title: Evolved Levels of Placental Invasion in Human and Bovine Endometrial Stroma

status: Public on Oct 24 2019

city: Farmington

first: Yasir

last: Suhail

state: Connecticut

address: 263 Farmington Avenue

department: BME

institute: UCHC

summary: Among mammals, the extent of placental invasion is correlated with vulnerability to malignancy. Animals with more invasive placentation (e.g. humans) are more vulnerable to malignancy, whereas animals with a non-invasive placenta (e.g. ruminants) are less likely to develop malignant cancer. To explain this correlation,we propose the hypothesis of Evolved Levels ofInvasibility (ELI) positing that the permissiveness of stromal tissue to invasion is a unitary character affecting both placental and cancer invasion. We provide evidence for this hypothesis by contrasting invasion of human and bovine cancer and placental cells into a lawn of stromal cells from different species. We find that both bovine endometrial andskin fibroblasts are more resistant to invasion of placental and cancer cells than their human counterparts. Gene expression profiling identified genes with high expression in human but not bovine fibroblasts. Knocking down of a subset of them in human fibroblasts leads to significantly stronger resistance to cancer cell invasion. Comparative analysis of gene expression among mammals suggests that humans evolved higher vulnerability to malignancy than the eutherian ancestor, possibly as a correlate of more invasive placentation, and boroeutherians evolved to decrease stromal invasibility. Identifying the evolutionary determinants of stromal invasibility can provide significant insights to developrational anti-metastatic therapeutics.

sample_organism:
Homo sapiens
Bos taurus

platform_organism:
Homo sapiens
Bos taurus

overall_design: 3 samples each of human and bovine endometrial stromal trophoblasts were sequenced with and without co-culture with their respective trophoblasts

first: Günter

middle: P

last: Wagner

first: Kshitiz

last: Gupta


title: Profiling the effect of Nafcillin on HA-MRSA D712 using bacteriological and physiological media

status: Public on Oct 22 2019

city: San Diego

first: Akanksha

last: Rajput

state: California

address: 417 Powell-Focht Bioengineering Hall, 9500 Gilman Drive La Jolla, CA 92093-0412  Contact Us  In Silico Lab:  858-822-1144

department: Bioengineering

country: USA

institute: University of California San Diego

type: Expression profiling by high throughput sequencing

summary: Vancomycin Intermediate Staphylococcus aureus (VISA) strain originated during the prolonged hospitalization, chronic infection and vancomycin treatment. The hospital acquired  D712 VISA strain were subjected to various sub-inhibitory concentration of nafcillin in Cation Adjusted Mueller Hinton Broth (CA-MHB) and Roswell Park Memorial Institute (RPMI) medium. The MIC of has dropped from 256 ug/ml to 1ug/ml in CA-MHB and RPMI media respectively. The cells were harvested and expression profiling were measured using RNA sequencing at time point of 03 hours.

overall_design: Staphylococcus aureus were treated with various sub-inhibitory concentration of Nafcillin in CA_MHB and RPMI + 10% LB media.


title: Reciprocal reprogramming of host and endophyte metabolic pathways upon symbiosis of Arabidopsis with Enterobacter sp. SA187

status: Public on Nov 10 2019

city: Thuwal

first: Hanin

last: ALZUBAIDY

address: 4700 KAUST

country: Saudi Arabia

institute: KAUST

summary: Dual transcriptome of Enterobacter sp. SA187 along with Arabidopsis thaliana root

overall_design: mRNA-seq of Enterobacter sp.SA187 and Arabidopsis thaliana

last: Alzubaidy

first: Cristina

last: Andres-Barrao

first: Rewaa

last: Jalal

first: Axel

last: de Zelicourt

first: Maged

last: Saad

first: Ameerah

last: Bokhari

first: Heribert

last: Hirt


title: MiRNA expression profiling in cholangiocarcinoma (CCA) cells compared to non-malignant human cholangiocyte

status: Public on Oct 19 2019

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: 10-1 tebiro 6-chome

country: Japan

institute: Toray Industries,Inc.

summary: Expression profiling of 2555 miRNAs was performed using microarray. Of these, 508 miRNAs expressed in both of CCA and non-malignant human cholangiocyte.

overall_design: In the study presented here, we used CCA cells, HuccT1 and non-malignant human cholangiocyte, MMNK-1 cells. MiRNAs expression was analyzed by comparing in HuccT1 cells and MMNK-1 cells.

first: Kenji

last: Takahashi

first: Yu

last: Ota


title: Thermo Fisher Scientific OncoScan expression array data for undifferentiated uterine sarcomas (expression)

status: Public on Aug 23 2019

city: Stockholm

first: Joseph

middle: Woodward

last: Carlson

address: P1:02 Radiumhemmet

department: Oncology-Pathology

country: Sweden

institute: Karolinska Institutet

overall_design: undifferentiated uterine sarcomas


title: Pooled CRISPR screens with imaging on microRaft arrays reveals stress granule-regulatory factors

status: Public on Nov 02 2019

city: La Jolla

first: Gene

last: Yeo

state: CA

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

institute: UCSD

summary: Here, we introduce CRaft-ID (CRISPR-based microRaft followed by gRNA identification) to enable the screening of image-based phenotypes such as subcellular protein localization from a pool of lenti-CRISPR bulk infected cells. Clonal colonies selected from microRaft arrays are isolated after phenotyping for a targeted-sequencing library preparation to identify the infected sgRNA in each colony. sgRNA representation in the pool of cells is measured with a targeted-sequencing library preparation from the bulk sample.

overall_design: Targeted-sequencing of sgRNA insert in the genome from a bulk sample of cells or individual microRaft cell colonies.

first: Emily

middle: C

last: Wheeler

first: Anthony

middle: Q

last: Vu

first: Matthew

last: DiSalvo

first: Jaclyn

middle: M

last: Einstein

first: Noorsher

last: Ahmed

first: Wenhao

last: Jin

first: Nancy

middle: L

last: Allbritton

middle: W

first: Eric

last: Van Nostrand

first: Alexander

middle: A

last: Shishkin


title: Thermo Fisher Scientific OncoScan expression array data for undifferentiated uterine sarcomas (CNV)


title: Chronic stress induces activity, synaptic and transcriptional remodeling of the lateral habenula associated with deficits in motivated behaviors

status: Public on Sep 16 2019

city: Zurich

first: Csaba

last: Földy

state: Zurich

address: Winterthurerstrasse 190

department: Brain Research Institute

country: Switzerland

institute: University of Zurich

summary: Chronic stress (CMS) affects many brain functions and is a major risk factor for the development of depression. Here, we demonstrate that CMS-induced hyperactivity in VTA-projecting lateral habenula (LHb) neurons is associated with increased passive coping (PC) but not anxiety or anhedonia. LHb→VTA neurons in mice with increased PC show increased burst and tonic firing as well as synaptic adaptations in excitatory inputs from the entopeduncular nucleus (EP). In-vivo manipulations of EP→LHb or LHb→VTA neurons selectively alter PC and effort-related motivation. Conversely, dorsal raphe (DR)-projecting LHb neurons do not show CMS-induced hyperactivity and are targeted indirectly by the EP. Using single-cell transcriptomics we reveal a set of genes that can collectively serve as biomarkers to identify mice with increased PC and differentiate LHb→VTA from LHb→DR neurons. Together, we provide a set of biological markers at the level of genes, synapses, cells and circuits that define a distinctive CMS-induced behavioral phenotype.

overall_design: 20 mice were analyzed for a total of 73 LHb cells. 6 mice (27 cells) were stressed, and 14 mice (46 cells) were not stressed. 19 cells were projecting to the Dorsol Raphe, and 54 cells were projecting to the VTA

first: Ignas

last: Cerniauskas

first: Jochen

last: Winterer

first: Johannes

last: de Jong

first: David

last: Lukacsovich

first: Hongbin

last: Yang

first: Fawwad

last: Khan

first: James

middle: R

last: Peck

first: Sophie

middle: K

last: Obayashi

first: Varoth

last: Lilascharoen

first: ByungKook

last: Lim

last: Földy

first: Stephan

last: Lammel


title: Expression data from human foreskin fibroblast and human iduced pluripotent stem cell

status: Public on Aug 06 2019

city: Solna

first: Pierre

last: Sabatier

address: Solnavägen 9

department: Medical Biochemistry and Biophysics

summary:
Pluripotent cells are important and unique because of unprecedently high proliferation and differentiation potentials. The state of pluripotency is robust enough to sustain years of uninterrupted proliferation in vitro, but, once lost, there is a significant barrier for differentiated cells to regain pluripotency. By now, reprogramming of somatic cells into a pluripotent state is unambiguously proven only for methods that necessarily involve ectopic expression or direct delivery of exogenous factors inside the cells. Molecular mechanisms that provide robustness to the state of pluripotency and sustain the barrier between pluripotent and differentiated cells are not fully understood.
We reprogrammed human foreskin fibroblasts into human induced pluripotent stem cells using CoMiP 4in1 plasmid without shRNA p53.

overall_design: Human foreskin fibroblasts were reprogrammed into human induced pluripotent stem cells and both cell lines were grown until exponential growth phase. We then extracted mRNA for hybridization on Affymetrix microarrays.


title: Gene expression predicts histological severity and reveals distinct molecular profiles of nonalcoholic fatty liver disease

status: Public on Aug 15 2019

city: Charlottesville

first: Stephen

middle: Aurelien

last: Hoang

state: Virginia

address: 501 Locust Ave, Suite 301

institute: HemoShear Therapeutics

summary: Transcriptomic analysis of liver biopsies that cover the spectrum of nonalcoholic fatty liver disease reveals genes that are progressively regulated over the course of the disease. This study demonstrates that progressive changes in expression of these genes can be used to approximate the histological grade of a liver biopsy. Furthermore, the relative progression profiles of these disease-responsive genes are shown to be distinct across patient biopsies. This observation suggests that there may be distinct biological processes that drive disease progression across individuals

overall_design: This dataset contains transcriptomic profiles of 78 distinct human liver biopsies.  Of these, 6 are histologically normal, and 72 cover the full spectrum of nonalcoholic fatty liver disease (NAFLD activity score 0-6, fibrosis stage 0-4).

first: Abdul

last: Oseini

first: Ryan

middle: E

last: Feaver

first: Banumathi

last: Cole

first: Amon

last: Asgharpour

first: Robert

last: Vincent

first: Mohammad

last: Siddiqui

first: Mark

middle: J

last: Lawson

first: Nathan

last: Day

first: Justin

last: Taylor

first: Brian

last: Wamhoff

first: Faridoddin

last: Mirshahi

first: Melissa

last: Contos

first: Michael

last: Idowu

first: Arun

last: Sanyal


title: LncRNA Expression Profile and Identification of Novel LncRNA Biomarkers for Diagnosing Coronary Artery Disease

status: Public on Aug 17 2019

city: Beijing

first: Lin

last: Li

state: Beijing

address: Xicheng District, No.167 Beilishi Road

department: Department of Epidemiology

country: China

institute: Department of Epidemiology, State Key Laboratory of Cardiovascular Disease

summary: Dysregulation of long non-coding RNAs (lncRNAs) has been proven to be involved in the pathogenesis of coronary artery disease (CAD). However, it remains to be extensively explored.Using microarray, we performed the transcriptome-wide lncRNA and mRNAs expression profile in peripheral blood mononuclear cells (PBMCs) of 93 CAD patients and 48 healthy controls. Gene Ontology (GO) and pathway analysis for differentially expressed mRNAs was used to investigate underlying biological associations of differentially expressed lncRNAs and create path-net to depict interactions of significant pathways.  We identified 1,210 lncRNAs and 890 mRNAs differentially expressed from the expression profile and validated selected 7 lncRNAs. Two novel lncRNA biomarkers, ENST00000444488.1 and uc010yfd.1, together with CAD risk factors had the better predictive performance for discriminating CAD patients from healthy controls, and ENST00000444488.1 could diagnose acute myocardial infarction (AMI) patients from non-AMI patients.

overall_design: 93 Coronary Artery Disease patients and 48 healthy controls

first: Laiyuan

last: Wang


title: N4-cytosine DNA methylation is involved in the maintenance of genomic stability in Deinococcus radiodurans

status: Public on Jul 27 2019

city: Hangzhou

first: Shengjie

address: No. 268, Yuhang Tang Road

institute: Zhejiang University

summary:
Purpose: DNA methylation has a global impact on gene expression
Methods: Gene expression profiles of D. radiodurans R1 wild type and ΔM.DraR1 strains were generated by deep sequencing using Illumina HiSeqTM2500.
Results: RNA-seq was used for differential expression gene analysis between wild-type and ΔM.DraR1 strains. A total of 1158 genes (766 upregulated genes and 392 downregulated genes) were differentially expressed in ΔM.DraR1 strain. GO enrichment analysis revealed that upregulated unigenes were significantly enriched in twelve subcategories. The majority of unigenes in the biological process category were associated with macromolecule metabolic processes. Interestingly, a number of unigenes were also associated with DNA recombination. Within the molecular function category, most unigenes were assigned to nucleic acid, DNA binding and hydrolase, and nucleoside triphosphatase activity. The KEGG enrichment analytical scatter diagram showed that the major pathways affected in the deletion strain belonged to ABC transport, two-component systems, DNA replication, homologous recombination, and protein export pathways. The majority of DNA damage response genes, such as ddrA, ddrB, ddrO, ddrG, ddrJ, ddrK, ddrD and pprA, were significantly upregulated. Several genes involved in DNA recombinational repair pathway including recA, recO, rexD, and ruvB were also significantly upregulated. Putative competence genes, including those encoding prepilin peptidase, CRP and CinA, were upregulated in the mutant strain. This gene expression pattern of the ΔM.DraR1 strain resembled that of D. radiodurans during recovery after exposure to acute radiation, indicating that the absence of N4-cytosine DNA methylation may result in intracellular stress.
Conclusion: Absence of N4-cytosine DNA Methylation in D. radiodurans Leads to Expression Changes of Proteins Involved in DNA Damage Response

overall_design: Gene expression profiles of D. radiodurans R1 wild type and ΔM.DraR1 strains were generated by deep sequencing using Illumina HiSeqTM2500. The raw reads were deposited in the Sequence Read Archive (SRA) database of NCBI. The bioProject accession is PRJNA532990, and the SRA Study accession is SRP192667.

first: Yuejin

last: Hua


title: Neurosphere cultures transfected with nonsense & miRNA-335 knockout reagents

status: Public on Jul 31 2019

city: Bryan

first: Rajesh

last: Miranda

address: 8447 Riverside Parkway

institute: Texas A&M University

summary: To understand the mechanism by which miR-335 acts anti proliferative factor, we profiled mRNA expression using microarray platform ( codelink array). Embryonic day 12.5 neural cortical epithelium was isolated and grown as neurospheres in defined medium. Cultures were transfected with 2'-O-methyl (2'OMe)-base modified miRNA-335 antisense (2'OMe-335) and control (2' O Me-EGFP). To verify the suppression of miR-335 after the 2'-OMe treatment, we used real time RT-PCR which confirmed the down regulation of miR-335 up to ~4.5 cycles (~24 fold). For the microarray experiment, mRNA isolated from these cells was hybridized to codelink microarrays. Three independent replicate were done for treatment and control, six independent single channel intensity values were uploaded  after normalization for analysis.   Our array results indicated that there is general up-regulation in gene expression due to miR-335 Knock Out ( KO).  We identified 116 genes statistically significant genes (adjusted p value < 0.05), out of these 95.7% were up-regulated genes. The highest fold difference we observed was between 2 and 3 fold, indicating the role of this miRNA in moderately controlling expression hundreds of genes. Of the several genes the highly expressed are important in maturation of neural stem cells and downstream signaling pathway genes

overall_design: Three independent replicates were done for treatment and control, six independent single channel intensity values were uploaded  after normalization for analysis


title: Longitudinal Blood Transcriptomic Changes Predict Lung Function Decline in patients with Idiopathic Pulmonary Fibrosis

status: Public on Sep 30 2019

first: Yong

last: Huang

state: VA

address: 1340 Jefferson Park Ave

department: Medicine

institute: University of Viginia

summary:
Rationale: Molecular markers of disease progression in idiopathic pulmonary fibrosis are needed.
Objective: Derive and validate a blood transcriptomic predictor of forced vital capacity (FVC) decline.
Methods: A training cohort (n=74) of IPF patients was stratified according to the presence of progressive disease, defined as ≥10% relative decline in FVC over 12 months. Baseline to 4-month within-patient changes in gene expression were correlated with categorical FVC decline. Genes predictive of FVC decline were identified by two-group comparison with false discovery rate <5% followed by logistic LASSO regression and 10-Fold Cross-Validation for gene list prioritization. Independent validation cohorts with differing transcriptome assay platforms and blood transcriptome sampling times from UChicago (n=27), UPMC (n=35), and Imperial (n=24) underwent receiver operating characteristic with area under the curve (AUC) analyses for validation.
Results: A longitudinally-derived FVC-gene predictor accurately discriminated most patients with stable and progressive IPF across four independent IPF cohorts with variable transcriptomic assay platforms and sampling times. The FVC-gene predictorand demonstrated sensitivity and specificity of 74.3% and 82.4% in the combined replication cohort. The likelihood ratio, LR+ and LR- were 4.11 and 0.32, respectively. TGF-beta was the highest-ranking canonical pathway by Gene Set Enrichment Analysis. An approach using longitudinal gene expression changes approach dramatically reduced within-group variation compared to cross-sectional expression for improved prediction modeling.
Conclusions: This novel FVC-gene predictor developed from short-term longitudinal gene expression changes successfully discriminates most patients with high likelihood of one-year 10% FVC decline. This tool may better reflect disease activity and prove useful for predictive enrichment of clinical trial populations.

overall_design:
Study populations were collected from the University of Chicago Medical Center and was approved by the institutional review board (IRB#14163) and informed consent was provided by all study subjects. All patients with IPF met American Thoracic Society/European Respiratory Society (ATS/ERS) diagnosis criteria. Demographic information, clinical characteristics, and pulmonary function tests were collected from all patients with IPF. Spirometry testing, including forced vital capacity percent predicted (FVC% predicted), diffusion capacity for carbon monoxide percent predicted (DLCO % predicted) as well as lung volumes by plethysmography were obtained per ATS guidelines. The prognosis of IPF subjects was dichotomously categorized as FVC stable (FVC-S) or FVC decline (FVC-D) defined by < or ≥10% reduction in FVC% predicted from the baseline to over 2 years of follow-up.
PBMC samples were analyzed.

last: Oldham

first: Shwu-Fan

last: Ma

first: Fernando

last: Martinez

first: Imre

last: Noth


title: SP80-3280 growth and maturation field 2

status: Public on Sep 20 2019

city: São Paulo

first: Glaucia

middle: Mendes

last: Souza

state: SP

address: Av Prof Lineu Prestes, 748

department: Biochemistry

country: Brazil

institute: Instituto de Quimica da Universidade de São Paulo

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

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

first: Carolina

middle: G

last: Lembke


title: Selective Disruption of Core Regulatory Transcription [ChIP-seq]

status: Public on Jul 16 2019

city: Bethesda

first: Javed

last: Khan

state: MD

address: 37 Convent Dr.

department: Genetics Branch

institute: NCI, NIH

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Activation of identity determining transcription factors (TFs), or core regulatory TFs, is governed by cell-type specific enhancers, an important subset of these being super enhancers (SEs).  This mechanism is distinct from constitutive expression of housekeeping genes.  The characterization of drug-like small molecules to selectively inhibit core regulatory circuitry is of high interest for treatment of cancers, which are addicted to core regulatory TF function at SEs.  Surprisingly, we find histone deacetylases (HDAC) to be an indispensable component of SE-driven transcription.  While histone acetylation is a marker for active genes, over accumulation of acetylation selectively halts core regulatory transcription. We show this conundrum may in part be explained by a SE-specific need for resetting histones to maintain SE boundaries, to facilitate enhancer-promoter looping and high levels of transcription.

overall_design: Genome-wide profiles for histone marks, chromatin remodelers, ATAC, transcription factors, coactivators, RNA Polymerase and architectural proteins in Rhabdomyosarcoma (RMS) cell lines before and after HDAC inhibition

first: Berkley

last: Gryder

first: Xinyu

last: Wen


title: RNA-Seq profiling in two chicken cell lines, LMH and DF1 with different susceptibiltiy to H9N2 avian influenza virus

status: Public on Jul 04 2019

city: Guangzhou

first: Min

last: Feng

address: wushan road

institute: South China Agricultural University

summary: We utilize the natural cell line model (LMH and DF1) with different susceptibiltiy to H9N2 avian influenza virus to find out more and new potential key factors of influencing AIV infection and replication via a high-throughput RNA sequencing (RNA-seq).

overall_design: DF1 and LMH cells were infected with H9N2 subtype HN strain at 0.1 MOI.Viral replication waw detected at  4, 6, 12, 24, 36 and 48 hours post infection (h. p. i).Total RNA were respectively extracted from DF1 or LMH cells infected with HN strain at 6 h. p. i and 12 h. p. i using Trizol reagent kit (Invitrogen, Carlsbad, CA,USA) according to the manufacturer’s protocol. For every time point, each sample was collected in duplication. RNA quality was assessed on an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA) and checked using RNase free agarose gel electrophoresis. The samples were used for RNA-Seq

first: Manman

last: Dai

first: Keyi

last: Shi

first: Ming

last: Liao


title: Gastric bypass vs. ‘Medical Bypass’ - Impact on experimental diabetic kidney disease

status: Public on Jul 10 2019

city: Dublin

first: Meera

last: Nair

address: Conway Institute

country: Ireland

institute: University College Dublin

summary: Albuminuria is significantly reduced following Roux-en-Y gastric bypass (RYGB) surgery, suggesting a renoprotective effect of the intervention. Herein, we assess the relative impact of RYGB and RYGB equivalent non-surgical weight loss and glycaemic improvement on glomerular injury and global renal transcriptomic responses in the Zucker diabetic fatty rat (ZDF) model of diabetic nephropathy. We coined the term "medical bypass" (MB) to describe the intensive diet and pharmacotherapy based non-surgical intervention Adult ZDF rats underwent sham surgery (n=15) or RYGB (n=9). Nine sham-operated rats were calorie restricted and received insulin, liraglutide, metformin, ramipril, rosuvastatin and fenofibrate for 2 months (MB). Zucker fa/+ rats acted as healthy controls throughout. Bodyweight, glycaemia, albuminuria and glomerular injury specifically podocyte number, density and ultrastructure were assessed at follow up. Renal transcriptomes were compared by RNA-seq. RYGB resulted in 20-30% weight loss, normalized glycaemia and albuminuria and reduced indices of glomerular injury, specifically podocyte injury (foot process effacement). RYGB equivalent outcomes were obtained on all parameters following MB.

overall_design: RNA-seq was performed to identify the renal transcriptomic profile of kidney disease in the ZDF rat,  and to investigate the relative effects of Medical bypass intervention on the renal transcriptome. N=9 replicates were profiled.

first: Carel

last: le Roux

first: Neil

last: Docherty


title: Roux-en-Y Gastric Bypass Reduces Podocyte Injury in Diabetic Kidney Disease

summary: Podocyte injury in diabetic kidney disease contributes to the development of albuminuria and subsequent renal decline. Clinically, gastric bypass surgery is associated with reductions in albuminuria, and rodent studies demonstrate coherent improvements in renal histology. We aimed to investigate the mechanisms underpinning remission of albuminuria following gastric bypass focussing on podocyte injury. Firstly, we tracked the evolution of albuminuria and cognate evidence of histological and ultrastructural damage to the glomerulus in male Zucker Diabetic Fatty rats. Secondly, we examined the impact of gastric bypass in these rats, focussing on podocyte injury. Thirdly, we conducted a global transcriptomic study profiling the shift in the renal transcriptome in the Zucker Diabetic Fatty rats rat and its relevance to human disease. Lastly, we explored whether gastric bypass could reverse the changes seen in the disease associated transcriptome. Albuminuria in the Zucker Diabetic Fatty rat developed by 12 weeks of age. This was accompanied by glomerulomegaly, podocyte stress and ultrastructural evidence of podocyte dedifferentiation. When animals underwent gastric bypass at 12 weeks of age, marked reductions in albuminuria in association with normalisation of glomerular tuft size, attenuation of podocyte stress and improvements in podocyte foot process morphology were observed within 2 months of surgery. A characteristic disease associated gene expression signature was observed in the kidneys of Zucker Diabetic Fatty rats, with a core set of alterations conserved in global analysis of the human DKD transcriptome. Many of the shared gene expression alterations were reversed by gastric bypass. Reductions in podocyte injury represent a key mechanism underpinning the remission of albuminuria following gastric bypass.

overall_design: RNA-seq was performed to identify the renal transcriptomic profile of kidney disease in the ZDF rat,  and to investigate the relative effects of Roux-en-Y gastric bypass intervention on the renal transcriptome. N=6 replicates were profiled.

first: Aoife

last: Canney

first: Jessie

last: Elliott

first: Naomi

last: Fearon

first: Eoin

last: Brennan


title: Effect of sodium houttuyfonate on transcriptome of Pseudomonas aeruginosa

status: Public on Jun 28 2019

city: hefei

first: Yeye

last: zhao

state: anhui

address: qianjiang

institute: Anhui University of Chinese Medicine

summary: The purpose of this experiment is to analyze the changes of transcriptome in Pseudomonas aeruginosa under the action of sodium houttuyfonate (SH), thus revealing the possible mechanism of sodium houttuyfonate inhibiting P. aeruginosa. We analyzed these data in order to compare the transcriptional differences of P. aeruginosa in SH medication group and blank control group.

overall_design: The expression of transcription group in SH group and blank control group was detected

last: Zhao

first: Yuanqing

last: Si

first: Longfei

last: Mei

first: Jiadi

last: Wu

first: Jing

last: Shao

first: Changzhong

last: Wang

first: Daqiang


title: Chromatin accessibility maps of muscle infiltrating macrophages.

status: Public on Jul 02 2019

city: Debrecen

first: Halasz

last: Laszlo

address: Egyetem tér 1

department: Department of Biochemistry and Molecular Biology

country: Hungary

institute: University of Debrecen

summary: Genome-wide chromatin accessibility maps of muscle infiltrating macrophages isolated at day 1 to 4 following acute sterile cardiotoxin injury.

overall_design: ATAC-seq timecourse from muscle infiltrating macrophage samples after CTX injury.

first: Andreas

last: Patsalos

first: Petros

last: Tzerpos

first: Laszlo

last: Halasz

first: Gergely

last: Nagy

first: Nikolas

last: Giannakis


title: Thermo Fisher Scientific OncoScan expression array data for undifferentiated uterine sarcomas

first: Joseph

last: Carlson

type:
Expression profiling by array
Genome variation profiling by array

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

overall_design: Refer to individual Series


title: PTEN modulates gene transcription by redistributing genome-wide RNA polymerase II occupancy

status: Public on Jun 04 2019

city: Cleveland

first: Ata

last: Abbas

state: OH

address: 10900 Euclid Ave

department: Division of Hematology & Oncology

institute: Case Western Reserve University


title: PTEN modulates gene transcription by redistributing genome-wide RNA polymerase II occupancy [RNA-seq]

summary: Control of gene expression is one of the most complex yet continuous physiological processes impacting cellular homeostasis. RNA polymerase II (Pol II) transcription is tightly regulated at promoter-proximal regions by intricate dynamic processes including Pol II pausing, release into elongation, and premature termination. Here, we identify PTEN interacting with the Pol II transcription machinery and dephosphorylating Pol II C-terminal domain in vitro. PTEN alters the expression of hundreds of genes, and its restoration establishes Pol II promoter-proximal pausing in PTEN null cells. Furthermore, PTEN re-distributes genome-wide Pol II occupancy and possibly impacts Pol II pause duration, release, and elongation rate in order to enable precise gene regulation at genome-wide scale. Our observations demonstrate a direct and imperative role of PTEN in global transcriptional regulation.

overall_design: Total RNA was extracted from cells using the Qiagen RNeasy kit with on-column DNase treatment. RNA quality was assessed via the Agilent 2100 Bioanalyzer. All samples have RIN numbers ≥ 9.5. Two independent biological replicates (each containing two technical replicates) were used for RNA-sequencing. The library was prepared using Illumina TruSeq stranded total RNA kit. Sequencing was performed using Illumina HiSeq 2500 using 100-bp paired-end rapid run format.

first: Roshan

last: Padmanabhan

first: Todd

last: Romigh

first: Charis

last: Eng


title: FGF2-mediated regulation of TGF-β-induced endothelial-to-myofibroblast transition

status: Public on May 15 2019

city: Tokyo

first: Yasuhiro

last: Yoshimatsu

address: M&D tower N-707, 1-5-45 Yushima, Bunkyo-ku

institute: Tokyo Medical and Dental University

summary:
Tumor microenvironment contains various components including cancer cells, tumor vessels, and cancer associated fibroblasts (CAFs), comprising of tumor-promoting myofibroblasts and tumor-suppressing fibroblasts. Multiple lines of evidence indicated that transforming growth factor-β (TGF-β) induces the formation of myofibroblasts and other types of mesenchymal (non-myofibroblastic) cells from endothelial cells. Recent reports showed that fibroblast growth factor 2 (FGF2) modulates TGF-β-induced mesenchymal transition of endothelial cells, but the molecular mechanisms regarding the signals that control the transcriptional networks during the formation of different groups of fibroblasts remain largely unclear. Here, we studied the roles of FGF2 during the regulation of TGF-β-induced mesenchymal transition of tumor endothelial cells (TECs). We demonstrated that auto/paracrine FGF signals in TECs inhibit TGF-β-induced endothelial-to-myofibroblast transition (End-MyoT), leading to suppressed formation of contractile myofibroblast cells, but on the other hand can also collaborate with TGF-β in promoting the formation of active fibroblastic cells which have migratory and proliferative properties. FGF2 modulated TGF-β-induced formation of myofibroblastic and non-myofibroblastic cells from TECs via transcriptional regulation of the array of various mesenchymal markers and growth factors. Furthermore, we observed that TECs treated with TGF-β were more competent in promoting in vivo tumor growth than TECs treated with TGF-β and FGF2. Mechanistically, we showed that Elk1 mediated this FGF2-induced inhibition of End-MyoT via inhibition of TGF-β-induced transcriptional activation of α-SMA promoter by myocardin-related transcription factor (MRTF)-A. Our data suggest that TGF-β and FGF2 oppose and cooperate with each other during the formation of myofibroblastic and non-myofibroblastic cells from TECs to determine the characteristics of the mesenchymal cells in tumor microenvironment.
Identification of marker genes for  TGF-β-induced endothelial-to-myofibroblast transition

overall_design:
Samples 1..4: The effect of FGF2 on TGF-β-induced endothelial-to-myofibroblast transition was examined. Tumor endothelial cells were cultured in the absence or presence of 1 ng/mL of TGF-β2 in combination with 50 ng/mL of FGF2  for 72 h.
Samples 5..8: The effect of FGF2 and infigratinib (a pan-inhibitor of FGF receptors) on TGF-β-induced endothelial-to-myofibroblast transition was examined. Tumor endothelial cells were cultured in the absence or presence of 1 ng/mL of TGF-β2 in combination with 50 ng/mL of FGF2 or 3 mM infigratinib  for 72 h.

first: Yuichi

last: Akatsu

first: Naoya

last: Takahashi

first: Shiori

last: Kimuro

first: Tomoki

last: Muramatsu

first: Akihiro

last: Katsura

first: Nako

last: Maishi

first: Hiroshi

middle: I

last: Suzuki

first: Johji

last: Inazawa

first: Kyoko

last: Hida

first: Kohei

last: Miyazono

first: Tetsuro

last: Watabe


title: The Methylome-Genome Interactions in Localized Prostate Cancer Define Disease Aggression

status: Public on Jun 30 2019

city: Toronto

first: Yu-Jia

last: Shiah

state: Ontario

address: MaRS Centre 661 University Avenue Suite 510

department: Informatics and Bio-computing

country: Canada

institute: Ontario Institute for Cancer Research

type: Methylation profiling by genome tiling array

summary: Localized prostate cancer exhibits profound genomic, pathologic, and clinical heterogeneity, and current clinical prognostic factors do not accurately distinguish aggressive from indolent disease for an individual man. We and others have demonstrated that aberrant DNA methylation may be an important driver of aggressive disease. Herein, we analyze the tumor methylomes of 619 localized prostate cancers and assess the interactions between methylation and somatic tumor genomic profiles. We identify three distinct methylation subtypes, including a hypermethylation subtype which is associated with early biochemical recurrence. DNA methylation and gene copy number status synergistically regulate mRNA abundance, and aberrant methylation is strongly associated with common prostate cancer driver aberrations, including mutation density, and with altered RNA abundance profiles. Finally, we identify a set of multivariate methylation biomarkers that are prognostic of rapid biochemical recurrence. Taken together, our data provide the first comprehensive assessment of the interplay between somatic molecular phenotypes and aberrant DNA methylation in localized, non-indolent prostate cancer, and suggest that integrated genome-epigenome analyses may accurately identify men at risk for adverse clinical outcomes in this patient cohort.

overall_design: In total, we have methylation profiles for 394 samples (corresponding to 286 unique samples).

first: Paul

last: Boutros

first: Robert

last: Bristow

first: Michael

last: Fraser


title: RNA-Seq of isogenic human iPS cell-derived cardiomyocytes with RBM20 mutations created by genome editing [RNA-Seq]

status: Public on May 02 2019

city: Cincinnati

first: Nathan

last: Salomonis

address: 3333 Burnet Avenue

department: Biomedical Informatics

institute: Cincinnati Children's Hospital

summary: RBM20 heterozygous (Het) and homozygous (Homo) R636S and homozygous 8-bp deletion (which causes nonsense-mediated decay) mutations were created by genome editing in an iPS cell line generated from a healthy male patient. Those cells were differentiated into cardiomyocytes by modulating the WNT signaling pathway, and then are subjected to the lactate purification method.

overall_design: RNAseq of iPS cell-derived cardiomyocytes with 4 different genotypes as replicates

first: Yuichiro

last: Miyaoka

first: Steven

last: Mayerl

first: Amanda

middle: H

last: Chan

first: Bruce

last: Conklin


title: Bisulfite (methylome) sequencing of msh1 memory line treated with 5-azacytidine in Arabidopsis

status: Public on May 18 2019

city: University Park

first: Hardik

last: Kundariya

state: PA

address: 361 N. Frear

institute: The Pennsylvania State University

type: Methylation profiling by high throughput sequencing

summary: Germination of the memory line and isogenic Col-0 wild type on media containing 100 uM 5-azacytidine alleviated the phenotype differences between the two lines, resulting in similar growth rates. Here we generate methylome profile for wild type and  msh1 memory line under 100 uM 5-azacytidine treatment to investigate the  effect of 5-azacytidine on msh1 memory line methylation profile.

overall_design: Three biological replicates for each treatment and control condition were sequenced.

first: Xiaodong

last: Yang

first: Sally

last: Mackenzie


title: Bypass and diabetic kidney disease

first: Meera

last: Nair


title: PTEN modulates gene transcription by redistributing genome-wide RNA polymerase II occupancy [ChIP-seq]

first: Ata

last: Abbas

overall_design: Nuclei were isolated from formaldehyde (1% w/v, methanol-free) crosslinked cells by using NEXSON method followed by chromatin preparation using a Covaris sonicator. Chromatin was immunoprecipitated using an appropriate antibody, washed, reverse-crosslinked, and DNA isolated using the phenol-chloroform method. 10ng precipitated DNA was used to prepare library using Illumina TruSeq ChIP library preparation kit. Libraries were quantified for cluster generation using KAPA Library Quantification Kit. Sequencing was performed using Illumina HiSeq2500 using 50-bp paired end rapid run format. Each experiment was performed using two independent biological replicates (each containing two technical replicates).

first: Roshan

last: Padmanabhan

first: Todd

last: Romigh

first: Charis

last: Eng


title: Designing a single cell RNA sequencing benchmark dataset to compare protocols and analysis methods [5 Cell Lines Cel-seq]

status: Public on Feb 22 2019

city: Melbourne

first: Shian

last: Su

state: Victoria

address: 1G Royal Parade

department: Molecular Medicine

country: Australia

institute: Walter and Eliza Hall Institute of Medical Research

summary: Single cell RNA sequencing (scRNA-seq) technology has undergone rapid development in recent years and brings new challenges in data processing and analysis. This has led to an explosion of tailored analysis methods for scRNA-seq to address various biological questions. However, the current lack of gold-standard benchmarking datasets makes it difficult for researchers to evaluate the performance of the many methods available in a systematic manner. Here, we designed and generated a cross-platform benchmark dataset that has in-built truth in various forms and varying levels of biological noise. We used this dataset to compare different protocols and data analysis methods.  We found that different protocols have different data quality and ERCC spike-in works independently to endogenous RNA. We found significant differences in the results from the methods compared and we associated the results with data characteristics to identify methods that perform well in different situations. Our dataset and analysis provide a valuable resource for algorithm selection in different biological settings.

overall_design: our experiment utilized the 5 human lung adenocarcinoma cell lines H2228, H1975, A549, H838 and HCC827. For the single cell designs, the five cell lines were mixed equally and processed by 10X chromium and CEL-seq2, referred to as sc_10X_5cl, and sc_CEL-seq2_5cl respectively in analysis that follows. For CEL-seq2, three plates were sorted and processed.

first: Luyi

last: Tian

first: Daniela

last: Amann-Zalcenstein

first: Matthew

last: Ritchie


title: Transcriptional profiling (RNA-seq) of wild-type and Arhgap35 knockout embryonic motor neurons (E12.5)

status: Public on May 01 2019

city: La Jolla

first: Samuel

last: Pfaff

address: 10010 N Torrey Pines Rd

institute: Salk Institute for Biological Studies

summary: Ventral spinal cord regions micro-dissected from E12.5 Arhgap35 (aka, p190) knockout embryos or control littermates (wild-type or p190+/-) were pulled and dissociated with papain (Worthington Biochemical Cat# LK003153) according to the manufacturer’s instructions. Cells were sorted on a Becton Dickinson FACS Vantage SE DiVa using Coherent Sapphire 488 nm solid state laser and collected directly into RLT lysis buffer containing β-mercaptoethanol (Qiagen). RNA was isolated using the RNeasy Mini Kit (Qiagen) with on-column DNase digestion (Qiagen RNase-Free DNase Set). Each sample contained between 100,000 and 200,000 GFP+ motor neurons isolated from 2-5 spinal cords during a single experimental session. Five p190-/- and five control RNA samples were quantified with Agilent 2200 TapeStation system prior to preparation of mRNA-sequencing libraries (50 bp single-end) using the Illumina TruSeq RNA Library Preparation Kit (v2) according to the manufacturer’s instructions. Libraries were sequenced with Illumina HiSeq 2500 platform. "Negative" samples are from FACS-sorted Hb9:GFP-negative cells.

overall_design: FACS sorting and RNA-seq of motor neurons expressing Hb9:GFP reporter from either control or Arhgap35 knockout embryos (E12.5)

first: Dario

last: Bononomi

first: Shawn

last: Driscoll


title: Transcriptome profiling of hindlimb-derived adult satellite cells

status: Public on Feb 13 2019

city: Minneapolis

first: Alessandro

last: Magli

state: MN

address: 2231 6th St SE

institute: University of Minnesota

summary: Optimal cell-based therapies for the treatment of muscle degenerative disorders should not only regenerate fibers, but provide a quiescent satellite cell pool ensuring long-term maintenance and regeneration. Conditional expression of Pax3/Pax7 in differentiating pluripotent stem cells (PSC) allows the generation of myogenic progenitors endowed with satellite cell-like abilities.  To identify the molecular determinants underlying their regenerative potential, we performed transcriptome analyses of these cells along with primary myogenic cells from several developmental stages. Here we show that in vitro generated PSC-derived myogenic progenitors possess a molecular signature similar to embryonic/fetal myoblasts. However, compared to fetal myoblasts, following transplantation they show superior myofiber engraftment and ability to seed the satellite cell niche, respond to multiple re-injuries and contribute to long-term regeneration. Upon engraftment, the transcriptome of Pax3/Pax7-induced PSC-derived myogenic progenitors changes dramatically, acquiring similarity to that of satellite cells, particularly in genes involved in extracellular matrix remodeling. Single cell profiling reveals that these changes are induced, not selected, by the in vivo environment.  These findings demonstrate that Pax3/Pax7-induced PSC-derived myogenic progenitors possess proliferative and migratory abilities characteristic of earlier developmental stages, and an intrinsic ability to respond to environmental cues upon skeletal muscle regeneration.

overall_design: Murine muscle stem cells (also called satellite cells) were isolated from hindlimb muscles of Pax7-ZsGreen mice. Hindlimb muscles from multiple aged matched animals were collected, rinsed in PBS, triturated using a razor blade and sequentially digested with Collagenase II and CollagenaseII/Dispase following the protocol described in Ippolito J et al, Skelet Muscle. 2012; 2: 13. Approximately 200,000 ZsGreen+ cells/sample were sorted using FACS AriaII and processed for RNA isolation.

first: Magli

last: Alessandro

first: Arpke

last: Robert

first: Swanson

last: Scott

first: Perlingeiro

last: Rita


title: Therapeutic targeting of KDM1A/LSD1 in Ewing sarcoma engages the ER-stress response II

status: Public on May 03 2019

city: Columbus

first: Cenny

last: Taslim

address: 700 Children's Drive

institute: Nationwide Children's Hospital

summary: The transcriptional profile of LSD1 knockdown in A673 Ewing sarcoma cells mirrors that of EWS/FLI knockdown and LSD1 small molecule inhibition (SP-2509)

overall_design: RNA-seq data for A673 cells infected with retroviral vector expressing shRNA for Luciferase or KDM1a.  Four biological replicates were performed for each group.

first: Ranajeet

middle: S

last: Saund

first: Stephen

last: Lessnick


title: β-Hydroxy-β-Methylbutyrate Supplementation Inhibits Pancreatic Tumor Growth and Preserves Muscle Mass in Obese Mice

status: Public on Dec 30 2018

city: chapel hill

first: michael

middle: francis

last: coleman

state: North Carolina

address: 235 dauer drive

institute: UNC

summary: Cachexia, a complex catabolic state, frequently accompanies pancreatic ductal adenocarcinoma (PDAC), the fourth leading cause of cancer-related death in the US. We previously showed in a murine PDAC model that leucine supplementation improves muscle protein synthesis, but unfortunately also enhances PDAC cell growth, through activation of the mechanistic target of rapamycin (mTOR) signaling pathway. Utilizing the same murine PDAC model, herein we test the hypothesis that the leucine metabolite β-hydroxy-β-methylbutyrate (HMB) enhances muscle protein synthesis but (unlike leucine) suppresses PDAC cell growth. Male C57BL/6 mice received either control diet (n=60) or a diet-induced obesity (DIO) regimen (n=60) for 10 weeks, then were subcutaneously injected (right flank) with Panc02 PDAC cells and further randomized to continue their diets ± HMB supplementation and ± gemcitabine chemotherapy. We determined that: a) DIO, relative to control diet, significantly increased Panc02 tumor growth (nearly 4-fold) and impaired chemotherapeutic response to gemcitabine; b) HMB significantly increased muscle fiber size and muscle mTOR activity in both DIO- and control-fed mice; c) HMB decreased tumor growth and partially rescued gemcitabine responsiveness in DIO-fed mice, but had no antitumor effect in control mice; d) gene expression profiling and additional qPCR, immunohistochemistry and in vitro studies indicate DIO promotes an immunosuppressive tumor microenvironment that is normalized by treatment with HMB. These preclinical findings suggest that HMB has muscle-sparing and anti-tumor activities against PDAC in the context of obesity.

overall_design: 13 samples were analyzed each representing a tumor sample from a different mouse. 3 control diet un-supplemented, 3 control diet HMB supplemented, 3 diet induced obesity (high fat diet) un-supplemented, and 4 diet induced obesity HMB supplemented.

first: Kristyn

last: Liu

first: Michael

middle: F

last: Coleman

first: Xiaohu

last: Tang

first: Edward

last: Mills

first: Emily

last: Rossi

first: Laura

last: Bowers

first: Hannah

last: Ruisi

first: Salvador

last: Fabela

last: Lashinger

first: Zhengrong

last: Cui

middle: D

last: Hursting


title: Microarray analysis of gene expression of Atlantic cod from different Baltic Sea regions

status: Public on Jan 21 2019

city: Sopot

first: Magdalena

last: Malachowicz

address: Powstańców Warszawy

country: Poland

institute: Institute of Oceanology Polish Academy of Sciences

summary: The Atlantic cod (Gadus morhua L.) is one of the most important species in the Baltic Sea with high ecological and economical value. To explore the differences in adaptation to salinity between Baltic cod from different regions, western (Kiel Bight) and eastern (Gdańsk Bay) samples were analyzed through oligonucleotide microarray.

overall_design: Atlantic cod samples (n=8) were collected from two subdivisions: the Schleifjord, Kiel Bight (KIEL-18PSU) - SD22 and Gdańsk Bay (GDA - 8PSU) - SD 26. Gene expression changes in gills were assessed with 44 k oligonucleotide microarray

first: Roman

last: Wenne


title: Characterization of murine hepatoma cells with regard to their dependence on cyclin E1

status: Public on Feb 25 2019

city: Cologne

first: Ali

middle: T

last: Abdallah

address: Joseph Stelzmann Str. 26

department: Medical Faculty

country: Germany

institute: University of Cologne

summary: In C57BL/6 mice with a floxed cyclin E1 (CcnE1) gene (CcnE1f/f), hepatocellular carcinomas were induced using diethylnitrosamine (DEN). Hepatocyte-derived cells from pre-cancerous but tumor-free liver tissue (referred to as CcnE1f/fpreCL) and from large, solid HCC nodules (referred to as CcnE1f/fHCC) were isolated and immortalized in vitro. Deletion of CcnE1 in CcnE1f/fpreCL cells resulted in cell cycle arrest and death while CcnE1f/fHCC cells grew almost normal after loss of CcnE1. The underlying differences of both cell types regarding the transcriptome were analyzed in the present experiment.

overall_design: Four independent CcnE1f/fpreCL cell lines (R1-R4) and 3 independent HCC-derived cell lines (CcnE1f/fHCC, NR1-3) were infected with an adenovirus encoding cre-recombinase (adv-cre) in order to delete CcnE1. For the control experiment the same cell lines were infected with adenovirus expressing GFP (adv-GFP). Please note that 2 out of 4 preCL cell lines (CcnE1f/fpreCL clone 3 and clone 4) also contained a floxed Cdk2 allele. All preCL cell lines underwent cell cycle arrest after CcnE1 deletion, and all HCC cells grew normal in absence of CcnE1. Cells were harvested 3 days after infection and analyzed. Cells were compared to primary hepatocytes from CcnE1f/f mice (Ref-Hep1-3).

first: Roland

last: Sonntag

first: Nives

last: Giebeler

first: Yulia

last: Nevzorova

first: Jörg-Martin

last: Bangen

first: Dirk

last: Fahrenkamp

first: Daniela

last: Lambertz

first: Ute

last: Haas

first: Wei

last: Hu

first: Nikolaus

last: Gassler

first: Francisco

last: Cubero

first: Gerhard

last: Müller-Newen

first: Ralf

last: Weiskirchen

first: Fabio

last: Ticconi

first: Ivan

last: Costa

first: Mariano

last: Barbacid

first: Christian

last: Trautwein

last: Liedtke


title: Genome wide transcriptome analysis of patient matched prostate cancer using NGS technology

city: Illkirch

first: Hinrich

last: Gronemeyer

address: 1 rue Laurent Fries

department: Functional genomics and cancer

country: France

institute: IGBMC

summary:
Purpose: The goal of present study is to compare transcript level changes between normal and tumor of same individual
Methods: Total RNA was isolated, strand specific RNA seq was performed after Ribosomal RNA removal, global transcript profiles were generated by deep sequencing, in duplicate, using Illumina Hiseq. Initial quality check was performed using FASTQC, Alignment was performed using Hisat2 against human hg19 genome. Raw read count was performed using SummarizedExperiment (R package). Differential analysis was done using DEseq2
Results: This study provides insights in terms of global trancriptome changes between normal and tumor of same patient.
Conclusions: This study provides in depth analysis of transcriptomoc data in patient specific manner.

overall_design: Strand specific total RNA seq was performed using frozen patient matched prostate cancer tissue in biological duplicate

first: Akinchan

last: Kumar


title: Single-cell analysis RNA sequencing of whole mouse skin at embryonic day 13.5 and 14.5

status: Public on Dec 27 2018

city: New Haven

first: Jonathan

last: Levinsohn

state: CT

address: 333 Cedar

department: Genetics

institute: Yale University

summary: A major challenge in delineating molecular and cellular events that precede appendage morphogenesis stems from the inability to distinguish quantitative molecular differences between cells that lack histological distinction. The hair follicle (HF) dermal condensate (DC) is a cluster of cells critical for HF development and regeneration. Events that presage emergence of this distinctive population are poorly understood. Using unbiased single-cell RNA sequencing and in vivo methods, we infer a sequence of transcriptional states through which DC cells pass that begins prior to HF morphogenesis. Our data indicate that Wnt/b-catenin signaling is required to progress into an intermediate stage that precedes quiescence and differentiation. Further, we provide evidence that quiescent DC cells are recent selective progeny of proliferating cells present prior to morphogenesis and that are identified in the peri-DC zone during DC expansion. Together, these findings provide an inferred path of molecular states that lead to DC cell differentiation.

overall_design: 6 embryo samples total, 3 collected at E13.5 and 3 collected at E14.5. Embryonic dorsolateral/flank skin was micro-dissected and pooled (3-4 embryos per sample) and dissociated into a single-cell suspension using 0.25% trypsin (Gibco, Life Technologies) for 30 minutes at 37° C. Single-cell suspensions were then stained with DAPI (Fisher Scientific, NBP2-31156) just prior to fluorescence-activated cell sorting. DAPI-excluded live skin cells were sorted on a BD Facs Aria II (Biosciences) sorter with a 100 µm nozzle. Cells were sorted in bulk for 10X Genomics platform. Chromium Single cell 3’ Library and Gel Bead Kit v2 Chromium Single Cell 3′ Library & Gel Bead Kit v2 (PN- 120237), Chromium Single Cell 3′ Chip kit v2 (PN-120236) and Chromium i7 Multiplex Kit (PN-120262) were used according to the manufacturer’s instructions in the Chromium Single Cell 3′ Reagents Kits V2 User Guide. After cDNA libraries were created, they were subjected to HiSeq 2500 (Illumina) sequencing.

first: Peggy

last: Myung

first: Kushali

last: Gupta


title: BORG-dependent alterations in the transcriptome of D2.OR cells

status: Public on Mar 27 2019

first: William

last: Schiemann

address: 2103 Cornell Rd Rm 2404

summary: The ubiquitous nature of lncRNAs to comprehensively alter cellular transcriptional networks led us to hypothesize that BORG is capable of compelling metastasic, chemoresistant, and pro-survival activities in triple-negative breast cancers by inducing global transcriptomic reprogramming. As such, we performed RNA-seq to garner mechanistic insights into BORG-dependent pathways within D2.OR cells. Accordingly, transcriptional profiles associated with aggressive breast cancers and adaptive survival programs were amongst the top enriched pathways in BORG-expressing D2.OR cells. Most notably, BORG enriched for gene signatures that were critical for the development of chemoresistance towards doxorubicin, as well as a core set of genes upregulated in response to hypoxia, radiotherapy, and serum-deprivation.

overall_design: We performed RNA-seq on parental and BORG-expressing D2.OR organoids propagated in 3D-cultures for 7 days. Sequencing was performed on biological duplicates using Illumina HiSeq 2500 Platform. Two replicate RNA-seq experiments were performed for each condition (total of 4 samples) with an average of ~66 million paired end, 100 nucleotide long reads obtained for each sample.

first: Alex

last: Gooding

middle: P


title: Identification of molecular controls over corticospinal motor neuron segmental target specificity

status: Public on Dec 31 2018

city: Cambridge

first: Vibhu

last: Sahni

address: 7 Divinity Avenue

institute: Harvard University

summary:
Molecular mechanisms over differentiation and differential axonal targeting of distinct neuron subtypes in the cerebral cortex are beginning to be elucidated. These studies have focused on controls that specifically distinguish one subtype of neocortical projection neurons, e.g. corticospinal motor neurons (CSMN), from closely related corticothalamic projection neurons (CThPN) or intracortical callosal projection neurons (CPN). CSMN are located in layer V of the neocortex and make synaptic connections to motor output circuitry in the spinal cord and brainstem. CSMN axons form the corticospinal tract (CST), which is the major motor output pathway from the motor cortex and critically controls voluntary movement. CSMN somatotopically and precisely target specific segments along the rostrocaudal axis of the spinal cord, the molecular basis for which remains unknown.
We used microarrays to examine gene expression differences between two CSMN subpopulations that target different levels of the spinal cord - CSMN-C (which extend axons to the brainstem and cervical spinal cord) and CSMN-L (which preferrrentially extend axons to the thoracic and lumbar spinal cord). We  compared CSMN-C vs CSMN-L gene expression at 3 critical developmental time points (previously described in Arlotta et a., 2005)

overall_design: All CSMN were retrogradely labeled with fluorescent microespheres injected into either the cerebral peduncle at P0 or the cervical spinal cord at P3 and P5.5. Rostrolateral (for CSMN-C) and caudomedial (for CSMN-L) cortices were microdissected and the labeled CSMN subpopulations in these distinct cortical areas were FACS purified at 3 developmental stages for RNA extraction and hybridization on Affymetrix microarrays.

first: Sara

last: Shnider

first: Denis

last: Jabaudon

first: Jeffrey

last: Macklis


title: Designing a single cell RNA sequencing benchmark dataset to compare protocols and analysis methods [5 Cell Lines 10X]

first: Shian

last: Su

first: Luyi

last: Tian

first: Azadeh

last: Seidi

first: Shalin

last: Naik

first: Jafar

last: Jabbari

first: Matt

last: Ritchie


title: Designing a single cell RNA sequencing benchmark dataset to compare protocols and analysis methods (RNAmix_CEL-seq2 )

status: Public on Aug 19 2018

overall_design: our experiment utilized the 3 human lung adenocarcinoma cell lines H2228, H1975 and HCC827. The experiment included mixtures of RNA and single cells from these cell lines. For the single cell designs, the three cell lines were mixed equally and processed by 10X chromium, Drop-seq and CEL-seq2, referred to as sc_10X, sc_Drop-seq and sc_CEL-seq2 respectively in analysis that follows. For the mixture designs, we used plate-based protocols to mix and dilute samples in 2 different ways. 9 cell mixtures from the 3 cell lines were sorted in different combinations in the cell mixture experiment and data were generated by CEL-seq2, the material after pooling from 384 wells were subsampled in either 1/9 or 1/3 to simulate cells of different sizes, with different PCR product clean up ratios ranging from 0.7 to 0.9, referred to as cellmix1 to cellmix4. For the cell mixture experiment, we also sorted wells with 10 times more cells (90 cells) to provide a pseudo bulk reference for each mixture (referred to as cellmix5).  Distinct RNA mixtures which were diluted down to create single cell equivalents (ranging from 3.75, 7.5, 15 to 30 pg per well) were generated using CEL-seq2 and SORT-seq (referred to as RNAmix_CEL-seq2 and RNAmix_Sort-seq. This is the RNAmix_CEL-seq2 dataset.

first: Daniela

last: Amann-Zalcenstein

first: Matthew


title: Transcriptional profiling reveals running promotes cerebrovascular remodeling in young but not midlife mice

status: Public on Jun 19 2019

city: Bar Harbor

first: Kate

last: Foley

state: ME

address: 600 Main St

institute: The Jackson Laboratory

summary: We report that running at a young age showed ECM-related changes as well as angiogenesis-related pathways. Midlife running did not show this same affect.

overall_design: Young running vs. young sedentary. Midlife running vs midlife sedentary

first: Gareth

last: Howell


title: Designing a single cell RNA sequencing benchmark dataset to compare protocols and analysis methods (9 cell mixture dataset).

overall_design: our experiment utilized the 3 human lung adenocarcinoma cell lines H2228, H1975 and HCC827. The experiment included mixtures of RNA and single cells from these cell lines. For the single cell designs, the three cell lines were mixed equally and processed by 10X chromium, Drop-seq and CEL-seq2, referred to as sc_10X, sc_Drop-seq and sc_CEL-seq2 respectively in analysis that follows. For the mixture designs, we used plate-based protocols to mix and dilute samples in 2 different ways. 9 cell mixtures from the 3 cell lines were sorted in different combinations in the cell mixture experiment and data were generated by CEL-seq2, the material after pooling from 384 wells were subsampled in either 1/9 or 1/3 to simulate cells of different sizes, with different PCR product clean up ratios ranging from 0.7 to 0.9, referred to as cellmix1 to cellmix4. For the cell mixture experiment, we also sorted wells with 10 times more cells (90 cells) to provide a pseudo bulk reference for each mixture (referred to as cellmix5).  Distinct RNA mixtures which were diluted down to create single cell equivalents (ranging from 3.75, 7.5, 15 to 30 pg per well) were generated using CEL-seq2 and SORT-seq (referred to as RNAmix_CEL-seq2 and RNAmix_Sort-seq. This is the 9 cell mixture dataset.


title: Designing a single cell RNA sequencing benchmark dataset to compare protocols and analysis methods (Drop-Seq)

status: Public on Aug 18 2018


title: Designing a single cell RNA sequencing benchmark dataset to compare protocols and analysis methods (Cel_Seq)


title: Deep sequencing and flow cytometric characterization of expanded effector memory CD8+CD57+ T cells frequently reveals T-cell receptor Vβ oligoclonality and CDR3 homology in acquired aplastic anemia

status: Public on May 05 2018

city: Bethesda

first: Valentina

last: Giudice

address: 10 Center Drive

department: Hematology Branch

institute: NHLBI

summary: In this work, we investigated the frequency and oligoclonal expansion of effector CD28-CD57+ memory cells in CD8+ T cell compartments and the T-cell Receptor (TCR) Vβ repertoire in acquired aplastic anemia (AA) to provide additional evidence to the immune hypothesis in AA pathophysiology. Using flow cytometry, deep sequencing, and computational methods, we examined the blood of 32 AA patients and 29 appropriate controls for Vβ usage; eight of these patients showing CD8+CD57+ expansion and three healthy subjects were subjected to TCR deep sequencing to confirm the clonality. We showed that CD8+CD57+ cells were frequently expanded with oligoclonal characteristics in AA, and patients and healthy donors shared CD8+ clonotypes by complementarity-determining region 3 sequences analysis.

overall_design: For VDJ combination and CDR3 sequence profiling, DNA was isolated from FACS-sorted CD4+ and CD8+ T cells from nine SAA patients with CD8+CD57+ cell expansion and four healthy subjects (mean, 2.4 μg of DNA; range, 1.2 – 3.4 μg). DNA was also isolated from beads-sorted (Miltenyi Biotec Inc., San Diego, CA) CD8+CD57+ cells from two of the eight SAA patients with enough cells for further analysis (mean, 1.6 μg of DNA; range, 1.0 – 2.3 μg). TCR repertoire sequencing was performed with Illumina HiSeq 2000 sequencer (Illumina, Inc., San Diego, CA).

first: Xingmin

last: Feng

first: Zenghua

last: Lin

first: Maria

last: del Pilar Fernandez Ibanez

first: Olga

last: Rios

first: Neal

last: Young


title: XCT is a novel regulator of chromatin functionally conserved across eukaryotes

city: Davis

first: Stacey

last: Harmer

address: 1002 Green Hall, One Shields Ave.

department: Plant Biology

institute: UC Davis

summary: XCT was originally identified due to the short circadian period observed in plants mutant for this gene.  Proteins with homology to XCT are found across eukaryotes, but their molecular function is unknown.  We have recently demonstrated that in Schizosaccharomyces pombe, the XCT ortholog Xap5 is a chromatin-associated protein that acts in a similar manner as the histone variant H2A.Z to suppress aberrant gene expression.  Here, we demonstrate that although XCT and H2A.Z act in similar pathways to control plant development, XCT's role in the circadian clock is independent of H2A.Z.

overall_design: Analysis of DNA methylation and gene expression in various xct mutants.

first: Cory

last: Ellison

first: Assaf

last: Zemach

first: Shajahan

last: Anver

first: Roderick

middle: W

last: Kumimoto

first: Elisa

last: Fiume

first: Julin

middle: N

last: Maloof

first: Daniel

last: Zilberman

middle: L


title: Single cell profiling of 3 Human Lung Adenocarcinoma cell lines.

status: Public on Feb 28 2018

first: Shian

last: Su

summary: An equal mixture of cells from the 3 Human Lung Adenocarcinoma cell lines (H2228, NCI-H1975 and HCC827) were processed on the Chromium 3' single cell platform (10X Genomics) and sequenced on an Illumina NextSeq 500. FASTQ data were preprocessed using both scPipe and CellRanger.

overall_design: The cell lines H2228, NCI-H1975 and HCC827 were retrieved from ATCC (https://www.atcc.org/) and cultured in Roswell Park Memorial Institute (RPMI) 1640 medium with 10% fetal calf serum (FCS) and 1% Penicillin-Streptomycin. The cells were grown independently at 37˚C  with 5% carbon dioxide until near 100% confluency. Cells were PI stained and 120,000 live cells were sorted for each cell line by FACS to acquire an accurate equal mixture of live cells from the three cell lines. This mixture was then processed by the Chromium single cell platform using the manufacturer’s (10X Genomics) protocol and sequenced with the Illumina Nextseq 500. Filtered gene expression matrices were generated using CellRanger (10X Genomics) and scPipe independently. For CellRanger, we used the default parameters, with --expect-cells=4000. For scPipe, we processed the 4000 most enriched cell barcodes, with comp=2 used for quality control to remove poor quality cells. The GRCh38 human genome and associated annotation were used for both the scPipe and CellRanger analysis.

first: Luyi

last: Tian

first: Azadeh

last: Seidi

first: Shalin

last: Naik

first: Matt

last: Ritchie


title: RNA-sequencing of smpB-dependent gene expression in A. Veronii C4

status: Public on Sep 29 2018

city: Haikou

first: Hong

last: Li

address: NO. 58, Renmin Avenue

institute: Hainan Unversity

summary: We generated A. veronii strains that express SmpB(wt) or not(△smpB) in trans to evaluate the changes in gene expression upon SmpB expression. As SmpB participate in transtranslation sysytem, this allows us to explore the gene regulaton in A.veronii.

overall_design: wild type and △smpB of A.veronii were grown in M9 medium. mRNA profiles were generated by deep sequencing, in triplicate, using Illumina Hiseq xTen.

first: Zhu

last: Liu

first: Dan

last: Wang


title: The IL-4/STAT6/PPARγ signaling axis is driving the expansion of the RXR heterodimer cistrome, providing complex ligand responsiveness in macrophages [GRO-Seq]

status: Public on Feb 12 2018

city: Debrecen

first: Gergely

last: Nagy

address: Egyetem ter 1.

institute: University of Debrecen

summary: Retinoid X receptor (RXR) is an obligate heterodimeric partner of several nuclear receptors (NRs), and as such a central component of NR signaling regulating the immune and metabolic phenotype of macrophages. Importantly, the binding motifs of RXR heterodimers are enriched in the tissue-selective open chromatin regions of resident macrophages, suggesting specific roles in subtype specification. Recent genome-wide studies revealed that RXR binds to thousands of sites in the genome, but the mechanistic details how the cistrome is established and serves ligand-induced transcriptional activity remained elusive. Here we show that IL-4-mediated macrophage plasticity results in a greatly extended RXR cistrome via the direct and indirect actions of the transcription factor STAT6. Activation of STAT6 leads to chromatin remodeling and RXR recruitment to de novo enhancers. In addition, STAT6 triggers a secondary transcription factor wave, including PPARγ. PPARγ appears to be indispensable for the development of RXR-bound de novo enhancers, whose activities can be modulated in a very restricted manner by the ligands of the PPARγ:RXR heterodimer. Collectively, these data reveal the mechanisms leading to the dynamic extension of the RXR cistrome, identify the lipid-sensing enhancer set of alternatively polarized macrophages and suggest a pervasive ligand-independent mechanism of action of the receptors.

overall_design: GRO-Seq analysis of Wt mouse BMDM cells differentiated in the presence of MCSF

first: Laszlo


title: Expression data from thymic non-hematopoietic stromal cells after damage

status: Public on Feb 01 2018

city: Seattle

first: Kirsten

last: Cooper

state: WA

address: 1100 Fairview Ave. N, Rm S3-208

institute: Fred Hutchinson Cancer Research Center

summary:
The thymus is extremely sensitive to damage but also has a remarkable ability to repair itself. However, the mechanisms underlying this endogenous regeneration remain poorly understood and this capacity diminishes considerably with age. To identify alternate regeneration pathways in the thymus, we performed an unbiased transcriptome analysis of the non-hematopoietic (CD45-) stromal cell compartment of the thymus, which is less sensitive to thymic damage compared to the CD45+ hematopoietic compartment.
Concentrating on a model of thymic damage caused by a sublethal dose of total body irradiation (SL-TBI), where after an initial depletion of thymic cellularity with regeneration initiated after a nadir between days 3-4 and complete recovery by day 42, we found significant upregulation at both days 4 and 7 of several genes known to be involved in thymic function.

overall_design: Thymic non-hematopoietic stromal cells were isolated using CD45 MACS cell depletion. Microarray analysis was performed on an Affymetrix MOE 430 2.0 platform in triplicate in untreated mice, and day 4 and day 7 after SL-TBI.

first: Tobias

last: Wertheimer

first: Enrico

last: Velardi

first: Jennifer

last: Tsai

first: Jarrod

middle: A

last: Dudakov

first: Marcel

middle: R

last: van den Brink


title: Primary T cells from cutaneous T-cell lymphoma skin explants display an exhausted  immune checkpoint profile

status: Public on Aug 21 2018

city: Duarte

first: Xiwei

last: Wu

state: CA

address: 1500 E. Duarte Rd.

department: Computational and Quantitative Medicine

institute: City of Hope National Medical Center

summary: Cutaneous T-cell lymphoma (CTCL) develops from clonally expanded CD4+ T cells in a  background of chronic inflammation. Dendritic cells (DCs) are potent T-cell stimulators; yet  despite DCs’ extensive presence in skin, cutaneous T cells in CTCL do not respond with  effective anti-tumor immunity. We evaluated primary T-cell and DC émigrés from epidermal and  dermal explant cultures of skin biopsies from CTCL patients (n = 37) and healthy donors (n = 5).  Compared with healthy skin, CD4+ CTCL populations contained more T cells expressing PD-1,  CTLA-4, and LAG-3; and CD8+ CTCL populations comprised more T cells expressing CTLA-4  and LAG-3. CTCL populations also contained more T cells expressing the inducible T-cell  costimulator (ICOS), a marker of T-cell activation. DC émigrés from healthy or CTCL skin  biopsies expressed PD-L1, indicating that maturation during migration resulted in PD-L1  expression irrespective of disease. Most T cells did not express PD-L1. Using skin samples  from 49 additional CTCL patients for an unsupervised analysis of genome-wide mRNA  expression profiles corroborated that advanced T3/T4 stage samples expressed higher levels of  checkpoint inhibition genes compared with T1/T2 stage patients or healthy controls. Exhaustion  of activated T cells is therefore a hallmark of both CD4+ and CD8+ T cells directly isolated from  the lesional skin of patients with CTCL, with a continuum of increasing expression in more  advanced stages of disease. These results justify identification of antigens driving T-cell  exhaustion and the evaluation of immune checkpoint inhibition to reverse T-cell exhaustion  earlier in the treatment of CTCL.

overall_design: RNA-seq correlated with tumor stages

first: Christiane

last: Querfeld

first: Sung

last: Kil


title: High-throughput RNAi cell viability screen to identify selective targets for EWS-FLI1 positive Ewing sarcoma

status: Public on Sep 16 2018

city: Espoo

first: Kristiina

last: Iljin

address: Tietotie 2

country: Finland

institute: VTT

summary: We have performed a high-throughput RNA interference screen to identify targets inhibiting EWS-FLI1 driven cell proliferation in Ewing sarcoma cells. EWS-FLI1 expressing A673 Ewing sarcoma cells were screened both in presence and absence of EWS-FLI1 shRNA induction with druggable siRNA library. Leucine rich repeats and WD repeat Domain containing 1 (LRWD1) targeting siRNA pool was the strongest anti-proliferative hit identified only in presence of EWS-FLI1. Validation experiments confirmed the anti-proliferative effect of LRWD1 depletion especially in EWS-FLI1 expressing cells. Functional analysis of differentially expressed genes in LRWD1 depleted Ewing sarcoma cells showed over-representation of connective tissue development, cell projection morphogenesis and neuronal processes.

overall_design: Examination of the effect of two LRWD1 targeting siRNA molecules vs. scrambled siRNA in one cell line

first: Tao

last: He


title: The IL-4/STAT6/PPARγ signaling axis is driving the expansion of the RXR heterodimer cistrome, providing complex ligand responsiveness in macrophages I

status: Public on Jan 01 2018

overall_design: CTCF and RAD21 binding sites


title: The IL-4/STAT6/PPARγ signaling axis is driving the expansion of the RXR heterodimer cistrome, providing complex ligand responsiveness in macrophages II

overall_design: RXR cistrome


title: Comprehensive Analysis of Gene Expression Patterns in Friedreich’s Ataxia Fibroblasts by RNA Sequencing Reveals Altered Levels of Protein Synthesis Factors and Solute Carriers

status: Public on Sep 27 2017

city: Dallas

first: Marek

last: Napierala

state: TX

address: Marek Napierala

institute: University of Texas Southwestern Medical Center

summary: Friedreich’s ataxia (FRDA) is an autosomal recessive neurodegenerative disease usually caused by large homozygous expansions of GAA repeat sequences in intron 1 of the frataxin (FXN) gene.  FRDA patients have low FXN mRNA and frataxin protein levels when compared with heterozygous carriers or healthy controls.  Presently, there is no effective treatment for FRDA, and biomarkers to measure therapeutic trial outcomes and/or to gauge disease progression are lacking.  Peripheral tissues, including blood cells, buccal cells, and skin fibroblasts, can readily be isolated from FRDA patients and used to define molecular hallmarks of disease pathogenesis.  However, because these tissues are not directly involved in disease pathogenesis, their relevance as models of the molecular aspects of the disease is yet to be decided.  Transcriptome profiling of FRDA skin fibroblasts revealed significantly upregulated expression of genes encoding plasma membrane solute carrier proteins.  Conversely, the expression of genes encoding accessory factors and enzymes involved in cytoplasmic and mitochondrial protein synthesis was consistently decreased in the FRDA cells.  Finally, comparison of genes differentially expressed in FRDA fibroblasts to 3 previously published gene expression signatures defined for FRDA blood cells showed substantial overlap between the independent datasets, including correspondingly deficient expression of antioxidant defense genes.  Together, these results indicate that gene expression profiling of cells derived from peripheral tissues can, in fact, consistently reveal novel molecular pathways of the disease.

overall_design: We used RNA sequencing to profile the transcriptomes of primary fibroblast cell lines derived from 18 FRDA patients and 17 unaffected control individuals.

first: Jill

first: Yanjie

first: Yue

last: Lu

first: Kevin

last: Lin

first: Lauren

last: Hauser

first: David

last: Lynch


title: FGF2 regulation of gene expression in stable inducible Neurons

status: Public on Dec 28 2017

city: Ann Arbor

first: Fan

last: Meng

state: MI

address: 205 Zina Pitcher Place

department: Psychiatry

institute: U of Michigan

summary: Stable inducible neurons were generated using Tol2 recombinase to generate human embryonic stem cells that expressed human NEUROG2 in a doxycycline regulated maner.  Treatment with doxycycline caused neuronal differentiation of the stem cells (samples 55649-55653). The post-mitotic excitatory neurons derived from the stem cells were used to examine FGF2 regulation of gene expression (samples 57089-57096).

overall_design: Forced overexpression of human NEURGO2 was used to differentiate human embryonic stem cells (H9) into a homogeneous population of post-mitotic excitator neurons

first: Michael

last: Uhler


title: Designing a single cell RNA sequencing benchmark dataset to compare protocols and analysis methods (RNAmix_Sort-seq)

status: Public on Jul 25 2018

city: Melbourne

first: Shian

last: Su

address: 1G Royal Parade

institute: Walter and Eliza Hall Institute of Medical Research

summary: Single cell RNA sequencing (scRNA-seq) technology has undergone rapid development in recent years and brings new challenges in data processing and analysis. This has led to an explosion of tailored analysis methods for scRNA-seq to address various biological questions. However, the current lack of gold-standard benchmarking datasets makes it difficult for researchers to evaluate the performance of the many methods available in a systematic manner. Here, we designed and generated a cross-platform benchmark dataset that has in-built truth in various forms and varying levels of biological noise. We used this dataset to compare different protocols and data analysis methods.  We found that different protocols have different data quality and ERCC spike-in works independently to endogenous RNA. We found significant differences in the results from the methods compared and we associated the results with data characteristics to identify methods that perform well in different situations. Our dataset and analysis provide a valuable resource for algorithm selection in different biological settings.

overall_design: our experiment utilized the 3 human lung adenocarcinoma cell lines H2228, H1975 and HCC827. The experiment included mixtures of RNA and single cells from these cell lines. For the single cell designs, the three cell lines were mixed equally and processed by 10X chromium, Drop-seq and CEL-seq2, referred to as sc_10X, sc_Drop-seq and sc_CEL-seq2 respectively in analysis that follows. For the mixture designs, we used plate-based protocols to mix and dilute samples in 2 different ways. 9 cell mixtures from the 3 cell lines were sorted in different combinations in the cell mixture experiment and data were generated by CEL-seq2, the material after pooling from 384 wells were subsampled in either 1/9 or 1/3 to simulate cells of different sizes, with different PCR product clean up ratios ranging from 0.7 to 0.9, referred to as cellmix1 to cellmix4. For the cell mixture experiment, we also sorted wells with 10 times more cells (90 cells) to provide a pseudo bulk reference for each mixture (referred to as cellmix5).  Distinct RNA mixtures which were diluted down to create single cell equivalents (ranging from 3.75, 7.5, 15 to 30 pg per well) were generated using CEL-seq2 and SORT-seq (referred to as RNAmix_CEL-seq2 and RNAmix_Sort-seq.

first: Luyi

last: Tian

first: Daniela

last: Amann-Zalcenstein

first: Matthew

middle: E

last: Ritchie


title: Next Generation Sequencing Facilitates Quantitative Analysis of ZEB1-Regulated Transcriptomes

status: Public on Aug 10 2017

city: Houston

first: Xiaofeng

last: Zheng

address: 7007 Bertner Ave

department: Bioinformatics & Computational Biology

institute: UT MD Anderson Cancer Center

summary: The goal of this study is to analyze the transcripts regulated by ZEB1.

overall_design: Genome-wide profiling of the trancripts in mouse lung cancer cells transfected with ZEB1 expression vector or control vector

first: Jonathan

middle: M

last: Kurie


title: Integrative Transcription Start Site Analysis and Physiological Phenotyping Reveal Torpor-specific Expressions in Mouse Skeletal Muscle

status: Public on Aug 01 2018

city: Tokyo

first: Ruslan

last: Deviatiiarov

address: Hongo 2-1-1, Bunkyo-ku

department: Intractable Disease Research Center

institute: Juntendo University

summary: Soleus muscle CAGE profiles of mice (C57BL/6J) under normal conditions, torpid by fasting, under high ambient temperature (32°C), torpor deprived were generated by deep sequencing, in two runs and 2-8 replicates, using Illumina NextSeq.

overall_design: CAGE RNA-seq from soleus muscle of mice in six conditions: ad. lib. fed on day 1 (Pre), food withdrawn on day 2 to induce torpor (Mid), food returned on day 3 (Post), high ambient temperature and with food, day 2 (HiT), torpor deprivation by touching, day 2 (Dep) and normally fed, day 2 (Fed).

first: Kiyomi

last: Ishikawa

first: Guzel

last: Gazizova

first: Takaya

last: Abe

first: Hiroshi

last: Kiyonari

first: Masayo

last: Takahashi

first: Oleg

last: Gusev

first: Genshiro

last: Sunagawa


title: Gene expression from human discoid (DLE) and subacute (sCLE) cutaneous lupus subtypes

status: Public on Jul 03 2017

first: Celine

middle: C

last: Berthier

address: 1150 W. Medical Center Dr, MSRB2

institute: University of Michigan

summary: Cutaneous lupus erythematosus (CLE) is a disfiguring disease that can exist as an independent entity or as a manifestation of systemic lupus erythematosus (SLE) where up to 70% of patients experience lesions during their disease course.  Subacute CLE (sCLE) is an inflammatory lesion with associated erythema in papulosquamous or annular formations.  Typically, sCLE does not scar but depigmentation can occur. Importantly, sCLE is associated with a higher progression to SLE. Discoid lesions (DLE) are often circular and frequently lead to alopecia and scar formation.  sCLE lesions have a higher propensity for photoprovocation and a more robust inflammatory infiltrate following ultraviolet (UV) B exposure. The pathogenic mechanisms which govern the differences between DLE and sCLE remain poorly defined, and this is reflected by the refractory nature of cutaneous lesions to usual lupus therapies. In this study, we evaluated the transcriptional profiles of 26 DLE and 23 sCLE biopsies and compared them to control skin and to each other in order to develop a comprehensive understanding of the similarities and differences between these two clinical subtypes.

overall_design: RNA from FFPE blocks of skin biopsies was extracted and processed for hybridization on Affymetrix microarrays.

first: Lam

last: Tsoi

first: Tamra

middle: J

last: Reed

first: Jasmine

last: Stannard

first: Emily

last: Myers

first: Rajaie

last: Namas

first: Xianying

last: Xing

first: Stephanie

last: Lazar

first: Lori

last: Lowe

first: Matthias

last: Kretzler

first: Johann

last: Gudjonsson

first: J

last: Kahlenberg


title: Mammary gland transcriptome study in heifers

status: Public on Jul 12 2017

city: Zaragoza

first: Jorge

last: Calvo

address: Avd. Montañana 930

department: Producción y Sanidad animal

country: Spain

institute: CITA

summary: A better understanding of impacts of nutrition during pre- weaning and post- weaning period is needed in order to design feeding strategies that optimize lifetime productivity. Therefore, the objectives of the present study were three-fold: to evaluate nutrition-induced changes of 1) growth from birth to first calving in heifers, 2) its impact on first-lactation milk yield and composition and 3) evaluate nutrition-induced changes in gene expression of mammary gland in Parda de Montaña heifers. Sixteen Parda de Montaña heifers, were randomly but equally assigned at birth to one of four management strategies, in a 2 x 2 factorial experiment. In the pre-weaning period (0-6 months of age), all the heifers suckled their dams twice daily for 30 minutes. Half of the heifers (n=8) were supplemented a starter concentrate (CON) while the other half only had access to their dam’s milk (NOCON). In the post-weaning period (6-15 months), half of the heifers of each pre-weaning feeding treatment received alfalfa hay ad libitum plus concentrates, with a different forage to concentrate ratio (F:C), 67:33 (67F:33C) or 87:13 (87F:13C). Plasma metabolites and hormones concentration at weaning was determined, and cows and their calves weigh was recorded once/week throughout the first lactation, and their ADG was calculated. Milk composition and quantity was determined during the first 4 months of lactation. Mammary tissue samples were taken by biopsy at weaning at the end of first lactation.  RNA mammary gland samples (n=16, 8 samples from each treatment) were analyzed by using Bovine Gene 1.1 ST Array Strip. The results of the present study showed that heifers that received concentrate during pre- weaning period had greater BW at weaning when compared to NOCON heifers. Concentrate supplementation during the pre-weaning period increased heifers’ weight gains in the pre-weaning period (P < 0.001) but decreased weight gains in the post-weaning period (P < 0.01) and during pregnancy (P < 0.05). In addition, CON cows had lower milk production throughout the 4 months of the first lactation when compared with NOCON (P < 0.01). Moreover CON cows had decreased milk crude protein, crude fat, lactose, extract and casein content in their first lactation. In addition, cows that received concentrate during pre- weaning period showed greater SCC at the third and fourth month of lactation. Different gene expression patterns were found between CON and NOCON animals. Overall, concentrate supplementation at pre- weaning resulted in up –regulation of genes related with immune response and chemokine activity, suggesting that these animals might be in a compromised immune status, probably being at greater risk to develop mastitis in the later periods.

overall_design: Sixteen Parda de Montaña heifers, were randomly but equally assigned at birth to one of four management strategies, in a 2 x 2 factorial experiment. In the pre-weaning period (0-6 months of age), all the heifers suckled their dams twice daily for 30 minutes. Half of the heifers (n=8) were supplemented a starter concentrate (CON) while the other half only had access to their dam’s milk (NOCON). In the post-weaning period (6-15 months), half of the heifers of each pre-weaning feeding treatment received alfalfa hay ad libitum plus concentrates, with a different forage to concentrate ratio (F:C), 67:33 (67F:33C) or 87:13 (87F:13C). Mammary tissue samples were taken by biopsy at weaning at the end of first lactation.

first: Elda

last: Dervishi

first: Mireia

last: Blanco


title: The Heritage family study - skeletal muscle gene expression

status: Public on Jul 14 2018

city: Baton Rouge

first: Claude

last: Bouchard

state: LA

address: 6400 Perkins Rd

institute: Pennington Biomedical Research Center

summary: Gene expression profiles generated from skeletal muscle biopsies taken from participants of the HERITAGE family study. Participants completed an endurance training regime in which a skeletal muscle biopsy was taken prior to the start and after the final session of the program. Biopsies were used to generate Affymetrix gene expression microarrays.

overall_design: The experimental design and exercise training protocol of the HERITAGE Family Study have been described previously (Bouchard et al., 1995). Participants were sedentary at baseline and normotensive. Each participant exercised three times per week for 20 weeks on cycle ergometers controlled by direct heart rate (HR) monitoring. Muscle biopsies of vastus lateralis were obtained at baseline and post-training.

first: C


title: Genome-wide binding of Cyclin G in Drosophila melanogaster third instar larva wing imaginal discs.

status: Public on Jul 01 2017

city: Paris

first: Frédérique

last: Peronnet

address: 9, quai saint-Bernard

department: UMR7622-Developmental biology

institute: CNRS-SU

summary: We describe here the genome-wide binding sites of Cyclin G in Drosophila melanogaster wing imaginal discs from third instar female larvae. We used a transgenic line expressing a version Cyclin G deleted of the PEST domain (the 25 COOH-terminal amin-acids) and tagged by Myc under the control of the daugterless-Gal4 ubiquitous driver.

overall_design: Genomic binding sites of Myc-CycGΔP in Drosophila melanogaster  third instar larvae wing imaginal discs

first: Delphine

last: Dardalhon-Cuménal

first: Jérôme

last: Deraze


title: Plant abiotic stress tolerance conferred by the desert endophytic bacterium Enterobacter sp. SA187 is mediated through enhanced ethylene signalling

status: Public on Feb 27 2018

city: Thuwal

first: Prof. Heribert

last: HIRT

address: 4700 KAUST

institute: KAUST

summary: Recent studies have shown that several plant species require microbial associations for stress tolerance and survival. In this work, we show that the desert endophytic bacterium Enterobacter sp. SA187 enhances yield and biomass of alfalfa in field trials, revealing a high potential for improving desert agriculture. To understand the underlying molecular mechanisms, we studied SA187 interaction with Arabidopsis thaliana. SA187 colonized surface and inner tissues of Arabidopsis roots and shoots and conferred tolerance to salt and osmotic stresses. Transcriptome, genetic and pharmacological studies revealed that the ethylene signaling pathway plays a key role in mediating SA187-triggered abiotic stress tolerance to plants. While plant ethylene production is not required, our data suggest that SA187 induces abiotic stress tolerance by bacterial production of 2-keto-4-methylthiobutyric acid (KMBA), known be converted into ethylene in planta. These results reveal a part of the complex molecular communication process during beneficial plant-microbe interactions and unravel an important role of ethylene in protecting plants under abiotic stress conditions.

overall_design:
4 samples, 3 biological replicates
Sterilized seeds were stratified for 3 days and then plated on ½ MS agar plates (Murashige and Skoog basal salts, Sigma), grown vertically for 5 days at 22 C and 16h light, then transferred to fresh ½ MS agar plates with (samples S, SB) or without (samples M, B) 100 mM NaCl (6 seedlings per plate) and cultivated for additional 12 days.
Initial plates for sterilized seeds germination containing bacterial strain SA187 (2·10E+5 cfu·mL-1) were used to prepare samples B and SB. Control plates for samples M and S were non-inoculated.

first: Axel

last: de Zélicourt

first: Lucas

last: Synek

first: Maged

last: Saad

first: Hanin

last: Alzubaidy

first: Rewaa

last: Jalal

first: Yakun

last: Xie

first: Cristina

last: Andrés-Barrao

first: Eleonora

last: Rolli

first: Florence

last: Guerard

first: Kiruthiga

middle: G

last: Mariappan

first: Ihsanullah

last: Daur

first: Moussa

last: Benhamed

first: Thomas

last: Depeape

first: Dominique

last: Van Der Straeten

first: Heribert

last: Hirt


title: MiRNA expression profiling in cholangiocarcinoma (CCA) cells treated with TGF-b

status: Public on Apr 18 2018

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, 451 miRNAs expressed in CCA cells. Microarray identified 17 miRNAs that were increased by > 1.5-fold  and 56 miRNAs that were decreased by < 0.67-fold in CCA cells treated with TGF-β.

overall_design: In the study presented here, we used CCA cells, HuccT1 and miRNAs expression was analyzed by comparing in HuccT1 cells treated with or without TGF-β.

first: Kenji

last: Takahashi

first: Yu

last: Ota


title: High frequency of β-catenin mutations in mouse HCCs induced by a non-genotoxic CAR agonist

status: Public on Apr 27 2018

city: CAGLIARI

first: AMEDEO

last: COLUMBANO

address: VIA PORVELL 4

department: DIPARTIMENTO DI SCIENZE BIOMEDICHE

country: Italy

institute: UNIVERSITA' DEGLI STUDI DI CAGLIARI

summary: Activation of Wnt/β-catenin signaling is frequent in human and rodent hepatocarcinogenesis. Although in mice, the tumor promoting activity of agonists of constitutive androstane receptor (CAR) occurs via selection of carcinogen-initiated cells harbouring β-catenin mutations, the molecular alterations leading to hepatocellular carcinoma (HCC) development by The CAR agonist 1,4-bis[2-(3,5-dichloropyridyloxy)]benzene (TCPOBOP), in the absence of genotoxic injury are unknown. Here we show that CAR activation per se induced HCC in mice and that 91% of them carried β-catenin point mutations or large in-frame deletions/exon skipping targeting Ctnnb1 exon 3. Point mutations in HCCs induced by TCPOBOP alone displayed different nucleotide substitutions compared to those found in HCCs from mice pre-treated with diethylnitrosamine (DENA). Moreover, unlike those occurring in HCCs from DENA+TCPOBOP mice, they did not result in increased expression of β-catenin target genes, such as Glul, Lgr5, Rgn, Lect2 and Ccnd1, or nuclear translocation of β-catenin when compared to the control liver. Remarkably, in the non-tumoral liver tissue, chronic CAR activation led to down-regulation of these genes and to a partial loss of glutamine synthetase (GS)-positive hepatocytes. These results thus show that while chronic CAR activation per se induces HCCs carrying β-catenin mutations, it concurrently down-regulates the Wnt/β-catenin pathway in non-tumoral liver. They also indicate that the relationship between CAR and β-catenin may be profoundly different between normal and neoplastic hepatocytes.

overall_design: 3 Controls, 7 TCP 42 w, 9 Dena + TCP, 3 TCP 28 w.

first: Amedeo

last: Columbano

first: Sandra

last: Mattu

first: Pia

last: Sulas


title: The IL-4/STAT6/PPARγ signaling axis is driving the extension of the RXR heterodimer cistrome, providing complex ligand responsiveness in macrophages

status: Public on Feb 12 2018

first: Gergely

last: Nagy

department: Department of Biochemistry and Molecular Biology

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

overall_design: Refer to individual Series


title: RNA sequencing for transcriptome comparison between HTLV-1 Tax(-) and Tax(+) cells in Adult T-cell leukemia cell lines (MT-1 and KK-1)

status: Public on Feb 02 2018

city: St. Louis

first: David

last: Spencer

state: MO

address: 660 South Euclid Avenue

department: Department of Medicine

country: USA

institute: Washington University in St. Louis

summary: Initially, ATL cell lines (MT-1 or KK-1) were stably transfected  with reporter plasmid for HTLV-1 Tax expression, and single clones were isolated . This reporter in composed of Tax responsive element upstream of d2EGFP fluorescent protein. d2EGFP is expressed upon Tax expression in any individual cell. To compare transcriptomes of Tax(-) and Tax(+) cells, FACS sorting was done for d2EGFP(-) and d2EGFP(+) populations and RNA sequencing was performed.

overall_design: Two ATL reporter cell lines were used in this study (MT1GFP and KK1GFP). For Each cell line, two samples were analyzed:  d2EGFP(-) and d2EGFP(+). In total 4 samples were used in this study.

first: Mohamed

last: Mahgoub

first: Jun-ichirou

last: Yasunaga


title: Production of BMP4 by endothelial cells is crucial for endogenous thymic regeneration

status: Public on Feb 01 2018

first: Kirsten

last: Cooper


title: Targeted RNA-Seq of Human Lymphoma Cell Line

city: Bellinzona

first: Francesco

last: Bertoni

state: Ticino

address: Via V. Vela 6

department: Lymphoma & Genomics Research Program

institute: IOR

summary: Thirty-seven (37) human cell lines were submitted to HTG Molecular for analysis using the HTG EdgeSeq Oncology Biomarker Panel. The goal of this work is to characterize the gene expression pattern of different cell lines bearing sensitivity or resistance for specific drugs.

overall_design: Cell lines were deep sequenced on an Illumina NextSeq using High Output, PhiX was spiked into the library at 5%.

first: Chiara

last: Tarantelli

first: Eugenio

last: Gaudio

first: Luciano

last: Cascione