title: The LC3 conjugation machinery specifies the loading of RNA-binding proteins into extracellular vesicles

status: Public on Dec 22 2019

first: Jayanta

last: Debnath

institute: University of California, San Francisco


title: Microarray Analysis of LncRNA Expression Profiles in Monocytic Myeloid-derived Suppressor Cells in Echinococcus granulosus-infected mice

status: Public on Dec 23 2019

city: shanghai

first: yujuan

last: shen

address: Rui jin Er road

country: China

institute: National Institute of Parasitic Diseases

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

summary: To investigate the lncRNA and mRNA expression profiles in the splenic M-MDSCs of normal and Eg-psc-infected mice, and performed bioinformatics analysis of the differentially expressed lncRNAs to explore the possible biological processes and pathways associated with M-MDSCs.

overall_design: The expression patterns of lncRNAs and mRNAs were detected in the splenic M-MDSCs of three Eg-psc–infected mice and normal mice each 8 months after infection.

first: Aiping

last: Yu

first: Yujuan

last: Shen

first: Jianping

last: Cao


title: Microarray Analysis of miRNA Expression Profiles in Monocytic Myeloid-derived Suppressor Cells in Echinococcus granulosus-infected mice

summary: To investigate the miRNA expression profiles in the splenic M-MDSCs of normal and Eg-psc-infected mice, and performed bioinformatics analysis of the differentially expressed miRNAs to explore the possible biological processes and pathways associated with M-MDSCs.

overall_design: The expression patterns of miRNAs were detected in the splenic M-MDSCs of three Eg-psc–infected mice and normal mice each 8 months after infection.


title: The role of Lhx4 and Bsx homeobox genes in the rat adult pineal gland

status: Public on Dec 21 2019

city: Bethesda

first: Steven

middle: L.

last: Coon

state: MD

address: 10 Center Dr; Room 8S261A

department: NICHD

country: USA

institute: National Institutes of Health

type: Expression profiling by high throughput sequencing

summary: Homeobox genes generally encode transcription factors involved in regulating developmental processes. In the pineal gland, a brain structure devoted to nocturnal melatonin synthesis, a number of homeobox genes are also expressed postnatally; among these are the LIM homeobox 4 gene (Lhx4) and the brain‐specific homeobox gene (Bsx). As part of a larger study, we used of siRNA technology to knock down Lhx4 or Bsx expression in cultured adult rat pinealocytes.  For RNAseq, nine barcoded libraries were pooled and sequenced on one Flow Cell of a HiSeq2500 (Illumina) in Rapid Run Mode yielding a total of 410 million 2∙x 100‐bp read‐pairs (average reads per sample: 45.6∙106 ± 3.3∙106 SEM). Analysis of control and siRNA‐treated pinealocytes revealed downstream target genes and insights into the role these homeobox genes play in the adult pineal gland. The two processed data file present siLhx4 vs siNT, or siBsx vs siNT.

overall_design: There are nine sample total of RNA extracted from adult rat pinealocytes treated with short-interfering RNAs (siRNA). There are triplicates of Control nontargeting siRNA (siNT), siRNA targeting Lhx4 (siLhx4), or siRNA targeting Bsx (siBsx).

first: Henrik

last: Hertz

first: Martin

middle: F

last: Rath

first: David

middle: C

last: Klein

middle: L


title: Swarming motility induces multidrug resistance

city: Burnaby

first: Travis

last: Blimkie

state: British Columbia

address: 8888 University Drive

department: MBB

country: Canada

institute: Simon Fraser University

summary: Multidrug adaptive resistance of Pseudomonas aeruginosa swarming cells

overall_design: Studying the effects of swarming motility on antibiotic resistance in Pseudomonas aeruginosa UCBPP-PA14, using subinhibitory concentrations

first: Shannon

last: Coleman

first: Reza

last: Falsafi

first: Robert

middle: W

last: Hancock


title: Next Generation Sequencing Facilitates Quantitative Analysis of Spermidine Inhibited Transcriptomes

city: Shanghai

first: Haibo

last: Zhou

address: No.160, Pujian Road

department: Department of Rheumatology

institute: Renji Hospital

summary:
Purpose: Spermidine inhibits the activation of interferon primed dendritic cells. The goals of this study are to identify genes and pathways invovled in the regulation.
Methods: Mouse monocyte derived dendritic cells were primed with interferon α for 24 hours, and then cultured with R837, together with or without spermidine for 18 hours. Then, the next-generation libraries of mRNA were prepared using VAHTS mRNA-seq v2 Library Prep Kit for Illumina® (Vazyme, Nanjing, China). The Library quality was determined by Bioanalyzer 4200 (Agilent, Santa Clara, CA, USA). Then the mRNA-seq libraries were sequenced in HiSeq X10 system (Illumina, San Diego, CA, USA) on a 150bp paired-end run. The differentially expressed genes were selected as having more than 1 fold difference in their geometrical mean expression between the compared groups and a statistically significant p-value (<0.05) by analysis of DEseq2. The GO analysis on differentially expressed genes was performed with an R package: Clusterprofiler using a p<0.05 to define statistically enriched GO categories. Pathway analysis was used to determine the significant pathway of the differential genes according to Kyoto Encyclopedia of Genes and Genomes Database (http://www.genome.jp/kegg/) and DAVID Bioinformatics Resources 6.8 (https://david.ncifcrf.gov/).
Results: Genes in the JAK/STAT pathway and the NF-κB pathway were inhibited by spermidine. As a result, the pro-inflammatory cytokines including IL-1β, IL-12a, IL-12b (IL-12/23 p40), IL-6 and IL-23a decreased obviously upon spermidine treatment

overall_design: MRNA profiles of Control, R837 stimulated and R837 plus Spermidine treated moDCs were generated by deep sequencing, in triplicate, using illumina HiSeq X10 system


title: siRNA-mediated knockdown

city: San Francisco

first: Hani

last: Goodarzi

state: CA

department: Biochemistry and Biophysics

institute: UCSF

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

overall_design: Refer to individual Series


title: Phase separation of TAZ compartmentalizes the transcription machinery to promote gene expression

city: Berkeley

first: Kunxin

last: Luo

address: 375E Li Ka Shing Center for Biomedical and Health Sciences

department: Department of Molecular and Cell Biology

institute: University of California, Berkeley

summary: TAZ promotes cell proliferation, development, and tumorigenesis by regulating target gene transcription. However, how TAZ orchestrates the transcriptional responses remains poorly defined. Here we demonstrate that TAZ forms nuclear condensates via liquid-liquid phase separation to compartmentalize its DNA binding co-factor TEAD4, the transcription co-activators BRD4 and MED1 and the transcription elongation factor CDK9 for activation of gene expression. TAZ, but not its paralog YAP, forms phase-separated droplets in vitro and liquid-like nuclear condensates in cells and tissues, and this ability is negatively regulated by Hippo signaling via LATS-mediated phosphorylation and mediated by the coiled-coil domain. Deletion of the TAZ coiled-coil domain or substitution with the YAP coiled-coil domain does not affect the interaction with its partners, but prevents its phase separation and more importantly, its ability to induce expression of TAZ-specific target genes. Thus, our study has identified a novel mechanism for the transcriptional activation by TAZ and demonstrated for the first time that pathway-specific transcription factors also engage the phase separation mechanism for efficient and specific transcription activation.

overall_design: RNA profiles of WT, TAZ-KO, TAZ-KO+Flag-TAZ, TAZ-KO+Flag-TAZ-deltaCC, and YAP-KO MDA-MB-231 cells were generated by deep sequencing, using Illumina NovaSeq.

first: Yi

last: Lu


title: TREM2 regulates microglial lipid metabolism during aging in mice [RNA-Seq]

city: South San Francisco

first: Thomas

last: Sandmann

email: genomics@dnli.com, sandmann@dnli.com

state: California

address: 161 Oyster Point Blvd

institute: Denali Therapeutics

summary: TREM2 is a microglial-specific gene implicated in late-onset Alzheimer's Disease (AD). Recent studies have identified that Trem2-deficient mice exhibit transcriptional changes in microglial gene expression that minimize the upregulation of lipid metabolism and lysosomal genes in AD disease models. We detect similiarly attenuated expression of lipid metabolism genes in microglia isolated from brains of aged Trem2 knockout mice.

overall_design: Microglia and astrocytes were purified from brains of Trem2 wildtype and homozygous knockout mice of young (2 months) and old (16-18 months) mice using fluorescent activated cell sorting (FACS). Gene expression was assessed using 3' tag sequencing of poly-adenylated RNA (QuantSeq, Lexogen, Vienna, Austria) with unique-molecular identifiers (UMIs).

first: Alicia

middle: A

last: Nugent

first: Kathryn

middle: M

last: Monroe

first: Gilbert

last: Di Paolo


title: Single cell RNA-sequencing reveals cellular heterogeneity and trajectories of lineage specification during murine embryonic limb development

city: St. Louis

first: Farshid

last: Guilak

state: MO

address: 4515 McKinley Ave

institute: Washington University in St. Louis

summary: The coordinated spatial and temporal regulation of gene expression in the murine hindlimb determines the identity of mesenchymal progenitors and the development of diversity of musculoskeletal tissues they form. Hindlimb development has historically been studied with lineage tracing of individual genes selected a priori, or at the bulk tissue level, which does not allow for the determination of single cell transcriptional programs yielding mature cell types and tissues. To identify the cellular trajectories of lineage specification during limb bud development, we used single cell mRNA sequencing (scRNA-seq) to profile the developing murine hindlimb between embryonic days (E)11.5-E18.5. We found cell type heterogeneity at all time points, and the expected cell types that form the mouse hindlimb. In addition, we used RNA fluorescence in situ hybridization (FISH) to examine the spatial locations of cell types and cell trajectories to understand the ancestral continuum of cell maturation. This data provides a resource for the transcriptional program of hindlimb development that will support future studies of musculoskeletal development and generate hypotheses for tissue regeneration.

overall_design: Four samples from murine embryonic hindlimb tissue at E11.5, E13.5, E15.5, and E18.5

first: Natalie

middle: H

last: Kelly

first: Nguyen

middle: P

last: Huynh


title: TREM2 regulates microglial cholesterol metabolism upon chronic phagocytic challenge [single-cell RNA-Seq]

summary: TREM2 is a microglial-specific gene implicated in late-onset Alzheimer's Disease (AD). Recent studies have identified that Trem2-deficient mice exhibit transcriptional changes in microglial gene expression that minimize the upregulation of lipid metabolism and lysosomal genes in AD disease models. We find that chronic phagocytic challenge from demyelination generates similiarly attenuated expression of lysosomal and lipid metabolism genes in microglia isolated from Trem2 knockout mouse brain.

overall_design: Trem2 wildtype, heterozyogus knockout, and homozygous knockout mice were fed a control or 0.2% cuprizone diet for 5 weeks or 12 weeks to generate acute or chronic demyelination, respectively. Single-cell microglial gene expression was assessed using the Chromium Single Cell 3' Reagent Kit with v2 Chemistry (10X Genomics).

first: Steve

last: Lianoglou


title: TREM2 regulates microglial cholesterol metabolism upon chronic phagocytic challenge [bulk RNA-seq]

overall_design: Trem2 wildtype, heterozyogus knockout, and homozygous knockout mice were fed a control or 0.2% cuprizone diet for 5 weeks or 12 weeks to generate acute or chronic demyelination, respectively. Microglial and pooled non-microglial cell type gene expression was assessed using 3' tag sequencing of poly-adenylated RNA (QuantSeq, Lexogen, Vienna, Austria).


title: TREM2 regulates microglial cholesterol metabolism upon chronic phagocytic challenge


title: Glioma-derived miRNA-containing extracellular vesicles induce angiogenesis by reprogramming brain endothelial cells (DNA methylation)

status: Public on Dec 20 2019

city: Houston

first: Aleksandar

last: Milosavljevic

state: Texas

address: 1 Baylor Plaza

department: Genetics and Genomics

institute: Baylor College of Medicine

type: Methylation profiling by genome tiling array

summary: Glioblastoma multiforme (GBM) is characterized by the close relationship of glioma stem cells (GSC) with aberrant vascularization. It has been established that GSC-derived extracellular vesicles (GSC-EVs) and their cargoes are proangiogenic in vitro. To elucidate gene regulatory mechanisms of neovascularization both in vitro and in vivo, we performed RNA-seq and DNA methylation profiling of the response of human brain endothelial cells to GSC-EVs as well as histoepigenetic analysis of GBM molecular profiles in the TCGA collection. The gene regulatory responses showed a footprint of post-transcriptional gene silencing by EV-derived miRNAs. Remarkably, EVs and normal vascular growth factors stimulated highly distinct gene regulatory responses, both converging on angiogenesis, providing exciting new insight into targetable angiogenic signaling in GBM.

overall_design: In this study, DNA methylation and gene expression profiling by long-RNA-seq and small-RNA-seq were performed on cultured human brain microvascular endothelial cells to investigate expression patterns of angiogenesis.

first: Rocco

middle: D

last: Lucero

first: Valentina

last: Zappulli

first: Xandra

middle: O

last: Breakefield


title: RNAseq experiments for "THAP11F80L cobalamin disorder-associated mutation reveals normal and pathogenic THAP11 functions in gene expression and cell proliferation"

city: Lausanne

first: Nicolo

last: Riggi

state: VD

address: Bugnon 25

department: Département de Pathologie Expérimentale

country: Switzerland

institute: CHUV

summary: Twelve human THAP proteins share the THAP domain, an evolutionary conserved zinc-finger DNA-binding domain.  Studies of different THAP proteins have indicated roles in gene transcription, cell proliferation and development. We have analyzed this protein family, focusing on THAP7 and THAP11. We show that human THAP proteins possess differing homo- and heterodimer formation properties and interaction abilities with the transcriptional co-regulator HCF-1. HEK-293 cells lacking THAP7 were viable but proliferated more slowly. In contrast, HEK-293 cells were very sensitive to THAP11 alteration. Nevertheless, HEK-293 cells bearing a human THAP11 mutation identified in a patient suffering from cobalamin disorder (THAP11F80L) were viable although proliferated more slowly. Cobalamin disorder is an inborn vitamin deficiency characterized by neurodevelopmental abnormalities, most often due to biallelic mutations in the MMACHC gene, whose gene product MMACHC is a key enzyme in the cobalamin metabolic pathway. We show that THAP11F80L selectively affected promoter binding by THAP11, having more deleterious effects on a subset of THAP11 targets, and resulting in altered patterns of gene expression. In particular, THAP11F80L exhibited a strong effect on association with the MMACHC promoter and led to a decrease in MMACHC gene transcription, suggesting that the THAP11F80L mutation is directly responsible for the observed cobalamin disorder.

overall_design: THAP11(F80L) mutant cells were generated by CRISPR/Cas9-mediated genome editing. Total RNA from parental and mutant cells was extracted and subsequently used to prepare ribosomal RNA-depleted libraries for 50-nucleotides single-read high-throughput sequencing using an Illumina HiSeq 2100 device with 6 samples per line (multiplexing). Each sample was done in duplicate.

first: Maykel

last: Lopes

first: Philippe

last: L’Hôte

first: Hamonie

last: Dehaene

first: Viviane

last: Praz

first: Winship

last: Herr


title: Glioma-derived miRNA-containing extracellular vesicles induce angiogenesis by reprogramming brain endothelial cells (miRNA-seq)

type: Non-coding RNA profiling by high throughput sequencing

first: Alessandro

last: Sammarco

first: Oscar

last: Murillo

first: Pike

middle: S

last: Cheah

first: Srimeenakshi

last: Srinivasan

first: Eric

last: Tai

first: David

middle: T

last: Ting

first: Zhiyun

last: Wei

first: Matthew

middle: E

last: Roth

first: Louise

last: Laurent

first: Anna

last: Krichevsky


title: Multiplatform molecular profiling reveals epigenomic intratumor heterogeneity in ependymoma, DNA Methylation

city: SAN FRANCISCO

first: John

last: Liu

address: 35 Medical Center Way

summary: Ependymomas exist within distinct genetic subgroups, but the molecular diversity within individual ependymomas is unknown. We performed multiplatform molecular profiling of 6 spatially-distinct samples from an ependymoma with C11orf95-RELA fusion. DNA methylation and RNA sequencing distinguished clusters of samples according to neuronal development gene expression programs that could also be delineated by differences in magnetic resonance blood perfusion. Exome sequencing and phylogenetic analysis revealed epigenomic intratumor heterogeneity, and suggested that chromosomal structural alterations may precede accumulation of single nucleotide variants during ependymoma tumorigenesis. In sum, these findings shed new light on the oncogenesis and intratumor heterogeneity of ependymoma.

overall_design: illumina EPIC methylation profiles of 6 regional samples from one anaplastic ependymoma

first: S

middle: J

first: Stephen

last: Magill

first: Harish

middle: N

last: Vasudevan

middle: R

last: Raleigh


title: Transcriptome analysis-identified long noncoding RNA CRNDE in maintaining endothelial cell proliferation, migration, and tube formation

city: Lincoln

last: Moran

state: NE

address: 1901 Vine St.

department: Biochemistry

institute: University of Nebraska-Lincoln

summary: Obesity is a leading risk factor for type-2 diabetes. Diabetes often leads to the dysregulation of angiogenesis, although, the mechanism is not fully understood. Previously, long noncoding RNAs (lncRNAs) have been found to modulate angiogenesis. In this study, we asked how the expression levels of lncRNAs change in endothelial cells in response to excessive palmitic acid treatment, an obesity-like condition. Bioinformatics analysis revealed that 305 protein-coding transcripts were upregulated and 70 were downregulated, while 64 lncRNAs were upregulated and 46 were downregulated. Gene ontology and pathway analysis identified endoplasmic reticulum stress, HIF-1 signaling, and Toll-like receptor signaling as enriched after palmitic acid treatment. In addition, we newly report enrichment of AGE-RAGE signaling pathway in diabetic complications, IL-17 signaling, and cysteine and methionine metabolism by palmitic acid. One lncRNA, Colorectal Neoplasia Differentially Expressed (CRNDE), was selected for further investigation. Palmitic acid induces CRNDE expression by 1.9-fold. We observed that CRNDE knockdown decreases endothelial cell proliferation, migration, and capillary tube formation. These decreases are synergistic under palmitic acid stress. These data demonstrated that CRNDE is a regulator of endothelial cell proliferation, migration, and tube formation in response to palmitic acid, and a potential target for therapies treating the complications of obesity-induced diabetes.

overall_design: Human Umbilical Vein Endothelial Cells (HUVECs) were treated with 100 µM palmitic acid conjugated to BSA for 8 hours or BSA alone as a control. Three biological replicates were done. RNA was harvested and sequenced.

first: Xinghui

last: Sun


title: The non-canonical RNA polyadenylation polymerase FAM46C is essential for fastening sperm head and flagellum in mice

city: Beijing

first: Xiwen

last: Lin

address: 1 Beichen West Road, Chaoyang District

institute: Institute of Zoology,CAS

summary: FAM46C has been proved to be a RNA polyadenylation polymerase. Fam46c KO resulted in male infertility caused by the production of acephalic sperm. we performed RNA sequencing to identify genes regulated by FAM46C

overall_design: We conducted RNA-sequencing (RNA-seq) analysis to identify FAM46C-regulated genes that were differentially expressed in testis of Fam46c KO and WT mice.

first: Chunwei

last: Zheng

first: Chunsheng

last: Han


title: THAP11F80L cobalamin disorder-associated mutation reveals normal and pathogenic THAP11 functions in gene expression and cell proliferation

first: Nicolo

last: Riggi

type: Genome binding/occupancy profiling by high throughput sequencing


title: Tissue-infiltrating cytotoxic T cells and endothelial cell apoptosis in systemic sclerosis

status: Public on Dec 28 2019

city: Cambridge

first: Jesper

last: Kers

state: MA

address: 400 Technology Square

institute: Ragon Institute of MGH, MIT & Harvard

summary: We report RNA sequencing profiles of CD4+ cytotoxic T cell subsets in patients with systemic sclerosis

overall_design: Examination of six samples

first: Takashi

last: Maehara

first: Naoki

last: Kaneko

first: Cory

last: Perugino

first: Hamid

last: Mattoo

first: Hugues

last: Allard-Chamard

first: Vinay

last: Mahajan

first: Hang

first: Samuel

last: Murphy

first: Musie

last: Ghebremichael

last: Fox

first: Robert

last: Lafyatis

last: Stone

first: Dinesh

last: Khanna

first: Shiv

last: Pillai


title: Determination of ErfA regulon by RNA-seq in IHMA87 and PAO1

city: Zurich

first: Julian

last: Trouillon

address: Otto-Stern-Weg 3

department: Institute of Molecular Systems Biology

institute: ETH Zurich

summary: ErfA is a transcription factor of Pseudomonas aeruginosa. We here define the genes impacted by the deletion of erfA by RNA-seq.

overall_design: RNA-seq analysis of WT vs erfA mutant, in both P. aeruginosa PAO1 and IHMA87 in LB liquid culture at OD=1, in duplicates.

first: Ina

last: Attrée

first: Sylvie

last: Elsen


title: Glioma-derived miRNA-containing extracellular vesicles induce angiogenesis by reprogramming brain endothelial cells

first: Aleksandar

last: Milosavljevic


title: Transcriptome analysis of 125 ESCC samples

city: Shantou

first: Yang

last: Chen

address: Department of Biochemistry and Molecular Biology, Shantou University Medical College, 22 Xinling Road, Shantou

institute: Shantou University Medical College

summary: In order to explore the clinical significance of several key genes, an Affymetrix IVT microarray of 125 ESCC patients were used to find the potential prognostic factors

overall_design: There were 125 ESCC samples and  the raw data (.cel file) is normalized by Affy package in R software, the normalized signal value is the value calculated by log2

first: En-Min

last: Li

first: Li-Yan

last: Xu


title: Glioma-derived miRNA-containing extracellular vesicles induce angiogenesis by reprogramming brain endothelial cells (longRNA-seq)

first: Rocco

last: Lucero

first: Valentina

last: Zappulli

first: Alessandro

last: Sammarco

first: Oscar

last: Murillo

first: Pike

last: Cheah

first: Srimeenakshi

last: Srinivasan

first: Eric

last: Tai

first: David

last: Ting

first: Zhiyun

last: Wei

first: Matthew

last: Roth

first: Louise

last: Laurent

first: Anna

last: Krichevsky

first: Xandra

last: Breakefield


title: Determination of ErfA regulon by ChIP-seq in IHMA87 and PAO1

first: Julian

last: Trouillon

summary: ErfA is a transcription factor of Pseudomonas aeruginosa. We here define the genome-wide binding sites of ErfA by ChIP-seq.

overall_design: ChIP-seq analysis of VSVG-tagged ErfA protein, in both P. aeruginosa PAO1 and IHMA87 in LB liquid culture at OD=1, in duplicates.

first: Ina

last: Attrée

first: Sylvie

last: Elsen


title: Altered cervical mucosal gene expression and lower IL-15 levels in women with S. haematobium but not S. mansoni infection.

city: New York

first: Jennifer

last: Downs

address: 1300 York Ave.

institute: Weill Cornell Medicine

summary: Schistosomiasis increases the risk of HIV acquisition in women, by mechanisms that are incompletely defined. Our objective was to determine how the cervical environment is impacted by Schistosoma haematobium or S. mansoni infection using mucosal gene expression and cervicovaginal lavage cytokine levels. We recruited women with/without S. haematobium and with/without S. mansoni infections from separate villages in rural Tanzania, as determined by urine and stool microscopy and serum circulating anodic antigen. RNA was extracted from cervical cytobrush samples for transcriptome analysis. Cytokine levels were measured by magnetic bead immunoassay. In the S. haematobium village, 110 genes were differentially expressed in the cervical mucosa of women with (n=18) versus without (n=39) S. haematobium. Among the 27 cytokines analyzed in cervicovaginal lavage fluids, interleukin 15 (IL-15) was lower in women with S. haematobium (62.8 versus 102.9 pg/mL, adjusted p=0.0013). Differences were not observed in the S. mansoni setting between women with (n=11) or without (n=29) S. mansoni. We demonstrate altered cervical mucosal gene expression and lower IL-15 levels in women with S. haematobium but not S. mansoni, which may impact HIV acquisition and cancer risks. Studies to determine effects of anti-schistosome treatment on these mucosal alterations are needed.

overall_design: Comparisons of two sets of women (18 with S. haematobium versus 39 with no schistosome infection; 11 with S. mansoni versus 29 with no schistosome infection)


title: A molecularly distinct subset of glioblastoma requires serum-containing media to establish sustainable bona fide glioblastoma stem cell cultures

city: Uppsala

first: Lene

last: Uhrbom

address: Dag Hammarskjölds väg 20

department: Immunology, Genetics and Pathology

country: Sweden

institute: Uppsala University

summary: Glioblastoma (GBM) is the most frequent and deadly primary malignant brain tumor. Hallmarks are extensive intra- and inter-tumor heterogeneity and highly invasive growth, which provide great challenges for treatment. Efficient therapy is lacking for GBM and the majority of patients survive less than one year from diagnosis. GBM progression and recurrence is caused by treatment-resistant glioblastoma stem cells (GSCs). GSC cultures are considered important models to use in target identification and drug screening. The current state of the art method to isolate and maintain GSC cultures that faithfully mimic the primary tumor, is to use serum-free (SF) media conditions developed for neural stem cells (NSCs). Here we have investigated the outcome of explanting 230 consecutively collected GBM patient samples under both SF and standard, serum-containing media conditions. The establishment of maintainable SF cultures (SFCs) was most frequent, but for a subgroup of GBM specimens a viable culture could only be established in serum-containing media, called exclusive serum culture (ESC). ESCs expressed nestin and SOX2, and displayed all functional characteristics of GSCs, i.e. extended proliferation, sustained self-renewal and orthotopic tumor initiation. Once adapted to the in vitro milieu they were also sustainable in SF media. Molecular analyses showed that ESCs formed a discrete group that was most related to the mesenchymal GBM subtype. This distinct subgroup of GBM that had evaded modeling under SF conditions provide unique cell models of GBM intertumor heterogeneity.

overall_design: Transcriptome analysis of 2 ESC (U3040MG, U3097MG) and 6 ESC_to_SFC (U3040MG, U3045MG, U3097MG, U3112MG, U3138MG, U3158MG) cell cultures on Affymetrix Human Transcriptome 2.0 arrays. ESC cultures are patient-derived glioblastoma cell cultures that were exclusively established in serum-containing media and not viable in serum-free defined NSC media. ESC_to_SFC cultures are ESC cultures that were cultured in serum-free defined NSC media for at least two passages. All cells were cultured adherently.

first: Naga

last: Maturi

first: E-Jean

last: Tan

first: Yuan

last: Xie

first: Anders

last: Sundström

first: Tobias

last: Bergström

first: Yiwen

last: Jiang


title: Expression data from ex vivo and cultured adipose-derived mesenchymal stromal cells (AdMSC, also known as ASC)

city: Auckland

first: Hilary

last: Sheppard

address: Symonds St

country: New Zealand

institute: Auckland University

summary: The effect of standard tissue culture on AdMSC is not well defined, therefore we sought to analyse global changes in microRNA expression when a defined ex vivo population of AdMSC was subjected to standard tissue culture conditions.

overall_design: A cocktail of antibodies and immunomagnetic beads were used to enrich for untouched ex vivo AdMSC from the stromal vascular fraction of adipose tissue. We used microarrays to detail the global changes in microRNA expression when these cells are freshly sorted and compared to when these cells are grown in standard tissue culture conditions for different time periods


title: Determination of ErfA regulon by DAP-seq in several Pseudomonas species

summary: ErfA is a transcription factor of Pseudomonas aeruginosa. We here define the genome-wide binding sites of ErfA by DAP-seq in Pseudomonas aeruginosa PAO1 and IHMA87, Pseudomonas chlororaphis PA23, Pseudomonas protegens CHA0 and Pseudomonas putida KT2440.

sample_organism:
Pseudomonas aeruginosa
Pseudomonas putida
Pseudomonas protegens
Pseudomonas chlororaphis

overall_design:
DAP-seq analysis of His-tagged purified ErfA protein binding to sheared genomic DNA of Pseudomonas aeruginosa PAO1 and IHMA87, Pseudomonas chlororaphis PA23, Pseudomonas protegens CHA0 and Pseudomonas putida KT2440.

DAP-seq was performed with ErfA protein from P. aeruginosa or P. chlororaphis. Samples  with P. chloroaphis ErfA include "chlo" in the sample title.


title: Global mammary luminal cells gene expression data from C451A-ERα and WT female mice treated by E2 or E2+Pg during 21 days.

status: Public on Dec 19 2019

city: Toulouse

first: Francoise

middle: B.

last: LENFANT

address: 1 avenue J. Poulhès

department: Team 9- I2MC

country: France

institute: INSERM U1048

summary: We used microarrays to detail the global programme of gene expression in mammary luminal cells C451A-ERα and WT female mice treated by E2 0.01 MG and E2 0.01 MG +Pg 1.5 MG during 21 days.

overall_design: There are 20 luminal cells samples, each from an individual mouse. The samples are from C451A-ERα and WT female mice of 8 week-old from the same genetic background (C57Bl/6N), N=5 for each experimental condition

first: LAURINE

last: GAGNIAC

first: FRANCOISE

first: Claire

last: Naylies

first: Yannick

last: Lippi


title: Small RNA-seq of breast tumor biopsies prior to treatment with letrozole or letrozole with bevacizumab

city: Huntsville

first: Brian

middle: Scott

last: Roberts

state: AL

address: 601 Genome Way

institute: HudsonAlpha Institute for Biotechnology

summary: Biopsies were collected from post-menopausal women with ER+ HER2- breast cancer who were subsequently treated with either letrozole or letrozole plus bevacizumab.

overall_design:
In one arm of the trial, the women received letrozole.  In the other arm they received letrozole plus bevacizumab.  Clinical responses were collected .  Small RNA-seq was performed on biopsy isolated RNA and the abundances correlated to clinical outcomes.  A classifier model for response to the combination therapy was derived.

Patient outcome definitions:
CR_DS = Complete Response and Down Staged
DS = Down Staged
PD = Progressed Disease
PR = Partial Response
PR_DS = Partial Response and Down Staged
SD = Stable Disease

first: Christos

last: Vaklavas


title: NGS based identification of GD2-positive tumor-specific phenotype for cancer diagnostics and therapy

city: Moscow

first: Maria

middle: Vladimirovna

last: Suntsova

address: Miklukho-Maklaya, 16/10

department: Department of Genetics and Postgenomic Technologies

country: Russia

institute: M.M. Shemyakin and Yu.A. Ovchinnikov  Institute of  bioorganic chemistry of the Russian Academy of Sciences

summary: The tumor-associated glycosphingolipid ganglioside GD2 presents an attractive target for cancer immunotherapy. This molecule is abundant on different types of cancer cells and is characterized  by restricted expression on healthy cells. Tumors exhibit heterogeneity in the expression level of GD2 and, therefore, development of methods for determination of the GD2-positive tumor  phenotype for the pertinent application of targeted therapies is required. In this work, we have developed a gene expression-based classifier for the prediction of the GD2-positive tumor  phenotype. We analyze RNA-seq data from GD2-positive and GD2-negative cell lines of different tumor types as well as neuroblastoma biopsy material for gene expression levels of  enzymes that participate in ganglioside biosynthesis and determine the role of gene expression of these enzymes in the formation of the GD2-positive tumor phenotype. We also apply gene  expression patterns known from literature to our data and use large public RNA-seq datasets to identify novel gene expression patterns associated with GD2 expression to validate the findings  in our data. The results of the study may be used for the development of a gene signature which separates GD2-positive from GD2-negative tumors and for prediction of the GD2 phenotype in  clinical specimens from cancer patients, and thus be used as a companion diagnostic for anti-GD2 therapy.

overall_design: 7 human tumor cell lines were tested for the expression of the glycosphingolipid ganglioside GD2. These cell lines were stored in RNAlater prior to RNA extraction. 3 tumor biopsies were stored as Formalin-Fixed Paraffin-Embedded (FFPE) blocks prior to RNA extraction. Following ribosomal RNA depletion and RNA libraries construction transcription profiles of the samples were obtained using Illumina HiSeq 3000.

first: Maxim

last: Sorokin

first: Irina

middle: V

last: Kholodenko

first: Daniel

last: Kalinovsky

first: Tatyana

last: Shamanskaya

first: Igor

middle: I

last: Doronin

first: Dmitry

last: Konovalov

first: Aleksei

last: Mironov

first: Sergey

last: Deyev

first: Anton

last: Buzdin

first: Roman


title: Transcriptomic dysregulation of SDCCGA8 KO retinal epithelial and immature neuronal cells.

city: Galway

first: Mairead

last: Flynn

address: Corrib village, NUI Galway

department: Centre for Chromosome Biology

country: Ireland

institute: NUI Galway

summary: RNA-seq transcirptomic profiling of SDCCAG8-deficient cells generated by gene-editing, identified differentially expressed genes that are enriched for in neurodevelopmental processes and extracellular matrix deposition and maintenance

overall_design: RPE1 WT, RPE1 SDCCAG8 -/-, SH-SY5Y WT and SH-SY5Y SDCCAG8 -/- cells were sequenced in triplicate at baseline conditions and after serum starvation.


title: Context and number of non‐canonical repeat variable diresidues (RVDs) impede the design of TALE proteins with improved DNA targeting

city: Boston

first: James

last: Anderson

address: 77 Avenue Louis Pasteur

department: Genetics

institute: Brigham and Women's Hospital

summary: A particularly promising approach for engineering more precise TALE proteins is to better understand non-canonical RVDs. The RVD repertoire employed by Xanthomonas extends well beyond just the four canonical RVD types, and natural TALE repeat arrays often utilize serial combinations of both canonical and non-canonical RVDs in a manner which is not fully understood. Attempts to characterize these non-canonical RVDs have utilized various approaches, in terms of both TALE design and experimental method. Some studies have considered just TALEs of particular biological relevance, others have looked at large numbers of different RVDs within a fixed repeat-array-context, and still others have designed custom TALEs to address hypotheses about optimal RVD positioning within the repeat array. Methods for inferring the DNA binding activity of these TALEs have included sequencing of cleaved DNA fragments from TALE-nuclease fusions; ELISA assays for TALE-oligonucleotide binding; reporter assays for TALEs’ transcriptional-activating effects; and in silico modeling. In this study we employ a novel “wholesale swap-out” approach to characterize 3 non-canonical RVDs for thymine and 4 non-canonical RVDs for guanine.

overall_design: In this study we employ a novel “wholesale swap-out” approach to characterize 3 non-canonical RVDs for thymine and 4 non-canonical RVDs for guanine. We assemble a library of 46 TALE proteins, comprising 11 reference TALEs bearing exclusively canonical RVDs, and 54 variant TALEs for characterizing the 7 non-canonical RVDs of interest. We design custom protein-binding microarrays (PBMs) which bear probes for the predicted target sequence of each TALE, in addition to probes for all possible mono- and di-nucleotide substitutions of these target sequences. The resulting quantitative binding data for the TALE proteins to ~5,000 unique DNA probes allows us to infer the relative affinity and specificity of each non-canonical RVD to each of the four nucleotides.

first: Julia

last: Rogers

first: Luis

middle: A

last: Barrera

first: Martha

last: Bulyk


title: Analysis of gene expression in shMETTL7B-A549 lung cancer cells

city: guangzhou

first: Dongcheng

last: Liu

state: guangdong

address: zhongshan 2nd road

department: Institute of Human Virology and Ministry of Education Key Laboratory of Tropical Disease Control

institute: Sun Yat-sen University

summary: Deletion of shMETTL7B significantly decreased number of colony in colony forming assay and cell number in proliferation assay for NSCLC cells in in vitro and inhibited the tumorigenesis in vivo. In order to explore the mechanism, gene expression profiles of NSCLC cells were investigated.

overall_design: NSCLC cells were plated at 80% confluency in 6 well plate 24 hours before lentivirus infection. Two days after infection, total RNA from cells treated with METTL7B shRNA or control shRNA was extracted for microarray analysis

first: Wei

last: Li

first: Chang

last: Zou


title: Transcriptomic Changes in the Nasal Epithelium Associated with Diesel Engine Exhaust Exposure

first: Eduard

middle: Iosifovich

last: Drizik

address: 72 East Concord Street

department: Computational Biomedicine

institute: Boston University

summary: Diesel engine exhaust (DEE) is one of the major contributors to air pollution around the world, and exposure to DEE is associated with lung cancer and other airway diseases. Although recent studies have investigated the effects of exposure to DEE, the mechanisms by which it leads to lung cancer pathogenesis are not well understood. We have previously investigated the transcriptomic changes that occur due to exposure to cigarette smoke and burning of bituminous (smoky) as well as anthracite (smokeless) coal in the airway epithelium, and in this study we assess the gene expression alterations in the nasal epithelium that are associated with chronic DEE exposure of diesel engine factory workers to better understand which molecular changes may lead to pathogenesis of lung cancer.

overall_design: Nasal brushings were collected from workers in diesel engine factories with diesel engine exhaust exposure (n=41) as well as from workers in factories without any known diesel engine exhaust exposure (n=38). RNA was isolated and profiled using Affymetrix Human Gene 1.0ST GeneChips.

first: Sean

last: Corbett

first: Yuxin

last: Zheng

first: Roel

last: Vermeulen

first: Yufei

last: Dai

last: Hu

first: Dianzhi

last: Ren

first: Huawei

last: Duan

first: Yong

last: Niu

first: Jun

last: Xu

last: Fu

first: Kees

last: Meliefste

first: Baosen

last: Zhou

first: Xiaohui

last: Zhang

first: Jufang

last: Yang

first: Hanqiao

first: Meng

last: Ye

first: Gang

first: Xiaowei

last: Jia

first: Tao

last: Meng

first: Ping

last: Bin

first: Junfang

first: Debra

last: Silverman

first: Avrum

last: Spira

first: Nathaniel

last: Rothman

first: Marc

last: Lenburg

first: Qing

last: Lan


title: Silencing of BEX2 promotes colorectal cancer metastasis through Hedgehog signaling pathway

city: Hangzhou

first: Kefeng

last: Ding

state: Zhejiang Province

address: 88 Jiefang Road

department: Department of Colorectal Surgery

institute: The Second Affiliated Hospital of Zhejiang University School of Medicine

summary: Colorectal cancer is one of the most common cancers worldwide with increasing incidence, the presence of metastasis is one of the major causes for poor outcome. BEX2 has been reported to be involved in tumor development in several types of cancer, but is poorly understood in metastatic colorectal cancer. Here we demonstrated that knockout of BEX2 resulted in the enhancement of the migratory and metastatic potential of colorectal cancer cells in vivo and in vitro, re-expression of BEX2 in knockout cells could reverse the migratory enhancement. Expression profile chip indicated that hedgehog signaling pathway was activated after knockout of BEX2, and hedgehog Signaling inhibitor GANT61 and GDC-0449 could somehow reverse the migratory enhancement of BEX2-/- colorectal cancer cells. We also demonstrated that it is the nucleus translocation of Zic2 after BEX2 silenced, that activated hedgehog signaling pathway, while knockdown Zic2 could also abrogated migratory enhancement of BEX2-/- cells. In summary, our findings suggest that BEX2 is a negative modulator of hedgehog signaling pathway by retaining Zic2 in the cytoplasm of colorectal cancer cells, thus to inhibit colorectal cancer cell migration and metastasis.

overall_design: mRNA profiles of colorectal cancer cell DLD1 (WT) and BEX2 knocked out DLD1 cells (DLD1 KO1 and DLD1 KO2) were generated by deep sequencing, using Illumina Hiseq 3000.

first: Yinuo

last: Tan

first: Yeting

last: Hu

first: Qian

last: Xiao

first: Yang

last: Tang

first: Haiyan

last: Chen

first: Jinjie

last: He

first: Liubo

first: Kai

last: Jiang

first: Zhanhuai

last: Wang

first: Yue

last: Liu

first: Lifeng

last: Sun

first: Ying

last: Yuan


title: MiR-543 regulates the epigenetic landscape of myelofibrosis by targeting TET1 and TET2

status: Public on Dec 18 2019

city: Houston

first: George

last: Calin

state: TX

address: 1881 East Road

department: Experimental Therapeutics

institute: MD Anderson Cancer Center

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

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

platform_organism:
Homo sapiens
synthetic construct

overall_design: Refer to individual Series


title: ChIP-seq experiments for "THAP11F80L cobalamin disorder-associated mutation reveals normal and pathogenic THAP11 functions in gene expression and cell proliferation"

city: Lausanne

first: Nicolo

last: Riggi

address: Bugnon 25

institute: CHUV

summary: Twelve human THAP proteins share the THAP domain, an evolutionary conserved zinc-finger DNA-binding domain.  Studies of different THAP proteins have indicated roles in gene transcription, cell proliferation and development. We have analyzed this protein family, focusing on THAP7 and THAP11. We show that human THAP proteins possess differing homo- and heterodimer formation properties and interaction abilities with the transcriptional co-regulator HCF-1. HEK-293 cells lacking THAP7 were viable but proliferated more slowly. In contrast, HEK-293 cells were very sensitive to THAP11 alteration. Nevertheless, HEK-293 cells bearing a human THAP11 mutation identified in a patient suffering from cobalamin disorder (THAP11F80L) were viable although proliferated more slowly. Cobalamin disorder is an inborn vitamin deficiency characterized by neurodevelopmental abnormalities, most often due to biallelic mutations in the MMACHC gene, whose gene product MMACHC is a key enzyme in the cobalamin metabolic pathway. We show that THAP11F80L selectively affected promoter binding by THAP11, having more deleterious effects on a subset of THAP11 targets, and resulting in altered patterns of gene expression. In particular, THAP11F80L exhibited a strong effect on association with the MMACHC promoter and led to a decrease in MMACHC gene transcription, suggesting that the THAP11F80L mutation is directly responsible for the observed cobalamin disorder.

overall_design: THAP11(F80L) mutant cells were generated by CRISPR/Cas9-mediated genome editing. For each ChIP sample, 5 IPs were performed in parallel and subsequently pooled, each time by incubating the crosslinked and sonicated chromatin with anti-THAP11 antibody and further with protein G agarose beads. Pre-IP samples (total chromatin — input sample) were prepared in parallel. Each ChIP and input purified DNA were used to prepare paired-end sequencing libraries for 100-nucleotide paired-end high-throughput sequencing (Illumina, HiSeq 2100) with 3 samples per line (multiplexing).

first: Maykel

last: Lopes

first: Philippe

last: L’Hôte

first: Hamonie

last: Dehaene

first: Viviane

last: Praz

first: Winship

last: Herr


title: MiR-543 regulates the epigenetic landscape of myelofibrosis by targeting TET1 and TET2 [mRNA]

summary:
We analyzed mK562 cells with miR-543 overexpressed or empty vector to determine the mRNA profile of miR-543 overexpressed K562 cells.
We used Affymetrix Clariom S Human Array  to profile the differentially expressed mRNA in miR-543 overexpressed and control cells

overall_design: Here, we performed a global profiling of differentially expressed mRNAs in miR-543 overexpressed K562 cells and control cells.

first: Recep

last: Bayraktar


title: MiR-543 regulates the epigenetic landscape of myelofibrosis by targeting TET1 and TET2 [miRNA]

summary:
We analyzed 14 patients with Myelofibrosis (MF) to determine the miRNA profile of patients not responding to current MF treatment.
We used Affymetrix miRNA-3 array to profile the differentially expressed miRNA in bone-marrow between patients with MF that respond to current MF treatment and the patients with MF that do not respond to current MF treatment.

overall_design: Here, we performed a global profiling of differentially expressed miRNAs in bone-marrow-derived skeletal cells


title: Murine RT2-cancer cells: Control vs. Cdk2na deficient RT2-cancer cells

city: Tübingen

first: Ellen

last: Brenner

state: Baden-Württemberg

address: Liebermeisterstraße 25

department: Dermatology

country: Germany

institute: Eberhard Karls University Tuebingen

type: Genome variation profiling by genome tiling array

summary: Immune checkpoint blockade (ICB)-based or natural cancer immune responses largely eliminate tumours but require additional mechanisms to arrest cancer cells that escape from cytotoxic immune responses. We show that cancer immune control needs, in addition to cytotoxicity, senescence-inducing cell cycle regulators.

overall_design:
Three control RT2 cell lines vs. Seven Cdkn2a deficient RT2-cancer cell lines.
DNA was isolated from RT2-cancer cells or reference spleen (wildtype male) tissue with the DNeasy Blood & Tissue Kit (Qiagen) according to the manufacturer's instructions. DNA was labeled using the SureTag Complete DNA Labelling Kit (Agilent Technologies) and hybridized on an Agilent Mouse Genome CGH Microarray, 2x105K (Agilent Technologies), and the image was analysed using Feature Extraction 10.5.1.1 and Agilent Genomic Workbench Lite Edition 6.5 with Genome Reference Consortium Mouse Build 38.

first: Nadine

last: Simon


title: Single cell hierarchy of the mouse vaginal epithelium

city: Sydney

first: David

last: Gallego Ortega

address: 384 Victoria St

country: Australia

institute: Garvan Institute of Medical Research

summary: In this study, using genetic cell lineage tracing, vaginal organoids, targeted gene deletion and single cell sequencing approaches; we revealed a unique population of vaginal epithelial stem cells and provided evidence that canonical Wnt/b-catenin signaling is required for the proliferation and differentiation of these stem cells.

overall_design: Mice vaginae of Wild Type (WT) or Ovarectomised (OVX) C57BL/6 mice were analysed using Dropseq. Each group in the dataset was produced by pooled samples of 5 individuals and run in duolicate (i.e. N701 WT1 (5 mice pooled); N702 WT2 (5 mice pooled); N703 OVX1 (5 mice pooled) and N704 OVX2 (5 mice pooled))

first: Yolanda

last: Colino-Sanguino

last: Gallego-Ortega


title: Regulatory T cells restrain IL-2- and Blimp-1-dependent acquisition of cytotoxic function by CD4+ T cells

city: London

first: Maria

last: Vila de Mucha

address: 72 Huntley Street

country: United Kingdom

institute: UCL Cancer Institute

summary: In addition to helper and regulatory potential, CD4+T cells also acquire cytotoxic activity marked by granzyme B (GzmB) expression and the ability to promote rejection of established tumors. Here we examined the molecular and cellular mechanisms underpinning the differentiation of cytotoxic CD4+T cells following immunotherapy. CD4 transfer into lymphodepleted animals or regulatory T cell (Treg)depletion promoted GzmB expression by tumor-infiltrating CD4+which was prevented by IL-2 neutralization. Transcriptional analysis revealed a polyfunctional helper and cytotoxic phenotype characterized bythe expression of the transcription factors T-bet and Blimp-1. Whilst T-bet ablation restrictedIFN-gproduction, lossof Blimp-1preventedGzmB expressionin response to IL-2, suggesting these are two independent programs required forpolyfunctionality of tumor-reactive CD4+T cells. The data underscores the role of Treg, IL-2 and Blimp-1 controlling the differentiation of cytotoxic T cells and offers a pathway to enhancement of anti-tumor activity through their manipulation.

overall_design: To investigate gene expression of TCR-transgenic Trp1 CD4+ T cells in B16 melanoma, tumor-bearing mice were left untreated or treated at day 8 with total body irradiation (RT)+Trp1+aCTLA-4 (Trp1 Th-ctx), Trp1+GVAX+aCTLA-4 (Trp1 Th), or Trp1 cells in the absence of irradiation or vaccine as a control (Trp1 ctrl). Foxp3- cells were isolated from tumours of Th and Th-ctx treated mice and draining lymph nodes of ctrl treated mice 8 days after treatment initiation.

first: Sergio

last: Quezada


title: STAT4 activation by leukemia inhibitory factor confers a therapeutic effect on intestinal inflammation

city: Suzhou

first: Yanan

last: Zhang

state: Jiangsu

address: 199 Renai Road

department: Institutes of Biology and Medical Sciences

institute: Soochow University


title: STAT4 activation by leukemia inhibitory factor confers a therapeutic effect on intestinal inflammation [array]

summary: T helper 17 (Th17) cell differentiation triggered by interleukin-6 (IL-6) via STAT3 activation promotes inflammation in inflammatory bowel disease (IBD) patients. However, leukemia inhibitory factor (LIF), an IL-6 family cytokine, restricts inflammation by blocking Th17 cell differentiation via an unknown mechanism. Here, we report that microbiota dysregulation promotes LIF secretion by intestinal epithelial cells (IECs) in a mouse colitis model. LIF greatly activates STAT4 phosphorylation on multiple SPXX elements within the C-terminal transcription regulation domain. STAT4 and STAT3 act reciprocally on both canonical cis-inducible elements (SIEs) and noncanonical “AGG” elements at different loci. In lamina propria lymphocytes (LPLs), STAT4 activation by LIF blocks STAT3-dependent Il-17a/Il-17f promoter activation, whereas in IECs, LIF bypasses the extraordinarily low level of STAT4 to induce YAP gene expression via STAT3 activation. In addition, we found that the administration of LIF is sufficient to restore microbiome homeostasis. Thus, LIF effectively inhibits Th17 accumulation and promotes repair of damaged intestinal epithelium in inflamed colon, and serves as a potential therapy for IBD.

overall_design: The gene expression in lamina propria lymphocytes (LPLs) of wild-type and Stat4-knockout mice were measured on day 10 after exposure to dextran sulfate sodium (DSS) solution, or DSS solution and LIF-treatment. Five mice were used to isolate LPLs for each group.

first: Y

last: Chin


title: Epigenomic analysis of gastrulation identifies a unique chromatin state for primed pluripotency

city: Beijing

first: Wei

last: Xie

address: Haidian District

department: School of Life Science

institute: Tsinghua University

type: Methylation profiling by high throughput sequencing

summary: Around implantation, the epiblast transits from naïve to primed pluripotency, before giving rise to the three germ layers. How chromatin is reconfigured during this developmental window remains poorly understood. We performed a genome-wide investigation of chromatin landscapes during this period. We find that enhancers in ectoderm are already pre-accessible in embryonic day 6.5 (E6.5) Epi when cells enter a primed pluripotent state. Unexpectedly, strong H3K4me3 emerges at developmental gene promoters in E6.5 epiblast and positively correlates with H3K27me3, thus establishing bivalency. These genes also show enhanced spatial interactions. Both the strong bivalency and spatial clustering are virtually absent in preimplantation embryos and are markedly reduced in fate-committed lineages. Finally, we show that KMT2B is essential for establishing bivalent H3K4me3 at E6.5 but becomes partially dispensable later. Its deficiency leads to impaired activation of developmental genes and subsequent embryonic lethality. Thus, our data characterize lineage-specific chromatin reconfiguration and a unique chromatin state for primed pluripotency.

overall_design: To determine the dynamics of chromatin states during gastrulation in mouse early embryos, male (DBA2) and female (C57BL/6N) were mated and multiple lineages were separated from embryos, including epiblast (Epi) and visceral endoderm (VE) at embryonic day 6.5 (E6.5), ectoderm (Ect), primitive streak (PS), mesoderm (Mes) and endoderm (End) at E7.5. We then conducted miniATAC-seq and STAR ChIP-seq for H3K4me3, H3K27ac, and H3K27me3 in these tissues. We also performed RNA-seq, ChIP-seq, MethylC-seq, and sisHi-C in E6.5Epi and/or E8.5 head tissues to determine the chromatin configuration in embryos upon loss of Kmt2b.

first: Yunlong

last: Xiang

first: Yu


title: STAT4 activation by leukemia inhibitory factor confers a therapeutic effect on intestinal inflammation [RNA-Seq]

summary: We report that microbiota dysregulation promotes LIF secretion by intestinal epithelial cells (IECs) in a mouse colitis model. LIF greatly activates STAT4 phosphorylation on multiple SPXX elements within the C-terminal transcription regulation domain. STAT4 and STAT3 act reciprocally on both canonical cis-inducible elements (SIEs) and noncanonical “AGG” elements at different loci. In lamina propria lymphocytes (LPLs), STAT4 activation by LIF blocks STAT3-dependent Il-17a/Il-17f promoter activation, whereas in IECs, LIF bypasses the extraordinarily low level of STAT4 to induce YAP gene expression via STAT3 activation. In addition, we found that the administration of LIF is sufficient to restore microbiome homeostasis. Thus, LIF effectively inhibits Th17 accumulation and promotes repair of damaged intestinal epithelium in inflamed colon, and serves as a potential therapy for IBD.

overall_design: mRNA profiles in intestinal epithelial cells of wild type (WT) and Stat4-/- mice were generated by deep sequencing, in duplicate, using Illumina-HiSeq2500/4000.


title: Manila clam - Perkinsus olseni interaction based on gene expression analysis of clam hemocytes and parasite trophozoites [Manila clam]

city: LUGO

first: Belen

middle: G

last: Pardo

state: LUGO

address: Avda. Carballo Calero s/n

department: Zoology, Genetics and Physical Anthropology

country: Spain

institute: University of Santiago de Compostela

summary: The Manila clam (Ruditapes philippinarum) is the bivalve species with the highest world production from both fisheries and aquaculture, but its production is seriously threatened by perkinsosis, a disease caused by the protozoan parasite Perkinsus olseni. To understand the molecular mechanisms underlying R. philippinarum–P. olseni interaction, we analyzed the gene expression profiles of in vitro challenged clam hemocytes and P. olseni trophozoites, using two oligo-microarray platforms, one previously validated for R. philippinarum hemocytes and a new one developed and validated in this study for P. olseni. Manila clam hemocytes were in vitro challenged with trophozoites, zoospores, and extracellular products from P. olseni in vitro cultures, while P. olseni trophozoites were in vitro challenged with Manila clam plasma along the same time-series (1 h, 8 h, and 24 h). The hemocytes showed a fast activation of the innate immune response, particularly associated with hemocyte recruitment, in the three types of challenges. Nevertheless, different immune-related pathways were activated in response to the different parasite stages, suggesting specific recognition mechanisms. Furthermore, the analyses provided useful complementary data to previous in vivo challenges, and confirmed the potential of some proposed biomarkers. The combined analysis of gene expression in host and parasite identified several processes in both the clam and P. olseni, such as redox and glucose metabolism, protease activity, apoptosis and iron metabolism, whose modulation suggests cross-talk between parasite and host. This information might be critical to determine the outcome of the infection, thus highlighting potential therapeutic targets. Altogether, the results of this study aid to understand the response and interaction between R. philippinarum–P. olseni and will contribute for developing effective control strategies for this threatening parasitosis.

overall_design: R. philippinarum hemocytes (5x106) were challenged in vitro with P. olseni trophozoites (5x106), zoospores (5x106) and extracellular products (2.5 mL of culture media enriched with extracellular products) separately in IWAKI 6-well plates. Each challenge included three biological replicates for both treatment and control (only culture media) groups, and each biological replicate was a pool of hemocytes from 10 different clams, thus averaging individual biological variation. Samples for RNA extraction were collected at 1, 8 and 24 h after the start of the challenge. Thirty-two microarrays (four slides) were used. R. philippinarum control replicates at each time point were pooled, so a single control microarray was used for each sampling time (1-C, 8-C, 24-C); in addition, the low RNA amount in the controls of the zoospore challenge determined pooling all controls in a single microarray hybridization.

first: Abul

last: Hasanuzzaman

first: Asunción

last: Cao

first: Paolo

last: Ronza

last: Fernández-Boo

first: Juan

last: Rubiolo

first: Diego

last: Robledo

first: Antonio

last: Gómez-Tato

first: Jose

last: Alvarez-Dios

last: Villalba

first: Paulino

last: Martínez


title: tt1-gr-TT1 gene network

city: Orsay

first: Stéphanie

last: Pateyron

address: Rue de Noetzlin _ Batiment 630

institute: IPS2_Institute of Plant Sciences Paris-Saclay

summary: ra15-05_tt1 - tt1-gr - Discover TT1 donwstream targets - An inducible line carrying TT1, an early marker of endothelium development, fused to the rat glucocorticoid receptor (GR), that allows a dexamethasone (DEX)-mediated posttranslational induction of the proteins, has been created. Siliques have been first treated with cycloheximide, an inhibitor of protein synthesis, to prevent indirect transcriptional effects of the inducible TT1 transcription factor. RNA profiling experiments (CATMA microarrays) will be then conducted before and after DEX induction of TT1. These experiments will unveil direct downstream target genes of the TT1 transcription factor.

overall_design: 6 dye-swap - normal vs transgenic comparaison,treated vs untreated comparison

first: Didier

last: MARION

first: Enrico

last: Magnani

first: Sandrine

last: Balzergue

first: Marie-Laure

last: Martin-Magniette


title: Coronary disease associated gene TCF21 inhibits smooth muscle cell differentiation by blocking the myocardin-serum response factor pathway

city: Stanford

first: Thomas

last: Quertermous

address: 300 Pasteur Drive

department: Medicine Cardiology

institute: Stanford University

overall_design:
SRF, H3K27ac and TCF21 ChIP-seq  and ATAC-seq on Cultured coronary artery smooth muscle cells

This series includes re-analyzed samples from GSE61369 and GSE72696. These re-analyzed samples have been included here.

first: Manabu

last: Nagao

first: Quanyi

last: Zhao

first: Milos

last: Pjanic


title: Bonn Dataset 3 of meta-analysis on AML classification, RNAseq dataset

city: Bonn

first: Joachim

last: Schultze

state: NRW

address: Carl-Troll-Strasse 31

department: Genomics and Immunoregulation

institute: LIMES (Life and Medical Sciences Center Genomics and Immunoregulation)

summary:
The present dataset ("dataset 3") is a subset of a large metastudy on AML classfication. It contains normalized gene expression values of  1181 samples.
In total, three datasets were generated, each containing data of a different platforms: dataset 1 (Affymetrix HG-U133 A microarrays), dataset 2 (Affymetrix HG-U133 2.0 microarrays) and dataset 3 (RNA-seq). Dataset 3 was generated using the following strategy: All data sets published in the National Center for Biotechnology Information Gene Expression Omnibus (GEO) on 20 September 2017 were reviewed for inclusion in the present study. Basic criteria for inclusion were the cell type under study (human peripheral blood mononuclear cells (PMBCs) and/or bone marrow samples) as well as the species (Homo sapiens). Furthermore, GEO SuperSeries were excluded to avoid duplicated samples. We filtered the datasets for data generated with high-throughput RNA sequencing (RNA-seq) and excluded studies with very small sample sizes (< 10 samples). We then applied a disease-specific search, in which we filtered for acute myeloid leukemia, other leukemia and healthy or non-leukemia-related samples.  The results of this search strategy were then internally reviewed and data were excluded based on the following criteria: (i) exclusion of duplicated samples, (ii) exclusion of studies that sorted single cell types (e.g. T cells or B cells) prior to gene expression profiling, (iii) exclusion of studies with inaccessible data. Other than that, no studies were excluded from our analysis. In total, the datasets contained samples from the following GSE Series:  GSE63085, GSE32874, GSE58335, GSE86884, GSE63703, GSE63646, GSE63816, GSE72790, GSE81259, GSE85712, GSE45735, GSE64655, GSE87186, GSE49642, GSE52656, GSE62190, GSE66917, GSE67039, GSE61162, GSE67184, GSE49601, GSE78785, GSE79970.         All raw data files were downloaded from GEO. Transcript abundances were calculated using kallisto version 0.43.0 and all data was normalized with the R package DESeq2 (R version R-3.2.4, DESeq2 version 1.12.4) with standard parameters.  Genome build hg38 was used for read alignment.  No filtering of low-expressed genes was performed.

overall_design: [Dataset_3_ensembl.txt]  count matrix of 1181 samples and 37045 genes (ensembl IDs)

first: Stefanie

last: Warnat-Herresthal

last: Ulas

middle: L


title: Candidate silencer elements in the human and mouse genome

city: Seattle

first: David

last: Hawkins

state: WA

address: 1959 NE Pacific St, HSB K226

department: Division of Medical Genetics, Department of Genome Sciences

institute: University of Washington

summary: STARR-seq assay performed on uncharacterized cis-regulatory elements to find candidate silencer elements in K562 cells.

overall_design: Five wells of 6 well plates, each with about 1 million K562 cells, were transfected with 20 ug of plasmid containing our library. Cells were grown in antibiotic-free media for 24 hours and then harvested for RNA and DNA extraction.

first: R

middle: D

first: Naresh

last: Jayavelu


title: Genome-wide occupancy of linker histone variant H1t in pachytene spermatocytes

status: Public on Dec 17 2019

city: Bangalore

first: Manchanahalli

middle: Rangaswamy

last: Satyanarayana Rao

state: Karnataka

address: Jakkur, Bengaluru, Karnataka

department: Molecular Biology and Genetics Unit (MBGU)

country: India

institute: Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR)

summary: We report the localization of linker histone variant H1t in pachytene spermatocytes determined by ChIP-sequencing analysis

overall_design: Genome-wide occupancy of linker histone variant H1t in mouse P20 testicular cells

first: Iyer

last: Mahadevan

first: Sanjeev

last: Kumar

first: M

last: Rao


title: Molecular and genetic analysis of resistance to METI-I acaricides in Iranian populations of the citrus red mite Panonychus citri

city: Ghent

first: Wannes

last: Dermauw

address: Coupure Links 653

department: Crop Protection

country: Belgium

institute: University Ghent

summary: The citrus red mite, Panonychus citri, is a major pest on citrus all around the world. Mitochondrial Electron Transport Inhibitors of complex I (METI-I) acaricides such as fenpyroximate have been used extensively to control P. citri populations, which resulted in multiple reports of METI-I resistant populations in the field. In this study, gene expression profile differences between METI-I resistant P. citri populations (Lahijan, Ramsar and Sari) and a susceptible P. citri population (Rasht) from Iran were compared using Illumina RNAseq.

overall_design: In total 16 RNA-seq samples (4 populations, 4 biological replicates per population) from Panonychus citri, were generated. RNA was collected from adult P. ctiri females. For each sample, Illumina mRNA-seq libraries were constructed and strand-specific, paired-end 125 bp RNA-seq Illumina reads were generated. The obtained reads were used to quantify gene expresison in each sample.

first: Simon

last: Snoeck

first: Elaheh

middle: S

last: Alavijeh

first: Jahangir

last: Khajehali

last: Van Leeuwen


title: ZBTB7B (ThPOK) IS REQUIRED FOR PATHOGENESIS OF CEREBRAL MALARIA AND PROTECTION AGAINST PULMONARY TUBERCULOSIS

city: MONTREAL

last: Langlais

state: QC

address: 740 Ave Dr Penfield, rm 4203, McGill Genome Centre

department: Human Genetics

institute: McGill University

summary: We used a genome-wide screen in N-ethyl-N-nitrosourea (ENU)-mutagenized mice to identify genes in which recessive loss-of-function mutations protect against pathological neuroinflammation. We identified an R367Q mutation in the ZBTB7B (ThPOK) protein in which homozygosity causes protection against experimental cerebral malaria (ECM) caused by infection with Plasmodium berghei ANKA. Zbtb7bR367Q homozygous mice show a defect in the lymphoid compartment expressed as severe reduction in the number of single-positive CD4 T cells in the thymus and in the periphery, reduced brain infiltration of proinflammatory leukocytes in P. berghei ANKA-infected mice, and reduced production of proinflammatory cytokines by primary T cells ex vivo and in vivo. Dampening of proinflammatory immune responses in Zbtb7bR367Q mice is concomitant to increased susceptibility to infection with avirulent (Mycobacterium bovis BCG) and virulent (Mycobacterium tuberculosis H37Rv) mycobacteria. The R367Q mutation maps to the first DNA-binding zinc finger domain of ThPOK and causes loss of base contact by R367 in the major groove of the DNA, which is predicted to impair DNA binding. Global immunoprecipitation of ThPOK-containing chromatin complexes coupled to DNA sequencing (ChIP-seq) identified transcriptional networks and candidate genes likely to play key roles in CD4+ CD8+ T cell development and in the expression of lineage-specific functions of these cells. This study highlights ThPOK as a global regulator of immune function in which alterations may affect normal responses to infectious and inflammatory stimuli.

overall_design: Chromatin immunoprecipitations followed by high throughput sequencing of Zbtb7b transcription factors ChIP on wild-type (B6) Th1 polarized Cd4+ T cells.

first: Philippe

last: Gros


title: Aberrant activation of hepatocyte growth factor/MET signaling promotes β-catenin–mediated prostatic tumorigenesis

city: Duarte

first: Zijie

last: Sun

state: CA

address: 1500 E. Duarte Rd.

department: Cancer Biology

institute: City of Hope

summary: Co-occurrence of aberrant hepatocyte growth factor (HGF)/MET proto-oncogene receptor tyrosine kinase (MET) and Wnt/β-catenin signaling pathways has been observed in advanced and metastatic prostate cancers. This co-occurrence positively correlates with prostate cancer progression and castration-resistant prostate cancer (CRPC) development. However, the biological consequences of these abnormalities in these disease processes remain largely unknown. Here, we investigated the aberrant activation of HGF/MET and Wnt/β-catenin cascades in prostate tumorigenesis by using a newly generated mouse model in which both murine Met transgene and stabilized β-catenin are conditionally co-expressed in prostatic epithelial cells. These compound mice displayed accelerated prostate tumor formation and invasion compared with their littermates that expressed only stabilized β-catenin.RNA-Seq and qRT-PCR analyses revealed increased expression of genes associated with tumor cell proliferation, progression,and metastasis. Moreover, Wnt signaling pathways were robustly enriched in prostate tumor samples from the compound mice.ChIP-qPCR experiments revealed increased β-catenin recruitment within the regulatory regions of the Myc gene in tumor cellsof the compound mice. Interestingly, the occupancy of MET on the Myc promoter also appeared in the compound mouse tumor samples,implicating a novel role of MET in β-catenin–mediated transcription. Results from implanting prostate graft tissues derived from the compound mice and controls into HGF-transgenic mice further uncovered that HGF induces prostatic oncogenic transformation and cell growth. These results indicate a role of HGF/MET in β-catenin–mediated prostate cancer cell growth and progressionand implicate a molecular mechanism whereby nuclear MET promotes aberrant Wnt/β-catenin signaling–mediated prostate tumorigenesis.

overall_design: RNA samples were isolated from prostate tumors of age-matched mice from the two genotypes as indicated


title: Differences in bone marrow serum proteins in acute myeloid leukemia patients and normal controls

city: Chongqing

first: Jun

address: No 183, Xinqiao street, Shapingba

department: Medical center of hematology

institute: Xinqiao hospital

summary:
we evaluated cytokine profiling of bone marrow serum samples in AML patients and healthy controls. Protein expression profiling of serum from 9 AML patients and 5 healthy controls was obtained using biotinylated antibody chip. Total 507 cytokines and growth factors were analyzed.
Compared with healthy people, AML patients expressed 31 signature proteins, among which, 27 were found significantly higher expressed and 4 proteins were lower.

overall_design: 9 AML patients and 5 healthy controls were enrolled in this study, Whole blood was collected in vacutainer serum tubes, and then 507 serum proteins were analyzed simultaneously using an antibody-based array.

first: Lidan

last: Zhu


title: Transcriptional data of inflamatory arthritis B cells

city: Newcastle upon Tyne

first: Arthur

last: Pratt

address: Framlington Place

department: Faculty of Medical Sciences

institute: Newcastle University

type:
Expression profiling by array
Third-party reanalysis

summary: With a focus on rheumatoid arthritis (RA), we sought new insight into genetic mechanisms of adaptive immune dysregulation to help prioritise molecular pathways for targeting in this and related immune pathologies. Whole genome methylation and transcriptional data from isolated CD4+ T cells and B cells of >100 genotyped and phenotyped inflammatory arthritis patients, all of whom were naïve to immunomodulatory treatments, were obtained. Analysis integrated these comprehensive data with GWAS findings across IMDs and other publically available resources.

overall_design: Suspected inflammatory arthritis patients of Northern European ancestry were recruited prior to treatment with immunomodulatory drugs. RA patients were classified using current, internationally accepted criteria, and matched with disease controls in respect of demographic and clinical characteristics. CD19+ B cells were isolated from fresh peripheral blood using magnetic bead-based positive selection, with isolation of paired, high-integrity RNA and DNA using the AllPrep DNA/RNA Mini Kit (Qiagen, UK). The majority of samples are from GSE100648.

first: Alexander

last: Clark

first: Nisha

last: Nair

first: Amy

last: Anderson

first: Nishanthi

last: Thalayasingam

first: Najib

last: Naamane

first: Andrew

last: Skelton

first: Julie

last: Diboll

first: Anne

last: Barton

first: Stephen

last: Eyre

first: John

last: Isaacs

first: Louise

last: Reynard


title: Transcriptional data of inflamatory arthritis T cells.

overall_design: Suspected inflammatory arthritis patients of Northern European ancestry were recruited prior to treatment with immunomodulatory drugs. RA patients were classified using current, internationally accepted criteria, and matched with disease controls in respect of demographic and clinical characteristics. CD4+ cells were isolated from fresh peripheral blood using magnetic bead-based positive selection, with isolation of paired, high-integrity RNA and DNA using the AllPrep DNA/RNA Mini Kit (Qiagen, UK). The majority of samples are from GSE80513.


title: Early arthritis B cell DNA methylation profiling

summary: With a focus on rheumatoid arthritis (RA), we sought new insight into genetic mechanisms of adaptive immune dysregulation to help prioritise molecular pathways for targeting in this and related immune pathologies. Whole genome methylation data from isolated B cells of >100 genotyped and phenotyped inflammatory arthritis patients, all of whom were naïve to immunomodulatory treatments, were obtained. Analysis integrated these comprehensive data with GWAS findings across IMDs and other publically available resources.

overall_design: DNA material was extracted from CD19+ B cells isolated from fresh peripheral blood of suspected inflammatory arthritis patients of Northern European ancestry prior to treatment with immunomodulatory drugs. RA patients were classified with reference to the 2010 ACR/EULAR criteria, and matched with disease controls in respect of demographic and clinical characteristics. 400ng of DNA was bisulphite-converted and DNAm quantified using the Infinium MethylationEPIC BeadChip (Illumina).


title: Early arthritis CD4+ T cell DNA methylation profiling

summary: With a focus on rheumatoid arthritis (RA), we sought new insight into genetic mechanisms of adaptive immune dysregulation to help prioritise molecular pathways for targeting in this and related immune pathologies. Whole genome methylation data from isolated CD4+ T cells of >100 genotyped and phenotyped inflammatory arthritis patients, all of whom were naïve to immunomodulatory treatments, were obtained. Analysis integrated these comprehensive data with GWAS findings across IMDs and other publically available resources.

overall_design: DNA material was extracted from CD4+ T cells isolated from fresh peripheral blood of suspected inflammatory arthritis patients of Northern European ancestry prior to treatment with immunomodulatory drugs. RA patients were classified with reference to the 2010 ACR/EULAR criteria, and matched with disease controls in respect of demographic and clinical characteristics. 400ng of DNA was bisulphite-converted and DNAm quantified using the Infinium MethylationEPIC BeadChip (Illumina).


title: Effect of Pirfenidone on NSCLC [A549/H1975 0.75 mg/ml Pirf]

city: Borstel

first: Sebastian

last: Marwitz

address: Parkallee 3a

department: Histology

institute: Research Center Borstel - Leibniz Lung Center

summary:
Investigating the effect of Pirfenidone on NSCLC cells
Although immune checkpoint and targeted therapies offer remarkable benefits for lung cancer treatment, some patients do not qualify for these regimens or do not exhibit consistent benefit. Provided that lung cancer appears to be driven by transforming growth factor beta signaling, we investigated the single drug potency of Pirfenidone, an approved drug for the treatment of lung fibrosis which is known to inhibit TGFB1 mRNA. Human A549 and H1975 lung adenocarcinoma cell lines were stimulated for 6h and 25h with 0.75 mg/ml or 1.5 mg/ml Pirfenidone or the respective volume of PBS as vehicle control. Total RNA was extracted and subjected to transcriptome analysis by microarrays.

overall_design: stimulation of A549 and H1975 cell line with 0.75 mg/ml Pirfenidone or equal volume of PBS and incubation for 6h or 24h


title: Single-cell analysis of olfactory neurogenesis and differentiation in adult humans

city: Miami

first: Michael

last: Durante

state: FL

department: Ophthalmology

institute: University of Miami Miller School of Medicine

summary: We performed single-cell RNAseq of human olfactory and respiratory epithelium and found evidence of olfactory neurogenesis and differentiation in adult humans.

overall_design: Single cell 3' RNAseq of olfactory epithelium from 2 patients and respiratory epithelium from 2 patients using the 10X Genomics Chromium platform and sequenced on Illumina Nextseq 500.

first: Stefan

last: Kurtenbach


title: Tissue-resident memory T cells mediate immune homeostasis in the human pancreas through the PD-1/PD-L1 pathway

city: New York

first: Stuart

last: Weisberg

state: NY

address: 650 W 168th Street

department: Pathology and Cell Biology

institute: Columbia University

summary: We investigated the distinct state of pancreas resident memory T cells (TRM) by whole transcriptome profiling of sorted CD8+TRM cells from donor-matched pancreata, jejunum, and PLN compared to circulating blood CD8+TEM cells from living healthy donors. We identified 2029 genes differentially expressed in pancreas TRM with comparison to both PLN and jejunum TRM. Strong correlation was observed in the differentially upregulated and downregulated genes between pancreas vs. jejunum TRM and pancreas vs. PLN TRM which together define a pancreas-specific gene signature.

overall_design: Examination of TRM gene expression profiles from donor-matched pancreas, jejunum, pancreas draining lymph node (PLN) and blood CD8+ TEM from living healthy donors.

middle: P

first: Donna

last: Farber


title: HELLS and PRDM9 from a pioneer complex to open chromatin at meiotic recombination hotspots

city: Bar Harbor

first: Christopher

middle: Lee

last: Baker

state: ME

address: 600 Main Street

department: Research

institute: The Jackson Laboratory

summary: Chromatin barriers prevent spurious interactions between regulatory elements and DNA-binding proteins. One such barrier, whose mechanism for overcoming is poorly understood, is access to recombination hotspots during meiosis. Here we identify that the DNA-binding protein PRDM9 and chromatin remodeler HELLS function together to open chromatin at hotspots providing access to the DNA double-strand break (DSB) machinery. Recombination hotspots are decorated by a unique combination of histone modifications, not found at other regulatory elements. HELLS is recruited by PRDM9, and is necessary for both histone modification and DNA accessibility at hotspots. In male mice lacking HELLS, DSBs are retargeted to other sites of open chromatin, leading to germ cell death and sterility. Together, these data provide a model for hotspot activation where HELLS and PRDM9 function as a pioneer complex to create a unique epigenomic environment to open chromatin in preparation for proper placement and repair of DSBs.

overall_design: Measure histone modifications and chromatin accessibility in male germ cells collected from various mouse backgrounds


title: Lymphocyte DNA methylation mediates genetic risk at shared immune mediated disease loci

first: Arthur

last: Pratt

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

overall_design: Refer to individual Series


title: Identification and characterization of miRNAs involved in cold acclimation of zebrafish ZF4 cells

city: shanghai

first: xiangqin

last: ji

address: hucheng ring road 999

department: College of Fisheries and Life Science

institute: Shanghai Ocean University

summary: MicroRNAs (miRNAs) play vital roles in various biological processes by leading to mRNA cleavage or translational repression, and are also involved in multiple stress conditions. However, the detailed roles of miRNAs in cold acclimation in fish are still unclear. In the present study, high-throughput sequencing was performed to identify miRNAs from 6 small RNA libraries from the zebrafish embryonic fibroblast ZF4 cells under control (28°C, 30 days) and cold-acclimation (18°C, 30 days) conditions. A total of 414 miRNAs, 349 known and 65 novel, were identified. Among those miRNAs, 24 (19 known and 5 novel) were up-regulated, and 23 (9 known and 14 novel) were down-regulated in cold acclimated cells. The Gene Ontology (GO) and Kyoto Encyclopaedia of Genes and Genomes (KEGG) enrichment analyses indicated that the known differentially expressed miRNAs (DE-miRNA) are involved in cold acclimation by regulation of phosphorylation, cell junction, intracellular signal transduction, ECM-receptor interaction and so on. Moreover, dre-miR-100-3p inhibitor or dre-miR-16b mimics could protect ZF4 cells under cold stress, indicating the involvement of miRNA in cold acclimation. In summary, the present data show that miRNAs are closely involved in cold acclimation in fish and provide information for further understanding of the roles of miRNAs in cold acclimation.

overall_design: ZF4 cells were cultured at 28 °C as control and at 18 °C for 30 days, seperately. Each condition has three biological replica.

first: Xiangqin

last: Ji

first: Penglei

last: Jiang

first: Juntao

last: Luo

first: Mengjia

last: Li

first: Yajing

last: Bai

first: Junfang

last: Zhang

first: Bingshe

last: Han


title: Intron 1-Mediated Regulation Of EGFR Expression In EGFR-Dependent Malignancies [ChIP-Seq]

city: La Jolla

first: Nathan

last: Jameson

state: CALIFORNIA

address: 9500 Gilman Dr

department: Pathology

institute: UC San Diego

summary: Here, we performed ChIP-seq and ATAC-seq and identified two novel super enhancers (SE1 and SE2) responsible for EGFR transcription present within the first intron of the EGFR gene in HNSCC and GBM. SE1 and SE2 span 37kb and 33kb respectively, contain H3K27Ac enhancer histone marks and open chromatin, functionally enhance transcription in reporter assays, interact with the EGFR promoter, and negatively impact EGFR transcript levels and anchorage-independent growth when perturbed by CRISPR/Cas9-deletion and dCas9-KRAB-silencing. We utilize in silico methods to identify AP-1 family transcription factors as critical for EGFR enhancers in HNSCC and GBM, and confirm their role through ChIP-qPCR and a dominant-negative c-Jun. Our results identify and characterize these novel enhancers, shedding light on the role that epigenetic mechanisms play in regulating EGFR transcription in EGFR-dependent cancer types and presents a novel angle by which these malignancies can be treated.

overall_design: H3K27Ac ChIP-seq in 3 HNSCC and 7 GBM cell lines

middle: M

first: Frank

last: Furnari


title: Intron 1-Mediated Regulation Of EGFR Expression In EGFR-Dependent Malignancies [ATAC-Seq]

overall_design: ATAC-seq in 3 HNSCC and 7 GBM cell lines


title: RUVBL1/RUVBL2 ATPase Activity Drives PAQosome Maturation, DNA Replication and Radioresistance in Lung Cancer

city: Dallas

first: Ralf

last: Kittler

state: Texas

address: 5323 Harry Hines Blvd

institute: University of Texas Southwestern Medical Center

summary: RUVBL1 and RUVBL2 (collectively RUVBL1/2) are essential AAA+ ATPases that function as co-chaperones and have been implicated in cancer. Here we investigated the molecular and phenotypic role of RUVBL1/2 ATPase activity in non-small cell lung cancer (NSCLC). We find that RUVBL1/2 are overexpressed in NSCLC patient tumors, with high expression prognostic of poor survival. Utilizing a highly specific inhibitor of RUVBL1/2 ATPase activity, we show that RUVBL1/2 ATPase activity is necessary for the maturation of the PAQosome, a large RUVBL1/2-dependent multiprotein complex. We also show that RUVBL1/2 have roles in DNA replication, as inhibition of their ATPase activity impedes RPA loading at replication forks, decreases fork stability, and ultimately results in replication catastrophe and cancer cell death. While in vivo pharmacological inhibition of RUVBL1/2 results in modest antitumor activity, it synergizes with radiation in NSCLC, but not normal cells, an attractive property for future preclinical development.

overall_design: Analyze the transcriptomic response of RUVBL1 knockdown (siBL1) or RUVBL1 inhibition (compB) in two different non-small cell lung cancer cell lines (H2009 and H596)

first: Paul

last: Yenerall

first: Amit

middle: K

last: Das

first: Shan

last: Wang

first: Rahul

last: Kollipara

first: LongShan

first: Pamela

last: Villalobos

first: Josiah

last: Flaming

first: Yu-Fen

last: Lin

first: Kenneth

last: Huffman

first: Brenda

middle: C

last: Timmons

first: Collin

last: Gilbreath

first: Rajni

last: Sonavane

first: Lisa

middle: N

last: Kinch

first: Jaime

last: Rodriguez-Canales

first: Cesar

last: Moran

first: Carmen

last: Behrens

first: Makoto

last: Hirasawa

first: Takehiko

last: Takata

first: Ryo

last: Murakami

first: Koichi

last: Iwanaga

first: Benjamin

last: Chen

first: Nick

last: Grishin

first: Ganesh

last: Raj

first: Ignacio

last: Wistuba

first: John

last: Minna


title: Intron 1-Mediated Regulation Of EGFR Expression In EGFR-Dependent Malignancies

first: Nathan

last: Jameson


title: RNA-seq of Bacillus subtilis WT W168 treated with the antimicrobial peptide YydF (0.5µM) compared to untreated control

status: Public on Dec 16 2019

city: Dresden

first: Thorsten

last: Mascher

address: Zellescherweg 20b

institute: TU Dresden

summary: To obtain global cellular response of Bacillus subtilis WT W168 against the intrinsically produced antimicrobial peptide YydF, we performed RNA-seq experiments. For this, we synthesized YydF, extrinsically added 0.5µM to logarithmic phase growing cells and harvested cells after 10 min exposure. Experiments were performed in triplicates and non-induced Bacillus subtilis WT W168 was used as reference condition.

sample_organism: Bacillus subtilis subsp. subtilis str. 168

overall_design: Examination of YydF induced Bacillus subtilis WT cells compared to non-induced Bacillus subtilis WT cells

first: Philipp

middle: F

last: Popp


title: A large peptidome dataset improves HLA class I epitope prediction across most of the human population

city: Cambridge

first: Nir

last: Hacohen

state: MA

address: 415 Main Street

institute: Broad Institute

summary: Prediction of HLA epitopes is important for the development of cancer immunotherapies and vaccines. However, current prediction algorithms have limited predictive power, in part because they were not trained on high-quality epitope datasets covering a broad range of HLA alleles. To enable prediction of endogenous HLA class I-associated peptides across a large fraction of the human population, we used mass spectrometry to profile >185,000 peptides eluted from 95 HLA-A, -B, -C and -G mono-allelic cell lines. We identified canonical peptide motifs per HLA allele, unique and shared binding submotifs across alleles and distinct motifs associated with different peptide lengths. By integrating these data with transcript abundance and peptide processing, we developed HLAthena, providing allele-and-length-specific and pan-allele-pan-length prediction models for endogenous peptide presentation. These models predicted endogenous HLA class I-associated ligands with 1.5-fold improvement in positive predictive value compared with existing tools and correctly identified >75% of HLA-bound peptides that were observed experimentally in 11 patient-derived tumor cell lines.

overall_design: RNA transcript expression was quantified for mono-allelic HLA-C cell lines (HLA-C*04:01 and HLA-C*07:01, 4 replicates each) in order to assess its contribution to Class I peptide prediction and compare it against HLA-A and HLA-B.

first: Catherine

middle: J

last: Wu

first: Derin

middle: B

last: Keskin


title: Toll-like receptor signaling rewires macrophage metabolism and promotes histone acetylation via ATP-citrate lyase

city: Bonn

first: Eicke

last: Latz

address: Sigmund-Freud-Straße 25

department: Institute of Innate Immunity

institute: University Hospital Bonn

summary: TLR activation induces inflammatory responses in macrophages by activating temporally defined transcriptional cascades within the first hours after stimulation. Whether concurrent changes in the cellular metabolism that occur upon TLR activation influence the quality of the transcriptional responses remain unknown. Here we investigated how macrophages adopt their metabolism early after activation to regulate TLR-inducible gene induction. Macrophages increase glucose metabolism and adopt fluxes through the TCA cycle to foster Citrate synthesis. We concomitantly observe activation of ATP-Citrate Lyase (Acly), resulting in augmented acetyl-CoA synthesis and histone acetylation. To investigate which genes and genes classes require ATP-citrate lyase activity for induction we stimulated bone marrow derived macrophages with LPS after ATP-citrate lyase inhibition.

overall_design: Bone marrow-derived macrophages were stimulated with LPS for 4 hours in the presence or absence of the ATP-Citrate Lyase inhibitor BMS303141.

first: Mario

last: Lauterbach

first: Christian

last: Kolbe

first: Timo

last: Hess

first: Jan

last: Gehlen


title: Transcriptome-wide study of the response of human trabecular meshwork cells to the substrate stiffness increase

city: Wuhan

first: Dong

state: Hubei

address: 388 GaoXin 2nd Road, East Lake Hi-Tech Development Zone

department: Center for Genome Analysis

institute: ABLife, Inc.

summary: Elevated intraocular pressure, a major risk factor of glaucoma, is caused by the abnormal function of trabecular outflow pathways. Human trabecular meshwork (HTM) tissue plays an important role in the outflow pathways. However, the molecular mechanisms that how TM cells respond to the elevated IOP are largely unknown. We cultured primary HTM cells on polyacrylamide gels with tunable stiffness corresponding to Young's moduli ranging from 1.1 to 50 kPa. Then next‐generation RNA sequencing (RNA‐seq) was performed to obtain the transcriptomic profiles of HTM cells. Bioinformatics analysis revealed that genes related to glaucoma including DCN, SPARC, and CTGF, were significantly increased with elevated substrate stiffness, as well as the global alteration of HTM transcriptome. Extracellular matrix (ECM)‐related genes were selectively activated in response to the elevated substrate stiffness, consistent with the known molecular alteration in glaucoma. Human normal and glaucomatous TM tissues were also obtained to perform RNA‐seq experiments and supported the substrate stiffness‐altered transcriptome profiles from the in vitro cell model. The current study profiled the transcriptomic changes in human TM cells upon increasing substrate stiffness. Global change of ECM‐related genes indicates that the in vitro substrate stiffness could greatly affect the biological processes of HTM cells. The in vitro HTM cell model could efficiently capture the main pathogenetic process in glaucoma patients, and provide a powerful method to investigate the underlying molecular mechanisms.

overall_design: Normal HTM cells with two different densities (cultured by 3 and 5 days, respectively) were cultured on collagen-coated polyacrylamide gels of tunable stiffness with Young’s moduli ranging from 1.1 kPa to 50 kPa. TM tissues of glaucoma patients were also obtained. RNA-seq experiments were performed for all the samples.

first: Yi

last: Zhang

first: Jiantao

last: Wang


title: Determination of CNVs in SKOV3 cells knocked down in BECN1 or MAP1LC3B

city: Charleston

first: Joe

middle: R

last: Delaney

state: SC

address: 173 Ashley Avenue

department: Biochemistry and Molecular Biology

institute: Medical University of South Carolina

summary: SKOV3 ovarian cancer cells have high basal autophagy levels and were used as a model cell line to enable knockdown of autophagy genes and study the changes of DNA copy number as a consequence of impaired autophagy.

overall_design: Four genomic DNA samples per genotype, including control (shScr), shBECN1, and shLC3B were analyzed after passaging 30 times in normal media.  Ploidy was verified and normalized in part by the known single allele of chromosome 7 and homozygous deletion of CDKN2A


title: Hepatic microRNA Expression by PGC-1α and PGC-1β in the Mouse I

status: Public on Dec 14 2019

city: Bari

first: Elena

last: Piccinin

state: Bari

address: Piazza Giulio Cesare, 11

department: Department of Translational Biomedicine and Neuroscience

country: Italy

institute: University of Bari

summary: The fine-tuning of liver metabolism is essential to maintain the whole-body homeostasis and to prevent the onset of diseases. The peroxisome proliferator-activated receptor-γ coactivators (PGC-1s) are transcriptional key players of liver metabolism, able to regulate mitochondrial function, gluconeogenesis and lipid metabolism. Their activity is accurately modulated by post-translational modifications. Here, we showed that specific PGC-1s expression can lead to the upregulation of different microRNAs widely implicated in liver physiology and diseases development and progression, thus offering a new layer of complexity in the control of hepatic metabolism.

overall_design: Total RNA obtained from liver isolated from LivPGC-1α (mice overexpressing PGC-1α selectively in the liver) compared to Wild Type mice.

first: E

first: M

last: Arconzo

last: Graziano

last: Vacca

first: C

last: Peres

last: Bellafante

first: G

last: Villani

first: A

last: Moschetta


title: Gene expression profiling study by RNA-seq in Arabidopsis thaliana treated with Chlorella

city: Daejeon

first: Seon-Kyu

last: Kim

address: 125 Gwahak-ro, Yuseong-gu, Daejeon 305-806, Korea

department: Personalized Genomic Medicine Research Center

country: South Korea

institute: Korea Research Institutue of Bioscience & Biotechnology

summary: The objective of this study is to assess gene expression changes in Arabidopsis thaliana after Chlorella treatment. We performed transcript profiling using 4 RNA-seq samples of Arabidopsis obtained at 0h and 12h after Cholorella treatment. To compare them with control sample groups, 6 RNA-seq samples treated with additional DC3000 pathogen or only water were generated. Through various statistical tests, differentially expressed genes at each time point were obtained and enriched biological functions were compared between treatment time points. Many enriched functions associated with immune or defence systems of plant were common in all treatment times.

overall_design: RNA-seq data of 10 samples were generated. Total RNA was isolated by RNeasy Mini Kit (Qiagen, CA, USA), according to the manufacturer's protocol. The quality and integrity of the RNA were confirmed by agarose gel electrophoresis and ethidium bromide staining, followed by visual examination under ultraviolet light. Sequencing library was prepared using TruSeq RNA Sample Preparation kit v2 (Illumina, CA, USA) according to the manufacturer’s protocols. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads, fragmented, and converted into cDNAs. Then, adapters were ligated and the fragments were amplified on a PCR. Sequencing was performed in paired end reads (2x100 bp) using Hiseq-2000 (Illumina).

first: Sang-Moo

last: Lee

first: Choong-Min

last: Ryu


title: Hepatic microRNA Expression by PGC-1α and PGC-1β in the Mouse II

overall_design: Total RNA obtained from liver isolated from LivPGC-1β (mice overexpressing PGC-1β selectively in the liver) compared to Wild Type mice.