title: Gene expression profile of primary cultures of neonatal cardiomyocytes treated with specific GapmeRs

summary: The eRNAs are non coding transcripts involved in the control of gene expression. To verify the biological effects of IRENE-SS and -div (Intergenic Regulatory Element Nkx2-5 Enhancer -same strand and -divergent)  knockdown, we analyzed the differentially gene expression profile of cells treated with either of the two specific gapmers versus cardiomyocytes transfected with a scrambled sequence control. We also determined whether IRENE-SS or -div silencing modified the expression of NKX2-5 target genes.

overall_design: Profiling of the neonatal cardiomyocytes transcriptome after gapmers treatment. Three biological replicates were profiled for each condition.


title: Autophagic adaptation to oxidative stress alters peritoneal residential macrophage survival and ovarian cancer metastasis [macrophages]

status: Public on Sep 09 2020

city: ANN ARBOR

first: Shasha

last: Li

state: MI

address: 1109 Maiden Ln, ct apt 104

country: USA

institute: University of Michigan

type: Expression profiling by high throughput sequencing

summary: Tumor-associated macrophages (TAMs) affect cancer progression and therapy. Ovarian carcinoma often metastasizes to the peritoneal cavity. Here, we found two peritoneal macrophage subsets in mice bearing ID8 ovarian cancer based on the Tim-4 (T-cell immunoglobulin and mucin domain containing 4) expression. Tim-4+ TAMs were embryonically originated and locally sustained while Tim-4- TAMs were replenished from circulating monocytes. Tim-4+ TAMs, but not Tim-4- TAMs, promoted tumor growth in vivo. Relative to Tim-4- TAMs, Tim-4+ TAMs manifested high oxidative phosphorylation and adapted mitophagy to alleviate oxidative stress. High levels of arginase-1 in Tim-4+ TAMs contributed to potent mitophagy activities via weakened mTORC1 activation due to low arginine resultant from arginase-1-mediated metabolism. Furthermore, genetic deficiency of autophagy element FIP200 resulted in Tim-4+ TAM loss via ROS-mediated apoptosis, and elevated T cell-immunity and ID8 tumor inhibition in vivo. Moreover, human ovarian cancer-associated CRIg (complement receptor of the Immunoglobulin superfamily) positive macrophages were transcriptionally, metabolically, and functionally similar to murine Tim-4+ TAMs. Thus, targeting CRIg+ (Tim-4+) TAMs may potentially treat ovarian cancer patients with peritoneal metastasis.

overall_design: Bulk mRNA profiles of Tim4+ and Tim4- tumor associated peritoneal macrophages in ID8 bearing mice. Each library was sequenced in two lanes and analyzed separately. Each lane of data is represented as an individual sample/GSM.

first: Houjun

last: Xia


title: Circulating exosomal microRNA as potential biomarkers of hepatic injury and inflammation in glycogen storage disease type 1a

city: Genova

first: Roberta

last: Resaz

address: via Gerolamo Gaslini 5

country: Italy

institute: IRCCS Istituto Giannina Gaslini

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

summary: Most patients affected by glycogen storage disease type 1a (GSD-1a), an inherited metabolic disorder caused by mutations in the enzyme glucose-6-phosphatase-alpha (G6Pase- α), develop renal and liver complications, including development of hepatocellular adenoma/carcinoma. The purpose of this study was to identify potential biomarkers of the pathophysiology of the GSD1a affected liver. To this end, we utilized the plasma exosomes of a murine model of GSD-1a, LS-G6pc-/- mice, to uncover microRNA expression modulation associated with the disease. Differentially expressed microRNA between LS-G6pc-/- and wild type mice, LS-G6pc-/- mice with hepatocellular adenoma and LS-G6pc-/- mice without adenoma, and LS-G6pc-/- mice with amyloidosis and LS-G6pc-/- mice without amyloidosis were identified. Pathway analysis demonstrated that the target genes of the differentially expressed miRNAs were significantly enriched for insulin signaling pathway, glucose and lipid metabolism, Wnt-beta catenin, telomere maintenance and hepatocellular carcinoma, and chemokine and immune regulation signaling pathways. While some microRNA were common to the different pathologic conditions, others were unique to cancerous or inflammatory status of the animals. Therefore, the altered expression of several microRNA correlates with various pathologic liver statuses and may help discriminate during the progression of the disease and the development of late GSD1-associated complications.

platform_organism:
Mus musculus
Rattus norvegicus

overall_design: Exo-miR were analyzed by the TaqMan Array Card Technology. Exo-miR were reverse transcribed with the TaqMan microRNA Reverse Transcription Kit, using the MegaplexTM RT primers Rodent Pool A (Thermo Fisher Scientific, Monza, MB, Italy). Pre-amplification of cDNA was performed with TaqMan PreAmp Master Mix and MegaplexTM Pre-Amp primers Rodent Pool A. The pre-amplification product was diluted according to the manufacturer’s instructions and used to perform microRNA profiling on the ViiATM 7 Real-Time PCR System. The Exo-miR modulation of expression in LS-G6pc-/- mice was validated for five microRNA by qRT-PCR on the ViiATM 7 Real-Time PCR System.

first: Alessandra

last: Eva


title: Chidamide used in MM primary cells [RNA-seq]

city: Shanghai

first: Yifeng

last: Sun

country: China

institute: Zhongshan Hospital, Fudan University

summary: Most patients with multiple myeloma (MM) will eventually relapse and current treatments have limited effect. Herein, we demonstrate that succinate dehydrogenase subunitA (SDHA) was low expressed in MM patients, and patients with SDHA relatively high expression had long overall survival and progression-free survival. Furthermore, SDHA high expression inhibited proliferation and invasion in multiple myeloma (MM) cell lines and enhanced the anti-tumor and synergistic effect of chemotherapeutics.  We conducted transcriptome comparison of BMMCs of three MM patients treated with DMSO or chidamide.

overall_design: RNA-Seq profiles for BMMCs of three initial MM patients treated with DMSO. RNA-Seq profiles for BMMCs of three initial MM patients treated with chidamide.

first: Zhao

last: Xu

first: Tianhong

first: Jiadai

first: Peng

last: Liu


title: Mechanisms of immune evasion in P. falciparum malaria revealed by integrative gene expression profiling [RNA-seq]

status: Public on Sep 05 2020

city: Abu dhabi

first: Youssef

last: Idaghdour

state: Abu dhabi

address: Saadiyat Marina District

department: Biology

country: United Arab Emirates

institute: NYUAD

summary: We performed a genome-wide profiling of miRNAs and mRNA, DNA sequencing of human whole blood sample to identify miRNAs responsive to P.falciparum (P.f) infection and/or associated with parasite load. We identified a set of 72 miRNAs that are positively or negatively associated with parasitemia. We also performed expression quantitative trait loci of miRNAs(miR-eQTL) of P.f infected individuals. The miR-eQTL dataset allowed us to determine relevant genetic variant responsible for miRNAs expression differences between P.f infected individuals and find novel malaria-associated miRNAs

overall_design: A longitudinal pediatric cohort of 150 healthy children was recruited in Banfora, Burkina Faso. Enrolment took place at the end of the dry season and none of the children were Plasmodium. -infected at the time of the first sample collection. The children were of age 2 to 10 years, had no disease symptoms or chronic disease history (including sickle cell disease) based on medical records and thorough physical assessment. In this study, a subset of 72 children were included. All of them were not P. falciparum-infected when initially sampled and were subsequently followed on a weekly basis for up to 6 months. For the discovery cohort, clinical phenotyping, sampling and genomic profiling were done at four time points: (i) before infection (at enrolment = V1), (ii) during asymptomatic parasitemia (=V2), (iii) at the beginning of symptomatic parasitemia (=V3), and (iv) three weeks after treatment (=V4). When asymptomatic parasitemia was detected, a closer follow-up of the children was done to sample the early stage of symptomatic infection and immediately followed by Artemether/lumefantrine treatment, as per Burkina Faso’s national malaria treatment guidelines. A replication set of infected children was sampled the following year during the wet season. miRNAs and mRNA expression profiling were performed using whole-blood RNA-sequencing of 68 samples of the discovery. Whole blood was taken and immediately store in a Tempus Blood RNA tube at room temperature for 2h and then stored at -20 ̊C until RNA extraction. The total RNA was extracted using the Tempus Spin RNA Isolation Kit (Thermo scientific). miRNAs and mRNA libraries were constructed using Truseq small rna library prep kit (Illumina) and KAPA Stranded RNA-Seq kit with RiboErase (Kapa Biosystems), respectively. Small RNA libraries were sequenced using HiSeq Rapid kit (50 cycles, Illumina). mRNA libraries were 100 bp paired-end sequenced using the TruSeq SBS Kit v3 – HS kit using Illumina HiSeq 2500 platform. Genomic DNA libraries were constructed using the TruSeq Nano DNA Library Prep Kit (Illumina) and sequenced at 30X coverage on the HiSeq X platform (Illumina).

first: Mame

middle: M

last: Dieng

first: Aissatou

last: Diawara

first: Vinu

last: Manikadan

first: Hala

middle: T

last: El Jarkass

first: Samuel

middle: S

last: Sereme

first: Salif

last: Sombie

first: Amidou

last: Diarra

first: Nizar

last: Drou

first: Marc

last: Arnoux

first: Ayman

last: Yousif

first: Alfred

middle: B

last: Tiono

first: Sam

last: Coulibaly

first: Sodiomon

last: Sirima

first: Soulama

last: Issiaka


title: Mechanisms of immune evasion in P. falciparum malaria revealed by integrative gene expression profiling [miRNA]

type: Non-coding RNA profiling by high throughput sequencing

overall_design: A longitudinal pediatric cohort of 150 healthy children was recruited in Banfora, Burkina Faso. Enrolment took place at the end of the dry season and none of the children were Plasmodium. -infected at the time of the first sample collection. The children were of age 2 to 10 years, had no disease symptoms or chronic disease history (including sickle cell disease) based on medical records and thorough physical assessment. In this study, a subset of 68 children were included. All of them were not P. falciparum-infected when initially sampled and were subsequently followed on a weekly basis for up to 6 months. For the discovery cohort, clinical phenotyping, sampling and genomic profiling were done at four time points: (i) before infection (at enrolment = V1), (ii) during asymptomatic parasitemia (=V2), (iii) at the beginning of symptomatic parasitemia (=V3), and (iv) three weeks after treatment (=V4). When asymptomatic parasitemia was detected, a closer follow-up of the children was done to sample the early stage of symptomatic infection and immediately followed by Artemether/lumefantrine treatment, as per Burkina Faso’s national malaria treatment guidelines. A replication set of infected children was sampled the following year during the wet season. miRNAs and mRNA expression profiling were performed using whole-blood RNA-sequencing of 68 samples of the discovery. Whole blood was taken and immediately store in a Tempus Blood RNA tube at room temperature for 2h and then stored at -20 ̊C until RNA extraction. The total RNA was extracted using the Tempus Spin RNA Isolation Kit (Thermo scientific). miRNAs and mRNA libraries were constructed using Truseq small rna library prep kit (Illumina) and KAPA Stranded RNA-Seq kit with RiboErase (Kapa Biosystems), respectively. Small RNA libraries were sequenced using HiSeq Rapid kit (50 cycles, Illumina). mRNA libraries were 100 bp paired-end sequenced using the TruSeq SBS Kit v3 – HS kit using Illumina HiSeq 2500 platform. Genomic DNA libraries were constructed using the TruSeq Nano DNA Library Prep Kit (Illumina) and sequenced at 30X coverage on the HiSeq X platform (Illumina).  The libraries of the discovery set were prepared in 3 differents batches. Those of the replication were prepared in one batch.


title: Genome-wide translational profiling of amygdala Crh-expressing

city: Belmont

first: Nikolaos

last: Daskalakis

state: MA

address: Oaks Building 328, Mailstop 212, 115 Mill Street

department: Department of Psychiatry

institute: McLean Hospital/ Harvard Medical School

summary: Here we translationally profiled the transcriptome of Crh-expressing neurons (Crh neurons) within the CeA following fear conditioning (FC) and fear extinction (EXT) in mice using translating ribosome affinity purification (TRAP) followed by RNA sequencing. A tone alone group (TA) was used as a control group.

overall_design: Individual animals were used as each sample (3 groups: FC, EXT and TA; n=10  males and females per group).

first: Kenneth

last: McCullough

first: Christos

last: Chatzinakos

middle: P

first: Kerry

middle: J

last: Ressler


title: Sex Diversity in Proximal Tubule and Endothelial Gene Expression in Mice with Ischemic Acute Kidney Injury

city: Ottawa

first: Theodore

last: Perkins

state: ON

address: 501 Smyth Rd.

department: Cellular and Molecular Medicine

country: Canada

institute: Ottawa Hospital Research Institute

summary: Female sex protects against development of acute kidney injury (AKI). While sex hormones may be involved in protection, the role of differential gene expression is unknown. We conducted gene profiling in male and female mice with or without kidney ischemia-reperfusion injury. Mice underwent bilateral renal pedicle clamping (30 min), and tissues were collected 24 hours after reperfusion. RNA-sequencing was performed on proximal tubules and kidney endothelial cells. Female mice were resistant to ischemic injury compared to males, determined by plasma creatinine, histologic scores, neutrophil infiltration, and extent of apoptosis. Sham mice had sex-specific gene disparities in proximal tubule and endothelium, and male mice showed profound gene dysregulation with ischemia-reperfusion compared to females. After ischemia proximal tubules from females exhibited smaller increases compared to males in injury-associated genes Lcn2, Havcr1, and Krt18, and no upregulation of Sox9 or Krt20. Endothelial upregulation of adhesion molecules and cytokines/chemokines occurred in males, but not females. Upregulated genes in male ischemic proximal tubules were linked to tumor necrosis factor and Toll-like receptor pathways, while female ischemic proximal tubules showed upregulated genes in pathways related to transport. The data suggest that sex-specific gene expression profiles in male and female proximal tubule and endothelium may underlie disparities in susceptibility to AKI.

overall_design:
Transcriptomic profile of endothelial cells from control (sham) FVB female mice (n=2), sham  male mice (n=3), acute kidney injury (AKI) female mice (n=3) and AKI male mice (n=3). The experiment also includes the same experimental groups with samples of proximal tubular cells from sham female mice (n=3), sham male mice(n=3), AKI female mice (n=3) and AKI male mice (n=3)
Please note that wwo libraries sequenced from the 'Sham M PTs rep 3' and quantified separately (i.e. rep3 and rep3B). Technical replicates combined in DESeq2 analysis

first: Jose

middle: L

last: Vinas

first: Christopher

last: Porter

first: Adrianna

last: Douvris

first: Matthew

last: Spence

first: Alex

last: Gutsol

first: Joseph

middle: A

last: Zimpelmann

first: Karishma

last: Tailor

first: Pearl

last: Campbell

first: Kevin

middle: D

last: Burns


title: Differentially expressed genes in cotyledon of ewes fed mycotoxins

status: Public on Sep 08 2020

city: Clemson

first: Susan

middle: K

last: Duckett

state: SC

address: 112 Biosystems Research Complex

department: Animal and Veterinary Sciences

institute: Clemson University

summary: Consumption of ergot alkaloids, specifically ergovaline, found in endophyte-infected tall fescue causes potent vasoconstriction and has been linked to reductions in placental mass and fetal growth and development. The objective of this study was to elucidate differences in the cotyledonary transcriptome of ewes consuming ergovaline during gestation through RNA-sequencing.

overall_design: Cotyledon mRNA profiles from ewes d 133 +/- 1 gestation fed endophyte-free or endophyte-infected tall fescue seed

first: Jessica

last: Britt

first: Rooksana

middle: E

last: Noorai


title: Mechanisms of immune evasion in P. falciparum malaria revealed by integrative gene expression profiling

first: Youssef

last: Idaghdour

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

overall_design: Refer to individual Series


title: Quantitative RNAseq Analysis of Treatment Outcomes with Talazoparib, Romidepsin or Combination in MBL2 cell line

status: Public on Sep 04 2020

city: Pittsburgh

first: Oleg

last: Akilov

state: PA

address: 200 Lothrop Street

department: Dermatology

institute: University of Pittsburgh

summary: To explore the molecular mechanisms by which romidepsin potentiates the effect of talazoparib, RNA sequencing analysis of MBL2 cell lines treated with talazoparib, romidepsin, or talazoparib plus romidepsin was performed. 40% of the 2023 genes in combination were from talazoparib, whereas only 5.9% of the genes deregulated during the treatment with the combination of talazoparib plus romidepsin were from the effect of romidepsin. 94 genes were presented in all three treatment groups and included upregulation of Prdm1, Dusp5, and CD74, among others. Analysis of genes responsible for DNA repair, cell cycle arrest and apoptosis demonstrated the contribution of romidepsin to downregulation of DNA repair, the synergistic effect of romidepsin and talazoparib on downregulation of genes of cell cycle leading to cell cycle arrest, and activation of apoptosis by talazoparib predominantly.

overall_design: mRNA profile 24 hrs after treatment of MBL2 cells with talazoparib, romidepsin, or talazoparib with romidepsin

last: Kruglov


title: Human Cytomegalovirus-Induced Interleukin-10 Production Promotes the Proliferation of Mycobacterium massiliense in Macrophages

city: Seoul

first: Hailian

last: Quan

address: 103 Daehak-ro, Jongno-gu,

department: Department of Microbiology and Immunology, and Institute of Endemic Disease

country: South Korea

institute: Seoul, South Korea

summary: We profiled the transcriptome of HCMV-, HCMV/M. mass- and M. mass-infected macrophages. Comparison of hierarchical clustering with the 880 differentially expressed genes (DEGs) between the HCMV-infected and control macrophages revealed that M. mass co-infection did not globally change the transcriptome of HCMV-infected macrophages. Low immune responsiveness upon M. mass challenge was due to the existence of HCMV, which was clearly shown in the gene ontology (GO) analysis. M. mass single-infected macrophages showed enriched GO pathways including response to lipopolysaccharide (LPS) and cellular response to TNF/IL-1 compared to GO pathways enriched in the co-infected group.

overall_design: Total RNA profiles of THP-1 cells were used for the hierarchical clustering and gene ontology analysis using the MeV softwared and DAVID bioinformatics resourses 6.8.

first: Yi

middle: R

first: Seung

middle: H

last: Seok


title: Genome-wide Chromatin Accessibility is Restricted by ANP32E [CUT&Tag]

city: Rochester

first: Fanju

last: Meng

state: NY

address: 601 Elmwood Avenue

department: Biomedical Genetics

institute: University of Rochester Medical Center

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Genome-wide chromatin state underlies gene expression potential and cellular function. Epigenetic features and nucleosome positioning contribute to the accessibility of DNA, but widespread regulators of chromatin state are largely unknown. Our study investigates how coordination of ANP32E and H2A.Z contributes to genome-wide chromatin state in mouse fibroblasts. We define H2A.Z as a universal chromatin accessibility factor, and demonstrate that ANP32E antagonizes H2A.Z accumulation to restrict chromatin accessibility genome-wide. In the absence of ANP32E, H2A.Z accumulates at promoters in a hierarchical manner. H2A.Z initially localizes downstream of the transcription start site, and if H2A.Z is already present downstream, additional H2A.Z accumulates upstream. This hierarchical H2A.Z accumulation coincides with improved nucleosome positioning, heightened transcription factor binding, and increased expression of neighboring genes. Thus, ANP32E dramatically influences genome-wide chromatin accessibility through subtle refinement of H2A.Z patterns, providing a means to reprogram chromatin state and to hone gene expression levels.

overall_design: Gene expression profiles, chromatin accessibility and CUT&Tag profiles in wildtype (WT) and Anp32e null mouse embryonic fibroblasts were generated by next-generation sequencing, in triplicates.


title: RNA-seq of WT ileum with DEX, Zn and untreated controls

status: Public on Sep 07 2020

city: Gent

first: Steven

last: Timmermans

address: Technologiepark 71

country: Belgium

institute: VIB-UGent

summary: The cytokine TNF drives inflammatory diseases, e.g. Crohn disease. In a mouse model of TNF-induced systemic inflammatory response syndrome (SIRS), severe impact on intestinal epithelial cells (IECs) is observed. Zinc confers complete protection in this model. We found that zinc no longer protects in animals which lack glucocorticoids (GCs), or express mutant versions of their receptor GR in IECs, nor in mice which lack gut microbiota. RNA-seq studies in IECs showed that zinc caused reduction of expression of constitutive (STAT1-induced) interferon-stimulated response (ISRE) genes and Interferon Regulatory Factor (IRF) genes. Since some of these genes are involved in TNF-induced cell death in intestinal crypt Paneth cells, and since zinc has direct effects on the composition of the gut microbiota (such as several Staphylococcus species) and on TNF-induced Paneth cell death, we postulate a new zinc-related anti-inflammatory mechanism. Zinc modulates the gut microbiota, causing less induction of ISRE/IRF genes in crypt cells, less TNF-induced necroptosis in Paneth cells and less fatal evasion of gut bacteria into the system.

overall_design: Examination of changes in gene expresion in ileum of mice after treatment with DEX, Zinc or DEX+Zinc and a control group  a total of 12 samples was sequenced in 4 conditions with 3 (biological) replicates/condition

first: Jolien

last: Souffriau

first: Tineke

last: Vanderhaeghen

first: Charlotte

last: Wallaeys

first: Kelly

last: Van Looveren

first: Lindsy

last: Aelbrecht

first: Sylviane

last: Dewaele

last: Vandewalle

first: Evy

last: Goossens

first: Serge

last: Verbanck

first: Filip

last: Boyen

first: Melanie

last: Eggermont

first: Lindsey

last: De Commer

first: Riet

last: De Rycke

first: Michiel

last: De Bruyne

first: Raul

last: Tito

first: Marlies

last: Ballegeer

first: Sofie

last: Vandevyver

first: Tiago

last: Velho

first: Luis

middle: F

last: Moita

first: Tino

last: Hochepied

first: Karolien

last: De Bosscher

first: Jeroen

last: Raes

last: Van Immerseel

first: Rudi

last: Beyaert

first: Claude

last: Libert


title: Argonaute-CLIP delineates versatile, functional RNAi networks in Aedes aegypti, a major vector of human viruses

city: New York

first: Kathryn

last: Rozen-Gagnon

address: 1230 York Avenue, Box 64

institute: The Rockefeller University

summary: Argonaute (AGO) proteins bind small RNAs to silence complementary RNA transcripts and are central to RNA interference (RNAi). AGO-crosslinking immunoprecipitation (AGO-CLIP) has illuminated RNAi networks, but bioinformatic analysis is laborious and lack of experimental tools hinders its application outside of model organisms. RNAi is critical for regulation of gene expression and defense against viral infection in the Aedes aegypti mosquito, which transmits Zika, chikungunya, dengue, and yellow fever viruses to cause human disease. We developed AGO-CLIP for both mosquito AGO proteins and a universal, streamlined software package for CLIP analysis, identifying 230 novel small RNAs and 5,447 small RNA targets that comprise a comprehensive RNAi network map. We used this unique resource to predict repression of small RNA targets in specific mosquito tissues. Notably, this resource revealed unexpected AGO target preferences and uncovered a new mode of AGO-mediated repression, findings that have broad implications for the study of antiviral RNAi.

overall_design: CLIP libraries were prepared using custom Ago1, Drosophila Ago2 (9D6; a kind gift from M. Siomi), or paired irrelevant IgG control antibodies, from Aag2 cells or whole homogenized female Aedes aegypti mosquitoes (a kind gift from L.D. Kramer).

first: Meigang

last: Gu

first: Joseph

last: Luna

first: Ji-Dung

last: Luo

first: Soon

last: Yi

first: Sasha

last: Novack

first: Eliana

last: Jacobson

first: Wei

last: Wang

first: Matthew

last: Paul

first: Troels

last: Scheel

first: Thomas

last: Carroll

first: Charles

last: Rice


title: Genome-wide Chromatin Accessibility is Restricted by ANP32E [ATAC-seq]

first: Fanju

last: Meng


title: ANP32E Restricts Widespread Chromatin Accessibility Through Regulation of H2A.Z


title: Epigenomic and transcriptomic analysis of Systemic Sclerosis CD4+ T cells

city: Badalona, Barcelona

first: Esteban

last: Ballestar

state: N/A = Not Applicable

address: Ctra de Can Ruti, Camí de les Escoles s/n

country: Spain

institute: Josep Carreras Research Institute (IJC)

type:
Expression profiling by array
Methylation profiling by array


title: ANP32E Restricts Widespread Chromatin Accessibility Through Regulation of H2A.Z [RNA-seq]

summary: Genome-wide chromatin state underlies gene expression potential and cellular function. Epigenetic features and nucleosome positioning are major factors in determining chromatin accessibility. Our study investigates how genomic localization of the histone variant H2A.Z regulates chromatin state in mouse fibroblasts. We define H2A.Z as a universal chromatin accessibility factor, and demonstrate that ANP32E antagonizes H2A.Z accumulation to restrict chromatin accessibility genome-wide. In the absence of ANP32E, H2A.Z accumulates in a hierarchical manner at promoters. H2A.Z initially localizes at the +1 nucleosome, and then if H2A.Z is already present at the +1 nucleosome position in WT, additional H2A.Z accumulates at the -1 nucleosome position. This hierarchical H2A.Z accumulation coincides with improved nucleosome positioning, heightened transcription factor footprint protection, and increased expression for neighboring genes. Thus, ANP32E dramatically influences genome-wide chromatin accessibility through refinement of H2A.Z patterns, providing a means to reprogram chromatin state and to hone gene expression levels.

overall_design: Gene expression profiles and chromatin accessibility in wildtype (WT) and Anp32e null mouse embryonic fibroblasts were generated by next-generation sequencing, in triplicates.


title: Extensive SUMO modification of chromatin factors distinguishes pluripotent from somatic cells

city: Paris

first: Jack-Christophe

last: Cossec

address: 28 rue du Dr. Roux

country: France

institute: Institut Pasteur

summary: The post-translational modification of proteins by SUMO acts as a key gatekeeper of cell identity. In mouse embryonic fibroblast (MEFs), SUMO impedes reprogramming to pluripotency, while in embryonic stem cells (ESCs), it represses the emergence of totipotent-like cells, suggesting that SUMO targets distinct sets of substrates to preserve the somatic and pluripotent states. Using MS-based proteomics, we show here that the composition of the endogenous SUMOylomes differs dramatically between MEFs and ESCs. In MEFs, SUMOylated proteins organize in a rather diffuse functional network enriched in nuclear factors with general cellular functions. In contrast, in ESCs, SUMOylated proteins form a tightly interconnected network mainly composed of repressive chromatin complexes. We also characterized several SUMOylated pluripotency factors and show that SUMO modification of Dppa2 and Dppa4 hampers their ability to induce a totipotent-like state. Altogether, we propose that rewiring the repertoire of SUMO target networks is a major driver of cell fate transition during embryonic development.

overall_design: MERVL:tdTomato Dppa2/4 knock out embryonic stem cells were transfected with Dppa2 and Dppa4 WT-GFP plasmids or SUMO deficient Dppa2 and Dppa4 GFP plasmids using lipofectamine. GFP+ cells were selected by flow cytometry and total RNA was prepared by TRIzol extraction (Invitrogen).

first: Ilan

last: Theurillat

first: Anne

last: Dejean


title: Characterization of the intergenerational impact of in utero and postnatal oxycodone exposure

status: Public on Sep 03 2020

city: OMAHA

first: Sowmya

middle: V

last: Yelamanchili

state: Nebraska

address: 984455 Nebraska Medical Center

department: Anesthesiology

institute: UNIVERSITY OF NEBRASKA MEDICAL CENTER

summary: Based on the significant physical attributes observed at P14 in the F1 and F2 generations exposed to oxycodone in utero (IUO) and postnatally (PNO), we performed RNA-Seq analysis on the nucleus accumbens (NAc). The NAc was chosen given its association with the reward pathway. RNA-Seq analysis showed several up-and down-regulated genes among the IUO, PNO, and saline groups in both the F1 and F2 generations

overall_design: RNA was isolated from the nucleus accumbens (NAc) of P14 Sprague Dawley rats that were exposed to oxycodone in utero (IUO) or postnatally (PNO). Samples were taken from F1 and F2 generations, allowing for intergenerational comparison. Biological replicates (n=4) taken from separate litters were used for each group.

first: Katherine

last: Odegaard

first: Jagadesan

last: Sankarasubramanian

first: S


title: Next Generation Sequencing Facilitates Quantitative Analysis of IFN-γ induced-MMP2/9 inhibition compared to vehicle control cells' Transcriptomes

first: Youqiong

last: Ye

address: 280 Chongqing south road

institute: Shanghai Jiao Tong University School of Medicine

summary: Expression profiles of SB-3CT treated A375 human melanoma cell lines and vehicle control group with or without induced by IFN-γ.

overall_design: Expression profiles were generated from SB-3CT treated A375 human melanoma cell lines with or without induced by IFN-γ, which were collected to extract total RNA, and mRNA sequencing was performed.

first: Xinwei

last: Kuang


title: Photoactivatable-Ribonucleotide-Enhanced Crosslinking and Immunoprecipitation (PAR-CLIP) of the RNA-binding protein (RBP) RBM4 in KBM-7 derived near-haploid human cell line, HAP1.

city: Bethesda

first: Stefan

last: Muljo

state: MD

address: 10 CENTER DR RM 11N306

institute: NIH/NIAID

summary: We hypothesized that RBM4 regulates HERVs by directly binding to their transcripts. To test this possibility, we performed photoactivatable ribonucleoside-enhanced crosslinking and immunoprecipitation (PAR-CLIP). We performed four independent PAR-CLIP replicates of our own using HAP1 cells stably expressing a FLAG-tagged RBM4 (FLAG-RBM4) transgene under control of a doxycycline-inducible promoter. Following metabolic labeling with 4-thiouridine (4SU) and crosslinking with ultraviolet light (UV) of 312 nm wavelength, we isolated RNA covalently linked to FLAG-RBM4. The RNA recovered from four biological replicates was converted into cDNA libraries and deep sequenced.

overall_design: Four replicate pairs of RBM4 PAR-CLIP libraries were sequenced. For each pair, one library was generated from a FLAG-RBM4 HAP1 sample treated with doxycycline (RBM4 induced) while the other one, as a Control, was not (no RBM4 induction). Dox-treated RBM4 ("RBM4_#_", 4 replicates). noDox (noDox_RBM4_#_", 4 replicates).

first: Amir

last: Foroushani

first: Bryan

last: Chim

first: Madeline

last: Wong

first: Markus

last: Hafner


title: The neurotransmitter receptor Gabbr1 regulates proliferation and function of hematopoietic stem and progenitor cells

city: Madison

first: Owen

middle: James

last: Tamplin

state: WI

address: 1111 Highland Ave

department: Cell and Regenerative Biology

institute: University of Wisconsin-Madison

summary: To better understand molecular phenotypes of Gabbr1 null mutant hematopoietic stem and progenitor cells (HSPCs), we sorted and pooled ~12,000 HSPCs (LSK population) from WT or Gabbr1 null P15 bone marrow for bulk RNA-seq analysis.

overall_design: HSPCs (~12,000 cell/LSK population) from P15 wild-type (n=2) or Gabbr1 null (n=3) BM were sorted (MoFlo Astrios) and collected in Trizol LS (Invitrogen).

first: Kostandin

last: Pajcini


title: RNA-sequencing experiments to identify differentially expressed genes between Wild Type and RBM4 KO HAP1 cell line samples

summary: Here, we implemented a computational pipeline to determine the correlation of expression between individual RBPs and ERVs from single-cell or bulk RNA sequencing data. One of our top candidates for an RBP negatively regulating ERV expression was RNA-Binding Motif Protein 4 (RBM4). This set of bulk RNA-sequencing experiments was performed to identify differentially expressed genes and repetitive elements, particularly HERVs, between independent Wild Type and RBM4 KO clones  in the KBM-7 derived, near-haploid human cell line, HAP1

overall_design: Multiple replicates are provided for each HAP1 sample: Wild Type ("WT_" ,3 replicates), RBM4 KO Clone 1 ("1B2_", 3 replicates)  RBM4 KO Clone 2 ("1B6_", 2 replicates), Single-end Wild Type ("HAP1_WT_", 1 replicate) and Single-end KO Clone (HAP1_RBM4_KO_", 1 replicate)


title: Transport of DNA within cohesin involves clamping on top of engaged heads by Scc2 and entrapment within the ring by Scc3

city: Oxford

first: Kim

last: Nasmyth

address: South Parks Road

department: Biochemistry

country: United Kingdom

institute: University of Oxford

summary: In addition to extruding DNA loops, cohesin entraps within its SMC-kleisin ring (S-K) individual DNAs during G1 and sister DNAs during S-phase. All three activities require related hook-shaped proteins called Scc2 and Scc3. Using thiol-specific crosslinking we provide rigorous proof of entrapment activity in vitro. Scc2 alone promotes entrapment of DNAs in the E-S and E-K compartments, between ATP-bound engaged heads and the SMC hinge and associated kleisin, respectively. This does not require ATP hydrolysis nor is it accompanied by entrapment within S-K rings, which is a slower process requiring Scc3. Cryo-EM reveals that DNAs transported into E-S/E-K compartments are “clamped” in a sub-compartment created by Scc2’s association with engaged heads whose coiled coils are folded around their elbow. We suggest that clamping may be a recurrent feature of cohesin complexes active in loop extrusion and that this conformation precedes the S-K entrapment required for sister chromatid cohesion.

sample_organism:
Saccharomyces cerevisiae
Nakaseomyces glabratus

overall_design: Characterisation of the effect of WT and mutant cohesin complexes and associated factors on loading onto chromosomes in S. cerevisiae, assessed by calibrated ChIP-seq on an Ion Torrent Proton (Life Technologies).

first: Naomi

last: Petela


title: Kevetrin induces apoptosis in TP53 wild-type and mutant acute myeloid leukemia cells

city: Meldola

first: Giorgia

last: Simonetti

state: FC

address: Via Piero Maroncelli, 40

institute: IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori"

summary: Tumor protein p53 is a key regulator of several cellular pathways, including DNA repair, cell cycle and angiogenesis. Kevetrin exhibits p53-dependent as well as independent activity in solid tumors, while its effects on leukemic cells remain unknown. We analyzed the response of acute myeloid leukemia (AML) cell lines (TP53 wild-type: OCI-AML3 and MOLM-13; and TP53-mutant: KASUMI-1 and NOMO-1) to kevetrin at a concentration range of 85-340 μM. Kevetrin induced cell growth arrest and apoptosis in all cell lines and in primary cells, with TP53-mutant models displaying a higher sensitivity and p53 induction. Gene expression profiling revealed a common core transcriptional program altered by drug exposure and the downregulation of glycolysis, DNA repair and unfolded protein response signatures. These findings suggest that kevetrin may be a promising therapeutic option for patients with both wild-type and TP53-mutant AML.

overall_design: MOLM-13 and KASUMI-1 cell lines treated with Kevetrin (or vehicle) for 6h and 48h were used for RNA extraction and hybridization on microarrays.

first: Roberta

last: Napolitano

first: Serena

last: De Matteis

first: Giovanni

last: Martinelli


title: Single-cell transcriptomics of mouse kidney transplants reveals a potentially novel myeloid cell pathway for transplant rejection

status: Public on Sep 02 2020

city: Durham

first: Shyni

last: Varghese

state: NC

address: 203 Research Drive

department: Department of Biomedical Engineering

institute: Duke University

summary: We used a murine kidney transplantation model and single-cell transcriptomics to dissect the contribution of myeloid cell subsets and their potential signaling pathways to kidney transplant  rejection. Using a variety of bioinformatic techniques including  machine learning, we demonstrated that kidney allograft-infiltrating myeloid cells followed a trajectory of differentiating from monocytes to pro-inflammatory  macrophages, and exhibited distinct interactions with kidney allograft parenchymal cells. While this process correlated with a unique pattern of myeloid cell transcripts, a top gene identified was Axl, a member of the receptor tyrosine kinase familyTAM(Tyro3/Axl/Mertk).

overall_design: Kidneys from 6-7 weeks old  BALB/c (male  or  female) mice were transplanted into bilaterally nephrectomized B6 (WT or KO) male recipients. In some of the experiments, kidney allograft tolerance was induced in the recipients by infusions of donor apoptotic cells.

first: Naveen

last: Natesh

first: Anil

last: Dangi

first: Xunrong

last: Luo


title: Post-transcriptional regulation of human endogenous retroviruses by RNA-Binding Motif Protein 4, RBM4

first: Stefan

last: Muljo


title: Impact of metformin treatment on CD8 in non and BCG-vaccinated mice

city: Singapore

first: Nicholas

last: Ang

address: 8a Biomedical Grove, Singapore 138648

country: Singapore

institute: Singapore Immunology Network (SIgN)

summary: The aim is to identify important metabolic and immune signaling pathways in memory CD8 T cells regulated by metformin and understand its implications on BCG-vaccination

overall_design: CD8 T cells sorted via MACS from mouse spleen, followed by sorting of memory CD8 T cells via FACS

first: Josephine

last: Lum

first: Bernett

last: Lee

first: Amit

last: Singhal

first: Julia

last: Bӧhme

first: Srini

last: Nicholas


title: Maternal High Fat Diet and Diabetes Disrupts Transcriptomic Pathways that Regulate Cardiac Metabolism and Cell Fate in Newborn Rat Hearts

city: Sioux Falls

first: Randolph

last: Faustino

state: SD

address: 2301 East 60th Street North

department: Genetics and Genomics

institute: Sanford Research

summary:
Children born to diabetic and obese or overweight mothers have a higher risk of heart disease at birth and later in life. Our previous work using chromatin immunoprecipitation sequencing revealed that late-gestation diabetes in combination with maternal high fat diet causes a distinct fuel-mediated epigenetic reprogramming of cardiac tissue during fetal cardiogenesis.
We used gene expression profiling to investigate the overall transcriptional signature of newborn rat offspring exposed to the combination of maternal diabetes and maternal high fat diet.

overall_design: Newborn rats, at postnatal day 1, were selected from different exposure groups for RNA extraction and hybridization on Rat Gene 1.0 ST Whole-transcript Affymetrix microarrays. Transcriptional signature from hearts of diabetes exposed, high fat diet exposed, diabetes + high fat diet exposed and control newborn rats was compared for differential transcriptome expression.

first: Claudia

middle: C

last: Preston

first: Michelle

last: Baack


title: Arsenic-induced polyadenylation of canonical histone H3.1 mRNA displaces histone variant H3.3 from critical gene regulatory regions

city: Charlottesville

first: Zhenjia

last: Wang

state: VIRGINIA

address: 1300 Jefferson Park Avenue

department: Center for Public Health Genomics

institute: University of Virginia

summary: The replication-dependent canonical histone genes are the only genes found in multicellular organisms whose messenger RNA (mRNA) does not terminate with a poly(A) tail at the 3’ end. We previously demonstrated that arsenic exposure induces polyadenylation of canonical histone H3.1 mRNA in tissue culture system. We report that arsenic is capable of inducing high levels of H3.1 mRNA polyadenylation and marked loss of the Stem-loop binding protein (SLBP) in vivo, which is critical for canonical histone pre-mRNA processing. Ectopic expression of polyadenylated H3.1 mRNA enhances anchorage-independent cell growth and tumor formation in nude mice. Moreover, polyadenylation of H3.1 mRNA causes transcriptional deregulation, G2/M arrest, chromosome aneuploidy and aberration. Importantly, overexpression of H3.3 attenuates arsenic-induced cell transformation. Through ChIP-Seq and RNA-Seq, we try to decipher if polyadenylated H3.1 mRNA could result in depletion of histone variant H3.3 at critical gene regulatory regions. Our study uncovers polyadenylation of H3.1 and resulting displacement of variant H3.3 as a potential new mechanism for arsenic-induced carcinogenesis.

overall_design: BEAS-2B cells were stably transfected with pcDNA3.1-NT-Empty or pcDNA3.1-NT-H3.1poly(A) plasmid. Through RNA-Seq, it will reveal the role of polyadenylated H3.1 mRNA in different cellular pathways. For ChIP-Seq, BEAS-2B cells were stably transfected with pcDNA3.1-FLAG-H3.3, and then pcDNA3.1-NT-H3.1poly(A), to obtain BEAS-2B FLAG-H3.3 and BEAS-2B FLAG-H3.3&NT-H3.1poly(A) stable cell lines. Then use FLAG-ChIP to pull down H3.3 specific binding DNA for ChIP-Seq.

first: Danqi

last: Chen

first: Qiao

middle: Y

first: Chongzhi

last: Zang

first: Chunyuan

last: Jin

first: Max

last: Costa


title: Epigenomic and transcriptomic analysis of Systemic Sclerosis CD4+ T cells [Illumina]

first: Esteban

last: Ballestar

summary:
Epigenomic and transcriptomic analysis of Systemic Sclerosis CD4+ T cells reveals long range dysregulation of key inflammatory pathways mediated by disease-associated susceptibility loci range dysregulation of key inflammatory pathways mediated by disease-associated
System sclerosis (SSc) is a genetically complex autoimmune disease mediated by the interplay between genetic and epigenetic factors in a multitude of immune cells, with CD4+ T lymphocytes as one of the principle drivers of pathogenesis. In this study, we obtained DNA methylation and RNA expression profiles of CD4+ T cells from 48 SSc patients and 16 healthy controls. Consequently, we identified 9112 and 3929 differentially methylated CpGs positions (DMPs) and differentially expressed genes (DEGs) respectively. These DMPs and DEGs are enriched in functional categories related to inflammation and T cell biology. Furthermore, correlation analysis identified 17,500 possible DMP-DEG interaction pairs within a window of 5 Mb, and utilizing promoter capture Hi-C data, we confirmed 168 pairs of DMP-DEG physical interactions. Finally, utilizing SSc GWAS data, we identified three important SSc-associated susceptibility loci, CSK (rs1378942), IL12RB1 (rs2305743) and IKZF3-GSDMB (rs9303277), that physically interact with cg11062629-ULK3, cg10808810-JUND and cg19458020-CCR7 respectively. Overall, our study reveals a solid link between genetic, epigenetic and transcriptional deregulation in CD4+ T cells of SSc patients, providing further understanding to SSc pathogenesis.

overall_design: CD4+ T cells were isolated from peripheral blood of 48 SSc patients and 16 healthy donors by positive cell sorting. Bisulfite-converted DNA was hybridized on the Infinium MethylationEPIC BeadChip array (Illumina).

first: Tianlu

last: Li

first: Lourdes

last: Ortiz

first: Eduardo

last: Andrés-León

first: Laura

last: Ciudad

first: Biola

middle: M

last: Javierre

first: Elena

last: López-Isac

first: Alfredo

last: Guillén-Del-Castillo

first: Carmen

last: Simeón-Aznar

first: Javier

last: Martin


title: Transcriptome profiling of ovarian tissues from pigs with extreme phenotypes for reproductive efficiency during the luteal and follicular phases of the estrous cycle

city: Baoding

first: Huiyan

last: HU

address: Lekai South Street No. 2596

institute: Hebei Agricultural University

summary:
Purpose:The goal of this study was to enrich understanding of the reproductive difference
Methods:Multiparous Canadian Large White cyclic sows were divided into two parts: high (H; total number of piglets born > 15.73) and low (L; total number of piglets born < 11.11) fecundity. Eight sows with similar parity from each part were chosen (n=16). Ovarian tissues were obtained on the 14 day (day 1 = first day of estrus) after estrus as in the luteal phase (L) and 20 day of the estrous cycle as in the follicular phase (F). Transcriptome profiling of ovarian tissues were generated by deep sequencing, in quadruplicate, using Illumina HiSeq X10 instrument.
Results: Using an optimized data analysis workflow, we obtained the differentially expressed RNAs between the high and low fecundity, with a fold change ≥1.5 and p value < 0.05. These results provide further insight into fecundity in pigs.
Conclusions: Our study represents the first detailed analysis of ovary transcriptome. It will be significantly helpful to display a novel regulatory mechanism for further investigation of prolificacy in pigs.

overall_design: Eight sows with similar parity from high and low fecundity group were chosen, respectively. Ovarian tissues were obtained on the 14 day (day 1 = first day of estrus) after estrus as in the luteal phase (L) and 20 day of the estrous cycle as in the follicular phase (F). Transcriptome profiling of ovarian tissues were generated by deep sequencing, in quadruplicate, using Illumina HiSeq X10 instrument.

last: Hu

first: Qing

last: Jia


title: Profiling in ovarian tissues of pigs with extreme phenotypes for reproductive efficiency during the luteal and follicular phases of the estrous cycle

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

overall_design: Refer to individual Series


title: MicroRNA transcriptome profiling in ovarian tissues of pigs with extreme phenotypes for reproductive efficiency during the luteal and follicular phases of the estrous cycle

summary:
Purpose:The goal of this study was to enrich understanding of the reproductive difference
Methods: Multiparous Canadian Large White cyclic sows were divided into two parts: high (H; total number of piglets born > 15.73) and low (L; total number of piglets born < 11.11) fecundity. Eight sows with similar parity from each part were chosen (n=16). Ovarian tissues were obtained on the 14 day (day 1 = first day of estrus) after estrus as in the luteal phase (L) and 20 day of the estrous cycle as in the follicular phase (F). Transcriptome profiling of ovarian tissues were generated by deep sequencing, in quadruplicate, using Illumina HiSeq X10 instrument.
Results: Using an optimized data analysis workflow, we obtained the differentially expressed miRNAs between the high and low fecundity, with a fold change ≥1.5 and p value < 0.05. These results provide further insight into fecundity in pigs.
Conclusions: Our study represents the first detailed analysis of ovary transcriptome. It will be significantly helpful to display a novel regulatory mechanism for further investigation of prolificacy in pigs.


title: Disturbed mitochondrial dynamics in CD8+ TIL reinforce epigenetic programming linked with T cell exhaustion [RNA-Seq]

status: Public on Sep 01 2020

city: Vienna

first: Hana

last: Imrichova

address: Lazarettgasse 14, AKH BT 25.3

country: Austria

institute: CeMM, Vienna

summary: The metabolic challenges present in tumors attenuate the metabolic fitness and anti-tumor activity of tumor-infiltrating T lymphocytes (TILs). However, it remains unclear whether persistent metabolic insufficiency can imprint permanent T cell dysfunction. We found that TILs accumulating depolarized mitochondria as a result of declined mitophagy activity display functional, transcriptomic and epigenetic characteristics of terminally exhausted T cells. Mechanistically, declined mitochondrial fitness in TILs is induced by the coordination of T cell receptor stimulation, microenvironmental stressors and PD-1 signal. Forcing the accumulation of depolarized mitochondria with pharmacological interventions induces epigenetic reprogramming for terminal exhaustion, indicating that mitochondrial deregulation is indeed a cause – rather than a consequence – of T cell exhaustion. Furthermore, supplementation with nicotinamide riboside enhances T cell mitochondrial fitness and improved responsiveness to anti-PD-1 treatment. Together, our results reveal new insights on how mitochondrial dynamics and quality orchestrate T cell anti-tumor responses and commitment to the exhaustion program.

overall_design: Examination of gene expression in in vivo-generated T cells

first: Yi-Ru

last: Yu

first: Haiping

last: Wang

first: Ping-Chih

last: Ho


title: Ancestral function of  Inhibitors-of-kappaB regulates Caenorhabditis elegans development (RNA-Seq)

city: Barcelona

first: Yolanda

last: Guillén

address: Dr. Aiguader 88 Planta 2 IMIM

institute: IMIM

summary: NF-κB-mediated signaling is maintained silent by the action of IκB proteins, whose canonical role is to sequester NF-κB in the cytoplasm. An alternative chromatin role for IκB members have been shown to affect stemness and cell differentiation but the involvement of NF-κB in this function has not been excluded.  NFKI-1 and IKB-1 are IκB homologs  in Caenorhabditis elegans, which lacks NF-κB nuclear effectors. nfki-1 and ikb-1 mutants present developmental defects that phenocopy mutations in Polycomb genes and demethylases as utx-1. suggesting a role for C. elegans IKB proteins in chromatin regulation, which is supported by various lines of evidence:(i) we detected NFKI-1 in the nucleus; (ii) NFKI-1 and IKB-1 bind to histones and Polycomb proteins, (iii) NFKI-1 and IKB-1 bind to chromatin in vivo, and (iv) mutations in nfki-1 and ikb-1 alter chromatin marks . Thus, ancestral IκB inhibitors may exert  nuclear functions regulating of gene expression and development.

overall_design: To study the transcriptional alterations in nfki-1 and ikb-1 mutants during animal development, we performed RNA-seq at two different timepoints: L1 (5 hours fed and 3 hours starved at 25ºC after synchronization, 1 replicate per strain) and L4 (36 hours at 25ºC after synchronization, 2 replicates per strain) developmental stages. We used different mutant strains for nfki-1 and ikb-1 to avoid mutant-specific alterations. cer1 allele is a CRISPR-generated 368 bp deletion near nfki-1 exon 2. cer2 is a 434 bp deletion and 50 bp insertion at exon 2. Both modifications generate premature stop codons. cer9 allele is a 462 bp deletion that includes the ATG start codon of ikb-1. nr2027 is a 1911 bp deletion of ikb-1 that includes the ankyrin-repeat domains encoding sequence (Pujol et al., 2001). N2(Bristol) was used for all analyses as wildtype (WT) control. 50 bp single-end sequencing was done on an Illumina HiSeq 2000.

first: David

last: Brena

first: Montserrat

last: Porta-de-la-Riva

first: Joan

last: Bertran

first: Lluís

last: Espinosa

first: Julián

last: Cerón


title: Ancestral function of  Inhibitors-of-kappaB regulates Caenorhabditis elegans development


title: Ancestral function of  Inhibitors-of-kappaB regulates Caenorhabditis elegans development (ChIP-Seq)

overall_design: To study chromatin alterations in nfki-1(cer1) and ikb-1(nr2027) mutants, we performed ChIP-seq for H3K27me3 and H3K36me3 chromatin marks at L4 stage (36 hours at 25ºC after synchronization, from the same worm extracts used for RNA-seq). cer1 allele is a CRISPR-generated 368 bp deletion near nfki-1 exon 2. nr2027 is a 1911 bp deletion of ikb-1 that includes the ankyrin-repeat domains encoding sequence (Pujol et al., 2001). N2(Bristol) was used as a wildtype control.  To detect direct chromatin targets of nfki-1 and ikb-1, we performed ChIP-seq at L1 (5 hours fed 3 hours at 25ºC starved after synchronization) on the endogenous tagged strain CER425[ikb-1(syb267[ikb-1::mCherry])I;nfki-1(cer102[nfki-1::3xFLAG)])X], using 3 independent biological replicates per strain. 50 bp single-end sequencing was done on an Illumina HiSeq 2000.


title: Disturbed mitochondrial dynamics in CD8+ TIL reinforce epigenetic programming linked with T cell exhaustion

type: Methylation profiling by high throughput sequencing

overall_design: Examination of DNA methylation in in vivo-generated T cells.

first: Yi

first: Ping


overall_design: Examination of chromatin accessibility in in vitro and in vivo-generated T cells.


title: Epigenomic and transcriptomic analysis of Systemic Sclerosis CD4+ T cells [Affymetrix]

first: Esteban

last: Ballestar

summary:
Epigenomic and transcriptomic analysis of Systemic Sclerosis CD4+ T cells reveals long range dysregulation of key inflammatory pathways mediated by disease-associated susceptibility loci  range dysregulation of key inflammatory pathways mediated by disease-associated
System sclerosis (SSc) is a genetically complex autoimmune disease mediated by the interplay between genetic and epigenetic factors in a multitude of immune cells, with CD4+ T lymphocytes as one of the principle drivers of pathogenesis. In this study, we obtained DNA methylation and RNA expression profiles of CD4+ T cells from 48 SSc patients and 16 healthy controls. Consequently, we identified 9112 and 3929 differentially methylated CpGs positions (DMPs) and differentially expressed genes (DEGs) respectively. These DMPs and DEGs are enriched in functional categories related to inflammation and T cell biology. Furthermore, correlation analysis identified 17,500 possible DMP-DEG interaction pairs within a window of 5 Mb, and utilizing promoter capture Hi-C data, we confirmed 168 pairs of DMP-DEG physical interactions. Finally, utilizing SSc GWAS data, we identified three important SSc-associated susceptibility loci, CSK (rs1378942), IL12RB1 (rs2305743) and IKZF3-GSDMB (rs9303277), that physically interact with cg11062629-ULK3, cg10808810-JUND and cg19458020-CCR7 respectively. Overall, our study reveals a solid link between genetic, epigenetic and transcriptional deregulation in CD4+ T cells of SSc patients, providing further understanding to SSc pathogenesis.

overall_design: CD4+ T cells were isolated from peripheral blood of 48 SSc patients and 16 healthy donors by positive cell sorting.

first: Tianlu

last: Li

first: Lourdes

last: Ortiz

first: Eduardo

last: Andrés-León

first: Laura

last: Ciudad

first: Biola

last: Javierre

first: Elena

last: López-Isac

first: Alfredo


title: IER5 is required for Notch-mediated induction of squamous cell differentiation [ChIP-seq RBPJ & MAML1]

status: Public on Aug 31 2020

city: Boston

first: Li

last: Pan

address: 77 Ave Louis Pasteur

department: Pathology

institute: Brigham and Women's Hospital

summary: Conditional activation of Notch in squamous cells activates a context-specific gene  expression program through lineage-specific regulatory elements. IER5 is a direct Notch-regulated gene and required for  Notch-induced differentiation of squamous carcinoma cells.

overall_design: To create a squamous cell carcinoma (SCC) model in which GSI (ɣ-secretase inhibitor) washout activates NOTCH1,  we engineered a cDNA encoding a mutated truncated form of NOTCH1, ΔEGF-L1596H, that  cannot respond to ligand and that has a point substitution in its negative regulatory region that  produces ligand-independent, ɣ-secretase-dependent Notch activation. ΔEGF-L1596H was transduced into human SCC cell line IC8 that have biallelic inactivating mutation in NOTCH1. GSI washout was performed for 4 hours to activate the Notch signaling pathway in IC8-ΔEGF-L1596H cells.

first: Madeleine

last: Lemieux

first: Jon

last: Aster


title: Florigen family chromatin recruitment, competition and targets

city: Philadelphia

first: Doris

last: Wagner

address: 103G Carolyn Lynch Laboratory

department: Department of Biology

institute: University of Pennsylvania


title: IER5 is required for Notch-mediated induction of squamous cell differentiation


title: IER5 is required for Notch-mediated induction of squamous cell differentiation [H3K27ac ChIP-seq]

overall_design: To create a squamous cell carcinoma (SCC) model in which GSI (ɣ-secretase inhibitor) washout activates NOTCH1,  we engineered a cDNA encoding a mutated truncated form of NOTCH1, ΔEGF-L1596H, that  cannot respond to ligand and that has a point substitution in its negative regulatory region that  produces ligand-independent, ɣ-secretase-dependent Notch activation. ΔEGF-L1596H was transduced into human SCC cell line IC8 that have biallelic inactivating mutation in NOTCH1. GSI washout was performed for 1,2 and 4 hours to activate the Notch signaling pathway in IC8-ΔEGF-L1596H cells.


title: IER5 is required for Notch-mediated induction of squamous cell differentiation [RNA-seq]

overall_design: To create a squamous cell carcinoma (SCC) model in which GSI (ɣ-secretase inhibitor) washout activates NOTCH1,  we engineered a cDNA encoding a mutated truncated form of NOTCH1, ΔEGF-L1596H, that  cannot respond to ligand and that has a point substitution in its negative regulatory region that  produces ligand-independent, ɣ-secretase-dependent Notch activation. ΔEGF-L1596H was transduced into human SCC cell line IC8 that have biallelic inactivating mutation in NOTCH1. SC2 cells were isolated as a single clone from IC8/ΔEGF-L1596H cells. GSI washout was performed for 4, 24 and 72 hours with SC2, I5 (SC2 cells with IER5 deleted) and I5/IER5 (I5 cells with IER5 addback) cells. Biological triplicates were analyzed for each of 12 conditions. Two runs for all 36 RNA-seq library samples


title: Escherichia coli transcriptome reorganization caused by nutritional changes

city: Tsukuba

first: Bei-Wen

last: Ying

state: Ibaraki

address: 1-1-1 Tennoudai

country: Japan

institute: University of Tsukuba

summary: Escherichia coli K-12 BW25113 were cultured in the LB and M63 media. Exponetially growing populations  were collected for RNAseq. The culture medium-induced transcriptional changes were analyzed.

overall_design: Whole mRNA sequencing of E.coli strain BW25113 growing under the LB and M63 media, respectively.

first: Masaomi

last: Kurokawa


title: Matrix rigidity and cardiac reprogramming

status: Public on Aug 28 2020

city: Tokyo

first: Shota

last: Kurotsu

address: 35 Shinanomachi, Shinjuku-ku

department: Department of Cardiology

institute: Keio University School of Medicine

summary: Direct cardiac reprogramming from fibroblasts holds great potential for disease modeling, drug screening, and regeneration. However, cardiac reprogramming remains inefficient in vitro, and induced cardiomyocytes (iCMs) generated in vitro are less mature than those in vivo, suggesting undefined biophysical factors may inhibit cardiac reprogramming. Previous studies mainly used conventional polystyrene dishes, and thus the effect of matrix rigidity on cardiac reprogramming remains unclear. Here, we developed a Matrigel-based hydrogel culture system to determine the effect of matrix rigidity and mechanotransduction on cardiac reprogramming. We found that soft matrix rigidity comparable to myocardium greatly enhanced cardiac reprogramming in combination with Gata4, Hand2, Mef2c, and Tbx5. Mechanistically, soft matrix enhanced cardiac reprogramming via inhibition of Rho/ROCK, actomyosin, and YAP/TAZ pathway, and suppression of fibroblast program, which were activated on rigid substrate. Intriguingly, inhibition of YAP/TAZ further suppressed integrin-mediated signaling to create a positive feedback loop for robust reprogramming. Thus, mechanotransduction may represent a new target for cardiac reprogramming.

overall_design: To identify the effect of ECM stiffness on cardiac reprogramming, we compared the global gene expression patterns of retroviral GHMT-transduced fibroblasts on 8 kPa (similar to native myocardium) and 126 kPa (similar to collagenous bone) hydrogels. RNA was extracted 2 weeks after transduction. Arrays were performed using Clariom S Mouse Arrays. Microarray analyses were performed in duplicate, using independent biological samples.

first: Masaki

last: Ieda


title: Functional evidence that Activin/Nodal signaling is required for establishing the dorsal-ventral axis in the annelid Capitella teleta

city: Saint Augustine

first: Elaine

last: Seaver

state: Florida

address: 9505 Ocean Shore Blvd.

department: Whitney Laboratory for Marine Bioscience

institute: University of Florida

summary: Transcript abundances were examined in single Capitella teleta embryos at three timepoints: 8-cell, 16-cell, and 32-cell stage.

overall_design: 12 whole embryos were sequenced individually using CEL-Seq (https://github.com/yanailab/CEL-Seq-pipeline commit version fecc97e ) . There were 4 replicates of 8-cell stage embryos, 3 replicates of 16-cell stage embryos, and 5 replicated of 32-cell stage embryos.

first: Alexis

last: Lanza

first: Itai

last: Yanai

first: Tamar

last: Hashimshony


title: Differential effects of voclosporin and tacrolimus on insulin secretion from human islets

status: Public on Aug 27 2020

city: Vancouver

first: James

last: Johnson

state: BC

address: 2350 Health Sciences Mall

department: Cellular and Physiological Sciences

institute: University of British Columbia

summary: The incidence of new onset diabetes after transplant (NODAT) has increased over the past decade, likely due to calcineurin inhibitor-based immunosuppressants, including tacrolimus (TAC) and cyclosporin (CsA). Voclosporin (VCS), a next generation calcineurin inhibitor is reported to cause fewer incidences of NODAT but the reason is unclear. Whilst calcineurin signaling plays important roles in pancreatic beta-cell survival, proliferation, and function, its effects on human beta-cells remain understudied. In particular, we do not understand why some calcineurin inhibitors have more profound effects on the incidence of NODAT. Here, we compared the the effects of TAC and VCS on the transcriptomic profile of human islets.

overall_design: There are 3 conditions. Groups of 200 islets from 7 independent donors were treated for 48 hours with vehicle (DMSO), TAC (30 ng/ml) or VCS (60 ng/ml) then immediately flash-frozen in liquid nitrogen and stored at -80°C until RNA isolation and sequencing was performed.

first: Jelena

last: Kolic


title: Loss of G protein pathway suppressor 2 in human adipocytes triggers lipid remodeling through upregulation of ATP binding cassette subfamily G member 1

city: Huddinge

first: Serena

last: Barilla

state: Huddinge

address: Hälsovägen 7C

country: Sweden

institute: Karolinska Institutet

summary: Here we demonstrate that the loss of GPS2 triggers the reprogramming of cellular processes related to adipocyte differentiation by increasing the responses to the adipogenic cocktail. Moreover, GPS2-depleted human adipocytes are characterized by hypertrophy, triglyceride and phospholipid accumulation, and sphingomyelin depletion. These changes are likely a consequence of the increased expression of ATP-Binding cassette subfamily G member 1 (ABCG1) that mediates sphingomyelin efflux from adipocytes and modulates lipoprotein lipase (LPL) activity. We identify ABCG1 as a direct transcriptional target, as GPS2 depletion leads to coordinated changes of transcription and H3K27 acetylation at promoter and enhancers which are occupied by GPS2 in wild-type adipocytes. Finally, we find that in omental adipose tissue of obese humans GPS2 levels correlate with ABCG1 levels, type 2 diabetic status, and lipid metabolic status.

overall_design: Transcriptome signature of GPS2-regulated genes between shGFP and shGPS2 during adipognesis was assessed through RNAseq analysis. Epigenomic status of shGFP and shGPS2 preadipocytes and adipocytes was analyzed using histone marker H3K27ac ChIPseq. GPS2 cistrome was analyzed in hMADS cells at day 0 and day 14 of differentiation. Transcriptome signature of non-diabetic and diabetic obese patients was assessed through RNAseq.

first: Ning

last: Liang

first: Nicolas

last: Venteclef

first: Eckardt

last: Treuter


title: Gata3 controls stem/progenitor maintenance potential in prostate organoids

city: Montreal

first: mathieu

last: tremblay

state: QC

address: 2950 Chemin de Polytechnique, pav marcelle-coutu 1432

institute: Université de Montréal/IRIC

summary: The adult stem/progenitor cell maintenance in the prostate is regulated by a balance between BMP5 self-renewal signal and GATA3 dampening activity. Here we report that the transcription factor GATA3 controls basal stem/progenitor cell maintenance in the prostate by directly controling the expression of BMP5, a key effector of this activity.

overall_design: Wild type and PbCreGata3f/f prostate organoids were harvested at day 4 after 0, 2, 3 and 4 passages. Gene expression profiles were compared to identify candidate genes that lead to the amplification of the stem cell pool upon Gata3 inactivation in basal stem/progenitor cells from 8 week old adult mice.

first: Mathieu

last: Tremblay

first: Maxwell

last: Shafer

first: Maxime

last: Bouchard


title: MYB30 orchestras ROS wave-triggered systemic transcriptomic responses and plant acclimation in Arabidopsis

city: Memphis

first: Soham

last: Sengupta

state: TN

address: 262 Danny Thomas Place

institute: St. Jude Children's Research Hospital

summary: MYB30 was found to regulate reactive oxygen species (ROS) - mediated systemic transcriptomics responses to light stress in Arabidopsis

overall_design: 48 samples were analyzed; included two genotypes (Col-0 and myb30 knockout); 4 time points (0,2,8,30min); local and systemic leaves; 3 repeats composed from 20 plants for each genotype in each time point; Col-0 and 0min were control/refernce samples

first: Yosef

last: Fichman

first: Sara

middle: I

last: Zandalinas

first: David

last: Burks

first: Ronald

last: Myers

first: Rajeev

last: Azad

first: Ron

last: Mittler


title: Histone H3.3 fills gaps in heterochromatin generated by Smarcad1 in mouse embryonic stem cells (ESC)

city: Solna

first: Simon

last: Elsässer

address: Tomtebodavägen 23A

department: Medical Biochemistry and Biophysics

summary: Nucleosome turnover concomitant with incorporation of the replication-independent histone variant H3.3 is a hallmark of regulatory regions in the animal genome. In our current understanding, nucleosome turnover is universally linked to DNA accessibility and histone acetylation. In mouse embryonic stem cells, H3.3 is also highly enriched at interstitial heterochromatin, most prominently intracisternal-A particle endogenous retroviral elements. Interstitial heterochromatin is established over confined domains by the TRIM28/SETDB1 corepressor complex and has stereotypical features of repressive chromatin, such as H3K9me3 and recruitment of all HP1 isoforms. Here, we demonstrate that fast histone turnover and H3.3 incorporation is compatible with these hallmarks of heterochromatin. We identify Smarcad1 to be a chromatin remodeler that generates nucleosome-free regions which are subsequently filled with histone H3.3, generating a surprisingly dynamic heterochromatin state. Loss of histone H3.3 elicits a highly specific opening of interstitial heterochromatin demonstrating that in the wake of Smarcad1 remodeling, H3.3 is required to maintain minimal DNA accessibility by reassembling nucleosomes.

overall_design: Chromatin accessibility was assessed using Omni-ATAC (Corces et al. 2017). Wildtype and H3.3 knockout (H3.3KO) cell lines were compared to following rescue cell lines: H3.3 (H3.3KO+H3.3), H3.2 (H3.3KO+H3.2) or H3.3 L126A I130A (H3.3KO+H3.3LI->AA). Further, Smarcad1 or ATRX was knocked down using RNAi. ATAC-Seq experiments were performed in two batches as indicated. Histone H3.3 and H3K9me3 occupancy was assessed using a crosslinking ChIP-Seq protocol described below.

first: Jing

last: Lyu

first: Anna-Maria

last: Katsori

first: Rozina

last: Caridha

first: Carmen

last: Navarro


title: Synergism of chemotherapy and PD-1 immune checkpoint blockade in the PyMT mammary carcinoma mouse model

city: Frankfurt

first: Andreas

last: Weigert

address: Theodor-Sern-Kai 7

department: Medicine

country: Germany

institute: Goethe-University

summary: We studied the impact of a combination of chemotherapy and PD-1 immune checkpoint blockade on tumor progression in the PyMT mammary carcinoma mouse model compared to each treatment as monotherapy. To gain insight into the reasons underlying improved efficacy of combined chemoimmunotherapy, whole transcriptome profiling of tumors of mice receiving either a control antibody, anti-PD-1 antibody, doxorubicin chemotherapy + a control antibody or doxorubicin chemotherapy + anti-PD-1 antibody was performed via next generation mRNA sequencing, in triplicates, on a NextSeq 550 high-throughput bench top sequencer.

overall_design: Tumor mRNA profiles of mice bearing polyoma middle T oncogene (PyMT)-induced tumors were generated after treatment with chemotherapy, PD-1 immunotherapy or both for 5 weeks in triplicates.

first: Evelyn

last: Sirait-Fischer


title: Whole-genome analysis of noncoding genetic variations identifies multigranular regulatory element perturbations associated with Hirschsprung disease

status: Public on Aug 30 2020

city: Hong Kong

first: Elly

middle: Sau-Wai

last: NGAN

address: 2/F, Professorial Block  Queen Mary Hospital  102 Pokfulam Road  Hong Kong SAR, China

department: Department of Surgery, Li Ka Shing Faculty of Medicine

country: Hong Kong

institute: The University of Hong Kong

summary: It is widely recognized that the missing heritability of many human diseases is partially due to noncoding genetic variants, but there are multiple challenges that hinder the identification of functional disease-associated noncoding variants. The number of noncoding variants can be many times of coding variants; many of them are not functional but in linkage disequilibrium with the functional ones; different variants can have epistatic effects; different variants can affect the same genes or pathways in different individuals, and some variants are related to each other not by affecting the same gene but by affecting the binding of the same upstream regulator. To overcome these difficulties, we propose a novel analysis framework that considers convergent impacts of different genetic variants on protein binding, which provides multi-granular information about disease-associated perturbations of regulatory elements, genes, and pathways. Applying it to our whole-genome sequencing data of 918 short-segment Hirschsprung disease patients and matched controls, we identify various novel genes not detected by standard single-variant and region-based tests, functionally centering on neural crest migration and development. Our framework also identifies upstream regulators whose binding is influenced by the noncoding variants. Using human neural crest cells, we confirm cell-stage-specific regulatory roles three top novel regulatory elements on our list, respectively in the RET, RASGEF1A and PIK3C2B loci. In the PIK3C2B regulatory element, we further show that a noncoding variant found only in the affects the binding of the gliogenesis regulator NFIA, with a corresponding down-regulation of multiple genes in the same topologically associating domain.

overall_design: Examination of H3K4me1, H3K27ac and chromatin accessibility in human induced pluripotent stem cells (hPSC) and neural crest cells (hNC)

first: Alexander

middle: X

last: Fu

first: Kathy

middle: N

last: Lui

first: Clara

middle: S

last: Tang

first: Ray

last: Ng

first: Frank

last: Lai

first: Sin-Ting

last: Lau

first: Zhixin

last: Li

first: Maria-Mercè

last: Gracia-Barcelo

first: Pak-Chung

last: Sham

first: Paul

last: Tam

last: Ngan

first: Kevin

last: Yip


title: RNA-Seq analysis of galaninergic neurons from ventrolateral preoptic nuleus identifies expression changes between sleep and wake

first: Allan

last: Pack

address: 125 South 31st St

summary: Galanin neurons at ventrolateral preoptic nuleus (VLPO) have been hypothesized to be sleep-active neurons. With the use of laser capture microdissection (LCM), we specifically isolated single galanin neurons, and our goal was to assess expression changes in VLPO galanin cells between sleeping mice and mice kept awake using gentle handling.

overall_design: Tg(Gal-EGFP)HX109Gsat mice that express eGFP under the control of galanin promoter was used for LCM isolation of galanin-expressing neurons in VLPO. Fifty-four mice were separated into 9 groups (up to n=6 per condition) corresponding to baseline (Z0; lights-on), sleep(SS) or sleep deprivation (SD) for 3, 6, 9, and 12 hours.

first: Xiaofeng

last: Guo

first: Brendan

middle: T

last: Keenan

first: Dimitra

last: Sarantopoulou

first: Xiaoling

last: Gao

first: Jingxu

last: Zhu

first: Gregory

last: Grant


title: Whole Tissue Transcriptome of HS Lesional, HS Nonlesional, and Healthy Skin

city: San Francisco

first: Margaret

last: Lowe

state: CA

address: 513 Parnassus Avenue, HSW1201B

institute: UCSF

summary: NOT PROVIDED; REQUESTED

overall_design: The whole tissue transcriptome of lesional and nonlesional skin of donors with HS prior to initiation on anti-TNF therapy (PRE), while on anti-TNF therapy (ON), or of donors who did not have disease severe enough for anti-TNF therapy (TxNaive) was compared to healthy skin

first: Michael

middle: D

last: Rosenblum


title: PPP2R2D suppresses interleukin-2 production and regulatory T cell function

first: George

middle: C.

last: Tsokos

state: MA

address: CLS-928, 3 Blackfan Circle

institute: Beth Israel Deaconess Medical Center, Harvard Medical School

summary: Upon ATAC-seq, we found that lack of PPP2R2D expression in Tconv cells boosts chromatin opening of a large number of genes, while in Treg cells chromatin remodeling is limited. These findings demonstrate that PPP2R2D is more important in the direct regulation of Tconv cell function (IL-2 production) rather than Treg cell function.

overall_design: Examination of chromatin accessibility in 2 cell types

first: Wenliang

last: Pan


title: SOX1 Determines the Regional Identity of Neural Progenitors Differentiated from Human Embryonic Stem Cells

status: Public on Aug 26 2020

city: Stanford

first: Zhuoqing

last: Fang

state: California

address: 300 Pasteur Drive

institute: Stanford

summary: During human embryogenesis, primitive neural cells start to be generated at the time of gastrulation and gradually acquire regional identities, which is a process called neural patterning. But how intrinsic factors respond to exogenous patterning signals remains poorly understood. Human Embryonic Stem Cells (hESCs) provide a great model to recapitulate this process. Through exogenous manipulation of canonical WNT signaling activation during neural differentiation, dose-dependent specification of regionally defined neural progenitors ranging from the telencephalic forebrain to posterior hindbrain could be rapidly and efficiently induced. Unexpectedly, we find that SOX1, generally referred as a pan-neural gene, displays a regional specific distribution in the human neural patterning process. To investigate the expression and function of SOX1 efficiently, we have generated the SOX1-EGFP reporter and SOX1-knockout (KO) hESC lines using the CRISPR/Cas9 system. SOX1 is initially expressed across the mes–met border and peaked in the metencephalon region at the early regional specification stage. Its depletion leads to the posterior shift of the mes–met border. Therefore, SOX1 is required to define the border at a correct region. In-depth analysis of SOX1 ChIP-sequencing and transcriptome data will provide more insights into how SOX1 determines the mes-met border formation and identify the downstream targets of SOX1. This study identifies SOX1 as one of the intrinsic factors key for the prepattern establishment in the developing central nervous system, particularly for defining the isthmus position.

overall_design: To analysis the function of SOX1 in early neural differentiation, we compared the gene expression profiles between wild type and SOX1-/- cells at 3 time points (Day 0, 4, 8) during neural differentiation by mRNA sequencing.

first: Xinyuan

last: Liu

first: Ying

last: Jin


title: Transcriptome sequencing data of goat submandibular glands at different ages

city: Tai’an

first: Chao

last: Tianle

state: Shandong

address: Daizong street, no. 61, 6/5000 Shandong Agricultural University

institute: 6/5000 Shandong Agricultural University

summary: 9 submandibular gland tissue samples were collected from goats in 1-month-old, 12-month-old and 24-month-old groups (3 samples from each group), and high-throughput transcriptome sequencing was conducted on these samples.

overall_design: Goats were separated into 3 different age groups: 1-month-old, 12-month-old and 24-month-old. Three healthy female goats (Lubo goats) from each group (total, 9 goats) were selected as experimental animals. The animals were obtained from Shandong Fengxiang Animal Husbandry and Seed Industry Technology Co., Ltd. (Laiwu District, Jinan, Shandong Province, China). All goats were raised under the same conditions, including natural lighting and free access to food. And high-throughput transcriptome sequencing was conducted on these samples.

first: Wang

last: Aili


title: AP-1 and TGFb-dependent transcriptomic changes in resistant basal cell carcinoma cell line

status: Public on Aug 25 2020

first: Anthony

last: Oro

address: 269 Campus Drvie

department: Dermatology

institute: Stanford University

summary: Tumor heterogeneity and lack of knowledge about resistant cell states remain a significant barrier to effective targeted cancer therapies. Basal cell carcinomas (BCCs) uniformly depend on Hedgehog (Hh)/Gli signaling for cell growth. We previously identified a nuclear myocardin-related transcription factor (nMRTF) resistance pathway that amplifies Gli1 activity, but nMRTF cell state and key factors driving its accumulation remain unknown. We have determined that AP-1 and TGFb transcription factor activity is essential to maintain MRTF activation. Here, we treat a murine BCC cell line with small molecule AP-1 and ALK5 inhibitors and analyze transcriptomic profiles.

overall_design: ASZ001 cells were plated and serum-starved and treated with 20 uM of AP-1 inhibitor T-5224 or 10 uM of ALK5 inhibitor SB431542 for 24 hours, then processed for ATAC-seq. Two or three biological replicates were sequenced per treatment group.

first: Catherine

last: Yao

first: Sadhana

last: Gaddam


title: Detection of early stage pancreatic cancer using 5-hydroxymethylcytosine signatures in circulating cell free DNA

city: San Diego

first: Samuel

last: Levy

address: 10578 Science Center Drive, Suite 210

institute: Bluestar Genomics

summary: Pancreatic cancers are typically diagnosed at late stage where disease prognosis is poor as exemplified by a 5-year survival rate of 10%. Earlier diagnosis would be beneficial by enabling surgical resection or earlier application of therapeutic regimens.  We investigated non-invasive detection of pancreatic ductal adenocarcinoma (PDAC) by interrogating changes in 5-hydroxymethylation cytosines (5hmC) of circulating cell free DNA in the plasma of a PDAC cohort (n=64) in comparison with a non-cancer cohort (n=243). 5hmC density is reduced in promoters and enhancers, whereas it is increased over 3’UTR, intron and TTS regions in PDAC compared to non-cancer cfDNA. Differential hydromethylation is rampant and found in thousands of genes. Stringent filtering by significance reveals genes related to pancreas function or development (GATA4, GATA6, PROX1, ONECUT1, MEIS2), and/or cancer pathogenesis (YAP1, TEAD1, PROX1, ONECUT1, ONECUT2 and IGF1). Furthermore, we observe enrichment for genes that are de-regulated upon activation of KRAS and inactivation of TP53, both of which are commonly observed in PDAC tumors. Regularized regression models, built using 5hmC densities in genes with the most variable 5hmC counts, performed with AUC of 0.92 on discovery dataset and 0.92-0.94 on two independent test sets. Furthermore, investigation of 5hmC occupancy in PDAC tumor tissue revealed that tissue-derived features can be used to accurately classify PDAC cfDNA (AUC=0.88). These findings suggest that 5hmC changes, at least partially derived from tumor tissue, enable classification of PDAC patients with high fidelity and are worth further investigation on larger cohorts of patient samples.

overall_design:
Examination of the 5-hydroxymethyl cytosine (5-hmC) profiles from cell-free DNA from pancreatic adenocarcinoma in comparison to non-cancer patients. Inclusion of PDAC tumor samples and normal pancreas tissue 5-hmC profiles and ChIP-seq.

**Submitter declares that raw data are not provided for this submission due to patient privacy concerns. Fastq files can be made available upon written request for submission to the study institutional review board for approval.**

first: Gulfem

last: Guler


title: AP-1 dependent changes in chromatin accessibility in resistant basal cell carcinoma cell line

summary: Tumor heterogeneity and lack of knowledge about resistant cell states remain a significant barrier to effective targeted cancer therapies. Basal cell carcinomas (BCCs) uniformly depend on Hedgehog (Hh)/Gli signaling for cell growth. We previously identified a nuclear myocardin-related transcription factor (nMRTF) resistance pathway that amplifies Gli1 activity, but nMRTF cell state and key factors driving its accumulation remain unknown. We have determined that AP-1 transcription factor activity is essential to maintain MRTF activation. Here, we treat a murine BCC cell line with small molecule AP-1 inhibitor and analyze chromatin accessibility profiles.

overall_design: ASZ001 cells were plated and serum-starved with or without 20 uM of AP-1 inhibitor T-5224 for 24 hours, then processed for ATAC-seq. Two biological replicates were sequenced per treatment group.


title: Genome-wide transcriptomic analysis of MRTF-active subpopulations in naïve human basal cell carcinoma

summary: Tumor heterogeneity and lack of knowledge about resistant cell states remain a significant barrier to effective targeted cancer therapies. Basal cell carcinomas (BCCs) uniformly depend on Hedgehog (Hh)/Gli signaling for cell growth. We previously identified a nuclear myocardin-related transcription factor (nMRTF) resistance pathway that amplifies Gli1 activity, but nMRTF cell state and key factors driving its accumulation remain unknown. Here, we use three surface markers (LYPD3, TACSTD2, and LY6D) to isolate the nMRTF subpopulation and analyze transcriptomic profiles.

overall_design: naïve human BCC tumors were processed into single-cell suspension and FACS sorted based on ItgA6, LYPD3, TACSTD2, and LY6D expression levels. Two tumors from different patients were sorted into surface marker positive and surface marker negative groups, with two biological replicates per group.


title: Effects of glucose exposures on gene expressions in HepG2 cells

city: RTP

first: NIEHS

last: Microarray Core

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

summary: SULT1E1, the enzyme that specifically and effectively sulfates estrogens to its inactive forms-sulfated estrogens has been found to be highly induced in high glucose (450 mg/dL) cultured human liver hepatocellular carcinoma HepG2 cells. To confirm the SULT1E1 transcription in response to glucose exposures and to investigate whether glucose signal may alter the other xenobiotic metabolizing enzyme transcripts in HepG2 cells, we have conducted whole genome microarray expression profiling as a platform to identify genes that may response to glucose exposures. HepG2 cells were exposed to low glucose (40 mg/dL) or high glucose (450 mg/dL) DMEM for 48 hours respectively. The xenobiotic metabolic enzyme transcripts such as SULTs, CYPs, UGTs and GSTs were significantly altered in response to glucose exposures.

overall_design: Glucose responsive gene expression in HepG2 cells was measured after exposure to low glucose (40 mg/dL) and high glucose (450 mg/dL) conditons for 48 hours. 4 replicates were preformed for each experiment.

first: Hao

last: Hu

first: Masahiko

last: Negishi


title: AP-1 and TGFb cooperativity drives non-canonical Hedgehog signaling in resistant basal cell carcinoma

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: Role of circulating microRNAs in patients with dengue infection

city: Faridabad

first: Abhay

middle: Deep

last: Pandey

address: 3rd Milestone, Faridabad-Gurgaon Expressway

department: Virology

country: India

institute: Regional Centre for Biotechnology

summary: miRNAs are found to be extremely stable in extracellular fluids of mammals, such as blood plasma, serum, etc. The expression profiles of these circulating miRNAs have immense potential for use as novel minimally invasive markers in monitoring Dengue diseases progression.

overall_design:
Here Using high-throughput small RNA sequencing methods followed by in silico analysis, the levels of circulating miRNAs analysed between patients with uncomplicated dengue infection (DI, n=9), Dengue with a warning sign (DWS, n=14), and severe dengue (DS, n=16). We also used plasma from nine dengue patients followed–up at two-time points (Day ’0’ and Day ’5”) for small RNA sequencing.

The total_miRNA_count_low2up.txt (containing normalized miRNAs counts) is a follow-up study, comparing Dengue severe samples with 5 days followup.
The total_miRNA_count_up2low.txt (containing normalized miRNAs counts) is a follow-up study two, comparing Dengue infection samples with 5 days followup.

first: Arup

last: Banerjee

first: Sudhanshu

last: Vrati

first: V

middle: G

last: Ramachandran

first: Bhaswati

last: Bandyopadhyay


title: Analysis of AP-1 regulation on Smad3 genome-wide DNA binding sites in resistant basal cell carcinoma

country: USA

summary: Tumor heterogeneity and lack of knowledge about resistant cell states remain a significant barrier to effective targeted cancer therapies. Basal cell carcinomas (BCCs) uniformly depend on Hedgehog (Hh)/Gli signaling for cell growth. We previously identified a nuclear myocardin-related transcription factor (nMRTF) resistance pathway that amplifies Gli1 activity, but nMRTF cell state and key factors driving its accumulation remain unknown. Epigenetic analysis of isolated nMRTF human tumor subpopulations demonstrates that cooperative AP-1 and TGFß signaling drive nMRTF activation. In this study, we find that AP-1 signaling drives changes in chromatin accessibility leading to differential Smad3 DNA binding and a transcriptional program of upstream activators of Rho, including RhoGEFs, that facilitate nMRTF activity.

overall_design: Chromatin immunoprecipitation was performed on murine resistant BCC cell line ASZ001 that were serum starved and treated with 20 uM AP-1 inhibitor T-5224 or 5 ng/ml TGFB3 ligand for 24 hours. 50 million cells were used per replicate. Briefly, cells were fixed with 1% formaldehyde, lysed in modified RIPA buffer, then sonicated using Covaris B208 ultrasonicator. Immunoprecipitation was performed with anti-phospho-Smad2/3 antibody (abcam 52903). Biological duplicate ChIP-seq libraries were generated using the standard protocol for the NEBNext Ultra II DNA Library Prep Kit for Illumina, then sequenced on the Illumina Nextseq (400M) platform. Pre-immunoprecipitation total extract DNA was sequenced as input.


title: Genome-wide chromatin accessibility analysis of MRTF-active subpopulations in human basal cell carcinoma

summary: Tumor heterogeneity and lack of knowledge about resistant cell states remain a significant barrier to effective targeted cancer therapies. Basal cell carcinomas (BCCs) uniformly depend on Hedgehog (Hh)/Gli signaling for cell growth. We previously identified a nuclear myocardin-related transcription factor (nMRTF) resistance pathway that amplifies Gli1 activity, but nMRTF cell state and key factors driving its accumulation remain unknown. Here, we use three surface markers (LYPD3, TACSTD2, and LY6D) to isolate the nMRTF subpopulation and analyze chromatin accessibility profiles.

overall_design: naive human BCC tumors were processed into single-cell suspension and FACS sorted based on ItgA6, LYPD3, TACSTD2, and LY6D expression levels. Two tumors from different patients were sorted into surface marker positive and surface marker negative groups, with two biological replicates per group. One BCC tumor from a patient with Gorlin syndrome was split into two biological replicates and sorted based on ItgA6 expression only.


title: Genome wide map of SOX1 occupancy in human embryonic stem cell derived neural progenitors

first: Zhuoqing

last: Fang

summary: To understand how SOX1's binding profile in neural progenitor with different regional identities, we differentiated hESC into neural progenitors with rostral and caudal identies throught modulating Wnt signaling pathway. We collected cells at neural differentiation day 4 and 8, and performed SOX1 ChIP-seq to investigate SOX1's genome wide binding profiles. These results provide important information for the mechanism underlying SOX1's functions in early regionalization.

overall_design: Examination of genome wide binding profile of SOX1 in human embryonic stem cell derived neural progenitors.

first: Xinyuan

last: Liu


title: A single metabolite which modulates lipid  metabolism alters hematopoietic stem/progenitor  cell behavior and promotes lymphoid reconstitution

city: Lausanne

first: Sylvain

last: Pradervand

address: Genopode

department: CIG

country: Switzerland

institute: UNI Lausanne

summary: Fatty acid beta-oxidation (FAO), the breakdown of lipids, is a metabolic pathway used by various stem cells. FAO levels are generally high during quiescence and downregulated with proliferation. The endogenous metabolite malonyl-CoA modulates lipid metabolism as a reversible FAO inhibitor and as a substrate for de novo lipogenesis. Here we assessed whether malonyl-CoA can be exploited to steer the behavior of hematopoietic stem/progenitor cells (HSPCs), quiescent stem cells of clinical relevance. Treatment of mouse HSPCs in vitro with malonyl-CoA increases HSPC numbers compared to non-treated controls and ameliorates blood reconstitution capacity when transplanted in vivo, mainly through enhanced lymphoid reconstitution. Similarly, human HSPC numbers also increase upon malonyl-CoA treatment in vitro. These data corroborate that lipid metabolism can be targeted to direct cell fate and stem cell proliferation. Physiological modulation of metabolic pathways, rather than genetic or pharmacological inhibition, provides unique perspectives for stem cell manipulations in health and disease.

overall_design: Four biological replicates of malonyl-CoA treated and control mouse HSPCs cells

first: Sonja

last: Giger

first: Larisa

last: Kovtonyuk

first: Sebastian

last: Utz

first: Mergim

last: Ramosaj

first: Werner

middle: J

last: Kovacs

first: Emanuel

last: Schmid

first: Vassilios

last: Ioannidis

first: Melanie

last: Greter

first: Markus

last: Manz

first: Matthias

middle: P

last: Lutolf

last: Jessberger

first: Marlen

last: Knobloch


title: Embryonic erythropoiesis and hemoglobin switching require transcriptional repressor ETO2 to modulate chromatin accessibility and looping

city: bethesda

first: Xiang

last: Guo

address: 50 south drive, blg50

department: NIDDK

institute: NIH


title: Embryonic erythropoiesis and hemoglobin switching require transcriptional repressor ETO2 to modulate chromatin accessibility and looping [RNA-Seq 2]

summary: During the human cord blood CD34+ cell differentiation, expression of the genes which contribute to erycyte maturation are increased, inculding ALAS2, SLC25A37, GYPA and KLF1. ETO2 functions as a transcription repressor and is required for the erythrocyte maturation and the hemoglobin switch. During mouse embryonic erythropoiesis, RNA-seq data in E8.5 yolk sac /E12.5, E14.5 fetal liver cells indicated that eto2 promoted a critical developmental transition and played an important role in globin switch from embryonic to adult β-globin transcription since its function is essential for erythorid maturation regulators (Alas2,Slc25a37,Epb42,Gypc,Klf1) and globin genes (Hbb-y and Hba-x) regulation.

overall_design: RNA-seq was performed using CD34 cells at differentiation day 8, 10 and 12 to identify the key genes essential for erythrocyte maturation. RNA-seq was also perfromed using embryonic day 8.5 (E8.5) yolk sac and  E12.5 fetal liver cells between control and Eto2 knockout mice to identify the differentially expressed genes which are essential for mouse development and embryonic erythropoiesis.

first: Jennifer

last: Plank-Bazinet

first: Ivan

last: Krivega

first: Ryan

last: Dale

first: Ann

last: Dean


title: Embryonic erythropoiesis and hemoglobin switching require transcriptional repressor ETO2 to modulate chromatin accessibility and looping (RNA-Seq)

summary: ETO2 functions as a transcription repressor and is required for the embryonic erythropoiesis and the hemoglobin switch. To gain insight into ETO2 regulatory function during human erythropoiesis, we performed RNA-seq for WT and ETO2 KO K562 cells and found that up-regulated genes upon ETO2 loss in human cells included many markers of mature erythroid cells EPB42, ALAS2, GYPA and SLC25a37. Notably, the α-globin genes (HBA1, HBA2 and HBZ) and embryonic and fetal β-globin genes (HBE1, HBG1, and HBG2) were significantly increased after deletion of ETO2. By contrast, deletion of ETO2 down-regulated the transcription factor genes (ETS1, KLF8 and SOX6) which play a negative role in globin gene expression and hemoglobin synthesis. To further explore different domain function of ETO2, we have analyzed our RNA-seq data from domain deletion cell lines compared to the cell line expressing wild type ETO2. Generally, 702 genes were found to co-regulated by three domain function of ETO2. Interestingly, the regulation of fetal globin genes, erythroid regulator (SOX5) as well as epigenetic factor (HDAC7) is required by three domain function of ETO2. During mouse embryonic erythropoiesis, our FACS-sorted and normal RNA-seq data in E14.5 fetal liver cells indicated that eto2 promoted a critical developmental transition and played an important role in globin switch from embryonic to adult β-globin transcription since its function is essential for key regulators (PU.1, BCL11A and ZBTB7A) and globin genes (Hbb-y and Hba-x) regulation.

overall_design: RNA-seq was performed between human erythroleukemia K562 control cells and ETO2 KO cells in order to identify the differentially expressed genes. RNA-seq was performed in WT control, KO control, rescued ETO2 full length (FL), rescued ETO2 full length without domain TAF110 (D1), rescued ETO2 full length without domain HHR (D2) and rescued ETO2 full length without domain ZF (D4) K562 cells to identify the differentially expressed genes and genes regulated by different functional domains. RNA-seq was performed using FACS-sorted and total embryonic day 14.5 (E14.5) fetal liver cells between control and Eto2 knockout mice to identify the differentially expressed genes which are essential for mouse development and embryonic erythropoiesis.


title: Embryonic erythropoiesis and hemoglobin switching require transcriptional repressor ETO2 to modulate chromatin accessibility and looping (ChIP-Seq)

summary: To determine direct targets and the regulatory role of ETO2 in gene expression, we performed ChIPmentation with antibodies to unmodified ETO2 and ETO2 interacted factor LDB1. A de novo MEME search performed on ETO2-occupied sites, revealed enrichment for GATA and TAL binding motifs, which are the components in LDB1 complex. Nearly 86% of ETO2-binding sites were intergenic or intronic, suggesting ETO2 functions primarily in regions of the genome likely to encompass enhancers. Notabley, ETO2 occupancy was almost completely coincident with LDB1 (97% of 7,761 sites), consistent with the presence of ETO2 exclusively within the LDB1 complex and their co-function in gene regulation.

overall_design: ChIPmentation was performed using antibodies of ETO2 and LDB1 to identify global occupancy of these two factors.


title: Transcriptome profiling of A549 RB1 wild-type/knockout cell lines

city: Macau

first: Joong

middle: Sup

last: Shim

address: Avenida da Universidade, Taipa

department: Faculty of Health Science

country: Macau

institute: University of Macau

summary: A549 cells were co-transfected with CRISPR/Cas9 (containing sgRNA and GFP) and HDR donor plasmids (containing RFP and puromycin). The genetic editing cells were selected by puromycin. And then, we performed RNA sequencing for transcription profiling of A549 RB1 RB1 wild-type/knockout cell lines. The raw data were processed with Tophat and cuffdiff for gene expression analysis.

first: Junfang

last: Lyu