title: Transcriptomic responses of Arabidopsis thaliana lines WS and sku5 to the Blue Origin NS-12 and Virgin Galactic VP-03 suborbital flights

city: Gainesville

middle: J.

last: Ferl

state: Florida

address: 1301 Fifield Hall PO Box 110690

department: Horticultural Sciences

institute: University of Florida

summary: The increasing availability of flights on suborbital rockets creates new avenues for the study of spaceflight effects on biological systems, in particular the transitions between hypergravity and microgravity. This paper presents an initial comparison of the responses of Arabidopsis thaliana to suborbital and atmospheric parabolic flights as an important step toward characterizing these emerging suborbital platforms and their effects on biology. Transcriptomic profiling of the response of the Arabidopsis ecotype Wassilewskija (WS) to the aggregate spaceflight experiences in the Blue Origin New Shepard and Virgin Galactic SpaceShipTwo rockets revealed that the transcriptomic load induced by flight differed greatly between the two flights, yet was biologically related to traditional parabolic flight responses. The sku5 skewing mutant and 14-3-3κ:GFP regulatory protein overexpression lines each showed altered intra-platform responses compared to WS in the Blue Origin and parabolic flights, respectively. An additional parabolic flight using the F-104 Starfighter showed that the response of 14-3-3κ:GFP to flight was modulated in a similar manner to the WS line. Despite the differing genotypes, experimental workflows, flight profiles and platforms, alteration of gene expression remodeling central metabolic processes was commonly observed as a response to the flights. The processes included carbon and nitrogen metabolism, branched-chain amino acid degradation, and hypoxic responses. The timing and directionality of differentially-expressed genes involved in the conserved pathways differed among the platforms. The data presented herein highlight the potential for various suborbital platforms to contribute insights into biological responses to spaceflight, and further suggest that in-flight fixation during suborbital experiments will provide insights into responses to each phase of flight.

overall_design: Multiple genotypes of Arabidopsis thaliana seedlings were flown on either the Virgin Galactic SpaceShipTwo (VG VP-03; Col-0 and WS) or Blue Origin New Shepard (BO NS-12; WS and sku5) suborbital flight platforms. Plates containing the seedlings, 10 days and 11 days old in VG and BO, respectively, were wrapped in Duvetyne™ Black-Out cloth and mounted to the internal wall of the FLEX imaging system payload used in these flights. Gene expression was compared between the ground control and spaceflight-exposed seedlings via RNA-Seq analysis of extracted total RNA from the roots of these seedlings.

first: Brandon

last: Califar

first: Agata

last: Zupanska

first: Jordan

last: Callaham

first: Matthew

last: Bamsey

first: Thomas

last: Graham

first: Anna-Lisa

last: Paul


title: Molecular profiling of 16 week aromatase inhibitor-treated post-menopausal breast tumors

status: Public on Apr 01 2021

city: Dunedin

first: Anita

last: Dunbier

address: 710 Cumberland Street

department: Biochemistry

country: New Zealand

institute: University of Otago

summary: To identify the effect of 16 weeks of neoadjuvant anastrozole treatment on gene expression profiles of oestrogen receptor positive breast tumours from post-menopausal patients.

overall_design: Global gene-expression measured in core-cut biopsies, from 28 postmenopausal women with stage I to IIIB ER+ early breast cancer  after 16-weeks’ anastrozole monotherapy in a neoadjuvant trial.

first: A

middle: K


title: Next generation sequencing of chicken otocyst with pharmacologicaly induced loss-of-Wnt signalling

city: London

first: Magdalena

last: Zak

address: 332 Grays Inn Road

country: United Kingdom

institute: UCL Ear Institute

type: Expression profiling by high throughput sequencing

summary: Bulk RNA-sequencing of individual E2.5 chicken otocyst incubated in media enriched with Wnt signalling inhibitor IWR-1 or control condition (DMSO) for 24h. Transcripts abundance was mapped to a chicken reference genome using Kallisto package and differentially expressed genes were identify using Sleuth package (genes with p-value < 0.05 were considered as significant). Biological Function enrichment analysis (Toppgene online tool) showed that many of these genes were associated with neurogenesis.

overall_design: Identification of genes deregulated in E3 otic explants treated with IRW-1 or DMSO for 24h

last: Żak

first: Nicolas

last: Daudet


title: Cx3cl1 expression in the adipose tissue is downregulated during development of obesity

city: Kanazawa

first: Mayumi

last: Nagashimada

address: 5-11-80 Kodatsuno

country: Japan

institute: Kanazawa University

summary: To assess changes in expression level of various chemokines and their receptors on diet-induced obesity, we analysed gene expression in adipose tissue of C56BL/6J mice fed a high-fat (HF) diet or normal chow diet for 8 weeks. HF diet-induced obese (DIO) mice showed adipose tissue inflammation and insulin resistance.  Comprehensive gene expression analysis showed that MCP-1–CCR2 and CCL5–CCR5 signalling in epididymal white adipose tissue (eWAT) were enhanced during the development of obesity. Surprisingly, the gene expression of Cx3cl1 was decreased in the eWAT of DIO mice compared with lean mice. While Cx3cr1 expression showed no significant difference between DIO and lean mice. Decreased CX3CL1-CX3CR1 signalling in adipose tissue may also be involved in the development of obesity-induced adipose tissue inflammation and insulin resistance.

overall_design: Eight-week old male C57BL/6J mice were fed for 8 weeks on a normal chow (CRF-1) or high-fat diet consisting of 60% fat.

first: Masuko

last: Kobori


title: Cardiac cell type-specific gene regulatory programs and disease risk association [ATAC-seq]

city: La Jolla

first: Sebastian

last: Preissl

state: CA

address: 9500 Gilman Drive

country: USA

institute: UCSD

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Misregulated gene expression in human hearts can result in cardiovascular diseases that are leading causes of morbidity and mortality worldwide. However, the limited information on the genomic location of candidate cis-regulatory elements (cCRE) such as enhancers and promoters in distinct cardiac cell types has restricted the understanding of these diseases. Here, we defined >287,000 cCREs in the four chambers of the human heart at single-cell resolution, which revealed cCREs and candidate transcription factors associated with cardiac cell types in a region-dependent manner and during heart failure. We further discovered cardiovascular disease-associated genetic variants enriched within these cCREs including 38 candidate causal atrial fibrillation variants localized to cardiomyocyte cCREs. Additional functional studies revealed that two of these variants affect a cCRE controlling KCNH2/HERG expression and action potential repolarization. Overall, this comprehensive atlas of human cardiac cCREs provides the foundation for illuminating cell type-specific gene regulation in human hearts during health and disease.

overall_design:
We performed single nucleus ATAC-seq to define a comprehensive catalogue of candidate cis-regulatory elements (cCREs) for the cell types in four regions of non-failing human hearts and generate in parallel snRNA-seq datasets for a subset to delineate gene expression patterns. We used the cCRE catalogue to computationally deconvolute dynamic enhancers in failing hearts and to assign cardiovascular disease risk variants to cCREs in individual cardiac cell types. Finally, we applied reporter assays, genome editing and electrophysiogical measurements in in vitro differentiated human cardiomyocytes to validate the molecular mechanisms of cardiovascular disease risk variants.

The raw sequencing data are available through dbGaP (controlled access): phs002204.v1.p1

first: James

middle: D

last: Hocker

first: Olivier

middle: B

last: Poirion

first: Fugui

last: Zhu

first: Justin

last: Buchanan

first: Kai

last: Zhang

first: Joshua

last: Chiou

first: Tsui-Min

last: Wang

first: Xiaomeng

last: Hou

first: Qingquan

first: Yang

middle: E

last: Li

first: Yanxiao

first: Elie

middle: N

last: Farah

first: Allen

first: Andrew

last: McCulloch

first: Kyle

middle: J

last: Gaulton

first: Bing

last: Ren

first: Neil

middle: C

last: Chi


title: Establishing a molecular phenotype for Angelman Syndrome stem cell-derived neurons

city: Madison

first: Carissa

middle: L

last: Sirois

state: WI

address: 1500 Highland Ave T515

department: Waisman Center

institute: University of Wisconsin-Madison

summary: mRNAseq on (1) isogenic control and Angelman Syndrome pluripotent stem cell-derived neurons or (2) antisense oligonucleotide-treated H9 hESC-derived neurons

overall_design: Stranded mRNAseq was performed on six (6) replicates of 12-week isogenic iPSC-derived or hESC-derived neurons (Angelman Syndrome or control) and on six (6) replicates of 10-week UBE3A ASO or scramble ASO-treated H9 hESC-derived neurons

first: Stormy

last: Chamberlain


title: ACME dissociation: a versatile cell fixation-dissociation method for single-cell transcriptomics

city: Barcelona

first: Arnau

last: Sebe-Pedros

address: Dr. Aiguader 88

department: Systems Biology

country: Spain

institute: Centre for Genomic Regulation

summary: We performed single-cell transcriptome analysis (using 10x genomics 3' scRNA-seq v3.1 chemistry) in the sea anemone Nematostella vectensis (Cnidaria).

overall_design: Several juvenile polyps were dissociated using ACME method and then single-cells were FACS-sorted before 10x encapsulation and transcriptome capture.

first: Marta

last: Iglesias

first: Anamaria

last: Elek

first: Helena

last: Garcia-Castro

first: Nathan

last: Kenny

first: Jordi

last: Solana


title: Cardiac cell type-specific gene regulatory programs and disease risk association

first: Sebastian

last: Preissl

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

overall_design: Refer to individual Series


title: Arabidopsis thaliana in altered gravity: the 14-3-3κ:GFP overexpression line on the F-104 Starfighter, first flight

first: Robert

last: Ferl

overall_design: 10-day-old seedlings overexpressing 14-3-3κ:GFP, from a WS background, were transferred from 0.5x MS media plates to three Kennedy Space Center fixation tubes (KFTs), which were sealed. KFTs were actuated in-flight, exposing the seedlings to RNAlater, following the transition out of microgravity and about 1.5 min after the return to level flight. A ground control KFT was also actuated during the flight. Seedlings and RNAlater were transferred from KFTs to 50 mL Falcon tubes. Roots from fixed seedlings were dissected from shoots. Whole roots were separated into three biological replicates for each condition. Total RNA was extracted from roots comprising each replicate and submitted for microarray analysis. The Affymetrix GeneChip Arabidopsis Gene (AraGene) 1.0 ST array was used to measure gene expression levels. The transcriptomic data from the flight-actuated samples were then compared to those of the ground controls in order to identify differentially-expressed genes between the ground control and the two flight conditions.

first: Brandon

last: Califar

first: Agata

last: Zupanska

first: Jordan

middle: A

last: Callaham

first: Matthew

last: Bamsey

first: Thomas

last: Graham

first: Anna-Lisa

last: Paul


title: Resistance to AR Signaling Inhibition Does Not Necessitate Prostate Neuroendocrine Differentiation

city: Seattle

first: Ilsa

last: Coleman

state: WA

address: 1100 Fairview Ave N, E2-112

department: Human Biology

institute: Fred Hutchinson Cancer Center

summary: Resistance to 2nd generation androgen receptor (AR) signaling inhibitors (ARSi) occurs in a subset of metastatic castration-resistant prostate cancer (mCRPC) patients with the emergence of a neuroendocrine (NE) phenotype. This NE phenotype is typically accompanied by loss of AR expression coupled with mutations/deletions in PTEN, TP53, and/or RB1, in addition to overexpression of DNMTs, EZH2, and/or SOX2. A combination of cell and molecular biology analyses of 29 prostate cancer patient-derived xenografts (PDXs) recapitulating the full spectrum of proposed genetic alterations driving NE differentiation, in addition to CRISPR-Cas9 AR-knockout cells were utilized. These analyses document that: 1) ARSi-resistance in mCRPC cells that lack AR expression in the context of a TP53 mutation and PTEN deletion does not necessitate acquiring a NE phenotype, but alternatively can occur via emergence of an AR-/NE- double negative (DN) cancer; 2) NE cancers lack AR expression due to transcriptional silencing via promoter hypermethylation; and 3) in contrast, the lack of AR expression in DN cancers is not due to promoter hypermethylation-dependent silencing. Regardless of their cell of origin, the prevalence of both AR-/NE- DN and AR-/NE+ ARSi-resistant cancers is increasing clinically, highlighting the urgent need to develop therapies that target vulnerabilities beyond AR pathway inhibition.

overall_design: RNA sequencing of patient-derived xenograft (PDX) models using Illumina TruSeq Library prep and sequenced on Illumina HiSeq 2500 and NovaSeq

first: W

last: Brennen

first: Yezi

last: Zhu

middle: M

first: Susan

last: Dalrymple

first: Lizamma

last: Antony

first: Radhika

last: Patel

first: Brian

last: Hanratty

first: Alan

last: Meeker

first: S

last: Zheng

first: Jody

last: Hooper

first: Jun

last: Luo

first: Angelo

last: De Marzo

first: Eva

last: Corey

first: Jianfeng

last: Xu

first: Michael

last: Haffner

first: Srinivasan

last: Yegnasubramanian

first: Peter

middle: S

last: Nelson

first: William

middle: G

last: Isaacs

first: John

middle: T


title: Arabidopsis thaliana in altered gravity: WS in C-9 parabolic flight, 2015

first: Robert

last: Ferl

overall_design: Sterilized seeds were planted on 0.5x MS Phytagel™ media, and maintained at the University of Florida at 19 ± 2 °C, with 24-h fluorescent lighting of about 80 m-2 s-1 PAR. Plates were transported to Ellington Airport, TX, inside a cooler lit with an LED light bank. A makeshift grow area was set up at the experimental location using a fluorescent light bank. Kennedy Space Center Fixation Tubes (KFTs) were preloaded with RNAlater™ fixative.  The morning before the C-9 parabolic flight experiment, seedlings were transplanted to the sample chambers of the KFTs, onto moistened Kimwipes shaped roughly into a cylinder. The following day, KFTs were taken onboard the C-9 aircraft. KFTs were actuated in level flight before the onset of parabolic flight, immediately at the start of the first parabola, mid-way through the first parabola at the hypergravity to microgravity, and after the first, third, and tenth parabolas. Samples were stored at 4 °C, and transported on ice back to UF, where they were stored at -80 °C. Samples were later removed from -80 °C, roots were dissected from shoot tissues, and roots were grouped into 3 replicates per condition. Total RNA was extracted from roots and submitted for microarray analysis. The Affymetrix GeneChip Arabidopsis Gene (AraGene) 1.0 ST array was used to measure gene expression levels. The transcriptomic data from the samples fixed in parabolic flight were then compared to those fixed during level flight in order to identify differentially-expressed genes associated with parabolic flight patterns.

first: Brandon

last: Califar

first: Agata

last: Zupanska

first: Jordan

last: Callaham

first: Matthew

last: Bamsey

first: Thomas

last: Graham

first: Anna-Lisa

last: Paul


title: Arabidopsis thaliana in altered gravity: the 14-3-3κ:GFP overexpression line in C-9 parabolic flight, 2013

overall_design: Sterilized seeds were planted on 0.5x MS Phytagel™ media, and maintained at the University of Florida at 19 ± 2 °C, with 24-h fluorescent lighting of about 80 m-2 s-1 PAR. Plates were transported to Ellington Airport, TX, inside a cooler lit with an LED light bank. A makeshift grow area was set up at the experimental location using a fluorescent light bank. Kennedy Space Center Fixation Tubes (KFTs) were preloaded with RNAlater™ fixative.  The morning before the C-9 parabolic flight experiment, seedlings were transplanted to the sample chambers of the KFTs, onto moistened Kimwipes shaped roughly into a cylinder. The following day, KFTs were taken onboard the C-9 aircraft. KFTs were actuated in level flight before the onset of parabolic flight, and after the first, third, and tenth parabolas. Samples were stored at 4 °C, and transported on ice back to UF, where they were stored at -80 °C. Samples were later removed from -80 °C, and seedling roots were dissected from shoot tissues. Roots were grouped into 3-4 replicates per condition, and total RNA was extracted from roots and submitted for microarray analysis. The Affymetrix GeneChip Arabidopsis Gene (AraGene) 1.0 ST array was used to measure gene expression levels. The transcriptomic data from the samples fixed in parabolic flight were then compared to those fixed during level flight in order to identify differentially-expressed genes associated with parabolic flight patterns.


title: Cytotoxic lymphocytes use mechanosurveillance to target biophysical vulnerabilities in cancer

city: CHICAGO

first: Ekrem Emrah

last: Er

state: IL

address: 909 S  WOLCOTT AVE

department: Physiology and Biophysics

institute: The University of Illinois at Chicago

summary: Immune cells identify cancer cells by recognizing characteristic biochemical features indicative of oncogenic transformation. Cancer cells have characteristic mechanical features, as well, but whether these biophysical properties also contribute to destruction by the immune system is not known. In the present study, we found that enhanced expression of myocardin related transcription factors (MRTFs), which promote migration and metastatic invasion, paradoxically compromised lung colonization by melanoma and breast carcinoma cells in an immune-mediated manner. Cancer cells with increased MRTF signaling were also more sensitive to immune checkpoint blockade therapy in mice and humans. The basis for this vulnerability was not biochemical, but biophysical. MRTF expression strengthened the actin cytoskeleton, increasing the rigidity of cancer cells and thereby making them more vulnerable to cytotoxic T lymphocytes and natural killer cells. These results reveal a mechanical dimension of immunosurveillance, which we call mechanosurveillance, that is particularly relevant to the targeting of metastatic disease.

overall_design: We report the genes induced by MRTFA or MRTFB overexpression in two mouse cancer cell lines E0771 and B16F10

first: Maria

last: Tello-Lafoz

first: Morgan

last: Huse

first: Ekrem

last: Emrah Er


title: Profiling the response of Arabidopsis thaliana to altered gravity environments: Exposure of the 14-3-3κ:GFP overexpression line on the F-104 Starfighter, second flight


title: Regulatory diversity contributes to divergent transcriptional response to dietary changes in mammals

city: Cambridge

first: Kevin

middle: Richard

last: Costello

state: Cambridgeshire

address: Genetics Building Downing St.

department: Department of Genetics

institute: Univerity of Cambridge

summary: Regulatory innovation is central to the evolution of species. Different nutritional sources are one environmental pressure that can select for novel regulatory elements. Dietary composition changes, including exposure to “western” diets with excess fat content, can lead to transcriptional regulatory changes in the liver. In order to investigate how transcriptional regulatory changes in response to a high fat diet diverge across species, we profiled chromatin accessibility, histone modifications and the transcriptome in livers of rhesus macaques and mice fed high fat and normal diets.

overall_design: To determine the impact changes in diet have on chromatin accessibility and transcription in adult rhesus macaques, we performed the ATAC-seq, ChIP-seq, and RNA-seq on rhesus macaque liver biopsies that were collected before and after the animals were fed a high fat diet for a 6 month period.

middle: R

first: Heon

last: Shin

first: Candi

last: Trac

first: Oleg

last: Varlamov

first: Dustin

last: Schones


title: YBX1 is selectively required for maintaining myeloid leukemia cell survival by regulating mRNA stability in an m6A-dependent manner [RNA-Seq]

city: wuhan

first: Haojian

last: Zhang

state: Hubei

address: Donghu Rd

department: Medical Research Institute

country: China

institute: Wuhan university

summary: we show that YBX1 is specifically required for maintaining myeloid leukemia cell survival but is dispensable for normal hematopoiesis. We found that expression of YBX1 is significantly upregulated in myeloid leukemia cells, and deletion of YBX1 significantly induces apoptosis, coupled with reduced proliferation and impaired leukemic capacity of primary human and mouse acute myeloid leukemia (AML) cells in vitro and in vivo. Loss of YBX1 does not obviously affect normal hematopoiesis. Mechanistically, YBX1 interacts with IGF2BPs and stabilizes m6A-tagged RNA. Moreover, YBX1 deficiency promotes mRNA decay of MYC and BCL2 in an m6A-dependent manner, which contributes to the defective survival due to YBX1 deletion. Thus, our findings uncover a selective and critical role of YBX1 in maintaining myeloid leukemia survival that might provide a rationale for the therapeutic targeting of YBX1 in myeloid leukemia.

overall_design: RNAseq of leukemia cells from WT and YBX1-/- mice

first: Mengdie

last: Feng

first: Xueqin

last: Xie

first: Guoqiang

last: Han


title: Gene expression changes in medulloblastoma due to Myc overexpression and Mitotic inhibition with AZD1152 Aurora Kinase  B Inhibitior

city: Montreal

first: Roberto

middle: Jose

last: Diaz

state: QC

address: 3801 Rue University, Rm 109, 3801 Rue University, Rm 122D

department: Neurosurgery

country: Canada

institute: Montreal Neurological Institute and Hospital, McGill University

summary: Sonic hedgehog medulloblastoma cells with stable overexpression of Myc (UW426-Myc) become sensitized to apoptosis induction when exposed to Aurora kinase B inhibitor AZD1152. We sought to determine the gene expression changes that take place when Myc is overexpressed in UW426 and to determine the genes differentially expressed in UW426-Myc cells compared to wild-type UW426 when exposed tothe drug  AZD1152 that specifically inhibits Aurora kinase B activity.

overall_design: Expression profiles were generated on the Illumina Human HT-12 v4.0 BeadChip platform for UW426-Myc and UW426 cells grown in standard culture media and exposed to no drug, 0.01% DMSO vehicle, or 100 nM AZD1152-HQPA for 48 hrs


title: Acute Ozone-Induced Changes in Metabolic Processes and Liver Gene Expression: The Impact of Hepatic Vagotomy

city: RTP

first: John

middle: S.

last: House

state: NC

address: 111 TW Alexander Drive

department: Biostatistics & Computational Biology Branch

institute: National Instititute of Environmental Health Sciences

summary: The effects of ozone exposure were examined in rats that have undergone sham surgery or hepatic vagotomy

overall_design: Two-factor design with 5-6 rats each.   Factor 1 = Air vs. Ozone.  Factor 2 = Sham vs. Hepatic Vagotomy

first: Catherin

last: Colonna

first: Andres

last: Henriquez

last: house

first: Alison

last: Motsinger-Reif

first: Devin

last: Alewel

first: Anna

last: Fisher

first: Hongzu

last: Ren

first: Samantha

last: Snow

first: Mette

last: Schladweiler

first: Collete

last: Miller

first: Prasada

last: Kodavanti

first: Urmila

middle: P


title: YBX1 is selectively required for maintaining myeloid leukemia cell survival by regulating mRNA stability in an m6A-dependent manner [RIP-Seq]

first: Haojian

last: Zhang

summary: we show that YBX1 is specifically required for maintaining myeloid leukemia cell survival but is dispensable for normal hematopoiesis. We found that expression of YBX1 is significantly upregulated in myeloid leukemia cells, and deletion of YBX1 significantly induces apoptosis, coupled with reduced proliferation and impaired leukemic capacity of primary human and mouse acute myeloid leukemia (AML) cells in vitro and in vivo. Loss of YBX1 does not obviously affect normal hematopoiesis. Mechanistically, YBX1 interacts with IGF2BPs and stabilizes m6A-tagged RNA. Moreover, YBX1 deficiency promotes mRNA decay in an m6A-dependent manner, which contributes to the defective survival due to YBX1 deletion. Thus, our findings uncover a selective and critical role of YBX1 in maintaining myeloid leukemia survival that might provide a rationale for the therapeutic targeting of YBX1 in myeloid leukemia.

overall_design: RIP-seq in 293T cells


title: YBX1 is selectively required for maintaining myeloid leukemia cell survival by regulating mRNA stability in an m6A-dependent manner [SLAM-seq]

overall_design: SLAMseq of leukemia cells from WT and YBX1-/- mice

first: Mengdie

last: Feng


title: YBX1 is selectively required for maintaining myeloid leukemia cell survival by regulating mRNA stability in an m6A-dependent manner

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: RUNX1/ETO and mutant KIT both contribute to programming the transcriptional and chromatin landscape in t(8;21) AML (RNA-Seq)

city: Birmingham

first: Salam

middle: Adli

last: Assi

address: IBR

department: Institute for Cancer and Genomic Sciences

institute: University of Birmingham

summary: Acute myeloid leukemia development occurs in a step-wise fashion whereby an original driver mutation is followed by additional mutations. The first type of mutations tends to be in genes encoding members of the epigenetic/transcription regulatory machinery (i.e. RUNX1, DNMT3, TET2), while the secondary mutations often involve genes encoding members of signalling pathways that cause uncontrolled growth of such cells such as the growth factor receptors c-KIT of FLT3. Patients usually present with both types of mutations, but it is currently unclear how both mutational events shape the epigenome in developing AML cells. To this end we generated an in vitro model of t(8;21) AML by expressing its driver oncoprotein RUNX1-ETO with or without a mutated (N822K) KIT protein. The expression of N822K–c-KIT strongly increases the self-renewal capacity of RUNX1-ETO expressing cells. Global analysis of gene expression changes and alterations in the epigenome show that N822K–c-KIT expression profoundly influences the open chromatin landscape and transcription factor binding. However, our experiments also show that double mutant cells still differ from their patient derived counterparts, highlighting the importance of studying patient cells to obtain a true picture of how gene regulatory networks have been reprogrammed during tumourigenesis.

overall_design: RNA sequencing data were used to study mutant KIT in t(8;21) AML

first: Paulynn

last: Chin

first: Anetta

last: Ptasinska

first: Maria

last: Imperato

first: Peter

last: Cockerill

first: Constanze

last: Bonifer


title: RUNX1/ETO and mutant KIT both contribute to programming the transcriptional and chromatin landscape in t(8;21) AML (ATAC-Seq)

overall_design: ATAC sequencing data were used to study mutant KIT in t(8;21) AML


title: RUNX1/ETO and mutant KIT both contribute to programming the transcriptional and chromatin landscape in t(8;21) AML (ChIP-Seq)

overall_design: ChIP sequencing of ETO, RUNX1, GATA2 and JUND transcription factors are used to study mutant KIT in t(8;21) AML


title: Transcriptome analysis of EDS1 4h after Pst AvrRps4- triggered immunity

city: Cologne

first: Deepak

middle: Dharamchand

last: Bhandari

email: bhandari@mpipz.mpg.de, dharamch@msu.edu

state: nrw

address: Carl-von-linne-weg, 10

department: Plant-Microbe interactions

country: Germany

institute: Employer

summary: We present here the transcriptominc changes occuring after TNL-triggered immunity after infection with pst AvrRps4 in a point mutant of EDS1, EDS1-R493A. This data of 4 h treatment, adds upon the previous study GSE116269.

overall_design: mRNA transcripts of Col-0, eds1-2, cEDS1(wt) and EDS1-R493A at 4 hpi with pst AvrRps4 were deep sequenced, in triplicates using illumina. 4 week old plant leaves were syringe infiltrated at a concentration of 0.005

first: Jane

last: Parker

middle: D


title: Endonuclease enrichment TAPS for cost-effective genome-wide base-resolution DNA methylation detection

city: Oxford

first: Jingfei

last: Cheng

state: Oxfordshire

address: Roosevelt Drive

institute: University of Oxford

type: Methylation profiling by high throughput sequencing

summary: We described endonuclease enrichment TAPS (eeTAPS), which utilizes dihydrouracil (DHU)-sensitive endonuclease digestion after TAPS to enrich methylated CpG (mCpG). eeTAPS can accurately detect 87% of methylated CpGs in the mouse genome with a sequencing depth comparable to 4x whole genome sequencing. In comparison, reduced representation TAPS (rrTAPS) detected less than 4% of methylated CpGs with 2.5x sequencing depth. Our results demonstrate eeTAPS to be a new strategy for cost-effective genome-wide methylation analysis at single-CpG resolution that can fill the gap between whole-genome and reduced representation sequencing.

overall_design: 5-Methylcytosine and 5-hydroxymethylcytosine detection with eeTAPS and rrTAPS in E14 mESC cell line.

first: Paulina

last: Siejka-Zielińska

first: Chun-Xiao

middle: X

last: Song


title: LncRNA and mRNA expression profiling reveals the molecular mechanism of hyperthermia sensitizing human gastric cancer cisplatin- resistant cell line SGC-7901/DDP

city: Lanzhou

first: Dongmei

last: Chen

address: No. 35 Dingxi east road, chengguan district, Lanzhou, Gansu province

institute: Gansu University of Chinese Medicine

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

summary: Gastric cancer (GC) is the second leading cause of cancer-related death in the world, but due to the emergence of drug resistance, the chemotherapy effect of GC has not been improved. Hyperthermia (HT) can increase the sensitivity of tumor cells to chemotherapeutic drugs and cause the specific expression of related genes. Therefore, we want to confirm that HT can enhance the sensitivity of SGC-7901/DDP cells to cisplatin (DDP) and explore the molecular mechanism of sensitization. To study the optimal experimental conditions with synergistic effect, temperature gradients (41 ℃, 44 ℃, 47 ℃, 50 ℃), time gradients (12 h, 24 h, 36 h) and DDP concentration gradients (1 μg/ml, 2 μg/ml, 3 μg/ml) were established. Then the microarray analysis was performed to explore the molecular mechanism of HT sensitization. Our results showed that 47 ℃ HT+ 2 μg/ml DDP for 24 h could synergistically inhibit the proliferation of SGC7901/DDP cells and significantly promote early apoptosis. Differentially expressed lncRNAs and mRNAs between groups were obtained. ENST00000434470.1(IDI2-AS1), ENST00000592689.1(TTN-AS1) and ENST00000412526.1(LINC00161) may play a pro-apoptotic role, while asRNAs could be a potential target for the treatment of GC. KEGG pathway enrichment showed that DDP+HT may induce apoptosis of SGC7901/DDP cells through GPCR signaling pathway, BARD signaling pathway and TRAIL signaling pathway. In summary, HT can enhance the sensitivity of SGC-7901/DDP cells to DDP by activating related apoptotic genes and pathways.

overall_design: The gene expression in SGC-7901/DDP cells was measured after treatment with 2 μg/ml cisplatin, 47 ℃ hyperthermia for 24 h, and 2 μg/ml cisplatin+47 ℃ hyperthermia for 24 h.

first: Jiajia

last: Liu

first: Jie

last: Meng

first: Che

first: Jing

last: Wang


title: The impact of the genes BBX32 and HY5 on the high light - responsive transcriptome of Arabidopsis thaliana

city: Colchester

first: Ellie

middle: Jane

last: Stallard

state: Essex

address: University of Essex

department: School of Life Sciences

institute: University of Essex

summary: Exposure of mature fully expanded leaves of Arabidopsis to a 7.5 fold increased light intensity  above  growth light conditions (high light; HL) tirggers stress defensive responses  but also initiates cellular processes, that if such conditions persist, can lead to increased photosynthetic capacity. This process is called dynamic acclimation. By using variational Bayesian state space modelling on eariler GEO deposited time series HL data (see GSE78251) a gene regulatory network of (co) transcription factor genes was inferred. The most connected gene in this network is BBX32, which was subequently shown  to be a negative regulator of dynamic acclimation. Also present in the inferred network is HY5, which is known from studies on seedling photomorphogenesis to be antagonistic in its action to BBX32. Subsequently, it was demonstrated that HY5 is indeed a positive regulator of dynamic acclimation.  This RNAseq-based study seeks  to provide gene expression data that will help to link the immediate impact of these genes on the HL transcriptome to the longer term (several days) physiological manifestation of dynamic acclimation.

overall_design: Arabidopsis thaliana (genotype Col-0) that over-express BBX32 (BBX32-10; Holtan et al. (2011) Plant Physiology 156: 2109-2123) and are null for HY5 (hy5-2; Ruckle et al. (2007) Plant Cell 19: 3944-3960) produce the same degree of inhibition of the quantum efficiency of photosynthetic elecron transport upon sustained expsure to HL, both genotypes failing to undergo dynamic acclimation.  Therefore, similar cohorts of genes may be affected in short term HL exposure. Therefore, plants were exposed to HL for 3.5h and then sampled for RNA from their fully expanded leaves. low light control samples were to be run in parallel. The duration of the HL exposure was chosen because based on time sereis daat most inductio of differential expression of genes was completed after this time. These data allow for the initial validation of the gene regulatory network centred on BBX32 (as well as future iterations and variations of this network), but will also, with further analysis yet to be done,  allow the identification of key genes downstream from BBX32 and HY5 that control both initial responses to HL and the establishment of dynamic acclimation.

middle: J

first: Philip

last: Mullineaux

first: Marino

last: Exposito-Rodriguez

first: Irabonosi

last: Obomighie


title: The expression profiling of the anterior cingulate cortex and hippocampus in chronic inflammatory pain mice

city: Hirosaki

first: Shuji

last: Shimoyama

state: Aomori

address: 5 Zaifu-cho

department: Department of Neurophysiology

institute: Hirosaki University Graduate School of Medicine

summary:
Chronic pain is a persistent unpleasant sensation that produces pathological synaptic plasticity in the central nervous system. Some of the studies demonstrate that the anterior cingulate cortex (ACC) is a critical area for nociceptive and chronic pain processing. Our previous study revealed that animal models of chronic pain alter excitatory and inhibitory synaptic transmission in the ACC. However, it is not clear what molecules are involved in the alterations of synaptic plasticity in the ACC of chronic pain models.
To identify genes with altered expression in the ACC of a chronic pain model, whole transcriptome analysis were performed. In addition to the ACC, whole transcriptome analysis was also performed in the hippocampus, a brain region that has not been reported to be associated with chronic pain. Complete freund's adjuvant (CFA, Sigma-Aldrich, #F5881) into the left hind paw was used for induce chronic inflammatory pain in this study.

overall_design: Control or 50% of CFA were injected into the dorsal surface of the left hindpaw of mice (n=3, respectively). Two days after the injection, the mice were deeply anesthetized and transcardially perfused, then brains were quickly removed and punched out the ACC and hippocampus. The samples were subjected to whole transcriptome analysis or qRT-PCR.

first: Kohei

last: Koga


title: ATAC-Seq of the Yeast Metabolic Cycle

city: Boston

first: Salvador

last: Casani

state: MA

address: 450 Brookline Avenue

department: Cancer Biology

institute: Dana Farber Cancer Institute

summary: Time course extraction of the Yeast Metabolic cycle, followed by ATAC seq processing. These files are used in a multi-omics study to complement a series of datasets that cover other moluecular layers of the Yeast Metabolic Cycle, including metabolomics, gene expression and histone modificaiton datasets. Our goal in this project is to create statistical integratory tools to comprehend YMC regulatory mechanism.

overall_design: 18 Samples were extracted at 18 different Timepoints throught the Yeast Metabolic Cycle. Samples were collected in two batches.

first: Casani

last: Salvador

first: Xi

last: Shidong

first: Tarazona

last: Sonia

first: Mellor

last: Jane

first: Conesa

last: Ana


title: Lignin deposits in xylem vessels of pedicel regulate water transport during seed maturation in soybean (Glycine max L. Merr.)

city: Fukuoka

first: Yushi

last: Ishibashi

state: Fukuoka

address: 744 Motooka, Nishi-ku

department: Department of Bioresource Sciences

institute: Kyushu University, Faculty of Agriculture

summary: Seed desiccation during maturation is important process for seed post-maturation behavior and harvest. However, the desiccation mechanism in soybean seed maturation is hardly known. In this study, water content in seed, pod and pedicel decreased faster than that in peduncle and stem. Therefore, we focus on the pedicel during seed maturation. By morphological analysis, the deposits in xylem vessels were confirmed in pedicel at 61 day after flowering (DAF), when there are not the deposits in peduncle. It was clarified by microarray analysis that lignin biosynthesis related genes expressed in pedicel at 61 DAF. Indeed, GmPAL, Gm4CL, GmC3H and GmCAD, which are lignin biosynthesis related genes, increased in pedicel during seed maturation. Furthermore, lignin content in pedicel also increased toward at 61 DAF and accumulated in the xylem vessels. These results suggested that lignin deposits into xylem vessels in pedicel cause the soybean seed desiccation during seed maturation.

overall_design: Differentially expressed genes between the pedicels at 51 and 66 days after flowering in soybean.

first: Haruka

last: Itoyama

first: Andressa

middle: C

last: Nakagawa

first: Yuri

last: Ariyoshi

first: Nobuyuki

last: Ario

first: Takashi

last: Yuasa

first: Mari

last: Iwaya-Inoue


title: A dynamic network reveals the novel characteristics of miRNA regulation over time in response to the ABA hormone in Arabidopsis (microRNA)

city: Beijing

first: Xu

middle: Zhao

last: Gao

state: Beijing

address: The Summer Palace Road No. 5

department: College of Biological Sciences

institute: Peking University

type: Non-coding RNA profiling by high throughput sequencing

summary: MicroRNAs (miRNAs) participate in post-transcriptional regulation as short non-coding RNAs together with the transcription factors (TFs) and other regulatory factors such as alternative splicing (AS), which constitute complex gene regulatory networks. Following stimulation with ABA in Arabidopsis, we performed RNA-seq and small RNA-seq simultaneously at consecutive time points, and found that miRNAs respond rapidly under stress condition. Further functional analyses revealed that miRNAs classified according to different response time points play a role by binding different target genes. Systematic analysis including the static network of TF-target, TF-miRNA, miRNA-target and the time series DEGs and DE-miRNAs revealed a miRNA-mRNA dynamic regulatory network. We found that miRNAs in miRNA-containing feed-forward loops (M-FFLs) could enhance co-expression and crosstalks between different FFLs of network. Additionally, the differential transcript usage (DTU) and differential alternative splicing (DAS) analysis increased regulatory diversity between miRNA and its target genes. Collectively, our findings highlighted the systematical and precise post-transcriptional regulation of miRNAs in plant.

overall_design: Totally fifty-six samples, two treatments with seven time points and two replicates, and each sample has two files of paired-end data.

first: Z

first: R

last: Yu

first: L

last: Li

first: X

middle: W

last: Deng

first: H

last: He


title: A dynamic network reveals the novel characteristics of miRNA regulation over time in response to the ABA hormone in Arabidopsis

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

overall_design: Refer to individual Series


title: A dynamic network reveals the novel characteristics of miRNA regulation over time in response to the ABA hormone in Arabidopsis (mRNA)


title: Harsh Parenting Predicts Novel HPA Receptor Gene Methylation and   NR3C1 Methylation Predicts Cortisol Daily Slope in Middle Childhood

city: Phoenix

first: Ignazio

middle: Stefano

last: Piras

state: Arizona

address: 445 N. Fifth Street, Phoenix

institute: Translational Genomic Research Institute

summary: Adverse experiences in childhood are associated with altered hypothalamic pituitary adrenal axis function and negative health outcomes throughout life. It is now commonly accepted that abuse and neglect can alter epigenetic regulation of HPA genes. Accumulated evidence suggests harsh parenting practices such as spanking are also strong predictors of negative health outcomes. We predicted harsh parenting at 2.5 years old would predict HPA gene DNA methylation similarly to abuse and neglect, and cortisol output at 8.5 years old. Saliva samples were collected three times a day across three days to estimate cortisol diurnal slopes. Methylation was quantified using the Illumina Infinium MethylationEPIC array BeadChip (850K) with DNA collected from buccal cells. We used principal components analysis to compute a summary statistic for CpG sites across candidate genes. The first and second components were used as outcome variables in mixed linear regression analyses with harsh parenting as a predictor variable. We found harsh parenting significantly predicted methylation of several HPA axis genes, including novel gene associations with AVPRB1, CRHR1, CRHR2, and MC2R (FDR corrected p < 0.05). Further, we found NR3C1 methylation predicted a steeper diurnal cortisol slope. Our results extend the current literature by demonstrating harsh parenting may influence DNA methylation similarly to more extreme early life experiences such as abuse and neglect. Further, we show NR3C1 methylation is associated with diurnal HPA function. Elucidating the molecular consequences of harsh parenting on health can inform best parenting practices and provide potential treatment targets for common complex disorders.

overall_design: Participants were recruited from state birth records for a longitudinal study investigating genetic and environmental influences on childhood health (Lemery-Chalfant et al. 2013). We recruited a sub-sample of monozygotic (MZ) twins (N = 96 individuals; 51% male; 50% Non-Hispanic White, 14.6% Hispanic/Latinx, 8.3% African American, 4.2% Asian American), Mage = 8.5 years, SD = .45. Seventy-one percent of primary caregivers reported currently being married and 91% were moms. Total household income ranged from $6,400 - $300,000 USD (M = $97,057, SD = $64,893) and 21% of families met Federal Medicaid Eligibility based on 2016 standards (Arizona Median Household Income = $53,510, US Census Bureau). Socioeconomic status (SES) was calculated as a mean composite of the family income, primary caregiver education level, and spouse/partner education level. All study procedures were approved by institutional review boards and are in accordance with the Helsinki Declaration of 1975.

first: Candace

last: Lewis

first: Reagan

middle: S

last: Breitenstein

first: Adrienne

last: Henderson

first: Hayley

middle: A

last: Sowards

first: Matthew

last: Huentelman

first: Leah

last: Doane

first: Kathryn

last: Lemery-Chalfant


title: TEM modulates salt tolerance by regulating hormonal components and photo-protection in Arabidopsis

city: Bellaterra

first: Jose Luis

last: Riechmann

state: Barcelona

address: Campus UAB - Edifici CRAG

institute: Center for Research in Agricultural Genomics

summary: Members of the plant specific RAV family of Transcription Factors regulate several developmental and physiological processes. In the model plant Arabidopsis thaliana, the RAV TEMPRANILLO 1 (TEM1) and TEM2 were previously described as negative regulators of the floral transition. Nevertheless, a transcriptomics analysis of transgenic plants overexpressing TEM1 revealed over-representation of GO categories related to abiotic stress response.

overall_design: Examination of TEM1 overexpression plants and wild-type plants, two replicates each (4 samples)

first: Andrea

middle: E

last: Aguilar-Jaramillo

first: Soraya

last: Pelaz

first: Jose

middle: L


title: Prostate H3K4me3 ChIP-seq and the transgenerational effects of pesticide chlordecone on prostate

city: Rennes

first: Fatima

last: SMAGULOVA

address: 9 av. Prof. Léon Bernard

country: France

institute: Irset - U1085


title: Ovulation suppression prevents the increase in egg aneuploidy with maternal age in mammals

city: Vienna

first: Kikuë

last: Tachibana

state: --- Select a state ---

address: Dr.-Bohr-Gasse 3

country: Austria

institute: IMBA

summary: Multiple mechanisms likely contribute to the increase in chromosome missegregation that leads to production of aneuploid eggs and fetuses at advanced maternal age.  It is therefore considered unlikely that a single approach could prevent age-related egg aneuploidy. Here we show using three independent approaches that ovulation reduction is sufficient to prevent egg aneuploidy in aged mammals. To gain insights into the mechanism underlying the rescue in egg aneuploidy, we show that ovulation suppression correlates with retention of chromosomal Rec8-cohesin, implying that ovulations are linked to cohesin deterioration. Moreover, we discovered that ageing alters 3D chromatin organization by single-nucleus Hi-C (snHi-C). Extruded loops increase in size with age and this is retarded by ovulation reduction. We conclude that reducing ovulations leads to retention of chromosomal Rec8, which maintains interphase chromatin structure and promotes chromosome segregation and production of euploid eggs. Importantly, our data suggest that ovulation itself contributes to the maternal age effect. This work provides the first experimental evidence that progesterone treatment reduces egg aneuploidy and suggests that hormonal contraception can reduce the risk of trisomic pregnancies like Down’s syndrome at advanced maternal age.

overall_design: We generated 67 Hi-C libraries from oocytes of 2-2.5 month old (young), 14-18 month old (aged), 14-15 month old virgin (virgin) and 14-15 month old constant-mated (mated) mice. (20 young, 20 aged, 12 virgin aged, 15 mated aged).

first: Emmanouella

last: Chatzidaki

first: Johanna

last: Gassler

first: Sean

last: Powell


title: mRNA expression in endothelial cells stimulated with isolated mitochondria

first: Christoph

last: Binder

address: Lazarettgasse 14

department: Laboratory Medicine

institute: Medical University of Vienna

summary:
Purpose: To compare gene expression profiles in endothelial cells stimulated with mitochondria isolated from vehicle-(MitoCo) or LPS-activated(MitoStress) THP-1 cells.
Result: We identified Type I Interferon and TNF pathways induced by mitochondria isolated from activated cells.

overall_design: HUVECs stimulated for 6 hours with mitochondria isolated from vehicle- or LPS-activated THP-1 cells

first: Afonyushkin

last: Taras

first: Florian

last: Puhm

first: Michael

last: Schuster

first: Thomas

last: Penz


title: The transgenerational effects of pesticide chlordecone on prostate

summary: The environmental factors such as pesticides could affect the developmental processes and cause the phenotypic changes. Moreover, the changes could be transferred to a subsequent generation via gametes. In this project we studied whether the pesticide chlordecone could cause the developmental effects and cause the transgenerational inheritance in outbred mouse strain (Swiss). Mice were treated during development (E6.5-E15.5) at dose 100 µg/kg/day and the progeny of exposed mice (F1) were crossed for three generations. The prostate of the first (F1) and third generation males (F3) were used for RNA-seq-analysis. We used three biological replicates for each condition.

overall_design: 3 control samples and 3 chlordecone (kepone)-treated samples for both F1 and F3 generations

last: Smagulova

first: Louis

last: Legoff


title: Antibiotics treatment ameliorates TET2 loss-of-function associated hematological malignancies

city: Houston

first: Jia

last: Li

state: Texas

address: 2121 W HOLCOMBE BLVD

department: CEDP

institute: Guangzhou Medical University

summary: TET2 is one of the most frequently mutated genes in hematological malignancies. TET2 mutations are also frequently observed in healthy individuals with clonal hematopoiesis. Additional factors, such as inflammatory stress, might promote the expansion and initiate the pre-leukemic condition of Tet2 deficient hematopoietic stem cells. Antibiotics treatment is frequently used in normal individuals and patients with hematological malignancies treatment to suppress infection-induced inflammation. However, prolonged antibiotics treatment resulted in bone marrow suppression and gut microbiota alteration. In our study, we observed that the expansion of Tet2 deficient myeloid cells are positively correlated with serum cytokine levels at pre-malignant stages. We then evaluated the effect of antibiotic treatment in Tet2 deficient myeloid and lymphoid tumors in vivo. We found that antibiotics treatment suppressed the growth of Tet2 deficient malignant cells in vivo. RNA-seq analysis revealed significant changes in immune related signaling pathways (e.g., Tnf-α signaling) in antibiotics treated Tet2 deficient myeloid and lymphoid tumor cells. Suppression of Tnf-α signaling using pharmacological inhibitors partially suppressed Tet2 deficient tumor cell growth in vivo. In summary, our results suggest that the expansion of Tet2 deficient blood cells are positively associated with a pre-inflammatory condition and suppression of inflammatory pathways may attenuate the progression of TET2 inactivation-associated hematological malignancies.

overall_design:
Normal Tet2KO CD4+ T cells and lymphoma cells were isolated from Tet2 deficient mouse model to identify the differential expressed genes. Tet2KO lymphoma mouse and CMML mouse were treated with and without antibiotics cocktail (ABX). Cells were isolated from these groups to identify the differential expressed genes between ABX treated and untreated groups.
Third-party re-analysis:  LK1 (GSM1902319) and LK2 (GSM1902320) processed data are represented in LK_KO-Tet2KO_CMML_vehicle-Tet2KO_CD4_Tcell-Tet2KO_lymphoma.normalized.txt.

first: Deqiang

last: Sun

first: Yun

last: Huang


title: RNA Sequencing of Tex19.1-/- Mouse Embryonic Stem Cells [RNA-seq]

city: Edinburgh

first: Ian

last: Adams

address: Crewe Road

department: Genome Regulation

institute: MRC Human Genetics Unit

summary: Analysis of the transcriptome of Tex19.1-/- mouse embryonic stem cells generated by sequential gene targeting in E14Tg2a (129/Ola) parental embryonic stem cells.

overall_design: mRNA profiles of Tex19.1+/- and Tex19.1-/- mouse embryonic stem cells were generated by deep sequencing, in triplicate, using Illumina HiSeq.

middle: R

first: Christopher

last: Playfoot


title: Co-expression Networks of mRNAs and non-coding RNAs of bones around implants in hyperlipidemic rats (miRNA-seq data sets)

city: Nanjing

first: Chen

last: Jishuang

state: Jiangsu

address: NO.30 Puzhu Road(S)

department: College of Biotechnology and Pharmaceutical Engineering

institute: Nanjing Tech University

summary: Purpose: Hyperlipidemia has been shown to contribute to reduced implant osseointegration, but the underlying mechanism remains poorly understood. Recently, non-coding RNAs (ncRNAs) have been established as key regulators of various pathophysiological processes. Therefore, the current study aims to examine the expression profiles of mRNAs and ncRNAs in femoral tissues around surgical implants in a murine hyperlipidemia model via RNA sequencing.Materials and method: Twenty adult male Wistar rats were equally divided between an experimental group and a control group, which were fed a high-fat diet and a normal diet, respectively. Titanium root-form implants was inserted into both femoral shafts of each rat in eight weeks. Bone tissues were collected at day 10 after the insertion of the implants and subsequently used for RNA extraction and sequencing. The sequenced reads were refined, assembled and annotated to obtain mRNA, microRNA (miRNA), long non-coding RNA (lncRNA) and circular RNA (circRNA) transcripts. The levels of all types of RNA molecules in both animal groups were quantified and differentially expressed candidates were identified. The function of the identified RNAs were predicted by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis. LncRNA-miRNA-mRNA and circRNA-miRNA-mRNA co-expression network of differentially expressed RNAs were constructed. Real-time polymerase chain reactions (RT-PCR) were performed to validate the expression levels of selected candidates.Results: The serum lipid levels of the experimental group were significant higher than those of the control group (p < 0.05). In total, 389 mRNAs, 73 miRNAs, 770 lncRNAs and 7 circRNAs were shown to be differentially expressed (p < 0.05, fold change > 2). GO analysis found that regulation of bone mineralization, negative regulation of chondrocyte differentiation and bone development changed significantly. The network that maybe related to osteogenesis included 6 mRNAs, 8 miRNAs, 6 circRNAs, 119 lncRNAs and 362 associations. Expression level of most RNAs detected by RT-PCR was consistent with that by RNA sequencing. Conclusion: Functional analysis predicted a panel of differentially expressed mRNAs and ncRNAs associated with osteogenesis. The results of the current study will greatly contribute to the elucidation of the mechanism for implant osseointegration under hyperlipidemia.

overall_design: The expression profiles of miRNAs of femur bones at 10 days after implantation in hyperlipidemic and normal rats

first: Xiaofei

last: Dong

first: Jing

last: Lan


title: H3K9me3 ChIP Sequencing of Tex19.1-/- Mouse Embryonic Stem Cells [ChIP-seq]

summary: Analysis of anti-histone H3K9me3 chromatin immunoprecipitation profiles of Tex19.1-/- mouse embryonic stem cells generated by sequential gene targeting in E14Tg2a (129/Ola) parental embryonic stem cells.

overall_design: H3K9me3 chromatin profiles of Tex19.1+/- and Tex19.1-/- mouse embryonic stem cells were generated by deep sequencing anti-histone H3K9me3 chromatin immunoprecipitates, in triplicate, using Illumina HiSeq.


title: H3K9me3 ChIP-Seq and RNA-seq of Tex19.1-/- Mouse Embryonic Stem Cells


title: CCNE1 Overexpression Causes Chromosome Instability in Liver Cells and Liver Tumor Development in Mice

city: Rochester

first: Hu

state: MN

address: 200 First Street, Gonda Building G19-408

department: Molecular Pharmacology & Experimental Therapeutics

institute: Mayo Clinic

summary: Background & Aims: The CCNE1 locus, which encodes cyclin E1, is amplified in many types of cancer cells and is activated in hepatocellular carcinomas (HCCs) from patients infected with hepatitis B virus or adeno-associated virus type 2, due to integration of the virus nearby. We investigated cell cycle and oncogenic effects of cyclin E1 overexpression in tissues of mice.    Methods: We generated mice with doxycycline-inducible expression of Ccne1 (Ccne1T mice) and activated overexpression of cyclin E1 from age 3 weeks onwards. At 14 months of age, livers were collected from mice that overexpress cyclin E1 and non-transgenic mice (controls) and analyzed for tumor burden and by histology. Mouse embryonic fibroblasts (MEFs) and hepatocytes from Ccne1T and control mice were analyzed to determine the extent to which cyclin E1 overexpression perturbs S-phase entry, DNA replication, and numbers and structures of chromosomes. Tissues from 4-month-old Ccne1T and control mice (at that age were free of tumors) were analyzed for chromosome alterations, to investigate the mechanisms by which cyclin E1 predisposes hepatocytes to transformation.     Results: Ccne1T mice developed more hepatocellular adenomas and HCCs than control mice. Tumors developed only in livers of Ccne1T mice, despite high levels of cyclin E1 in other tissues. Ccne1T MEFs had defects that promoted chromosome missegregation and aneuploidy, including incomplete replication of DNA, centrosome amplification, and formation of non-perpendicular mitotic spindles. Whereas Ccne1T mice accumulated near-diploid aneuploid cells in multiple tissues and organs, polyploidization was observed only in hepatocytes, with losses and gains of whole chromosomes, DNA damage, and oxidative stress.     Conclusions: Livers, but not other tissues of mice with inducible overexpression of cyclin E1, develop tumors. More hepatocytes from the cyclin E-overexpressing mice were polyploid than from control mice, and had losses or gains of whole chromosomes, DNA damage, and oxidative stress – all of these have been observed in human HCC cells. The increased risk of HCC in patients with hepatitis B virus or adeno-associated virus type 2  infection might involve activation of cyclin E1 and its effects on chromosomes and genomes of liver cells.

overall_design: Liver, kidney and lung tissue from Ccne1-overexpressing or control mice were subjected to RNA-sequencing. Tet-inducible Ccne1; rtTA mice and rtTA control mice were treated with doxycyclin (dox) from weaning age (3wks) onwards. Mice were euthanized at 4 months of age and tissues were subjected to RNA-sequencing.

first: Jan

last: van Deursen


title: BMI1 Maintains the Regulatory T cell Epigenomic Landscape to Prevent Inflammatory Bowel Disease (Mouse ATAC-Seq)

status: Public on Mar 31 2021

first: Aditya

last: Bhagwate

address: 200 1st Street SW

summary: FOXP3+ Treg cells are expanded within the inflamed intestine of human Crohn’s disease, yet FOXP3-mediated gene repression within these cells is lost. The Polycomb repressive complexes play a role in FOXP3 target gene regulation, but deeper mechanistic insight is incomplete. We have now specifically identified the Polycomb Repressive Complex 1 (PRC1) family member, BMI1 in the regulation of a pro-inflammatory enhancer network in both human and murine Tregs. Using human Tregs and lamina propria T cells, we inferred PRC1 to regulate Crohn’s associated gene networks through assays of chromatin accessibility. Conditional deletion of BMI1 in murine FOXP3+ cells led to systemic inflammation. BMI1-deficient Tregs beared a TH1/TH17-like phenotype as assessed by assays of genome wide transcription, chromatin accessibility and proteomic techniques. Finally, BMI1 mutant FOXP3+ cells did not suppress colitis in the adoptive transfer model of human inflammatory bowel disease. We propose that BMI1 plays an important role in enforcing Treg identity in vitro and in vivo. Loss of Treg identity via genetic or transient BMI1 depletion perturbs the epigenome and converts Tregs into Th1/Th17-like proinflammatory cells, a transition relevant to human Crohn’s disease associated CD4+ T cells.

overall_design: Comparison of accessible chromatin regions between EZH2- and BMI1-deficient to WT murineTreg cells.

first: Michelle

middle: M

last: Gonzalez

first: Adebowale

middle: O

last: Bamidele

first: Phyllis

last: Svingen

first: Mary

last: Sagstetter

last: Smyrk

first: Joseph

last: Gaballa

first: Feda

middle: H

last: Hamdan

first: Robyn

last: Kosinsky

first: Hunter

last: Gibbons

first: Zhifu

first: Zhenqing

last: Ye

first: Asha

last: Nair

first: Guilherme

last: Ramos

first: Manuel

middle: B

last: Braga Neto

first: Alexander

middle: Q

last: Wixom

first: Angela

last: Mathison

first: Steven

last: Johnsen

first: Raul

last: Urrutia

first: William

last: Faubion


title: BMI1 Maintains the Regulatory T cell Epigenomic Landscape to Prevent Inflammatory Bowel Disease (ChIP-Seq)

first: Aditya

last: Bhagwate

overall_design: Cultured Jurkat cells were harvested from suspension and pelleted down. Jurkat T cells were transiently transfected with indicated plasmids by electroporation at 315 mV for 10 ms and harvested 36 to 48 hours later. 2 x 10^6 Jurkat cells were transfected with 120 nM of ON-TARGETplus Human BMI1 siRNA (648) (Dharmacon cat# L-005230-01-0005) or 100 nM of ON-TARGETplus Human EZH2 siRNA (2146) (Dharmacon, cat# L-004218-00-0005). After treatment, he cells were incubated with 2 μg of histone modification-specific antibodies overnight at 4 °C. The following antibodies were used: anti-H3K27ac (Abcam, Cat# ab4729), anti-H3K27me3 (Cell Signaling Technology, Cat# 9733S). ChIP DNA was purified using the Mini-Elute PCR purification kit (Qiagen) after treatment with DNase-free RNase A (10 mg/mL, Thermo Scientific Cat #EN0531) and Proteinase K (20 mg/mL, Ambion, Cat #AM2546). Purified DNA was subjected to targeted real-time PCR to confirm enrichment. ChIP DNA library preparation was performed using 10 ng per reaction, and input DNA using the Ovation Ultralow DR Multiplex System (NuGen). The ChIP-seq libraries were subjected to sequencing by the Mayo Clinic Medical Genomics Core. These were sequenced to 50 base pairs from both ends using the Illumina HiSeq 2000.   After adding 30 μL of protein G-agarose magnetic beads, the reactions were incubated for another 3 h. Beads were washed extensively with ChIP buffer, high-salt buffer, LiCl2 buffer, and TE buffer. Bound chromatin was eluted and reverse-crosslinked at 65 °C overnight. DNA was purified using the Mini-Elute PCR purification kit (Qiagen) after treatment with RNase A and proteinase K. Enrichment was confirmed by targeted real-time PCR in positive and negative genomic loci. For next-generation sequencing, ChIP-seq libraries were prepared from 10 ng of ChIP, and input DNA with the Ovation Ultralow DR Multiplex system (NuGEN). The ChIP-seq libraries were sequenced to 51 base pairs from both ends using the Illumina HiSeq 2000 in the Mayo Clinic Medical Genomics Core.

first: Michelle

last: Gonzalez

first: Adebowale

last: Bamidele

first: Thomas

last: Sun

middle: P


title: Co-expression Networks of mRNAs and non-coding RNAs of bones around implants in hyperlipidemic rats

first: Chen

last: Jishuang


title: BMI1 Maintains the Regulatory T cell Epigenomic Landscape to Prevent Inflammatory Bowel Disease (Human ATAC-Seq)

overall_design: Examined average binding profiles representing open chromatin state at ATAC peaks associated with Crohn’s disease-related genes in in vitro generated Tregs derived from PBMCs.

first: Phyllis

last: Svingen

first: Mary

last: Sagstetter

last: Smyrk

first: Joseph

last: Gaballa

first: Feda

last: Hamdan

first: Robyn


title: Co-expression Networks of mRNAs and non-coding RNAs of bones around implants in hyperlipidemic rats (RNA-seq data sets)

overall_design: The expression profiles of mRNAs and non-coding RNAs of femur bones at 10 days after implantation in hyperlipidemic and normal rats

first: Xiaofei

last: Dong

first: Jing

last: Lan


title: TIGIT expression on CD8+ T cells correlates with higher cytotoxic capacity

city: Bethesda

first: Jana

last: Blazkova

address: 9000 Rockville Pike

institute: NIH

summary: Persistent exposure to antigen leads to T cell exhaustion and immunologic dysfunction. We examined the immune exhaustion markers TIGIT and PD-1 in HIV-infected and healthy individuals and the relationship with cytotoxic CD8+ T lymphocyte (CTL) activity. Frequencies of TIGIT but not PD-1 positively correlated with CTL activity in HIV-aviremic and healthy individuals; however, there was no correlation in HIV-viremic individuals. Transcriptome analyses revealed upregulation of genes associated with antiviral immunity in TIGIT+ versus TIGIT-CD8+ T cells. Our data suggest that TIGIT+CD8+ T cells do not necessarily represent a state of immune exhaustion and maintain an intrinsic cytotoxicity in HIV-infected individuals.

overall_design: 29 total patients, with 8 aviremic, 6 viremic, and 15 negative. For each patients, expression was measured in CD8+ T-cells, both TIGIT+ and TIGIT-

first: Erin

middle: D

last: Huiting

first: Arun

middle: K

last: Boddapati

first: Victoria

last: Shi

first: Emily

last: Whitehead

first: Jesse

last: Justement

first: Jeffrey

last: Nordstrom

first: Susan

last: Moir

first: Justin

last: Lack

first: Tae-Wook

last: Chun


title: BMI1 Maintains the Regulatory T cell Epigenomic Landscape to Prevent Inflammatory Bowel Disease (Microarray)

first: Aditya

last: Bhagwate

overall_design: We freshly isolated splenic Tregs (CD4+ CD25++ FOXP3+ GFP+) from WT and BMI1-/- animals. These were then stimulated with αCD3/CD28 for 24 hours.

first: Michelle

last: Gonzalez

first: Adebowale

last: Bamidele

first: Phyllis

last: Svingen

first: Thomas

middle: C

last: Kosinsky

first: Hunter

last: Gibbons

first: Zhifu

last: Sun

first: Zhenqing

last: Ye

first: Asha

last: Nair

first: Guilherme

last: Ramos

first: Manuel

last: Braga Neto

first: Alexander

last: Wixom

first: Angela

last: Mathison

first: Steven

last: Johnsen

first: Raul

last: Urrutia

first: William

last: Faubion


title: Differential gene expression analysis of Wildtype and pgp1 mutant at 16°C Long day condition

city: Anam-ro 145, Seongbuk-Gu

first: Hendry

last: Susila

state: Seoul

address: Anam-ro 145

department: Life Science

country: South Korea

institute: Korea University

summary: We sequence mRNA of WT and pgp1 seedling grown at 16°C, day 8 after germination, ZT 16

overall_design: Examination of mRNA level in WT and pgp1 seedling grown at 16°C

first: Snježana

last: Jurić

first: Ji

last: Ahn


title: Splicing patterns in SF3B1 mutated uveal melanoma generate shared immunogenic tumor-specific neo-epitopes [bulk TCR-seq]

city: Paris

first: Paul

last: Gueguen

address: 26 rue D'Ulm

department: Inserm U932

institute: Institut Curie

summary: Purpose: In this study, we show that mutations of the splicing factor SF3B1 in uveal melanoma (UM) generate immunogenic neo-antigens.

overall_design: Thawed  PBMC  from  patient  UM1 were  stained  with PE  and  APC  tetramers  loaded with  peptide 37,  then  tetramer  positive  cells  were  positively enriched  using  anti-APC  and  anti-PE  microbeads (Miltenyi Biotech), stained with CD3 A700 and CD8 FITC and finally with DAPI. The positive fraction was sorted in a FACS ARIA (BD). To combine 5 tetramer positive populations from 2 donors (14, 17, 26  and  37  for  UM2  and  18  for  UM3)  the  tetramers  were  prepared  using  5  different  TotalSeq-PE streptavidins  (BioLegend)  and  1  classical  fluorochrome-streptavidin  (APC,  PE-CF594,  PE-Cy5,  PE-Cy7), PE-CF594 was used for UM3 who had only one population sorted. The PBMC were stained with the 4 pairs of tetramers for patient UM2 and 1 pair of tetramers for patient UM3, enriched with anti PE-microbeads (Milteny Biotech), stained with CD3 A700 and CD8 FITC and DAPI and sorted separately. The  cells  were  then  counted,  mixed  and  loaded  onto  a  Chromium  controller  using  Chromium  next GEM  Single  Cell  V(D)J  reagent  kit  with  feature  barcoding  technology  according to manufacturer’s instructions

first: Jeremy

last: Bigot

first: Ana

middle: I

last: Lalanne


title: Skeletal muscle DNA methylation profiles in young, healthy men and women before and after 4, 8 and 12 weeks of HIIT, or after a 4-week control period

city: Footscray

first: Sarah

middle: Amandine Caroline

last: Voisin

state: VIC

address: Ballarat Road

department: Institute for Health and Sport

country: Australia

institute: Victoria University

summary:
This dataset is an extension of GSE151407. It contains 160 vastus lateralis muscle samples from young, healthy men and women who underwent 4, 8 or 12 weeks of HIIT. Some of them also underwent a 4-week control period prior to commencing the HIIT program.
Some individuals in GSE151407 also appear in this dataset as they did two HIIT interventions, as indicated in the "description" field in the corresponding sample records (to link the individuals between the two datasets).

overall_design:
This dataset contains 160 vastus lateralis muscle samples from young, healthy men and women who underwent 4, 8 or 12 weeks of HIIT.
From the 160 samples, 57 were taken at baseline, 57 after four weeks of exercise training, 17 after eight weeks of exercise training, and 15 after twelve weeks of exercise training; 13 samples were taken four weeks before the baseline timepoint to see whether DNA methylation patterns would change without exercise over a four-week time period (57 + 57 + 17 + 15 + 13 = 159 samples). The remaining sample was a replicate.

Please note that total 35 sample records (from GSE151407) are also included in the current Series records.

first: Nir

last: Eynon


title: Gene expressions of CD4+ T cells from patients with rheumatoid arthritis in each developmental stages

city: sinjuku-ku

first: Masaru

last: Takeshita

state: Tokyo

address: 35 shinanomachi

department: Division of Rheumatology

institute: Keio University

summary:
The development of T cells has been characterized as taking place over three stages: naïve (Tn), central memory (Tcm), and effector memory (Tem) cells.
Recently, stem cell memory T cells (Tscm) were found to be the least-developed memory subset.
We performed detailed analysis of the gene expression of human CD4+ T cells from patients with rheumatoid arthritis with clear distinction of the Tn, Tscm, Tcm, and Tem stages.

overall_design: We sorted Tn, Tscm, Tcm, and Tem CD4+ T cells from the peripheral blood of six patients with rheumatoid arthritis to see the differences of gene expression between each developmental stage.

first: Tsutomu

last: Takeuchi


title: BMI1 Maintains the Regulatory T cell Epigenomic Landscape to Prevent Inflammatory Bowel Disease

first: Aditya

last: Bhagwate

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

overall_design: Refer to individual Series


title: Histone lysine demethylase JMJD3/KDM6B is required for the establishment of adult hippocampal neurogenesis

city: SAN FRANCISCO

first: John

last: Liu

state: California

address: 35 Medical Center Way

institute: UCSF

summary: Mutations in the JMJD3 (KDM6B) chromatin regulator are causally associated with autism spectrum disorder and syndromic intellectual disability, but the neurodevelopmental roles of this histone 3 lysine 27 (H3K27) demethylase are poorly understood.  Neural stem cells (NSCs) in the hippocampal dentate gyrus (DG) generate new granule neurons throughout life, and deficits in DG neurogenesis are associated with cognitive and behavioral problems.  Here we show that Jmjd3 is required for the establishment of adult neurogenesis in the mouse DG.  Conditional deletion of Jmjd3 in embryonic DG precursors results in an adult hippocampus that is essentially devoid of NSCs.  While early postnatal mice with Jmjd3-deletion have near normal numbers of DG NSCs, at later stages, Jmjd3-deleted NSCs fail to propagate normally.  In addition to the loss of NSCs during postnatal development, neurogenesis from Jmjd3-deleted NSCs is impaired, corresponding to defective neurogenic gene expression.  Without Jmjd3, NeuroD2 and Bcl11b(Ctip2) are not properly expressed and exhibit increased levels of H3K27me3, underscoring the role of Jmjd3 in the regulation of transcription for neuronal differentiation.  Thus, these data indicate that Jmjd3 plays dual roles in postnatal DG neurogenesis, being critical for the establishment of the NSC pool as well as the differentiation of young DG granule neurons.  More broadly, our results suggest a neurodevelopmental link between JMJD3 mutations and hippocampal dysfunction, providing new insights into how mutations in chromatin regulators may contribute to learning disorders.

overall_design: RNA-seq of JMJD3 wt and null dentate gyrus

first: Dae

last: Park

first: Siyuan

middle: J

first: Daniel

last: Lim


title: Role of OxyR in Prevotella intermedia

city: Richmond

first: Janina

last: Lewis

state: VA

address: 521 North 11th Street

department: Philips Institute of OCMB

institute: Virginia Commonwealth University

summary: Wild type Prevotella intermedia OMA14 strain (V3203) was used to compare to the OxyR-deficient strain (V3147).

overall_design: OxyR mutant and wild type with iron replete and deplete.

first: Qin

last: Gui


title: Differential transcriptome of human dendritic cells at first contact with Trypanosoma cruzi reveals response to virus as a central unexplored pathway

city: Brasília

first: Taina

last: Raiol

state: DF

address: Av. L3 Norte, Campus Universitário Darcy Ribeiro

department: Fiocruz Brasília (GEREB)

country: Brazil

institute: Oswaldo Cruz Foundation - Fiocruz

summary: Chagas disease is a notorious public health problem worldwide. However, the pathology is still poorly understood in humans and dendritic cells (DCs) have a determinant role during infection that could help to understand what happens with immune response during the first contact. Here we performed a transcriptomic analysis of the interaction between DCs from three human donors and the infective forms of T. cruzi for 12 h. 468 differentially expressed genes (DEGs) were found in DCs after infection. KEGG and GO enrichment analysis showed that most of DEGs are involved in pathways related to virus infection and intracellular receptors, as NOD and RIG-I -like receptors. Some of these DEGs were validated through RT-qPCR, corroborating the transcriptome data. Cytokine measurement partially corresponded to the transcript levels. In conclusion, this study has revealed the virus response as an unexplored pathway in Chagas disease, which brings new perspectives for this pathology.

sample_organism:
Trypanosoma cruzi
Homo sapiens

platform_organism:
Trypanosoma cruzi
Homo sapiens

overall_design: 3 human donors, 2 replicates each, with control and infected samples for each experiment. A total of 12 samples were analyzed.

first: Natalia

last: Gil-Jaramillo

first: Amanda

last: Rocha

first: Tainá

first: Flávia

middle: N

last: Motta

first: Cecília

last: Favali

first: Marcelo

last: Brigido

first: Izabela

last: Bastos

first: Jaime

last: Santana


title: Targeted radionuclide therapy for pigmented BRAF- and NRAS-mutated melanoma: [131I]ICF01012 efficacy and combination with MAPK/ERK pathway inhibitors

city: Orsay

first: Lionel

last: Larue

address: Centre universitaire Bat 101B-110-111-112 Rue Henri Becquerel CS 90030

department: CNRS UMR3347, INSERM  U1021

summary: Purpose: Tumor radioresistance can be driven by ERK phosphorylation and its downstream targets. In this context, melanomas harboring constitutive MAPK/ERK activation have been considered for targeted radionuclide therapy (TRT) with a radiolabeled melanin tracer ([131I]ICF01012), alone or in combination with MEK inhibitors (MEKi).   Experimental design: We used three dimensional (3D) melanoma spheroid models to evaluate the effects of TRT in combination with MEKi, in human BRAFV600E SK-MEL-3, NRASQ61K 1007 and WT B16F10 murine melanomas. TRT was assessed in vivo using the syngeneic model C57Bl5/NRAS 1007 for biodistribution, dosimetry, efficiency and molecular mechanisms.  Results: In spheroids, TRT cooperated with MEKi to increase apoptosis in both BRAF- and NRAS-mutant models that were resistant to TRT-induced apoptosis. However NRASQ61K spheroids were highly radiosensitive towards [131I]ICF01012-TRT. Actually, mice bearing NRAS1007 melanoma and receiving 18.5MBq of [131I]ICF01012 had a significant extended survival (median: 92 vs 44 days, p < 0.0001), associated with a 93 Gy tumor deposit, leading to a dramatic decrease of tumor growth. Furthermore, the number of lymph node metastases was reduced in mice receiving [131I]ICF01012. Comparative transcriptomic analyses confirm a decrease of mitosis, proliferation and metastasis signature in TRT-treated tumors vs control tumors. These analyses also suggest that in this NRAS-melanoma, TRT acts through an increase of oxidation and inflammation as well as P53 activation.   Conclusions: Our data support the view that combining [131I]ICF01012-TRT with MEKi can be of benefit for the treatment of advanced pigmented BRAF-mutant melanoma. Likewise, [131I]ICF01012 alone can be considered as a new potential NRAS-mutant melanoma treatment.

overall_design: To understand how [131I]ICF01012 disrupts melanoma growth, 1007 NRAS mouse melanoma cells (1.10e5) were injected subacutaneously in the right flank of 5 weeks old C57BL/6J mice. 36 days after cell injection, a single administration of either 18.5 MBq/100 µL of [131I]ICF01012 (n=3) or with 100 µL of saline (n=6) was given intravenously to the mice. Tumors were harvested 10 days after treatment and snap-frozed in liquid nitrogen. Total RNA was extracted and sequenced (RNA-seq).The results confirm that [131I]ICF01012 inhibits cell growth and suggest different mechanism of action : 1) through oxydation, 2) linked with p53 activation and 3) via an immune response.

first: H

last: Akil

first: M

last: Quintana

first: Jeremy

last: Raymond

first: T

last: Billoux

first: V

last: Benboubker

first: S

last: Besse

first: P

last: Auzeloux

last: Delmas

last: Petit

first: L

last: D'Incan

first: F

last: Degoul

first: J

last: Rouanet


title: Gene expression profiling of AGS Gastric Cancer cells upon YY1 knock down

city: Madurai

first: Kumaresan

last: Ganesan

state: Tamil Nadu

address: School of Biological Sciences,

department: Genetics

country: India

institute: Madurai Kamaraj University

summary: Yin Yang 1 (YY1) is a ubiquitous transcription factor belonging to the GLI-Kruppel class of zinc finger proteins regulating diverse biological processes including cell proliferation, development, DNA damage responses and also involved in carcinogenesis. The protein is involved in repressing and activating a diverse number of promoters.In order to study the role of the transcription factor YY1 in gastric cancer, transcriptome wide gene expression analysis was performed upon silencing the YY1 gene in gastric cancer cell line, AGS using Affymetrix Human Transcriptome 2.0 array. Transcriptome Analysis Console (TAC) Software was used for the analysis of differentially expressed genes between AGS_YY1_siRNA transfected and AGS_NTC_siRNA transfected cells.

overall_design: Total RNA was extracted from AGS gastric cancer cells transfected with YY1siRNA and NTC siRNA and profiled using GeneChip® Human Transcriptome Array 2.0 (HTA-2_0).

first: B

last: DIVYA

first: G

last: KUMARESAN


title: Apoplastic lipid barriers regulated by conserved homeobox transcription factors extend seed longevity in multiple plant species

city: Valencia

first: Eduardo

last: Bueso

state: Valencia

address: Ingeniero Fausto Elio, s/n

department: IBMCP

institute: Universitat Politècnica de València

summary:
•Cutin and suberin are lipid polyesters deposited in specific apoplastic compartments. Their fundamental roles in plant biology include controlling the movement of gases, water and solutes, and conferring pathogen resistance. Both cutin and suberin have been shown to be present in the Arabidopsis seed coat where they regulate seed dormancy and longevity.
•In this study, we use accelerated and natural aging seed assays, glutathione redox potential measures, optical and transmission electron microscopy and gas chromatography-mass spectrometry to demonstrate that increasing the accumulation of lipid polyesters in the seed coat is the mechanism by which the AtHB25 transcription factor regulates seed permeability and longevity.
•Chromatin immunoprecipitation during seed maturation revealed that the lipid polyester biosynthetic gene LACS2 (long-chain acyl-CoA synthetase 2) is a direct AtHB25 binding target. Gene transfer of this transcription factor to wheat and tomato demonstrates the importance of apoplastic lipid polyesters for the maintenance of seed viability.
•Our work establishes AtHB25 as a trans-species regulator of seed longevity and has identified the deposition of apoplastic lipid barriers as a key parameter to improve seed longevity in multiple plant species.

overall_design: A ChIP-seq experinent in developing seeds of the Arabidopsis thaliana AtHB25 HA-tagged TF to obtain its genomic binding sites

first: Joan

last: Renard


title: Affymetrix SNP array data for pharmacogenomic profile of Benzidazole adverse reactions.

city: Sao Paulo

first: Roberta

last: Martins

address: Av. Dr. Eneas Carvalho de Aguiar, 470

institute: FMUSP

summary: Search for SNPs associated with the pharmacogenomic profile of Benzidazole adverse reactions in Chagas Disease Homo sapiens patients.

overall_design: Affymetrix SNP arrays were performed according to the manufacturer's directions on DNA extracted from cryopreserved buffy-coat of peripheral blood of diagnostic Homo sapiens with Chagas disease treated with Benznidazole.

first: Lucas

middle: A

last: Franco


title: Transcriptome analysis of p35S:AtBBD1 and atbbd1 (Knock-out) under PEG-induced drought stress condition

city: Seoul

first: Zeeshan

last: Nasim

address: Anam-ro 145, Seongbuk-Gu

department: School of Life Sciences and Biotechnology

summary: We sequenced mRNA of WT, p35S:AtBBD1 (OX) and atbbd1 (KO) plants. Plants were grown in soil for three weeks at 23 ℃ with 60% relative humidity. mRNA was isolated 6 hours after threating with  20% PEG.

overall_design: Examination of mRNA level in WT, p35S:AtBBD1 (OX) and atbbd1 (KO) plants under drought stress condition.

first: A

last: Huque

first: Min

last: You

first: Jeong

middle: S

last: Shin


title: Analysis of NFE2L2 (NRF2) binding to chromatin in primary human keratinocytes

city: Manchester

first: Svitlana

last: Kurinna

address: Dover Street

institute: University of Manchester

overall_design: ChIPseq using antibody to human NRF2 and human primary keratinocytes treated with control vehicle or sulfarophane (SFN) for 3 hours, 5μM


title: SCITO-seq: single-cell combinatorial indexed cytometry sequencing

city: San Francisco

first: Chun

middle: Jimmie

last: Ye

address: 513 Parnassus Ave

department: IHG

summary: We introduce single cell combinatorial indexed cytometry by sequencing (SCITO-seq), a single cell proteomics workflow that combines split-pool indexing and droplet-based sequencing

overall_design: Human/Mouse cell line experiment, Human mixture experiment using T/B cells and whole PBMC (two human donors used)

first: Byungjin

last: Hwang


title: The RelA hydrolase domain acts as a molecular switch for (p)ppGpp synthesis

city: Copenhagen

first: Kristoffer

middle: Skovbo

last: Winther

address: Ole Maaloesvej 5

department: Department of Biology

country: Denmark

institute: University og Copenhagen

summary: Bacteria synthesize guanosine tetra- and penta phosphate (commonly referred to as (p)ppGpp) in response to environmental stresses. (p)ppGpp reprograms cell physiology and is essential for stress survival, virulence and antibiotic tolerance. Proteins of the RSH superfamily (RelA/SpoT Homologues) are ubiquitously distributed and hydrolyze or synthesize (p)ppGpp. Structural studies have suggested that the shift between hydrolysis and synthesis is governed by conformational antagonism between the two active sites in RSHs. RelA proteins of γ-proteobacteria exclusively synthesize (p)ppGpp and encode an inactive pseudo-hydrolase domain. Escherichia coli RelA synthesizes (p)ppGpp in response to amino acid starvation with cognate uncharged tRNA at the ribosomal A-site, however, mechanistic details to the regulation of the enzymatic activity on the ribosome remain elusive. Here, we show a novel role of the enzymatically inactive hydrolase domain in modulating the activity of the synthetase domain of RelA. Using random mutagenesis screening and functional studies, we identify a loop region (residues 114-130) in the hydrolase domain, which controls the synthetase activity. We show that a synthetase-inactive loop mutant of RelA is not affected for tRNA binding, but binds the ribosome less efficiently than wildtype RelA. Our data provide strong evidence to support the model that the hydrolase domain acts as a molecular switch to regulate the synthetase activity.

overall_design: The relA locus of Escherichia coli was fused to a dual affinity His-TEV-FLAG tag.  Strains expressing relA-HTF (RelA), relAA21E-HTF (A121E) were grown exponentially in MOPS minimal medium. Cell samples were UV-C irradiated (100sec of 1800mJ) before and 5 or 30 min after isoleucine starvation (indicated by 5 or 30) and harvested. Cells were washed with ice-cold PBS before snap freezing in liquid nitrogen. RNA-RelA complexes were purified on M2-anti-FLAG resin and Ni-NTA resin. Sequencing libraries were prepared from purified complexes essentially per, Sinha and Winther 2020. Amplified libraries were sequenced by Illumina Miseq.

first: Anurag

last: Sinha


title: Expression data from SNK6 cell

first: Joo Hyun

last: Kim

address: 50 Irwon-dong

institute: Sungkyunkwan University

summary:
Differential expression in the presence and absence of sildenafil following romidepsin
We performed cDNA microarray analysis using an GeneChip® Human Gene 2.0 ST Array to identify cellular genes that may be differentially expressed in the presence and absence of sildenafil following romidepsin treatment in SNK6

overall_design: SNK6 cells were treated with romidepsin in the presence or absence of sildenafil for 72hr.

first: Won

first: Chaehwa

last: Park


title: Chromothripsis is a prognostic factor in early-onset breast cancer [OncoScan]

city: Salamanca

first: Juan Luis

last: Garcia

state: Salamanca

address: Campus Miguel de Unamuno

institute: Centro de Investigación del Cáncer IBMCC-CIC

summary: Breast cancer in Spain remains the first leading cause of cancer-related death in women from all age, and in younger women breast tumors often exhibit more aggressive phenotypes, worse prognosis and more frequently germline mutation in BRCA1/2 genes. Chromothripsis, a massive genome rearrangement, has been recently described but its etiology and effect on cancer cells remain unknown. Chromothripsis in breast cancer has been poorly studied and prevalence rates vary between 11-61%. We have studied chromothripsis-like patterns (CTLPs) in 58 DNA extracted from formalin-fixed paraffin-embedded (FFPE) breast cancer tissues from patients below 40 years old. Chromothripsis was confirmed with website tool CTLPScanner in 10/58 (17%) and most frequently involved chromosomal segment was 17q12-q21 (5/10 cases, 50%). We have also find that chromothripsis was related to low recurrence rates and familial history of breast cancer. In summary, we have analyzed chromothripsis in early-onset breast cancer for the first time and could have a prognostic value for this patients

overall_design: We performed OncoScan™ FFPE Assay and Affymetrix® CytoScan™ 750k Assay to asses copy number alterations in 32 and 26 FFPE samples from women breast cancer tumors, respectively

first: Athenea

last: Pascual-Rodríguez

first: Eva

last: Lumbreras

first: Luis

last: Corchete

first: Juan

middle: L

last: García-Hernández

first: Rogelio

last: González-Sarmiento


title: Expression data from FSTL1 antibody treatment for 6 hours in CL1-0 lung cancer cell line.

city: Taipei

first: Jean

last: Chiou

address: No. 128, Academia Road, Section 2, Nankang,

country: Taiwan

institute: Genomics Research Center, Academia Sinica

summary:
We demonstrate that FSTL1 down-regulation shRNAs significantly increased cell migration and invasion in lung cancer cell lines in vitro, as well as in lung metastases in vivo
We used microarrays to analyze the FSTL1 regulated gene expression underlying invasion-metastasis cascade.

overall_design: CL1-0 lung adenocarcinoma cells treated with FSTL1 antibody for 6 hours were selected for RNA extraction and hybridization on Affymetrix microarrays.

first: Michael

last: Hsiao


title: Indazole-Cl inhibition of hypoxia-induced cyclooxygenase-2 expression in vascular smooth muscle cells

first: Youngjoo

last: Lee

address: 209, Neungdong-ro, Gwangjin-gu

department: Bioscience and Biotechnology

institute: Sejong University

summary: We used RNA-sequencing analysis to identify changes in inflammation-related genes by ER agonist treatment in the hypoxic state.

overall_design: Examination of 3 different ER agonist in hypoxia

first: Choa

first: Young-Joo


title: Chromothripsis is a prognostic factor in early-onset breast cancer [CytoScan750K_Array]


title: Radiation Impacts Early Atherosclerosis by Suppressing Intimal LDL Accumulation

city: Toronto

first: Corey

last: Scipione

state: Ontario

address: 101 College Ave., TMDT 3-307 G,

department: Toronto General Hospital Research Institute

institute: University Health Network

summary: We report that bone marrow transplantation suppresses atherosclerosis by reducing LDL accumulation in the intima. Radiation exposure enhances endothelial endolysosomal trafficking and cholesterol efflux pathways, thus preventing reducing the abundance of LDL particles that traverse the endothelial layer to deposit in the sub-endothelial space.

overall_design: A comparison of Ldlr mouse aortic arch isolates from Control and bone marrow transplanted mice. Each group is represented in standard chow fed and cholesterol rich diet fed (5 days). There are 2-3 replicates per sample. In addition, aortic arch intimal samples from standard chow fed Ldlr and bone marrow transplanted mice (10 mice each, pooled) were subjected to single cell RNA seq.

first: Sharon

last: Hyduk

first: Myron

last: Cybulsky


title: Chromothripsis is a prognostic factor in early-onset breast cancer

overall_design: Refer to individual Series


title: Next Generation Sequencing to assess pesticides capacity in vitro to act as agonists/antagonists of the thyroid hormone nuclear receptors

status: Public on Mar 30 2021

city: Lyon

first: Yanis

last: ZEKRI

address: 32-34 Avenue Tony Garnier

institute: IGFL-ENS

summary: We combined in vitro tests to fully assess the capacity of pesticides to act as thyroid hormone disruptors (THD). Pesticides which were active in these tests were selected for a transcriptome analysis of neural cells. We took advantage of this technique to decipher what were the transcriptomic effects of these chemical in vitro. We also compared the expression of thyroid hormone responsive genes in presence or absence of the pesticides to determine if the transcriptomic changes could impact thyroid hormone receptor signaling. Although some pesticides elicit a cellular response, which sometimes interferes with thyroid hormone signaling, we found no evidence that they can act as TRα1 agonists or antagonists. We conclude that their neurodevelopmental toxicity in mammals is not explained by an alteration of the neural cell response to thyroid hormone.

overall_design: C17.2 neural cells exposed to different concentrations of pesticides (n=1) or vehicle (n=2, DMSO)

last: Zekri

first: Laure

last: Dall'Agnol

first: Frédéric

last: Flamant

first: Romain

last: Guyot


title: Control ChIP-seq from SK-N-SH (ENCSR697UDH)

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

institute: ENCODE DCC

summary:
ChIP-Seq on SK-N-SH

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: ATAC-seq from mucosa of gallbladder (ENCSR695FLC)

summary:
ATAC-seq on human mucosa of gallbladder

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Control ChIP-seq from HepG2 (ENCSR690IYP)

summary:
ChIP-Seq on HepG2

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


city: La Jolla

first: Ferran

last: soldevila

address: 9420 Athena Cir

institute: La Jolla Institute for Immunology

summary:
System level view of the vaccine induced immune response to identify perturbations at the level of gene expression in whole PBMC  specifically in response to pertussis antigenic challenge in vivo (Tdap vaccine boost) as a proxy of infectious challenge, and whether this response differed in aP vs. wP primed individuals 15 years or more after the original vaccination.
RNA-Seq analysis on PBMC samples collected longitudinally at baseline and following Tdap booster vaccination. For this purpose, we recruited addults primed with either aP and wP and proceeded  to booster vaccination with aP.  PBMCs were collected for transcriptomics at 0 days post boost (baseline) followed by 1, 3, 7 and 14 days post boost. Bulk PBMC RNA sequencing was performed for 39 donors with 5 timepoints (0, 1, 3, 7 and 14 days post boost) +1 donor with 3 timepoints (0, 1 and 3 days post boost)

overall_design: To determine immunological differences associated with aP vs. wP priming, we performed RNA expression profiling of the immune response in adults primed with aP vs. wP vaccine in infancy following the Tdap booster vaccination. A four part format of the samples was used internally using Sample number_DonorID_visit_Timepoint. Ex: 1_2685_1_TimePoint1 where 1 accounts for sample number in RNA sequencing plate, 2685 is the donor ID, 1 is the internal visit number where the blood was collected and Timepoint1 accounts for 0 days post boost (Baseline). Thus, Timepoint2, 3, 4 and 5 account for 1, 3, 7 and 14 days post boost.

first: Ricardo

last: da Silva Antunes

first: Bali

last: Pulendram

first: Bjoern

last: Peters

first: Alessandro

last: Sette


title: Control ChIP-seq from brain (ENCSR688WUZ)

summary:
Control ChIP-seq on brain female embryo (5 days)

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Control ChIP-seq from H9 (ENCSR686HII)

summary:
Control ChIP-seq on H9 originated from H9

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: ATAC-seq from left lung (ENCSR682ETE)

summary:
ATAC-seq on human left lung

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Control ChIP-seq from A549 (ENCSR663DVJ)

summary:
ChIP-seq on human A549

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Control ChIP-seq from A549 (ENCSR650VIH)


title: Control ChIP-seq from left lung (ENCSR650AIN)

summary:
Control ChIP-seq on left lung female child (16 years)

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Anti-Interleukin-10 unleashes transcriptional response to leishmanial antigen in whole blood of visceral leishmaniasis patients

city: Milan

first: Michaela

last: Fakiola

address: Via Francesco Sforza 35

country: Italy

institute: INGM

summary: Visceral leishmaniasis (VL; Leishmania donovani) cases produce interferon- (IFN) and tumour necrosis factor (TNF) in response to soluble leishmanial antigen (SLA) in whole blood assays. These pro-inflammatory cytokines are crucial for activation of macrophages to kill L. donovani parasites.  Detailed immunological studies comparing active with cured patients suggest that a balance exists between the pro-inflammatory cytokines TNF and IFN, and anti-inflammatory interleukin-10 (IL10). Our interest was to obtain a global understanding of the response to SLA in whole blood from active VL cases, and to determine what effect neutralising anti-IL10 would have on this response.  Transcriptional profiles following SLA stimulation of whole blood from VL patients showed very few differentially expressed genes (DEGs), the majority belonging to a single network with TNF at the hub.  In contrast, when anti-IL10 was added with SLA, hundreds of DEGs were observed, 65% belonging to a single network with TNF, IFNG, NFKBIA, IL6 and IL1B as hub genes in concert with a remarkable chemokine/cytokine storm.  Our data demonstrate the singular impact of IL10 as a potent immune modulator in VL.

overall_design: Whole blood from active cases (pre-treatment; day 0) was stimulated with SLA with/without isotype control antibody or anti-IL10.  Whole blood collected at day 30 post-treatment was unstimulated or stimulated with SLA alone. Samples from different experimental groups were distributed evenly across 4 Illumina HT12v4 expression beadchips.

first: Om-Prakash

last: Singh

first: Genevieve

last: Syn

first: Susanne

last: Nylén

first: Christian

last: Engwerda

first: David

last: Sacks

first: Mary

middle: E

last: Wilson

first: Jaya

last: Chakravarty

first: Shyam

last: Sundar

first: Jenefer

middle: M

last: Blackwell


title: Chromothripsis is a prognostic factor in early-onset breast cancer [OncoScan_CNV]

first: Juan Luis

last: Garcia

first: Athenea

last: Pascual-Rodríguez

first: Eva

last: Lumbreras

first: Luis

last: Corchete

first: Juan

last: García-Hernández

first: Rogelio

last: González-Sarmiento