title: Defining the Independence of the Liver Circadian Clock

status: Public on Jun 13 2019

city: Irvine

first: Jiejun

last: Shi

address: 5270 California Ave

department: School of Medicine

institute: University of California Irvine

summary: Mammals rely on a network of circadian clocks to control daily systemic metabolism and physiology. The central pacemaker in the suprachiasmatic nucleus (SCN) is considered hierarchically dominant over peripheral clocks, whose degree of independence, or tissue-level autonomy, has never been ascertained in vivo. Using arrhythmic Bmal1-null mice, we generated animals with reconstituted circadian expression of BMAL1 exclusively in the liver (Liver-RE). High-throughput transcriptomics and metabolomics show that the liver has independent circadian functions specific for metabolic processes such as the NAD+ salvage pathway and glycogen turnover. However, although BMAL1 occupies chromatin at most genomic targets in Liver-RE mice, circadian expression is restricted to ∼10% of normally rhythmic transcripts. Finally, rhythmic clock gene expression is lost in Liver-RE mice under constant darkness. Hence, full circadian function in the liver depends on signals emanating from other clocks, and light contributes to tissue-autonomous clock function.

overall_design: BMAL1 ChIP-seq in mouse liver harvested at Zeitgeber Time (ZT) 8 and ZT20

first: Kevin

middle: B

last: Koronowski

first: Paolo

last: Sassone-Corsi


title: 5-hydroxymethylcytosine and gene activity in mouse intestinal differentiation (RNA-Seq).

city: Bath

first: Adele

last: Murrell

address: The Avenue

department: Biology and Biochemistry

country: United Kingdom

institute: University of Bath

type: Expression profiling by high throughput sequencing

summary: Background: Cytosine hydroxymethylation (5hmC) was recently identified in mammalian DNA as the product of oxidation of methylated cytosines (5mC) by Ten-Eleven-Translocation (TET) enzymes. The TETs have been shown to influence 5mC metabolism, pluripotency and differentiation during early embryonic development. However, a functional relationship between gene expression and 5hmC in adult (somatic) stem cell differentiation is however mainly unknown. To explore the role of this novel DNA modification in adult stem cell differentiation we profiled 5hmC and gene activity in purified mouse intestinal progenitors and differentiated progeny.  Results: We show that the hydroxymethylome is highly dynamic with tens of thousands of differentially hydroxymethylated regions between progenitors and differentiated progeny.  In progenitors 5hmC does not correlate with gene expression levels, however, upon differentiation a global increase in 5hmC is observed with an overall positive correlation between 5hmC and gene expression together with prominent associations with histone modifications that typify active genes and enhancer elements.   Conclusions: In the context of recent evidence of near identical methylomes between mouse intestinal stem and differentiated cells, our data imply that a gene regulatory role for 5hmC is predominant over its role in controlling DNA methylation states. Our study provides an insight into the dynamics of 5hmC and of epigenetic machineries in differentiation of the mouse intestine.

overall_design: Four biological replicates were analysed per cell type purified by flow cytometry using the CD24 marker and depletion of CD45 and Ulex lectin positive cells. See Wong et al. NatCellBiol 2012 Mar 4;14(4):401-8 or Buczacki et al. Nature 2013 Mar 7;495(7439):65-9. CD24Mid are also referred to as CD24low in the manuscript.

first: Santiago

last: Uribe-Lewis

first: Suraj

last: Menon

first: Silvia

last: Halim


title: AGO CLIP reveals an activated network for acute regulation of brain glutamate homeostasis in ischemic stroke [dataset 6]

status: Public on Jun 14 2019

city: New York

first: Mariko

last: Kobayashi

state: NY

address: 1230 York Avenue

department: Molecular Neuro-Oncology

country: USA

institute: Rockefeller University

summary: Human motor cortex (brodmann’s area 9) tissues analyzed by Argonaute HITS-CLIP to determine human transcriptome-wide AGO binding pattern.

overall_design: Frozen tissues were crushed, UV-irradiated and analyzed by CLIP protocol.  For each CLIP sample, high and low molecular weight AGO:RNA complexes (~110-130 kDa, Supplementary figure 1B) were pooled for library construction.  Individual replicates were taken through AGO CLIP separately, aligned reads were then combined into 2 pools prior to informatic analysis.  Complete protocol detailed in referenced publication.

first: Aldo

last: Mele


title: 5-hydroxymethylcytosine and gene activity in mouse intestinal differentiation (hmeDIP-seq).

type: Methylation profiling by high throughput sequencing

first: Thomas

last: Carroll


title: Paternal overdiet drives intergenerational transmission of metabolic disorders through sperm epigenetic alteration [MeDIP-Seq]

city: Wuhan

first: Jing-Jing

last: Zhang

state: Hubei

address: 1 Lion Rock Street

department: Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction

country: China

institute: Huazhong Agricultural University

summary: We using a mouse model of paternal famine to simulate famine, our data show that paternal famine increases the susceptibility to metabolic disease in offspring through gametic epigenetic alterations.

overall_design: Sperm DNA profiles of 12 week old control male F0 and Famine male F0 mice were generated by deep sequencing

first: Ying-Ying

last: Gao

first: Yi-Liang

last: Miao


title: Scavenger Receptor A1 Prevents Non-Small Cell Lung Cancer Metastasis by Suppressing Macrophage Serum Amyloid A1 Expression

status: Public on Jun 16 2019

city: Nanjing

first: jingjing

last: ben

address: Longmian road 101

institute: Nanjing Medical University

summary: Metastasis is the key determinant of poor prognosis for advanced-stage NSCLC patients. Although an important contributor to metastasis is cross-talk between tumor-associated macrophages (TAMs) and tumor cells, its regulation is not fully understood. Expressed primarily in macrophages, scavenger receptor A1 (SR-A1) has been associated with lung tumorigenesis. Here, the mechanistic basis for the involvement of SR-A1 in lung cancer prognosis was investigated using population genetics, transcriptomics, and functional analyses. SR-A1 genetic variants were investigated for possible association with survival of advanced-stage NSCLC patients in the Harvard Lung Cancer Study cohort. Two SNPs (rs17484273, rs1484751) in SR-A1 were significantly associated with poor overall survival of NSCLC patients. Further, data from The Cancer Genome Atlas showed a considerable down-regulation of SR-A1 in lung tumor tissues. The association of SR-A1 with prognosis was validated in animal models in the context of lung cancer metastasis. Macrophages derived from SR-A1 knockout mice accelerated metastasis in a lung cancer mouse model. On the other hand, tumor cell seeding, migration, and invasion as well as macrophage accumulation in lung cancer tissue were enhanced in SR-A1 knockout mice. Furthermore, SR-A1 deficiency promoted up-regulation of serum amyloid A1 (SAA1) in macrophages, which appeared to be mediated by MAPK/Ikappa-B/NF-kappaB signaling. Further, SAA1 exposure promoted tumor cell invasion and macrophage migration in vitro and in vivo, but these effects were blocked by administration of an anti-SAA1 antibody. These findings suggest that SR-A1 may suppress lung cancer metastasis by down-regulating SAA1 production in macrophages.

overall_design: In the experimental metastasis model, 3 × 105 LLC cells were re-suspended in 200 uL phosphate-buffered saline (PBS) and injected into the tail vein of 8-week-old WT and SR-A1 KO female mice (B6.Cg-Msr1tm1Csk/J) to induce the pulmonary metastasis. Mice were euthanized after three weeks and the lungs were collected for analysis. Total RNA was extracted, purified, and assessed by formaldehyde agarose gel electrophoresis and quantitated spectrophotometrically. cDNA labeled with a fluorescent dye (Cy3-dCTP) was produced by Eberwine’s linear RNA amplification method and subsequent enzymatic reaction. Array hybridization, washing, scanning, and data analysis were carried out according to NimbleGen Expression user’s guide and performed at Capital Biotech Corporation (Beijing, China).

first: Yan

first: Yongyue

last: Wei

first: Jingjing

last: Ben

first: Chen

last: Qi


title: A technology-agnostic long-read analysis pipeline for transcriptome discovery and quantification

status: Public on Jun 15 2019

first: Ali

last: Mortazavi

state: CA

address: 2218 Biological Sciences III

department: Developmental and Cell Biology

institute: University of California: Irvine

summary: Alternative splicing is widely acknowledged to be a crucial regulator of gene expression and is a key contributor to both normal developmental processes and disease states. While cost-effective and accurate for quantification, short-read RNA-seq lacks the ability to resolve full-length transcript isoforms despite increasingly sophisticated computational methods. Long-read sequencing platforms such as Pacific Biosciences (PacBio) and Oxford Nanopore (ONT) bypass the transcript reconstruction challenges of short-reads. Here we describe TALON, the ENCODE4 pipeline for analyzing PacBio cDNA and ONT direct-RNA transcriptomes. We apply TALON to three human ENCODE Tier 1 cell lines and show that while both technologies perform well at full-transcript discovery and quantification, each technology has its distinct artifacts. We further apply TALON to mouse cortical and hippocampal transcriptomes and find that a substantial proportion of neuronal genes have more reads associated with novel isoforms than annotated ones. The TALON pipeline for technology-agnostic, long-read transcriptome discovery and quantification tracks both known and novel transcript models as well as expression levels across datasets for both simple studies and larger projects such as ENCODE that seek to decode transcriptional regulation in the human and mouse genomes to predict more accurate expression levels of genes and transcripts than possible with short-reads alone.

overall_design: We performed direct RNA-sequencing using ONT on 3 tier1 ENCODE cell lines to be able to compare to PACBIO data using TALON

first: Fairlie

last: Reese


title: Dynamic Enhancer DNA Methylation as Basis for Transcriptional and Cellular Heterogeneity of ESCs [BiSulfite-seq]

city: Cambridge

first: Rudolf

last: Jaenisch

state: MA

address: 455 Main Street

department: Biology

institute: Whitehead Institute for Biomedical Research

summary: Variable levels of DNA methylation have been reported at tissue-specific differential methylation regions (DMRs) overlapping enhancers, including super-enhancers (SEs) associated with key cell identity genes, but the mechanisms responsible for this intriguing behavior are not well understood. We used allele-specific reporters at the endogenous Sox2 and miR290 super-enhancers (SE) in embryonic stem cells and found that the allelic DNA methylation state is dynamically switching, resulting in cell-to-cell heterogeneity. Dynamic DNA methylation is driven by the balance between DNA methyl-transferases and transcription factor binding on one side, and co-regulated with the Mediator complex recruitment and H3K27ac level changes at regulatory elements on the other side. DNA methylation at the Sox2 and the miR290 SEs is independently regulated and has distinct consequences on the cellular differentiation state. Dynamic allele-specific DNA methylation at the two SEs was also seen at different stages in preimplantation embryos, revealing that methylation heterogeneity occurs in vivo.

overall_design: Illumina next generation sequencing was performed on miR290 SE DMR bisulfite-PCR amplicons from Dnmt3a/b DKO ESCs, miR290-SE Nanog+RGM+ ESCs, and untargeted ESCs

first: Yuelin

last: Song

first: Bingbing

last: Yuan


title: The 19S proteasome regulates subtelomere silencing and facultative heterochromatin formation

city: Daejeon

first: Hogyu David

last: Seo

address: 291 Daehak-ro

country: South Korea

institute: KAIST

type: Genome binding/occupancy profiling by high throughput sequencing

summary: The non-proteolytic role of the proteasome in heterochromatin regulation

overall_design: For ChIP experiment : ChIP against H3K9me2, anti-FLAG was performed for a wild type strain and strains lacking Clr4, Leo1, Rpt4 point-mutation and FLAG-tagged Epe1.

first: H

middle: D

first: D

last: Lee


title: Dynamic Enhancer DNA Methylation as Basis for Transcriptional and Cellular Heterogeneity of ESCs [RNA-seq]

overall_design: RNA-seq experiments were performed on sorted T+G+, T+G-, T-G+, and T-G- cells from the SOX2-SE-TG and MIR290-SE-TG mouse ESC lines

first: Patrick

middle: R

last: van den Berg

first: Stefan

last: Semrau


title: RNA-sequencing of RNAs found on eRpL22 paralogue-specific ribosomes in Drosophila melanogaster testis

city: Bethlehem

first: Catherine

middle: M

last: Mageeney

state: PA

address: 111 Research Drive, B217

department: Biological Sciences

institute: Lehigh Univeristy

summary: This study uncovers a population of eRpL22 paralogue-specific specialized ribosomes in the fly testis. Wildtype testes were used to isolate eRpL22 paralogue-specific ribosomes complexed with RNA molecules.  RNA-sequencing determined the distribution of RNAs (mRNA and ncRNA) on each type of eRpL22 paralogue-specific ribosome, revealing unique translatomes for both eRpL22- and eRpL22-like- ribosomes, as well as an overlapping translatome.

overall_design: Examination of RNAs associated with two different ribosome population denoted by eRpL22 paralogues in Drosophila melanogaster testis

first: Vassie

middle: C

last: Ware


title: Mitosis-related phosphorylation of the eukaryotic translation suppressor 4E-BP1 and its interaction with eukaryotic translation initiation factor 4E (eIF4E)

city: Pittsburgh

first: Rui

last: Sun

address: 5117 Centre Avenue, UPMC Hillman Cancer Center Research Pavilion 1.8

department: Department of Microbiology and Molecular Genetics

institute: University of Pittsburgh

summary: Eukaryotic translation initiation factor 4E (eIF4E)–binding protein 1 (4E-BP1) inhibits cap-dependent translation in eukaryotes by competing with eIF4G for an interaction with eIF4E. Phos-phorylation at Ser-83 of 4E-BP1 occurs during mitosis through the activity of cyclin-dependent kinase 1 (CDK1)/cyclin B rather than through canonical mTOR kinase activity. Here, we investi-gated the interaction of eIF4E with 4E-BP1 or eIF4G during interphase and mitosis. We observed that 4E-BP1 and eIF4G bind eIF4E at similar levels during interphase and mitosis. The most highly phosphorylated mitotic 4E-BP1 isoform (δ) did not interact with eIF4E, whereas a distinct 4E-BP1 phospho-isoform, EB-γ—phosphorylated at Thr-70, Ser-83, and Ser-101—bound to eIF4E during mitosis. Two-dimensional gel electropho-retic analysis corroborated the identity of the phosphorylation marks on the eIF4E-bound 4E-BP1 isoforms and uncovered a population of phosphorylated 4E-BP1 molecules lacking Thr-37/Thr-46–priming phosphorylation. Moreover, proximity ligation assays for phospho–4E-BP1 and eIF4E revealed different in situ interactions during interphase and mitosis. The eIF4E:eIF4G interaction was not inhibited, but rather increased in mitotic cells, consistent with active translation initiation during mitosis. Phospho-defective substitution of 4E-BP1 at Ser-83 did not change global translation or individual mRNA translation profiles as measured by single-cell nascent protein synthesis and eIF4G RNA-immunoprecipitation sequencing. Mitotic 5’-terminal oligopyrimidine RNA translation was active and, unlike interphase translation, resistant to mTOR inhibition. Our findings reveal the phosphorylation profiles of 4E-BP1 isoforms and their interactions with eIF4E throughout the cell cycle and indicate that 4E-BP1 does not specifically inhibit translation initiation during mitosis.

overall_design: 1) eIF4G RIP-seq in HeLa cells. 4 groups of samples (M_CtrL, M_PP242, PM_CtrL, PM_PP242) were included. Each group contains Input and IP. 2) eIF4G RIP-seq in mitosis-enriched 4E-BP1WT and 4E-BP1S83A cells. 2 groups of samples (WT, S83A) were included. Each group contains Input and IP. Three independent biological experiments were performed.

first: Yuan

last: Chang

middle: S

last: Moore


title: Functional Comparison of the HGF/Met and MSP/Ron Systems in a Pancreatic Cancer Model

city: Pullman

first: Brett

last: Vanderwerff

state: WA

address: PO Box 647620, Washington State University

institute: Washington State University

summary: Pancreatic cancer is an aggressive disease with a poor prognosis for which current standard chemotherapeutic treatment options offer little survival benefit. In recent years, receptor tyrosine kinases (RTK)s have garnered interest as therapeutic targets to augment or replace standard chemotherapeutic therapies because of their high expression levels in various cancers and their ability to promote cell growth, migration, and survival. Met and Ron, which are homologous RTKs activated by the ligands hepatocyte growth factor (HGF) and macrophage stimulating protein (MSP), respectively, are over-activated in many of the least treatable cancers. In pancreatic adenocarcinoma, Met expression is linked to poor patient survival and Ron expression is generally higher in tumor samples relative to normal tissue, although its prognostic significance in pancreatic cancer remains unclear. Despite the structural homology between Met and Ron, studies that have directly compared the functional outcomes of these systems in any context are limited. To address this, we sought to determine if the HGF/Met and MSP/Ron systems produce overlapping or divergent contributions towards a malignant phenotype by performing a characterization of MSP and HGF driven signaling, behavioral, and transcriptomic responses in pancreatic cancer cells in vitro. We found HGF and MSP both encouraged cell migration and activated the MAPK/Erk pathway both at the transcript and protein level. HGF uniquely increased proliferation in addition to regulating a wider variety of transcripts compared to MSP. Although HGF and MSP produced a differing breadth of responses, overlapping pro-cancer signaling, behavioral, and transcriptional effects suggest dual inhibition of the MSP/Ron and HGF/Met systems in pancreatic cancer may provide a more complete anti-cancer effect compared to individually targeting either system.

overall_design: BxPC-3 cells were treated with vehicle control (PBS), HGF (80 ng/ml), or MSP (100 ng/ml) in triplicate. Total RNA was collected at 1 and 4 hours post-treatment. Libraries were prepped with a KAPA mRNA HyperPrep Kit. Libraries were sequenced on an Illumina HiSeq 4000. All samples were sequenced in duplicate across two lanes.

first: Joseph

middle: W

last: Harding

first: Leen

middle: H

last: Kawas

first: Kevin

middle: J

last: Church


title: Increased sulfation of bile acids in mice and human subjects with sodium taurocholate cotransporting polypeptide deficiency

city: Beijing

first: Wenhui

last: Li

address: 7 Science Park Road ZGC Life Science Park

institute: National Institute of Biological Sciences

summary:
Purpose: To decipher the biochemical basis for the declining of total bile acids (TBA) levels in the late age of Slc10a1-/- mice, we performed a serial liver RNA-Seq analysis of mRNA expression with male mice at different ages.

Methods: Liver mRNA profiles of 4-week, 8-week, 20-month-old wild-type (WT) and sodium taurocholate cotransporting polypeptide knockout (Slc10a1-/-) mice were generated by deep sequencing, in triplicate, quadruplicate or sextuplicate, using  Illumina Hiseq-2500 platform. Clean mRNA-seq reads were aligned to the mouse reference genome (GRCm38) with TopHat (v2.0.13), guided by Ensembl gene annotation v83. Only uniquely aligned and properly paired reads were retained for further analysis. Gene-level read counts were calculated with HTseq (v0.6.1p1) with the union mode. Genes with less than a total of 11 non-normalized reads across all samples were excluded. Data normalization and statistical analysis of differential expression were performed with the DEseq2 (v1.10.0) R package. Pair-wise Spearman correlation between samples across all quantified genes used for hierarchical clustering.

Results: At 4 weeks and 8 weeks, WT and Slc10a1-/- mice exhibited clear different pattern in terms of transcriptome similarity and were well separated, however, the difference was indistinguishable at 20 months.And changes of pathways involved in the metabolism of xenobiotics in Slc10a1-/- mice.

Conclusions: Our study reveal that enhanced BA sulfation is a major mechanism for BA detoxification and elimination in Slc10a1-/- mice with hypercholanemia.

first: Hanqing

last: Zhao


title: A Role for FACT in RNA Polymerase II Promoter-Proximal Pausing

city: KANSAS CITY

first: Joan

last: Conaway

state: Missouri

institute: Stowers Institute for Medical Research

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

FACT (Facilitates Chromatin Transcription) is an evolutionarily conserved histone chaperone that was initially identified as an activity capable of promoting RNA polymerase II transcription through nucleosomes in vitro. In this report, we describe a global analysis of FACT function in Pol II transcription in Drosophila. We present evidence that loss of FACT has a dramatic impact on Pol II elongation-coupled processes including H3K4 and H3K36 methylation, consistent with a role for FACT in coordinating histone modification and chromatin architecture during Pol II transcription. Importantly, we identify a role for FACT in the maintenance of promoter proximal Pol II pausing, a key step in transcription activation in higher eukaryotes. These findings bring to light a broader role for FACT in the regulation of Pol II transcription.

overall_design: Refer to individual Series


title: AGO CLIP reveals an activated network for acute regulation of brain glutamate homeostasis in ischemic stroke

first: Mariko

last: Kobayashi

type: Non-coding RNA profiling by high throughput sequencing

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: AGO CLIP reveals an activated network for acute regulation of brain glutamate homeostasis in ischemic stroke [dataset 7]

summary: In vivo microRNA-target interactions from adult mouse cortex were identified with CLEAR-CLIP, a modified AGO HITS-CLIP approach that allows direct ligation of microRNA and target within purified, endogenous AGO-RNA complexes.

overall_design:
Native AGO-RNA complexes were purified under stringent conditions selectively preserve cross-linked AGO-target interactions, then microRNA and target mRNA were ligated within the AGO complex to form miRNA-target chimeras in addition to standard AGO CLIP reads. AGO-bound RNAs were cloned by addition of a pre-adenylated 3' linker, a 5' RNA linker containing a 4 nt degenerate barcode followed by a G (NNNNG), and RT-PCR amplification. A second round of PCR amplification added a 4 nt index (for multiplexing) followed by a 16 nt common priming sequence. Raw data files have been de-multiplexed, but are otherwise not modified.
DATA PROCESSING: base calling: Casava 1.8.2  quality filtering: minimum quality filter applied for barcode and insert; fastq_filter.pl; -if sanger -f min:0-3:20,mean:20-40:20 -maxN -1 -v -of fasta ; http://sourceforge.net/projects/ngs-cims/files/CIMS.v1.0.5.tgz/download  collapse exact sequences: exact duplicate sequences removed; fasta2collapse.pl; ; http://sourceforge.net/projects/ngs-cims/files/CIMS.v1.0.5.tgz/download  remove 3' adapter sequene: 3' adapter GTGTCAGTCACTTCCAGCGG clipped; fastx Clipper; -l 20 -a GTGTCAGTCACTTCCAGCGG -n; http://hannonlab.cshl.edu/fastx_toolkit/  trim 5' adapter sequence: 5' 20 nucleotides trimmed (NNNNAGGGAGGACGATGCGG, where NNNN is 4 nucleotide index for multiplexing); fastx Trimmer; -f 21; http://hannonlab.cshl.edu/fastx_toolkit/  strip 5' degenerate linker: 5 nucleotide (NNNNG) degenerate barcode stripped and appended to read IDs; stripBarcode.pl; -linker 5 ; http://sourceforge.net/projects/ngs-cims/files/CIMS.v1.0.5.tgz/download  alignment against micoRNA database: microRNA database mapped against sample file (treated as reference genome) to identify potential chimeric reads containing microRNA sequence; Bowtie; -n 1 -l 8 -e 35; http://bowtie-bio.sourceforge.net/index.shtml  extract chimeric read: extract potential chimeric sequence 5' or 3' of mapped microRNA sequence; text manipulation in R; ;  alignment against genome reference: alignment ofpotential chimeric reads against reference genome to identify target sites; Bowtie; -n 1 -l 8 -e 35; http://bowtie-bio.sourceforge.net/index.shtml  collapse PCR duplicates: mapped reads with same 5' end and same degenerate barcode consolidated; tag2collapse.pl; keep-tag-name --keep-max-score --random-linker -EM 30 --seq-error-model em-local --weight --weight-in-name ; http://sourceforge.net/projects/ngs-cims/files/CIMS.v1.0.5.tgz/download  clustering : chimera interactions with the same ligated microRNA and overlapping genomic coordinates were clustered; Genome_Intervals R package; ;
mm10 genomic coordinates of 126,295 CLEAR CLIP chimeras, chromosome, start, end, associated mmu miRNA, strand info

first: Michael


title: Small intestinal inflammation shapes the transcriptomic signature of incoming monocytes in a partially Trem1-dependent mechanism

status: Public on Jun 12 2019

city: Aachen

first: Oliver

last: Pabst

address: Pauwelsstrasse 30

department: Institute of Molecular Medicine

country: Germany

institute: RWTH Aachen University

summary: In this study we showed that Trem1 is one of genes that were differentially regulated in donor monocytes recovered from non-inflamed and inflamed small intestine of recipient mice. We, therefore, aimed at investigating the role of Trem1 on regulating the monocyte adapatation and differentiation in a context-dependent manner. Thus, the gene expression of WT and Trem1-deficient donor monocytes that are recruited to non-inflamed and inflamed small intestine one day after transfer.

overall_design: Transferred monocytes recovered and FACS-sorted from the small intenstine of recipient mice at different time points and used for gene expression analysis. Following sorting, cDNA was made immediately and preamplified with Multiplexed target enrichment (MTE) primers. Hybridization of pre-amplified DNA with target specific oligonucleotide probe pairs were performed using a nanostring technology.

first: Girmay

last: Desalegn


title: AGO CLIP reveals an activated network for acute regulation of brain glutamate homeostasis in ischemic stroke [dataset 3]

summary: Adult mouse cortical tissues after MCAO or sham surgery were analyzed by small RNAseq at various time points after reperfusion to assess differences in miRNA abundance in I/R injury model of stroke.

overall_design: Mice were anesthetized briefly with 1.5–2% isoflurane.  A heat-blunted nylon suture (6/0) was inserted into the right external carotid artery and advanced until it obstructed the MCA together with the ligation of the common carotid artery for 35 min.  Regional cerebral blood flow (CBF, bregma coordinates: 2-mm posterior, 5-mm lateral) was continuously recorded by transcranial laser Doppler flowmetry from the induction of ischemia until 30 min after reperfusion.  Surgery success was determined by monitoring regional cerebral blood flow (CBF, bregma coordinates: 2-mm posterior, 5-mm lateral) using transcranial laser Doppler flowmetry, and required a residual CBF <15%, followed by >80% recovery within 10 min of reperfusion.   Following MCAO, mice were placed in temperature-controlled recovery cages for 3, 6, 12 or 24 hrs to prevent post-surgery hypothermia and sacrificed.  Sham animals were similarly anestheized, arteries exposed for surgical time period without filament insertion.  Cortical tissues from ipsilateral or contralateral hemispheres of MCAO, or sham animals were dissected for RNA extraction and library construction.  Each set of biological replicates represent animals from a distinct day of surgery.  Complete protocol detailed in referenced publication.


title: RNAseq transcriptome analysis of K. pneumoniae MS6671 and E. coli MS8345 treated with PBT2

city: Brisbane

first: David

middle: Manuel Pereira

last: De Oliveira

state: QLD

address: St Lucia

department: School of Chemistry and Molecular Biosciences

country: Australia

institute: The University of Queensland

summary: The emergence of colistin resistance in carbapenem-resistant and extended-spectrum ß-lactamase (ESBL)-producing bacteria is a significant threat to human health, and new treatment strategies are urgently required. Here we investigated the ability of the safe-for-human use ionophore PBT2 to restore antibiotic sensitivity in several polymyxin-resistant, ESBL-producing, carbapenem resistant Gram-negative human pathogens. PBT2 was observed to resensitize Klebsiella pneumoniae, Escherichia coli, Acinetobacter baumannii, and Pseudomonas aeruginosa to last-resort polymyxin class antibiotics, including a ‘next generation’ polymyxin derivative, FADDI-287. To gain additional insight into the potential mechanism of action of PBT2, we analyzed the transcriptome of K. pneumoniae and E. coli in the presence of sub-inhibitory concentrations of PBT2. Treatment with PBT2 was associated with multiple stress responses in both K. pneumoniae and E. coli. Significant changes in the transcription of transition metal ion homeostasis genes were observed in both strains.

sample_organism:
Escherichia coli
Klebsiella pneumoniae

platform_organism:
Escherichia coli
Klebsiella pneumoniae

overall_design: For each species of bacteria, 2 sample conditions were analyzed. Sample conditions included: 1) bacterial treatment with cation-adjusted Muller Hinton broth (CA-MHB; reference sample); or 2)  CA-MHB+PBT2 (7 µM for E. coli and 64 µM for K. pneumoniae).

middle: P

first: Minh-Duy

last: Phan

first: Mark

last: Walker


title: Transcriptome and proteome profiling of neural stem cells from the human subventricular zone in Parkinson's disease

city: Utrecht

first: Onur

last: BASAK

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute

summary: It is currently accepted that the human brain has a limited neurogenic capacity and an impaired regenerative potential. We have previously shown the existence of CD271-expressing neural stem cells (NSCs) in the subventricular zone (SVZ) of Parkinson’s disease (PD) patients, which proliferate and differentiate towards neurons and glial cells in vitro. To study the molecular profile of these NSCs in detail, we performed RNA sequencing and mass spectrometry on CD271+ NSCs isolated from human post-mortem SVZ and on homogenates of the SVZ. CD271+ cells were isolated through magnetic cell separation (MACS). We first compared the molecular profile of CD271+ NSCs to the SVZ homogenate from control donors to assess the CD271+ NSCs gene signature and finally made a comparison between controls and PD patients to establish a specific molecular profile of NSCs and the SVZ in PD. While our transcriptome analysis did not identify any differentially expressed genes in the SVZ between control and PD patients, our proteome analysis revealed several proteins that were differentially expressed in PD. Some of these proteins are involved in cytoskeletal organization and mitochondrial function. Transcriptome and proteome analyses of NSCs from PD revealed changes in the expression of genes and proteins involved in metabolism, transcriptional activity and cytoskeletal organization. Our results not only confirm pathological hallmarks of PD (e.g. impaired mitochondrial function), but also suggest that NSCs may transit into a primed-quiescent state, that is in an “alert” non-proliferative phase in PD.

overall_design: From post-mortem human SVZ of control and Parkinson disease donors we isolated CD271+ NSCs and Cd11b+ microglia by MACS and the whole SVZ to generate RNA sequencing libraries using Celseq2 method. We aimed for low coverage sequencing (~2 million mapped to the coding regions) per sample to investigate the gross changes in the transcriptome. Libraries (rpi small primer) were sequenced in 3 runs, 2 on an Illumina NextSeq500 using 75-bp paired-end sequencing at the Utrecht Seuqencing center (USEQ) and the third on a HiSeq4000 using 150-bp paired-end sequencing at Genomescan. All the samples were mapped in a single run to an average depth of ~10 million reads per sample. Reads were mapped to the latest human coding transcriptome using bwa, normalized and analyzed using the standard DESEQ2 package.

first: Vanessa

last: Donega

first: Saskia

last: Burm

first: Miriam

middle: E

last: van Strien

first: Emma

last: van Bodegraven

first: Iryna

last: Paliukhovich

first: Hanneke

last: Geut

first: Wilma

last: van de Berg

first: Ka

first: August

last: Smit

last: Basak

first: Elly

last: Hol


title: Effect of BRD4 inhibition in leukemic stem cells (Microarray)

city: Birmingham

first: Rui

last: Lu

state: AL

address: 1824 6th Ave S

institute: Univ of Alabama at Birmingham

summary:
DNA Methyltransferase 3A (DNMT3A) is frequently mutated in various hematopoietic malignancies. We report that DNMT3A mutational ‘hotspot’ at Arg882 (i.e., DNMT3A-R882H) cooperates with constitutively activated RAS in transforming murine hematopoietic stem/progenitor cells (HSPCs) ex vivo and inducing acute leukemias in vivo. Mechanistically, DNMT3A-R882H induced DNA hypomethylation facilitates gene enhancer/promoter activation.
In this dataset, we provided microarray data showing effect of BRD4 inhibitor I-BET151 on gene expression in leukemic stem cells transformed by DNMT3A R882H and NRAS G12D.

overall_design: Gene expression data were generated using RH-RAS leukemia stem cell lines (transformed by DNMT3A R882H and NRAS G12D) treated with 100 nM I-BET-151 (a Brd4-specific small-molecule inhibitor) for 24 hours.

first: Gang

middle: G

last: Wang


title: Paternal overdiet drives intergenerational transmission of metabolic disorders through sperm epigenetic alteration [RNA-Seq]

first: Jing-Jing

last: Zhang

summary: We used a mouse model of paternal famine to simulate famine, our data show that paternal famine increases the susceptibility to metabolic disease in offspring through gametic epigenetic alterations.

overall_design: Livers mRNA profiles of 8 week old control male F1 and FR male F1 mice were generated by deep sequencing

first: Ying-Ying

last: Gao

first: Yi-Liang

last: Miao


title: Evidence supporting a dominant negative mechanism for DNMT3A hotspot mutation-mediated leukemic cell transformation

type: Methylation profiling by genome tiling array

summary: Mutation of DNA methyltransferase 3A at arginine 882 (DNMT3AR882mut) is prevalent in various hematological cancers. DNMT3AR882mut was recently shown to carry partially defective, dominant-negative or gain-of-function activities under different in vitro contexts. However, the causal roles for such a multifaceted effect of DNMT3AR882mut on leukemogenesis remain undefined. Here we report TF-1 leukemia cells as a robust system for modeling DNMT3AR882mut-dependent cell transformation phenotypes and for performing structure-function relationship studies of DNMT3AR882mut. We show that expression of DNMT3AR882mut and not its wildtype counterpart promotes TF-1 cell transformation and induces CpG hypomethylation predominantly at enhancers. Such effect by DNMT3AR882mut is dose-dependent, acts synergistically with that of IDH1 mutation, and resembles what was seen in human leukemia patients with DNMT3AR882mut. Both transformation- and hypomethylation-inducing capacities of DNMT3AR882mut rely on a motif involved in heterodimerization whereas its various chromatin-binding and enzymatic domains were dispensable. We also show bromodomain inhibition as a therapeutic means for treatment of murine leukemia carrying DNMT3AR882mut. Collectively, this study describes a useful model system for studying DNMT3AR882mut and supports a requirement for the dominant-negative effect of DNMT3AR882mut during leukemogenesis.

overall_design: TF-1 cells were stably expressed with either wild-type DNMT3A or its hematopoietic cancer-associated mutants. Genomic DNA was extracted and analyzed by the Illumina 450k Methylation array. Part of the data were submitted previously in GSE93727, including empty vector (GSM2461097, GSM2461098, GSM2461099, GSM2461100, and GSM2461101) and wild-type DNMT3A (GSM2461105, GSM2461106, and GSM2461107).

first: Greg


title: Log-term effects of proton irradiation on DNA methylation and metabolomic pathways in the hippocampus and heart.

city: Portland

first: Soren

last: Impey

state: OR

address: 3181 SW Sam Jackson Park Rd, LBRB Rm 709

department: Dept of Pediatric

institute: OHSU

summary: The goal of this experiment was to identify methylation and metabolomic pathways the respond to proton irradiation and examine whether these two pathways coregulate biological pathways.

overall_design: DNA was isolated 20 weeks after 0 Gy (sham) or 1 Gy Proton irradiation.  1 ug of hippocamal or left ventricular DNA from 5 mice in each treatment group was pooled, resulting in two pooled biological replicates for each treatment condition. Pooled DNA was subjected to 5hmC DIP and Illumina TrueSeq libraries were constructed.

first: Jacob

last: Raber

first: Carl

last: Pelz


title: Gene expression analysis of Mulberry root after inoculation with Ralstonia solanacearum.

city: Guangzhou

first: fanwei

last: dai

state: Guangdong

address: The Sericulture and Agri-Food Research Institute, Guangdong Academy of Agricultural Sciences

summary: Bacterial wilt, caused by the soil-borne bacterium Ralstonia solanacearum, is a lethal disease of mulberry, but the molecular mechanisms of the host resistance responses to R. solanacearum remain unclear. In order to better understand molecular resistance mechanisms to R. solanacearum in mulberry, we set out to define the changes in gene expression of resistance and susceptible mulberry cultivars after inoculation with R. solanacearum. Susceptible cultivar YSD10, resistance cultivar KQ10 and YS283 were inoculation with R. solanacearum, mulberry root samples were collected at 1 dpi and non-treated control in all cultivars. Then we performed RNA-Seq analyses on all mulberry root samples using Illumina HiSeq 2000.

overall_design: Mulberry root mRNA profiles of resistance and susceptible cultivar after inoculation with R. solanacearum were generated by deep sequencing using Illumina HiSeq 2000.

first: Fanwei

last: Dai

first: Cuiming

last: Tang

first: Zhenjiang


title: Transcriptome analysis upon C6orf203 silencing

city: Warsaw

first: Sylwia

last: Czarnomska

state: Mazowieckie

address: Pawinskiego 5a

country: Poland

institute: Institute of Biochemistry and Biophysics Polish Academy of Sciences

summary: In our studies we were searching for the new factors engaged in mitochondrial nucleic acids metabolism under stress conditions in humans. Quantitative proteomic approach revealed C6orf203 protein as a potential new factor engaged in response to perturbed mitochondrial gene expression. We showed that C6orf203 is a mitochondrial RNA binding protein which is able to rescue diminished mitochondrial transcription in stress conditions.

overall_design: The dataset corresponds to RNAseq studies and comprises experiment performed in triplicate. The aim of this study was to examine the influence of C6orf203 silencing on mitochondrial transcriptome. To this end we engineered two stable cell lines with the use of human 293 Flp-In T-Rex cells as parental. First cell line inducible expressed miRNAs silencing endogenous copy of C6orf203 gene while second one expressed additionally transgenic version of FLAG-tagged C6orf203 which contained silent mutations causing insensitivity to miRNA. We also analyzed RNA isolated from parental 293 Flp-In T-Rex cells. RNAseq libraries were prepared with the use of strand-specific library preparation procedures. RNAs were random fragmented and reverse transcribed using random oligomers as primers (dUTP-based protocol, see PMID: 29590189, PMID: 22609201; this pipeline enables analysis of RNAs (> ~100 nucleotides)). RNA was isolated from unfractionated cells using TRI-Reagent. Before preparation of the libraries total RNA was subjected to depletion of nuclear-encoded rRNAs (Ribo-Zero rRNA Removal Kit (Human/Mouse/Rat), Epicenter). Libraries were sequenced with the help of Illumina sequencing platform.

first: Anna

middle: V

last: Kotrys

first: Roman

last: Szczesny


title: Antagonizing increased miR-135a levels at the chronic stage of experimental TLE reduces spontaneous recurrent seizures

first: Ronald

middle: Jeroen

last: Pasterkamp

state: Utrecht

address: Universiteitsweg 100

department: Translational Neuroscience

institute: UMC Utrecht

summary: Increased miR-135a levels are observed in human patients with temporal lobe Epilepsy (TLE) and in experimental animal models. Upon targeting the increased miR-135a levels in vivo using antagomirs in kainic acid induced status epilepticus mouse model of TLE, we observed a strong reduction of spontaneous recurrent seizures. To understand this further and to find target mRNAs that potentially mediate the seizure suppressive function of miR-135a, we performed immunoprecipitation using biotin tagged miRNA mimics, followed by RNAsequencing (RNAseq). We found several novel neuronal targets of miRNA-135a and identified Mef2a as a key target in this study. Here we report the total RNAseq data.

overall_design: N2A cells were transfected with biotin tagged miRNA mimics for miR-135a and negative control and immunoprecipitations were performed. N = 3 replicates of IP and input samples for each condition were generated and sequenced on illumina platform for total RNA for identification of novel targets of miR-135a.

first: Vamshidhar

last: Vangoor

first: Giuliano

last: Giuliani

first: Roel

last: Schaapveld

first: R


title: microRNA profiling in different stages of rheumatoid arthritis

city: Zacatecas

first: María

middle: Fernanda

last: Romo García

state: Zacatecas

address: Alameda

country: Mexico

institute: IMSS

summary: Determine the comprehensive miRNA expression profile in RNA extracted from whole blood samples from healthy controls (CTRL), individuals positive to  CCP antibodies >25UI/ml (CCP+), early rheumatoid arthritis (ERA) and established rheumatoid arthritis (CRA) according to the ACR/EULAR 2010 classification criteria. Several miRNAs were overexpressed on ERA patients. We  selected 5 miRNAs (miR-361-5p, miR-23a-3p, miR-223-3p, miR-4634 and miR-128-3p)  for its quantification on a bigger group of subjects by RT-qPCR and the results showed good concordance with microarray expression data.

overall_design: A convenience sampling for the study was made with Individuals recruited in rheumatology clinics between January 2013 and November 2017. We collected 4 to 5 ml of whole blood in EDTA tubes plus 1ml of RNA later  and homogenized immediately to prevent changes in their transcriptional profiles. Samples were stored at -70°C until processed for RNA extraction. The groups were divided according to classification criteria by ACR/EULAR 2010 by certified clinical rheumatologists.  For the stratification of early and established RA the main criteria was the symptoms persistence for less or more than one year respectively. Healthy controls were considered as individuals with no relevant medical history, normal results on the COPCORD questionnaire, CCP levels <25U/ml and a normal ESR. The criteria for CCP+ group was CCP values >25U/ml and no RA clinical symptoms. A sample of whole blood for each subject was mixed with Tri-Pure reagent (ROCHE, USA) and centrifuged at 13,000xg for 15 minutes at 4°C. The aqueous phase was then transferred to a pre-filter column of Absolutely-miRNA RNA kit (Agilent) following the manufacturer’s instructions. 100ng of total rna were used for microarray analysis.

middle: F

last: Romo-García

first: Yadira

last: Bastian

first: Mátín

last: Zapata-Zuñiga

first: Noé

last: Macías-Segura

first: Edgar

last: Lara-Ramírez

first: Julio

last: Fernández-Ruíz

first: Antonio

last: Berlanga-Taylor

first: Roberto

last: González-Amaro

first: José

middle: A

last: Enciso-Moreno

last: Castañeda-Delgado


title: Characterization of Streptococcus pneumoniae phage-like element SpnCI reveals an enhanced virulent phenotype in the acute invertebrate infection model Galleria mellonella

city: Oklahoma City

first: William

middle: Michael

last: McShan

state: OK

address: 1110 N. Stonewall Ave.

department: Pharmaceutical Sciences

institute: University of Oklahoma Health Sciences Center

summary: Phage-like elements are found in a multitude of streptococcal species, including pneumococcal strain Hungary19A-6 (SpnCI). The aim of our research was to investigate the role of phage-like element SpnCI in enhanced virulence and phenotypic modulation within Streptococcus pneumoniae. SpnCI was found to significantly enhance virulence within the invertebrate infection model Galleria mellonella. Infections with SpnCI led to a lower mean health score (1.6) and survival percentage (20%) compared to SpnCI null TIGR4 infections (3.85 mean health score and 50% survival). SpnCI remained integrated throughout growth, conferring greater sensitivity to UV irradiation. Change in transcriptional patterns occurred, including downregulation of operons involved with cell surface modelling in the SpnCI containing strain of TIGR4. Kanamycin-tagged SpnCI strain in Hungary19A-6 was inducible and isolated from lysate along with both annotated prophages. No phages were identified by PCR nor electron microscopy (EM) following induction of TIGR4 SpnCI∆strA suggesting helper-phage dependence for dissemination. EM of lysate showed typical siphoviridae morphology with an average capsid size of 60 nm. Two of sixty capsids were found to be smaller, suggesting SpnCI disseminates using a similar mechanism described for Staphylococcus aureus phage-like element SaPI. SpnCI from lysate  infected capsule null strain T4R but was incapable of infecting the encapsulated TIGR4 strain suggesting that capsule impedes phage infection. Our work demonstrates that SpnCI can modulate virulence, UV susceptibility, alter transcriptional patterns, and furthermore, can disseminate via infection within pneumococcus. Further research is necessary to elucidate how SpnCI modulates virulence and what genes are responsible for the enhanced virulence phenotype.

overall_design: Comparison of two strains of Streptococcus pneumoniae that differ only by the presence or absence of phage-like chromosomal island SpnCI

first: Kimberly

last: McCullor


title: Cistromic re-programming by truncating GATA3 mutations promotes mesenchymal transformation in vitro, but not mammary tumour formation in mice [ChIP-seq]

city: Amsterdam

first: Lisette

last: Cornelissen

address: Plesmanlaan 121

institute: The Netherlands Cancer Institute

summary: Heterozygous mutations in the transcription factor GATA3 are identified in 10-15% of all breast cancer cases. Most of these are protein-truncating mutations, concentrated within or downstream of the second GATA-type zinc-finger domain. Here, we investigated the functional consequences of expression of two truncated GATA3 mutants, in vitro in breast cancer cell lines and in vivo in the mouse mammary gland. We found that the truncated GATA3 mutants display altered DNA binding activity caused by preferred tethering through FOXA1. In addition, expression of the truncated GATA3 mutants reduces E-cadherin expression and promotes anchorage-independent growth in vitro. However, we could not identify any effects of truncated GATA3 expression on mammary gland development or mammary tumor formation in mice. Together, our results demonstrate that both truncated GATA3 mutants promote cistromic re-programming of GATA3 in vitro, but these mutants are not sufficient to induce tumor formation in mice.

overall_design: Binding of HA-tagged wild-type GATA3 (HA_GATA3_wt) and two truncated variants (HA_GATA3_TR1 and HA_GATA3_TR2) exogenously introduced in T47D cells profiled by ChIP-seq (Chromatin Immunoprecipitation followed by deep sequencing).

first: Roebi

last: de Bruijn

first: Linda

last: Henneman

first: Yongsoo

last: Kim

first: Wilbert

last: Zwart

first: Jos

last: Jonkers


title: Cistromic re-programming by truncating GATA3 mutations promotes mesenchymal transformation in vitro, but not mammary tumour formation in mice [RNA-seq]

overall_design: RNAseq data of T47D cells expressing HA-tagged wild-type GATA3 (HA_GATA3_wt) or one of two truncated variants (HA_GATA3_TR1 and HA_GATA3_TR2).


title: Cistromic re-programming by truncating GATA3 mutations promotes mesenchymal transformation in vitro, but not mammary tumour formation in mice

overall_design: Refer to individual Series


title: ZEB1 insufficiency causes corneal endothelial cell state transition and altered cellular processing

city: Los Angeles

first: Anthony

middle: J.

last: Aldave

address: 200 Stein Plaza DSERC 3-143

department: Ophthalmology

institute: Stein Eye Institute, UCLA

summary: The zinc finger e-box binding homeobox 1 (ZEB1) transcription factor is a master regulator of the epithelial to mesenchymal transition (EMT), and of the reverse mesenchymal to epithelial transition (MET) processes. ZEB1 plays an integral role in mediating cell state transitions during cell lineage specification, wound healing and disease. EMT/MET are characterized by distinct changes in molecular and cellular phenotype that are generally context-independent. Posterior polymorphous corneal dystrophy (PPCD), associated with ZEB1 insufficiency, provides a new biological context in which to understand and evaluate the classic EMT/MET paradigm. PPCD is characterized by a cadherin-switch and transition to an epithelial-like transcriptomic and cellular phenotype, which we study in a cell-based model of PPCD generated using CRISPR-Cas9-mediated ZEB1 knockout in corneal endothelial cells (CEnCs). Transcriptomic and functional studies support the hypothesis that CEnC undergo an MET-like transition in PPCD, termed endothelial to epithelial transition (EnET), and lead to the conclusion that EnET may be considered a corollary to the classic EMT/MET paradigm.

overall_design: Three independent clones for each genotype were generated. ZEB1+/+ and ZEB1+/- (generated using CRISPR-Cas9 gene editing) parental lines were initially generated, then transduced with lentivirus containing ZEB1 cDNA to generate ZEB1 transgenic lines of the parental lines.

first: Ricardo

last: Frausto

first: Vinay

last: Swamy

first: Marco

last: Morselli

first: Matteo

last: Pellegrini


title: Expression of deregulated MYC with activated NeuNT in mammary gland developed mammary tumors with  molecular heterogeneity

first: Tyler

last: Risom

state: Oregon

address: 2730 SW Moody Ave

department: Molecular Medical Genetics

institute: Oregon Health & Science University

summary: The goal of this study is to investigate the role of deregulated c-MYC in cooperation with activated NeuNT (mutated rat HER2) in mammary tumor molecular heterogeneity.  We monitored female mice through two cycles of pregnancy/lactation in order to activate Blg-Cre expression in mammary gland after the second cycle.  MYC-NeuNT mice develop tumors between 4 and 12 weeks post Blg-Cre activation, H&E images from these tumors showed histologic heterogeneity.  NeuNT mice developed tumors between 28 to 44 weeks post Blg-Cre activation that also showed histologic heterogeneity.

overall_design: ROSA-LSL-MYC mice were crossed with LSL-NeuNT and Blg-Cre mice to get mice that express both MYC and NeuNT in response to Cre-mediated recombination in the mammary gland. We monitored the female mice through two cycles of pregnancy/lactation then activated and waited for tumors to reach 20mm in diameter (end point).  We collected 14 tumors from MYC-NeuNT mice,  4 tumors from NeuNT mice , and 3 normal mammary gland samples from control Myc mice without Blg-Cre.  One piece of tissue from each sample was used to extact total RNA with Trizol according to manufactuer's protocol.

first: Rosalie

last: Sears

first: Xiaoyan

last: Wang


title: Primary peri-aorta adipose tissue stromal vascular fraction single cell RNA sequencing

city: London

first: Wenduo

last: Gu

state: Select One

address: James Black Centre, 125 Coldharbour Lane

institute: King's College London

summary: Peri-aorta adipose tissue were digested with collagense I (2mg/ml) at 37 C for 30 mins

overall_design: digested cells were sorted for CD144-/CD45-/CD29+/Sca1+ cells and subjected for scRNAseq

first: Witold

last: Nowak

first: Yao

last: Xie

first: Qingbo

last: Xu


title: Spatial chromosome folding and active transcription drive DNA fragility and formation of oncogenic MLL translocations

city: Mainz

first: Vassilis

last: Roukos

address: Ackermannweg 4

institute: Institute of Molecular Biology gGmbH

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


title: Spatial chromosome folding and active transcription drive DNA fragility and formation of oncogenic MLL translocations [BLISS-Seq]

summary: How spatial chromosome organization influences genome integrity is still poorly understood. Here we show that DNA double-strand breaks (DSBs) mediated by topoisomerase 2 (TOP2) activities, are enriched at chromatin loop anchors with high transcriptional activity. Recurrent DSBs occur at CTCF/cohesin bound sites at the bases of chromatin loops and their frequency positively correlates with transcriptional output and directionality. The physiological relevance of this preferential positioning is indicated by the finding that genes recurrently translocating to drive leukemias, are highly transcribed and are enriched at loop anchors. These genes accumulate DSBs at recurrent hot spots that give rise to chromosomal fusions relying on the activity of both TOP2 isoforms and on transcriptional elongation. We propose that transcription and 3D chromosome folding jointly pose a threat to genomic stability, and are key contributors to the occurrence of genome rearrangements that drive cancer.

overall_design: Genome wide profiling of DNA double-strand breaks upon etoposide using Breaks Labeling In Situ and Sequencing (BLISS) in hematopoietic cell lines TK6 and K562 and primary CD34+ bone marrow cells.


city: Balice

first: Kacper

last: Zukowski

address: Krakowska 1 Street

institute: National Research Institute of Animal Production

summary: In Poland, conducted for years porcine breeding works focused on improving meat content in the carcass without undertaken to accomplish the more effectiveness of fattening indicators that impact on feed efficiency. At present, feeding and feed conversion became important factors that are especially evident in the countries where the production of fattening pigs is conducted in large farms. In the present study, was attempted to indicate pituitary candidate genes depending on feed conversion ratio (FCR) in native Polish pig breed, Złotnicka White. The whole pituitary transcriptome was sequenced using next-generation sequencing technology. The obtained results show the differences in gene expression for pathways associated with hormonal regulation and also with Notch and Wnt signaling. Moreover, it was observed that worse FCR in Złotnicka pigs was associated with a higher fat level in a carcass and a significant higher level of prolactin expression in the pituitary.

overall_design: The pituitary hormonal changes related to feed efficiency in pigs experiment was supported by BIOSTRATEG2/297267/14/NCBR/2016

first: K

last: Piórkowska

last: Żukowski

first: M

last: Tyra

last: Ropka-Molik


title: Conjoint analysis of transcriptional and protein changes in heterosis of hybrid yellow catfish Huangyou-1 uncovers key roles for miRNAs

city: Nanjing

first: Shaowu

last: Yin

state: jiangsu

address: College of Life Sciences, Nanjing Normal University, 1 Wenyuan Road,  210023, China.

institute: Nanjing Normal University

sample_organism: Tachysurus fulvidraco x Tachysurus vachelli


title: Spatial chromosome folding and active transcription drive DNA fragility and formation of oncogenic MLL translocations [RNA-Seq]

overall_design: Nuclear RNA profiling in lymphoblastoid TK6 cell line


title: Gastric carcinoma patients and healthy subjects

city: shanghai

first: Mingjie

address: 197 Ruijin Er Road

institute: Ruijin Hospital,Shanghai Jiaotong University,School of Medicine

summary: Gastric cancer is one of the most aggressive cancers and is the second leading cause of cancer death worldwide. Approximately 40% of global gastric cancer cases occur in China, with peritoneal metastasis being the prevalent form of recurrence and metastasis in advanced disease (>50%). Currently, there are limited clinical approaches for predicting and treatment of peritoneal metastasis, resulting in a 6- month average survival time. By comprehensive genome analysis will uncover the pathogenesis of peritoneal metastasis. Here we describe a comprehensive whole-genome and transcriptome sequencing analysis of one advanced gastric cancer case, including non-cancerous mucosa, primary cancer and matched peritoneal metastatic cancer. The peripheral blood is used as normal control.

first: Yingyan

last: Yu

first: Jinyan

last: Huang


title: Conjoint analysis of transcriptional and protein changes in heterosis of hybrid yellow catfish Huangyou-1 uncovers key roles for miRNAs [RNA-Seq]

summary: In this study, we used next-generation sequencing technologies and tandem mass tags to characterize mRNA-seq, miRNA-seq and proteomic of Pelteobagrus fulvidraco, P. vachelli and hybrid yellow catfish Huangyou-1 (P. fulvidraco female×P. vachelli male) livers and in doing so, offer deeper insight into the transcriptional and protein changes in heterosis uncovers key roles for miRNAs.

platform_organism: Tachysurus fulvidraco x Tachysurus vachelli

overall_design: RNA-sequencing analysis was performed on an Illumina Hiseq 2500 (LC Sciences, USA) following the vendor's recommended protocol

first: Guosong

last: Zhang


title: Conjoint analysis of transcriptional and protein changes in heterosis of hybrid yellow catfish Huangyou-1 uncovers key roles for miRNAs [miRNA-Seq]

summary: In this study, we used next-generation sequencing technologies and tandem mass tags to characterize mRNA-seq, miRNA-seq and proteomic of Pelteobagrus fulvidraco, P. vachelli and hybrid yellow catfish Huangyou-1 (P. fulvidraco female ×P. vachelli male) livers and in doing so, offer deeper insight into the transcriptional and protein changes in heterosis uncovers key roles for miRNAs.

overall_design: miRNA-sequencing analysis was performed on an Illumina Hiseq 2500 (LC Sciences, USA) following the vendor's recommended protocol


title: Next Generation Sequencing to Study LUX-affected genes.

city: Baltimore

first: HUA

last: LU

state: MD

address: 1000 Hilltop Circle

institute: University of Maryland Baltimore County

summary:
Purpose: The goals of this study are to compare RNA-seq profiles of Col-0, acd6-1, Iux-1, and acd6-1lux-1 to identify genes affected by LUX.
Methods: Total RNA was extracted from 25-d old Col-0, lux-1, acd6-1, or acd6-1lux-1 plants collected at ZT1 or ZT13. Triplicate biological samples were used for most genotypes at each time point, except acd6-1 and acd6-1lux-1 at ZT13, which had duplicate samples. 0.5 ug RNA per replicate was used to generate cDNA libraries using Illumina TruSeq RNA sample preparation kit (catalog no. RS-122-2001). The samples were multiplexed and sequenced using the Illumina HiSeq sequencing platform in Genomics Resources Core Facility at Weill Cornell Medical College. Sequencing was conducted with a standard run of 51 cycles and single reads. At least 150 million reads per lane were obtained for sequencing. qRT–PCR validation was performed using TaqMan and SYBR Green assays for some selected genes.
Results: We found that over 1500 genes are affected by lux-1 based on the RNAseq analysis. GO analysis revealed that LUX-affected genes are enchriched in response to abiotic and biotic stimuli. In particular, genes involved in basal defense, salicyclic acid signaling, and jasmonic acid signaling are affected by lux-1. We also found LUX regulation of the clock genes, including core clock components and  those acting in the output pathways.
Conclusions: The RNAseq analysis support a role of LUX in regulation of the circadian clock and plant defense.

overall_design: 25-d old Col-0, lux-1, acd6-1, or acd6-1lux-1 plants  were collected at ZT1 or ZT13 for RNA extraction followed by cDNA library preparation and high throughput.

first: Hua

last: Lu


title: Gene expression comparison between human embryonic stem cell lines with a normal karyotype and after acquiring a duplication of 20q11.21

city: Leuven

first: Rekin's

last: Janky

address: Herestraat 49 Box 816

department: Nucleomics Core

country: Belgium

institute: VIB

summary: Since the introduction of high-resolution molecular cytogenetic methods for the screening for chromosomal abnormalities in human embryonic stem cells (hESC), numerous laboratories worldwide have reported the gain of 20q11.21 as a recurrent mutation. Recently, in a large joint study, the International Stem Cell Initiative (ISCI) screened 125 hESC lines worldwide and found this aberration in over 20% of the lines. In our laboratory, we found an increased copy number of 20q11.21 in four hESC lines, VUB01, VUB02, VUB03 and VUB07. We first carried out Affymetrix HG-U133-Plus2 gene-expression microarray analysis of pairs of the mutant and wild type sublines. We identified a small group of very significantly deregulated genes, but none of them were located in the region of duplication. Validation of these results by qRT-PCR revealed that CHCHD2 and TRPC6 were most consistently deregulated.

overall_design: Gene expression was compared between four karyotypically normal hESC lines: VUB01, VUB02, VUB03 and VUB07 and their  subline containing a duplication of 20q11.21.

first: Ha

last: Nguyen

first: Mieke

last: Geens

first: Afroditi

last: Mertzanidou

first: Kurt

last: Jacobs

first: Claudia

last: Spits


title: Gene expression profiling of Dermal Papilla (DP) cells isolated from wild type (WT) and DP-specific Smo gain-of-function (Smo*) mutant mice during both telogen (at P20) and anagen (at P28).

city: Safed

first: David

last: Enshell-Seijffers

address: 8 Henrietta Szold

department: The Azrieli Faculty of Medicine

country: Israel

institute: Bar Ilan University

summary: Gene expression analysis revealed that the DP transcriptome is  altered in the Smo* mutant. At P28 the expression of 2226 genes was significantly altered. The expression of 473 genes was altered in the Smo* mutant during telogen (P20).

overall_design: 3 samples of wt at telogen (p20), 3 samples of Smo* mutant at telogen (p20), 3 samples of wt at anagen (p28), 3 samples of Smo* mutant at anagen (p28)

first: Efrat

last: Laron


title: Array comparative genomic hybridization (CGH) analysis of ameloblastoma tumor

status: Public on Jun 11 2019

city: Nagoya

first: Akinobu

last: Ota

state: Aichi

address: 1-1 Yazakokarimata

department: Food and Nutritional Environment

country: Japan

institute: Kinjo Gakuin University

summary: To investigate the minimal genomic alterations in ameloblastoma, we have employed high-resolution CGH as a discovery platform to identify somatic genomic gains and losses in ameloblastoma tumors.

overall_design: 8 ameloblastoma-derived DNA and patients-matched DNA were hybridised to the SurePrint G3 human 400k CGH microarray.

first: Sayuri

last: Kondo

first: Sivasundaram

last: Karnan


title: Gene expression profiling and aCGH of ameloblastoma tumor

type:
Expression profiling by array
Genome variation profiling by array


title: Evolution of Escherichia coli to 42 °C and Subsequent Genetic Engineering Reveals Adaptive Mechanisms and Novel Mutations

city: San Diego

first: Anand

last: Sastry

state: CA

address: 9500 Gilman Dr

department: Bioengineering

institute: University of California, San Diego

summary: mRNA sequencing was performed on E. coli evolved at 42C on M9 Minimal Media with Glucose

sample_organism: Escherichia coli str. K-12 substr. MG1655

overall_design: Growth of evolved E. coli was characterized under the same conditions as the evolution and compared to the wild type parent strain

first: Troy

last: Sandberg

first: Margit

last: Pedersen

first: Ryan

last: LaCroix

first: Ali

last: Ebrahim

first: Mads

last: Bonde

first: Markus

last: Herrgard

first: Bernhard

middle: O

last: Palsson

first: Morten

last: Sommer

first: Adam

middle: M

last: Feist


title: Single cell RNA sequencing of in vitro differentiation NMP protocols

city: Cambridge

first: Alfonso

last: Martinez Arias

address: Downing

department: Genetics

institute: University of Cambridge

summary: The mammalian embryos Caudal Lateral Epiblast (CLE) harbours bipotent progenitors, called Neural Mesodermal Progenitors (NMPs), that contribute to the spinal cord and the paraxial mesoderm throughout axial elongation. Here we performed a single cell analysis of different in vitro NMPs populations produced either from embryonic stem cells (ESCs) or epiblast stem cells (EpiSCs) and compared them to E8.25 CLE mouse embryos. In our analysis of this region our findings challenge the notion that NMPs can be defined by the exclusive coexpression of Sox2 and T at mRNA level. We analyse the in vitro NMP-like populations using a purpose-built Support Vector Machine (SVM) based on the embryo CLE and use it as a classification model to compare the in vivo and in vitro populations. Our results show that NMP differentiation from ESCs, leads to heterogeneous progenitor populations with few NMP-like cells, as defined by the SVM algorithm, whereas starting with EpiSCs, yields a high proportion of cells with the embryo NMP signature. We find that the population from which the Epi-NMPs are derived in culture contains a node-like population, which leads to suggest that this population probably maintains the expression of T in vitro and thereby a source of NMPs. In conclusion, differentiation of EpiSCs into NMPs reproduces events in vivo and suggests a sequence of events for the emergence of the NMPs population.

overall_design: We performed single cell RNA sequencing (RNA-seq) for different in vitro NMPs populations produced either from ESCs or EpiSCs: ES-NMP, Epi-CE as well as of the T expressing cells from the Epi-CE population (Epi-CE-T) and Epi-NMP. 10x Genomics single cell transcriptomic service was used to sequence our 4 samples.

first: Shlomit

last: Edri

first: Penelope

last: Hayward


title: The nucleosome acidic patch directly interacts with subunits of the Paf1 and FACT complexes and controls chromatin architecture in vivo

city: Pittsburgh

first: Karen

middle: M.

last: Arndt

state: Pennsylvania

address: 4249 Fifth Avenue

institute: University of Pittsburgh

summary: We employed MNase-seq and ChIP-seq to determine irregularities in chromatin architecture in mutants of the nucleosome acidic patch. Indeed, the acidic patch mutant showed defects in nucleosome positioning and occupancy at genes with high expression and H2B K123ub levels, linking the acidic patch to transcription-dependent chromatin changes. Our results emphasize the importance of the nucleosome core as a hub for proteins that regulate chromatin during transcription.

overall_design: MNase-seq and ChIP-seq (histone H3) in biological duplicate samples of an H2A E57A mutant compared to biological duplicate samples of a wild-type control.

first: Christine

last: Cucinotta

first: A

last: Hildreth

first: Brendan

last: McShane

first: Margaret

middle: K

last: Shirra


title: Molecular consequences of fetal alcohol exposure on amniotic exosomal miRNAs with functional implications for stem cell potency and differentiation

first: Yong

last: Kim

address: 10833 Le Conte Ave, 73-022 CHS

institute: UCLA

summary: Alcohol (ethanol, EtOH) consumption during pregnancy can result in fetal alcohol spectrum disorders (FASDs), which are characterized by prenatal and postnatal growth restriction and craniofacial dysmorphology. The specific mechanisms by which alcohol mediates these injuries have yet to be determined. Cell-derived extracellular vesicles, including exosomes and microvesicles containing several species of RNAs (exRNAs), have recently emerged as a mechanism of cell-to-cell communication. However, EtOH’s effects on the biogenesis and function of non-coding exRNAs during fetal development have not been explored. Therefore, we studied the effects of maternal EtOH exposure on the composition of exRNAs in the amniotic fluid (AF) using a rat fetal alcohol exposure (FAE) model. Timed pregnant Sprague Dawley rats received 0 or 2.5 g/kg of 20% EtOH by oral gavage on embryonic days 5, 8, 10, 12 and 15. Through RNA-Seq analysis we identified and verified AF exosomal miRNAs with differential expression levels specifically associated with maternal EtOH exposure.

overall_design: RNA-seq analysis of amniotic exosomal miRNAs from rat fetal alcohol exposure model


title: The Paf1 complex broadly impacts the transcriptome of Saccharomyces cerevisiae

type: Expression profiling by genome tiling array

summary: The polymerase associated factor 1 complex (Paf1C) is a multifunctional epigenetic regulator of RNA polymerase II (Pol II) transcription. Paf1C controls gene expression by stimulating the placement of co-transcriptional histone modifications, influencing nucleosome occupancy in coding regions, facilitating transcription termination, and regulating nuclear export of RNAs. In this study, we investigate the extent to which these functions of Paf1C combine to influence the Saccharomyces cerevisiae transcriptome. Using conditions that enrich for unstable transcripts, we show that deletion of PAF1 affects all classes of Pol II-transcribed RNAs including multiple classes of noncoding transcripts. Gene ontology analysis revealed that mRNAs encoding genes involved in iron and phosphate homeostasis were differentially affected by deletion of PAF1. We further investigated these two groups of mRNAs with the goal of identifying overarching mechanisms of up and down-regulation in cells lacking Paf1. Our results indicate that only a subset of the observed changes result from loss of Paf1C-promoted histone modifications. We also found that transcription of the FET4 gene is differentially regulated by Paf1 and an upstream CUT. Together these data highlight the complexity of the epigenetic regulation of Pol II transcription imposed by Paf1C and identify a role for Paf1C in promoting CUT transcription.

overall_design: Four yeast strains were tested and arrays were performed in triplicate

first: Mitchell

last: Ellison

first: Alex

middle: R

last: Lederer

first: Marcie

middle: H

last: Warner

first: Travis

last: Mavrich

first: Lawrence

last: Heisler

first: Marinella

last: Gebbia

first: Corey

last: Nislow

first: Miler

middle: T

last: Lee


title: CD10 expression in human adventitial cells

city: Nanjing City

first: Lijun

last: Ding

address: 321#，Zhongshan Road

department: Department of Obstetrics and Gynecology

institute: the Affiliated Drum Tower Hospital of Nanjing University Medical School

summary: The tunica adventitia ensheaths arteries and veins and contains presumptive mesenchymal stem cells (MSCs) involved in vascular remodeling. We show here that a subset of human adventitial cells expresses the CD10/CALLA cell surface metalloprotease. Sorted CD10+ adventitial cells developed promptly in culture into MSCs, exhibiting higher proliferation, clonogenic and osteogenic potentials than CD10- counterparts. CD10+ adventitial cells increased expression of the cell cycle protein CCND2 via ERK1/2 and prompted NELL1 expression via NF-κB. CD10 expression was upregulated in CD10+ adventitial cells through neural secreted protein sonic hedgehog-mediated Gli1 signaling. These results suggest that CD10 expression, which marks rapidly dividing cells in other normal and malignant cell lineages, plays a role in MSC homeostasis in human tissues.

overall_design: two samples, sorted CD10+ and CD10- adventitial cells

first: Bianca

last: Vezzani

first: Nusrat

last: Khan

first: Jing

last: Su

first: Lu

last: Xu

first: Guijun

last: Yan

last: Liu

first: Ruotian

last: Li

first: Zhongzhou

last: Yang

first: Anushri

last: Gour

first: Zhenyu

last: Diao

first: Yali

last: Hu

first: Aaron

last: James

first: Haixiang

last: Sun

first: Bruno

last: Péault


title: Genome-wide analysis identifies NR4A1 as a key mediator of T cell dysfunction (Microarray)

status: Public on Jun 10 2019

city: Seattle

first: Raymond

last: Doty

state: WA

department: Division of Hematology

institute: University of Washington

summary: T cells become dysfunctional when they encounter self antigens or are exposed to chronic infection or to the tumour microenvironment1. The function of T cells is tightly regulated by a combinational co-stimulatory signal, and dominance of negative co-stimulation results in T cell dysfunction2. However, the molecular mechanisms that underlie this dysfunction remain unclear. Here, using an in vitro T cell tolerance induction system in mice, we characterize genome-wide epigenetic and gene expression features in tolerant T cells, and show that they are distinct from effector and regulatory T cells. Notably, the transcription factor NR4A1 is stably expressed at high levels in tolerant T cells. Overexpression of NR4A1 inhibits effector T cell differentiation, whereas deletion of NR4A1 overcomes T cell tolerance and exaggerates effector function, as well as enhancing immunity against tumour and chronic virus. Mechanistically, NR4A1 is preferentially recruited to binding sites of the transcription factor AP-1, where it represses effector-gene expression by inhibiting AP-1 function. NR4A1 binding also promotes acetylation of histone 3 at lysine 27 (H3K27ac), leading to activation of tolerance-related genes. This study thus identifies NR4A1 as a key general regulator in the induction of T cell dysfunction, and a potential target for tumour immunotherapy.

overall_design: Microarray data from Ttol cells were normalized with GC robust multi-array average (GCRMA) and compared with gene expression profiles from other T cells including TH1, TH2, TH17, nTreg and naive T cells.

first: Liu

last: Xindong

first: Dong

last: Chen


title: Second-generation molecular subgrouping of medulloblastoma: an international meta-analysis of Group 3 and Group 4 subtypes

city: Newcastle upon Tyne

first: Ed

last: Schwalbe

address: Ellison Place

department: Applied Sciences

institute: Northumbria University

summary: We undertook a meta-analysis based on DNA methylation patterns of Group3/4 subgroup medulloblastoma from three published studies, alongside additional unpublished tumours (total n=1501).

overall_design: We used 267 samples from GSE93646, 356 samples from GSE85212, 725 samples from Northcott et al., 2017 (PMID: 28726821) and 153 previously unpublished samples from the St. Jude collection. Bisulfite-converted DNA from medulloblastoma samples were hybridised to the Illumina Infinium 450k and Infinium MethylationEPIC BeadChips.

first: Edward

middle: C

first: Tanvi

last: Sharma


title: Gene expression from AsPC-1 cells treated with PTC596 and DMSO

city: Munich

first: Hans

middle: Carlo

last: Maurer

state: Bavaria

address: Ismaninger Str. 22

department: II. Medizinische Klinik

institute: Klinikum rechts der Isar

summary: This study examines the transcriptional changes invoked by the novel anti-cancer agent PTC596 in AsPC-1 pancreatic cancer cells as compared to DMSO.

overall_design: Gene expression data are presented for 6 replicates of AsPC-1 cells from 3 time points at 8, 16 and 24 hours, respectively, that were either treated with PTC596 or DMSO.

first: Jaime

last: Eberle-Singh

first: Kenneth

middle: P

last: Olive


title: LSF small molecule inhibitors phenocopy LSF-targeted siRNAs causing mitotic defects and senescence in cancer cells

city: Ipswich

first: HANG GYEONG

middle: GYEONG

last: CHIN

state: MA

address: 240 County Road, NEB

department: Research

institute: New England Biolabs, Inc

summary: The oncogene LSF has been proposed as a novel target with therapeutic potential for multiple cancers. LSF overexpression correlates with poor prognosis for both liver and colorectal cancers, for which there are currently limited therapeutic treatment options. In particular, molecularly targeted therapies for hepatocellular carcinoma targeting cellular receptors and kinases have yielded disappointing clinical results, providing impetus for targeting distinct mechanisms. LSF small molecule inhibitors, Factor Quinolinone Inhibitors (FQIs), have exhibited robust anti-tumor activity in multiple pre-clinical models of hepatocellular carcinoma, with no observable toxicity. To understand how the inhibitors impact cancer cell proliferation, we characterized the cellular phenotypes that result from loss of LSF activity. Phenotypically, inhibition of LSF activity induced a mitotic delay with condensed, but unaligned, chromosomes. This mitotic disruption resulted in improper cellular division leading to multiple outcomes: multi-nucleation, apoptosis, and cellular senescence. The cellular phenotypes observed upon FQI1 treatment were due specifically to the loss of LSF activity, as siRNA specifically targeting LSF produced nearly identical phenotypes. Taken together, these findings confirm that LSF is a promising therapeutic target for cancer treatment. In order to identify potential LSF target genes in human cells, we performed LSF-ChIP-seq in a LSF-inducible, stable HEK293T cell line.

overall_design: Establishment of HA-tagged LSF inducible, permanent HEK293T cell line by using the RheoSwich inducible system---> Crosslinking, followed by micrococcal nuclease digestion to fragment chromatin to yield mono- and di-nucleosomes---> ChIP using antibody against HA tag---> Library preparation separately of DNA-sized fragments representing mono- versus di-nucleosomes---> ChIP-seq analysis.

first: Hang

middle: G

last: Chin

first: Hyunjin

last: Shin

first: Chandra

middle: S

last: Pedammallu

first: Ulla

last: Hansen


title: Tissue-specific alteration of gene expression and function by RU486 and the GeneSwitch system

city: Memphis

first: David

last: Finkelstein

state: TN

address: 332 N. Lauderdale St.

department: Computational Biology

institute: St Jude Children's Research Hospital

summary: The drug-inducible GeneSwitch (GS)-Gal4 transgene expression system is routinely used in Drosophila aging and behavioral studies to avoid the confounding effects related to genetic background mutations. Here, we report transcriptional and functional defects that are induced by RU486 in a stock- and tissue-dependent manner, such as defects in flight and mitochondrial gene expression. Our findings indicate that side effects induced by RU486 need to be considered when interpreting the observed phenotypes, and proper controls, consisting of ethanol-treated GS-Gal4 flies and RU486-induced expression of mock transgenes, should always be included

overall_design: Studies of the RU486 gene switch, 2 with a Gal4 transgene one w1118.  3 drug treated samples and 3 controls in each study.

first: Maricela

last: Robles-Murguia

first: Liam

last: Hunt

first: Yiping

last: Fan

first: Fabio

last: Demontis


title: Sorted MDMs with RFP+GFP+ or RFP+GFP- Mtb

first: Bryan

last: Bryson

address: 400 Technology Square

department: Biological Engineering

institute: MIT

summary: Human serum derived macrophages were infected with Mtb expressing a transcriptional reporter of viability and on day 5, the cells were sorted for RFP+GFP+ macrophages or RFP+GFP- macrophages.

overall_design: 3 individual donors were analyzed in biological triplicate.

first: Sarah

last: Fortune


title: Modular architecture of the STING C-terminal tail allows interferon and NF-κB signaling adaptation

city: Boston

first: Amy

middle: Si-Ying

last: Lee

address: 450 Brookline Ave SM520

department: Cancer Immunology and Virology

institute: DFCI

summary: Stimulator of Interferon Genes (STING) is a key regulator of type I interferon and pro-inflammatory responses during infection, cellular stress, and cancer. Here we reveal a mechanism for how STING balances activation of IRF3- and NF-κB-dependent transcription, and discover that acquisition of discrete signaling modules in the vertebrate STING C-terminal tail (CTT) shapes downstream immunity. As a defining example, we identify a motif appended to the CTT of zebrafish STING that inverts the typical vertebrate signaling response and results in dramatic NF-κB activation and weak IRF3-interferon signaling. We determine a co-crystal structure that explains how this CTT sequence recruits TRAF6 as a new binding partner, and demonstrate that the minimal motif is sufficient to reprogram human STING and immune activation in macrophage cells. Together, our results define the STING CTT as a linear signaling hub that can acquire modular motifs to readily adapt downstream immunity.

overall_design: Sting-/- mouse macrophages stably expressing different STING proteins were stimulated with 10-carboxymethyl-9-acridanone (CMA) for 4 hours

first: Carina

last: de Oliveira Mann

first: Philip

middle: J

last: Kranzusch


title: 16s rDNA-sequencing of gastric flora in mouse fed with high salt with or without buckwheat

city: jinan

first: yundong

last: sun

address: wenhua west road 44

institute: shanda university

summary: Divided into four groups,CTL,Salt,(S+B),B.CTL group was fed with normal salt diets for 4 weeks,Salt group were fed with high salt diets(5% NaCl)for 4 weeks,(S+B)group were fed with  high salt diets mixed with buckwheat (1:1)for 4 weeks ,B group: first fed high salt diets for 4 weeks and then fed with buckwheat for 4 weeks. Extract mouse gastric flora DNA and sequence.

overall_design: 16s rDNA-sequencing  for 36 samples

first: Ya

last: Li


title: CD271 is a molecular switch with divergent roles in melanoma and melanocyte development

city: Merced

first: Fabian

middle: Volker

last: Filipp

state: California

address: 5200 North Lake Road

department: Systems Biology and Cancer Metabolism, Program for Quantitative Systems Biology

institute: University of California Merced

summary:
Dysregulation of signaling networks controlling self-renewal and migration of developmental cell lineages is closely linked to the proliferative and invasive properties of tumors. Identification of such signaling pathways and their critical regulators is vital for successful design of effective targeted therapies against neoplastic tissue growth. The neurotrophin receptor (CD271/NGFR/p75/NTR) is a key regulator of the melanocytic cell lineage through its ability to mediate cell growth, survival, and differentiation. Using clinical melanoma samples, normal melanocytes and global gene expression profiling we have investigated the role of CD271 in rewiring signal transduction networks of melanoma cells during neoplastic transformation. Our analysis demonstrates that depending on the cell fate, tumor initiation vs normal development, elevated levels of CD271 can serve as a switch between proliferation/survival and differentiation/cell death. Two divergent arms of neurotrophin signaling hold the balance between positive regulators of proliferation, selfrenewal, and survival controlled by E2F, MYC, SREBP1 and AKT3 pathways on the one hand, and differentiation, senescence, and apoptosis controlled by TRAF6/IRAK-dependent activation of AP1 and TP53 mediated processes on the other hand. A molecular network map revealed in this study uncovers CD271 as a context-specific molecular switch between normal development and malignant transformation.
https://doi.org/10.1038/s41598-019-42773-y
http://orcid.org/0000-0001-9889-5727

overall_design: Flow cytometry in combination with lineage- and CD271-specific monoclonal antibodies was used to purify distinct CD271+ and CD271- tumor cell subsets from surgically removed, human melanoma tumor tissue specimens. In addition, the same approach was used to purify CD271+ and CD271- cell population from epidermal melanocytes separately isolated from healthy human skin tissue. All CD271+ and CD271- cell populations were then subjected to RNA extraction, transcriptomic profiling, and systems biology analysis.

middle: V

first: Chen

first: Alex

last: Boiko


title: TFEB-driven lysosomal biogenesis is pivotal for PGC1a-dependent renal stress resistance

first: Manoj

last: Bhasin

address: 330 Brookline Avenue  RN 380E

institute: Beth Israel Deaconess Medical Center

summary: Because injured mitochondria can accelerate cell death through the elaboration of oxidative free radicals and other mediators, it is somewhat paradoxical that proliferator gamma coactivator 1-alpha (PGC1a), a stimulator of increased mitochondrial abundance, protects stressed renal cells instead of potentiating injury. Here we report that PGC1a’s induction of lysosomes via transcription factor EB (TFEB) may be pivotal for kidney protection. CRISPR and stable gene transfer showed that PGC1a knockout tubular cells were sensitized to the genotoxic stressor cisplatin whereas transgenic cells were protected. The biosensor mtKeima unexpectedly revealed that cisplatin blunts mitophagy both in cells and mice.  PGC1a not only counteracted this effect but also raised basal mitophagy, as did the downstream mediator nicotinamide adenine dinucleotide (NAD+). PGC1a did not consistent affect known autophagy pathways modulated by cisplatin. Instead RNA sequencing identified coordinated regulation of lysosomal biogenesis via TFEB. This effector pathway was sufficiently important that inhibition of TFEB or lysosomes unveiled a striking harmful effect of excess PGC1a in cells and conditional mice. These results uncover an unexpected effect of cisplatin on mitophagy and PGC1a’s exquisite reliance on lysosomes for kidney protection. Finally, the data illuminate TFEB as a novel target for renal tubular stress resistance.

overall_design: 12 samples in total = 3 replicates each from 4 groups

first: Mei

last: Tran

first: Matthew

last: Lynch

first: Kenneth

last: Ralto

first: Swati

first: Samir

last: Parikh


title: Expression data from knockdown of IARS2 in A549 cells

city: Changchun/Jilin

first: Ke

last: Wang

address: Ziqiang street

institute: The Second Hospital of Jilin University

summary:
Isoleucyl-tRNA synthetase 2, mitochondrial (IARS2) is a nuclear gene encoding a mitochondrial ARS.
We used microarray analysis to identify the genes that are regulated by IARS2 in A549 cells.

overall_design: IARS2 expression was stably knocked-down in A549 cells. RNA from this clone and parental (control) cells were purified for microarray analysis.

first: Xin

last: Di


title: RNA-seq data from VavCre;Jak2+/+; Cdk6+/+, VavCre;Jak2V617F; Cdk6+/+, VavCre;Jak2V617F; Cdk6-/-, VavCre; Jak2+/+; Cdk6-/- murine bone marrow LSK cells and VavCre; Jak2V617F; Cdk6+/+ Palbociclib treated murine bone marrow LSK cells

city: Vienna

first: Veronika

last: Sexl

address: Veterinaerplatz 1

country: Austria

institute: Vetmeduni Vienna

summary: We describe a critical role for Cdk6 in JAK2V617F+ MPN evolution. The absence of Cdk6 ameliorates clinical symptoms and prolongs survival of JAK2V617F fl/+ vav-Cre mice. The Cdk6 protein interferes with three hallmarks of disease: besides regulating malignant stem cell quiescence, it promotes NFkB signaling and contributes to cytokine production while inhibiting apoptosis. The treatment with palbociclib did not mirror these effects, showing that the functions of Cdk6 in MPN pathogenesis are largely kinase-independent.

overall_design: LSK-sorted (FACS) bone marrow cells from 8-week-old VavCre;Jak2+/+; Cdk6+/+, VavCre;Jak2V617F; Cdk6+/+, VavCre;Jak2V617F; Cdk6-/-, VavCre; Jak2+/+; Cdk6-/- mice, and the same cell type from palbociclib-treated (38mg/kg, 3x in one week) VavCre;Jak2V617F; Cdk6+/+ mice, n=3 for all genotypes

first: Iris

middle: Z

last: Uras

first: Harini

last: Nivarthi

first: Philipp

last: Jodl

first: Reinhard

last: Grausenburger

first: Christoph

last: Bock

first: Robert

last: Kralovics


title: Differential gene expression stimulated by acGM in bone marrow derived macrophages

city: Maucau

first: Feng

last: Yanxian

address: Tapai

department: Institute of Chinese Medical Sciences

country: Macau

institute: University of Maucau

summary: To explore the mechanism of inflammation caused by glucomannan with increasing degree of acetyl substitution (acGM) in  bone marrow derived macrophages (BMDM), BMDM was treated with acGM-0.2 and acGM-1.8 for 24h.

overall_design: After co-incubation of acGM-0.2 and acGM-1.8 with the same dose in BMDM for 24h, cells were collected, the whole genome microarray expression was compared with untread BMDM to explain the possible mechanism of the induced-inflammation.

first: Yanxian

last: Feng

first: Chunming


title: No effect of calcifediol supplementation on skeletal muscle transcriptome in vitamin D deficient frail older adults.

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

institute: Wageningen University

summary: Vitamin D deficiency is common among older adults and has been linked to muscle weakness. Vitamin D supplementation has been proposed as a strategy to improve muscle function in older adults. The aim of this study was to investigate the effect of calcifediol (25-hydroxycholecalciferol) on whole genome gene expression in skeletal muscle of vitamin D deficient frail older adults. A double-blind placebo controlled trial was conducted in vitamin D deficient frail older adults (aged above 65), characterized by blood 25-hydroxycholecalciferol concentrations between 20 and 50 nmol/L. Subjects were randomized across the placebo group (n=12) and the calcifediol group (n=10, 10 µg per day). Muscle biopsies were obtained before and after six months of calcifediol or placebo supplementation and subjected to whole genome gene expression profiling using Affymetrix HuGene 2.1ST arrays. Expression of the vitamin D receptor gene was virtually undetectable in human skeletal muscle biopsies. Calcifediol supplementation led to a significant increase in blood 25-hydroxycholecalciferol levels compared to the placebo group. No difference between treatment groups was observed on strength outcomes. The whole transcriptome effects of calcifediol and placebo were very weak. Correcting for multiple testing using false discovery rate did not yield any differentially expressed genes using any sensible cut-offs. P-values were uniformly distributed across all genes, suggesting that low p-values are likely to be false positives. Partial least squares-discriminant analysis and principle component analysis was unable to separate treatment groups. Calcifediol supplementation did not affect the skeletal muscle transcriptome in frail older adults. Our findings indicate that vitamin D supplementation has no effects on skeletal muscle gene expression, suggesting that skeletal muscle may not be a direct target of vitamin D in older adults.

overall_design: Microarray analysis was performed on skeletal muscle biopsies (m. vastus lateralis) from vitamin D deficient frail older adults before and after supplementation with 25-hydroxycholecalciferol.

first: Roland

middle: W

last: Hangelbroek

first: Anouk

middle: M

last: Vaes

first: Mark

last: Boekschoten

first: Sander

last: Kersten


title: De novo transcriptome sequencing in Anopheles aquasalis using RNA-seq

city: Lisbon

first: Henrique

last: Silveira

address: Rua da Junqueira, 100

department: Global Health and Tropical Medicine

country: Portugal

institute: Instituto de Higiene e Medicina Tropical, IHMT, UNL

summary: Anopheles aquasalis transcriptome in response to Plasmodium vivax invasion of midgut

overall_design: A. aquasalis mosquitoes  were: i) membrane-fed on P. vivax infected blood, ii) membrane-fed on blood with inactivated gametocytes or iii) fed on 10 % sugar solution. 18-24 hours after feeding, mosquitoes were dissected and pools of 30 midguts were collected from each group. Three independent biological replicates of each experiment were performed.

first: Rosa

middle: A

last: Santana

first: Patrícia

last: Abrantes

first: Maria

last: Guerra


title: Identification of key molecules involved in tertiary lymphoid organ formation in the central nervous system

city: Würzburg

first: Richa

last: Bharti

address: Josef-Schneider-Straße 2 / Bau D15

department: IMIB,Core Unit Systemmedizin

institute: University of Wuerzburg

summary: We have induced experimental autoimmune encephalomyelitis (EAE) in mice to mimic B cell aggregate formation as seen in progressive multiple sclerosis patients. Aggregates and regular central nervous system infiltrates were dissected using laser capture microdissection. RNA was collected using commercially available kits and subjected to RNA sequencing. Samples were compared to draining lymph nodes and to another EAE model, which had no involvement of B cells.

overall_design: Examinations of RNA experession profiles in cerebellar B cell aggregates, central nervous system infiltrates and draining lymph nodes in two different EAE models.

first: Stefanie

last: Kürten

first: Verena

last: Schropp


title: UCP1-expression associated gene signatures of human epicardial adipose tissue.

city: Quebec

first: Kanta

last: Chechi

address: 2275 Chemin Sainte Foy

department: Physiology

country: Canada

institute: Quebec Heart and Lung Institute, Laval University

summary: The primary objective of the study was to investigate the uncoupling protein-1 (UCP1) associated features of human epicardial adipose tissue (eAT) using next generation deep sequencing.  In addition, paired mediastinal adipose tissue (mAT) and subcutaneous adipose tissue (sAT) samples colleced from patients undergoing cardic surgeries at our center were included in the study.

overall_design: Paired biopsies of eAT, mAT and sAT obtained from cardiac surgery patients (n=10), with specific criteria of high- and low- expression of UCP1 in eAT, were subjected to RNA sequencing. While the primary objective was to compare high- vs. low UCP1 expression in eAT, our study design further allowed us to investigate depot- and disease specific transcriptomic shifts in these patients. Specifically, 10 patients provided 30 samples (n = 10 each for eAT, mAT and sAT) that could be compared based on depot specificity (n = 10), obesity (n = 5 lean, n = 5 obese) and coronary artery disease (CAD) (n = 6 CAD, 4 = Non-CAD).

first: Jinchu

last: Vijay

first: Elin

last: Grundberg

first: Denis

last: Richard


title: Salmonella enterica serovar Typhimurium strain 14028s transcriptome response to lettuce media

city: Braunschweig

first: Jasper

last: Schierstaedt

address: Messeweg 11-12

department: EP

institute: Julius kühn-Institute

summary:
Summary: Salmonella enterica serovar Typhimurium strain 14028s transcriptome response to lettuce medium (LM) and lettuce root exudates (LX) to minimal medium (MM).
Purpose: Salmonella mRNA profile, when grown in different media was compared to minimal medium to reveal environment specific transcriptional changes.
Methods: mRNA profiles were generated using Illumina HiSeq in triplicates. The sequences were analysed using Bowtie2 followed by Cufflinks.

overall_design: mRNA profiles of Salmonella were generated using Illumina HiSeq in triplicates.

first: Sven

last: Jechalke

first: Klaus

last: Neuhaus

first: Adam

last: Schikora


title: Transcriptomic analysis of WM-266-4 GFP cells transfected with miR-199a-3p

city: Paris

first: Paola

last: Arimondo

address: 28 rue du Dr Roux

department: Institut Pasteur

country: France

institute: CNRS

summary: To identify the genes targeted by miR-199a-3p in metastatic melanoma cells, we compared global gene expression in miR-199a-3p vs control miR transiently transfected cells by transcriptomic microarrays.

overall_design: Cells were transfected with miR199-3p at 0.5nM (Mo5) and 0.25nM  (Mo25), after 48h total RNA were collected and compared to the cells transfected with a control miR (CTM), in biological triplicates.

middle: B

first: Jcécile

last: Desjobert


title: Microglia in developing retina transition through a disease-like functional state that does not require CSF1R signaling for survival

city: Salt Lake City

first: Monica

middle: L.

last: Vetter

state: UT

department: Neurobiology & Anatomy

institute: University of Utah

summary: Microglia have important remodeling functions in development and disease. There is evidence for molecular diversity of microglia suggesting they may exist in distinct functional states to differentially impact CNS health and function. To better understand this in development, we profiled microglia of a discrete developing CNS region, the murine retina. We find that retinal microglia transition through unique transcriptional states and identify a population with peak density postnatally that resemble adult disease-associated microglia (DAM) and CD11c+ microglia of developing white matter, we term DAM-like. Developmental cell death is a major driver of the DAM-like phenotype, and TREM2 signaling is required for select DAM gene expression. Notably, DAM-like cells that highly express CD11c are not dependent on CSF1R signaling for survival, and TREM2 signaling is required for CSF1R independence in a subset of microglia. Thus, microglial phenotype in development is influenced by local developmental events and may share features with microglia in disease.

overall_design: mRNA profiles of whole retina and sorted retinal microglia from embryonic day (e)16.5, postnatal day (P)7 and adult (P60) mice were generated by deep sequencing.

first: Sarah

middle: R

last: Anderson

first: Jacqueline

last: Roberts

first: Jianmin

last: Zhang

first: Michael

last: Steele

first: Cesar

middle: O

last: Romero

first: Alejandra

last: Bosco

middle: L