2BGFP label retention as a proxy for divisional history. 3 replicates for each HSC popultion: 1 Total HSC population and 4 subdivided HSC populations.

first: Jeffrey

last: Bernitz

first: Michael

last: Daniel

first: Dmitrii

last: Scherbinin

first: Ye

last: Yuan

first: Andreia

last: Gomes

first: Avinash

last: Waghray

first: Katrina

last: Rapp

first: Ran

last: Brosh

first: Alexander

last: Lachmann

first: Avi

last: Ma'ayan

first: Dmitri

last: Papatsenko