title: Redefining the sRNA transcriptome of Streptococcus pneumoniae serotype 2 strain D39

status: Public on May 13 2019

city: Bloomington

first: Malcolm

last: Winkler

address: 1001 E. Third Street

department: Biology

institute: Indiana University

summary: Streptococcus pneumoniae (pneumococcus) is a major human respiratory pathogen and a leading cause of bacterial pneumonia worldwide. Small regulatory RNAs (sRNAs), which often act by post-transcriptionally regulating gene expression, have been shown to be crucial for the virulence of S. pneumoniae and other bacterial pathogens. Over 170 putative sRNAs have been identified in S. pneumoniae TIGR4 strain (serotype 4) through transcriptomic studies, and a subset of these sRNAs have been further implicated in regulating pneumococcal pathogenesis. However, there is little overlap in the sRNAs identified among these studies, which indicates that the approaches used for sRNA identification were not sufficiently sensitive and robust and that there are likely many more undiscovered sRNAs encoded in the S. pneumoniae genome. Here, we sought to comprehensively identify sRNAs in Avery's virulent S. pneumoniae strain D39 using two independent RNA-seq based approaches. We developed an unbiased method for identifying novel sRNAs from bacterial RNA-seq data and have further tested the specificity of our analysis program towards identifying sRNAs encoded by both strains D39 and TIGR4. Interestingly, the genes for 15% of the putative sRNAs identified in strain TIGR4 including ones previously implicated in virulence are not present in strain D39 genome suggesting that the differences in sRNA repertoires between these two serotypes may contribute to their strain-specific virulence properties. Finally, this study has identified 67 new sRNA candidates in strain D39, 28 out of which have been further validated, raising the total number of sRNAs that have been identified in strain D39 to 112.

overall_design: For samples 1-6 and 8-9, the library was generated by removing DNA by DNase treatment, depleting rRNA with Ribo-Zero rRNA removal kit for gram-positive bacteria and subsequently utilizing the ScriptSeqTM v2 RNA-Seq Library Preparation kit (Epicenter).  For samples 7 and 10, the same protocol excpet for TruSeq® Stranded RNA kit (Illumina Inc.) was used to prepare sRNA libraries using 145 - 500 bp size selection.

first: Dhriti

last: Sinha

first: Kurt

last: Zimmer

first: Todd

last: Cameron

first: Douglas

middle: B

last: Rusch

first: Nicholas

last: De Lay


title: Corrupted DNA-binding specificity and ectopic transcription underpin dominant neomorphic mutations in KLF/SP transcription factors

status: Public on May 14 2019

city: Woolloongabba

first: Melissa

middle: D

last: Ilsley

state: Queensland

address: 36 Kent street

country: Australia

institute: Mater Research

type: Expression profiling by high throughput sequencing

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Study of mutations in the DNA-binding domain

overall_design: ChIP-seq of CDA(E339K)-KLF1 in erythroid cell lines. 4sU-RNA-seq before and after induction of CDA(E339K)-KLF1 in erythroid cell lines.

first: Kevin

middle: R

last: Gillinder

first: Andrew

middle: C

last: Perkins


title: Transcriptomic Analysis of Wild Type and FOXA2-/- ES-derived Pancreatic Progenitors

city: New York

first: Hyein

middle: Sophia

last: Cho

state: NY

address: 430 E 67th St

department: Developmental Biology

country: USA

institute: Memorial Sloan Kettering Cancer Center

overall_design: Examination of triplicates per genotypes for each differentiation stage

first: Danwei

last: Huangfu

first: Christina

middle: S

last: Leslie


title: A Preformed Chromatin Architecture Ensures Robust Shh Transcription during Limb Development [RNA-Seq]

city: Berlin

last: Paliou

address: Ihnestrasse 63-73

country: Germany

institute: Max Planck Institute for Molecular Genetics

summary: During embryogenesis, enhancer-promoter interactions control gene transcriptional activation. These interactions can be tissue-specific or tissue-invariant and occur mostly within larger insulated regulatory domains called Topologically Associating Domains (TADs). Boundary elements, which delineate the extent of TADs, frequently interact with each other and have been associated with constitutive transcription and CTCF/Cohesin binding. In this work, we set out to investigate the regulatory role of a tissue-invariant, preformed interaction between two boundaries that involve the Shh gene and its unique limb enhancer, the ZRS, located one megabase away. Using CRISPR/Cas9 we specifically perturb CTCF binding sites or constitutive transcription at the ZRS-containing boundary, without altering the enhancer sequence. Using capture-HiC (cHiC) we show that both types of perturbation result in altered preformed chromatin interactions and lead to a reduction of Shh expression in developing limb buds. Finally, we demonstrate that the disruption of the chromatin structure in combination with a hypomorphic ZRS allele results in a dramatic Shh loss- of- function and digit agenesis. We thus propose that preformed chromatin structures can ensure stable enhancer promoter communication during development and robustness of gene transcriptional activation.

overall_design: We performed transcriptome analysis to confirm the complete loss of the Lmbr1 transcript due to the deletion of its promoter and to detect other potential non-coding transcripts at the locus.

first: Guillaume

last: Andrey


title: A Preformed Chromatin Architecture Ensures Robust Shh Transcription during Limb Development [ChIP-Seq]

overall_design: We used ChIP-seq in E10.5 Wildtype and mutant limb buds to assess the binding of transcription factors CTCF and Rad21, but also of the histone marks H3K27ac and H3K36me3


title: A Preformed Chromatin Architecture Ensures Robust Shh Transcription during Limb Development [ATAC-seq]

overall_design: We used ATAC-seq to compare chromatin accessibility in 3 different tissues and to compare the accessibility of the enhancer in WT and mutant animals.


title: A Preformed Chromatin Architecture Ensures Robust Shh Transcription during Limb Development [4C-seq]

summary: During embryogenesis, enhancer-promoter interactions control gene transcriptional activation. These interactions can be tissue-specific or tissue-invariant and occur mostly within larger insulated regulatory domains called Topologically Associating Domains (TADs). Boundary elements, which delineate the extent of TADs, frequently interact with each other and have been associated with constitutive transcription and CTCF/Cohesin binding. In this work, we set out to investigate the regulatory role of a tissue-invariant, preformed interaction between two boundaries that involve the Shh gene and its unique limb enhancer, the ZRS, located one megabase away. Using CRISPR/Cas9 we specifically perturb CTCF binding sites or constitutive transcription at the ZRS-containing boundary, without altering the enhancer sequence. Using capture-HiC (cHiC) we show that both types of perturbation result in altered preformed chromatin interactions and lead to a reduction of Shh expression in developing limb buds. Finally, we demonstrate that the disruption of the chromatin structure in combination with a hypomorphic ZRS allele results in a dramatic Shh loss of function and digit agenesis. We thus propose that preformed chromatin structures can ensure stable enhancer promoter communication during development and robustness of gene transcriptional activation.

overall_design: We performed Circular Chromosome Conformation Capture (4C seq) on E10.5 mouse limb buds to determine the regulatory domain of Shh gene in wildtype and mutants.


title: Transcriptome time course of mouse acute myeloid leukemia cells upon PU.1 restoration and knockdown

city: Roseworthy

first: Ruijie

last: Liu

state: South Australia

address: Mudla Wirra Rd

institute: the university of Adelaide

summary: We have utilized advanced RNAi technology to dynamically restore and subsequently knock down endogenous PU.1 expression in p53-deficient AML cells, which respectively causes differentiation and de-differentiation

overall_design: RNA-seq was performed on AML246 cells following Dox treatment or withdrawal over a 24 day time course

first: Ethan

middle: P

last: Oxley

first: Ross

middle: A

last: Dickins

first: Matthew

middle: E

last: Ritchie


title: PU.1 ChIP-seq time course in mouse acute myeloid leukemia cells upon PU.1 restoration and knockdown

overall_design: ChIP-seq was performed on AML246 cells following Dox treatment or withdrawal over a 24 day time course

first: Michael

last: Chopin

first: Stephen

middle: L

last: Nutt


title: Single cell expression profiling of murine p53-/- shPU.1 AML cells following PU.1 restoration

city: Melbourne

first: Shian

last: Su

state: Victoria

address: 1G Royal Parade

department: Molecular Medicine

institute: Walter and Eliza Hall Institute of Medical Research

summary: We have utilized advanced RNAi technology to dynamically restore endogenous PU.1 expression in p53-deficient AML cells.

overall_design: RNA-seq was performed on individual clone 2 AML246 cells either untreated or treated with doxycycline for 14 days, compared with normal mouse peripheral blood neutrophils.

first: Mark

last: McKenzie

first: Tracey

middle: M

last: Baldwin

first: Shalin

middle: H

last: Naik

first: Daniela

last: Zalcenstein


title: Next generation sequencing of human hepatic stellate cell line, LX-2 treated with recombinant human TGF-β1, with DMSO or ML290 (5 µM) for 72h.

city: Miami

first: Alexander

last: Agoulnik

state: FL

department: Human and Molecular Genetics

institute: Florida International University Herbert Wertheim College of Medicine

summary: The overall aim of this experiment was to identify specific genes and molecular pathways regulated by ML290, a small molecule agonist of the relaxin receptor, RXFP1, in the context of liver fibrosis.

overall_design: Whole transcriptome mRNA sequencing of transformed LX-2 cells using HiSeq platforms with paired-end 150 bp (PE 150) sequencing strategy, with four biological replicates in each treatment group.

middle: I


title: Single-cell reference cell state map of early mouse development

first: Helene

last: Kretzmer

address: Ihnestraße 63

department: Genome Regulation

summary: Ontogeny describes the orchestrated assembly of a complex multicellular organism from a single totipotent zygote. As the embryo grows, proliferating cells become restricted in their fate to realize one of many encoded phenotypes, which are subsequently maintained through the combined action of cell-type specific transcription factors and broadly expressed regulatory machinery. Here, we provide a reference map of mouse development through gastrulation and early organogenesis, which can be used to explore the partitioning of early lineages and discrete cell states.

overall_design: Single-cell RNAseq data was collected on whole early mouse embryos. Each experiment consists of 4-10 replicates of developmental stages 6.5, 7.0, 7.5, 8.0, 8.5 for wild-type sequenced with 10X Genomics single-cell RNA sequencing system.

first: Stefanie

last: Grosswendt

first: Zachary

last: Smith

first: Abhishek

last: Sampath Kumar

first: Sven

last: Klages

first: Shankar

last: Mukherji

last: Meissner


title: Aging Human Hematopoietic Stem Cells Manifest Profound Epigenetic Reprogramming of Enhancers That May Predispose to Leukemia (RNA-seq of KLF6 KO)

first: Maria

last: Figueroa

address: 1501 NW 10th Avenue

department: Biochemistry

institute: University of Miami

summary: Aging is associated with functional decline of hematopoietic stem cells (HSC) as well as an increased risk of myeloid malignancies. We performed an integrative characterization of epigenomic and transcriptomic changes, including single-cell RNA-seq, during normal human aging. Lineage-CD34+CD38- cells (HSC-enriched, HSCe) undergo age-associated epigenetic reprogramming consisting of redistribution of DNA methylation and reductions in H3K27ac, H3K4me1 and H3K4me3. This reprogramming of aged HSCe globally targets developmental and cancer pathways which are comparably altered in AML of all ages; encompassing loss of 4,656 active enhancers, 3,091 bivalent promoters, and deregulation of several epigenetic modifiers and key hematopoietic transcription factors, such as KLF6, BCL6 and RUNX3. Notably, in vitro downregulation of KLF6 results in impaired differentiation, increased colony forming potential and changes in expression that recapitulate aging and leukemia signatures. Thus, age-associated epigenetic reprogramming may form a predisposing condition for the development of age-related AML.

overall_design: CRISPR-Cas9 mediated knockout of KLF6 was performed in human peripheral blood CD34+ cells (n=4 replicates). RNA-seq was utilized to determine the effect of KLF6 knockout compared to a non-targeting control control.

first: Emmalee

last: Adelman

first: Hsuan-Ting

last: Huang

first: Alejandro

last: Roisman

first: André

last: Olsson

first: Antonio

last: Colaprico

first: Tingting

last: Qin

first: R

last: Lindsley

first: Rafael

last: Bejar

first: Nathan

last: Salomonis

first: H

last: Grimes


title: ATAC-seq time course in mouse acute myeloid leukemia cells upon PU.1 restoration and knockdown

first: Ruijie

last: Liu

overall_design: ATAC-seq was performed on AML246 cells following Dox treatment or withdrawal over a 24 day time course

first: Ethan

last: Oxley

first: Charles

last: Bell

first: Mark

last: Dawson

first: Ross

last: Dickins

first: Matthew

last: Ritchie


title: Aging Human Hematopoietic Stem Cells Manifest Profound Epigenetic Reprogramming of Enhancers That May Predispose to Leukemia (H3 ChIPseq)

first: Maria

last: Figueroa

overall_design: ChIP-sequencing was performed on FACS isolated human bone marrow derived HSCe (Lineage-, CD34+, CD38-) from young (18-30 yo) and aged (65-75 yo) donors. Donors had no known hematological malignancy. ChIP-seq was performed for total histone 3, using 10,000-15,000 cells per immunoprecipitation, and 2 biological replicates per age group.


title: Expression profiling of murine monosomal karyotype p53-/- shPU.1 AML cells following gradual PU.1 restoration

summary: We have utilized advanced RNAi technology to dynamically restore endogenous PU.1 expression in p53-deficient AML cells. This causes rapid cell cycle shutdown and myeloid differentiation. PU.1 restoration results in regression and clearance and prolongs survival.

overall_design: RNA-seq was performed on AML410 cells isolated from duplicate untreated or duplicate Dox-treated mice.

last: McKenzie

first: Cynthia


title: Expression profiling of murine cytogenetic normal p53-/- shPU.1 AML cells following gradual PU.1 restoration

summary: We have utilized advanced RNAi technology to dynamically restore endogenous PU.1 expression in p53-deficient AML cells . This causes rapid cell cycle shutdown and myeloid differentiation. PU.1 restoration results in regression and clearance and prolongs survival.

overall_design: RNA-seq was performed on AML246 cells isolated from triplicate untreated or triplicate Dox-treated mice.


title: Expression profiling of p53-/- shPU.1 AML cells single cell clones

summary: We have utilized advanced RNAi technology to dynamically restore endogenous PU.1 expression in p53-deficient shPU.1 AML single cell clones in vitro. This causes rapid cell cycle shutdown and reversible myeloid differentiation.

overall_design: RNA-seq was performed in  biological triplicate single cell clones that were either untreated, treated with Dox for 14 days or treated with Dox for 14 days washed and left untreated


title: Cow mammary glande miRNomes

status: Public on May 12 2019

city: saint-genes-champanelle

first: Pierre-Alexis

last: Billa

address: route de theix

department: UMRH

country: France

institute: INRA

type: Non-coding RNA profiling by high throughput sequencing

summary:
Effect of breed in mid lactation Holstein (H) and Montbéliarde (M) cows on mammary glande miRNA profile.
Genetic polymorphisms are known to influence milk production and composition. However, genomic mechanisms involved in the genetic regulation of milk component synthesis are not completely understood. MicroRNAs (miRNA) regulate gene expression. The objective of the present study was to compare mammary gland miRNomes of two dairy cow breeds, Holstein and Montbéliarde, with different dairy performances.  Milk, fat, protein, and lactose yields were lower in Montbéliarde than in Holstein cows. MiRNomes obtained using RNA-Seq technology from the mammary glands of Holstein (n = 5) and Montbéliarde (n = 6) lactating cows revealed 623 distinct expressed miRNAs, among which 596 were known and 27 were predicted miRNAs. The comparison of their abundance in the mammary gland of Holstein versus Montbéliarde cows showed 22 differentially expressed miRNAs (Padj ≤ 0.05). Among them, 11 presented a fold change ≥2, with 2 highly expressed miRNAs (miR-100 and miR-146b). Without taking into account the fold change, the differential miRNA with the highest abundance was miR-186, which is known to inhibit cell proliferation and epithelial-to-mesenchymal transition. Data mining showed that the 17 differentially expressed miRNAs with more than 20 reads on average, regulate mammary gland plasticity and may be related to the observed differences in milk production between Holstein and Montbéliarde, which are two breeds with different mammogenic potential. Some of the 17 miRNAs could potentially target mRNAs involved in signaling pathways (such as mTOR) and in lipid metabolism, thereby suggesting that they could influence milk composition.  In conclusion, we showed differences in mammary gland miRNomes of two dairy bovine breeds. These differences suggest a potential role of miRNAs in mammary gland plasticity and in milk component synthesis related to milk production and composition.

overall_design: Comparaison of miRNome of mammary gland obtain by biopsies between two breeds of dairy cows (Holstein and Montbéliarde)

first: Christine

last: Leroux

first: Ye

last: Tao

first: Faulconnier

last: Yannick


title: Estrogen receptor and mTOR signaling rewires cancer metabolism in obesity-associated breast cancer

status: Public on May 11 2019

city: Urbana

first: Zeynep

last: Madak-Erdogan

state: Illinois

address: 1201 W. Gregory Dr, 359 ERML Hall

department: Food Science and Human Nutrition

institute: University of Illinois at Urbana-Illinois

summary: Obesity is a risk factor for postmenopausal ERα (+) breast cancer. Molecular mechanisms activated by the factors from serum that contribute to this risk and how these mechanisms affect ERα signaling are yet to be elucidated. To identify such mechanisms, we performed whole metabolite and protein profiling in serum samples, which enabled us to focus on factors that were differentially present in serum from cancer-free vs. breast cancer susceptible and obese vs. non-obese post-menopausal women. These studies combined with in vitro assays identified free fatty acids (FFAs), as serum factors that correlate with increased proliferation and aggressiveness in ERα(+) breast cancer cells by. FFAs activated both ERα and mTOR pathways and rewired metabolism in breast cancer cells. Pathway preferential estrogen-1 (PaPE-1), which target ERα and mTOR signaling, was able to block changes induced by FFAs. In fact, PaPEs were more effective in the presence of FFAs, suggesting a role for obesity-associated gene and metabolic rewiring in providing new targetable vulnerabilities for ERα-(+) breast cancer in postmenopausal women. Our findings provide a basis for preventing or inhibiting obesity-associated breast cancer by using PaPEs that would reverse these newly appreciated metabolic properties of breast tumors in obese postmenopausal women.

overall_design:
Data set 1 (6 samples): For gene expression analysis, total RNA was extracted from 3 biological replicates for each ligand treatment using Trizol reagent and further cleaned using the RNeasy kit (QIAGEN). MCF-7 cells were treated with Veh (0.1% EtOH), 100 nM oleic acid (OA) in presence or absence of 1 μM PaPE-1 for 24 h. Once the sample quality and replicate reproducibility were verified, 2 samples from each group were subjected to sequencing.

Data set 2 (15 samples): For gene expression analysis, total RNA was extracted from 3 biological replicates for each ligand treatment using Trizol reagent and further cleaned using the RNAeasy kit (QIAGEN). MCF-7 cells were treated with Veh (0.1% EtOH) or 100 nM OA, LA, PA or SA  for 24 h. Once the sample quality and replicate reproducibility were verified, 2 samples from each group were subjected to sequencing.


title: ChIP-seq of TREX complex proteins in HEK293T cells

status: Public on May 10 2019

city: Sheffield

first: Ian

last: Sudbery

address: Firth Court, Western Bank

department: Molecular Biology and Biotechnology

country: United Kingdom

institute: University of Sheffield

summary: During gene expression, RNA export factors are mainly known for driving nucleocytoplasmic transport. While early studies suggested that the Exon Junction Complex (EJC) may provide a binding platform for them, subsequent work proposed that they are only recruited by the Cap-Binding Complex (CBC) to the 5’ end of RNAs, as part of the TREX complex. Using iCLIP, we show that the export receptor Nxf1 and two TREX subunits, Alyref and Chtop, are actually recruited to the whole mRNA co-transcriptionally via splicing but before 3’-end processing. Consequently, Alyref can alter splicing decisions and Chtop regulates alternative polyadenylation. Surprisingly, we observe that eIF4A3 stimulates Alyref deposition on single exon or spliced RNAs close to EJC sites. Additional experiments suggest that Alyref is recruited to the 5’-end of RNAs by CBC before binding RNAs near EJCs. Our study reveals mechanical insights into the co-transcriptional recruitment of mRNA export factors and how this shapes the human transcriptome.

overall_design: ChIP-seq of FLAG pull down from HEK293T cells stabally transgenic for  FLAG tagged Alyref, Chtop or Nxf1 fusion proteins.

first: Nicolas

last: Viphakone

first: Catherine

last: Heath

first: David

last: Sims

first: Stuart

last: Wilson


title: Aging Human Hematopoietic Stem Cells Manifest Profound Epigenetic Reprogramming of Enhancers That May Predispose to Leukemia (RNA-Seq of LMNA KD)

overall_design: shRNA-mediated knockdown of LMNA was performed in human peripheral blood CD34+ cells (n=8 biological replicates). RNA-seq was utilized to determine the effect of LMNA knockdown compared to empty vector control.

first: Emmalee

last: Adelman

first: Hsuan-Ting

last: Huang

first: Alejandro

last: Roisman

first: André

last: Olsson

first: Antonio

last: Colaprico

first: Tingting

last: Qin

first: R

last: Lindsley

first: Rafael

last: Bejar

first: Nathan

last: Salomonis

first: H

last: Grimes


title: Pyruvate dehydrogenase kinase is a metabolic checkpoint for polarization of macrophages to the M1 phenotype

city: Seoul

first: Do Young

last: Hyeon

state: Select State

address: 1 Gwanak-ro, Gwanak-gu

department: School of Biological Sciences

country: South Korea

institute: Seoul National University

summary: Metabolic reprogramming during macrophage polarization supports the effector functions of these cells in health and disease. Although the importance of glycolytic and oxidative metabolism in M1 and M2 macrophages, respectively, is well established, our knowledge of metabolic checkpoints controlling these effector states is limited. Here we demonstrate that pyruvate dehydrogenase kinase (PDK), which inhibits the conversion of cytosolic pyruvate to mitochondrial acetyl-CoA by pyruvate dehydrogenase, functions as a metabolic checkpoint in M1 macrophages. Genetic deletion or pharmacological inhibition of PDK2/4 prevents polarization of macrophages to the M1 phenotype in response to inflammatory stimuli (lipopolysaccharide plus IFN-γ). The therapeutic potential of attenuation of pro-inflammatory responses by PDK inhibition was tested, both genetically and pharmacologically, in obesity-induced insulin resistance, a disease process in which M1 macrophages contribute to adipose tissue inflammation and insulin resistance. Taken together, these studies identify PDK2/4 as a metabolic checkpoint for M1 phenotype polarization of macrophages.

overall_design: mRNA expression profiles of Mus musculus peritoneal macrophages (PMs) at the following three conditions were examined by Illumina Hi-seq 2500: wild-type PMs untreated (Cont-WT) or treated with LPS (100 ng/ml) and IFN-γ (10 ng/ml) for 12 hr (M1-WT), and PDK2/4 double knock-out PMs treated with LPS and IFN-γ for 12 hr (M1-DKO).

first: In-kyu

last: Lee

first: Daehee

last: Hwang


title: Mubritinib Targets the Electron Transport Chain Complex I and Reveals the Landscape of OXPHOS Dependency in Acute Myeloid Leukemia

city: Toronto

first: Micheal

last: Tyers

state: Ontario

address: 555 University Avenue

country: Canada

institute: The Hospital for Sick Children

summary: To identify novel therapeutic targets in Acute Myeloid Leukemia (AML), we chemically interrogated 200 sequenced primary specimens. We identified Mubritinib, a known ERBB2 inhibitor, as a strong in vitro and in vivo anti-leukemic compound. We demonstrate that, in the context of AML, Mubritinib functions through ubiquinone-dependent inhibition of Electron Transport Chain (ETC) complex I activity. Resistance to Mubritinib characterized normal CD34+ hematopoietic cells and chemotherapy-sensitive AMLs, which displayed transcriptomic hallmarks of hypoxia. Conversely, sensitivity correlated with mitochondrial function-related gene expression levels and characterized a large subset of chemotherapy-resistant AMLs with oxidative phosphorylation (OXPHOS) hyperactivity. Altogether, our work thus identifies a novel ETC complex I inhibitor and reveals for the first time the genetic landscape of OXPHOS dependency in this disease.

overall_design: Nalm-6 cells infected with the EKO sgRNA library (Bertomeu et al. 2017, PMID:29038160), after 7 days of Cas9 induction with doxycycline, were exposed to either 200nM mubritinib or 0.1% DMSO for 8 days. sgRNA abundance was then assessed by high-throughput sequencing. Cells collected before the treatment and DMSO-treated cells served as controls.

first: Irène

last: Baccelli

first: Corinne

last: St-Denis

first: Thierry

last: Bertomeu

first: Jasmin

last: Coulombe-Huntington

first: Michael

first: Guy

last: Sauvageau


title: Single-cell RNA-sequencing of GM-CSF derived macrophages

status: Public on May 09 2019

city: Cambridge

first: Brian

last: Hie

state: MA

address: 77 Massachusetts Ave

institute: MIT

summary: We obtained single-cell RNA-sequencing (scRNA-seq) profiles of GM-CSF derived macrophages from CD14+ monocytes isolated from human peripheral blood with 6 days of GM-CSF stimulatio across multiple donors.

overall_design: scRNA-seq of GM-CSF derived macrophages

first: Bryan

last: Bryson

first: Bonnie

last: Berger


title: Mammalian SWI/SNF collaborates with a polycomb-associated protein to regulate germ line transcription in the mouse [CUT&RUN]

city: Chapel hill

first: Terry

last: Magnuson

state: NC

address: 120 Mason Farm Road, Genetics Medicine Bldg.,

department: Genetics

institute: University of North Carolina at Chapel Hill

summary: CUT&RUN to monitor SCML2 localization in  BRG1-WT and BRG1-cKO spermatogenic cells

overall_design: CUTnRUN was performed on P12 Brg1WT and Brg1cKO (conditional knockout generated with Mvh-cre) spermatogenic cells.

first: Debashish

last: Menon

first: Yoichiro

last: Shibata

first: Weipeng

last: Mu


title: Reversible transitions between transformed and differentiated states in AML

first: Ruijie

last: Liu

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

overall_design: Refer to individual Series


title: Mammalian SWI/SNF collaborates with a polycomb-associated protein to regulate germ line transcription in the mouse [RNA-seq]

summary: RNA-seq on spermatogenic cells from P12 testes

overall_design: RNA-seq was performed on spermatogenic cells obtained from P12 Brg1WT and BrgcKO testes. A total of 4 biological replicates per genotype were analyzed to determine differential gene expression.


title: PU.1 ChIP-seq in p53-/- shPU.1 AML cells following acute PU.1 restoration

summary: We have utilized advanced RNAi technology to dynamically restore endogenous PU.1 expression and perform PU.1 ChIP-seq in p53-deficient shPU.1 AML cells in vivo. This causes rapid cell cycle shutdown and myeloid differentiation. PU.1 restoration results in regression and clearance and prolongs survival.

overall_design: ChIP-seq was performed on AML-246 cells isolated from untreated or 2d Dox-treated mice

first: Mark

last: McKenzie

first: Ross

last: Dickins

first: Matthew

last: Ritchie


title: Mammalian SWI/SNF collaborates with a polycomb-associated protein to regulate germ line transcription in the mouse [ATAC-seq]

summary: ATAC-seq on spermatogenic cells from P12 and P18 testes

overall_design: ATAC-seq was performed in duplicates  on spermatogenic cells obtained from P12 Brg1WT and Brg1cKO (conditional knockout generated with Mvh-cre) testes. At P18, ATAC-seq was performed on  spermatogenic cells obtained from Brg1WT and Brg1Het testes.


title: Mammalian SWI/SNF collaborates with a polycomb-associated protein to regulate germ line transcription in the mouse [ChIP-seq]

summary: ChIP-seq of BRG1 and histone modifications from spermatogenic cells

overall_design: BRG1 ChIPs were performed in duplicates on spermatogenic cells obtained from wild type P12 and P18 mouse testes. For histone modifications, H2AK119ub1 and H3K27ac ChIPs were performed in duplicates on spermatogenic cells obtained from P12 Brg1WT and Brg1cKO (conditional knockout generated with Mvh-cre) testes.


title: Mammalian SWI/SNF collaborates with a polycomb-associated protein to regulate germ line transcription in the mouse


status: Public on May 08 2019

city: Utrecht

first: Anna

last: Alemany

state: Utrecht

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institue

summary:
Single-Cell Analysis of the Liver Epithelium Reveals Dynamic Heterogeneity and an Essential Role for YAP in Homeostasis and Regeneration
The liver is an essential organ with compartmentalized metabolic processes  and significant regenerative capabilities. Repopulation of the liver  parenchyma can transpire from both main epithelial cell types, hepatocytes  and biliary epithelial cells (BECs). Here, we harness high-throughput  single-cell RNA sequencing (scRNA-seq) to dissect the transcriptional  heterogeneity and cellular diversity of these epithelial compartments in  homeostasis and injury. Our data argue against the idea of a rigidly  defined liver progenitor cell in BECs, finding instead that heterogeneity  in homeostatic BECs is principally distinguished by a YAP-dependent  program that defines a dynamic cellular state. We report that this  cellular state dynamically fluctuates between BECs and can be induced in  the majority of BECs in response to environmental stimuli and injury.  Functional studies demonstrate that YAP is distinctly required for BEC  survival in homeostasis, uncovering a tight physiological necessity for  YAP signaling in BECs compared to other tissues. YAP is also essential for  hepatocyte reprogramming towards a ductal progenitor fate upon injury.  Finally, our data demonstrate that this YAP-driven cellular state is  highly responsive to injury by physiological exposure to bile acids (BAs)  via apical sodium-bile acid transporter, and that sequestration of  endogenous BAs rescues the cell loss phenotype associated with homeostatic  Yap deletion. Together, our findings uncover previously undescribed  molecular heterogeneity within the ductal epithelium and highlight a  distinct and potent role for YAP as a protective rheostat and regenerative  regulator in the mammalian liver.

overall_design: RNA sequencing data from single biliary epithelial cells isolated from mouse livers

middle: J

last: Pepe-Mooney

middle: T

last: Dill

first: Jose

last: Ordovas-Montanes

first: Yuki

last: Matsushita

first: Anuradha

last: Rao

first: Anushna

last: Sen

first: Makoto

last: Miyazaki

first: Sayeepriyadarshini

last: Anakk

first: Paul

last: Dawson

first: Noriaki

last: Ono

first: Alex

middle: K

last: Shalek

first: Alexander

last: van Oudenaarden

first: Fernando

last: Camargo


title: SR9009 has REV-ERB-independent effects on cell proliferation and metabolism

city: Philadelphia

first: Chunjie

last: Jiang

state: PA

address: 3400 Civic Center Boulevard

department: Institute for Diabetes, Obesity, and Metabolism

institute: University of Pennsylvania

summary: The nuclear receptors (NRs) REV-ERBα and β, encoded by Nr1d1 and Nr1d2, link circadian rhythms and metabolism. REV-ERB lacks the canonical NR activation domain, and thus functions as a transcriptional repressor. Like other NRs, REV-ERBs can be regulated by ligands, including naturally occurring heme, which potentiate their repressive activity. Attempts to pharmacologically target REV-ERBs by the use of putatively specific synthetic agonists, particularly SR90096, have suggested a wide range of beneficial effects in healthy as well as diseased animal models and cell systems. For instance, Sulli et al. recently reported that REV-ERB activation by SR9009 is specifically lethal to cancer (stem) cells but not other cell types. Because REV-ERBs are core components of the molecular clock, the results were interpreted as a link between the body’s circadian timekeeping system and cancer. Moreover, increased energy expenditure after SR9009 administration decreases obesity in mice, and the reported activity of SR9009 as an exercise mimetic in skeletal muscle have resulted in online sales of the compound as a performance-enhancing drug, with advertisements reassuringly highlighting REV-ERBs as the molecular target (https://www.evolutionary.org/stenabolic-sr9009-review; https://www.simplyanabolics.com/sarms/sr9009-stenabolic/).

overall_design: Mouse hepatocytes were derived from 10-week-old male REV-ERBab double floxed animals two weeks after AAV8-TBG-Cre-GFP (vs AAV8-TBG-GFP as a control) injection. Hepatocytes were treated with DMSO vs SR9009 for 8 hours.

first: Pieterjan

last: Dierickx


title: QBiC-Pred: Quantitative Predictions of Transcription Factor Binding Changes Due to Sequence Variants

city: Durham

first: Raluca

last: Gordan

address: 101 Science Dr, CIEMAS 2179

department: Center for Genomic and Computational Biology

institute: Duke University

sample_organism:
Arabidopsis thaliana
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
synthetic construct


title: Allelic specificity of IGH-DUX4 translocation in acute lymphoblastic leukemia (ALL) [H3K27ac ChIP-seq]

city: Memphis

first: Jinghui

last: Zhang

state: TN

address: 262 Danny Thomas PL, Mail stop 1135

institute: St. Jude Children's Research Hospital

summary: In Nalm6, allelic imbalance was found at IGH-DUX4 translocation locus from H3K27ac ChIP-seq data.

overall_design: H3K27ac ChIP-seq

first: Liqing

last: Tian

first: Ying

last: Shao

first: Beisi

last: Xu

first: Xiaotu

last: Ma

first: Yongjin

last: Li

first: Bensheng

last: Ju

first: Scott

last: Newman

first: Xin

last: Zhou

first: Elizabeth

last: Tseng

first: Ting

last: Hon

first: Meredith

last: Ashby

first: John

last: Easton


title: Allelic specificity of IGH-DUX4 translocation in acute lymphoblastic leukemia (ALL) [Capture-C]

summary: In Nalm6, mono-allelic interaction between IGH enhancer and IGH promoter was found from Capture-C data.

overall_design: Capture-C


title: Allelic specificity of IGH-DUX4 translocation in acute lymphoblastic leukemia (ALL) [H3K27Ac HiChIP]

summary: In Nalm6, mono-allelic interaction between IGH enhancer and IGH promoter was found from H3K27ac HiChIP data.

overall_design: H3K27ac HiChIP


title: Allelic specificity of IGH-DUX4 translocation in acute lymphoblastic leukemia (ALL) [ATAC-seq]

summary: In Nalm6, allelic imbalance was found at IGH-DUX4 translocation locus from ATAC-seq data.

overall_design: ATAC-seq


title: A gain-of-function p53 mutant oncogene promotes cell fate plasticity and myeloid leukemia through the pluripotency factor Foxh1

first: Yu-Jui

last: Ho

state: New York

address: 417 E 68th St

department: Cancer Biology & Genetics Program

institute: Memorial Sloan Kettering Cancer Center

summary: Mutations in the TP53 tumor suppressor gene are common in many cancer types, including the acute myeloid leukemia (AML) subtype known as complex karyotype (CK) AML. Here, we identify a gain-of-function (GOF) p53 mutation that accelerates CK-AML initiation beyond p53 loss and, surprisingly, is required for disease maintenance. The p53R172H mutation (TP53R175H in humans) exhibits a neomorphic function by promoting aberrant self-renewal in leukemic cells, a phenotype that is present in hematopoietic stem and progenitor cells (HSPCs) even prior to their transformation. We identify the Forkhead box H1 transcription factor (Foxh1) as a critical mediator of mutant p53 function that binds to and regulates stem cell-associated genes and transcriptional programs. Our results identify a context where mutant p53 acts as a bona fide oncogene that contributes to the pathogenesis of CK-AML and suggests a common biological theme for TP53 gain-of-function in cancer.

overall_design:
RNA-sequencing of duplicated samples per condition were derived from idependent biological replicates and were then sequenced using Illumina Hiseq 2500
ChIP-sequencing of Foxh1 in p53R172H mutant murine AML cells

first: Evangelia

last: Loizou

middle: W

last: Lowe

first: Richard

last: Koche


title: KLF4 as a rheostat of osteolysis and osteogenesis in prostate tumors in the bone

city: New York City

first: Alireza

last: Khodadadi-Jamayran

address: 550 1st Ave, MSB 304

department: Division of Advanced Research Technologies (DART)

institute: New York University, NYU Langone Medical Center

summary: We previously found that KLF4, a gene highly expressed in adult prostate stem cells, blocks the progression of indolent intraepithelial prostatic lesions into aggressive and rapidly growing tumors. To test whether this anti-cancer effect of KLF4 can also prevent prostate cancer-induced damage to the bone, we ablated KLF4 in human PC3 prostate cancer cells using CRISPR/Cas9-mediated genome editing and compared their behavior to null cells transduced with a DOX inducible KLF4 expression system. KLF4 re-expression inhibited growth of PC3 null cells in monolayer and as colonies in soft agar in a dose-dependent manner. When injected into the mouse femurs, PC3 null cells proliferated rapidly, forming very large, invasive and osteolytic tumors. Induction of KLF4 expression in PC3 null cells immediately after their intra-femoral inoculation blocked the development of tumors while preserving the normal bone architecture. KLF4 re-expression in established PC3 bone tumors inhibited osteolytic effects of PC3 null cells, preventing bone fractures and inducing a significant osteogenic response with regions of new bone formation. Transcriptome analyses of PC3 cells with no or high KLF4 expression revealed KLF4-dependent osteolytic or osteogenic transcriptional programs, respectively. Importantly, these KLF4-dependent functions significantly overlapped with metastatic prostate cancers in patients.

overall_design: Uninfected PC3 KLF4 wild-type cells and uninfected PC3 KLF4 null cells were grown for 48 hours and collected for RNA extraction. Another cohort of PC3 KLF4 null cells was infected with lentiviruses expressing a DOX inducible KLF4 expression construct (BFP-T2A-hKLF4) or the control empty vector (BFP-T2A). After 48 hours, DOX (10 ng/ml) was added to the culture medium to induce KLF4 expression. Control and KLF4-overexpressing cells were collected for RNA extraction after a 48-hour incubation with DOX. Total RNA was extracted using the RNeasy kit (Qiagen, CA, USA). RNA-Seq libraries were prepared with the TruSeq sample preparation kit (Illumina, CA, USA).

first: Evelyne

last: Tassone

first: Markus

last: Schober

first: Ana

last: Sastre Perona

first: Elaine

last: Wilson


title: Allelic specificity of IGH-DUX4 translocation in acute lymphoblastic leukemia (ALL) [Hi-C]

first: Jinghui

last: Zhang

summary: In Nalm6, mono-allelic interaction between IGH enhancer and IGH promoter was found from Hi-C data.

overall_design: Hi-C

first: Liqing

last: Tian

first: Ying

last: Shao

first: Beisi

last: Xu

first: Xiaotu

last: Ma

last: Li


title: Effects of hydroxyurea on CNV induction in the mouse germline

city: Ann Arbor

first: Thomas

middle: E.

state: MI

address: 2065 BSRB, 109 Zina Pitcher

department: Department of Pathology

institute: University of Michigan

type: Genome variation profiling by genome tiling array

summary: We examined the effects of hydroxyurea (HU) treatment on germline copy number variants (CNVs) in vivo in male mice. Several trials of HU administration were performed by oral gavage and subcutaneous pump, with CNVs characterized in C57BL/6 x C3H/HeJ hybrid mouse offspring by microarray and mate-pair sequencing. This accession contains the Nimblegen aCGH microarray data from mice treated by oral gavage or by subcutaneous pump.

overall_design: Comparison of genomes from individual pups to all other pups from C3H/HeJ x C57BL/6 crosses, to detect de novo CNVs. C57BL/6 males were treated with hydroxyurea or served as untreated controls, while C3H/HeJ females were untreated.

first: Martin

middle: F

last: Arlt

first: Sountharia

last: Rajendran

first: Sandra

middle: N

last: Holmes

first: Kathleen

last: Wang

first: Ingrid

last: Bergin

first: Samreen

last: Ahmed

last: Glover


title: Temporal patterning of apical progenitors and their daughter neurons in the developing neocortex

city: Geneva

first: Julien

last: Prados

address: Rue Michel Servet 1

department: SCMU

country: Switzerland

institute: University of Geneva

summary: During cortical development, distinct subtypes of glutamatergic neurons are sequentially born and differentiate from dynamic populations of progenitors. How progenitors and their daughter cells are temporally patterned remains unknown. Here, we trace the transcriptional trajectories of successive generations of apical progenitors (APs) and isochronic cohorts of their daughter neurons in the developing mouse neocortex using high temporal resolution parallel single-cell RNA sequencing. We identify and functionally characterize a core set of evolutionarily-conserved temporally patterned genes which drive APs from internally-driven states to more exteroceptive states, revealing a progressively increasing role for extracellular signals as corticogenesis unfolds. These embryonic age-dependent AP molecular states are reflected in their neuronal progeny as successive ground states, onto which essentially conserved early post-mitotic differentiation programs are applied. Thus, temporally unfolding molecular birthmarks present in progenitors act in their post-mitotic progeny as seeds for adult neuronal diversity.

overall_design: Investigation of the transcriptional dynamics in time-locked cohorts of cortical cells across embryonic neurogenesis. Flashtag is injected at 4 ages (E12, E13, E14, E15), and cells collected 1H, 24H, 96H after birth (= a total of 12 conditions) and analyzed by single cell transcriptomics.

first: Ludovic

last: Telley

first: Gulistan

last: Agirman

first: Nicole

last: Amberg

first: Sabine

last: Fièvre

first: Polina

last: Oberst

first: Giorgia

last: Bartolini

first: Ilaria

last: Vitali

first: Christelle

last: Cadilhac

first: Simon

last: Hippenmeyer

first: Laurent

last: Nguyen

first: Alexandre

last: Dayer

first: Denis

last: Jabaudon


title: Identification of genes regulated by long noncoding RNA H19 in the ovary.

city: Farmington

last: Zhang

state: CT

address: 400 Farmington Ave

department: Genetics and Genome Sciences

institute: UConn Health

summary: In order to identify genes regulated by long noncoding RNA H19 in the ovary, we performed RNA-Seq with WT and H19KO ovaries from 8-week old mice. Among the differentially expressed genes, we found anti-mullerian hormone (AMH), which potentially plays an important role in regulating ovarian follicular development, might be a target of H19 mediated regulation.

overall_design: Ovaries were harvested from 8-week old WT and H19KO mice, followed by total RNA extraction, library preparation and RNA-seq analysis to compare gene expression profiles between WT and H19KO conditions.

first: Gordon

middle: G

last: Carmichael

first: Amanda

last: Kallen


title: Allelic specificity of IGH-DUX4 translocation in acute lymphoblastic leukemia (ALL)

first: Jinghui

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

overall_design: Refer to individual Series


title: Microarray analysis of liver biopsies at baseline and after one year follow up from 21 patients with histologically proven NASH (responders, bariatric surgery).

city: Lille

first: Lefebvre

last: Philippe

address: Bld Pr Jules Leclerc

institute: Inserm

summary: We used microarray analysis to study the global program of gene expression in the liver of 21 patients with histologically proven NASH who had an improvement in disease activity, including a decrease of lobular inflammation and/or ballooning, one year after Roux-en-Y gastric bypass.

overall_design: High quality RNA appropriate for microarray analysis was isolated from liver biopsies at baseline and after one year follow up.

last: Mogilenko

first: Luisa

last: Vonghia

first: Philippe

last: Lefebvre

first: Bart

last: Staels

first: Sven

last: Francque

first: David

last: Dombrowicz


title: Identification of key genes and molecular mechanisms associated with low egg production of broiler breeder hens in ad libitum

city: Yangling

first: Cunling

last: Jia

state: Shaanxi

address: Xinong road 22#

department: Animal science

country: China

institute: Northwest A&F University

summary: Overfeeding reduces laying performance in broiler breeder hens (Gallus gallus domesticus). To unravel the effect of feeding regimes on energy metabolism and egg production, high-throughput RNA sequencing was utilized to identify differentially expressed genes (DEGs) in ovary, liver and adipose tissues of broiler chickens under ad libitum and restricted feeding. The transcriptome analysis showed that 289, 388 and 204 DEGs were identified in the adipose tissue, liver and ovary, respectively, between ad libitum and restricted feeding groups. Bioinformatics analysis by STRING further revealed DEGs were significantly enriched in phagosome pathway, lipid transport and location biological process, and the molecular function of lipid transporter activity and nutrient reservoir activity in ovary; the pathways of “steroid hormone biosynthesis” and “metabolism of xenobiotics by cytochrome P450”, and the molecular function of nutrient reservoir activity in adipose tissue; the metabolic pathways, Jak-STAT signaling pathway and PPAR signaling pathway in liver.

overall_design: Gene expression from 3 tissues including adipose, liver and ovary of hens under ad libitum（3 hens） and restricted feeding（3 hens） was measured by Illumina HiSeqTM PE125.

first: Zehui

last: Wei


title: KH-type splicing regulatory protein controls colorectal cancer cell growth and modulates the tumor microenvironment

city: San Francisco

first: Francesco

last: Caiazza

state: CA

address: 600 16th street, Room S-514

department: Pharmaceutical Chemistry

institute: UCSF

summary:
KH-type splicing regulatory protein (KHSRP) is a multifunctional nucleic acid binding protein. KHSRP regulates transcription, mRNA decay and translation, and miRNA biogenesis that influence distinct functions associated with cancer cell biology, such as inflammation and cell-fate determination. Our study uncovered novel mechanistic-based data on the tumor-promoting effects of KHSRP in colorectal cancer.
We used microarrays to detail changes in gene expression upon specific knockdown of KHSRP in SW480 cells

overall_design: SW480 cells were transiently transfected with KHSRP siRNA for RNA extraction and hybridization on Affymetrix microarrays.

first: Elizabeth

last: Ryan


title: RNA-Seq from human ILC transitional populations

status: Public on May 07 2019

city: St. Louis

first: Marco

last: Colonna

state: MO

address: 660 S. Euclid Ave.

institute: Washington University in St. Louis

summary: Innate lymphoid cells (ILCs) are tissue-resident lymphocytes subdivided into ILC1s, ILC2s and ILC3s based on core regulatory programs and signature cytokines secreted. ILCs exhibit functional plasticity: for instance, human IL-22-producing ILC3s convert into IFN-γ-producing ILC1-like in vitro. Whether this conversion occurs in vivo is unclear. Using flow cytometry, mass cytometry and scRNAseq, here we found that ILC3s and ILC1s occupy opposite ends of a spectrum including discrete subsets in human tonsils. RNA velocity suggested strong directionality toward ILC1s for one ILC3-ILC1 intermediate cluster. Clonal analysis revealed graded ability of ILC3-ILC1 subsets to convert into ILC1-like cells. When examined in humanized mice, ILC3 acquisition of ILC1 features showed tissue-dependency. In chromatin studies, Aiolos emerged as a nuclear factor that cooperates with Tbet to repress evolutionarily conserved regulatory elements active in ILC3s. The human intestine also exhibited an ILC3–ILC1 transitional population. We conclude that conversion of ILC3s to ILC1-like occurs in vivo in human tissues, and that tissue factors and Aiolos are crucial for this process.

overall_design: ILCs were sorted from human tonsils. 3-4 biological replicates were analyzed per cell type.

first: Cella

last: Marina

first: Peng

last: Vincent

first: Colonna

last: Marco


title: Microarray data from human ILC transitional populations

overall_design: ILCs were sorted from  human tonsils. 3-4 biological replicates were analyzed per cell type.

first: Marina

last: Cella

first: Michelle

last: Robinette

first: Vincent

last: Peng


title: Expression profiling of ILC transitional populations and Aiolos accessability and H3K27ac histone modifications in transfected MNK3 cells

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: Membralin deficiency dysregulates astrocytic glutamate homeostasis leading to ALS-like impairment

city: La Jolla

first: Timothy

last: Huang

address: 10901 N Torrey Pines Rd.

institute: Sanford Burnham Prebys Medical Discovery Institute

summary: Mechanisms underlying motor neuron degeneration in amyotrophic lateral sclerosis (ALS) are yet unclear. Specific deletion of the ER-component membralin in astrocytes manifested postnatal motor defects and lethality in mice, causing the accumulation of extracellular glutamate through reducing the glutamate transporter EAAT2. Restoring EAAT2 levels in membralin KO astrocytes limited astrocyte-dependent excitotoxicity in motor neurons. Transcriptomic profiles from mouse astrocytic membralin KO motor cortex indicateed significant perturbation in KEGG pathway components related to ALS, including downregulation of Eaat2 and upregulation of Tnfrsf1a. Changes in gene expression with membralin deletion also overlapped with mouse ALS models and reactive astrocytes. Our results shown that activation of TNF receptor (TNFR1)-NFkB pathway known to suppress Eaat2 transcription was upregulated with membralin deletion. Further, reduced membralin and EAAT2 levels correlated with disease progression in spinal cord from SOD1-mutant mouse models, and reductions in membralin/EAAT2 were observed in human ALS spinal cord. Importantly, overexpression of membralin in SOD1G93A astrocytes decreased TNFR1 levels and increased EAAT2 expression, and improved motor neuron survival. Importantly, upregulation of membralin in SOD1G93A mice significantly prolonged mouse survival. Together, our study provides a mechanism for ALS pathogenesis where membralin limits glutamatergic neurotoxicity, suggesting that modulating membralin has potential in ALS therapy

overall_design: Motor cortex mRNA profiles from 22-day old wild type (WT) and membralin astrocyte conditional knockout (Astro-mem KO) were generated by RNAseq. Five biological repeats were included per genotype.

first: LuLin

last: Jiang

first: Huaxi

last: Xu


title: RNA-Seq JunB WT and KO Tregs Mus musculus

city: Heidelberg

first: Guoliang

last: Cui

address: Im Neuenheimer Feld 280

institute: German cancer research center (DKFZ)

overall_design: To study if JunB regulated Treg suppressive function, we created a mouse strain with Treg-specific ablation of Junb (Foxp3YFP-Cre×JunbFlox/Flox) by crossing the Foxp3YFP-Cre mice and the JunbFlox/Flox strain. Non-Treg CD4+ T cells and CD8+ T cells in the KO mice produced a larger amount of IFNγ and TNFα after PMA and ionomycin stimulation, whereas IL-17 production was not influenced. To understand the mechanisms through which JunB regulates Tregs-mediated immune regulation, we examined the global gene expression profiles in the JunB WT and KO Tregs by performing RNA sequencing (RNA-seq) analysis. The subsequent Ingenuity Pathway Analysis (IPA) revealed that the JunB deficiency reduced the expression of a panel of genes reported to be enriched in Tregs.

first: Jingxia

last: Wu


title: Endothelial ERK1/2 signaling maintains integrity of the quiescent endothelium

city: new haven

first: Nicolas

last: Ricard

address: 300 george street

department: internal medicine

institute: yale university

summary: Endothelial ERK1/2 pathway plays a crucial role in maintenance of endothelial homeostasis.  Its suppression results in activation of TGFΒ signaling, leading to hypertension, renal failure, fibrosis and sudden death, findings similar to those observed in patients treated with anti-VEGF agents.

overall_design: Examination of siERK1/2 (N=19) and siSCR (N=18) in HUVEC cells

first: Rizaldy

last: Scott

first: Carmen

last: Booth

first: Heino

last: Velazquez

first: Nicholas

last: Cilfone

first: Javier

last: Baylon

first: Jeffrey

middle: R

last: Gulcher

first: Susan

last: Quaggin

first: Thomas

last: Chittenden

first: Michael

last: Simons


title: Genome Wide Chromatin Mapping of Aiolos accessability and H3K27ac histone modifications in transfected MNK3 cells

first: Marco

last: Colonna

overall_design: Examination of H3K27Ac and IKZF3 binding sites in MNK3 transfected with control, pTbet, or pTbet + pIKZF3 expression vectors

first: Patrick

last: Collins

first: Marina

last: Cella


title: Tie2 regulates endocardial sprouting and myocardial trabeculation

city: Nashville

first: Xianghu

last: Qu

address: 2213 Garland Ave

institute: Vanderbilt medical center

summary: The ang1-Tie2 pathway is required for normal vascular development, but its molecular effectors are not well-defined during cardiac ontogeny. Here we show that endocardial specific attenuation of Tie2 results in mid-gestation lethality due to heart defects associated with a hyperplastic but simplified trabecular meshwork (fewer but thicker trabeculae). Reduced proliferation and production of endocardial cells (ECs) following endocardial loss of Tie2 results in decreased endocardial sprouting required for trabecular assembly and extension. The hyperplastic trabeculae result from enhanced proliferation of trabecular cardiomyocyte (CMs), which is associated with upregulation of Bmp10, increased retinoic acid (RA) signaling, and Erk1/2 hyperphosphorylation in the myocardium. Intriguingly, myocardial phenotypes in Tie2-cko hearts could be partially rescued by inhibiting in utero RA signaling with pan-retinoic acid receptor antagonist BMS493. These findings reveal two complimentary functions of endocardial Tie2 during ventricular chamber formation: ensuring normal trabeculation by supporting EC proliferation and sprouting, and preventing hypertrabeculation via suppression of RA signaling in trabecular CMs.

overall_design: mRNA profiles of  hearts isolated from  littermate control (Tie2 flox/wild-type, n=18) and conditional knockout (Nfatc1Cre:Tie2 flox/flox, n=18) embryos at day 11.5 of gestation. RNA for each genotype was pooled, then separated into three replicates for sequencing using the Illumina HiSeq 2500 system.

first: Cristina

last: Harmelink

first: Harold

middle: S

last: Baldwin


title: CBX2 is required to stabilize the testis pathway by repressing Wnt signaling

first: Sara

middle: A.

last: Garcia-Moreno

state: North Carolina

address: Nanaline Bldg. Research Drive

summary:
Purpose: Determine whether sex-determining genes are bivalent at the bipotential stage, poised between the testis and ovary fate, and whether H3K4me3 and H3K27me3 resolve into sex-specific patterns after sex determination, contributing to the canalization and stabilization of either the testis or ovary fate.
Methods: XX and XY supporting cells of the gonad were FACS-purified before sex determination (at E10.5) and after sex determination (at E13.5), and submitted to ChIP-seq for H3K4me3, H3K27me3 and H3 as a means to normalize across cell populations.
Results: We found that key sex-determining genes are bivalent at the bipotential stage. Genes that are upregulated affter sex determination are stripped of their repressive H3K27me3 mark, whereas repressed genes that promote the alternate pathway remain bivalent even after sex determination.

overall_design:
ChIP-seq for H3, H3K27me3, and H3K4me3 was performed in duplicate on FACS-sorted  XX and XY gonadal supporting cells from E10.5 and E13.5 mouse embryonic gonads.
NOTE: processed data was generated from both replicates and is linked to the corresponding rep1 sample records

first: S


title: Gene expression profiling of human neuroblastoma cell line BE(2)-C treated with the PHGDH inhibitor NCT-503 at 10 µM for 2 days

city: Birmingham

first: Han-Fei

last: Ding

state: Alabama

address: WTI 602D, 1824 6th Avenue South

department: Pathology

institute: University of Alabama at Birmingham

summary: Microarray gene expression profiling reveals that PHGDH inhibition by NCT-503 activates a metabolic stress response characterized by downregulation of cell cycle genes and induction of stress response genes.

overall_design: Affymetrix microarray assays were performed according to the manufacturer's directions on total RNA isolated from three independent samples of BE(2)-C cells treated with vehicle control DMSO or 10 µM NCT-503 for 2 days.

first: Han-Fe

last: i Ding

first: Jane

first: Bingwei

last: Ye


title: Chronic dysfunction of Store-operated calcium entry by pulsed RNAi induction in fat tissue impairs organismal energy homeostasis in Drosophila

city: Goettingen

first: Ronald

last: Kühnlein

state: Lower Saxony

address: Am Fassberg 11

department: Department of Molecular Developmental Biology

institute: Max Planck Institute for Biophysical Chemistry

summary:
The purpose is to have a overview on how chronic dysfunction of store-operated calcium entry change transcription profiles of  adult fly fat tissue.
Methods:To achieve chronic dysfunction of store-operated calcium entry, we carried out the Temperature-caused RNAi Pulse Induction of Stim (29 celcius degree incubation, Stim-TRiPI, or Stim-TRIP in data file) in fat storage tissue of 6 days old adult male flies. At day 10 and 11 after Stim-TRiPI (Stim-TRIP), we isolated the fat tissues and carried out RNAseq analysis based gene-level read counts.

overall_design: Fat body tissue mRNA profiles of day 10-11 Stim-TRiPI (Stim-TRIP) On and Off adult male flies were generated by deep sequencing, in triplicate, using Illumina 2500.

first: Yanjun

last: Xu


title: The Blue-Light Photoreceptor Sfwc-1 Gene Regulates the Phototropic Response and Fruiting-Body Development in the Homothallic Ascomycete Sordaria fimicola

status: Public on May 06 2019

city: Taipei

first: Kulsumpun

last: krobanan

address: No.1, Sec. 4, Roosevelt Rd., Zhongzheng Dist.

country: Taiwan

institute: National Taiwan University

summary:
Purpose: The goal of this stufy is to elucidate the transcriptional regulatory network in response to light in S. fimicola. We analyzed blue-light-induced genome-wide transcriptional responses by high-throughput RNA-seq to determine the transcriptional profiles between the wild type and Sfwc-1(∆lov) mutant. Untreated mycelia (constant darkness sample) and mycelia treated with blue light for 15 and 45 min were used to explore.

Method: the S. fimiocla wild type and Sfwc-1(∆lov) mutant were grown on malt extract agar I in constant dark for 2 days. The drak grown  samples were exposed to blue light for 15 and 45 min. The cDNA was synthesized from mRNA by using the TruSeq Stranded mRNA Library Prep Kit (Illumina, USA)and then sequencing involved using Illumina NextSeq 500. The clean RNA-seq reads were then de novo assembled into a transcript sequence by using the Trinity platform and the jaccard_clip option. The quantified gene and isoform abundances (transcript abundance estimation) were obtained by using RNA-seq by expectation-maximization (RSEM) software with the default setting of Bowtie. Then differentially expressed genes (DEGs) were identified by using the EdgeR Bioconductor package in Trinity platform. The normalized RSEM-estimated abundances weighted by Trimmed Mean of M values (TMM) method counted by EdgeR was used for pairwise comparison of each of the sample pairs.

Conclusion: Our study represents  the transcription regulatory nextwork existing in S. fmicola, generated by RNA-seq technology. The data analysis  has been providing a framework for comparative investigations of expression profiles. We conclude that RNA-seq based transcriptome characterization would expedite genetic network analyses and contribute the understanding of biologic functions in S. fimicola.

overall_design:
The mRNA profile of S. fimiocla Wild Type and Sfwc-1(∆lov) illuminated by light for 15 and 45 min were generated by using Illumina NextSeq 500.

Please note that  feature Ids like “TR4637|c0_g1” (in the processed data files) are generated in this study (de novo transciptome assembly: SF_denovo_trinity.fasta) and the corresponding public gene Id was included in the last column (https://www.ncbi.nlm.nih.gov/bioproject/13841). However, as the species Sordaria fimicola and the reference Neurospora crassa OR74A genome (used for annotation) are closely related but different species, there are 26 out of 53,338 transcripts which do not  match to the reference genome.

last: Krobanan

first: Wei-Chiang

last: Shen

first: Syun-Wun

last: Liang


title: Multi Omics analysis of fibrotic kidneys in two mouse models [RNA-Seq]

city: Boston

first: Lorena

last: Pantano

address: 655 Huntington Ave

department: Biostatistics

institute: Harvard Chan School of Public Health

summary: Kidney fibrosis represents an urgent unmet clinical need due to the lack of effective therapies and inadequate understanding of the molecular pathogenesis. We have generated a comprehensive and integrated multi-omics data set (proteomics, mRNA and small RNA transcriptomics) of fibrotic kidneys that is searchable through a user-friendly web application. Two commonly used mouse models were utilized: a reversible chemical-induced injury model (folic acid (FA) induced nephropathy) and an irreversible surgically-induced fibrosis model (unilateral ureteral obstruction (UUO)). mRNA and small RNA sequencing as well as 10-plex tandem mass tag (TMT) proteomics were performed with kidney samples from different time points over the course of fibrosis development. The bioinformatics workflow used to process, technically validate, and integrate the single data sets will be described. In summary, we present temporal and integrated multi-omics data from fibrotic mouse kidneys that are accessible through an interrogation tool to provide a searchable transcriptome and proteome for kidney fibrosis researchers.

overall_design: mRNA and small RNA sequencing (n=3 per time point, respectively) as well as proteomics (n=2 per time point) with kidney samples from different time points (day 1, 2, 3, 7 and 14) over the course of fibrosis development in two mouse models. Kidneys from day 0 were used as normal control samples i.e. as reference.

first: Mira

last: Pavkovic


title: Multi Omics analysis of fibrotic kidneys in two mouse models [miRNA-Seq]


title: Multi Omics analysis of fibrotic kidneys in two mouse models (Folic acid (FA) model MS data set)

overall_design:
mRNA and small RNA sequencing (n=3 per time point, respectively) as well as proteomics (n=2 per time point) with kidney samples from different time points (day 1, 2, 3, 7 and 14) over the course of fibrosis development in two mouse models. Kidneys from day 0 were used as normal control samples i.e. as reference.

Raw MS data deposited in PRIDE:
https://www.ebi.ac.uk/pride/archive/projects/PXD011453

first: Pantano

last: Lorena

first: Pavkovic

last: Mira


title: CtIP is essential for early B cell proliferation and development in mice

city: New York

first: Xiaobin

middle: Summer

last: Wang

state: NEW YORK

address: 1130 Siant Nicholas Ave, Room 501

department: Institute for Cancer Genetics

institute: Columbia University Medical Center

summary: B cell development requires efficient proliferation and successful assembly and modifications of the immunoglobulin gene products. CtIP is an essential gene implicated  in end-resection and DNA repair. Here we show that CtIP is essential for early B cell development, while dispensable in naïve B cells. CtIP loss is well-tolerated in G1 arrested B cells and during V(D)J recombination. But, in proliferating B cells, CtIP loss leads to a progressive cell death characterized by ATM hyper-activation, G2/M arrest,  genomic instability, and 53BP1 nuclear body formation, indicating that the essential role of CtIP during proliferation underscores its stage-specific requirement in B cells. B cell proliferation requires phosphorylation of CtIP at T847 presumably by CDK, but not its interaction with CtBP, Rb, nor its nuclease activity. CtIP phosphorylation by ATM/ATR at T859 (T855 in mice) promotes end-resection in G1 arrested cells, but dispensable for B cell development and class switch recombination, suggesting distinct roles for T859 and T847 phosphorylation in B cell development.

overall_design: Despite a moderate and transient delay at day 3, CtipT855A/T855A B cells undergo robust CSR upon activation in vitro. Consistent with the partial rescue in the reconstitution experiments, activated CtipT855A/T855A B cells show a moderate reduction in overall proliferation. Yet, the frequency of IgG1+ B % cells does not significantly differ in CtipT855A/T855A B cells vs the control (p=0.74) at each cell division, suggesting T855A-CtIP does not directly compromise IgG1 switching beyond cell proliferation. Moreover, high throughput sequencing analyses of over 10,000 CSR junctions between Sμ and downstream switch regions show that the usage of peripheral switch regions (an indicator of end-resection) and the number of micro-homologies at the junction (an indicator of Alt-EJ) are also not affected by the T855A mutation of CtIP. Taken together these findings indicate that ATR/ATM-mediated phosphorylation of CtIP at T859 promotes end-resection, but is largely dispensable for CSR in vivo.

first: Zhengping

last: Shao

first: Shan

last: Zha


title: Multi Omics analysis of fibrotic kidneys in two mouse models (Unilateral ureter obstruction (UUO) model MS data set)

overall_design:
mRNA and small RNA sequencing (n=3 per time point, respectively) as well as proteomics (n=2 per time point) with kidney samples from different time points (day 1, 2, 3, 7 and 14) over the course of fibrosis development in two mouse models. Kidneys from day 0 were used as normal control samples i.e. as reference.

Raw MS data deposited in PRIDE:
https://www.ebi.ac.uk/pride/archive/projects/PXD010861


title: Differential gene expression and physiological changes during acute or persistent plant virus interactions may contribute to viral symptom differences (microarray)

city: Budapest

first: <Up loaded by Bioinformatics core  facility>

last: <PI shown in the article>

address: Szigony st 43.

country: Hungary

institute: HUN-REN Institute of Experimental Medicine

summary:
Viruses have different strategy to infect their hosts. Acute type infection is fast resulting in severe symptoms or in the death of the plant, while in persistent type of interaction the virus can survive within its host for a long period of time with mild symptoms. During our studies we investigated gene expression changes of virus infected Nicotiana benthamiana and Solanum lycopersicum after systemic spread of the virus by two different methods: microarray hybridization and RNA sequencing. Using these high throughput techniques we could easily differentiate between acute and persistent type of infection and validate key expression changes by Northern blot hybridization. We also demonstrated that in persistent infection not only drastic downregulation of important housekeeping genes, but induction of stress genes are missing, making possible for the virus to survive in its host for a long period of time. Symptoms of acute and persistent type virus infection differ markedly and according to our results the type of infection can be distinguished even at an early point by characterizing the photosynthetic activity of virus infected plants.
RNA-Seq was made from PVX, TMV infected and mock inoculated leafs in 3 biological replicates and 1 technical repeat

overall_design: Réka, Pesti

first: Réka

last: Pesti

first: Levente

last: Kontra

first: Kenny

last: Paul

first: Imre

last: Vass

first: T

last: Csorba

first: Zoltán

last: Havelda

first: Éva

last: Várallyay


title: Effects of gene-by-environment interaction on the methylome of mice deficient for tryptophan hydroxylase 2 [MBD-seq]

city: Cologne

first: Konrad

middle: U.

last: Förstner

state: North Rhine-Westphalia

address: Gleueler Str. 60

department: Information Services

institute: ZB MED - Information Centre for Life Sciences

type: Methylation profiling by high throughput sequencing

summary:
Purpose: Investigation of effects of early adversity in mice deficient for brain serotonin on the methylome

Methods: Following materal separation in early childhood and behavioural screening in adulthood, 4 moth old males, either wildtype or carrying a hetero- or homozygous knockout of the thryptophan hyroxylase 2 gene, were sacrificed, brains extracted, the amygdalae of both hemispheres dissected, blended and separated in two protions. From one of these portions DNA was processed by an external company, i.e. Nxt-Dx (Ghent, Belgium). DNA was sheared by sonication, followed by methyl binding domain (MBD) based capture, leading to an enrichment of methylated fragments. Subsequently, library preparation was performed followed by multiplexed paired-end sequencing with a read-length of 50 bp and an approximate output of 20 million reads/sample on the Illumina HiSeq4000 platform. Reads were mapped to the Mus musculus GRCm38.p5 genome  using Bowtie2 (v2.1.0) software in end-to-end & sensitive-mode. After mapping, coverage peaks were generated using MACS 14 peak caller (Zhang et al. 2008).

Results: Either Tph2 genotype, early adversity as well as their interaction resulted in unique profiles of differentially enriched methylated peaks as well as expressed RNA. As expected, the effect sizes and significances were rather subtle and the overlap between top hits of methylome and transcriptome were marginal.

Conclusion: Tph2, MS and their interaction induced changes in gene expression and DNA methylation, within a physiological range. The observed changes by MS seemed furthermore strongly influenced by the Tph2 genotype, ergo brain 5-HT availability.

overall_design:
RNA expression adn DNA methylation profiles affected by maternal separation, brain 5-HT deficiency and their interaction in adult male mice, were generated using MBD enrichment based and RNA deep sequencing
MBD based capture (performed by Nxt-Dx, Ghent Belgium, http://www.nxt-dx.com/)

first: K

middle: P

last: Lesch

first: D

last: van den Hove

first: M

last: Weidner

middle: U

last: Förrstner

first: L

last: Eijsen

first: R

last: Lardenoije


title: Effects of gene-by-environment interaction on the transcriptome of mice deficient for tryptophan hydroxylase 2 [RNA-seq]

summary:
Purpose: Investigation of effects of early adversity in mice deficient for brain serotonin on the transcriptome

Methods: Following materal separation in early childhood and behavioural screening in adulthood, 4 moth old males, either wildtype or carrying a hetero- or homozygous knockout of the thryptophan hyroxylase 2 gene, were sacrificed, brains extracted, the amygdalae of both hemispheres dissected, blended and separated in two protions. From one of these portions RNA was extracted. Extracted RNA was further processed by an external company, i.e. IGA Technologies (Udine, Italy). , library preparation was performed using TruSeq Stranded Total RNA Library Prep Kit (Illumina, San Diego, CA, US) that captures coding RNA and multiple forms of non-coding RNA, with a total input of 300 ng of RNA, as measured with Qubit 2.0 Fluorometer (Invitrogen, Carlsbad, CA) following manufacturer’s recommendations. The sequencing was performed using the Illumina HiSeq 2500 platform at a read-length of 125 bp with paired end reads yielding 60 million reads/sample. Reads were mapped to the Mus musculus GRCm38.p5 genome using STAR (Dobin et al. 2013). Following mapping, the reads per position were determined using HTSeq (Anders et al. 2015).

Results: Either Tph2 genotype, early adversity as well as their interaction resulted in unique profiles of differentially expressed RNA. As expected, the effect sizes and significances were rather subtle.

Conclusion: Tph2, MS and their interaction induced changes in gene expression and DNA methylation, within a physiological range. The observed changes by MS seemed furthermore strongly influenced by the Tph2 genotype, ergo brain 5-HT availability.

overall_design: RNA expression profiles affected by maternal separation, brain 5-HT deficiency and their interaction in adult male mice, were generated using RNA deep sequencing


title: Ribosome profilling and RNA Sequencing of WT and Rasgrp1Anaef mouse CD4+ T cells

first: Darienne

middle: Ross

last: Myers

address: 513 Parnassus Ave, HSW 1330A, Box 0452

department: Anatomy

summary: To determine what mRNAs are translated at baseline in CD4+ T cells, and whether these are altered in Rasgrp1Anaef CD4+ T cells, which have a point mutation in the Ras GEF Rasgrp1, before the onset of autoimmunity, we performed sequencing of ribosome-protected fragments as well as total RNA from WT and Anaef T cells. We identified a number of target genes that are translated at baseline, many of which have been shown to be downstream of the kinase mTOR.

overall_design: CD4+ T cells from the lymph nodes of mice that are WT/WT or Rasgrp1Anaef/Rasgrp1Anaef were purified by a negative isolation magnetic bead-based kit. 20000 cells were lysed and total RNA was isolated (4 samples per genotpye) and RNA was sequenced (Illumina HiSeq 4000); from the rest of the cells in the pool. samples were pooled 2 by 2 (for 2 total samples per genotype), lysed, and ribosome-associated mRNAs were isolated and sequenced (Illumina HiSeq 4000)

first: Jeroen

last: Roose


title: Expression data comparing CD133+ and CD133- B16-F10 melanoma cells

status: Public on May 03 2019

first: Chris

last: Shidal

address: 2525 West End Ave 6th Floor

department: Medicine

institute: Vanderbilt University Medical Center

summary: Cancer stem cells (CSC) were isolated based on the putative stem cell marker CD133. This subset of cells has been shown to have superior tumorigenicity and metastatic ability compared to cells in the non-CSC compartment (i.e. CD133-). We compared microRNA expression profiles of CSCs to non-CSCs to identify disparities in miRNA expression and explore how these miRNAs may provide a selective survival advantage to cancer stem cells.

overall_design: B16-F10 murine melanoma cells were labelled with a monocloncal antibody against CD133 (Prominin-1) and subjected to FACS to collect CD133-negative and -positive populations arising from the parental cell population. Total RNA was isolated and hybridized on Affymetrix GeneChips (miRNA 4.0 platform). Chips were scanned using a GeneChip Scanner (Affymetrix) and microarray images were analyzed using Affymetrix Power Tools. Transcriptome Analysis Software (TAC, Affymetrix) was used to analyze and visualize microarray data.

first: Narendra

last: Singh

first: Prakash

last: Nagarkatti

first: Mitzi


title: CGH analysis of DENA-induced liver tumor in pigs (Sus scrofa)

city: Saarbrucken

first: Sonja

middle: M.

last: Kessler

address: Campus C2 3

institute: Saarland University

summary: We have employed aCGH analysis of tumor tissue compared to non-tumourous tissue in pigs treated with diethylnitrosamine (DENA). Beside other liver tumors angiosarcoma-like tumors were observed in the DENA-treated livers.

overall_design: Pigs were treated with 200 mg/kg body weight DENA. Liver was resected 10 months later. Labeling was performed following the BioPrime aCGH Genomic Labeling Module protocol (Invitrogen). The samples were hybridized on an 8x15k CGH Array under the conditions of the Agilent protocol (Version 7.2). The arrays were analyzed with an Agilent DNA Microarray Scanner G2505C and the extraction software Agilent Feature Extraction 11.0.1.1.

first: S

first: N

last: Golob-Schwarzl

first: J

last: Haybaeck


title: Differential gene expression and physiological changes during acute or persistent plant virus interactions may contribute to viral symptom differences

first: <Up loaded by Bioinformatics core  facility>

last: <PI shown in the article>

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

sample_organism:
Solanum lycopersicum
Nicotiana benthamiana

platform_organism:
Solanum lycopersicum
Nicotiana tabacum

overall_design: Refer to individual Series


title: Transcriptome and differential gene expression analysis for nacRNAi and non-transgenic sibling

status: Public on May 04 2019

city: Piscataway

first: Joachim

last: Messing

state: NJ

address: 190 Frelinghuysen Rd

institute: Waksman Institute of Microbiology, Rutgers University

summary: We report the transcriptome profile of the developing maize endosperm of nacRNAi. The nacRNAi is the transgenic maize which knocks down the expression of both ZmNAC128 and ZmNAC130 in the developing endosperm.ZmNAC128 and ZmNAC130 are the two maize endosperm-specific NAC-type transcription factors. This study finds that nacRNAi has a broad effect on the accumulation of starch and protein by regulating their main synthetic genes.

overall_design: The 20-DAP endosperm of wild type (B73) and nacRNAi siblings (Ni4) are used to do RNA-seq. There are three replicats per line, total six samples.

first: Zhiyong

last: Zhang


title: Multi Omics analysis of fibrotic kidneys in two mouse models

first: Lorena

last: Pantano

state: MA


title: Differential gene expression and physiological changes during acute or persistent plant virus interactions may contribute to viral symptom differences (RNA-Seq)

summary: Viruses have different strategy to infect their hosts. Acute type infection is fast resulting in severe symptoms or in the death of the plant, while in persistent type of interaction the virus can survive within its host for a long period of time with mild symptoms. During our studies we investigated gene expression changes of virus infected Nicotiana benthamiana and Solanum lycopersicum after systemic spread of the virus by two different methods: microarray hybridization and RNA sequencing. Using these high throughput techniques we could easily differentiate between acute and persistent type of infection and validate key expression changes by Northern blot hybridization. We also demonstrated that in persistent infection not only drastic downregulation of important housekeeping genes, but induction of stress genes are missing, making possible for the virus to survive in its host for a long period of time. Symptoms of acute and persistent type virus infection differ markedly and according to our results the type of infection can be distinguished even at an early point by characterizing the photosynthetic activity of virus infected plants.

overall_design: RNA-Seq was made from PVX, TMV infected and mock inoculated leafs in 3 biological replicates and 1 technical repeat

first: Réka

last: Pesti

first: Levente

last: Kontra

first: Kenny

last: Paul

first: Imre

last: Vass

first: T

last: Csorba

first: Zoltán

last: Havelda

first: Éva

last: Várallyay


title: Transcriptome of Chinese sturgeon (Acipenser sinensis) from the hypothalamic-pituitary-gonad axis in two sex development stages

status: Public on May 15 2019

city: Shenzhen

first: Jianwei

last: Chen

address: Yantian

institute: BGI-Shenzhen

summary: Here, the HPG axis transcriptomes of A. sinensis were sequenced using Illumina HiSeq 2000 and 4000 platforms. A total of 271.19 Gb filtered data from 45 samples belonging to 15 individuals (six individuals in stage I, six males and three females in stage II) were obtained, and 74.50% of 121,952 assembled unigenes were annotated to the non-redundant (NR), Swiss-Prot, Kyoto Encyclopedia of Genes and Genomes (KEGG), Cluster of Orthologous Groups of proteins (COG), InterPro, Gene Ontology (GO) and NT databases. Additionally, 78,770 unigenes contained complete open reading frames (ORFs). A total of 51,570 simple sequence repeats (SSRs) were detected, and the number of differentially expressed genes (DEGs) from 1,531 to 34,439 in 18 pairwise comparisons were identified for HPG samples of male and female A. sinensis in two stages. We reported the first integrated transcriptome data from HPG samples of male and female A. sinensis in stage I and II of gonadal development. These data offer valuable resources for research into reproductive regulation and the HPG axis interaction in A. sinensis and other sturgeons.

first: Hejun

last: Du

first: Binzhong

last: Wang


title: Effects of gene-by-environment interaction on the transcriptome and methylome of mice deficient for tryptophan hydroxylase 2

first: Konrad

last: Förstner


title: Structural Basis for Target-Directed MicroRNA Degradation

status: Public on May 02 2019

city: New Haven

first: Paulina

last: Pawlica

address: 295 Congress Avenue, BCMM Room 131

department: MBB

institute: Yale University

summary: We used HSUR1 – a small non-coding RNA from Herpesvirus saimiri that induces degradation of host miR-27 – to validate structural insights into target-directed miRNA degradation (TDMD). While performing systematic mutagenesis of HSUR1 we noticed that HSUR1 mutants exhibiting complementarity to the extreme 3' end of miR-27, lead to generation of extended miR-27 isoforms (isomiRs). These isomiRs likely represent failed products of TDMD and could mean that features of the pairing between the TDMD target and miRNA dictate which enzymes are recruited to modify the miRNA 3′ end. Small RNA sequencing revealed that a mixture of adenylates and uridylates is added to the 3′ end of miR-27 during TDMD.

overall_design: miRNA-seq from BJAB cells transduced with either empty vector control or HSUR1 constructs; three biological replicates

first: Jessica

last: Sheu-Gruttadauria

first: Shannon

middle: M

last: Klum

first: Sonia

first: Therese

middle: A

last: Yario

first: Nicole

last: Oakdale

first: Joan

last: Steitz

first: Ian

middle: J

last: MacRae


title: High-throughput combinatorial indexing enables scalable single-cell chromatin accessibility profiling [GM12878]

first: Caleb

last: Lareau

address: 417 E 68th St, Zuckerman - ZRC 1132

institute: Memorial Sloan Kettering

summary: While recent technical advancements have facilitated the mapping of epigenomes at the single-cell resolution, the throughput and quality of these methods have limited the widespread application of these technologies. Here, we describe a high-throughput platform for single-cell assay for transposase accessible chromatin (scATAC-seq) using droplet microfluidics that yields essential qualities for high-throughput profiling, including improvements in per-cell library complexity and throughput. This approach enables robust cell-typing of complex tissues and reveals a de novo atlas of cellular and epigenomic diversity across many cell types and cell stages.

overall_design: Variable bead concentrations and loading conditions for testing species mixing and data quality from SureCell scATAC-seq on GM12878 cells


title: YAP/TAZ inhibition induces metabolic and signaling rewiring resulting in new targetable vulnerabilities in NF2-deficient tumor cells

city: Washington

first: Chunling

last: Yi

state: DC

address: 3970 Reservoir Rd NW

institute: Georgetown University

summary: The NF2 gene, which encodes the Merlin protein, is a bona fide tumor suppressor whose mutations underlie inherited tumor syndrome Neurofibromatosis Type 2 (NF2). Recent large-scale genome sequencing studies have also identified NF2 as one of the most frequently mutated genes in VHL-wild-type kidney cancers. Even though a wide array of downstream signaling pathways has been described for Merlin/NF2, the molecular mechanisms underpinning the growth and survival of NF2 mutant tumors remain poorly understood. Using an inducible orthotopic kidney tumor model, we demonstrate for the first time that silencing of YAP/TAZ is sufficient to induce regression of pre-established NF2 deficient kidney tumors. Mechanistically, we show  that YAP/TAZ ablation severely diminishes glycolysis by downregulating the transcription of several glycolytic enzymes and growth factors and RTK-PI3K-AKT signaling, resulting in growth arrest. On the other hand, YAP/TAZ depletion  significantly increases mitochondrial respiration and overproduction of mitochondrial ROS, resulting in redox imbalance and oxidative stress cell death when challenged by nutrient stress. Furthermore, we identify lysosome-mediated cAMP-PKA/EPACdependent activation of the RAF-MEK-ERK pathway to be a novel resistance mechanism that allows NF2 deficient tumor cells to survive YAP/TAZ inhibition in vitro and in vivo. Finally, unbiased analysis of TCGA primary kidney tumor transcriptomes confirms strong correlations of a YAP/TAZ signature with the expression of glycolysis, oxidative phosphorylation and lysosomal genes, validating the clinical relevance of our findings.

overall_design: SN12C cells with either vector control or shRNAs targeting YAP and TAZ, each containing 3 technical repeats, are included in this analysis.

last: White


title: High-throughput combinatorial indexing enables scalable single-cell chromatin accessibility profiling [human K562 and muring 3T3]

overall_design: A mixture of human K562 and murine 3T3 cells was profiled in various quantities to access cross-talk between cells in our combinatorial setting using 48-plex barcoded Tn5


title: High-throughput combinatorial indexing enables scalable single-cell chromatin accessibility profiling [Bone marrow]

overall_design: In a single experiment, we utilized 96 barcoded Tn5 to profile human bone marrow mononuclear cells from two donors before (untreated controls) and after stimulation. After the tagmentation reaction, all cells were pooled, washed and processed in 16 different channels (16 "samples") on the SureCell platform (thus, data from 16 samples should be collapsed for analysis)


title: Expression profile of primary Keratinocytes and E13.5 MEFs

city: Izmir

first: Hani

last: Alotaibi

address: Dokuz Eylül University Health Campus

country: Turkey

institute: Izmir Biomedicine and Genome Center

summary: We used microarray analysis to study the expression profiles of primary keratinocyes and MEFs. İn an effort to identify transcription factors with epithelial specific expression pattern.

first: Marc

last: Stemmler


title: High-throughput combinatorial indexing enables scalable single-cell chromatin accessibility profiling [species mixture]

overall_design: A mixture of human K562 and murine 3T3 cells was profiled in various quantities to access cross-talk between cells in our combinatorial setting using 24-plex barcoded Tn5


title: High-throughput combinatorial indexing enables scalable single-cell chromatin accessibility profiling [PBMC]

overall_design: Human peripheral blood mononuclear cells from 2 donors were processed using the BioRad SureCell scATAC-seq platform across multiple channels in the instrument.


title: MARS-seq2.0 an experimental and analytical pipeline for indexed sorting combined with Single-cell RNA sequencing

city: Rehovot

first: Ido

last: Amit

address: 234 Herzl st.

department: Immunology

country: Israel

institute: Weizmann Institute of Science

summary: Human tissues are composed of trillions of cells that populate a complex space of molecular phenotypes and functions that vary in abundance by 4-9 orders of magnitude. Relying solely on unbiased sampling to characterize cellular niches becomes non-feasible, as the marginal utility of collecting more cells is diminishing quickly. Further, in many clinical samples, the relevant cell types are scarce and efficient processing is critical. We developed an integrated pipeline for index-sorting and massively parallel single-cell RNA-seq (MARS-seq2.0) that is based on over 1 million cells sequenced with this pipeline. These include, identification of unique cell types across different tissues, diseases, and unique model systems and organisms. In addition we developed several modalities that are based on MARS-seq2.0, including genetic perturbations (CRISP-seq) and spatial reconstruction (NICHE-seq). Here we present a detailed step-by-step procedure to apply the method. We combine sub microliter reaction volumes, optimization of enzymatic mixtures and enhanced analytical pipeline (http://compgenomics.weizmann.ac.il/tanay/?page_id=672) to significantly lower cost, improve reproducibility and reduce the well-to-well contamination. Data analysis combines multiple layers of quality assessment and error detection and correction, graphically presenting key statistics of library complexity, noise distribution and sequencing saturation. Importantly, our combined FACS and single cell RNA-seq workflow enables for intuitive approaches to deplete or enrich for cell populations in a data driven manner that is essential for efficient sampling of complex tissues. The experimental protocol, from sorted plates to a ready to sequence library, takes 2 days. Sequencing and running the analytical pipeline takes another 1-2 days.

overall_design:
Transcriptional profiling of single cells from cell lines and mouse models of, generated from deep sequencing of thousands of cells, sequenced in several batches on illumina Nextseq500. For the BM experiments (samples 1-16), cells were extracted from the BM of 4 individual mice, enriched for the eindicated population and sorted for MARS-seq2.0 cell capture plates. During library preparation, in order to calibrate and optimize the MARS-seq protocol, we have used different compositions of secon strand synthesis mixes as described in the 'description' column. For the mixed species experiments (samples 17-20), human and mouse cell lines were disocciated and mixed in 1:1 ratio. For the cell line experiments (samples 21-30), either ES, MEF or a mixture of ES and MEF cell lines, in at least duplicates, were disocciated and sorted into MARS-seq2.0 cell capture plates. Different conditions were used in the library prepartion protocol in order to optmize the protocol, as described in the 'description' column.
The 'metadata.txt' file associating each single cell with its amplification batch and index sorting readouts is provided.

first: Hadas

last: Keren-Shaul

first: Ephraim

last: Kenigsberg

first: Diego

last: Jaitin

first: Eyal

last: David

first: Franziska

last: Paul

first: Amos

last: Tanay


title: Comprehensive Characterization of the Tumor Immune Micromilieu and its Interference with Outcome After Concurrent Chemoradiation in Patients with Locally Advanced Oropharyngeal Carcinomas

city: Berlin

first: Ingeborg

last: Tinhofer

address: Chariteplatz 1

department: Dept of Radiooncology and Radiotherapy

institute: Charite University Hospital

summary: Intratumoral CD8+ T-cell infiltration in squamous cell carcinoma of the head and neck (HNSCC) has previously been linked to the efficacy of chemoradiation (CRTX) and immune checkpoint inhibitor (ICI) monotherapy. Further detailed characterization of the tumor immune-micromilieu and its influence on outcome may suggest rational CRTX-ICI combinations. In this study, the complex interaction of the tumor immune microenvironment with the efficacy of CRTX in HNSCC was analyzed. Comprehensive immune transcriptome analysis of FFPE tumor samples from patients with oropharyngeal carcinoma was used for establishing differences in tumor immune profiles according to the overall survival status. Furthermore, a composite immune signature risk score for survival prediction was developed.

overall_design: Immune profiles were established in a training set of FFPE tumor specimens from oropharyngeal squamous cell carcinoma (OPSCC) patients treated with cisplatin-based CTRX in the ARO-0401 phase III study (n=33) using the nCounter PanCancer Immune Profiling Panel and the nCounter Digital Analyzer. Differences in basal mRNA levels of 730 immune-related genes and the abundance of immune-cell subsets according to the overall survival (OS) status were established. A composite immune signature risk score for survival prediction was developed in the training set and validated in two independent OPSCC CRTX cohorts (validation 1, n=31; validation 2, n=36) and the OPSCC subset of the TCGA HNSCC cohort (validation 3, n=79), data of which is publicly available from the TCGA project.

first: Anne

middle: K

last: Hess

first: Korinna

last: Jöhrens

first: Andre

last: Zakarneh

first: Panagiotis

last: Balermpas

first: Claus

last: Rödel

first: Wilko

last: Weichert

first: Michael

last: Hummel

first: Ulrich

last: Keilholz

first: Volker

last: Budach


title: Interference of tumor mutational burden with outcome of patients with head and neck cancer treated with definitive chemoradiation: A multicenter retrospective study of the German Cancer Consortium Radiation Oncology Group (DKTK-ROG)

summary: It has been postulated that a high number of mutations resulting in the expression of neoantigens promotes T-cell-mediated inflammation and, as a consequence leads to the activation of immune checkpoints Hence, we determined if high tumor mutational burden (TMB) was associated with a distinct immune expression signature. For this analysis, 37 cases with tumor material for nanoString mRNA expression analysis were available. Overall, only minor differences in the expression levels of the immune-related genes were observed. Specific features of immune checkpoint activation such as high CD8+ T-cell scores and the IFNG signature were downregulated per trend in high compared to low TMB cases. In contrast, genes involved in neutrophil functions were found to be overexpressed in the high TMB group.

overall_design: Immune gene expression profiles were established in a cohort of patients with histologically proven locally advanced squamous cell carcinoma of the oral cavity (N=5), oropharynx (N=18) or hypopharynx (N=14) from a retrospective multicenter DKTK-ROG biomarker study. Treatment protocol was according to standard concurrent chemoradioation (cCRTX) including cisplatin/5-fluorouracil (N=33) or mitomycin-C/5-fluorouracil (N=4). RNA was isolated from FFPE tumor specimens and analysed by using the nCounter PanCancer Immune Profiling Panel and the nCounter Digital Analyzer. Differences in basal mRNA levels of the included immune-related genes and the abundance of immune-cell subsets according to the TMB status were established.

first: Theresa

last: Eder

first: Anne-Kathrin

first: Carmen

last: Stromberger

first: Vanessa

last: Fleischer

first: Annett

last: Linge

first: Mechthild

last: Krause

first: Martin

last: Stuschke

first: Daniel

last: Zips

first: Anca-Ligia

last: Grosu

first: Amir

last: Abdollahi

first: Jürgen

last: Debus

last: Belka

first: Steffi

last: Pigorsch

first: Stephanie

middle: E

last: Combs


title: slmp mutant in tomato leaf primordia

status: Public on May 01 2019

first: Idan

last: Efroni

address: POB 12

department: Plant Sciences

institute: Hebrew University

summary: The dataset described the transcriptional response to the loss of the tomato mp/arf5 gene

overall_design: three replicates of P5 stage of the fifth leaf primordia of slmp mutant.

first: Alon

last: Israeli


title: High-throughput combinatorial indexing enables scalable single-cell chromatin accessibility profiling [Blood]

first: Caleb

last: Lareau

overall_design: Human isolated bone marrow CD34+ stem/progenitor cells, and isolated peripheral blood CD4+ T cells, CD8+ T cells, Monocytes, B cells and NK cells were were processed using the BioRad SureCell scATAC-seq platform across multiple channels in the instrument.


title: Cryptochromes-mediated Inhibition of the CRL4Cop1-Complex Assembly Defines an Evolutionary Conserved signaling mechanism

first: Luca

last: Rizzini

state: NY

address: 522 1st Ave

department: Department of Pharmacology

institute: NYU Langone

summary:
Purpose: The goal of this study is to analyze the Cryptochrome-Cop1 axis in mammals
Methods: mouse embryonic fibroblasts treated with dexamethasone, KL001 and/or Cop1 knockdown.
Results: The transcriptomic analysis helps us to support our finding that the Cryptochromes-dependent repression of the glucocorticoid receptor is mediated by Cop1.

overall_design: All samples generated by deep sequencing in triplicate

first: Michele

last: Pagano


title: High-throughput combinatorial indexing enables scalable single-cell chromatin accessibility profiling [mouse brain]

overall_design: Whole brains from two adult mice were collected and processed using the BioRad SureCell scATAC-seq platform across multiple channels in the instrument.