title: RNA sequencing on the infarct zone after ischemia reperfusion (I/R)

status: Public on Jun 30 2020

city: Utrecht

first: Eva

last: van Rooij

state: Utrecht

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute

type: Expression profiling by high throughput sequencing

summary: Hearts received a sham or an I/R surgery. After indicated timepoints, the infarct region was isolated and used for RNA sequencing

overall_design: RNA sequencing was performed on the infarct region of 3 sham mice, 3 mice 1 day after I/R and 3 mice 14 days after IR

first: Bas

last: Molenaar

first: Sebastiaan

last: van Kampen

first: Alexandre

last: Bossu

last: van Heesch

first: Jorge

last: Ruiz-Orera

first: Benedikt

last: Obermayer

first: Kamila

last: Kutz

first: Marta

last: Vigil-Garcia

first: Jantine

last: Monshouwer-Kloots

first: Mauro

last: Giacca

first: Norbert

last: Hubner

first: Toon

middle: A

last: van Veen

first: Teun

middle: P

last: de Boer


title: Chromatin assembly factor HIRA is essential for the maintenance of hematopoiesis

city: Bethesda

first: Mingan

last: Sun

state: Maryland

address: Building 6B, 6 Center Drive

department: Eunice Kennedy Shriver National Institute of Child Health and Human Development

country: USA

institute: National Institute of Health

type: Genome binding/occupancy profiling by high throughput sequencing

summary: HIRA is a histone chaperone that deposits the histone variant H3.3 in transcriptionally active genes. HIRA is essential for mouse development, as the standard knockout (KO) results in early embryonic death.  However, the role of HIRA in hematopoiesis is poorly understood.  We investigated the effect of Hira KO on hematopoiesis using Vav-Cre Loxp system. We show that Hira KO dramatically reduces bone marrow LSK cells, resulting in anemia, thrombopenia and severe, combined immunodeficiency. To investigate the molecular mechanisms, RNA-seq and ATAC-Seq were performed using LSK cells isolated from WT and Hira conditional KO mice.

overall_design: Examination of the alteration of gene expression and chromatin accessibilty in LSK (Lin-Sca1+cKit+) cells sorted from WT or Hira KO bone marrow cells by FACS

first: Chao

last: Chen

first: Keiko

last: Ozako


title: A novel class of CLK inhibitors that targets SRSF10 and promote p53-mediated cytotoxicity on human colorectal cancer cells

city: Sherbrooke

first: Philippe

last: Thibault

state: Quebec

address: 3201, Jean-Mignault

department: faculty of medecine and health sciences

country: Canada

institute: Université de Sherbrooke

summary: The expression of the splicing regulator SRSF10 is elevated in metastatic colorectal cancer (CRC) where it promotes the production of the pro-tumorigenic Bclaf1-L splice variant. We discovered a group of small molecules with an aminothiazole carboxamide core (GPS167, GPS192 and others) that decrease production of Bclaf1-L. Additional alternative splicing events regulated by SRSF10 in HCT116 cells were affected by GPS167/192 (e.g. Mdm4 and Wtap), and other events also shifted in a SRSF10-independent manner (e.g. Mdm2, Nab2, Tra2a). GPS167/192 increased the interaction of SRSF10 with CLK1 and CLK4 kinases, leading us to show that GPS167/192 were CLK kinase inhibitors impacting the activity of SRSF10. Notably, GPS167 impaired the growth of colorectal cancer cell lines and organoids, inhibited anchorage-independent colony formation, cell migration and promoted cytoxicity that required SRSF10 and p53. The anti-cancer potential of this new class of CLK kinase inhibitors is further supported by the observation that GPS167 only minimally affected normal colonocytes and normal colorectal organoids. Thus, while SRSF10 promotes tumorigenesis, DNA damage promoted by GPS167 redirects SRSF10 activity towards cell death in a p53-dependent manner.

overall_design: Impact of GPS167 or GPS192 on alternative splicing and gene expression profiles of HCT116 cells.

first: Muhammad

last: Sohail

first: Benoit

last: Chabot


title: Gene expression profiling of tissue and hMSC xenografts in a rat postpartum urinary injury model

city: Cleveland

first: Mark

last: Cameron

state: OH

address: 10900 Euclid Ave

department: Population and Quantitative Health Sciences

institute: Case Western Reserve University

summary: Periurethral human mesenchymal stem cell (hMSC) injections are associated with functional improvement in animal models of post-partum stress urinary incontinence (SUI). However, limited data exists on the role of hMSCs in modulating gene expression in tissue repair after urethral injury. We quantified temporal gene expression modulation in hMSCs, and injured rat urethral tissue, using RNA seq in an animal model of SUI, over a 3-day time period following urethral injury, and local hMSC therapy.     We injected PKH fluorescent-labeled human hMSC into the periurethral space of rats, following a 4h vaginal distention (3 rats per time point). Control rats underwent vaginal distention injury only, and were sacrificed at 12h, 24h, 36h, 72h post injury. Rat urethral and vaginal tissues were frozen and sectioned. Fluorescent labeled hMSCs were distinguished from adjacent, unlabeled rat urethral tissue. RNA was prepared from urethral tissue obtained by laser dissection of frozen tissue sections and sequenced on an Illumina HiSeq 2500. Differentially expressed genes (DEGs) over 72h were evaluated using a 2-group t-test (p<0.05).    Our transcriptional analyses identified candidate genes involved in tissue injury, that were broadly sorted by injury and exposure to hMSC, throughout the first 72h of acute phase of injury. DEGs in treated urethra, compared with untreated urethra, were functionally associated with tissue repair, angiogenesis, neurogenesis, and oxidative stress suppression. DEGs included a variety of cytokines, extracellular matrix stabilization and regeneration genes, cytokine signaling modification, cell cycle regulation, muscle differentiation and stabilization. Moreover, our results revealed DEGs changes in the hMSCs (PKH-labelled), which were harvested from injured urethra. The expressions are related to DNA damage repair, transcription activation, stem cell regulation, cell survival, apoptosis, self-renewal, cell proliferation, migration and injury response.

sample_organism:
Homo sapiens
Rattus norvegicus

platform_organism:
Homo sapiens
Rattus norvegicus

overall_design: Laser captured rat urethral tissue or PKH labeled hMSC were obtained from 12 hr, 24 hr, 36 hr, or 72 hr post injury. Our submission contains the following samples: Urethral tissues from 3 control rats for every timepoint; urethral tissue and hMSC from 2 rats at 12 hr; urethral tissue and hMSC from 3 rats per timepoint at 24 hr, 36 hr, and 72 hr post-injury. In total we submitted 31 tissue samples for RNA seq analysis.

first: Z

last: Sadeghi

first: J

last: Kenyon

first: B

last: Richardson

first: A

last: Khalifa

first: S

last: El-Kom

first: M

last: Cartwright

last: Conroy

last: Caplan

last: Hijaz


title: Heme oxygenase-1 orchestrates the immunosuppressive program of tumor-associated macrophages [RNA-Seq]

status: Public on Jun 29 2020

city: Gosselies

first: Stanislas

last: Goriely

address: Rue Adrienne Bolland 8

country: Belgium

institute: Université Libre de Bruxelles

summary: Tumor-Associated Macrophages (TAMs) contribute to the maintenance of a strong immunosuppressive environment, supporting tumor progression and resistance to treatment. To date, the mechanisms that drive acquisition of these immunosuppressive features are still poorly defined. Heme oxygenase-1 (HO-1) is the rate-limiting enzyme that catabolizes free heme. It displays important cytoprotective, anti-inflammatory and antioxidant properties. A growing body of evidence suggests that HO-1 may also promote tumor development. Herein, we show that HO-1 is highly expressed in monocytic cells in the tumor microenvironment (TME) once they differentiate into TAMs. Deletion of HO-1 in the myeloid compartment enhances the beneficial effects of a therapeutic antitumor vaccine by restoring CD8 T-cell proliferation and cytotoxicity. We further show that induction of HO-1 plays a major role on monocyte education by tumor cells by modulating their transcriptional and epigenetic programs. These results identify HO-1 as a valuable therapeutic target to reprogram the TME and synergize with current cancer therapies to facilitate antitumoral response.

overall_design: RNA-seq in mouse macrophages from HO1-KO and wild type samples

first: Emmanuelle

last: Alaluf

first: Benoît

last: Vokaer

first: Aurélie

last: Detavernier

first: Abdulkader

last: Azouz

first: Marion

last: Splittgerber

first: Alice

last: Carrette

first: Louis

last: Boon

first: Frédérick

last: Libert

first: Miguel

last: Soares

first: Alain

last: Le Moine


title: Imaging resident and recruited macrophage contributions to Wallerian degeneration

city: PARIS

first: Alexandre

last: Boissonnas

address: 91 Boulevard de l'hopital

department: CIMI

country: France

institute: INSERM

summary:
Abstract: Wallerian degeneration (WD) is a process of autonomous distal degeneration of axons upon injury. Macrophages (MP) of the peripheral nervous system (PNS) are main cellular agent controlling this process. Some evidences suggest that resident PNS-MP along with MP of hematogenous origin may be involved but whether these two subsets exert distinct functions is unknown. Combining MP-designed fluorescent reporters mice, and coherent anti-stoke raman scattering (CARS) imaging of the sciatic nerve, we deciphered the spatio-temporal choreography of resident and recently recruited MP after injury and unveiled distinct functions of these subsets with recruited MP responsible of efficient myelin stripping and clearance while resident MP were involved in axonal regrowth.  This work provides clues to tackle selectively cellular processes involved in neurodegenerative diseases.
Methods: (relevant for this GEO dataset): RNAseq of sciatic nerve macrophages from mice after CCI: Sorted cells were lysed in 100µl of RA1/TCEP buffer (NucleoSpin RNA XS, Macherey-Nagel), snap frozen in liquid nitrogen and stored at -80C until RNA extraction. All samples were processed in parallel and RNA extraction (without Carrier RNA but with on-column DNase treatment) was performed according to manufacturer's instructions (NucleoSpin RNA XS, Macherey-Nagel). RNA was eluted in RNAse-free water. Preparation of cDNA libraries for RNAseq was done using the SmartSeq method according to manufacturer's instructions (SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing, Clontech/TaKaRa). Due to the low number of cells, the total amount of eluted RNA was used as starting material for reverse transcription, followed by 18 cycles of pre-amplification. 1ng of cDNA were used for RNAseq sequencing library preparation, according to manufacturer's instructions (Nextera XT DNA Library Preparation, Illumina). Final samples pooled library prep were sequenced on a Nextseq 500 ILLUMINA with MidOutPut cartridge (2x130Millions of 75 bases reads) with 2 runs (4plex and 5plex), corresponding to 2x30Millions of (paired-end) reads per sample after demultiplexing.

overall_design: EGFP+/CD64+/CD11b+/SiglecF-/Ly6G- or ECFP+/CD64+/CD11b+/SiglecF-/Ly6G- macrophages were sorted by flow cytometry from a cell suspension of three pooled sciatic nerves from Macblue x Cx3cr1egfp/+ mice (one sciatic nerve per mouse; with 3 mice pooled for one group; repeated three times) at D14 after CCI. Two populations were analyzed: (1) EGFP+/CD64+/CD11b+/SiglecF-/Ly6G- macrophages sorted from ipsi lateral nerves representing resident macrophages in injured nerves, which are represented by the 3 following samples (each being a pool of 3 mice): Res1/Res2/Res/3; and (2) ECFP+/CD64+/CD11b+/SiglecF-/Ly6G-macrophages sorted from ipsi lateral nerves representing recently recruited macrophages in injured nerves, which are represented by the 3 following samples (each being a pool of 3 mice): Res1.1/Res2.1/Res/3.1.

first: C

last: Lobsiger

middle: M

last: Parsadaniantz

last: Combadière


title: Heme oxygenase-1 orchestrates the immunosuppressive program of tumor-associated macrophages [ATAC-Seq]

overall_design: ATAC-seq in mouse macrophages from HO1-KO and wild type samples


title: Circulating microRNA expression profiling of  Hashimoto's Thyroiditis

city: zhenjiang

first: xiangmei

last: ding

address: No. 8 of Power Road

country: China

institute: The Affiliated People’s Hospital of Jiangsu University

type: Non-coding RNA profiling by high throughput sequencing

summary: NGS was performed to detect human miRNAs.  We found many upregulated and downregulated miRNAs in HT patients.  A total of 1310 dysregulated miRNAs were identified in PBMCs from HT patients and healthy volunteers, of which 659 were upregulated and 651 were  Downregulated. Among them, a total of 655 miRNAs, 331 upregulated and 324 downregulated.

overall_design: Circulating miRNA profiles of five Hashimoto's Thyroiditis patients and five healthy volunteers were generated by deep sequencing,using Illumina HiSeq 4000

first: Yingzhao

last: Liu

first: Huiyong

last: Peng

first: Si

last: Xiong

first: Xiangmei

last: Ding

first: Xuehua

last: Wang


title: A Transcriptomic Analysis of Neuropathic Pain in Rat Dorsal Root Ganglia Following Peripheral Nerve Injury

city: Shenzhen

first: SHAO

middle: MIN

last: YANG

state: guangdong

address: Nanshan

department: Shenzhen Nanshan People's Hospital and the 6th Affiliated Hospital of Shenzhen University Health Science Center

institute: Department of Pain Medicine and Shenzhen Municipal Key Laboratory for Pain Medicine

summary: In this study, we screened the differentially expressed genes (DEGs) in the dorsal root ganglia (DRG) from rats with sham or partial sciatic nerve ligation (pSNL) surgery 7 days using RNAseq technique to explore the molecular mechanisms of neuropathic pain

overall_design: Examination of the DRG from rats with sham or partial sciatic nerve ligation

first: Wuping

last: Sun

first: Shaomin

last: Yang


title: RNAseq analysis of cell lines established from patient-derived luminal breast cancer xenografts

city: Aurora

first: Jessica

last: Finlay-Schultz

state: CO

department: Pathology

institute: University of Colorado Denver Anschutz Medical Campus

summary: Breast cancer cell lines from PDX models

overall_design: Six breast cancer cell lines grown in regular media

first: Britta

last: Jacobsen

first: Kiran

middle: V

last: Paul

first: Peter

last: Kabos

first: Carol

last: Sartorius


title: Anti-inflammatory properties of deep sea water in-vitro and in-vivo models of inflamed intestinal epithelium

city: Seoul

first: Ji Yeon

last: Kim

state: Nowon

address: 232 Gongneung-ro

department: Food science & technology

country: South Korea

institute: Seoul National Universiti of Science & Technology

summary:
Purpose: This study aimed to determine the effect of deep sea  water (DSW) containing minerals on intestinal health, using a cell model and dextran sulfate sodium (DSS)-induced enteritis animal model.
Methods: In vivo, the role of DSW was determined in DSS-induced colitis mouse model.
Results: In comparison to the DSS group, colon shortening was inhibited, and disease activity and colon injury were suppressed in DSW-treated mice. RNA isolated from colonic tissues of mice in the control and experimental groups was subjected to RNA-seq. Gene expression of inflammatory genes was similar among control and HMLS mice. In the HMLS group, inflammatory pathways were suppressed through reductions in the expression of genes such as TNF-a, Nos2, and inflammatory chemokines.
Conclusions: Our findings suggest that DSW intake can help to colitis, and the effects may be partially regulated by magnesium and other minerals.

overall_design: Intestinal colitis was induced for one week with DSS from 8-weeks old mice that has consumed deep sea water for three weeks. This is the RNA-seq data shown by  intestinal tissue using  Illumina 6000.

first: Jain

last: Nam

first: Kyeong Jin


title: Integrative tissue analysis of men with prostate cancer

first: Adam

middle: G.

last: Sowalsky

state: MD

address: 37 Convent Drive Building 37 Room 1062B

department: Genitourinary Malignancies Branch

institute: National Cancer Institute

summary: Prostate cancer is a multi-focal disease and understanding the relationship between primary disease and relapse has remained a challenge.

overall_design:
To identify the genetic events that drive tumor aggressivity, we performed whole transcriptome sequencing and gene expression analysis of multiple foci of prostate cancer from men who underwent radical prostatectomy as definitive therapy.

*Submitter declares that the raw data will be submitted to dbGaP (https://www.ncbi.nlm.nih.gov/gap) because of patient privacy concerns.*

first: Shana

middle: Y

last: Trostel

first: Nichelle

middle: C

last: Whitlock

first: Huihui

last: Ye

middle: G


title: Grouped ensemble coding of behavioral states by combinations of molecularly defined cell types

city: New York

first: Vilas

last: Menon

state: NY

department: Neurology

institute: Columbia University Medical Center

summary: We used a plate-based method (SMART-SCRB) to transcriptionally profile manually picked single neurons from the paraventricular nucleus of hypothalamus (PVH) from 10 male Agrp-IRES-Cre crossed with Ai9 reporter mice, all >7 weeks old. For each mouse, the PVH was dissected and cells expressing the tdTomato reporter were manually selected and placed into wells of a series of 96-well plates. We used a plate-based method with cell and transcript barcording and reverse transcription in each well, followed by pooling and amplification using a modified SMART-Seq technology that yields digital 3' end counts of transcripts.

overall_design: We processed a total of 8 96-well plates, of which some wells were deliberately left empty. External RNA controls (ERCCs) were spiked into each well to allow for QC and accurate transcript quantification.

first: Shengjin

last: Xu


title: Transcriptomic response of SIM-A9 microglia to neuro-probes

city: Berkeley

first: Markita

last: Landry

state: CA

address: 106 Gilman Hall

department: Chemical Engineering

institute: University of California, Berkeley

summary: This study aims to elucidate the response of microglial cells to various molecular probes used in neuroscience for the detection of neurotransmission. Particularly, we aim to quantify the degree of inflammatory activation observed in these cells upon exposure to carbon nanotube catecholamine sensors. We compare these results to carboxylic acid functionalized carbon nanotubes which have previously been implicated in macrophage activation, and lipopolysaccharide as a positive control.

overall_design: Study of effects of neuro-probes, including novel carbon nanotube based platforms, on SIM-A9 mouse microglial cells. Inflammatory response compared to LPS positive control

first: Darwin


title: Sacrificial cell death of adipose mesenchymal stem cells by autophagy facilitates cartilage formation in co-cultures with chondrocytes

city: Rochester

first: Asha

last: Nair

address: 200 1ST ST SW

institute: Mayo Clinic

summary: Objective: Cartilage formation is stimulated in mixtures of chondrocytes and human adipose-derived mesenchymal stem cells (MSCs) both in vitro and in vivo. During co-culture, human MSCs perish through an unknown process.  The goal of this study is to elucidate the mechanism by which adipose tissue-derived MSC cell death occurs in the presence of chondrocytes.   Methods: Human primary chondrocytes were co-cultured with human MSCs derived from three donors. The cells were cultured in mono-culture or co-culture (20% chondrocytes and 80% MSCs) in pellets (200.000 cell/pellet) for 7 days in chondrocyte proliferation media in hypoxia (2% O2). RNA sequencing was performed to assess for differences in gene expression between monocultures or co-culture. Western blot and immune fluorescence assays were performed to quantify the level of Caspase-3, LC3B and P62.  Results: RNA sequencing revealed significant up-regulation of >90 genes in the three co-cultures when compared to monocultures. STRING analysis showed interconnections between >50 of these genes. Remarkably, 75% of these genes play a role in cell death pathways such as apoptosis and autophagy. Western blotting shows a clear up-regulation of the autophagic machinery with no substantial activation of the apoptotic pathway.   Conclusion: In co-cultures of human MSCs with primary chondrocytes, MSCs perish through autophagy. We propose that this sacrificial cell death may perhaps contribute to the trophic effects of MSCs on cartilage formation.

overall_design: Cell pellets were generated by seeding 200,000 cells per well in a 96 well plate. Cells were cultured as monocultures or as co-cultures with a ratio of 80% MSCs/20% human chondrocytes. Both MSCs and chondrocytes were cultured in chondrogenic proliferation media (Gilco’s advance MEM, 10% FBS, 1% pen/strep, 1% GLUTAmax) under hypoxia (2% oxygen). Medium was changed every three days. Pellets were harvested on day 7.

first: Amel

last: Dudakovic

first: Andre

middle: J

last: van Wijnen


title: LncRNA sequencing of oocytes at germinal vesicle (GV) and metaphase of second meiotic division (MⅡ) stages of Chinese local sheep

city: Qingdao

first: Jun-Jie

last: Wang

state: Shandong

address: Changcheng 700

department: Qingdao Agricultural University

institute: College of Life Sciences

summary: The molecular mechanism of lncRNA involving oocyte differentiation from GV to MⅡ stage had been investigated in the study, and it is expected to extend the knowledge of lncRNA-mediated regulation connected to oocyte fate determination in ovarian development

overall_design: In present study, the GV stage oocytes isolated from Chinese local sheep, and MⅡ oocytes derived from cumulus oocyte complexes (COCs) for in vitro mature were sequence respectively. Through RNA data analysis, the lncRNAs and coding genes were identified, also the co-expression and cis-regulation analysis were implemented with differentially expressed lncRNAs (DELs) and genes (DEGs) to explore the regulatory network involving oocytes differentiated transition from GV to MⅡ period.

first: Wei

last: Shen

first: Hong-Guo

last: Cao


title: SINGLE FLOWER TRUSS and SELF-PRUNING differentially regulate developmental and metabolic genetic networks to guide cotton (Gossypium hirsutum) architectures [GEO_SFT_SP]

city: Denton

first: Roisin

last: McGarry

state: TX

address: 1511 West Sycamore

department: Dept. of Biological Sciences, BioDiscovery Institute

institute: University of North Texas

summary: Patterns of indeterminate and determinate growth specify plant architecture and influence crop productivity. In cotton (Gossypium hirsutum), SINGLE FLOWER TRUSS (SFT) stimulates the transition to flowering and determinate growth while its closely related antagonist SELF-PRUNING (SP) maintains meristems in indeterminate states to favor vegetative growth. To identify the molecular programs regulating cotton growth habits, and understand how altered expression of GhSFT and GhSP perturbs these programs, we used RNA-Seq to determine the gene expression networks involved in wild photoperiodic, domesticated day-neutral, and GhSFT- and GhSP-regulated architectures. GhSFT or GhSP affected the expression of genes regulating meristem fate and metabolic pathways. Gene ontology analysis predicted enrichment of transcripts involved in photosynthesis, secondary metabolism, and cell wall biosynthesis, and these hypotheses were functionally verified. Weighted gene co-expression network analyses using multiple cotton datasets identified diverse genetic modules highly correlated with SFT or SP, including those that may benefit crop management.

overall_design: We used virus-mediated transient gene manipulation to over-express GhSFT from a disarmed Cotton leaf crumple virus (dCLCrV) or silence GhSP from Tobacco rattle virus (TRV) in wild photoperiodic Texas 701 (TX701) and domesticated day-neutral Delta Pine 61 (DP61) cotton varieties.

first: Xiaolan

last: Rao

first: Brian

last: Ayre


title: Identification of Cpeb4 binders in cardiomyocyte

city: Heidelberg

first: Mirko

last: Volkers

address: INF 410

country: Germany

institute: University Hospital Heidelberg

summary: Mutations or decreased expression of RNA-binding proteins (mRBPs) can lead to cardiomyopathies in humans. Here we defined RBPs in healthy and diseased primary cardiomyocytes at a system-wide level by RNA Interactome Capture. This identified 67 novel cardiomyocyte specific RBPs including several contractile proteins. Furthermore, we identified Cytoplasmic polyadenylation element binding protein 4 (Cpeb4) as a dynamic mRBP in diseased cardiomyocytes, regulating cardiac growth both in vitro and in vivo. To study Cpeb4 in cardiomyocytes, we identified mRNAs bound to and regulated by Cpeb4. Cpeb4 regulates cardiac remodeling by differential expression of transcription factors. Among Cpeb4 target mRNAs, two Zinc finger transcription factors (Zeb1 and Zbtb20) were identified. We show that Cpeb4 regulates the translation of these mRNAs and that Cpeb4 depletion increases their expression. Thus, Cpeb4 emerges as critical regulator of cardiomyocyte function by differential binding of specific mRNAs in response to pathological growth stimulation.

overall_design: Purified mRNA from immunoprecipitated Cpeb4 and Input total RNA

last: Völkers


title: RNA-seq in murine acute myeloid leukemia (AML) cells with and without knockdown of Tet1

city: Monrovia

first: Jianjun

last: Chen

department: Systems Biology

institute: Beckman Research Institute of City of Hope

summary: To explore the global targets and dissect the mechanism underlying the oncogenic function of TET1 in AML, we performed deep sequencing for mRNA isolated from mouse MLL-ENL-ERtm cells with and without knockdown of Tet1.

overall_design: We transduced pGFP-V-RS-based retroviral shRNA targeting Tet1 (i.e., shTet1) as reported in Huang H et al., PNAS, 2013 (reported as shTet1-a+b), or scramble shRNA (i.e., shNS), into mouse MLL-ENL-ERtm cells. After puromycin selection (1 µg/mL) for three passages and SILAC adaption, cells were collected and RNA was extracted using miRNeasy kit (Qiagen). PolyA RNA was subsequently purified from 50-100 ng total RNA using NEBNext Poly(A) mRNA Magnetic Isolation Module. NEBNext Ultra Directional RNA Library Prep Kit (New England BioLabs, Ipswich, MA) was used for library preparation. Each group was sequenced in triplicate by Illumina Hiseq 1000 with single end 51-bp read length.

first: Hengyou

last: Weng

first: Huilin

last: Huang


title: SINGLE FLOWER TRUSS and SELF-PRUNING differentially regulate developmental and metabolic genetic networks to guide cotton (Gossypium hirsutum) architectures.

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

overall_design: Refer to individual Series


title: beta-glucan-induced trained immunity protects against Leishmania braziliensis infection: a crucial role for IL-32

city: Bonn

first: Branko

last: Cirovic

address: Carl-Troll Str 31

institute: LIMES

summary: We reported the first definitive characterization of the role of IL-32 in the trained phenotype, the results of which improve our understanding of the molecular mechanisms governing trained immunity and Leishmania infection control.

overall_design: Examination of the influence of IL32 rs4786370 SNP in the gene expression in bone marrow granulocyte macrophage progenitors (GMP) of healthy volunteers prior and on day 0 and day 90 (M3) post BCG vaccination. GMPs were identified as Lin-CD34+CD38+CD45RA+CD10- events and purified using FACS.

first: Jéssica

last: dos Santos

first: Charlotte

middle: L

last: de Bree

first: Joachim

last: Schultze

first: Mihai

last: Netea

first: Andreas

last: Schlitzer

first: Leo

last: Joosten


title: Comparison of gene expression in the Red Imported Fire Ant, Solenopsis invicta Buren, in different temperature conditions

city: Gimcheon

first: Mohammad

last: Vatanparast

address: 167, Yongjeon-ro

department: Plant quarantine technology center

institute: Animal and Plant Quarantine Agency

summary:
Purpose: We aimed to provide a basis for the adaptive mechanism and a rich resource for the discovery and identification of novel genes involved in the cold and heat stress response in Solenopsis invicta. retinal transcriptome profiling (RNA-seq) to microarray and quantitative reverse transcription polymerase chain reaction (qRT–PCR) methods and to evaluate protocols for optimal high-throughput data analysis
Methods: Solenopsis invicta was reared at lab condition, and incubated at 4 different temperature for 24h (10, 20, 30 and 40℃). RNA was extracted using Trizol reagent and Illumina sequencing was performed at Macrogen. Illumina short reads were quality-filtered and Illumina-based de novo transcriptome assembly was performed. Differential Gene Expression Analysis was studied for different tempearture conditions.
Results: Totally 99,085 unigenes was obtained which at least 19,154 were annotated with gene descriptions, gene ontology terms, and metabolic pathways. 86 GO functional sub-groups and 23 EggNOG terms resulted. DEGs with log2FC≥10 were screened and were compared at different temperatures. We found 203, 48 and 66 specific DEGs co-regulated at 10, 20 and 40℃, respectively compare with 30℃. Comparing transcriptome profiles for differential gene expression resulted various DE proteins and genes, including cytochrome P450, NADH dehydrogenase subunit 1, cuticle protein and HSP which have previously been reported to be involved in cold and high temperature resistance. GO analysis revealed that antioxidant activity up-regulated under high temperature stress.
Conclusions: we compared the transcriptomes of S. invicta under high- and low-temperature stresses using RNA-Seq technology based on the high-throughput sequencing. Comparative transcriptome analysis identified many genes and a large number of changes were discovered in metabolic pathway through the GO and KEGG enrichment analysis. Our data will facilitate further molecular investigations and genomic research. Many high- and low-temperature significantly up-regulated genes were first identified in this study. These newly found genes may be important and necessary to RIFA overwintering and its behavior for adaptation in new environment as well as quarantine area.

overall_design: Total RNA of Solenopsis invicta for four different treated temperature that 30℃ was used as control.

first: Youngjin

last: Park


title: SINGLE FLOWER TRUSS and SELF-PRUNING differentially regulate developmental and metabolic genetic networks to guide cotton (Gossypium hirsutum) architectures [meristems]

last: McGarry

summary: Each plant's architecture, composed of patterns of indeterminate and determinate growth, is defined through the activities of meristems. Understanding the regulation of meristem identity can benefit plant architecture and crop yield. To understand how meristem activities contribute to different architectures in cotton (Gossypium hirsutum), we used RNA-Seq to determine the transcriptomes from meristems isolated from different developmental stages of wild photoperiodic and domesticated day-neutral cotton grown under different photoperiods.

overall_design: Meristems were isolated from wild photoperiodic Texs 701 (TX701) and domesticated day-neutral Delta Pine 61 (DP61) cotton grown at different stages of development and from different growth regimes.  Each developmental stage was comprised of 3 biological replicates, and each replicate consisted of 4 isolated meristems. RNA was extracted, mRNA amplified with TargetAmp Amplification kit (Epicenter, Madison, WI, USA), and 125 ng of amplified mRNA was used to prepare Illumina TruSeq mRNA stranded libraries (Illumina, Inc., San Diego, CA, USA).


title: SIRT7 counteracts mesenchymal stem cell senescence via stabilizing heterochromatin

city: Beijing

first: Zunpeng

last: Liu

address: Beichen West Road

department: Institute of Zoology, Chinese Academy of Sciences

institute: State Key Laboratory of Stem Cell and Reproductive Biology

summary: Human mesenchymal stem cell (hMSC) senescence contributes to the imbalance of tissue homeostasis during aging. However, the connection between Sirtuin 7 (SIRT7) and hMSC homeostasis remains unclear. Here, we discovered a pivotal role of SIRT7 in protecting hMSC from senescence. We detected a decreased expression of SIRT7 during hMSC aging, while overexpression of which reversed premature hMSC senescence phenotypes. Mechanistically, we proved SIRT7 as a novel interacting protein of the heterochromatin complex, whose deficiency disrupted heterochromatin organization, thereby contributing to the derepression of the retrotransposon Long Interspersed Element 1 (LINE1 or L1). SIRT7-deficient hMSCs accumulated LINE1 in cytoplasm stimulating innate immune response by activated the cyclic GMP-AMP synthase (cGAS) and its downstream signaling effector stimulator of interferon genes (STING). Moreover, reverse-transcriptase inhibitors (RTis), such as Lamivudine (3TC), attenuated these senescence phenotypes of SIRT7-deficient hMSCs. Taken together, our findings identify SIRT7-heterochromatin via LINE1-cGAS/STING influence innate immune response, which contributes more comprehensive understanding of the physiological and function of SIRT7 and help us to find novel targets for the treatment of aging and aging relative diseases.

overall_design: Multi-omics sequencing of WT and SIRT7 defecient hMSCs.

first: Guanghui


title: Heme oxygenase-1 orchestrates the immunosuppressive program of tumor-associated macrophages

first: Stanislas

last: Goriely

institute: Université Libre de Bruxelles


title: Longitudinal mRNA expression analysis of the adaptive response to Enzalutimde in LNCaP cells

city: Brisbane

first: Colleen

last: Nelson

state: Queensland

address: 199 Ipswich Road

department: Institute of Health and Biomedical Innovation; Vancouver Prostate Centre

country: Australia

institute: Queensland University of Technology; University of British Columbia

summary: The aim of this study is to investigate metabolic alterations involved in the adaptive response of prostate cancer cells to androgen-deprivation therapy (ADT) and AR-targeted therapies (ATTs) in hopes of identifying novel targets to help delay progression to castrate-resistant prostate cancer (CRPC). We developed an in vitro model of long-term ATT and used transcriptomics, proteomics and lipidomics to identify metabolic pathways contributing to cell survival.

overall_design: LNCaP cells were treated for up to 21 days with 10 µM Enzalutamide (ENZ) in DMSO (vehicle control). Samples were collected on day 0 (DMSO control), 7, 14 and 21. 3 biological repeats of each sample were processed for microarray analysis.

first: Kaylyn

middle: D

last: Tousignant

first: Martin

last: Sadowski

first: Anja

last: Rockstroh

first: Atefeh

last: Taherian Fard

first: Melanie

last: Lehman


title: Gene expression of 6 FFPE tissues of adults with T-cell lymphoblastic lymphoma

city: Guangzhou

first: Xiao-Peng

last: Tian

address: 651 Dong Feng RD East

department: Department of Medical Oncology

institute: Sun Yat-sen University Cancer Center

summary: Affymetrix Human Gene 2.0 ST microarray (ThermoFisher Scientific, Waltham, MA, USA) was used to select differentially expressed genes.

overall_design: Our microarray identified differentially expressed mRNAs between 3 drug susceptibility and 3 drug resistance T-LBL patients.

first: Xiaopeng


title: Transcriptome network analysis of Smug1 knock-out cells by using CRISPR/Cas9 system

first: Jung-Woong

last: Kim

address: 84 Heuksuk-ro Dongjak-ku

department: Life Science

institute: Chung-Ang University

summary:
Purpose: To build a differential transcriptome network in Smug1 knock-out HepG2 hepatocarcinoma cells.
Methods: Transcriptome analysis by the RNA-seq via mRNA pull-down.
Results: We constructed transcriptome from Smug1 knock-out cells by using RNA-seq analysis. Nucleosome and miRNA related genes were highly enriched in Smug1 KO HepG2 cells.
Conclusions: Smug1 regulate the gene expression related with nucleosome assembly and histone function.

overall_design: The start codon region of Smug1 gene was targeted for CRISPR/Cas9 to generate Smug1 KO HepG2 cells. After generate KO cells, we isolated total RNA from KO and WT HepG2 cells and performed directional mRNA-sequencing.


title: Combinatorial single-cell analyses of granulocyte-monocyte progenitor heterogeneity reveals an early uni-potent neutrophil progenitor

city: SINGAPORE

first: JIA CHI

last: TAN

address: 8a Biomedical Grove

country: Singapore

institute: SIgN

summary: Granulocyte-monocyte progenitors (GMPs) have been previously defined for their potential to generate various myeloid progenies such as neutrophils and monocytes. Although studies have proposed lineage heterogeneity within GMPs, it is unclear if committed progenitors already exist among these progenitors and how they may behave differently during inflammation. By combining single-cell transcriptomic and proteomic analyses, we identified the early committed progenitor within the GMPs responsible for the strict production of neutrophils, which we designate as proNeu1. Our dissection of the GMP hierarchy led us to further identify a previously unknown intermediate proNeu2 population. Similar populations could be detected in human samples. proNeu1s, but not proNeu2s, selectively expanded during the early phase of sepsis at the expense of monocytes. Collectively, our findings help shape the neutrophil maturation trajectory roadmap and challenge the current definition of GMPs.

overall_design: Examination of transcriptomic heterogeneity of GMPs

first: Jinmiao

last: Chen

first: Immanuel

last: Kwok

first: Ng

last: Guan


title: Photothermal Modulation of Human Stem Cells Using Light-responsive 2D Nanomaterials

city: Bryan

first: Irtisha

last: Singh

address: 8447 Riverside Pkwy Medical Research and Education Building II

institute: Texas A&M Health Science Center

summary: Two-dimensional (2D) molybdenum disulfide (MoS2) nanomaterials are an emerging class of biomaterials that are photo-responsive at near-infrared wavelengths (NIR). Here, we demonstrate for the first time the ability of 2D MoS2 to modulate cellular functions of human stem cells through photothermal mechanisms. The interaction of MoS2 with human stem cells is investigated using whole transcriptome sequencing (RNA-seq). Global gene expression profile of stem cells reveals significant influence by NIR stimulation of MoS2 on integrins, cellular migration and wound healing. Overall, the combination of MoS2 and NIR light may provide new approach to control and regulate cellular migration and functions.

overall_design: Examination of effect of MoS2 and NIR on human mesenchymal stem cells (hMSCs)

first: Carrow

middle: K

last: Jake

first: Singh

last: Kanwar

last: Irtisha

first: Gaharwar

last: Akhilesh


title: Exposure to low and moderate dose rate of ionizing radiation induces promoter hypomethylation znf deregulation of developmental genes in zebrafish

city: Saint Paul lez Durance

first: olivier

last: ARMANT

address: Cadarache BP3

department: SERIS

institute: IRSN

summary: Following nuclear accidents and the increasing use of radionuclides, environmental radiation  radiological protection is a source of major concern, particularly in the context of low doses. Ionizing radiation (IR) may lead to genetic mutations, chromosomal rearrangements and epigenetic modifications. The present study focuses on the in vivo effects of low to moderate doses of IR on zebrafish early embryonic development. The effects of IR on the transcriptome were studied at the shield stage (6 hours post-fertilization, hpf) and at dose rates from 50 mGy/h to 0.005 mGy/h. The effects on the methylome by whole genome bisulfite sequencing were investigated at the same stage and at dose rates of 50 mGy/h and 5 mGy/h.IR exposure impacted the expression of genes involved in germ layers specification during gastrulation of zebrafish embryos. Moreover, changes in mitochondrial energetic metabolism were detected at all dose rates. Different transcriptomic responses were observed between groups irradiated at the two highest dose rates, 50 mGy/h and 5 mGy/h and those irradiated at the three lower dose rates. However, the transcriptomic analysis revealed an impact of IR on development, neurogenesis and muscular development at 50 mGy/h, 5 mGy/h and 0.5 mGy/h. The global level of methylation was not changed after exposure to IR, and no widespread changes in transposable elements were detected. Rather, we observed that IR induced loci specific demethylation in the promoter of genes involved in development, neurogenesis and myogenesis. Interestingly, this promoter hypomethylation was equally associated with a change in gene expression. In this study, both DMR and gene expression analysis pointed toward a specific deregulation of genes involved in development, neurogenesis and myogenesis. The modification of the methylation pattern in promoters of genes involved in central nervous system development and muscle development seems to be responsible of transcriptomic changes. This study confirms previous results obtained at later developmental stages, showing that neurogenesis and muscle development were also impacted at 50 mGy/h, 5 mGy/h and 0.5 mGy/h with phenotypic alterations in terms of muscle histology and swimming behaviour. This suggests that early developmental perturbations are predictive of functional defects at later developmental stages.

overall_design: RNAseq analysis of zebrafish embryos (shield stage) exposed chronically to 5 dose rates of gamma ionizing radiation. All experiments made in at least 3 biological replicates

first: Olivier

last: Armant

first: Sophia

last: Murat El Houdigui


title: Loss of TET2 results in gene expression represssion in mouse naïve B-cells and lymphoma cells

city: Farmington

first: Sheng

last: Li

state: CT

address: 10 Discovery Drive

institute: The Jackson Laboratory


title: Loss of TET2 results in gene expression represssion in mouse naïve B-cells and lymphoma cells [DNA-Seq]

summary: Absence of Tet2 at mouse cells does not result in decreased somatic hypermutation

overall_design: PCR amplification and HTS sequencing of JH4 (mm10:chr12:113,427,959-113,428,543) and Su (mm10:chr12:113,425,655-113,426,278) in TET2 WT and TET2 KO mouse GC B-cells.

first: Ari

last: Melnick

first: Maria

last: Dominguez

first: Xiaowen

first: Wojciech

last: Rosikiewicz


title: NCX1 represents an ionic Na+ sensing mechanism in macrophages

first: Joachim

last: Schultze

state: NRW

address: Carl-Troll-Strasse 31

department: Genomics and Immunoregulation

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

summary: Inflammation and infection can trigger local tissue Na+-accumulation. This Na+-rich environment boosts pro-inflammatory activation of monocyte/macrophage-like cells (MΦ) and their antimicrobial activity. Enhanced Na+-driven MΦ-function requires the osmoprotective transcription factor nuclear factor of activated T cells 5 (NFAT5), which augments NO production and contributes to increased autophagy. However, the mechanism of Na+-sensing in MΦ remained unclear. High extracellular Na+ levels (HS) trigger a substantial Na+-influx and Ca2+ loss. Here, we show that the Na+/ Ca2+-exchanger 1 (NCX1/ solute carrier family 8 member A1 (SLC8A1)) plays a critical role in HS-triggered Na+-influx, concomitant Ca2+ efflux and subsequent NFAT5 accumulation. Moreover, interfering with NCX1-activity impairs HS-boosted inflammatory signaling, infection-triggered autolysosome formation and subsequent antibacterial activity. Taken together, this demonstrates that NCX1 is able to sense Na+ and is required for amplifying inflammatory and antimicrobial MΦ responses upon HS exposure. Manipulating NCX1 offers a new strategy to regulate MΦ function.

overall_design:
Examination of Slc8a1 (NCX1) isoform expression in RNA-seq data of 3 unstimulated murine BMDM samples.

We analyzed the isoform expression of Slc8a1 (NCX1) in RNA-seq data of murine bone-marrow derived macrophages (BMDM). RNA of 3 samples differentiated in vitro for 8 days using M-CSF was isolated with trizol and miRNeasy micro kit (Qiagen) according to the manufacturer’s protocol and 100 ng of RNA was converted into cDNA libraries using the TruSeq RNA library preparation kit v2 for 75 bp single read sequencing performed on a HiSeq1500. We aligned the reads using Hisat2 and and performed genome-guided transcriptome assembly using Stringtie followed by transcript abundance estimation using Ballgown as delineated in the "new tuxedo" protocol (Pertea et al., 2016: Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown). The transcriptome assembly identified two additional multi-exon transcripts variants for Slc8a1 and transcript abundance estimation determined one of the novel variants to be dominantly expressed.

first: Jonas

last: Schulte-Schrepping

first: Patrick

last: Neubert

first: Jonathan

last: Jantsch

first: Waldemar

last: Kolanus


title: Design and experimental evaluation of a minimal, innocuous watermarking strategy to distinguish near-identical DNA and RNA sequences

city: Delft

first: Jean-Marc

last: Daran

address: Julianalaan 67

department: Department of Biotechnology

institute: Delft University of Technology

summary: The construction of powerful cell factories requires intensive and extensive remodelling of microbial genomes. Considering the rapidly increasing number of these synthetic biology endeavours, there is an increasing need for DNA watermarking strategies that enable the discrimination between synthetic and native gene copies. While it is well documented that codon usage can affect translation, and most likely mRNA stability in eukaryotes, remarkably few quantitative studies explore the impact of watermarking on transcription, protein expression and physiology in the popular model and industrial yeast Saccharomyces cerevisiae. The present study, using S. cerevisiae as eukaryotic paradigm, designed, implemented and experimentally validated a systematic strategy to watermark DNA with minimal alteration of yeast physiology. The thirteen genes encoding proteins involved in the major pathway for sugar utilization (i.e glycolysis and alcoholic fermentation) were simultaneously watermarked in a yeast strain using the previously published pathway swapping strategy. Carefully swapping codons of these naturally codon optimized, highly expressed genes, did not alter transcript abundance, protein activity and yeast physiology. The markerQuant bioinformatics method could reliably discriminate native from watermarked genes and transcripts. Furthermore, presence of watermarks enabled selective CRISPR/Cas genome editing, specifically targeting the native gene copy while leaving the synthetic, watermarked variant intact. This study offers a validated strategy to simply watermark genes in S. cerevisiae.

overall_design: Comparing expression of native and watermarked gene copies in Saccharomyces cerevisiae.

first: Pascale

last: Daran-Lapujade

first: Jean

first: Marcel

last: van den Broek


title: Integration of systemic signals in plants

city: Memphis

first: Soham

last: Sengupta

state: TN

address: 262 Danny Thomas Place

institute: St. Jude Children's Research Hospital

summary: Transcriptome profiling (RNA-seq) of local and systemic tissue of Arabidopsis Col plants exposed to a local treatment of high light, heat stress and a combination of high light and heat stress on the same leafs or in different leaves

overall_design: Local leaves of bolting Col plants were exposed to a light intensity of 1700 µmol m-2 sec-1 using a gooseneck light source (ACE I; Schott), or heat stress by placing a heat block 2 cm underneath the treated leaf, or to the combination of both stresses in the same leaf or in two different leaves for periods of 0, 2 and 8 min. Total RNA of local treated leaves as well as systemic tissue (stem) were  used and single-end sequenced reads were obtained from the Illumina NExtSeq platform.

first: Sara

middle: I

last: Zandalinas

first: Yosef

last: Fichman

first: Amith

middle: R

last: Devireddy

first: Rajeev

last: Azad

first: Ron

last: Mittler


title: Loss of TET2 results in gene expression represssion in mouse naïve B-cells and lymphoma cells [RNA-seq]

first: Sheng

last: Li

summary: Absence of Tet2 at mouse cells results in reduced gene expression

overall_design: Genome-wide profiling of total RNA transcript levels in mouse cells: TET2 WT and KO naïve B-cells

first: Ari

last: Melnick

first: Maria

last: Del Pilar Dominguez

first: Xiaowen

last: Chen


title: Oct4-mediated inhibition of Lsd1 activity promotes the active and primed state of pluripotency enhancers

city: West Lafayette

first: Humaira

last: Gowher

state: IN

address: 175 South University St.

department: Department of Biochemistry

institute: Purdue University

type: Methylation profiling by high throughput sequencing


title: Oct4-mediated inhibition of Lsd1 activity promotes the active and primed state of pluripotency enhancers [methylRAD-seq]

summary: Enhancer reactivation and pluripotency gene (PpG) expression could induce stemness and enhance tumorigenicity in cancer stem cells. Silencing of PpG enhancers (PpGe) during embryonic stem cell differentiation involves Lsd1–mediated H3K4me1 demethylation followed by DNA methylation. Here, we observed a widespread retention of H3K4me1 and DNA hypomethylation at PpGe associated with a partial repression of PpGs in F9 embryonal carcinoma cells (ECCs) post-differentiation. The absence of H3K4me1 demethylation could not be rescued by Lsd1 overexpression. Based on the observation that H3K4me1 demethylation is accompanied by strong Oct4 repression in P19 ECCs, we tested if Lsd1-Oct4 interaction affects Lsd1 catalytic activity. Our data show a dose-dependent inhibition of Lsd1 by Oct4 in vitro and retention of H3K4me1 at PpGe post-differentiation in Oct4 overexpressing P19 ECCs. These data suggest that Lsd1-Oct4 interaction in cancer stem cells may establish a primed enhancer state that is susceptible to reactivation leading to aberrant PpG expression.

overall_design: To understand the mechanism by which cancer cells retain PpG expression, we investigated the mechanism of enhancer-mediated regulation of PpG expression in ECCs. This data correspond to genome-wide methylRAD sequencing experiment performed with undifferentiated (UD) and day four (D4) samples. Raw data is provided as FASTQ files. Processed data is provided as BedGraph files and TSV files. TSV files describe all methylated sites and columns are Chr, Sites, CgarType (cigar string – shows match, substitution, etc), count, and type of site (CCGG, CCAGG< or CCTGG).

first: Lama

last: AlAbdi

first: Debapriya

last: Saha

first: Ming

last: He

first: Mohd

middle: S

last: Dar

first: Sagar

last: Utturkar

first: Putu

last: Sudyanti

first: Stephen

last: McCune

first: Brice

last: H Spears

first: James

last: Breedlove

first: Nadia

last: Lanman


title: Oct4-mediated inhibition of Lsd1 activity promotes the active and primed state of pluripotency enhancers [ChIP-seq]

overall_design: To understand the mechanism by which cancer cells retain PpG expression, we investigated the mechanism of enhancer-mediated regulation of PpG expression in ECCs. This data correspond to ChIP-Seq experiment performed with undifferentiated (UD) and day four (D4) samples and  corresponding input controls. Raw data is provided as FASTQ files. Processed data includes BedGraph files for each sample and annotated epic2 peaks (excel) for each sample.


title: Transcriptomic changes during regeneration in demosponge Cinachyyrella cf cavernosa

city: Dona Paula

first: Aabha

last: Deshpande

state: Goa

address: Dona Paula circle

department: Chemical Oceanography Department

country: India

institute: CSIR- National Institute of Oceanography

summary: In this study, the differential regeneration process in sponge Cinachyrella cf cavernosa was examined by creating a wound at basal and non-basal tissues. The differences in wound healing were investigated based on qualitative and quantitative changes in collagen at both wound locations. The variation at the cellular level was also studied during regeneration. To understand the molecular process of gene regulation during regeneration in C.cf cavernosa, differential gene expression (transcriptomics) analysis was carried out using Illumina NextSeq 500. The basal tissue was found to heal faster than non-basal tissue and collagen was found to be the responsible factor for this increased rate of wound healing.  There was no apparent difference in the types and density of cells present in regenerative basal and non-basal tissue. The differential analysis of fast regenerating basal tissue showed up-regulation in collagen-related gene Col and actin-related genes during progressive stages of regeneration. Contrary to other metabolism-related genes, lipid metabolism related genes are expressed in more numbers with consecutive stages of regeneration highlighting their role in stress management of the sponge. This study serves to advance our understanding of the regeneration process, factors affecting the rate of this process and transcriptomic changes in regenerating sponge.

overall_design: Three samples were analysed, viz., before wound infliction, during regeneration, after regeneration. The sample before wound infliction is also the control of the experiment. Replicates were not used.

first: Narsinh

last: Thakur


title: ERK inhibitor treatment in Pa16C pancreatic cancer cells

city: Chapel Hill

first: Joel

last: Durand

state: NC

address: 450 West Drive

department: Lineberger Comprehensive Cancer Center

institute: The University of North Carolina at Chapel Hill

type: Methylation profiling by genome tiling array

summary: Pa16C cells treated every other day with the ERK inhibitor SCH772984 and assayed at 3 or 7 days post-treatment

overall_design: Bisulphite converted DNA from the samples were hybridised to the Illumina Infinium MethylationEPIC BeadChip


title: A comprehensive comparison of differential accessibility analysis methods for ATAC-seq data

city: Saint Louis

first: Bo

last: Zhang

state: Missouri

address: 4515 McKinley Research Bldg 03212

department: Developmental Biology

institute: Washington University School of Medicine

summary:
Background:  ATAC-seq is widely used to measure the chromatin accessibility and identify the open chromatin regions (OCRs). OCRs usually indicate the active regulatory elements in the genome and are directly associated with gene regulatory networks. Identification of differential accessibility regions (DARs) between different biological conditions is critical to measure the differential activity of regulatory elements. Differential analysis of ATAC-seq shares many similarities to differential expression analysis of RNA-seq data. However, the distribution of ATAC-seq signal is different from RNA-seq data, and higher sensitivity is desired for DARs identification. Many different tools can be used to perform differential analysis of ATAC-seq data, but a comprehensive comparison and benchmarking of these methods is still missing.
Methods: Here, we used simulated datasets to systematically measure the sensitivity and specificity of 6 different methods. We further discussed the statistical and signal density cutoff in the differential analysis of ATAC-seq by applying to real data. Batch-effect is very common in high-throughput sequencing experiments.
Results: We illustrated that batch-effect correction can dramatically improve the sensitivity in differential analysis of ATAC-seq data. Finally, we developed an easily usable package, BeCorrect, to perform batch-effort correction for visualizing corrected ATAC-seq signals on a genome browser.
Conclusions: It is important to use PCA to check the samples distribution, and the Remove Unwanted Variation strategy can be used to correct the data to improve the sensitivity when strong batch effects are found in the data. Finally, BeCorrect can be used to correct the batch-effect of ATAC-seq data signal based on DARs analysis, and generate a proper visualization on a genome browser.

overall_design: This represents the dentate gyrus and Ammon’s horn samples only

first: Paul

last: Gontarz

first: Anna

last: Moszczynska


title: Reduced levels of the hepatokine IGFBP2 associate with degree of NAFLD

city: Duesseldorf

first: Birgit

last: Knebel

address: Auf'm Hennekamp 65

department: Cinical Biochemistry and Pathobiochemistry

institute: German Diabetes Center

summary: Background and aim: The Insulin-like growth factor (IGF) axis is increasingly suggested to be involved in fatty liver disease and progression. We identified IGFBP2 as transcriptional regulatory effect network in liver steatosis and conducted a translational approach of its role in liver pathology from mouse to human, and whether it is influenced by conventional clinical intervention that mitigate hepatic steatosis.  Methods: Primary hepatocytes from either C57Bl6 controls, alb-SREBP-1c mice with moderate transgene induced hepatic lipid accumulation or aP2-SREBP-1c mice with massive ectopic hepatic lipid accumulation, were analyzed to identify regulatory networks based on differentially regulated hepatic gene expression. In a translational approach, serum of morbidly obese patients with and without diabetes and biopsy-proven NAFLD were used for ELISA-based validation of mouse data. Moreover, sera of patients undergoing intervention were analyzed and correlated to liver fat content.  Results: Comparative knowledge-based transcriptome analysis identified IGFBP2 as top score regulatory effect network between moderate and aggravated fatty liver in mouse models. The reduced expression of IGFBP2 in aP2-SREPB-1c progressed fatty liver associated with Igfbp2 promoter hypermethylation. Reduced secretion of IGFBP2 from aP2-SREBP-1c hepatocytes was reflected in the circulation of the animals. In this phenotype, reductions of IGFBP2 were accompanied by reduced fatty acid oxidation and increased methyltransferase and SIRT activity. Physiologically, IGFBP2 has no direct impact on lipid metabolism but might modulate IGF1 action on de novo lipogenesis. In humans, IGFBP2 levels declined from non-obese men to morbidly obese men with NAFLD and NASH. In intervention study reductions in liver fat correlated with restoration of IGFBP2 serum levels to values found in healthy individuals in morbidly obese patients following bariatric surgery.  Conclusion: In hepatic metabolism changes of IGFBP2 abundance is connected to lipid metabolism whereas changes in IGFBP2 secretion were directly reflected in the circulation. IGFBP2 serum concentration correlates with the degree of fatty liver, which seems to be related to plasticity of the adipose tissue. These data provide IGFBP2 as a potential non-invasive biomarker for fatty liver disease directly reflecting the degree of impaired liver function with the potential to indicate progressed fatty liver disease.

overall_design: C57Bl6-TgN aP2-HA-hSREBP-1c-NT (aP2-SREBP-1c) mice were bred and maintained under standard conditions to until aP2-SREBP-1c mice develop fatty liver and adipositas phenotype (24 weeks of age).

first: Jorg

last: Kotzka

first: Dirk

last: Müller-Wieland

first: Pia

last: Fahlbusch


title: Characterization of schistosomal microRNA by species, sex and developmental stage

city: Jerusalem

first: Iddo

middle: Z.

last: Ben-Dov

address: Ein Kerem

department: Nephrology and Hypertension

country: Israel

institute: Hadassah Medical Center

summary: To date, 115 miRNAs genes (precursors) have been registered in miRBase for Schistosoma mansoni, and 56 for Schistosoma japonicum (225 and 79 mature miRNA, respectively). miRNAs have not been systematically described in Schistosoma haematobium. Our aim in this study was to systematically characterize and quantify miRNA in Schistosoma by species, developmental stage and sex and to test the usefulness of this characterization in biomarker discovery for infection. We found read evidence for the expression of 65/225 (36 precursors) known S. mansoni miRNA and 76/79 (55 precursors) of the known S. japonicum miRNA. We report a handful of novel miRNA in each of these species and provide a curated list of S. haematobium miRNA. We report differences of miRNA expression by species, sex and developmental stages. Lastly, we present preliminary results of miRNA deep sequencing from infected specimens (mouse and human).

sample_organism:
Schistosoma japonicum
Schistosoma mansoni
Schistosoma haematobium

overall_design:
Total RNA from twenty Schistosoma specimens of different species, sex and developmental stages were obtained from the BEI Resources (https://www.beiresources.org/). Total RNA was also extracted from infected mouse livers and infected human serum. miRNAs were profiled by small RNA deep sequencing. Output files were analyzed using miRDeep2 followed by manual curation to identify previously reported and novel miRNA in parasite and clinical specimens.
Funding source: I-CORE Program of the Planning and Budgeting Committee and the Israel Science Foundation (grant no. 41/11)

first: Refael

last: Kohen

first: Dror

last: Avni

first: Eli

last: Schwartz

first: Tal

last: Meningher

first: Devorah

last: Gur-Wahnon

middle: Z


title: Transcriptomic changes from iPSC-derived RPE due to MFRP and C1QTNF5

status: Public on Jun 28 2020

city: Milwaukee

first: Steven

last: Henle

state: WI

address: 8701, W Watertown Plank Rd

department: Cell Biology, Neurobiology, and Anatomy

institute: Medical College of Wisconsin

summary: RNA-seq from iPSC-derived RPE looking at both loss of MFRP and treatment with C1QTNF5

overall_design: Human iPSCs were differentiated into RPE, including a line in which had a MFRP knockout. RNA-seq profiles were then created from untreated and C1QTNF treated cells

first: Brian

middle: A

last: Link


title: Upf2-mediated inhibition of nonsense mediated decay causes memory and social deficits by activating the immune response

city: Stockholm

first: Ola

last: Larsson

department: Department of oncology-pathology

country: Sweden

institute: Karolinska Institutet

summary: Nonsense-mediated decay (NMD) is an evolutionarily conserved surveillance mechanism that targets mRNAs undergoing premature translation termination for rapid degradation as well as normal physiological transcripts. From yeast to humans, NMD requires the function of three conserved Up-frameshift (Upf) factors (Upf1, Upf2, Upf3). Interestingly, in humans, mutations in UPF2 and UPF3B are associated with intellectual disability and autism spectrum disorder (ASD). However, the neurobiological mechanism by which deficient NMD leads to neurodevelopmental disorders remains unknown. Consequently, no treatment is currently available. Here we report that mice lacking Upf2 in the murine forebrain (Upf2 fb-KO mice) show endophenotypes associated with ASD and deficits in learning and memory. In addition, Upf2-mediated deficient NMD leads to abnormal long-term potentiation (LTP) in the hippocampus. Like patients with mutations in UPF2, Upf2 fb-KO mice showed neuroanatomical abnormalities including a smaller corpus callosum. Surprisingly, transcriptomic analysis revealed elevated mRNA expression of immune-related genes in the hippocampus of Upf2-fb-KO mice, which was accompanied by increased inflammation and progressive infiltration of peripheral immune cells. More importantly, treatment with an FDA-approved immunosuppressant, cyclophosphamide (CyP), significantly reduces brain inflammation, improves the neuroanatomical defects and the deficits in LTP and memory deficits, and reverses some of the ASD-like behaviors, notably the social deficits. Collectively, our results reveal the biological basis underlying neurodevelopmental disorders associated with dysfunctional NMD. Moreover, these findings suggest that immunosuppressant drugs, like CyP, may provide a new therapeutic approach for the treatment of patients with mutations in core NMD components.

overall_design: Comparison of gene expression of fore brains (fb) bewteen Upf2 WT and fb-knock out mice.


title: Next Generation Sequencing Based RNAseq Analysis of lri35-/- mutant zebrafish larvae at 5 dpf

status: Public on Jun 27 2020

city: Cleveland

first: Takuya

last: Sakaguchi

address: 9500 Euclid Ave.

institute: Cleveland Clinic Foundation

summary: Gene expression profiles in lri35 mutant zebrafish larvae at 5 dpf based on RNAseq data.

overall_design: Total RNA was isolated from homozygous lri35 mutant and their clutchmate wild-type larvae at 5 dpf.  Gene expression difference between wild-type and lri35 mutant larvae was determined based on the RNAseq data.


title: Analysis of Differentially Expressed Genes in sorted CD69+ double positive (DP) thymocytes from wild type (WT) and NSRP1CD4Cre (KO) mice

city: Gwangju

first: Chang-Hyun

last: Kim

address: 123, Cheomdangwagi-ro, Buk-gu

department: School of Life Sciences

institute: Gwangju Institute of Science and Technology (GIST)

summary: NSrp70 deficiency (NSRP1f/fCD4Cre) profoundly perturbed the late development of DP thymocytes, leading to a significant reduction of single positive (SP) cells in the thymus and peripheral lymphoid tissues. To gain further insight into how NSrp70 controls thymocyte development from CD69+ DP stage, we performed RNA-seq analysis after sorting CD69+ DP thymocytes from WT and Nsrp1 cKO mice.

overall_design: Gene profiles differentially expressed in NSRP1-deficient CD69+ DP thymocytes compared to wild-type thymocytes.

first: Sang-Moo

last: Park

first: Hye-Ran

first: Young-Dae

first: Chang-Duk

last: Jun


title: Transcriptome defense response of orange fruit Induced with Rhodoturola mucilaginosa enhanced with salicylic acid

city: Zhenjiang

first: Solairaj

last: Dhanasekaran

state: Jiangsu

address: Jiangsu University

department: School of Food and Biological Engineering

institute: Jiangsu University

summary:
Purpose: The goal of this study is to looked at the expression levels of defense genes in orange fruit in response to the application of the antagonist R. mucilaginosa enhanced with SA
Methods: Three identical and evenly distributed wounds (5 mm diameter and 3 mm deep) made at the equator of each fruit were inoculated with 30 µL cell suspension of R. mucilaginosa (1×108 cells/mL) + 0.2 mM SA, whiles cell suspension of R. mucilaginosa alone (1×108 cells/mL) was used as a control. Treated fruits were then kept in plastic baskets and covered with film wraps to maintain relative humidity of 95% at storage temperature of 20 ºC. After 72 h of storage the wound tissues were excise and immediately kept in liquid nitrogen and maintained at -80 ºC for the analysis of the RNA. There were three replications per each sample.
Results: The results showed that 46 genes were identified as DEGs. Among these 34 were up-regulated and 12 were down regulated, 10 of the RNA-seq
these were validated using qRT-PCR. RNA-seq data had a linear relationship withqRT_PCR with a corelation coefficent value of (R2) 0.8388.
Conclusion: Our finding showed that the defense genes of orange fruit were up-regulated by the innoculation of R. mucilaginosa enhanced with 0.2 mM SA in the fruit.

overall_design: Examine expression levels of defense genes in orange fruit in response to the application of the antagonist R. mucilaginosa enhanced with SA

first: Joseph

last: Ahima

first: Hongyin

last: Zhang

first: Meiqiu

last: Xu


title: Integrated Genomic Analysis of a Stem Cell Model of Overgrowth Syndrome with Intellectual Disability (WGBS)

city: Los Angeles

first: Andrew

last: King

address: Gonda Bldg Rm. 6554, P.O.Box 957088

department: Human Genetics

institute: UCLA

summary: We profiled genome-wide DNA methylation, H3K27me3 histone modification, and gene transcription in embryonic stem cell-derived neural stem cells harboring mutations in Dnmt3a associated with overgrowth syndrome with intellectual disability.

overall_design: Whole genome bisulfite sequencing (WGBS) performed on wild-type and Dnmt3a knock-out embryonic stem cells. Additionally, WGBS was performed on wild-type, Dnmt3a knock-out, I306N, G528S, M544K, and P900L embryonic stem cell-derived neural stem cells.

first: Guoping

last: Fan


title: Silencing core spliceosome Sm gene expression induces a cytotoxic splicing switch in the proteasome subunit beta 3 mRNA in non-small cell lung cancer cells

city: Amsterdam

first: Victor

middle: W

last: van Beusechem

address: De Boelelaan 1117

department: Medical Oncology

institute: Amsterdam UMC

summary: The core spliceosomal Sm proteins were recently proposed as cancer-selective lethal targets in non-small cell lung cancer (NSCLC). In contrast, loss of commonly mutated cancer target SF3B1 appeared to be toxic to non-malignant cells as well. In the current study, the transcriptomes of A549 NSCLC cells in which SF3B1 or SNRPD3 was silenced were compared using RNA sequencing. Skipping of exon 4 of the proteasomal subunit beta type-3 (PSMB3) mRNA, resulting in a shorter PSMB3-S variant, occurred only after silencing SNRPD3. This observation was extended to the other six Sm genes. Remarkably, alternative splicing of PSMB3 mRNA upon Sm gene silencing was not observed in non-malignant IMR-90 lung fibroblasts. Furthermore, PSMB3 was found overexpressed in NSCLC clinical samples and PSMB3 expression correlated with Sm gene expression. Moreover, high PSMB3 expression corresponds to worse survival in patients with lung adenocarcinomas. Finally, silencing the canonical full-length PSMB3-L but not the shorter PSMB3-S variant was cytotoxic and was accompanied by a decrease in proteasomal activity. Together, silencing Sm genes, but not SF3B1, causes a cytotoxic alternative splicing switch in the PSMB3 mRNA in NSCLC cells only.

overall_design: Examination of the transcriptome of A549 NSCLC cells transfected with a non-targeting negative control siRNA or siRNAs targeting either SF3B1 or SNRPD3

first: Maxime

last: Blijlevens

first: Malgorzata

last: Komor

first: Rocco

last: Sciarrillo

first: Egbert

middle: F

last: Smit

first: Remond

last: Fijneman


title: Next Generation Sequencing analysis of control and serotonin, pergolide and dexfenfluramine treated tricuspid valves

city: Liege

first: Alexia

last: Hulin

address: Avenue de l'hopital 1

department: Cardiovascular Science

institute: GIGA

summary:
Identify biological processes leading to heart valve disease upon long-term oral administration of serotonin, pergolide and dexfenfluramine
Transcriptome profiling of tricuspid valves isolated from the drug treateds rabbit groups and compared to control rabbits using RNA sequencing
Distinct patterns of differentially expressed genes (DEGs) highlight common and specific biological processes of drug treatment in tricuspid valves

overall_design: Total RNA, extracted from tricuspid heart valves (n=5 for each treatment and control),  was sequenced with an Illumina NextSeq500 sequencer generating a total of around 10 millions mapped reads per library on average.

first: Latifa

last: Karim

first: Benoit

last: Charloteaux

first: Wouter

last: Coppieters

first: Cecile

last: Oury

first: John

last: Dibato

first: Patrizio

last: Lancellotti

first: Laurence

last: Servais

first: Alexandre

last: Hego

first: Nathalie

last: Donis

first: Alain

last: Nchimi


title: Transcriptome Analysis of Duck Spleen Infected by Duck enteritis virus

city: Guiyang

first: wu

last: liangtao

address: huaxi district

institute: Guizhou University

summary: Purpose:To understand the transcriptome regulator of duck spleen infected with duck enteritis virus (DEV).Methods:50-day-old ducks were inoculated with 100 titer (The TCID50 of DEV was 10-9/0.1mL) and 10-2 titer two different viral titer of DEV in leg muscle for different durations (66 h, 90 h and 114 h) and seronegative control (0 h) were analyzed using next-generation RNA sequencing.Furthermore, the data were validated using quantitative real-time PCR.Results:There were 534, 685 and 580 genes differentially expressed in 100 titer, moreover, 511, 485 and 531 differentially expressed genes (DEGs) were obtained from 10-2 titer for 66 h, 90 h and 114 h, respectively. These genes were mainly involved in functional categories including immune response, extracellular space, heparin binding, oxygen transport, extracellular region, cellular response to interleukin-4, MHC class II protein complex, antigen processing and presentation of peptide or polysaccharide antigen via MHC class II, and pathways such as ribosome, ECM-receptor interaction, cell adhesion molecules, JAk-STAT signaling pathway, PPAR signaling pathway, neuroactive ligand-receptor interaction, phagosome.Conclusions: Different titers of DEV infection can stimulate different biological processes and signaling pathways in the spleen, and regulated the complex biological processes, metabolic and signaling pathways in the process of DEV infection.This transcriptome analysis of duck spleen infected with DEV in different time points is reported for the first time, it laid the foundation for further understanding of interactions between DEV and duck spleen tissue, molecular mechanisms of duck defend against DEV infection, and screening key functional genes.

overall_design: Spleen mRNA profiles of 50-day old duck infected  with 100 titer (The TCID50 of DEV was 10-9/0.1mL) and 10-2 titer two different viral titers of DEV for different durations (66 h, 90 h and 114 h) and seronegative control (0 h) were generated by deep sequencing  using IonProton

first: Liangtao

last: Wu

first: Ming

last: Wen


title: Comparative transcriptomic analysis of peach fruits in common and high temperature conditions

city: Wuhan

first: xiao

last: wang

address: No.1 Shizishan street, Hongshan district, Wuhan City, Hubei Province

institute: Huazhong Agricutural University

summary:
Purpose: This study was to explore the underlying molecular mechanism of temperature effects on fruit quality during shelf life. The transcriptome data of peach fruits stored in high temperature (HT, 35 °C) and common temperature (CT, 25 °C) conditions were measured and compared.

Methods: Red flesh peach (Prunus persica L. Batsch cv. Tianxianhong) fruits with consistent color, shape and weight were selected and kept at 5 °C for 2 days after the day of harvest. Then, these fruits were randomly divided into two groups. One group was stored at CT for 7 days, and the other was stored at HT for 7 days. During storage, fruits were sampled at day 1, 2 and 3 as early stage as well as day 5, 6 and 7 as later stage. Total RNA of each sample was extracted and used to construct 24 RNA libraries. RNA sequencing was performed on an Illumina HiSeq 2500 platform. The differences in transcriptome, ethylene production, pulp softening of postharvest peach fruits were compared between CT and HT storage conditions

Results: Our results showed that HT conditioning after 5 °C is better than CT to maintaining fruit quality during shelf life due to MEKK1-MKK2-MPK4/6 signal transduction and low level of ethylene and auxin biosynthesis enzymes which may affect genes related to softening and membrane stability through ethylene response factors (ERFs) and auxin response factors (ARFs).

overall_design: The mRNA profiles of postharvest peach fruits in 25 °C and 35 °C conditions at 6 time points using Illumina HiSeq.

first: Xiao

last: Wang

first: Binguang

last: Ma

first: Binzhong


title: Expression data from  plumbagin-treated B16F10

city: Tsukuba,

first: Meriem

last: Bejaoui

state: Ibaraki

address: 1 Chome-1-1 Tennodai

country: Japan

institute: University of Tsukuba

summary:
Gene expression profiling reveals a potential role of plumbagin on the induction of B16F10 metastasis
cells were treated with 0 and 2 µM plumbagin for 24 h ; Microarray gene expression profiling was conducted.

overall_design: RNA was extracted using Isogen (Nippon Gene Co. Ltd., Toyama, Japan). The integrity of RNA was quantified using NanoDrop 2000 spectrophotometer (Thermo Scientific, Wilmington, DE, USA). RNA samples were prepared for gene expression profiling analysis with GeneChip® 3' Expression Arrays using 3' IVT PLUS Reagent Kit (Affymetrix Inc., Santa Clara, CA, USA). Two hundred and fifty ng of total RNA from each sample was used to generate amplified and biotinylated complementary RNA (cRNA) from poly (A) RNA in a total RNA sample according to the user manual. IVT Incubation time was 16 hour. GeneAtlas® Hybridization, Wash and Stain Kit was used for hybridizing 3' IVT Array Strips according to the user manual . Mouse genome array strips  were hybridized for 16 hours in a 45oC incubator, washed and stained and finally imaging was done with the GeneAtlas Fluidics and Imaging Station.


title: Notch signaling between cerebellar granule cell progenitors

city: Heidelberg

first: Konstantin

last: Okonechnikov

state: Germany

address: Im Neuenheimer Feld 280

department: Pediatric Neurooncology

institute: German Cancer Research Center

summary: During cerebellar development, maternal granule cell progenitors (GCPs) divide to produce not only postmitotic granule cells (GCs) but also sister GCPs. However, molecular machinery to proportionally produce distinct sister cell types from seemingly uniform GCPs is still elusive. Here we report Notch signaling makes a difference among GCPs, leading to their proportional differentiation.

overall_design: P7 cerebella cells were extrated using percoll density gradient centrifugation and further captured via the C1 Fluidigm systems with 96-well chips

first: Toma

last: Adachi

first: Daisuke

last: Kawauchi


title: Transcriptomic responses to oil, a pathogen, or both in spleen tissues from juvenile red snapper (Lutjanus campechanus)

status: Public on Jun 26 2020

city: Ocean Springs

first: Maria

last: Rodgers

state: Mississippi

address: 103 McIlwain Drive

department: Coastal Sciences

institute: University of Southern Mississippi

summary: The objective of this study was to determine how transcriptomic responses in the spleen are altered in juvenile red snapper exposed to oil, a known fish pathogen (Vibrio anguillarum), or both.

overall_design: Red snapper juveniles were exposed to oil, a pathogen (Vibrio anguillarum) or both.  Oil exposure was for 8 days and pathogen exposure was for 1 hour, 24 hours before takedown.  Oil solutions used in exposures were derived from high energy water accommodated fractions (HEWAF) prepared using Macondo well oil from the Deepwater Horizon oil spill following established procedures.  At the end of the experiments, spleens were taken from organisms, RNA was extracted and sequenced.

first: Robert

last: Griffitt


title: Differential chromatin accessibility landscape reveals the structural and functional features of the allopolyploid wheat chromosomes

city: Manhattan

first: Eduard

last: Akhunov

state: Kansas

address: 1712 Claflin Road

department: Plant Pathology

institute: Kansas State University

summary: We have a limited understanding of how the complexity of the wheat genome influences the distribution of chromatin states along the homoeologous chromosomes. Using a differential nuclease sensitivity (DNS) assay, we investigated the chromatin states in the coding and transposon element (TE) -rich repetitive regions of the allopolyploid wheat genome.

overall_design: The raw data was deposited in BioProject: PRJNA564769, including SRR10098334, SRR10098333, SRR10098332, and SRR10098331.

first: Katherine

last: Jordan

first: Fei

last: He

first: Monica

last: Fernandez de Soto

first: Alina

last: Akhunova


title: Epigenome-wide DNA methylation of the BEAS-2B cells post-chronic exposure to SWCNTs for 60 days

city: Suzhou

first: Jianxiang

last: Li

address: No. 199 Renai Road

department: Department of Toxicology, School of Public Health, Medicine College

institute: Soochow university

summary:
As environmental pollutants and possible carcinogens, carbon nanotubes (CNTs) have recently been found to promote tumorigenesis and tumor metastasis after long-term pulmonary exposure. However, whether CNT-induced carcinogenesis can be inherited and last for generations remains unknown. Here, we establish a post-chronic single-walled carbon nanotubes (SWCNTs) exposed human bronchial epithelium BEAS-2B cell model to investigate SWCNTs-induced carcinogenesis. At a tolerated sublethal dose level, post-chronic SWCNTs exposure significantly increases the migration and colony formation abilities of BEAS-2B cells, leading to cell malignant transformation. Notably, the malignant transformation of BEAS-2B cells is irreversible within 60 days recovery period after SWCNTs exposure, and the malignant transformation activities of cells gradually increase during the recovery period. Mechanism analyses show that post-chronic exposure to SWCNTs causes substantial DNA methylation and transcriptome dysregulation of BEAS-2B cells. Subsequent enrichment and clinical database analyses reveal that differentially expressed/methylated genes of BEAS-2B cells are enriched in cancer-related biological pathways, and several of these genes are validated in lung cancer patients.
As environmental pollutants and possible carcinogens, carbon nanotubes (CNTs) have recently been found to promote tumorigenesis and tumor metastasis after long-term pulmonary exposure. However, whether CNT-induced carcinogenesis can be inherited and last for generations remains unknown. Here, we establish a post-chronic single-walled carbon nanotubes (SWCNTs) exposed human bronchial epithelium BEAS-2B cell model to investigate SWCNTs-induced carcinogenesis. At a tolerated sublethal dose level, post-chronic SWCNTs exposure significantly increases the migration and colony formation abilities of BEAS-2B cells, leading to cell malignant transformation. Notably, the malignant transformation of BEAS-2B cells is irreversible within 60 days recovery period after SWCNTs exposure, and the malignant transformation activities of cells gradually increase during the recovery period. Mechanism analyses show that post-chronic exposure to SWCNTs causes substantial DNA methylation and transcriptome dysregulation of BEAS-2B cells. Subsequent enrichment and clinical database analyses reveal that differentially expressed/methylated genes of BEAS-2B cells are enriched in cancer-related biological pathways, and several of these genes are validated in lung cancer patients.

overall_design: The level of epigenome-wide DNA methylation of normal BEAS-2B cells and the cells treated with SWCNT for 60 days were analyzed by Infinium Methylation EPIC 850K Beadchip (Illumina Inc., USA), There were 3 replicates in each group

first: Jin

first: Tian

last: Xin

first: Jie

last: Zhang

last: OUYang

first: Lirong

last: Tan

first: Beibei

last: Jia

first: Cuicui

last: Ge


title: Transcriptional changes induced by miR-21 antagonism in T helper cells abrogates Th17 tumor promoting functions

city: Cosenza

first: Cirino

last: Botta

address: Via Migliori

department: Hematology Unit

country: Italy

institute: "Annunziata" Hospital of Cosenza

summary: Multiple myeloma (MM) is a hematologic malignancy tightly dependent on inflammatory bone marrow microenvironment. IL-17 producing CD4+ T cells (Th17) sustain MM cells growth and osteclast-dependent bone damage. In turn, Th17 generation and function rely on inflammatory stimuli. There is compelling evidence that miR-21 is involved in Th17 differentiation and effector functions. Here, we investigated the role of miR-21, which is an inflammation induced miRNA, in Th17-mediated MM tumor growth and bone disease. We found that inhibition of miR-21 in naive T cells (miR-21i-T cells) impaired differentiation towards Th17 in vitro. Analysis of miR-21-related molecular pathways in Th17 cells demonstrated upregulation of STAT-1/-5a-5b, downregulation of STAT-3 and redirection of Th17 to Th1/activated like cells as shown by a pair-to-pair RNAseq and proteome/phosphoproteome analysis. Inhibition of miR-21 impaired Th17 mediated MM cell proliferation and osteoclast activity in vitro. We recapitulated and validated these findings in NOD/SCID gNULL mice, injected intratibially with miR-21i-T cells and MM cells. Our findings disclose the critical involvement of miR-21 in pathogenic Th17 development and activity and open the avenue to the design of miR-21-targeting strategies to counteract microenviromental dependence of MM growth and bone disease.

overall_design: 50,000 Th17 cells differentiated from naïve CD4+ T cells exposed to NC or miR-21i were sequenced

first: Emanuela

last: Altomare

first: Sarai

last: Sarvide

first: Bruno

last: Paiva

first: Marco

last: Rossi


title: Gene expression data of stromal cell subpopulations isolated from human lymph nodes (LNs) infiltrated with melanoma

city: Auckland

first: Jennifer

last: Eom

address: 3A Symonds Street

country: New Zealand

institute: University of Auckland

summary:
Metastasis of human tumours to LNs is a universally negative prognostic factor. LN stromal cells (SCs) play a crucial role in enabling T cell responses, and since tumour metastases modulate their structure and function, this interaction may suppress immune responses to tumour antigens. However the SC subpopulations that respond to infiltration of malignant cells into human LNs have not been defined. Using microarray, we sought to assess gene expression profiles of two distinct SC subpopulations isolated from melanoma-infiltrated LNs.
Our data demonstrate distinct profiles of two SC subpopulations isolated from melanoma-infiltrated LNs using fluorescence-activated cell sorting (FACS). FRCs express T cell modulating cytokines, chemokines and adhesion molecules, while CD34+ SCs predominantly express genes associated with ECM organization. Distinguishing between these two SC subpopulations in human LNs will now allow study of their respective impact on T cell responses to tumour antigens and clinical outcomes.

overall_design: FRCs and CD34+ SCs isolated from 7 different melanoma-infiltrated LNs were examined by microarray. Transcriptomic analysis revealed the genes that were differentially expressed between these two SC populations.

first: Saem

middle: M

last: Park

first: Michael

last: Black

first: Rod

last: Dunbar


title: Identification of dynamic RNA-binding proteins uncovers key regulators of gene expression in diseased cardiomyocytes

first: Christoph

last: Sandmann

address: Im Neuenheimer Feld 669

institute: Heidelberg University Hospital

summary: Mutations or decreased expression of RNA-binding proteins (RBPs) can lead to cardiomyopathies in humans. Here we defined RBPs in healthy and diseased primary cardiomyocytes at a system-wide level by RNA Interactome Capture. This identified 67 novel cardiomyocyte specific RBPs including several contractile proteins. Furthermore, we identified Cytoplasmic polyadenylation element binding protein 4 (Cpeb4) as a dynamic RBP in diseased cardiomyocytes, regulating cardiac growth both in vitro and in vivo. To study Cpeb4 in cardiomyocytes, we identified mRNAs bound to and regulated by Cpeb4. Cpeb4 regulates cardiac remodeling by differential expression of transcription factors. Among Cpeb4 target mRNAs, two Zinc finger transcription factors (Zeb1 and Zbtb20) were identified. We show that Cpeb4 regulates the translation of these mRNAs and that Cpeb4 depletion increases their expression. Thus, Cpeb4 emerges as critical regulator of cardiomyocyte function by differential binding of specific mRNAs in response to pathological growth stimulation.

overall_design: Effect of Cpeb4 Knock-down in isolated cardiac myocytes

first: Mirko

last: Völkers


title: Steroid sulfatase is a therapeutic target for advanced prostate cancer

city: SACRAMENTO

first: Cameron

middle: Michelle

last: Armstrong

state: CA

address: 4645 2nd Ave.Research Bldg. III, Ste. 1300

institute: UC Davis Medical Ctr.

summary: The conversion of DHEAS into DHEA by steroid sulfatase (STS) may contribute to sustained intracrine androgen synthesis. Here, we determine the contribution of STS to treatment resistance and explore the potential of targeting STS using novel inhibitors to overcome resistance in prostate cancer.

overall_design: VCaP cells were seeded in 60mm dishes and treated overnight with DMSO or 5 µM SI1 or SI-2 for a total of 3 samples. RNA was isolated using Trizol.

first: Allen

last: Gao


title: FiTAc-seq: Fixed-Tissue ChIP-seq for H3K27Ac profiling and super-enhancer analysis on FFPE tissues [human]

city: Boston

first: Henry

last: Long

state: MA

address: 450 Brookline ave

institute: Dana Farber Cancer Institute

summary: Fixed-Tissue ChIP-seq for H3K27Ac profiling (FiTAc-seq) is an epigenetic method for profiling active enhancers and promoters in FFPE tissues. We previously developed a modified ChIP-seq protocol (FiT-seq) for chromatin profiling in FFPE. FiT-seq produces high-quality chromatin profiles particularly for methylated histone marks but is not optimized for H3K27Ac profiling. FiTAc-seq is a modified protocol that replaces the proteinase K digestion applied in FiT-seq with extended heating at 65°C in more stringent detergent conditions and a minimized sonication step, to produce robust genome-wide H3K27Ac maps from clinical samples. We demonstrate FiTAc-seq suitability to generate high quality enhancer landscapes and SE annotation in a number of archived FFPE samples from distinct tumor types. This approach will be of great interest both for basic and clinical researchers. The entire protocol from FFPE blocks to sequence ready library can be accomplished within 4 days.

overall_design: 3 samples per tissue type for bladder, melanoma, and seminoma. 1 brain cancer breast metastasis sample. RT4 cell line open chromatin assessed to compare bladder.

first: Alba

last: Font-Tello

first: Nikolas

last: Kesten

first: Paloma

last: Cejas


title: Targeted RNA quantification of 770 genes in primary salivary gland carcinomas

city: Cologne

last: Arolt

address: Kerpener Strasse 62

department: Institute of Pathology

institute: University of Cologne

summary: The RNA of 770 genes was profiled using the Nanostring platform in a set of 34 primary salivary gland carcinomas to detect global and entity-specific features

overall_design: 34 primary salivary gland carcinomas including adenoid cystic, mucoepidermoid and salivary duct carcinomas were analyzed using the Nanostring panCancer pathways RNA quantification panel.

first: Alexander

last: Quaas


title: Combining imaging- and gene-based hypoxia biomarkers in cervical cancer improves prediction of treatment failure independent of intratumor heterogeneity

city: Oslo

first: Heidi

last: Lyng

address: Montebello

department: Department of Radiation Biology

country: Norway

institute: Oslo University Hospital

summary: Emerging biomarkers based on medical images and molecular characterization of tumor biopsies open up for combining the two disciplines and exploiting their synergy in treatment planning. We compared pretreatment classification of cervical cancer patients by two previously validated imaging- and gene-based hypoxia biomarkers, evaluated the influence of intratumor heterogeneity, and investigated the benefit of combining them in prediction of treatment failure. The imaging-based biomarker was hypoxic fraction, determined from diagnostic dynamic contrast enhanced (DCE)-MR images. The gene-based biomarker was a hypoxia gene expression signature determined from tumor biopsies. Paired data were available for 118 patients. Intratumor heterogeneity was assessed by variance analysis of MR images and multiple biopsies from the same tumor. The two biomarkers were combined using a dimension-reduction procedure. The biomarkers classified 75% of the tumors with the same hypoxia status. Both intratumor heterogeneity and distribution pattern of hypoxia from imaging were unrelated to inconsistent classification by the two biomarkers, and the hypoxia status of the slice covering the biopsy region was representative of the whole tumor. Hypoxia by genes was independent on tumor cell fraction and showed minor heterogeneity across multiple biopsies in 9 tumors. This suggested that the two biomarkers could contain complementary biological information. Combination of the biomarkers into a composite score led to improved prediction of treatment failure (HR:7.3) compared to imaging (HR:3.8) and genes (HR:3.0) and prognostic impact in multivariate analysis with clinical variables.  In conclusion, combining imaging- and gene-based biomarkers enables more precise and informative assessment of hypoxia-related treatment resistance in cervical cancer, independent of intratumor heterogeneity.

overall_design: Totally 118 samples using pooled RNA isolated from 1-4 biopsies (median 2) per tumor were analysed; 84 with Illumina WG-6 v3 and 34 with Illumina HT-12 v4. In addition, each of 2-4 biopsies in nine tumors (24 samples in total) were analyzed with Illumina HT-12 v4.

first: Christina

last: Fjeldbo

first: Tord

last: Hompland

first: Tiril

last: Hillestad

first: Eva

last: Aarnes

first: Clara

last: Günther

first: Gunnar

middle: B

last: Kristensen

first: Eirik

last: Malinen


title: YBX1 indirectly targets heterochromatin-repressed inflammatory response genes through binding to CBX5 [PAR-CLIP]

city: Braunschweig

first: Andreas

last: Kloetgen

state: NI

address: Inhoffenstr 7

department: Department for Computational Biology of Infection Research

institute: Helmholtz Centre for Infection Research

summary: The RNA- and DNA-binding protein YBX1 is involved in various cellular processes. We here focused on investigating its role in posttranscriptional gene regulation in medulloblastoma, in which CRISPR screens have shown its essentiality for cellular survival. We found that YBX1 knockdown leads to broad upregulation of genes related to neuroinflammation, and directly regulates mRNA stability of various mRNA targets. More specifically, target CBX5, also called heterochromatin-protein 1 alpha (HP1-alpha), is downregulated upon YBX1 KD. It associates strongly with heterochromatin, and upon downregulation allows for upregulation of heterochromatin repressed genes related to inflammation.

overall_design:
We performed survival assays and RNA-seq upon YBX1 knockdown to elucidate the role of transcriptional control of YBX1 in medulloblastoma. Differential expresion analysis and pathway analysis elucidated the role of YBX1 in transcriptional control. We further performed PAR-CLIP of YBX1 to identify direct binding targets, and integrated results with differential expression analysis.
Please note that processed data was generated from both replicates and is linked to the rep1 sample records.

first: Alice

last: McHardy

first: Jessica

last: Hoell


title: FiTAc-seq: Fixed-Tissue ChIP-seq for H3K27Ac profiling and super-enhancer analysis on FFPE tissues [human PNET]

last: Long

summary: Fixed-Tissue ChIP-seq for H3K27Ac profiling (FiTAc-seq) is an epigenetic method for profiling active enhancers and promoters in FFPE tissues. We previously developed a modified ChIP-seq protocol (FiT-seq) for chromatin profiling in FFPE. FiT-seq produces high-quality chromatin profiles particularly for methylated histone marks but is not optimized for H3K27Ac profiling. FiTAc-seq is a modified protocol that replaces the proteinase K digestion applied in FiT-seq with extended heating at 65°C in more stringent detergent conditions and a minimized sonication step, to produce robust genome wide H3K27Ac maps from clinical samples. We demonstrate FiTAc-seq suitability to generate high quality enhancer landscapes and SE annotation in a number of archived FFPE samples from distinct tumor types. This approach will be of great interest both for basic and clinical researchers. The entire protocol from FFPE blocks to sequence ready library can be accomplished within 4 days.

overall_design: H3K27Ac chip-seq on 3  pancreatic neuroendocrine tumor samples (FFPE)


title: The possible mechanisms involved in induced disease resistance of peaches by Pichia membranaefaciens

city: zhenjiang

first: wu

last: feng

state: jiangsu

address: xuefu road 301

institute: jiangsu university

summary: We report the application of next-generation sequencing technology for analyzing the differentially expressed genes of peaches after treated with or without P. membranaefaciens. After analyzing the differentially expressed genes, we selected some important genes related to the resistance of peaches to do RT-qPCR.

overall_design: Examination of differentially expressed genes related to the resistance of 2 types of peach tissues which treated with or without P. membranaefaciens. RT-qPCR was performed using SYBR Green assays.

first: Hongyin

last: Zhang

first: Xiaoyun


title: YBX1 indirectly targets heterochromatin-repressed inflammatory response genes through binding to CBX5 [RNA-Seq]

overall_design: We performed survival assays and RNA-seq upon YBX1 knockdown to elucidate the role of transcriptional control of YBX1 in medulloblastoma. Differential expresion analysis and pathway analysis elucidated the role of YBX1 in transcriptional control. We further performed PAR-CLIP of YBX1 to identify direct binding targets, and integrated results with differential expression analysis.


title: FiTAc-seq: Fixed-Tissue ChIP-seq for H3K27Ac profiling and super-enhancer analysis on FFPE tissues

first: Henry

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: FiTAc-seq: Fixed-Tissue ChIP-seq for H3K27Ac profiling and super-enhancer analysis on FFPE tissues [mouse]

overall_design: FitAc-seq optimization on FFPE normal mouse liver tissue, testing different tissue homogenization temperatures and sonication times. Fit-seq protocol performance for H3K4me2 and H3K27Ac on FFPE normal mouse liver tissue. Matched fresh frozen mouse liver H3K27Ac ChIP-seq as control.

first: Alba

last: Font-Tello

first: Nikolas

last: Kesten

first: Paloma

last: Cejas