title: BCL6 corepressor regulates androgen signaling and viability of prostate cancer cells

city: Kuopio

first: Einari

middle: A

last: Niskanen

address: Yliopistonranta 8

department: School of Medicine

country: Finland

institute: University of Eastern Finland

summary: To analyze the role of BCOR (BCL6 corepressor) in androgen signaling, we used ChIP-seq to analyze chromatin binding of BCOR and positioning of H2AK119ub histone mark in androgen and vehicle treated VCaP cells. The role of BCOR in transcription regulation and positioning of H2AK119ub histone mark was analyzed from BCOR depleted (siBCOR) and control (siNON) treated VCaP cells in andorgen and vehicle treatments.

overall_design:
For ChIP-seq, VCaP cells were silenced using siRNA transfection for three days when indicate, grown on steroid-depleted medium for two days and treated for 1h with R1881 (10mM) or equal volume of vehicle (ethanol). Samples were fixed for 10 min. in room temperature with 1% (v/v) formaldehyde, fragmented to 200-400bp fragments by sonication (Bioruptor, Diagenode), chromatin immunoprecipitation was done using rabbit polyclonal anti-BCOR antibody (A310-672A, Bethyl Laboratories), antiserum against androgen receptor (AR) or anti-H2AK119ub antibody (#8240, Cell Signaling Technology), and libraries were prepared using NEBNext Ultra II kit (New England Biolabs). Two biological replicates of all conditions were sequenced using Illumina HiSeq 2000 at EMBL GeneCore (Heidelberg, Germany).

For RNA-seq, VCaP cells were transfected with siRNA against BCOR (siBCOR, 20nM, Dharmacon, ON-TARGETplus SMARTpool, L-004584-01-0005) or control siRNA (siNON, Dharmacon, non-targeting pool) using Lipofectamine RNAiMAX (Invitrogen). After three days, medium was changed to steroid-depleted medium for 32h, followed by treatment with dihydrotestosterone (DHT, 100nM) or equal volume of vehicle (ethanol) for 16h. RNA was extracted using RNeasy Plus Mini kit (Qiagen) and mRNA isolated using NEBNext Poly(a) mRNA Magnetic Isolation Module (New England Biolabs). Libraries were prepared using NEBNext Ultra II kit (New England Biolabs) and sequenced with HiSeq 2000 at EMBL GeneCore (Heidelberg, Germany).

Please note that the tdf processed data (for GSM4253755-GSM4253774 ChIP-seq samples) was generated from both replicates and is linked to the corresponding rep1 sample records

first: Joanna

last: Lempiäinen

first: Marjo

last: Malinen

first: Jorma

middle: J

last: Palvimo


title: Expression data from enteroid deleted for HDAC1 or HDAC2

status: Public on Dec 31 2019

city: Sherbrooke

first: Alexis

last: Gonneaud

state: QC

address: 3201 rue Jean-Mignault

department: Anatomie et biologie cellulaire

country: Canada

institute: Université de Sherbrooke

type: Expression profiling by high throughput sequencing

summary: Both HDAC1 and HDAC2 are epigenetic erasers that drive specific and redundant gene expression patterns, in part by removing acetyl groups on histones. Deletion of these Hdac in intestinal epithelial cell (IEC) in vivo alters intestinal homeostasis, dependent on the Hdac deleted and the level of expression of both. To determine the intrinsic specific IEC function of HDAC1 and HDAC2, we have performed transcriptomic and quantitative proteomic approaches on enteroids deficient in Hdac1 or Hdac2. We have defined changes in both mRNA and protein expression patterns affecting IEC differentiation. We have identified IEC Hdac1- and Hdac2-dependent common as well as specific pathways and biological processes. These findings uncover unrecognized similarities and differences between Hdac1 and Hdac2 in IEC.

overall_design: Total RNAs from wild-type, Hdac1- or Hdac2-deleted enteroids were purified with the RNeasy mini kit (Qiagen), and quantified with a NanoDrop ND-1000 spectrophotometer (Thermo Fisher Scientific).

first: Claude

last: Asselin


title: The KRAB zinc finger protein SNERV represses proviral endogenous retroviruses and underlies the Sgp3 and Gv1 loci

city: New Haven

first: Akiko

last: Iwasaki

state: CT

address: 300 Cedar Street

country: USA

institute: Yale University School of Medicine

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Transcriptional silencing of endogenous retroviruses (ERV) defends against active retrotransposition and disease, including overproduction of non-ecotropic ERV (NEERV) envelope and resultant nephritis observed in lupus-prone mice. However, a repressor targeting NEERV loci has not yet been identified. In this study, we identified suppressor of NEERV (Snerv), a Krüppel-associated box zinc finger protein gene responsible for NEERV repression in multiple inbred mouse strains. We show that SNERV binds to the NEERV long terminal repeat and recruits the transcriptional regulator KAP1. Germline deletion of Snerv leads to increased activating chromatin modifications, transcription, and expression of envelope glycoprotein, gp70, from NEERV loci. We found that the NZB and 129 genomes, which overexpress NEERV gp70, cannot rescue defective NEERV repression in F1 crosses to Snerv-/- mice, thus mapping the long sought-after Sgp3 and Gv1 loci to Snerv and demonstrating that loss of SNERV is responsible for the overexpression of the lupus autoantigen gp70. We also found elevated expression of human ERV transcripts in lupus patients compared to healthy controls, and identify putative KRAB-ZFP genes whose expression inversely correlates with human ERV levels. Collectively, our study highlights a role for the KRAB-ZFP, Snerv, in mouse NEERV repression, and suggests similar ERV dysregulation in human lupus disease.

overall_design:
Paired-end RNAseq and ChIPseq of various immune tissues comparing B6N to B6J mice

Please note that BioProject PRJNA482844 (SRA submission SUB4310516) contains all of our whole genome sequencing data for this same study.

first: Rebecca

last: Treger

first: Scott

last: Pope

first: Yong

last: Kong

first: Maria

last: Tokuyama

first: Manabu

last: Taura


title: Gene expression in pancreatic beta-cells post EMC-D virus infection

city: Saga City

first: Keiichiro

last: Mine

state: Saga

address: 5-1-1 Nabeshima

country: Japan

institute: Saga university

summary: In order to reveal context specific gene expression in pancreatic beta-cells, beta-cells were purified by flow cytometry from two days after EMC-D virus infected mice, and performed microarray analysis.

overall_design: Three independent experiments were performed among C57BL/6J, DBA/2N, and B6D2F1 mouse. C57BL/6J data was using as control data.

first: Seiho

last: Nagafuchi

first: Yasunobu

last: Yoshikai


title: Expression data from liver tissue of mice (Mus musculus)

city: Valencia

first: Francisco

middle: García

last: García

address: Eduardo Primo Yúfera, 3

department: Bionformatics & Biostatistics Unit

country: Spain

institute: CIPF

summary:
The aim of this study was to assess whether chronic treatment with RPV can modulate the progression of chronic liver disease, especially of non-alcoholic fatty liver disease (NAFLD), through a nutritional model in wild-type mice
Mice were daily treated with RPV (p.o.) and fed with normal or high fat diet during 3 months to induce fatty liver disease

overall_design: Comparison between two experimental groups: RPV vs. control

first: Alberto

last: Marti Rodrigo

first: Ana

last: Blas

last: Garcia-Garcia

first: Nadezda

last: Apostolova


title: Global transcriptome analysis of paracancerous lung tissues from the B16 metastasis mice model under the influence of lactoferrin knockout

city: Changsha

first: Jian

last: Ma

state: Hunan

address: 110  Xiangya  Road

department: Cancer  Research Institute

country: China

institute: Central South University

summary:
Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are using transcriptome profiling (RNA-seq) to evaluate the effects of lactoferrin deficiency on the global transcriptome of the lung microenvironment of the B16 metastasis mice model.
Methods: 2×10^5 B16-F10 cells were injected into WT and lactoferrin kncoutout (Lf-/-) mice (each group has 10 eight-weeks-old male mice) through tail vein. At 3 weeks post injection,the paracancerous lung tissue were isolated (not including any metastatic colonies). RNAs were extracted by Trizol and sequenced by Solexa high-throughput sequencing service (Oebiotech, Shanghai, China). Data were extracted and normalized according to the manufacturer’s standard protocol.Each group has two mice paracancerous lung tissues be tested.
Results: There are significant gene expression profile changes between WT and Lf-/- tumor-bearing mice.
Conclusions: Our study describes the global transciptome changes of paracancerous lung tissues from the B16 metastasis mice model under the influence of lactoferrin kncokout.

overall_design: Mice paracancerous lung tissues mRNA profiles of “WT” (wild type), “KO”(lactoferrin konckout, Lf-/-) were generated by RNA sequecning, using Solexa high-throughput sequencing service (Oebiotech, Shanghai, China).

first: Lingyu

last: Wei


title: Placental effects on maternal brain revealed by disrupted placental gene expression in mouse hybrids

city: Riverside

first: Polly

last: Campbell

state: CA

address: 3401 Watkins Drive

department: Evolution, Ecology, and Organismal Biology

institute: University of California Riverside

summary: The mammalian placenta is both the physical interface between mother and fetus, and the source of endocrine signals that target the maternal hypothalamus, priming females for parturition, lactation and motherhood. Despite the importance of this connection, the effects of altered placental signaling on the maternal brain are understudied. Here, we show that placental dysfunction alters gene expression in the maternal brain, with the potential to affect maternal behavior. Using a cross between the house mouse and the Algerian mouse in which hybrid placental development is abnormal, we sequenced late gestation placental and maternal medial preoptic area transcriptomes and quantified differential expression and placenta-maternal brain co-expression between normal and hybrid pregnancies. The expression of Fmn1, Drd3, Caln1 and Ctsr was significantly altered in the brains of females exposed to hybrid placentas. Most strikingly, expression patterns of placenta-specific gene families and Drd3 in the brains of house mouse females carrying hybrid litters matched those of female Algerian mice, the paternal species in the cross. Our results indicate that the paternally-derived placental genome can influence the expression of maternal-fetal communication genes, including placental hormones, suggesting an effect of the offspring's father on the mother’s brain.

sample_organism:
Mus musculus domesticus
Mus spretus
Mus musculus domesticus x Mus spretus

overall_design: Analysis of 15 RNA samples of the maternal medial preotic area at e17.5 of pregnancy (3 groups, 5 biological replicates each) and 29 samples of placental DNA at e17.5 of the same pregnancies (3 groups, 4-5 biological replicates per sex, per group)

first: Lena

last: Arévalo


title: Identification and comprehensive analysis of microRNAs and phased small interfering RNAs in Rosa rugosa Thunb

city: Kunming

first: Yun

last: Zheng

state: Yunnan

address: 452 Fengyuan Road

institute: Yunnan Agricultural University

type: Non-coding RNA profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Next generation sequencing facilitates analysis of the role of PRMT5 in diffuse large B-cell lymphoma (DLBCL)

city: Madison

first: Lixin

last: Rui

state: WI

address: 1111 Highland ave, Room 4053

institute: Wisconsin Ins for Medical Res

summary: Whole transcriptome profiling in Diffuse large B cell lymphoma (DLBCL) cells with and wothout PRMT5 knockout revealed important pro-survival pathways that are regulated by PRMT5.

overall_design: TMD8 and OCI-LY7cells expressing doxycycline inducible sgRNA targeting PRMT5 were culture in the presence of 20ng/ml of doxycycline for 0, 3 or 6 days. Duplicated samples were used for each time point. RNA were isolated from above cells and used for RNA sequencing analysis.

first: Li

last: Lu

first: Fen

last: Zhu


title: Astrocytic trans-differentiation completes a multicellular paracrine feedback loop required for medulloblastoma tumor growth

city: Charlottesville

first: Hui

last: Zong

state: VA

address: 7046 Jordan Hall, 7th Floor, 1340 JPA

department: Microbiology, immunology and cancer biology

institute: University of Virginia

summary: We report the application of RNA-sequencing technology for high-throughput profiling of tumor-associated microglia/macrophage (TAMs). First, we checked the purity of sample by qRT-PCR. We confirmed the high purity of TAMs with rare other cell type contamination. By profiling samples of TAMs purified from five individual medulloblastoma of mouse model, we find that TAMs maintain microglia gene signature even there are decrease of microglia genes and increase of macrophage genes. This study provides the evidence for the application of comprehensive gene profiling towards characterization of cellular origin of cell populations in tumor microenvironment.

overall_design: Comparing the gene profile between tumor associated microglia/macrophage and normal microglia

first: Maojin

last: Yao


title: The histone methyltransferase SETDB1 contributes to melanoma tumorigenesis and serves as a new potential therapeutic target in BRAF/MEK inhibitor-resistant melanoma

city: Heidelberg

first: Jochen

last: Utikal

address: Im Neuenheimer Feld 280

department: Clinical Cooperation Unit Dermato-Oncology

country: Germany

institute: German Cancer Research Center


title: The histone methyltransferase SETDB1 contributes to melanoma tumorigenesis and serves as a new potential therapeutic target in BRAF/MEK inhibitor-resistant melanoma [HT144]

summary: The aim of this work is to establish the impact of SETDB1 expression in melanoma. SETDB1 was overexpressed in melanoma cell lines (SETDB1 OE) and  whole-genome expression profiles were compared to the control ( melanoma cells carrying an empty vector).

overall_design: Total RNA from SETDB1 overexpressing HT144 melanoma cells was compared to  HT144 melanoma cells carrying an empty vector (control) and mutant HC/KA-SETDB1 overexpressing HT144 melanoma cells.

first: Elias

middle: O

last: Aniello Federico


title: N6-methyladenosine (m6A) profiling of mouse liver

city: CHICAGO

first: Zijie

last: Zhang

state: IL

department: Chemistry

institute: University of Chicago

type: Methylation profiling by high throughput sequencing

summary: We developed RADAR , a method for detecting differential methylated loci in MeRIP-seq data. RADAR uses a flexible model to accommodate increased noise due to RNA immunoprecipitation and are compatible with complex study design. RADAR enabled accurate identification of altered methylation sites in patient  samples where covariates need to be accounted for. We use the m6A-profiling of mouse liver data as an example data set to benchmart the performance of RADAR and a few alternative methods.

overall_design: Four mouse liver tissues were collected from wild type mice and four from METTL14 liver specific knockout mice. Total RNA was extracted from the tissue by TRIzol followed by polyT bead mRNA purification. mRNA was subject to fragmentation with Bioruptor ultrasonicator. m6A-immunoprecipitation were performed using EpiMark N6-Methyladenosine enrichment kit (NEB cat. E1610S). Kapa RNA hyper kit for Illumina was used to construct library from mRNA. The libraries were sequenced by the Hiseq 4000 platform at SE50 mode.

first: Decheng

last: Ren

first: Chuan

last: He


title: Identification and comprehensive analysis of microRNAs and phased small interfering RNAs in Rosa rugosa Thunb [ncRNA-seq]

summary: MicroRNAs (miRNAs) are small non-coding RNAs that regulate target mRNAs by inducing degradation or preventing translation of their target mRNAs. Rose, Rosa rugosa Thunb., is an important ornamental and edible plant, yet there are only a few studies on the miRNAs of rose. Here we carried out computational and experimental analysis of miRNAs and phased small interfering RNAs (phasiRNAs) in rose by analyzing 10 small RNA profiles from roots, petals, pollens, stamens, and leaves. To identify the targets of miRNAs and phasiRNAs, we generated a degradome profile for rose leaf which is analyzed using the SeqTar algorithm. This study identified 25 conserved pre-miRNAs, of which 24 have not been reported previously. We also found 22 novel pre-miRNAs. Three hundred and thirty nine 21 nucleotide (nt) PHAS loci, and forty nine 24 nt PHAS loci were also identified. We identified more than 4000 putative targets of the conserved miRNAs using a criteria of less than 4 mismatches between miRNA and targets. Among these targets, at least 171 have shown significant accumulation of degradome reads. Our results demonstrate that the miR482 family triggers the generations of phasiRNAs by targeting nucleotide-binding, leucine-rich repeat (NB-LRR) disease resistance genes in rose. These results significantly enhanced our knowledge of the miRNAs and phasiRNAs, as well as their potential functions in rose.

overall_design: Identification and comprehensive analysis of conserved microRNAs, phased small interfering RNAs and their targets in rose using Illumina HiSeq 2000 sequencer.


title: A role for Pak2 kinase in cellular senescence and organismal aging

city: New York

first: zhiguo

last: zhang

state: NY

address: 1130 St. Nicholas Avenue

department: Pediatric and Genetics and Development

institute: Columbia University

summary: Cellular senescence is an irreversible cell growth arrest state linked to loss of tissue function and aging in mammals. The cellular transition from proliferation to senescence is marked by increased expression of the cell-cycle inhibitor p16INK4A and formation of senescence-associated heterochromatin foci (SAHF). It is known that SAHF formation depends primarily on HIRA-mediated nucleosome assembly of H3.3, and that the serine/threonine protein kinase Pak2 regulates HIRA-mediated nucleosome assembly of histone H3.3. Here, we tested the role of Pak2 in the regulation of cellular senescence. Depletion of Pak2 delays premature cellular senescence in both oncogene-induced senescence in human fibroblasts IMR90 cells and in oxidative stress induced senescence of mouse embryonic fibroblasts. Furthermore, overexpression of Pak2 promotes senescence of IMR90 cells. Importantly, depletion of Pak2 in mice delays the onset of some of the aging-associated phenotypes and extend life span of a progeroid mouse model. Lastly, we showed that Pak2 is required for expression of a group of genes involved in cellular senescence and regulates the deposition of newly synthesized H3.3 onto chromatin in senescent cells. Together, our results demonstrate that Pak2 is an important regulator of cellular senescence and organismal aging, in part through the regulation of gene expression and H3.3 nucleosome assembly.

overall_design: To understand the impact of Pak2 on senescence, we performed RNA-seq analysis on wild type Pak2 MEFs and Pak2H/H MEFs at two different time points, P3 and P7, representing the proliferating and senescent states of WT MEF cells, respectively .

first: Jong-Sun

last: Lee

first: Haiyun

last: Gan

first: Zhiguo


title: The histone methyltransferase SETDB1 contributes to melanoma tumorigenesis and serves as a new potential therapeutic target in BRAF/MEK inhibitor-resistant melanoma [SETDB1]

summary: The aim of this work is to establish the impact of SETDB1 expression in melanoma. SETDB1 was overexpressed in melanoma cell lines (SETDB1 OE) and  whole-genome expression profiles were compared to the control ( melanoma cells carrying an empty vector). .

overall_design: Total RNA from SETDB1 overexpressing SK-NL-SETDB1 (a SKMEL28 subcblone with normale SETDB1 gene copy) melanoma cells was compared to  SK-NL-SETDB1 melanoma cells carrying an empty vector (control).


title: RIP-seq for hnRNPK in Min6 cells

city: Philadelphia

first: Austin

middle: Lewis

last: Good

state: PA

address: 3400 Civic Center Blvd

institute: University of Pennsylvania

summary: RNA immunoprecipitation followed by RNA-seq (RIP-seq) for hnRNPK was performed in Min6 cells treated with high glucose and palmitate levels for 30hrs. RNA-seq was performed on both immunoprecipitated RNA and total RNA for enrichment analysis.

overall_design: RNA-seq performed on IP RNA and Total RNA in triplicate for Min6 cells.

middle: L

first: Doris

last: Stoffers


title: CD271/p75NTR is a novel diagnostic marker, prognostic indicator and therapeutic target in SHH medulloblastoma

city: Winnipeg

first: Tamra

last: Werbowetski-Ogilvie

state: Manitoba

address: 611-745 Bannatyne Avenue

department: Biochemistry & Medical Genetics

institute: University of Manitoba

summary: The extensive heterogeneity both between and within the medulloblastoma (MB) subgroups underscores a critical need for variant-specific biomarkers and therapeutic strategies. We previously identified a role for the CD271/p75 neurotrophin receptor (p75NTR) in regulating stem/progenitor cells in the SHH MB subgroup. Here, we demonstrate the utility of CD271 as a novel diagnostic and prognostic marker for SHH MB using immunohistochemical analysis as well as transcriptome data across 763 primary tumors. Characterization of CD271+ and CD271- cells by RNA sequencing revealed that these two subpopulations are molecularly distinct, co-existing cellular subsets both in vitro and in vivo. MAPK/ERK signaling is upregulated in the CD271+ population and inhibiting this pathway reduced CD271 levels, stem/progenitor cell proliferation and cell survival as well as cell migration in vitro. Importantly, the MEK inhibitor selumetinib extends survival and reduces CD271 levels in vivo. Our study demonstrates the clinical utility of CD271 as both a diagnostic and prognostic tool for SHH MB tumors and reveals a novel role for MEK inhibitors in targeting CD271+ SHH MB cells.

overall_design: UI226 tumorspheres were dissociated and counted using an automated cell counter.  Cells were stained with CD271 and 7-Aminoactinomycin D (7AAD) viability dye (Beckman Coulter, Inc., Mississauga ON, Canada) and then FACS sorted on the basis of CD271+ and CD271- expression using a MoFlo XDP cell sorter (Beckman Coulter, Inc.) at the University of Manitoba. Analysis was performed using FlowJo software (Tree Star Inc., Ashland, OR, USA). Sorted CD271+ and CD271- cells were collected and RNA was isolated using the Norgen RNA extraction kit (Norgen Biotek) according to manufacturer’s instructions for mammalian cultured cells

first: Lisa

last: Liang

first: Ludivine

last: Coudière Morrison

first: Nazanin

last: Tatari

first: Margaret

last: Stromecki

first: Agnes

last: Fresnoza

first: Christopher

last: Porter

first: Marc

last: Del Bigio

first: Cynthia

last: Hawkins

first: Jennifer

last: Chan

first: Michael

middle: D

last: Taylor

first: Vijay

last: Ramaswamy


title: Fetal monocytes possess increased metabolic capacity and replace primitive macrophages in tissue macrophage development

status: Public on Dec 30 2019

city: Zürich

first: Manfred

last: Kopf

address: Otto-Stern-Weg 7

department: Biologie

country: Switzerland

institute: ETH Zürich

summary: We studied alveolar macrophage (AM) development after single and competitive transplantation of different precursors from YS, fetal liver, and lung into neonatal Csf2ra-/- mice, which lack endogenous AM. Fetal monocytes, promoted by Myb, outcompeted primitive MΦ (pMΦ) in empty AM niches and preferentially developed to mature AM, which is associated with enhanced mitochondrial respiratory and glycolytic capacity and repression of the transcription factors c-Maf and MafB. Interestingly, AM derived from pMΦ failed to efficiently clear alveolar proteinosis and protect from fatal lung failure following influenza virus infection. Thus, our data demonstrate superior developmental and functional capacity of fetal monocytes over pMΦ in AM development and underlying mechanisms explaining replacement of pMΦ in fetal tissues.

first: Fengqi

last: Li

first: Katarzyna

middle: M

last: Okreglicka

first: Lea

last: Pohlmeier

first: Christoph

last: Schneider


title: In situ dissection of domain boundaries affects genome topology and gene transcription in Drosophila [RNA-seq]

city: Ciudad de Mexico

first: Felix

last: Recillas-Targa

address: Circuito Exterior s/n Ciudad Universitaria

department: Genetica Molecular

country: Mexico

institute: Instituto de Fisiologia Celular, UNAM

summary: The molecular mechanisms responsible for Topologically Associated Domains (TADs) formation are not yet fully understood. In Drosophila, it has been proposed that transcription is fundamental for TAD organization while the participation of genetic sequences bound by Architectural Proteins (APs) remains controversial.  Here, we investigate the contribution of domain boundaries to TAD organization and the regulation of gene expression at the Notch gene locus in Drosophila. We find that deletion of domain boundaries results in TAD fusion and long-range topological defects that are accompanied by loss of APs and RNA Pol II chromatin binding as well as in defects in transcription. Together, our results provide compelling evidence on the contribution of discrete genetic sequences bound by APs and RNA Pol II in the partition of the genome into TADs and in the regulation of gene expression in Drosophila

overall_design: RNA-seq experiments on wild-type and CRISPR mutants S2R+ cells

first: Rodrigo

middle: G

last: Arzate-Mejía

first: Ángel

last: Cerecedo-Castillo

first: Georgina

last: Guerrero

first: Mayra

last: Furlan-Magaril

first: Félix


title: Gestational diabetes adversely affects pancreatic islet development and function in the rat offspring

first: Dr. Vernon

last: Dolinsky

address: 601 John Buhler Research Centre, 715 McDermot Avenue

department: Department of Pharmacology and Therapeutics

summary: Gestational diabetes mellitus (GDM) exposure and obesity are strong risk factors for type 2 diabetes development; however, the connections between GDM exposure, postnatal diet and islet dysfunction in offspring metabolic health remain unclear. Reduced glucose-stimulated insulin secretion was observed in islets isolated from 15-week-old offspring prenatally exposed to GDM, which was exacerbated by postnatal HFS consumption. In the HFS-fed offspring of Lean dams, islet size and number increased, an adaptation that was not observed in the HFS-fed offspring of GDM dams. Islets from GDM exposed offspring revealed upregulation of 102 genes (e.g. Sod2, Il1b) and 13 downregulated genes. In the GDM offspring that consumed a postnatal HFS-diet, 126 genes were significantly upregulated (e.g. Ccl2, Rps14, Atp5f1) and 17 genes were downregulated (e.g. Hnf1a, Slc2a2). These results demonstrate that GDM exposure induced changes in gene expression in the young adult rat offspring that worsen islet function and whole-body glucose homeostasis.

overall_design: GDM was induced in female Sprague-Dawley rats using a high fat and sucrose (HFS) diet and litters from Lean (low-fat or LF) fed dams or the GDM (HFS-fed) dams. Pups were weaned on to a LF or HFS diets for 12 weeks. Islets and pancreata were isolated to analyze endocrine pancreas morphology, gene expression (RNA-seq) and hormone contents.

first: Taylor

last: Morriseau

first: Prasoon

last: Agarwal

first: Mario

last: Fonseca

first: Vern


title: Analysis of microRNAs, phased small interfering RNAs and their functions in Rosa rugosa Thunb

first: Yun

last: Zheng

summary: MicroRNAs (miRNAs) are small non-coding RNAs that play important roles by regulating other genes. Rose, Rosa rugosa Thunb., is an important ornamental and edible plant, yet there are only a few studies on the miRNAs and their functions in rose. Here we carried out computational and experimental analysis of miRNAs, phased small interfering RNAs (phasiRNAs) and mRNAs in rose by analyzing 10 small RNA sequencing profiles from roots, petals, pollens, stamens, and leaves and 4 RNA-seq profiles in leaves and petals of rose. To identify the targets of miRNAs and phasiRNAs, we produced a degradome profile for rose leaf which is analyzed using the SeqTar algorithm. This study identified 25 conserved pre-miRNAs, of which 24 have not been reported previously. We also found 22 novel pre-miRNAs. Three hundred and thirty nine 21 nucleotide (nt) PHAS loci, and forty nine 24 nt PHAS loci were also identified. We identified more than 19,000 putative targets of the conserved miRNAs/tasiRNAs using a criteria of less than 4 mismatches between miRNA and targets. Among these targets, 592 have shown significant accumulation of degradome reads. Our results demonstrate that the miR482 family triggers the generations of phasiRNAs by targeting nucleotide-binding, leucine-rich repeat (NB-LRR) disease resistance genes in rose. Our results also suggest that the deregulated genes in leaves and petals are significantly enriched in GO and KEGG pathways related to metabolic processes and photosynthesis. These results significantly enhanced our knowledge of the miRNAs and phasiRNAs, as well as their potential functions in rose.

overall_design: Identification and comprehensive analysis of conserved microRNAs, phased small interfering RNAs and their targets in rose using Illumina HiSeq 4000 sequencer.


title: A lncRNA-SWI/SNF complex crosstalk controls transcriptional activation at specific promoter regions [RNA-seq]

first: Elena

last: Grossi

address: 1470 Madison Ave

department: Oncological Sciences

institute: Icahn School of Medicine at Mount Sinai

summary: RNA is an essential component of the chromatin, influencing genome organization and expression. To investigate the role of lncRNAs in epigenetic activation, we profiled the RNA interactome of SWI/SNF complexes in proliferating and senescent conditions, when cells undergo widespread chromatin rearrangements. The isolation of transcripts associated to SMARCB1 core subunit, together with its chromatin binding profiling, showed prevalent association to active regions where it differentially binds ncRNAs locally transcribed.  Among them, LINC00565 interacts with SMARCB1 exclusively in proliferating conditions, exerting a pro-oncogenic role in tumors with intact SWI/SNF complexes. LINC00565 is transcribed from an enhancer region and through binding to SMARCB1, controls the activation of GAS6 oncogene as part of a topologically organized region, as well the activation of a larger set of genes by favoring SMARCB1 binding. Our results indicate that LINC00565 influences the ability of the SWI/SNF complexes to drive epigenetic activation of specific promoters, suggesting a SWI/SNF-RNA cooperation to achieve transcriptional activation.

overall_design: Gene expression analysis of H226 lung squamous carcinoma cells depleted of LINC00565

first: Enrique

last: Goñi

first: Maite

last: Huarte


title: MicroRNA expression profiling of peripheral blood mononuclear cells associated with syphilis

status: Public on Dec 28 2019

city: Guangzhou

first: li

middle: xue

last: fei

state: Guangdong

address: Wushang Road  No.483

institute: SMUDH

summary: Treponema pallidum (Tp) infection evokes vigorous immune responses, resulting in tissue damage. The immune mechanism after Treponema pallidum infection is still not clear. MicroRNAs (miRNAs) have been shown, however, to influence immune cell function and consequently the generation of antibody responses during other microbe infections, but these values are unknown for Tp. In this study, we performed a comprehensive analysis of differentially expressed miRNAs in healthy persons, untreated patients with syphilis, patients in the serofast state, and serologically cured patients. MiRNAs were profiled from patient peripheral blood obtained at the time of serological diagnosis. There were 89 differentially regulated miRNA identified in total. Then both the target sequence analysis on these different miRNAs and pathway analysis were performed to identify important immune and cell signaling pathways. Following RT-qPCR confirmation, three miRNAs (hsa-miR-195-5p, hsa-miR-223-3p, hsa-miR-589-3p) showed significant difference among serofast state, and serological cure (P<0.05). Two miRNAs (hsa-miR-195-5p, hsa-miR-1204) showed significant differences among untreated patients and healthy individuals. This is the first study of miRNA expression difference in PBMC in different stages of T. pallium infection. Our study suggests that the combination of three miRNAs has great potential to serve as non-invasive biomarkers of Treponema pallidum infections, which will facilitate better diagnosis and treat of T. pallium infections.

overall_design: This study examined 4 groups of healthy controls, syphilitic patients, serofast state and serologically cured patients. There are 6 samples per group. Sample A1-A6 mean healthy controls, B1-B6 mean serofast state, C1-C6 mean syphilitic patients, D1-D6 mean serologically cured patients.

first: Tao

last: Huang

first: Jun

last: Zhang

first: Wujian

last: Ke

first: Xiaohui

first: Wentao

last: Chen

first: Jieyi

last: Yang

first: Yiwen

last: Liao

first: Fangwen

last: Liang

first: Shuqing

last: Mei

first: Mingjiu

last: Li

first: Zhenzhou

last: Luo

first: Qiwei

first: Bin

first: Heping


title: A lncRNA-SWI/SNF complex crosstalk controls transcriptional activation at specific promoter regions [RIP-seq]

first: Elena

summary: RNA is an essential component of the chromatin, influencing genome organization and expression. To investigate the role of lncRNAs in epigenetic activation, we profiled the RNA interactome of SWI/SNF complexes in proliferating and senescent conditions, when cells undergo widespread chromatin rearrangements. The isolation of transcripts associated to SMARCB1 core subunit, together with its chromatin binding profiling, showed prevalent association to active regions where it differentially binds ncRNAs locally transcribed.

overall_design: Analysis of SMARCB1 RNA interactome by native RIP-seq in proliferating and senescent human fibroblasts

first: Enrique


title: Genome-wide map of AR-targets in human endometrial stromal cells treated with DHT.

city: Swansea

first: Marcos

last: Quintela

address: Singleton Park

country: United Kingdom

institute: Swansea University

summary: Polycystic ovary syndrome (PCOS) is a common gynaecological disorder, characterised by elevated circulating androgens and aberrant expression of androgen receptor (AR) in the endometrium: The objective of this study is to evaluate the targets of AR in PCOS patients. Overexpression of AR and altered endometrial signalling pathways in PCOS patients may impact on a correct decidualization response, critically affecting the events surrounding embryo implantation and causing infertility.

overall_design: Endometrial stromal cells isolated from 3 PCOS patients were pooled together, grown to confluency and treated with DHT for 72h. One chromatin sample (containing genetic background from 3 different patients) was immunoprecipitated with an anti-AR antibody and subsequently submitted to ChIP-Seq

first: R

middle: S

last: Conlan

first: Lewis

middle: W

last: Francis


title: The histone methyltransferase SETDB1 contributes to melanoma tumorigenesis and serves as a new potential therapeutic target in BRAF/MEK inhibitor-resistant melanoma [ChIP-seq]

first: Jochen

last: Utikal

summary: Histone modifications play a crucial role in the progression of various cancers. The histone methyltransferase SETDB1 catalyzes the addition of methyl groups to histone H3 at lysine 9. Here, we describe SETDB1 contribution to melanoma tumorigenesis. SETDB1 is highly amplified in melanoma cells and in patients’ tumors. Increased SETDB1 expression, which correlates with SETDB1 amplification, is associated with a more aggressive phenotype in in vitro and in vivo studies. SETDB1 implements its effects through the regulation of Thrombospondin 1. SETDB1’s SET-domain is essential to maintain its tumorigenic effects. SETDB1 inhibition reduces cell growth in melanomas resistant to targeted treatments. In essence, we support SETDB1 as a major driver of melanoma development, highlighting a role as potential future target for the treatment of this disease.

overall_design: Chromatin obtained from SETDB1-OE (C32) and -knockdown (SK-HI-SETDB1) melanoma cell lines, together with the corresponding control cells, was immunoprecipitated with anti-H3K9me3 and anti-H3K4me1 antibodies. Next, chromatin-immunoprecipitated DNA libraries were prepared and sequenced.

first: Elias

last: Orouji

first: Aniello

last: Federico


title: The effects of vitamin B12 on the expression of genes of mouse proximal tubular cells treated with hypoxia/reperfusion (H/R)

city: Chapel Hill

first: Feng

middle: of

state: NC

address: 101 Meical Drive

department: Pathology

institute: UNC-CH

summary: After treatment with H/R, H/R plus B12 or control, control plus B12, cells were collected and total RNA was isolated using Trizol. RNA was purified using RNeasy Mini Kit (QIAGEN), and RNA samples were submitted to the microarray core at UNC-CH to assess RNA quality and analyze the transcriptome using ClariomTM S Mouse WT (Affymetrix).

first: Nobuyo

last: Maeda-Smithies


title: Transcriptional profiles of wild-type and pheta1/2 mutant zebrafish larvae

city: Roanoke

first: Yuchin

middle: Albert

last: Pan

address: 2 Riverside Circle

institute: Virginia Tech

summary: The purpose of the experiment was to identify the effects of pheta1 and pheta2 on the expression of genes associated with chondrogenesis and osteogenesis

overall_design: Total RNA from 5 days-post fertizliation larvae. Each sample is from a pool of 10 larvae. 3 replicates each for wild-type, pheta1 mutant, and pheta1/2 double mutant.


title: Inflammatory mediators regulate long non-coding RNA-PPTG1-1:1 in myeloid leukemia.

city: Seoul

first: Marc

last: Diederich

address: Gwanak-ro, Gwanak-gu, 1

department: College of Pharmacy

country: South Korea

institute: Seoul National University

summary: The experiment aims to distinguish the transcriptome influenced by the extinction of the lncRNA, after treatment with TNF_ with or without PPTG1-1:1 extinction.

overall_design: Comparison of K562 cells treated with or without TNFa after transfection with siRNA and GapmeR (control or targeting a specific lncRNA): 4 conditions in 3 biological replicates.

first: S

last: Chateauvieux

first: A

last: Gaigneaux

first: M

first: Déborah

last: Gérard


title: RT² Profiler PCR Array analysis of different human HCT116 cell lines

city: Erlangen

first: Pablo

last: Lindner

state: Bavaria

address: Universitaetsstr. 22

institute: Universityclinic Erlangen

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

overall_design: Refer to individual Series


title: New insights into the Manila clam – Perkinsus olseni interaction based on gene expression analysis of clam hemocytes and parasite trophozoites through in vitro challenges [Perkinsus olseni]

status: Public on Dec 27 2019

city: LUGO

first: Belen

last: Pardo

state: LUGO

address: Avda. Carballo Calero s/n

department: Zoology, Genetics and Physical Anthropology

institute: University of Santiago de Compostela

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

overall_design: P. olseni trophozoites (~ 5x10e6) resuspended in 2.5 mL filtered seawater (FSW) were placed in IWAKI 6-well plates, and 2.5 mL of plasma (treatment) or FSW (control) were added into a permeable insert (0.2 µm Anopore® membrane NUNC 25 mm) set in the plate-wells. Four or three pseudo-replicates (trophozoites from the same culture) for both control and treatment groups were collected at 1, 8 and 24 h since the onset of the challenge.

first: Abul

middle: F

last: Hasanuzzaman

first: Asunción

last: Cao

first: Paolo

last: Ronza

first: Sergio

last: Fernández-Boo

first: Juan

last: Rubiolo

first: Diego

last: Robledo

first: Antonio

last: Gómez-Tato

first: Jose

last: Alvarez-Dios

last: Villalba

first: Paulino

last: Martínez


title: RT² Profiler PCR Array analysis of different human HCT116 cell lines [chromatin modification enzyme]

summary: Three HCT116 cell lines (HCT WT, HCT p21-/-, HCT p53-/-) were analyzed by RT-qPCR array analysis for chromatin modification enzymes to identify potential target genes,   that depend on the cell cycle regulator p21 and that are indpendent of p53. HCT116 cell lines (HCT WT, HCT p21-/-, HCT p53-/-) were cultured at 37°C in a humidified atmosphere   with 5% CO2. Cells were harvested at a confluency of ~60-80% and RNA was isolatd using QIAzol an Rneasy Kits from Qiagen. cDNA was produced from equal amounts of RNA   using the RT² First Strand Ki from Qiagen and RT-qPCR analysis was performed following the manufacturer's instructions using the Epigenetic Chromatin Modification Enzymes   RT² Profiler PCR Array from Qiagen. The CFX96TM Real-Time System and the C1000TM Thermal Cycler from Bio-Rad were used to perform the RT-PCR runs. The three different   cell lines were analyzed in three biological triplicates. The mean expression Ct values of the target genes were normalized against the mean Ct value for GAPDH to calculate the   Fold Change values. The Raw Data was processed using the RT² Profiler PCR Array Data Analysis version 3.5 software from SABiosciences.

overall_design: RT² Profiler PCR Array analysis of different HCT116 cell lines (HCT WT, HCT p21-/-, HCT p53-/-) for expression patterns of chromatin modification enzymes.

first: Regine

last: Schneider-Stock


title: SUV39H1 regulates human colon carcinoma apoptosis and cell cycle to promote tumor growth

city: Augusta

first: Kebin

last: Liu

state: GA

address: 1410 Laney Walker Blvd

department: Biochemistry and Molecular Biology

institute: Medical College of Georgia

summary: Transcriptional profiling of histone methyltransferase SUV39H1-selective small molecule inhibitor F5446-induced genes in human colon carcinoma cells. Tumor cells were treated with F5446 for 48h and used for RNA isolation. The treated cells were compared to untreated control cells. The objective is to identify genes that are regulated by H3K9me3 in the metastatic human colon carcinoma cells.

overall_design: Two-condition experiments. Control (untreated) vs F5446 treatment. Biological replicates: 2 replicates for the comparison.

first: Chunwan

last: Lu

first: John

last: Klement

first: Dafeng

last: Yang

first: Thomas

last: Albers

first: Iryna

last: Lebedyeva

first: Jennifer

last: Waller


title: Effect of Th2 cytokines on AEC2 transcriptome

city: Durham

first: Christina

middle: E

last: Barkauskas

address: BOX 2629 DUMC

department: Medicine / Pulmonary

institute: Duke University

summary: We report the effect of exposure to IL13 or IL4 of alveolar epithelial type 2 cells (AEC2s) in organoid culture

overall_design: Examination of transcriptome of AEC2s after exposure to IL13 or IL4 for 16 days in organoid culture (compared to untreated, cultured AEC2s and primary, non-cultured AEC2s)


title: A lncRNA-SWI/SNF complex crosstalk controls transcriptional activation at specific promoter regions [ChIP-Seq]

first: Elena

last: Grossi

summary: RNA is an essential component of the chromatin, influencing genome organization and expression. To investigate the role of lncRNAs in epigenetic activation, we profiled the RNA interactome of SWI/SNF complexes in proliferating and senescent conditions, when cells undergo widespread chromatin rearrangements. The isolation of transcripts associated to SMARCB1 core subunit, together with its chromatin binding profiling, showed prevalent association to active regions where it differentially binds ncRNAs locally transcribed. Among them, LINC00565 interacts with SMARCB1 exclusively in proliferating conditions, exerting a pro-oncogenic role in tumors with intact SWI/SNF complexes. LINC00565 is transcribed from an enhancer region and through binding to SMARCB1, controls the activation of GAS6 oncogene as part of a topologically organized region, as well the activation of a larger set of genes by favoring SMARCB1 binding. Our results indicate that LINC00565 influences the ability of the SWI/SNF complexes to drive epigenetic activation of specific promoters, suggesting a SWI/SNF-RNA cooperation to achieve transcriptional activation.

overall_design: Analysis of SMARCB1 and histone marks genomic occupancy by ChIP-seq in proliferating human fibroblasts

first: Enrique

last: Goñi

first: Maite

last: Huarte


title: Chronic IL-1β-induced inflammation regulates epithelial-to-mesenchymal transition memory phenotypes via epigenetic modifications in non-small cell lung cancer

city: Los Angeles

first: Linh

middle: My

last: Tran

state: California

department: Medicine - Pulmonary & Critical Care

institute: University of Los Angeles

summary: Chronic inflammation facilitates tumor progression. We discovered that a subset of non-small cell lung cancer cells underwent a gradually progressing epithelial-to-mesenchymal (EMT) phenotype following a 21-day exposure to IL-1β, an abundant proinflammatory cytokine in the at-risk for lung cancer pulmonary and the lung tumor microenvironments. Pathway analysis of the gene expression profile and in vitro functional studies revealed that the EMT and EMT-associated phenotypes, including enhanced cell invasion, PD-L1 upregulation, and chemoresistance, were sustained in the absence of continuous IL-1β exposure. We referred to this phenomenon as EMT memory. Utilizing a doxycycline-controlled SLUG expression system, we found that high expression of the transcription factor SLUG was indispensable for the establishment of EMT memory. High SLUG expression in tumors of lung cancer patients was associated with poor survival. Chemical or genetic inhibition of SLUG upregulation prevented EMT following the acute IL-1β exposure but did not reverse EMT memory. Chromatin immunoprecipitation and methylation-specific PCR further revealed a SLUG-mediated temporal regulation of epigenetic modifications, including accumulation of H3K27, H3K9, and DNA methylation, in the CDH1 (E-cadherin) promoter following the chronic IL-1β exposure. Chemical inhibition of DNA methylation not only restored E-cadherin expression in EMT memory, but also primed cells for chemotherapy-induced apoptosis.

overall_design: Compare transcriptome profiles between IL-1β treated and control untreated A549 cells at different time points. Each biological condition was represented by triplicate.

first: Rui

last: Li

first: Stephanie

last: Ong

first: Zhe

last: Jing

first: Zi

last: Huang

first: Bin

first: Gina

last: Lee

first: Ramin

last: Salehi-Rad

first: Kostyantyn

last: Krysan

first: Paul

middle: C

last: Pagano

first: Manash

middle: K

last: Paul

first: Shili

last: Xu

first: Harvey

middle: R

last: Herschman

first: Steven

last: Dubinett

first: Stacy

last: Park

first: Tonya

last: Walser

first: Eileen

last: Heinrich

first: William

middle: P

last: Crosson


title: Identifying target genes which are heterogeneously expressed

city: Toronto

first: Philip

last: Marsden

address: 209 Victoria St

institute: St. Michael's hospital/University of Toronto

summary: We have identified that VCAM1 is heterogeneously expressed in human umbilical vein endothelial cells (HUVEC). In this experiment, we aimed to identify genes which are regulated by TNF and genes which are differentially regulated in the highest and lowest 5% VCAM1 expressing cells.

overall_design: In this experiment, we use total cellular RNA from HUVEC  treated with TNF for 4 hr (TNF4) or 24 hr (TNF24) and vehicle control (TNF0). Total cellular RNA from the 5% highest (HIGH) and lowest (LOW) HUVEC  treated with TNF for 4 hr were used. We have paired comparisons of 0 hr versus 4hr or 24 hr in four biological lines of HUVEC. Pairwise comparisons were also performed on the 5% highest and lowest HUVEC

middle: J

last: Turgeon

middle: A


title: Super-enhancer-associated oncogenes as novel therapeutic targets in osteosarcoma

first: Jiajun

last: Zhang

address: #58，Zhongshan 2nd Road

institute: the First Affiliated Hospital of Sun Yat-Sen University


title: Deletion of the Cardiomyocyte Glucocorticoid Receptor Leads to Sexually Dimorphic Changes in Cardiac Gene Expression and Progression to Heart Failure

city: RTP

first: Xiaojiang

state: North Carolina

address: 111 T. W. Alexander Dr.,

institute: NIEHS

summary:
Background
The contribution of glucocorticoids to sexual dimorphism in the heart is essentially unknown. Therefore, we sought to determine the sexually dimorphic actions of glucocorticoid signaling in cardiac function and gene expression. To accomplish this goal, we conducted studies on mice lacking glucocorticoid receptors (GR) in cardiomyocytes (cardioGRKO mouse model).

Methods and Results
Deletion of cardiomyocyte GR leads to an increase in mortality because of the development of spontaneous cardiac pathology in both male and female mice; however, females are more resistant to GR signaling inactivation in the heart. Male cardioGRKO mice had a median survival age of 6 months. In contrast, females had a median survival age of 10 months. Transthoracic echocardiography data showed phenotypic differences between male and female cardioGRKO hearts. By 3 months of age, male cardioGRKO mice exhibited left ventricular systolic dysfunction. Conversely, no significant functional deficits were observed in female cardioGRKO mice at the same time point. Functional sensitivity of male hearts to the loss of cardiomyocyte GR was reversed following gonadectomy. RNA‐Seq analysis showed that deleting GR in the male hearts leads to a more profound dysregulation in the expression of genes implicated in heart rate regulation (calcium handling). In agreement with these gene expression data, cardiomyocytes isolated from male cardioGRKO hearts displayed altered intracellular calcium responses. In contrast, female GR‐deficient cardiomyocytes presented a response comparable with controls.

Conclusions
These data suggest that GR regulates calcium responses in a sex‐biased manner, leading to sexually distinct responses to stress in male and female mice hearts, which may contribute to sex differences in heart disease, including the development of ventricular arrhythmias that contribute to heart failure and sudden death.

overall_design: Examination of transcriptome under two different conditions (Normal GR levels in cardiomyocytes vs. no GR expression in cardiomyocytes)

first: Diana

last: Cruz-Topete

first: Robert

last: Oakley

first: Natalie

last: Burford

first: Page

last: Myers

first: John

last: Cidlowski


title: Super-enhancer-associated oncogenes as novel therapeutic targets in osteosarcoma (ChIP-seq)

summary: Despite the development of diagnostic and advanced treatment strategies, the prognosis of patients with osteosarcoma remains poor. A limited understanding of the pathogenesis of osteosarcomas has impeded any improvement in patient outcomes over the past 4 decades. It is thus urgent to identify novel effective targets and treatment regimens for osteosarcoma patients. In this study we delineated the super-enhancer landscape in osteosarcoma cells on the basis of H3K27ac signal intensity by ChIP-Seq and found that super-enhancer-associated genes contribute to the malignant potential of osteosarcoma. THZ2, a novel small molecular inhibitor, shows a powerful anti-osteosarcoma ability through suppress super-enhancer-associated genes selectively. Utilizing the characteristics of super-enhancers in cancer cells, we identified 5 critical super-enhancer-associated oncogenes. With the comparative and retrospective analysis in large numbers of human specimens from patients, these 5 oncogenes were observed closely related with patient prognosis. Our findings determined that targeting super-enhancer-associated oncogenes with transcriptional inhibitor, THZ2, was a promising therapeutic strategy in osteosarcoma, and provided novel candidate targets for patients with osteosarcoma.

overall_design: ChIP-seq for H3K27Ac in two esophageal cell lines U2-OS and SJSA-1.

first: Weihai

last: Liu

first: Changye

last: Zou

first: Zhiqiang

last: Zhao

first: Yuanying

last: Lai

first: Zhi

last: Shi

first: Xianbiao

last: Xie

first: Gang

last: Huang

first: Yongqian

last: Wang

first: Xuelin

first: Zeipei

last: Fan

first: Qiao

last: Su

first: Junqiang

last: Yin

first: Jingnan

last: Shen


title: Super-enhancer-associated oncogenes as novel therapeutic targets in osteosarcoma (Microarray gene expression data)

first: Jiajun

last: Zhang

summary:
CDK7 is a component of the general transcription factor IIH, which regulates RNAPII initiation and elongation.THZ2, a new molecular inhibitor, can completely inhibit the phosphorylation of the established intracellular CDK7 substrate RNAPII CTD at Ser-2, -5 and -7 through irreversible covalent binding to CDK7.
Gene expression profiling was then performed to investigate the THZ2-induced transcription effect, and search the subset of sensitive genes in these 2 osteosarcoma cell lines.

overall_design: Total RNA was extracted from U2-OS or SJSA-1 cells treated with DMSO (control), 25, 100, and 400 nM THZ2 for 6 hours, respectively, using TRIzol reagent.An Affymetrix GeneChip® PrimeView™ Human Gene Expression Array was used for the microarray analysis. The hybridization data were analyzed using Affymetrix GeneChip Command Console Software.


title: A lncRNA-SWI/SNF complex crosstalk controls transcriptional activation at specific promoter regions

status: Public on Dec 29 2019

city: New York

first: Elena

last: Grossi


title: FLANC, a novel primate-specific long non-coding RNA, is involved in colorectal carcinogenesis and holds potential as a novel therapeutic target (shRNA)

city: Houston

first: George

last: Calin

state: TX

address: 1881 East Road

department: Experimental Therapeutics

institute: MD Anderson Cancer Center

summary: FLANC is significantly up-regulated in two cohorts of CRC samples and high level of FLANC is associated with poor patient survival in two additional independent cohorts. FLANC influences cellular growth, apoptosis, migration and metastases formation of CRC cells.

overall_design: We performed genome-wide microarray expression profiling to study the genetic landscape alterations induced by the knock-down of FLANC by shRNA in HCT-116 cells.

first: Mihnea

last: Dragomir


title: Exome-seq of Glioblastoma Tumors and GBOs

status: Public on Dec 26 2019

city: Philadelphia

first: Daniel

address: 3400 Civic Center Boulevard

institute: University of Pennsylvania

summary: Analysis of glioblastoma tissue and corresponding glioblastoma organoids by Exome sequencing.

overall_design: Exome sequencing of glioblastoma tumor samples and corresponding glioblastoma organoids

middle: Y

first: Hongjun

last: Song


title: Single Cell RNA-seq of Glioblastoma Tumors and GBOs

summary: Analysis of glioblastoma tissue and corresponding glioblastoma organoids by single cell RNA sequencing.

overall_design: Single cell RNA-sequencing of glioblastoma tumor samples and corresponding glioblastoma organoids


title: Glioblastoma Tumors and GBOs


title: In situ dissection of domain boundaries affects genome topology and gene transcription in Drosophila [Hi-C]

first: Felix

last: Recillas-Targa

address: Circuito Exterior s/n Ciudad Universitaria

institute: Instituto de Fisiologia Celular, UNAM

summary: The molecular mechanisms responsible for Topologically Associated Domains (TADs) formation are not yet fully understood. In Drosophila, it has been proposed that transcription is fundamental for TAD organization while the participation of genetic sequences bound by Architectural Proteins (APs) remains controversial.  Here, we investigate the contribution of domain boundaries to TAD organization and the regulation of gene expression at the Notch gene locus in Drosophila. We find that deletion of domain boundaries results in TAD fusion and long-range topological defects that are accompanied by loss of APs and RNA Pol II chromatin binding as well as in defects in transcription. Together, our results provide compelling evidence on the contribution of discrete genetic sequences bound by APs and RNA Pol II in the partition of the genome into TADs and in the regulation of gene expression in Drosophila

overall_design: Hi-C experiments on wild-type and CRISPR mutants S2R+ cells

first: Rodrigo

last: Arzate-Mejía

first: Ángel

last: Cerecedo-Castillo

first: Georgina

last: Guerrero

first: Mayra

last: Furlan-Magaril

first: Félix


title: Germline development in rat revealed by visualization and deletion of Prdm14

city: Kashihara

first: Hisato

last: Kobayashi

state: Nara

address: 840 Shijo-Cho

department: Department of Embryology

institute: Nara Medical University

summary: Primordial germ cells (PGCs), the founder cells of the germline, are specified in pre-gastrulating embryos in mammals, and subsequently migrate towards gonads to mature into functional gametes. Here, we investigated PGC development in rats, by genetically modifying Prdm14, a unique marker and a critical PGC transcriptional regulator. We trace PGC development in rats, for the first time, from specification until sex determination stage in fetal gonads using Prdm14 H2BVenus knock-in rats. We uncover that Prdm14’s crucial role in PGC specification is conserved between rat and mice, by analyzing Prdm14 deficient rat embryos. Notably, loss of Prdm14 completely abrogates the PGC program: failure in maintenance and/or activation of germ cell markers and pluripotency genes. Finally, we profile the transcriptome of the postimplantation epiblast and all PGC stages in rat, to reveal enrichment of distinct gene sets at each transition point, thereby providing an accurate transcriptional time-line for rat PGC development. Thus, the novel genetically modified rats and data sets obtained in this study will advance our knowledge on conserved vs species-specific features for germline development in mammals.

overall_design: RNA-seq of rat primordial germ cells and epiblasts.

first: Toshihiro


title: The LC3 conjugation machinery specifies the loading of RNA-binding proteins into extracellular vesicles (smRNA-seq dataset)

city: San Francisco

first: Jayanta

last: Debnath

state: CA

address: 513 Parnassus Ave, HSW-475 Campus Box 0502

institute: University of California, San Francisco

summary: We employed small non-coding RNA  sequecing to profile the small RNAs in extracellular vesicles (EVs) from WT cells and cells deficient for the LC3 conjugation machinery

overall_design: EVs from wild-type, ATG7-/- and ATG12-/- HEK293T cells and corresponding cell samples were collected after 24h of serum starvation. Total RNA from wild-type, ATG7-/- and ATG12-/- HEK293T EVs and cells was isolated and used for the preparation of uniquely barcoded small RNA sequencing libraries (n=3). Results of single-end 50 base pair sequencing on two separate lanes of a HiSeq4000 for these samples revealed dramatic differences in the small RNA profiles of EVs from ATG7-/- and ATG12-/- cells relative to EVs from wild-type cells. Specifically, EVs from ATG7-/- and ATG12-/- cell were found to have reduced levels of numerous small nucleolar RNAs (snoRNAs), and more limited affects upon discrete microRNA and transfer RNA (tRNA) species. Overall, these results are supportive of a role for the LC3-conjugation machinery in specifying RNA-binding proteins and RNAs into EVs for secretion outside the cell.

first: Andrew

middle: M

last: Leidal

first: Hani

last: Goodarzi


title: The LC3 conjugation machinery specifies the loading of RNA-binding proteins into extracellular vesicles (lrgRNA-seq dataset)

summary: We employed RNA sequecing to profile large RNAs (mRNAs and lincRNAs) packaged into extracellular vesicles (EVs) from WT cells and cells deficient for the LC3 conjugation machinery

overall_design: EVs from wild-type, ATG7-/- and ATG12-/- HEK293T cells and corresponding cell samples were collected after 24h of serum starvation. Total RNA from wild-type, ATG7-/- and ATG12-/- HEK293T EVs and cells was isolated and used for the preparation of uniquely barcoded large RNA sequencing libraries (n=3). Results of single-end 50 base pair sequencing on two separate lanes of a HiSeq4000 for these samples revealed negligible differences in the large RNA profiles of EVs from ATG7-/- and ATG12-/- cells relative to EVs from wild-type cells. These results suggest that large RNAs are packaged into EVs via mechanisms independent of the LC3 conjugation machinery.


title: In situ dissection of domain boundaries affects genome topology and gene transcription in Drosophila

city: Ciudad de Mexico

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

overall_design: Refer to individual Series


title: New insights into the Manila clam – Perkinsus olseni interaction based on gene expression analysis of clam hemocytes and parasite trophozoites through in vitro challenges

first: Belen

middle: G

last: Pardo

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

sample_organism:
Perkinsus olseni
Ruditapes philippinarum

overall_design:
R. philippinarum collected from a P. olseni-free area (Camariñas, NW Spain) were used to collect hemocytes for the in vitro challenge with P. olseni trophozoites, zoospores  and extracellular products (proteins released into the culture medium by P. olseni trophozoites). Similarly, P. olseni trophozoites were challenged in vitro with R. philippinarum plasma collected from clams of the P. olseni-free area. The details for collection of hemocytes, trophozoites, zoospores and extracellular products have been described in Hasanuzzaman et al. (2017). The procedures to collect trophozoites from in vitro cultures (1-2 months old) and the isolation of Manila clam plasma have been described in Hasanuzzaman et al. (2016). Absence of P. olseni infection in every used clam was confirmed by PCR and incubation of gill pieces in Ray’s fluid thioglycollate medium. All experiments were carried out in the facilities of Centro de Investigacións Mariñas (CIMA; Spain).
R. philippinarum hemocytes (5x10e6) were challenged in vitro with P. olseni trophozoites (5x10e6), zoospores (5x10e6) and extracellular products (2.5 mL of culture media enriched with extracellular products) separately in IWAKI 6-well plates (Fig.1A). Each challenge included three biological replicates for both treatment and control (only culture media) groups, and each biological replicate was a pool of hemocytes from 10 different clams, thus averaging individual biological variation. For the challenges, trophozoites and zoospores, obtained just before the challenge, were separately suspended in 2.5 mL filtered seawater (FSW) and added into a permeable insert (0.2 μm Anopore® membrane NUNC 25 mm) in each well. For hemocyte-extracellular products challenge, 2.5 mL of culture media enriched with hemocyte extracellular products were added into the inserts of the respective wells. The inserts allowed the flow of media but not the cells; hence, hemocytes and parasite cells were never in contact. Samples for RNA extraction were collected at 1, 8 and 24 h after the start of the challenge. Further details are available in Hasanuzzaman et al. (2017).
P. olseni trophozoites (~ 5x10e6) resuspended in 2.5 mL FSW were placed in IWAKI 6-well plates, and 2.5 mL of plasma (treatment) or FSW (control) were added into a permeable insert (0.2 µm Anopore® membrane NUNC 25 mm) set in the plate-wells (Fig. 1B). Four pseudo-replicates (trophozoites from the same culture) for both control and treatment groups were collected at 1, 8 and 24 h since the onset of the challenge. Further details are available in Hasanuzzaman et al. (2016).
The design of the R. philippinarum oligo-microarray has been described and validated in Hasanuzzaman et al. (2018). Briefly, this microarray was designed on an 8 × 15 k Agilent format and included 14,621 probes representing 11,052 transcripts of which 10,813 were annotated (97.8%).
Thirty-two microarrays (four slides) were used. R. philippinarum control replicates at each time point were pooled, so a single control microarray was used for each sampling time (1-C, 8-C, 24-C); in addition, the low RNA amount in the controls of the zoospore challenge determined pooling all controls in a single microarray hybridization.
To construct the P. olseni oligo-microarray, we selected 10,104 sequences from our previously published P. olseni trophozoite transcriptome (Hasanuzzaman et al., 2016). A total of 9,369 sequences were selected because they were annotated to transcripts in the NCBI nr protein database, while the remaining 735 non-annotated sequences were selected by their notable differential expression in our preliminary evaluation (Hasanuzzaman et al., 2016). One oligo-probe was designed for annotated sequences (known sense) and two probes (sense and antisense) were designed for the non-annotated sequences. We also included 4,158 technical replicates for microarray reproducibility evaluation. All processes for oligo-probe design and Agilent oligo-microarray procurement were similar to those followed for the Manila clam microarray (Hasanuzzaman et al., 2018).
A total of 16 microarrays (two slides) were used for the experiment. A single pooled control was hybridized in two microarrays per slide as technical replicates. Twelve microarrays were used for the treatments across the time-series (1 h, 8 h and 24 h) including four replicates per time point.
Hybridizations were performed at the Universidade de Santiago de Compostela (USC) Functional Genomics Platform using the Agilent Technology Gene Expression Unit following a one-color gene expression analysis protocol. All hybridizations were carried out by the same researcher in the same day. Hybridized slides were scanned using an Agilent scanner (G2565B, Agilent Technologies) and signals were captured and processed. The microrarray platforms (Agilent-072098 and Agilent-xxx) and data presented in this publication has been deposited in the NCBI’s Gene Expression Omnibus (GEO, http://www.ncbi.nlm.nih.gov/geo/) and are available under accession number xxxx. Microarray hybridization, data processing and quality filtering were carried out as previously described (Hasanuzzaman et al., 2018).


title: Histone H2AK119 Mono-Ubiquitination is Essential for Polycomb-Mediated Transcriptional Repression

city: Milano

first: Diego

last: Pasini

address: Via Adamello, 16

country: Italy

institute: European Institute of Oncology

summary: The major function of Polycomb group proteins (PcG) is to maintain transcriptional repression to preserve cellular identity. This is exerted by two distinct repressive complexes, PRC1 and PRC2, that modify histones by depositing H2AK119ub1 and H3K27me3, respectively. Both complexes are essential for development and are deregulated in several types of human tumors. PRC1 and PRC2 exist in different variants and show a complex regulatory cross-talk. However, the contribution that H2AK119ub1 plays in mediating PcG repressive functions remains largely controversial. Coupling an inducible system with the expression of a fully catalytic inactive RING1B mutant, we demonstrated that H2AK119ub1 deposition is essential to maintain PcG-target genes repressed in ESC. Loss of H2AK119ub1 induced a rapid displacement of PRC2 activity and a loss of H3K27me3 deposition. This affected both PRC2.1 and PRC2.2 variants and further correlated with a strong displacement and destabilization of canonical PRC1. Finally, we find that variant PRC1 forms can sense H2AK119ub1 deposition, which contributes to their stabilization specifically at sites where this modification is highly enriched. Overall our data place H2AK119ub1 deposition as central hub that mount PcG repressive machineries to preserve cell transcriptional identit

overall_design: This data series consists of ChIPseq and RNAseq samples. RNAseq samples consist of 2 biological replicates. For all ChIP-seq samples the E14 input has been used to call peaks. The inputs for H3K27me3 and H2AK119ub1 are used to correct the variability introduced in the quantification of the chromatin before adding the spike-in (see methods of the paper).

last: Fernande-Perez


title: Total RNA-seq of siRNA-mediated TARBP2 knockdown

department: Biochemistry and Biophysics

institute: UCSF

summary: To identify changes in splicing patterns following TARBP2 knockdiwn, RNA-sequencing was performed on breast cancer cells transfected with siRNAs targeting TARBP2.

overall_design: Libraries were generated using ScriptSeq v2 RNA-seq Library Preparation Kit (Epicentre) and run on Illumina HiSeq 2500.

first: L

last: Fish

first: H

last: Nguyen


title: Total RNA-seq of siRNA-mediated WTAP and TPR knockdown

summary: To identify changes in splicing patterns following WTAP and TPR knockdown, RNA-sequencing was performed on breast cancer cells transfected with siRNAs targeting WTAP or TPR.

overall_design: Libraries were generated using ScriptSeq v2 RNA-seq Library Preparation Kit (Epicentre) and run on Illumina NextSeq 500.


title: Nuclear RNA-seq of shRNA-mediated TARBP2 knockdown

summary: To identify changes in splicing patterns following TARBP2 knockdown, RNA-sequencing was performed on nuclear RNA extracted from cells expressing shRNAs targeting TARBP2 or a non-targeting shRNA (shControl).


title: Total RNA-seq of shRNA-mediated TARBP2 knockdown

summary: To identify changes in splicing patterns following TARBP2 knockdown, RNA-sequencing was performed on breast cancer cells transduced with shRNAs targeting TARBP2.

last: Goodarzi H


title: FLANC, a novel primate-specific long non-coding RNA, is involved in colorectal carcinogenesis and holds potential as a novel therapeutic target (overexpression)

first: George

last: Calin

overall_design: We performed genome-wide microarray expression profiling to study the genetic landscape alterations induced by the overexpression of FLANC in HCT-116 cells.

first: Mihnea

last: Dragomir


title: FcgRIIB+ and FcgRIIB- OT-I T cells d14 post OVA skin graft

city: Atlanta

first: Chris

last: Scharer

address: 1510 Clifton Rd, Suite 3086A

department: Microbiology and Immunology

institute: Emory University

summary: Here, we sought to characterize the transcriptomes of FcγRIIB+ versus FcγRIIB- CD8+ T cells in a mouse model of transplant rejection to understand the function of FcγRIIB in programming CD8 T cells responses.

overall_design: 3 spleens were pooled for each of the 4 replicates and then from each replicate FcgRIIB+ and FcgRIIB- cells were sorted.

first: C

middle: D

first: M

middle: L

last: Ford

first: A

middle: B

last: Morris


title: RNA-sequencing analysis to investigate genes regulated by CASZ1 in C2C12 cells

city: bethesda

first: Jack

last: Shern

state: MD

address: 10 Center drive

institute: NCI

summary: In this study we identified genes regulated by CASZ1b in C2C12 cells

overall_design: 1) RNA was isolated from C2C12 cells that transfected with empty vector (EV), CASZ1a or CASZ1b and cultured in regular growth medium for 48 hr; 2) RNA was isolated from C2C12 cells that stably transfected with  shCtrl or shCasz1 and cultured in differentiation medium for 48 hr.

first: Zhihui

last: Liu

first: Carol

last: Thiele


title: Nuclear RNA-seq of siRNA-mediated METTL3 knockdown

summary: To identify changes in splicing patterns following METTL3 knockdown, RNA-sequencing was performed on nuclear RNA extracted from cells transfected with METTL3-targeting siRNA or a non-targeting siRNA (siControl).

overall_design: Libraries were generated using ScriptSeq v2 RNA-seq Library Preparation Kit (Epicentre) and run on Illumina HiSeq 4000.


title: Genome-wide mapping of CASZ1 binding sites in differentiated SMS-CTR cells [Trametinib]

summary: MEK inhibitor trametinib induces SMS-CTR cell differentiation and up-regulates CASZ1 expression. We identified genome-wide binding sites of CASZ1 in differentiated SMS-CTR cells.

overall_design: SMS-CTR cells were treated with DMSO control or 100 nM trametinib for 48 hr, and ChIP seq was performed using anti-CASZ1 antibody.

first: Xiyuan

last: Zhang


title: RNA-seq of shRNA-mediated EXOSC10 and XRN2 knockdown

summary: To identify changes in gene expression following EXOSC10 and XRN2 silencing, 3'-end RNA-sequencing was performed on RNA extracted from shEXOSC10 and shXRN2 cells.

overall_design: Libraries were generated using QuantSeq 3’ mRNA-Seq library prep kit fwd (Lexogen) and run on Illumina HiSeq 4000.

first: B

last: Culbertson


title: Genome-wide mapping of CASZ1b binding sites and investigate its effect on chromatin status in SMS-CTR cells [CTRtetCASZ1b]

summary: In SMS-CTR cells, we identified genomewide binding sites of CASZ1b. The overexpression of CASZ1b in SMS-CTR cells led to a regional epigenetic modification.

overall_design: In the CASZ1b stably transfected SMS-CTR cells (CTRtetCASZ1b), CASZ1b expression is Doxcycline (Dox) inducible . The CTRtetCASZ1b cells were treated with or without Dox for 48 hr, and ChIP seq was performed using anti-CASZ1 antibody and antibodies of histone markers and RNA Pol II.


title: SRSF1 HITS-CLIP in MDA-LM2

last: Goodarzi

summary: To identify SRSF1 binding sites on RNAs, we performed HITS-CLIP of endogenous SRSF1 in MDA-LM2 cells

overall_design: MDA-LM2 cells were subjected to the HITS-CLIP procedure (Licatalosi D, et al. 2008, Nature 456:464-U22)

first: S

last: Tavazoie


title: Investigate the affect of CASZ1b on chromatin accessibility in SMS-CTR cells

summary: In SMS-CTR cells, the overexpression of CASZ1b in SMS-CTR cells led to a modification of regional chromation accessibility.

overall_design: In the CASZ1b stably transfected SMS-CTR cells (CTRtetCASZ1b), CASZ1b expression is Doxcycline (Dox) inducible. The CTRtetCASZ1b cells were treated with or without Dox for 48 hr and ATAC seq was performed.


title: The affect of loss of Casz1 in C2C12 cells on super-enhancers

summary: In the differereniated C2C12 cells, knockdown of Casz1 leads to a re-establishment of super-enhancers

overall_design: C2C12 cells infected with control shRNA (shCtrl) or Casz1 shRNA (shCasz1) were induced to differentiate, then ChIP experiment was performed using anti-H3K27ac antibody and anti-H3K4me3 antibody.


title: Decapping enzyme NUDT12 partners with BLMH for cytoplasmic surveillance of NAD-capped RNAs

status: Public on Dec 25 2019

city: Gneveva

first: Ramesh

last: Pillai

address: 30, Quai Ernest-Ansermet

department: Department of Molecular Biology

institute: University of Geneva

summary: RNA polymerase II transcripts receive a protective 5ʹ m7G cap early during transcription. An alternative cap can be acquired when RNA pol II initiation uses the redox cofactor nicotinamide adenine dinucleotide (NAD) to generate NAD-capped RNAs. The biology of mammalian NAD-RNAs, including its turnover and physiological roles are not completely understood. Here we identify NUDT12 as a cytosolic decapping enzyme for NAD-RNAs. Structural, biochemical and functional studies reveal how homodimerization modulates specificity of NUDT12 for NAD-RNAs as substrate. NUDT12 is localized within a few discrete cytoplasmic granules that are distinct from P-bodies. We identity Bleomycin hydrolase (BLMH) as a factor that associates with NUDT12 in a large ~600 kDa dodecamer complex, and we demonstrate that BLMH is required for correct localization of NUDT12 into these granules. This complex is functional in human cell cultures, as artificial tethering of BLMH to a reporter mRNA results in downregulation of reporter expression, similar to that seen with tethering of NUDT12. Analysis of mouse liver transcriptome from the Nudt12 knockout mouse reveals that a select set of RNAs are regulated, including a significant upregulation of circadian clock transcripts. Given that NAD biosynthesis is under circadian control, our study points to a physiological role for the cytosolic surveillance of NAD-RNAs.

overall_design: RNA sequencing was used to identify transcript abundance differences between Nudt12-/- and Nudt12+/+  in mouse liver and kidney.   To characterize the effect of NUDT12 absence on circadian gene expression, the RNA sequencing was used to compare gene expression in relation to dark-light cycle.

first: Hao

last: Wu

first: Lingyun

last: Li

first: Kuan-Ming

last: Chen

first: David

last: Homolka

first: Pascal

last: Gos

first: Fabienne

last: Fleury-Olela

first: Andrew

last: McCarthy

middle: S


title: MeRIP-seq of control and TARBP2 knockdown cells

first: Hani

summary: To identify changes in methylation patterns following TARBP2 knockdown, m6A-IP followed by RNA-seq was performed on breast cancer cells expressing shRNAs against TARBP2 (and non-targeting shControl cells).

first: C

last: Alarcon

first: H


title: Single cell analysis of circulating B lymphocytes and myocardial B lymphocytes in naïve C57/B6 mice

status: Public on Dec 24 2019

first: Maxim

middle: N.

last: Artyomov

state: MO

address: 660 S. Euclid Avenue, Campus Box 8118

department: Immunology&Pathology

institute: Washington University in St.Louis

summary: Perfused naïve murine hearts harbor a sizeable population of B lymphocytes. In order to assess any differences between "myocardial" B cells and circulating B cells we FACS sorted B cells collected from the peripheral blood via cheek bleed and B cells isoalted from the heart after enzymatic digestion. CD45+, CD19+, Aqua- cells were facs sorted into PBS - with 0.04% BSA and processed for single cell RNA sequencing. Peripheral blood was colelcted immediately prior to sacrificing mice in a CO2 chamber. the blood and heart of 3 10 weeks old female mice was pooled together prior to FACS sorting.

overall_design:
Droplet-based 5′ end massively parallel single-cell RNA sequencing was performed by isolating single cells from mouse peripheral blood and heart
myocardial cells and peripheral blood cells from 3 independent mice were pooled in this experiment

first: Luigi

last: Adamo

first: Cibele

last: Rocha-Resende

first: Chieh-Yu

last: Lin

first: Sarah

last: Evans

first: Jesse

last: Williams

last: Dun

first: Wenjun

first: Cedric

last: Mpoy

first: Prabhakar

last: Andhey

first: Kory

last: Lavine

first: Buck

last: Rogers

first: Daniel

last: Kreisel

first: Gwendalyn

last: Randolph

first: Douglas

last: Mann


title: Total RNA-seq of siRNA-mediated SRSF1 knockdown

first: Hani

last: Goodarzi

summary: To identify changes in splicing patterns following SRSF1 knockdown, RNA-sequencing was performed on breast cancer cells transfected with siRNAs targeting SRSF1.

first: L

last: Fish

last: Nguyen

last: Goodarzi H


title: SRSF1 HITS-CLIP

summary: To identify METTL3 binding sites on RNAs, we performed HITS-CLIP of endogenous SRSF1

overall_design: H1299 cells were subjected to the HITS-CLIP procedure (Licatalosi D, et al. 2008, Nature 456:464-U22)

first: Y

last: Xu

first: D

last: Ruggero

first: H


title: Differential Expression of the Transcription Factor GATA3 Specifies Lineage and Functions of Innate Lymphoid Cells

city: Morgantown

first: Gangqing

last: Hu

state: West Virginia

address: 64 Medical Center Drive

department: MicroBiology, Immunology, and Cell Biology

institute: West Virginia University

summary: Lymphoid tissue inducer (LTi) cells are regarded as a subset of innate lymphoid cells (ILCs). However, these cells are not derived from the ILC common progenitor, which generates other ILC subsets and is defined by the expression of the transcription factor PLZF.  Here we examined transcription factor(s) determining the fate of LTi progenitor versus non-LTi ILC progenitor.  Conditional deletion of Gata3 resulted in the loss of PLZF+ non-LTi progenitors but not the LTi progenitors that expressed the transcription factor RORγt.  Consistently, PLZF+ non-LTi progenitors expressed high amounts of GATA3 whereas GATA3 expression was low in RORγt+ LTi progenitors. The generation of both progenitors required the transcriptional regulator Id2, which defines the common helper-like innate lymphoid progenitor, but not cytokine signaling. Nevertheless, low GATA3 expression was necessary for the generation of functionally mature LTi cells. Thus, differential expression of GATA3 determines the fates and functions of distinct ILC progenitors.

overall_design: To identify transcriptome changes from common lymphoid progenitor (CLP) to common helper-like innate lymphoid progenitor (ChILP) with RNA-Seq; To identify unique genes expressed by PD-1+ non-LTi ILC progenitor and CCR6+ LTi progenitor with RNA-Seq.

first: Chao

last: Zhong

first: Mingzhu

last: Zheng

first: Kairong

last: Cui

first: Andrew

last: Martins

first: Dan

last: Li

first: Lino

last: Tessarollo

first: Serguei

last: Kozlov

first: Jonathan

last: Keller

first: John

last: Tsang

first: Keji

last: Zhao

first: Jinfang

last: Zhu


title: Pachytene piRNA Genes Are Rapidly Diverging Among Modern Humans

status: Public on Dec 23 2019

city: Worcester

first: Tianxiong

last: Yu

state: MA

address: 364 Plantation St

institute: Umass Med

summary: In the fetal mouse testis, PIWI Interacting RNAs (piRNAs) guide PIWI proteins to silence transposons, but after birth, most post-pubertal pachytene piRNAs map to genome uniquely and are thought to regulate genes required for male fertility. In human males, the developmental classes, precise genomic origins, and transcriptional regulation of post-natal piRNAs remain undefined. Here, we demarcate the genes and transcripts that produce post-natal piRNAs in human juvenile and adult testes. As in mouse, A‑MYB in humans drives transcription of both pachytene piRNA precursor transcripts and the mRNAs encoding piRNA biogenesis factors. Although human piRNA genes are syntenic to those in other placental mammals, their sequences are poorly conserved. In fact, pachytene piRNA loci are rapidly diverging even among modern humans. Our findings suggest that during mammalian evolution, pachytene piRNA genes are under fewer selective constraints. We speculate that pachytene piRNA diversity may provide a hitherto unrecognized driver of reproductive isolation.

sample_organism:
Macaca mulatta
Homo sapiens
Mus musculus

overall_design: RNA-seq, small RNA-seq and ChIP-seq for human, mouse, and rhesus macaque.

first: Yu

last: Tianxiong

first: Özata

last: Deniz


title: Effects of a gastrin receptor antagonist (NTZ, previously named YF) on the gastric corpus mucosa of HKATPase betasubunit  knockout (KO) mice

city: Trondheim

first: Reidar

last: Fossmark

address: Prinsesse Kristinas gate 1

department: Department of Clinical and Molecular Medicine

country: Norway

institute: Norwegian University of Science and Technology

summary:
Purpose: the effects of a gastrin receptor antagonist has been studies in patients with gastrin neuroendocrine (NE) tumours due to hypergastrinemia. This mouse model of hypergastrinemia is a model for studying long term acid inhibition, including NE hyperplasia and formation of Spasmolytic polypeptide expressing metaplasia (SPEM), a proposed premalignant alteration of the stomach.
Methods: RNA was isolated from the oxyntic mucosa. RNA was sequenced using standard Illumina protocols on a NextSeq 500 instrument.
Results: NTZ reduced oxyntic mucosal hypertropohy and stomach weight. Neuroendocrine cell hyperplasia and NE markers were also reduced. Spasmolytic polypeptide expressing metaplasia (SPEM) was expressed in KO mice and was not affected by the gastrin receptor antagonist.
Conclusions: The gastrin receptor antagonist YF reduced gastric corpus mucosal hypertrophy and NE cell hyperplasia in HKATPase KO mice, but did not affect SPEM or SPEM related genes.

overall_design: Gastric corpus mRNA profiles of 13 months old WT and KO mice, given YF or vehicle (PEG) were generated by  sequencing using an Illumina NextSeq 500 instrument  to examine the effect of genotype and NTZ.

first: Flatberg

last: Arnar


title: DDX18 safeguards rDNA epigenetic landscape by counteracting PRC2 and maintains ESC identity

city: Rochester

first: jinlong

last: lu

state: NY

address: 213 Hutchinson Hall

institute: University of Rochester

summary: Here we have RNA binding protein DDX18 connecting rRNA transcription to early embryo development and embryonic stem cell (ESC) identity maintenance. DDX18 mutant embryos suffer lethality during preimplantation development. DDX18 depletion impairs ESC self-renewal and pluripotency, which phenotype-copies RNA polymerase I (RNAPI) inhibition. Mechanistically, DDX18 is recruited to rDNA by RNAPI transcription machinery and senses rRNA transcription by binding to pre-rRNA. In nucleolus, DDX18 surrounds DFC ring and interacts with PRC2. In the presence of transcribed pre-rRNA, DDX18 interaction with PRC2 makes EZH2 unstably binding to the other components of PRC2, thereby preventing PRC2 engagement and counteracting H3K27me3 mediated silencing at rDNA chromatin. Together, our study shows that DDX18 plays important roles in safeguarding ESCs identity through regulating epigenetic states of rDNA locus and maintaining euchromatin structure in nucleolus.

overall_design: RNA-seq (s) were designed to reveal DDX18 function in early embryo development and ESC idetity maintenance. Transcriptome comparison of RNA-seq (s) between DDX18 KD and RNAPI/CHX inhibition indicate that DDX18 functions through maintaing rRNA transcription. CLIP/TAP-seq (s) as well as ChIP-seq were designed to reveal DDX18 binding RNA and DNA.

first: Hui

last: Zhang

first: Jinlong

last: Lu

first: Zhongyang

last: Wu

first: Bo

last: Huang

first: Xiaohua

last: Shen


title: CASZ1 directly regulates expression of myogenic genes through regional epigenetic modifications to induce muscle and rhabdomyosarcoma cell differentiation

first: Jack

last: Shern

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: Gene expression profiles in SLC15A1/PEPT1-knockout human iPS cell-derived intestinal epithelial-like cells

city: Suita

first: Tomoki

last: Yamashita

state: Osaka

address: 1-6 Yamadaoka

department: Graduate School of Pharmaceutical Sciences

institute: Osaka University

summary: Because many peptide and peptide-mimetic drugs are substrates of peptide transporter 1, it is important to evaluate the peptide transporter 1-mediated intestinal absorption of drug candidates in the early phase of drug development. Although intestinal cell lines treated with inhibitors of peptide transporter 1 are widely used to examine whether drug candidates are substrates for peptide transporter 1, these inhibitors are not sufficiently specific for peptide transporter 1. In this study, to generate a more precise evaluation model, we established peptide transporter 1-knockout induced pluripotent stem cells (iPSCs) by using a CRISPR-Cas9 system and differentiated the cells into intestinal epithelial-like cells. The permeability value and uptake capacity of glycylsarcosine (substrate of peptide transporter 1) in peptide transporter 1-knockout intestinal epithelial-like cells were significantly lower than those in wild-type intestinal epithelial-like cells, suggesting that peptide transporter 1 was successfully depleted in the epithelial cells. Taken together, our model can be useful in the development of peptide and peptide-mimetic drugs.

overall_design: We generated SLC15A1/PEPT1-knockout human iPS cells based on a human iPS cell line, YOW-iPS (Takayama et al., 2014). Each SLC15A1/PEPT1-knockout iPS cells and wild type iPS cells were differentiated into intestinal epithelial-like cells (PEPT1-KO iPS-IEC and WT iPS-IEC, respectively). PEPT1-KO iPS-IEC and WT iPS-IEC were pooled from triplicate samples of one independent experiments, and then microarray analysis was performed.

first: Kanae

last: Kawai

first: Ryosuke

last: Negoro

first: Moe

last: Ichikawa

first: Sayaka

last: Deguchi

first: Kazuo

last: Harada

first: Kazumasa

last: Hirata

last: Takayama

first: Hiroyuki

last: Mizuguchi


title: RNA-sequencing analysis to investigate genes regulated by CASZ1 in SMS-CTR cells

summary: In this study we identified genes regulated by CASZ1b in SMS-CTR cells

overall_design: In the CASZ1b stably transfected SMS-CTR cells (CTRtetCASZ1b), CASZ1b expression is Doxcycline (Dox) inducible . RNA was isolated from CTRtetCASZ1b cells that treated with or without Dox for 48 hr

first: Zhihui

last: Liu

first: Carol

last: Thiele


title: Endogenous topoisomerase II-mediated DNA breaks drive thymic cancer predisposition linked to ATM deficiency

city: Madrid

first: Felipe

last: Cortés Ledesma

state: Madrid

address: Melchor Fernández Almagro 3

department: Molecular Oncology

institute: CNIO

type: Genome variation profiling by genome tiling array

summary: Copy-number variation by Comparative Genomic Hybridization (CGH) on thymocytes and Kidney (control) of Tdp2+/+Atm-/- and Tdp2-/-Atm-/- mice.

overall_design: 6 independent experiments of Tdp2+/+Atm-/- mice and 3 independent experiments of Tdp2-/-Atm-/ mice.

first: Alejandro

last: Álvarez-Quilón

first: Jose

last: Terrón-Bautista

first: Irene

last: Delgado-Sainz

first: Almudena

last: Serrano-Benítez

first: Rocío

last: Romero-Granados

first: Pedro

last: Martínez-García

first: Cristina

last: Bernal-Lozano

last: Quintero

first: Lourdes

last: García-Quintanilla

last: Cortés-Ledesma


title: Next generation sequencing analysis of transcriptomes at different timepoints after chlorprothixene treatment in NB4 and Kasumi-1 cells

city: Shanghai

first: Ji

last: Zhang

state: Select a State or Province

address: 197 Ruijin 2nd Road

institute: Shanghai Jiao Tong University School of Medicine

summary: To understand the mechanisms of chlorprothixene in acute myeloblastic leukemia (AML) therapy, gene expression changes of NB4 and Kasumi-1cells after chlorprothixene treatment were analyzed by RNA-seq

overall_design: RNA from NB4 and Kasumi-1cells treated with chlorprothixene at different timepoints were sequenced.

first: Yuxin

last: Du

first: Kening

last: Li


summary: The ATM kinase is a master regulator of the DNA damage response to double-strand breaks (DSBs) and a well-established tumour suppressor. Loss-of-function mutations in the gene are not only frequently found in many types of cancer, but constitute the underlying cause of the neurodegenerative and cancer-prone genetic syndrome Ataxia-Telangiectasia (A-T). A-T patients are particularly predisposed to develop lymphoid cancers, which are thought to arise from inefficient signalling and inaccurate repair of RAG-induced DSBs during V(D)J recombination, and which the Atm-/- mouse models recapitulate in the form of very aggressive T-cell malignancies. Here, we unexpectedly find that specifically disturbing the repair of DSBs produced by DNA topoisomerase II (TOP2) by genetically removing the highly specialised repair enzyme TDP2, strongly increases the incidence of thymic tumours in Atm-/- mice, but without changing their molecular characteristics or underlying genomic rearrangements, including a significant association with Tcr loci. Furthermore, we find that TOP2 strongly colocalizes with RAG, both in a genome-wide scale and specifically at sites undergoing V(D)J recombination, in a manner that is consistent with its involvement in solving topological problems associated to 3D genome organization, and which results in an increased chromosomal fragility of these regions. Thus, our findings demonstrate a strong causal relationship between accidental TOP2-induced DSBs and cancer development, putting forward these lesions as major drivers of the genome rearrangements that are characteristic of ATM-deficient lymphoid malignancies, and opening the door for their involvement in other conditions and cancer types.

overall_design: TOP2B and TOP2A ChIPseq in mouse isolated thymocytes.

first: José

last: Serrano-Benitez


title: RNA-sequencing analysis to investigate genes regulated by CASZ1 in RD cells

first: Jack

last: Shern

summary: In this study we identified genes regulated by CASZ1b in RD cells

overall_design: In CASZ1b stably transfected RD cells (RDtetCASZ1b), CASZ1b is tetracycline inducible . RNA was isolated from RDtetCASZ1b cells that treated with or without tetracycline (Tet) for 48 hr

last: Liu


title: Swarming motility in Pseudomonas aeruginosa

city: Burnaby

first: Travis

last: Blimkie

state: British Columbia

address: 8888 University Drive

department: MBB

institute: Simon Fraser University

summary: We report the transcriptome of Pseudomonas aeruginosa PA14 under swarming conditions as compared to a swimming control

overall_design: Examination of Pseudomonas aeruginosa PA14 transcriptome under swarming conditions

first: Shannon

last: Coleman

first: Reza

last: Falsafi

first: Robert

last: Hancock


title: Microglia and macrophages promote corralling, wound compaction and recovery in spinal cord injury via Plexin-B2

city: New York

first: Hongyan

last: Zou

address: 1425 Madison Avenue

department: Neuroscience

institute: Icahn School of Medicine at Mount Sinai

summary: Tissue repair after spinal cord injury (SCI) requires mobilization of immune and glial cells to form a protective barrier that seals the wound and facilitates debris clearing, inflammatory containment, and matrix compaction. This process involves corralling, wherein phagocytic immune cells become confined to the necrotic core surrounded by an astrocytic border. Here, we elucidate a temporally distinct gene signature in injury-activated microglia/macrophages (IAM), which engages axon guidance pathways. Plexin-B2 is upregulated in IAM, which is required for motosensory recovery after SCI. Plexin-B2 deletion in myeloid cells impairs corralling, leading to diffuse tissue damage, inflammatory spillover, and hampered axon regeneration. Corralling begins early and requires Plexin-B2 in both microglia and macrophages. Mechanistically, Plexin-B2 promotes microglia motility, steers IAM away from colliding cells, and facilitates matrix compaction. Our data thus establish Plexin-B2 as an important link that integrates biochemical cues and physical interactions of IAM with the injury microenvironment during wound healing.

overall_design: Investigation of transcriptional profile changes in microglia of mice with spinal cord injury at 3, 7 and 14 days post injury

first: Xiang

last: Zhou

first: Shalaka

last: Wahane

first: Marie-Sophie

last: Friedl

first: Michael

last: Kluge

first: Caroline

last: Friedel

first: Kleopatra

last: Avrampou

first: Venetia

last: Zachariou

first: Lei

last: Guo

first: Bin

first: Xijing

last: He

first: Roland

middle: H


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

city: shanghai

first: yujuan

last: shen

address: Rui jin Er road

institute: National Institute of Parasitic Diseases

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