title: Integrated analysis of mRNAs and lncRNAs repertoires involved immune response in panleukopenia virus-infected feline kidney cell line

city: Beijing

first: Lingling

last: Zhang

address: Yuanmingyuan West Road No.2

institute: Institute of Animal Sciences, Chinese Academy of Agricultural Sciences

type: Non-coding RNA profiling by high throughput sequencing

summary:
Purporse: FPV can cause a viral disease that occurs in cats, causing severe leukopenia, gastro-enteritis and nervous signs and leads to significant losses. LncRNAs biochemically resemble mRNAs posited by Jacob and Monod, yet do not template protein synthesis. Rather, lncRNAs functioning as RNA genes to play an important role in many biological and pathological processes such as inflammation and viral infection. However, lncRNAs have not been comprehensively identified in felines. Here, microarrays of mRNAs and lncRNAs were globally performed to identify the lncRNAs related to immune response of feline panleukopenia virus infection in F81 cells.
Methods:lncRNA and mRNA sequencing analysis was performed on an Illumina Hiseq 4000 (LC Sciences, USA) following the vendor's recommended protocol
Results: Through RNA sequencing, we performed a comprehensive analysis of lncRNAs and mRNAs in FPV infected F81 cells. F81 cells infected or uninfected FPV were used to prepare six libraries to generate 14.66 to 15.45 gigabytes (GB) clean reads per sample. We obtained 90588 novel lncRNAs, and 291 are differential expressed lncRNAs between FPV infected cells and uninfected cells. Consistent with previous studies, lncRNAs showed features distinct from mRNAs, such as shorter lengths, lesser exon numbers, and lower expression levels compared to mRNAs. The GO enrichment and KEGG pathway analyses showed that a majority of genes and lncRNAs were mainly related to the immune response of host cells with FPV infection. By differentially expressed target genes as well as co-expression network construction analysis, 21 key differentially expressed genes (19 upregulated & 2 downregulated) related to immune regulation of FPV infection in F81 cells were identified. Moreover, fifteen differentially expressed genes (five lncRNAs, ten mRNAs) were selected and independently validated by reverse-transcription qPCR and the results were consistent with the sequencing results.
Conclusion: The present study is the first to provide insights into the biological connection of lncRNAs and FPV infection, which can be further explore for the potential link between lncRNA expression and the pathogenesis of FPV infection.

overall_design: We designed two groups in this study, FPV group ( Feline Panleukopenia Virus infected) and Ctrl group ( Feline Panleukopenia Virus uninfected). Each group includes three replicates, so there are six library were constructed.

first: Shangjin

last: Cui


title: Upregulation of 5’-terminal oligopyrimidine mRNA translation upon loss of the tumor suppressor ARF

status: Public on Dec 20 2020

city: St. Louis

first: Kyle

middle: Aaron

last: Cottrell

state: MO

address: 660 S Euclid

country: USA

institute: Washington University in St. Louis

type: Expression profiling by high throughput sequencing

summary: Tumor cells require nominal increases in protein synthesis in order to maintain high proliferation rates. As such, tumor cells must acquire enhanced ribosome production. How many of the mutations in tumor cells ultimately achieve this aberrant production is largely unknown. The gene encoding ARF is the most commonly deleted gene in human cancer. ARF plays a significant role in regulating ribosomal RNA synthesis and processing, ribosome export into the cytoplasm, and global protein synthesis. Utilizing ribosome profiling, we show that 5’-terminal oligopyrimidine mRNA translation is upregulated following loss of ARF. Genes with increased translational efficiency following loss of ARF include many ribosomal proteins and translation factors.  Knockout of p53 largely phenocopies ARF loss, with increased protein synthesis and expression of 5’-TOP encoded proteins. The 5’-TOP regulators eIF4G1 and LARP1 are upregulated in ARF and p53 null cells.

overall_design: RNAseq and Ribosome profiling for three conditions with two replicates for each.

first: Jason

middle: D

last: Weber

middle: A


title: MicroRNA profile analysis of feline kidney cell line infected with Feline Panleukopenia Virus using deep sequencing

country: China

summary:
Purpose:MicroRNAs (miRNAs) are members of a rapidly growing class of small endogenous non-coding RNAs that play crucial roles in post-transcriptional regulator of gene expression in many biological processes. Feline Panleukopenia Virus (FPV) is a highly infectious pathogen that causes severe disease in pets, economically important animals and wildlife in worldwide. However, the molecular mechanisms underlying the pathogenicity of FPV have not been completely clear. To study the involvement of miRNAs in the FPV infection process, miRNAs expression profiles were identified via deep sequencing in the feline kidney cell line (F81) infected and uninfected with FPV.
Methods:miRNA-sequencing analysis was performed on an Illumina Hiseq 2500 (LC Sciences, USA) following the vendor's recommended protocol
Results:As a result, 673 known miRNAs belonging to 210 families and 278 novel miRNAs were identified. Then we found 57 significantly differential expression miRNAs by comparing the results between uninfected and FPV-infected groups. Furthermore, stem-loop qRT-PCR was applied to validate and profile the expression of the randomly selected miRNAs; the results were consistent with those by deep sequencing. Furthermore, the potential target genes were predicted. The target genes of differential expression miRNAs were analyzed by GO and KEGG pathway.
Conclusions:The identification of miRNAs in feline kidney cell line before and after infection with Feline Panleukopenia Virus will provide new information and enhance our understanding of the functions of miRNAs in regulating biological processes.

overall_design: We designed two groups in this study, FPV group ( Feline Panleukopenia Virus infected) and Ctrl group ( Feline Panleukopenia Virus uninfected). Each group includes three replicates, so there are six small RNA library were constructed.


title: Murine mononuclear phagocyte lineage cells

city: Yokohama

first: Tomohiko

last: Tamura

address: 3-9 Fukuura, Kanazawa-ku

department: Department of Immunology

country: Japan

institute: Yokohama City University

type: Genome binding/occupancy profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Genome-wide identification of myoblast circular RNAs

city: Xinyang

first: pengpeng

state: Henan

address: No.237 Nanhu Road Shihe District

institute: Xinayang Normal University

summary: We performed deep RNA-sequencing on ribosomal-depleted RNA isolated from a 6-day differentiation time-course of murine C2C12 myoblasts. We uncovered a total of 37,751 unique circRNA expressed from 6943 hosting genes.

overall_design: Examination of circRNA expression in 3 time points of myoblast differentiation.

first: Pengpeng

first: Yongjie

last: Xu


title: Expression data from ischemic myocardium of mice subjected to ischemia and reperfusion after protein DJ-1 pre-treatment

city: Barcelona

first: Lina

last: Badimon

address: St Antoni M Claret, 167

department: ICCC-Cardiovascular Program

country: Spain

institute: Research Institut- HSCSP

summary: We used microarrays to detail the global changes in myocardial gene expression induced by recombinant DJ-1 pre-treatment in a mice model of ischemia and reperfusion before MI induction.

overall_design: Mice full genome arrays were run with placebo (S12, S11, S9 and S10) and DJ-1-treated mice (S15, S13, S14 and S16) myocardial samples.

first: Judit

last: Cubedo

first: Gemma

last: Vilahur

first: Laura

last: Casaní

first: Guiomar

last: Mendieta

first: Efrem

last: Gomez-Jabalera

first: Esther

last: Peña

first: Oriol

last: Juan-Babot

first: Sandra

last: Camino-López

first: Teresa

last: Padró


title: Response of Chinese fir Seedlings to Low Phosphorus Stress and Analysis of Gene Expression Differences

city: Lin'an

first: Jianhui

last: Li

state: Zhejiang

address: Jincheng Street

institute: Zhejiang A & F University

summary: Chinese fir (Cunninghamia lanceolata) is an excellent fast-growing timber species occurring in southern China and has significant value in the forestry industry. In order to enhance the phosphorus utilization efficiency in Chinese fir, four clones named X6, S3, S39 and FK were used, and low phosphorus (LP) stress experiments were performed to analyze the response of different clones to phosphorus deficiency. According to the results on seedling height, maximum root length, leaf blade aspect ratio, root ratio, malondialdehyde content, acid phosphates activity, proline content, soluble protein level, and chlorophyll a and b levels of the tested clones, compared to the control groups (CK), the phosphorus high efficiency clone X6 was screen out for transcriptome sequencing experiments. De novo RNA-seq was then used to sequence the root transcriptomes of X6 under LP stress and CK, and we then compared the gene expression differences under the two conditions. A total of 3416 SDEGs were obtained by comparing the LP and CK groups, among which 1742 were up-regulated and 1682 were down-regulated. All SDEGs obtained from the LP and CK treated samples were subjected to KEGG annotation and classification. Through classification statistical analysis using WEGO software, 607 SDEGs obtained KEGG pathway annotations, which were related to 206 metabolic pathways. In Chinese fir subjected to LP stress, 53 SDEGs related with phosphorus metabolism, and phosphate uptake and transport were obtained from our transcriptome data. Based on the phosphorus metabolism pathway obtained by KEGG classification, combined with previously report on gene annotation related with phosphorus metabolism, the enzymes encoded by SDEG related with phosphorus metabolism and their expression pattern were mapped onto phosphorus metabolism pathway.

overall_design: Low phosphorus (LP, the phosphorus present in distilled water, which was determined to be less than 0.01mM) and phosphorus sufficient (CK, phosphorus concentration of 1mM) treated Chinese fir root were generated by deep sequencing, using Illumina Hiseq2000/2500.

first: Yongquan

last: Lu

first: Dingwei

last: Luo

first: Guifang

last: Ma


title: Transcriptome analysis of hIPSCs differentiation towards the skeletal muscle and motor neurons lineages

city: Marseille

first: Frederique

last: Magdinier

address: 27 Bvd Jean Moulin, Aix-Marseille Université. Faculté de Médecine. Campus La Timone

country: France

institute: Aix-Marseille Université - Marseille Medical Genetics

summary: We report the application of RNA sequencing technology for high-throughput expression profiling in human Induced Pluripotent Stem cells differentiated toward skeletal muscle and motor neurons lineages. Transcriptomic analysis was performed at different time points during the differentiation process

overall_design:
Transcriptome of biological duplicates at 3 key time point of the differentiation process. Briefly, hIPSCs derived from two different primary fibroblasts cell lines were processed throughout a differentiation protocol allowing the production of stable and mature muscle fibers along with motorneurones structures. A total of 6 Differenciation procedures were carried out with the same hIPSC clones for a total of 3 time point in biological duplicate. Results were analyzed to reveal transcritpome dynamics.
RNA Seq performed at different time point of a differentiation procedure; Each differentiation corresponds to one RNA Seq, as one cannot divide cells or split samples during this process. Thus, 6 differentiations correspond to 2 differentiations stopped at D8, 2 stopped at D17 and 2 stopped at D30.  Differentiations are performed from human Induced Pluripotent stem cells (hIPCs) derived from the primary fibroblast.

first: Mazaleyrat

last: Kilian

first: Chevalier

last: Raphaël

first: Magdinier

last: Frédérique


title: Targeting of the NOTCH transcription complex by a novel small molecule inhibitor CB-103 in KOPT-K1 cells

status: Public on Dec 19 2020

city: Lausanne

first: Nadine

last: Fournier

state: Vaud

address: Agora Cancer Research Center, Bugon 25A

country: Switzerland

institute: Agora Cancer Research Center & Swiss Institute of Bioinformatics

summary: We used microarrays to study the transcriptional networks controlled by CB-103 in KOPT-K1 human cell line.

overall_design: Human T-ALL cell line KOPT-K1 were treated with 10µM CB-103 or 0.1% DMSO control vehicle. RNA were collected 24 hours post-treatment. RNA were hybridized on Affymetrix Human Gene 1.0 ST Arrays.  The experiment was run twice independently, using each time a different siRNA to knockdown FOXC2, as previously described (Sabine et al, 2012, Dev Cell).

first: Rajwinder

last: Lehal

first: Jelena

last: Zaric

last: Zangger

first: Freddy

last: Radtke


title: Pharmacological disruption of the Notch transcription factor complex

summary: Notch pathway signaling is implicated in several human cancers. Aberrant activation and mutations of Notch signaling components are linked to tumor initiation, maintenance and resistance to cancer therapy. Several strategies, such as monoclonal antibodies (MAbs) against Notch ligands and receptors, as well as small molecule -secretase inhibitors (GSIs), have been developed to interfere with Notch receptor activation at proximal points in the pathway. However, the use of drug-like small molecules to target the downstream mediators of Notch signaling, the Notch transcription activation complex, remains largely unexplored. Using a Notch signaling dependent co-culture system, we developed a high-throughput small molecule screening assay. Herein we report the discovery of an orally active small molecule inhibitor (termed CB-103) of the Notch transcription activation complex. We show that CB-103 inhibits Notch signaling in primary human T-ALL and other Notch-dependent human tumor cell lines, and concomitantly induces cell cycle arrest, thereby impairing proliferation. Notably, CB-103 has the ability to downregulate Notch signaling in GSI-resistant human tumor cell lines that harbor chromosomal translocations and rearrangements in Notch genes. CB-103 mimics Notch loss-of-function phenotypes in flies and mice, retarding tumor growth in xenograft models of breast cancer and patient-derived xenograft models of human leukemia, notably without causing the frequently observed dose-limiting intestinal toxicity induced by other Notch inhibitors. In summary, we describe a pharmacological strategy to interfere with Notch signaling by disrupting the transcriptional regulatory complex it assembles, with therapeutic potential for the treatment of human tumors.

overall_design: Newly synthesized RNA expression profile comparisons of sorted RPMI-8402 cells treated with CB-103 or DMSO control after 1h, 4h or 24h treatment.

first: Linlin

last: Cao


title: Targeting of the NOTCH transcription complex by a novel small molecule inhibitor CB-103


title: Targeting of the NOTCH transcription complex by a novel small molecule inhibitor CB-103 in HPB-ALL cells

summary: We used microarrays to study the transcriptional networks controlled by CB-103 in HPB-ALL human cell line.

overall_design: Human T-ALL cell line HPB-ALL were treated with 10µM CB-103 or 0.1% DMSO control vehicle. RNA were collected 24 hours post-treatment. RNA were hybridized on Affymetrix Human Gene 1.0 ST Arrays.  The experiment was run twice independently, using each time a different siRNA to knockdown FOXC2, as previously described (Sabine et al, 2012, Dev Cell).


title: Construction of PYCARD-inducible system in two cancer cell lines, LNCaP (prostate cancer) and DLD1 (colorectal cancer)

city: Sendai

first: Shinichi

last: Fukushige

address: 2-1 Seiryo-machi, Aoba-ku

department: Department of Diabetes, Metabolism and Endocrinology

institute: Tohoku University Graduate School of Medicine

summary: Epigenetic gene silencing by aberrant DNA methylation is one of the important mechanisms leading to the loss of key cellular pathways in tumorigenesis. We previously reported that PYCARD (PYD and CARD domain containing), an apoptosis inducing gene, was frequently hypermethylated in prostate cancer in a tumor-specific manner (46/51: 90%), by methylation specific PCR (MSP). In order to examine the relationship between methylation status and level of the PYCARD protein expression in prostate cancer, we further performed immunohistochemical analyses of the 51 MSP-analyzed prostate cancer specimens and observed reduced or absent protein expression in tumors with aberrant methylation status of PYCARD. In contrast, PYCARD was unmethylated and expressed in normal prostatic tissues including epithelial, basal and inflammatory cells. Furthermore, we tried to identify downstream genes of PYCARD by microarray analyses using PYCARD inducible LNCaP prostate cancer cells. Interestingly, PYCARD induction upregulated PYDC1, another PYCARD homolog that associates with PYCARD and accelerates inflammation and apoptosis. Our present results suggest that aberrant methylation of PYCARD is an extremely frequent event and contributes to escape from apoptosis by reducing PYCARD expression in prostate cancer.

overall_design: Two cancer-derived cell lines, LNCaP_PYCARD and DLD1_PYCARD, that allow tetracycline-regulated PYCARD expression were constructed. The RNAs from LNCaP_PYCARD and DLD1_PYCARD with (4 days tetracycline treatment) or without tetracycline were prepared and analyzed by using Agilent whole human genome microarray (4×44K) v2.


title: MDA-MB-231-LM2 cells treated with sudemycin D6 (SD6)

status: Public on Dec 18 2020

city: Houston

first: Jarey

middle: Hao

last: Wang

state: Texas

address: 1 Baylor Plaza, 304B, Anderson Building

institute: Baylor College of Medicine

summary: The objective is to identify gene expression patterns that occur after spliceosome inhibition in triple-negative breast cancer.

overall_design: MDA-MB-231-LM2 cells were treated with vehicle (DMSO) or SD6 for 72 hours, in biological triplicate.

first: Elizabeth

last: Bowling

first: Thomas

last: Westbrook


title: The differential gene expression of the dentate gyrus between WT and KO mice as well as between Fst knockout and overexpressing mice

city: Taoyuan City

first: Yu-Ju

last: Chen

address: No.259, Wenhua 1st Rd.

country: Taiwan

institute: Chung Gang University

summary: we aim to find the possible pathway and mechanism whereby Fst mediates neurogenesis and spatial learning by utilising RNA-seq to identify differential hippocampal gene expression between WT and KO mice as well as between KO and Fst overexpression mice

overall_design: Three samples in each group and each sample was collected from three different mice.

first: Guo-Jen

last: Huang


title: SUM159 cells treated with sudemycin D6 (SD6)

overall_design: SUM159 cells were treated with vehicle (DMSO) or SD6 for 72 hours, in biological triplicate.


title: Drought responsiveness dynamics in wheat

city: Lincoln

first: Chi

last: Zhang

state: NE

address: 1901 Vine Street

institute: University of Nebraska - Lincoln

summary: Wheat seedling root transcritpome under well watered and water limited treatments for two genotypes, Svevo and IL20-2

overall_design: RNA deep sequencing

first: Harkamal

last: Walia

first: Harel

last: Bacher


title: Glucocorticoid Receptor (GR) ChIP-seq in A549 and U2OS cells

city: San Francisco

first: Delsy

last: Martinez

state: California

institute: UCSF

summary: Glucocorticoid (GC) response elements (GREs) are genomic segments that confer GC-regulated transcription by recruiting hormone-bound glucocorticoid receptor (GR) and nucleating assembly of transcriptional regulatory complexes (TRCs). The locations of GR binding, the functionality of those GR occupied regions (GORs) as GREs, and the molecular features and spatial organization that characterize active GREs are gene-, cell- and physiological-context specific, and poorly understood. Moreover, identification of the gene(s) targeted for regulation by a given GRE has been inferred by proximity, or examined outside the normal chromosomal context, rather than rigorously validated. We approached these issues in two human cell lines with distinct tissue origins, treated or not with a hormonal ligand that activates GR.

overall_design: ChIP-Seq profiling to examine GR occupancy differences  in A549 and U2OS cells treated with EtOH or 100 nM Dexamethasone (Dex) for 90 minutes.


title: The ZSWIM8 ubiquitin ligase mediates target-directed microRNA degradation [dataset3]

city: Cambridge

first: Charlie

middle: Y.

last: Shi

state: MA

address: 455 Main St.

department: Biology

institute: Whitehead Institute / MIT

summary: MicroRNAs (miRNAs) associate with Argonaute (AGO) proteins to direct widespread post-transcriptional gene repression.  Although association with AGO typically protects miRNAs from nucleases, extensive pairing to some unusual target RNAs can trigger miRNA degradation.  Here we found that this target-directed miRNA degradation (TDMD) required the ZSWIM8 Cullin-RING E3 ubiquitin ligase.  This and other findings suggested and supported a mechanistic model of TDMD in which target-directed proteolysis of AGO by the ubiquitin–proteasome pathway exposes the miRNA for degradation.  Moreover, loss-of-function studies indicated that the ZSWIM8 Cullin-RING ligase accelerates degradation of numerous miRNAs in cells of mammals, flies, and nematodes, thereby specifying the half-lives of most short-lived miRNAs.  These results elucidate the mechanism of TDMD and expand the inferred role of TDMD in shaping miRNA levels in bilaterian animals.

sample_organism:
Drosophila melanogaster
Homo sapiens

platform_organism:
Drosophila melanogaster
Homo sapiens

overall_design: miRNA expression profiling by small-RNA sequencing of clonal K562 or Drosophila S2 cell lines that are either wild-type or knockout for ZSWIM8 (zswim8/Dora).  Clonal lines were generated by single-cell sorting of parental lines transiently transfected with Cas9 and either a gRNA targeting ZSWIM8 (zswim8/Dora) or a non-targeting control gRNA.  This study consists of libraries generated from three clonal  lines per genotype for each of the two cell types.

middle: Y

first: David

middle: P

last: Bartel


title: The ZSWIM8 ubiquitin ligase mediates target-directed microRNA degradation [datatset 7]

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: mRNA expression profiling by RNA sequencing of polyclonal mammalian cell lines expressing either Cas9 and one of three non-targeting control gRNAs, or KRAB-dCas9 and either a non-targeting control gRNA, a CYRANO-targeting gRNA, or one of two ZSWIM8-targeting gRNAs.  This study consists of libraries generated from two to three biological replicates.


title: Genome-wide maps of nucleolus interactions in human cells using 4xAP3 DamID

city: Amsterdam

first: Bas

last: van Steensel

address: Plesmanlaan 121

department: division of Molecular Biology

country: Netherlands

institute: Netherlands Cancer Institute

summary: We used DamID to map nucleolus interactions in human cells using a 4x tandem repeat of the nucleolar targeting sequence of AP3D1 (Scott, 2010) ("4xAP3"). These interactions are mapped in various human cell lines, including human K562 cells

overall_design: A DamID expression vector was created where Dam was fused to the 4xAP3 sequence described above to target to the nucleolus. Wild-type K562 cells were transduced with lentiviral constructs in more replicates, Dam-4xAP3 or Dam only and collected by three days after transduction for quantification of genome-wide methylation levels via next-generation sequencing.

first: Tom

last: van Schaik

first: Daan

last: Peric-Hupkes


title: Differentiation of IMR32 neuroblastoma is accompanied by a global change in the transcriptome

city: Moscow

first: Tatiana

last: Portseva

address: Vavilova street 32

country: Russia

institute: Engelhardt Institute of Molecular Biology, Russian Academy of Sciences

summary: The aim of this study is to compare human transcriptomes based on NGS (RNA-seq). The transcriptome of neuroblastoma IMR32 was compared with the transcriptome of neuroblastoma IMR32, which was differentiated for 16 days in the presence of 2.5 mkM BrdU. Methods. Human mRNA profiles of 16-day differentiation of IMR32 neuroblastoma and non-differentiated IMR32 neuroblastoma were obtained by deep three-fold sequencing using Illumina NovaSeq. The mapping is read into the human genome (hg38) using the hisat program. On average, about 89-90% of all data received was unambiguously aligned in each library. The htseq-count utility has counted the number of reads that have been matched against known genes (ncbi - entrezID). The obtained values (cpm - countpermillion) for each gene for each library were combined into one matrix for further analysis. Results: Using an optimized data analysis workflow, we matched about 30 million sequence reads per sample to the human genome (hg38). Filtration, normalization by the method (TMM), variance estimation and differentially expressed genes estimation were performed in the edgeR module. Genes in which the cpm did not exceed 1 in any three libraries were considered low expressing.

overall_design: Human neuroblastoma mRNA profiles of 16-days differentiating neuroblastoma IMR32  and untreated  neuroblastoma  IMR32. Differentiation in MEM, 10% FCS, 2.5 mkM BrdU.

first: E

middle: V

last: Pankratova E.V.

first: A

middle: G

last: Stepchenko

first: T

middle: N


title: RNA sequencing data from primary atypical teratoid rhabdoid tumor (ATRT) samples

city: Hamburg

first: Dörthe

last: Holdhof

address: Martinistraße 52

country: Germany

institute: University Medical Center Hamburg-Eppendorf

summary: Atypical teratoid/rhabdoid tumors (ATRTs) are very aggressive childhood malignancies of the central nervous system. The underlying genetic cause are inactivating bi-allelic mutations in SMARCB1 or (rarely) in SMARCA4. The purpose of this study was to compare the transcriptomes of ATRTs with SMARCA4 mutations to those carrying SMARCB1 mutations.

overall_design: 6 SMARCA4 mutated and 4 SMARCB1 mutated ATRT samples were selected for RNA extraction from formalin fixed paraffin embedded (FFPE) tissue followed by RNA sequencing.

first: U

last: Schüller

first: D


title: The ZSWIM8 ubiquitin ligase mediates target-directed microRNA degradation [dataset 2]

overall_design: miRNA expression profiling by small-RNA sequencing of polyclonal mammalian cell lines expressing Cas9 and either one of three control guide RNAs (gRNAs), or one of three gRNAs targeting ZSWIM8.  This study consists of libraries generated from two to three biological replicates per cell ine, with the expressied gRNA indicated.


title: Next Generation Sequencing Facilitates Quantitative Analysis of original and mutant E. coli K-12 MG1655 Transcriptomes

city: Brisbane

first: Min

last: Jin

address: st lucia,QLD

country: Australia

institute: The University of Queensland

summary: The goals of this study are to use Next-generation sequencing (NGS)to detect bacterial mRNA profiles of original E. coli K-12 MG1655 and fluoxetine induced E. coli mutants in response to 100 mg/L fluoxetine for 8 h, in triplicate, using Illumina HiSeq 2500.The NGS QC toolkit (version 2.3.3) was used to treat the raw sequence reads to trim the 3’-end residual adaptors and primers, and the ambiguous characters in the reads were removed. Then, the sequence reads consisting of at least 85% bases were progressively trimmed at the 3’-ends until a quality value ≥ 20 were kept. Downstream analyses were performed using the generated clean reads of no shorter than 75 bp. The clean reads of each sample were aligned to the E. coli reference genome (NC_000913) using SeqAlto (version 0.5). Cufflinks (version 2.2.1) was used to calculate the strand-specific coverage for each gene, and to analyze the differential expression in triplicate bacterial cell cultures. The statistical analyses and visualization were conducted using CummeRbund package in R (http://compbio.mit.edu/cummeRbund/). Gene expression was calculated as fragments per kilobase of a gene per million mapped reads (FPKM, a normalized value generated from the frequency of detection and the length of a given gene.

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

overall_design: Bacterial mRNA profiles of original E. coli K-12 MG1655 and fluoxetine induced E. coli mutants in response to 100 mg/L fluoxetine for 8 h, in triplicate, using Illumina HiSeq 2500

first: Ji

last: Lu

first: Jianhua

last: Guo

first: Likai

last: Mao


title: RNA-seq profiling of C/EBPβ-overexpressing myoblasts [proliferating myoblasts]

city: Ottawa

first: Nadine

last: Wiper-Bergeron

state: Ontario

address: 451 Smyth Road

department: Cellular and Molecular Medicine

country: Canada

institute: University of Ottawa

summary: We previously identified C/EBPβ as an inhibitor of myogenic differentiation and a regulator of muscle satellite cell self-renewal. We found that C/EBPβ is regulated during the transition from proliferation to growth arrest in myoblasts and overexpression of C/EBPβ in myoblasts promotes cell growth arrest in vitro and improves engraftment of satellite cells into the stem cell niche in vivo. To identify the molecular mechanism by which C/EBPβ regulates myoblast proliferation and growth arrest, we performed RNA-seq on C/EBPβ-overexpressing myoblasts.

overall_design: mRNA profiles of C/EBPβ-overexpressing C2C12 cells and empty vector controls in growth media.

first: Hamood

last: AlSudais


title: The ZSWIM8 ubiquitin ligase mediates target-directed microRNA degradation [dataset 6]

first: Charlie

overall_design: Profiling of gRNA cassettes from K562 cells expressing a miR-7 fluorescent reporter and the human CRISPRi v2 library.  Cells were sorted by mCherry:GFP ratio, and those in the top 5% and bottom 5% of this metric were collected. This study consists of libraries generated from these populations.

first: David


title: The ZSWIM8 ubiquitin ligase mediates target-directed microRNA degradation [dataset 4]

overall_design: miRNA expression profiling by small-RNA sequencing of wild-type (N2) and ebax-1 (tm2321 or CZ9907) mutant C. elegans gravid adults.  This study consists of libraries generated from three biological replicates.


title: Mammalian AMP-activated protein kinase has only a partial functional redundancy with Snf1 in Saccharomyces cerevisiae

city: Kgs. Lyngby

first: Jie

last: Zhang

address: Kemitorvet 220

department: CFB

country: Denmark

institute: Technical University of Denmark

summary: Snf1/AMPK functions as a heterotrimeric complex, consisting of a regulatory subunit that is senses the energy status, a catalytic subunit with the canonical kinase domain and a scaffolding subunit to secure the complex together. The high degree of conservation in the sequence, structure and function of yeast Snf1 and mammalian AMPK, it is only logical to investigate the extent of conservation in the downstream effects that are controlled by these kinases.

platform_organism:
Schizosaccharomyces pombe
Saccharomyces cerevisiae

overall_design: The reference yeast strain is the mutant strain snf1Δ carrying the plasmid HA-Snf1. The mutant strain Alpha1 is the mutant strain snf1Δ carrying the plasmid HA-Alpha1, which is the katalytic domain of Alpha1 subunit of AMPK fused to the regulatory domain of Snf1. The mutant strain HA-T210A is the mutant strain snf1Δ carrying the plasmid HA-T210A, which is the native Snf1 but Thr210 (the phosphorylation and activation site) was mutated into Ala.

first: J

first: S

middle: K

last: Nandy

last: Nielsen

first: G

last: Vemuri


title: High expression of circZBTB46 predicts poor prognosis in patients with myelodysplastic syndrome and acute myeloid leukemia

status: Public on Dec 17 2020

city: Shanghai

first: Shuang

last: Li

address: 12 Wulumuqi Road Central

institute: Huashan Hospital of Fudan University

summary: This study aimed to find the functional circular RNA and further analyze its biological and clinical significance in myelodysplastic syndrome (MDS) and acute myeloid leukemia (AML) patients.The circRNAs profiles were analyzed using the Arraystar human circRNA microarray with bone marrow samples from 5 MDS patients, 5 AML patients and 4 controls. Real-time quantitative polymerase chain reaction was carried on circZBTB46 in bone marrow samples from 124 MDS patients, 116 AML patients and 37 controls, and subsequently associated with clinicopathological characteristics and survival of MDS and AML patients.Furthermore, functional studies were conducted by silencing and rescuing/increasing circZBTB46 expression in SKM-1, THP-1 and K562 cell lines. Our results suggested the essential role of circZBTB46 in the progression of MDS and AML, and might be a poor indicator of hematological malignancies.

overall_design: The circRNAs profiles were analyzed using the Arraystar human circRNA microarray with bone marrow samples from 5 MDS patients, 5 AML patients and 4 controls. CircRNAs from 14 samples were detected by the Arraystar Human circRNA Array V2 (8 × 15 K, Arraystar, Rockville, MD, USA) including 15,000 probes detecting 13,617 circRNAs ever obtained from circbase and other databases. Total RNA from each sample was quantified using the NanoDrop ND-1000 (Thermo Scientific, DE, USA). The sample preparation and microarray hybridization were performed based on the Arraystar’s standard protocols.

first: Xiaoqin

last: Wang

first: Wanling

last: Wu


title: Integrated miRNA-mRNA transcriptomic analysis reveals antler growth regulatory network.

city: Changchun

first: Boyin

last: Jia

state: Jilin

address: 2888 Xincheng Street

department: College of Animal Science and Technology

institute: Jilin Agricultural University

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

overall_design: Refer to individual Series


title: Integrated miRNA-mRNA transcriptomic analysis reveals antler growth regulatory network [RNA-seq]

summary: As the only regenerative organ of mammals, antler could grow rapidly without carcinogenesis. To understand the molecular mechanisms of the growth of sika deer antler, we used de novo RNA-seq analyses to determine the diﬀerential expression of unigenes and miRNAs from antler at 15, 60, 90, and 110-day. A total of 55004 unigenes, 208 known miRNAs and 38 novel miRNAs were identified. 10182 unigenes and 35 miRNAs were differentially expressed between 60-day and 15-day antler, 13258 unigenes and 53 miRNAs were differentially expressed between 90-day and 60-day antler, and 10740 unigenes and 27 miRNAs were differentially expressed between 110-day and 90-day antler. GO and KEGG analyses showed that DE unigenes and miRNA were mainly related to chondrogenesis, osteogenesis and inhibition of oncogenesis, that were closely associate with antler growth. We also constructed mRNA-mRNA and miRNA-mRNA interaction networks related to chondrogenesis, osteogenesis and inhibition of oncogenesis of antler. The results showed that mRNA (COL2A1, SOX9, WWP2, FGFR1, SPARC, LOX etc.) and miRNAs (miR-145, miR-199a-3p, miR-140, miR-199a-5p etc.) may play important roles in chondrogenesis and osteogenesis of antler, and mRNA (TP53, Tpm3 and ATP1A1 etc.) and miRNAs (miR-106a, miR-145, miR-1260b and miR-2898 etc.) may have key roles in inhibiting the carcinogenesis of antlers. In this study, we identified miRNAs and unigenes related to chondrogenesis, osteogenesis and inhibition of oncogenesis of antler. This will provide a reference for in-depth analysis of the molecular mechanism of antler growth without carcinogenesis, and also provide valuable information for cartilage- and bone-related disease treatment, cancer treatment.

overall_design: The miRNA expression profiles of antler at 15, 60, 90, and 110-day in sika deer were generated by Illumina HiSeq2500 sequencing

first: Dongdong

last: Liu

first: Fuhe

last: Yang


title: The ZSWIM8 ubiquitin ligase mediates target-directed microRNA degradation [dataset 5]

last: Shi

overall_design: miRNA expression profiling by small-RNA sequencing of input and eluate from tandem ubiquitin binding entity (TUBE) pulldown with lysates generated from Drosophila S2 cell lines that are either wild-type or knockout for zswim8/Dora.  Clonal lines were generated by single-cell sorting of parental lines transiently transfected with Cas9 and either a gRNA targeting zswim8/Dora or a non-targeting control gRNA.  This study consists of libraries generated from three clonal lines per genotype.

last: Bartel


title: Integrated miRNA-mRNA transcriptomic analysis reveals antler growth regulatory network [miRNA-seq]


title: Histone deacetylase 9 promotes vascular inflammation by activating IKK

city: Martinsried

first: Tobias

last: Straub

address: Großhadener Str. 9

department: Biomedical Center, Bioinformatics

institute: LMU Munich

summary: Comparison of TNFα activated BMDM from B6.129P2-Apoetm1Unc/J mice treated with the inhibitors TMP195 or TPCA-1.

overall_design: Cells were treated for 1h with the respective inhibitors, followed by 24h stimulation with TNFα and subsequently lysed in Trizol.

first: Yaw

last: Asare

first: Thomas

last: Campbell-James

first: Yury

last: Bokov

first: Lydia

middle: L

last: Yu

first: Matthias

last: Prestel

first: Omar

last: El Bounkari

first: Stefan

last: Roth

first: Remco

middle: T

last: Megens

first: Kyra

last: Thomas

first: Guangyao

last: Yan

first: Melanie

last: Schneider

first: Natalie

last: Ziesch

first: Steffen

last: Tiedt

first: Carlos

last: Silvestre-Roig

first: Quinte

last: Braster

first: Yishu

last: Huang

first: Rainer

last: Malik

first: Manuela

first: Christof

last: Haffner

first: Arthur

last: Liesz

first: Oliver

last: Soehnlein

first: Jürgen

last: Bernhagen

first: Martin

last: Dichgans


title: Expression data from the liver of high fat diet fed control and treated mice

city: New Delhi

first: Neeru

last: Saini

state: Delhi

address: Mall road

department: FGU

country: India

institute: CSIR-IGIB

summary:
MicroRNAs co-ordinate various developmental and physiological processes, including cholesterol metabolism. High fat diet can induce abnormalities in systemic microRNA expression that can aid in the progression or diet-induced hypercholesterolemia. Since a microRNA can regulate a range of mRNAs, alterations in the endogenous level of microRNA can significantly alter the global gene expression.
We performed the microarray experiment to understand the changes in the global gene expression in the liver of mice following down-regulation of endogenous miR-128-3p

overall_design: A diet induced hypercholesterolemic mouse model was prepared. The mice were randomly segregated I nto two groups (n=4) that received five intra-peritonial injection of either anti-miR-128-3p or control

first: Amit

last: Chandra

first: Kritika

last: Sharma

first: Kunal

last: Pratap

first: Vijaypal

last: Singh


title: Analysis of the microbiota composition of colorectal mucosa tissues and adjacent healthy tissues of 40 patients affected by colorectal cancer.

city: Firenze

first: Matteo

last: Ramazzotti

address: viale Morgagni 50

department: Experimental and Clinical Biomedical Sciences

country: Italy

institute: University of Florence

summary: Colorectal cancer is a chronic inflammation-associated tumor and the immune system, besides protecting the host from developing tumors, can support the CRC progression. In this scenario, due to its capability to elicit the production of cytokines, gut microbiota is essential to modulate immune response, influencing immunostimulatory or immunosuppressive reactions. So, the investigation of the microbiota-immunity axis in healthy and tumor mucosa is crucial to well understand the cancer development with positive relapses in prevention and treatment.

overall_design: Total DNA was extracted from tumoral and surrounding healthy mucosa samples of 40 patients affected by colorectal cancer CRC patients and amplicons of variable V3–V4 regions of the bacterial 16s rRNA gene were sequenced.

first: Amedeo

last: Amedei


title: DNA methylation of normal kidney, Wilms tumor and metastatic (lung) samples

city: Campinas

first: Mariana

last: Maschietto

state: São Paulo

address: Rua Márcia Mendes, 619

department: Research Center

country: Brazil

institute: Boldrini Children's Hospital

type: Methylation profiling by genome tiling array

summary: To identify underlying mechanisms involved with metastasis formation in Wilms tumors (WTs), we performed comprehensive DNA methylation and gene expression analyses of matched normal kidney (NK), WT blastemal component, and metastatic tissues (MT) from patients treated under SIOP 2001 protocol. A linear Bayesian framework model identified 497 differentially methylated positions (DMPs) between groups that discriminated NK from WT, but MT samples were divided in two groups. Accordingly, methylation variance grouped NK and three MT samples tightly together and all WT with four MT samples that showed high variability. WT were hypomethylated compared to NK, and MT had a hypermethylated pattern compared to both groups. The methylation patterns were in agreement with methylases and demethylases expression. Methylation data pointed to the existence of two groups of metastases. While hierarchical clustering analysis based on the expression of all 2569 differentially expressed genes (DEGs) discriminated WT and MT from all NK samples, the hierarchical clustering based on the expression of 44 genes with a differentially methylated region (DMR) located in their promoter region revealed two groups: one containing all NKs and three MTs and one containing all WT and four MTs. Methylation changes might be controlling expression of genes associated with WT progression. The 44 genes are candidates to be further explored as a signature for metastasis formation in WT.

overall_design: Bisulphite converted DNA from the 21 samples were hybridised to the Illumina Infinium Human Methylation 450K Beadchip v1.2

first: João

last: Guerra

first: Bruna

middle: M

last: Pereira


title: Transcriptome sequencing reveals high-salt diet-induced abnormal liver metabolic pathways in mice

city: Beijing

first: Li

last: Yanping

address: 1# Gaojingjia

institute: Civil Aviation General Hospital

summary: we analyzed the influence of a high-salt diet on liver by transcriptome sequencing. We found that after high-salt feeding, many metabolic abnormalities had formed based on transcriptome sequencing results. Analyses of differentially expressed genes revealed that at least 15 enzyme activities and the metabolism of multiple substances were affected by a high-salt diet. Moreover, a variety of signaling, and metabolic pathways, as well as biological functions, including some known pathways and many novel ones, such as retinol metabolism, linoleic acid metabolism, steroid hormone biosynthesis, and signaling pathways, were involved in liver dysfunction due to a high-salt diet.

overall_design: Liver mRNA profiles of  normal mice (fed with normal chow) and the high salt group (fed with sodium-rich chow (containing 6% NaCl)) for 6 weeks.

first: Lyu

last: Yufei


title: Gene expression profiling of human angiosarcoma

city: Minneapolis

first: Lauren

last: Mills

state: MN

address: 420 Delaware St SE

department: Department of Pediatrics

institute: University of Minnesota

summary: We generated RNA-Seq data from human angiosarcoma tissues (N=13) and non-malignant tissue samples (N=6). The goal of this study was to determine differentially expressed genes in the tumors compared to controls. We sequenced about 80 – 100 million sequence reads per sample and mapped to the human reference genome (GRCh38). We identified 1,237 differentially expressed genes between the tumors and non-malignant controls (FDR P-value < 0.05): 490 genes were upregulated and 747 genes were downregulated in angiosarcomas. Our results show a comprehensive data of fusion genes and gene expression profile in human angiosarcomas using RNA-seq technology.

overall_design: Genome-wide gene expression profiling between human angiosarcomas and non-malignant control tissues using RNA-seq.

first: Jong

middle: H

last: Kim

first: Jaime

middle: F

last: Modiano

first: Aaron

last: Sarver


title: Analysis of effects of TM4SF5 deficiency in inguinal white adipose tissue

city: Seoul

first: CheolJun

last: Choi

address: 1, Gwanak-ro, Gwanak-gu, 29-310

country: South Korea

institute: Seoul National University

summary: There are limited studies of TM4SF5, even though it plays a role in cell proliferation functions as lysosomal membrane amino acid sensor. In current studies, we aimed to study the role of TM4SF5 in mitochondrial homeostasis in adipocytes.

overall_design: White adipose tissue mRNA profiles of wild type(WT) and TM4SF5-/- mice were generated by deep sequencing. Three biological replicates were analyzed for each of two conditions.

first: Yun-Hee

last: Lee

first: Cheoljun


title: Topical application of an irreversible small molecule inhibitor of Lysyl Oxidases ameliorates skin scarring and fibrosis

city: Perth

first: Zhenjun

last: Deng

state: Western Australia

address: 35 Stirling Highway

institute: The University of Western Australia

summary: Next-generation sequencing (NGS) has been performed to investigate the effect of Lysyl oxidase inhibition by PXS-4787A on transcriptome of normal skin derived fibroblasts and keratinocytes. Fibroblasts and keratinocytes of low passage (p2-5) were cultured onto T25 flasks until ~70% confluence was reached. Fibroblasts were treated with or without 10 µM PXS-4787A in complete fibroblast growth media for 48 hours at 37°C. Keratinocytes were treated with 10 µM PXS-4787A with basal keratinocyte medium supplemented with 1.2 mM calcium chloride for 48 hours at 37°C. Cells were then collected using 0.05% trypsin and washed in Phosphate Buffered Saline (PBS). RNA was extracted using the RNeasy Mini kit protocol. Samples were then sent to the Australian Genome Research Facility (AGRF) where 1μg of RNA was submitted for next-generation sequencing. Once raw data returned, bioinformatics analyses were conducted. This study found that the exposure of PXS-4787A only had minor impact on gene expression in both fibroblasts and keratinocytes. In fibroblasts, 3 genes were significantly upregulated and only one gene was significantly downregulated. Besides, There were only two upregulated genes in the whole genome analysis after LOX inhibition in keratinocytes. In conclusion, this study highlights the safety of LOX-inhibition through PXS-4787A on primary human epidermal cells. The results of the transcriptome analysis intimate that PXS-4787A treatment has no adverse effects on the healthy keratinocytes. Taken together, this study suggests that LOX-inhibition has no potential effects on the epidermal differentiation in human skin.

overall_design: 6 normal skin fibroblasts and 5 normal skin keratinocytes with and without treatment of Lysyl Oxidases inhibitor (10 µM PXS-4787A)

first: Nutan

last: Chaudhari


title: Expession data from Human keratinocytes treated with IL4,13,and 31 for 18hrs.

city: Denver

first: Donald

last: Leung

state: CO

address: 1400 Jackson Street

department: Pediatrics

country: USA

institute: National Jewish Health

summary: Human epidermal keratinocytes were treated with cytokines in cell culture for 18 hours

overall_design: Five samples including media, comparision made between groups and filtered by p value

first: Elena

last: Goleva

first: Clifton

last: Hall


title: SUM159 cells treated with H3B-8800 or DMSO, J2 enrichment for dsRNA

city: Houston

first: Jarey

last: Wang

address: 1 Baylor Plaza, 304B, Anderson Building

institute: Baylor College of Medicine

summary: The objective is to identify splicing and expression changes that occur after spliceosome inhibition in triple-negative breast cancer, specifically after the RNA has been enriched for double-stranded structure using the J2 antibody.

overall_design: SUM159 cells treated with H3B-8800 (spliceosome inhibitor) or vehicle (DMSO) for 12 hours in biological duplicate. Then RNA was enriched for double-stranded structure using the J2 antibody prior to library prep.

first: Elizabeth

last: Bowling

first: Thomas

last: Westbrook


title: Expression data of LMP1-B cells, CD40-activated B cells, and their respective controls

city: Boston

first: Baochun

last: Zhang

address: 450 Brookline Ave

department: Medical Oncology

institute: Dana-Farber Cancer Institute

summary: In this study, by microarray we analyzed gene expression changes due to LMP1 signaling and CD40 signaling in B cells, in order to identify similarly as well as differentially induced candidate tumor-associated antigens (TAAs) and co-stimulatory ligands.

overall_design: In this experiment, two LMP1-expressing B cell samples and two YFP-expressing control B cell samples, two anti-CD40-treated B cell samples and two untreated (naive) control B cell samples were analyzed together. This allows comparison of gene expression of LMP1-B cells versus YFP control B cells, CD40-activated B cells versus naive control B cells, as well as comparison of gene expression of LMP1-B cells versus CD40-activated B cells.


title: Expression of genes related to H. pylori infection and its virulence factor CagA, in AGS cells

city: Athens

first: Eleftherios

last: Kontizas

address: Vasilissis Sofias 127

department: Microbiology

country: Greece

institute: Hellenic Pasteur Institute

summary: Helicobacter pylori infection promotes chronic inflammation and plethora of DNA damages including strand breaks, base alterations, point mutations, microsatellite instability and epigenetic alterations. The gastric epitheliaI cells, in order to prevent genomic instability, require an integrous DNA damage repair (DDR) machinery which, however, has been reported to be modulated by the infection. CagA is a major Hp virulence factor that deregulates host cell functions such as proliferation, apoptosis and chromosomal integrity. Its pathogenic activity is partly regulated by tyrosine phosphorylation on repeated EPIYA-motifs. Our aim was to identify putative effects of H. pylori infection and CagA protein on DDR machinery, investigating the transcriptome of AGS cells, infected with P12 H. pylori wild-type strain, as well as, its corresponding CagA knock-out and the CagA phosphorylation-defective mutant following tyrosine (EPIYA) substitution by phenylalanine (EPIFA) in the EPIYA-C motifs. Upon RNA-Sequencing on polyA-selected transcripts we performed Differential Expression Analysis, Pathway Enrichment Analysis and visualization on KEGG Pathway Maps per DDR mechanism. Key DDR components that were observed to be downregulated in a CagA-related manner were validated via Western Blot utilizing AGS and the non-cancerous GES1 cell lines. Transcriptome analysis revealed that a notable number of DDR genes were downregulated during H. pylori infection resulting to potential modulation of Base Excision Repair, Mismatch Repair and a more intricate deregulation of Nucleotide Excision Repair, Homologous Recombination and Non-Homologous End-Joining. CagA contributes to MUTYH, FEN1, APE1, POLD1 and LIG1 downregulation and those observations were verified on the protein expression level, with the exception of APE1 that was on contrary observed to be upregulated. Our study accentuates the role of CagA, as a significant contributor of the H. pylori infection-mediated DDR modulation, disrupting the balance between DNA damage introduction and repair thus favoring genomic instability and potentially contributing to gastric carcinogenesis.

overall_design: For the 4 different conditions (uninfected AGS cells, AGS cells infected with wild-type H. pylori strain, AGS cells infected with CagA-phosphorylation-defective H. pylori strain, AGS cells infected with CagA-knock-out H. pylori strain), 8 samples were analyzed. Experiments conducted in biological duplicate.

first: Spyros

last: Tastsoglou

first: Timokratis

last: Karamitros

first: Yiannis

last: Karayiannis

first: Panagoula

last: Kollia

first: Artemis

last: Hatzigeorgiou

first: Dionyssios

last: Sgouras


title: Fate and Functional Roles of Prominin 1+ Cells in Liver Injury and Cancer [scRNA-seq]

city: Los Angeles

first: Hidekazu

last: Tsukamoto

state: CA

address: 1333 San Pablo Street MMR414

department: Pathology

institute: University of Southern California

summary:
Purpose: The goal of the study is to understand gene expression profiles of Prom1+ cells at single cell level in mouse liver cancer.
Method: DEN-WAD liver from Col1a1Cre;Rosa26mTmG was perfused with collagenase.  GFP+UV- cells were FACSsorted.  Single cell library was constructed with 10X single gene expression v3 with 10X chromium technology.
Conclusion: We identified Prom1+Afp+, Prom1+Afp-, Prom1-Afp+ gene expression profiles.  These gene expression profiles revealed the markers previously observed for liver tumor intiating cells and ductular cells.  In addition, they revealed novel specific markers.

overall_design: Single cell RNA sequencing analysis of Prom1+ cells in stellate cells depleted non-parachymal cell fraction of mouse model of liver cancer

first: Raymond

last: Wu

first: Yibu

last: Chen


title: Microarray Expression Profiles and bioinformatics analysis of mRNAs, lncRNAs and circRNAs in the secondary temozolomide-resistant glioblastoma

city: zhengzhou

first: zhao

middle: cheng

last: bin

address: jianshe road

country: China

institute: zhengzhou university

summary: Glioblastoma multiforme (GBM) is the most common and aggressive primary human brain tumor. Although comprehensive therapies combining radiotherapy and chemotherapy after surgery can prolong survival, the prognosis is still poor with a median survival of only 14.6 months. Chemoresistance is one of the major causes of relapse as well as poor survival in glioma patients. Therefore, novel strategies to overcome chemoresistance are desperately needed for improved treatment of human GBM. Recent studies have demonstrated that long non‑coding RNAs are closely related to resistance to cancer chemotherapy. Here, we simultaneously detected, for the ﬁrst time, the expression proﬁles of mRNAs, lncRNAs, and circRNAs in three pairs of secondary temozolomide-resistant glioblastoma (STRG) and matched primary glioblastoma tissues by microarrays. A total of 92 mRNA, 299lncRNAs, and 53 circRNAs were altered during the Chemoresistance. The functions of these differentially expressed RNAs were predicted by Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis. Co-expression networks of lncRNA-mRNA and circRNA-miRNA were conducted to uncovered the hidden ceRNA mechanisms. Our findings revealed the alteration of expression patterns of mRNAs, lncRNAs, and circRNAs in the secondary temozolomide-resistant glioblastoma. These mRNAs, lncRNAs, and circRNAs might be potential therapeutic targets for the treatment of glioblastoma.

overall_design: The STRG samples included the standard resection of GBM performed on these patients and treatment with a 100 mg / (m2 d) dose of temozolomide was applied for the postoperative period. These patients underwent surgery again owing to GBM recurrence, and the daily dose of temozolomide was increased to 200 mg / (m2 d), postoperatively

first: Chengbin

last: Zhao

first: Bo

last: Yang


title: Fate and Functional Roles of Prominin 1+ Cells in Liver Injury and Cancer

overall_design: Refer to individual Series


title: Concurrent depletion of Vps37 proteins evokes inflammatory response and cell growth inhibition via ESCRT-I destabilization.

city: Warszawa

first: Krzysztof

last: Goryca

address: Banacha 2c

department: CeNT

country: Poland

institute: Uniwersytet Warszawski

summary: Ample evidence points to the contribution of endocytosis to oncogenesis at the cellular level but molecular details still remain obscure. Our analysis of The Cancer Genome Atlas data involving cohorts of colorectal cancer (CRC) patients revealed stage-dependent alterations in the expression of 113 genes whose function is related to endocytic transport. Among differentially expressed genes we observed decreased transcription of VPS37B and to a lesser extent VPS37A in the advanced stages of CRC. One member of the Vps37 protein family (Vps37A, Vps37B, Vps37C, Vps37D) together with Tsg101 and Vps28 forms the core of the Endosomal Sorting Complex Required for Transport (ESCRT)-I mediating membrane-remodeling processes. Our analysis of an independent cohort of CRC patients corroborated that both VPS37B and VPS37A genes are downregulated at mRNA and protein levels. Depletion of both Vps37A and Vps37B proteins elicits multifaceted transcriptional alterations, including cell growth arrest and induction of sterile inflammatory response, which are further potentiated by co-silencing of VPS37C. Among analyzed silencing condition, concurrent knockdown of VPS37A, VPS37B and VPS37C evokes the greatest magnitude of p21-mediated inhibition of cell proliferation and activation of Nuclear Factor-κB and mitogen-activated protein kinases signaling. These processes are independently induced after co-silencing of VPS37 paralogs. We further show that the type and magnitude of transcriptional responses correlate with the ESCRT-I stability, which is differentially affected upon individual and concurrent Vps37 depletion. Our study provides novel insights into cancer cell biology by describing a cellular stress response that is associated with ESCRT-I destabilization, which might occur in CRC patients

overall_design: The aim of the study was to analyze transcriptional changes upon single, double and triple depletion of VPS37 paralogs (VPS37A, VPS37B, VPS37C) in human colorectal DLD1 cell line. For RNA-seq analysis 3 biological replicates were prepared, each encompassing following samples: 1) non-transfected DLD1 (NT), 2) DLD1 transfected with a combination of non -targeting siRNA (siCTRL#1), 3) DLD1 transfected with siRNA targeting VPS37A, sequence #1 (siVPS37A#1), 4) DLD1 transfected with siRNA targeting VPS37B, sequence #1 (siVPS37B#1), 5) DLD1 transfected with siRNA targeting VPS37C, sequence #1 (siVPS37C#1), 6) DLD1 transfected with a combination of siRNAs targeting VPS37A, sequence #1 and VPS37B, sequence #1 (referred thereafter as siVPS37AB#1), 7) DLD1 transfected with a combination of siRNAs targeting VPS37A, sequence #1 and VPS37C, sequence #1 (referred thereafter as siVPS37AC#1), 8) DLD1 transfected with a combination of siRNAs targeting VPS37B, sequence #1 and VPS37C, sequence #1 (referred thereafter as siVPS37BC#1), 9) DLD1 transfected with a combination of siRNAs targeting VPS37A, sequence #1, VPS37B, sequence #1 and VPS37C, sequence #1 (referred thereafter as siVPS37ABC#1). Non-transfected and siCTRL#1-transfected cells served as reference samples.

last: Kolmus

first: Purevsuren

last: Erdenebat

first: Blair

last: Stewig

first: Ewelina

last: Szymańska

first: Edyta

last: Derezińska-Wołek

first: Anna

last: Szumera-Ciećkiewicz

first: Marta

last: Brewińska-Olchowik

first: Katarzyna

last: Piwocka

first: Monika

last: Prochorec-Sobieszek

first: Michał

last: Mikula

last: Miączyńska


title: Fate and Functional Roles of Prominin 1+ Cells in Liver Injury and Cancer [Quant-seq]

last: Tsukamoto

summary:
Purpose: The goal of the experiment is to obtain RNAseq profiles of Prom1+ Ductular Reactive Progenitors (DRPs) from mouse model of severe alcoholic liver injury
Method: mRNA-seq analysis was performed in FACS sorted Prom1+CD49f+CD45-, Prom1-CD49f+CD45-, Prom1+CD49f+CD45+ cells and presorted CD45- liver cells.
Conclusion: We obtained liver specific Prom1+ genes from analysis.

overall_design: The livers from AH mouse liver were digested with collagenase.  Hepatocytes were removed by low centrifugation.  Non-parachymal cells stained with CD45 magnetic beads to remove CD45+ cells with MACS.  Presorted CD45- liver cells were stained with Prom1 antibody and CD49f antibody.  The cells were FACS sorted for three different populations:  Prom1+CD49f+CD45- (R6), Prom1-CD49f+CD45- (R5) and Prom1+CD49f+CD45+ (R8).  Total RNA from R6, R5, R8 and presorted CD45- cells were extracted.  The RNA from two mice were pooled for RNA-seq analysis.

last: Wu


title: The Effect of Chronic Hypoxia on Cardiac Gene Expression in Rattus Norvegicus

first: Yiwei

last: Liu

address: No.167 North Lishi Road, Xicheng District

department: Pediatric Cardiac Surgery

institute: fuwai hosptial, PUMC & CAMS

summary: To explore the gene expression prolife in the chroniclly hypoxic myocardium, 8 rats were divided randomly into normoxic (n=4) or chroniclly hypoxic (n=4) group, and were exposed to room air (21% O2) or continued hypoxia (10% O2) for 4 weeks. Heart tissues were collected and RNA sequencing was applied to detect the overall gene expression prolife. Genes with adjusted P-value ≤0.01 (corrected by Benjamini-Hochberg) and |log2_ratio|≥0.585 are identified as differentially expressed genes. RNA sequencing identified a total of 2014 gene with statistical significances, among which 1260 genes were significantlly increased and 754 genes were significantlly decreased. The results showed that gene expression profiling was perturbed in chronically hypoxic myocardium.

overall_design: Quantification of gene expression in heart tissues harvested from rats exposed to chronic hypoxia

first: Hao

last: Zhang


title: Transcriptomic effects of combination Menin-MLL1 inhibition and FLT3 inhibition on human AML cells

city: Indianapolis

first: James

last: Ropa

state: IN

address: 950 W Walnut St

institute: Indiana University

summary: Chromosomal translocations of the MLL1 gene cooccur with the activating mutations in FLT3 kinase in acute myeloid leukemia patients, providing the rationale to explore combination of the menin-MLL1 inhibitor (MI-3454) and FLT3 inhibitor (Gilteritinib) in leukemia models. Here, we pursued global gene expression studies after 7 days of treatment of MOLM13 cells (harboring MLL-AF9 and FLT3-ITD) with MI-3454 and Gilteritinib used as single agents and in combination. We observed that MYC, differentiation and stemness-associated gene programs were disrupted by the single agent treatments, but the effect was enhanced upon combinatorial treatment. These results provide a mechanistic input on the increased activity of MI-3454 when combined with Gilteritinib in leukemia models versus single agent treatment.

overall_design: Total RNA was prepared from MOLM13 cells treated for 8 days with DMSO, MI-3454, Gilteritnib or combination of these two agents. Libraries were prepped from total RNA and sequenced. Differential expression was performed by comparing each single agent or combination treatment to DMSO separately, then comparing the overlap of differentially expressed genes.

first: Jolanta

last: Grembecka

first: Tomasz

last: Cierpicki


title: Illumina Sequencing of Wild Type, nerd-1 and cpsf30-1 mutant plants

city: Perpignan

first: Thierry

last: Lagrange

address: 58 Avenue Paul Alduy

country: France

institute: CNRS

summary: The goals of this study are to compare plant transcriptome profiling (RNA-seq) obtained from various plant lines, including a Wild Type control, the nerd-1 mutant , and the cpsf30-1 mutant plants.

overall_design: Plant mRNA profiles of 9-day old wild typeType, nerd-1, and cpsf30-1 plants were generated by deep sequencing, in duplicate using Illumina with paired-end reads, 2x 125bp and 37-53x106 reads per library

last: LAGRANGE


title: T11, AT3, PyMT-M, 2208L GEMM tumors treated with H3B-8800

first: Jarey

last: Wang

summary: The objective is to identify splicing and expression changes that occur after spliceosome inhibition in triple-negative breast cancer using immune competent GEMM tumors.

overall_design: 4 different GEMM models of TNBC were transplanted orthotopically into C57BL/6 or Balbc females and then randomized onto 8800 or Vehicle. RNA was obtained from whole tumor. RNA from 3 or 4 biological replicate tumors were sequenced for each model for each condition.

first: Elizabeth

last: Bowling

first: Thomas

last: Westbrook


title: SUM159 cells treated with H3B-8800 or DMSO, Cytoplasmic fraction RNA-seq

summary: The objective is to identify splicing changes that occur after spliceosome inhibition in triple-negative breast cancer, specifically in cytoplasmic RNA.

overall_design: SUM159 cells treated with H3B-8800 (spliceosome inhibitor) or vehicle (DMSO) for 12 hours in biological duplicate. RNA was isolated from the cytoplasm for downstream processing.


title: Expression data from transgenic mice overexpressing TFEB specifically in liver

city: Napoli

first: Annamaria

last: Carissimo

address: via Castellino

institute: Tigem

summary:
In order to identify the effects of TFEB overexpression on liver transcriptome, we performed Affymetrix Gene-Chip hybridization experiments for transgenic mice at P9
Transcriptome analysis of transgenic mice overexpressing TFEB specifically in liver

overall_design: For the analysis on transgenic  mice overexpressing TFEB, total RNA was extracted from the liver of three mice; RNA extracted from the liver of wild-type mice was used as control.

first: Nunzia

last: Pastore


title: Comparative transcriptome analysis to reveal putative genes responsible for high theacrine content in Kucha (Camellia kucha (Chang et Wang) Chang)

status: Public on Dec 16 2020

city: Guangzhou

first: Hongjian

last: Li

address: No.6 Dafeng Road, Tianhe District

department: Department of tea resources and breeding

institute: Tea Research Institute, Guangdong Academy of Agricultural Sciences

summary: To identify the putative genes involved in theacrine biosynthesis in tea plant, we carried out comparative transcriptome analysis of Kucha (K6 and K11) and conventional varieties (YH 9 and QX 1).

overall_design: Two Kucha genotypes (Kucha-6 (K6) and Kucha-11 (K11)) and two conventional varieties (Yinghong 9 (YH9) and Qingxin 1 (QX1)) with extremely contrasting theacrine content were used in this study.

first: Li

last: Hongjian


title: Global analysis of the interplay between site-specific CREB O-GlcNAc glycosylation and phosphorylation

city: Pasadena

middle: Hwang

last: Jensen

address: 1200 E California Blvd, MC 164-30

department: CCE

institute: Caltech

summary:
Purpose: CREB (cAMP response element binding protein) is a transcription factor that is critical for learning and memory. The activity of CREB is mediated through its post-translational modifications (PTMs); specifically, phosphorylation at serine 133 and glycosylation at serine 40.  In this study, we used RNA-Seq and weighted gene network coexpression analysis (WGCNA) to determine the CREB-mediated transcriptional programmes that are regulated by phosphorylation at serine 133 and glycosylation at serine 40 through the use of various PTM-deficient CREB mutants.
Methods: The mRNA profiles of E16.5 Creb1-/- mouse cortical neurons expressing GFP, WT CREB, S40A-CREB, S133A-CREB, and S40A-S133A-CREB were generated by deep sequencing, in triplicate, using Illumina HiSeq 2500. The sequence reads that passed quality filters were analyzed using Bowtie, aligned using TopHat, and quantified using Cufflinks in Galaxy.
Results: Through differential expression analysis with glycosylation-deficient (S40A) and phosphorylation-deficient (S133A) CREB mutants, we show that CREB O-GlcNAcylation is important for neuronal activity and excitability, while phosphorylation at serine 133 regulates the expression of genes involved in neuronal differentiation. Furthermore, many of the S40A and S133A differentially-expressed genes were directly bound by (1) CREB and its co-activators, CREB-binding protein and p300, (2) activating histone modifications, (3) OGT and O-GlcNAc, and (4) Tet1, an critical regulator of neuronal activity and differentiation. Finally, we observed a positive correlation between S40A and activity- and excitotoxicity-related gene networks and a negative correlation between S133A and neuronal differentiation and amino and fatty acid metabolism-related gene networks. This study demonstrates that CREB O-GlcNAcylation at serine 40 and phosphorylation mediate mutually exclusive gene networks. Together, O-GlcNAc and phosphorylation impart a TF code, which CREB must integrate and decode to modulate neuronal activity, differentiation, and metabolism.

overall_design: The mRNA profiles from E16.5 Creb1-/- mouse cortical neurons expressing glycosylation- and/or phosphorylation-deficient and WT CREB using HSV (herpes simplex virus) were generated by deep sequencing, in duplicate or quadruplicate, using the Illumina HiSeq 2500.


title: Secretory Cells Dominate Airway CFTR Expression and Function in Human Airway Superficial Epithelia [bulk RNA]

city: Chapel Hill

first: Kenichi

last: Okuda

state: NC

address: 125 Mason Farm Road

department: Department of Medicine, Cystic Fibrosis/Pulmonary Research and Treatment Center

institute: University of North Carolina at Chapel Hill

summary:
Purpose: To identify the cell types that contribute to CFTR expression and function within the proximal-distal axis of the normal human lung.
Methods: Single cell RNA-seq (scRNA-seq) was performed on freshly isolated human large and small airway epithelial cells. Single cell-based RNA in situ hybridization (scRNA-ISH) and quantitative RT-PCR (scqRT-PCR) were performed for validation. In vitro culture systems correlated CFTR function to cell types. Lentiviruses were used for cell-type specific transduction of wild-type CFTR in CF cells.
Results: scRNA-seq identified secretory cells as dominating CFTR expression in normal human large and particularly small airways, followed by basal cells. Ionocytes expressed the highest CFTR levels but were rare, while expression in ciliated cells was infrequent and low. scRNA-ISH, and scqRT-PCR confirmed the scRNA-seq findings. CF lungs exhibited distributions of CFTR and ionocytes similar to normal controls. CFTR-mediated Cl- secretion tracked secretory cell, not ionocyte, densities. Further, the nucleotide-purinergic regulatory system that controls CFTR-mediated hydration was associated with secretory cells. Lentiviral transduction of wild-type CFTR produced CFTR-mediated Cl- secretion in CF airway secretory cells but not ciliated cells.
Conclusions: Secretory cells dominate CFTR expression and function in human airway superficial epithelia. CFTR therapies may need to restore CFTR function to multiple cell types, with a focus on secretory cells.

overall_design: mRNA profiles of in vitro primary human large and small airway epithelial cells

first: Richard

middle: C

last: Boucher

first: Hong

last: Dang


title: Secretory Cells Dominate Airway CFTR Expression and Function in Human Airway Superficial Epithelia

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


title: Secretory Cells Dominate Airway CFTR Expression and Function in Human Airway Superficial Epithelia [single-cell RNA-seq]

overall_design: single cell-based mRNA profiles of normal human large and small airway epithelia


title: MLL3 is a de novo Cause of Endocrine Therapy Resistance

city: Nashville

middle: Paul

last: Stricker

state: TN

address: 1161 21st Ave South, CC3309A

department: Pathology, Microbiology and Immunology

institute: Vanderbilt University

summary:
a.Background Cancer resequencing studies have revealed epigenetic enzymes as common targets for recurrent mutations. The monomethyltransferase MLL3 is among the most recurrently mutated enzymes in ER+ breast cancer. The H3K4me1 marks created by MLL3 can define enhancers. In ER+ breast cancer, ERα genome binding sites are primarily distal enhancers. Thus, we hypothesize that mutation of MLL3 will alter the genomic binding and transcriptional regulatory activity of ERα.
b.Methods We investigated the genomic consequences of knocking down MLL3 in an MLL3/PIK3CA WT ER+ breast cancer cell line.
c. Results Loss of MLL3 led to large loss of H3K4me1 across the genome, and a shift in ERα binding sites, which was accompanied by a re-organization of the breast cancer transcriptome. Enrichment analyses of ERα binding sites in MLL3 KD identified endocrine therapy resistance terms, and we show that MLL3 KD cells are resistant to tamoxifen and fulvestrant. Many differentially expressed genes are controlled by new locations of H3K4me1 deposition and ERα binding, suggesting that loss of functional MLL3 leads to new transcriptional regulation of essential genes. Motif analysis of RNA-seq and ChIP-seq data highlighted SP1 as a critical transcription factor in the MLL3 KD cells.  Loss of ERα binding is accompanied by a massive increase in SP1 binding at differentially expressed genes.
d.Conclusions Our data show that loss of functional MLL3 leads to endocrine therapy resistance. This highlights the importance of genotyping patient tumor samples for MLL3 mutation upon initial resection, prior to deciding upon treatment plans.

overall_design: MLL3 expression was knocked down via shRNA. shLucif was used as a control, and both RNAseq and ChIPseq experiments were performed with biological replicates.

first: Kimberly

last: Stauffer


title: Early alterations in stem-like/marrow-resident T cells, innate and myeloid cells in preneoplastic gammopathy

city: Atlanta

first: Samuel

middle: Spence

last: McCachren

state: GA

address: 1760 Haygood Dr. NE

institute: Emory University

summary: We report an alteration in bone marrow immune cell subset composition and function in multiple myeloma and monoclonal gammopathy of unkown significance (MGUS).

overall_design: Examination of bone marrow immune cell transcriptomes in 8 healthy donors, 14 MGUS, and 11 myeloma patient samples

first: Jithendra

last: Bailur

middle: S

first: Deon

middle: B

last: Doxie

first: Mahesh

last: Shrestha

first: Katherine

last: Pendleton

first: Ajay

last: Nooka

first: Natalia

last: Neparidze

first: Terri

last: Parker

first: Noffar

last: Bar

first: Jonathan

last: Kaufman

first: Craig

last: Hofmeister

first: Lawrence

last: Boise

first: Sagar

last: Lonial

first: Melissa

last: Kemp

first: Kavita

last: Dhodapkar

first: Madhav


title: Comprehensive Dissection of CircRNA-Associated-ceRNA Networks in Cardiac Transplant Rejection Immunity

city: Harbin

first: Maomao

last: Zhang

address: No.246  Xuefu Road, Nangang District

institute: Second Affiliated Hospital of Harbin Medical University

summary: Transplant rejection is a major factor limiting allograft survival. CircRNAs are reported to be strongly associated with various diseases pathogenesis. However, the potential role of circRNAs in cardiac transplant rejection are rarely reported. Here,  differentially expressed mRNAs and circRNAs were determined by microarrays in allogeneic cardiac allografts. Functional analysis was then performed and a full-scale functional blueprint of the  circRNA-associated-ceRNA networks was constructed. Among the circRNA networks, circ23123 expression was negatively linked with cytolytic molecules of CD8+ T cells by targeting miR155-SOCS1 axis. We illustrated a new comprehensive view of circRNAs and their potential functional impact in cardiac transplantation. It may provide a prospective for therapeutic strategy on organ transplant rejection in the future.

overall_design: For mRNA microarrays, total RNA from each sample was linearly amplified and labeled with Cy3-UTP. The Labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000. Sample labeling and array hybridization were performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology). The microarray was to confirm the differentially expressed  mRNAs in three pairs of heart grafts, comparing cardiac allograft mice and syngraft mice.


title: Identification of differentially expressed genes through miR-7 overexpression in H1299 cells

city: Daejeon

first: Seong-Lan

last: Yu

address: Gasuwon-dong

department: Myunggok Medical Research Institute

institute: Konyang university

summary: Transcription profiling comparing control H1299 with hsa-miR7-5p overexpressing H1299 cells

overall_design: Two-condition experiment, H1299_control vs. H1299_miR-7_overexpression cells.


title: Kisspeptin influences the reproductive axis and circulating levels of microRNAs in Senegalese sole

city: Faro

first: Elvira

last: Fatsini

address: Universidade do Algarve

country: Portugal

institute: UALG

summary: The kiss system is known to regulate puberty and to be involved in the onset of reproduction, acting upstream of the Brain-Pituitary-Gonad axis in gonadotrophin releasing hormone neurons and stimulating secretion of GnRH. Kisspeptin has been proven to be a novel therapeutic for fertility disorders in humans. In fish, positive results have also observed the prospective of this hormone to induce gamete development. During the last two decades, support has been obtained describing the key role of microRNAs (miRNA) in regulating gene expression at the post-transcriptional level and they have been recommended as relevant biomarkers in reproductive studies. Senegalese sole is a marine flatfish species with high importance in the European aquaculture industry, due to its good growth rate and high market value. However, this species presents a bottleneck in terms of reproduction, which does not allow to close the cycle in captive conditions. Hence, this study aimed to observe the effect of a novel hormonal treatment using kisspeptin in miRNA expression related to reproductive performance in cultured Senegalese sole breeders. For this purpose, Senegalese sole F1 broodstock were held at CCMAR facilities in 4 tanks of 3m3 (n = 12/per tank, sex ratio 1:1) under natural photoperiod and temperature conditions. During the reproductive season, the animals from each 2 of the tanks were treated either with SSkiss2_v2 decapeptide in a single intramuscular injection, or with a PBS injection for control groups. After the treatment (2 and 4 days), all fish were anesthetized and sampled for blood collection. Afterwards, plasma was obtained to determine several parameters related to reproductive physiology (Fsh, Lh and sexual esteroids (T, 11-KT and E2)) and miRNAs regulation. After observing the high implication of this treatment in the gonadotrofins, above all in Fsh and sexual esteroids, above all in T, the RNA was extracted from blood plasma using miRNeasy Serum/Plasma Kit (Qiagen, Germany) and libraries were prepared using NEXTflex Small RNA-Seq kit v3 (Bioo Scientific, USA). Small RNA sequencing (sRNA-seq) (NextSeq 500) was performed on sole treated with kisspeptin (n = 16) and non-treated control fish (n = 14). A total of 1,467 unique miRNAs were expressed in Senegalese sole plasma. A multidimensional scaling (MDS) plot showed no clear clustering of the samples with the kisspeptin treatment. However, the differential expression analysis revealed one miRNA, miR-1-3p, to be highly up-regulated in both males and females treated with kisspeptin compared to control sole. This miRNA is linked with myogenesis and angiogenesis, and skeletal muscle development in fish. Three isomirs (let 7e, miR-199a-3p, miR-100-5p) were differentially expressed between females treated and control fish. MicroRNA let-7e is an important regulator of endothelial function and inflammation, related to testosterone pathway release; miR-199a-3p plays an important role in inflammation and women fertility and miR-100-5p might be implicated in the regulation of cell growth and oocytes maturation. In conclusion, kisspeptin treatment may affect gonad maturation in females and muscle growth in males. Our data support the possibility of using circulating miRNAs as less invasive physiological biomarkers in fish reproduction.

overall_design: Examination of the application of a hormonal treatment in blood samples of Senegalese sole species at several levels (endocrine, physiological and circulating miRNAs)

first: Catarina

last: Oliveira

first: Ignacio

last: Fernández

last: Anjos

first: François

last: Chauvigné

first: Joan

last: Cerdà

first: Robin

last: Mjelle

first: Jorge

last: Fernandes

first: Elsa

last: Cabrita


title: A Roadmap from Single-Cell Transcriptome to Patient Classification for the Immune Response to Trauma

city: Pittsburgh

first: Timothy

last: Billiar

state: Pennsylvania

address: 200 Lothrop Street

department: Surgery

institute: University of Pittsburgh

summary: Immune dysfunction is an important factor driving mortality and adverse outcomes after trauma but remains poorly understood, especially at cellular level. To deconvolute the trauma-induced immune response, we applied single-cell RNA sequencing to circulating and bone marrow mononuclear cells in injured mice and circulating mononuclear cells in trauma patients. In mice, the greatest changes in gene expression were seen in monocytes across both compartments. After systemic injury, the gene expression pattern of monocytes markedly deviated from steady state with corresponding changes in critical transcription factors (TFs), which can be traced back to myeloid progenitors. These changes were largely recapitulated in the human single-cell analysis. We generalized the major changes in human CD14+ monocytes into six signatures, which further defined two trauma patient subtypes (SG1 vs. SG2) identified in the whole blood leukocyte transcriptome in the initial 12h after injury. Compared with SG2, SG1 patients exhibited delayed recovery, more severe organ dysfunction and a higher incidence of infection and non-infectious complications. The two patient subtypes were also recapitulated in burn and sepsis patients, revealing a shared pattern of immune response across critical illness. Our data will be broadly useful to further explore the immune response to inflammatory diseases and critical illness.

overall_design: We longitudinally single-cell RNA sequenced circulating and bone marrow mononuclear cells in injured mice (3hrs, 6hrs and 24hrs representing escalating, peak and recovery phase of inflammation) and circulating mononuclear cells in trauma patients (<4hrs, 24hrs and 72hrs mainly representing the early changes after systematic injury) along with paired healthy controls.

middle: R

first: Jason

last: Sperry

first: Rami

middle: A

last: Namas

first: Kong

last: Chen

first: Wei

first: Yoram

last: Vodovotz

first: Julia

last: Conroy

first: Tianmeng


title: Analysis of normal human lung small and large airway epithelium.

first: Gianni

last: Carraro

address: 8700 Beverly Blvd

department: Medicine

institute: Cedars-Sinai Medical Center

summary: Single cell RNA sequencing of normal human lung airway epithelium

overall_design: Single cell RNA-seq using 10x chromium system on FACS isolated epithelial cells (DAPI-,CD45-,CD31-,CD326+) from control lung explant tissue. The barcoded sequencing libraries were quantified by qPCR using the KAPA Library Quantification Kit (KAPA Biosystems). Sequencing libraries were loaded on a NovaSeq 6000 (Illumina).

first: Barry

last: Stripp


title: Gene expression profiling in neuronal cells identifies a different type of transcriptome modulated by NF-Y [YAYC_Affymetrix]

city: Niigata

first: Tomoyuki

last: Yamanaka

address: 1-757 Asahimachidori, Chuo-ku

department: Brain Research Institute

country: Japan

institute: Niigata University

summary: We knocked down NF-Y in two types of neuronal cells, neuro2a neuroblastoma cells and sorted brain striatal cells, and performed gene expression profiling. We found that the down-regulated genes preferentially contained NF-Y-binding motifs in their proximal promoters, and notably enriched genes related to ER functions rather than those for cell cycle. These are highly contrast to the profiling data of HeLa and embryonic stem cells in which distinct down-regulation of cell cycle-related genes was observed by NF-Y knockdown. Clustering analysis further identified several functional clusters where populations of the down-regulated genes were highly distinct. Further analyses using chromatin immunoprecipitation and RNA-seq data revealed that transcriptomic difference was not correlated with the DNA binding of NF-Y but with splicing of NF-YA. These data suggest that neuronal cells have a different type of transcriptome in which ER-related genes are dominantly modulated by NF-Y, and imply that NF-YA splicing alteration rather than DNA-binding preference could be involved in this cell type-specific gene modulation.

overall_design: To screen differentially expressed genes in mouse neuro2a cells, the cells were transfected with miR RNAi vectors for NF-YA and NF-YC or an empty vector, and then subjected to microarray analysis using Affymetrix Mouse Gene 1.0 ST Arrays. Obtained microarray data were analyzed using an Agilent GeneSpring GX software to identify differentially expressed genes (DEGs) by gene knockdown.

first: Nobuyuki

last: Nukina


title: Gene expression profiling in neuronal cells identifies a different type of transcriptome modulated by NF-Y

overall_design: The AAV vectors expressing EmGFP with miR RNAi for NF-YA and -YC (YA-8/YC-2) or control non-targeting miR RNAi (NT-2) under CAG promoter were stereotaxically injected into striatum in both hemispheres of 6-week-old wild-type male B6 mice . Total 5 (YA-8/YC-2) and 6 (NT-2) mice were injected. Three weeks after the injection, stirata were surgically isolated and dissociated by Papain. To isolate RNAi-expressing cells positive for green fluorescence (EmGFP), dissociated and sorted by FACS. Total RNAs were prepared from the sorted cells by RNeasy Micro Kit (Qiagen). Clontech SMARTer Ultra Low Input RNA Kit for Sequencing (v3) was used for amplification of cDNA after reverse transcription. Libraries for sequencing were prepared by Nextera XT Sample Prep Kit, and sequenced by an Illumina HiSeq 2500 system. Obtained seq data were analyzed using Agilent Strand NGS to identify differentially expressed genes (DEGs) by NF-Y knockdown.


title: Gene expression profiling in neuronal cells identifies a different type of transcriptome modulated by NF-Y [Grp94]

overall_design:
To screen differentially expressed genes in mouse neuro2a cells, the cells were transfected with miR RNAi vectors for Grp94 (Hsp90b1) or an empty vector, and then subjected to microarray analysis using Affymetrix Mouse Gene 1.0 ST Arrays. Obtained microarray data were analyzed using an Agilent GeneSpring GX software to identify differentially expressed genes (DEGs) by gene knockdown.
Please note that the differentially expressed data is provided in the 'Affy_N2a_Grp94_Filt20_P0.01.txt' since the normalized data for each sample is unavailable.


title: Gene expression profiling in neuronal cells identifies a different type of transcriptome modulated by NF-Y [YAYC_Agilent]

overall_design: To screen differentially expressed genes in mouse neuro2a cells, the cells were transfected with miR RNAi vectors for NF-YA and NF-YC or an empty vector, and then subjected to microarray analysis using Agilent SurePrint G3 Mouse GE 8x60K Microarrays. Obtained microarray data were analyzed using an Agilent GeneSpring GX software to identify differentially expressed genes (DEGs) by gene knockdown.


title: Role of Jagged1 in cochlear supporting cell differentiation and maintenance

city: Baltimore

first: Angelika

last: Doetzlhofer

state: MD

address: 855 North Wolfe St.

department: Neuroscience

institute: The Johns Hopkins University School of Medicine

summary: Inner ear cochlear supporting cells (SCs) are highly specialized glia-like cells that structurally and functionally support neighboring mechano-sensory hair cells. Despite their importance for proper auditory function, little is known about the molecular mechanisms that control their development. In this study we investigated the function of the Notch ligand Jagged1 (Jag1) in cochlear SC differentiation and maintenance. To address the function of Jag1 in the differentiation of SCs, we conditionally deleted Jag1 in stage E14.5 SC precursors using the recently established Sox2-CreER/+ and Jag1 fx/fx mouse lines. Analysis of  stage P0 Jag1 mutant and control animals revealed that Hensen cells, a highly specialized SC-subtype located at the lateral edge of the auditory sensory epithelium, failed to form in the absence of Jag1. Other SC-subtypes did form in the absence of Jag1, however, their morphology and cellular arrangement was abnormal and SC-subtype specific genes and genes associated with mitochondrial function and protein synthesis were significantly reduced, indicating global defects in SC differentiation and SC homeostasis.

overall_design: To delete the Jag1 gene at the onset of supporting cell differentiation, we co-administered tamoxifen and progesterone to pregnant dams at stage E14.5. Five days later we harvested cochlear epithelia from P0 Sox2-CreER/+ Jag1 fx/fx (Jag1 mutant) and Jag1 fx/fx (Jag1 wild type) mice, isolated total RNA and analyzed gene expression using Clariom D arrays.  The three biological replicates of each class, mutants and wildtype controls, were compared.

first: Elena

last: Chrysostomou


title: Genotoxicity induces epithelial hyperplasia and lineage infidelity via fibroblast IL-1β

first: Lindsey

last: Seldin

address: 465 21st Avenue South U3200 MRBIII

summary: Epithelial tissues possess a barrier function that must be restored following injury. Repair often involves changes in cell fate, but it remains poorly understood how cell plasticity is induced and whether responses vary with distinct types of damage. Here, we reveal that genotoxic agents, but not mechanical damage, induce hyperplasia and lineage infidelity in the interfollicular epidermis, as well as in two epidermal subappendages: the mammary gland and hair follicle. DNA damage to the epidermis promotes stromal proliferation, and induces basal cell hyperplasia with formation of abnormal, multi-layered K14+/K10+ cells. Unexpectedly, this behavior is epithelial cell non-autonomous, but independent of immunity. Instead, dermal fibroblasts are both necessary and sufficient to induce the epithelial response. We identify a previously unrecognized fibroblast-specific NLRP3 inflammasome that drives this response via IL-1β. Thus, genotoxic agents, used chemotherapeutically to promote cancer cell death, can have the opposite effect on wild-type epithelia, paradoxically promoting hyperplasia and inducing both stemness and lineage infidelity via a non-autonomous, fibroblast-driven mechanism.

overall_design: Analysis of gene expression changes in dermal fibroblasts following Cisplatin treatment; 2 vehicle replicates, 2 Cisplatin replicates

first: Ian

last: Macara


title: m6A-seq of the mouse ESC transcriptome expressing wild-type (R-WT) or non-phosphorylatable (R-3A2A) METTL3/WTAP

city: Chicago

first: Allen

last: Zhu

state: Illinois

address: 929 E 57th St, Room E331

institute: University of Chicago

summary:
We performed immunoprecipitation of m6A-modfiied poly-A tailed RNA in mouse ESCs expressing either wild-type or non-phosphorylatable METTL3/WTAP. By sequencing over 4 billion bases across both Input and Immunoprecipitated (IP) samples, we generate a transcriptome-wide map of m6A methylation enrichment across both cell types. We find that m6A peaks that are differentially methylated between R-WT and R-3A2A mouse ESCs. Several pluripotency transcripts show reduced m6A methylation in R-3A2A cells compared to R-WT.
For the CRISPR screen, we transduced a circular RNA GGACU-containing GFP reporter plasmid, followed by transduction of a genome-wide CRISPR sgRNA library. We selected for the top and bottom 5% of GFP expression in HeLa cells and sequenced the sgRNAs.

overall_design:
Profiles of m6A methylation on mRNA of wild type (WT) and mutant (3A2A) mouse ESCs were generated by deep sequencing, in triplicate, using Illumina HiSeq 4000.
CRISPR sgRNA sequencing was performed on HeLa cells expressing the highest and lowest 5% of GFP signal.

first: Hui-Lung

last: Sun


title: Genome-wide binding of EHMT2 in RD18 ERMS cells

city: Singapore

first: Reshma

last: Taneja

state: Singapore

address: 2 Medical Drive, MD9, National University of Singapore

department: Department of Physiology

country: Singapore

institute: National University of Singapore

summary: We report the genome-wide occupancy of EHMT2/G9a in the RD18 embryonal rhabdomyosarcoma cell line.

overall_design: Examination of G9a peaks in RD18 cells.

first: R


title: Change in transcriptome upon G9a knockdown in RD ERMS (Embryonal Rhabdomyosarcoma) cells

summary: The Wnt signaling pathway is down-regulated in embryonal rhabdomyosarcoma (ERMS) and contributes to the block of myogenic differentiation. Epigenetic mechanisms leading to its suppression are unknown and could pave the way towards novel therapeutic modalities. In this study, we demonstrate that the lysine methyltransferase G9a suppresses the canonical Wnt signalling pathway by activating expression of the Wnt antagonist DKK1. Inhibition of G9a expression or activity reduced DKK1 expression and elevated canonical Wnt signalling resulting in myogenic differentiation in vitro and in vivo. Mechanistically, G9a impacted Sp1 and p300 enrichment at the DKK1 promoter in a methylation-dependent manner. The reduced tumor growth upon G9a deficiency was reversed by recombinant DKK1 or LGK974, which also inhibits Wnt signaling. Consistently, among thirteen drugs targeting chromatin modifiers, G9a inhibitors were highly effective in reducing ERMS cell viability. Together, our study demonstrates that ERMS cells are vulnerable to G9a inhibitors and suggest that targeting the G9a-DKK1--catenin node holds promise for differentiation therapy.

overall_design:
We report the transcriptomic changes through RNA sequencing analysis upon transient knockdown of G9a in RD Embryonal Rhabdomyosarcoma cell line
Three biological replicates for control RD cells (siscm) and three biological replicates for siG9a knockdown RD cells were analyzed .


title: Cooperation between distinct cancer drivers dictates inter-tumor heterogeneity in hepatocellular carcinoma

city: New York

first: Tiphaine

middle: Christiane

last: Martin

address: 1470 Madison Ave

department: Oncological Sciences

institute: Icahn School of Medicine at Mount Sinai, Tisch Cancer Institute

summary: We generate multiple models of liver cancer to study heterogeneity at different levels

overall_design: Examination of transcriptional profiles in 9 different tumor genotypes, normal liver, and derived cell lines.

first: Amaia

last: Lujambio

first: Pedro

last: Molina-Sánchez


title: The mRNA profile after knockdown of Bmi1 in QBC939 cells

status: Public on Dec 15 2020

city: Jinan

first: Xin

last: Zhang

state: Shandong

address: 107 Wenhua Xi Road

institute: Qilu Hospital, Shandong University

summary: We profile the expression of mRNAs upon Bmi1 Knockdown in QBC939 cells

overall_design: Comparison of Bmi1 knockdown in QBC939 cells against cells transfected with scrambled siRNA. 3 independend transfections per shRNA were used.


title: A single missense mutation in hilD is responsible for further adaptation of a Salmonella Derby lineage to swine and reduced risk to human health

city: Parma

first: Stefano

last: Pongolini

state: PR

address: Strada dei Mercati 13/A

department: Risk Analysis and Genomic Epidemiology Unit

institute: Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia-Romagna

summary:
Salmonella enterica variants exhibit diverse host adaptation, outcome of infection, and associated risk to humans. Analysis of 6,335 Salmonella isolates recovered from integrated human-animal surveillance in Emilia Romagna region, Northern Italy, (human population ca 4,500,000), from 2012 to 2017 showed that Salmonella enterica serovar Derby constitutes a swine associated serovar in this epidemiological context while representing also a significant causative agent of human infections. Comparison of the distribution of subtypes of Salmonella Derby from human and swine identified isolates with a distinct PFGE profile that were significantly less isolated in human infections than in swine infections compared to all other subtypes.
Here we show that isolates with this PFGE profile form a distinct phylogenetic sub-clade within Salmonella Derby and exhibit a marked reduction in invasion and replication in human epithelial cells but a relatively small reduction in swine epithelial cells, in line with the epidemiological evidence. A single missense mutation in hilD, that encodes the master-regulator of the Salmonella Pathogenicity Island 1 (SPI-1), was identified in this lineage of Salmonella Derby. Since SPI-1 encodes for a primary system of Salmonella invasion into epithelial cells, we investigated the role of the observed mutation in detail. We demonstrated that the missense mutation results in a loss of function of HilD that accounts for the reduced invasion and replication in human epithelial cells while showing a relatively small impact on the interaction with swine cells. This finding is suggestive of a mechanism of invasion alternative to SPI-1 in the Salmonella-swine combination

sample_organism: Salmonella enterica subsp. enterica serovar Derby

overall_design: Transcriptome analysis of Salmonella Derby ER1175, ER278 strains and their hilD mutants

first: M

last: Tambassi

last: Berni

first: C

last: Bracchi

first: E

last: Scaltriti

last: Morganti

first: L

last: Bolzoni

first: J

last: Tanner

first: G

last: Thilliez

last: Kingsley

first: S

last: Casadei


title: RNA-Seq for ALV-J-susceptible and ALV-J-resistant chickens

first: Yiming

last: Yan

address: Wushan Road

institute: South China Agricultural University

summary: We bed ALV-J-susceptible and ALV-J-resistant chickens. In this work, we find the different gene expression between ALV-J-susceptible and ALV-J-resistant chickens

overall_design: Examination of different gene expression in ALV-J-susceptible and ALV-J-resistant chickens.