title: Functional analysis of the methyltransferase SMYD in the single-cell model organism Tetrahymena thermophila

status: Public on Oct 02 2019

city: Ann Arbor

first: Fengbiao

last: Mao

state: Michigan

address: 1301 Catherine St

department: Department of Pathology

institute: University of Michigan

summary: In order to resolve controversies concerning SMYD's substrates and functions, we studied SMYD1 (TTHERM_00578660), the only homologue in the unicellular eukaryote Tetrahymena thermophila. We epitope-tagged SMYD1, and analyzed its localization and interactome. We also characterized ΔSMYD1 cells, focusing on the replication and transcription phenotype. Our results show that: 1) SMYD1 is present in both cytoplasm and transcriptionally active macronucleus and shuttles between cytoplasm and macronucleus, which is consistent with its association with both histone and non-histone substrates; 2) SMYD1 is involved in DNA replication and regulates transcription of metabolism-related genes; 3) HSP90 is an potential substrate for SMYD1 and it may regulate target selection of HSP90, leading to pleiotropic effects in both the cytoplasm and the nucleus.

overall_design: To investigate the roles of SMYD1 in regulating gene transcription, we carried out RNA-seq analysis in wild-type (CU428) and the isogenic △SMYD1 cells. In total, 21461 well-annotated genes were included, among which 4841 (23%) were up-regulated (> 2-fold) and 1507 (7%) down-regulated (< 0.5-fold). KEGG pathway analysis revealed that the most affected pathways in △SMYD1 cells were metabolic pathway (ko01100) and biosynthesis of secondary metabolites (ko01110), supporting that SMYD1 plays important roles in regulating metabolic genes in Tetrahymena. The result of Gene Ontology (GO) term enrichment analysis  was consistent with that of the KEGG pathway analysis, which revealed the single organism metabolic process as the most enriched pathway for the up-regulated genes in △SMYD1 cells. These results suggested that SMYD1 is involved in regulation of metabolism.

first: Shan

last: Gao


title: Melatonin protects against defects induced by malathion during porcine oocyte maturation

status: Public on Jun 13 2019

city: Wuhan

first: Jing-Jing

last: Zhang

state: Hubei

address: 1 Lion Rock Street

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

country: China

institute: Huazhong Agricultural University

type: Expression profiling by high throughput sequencing

summary: We used porcine oocytes as model and found that MAL exposure significantly impaired porcine oocyte maturation in a dose dependent manner. RNA-seq analyses showed that MAL altered the mRNA level of 2917 genes in the porcine maturated oocytes and most of these genes were related to ROS, the lipid droplet process and the energy supplement.

overall_design: RNA-seq analysis was used to investigate how MAL affects intracellular stored mRNA in oocytes

first: Li

last: Chen

first: Yi-Liang

last: Miao


title: Transcriptome of non-involved lung parenchyma from ever and never smoker lung adenocarcinoma patients from Milan, Italy.

status: Public on Oct 01 2019

city: Milan

first: Matteo

last: Dugo

address: via Olgettina 60

department: Department of Medical Oncology

country: Italy

institute: IRCCS Ospedale San Raffaele

summary: Alteration of gene expression profile of target organs may signal exposure of that organ to toxic chemicals. We analyzed the transcriptome of the non-involved lung tissue, excised from 176 surgically treated lung adenocarcinoma patients, to identify genes whose expression levels were altered by individual habit to cigarette smoking. Of 17.097 genes analyzed, 357 resulted to be differentially expressed between never smokers and ever smokers (FDR <0.05). The gene that resulted to be the most significantly differentially expressed was MYO1A (FDR = 6.9 x 10-4 and ever versus never smokers fold change of 1.42). We compared our results with those of five independent datasets and found that more than one third (38.6%) of the transcripts associated with smoking habit in our dataset overlapped with at least one of the other datasets, with 7 genes (KMO, CD1A, SPINK5, TREM2, CYBB, DNASE2B, FGG) resulting significantly differentially expressed between ever and never smokers in all five datasets, with concordant higher expression in ever smokers than in never smokers. Most of the genes that we found significantly differentially expressed between ever and never smokers participate in pathways/networks that are directly or indirectly associated with immunity and inflammation, in particular, the most significantly enriched pathway was that of eicosanoid signaling. Overall, present results further points to the inflammatory condition that characterize the lung tissue of smokers.

overall_design: 176 samples of non-involved (apparently normal) lung parenchyma excised from patients (118 smokers and 58 non-smokers) who underwent lobectomy for lung adenocarcinoma in the area around Milan, Italy.

first: Giulia

last: Pintarelli

first: Sara

last: Noci

first: Loris

last: De Cecco

first: Tommaso

middle: A

last: Dragani

first: Francesca

last: Colombo


title: Determination of an Interaction Network between an Extracellular Bacterial Pathogen and the Human Host

status: Public on May 30 2019

city: Indianapolis

first: Brad

last: Griesenauer

state: Indiana

address: 635 Barnhill Dr, MS 420

department: Microbiology and Immunology

country: USA

institute: Indiana University School of Medicine

summary: A major gap in understanding infectious diseases is the lack of information about molecular interaction networks between pathogens and the human host. Haemophilus ducreyi causes the genital ulcer disease chancroid in adults and is a leading cause of cutaneous ulcers in children in the tropics. We developed a model in which human volunteers are infected on the upper arm with H. ducreyi until they develop pustules. To define the H. ducreyi and human interactome, we determined bacterial and host transcriptomic and host metabolomic changes in pustules. We found in vivo H. ducreyi transcripts were distinct from those in the inocula as were host transcripts in pustule and wounded control sites. Many of the upregulated H. ducreyi genes were involved in ascorbic acid and anaerobic metabolism and inorganic ion/nutrient transport. The top 20 significantly expressed human pathways showed that all were involved in immune responses. We generated a bipartite network for interactions between host and bacterial gene transcription; multiple positively correlated networks contained H. ducreyi genes involved in anaerobic metabolism and host genes involved with the immune response. Metabolomic studies showed that pustule and wounded samples had different metabolite compositions; the top ion pathway involved ascorbate and aldarate metabolism, which correlated with the H. ducreyi transcriptional response and upregulation of host genes involved in ascorbic acid recycling. These data show that an interactome exists between H. ducreyi and the human host and suggests that H. ducreyi exploits the metabolic niche created by the host immune response.

sample_organism:
[Haemophilus] ducreyi
Homo sapiens

platform_organism:
[Haemophilus] ducreyi
Homo sapiens

overall_design: mRNA profiles from four human pustules infected with H. ducreyi from four different volunteers, their four corresponding wound controls, and their four H. ducreyi inocula samples grown to mid-log phase.

first: Stanley

middle: M

last: Spinola


title: Paternal overdiet drives intergenerational transmission of metabolic disorders through sperm epigenetic alteration

type: Methylation profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Self-organizing human neuruloids allow disease modeling in the developing ectodermal compartment

status: Public on Sep 08 2019

city: New York

first: Tiago

last: Rito

state: NEW YORK

address: 1230 York Avenue

institute: Rockefeller University

summary: Harnessing the self-organizing abilities of human embryonic stem cells to mimic normal and aberrant development is a pressing challenge. Generation of highly reproducible and standardized models would allow drug screening with unprecedented accuracy. Here we report single-cell RNA-seq data (10xGenomics) of human "neuruloids". Using micro-patterned technologies we recapitulate the self-organization of the complete human embryonic ectodermal compartment during neurulation containing: neural progenitors, neural crest, sensory placode and epidermis. Single-cell transcriptomics allowed the precise molecular characterization of each cell type in a faithful model of human neurulation. Additionally, isogenic neuruloids coupled to deep neural network analysis provide a unique opportunity to model human neuropathological disorders as demonstrated for Huntignton’s disease.

overall_design: Two single-cell RNAseq data sets of neuruloid day 7 (3ng/mL of BMP4) starting from hESCs (RUES2 and isogenic HTT 56CAG cell line).

first: Tomomi

last: Haremaki

first: Ali

last: Brivanlou


title: Single cell RNA-seq shows cellular heterogeneity and lineage expansion in a mouse model of SHH-driven medulloblastoma support resistance to SHH inhibitor therapy

status: Public on Apr 13 2019

city: Chapel Hill

first: Timothy

last: Gershon

state: NC

address: 6129 NRB, 115 Mason Farm Rd

department: Neurology

institute: University of North Carolina

summary: Cellular diversity within tumors and reduced lineage commitment can undermine targeted therapy by increasing the probability of treatment-resistant populations. Using single-cell RNA-seq, we analyzed cellular diversity and lineage in medulloblastomas in transgenic, medulloblastoma-prone mice, and responses to the SHH-pathway inhibitor vismodegib.

overall_design: Drop-Seq single-cell transcriptome sequencing of 15 mice: 5 Wild Type cerebella, 5 Drug-treated cerebellar tumors and 5 vehicle-treated cerebellar tumros.

first: Benjamin

last: Babcock

first: Jennifer

last: Ocasio


title: Single-cell RNA sequencing-based CRISPRi screening resolves molecular drivers of early human endoderm development [set 2]

status: Public on Apr 16 2019

city: Worcester

first: Rene

last: Maehr

state: MA

address: 55 Lake Ave N

department: Program in Molecular Medicine

institute: UMass Medical School

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Studies in vertebrates have outlined conserved molecular control of definitive endoderm (END) development. Yet, recent work also shows that key molecular aspects of human END regulation differ even from rodents. Differentiation of human pluripotent stem cells (hPSCs) to END offers a tractable system to study the molecular basis of normal and defective human-specific END development. Here, we interrogated dynamics in chromatin accessibility during differentiation of hPSCs to END, predicting DNA-binding proteins that may drive this cell fate transition. We then combined single-cell RNA-seq with parallel CRISPR-perturbations to comprehensively define the loss-of-function phenotype of those factors in END development. Following a few candidates, we revealed distinct impairments in the differentiation trajectories for mediators of TGFβ signaling and expose a role for the FOXA2 transcription factor in priming human END competence for human foregut and hepatic endoderm specification. Together, this single-cell functional genomics study provides high-resolution insight on human END development.

overall_design: CRISPRi screen of endodermal differentiation with a single-cell RNA readout. This submission contains the chromatin data from the paper.

first: Ryan

last: Genga

first: Eric

last: Kernfeld

first: Krishna

last: Parsi

first: Teagan

last: Parsons

first: Michael

last: Ziller


title: Mapping of low-salt soluble chromatin identifies known and novel transcriptionally active genes in chicken erythrocytes

status: Public on Jul 24 2019

city: Winnipeg

first: James

middle: Ronald

last: Davie

state: Manitoba

address: 745 Bannatyne Avenue, RM 333A

department: Biochemistry and Medical Genetics

country: Canada

institute: University of Manitoba

summary: Transcriptional regulation is regulated by the organization of the genome into chromatin compartments and domains. Here, we present the detailed characteristics, including location of nucleosome-free regions, of several novel transcriptionally active/poised chromatin compartments exhibiting a range of transcriptional activities. These chromatin patterns illustrate how the salt solubility profile of a genomic region aids in the annotation of genes expressed in erythroid cells and contributes to the identification of functional features such as regulatory regions.

overall_design: Examination of open chromatin regions in Chicken Immature erythrocyte cells.

first: Sanzida

last: Jahan

first: Tasnim

middle: H

last: Beacon

first: H

last: Shihua

first: Carolina

last: Gonzalez

first: Wayne

last: Xu

first: Geneviève

middle: P

last: Delcuve

middle: R


title: Cell Type- and Sex-Dependent Transcriptome Profiles of Rat Anterior Pituitary Cells

status: Public on Aug 23 2019

city: Bethesda

first: Patrick

middle: Allen

last: Fletcher

state: Maryland

address: 9000 Rockville Pike

institute: NIDDK

summary: Understanding of physiology and pathology of an organ composed of variety of cell populations depends critically on genome-wide information on each cell type. Here, we report single-cell transcriptome profiling of over 6800 freshly dispersed anterior pituitary cells from postpubertal male and female rats. Six pituitary-specific cell types were identified based on known marker genes and characterized: folliculostellate cells and hormone producing corticotrophs, gonadotrophs, thyrotrophs, somatotrophs, and lactotrophs. Also identified were endothelial and blood cells from the pituitary capillary network. The expression of numerous developmental and neuroendocrine marker genes in both folliculostellate and hormone producing cells supports that they have a common origin. For several genes, the validity of transcriptome analysis was confirmed by qRT-PCR and single cell immunocytochemistry. Folliculostellate cells exhibit impressive transcriptome diversity, indicating their major roles in production of endogenous ligands and detoxification enzymes, and organization of extracellular matrix. Transcriptome profiles of hormone producing cells also indicate contributions toward those functions, while also clearly demonstrating their endocrine function. This survey highlights many novel genetic markers contributing to pituitary cell type identity, sexual dimorphism, and function and points to relationships between hormone producing and folliculostellate cells.

overall_design:
Examination of single-cell transcriptomes from female and male rats

Grants:
Z01 DK013028-10, "Mathematical Modeling of Neurons and Endocrine Cells", Arthur Sherman, National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK).

Z01 HD000195-25, "Intracellular Signaling In Endocrine Cells", Stanko S. Stojilkovic, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD).

Z01 HD008958-02, "Molecular Genomics Sequencing Core Facility", Steven L. Coon, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD).

last: Iben


title: H3K27ac ChIP-Seq and mRNA-Seq analysis of five human B-lymphoblastoid cell lines (LCLs) prepared from the same healthy male individual (CEPH/UTAH).

status: Public on Mar 27 2019

city: Debrecen

first: Lilla

last: Ozgyin

address: Egyetem ter 1

country: Hungary

institute: University of Debrecen

summary:
Purpose: We examined the extent and nature of non-genetic variability at the gene regulatory activity and gene expression levels in isogenic LCLs, highlighting features of the LCL model that might aid the rational design of genetic association studies.
Brief method:
H3K27ac ChIP-Seq: Crosslinked chromatin corresponding to 5 million cells was immunoprecipitated with 2.5 ug anti-histone H3 (acetyl K27) antibody (Abcam, cat. ab4729) or isotype control antibody (Santa Cruz Biotechnology, cat. sc-2027 X). in biological duplicates. Library preparation was performed by the Genomic Medicine and Bioinformatics Core Facility at the University of Debrecen, Debrecen, Hungary from 10 ng of ChIP material based on the “TruSeq ChIP Sample Preparation Guide 15023092 B” with minor modifications. Cluster generation, sequencing (50-bp, single-end) and demultiplexing (bcl2fastq Conversion Software) were performed either at the Genomic Medicine and Bioinformatic Core Facility at the University of Debrecen or at the EMBL Genomics Core Facility, Heidelberg, Germany. BWA 0.7.10 was used to align ChIP-Seq reads to the hg19 (GRCh37) genomic build. HOMER 4.9.1. was used to predict genomic regions with H3K27ac enrichment. We used the R package DiffBind (Bioconductor) to define a consensus set of predicted gene regulatory elements, calculate RPKM values, cluster the samples and create a correlation matrix.
RNA-Seq: Total RNA was extracted from two million cells with TRIzolate reagent in biological duplicates. Sequencing libraries were prepared following Illumina’s TruSeq RNA Sample Preparation v2 Guide with poly(A) selection using 1 μg total RNA as the starting material. Indexed libraries were pooled and subjected to single-end sequencing on a NextSeq 500 sequencer (Illumina, San Diego, CA, USA) with 50-bp read length. Library preparation, cluster generation, sequencing and base calling were performed at the Genomic Medicine and Bioinformatic Core Facility at the University of Debrecen, Hungary. Demultiplexing was performed using the bcl2fastq Conversion Software (Illumina). RNA-Seq reads were aligned to the hg19 (GRCh37) genomic build using TopHat v2.0.7 (--max-multihits option set to 1). Transcript abundances were calculated and batch effect was accounted for using edgeR and UCSC gene annotation track (hg19, downloaded from Illumina's iGenomes database in 07/17/2015), and are expressed as RPKM values. Genes with CPM values (read counts per million mapped reads) below 5 across all samples were considered unexpressed and were discarded.
Results: We found extensive gene regulatory region activity differences between the five isogenic LCLs affecting mostly typical enhancers. clustered enhancers (super-enhancers). H3K27ac variability is coupled with a modest gene expression variability. The set of variable genes was enriched for genes involved in lymphocyte-specific signaling pathways and drug response.

Principal investigator: Balint L. Balint, lbalint@med.unideb.hu

overall_design: H3K27ac ChIP-Seq and mRNA profiles of five LCLs in biological duplicates.

first: Attila

last: Horvath

first: Zsuzsanna

last: Hevessy

first: Balint

middle: L

last: Balint


title: Early Loss of Histone H2B Monoubiquitylation Alters Chromatin Accessibility and Activates Key Immune Pathways That Facilitate Progression of Ovarian Cancer

status: Public on Feb 26 2019

city: Santa Monica

first: Dave

last: Hoon

state: CA

address: 2200 Santa Monica Boulevard

department: Translational Molecular Medicine

institute: Saint John's Cancer Institute

type: Genome variation profiling by high throughput sequencing

summary:
We identified that downregulation of RNF20/H2Bub1 is involved in HGSOC progression through altering key immune signaling pathways.
The goal of ATAC-seq analysis was to profile chromatin conformation in FTSEC cells (FT190 and FT194 cell lines) with RNF20 knockdown (shRNF20) or control shRNA. The data generated by ATAC-Seq was integrated with RNA-seq data analysis for the same samples.

overall_design: The mRNA profiles of FT190 and FT194 shRNF20 (RNF20 knockdown) or control shRNA cells were generated by RNA-Seq using Illumina HiSeq 2500, in triplicates.

first: Ronny

last: Drapkin

first: Jagmohan

last: Hooda

first: Matthew

last: Salomon

middle: B


title: A Preformed Chromatin Architecture Ensures Robust Shh Transcription during Limb Development

status: Public on May 13 2019

city: Berlin

first: Christina

last: Paliou

address: Ihnestrasse 63-73

country: Germany

institute: Max Planck Institute for Molecular Genetics

summary:
During embryogenesis, enhancer-promoter interactions control gene transcriptional activation. These interactions can be tissue-specific or tissue-invariant and occur mostly within larger insulated regulatory domains called Topologically Associating Domains (TADs). Boundary elements, which delineate the extent of TADs, frequently interact with each other and have been associated with constitutive transcription and CTCF/Cohesin binding. In this work, we set out to investigate the regulatory role of a tissue-invariant, preformed interaction between two boundaries that involve the Shh gene and its unique limb enhancer, the ZRS, located one megabase away. Using CRISPR/Cas9 we specifically perturb CTCF binding sites or constitutive transcription at the ZRS-containing boundary, without altering the enhancer sequence. Using capture-HiC (cHiC) we show that both types of perturbation result in altered preformed chromatin interactions and lead to a reduction of Shh expression in developing limb buds. Finally, we demonstrate that the disruption of the chromatin structure in combination with a hypomorphic ZRS allele results in a dramatic Shh loss- of- function and digit agenesis. We thus propose that preformed chromatin structures can ensure stable enhancer promoter communication during development and robustness of gene transcriptional activation.

This SuperSeries is composed of the SubSeries listed below.


title: Regulation of ectopic heterochromatin-mediated epigenetic diversification by the JmjC family protein Epe1.

status: Public on Apr 24 2019

city: Kobe

first: Atsushi

last: Matsuda

address: 588-2, Iwaoka, Iwaoka-cho, Nishi-ku

country: Japan

institute: National Institute of Information and Communications Technology

summary: H3K9 methylation (H3K9me) is a conserved marker of heterochromatin, a transcriptionally silent chromatin structure. Knowledge of the mechanisms for regulating heterochromatin distribution is limited. The fission yeast JmjC domain-containing protein Epe1 localizes to heterochromatin mainly through its interaction with Swi6, a homologue of heterochromatin protein 1 (HP1), and directs JmjC-mediated H3K9me demethylation in vivo. Here, we found that loss of epe1 (epe1∆) induced a red-white variegated phenotype in a red-pigment accumulation background that generated uniform red colonies. Analysis of isolated red and white colonies revealed that silencing of genes involved in pigment accumulation by stochastic ectopic heterochromatin formation led to white colony formation. In addition, genome-wide analysis of red- and white-isolated clones revealed that epe1∆ resulted in a heterogeneous heterochromatin distribution among clones. We found that Epe1 had an N-terminal domain distinct from its JmjC domain, which activated transcription in both fission and budding yeasts. The N-terminal transcriptional activation (NTA) domain was involved in suppression of ectopic heterochromatin-mediated red-white variegation. We introduced a single copy of Epe1 into epe1∆ clones harboring ectopic heterochromatin, and found that Epe1 could reduce H3K9me from ectopic heterochromatin but some of the heterochromatin persisted. This persistence was due to a latent H3K9me source embedded in ectopic heterochromatin. Epe1H297A, a canonical JmjC mutant, suppressed red-white variegation, but entirely failed to remove already-established ectopic heterochromatin, suggesting that Epe1 prevented stochastic de novo deposition of ectopic H3K9me in an NTA-dependent but JmjC-independent manner, while its JmjC domain mediated removal of H3K9me from established ectopic heterochromatin. Our results suggest that Epe1 not only limits the distribution of heterochromatin but also controls the balance between suppression and retention of heterochromatin-mediated epigenetic diversification.

overall_design: Gene expression profile at exponentially-growing phase in the fission yeast epe1 mutants.

first: Masato

last: Sorida

first: Takahiro

last: Hirauchi

first: Hiroaki

last: Ishizaki

first: Wataru

last: Kaito

last: Shimada

first: Chie

last: Mori

first: Yuji

last: Chikashige

first: Yasushi

last: Hiraoka

first: Yutaka

last: Suzuki

first: Yasuyuki

last: Ohkawa

last: Kato

first: Shinya

last: Takahata

first: Yota

last: Murakami


title: A Preformed Chromatin Architecture Ensures Robust Shh Transcription during Limb Development [Capture Hi-C]

summary: During embryogenesis, enhancer-promoter interactions control gene transcriptional activation. These interactions can be tissue-specific or tissue-invariant and occur mostly within larger insulated regulatory domains called Topologically Associating Domains (TADs). Boundary elements, which delineate the extent of TADs, frequently interact with each other and have been associated with constitutive transcription and CTCF/Cohesin binding. In this work, we set out to investigate the regulatory role of a tissue-invariant, preformed interaction between two boundaries that involve the Shh gene and its unique limb enhancer, the ZRS, located one megabase away. Using CRISPR/Cas9 we specifically perturb CTCF binding sites or constitutive transcription at the ZRS-containing boundary, without altering the enhancer sequence. Using capture-HiC (cHiC) we show that both types of perturbation result in altered preformed chromatin interactions and lead to a reduction of Shh expression in developing limb buds. Finally, we demonstrate that the disruption of the chromatin structure in combination with a hypomorphic ZRS allele results in a dramatic Shh loss- of- function and digit agenesis. We thus propose that preformed chromatin structures can ensure stable enhancer promoter communication during development and robustness of gene transcriptional activation.

overall_design: We used capture Hi-C enriching a 3Mb region at the Shh locus in Mus musculus. We analysed two biological replicates of wild type and two technical replicates of CRISPR-Cas9 genome engineered mutant tissue to compare the structural changes at the locus.

first: Guillaume

last: Andrey


title: Transcriptome Analyses of LncRNA Metabolic Regulators from High Fat Diet Induced T2DM Mouse Adipose Tissue

status: Public on Jun 01 2019

city: Shenzhen

first: yao

last: zhenyu

state: Guang dong province

address: No. 1068 xueyuan road Nanshan District Shenzhen

department: Institute of biomedical and Health Engineering

institute: Shenzhen institutes of advanced technology, chinese academy of science

summary: To search long noncoding RNAs (lncRNAs) which regulating energy metabolism in high fat diet induced T2DM mouse, we performed transcriptome analyses to simultaneously profile mRNAs and lncRNAs in epididymal adipose tissue in normal and high fat diet induced mouse. Combining genome-wide screens, bioinformatics function predictions, and cell-based analyses, we developed an integrative roadmap to identify lncRNA metabolic regulators in epididymal adipose tissue under high fat diet induced T2DM mouse.

overall_design: To identify regulated lncRNAs in adipose tissues and to establish an inclusive data set to predict lncRNA functions in energy metabolism on the basis of their correlation with mRNAs, we simultaneously profiled all mRNAs and lncRNAs in epididymal adipose tissue in mice（C57BL/6J）under long-term (12 weeks) HFD (high fat diet) feeding, a widely used model mimicking dietary obesity in humans，the ND（normal diet） feeding animals as control. We performed 6 microarray analyses for each group of three mice for RNA extraction and hybridization on Affymetrix microarrays .

first: Zhenyu

last: Yao

first: Pei-Gen

last: Ren


title: Genome-wide gene expression analysis in ARID1A-proficient and ARID1A-deficient cancer cells

status: Public on Jan 28 2019

city: Chuo-ku

first: Takashi

last: Kohno

state: Tokyo

address: 1-1, Tsukiji 5-chome

institute: National Cancer Center Research Institute

summary: To investigate that ARID1A regulates transcription of genes encoding components of the GSH synthesis pathway, a genome-wide expression analysis of a panel of ARID1A-proficient and ARID1A-deficient cancer cells was performed.

overall_design: 12 samples are analyzed.

first: Hideaki

last: Ogiwara


title: Single-cell RNA sequencing-based CRISPRi screening resolves molecular drivers of early human endoderm development

first: Rene

last: Maehr


first: Dave

last: Hoon

overall_design: Chromatin conformation profiles of FT190 and FT194 shRNF20 (RNF20 knockdown) or control shRNA cells were generated by using Illumina HiSeq 2500, in triplicates.

first: Ronny

last: Drapkin

first: Jagmohan

last: Hooda

first: Matthew

last: Salomon


status: Public on Feb 25 2019


title: TOP2B disturbed the quality of human oocytes with advanced maternal age

status: Public on Jan 19 2019

first: Jing-Jing

last: Zhang

summary: STUDY QUESTION: Does maternal age affect the maturated oocyte quality and the fol-lowing development after fertilization in human?   SUMMARY ANSWER: Maternal age affects the quality of maturated oocytes by altering the stored mRNA levels in human, such as TOP2B.   WHAT IS KNOWN ALREADY: Intracellular mRNAs in maturated oocytes are tran-scripted from the maternal genome during oogenesis and important for the zygotic genome activation (ZGA) after fertilization. Microarray data showed that maternal age affected polyadenylated transcript abundance in human oocytes. These genes are involved in in signaling pathway related to cell cycle regulation, chromosome alignment. However, which genes are the key genes affected by maternal age and important for the development after fertilization had not been reported. Therefore, single-cell RNA sequencing (scRNA-Seq) technology is employed in this study to screen the key genes affected by maternal age in human maturated oocytes.  STUDY DESIGN, SIZE, DURATION: We isolated mRNA from maturated (MII) oo-cytes donated by IVF or ICSI patients (three oocytes from young (≤ 30 years) and three oocytes from advanced maternal age (≥ 40 years) patients) undergoing controlled ovarian stimulation. Thus, a total of six maturated oocytes were individually processed for scRNA-seq analysis. The key genes screened from scRNA-seq analysis are confirmed using mouse model.   PARTICIPANTS/MATERIALS, SETTING, METHODS:  Patients undergoing infertility treatment at the Yuhuangding Hospital of Yantai underwent ovarian stimulation with FSH and received hCG for final follicular maturation prior to ul-trasound guided oocyte retrieval. We isolated RNA, generated single cell RNA-seq librar-ies (Smart-Seq2) and sequenced by Illumina Hiseq X-ten platform with 150 bp paired-end. Bioinformatics analysis of the sequencing data was done to find the biological processes and key genes that led to the decline in the quality of oocytes with advanced maternal age. To validate the findings, we used mouse model and validated candidate genes by RT-PCR and knockdown experiments.  MAIN RESULTS AND THE ROLE OF CHANCE:  We identified 1439 genes differentially expressed between older and younger women's maturated oocytes (|foldchange|>2, P < 0.05). These genes are significantly enriched with annotations related to transporter activity, cytoskeleton, oxidative stress, catalytic activity, immune function, cellular senescence and biosynthesis. The key candidate gene TOP2B was found by protein interaction network analysis, and knockdown verification on young mouse maturated oocytes showed that TOP2B was a key gene affecting the oocyte quality and disturbing early embryo development.  LARGE SCALE DATA  Raw data from this study can be accessed through GSE.  LIMITATIONS, REASONS FOR CAUTION:   The human maturated oocytes used in this study were from patients with different causes of infertility and may affect oocyte gene expression. In addition, the study was based on a lim-ited number of patients, and there are possible natural biological variance existed in human samples.  WIDER IMPLICATIONS OF THE FINDINGS:  For the first time, we used scRNA-seq to detect global gene transcriptome of maturated oocytes in young and older women. These results are useful to indicate the molecular mechanisms of female ovary aging and establishing a criterion to evaluate the quality of oocytes in women with advanced maternal age.  STUDY FUNDING/COMPETING INTERESTS:  This research was supported by the National Key Research and Development Program of China (2018YFC1004304, 2016YFA0100203), Medical and Health Science Technology Development Plan Project of Shandong Province (Grant#. 2017WS566). There are no competing interests.

overall_design: We isolated mRNA from maturated (MII) oocytes donated by IVF or ICSI patients (three oocytes from young (≤ 30 years) and three oocytes from advanced maternal age (≥ 40 years) patients) undergoing controlled ovarian stimulation. Thus, a total of six maturated oocytes were individually processed for scRNA-seq analysis. The key genes screened from scRNA-seq analysis are confirmed using mouse model.

first: Xiaoyan

last: Liu

first: Yi-Liang

last: Miao


title: Atopic Dermatitis, Psoriasis and healthy control RNA-seq cohort

status: Public on Jan 18 2019

first: Lam

last: Tsoi

state: MI

address: Medical Sciences 1 Bldg. 1301 E. Catherine

summary: To gain a deeper understanding of the pathophysiology of AD, we conducted a large-scale transcriptomic study of AD with deeply-sequenced RNA-seq samples using long (125b) paired-end reads. By integrating deep sequencing-based skin transcriptome profiling with systems biology analysis, we are able to provide deep characterization for the expression signatures for AD, and by including psoriasis samples in the analysis, we can reveal the distinct molecular features of uninvolved and lesional skin of AD that have not been previously described.

overall_design: We performed high-depth sequencing of 147 skin transcriptomes obtained from a carefully matched and tightly defined cohort of 27 AD patients, 28 PSO patients, and 38 healthy controls, whom were recruited within an ongoing investigator-initiated clinical study to identify shared and distinct disease mechanisms of AD and Psoriasis.

first: Stephan

last: Weidinger

first: Elke

last: Rodriguez

middle: C

first: Johann

last: Gudjonsson


title: RNA over-editing leads to aggressiveness of intrahepatic cholangiocarcinoma

status: Public on Dec 12 2018

city: Beijing

first: Pengbo

last: Cao

address: 27 Taiping Road

institute: Beijing Institute of Radiation Medicine


title: RNA over-editing leads to aggressiveness of intrahepatic cholangiocarcinoma [RNA-Seq]

summary: Alteration in RNA editing has been connected to tumor progression and many other important human diseases. However, the role of RNA editing in intrahepatic cholangiocarcinoma (ICC) remains unclear. Here we conducted a transcriptome-wide investigation in ICCs, and revealed ADAR-associated over-editing occurred uniformly in ICCs. Collectively, these results reveal a previously unrecognized role of RNA editing in malignant transformation into ICC, and ADAR1 inhibition may obviate progression and relapse of this malignancy.

overall_design: We performed RNA-seq using Illumina HiSeq2000 on 15 pairs of ICC tumors and matched non-tumor liver tissues, with a mean of 30 million paired-end reads per sample. RNA-seq was performed by MyGenostics Inc. (Beijing, China).

first: Gangqiao

last: Zhou

first: Yuanfeng

last: Li


title: Next Generation Sequencing of Transcriptomes of Cutaneous Melanocytes and Metastatic Melanoma Cell Lines

status: Public on Jan 16 2019

city: MADISON

first: Vijayasaradhi

last: Setaluri

address: 1300 University Avenue

department: Dermatology

institute: University of Wisconsin-Madison

type: Non-coding RNA profiling by high throughput sequencing


title: Differential expression of long non‑coding RNA and mRNA in children with Henoch‑Schönlein purpura nephritis

status: Public on Dec 04 2018

city: Shenyang

first: shuang

last: pang

state: China

address: No.79 Chong Shan Dong Lu Street

institute: Liaoning University of Traditional Chinese Medicine

summary: Long non‑coding RNAs (lncRNAs) serve an essential role in regulating immunological functions. However, their impact on Henoch‑Schönlein purpura nephritis (HSPN), has remained elusive.

overall_design: The present study determined the expression of lncRNAs and mRNAs in the peripheral blood of 6 children with HSPN and recruited 4 healthy children for comparative study. High‑throughput sequencing revealed outstanding differences in lncRNA and mRNA expression, which were verified through reverse transcription‑quantitative polymerase chain reaction. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway analyses were used to investigate the associated biological functions and possible mechanisms of lncRNAs and mRNAs in HSPN.

first: Shuang

last: Pang

first: Jun


title: Induction of autonomous memory alveolar macrophages requires T-cell help and is critical to trained immunity

status: Public on Nov 06 2018

city: Hamilton

first: Zhou

last: Xing

state: Ontario

address: 1280 Main Street West

department: Pathology and Molecular Medicine

institute: McMaster University

summary: Innate immune memory is a new important area of research. However, innate immune memory at the major mucosal sites remains poorly understood. Here we show that respiratory viral infection induces long-lasting memory alveolar macrophages (AM). Memory AM are programed to express high MHC II, carry a defense-ready gene signature, and produce, upon re-stimulation, neutrophil chemokines. Using a multitude of approaches, we reveal that the priming, but not maintenance, of memory AM requires the help from effector CD8 T cells. T cells jump-start this process in AM via IFN-γ production. We further find that formation/maintenance of memory AM are independent of monocytes or bone marrow progenitors. Finally, we demonstrate that memory AM are poised for robust trained immunity against bacterial infection in the lung via rapid induction of chemokines and neutrophilia. Our study thus establishes a new paradigm of immunological memory formation whereby adaptive T-lymphocytes render innate memory of mucosal-associated macrophages.

overall_design: Acute respiratory viral infection was elicited by intranasal inoculation with a recombinant human serotype 5 adenovirus expressing an Mtb protein Ag85A at 5×107 PFU per mouse. PBS inoculated mice were used as control. At 4 weeks post infection, CD11b-CD11c+ alveolar macrophages (AM) were purified from bronchoalveolar lavage fluid by using magnetic selection. AM from each 3 mice were pooled and used as one sample and triplicate samples/group were set up for RNA extraction and gene microarray analysis. Quality of RNA and subsequent microarray was carried out by the Center for Applied Genomics of The Hospital for Sick Children (Toronto, ON). The quality of RNA samples was analyzed using the Agilent 2100 bioanalyzer, which uses RNA 6000 Nano LabChip platform (Agilent Technologies Canada, Mississauga, ON). RNA samples were then subjected to RNA microarray expression analysis using the Affymetrix Mouse Gene 2.0 ST array. This array contains protein-coding regions.

first: Yushi

last: Yao

first: Mangalakumari

last: Jeyanathan

first: Siamak

last: Haddadi

first: Nicole

middle: G

last: Barra

first: Maryam

last: Vaseghi-Shanjani

first: Daniela

last: Damjanovic

first: Rocky

last: Lai

first: Sam

last: Afkhami

first: Yonghong

last: Chen

first: Anna

last: Dvorkin-Gheva

first: Clinton

middle: S

last: Robbins

first: Jonathan

middle: D

last: Schertzer


title: Next Generation Sequencing of Transcriptomes of Cutaneous Melanocytes and Metastatic Melanoma Cell Lines (mRNA-Seq)

first: Vijayasaradhi

summary: The goal of the study is to compare NGS-derived transcriptome (mRNA-seq) profiles of melanocytes and metastatic melanoma cells and identify genes involved in melanomagenesis

overall_design: mRNA profiles are generated for low passage primary melanocytes and melanoma cells using Illumina’s HiSeq 2500 platform

first: Ranjan

last: Perera


title: RNA over-editing leads to aggressiveness of intrahepatic cholangiocarcinoma [SNP]

first: Pengbo

last: Cao

overall_design: To detect copy number variations (CNVs) for the 15 ICCs in discovery stage, we performed genome-wide single nucleotide polymorphisms (SNPs) genotyping by Affymetrix Genome-Wide Human SNP Array 6.0, which includes more than 906,600 single nucleotide polymorphisms (SNPs) and more than 946,000 probes. Copy-number estimation using Robust Multichip Analysis (CRMA, v2) method was used to pre-process the probe signal intensities from each raw .CEL file. This procedure consists of a calibration for offset and global crosstalk between alleles, and normalized for probe sequence effects. Once the data has been preprocessed using CRMA, fragment-length effects were normalized. Next, raw copy numbers was calculated by paired analysis, which takes the matched non-tumor liver tissue as reference for each tumor. Segmented copy number profiles were analyzed using Circular binary segmentation (CBS) algorithm with default parameters in the R package “DNA-copy”.

first: Gangqiao

last: Zhou

first: Yuanfeng

last: Li


title: Comparative RNA-Seq transcriptome analyses of diabetic nerve and kidney disease I

status: Public on Dec 15 2018

city: Grand Forks

first: Junguk

last: Hur

state: ND

address: 1301 N. Columbia Rd. Stop 9037

department: Biomedical Sciences

institute: University of North Dakota

summary: Treating insulin resistance with pioglitazone normalizes renal function and improves small nerve fibre function and architecture; however, it does not affect large myelinated nerve fibre function in mouse models of type 2 diabetes (T2DM), indicating that pioglitazone affects the body in a tissue-specific manner. To identify distinct molecular pathways regulating diabetic peripheral neuropathy (DPN) and nephropathy (DN), as well those affected by pioglitazone, we assessed DPN and DN gene transcript expression in control and diabetic mice with or without pioglitazone treatment. Differential expression analysis and self-organizing maps were then used in parallel to analyse transcriptome data. Differential expression analysis showed that gene expression promoting cell death and the inflammatory response was reversed in the kidney glomeruli but unchanged or exacerbated in sciatic nerve by pioglitazone. Self-organizing map analysis revealed that mitochondrial dysfunction was normalized in kidney and nerve by treatment; however, conserved pathways were opposite in their directionality of regulation. Collectively, our data suggest inflammation may drive large fibre dysfunction, while mitochondrial dysfunction may drive small fibre dysfunction in T2DM. Moreover, targeting both of these pathways is likely to improve DN. This study supports growing evidence that systemic metabolic changes in T2DM are associated with distinct tissue-specific metabolic reprogramming in kidney and nerve and that these changes play a critical role in DN and small fibre DPN pathogenesis. These data also highlight the potential dangers of a 'one size fits all' approach to T2DM therapeutics, as the same drug may simultaneously alleviate one complication while exacerbating another. PMID: 28272773

overall_design: mRNA profiles of four diabetic complication-prone tissues (sciatic nerve, dorsal root ganglia, kidney glomeruli and kidney cortex) from 16-week old BKS.Cg-m +/+ Leprdb/J mice with/without pioglitazone treatment of 15 mg/kg for 11 weeks. db/db genetic model was used for type 2 diabetes model. Deep sequencing of six biological replicates in each tissues using Illumina HiSeq 2000.

first: Eva

last: Feldman


title: Next Generation Sequencing of Transcriptomes of Cutaneous Melanocytes and Metastatic Melanoma Cell Lines (miRNA-Seq)

last: Setaluri

summary: The goal of the study is to compare NGS-derived transcriptome (miRNA-seq) profiles of melanocytes and metastatic melanoma cells and identify microRNAs involved in melanomagenesis

overall_design: miRNA profiles are generated for low passage primary melanocytes and melanoma cells using Illumina’s HiSeq 2500 platform


title: Disruption of Autism Spectrum Disorder-Susceptibility Genes Predominantly Reduces Functional Connectivity of Isogenic Human Neurons

status: Public on Nov 01 2018

city: Toronto

first: Stephen

middle: W

last: Scherer

address: 686 Bay Street

department: Genetics and Genomic Biology

institute: The Hospital for Sick Children

summary: Autism Spectrum Disorder (ASD) is phenotypically and genetically heterogeneous, but genomic analyses have identified candidate susceptibility genes. We present a CRISPR gene editing strategy to insert a protein tag and premature termination sites creating an induced pluripotent stem cell (iPSC) knockout resource for functional studies of 10 ASD-relevant genes (AFF2/FMR2, ANOS1, ASTN2, ATRX, CACNA1C, CHD8, DLGAP2, KCNQ2, SCN2A, TENM1). Neurogenin 2 (NEUROG2)-directed differentiation of iPSCs allowed production of cortical excitatory neurons, and mutant proteins were not detectable. Using both patch-clamp and multi-electrode array approaches, the electrophysiological deficits measured were distinct for different mutations. However, they culminated in a consistent reduction in synaptic activity, including reduced spontaneous excitatory post-synaptic current frequencies in AFF2/FMR2-, ASTN2-, ATRX-, KCNQ2- and SCN2A-null neurons. RNAseq revealed convergence of several neuronal networks. Despite ASD susceptibility genes belonging to different gene ontologies, isogenic stem cell resources can reveal common functional phenotypes, such as reduced functional connectivity.

overall_design: RNAseq profile of 1 control sample and 10 isogenic knokout human induced pluripotent stem cells (iPSCs) samples with 2-4 replicates per sample, as well as their corresponding 28-day old differentiated glutamatergic neuron samples with 3-5 replicates per sample.

first: Eric

last: Deneault

first: Sean

last: White

first: Deivid

last: Rodrigues

first: P

middle: J

last: Ross

first: Muhammad

last: Faheem

first: Kirill

last: Zaslavsky

first: Zhuozhi

last: Wang

first: Roumiana

last: Alexandrova

first: Giovanna

last: Pellecchia

first: Wei

last: Wei

first: Alina

last: Piekna

first: Gagan

last: Kaur

first: Jennifer

last: Howe

first: Vickie

last: Kwan

first: Bhooma

last: Thiruvahindrapuram

first: Susan

last: Walker

first: Peter

last: Pasceri

first: Daniele

last: Merico

first: Ryan

middle: K

last: Yuen

first: Karun

last: Singh

first: James

last: Ellis


title: A Systems Genetics Approach to Fracture Healing

status: Public on Dec 25 2018

city: Boston

first: Boston University

last: Microarray and Sequencing Resource

address: 72 East Concord Street, E631

department: Microarray and Sequencing Resource

institute: Boston University

summary:
Phosphate is essential for healthy bone growth and plays an essential role in fracture repair. Although phosphate deficiency has been shown to impair fracture healing, the mechanisms involved in impaired healing are unknown. More recently, studies have shown that the effect of phosphate deficiency on the repair process varied based on the genetic strain of mice, which is not characterized.
We used data from microarrays to (1) determine the effects of phosphate restriction on the biologic functions identified from the gene expression in fracture calluses; and (2) examine whether there are genetic differences within the primary biologic functions.

overall_design: Closed stabilized fractures were generated in the femora of three strains of male mice: A/J (AJ), C57BL/6J (B6), and C3H/HeJ (C3) (age: 8- to 12-weeks) (Gerstenfeld LC et al. J Histochem Cytochem, 2006;54(11):1215-28). Phosphate deficiency (Pi) was initiated 2 days prior to fracture and was maintained for 15 days by supplying the mice with a low phosphate diet (Harlan Laboratories, Madison, WI). Phosphate was then replenished and bone healing was allowed to continue until 35 days. For the three strains of mice, control groups were included where the mice were given normal diet throughout the study. The fracture calluses were harvested at various time-points: 3, 5, 7, 10, 14, 18, 21, 28, and 35 post-operative days (n=6 per time-point for each mouse strain and diet condition).

first: Louis

last: Gerstenfeld

first: Amira

middle: I

last: Hussein


title: The Association of Genomic Lesions and PD-1/PD-L1 Expression in Resected Triple Negative Breast Cancers

status: Public on Nov 15 2018

city: Scottsdale

first: Michael

middle: Thomas

last: Barrett

state: AZ

address: 13400 East Shea Boulevard

department: Molecular Pharmacology and Experimental Therapeutics

institute: Mayo Clinic Arizona

type: Genome variation profiling by genome tiling array

summary: We used DNA content-based flow cytometry to distinguish and isolate nuclei of clonal tumor populations from resected triple negative breast cancer tissues. We then interrogated each sorted tumor population with whole genome aCGH and next generation sequencing (NGS). The genomic data was correlated with IHC staining for PD-1 and PD-L1.

overall_design: We applied DNA content based flow sorting to isolate the nuclei of clonal populations from tumor biopsies obtained from resected TNBCs. We coupled this strategy with oligonucleotide array CGH (aCGH) and next generation resequencing, thereby obtaining high definition genomic profiles of clonal populations from each tumor. These data were then correlated with the presence or absence of PD-1 and PD-L1 expression as measured by IHC.

first: Elizabeth

last: Lenkiewicz

first: Smriti

last: Malasi

first: Anamika

last: Basu

last: Holmes Yearly

first: Lakshmanan

last: Annamalai

first: Ann

middle: E

last: McCullough

first: Pooja

last: Narang

first: Melissa

middle: A

last: Wilson Sayres

first: Karen

last: Anderson

first: Barbara

last: Pockaj

middle: T


title: Neonatally imprinted mesenteric lymph node stromal cell subsets induce tolerogenic dendritic cells [Tx FSC]

status: Public on Sep 25 2018

city: Lausanne

first: Joern

last: Pezoldt

address: Station 19, SV 3818.A

department: SV

country: Switzerland

institute: EPFL

summary: Gut-draining mesenteric lymph nodes (mLNs) play a key role in peripheral tolerance towards food and commensal antigens by providing an optimal microenvironment for efficient de novo induction of Foxp3+ regulatory T cells (Tregs). We recently identified mLN stromal cells as critical cellular players in this process and demonstrated that their tolerogenic properties are imprinted by microbiota. Here, we show that this imprinting process already takes place in the neonatal phase and renders the mLN stromal cell compartment resistant to inflammatory perturbations later in life. Utilizing LN transplantation, RNA-seq and single-cell RNA-seq allowed identification of stably imprinted expression signatures in mLN fibroblastic stromal cells. We dissected common stromal cell subsets across gut-draining mLNs and skin-draining LNs with location-specific immunomodulatory functions, such as subset-specific expression of Aldh1a2/3. Accordingly, mLN stromal cells shaped resident dendritic cells to attain high Treg-inducing capacity in a Bmp2-dependent manner. Thus, crosstalk between mLN stromal and resident dendritic cells provides a robust feedback mechanism for the maintenance of intestinal tolerance.

overall_design: Transcriptomic analysis of fibroblastic stromal cells of skin-draining and intestinal-draining lymph nodes from endogenous and transplanted lymph nodes at the popliteal fossa.

first: Maria

last: Pasztoi

first: Mangge

last: Zou

first: Carolin

last: Wiechers

last: Beckstette

first: Guilhem

last: Thierry

first: Ehsan

last: Vafadarnejad

first: Stefan

last: Floess

first: Panagiota

last: Arampatzi

first: Manuela

last: Buettner

first: Janina

last: Schweer

first: Diana

last: Fleissner

first: Marius

last: Vital

first: Dietmar

middle: H

last: Pieper

first: Marijana

last: Basic

first: Petra

last: Dersch

first: Till

last: Strowig

first: Mathias

last: Hornef

first: André

last: Bleich

first: Ulrike

last: Bode

first: Oliver

last: Pabst

first: Marc

last: Bajenoff

first: Antoine-Emmanuel

last: Saliba

first: Jochen

last: Huehn


title: Neonatally imprinted mesenteric lymph node stromal cell subsets induce tolerogenic dendritic cells [resDCs]

first: Joern

last: Pezoldt

overall_design: Transcriptomic analysis of resident dendritic cells of skin-draining and intestinal-draining lymph nodes from endogenous and lymph nodes transplanted to the popliteal fossa.

first: Maria

last: Pasztoi

first: Mangge

last: Zou

first: Carolin

last: Wiechers

first: Michael

last: Beckstette

first: Guilhem

last: Thierry

first: Ehsan

last: Vafadarnejad

first: Stefan

last: Floess


title: Leptin and fractalkine: Novel subcutaneous cytokines in burn injury.

status: Public on Aug 31 2018

city: London

first: Istvan

last: Nagy

address: 369 Fulham Road

country: United Kingdom

institute: Imperial College London

summary: Burn injury remains a major clinical challenge to both survival and to quality of life. Its progressive, aberrant inflammation underlies the lethal dysfunction of various organs and the pain it induces is excruciating and notoriously difficult to manage. While it is known that burn injury’s complex local and disseminating pathology is orchestrated from the burned tissue, few studies have sought to characterise the local signalling environment. An enhanced understanding of the local and acutely temporally-dynamic processes defining burn injury and its progression is required for the development of novel therapeutic interventions. Microdialysis was used as an interstitial sampling technique, conducted over three hours post-burn. Samples were analysed by metabolomics and a multiplex cytokine immunoassay. Next-Generation sequencing libraries of the burn and control microdialysis sites were prepared to measure transcriptional changes potentially underlying the interstitial profile characterising burn injury.

overall_design: All microdialysis sites in the study were excised for the extraction of RNA; 4 burn site and 4 control site samples were analysed.

first: Dominic

last: Friston

first: Sini

last: Junttila

first: Helen

last: Laycock

first: Jose

middle: V

last: Torres-Perez

first: Attila

last: Gyenesei


title: ImmGen ULI: OpenSource Mononuclear Phagocytes Project

status: Public on Nov 03 2018

first: Liang

last: Yang

address: 77 Avenue Louis Pasteur

department: Pathology

institute: Harvard Medical School

summary: Primary RNASeq data for progenitor, resident, and stimulated (C.alb, LPS, injury, APAP+ starved overnight and pIC) mononuclear phagocytes from fourteen organs.

overall_design:
RNASeq data for over 400 samples comprising of 130 populations submitted by 16 labs (both non-ImmGen and ImmGen labs) from 8 locations around the world for ImmGen OpenSource Mononuclear Project. Samples were sorted in these facilities using ImmGen’s stringent ULI protocol and shipped to one location for library preparation and sequencing.

Contributor: Immunological Genome Project Consortium


title: Neonatally imprinted mesenteric lymph node stromal cell subsets induce tolerogenic dendritic cells [migDC]

overall_design: Transcriptomic analysis of migratory dendritic cells of skin-draining and intestinal-draining lymph nodes from endogenous and lymph nodes transplanted to the popliteal fossa.

first: Panagiota

last: Arampatzi

first: Manuela

last: Buettner

first: Janina

last: Schweer

first: Diana

last: Fleissner

first: Marius

last: Vital

first: Dietmar

last: Pieper

first: Marijana

last: Basic

first: Petra

last: Dersch

first: Till

last: Strowig

first: Mathias

last: Hornef

first: André

last: Bleich

first: Ulrike

last: Bode

first: Oliver

last: Pabst

first: Marc

last: Bajenoff

first: Antoine-Emmanuel

last: Saliba


title: Expression data from orthotopic U-87 MG xenograft mouse models

status: Public on Jul 17 2018

city: Busan

first: Beomseok

last: Son

address: 322 Biology Building, 2 Busandaehakro 63beon-gil, Geumjeong-gu

country: South Korea

institute: Pusan National University

summary:
Glioblastoma (GBM) is classified as World Health Organization grade IV tumors of the central nervous system, and it is the most malignant form of glioma. The current GBM therapies could not completely eliminate the tumor mass and the occurrence of therapeutic resistance of surviving GBM cells is considered as an obstacle to be overcome.
We used microarrays to detail the global program of gene expression underlying development of radioresistance of GBM and identified a variety of genes whose expressions were regulated during this process.

overall_design: 5x105 U-87 MG GBM cells were injected into the brain of seven-week-old BALB/c athymic nude mice. Fourteen days after the injection date, the brains of the mice were irradiated with 2 Gy daily for 5 days at a dose rate of 0.4 Gy/min. At the end of the treatment period, animals were euthanized and brain samples were harvested.

first: Sungmin

last: Lee

first: Hyunkoo

last: Kang

first: BuHyun

last: Youn


title: Neonatally imprinted mesenteric lymph node stromal cell subsets induce tolerogenic dendritic cells [endogenous FSCs]

first: Joern

last: Pezoldt

overall_design: Identification of differentially expressed genes in fibroblastic stromal cells from mesenteric or skin-draining lymph nodes of germ-free or specific-pathogen-free housed mice.

first: Maria

last: Pasztoi

first: Mangge

last: Zou

first: Carolin

last: Wiechers

first: Michael

last: Beckstette

first: Guilhem

last: Thierry

first: Ehsan

last: Vafadarnejad

first: Stefan

last: Floess

first: Panagiota

last: Arampatzi

first: Manuela

last: Buettner

first: Janina

last: Schweer

first: Jochen

last: Huehn


title: Neonatally imprinted mesenteric lymph node stromal cell subsets induce tolerogenic dendritic cells

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

overall_design: Refer to individual Series


title: Whole blood gene expression profiling of multiplex multiple sclerosis family

status: Public on Aug 01 2018

city: Milan

first: Ana Maria

last: Osiceanu

address: via Olgettina 58

department: INSPE

institute: IRCCS San Raffaele Scientific Institute

summary: This experiment was carried out in the context of a whole-genome sequencing study in 4 affected and 4 unaffected relatives of a consanguineous Italian family characterized by the high prevalence of multiple sclerosis. These data were used to evaluate differences in GRAMD1B gene expression in whole blood comparing healthy and affected subjects of the family. Functional experiments have been subsequently performed to evaluate the involvement of this gene in multiple sclerosis.

overall_design: Total RNA from whole blood was collected from 10 family members (4 affected with multiple sclerosis and 6 unaffected) using the PaxGene System (PreAnalytix). Sample collection was performed at baseline and after 6 months.

first: Ana

middle: M

first: Federica

last: Esposito

first: Melissa

last: Sorosina

first: Filippo

last: Martinelli Boneschi


title: Neonatal imprinting of mesenteric lymph node stroma modulates tolerogenic properties of dendritic cells [scRNA-seq]

first: Joern

overall_design: Single-cell transcriptomic analysis of skin-draining pLNs (inguinal and axillary) or mLNs (small intestinal and colon/caecum-draining) cell populations.

first: Diana

last: Fleissner

first: Marius

last: Vital

first: Dietmar

last: Pieper

first: Marijana

last: Basic

first: Petra

last: Dersch

first: Till

last: Strowig

first: Mathias

last: Hornef

first: André

last: Bleich

first: Ulrike

last: Bode

first: Oliver

last: Pabst

first: Marc

last: Bajenoff

first: Antoine-Emmanuel

last: Saliba


title: Ubiquitin C-terminal hydrolase isozyme L1 (UCHL1) is associated with shelterin complex at interstitial telomeric sites

status: Public on Feb 23 2018

city: Winnipeg

first: James

middle: Ronald

last: Davie

address: 745 Bannatyne Avenue, RM 333A

institute: University of Manitoba

summary: Ubiquitin C-terminal hydrolase isozyme L1 (UCHL1) is primarily expressed in neuronal cells and neuroendocrine cells. It is a multifunctional protein involved in deubiquitination, ubiquitination, and ubiquitin homeostasis. UCHL1 has been associated with various diseases, including many cancers, but its specific roles are disputed and still generally undetermined. Herein, we demonstrate that UCHL1 is associated with genomic DNA in certain prostate cancer cell lines, including DU 145 cells derived from a brain metastatic site, and in HEK293T embryonic kidney cells with a neuronal lineage. Chromatin immunoprecipitation and sequencing revealed that UCHL1 localizes to TTAGGG repeats at telomeres and interstitial telomeric sequences, as do TRF1 and TRF2, components of the shelterin complex. A weak or transient interaction between UCHL1 and the shelterin complex was confirmed by immunoprecipitation and proximity ligation assays. UCHL1 and TERF2IP, also a component of the shelterin complex, were bound to the nuclear scaffold. UCHL1 may play a role in regulating gene expression by affecting the stabilization of the shelterin proteins or influencing nuclear targeting. As several shelterin proteins (TRF1, TRF2, POT1 and TERF2IP) are ubiquitinated, UCHL1 may have a role in regulating the stability of these proteins. UCHL1 may also regulate the nuclear location of shelterin-associated genomic regions.

overall_design: A total of six samples were analyzed in the examination of genomic distribution of UCHL1 in DU 145 and HEK293T cells. Firstly, UCHL1 ChIP seq was performed in DU 145 1% formaldehyde cross-linked cells. Then, UCHL1 ChIP seq was performed in dual cross-linked (1mM DSP and 1% formaldehyde) DU 145 and HEK293T cells. All three UCHL1 ChIP seq samples were analyzed compared to their respective DNA inputs.

first: Aleksandar

last: Ilic

first: Sumin

last: Lu

first: Vikram

last: Bhatia

first: Farhana

last: Begum

first: Thomas

last: Klonisch

first: Prasoon

last: Agarwal

first: Wayne

last: Xu

middle: R


title: CRP and FIS

status: Public on Oct 03 2017

city: Parul

first: Parul

last: Singh

address: 25-28, rue du Docteur Roux

country: France

institute: Institut Pasteur

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


title: Differential and overlapping effects of 20.23(OH)2D3 and 1,25(OH)2D3 on gene expression in human epidermal keratinocytes

status: Public on Jul 19 2018

city: Birmingham

first: Tae-Kang

last: Kim

state: AL

institute: University of Alabama at Birmingham

summary:
Neonatal keratinocytes from African American donors of passage 2 or 3 were treated with 20,23(OH)2D3, 1,25(OH)2D3 or 0.1% ethanol (control) for 6 and 24 hours.
The cells were harvested separately, RNA isolated and submitted for microarray analysis at the Molecular Resources Center at the UTHSC.

overall_design: Neonatal foreskins of African American donors were used to isolate neonatal human epidermal keratinocytes. Petrie dishes (100 mm in diameter) were seeded with human neonatal keratinocytes that were combined from 4 different black donors of  either passage 2  or 3.  After reaching 70-80% of confluence cells were treated with 10-7M of either 20,23(OH)2D3 or  1,25(OH)2D3  or 0.1% of ethanol  (EtOH solvent control) for 6 or 24 hours. After 6 or 24 h of incubation  cells were isolated from 3 plates per each experimental condition and combined for passage 2 and 3, separately. The RNA from HEK treated with either 20,23(OH)2D3 or 1,25(OH)2D3 or 0.1% ethanol (control), was isolated using the Absolutely RNA Miniprep Kit (Stratagene). High purity RNA samples were submitted for microarray analysis at the Molecular Resources Center at the UTHSC. Expression profiling was accomplished using whole-genome gene expression direct hybridization assay using Illumina’s HumanWG-6_V2 (Platform GPL13376) chip/array  (Illumina, San Diego, CA).

first: Andrzej

last: Slominski


title: Integrative multi-omics analysis of intestinal organoid differentiation

status: Public on Jun 22 2018

city: Hinxton

first: Rik

last: Lindeboom

address: Wellcome Trust Genome Campus

department: Cellular Genetics

institute: Wellcome Sanger Institute

summary: Intestinal organoids accurately recapitulate epithelial homeostasis in vivo, thereby representing a powerful in vitro system to investigate lineage specification and cellular differentiation. Here, we applied a multi-omics framework on stem cell-enriched and stem cell-depleted mouse intestinal organoids to obtain a holistic view of the molecular mechanisms that drive differential gene expression during adult intestinal stem cell differentiation. Our data revealed a global rewiring of the transcriptome and proteome between intestinal stem cells and enterocytes, with the majority of dynamic protein expression being transcription-driven. Integrating absolute mRNA and protein copy numbers revealed post-transcriptional regulation of gene expression. Probing the epigenetic landscape identified a large number of cell-type-specific regulatory elements, which revealed Hnf4g as a major driver of enterocyte differentiation. In summary, by applying an integrative systems biology approach, we uncovered multiple layers of gene expression regulation, which contribute to lineage specification and plasticity of the mouse small intestinal epithelium.

overall_design: We use minor modifications of the organoid culture medium to generate cell type enriched mouse intestinal organoids, e.g. stem cell or enterocyte. These cell type enriched organoids are used in combination with a multi-omics framework to decipher the molecular mechanisms that drive cell fate changes in small intestinal organoids.

first: Lisa

last: van Voorthuijsen

first: Michiel

last: Vermeulen


title: ChIP-seq profiling of transcriptional co-activator p300 during early myogenic differentiation

status: Public on Jul 30 2018

city: Ottawa

first: Qiao

last: Li

address: 451 smyth road

department: Cellular and Molecular Medicine

institute: University of Ottawa

summary: Molecular regulation of stem cell differentiation is exerted through both genetic and epigenetic determinants over distal regulatory or enhancer regions. Understanding the mechanistic action of active or poised enhancers is thus imperative for control of stem cell differentiation. Based on a genome-wide co-occurrence of different epigenetic marks in committed proliferating myoblasts, we have previously generated a 14-state chromatin state model to profile residue-specific histone acetylation in early myoblast differentiation. Here, we use genome-wide chromatin state association to delineate the functional mode of transcription regulators in early myogenic differentiation. We define a role of transcriptional coactivator p300, when recruited by master muscle regulator MyoD, in the establishment and regulation of myogenic loci at the onset of terminal differentiation. In addition, we reveal an enrichment of residue- and loci-specific histone acetylation at p300 associated active or poised enhancers, particularly when enlisted by MyoD. We provide novel molecular insights into the regulation of myogenic enhancers by p300 in concert with MyoD. Our studies present a valuable aptitude for driving stage specific chromatin state or enhancers pharmacologically to treat muscle related diseases and for the identification of additional myogenic targets and molecular interactions for therapeutic development.

overall_design: We examined the genome-wide enrichment of transcriptional co-activator p300 in proliferating C2C12 myoblasts and myoblasts differentiated for 24 hours. Input chromatin DNA was used as control.

first: Munerah

last: Hamed

first: Saadia

last: Khilji


title: Genome-wide transcription profiling of oxic and anoxic cultures

status: Public on Sep 01 2016

city: Midreshet Ben Gurion

first: Bihter

last: Bayramoglu

address: Albert Katz International School, Jacob Blaustein Institute

department: Aquatic and Environmental Microbiology

country: Israel

institute: Ben Gurion University of the Negev

summary: We compared the transcriptome of stationary-phase cells with mature biofilm cultured with and without oxygen. The reads were mapped to the genome and then normalized counts for each gene were calculated, thus enabling the comparison of gene-expression levels between samples. Our results depicts the severe stress the lack of oxygen imposes on biofilms by altered gene expression

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

overall_design: mRNA profiles of aerobic and anaerobic biofilm and planktonic cultures were generated by deep sequencing

first: David

last: Toubiana

first: Osnat

last: Gillor


title: Chromatin remodeler CHD7 regulates the stem cell identity of human neural progenitors

status: Public on Mar 28 2018

city: Shinjuku-ku

first: Tsukasa

last: Sanosaka

address: 35 Shinanomachi

department: Department of Physiology

institute: Keio University School of Medicine


title: Expression-based clustering of CAZyme-encoding genes of Aspergillus niger

status: Public on Jan 29 2018

city: Utrecht

first: Ronald

last: de Vries

address: Uppsalalaan 8

department: fungal physiology

country: Netherlands

institute: Centre of fungal biodiversity

summary: The Aspergillus niger genome contains a large repertoire of genes encoding carbohydrate active enzymes (CAZymes) that are targeted to plant polysaccharide degradation enabling A. niger to grow on a wide range of plant biomass substrates. Which genes need to be activated in certain environmental conditions depends on the composition of the available substrate. Previous studies have demonstrated the involvement of a number of transcriptional regulators in plant biomass degradation and have identified sets of target genes for each regulator. In this study, a broad transcriptional analysis was performed of the A. niger genes encoding (putative) plant polysaccharide degrading enzymes. Microarray data focusing on the initial response of A. niger to the presence of plant biomass related carbon sources were analyzed of a wild-type strain N402 that was grown on a large range of carbon sources and of the regulatory mutant strains ΔxlnR, ΔaraR, ΔamyR, ΔrhaR and ΔgalX that were grown on their specific inducing compounds.

overall_design: We aim to evaluate co-regulation/co-expression of characterized and putative CAZymes to gain more insight in the function of uncharacterized CAZyme encoding genes in plant biomass utilization and to identify new targets of transcriptional regulators. The focus of the study was on the initial response of A. niger to the presence of a carbon source. For this, microarray data were analyzed of A. niger N402 (wild type) that was grown on a set of 23 carbon sources (including eight monosaccharides, two oligosaccharides, 11 polysaccharides, a crude plant biomass substrate and ferulic acid), and of regulatory mutant strains (ΔxlnR, ΔaraR, ΔamyR, ΔrhaR and ΔgalX) that were grown on their specific inducing compounds. Biological duplicates were grown for each of the conditions and Affymetrix microarray experiments were performed on these samples.

first: Birgit

last: Gruben

first: Miia

last: Mäkelä

first: Joanna

last: Kowalczyk

first: Miaomiao

last: Zhou

first: Isabell

last: Benoit-Gelber

middle: P


title: Non-coding mechanisms of tolerance, persistence and resistance to EGFR inhibition in lung cancer [microRNA-seq]

status: Public on Jan 11 2018

first: Wen Cai

last: Zhang

state: MASSACHUSETTS

address: 330 BROOKLINE AVENUE, CLS417

institute: Beth Israel Deaconess Medical Center

summary:
Purpose: To characterize microRNA signatures for tolerance, persistence and resistance to EGFR tyrosine kinase inhibitors (TKIs) in human lung cancer.
Methods: microRNA profiles of gefitinib- and osimertinib-tolerant cells in PC9 and HCC827 cells were generated by deep microRNA sequencing using Illumina. In addition, microRNA profiles of PC9 subpopulations cells with characterizations of persistence and resistance to gefitinib were generated by deep microRNA sequencing. The mappable reads were aligned to the human genome and miRbase using Bowtie.
Results: We identified a specific microRNA profile distinguishing tolerance, persistence and resistance to gefitinib or osimertinib from parental human lung cancer cells with mutated EGFR. The expressions of those microRNAs in lung cancer cells were validated by qRT-PCR. Functionally, knocking down top-upregulated microRNAs reduced the tolerance, persistence and resistance to gefitinib or osimertinib in those tolerant and resistant cells. Conversely, overexpression of those microRNAs enhanced the tolerance and resistance to EGFR inhibition in cells sensitive to gefitinib and osimertinib.
Conclusions: Our work identifies a panel of microRNAs that mediate EGFR-TKI tolerance and resistance in lung cancer. Our study provides potential non-coding targets to improve the efficacy of EGFR-TKIs therapy in cancer pagtients.

overall_design: microRNA profiles of gefitinib and osimertinib tolerant cells in PC9 (PC9GTR and PC9OTR) and HCC827 (HCC827GTR and HCC827OTR) were generated by deep sequencing using Illumina. In addition, microRNA profiles of PC9 persisters and resistant cells treated by gefitinib and WZ4002 were generated by deep sequencing.

first: Wencai

first: Frank

last: Slack


title: CHARGE syndrome modeling using patient-derived iPSC reveals defective migration of neural crest cells harboring CHD7 mutations

status: Public on Oct 23 2017

summary: CHARGE syndrome is caused by heterozygous mutations in a chromatin remodeler CHD7 and characterized by a set of malformations historically postulated to arise from defects in the neural crest formation during embryogenesis. To better delineate neural crest defects in CHARGE syndrome, we generated induced pluripotent stem cells (iPSCs) from two patients with typical syndrome manifestations, and characterized neural crest cells differentiated in vitro from these iPSCs (iPSC-NCCs). We found that expression of genes associated with cell migration was altered in CHARGE iPSC-NCCs as compared to control iPSC-NCCs. Consistently, CHARGE iPSC-NCCs showed defective delamination, migration and motility in vitro, and their transplantation in ovo revealed overall defective migratory activity in the chick embryo. Altogether, our results support the historical inference that CHARGE syndrome patients have defects in neural crest migration and provide the first successful application of patient-derived iPSCs in modeling craniofacial disorders.

overall_design: 8 samples

first: Hironobu

last: Okuno


title: RNA-seq profiling of rexinoid responsive gene expression during early myogenic differentiation

status: Public on Sep 13 2017

first: Qiao

summary: While skeletal myogenesis is tightly coordinated by myogenic regulatory factors including MyoD and myogenin, chromatin modifications have emerged as vital mechanisms of myogenic regulation. We have previously established that bexarotene, a clinically approved agonist of retinoid X receptor, promotes the specification and differentiation of skeletal muscle lineage. Here, we examine a genome-wide impact of rexinoids on myogenic differentiation through integral RNA-seq and ChIP-seq analyses. We found that bexarotene promotes myoblast differentiation through the coordination of exit from the cell cycle and the activation of muscle-related genes. We uncovered a new mechanism of rexinoid action which is mediated by the nuclear receptor and largely reconciled through a direct regulation of MyoD gene expression. In addition, we determined a rexinoid-responsive residue-specific histone acetylation at a distinct chromatin state associated to MyoD and myogenin. Thus, we provide novel molecular insights into the interplay between retinoid X receptor signaling and chromatin states pertinent to myogenic programs in early myoblast differentiation.

overall_design: We have profiled the global effect of bexarotene, a selective agonist of retinoid X receptor on myoblast gene expression by RNA-seq analysis using RNA isolated from C2C12 myoblasts following 12 or 24 hours of differentiation in the presence and absence of 50 nM bexarotene, with 2 biological replicates. Proliferating myoblasts were used as controls.


title: Poly(ADP-ribosyl)ation dependent changes in CTCF-chromatin binding and gene expression in breast cells

status: Public on Aug 11 2017

city: Colchester

first: Vladimir

middle: B

last: Teif

address: Wivenhoe Park

department: School of Life Sciences

institute: University of Essex

summary: CTCF is an evolutionary conserved and ubiquitously expressed architectural protein, which regulates a plethora of cellular functions using different molecular mechanisms. The main form of CTCF with an apparent molecular mass of 130 kDa (CTCF130) has been extensively studied, however the properties of CTCF180, highly modified by poly(ADP-ribosyl)ation (PARylation) are not well understood. In this study we performed ChIP-seq and RNA-seq analyses in breast cells 226LDM, proliferating (with CTCF130 as the most abundant CTCF form) and arrested in the cell cycle (with only CTCF180).  A dramatic reorganization of CTCF binding was observed during this transition, whereby CTCF was evacuated from many sites ("lost" group), although some sites retained modified CTCF ("common") and others acquired CTCF180 ("gained"). The classic CTCF binding motifs were identified for the former two groups, whereas the latter had no CTCF binding motif.  Changes in CTCF occupancies in lost/common (but not gained) sites were associated with increased chromatin densities and altered expression from the neighboring genes. We propose a model integrating CTCF130/180 transition with CTCF-DNA binding and gene expression patterns, and functional outcomes. This study issues an important cautionary note concerning design and interpretation of any experiments using cells and tissues where CTCF180 may be present.

overall_design: ChIP-Seq and RNA-Seq analyses to investigate CTCF binding, histone patterns and gene expression profiles in breast cells, 226LDM, proliferating (with CTCF130 as the most abundant CTCF form) and chemically arrested in the cell cycle (with only CTCF180)

first: Ioanna

last: Pavlaki

first: France

last: Docquier

first: Igor

last: Chernukhin

first: Elena

last: Klenova


title: Transcriptome of non-involved lung parenchyma from smoker lung adenocarcinoma patients from Milan, Italy.

status: Public on Jan 20 2016

first: Matteo

last: Dugo

address: via Olgettina 60

department: Department of Medical Oncology

institute: IRCCS Ospedale San Raffaele

summary: Scientific evidence indicates that genetic factors may contribute to differences in lung cancer risk for individuals with similar levels of tobacco exposure, which is the main environmental risk factor of lung cancer. Moreover, lung cancer patients show large differences in clinical staging and survival; these differences seem to be attributable, at least partially, to the genetic background. The analysis of the molecular properties (e.g., germline variations and genome-wide expression levels) of non-involved tissue from lung cancer patients may contribute in the identification of genetic factors involved in the development and progression of this pathology. To this aim, we analyzed two series (discovery series, n = 204, and validation series, n = 78) of non-tumor lung tissue samples from smokers that underwent surgical lobectomy for adenocarcinoma in Milan, Italy. First, we examined the whole transcriptome of these two series to define the candidate genes and pathways associated with either lung cancer risk or prognosis in this cohort. Moreover, as sex and age are known to strongly influence the pathophysiology of human lungs, we used transcriptome data from the same samples to identify sex- and age-related transcriptional differences in lung.

overall_design: Samples of non-involved (apparently normal) lung parenchyma excised from patients who underwent lobectomy for lung adenocarcinoma in the area around Milan, Italy. The samples were analyzed in two sets: a discovery series (n = 204) and a validation series (n = 78).

first: Francesca

last: Colombo

first: Chiara

last: Cotroneo

first: Loris

last: De Cecco

first: Tommaso

last: Dragani

first: Antonella

last: Galvan

first: Sara

last: Noci


title: Molecular characterization of chronic antibody mediated rejection in kidney transplantation (mRNA)

status: Public on Dec 10 2015

city: Bari

first: Paola

last: Pontrelli

address: Piazza G.Cesare 11

department: Dept. of Precision and Regenerative Medicine and Ionian Area (DIMEPRE-J)

institute: University of Bari

summary:
Chronic antibody-mediated rejection (CAMR) represents the main cause of kidney graft loss, but its pathogenesis is unclear. In order to uncover the molecular mechanisms underlying this condition, we characterized the molecular signature of circulating peripheral blood mononuclear cells and, separately, of CD4+ T lymphocytes isolated from CAMR patients compared to kidney transplant recipients with normal graft function and histology.
In total peripheral lympho-monocytes, forty-five genes resulted differentially expressed between the two groups, most of them were up-regulated in CAMR and were involved in type I interferon signaling. In addition, in the same set of patients, 16 microRNAs resulted down-regulated in CAMR subjects compared to controls: 4 were predicted modulators of 6 mRNAs identified in the transcriptional analysis. In silico functional analysis supported the involvement of type I interferon signaling. To further confirm this hypothesis, we investigated the transcriptomic profiles of CD4+ T lymphocytes in an independent group of patients and we observed that the activation of type I interferon signaling was a specific hallmark of CAMR. In addition, in CAMR patients we detected a reduction of circulating BDCA2+ dendritic cells, the natural type I interferon- producing cells and their recruitment into the graft along with an increased expression of MXA, a type I interferon-induced protein, at tubulointerstitial and vascular level.
In conclusion, our data suggest that type I interferon signaling may represent the molecular signature of CAMR.

overall_design: For microarray analysis, we studied 8 patients included into the control-group and 10 included into the study group. The control group was represented by renal transplant recipients undergoing protocol graft biopsies, with normal renal function and histology, in the absence of circulating anti-HLA antibodies. Study group patients showed clinical and histological evidence of CAMR according to Banff 2011 criteria.

first: Federica

last: Rascio

last: Accetturo

first: Annarita

last: Oranger

first: Margherita

last: Gigante

first: Giuseppe

last: Castellano

first: Maddalena

first: Anna

last: Zito

first: Gianluigi

last: Zaza

first: Antonio

last: Lupo

last: Ranieri

first: Giovanni

last: Stallone

first: Loreto

last: Gesualdo

last: Grandaliano


title: Dose-Response Analysis of RNA-Seq Profiles in Archival Formalin-Fixed Paraffin-Embedded (FFPE) Samples

status: Public on Aug 30 2016

city: RTP

first: Susan

last: Hester

address: 109 TW Alexander Dr

institute: US EPA

summary: Use of archival resources has been limited to date by inconsistent methods for genomic profiling of degraded RNA from formalin-fixed paraffin-embedded (FFPE) samples. RNA-seq offers a novel way to address this problem. In this study we evaluated transcriptomic dose responses using RNA-seq in paired FFPE and frozen (FROZ) samples from two archival studies in mice, one recent (<2 years old) and the other older (>20 years old). Experimental treatments included di(2-ethylhexyl)phthalate (DEHP) and dichloroacetic acid (DCA) for the <2 and >20 year-old studies, respectively. Total RNA was ribodepleted and sequenced using the Illumina HiSeq platform. In the recent study, FFPE samples showed high concordance in total reads (98% vs FROZ), fold-change values of differentially expressed genes (DEGs) (R2 = 0.99), highly enriched target pathways (90% overlap with FROZ), and benchmark dose estimates for preselected target genes (-2% overall vs FROZ). In contrast, RNA-seq data from older FFPE samples had lower total reads (70% vs FROZ) and poor concordance in global DEGs and pathways. Despite a 99% loss of counts, dose responses were still evident for target genes in FFPE samples and positively correlated with paired FROZ samples. These findings highlight potential variability in the quality of RNA-seq data from FFPE samples. More recent FFPE samples were highly similar to FROZ samples in sequencing quality metrics, DEG profiles, and dose-response parameters, while further methods development is needed for older or lower-quality FFPE samples. This work should help broaden the use of archival resources in both chemical safety and translational science.

overall_design: Trancriptomic profiles obtained using from paired frozen (FROZ) and formalin-fixed paraffin-embedded (FFPE) liver samples collected in 2013 for the DEHP study  (n=16 FROZ, n=16 FFPE, with four dose groups at 0, 1500, 3000, and 6000 ppm DEHP, n=4 per dose group) and 1994 for the DCA study (n=24 FROZ, n=24 FFPE, with four dose groups at 0, 1.0, 2.0, and 3.5 g/L DCA, n=6 per dose group) using Illumina HiSeq platform.

first: Virunya

last: Bhat

first: Brian

middle: N

last: Chorely

first: Gleta

last: Carswell

first: Wendell

last: Jones

first: William

last: Ward

first: Leah

last: Wehmas

first: Charles

last: Wood


title: Gene expression profiles of livers from male LMNA+/+, LMNA flx/+, and LMNA flx/flx; Alb-Cre+ C57BL/6 mice fed normal chow or high fat diet

status: Public on Jan 16 2017

city: Ann Arbor

first: Raymond

last: Kwan

address: 7720 Med Sci II

department: Molecular and Integrative Physiology

institute: University of Michigan, Ann Arbor

summary:
To investigate the molecular basis for male-specific steatohepatitis in Lamin A/C-deficient livers, microarray gene expression analysis was performed on total liver RNA isolated from 26- to 39-week-old, male LMNA+/+, LMNA flx/+, and LMNA flx/flx; Alb-Cre+ C57BL/6 mice fed either normal chow (NC) or high fat diet plus carbohydrate-supplemented water (HFD).
Lamins are nuclear intermediate filament proteins that comprise the major components of the nuclear lamina in metazoan cells. Mutations in LMNA, which encodes lamins A/C, cause diseases termed laminopathies, including lipodystrophy, cardiomyopathy, and premature aging. The lamin A/C mutation-associated Dunnigan familial partial lipodystrophy is typically accompanied by fatty liver disease. The role of lamins in the liver is unknown, and it is unclear whether laminopathy-associated liver disease is due to primary hepatocyte defects or systemic alterations. To address these questions, mice carrying a hepatocyte-specific deletion of Lmna (KO mice) were generated. KO hepatocytes manifested abnormal nuclear morphology, and KO mice developed spontaneous male-selective hepatosteatosis, with increased susceptibility to high fat diet-induced steatohepatitis and fibrosis. The molecular mechanism by which liver-specific Lamin A/C deficiency induces male-specific steatohepatitis is unknown. The microarray data presented here demonstrates that hepatic Lmna deficiency is associated with upregulated expression of fatty acid transporters, lipid biosynthetic enzymes, lipid-droplet associated proteins, and interferon-regulated genes and other pro-inflammatory mediators.

overall_design: Global gene expression profiling of liver RNA isolated from 26- to 39-week-old LMNA+/+, LMNA flx/+, and LMNA flx/flx; Alb-Cre+ C57BL/6 mice fed either normal chow (NC) or high fat diet plus carbohydrate-supplemented water (HFD). The following mouse livers were used in gene expression profiling: LMNA+/+; Alb-Cre+, NC-fed (n=2); LMNA flx/+; Alb-Cre+, NC-fed (n=3); LMNA flx/flx; Alb-Cre+, NC-fed (n=3); LMNA flx/+; Alb-Cre+, HFD-fed (n=3); and LMNA flx/flx; Alb-Cre+, HFD-fed (n=3).

first: Bishr

last: Omary


title: The role of CHD7 in human central nervous system development (ChIP-Seq)

first: Tsukasa

last: Sanosaka

summary: CHARGE syndrome is a congenital disorder caused by mutations in Chromodomain Helicase DNA-binding domain 7 (CHD7) gene. We generated a cell line carrying HA-tag knock-in into the human CHD7 locus, mediated by CRISPR-Cas9 system. We then performed ChIP against HA antibody using the validated knock-in cells and subsequent high-throughput sequencing analysis.

overall_design:
Examination of histone modification and CHD7 binding sites in WT, CHD7-KD and CHARGE patient cells.
CHARGE patient raw data is not available in GEO due to patient privacy restrictions. The raw data is available via controlled access through JGA (Japanese Genotype-Phenotype Archive) by accession number JGAS00000000131.


status: Public on Dec 13 2016

first: Parul

last: Singh

summary: We have performed ChIP-Seq experiment for the global regulators, CRP and Fis in early and mid exponential growth phases respectively in Escherichia coli K12 MG1655. The dataset contains the genome wide binding patterns of Fis and CRP in the wildtype and the mutant strains

overall_design: To understand the influence of global transcription regulators Fis and CRP on DNA binding property in different growth phases as well as of E. coli

first: Aswin

middle: S

last: Seshasayee


title: High Density Rice Array (HDRA6.4) developed by the McCouch-Rice Lab at Cornell University

status: Public on Feb 25 2016

city: Ithaca

middle: R.

last: McCouch

state: NY

address: 162 Emerson Hall

department: Plant Breeding & Genetics

institute: Cornell University

summary: A High Density Rice Array (HDRA) was developed as an Affymetrix Custom GeneChip Array by the McCouch Rice Lab at Cornell University. The HDRA assays 700,000 SNPs, or approximately one SNP every 0.54 Kb across the rice genome (genome size = 380 Mb). It was designed to capture most of the haplotype variation observed in a discovery panel consisting of 16M SNPs (generated by sequencing 125 rice genomes at ~7X genome coverage) and to maximize the inclusion of non-synonymous SNPs. Six probes per SNP target were designed as 3 A-allele and 3 B-allele probes at offsets from center ranging from -6 to +6. A small fraction of SNPs have only 4 probes (2-A, 2-B). For all SNPs, the “A” allele is the reference allele (Os-Nipponbare-Reference-IRGSP-1.0 assembly). Additionally, we designed 23,656 x 25-bp probes complimentary to invariant regions of the genome that were used to normalize systematic differences between samples. An estimated 45% of HDRA SNPs map within genes, hitting all 39,045 unique, non-TE rice gene models (MSUv7 rice genome annotation, GFF3 file, Feb. 7, 2012, http://rice.plantbiology.msu.edu/), while 55% of SNPs map to intergenic regions. Non-synonymous are found in 91% of unique, non-TE gene models, and 57% of genic SNPs are distributed within exons, 36% within introns, 5% within 5’ UTRs and 2% within 3’ UTRs. Of the intergenic SNPs, 40% are located in putative regulatory regions within 2 Kb of a transcriptional start site.

overall_design: Using the HDRA, SNP variation was assayed in a collection of 1,568 diverse O. stiva accessions and the resulting genotypic dataset was analyzed for population structure and used for Genome Wide Association Studies (GWAS).

first: Mark

last: Wright

first: Chih-Wei

last: Tung

first: Genevieve

last: DeClerck

first: Francisco

last: Agosto-Pérez

first: Sandra

last: Harrington

first: Yuxin

last: Shi

first: Namrata

first: Kenneth

middle: L

last: McNally

first: Kowaru

last: Ebana

first: Masahiro

last: Yano

first: Georgia

last: Eizenga

first: Anna

last: McClung

first: Jason

last: Mezey


title: AdipoQ-LPL transgene alters gene expression and alternative splicing in perigonadal adipose tissue

status: Public on Oct 06 2016

city: Lexington

first: Brian

last: Finlin

state: KY

address: 900 S. Limestone CTW 575

department: Internal Medicine

institute: University of Kentucky

summary:
Specific expression lipoprotein lipase in adipose by the adiponectin promoter alters the transcriptional response of adipose tissue to an acute high fat diet challenge.
We include transcriptional changes in adipose tissue from 12 littermate control and 12 AdipoQ-LpL mice.  Gene expression and alternative splicing were analyzed.

overall_design: 24 samples were analyzed.  We identified changes in gene expression and alternative splicing.


title: Aging induces de novo rhythmic expression of oxidative stress-responsive genes

status: Public on Jan 14 2017

city: Corvallis

first: David

middle: Anthony

last: Hendrix

state: OR

address: 2011 Ag & Life Sciences Bldg

department: Biochemistry and Biophysics/EECS

institute: Oregon State University

summary:
Disruption of the circadian clock, which directs rhythmic expression of numerous
genes, accelerates aging. To inquire how the circadian system protects organisms
during aging, we compared circadian transcriptomes in heads of young and old
Drosophila melanogaster. These data revealed a class of genes that adopt de novo
rhythmicity during aging, termed "late life cyclers" (LLCs). We show that application of exogenous oxidative stress in young flies mimics aging by inducing robust, rhythmic LLC upregulation in a light- and CLOCK-dependent fashion. Additionally, we identified age-onset rhythmicity in some primary piRNA transcripts that overlap antisense transposable elements. To share our data, we developed a database for public viewing of graphical RNA-seq results for coding and non-coding RNAs in young and old flies. Taken together, our results suggest that aging organisms recruit the circadian system to launch a temporally coordinated defense to cope with their increasingly stressful cellular environments.

overall_design: RNA-Seq was collected around the clock every 4 hours for young (5 day) and old (55 day) Drosophila melanogaster heads.

first: Rachael

middle: C

last: Kuintzle


title: Genome-wide mapping of immature erythrocyte transcribed chromosomal domains (F1-seq)

status: Public on Jan 01 2016

first: James

last: Davie

department: Biochemistry and Medical Genetics

institute: University of Manitoba

summary: Transcriptional regulation is impacted by multiple layers of genome organization. Here, we  identified and mapped out all the transcriptionally active chromosomal domains in the chicken  immature erythrocyte genome, including the known β- and α-globin domains, by combining a  powerful chromatin fractionation method with next generation DNA and RNA sequencing.

overall_design: To characterize transcriptionally active chromatin domains, we used two biological replicates. Each replicate set has one control SE fraction and one transcriptionally active chromatin fraction (F1)

first: Sanzida

last: Jahan

first: Wayne

last: xu

first: Shihua

last: He

first: Carolina

last: Gonzalez

first: Geneviève

last: Delcuve


title: Ser7 of RNAPII-CTD facilitates heterochromatin formation by linking ncRNA to RNAi

status: Public on Dec 13 2017

city: Kobe

first: Atsushi

last: Matsuda

address: 588-2, Iwaoka, Iwaoka-cho, Nishi-ku

institute: National Institute of Information and Communications Technology

summary: Some long noncoding RNAs (ncRNAs) transcribed by RNA polymerase II (RNAPII) are retained on chromatin, where they regulate RNAi and chromatin structure. The molecular basis of this retention remains unknown. We show that in fission yeast serine 7 (Ser7) of the C-terminal domain (CTD) of RNAPII is required for efficient siRNA generation for RNAi-dependent heterochromatin formation. Surprisingly, Ser7 facilitates chromatin retention of nascent heterochromatic RNAs (hRNAs). Chromatin retention of hRNAs and siRNA generation requires both Ser7 and an RNA-binding activity of the chromodomain of Chp1, a subunit of the RNA-induced transcriptional silencing (RITS) complex. Furthermore, RITS associates with RNAPII in a Ser7- dependent manner. We propose that Ser7 promotes cotranscriptional chromatin retention of hRNA by recruiting the RNA-chromatin connector protein Chp1, which facilitates RNAi-dependent heterochromatin formation. Our findings reveal a function of the CTD code: linking ncRNA transcription to RNAi for heterochromatin formation.

overall_design: Gene expression profile at exponentially-growing phase in the fission yeast mutants of rpb1. Repression of otr1R::ade6+ by heterochromatin in wild-type cells resulted in the formation of red colonies on a solid medium containing a limiting amount of adenine (Low Ade), because lack of the ade6+ gene product results in the accumulation of a red pigments in the cells. By contrast, the ctdS2A and ctdS7A mutants of rpb1 produced a mixture of pink and white colonies showing these mutants are defective in heterochromatin. The microarray analysis was performed respectively on pink and white cells.

first: Takuya

last: Kajitani

first: Hiroaki

last: Kato

first: Yuji

last: Chikashige

first: Chihiro

last: Tsutsumi

first: Yasushi

last: Hiraoka

first: Hiroshi

last: Kimura

first: Yasuyuki

last: Ohkawa

first: Chikashi

last: Obuse

first: Damean

last: Hermand

first: Yota

last: Murakami


title: The chicken erythrocyte epigenome

first: James

last: Davie

address: 745 Bannatyne Avenue, RM 333A

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

overall_design: Refer to individual Series


title: Genome-wide mapping of H3K4me3 and H3K27ac in chicken immature erythrocyte cells

summary: Transcriptional regulation is impacted by multiple layers of genome organization. Here, we report that highly expressed genes were associated with H3K4me3 and H3K27ac.Our data provide a genome-wide profile of chromatin signatures in relation to expression levels in chicken immature erythrocytes.

overall_design: Examination of two different histone modifications in immature erythrocyte cells

first: Sanzida

last: Jahan

last: Xu


title: Cell-specific methylation patterns in TB patients and household contacts

status: Public on Aug 25 2015

city: Berlin

first: January

last: Weiner

address: Charitéplatz 1

department: CUBI

institute: Berlin Institute of Health, Charité Medical University of Berlin

type: Methylation profiling by genome tiling array

summary: Monocytes and granulocytes were isolated from blood of TB patients and household contacts. DNA was isolated and methylation profile was measured using Illumina HumanMethylation450.

overall_design: House-hold contacts were matched to TB patients by gender and age. From each subject, two profiles (monocytes and granulocytes) were collected.

first: Maria

last: Esterhuyse

first: Hans-Joachim

last: Mollenkopf