title: Transcriptome analysis of Arabidopsis thaliana roots, H2O2 and Rose Bengal [20180920_173313_H2O2_RB]

summary: In order to better understand the context of root water stress and its relationship to other stresses, I undertook an evaluation of osmotic water stress by transcriptome analyses. Whole transcriptome MARSeq (Diego Adhemar Jaitin, 2017) analysis can enable us to study the changes in gene expression (changes in transcript prevalence) in depth under different treatments. It is a cost effective method to develop transcriptional activity. It uses relatively small amounts of RNA and reads sequences from the 3’-polyA containing end. This method can reveal underlying trends that can help us understand the less obvious processes happening in our system. To carry this out I processed whole transcriptome data separately from WT seedling roots exposed to 5 mM H2O2 or 10  µM RB for 0, 1, 2, 3 h or  5 mM H2O2 or 10  µM for 2h .

overall_design: WT Arabidopsis thaliana seedling roots were exposed to 5 mM H2O2 or 10  µM RB for 0, 1, 2, 3 h or  5 mM H2O2 and 10  µM for 2h ., and root RNA was extracted sequenced using the MARSeq protocol.


title: Changes of H3K9ac and H3K27ac recruitment and gene expression in pachytene spermatocytes and round spermatids depleted of HDAC3

status: Public on May 26 2021

city: Nanjing

first: Lan

last: Ye

state: Jiangsu

address: B112 Xuehai Building,101 Longmian Avenue, Jiangning district

country: China

institute: Nanjing Medical University

type: Expression profiling by high throughput sequencing

type: Genome binding/occupancy profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Changes of H3K9ac and H3K27ac recruitment in pachytene spermatocytes and round spermatids from testes-specific HDAC3-depleted mice and genome-wide maps of HDAC3,NCOR and Sox30 in wild-type and Sox30 KO testes

summary: We reported changes in the recruitment of H3K9ac and H3K27ac in HDAC3-depleted mouse testes in the late meiotic and early haploid stages. We also investigated genome-wide occupancy of HDAC3, NCOR and Sox30 to the mouse testes from wild-type and Sox30 KO mice.

overall_design: ChIP-seq of H3K9ac and H3K27ac in pachytene spermatocytes and round spermatids isolated from adult wild-type and HDAC3-depleted mice. ChIP-seq profiling of HDAC3, NCOR and Sox30 in mouse testes from wild-type and Sox30 KO mice at postnatal day 20.

first: Z

last: Kang

first: H

last: Yin

first: L


title: Transcriptome analysis of Arabidopsis thaliana shoots and roots, exposed to PEG-induced osmotic shock, PEG+Histidine, PEG+SHAM [20191204_130529_uLox_PEG_Shock]

city: Rehovot

first: Tomer

last: Chen

address: P.O.box 26

department: Plant and Environmental Sciences

country: Israel

institute: Weizmann Institute of Science

summary: In order to better understand the context of root water stress and its relationship to other stresses, I undertook an evaluation of osmotic water stress by transcriptome analyses. Whole transcriptome MARSeq (Diego Adhemar Jaitin, 2017) analysis can enable us to study the changes in gene expression (changes in transcript prevalence) in depth under different treatments. It is a cost effective method to develop transcriptional activity. It uses relatively small amounts of RNA and reads sequences from the 3’-polyA containing end. This method can reveal underlying trends that can help us understand the less obvious processes happening in our system. To carry this out I processed whole transcriptome data separately from WT and µlox seedling roots and shoots under 30% PEG -induced osmotic shock and control conditions and after 0, 1, 2, 3 h.

overall_design: µlox Arabidopsis thaliana seedlings were exposed to 30% PEG, for 0, 1, 2, 3 h, and root RNA was extracted sequenced using the MARSeq protocol.

first: Robert

last: Fluhr


title: Transcriptome analysis of Arabidopsis thaliana shoots and roots, exposed to PEG-induced osmotic shock, PEG+Histidine, PEG+SHAM [20190311_172119_Peg_SHAMf1_res]

summary: In order to better understand the context of root water stress and its relationship to other stresses, I undertook an evaluation of osmotic water stress by transcriptome analyses. Whole transcriptome MARSeq (Diego Adhemar Jaitin, 2017) analysis can enable us to study the changes in gene expression (changes in transcript prevalence) in depth under different treatments. It is a cost effective method to develop transcriptional activity. It uses relatively small amounts of RNA and reads sequences from the 3’-polyA containing end. This method can reveal underlying trends that can help us understand the less obvious processes happening in our system. To carry this out I processed whole transcriptome data separately from WT seedling roots exposure to PEG, and from roots under 30% PEG + 5mM HIS, 30% PEG + 1mM SHAM for 0, 1, 2, 3 h.

overall_design: WT Arabidopsis thaliana seedlings were exposed to 30% PEG + 5mM HIS, 30% PEG + 1mM SHAM 0, 1, 2, 3 h, and root RNA was extracted sequenced using the MARSeq protocol.


title: A role for lipoxygenase in the production of 1O2 and promoting the root's response to osmotic stress in Arabidopsi


title: DNA methylation deregulation in murine cutaneous squamous cell

city: Ghent

first: Jeroen

last: Galle

address: Coupure Links 653

department: Dept. Of Mathematical Modelling, Statistics and Bioinformatics

country: Belgium

institute: Ghent University

type: Methylation profiling by high throughput sequencing

summary:
Background: Cutaneous squamous cell carcinomas (cSCC) are among the most common and highly mutated human malignancies, with rising incidence rates. There are limited treatment options for advanced and metastatic cSCC and particularly high-risk groups, such as organ transplant recipients, are in urgent need for strategies to treat aggressive cSCC. We have previously developed a preclinical murine model for cSCC, with remarkably similar histopathology and genetics to human cSCC. Understanding the impact of DNA methylation in cSCC may provide avenues to develop new treatment or prevention strategies. Here, we perform reduced-representation bisulfite sequencing based DNA methylation analysis of a murine cSCC model (6 tumors, 6 controls, 2 independent healthy skin samples) and compare results with publicly available human cSCC methylation data for two cSCC subtypes, stem-cell like and keratinocyte like tumors.
Results: Contrasting most cancers, general DNA hypermethylation was previously reported for high-risk human cSCC. Similarly, we found significantly increased average methylation in mouse cSCC as well as in stem-cell like, but not keratinocyte like, human cSCC. Locus specific methylation changes in mouse cSCC often occurred in regions of potential regulatory function, including enhancers and promoters. One differentially methylated region was located in a potential enhancer of the tumor suppressor gene Filip1l and expression of this gene was significantly reduced in mouse tumors and human cSCC cell lines. Furthermore, comparison of differentially methylated genes revealed remarkable similarities between human and mouse cSCC.
Conclusion: Our data suggest that, in addition to mutations, deregulation of DNA methylation is an important feature of murine and human cSCC. DNA methylation likely contributes to silencing of tumor suppressor genes, as shown for the Filip1l gene. The similarities between mouse and human cSCC, particularly stem-cell like, highlight the clinical relevance of our model and presents unique opportunities to identify new treatment strategies.

overall_design: We performed reduced-representation bisulfite sequencing based DNA methylation analysis of a murine cSCC model (6 tumors, 6 controls, 2 independent healthy skin samples) and compared results with publicly available human cSCC methylation data for two cSCC subtypes, stem-cell like and keratinocyte like tumors.

first: Kevin

last: Roth

first: Louis

last: Coussement

first: Elena

middle: V

last: Knatko

first: Maureen

last: Higgins

first: Sandra

last: Steyaert

first: Charlotte

middle: M

last: Oroby

first: Tim

last: de Meyer

first: Albena

middle: T

last: Dinkova-Kostova


title: Transcriptome analysis of Arabidopsis thaliana shoots and roots, exposed to PEG-induced osmotic shock, PEG+Histidine, PEG+SHAM [20191204_125511_PEG_SHOCK_II]

overall_design: WT Arabidopsis thaliana seedlings were exposed to 30% PEG, for 0, 1, 2, 3 h, and root RNA was extracted sequenced using the MARSeq protocol.


title: Small RNA-dependent epigenetic modifications in Arabidopsis thaliana embryos

city: Ottawa

first: Jean-Sebastien

last: Parent

state: Ontario

address: 960 Carling Avenue

country: Canada

institute: Agriculture and Agri-Food Canada

summary: We report the survey of two repressive epigenetic marks in hand-dissected mature Arabidopsis embryos. DNA from approximately 2500 embryos was extracted for each samples. DNA was  treated with bisulfite and fractionated for whole genome bisulfite sequencing to reveal methylated cytosines. Chromatin was fractionnated and immuno-precipited with either anti-H3K9me2 or anti-H3 to test for histone methylation. Both profiles were compared in different mutant backgrounds to survey how small RNA influence reprogramming in the embryo.

overall_design: Examination of two repressive epigenetic marks in embryos of different mutant backgrounds.

first: Jean-Sébastien

first: Daniel

last: Grimanelli

middle: A

last: Martienssen


title: Transcriptome analysis of Arabidopsis thaliana roots, H2O2 and Rose Bengal [20180920_172844_1O_H2O2]


title: Epigenetic drift during long-term culture of cells in vitro [ChIP-seq]

city: Aachen

first: Wolfgang

last: Wagner

address: Pauwelsstrasse 20

department: Helmholtz Institute for Biomedical Engineering

country: Germany

institute: RWTH Aachen University

summary: Culture expansion of primary cells evokes highly reproducible DNA methylation (DNAm) changes at specific sites in the genome. These changes might be due to an directly regulated epigenetic process, or to gradual deregulation of the epigenetic state, which is often referred to as “epigenetic drift”. We have identified CG dinucleotides (CpGs) that become continuously hyper- or hypomethylated in the course of culture expansion of mesenchymal stem cells (MSCs) and other cell types. During reprogramming into induced pluripotent stem cells (iPSCs) the long-term culture-associated hypomethylation is reversed simultaneously with pluripotency-associated DNAm changes. Bisulfite barcoded amplicon sequencing (BBA-seq) demonstrated that upon passaging the DNAm patterns of neighboring CpGs become more complex without evidence of continuous pattern development and without association to dominant subclones at later passages. Circularized chromatin conformation capture (4C) revealed reproducible changes in nuclear organization between early and late passages, while there was no preferential interaction with other genomic regions that also harbor culture-associated DNAm changes. Chromatin immunoprecipitation of CTCF did not show significant differences during long-term culture of MSCs, however culture-associated hypermethylation was enriched at CTCF binding sites and hypomethylated CpGs were devoid of CTCF. Taken together, the DNAm changes during culture-expansion of cells cannot be attributed to cellular subsets, whereas they seem to resemble epigenetic drift in relation to chromatin conformation.

overall_design: Examination of CTCF binding in three donors of mesenchymal stromal cells in early (P=2) and late (P8-P14) passages

first: Julia

last: Franzen

first: Theodoros

last: Georgomanolis

first: Anton

last: Selich

first: Chao-Chung

last: Kuo

first: Reinhard

last: Stöger

first: Lilija

last: Brant

first: Melita

middle: S

last: Mulabdić

first: Eduardo

last: Fernandez-Rebollo

first: Clara

last: Grezella

first: Alina

last: Ostrowska

first: Matthias

last: Begemann

first: Miloš

last: Nikolić

first: Björn

last: Rath

first: Anthony

middle: D

last: Ho

first: Michael

last: Rothe

first: Axel

last: Schambach

first: Argyris

last: Papantonis


title: Identification of molecular signatures associated with early relapse after complete resection of lung adenocarcinomas

city: Ulm

first: Ole

last: Ammerpohl

address: Albert-Einstein-Allee 11

institute: UK Ulm

type: Methylation profiling by genome tiling array

summary: The study comprised 97 patients with totally resected stage IA-IIIA lung adenocarcinoma. Patients suffering from an early relapse within two years after surgery were compared to patients without a relapse in two years.

overall_design: Bisulphite converted DNA from the 97 samples were hybridized to the Illumina MethylationEPIC Beadchip. Data from 9 donors have to be excluded from the study due to insufficient clinical information


title: Epigenetic drift during long-term culture of cells in vitro

first: Wolfgang

last: Wagner


title: Akkermansia muciniphila associated with improved  child health produces the peptode larazotide that affects colonic epithelial cells

status: Public on May 25 2021

city: Baltimore

first: Oscar

middle: Colin

last: Stine

state: Maryland

address: 660 W. Redwood St.

department: Epidemiology and Public Health

country: USA

institute: University of Maryland Baltimore

summary: Akkermansia muciniphila, a bacterium, is associated with good health, but data are lacking whether it confers health benefits on children in low income countries and by which mechanisms. In a case-control study of children <5 years old with (n=1717) or without (n=1524) diarrhea, the presence of A. muciniphila reduces the odds ratio of symptoms of diarrhea from six diarrheal pathogens. A. muciniphila is found more frequently among children who are growing well compared with those who are growing poorly. In silico analysis of 1487 A. muciniphila genomes revealed the presence of DNA encoding the peptide larazotide known to benefit human health by improving tight junctions. Although previously considered synthetic, we demonstrated that larazotide is secreted by A. muciniphila. Larazotide is found in the nucleus of colonic epithelial cells and its exogenous application alters gene expression. When larazotide is applied to colonic organoid cultures, the amount of mucin (MUC2) is increased significantly (p<0.005). Our analyses are consistent with A. muciniphila secreting larazotide and intestinal epithelial cells responding by increasing MUC2, potentially creating a positive feedback loop that increases mucin production, which may itself increase abundance of the mucin-metabolizing A. muciniphila.  This cycle may confer positive health outcomes for children.

overall_design: Six samples, three untreated and three treated with larazotide

first: Mathieu

last: Almeida

first: Richard

last: Smith

first: Laura

last: Gonya

first: Colin

last: Robertson

first: John

middle: B

last: Ochieng

first: Martin

last: Antonio

first: Shan

last: Li

first: Hector

middle: C

last: Bravo

first: Elizabeth

last: Humphries

first: Ashkan

last: Emadi

first: James

middle: P

last: Nataro

first: O


title: CD8 T cell transcriptional changes induced by MDSCs during TCR stimulation

city: Boston

first: Kai

middle: W

last: Wucherpfennig

state: MA

address: 1 Jimmy Fund Way

department: Cancer Immunology and Virology

institute: Dana Farber Cancer Institute

summary: Single cell RNA-seq analyiss of FACS enriched OT-I CD8+ T cells following co-culture with SIINFEKL-pulsed bone marrow-derived DCs and bone marrow-derived myeloid-derived suppressor cells (T cell:DC:MDSC = 1:0.2:2)

overall_design: FACS enricgment of CD8+ T cells at 0, 24, and 72 hours post-co-culture with SIINFEKL-pulsed DCs ± MDSCs

first: Adam

middle: N

last: Cartwright


title: lncRNA UC.145 and PRKG1-AS1 determine the functional output of DKK1 in regulating the Wnt signaling pathway in gastric cancer

city: Seoul

first: Sang Kil

last: Lee

address: 50-1 Yonsei-ro, Seodeamun-gu

department: Internal Medicine

country: South Korea

institute: Yonsei University Colloge of Medicine

summary: In this study we show that UC.145 may serve as an effective therapeutic target for molecular-targeted therapy resulting in the inhibition of Wnt signaling within gastric cancer cells.

overall_design: To select differentially expressed T-UCRs in gastric cancer, we performed a microarray analysis using RNA samples collected from three patients with gastric cancer.

first: Sang

middle: K

first: George

last: Calin

first: Jung-Ho

last: Yoon

first: Cristina

last: Ivan


title: Mechanical overload-induced muscle-derived extracellular vesicles promote adipose tissue lipolysis

city: Lexington

first: Ivan

last: Vechetti

state: KY

address: 800 Rose St.  Medical Science Build

institute: University of Kentucky

summary:
How regular physical activity is able to improve health remains poorly understood, but release of substances from skeletal muscle following exercise is one proposed mechanism. Here we describe a novel mechanism through which physical activity initiates extracellular vesicle (EV)-mediated communication between skeletal muscle and adipose tissue causing increased adipocyte lipolysis as a result of enhanced catecholamine sensitivity. In response to a hypertrophic stimulus induced by mechanical overload (MOV), skeletal muscle released EVs containing muscle-specific miR-1 which were preferentially taken up by epididymal white adipose tissue (eWAT) and were associated with elevated adrenergic signaling and lipolysis.
Inhibiting EV release by GW4869 treatment prevented the MOV-induced increase in eWAT miR-1 abundance and expression of lipolytic factors. miR-1 was shown to induce adrenergic receptor beta β3 (Adrβ3) expression in adipocytes by targeting transcription factor AP-2, alpha (Tfap2α, a known repressor of Adrβ3 expression. Ex vivo experiments showed enhanced catecholamine sensitivity and elevated fatty acid oxidation in eWAT following MOV. Following a bout of resistance exercise in humans, skeletal muscle miR-1 expression was decreased with a concomitant increase in EV miR-1 abundance, suggesting that a skeletal muscle-adipose tissue axis is operative in humans.  Altogether, our highly novel findings demonstrate that skeletal muscle promotes metabolic adaptations in adipose tissue in response to MOV via EV-mediated delivery of miR-1.

overall_design: 4 samples: 1 Veh-Sham, 1 Veh-SA, 1 GW-Sham, 1 GW-SA. Veh:Vehicle (DMSO), GW: GW4869 (EV inhibitor), SA (Mechanical Overload, synergist ablation)

first: Bailey

last: Peck

first: Yuan

last: Wen

first: R

middle: G

last: Walton

first: Alexander

last: Alimov

first: Taylor

last: Valentino

first: Cory

last: Dungan

first: Douglas

last: Van Pelt

first: Ferdinand

last: von Walden

first: Bjorn

last: Alkner

first: Charlotte

last: Peterson

last: McCarthy


title: The RNA binding protein MEX3A controls G1/S transition via regulating RB/E2F pathway in clear cell renal cell carcinoma [eCLIP-Seq]

city: guangzhou

first: yuntan

last: qiu

state: guangdong

address: 107 Yanjiang West Road, Guangzhou City, Guangdong Province

department: Research Center of Medicine

institute: Sun Yat-Sen Memorial Hospital

summary: Flag_eCLIP_Seq was performed in MEX3A-flag overexpressing ACHN cells.

overall_design: MEX3A-Flag was over-expressed in ACHN cells. The potent RNA  was immunoprecipitated by Flag or IgG antibodies using eCLIP assay. Then, all the potent MEX3A-binding target RNAs were identified by deep sequencing, using Hiseq Xten.

first: Yuntan

last: Qiu


title: Bulk and single-cell RNA-seq reveal the role of dmrtb1 in a sequentially hermaphroditic fish, Mastacembelus armatus

city: Fuzhou

first: Zhen

last: Huang

state: Fujian

address: 1 keji road, college of life science, Fujian Normal University (Qishan campus)

institute: Fujian Normal University

summary: Sequential hermaphroditism, whereby the sex of one individual changes during its development, has been described in many fish species. Yet, the genetic regulation of this dynamic process of sexual differentiation is not well understood. Here, we report the characterization of sequential hermaphroditism in an aquacultural fish, the zig-zag eel (Mastacembelus armatus), based on 4 years of artificial breeding. All M. armatus individuals initially developed as females, with approximately half of them then becoming males after going through an intersex phase.

overall_design: The ovotestes of three individual 2-year-old zig-zag eels were dissected, and mixed to a single sample of ovotestis.

first: Lingzhan

last: Xue


title: Regulation of cortical folding by niche progenitor cells that co-express cross-repressive transcription factors Neurog2 and Ascl1

city: Lethbridge

first: Yaroslav

last: Ilnytskyy

state: AB

address: 4401, University Drive W

department: Biology

institute: University of Lethbridge

summary: Humans exemplify gyrencephalic species with folded cerebral cortices, contrasting with lissencephalic mammals such as mice. Here we investigated how proneural genes Neurog2 and Ascl1 control cortical folding by regulating neurogenic patterns. Cortical neural progenitor cells (NPCs) stratify into four pools (proneural negative, Neurog2+, Ascl1+, double+) that are distributed evenly in mouse cortices and modular in gyrencephalic macaque cortices and pseudo-folded human cerebral organoids. Each pool has distinct developmental potentials, transcriptomes, epigenomes, and gene regulatory networks. Neurog2-Ascl1 form a bistable toggle switch double+ NPCs to prevent lineage commitment observed in single+ NPCs. Neurog2 and Ascl1 act redundantly to control neurogenic timing, with NPCs precociously depleted in Neurog2-/-;Ascl1-/- cortices. Finally, selective killing of Neurog2/Ascl1 double+ NPCs using Neurog2/Ascl1 split-Cre;Rosa-DTA transgenics breaks neurogenic symmetry in mice by locally disrupting Notch signaling, leading to cortical folding. Our findings suggest that Neurog2/Ascl1 double+ NPCs are Notch-ligand expressing ‘niche’ cells that regulate neurogenic continuity and cortical gyrification.

overall_design: Atac-seq. CD15+ GFP/mCherry negative, single, double positive, double negative cortical progenitors were isolated from E12.5 Neurog2Flag-mcherryKI/+;Ascl1GFPKI/+ dorsal telencephalic tissue by FACS. ATAC-seq was performed on each cell type using 50,000 cells as input material for the transposase reaction (Buenrostro et al., 2015).


title: Gene expression profiling for cigarette smoke (CS) exposed lung treated with human umbilical cord mesenchymal stem cells derived extracellular vesicle (hUCMSC-EV) and human umbilical cord derived mesenchymal stem cells (hUC-MSC)

city: Kepala Batas

first: Noridzzaida

last: Ridzuan

state: pulau pinang

address: BERTAM

country: Malaysia

institute: Institut perubatan dan pergigian termaju, Universiti Sains Malaysia

summary: To study the genes and pathway involved in cigarette smoke induced lung inflammation, and treatment with hUC-MSC-EV and hUC-MSC we have employed microarray expression profiling to identify the differentially expressed genes

overall_design: Treatment of hUC-MSC-EV and hUC-MSC were given to the animals after 12 weeks of CS exposure

first: Badrul

middle: H

last: Yahaya


title: The RNA binding protein MEX3A controls G1/S transition via regulating RB/E2F pathway in clear cell renal cell carcinoma [RNA-Seq]

summary: RNA-Seq was performed after siRNA transfection in ACHN cells.

overall_design: After transfection for 48 h, total RNA was extracted using RNAiso Plus. Then,total RNA were identified by deep sequencing, using BGI500.

first: Meng

last: Meng


title: The RNA binding protein MEX3A controls G1/S transition via regulating RB/E2F pathway in clear cell renal cell carcinoma [RIP-Seq]

summary: Flag_RIP_Seq was performed in MEX3A-flag overexpressing ACHN cells.

overall_design: MEX3A-Flag was over-expressed in ACHN cells. The potent RNA  was immunoprecipitated by Flag or IgG antibodies using RIP assay. Then, all the potent MEX3A-binding target RNAs were identified by deep sequencing, using Hiseq Xten.


title: RNA sequencing to determine gene expression changes in Siglec-15 knockdown oteosarcoma cells

city: Shijiazhuang

first: Mengke

last: Fan

address: Ziqiang Road, Qiaoxi District

department: Bone research institute

institute: The Third Hospital of Hebei Medical University

summary: In our study, we found that Siglec-15 was critical to osteosarcoma characteristics. To identify the downstream target genes of Siglec-15 in osteosarcoma, we conducted the RNA-seq analysis of Siglec-15 knockdown in osteosarcoma cell line 143B cells.

overall_design: Compare negative control siRNA and Siglec-15 knockdown 143B cancer cells using RNA-seq.


title: mRNA expression profiling in MDA-MB-231 and HepG2 cells with 2 µM of ACP52C peptide treatment for 0, 12, 24, and 48 hours

first: Chul Geun

last: Kim

address: wangsimni-ro 222

department: Life Science

institute: Hanyang University

summary: The goal of this study is to compare mRNA expression profiles of the ACP52C-treated cells in time dependent manner. All cell lines were maintained in DMEM supplemented with 10% fetal bovine serum and 1% penicillin/streptomycin. For the drug treatment, MDA-MB-231 and HepG2 cells were incubated in the presence of 2 μM ACP52C for 0, 12, 24, and 48 hours. Total cellular RNAs were extracted using Qiazol reagent. The RNA quality was examined by spectrophotometry, agarose gel electrophoresis (calculating the 18S and 28S rRNA ratio) and an Agilent Technologies 2100 Bioanalyzer (ensuring a RIN value greater than 7). The library was prepared using the RNA seq3’ mRNA-Seq Library Prep Kit FWD. The constructed libraries were subjected to 150-bp two-end sequencing using an Illumina NextSeq 500 sequencer at Insilicogen. All procedures were performed following the manufacturer’s instructions. Tophat 2 and cufflinks were used for reads mapping and expected read counts, respectively. DEGs were analyzed using an edgeR program and functional annotation of genes were achieved using a DAVID program.

overall_design: Duplicated mRNA profiles of ACP52C treated MDA-MB-231 and HepG2 cells are generated by 150 bp two end sequencing using Illumina NextSeq 500 and then analyze the differential expressed gene among these groups of cells.

first: C


title: MeRIP sequencing

city: Beijing

first: wenhao

last: ju

address: chaoyang

institute: pumc

summary: In this study, we aimed to systematically profile global RNA N6-methyladenosine (m6A) modification patterns in a mouse model of diabetic cardiomyopathy (DCM). Patterns of m6A in DCM and normal hearts were analyzed via m6A-specific methylated RNA immunoprecipitation followed by high-throughput sequencing (MeRIP-seq) and RNA sequencing (RNA-seq). A total of 973 m6A peaks were detected in DCM samples and 296 differentially methylated sites were selected for further study, including 106 hypermethylated and 190 hypomethylated m6A sites (fold change (FC) > 2, p < 0.05). Gene ontology and KEGG Pathway analyses indicated that unique m6A-modified transcripts in DCM were closely linked to cardiac fibrosis, myocardial hypertrophy, and myocardial energy metabolism. Overall, m6A modification patterns were altered in DCM, and modification of epitranscriptomic processes, such as m6A, is a potentially interesting therapeutic approach.

overall_design: To establishe a transcriptome-wide m6A methylome profile of diabetic cardiomyopathy and healthy heart

first: Ju

last: wenhao

first: Liu

last: kai


title: Development of gene expression signatures for SL-13R

city: Fukuoka

first: Daisuke

last: Sugiyama

state: Fukioka

address: 3-1-1, Maidashi, Higasi-ku

department: Incubation Center for Advanced Medical Science (ICAMS)

country: Japan

institute: Kyushu university

summary: To further development of our gene expression, we have employed whole genome microarray expression profiling. Human cord blood CD34+ cells from healthy donors was cultured for 2 days with or without SL-13R.

overall_design: SL-13R induced gene expression in human cord blood CD34+ cells was measured at 2 day after addition of SL-13R or PBS (control).


title: Interplay between Histone and DNA Methylation Seen through Comparative Methylomes in Rare Mendelian Disorders

city: Paris

first: Guillaume

last: Velasco

address: 35 rue Hélène Brion

department: UMR7216 Epigenetics and Cell Fate

country: France

institute: Université Paris Cité

summary: Genome wide DNA methylation profiling of blood samples from patients with genetic diseases of the epigenetic machineries. The Illumina Infinium HumanMethylation450  and the Infinium MethylationEPIC BeadChips were used to obtain DNA methylation profiles across approximately 450,000 and 850,000 CpGs in whole blood from patients with ICF and overgrowth syndrome. Samples included 1 ICF1, 2 ICFX, 2 TBRS and 2 Luscan-Lumish patients.

overall_design: Bisulphite converted DNA from 7 samples

first: Claire

last: Francastel


title: Effects of circALTO on gene expression of 293T cells

city: Dallas

first: Richard

last: Wang

state: TX

address: 5323 Harry Hines Blvd

department: Dermatology

institute: UT Southwestern

summary: Purpose: The goal of the study was to determine the potential effects of ALTO expression on the human transcriptome. Method: 293T cells were transfected with circALTO1 or a control plasmid, in triplicate, and mRNA profiles sequenced. Results: mRNA profiles from circALTO1 and control cells were distinct. ALTO expressing cells induced the transcription of multiple genes previoulsy implicated in polyomavirus infections.

overall_design: mRNA profile of ALTO1 or vector transfected 293T cells

first: Rong

last: Yang

first: Jiwoong


title: AMPKalpha1,  AMPKalpha2 and AMPKalpha1/2 double knock-down RNA-Seq

city: Manchester

first: Michela

last: Garofalo

address: Wilmslow Road

country: United Kingdom

institute: University of Manchester

summary: In non-small cell lung cancer the role of AMPKα is controversial and its contribution to lung carcinogenesis is not well-defined. To shed light on the molecular mechanisms through which AMPKα could be involved in lung tumorigenesis, we analysed by RNA-sequencing the whole transcriptome upon AMPKα1, AMPKα2 or AMPKα1/α2 knockdown (KD). Furthermore, it remains largely unknown whether long non-coding RNAs (lncRNAs) are involved in the regulation of AMPKα-mediated pathways. Therefore, we examined the lncRNA expression profile and searched for lncRNAs differentially expressed in the same conditions (AMPKα1, AMPKα2 or AMPKα1/α2 KD versus control) in H1299 cells.

overall_design: H1299 cells were stably transduced with shRNA lentivruses targeting human PRKAA1 (AMPKα1), PRKAA2 (AMPKα2) and a negative non-targeting control. Total RNA was isolated according to manufacturer’s instructions and submitted for RNA-seq.

first: Manuela

last: La Montagna

first: Sudhakar

last: Sahoo


title: Epigenetic drift during long-term culture of cells in vitro

first: Wolfgang

last: Wagner

address: Pauwelsstrasse 20

institute: RWTH Aachen University

summary: Culture expansion of primary cells evokes highly reproducible DNA methylation (DNAm) changes These changes might be directly regulated or caused by gradual deregulation of the epigenetic state, which is often referred to as “epigenetic drift” We have identified CG dinucleotides (CpGs) that become continuously hyper- or hypomethylated in the course of culture expansion of mesenchymal stem cells (MSCs) and other cell types During reprogramming into induced pluripotent stem cells (iPSCs) particularly the culture-associated hypomethylation is reversed simultaneously with age-associated and pluripotency-associated DNAm changes Bisulfite barcoded amplicon sequencing (BBA-seq) demonstrated that upon passaging the DNAm patterns of neighboring CpGs become more complex without evidence of continuous pattern development and without association to oligoclonal subpolulations of MSCs at later passages Circularized chromatin conformation capture (4C) revealed reproducible changes in nuclear organization between early and late passages, while there was no preferential interaction with other genomic regions that also harbor culture-associated DNAm changes Chromatin immunoprecipitation of CTCF did not show significant differences during long-term culture of MSCs, however culture-associated hypermethylation was enriched at CTCF binding sites and hypomethylated CpGs were devoid of CTCF Taken together, our results indicate that DNAm changes during culture-expansion resembles epigenetic drift

overall_design: Bisulfite converted DNA from different passages of three donors of human umbilical vein endothelial cells and three donors of mesenchymal stromal cells was hybridised to the Illumina Infinium 450k Human Methylation Beadchip In addition, DNA of the same donors of mesenchymal stromal cells was oxidized prior to bisulfite treatment and hybridization to the Illumina 450k Human Methylation Beadchip with the TrueMethyl Array kit (Cambridge Epigenetix) to investigate 5-hyxdroxymethylation int these cells

first: Julia

last: Franzen

first: Theodoros

last: Georgomanolis

first: Anton

last: Selich

first: Chao-Chung

last: Kuo

first: Reinhard

last: Stöger

first: Lilija

last: Brant

first: Melita

last: Mulabdić

first: Eduardo

last: Fernandez-Rebollo

first: Clara

last: Grezella

first: Alina

last: Ostrowska

first: Matthias

last: Begemann

first: Miloš

last: Nikolić

first: Minseung

last: Choi

first: Björn

last: Rath

first: Anthony

last: Ho

first: Michael

last: Rothe

first: Axel

last: Schambach

first: Argyris

last: Papantonis


title: Targeting of CAT and VCAM1 as novel therapeutic targets for DMD cardiomyopathy

city: Shanghai

first: Bin

last: Li

address: Dong'an Road

department: Department of Physiology and Pathophysiology

institute: Fudan University

summary: Novel targets for DMD cardiomyopathy

overall_design: Whole transcriptomic analyses of wild type and DMD mutant hiPSCs-derived cardiomyocytes.

first: Alex

last: Chang

first: Weiyao

last: Xiong


title: Single-cell RNAseq profiling in a patient with discordant primary cutaneous B and T cell lymphoma reveals micromilieu-driven immune skewing

city: Vienna

first: Natalia

last: Alkon

address: Währinger Gürtel 18-20

department: Department of Dermatology

country: Austria

institute: Medical University of Vienna

summary:
Background: Primary cutaneous lymphomas comprise a heterogeneous group of B and T cell malignancies which often show an indolent course, but can progress to aggressive disease in a subset of patients. Diagnosis is often delayed due to clinical and histopathological similarities with benign inflammatory conditions. Especially during early disease, cancer cells are present at relatively low percentages in comparison to the inflammatory infiltrate, an interplay that is currently only insufficiently understood.
Objectives: To improve diagnostics and perform molecular characterization of a complex type of primary cutaneous lymphoma.
Methods: Single-cell RNA sequencing (scRNA-seq) combined with T and B cell receptor sequencing.
Results: We were able to diagnose a patient with concurrent mycosis fungoides (MF) and primary cutaneous follicle center lymphoma (PCFCL), appearing in mutually exclusive skin lesions. Profiling of tumor cells and the tissue microenvironment revealed a type-2 immune skewing in MF, most likely guided by the expanded clone that also harbored upregulation of numerous pro-oncogenic genes. By contrast, PCFCL lesions exhibited a more type-1 immune phenotype, consistent with its indolent behavior.
Conclusions: These data not only illustrate the diagnostic potential of scRNA-seq, but also allow the characterization of specific clonal populations shaping the unique tissue microenvironment in clinically distinct types of lymphoma skin lesions.

overall_design:
Comparison of skin cells from two histologically different tumors in a single patient
>>> Raw data are unavailable due to patient privacy concerns. <<<

first: Constanze

last: Jonak

first: Katharina

last: Rindler

first: Thomas

last: Rojahn

first: Lisa

middle: E

last: Shaw

first: Stefanie

last: Porkert

first: Wolfgang

last: Weninger

first: Franz

last: Trautinger

first: Georg

last: Stingl

first: Philipp

last: Tschandl

first: Lorenzo

last: Cerroni

last: Farlik

first: Patrick

last: Brunner


title: Distinct transcriptional profile of blood mononuclear cells in Behcet’s disease: insights into the central role of neutrophil chemotaxis

city: Athens

first: Maria

middle: G.

last: Tektonidou

state: Please choose a State

address: Mikras Asias 75

country: Greece

institute: National and Kapodistrian University of Athens

summary: Both innate and adaptive immune responses are reportedly increased in Behcet’s disease  (BD), a chronic-relapsing systemic vasculitis lying at the intersection between autoinflammation and  autoimmunity. To further study pathophysiologic molecular mechanisms operating in BD we searched  for transcriptome-wide changes in blood mononuclear cells from these patients. We performed 3’ mRNA next generation sequencing-based genome-wide transcriptional  profiling followed by analysis of differential expression signatures, KEGG pathways, GO biological  processes and transcription factor signatures al 25 samples (11 healthy controls and 14 BD).

overall_design: 25 human samples out of with 11 healthy controls and 14 with Behcet’s disease

first: Kleio-Maria

last: Verrou

first: Nikolaos

middle: I

last: Vlachogiannis

first: Giannis

last: Ampatziadis-Michailidis

first: Panagiotis

last: Moulos

first: Georgios

last: Pavlopoulos

first: Pantelis

last: Hatzis

first: George

last: Kollias

first: Petros

last: Sfikakis


title: Next Generation Sequencing Facilitates Quantitative Analysis of human multiple myeloma derived CD84 activated M-MDSCs or IgG (control) treated M-MDSCs

city: Rehovot

first: Idit

last: Shachar

address: Herzl 234

department: Immunology

institute: Weizmann Institute of science

summary:
Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare CD84 activated to control treated primary human M-MDSCs from multiple myeloma patients transcriptome profiling (RNA-seq) to understand the role of CD84 on these cells
Methods: mRNA profiles from sorted M-MDSCs from patient bone marrow samples were generated by deep sequencing, in triplicate, using a bulk adaptation of the MARS-Seq protocol.

overall_design: mRNA profiles of human multiple myeloma derived CD84 activated M-MDSCs or IgG (control) treated M-MDSCs

first: Hadas

last: Lewinsky


title: Next Generation Sequencing Facilitates Quantitative Analysis of human multiple myeloma derived CD84 activated G-MDSCs or IgG (control) treated G-MDSCs

summary:
Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare CD84 activated to control treated primary human G-MDSCs from multiple myeloma patients transcriptome profiling (RNA-seq) to understand the role of CD84 on these cells
Methods: mRNA profiles from sorted G-MDSCs from patient bone marrow samples were generated by deep sequencing, in triplicate, using a bulk adaptation of the MARS-Seq protocol.

overall_design: mRNA profiles of human multiple myeloma derived CD84 activated G-MDSCs or IgG (control) treated G-MDSCs


title: Context-specific action of macrolide antibiotics on the eukaryotic ribosome

city: chicago

first: Maxim

last: Svetlov

state: ILLINOIS

address: 900 south ashland ave

department: Department of Medicinal Chemistry and Pharmacognosy

institute: University of Illinois at Chicago

summary: 80S ribosomes of S.cerevisiae carry G2400A mutation in the 25S rRNA which makes them sensitive to macrolide antibiotics

overall_design: Ribosome profiling was performed on the G2400A mutant S.cerevisiae cells (2 biological replicates) and compared to the same cells treated with telithromycin (2 biological replicates)

first: Timm

middle: O

last: Koller

first: Sezen

last: Meydan

first: Vaishnavi

last: Shankar

first: Dorota

last: Klepacki

first: Norbert

last: Polacek

first: Nicholas

middle: R

last: Guydosh

first: Daniel

last: Wilson

first: Nora

last: Vázquez-Laslop

first: Alexander

last: Mankin


title: LGR6 marks nephron progenitor cells

city: UTRECHT

first: PHILIP

last: LIJNZAAD

state: Utrecht

address: HEIDELBERGLAAN 25

department: Single Cell Facility

country: Netherlands

institute: Princess Maxima Center for Pediatric Oncology

summary: Background: Nephron progenitor cells (NPCs) undergo a stepwise process to generate all mature nephron structures. Mesenchymal to epithelial transition (MET) is considered a multi-step process of NPC differentiation to ensure progressive establishment of new nephrons. However, despite this important role, to date, no marker for NPCs undergoing MET in the nephron exists. Results: Here, we identify LGR6 as a NPC marker, expressed in very early cap mesenchyme, pre-tubular aggregates, renal vesicles and in segments of S-shaped bodies, following the trajectory of MET. By using a lineage tracing approach in embryonic explants in combination with confocal imaging and single-cell RNA sequencing, we provide evidence for the multiple fates of LGR6+ cells during embryonic nephrogenesis. Moreover, by using long-term in vivo lineage tracing, we show that postnatal LGR6+ cells are capable of generating the multiple lineages of the nephrons.   Conclusion: Given the profound early mesenchymal expression and MET signature of LGR6+ cells, together with the lineage tracing of mesenchymal LGR6+ cells, we conclude that LGR6+ cells contribute to all nephrogenic segments by undergoing MET. LGR6+ cells can therefore be considered an early committed NPC population during embryonic and postnatal nephrogenesis with potential regenerative capability.

overall_design: lineage tracing using single-cell RNA sequencing of in vivo and ex vivo cultured mouse embryonic kidney cells

first: Ravian

middle: L

last: van Ineveld

first: Thanasis

last: Margaritis

first: Berend

last: Kooiman

first: Femke

last: Groenveld

first: Hendrikus

last: Ariese

first: Philip

last: Lijnzaad

first: Hannah

last: Johnson

first: Jeroen

last: Korving

first: Ellen

middle: J

last: Wehrens

first: Frank

last: Holstege

first: Jacco

last: van Rheenen

first: Jarno

last: Drost

first: Anne

last: Rios

last: Bos


title: Transcriptome profiling of cold exposure induced browning of white fat

first: Yu

last: Li

address: Minhang Dongchuan Road No.500

institute: East China Normal University

summary: We revealed the common alterations and highlighted the differential effects between cold and β-AR agonists exposure on beige fat

overall_design: Total RNA obained from the beige fat which mice were housed at either 22℃ or 4℃ for 7 days in a temperature-controlled incubator

first: Xiaodan

last: Ping

first: Yankang

last: Zhang


title: Comparing Co-morbid Crohn's-Spndyloarhtritis to each of the underlying dieases

city: Aurora

first: Kristine

middle: A

last: Kuhn

state: Colorado

address: 1775 Aurora Ct. Mail Stop B115

department: Medicine

institute: University of Colorado School of Medicine

summary: This study was carried out to determine how immunological signatures related in the colon and periperhal blood between indivudals with Crohn's, Spondyloarhtritis, and individuals with both diseases.  We carried out one experiments with 1 patient in each condition (1 Crohn's, 1 Spondyloarthritis, 1 Co-morbid, 1 HC), which we then repeated for a total of 8 subjects.

overall_design: We carried out scRNA-seq on CD45+ cells isolated from colon biopsy tissue


title: Co-transcriptional splicing efficiencies differ within genes and between cell types

city: Ann Arbor

first: Mats

last: Ljungman

state: Michigan

address: NCRC, B520 Room 1346 2800 Plymouth Rd.

institute: University of Michigan

summary: Pre-mRNA splicing is carried out by the spliceosome and involves splice site recognition, removal of introns, and ligation of exons. Components of the spliceosome have been shown to interact with the elongating RNA polymerase II (RNAPII), which is thought to allow splicing to occur concurrently with transcription. However, little is known about the regulation and efficiency of cotranscriptional splicing in human cells. In this study, we used Bru-seq and BruChase-seq to determine the cotranscriptional splicing efficiencies of 17,000 introns expressed across six human cell lines. We found that less than half of all introns across these six cell lines were cotranscriptionally spliced. Splicing efficiencies for individual introns showed variations across cell lines, suggesting that splicing may be regulated in a cell type–specific manner. Moreover, the splicing efficiency of introns varied within genes. The efficiency of cotranscriptional splicing did not correlate with gene length, intron position, splice site strengths, or the intron/neighboring exons GC content. However, we identified binding signals from multiple RNA binding proteins (RBPs) that correlated with splicing efficiency, including core spliceosomal machinery components—such as SF3B4, U2AF1, and U2AF2 showing higher binding signals in poorly spliced introns. In addition, multiple RBPs, such as BUD13, PUM1, and SND1, showed preferential binding in exons that flank introns with high splicing efficiencies. The nascent RNA splicing patterns presented here across multiple cell types add to our understanding of the complexity in RNA splicing, wherein RNA-binding proteins may play important roles in determining splicing outcomes in a cell type– and intron-specific manner.

overall_design: Nascent RNA Bru-seq and BruChase-seq used to determine co-transcriptional splicing efficiencies of 17000 introns expressed across 6 diverse human cell lines

first: K

last: Bedi

first: B

last: Magnuson

first: Narayanan

last: Venkata

first: M

middle: T

last: Paulsen

first: T

last: Wilson


title: Splicing factor SRSF1 promotes breast cancer progression via regulating alternative splicing

first: Junxian

last: Du

state: Shanghai

address: Fudan university,Shanghai,China

institute: Fudan university

summary:
Purpose:Intensive evidence have highlighted the effect of aberrant alternative splicing (AS) events triggered by dysregulation of SR protein family on cancer progression. Nonetheless, the underlying mechanism in breast cancer (BRCA) remains elusive. Here we sought to explore the molecular function of SRSF1 and identify the key AS events regulated by SRSF1 in BRCA.
Methods:We conducted comprehensive analysis for the expression and the clinical correlation of SRSF1 in BRCA based on TCGA, Metabric database, clinical tissue samples and BRCA cell lines. Functional analysis of SRSF1 in BRCA was conducted in vitro and in vivo. SRSF1-mediated AS events and its binding motif were identified by RNA-seq, RNA immunoprecipitation-PCR (RIP-PCR) and in vivo crosslinking followed by immunoprecipitation (CLIP), which was further validated by the minigene reporter assay. Finally, the expression and their clinical significance were validated in clinical samples and TCGA database.
Results:SRSF1 was upregulated in BRCA samples, associated positively with tumor grade and Ki-67 index, and correlated with poor prognosis in hormone receptor positive (HR+) cohort, which facilitated tumor progression in vitro and in vivo. We identified SRSF1-mediated AS events and discovered the SRSF1 binding motif in the regulation of PTPMT1. Furthermore, PTPMT1 splice switching regulated by SRSF1 partially mediated the oncogenic role of SRSF1 via the AKT/C-MYC axis. Additionally, PTPMT1 splice switching was validated in tissue samples of BRCA patients.
Conclusions:Collectively, SRSF1 exerts the oncogenic roles in BRCA partially through regulating AS of PTPMT1, which could be a candidate prognostic factor and therapeutic target in HR+ BRCA cohort.

overall_design: mRNA alternative splicing profiles of MCF7 NC and MCF7 sh SRSF1 cells

first: Wei

last: Zhu


title: Cholesterol-induced M4-like Macrophages in Non-alcoholic Steatohepatitis recruit Neutrophils and induce NETosis

city: Los Angeles

first: Ana

last: Maretti-Mira

state: CA

address: 1450 Biggy Street, NRT 3514

institute: USC

summary: The liver is the central organ for cholesterol synthesis and homeostasis. The effects of dietary cholesterol on hepatic injury, mainly of oxidized low-density lipoproteins (OxLDL), are not fully understood. Here, we show that the degree of cholesterol oxidation had different impacts on the global gene expression of human M2-like macrophages, with highly oxidized LDL causing the most dramatic changes. M2-like macrophages and Kupffer cells undergo M4-like polarization, decreasing the expression of important markers, such as IL10, MRC1, and CD163. These cells also displayed functional changes, with reduced phagocytic capacity, increased neutrophil recruitment, and more effective neutrophil extracellular traps (NETs) induction. Our findings provide a link between the accumulation of OxLDL and NASH progression, offering a new target for NAFLD treatment.

overall_design: Human CD14+ monocytes were isolated from five healthy control PBMCs using the CD14 MicroBeads human kit according to the manufacturer’s protocol (Miltenyi).  CD14+ monocytes were plated at 1x10e6 /well in 6-well plate in RPMI 1640 with 50ng/mL of M-CSF plus 5% FBS for 5 days at 37˚C/ 5% CO2. After differentiation, M2-like macrophages were stimulated for 24h with RPMI + 5%FBS media plus PBS (unstimulated control), or 50ug/mL of native low-density lipoprotein (Kalen Biomedical LLC), medium oxidized LDL (Kalen Biomedical LLC), or high oxidized LDL (Kalen Biomedical LLC). Cells were then harvested in Buffer RLT (Qiagen) + 1% 2-Mercaptoethanol (Sigma-Aldrich) and processed for low pass RNAseq using Illumina Truseq Stranded mRNA library preparation kit according to the manufacturer’s protocol (Illumina). Prepared libraries were sequenced on the Illumina Nextseq 500 at 3 million reads per sample at 2x75 cycles.

first: Lucy

last: Golden-Mason

first: Matthew

last: Salomon


title: Transcript changes in primary Leydig cells treated with Sertoli cell released exosomes

first: Yi

last: Ma

address: 1630, Dongfang road.

institute: Renji hospital

summary: In this study, we aim to figure out if Sertoli cells released exosomes can regulate the survival and steroidogenesis of Leydig cells. We found Sertoli cells released exosomes can cross the blood-testis barrier, deliver their contents into the Leydig cells, and promote the survival of Leydig cells through CCL20.

overall_design: Two groups of RNA samples isolated from Leydig cells were included, each group has three replicates (n=3). Group A was reference, the cells were not treated with exoxomes. The cells in Group B  were treated with exoxomes.

first: Yan

last: Zhou

first: Shasha

last: Zou

first: Yun

last: Sun

first: Xiangfeng

last: Chen


title: ATRX alteration contributes to tumor growth and immune escape in pleomorphic sarcomas

city: Toulouse

first: Christel

last: Devaud

address: 2 Avenue Hubert Curien

institute: INSERM

summary: Whole genome and transcriptome sequencing of a cohort of 67 leiomyosarcomas revealed ATRX to be one of the most frequently mutated genes in LMS after TP53 and RB1. While its function is well described in the ALT mechanism, we wondered whether its alteration could have complementary effects on sarcoma oncogenesis. ATRX alteration is associated with the down-expression of genes linked to differentiation in LMS, and to immunity in an additional cohort of 60 poorly differentiated sarcomas. In vitro and in vivo models showed that ATRX loss increases tumor growth rate and immune escape by decreasing the immunity load of active mast cells in sarcoma tumors. These data indicate that an alternative to unsuccessful targeting of the adaptive immune system in sarcoma could be to target the innate system. This might lead to a better outcome for sarcoma patients in terms of ATRX status.

overall_design: Differential gene expression was performed by R package DESeq, between ATRXKD and ATRXCT tumors

first: Lucie

last: Darmusey

first: Noémie

last: Thébault

first: Frédéric

last: Chibon


title: NAD+ supplementation counteracts senescence mediated by STING in Ataxia Telangiectasia models by improving mitophagy (Mouse)

city: Baltimore

first: Supriyo

last: De

address: 251 Bayview Blvd

department: Laboratory of Genetics and Genomics

institute: NIA-IRP, NIH

summary: Senescence phenotypes and mitochondrial dysfunction are implicated in aging and neurodegeneration, and in the premature aging disease, including A-T. Loss of mitochondrial function can drive age-related decline in the brain, but little is known about whether improving mitochondrial homeostasis alleviates senescence phenotypes. Here we demonstrate impaired mitochondrial function and increased senescence growth arrest with senescence-associated secretory phenotype (SASP) in A-T patient fibroblasts, and in ATM-deficient cells and mice. We find that boosting intracellular NAD+ levels with nicotinamide riboside (NR) reduces senescence, suppresses neuroinflammation, and improves motor function in Atm-/- mice. We further show that the senescence responses are mediated by stimulator of interferon genes (STING), which is activated by cytoplasmic mtDNA and that NR prevents senescence and neuroinflammation through stimulation of mitophagy. Our findings suggest a pivotal role for mitochondrial dysfunction induced senescence in A-T pathogenesis, and that enhancing mitophagy is a potential therapeutic intervention.

overall_design: Six week old male B6;129S4-Atmtm1Bal/J mice from either wild-type (WT) or Atm homozygous (Atm-/-, ATM) were given 3.5 mg/ml (12 mM)  nicotinamide riboside (NR) at in their drinking water while the control groups  received only water (Veh) for 2 months, using four biological replicates for each of the four experimental groups.

first: Beimeng

last: Yang

first: Jong-Hyuk

last: Lee

first: Yujun

last: Hou

first: Xiuli

last: Dan

first: Noah

last: Wechter

first: Sudarshan

last: Krishnamurthy

first: Risako

last: Kimura

first: Mansi

last: Babbar

first: Ross

last: McDevitt

first: Shiliang

last: Zhang

first: Tyler

last: Demarest

first: Yongqing

first: Mark

last: Mattson

first: Deborah

last: Croteau

first: Vilhelm

last: Bohr


title: NAD+ supplementation counteracts senescence mediated by STING in Ataxia Telangiectasia models by improving mitophagy

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: Expression data of human stromal cells isolated from Follicular lymphoma  (FL) or non-malignant reactive (RLN) lymph nodes

city: RENNES

first: Celine

last: Pangault

address: 2, avenue du Léon Bernard

department: Medical School of Rennes

institute: Rennes University Hospital

summary: GEP on Affymetrix U133+2.0 microarrays was performed on in vitro expanded stromal cells

overall_design: GEP was performed on 8 FL-LN and 8 RLN

first: Karin

last: Tarte


title: Global expression profile of uterine cervical carcinoma in Indian patients.

city: Kolkata

first: Susanta

last: Roychoudhury

state: West Bengal

address: Mahatma Gandhi Road, Thakurpukur

country: India

institute: Saroj Gupta Cancer Centre & Research Institute

summary: Cervical cancer (CACX) is the tumor of the uterine cervix and its primary etiological factor is the infection of high risk human papilloma virus (hrHPV), primarily HPV16 and HPV18. CACX is the third most commonly diagnosed cancer and the fourth leading cause of cancer deaths in women worldwide. In India, CACX accounts for approximately 1,22,844 new cases and 67,477 deaths annually. It is evident that Indian women are getting diagnosed at invasive stages of CACX leading to poor prognosis. Here, we tried to understand the change in the expression profile during the development of the tumor starting from HPV-negative normal samples to invasive CACX samples and try to understand the pathogenesis of cervical carcinoma in Indian patients.

overall_design: Gene expression analysis was carried out on 11 invasive CACX samples and 5 HPV Negative Normal Controls. Moreover, cervical cancer cell lines with varying Human Papilloma virus (HPV) status namely, SiHa (HPV16 positive), Hela (HPV18 positive) and C33A (HPV negative) were also included.

first: Anirban

last: Roychowdhury

first: Sudip

last: Samadder

first: Ankita

last: Chatterjee

first: Chinmay

last: Panda


title: Comparison of Corynebacterium glutamicum ATCC 13032 + pAN6-cg1978 with ATCC 13032 + pAN6

city: Jülich

first: Max

last: Hünnefeld

address: Wilhelm-Johnen-Straße

department: Institute for Bio- and Geosciences 1: Biotechnology

institute: Forschungszentrum Jülich

summary: Investigation of the impact of an overexpression of cg1978 on gene expression under standard conditions (CGXII-Glucose)

platform_organism: Bacillus subtilis subsp. subtilis str. 168

overall_design: To identify genes which are differentially expressed in Corynebacterium glutamicum ATCC13032 pAN6-cg1978 in comparison to the empty vector control ATCC13032 pAN6 , DNA microarray analyses with these strains were performed. For this purpose RNA was isolated from cells cultivated in CGXII minimal medium with 2% glucose (w/v) and harvested at OD600 = 6. Three biological replicates were performed.

first: Larissa

last: Kever

first: Julia

last: Frunzke


title: Implication of repeat insertion domains in the trans-activity of the long non-coding RNA ANRIL [ANRIL_LNA_Affy]

city: Vandoeuvre-lès-Nancy

first: Sylvain

last: Maenner

address: 9 Avenue de la Forêt de Haye

department: CNRS-UL

institute: IMoPA

summary: To identify the genes differentially expressed upon the knockdown of the lncRNA ANRIL using LNA GapmeRs in HEK293 cells

overall_design: We analyzed WT and ANRIL knockdown HEK293 cells using the Affymetrix Human Clariom D chips. Array data were processed using the Transcriptome Analysis Console (TAC) Software. Five biological replicates were included in the analysis.

first: Charbel

last: Alfeghaly

first: Aymeric

last: Sanchez

first: Raphael

last: Rouget

first: Quentin

last: Thuillier

first: Valérie

last: Igel-Bourguignon

first: Virginie

last: Marchand

first: Christiane

last: Branlant

first: Yuri

last: Motorin

first: Isabelle

last: Behm-Ansmant


title: NAD+ supplementation counteracts senescence mediated by STING in Ataxia Telangiectasia models by improving mitophagy (Human)

first: Supriyo

last: De

state: Maryland

overall_design: Gene expression profiles from cultured fibroblasts from healthy controls (N=5) and Ataxia-Telangiectasia (ATM) cases (N=5) were compared by microarray analysis.

first: Beimeng

last: Yang

first: Jong-Hyuk

last: Lee

first: Yujun

last: Hou

first: Xiuli

last: Dan

first: Noah

last: Wechter

first: Sudarshan

last: Krishnamurthy

first: Risako

last: Kimura

first: Mansi

last: Babbar

first: Ross

last: McDevitt

first: Shiliang

last: Zhang

first: Tyler

last: Demarest

first: Yongqing

first: Mark

last: Mattson

first: Deborah

last: Croteau

first: Vilhelm

last: Bohr


title: Expression data from splenocytes - Wild type Myd88 or mutated MYD88-L252P mice

city: Limoges

first: Lilian

last: Roland

address: rue Bernard Descottes

department: Haute Vienne

institute: Contrôle de la Réponse Immune B et Lymphoproliférations Limoges

summary: The MYD88 L265P mutation, activator of NF-kappa B (NF-kB), is found in 80% to 90% of WM. So far, there is no existing animal model for WM to evaluate the role of MYD88 activation, and the only published mouse model harboring the mouse ortholog MYD88 L252P mutation develops aggressive B-cell lymphomas in aged mice. The MYD88 L252P coding sequence was attached to YFP cDNA with an IRES sequence. This construct was flanked with loxP sites and inserted in the Rosa26 locus. The expression of MYD88 L252P protein is induced only in B cells after crossing with CD19_Cre mice.

overall_design: Total mRNA was extracted from whole spleen tissues. Amplification of RNAs and hybridization onto microarrays were performed on an Affymetrix Gene Atlas system® with the MoGene-2_1-st-v1 Affymetrix chip (Affymetrix, Santa Clara, CA) as described (Chanut A et al, Leukemia 2013).

first: Jean

last: Feuillard

first: Christelle

middle: V

last: Fabert

first: Nathalie

last: Gachard


title: RNA-Seq of silenced MYB123 stable transgenic plants

city: Cordoba

first: Antonio

middle: Rodriguez

last: Franco

state: CORDOBA

address: Rabanales. Ed Severo Ochoa

department: Bioquímica y Biología Molecular

country: Spain

institute: Universidad de Córdoba

summary: Report of an RNA-Seq analysis done with strawberries taken from MYB123 RNAi silenced and stable transgenic plants vs control  plants transformed with the pFRN empty vector

overall_design: RNA-Seq analysis done with 3 biological replicates

first: Juan

last: Muñoz Blanco


title: Integrative Analysis of ovarian cancer cell behavior reveals a miRNA signature associated with Intrinsic Platinum Resistance in ovarian cancer.

city: Brisbane

first: Dominic

last: Guanzon

state: Queensland

address: Building 71/918 RBWH Herston

department: UQCCR

country: Australia

institute: University of Queensland

type: Non-coding RNA profiling by high throughput sequencing

summary: The aim of this study was to identify a set of miRNAs which are associated with chemotherapy resistance in ovarian cancer, and to evaluate if these miRNAs are enrich in small nanovesicles, called exosomes, released from ovarian cancer cells.

overall_design: miRNAs were profiled from cells using next generation seqeuencing (Illumina NextSeq 500 platform).

first: Mona

last: Alharbi

first: Carlos

last: Salomon


title: Effect of fasting and ketogenic diet on hippocampal astrocytes in vivo

status: Public on May 24 2021

first: Michael

middle: J.

last: Wolfgang

state: MD

address: 855 N Wolfe Street

department: Institute for Basic Biomedical Sciences

institute: The Johns Hopkins University School of Medicine

summary: To understand the transcriptional effect of fasting and feeding a ketogenic diet on mouse CNS astrocytes, we performed translating ribosomal affinity purification (TRAP)  of mRNAs immunoprecipitated from hippocampus.  TRAP mice express a ribosomal epitope tag upon Cre-induced recombination that can be immunoprecipitated following activation. We measured the abundance of actively translating mRNAs from a ribosomal pull-down that came from adult astrocyte (Aldh1l1-Cre)-specific TRAP mice that were subjected to one of three dietary conditions: four weeks of normal chow diet, four weeks of ketogenic diet (high-fat, low-carbohydrate)43, or an 18-hour fast. Immediately following the respective diets, forebrain and hippocampus was harvested from all groups, ribosomes were immunoprecipitated, and actively translating mRNAs in the ribosomes were purified.

overall_design: 11 total samples were analyzed.  4 Fed, 3 Fasted, and 4 Ketogenic diet fed mice.

first: M

first: J

middle: M

last: Ellis


title: YTHDC1-Hyper tribe uncover YTHDC1 binding sites in human leukemia cells

city: New York

first: Yuanming

last: Cheng

state: New York

address: 417 E68 Street

institute: MSKCC

summary: The goal of this study is to identify YTHDC1 binding targets in MOLM13 cells(AML).

overall_design: MOLM-13 cells overexpressing YTHDC1-ADAR fusion or empty vector for 48 hours were harvested for RNA-seq to look for A-G editing events.

first: Karen

last: Chu

last: Kharas


title: Fibroblast Dedifferentiation as a Determinant of Successful Regeneration

city: Heidelberg

first: Tobias

last: Gerber

address: Meyerhofstr. 1

department: Developmental Biology

institute: EMBL Heidelberg

summary: Limb regeneration, while observed lifelong in salamanders, is restricted to pre-metamorphic stages in Xenopus laevis frogs. After amputation, post-metamorphic frogs form a blastema that grows only an unsegmented cartilage rod. Whether this loss is due to systemic factors such as the immune system or due to an intrinsic incapability of cells to form competent stem cells has been unclear. Here, we use genetic fate mapping to establish that, as in axolotl, connective tissue (CT) cells form the post-metamorphic frog blastema. Using heterochronic transplantation into the limb bud and single-cell transcriptomic profiling, we show that axolotl CT cells fully dedifferentiate and integrate to form lineages including cartilage in the developing limb. In contrast, frog blastema CT cells do not fully re-express the limb bud progenitor program, even when transplanted into the limb bud. Correspondingly, transplanted cells contribute to extraskeletal CT but not to developing cartilage. Further, using single-cell RNA-seq analysis we find that the embryonic and the adult frog cartilage differentiation programs are molecularly distinct. This work defines intrinsic restrictions in CT dedifferentiation as a limitation in adult regeneration.

sample_organism:
Ambystoma mexicanum
Xenopus laevis

platform_organism:
Ambystoma mexicanum
Xenopus laevis

overall_design: Tissue grafting, single-cell transcriptomics, reporter lineage tracking and cell transplantions were used to deconstruct cell compositions and to reconstruct lineage relationships aiming to find determinants of the successful regeneration in axolotl compared to the incomplete regenration in frogs.

first: Barbara

last: Treutlein


title: RNA-seq identifies differential expressed genes upon YTHDC1 knockdown in MOLM13 human acute myeloid leukemia cells

summary: The goal of this study is to identify differential expressed genes upon YTHDC1 depletion in MOLM13 cells(AML).

overall_design: RNAs were purified from MOLM13 cells transduced with control and  YTHDC1 shRNAs and then used for RNA-seq.


title: RNA-seq data for tumor tissues from mice fed with normal diet (ND) or high cholesterol diet (HCD) II

city: shanghai

first: Fu

last: jing

address: No.225 Changhai road

department: Liver Centre of SMMU

country: China

institute: Eastern Hepatobiliary Surgery Hospital

summary: To address how serum cholesterol affected tumor progression, C57BL/6J mice were placed on either normal diet or high cholesterol diet for 4 weeks, and then B16F10 cells were subcutaneously injected into the right flanks of mice. We performed transcriptome sequencing analysis (RNA-seq) on tumor tissues from ND and HCD groups.

overall_design: Tumor tissues from ND and  HCD group were analyzed.

first: Wenhao

last: Qin

first: Zhishi

last: Yang

first: Jing

last: Fu

first: Hongyang

last: Wang


title: Xrn1 influence on gene transcription results from the combination of general effects on elongating RNA pol II and gene-specific chromatin configuration

city: Burjassot

first: Antonio

last: Jordan

state: Valencia

address: Doctor Moliner 50

institute: Universitat de Valencia


title: Gene expression of MOLM14 (AML cell line) transfected with siATF4 or siCTRL

city: Strassen

first: Tony

last: KAOMA

address: 1 A-B Rue Thomas Edison

department: Quantitative Biology Unit

country: Luxembourg

institute: Luxembourg Institute of Health

summary: Assessment of the impact of ATF4 silencing in FLT3-ITD/MLL AML cell lines

overall_design: siATF4 versus siCTL MOLM14 transcriptome

first: Joffre

last: Carine

first: Heyndt

last: Questin

first: Sarry

last: Jean-Emmanuel

first: Kaoma

last: Tony


title: Xrn1 influence on gene transcription results from the combination of general effects on elongating RNA pol II and gene-specific chromatin configuration [RNA-seq]

summary: mRNA homeostasis is favored by crosstalk between transcription and degradation machineries. Both the Ccr4-Not and the Xrn1-decaysome complexes have been described to influence transcription. While Ccr4-Not has been shown to directly stimulate transcription elongation, the information available on how Xrn1 influences transcription is scarce and contradictory. In this study we have addressed this issue by mapping RNA polymerase II (RNA pol II) at high resolution, using CRAC and BioGRO-seq techniques in Saccharomyces cerevisiae. We found significant effects of Xrn1 perturbation on RNA pol II profiles across the genome. RNA pol II profiles at 5’ exhibited significant reductions in slope that were compatible with decreased elongation rates. This phenomenon was also observed soon after the nuclear pool of Xrn1 was depleted. Nucleosome mapping confirmed drastically altered chromatin dynamics. We also found an accumulation of arrested RNA pol II at the 3’ end, immediately upstream of polyadenylation sites of most genes, with particular incidence in those functionally related to regulatory processes. Lack of Xrn1 provoked alterations in RNA pol II CTD phosphorylation and increased recruitment of 3’ pre-mRNA processing factors. However, accumulation of RNA pol II at 3’ ends was rather related to the nucleosomal configuration of those regions.

overall_design: 2 RNA-seq samples: 1 wt and 1 mutant.

first: A

last: Jordán-Pla

first: M

last: Barneo-Muñoz

last: Pérez-Martínez

last: Pérez-Ortín


title: Genetic regulation of the ATP synthase in neurons modulates cognition

city: Madrid

first: Pau

middle: B.

last: Esparza-Molto

state: Madrid

address: Calle Nicolas Cabrera, 1

institute: Universidad Autonoma de Madrid

summary:
The goal of this analysis was to profile the gene expression signatures associated to different neuronal doses of IF1.
The mitochondrial ATP synthase produces ATP by oxidative phosphorylation and integrates different signals to regulate cellular functions and fate. The ATPase inhibitory factor 1 (IF1) is a structurally-disordered protein that inhibits the ATP synthase, contributing to metabolic reprogramming and signalling through mitochondrial reactive oxygen species (mtROS). mtROS regulate kinases and transcription factors in mitohormetic responses that favour adaptation to toxic insults. IF1 is tissue-specifically expressed and in human and mouse brain is in molar excess over the ATP synthase. Herein, we have used genetic approaches to ablate or overexpress IF1 in neurons to investigate its role in brain functions. IF1 inhibits a fraction of the ATP synthase under physiological conditions and regulates respiration, mtROS production and mitochondrial structure. Transcriptomic, proteomic and metabolomic analyses indicate that IF1 regulates synaptic transmission and cognition. Ablation of IF1 impairs short-term memory whereas IF1 overexpression increases basal synaptic transmission and learning by mtROS-dependent activation of the extracellular signal-regulated kinases 1/2 (ERK 1/2). Overall, we show that IF1 dose plays a fundamental role in the regulation of neuronal function by controlling the fraction of inhibited ATP synthase that acts as source of mitohormetic mtROS, further emphasizing the ATP synthase/IF1 as promising targets to treat cognitive disorders.

overall_design: RNA was extracted from the hippocampus of 9-month old mice of the following genotypes: IF1-KO, control (CRL) and IF1-overexpressing transgenic (TG) mice. Three mice were processed for each genotype for hybridization onto Agilent microarrays.

middle: B

first: Jose

last: Cuezva


title: Xrn1 influence on gene transcription results from the combination of general effects on elongating RNA pol II and gene-specific chromatin configuration [Mnase-seq]

overall_design: 5 MNase-seq samples: 1 WT, 1 Xrn1 mutant (2 replicates each), 1 Naked DNA control.

first: G

last: Gutiérrez

last: Mitjavila

first: V

last: Begley

first: X

last: Peñate

first: S

last: Chávez


title: Dnmt1/3a deletion in prefrontal cortical neurons reduces palatable food intake

city: Charlottesville

first: Michael

middle: Murray

last: Scott

state: VA

address: 1340 Jefferson Park Ave

department: Pharmacology

institute: University of virginia

summary: DNA methylation is an important regulatory mechanism in the control of neuronal function. Both during development and following exposure to salient stimuli, plasticity in the methylation of cytosine residues leads to a change in neuron excitability that subsequently sculpts animal behavior. However, while the response of DNA methyltransferase enzymes in adult neurons to stimuli such as drugs of abuse have been described, less is known about how these enzymes regulate methylation at specific loci to change an animal’s inclination to ingest natural rewards.  Specifically, we do not understand how changes in methylation within important brain areas known to regulate palatable food intake can affect ingestion, and detailed investigation of the neurophysiological and genomic effects of perturbing methyltransferase function has not been pursued.  By deleting DNA methyltransferase 1 and 3a in the mouse prefrontal cortex, we observed the requirement for these enzymes in the regulation of nutrient rich food consumption in the absence of any effect on the intake of low fat and low sugar chow. We also determined that the deletion profoundly affected neuron excitability within pyramidal cells resident in superficial layers II/III of the cortex but had little effect in deep layer V neurons.  Finally, reduced representation bisulfite sequencing revealed both hypo and hypermethylation in response to methyltransferase deletion, an effect that was observed in binding sites for retinoic acid receptor beta (RARβ) located within regulatory regions of genes known to affect neuronal function. Together, our data suggest that alterations in the actions of RARβ could shift neuronal activity to reduce palatable food intake.

overall_design: C57BL/6 and, DNMT1 and DNMT3a floxed mice were injected with Synapsin promoter-driven Cre-GFP AAV. Methylomes of medial prefrontal cortex pyramidal neurons with and without DNMT1 and DNMT3a were profiled.

first: Amelie

last: Kuchler

first: Nathan

last: Sheffield

first: Mohan

middle: C

last: Manjegowda


title: PLZF acetylation levels regulate NKT cell diffrentiation

city: Paris

first: Marc

last: Delord

address: Hopital Saint-Louis, 1 avenue Claude Vellefaux

department: Recherche clinique

institute: Centre hospitalier de Versailles

summary:
The transcription factor PLZF (promyelocytic leukemia zinc finger) is encoded by the BTB domain-containing 16 (Zbtb16) gene. Its repressor function regulates specific transcriptional programs. During the development of invariant natural killer T (NKT) cells, PLZF is expressed and directs their effector program but the detailed mechanisms underlying PLZF regulation of multi-stage NKT cell developmental program are not well understood. This study investigated the role of acetylation-induced PLZF activation on NKT cell development by analyzing mice expressing a mutant form of PLZF mimicking constitutive acetylation (PLZFON mice). NKT populations in PLZFON mice were reduced in proportion and numbers of cells, and the cells present were blocked at the transition from developmental stage 1 to stage 2. NKT cell subset differentiation was also altered, with T-bet+ NKT1 and RORt+ NKT17 subsets dramatically reduced, and the emergence of a T-bet-RORt- NKT cell subset with features of cells in early developmental stages rather than mature NKT2 cells. Preliminary analysis of DNA methylation patterns suggested that activated PLZF acts on the DNA methylation signature to regulate NKT cells’ entry into the early stages of development, while repressing maturation. In wild-type NKT cells, deacetylation of PLZF is possible, allowing subsequent NKT cell differentiation. Interestingly, development of other innate lymphoid and myeloid cells, that are dependent on PLZF for their generation, is not altered in PLZFON mice highlighting lineage specific regulation. Overall, we propose that specific epigenetic control of PLZF through acetylation levels is required to regulate normal NKT cell differentiation.
Key points:
Constitutive acetylation of PLZF (PLZFON) blocks NKT cell development.
PLZFON might act on the DNA methylation signature to control gene expression.
PLZF acetylation levels regulate normal NKT cell differentiation.

overall_design:
We investigate the transcriptional difference of iNKT cells between mice expressing a constitutive acetylated form of PLZF (PLZFon mice) vs control (WT mice)

Samples WT_control_rep_1, PLZF_ON_rep_1, WT_control_rep_2 and PLZF_ON_rep_2 where used in the analyses.

first: Jihene

last: Klibi

first: Claudine

last: Joseph

first: Veronique

last: Parietti

first: Marika

last: Pla

first: Bruno

last: Lucas

first: Christine

last: Chomienne

first: Antoine

last: Toubert

first: Fabien

last: Guidez

first: Kamel

last: Benlagha


title: Effect of RP58 deletion on neural cell transcriptional programs

first: Nadia

last: Dahmane

state: NY

address: 525 East 68 Street, Box 99

institute: Cornell University

summary: The goal of our study is to identify RP58 transcriptional traget that may play a role in its fucntion during neuronal differentiation.

overall_design: RNA-seq of E14.5 postmitotic neurons from Rp58+/+ (control) and Rp58-/- (Rp58 mutant) mouse cortices

first: Yingtao

last: Bi


title: MicroRNA sequencing and analysis of the newt heart

city: Bad Nauheim

first: Carsten

last: Kuenne

address: Ludwigstrasse 43

department: Bioinformatics

institute: Max Planck Institute for Heart and Lung Research

summary: MicroRNA sequencing using Ion Torrent Proton platform of the undamaged heart of the red spotted newt Notophthalmus viridescens. MicroRNAS were identified using MIRPIPE

overall_design: Examination of miRNA expression in the undamaged heart of Notophthalmus viridescens by IonTorrent Proton sequencing

first: Ettore

last: Lignelli

first: Stefan

last: Guenther

first: Mario

last: Looso

first: Thomas

last: Braun


title: Transcriptome profiling of prefrontal cortex (BA9) in neurodegenerative dementia using Affymetrix Human Transcriptome Array 2.0

city: Singapore

first: Michelle

middle: GK

last: Tan

address: 20 College Road

department: Clinical Translational Research

country: Singapore

institute: Singapore General Hospital

summary:
We investigated transcriptome alterations in the prefrontal cortex (BA) of patients with Alzheimer’s disease (AD), dementia with Lewy bodies (DLB) and Parkinson's disease dementia (PDD) when compared with elderly controls without neurological or psychiatric diseases (CTRL) using Affymetrix Human Transcriptome Array 2.0
All brain samples were provided by the Brains for Dementia Research (BDR), UK. All cases were prospectively assessed by experienced clinicians using validated clinical rating instruments. The samples processed in each group were matched for age, sex and postmortem interval (PMI) as far as possible.

overall_design: Postmortem brains (BA9) derived from 9 CTRL (5F/4M), 9  AD (5F/4M), 12 DLB (6F/6M) and 12PDD (6F/6M) were extracted for RNA and subjected to transcriptome profiling using HTA 2.0 array.

middle: G

first: Mitchell

middle: K

last: Lai


title: RenalMSCvsJGcells_MouseMicroarray

city: Nashville

first: Jose

last: Gomez

state: Tennessee

address: 2220 Pierce Ave, 502 RRB

institute: Vanderbilt University Medical Center

summary: Microarray data comparison of renal mesenchymal stromal cells (MSC) vs Juxtaglomerular cells using Affimetric Mouse 430 2.0

overall_design: Juxtaglomerualr (JG) cells were FACSorted and Renal MSC were FACSorted using CD44 from the C56Bl6 Ren1c YFP mice. MSC culture to confluence. RNA isolated from MSC and JG cells for microarray analysis

first: Victor

last: Dzau


title: Identification and comparative analysis of long non-coding RNA in the skeletal muscle of two Dezhou donkey strains (Equus asinus)

city: Beijing

first: Haobin

last: Hou

address: 2 Yuanmingyuan West Road, Haidian District

institute: Chinese Academy of Agricultural Sciences

summary: In this study, 3,869 donkey skeletal muscle lncRNAs were identified using RNA-Seq along with a stringent screening procedure in the longissimus dorsi (LD) and gluteal (G) muscles. These lncRNAs share many characteristics with other mammalian lncRNAs, such as shorter open reading frames (ORFs) and lower expression levels than mRNAs. Furthermore, in pairwise comparisons between libraries of the same stage for two genetic types of male Dezhou donkey, 73 differentially expressed lncRNAs were common to all muscle tissues.

overall_design: Twelve skeletal muscle samples were taken from the longissimus dorsi and gluteal muscles of six Dezhou donkeys, respectively.

first: Hou

last: Haobin

first: Zhang

last: Li


title: long read RNA-seq from lower lobe of left lung (ENCSR986WKB)

status: Public on May 23 2021

city: Stanford

first: ENCODE

last: DCC

address: 300 Pasteur Dr

institute: ENCODE DCC

summary:
ENC4_39 W78 left lobe of 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: long read RNA-seq from heart right ventricle (ENCSR984OAE)

summary:
ENC4_52 W76 heart right ventricle

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: long read RNA-seq from heart left ventricle (ENCSR994YZY)

summary:
ENC4_53 W76 heart left ventricle

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 fibroblast of lung (ENCSR000AMZ)

summary:
Control ChIP-seq on human NHLF

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: long read RNA-seq from K562 (ENCSR983KDL)

summary:
K562

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 foreskin keratinocyte (ENCSR982AYN)

summary:
ChIP-seq control (input DNA) on primary keratinocytes in day 0 of differentiation

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 SK-N-SH (ENCSR759IVF)

summary:
ChIP-seq on human 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: Gene expression profiling following the overexpression or the knockdown of Ambra1 in A375 melanoma cell lines

first: Milad

last: Ibrahim

address: 550 1st Avenue

department: Dermatology

institute: NYU Langone

summary:
Melanoma is the most deadly type of skin cancers and, there is a continuous need to develop early biomarkers as well as treatments to improve the survivability of patients. Ambra1 is an essential regulator in
autophagy and it has been recently shown to have a role in cell proliferation. We used microarrays to analyse the transcriptomic changesi n A375 melanoma cell lines following Ambra1 differential expression

overall_design: Four stably transfected A375 melanoma cell lines were utilized for this study. Overexpressions of Ambra1 and its matching control, β-galactosidase were performed by retroviral infection. While knockdown of Ambra1 was performed by lentiviral infection that expresses a shRNA construct targeted to Ambra1 and the control cell line expressed a scrambled shRNA control. Total RNA was extracted and hybridized on Affymetrix microarrays. Three biological replicates of each cell line were used for eah group.

first: Noel

last: Carter

first: Jane

last: Armstrong


title: long read RNA-seq from adrenal gland (ENCSR995WKW)

summary:
Adrenal Gland 2-1 ENTEX51

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: long read RNA-seq from GM12878 (ENCSR962BVU)

summary:
GM12878 Ljungman

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: long read RNA-seq from PC-3 (ENCSR947JHA)

summary:
PC-3 cell line

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: Histone ChIP-seq from middle frontal area 46 (ENCSR965CIV)

summary:
H3K4me3 ChIP-seq on dorsolateral prefrontal cortex tissue male adult (86 years) originated from dorsolateral prefrontal cortex

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 HEK293 (ENCSR938LXW)

summary:
Control ChIP-seq on human HEK293

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: TF ChIP-seq from nephron (ENCSR966OUM)

summary:
CTCF ChIP-seq on nephron female embryo (5 days) 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: long read RNA-seq from ovary (ENCSR507WZC)

summary:
ENC4_72 W80 ovary

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: Histone ChIP-seq from left lung (ENCSR510RPC)

summary:
H3K27ac ChIP-seq on left lung tissue 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: Control ChIP-seq from middle frontal area 46 (ENCSR917XOL)

summary:
Control ChIP-seq on dorsolateral prefrontal cortex tissue female adult (90 or above years) originated from dorsolateral prefrontal cortex

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: Histone ChIP-seq from left lung (ENCSR904KDP)

summary:
H3K4me3 ChIP-seq on left lung tissue 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: long read RNA-seq from endodermal cell (ENCSR904KAT)

summary:
H9-derived definitive endoderm

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: In Vivo CRISPR Screens Identify E3 Ligase Cop1 as a Modulator of Macrophage Infiltration and Cancer Immunotherapy Target

city: Boston

first: Xiaoqing

last: Wang

state: MA

address: 450 Brookline Ave

institute: Dana Farber Cancer Institute

summary: Cop1 regulates stability of transcription factors. We found that Cop1 can regulate the proteasomal degradation of Cebpd. We generated 4T1 breast cancer cells with CRISPR/Cas9 mediated Cop1 (gene symbol RFWD2) knockout. We used Cebpd antibody to pulldown the DNA fragments binding with Cebpd and did ChIP-seq.

overall_design: Examination of Cebpd ChIP-seq under two condtions in 4T1 breast cancer cells: Rosa26 and Cop1 knockout. Additionally, we used two different gRNAs to knockout Cop1. Two replicaters per condition.

first: Collin

last: Tokheim

first: Binbin

first: Myles

last: Brown

first: Xiaole

middle: S

last: Liu


title: TF ChIP-seq from progenitor cell of endocrine pancreas (ENCSR901NIN)

summary:
CTCF ChIP-seq on progenitor cell of endocrine pancreas originated from progenitor cell of endocrine pancreas

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: TF ChIP-seq from heart right ventricle (ENCSR505RTK)

summary:
CTCF ChIP-seq on heart right ventricle female adult (46 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: Histone ChIP-seq from HEK293 (ENCSR910LIE)

summary:
H3K36me3 ChIP-seq on human HEK293

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: TF ChIP-seq from brain (ENCSR930SOT)

summary:
CTCF 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: Histone ChIP-seq from testis (ENCSR503QSX)

summary: 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: Histone ChIP-seq from middle frontal area 46 (ENCSR901EDL)

summary:
H3K4me3 ChIP-seq on dorsolateral prefrontal cortex tissue male adult (89 years) originated from dorsolateral prefrontal cortex

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: Histone ChIP-seq from pancreas (ENCSR499GKR)

summary:
H3K27me3 ChIP-seq on pancreas tissue female adult (41 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: Histone ChIP-seq from middle frontal area 46 (ENCSR495HIT)

summary:
H3K27ac ChIP-seq on dorsolateral prefrontal cortex tissue male adult (71 years) originated from dorsolateral prefrontal cortex

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: long read RNA-seq from Right ventricle myocardium superior (ENCSR899GAP)

summary:
ENC4_56 W78 right ventricle myocardium superior

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: TF ChIP-seq from excitatory neuron (ENCSR489QDF)

summary:
CTCF ChIP-seq on excitatory neuron

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: long read RNA-seq from HL-60 (ENCSR887LTD)

summary:
Homo sapiens HL-60

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 SK-N-SH (ENCSR481DSF)

summary:
ChIP-seq on human 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: Control ChIP-seq from foreskin keratinocyte (ENCSR488AHQ)

summary:
ChIP-seq control (input DNA) on primary keratinocytes in day 3 of differentiation

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: Histone ChIP-seq from middle frontal area 46 (ENCSR882ZTE)

summary:
H3K27me3 ChIP-seq on dorsolateral prefrontal cortex tissue male adult (71 years) originated from dorsolateral prefrontal cortex

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: Histone ChIP-seq from middle frontal area 46 (ENCSR889TEU)

summary:
H3K27ac ChIP-seq on dorsolateral prefrontal cortex tissue female adult (87 years) originated from dorsolateral prefrontal cortex

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: Histone ChIP-seq from adrenal gland (ENCSR886FKD)

summary:
H3K9me3 ChIP-seq on adrenal gland tissue female adult (41 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: long read RNA-seq from ovary (ENCSR477HHG)

summary:
ENC4_71 W73 ovary

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: TF ChIP-seq from heart right ventricle (ENCSR473DVS)

summary:
CTCF ChIP-seq on heart right ventricle male adult (40 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: Control ChIP-seq from mucosa of descending colon (ENCSR856YCA)

summary:
Control ChIP-seq on mucosa of descending colon tissue male adult (40 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: Histone ChIP-seq from middle frontal area 46 (ENCSR855NCG)

summary:
H3K27ac ChIP-seq on dorsolateral prefrontal cortex tissue female adult (83 years) originated from dorsolateral prefrontal cortex

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: TF ChIP-seq from astrocyte (ENCSR461VHZ)

summary:
CTCF ChIP-seq on astrocyte originated from astrocyte

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: TF ChIP-seq from H9 (ENCSR871MKQ)

summary:
CTCF 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: Control ChIP-seq from SK-N-SH (ENCSR451BHD)


title: long read RNA-seq from right cardiac atrium (ENCSR435UUS)

summary:
ENC4_58 W78 right cardiac atrium

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: long read RNA-seq from kidney (ENCSR432YKA)

summary:
ENC4_42 W71 kidney

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 middle frontal area 46 (ENCSR437DCH)

summary:
Control ChIP-seq on dorsolateral prefrontal cortex tissue female adult (90 or above years) originated from dorsolateral prefrontal cortex

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: long read RNA-seq from GM12878 (ENCSR838WFC)

summary:
Homo sapiens GM12878 immortalized cell line

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: long read RNA-seq from aorta (ENCSR425HFS)

summary:
ENC4_103 W73 aorta

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 SK-N-SH (ENCSR411AFQ)


title: Control ChIP-seq from K562 (ENCSR409VQS)

summary:
ChIP-seq on human K562

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: Histone ChIP-seq from adrenal gland (ENCSR837CSL)

summary:
H3K27ac ChIP-seq on adrenal gland female adult (41 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: TF ChIP-seq from type B pancreatic cell (ENCSR458PYQ)

summary:
CTCF ChIP-seq on type B pancreatic cell originated from type B pancreatic cell

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: Histone ChIP-seq from pancreas (ENCSR829EYM)

summary:
H3K4me1 ChIP-seq on pancreas tissue female adult (41 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: Control ChIP-seq from SK-N-SH (ENCSR823HRT)

summary:
ChIP-seq on human 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: Control ChIP-seq from middle frontal area 46 (ENCSR822YWX)

summary:
Control ChIP-seq on dorsolateral prefrontal cortex tissue female adult (86 years) originated from dorsolateral prefrontal cortex

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