title: Microarray on proximal epididymis from Ctl and cKO mouse

status: Public on Jun 23 2022

city: Québec

first: Antoine

last: BODEIN

state: QC

address: 2705 Bd Laurier

institute: Université Laval

summary:
Microarray were performed on Ctl and cKO mouse after surgery, proximal epididymis of SHAM and the EDL epididymides were collected
We used microarrays to detail the global programme of gene expression underlying regeneration of the tissue depending on ARL13b expression on basal cell

overall_design: Eight weeks old mice from control (Ctl) or cKO (conditional knock out of Arl13b in Krt5-positive basal cell) undergo surgery. In each mice, one epididymis was used as a control (Sham) and the other had an efferent duct ligation (EDL). RNA extraction and hybridization on Affymetrix microarrays were then assessed. We then compared the gene expression between Ctl and cKO mice depending on their surgical condition (SHAM/EDL).

first: Laura

last: Girardet

first: Clémence

last: Belleannée


title: IRdb: an insect resistance database

city: Beijin

first: Ruiyan

last: Hou

state: Beijin

address: Datun Road

department: State Key Laboratory of Integrated Management of Pest Insects and Rodents

country: China

institute: Institute of Zoology, Chinese Academy of Sciences

type: Expression profiling by high throughput sequencing

summary: Pesticides are widely used to protect growth of crops and prevent the spread of diseases. However, more and more pest insects have developed resistance to chemical pesticides along with the long-term application of the pesticides. It is very important to explore the molecular mechanisms of insecticide resistance not only for reversing the resistance in insects, but also for finding out new function targets of the insecticides. Recently, the next-generation sequence technique has become an effective tool to screen resistance genes and has developed transcriptome profiles of various species. However, a comprehensive database to collect these transcriptome data remains poorly developed. In this study, we constructed a database for insect resistance called IRdb, which contains gene count data from various insect species analyzed by a unified process. In addition to the gene data, IRdb also contains 430 unique resistance proteins (experimentally verified proteins manually extracted from literature). Users can discriminate the resistance proteins by submitting fasta sequence of proteins of interest, which can provide clues to detect resistance proteins. The application of resistance protein part in IRdb indicates the accuracy of prediction of IRdb by extracting CTD features and employing random forest. The database IRdb online web server (http://120.27.24.199:20609/) was provided for users to download the transcriptome and protein data for resistance of insects to insecticides and to predict potential resistance proteins.

overall_design: Compare the RNA-seq between sensitive and resistance in third-instar larva and adult Drosophila melanogaster

first: Liang

last: Luo

first: Quan

last: Zou

first: Yi-jun

last: Wu


title: Single cell transcriptomic analysis of human retina and RPE/choroid

city: Philadelphia

first: Dwight

middle: Edward

last: Stambolian

state: PA

address: 422 Curie Blvd.

department: Opthalmalogy

country: USA

institute: University of Pennsylvania

summary: Single-cell gene expression profiling by high throughput sequencing

overall_design: Human retina and RPE/choroid from healthy and age-related macular degeneration donors


title: Investigating human T cell development in the human pediatric thymus using scRNA-seq

city: Ghent

first: Tom

last: Taghon

address: Corneel Heymanslaan 10

country: Belgium

institute: Ghent University

summary: To study human T cell development at the single cell level we profiled thymocytes from 3 pediatric donors using scRNA-seq. The data was subsequently used in the construction of a cell atlas of human thymic development across the life span. This allowed the identification of over 50 cell states in the human thymus and helped map the developmental trajectories of conventional and unconventional T cells throughout development.

overall_design: Single cell transcriptional libraries were generated from human CD3+ and CD3- thymocytes obtained from pediatric donors using the 10X Genomics Chromium 3’ sequencing V2 kit.

first: Marieke

last: Lavaert

first: Niels

last: Vandamme


title: Expression of myeloid inflammation genes in HLADR+ve blood monocytes from healthy control and patients with ARDS

city: Edinburgh

first: John

middle: P

last: Thomson

state: Lothian

address: 27, Strathalmond Road

country: United Kingdom

institute: Thomson Bioinformatics

summary:
Gene expression of HLADR+ve blood monocytes from healthy control and patients with ARDS assayed on NanoString nCounter Human Myeloid Innate Immunity Panel panel.
Nanostring expression data

overall_design: Gene expression of HLADR+ve blood monocytes from healthy control and patients with acute respiratory distress syndrome (ARDS) assayed on NanoString nCounter Human Myeloid Innate Immunity Panel panel.

first: Ananda

middle: S

last: Mirchandani

first: Sarah

middle: R

last: Walmsley


title: Expression of myeloid inflammation genes in blood monocytes from mouse models of hypoxic acute lung injury (ALI) housed in normoxia, hypoxia and hypoxia+CSF1 conditions

summary: Gene expression of blood monocytes from mouse models of hypoxic acute lung injury (ALI) housed in normoxia, hypoxia and hypoxia+CSF1 conditions, assayed on NanoString nCounter Mouse Myeloid Innate Immunity Panel panel (GPL30135)

overall_design: 5000 mouse classical monocytes were sorted from mice treated with LPS and housed in normoxia, hypoxia and hypoxia+CSF1 gating on single DAPI-CD45+LinCD115+Ly6Chi cells into 2ul RLT. Cell pellets were vortexed and centrifuged prior to immediate freezing until ready for processing.  mouse myeloid inflammation NanoString gene expression plates were run as per manufacturer’s instructions


title: RNA-sequencing after sevoflurane exposion in  Rhesus macaque

city: shanghai

first: yanyong

last: cheng

address: 639 Zhizaoju Road

department: Department of Anesthesiology

institute: Shanghai Ninth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine

summary: RNA-sequencing of 4 Rhesus macaque Samples

overall_design: examing 2 conditions, each with 2 replicates

first: Lei

last: Zhang


title: Biological Aging of CNS-Resident Cells Alters the Clinical Course and Immunopathology of Autoimmune Demyelinating Disease

city: Columbus

first: Cankun

last: Wang

state: OH

address: 281 W Lane Ave, Columbus, OH 43210

institute: The Ohio State University Wexner Medical Center

summary: Biological aging is the strongest factor associated with the clinical phenotype of multiple sclerosis (MS). Relapsing remitting MS (RRMS) typically presents in the third or fourth decade, while the mean age of presentation of progressive MS (pMS) is 45 years old. Here we show that experimental autoimmune encephalomyelitis (EAE), induced by the adoptive transfer of encephalitogenic CD4+ Th17 cells, is more severe, and less like to remit, in middle-aged compared with young adult mice. Donor T cells and neutrophils are more abundant, while B cells are relatively sparse, in central nervous system (CNS) infiltrates of the older mice. Experiments with reciprocal bone marrow chimeras demonstrate that radio-resistant, non-hematopoietic cells play a dominant role in shaping age-dependent features of the neuroinflammatory response, as well as the clinical course, during EAE. Reminiscent of pMS, EAE in middle-aged adoptive transfer recipients is characterized by widespread microglial activation. Microglia from older mice express a distinctive transcriptomic profile, suggestive of enhanced chemokine synthesis and antigen presentation. Collectively, our findings suggest that drugs that suppress microglial activation, and acquisition or expression of aging-associated properties, may be beneficial in the treatment of progressive forms of inflammatory demyelinating disease.

overall_design: CD45+ cells were isolated from spinal cord tissue via Fluorescence-activated cell sorting (FACS)

first: Jeffrey

last: Atkinson

first: Anjun

last: Ma

first: Benjamin

last: Segal


title: Hepatocyte-specific knock-out of Nfib aggravates hepatocellular tumorigenesis via enhancing urea cycle

city: Chongqing

first: Li

last: Zhou

state: China

address: No. 76, Linjiang Road, Yuzhong District, Chongqing, China 400010, Telephone:86-023-62887681, Fax:86-

institute: Department of Gastroenterology, Second Affiliated Hospital of Chongqing Medical University

summary:
Purpose: Nuclear Factor I B (NFIB) has been reported to promote tumor growth, metastasis, and liver regeneration, but its mechanism in liver cancer is not fully elucidated. The present study aims to reveal the role of NFIB in hepatocellular carcinogenesis
Methods:In our study, we constructed hepatocyte-specific NFIB gene knockout mice with CRISPR/Cas9 technology (Nfib-/-; Alb-cre), and induced liver cancer mouse model by intraperitoneal injection of DEN/CCl4
Results: First, we found that Nfib-/-; Alb-cre mice developed more tumor nodules and had heavier livers than wild-type mice. H&E staining indicated that the liver histological severity of Nfib-/- group was more serious than that of WT group. Then we found that the differentially expressed genes in the tumor tissue between Nfib-/- mice and wild type mice were enriched in urea cycle. Furthermore, ASS1 and CPS1, the core enzymes of the urea cycle, were significantly upregulated in Nfib-/- tumors. Subsequently, we validated that the expression of ASS1 and CPS1 increased after knockdown of NFIB by lentivirus in normal hepatocytes and also promoted cell proliferation in vitro. In addition, ChIP assay confirmed that NFIB can bind with promoter region of both ASS1 and CPS1 gene
Conclusions:Our study reveals for the first time that hepatocyte-specific knock-out of Nfib aggravates hepatocellular tumor development by enhancing the urea cycle.

overall_design: Liver mRNA profiles of wild-type mice and Nfibf/f Alb-Cre mice aged 14-16 days

first: Song

last: He


title: Expression of myeloid inflammation genes in Lung digest CD64hiSiglecF-Ly6C-MHC- macrophages from PBS-treated mice and CD64hiSiglecF-Ly6C-MHC-Lyve1+ macrophages

summary:
Gene expression in Lung digest CD64hiSiglecF-Ly6C-MHC- macrophages from PBS-treated mice and CD64hiSiglecF-Ly6C-MHC-Lyve1+ macrophages, assayed on NanoString nCounter Mouse Myeloid Innate Immunity Panel panel (GPL30135)
Nanostring expression data

overall_design: C57BL/6J mice were challenged with LPS and housed in 10% hypoxia for 5 days. Mice received i.p PBS or CSF1-Fc daily (4 days) until sacrificed on day 5. Lung digest CD64hiSiglecF-Ly6C-MHC- macrophages from PBS-treated mice and CD64hiSiglecF-Ly6C-MHC-Lyve1+ macrophages were sorted by flow cytometry and analysed by nanostring platform.


title: Hydrogen peroxide treatment of Jurkat T lymphoma cells leads to upregulation of genes involved in intracellular signalling pathways

city: Dunedin

first: Elizabeth

middle: C.

last: Ledgerwood

address: 710 Cumberland St

department: Biochemistry

country: New Zealand

institute: University of Otago

summary: The transcriptomic response of Jurkat T lymphoma cells to hydrogen peroxide was investigated to determine the global effects of hydrogen peroxide on cellular gene expression.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for Jurkat WT and Jurkat WT cells resuspended in PBS, treated with 10 µM hydrogen peroxide per 1 x 10^6 cells and harvested after 4 hours.

first: Megan

middle: F

last: Taylor

middle: C

first: Mark

middle: B

last: Hampton

first: Mik

middle: A

last: Black


title: Hierarchical accumulation of histone variant H2A.Z regulates transcriptional states and histone modifications in early mammalian embryos [ChIP-seq]

status: Public on Jun 24 2022

city: Wuhan

first: Jing-Jing

state: Hubei

address: 1 Lion Rock Street

department: Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction

institute: Huazhong Agricultural University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Early embryos undergo extensive epigenetic reprogramming to achieve gamete-to-embryo transition, which involves the loading and removal of histone variant H2A.Z on chromatin. Although the H2A.Z landscapes in sperm have been investigated, its dynamics during early development remain unrevealed. Here, by using ultra-low-input native chromatin immunoprecipitation and sequencing (ULI-NChIP-seq), we map the genome-wide distribution of H2A.Z in mouse oocytes and early embryos. We find that paternal H2A.Z is removed upon fertilization, followed by unbiased accumulation on parental genomes during zygotic genome activation (ZGA). More importantly, H2A.Z exhibits hierarchical accumulation as different peak types at promoters. We identify that double H2A.Z peaks co-localizes with H3K4me3 and facilitates transcriptional activation, bivalent markers (H3K4me3+H3K27me3) prefer to occupy single H2A.Z peak and inhibits developmental gene expression, while promoters with no H2A.Z accumulation exhibit gene silencing in early embryos. Remarkably, H2A.Z depletion changes the enrichments of histone modifications and RNA polymerase II (Pol II) binding at promoters, resulting in abnormal gene expression and developmental arrest during lineage commitment. Hence, H2A.Z plays dual roles in regulating the epigenomes required for proper gene expression during preimplantation development.

sample_organism:
Sus scrofa
Mus musculus

platform_organism:
Sus scrofa
Mus musculus

overall_design: The ChIP-Seq experiments of the control and H2A.Z KD embryos at the 2-cell, morula and blastocyst stage.

first: Xin

last: Liu

first: Jingjing

first: Yi

middle: L

last: Miao


title: Identification of novel AR and O-GlcNAc co-regulated genes in prostate cancer cells

city: Belfast

first: Ian

middle: G

last: Mills

address: 97 Lisburn Road

department: Centre for Cancer Research and Cell Biology

institute: Queens University

summary: Androgen receptor (AR) plays a central role in the development of prostate cancer. Increased expression of O-GlcNAc transferase (OGT) and O-GlcNAcylation are also implicated in metastatic prostate cancer. Increased O-GlcNAcylation in prostate cancer cells is associated with poor prognosis in patients. In this study, we employed chromatin immunoprecipitation coupled with massive parallel sequencing (ChIP-seq) to identify AR and O-GlcNAc binding sites in an attempt to identify novel co-regulatory mechanisms, biomarkers/druggable targets.

overall_design: ChIP-seq studies were carried out in vehicle (ethanol) vs. R1881 treated LNCaPs using antibody against AR (Abcam, ab74272) and O-GlcNAc (RL2, Abcam, ab2739).

first: Ninu

last: Poulose

first: Rebecca

middle: E

last: Steele

first: Simon

last: McDade

first: Sarah

last: Maguire


title: High Expression Level of ROR1 and ROR1-signaling Associates With Venetoclax Resistance In Chronic Lymphocytic Leukemia

city: La Jolla

first: Emanuela

middle: Maria

last: Ghia

state: CA

address: 9310 Athena Circle

department: Center For Novel Therapeutics

institute: University of California San Diego

summary:
We examined the CLL cells transcriptome data of six patients who fail to clear their leukemia cells and develop progressive disease on venetoclax therapy.
Methods: CLL cells were collected prior to venetoclax therapy (Sample Collection 1 (SC1)) and then more than 1 year later (Sample Collection 2 (SC2)). Negative isolation of CLL cells to ≥95% purity was performed prior to RNA isolation.

overall_design: Transcriptome profiles of CLL cells prior to venetoclax therapy and more than 1 year later on venetoclax

middle: M

first: Elvin

last: Chu


title: Single-cell RNA sequencing characterizes the comparision between Granulocyte-colony stimulating factor (G-CSF) primed human bone marrow and unstimulated bone marrow

city: Beijing

first: Guoju

last: You

state: Beijing

address: 30 Shuangqing Street

institute: Tsinghua University

summary:
Purpose: The goal of the study is to obatin a comprehensive landscape of G-CSF primed bone marrow (G-BM) and to deciphering the underlying mechanisms of immune modulatory effect induced by G-CSF treatment.
Methods: We recruited two healthy donors and treated them with recombinant G-CSF  at a dosage of 5μg/kg body weight per day for 5 consecutive days. The bone marrow samples were collected by aspiration on the fourth day of G-CSF treatment.  Bone marrow samples from healthy donors were treated with lysing solution to remove erythrocytes and were then labeled with antibodies. Through flow sorting, the final cells used for single-cell RNA sequencing (scRNA-seq) contained CD45+CD66b- population (90%), CD66b+ population (5%), and CD45- population (5%).
Results and Conclusion:  Through unbiased analysis, our data systematically showed the alterations in the transcriptional landscape of hematopoietic cells in G-BM, and illustrated the mechanisms of hyporesponsiveness of T cells and natural killer (NK) cells caused by G-CSF stimulation.

overall_design: ScRNA-seq of bone marrow samples from two healthy donors before and after G-CSF administration

first: Yandong

last: Gong

first: Man

last: Zhang

first: Zhilei

last: Bian


title: LncRNA ICR regulates endothelium inflammation through feedback activation of NF-κB signaling

first: shuangjin

last: ding

address: No.5 YiHeYuan Road, Haidian District Beijing 100871, China

department: College of Future Technology

institute: Peking University

summary: The responsive and abundant lncRNAs to pro-inflammatory factors in human ECs were screened and validated by RNA sequencing and qPCR. ICAM1-related non-coding RNA (ICR) was identified as the most potential candidate. In vivo data confirmed ICR was upregulated in atherosclerotic plaque. Knock down and overexpression experiments showed that ICR plays an essential role for EC adhesion and migration as well as for the expression of its adjacent ICAM1 gene.  Mechanistically, we unexpectedly found in quiescent ECs, ICR regulates mRNA stabilization of ICAM1 through a RNA duplex formation mechanism while in activated ECs, ICR modulated ICAM1 transcription via a NF-κB-dependent manner. RNA-seq and PCR analysis demonstrated a vast number of pro-inflammatory genes downstream of NF-κB were regulated by ICR. Further, CHIP assay showed p65 directly binds to ICR promoter and facilitate the transcription. Interestingly, we found p65 phosphorylation and degradation was in turn regulated by ICR, forming a feedback activation of NF-κB signaling. Finally, we screened siRNA of mouse ICR and delivered the shRNA adenovirus by intravenous injection in a high fat diet induced ApoE-/- atherosclerosis model, it was found that both aortic root stenosis and plaque area could be markedly inhibited by suppressing ICR.

overall_design: silenced ICR with or without TNF-α treatment performed RNA-seq in endothelial cells

first: Shuangjin

last: Ding


title: Identification of candidate genes involved in salt stress response at germination and seedling stages by QTL mapping in upland cotton

first: Anhui

last: Guo

address: College of Agronomy and Biotechnology,

institute: College of Agronomy and Biotechnology, China Agricultural University

summary: Salinity is a major abiotic stress at critical stages of seed germination and seedling establishment. Germination rate (GR) and field emergence rate (FER) are the key traits that determine the basic number of plants stand under field conditions. To explore molecular mechanisms in upland cotton under salt stress, a population of 177 recombinant inbred lines (RILs) and their parents were evaluated for seed germination traits (GP, germination potential; GR; FW, fresh weight; DW, dry weight; GL, germinal length) and seedling traits (FER; SH, seedling height; NL, Number of main stem leaves) in 2016-2018. Based on the linkage map contained 2,859 single nucleotide polymorphism (SNP) and simple sequence repeats (SSR) markers, traits under salt stress (E1) and normal condition, (E2) and the converted relative index (R-value) of three years’ trials were used to map quantitative trait loci (QTL). A total of three QTL and two clusters were detected as salt-tolerant QTL. Three QTL (qGR-Chr4-3, qFER-Chr12-3, qFER-Chr15-1) were detected under salt stress and R-value, which explained phenotypic variance of 9.62%-13.67%, and 4.2%-4.72%, 4.75%-8.96%, respectively. Two clusters (Loci-Chr4-2 and Loci-Chr5-4) harboring the QTL for four germination traits (GR, FER, GL, NL) and six seedling traits (GR, FER, DW, FW, SH, NL) were detected related under salt stress. A total of 691 genes were found in the candidate QTL or clusters. Among them, four genes (Gh_A04G1106, Gh_A05G3246, Gh_A05G3177, Gh_A05G3266) showed expression changes between sensitive and tolerant lines under salt stress, and were assigned as candidate genes in response to salt stress. The consistent salt-tolerance QTL identified in both germination and seedling stages will facilitate new information for cotton breeding.

overall_design: RNA-seq profiles of five time points after 150 mM NaCl treatment in two upland cotton varieties.

first: Ying

last: Su

first: Hushuai

last: Nie

first: Bin

last: Li

first: Xingkun

last: Ma

first: Jinping

last: Hua


title: Classification of developmental toxicants in a human iPSC transcriptomics-based test

city: Dortmund

first: Jan

middle: Georg

last: Hengstler

address: Ardeystraße 67

department: Toxikologie / Systemtoxikologie

country: Germany

institute: Leibniz-Institut für Arbeitsforschung an der TU Dortmund

summary: There is a great need for in vitro tests that identify developmental toxicants in relation to human oral doses and blood concentrations. In the present study, we used the hiPSC-based UKK-24h-test and analyzed genome-wide expression profiles of 23 known teratogens and 16 non-teratogens. All compounds were analyzed at the maximal plasma concentration (Cmax) and the 20-fold Cmax for a 24 h incubation period in three independent experiments. Using the 1,000 probe sets with the highest variability and including information on cytotoxicity, a penalized logistic regression based classifier (top-1,000 classifier) reached an AUC, accuracy, sensitivity, and specificity of 0.96, 0.92, 0.96 and 0.88, respectively to correctly classify the compounds as teratogens or non-teratogens. This top-1,000 classifier reached a higher AUC, accuracy and sensitivity than a second classifier (SPS-classifier), which used the number of significant probe sets to classify the compounds. At least, the SPS-classifier had a specificity of 1.  Classification at 20-fold Cmax did not lead to better performance metrics than testing at 1-fold Cmax. Finally, inclusion of cytotoxicity information into the classifier clearly improved the performance metrics. In conclusion, although further optimization by additional readouts and inclusion of cell systems that model different developmental processes is required, the UKK-24h-test will support the early discovery-phase detection of human developmental toxicants already in its present form.

overall_design: Human iPSCs wered differentiated for 24 h according to a cardiomyogenic protocol and incubated with compounds at the same time. RNA was isolated from these cells and a whole transcritpome analysis was performed. Compound-induced gene expression changes were determined with statistical models

first: Anna

last: Cherianidou

first: Florian

last: Seidel

first: Franziska

last: Kappenberg

first: Nadine

last: Dreser

first: Jonathan

last: Blum

first: Tanja

last: Waldmann

first: Nils

last: Blüthgen

first: Johannes

last: Meisig

first: Katrin

last: Madjar

first: Margit

last: Henry

first: Tamara

last: Rotshteyn

first: Rosemarie

last: Marchan

first: Karolina

last: Edlund

first: Marcel

last: Leist

first: Jörg

last: Rahnenführer

first: Agapios

last: Sachinidis


title: Quantitative transcriptome analysis of the repair mechanism of AKBA on the treatment of rat sciatic nerve injury

city: Harbin

first: Yao

last: Wang

address: 59 Mucai Street, Xiangfang District

department: Department of Veterinary Medicine

institute: Northeast Agricultural university

summary: The data obtained through differential mRNA expression analysis showed that 258 genes were significantly differentially expressed at the mRNA level in the AKBA group relative to in the model group . These genes included 189 upregulated genes and 69 downregulated genes. A total of 355 genes, including 194 upregulated genes and 161 downregulated genes, were significantly differentially expressed at the mRNA level in the AKBA group relative to in the sham operation group . A total of 410 genes, among which 171 were upregulated and 239 were downregulated, were significantly differentially expressed at the mRNA level in the sham operation group relative to in the model group. The results showed that significantly differentially expressed genes in the AKBA and model control groups were enriched in 193 pathways. The the highest enrichment the phagosome pathways.

overall_design:
SD rats with sciatic nerve injury model, model group treated with AKBA, and sham operation group

Please note that the data columns in the 'mRNA_Expression_Summary.xlsx" correspond to the samples as following:
GYZ = A
KBZ = M
JSSZ = S

first: Wenhui

last: Yu

first: Xiaowen

last: Jiang


title: Chromosome-specific retention of cancer-associated DNA hypermethylation following pharmacological inhibition of DNMT1

city: Grand Rapids

first: Peter

last: Jones

state: MI

address: 333 Bostwick Ave

department: Center for Epigenetics

institute: Van Andel Research Institute

type: Methylation profiling by genome tiling array

summary: The DNA methylation status of the X-chromosome in cancer cells is often overlooked because of computational difficulties. Most of the CpG islands on the X-chromosome are mono-allelically methylated in normal female cells and only present as a single copy in male cells.  We treated two colorectal cancer cell lines from a male (HCT116) and a female (RKO) with increasing doses of a novel DNA methyltransferase 1 (DNMT1)-specific inhibitor (GSK3685032/GSK5032) over a long time period to remove as much non-essential CpG methylation as possible. Analysis of the residual methylation patterns in the heavily treated cells showed a very surprising non-uniform distribution of retained methylation on specific chromosomes. For example, probes on the X-chromosome preferentially retained methylation 2-3-fold more frequently compared to those on autosomes. This was true for probes methylated on the active X chromosome in normal cells such as XIST and also for genes which acquired methylation in cancer such as ARMCX2 and MAGEH1. The maintenance of high DNA methylation on a subset of probes after such exhaustive treatment suggests that it might have functional significance for cell survival. Importantly, the same X-linked probes we found in the treated cells were also methylated in a large number of colorectal/rectal cancers in the TCGA data set and to a lesser extent in other cancer types. These results suggest that a re-examination of tumors for X-linked DNA methylation changes may enable greater understanding of the importance of epigenetic silencing of cancer related genes.

overall_design: Genomic DNA was isolated from parental HCT116, HCT116 DKO1, or RKO cells and HCT116 and RKO cells that had been treated for >100 days with >IC90 of the DNMT1-specific inhibitor GSK5032.

first: Ashley

middle: K

last: Wiseman

first: Rochelle

last: Tiedemann

first: Huihui

last: Fan

first: Hui

last: Shen


title: MicroRNA (miRNA) Expression in Circulating Leukocytes and Bioinformatic Analysis of Patients with Moyamoya Disease (MMD)

first: Kaijiang

last: Kang

address: No.119 South Fourth Ring West Road, Fengtai District

department: Department of Neurology

institute: Beijing Tiantan Hospital, Capital Medical University

summary: To investigate the differential expression of miRNAs in circulating leukocytes of patients with MMD. The results showed 12 differentially expressed miRNAs in leukocytes of MMD patients compared with controls (fold change > 2.0 and P < 0.05), of which 7 were up-regulated and 5 were down-regulated.

overall_design: A total of 30 MMD patients and 10 healthy adults were enrolled. The gene microarray was used to detect the differential expression profiles of miRNAs in leukocytes between patients with moyamoya disease and healthy controls.

first: Xingquan

last: Zhao


title: A multi-omics approach identifies pancreatic cancer cell extracellular vesicles as mediators of the unfolded protein response in normal pancreatic epithelial cells

city: Washington

first: Amrita

last: Cheema

state: District of Columbia

address: 3900 Reservoir Road NW

institute: Georgetown University

summary: The early molecular mechanisms of pancreas cancer development remain elusive. A key driver of poor patient outcomes remains late-stage diagnosis of disease, typically when patients present with pancreatic ductal adenocarcinoma (PDAC). Currently, no diagnostics exist to identify indolent disease. It is crucial to identify the early molecular events that drive the transformation of naïve cells to a neoplastic phenotype. Extracellular vesicles (EVs) are nanometer sized lipid-bilayer particles released from cells of almost all known tissue types. EVs carry an array of biomolecules which are internalized by neighboring and distant cells, critical for facilitating intracellular communication. Although cancer derived EVs impact a myriad of cancer progression events including tumor proliferation, immune escape, and metastasis, their role in mediating early onset of PDAC is unknown.  In this study, we report on alterations in the gene expression profiles of normal pancreatic epithelial cells upon internalization of PDAC cell derived EVs (cEVs). Leveraging a layered multi-omics approach, we show that cEVs induce endoplasmic reticulum (ER) stress and the unfolded protein response in recipient normal pancreatic epithelial cells within 24 hours. Consequently, cEV treated cells demonstrated increased proliferation. cEV cargo was enriched for an array of biomolecules which can induce or regulate ER stress and the UPR, including lipid species esterified to palmitic acid, sphingomyelins, metabolites which regulate tRNA charging and protein trafficking and degradation proteins. These results highlight a role for pancreatic cancer cEVs to induce stress in recipient normal pancreas cells; studying these genetic, metabolic and proteomic perturbations may lead to valuable insight to disease etiology and early biomarker identification.

overall_design: 24 samples in biological triplicate over 8 conditions, comparing effects of pancreas cancer cell EVs on normal pancreas cells (hTERT-HPNE and HPDE-H6c7) vs. untreated normal pancreas cells and a negative control (residual cell culture media left after EV isolation).

first: Charles

last: Hinzman

first: Shivani

last: Bansal

first: Yaoxiang

last: Li

first: Anton

last: Iliuk

first: Michael

last: Girgis

first: Jose

last: Trevino

first: Partha

last: Banerjee


title: Transcriptome analysis of eutopic endometrium stromal cells by RNA-sequencing in patients with adenomyosis

city: Nanjing

first: Tao

last: Gui

state: Jiangsu

address: NO.100 Shizi Street, Hongshan Road

institute: Affiliated Hospital of Integrated Traditional Chinese and Western Medicine, Nanjing University of Chinese Medicine

summary: To identify differentially expressed genes (DEGs) and molecular pathways in eutopic endometrial stroma cells (EuESCs) from adenomyosis patients and provide a new insight into disease mechanisms at transcriptome level.Gene expression profiling of normal endometrial stromal cells (N-ESCs) and adenomyotic eutopic endometrial stroma cells (A-EuESCs) were analyzed by using RNA-sequencing.

first: Guiping

last: Wan

first: Quan


title: Deciphering the transcriptional changes in Escherichia coli strains C41(DE3) and C43(DE3) that makes them a superior choice for membrane protein production.

city: Clayton

first: Kirill

last: Tsyganov

state: Victoria

address: Wellington Road

department: Monash Bioinformatics Platform

country: Australia

institute: Monash University

summary: This study assessed the differential gene expression of C41(DE3) and C43(DE3) strains in comparison to their parental strain BL21(DE3), in the presence and absence of a prototypical protein expression vector with or without the inducer IPTG.

overall_design:
Part 1 of this two part study assessed the differential expression of E. coli strains C41(DE3) and C43(DE3) compared to BL21(DE3).  assessed  the differential expression of E. coli strains C41(DE3) and C43(DE3) compared to BL21(DE3) that had been transformed with a plasmid, pACYCDuet-1, and grown in the presence of the inducer IPTG. All samples were performed in triplicate.
This part 2 of the study assessed  the differential expression of E. coli strains C41(DE3) and C43(DE3) compared to BL21(DE3) that had been transformed with the plasmid, pACYCDuet-1, and grown in the presence of the inducer IPTG for two hours. All samples were performed in triplicate.

first: Chaille

middle: T

last: Webb

first: Treveor

last: Lithgow


title: Study of the effect of Protein Kinase CK2 alpha prime in the transcriptional deficits associated with Huntington's disease

city: Minneapolis

first: Ying

last: Zhang

state: MN

address: 117 Pleasant St S.E.

department: Minnesota Supercomputing Institute

institute: University of Minnesota

summary: Protein kinase CK2 alpha prime (CK2a') is preferentially upregulated in the striatum of patients with HD and in different cellular and mouse models of HD. CK2a' happloinsufficiency in the zQ175 HD mouse model restored several HD-like phenotypes. We hypothesized that CK2a' neuronal up-regulation is linked to key transcriptional alterations in the zQ175 mouse model. We found that CK2a' haploinsufficiency rescued the expression of genes associated with synaptogenesis and glutamatergic signaling whose upstream regulator seems to be alpha-synuclein. These transcriptomic studies revealed a conection between CK2a', alpha-synuclein dysfunction and transcriptional changes in key signaling pathways.

overall_design: Striatum transcriptional profiles in zQ175 mice with and without one allele of CK2a'. RNA-seq analyses in samples obtained from the striatum of 12-14 months old mice using four different genotypes: WT, CK2a' (+/-), zQ175 and zQ175:CK2a'(+/-). All mice are in the C57BL/6 background. Animals were anesthesized with Avertin and intracardially perfused with Heparin+PBS. Brains were dissected and striatum samples were flash frozen in N2 prior to RNA extraction.

first: Nicole

last: Zarate

first: Rocio

last: Gomez-Pastor


title: Metabolic disorder and gut microbiota feature in high energy diet

status: Public on Jun 22 2022

city: Shanghai

first: Weize

last: Zhu

address: Zhangjiangzhen

institute: Shanghai University of Traditional Chinese Medicine

summary: To study dynamic and diversied impacts of fat and sugar.

overall_design: In our current study, we investigated the dynamic changes of gut microbiota, and host metabolism in mice that were fed with either chow diet, HFD or chow diet with 30% sucrose in drinking water (HSD) for continued 12 weeks. The gut microbiota was analyzed with 16S rDNA sequencing on feces. Hepatic gene expression profile was tested with transcriptomics analysis on liver tissue. The host metabolism was evaluated by measuring body weight, insulin sensitivity, serum lipids and expression of proteins involved in lipid metabolism of liver.

last: Hong


title: RNAseq of human macrophages obtained from in vitro treatments with M-CSF/GM-CSF/CM-WSU-FSCCL

city: Barcelona

first: Luis

last: Hernandez

address: Rossello 153, CEK building

department: Molecular Pathology

country: Spain

institute: IDIBAPS

summary: RNAseq analysis of 12 human macrophage samples was performed using ribosomal-depleted total RNA to analyze long non-coding RNA and coding transcript expression profiles comparing macrophage in vitro subtypes (M2, M1 and TAM) obtained from peripheral blood normal monocytes.

overall_design: Dataset included RNA-seq data (Four Fastq files per sample as paired end sequencing was performed and two replicates per sample were included to increase the total number of reads to 100M) from ribosomal-depleted total RNA of macrophage in vitro subtypes obtained from peripheral blood normal monocytes to analyze their long non-coding RNA and coding transcript expression profiles. Sample metadata is referred to the in vitro treatments performed on to the different monocyte samples to obtain the macrophage subtypes of interest: M2 using M-CSF (N=3), M1 using GM-CSF (N=6), TAM using conditioned media from the follicular lymphoma cell line WSU-FSCCL (N=3).

first: Alejandro

last: Roisman

first: Giancarlo

last: Castellano


title: Discovery and validation of blood methylation variation associated with the response tumor necrosis factor inhibitors in rheumatoid arthritis

first: Antonio

last: Gomez

address: Pg Vall d'Hebron 119-129

department: Rheumatology research Group

institute: VHIR

summary: Rheumatoid arthritis (RA) is a chronic inflammatory disease of the joints that has been associated with changes in the blood methylome. There is high interest to determine if this accessible epigenetic variation is associated with relevant clinical outcomes.

overall_design: An initial longitudinal cohort of n=62 RA patients starting anti-TNF therapy was analyzed by means of the EPIC methylation array (850,000 probes). Methylation profiles were analyzed at baseline and at week 12 of treatment. Association of whole blood epigenetic variation with the clinical response to therapy and with disease activity were performed both at the CpG and biological pathway levels

last: Julià

last: Gómez

first: Sara

last: Marsal


title: Efficient detection of alternative spliced human proteome using translatome sequencing

city: guangzhou

first: Gong

address: Jinan University, No.601, West Huangpu Avenue ，Guangzhou, Guangdong, China.

institute: Jinan University

summary: Alternative splicing (AS) isoforms create numerous proteoforms, expanding the complexity of the genome. Highly similar sequences, incomplete reference databases and the insufficient sequence coverage of mass spectrometry limit the identification of AS proteoforms.In this work, we compared RNC-seq and Ribo-seq in the context of proteome identification, especially when identifying protein isoforms from AS. We also demonstrated that the single-molecule long read sequencing technique identified thousands of new splice variants and guided the MS identifications of new protein isoforms.

overall_design: Getting translatome data of MHCC97H RNC and RPF.And we performed the direct full-length RNC-seq on MHCC97H using Nanopore MinION sequencer

first: Xiaolong

last: Lu

first: Chun

last: Wu

first: Hongwei

last: Wang

first: Yang

last: Chen


title: Hyaluronan And Proteoglycan Link Protein 1 (HAPLN1) promotes Proliferation and Pro-inflammatory phenotype but not mobility of Fibroblast-like Synoviocytes

city: Shenzheng

first: Yong

address: No. 1017, Dongmen North Road, Luohu District, Shenzhen, Shenzhen P. R. China.

institute: Shenzhen People's Hospital

summary:
Objectives: HAPLN1 stabilize the macromolecular structure of the extracellular matrix (ECM) and its expression is increased in a few types of musculoskeletal diseases including rheumatoid arthritis (RA). However, its functions are obscure.
Methods: Here, how HAPLN1 contributes to the viability, proliferation, mobility and pro-inflammatory phenotype of RA-FLSs was investigated using small interfering RNA (siHAPLN1), over-expression vector (HAPLN1OE) and a recombinant HAPLN1 (rHAPLN1) protein.
Results: Interestingly, HAPLN1 promoted proliferation but inhibited migration of RA-FLSs. Earlier we reported the function of metformin, an AMPK activator, in the inhibition of FLSs activation but promotion of HAPLN1 secretion. In this study, we confirmed the findings of up-regulated HAPLN1 in RA patients, and it is positively correlated with AMPK. Both si-HAPLN1 and HAPLN1OE treatment has down-regulated the expression of AMPK-ɑ gene but the levels of phosphorylated AMPK-ɑ were found to be up-regulated in RA-FLSs. Furthermore, si-HAPLN1 had down-regulated the gene and protein expression of proinflammatory factors like TNF-ɑ, MMPs and IL-6, while HAPLN1OE up-regulated their levels. qPCR assay also indicated down regulated TGF-β, ACAN, Fibronectin, collagen Ⅱ, and Ki-67 by si-HAPLN1 treatment, while up-regulated ACAN, Ki-67 and down regulated cyclin-D1 by HAPLN1OE treatment. Proteomics of si-HAPLN1, rHAPLN1 and mRNA-Seq analysis of rHAPLN1 confirmed the functions of HAPLN1 in the activation of inflammation, proliferation, increased cell adhesion, and strengthening of ECM function.
Conclusions: Collectively, these findings demonstrate HAPLN1 function in promoting proliferation and pro-inflammatory phenotype of RA-FLSs, which in turn could contribute to RA pathogenesis.

overall_design: High-throughput RNA sequencing was performed using FLSs after treatment with rHAPLN1 50 ng/ml for 48 h. Each concentration was tested thrice.

first: Baojiang

first: Yanjuan

first: Qunyan

first: Youlai

last: Wei

first: Kutty

last: Selva Nandakumar

first: Dongzhou

last: Liu


title: Gene expression profile in the rat heart across hear regions [array]

city: Akita

first: Yosuke

last: Okamoto

address: 1-1-1 Hondo

department: Cell Physiology

country: Japan

institute: Akita University Graduate School of Medicine

summary: To characterize a expression patterns in the heart, we used rat. 12 Wistar male rats (8 - 11 weeks) were sacrificed. Left atrium (LA) adjacent to the pulmonary vein (PV), a mass of left ventricle (LV), and free-wall of the right ventricle (RV) was isolated. Each LV mass was dissected into three pieces as samples. Because the SAN isolation procedure takes approximately 20 minutes, SA was isolated separately. The SA region was delimited by the borders of the crista terminalis, the interatrial septum, the superior vena cava, and right atrium (RA). In addition to PV, LV, RV, SA, and RA samples, pulmonary arteries were added to the samples for the rat microarray.

overall_design: 23 samples

first: Miho

last: Oka

first: Daigo

last: Okada


title: Gene expression profile in the human and rat heart across regions

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

sample_organism:
Homo sapiens
Rattus norvegicus

platform_organism:
Homo sapiens
Rattus norvegicus

overall_design: Refer to individual Series


title: Improved T cell immunity following neoadjuvant chemotherapy in ovarian cancer

city: Boston

first: Livius

last: Penter

state: MA

address: 450 Brookline Avenue

department: Medical Oncology

institute: Dana-Farber Cancer Institute

summary:
To investigate effects of standard-of-care neoadjuvant carboplatin and paclitaxel chemotherapy on T cell immunity, we surveyed changes in the peripheral T cell receptor repertoire.
We performed bulk TCR sequencing of peripheral blood before chemotherapy (baseline), after 3 cycles (C3) and after 6 cycles (C6).

overall_design: Bulk rhTCR-seq of peripheral blood before and following chemotherapy (standard-of-care neoadjuvant carboplatin and paclitaxel chemotherapy)

first: Min


title: Bace-1 inhibition facilitates the transition from homeostatic microglia to DAM-1

city: Farmington

first: Marc

last: Benoit

address: 263 Farmington Ave

institute: UConn Health

summary: Single-cell RNA sequencing data from purified mouse microglia with and without 5xFAD Alzheimer's disease model and with and without Bace-1 knockout

overall_design: Examation of microglial subtypes in response to Alzheimer's disease pathology

first: Neeraj

last: Singh

first: Riqiang

last: Yan


title: RNA-seq reveals important sRNAs in E.coli O157:H7

first: Bin

address: Hai Dian

department: School of Life Sciences

institute: Tsinghua University

summary: We report the different expression level of in vivo transcriptome and DMEM cultured bacteria E.coli O157:H7 samples. After obtaining RNA from mice colon and LB cultured free living cells, RNA samples were purified using an RNeasy Mini Kit (Qiagen) and bacterial rRNAs were depleted using the Ribo-Zero rRNA Removal Kit (Epicentre; #RZNB1056). Library construction of RNA samples was carried out using a NEBNext R UltraTM Directional RNA Library Prep Kit for Illumina R (NEB, USA), following the manufacturer’s recommendations. After cluster generation, library preparations were sequenced on an Illumina Hiseq platform to generate paired-end reads.We find that a novel sRNA s77 significantly upregulated compared in vivo samples and LB-cultured sample. This study provides a novel sRNA for further identifications.

overall_design: In this study, we intend to verify the expression of small RNA s77 in mice and LB medium. Meanwhile, we want to see genes being regulated by s77 by comparison mRNA expression levels between o157 and △s77 strains.

first: Tianyuan

last: Jia


title: FOXA2 suppresses endometrial carcinogenesis and epithelial-mesenchymal transition through its actions as chromatin remodeler [WT41]

city: Dallas

first: Subhransu

last: Sahoo

state: Texas

address: 5323 Harry Hines Blvd

department: Pathology

institute: UT Southwestern Medical Center

summary: FOXA2 encodes a transcription factor mutated in 10% of endometrial cancers (ECs), with a higher mutation rate in aggressive variants. FOXA2 has essential roles in embryonic and uterine development. However, FOXA2’s role in EC is not understood. Functional investigations using human and mouse EC cell lines revealed that FOXA2 controls endometrial epithelial gene expression programs regulating cell proliferation, adhesion, and endometrial-epithelial transition. In live animals, conditional inactivation of Foxa2 or Pten alone in endometrial epithelium did not result in ECs, but simultaneous inactivation of both genes resulted in lethal ECs with complete penetrance, establishing potent synergism between Foxa2 and PI3K signalling. Organoids and tumor-derived cell line studies highlighted additional invasion and cell growth phenotypes associated with malignant transformation and identified key mediators including Myc and Cdh1. Transcriptome and cistrome analyses revealed that FOXA2 broadly controls gene expression programs through chromatin remodeling and modification of enhancer activity in addition to regulating specific target genes, rationalizing its tumor suppressor functions. By integrating results from our cell lines, organoids, animal models, and patient data, our findings demonstrate that FOXA2 is an endometrial tumor suppressor associated with aggressive disease and with shared commonalities among its roles in endometrial function and carcinogenesis.

overall_design: Transcriptomic profiling of Ishikawa (ISK) and ISK-FOXA2 cells.

first: Diego

middle: H

last: Castrillon

first: Chao

last: Xing

first: Ashwani

last: Kumar


title: FOXA2 suppresses endometrial carcinogenesis and epithelial-mesenchymal transition through its actions as chromatin remodeler.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: T cell receptor repertoire in premature infants

first: Sarah

last: Morton

address: 300 Longwood Ave

institute: Boston Children's Hospital

summary: We analyzed the TCRR beta for premature infants at various postmenstrual ages along with term born control infants.

overall_design: Collected 40 200ul blood samples, isolated RNA, sent to iRepertoire for library prep and sequencing. Analyzed data via immunarch program in R.

first: Amy

last: O'Connell


title: m6A modification involves in enriched environment-induced neurogenesis and cognition enhancement

city: hangzhou

first: wenzheng

last: qu

address: Kaixuan Road

institute: Zhejiang University

summary: Our results suggest that different environment induces differential m6A mRNA modification, and add novel layer of the interaction between environment and epigenetics during the postnatal neuronal development.

overall_design: New born pups were randomly grouped, and housed in standard cage and different environment.

first: Wenzheng

last: Qu

first: Xuekun

last: Li


title: FOXA2 suppresses endometrial carcinogenesis and epithelial-mesenchymal transition through its actions as chromatin remodeler [WT106]

overall_design: Transcriptomic profiling of FP and FP-Foxa2 cells.


title: Fasciola hepatica Fatty Acid Binding Protein 1 modulates T cell polarization by promoting dendritic cell thrombospondin-1 secretion without affecting metabolic homeostasis in obese mice

city: Leiden

first: Bruno

last: Guigas

address: Albinusdreef 2

department: Parasitology

country: Netherlands

institute: Leiden University Medical Center

summary: The immunomodulatory effects of recombinant F. hepatica FABP1 (fhFABP1) on monocyte-derived human DCs (moDCs) and the underlying mechanism were investigated using various approaches, including DC-allogenic T cell co-culture and DC phenotyping through transcriptomic, proteomic and FACS analyses. We found that fhFABP1 induced a tolerogenic-like phenotype in LPS-stimulated moDCs characterized by a dose-dependent increase in the cell-surface tolerogenic marker CD103 and IL-10 secretion, while DC co-stimulatory markers were not affected. A significant decrease in secretion of the pro-inflammatory cytokines IL-12p70 and IL-6 was also observed. In addition, these effects were associated with an increase in both Th2-on-Th1 ratio and IL-10 secretion by CD4+ T cells following DC-T cell co-culture. RNA sequencing and targeted proteomic analyses identified thrombospondin-1 (TSP-1) as a non-canonical factor highly expressed and secreted by fhFABP1-primed moDCs. The effect of fhFABP1 on T cell skewing was abolished when using an TSP-1 blocking antibody during DC-T cell co-culture. Immunomodulation by helminth molecules has also been linked to improved metabolic homeostasis during obesity. In vivo, although fhFABP1 injection in high-fat diet-fed obese mice induced a potent Th2 immune response in adipose tissue, it did not improved insulin sensitivity or glucose homeostasis.

overall_design: mRNA sequencing of human monocyte-derived dendritic cells from 3 donors that were treated with fhFABP1 and LPS, or LPS only, as a control

first: Anna

last: Zawistowska-Deniziak

first: Maciej

last: Łapiński


title: Nicotinamide mononucleotide improves the quality of porcine oocytes deteriorated by heat stress

first: Li

last: Yu

address: No. 1 Weigang, Nanjing City, Jiangsu Province

institute: College of Animal Science and Technology, Nanjing Agricultural University

summary: Elevated ambient temperature results in heat stress which is a major concern for productivity and product quality due to its negative impact on animal health, productivity and product quality. As global warming becomes more and more serious, the impact of heat stress (HS) on animal husbandry cannot be ignored. However, the effect of NMN on the quality of porcine oocytes after heat stress and the prevention strategies are not yet fully understood. Here, we report that nicotinamide mononucleotide (NMN) treatment ameliorates the quality of porcine oocytes exposed to heat stress. Specifically, we found that HS caused oocyte meiosis failure by disrupting the dynamics and arrangement of meiotic organelles, showing obvious damage to cytoskeleton assembly. Furthermore, heat stress can cause damage to oocyte mitochondria, which is an indicator of oocyte cytoplasmic maturation. On the contrary, supplementation of NMN can improve this phenomenon, maintain the normal chromosome/spindle structure, and the dynamics of CGs and its core content ovastacin.

overall_design: Transcriptomic analysis of porcine oocytes at the GV phase for 24 hours was carried out using a protocol for RNA-Seq. The constructed library was sequenced with Illumina Novaseq6000 platform.

first: Bo

last: Xiong


title: Gene expression profile in the human heart across hear regions [RNA-Seq]

first: Yosuke

last: Okamoto

summary: High-througput sequence was demonstrated with NovaSeq 6000 (Illumina). First, extracted RNAs were purified by poly(A) capture. Resultant mRNAs were then fragmented and reverse-transcribed into single-stranded complementary DNAs (cDNAs). Subsequently, cDNAs were double-stranded by a DNA polymerase. During the polymerase reactions, deoxy UTP (dUTP) were mixed in nucleotide materials. Both ends of double-stranded DNA (ds DNA) were ligated to a 13 bp adapter sequence. Next, the ds DNAs were subjected to PCR amplification for the multi-sized DNA library preparation. NovaSeq Control software v1.4.0 analyzed the sequencing runs and tag sequences classified each read in the raw sequencing data. A total of 21 RNA-seq data were used for human data, three samples each of LA, left atrial appendage (LAA), LV, pulmonary vein (PV), RA, RV, and SA. fastp software (version 0.12.4) was used for Read quality control and adapter removal. Reads were aligned using STAR software (version 2.7.0a).

overall_design: mRNA profiling of seven different cardiac regions

first: Miho

last: Oka

first: Toshiro

last: Io

first: Daigo

last: Okada


title: Single-cell analysis reveals fibroblast heterogeneity in chronic pancreatitis

first: Yang

middle: yang

last: Guo

address: Dongan Road

institute: 复旦大学

summary: We used 10x Genomics Single Cell 3’v3.1 scRNA sequencing to investigate the cellular heterogeneity in chronic pancreatitis using pancreases of three CP mice. Mice were induced by daily subcutaneous re-injections of caerulein for 28 days

overall_design: ScRNA profiles of three pancreas tissue from CP mice day 28 post-Cearulein exposed. 10480 individual cells were obtained with 1303 median genes detected per cell.

first: Yuli

last: Lin

first: Xuguang

last: Yang

last: Yin

first: Wenxue

last: Feng

first: Yangyang


title: RNA-seq and sRNA-seq analysis of rice lines of wild type and its mutant

city: Hangzhou

first: Xiaoli

last: Jin

state: Zhejiang

address: Yuhangtang road 866

summary:
The study was conducted to characterize the  mutant; identify the candidate gene for the mutant trait with the map-based cloning approach; investigate the segregation of target gene with the mutant characteristics, and examine the metabolic pathways of differentially expressed genes between WT and its mutant with comparative transcriptome analysis.
We then performed gene expression profiling analysis using data obtained from RNA-seq of  wild type and its mutant.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for Nipponbare and its mutant.

first: Yohannes

last: Tsago


title: Genome-wide placental gene methylations in gestational diabetes mellitus, fetal growth and metabolic health biomarkers in cord blood

city: Toronto

first: Zhong-Cheng

last: Luo

state: Ontario

address: 60 Murray, L5-240, LTRI

department: Lunenfeld-Tanenbaum Research Institute

country: Canada

institute: Mount Sinai Hospital, University of Toronto

summary: Gestational diabetes mellitus (GDM) “program” an elevated risk of metabolic syndrome in the offspring.  Epigenetic alterations are a suspected mechanism. GDM has been associated with placental DNA methylation changes in some epigenome-wide association studies. It remains unclear which genes or pathways are affected, and whether any placental differential gene methylations are correlated to fetal growth or circulating metabolic health biomarkers. In an epigenome-wide association study using the Infinium MethylationEPIC Beadchip, we sought to identify genome-wide placental differentially methylated genes and enriched pathways in GDM, and to assess the correlations with fetal growth and metabolic health biomarkers in cord blood. The study samples were 30 pairs of term placentas in GDM vs. euglycemic pregnancies (controls) matched by infant sex and gestational age at delivery in the Shanghai Birth Cohort. Cord blood metabolic health biomarkers included insulin, C-peptide, proinsulin, IGF-I, IGF-II, leptin and adiponectin. Adjusting for maternal age, pre-pregnancy BMI, parity, mode of delivery and placental cell type heterogeneity, 256 differentially methylated positions (DMPs,130 hypermethylated and 126 hypomethylated) were detected between GDM and control groups accounting for multiple tests with false discovery rate <0.05 and beta-value difference >0.05. WSCD2 was identified as a differentially methylated gene in both site- and region-level analyses. We validated 7 hypermethylated (CYP1A2, GFRA1, HDAC4, LIMS2, NAV3, PAX6, UPK1B) and 10 hypomethylated (DPP10, CPLX1, CSMD2, GPR133, NRXN1, PCSK9, PENK, PRDM16, PTPRN2, TNXB) genes reported in previous epigenome-wide association studies. We did not find any enriched pathway accounting for multiple tests. DMPs in 11 genes (CYP2D7P1, PCDHB15, ERG, SIRPB1, DKK2, RAPGEF5, CACNA2D4, PCSK9, TSNARE1, CADM2, KCNAB2) were correlated with birth weight (z score) accounting for multiple tests. There were no significant correlations between placental gene methylations and cord blood biomarkers. In conclusions, GDM was associated with DNA methylation changes in a number of placental genes, but these placental gene methylations were uncorrelated to the observed metabolic health biomarkers (fetal growth factors, leptin and adiponectin) in cord blood. We validated 17 differentially methylated placental genes in GDM, and identified 11 differentially methylated genes relevant to fetal growth.

overall_design: Bisulphite converted DNA extracted from the placentas (fetal-side) of 30 GDM and 30 euglycemic pregnancies were hybridised to the Illumina Infinium HumanMethylation850 BeadChip

first: Wenjuan

last: Wang

first: Rong

last: Huang

first: Tao

last: Zheng

first: Qinwen

last: Du

first: Meng-nan

first: Ya-jie

last: Xu

first: Xin

last: Liu

first: Min-Yi

last: Tao

first: Hua

last: He

first: Fang

last: Fang

first: Fei

last: Li

first: Jian-Gao

last: Fan

first: Jun

last: Zhang

first: Laurent

last: Briollais

first: Fengxiu

last: Ouyang


title: Concurrent Activation of Kras and Canonical Wnt Signaling Induces Premalignant Lesions That Progress to Extrahepatic Biliary Cancer in Mice

city: Kyoto

first: Munemasa

last: Nagao

state: Kyoto

address: 54 Kawaharacho, Shogoin, Sakyoku

department: Gastroenterology

institute: Kyoto University Graduate School of Medicine

summary:
We revealed that concurrent activation of the Kras and canonical Wnt pathways resulted in formation of ICPN and BilIN, which could develop into biliary cancer.
We found that c-Myc contributed to tumorigenesis, whereas Tgf-β pathway inhibited it.

overall_design: Hnf1bCreER, Hnf1bCreER;Kras, Hnf1bCreER;Ctnnb1, and Hnf1bCreER;Kras;Ctnnb spheroids were analyzed (n=3/group).

first: Akihisa

last: Fukuda


title: FOXA2 suppresses endometrial carcinogenesis and epithelial-mesenchymal transition through its actions as chromatin remodeler [WT67]

first: Subhransu

middle: S

last: Sahoo

overall_design: Transcriptomic profiling of HEC1B and FOXA2KD HEC1B cells.

first: Diego

last: Castrillon

first: Chao

last: Xing

first: Ashwani

last: Kumar


title: Single cell transcriptome atlas of microenvironment in preovulation follicle

city: Suzhou

first: Huihua

last: Wu

address: NO. 26, Daoqian road

institute: The Affiliated Suzhou Hospital of Nanjing Medical University

summary: The follicular microenvironment, including intra-follicular granulosa cells (GCs),are responsible for the dynamics of ovarian function. However the cellular component of follicular microenvironment as well as the different functional clusters of GCs and the other type cells  in preovulatory follicle  have not been extensively explored. Here we surveyed the single-cell transcriptome of follicular microenvironment around MII oocytes in six human preovulatory follicles in in-vitro fertilization. There were 6 different cell types in preovulatory follicles, including GCs, epithelial cells, and various immune cells.We identified 9 different functional clusters with different functional transcriptomic profiles in GCs and 5 different functional clusters with different functional transcriptomic profiles in macropahge.Our results provide a comprehensive understanding of the transcriptomic landscape of the preovulatory follicular microenvironment at the single-cell level.

overall_design:
We surveyed the single-cell transcriptome of the follicular microenvironment cells in six human preovulatory follicles in IVF.
Raw data not provided due to patient privacy concerns.

first: Hong

first: Rui

last: Zhu


title: A bipotential organoid culture of respiratory epithelium for modeling SARS-CoV-2 infection

city: Hong Kong

first: Jie

last: Zhou

address: 102 Pokfulam Road, Pokfulam, Hong Kong

department: Microbiology

country: Hong Kong

institute: The University of Hong Kong

summary: The airways and the alveoli of the human respiratory tract are lined by two distinct types of epithelium. We previously established long-term expanding human lung epithelial organoids from lung tissues and developed a ‘proximal’ differentiation protocol to generate mucociliary airway organoids, yet the derivation of alveolar organoids from adult lung has remained a challenge. Here we defined a ‘distal’ differentiation approach to generate alveolar organoids from the same source that allows the establishment of airway organoids. Alveolar organoids are enriched for AT1 and AT2 cells and functionally simulate the alveolar epithelium. AT2 cells in lung organoids act as the progenitor cells from which alveolar organoids emerge. Moreover, we demonstrate productive SARS-CoV-2 infection of alveolar organoids. We further optimize 2-dimensional (2D) airway organoids. When differentiated under a slightly acidic pH, these 2D airway organoids sustain enhanced viral replication and better recapitulate the high infectivity of SARS-CoV-2. Moreover, the optimized 2D airway organoids can model IgG transcytosis across the airway epithelium. Collectively, we establish a bipotential organoid culture system that can reproducibly expand the entire human respiratory epithelium in vitro for modeling respiratory diseases, including COVID-19.

overall_design: Human lung organoids were induced to generate 3D airway organoids, 2D airway organoids and 3D alveolar organoids in triplicate as described above or previously (Zhou et al., 2018). Three biological replicates of lung organoids and derived organoids were harvested for RNA extraction using RNeasy Mini Kit (Qiagen, Cas.74106). After a quality check with Bioanalyzer, RNA specimens were applied to library preparation by KAPA mRNA HyperPrep Kit. In brief, Poly-A containing mRNA was collected by using poly-T oligo-attached magnetic beads. The purified mRNA was fragmented to 200 ~ 300 bp by incubating at 94°C for 6 min in the presence of magnesium ions. The fragmented mRNA was then applied as a template to synthesize the first-strand cDNA by using random hexamer-primer and reverse transcriptase. In the second strand cDNA synthesis, the mRNA template was removed and a replacement strand was generated to form the blunt-end double-stranded (ds) cDNA. The ds cDNA underwent 3’ adenylation and indexed adaptor ligation. The adaptor-ligated libraries were enriched by 15 cycles of polymerase chain reaction (PCR). The libraries were denatured and diluted to optimal concentration. Illumina NovaSeq 6000 was used for Pair-End 151bp sequencing. Sequencing reads were assigned into individual samples, with each sample having an average throughput of 9.6 GB and a total throughput of 111.5 Gb. In terms of sequence quality, an average of 93% of the bases achieved a quality score of Q30 where Q30 denotes the accuracy of a base call to be 99.9%. Sequencing reads were mapped to the human reference genome GRCh38 with RNA-Seq aligner STAR. Clean reads were quantified based on the number of reads spanning the back-splicing junction, and their fragments per kb for a million reads (FPKM) were calculated using HTSeq 0.13.5. Aligned BAM files were sorted by SAMtools. GenomicAlignments and DESeq2 R packages (version 1.18.1) were used for read counting and differential expression analysis. Genes with an absolute value of log2 fold change greater than 1 and adjusted P-value (Benjamini-Hochberg) less than 0.05 were considered as differentially expressed.

first: Man

last: Chiu

first: Cun

first: Xiaojuan

last: Liu

first: Yifei

last: Yu

first: Jingjing

last: Huang

first: Zhixin

last: Wan

first: Hin

last: Chu

first: Jian

middle: P

last: Cai

first: Biao

first: Ko

middle: Y

last: Sit

first: Wing

last: Au

first: Kenneth

last: Wong

first: Jasper

last: Chan

first: Kelvin

last: To

first: Zhiwei

last: Chen

first: Hans

last: Clevers

first: Kwok

last: Yuen


title: m6A modification maps of mRNA in colonic epithelial cells from mouse

city: Chicago

first: Jie

last: Du

address: 900 E. 57th Street

institute: University of Chicago

summary: We report the application of sequencing technology for high-throughput profiling of mRNA m6A methylation in mice colonic epithelial cells with or without  mettl14 deletion. By obtaining over thirty billion bases of sequence from m6A antibody immunoprecipitated mRNA, we generated m6A methylation maps of mouse colonic epithelial cells with or with mettl14 deletion. We find that GsdmC2, GsdmC3, GadmC3 mRNA methylation is robustly decreased in colonic epithelial cells upon mettl14 deletion, leading to the decrease of Gsdmc expression.

overall_design: Examination of mRNA m6A modifications in mice colonic epithelial cells with or without mettl14 deletion.

first: Yanchun

last: Li

first: Wang

last: Liao


title: Chromosome conformation capture-on-chip sequencing (4C) analysis of the FCGR2A promoter.

city: Cambridge

first: Johanna

last: Dahlqvist

address: 415 Main street

institute: Broad Institute of MIT and Harvard

summary: We performed 4C analysis of the immunity-related FCGR2A gene promoter in the U937 monocytic cell line, using cells in resting conditions. The FCGR2A transcription start site was used as bait.

overall_design: 4C analysis of cross-linked resting U937 cells, using the FCGR2A transcription start site as a bait and next-generation sequencing as read-out.

first: John

last: Ray


title: Murine model and pathogenesis of radiation induced liver fibrosis.

city: Bern

first: Daniel

last: Sanchez-Taltavull

address: Murtenstrasse 35

department: Department of BioMedical Research

country: Switzerland

institute: University of Bern

summary: We have developed a new model of radiation-induced liver fibrosis and aimed to understand the underlying mechanism using RNAseq.

overall_design: We have collected the liver sample at different points post-irradiation (Day 1, Day6, Week 6, week 20). For each mouse, we have harvested liver from the liver area highly irradiated (≈50 Gy - that develops the late fibrosis) called HIGH, and from the area of the liver that is not irradiated or exposed to very low doses (that does not develop the fibrosis) called LOW.

first: Nicolas

last: Melin

last: Sánchez-Taltavull

first: Tural

last: Yaramadov

first: Deborah

last: Stroka


title: Genetic Networks of Bract Suppression in Maize

city: Provo

first: Clinton

last: Whipple

state: UT

institute: Brigham Young University

summary: This project is to generate and analyze the transcriptomes of bract primordium of maize, and to identify the genes, pathways and networks that suppress bract outgrowth in maize inflorescence.

overall_design: RNA profilings of bract primordia of wildtype, tsh1, tsh4 and tsh1;tsh4 double mutants. three biological replicates were used per genotype

first: Yuguo

last: Xiao

first: Jinyan

last: Guo

first: Mike

last: Scanlon


title: RNA-seq analysis of sporadic and Basal Cell Nevus Syndrome-associated odontogenic keratocysts (OKCs)

city: Athens

first: Konstantinos

middle: I

last: Tosios

address: Thivon 2

country: Greece

institute: National and Kapodistrian University of Athens

summary: The aim of this study was to decode the gene expression program characterizing odontogenic keratocyst (OKC) development, by performing a comprehensive transcriptomics analysis applied on whole OKC tissue derived from sporadic and Basal Cell Nevus Syndrome (BCNS)-associated OKCs, and control samples of pericoronal tissues of impacted teeth (dental follicles, DFs) derived from healthy individuals.

overall_design: Formalin-fixed and paraffin-embedded tissue samples from 6  cases of sporadic OKCs, 6 cases of BSCN-associated OKCs and 6 cases of pericoronal tissues of impacted teeth (dental follicles, DFs) were included in RNA-seq analysis. 150-bp paired-end multiplexed sequencing was implemented using an Illumina Hiseq4000 sequencer (Illumina Inc., San Diego, CA). DFs were selected as the control group, as they represent a source of dental lamina rests, proposed to be a potential tissue of origin of OKC. Transcriptomics analysis of the whole OKC tissue was perfomed, composed of the lining epithelium and the fibrous capsule, as the former harbors the pathognomonic features of OKC and the latter is thought to effect its epithelial structure and biological behavior. Validation of RNA-seq results for selected gene markers via immunohistochemistry was performed in all cases.

first: Eleni-Marina

last: Kalogirou

first: Spyros

last: Foutadakis

first: Marios

last: Agelopoulos


title: Deciphering defense mechanisms primed by a rhamnolipid in wheat towards Zymoseptoria tritici

city: Villeneuve d'Ascq

first: Anca

last: Lucau-Danila

address: Cité Scientifique SN2 303

department: Biology

country: France

institute: University of Lille

summary: We revealed that a rhamnolipid protects wheat against the hemibiotrophic fungal pathogen Zymoseptoria tritici. Foliar application of the biomolecule primes, during the early stages of infection, the expression of genes associated with different functional groups of genes.

overall_design: Wheat plants treated with rhamnolipid (R) or not (control, C), and inoculated with Z. tritici (i) or not (Ni) were analyzed for their gene expression.

first: Rémi

last: Platel

first: Ali

last: Siah


title: RNA-Seq of TET2 uniallelic mutated and wild type CFU colonies from rhesus macaque HSPCs

city: Bethesda

first: Taehoon

last: Shin

address: 9000 Rockville Pike

institute: National Institutes of Health

summary: Gene expression profile of individual CFU-GM colonies identified as uniallelic TET2 mutant versus TET2 wild type was analyzed via RNA-Seq to verify the impact of TET2 editing on gene expression in the rhesus macaque clonal hematopoiesis model.

overall_design: Mobilized CD34+ cells were treated with CRISPR/Cas9, followed by transplanted autologously to generate a non-human primate model of clonal hematopoiesis. CD34+ HSPCs were enriched from the bone marrow at 15 months post-transplantation and plated for CFUs. At 14 days, individual CFUs were picked and genotyped, and three TET2 wild type and three TET2 uniallelic CFU-GM CFUs with predicted loss-of-function mutations were analyzed via RNA-Seq.

first: Kyung-Rok

last: Yu

first: Cynthia

last: Dunbar


title: Transcriptomics profiles in human keratinocytes after PM2.5 exposure

city: Goyang-si

first: Young Rok

last: Seo

address: Dongguk-ro 32

department: Life science

country: South Korea

institute: Dongguk University

summary: RNA-seq in normal human epidermal keratinocytes (NHEK) for understanding PM2.5-induced effects

overall_design: 24hr exposure to PM2.5 (100ug/ml). Replicates: Control: 3, PM treated: 3

first: Hye-Won

first: Hyun Soo

last: Kim

first: Hyoung-june


title: Systematic genome-scale identification of host factors for SARS-CoV-2 infection across models yields a core single gene dependency; ACE2

first: Jason

last: Moffat

state: ON

address: 686 Bay Street, Room 13.9705

department: Molecular Genetics

institute: University of Toronto

summary: SARS-CoV-2 depends on host cell components for replication, therefore the identification of virus-host dependencies offers an effective way to elucidate mechanisms involved in viral infection. Such host factors may be necessary for infection and replication of SARS-CoV-2 and, if druggable, presents an attractive strategy for anti-viral therapy. We performed genome-wide CRISPR knockout screens in Vero E6 cells and 4 human cell lines including Calu-3, Caco-2, Hek293 and Huh7 to identify genetic regulators of SARS-CoV-2 infection. Our findings identified only ACE2, the cognate SARS-CoV-2 entry receptor, as a common host dependency factor across all cell lines, while all other host genes identified were cell line-specific, including known factors TMPRSS2 and CTSL. Several of the discovered host-dependency factors converged on pathways involved in cell signalling, lipid metabolism, immune pathways and chromatin modulation. Notably, chromatin modulator genes KMT2C and KDM6A in Calu-3 cells had the strongest impact in preventing SARS-CoV-2 infection when perturbed. Overall, the network of host factors that have been identified will be broadly applicable to understanding the impact of SARS-CoV-2 on human cells and facilitate the development of host-directed therapies.

sample_organism:
Homo sapiens
Chlorocebus sabaeus

platform_organism:
Homo sapiens
Chlorocebus sabaeus

overall_design: CRISPR screens in Vero E6, Huh7, Calu-3, Caco-2, and HEK293+ACE2+TMPRSS2 cell lines in the presence or absence of SARS-CoV-2 virus  (SARS-CoV-2/SB3 isolate)

first: Kevin

middle: R

last: Brown

first: Katherine

last: Chan


title: Nox4 expression in osteo-progenitors controls bone development in mice during early life

city: New Orleans

first: Jovanny

last: Zabaleta

state: LA

address: 1700 Tulane Ave

department: Interdisciplinary Oncology

institute: LSUHSC

summary: Tightly regulated and cell-specific NADPH-oxidases (Nox) represent one of the major sources of reactive oxygen species (ROS) signaling molecules that are involved in tissue development and stem cell self-renewal. We have characterized the role of Nox4 in osteo-progenitors during postnatal bone development. Nox4 expression in bone and ROS generation were increased during early osteoblast differentiation and bone development. Stromal osteoblastic cell self-renewal, proliferation and ROS production were significantly lower in samples from whole body Nox4 knockout mice (Nox4-/-) and conditional knockout (CKO) mice with depletion of Nox4 in the limb bud mesenchyme compared with those from control mice (Nox4fl/fl), but they were reversed after 9 passages. In both sexes, bone volume, trabecular number and bone mineral density were significantly lower in 3-week old CKO and Nox4-/- mice compared with Nox4fl/fl controls. This was reflected in serum levels of bone formation markers alkaline phosphatase (ALP) and procollagen 1 intact N-terminal propeptide (P1NP). However, under-developed bone formation in 3-week old CKO and Nox4-/- mice quickly caught up to levels of control mice by 6-week of age, remained no different at 13-week of age, and was reversed in 32-week old male mice. Osteoclastogenesis showed no differences among groups, however, CTX1 reflecting osteoclast activity was significantly higher in 3-week old male CKO and Nox4-/- mice compared with control mice, and significantly lower in 32-week old Nox4-/- mice compared with control mice. These data suggest that Nox4 expression and ROS signaling in bone and osteoblastic cells coordinately play a role on osteoblast differentiation, proliferation and maturation.

overall_design: We did RNA-seq in 80 colon cancer tissue samples from African American and Caucasian individuals (20 tumor tissues and 20 adjacent non-tumor tissues per ethnic group). RNA was extracted, qualified by Agilent 2100, quanitfied by qubit. Librarires were prepared using the Illumina's TruSeq Stranded mRNA kit and sequenced at 2 x 75bp (50M reads/sample)

first: Jin-Ran

last: Chen

first: Oxana

last: Lazarenko

first: Michael

last: Blackburn

first: Katrin

last: Schroder

first: Kim

middle: B

last: Pedersen

first: Martin

middle: J

last: Ronis


title: MicroRNA in plasma, Newly diagnosed untreated diabetic cases and healthy controls

city: Wuhan

first: Hua

last: Hu

address: 13 Hangkong Road

department: School of Public Health, Tongji Medical College

institute: Huazhong University of Science & Technology

summary: We examined the plasma miRNA among 113 newly diagnosed untreated diabetic cases and 113 healthy controls from DFTJ cohort by miRNA array screening and Taqman real-time PCR validation. After prediction of miRNA target genes, the low-abundance proteins coded by miR-193b-3p target genes were explored in plasma of the same population. We further validated the target effect and potential cell function of differentially expressed miRNA in HepG2 cells.

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus

overall_design: we examined the plasma miRNA among 113 newly diagnosed untreated diabetic cases and 113 healthy controls from DFTJ cohort

first: Meian

last: He


title: SME1 deficiency results in oxidative stress tolerance

city: Gent

first: Patrick

last: Willems

address: Technologiepark 927

department: PSB

institute: Ghent University

summary: In this work, we describe a nonsense mutation in SME1 that alleviates photorespiratory cell death in the Arabidopsis thaliana cat2-2 mutant. A SME1 loss-of-function mutant (sme1-1) and wild-type Col-0 were subjected to mRNA-seq for differential gene expression and alternative splicing analysis. This revealed a massive transcript reprogramming and occurrence of splicing defects caused by SME1 deficiency. For more details see the publication.

overall_design: 2 genotypes: sme1-1 and wild-type Col-0  X  3 replicates = 6 samples

first: Katrien

last: Van der Kelen

first: Valerie

last: Van Ruyskensvelde

first: Frank

last: Van Breusegem


title: Secretory pathway differences between HEK293 and CHO enable rescue of difficult to express human proteins

city: La Jolla

first: Nathan

last: Lewis

address: 9500 Gilman Dr

institute: UCSD

summary: Biologics have emerged as leading blockbuster therapeutics, but many advanced recombinant protein moieties remain difficult to produce. Here we identify bottlenecks limiting expression of challenging recombinant human proteins through a systems biology analysis of the transcriptomes of CHO and HEK293. Surprisingly, one third of the challenging human proteins displayed an improved secretion upon host cell swapping from CHO to HEK293. While most components of the secretory machinery showed comparable expression levels in both expression hosts, a key set of genes with extreme expression variation was identified. Among these, ATF4 and SRP9 were validated as general productivity boosters in CHO. Further, we found that more heavily glycosylated products benefit more from the elevated activities of the N- and O-glycosyltransferases found in HEK293 cells. Collectively, our results demonstrate the utilization of HEK293 cells for expression rescue of human proteins and suggest a strategy for identification of secretory pathway components improving yield and quality in HEK293 and CHO.

sample_organism:
Homo sapiens
Cricetulus griseus

platform_organism:
Homo sapiens
Cricetulus griseus

overall_design: Expression profiling and comparative analysis of CHO and HEK293 cells producing a panel of recombinant proteins.


title: Illumina NGS RNA-seq and RRBS Sequencing on Rat Kidney

city: Loma Linda

first: Charles

last: Wang

address: 11021 Campus Street

department: Department of Basic Sciences

institute: Loma Linda University

type: Methylation profiling by high throughput sequencing

summary: We reported the kidney transcriptome and methylome profiles of rat Brown Norway (BN) and Sprague Dawley (CD) strains at late pregnancy (day 18/21) compared to non-pregnancy. The renal transcriptome was characterized from 326 million single-end 100bp RNA-seq data. The methylome dataset included 234 million 75-bp RRBS DNA methylation reads. We identified 297 differentially expressed genes (DEGs) induced by pregnancy in CD rats and 174 DEGs induced in BN rats, based on the RNA-seq dataset.  237 of the 297 DEGs in CD pregnant rats and 114 of the 174 DEGs in BN pregnant rats are strain specific, indicating differential adaptation to pregnancy. Methylome data reveals that strain differences is the major factor in determining methylation differences. We also found that pregant BN showed higher methylation than non-pregnant BN at transcription starter site (TSS) and promoter regions. Functional analysis based on DEGs and DMGs revealed that pregnant BN rats showed renal transcriptomic changes that induce vitamin D deficiency and renal pro-inflammatory gene expression that can partly explain pregnancy-specific proteinuria. Integrated analysis based on transcriptome and methylome  suggested that modifications on DNA methylation were correlated with transcriptome changes for several significant biological processes and/or pathways.

overall_design: Brown Norway (BN) rat pregnancies are characterized by preeclampsia-like symptoms, while Sprague-Dawley (CD) rats are regarded as a model of normal pregnancy. Using these two rat strains, we characterized the transcriptomic and methylomic changes in both BN and CD rats during pregnancy as compared to non-pregnancy, in aim to understand the temporal changes in renal physiological adaptation during pregancy.

first: Eugenia

last: Mata-Greenwood


title: Integrated analysis of immune parameters, miRNA-mRNA interaction, and immune genes expression in the liver of rainbow trout following infectious hematopoietic necrosis virus infection

status: Public on Jun 21 2022

city: Xining

first: Delin

last: Qi

address: No. 251, Ningda Road

institute: Qinghai university

summary: Rainbow trout (Oncorhynchus mykiss) is an important economical cold-water fish worldwide. However, infection with infectious hematopoietic necrosis virus (IHNV) has severely restricted the development of aquaculture and caused huge economic losses. Currently, little is known about the immune defense mechanisms of rainbow trout against IHNV. In this study, we detected the changes of immune parameters over different post-infection periods (6-, 12-, 24-, 48-, 72-, 96-, 120-, and 144 hours post-infection (hpi)), mRNA and miRNA expression profiles under 48 hpi (T48L) compared to control (C48L), and key immune-related genes expression patterns in rainbow trout liver following IHNV challenge through biochemical methods, RNA-seq, and qRT-PCR, and the function of miR-330-y was verified by overexpression and silencing in vitro and in vivo. The results revealed that AKP, ALT, CAT, and T-SOD activities, and LZM content showed significant peaks at 48 hpi (P < 0.05), whereas MAD content and AST activity decreased continuously during infection (P < 0.05), and ACP activity varied slightly. From RNA-seq, a total of 6844 genes and 86 miRNAs were differentially expressed, and numerous immune-related differentially expressed genes (DEGs) involved in RIG-I-like receptor signaling pathway, Toll-like receptor signaling pathway, NOD-like receptor signaling pathway, cytokine-cytokine receptor interaction, and antigen processing and presentation were significantly upregulated in T48Lm group, including IFIH1, DHX58, MAVS, TRAF3, IRF3, IRF7, MX1, TLR3, TLR8, MYD88, NOD1, NOD2, IL-8, CXCR1, CD209, CD83, and TAP1. Integrated analysis identified seven miRNAs (miR-425-x, miR-185-x, miR-338-x, miR-330-y, miR-361-x, miR-505-y, and miR-191-x) that target at least three key immune-related DEGs. Expression analysis showed that IFIH1, DHX58, IRF3, IRF7, MX1, TLR3, TLR8, and MYD88 showed a marked increase after 24 hpi during infection. Further research confirmed TAP1 as one of the targets of miR-330-y, overexpression of miR-330-y with mimics or agomir significantly reduced the expression levels of TAP1, IRF3, and IFN, and the opposite effects were obtained by inhibitor. These results facilitate in-depth understanding of the immune mechanisms in rainbow trout against IHNV and will provide valuable information for disease resistance breeding.

overall_design: In this study, both biochemical methods and RNA-seq were performed to analyze the changes of immune parameters and miRNA-mRNA expression profiles in the rainbow trout liver against IHNV infection.

first: Jinqiang

last: Huang

first: Shenji

last: Wu


title: Aberrant EVI1 splicing contributes to EVI1-rearranged leukemia (ChIP-Seq)

city: Suita

first: Masaki

last: Nomura

state: Osaka

address: 2-2, Yamadaoka

department: Department of Cancer Pathology

institute: Graduate School of Medicine, The University of Osaka

summary: Detailed genomic and epigenomic analyses of MECOM (the MDS1 and EVI1 complex locus) have revealed that inversion or translocation of chromosome 3 at MECOM drive inv(3)/t(3;3) myeloid leukemias and revealed MECOM germline mutations in patients with MECOM-associated bone marrow failure syndromes. Here we identify a novel, previously unannotated oncogenic RNA-splicing derived isoform of EVI1 which is frequently present in inv(3)/t(3;3) AML and directly contributes to leukemic transformation. Expression of this EVI1 splice variant enhanced the self-renewal of hematopoietic stem cells and introduction of mutant SF3B1 in mice bearing the humanized inv(3)(q21;26) allele hastened leukemogenesis in vivo. These data provide a mechanistic basis for the frequent co-occurrence of SF3B1 mutations as well as new insights into the pathogenesis of myeloid leukemias harboring inv(3)/t(3;3).

overall_design: Examination of different DNA binding of EVI1 in 3q-rearranged hematopoietic cells with or without SF3B1 mutations .

first: Ruud

last: Delwel

first: Daichi

last: Inoue

first: Omar

last: Abdel-Wahab


title: Lack of major genome-wide DNA methylation changes in succinate-treated human epithelial cells

city: Grand Rapids

first: Gerd

last: Pfeifer

address: 333 Bostwick Ave. NE

institute: Van Andel Research Institute

summary: We treated human bronchial epithelial cells with succinate for five days and confirmed its effect on TET protein function by observing diminished formation of 5-hydroxymethylcytosine. We then analyzed global DNA methylation patterns by performing whole genome bisulfite sequencing.

overall_design: Comparative DNA methylation analysis of WGBS data for non-treatedand dimethyl-succinate-treated  human bronchial epithelial cells.

first: Wei

last: Cui

first: Zhijun


title: Aberrant EVI1 splicing contributes to EVI1-rearranged leukemia (RNA-Seq)

overall_design: mRNA profiles of wild type mouse hematopoietic stem or progenitor cells expressing EVI1-WT or EVI1+18.

first: Atsushi

last: Tanaka

first: Weijia

last: Zang


title: Aberrant EVI1 splicing contributes to EVI1-rearranged leukemia [mouse_RNA-seq]

overall_design: 1.0 x 10E6 total BM cells of Mx1-Cre control, Mx1-Cre inv(3), Mx1-Cre Sf3b1K700E/WT, and Mx1-Cre inv(3) Sf3b1K700E/WT CD45.2+ mice were mixed with 1.0 x 10E6 WT CD45.1+ support BM and transplanted via tail vein injection into lethally irradiated (two times 450 cGy) CD45.1+ recipient mice. Four weeks after BMT, the recipient mice received 20 mg/kg pIpC injection every other day for a total of 3 doses. Six months after pIpC injection, the recipient mice were sacrificed for sample preparation.

first: Alex

last: Penson


title: Isopimaric acid, an ion channel regulator, regulates calcium and oxidative phosphorylation pathways to inhibit breast cancer proliferation and metastasis

city: Hangzhou

first: Mingqian

last: Li

address: Gucui Road 234

institute: Tongde hospital of Zhejiang Province

summary: Breast cancer is the globally most common malignant tumor and the biggest threat to women. Even though the diagnosis and treatment of breast cancer are progressing continually, a large number of breast cancer patients eventually develop a metastatic tumor, especially triple-negative breast cancer (TNBC). Recently, metal ion homeostasis and ion signaling pathway have become important targets for cancer therapy. In this study, We analyzed the effects and mechanisms of isopimaric acid (IPA), an ion channel regulator, on the proliferation and metastasis of breast cancer cells (4T1, MDA-MB-231and MCF-7) by cell functional assay, flow cytometry, western blot, proteomics and other techniques in vitro and in vivo. Results found that IPA significantly inhibited the proliferation and metastasis of breast cancer cells (especially 4T1). Further studies on the anti-tumor mechanism of IPA suggested that IPA might affect EMT and Wnt signaling pathways by targeting mitochondria oxidative phosphorylation and Ca2+ signaling pathways, and then inducing breast cancer cell cycle arrest and apoptosis. Our research reveals the therapeutic value of IPA in breast cancer and provides a theoretical basis for the new treatment of breast cancer.

overall_design: The 4T1 cells were seeded in a six-well plate at the number of 5×105 cells/well. After overnight, 10 μg/mL IPA was added for 24 h, and the cells were extracted by the Trizol method.

first: Qun


title: Construction and comprehensive analysis of the ceRNA network to reveal key genes for benign tracheal stenosis.

city: shijiazhuang

first: Yanpeng

last: He

state: hebei

address: No.215 Heping West Road

department: The First Department of Pulmonary and Critical Care Medicine

institute: The Second Hospital of Hebei Medical University

type: Non-coding RNA profiling by high throughput sequencing

summary: Whole transcriptome sequencing was performed on blood samples collected from patients with benign tracheal stenosis and normal controls. To explore the possible biological functions of the differentially expressed genes in patients with benign tracheal stenosis, and to provide a valuable molecular basis for investigating the pathogenesis of benign tracheal stenosis.

overall_design: The benign tracheal stenosis blood samples and normal control samples were collected in the Second Hospital of Hebei Medical University, including 6 benign tracheal stenosis samples and 5 normal control samples.The samples wered stored in the refrigerator at -80℃ for long-term storage for high-throughput sequencing.

first: Zhigang

last: Cai


title: Transcriptome comparative analysis of heat-induced domesticated zebrafish during gonadal differentiation

city: Xiangtan

first: chen

middle: chen

last: Wang

state: Hunan province

address: Heping Street

department: School of Life and Health Sciences

institute: Hunan University of Science and Technology

summary: The influence of environmental factors, especially temperature, on sex ratio is of great significance to elucidate the mechanism of sex determination. However, the molecular mechanisms by which temperature affects sex determination remains unclear, although a few candidate genes have been found to play a role in the process. In this study, we conducted transcriptome analysis of the effects induced by high temperature on zebrafish during gonad differentiation period. 1171, 1022 and 2921 differentially expressed genes (DEGs) between high temperature and normal temperature were identified at 35, 45 and 60 days post-fertilization (dpf) respectively, revealing that DNA methyltransferases (DNMTs) and heat shock proteins (HSPs) were involved in the heat-exposed sex reversal. The Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway that were enriched in individuals after heat treatment included Fanconi anemia pathway, cell cycle, oocyte meiosis and homologous recombination. These results provide insights into the network of genes involved in heat-induced masculinization, and improve our understanding the molecular mechanisms of vertebrate sex determination.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for heat-induced domesticated zebrafish during gonadal differentiation

first: Chenchen

first: Xuhuai

last: Chen

first: Yu

last: Dai

first: Yifei

last: Zhang

first: Yuandong

last: Sun

first: Xiaojuan


title: Genetic and epigenetic mechanisms deregulate the CRL2pVHL complex in hepatocellular carcinoma

city: Vancouver

first: Wan

middle: L

last: Lam

address: 675 West 10th Ave

institute: BC Cancer Research Centre

summary: Dysregulation of ubiquitin-proteasome pathway genes through copy number alteration, promoter hypomethylation, and miRNA deregulation is involved in cancer development and progression. Further characterizing alterations in these genes may uncover novel drug targets across a range of diseases in which druggable alterations are uncommon, including hepatocellular carcinoma (HCC). We analyzed 377 HCC and 59 adjacent non-malignant liver tissue samples, focusing on alterations to component genes of the widely studied CRL2pVHL complex. Patient outcome was significantly worse when complex components VHL, CUL2, ELOC, or RBX1 were overexpressed in tumours. DNA hypomethylation and copy number increase were correlated with this overexpression, but many tumours had mRNA upregulation that was not explained by either mechanism. To assess the potential role of miRNA downregulation in component gene upregulation, we first acquired a wide-ranging view of the liver miRNA transcriptome by finding all miRNAs that were expressed in fetal liver, HCC, or adjacent non-malignant samples.  Interestingly, we found 66 miRNAs, including 39 previously unannotated miRNAs, that were downregulated in HCC and predicted to target one or more CRL2pVHL components. Several miRNAs, including hsa-miR-101-3p and hsa-miR-139-5p, were negatively correlated with multiple component genes, suggesting that miRNA deregulation may contribute to CRL2pVHL overexpression. Combining miRNA and mRNA expression, DNA copy number, and methylation status into one multidimensional survival analysis, we found a significant association between greater numbers of alterations and poorer overall survival for multiple component genes. While the intricacies of CRL2pVHL complex gene regulation require additional research, it is evident that multiple causes for the deregulation of these genes must be considered in HCC, including non-traditional mechanisms. A better understanding of the CRL2pVHL components and further elucidation of their regulation could expand our understanding of HCC oncogenesis and aid in the development of novel inhibitors.

overall_design: Ten fetal liver samples were subjected to miRNA sequencing, in order to quantify their expression of both known and unannotated ('novel') miRNAs.


title: Altered transcriptional responses in the lungs of aged mice after influenza infection

city: Providence

first: Gerard

last: Nau

state: RI

address: 593 Eddy St.

department: Medicine

institute: Alpert School of Medicine at Brown University

summary: This study used transcriptomic analysis to evaluate how aging specifically affects the functional host response to influenza in the mouse lung.  Adult (12-16 weeks) and aged (72-76 weeks) female BALB/c mice were infected with influenza (A/Puerto Rico/8/34 (H1N1) (A/PR8))  intranasally (instilled with 50 μl of PBS containing 50-100 pfu PR8). Lungs were processed for RNA expression analysis via Agilent microarray at various time points. Time points were 0, 1, 3, 5, 7, 9 days post infection.

overall_design: Factorial experiment. Two mouse age classes: Adult (12-16 weeks); and Aged (72-76 weeks), both tested in six timepoints (0, 1, 3, 5, 7, 9 days post-influenza infection). There were three replicates for each Age x timepoint combination except timepoint = 3 days. In the 3 day treatments, there were two replicates per timepoint. There were a total of 34 samples.

first: Jim

middle: A

last: Mossman


title: Aberrant EVI1 splicing contributes to EVI1-rearranged leukemia II

first: Masaki

last: Nomura

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

overall_design: Refer to individual Series


title: High-Yield Monocyte, Macrophage, and Dendritic Cell Differentiation from Induced Pluripotent Stem Cells

city: Gainesville

first: Clayton

middle: E

last: Mathews

state: FL

address: 1275 Center Drive

department: Pathology

institute: University of Florida

summary: Differentiation of induced pluripotent stem cells (iPSC) into monocytes, monocyte-derived macrophages (MDM), and monocyte-derived dendritic cells (moDC) represents a powerful tool for studying human innate immunology and developing novel iPSC-derived immune therapies. Challenges include inefficiencies in iPSC-derived cell cultures, labor-intensive culture conditions, low purity of desired cell types, and feeder cell requirements. Here, a highly efficient method for differentiating monocytes, MDMs, and moDCs that overcomes these challenges is described. The process utilizes commercially-available materials to derive CD34+ progenitor cells that are apically released from a hemogenic adherent fraction (HAF). Subsequently, the HAF gives rise to highly pure (>95%), CD34-CD14+ monocytes in 19-23 days and yields 13.5-fold more monocytes by day 35 when compared to previous methods. These iPSC-monocytes are analogous to human blood-derived monocytes and readily differentiate into MDM and moDC. The efficient workflow and increase in monocyte output heightens feasibility for high throughput studies and enables clinical-scale iPSC-derived manufacturing processes.

overall_design: Comparing gene expression (RNA-seq) of PSC-derived monocytes, PSC-monocyte derived macrophages, and PSC-monocyte derived dendritic cells to their primary counterparts. All 6 cell types had 3 replicates. The primary monocytes, primary monocyte-derived macrophages, and primary monocyte-derived dendritic cells were the controls for the PSC counterparts

first: Lucas

last: Armitage

first: Mohsen

last: Khosravi-Maharlooei

first: Similoluwa

middle: O

last: Ogundare

first: Amy

last: Meacham

first: Edward

last: Butfiloski

first: Dieter

last: Egli

first: Megan

last: Sykes

first: Mark

last: Wallet


title: Aberrant EVI1 splicing contributes to EVI1-rearranged leukemia


title: Delamination of trophoblast-like syncytia from the amniotic ectodermal analogue in human primed embryonic stem cell-based differentiation model [scRNA-seq]

city: Kyoto

first: Masatoshi

last: Ohgushi

address: 53 Shogoin Kawahara-cho, Sakyo-ku

department: Instutute for Frontier Life and Medical Sciences

institute: Kyoto University

summary: Human embryonic stem cells were converted into GATA3-expressing extraembryonic cells (GATA3+ ExE cells) when they were exposed to chemical inhibitors for ACTIVIN/NODAL (A83-01, 1uM) and FGF signaling (PD173074, 100nM). We refer here to this inhibitor-induced differentiation method as an 'AP' protocol. To understand the transcriptional properties of the AP-induced GATA3+ ExE cells, we obtained the gene expression profile from the single cells treated with AP for 2, 3 and 4 days.

overall_design: The GATA3 reporter human ESCs were exposed to AP for 2, 3, and 4 days.