title: OsbZIP76 interacts with OsNF-YBs and regulates endosperm cellularization in rice (Oryza sativa)

status: Public on Dec 28 2019

city: Yangzhou

first: Chen

state: Jiangsu

address: 12 E. Wenhui Rd.

department: Agricultural College

institute: Yangzhou University

summary: Cellularization is a key event during the development of the endosperm. Our understanding of the developmental regulation of cellularization has been limited for plants other than  Arabidopsis. We found that the activation of OsbZIP76 coincided with the initiation of cellularization of rice. Either knockdown or knockout of OsbZIP76 led to precocious cellularization. Many genes involved in endosperm development or starch biosynthesis were prematurely activated in the caryopsis at two days after fertilization. The results implied that OsbZIP76 is involved in the regulation of cellularization in rice. As a putative transcription factor, OsbZIP76 alone lacked transcriptional activation activity. However, it was able to interact with OsNF-YB9 and OsNF-YB1, two nuclear factor Y (NF-Y) family transcription factors, both in yeast and in planta. OsbZIP76 and OsNF-YB9 showed similar endosperm-preferential expression patterns and the transiently expressed proteins were colocalized in the epidermal cells of tobacco. As with osnf-yb1 mutants, the osbzip76 mutants showed reduced seed size and reduced apparent amylose content of the seeds. We also confirmed that OsbZIP76 is an imprinted gene in rice, the expression of which depended on the genetic background. Our results suggested that OsbZIP76 is an endosperm-expressed imprinted gene to regulate development of the endosperm in rice.

overall_design: The process of cellularization in rice typically occurs from 3 through 5 DAF. OsbZIP76 coincided with the initiation of cellularization of rice. Either knockdown or knockout of OsbZIP76 led to precocious cellularization.Due to the high environmental temperature at the reproductive stage in the summer of 2018, the developmental process of rice caryopsis was promoted, which reflected by precocious cellularization at 2 DAF in WT as well as the mutant. We therefore used 2DAF samples to analyze the transcriptome changes in the caryopses of the osbzip76 mutants. RNA isolated from caryopses of the WT, osbzip76-1 and osbzip76-2 at 2 DAF was used for RNA-Seq. We set up three biological replicates for WT and two replicates for osbzip76-1 and osbzip76-2, two independent mutant alleles of OsbZIP76.


title: Transcriptome changes in bovine oocytes caused by microinjection

status: Public on Dec 20 2019

city: Utrecht

first: Bernard

last: Roelen

state: The Netherlands

address: Uppsalalaan 8

department: Department of Farm Animal Health

country: Netherlands

institute: Utrecht University

type: Expression profiling by high throughput sequencing

summary:
Purpose: In this study, we investigated the effect of microinjection on oocytes transcriptome changes through scrambled siRNA injection.
Method: Scrambled siRNA injection followed by RNA-seq of single oocytes.
Result:Our result showed 119 transcripts were differentially expressed of which 76 were down-regulated after scrambled siRNA injection.

overall_design: Conculsion: Biology process of ATP synthesis, molecular transportation and regulation of protein polyubiquitination can act as reference of background effect when conduct siRNA injection experiment with oocytes.

first: Minjie

last: Tan

first: Helena

middle: T

last: van Tol

first: Michal

last: Mokry

first: Tom

middle: A

last: Stout


title: Benchmarking Single-Cell RNA Sequencing Protocols for Cell Atlas Projects (10 X V3)

status: Public on Dec 10 2019

city: Barcelona

first: Atefeh

last: Lafzi

address: Baldiri Reixac 4

department: CNAG

country: Spain

institute: Center for Genomic Regulation

summary: Single-cell RNA sequencing (scRNA-seq) is the leading technique for charting the molecular properties of individual cells. The latest methods are scalable to thousands of cells, enabling in- depth characterization of sample composition without prior knowledge. However, there are important differences between scRNA-seq techniques, and it remains unclear which are the most suitable protocols for drawing cell atlases of tissues, organs and organisms. We have generated benchmark datasets to systematically evaluate techniques in terms of their power to comprehensively describe cell types and states. We performed a multi-center study comparing 13 commonly used single-cell and single-nucleus RNA-seq protocols using a highly heterogeneous reference sample resource. Comparative and integrative analysis at cell type and state level revealed marked differences in protocol performance, highlighting a series of key features for cell atlas projects. These should be considered when defining guidelines and standards for international consortia, such as the Human Cell Atlas project.

sample_organism:
Homo sapiens
Canis lupus familiaris
Mus musculus

overall_design: The samples consists of two complex tissues (human PBMC and mouse colon) and three cell lines (HEK293-RFP, NIH3T3-GFP, MDCK-Turbo650). The primary PBMC and the colon sample constitute 90% and the cell lines 10%. The sample preparation aims to be standardized for all methods to allow a comparison of library preparation performance (6% HEK293T-RFP, 3% NIH3T3-GFP, 1% MDCK-Turbo650) of the sample content.

first: Holger

last: Heyn

first: Elisabetta

last: Mereu


title: Comparison of Kidney Transcriptomic Profiles of Early and Advanced Diabetic Nephropathy Reveals Potential New Mechanisms for Disease Progression

status: Public on Dec 14 2019

city: New York

first: Weijia

last: Zhang

state: NY

address: 1 Gustave L. Levy Pl

department: Renal

country: USA

institute: Icahn School of Medicine at Mount Sinai

summary: To identify the factors mediating the progression of di- abetic nephropathy (DN), we performed RNA sequencing of kidney biopsy samples from patients with early DN, advanced DN, and normal kidney tissue from nephrectomy samples. A set of genes that were upregulated at early but downregulated in late DN were shown to be largely renoprotective, which included genes in the retinoic acid pathway and glucagon-like peptide 1 receptor. Another group of genes that were downregulated at early but highly upregulated in advanced DN consisted mostly of genes associated with kidney disease pathogenesis, such as those related to immune response and fibrosis. Correlation with estimated glomerular filtration rate (eGFR) identified genes in the pathways of iron transport and cell differentiation to be positively associated with eGFR, while those in the immune response and fibrosis pathways were negatively associated. Correlation with various histopathological features also identified the association with the distinct gene ontological pathways. Deconvolution analysis of the RNA sequencing data set indicated a significant increase in monocytes, fibroblasts, and myofibroblasts in advanced DN kidneys. Our study thus provides potential molecular mechanisms for DN progression and association of differential gene expression with the functional and structural changes observed in patients with early and advanced DN.

overall_design: A total of 28 patients with biopsy-proven DN hospitalized from January 2015 to December 2016 in Shanghai Jiao Tong University Affiliated Sixth People’s Hospital were enrolled in the study. Nine control human kidney samples were obtained from the unaffected portion of tumor nephrectomies. RNA-seq was performed on 28 DN and 9 control samples.

first: Ying

last: Fan

first: Zhengzi

last: Yi

first: Kyung

last: Lee

first: John

middle: C

last: He


title: Benchmarking Single-Cell RNA Sequencing Protocols for Cell Atlas Projects (inDrop)

platform_organism:
Homo sapiens
Canis lupus familiaris
Mus musculus


title: Leptin deficiency leads to a unique natural history of NASH in rats

status: Public on Dec 31 2019

city: Shanghai

first: Gran

last: Young

state: --- Select a state ---

address: 1239th, Siping Road, Yangpu district

country: China

institute: Tongji University

summary: Nonalcoholic steatohepatitis (NASH) is an aggressive liver disease threatening public health, however its natural history is poorly understood. Unlike ob/ob mice, Lep∆I14/∆I14 rats develop unique NASH phenotype with an inflection point of inflammation at postnatal week 16. Using Lep∆I14/∆I14 rats, we studied the natural history of NASH progression by performing an integrated analysis of hepatic transcriptome from postnatal week 4 to 48. Leptin deficiency leads to the precipitously increasing expression of genes encoding rate-limiting enzymes in lipid metabolism. However, hepatic inflammation related genes, pathways and immune-cell infiltration are restricted after week 16, implying an essential role of LEPTIN in regulating hepatic inflammation. Lep∆I14/∆I14 rats share more genes with NASH patients than known mouse models, therefore will provide a better genetic platform for studying NASH than mice.

sample_organism:
Macaca fascicularis
Rattus norvegicus

platform_organism:
Macaca fascicularis
Rattus norvegicus

overall_design: We collected liver samples/biopsies from detailed 5 timepoints of both wild-type rats, leptin Knock-out rats and crab-eating monkeys and then conduct RNA-seq. Each sample contain 2~3 replicates.

first: Ping

last: Lu

first: Guang

last: Yang

first: Wen

first: Wanwan

last: Wu

first: Lingbin

last: Qi

first: Shijun

last: Shen

first: Guoping

first: Zhigang

last: Xue

first: Peng

first: Cizhong

last: Jiang

first: Xianmin

last: Zhu


title: Benchmarking Single-Cell RNA Sequencing Protocols for Cell Atlas Projects (ddSEQ)

first: Atefeh

last: Lafzi

first: Holger

first: Elisabetta


title: Benchmarking Single-Cell RNA Sequencing Protocols for Cell Atlas Projects (SingleNuclei)

last: Heyn


title: Benchmarking Single-Cell RNA Sequencing Protocols for Cell Atlas Projects (SMART-Se2q)

last: Mereu


title: Benchmarking Single-Cell RNA Sequencing Protocols for Cell Atlas Projects

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

overall_design: Refer to individual Series


title: Benchmarking Single-Cell RNA Sequencing Protocols for Cell Atlas Projects (QUARTZ-Seq2)


title: Benchmarking Single-Cell RNA Sequencing Protocols for Cell Atlas Projects (DROP-Seq)


title: Benchmarking Single-Cell RNA Sequencing Protocols for Cell Atlas Projects (CEL-Seq2)


title: Benchmarking Single-Cell RNA Sequencing Protocols for Cell Atlas Projects (gmSCRB-seq)


title: Benchmarking Single-Cell RNA Sequencing Protocols for Cell Atlas Projects  (ICELL8)


title: Cancer avatars derived from genetically engineered pluripotent stem cells allow for longitudinal assessment of tumor development

city: La Jolla

first: Gene

last: Yeo

state: CA

address: 2880 Torrey Pines Scenic Dr. Room 3805/Yeo Lab

institute: UCSD

summary: Many current cellular models aimed to elucidate cancer biology do not recapitulate pathobiology including tumor heterogeneity, an inherent feature of cancer that underlies treatment resistance. Here we introduce a new cancer modeling paradigm using genetically engineered human pluripotent stem cells (hiPSCs) that capture authentic cancer pathobiology. Orthotopic engraftment of the neural progenitor cells derived from hiPSCs introduced with tumor-associated genetic driver mutations revealed by The Cancer Genome Atlas project for glioblastoma (GBM) results in formation of brain tumors. As observed in GBM patient samples, these models harbor  inter-tumor heterogeneity resembling different GBM molecular subtypes, and intra-tumor heterogeneity. Further, re-engraftment of these tumor cells generate tumors with features characteristic of patient samples and present mutation-dependent patterns of tumor evolution. Thus, these cancer avatar models provide a platform for a comprehensive longitudinal assessment of human tumor development as governed by molecular subtype mutations.

overall_design: Analyses on inter- and intra-tumor heterogeneity of different glioblastoma derived from differentially engineered isogenic human induced pluripotent stem cells.

first: Tomoyuki

last: Koga

first: Isaac

last: Chaim

first: Jorge

last: Benitez

first: Sebastian

last: Markmiller

first: Alison

middle: D

last: Parisian

first: Kristen

middle: M

last: Turner

first: Florian

last: Hessenauer

first: Matteo

last: D’Antonio

first: Nam-phuong

last: Nguyen

first: Shahram

last: Saberi

first: Jianhui

last: Ma

first: Shunichiro

last: Miki

first: Antonia

last: Boyer

last: Ravits

first: Kelly

last: Frazer

first: Vineet

last: Bafna

first: Clark

last: Chen

first: Paul

middle: S

last: Mischel

middle: W

first: Frank

middle: B

last: Furnari


title: Benchmarking Single-Cell RNA Sequencing Protocols for Cell Atlas Projects (C1HT)

first: Atefeh

last: Lafzi

first: Holger

last: Heyn

first: Elisabetta

last: Mereu


title: CEBPA Dysfunction Intiates CSF3R Mutant Acute Myeloid Leukemia Through Disruption of Myeloid Lineage Enhancers (RNA-seq - simultaneous)

status: Public on Dec 02 2019

city: Portland

first: Theodore

middle: Paul

last: Braun

state: OR

address: 3181 SW Sam Jackson Park Road

department: Knight Cancer Institute

institute: OHSU

summary: Acute Myeloid Leukemia (AML) develops due to the acquisition of mutations from multiple functional classes. Here, we demonstrate that activating mutations in the granulocyte colony stimulating factor receptor (CSF3R), cooperate with loss of function mutations in the transcription factor CEBPA to promote acute leukemia development. Terminal myeloid differentiation in response to granulocyte colony-stimulating factor  signaling requires wild type CEBPA and is blocked by mutations in CEBPA. Inhibition of the histone demethylase LSD1, restores differentiation and in combination with JAK/STAT blockade, produces significant disease response in vivo. Mutant CEBPA blocks myeloid differentiation by preventing the activation of differentiation-associated enhancers. As enhancer activation precedes promoter activation, CEBPA mutations must occur prior to CSF3R mutations to effectively block differentiation and promote leukemia formation in vivo. This study demonstrates that order-dependent oncogene interaction is a fundamental process in AML. Dissecting this process is critical for understanding disease evolution to enable the development of effective therapeutics.

overall_design: Comparison of gene expression across mouse (C57BL/6 ) lineage negative bone marrow cells simultanously transduced with different combinations of CEBPA and CSF3R mutant vectors or empty vector (negative control). Each treatment has three biological replicates, indiciated with letters A, B or C.

first: Mariam

last: Okhovat

middle: P

first: Julia

middle: E

last: Maxson


title: Effect of BRCA1 overexpression on genetic expressions of cervical cancer based on next generation sequencing

status: Public on Dec 06 2019

city: Changchun

first: Xin

last: Wen

address: Ziqiang Stree No.218

institute: Jilin University

summary: The cells were cultured in DMEM medium supplemented with 10% fetal bovine serum (Sangon, China) and 1% antibiotic-antimitotic solution (Gibco, USA). The SiHa cells were transfected using Lipofectamine 3000 reagent following the manufacturer’s protocol and incubated for 48h for further analysis.The gene expression profiles were analyzed of SiHa cells transfected with GV230-BRCA1 or GV230 plasmid to assess effect of BRCA1 overexpression on genetic expressions of cervical cancer.

overall_design: High-throughput sequencing raw data for 6 samples, A1;A2;A3 are three samples from experimental group (SiHa cells with GV230-BRCA1 plasmid transfection),and C1;C2;C3 are three samples from negative control group (SiHa cells with GV230 plasmid transfection).


title: CEBPA Dysfunction Intiates CSF3R Mutant Acute Myeloid Leukemia Through Disruption of Myeloid Lineage Enhancers (RNA-seq - orders)

overall_design: Comparison of gene expression across lineage negative mouse (C57BL/6 ) bone marrow cells transduced with CEBPA and CSF3R mutant vectors in different orders: CSF3R-only (control, 4 replicates), CEBPA-first (CSF3R-second, 4 replicates), and CSF3R-first (CEBPA-second, 3 replicates). Replicates are indicated with letters A, B, C and D.


title: CEBPA Dysfunction Intiates CSF3R Mutant Acute Myeloid Leukemia Through Disruption of Myeloid Lineage Enhancers

type: Genome binding/occupancy profiling by high throughput sequencing


title: Benchmarking Single-Cell RNA Sequencing Protocols for Cell Atlas Projects (10X 2x 5K cells 250K reads)


title: Benchmarking Single-Cell RNA Sequencing Protocols for Cell Atlas Projects  (C1HT small)


title: Transcriptomic analysis of blastocyst according to peripubertal age of bull (10 vs 16 months)

status: Public on Apr 02 2020

city: Québec City

first: Marc-André

last: Sirard

state: Quebec

address: Offfice 2732, 2440 Hochelaga Blvd.

department: Sciences Animales

country: Canada

institute: Université Laval

summary: The transcriptome pattern in blastocyst produced by bulls at different age was investigated. Embryos were in vitro fertilized from 4 different bulls at 10 and 16 month each with matched adult cows. Genome-wide DNA methylation analysis was performed by micro array using EDMA platform.

overall_design: Two condition experiment,  4 bulls, all collected at 10 and 16 months old

first: Chongyang

last: Wu

first: Patrick

last: Blondin

first: Christian

last: Vigneault

first: Rémi

last: Labrecque


title: CEBPA Dysfunction Intiates CSF3R Mutant Acute Myeloid Leukemia Through Disruption of Myeloid Lineage Enhancers (ChIP-seq)

overall_design: Characterization and comparison of chromatin states across murine hematopoietic cell lines immortalized through retroviral transduction of different combinations of CSF3R and CEBPA mutations: CSF3R.T618I only,CEBPA.v314vw only and CSF3R.T618I+CEBPA.v314vw. Cells transduced with empty vector were used as control. Each treatment group had two replicates.


title: RNA-seq total KO experiments for "Chronic repression by MAF1 supports futile RNA cycling as a mechanism for obesity resistance"

status: Public on Nov 04 2019

city: Lausanne

first: Nicolo

last: Riggi

state: VD

address: Bugnon 25

department: Département de Pathologie Expérimentale

country: Switzerland

institute: CHUV

summary: To examine the effect of MAF1 on the RNA polymerase II transcriptome, RNA-seq was performed on samples of liver from overnight fasted and four hour refed wild-type and whole-body Maf1-/- mice.

overall_design: RNA-seq, wild-type and Maf1 KO

first: Nicolas

last: Bonhoure

first: Viviane

last: Praz

first: Ian

last: Willis

first: Nouria

last: Hernandez


title: Expression data from human epidermal keratinocytes treated with hydrolyzed wheat protein

status: Public on Dec 01 2019

city: Ichikai, Haga

first: Yasutaka

last: Kuroda

state: Tochigi

address: Akabane 2606

country: Japan

institute: Kao Corporation

summary:
Hydrolyzed wheat proteins (HWPs) contained in cosmetics have occasionally caused immediate-type hypersensitivity following repeated skin exposure. Although the Cosmetic Ingredient Review Expert Panel concluded that <3,500 Da HWP is safe for use in cosmetics, it remains biologically unknown how allergenic HWPs evoke immediate-type allergy percutaneously. Keratinocyte-derived thymic stromal lymphopoietin (TSLP) induces type 2 immune responses, which play an essential role in the pathogenesis of immediate-type allergy. Previously, we demonstrated that protein allergens in cultured human keratinocytes strongly induced long-form TSLP (loTSLP) transcription. However loTSLP-regulating signaling by HWP is poorly understood.
In this study, we performed global gene expression analysis by microarray to investigate how the allergenic HWP acts on epidermal keratinocytes and the induction of loTSLP.

overall_design: According to our previous work, the hydrolyzed wheat protein (GP19S), unlike human serum albumin (HSA), induced potent loTSLP transcription. To elucidate this difference, the gene expression profiles of keratinocytes exposed to 3 mg/mL GP19S, 66 mg/mL HSA, and their solvents were compared.

first: Takuo

last: Yuki

first: Yutaka

last: Takahashi

first: Hitoshi

last: Sakaguchi

first: Kayoko

last: Matsunaga

first: Hiroshi

last: Itagaki


title: Benchmarking Single-Cell RNA Sequencing Protocols for Cell Atlas Projects (10X 8x 10K cells 25K reads)

first: Atefeh

last: Lafzi

first: Holger

last: Heyn

first: Elisabetta

last: Mereu


title: miRNA array experiment of NC-Exo and GATA4-Exo

status: Public on Nov 28 2019

city: Nanjing

first: chunshu

last: Hao

address: No.87 Dingjiaqiao street

department: Cardiology

institute: Southeast university

summary:
Exosomes carry cell-specific proteins or mRNAs/miRNAs that mediate the functional effect of exosomes. To investigate whether miRNAs within GATA4-Exo are important for their cardioprotective effects, we utilized an unbiased approach by performing an exosomal miRNA array analysis.
Total RNA was extracted from CDCs-Exo by using a Qiagen miRNeasy Mini Kit. Global expression patterns of miRNAs were then examined by using Affymetrix GeneChip miRNA 4.0 arrays.Expression data were generated by using Affymetrix Expression Console software and normalized according to the MAS5 method. The RVM t test was applied to filter the differentially expressed genes for the control and experimental groups. Differentially expressed genes were defined based on a P-value threshold and fold-change analysis.

overall_design: Exosomes were obtained from the CDC and CDCGATA4 culture supernatants by ultracentrifugation.  Exosomes were harvested from CDCs by ultracentrifugation. miRNA arrays were performed to test the differential miRNA expression between exosomes derived from GATA4-overexpressing CDCs (GATA4-Exo) and control CDCs (NC-Exo). Microarray analysis revealed significantly increased and decreased miRNAs expression in GATA4-Exo.

first: Chunshu

first: Lijuan

last: Chen


title: PHYB and PHYC–mediated transcriptomic responses to short and long day photoperiods in wheat

status: Public on Nov 26 2019

city: Harpenden

first: Stephen

last: Pearce

state: Hertfordshire

address: West Common

department: Sustainable Soils and Crops

country: United Kingdom

institute: Rothamsted Research

summary: The phytochromes (PHYs) are a family of photoreceptors which absorb red and far-red light to modulate developmental responses in photosynthetic organisms. We developed knockout mutants of PHYB and PHYC in tetraploid wheat and performed RNA-seq studies to analyze and compare the regulons of each phytochrome under short day photoperiods.

overall_design: Illumina Truseq v2 RNA-seq libraries were constructed from four biological replicates of Wild-type controls, phyBnull and phyCnull mutants. Raw reads were trimmed for quality and adapter contaminations and mapped to the IWGSC RefSeqv1.0 wheat genome assembly. Sequencing reads mapping uniquely within regions annotated as high confidence and low confidence gene models were used to determine relative expression profiles. We provide tables of raw counts and TPM data for each gene.

first: Nestor

last: Kippes

first: Ani

last: Akpinar

first: Hikmet

last: Budak

first: Jorge

last: Dubcovsky


title: DNA copy number profiling of lung adenocarcinomas and patient-matched non-malignant lung

status: Public on Oct 23 2019

city: Vancouver

first: Katey

middle: SS

last: Enfield

state: BC

address: 675 West 10th Ave

institute: BC Cancer Research Centre

summary:
Gene function in cancer is often cell type-specific.
The epithelial cell-specific transcription factor ELF3 is a documented tumour suppressor in many epithelial tumours yet displays oncogenic properties in others.
Here, we show that ELF3 is an oncogene in the adenocarcinoma subtype of lung cancer (LUAD), providing genetic, functional, and clinical evidence of subtype specificity.
We discover a region of focal amplification at chromosome 1q32.1 encompassing the ELF3 locus in LUAD which is absent in the squamous subtype.
Gene dosage and promoter hypomethylation affect the locus in up to 80% of LUAD analysed.
ELF3 expression was required for tumour growth and a pan-cancer expression network analysis supports its subtype and tissue specificity.
We further show that ELF3 displays strong prognostic value in LUAD but not LUSC.
We conclude that, contrary to many other tumours of epithelial origin, ELF3 is an oncogene and putative therapeutic target in LUAD.
A subset of this data has been previously published (https://edrn.jpl.nasa.gov/ecas/data/dataset/urn:edrn:COPY_NUMBER_LEV1) PMID: 22412972

overall_design: 83 lung adenocarcinomas and 83 matched non-malignant lung samples were profiled on Affymetrix SNP6.0 arrays

first: Wan

middle: L

last: Lam


title: Expression data of LncRNA from Human rectal cancer tissues and adjacent non-cancerous tissues

status: Public on Nov 02 2019

city: Beijing

first: 唐

last: 伟评

address: 2 Anzhen Rd, Chaoyang District,

institute: Beijing Institute of Heart Lung and Blood Vessel Diseases

summary:
Rectal carcinoma(RC) is one of the most common malignant tumor of the digestive tract in humans.Long non-coding RNA (lncRNA) plays a vital role in tumor regulation.Nevertheless, the exact expression features and functions of lncRNAs are still obscure.To investigate aberrantly expressed lncRNAs and mRNAs in RC, we screened the crucial differentially expressed lncRNA and mRNA in RC tissues and paire-matched adjacent non-cancerous tissues.These differentially expressed lncrnas are likely to play a key role in the tumorigenesis and development of RC, and may be used as a novel tumor biomarker for the diagnosis or prognosis of RC.
We used Affymetrix human GeneChip to screen the candidate differentially expressed lncRNAs and mRNAs in RC tissues and paire-matched adjacent non-cancerous tissues.Subsequently, the candidate differentially expressed lncRNAs and mRNAs were verified by qRT-PCR.

overall_design: We selected 6 cases of rectal cancer patients with cancer tissues and adjacent non-cancerous tissues for total RNA extraction and Clariom D Assay (human,Affymetrix) analysis. At the same time, in order to deeply understand the relationship between differential lncRNA and mRNA, we carried out in-depth analysis, including GO Enrichment Analysis,Hierarchical Clustering,Pathway enrichment Analysis and co-expression regulatory network analysis under the basic analysis. We are trying to find out an instructive tumor marker which is of guiding significance for the diagnosis and prognosis of rectal cancer.

first: Dezhong

last: Wang

first: Yifeng

last: Li


title: Lead-seq: transcriptome-wide in vivo structure probing with lead

status: Public on Nov 20 2019

city: Bochum

first: Franz

last: Narberhaus

state: NRW

address: Universitätsstraße 150

department: Microbial Biology

country: Germany

institute: Ruhr University Bochum

summary: In vivo probing of the Yersinia pseudotuberculosis YPIII transcriptome at 25 °C and 37 °C

overall_design: RNA-seq of Yersinia pseudotuberculosis YPIII transcriptome at 25 °C and 37 °C with and without lead acetate

first: Christian

last: Twittenhoff

first: Vivian

last: Brandenburg

first: Francesco

last: Righetti

first: Aaron

last: Nuss

first: Axel

last: Mosig

first: Petra

last: Dersch


title: Benchmarking Single-Cell RNA Sequencing Protocols for Cell Atlas Projects (MARS-Seq)

first: Atefeh

last: Lafzi

overall_design: The samples consists of two complex tissues (human PBMC and mouse colon) and three cell lines (HEK293-RFP, NIH3T3-GFP, MDCK-Turbo650). The primary PBMC and the colon sample constitute 90% and the cell lines 10%. The sample preparation aims to be standardized for all methods to allow a comparison of library preparation performance (6% HEK293T-RFP, 3% NIH3T3-GFP, 1% MDCK-Turbo650) of the sample content.

first: Holger

last: Heyn

first: Elisabetta

last: Mereu


title: DNA methylation profiling of lung adenocarcinomas and patient-matched non-malignant lung

summary:
Gene function in cancer is often cell type-specific.
The epithelial cell-specific transcription factor ELF3 is a documented tumour suppressor in many epithelial tumours yet displays oncogenic properties in others.
Here, we show that ELF3 is an oncogene in the adenocarcinoma subtype of lung cancer (LUAD), providing genetic, functional, and clinical evidence of subtype specificity.
We discover a region of focal amplification at chromosome 1q32.1 encompassing the ELF3 locus in LUAD which is absent in the squamous subtype.
Gene dosage and promoter hypomethylation affect the locus in up to 80% of LUAD analysed.
ELF3 expression was required for tumour growth and a pan-cancer expression network analysis supports its subtype and tissue specificity.
We further show that ELF3 displays strong prognostic value in LUAD but not LUSC.
We conclude that, contrary to many other tumours of epithelial origin, ELF3 is an oncogene and putative therapeutic target in LUAD.

overall_design: 77 lung adenocarcinomas and 77 matched non-malignant lung samples were profiled on Illumina HumanMethylation27 BeadChip arrays.


title: Identifying a novel candidate diagnostic and prognostic biomarker SPRR3 for oral squamous cell carcinoma via mRNA Sequencing and Bioinformatics

status: Public on Nov 21 2019

city: Jinan

first: Lu

last: Yu

state: Shandong

address: No.44-1 Wenhua Road West

department: Department of Implantology

institute: School and Hospital of Stomatology, Shandong University

summary: Oral squamous cell carcinoma (OSCC) has always been one of the most aggressive and invasive malignancies among the numerous oral and maxillofacial malignancies. we collected three tumorous and adjacent tissues from OSCC sufferers, and we obtained differentially expressed genes (DEGs) via high throughput RNA sequence.

overall_design: We obtained 229 DEGs between tumor and normal tissues. Function and pathway enrichment analyses for DEGs were conducted to find correlation between tumorigenesis status and differentially expressed genes.Protein interaction network and molecular complex detection were constructed to find meaningful modules. Two core modules were enriched in MCODE. The diagnostic and prognostic values of the candidate genes were analyzed, which provide evidence for the candidate genes as new tumor markers.

first: Y

last: Lu

first: Zongcheng

last: Yang


title: G3BP1-linked mRNA partitioning supports selective protein synthesis in response to oxidative stress

status: Public on Nov 01 2019

first: Syam Prakash

last: Somasekharan

address: 2660 Oak St

institute: Vancouver Prostate Centre

summary: Cells limit energy-consuming mRNA translation during stress to maintain metabolic homeostasis. Sequestration of mRNAs by RNA binding proteins (RBPs) into stress granules (SGs) reduces translation, but it remains unclear whether SGs also function in partitioning of specific transcripts to polysomes (PSs) to guide selective translation and stress-adaptation in cancer. Transcripts enriched in PSs, defined by polysome fractionation and RNAseq, were compared with mRNAs complexed with the SG-nucleator protein, G3BP1, defined by spatially-restricted enzymatic tagging. Short-term oxidative stress profoundly altered mRNA translation by promoting selective enrichment of transcripts within SGs or PSs. G3BP1 participates in this compartmentalisation by sequestering transcripts in SGs. Under stress, G3BP1-bound transcripts are PS-depleted and encode proteins involved in mRNA translation, pro-apoptosis, and mitochondrial function. In contrast, specific PS-enriched transcripts disassociate from G3BP1 under stress to encode proteins involved in diverse cellular cytoprotective pathways. Therefore, G3BP1 partitioning guides selective translation to support stress adaptation and cell survival.

overall_design: G3BP1-interacting RNAs were identified in untreated and arsenite treated cells by APEX method, polysome-associated mRNAs in untreated arsenite treated conditions were idnetified by sucroses gradient polysomal fractionation (SGPF) and RNAseq.

first: Syam


title: A Digital mRNA Expression Signature to Classify Challenging Spitzoid Melanocytic Neoplasms

status: Public on Oct 25 2019

city: Maastricht

first: Lisa

middle: Maria

last: Hillen

state: Limburg

address: P. Debyelaan 25

department: Department of Pathology

institute: Maastricht University Medical Center

summary: Spitzoid neoplasms are a challenging group of cutaneous melanocytic proliferations that occur in children or adolescents but can also arise in the elderly. They are characterized by epithelioid and/ or spindle-shaped melanocytes with a stromal background of variable amounts of lymphocytes, blood vessels and sclerosis. According to the WHO 2018 classification, Spitzoid melanocytic lesions are classified as benign Spitz nevi (SN), atypical Spitz tumors (AST) or malignant Spitz tumors (MST). The intermediate AST category represents a diagnostically challenging group since on purely histopathological grounds, their benign or malignant character remains unpredictable. This results in uncertainties in patient management and prognosis. The molecular properties of Spitzoid lesions, especially their transcriptomic landscape, remain poorly understood and genomic alterations in melanoma-associated oncogenes are typically absent. The aim of this study was to characterize the transcriptome of Spitzoid melanocytic neoplasms with digital mRNA expression profiling. Formalin-fixed-paraffin-embedded samples (including 27 SN, 10 AST and 14 MST) were analyzed using the RNA NanoString nCounter PanCancer Pathways Gene Expression panel. The number of significantly differentially expressed genes in SN vs. MST, SN vs. AST and AST vs. MST was 68, 167 and 18, respectively. Gene set enrichment analysis revealed an upregulation of pathways related to epithelial mesenchymal transition, immunomodulatory-, angiogenesis- as well as myogenesis associated processes in AST and MST.  In addition, a specific gene expression signature of SN vs. MST was discovered based on the top-ranked six most informative gene expression markers: NRAS, NF1, BMP2, EIF2B4, IFNA17 and FZD9. The AST samples showed intermediate levels of the identified signature. This implies that the identified gene expression signature can potentially be used to distinguish high-grade from low-grade AST. This combined histopathological and transcriptomic methodology is promising for diagnostics of Spitzoid neoplasms and patient management in dermatological oncology in the future.

overall_design: mRNA expression of 27 Spitz nevi (SN), 10 atypical Spitz tumors (AST) and 14 malignant Spitz tumors (MST) were analyzed. Molecular profiling was done using the RNA NanoString nCounter Gene Expression Platform (No. of genes = 770). Gene expression counts were normalized based on total library size. As such, both the housekeeping and endogenous genes were used for normalization. The studied samples showed a mean library size of 307914 counts (median 292412; range 789054 (sample AST4) to 19042 (sample MST4)). All analyses were performed using R and Bioconductor packages. Marker Discovery and Validation of differentially expressed genes from the nCounter data was done using the limma and voom method in R. Three conditions were studied: (i) SN vs. MST, (ii) SN vs. AST, and (iii) AST vs. MST. The limma procedure borrows information across all genes, which makes the analysis robust even when the sample size is small (Ritchie, Phipson et al. 2015). The voom procedure was applied to non-parametrically estimate the mean-variance relationship of the log-transformed gene counts, which is important when dealing with expression count data

first: Milan

last: Geybels

first: Ivelina

last: Spassova

first: Jürgen

last: Becker

first: Thilo

last: Gambichler

first: Marjan

last: Garmyn

last: zur Hausen

first: Joost

last: van den Oord

first: Véronique

last: Winnepenninckx


title: CEBPA Dysfunction Intiates CSF3R Mutant Acute Myeloid Leukemia Through Disruption of Myeloid Lineage Enhancers (Microarray)

first: Theodore

last: Braun

overall_design: 12 total samples were analyzed (4 groups, with 3 biological replicates in each group). We generated 6 total pairwise comparisons between the following groups in HoxB8 cells 24 hours after estrogen withdrawal: Empty Vector, CSF3R_T618I, CEBPA_V314VW, CSF3R_T618I+CEBPA_V314VW (each has three biological replicates, indicated with A, B and C). Genes with an FDR<5% and Fold change of +/-2 were selected.

first: Mariam

last: Okhovat

first: Julia

last: Maxson


title: Gut dysbiosis modulates the immune response to factor VIIII in murine hemophilia A

status: Public on Oct 04 2019

city: Kingston

first: David

last: Lillicrap

state: ON

address: 88 Stuart Street

department: Pathology and Molecular Medicine

institute: Queen's University

sample_organism:
Mus musculus
mouse gut metagenome

platform_organism:
Mus musculus
mouse gut metagenome

overall_design: Refer to individual Series


title: Epithelial Tumour Suppressor ELF3 is a Lineage-Specific Amplified Oncogene in Lung Adenocarcinoma

first: Katey

last: Enfield

type:
Expression profiling by array
Methylation profiling by array
Genome variation profiling by SNP array


title: RNA-Sequencing of HepG2 cells treated with TGFBeta

status: Public on Oct 18 2019

city: Rochester

first: Asha

last: Nair

address: 200 1ST ST SW

institute: Mayo Clinic

summary: We report a subset of genes upregulated by TGFBeta after three hours of treatment

overall_design: We used RNA-seq to determines changes in expression profiles of HepG2 cells treated with TGFBeta or Vehicle to determine  unique TGFB responsive genes

first: Angela

last: McCleary-Wheeler

first: Luciana

last: Almada

first: Brooke

last: Paradise

first: Martin

last: Fernandez-Zapico


title: Genetic and microstructural differences in the cortical plate of gyri and sulci during gyrification in fetal sheep

status: Public on Dec 03 2019

city: Bundoora

first: Sebastian

last: Quezada

state: VIC

address: 225-245 Plenty Rd

department: School of Health and Biomedical Sciences

country: Australia

institute: RMIT University

summary: Gyrification of the cerebral cortex is a developmentally important process, however the mechanisms that drive cortical folding remain unknown. Theories propose that changes within the cortical plate (CP) cause gyrification, yet differences between the CP below gyri and sulci have not been investigated. Here we report genetic and microstructural differences in the CP below gyri and sulci assessed before (gestational age (GA) 70), during (GA 90) and after (GA 110) gyrification in fetal sheep. The areal density of BDNF-, CDK5-, and NeuroD6-immunopositive cells were increased, and HDAC5 and MeCP2 mRNA levels were decreased, in the CP below gyri compared to sulci during gyrification, but not before. Only the areal density of BDNF-immunopositive cells remained increased after gyrification. MAP2-immunoreactivity was also increased in the CP below gyri compared to sulci at GA 90, and this was associated with microstructural changes assessed via neurite orientation dispersion and density imaging (NODDI) at GA 98. Differential neurite outgrowth may therefore be a strong candidate to explain local changes in CP architecture during gyrification.

overall_design: Total RNA of cells coming from gyri or sulci cortical plate from fetal sheep brains at gestational age 90. Four biological replicates, eight samples in total (gyri and sulci per specimen). SPIA sequencing, 7 cycles in Illumina HiSeq3000 sequencer. No technical replicates.

first: Yohan

last: van de Looij

first: Nadia

last: Hale

first: Shreya

last: Rana

first: Stéphane

middle: V

last: Sizonenko

first: Margie

last: Castillo-Melendez

first: Mary

last: Tolcos

last: Walker


title: Ampicillin treatment casues dysbiosis that persists until study endpoint [RNA-seq]

summary:
The development of neutralizing FVIII antibodies is the most serious complication of hemophilia A treatment. The currently known patient- and treatment-related risk factors for inhibitor development do not accurately predict this adverse event in all patients. The composition of the gut microbiota has been shown to influence immune mediated diseases at distant anatomical sites (e.g. lungs, brain and joints). We demonstrate that a disrupted gut microbiome can be created in a mouse model of hemophilia A using a broad-spectrum antibiotic. Under controlled conditions, this sustained dysbiosis was associated with an enhanced anti-FVIII immune response as evidenced by increased splenic B cells and the development of higher titre FVIII specific IgG antibodies following FVIII challenge. Splenic and mesenteric lymph node cytokines, T cells and dendritic cells were unaffected prior to FVIII administration. However, the immune transcriptome of both aforementioned secondary lymphoid organs was significantly modified. Short chain fatty acids (SCFA), which are microbial metabolites, were depleted in cecal contents of the dysbiotic mice. Furthermore, supplementation of the drinking water with the most immunologically active SCFA, butyrate, successfully achieved attenuation of the FVIII immune response. Collectively, our data suggest that the composition of the gut microbiome alters the FVIII immune response via the action of specific microbial metabolites on the immune cell transcriptome and that oral butyrate supplementation effectively reduces the FVIII immune response.
Mice treated with one week of ampicillin at 3 weeks of age have a dysbiotic gut microbiome at 6 weeks of age and at the study endpoint. The immune response to FVII was compared between the two cohorts. The dysbiotic cohort had a greater immune response to FVIII

overall_design: Mice are treated with ampicillin by gavage at 3 weeks of age. Microbiota of cecal content is assessed at 6 weeks of age and at 10 weeks of age. Mice are euthanised and cecums dissected to access cecal contents.

first: Julie

last: Tarrant

first: Matthew

last: Cormier


title: MiRNA expression profiling in pancreatic ductal adenocarcinoma (PDAC) cells treated with TGF-b

status: Public on Oct 17 2019

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: 10-1 tebiro 6-chome

institute: Toray Industries,Inc.

summary: Expression profiling of 2555 miRNAs was performed using microarray. Of these, 1719 miRNAs expressed in PDAC cells.

overall_design: In the study presented here, we used PDAC cells, Panc-1 and miRNAs expression was analyzed by comparing in Panc-1 cells treated with or without TGF-β.

first: Kenji

last: Takahashi

first: Yu

last: Ota


title: RNA-seq analysis reveals profound changes in transcript profiles between siCon- and siH19-transfected uterine smooth muscle cells (USMC)

status: Public on Oct 01 2019

city: New Haven

first: Ying

last: Jiang

address: 310 Cedar Street

institute: Department of Obstetrics, Gynecology & Reproductive Sciences

summary: We used high throughput sequencing to analyze the gene expression profiling of human uterine smooth muscle cells (USMC). By comparing the gene expression profiling of USMC with or without H19 knockdown, 215 genes were found at least 1.5-fold up-regulated in siH19 relative to siCon cells, meanwhile 228 genes were found at least 1.5-fold down-regulated in siH19 over siCon cells.

overall_design: USMC cells were transfected with either control siRNA or siH19. 48h after transfection, total RNA was extracted for library preparation and RNA-seq analysis to compare gene expression profiles between siCon and siH19 cells.

last: Zhang

first: Gordon

middle: G

last: Carmichael

first: Yingqun

last: Huang


title: Trophectoderm specific function of Atypical Protein Kinase C iota (PKCi) is essential for post-implantation mammalian development.

status: Public on Oct 15 2019

city: Kansas City

first: Bhaswati

last: Bhattacharya

state: Kansas

address: 3901 Rainbow Blvd

department: Pathology and Laboratory Medicine

institute: University of Kansas Medical Center

summary: Atypical protein kinase C iota (Prkci) knockout mice are embryonic lethal at gestation day 9.5 but the underlying molecular mechanisms is not known. Here , using Prkci knockout mouse model , we show that trophectoderm specific function of PKCi is essential for post-implantation mammalian development. We observed that PKCi is expressed predominantly in the trophectoderm lineage and developing placenta region in post-implantation mouse embryos. Prkci knockout or homozygous embryos show severe defect in placenta formation compared to wildtype and heterozygous embryos.  Using RNA seq analysis in PKCi knockdown mouse trophoblast stem cells, we identified certain genes which are significantly upregulated upon PKCi depletion , one among them is Bone Morphogenetic protein 13 (Bmp13). Our study shows that PKCi is one of key players involved in proper development of the placenta, loss of which might be one of the reasons for early pregnancy failure.

overall_design: Mouse trophoblast stem cells were cultured using MEF conditioned media along with FGF4 and Heparin. Short hairpin RNA against Prkci mRNA was cloned in PLKO1 vector and a scrambled control was also used. Lentiviral supernatants were obtained from HEK 293T cells and were used to transduce TS cells described before. Transduced cells were selected using 1µg/ml puromycin. Knockdown efficiency was validated by real-time PCR analysis and western blotting. Whole cell-lysates were used to prepare RNA using Qiagen RNeasy Mini Kit with on column DNase digestion. RNA-seq analysis were performed using Illumina HiSeq2500 platform.

first: Paul

last: Soumen

first: Bhattacharya

last: Bhaswati


title: Next generation sequencing comparing effects of FFSS, FAK inhibitor and FAK gene deletion.

status: Public on Oct 31 2019

city: Boston

first: Marc

last: Wein

state: MA

address: 15 Fruit Street

department: Massachusetts General Hospital, Department of Medicine

institute: Harvard Medical School

summary: Purpose: The goals of this study are to compare the effect of FFSS, FAK inhibitor, and FAK gene deletion on gene expression of NGS-derived RNA-sequencing.

overall_design: Methods: Ocy454 cells were grown at 37c for 14 days. Cells were then treated with FFSS (3h), or FAK inhibitor (2.5uM PF562271, 4h). Total RNA was isolated using PureLink RNA mini columns, and submitted for NGS library generation and sequenccing. All experiments performed in duplicate.

first: Tadatoshi

last: Sato

first: Murat

last: Cetinbas


title: Placental Accreta Spectrum: Upregulated Cytotrophoblast DOCK4 Contributes to Over Invasion

status: Public on Sep 30 2019

city: San Francisco

first: M.

middle: Yvonne

last: Kim

address: 3rd st.

institute: UC San Francisco

summary: In humans, a subset of placental cytotrophoblasts (CTBs) invades the uterus and its vasculature, anchoring the pregnancy and ensuring adequate blood flow to the fetus. Appropriate depth is critical. Shallow invasion increases the risk of pregnancy complications, e.g., severe preeclampsia. Overly deep invasion, the hallmark of placenta accreta spectrum (PAS), increases the risk of pre-term delivery, hemorrhage and death. Previously a rare condition, the incidence of PAS has increased to 1:731 pregnancies, likely due to the rise in uterine surgeries (e.g., Cesarean sections). CTBs track along the scars deep into the myometrium and beyond. Here we compared the global gene expression patterns of CTBs from PAS cases to gestational age-matched control cells that invaded to the normal depth from preterm birth (PTB) deliveries. The mRNA encoding the guanine nucleotide exchange factor, DOCK4, mutations of which promote cancer cell invasion and angiogenesis, was the most highly differentially expressed molecule in PAS samples. Over-expression of DOCK4 increased CTB invasiveness, consistent with the PAS phenotype. Also, this analysis identified other genes with significantly altered expression in this disorder, potential biomarkers. These data suggest that CTBs from PAS cases up regulate a cancer-like pro-invasion mechanism, suggesting molecular as well as phenotypic similarities in the two pathologies.

overall_design: Expression profiling of placental cytotrophoblasts from PAS patients and healthy controls.

first: Leah

last: McNally

first: Yan

last: Zhou

first: Joshua

middle: F

last: Robinson

first: Guangfeng

last: Zhao

first: Lee-May

last: Chen

first: Hao

first: M

middle: Y

first: Mirhan

last: Kapidzic

last: Gormley

first: Susan

middle: J

last: Fisher


title: Identification of gene signature in ascitic fluid-isolated mesothelial cells from high grade serous ovarian cancer patients

status: Public on Sep 20 2019

city: Houston

first: Chi Lam

last: Au Yeung

state: TX

address: 1515 Holcombe Blvd

institute: UT MD Anderson Cancer Center

summary: RNA-sequencing analysis was carried out on ascitic fluid-isolated mesothelial cells from ovarian cancer patients compared to control human peritoneal mesothelial cells.

overall_design: Three control human peritoneal mesothelial cell samples isolated from omentum obtained from non-oncologic patients undergoing abdominal surgery and four ascitic fluid-isolated mesothelial cell samples obtained from the peritoneal effucsions of stage III/IV

first: Chi

first: Tsz

last: Yeung

first: Samuel

middle: C

last: Mok


title: Transcriptome Comparison of staphylococcus aureus phoU Homologies: Genes Deletion strain and the Parent Strain in stationary phase (12 h)

status: Public on Oct 19 2019

city: Shanghai

first: Yongpeng

last: Shang

address: Zhidao building, Dong'an road, Xuhui district

department: Department of Medical Microbiology And Parasitotology

institute: Fudan University

summary:
Purpose: The goals of this study are to compare the wild type and phoU1 or phoU2 gene knock out transcriptome profiling (RNA-seq)  to analysis  gene expression change
Methods: Samples was prepared according to the Illumina RNA Sequencing Sample Preparation Guide. In brief, three biological replicates for each of the S. aureus and derivative strains were treated with RNase-free DNase I (Takara) to remove the genomic DNA. BioAnalyzer 2100 system used to evaluate the RNA quality. Samples were treated with RiboZero rRNA removal kit (gram-positive organisms) to remove ribosomal RNA. Fragmented RNA was reverse transcribed using random primers. The cDNA library included the fragment size (200–300 bp) were prepared by the mRNA-Seq Sample Prep kit and verified on a BioAnalyzer 2100 system. Then, the fragment size is amplified by Illumina cBot and sequenced by Illumina HiSeq 2500. Quality control involves discards of rRNA reads, sequencing adapters, short-fragment and other low-quality reads. The remaining reads were multi-mapped to the genome of S. aureus USA500 2395 at the NCBI website with Bowtie2 software. BED Tools software was used to count the transcript expression levels. Per Kilobase of Gene Per Million Mapped Reads (RPKM) reported RNA-seq gene expression values. Integrated Genomics Viewer was used to visualize the date. DEGseq software was used to quantify differential expression of different transcripts. Significant differences in expression ratios were defined at least a 2.0-fold or 0.5-fold change in transcript level.
Results:Transcriptome analysis revealed that 573 or 285 genes were differentially expressed by at least 2.0-fold in the ΔphoU1 or ΔphoU2 mutant’s vs the wild type. Genes involved in carbon and pyruvate metabolism were changed, and virulence genes and virulence regulatory genes were downregulated
Conclusions:  In conclusion, both PhoU1 and PhoU2 in S. aureus regulate virulence and persister via the metabolism.

overall_design: RNA profiles of  ΔphoU1 or ΔphoU2 mutant and the wild type grown for 12h were generated by deep sequencing, in triplicate, using Illumina HiSeq 2500.

first: Xiaofei

last: Wang

first: Di

last: Qu


title: Estrogen-like effects of arsenite and cadmium

city: Washington

first: Henghong

last: Li

state: DC

address: 3970 Reservoir Rd., NW

department: Biochemistry

institute: Georgetown University

summary: Microarray data indicate estrogen-like effects of arsenite and cadmium

overall_design: This experiment examined the whole genome transcriptional response of MCF7 cells treated with estradiol (1nM), arsenite (1μM), or cadmium (1μM) in the absence or presence of the antiestrogen ICI-182,780 (500nM) for 24 hours

first: Heng-Hong

first: Renxiang

first: Albert

last: Fornace


title: Tbx3 governs a transcriptional program to maintain atrioventricular conduction system form and function

city: Amsterdam

first: Vincent

middle: M.

last: Christoffels

state: N/A (NA)

address: Meibergdreef 15  K2-159

department: Medical Biology

institute: Amsterdam UMC

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


title: Tbx3 governs a transcriptional program to maintain atrioventricular conduction system form and function [ATAC-seq]

summary: Rationale: The atrioventricular conduction system controls ventricular activation and is delineated by expression of Tbx3. Genome-wide association studies identified genetic variants near TBX3 associated with conduction velocities (PR interval and QRS duration), suggesting minor changes in TBX3 dose affect conduction system function. Objective: To assess whether and how Tbx3 dose reduction affects the integrity of the atrioventricular conduction system. Methods and Results: Electrocardiograms revealed a PR interval shortening and prolonged QT interval and QRS duration in heterozygous Tbx3 mutants compared to wild-types. We observed that the atrioventricular bundle and proximal bundle branches of Tbx3+/- mice after birth became hypoplastic, whereas the size of the atrioventricular node was not affected. The transcriptomes of wild-type and Tbx3+/- atrioventricular nodes were analyzed using BAC-Tbx3-Egfp mice enabling specific isolation of the atrioventricular node by laser capture microdissection followed by RNA-sequencing. Hundreds of genes were slightly but consistently deregulated. Cross-referencing with transcriptome data of isolated cardiomyocytes of the conduction system and chamber myocardium derived from Tbx3+/Venus;BAC-Nppb-Katushka hearts revealed that a set of chamber-enriched genes, including Kcne1 (MinK), Ryr2, and Scn5a, were upregulated in Tbx3+/- atrioventricular nodes, whereas conduction system-enriched genes, including Hcn4 and Cacna2d2, were downregulated. We performed ATAC-sequencing on purified fetal Tbx3+ atrioventricular cardiomyocytes to identify potential atrioventricular-specific regulatory DNA elements on a genome-wide scale, and identified regulatory elements mediating the Tbx3-dependent regulation of Ryr2 and other target genes in the atrioventricular node. Conclusions: Tbx3 dose reduction results in deregulation of a large number of genes affecting the electrical properties of the atrioventricular node and causes failure to maintain the structural integrity of the atrioventricular bundle. These data provide a mechanism underlying differences in PR interval and QRS duration in individuals carrying associated variants in the TBX3 locus.

overall_design: ATAC-seq on microdissected and FACS-sorted E13.5 Tbx3-Venus+ atrioventricular junction cardiomyocytes

first: Rajiv

last: Mohan

first: Jan

middle: H

last: van Weerd

first: Karel

last: van Duijvenboden

middle: M


title: Expression profiling of isogenic A549 cell lines with and without ELF3 knock-down

city: Vancouver

first: Katey

last: Enfield

address: 675 West 10th Ave

institute: BC Cancer Research Centre

summary:
Gene function in cancer is often cell type-specific.
The epithelial cell-specific transcription factor ELF3 is a documented tumour suppressor in many epithelial tumours yet displays oncogenic properties in others.
Here, we show that ELF3 is an oncogene in the adenocarcinoma subtype of lung cancer (LUAD), providing genetic, functional, and clinical evidence of subtype specificity.
We discover a region of focal amplification at chromosome 1q32.1 encompassing the ELF3 locus in LUAD which is absent in the squamous subtype.
Gene dosage and promoter hypomethylation affect the locus in up to 80% of LUAD analysed.
ELF3 expression was required for tumour growth and a pan-cancer expression network analysis supports its subtype and tissue specificity.
We further show that ELF3 displays strong prognostic value in LUAD but not LUSC.
We conclude that, contrary to many other tumours of epithelial origin, ELF3 is an oncogene and putative therapeutic target in LUAD.

overall_design: Three biologically independent isogenic controls were derived by stable transfection of empty vector, and three biologically independent ELF3 knock-down lines were prepared by stable transfection of a vector containing an ELF3-targeting shRNA. Knock-down lines were derived from single cell clones. RNA was extracted and 150ng was submitted for expression profiling to The Centre for Applied Genomics.

first: Wan

last: Lam


title: Ampicillin treatment casues dysbiosis that affects transcriptome in spleen and mesenteric lymph nodes [nCounter Mouse Immunology Panel]

first: David

last: Lillicrap

summary:
The development of neutralizing FVIII antibodies is the most serious complication of hemophilia A treatment. The currently known patient- and treatment-related risk factors for inhibitor development do not accurately predict this adverse event in all patients. The composition of the gut microbiota has been shown to influence immune mediated diseases at distant anatomical sites (e.g. lungs, brain and joints). We demonstrate that a disrupted gut microbiome can be created in a mouse model of hemophilia A using a broad-spectrum antibiotic. Under controlled conditions, this sustained dysbiosis was associated with an enhanced anti-FVIII immune response as evidenced by increased splenic B cells and the development of higher titre FVIII specific IgG antibodies following FVIII challenge. Splenic and mesenteric lymph node cytokines, T cells and dendritic cells were unaffected prior to FVIII administration. However, the immune transcriptome of both aforementioned secondary lymphoid organs was significantly modified. Short chain fatty acids (SCFA), which are microbial metabolites, were depleted in cecal contents of the dysbiotic mice. Furthermore, supplementation of the drinking water with the most immunologically active SCFA, butyrate, successfully achieved attenuation of the FVIII immune response. Collectively, our data suggest that the composition of the gut microbiome alters the FVIII immune response via the action of specific microbial metabolites on the immune cell transcriptome and that oral butyrate supplementation effectively reduces the FVIII immune response.
Mice treated with one week of ampicillin at 3 weeks of age have a dysbiotic gut microbiome throughout the study and an enhanced immune response to FVIII which was administered at 6 weeks of age. Here we assess the immune transcriptome in the mice spleen and Mesenteric lymph nodes at 6 weeks of age, just prior to exposure to FVIII challenge.

overall_design: Mice are treated with ampicillin by gavage at 3 weeks of age. At 6 weeks of age, a subset of each cohort of mice are euthanised and spleen and mesenteric lymphnodes are immediately dissected and stored in RNAlater (Invitrogen). mRNA was isolated using RNeasy Plus Mini Kit (Qiagen) and quantified, normalized and analyzed using the NanoString Mouse Immunology panel (NanoString Technologies Inc, Seattle, WA). All data was normalized to 14 housekeeping genes (nSolver). Up/down regulated genes defined as transcript fold change > 1.25 with an  = 0.05. After checking assumptions, Welch’s T Test was used to calculate p values. Expression data was standardized by calculating Z-scores and visualized in a heat map using squared Pearson distance metric with Ward’s clustering method.

first: Julie

last: Tarrant

first: Matthew

last: Cormier


title: Endogenous retroviruses are a source of oncogenic enhancers in acute myeloid leukemia [DNase-Seq]

status: Public on Sep 04 2019

city: London

first: Miguel

middle: R

last: Branco

address: 4 Newark Street

institute: Blizard Institute

summary: Endogenous retroviruses (ERVs) and other transposons can act as tissue-specific regulators of gene expression in cis, with potential to affect biological processes. In cancer, epigenetic alterations and transcription factor misregulation may uncover the regulatory potential of typically repressed ERVs, which could contribute to tumour evolution and progression. Here, we asked whether transposons help to rewire oncogenic transcriptional circuits in acute myeloid leukaemia (AML). Using epigenomic data from both primary cells and cell lines, we have identified six ERV families that are frequently found in an open chromatin state in AML when compared to differentiated myeloid cells. A subset of these AML-associated ERVs harbour enhancer-specific histone modifications, and are bound by transcription factors that play key roles in haematopoiesis and in the pathogenesis of AML. Using CRISPR-mediated genetic and epigenetic editing, we have established causal links between ERV deregulation in AML and expression changes of adjacent genes. Finally, we show that deletion and epigenetic silencing of an ERV associated with the APOC1 gene leads to growth suppression by inducing apoptosis in leukemia cell lines. Our results suggest that ERV derepression provides an additional layer of gene regulation in AML that may be exploited by cancer cells to help drive oncogenic phenotypes.

overall_design: Dnase-seq libraries were generated from OCI-AML3, Molm13 and HL-60 cell lines.

first: Ozgen

last: Deniz

first: Mamataz

last: Ahmed

first: Christopher

middle: D

last: Todd

first: Mark

middle: A

last: Dawson


title: Dts-seq: a simple method of library preparation for a highly reproducible characterization of the tRNA epitranscriptome by deep sequencing

status: Public on Aug 19 2019

city: Gif-sur-Yvette

first: Claire

last: Toffano-Nioche

address: Avenue de la Terrasse, b. 21

department: UFR des Sciences

country: France

institute: CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay

type: Non-coding RNA profiling by high throughput sequencing

summary: High-throughput sequencing of cellular tRNAs is severely hindered by the presence of base modifications. These modifications impair the reverse transcription (RT) enzyme and prevent a large fraction of transcripts to be converted into cDNA in conventional sequence library preparation. Recent attempts to circumvent this issue made use of enzymatic treatments to remove methyl groups (Cozen et al. 2015; Zeng et al. 2015). This approach is, however, not fully satisfactory because it can clear the way to the RT enzyme for only a fraction of all tRNAs. Another approach takes advantage of the interference of modifications with RT enzymes to detect and identify them in fragmented RNA transcripts (Hauenschild et al. 2015; Helm and Motorin 2017; Schwartz and Motorin 2017). In line with this second approach, we present results of an alternate method that is simpler and fully adapted to the direct characterization and quantification of mature tRNA transcripts. An analysis of the obtained read coverages enables to generate highly reproductible patterns of termination signals that can be used to assess the modification state of all tRNAs.

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

overall_design: ENA Study accession : ERP116057 ; BioProject accession: PRJEB33277

first: Ji

last: Wang

first: Florence

last: Lorieux

first: Daniel

last: Gautheret

first: Jean

last: Lehmann


title: CTCF orchestrated enhancer hijacking accelerated tumorigenesis through remodeling 3D chromosomal architecture in NTS locus [RNA-seq]

status: Public on Aug 27 2019

first: Peiwei

last: Chai

state: Shanghai

address: No.833 Zhizaoju Road

department: Opthalmology

institute: Shanghai Ninth people's hospital

summary: We identified aberrant CTCF binding lead to a 3D chromosomal interactional driver in NTS locus that accelerates tumorigenesis of uveal melanoma. Both enhancer deletion and abolishing CTCF binding lead to the loss of chromosomal looping and triggered therapeutic efficacy in inhibiting tumorigenesis. Our study shed light on a functional chromosomal architecture induced enhancer hijacking, thereby provide novel concept of 3D-chromosomal conformation exploration.

overall_design: We performed CTCF ChIP-Seq in melanoma cells and RNA-seq in 2 types of ocular melanoma cells with or without NTS promoter deletion.  Both deleted enhancer (RNAseq OCM1 sgRNA-1 RNAseq OCM1 sgRNA-2) was located in LRRIQ1 intron: 'Hg19 chr12:85,469,730-85,470,916 del'.

first: Xianqun

last: Fan


title: Endogenous retroviruses are a source of oncogenic enhancers in acute myeloid leukemia

overall_design: Refer to individual Series


title: Endogenous retroviruses are a source of oncogenic enhancers in acute myeloid leukemia [ChIP-Seq]

overall_design: H3K27ac ChIP-seq were generated from WT HL-60 and Molm13 cell lines. LRT2/2B elements were silenced in K562 and OCI-AML3 cell lines by CRISPRi with 4 sgRNAs, using the empty sgRNA vector as a control. H3K27ac and H3K9me3 ChIP-seq libraries for K562 and OCI-AML3, and dCas9 ChIP-seq libraries for K562 were generated.


title: Proteasome Inhibition as a Therapeutic Approach in Atypical Teratoid/Rhabdoid Tumors

status: Public on Sep 21 2019

city: Aurora

last: Mulcahy Levy

state: CO

institute: University of Colorado - Anschutz

summary: Generation of fpkm lists for 6 cell lines

overall_design: 6 cell lines were grown, and total mRNA extracted

first: Andrew

last: Morin

first: Bridget

last: Sanford


title: Pitfalls in Single Clone CRISPR-Cas9 Mutagenesis to Fine-map Regulatory Intervals

city: Atlanta

first: Greg

last: Gibson

state: Georgia

address: 950 Atlantic Drive

institute: Georgia Institute of Technology

summary: We report gene expression of four and three single-cell derived clones from HL60 and HL60/S4 cell lines, respectively, and the gene expression of bulk parental lines. We also report gene expression of control and mnocyte-derived HL60 (n=2, n=2, respectively) and HL60/S4 (n=2, n=2, respectively) single-cell clones, and control and neutrophil-derived HL60 (n=4, n=4, respectively) and HL60/S4 (n=4, n=4, respectively) single-cell clones.

overall_design: Single-cell clones were derived from HL60 and HL60/S4 cell lines. The transcriptome of parental clones and bulk cells was profiled by RNA-Seq. Those single-cell derived clones were then differentiated into neutrophils and monocytes. The gene expression of vehicle controls and differentiated clones was profiled by RNA-Sequencing.  Each clone with the same type of treatment or control has  two replicates.

first: Ruoyu

last: Tian

first: Yidan

last: Pan

first: Thomas

last: Etheridge

first: Harshavardhan

last: Deshmukh

first: Dalia

last: Gulick

first: Gang

last: Bao

first: Ciaran

last: Lee


title: Diversification of DNA-binding specificity via permissive and specificity-switching mutations in the ParB/Noc protein family

status: Public on Aug 05 2019

city: Norwich

first: Tung

middle: Ba  Khanh

last: Le

state: Norfolk

address: Colney Lane

department: Department of Molecular Microbiology

institute: John Innes Centre

summary: Specific interactions between proteins and DNA are essential to many biological processes.  Yet it remains unclear how the diversification in DNA-binding specificity was brought about, and what were the mutational paths that led to changes in specificity. Using a pair of evolutionarily related DNA-binding proteins, each with a different DNA preference (ParB and Noc: both having roles in bacterial chromosome maintenance), we show that specificity is encoded by a set of four residues at the protein-DNA interface. Combining X-ray crystallography and deep mutational scanning of the interface, we suggest that permissive mutations must be introduced before specificity-switching mutations to reprogram specificity, and that mutational paths to a new specificity do not necessarily involve dual-specificity intermediates. Overall, our results provide insight into the possible evolutionary history of ParB and Noc, and in a broader context, might be useful in understanding the evolution of other classes of DNA-binding proteins.

overall_design: Chromatin-immunoprecipitation with deep sequencing experiments (ChIP-seq) were performed on exponential-growing Escherichia coli (see the supplementary Materials and Methods for the exact treatment that were applied to each strain). Bacterial one-hybrid (B1H) with deep seqeuncing i.e. deep mutational scanning experiments were performed using plasmid DNA extracted from cells that were either selected on M9 minimal medium lacking (or supplemented) with histidine.

first: T

middle: B

first: N

middle: T

last: Tran

first: A

middle: S

last: Jalal

first: S

middle: E

last: Stevenson

first: X

last: Tan

first: D

last: Lawson

first: R

last: Lo

first: E

middle: W

last: Chan

last: Noy


title: Gene expression changes in Retinoic Acid-treated zebrafish Vagus motor neurons

status: Public on Aug 14 2019

city: Seattle

first: Adam

last: Isabella

state: WA

address: 1100 Fairview Ave N B2-123

institute: Fred Hutchinson Cancer Research Center

summary: Weprofiled the transcriptomes of DMSO-treated (control) and Retinoic Acid-treated zebrafish Vagus motor neurons at 38 hours post fertilization to identifiy genes that are differentially expressed between these two treatments.

overall_design: We obtained cells by dissecting the hindbrains of Tg(isl1:Kaede)-expressing embryos, dissociating to single cell suspension, and sorting for Kaede-positive cells by flow cytometry.  We sequenced 3 replicates of 4500-10000 cells per condition.

first: Cecilia

last: Moens


title: Anterior-Posterior gene expression differences in zebrafish Vagus motor neurons

summary: We profiled the transcriptome of anterior and posterior zebrafish Vagus motor neurons at 28-30 hours post fertilization to identify genes that are differentially expressed between these two cell populations.

overall_design: We obtained cells by photoconverting the  anterior or posterior 1/4 of Kaede-expressing Vagus motor neurons, dissecting the posterior hindbrain, dissociating to single cell suspension, and manually picking photoconverted cells.  We sequenced 3 replicates of 100 cells per population.

first: Gabrielle

last: Barsh


title: Identification of differentially expressed gene signature in ITLN1-treated ovarian cancer cells

first: Chi Lam

last: Au Yeung

summary: Microarray analysis was used to identify differentially expressed gene signature in ovarian cancer A224 cells treated with recombinant human ITLN1 protein. MMP1 was found to be significantly upregulated in ITLN1-treated A224 cells. Further studies revealed that MMP1 is an important mediator for the ITLN1 suppression of ovarian cancer cell motility and invasion potential.

overall_design: Ovarian cancer A224 cells were treated with PBS (Control) or 500 ng/mL recombinant human ITLN1 protein for 24 h before total RNA extraction.

first: Chi

first: Tsz

last: Yeung

first: Samuel

last: Mok


title: Discovering the anti-cancer potential of non-oncology drugs by systematic PRISM profiling

status: Public on Aug 08 2019

city: Cambridge

first: Steven

last: Corsello

address: 415 Main Street

institute: Broad Institute


title: Comparative transcriptomic analysis of WT and XP-C fibroblasts cultured in 3D-dermal equivalents

status: Public on Sep 19 2019

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

institute: IPMC/CNRS

summary: Xeroderma Pigmentosum (XP) is a rare autosomal genetic disease. XP patients present a default in the mechanism responsible for the repair of UV-induced DNA lesions. They are prone to develop skin cancers with high frequencies early in their life. To identify microenvironment factors that could contribute to the progression of skin cancers in XP-C group we did comparative transcriptomic analysis of WT and XP-C dermal patient’s fibroblasts.

overall_design: We examined the genome-wide expression profile of six primary independent fibroblast cell lines (3 WT, 3 XP-C) cultured in 3D-collagen matrices.

first: M

last: Goncalves-Maia

first: F

last: Bernerd

last: Magnaldo


title: H3K79me2 ChIP-seq and RNA-seq analysis of murine AML with DOT1L overexpressed

status: Public on Jul 10 2019

city: Philadelphia

first: Kathrin

last: Bernt

state: PA

address: 3501 Civic Center Boulevard,

institute: Children's Hospital of philadelphia


title: The pH Signaling Transcription Factor PAC-3 Regulates Metabolic and Developmental Processes in Pathogenic Fungi

status: Public on Sep 10 2019

city: Ribeirão Preto

first: Pablo

middle: Rodrigo

last: Sanches

state: SP

address: Av. Bandeirantes, 3900

department: Genetics

country: Brazil

institute: University of São Paulo

summary:
Purpose: We utilized high-throughput genomic approach to investigate transcriptional changes in two Neurospora crassa strains, the Δpac-3 knockout strain, and the Δmus-52 strain, under limited and sufficient Pi availability conditions, to evaluate the effects of the Δpac-3 deletion in gene modulation, from a plant-pathogen perspective.
Methods: All strains were maintained on solid Vogel’s Minimal (VM) medium supplemented with 2 % sucrose at 30 °C and pH 5.8. Conidia were germinated in an orbital shaker for 5 h at 30°C (200 rpm) in low- and high-Pi media (final concentrations, 10 μM or 10 mM Pi, respectively). Total RNA was isolated from both strains and a total of 4 cDNA libraries were sequenced, with their respective biological triplicates corresponding to the paired libraries, using an Illumina HiSeq2000 sequencer, to generate 100 bp paired-end reads. To assess the library quality prior to and after trimming, we used the FastQC software. To remove the sequencing bases from the end of the reads, we applied a minimum Phred score of 20. Filtered reads were mapped onto the N. crassa genome using Bowtie2 software. The reads count values were obtained and used to calculate the expression variation of the transcripts from different conditions, considering the statistical significance of the differential gene expression. qRT–PCR validation was performed using SYBR Green assays.
Results: Results from Bowtie2 analysis revealed that approximately 84% - 86% of the total high-quality reads were found to align with the reference genome of N. crassa. Furthermore, we identified 145 DEGs that were modulated regardless of the Pi concentration, however, were responsive to deletion of pac-3; while 171 DEGs were found to be modulated concomitantly with the deletion of pac-3 and with low-Pi availability. An additional 111 DEGs were found to be responsive to pac-3 deletion and high-Pi concentration. Extracellular Pi availability influenced the expression of genes involved in several biological functions.
Conclusions: We have generated a robust dataset, which advances our knowledge on regulatory mechanisms of PAC-3 within a fungus-host system. We found that in a mutually beneficial, symbiotic fungus-plant relationship (as occurs during interactions in mycorrhizal symbiosis) or during a pathogenic interaction, PAC-3 functions to regulate ambient pH while also affecting myriad of physiological functions, including adaptation to nutritional conditions, regulation of virulence, or regulating the transcription of genes associated with structural and metabolic features. Herein, we highlight the role of PAC-3 in Pi adaptation, acting as a critical regulator of environmental challenges. The widespread regulatory activity of PAC-3 in fungal physiology confirms its role in the propagation of successful infections within hosts.

overall_design: Transcriptional profile of N. crassa Δpac-3 strains using RNA-sequencing technique highlight the role of PAC-3 in Pi adaptation, acting as a critical regulator of environmental challenges.

first: Maíra

middle: P

last: Martins

first: Nilce

last: Martinez-Rossi

first: Maria

last: Bertolini

first: Eriston

middle: V

last: Gomes

first: Wellington

last: Pedersoli

first: Roberto

middle: N

last: Silva

first: Antonio

last: Rossi


title: Identification of gene signature in microdissected omental adipose tissue from high grade serous ovarian cancer patients

first: Chi Lam

last: Au Yeung

summary: Advanced ovarian cancer usually spreads to the omentum. However, the omental cell-derived molecular determinants modulating its progression have not been thoroughly characterized. Transcriptome profiling was performed on microdissected omental adipose tissue obtained from patients with benign gynecologic diseases and on cancer-associated omental tissue obtained from patients with advanced-stage, high grade serous ovarian cancer.

overall_design: Microarray analysis was performed on four microdissected omental adipose tissue from patients with benign gynecologic diseases and ten cancer-associated omental tissue obtained from patient with high grade serous ovarian cancer

middle: L

middle: C


title: H3K79me2 ChIP-seq analysis of murine AML with DOT1L overexpressed

summary: We transduced two individual murine KMT2A-MLLT3 AML samples with DOT1L and three days after sorting for DOT1L+ cells were collected for ChIP-Seq. Before beginning the ChIP protocol drosophila melanogaster (S2) cells were spiked in at a 1:2 ratio.

overall_design: Examination of H3K79me2 profiles murine KMT2A-MLLT3 AML cells with DOT1L overexpressed

first: Molly

last: Kingsley


title: RNA-seq analysis of murine KMT2A-MLLT3 with DOT1L overexpressed

summary:
We transduced two individual murine KMT2A-MLLT3 AML samples with DOT1L and three days after sorting for DOT1L+ cells collected for RNA-seq
MLL-rearranged leukemias have been previously shown to be dependent on the presence of histone 3 lysine 79 (H3K79) dimethylation on the genomic targets of the fusion, and an inhibitor of the H3K79 methyltransferase DOT1L is in clinical trials for MLL-rearranged leukemia. In order to ask what biologic effects overexpression of DOT1L would have on the H3K79me2 ChIP-Seq profiles and MLL-fusion target gene expression,  murine leukemias generated by transplanting MSCV-MLL-AF9-GFP transduced lin- cKit+ Sca1+ bone marrow cells were subjected to overexpression of DOT1L. Cells were sorted into low (low level of DOT1L overexpression), high (high level of DOT1L overexpression) and bulk (entire population) samples, and subjected to H3K79me2 ChIP-Seq (using a drosophila spike in for normalization) and RNA-Seq analysis 3 days after transduction.

overall_design: mRNA from murine KMT2A-MLLT3 AML with DOT1L overexpressed was submitted for RNA-seq


title: Quinoa gene expression under shoot or root heating

status: Public on Jul 31 2019

city: St. Louis

first: Malia

last: Gehan

state: MO

address: 975 N Warson Road

institute: Donald Danforth Plant Science Center

summary: Quinoa is a highly nutritious seudocereal crop that is not well adapted to heat. Improving understanding of quinoa responses to heat would help expand its cultivation to regions with warmer climates. This study profiled gene expression of quinoa plants from accession QQ74 (PI 614886) treated with high tempreatures during anthesis of the main panicle, which lasted 11 days. Heat was applied in four different treatments to profile gene expression changes from root or shoot heating. Treatments were: 1. control with both roots and shoots at 22°C, 2. heated roots with roots at 30°C and shoots at 22°C, 3. heated shoots with roots at 22 °C and shoots at 35°C, and 4. heated roots and shoots with roots at 30°C and shoots at 35°C. Healthy leaves from 3 plants per treatment were sampled from the mid section of the plants, during the first (day 1) and last day (11) of heat treatment, at Zeitgeber time 2. Gene expression of each of the three heat treatments was compared to control using the Kallisto-Sleuth pipeline. These gene expression profiles of quinoa under heat are made available as a community resource to improve understanding of quinoa responses to heat.

overall_design: Quinoa QQ74 (PI 614886) root vs. shoot heating 2x2 factorial design, with 4 treatments: 1. control with both roots and shoots at 22°C, 2. heated roots with roots at 30°C and shoots at 22°C, 3. heated shoots with roots at 22 °C and shoots at 35°C, and 4. heated roots and shoots with roots at 30°C and shoots at 35°C. Heat treatment started at first anthesis and lasted 11 days. Leaf tissue from 3 plants was sampled from each treatment, during days 1 and 11 of heat, for a total of 24 samples analyzed. Each plant was considered a replicate.

first: Jose

last: Tovar

first: Carlos

last: Quillatupa

last: Callen

first: Sonia

last: Castillo

first: Paige

last: Pearson

first: Anastasia

last: Shamin

first: Haley

last: Schuhl

first: Noah

last: Fahlgren


title: Transcriptome analysis by expression microarrays of endometrial cancer derived from the Cancer Institute Hospital of Japanese Foundation for Cancer Research.

status: Public on Sep 13 2019

city: Koto

first: Akihisa

last: Takahara

state: Tokyo

institute: Japanese Foundation For Cancer Research

summary: We performed the expression microrarray experiments for mRNA of endometrial cancer tissue.

overall_design: Messenger RNA were extracted from primary tumor of 66 endometrial cancer patients (64 Carcinoma samples and 33 Hyperplasia samples), hybridized and scanned with Affymetrix?HG-U133 plus2.0 Array.

first: Yuko

last: Sugiyama


title: Effect of Bangle extract and cis-Banglene on human NSC neuronal differentiation

status: Public on Jun 30 2019

city: Tsukuba

first: Kazumi

last: Hirano

state: Ibaraki

address: 1-1-1 Higashi

department: Biomedical

institute: AIST

summary: To trace the mechanisms by which Bangle extract and cis-Banglene (c-Banglen) promote neurogenesis of hfNSCs, we performed genome-wide gene expression profiling by microarray analysis in control hfNSCs and these extracts treated cells.

overall_design: Treatment of Bangle extract and cis-Banglene for 2 days during neuronal differentiation of hfNSCs.

first: Masakazu

last: Namihira


title: E-cadherin suppresses invasion and promotes metastasis in multiple breast cancer models

status: Public on Jun 24 2019

city: Baltimore

first: Andrew

last: Ewald

state: MD

address: 855 N. Wolfe Street, 452 Rangos Bldg.

department: Cell Biology

institute: Johns Hopkins University

summary: E-cadherin (E-cad) mediates cell-cell adhesion and has been proposed to suppress both invasion and metastasis. However, invasive ductal cancers retain E-cad expression in the primary tumor, circulating tumor cells, and distant metastases. We recently demonstrated that cancer cell clusters are efficient metastatic seeds. Since clusters organize through cell-cell adhesion, we tested the requirement for E-cad in genetically engineered mouse models of luminal and basal breast cancer. Loss of E-cad increased invasion and dissemination in 3D culture and in the mammary gland. However, E-cad loss also reduced cancer cell proliferation, survival, tumor cell seeding, and metastatic outgrowth in the lungs. At the transcript level, loss of E-cad was associated with increased apoptosis. Consistent with these results, inhibition of apoptosis partially rescued the metastatic phenotype of E-cad null cancer cells. We therefore propose that E-cad is an invasion suppressor, survival factor, and metastasis promoter in invasive ductal cancers.

overall_design: Differential gene expression analysis between organoids isolated from  adeno-Cre transduced MMTV-PyMT E-cad+/+ (r = 4 biological replicates) and adeno-Cre transduced MMTV-PyMT E-cadfl/fl (r = 5 biological replicates)

middle: J

first: Joel

last: Bader


title: Endogenous retroviruses are a source of oncogenic enhancers in acute myeloid leukemia [RNA-Seq]

first: Miguel

last: Branco

summary: Endogenous retroviruses (ERVs) and other transposons can act as tissue-specific regulators of gene expression in cis, with potential to affect biological processes. In cancer, epigenetic alterations and transcription factor misregulation may uncover the regulatory potential of typically repressed ERVs, which could contribute to tumour evolution and progression. Here, we asked whether transposons help to rewire oncogenic transcriptional circuits in acute myeloid leukaemia (AML). Using epigenomic data from both primary cells and cell lines, we have identified six ERV families that are frequently found in an open chromatin state in AML when compared to differentiated myeloid cells. A subset of these AML-associated ERVs harbour enhancer-specific histone modifications, and are bound by transcription factors that play key roles in haematopoiesis and in the pathogenesis of AML. Using CRISPR-mediated genetic and epigenetic editing, we have established causal links between ERV deregulation in AML and expression changes of adjacent genes. Finally, we show that deletion and epigenetic silencing of an ERV associated with the APOC1 gene leads to growth suppression by inducing apoptosis in leukemia cell lines. Our results suggest that ERV derepression provides an additional layer of gene regulation in AML that may be exploited by cancer cells to help drive oncogenic phenotypes.

overall_design: LRT2/2B elements were silenced in K562 and OCI-AML3 cell lines by CRISPRi with 4 sgRNAs, using the empty sgRNA vector as a control. RNA-seq libraries were generated.

first: Ozgen

last: Deniz

first: Mamataz

last: Ahmed

first: Christopher

last: Todd

first: Mark

last: Dawson


title: Transcriptome Analysis and Functional Identification of Adipose-Derived Mesenchymal Stem Cells in Secondary Lymphedema

status: Public on Jun 19 2019

city: Beijing

first: Zhou

last: Zhou

address: Beilishi Street 167, Xi Cheng District

institute: Fuwai Hospital, the Chinese Academy of Medical Sciences

summary: We isolated adipose-derived mesenchymal stem cells (ASCs) from the lymphedema adipose tissue from liposuction specimens of 10 patients with malignancy-related extremity lymphedema, and we used adipose tissue from the normal upper abdomen of the same patients as control tissue. We compared the proliferation and adipogenic differentiation capacity between the two kinds of ASCs, and we explored the transcriptomic differences between them. We found that lymphedema-associated ASCs had more rapid proliferation and a higher adipogenic differentiation capacity. CDK1 inhibitors could return the abnormal biological characteristics of these cells to normal phenotype, suggesting that CDK1 is a key driver of proliferation and adipogenic differentiation in these cells, which might expound the accumulation of adipose tissue extensively observed in secondary lymphedema, indicating the CDK1 may be a potential target for lymphedema therapy. On the other hand, our finding showed that ASCs from lymphedema adipose tissues have higher immunosuppressive effect, and the inhibition of up-regulated cytokine CHI3L1 may be clinically beneficial. In summary, explore the underlying mechanisms of fat deposition in lymphedema may provide powerful strategies for the treatment of lymphedema.

overall_design: mRNA sequencing of ASCs from the affected thighs of 10 patients with lymphedema, and as control, ASCs from the normal upper abdomen of the same patients were also sequenced.

first: Xuanyu

last: Liu


title: Transcriptional profiling of LS1034 cells treated with tepoxalin

first: Steven

last: Corsello

summary:
LS1034 colorectal cancer cells were treated with DMSO vehicle control or 12 uM tepoxalin for 6 hours.
Anti-cancer uses of non-oncology drugs have been found on occasion, but such discoveries have been serendipitous and rare. To fully discover activity against multiple tumor types, resource-intensive screening across hundreds of cancer cell lines is needed. We sought to create a public resource containing the growth inhibitory activity of 4,518 drugs tested across 578 human cancer cell lines. To accomplish this, we used PRISM, which involves the molecular barcoding of each cell line, followed by pooling of the barcoded lines. Relative barcode abundance following drug treatment versus controls thus reflects cell viability following drug treatment. We found that an unexpectedly large number of non-oncology drugs selectively inhibited subsets of cancer cell lines. Moreover, the killing activity of the majority of these drugs was predictable based on the molecular features of the cell lines. Mechanistic follow-up of several of these compounds revealed novel mechanisms. These results illustrate the potential of the PRISM drug repurposing resource as a starting point for new oncology therapeutic development.

overall_design: 6 samples total:  LS1034 cells treated with tepoxalin for 6 hours (triplicate) or DMSO vehicle control (triplicate)

first: Todd

last: Golub

middle: M

first: Vickie

last: Wang


title: Genetic and Epigenetic Fine Mapping of Complex Trait Associated Loci in the Human Liver

status: Public on Jun 13 2019

first: Minal

last: Caliskan

address: 415 Curie Blvd., Room 540

institute: University of Pennsylvania

summary: Deciphering the impact of genetic variation on gene regulation is fundamental to understanding common, complex human diseases. In this study, we obtained genome-wide RNA-Seq and ChIP-Seq (for H3K4me3 and H3K27ac histone modifications) data in the human liver. We mapped quantitative trait loci (QTLs) of gene expression levels and histone modification states. We integrated our findings with summary statistics of genome-wide association studies (GWAS) and identified candidate genes, gene regulatory regions, and variants in GWAS loci.

overall_design: RNA-Seq data were obtained from 49 (Penn Cohort 1) + 96 (Penn Cohort 2) individuals. ChIP-Seq data were obtained from 9 and 18 individuals (Penn Cohort 1) for H3K4me3 and H3K27ac marks, respectively.

last: Brown


title: Transcriptional profiling of SF295 cells following MTF1 knockout by CRISPR/Cas9

summary:
SF295 glioblastoma cells were subjected to CRISPR/Cas9-mediated knockout of the MTF1 (metal regulatory transcription factor 1) gene or non-targeted control (GFP). Two guides targeting MTF1 and one guide targeting GFP were cloned into the pXPR_023 all-in-one CRISPR/Cas9 vector. SF295 cells were transduced by lentiviral infection and selected using puromycin. Following selection, RNA was harvested from cell lines growing in culture. Wild-type SF295 cells were also included as a control.
Anti-cancer uses of non-oncology drugs have been found on occasion, but such discoveries have been serendipitous and rare. To fully discover activity against multiple tumor types, resource-intensive screening across hundreds of cancer cell lines is needed. We sought to create a public resource containing the growth inhibitory activity of 4,518 drugs tested across 578 human cancer cell lines. To accomplish this, we used PRISM, which involves the molecular barcoding of each cell line, followed by pooling of the barcoded lines. Relative barcode abundance following drug treatment versus controls thus reflects cell viability following drug treatment. We found that an unexpectedly large number of non-oncology drugs selectively inhibited subsets of cancer cell lines. Moreover, the killing activity of the majority of these drugs was predictable based on the molecular features of the cell lines. Mechanistic follow-up of several of these compounds revealed novel mechanisms. These results illustrate the potential of the PRISM drug repurposing resource as a starting point for new oncology therapeutic development.

overall_design: Eleven biological samples are included in the study. SF295 wild-type cells (control, duplicate), SF295 GFP sg1 (non-targeting guide control, triplicate), SF295 MTF1 sg1 (triplicate), and SF295 MTF1 sg2 (triplicate).

middle: R


title: Transcriptomic comparison between nickel hyperaccumulator and non-accumulator plant species from the Psychotria genus (Rubiacaeae) endemic from New Caledonia

status: Public on Jun 05 2019

city: Auzeville Tolosane

first: Sylvain

last: MERLOT

address: 24, chemin de Borde Rouge

department: Biological Sciences

institute: CNRS

summary: The leaf transcriptome of the nickel hyperaccumulator Psychotria gabriellae (Rubiaceae) endemic from New Caledonia was compared to the closely related non-accumulator Psychotria semperflorens, living in sympatry with P. gabriellae in rain forest on serpentine soil, to identity differentially expressed genes potentially involved in Ni hyperaccumulation.

sample_organism:
Psychotria gabriellae
Psychotria semperflorens

overall_design: Leaves from 3 independant individual plants of Psychotria gabriellae and Psychotria semperflorens were collected in their natural environment. RNA of the 6 independant samples were extracted and sequenced using the Illumina paired-end sequencing technology. Reads from one individual plant per species were assembled de novo to generate transcriptome sequences. The transcriptome of P. gabriellae was used as a reference to compare the expression of genes in both species.

first: Vanesa

last: Garcia de la Torre

first: Clarisse

last: Majorel-Loulergue

first: Louis-Charles

last: Brinon

first: Ludivine

last: Soubigou-Taconnat

first: Valérie

last: Burtet-Sarramegna

first: Bruno

last: Fogliani

last: Merlot


title: Transcriptomic comparison between nickel hyperaccumulator and non-accumulator plant species from the Geissois genus (Cunoniaceae) endemic from New Caledonia

summary: The leaf transcriptome of the nickel hyperaccumulator Geissois pruinosa (Rubiaceae) endemic from New Caledonia was compared to the closely related non-accumulator Geissois racemosa, living respectively in serpentine maquis or rainforest on limestone, to identity differentially expressed genes potentially involved in Ni hyperaccumulation.

sample_organism:
Geissois pruinosa
Geissois racemosa

platform_organism:
Geissois pruinosa
Geissois racemosa

overall_design: Leaves from 3 independant individual plants of Geissois pruinosa and Geissois racemosa were collected in their natural environment. RNA of the 6 independant samples were extracted and sequenced using the Illumina paired-end sequencing technology. Reads from one individual plant per species were assembled de novo to generate transcriptome sequences. The transcriptome of G. pruinosa was used as a reference to compare the expression of genes in both species.


title: Transcriptomic comparison between nickel hyperaccumulator and non-accumulator plant species from the Noccaea genus (Brassicaceae) from France

summary: The leaf transcriptome of the nickel hyperaccumulator specie Noccaea caerulescens subsp. fimiensis living on serpentine soils were compared to the closely related non-nickel-accumulators   Noccaea caerulescens "Viviez" growing on a zinc mining site and Noccaea montana living on serpentine soil, to identity differentially expressed genes potentially involved in Ni hyperaccumulation.

sample_organism:
Noccaea caerulescens
Thlaspi montanum

platform_organism:
Noccaea caerulescens
Thlaspi montanum

overall_design: Leaves from 2 independant individual plants of  Noccaea caerulescens subsp. fimiensis, Noccaea caerulescens "Viviez" and Noccaea montana were collected in their natural environment. Leaves and roots were also collected from Noccaea caerulescens subsp. firmensis and Noccaea montana hydroponically grown (Araponics, Liège, Belgium) with modified Hoagland’s  solution, supplemented with 20 μM Fe-HBED and 37.5 μM NiCl2 during 7 weeks. RNA of the 10 independant samples were extracted and sequenced using the Illumina paired-end sequencing technology. Reads of roots and leaves from one individual sample hydroponically  grown were assembled de novo to generate transcriptome sequences. The transcriptome of Noccaea caerulescens subsp. fimiensis was used as a reference to compare the expression of genes in the three species


title: Transcriptome Analysis of Tomato Genotypes in Response to Bacterial spot (Xanthomonas perforans) Race T4 Inoculation

status: Public on Aug 02 2019

city: Raleigh

first: Ramsey

last: Lewis

state: NC

address: 101 Derieux PI

department: Crop and Soil Sciences Department

institute: North Carolina State University

summary:
Purpose: Investigate genes associated to resistance of  Xanthomonas perforans race T4 in tomato line with different resistance level
Methods: Resistant and susceptible tomato breeding lines were subjected to the inoculation with Xanthomonas perforans race T4 followed by sample collection at 48 hpi and RNA-seq analysis for screening differential expressed genes associated with inoculation of pathogen.
Results: Revealed gene expression profiles associated disease resistance and susceptiblilty.

first: Dillip

last: Panthee

first: Rui

last: Shi


title: Transcriptomic Analysis of Cellular Pathways during Healing of Flexor Tendons in Plasminogen Activator Inhibitor Type 1, Member 1 (PAI-1/Serpine1) Null Mice

status: Public on May 31 2019

city: Rochester

first: Hani

last: Awad

state: NY

address: 601 Elmwood Avenue

department: Biomedical Engineering

institute: University of Rochester

summary: Injuries to flexor tendons can be complicated by fibrotic adhesions, which severely impair the function of the hand. Adhesions have been associated with PAI-1, a master suppressor of protease activity including matrix metalloproteinases (MMP). In the present study, we used next generation RNA sequencing (RNA-seq) to assess genome-wide differences in mRNA expression due to PAI-1 deficiency after zone II flexor tendon injury. Ingenuity pathway analysis was used to characterize molecular pathways and biological drivers associated with differentially expressed genes. Analysis of hundreds of overlapping and differentially-expressed genes in PAI-1 knockout and C57Bl/6J mice during tendon healing revealed common and distinct biological processes associated with the regulation of matrix organization, cell cycle, and immune response. Most importantly, we identified the activation of PTEN signaling and the inhibition of FOXO1-associated biological processes as a unique transcriptional signature of the healing tendon in the PAI-1 KO mice. The differences in transcriptomics between the two mouse strains are transcriptionally related to complex cross-talk between PI3K/Akt/mTOR, PKC, and MAPK signaling cascades that drive differences in transcriptional regulation of cell proliferation, survival and senescence, and chronic inflammation as potential drivers of fibrotic healing and adhesions in the C57Bl/6J injured tendons. These transcriptional observations should guide future studies to develop an improved understanding of the biological limitations of tendon healing as the basis for rational design of targeted therapeutics for scar-free regenerative healing of tendon.

overall_design: Tendon tissue (n = 3 per group) was harvested from uninjured, 2-weeks, and 4-weeks post injury tendons of WT and PAI-1 KO mice