title: The effects of Myricitrin on Rheumatoid Synovial Fibroblast-like Synoviocytes

status: Public on Jul 31 2022

city: Guangzhou

first: Yu

last: Kuang

state: Guangdong

address: 58 Zhongshan 2nd Road, Yuexiu District

department: Rheumatology and Immunology

country: China

institute: The First Affiliated Hospital, Sun Yat-sen University

type: Expression profiling by high throughput sequencing

summary: To explored the mechanism by which Myr regulates the biological function of RA FLSs. RNA sequencing was used to identify the differentially expressed transcriptome of Myr-treated RA FLSs compared with the DMSO control.

overall_design: Analysis of transcriptional changes in human RA FLSs treated with or without Myr for 24h.

first: Chuyu

last: Shen


title: Inhibition of PC reverse metformin resistance pancreatic cancer

city: shanghai

first: chang

last: liu

state: China

address: 上海瑞金二路瑞金医院7号楼4楼核医学科实验室

institute: Ruijin Hospital

summary: Using lentivirus infection PDAC cells to construct PC stably knocking down cell lines and detecting its effect on PDAC progression in vivo and vitro. RNA-sequencing analysis on PC knocked down in PDAC cells and the results were verified by RT-qPCR. Seahorse XF flux analyzer used to analyze mitochondrial oxygen consumption rate (OCR) and extracellular acidification rate (ECAR) changed with or without metformin. The therapeutic efficiency of metformin combined with PC interference in PDAC were evaluate in vitro.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for PDAC cells (n=3) and its PC stably knocking down cell lines（n=3).

first: Chang

last: Liu

first: Huijun

last: Ju

first: Yifan

last: Zhang


title: Circulating cardiac microRNA-FOXO3 axis safeguards against dilated cardiomyopathy

city: Nanjing

first: xiaolei

last: cheng

state: jiangsu

address: 321 Zhongshan Road

department: Department of Anesthesiology

institute: Affiliated Drum Tower Hospital of Medical School of Nanjing University

type: Non-coding RNA profiling by high throughput sequencing

summary:
Background - Cardiac microRNAs (miRNAs) could be released into circulation thus becoming circulating cardiac miRNAs, which are increasingly recognized as noninvasive and readily accessible biomarker for multiple heart diseases. A global loss of cardiac miRNAs due to dicer or dgcr8 depletion has been reported to lead to dilated cardiomyopathy (DCM). However, DCM-associated circulating miRNAs (DACMs) and their roles in regulating DCM progression remain largely unexplored.
Methods and Results - Through miRNA sequencing of human plasma procured from DCM patients and healthy control people, DCM was characterized with a unique expression pattern for circulating miRNAs. Among them, miR-26a-5p, miR-30c-5p, miR-126-5p, and miR-126-3p were all identified with dramatic reductions in DCM mouse myocardium as in the plasma of DCM patients. FOXO3, highlighted as a predicted common target gene, was experimentally demonstrated to be repressed within cardiomyocytes by these miRNAs except miR-26a-5p. Mechanistically, miRNA combination (miR-30c-5p, miR-126-5p, and miR-126-3p) significantly attenuated FOXO3-induced apoptosis and autophagy observed in cardiomyocytes as well as in DCM murine heart. Cardiac-specific knockout of FOXO3 conspicuously mitigated myocardial apoptosis and autophagy in DCM development. Moreover, stymieing the interaction between these miRNAs and FOXO3 mRNA extremely crippled the cardioprotection of these miRNAs against DCM progression.
Cardiac miRNA-FOXO3 axis plays a pivotal role in safeguarding against myocardial apoptosis and autophagy, thereby maintaining cardiac homeostasis and potently preventing DCM development. These findings may provide serological clues for the noninvasive diagnosis of DCM in the future, and unambiguously shed new light on DCM pathogenesis and associated therapeutic targets

overall_design: Ten Control human plasma RNA  from N1~N10 and Ten DCM patient plasma RNA from T1,T3,T4,T5,T6,T7,T9,T10,T11,T13 respectively

first: Xiaolei

last: Cheng

first: Dongdong

last: Jian

first: Junyue

last: Xing


title: RNAseq bovine subcutaneous adipose tissue in periparturient stage

city: Nouzilly

first: joelle

last: dupont

address: Centre Val de Loire

country: France

institute: INRA

summary: The severity of negative energy balance (NEB) in high-producing dairy cows has a high incidence among health diseases. The periparturient period is crucial for the health status and reproductive performance of dairy cows. During this period, dairy cows experience a transition from a pregnant, non-lactating state to a non-pregnant, lactating state. At the beginning of lactation, the energy needs for milk production are higher than the available energy consumed from feed intake, resulting in a negative energy balance (NEB)]. While in a NEB, cows mobilise their reserves from adipose tissue, resulting in elevated plasma concentrations of non-esterified fatty acids (NEFAs), which are used as a fuel source by peripheral tissues and the mammary gland for milk fat synthesis. Thus, white adipose tissue is one of the main tissue involved in the energy production during this transition period. So the objectives of our study were to dentify mRNA differentially expressed in white adipose before and after calving in dairy cow fed with low (LE) and high (HE) energy diet.

overall_design: Identify mRNA differentially expressed before and after calving in dairy cow fed with low (LE) and high (HE) energy diet

first: Joelle

last: Dupont


title: Single-cell genome-wide association reveals a nonsynonymous variant in ERAP1 confers increased susceptibility to influenza virus

status: Public on Jul 29 2022

city: Durham

first: Benjamin

middle: Huston

last: Schott

state: North Carolina

address: 0048B CARL, Box 3053 DUMC

department: MGM

country: USA

institute: Duke University

summary: Diversity in the human genome is one factor that confers resistance and susceptibility to infectious diseases. This is observed most dramatically during pandemics, where individuals exhibit large differences in risk and clinical outcomes against a pathogen infecting large portions of the world’s populations. Here, we developed scHi-HOST (single cell High-throughput Human in vitrO Susceptibility Testing), a method for rapidly identifying genetic variants that confer resistance and susceptibility to pathogens. scHi-HOST leverages scRNA-seq (single-cell RNA-sequencing) to simultaneously assign genetic identity to individual cells in mixed infections of cell lines of European, African, and Asian origin, reveal associated genetic variants for viral entry and replication, and identify expression quantitative trait loci (eQTLs). Applying scHi-HOST to influenza A virus (IAV), we identified eQTLs at baseline and in genes that are induced by IAV infection. Integration of scHi-HOST with a human IAV challenge study (Prometheus) revealed that a missense variant in ERAP1 (Endoplasmic reticulum aminopeptidase 1; rs27895) was associated with IAV burden in cells and human volunteers. Functional studies using RNA interference, ERAP1 inhibitor, and overexpression of alternative alleles demonstrated that ERAP1 is exploited by IAV to promote infection. Specifically, the nonsynonymous substitution, which results in a glycine to aspartate substitution at ERAP1 residue 348, would disrupt the substrate binding pocket of ERAP1, likely resulting in a significantly altered preference for substrates, poorer catalytic efficiency, or both. Finally, rs27895 exhibits substantial population differentiation, with the higher frequency of the minor T allele in two African populations likely contributing to the greater permissivity of cells from these populations to IAV infection. scHi-HOST is an important resource for understanding susceptibility to influenza and is a broadly applicable method for decoding human genetics of infectious disease.

overall_design: 96 human lymphoblastoid cell lines (LCLs) from the 1000 Genomes project were infected with influenza A virus and analyzed using single-cell RNA-seq in two batches (scHH_EIK and scHH_LGC). Uninfected samples were included as controls.

middle: H

first: Liuyang

last: Wang

first: Dennis

middle: C

last: Ko


title: Transcriptomic analysis of an E. coli deletion mutant of the two C-terminal OB fold domains of r-protein S1

city: Strasbourg

first: Stefano

last: Marzi

address: 2 allée Konrad Roentgen

department: UPR9002 - IBMC

institute: CNRS

summary: Escherichia coli ribosomal protein S1 is essential for cellular viability through translation initiation of mRNAs. Here, we have addressed the roles of the two distal OB fold domains located in the C-terminus, which are dispensable for growth. Their deletion causes a cold-shock phenotype and a loss of motility accompanied by deregulation of the expression of several small regulatory RNAs (sRNAs) and many mRNAs involved in stress responses. Surprisingly, the expression of the sRNA RyhB and one of its repressed target mRNA, sodB, were found enhanced in the mutant strain. We used a combination of in vivo and in vitro approaches to address the roles of S1 in RyhB-dependent regulation. We found that the RyhB-dependent repression of sodB translation was not altered but instead rapid RNase E-mediated depletion of the repressed sodB mRNA was strongly impaired in the mutant strain. This unexpected effect was also generalized to other RyhB-dependent targets. In addition, deletion of the last two OB domains of S1 causes a defect of the final step of the RNase E-dependent maturation of the 16S rRNA. This work unveils an unexpected function of S1 in enhancing the kinetics of ribosome biogenesis and RyhB-dependent mRNA decay mediated by the RNA degradosome. Through its RNA chaperone activity, S1 facilitates the existing coupling between ribosome biogenesis, translation, and RNA decay.

sample_organism: Escherichia coli str. K-12 substr. MG1655

overall_design: Total RNA-seq analysis of WT and rpsA∆56 mutant strains. rpsA∆56 is a strain where the last two C-terminal OB-fold domains of r-protein S1 have been deleted.


title: Oxidative Phosphorylation Regulates Interleukin-10 Production in Regulatory B Cells via the Extracellular Signal-related Kinase Pathway

city: guangzhou

first: Yinhong

last: Zhu

state: guangdong

address: zhongshan Second Road

institute: 无

summary: Regulatory B cells (Bregs) are immune cells that constrain the immune response and restrict inflammation via their expression of interleukin (IL)-10. However, the molecular mechanisms underlying Breg differentiation and IL-10 secretion remain unclear. Previous data suggest that cellular metabolism determines both the fate and function of these cells. Here, we suggest an essential role for mitochondrial oxidative phosphorylation (OXPHOS) in the regulation of IL-10 in these Bregs. We found that IL-10+ B cells from IL-10-green fluorescent protein-expressing mice had higher oxygen consumption rate than IL-10- B cells. In addition, inhibition of OXPHOS decreased the expression of IL-10 in B cells. Further, suppression of OXPHOS diminished the expression of surface markers for Bregs and impaired their therapeutic effects in dextran sulfate sodium-induced colitis. Mechanistically, mitochondrial OXPHOS was found to regulate the transcription factor HIF-1α through the extracellular signal-related kinase pathway. Taken together, this study reveals a strong correlation between mitochondrial OXPHOS and Breg phenotype/function, indicating OXPHOS as a therapeutic target in autoimmune diseases driven by Breg dysfunction.

overall_design: After splenic B cells from IL-10-eGFP Tiger mice were stimulated with 3 µg/ml LPS for 48 h, IL-10+ B cells and IL-10- B cells were sorted.And mRNA profiles of them were  examined.

first: Xiaoran

first: Shujuan

last: Xie

first: Yanwen

last: Peng


title: Effect of horizontal microbiome transmission on the development of bleomycin induced pulmonary fibrosis

city: Ann Arbor

first: Stephen

middle: J.

last: Gurczynski

state: MI

address: 109 Zina Pitcher Pl, Room 4062

department: Internal Medicine

institute: University Of Michigan

summary: Pulmonary fibrosis is a chronic progressive and often fatal disease. The pathogenesis is characterized by aberrant repair and remodeling of the lung parenchyma resulting in loss of physiological homeostasis, respiratory failure and death. The immune response in pulmonary fibrosis is dysregulated. The gut microbiome is a key regulator of immunity. The role of the gut microbiome in regulating the pulmonary immunity in lung fibrosis is unknown. Here, we have utilized a strategy of cage randomization to study how the horizontal transmission of gut microbiome influences the development of pulmonary fibrosis.

overall_design: Mice from various vendors were cage randomized or left non-randomized for 2 weeks.  Mice were subsequently treated o.n. with .75 / kg units of bleomycin for 14 days to induce pulmonary fibrosis.

middle: J

first: David

middle: N

last: O'Dwyer


title: ChIP-seq analysis of IMR32

status: Public on Jul 28 2022

city: Kitaadachi-gun

first: Hisanori

last: Takenobu

state: Saitama

address: 818, Komuro, Ina-machi

department: Research Institute for Clinical Oncology

country: Japan

institute: Saitama Cancer Center

type: Genome binding/occupancy profiling by high throughput sequencing

summary: In the present study, we found that EZH1 depletion in MYCN-amplified neuroblastoma cells resulted in significant cell death as well as xenograft inhibition. EZH1 depletion decreased the level of H3K27me1; the interaction and protein stabilization of MYCN and EZH1 appear to play roles in epigenetic transcriptional regulation. Transcriptome analysis of EZH1-depleted cells resulted in down-regulation of the cell cycle progression-related pathway. In particular, GSEA revealed down-regulation of reactome E2F-mediated regulation of DNA replication along with key genes of this process, TYMS, POLA2, and CCNA1. TYMS and POLA2 were transcriptionally activated by MYCN and EZH1-related epigenetic modification. Treatment with the EZH1/2 inhibitor UNC1999 also induced cell death, decreased H3K27 methylation, and reduced the levels of TYMS in NB cells. Previous reports indicated neuroblastoma cells are resistant to 5-fluorouracil (5-FU) and TYMS (encoding thymidylate synthetase) has been considered the primary site of action for folate analogues. Intriguingly, UNC1999 treatment significantly sensitized MYCN-amplified neuroblastoma cells to 5-FU treatment, suggesting that EZH inhibition may be an effective strategy for development of a new epigenetic treatment for neuroblastoma.

overall_design: ChIP seq analysis of parental neuroblastoma cell line IMR32

first: Yoshitaka

last: Shinno

first: Ryuichi

middle: P

last: Sugino

first: Miki

last: Ohira

first: Takehiko

last: Kamijo


title: The critical and diverse roles of CD4-CD8- double negative T cells in non-alcoholic fatty liver disease II

city: Beijing

first: Changying

last: Li

address: Panjiayuan Street 17, Chaoyang District

institute: Chinese Academy of Medical Sciences and Peking Union Medical College

summary: Methods: RNA transcription profiling of intrahepatic CD4-CD8- double negative T cells with or without arachidonic acid stimulation for 48 hours. Results: RNA sequencing data showed that intrahepatic DNT in NAFLD mice promoted cell apoptosis, decreased GZMB expression, and increased IL-17A expression.

overall_design: Examination of  differential genes in intrahepatic double negative T cells with or without arachidonic acid

first: Guangyong

last: Sun

first: Dong

last: Zhang


title: RNA sequencing data of SK-BR-3 Parental vs lapatinib resistance (LR) cells

city: Seoul

first: Daeun

last: Jeong

address: Daehak-ro 101

department: Cancer research institute

country: South Korea

institute: Seoul National University

summary:
Transcriptional profiling of SK-BR-3 lapatinib resistance cells comparing control SK-BR-3 parental cells. Randomly fragmented the purified RNA for sequencing with a short read and reverse-transcrived. Attached different adapters to both end of cDNA and ligated them and amplified.
Calculate the amount of expression obtained by transcript quantification of each sample as a normalization value considering transcript length and depth of coverage.

overall_design: Two-condition experiment, SK-BR-3 parental cells vs. SK-BR-3 LR cells. Biological replicates: 1 SK-BR-3 parental cell, 1 SK-BR-3 LR cell, independently grown and harvested. One replicate per array.

first: Seock-Ah

last: Im


title: DARPP32, a target of hyperactive mTORC1 in the retinal pigment epithelium

city: Oklahoma city

first: Yan

last: Chen

state: Oklahoma

address: 608 Stanton L Young Blvd

institute: The University of Oklahoma Health Sciences Center/DMEI

summary: The mechanistic target of rapamycin (mTOR) is assembled into signaling complexes of mTORC1 or mTORC2, and plays key roles in cell metabolism, stress response, nutrient and growth factor sensing. Accumulating evidence from human and animal model studies has demonstrated a pathogenic role of hyperactive mTORC1 in age-related macular degeneration (AMD). The retinal pigment epithelium (RPE) is a primary injury site in AMD. In mouse models of RPE-specific deletion of Tuberous sclerosis 1 (Tsc1), which encodes an upstream suppressor of mTORC1, the hyperactivated mTORC1 metabolically reprogrammed the RPE and led to the degeneration of the outer retina and choroid (CH). In the current study, we used single-cell RNA sequencing (scRNA-seq) to identify a novel RPE mTORC1 downstream protein, dopamine and cyclic AMP-regulated phosphoprotein of molecular weight 32,000 (DARPP-32). DARPP-32 was not found in healthy RPE but localized to drusen and basal linear deposits in human AMD eyes. In animal models, overexpressing DARPP-32 by adeno-associated virus (AAV) led to abnormal RPE structure and function. The data indicate that DARPP-32 is a previously unidentified signaling protein subjected to mTORC1 regulation and may contribute to RPE degeneration in AMD.

overall_design: Single-cell suspension of RPE/choroid tissue prepared from 10-week-old animals was used for single-cell RNAseq experiments.  Each sample includes tissues pooled from one male and one female.  TSC1 flox (Tsc1tm1Djk/J) and the RPE-specific TSC1 KO (Tsc1tm1Djk/J; Best-Cre) were analyzed and compared.  The scRNA experiments were performed using 10 X genomics chromium platforms.

first: Cai

last: Jiyang

first: Litwin

last: Christopher

first: Cheng

last: Rui

first: Ma

last: Jian-Xing

first: Chen

last: Yan


title: Transcriptome of eight rooster (Leghorn) tissues for identification of differentially expressed genes

city: NOUZILLY

first: Sophie

last: Fouchécourt

state: FRANCE

summary: The aim of this study is to obtain mRNA profiles of chicken tissues to perform differential transcriptome analysis

overall_design: mRNA profiles of 8 male tissues from 5 adult roosters: testis, liver, lung, brain, kidney, intestine, muscle, heart

first: Benoit

last: Piégu

first: Marine

last: Milhes


title: Expression data from 4T1 parental breast cancer cell line and 4T1-3R liver metastatic cells (4T1-3R_L).

city: Taipei

first: Min-Ying

last: Lin

address: No. 155, Sec. 2, Linong St. Beitou District,

country: Taiwan

institute: National Yang Ming Chao Tung University

summary:
We used 4T1 murine breast cancer cells to establish a syngeneic tumor model and found that liver metastatic cells exhibited serveral biological and molecular characteristic that are distinct from parental 4T1 cells.
We used microarrays to analyze 4T1-3R_L cells exhibited several CSC related genes compared to 4T1 cells.

overall_design: 4T1 parental breast cancer cells and 4T1-3R liver metastatic cells were selected for RNA extraction and hybridization on Affymetrix microarrays.

first: Yi-Jang

last: Lee


title: Uterine infection-induced transcriptomic changes in the bovine endometrium

city: Honolulu

first: MAHFUZ

middle: RAHMAN

last: ADNAN

state: HI

address: 1955 East-West Road

department: Human Nutrition, Food and Animal Sciences

institute: University of Hawaii at Manoa

summary:
Purpose: Perform RNA-seq study on infectious bovine endometrial tissues to reveal important genes and biological pathways regulating uterine physiology following uterine infections
Methods:RNA sequencings were done using Illumina platform. Single-end reads in the FASTQ format were explored using FastQC, low-quality reads were trimmed from both 3’ and 5’ ends until a base pair of Phred quality score of 30 (99.9% accurate) or greater was found, reads having a mean quality score less than 30 and length below 30 nucleotides were filtered out. Cleaned reads were aligned against the bovine reference genome (Bos_taurus.ARS-UCD1.2) using HiSAT2. The resulting SAM files were sorted, converted to BAM files using SAMtools. Read counts mapped to bovine gene models were generated using htseq-count script from HTSeq package. Bioconductor DESeq2 was used to get the differentially expressed genes among infectious vs normal uterine tract groups
Conclusions: The study demonstrated that uterine infections altered several genes and pathways related to inflammatory response, immune response, uterine physiology, uterine enviroment and fertility in the intercaruncular region of bovine endometrium.

overall_design: There are 4 normal uterine tract and 5 infectious uterine tract samples. Differential gene expression between each group (Infectious vs. Normal) are compared.

first: Birendra

last: Mishra

first: Vedbar

last: Khadka

first: Adnan

last: Mahfuz Rahman


title: RNA sequence of gene expression in LPA or PBS treated human ARP1 multiple myeloma cells

city: Houston

first: Pan

last: Su

state: TX

address: 6550 FANNIN STREET

institute: Houston Methodist Research Institute

summary: we use RNA sequence to detect the global gene expression in human ARP1 MM cells after 24 hours of LPA or PBS treatment in vitro

overall_design: ARP1 cells were cultured with or without LPA in vitro for 24 hours, and then the cells were collected and their mRNA profiles were detected.


title: Expression data from WT and BMPR2 knockout hematopoietic stem cells extracted from mice.

city: Lund

first: Sarah

last: Warsi

address: BMC, Sölvegatan 17

country: Sweden

institute: Lund University

summary:
Abstract copied in below, from Warsi et al. 2021 BMP signaling is required for postnatal murine hematopoietic stem cell self-renewal, published in Haematologica. DOI 10.3324/haematol.2019.236125
Life-long production of blood from hematopoietic stem cells (HSCs) is a process of strict modulation. Intrinsic and extrinsic signals govern fate options like self-renewal - a cardinal feature of HSCs. Bone morphogenetic proteins (BMP) have an established role in embryonic hematopoiesis, but less is known about its functions in adulthood. Previously, SMAD-mediated BMP signaling has been proven dispensable for HSCs. However, the BMP Type II receptor (BMPR-II) is highly expressed in HSCs, leaving the possibility that BMPs function via alternative pathways. Here, we establish that BMP signaling is required for self-renewal of adult HSCs. Through conditional knockout we show that BMPR-II deficient HSCs have impaired self-renewal and regenerative capacity. BMPR-II deficient cells have reduced p38 activation, implying that non-SMAD pathways operate downstream of BMPs in HSCs. Indeed, a majority of primitive hematopoietic cells do not engage in SMAD-mediated responses downstream of BMPs in vivo. Furthermore, deficiency of BMPR-II results in increased expression of TJP1, a known regulator of self-renewal in other stem cells, and knockdown of TJP1 in primitive hematopoietic cells partly rescues the BMPR-II null phenotype. This suggests TJP1 may be a universal stem cell regulator. In conclusion, BMP signaling, in part mediated through TJP1, is required endogenously by adult HSCs to maintain self-renewal capacity and proper resilience of the hematopoietic system during regeneration.

overall_design: HSCs (LSK CD9hi CD48- CD150+) were sorted from c-kit enriched mouse bone marrow using FACS. Samples were frozen at -80 in RLT buffer and sent to KFB (Regenburg, Germany) for RNA extraction and hybridization on Affymetrix microarrays. Cells were sorted from fourBMPR2 knockout C57Bl/6 mice and four WT control mice (littermates). Please see further information in the associated pubilcation by Warsi et al. 2021.

first: Ulrika

last: Blank

first: Stefan

last: Karlsson


title: 3D Chromosome Structure of SSCs, iGSCs and FGSCs

city: Shanghai

first: Ji

last: Wu

address: No.800, Dongchuan Road, Minhang District

institute: Shanghai Jiao Tong University

summary: We use in situ Hi-C to report the most comprehensive survey to date of chromatin organization in germline stem cells

overall_design: Examination of the chromatin architecture in 3 cell types.

first: Xiaoyong

last: Li

first: Geng

middle: G

last: Tian


title: RNA-seq profiling of NKX6.1+/C-pep+ sorted pancreatic beta cells differentiated from MODY3 hiPSCs and corrected controls to investigate the mechanism behind MODY3

city: Vanløse

first: Florian

middle: Malte

last: Hermann

address: Dybendalsvej 61, 1.tv

country: Denmark

institute: University of Copenhagen

summary: We report differential gene expression of hiPSC-derived beta cells from a MODY3 donor and a corrected control. The aim of the study was to investigate the underlying mechanism behind MODY3 in beta cells. The findings were coupled to functional assays of the in vitro differentiated beta cells to propose a mechanism for the dysfunction of the beta cells.

overall_design: mRNA profiles of beta-cells derived from a MODY3 hiPSC line and a corrected control line. The data set consists of four replicates coming from four independent in vitro differentiations. RNA seq was performed on bulk NKX6.1+/Cpep+ FACS sorted population.

first: Maya

last: Kjaergaard

first: Henrik

last: Semb


title: A Missense Mutation in Kcnc3 Causes Hippocampal Learning Deficits in Mice

city: Dallas

first: Joseph

middle: S.

last: Takahashi

address: 5323 Harry Hines Blvd., NA4.118

institute: University of Texas Southwestern Medical Center

summary: Although a wide variety of genetic tools have been developed to study learning and memory, the molecular basis of memory encoding remains incompletely understood. Here, we undertook an unbiased approach to identify novel genes critical for memory encoding. From a large-scale in vivo mutagenesis screen using contextual fear conditioning, we isolated a mutant, named Clueless, with spatial learning deficits. A causative missense mutation (G434V) was found in the voltage gated potassium channel, subfamily C member 3 (Kcnc3) gene in a region that encodes a transmembrane voltage sensor. Generation of a Kcnc3G434V CRISPR mutant mouse confirmed this mutation as the cause of the learning defects. While G434V had no effect on transcription, translation, or trafficking of the channel, electrophysiological analysis of the G434V Kcnc3 mutant channel revealed a complete loss of voltage-gated conductance, a broadening of the action potential, and decreased neuronal firing. Together, our findings have revealed a previously unrecognized role for Kcnc3 in learning and memory.

overall_design: Comparative gene expression profiling analysis of RNA-seq data (4 replicates) in the dorsal and ventral parts of DG and CA in mice hippocampus after contextual fear conditioning training

first: Pin

last: Xu

first: Kazuhiro

last: Shimomura

first: Changhoon

first: Xiaofei

last: Gao

first: Eleanor

last: Simpson

first: Guocun

last: Huang

first: Chryshanthi

middle: M

last: Joseph

first: Vivek

last: Kumar

first: Woo-Ping

last: Ge

first: Karen

middle: S

last: Pawlowski

first: Mitchell

middle: D

last: Frye

first: Saïd

last: Kourrich

first: Eric

middle: R

last: Kandel


title: Early life exposure of pigs to topsoil alters miRNA and mRNA expression in peripheral blood mononuclear cells

city: Ames

first: James

last: Koltes

state: Iowa

address: 239A Kildee Hall

department: Animal Science

institute: Iowa State University

summary: Exposure to less hygienic conditions during early childhood has been associated with stimulation and development of the immune system. A recent study indicated exposure of piglets to soil-borne microbes during lactation was related with modulation of gut microbiota and immune function. To identify potential molecular mechanisms and pathways impacted by early life topsoil exposure, we analyzed gene expression (mRNA and miRNA) in peripheral blood mononuclear cells (PBMC) from these piglets. Total RNA was extracted from PBMC of piglets exposed to topsoil only from d 4-d 21 of life (mRNA n=6; miRNA n=5) or unexposed control pigs (mRNA n=6; miRNA n=8) at 11, 20, and 56 days of age. Small RNA and mRNA were sequenced with 50-bp single-end reads using Illumina chemistry. Differential expression (DE) analysis was performed using PROC Glimmix of SAS to evaluate changes in expression due to topsoil exposure over time with genes declared DE at a false discovery rate (FDR) of q<0.10. A total of 138 mRNA and 21 miRNAs were identified as DE for the treatment by age interaction. Ontology enrichment analysis of DE mRNA revealed GO terms directly involved in the connection between T-cell and antigen-presenting cells that are associated with T-cell activation. Key regulatory genes identified include PTPRJ, ITGB3, TRBV30, CD3D, mir-143, mir-29, and mir-148a. While these results require validation, this study provides data supporting the hypothesis that less hygienic environments during early life may contribute to the development of the immune system

overall_design: RNA-Seq mRNA and miRNA. Piglets exposed to topsoil from days 4 to 21 of life (mRNA n=6; miRNA n=5) or unexposed control pigs (mRNA n=6; miRNA n=8). Samples were collected at 11, 20, and 56 days of age.

first: Marcela

last: de Souza

first: Dawn

middle: A

first: Hamid

last: Beiki

first: Marites

last: Sales

first: Tsungcheng

last: Tsai

first: Charles

last: Maxwell

first: Jiangchao

last: Zhao

middle: E


title: Combined double knockout of Ezh2 and G9a leads to expression change in murine retinal ganglion cells

city: Boston

first: Dong Feng

last: Chen

state: Massachusetts

address: 20 Staniford St

institute: Schepens Eye Research Institute

summary: Purpose: The goal of this study is to evaluate H3K27me3 histone marks in retinal ganglion cells in Ezh2 (Math5Cre, Ezh2-/-) and combined G9a-Ezh2 (Math5Cre; G9a+/-Ezh2-/-) knockout mutant mice at P1. Both Ezh2 and G9a are major epigenetic silencing machineries. Ezh2 mediates the trimethylation of lysine 27 on histone 3. Emerging evidences show an interdependence between Ezh2 and G9a to facilitate K27 trimethylation.   Methods: P1 retinal ganglion cells were collected and chromatin immunoprecipitation was performed with EZ- CHIP kit from Millipore. Library preparation was done with Rubicon Genomics Thruplex DNAseq.  Results: Here, we find a pool of common K27me3 target genes of Ezh2 and G9a in double knockout that leads to dysfunction in double mutant RGCs.  Conclusion: This study provides the first Chip-seq analysis of K27me3 in murine RGCs. Our data supports that an interaction between Ezh2 and G9a is also evident in murine retinal ganglion cells. This work should be a framework for further study of retinal ganglion cells and retinal diseases.

overall_design: Examination of H3K27me3 marks in single Ezh2 (Math5Cre; Ezh2-/-) and combined G9a-Ezh2 (Math5Cre; G9a+/-Ezh2-/-) knockout murine retinal ganglion cells

first: Lucy

last: Wong

first: Dong

middle: F


title: R848 treated DNMT3A-mutant AML [RNA-seq]

city: Philadelphia

first: Sara

last: Meyer

state: PA

department: Cancer Biology

institute: Thomas Jefferson University

summary: microRNA (miRNA or miR) are aberrantly expressed in acute myeloid leukemia (AML), and clinically may have diagnostic, prognostic, and therapeutic value. We identify miR-196b, is overexpressed in high-risk subset of DNMT3A-mutant AML and its activity is important to maintain a differentiation block and limit innate immune signaling pathways in AML. We interrogated previously published experimentally defined and computationally predicated miR-196b targets demonstrating that miR-196b regulates Toll-like Receptor Signaling. This work uncovered that miR-196b represses TLR7/8 activation and innate immune signaling in AML and that TLR7/8 activates a Stat1 transcriptional response associated with induced co-stimulatory molecule expression on the surface of AML-derived monocytes and dendritic-like cells.

overall_design: To identify the gene expression and pathway changes assoicated with Resiquimod (R848) treatment in murine Dnmt3a/Flt3ITD-mutant leukemia cells.

first: Holly

last: Gamlen

first: Jennifer

last: Romer-Seibert

first: Michael

last: Lawler

first: Amanda

last: Versace

first: Yang

last: Feng

first: Olga

last: Guryanova

first: Neil

last: Palmisiano


title: MiR-219-5p attenuates OC cisplatin resistance by inactivating Wnt/β-catenin signaling and autophagy via targeting HMGA2

status: Public on Jul 30 2022

first: Feng

last: Xing

address: 619 Zhonghua New Road, Zhabei District

department: gynecology

institute: Zhabei District Centre Hospital

summary: To investigate the miR-219-5p decreases the resistance of OC cells to cisplatin via Wnt/β-catenin signaling and autophagy by regulating HMGA2, we tested the A2780 and A2780-DDP cell lines with miRNA-Seq.

overall_design: We tested the A2780 and A2780-DDP cell lines with miRNA-Seq.

first: Zhijiao

last: Song

first: Caihe

last: Liao

first: Liqun

last: Yao


title: Chloroplast activity provides invitro regeneration capability in contrasting cultivars

city: Uttarakhand

first: Harsh

last: Chauhan

state: Haridwar

address: Roorkee-Haridwar Highway, Roorkee

department: Department of Biosciences and Bioengineering

country: India

institute: Indian Institute of Technology Roorkee

summary: Existence of potent in vitro regeneration system is a prerequisite for efficient genetic transformation and functional genomics of crop plants. Little is known why only some cultivars in crop plants are tissue culture friendly? In this study, contrasting barley cultivars Golden Promise (GP) and DWRB91 (D91) were utilized for digging the molecular basis of regeneration efficiency. Multiomics studies involving transcriptomics, proteomics, metabolomics, and biochemical analysis were performed using GP and D91 callus to unravel the regulatory mechanisms. Transcriptomics analysis revealed 1487 differentially expressed genes (DEGs), in which 795 DEGs were upregulated and 692 DEGs were downregulated in the GP-D91 transcriptome. Genes encoding proteins localized in chloroplast and involved in ROS generation were upregulated in the embryogenic calli of GP. Moreover, proteome analysis by LC-MS revealed 3062 protein groups and 16989 peptide groups, out of these 1586 protein groups were differentially expressed proteins (DEPs). Eventually, GC-MS based metabolomics analysis also revealed the higher activity of plastids and alterations in key metabolic processes such as sugar metabolism, fatty acid biosynthesis, and secondary metabolism. Higher accumulation of sugars, amino acids and metabolites corresponding to lignin biosynthesis were observed in GP as compared to D91.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for barley callus (Hordeum vulagre cvs. Golden promise (GP) and DWR91 (D91)).

first: Parul

last: Sirohi

first: Chanderkant

last: Chaudhary


title: Retrospective study of 186 fetuses with sex chromosomal copy number variations

city: FuZhou

first: Haiwei

last: Wang

state: FuJian

address: Daoshan road 180

institute: Fujian Maternity and Child Health Hospital

type:
SNP genotyping by SNP array
Genome variation profiling by SNP array

summary: Sex chromosomal abnormalities areare associated with multiple defects. In this study, we retrospectively analyzed the single nucleotide polymorphism (SNP) arrays of 186 early embryos with sex chromosomal abnormalities. using single nucleotide polymorphism (SNP) array. Among them, 52 cases of Turner syndrome, 21 cases of triple X syndrome, 35 cases of Klinefelter syndrome and 14 cases of XYY syndrome were detected. Moreover, 27 cases of mosaic sex chromosomal abnormalities were determined. Sex chromosomal deletions and duplications were found in 37 cases. Overall, our results presented a detailed manifestation of sex chromosomal abnormalities.

overall_design:
From 2019 to 2022, more than 10,000 cases of SNP arrays were conducted in our center. In this study, we retrospectively analyzed the SNP arrays of 186 early embryos with sex chromosomal abnormalities. Chromosome Analysis Suite (ChAS) and online databases were used for analyzing the SNP arrays and prenatal diagnosis.
------------------------------------
Author state "43 CEL files from December 2016 to August 2019 were lost. CYCHP files of 186 early embryos were submitted."


title: Profiling of lung SARS-CoV-2 and influenza virus infection dissects virus-specific host responses and gene signatures

city: brisbane

first: Arutha

last: Kulasinghe

address: 37 kent st

country: Australia

institute: University of Queensland

summary: The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that emerged in late 2019 has spread globally, causing a pandemic of respiratory illness designated coronavirus disease 2019 (COVID-19). A better definition of the pulmonary host response to SARS-CoV-2 infection is required to understand viral pathogenesis and to validate putative COVID-19 biomarkers that have been proposed in clinical studies. Here, we use targeted transcriptomics of FFPE tissue using the Nanostring GeoMX™ platform to generate an in-depth picture of the pulmonary transcriptional landscape of COVID-19, pandemic H1N1 influenza and uninfected control patients. Host transcriptomics showed a significant upregulation of genes associated with inflammation, type I interferon production, coagulation and angiogenesis in the lungs of COVID-19 patients compared to non-infected controls. SARS-CoV-2 was non-uniformly distributed in lungs (emphasising the advantages of spatial transcriptomics) with the areas of high viral load associated with an increased type I interferon response. Once the dominant cell type present in the sample, within patient correlations and patient-patient variation had been controlled for, only a very limited number of genes were differentially expressed between the lungs of fatal influenza and COVID-19 patients. Strikingly, the interferon-associated gene IFI27, previously identified as a useful blood biomarker to differentiate bacterial and viral lung infections, was significantly upregulated in the lungs of COVID-19 patients compared to patients with influenza. Collectively, these data demonstrate that spatial transcriptomics is a powerful tool to identify novel gene signatures within tissues, offering new insights into the pathogenesis of SARS-COV-2 to aid in patient triage and treatment

overall_design: In this dataset, we capture GeoMx DSP RNA profiles of lung tissue from SARS-CoV2 infected patients aswell as pH1N1 and control specimens

first: A

middle: K

first: C

middle: W

last: Tan


title: Hsa-miR-200c-3p is down regulated in stable coronary artery disease: A pilot study

status: Public on Jul 26 2025

city: Paris

first: Noémie

last: Robil

address: 29, rue du Faubourg Saint-Jacques

department: Paris Biotech Santé

institute: GenoSplice technology

type: Methylation profiling by high throughput sequencing

summary: Four male patients were enrolled for this study in collaboration with the Cardiology Unit of Policlinico Tor Vergata-Fondazione PTV (Rome). The first group of patients has chronic coronary artery disease (CAD) confirmed by coronary angiography, the second group are subjects with clinically proven healthy coronary arteries (CTR). On our case study we have performed a genome-wide methylation study on genomic DNA bisulfite-converted and a miRNA-sequencing study using NextSeq 500 ILLUMINA platform. The methylation study showed different methylated regions (DMRs) and single CpG sites (DMCs) in patients sharing the same clinical and pathological features, allowing detecting distinctly different methylation patterns between CTR subjects and CAD patients. Moreover, miRNA-sequencing results displayed a differential expression of several significant miRNAs (p-value<0.05), defining a peculiar miRNAs profile in patients featuring the same clinical data. miRNA-sequencing and genome-wide methylation integreted results, showed hsa-miR-200c-3p down-regulated in CAD patients compared to control subjects (FC CAD=2.97 and p≤0.05) and with two hypermethylated sites (genomic coordinates: chr12:7073122-7073122 and chr12:7072599-7072599) in its promoter region (p-value=0.009). We extended the validation of these results on all case study (n=96; 24 CTR and 72 CAD).

overall_design: Analysis of genome-wide methylation level and miRNA-seq expression profile of two different groups of patients (CTR, CAD). In total we have analyzed 4 samples.

first: Chiara

last: Vancheri

first: Elena

last: Morini

first: Giuseppe

last: Novelli

first: Francesca

last: Amati


title: Abnormal inflammatory traits and downregulated caveolin-1 expression in monocytes of psoriasis patients may relate to psoriatic inflammation and atherosclerosis.

city: Yokohama-shi

first: Yukie

last: Yamaguchi

state: Kanagawa-Ken

address: 3-9 Fukuura Kanazawa-ku

institute: Yokohama City University Graduate School of Medicine

summary: Background: Monocytes and macrophages are implicated in inflammation and atherosclerosis, whereas monocytes are involved in psoriasis lesion formation. We previously reported a psoriatic inflammation-associated significant decrease in the membrane protein caveolin-1 (CAV-1) in psoriasis patient monocytes. However, the phenotype of circulating monocytes and their macrophage differentiation in psoriasis patients remain unclear.  Objective: We sought to clarify circulating monocyte and monocyte-derived macrophage (MDM) phenotypes in psoriasis patients with and without comorbidities.   Method: Thirty-one patients with psoriasis vulgaris and 28 control subjects were included. Surface macrophage markers and inflammatory status were examined in circulating monocytes and MDMs from both groups. Expression of CD36, which mediates macrophage uptake of oxidized low-density lipoprotein (oxLDL), was evaluated in these cells. CAV-1-silenced monocytes were differentiated into macrophages to investigate the effects of CAV-1 downregulation on psoriatic inflammation and atherosclerosis.  Results: Macrophage surface markers were detectable in circulating monocytes. A significant M1 shift was detected in monocytes and MDMs in psoriasis patients, including those without cardiovascular disease risk factors, as compared to controls. MDMs of psoriasis patients had more CD36-expressing cells, which are associated with atherosclerosis risk. Additionally, CAV-1-silencing in monocytes increased the likelihood of M1-biased macrophage differentiation and increased pro-inflammatory cytokine production.  Conclusions: Monocytes from psoriasis patients were more likely to differentiate into M1-dominant macrophages, correlating with inflammatory status and CAV-1 expression. These aberrant inflammatory monocytes not only contribute to psoriatic inflammation by producing psoriatic cytokines, but also have a phenotype that could increase atherosclerosis risk by uptake of oxLDL and formation of foam cells.

overall_design: The expression profiles of primary human macrophages from healthy donors were evaluated. The macrophages have two groups: a monocyte-derived group with suppressed Caveolin-1 (Cav-1) expression and an unsuppressed group (control).

first: Miho

last: Asami

first: Yasushi

last: Ototake

first: Naoko

last: Takamura

first: Yuko

last: Watanabe

first: Michiko

last: Aihara


title: TRANSCRIPTOMIC ANALYSIS OF BOVINE ENDOMETRIUM WITH SHORT UTERINE TRACT LEADING TO INFERTILITY

first: MAHFUZ

last: ADNAN

summary:
Purpose: Perform RNA-seq study on short bovine endometrial tissues to reveal important genes and biological pathways related to uterine development and physiology
Methods:RNA sequencings were done using Illumina platform. Single-end reads in the FASTQ format were explored using FastQC, low-quality reads were trimmed from both 3’ and 5’ ends until a base pair of Phred quality score of 30 (99.9% accurate) or greater was found, reads having a mean quality score less than 30 and length below 30 nucleotides were filtered out. Cleaned reads were aligned against the bovine reference genome (Bos_taurus.ARS-UCD1.2) using HiSAT2. The resulting SAM files were sorted, converted to BAM files using SAMtools. Read counts mapped to bovine gene models were generated using htseq-count script from HTSeq package. Bioconductor DESeq2 was used to get the differentially expressed genes among short vs normal uterine tract groups
Conclusions: Heifers with short uterine tract had significantly decreased endometrial layers, uterine glands, and altered transcriptomic profiles.  The decrease in uterine glands probably resulted in lower uterine secretions necessary to support embryo growth and development. As a result, heifers with short uteri were infertile even when they were bred by fertile bulls.

overall_design: There are 4 normal uterine tract and 5 short uterine tract samples. Differential gene expression between each group (Short vs. Normal) are compared.

first: Birendra

last: Mishra

first: Vedbar

last: Khadka

first: Adnan

last: Mahfuz Rahman


title: single cell RNA seq of mouse bone marow-derived hematopoietic stem progenitor cells

city: Tianjin

first: Hideo

last: Ema

state: Tianjin

address: 288#, Nanjing Road

department: State key laboratory of experimental hematolog

institute: Inatitute of Hematology & Blood Disease Hospital, Chinese Academy of Sciences.

summary: Hematopoietic stem cells (HSCs) have been considered to progressively lose the self-renewal and differentiation potentials towards the commitment to each blood lineage. However, recent studies have suggested megakaryocyte progenitors are generated in a close relation with HSCs. In this study, we identified CD201-CD48- or CD48+ CD150+CD34-Kit+Sca-1+Lin- cells as new early megakaryocyte progenitors (MegP) in adult mouse bone marrow by single-cell (sc) transplantation, sc colony assay, sc RT-PCR, and sc RNA-sequencing. These MegP had little repopulating potential in vivo but formed megakaryocyte colonies in vitro. Transcriptome analysis suggested that these MegP lie downstream of HSCs and upstream of multipotent progenitors in a megakaryocyte differentiation pathway. The polyinosinic-polycytidylic acid (polyIC) injection and long-term reconstitution data suggested that a proportion of MegP expand after inflammation and transplantation. Here we propose a new model of HSC differentiation where HSCs give rise to common myeloid progenitors and MegP with little repopulating activity.

overall_design: scRNA-Seq were successfully performed on 48 HSC1-P1 cells, 48 HSC1-P2cells, 44 HSC1-P3 cells, 44 HPC1-P1 cells, 48 HPC1-P2 cells, 44 HPC1-P3 cells, and 48 MPP2 cells.

first: Zixian

last: Liu

first: Sen

last: Zhang

first: Peng

last: Wu

first: Caiying

last: Zhu

first: Fang

last: Dong

first: Yan


title: RNAseq analysis of skeletal muscle transcriptomes from non-transgenic (NTG) and skeletal muscle specific overexpression a deletion mutant form of ornithine transcarbamylase (MCK-ΔOTC) mice.

city: Nanjing

first: Zhenji

last: Gan

address: 12 Xuefu Road

department: Model Animal Research Center of Nanjing University

institute: Nanjing University

summary: We analyzed the gene expression changes that result from mitochondria overloaded by unfolded proteins in skeletal muscles. Mitochondrial-retained mutant ornithine transcarbamylase (ΔOTC) is a known protein degraded by LONP1 and an established model for studying mitochondrial proteostasis imbalance. We generated transgenic mice overexpressing ΔOTC specifically in skeletal muscle using the muscle creatine kinase promoter (MCK-ΔOTC). Transcriptome analysis was performed by whole-genome gene expression profiling experiments in muscles from the MCK-ΔOTC mice and NTG littermate controls. The comparative mRNA profiling strategy revealed extensive genomic reprogramming in MCK-ΔOTC muscles, with 1051 genes up- and 519 genes down-regulated (1.5-fold change and p<0.05), respectively. GO analysis of the regulated genes in MCK-ΔOTC muscles revealed significant enrichment in unfolded protein response as well as RNA processing process. These data suggest that mitochondria overloaded by ΔOTC unfolded proteins induce extensive genomic reprogramming in skeletal muscle

overall_design: Gastrocnemius muscle mRNA profiles of 2-week-old NTG and MCK-ΔOTC mice were generated by deep sequencing, in duplicate, using Illumina HiSeq 4000.

first: Qiqi

last: Guo


title: Expression data from Hela cells treated with IHSF115, an inhibitor of HSF1.

city: Madrid

first: Nuria

last: Vilaboa

state: Madrid

address: Edificio IdiPAZ segunda planta, Hospital Universitario La Paz, Paseo de la Castellana 261

country: Spain

institute: Fundación para la Investigación Hospital La Paz, G83727057

summary:
IHSF115 induces a transcriptomic response that resembles but is not identical with a typical heat stress response.
The data suggest that mRNAs of a number of genes, most notably including histone genes, were stabilized in IHSF115-exposed cells. For the remaining genes, exposure of cells to IHSF115 apparently increased their rates of transcription.

overall_design: Transcriptomic changes in cells exposed to iHSF1 were analyzed in cells exposed for 6h to vehicle (DMSO) or IHSF, by triplicate. Transcript stabilization was analyzed in cells treated for 10min with DMSO or IHSF115 and then exposed fpor 1h to actinomycin D, by duplicate.

first: Richard

last: Voellmy


title: Single cell transcriptome of regional human embryonic stem cell-derived dorsal and ventral neurons from the hindbrain and spinal cord

city: Madison

first: Sushmita

last: Roy

state: WI

address: 330 N. Orchard St.

department: Dept. of Biostatistics and Medical Informatics

institute: University of Wisconsin-Madison

summary: We generated single RNA-seq data to measure transcriptional profiles of 14 hESC-derived neuronal populations, representing distinct regions along the dorsoventral and rostrocaudal axes of the developing hindbrain and human spinal cord. These cells are differentiated using a modular protocol that first induces collinear activation of region-specific HOX genes by exposure to FGF8 and Wnt signaling (Lippmann et al, 2015 PMID:25843047). By transitioning to media containing retinoic acid (RA), SB-431542, and LDN-193189, we generate dedicated posterior central nervous system progenitors with unique rostrocaudal identities. Dorsal patterning by BMP4 or ventral patterning by Sonic hedgehog agonists (smoothened agonist (SAG) and Purmorphamine (Pur)), followed by DAPT gave rise to somatosensory or locomotor neuronal cultures. In total we recovered the transcriptomes of 46,959 cells. Analysis verified expression of increasingly caudal HOX paralogs that could be correlated to hindbrain (HOX1-5; H24, H48, and H72), cervical (HOX1-8; H72 and H120), thoracic (HOX1-9; H168), and thoracolumbar (HOX1-11; H216 and H216R) spinal regions. The dataset also includes representation from major cardinal neuron types. Comparison with existing mouse and human datasets revealed the overall similarity between in vitro-derived and in vivo neurons. Moreover, we detect hundreds of transcriptional markers within region-specific neuronal phenotypes, enabling discovery of novel gene expression patterns along the human developmental axes.

overall_design: The data consist of single RNA-seq measurements taken from 14 hESC-derived cultures differentiated along the rostrocaudal axis by exposure to CHIR99021 (24-216hr), converted to posterior central nervous system progenitors by RA and dual SMAD inhibitors, then differentiated along the dorsoventral axis by exposure to RA with BMP4 or Shh agonists.

first: Nisha

last: Iyer

first: Junha

last: Shin

first: Randolph

last: Ashton


title: Examination of miRNA mimics and inhibitors on satellite cell proliferation in vitro

city: Clemson

first: Susan

last: Duckett

state: South Carolina

address: 105 Collings ST, RM 112 BRC

department: Animal and Veterinary Science

institute: Clemson University

summary:
Cultured satellite cells were transfected with either a mimic for miR-127 or Antagomir-22-3p and cultured for an additional 4 days. Samples were examined to determine potential mRNA targets of miR-127 or miR-22-3p.
This study is comprised of 8 samples. Mimic (n = 2) and AntagomiR (n = 2) experiemnts were preformed independantly of each other and so controls from both groups were sequenced (n = 4).

overall_design: Maslyn,A,Greene

first: William

middle: C

last: Bridges Jr.


title: Set1-mediated histone H3K4 methylation is conserved and required for azole induction of ergosterol biosynthesis genes and antifungal drug resistance in Candida glabrata

city: West Lafayette

first: Nadia

middle: Marie

last: Atallah

state: IN

address: 201 S. University St

department: Center for Cancer Research

institute: Purdue University

summary: Fungal infections are a major health concern because of limited antifungal drugs and development of drug resistance. Candida can develop azole drug resistance by overexpression of drug efflux pumps or mutating ERG11, the target of azoles. However, the role of epigenetic histone modifications in azole-induced gene expression and drug resistance is poorly understood in Candida glabrata. In this study, we show that Set1 mediates histone H3K4 methylation in C. glabrata. In addition, loss of SET1 and histone H3K4 methylation increases azole susceptibility in both C. glabrata and S. cerevisiae. This increase in azole susceptibility in S. cerevisiae and C. glabrata strains lacking SET1 is due to distinct mechanisms. For S. cerevisiae, loss of SET1 decreased the expression and function of the efflux pump Pdr5, but not ERG11 expression under azole treatment. In contrast, loss of SET1 in C. glabrata does not alter expression or function of efflux pumps. However, RNA sequencing revealed that C. glabrata Set1 is necessary for azole-induced expression of all 12 genes in the late ergosterol biosynthesis pathway, including ERG11 and ERG3. Furthermore, chromatin immunoprecipitation analysis shows histone H3K4 trimethylation increases upon azole-induced ERG gene expression. In addition, high performance liquid chromatography analysis indicated Set1 is necessary for maintaining proper ergosterol levels under azole treatment. Clinical isolates lacking SET1 were also hypersusceptible to azoles which is attributed to reduced ERG11 expression but not defects in drug efflux. Overall, Set1 contributes to azole susceptibility in a species-specific manner by altering the expression and consequently disrupting pathways known for mediating drug resistance.

overall_design: bulk RNA-seq was performed in wild-type and set1 deletion Candida glabrata, either untreated or treated with fluconazole.  Three biological replicates were performed for each condition.

first: Kortany

last: Baker

first: Smriti

last: Hoda

first: Debasmita

last: Saha

first: Livia-Maria

last: Georgescu

first: Yueping

first: Nina

last: Serratore

last: Lanman

first: Scott

last: Briggs


title: RNAseq analysis of skeletal muscle transcriptomes from wild-type, LONP1 skeletal muscle specific knockout (LONP1 mKO) and LONP1ATF4 skeletal muscle double-knockout (LONP1ATF4 DmKO) mice.

first: Zhenji

last: Gan

summary: Studying the molecular basis for the skeletal muscle mitochondrial stress response could potentially be targeted to counteract metabolic disorders such as obesity. We uncovered a crucial role for the mitochondrial protease LONP1 in controlling the muscle mitochondrial proteostasis stress response that governs systemic metabolic homeostasis. Skeletal muscle-specific ablation of LONP1 led to broad genomic reprogramming of muscle and protected the mice from HFD-induced obesity. To thoroughly analyze pathways that are affected by ATF4 deficiency in the context of LONP1 mKO, we performed RNA-Seq transcriptome analysis of skeletal muscles from WT, LONP1 mKO and LONP1ATF4 DmKO mice. We identified a total of 3017 differentially expressed genes with a cutoff of 1.5-fold, and p < 0.05. Surprisingly, we found that ATF4 loss blunted a subset of regulated genes in LONP1 mKO muscles, whereas the majority of differentially regulated genes in LONP1 mKO muscles were not affected by ATF4 ablation. GO analysis of ATF4-dependent genes regulated by LONP1 ablation revealed significant enrichment in amino acid metabolic processes, Interestingly, however, LONP1 deficiency induced activation of muscle UPR and UPR-related RNA processing as well as myokine pathways were not affected by ATF4 ablation. Therefore, our results highlight a ATF4-independent mechanism in mediating the UPRmt in mammals.

overall_design: Gastrocnemius muscle mRNA profiles of 6-week-old WT, LONP1 mKO and LONP1ATF4 DmKO mice were generated by deep sequencing, in duplicate, using Illumina HiSeq 4000.

first: Qiqi

last: Guo


title: Gene expression of the Dnmt1/3a/3b TKO ESCs which ubiquitously express full-length DNMT1(TKO_FL) or a deletion mutant DNMT1 lacking the N-terminal 602 amino acids(TKO_602).

city: Chiba

first: Musashi

last: Kubiura-Ichimaru

address: 2-2-1 Miyama, Funabashi-shi

institute: Toho University

summary: Gene expression analysis of TKO_FL ESCs and TKO_602 ESCs(day 0), differentiated cells from each ESCs(day4 and day7).

overall_design:
To form embryoid bodies (EBs), all ES cells were cultured in MEF medium without LIF.
EBs were placed in a cell culture plate, and adherent cells were cultured. To induce primitive streak formation, 10 ng/ml Activin A (R&D Systems) was added.
Total RNA was extracted using the RNeasy Plus Mini Kit (Qiagen). Microarray expression analysis was performed using RNA extracted from mouse ESCs and their derivatives.

first: Takamasa

last: Ito

first: Fumihito

last: Miura

first: Takashi

first: Shoji

last: Tajima

first: Nasako

last: Tada


title: Single cell transcriptome of  human embryonic stem cell-derived neurons spanning the rostrocaudal and dorsoventral axes

first: Sushmita

last: Roy

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

overall_design: Refer to individual Series


title: Glucose PTS modulates pyruvate metabolism, bacterial fitness, and microbial ecology in oral biofilm

city: Gainesville

first: Alejandro

last: Riveros Walker

state: Fl

address: 1395 Center Drive

department: Oral Biology

institute: University of Florida

summary: Recently identified spontaneous mutants of major glucose-PTS (manLMNO) in stocks of Streptococcus sanguinis SK36 showed enhanced fitness in low-pH environment. Transcriptomic and metabolomic analyses of the manL mutant (SK36/manL) revealed redirection of pyruvate from production of lactate to acetate for extra energy extraction, resulting in excretion of greater amounts of pyruvate and H2O2, and increased expression of multiple alkali-generating activities. Genes showing increased expression in SK36/manL also included several carbohydrate transporters, putative extracellular glycosidases, intracellular polysaccharide (IPS) locus, pathways for catabolism of acetoin, ethanolamine, ascorbate, and formate, genes required for membrane biosynthesis, and those for motility and attachment.

overall_design: A wild-type S. sanguinis strain SK36 and its isogenic mutant deficient in glucose-PTS (manL) were each cultured (n = 3) to exponential phase in TY medium supplemented with 20 mM glucose, treated with RNAprotect reagent, and harvested for RNA extraction and RNA-Seq analysis

first: Lin

last: Zeng

first: Zachary

last: Taylor

first: Robert

last: Burne

last: Walker


title: JUN Regulation of Injury-induced Enhancers in Schwann Cells

status: Public on Jul 27 2022

city: Chicago

first: Rajeshwar

last: Awatramani

state: Illinois

address: 320 E Searle

department: Neurology

institute: Northwestern University

summary: To determine gene expression differences between control transected sciatic nerves (from C57BL/6 WT mice) and mutant (Homozyous Shh 1/2/3 enhancer deletion). Our analysis revealed significant differential gene expression between the control samples and the mutants.

overall_design: mRNA profiling of control (C57BL/6) transected sciatic nerves, compared to age-matched homozyous Shh 1/2/3 enhancer deletion transected sciatic nerves (1DPI)

first: Raghu

last: Ramesh

first: Yanti

last: Manurung

first: Ki

middle: H

last: Ma

first: Todd

last: Blakely

first: Seongsik

last: Won

first: Oscar

last: Moreno-Ramos

first: Eugene

last: Wyatt

first: John

last: Svaren


title: Parathyroid Hormone Treatment Effect on Gene Expression in Primary Calvarial Osteoblasts

city: Charleston

first: Jeremy

last: Barth

state: SC

address: 173 Ashley Ave, BSB 627

institute: MUSC

summary: The effect of parathyroid hormone (PTH) treatment was tested on osteoblasts prepared from calvaria of C57BL/6J mice 7-10 days old. Osteoblasts were treated with either human parathyroid hormone (1-34), bovine (D-Trp12,Tyr34) parathyroid hormone (7-34) amide or vehicle control for 4 hr. Gene expression effects were evaluated by DNA microarray.

overall_design: Mouse osteoblasts were prepared independently for each biological replicate. Three biological replicates were used for each treatment. Osteoblasts were treated with either 100 nM human parathyroid hormone (1-34), 1 µM bovine (D-Trp12,Tyr34) parathyroid hormone (7-34) amide or vehicle for 4 hr. Total RNAs were collected and 100 ng analyzed for gene expression using Affymetrix Mouse Gene 2.0 ST GeneChips.

first: Louis

last: Luttrell

middle: L


title: Comparative transcriptome analysis reveals defense responses against soft rot in Chinese cabbage

city: Baoding

first: mengyang

last: liu

state: Hebei

address: Hebei Agricultural University West Campus, Lianchi District

institute: Hebei Agricultural University

summary: Pectobacterium carotovorum ssp. carotovorum (Pcc) is a necrotrophic bacterial species that causes soft rot disease in Chinese cabbage. In this study, plants harboring the resistant mutant sr gene, which confers resistance against Pcc,were screened from an 800 M2 population mutated by ethyl methane sulfonate (EMS) and scored in vitro and in vivo for lesion size. The transcript profiles showed ~512 differentially expressed genes (DEGs) between sr and WT plants occurring between 6 and 12 h postinoculation (hpi), which corresponded to the important defense regulation period (resistance) to Pcc in Chinese cabbage. The downstream defense genes (CPK, CML, RBOH MPK3, and MPK4) of pathogen pattern-triggered immunity (PTI) were strongly activated during infection at 12 hpi in resistant mutant sr; PTI appears to be central to plant defense against Pcc via recognition by three putative pattern recognition receptors (PRRs; BrLYM1-BrCERK1, BrBKK1/SERK4-PEPR1, BrWAKs). Pcc triggered the upregulation of the jasmonic acid (JA) and ethylene (ET) biosynthesis genes in mutant sr, but auxins and other hormones may have affected some negative signals.Endogenous hormones (auxins, JAs, and SA), as well as exogenous auxins (MEJA and BTH), were also verified as functioning in the immune system. Concurrently, the expression of glucosinolate and lignin biosynthesis genes was increased at 12 hpi in resistant mutant sr, and the accumulation of glucosinolate and lignin also indicated that these genes have a functional defensive role against Pcc. Our study provides valuable information and elucidates the resistance mechanism of Chinese cabbage against Pcc infection.

overall_design: The RNA-Seq data from three biological replicates of Chinese cabbage soft rot-resistant mutant sr and WT at 0, 6, 12, and 24 hpi (24 samples).

first: Mengyang

last: Liu

first: Fang

last: Wu

first: Shan

last: Wang

first: Yin

last: Lu

first: Xueping

last: Chen

first: Yanhua

first: Aixia

last: Gu

first: Jianjun

last: Zhao

first: Shuxing

last: Shen


title: A novel somatic mutation in GNAQ in Sturge-Weber Syndrome provides insight into disease pathogenesis

city: Durham

first: Daniel

last: Snellings

state: NC

address: 213 Research Drive

institute: Duke University

summary: Sturge-Weber syndrome (SWS) is a sporadic, congenital, neuro-cutaneous disorder characterized by a mosaic, capillary malformation. SWS and isolated capillary malformations are caused by a somatic activating mutation in GNAQ encoding the G protein subunit alpha-q protein.  The missense mutation R183Q is the sole GNAQ mutation identified thus far in affected tissues of 90% of SWS patients.  In this study, we sequenced skin biopsies of affected capillary malformations from 9 patients. We identified the R183Q mutation in nearly all samples, but one sample exhibited a Q209R mutation.  This new mutation occurs at the same residue as the constitutively-activating Q209L mutation, commonly seen in tumors.  However, Q209R is a rare variant in this gene.  To compare the effect of the Q209R mutation on downstream signaling, we performed reporter assays with a GNAQ-responsive reporter co-transfected with either GNAQ WT, R183Q, Q209L, Q209R, or C9X (representing a null allele). Q209L showed the highest reporter activation, with R183Q and Q209R showing significantly lower activation.  To determine whether these mutations had similar or different downstream consequences we performed RNAseq analysis in microvascular endothelial cells (HMEC-1) electroporated with the same GNAQ variants.  The R183 and Q209 missense variants caused extensive dysregulation of a broad range of transcripts compared to the WT or null allele, confirming that these are all activating mutations. However, the missense variants exhibited very few differentially expressed genes (DEGs) when compared to each other. These data suggest that these activating GNAQ mutations differ in magnitude of activation but have similar downstream effects.

overall_design: 5 conditions, 3 replicates per condition

first: Francesca

last: Galeffi

first: Sarah

last: Wetzel-String

first: Nicole

last: Kastelic

first: Jaye

last: Bullock

first: Carol

last: Gallione

first: Paula

last: North

first: Douglas

last: Marchuk


title: Expression data from CCL2 overexpression in MCF7 breast cancer cell line and CCL2 knockdown in MB231 breast cancer cell line.

city: Taipei

first: Michael

last: Hsiao

address: Academia Road, Section 2, Nankang, Taipei, 115, Ta

department: Genomics Research Center

institute: Academia Sinica

summary:
We demonstrate that AK4 down-regulation shRNAs significantly reduced cell migration and invasion in highly invasive lung cancer cell lines in vitro, as well as in lung metastases in vivo
We used microarrays to analyze the AK4 regulated gene expression underlying invasion-metastasis cascade.

overall_design: CL1-0 lung adenocarcinoma cells with AK4 overexpression and CL1-5 cells with AK4 knockdown were selected for RNA extraction and hybridization on Affymetrix microarrays.

first: Yuan-Feng

last: Lin


title: Gene expression profiling of BMMC derived-MMCs and BMMC-derived CTMCs.

city: Fukuoka

first: Yasuyuki

last: Ohkawa

address: 3-1-1 Maidashi

institute: Medical Institute of Bioregulation

summary: Mast cells are generally classified into two phenotypically distinct populations: mucosal-type mast cells (MMCs) and connective tissue-type mast cells (CTMCs). However, the molecular basis determining the different characteristics of the mast cell subclasses still remains unclear.Here, we report the characterization of MMCs and CTMCs derived from mouse bone marrow mast cells (BMMCs).

overall_design: The gene expression profiles of BM-MMCs and BM-CTMCs.

first: Tomoko

last: Yamaguchi

first: Kenji

last: Kawabata


title: Hhigh-throughput sequencing of in vitro fecal fermentation samples

city: Hangzhou

first: zuorui

last: xie

address: Zhejiang Gongshang University

institute: ZFM

summary: We report the use of high-throughput sequencing technology to detect the microbial composition and abundance of mice grastic contents before and after Helicobacter pylori infection or Lactobacillus paracasei ZFM54 pretreatment/treatment. The genomic DNA was obtained by the QIAamp PowerFecal DNA Kit. Then, the DNA samples were sent to BGI Genomics Co., Ltd. (Shenzhen, China) for V3-V4 region of the 16S rRNA gene high-throughput sequencing with an Illumina MiSeq platform. DNA samples were sequenced using primers 338F (forward primer sequence ACTCCTACGGGAGGCAGCAG)-806R (reverse primer sequence GGACTACHVGGGTWTCTAAT). The sequencing analyses were carried out using silva138/16s database as a reference for the assignation of Amplicon Sequence Variant (ASV) at 100% similarity.

overall_design: Examination of microbial composition and abundance differences in gastric  contents.

first: Qing

first: Ping

last: Li

first: Qingqing

last: Zhou

first: Nuzhat

last: Qureshi

first: Bingyao

last: Xue

first: Zuorui

last: Xie


title: Luteolin protects against obese sarcopenia in mice with high-fat diet-induced obesity by ameliorating inflammation and protein degradation in muscle

city: Daegu

first: Myung-Sook

last: Choi

address: 1370, Sankyuk-Dong, Buk-gu

department: Food and Nutrition

institute: Kyungpook National University

summary: Although there are studies on obesity and sarcopenia, our understanding of obesity-mediated sarcopenia is insufficient. Additionally, no studies have investigated the application of luteolin in sarcopenia. We attempted to determine the effect of luteolin on obese sarcopenia in mice with high-fat diet (HFD)-induced obesity. Luteolin exerted suppressive effects on obesity, inflammation, and protein degradation in HFD-fed obese mice. Luteolin inhibited lipid infiltration into the muscle and decreased p38 and JNK activity and mRNA expression of inflammatory factors, such as TNFα, Tlr2, Tlr4, MCP1, and MMP2, in the muscle. Suppression of muscle inflammation by luteolin led to the inhibition of myostatin, FoxO, atrogin, and MuRF expression, which reduced protein degradation and improved muscle function. This is the first study to demonstrate that luteolin exerts a protective effect against obese sarcopenia, as its anti-obesity and anti-inflammatory activities inhibited protein degradation. Therefore, luteolin may be a useful supplement for prevention of obese sarcopenia.

overall_design: Total RNA of liver and adipose tissues was obtained from normal diet, high-fat diet and luteolin added high-fat diet-fed mice and mRNA expression-associated with protein metabolism was measured.

first: Ji-Won

last: Kim

first: Su-Kyung

last: Shin

first: Eun-Young

last: Kwon


title: Human - murine concordance of molecular signatures in nerve-sparing murine partial bladder outlet obstruction (NeMO)

city: Toronto

first: Paul

last: Delgado-Olguin

state: Ontario

department: Molecular Genetics

country: Canada

institute: University of Toronto

summary: Recently, we described a nerve-sparing mid-urethra model of partial outlet obstruction (NeMO) that has high consistency and minimal mortalities, unlike the traditional model of obstruction proximal to the bladder neck. To uncover pathogenic pathways in PBO, we performed NeMO and examined the transcriptional responses in the bladder. NeMO increased bladder mass, relative bladder mass, hyperactivity and decreased voiding efficiency. In NeMO vs. sham bladders, there were 831 differentially expressed genes, which correlated significantly with physiologic parameters. Of the 796 genes mapped to human orthologues, upregulated genes were enriched for functions related to extracellular matrix, and cytokine activation, and downregulated genes were enriched for functions relating to muscle contraction and metabolism. To identify candidate drug targets for the treatment of PBO, we analysed the conserved transcriptional response to PBO in human and mouse. Gene sets related to cytokine activation, including the TNF pathway, were consistently upregulated in both human and mouse bladders affected by obstruction, revealing a potential therapeutic target. Accordingly, we depleted macrophages, which are an important source of TNF, with clodronate (CL). In NeMO, CL significantly decreased hyperactive voiding, residual volumes and improved voiding efficiency (p<0.05). Moreover, the expression levels of cytokines/chemokines correlated with several bladder functional parameters. Thus, genes that control progression of pathology in bladder obstruction are consistently dysregulated in NeMO and human bladders affected by PBO, supporting the use of the nerve-sparing mouse obstruction model for therapeutic exploration.

overall_design: Examination of transcriptome profiles of bladder tissue isolated from Sham-operated or NeMO mice

first: Martin

last: Sidler

first: Abdalla

last: Ahmed

first: Jia-Xin

last: Jiang

first: Dursa

last: Koshkebaghi

first: Ryan

last: Huang

first: Priyank

last: Yadav

first: Dariush

last: Davani

first: Rosanna

last: Weksberg

first: Karen

middle: J

last: Aitken

first: Darius

last: Bägli


title: Single cell transcriptome of regional human embryonic stem cell-derived ventral cultures from the spinal cord

first: Sushmita

last: Roy

summary: We generated single RNA-seq data to measure transcriptional profiles of six hESC-derived ventral populations, representing distinct regions of the developing human spinal cord. These cells are differentiated using a protocol that induces collinear activation of region-specific HOX genes during exposure to FGF8 and Wnt signaling (Lippmann et al, 2015 PMID:25843047). By transitioning to media containing retinoic acid, smoothened agonist (SAG), Purmorphamine (Pur), and DAPT after varying durations of Wnt signaling, ventral neuronal cultures are generated with unique rostrocaudal identities. In total we recovered the transcriptomes of 12,540 cells. Analysis verified expression of increasingly caudal HOX paralogs that could be correlated to cervical (HOX1-8; H24-vN, H48-vN, and H72-vN), thoracic (HOX1-9; H120-vN), lumbar (HOX1-11; H168-vN), and lumbosacral (HOX1-13; H216-vN) spinal regions. However, inconsistent differentiation between samples resulted in a mix of neural progenitor, neuron, mesodermal, and neural crest derivatives.

overall_design: The data consist of single RNA-seq measurements taken from hESC-derived cultures that were exposed to CHIR99021 for different amount of time (24-216hr) prior to RA, SAG, Pur, and DAPT treatment.

first: Nisha

last: Iyer

first: Junha

first: Randolph

last: Ashton


title: Gene expression profile at single cell level of human cerebral organoid transplants harvested from the mouse brain.

city: Milwaukee

first: Yu-Chieh

last: Wang

address: 8701 Watertown Plank Rd.,

department: Dermatology and Cancer

institute: Medical College of Wisconsin

summary: Transplanted human cerebal organoids were developed from induced pluripotent stem cells that were reprogrammed from human urine-contained epithelial cells.  Immune-compromised mice with brain lesions caused by distal middle cerebral artery occlusion (dMCAO) were used as recipients for transplantation.  The organoids were grafted at the lesion cavity.  Each transplant sample was collected from the brain of a mouse, disassociated, and sequenced using a 10x Genomics single-cell RNA-sequencing platform.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Three tissue samples involved in this submitted single-cell RNA sequencing data set were human cerebral organoid transplants harvested from the mouse brain.

first: Jonnie

last: Hu

first: Jordan

middle: T

last: Bird

first: Stephanie

last: Byrum


title: Single cell evaluation of the developing pancreatic tumor microenvironment and its response to chronic jetlag

first: Sean

last: Ronnekleiv-Kelly

state: Wisconsin

address: 1400 University Ave

department: Surgery

institute: University of Wisconsin

summary: Chronic jetlag is a risk factor for cancer development, we subjected mice that develop pancreatic cancer to normal or chronic jetlag conditions and used scRNAseq to evaluate the developing tumor microenvironment

overall_design: 1 pololed Male/Female from 5 and 9 month old KrasG12D Pdx1-Cre pancreata subjected to either normal circadian or chonic jetlag conditions were compared with scRNAseq

first: Patrick

middle: B

last: Schwartz

first: Mark

last: Berres

first: Derek

last: Pavlec


title: Immune crosstalk between pancreas, gut and liver through lymph node sharing [scRNA-seq]

first: Daria

last: Esterhazy

state: IL

address: 924 E 57th Street

department: Pathology

institute: University of Chicago

summary:
To investigate tissue of origin effects on migratory dendritic cell (DC) gene expression in shared lymph nodes we performed bulk RNAseq of DCs from each tissue (liver, pancreas, duodenum).
We then performed single cell sequencing of the DCs within the draining lymph nodes.

overall_design: scRNAseq of FACs purified migratory dendritic cells from liver, pancreas and duodenum (n=4 each tissue, each tissue is 2 mice pooled) and single cell sequencing of YFP+ cells sorted from CD11c-YFP pancreatic-duodenal lymph nodes (n=3 each lymph node, each lymph node is 10 mice pooled).

first: Hailey

last: Brown


title: Immune crosstalk between pancreas, gut and liver through lymph node sharing [bulk RNA-seq]

overall_design: Bulk RNAseq of FACs purified migratory dendritic cells from liver, pancreas and duodenum (n=4 each tissue, each tissue is 2 mice pooled) and single cell sequencing of YFP+ cells sorted from CD11c-YFP pancreatic-duodenal lymph nodes (n=3 each lymph node, each lymph node is 10 mice pooled).


title: Immune crosstalk between pancreas, gut and liver through lymph node sharing


title: Gene expression profile at single cell level of hESC H9 derived hemognic niches at Day 18 of in vitro differentiation

city: Randwick

first: Jingjing

last: Li

state: New South Wales

address: UNSW, Gate 11 Botany Street

department: Graduate School of Biomedical Engineering

institute: UNSW

summary: Small drug (SB/CHIR) treatment and orbital shear treatment promotes the generation of hemogenic endothelium and multipotent hematopoieitic progenitor cells. We used single cell RNA sequencing (scRNA-seq) to analyze the diversity of hemogenic niches derived from hESC H9 line at day 18 of in vitro differentiation.

overall_design: Hemogenic niches derived from day 18 hESC H9 differentiation were harvested and anlyzed using scRNAseq. a 22 balanced experimental design was used to quantify the effect of circuilatory flow (shear) and small drug treatment (SB/CHIR).

first: Robert

last: Nordon

first: Ziqi

last: Yang

first: Nona

last: Farbehi


title: A robust machine learning approach for missing persons cases with high genotyping errors

city: Fort Worth

first: Jianye

last: Ge

state: TX

address: 3500 Camp Bowie Blvd

department: Center for Human Identification

institute: University of North Texas Health Science Center

type:
Genome variation profiling by SNP array
SNP genotyping by SNP array

summary: Estimating the relationships between individuals is one of the fundamental challenges in many fields. In particular, relationship estimation could provide valuable information for missing persons cases. The recently developed investigative genetic genealogy approach uses high-density single nucleotide polymorphisms (SNPs) to determine close and more distant relationships, in which hundreds of thousands to tens of millions of SNPs are generated either by microarray genotyping or whole-genome sequencing. The current studies usually assume the SNP profiles were generated with minimum errors. However, in the missing person cases, the DNA samples can be highly degraded, and the SNP profiles generated from these samples usually contain lots of errors. In this study, a robust machine learning approach was developed for estimating the relationships with high error SNP profiles. In this approach, a hierarchical classification strategy was employed first to classify the relationships by degree and then the relationship types within each degree separately. As for each classification, feature selection was implemented to gain better performance. Both simulated and real data sets with various genotyping error rates were utilized in evaluating this approach, and the accuracies of this approach were higher than individual measures; namely, this approach was more accurate and robust than the individual measures for SNP profiles with genotyping errors. In addition, the highest accuracy could be obtained by providing the same genotyping error rates in train and test sets, and thus estimating genotyping errors of the SNP profiles is critical to obtaining high accuracy of relationship estimation.

overall_design: 8 UTAH samples were genotyped using Illumina Infinium Omni5-4 Kit with various input DNA (i.e., 50ng, 500pg, 100pg); the genotyping error rates for different input DNA should be different

first: Meng

last: Huang

first: Muyi

last: Liu

first: Hongmin

first: Jonathan

last: King

first: Amy

last: Smuts

first: Bruce

last: Budowle


title: The RNA-seq in inguinal white adipose tissue in Cdo1flox/flox mice and Cdo1AKO mice

city: Shanghai

first: Ying-Ying

last: Guo

address: Dongan Road, Xuhui District

department: School of basic medical sciences

institute: Fudan University

summary: To investigate the function of cysteine dioxygenease 1 (Cdo1) in adipose tissue, we isolated RNA from control (Cdo1flox/flox) and Cdo1AKO (Konckout Cdo1 in adipose tissue ) mice for RNA seq

overall_design: The 8-week-old control (Cdo1folx/flox) and Cdo1AKO(Konckout Cdo1 in adipose tissue) were fed with high fat diet for 15 weeks to produce obesity model. Then the RNA from inguinal white adipose tissue were isolated for RNA-seq

first: Liang

first: Qi-Qun

last: Tang


title: RNA-seq and ATAC-seq in MEF and mESC sequenced on different instrument models

city: Brisbane

first: Christian

last: Nefzger

state: Queensland

address: 306 Carmody Road

department: Institute for Molecular Biology

institute: The University of Queensland

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

overall_design: Refer to individual Series


title: The Analysis of HBV-ACLF plasma-derived exosomal sncRNA-seq

city: Guangzhou

first: Wenli

last: Xu

state: Guangdong

address: Guangzhou, Guangdong Province, 510630, China.

institute: The Third Affiliated Hospital of Sun Yat-sen University

summary: To identify the sncRNAs related to HBV-ACLF, we performed small RNA-seq in plasma exosomes collected from 3 normal subjects, 4 chronic hepatitis B (CHB) patients with flare and 6 HBV-ACLF patients in the discovery cohort.

overall_design: Small RNA-seq profiles of the 13 subjects(3 normal subjects, 4 chronic hepatitis B (CHB) patients with flare and 6 HBV-ACLF patients) were generated by high-throughput sequencing , using Illumina 3000.The software SPORTS (version 1.1)was applied to annotate the raw sncRNA-seq data with one mismatch tolerance.

first: Mingxue

last: Yu

first: Yuankai

last: Wu

first: Yusheng

last: Jie

first: Xiangyong

first: Xinxin

last: Zeng

first: Fangji

first: Yutian

last: Chong


title: Transcription factor RUNX3 mediates plasticity of ThGM cells toward Th1 phenotype.

city: Philadelphia

first: Sankar

last: Addya

state: PA

address: 233 South 10th Street

department: Kimmel Cancer Center

institute: Thomas Jefferson University Hospital

summary: GM-CSF-producing T helper (Th) cells play a crucial role in the pathogenesis of autoimmune diseases such as multiple sclerosis (MS). Recent studies have identified a distinct population of GM-CSF-producing Th cells, named ThGM cells, that also express cytokines TNF, IL-2, and IL-3, but lack expression of master transcription factors (TF) and signature cytokines of commonly recognized Th cell lineages. ThGM cells are highly encephalitogenic in a mouse model of MS, experimental autoimmune encephalomyelitis (EAE). Similar to Th17 cells, in response to IL-12, ThGM cells upregulate expression of T-bet and IFN-g and switch their phenotype to Th1. Here we show that in addition to T-bet, TF RUNX3 also contributes to the Th1 switch of ThGM cells. T-bet-deficient ThGM cells in the CNS of mice with EAE had low expression of RUNX3, and knockdown of RUNX3 expression in ThGM cells abrogated the Th1-inducing effect of IL-12. Comparison of ThGM and Th1 cell transcriptomes showed that ThGM cells expressed a set of TFs known to inhibit the development of other Th lineages. Lack of expression of lineage-specific cytokines and TFs by ThGM cells, together with expression of TFs that inhibit the development of other Th lineages, suggests that ThGM cells are a non-polarized subset of Th cells with lineage characteristics.

overall_design: Human RNA-sequencing: Human ThGM, Th1, and GM-CSF+Th1 cells were isolated from peripheral blood of healthy donors using a combination of fllow cytometry cell sorting and cytokine sceretion assay. RNA from human ThGM, Th1, and GM-CSF+Th1 cells were isolated and their transcriptome were analyzed by RNA sequencing. MouseRNA sequencing: Mouse naive CD4+ T cells were polarized to ThGM and Th1 cells and RNA from several time points were isolated and analyzed using RNA sequencing.

first: Javad

last: Rasouli

first: Gaurave

last: Kumar

first: Adam

last: Ertel

first: Paolo

last: Fortina

first: Abdolmohamad

last: Rostami

first: Bogoljub

last: Ciric


title: ATAC-seq data in MEF and mESC sequenced by BGI DNBSEQ-G400 platform and Illumina HiseqX10 instruments

summary: We benchmark Illumina’s HiseqX10 instrument against Beijing Genomics Institute’s (BGI) DNBSEQ-G400 platform, a considerably cheaper sequencing alternative. For comparisons, the same bulk ATAC-seq libraries generated from pluripotent stem cells (PSCs) and fibroblasts were sequenced on both platforms. Both instruments generate sequencing reads with comparable mapping rates and genomic context. However DNBSEQ-G400 data contained a significantly higher number of small, sub-nucleosomal reads (>30% increase) and a reduced number of bi-nucleosomal reads (>75% decrease), which resulted in narrower peak-bases and improved peak calling, enabling the identification of 4% more differentially accessible regions between PSCs and fibroblasts. Ability to identify master TFs that underpin the PSC state relative to fibroblasts, including aggregate and de novo foot-printing capacity, were highly similar between data generated on both platforms.

overall_design:
Comparative open-chromatin profile (ATAC-seq) for PSCs and fibroblasts.
OMNI-ATACseq libraries were generated from FACS purified cells (in case of MEFs: Thy1+ ; in case of mESCs: Thy1-/Ssea1+/Epcam+)  according to the standard protocol (see doi: 10.1038/nmeth.4396). Afterwards, libraries were purified using a QIAGEN MinElute PCR purification kit (QIAGEN, Cat#28004) followed by Agencourt AMPure XP beads (Beckman Coulter, Cat#A63880) according to the manufacturer’s recommendations. Library fragments ranging from 150 to 700 bp were enriched and the final elution volume was 21 ul. The finalized libraries were provided to BGI for sequencing. HiSeqX10 sequencing was performed in 150bp PE mode followed by read trimming to 100bp PE for analysis. In case of sequencing on the DNBSEQ-G400 instrument libraries were converted to nanoballs and sequenced according to established workflows in 100bp PE mode (see doi: 10.1093/nargab/lqaa034).

first: Marina

last: Naval Sanchez

first: Nikita

last: Deshpande

first: Minh

last: Tran

first: Quan

last: Nguyen


title: Insight into the metabolic adaptations of electrically pulse-stimulated human myotubes using global analysis of the transcriptome and proteome

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

country: Netherlands

institute: Wageningen University

summary: Regular physical exercise evokes profound physiological responses which are strongly associated with many health benefits. However, the details of cellular networks and mechanisms underlying the adaptive responses to exercise remain to be elucidated. We have previously shown the usefulness of electrical pulse stimulation (EPS) to investigate metabolic effects of exercise in cultured human myotubes. The aim of the present study was to uncover networks of signaling pathways and regulatory molecules responsible for the metabolic effects of exercise in human skeletal muscle cells exposed to chronic EPS. Differentiated myotubes were subjected to two different EPS protocols (protocol 1; 2 ms, 10 V, 0.1 Hz for 24 h or protocol 2; 2 ms, 30 V, and 1 Hz for 48 h). Fuel handling was assessed using radiolabeled substrates. The transcriptome, cell proteome, and secreted proteins from EPS-treated and untreated myotubes were analyzed using a combination of high-throughput RNA sequencing, microarray, and high-resolution liquid chromatography mass spectrometry. Independent validation of selected putative myokines were measured using ELISA or multiplex assay.  Oxidative metabolism was enhanced in human myotubes exposed to EPS protocol 1. A total of 81 differentially regulated proteins and 952 differentially expressed genes (DEGs) were observed in the cells after EPS protocol 1. Gene ontology (GO) analysis indicated that significantly regulated proteins and genes were enriched in biological processes related to glycolytic pathways, positive regulation of fatty acid oxidation, and oxidative phosphorylation, as well as muscle contraction, autophagy/mitophagy, and oxidative stress. Moreover, proteomic identification of secreted proteins revealed extracellular levels of 137 proteins were changed in myotubes subjected to EPS protocol 1. We also found some degree of overlap between the DEGs found in myotubes submitted to EPS protocol 1 and protocol 2. Among these DEGs was a myokine, leukemia inhibitory factor, which showed to enhance the glucose uptake in skeletal muscle cells, indicating autocrine mechanism to maintain metabolic homeostasis. Collectively, our data provides new insight into the transcriptome, proteome and secreted proteins alterations following in vitro exercise and is a valuable resource for understanding the molecular mechanisms and regulatory molecules mediating the beneficial metabolic effects of exercise.

overall_design: Human myotubes from four donors were exposed to electrical pulse stimulation (EPS) or control for 48 h after which gene expression was profiled.

first: Abel

last: Mengeste

first: Natasa

last: Nikolic

first: Andrea

last: Fernandez

first: Yuan

middle: Z

last: Feng

first: Tuula

last: Nyman

first: Sander

last: Kersten

first: Fred

last: Haugen

first: Eili

last: Kase

first: Vigdis

last: Aas

first: Arild

last: Rustan

first: G

last: Thoresen


title: Massive accumulation of sphingomyelin affects the lysosomal and mitochondria compartments and promotes apoptosis in type A Niemann- Pick disease

city: Pieve Emanuele-Milan

first: Giulia

last: Solda'

address: via Rita Levi Montalcini 4

country: Italy

institute: Humanitas University

summary: Niemann-Pick type A disease (NPA) is a rare lysosomal storage disorder caused by mutations in the gene coding for the lysosomal enzyme acid sphingomyelinase (ASM). ASM deficiency leads to the consequent accumulation of its uncatabolized substrate, the sphingolipid sphingomyelin (SM), causing severe progressive brain disease.   To study the effect of the aberrant lysosomal accumulation of SM on cell homeostasis we loaded skin fibroblasts derived from a NPA patient with exogenous SM to mimic the levels of accumulation characteristic of the pathological neurons. In SM-loaded NPA fibroblasts we found the blockage of the autophagy flux and the impairment of the mitochondrial compartment paralleled by the altered transcription of several genes, mainly belonging to the electron transport chain machinery and to the cholesterol biosynthesis pathway. In addition, SM loading induces the nuclear translocation of the transcription factor EB that promotes the lysosomal biogenesis and exocytosis. Interestingly, we obtained similar biochemical findings in the brain of the NPA mouse model lacking ASM (ASMKO mouse) at the neurodegenerative stage. Our work provides a new in vitro model to study NPA etiopathology and suggests the existence of a pathogenic lysosome-plasma membrane axis that with an impairment in the mitochondrial activity is responsible for the cell death.

overall_design: mRNA profiles of fibroblasts from a NPA patient treated (3 replicates) or not (3 replicates) with sphingomyelin (SM) for 30 days

last: Soldà

first: Emma

last: Carsana

last: Lunghi

first: Simona

last: Prioni

first: Laura

last: Mauri

first: Nicoletta

last: Loberto

first: Rosanna

last: Asselta

first: Letizia

last: Straniero

first: Fabio

last: Zucca

first: Rosaria

last: Bassi

first: Alessandro

last: Prinetti

first: Elena

last: Chiricozzi

first: Sandro

last: Sonnnino

first: Stefano

last: Duga

first: Maura

last: Samarani

first: Massimo

last: Aureli


title: Comparing dormancy in two distantly related tunicates reveals morphological, molecular, and ecological convergences and repeated co-option

city: Santa Barbara

first: Laurel

middle: S.

last: Hiebert

state: CA

address: Molecular, Cellular, and Developmental Biology

institute: University of California Santa Barbara

summary: Many asexually-propagating marine invertebrates can survive extreme environmental conditions by developing dormant structures, i.e., morphologically simplified bodies that retain the capacity to completely regenerate a functional adult when conditions return to normal. Here, we examine the environmental, morphological, and molecular characteristics of dormancy in two distantly related clonal tunicate species: Polyandrocarpa zorritensis and Clavelina lepadiformis. In both species, we report that the dormant structures are able to withstand harsher temperature and salinity conditions compared to the adult, and are the dominant forms these species employ to survive the colder winter months. By finely controlling the entry and exit of dormancy in laboratory-reared individuals, we were able to select and characterize the morphology of dormant structures associated with their transcriptome dynamics. In both species, we identified putative stem and nutritive cells in structures that resemble the earliest stages of asexual propagation. By characterizing gene expression during dormancy and regeneration into the adult body plan (i.e., germination), we observed that genes which control dormancy and environmental sensing in other metazoans, notably HIF-α and insulin signaling genes, are also expressed in tunicate dormancy. Germination-related genes in these two species, such as the retinoic acid pathway, are also found in other unrelated clonal tunicates during asexual development. These results are suggestive of repeated exaptation of conserved eco-physiological and regeneration programs for the origin of novel dormancy-germination processes across distantly related animal taxa.

sample_organism:
Clavelina lepadiformis
Polyandrocarpa zorritensis

overall_design: Two species, 6 stages/tissues (zooid, bud, dormant stage, stolon, germination), 3 replicates of each, except germination had 6 replicates (half germinated at 18 degrees and half germinated at 24 degrees). All germination samples were allowed to germinate for 48hrs. Germination samples across temperatures were combined in analysis.

first: Marta

last: Scelzo

first: Alexandre

last: Alié

first: Anthony

last: De Tomaso

first: Federico

last: Brown

last: Tiozzo


title: The transcription factor KLF4, together with PAX6, is essential for the commitment of corneal epithelial cell fate

city: Kyoto

first: Koji

last: Kitazawa

state: Kyoto

address: 465 Kajiicho Kamigyoku

department: Ophthalmology

institute: Kyoto Prefectural University of Medicine

summary: Lineage-specific transcription factors (TFs) play key roles in maintaining the unique properties of cells, but the molecular mechanism that regulates the homeostasis of human corneal epithelial cells (CECs) is still poorly understood. We aimed to modulate KLF4 and PAX6 in human CECs using gene knockout system to clarify the regulatory network of KLF4, and then elucidate how KLF4 regulates the transcriptional genes of human CECs compared with PAX6. We performed a functional analysis of KLF4 via gene knockout using a lentivirus vector that carries both Cas9 and guide RNAs. We designed guide RNAs targeted for KLF4 and PAX6, and created KLF4-, PAX6-, and both KLF4- and PAX6-depleted CECs (KLF4-KO, PAX6-KO, and DKO, respectively).  An empty vector was used as a control. The morphology of KLF4-KO CECs displayed an epithelial-mesenchymal transition (EMT)-like change, including upregulation of mesenchymal genes and downregulation of epithelial genes, as well as downregulation of keratin (KRT) 3 and KRT12. Global analyses using NGS revealed that the downregulated genes in KLF4-KO CECs were enriched in more widely keratin-related genes than PAX6-KO CECs.  DKO cells showed disruption of the epithelial barrier due to downregulation of epithelial genes and showed more increase of KRT1 and KRT10 than PAX6-KO and KLF4-KO CECs, respectively. In conclusion,  KLF4 modulates keratin-related genes as well as EMT-related genes and, together with PAX6, co-regulates the human CEC identity.

overall_design: mRNA profiles of KLF4 depleted-corneal epithelial cells

first: Masahiro

last: Nakamura


title: RNA-seq data in MEF and mESC sequenced by HiSeq 3000

first: Christian

last: Nefzger

overall_design: Comparative RNA-seq  for PSCs and fibroblasts.

first: Marina

last: Naval Sanchez

first: Nikita

last: Deshpande

first: Minh

last: Tran

first: Quan

last: Nguyen


title: Mycobacterium abscessus HelR interacts with RNA Polymerase to confer intrinsic rifamycin resistance

city: Albany

first: Pallavi

last: Ghosh

state: NY

address: 150 New Scotland Ave

department: New York State Department of Health

institute: Wadsworth Center

summary: Using RNA sequencing we show that exposure of M. abscessus to sublethal doses of RIF results in ~25-fold upregulation of Mab_helR; an isogenic deletion mutant of Mab_helR is hypersensitive to RIF and RBT, and over-expression of Mab_helR confers RIF tolerance in M. tuberculosis, implying that Mab_helR constitutes a significant determinant of inducible RIF and RBT resistance.

overall_design: RNA-seq data for M. abscessus ATCC19977 in the presence and absence of rifampicin

first: Kelley

last: Hurst-Hess

first: Aavrati

last: Saxena

first: Pauami

last: Rudra