title: RNA Sequencing of intra-phagosomal Mtb populations

city: Bengaluru

first: Amit

last: Singh

state: KARNATAKA

address: Sir CV Raman Road

department: Microbiology and Cell Biology

institute: Indian Institute of Science

summary: Heterogeneity of host cells as well as bacteria residing within them has been known to induce drug tolerance in pathogens. In Mycobacterium tuberculosis, particularly, drug tolerance within host is a major hurdle in the path to attain a sterlising cure. Reports have shown how residence of Mtb within macrophages makes the pathogen refractory to anti-TB therapy. However, the mechanisms responsible for induction of tolerance to antibiotics, particularly in resting macrophages where Mtb continues to actively replicate, is yet to be deciphered. Reports have suggested that heterogeneity induced in Mtb by cues sensed in the host environment could be a contributing factor to drug tolerance. With regard to this, differences in redox physiology of intra-macrophage Mtb (mid-point potential of the major cytosolic redox buffer in Mtb, mycothiol- EMSH) have been shown to play a role in influencing antibiotic-mediated killing. In this study, we have attempted to analyse the trascriptomic profiles of individual redox sub-populations of Mtb from within macrophages- viz., the EMSH-reduced bacteria with mid-point potential ranging between -285 and -310 mV, shown to be most refractory to killing by front-line anti-TB antibiotics inside macrophages, as well as EMSH-basal bacteria with mid-point potential ranging between -270 and -280 mV, with a much higher degree of antibiotic susceptibility within macrophages. Analysing gene expression level differences between these bacterial sub-populations would help in providing a mechanistic understanding of drug tolerance in Mtb, bred from phenotypic heterogeneity in the pathogen.

overall_design:
The study involves profiling mRNA signatures of redox differential sub-populations of Mtb H37Rv (expressing the biosensor Mrx1-roGFP2) isolated from within PMA-differentiated THP1 monocytes at 24 hours post-infection. The profiles of EMSH-reduced and EMSH-basal intra-macrophage subpopulations were compared with in vitro grown Mtb, under similar conditions with the exception of the extracellular environment as faced within macrophages. Samples for all three conditions were prepared in duplicates.
Acidic pH is one of the earliest signals faced by Mtb within the host and possibly contributes to the emergence of the EMSH-reduced sub-population during infection. In order to determine the overlap of deregulated Mtb genes between the EMSH-reduced fraction arising inside macrophages and those induced under acidic pH exposure,  WT Mtb was exposed in vitro to neutral (6.6) and acidic (4.5) pH and genes induced at low pH were analyzed. Additionally, WhiB3 is a known regulator of acidic pH-mediated emergence of EMSH-reduced population of Mtb. As a control, a genetic knock-out of WhiB3 in the background of WT Mtb, along with its complemented strain, were also exposed to neutral and acidic pH. This in vitro analysis was conducted to determine the overlap of differentially expressed genes between the EMSH-reduced sub-population and the WhiB3-specific, low pH induced regulon of Mtb. Samples for all three strains at pH 6.6 and pH 4.5 were prepared in duplicates.

first: Richa

last: Mishra

first: Nitish

last: Malhotra

first: Aswin

last: Seshasayee


title: c-Maf regulates the plasticity of group 3 innate lymphoid cells by restraining the type 1 program [CUT&RUN]

status: Public on Sep 13 2019

city: Durham

first: Maria

last: Ciofani

state: NC

address: 207 Research Drive, 128 Jones Building

department: Integrative Immunobiology

country: USA

institute: Duke University School of Medicine

type: Genome binding/occupancy profiling by high throughput sequencing

summary: The transcription factor c-Maf is an essential regulator of group 3 ILC homeostasis and effector plasticity. c-Maf limits acquisition of the type 1 program and conversion to the ILC1 fate through restraint of T-bet expression and function.

overall_design: Evaluation of differential H3K27ac and H3K27me3 histone marks in cohoused Maf-deficient NKp46+ ILC3. The CUT&RUN  protocol was performed on replicate samples of  NKp46+ ILC3  isolated from the small intestine lamina propria of Maf+/+ Il7r-Cre and Maf fl/fl Il7r-Cre mice.

first: Morgan

middle: E

last: Parker

first: Alejandro

last: Barrera


title: Gene expression in liver and hypothalamus from ob/ob mice treated with γ-oryzanol-encapsulated nanoparticles

city: Okinawa

first: Chisayo

last: Kozuka

address: 207 Uehara, Nishihara

country: Japan

institute: University of the Ryukyus

summary:
Brown rice-specific bioactive substance, γ-oryzanol ameliorates fuel dysmetaborism, but it is hardly absorbed form the intestine. To increase the efficiency of its absorption, we therefore challenged to encapsulate γ-oryzanol in polymer poly (DL-lactide-co-glycolide) (PLGA) nanoparticles.
We assessed the metabolically-beneficial impact of PLGA-encapusulated γ-oryzanol on fuel dyshomeostasis in genetically obese-diabetic ob/ob mice.

overall_design: Obese diabetic ob/ob mice were orally administered with γ-oryzanol or γ-oryzanol-encapsulated nanoparticles for 4 weeks (n=3 animals per group). Liver and hypothalamus RNA was extracted and hybridized to Affimetrix microarrays and gene expression data was analyzed.

first: Chigusa

last: Shimizu-Okabe

first: Chitoshi

last: Takayama

first: Kaku

last: Nakano

first: Hidetaka

last: Morinaga

first: Asuka

last: Kamei

first: Akihito

last: Yasuoka

first: Takashi

last: Kondo

first: Keiko

last: Abe

first: Kensuke

last: Egashira

first: Hiroaki

last: Masuzaki


title: Repression of an activity-dependent autocrine insulin signal is required for sensory neuron development in C. elegans

status: Public on Sep 12 2019

city: New York

first: Lauren

last: Bayer Horowitz

state: NY

address: 540 1st Ave

department: Cell Biology

institute: NYU School of Medicine

type: Expression profiling by high throughput sequencing

summary: The nervous system comprises diverse and highly specialized neuron-types, each expressing a unique set of genes that defines its functional properties. What molecular mechanisms generate diverse neuron types remains a central question in neuroscience. Our study of C. elegans chemosensory BAG neurons showed that a p38 MAP kinase (MAPK), PMK-3, is required for their proper differentiation and function (Brandt, J. and Ringstad, N. 2015). How p38 MAPKs function in neurodifferentiation is poorly understood. To better understand how pmk-3 promotes the BAG cell fate, we purified wild-type and pmk-3 mutant chemosensory BAG neurons and determined their transcriptomes using RNA-Seq. Expression of a number of genes that encode neuropeptides, including insulin-like peptides (ILPs), were up-regulated in pmk-3 mutant BAG neurons. Through analysis of mutations that restore expression of a BAG-fate marker to pmk-3 mutants, we additionally found that genes required for the release of neuropeptides, including UNC-31/CAPS, suppress pmk-3 mutant gene expression defects. These two observations suggested that the differentiation defects of pmk-3 mutants are associated with dysregulated release of peptide hormones. Indeed, we find that increased synthesis and release of ILPs from BAG during development causes a significant fraction of the gene expression and functional defects of pmk-3 mutant neurons. Together our data delineate a mechanism through which p38 MAPKs promote proper sensory neuron differentiation by inhibiting an autocrine insulin signal that represses expression of a BAG neuron fate. These findings reveal an unexpected role for insulin signaling in nervous system development and suggest that insulin-like factors are at the nexus of intrinsic genetic programs and extrinsic signaling mechanisms that regulate cell fate and neuronal differentiation.

overall_design: Two biological replicates were analyzed for each of the 3 cell populations

middle: B

last: Horowitz

first: Niels

last: Ringstad

first: Igor

last: Dolgalev


title: Immune effector monocyte - neutrophil cooperation induced by the primary tumor prevents metastatic progression of breast cancer

city: San Francisco

first: Zena

last: Werb

state: CA

address: 513 Parnassus Avenue

department: Anatomy

institute: UCSF

summary: Metastatic behaviour varies significantly among breast cancers. Mechanisms explaining why the majority of breast cancer patients never develop metastatic outgrowth are largely lacking but could underlie the development of novel immunotherapeutic target molecules. Here we show interplay between non-metastatic primary breast cancer and innate immune response, acting together to control metastatic progression. The primary tumor systemically recruits IFNγ-producing immune effector monocytes to the lung. IFNγ upregulates Tmem173/STING in neutrophils and enhances their killing capacity. The immune effector monocytes and tumoricidal Tmem173/STINGhigh neutrophils target disseminated tumor cells in the lungs, preventing metastatic outgrowth. Importantly, our findings could underlie the development of immunotherapeutic target molecules that augment the function of immune effector monocytes and Tmem173high neutrophils.

overall_design: The aim is to compare the transcriptome of neutrophils and monocytes CCR2+ purified from lungs of NOD/scid mice bearing the highly metastatic tumors HCl-001 (TN1) and low metastatic tumors HCl-002 (TN2). RNA sequencing was performed on RNA extracted from FACS-sorted monocytes CCR2+ and neutrophils from lungs of mice bearing tumors HCl-001 and HCl-002 reaching end point, followed by purification using an RNeasy Micro Kit (Qiagen). cDNA synthesis and whole, transcriptome amplification was performed using the Smart-seq2 protocol, libraries were prepared using Illumina XT Library Preparation Kit and sequenced by HiSeq 2500 sequencer. Raw reads were aligned to reference transcriptome (Mus_musculus.GRCm38) and transcripts per million values were calculated using Kallisto50 quant, version 0.42.3 (2). AltAnalyze was used to analyze normalized read counts and to calculate differentially expressed genes.

first: Catharina

last: Hargerling

first: Hugo

last: Gonzalez


title: Novel drug-like RAR-Beta agonist induces BRCA1 to prevent neuropathic pain

city: Evry

first: Marco Antonio

last: Mendoza Parra

address: 2 Gaston Crémieux

country: France

institute: Genoscope

summary: Neuropathic pain (NP) is associated with profound gene expression alterations within  the nociceptive system. DNA mechanisms, such as epigenetic remodelling and repair  pathways have been implicated in NP. Here we have used a rat model of peripheral  nerve injury to study the effect of a novel RARβ-agonist, C286, currently under clinical  research, in NP. A four week treatment initiated two days after the injury normalised  pain sensation. Genome-wide and pathway enrichment analysis showed that multiple  mechanisms persistently altered in the spinal cord were restored to preinjury levels by  the agonist. Concomitant upregulation of DNA repair proteins, ATM and BRCA1, the  latter being required for C286 mediated pain modulation, suggest that early DNA repair  may be important to prevent phenotypic epigenetic imprints in NP. Thus, C286 is a promising drug candidate for neuropathic pain and DNA repair mechanisms may be useful therapeutic targets to explore.

overall_design: Frozen micro dissected spinal cord samples were lysed with Teflon-glass homogenisers and  QIAshredder columns (Qiagen). Total RNA was isolated with the Qiagen RNeasy® Mini kit.  The RNA was assessed for purity and quantity using the Nanodrop 1000 spectrophotometer  and assessed for quality on the Agilent Bioanalyzer 2100.  Four hundred ng of intact high-quality total RNA (RIN>7.9) from each sample was then used  as input to generate libraries for RNA-sequencing using the NEBNext Ultra II Directional kit  (NEB, Cat.no: E7760S) following the manufacturer’s recommendations. This protocol involved an initial step of mRNA selection using a poly-A isolation module (NEB, Cat.no:  E7490) to select for mRNA with a mature polyA tail, followed by fragmentation prior to first  cDNA synthesis and barcoding second-strand cDNA synthesised with indices for Illumina  sequencing for final library amplification (10-cycles). The resulting libraries (342-421bp) were assessed on the Bioanalyzer 2100 for purity. The NEBNext Library Quant Kit for Illumina (NEB, Cat.no: E7630L) was used to calculate the quantity of each library. The quantification data was used to pool the libraries in equal molarity prior to performing a QC run on the MiSeq (MiSeq Reagent Kit v3 (150-cycle); Cat no: MS-102-3001). Further deep sequencing was performed on the pooled library over 2 lanes using a HiSeq4000 (by GENEWIZ) to generate roughly 26 million reads per sample.

first: Bia-de-Castro

last: Vasconcelos Goncalves

first: Jonathan

middle: P

last: Corcoran

first: Marco

middle: A

last: Mendoza-Parra


title: Single-nucleus chromatin accessibility maps of IDH mutant gliomas  point to non-coding RNAs as a major influence on heterogeneity

city: Heidelberg

first: Ruslan

last: Al-Ali

state: Baden Wurttemberg

address: INF 400

country: Germany

institute: University Hospital Heidelberg

summary:
We generated chromatin accessibility maps from 5 tumors, 336 individual nuclei, using the Fluidigm HT IFC microfluidics platform (snATAC-Seq). We were able to identify variable promoter accessibility of non-coding RNAs in LGGs.
Our results point to increased CYTOR promoter accessibility in IDH-intact samples. We obtained two distinct clusters, primarily driven by histology, with a more constrained IDH-codel/oligodendroglioma cluster.

overall_design:
Examination of open chromatin accessibility in 336 nuclei from 5 low grade tumors

>>>Submitter states that raw data are unavailable due to patient privacy concerns<<<

first: Sevin

last: Turcan


title: RNA-seq from CymRSV-infected shoot apical meristem region

city: Godollo

first: Peter

last: Gyula

state: Pest

address: Szent-Gyorgyi Albert u. 4.

department: Department of Plant Biotechnology

country: Hungary

institute: Hungarian University of Agricultural and Life Sciences

summary:
Background: It has been observed in some plant-virus interaction under certain circumstances that the plants show a sign of healing from virus-infection, a phenomenon called symptom recovery. The nature of molecular processes behind symptom recovery has been an enigma in plant virology for a long time. Discovery of RNA silencing provided a possible mechanism to explain some aspects of recovery but not all.
Results: We provide evidence that silencing is not the reason for recovery in CymRSV-infected Nicotiana benthamiana plants. Transcriptome analysis followed by in situ hybridization experiments shed light on the expressional changes in the shoot apical meristem (SAM) region upon virus infection. We observed a severe loss of meristem function in the SAM which was accompanied by the downregulation of meristem-specific genes. Among the upregulated genes we found an enrichment of salicylate-metabolism and signalling, and autophagy-related functions (among many others) suggesting that these genes might play a role in shoot necrosis and symptom recovery.
Conclusion: Our data suggest that the loss of meristem function is a result of salicylate-induced programmed cell death.

overall_design: PolyA-selected mRNAs were sequenced from mock or CymRSV-infected SAM region of Nicotiana benthamiana plants in four biological replicates on Illumina HiSeq2000 platform (unstranded, 75bp single-end).

first: Anna

last: Medzihradszky

first: Péter

first: Anita

last: Sós-Hegedűs

first: György

last: Szittya

first: József

last: Burgyán


title: Histone deactylase 3 controls a transcriptional network required for B cell maturation

city: Nashville

first: Scott

last: Hiebert

state: TN

address: 2220 Pierce Ave

department: Biochemistry

institute: Vanderbilt University

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

overall_design: Refer to individual Series


title: Histone deactylase 3 controls a transcriptional network required for B cell maturation [ChIP-seq]

summary: We used Cd19-Cre to conditionally delete Hdac3 in order to define its role in germinal center B cells, which represent the cell of origin for many B cell malignancies. Cd19-Cre-Hdac3-/- mice showed impaired germinal center (GC) formation along with a defect in plasmablast generation.  Analysis of Hdac3-/- GCs revealed a reduction in dark zone centroblasts and accumulation of light zone centrocytes. RNA-seq revealed a significant correlation between genes up-regulated upon Hdac3 loss and those up-regulated in Foxo1-deleted GC B cells, even though Foxo1 typically activates transcription. Therefore, to determine whether gene expression changes observed in Hdac3-/- GCs were a result of direct effects of Hdac3 deacetylase activity on transcription, we used an HDAC3 selective inhibitor to examine nascent transcription in germinal center-derived cell lines. Transcriptional changes upon HDAC3 inhibition in cells highly correlated with transcriptional changes observed in GCs in vivo. Further comparison of PRO-seq data with ChIP-seq/exo data for BCL6, SMRT, FOXO1 and H3K27ac identified direct targets of HDAC3 function including CD86, CD83 and CXCR5 that are likely responsible for driving the light zone phenotype observed in vivo.

overall_design: ChIP-exo was performed from OCI-LY1 cells to detect H3K27ac following a 3 hour treatment with the HDAC3-selective inhibitor, RGFP966, or DMSO control. H3K27ac ChIPs were performed on biologic replicates. ChIP-exo was also performed on untreated OCI-LY1 cells to determine FOXO1 chromatin associations.

middle: W

first: Kristy

middle: R

last: Stengel


title: RNAseq transcriptome analysis of White Blood Cells (WBCs) from individuals with and without trisomy 21 [stranded]

city: Aurora

first: Matthew

middle: D

last: Galbraith

state: CO

department: Department of Pharmacology; Linda Crnic Institute for Down Syndrome

institute: University of Colorado Anschutz Medical Campus

summary: Poly(A)+ RNA extracted from WBCs obtained from chromosome 21 disomic (D21) and trisomic (T21) individuals to identify consistent changes in gene expression across individuals.

overall_design: 8 individuals with T21 and 6 individuals with D21.

first: Kelly

last: Sullivan

first: Keith

last: Smith

first: Ross

last: Granrath

first: Angela

middle: L

last: Rachubinski

first: Joaquin

middle: M

last: Espinosa


title: SIGNAL INTEGRATION AND TRANSCRIPTIONAL REGULATION OF THE INFLAMMATORY RESPONSE MEDIATED BY THE GM-/M-CSF SIGNALING AXIS IN HUMAN MONOCYTES [RNA-seq]

city: Derio

first: Ana

middle: Maria

last: Aransay

state: BIZKAIA

address: Parque tecnologico de Bizkaia, Building 801-A

department: Genome Analysis Platform

country: Spain

institute: CIC bioGUNE

summary: In recent years, the M-CSF and GM-CSF cytokines have been identified as opposing regulators of the inflammatory program. However, the two cytokines are simultaneously present in the inflammatory milieu, and it is not clear how cells integrate these signals. In order to understand the regulatory networks associated with the GM/M-CSF signaling axis we analyzed DNA methylation in human monocytes. Our results indicate that GM-CSF induces activation of the inflammatory program and extensive DNA methylation changes, while M-CSF-polarized cells are in a less differentiated state. This inflammatory program is mediated via JAK2 associated with the GM-CSF receptor and the downstream ERK signaling. However, PI3K signaling is associated with a negative regulatory loop of the inflammatory program and M-CSF autocrine signaling in GM-CSF-polarized monocytes. Our findings describe the regulatory networks associated with the GM/M-CSF signaling axis and how they contribute to the establishment of the inflammatory program associated with monocyte activation.

overall_design:
Two replicates were used per condition. Each sample was obtained from one individual. One replicate from the Trametinib sample group was excluded due to RNA degradation.
The RNA-seq samples and the ATAC-seq samples (GSE123569) are from the same biological samples.

first: Ramon

last: Rodriguez

first: Beatriz

last: Suarez-Alvarez

first: Jose

last: Lavín

first: Alex

last: Ascensión

first: Monika

last: González

first: Juan

middle: J

last: Lozano

first: Aroa

last: Raneros

first: Paula

last: Bulnes

first: Covadonga

last: Huidobro

first: Cristina

last: Martin-Martin

first: Amaya

last: Puig-Kröger

first: Angel

last: Corbí

first: Marcos

last: Araúzo-Bravo

first: Carlos

last: Lopez-Larrea

last: Vidal-Castiñeira

last: Sanz

first: Marta

last: Ruiz-Ortega


title: RNAseq transcriptome analysis of White Blood Cells (WBCs) from individuals with and without trisomy 21

first: Matthew

last: Galbraith


title: Histone deactylase 3 controls a transcriptional network required for B cell maturation [PRO-seq]

first: Scott

last: Hiebert

overall_design: PRO-seq was performed on three cell lines: OCI-LY1, NU-DUL-1 and SU-DHL4 following a 3 hour treatment with 10 uM RFP966, an HDAC3 selective inhibitor. Experiments were performed in duplicate, and DMSO-treated samples served as controls.

first: Kristy

last: Stengel


title: RNAseq transcriptome analysis of White Blood Cells (WBCs) from individuals with and without trisomy 21 [unstranded]

overall_design: 2 individuals with T21 and 3 individuals with D21.

first: Kelly

last: Sullivan

first: Keith

last: Smith

first: Ross

last: Granrath

first: Angela

last: Rachubinski

first: Joaquin

last: Espinosa


title: SIGNAL INTEGRATION AND TRANSCRIPTIONAL REGULATION OF THE INFLAMMATORY RESPONSE MEDIATED BY THE GM-/M-CSF SIGNALING AXIS IN HUMAN MONOCYTES [ATAC-seq]

first: Ana

last: Aransay

overall_design:
Two replicates were used per condition. Each sample was obtained from one individual.
The ATAC-seq samples and the RNA-seq samples (GSE123573) are from the same biological samples.

first: Ramon

last: Rodriguez

first: Beatriz

last: Suarez-Alvarez

first: Jose

last: Lavín

first: Alex

last: Ascensión

first: Monika

last: González

first: Juan

last: Lozano

first: Aroa

last: Raneros

last: Bulnes

last: Huidobro


title: Targeted exon skipping with AAV-mediated split adenine base editors.

city: Urbana

first: Alan

last: Luu

state: Illinois

address: 1110 W Green St.

department: Physics

institute: University of Illinois at Urbana Champaign

summary: Techniques for exclusion of exons from mature transcripts have been applied as gene therapies for treating many different diseases. Since exon skipping has been traditionally accomplished using technologies that have a transient effect, it is particularly important to develop new techniques that enable permanent exon skipping. We have recently demonstrated that this can be accomplished using cytidine base editors for permanently disabling the splice acceptor of target exons. We now demonstrate the application of adenine-deaminase base editors to disrupt the conserved adenosine within splice acceptor sites for programmable exon skipping. We also demonstrate that by altering the amino acid sequence of the linker between the adenosine deaminase domain and the Cas9 nickase or by coupling the adenine base editor with a uracil glycosylase inhibitor, the DNA editing efficiency and exon skipping rates improve significantly. Finally, we developed a split base editor architecture compatible with adeno-associated viral packaging. Collectively, these results represent significant progress towards permanent in vivo exon skipping through base editing and, ultimately, a new modality of gene therapy for the treatment of genetic diseases.

overall_design: 50 samples included. Samples with the same name except for their trailing numbers are replicates. Samples with GFP in their name are controls.

first: Jackson

last: Winter

first: Michael

last: Gapinske

first: Wendy

middle: S

last: Woods

first: Jun

last: Song

first: Pablo

last: Perez-Pinera


title: SIGNAL INTEGRATION AND TRANSCRIPTIONAL REGULATION OF THE INFLAMMATORY RESPONSE MEDIATED BY THE GM-/M-CSF SIGNALING AXIS IN HUMAN MONOCYTES

type: Methylation profiling by genome tiling array


title: SIGNAL INTEGRATION AND TRANSCRIPTIONAL REGULATION OF THE INFLAMMATORY PROGRAM ASSOCIATED WITH THE GM-/M-CSF SIGNALING AXIS IN HUMAN MONOCYTES [EXPRESSION DATA SET]

overall_design: Three replicates were used per cell type. Each sample of Monocytes, M1 and M2 were obtained from a pool of three individuals.

first: Paula

first: Covadonga

first: Cristina

last: Martin-Martin

first: Amaya

last: Puig-Kröger

first: Angel

last: Corbí

first: Marcos

last: Araúzo-Bravo

first: Carlos

last: Lopez-Larrea

last: Vidal-Castiñeira

last: Sanz

first: Marta

last: Ruiz-Ortega


first: Ana

last: Aransay


title: ER beta regulated transcriptome in endometriotic tissues

city: HOUSTON

first: Sang

middle: Jun

last: Han

state: Texas

address: One Baylor Plaza

department: Molecular Cellular Biology

institute: Baylor College of Medicine

summary: The Estrogen Receptor beta (ERβ) has an essential role in endometriosis progression. However, the molecular mechanism of how ERβ drives endometriosis progression is not elucidated, yet. To define the role of genomic ERβ in endometriosis progression, we have employed whole-genome microarray expression profiling as a discovery platform to identify ERβ-regulated transcriptome in endometriotic tissues. To get this transcriptome, we applied endometrium specific ERβ overexpression (ERBOE) mouse model by crossing mouse having a pCAG promoter-loxPSTOPloxP-ERβ cassette with PRCre knockin mice that Cre recombinase cDNA was inserted into exon 1 of PR gene. Endometriosis was surgically induced in ERBOE mice and PRCre mice as the control by transplantation of uterine tissues. The ectopic lesions and eutopic endometrium were harvested at the estrus cycle in 4th weeks after endometriosis induction.

overall_design:
ERβ-regulated transcriptome analysis in ectopic lesions: We isolated uteri from ERBOE female mice (eight weeks old) and its female control mice (PRCre/+, eight weeks old) and then made endometrium fragments by using Miltex Medical Biopsy Punch Dermal 2 mm OR Grade. The endometriosis was surgically induced by implanting one uterus fragment isolated from ERBOE female mouse to wild-type intact C57BL/6J mouse (n=9, eight weeks old).  We also made endometrial pieces from uteri of female control mice (PRCre/+), and then implanted one endometrial piece to wild-type intact C57BL/6J mouse (n=9, eight weeks old) as the control.  At estrus cycle in 4th weeks of endometriosis induction, We harvested ERβ overexpressing and ectopic control lesions and then isolated total RNA from them.  After that, we combined total RNA isolated from three ectopic lesions to form a single group. Therefore, we made three RNA groups from nine ERβ overexpressing ectopic lesions and nine ectopic control lesions.

ERβ-regulated transcriptome analysis in eutopic endometrium: We isolated uteri from wild-type C57BL/6J female (eight weeks old), and then made endometrium fragments by using Miltex Medical Biopsy Punch Dermal 2 mm OR Grade. The endometriosis was surgically induced by implanting one uterus fragment isolated from wild-type C57BL/6J into ERBOE female mouse (eight weeks old) and female control mouse (PRCre/+, n=9/group, eight weeks old). At estrus cycle in 4th weeks of endometriosis induction, we harvested ectopic lesions and then isloated total RNA from them. After that, we combine total RNA from three eutopic endometria to form a single group. Therefore, we made three RNA groups from nine ERβ overexpressing eutopic endometrium and nine eutopic control endometrium.

Transcriptome analysis in the uterus: We harvested uteri ERBOE female mouse, and it's female control mouse (PRCre/+) (n=9/group, 12 weeks old) at estrus cycle and isolated total RNA from them. We combined total RNA from three uteri to form a single group.  Therefore, we made three RNA groups from nine ERβ overexpressing uteri and nine control uteri.


title: Estrogen Receptor beta cistrome in mouse endometriotic tissue.

summary: Estrogen Receptor beta (ERβ) has an essential role in endometriosis progression. However, the role of genomic ERβ in the pathogenesis of endometriosis is not elucidated, yet. To get ERβ cistrome, we employed endometrium specific ERβ overexpression (ERBOE) mouse model by crossing mouse having pCAG promoter-loxPSTOPloxP-ERβ cassette with PRCre knockin mice that Cre recombinase cDNA was inserted into exon 1 of PR gene. Using ERBOE mouse model, we determine ERβ-cistrome in endometriotic lesions and eutopic endometrium of mice with endometriosis.

overall_design:
ERβ cistrome analysis in ectopic lesions: We isolated uteri from ERBOE female mice (eight weeks old) and then made endometrium fragments by using Miltex Medical Biopsy Punch Dermal 2 mm OR Grade. The endometriosis was surgically induced by implanting one uterus fragment from ERBOE female mouse to wild-type intact C57BL/6J mouse (n=9, eight weeks old). At estrus cycle in 4th weeks of endometriosis induction, we harvested ectopic lesions and then pooled them. Uaing pooled ectopic lesions; we conducted the ERβ-ChIP Seq.

ERβ cistrome analysis in eutopic endometrium: We isolated uteri from wild-type C57BL/6J female (eight weeks old) and then made endometrium fragments by using Miltex Medical Biopsy Punch Dermal 2 mm OR Grade. The endometriosis was surgically induced by implanting one uterus fragment isolated from wild-type C57BL/6J into ERBOE female mouse (eight weeks old) (n=9, eight weeks old). At estrus cycle in 4th weeks of endometriosis induction, we isolated eutopic endometrium and then pooled them. Using pooled eutopic endometria, we conducted the ERβ-ChIP Seq.


title: Body fluid from the parasitic worm Ascaris suum inhibits broad-acting pro-inflammatory programs in dendritic cells

status: Public on Sep 11 2019

city: Lyngby

first: Pankaj

last: Arora

email: sbrix@dtu.dk, sbp@bio.dtu.dk, panar@dtu.dk, panar.arora@sund.ku.dk

address: Søltofts Plads - blg. 224 room 218, DK-2800 Kgs. Lyngby

department: Department of Biotechnology and Biomedicine

country: Denmark

institute: Technical University of Denmark

summary:
Purpose:  To characterize the processes defining the end dendritic cell (DC) phenotype, including the type of early transcriptional changes in pro-inflammatory cues towards regulatory or type 2 immune-based cues induced by a variety of exogenous and endogenous molecules.

Methods: Human peripheral blood mononuclear cells (PBMCs) were isolated from buffy coats from human donors using Ficoll-Paque gradient centrifugation. CD14+ monocytes were isolated from PBMCs by magnetic-activated cell sorting (MACS) and cultured in complete medium consisting of RPMI 1640 supplemented with 10% heat-inactivated fetal bovine serum, 2 mM L-glutamine, 50 µM 2-Mercaptoethanol, 1% Penicillin-Streptomycin at 37°C and 5% CO2. During the differentiation stage, complete medium was added 150 U/mL recombinant human IL-4 and 160 U/mL recombinant human GM-CSF to obtain monocyte-derived dendritic cells (moDCs). Medium was replaced after 3 days of culturing, and moDCs were used 6 days after the start of culture. The cells were on average >70% CD1a-positive, and with <3% CD14+CD16+ cells, based on flow cytometry, and responded with high levels of  IL-12p70 production upon stimulation with LPS and IFN-y (mean IL-12p70 production of 4641.8 pg/mL; SD = 688.1 pg/mL). Cells were harvested and rested for 1 hour at 37°C and 5% CO2 before stimulation. At this point, moDCs were supplemented with complete medium containing TSLP (to final concentration of 25 ng/mL), IL-25 (25 ng/mL), TSLP+IL-25 (both 25 ng/mL), helminth PCF (100 μg dry matter/mL, tested in different doses in pre-study experiments), butyrate (2 mM),  or succinate (0.5 mM and 2 mM, di-sodium succinate hexahydrate). Unstimulated cells were supplemented with complete medium alone. Immediately afterwards,  medium containing Escherichia coli O26:B6 LPS (final concentration of 100 ng/mL) and IFN-γ (10 ng/mL) was added. Cells were stimulated for 4 or 20 h at 37°C, 5% CO2, and 95% humidity.

Results: Our data show that helminth PCF and butyrate treatment suppress the Th1-inducing pro-inflammatory DC phenotype through induction of different transcriptional programs in DCs. RNA sequencing indicated that helminth PCF treatment strongly inhibited the Th1 and Th17 polarizing ability of LPS+IFN-γ-matured DCs by downregulating myeloid differentiation primary response gene 88 (MyD88)-dependent and MyD88-independent pathways in TLR4 signaling. By contrast, butyrate treatment had a strong Th1-inhibiting action, while transcripts encoding important gut barrier defending factors such as IL18, IL1B and CXCL8 were upregulated.

Conclusion: Collectively, our results further our understanding of how compounds from parasites and gut microbiota-derived butyrate may exert immunomodulatory effects on the host immune system.

overall_design: The transcriptional profile of stimulated human moDCs was evaluated, in triplicates, after 4 hours of stimulation. After stimulation for 20 hours, the cell-free culture supernatants were harvested and frozen at -80°C until further analysis. IL-12p70 levels were determined using ELISA in triplicates.

first: Janne

last: Moll

first: Daniel

last: Andersen

first: Christopher

middle: T

last: Workman

first: Andrew

last: Williams

first: Karste

last: Kristiansen

first: Susanne

last: Brix


title: Medicago truncatula seed development under greenhouse conditions

city: Beaucouze

first: Julia

last: Buitink

address: 42 rue Georges Morel

department: BAP

institute: INRAE

summary: Transcriptional profiling of seeds of Medicago truncatula during maturation. To identify genes that are regulated during seed maturation in the model legume Medicago truncatula, plants at flowering stage were grown at variable light and temperature conditions under greenhouse environment (period March-June). Seeds were then collected at different stages of development. Using the Medicago NimbleGen chip, a transcriptomic analysis was performed to follow the differential expression of genes during seed maturation.

overall_design: Seeds of Medicago truncatula grown at 27-25°C were collected at different developmental stages, 8 developmental stages were analysed. Two replicates from each developmental stage were used for dye switch, each time the control was considered as the earlier developmental stage vs the treatment corresponding to the later developmental stage. For each repetition 4 hybridisation were made: 7DAP vs 9DAP, 11DAP vs 14DAP, 17DAP vs 20DAP, Abs vs DS. For each biological replicates, RNA was extracted from 50 seeds collected from 5 different plants, grown in the same conditions. One replicate per array.

first: Michaela

last: Hundertmark

first: Karima

last: Righetti


title: The transcriptomic landscape of MAIT cell development in the thymus (C006 RNAseq data set)

status: Public on Sep 26 2019

city: Melbourne

first: Shian

last: Su

state: Victoria

address: 1G Royal Parade

department: Molecular Medicine

country: Australia

institute: Walter and Eliza Hall Institute of Medical Research

summary: We report the transcriptomic landscape of MAIT cell development by examining thymic immature stage 1 and mature stage 3 MAIT cells from mouse thymus, and thymic immature stage 1, stage 2  mature stage 3 MAIT cells from human thymus using RNAseq.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: We bulk-sorted (100 cell) each MAIT cell subset by flow cytometry and compared the differentially expressed genes (DEGs) between subsets. In addition, we single-cell sorted mouse mature MAIT cell subsets, performed single cell RNAseq comparison of mature thymic MAIT cell populations via clustering analysis to obtain in-depth information about the heterogeneity of functionally diverse mouse MAIT cells.

first: Hui-Fern

last: Koay

first: Daniela

last: Zalcenstein

first: Tracey

last: Baldwin

first: Peter

last: Hickey

first: Shalin

last: Naik

first: Matthew

last: Ritchie


title: Downregulation of CFIm25 amplifies dermal fibrosis through Alternative Polyadenylation

city: Suzhou

first: Hang

last: Ruan

state: Jiangsu

address: 199 Ren'ai Road

department: IBMS

country: China

institute: Soochow University

summary: Systemic sclerosis (SSc - scleroderma) is a multi-system, fibrotic disease affecting skin and internal organs. Alternative polyadenylation (APA) involves the differential usage of polyadenylation signals, which gives rise to transcripts with variable 3'UTR length. The mammalian Cleavage factor I 25kDa subunit (CFIm25, encoded by NUDT21) is a key regulator of alternative polyadenylation APA and its depletion causes predominantly 3'UTR shortening through loss of stimulation of distal polyA sites resulting in increased used of proximal polyA sites. A shortened 3'UTR will often lack microRNA target sites, resulting in increased mRNA translation due to evasion of microRNA-mediated gene repression. Herein, we report that CFlm25 is downregulated in SSc skin, and primary dermal fibroblasts, andas well as in two murine models of dermal fibrosis.The purpose of this experiment is to identify the APA targets of CFIm25 in human skin fibroblasts. Following the knockdown of CFIm25 in normal human skin fibroblasts, we identified 971 genes with shortened 3’UTRs, including those involved in the transforming growth factor-beta signaling pathway.

overall_design: mRNA profiles of primary human skin fibroblasts transfected with control or CFIm25 siRNA were generated by RNA-Seq using Illumina GAIIx

first: Tingting

last: Weng Mills

first: Yu

last: Xiang

first: Ping

last: Ji

first: Leng

last: Han

first: Eric

last: Wagner

first: Shervin

last: Assassi


title: Gene expression profile of thymic AML generated by NP23 and NHD13 transgenes

status: Public on Sep 19 2019

city: Bethesda

last: Aplan

state: Maryland

address: 37 convent drive

department: Genetics

institute: CCR-NCI-NIH

summary: Gene expression profile of AML generated via 3 related transgenes is compared.

overall_design: Comparison of gene expression profile from NP23, NHD13, and NP23-NHD13 AML.

first: Vijay

last: Negi

first: Subhadip

last: Kundu


title: The transcriptomic landscape of MAIT cell development in the thymus

last: Su


title: Microarray analysis of miR-511-3p regulation of macrophage polarization

city: Baltimore

first: Danh

middle: Cong

last: Do

state: MD

address: 5501 Hopkins Bayview Circle, 3A.4

department: Medicine

institute: Johns Hopkins University

summary: The goal of this study is to identify potential mechanism in which miR-511-3p regulates macrophage polarization

overall_design: We examined the mRNA transcriptome of macrophages that were transfected with miR-511-3p or miRNA mock control followed by IL-4 and LPS stimulation.

first: Fauod

last: Ishmael

first: Peisong

last: Gao

middle: C


title: Proliferation-competent Tcf1+ CD8 T-cells in dysfunctional populations are CD4 T-cell help independent

city: Freising

first: Dietmar

last: Zehn

address: Weihenstephaner Berg 3

department: Division of Animal Physiology and Immunology

institute: Technical University of Munich

summary: Effector CD8 T-cell responses in chronic infection and cancer are maintained by proliferation competent progenitors, which share features with the progenitors of memory T-cells in acutely resolved infections. Combining classical assessment of population dynamics with single cell RNA-sequencing, we discovered a switch in the need for CD4 help between related populations in acute and chronic infection. While in acute infection memory T-cells but not effector T-cells are CD4 help dependent, we found the opposite in chronic infection. Thus, progenitor cells in chronic infection acquire a level of autonomous function that is not seen among their counterparts in acute infection. Vice versa, the dependece of the effector cells highlight why a functional antigen-specific CD4 T-cell compartment is critical in therapeutic settings.

overall_design: Single cell splenocyte suspensions were obtained by mashing total spleens through a 100 μm nylon cell strainer (BD Falcon) and red blood cells were lysed with a hypotonic ACK buffer. Transgenic CD8+ T-cells were isolated using the mouse CD8+ T-cell enrichment kit (Miltenyi Biotech, Bergisch-Gladbach, Germany). 2x10e3 CD45.1+ P14 TCRαβ were transferred into naïve CD45.2+ C57BL/6 mice. 5x10e6 pfu wild-type LCMV c13 was diluted in PBS and injected intravenously. In vivo depletion of CD4 lymphocytes was achieved by intraperitoneal injection of 300 µg anti-mouse CD4 antibody (clone GK1.5; Bio X Cell, USA) diluted in PBS and injected on day -2, +1, and thereafter on each fifth day after infection. At day 40 post infection, splenocytes were enriched for CD45.1 + P14 T-cells using anti-CD45.1 biotin/ anti-biotin conjugated microbeads and magnetic MACS cell separation (Miltenyi Biotech, Bergisch-Gladbach, Germany). Single-cells were sorted on BD FACS Fusion (100 micron nozzle, standard operation settings, single-cell purity, index sorting). Individual cells meeting the gating strategy were sorted directly in lysis buffer into individual wells of a low-binding PCR plate. Immediately after sorting, each plate was spun down, snap-freezed on dry ice and stored at -80oC until use. The single-cell libraries were generated using the previously described SCRB-seq protocol (doi: https://doi.org/10.1101/003236), with some modifications.  After RNA purification and reverse transcription, the generated single-cell cDNA was amplified for 22 cycles. The barcoded single-cell amplicons were purified with the use of (0.6x) Agencourt AMPure XP beads. 1 ng of the resulting amplified cDNA were used for library preparation with the Illumina Nextera XT DNA Library reagents (FC-131-1024, Illumina). After PCR amplification of the fragmented libraries, the samples were purified with (0.6x) Agencourt AMPure XP beads and eluted in 10 µl of molecular grade water. The quality of the resulting library was assessed with the use of Agilent High Sensitivity DNA Kit (5067-4626, Agilent). The library quantification was performed based on the Illumina recommendations (SY-930-1010, Illumina) with the use of KAPA SYBR FAST qPCR Master Mix (KK4600, Kapa Biosystems). The samples were sequenced on Illumina HiSeq 2500 system at the following conditions – high output run mode, paired-end, 16 bp read 1, 49 bp read 2, single-indexed sequencing resulting in 1 million reads per single-cell. A total of 1728 single-cells were sequenced – 864 ctrl and 864 w/o CD4 single-cells. The cells per each condition were derived from three experimental animals (288 single-cells from an animal).

first: Kristiyan

last: Kanev

first: Ming

last: Wu

first: Patrick

last: Roelli

first: Christine

last: Wurmser


title: Fe limitation decreases transcriptional regulation over the diel cycle in the model diatom Thalassiosira pseudonana

city: Seattle

first: Ginger

last: Armbrust

state: WA

address: 616 NE Northlake Pl

department: Oceanography

institute: University of Washington

summary: Iron (Fe) is an important growth limiting factor for diatoms and its availability is further restricted by changes in the carbonate chemistry of the water. We investigated the physiological attributes and transcriptional profiles of the diatom Thalassiosira pseudonana grown on a day:night cycle under different CO2/pH and iron concentrations, that in combination generated available iron (Fe’) concentrations of 1160, 233, 58 and 12 pM.  We found the light-dark conditions to be the main driver of transcriptional patterns, followed by Fe’ concentration and CO2 availability, respectively. At the highest Fe’ (1160 pM), 55% of the transcribed genes were differentially expressed between day and night, whereas at the lowest Fe’ (12 pM), only 28% of the transcribed genes displayed comparable patterns. While Fe limitation disrupts the diel transcriptional patterns for genes in most central metabolism pathways, the diel periodicity of light- signaling molecules and glycolytic genes, was relatively robust in response to reduced Fe’. Moreover, we identified a non-canonical splicing of transcripts encoding triose-phosphate isomerase, a key-enzyme of glycolysis, generating transcript isoforms that would encode proteins with and without an active site. Transcripts that encoded an active enzyme maintained a diel pattern at low Fe’, while transcripts that encoded the non-active enzyme lost the diel pattern. This work illustrates the interplay between nutrient limitation and transcriptional regulation over the diel cycle. Considering that future ocean conditions will reduce the availability of Fe in many parts of the oceans, our work identifies some of the regulatory mechanisms that may shape future ecological communities.

overall_design: Axenic Thalassiosira pseudonana (CCMP 1335) was grown in batch cultures using chelexed Aquil media with the addition of either 1000 nmol L-1 or 50 nmol L-1 iron (EDTA at 100 µmol L-1). Cells were grown at 20˚C under a 12:12 light:dark cycle at 50 µmol photons m-2 sec-1. Prior to start of the experiments, cells were grown at the same light and acclimated to iron-replete (1000 nM) or iron-limiting (50 nM) conditions for at least a month (~20 generations at Fe-limiting, ~40 generations at iron-replete), but not to their respective CO2/pH conditions. The media was bubbled with air containing 400 or 800 ppm CO2 prior to cell inoculation resulting in pH of 8.1 and 7.8 respectively. The starting cell concentration for the three experimental replicates was 30,000 cell/mL. The combination of Fe addition and pH resulted in four concentration of available Fe: 1160, 233, 58 and 12 pM . All experiments were performed in triplicate. Samples were collected in triplicate for each of the experimental replicate for: macronutrients, fluorescence, Fv/Fm, carbonate chemistry measurements, and flow cytometry. All experimental samples were drawn from the bottles via a syringe port 6 hours into the light (midday) and 6 hours into the dark phase (midnight). Samples for transcriptomes were collected over one day during the exponential growth phase at 6 hours into the light and 6 hours into the dark phase.

first: Johanna

last: Goldman

first: Megan

last: Schatz

first: Chris

last: Berthiaume

first: Sacha

middle: N

last: Coesel

first: Mónica

middle: V

last: Orellana

first: E


title: Genome Wide Chromatin Mapping of accessibility (ATAC-seq) Dichotomous effects of REV-ERBa on group 3 innate lymphoid cells

city: Columbus

middle: Leonard

last: Collins

state: OH

address: 770 BRT,  460 W 12th Ave

department: Microbial Infection and Immunity

institute: Ohio State University

summary: Circadian rhythm influences the functions of ILC3, and the circadian regulator, REV-ERB, has differential impacts on the development, metabolism, and cytokine secretion of ILC3 subsets.

overall_design: Examination of 2 different histone modifications and accessability in 2 different cell types

first: Eugene

last: Oltz

first: Qianli

last: Wang

first: Marco

last: Colonna


title: Tribolium castaneum experimental evolution

city: Münster

first: Joachim

last: Kurtz

address: Hüfferstraße 1

department: Evolution and Biodiversity

institute: University of Münster

summary: We report Illumina-generated RNASeq data of several populations of Tribolium castaneum larvae selected for higher or lower immune priming specificity as well as unselected control populations. From each of these populations, we injected groups of 20 larvae with either one of three bacteria species or left them untreated as controls. Whole body samples were taken 6h after injection and used for RNASeq Analysis.

overall_design: Examination of three selection treatments exposed to four different priming conditions

first: Kevin

last: Ferro


title: Genome-Wide Profiling of Allergic Asthma Peripheral Blood

city: South San Francisco

first: David

middle: Fong

last: Choy

address: 1 DNA Way

institute: Genentech, Inc.

summary: Gene expression microarray analysis of PAXgene of allergic asthma patients at baseline (www.clinicaltrials.gov  identifier NCT00314574)

overall_design: PAXgene mRNA analysis by Human Genome U133 Plus 2.0 Array (Affymetrix, Santa Clara, Calif)

middle: F


title: A Unique Epigenomic Landscape Defines Human Erythropoiesis (RNA-seq)

city: New Haven

first: Vince

last: Schulz

state: CT

address: 333 Cedar St. LMP 4085

department: Department of Pediatrics

institute: Yale University

summary: Mammalian erythropoiesis yields a highly specialized cell type, the mature erythrocyte, evolved to meet organismal needs of increased oxygen carrying capacity. To better understand regulation of erythropoiesis, we performed genome-wide chromatin accessibility studies, DNA methylation studies, and transcriptome analyses and correlated this with genomic organization in highly purified populations of primary human erythroid cells across the stages of erythroid development and differentiation. Gene expression patterns and chromatin state dynamics differed significantly between erythroid stages, with significant transitions between some stages indicating cell stage-specific gene regulation during erythropoiesis is a stepwise and hierarchical process involving many cis-regulatory elements. Numerous erythroid-specific, nonpromoter sites of chromatin accessibility were identified, many linked to erythroid cell phenotypic variation and inherited disease. A limited number of sites of chromatin accessibility identified in hematopoietic stem and progenitor cells were also identified in cells committed to the erythroid lineage, demonstrating limited early chromatin priming of erythroid genes during hematopoiesis. Chromatin accessibility of terminally differentiating erythroid cells defined a unique subset of highly specialized cells vastly dissimilar from other hematopoietic cell types. These epigenetic and transcriptome data are powerful tools to study human erythropoiesis

overall_design: Erythroid cell culture of human umbilical cord derived CD34+ human hematopoietic stem and progenitor cells (HSPCs) and fluorescence-activated cell sorting to purify discrete populations of progenitor cells at differing stages of erythroid development and differentiation were performed on three replicate sets of cells.  RNA-sequencing was then performed on the purified cells.  Single end  51 base reads were obtained on an Illumina HiSeq 2500 sequencer.  The data is similar to GSE61566 but with higher quality.

first: Vincent

middle: P

first: Hongxia

last: Yan

first: Kimberly

last: Lezon-Geyda

first: Yelena

last: Maksimova

first: Xiuli

last: An

first: John

last: Hale

first: Christopher

last: Hillyer

first: Narla

last: Mohandas

middle: G

last: Gallagher


title: A Unique Epigenomic Landscape Defines Human Erythropoiesis (ERRBS)

type: Methylation profiling by high throughput sequencing

overall_design: Erythroid cell culture of human umbilical cord derived CD34+ human hematopoietic stem and progenitor cells (HSPCs) and fluorescence-activated cell sorting to purify discrete populations of cells at differing stages of erythroid development and differentiation were performed on three replicate sets of cells.  Enhanced Reduced Representation Bisulfite sequencing was performed  to identify patterns of cytosine methylation.  Single end  51 base reads were obtained on an Illumina HiSeq 2000 sequencer.

middle: D

first: Patrick


title: A Unique Epigenomic Landscape Defines Human Erythropoiesis (ATAC-seq)

overall_design: Erythroid cell culture of human umbilical cord derived CD34+ human hematopoietic stem and progenitor cells (HSPCs) and fluorescence-activated cell sorting to purify discrete populations of cells at differing stages of erythroid development and differentiation were performed on two replicate sets of cells.  ATAC-sequencing was then performed on the purified cells to identify genomic regions with open chromatin.  Single end  76 base reads were obtained on an Illumina HiSeq 2500 sequencer.


title: A role for the RNA Polymerase II-CTD phosphatase, FCP1 in the oxidative stress response

status: Public on Sep 10 2019

city: Utrecht

first: Marian

last: Groot Koerkamp

state: Utrecht

address: Heidelberglaan 25

department: Research

country: Netherlands

institute: Princess Maxima Center for Pediatric Oncology

summary: Fcp1 is a protein phosphatase that facilitates transcription elongation and termination by dephosphorylating the C-terminal domain of RNA Polymerase II. Here, we report an unanticipated role in the repression of the oxidative stress induced genes. High-throughput genetic and gene expression profiling of FCP1 mutants uncovered a link to Skn7, a key transcription factor in the oxidative stress response pathways, as well as a link to the Mediator complex kinase subunit, Cdk8. Interestingly, loss of CDK8 suppressed FCP1 mutant growth phenotypes upon exposure to oxidative stress, an effect dependent on SKN7. Furthermore, FCP1 and CDK8 regulated Skn7 protein levels and stability, as well as the expression of target genes through interdependent mechanisms. Focusing on the latter, while the FCP1 mutant robustly increased mRNA levels of Skn7-dependent genes under basal and induced conditions, it decreased Skn7 promoter occupancy, both defects normalized by loss of CDK8. Intriguingly, both FCP1 and CDK8 also altered Skn7 phosphorylation levels, a modification known to control Skn7 function, although the significance of this effect and residues involved remain unclear. Loss of CDK8 also alleviated the sensitivity of FCP1 mutants to other stressors, implicating these factors in regulating the response to other environmental insults.

overall_design: Microarray expression profiling was performed in duplicate. Cultures were grown in a 24-well plate incubator/reader to mid-log phase, with spiked-in RNA controls to monitor global changes in mRNA levels. Since no global changes in mRNA levels were detected, expression values were normalized to total mRNA levels. Fold changes were determined by comparing mutant to wild type profiles, with differentially expressed genes having a p-value <0.01 and absolute fold change >1.7 .

first: Maria

last: Aristizabal

first: Kristy

last: Dever

first: Gian

middle: L

last: Negri

first: Mary

last: Shen

first: Nicole

last: Hawe

first: Joris

last: Benschop

first: Frank

last: Holstege

first: Nevan

last: Krogan

first: Ivan

last: Sadowski

first: Michael

last: Kobor


title: Non-core subunits of the PRC2 complex are collectively required for its target site specificity

city: Copenhagen N

first: Jonas

middle: Westergaard

last: Hojfeldt

address: Ole Maaloes Vej 5

department: BRIC

institute: University of Copenhagen

summary: The Polycomb repressive complex 2 (PRC2) catalyzes H3K27 methylation across the genome, which through involvement in transcriptional regulation is critical in establishment of cell identity. Because of its essential function during development and in cancer, understanding the establishment of genome-wide H3K27 methylation patterns has been the focus of intense investigation. PRC2 methylation activity is abundant and dispersed throughout the genome, but highest activity is specifically directed to a subset of target regions that are stably occupied by the complex and highly enriched for H3K27me3. Here we show, by systematically knocking out single and multiple non-core subunits of the PRC2 complex in mouse embryonic stem cells (mESCs), that they each contribute in directing PRC2 activity to targets sites. Furthermore, combined knockout of six non-core subunits reveal that, while dispensable for global H3K27 methylation levels, the non-core PRC2 subunits are collectively required for focusing H3K27me3 activity to specific sites in the genome.

overall_design: H3K27me3, SUZ12, JARID2, PCL2 and Flag enrichment profiles (ChIPseq) analyzed in mouse ES cells which are wildtype, knockout for one or multiple PRC2 subunits (SUZ12, AEBP2, EPOP, JARID2, PCL1, PCL2, PCL3), or expressing Flag-tagged SUZ12 fragment in SUZ12 KO cells or Flag-tagged PRC2 subunit (AEBP2, EPOP, JARID or PCL2) in cells with combined knockout of all non-core PRC2 subunits. RNAseq analysis in mouse ES cells which are wildtype or knockout for one or multiple PRC2 subunits (SUZ12, AEBP2, EPOP, JARID2, PCL1, PCL2, PCL3).

middle: W

first: Anne

last: Laugesen

first: Lin

last: Hedehus

first: Kristian

last: Helin

first: Tülin

last: Tatar

first: Laura

last: Wiehle


title: Expression of genes in red fruit of Andean tomato (Solanum lycopersicum) and Solanum pimpinellifolium

city: Rosario

first: Estela

middle: Marta

last: Valle

address: Ocampo y Esmeralda

country: Argentina

institute: IBR (CONICET-UNR)

summary:
In this study, we explored the metabolome and transcriptome of the ripe fruit in nine landrace accessions representing the seven genetic groups and compared them to the mature fruit of the wild progenitor S. pimpinellifolium.
The goal is to shed light in understanding the factors responsible for acquiring tomato fruit quality (taste and flavour) at molecular level during the domestication process.

sample_organism:
Solanum lycopersicum
Solanum pimpinellifolium

overall_design: The tomato cultivars analysed were 10 (in triplicate, that is 30 samples in total), 9 were local varieties (accessions numbers 549, 557, 560, 571, 572, 3806, 3815, 3836 and 3842) and one was S. pimpinellifolium (accession number LA1589).

first: Matilde

last: D´Angelo

middle: I

last: Zanor

middle: M


title: SUMO-chain-regulated proteasomal degradation timing exemplified in DNA replication initiation

city: Milan

last: Psakhye

address: Via Adamello 16

country: Italy

institute: IFOM, the FIRC Institute of Molecular Oncology

type: Genome binding/occupancy profiling by genome tiling array

summary: Similar to ubiquitin, SUMO forms chains, but the identity of SUMO-chain-modified factors and the purpose of this modification remain largely unknown. Here, we identify budding yeast SUMO protease Ulp2, able to disassemble SUMO chains, as a DDK interactor enriched at replication origins that promotes DNA replication initiation. Replication-engaged DDK is SUMOylated on chromatin, becoming a degradation-prone substrate when Ulp2 no longer protects it against SUMO-chain assembly. Specifically, SUMO chains channel DDK for SUMO-targeted ubiquitin ligase Slx5/Slx8-mediated and Cdc48 segregase-assisted proteasomal degradation. Importantly, the SUMOylation-defective ddk-KR mutant rescues inefficient replication onset and MCM activation in cells lacking Ulp2, suggesting that SUMO chains time DDK degradation. Using two unbiased proteomic approaches, we further identify subunits of the MCM helicase and other factors as SUMO-chain-modified degradation-prone substrates of Ulp2 and Slx5/Slx8. We thus propose SUMO-chain-/Ulp2-protease-regulated proteasomal degradation as a mechanism that times the availability of functionally-engaged SUMO-modified protein pools during replication and beyond.

overall_design: Protein binding profiles by ChIP-on-chip analysis were generated as described (Bermejo et al., 2009). BrdU incorporation profiles by BrdU IP-on-chip have been generated as described (Katou et al., 2003). Labeled probes were hybridized to Affymetrix S.cerevisiae Tiling 1.0 (P/N 900645) arrays and processed with TAS software.

first: Federica

last: Castellucci

first: Dana

last: Branzei


title: Transcriptome of activated human and mouse MAIT cells

city: Oxford

first: Timothy

last: Hinks

state: United Kingdom

address: John Radcliffe Hospital, Headley Way, Oxford

department: NDM Experimental Medicine - New College

country: United Kingdom

institute: University of  Oxford

summary: We sought to describe in detail the consequences of MAIT cell activation using a transcriptomic approach to define the basic transcriptome of a MAIT cell in both humans and mice and to determine how this is modulated by activation. Fresh human peripheral blood cells were obtained from three donors. These were cultured for 6 hours with (‘stimulated’) or without (‘unstimulated’) 10 nM 5-OP-RU, magnetically enriched on MR1-tetramer+ cells, and flow-sorted for RNA sequencing of live CD3+TCR Valpha7.2+ MR1-5-OP-RU tetramer+ MAIT cells, and of unstimulated naïve live CD8+CD45RA+ T cells as a comparator cell type. For the murine samples we  included within the same sequencing experiment live pulmonary CD3+45.2+19-MR1-5-OP-RU tetramer+ MAIT cells which were magnetically enriched and flow-sorted from the lungs of mice 7 days after infection with 1x104 CFU L. longbeachae (‘acute’), or at least 12 weeks post infection (‘resolution’) or 7 days after a second intranasal infection with 2x104 CFU L. longbeachae in mice that had recovered from infection 12 weeks previously (‘reinfection’). Live CD3+CD45.2+CD19-CD8+CD44-CD62L+ naïve T cells from uninfected mice were used as a comparator cell type.

overall_design: Illumina sequencing of human and murine MR1-5-OP-RU tetramer+ MAIT cells in comparison with naïve CD8 T cells. 3 biological replicates of each of the following conditions: Human peripheral blood MAIT cell unstimulated. Human peripheral blood MAIT cells stimulated for 6 h with 5-OP-RU. Human peripheral blood CD8+45RA+ T cells. Murine pulmonary MAIT cells 7 days after legionella infection, 12 weeks after legionella infection, 7 days after reinfection with legionella, Murine naive pulmonary CD8+CD45+44-62L+ T cells. Full details of the study can be downloaded at https://www.biorxiv.org/content/early/2018/12/09/490649?rss=1

first: Emanuele

last: Marchi

middle: S


title: Stage-specific combinations of opposing poly(A) modifying enzymes guide gene expression during early oogenesis

status: Public on Sep 09 2019

city: Martinsried

first: Assa

last: Yeroslaviz

state: Bavaria

address: Am Klopferspitz 18

department: computational Biology

institute: Max-Planck-Institute for biochemistry

summary: Comparision of mRNA abundance in C. elegans polyA polymerase (cytoPAP) and deadenylase (DeAd) mutants.

overall_design: Comparision of adult cytoPAP single and cytoPAP/DeAd double  mutants.

first: Marco

last: Nousch


title: Effect of EGC treatment on genome instability induced by cisplatin treatment

city: Kitakyushu

first: Masaoki

last: Kohzaki

state: Fukuoka

address: 1-1 Iseigaoka Yahatanishi-ku

department: Institute of Industrial Ecological Sciences

institute: University of Occupational and Environmental Health, Japan

type: Genome variation profiling by genome tiling array

summary: Cisplatin treatment causes genome instability by single-strand annealing (SSA) activation in some cancer cells. Therefore, we checked whether EGC, a RAD52 inhibitor, can restrain genome instability induced by cisplatin treatment.

overall_design: In total, 10 samples: 2 Input control (4 different conditions) in WT and RECQL4 KO cells.


title: Transcriptomic analysis of mouse subcutaneous tumor after intratumoral treatment with SLR14 or vehicle

status: Public on Sep 07 2019

first: Xiaodong

last: Jiang

address: 300 Cedar Street

summary: We subcutaneously injected 5x105 YUMMER1.7 melanoma into right flank of C57BL/6J mice. 7 days later, the mice were intratumorally treated with 1 mg/kg SLR14 or vehicle every 3 days, for a total of 3 cycles. We observed a significant tumor growth delay in SLR14-treated mice compared to vehicle-treated mice.

overall_design: The tumors were intratumorally treated with 1 mg/kg SLR14 or vehicle. After 3 cycles of treatment, tumors were harvested and total RNAs were extraced.

first: Akiko

last: Iwasaki


title: Single cell RNA-Seq of adult mouse pancreatic stem cells and early progenitors

city: Dresden

first: Anthony

last: Gavalas

address: Fetscherstr. 105

institute: TU Dresden

summary: Aldh1b1 expressing, adult mouse pancreatic stem cells, were isolated and subjected to single cell RNA Seq.

sample_organism:
Mus musculus
synthetic construct

platform_organism:
Mus musculus
synthetic construct

overall_design: Aldh1b1CreERT2 / ROSA26 LSLtdTomato double heterozygous 8 week-old mice were injected intraperitoneally with 1 mg of corn oil dissolved tamoxifen (at 20 mg/ml) for five consecutive days and tdTomato+ cells were isolated by FACS one day later.

first: Ekaterina

last: Mameishvili

first: Mathias

last: Lesche


title: Identifying differential expressed genes in LNvs with Atx2 knocked down or in LNvs of tyf mutant

status: Public on Sep 06 2019

city: Evanston

first: Ravi

last: Allada

state: IL

address: 2205 Tech Drive

department: Neurobiology

institute: Northwestern University

summary: We applied RNA-seq to FACS sorted LNvs (circadian neurons) in Pdf-Gal4 driven Atx2 RNAi flies and tyf mutant flies (tyf(e)) to look at gene expression differences compared to WT flies.

overall_design: mRNA profiles of LNvs from Pdf>Atx2 RNAi flies at ZT00 and ZT12 and from tyf(e) flies at ZT04 and ZT16.

first: Ela

last: Kula-Eversole

first: Fangke

last: Xu

first: Marta

last: Iwanaszko


title: Genome-wide long non-coding RNAs and mRNAs analysis of the tissues related to ovarian endometriosis

city: Beijing

first: Chen

last: Zhang

address: NO.11, Xizhimen South Street

department: Gynecological Oncology Center

institute: Peking University People’s Hospital

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

summary: To investigate the function of long non-coding RNA (lncRNA) in ovarian endometriosis and explore its pathogenesis from a new prospective pathway, we conducted genome-wide microarray expression profiling.GO and KEGG analysis demonstrated that the differential mRNAs in ECvsEU and NOvsEU mostly focused on cell adhesion and biological adhesion pathways, nevertheless ECvsNO on molecular metabolism pathways. CHL1 was the most up-regulated mRNA in EC than EU, and the expression of its two antisense lncRNAs, CHL1-AS1 and CHL1-AS2 exhibited the same tendency. They were significantly correlated with each other through bioinformatic calculation.GSEA analysis revealed that CHL1-AS1 and CHL1-AS2 were conspicuously concerned with the same gene set. Validated by qRT-PCR, CHL1-AS2 was higher expressed in EC than EU. It was also up-regulated in NO, and the relative fold changes in EC/EU and NO/EU showed no statistical significance (P>0.05). Furthermore, the value of EC/NO was more closed to 1 when sample size was enlarged, presenting the near expression of CHL1-AS2 in EC and NO. Consequently, we supposed that CHL1, CHL1-AS1 and CHL1-AS2 may play an important part in ovarian endometriosis.

overall_design: We collected ectopic endometrium (EC), normal ovarian (NO) and ectopic endometrium (EU) from four patients with ovarian endometriosis, and compared the lncRNA/mRNA expression files of these three kinds of tissues in pairs

first: Wei

last: Wu

first: Jianjun

last: Luo

first: Jing

last: Guan

first: Xiaohong

last: Chang


title: TGF-b-activated LncRNA LINC00115 is a critical regulator for glioma stem-like cell tumorigenicity

status: Public on Sep 08 2019

city: Shanghai

first: Haizhong

last: Feng

state: Shanghai

address: Pujian Road 160

department: Ren Ji Hospital

institute: Shanghai Jiao Tong University

summary: Long non-coding RNAs (lncRNAs) are critical regulators in cancer. However, the involvement of lncRNAs in TGF-beta-regulated tumorigenicity is still unclear. Here we identify TGF-beta-activated lncRNA LINC00115 as a critical regulator in glioma stem-like cell (GSC) self-renewal and tumorigenicity. LINC00115 is upregulated by TGF-beta, acts as a miRNA sponge and upregulates ZEB1 by competitively binding miR-200s, thereby enhancing ZEB1 signaling and GSC self-renewal.

overall_design: Examing of TGF-beta on long non-coding RNA expression in glioma stem-like cells


title: The expression level of  microRNA after  knockdown of GATA3 in MCF-7 cells

city: Tianjin

first: Yan

last: Wang

address: #22 Qixiangtai Road

department: Department of Biochemistry and Molecular Biology

institute: Tianjin Medical University

summary: GATA3 is a basic and essential transcription factor that regulates many pathophysiological processes that is required for the development of mammary luminal epithelial cells. Loss-of-function GATA3 alterations in breast cancer are associated with poor prognosis. However, its regulation and function in miRNAs expression has been less explored.

overall_design: We establish stable transfectants of shGATA3 in MCF-7 cells and analyze the miRNA expression level by microRNA microarray. MCF-7 cells transfected with shSCR were used as a control group.

first: Yi

last: Zeng


title: RNA-Seq analysis miR-455-3p overexpression effect on breast cancer cell line

summary: MiR-455-3p has been reported to suppress the expression of ROCK2, HOXB5, hTERT, and RUNX2, which are involved in multiple biological processes including renal fibrosis, chondrogenic development and differentiation, Alzheimer’s disease, preeclampsia, and tumorigenesis. Here, we showed that miR-455-3p broadly inhibited TGF-beta-induced EMT by repressing the expression of Smad2, ZEB1, and HDAC2 in breast cancer cells, and that miR-455-3p loss-of-function promotes the acquisition of cell invasive properties and the ability to metastasize. These results indicate that miR-455-3p represents an important node that inhibits metastasis of breast cancer.

overall_design: MiR-455-3p mimics or controls were transfected into MCF-7 cells (n=3 for each group) for 48 hours. Total RNA was isolated using Trizol reagent (Invitrogen, USA). Agilent 2100 Bioanalyzer (Agilent Technologies, USA) was used to evaluate the RNA quality.


title: Microarray profiling of in vitro expanded FRCs cultured alone or with activated T cells

city: Boston

first: Kevin

last: Bi

state: MA

address: 450 Brookline Ave.

department: Pediatric Oncology

institute: Dana-Farber Cancer Institute

summary: To investigate whether FRCs express molecules capable of promoting the functions of activated T cells, we expanded FRCs from primary lymph node stromal cell (LNSC) cultures as previously described (Lukacs-Kornek et al., Nature Immunology, 2011), and then cultured them alone or with splenocytes activated with soluble antibody (0.25μg/ml) against CD3 (anti-CD3) and anti-CD28 for 16 hours. FRCs co-cultured with activated T cells upregulated expression of genes encoding molecules known to dampen T cell function such as Arg1, CD274 and Nos2. However, in response to activated T cells, FRCs also upregulated molecules with immunostimulatory capabilities such as Icosl, Cd40 and Il6.

overall_design: In vitro expanded FRCs cultured alone (2 biological replicates) or with splenocytes activated with soluble antibody (0.25μg/ml) against CD3 (anti-CD3) and anti-CD28 (2 biological replicates) for 16 hours. The FRCs were sorted as previously described (Malhotra et al., Nature Immunology, 2012) and processed for microarray analysis.

first: Flavian

last: Brown


title: Muscle-secreted G-CSF as a metabolic niche factor ameliorates loss of muscle stem cell in aged mice

first: Yong

address: 5 Dong Dan San Tiao

institute: School of Basic Medicine, Peking Union Medical College

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

overall_design: Refer to individual Series


title: Transcatheter aortic valve replacements alter circulating serum factors to mediate myofibroblast deactivation

city: Boulder

first: Kristi

last: Anseth

state: CO- COLORADO

address: 3415 Colorado Ave, 596 UCB

institute: University of Colorado - Boulder

summary: The transcatheter aortic valve replacement (TAVR) procedure has emerged as a minimally invasive treatment for patients with aortic valve stenosis (AVS). However, alterations in serum factor composition and biological activity after TAVR remain unknown. Here, we quantified the systemic inflammatory effects of the TAVR procedure and hypothesized that alterations in serum factor composition would modulate valve and cardiac fibrosis. Serum samples were obtained from patients with AVS immediately before their TAVR procedure (pre-TAVR) and about one month afterwards (post-TAVR). Aptamer-based proteomic profiling revealed alterations in post-TAVR serum composition, and ontological analysis identified inflammatory macrophage factors implicated in myofibroblast activation and deactivation.  Hydrogel biomaterials used as valve matrix mimics demonstrated that post-TAVR serum reduced myofibroblast activation of valvular interstitial cells relative to pre-TAVR serum from the same patient. Transcriptomics and curated network analysis revealed a shift in myofibroblast phenotype from pre-TAVR to post-TAVR and identified p38 MAPK signaling as one pathway involved in pre-TAVR-mediated myofibroblast activation. Post-TAVR serum deactivated valve and cardiac myofibroblasts initially exposed to pre-TAVR serum to a quiescent fibroblast phenotype. Our in vitro deactivation data correlated with patient echocardiography data and multi-morbidity scores, and correlations were dependent upon hydrogel stiffness. Sex differences in cellular responses to male and female sera were also observed and may corroborate clinical observations regarding sex-specific TAVR outcomes. Together, our observations support the hypothesis that alterations in serum composition after a TAVR procedure may promote an anti-fibrotic fibroblast phenotype.

overall_design: Male and female porcine VICs were isolated, seeded on PEG-norbornene hydrogels (elastic modulus ~5.8 kPa), and cultured in Media 199 (Life Technologies) supplemented with 1% human serum, 50 U/mL penicillin, 50 μg/mL streptomycin, and 1 μg/mL amphotericin B for 48 hours. Pre-TAVR and post-TAVR serum from 8 patients (4 male and 4 female) were tested in this experiment, resulting in 16 total samples.

first: Brian

middle: A

last: Aguado


title: Whole-transcriptome sequencing reveals heightened inflammation and defective host-defense responses in inflammation and defective host-defense responses in chronic rhinosinusitis with nasal polyps

status: Public on Sep 05 2019

city: Singapore

first: Nicholas

last: Ang

address: 8a Biomedical Grove, Singapore 138648

country: Singapore

institute: Singapore Immunology Network (SIgN)

summary: The pathways underlying chronic rhinosinusitis with nasal polyps (CRSwNP) are unclear. We conducted genome-wide gene expression analysis to determine pathways and candidate gene sets associated with CRSwNP.

overall_design: We performed whole-transcriptome RNA sequencing on 42 polyp (CRSwNP-NP) and 33 turbinate samples from non-CRS controls (CS-IT). We analyzed the differentially expressed genes, and gene sets that enriched in functional pathways

first: Anand

middle: K

last: Andiappan

first: Wei-jie


title: Identifying genes exhibiting cycling pattern at mRNA level in LNvs at different food/temperature conditions

first: Ravi

last: Allada

summary: We applied RNA-seq to FACS sorted LNvs (circadian neurons) w1118 flies (expressing mGFP in the LNv neurons) to look at gene expression pattern at different time of the day under different food/temperature conditions.

overall_design: mRNA profiles of LNvs from Pdf>mGFP flies sampled at 2hr intervals raised at standard 1.5x sucrose-yeast (SY) food at 25°C, 1.5xSY at 18°C, or 0.5xSY at 25°C.

first: Ela

last: Kula-Eversole

first: Marta

first: Fangke


title: Muscle-secreted G-CSF as a metabolic niche factor ameliorates loss of muscle stem cell in aged mice (scRNA-seq)

summary: Function and number of muscle stem cells (satellite cells, SCs) declines with muscle aging. Although SCs are heterogeneous and different subpopulations have been identified, it remains unknown if a specific subpopulation of muscle SCs selectively decreases during aging. Here, we find Pax7Hi cells are dramatically reduced in aged mice and this aged-dependent loss of Pax7Hi cells is metabolically mediated by myofiber-secreted granulocyte-colony stimulating factor G-CSF as the Pax7Hi SCs are replenished by exercise-induced G-CSF in aged mice. Mechanistically, we show that transcription of G-CSF (Csf3) gene in myofibers is regulated by MyoD in a metabolism-dependent manner and the myofibers-secreted G-CSF acts as a metabolic niche factor required for establishing and maintaining the Pax7Hi SC subpopulation in adult and physiological aged mice by promoting the asymmetric division of Pax7Hi and Pax7Mi SCs. Together, our findings uncover a metabolic niche role of muscle metabolism in regulating Pax7 SC heterogeneity in mice.

overall_design: Three subpopulations of satellite cells (Pax7Hi, Pax7Mi and Pax7Lo) were isolated by FACS based on levels of GFP (Pax7) from tibialis anterior muscle of Pax7-nGFP transgenic mice and subjected to single cell RNA sequencing (scRNA-Seq).

first: Hu

last: Li

first: Qian

last: Chen

first: Changyin

first: Ran

last: Zhong

first: Yixia

last: Zhao

first: Qianying

first: Weimin

last: Tong

first: Dahai

last: Zhu


title: Expression data and Copy Number Variations from Diffuse Large B Cell Lymphoma (DLBCL) patients

city: Bron

first: Sylvain

last: Mareschal

address: Centre de Biopathologie Est, 59 boulevard Pinel

department: NGS-HCL platform

institute: Hospices Civils de Lyon


title: X chromosome domain architecture regulates Caenorhabditis elegans lifespan but not dosage compensation [RNA-seq]

city: San Francisco

first: Elphege

last: Nora

state: CA

address: 555 Mission Bay Blvd S

department: CVRI

institute: UCSF

summary: Mechanisms establishing higher-order chromosome structures and their roles in gene regulation are elusive. We analyzed chromosome architecture during nematode X-chromosome dosage compensation, which represses transcription via a dosage-compensation condensin complex (DCC) that binds hermaphrodite Xs and establishes megabase-size topologically associating domains (TADs). We show that DCC binding at high-occupancy sites (rex sites) defines eight TAD boundary locations. Single rex deletions disrupted boundaries, and single insertions created new boundaries, demonstrating one rex site is necessary and sufficient for DCC-dependent boundary formation. Deleting eight rex sites (8rexΔ) recapitulated TAD structure of DCC mutants, permitting analysis when chromosome-wide domain architecture was disrupted but most DCC binding remained. 8rexΔ animals exhibited no changes in X expression and lacked dosage-compensation mutant phenotypes. Hence, TAD boundaries are neither the cause nor consequence of gene repression during dosage compensation. Abrogating TAD structure did, however, reduce thermotolerance, accelerate aging, and shorten lifespan, implicating chromosome architecture in regulating stress responses and aging.

overall_design: We performed in RNA-seq on five replicates of wild-type and 8rexΔ embryos and three replicates of DCC mutant embryos. For each replicate, worms were grown and embryos collected for all genotypes in parallel. Gene expression in 8rexΔ and DCC mutant is compared to wild-type expression.

first: Erika

middle: C

last: Anderson

first: Phillip

last: Frankino

first: Ryo

last: Higuchi-Sanabria

first: Qiming

last: Yang

last: Bian

first: Katie

last: Podshivolova

first: Aram

last: Shin

first: Cynthia

last: Kenyon

first: Andrew

last: Dillin

first: Barbara

middle: J

last: Meyer


title: X chromosome domain architecture regulates Caenorhabditis elegans lifespan but not dosage compensation [Hi-C]

overall_design: We performed in situ Hi-C on nuclei isolated from mixed stage embryos and processed data as in (Brejc et al., 2017). We performed Hi-C for two biological replicates of wild type, TY5815 rex-47Δ, TY5824 6rexΔ, TY5827 8rexΔ, and TY0810 DCC mutant and a single replicate for TY5818 3rexΔ, TY5868 8rexΔ plus rex-32, TY5872 8rexΔ plus rex-32 & rex-8, TY5854 rex-32 insert, TY5859 3rexΔ plus rex-47 on I, TY5860 3rexΔ plus rex-47 & rex-8 on I, and TY5867 3rexΔ plus rex-14, rex-47 & rex-8 on I.

first: Qian


title: Morphogenesis and differentiation of embryonic vascular smooth muscle cells in zebrafish

city: Worcester

first: Nathan

middle: D.

last: Lawson

address: 364 Plantation Street

department: Molecular, Cell, and Cancer Biology

institute: University of Massachusetts Medical School

summary: Molecular and cellular analysis of mural cell development during zebrafish embryonic development

overall_design: RNAseq was performed on mural or endothelial cells isolated from transgenic zebrafish embryos

first: Thomas

last: Whitesell

first: Sarah

last: Childs

first: Rui

last: Li


title: Transcriptomic analysis of embryonic brown adipose tissue (BAT)

city: Lille

first: Jérôme

last: Eeckhoute

address: Bâtiment J&K, Faculté de Médecine de Lille-Pôle Recherche, Boulevard du Professeur Leclerc

institute: CNRS

summary: BAT obtained from embryos at E14.5, E15.5 or E16.5 of C57Bl6J mice used to prepare RNA which was then processed for analysis using MoGene-2_1-st Affymetrix microarrays according to standard procedures.

overall_design: For each stage, 3 independent preparations containing BAT of 3 embryos were performed and used to prepare RNA which was then processed for analysis using MoGene-2_0-st Affymetrix microarrays according to standard procedures.

first: Alicia

last: Mayeuf-Louchart


title: X chromosome domain architecture regulates Caenorhabditis elegans lifespan but not dosage compensation [ChIP-seq]

first: Elphege

last: Nora

overall_design: We performed two ChIP-seq replicates with wild-type and 8rexΔ embryos and one replicate with TY5872 8rexΔ plus rex-32 & rex-8 and TY5867 3rexΔ plus rex-14, rex-8 & rex-47 embryos.


title: Muscle-secreted G-CSF as a metabolic niche factor ameliorates loss of muscle stem cell in aged mice (RNA-seq)

first: Yong

last: Zhang

overall_design: Transcriptional profile of TA muscle from young and aged mice

first: Hu

last: Chen

first: Changyin

first: Ran

last: Zhong

first: Yixia

last: Zhao

first: Qianying

first: Weimin

last: Tong

first: Dahai

last: Zhu


title: Gene expression changes in PC12 cells expressing GFP-mHtt-74Q treated with Guanabenz analogues

city: SINGAPORE

first: SUJOY

last: GHOSH

address: 8 COLLEGE ROAD

department: Cardiovascular & Metabolic Diseases

institute: DUKE-NUS Graduate Medical School

summary: To gain an overview of the cellular impact of Guanabenz analogues, we analyzed the gene expression changes in PC12 cells expressing GFP-mHtt-74Q utilizing Affimatrix rat genome microarrays. Following exposure of PC12 cells expressing GFP-mHtt-74Q to Compound 6 for 48 hrs, we noted the enhanced expression of over 46 genes and the reduced expression of 8 genes compared to DMSO

overall_design: Genome-wide gene expression analyses (RTA-1_0, Affymetrix Rat Transcriptome Array 1.0, Affymetrix, Cleveland, OH, USA) were performed using RNA extracted from PC12 cells expressing GFP-mHtt-74Q, identified in four groups with 3 replicates for each group: non-induced and DMSO-treated, induced and DMSO-treated, induced and 10 µM Compound 3-treated and induced and 10 µM Compound 6-treated (at) for 48 hrs.

first: Shirish

last: Shenolikar

first: Jeyapriya

middle: R

last: Sundaram

first: Sujoy

last: Ghosh


title: Transcriptome profiling of tdc and agdi clusters deletion mutant of Enterococcus faecalis V583.

city: Villaviciosa

first: Victor

last: Ladero

state: Select if applicable

address: Paseo Rio Linares S/N

department: Technology and Biotechnology of dairy products

institute: IPLA-CSIC

summary: The aim was to study the transcriptional profiling of the tdc and agdi clusters delection mutant E. faecalis V583 ΔtdcΔagdi (non-tyramine non-putrescine producer) compared to the wild type strain E. faecalis V583 (tyramine producer). We compared the expression profile of the strains grown in M17 medium with glucose as carbon source and suplemented with tyrosine.

overall_design: E. faecalis V583 ΔtdcΔagdi cells (test) compared with E. faecalis V583 cells (reference). Both strains grown in GM17 medium.

first: Marta

last: Perez

first: Marina

last: Calles-Enriquez

first: Beatriz

last: del Rio

first: Begoña

last: Redruello

first: Anne

last: de Jong

first: Oscar

last: Kuipers

first: Jan

last: Kok

first: Maria

last: Martin

last: Fernandez

first: Miguel

last: Alvarez


title: Distinct imprinting signatures and biased differentiation of human androgenetic and parthenogenetic embryonic stem cells [RNA-Seq II]

city: Jerusalem

first: Ido

last: Sagi

address: Givat Ram

department: Genetics

country: Israel

institute: The Hebrew University of Jerusalem

summary: Genomic imprinting is an epigenetic mechanism that results in parent-of-origin monoallelic expression of specific genes, which precludes uniparental development and underlies various diseases. Here, we explored molecular and developmental aspects of imprinting in humans by generating exclusively paternal human androgenetic embryonic stem cells (aESCs) and comparing them with exclusively maternal parthenogenetic ESCs (pESCs) and bi-parental ESCs, establishing a pluripotent cell system of distinct parental backgrounds. Analyzing the transcriptomes and methylomes of human aESCs, pESCs, and bi-parental ESCs enabled the characterization of regulatory relations at known imprinted regions and uncovered imprinted gene candidates within and outside known imprinted regions. Investigating the consequences of uniparental differentiation, we showed the known paternal-genome preference for placental contribution, revealed a similar bias toward liver differentiation, and implicated the involvement of the imprinted gene IGF2 in this process. Our results demonstrate the utility of parent-specific human ESCs for dissecting the role of imprinting in human development and disease.

overall_design: RNA sequencing analysis was performed on a total of 48 samples, including undifferentiated human aESCs and bi-parental ESCs, as well as human aESCs, pESCs and bi-parental ESCs differentiated into teratomas, trophoblast cells and hepatic cells.

first: Nissim

last: Benvenisty

first: Dieter

last: Egli


title: Distinct imprinting signatures and biased differentiation of human androgenetic and parthenogenetic embryonic stem cells [microarray]

summary: Genomic imprinting is an epigenetic mechanism that results in parent-of-origin monoallelic expression of specific genes, which precludes uniparental development and underlies various diseases. Here we explored molecular and developmental aspects of imprinting in humans by generating exclusively-paternal human androgenetic embryonic stem cells (aESCs) and comparing them with exclusively-maternal parthenogenetic ESCs (pESCs) and bi-parental ESCs, establishing a pluripotent-cell system of distinct parental backgrounds. Analyzing the transcriptomes and methylomes of human aESCs, pESCs and bi-parental ESCs enabled the characterization of regulatory relations at known imprinted regions and uncovered new imprinted gene candidates within and outside known imprinted regions. Investigating the consequences of uniparental differentiation, we showed the known paternal-genome preference for placental contribution, revealed a novel bias towards liver differentiation, and implicated the involvement of the imprinted gene IGF2 in this process. Our results demonstrate the utility of parent-specific human ESCs for dissecting the role of imprinting in human development and disease.

overall_design: Genome-wide DNA methylation profiling by Illumina Infinium HumanMethylation 450K Beadchip was performed on a total of 14 samples, including undifferentiated human aESCs, pESCs and bi-parental ESCs, teratomas generated from these cells and sperm samples.


title: Different Diets Change the Expression of Bovine Serum Extracellular Vesicle-miRNAs

status: Public on Sep 04 2019

first: suyu

last: quan

address: Yuanmingyuan West Road No.2, Haidian Distric

institute: Institute of Animal Sciences, Chinese Academy of Agricultural Sciences

type: Non-coding RNA profiling by high throughput sequencing

summary: The effects of different diets on bovine serum extracellular vesicle (EV)-miRNAs are explored by small RNA Solexa sequencing. We partly replaced alfalfa hay with whole cotton seed and soybean hull in the feed formula of treat cows. Small RNAs are enriched in bovine serum EVs, including miRNAs, snRNAs, tiRNAs, Cis-regulatory elements, piRNAs, etc. Totally 359 bos taurus miRNAs are identified by sequencing. There are 15 immune-related miRNAs in the top 20 serum EV-miRNAs, accounting for about 80% of the total. Seven differently expressed known miRNAs were detected in responding to different diets. KEGG analysis showed differently expressed miRNAs are related to hormone signal pathways and protein metabolism.

overall_design: Examination the EV-miRNA profiling changes of bovine sera responding to two different diets

first: Suyu

last: Quan

first: Xuemei


title: Microbial metabolic reprogramming regulates intraspecific competition of Enterobacteriaceae in the inflamed gut

city: Ann Arbor

first: Richard

last: McEachin

state: United States

address: 2800 Plymouth Road

department: DCM&B

institute: University of Michigan

summary: Imbalance in beneficial and harmful bacteria underlies gastrointestinal diseases, such as inflammatory bowel disease. Here, we demonstrated that certain E. coli strains, specifically adherent-invasive E. coli (AIEC), utilize a serine metabolism pathway to outcompete other E. coli strains in the inflamed gut. In contrast, amino acid metabolism has a minimal effect on their competitive fitness in the healthy gut. The availability of luminal serine used for the competition of E. coli is largely dependent on dietary intake, as the inflammation-induced blooms of AIEC are significantly blunted when amino acids, particularly serine, are removed from the diet. Thus, intestinal inflammation regulates the intraspecific competition between Enterobacteriaceae by eliciting their metabolic reprogramming.

overall_design: GF mice were mono-colonized with AIEC LF82 for 1 week. E. coli mono-colonized mice were then treated with 1.5% DSS for 5 days. Cecal content was harvested and microbial gene expression was analyzed by RNA-seq (N=4).

first: Sho

last: Kitamoto

first: Nobuhiko

last: Kamada


title: Zebrafish (Danio rerio) neural crest cell RNA-sequencing

city: Charlottesville

first: Sarah

last: Kucenas

state: VA

address: 90 Galderd Dr, Rm 312

department: Biology

institute: University of Virginia

summary: RNA-sequencing of neural crest cells collected from Gt(foxd3:mCherry);Tg(sox10:mEGFP) embryos

overall_design: foxd3+/sox10+ double positive neural crest cells (NCC) were collected from the trunk of Gt(foxd3:mCherry);Tg(sox10:mEGFP) embryos at 36 and 72 hpf and sent for sequencing. 3 replicates for each condition.

first: Andrew

last: Latimer

first: Yunlu

last: Zhu


title: Self-renewing Endometrial Epithelial Organoids of the Human Uterus [bulk RNA-seq data]

city: Columbia

first: Thomas

last: Spencer

state: MO

address: 920 East Campus Drive

department: Animal Sciences

institute: University of Missouri

summary: The inner lining of the human uterus, termed the endometrium, is replete with glands that are hypothesized to be important for establishment of pregnancy through interactions with other endometrial cells and the embryo. A three-dimensional culture system was utilized to establish and generate endometrial epithelial organoids from normal human endometrium that display long-term expandability, can be cryopreserved, and are hormone responsive. Here, single cell RNA-seq was used to create a high-resolution gene expression atlas of the endometrial epithelial organoids and to define responsiveness to reproductive hormones.

overall_design: In order to investigate the roles of uterine glands in first trimester human pregnancy, we used an established protocol of Matrigel and WNT-activating conditions to generate three-dimensional human uterine gland organoid (HUGO) cultures from endometrial biopsies. The HUGO expand long-term, are genetically stable, differentiate following treatment with reproductive hormones, and can be cryopreserved. After passage, HUGO were grown for 4 days in expansion medium and then treated with estrogen (E2) for 2 days and then either nothing (Control), E2 and medroxyprogesterone acetate (MPA) or E2+MPA+cAMP for a further 6 days (n=3 replicates per patient and treatment). Total RNA was extracted from the organoids using a standard TRIzol-based protocol and Direct-zol RNA MiniPrep Plus isolation kit (Zymo Research, R2070). RNA quality and concentration was determined by a Fragment Analyzer (Advanced Analytical Technologies). RNA library preparation and sequencing was conducted by Illumnia platform by Novogene, California.

first: Harriet

last: Fitzgerald

first: Pramod

last: Dhakal

first: Susanta

last: Behura

first: Daniel

last: Schust

middle: E


title: Impaired adult hippocampal neurogenesis in a mouse model of familial hypercholesterolemia: a role for the LDL receptor and cholesterol metabolism in adult neural precursor cells

city: Dresden

first: Gerd

last: Kempermann

state: Saxony

address: Tatzberg 41

institute: German Center for Neurodegenerative Diseases (DZNE)

overall_design: Refer to individual Series


title: Impaired adult hippocampal neurogenesis in a mouse model of familial hypercholesterolemia: a role for the LDL receptor and cholesterol metabolism in adult neural precursor cells (LDL treatment)

summary: In familial hypercholesterolemia (FH), mutations in the low-density lipoprotein (LDL) receptor (LDLr) gene result in increased plasma LDL cholesterol. Clinical and preclinical studies revealed an association between FH and hippocampus-related memory and mood impairment. We here asked whether hippocampal pathology in FH might be a consequence of compromised adult hippocampal neurogenesis. We evaluated hippocampus-dependent behaviour and neurogenesis in adult C57BL/6JRj and LDLr-/- mice. Behavioural tests revealed that adult LDLr-/- mice showed reduced performance in a dentate gyrus (DG)-dependent metric change task. This phenotype was accompanied by a reduction in cell proliferation and adult neurogenesis in the DG of LDLr-/- mice, suggesting a potential direct impact of LDLr mutation on NPC. We thus investigated the effects of elevated cholesterol and the function of LDLr in neural precursor cells (NPC) isolated from adult C57BL/6JRj mice in vitro. Exposure of NPC to LDL as well as LDLr gene knockdown reduced proliferation and disrupted transcriptional activity of genes involved in endogenous cholesterol synthesis and metabolism. The LDL treatment also induced an increase in intracellular lipid storage. Functional analysis of differentially expressed genes revealed parallel modulation of distinct regulatory networks upon LDL treatment and LDLr knockdown. Together, these results suggest that high LDL levels and a loss of LDLr function, which are characteristic to individuals with FH, might contribute to a disease-related impairment in adult hippocampal neurogenesis and, consequently, cognitive functions.

overall_design: Adult mouse hippocampal progenitor cells propagated in vitro were treated with human LDL or saline as a conrol for 48 h prior RNA extraction. Three independent replicates from different passages were performed.

first: Daiane

last: Engel

first: Anna

middle: N

last: Grzyb

first: Jade

last: de Oliveira

first: Alexandra

last: Pötzsch

first: Tara

last: Walker

first: Patricia

last: Brocardo

first: Andreza

last: de Bem


title: Real-time quantitative PCR analysis of jejunal and ileal mucosa from postnatal growth retardation and healthy pigs

city: Changsha

first: Ming

last: Qi

state: Hunan

address: 644 Yuanda 2nd Rd

institute: Insititute of Subtropical Agriculture

summary: The purpose of this study was to investigate the relative mRNA expression related to hormone, antioxidant capacity and immune responses in jejunal and ileal mucosa of healthy and postnatal growth retardation pigs. At 42 d of age, after overnight fasting,  six postnatal growth retardation pigs and six healthy pigs  were pair-matched by litter were selected for sampling. Samples of the jejunal and ileal mucosa were scraped and immediately snap-frozen in liquid nitrogen and stored at −80°C for RNA extraction. We used Roche LightCycler ® 480 Instrument PCR assay panel to quantitate gene expression of hormone, antioxidant capacity and immune responses relevant genes from jejunal and ileal mucosa.

overall_design: qPCR gene expression profiling.  Jejunal and ileal mucosa from 12 donors were used as indicated in the summary. Healthy pig was regareded as control group. Equal amount total RNA from each donor was extracted prior to gene expression analysis.  All samples were tested in triplicate. β-actin was used as a housekeeping gene to normalize target gene transcript levels

first: Bie

last: Tan


title: RNA-seq profiling of parental and NLUCAT1-deleted A549 cells under hypoxia

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

institute: IPMC/CNRS

summary: Parental or NLUCAT1 CRISPR/Cas9-deleted A549 clones (WT A549 Hx, n = 1 clone; DEL A549 Hx, n = 1 clone) were exposed to hypoxia (Hx) at 1% O2 for 24 hours. Libraries were generated from 500 ng of total RNAs using TruSeq Stranded Total RNA kit with Ribo-Zero (Illumina) and sequenced on a NextSeq500 sequencer (Illumina) with 2x75bp paired-end chemistry. Reads were aligned to the human genome release hg19 using STAR v2.4.0a with default parameters.

overall_design: 2 samples in monoplicates: 1 clone WT in Hx and 1 clone DEL in Hx

first: R

last: Rezzonico

first: N

last: Nottet

first: B

last: Mari

first: P

last: Barbry

first: K


title: Hypoxic transcriptomic signature of A549 cells (RNA-Seq)

summary: To assess the transcriptomic response of the LUAD cell line A549 to hypoxia, cells were exposed to 1% (Hx) or 21% O2 (Nx) during 24 hours. Two µg of total RNAs were depleted from ribosomal RNA with the Ribozero kit (epicenter), libraries were generated with the NEBNext Small RNA Library Prep Set for SOLiD and sequenced on SOLiD 5500XL (Life Technologies) with single-end 50bp reads. Reads were aligned to the human genome release hg19 with the LifeScope software v2.5.1 (Life Technologies) using whole transcriptome pipeline for RNA‐seq libraries with default parameters.

overall_design: 2 samples in monoplicates: Nx versus Hx