title: Endocardial/endothelial angiocrines regulate cardiomyocyte development and maturation and induce features of ventricular non-compaction

status: Public on Dec 30 2021

city: Stanford

first: Lei

last: Tian

state: CA

address: 1215 Welch Rd

institute: Stanford's Postdoctoral Scholar programs

summary: Non-compaction cardiomyopathy is a devastating genetic disease caused by insufficient consolidation of ventricular wall muscle that can result in inadequate cardiac performance. Despite being the third most common cardiomyopathy, the mechanisms underlying the disease, including the cell types involved, are poorly understood. We have previously shown that endothelial cell-specific deletion of the chromatin remodeller gene Ino80 results in defective coronary vessel development that leads to ventricular non-compaction in embryonic mouse hearts. Here, we used single-cell RNA-sequencing to characterize endothelial and endocardial defects in Ino80-deficient hearts. We observed a pathological endocardial cell population in the non-compacted hearts and identified multiple dysregulated angiocrine factors that dramatically affected cardiomyocyte behaviour. We identified Col15A1 as a coronary vessel-secreted angiocrine factor, down-regulated by Ino80-deficiency, which functioned to promote cardiomyocyte proliferation. Furthermore, mutant endocardial and endothelial cells (ECs) AQ6 up-regulated expression of secreted factors, such as Tgfbi, Igfbp3, Isg15, and Adm, which decreased cardiomyocyte proliferation and increased maturation. These findings support a model where coronary ECs normally promote myocardial compaction through secreted factors, but that endocardial and ECs can secrete factors that contribute to non-compaction under pathological conditions.

overall_design: Endothelial cell sigle cell RNA sequencing of mouse embryonic heart (Control) and Ino80 cKO at E15.5

first: Siyeon

last: Rhee

first: David

middle: T

last: Paik

first: Daielle

last: Nagelberg

first: Ashby

last: Morrison

first: Joseph

last: Wu

first: Kristy

last: Red-Horse


title: Depletion of histone methyl transferase KMT9 inhibits lung cancer cell proliferation by inducing non-apoptotic cell death

status: Public on Dec 31 2021

city: Freiburg

first: Eric

last: Metzger

address: Breisacherstr. 66

country: Germany

institute: Uniklinik-Freiburg

type: Expression profiling by high throughput sequencing

summary: The aim of the study is to identify KMT9a target genes in A549 cells

overall_design: 6 samples correponding to 2 times 3 replicates were used for the study

first: Roland

last: Schüle

first: Dominica

last: Willmann

first: Hannah-Maria

last: Baumert


title: Transcriptional Profiling of Early and Late Phases of Bovine Tuberculosis

city: Seattle

first: Hazem

last: Abdelaal

state: WA

address: 1900 9th street

country: USA

institute: Seattle Children's Researcch Institute

summary: We report RNAseq analysis of Early and Late Phases of Bovine Tuberculosis

middle: M

first: Adel

last: Talaat


title: Single-cell RNA-sequencing of adult neural stem cells reveals novel molecular principles of stem cell activation and heterogeneity

city: Heidelberg

first: Haikun

last: Liu

address: INF 581

institute: DKFZ

summary: Neural stem cells (NSCs) in the subventricular zone (SVZ) and the subgranular zone of the hippocampus continuously give rise to glial cells and neurons and are the most important source for new neurons in the adult mammalian brain1-4. It has been suggested that the NSCs in the adult brain form a heterogeneous population5,7, akin to other tissue-specific adult stem cells6. However, a molecular basis of the presumed NSC heterogeneity has been lacking. Here, we sequenced the transcriptomes of 131 individual adult NSCs from the mouse SVZ. After filtering, 117 cells were used for further analysis. We  found that they consist of two distinct subgroups of about equal size, independent of the mouse’s age. These subgroups were separated by molecular markers of quiescence (quiescent NSCs, qNSCs) and cell-cycle progression (active NSCs, aNSCs). We identified novel cell surface markers belonging to the tetraspanin family of transmembrane proteins for the prospective purification of qNSCs and aNSCs. The individual NSC transcriptomes were ordered along a continuous progression from qNSCs to aNSCs, with the expression of molecular pathways decreasing (G-protein-coupled receptor signaling) or increasing (MAP kinase, PI3 kinase-mTOR, Hippo, and p53 pathways) in a coordinated manner. Within the aNSCs, transcription factors for neural cell lineage specification were expressed in patterns that indicate specific lineage commitment of individual aNSC. Together, these findings imply that the switch from qNSC to aNSC is irreversible in vivo, at least in a large fraction of cells, and is accompanied by lineage commitment already at the stem-cell stage. Thus our work reveals coherent patterns of molecular heterogeneity within adult NSCs that arise from the regulation of cell-cycle activity and differentiation pathways. We also sequenced 13 bulk populations.

overall_design: neural stem cells  expressing the nuclear receptor Tlx were isolated via FACS and subjected for single cell RNA sequencing. The project aims to discover heterogeneity of NSCs in vivo via single cell RNA-SEQ

first: HaiKun

first: Huiqin

last: Qu

first: Chunxuan

last: Shao


title: Effects of Mucosa associated fungi on IEC

city: New York

first: Gregory

last: Putzel

state: NY

address: 430 East 29th Street

department: Microbiology

institute: NYU Langone Health

summary: RNAseq of intestinal epithelial cells from ASF Mice colonized with a consortium of mucosa associated fungi

overall_design: 4 samples per group, 2 groups: ASF and ASF+ MUC

first: Irina

last: Leonardi


title: Porphyromonas gingivalis W50 wild type vs. FeoB mutant

city: Carlton

first: Catherine

last: Butler

state: VIC

address: 720 Swanston St

department: The Melbourne Dental School

country: Australia

institute: The University of Melbourne

summary: Transcriptomics profiling of P. gingivalis W50 wild type compared to a FeoB mutant.

sample_organism:
Porphyromonas gingivalis
Porphyromonas gingivalis W50

overall_design: Reference design to compare two conditions (wild type, FeoB mutant). 6 replicates for each condition, independently grown. Cy5-labelled genomic DNA from Porphyromonas gingivalis W50 was used as the reference sample.

middle: A

first: Helen

middle: L

last: Mitchell

first: Stuart

middle: G

last: Dashper

first: Christine

last: Seers

first: Nada

last: Slakeski


title: In Vivo Organ Regeneration via Stroma-Dependent Adult Lineage Reprogramming (miRNA)

city: Carrington Crescent

first: Andrew

middle: H

last: Sims

state: Edinburgh

address: Systems Medicine Building

department: Institute of Genetics and Molecular Medicine

country: United Kingdom

institute: University of Edinburgh

summary: Remarkable progress has been made in cell fate reprogramming by forced expression of a small number of transcription factors. Major challenges remain, however, in regenerative medicine regarding how to target multiple cell types and direct them to form a functional organ in vivo. Here, we demonstrate that, by changing their stromal microenvironment, adult differentiated cells of endodermal origin can be reprogrammed to generate a functional ectodermal organ. The process of organ regeneration is highly efficient and complete, and depends on epithelial-stromal interactions that lead to successful remodeling of the extracellular matrix and stromal cells that are essential for organ function. Furthermore, it is a multistep process consisting of changes in cell fate, where dedifferentiation occurs more rapidly than redifferentiation, and subsequent morphogenetic reprogramming. Remarkably, neither direct transdifferentiation nor a complete reversion to the pluripotency state is involved in the reprogramming process; instead it features dynamic activities of essential genes that regulate pluripotency and lineage development. Our data have important implications for stem cell biology, cancer biology, and regenerative medicine.

platform_organism:
Caenorhabditis elegans
Drosophila melanogaster
Danio rerio
Gallus gallus
Homo sapiens
Mus musculus
Rattus norvegicus

overall_design: Three replicates of adult and reprogrammed mouse lung and mammary cells were profiled for miRNAs


title: Control of sucrose accumulation in sugarcane (Saccharum spp. hybrids) involves miRNA-mediated regulation of genes and transcription factors associated with sugar metabolism

city: Nanning

first: Dong-Liang

last: Huang

email: hdl666@163.com, Huangdl@gxaas.net

address: 174 Daxue Road

country: China

institute: Sugarcane Research Institure of Guangxi Academy of Agricultural Sciences

type: Non-coding RNA profiling by high throughput sequencing

summary: Sugarcane established industrial crop providing sugar, ethanol and biomass-derived electricity around the world. Cane sugar content is an important, breeding target, but its improvement remains very slow in many breeding programmes. Biotechnology strategies to improve sucrose accumulation made little progress at crop level, mainly due to the limited understanding of its regulation. MiRNAs regulate many metabolic processes in plants. However, their roles and target genes associated with sugarcane sucrose accumulation remains unknown. Here, we conducted high-throughput sequencing of transcriptome, small RNAs and degradome of leaves and stem of two sugarcane genotypes with contrasting sucrose content from the early to late stages of sucrose accumulation stages, which provided more insights into miRNA-associated gene regulation during sucrose accumulation. Transcriptome analysis identified 18,722 differentially expressed genes (DEGs) between both genotypes during sucrose accumulation. The major DEGs identified were involved in starch and sucrose metabolism, and photosynthesis etc. miRNA sequencing identified 563 known and 281 novel miRNAs from both genotypes during sucrose accumulation. Of these, 311 miRNAs were differentially expressed.752 targets of 368 miRNAs (609 targets for 260 known miRNAs and 168 targets for 108 novel miRNAs) were identified by degradom sequencing.Several known and novel miRNAs and their target genes associated with sugar metabolism, sugar transport and sucrose storage were identified in this study.This new insight into the complex network of sucrose accumulation in sugarcane will help identify candidate targets for sucrose improvement in sugarcane through molecular means.

overall_design: High-throughput sequencing of transcriptome, small RNAs and degradome of leaves and stem of two sugarcane genotypes with contrasting sucrose content from the early to late stages of sucrose accumulation stages were conducted.

first: Huang

last: Dong-Liang

first: Wang

last: Miao

first: Li

last: Aomei

first: Liao

last: Fen

first: Qin

last: Cui-Xian

first: Chen

last: Zhong-Liang

first: Zhou

last: Li

last: Yang-Rui

last: Xiao-Feng

first: Lakshmanan

last: Prakash


title: Expression data from bone marrow mesenchymal stromal cells obtained from healthy donors and  myeloma patients

city: Toulouse

first: Lea

last: Lemaitre

address: IUCT, 1 Av. Irene Joliot-Curie

department: Hematology

country: France

institute: IUCT

summary: Multiple myeloma (MM) is a B-cell neoplasm characterized by clonal expansion of malignant plasma cells (MM cells) in the bone marrow (BM) compartment, where they acquire resistance to chemotherapy-mediated apoptosis. Natural history of patients include a premalignant stage, the MM diagnosis, the treatment, the remission, and for most of them the relapse. BM mesenchymal stromal cells (MSC) from newly diagnosed MM patients are functionally different from healthy donors (HD) MSC and display a distinct transcriptome. They have been largely involved in MM pathogenesis and chemoresistance acquisition. In order to determine if MM-MSC also participate to relapse, we focused on the characterization of MSC from patients with MM at different stages of the disease. We obtained patient MSC’s samples at diagnosis, at 2 years after intensive treatment without relapse and at the relapse from an intensive treatment. We used MCS from HD as control. All MSC were able to support MM cells growth through released factors, and still multipotent since able to differentiate into osteoblast and adipocyte. A transcriptomic analysis between these groups reveals differences in gene expression between HD and MM MSC whatever stage of the disease, suggesting that the difference in gene expression in MM-MSC persist with time. These data demonstrate an imprinting of MSC as soon as they were in contact with MM cells, which persist even after the disappearance of MM cells. This imprinting is in favour of an easier differentiation towards adipogenesis.

overall_design: Mesenchymal stromal cells (MSC) from bone marrow (BM) were selected at successive stages of multiple myeloma (MM) and in healthy donor (HD) for RNA extraction and hybridization on Affymetrix microarrays. We sought to compare expression profiles of MM vs HD BM MSC. To that end, we selected patients according to SliM CRAB and International Myeloma Working Group uniform response criteria: at diagnosis (D), at early relapse from an intensive treatment (<18 months) (ER), and in persistent complete response (CR) at least 2 years after an intensive treatment.

first: Léa

first: Jill

last: Corre

first: Bettina

last: Couderc


title: Next Generation Sequencing Facilitates Quantitative Analysis of HGF treated (HGF+) and matched control (HGF-) HepG2 cells

city: Chengdu

first: Xuan

last: Zheng

address: NO.17 of Section 3, Renmin south Road

department: State Key Laboratory of Biotherapy and Cancer Center

institute: West China Hospital, Sichuan University

summary: We report the high-throughput profiling of HGF treated liver cancer cell (HepG2) for differentiated genes analysis. We generated HGF stimulated and paired control HepG2 cells for 4 days. We find that tumor suppressor genes that are overexpressed and some tumor associated genes were downregulated, therefore reflect cell state and HGF induced anti-tumor potential. This study provides a potential framework for the research of HGF induced critical genes in the application of liver cancer therapy.

overall_design: HepG2 mRNA profiles of 4-day treated (HGF+) and control (HGF-) were generated by deep sequencing, in duplicate, using Illumina HiSeqTM 2000.

first: Junhong

last: Han

first: Xinyi

last: Zeng


title: MicroRNA map of Paralichthys olivaceus spleen at 6h and 24h after Streptococcus iniae infection

city: Qingdao

first: shuang

last: liu

address: 7 Nanhai Road

department: CAS Key Laboratory of Experimental Marine Biology

institute: Institute of Oceanology, Chinese Academy of Sciences

summary: In this study, we applied high-throughput sequencing technology to examine miRNAs in Japanese flounder (Paralichthys olivaceus) infected with Streptococcus iniae at different times.

overall_design: The expression profile of microRNA in Paralichthys olivaceus spleen at two different time points after Streptococcus iniae infection was examined.

first: Shuang

last: Liu

last: Sun


title: Matador,a multicenter clinical trial. Non-metastatic breast cancer patients were randomized between TAC or ddAC

city: Amsterdam

first: Mark

last: Opdam

address: 121, Plesmanlaan 121

country: Netherlands

institute: Netherlands Cancer Institute

summary: Between 2004 and 2012, patients with pT1-3, pN0-3, M0 breast tumors were randomised between adjuvant dose-dense doxorubicin-cyclophosphamide (ddAC) versus docetaxel-doxorubicin-cyclophosphamide (TAC). Trial registration numbers: ISRCTN61893718 and BOOG 2004-04.

overall_design: Total number of patients in the MATADOR study: 664. For 604 (90.9%) patients, tumor tissue was available for gene expression analysis. Library preparation failed in 7 patients. Six out of 597 sequenced samples did not meet the quality checks. 62 patients had a clinically low risk of recurrence according to the modified Adjuvant! Online and would not receive adjuvant chemotherapy according to current guidelines. In this group no events occurred. For one patient survival data was missing. The remaining 528 patients were used to develop DTS.

first: Sabine

middle: C

last: Linn

first: Rianne

last: Oosterkamp

first: Annelot

last: Rossum

first: Lennart

last: Kester

first: Jacco

last: van Rheenen

first: Marlous

last: Hoogstraat

first: Marleen

last: Kok

first: Gergana

last: Bounova

first: Ron

last: Kerkhoven

first: Iris

last: de Rink

first: Elise

last: van Leeuwen-Stok

first: Lodewyk

last: Wessels


title: Peroxidase plays important roles in soybean tolerance to Al toxicity

city: Nanjing

first: Ge

middle: Ju

address: Weigang No.1

institute: Nanjing Agricultural University

summary:
Aluminum (Al) toxicity is an important restraint to soybean (Glycine max L. Merr.) production on acid soils. However, little is known about the genes underlying Al tolerance in soybean.
We used microarrays to detail the global programme of gene expression  under control and Al stress  in two soybean  at 6, 12, and 24 h.

overall_design: The roots  of a Al-tolerant  and a Al-sensitive soybean varieties were harvested after 6,12,24h  of hydroponics under control and Al stress , each withone biological replicate.Then microarray chips were performed on the 12 samples. We aim to find key candidate genes and investigate their roles in soybean tolerance to Al toxicity. To that end, we analyzed the differently expressed genes in Al-tolerant (KF) and Al-sensitive (GF) soybean varieties under control and Al stress at 6, 12, and 24 h.

first: Juge

first: Xiangting

last: Wang

first: Ning

first: Yang

last: Li

first: Ting

last: Jin

first: Junyi

last: Gai

first: Yan


title: Whole genome methylation profiling in HepG2 cells using WGBS (Whole Genome Bisulfite Sequencing)

city: Huntsville

first: Eric

last: Mendenhall

state: AL

address: 601 Genome Way Northwest

institute: HudsonAlpha Institute

type: Methylation profiling by high throughput sequencing

summary: We performed WGBS analysis of HepG2 cells using ENCODE Consortium Data to study CpG methylation and their association with TFBS (transcription factor binding sites).

overall_design:
WGBS data was produced by ENCODE Production Lab and submitted to ENCODE Data Coordination Center. We further processed the data to generate whole genome methylation profile using Bismark and Bowtie2 aligner.
An alternative analysis of ENCODE data.

first: E

last: Partridge

first: Surya

middle: B

last: Chhetri

first: Richard

last: Myers


title: The gills  transcriptome analysis of yellow catfish  (Tachysurus fulvidraco♀ × P. vachellii♂) under transport stress

status: Public on Dec 29 2021

city: WuXi

first: Tao

last: Zheng

address: No.69, Xuejiali, Nanquan Town, Binhu District, Wuxi City, Jiangsu Province, China

institute: Wuxi Fisheries College, Nanjing Agricultural University

summary: Transport stress is a big threat to most teleost fish during production practice, causing mass loss to the aquaculture industry. Fish gills are mucosa-associated lymphoid tissue that directly contacted with water, which is the good choice to study the mechanism of transport stress. Gills transcriptome results revealed 1551 differentially expressed genes (744 up-regulated and 807 down- regulated) between the control and 16h transportation groups. The top 10 enriched KEGG pathways are all immune-related. After qRT-PCR validation, we found that the toll-like receptors and nod-like receptors signaling pathways mediate the gill’s immune response to transport stress: tlr5, tnfɑ, hsp90ɑ, il-1ß and map2k4 were significantly up-regulated and arrdc2 was significantly down-regulated under transport stress. These results suggested that the transport stress altered innate immunity responses and induced metabolic changes in gills of hybrid yellow catfish.   In conclusion, the results provide new perspectives on immune response in yellow catfish against transport stress and provide the possibility of mining resistance genes for future optimize transportation plan.

sample_organism: Tachysurus fulvidraco x Tachysurus vachelli

overall_design: The gills transcriptomes were examined  at control group and 16 h transport group.

first: Jun

last: Qiang

first: Yifan

last: Tao

first: Siqi

last: Lu


title: DNA methylation profiling of TF bound sites using ChIPBS (ChIP Bisulfite Sequencing)

type: Genome binding/occupancy profiling by high throughput sequencing

summary: ChIPBS analysis of HepG2 cells was performed using more direct assay approach, to study the methylation status of transcription factor bound sites and elucidate our understanding on TF-DNA methylation crosstalk

overall_design: ChIP followed by Bisulfite sequencing were performed in HepG2 cell lines. Methylation profile was measured for JUND, YY1, ZBTB33, POL2R and TAF1 and compared to the wgbs methylation profile for the same TF bound sites.


title: Identification of temporal regulatory modules associated with proliferation and differentiation in early maize endosperm development

city: Tucson

first: Ramin

last: Yadegari

state: Arizona

address: 1140 E. South Campus Dr.

department: Plant Sciences

institute: University of Arizona

summary: Endosperm is a product of double fertilization and functions as a nutritive tissue in the angiosperm seed to support the growth of the embryo or the germinating seedling. In cereal grains, endosperm comprises a large proportion of the mature seed and contains large amounts of carbohydrates and proteins. To identify a high-resolution temporal transcriptome of the earliest stages of endosperm development, we used laser-capture microdissection to isolate and profile mRNA populations of a developmental series of the endosperm from 0 to 4 DAP in maize inbred B73. These stages comprise the initial period of proliferation of the triploid endosperm coenocyte through cellularized endosperm that shows an overall polarity and indications of early cell differentiation. Using computational tools, we identified distinct temporal co-expression modules during this period of development. Analysis of the co-expressed transcription-factor genes and the associated cis-regulatory elements allowed us to hypothesize gene regulatory networks involved in early endosperm development in maize.

overall_design: mRNA populations of a developmental series of the central cell and endosperm from 0 to 4 days after pollination (DAP) (0, 1, 2, 3, and 4 DAP), and the whole embryo at 4 DAP in triplicates (18 samples) in maize inbred B73 were isolated using laser-capture microdissection and sequenced using an Illumina HiSeq 2500 platform.


title: Angiotensin-(1-7) analogue AVE0991 modulates astrocyte-mediated neuroinflammation via lnc RNA SNHG14/miR-223-3p/NLRP3 pathway and offers neuroprotection in a transgenic mouse model of Alzheimer’s disease

first: Siyu

state: Jiangsu

address: No.68, Changle Road

institute: Nanjing First Hospital

summary:
Objective: Emerging evidence suggested that brain angiotensin-(1-7) (Ang-(1-7)) deficiency contributed to the pathogenesis of Alzheimer’s disease (AD). Meanwhile, our previous studies revealed that restoration of brain Ang-(1-7) levels provided neuroprotection by inhibition of inflammatory responses during AD progress. However, the potential molecular mechanisms by which Ang-(1-7) modulates neuroinflammation remain unclear.
Materials and Methods: APP/PS1 mice were injected intraperitoneally with AVE0991 (a nonpeptide analogue of Ang-(1-7)) once a day for 30 consecutive days. Cognitive functions, neuronal and synaptic integrity, and inflammation-related markers were assessed. Since astrocytes played a crucial role in AD-related neuroinflammation whilst long noncoding RNAs (lncRNAs) were reported to participate in modulating inflammatory responses, astrocytes of APP/PS1 mice were then isolated for high-throughput lncRNA sequencing to identify the most differentially expressed lncRNA following AVE0991 treatment. Afterward, the downstream pathway of this lncRNA in the anti-inflammatory action of AVE0991 were investigated using primary astrocytes.
Results: The protection of AVE0991 against cognitive impairment and neuronal and synaptic damage in APP/PS1 mice was confirmed. For the first time, we demonstrated that AVE0991 suppressed astrocytic NLRP3 inflammasome-mediated neuroinflammation via a lncRNA SNHG14-dependent manner. SNHG14 acted as a sponge of miR-223-3p while NLRP3 represented a direct target of miR-223-3p in astrocytes. In addition, miR-223-3p participated in the AVE0991-induced suppression of astrocytic NLRP3 inflammasome.
Conclusion: These results suggest that AVE0991 inhibits astrocyte-mediated neuroinflammation via SNHG14/miR-223-3p/NLRP3 pathway. Moreover, these results reveal the underlying mechanisms by which Ang-(1-7) inhibits neuroinflammation under AD condition and uncovers the potential of its nonpeptide analogue AVE0991 in AD treatment.

overall_design: Astrocytes lncRNA profiles of 8 months old APP/PS1 mice and APP/PS1 mice were treated with AVE0991

first: Yingdong

last: Zhang

first: Teng

last: Jiang

first: Rui

last: Duan


title: Transcriptome profiling of cardiomyocytes treated with antiretroviral drugs

city: Orlando

first: Manish

last: Gupta

state: Florida

address: 6900 Lake Nona Blvd

department: Burnet School of Biomedical Sciences

institute: University of Central Florida

summary: The use of antiretroviral therapy (ART) improved the life expectancy of HIV patients through the suppression of HIV propagation in host. However, recent studies suggest that long-term use of ART induces comorbid conditions and heart failure in surviving HIV patients. The mechanism associated with the antiretroviral drugs (ARVs) induced cardiotoxicity and heart failure is not clear. In this study, we performed an RNA sequencing with ARV drugs-treated neonatal rat ventricular cardiomyocytes to explore drugs-induced cardiotoxicity. RNA-sequencing data analysis identified 1756 differentially expressed genes (padj<0.05) in cardiomyocytes. Out of 1756 genes, 701 genes were upregulated, and 1055 genes were downregulated in drug-treated cardiomyocytes. Functional enrichment analysis of differentially expressed genes was performed using clusterProfiler R and ingenuity pathway analysis. Our study showed that upregulated genes were linked with the biological processes associated with apoptosis, cellular movement or locomotion, cellular stress, and immune response. In contrast, down-regulated genes were involved in cell division and metabolism. Interestingly, we also found that ARV drugs treatment significantly upregulates the expression of a set of genes involved in cardiac enlargement and hypertrophy in the heart. Collectively, ARVs treatment in cardiomyocytes induces cardiotoxicity through differentially regulation of pathological genes expression in cardiomyocytes.

overall_design: Evalualtion of differentially expressed genes in antiretroviral drugs treated cardiomyocytes

first: Shiridhar

last: Kashyap


title: Differential expression of mitosis and cell cycle regulatory genes during recovery from an acute respiratory virus infection

city: Bethesda

first: Helene

middle: F.

last: Rosenberg

state: MD

address: 50 South Drive

institute: NIAID

summary: Acute respiratory virus infections can have profound and long-term effects on lung function that persist even after the acute responses have fully resolved. In this study, we examined gene expression by RNA sequencing in lung tissue of wild-type BALB/c mice that are recovering from a sublethal infection with pneumonia virus of mice (PVM) a natural rodent pathogen of the same virus family and genus as human respiratory syncytial virus. We compared these responses to gene expression in PVM-infected mice treated with Lactobacillus plantarum, an immunobiotic agent that limits inflammation and averts the negative clinical sequelae typically observed in response to acute infection with this pathogen. Our findings revealed prominent differential expression of inflammation-associated as well as numerous genes and gene families implicated in mitosis and cell-cycle regulation, including cyclins, cyclin-dependent kinases, cell division cycle genes, E2F transcription factors, kinesins, centromere proteins, and aurora kinases, among others. Of particular note was the differential expression of the cell division cycle gene Cdc20b, which was previously identified as critical for the differentiation of multi-ciliated cells ex vivo. Collectively, these findings provide us with substantial insight into post-viral repair processes and broaden our understanding of the mechanisms underlying Lactobacillus-mediated protection.

overall_design: 15 samples, 4 groups (WT, WT + PVM, WT + LP, WT + PVM + LP), 4 biological replicates per group, except 3 biological replicates for WT+PVM+LP

first: Ajinkya

middle: R

last: Limkar

first: Justin

last: Lack

first: Albert

last: Sek

first: Caroline

last: Percopo

first: Kirk

last: Druey

middle: F


title: Disruption of circadian rhythms by ambient light during neu-rodevelopment leads to autistic-like molecular and behavioral alterations in adult mice

city: Milwaukee

first: Victor

last: Jin

state: WI

address: 8701 Watertown Plank Rd

department: IHE

institute: Medical college of Wisconsin

summary: Although circadian rhythms are thought to be essential for maintaining body health, the effects of chronic circadian disruption during neurodevelopment remain elusive. Here, using the “Short Day” (SD) mouse model, in which an 8h/8h Light/Dark (LD) cycle was applied during E1-P42, we investigated molecular and behavioral changes after circadian disruption in mice. Adult SD mice fully entrained to the 8h/8h LD cycle and their circadian oscillations of clock protein PERI-OD1 and PERIOD2 were disrupted in the suprachiasmatic nucleus and the hippocampus. RNA-seq revealed changes in the transcriptome associated with neurodevelopment, translational control, and autism. Western blotting and immunostaining identified hyperactivation of the mTOR and MAPK signaling and enhanced global protein synthesis in the hippocampus of SD mice. Electrophysiological recording uncovered enhanced excitatory but attenuated inhibitory synaptic transmission in the hippocampal CA1 pyramidal neurons. These functional changes are corroborated by immature dendritic spine morphology in these neurons. Lastly, autistic-like be-havioral changes, including impaired social interaction and communication, increased repetitive behaviors and impaired novel object recognition and location memory, were found in SD mice. Together, these findings demonstrate autistic-like phenotypes in SD mice and highlight a critical role for circadian rhythm in neurodevelopment.

overall_design: RNA-seq experiment of control mice and short day mice, 3 biological replicates for each condition;

first: Kun

last: Fang

first: Dong

last: Liu


title: Transcriptomic alterations in fibroblast from parkinson's disease patients at high glucose levels

city: Barcelona

first: Mario

last: Ezquerra

state: Catalonia

address: Villarroel 170

department: Neurology

country: Spain

institute: Fundacio Clinic/IDIBAPS

summary: In this study, we evaluate the hypothesis that molecular pathways in a cell model of Parkinson’s disease (PD) could be altered depending of glucose levels. We cultured fibroblasts from sporadic PD (sPD; n=4), PD patients carrying LRRK2 mutations (LRRK2-PD; n=3) and healthy controls (HC; n=4) at high (25 mM) and low (5 mM) glucose and analysed the transcriptome profile by using whole RNA sequencing.   We found 1439 differentially expressed transcripts (DET) comparing HC with overall PD cases. These genes are related with THE gene ontology terms cytosqueleton, cell adhesion, protein translation and ribosomes, mitochondrial electron transport between others, when cultured at 25 mM of glucose. However, at 5 mM there are virtually no gene expression changes in PD compared to controls. When compared between 5 and 25 mM condition separately for each group HC and PD, we found 1482 DET in controls, and 3381 in PD cases, but only found altered significant gene ontology terms in PD.  These findings suggest that high glucose levels cause specific molecular changes in fibroblasts which is exacerbated in PD, potentially leading to non adaptive changes. This work emphasizes the importance of energetic balance in PD and the need of further research about the role of glucose levels in clinical studies.

overall_design: Examination of fibroblast expression by RNA seq at low (5 mM) and high (25 mM) glucose levels

first: Ruben

last: Fernandez-Santiago


title: Vitrification preserves murine ovarian follicular cell transcriptome in a 3D encapsulated in vitro follicle growth system

city: Piscataway

first: Yingzheng

last: Wang

state: New Jersey

address: 170 Frelinghuysen Rd, Rm 406

department: Pharmacology and Toxicology

institute: Rutgers University

summary: Vitrification is a method for long-term biological sample cryopreservation that transforms cells into a glass-like state by cooling without causing intra- and extra-cellular ice formation, which is a major driver of cell cryoinjury. Using an alginate hydrogel encapsulated in vitro follicle growth (eIVFG) system, we have recently demonstrated that compared to freshly-harvested follicles, vitrified follicles have normal follicle and oocyte reproductive outcomes as well as comparable expression levels of several genes that are essential for gonadotropin-dependent folliculogenesis and oogenesis. However, it is unknown whether vitrification preserves the molecular signatures of folliculogenesis at the whole transcriptomic level, which is the primary research focus in this study. Multilayered secondary follicles with a diameter of 130 -160 µm were mechanically isolated from 16-day-old CD-1 female mice and vitrified using the closed vitrification method. After a 2-week storage in liquid nitrogen, vitrified follicles were warmed, and together with freshly-harvested follicles, cultured for 8 days using the eIVFG method. Next, mature antral follicles from day 8 were collected for single-follicle RNA sequencing using the SMART-seq RNA-seq method. Principal component analysis (PCA) and Pearson’s correlation analysis revealed that vitrified follicles have similar transcriptomic profiles to fresh follicles. Using the criterion of fold change >2 or <0.5 and a false discovery rate (FDR) adjusted p-value < 0.05, there were 35 differentially expressed genes out of a total of 11,806 detected genes between vitrified and fresh follicles, among which 17 were up-regulated and 18 were down-regulated in vitrified follicles. To the best of our knowledge, none of those differentially expressed genes identified between vitrified and fresh follicles have been shown to be critical to folliculogenesis and oogenesis. Meanwhile, gene ontology (GO) and KEGG pathway analysis over these 35 genes using the functional annotation tool DAVID revealed that no GO terms or signaling pathways were significantly enriched. Furthermore, the expression of several genes essential for the gonadotropin-dependent folliculogenesis and oogenesis were comparable between vitrified and fresh follicles, including granulosa cell-specific genes (Cyp19a1, Amh, Inha, Inhba, Inhbb, and Fshr), theca cell-specific genes (Cyp17a1, Col1a2, and Col3a1), and oocyte-specific genes (Gdf9, Bmp15, Zp1, Zp2, and Zp3). Equally important, Lhcgr, the gene that is primarily expressed in theca cells of preantral follicles and then greatly induced in mural granulosa cells in antral follicles to prepare for the luteinizing hormone (LH) surge and ovulation, also had comparable mRNA expression levels between vitrified and fresh follicles. Taken together, these results demonstrate that vitrification preserves the follicular cell transcriptome and molecular signatures of gonadotropin-dependent folliculogenesis in the eIVFG system. In conclusion, our study re-evaluates individual follicle cryopreservation by using the closed vitrification method in a more in-depth perspective and proves that vitrification preserves the follicular cell transcriptome in the eIVFG system, thus providing a robust model for fertility preservation, conservation of endangered species, and also establishing a high-content ovarian follicle biobank for studying ovarian biology and female reproductive toxicology.

overall_design: Comparison of the transcriptomes of vitrified and fresh follicles

first: Daniela

middle: D

last: Russo

first: Pawat

last: Pattarawat

first: Qiang

first: Mary

last: Zelinski

first: Alex

middle: K

last: Shalek

first: Brittany

last: Goods

first: Shuo

last: Xiao


title: Expression data from NSCLC cells before and after berberine treatment

city: wuxi

first: jiangan

last: li

address: No 68, Zhongshan Road

institute: Wuxi NO.2 People's Hospital of Nanjing Medical University

summary:
Natural products play an important role in the prevention and treatment of lung cancer.
Gene chip technology to analyze the differentially expressed genes in adenocarcinoma after berberine treatment

overall_design: We found that cell cycle and DNA replication pathway were significantly enriched in patients with lung adenocarcinoma compared with normal tissues. After berberine treatment, the expression of FoxM1 closely related to survival and survival related genes in cell cycle and DNA replication pathway were significantly down regulated. Berberine could inhibit the survival of lung adenocarcinoma xenografts and down regulate the expression of FoxM1 in vivo. Berberine interfered with the expression of survival related gene POLE2 in DNA replication through FoxM1.

first: Lulu

last: Ni

first: Ping

last: Sun

first: Xiaochun

last: Fan

first: Zhongjie

last: Li

first: Jiangan

first: Hongli

last: Ren


title: Towards an integrative map of a single cell type's transcription factor landscape

first: Eric

last: Mendenhall

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

overall_design: Refer to individual Series


title: Persistent Cryptosporidium parvum infection leads to the development of tumor microenvironment in an experimental mouse model: Results of a microarray approach

city: Lille

first: David

last: Hot

address: 1 rue du professeur Calmette

department: Center for Infection and Immunity of Lille

institute: Institut Pasteur de Lille

summary: Cryptosporidium parvum has been reported to induce digestive adenocarcinoma in a rodent model of chronic cryptosporidiosis. In the current study, the transcriptomes of C. parvum infected ileo-caecal regions of mice developing tumours were analysed to identifie potential genes involved in development of cancer

overall_design: Whole genome microarray profiling was performed on the C. parvum infected caecum tissue at days 45 and 93 post-infection. The experimental setup consisted of total 15 mice wherein each mouse was considered as an independent experiment. (4 uninfected and 3 infected mice at day 45 post-infection ; 3 uninfected and 5 infected at 93 post-infection)

last: Viscogliosi

first: Gabriela

last: Certad

first: Manasi

last: Sawant


title: RNA-seq Analysis of Enterococcus faecalis in Response to Bacillus subtilis natto Supernatant Treatment

city: Taipei

first: Kung-Ta

last: Lee

address: No.1, Sec. 4, Roosevelt Road

department: Department of Biochemical Science & Technology

country: Taiwan

institute: National Taiwan University

summary: We found that biofilm formation ability of E. faecalis was impacted by culture supernatant of probiotic B. subtilis natto. To further understand how E. faecalis responded to B. subtilis natto supernatant, we searched for differentially expressed genes between E. faecalis treated with or without B. subtilis natto supernatant using RNA-seq analysis.

overall_design: E. faecalis was cultured with or without B. subtilis natto supernatant (10% v/v) anaerobically at 37 °C for 24 hours. Their RNA was then extracted and analyzed.

first: Yu-Chieh

last: Lin


title: Construction of a Competing Endogenous RNA Network and Identification of Potential Regulatory Axes in Gastric Cancer Chemoresistance

city: Guangzhou

first: Shu-Zhong

last: Cui

state: Guangdong

address: hengzhigang road NO78, yuexiu region

department: Department of Gastrointestinal Surgery II

institute: Affiliated Cancer Hospital & Institute of Guangzhou Medical University

summary:
Purpose: Emerging evidence highlights the multifunctional role of noncoding RNAs (ncRNAs) in gastric cancer (GC) chemoresistance. However, the comprehensive expression profile and competing endogenous RNAs (ceRNAs) regulatory network of GC chemoresistance remain unanswered.
Methods: The whole-transcriptome sequencing (RNA sequencing) was performed to comprehensively analyze the differentially expressed (DE) lncRNAs, miRNAs and mRNAs in cisplatin-resistant cells MGC-803/DDP and GC cells MGC-803. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were conducted to investigate the biological functions implicated with the DEncRNAs. Then, the cisplatin-resistant-related ceRNA network and potential regulatory axes were constructed by bioinformatic analysis.
Results: We successfully generated cisplatin-resistant GC cell line MGC-803/DDP. Differential expression analysis showed that a total of 1,936 DElncRNAs, 2,194 DEmRNAs and 174 DEmiRNAs were identified. Functional enrichment analysis indicated that those DEncRNAs were mainly involved in neuroactive ligand-receptor interaction, drug metabolism and Hippo signaling pathway. Subsequently, the cisplatin-resistant-related ceRNA network was constructed with the widely accepted vital chemo-resistant-related genes and signaling pathways. In addition, two constructed regulatory axes (include FAM66C/miR-129-5p/7 mRNAs and SFTA1P/miR-206/FN1 or NRP1) were successfully validated by the Genomic Data Commons (GDC) GC data.
Conclusion: The novel ceRNA network and the potential regulatory axes may provide the most comprehensive view of GC chemoresistance to date. Our findings uncovered potential biomarkers for prognostic prediction and novel therapeutic targets for reversing cisplatin resistance in GC.

overall_design: Transcriptomic profilling of MGC-803 and cisplatin-resistant GC cell line MGC-803/DDP

first: Xian-Zi

last: Yang


title: Transcriptomics of the Djungarian Hamster Hypothalamus

city: Ulm

first: Annika

last: Herwig

address: Albert-Einstein-Allee 11

department: Institute of Neurobiology

institute: Ulm University

summary: Transcriptome analyses were performed to further disentangle hypothalamic control of spontaneous daily torpor and seasonal adaptation, concentrating on the most extreme metabolic and seasonal states of the Djungarian hamster (Phodopus sungorus). The data must be interpreted with respect to the metabolic and seasonal context, as described in the manuscript of the original research.

overall_design: Sampling took place four hours after lights on (Zeitgeber-Time 4, ZT04) in spontaneous daily torpor, an energy-saving mechanism when adapted to short photoperiod (SPHT, n = 4, hypothermic core body temperature), on a torpor-free day when adapted to short photoperiod (SPNT, n = 4, normothermia), or when remained in long photoperiod (LPNT, n = 4, normothermia).

first: Elena

last: Haugg


title: Single cell RNAseq was conducted on mice with TIPE protein knockout to identify the effect of TIPE proteins on immune response [Lung]

city: Philadelphia

first: Mayassa

last: Bou-Dargham

state: Pennsylvania

address: 421 Curie Blvd

department: pathology and laboratory medicine

institute: University of Pennsylvania

summary: Mucosal surfaces are continuously exposed to, and challenged by, numerous commensal and pathogenic organisms. To guard against infections, a majority of the thymus-derived T lymphocytes are deployed at the mucosa. Although chemokines are known to be involved in the mucosal lymphocyte deployment, it is not clear whether lymphocytes enter the mucosa through directed migration or enhanced random migration.  Here we report that TIPE (tumor necrosis factor-a-induced protein 8 (TNFAIP8)-like) proteins mediate directed migration of T lymphocytes into lung, and they are crucial for mucosal immune defense against Streptococcus pneumoniae infection. Knockout of both Tnfaip8 and Tipe2, which encode polarity proteins that control the directionality of lymphocyte migration, significantly reduced the numbers of T lymphocytes in the lung of mice. Compared with wild-type mice, Tnfaip8−/− Tipe2−/− mice also developed more severe infection with more pathogens entering blood circulation upon nasal Streptococcus pneumoniae challenge. Single-cell RNA-sequencing analysis revealed that TIPE proteins selectively affected mucosal homing of a unique subpopulation of T cells, called “T cells-2”, which expresses high levels of Ccr9, Tcf7, and Rag1/2 genes. TNFAIP8 and TIPE2 appear to have overlapping functions since deficiency in both yielded the strongest phenotype. These data demonstrate that TIPE family of proteins are crucial for lung mucosal immunity. Strategies targeting TIPE proteins may help develop  mucosal vaccines or treat inflammatory diseases of the lung.

overall_design: Eight to 10-week-old female naïve mice of WT, TKO, and DKO genotypes (three mice per group) were perfused with PBS, and lungs were collected. Single cell RNAseq was done using Seurat to compare immune cell differences between the 3 genotypes in lung tissues.

first: Mingyue

middle: J

first: Jiyeon

last: Yu

first: Zienab

last: Etweb

first: Honghong

first: Youhai

last: Chen


title: Transcriptome analysis of Con-TD and MCK-TD muscle

city: Ann Arbor

first: Jun Hee

state: MI

address: 109 Zina Pitcher Pl

institute: University of Michigan

summary: RNA-seq data of GTN muscle tissues of Con-TD and MCK-TD mice

overall_design: 10 ug of DNAase I-treated total RNA, purified from GTN muscle tissues of Con-TD and MCK-TD mice, were submitted to BGI for mRNA enrichment, library construction and sequencing (BGISeq-50SE).

first: Chun-Seok

last: Cho

first: Jun

first: Myungjin

last: Kim


title: NFAT5 Controls the Integrity of Skin II

city: Mainz

first: Matthias

last: Klein

address: Langenbeckstrasse 1

department: Inst. for Immunology

institute: University Medical Center Mainz

summary: The skin protects the human body against dehydration and harmful challenges. Keratinocytes (KCs) are the most frequent epidermal cells, and it is anticipated that KC-mediated transport of Na+ ions creates a physiological barrier of high osmolality against the external environment. We studied in KCs the role of NFAT5, a transcription factor whose activity is controlled by osmotic stress. Cultured KCs from adult mice secrete more than 300 proteins, and upon NFAT5 ablation, the secretion of several matrix proteinases, including metalloproteinase-3 (Mmp3) and kallikrein-related peptidase 7 (Klk7), was markedly enhanced. An increase in Mmp3 and Klk7 RNA levels was also detected in transcriptomes of Nfat5-/- KCs, along with increases of numerous components of ‘Epidermal Differentiation Complex’ (EDC), as proline-rich Sprr and S100 proteins. NFAT5 and Mmp3 are co-expressed in basal KCs from fetal and adult skin but not in skin of newborn mice. This is correlated with a strong increase in Mmp3 and Klk7 expression in KCs of newborn mice and suggests, along with the fragile epidermis of adult Nfat5-/- mice, a suppressive effect of NFAT5 on the expression of matrix proteases in skin. Our data suggest that NFAT5 controls the expression of matrix proteases in skin and contributes to the many fold changes during embryonal skin development and skin integrity in adults.

overall_design: Expression profiling by high throughput sequencing of RNA from murine keratinocytes cultivated in vitro for one or for three weeks. Keratinocytes were prepared from the tail of adult mice (4 independent experiments)

first: Khalid

last: Muhammad

first: Edgar

last: Serfling

first: Stefan

last: Klein-Hessling


title: NFAT5 Controls the Integrity of Skin I

overall_design: Expression profiling by high throughput sequencing of RNA from in vitro cultivated keratinocytes prepared from the tail of adult WT or Nfat5-deficient mice (2 independent experiments for both genotypes)


title: Transcriptome-wide analysis of RNA N6-methyladenosine in Adriamycin-resistant acute myeloid leukemia cells

city: Beijing

first: Shu

last: Fang

address: 28 Fuxing Road, Haidian District

institute: Chinese PLA general hospital

summary: N6-Methyladenosine (m6A) is the most abundant post-transcriptional modification in eukaryotes, the imbalance of which is reported to be associated with various pathological processes, including drug resistance. In this study, we analyzed the methylated RNA immunoprecipitation combined with next-generation sequencing (MeRIP-seq) data of AML cell line HL60 and its adriamycin-resistant cell line HL60/ADR. We found a total of 40550 peaks, representing 15640 genes in HL60, and a total of 38834 peaks, representing 15285 genes in HL60/ADR. A total of 4437 differentially methylated m6A peaks within 3461 genes have been found between HL60 and HL60/ADR. Among them, 3587 differentially m6A peaks within 2790 genes were hyper-methylated, and 850 m6A peaks within 671 genes were hypo-methylated. KEGG pathway analysis showed that pathways were enriched in tumor and drug-resistant related signaling pathway. Results of MeRIP-seq showed that fold enrichment of global m6A peaks was higher in HL60/ADR compared to HL60. This study provides a framework for the application of comprehensive mRNA m6A profiling towards acute myeloid leukemia cell line (HL60) and its adriamycin-resistant acute myeloid leukemia cell line (HL60/ADR).

overall_design: mRNA N6-methyladenosine profiles of acute myeloid leukemia cell line (HL60) and its adriamycin-resistant acute myeloid leukemia cell line (HL60/ADR)

first: Chunji

last: Gao

first: Liping

last: Dou


title: NFAT5 Controls the Integrity of Skin


title: Epigenome analysis of doxorubicin-induced cardiotoxicity before and after treatemt of breast cancer patients

city: Little Rock

first: Michael

middle: Anton

last: Bauer

state: United States

address: 4301 W Markham  Slot 782

department: Biomedical Informatics

institute: University of Arkansas for Medical Sciences

summary: This study aimed to determine whether methylation signature of peripheral blood mononuclear cells (PBMCs) prior to the start of the first cycle of DOX-based chemotherapy could predict the risk of cardiotoxicity in breast cancer patients as well as determine if DOX treatment changed methlation profiles. The Illumina Infinium 450 Human DNA methylation Beadchip was used to obtain DNA methylation profiles across approximately 450k CpGs PBMCs samples before and after treatment. Samples included 10 samples from patients with normal ejection fraction after DOX treatment, 9 samples from patients with abnormal ejection fraction (indicative of cardiotoxicity) after DOX treatment.

overall_design: Bisulphite converted DNA from the 37 samples were hybridised to the Illumina Infinium 450k Human Methylation Beadchip

first: Valentina

last: Todorova


title: Modulation of macrophage polarization by HMB [tumor]

city: chapel hill

first: michael

middle: francis

last: coleman

state: North Carolina

address: 235 dauer drive

institute: UNC

summary: to determine whether hydroxymethyl butyrate alters PDAC response to anti-PD1 therapy, mice bearing PANC02 tumors were treated with anti-PD1 with or without HMB supplementation

overall_design: 7 untreated control, 7 anti-PD1 treated, 7 HMB treated, 6 HMB+anti-PD1 treated

last: Coleman

first: Stephen

last: Hursting


title: Modulation of macrophage polarization by HMB


title: Modulation of macrophage polarization by HMB [muscle]

summary: to determine whether hydroxymethyl butyrate alters PDAC response to anti-PD1 therapy, mice bearing PANC02 tumors were treated with anti-PD1 with or without HMB supplementation, gastroc mucsle was isolated from ctrl and HMB groups and analysed by microarray for HMB induced differences in gene expression

overall_design: 7 untreated control, 7 HMB treated,


title: Modulation of macrophage polarization by HMB [macrophage]

summary: to determine whether hydroxymethyl butyrate alters macrophage polarization bone marrow derived macrophages were treated with HMB alone or in combination with LPS for 48h

overall_design: 5 untreated control, 5 LPS treated, 5 HMB treated, 5 HMB+LPS treated


title: RNASeq Analysis of MirA Regulator in Agrobacterium tumefaciens C58

city: Bloomington

first: Clay

last: Fuqua

state: IN

address: 1001 E. Third Street

department: Biology

institute: Indiana University

summary: Performed RNASeq analysis comparing A. tumefaciens C58 (fabrum) harboring a plasmid driving ectopic expression of mirA regulator gene (ATU_RS08050) from Plac promoter with the isogenic strain haboring the same plasmid with no mirA (Vector control)

overall_design: Triplicate cultures of the two A. tumefaciens derivatives were grown in two mL minimal medium (ATGN) in the presence of 500 mM IPTG and 300 μg/mL to an optical density at 600 nm (OD600) of ~0.6, and total RNA was extracted for RNA Seq analysis.

first: Melene

last: Alakavuklar


title: Cubilin-, Megalin- and Dab2-dependent transcription revealed by CRISPR/Cas9 knockout in kidney proximal tubule cells

city: Pittsburgh

first: B. Rhodes

last: Ford

state: PA

address: 4401 Penn Ave.

department: Department of Pediatrics

institute: University of Pittsburgh

summary: The multiligand receptor megalin and its endocytic adaptor protein Dab2 play essential roles in maintaining the integrity of the apical endocytic pathway of proximal tubule cells, and have complex and poorly understood roles in the development of chronic kidney disease. Here we used RNASeq in CRISPR/Cas9 knockout technology in a well-differentiated cell culture model to identify PT-specific transcriptional changes that are directly consequent to the loss of megalin (Lrp2), cubilin (Cubn), or Dab2 (Dab2) expression.

overall_design: CRISPR/Cas9 knockout Opossum Kidney (OK) cells cultured under orbital shear stress to enhance differentiation were subjected to RNASeq.

first: B

first: Amanda

last: Poholek

first: Ora

last: Weisz


title: Rybp Modulates Embryonic Neurogenesis Involving the Notch Signaling Pathway in a PRC1-Independent Manner

city: hangzhou

first: wenzheng

last: qu

address: Kaixuan Road

institute: Zhejiang University

summary: Rybp plays pivotal roles in regulating organic development, spermatogenesis, apoptosis and cancer. However, it remains unknown regarding the function of Rybp in regulating neuronal development. In the present study, we have shown that the depletion of Rybp in embryonic neural progenitor cells (NPCs) impairs proliferation and promotes neuronal differentiation of embryonic NPCs. In additon, Rybp deficiency results in alterations in dendritic shape of neuron.

overall_design: two replicates in ctrl and shRybp group (proliferated neural progenitor cells)

first: Qian

last: Li

first: Junchen

last: Chen

first: Wenzheng

last: Qu

first: Xuekun


title: Transcriptome-wide N6-methyladenosine proﬁling of bovine skeletal myoblasts differentiation

city: Shenzhen

first: Xinran

last: Yang

state: --- Select One ---

address: Xueyuan street 1068, Shenzhen

department: Shenzhen Institute of Synthetic Biology

institute: Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences

summary: We ascertain that mRNA m6A methylation exhibits declined change during bovine skeletal myoblast myogenic differentiation. RNA-seq and m6A-seq (MeRIP-seq) analysis reveal that m6A methylation is an abundant modification in the mRNA of bovine myoblast and myotubes, and the m6A sites are mainly enriched near the stop codons and the 3′ untranslated regions.

overall_design: mRNA m6A methylation profiles in bovine proliferating myoblasts (GM, 80% confluence, cultured in growth medium) and differentiated myotubes (DM, 100% confluence, cultured in differentiation medium for 4 days) were generated by m6A-seq, in triplicate, using Illumina Novaseq 6000.

first: Linsen

last: Zan


title: Expression data from wild type and Bach1 knock out ventral mid brains of two month old mice.

city: Charleston

first: Michael

last: Ostrowski

state: SC

address: 86 Jonathan Lucas street

department: Biochemistry and Molecular Biology

institute: Medical University of South Carolina

summary: Bach1 is a known repressor of NRF2 transcription factor which governs oxidative stress during pathophysiology of Parkinson's disease. NRF2 activation in ventral midbrain is associated with protection against oxidative stress induced apoptosis of DA neurons. In this study we hve evaluated the effect of loss of Bach1 fucntion in ventral mid brains.

overall_design: Ventral mid brains from two month old male wilt type or Bach1 knock out mice were disected out and total RNA was prepared using Trizol method followed by quiagen easy cleanup. Total RNA was used for microarray.

first: Sudarshana

last: Sharma

first: Bobby

last: Thomas


title: Functionalized carbon nanotube toxicity in Arabidopsis leaves

city: Berkeley

first: Markita

middle: Patricia

last: Landry

state: California

address: Stanley Hall

department: Chemical and Biomolecular Engineering

institute: University of California Berkeley

summary: Polyethilenimine (PEI) functionalized single walled carbon nanotubes (SWNTs) and carbon-based nanomaterials enable delivery of DNA and RNA in plants. Given the broad-scale use of PEI-functionalized nanomaterials in plants, we sought to investigate the reaction of plant tissues to treatment with PEI-SWNTs and pristine SWNTs. To this end, we infiltrated Arabidopsis thaliana leaves with pristine single walled carbon nanotubes used in RNA silencing applications (SWNTs) and polyethyleneimine-functionalized SWNTs used for plasmid DNA delivery (PEI-SWNTs). We used Arabidopsis as it is a well characterized model plant, for which genomic and detailed gene function information is readily available. To minimize the effects caused by the introduction of exogenous nucleic acids, in SWNT preparations we used single stranded RNA targeting Green Fluorescent Protein (GFP) with no target sequence in the Arabidopsis genome, and a plasmid that expresses GFP in PEI-SWNT preparations. For our experiments herein, we used ~25-50 fold higher concentrations of SWNTs and PEI-SWNTs compared to standard concentrations used in biomolecule delivery assays. Water-infiltrated plant leaves served as a negative control to distinguish between the SWNT-specific response and the response to the infiltration process itself. We performed RNA sequencing (RNA-seq) with RNA extracted from leaves two days after infiltration to identify changes in the leaf transcriptomic profile in response to the three treatments, compared to non-infiltrated leaves.

overall_design: Young leaves of 6-week old wild-type Col-0 Arabidopsis thaliana plants in vegetative stage were selected to be fully infiltrated (approx. vol 40 µL) with a 1 mL needleless syringe (BD, cat. no. 14-823-434) loaded with water, SWNTs+ssRNA (50 ng/µL) or pDNA+PEI-SWNTs (50 ng/µL) prepared as described previously. Two days after infiltration, five biological replicates containing four leaves of each treatment from different plants and from non-treated plants were collected in a 2 mL Eppendorf tube with two 3.2 mm chrome steel beads (RPI, cat. no. 9840) and flash frozen in liquid N2 immediately. Frozen samples were ground in a Mini-beadbeater (Biospec Products, cat. no. 3110Bx) tissue homogenizer for 5 seconds at 25 Hz frequency, twice.  RNA was extracted using RNeasy Plant Mini Kit (Qiagen cat. 74904) using RNase-Free DNase (Qiagen cat. 79254) following manufacturer instructions. Total RNA concentration was measured using the Qubit™ RNA BR Assay Kit (Thermo Fisher). RNA quality was checked using the 2100 Bioanalyzer with RNA 6000 Nano Kit (Agilent). RNA integrity number (RIN) scores were confirmed to be >8. Libraries were prepared using Kapa Biosystems library preparation kit with mRNA selection with poly-A magnetic beads. Libraries were pooled and sequenced on an Illumina NovaSeq S4 flow cell in a NovaSeq 6000 Platform with 150 paired end reads.

first: Eduardo

last: Gonzalez-Grandio

first: Gozde

last: Sultan Demirer

first: Darwin

middle: P


title: Genome-wide maps in MDA-MB-231 cells treated with or without HET0016 (5 μM).

city: Nanjing

first: Lufeng

last: Zheng

address: Tongjia Xiang 24

department: School of Life Science and Technology, Jiangsu Key Laboratory of Carcinogenesis and Intervention

institute: China Pharmaceutical University

summary: Analysis of MDA-MB-231 cells following  HET0016 treatment or not. HET0016 regulates various mRNA expression in MDA-MB-231 cells.Results provide insight into the role of mRNAs-involved mechanisms underlying HET0016-mediated effects on breast cancer stemness.

overall_design: MRNA profiles of MDA-MB-231 cells treated with or without HET0016 were generated by deep sequencing, in two repeats, using Illumina GAIIx.

first: Tao

last: Xi


title: Effect of pyrvinium pamoate on transcriptome and signaling pathways in FLT3-ITD acute leukemic cell line Molm13

first: Yu-Hsuan

last: Fu

address: No.1, Chang-Te St

department: Department of Clinical Laboratory Sciences and Medical Biotechnology

summary: To identify molecular effects of a classical anthelmintic pyrvinium pamoate(PP), we applied gene expression profiling in human  acute leukemic cell line FLT3-ITD+ Molm13 using Whole Transcriptome Shotgun Sequencing (RNA-seq) after 6 h treatment with 50nM or 100nM pyrvinium. We got 94 and 219 differentially expressed genes (DEGs) compared with the control group, respectively. Among 94 DEGs in the 50nM pyrvinium group, 62 were upregulated and 32 were downregulated and corresponded 162 upregulated and 57 downregulated DEGs in the 100nM pyrvinium group.

overall_design: Gene expression in Molm13 was measured after exposure for 6h to 50nM or 100nM pyrvinium or to the vehicle control (DMSO).

first: Liang-In

last: Lin


title: Control and FOP Human iPSC derived myogenic cell single cell RNA sequencing

city: San Francisco

first: Emilie

last: Barruet

address: 513 Parnassus Av

institute: UCSF

summary: We compared the transcriptome of sorted muscle stem/progenitor cells differentiated from control and FOP (ACVR1 R206H (c.617>A)) human induced pluripotent stem cells.

overall_design: single cell RNA sequencing of sorted control and FOP HNK1-CD45-CD31- CXCR4+CD29+CD56dim cells derived from hiPSC myogenic differentiation day 50.

first: Tania

last: Moody


title: Expression data from MCF-10A cell lines stably expressed with EGFP or EGFP-ARHGAP4

city: Toyonaka

first: Shinji

last: Degcuhi

state: Osaka

address: Machikaneyama 1-3

department: Mechanical Science and Bioengineering

country: Japan

institute: Osaka University

summary: ARHGAP4 is a key cytoskeletal regulator in epithelial morphology and EMT process. We used microarrays to clarify the gene expression in ARHGAP4-induced anti-EMT mechanism.

overall_design: MCF-10A mammary epithelial cells were stabley expressed with either EGFP-ARHGAP4 or a EGFP vector were harvested for RNA extraction and hybridization on Affymertix microarrays.

first: Kang

first: Tsubasa

middle: S

last: Matsui

last: Deguchi


title: microRNA expression changes after knocking out MYEOV in two human pancreatic cancer cell lines

city: Shanghai

first: Haiyang

last: Hu

address: 320 Yueyang Road

institute: PICB

summary: Pancreatic cancer (PC) remains a highly lethal malignancy worldwide. As metastasis and malignant proliferation are primarily responsible for poor clinical outcomes of PC, it is imminent to dig out the pivotal gene involved in the process as well as its underlying molecular mechanism. In this study, through analysis of TCGA and GTEx data, we found that the expression level of MYEOV was obviously increased in carcinoma tissues relative to healthy ones and associated with poor survival in PC patients. The elevated abundance of MYEOV was positively correlated with enhanced cell proliferation, invasion and migration in vivo and in vitro. The global transcriptome analysis of MYEOV-depleted PC cells revealed the downregulation of various genes involved in active cell proliferation, which indicated that MYEOV overexpression was critical for PC progression. MiRNA-seq analysis showed that MYEOV had a regulatory effect on the expression levels of miR-17-5p and miR-93-5p, depletion of which resulted in reduced cell proliferation, invasion and migration as observed in MYEOV-knockdown PC cells. Such effect was imposed by MYEOV through affecting enrichment of the transcription factor c-myc at the gene promoter regions of the two miRNAs. Furthermore, a complex containing MYEOV and MYC was confirmed to exist in cell nucleus, providing convictive evidence for the association of MYEOV with MYC. Together, these results suggested that the axis of MYEOV-MYC-miR-17/93-5p could be vital for PC progression and could act as a potential therapeutic target to interrupt cell proliferation which will benefit treatment and management of PC patients.

overall_design: small RNAs after knocking out MYEOV in two human pancreatic cancer cell lines were isolated and sequenced by deep sequencing using Illumina HiSeq 4000 from novogene.

first: Juanjuan

last: Zhu


title: Integrative omics approaches revealed a crosstalk among phytohormones during tuberous root development in cassava

city: Yokohama

first: motoaki

last: seki

state: Kanagawa

address: Suehiro-cho 1-7-22, Tsurumi-ku

department: CSRS

institute: RIKEN

summary: Tuberous root formation is a complex process consisting of phase changes as well as cell division and elongation for radial growth. We performed an integrated analysis to clarify the relationships among metabolites, phytohormones, and gene transcription during tuberous root formation in cassava (Manihot esculenta Crantz). We also confirmed the effects of the auxin (AUX), cytokinin (CK), abscisic acid (ABA), jasmonic acid (JA), gibberellin (GA), brassinosteroid (BR), salicylic acid (SA), and indole-3-acetic acid conjugated with aspartic acid (IAAsp) on tuberous root development. An integrated analysis of metabolites and gene expression indicated the expression levels of several genes encoding enzymes involved in starch biosynthesis and sucrose metabolism are up-regulated during tuberous root development, which is consistent with the accumulation of starch, sugar phosphates, and nucleotides. An integrated analysis of phytohormones and gene transcripts revealed a relationship among AUX signaling, CK signaling, and BR signaling, with AUX, CK, and BR inducing tuberous root development. In contrast, ABA and JA inhibited tuberous root development. These phenomena might represent the differences between stem tubers (e.g., potato) and root tubers (e.g., cassava). On the basis of these results, a phytohormonal regulatory model for tuberous root development was constructed. This model may be useful for future phytohormonal studies involving cassava.

overall_design: The cassava samples were prepared in Rayong filed crop center at Thailand. Total RNA was prepared from the cassava samples and used for the microarray hybridization. Three replicative hybridization experiments were carried out using the independent biological samples.

first: Yoshinori

last: Utsumi

first: Maho

last: Tanaka

first: Chikako

first: Satoshi

last: Takahashi

first: Akihiro

first: Atsushi

last: Fukushima

first: Makoto

last: Kobayashi

first: Ryosuke

last: Sasaki

first: Akira

last: Oikawa

first: Miyako

last: Kusano

first: Kazuki

last: Saito

first: Hitoshi

last: Sakakibara

first: Mikiko

last: Kojima

first: Punchapat

last: Sojikul

first: Jarunya

last: Narangajavana

first: Motoaki

last: Seki


title: Loss of ATF4 leads to functional aging-like attrition of adult hematopoietic stem cells

city: Guangzhou

first: Yan

last: Sun

address: Zhong shan 2nd Road, Building 74

institute: Sun Yat-sen University

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: Comparison of children and adults’ lung tissues by scRNA-seq

city: NanJing

first: Fei

last: jia

state: Jiangsu

address: Xinghuo Road

institute: singleron

summary: The present study for the first time described the features of children’s lung by scRNA-seq and compared the results to the data acquired from healthy adults (GSE122960). We analyzed the expression levels of viral-entry associated genes in both children and adults’ lung tissues by single cell RNA sequencing (scRNA-seq) to explore whether the expression levels of these genes might contribute to the milder symptoms in SARS-CoV-2 infected children. The results of scRNA-seq showed comparable expression of the key genes for SARS-CoV-2 entry in children and adults, including ACE2, TMPRSS2 and FURIN, suggesting that instead of lower virus intrusion rate, other factors are more likely to be the key reasons for the milder symptoms of SARS-CoV-2 infected children.

overall_design: Normal lung tissues from 10 children undergoing biopsy or surgery for various reasons were collected for sc-RNA seq. The study was approved by the Institutional Review Board and the Ethics Committee of Shanghai Children’s Medical Center (SCMCIRB-K2020034), and written informed consent was obtained from the parents of each patient. The public data of 8 healthy adults were downloaded from Gene Expression Omnibus (GSE122960). We used Canonical Correlation Analysis (CCA) implemented in Seurat V3 (https://github.com/satijalab/seurat) to integrate the two datasets for the feature comparison of children and adults’ lung tissues.

first: Yue

last: Tao

first: Ruwen

last: Yang

first: Chen

last: Wen

first: Jue

last: Fan

first: Jing

last: Ma

first: Qiao

last: He

first: Zhiguang

last: Zhao

first: Xinyu

last: Song

last: Hao

first: Guocheng

last: Shi

first: Minzhi

last: Yin

last: Fang

first: Hao

last: Zhang

first: Huiwen

last: Chen

first: X

last: Mo


title: RNA sequencing profiling of placental tissues from placenta accreta and control pregnancies

city: Shenyang

first: Caixia

last: Liu

state: Liaoning

address: No.36 SanHao Street, HePing Area

department: Department of Obstetrics and Gynecology

institute: Shengjing Hospital of China Medical

summary: Placenta accreta is a major cause of maternal morbidity and mortality in modern obstetrics. The study aims to identify the differently expressed lncRNA and mRNA in placenta accreta patients compared with controls and to determine biological pathways, which provides a novel insight ingto thepathogenesis of placneta accreta.

overall_design: Total RNA from placental tissues obtained from 5 placenta accreta and 5 control patients at Caesarean section were extracted and performed RNA-seq.

first: Chong

last: Qiao


title: SP80-3280 growth and maturation field 1

city: Sao Paulo

first: Augusto

middle: Lima

last: Diniz

state: SP

address: Av Lineu Prestes

department: Biochemistry

country: Brazil

institute: University of Sao Paulo

summary: A field experiment was conducted at the Agricultural Sciences Center of the Federal University of Sao Carlos in Araras (22°21'25''S and 47°23'3''W) in the state of Sao Paulo, Brazil. Trial plots of SP-3280 consisted of four rows of 10 m long and spaced 1.35m apart. The field experiment was initiated in April 2012 and extended up until May 2013, representing the conditions under which one-year-and-a-half sugarcane crops are cultivated.

overall_design: Aiming to carry out observations throughout growth and development, tissue samples of the +1 leaves (L1) and upper (I1), immature (I5) and mature (I9) internodes were collected from two plots (two technical replicates) after 4, 8, 11 and 13 months of planting. RNA was extracted for four biological replicates, two from each plot, using the TriZol method, treated with DNase I and purified. A pool of samples from leaves and a pool of internodes was used as a 'reference sample' for hybridization experiments on a customized 4x44K oligoarray (Agilent Technologies) for sugarcane (CaneRegNet). The oligoarrays were read using the GenePix 4000B scanner device (Molecular Devices) and the fluorescence data was processed by Feature Extraction software 9.5.3 (Agilent Technologies).

first: Carolina

last: Lembke


title: Expression data from PC-3 cells with increased in vivo metastatic potential compared to parental tumor cells [RT-PCR]

city: Barcelona

first: Marta

last: Garcia Lopez

address: Pg. de la Vall d'Hebron, 119-129

department: Oncology

institute: Vall d'Hebron Research Institute

summary: Description of molecular changes of prostate cancer cells with increased in vivo metastatic potential

overall_design: The analysis is composed of two samples with high and low in vivo metastatic potential

last: Garcia


title: Impact of exogenous caffeine on regulatory networks of microRNAs in response to Colletotrichum gloeosporioides in tea plant.

first: Anburaj

last: Jeyaraj

address: No. 1 Weigang

institute: Nanjing Agricultural University

summary: Anthracnose, caused by Colletotrichum gloeosporioides is one of the most serious diseases of tea plant [Camellia sinensis (L.) O. Kuntze]. MicroRNAs are key modulators of gene expression in defense responses and plant immunity; although, foliar application of exogenous caffeine in anthracnose disease control management has proven to be effective, miRNA-mediated regulatory mechanisms underlying caffeine-induced plant defense response to C. gloeosporioides remain unexplored in tea plant. Using high-throughput-sequencing, 24 miRNA sequencing data sets and 8 degradome data sets were generated from the susceptible cultivar Longjing43 (LJ43) and the resistant cultivar Zhongcha108 (ZC108) leaves treated with CK (Water), C. gloeosporioides-inoculation (CgI), exogenous caffeine (CN) and CgI + CN. Using sRNA sequencing, 424 conserved miRNAs and 417 novel miRNAs were identified; of these, 146 and 130 miRNAs were differentially expressed under CgI + CN treatment in the LJ43 and ZC108, respectively. Degradome sequencing identified 599 targets predicted to be cleaved by 210 conserved and 70 novel miRNAs. Majority of the annotated targets were found to involve in regulation of transcription factors, oxidation-reduction and metabolic process for plant growth and development as well as stress responses in tea plant against C. gloeosporioides stress. The expression pattern of eight miRNAs and their targets were validated by qRT-PCR, and correlation analysis of csn-miR164a_R+1_1ss21AG/NAC-17 and csn-miR396b-5p/GRF-1 showed highly significant negative R-value at 7th dpi under CgI + CN in the LJ43. This study provides important insights into the novel approach of exogenous caffeine-induced miRNAs dynamically exerts its fungicidal activity through regulating JA/ET signaling pathway, thereby accurately switch on LJ43 susceptibility nature to resistance activity against C. gloeosporioides infection.

overall_design: In order to identify the microRNAs and their target genes in the tea plant, a total of 24 sRNA libraries and 8 degradome libraries were constructed from the susceptible cultivar Longjing (LJ43) and anthracnose-resistant cultivar Zhongcha (ZC108) leaves collected after 7 days of the mock-inoculated control (LJCK and ZCCK), the C. gloeosporioides-inoculated treatment (LJCg and ZCCg), the exogenous caffeine treatment (LJCN and ZCCN) and the C. gloeosporioides inoculation with exogenous caffeine treatment (LJCgCN and ZCCgCN); three independent replicates of each treatment were sequenced for sRNA sequencing using the Illumina Hiseq2500  platform.

first: Tamilselvi

last: Elango

first: Xinghui

last: Li


title: Gene expression changes in wide-type P2X7 overexpressed MLL-AF9 induced mouse acute myeloid leukemia (AML)

city: Tianjin

first: Guo Guang

last: Zheng

state: Tianjin

address: Blood Hospital,288 Nanjing Road,Heping District

department: Institute of Hematology & Blood Hospital

institute: Chinese Academy of Medical Science& Peking Union  Medical College

summary:
P2X7 was significantly up-regulated in leukemia patients, especially in AML (MLL-AF9) and often related to poor prognosis.We compared the transcriptomic changes in MLL-AF9 induced mouse AML and overexpressed wP2X7 in MLL-AF9 induced AML. Engaged to explore the mechanism of P2X7 in leukemia progression.
Mouse AML was induced by expressing MLL-AF9 in mouse HSPCs. Leukemia cells were divided into two groups, c-kit+ and c-kit-. Due to leukemia cells were nearly 95% c-kit+ in P2X7-overexpressed AML cells, we set up four groups of leukemia cells, namely leukemia total cells (V total), leukemia c-kit positive cells (V c-kit+), leukemia c-kit negative cells (V c-kit-), overexpressed wide type P2X7 leukemia cells (wP2X7).

overall_design: single-color experiment using Agilent Mouse GE 8x60K Microarray Cat.# G4858A-028005

first: Xiao

last: Yang

first: Wenli

last: Feng

first: Guoguang


title: Expression data from PC-3 cells with increased in vivo metastatic potential compared to parental tumor cells

type:
Expression profiling by array
Expression profiling by RT-PCR


title: RNA-Seq Analysis of mouse pancreatic cancer cell lines derived from KPC mice and Reprogrammed somatic cells

city: London

first: Yaohe

last: Wang

address: John Vane Science Centre,  Charterhouse Square

department: Centre for Molecular Oncology

institute: Barts Cancer Institute

summary: We report the gene expression profile of six murine pancratic cancer cell lines, and also compare the similarities of gene expression between KPC mice-derived tumor cells and Regrogrammed somatic cells-derived tumor cells.

overall_design: The whole RNA deep sequencing was performed for the six mouse pancreatic cancer cell lines. The gene experssion profiles were bioinformatically analyzed.

first: Shuangshuang

last: Lu


title: Expression data from PC-3 cells with increased in vivo metastatic potential compared to parental tumor cells [Array]

summary: Description of molecular changes of prostate cancer cells with increased in vivo metastatic potential compared to parental tumor cells


title: Transcriptomic alteration after miR-6126 tranfection into HepG2-NTCP

status: Public on Dec 28 2021

city: Takamatsu

first: Koji

last: Fujita

state: Kagawa

address: Saiwai 1-1

institute: Kagawa University

summary: Aim: Hepatitis B virus (HBV) infection is one of the most serious global health problems. Our previous study revealed that an increase in the miR-6126 serum level over one year of pegylated interferon therapy predicted a decrease in hepatitis B surface (HBs) antigens. We aimed to clarify whether miR-6126 downregulated the expression level of sodium taurocholate cotransporting polypeptide (NTCP), a host cell receptor required for HBV entry.   Methods: HepG2-NTCP and PXB cells were utilized to evaluate the expression level of NTCP after transfection with miR-6126. The protein expression level of NTCP was evaluated using Western blot analysis and immunostaining. The expression profile of messenger RNAs was evaluated using next-generation sequencing to search for direct targets of miR-6126.

overall_design: Samples were triplicated; miR-6126-transfected group and negative control.


title: Loss of ATF4 leads to functional aging-like attrition of adult hematopoietic stem cells [RNA-seq]

first: Yan

last: Sun

state: Guangdong

summary: We collected significant amount of phenotypic and mechanistic data from a ATF4 knockout mouse model and demonstrated that HSC defects with an aging-like phenotype (expanded pool of phenotypical HSCs, decreased number of functional HSCs, impaired repopulating and self-renewal capacities of HSCs and myeloid bias) occurred in the ATF4 KO mice, suggesting that not only ATF4 indeed represents a pivotal factor for adult HSC function but also we had successfully constructed an ideal and attractive model to study aging and aging-related disease.

overall_design: This dataset contains RNA-seq experiments of long-term HSCs isolated from ATF4WT or ATF4 CKO mice.

first: Mengfeng


title: Paternal high-fat diet elicits early-onset se-specific islet inflammation in rat progeny

city: Wallace Wurth Building, Sydney

first: Margaret

last: Morris

state: NSW

address: University of New South Wales

department: School of Medical Sciences

institute: University of New South Wales

summary: Progressive β–cell failure and apoptosis, resultant of innate immune system activation1,2 is gaining traction as a converging point for type 1 (T1D) and type 2 (T2D). Islet inflammation (insulitis), a hallmark of T1D, occurs typically during the initiation phase of the disease, subsequently orchestrating an autoimmune assault against β–cells. Whether this is a primary event or a consequence of glucotoxicity or lipotoxicity is undetermined3 but metabolic stress is demonstrated to prompt islet inflammation1,2. Here we show that paternal consumption of high fat diet (HFD) invoked distinct immuno-inflammatory transcriptional response in the pancreatic islets of their weanling daughters, in contrast to compensatory changes in the sons. Importantly, these changes occurred in conjunction with transition in islet repertoire resembling the spectrum of T2D, along with progressive development of β–cell dysfunction4. Note, these females were lean, normolipidaemic and insulin sensitive4. These findings provide experimental support for the notion that islet inflammation could be an antecedent event in T2D, leading to β–cell secretory defect, repair/regeneration and apoptosis. Importantly, these effects were transmitted via paternal nutrient stress to offspring.

overall_design: Male F0 Sprague Dawley founders were assigned to high fat diet (HFD) or control diet for 12 weeks, then mated with chow-fed female Sprague Dawley as previously decribed4. Litters from 8 control and 9 HFD fathers were included. Eligible litter size was 12-16 pups and litters were standardized to 12 pups at postnatal day-1 (P1). Additional animals were killed for post-mortem analysis. At P20, one cohort of animals was euthanized for pancreas histology and postmortem analyses. Littermates were weaned onto chow and islets harvested from another cohort killed at week-4 to -5. All animals were euthanized in a non-fasting state. Islet transcriptome data were extracted from Affymetrix GeneChip® Rat Gene ST 1.0 arrays [n = 10 controls and 10 HFD (5 females, 5 males), (Ramaciotti Centre for Genomics, UNSW)], representing one biological replicate per litter. Effects of paternal diets across both sexes were compared using two way ANOVA; data were also compared for each sex separately, based on robust multi-array average (RMA)3 normalized gene expression in log 2 space. Differentially expressed genes (P < 0.05, unadjusted) were then functionally annotated according to Gene Ontology (GO) terms and enriched terms were calculated using DAVID4,5. P < 0.05 was considered statistically significant. All experimental protocols were approved by the Animal Care and Ethics Committee, UNSW, Australia.

first: Sheau-Fang

last: Ng

first: Ruby

last: Lin


title: Loss of ATF4 leads to functional aging-like attrition of adult hematopoietic stem cells [ChIP-seq]

summary: Human acute myeloid leukemia (AML) KG1a cells  or mouse BM cells (mouse bone morrow cells were employed for each ChIP assay. The ChIP procedure was performed according to a previously described protocol (Lee et al., 2006; Ying et al., 2017), using anti-ATF4 antibody (Abcam)

overall_design: ChIP-sequencing (ChIP-seq) of ATF4  in human AML KG1a cells and mouse BM cells. Input samples included.


title: Small-Molecule-Driven Direct Reprogramming of Fibroblasts into functional Sertoli-like cells as a model for male reproductive toxicology

first: Quan

address: West Huangpu Avenue

institute: Jinan University

summary: We report the generation of functional Sertoli-like cells from mice fibroblasts using only chemical cocktails, I-bet151 and Riluzole (IR). CiSCs possess similar gene expression profiles and biological functions to endogenous Sertoli cells and are highly sensitive to reproductive toxicants.

overall_design: A total of 6 samples（2 CiSCs, 2 MEFs, 2 MSCs） were tested using the BGISEQ platform for this project to prove that the CiSC resemble Sertoli cell in genome-wide gene expression profile.


title: Effects of dietary obesity in fathers on gene expression of fat in the female offspring (miRNA data)

summary: The global prevalence of obesity is increasing across age and gender. The rising burden of obesity in young people contributes to the early emergence of type 2 diabetes. Having one parent obese is an independent risk factor for childhood obesity. While the detrimental impact of diet-induced maternal obesity on offspring is well established, the extent of the contribution of obese fathers is unclear, as is the role of non-genetic factors in the casual pathway. Here we show that paternal high fat diet exposure programmed β-cell ‘dysfunction’ in their F1 female offspring. Chronic high fat diet consumption in Sprague Dawley fathers led to increased body weight, adiposity, impaired glucose tolerance and insulin sensitivity. Relative to controls, their female offspring had lower body weight at day-1, increased pubertal growth rate, impaired insulin secretion and glucose tolerance, in the absence of obesity or increased adiposity.  Paternal high fat diet altered the expression of 211 pancreatic islet genes in adult female offspring (P < 0.001); genes belonged to 8 functional clusters, including calcium ion binding, primary metabolic processes and ATP binding, and organ/system development.  Broader KEGG pathway analysis of 2014 genes differentially expressed at the P < 0.01 level further demonstrated involvement of insulin and calcium signaling, and MAPK pathways. This is the first reported study in mammals describing non-genetic, intergenerational transmission of metabolic sequelae of high fat diet from father to offspring. These findings support a role of fathers in metabolic programming of offspring and form a framework for further studies.

overall_design: F0 founders were male Sprague Dawley rats, divided into two groups: high fat (HF) and control. The HF fathers were given commercially prepared high-fat pellets (43% as fat), while the controls ate standard laboratory chow (9% as fat). The two groups of fathers had distinct phenotypes; the HF fathers were significantly heavier with increased adiposity, and they were also glucose intolerant and insulin resistant. At 15 weeks of age, fathers were mated with normal females consuming chow to generate the F1 offspring. Only female offspring were studied. Female offspring were weaned unto standard laboratory chow at 3 weeks. At 6 and 12 weeks, an intraperitoneal glucose tolerance test (IpGTT) was performed to measure blood glucose and insulin profile; at 11 weeks, an intraperitoneal insulin tolerance test was done. The body weight and adiposity of these offspring were not different between the two groups. The HF offspring had glucose intolerance and impaired glucose-induced insulin response, mainly at the acute phase, observed since 6 weeks. The IpITT was not different between groups. At 14 weeks, fat was harvested from the two groups of offspring.

first: Sheau


title: Single Nuclei RNA Sequencing Analysis of Cardiac Microthrombi in Fatal Covid-19

city: Utica

first: Nathan

last: Tucker

state: NY

address: 2150 Bleecker St

institute: Masonic Medical Research Institute

summary: Cardiac microthrombi have been variably identified at autopsy of Covid-19 decedents. Little is known about the morphologic and molecular changes associated with cardiac microthrombi and whether predictive biomarkers exist. We sought to determine the prevalence, pathogenesis, and biomarker risk factors of Covid-19-associated cardiac microthrombi. In addition to histology and immunohistochemical analyses, we investigated right verticles from 8 Covid-19 decedents via single nuclei RNA sequencing for cell-type specific transcriptional differences between hearts with and without microthrombi, as well as between Covid-19 decedents and publicly available non-Covid-19 donor controls.

overall_design: Compare differential gene expression in right ventricles of fatal Covid-19 hearts between patients that developed microthrombi and those that did not.

first: Nobuaki

last: Fukuma

first: Michelle

last: Hulke

first: Michael

last: Brener

first: Stephanie

last: Golob

first: Robert

last: Zilinyi

first: Zhipend

last: Zhou

first: Christos

last: Tzimas

first: Ilaria

last: Russo

first: Claire

last: McGroder

first: Ryan

last: Pfeiffer

first: Alexander

last: Cong

first: Geping

last: Zhang

first: Daniel

last: Burkoff

first: Martin

last: Leon

first: Mathew

last: Maurer

first: Jeffery

last: Moses

first: Anne-Cartin

last: Uhlemann

first: Hibshoosh

last: Hanina

first: Nir

last: Uriel

first: Matthias

last: Szabolcs

first: Bjorn

last: Redfors

first: Charles

last: Marboe

first: Matthew

last: Baldwin

first: Emily

last: Tsai


title: Applying defective interfering viral genome bioinformatics for detection of coronavirus subgenomic RNAs

city: Paris

first: Rachel

last: Legendre

address: 28, rue du docteur Roux

department: Research and Resource Center for Scientific Informatics

institute: Institut Pasteur

summary: Coronavirus RNA-dependent RNA polymerases produce subgenomic RNAs (sgRNAs) that encode viral structural and accessory proteins. The kinetics and efficiency of sgRNAs production during viral replication in different cell types or sgRNA transcription by individual viral strains or variants are yet to be studied to shed light on fundamental mechanisms necessary for viral replication. User-friendly bioinformatic tools to detect and quantify sgRNA production are urgently needed to study a growing number of next-generation sequencing (NGS) data of SARS-CoV-2. Starting from DI-tector, a bioinformatic tool for the detection of viral defective interfering genomes, here we introduced sgDI-tector to identify and quantify sgRNA in SARS-CoV-2 NGS data. This new tool allowed detection of sgRNA without initial knowledge of the transcription-regulatory sequences. As a proof of principle, we analyzed new data sets and successfully detected the nested set of sgRNAs produced with the ranking M>ORF3a>N>ORF6>ORF7a>ORF8>S>E>ORF7b. Our study also compared, for the first time for SARS-CoV-2, the level of sgRNA production with other types of viral RNA products such as defective interfering viral genomes.

sample_organism: Severe acute respiratory syndrome coronavirus 2

overall_design: three biological replicates of SARS-CoV-2 infected  (MOI1)HEK293-ACE2 cells were performed.

first: Andrea

last: Di Gioacchino

first: Yannis

last: Rahou

first: Valérie

last: Najburg

first: Pierre

last: Charneau

first: Benjamin

last: Greenbaum

first: Frédéric

last: Tangy

first: Sylvie

last: van der Werf

first: Simona

last: Cocco

first: Anastasia

middle: V

last: Komarova


title: RNA-Sequencing of Aged Mouse Oocytes with in vivo Nicotinamide Mononucleotide (NMN) Treatment

city: Hong Kong

first: Tin Lap

last: Lee

address: The Chinese University of Hong Kong, Shatin, NT, Hong Kong

country: Hong Kong

institute: The Chinese University of Hong Kong

summary: We highlighted the effects of in vivo NMN administration on aged mouse oocyte transcriptome.

overall_design: RNA-sequencing data of GV and MII oocytes of in vivo NMN-treated aged mice and control young and aged mice

first: WingTung

first: TinLap


title: Effects of dietary obesity in fathers on gene expression of islets in the female offspring (miRNA data)

first: Margaret

last: Morris

overall_design: F0 founders were male Sprague Dawley rats, divided into two groups: high fat (HF) and control. The HF fathers were given commercially prepared high-fat pellets (43% as fat), while the controls ate standard laboratory chow (9% as fat). The two groups of fathers had distinct phenotypes; the HF fathers were significantly heavier with increased adiposity, and they were also glucose intolerant and insulin resistant. At 15 weeks of age, fathers were mated with normal females consuming chow to generate the F1 offspring. Only female offspring were studied. Female offspring were weaned unto standard laboratory chow at 3 weeks. At 6 and 12 weeks, an intraperitoneal glucose tolerance test (IpGTT) was performed to measure blood glucose and insulin profile; at 11 weeks, an intraperitoneal insulin tolerance test was done. The body weight and adiposity of these offspring were not different between the two groups. The HF offspring had glucose intolerance and impaired glucose-induced insulin response, mainly at the acute phase, observed since 6 weeks. The IpITT was not different between groups. At 13 weeks, islets were harvested from the two groups of offspring.

first: Sheau

last: Ng

first: Ruby

last: Lin


title: cAMP-induced nuclear condensation of CRTC2 promotes transcription elongation and cystogenesis in autosomal dominant polycystic kidney disease

first: Zeyun

last: Mi

address: Qi Xiang Tai Road

institute: Tianjin Medical University

summary: Formation of biomolecular condensates by phase separation has recently emerged as a new principle for regulating gene expression in response to extracellular signaling. However, the molecular mechanisms underlying the coupling of signal transduction and gene activation through condensate formation, and how dysregulation of these mechanisms contributes to disease progression, remain elusive. Here we report that CREB-regulated transcription coactivator 2 (CRTC2) translocates to the nucleus and forms phase-separated condensates upon activation of cAMP signaling. We show that intranuclear CRTC2 interacts with positive transcription elongation factor b (P-TEFb) and activates P-TEFb by disrupting the inhibitory 7SK snRNP complex. Aberrantly elevated cAMP signaling plays central roles in the development of autosomal dominant polycystic kidney disease (ADPKD). We find that CRTC2 localizes to the nucleus and forms condensates in cystic epithelial cells of both mouse and human ADPKD kidneys. Genetic depletion of CRTC2 suppresses cyst growth in an orthologous ADPKD mouse model. Using integrative transcriptomic and cistromic analyses, we identify CRTC2-regulated cystogenesis-associated genes, whose activation depends on CRTC2 condensate-facilitated P-TEFb recruitment and the release of paused RNA polymerase II. Together, our findings elucidate a mechanism by which CRTC2 nuclear condensation conveys cAMP signaling to transcription elongation activation and thereby promotes cystogenesis in ADPKD.

overall_design: For ChIP-seq. Cells were cross-linked with 1% formaldehyde in 1 mL PBS for 10 min at RT. The crosslink was quenched by adding 67 μL of 2.5 M glycine(150 mM final). Cells were washed with PBS and harvested using ChIP lysis buffer. Cells were then sonicated to obtain fragments (200-500 bp) with Sonicator. Immunoprecipitation was performed with indicated antibodies. After elution and reversal cross-linking, DNA was purified for library preparation.


title: cAMP-induced nuclear condensation of CRTC2 promotes transcription elongation and cystogenesis in autosomal dominant polycystic kidney disease (RNA-Seq)

summary: Forming biomolecular condensates by phase separation has recently emerged as a new principle for regulating gene expression in response to extracellular signaling. However, the molecular mechanisms underlying the coupling of signaling transduction and gene activation through condensate formation and how dysregulation of these mechanisms contributes to disease progression remain elusive. Here we report that CREB-regulated transcription coactivator 2 (CRTC2) translocates to nucleus and forms phase-separated condensates upon activation of cAMP signaling. We show that CRTC2 interacts with positive transcription elongation factor b (P-TEFb), and cAMP-induced CRTC2 condensate formation activates P-TEFb by extracting P-TEFb from its inhibitory complex. Aberrantly elevated cAMP signaling plays central roles in the development of autosomal dominant polycystic kidney disease (ADPKD). We demonstrate that, in contrast to a dispersed cytosolic distribution in the normal tubular epithelia cells, CRTC2 localizes in nucleus and forms condensates in cystic epithelial cells of mouse and human ADPKD kidneys. We show that genetic depletion of CRTC2 markedly suppresses cyst growth in an orthologous ADPKD mouse model. Using integrative transcriptomic and cistromic analyses, we identify CRTC2-regulated cystogenic genes, whose activation depends on CRTC2 condensation-facilitated P-TEFb recruitment and RNA polymerase II pausing release. Together, our findings elucidate a mechanism by which CRTC2 nuclear condensation conveys cAMP signaling to transcription elongation activation and promotes cystogenesis in ADPKD.

overall_design: RNA-sequencing of different condition: sgControl and sgCRTC2 in WT9-12.

first: Yupeng

last: Chen


title: cAMP-induced nuclear condensation of CRTC2 promotes transcription elongation and cystogenesis in autosomal dominant polycystic kidney disease (ChIP-Seq)

overall_design: ChIP sequencing with TY1 antibody in WT9-12 CELLS expressing CRTC2-TY1.


title: RNA profiling of etiolated Arabidopsis seedlings 2 days after UV-B treatment

city: Saint Paul

first: Stefanie

last: Dukowic-Schulze

state: Minnesota

address: 1970 Folwell Avenue

department: Horticultural Science

institute: University of Minnesota

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

overall_design: Refer to individual Series


title: Transcriptome profiling of etiolated Arabidopsis seedlings 2 days after UV-B treatment

summary: We applied mRNA-seq to excised hypocotyls of etiolated Arabidopsis seedlings 2 days after exposure of germinating seedlings to UV-B. Please cite: Dukowic-Schulze, Harvey, Garcia, Chen, Gardner et al. (exp.2021)

overall_design: 3 replicates for 3 treatments in 3 genotypes: 3 treatments (3,000 and 30,000 µmol m-2 UV-B and dark control), 3 genotypes (WT Columbia-0, xpf-3, uvr8-6)

first: Gary

last: Gardner

first: Changbin


title: Small RNA profiling of etiolated Arabidopsis seedlings 2 days after UV-B treatment

summary: We applied sRNA-seq to excised hypocotyls of etiolated Arabidopsis seedlings 2 days after exposure of germinating seedling to UV-B. Please cite: Dukowic-Schulze, Harvey, Garcia, Chen, Gardner et al. (exp.2021)


title: The DGCR8 E518K mutation found in Wilms tumors leads to a partial miRNA processing defect that alters gene expression and biological processes

city: Saarbrücken

first: Tim

last: Kehl

address: Campus E2.1, P.O. box 151150

department: Center for Bioinformatics

institute: Saarland University