title: RNA-sequencing of whole blood samples from biologic naïve rheumatoid arthritis patients initiating anti-TNF treatment

status: Public on Oct 23 2019

first: Victor

last: Farutin

address: 301 Binney St.

department: Research

institute: Momenta Pharmaceuticals, Inc.

summary:
Objective: use comprehensive molecular profiling to understand the molecular mechanisms that affect clinical response to anti-TNF therapy in rheumatoid arthritis (RA) and to identify predictive markers to differentiate good responders and non-responders.
Methods: two independent cohorts of 40 and 36 biologic-naïve RA patients were selected from the Corrona (Comparative Effectiveness Registry to study Therapies for Arthritis and Inflammatory coNditions) CERTAIN registry and categorized by EULAR response criteria. Whole-blood RNA and plasma samples from baseline and after 3 months of anti-TNF treatment were profiled using RNA-seq, shotgun proteomics and glycopeptide analysis. A cell type-specific transcriptional data analysis was applied to RNA-seq data to evaluate the impact of the most common immune cell sub-populations.
Results: a treatment-related molecular signature was identified that showed a high level of correlation (ρ=0.62; permutation p<0.01) between cohorts. Treatment led to a reduction of neutrophils, independent of the status of response. Gene expression differences between good responders and non-responders at baseline did not manifest statistically significant concordance genome-wide between the two cohorts. However, a cell type-specific analysis indicated increased representation of innate cell type signatures in good responders and, conversely, increased expression of adaptive cell type signatures in non-responders at baseline in both cohorts. This result was confirmed by applying the cell-type specific analysis to other publicly available RA datasets. Evaluation of the neutrophil to lymphocyte ratio (NLR) at baseline in the remaining patients (n=1962) from the CERTAIN database using a logistic regression model further confirmed the observation (odds ratio of good/moderate response = 1.20 [95% CI = 1.03 – 1.41; p = 0.02]).
Conclusion: differences in innate/adaptive immune cell type composition at baseline may be a major contributor to response to anti-TNF treatment within the first 3 months of therapy.

overall_design:
Whole blood mRNA profiles of biologic naive rheumatoid arthritis patients initiating treatment with infliximab or adalimumab were generated by RNA-sequencing using Illumina HiSeq 2500 from samples obtained at at baseline and after 3 months on anti-TNF treatment
***Due to consent limitations,  raw data are not available**

first: Thomas

last: Prod’homme

first: Kevin

last: McConnell

first: Jay

last: Duffner

first: Kristen

last: Getchell

first: Bryan

last: Gutierrez

first: David

last: DeLuca

first: Ishan

last: Capila


title: Whole-genome single-cell 5mC sequencing of human primordial germ cell-like cells

status: Public on Oct 21 2019

city: Santa Barbara

first: Alex

last: Chialastri

state: CA

address: 2002 BioEngineering Bldg

department: Chemical Engineering

country: USA

institute: University of California Santa Barbara

type: Methylation profiling by high throughput sequencing

summary: In this study, we evaluated the 5mC content of single cell human primordial germ cell-like cells (hPGCLCs) generated from a male human embryonic stem cell line (UCLA2, 46XY). tilizing a strand-specific, enzymatic based method of sequencing, we compared the 5mC content of the plus strand relative to the whole chromosome. We evaluated just specified hPGCLCs, at day 4 of differentiation (D4) and then D4 hPGCLCs that were cultured on a feeder layer for additional 10 days (D4C10).

overall_design: Evaluation of 5mC content at two different time periods in hPGCLCs using scMspJI-seq

first: Siddharth

middle: S

last: Dey

first: Joanna

middle: J

last: Gell

first: Wanlu

last: Liu

first: Enrique

last: Sosa

first: Grace

last: Hancock

first: Yu

last: Tao

first: Sissy

middle: E

last: Wamaitha

last: Bower

first: Amander

middle: T

last: Clark


title: Methylation profiling of Desmoplastic myxoid tumor

status: Public on Oct 01 2019

city: Münster

first: Christian

last: Thomas

address: Pottkamp 2

country: Germany

institute: Institute of Neuropathology Münster, Germany

type: Methylation profiling by genome tiling array

summary: Atypical teratoid/rhabdoid tumor (ATRT) is a highly malignant brain tumor predominantly occurring in infants. Mutations of the SMARCB1 gene are the characteristic genetic lesion. We characterized a series of SMARCB1-deficient intracranial tumors sharing distinct clinical, histopathological and molecular features. Median age of the four females and three males was 40 years (range: 15-61 years). All tumors were located in the pineal region. Histopathologically, these tumors displayed spindled and epithelioid cells embedded in a desmoplastic stroma alternating with a variable extent of a loose myxoid matrix. All cases showed loss of nuclear SMARCB1/INI1 protein expression. After DNA isolation from formalin-fixed paraffin-embedded tumor samples, purification and bisulfite conversion using standard protocols provided by the manufacturer, all samples were analyzed using the HumanMethylation450 BeadChip array or the MethylationEPIC BeadChip array (Illumina Inc., San Diego, CA). Six samples passed initial quality control and were further analyzed. Most DNA methylation profiles were not classifiable using the Heidelberg Brain Tumor Classifier (version v11b4). On unsupervised t-SNE analysis and hierarchical clustering analysis, however, all tumors grouped closely together and showed similarities with ATRT-MYC.

overall_design: Bisulphite converted DNA from the 6 samples were hybridised to either the Illumina HumanMethylation450 BeadChip array or the MethylationEPIC BeadChip array.

first: Martin

last: Hasselblatt


title: PRX2 and PRX25, peroxidases regulated by COG1, are involved in seed longevity in Arabidopsis

status: Public on Oct 15 2019

city: Valencia

first: Eduardo

last: Bueso

state: Valencia

address: Ingeniero Fausto Elio, s/n

department: IBMCP

country: Spain

institute: Universitat Politècnica de València

type: Expression profiling by high throughput sequencing

summary: Permeability is a crucial trait that affects seed longevity and is regulated by different polymers including proanthocyanidins, suberin, cutin and lignin located in the seed coat. By testing mutants in suberin transport and biosynthesis, we demonstrate the importance of this biopolymer to cope with seed deterioration. Transcriptomic analysis of cog1‐2D, a gain‐of‐function mutant with increased seed longevity, revealed the upregulation of several peroxidase genes. Reverse genetics analysing seed longevity uncovered redundancy within the seed coat peroxidase gene family, however after controlled deterioration treatment, seeds from the prx2 prx25 double and prx2 prx25 prx71 triple mutant plants presented lower germination than wild‐type plants. Transmission electron microscopy (TEM) analysis of the seed coat of these mutants showed a thinner palisade layer, but no changes were observed in proanthocyanidin accumulation or in the cuticle layer. Spectrophotometric quantification of acetyl bromide‐soluble lignin components indicated changes in the amount of total polyphenolics derived from suberin and/or lignin in the mutant seeds. Finally, the increased seed coat permeability to tetrazolium salts observed in the prx2 prx25 and prx2 prx25 prx71 mutant lines suggested that the lower permeability of the seed coats caused by altered polyphenolics is likely to be the main reason explaining their reduced seed longevity.

overall_design: Arabidopsis seedlings cog1-2D mutant RNA-seq analisis vs Col-0 plants

first: Joan

last: Renard


title: MTSS1 Suppresses Expansion and Activity of Mammary Tumor-initiating Cells by Mediating P65 Ubiquitination and Degradation

status: Public on Oct 29 2019

city: Shanghai

first: Guohong

last: Hu

address: 320 Yueyang Road

country: China

institute: Shanghai Institute of Nutrition and Health

summary: We conduct transcriptome comparison of control and Mtss1-overexpressed Py8119 cells to gain genomic insights on the biological processes that Mtss1 is involved in breast cancer cells. Through unsupervised cluster analysis of differentially expressed genes (DEGs), we found 1661 genes were significantly changed in Mtss1 cells. Single Site Analysis and Gene Set Enrichment Analysis show that Mtss1 downregualted numerous NF-κB targeted genes.

overall_design: In the study presented here, Mtss1 was overexpressed in the Py8119 mouse breast cancer cells. RNA sequencing profiling of mRNA levels was performed in the control and overexpression cells.

first: Min

last: Cong


title: Comparative transcriptional profiling of Arabidopsis arr6-3 mutant and wild-type (Col-0) plants mock-treated and after infection with Plectosphaerella cucumerina BMM

status: Public on Oct 04 2019

city: Pozuelo de Alarcón

first: Laura

last: Bacete

state: Madrid

institute: Centro de Biotecnología y Genómica de Plantas. Universidad Politécnica de Madrid.

summary: Cytokinin signaling pathway, that is mediated by Arabidopsis Response Regulators (ARRs) proteins, has gained functional relevance in the modulation of plant disease resistance responses. We describe here a novel function of ARR6 in the regulation of Arabidopsis immunity and cell wall composition. arr6 mutants were found to be more susceptible and resistant, respectively, to the vascular bacteria Ralstonia solanacearum GMI1000 and the necrotrophic fungus Plectosphaerella cucumerina BMM. In contrast, transgenic Arabidopsis lines overexpressing ARR6 showed the opposite phenotypes, further supporting a role of ARR6 in regulating disease resistance responses. Transcriptomics and metabolomics analyses of arr6 revealed that canonical immune pathways, like those modulated by defensive phytohormones or triggered by Microbe-Associated Molecular Patterns, are not altered in arr6 plants, suggesting that novel, uncharacterized defensive pathways explain arr6-mediated resistance. We identified alterations in the composition of arr6 cell walls in comparison to that of wild-type plants walls. Remarkably, pectin-enriched cell wall fractions extracted from arr6 walls trigger more intense immune responses than those activated by the corresponding wild-type fractions. Our data suggest that arr6 pectin wall fraction contained specific pentose-based oligosaccharides that would function as non-yet described wall-related Damage-Associated Molecular Patterns (DAMPs). These data supported a novel function of ARR6 in the regulation of cell-wall mediated immunity and reinforce the relevance of plant cell wall composition in the modulation of specific disease resistance responses.

overall_design: Eighteen-day-old wild-type (Col-0) and arr6-3 plants were mock-treated or Plectosphaerella cucumerina BMM-inoculated, and samples were collected at 1 day post infection (dpi). Each sample represented a pool of 25 rosettes from plants grown under short-day conditions. Three biological replicates were obtained for each combination of genotype and treatment were independently hybridized for each transcriptomic comparison. Fluorophore-marked (Cy3 and Cy5) complementary RNA was prepared and the product was used to hybridize Arabidopsis Oligonucleotide Microarrays (Qiagen-Operon Version 3.0.; Arizona University, USA) at the Genomic Unit of CNB-CSIC (Madrid). After hybridization, the array was scanned and the intensities were used to generate the array images. These images were then used to correct and normalize the data. The expression levels of the genes were visualized with the FIESTA Viewer.

first: Hugo

last: Mélida

first: Eva

last: Miedes

first: Gemma

last: López

first: Dominique

last: Tremousaygue

first: Nicolas

last: Denance

first: Vincent

last: Bulone

first: Deborah

last: Goffner

first: Antonio

last: Molina


title: 3’Pool-seq: an optimized cost-efficient and scalable method of whole-transcriptome gene expression profiling (Run0064)

status: Public on Sep 30 2019

city: Lexington

first: Hualin

last: Xi

state: Massachusetts

address: 34 webb st

institute: AbbVie

summary: The advent of Next Generation Sequencing has allowed transcriptomes to be profiled with unprecedented accuracy, but the steep costs associated with full-length library sequencing have posed a limit on the accessibility and scalability of the technology. To address these limitations, we developed 3’Pool-seq, a simple, cost-effective, and scalable RNA-seq method that focuses sequencing to the 3’ end of mRNA transcripts.

overall_design:
Transcriptomes (4 replicates each) from homozygous GFAP-IL6 mice were compared to those from wild-type C57BL/6 for differential gene expression using different amounts of cDNA input during the tagmentation step of 3'Pool-seq.
In this specific experiment, different amounts of total RNA were added to the Reverse Transcription reaction in order to optimize that step for 3'Pool-seq.

first: Gabriel

last: Sholder


title: 3’Pool-seq: an optimized cost-efficient and scalable method of whole-transcriptome gene expression profiling (Run0050)

overall_design:
Transcriptomes (3 replicates each) from homozygous GFAP-IL6 mice were compared to those from wild-type C57BL/6 for differential gene expression using different amounts of cDNA input during the tagmentation step of 3'Pool-seq.
In this specific experiment, different amounts of cDNA were added to the Tagmentation reaction in order to optimize that step for 3'Pool-seq.


title: 3’Pool-seq: an optimized cost-efficient and scalable method of whole-transcriptome gene expression profiling (Glitazone)

overall_design: Transcriptomes (4 replicates each) from HepG2 Cells treated with Troglitazone, Pioglitazone, or Vehicle (DMSO) for 2 or 16 hours post-plating were compared to those that were left Untreated, and Differential Genes were determined using 3'Pool-seq.


title: VAMP8 contributes to TRIM6-mediated type-I interferon antiviral response upon West Nile virus (WNV) infection

status: Public on Oct 24 2019

city: Galveston

first: Rajsbaum

last: Ricardo

state: TX

address: 301 University Blvd.

department: Microbiology and Immunology

institute: University of Texas Medical Branch at Galveston

summary:
Purpose: Several members of the tripartite motif (TRIM) family of E3 ubiquitin ligases regulate immune pathways including the antiviral type I interferon (IFN-I) system. Therefore, we aimed to investigate the mechanism of IFN-I regulation upon West Nile virus infection using TRIM6 knockout (TRIM6-KO) human airway epithelial cells (A549).
Methods: RNAs were extracted from wild-type (WT) and TRIM6KO A549 cells infected with WNV or mock-treated. RNA quality was assessed by visualization of 18S and 28S RNA bands using an Agilent BioAnalyzer 2100 (Agilent Technologies, CA); the electropherograms were used to calculate the 28S/18S ratio and the RNA Integrity Number. Poly-A+ RNA was enriched from total RNA (1 μg) using oligo dT-attached magnetic beads. First and second strand synthesis, adapter ligation, and amplification of the library were performed using the Illumina TruSeq RNA Sample Preparation kit as recommended by the manufacturer (Illumina, Inc). Library quality was evaluated using an Agilent DNA-1000 chip on an Agilent 2100 Bioanalyzer. Quantification of library DNA templates was performed using qPCR and a known-size reference standard. Cluster formation of the library DNA templates was performed using the TruSeq PE Cluster Kit v3 (Illumina) and the Illumina cBot workstation using conditions recommended by the manufacturer. Paired end 50 base sequencing by synthesis was performed using TruSeq SBS kit v3 (Illumina) on an Illumina HiSeq 1500 using protocols defined by the manufacturer. The alignment of NGS sequence reads was performed using the Spliced Transcript Alignment to a Reference (STAR) program, version  2.5.1b, using default parameters. We used the human hg38 assembly as a reference with the UCSC gene annotation file. The –quantMode GeneCounts option of STAR provided read counts per gene, which were input into the DESeq2 (version 1.12.1) differential expression analysis program to determine expression levels and differentially expressed genes. Processed data are presented as reads per kilobase transcript per million (RPKM).
Results: Using next generation sequencing, we identified VAMP8 as a factor involved in this TRIM6-mediated antiviral response. In support, VAMP8 knockdown resulted in reduced Jak1 and STAT1 phosphorylation and impaired induction of several ISGs following WNV infection or IFNβ treatment.
Conclusions: Our results provide evidence that TRIM6 contributes to the antiviral response against WNV and identified VAMP8 as a novel regulator of the IFN-I system

overall_design: A549 cells (WT and TRIM6KO) cells were infected with WNV at MOI = 5 or mock-treated with similar volumes of PBS. RNA was extracted at 24h post-infection and subjected to deep-sequencing analysis in duplicate using NSG on an Illumina HiSeq 1500 sequencing system.

first: Ricardo

last: Rajsbaum

first: Sarah

last: van Tol

first: Colm

last: Atkins

first: Preeti

last: Bharaj

first: Kendra

middle: N

last: Johnson

first: Adam

last: Hage

first: Alexander

last: Freiberg

first: Leopoldo

last: Aguilera-Aguirre

first: Steven

last: Widen


title: Investigating the role of GLI1 in SULF2-potentiated liver tumorigenesis

status: Public on Oct 25 2019

city: Rochester

first: Asha

last: Nair

address: 200 1ST ST SW

institute: Mayo Clinic

summary: The expression of the extracellular sulfatase, SULF2, has been strongly associated with increased hepatocellular carcinoma (HCC) tumor growth and poorer patient survival. However, to date, the molecular mechanisms underlying this phenomenon remain in part unclear. To address this issue, we developed a transgenic mouse overexpressing Sulf2 in hepatocytes under the control of the transthyretin promoter. In this mouse model Sulf2 overexpression potentiated DEN-induced HCC. Further analysis demonstrated a central role for the zinc finger transcription factor Gli1 as a mediator of Sulf2 during HCC development. The cross of the Sulf2 transgenic with Gli1 knockout mice showed that the inactivation of this transcription factor impaired Sulf2-induced HCC. Transcriptomic analysis revealed a Stat3 gene signatures associated with Sulf2 overexpression. Interestingly, Gli1 knockout abrogates Sulf2-induction of several Stat3 target genes including Socs2/3, Pim1 and Flt4. Human orthologues were similarly regulated by SULF2 and dependent on intact GLI1 and STAT3 function in human HCC cells. SULF2 overexpression not only resulted in GLI1 and STAT3 interaction, but also promoted enrichment of GLI1 and STAT3 at consensus sites at the target gene promoters. Interestingly, GLI1 was found to be enriched at select STAT3 consensus sites with SULF2 overexpression and vice versa. siRNA-mediated knockdown of STAT3 or GLI1 reduced promoter binding of GLI1 and STAT3 respectively. Finally, chromatin capture PCR confirmed long-range co-regulation of SOCS2 and FLT3 through changes in promoter conformation. Thus, these findings define a novel mechanism by which SULF2 drives HCC and highlights the role of GLI1-STAT3 transcriptional complex as an effector of this sulfatase.

overall_design: Compared transcriptome from DEN-induced liver tumors derived from SULF2-overexpressing mice (SULF2-TTR) with wildtype GLI1 and GLI1 knockout. Three replicates for each genotype were studied.

first: Ryan

middle: M

last: Carr

first: Martin

last: Fernandez-Zapico


title: 3’Pool-seq: an optimized cost-efficient and scalable method of whole-transcriptome gene expression profiling

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: 3’Pool-seq: an optimized cost-efficient and scalable method of whole-transcriptome gene expression profiling (Run0004)

overall_design:
Transcriptomes (4 replicates each) from homozygous GFAP-IL6 mice were compared to those from wild-type C57BL/6 for differential gene expression using different amounts of cDNA input during the tagmentation step of 3'Pool-seq.
In this specific experiment, the standard Illumina Truseq protocol was used for library preparation. The results were used as a reference for comparison to the 3'Pool-seq protocol.


title: Common DNA sequence variation influences 3-dimensional conformation of the human genome

status: Public on Oct 02 2019

city: La Jolla

first: Yunjiang

last: Qiu

address: 9500 Gilman Drive

institute: University of California, San Diego

type:
Other
Third-party reanalysis

summary: The 3-dimensional (3D) conformation of chromatin inside the nucleus is integral to a variety of nuclear processes including transcriptional regulation, DNA replication, and DNA damage repair. Aberrations in 3D chromatin conformation have been implicated in developmental abnormalities and cancer. Despite the importance of 3D chromatin conformation to cellular function and human health, little is known about how 3D chromatin conformation varies in the human population, or whether DNA sequence variation between individuals influences 3D chromatin conformation. To address these questions, we performed Hi-C on Lymphoblastoid Cell Lines (LCLs) from a panel of 20 individuals. We identify thousands of regions across the genome where 3D chromatin conformation varies between individuals and find that these conformational variations are often accompanied by variations in gene expression, histone modifications, and transcription factor (TF) binding. Moreover, we find that DNA sequence variation influences several features of 3D chromatin conformation including loop strength, contact insulation, contact directionality and density of local cis contacts. We map hundreds of Quantitative Trait Loci (QTLs) associated with 3D chromatin features and find evidence that some of these same variants are associated at modest levels with other molecular phenotypes as well as complex disease risk. Our results demonstrate that common DNA sequence variants can influence 3D chromatin conformation, pointing to a more pervasive role for 3D chromatin conformation in human phenotypic variation than previously recognized.

overall_design: Hi-C in 20 lymphoblastoid cell lines with two bilogical replicates

first: David

middle: U

last: Gorkin

first: Ming

last: Hu

first: Bing

last: Ren


title: The extracellular matrix protein TasA is a developmental cue that maintains a motile subpopulation within Bacillus subtilis biofilms

status: Public on Sep 26 2019

city: Rehovot

first: Tsviya

last: Olender

address: 234 Herzl St.

department: Molecular Genetics

country: Israel

institute: The Weizmann Institute

summary: In nature, bacteria form biofilms – differentiated multicellular communities attached to surfaces. In the otherwise sessile biofilms, a subset of cells continues to express motility genes. Here, we demonstrate a biological role for this subpopulation, which enabled biofilms of Bacillus subtilis to expand on high-friction surfaces. Moreover, we show that the extracellular matrix (ECM) protein TasA was required for the expression of flagellar genes. In addition to its structural role as an adhesive fiber for cell attachment, TasA served as a developmental signal similar to ECM proteins of multicellular organisms. Transcriptomic analysis revealed that TasA regulated a specific subset of genes, inducing genes involved in motility and repressing ECM production. A screen for suppressor mutations that restore motility in the absence of TasA revealed activation of the biofilm-motility switch by the two-component system CssRS, that alleviated Spo0A repression by TasA. Our results suggest that although mostly sessile, biofilms retain a degree of motility by maintaining a motile subpopulation.

overall_design: 8 samples. delTASA (3 biological replicates), delCSSRS (3 biological replicates), WT (2 biological replicates, control)

first: Nitai

last: Steinberg

first: Alona

last: Keren-Paz

first: Qihui

last: Hou

first: Shany

last: Doron

first: Keren

last: Yanuka-Golub

first: Gili

last: Rosenberg

first: Rotem

last: Hadar

first: Rakeshkumar

last: Jain

first: Sven

last: van Teeffelen

first: Ilana

last: Kolodkin-Gal


title: A whole-tissue RNA-seq toolkit for organism-wide studies of gene expression with PME-seq

city: Chicago

first: Nicolas

last: Chevrier

state: Illinois

address: 5640 South Ellis Avenue

department: Pritzker School of Molecular Engineering

institute: The University of Chicago

summary: The immune system operates at the scale of the whole organism in mammals. We currently lack experimental approaches to systematically track and study organism-wide molecular processes in mice. Here we describe an integrated toolkit for measuring gene expression in whole tissues, 3-prime mRNA extension sequencing, that is applicable to most mouse organs and any mouse model of interest. Further, the methods of RNA-seq described in this protocol are broadly applicable to other sample types beyond whole organs, such as tissue samples or isolated cell populations. We report procedures to collect, store and lyse a dozen organ types using conditions compatible with the extraction of high-quality RNA. In addition, we detail protocols to perform high-throughput and low-cost RNA extraction and sequencing, as well as downstream data analysis. The protocol takes 5 d to process 384 mouse organs from collecting tissues to obtaining raw sequencing data, with additional time required for data analysis and mining. The protocol is accessible to individuals with basic skills in (i) mouse perfusion and dissection for sample collection and (ii) computation using Unix and R for data analysis. Overall, the methods presented here fill a gap in our toolbox for studying organism-wide processes in immunology and physiology.

overall_design: To study immune processes at the organism-level, four replicates of 6 weeks old female mice were anasthesized, and transcardially perfused with PBS supplemented with 1 mM EDTA. 15 tissues (Liver, bone marrow, lung, inguinal lymph node, mesenteric lymph node, colon, small intestine, female reproductive tract, brain, kidney, thymus, peripheral blood mononuclear cells, heart, skin, spleen) were collected and stored in RNAlater at 4C overnight before freezing at -80C for long-term storage.

first: Surya

last: Pandey


title: Lineage Tracing of PSC-derived iAEC2 Differentiation Using Lentiviral Barcoding

status: Public on Sep 24 2019

city: Boston

first: Carlos

last: Villacorta-Martin

state: MA

address: 670 Albany St

institute: Center for Regenerative Medicine at Boston University

summary: Lineage tracing of individual cells during directed differentiation human iPSC into alveolospheres was performed using a lentiviral barcode labeling system (Weinreb et al., 2020) as described in Hurley et al., 2020.

overall_design: Human BU3 NGST iPSCs were differentiated in vitro, sorted on day 15 for NKX2-1GFP positive cells, which were grown in CK+DCI until D17 (as described in Hurley et al., 2020). At this point cells were infected with a lentiviral barcode to demarcate individual cells. Cells were then replated and grown out for an additional 10 days before being analyzed by single cell sequencing.

first: Michael

last: Herriges

first: Killian

last: Hurley

first: Darrell

last: Kotton


title: Developmental changes of rRNA ribose methylations in the mouse

city: Copenhagen

first: Nicolai

last: Krogh

address: Blegdamsvej 3B

department: Department of Cellular and Molecular Medicine

country: Denmark

institute: University of Copenhagen

summary: A sequencing-based profiling method (RiboMeth-seq) for ribose methylations was used to study methylation patterns in mouse adult tissues and during development. In contrast to previous reports based on studies of human cancer cell lines, almost all methylation sites were close to fully methylated in adult tissues. A subset of sites was differentially modified in developing tissues compared to their adult counterparts and showed clear developmental dynamics. This provides the first evidence for ribosome heterogeneity at the level of rRNA modifications during mouse development. In a prominent example, the expression levels of SNORD78 during development appeared to be regulated by alternative splicing of the Gas5 host-gene and to correlate with the methylation level of its target site at LSU-G4593. The results are discussed in the context of the specialized ribosome hypothesis.

overall_design: 11 samples analyzed in biological triplicates, in total 33 samples

first: Hebras

last: Jade

first: Marty

last: Virginie

first: Henrik

last: Nielsen

first: Jérôme

last: Cavaillé


title: Transcriptional modulation of Quoring-sensing signaling throught QslA in Pseudomonas aeruginosa PA14 and PAO1.

status: Public on Sep 23 2019

city: VALENCIA

first: LOMAS LOPEZ

last: RODRIGO

address: C/ Eduardo Primo Yúfera, 3 (junto Oceanogràfic)

institute: CIPF

summary: To further determine the origin of the increased virulence of Pseudomonas aeruginosa PA14  compared to Pseudomonas aeruginosa PAO1, we report a transcriptomic approach through RNA sequencing. Next-generation sequencing (NGS) has revolutioned sistems-based analsis of transcriptomic pathways. The goals of this study are to compare the transcriptomic profile of all 5263 orthologous genes of these nearly two strains of Pseudomonas aeruginosa.

sample_organism:
Pseudomonas aeruginosa PAO1
Pseudomonas aeruginosa PA14

overall_design: Transcriptomic analysis of 2 nearly bacterial strains of Pseudomonas aeruginosa.

first: Rodrigo

last: Lomas

first: Ana

last: Conesa

first: Sophie

last: Bleves

first: Romé

last: Voulhoux

first: Bérengère

last: Ize

first: Maxime

last: Gimenez

first: Aurélie

last: Laubier

first: Chatal

last: Soscia

first: Claire

last: Chauvet


title: Fasting-induced FGF21 signaling activates hepatic autophagy and lipid degradation via JMJD3 histone demethylase

city: Urbana

first: Jongsook

middle: Kim

last: Kemper

address: 524 Burrill Hall  407 S. Goodwin Ave

department: Department of Molecular & Integrative Physiology

institute: University of Illinois at Champaign-Urbana

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Autophagy is essential for cellular survival and energy homeostasis under nutrient deprivation. Despite the emerging importance of nuclear events in autophagy regulation, epigenetic control of autophagy gene transcription remains unclear. Here, we identify Jumonji-D3 (JMJD3/KDM6B) histone demethylase as a key epigenetic activator of hepatic autophagy. Upon fasting-induced fibroblast growth factor-21 (FGF21) signaling, JMJD3 epigenetically upregulated global autophagy-network genes, including Tfeb, Atg7, Atgl, and Fgf21, through demethylation of histone H3K27-me3, resulting in autophagy-mediated lipid degradation. Mechanistically, phosphorylation of JMJD3 at Thr-1044 by FGF21 signal-activated PKA increased its nuclear localization and interaction with the nuclear receptor PPARa to transcriptionally activate autophagy. Chronic administration of FGF21 in obese mice improved defective autophagy and hepatosteatosis in a JMJD3-dependent manner. Remarkably, in non-alcoholic fatty liver disease patients, hepatic expression of JMJD3, ATG7, LC3, and bKL were substantially decreased. These findings demonstrate that FGF21-JMJD3 signaling epigenetically links nutrient deprivation with hepatic autophagy and lipid degradation in mammals.

overall_design:
Liver ChIP-seq profiles were generated by deep sequencing, were profiled in mouse liver in which jmjd3-floxed mice were infected with either AAV-TBG-Cre or GFP for 12 weeks.

Please note that each processed data file was generated from both replicates and is linked to the corresponding rep1 sample records.

first: Sangwon

last: Byun

first: Sunmi

last: Seok

first: Young-Chae

last: Kim

first: Yang

last: Zhang

first: Peter

last: Yau

first: Naoki

last: Iwamori

first: H

last: Xu

first: Jian

last: Ma

first: Byron

middle: K


title: Hippocampal Subregions Express Distinct Dendritic Transcriptomes that Reveal Differences in Mitochondrial Function in CA2

city: Roanoke

first: Shannon

last: Farris

state: VA

address: 2 Riverside Circle

department: Fralin Biomedical Research Institute

institute: Virginia Tech


title: Live-animal imaging of native hematopoietic stem and progenitor cells

city: Torino

first: Raffaele

middle: A

last: Calogero

state: To

address: Via Nizza 52

department: Molecular Biotechnology Center

country: Italy

institute: University of Torino

summary: As the biology of hematopoietic stem cells (HSCs) has been predominantly studied under transplantation conditions, it has been challenging to study dynamic HSC behaviors in their native niche given under steady state conditions. Here, we describe the generation of a double knock-in fluorescent reporter that restricts the reporter labeling exclusively to the LT-HSC compartment. Single cell RNAseq comparing previously published LSK signatures (GEO: GSE90742) to our sorted fluorescently labeled cells (sorted without the use of any other cell surface markers) demonstrates that the fluorescently marked cells in our unique mouse model are exclusively found in the LT-HSC compartment in terms of their overal RNA content. This confirms that the generated mice label LT-HSCs in a highly specific manner.

overall_design: Single-cell mRNA sequencing of GFP+ long-term hematopoietic stem cells isolated from Mds1-GFP/+ Flt3-Cre mouse bone marrow. As GFP cells represent a very rare fraction of the BM, LT-HSC cells from wild type mice were sorted for the SLAM markers and mixed with the GFP LT-HSCs to ensure high quality of derived libraries. Sample GFP LT-HSCs represents 46 single cells in total after processing while the rest of cells are SLAM LT-HSCs (not used for analysis).

first: Constantina

last: Christodoulou

first: Joel

last: Spencer

first: Raphael

last: Turcotte

first: Konstantinos

middle: D

last: Kokkaliaris

first: Riccardo

last: Panero

first: Azucena

last: Ramos

first: Tatiana

middle: V

last: Esipova

first: Sergei

last: Vinogradov

first: Sarah

last: Rudzinskas

first: Yi

first: Archibald

last: Perkins

first: Timm

last: Schroeder

first: Charles

middle: P

last: Lin

first: Fernando

last: Camargo


title: Histone demethylase JMJD3 is a key epigenetic activator of FGF21 signaling-induced hepatic autophagy and lipid degradation

status: Public on Sep 18 2019

first: Young-Chae

last: Kim

state: IL

address: 394 Burrill Hall  407 S. Goodwin Ave

department: MIP

institute: University of Illinois at Urbana-Champaign

overall_design: Liver mRNA profiles were generated by deep sequencing, were profiled in mouse liver in which jmjd3-floxed mice were infected with either AAV-TBG-Cre or GFP for 12 weeks.

first: Sangwon

last: Byun

first: Sunmi

last: Seok

first: Yang

last: Zhang

first: Peter

last: Yau

first: Naoki

last: Iwamori

first: H

last: Xu

first: Matthew

last: Potthoff

first: Jian

first: Byron

last: Kemper

first: Jongsook


title: Identification of PIKfyve kinase as a target in multiple myeloma

status: Public on Sep 19 2019

city: Scottsdale

first: Cecilia

last: Bonolo de Campos

state: AZ

address: 13400 E Shea Blvd

summary: The cellular cytotoxicity of APY0201, a PIKfyve inhibitor, against multiple myeloma was initially identified in an unbiased in vitro chemical library screen. Activity was confirmed in all 25 cell lines tested and 40% of 100 ex vivo patient derived primary samples, and positively correlated with samples harboring trisomies and inversely related to t(11;14). The broad anti- multiple myeloma activity of PIKfyve inhibitors was further demonstrated in confirmatory screens and showed the superior potency of APY0201 when compared to the PIKfyve inhibitors YM201636 and apilimod, with a mid-point EC50 at nanomolar concentrations respectively in 65%, 40%, and 5% of the tested cell lines. An up-regulation of genes in the lysosomal pathway and increased cellular vacuolization was observed in vitro in cell lines following APY0201 treatment however this cellular response did not correlate well with responsiveness. We confirm that PIKfyve inhibition is associated with activation of the transcription factor EB, a master regulator of lysosomal biogenesis and autophagy. Furthermore, we established an assay measuring autophagy as a predictive marker of APY0201 sensitivity. Overall, these findings suggest promising activity of PIKfyve inhibitors secondary to disruption of autophagy in multiple myeloma and a strategy to enrich for likely responders.

overall_design: Five human myeloma cell lines were treated with a DMSO control or 100nM of APY0201 for 24 hours and four human multiple myeloma primary patient samples treated with a DMSO control or 50nM and 500nM of APY0201 for 24 hours and were sent for RNA sequencing

middle: B

last: de Campos

first: A

last: Stewart


title: Molecular profile of hidradenitis suppurativa

status: Public on Sep 10 2019

city: Dessau

first: Christos

middle: C

last: Zouboulis

address: Auenweg 38

department: Departments of Dermatology, Venereology, Allergology and Immunology

institute: Dessau Medical Center, Brandenburg Medical School Theodor Fontane

summary: Hidradenitis Suppurativa molecular taxonomy and key signaling pathways were studied by whole transcriptome profiling. Dysregulated genes were detected by comparing lesional and non lesional skin obtained from female HS patients and matched healthy controls using the Agilent array platform

overall_design: Total RNA was obtained from full thickness skin specimens taken from both lesional and non lesional sites in 8 female patients diagnosed with Hurley stage II-III Hidradenitis Suppurativa, and from clear skin sites in 8 healthy controls

first: Andre

last: Nogueira da Costa

first: Eugenia

last: Makrantonaki

first: Xiao

middle: X

last: Hou

first: Daifallah

last: Almansouri

first: Joel

last: Dudley

first: Hannah

last: Edwards

first: Ben

last: Readhead

first: Ottfried

last: Balthasar

first: G

last: Jemec

first: Nikolaos

middle: G

last: Bonitsis

first: Georgios

last: Nikolakis

first: Dietrich

last: Trebing

first: Konstantin

first: Amir

last: Hossini


title: Generation of mature lung alveolar epithelial cells from human pluripotent stem cells

first: Carlos

last: Villacorta-Martin

summary: We perform time-series global transcriptomic profiling of a directed differentiation protocol for generating alveolar epithelial type II cells (AEC2s) from pluripotent stem cells (PSCs). We analyzed 3 different timepoints in the RUES2 differentiation: 1) Day 0 undifferentiated cells, 2) Day 15 lung progenitors highly enriched in NKX2-1+ cells by CD47hi/CD26lo sorting, and 3) the outgrowth of these purified progenitors in 3D culture sorted again on Day 35 based on SFTPCtdTomato+ and SFTPCtdTomato- gating. For comparison to primary cells, we simultaneously sequenced RNA from purified primary fetal (21 week gestation) distal alveolar epithelial progenitors and purified adult human (HTII-280 sorted) AEC2s. In order to evaluate the effect of cell culture on primary fetal alveolar cells, parallel aliquots of the fetal cells were also exposed to 4 days of culture in DCI media. We find that AEC2 maturation involves downregulation of Wnt signaling activity, and that the highest differentially expressed transcripts in iPSC-derived AEC2s encode genes associated with lamellar body and surfactant biogenesis.

overall_design: Analysis of global transcriptomes of PSCs and their differentiated progeny (primordial lung progenitors and alveolar cells) compared to primary fetal (21 week) and adult alveolar epithelial type 2 cells in triplicate. Nine of the samples were re-analyzed from a previously publish study by Jacob et al. 2017 Cell Stem Cell (accession: GSE96642)

first: Anjali

last: Jacob

first: Darrell

last: Kotton

first: Killian

last: Hurley


title: Rice roots: Non-colonized (sterile) control vs. infected with Xanthomonas oryzae pv. oryzae strain PXO99 (Xan)

status: Public on Sep 01 2019

city: Bremen

first: Barbara

last: Reinhold-Hurek

state: Bremen

address: Leobener Str. 5

department: Microbe-Plant Interactions

institute: University of Bremen

summary: Transcriptional profiling of Oryza sativa japonica Nipponbare roots after 14 days post infection with Xanthomonas oryzae pv. oryzae strain PXO99 , the goal is to understand the transcriptomic response of rice roots to colonization by bacterial pathogen

overall_design: Two-conditon experiment, Biological replicates: 3, One dye-swap control, Biological replicate 1 consist of two technical replicates

first: Xi

last: Chen


title: Rice roots: Non-colonized (sterile) control vs. colonized with Azoarcus olearius BH72

summary: Transcriptional profiling of Oryza sativa japonica Nipponbare roots after 14 days post inoculation with Azoarcus olearius BH72, the goal is to understand the transcriptomic response of rice roots to colonization by bacterial endophyte

overall_design: Two-conditon experiment, Biological replicates: 3, One technical replicate with dye swap.


title: RNA sequencing of HCT116 and HKE3 colorectal cancer cell lines before and after stimulation with TGF-alpha

city: Adelaide

first: Sriganesh

last: Srihari

state: SA

address: North Terrace

department: Infection and Immunity

country: Australia

institute: South Australian Health and Medical Research Institute

summary: RNA sequencing was performed on HCT116 and HKE3 colorectal cancer cell lines before stimulation and at 15, 30, 60, 90 and 120 mins post-stimulation with transforming growth factor alpha (TGF-α) (0.01 µg/mL, Abcam). Three replicates were sequenced at each time point.

overall_design: RNAseq profiles from HCT116 and HKE3 cells before and after stimulation with TGF-alpha. In total, 36 cDNA libraries (2 cell lines X 6 time-points X 3 replicates per timepoint) were generated for sequencing.

first: Theodosia

last: Charitou

first: David

last: Lynn

first: Walter

last: Kolch


title: Target Gene Repression Based on Dismissal of Polymerase II from Estrogen Receptor Trans-bound Enhancers Is Associated With Clinical Outcome in Human Breast Cancer [ChIP-seq]

status: Public on Sep 04 2019

first: Yuliang

last: Tan

state: California

address: Room 345, CMM West, 9500 Gilman Drive, Mail Code 0648

department: School of Medicine

summary: We find that 17-β-estradiol (E2)-bound estrogen receptor α (ERα) is bound in trans to a cohort of FOXA1-dependent, constitutively activate enhancers, inactivating these enhancers by decommissioning/removing enhancer Polymerase II (Pol II), despite recruitment of coactivators. This is based on the surprising recruitment by the ERα DNA binding domain of the histone demethylase, KDM2A, which, functioning independently of its demethylase function. KDM2A mediates recruitment of NEDD4 complexes that ubiquitinate and dismisses Pol II from these "repressive" enhancers, resulting in the E2 down-regulated transcriptional program.

overall_design: Trans-bound estrogen receptor α (ERα) to the E2 repressed enhancers are proved by ERα pbox mutated ChIP-seq. ERα DNA binding domain interacts with histone demethylase, KDM2A, which mediates recruitment of NEDD4 complexes that dismisses Pol II from these "repressive" enhancers, resulting in the E2 down-regulated transcriptional program shown by GRO-seq and Pol II ChIP-seq. Overall, our data suggest that KDM2A plays central roles in a nuclear receptor-induced transcriptional repression program.

first: Michael

last: Rosenfeld


title: Target Gene Repression Based on Dismissal of Polymerase II from Estrogen Receptor Trans-bound Enhancers Is Associated With Clinical Outcome in Human Breast Cancer [GRO-seq]


title: Target gene profiles of 1,25(OH)2D3 and 25(OH)D3 in Cyp27b1 knockout mDCT cells.

status: Public on Aug 30 2019

city: Itabashi-ku

first: Takao

last: Susa

state: Tokyo

department: Department of Biochemistry

country: Japan

institute: Teikyo University School of Medicine

summary: Recently, it has been reported that 25(OH)D3 (25D3) has physiological bioactivity in certain tissues derived from the Cyp27b1 knockout mice. To investigate 25D3 function in the kidney as an informational crossroad of various calciotropic substances, we employed CRISPR-Cas9 system to knock out the Cyp27b1 gene in the mouse renal tubular cell line, mDCT cells. Unlike the previously reported mice targeted to the Cyp27b1 gene systemically, Cyp27b1 knockout mDCT cells did not produce any measurable 1a,25(OH)2D3 (1,25D3) after 25D3 administration. As was seen in the treatment with 10-8 M and higher dose of 1,25D3, we found that 10-7 M of 25D3 could translocate VDR into the nucleus and promoted expression of the representative 1,25D3-responsive Cyp24a1 gene in the Cyp27b1 knockout mDCT cells. The exhaustive target gene profiles of 25D3 showed results closely mimicking those of 1,25D3. Subsequently, we confirmed that 25D3 induced the expression of a calcium reabsorption-related gene, Calbindin-D9K gene, in a similar way to 1,25D3. As another example among others, we found that both 1,25D3 and 25D3 induced the expression of Megalin gene. Our ChIP assay identified that two VDRE sites at the upstream region of the Megalin gene contributed to such gene activation. Together, we surmise that the ability to stimulate VDR target genes may provide a novel perspective with 25D3 contribution in certain tissues.

overall_design: CRISPR-Cas9 mediated Cyp27b1 knockout mDCT cells were cultured as previously reported. Twenty-four hours before 1,25(OH)2D3 or 25(OH)D3 administration to the cells, culture medium was changed to the phenol red-free medium containing 2 % charcoal stripped fetal bovine serum (FBS), then the cells were exposed to the indicated hormones for another 24 h with the same medium. This study was analyzed 3 samples (N=1) described below. 128_siCT_V_1 was vehicle treated control sample, and 128_siCT_1_25D3_7_1 and 128_siCT_25D3_7_1 were 10-7 M of 1,25(OH)2D3 or 25(OH)D3 treated samples, respectively.

first: Takahiro

last: Kikuyama

first: Mimi

last: Tamamori-Adachi

first: Masayoshi

last: Iizuka

first: Miho

last: Akimoto

first: Hiroko

last: Okinaga

first: Yoshihide

last: Fujigaki

first: Shunya

last: Uchida

first: Shigeru

last: Shibata

first: Tomoki

last: Okazaki


title: Time series single-cell transcriptomic analysis of AEC2 directed differentiation

first: Carlos

last: Villacorta-Martin

overall_design: Transcriptional trajectories of individual cell states over time by scRNA-seq performed at the time intervals selected by our TPS algorithm. For each time point we profiled ~4000 cells, following PSC-derived cells sorted on NKX2-1GFP at the lung primordial progenitor stage of differentiation (day 15; Figure 3B) through day 31 of alveolar directed differentiation without further sorting. As a negative control we included a 7th sample, the day 15 non lung population, isolated based on GFP exclusion (NKX2-1GFP negative sorted). Flow cytometry monitoring of NKX2-1 and SFTPC locus activity at each of the 6 time points of alveolar differentiation (Figure 3B) indicated the expected emergence of SFTPCtdTomato expression over time in some cells, peaking on day 29 of differentiation, but a loss of NKX2-1GFP expression in other cells over time, predicting potential loss of lung cell fate in a subset of the population, consistent with our prior reports (McCauley et al., 2018)

first: Killian

last: Hurley

first: Darrell

last: Kotton


title: The lamin-like LITTLE NUCLEI 1 (LINC1) regulates jasmonic acid signaling and innate immunity

status: Public on Aug 31 2019

city: Thuwal

first: Prof. Heribert

last: HIRT

address: 4700 KAUST

country: Saudi Arabia

institute: KAUST

summary: We report the transcriptome composition of linc1-1 and ahl13-1  compared to WT (col-0) plant without treatment and after Pst hrcC-application

overall_design: Illumina high-sequencing plateform was used to analyse the transcriptome composition of linc1-1 under treated and untreated conditions

first: Mai

last: Jarad

first: Kiruthiga

last: Mariappan

first: Marilia

last: Almeida-Trapp

middle: F

last: Mette

first: Axel

last: Mithöfer

first: Naganand

last: Rayapuram

first: Heribert

last: Hirt


title: Hippocampal Subregions Express Distinct Dendritic Transcriptomes that Reveal Differences in Mitochondrial Function in CA2 [RNA-seq]

first: Shannon

last: Farris

summary: RNA localization is one mechanism that neurons use to spatially and temporally regulate gene expression at synapses. Here, we tested the hypothesis that cells exhibiting distinct forms of synaptic plasticity will have differences in dendritically localized RNAs. Indeed, we discovered that each major subregion of the adult mouse hippocampus expresses a unique complement of dendritic RNAs. Specifically, we uncovered a surprising number of cell type and compartment specific differences in RNA expression and alternative splicing, some of which pointed to differences within interneuron and non-neuronal cells present in dendritic laminae. Further, by focusing gene-ontology analyses on the plasticity-resistant CA2, we identified an enrichment of mitochondria-associated pathways in CA2 cell bodies and dendrites, and we provide functional evidence that these pathways influence plasticity and mitochondrial respiration in CA2. In sum, our results support accumulating evidence that thousands of RNAs are present in adult dendrites that likely function to regulate cell type specific processes in dendrites.

overall_design: Hippocampal cell-type and compartment specific transcriptomes were generated using laser capture microdissection on three adult male Amigo2-EGFP mice. The cell body (stratum pyramidale and granule cell layer) and dendritic layers (stratum radiatum and molecular layer) from CA1, CA2, CA3 and DG were multiplexed per mouse (8 regions per mouse) and each sequenced on an Illumina NextSeq500 instrument.

first: James

last: Ward


title: Comprehensive analysis of the mRNA-lncRNA co-expression profile and ceRNA networks patterns in chronic hepatitis B

status: Public on Aug 27 2019

city: Hangzhou

first: Wenbiao

last: Chen

address: Zhejiang University, Hangzhou

institute: Zhejiang University

summary: To explore the lncRNAs and mRNA expression profiles in CHB and asymptomatic HBsAg carriers (ASC) and construct mRNA-lncRNA co-expression profile and ceRNA networks to identify the potential targets of diagnosis and treatment in CHB.

overall_design: We determined the expression profiles of lncRNAs and mRNAs in CHB and ASC using microarray analysis.

first: Hongyan

last: Diao


title: Single-cell analysis of Crohn’s disease lesions identifies a pathogenic cellular module associated with resistance to anti-TNF therapy

status: Public on Aug 21 2019

city: Cincinnati

first: Yael

last: Haberman

address: 3333 Burnet Av

institute: CCHMC

summary:
Purpose:  IBD diagnosis correlation with failure to achieve corticosteroid-free durable remission upon anti-TNF therapy
Results:  Enrichment of the GIMATS module (unique cellular signature found in a small cohort of surgically resected iCD ileums by scRNAseq) was also present in early stages of disease, prior to any biological therapy
Conclusion:  Confirmed the presence of the GIMATS module in bulk expression dataset and revealed that the presence of the module at diagnosis is associated with failure to achieve durable corticosteroid-free remission upon anti-TNF therapy in a pediatric inception cohort

overall_design: Ileal gene expression profiles were analyzed for 199 treatment-naïve pediatric Crohn patients and non-IBD controls with 13 additional samples combined with samples from GSE101794

last: Haberman-Ziv

first: Lee

last: Denson

first: Rebekah

last: Karns


title: Identification of Functional Regulatory Elements in the Human Genome Using Pooled CRISPR Screens

city: Kansas City

first: Scott

last: Younger

state: MO

address: 2401 Gillham Road

institute: Children's Mercy Kansas City

summary: Genome-scale pooled CRISPR screens are powerful tools for identifying genetic dependencies across varied cellular processes.  The vast majority of CRISPR screens reported to date have focused exclusively on the perturbation of protein-coding gene function.  However, protein-coding genes comprise <2% of the sequence space in the human genome leaving a substantial portion of the genome uninterrogated.  Noncoding regions of the genome harbor important regulatory elements (e.g. promoters, enhancers, suppressors) that influence cellular processes but high-throughput methods for evaluating their essentiality have yet to be established.  Here, we describe a CRISPR-based screening approach that facilitates the functional profiling of thousands of noncoding regulatory elements in parallel.  We selected the tumor suppressor p53 as a model system and designed a pooled CRISPR library targeting thousands of p53 binding sites throughout the genome.  Following transduction into dCas9-KRAB-expressing cells we identified several regulatory elements that influence cell proliferation.  Moreover, we uncovered multiple elements that are required for the p53-mediated DNA damage response.  Surprisingly, many of these elements are located deep within intergenic regions of the genome that have no prior functional annotations.  This work diversifies the applications for pooled CRISPR screens and provides a framework for future functional studies focused on noncoding regulatory elements.

sample_organism:
Homo sapiens
Expression vector lentiGuide-Puro

overall_design: Pooled CRISPR screens targeting p53-regulated genes and p53 binding sites in human renal adenocarcinoma cells (769P)

first: Samantha

last: Borys


title: H3K4 methylation at active genes mitigates transcription-replication conflicts during replication stress

city: Taipei

first: Cheng-Fu

last: Kao

address: 128, Academia Rd., Sec. 2, Nankang

department: Institute of Cellular and Organismic Biology

country: Taiwan

institute: Academia Sinica

summary: Methylated H3K4 (H3K4me) is highly conserved and has been widely considered to be involved in transcriptional control. However, this once popular model was recently challenged by multiple groups, because blocking this modification does not appreciably affect transcription. Thus, the function of the H3K4me remains unclear. To investigate how H3K4 methylation influences the processes of transcription and replication under HU-stress, we used chromatin immunoprecipitation-sequencing (ChIP-seq) to identify genomic sites of active transcription marked by Rpb3, a subunit of RNA Polymerase II, and sites of replication pausing marked by DNA Pol2, a subunit of DNA Polymerase e. Our data lead us to the surprising conclusion that H3K4me pauses the progression of replication forks, and we propose that high levels of H3K4me deposited by high transcriptional activity result in a large cushioning effect on fork progression to protect against transcription-replication collisions (TRCs), which cause genome instability.

overall_design: 16 Samples of  RPB3 or DNA pol2 ChIP-Seq for S.cerevisiae in wild type and relevant mutant conditions.

first: Shin-Yen

last: Chong

first: Sam

last: Cutler

first: Jing-Jer

last: Lin

first: Sue

last: Biggins

first: Toshio

last: Tsukiyama

first: Yi-Chen

last: Lo


title: Identification of the genes exhibiting differential expression along the dorsoventral axis in the tracheoesophageal anlagen.

status: Public on Aug 16 2019

city: Nagoya

first: Atsushi

last: Kuroiwa

state: Aichi

address: Furo-cho, Chkusa-ku

department: Graduate School of Science

institute: Nagoya University

summary:
During development, morphogenetic movement occur that separate the single tube of tracheoesophageal anlagen to the esophagus on the dorsal side and trachea and lung on the ventral side. In this process, signaling factors from the mesoderm induce the function and structure that is specific for esophagus or respiratory system in the lining endoderm.
In order to elucidate the mechanism of demarcating these two regions and identify factors that involved in the  dorsal and ventral specific inductions, we attempted to identify genes that show different expression in the dorsal and ventral regions using a microarray.

overall_design: The tracheoesophageal anlagen is in a single tube structure and just begin to exhibit the lung bud formation as a swelling at the ventral region around E9.75. We isolated the tracheoesophageal anlagen by dissecting the tube from the posterior end of the pharynx to the posterior end of lung bud swelling and further divided this piece into the dorsal and ventral halves.

first: Kuroiwa

last: Atsushi


title: Spaceflight and simulated microgravity conditions increase virulence of Serratia marcescens in the Drosophila melanogaster infection model

status: Public on Sep 28 2019

city: Moffett Field

first: Rachel

middle: Rene

last: Gilbert

state: CA

department: Space Biosciences

institute: NASA Ames Research Center

summary: While it has been shown that astronauts suffer immune disorders after spaceflight, the underlying causes are still poorly understood and there are many variables to consider when investigating the immune system in a complex environment. Additionally, there is growing evidence that suggests that not only is the immune system being altered, but the pathogens that infect the host are significantly influenced by spaceflight and ground-based spaceflight conditions. In this study, we demonstrate that Serratia marcescens (strain Db11) was significantly more lethal to Drosophila melanogaster after growth on the International Space Station than ground-based controls, but that the host immune system is not significantly altered amongst known immune genes. High-throughput sequencing of wild-type (w1118) adult hosts infected with either space or ground-reared S. marcescens revealed few changes in gene expression, with 11 genes significantly differentially expressed (q-values <0.05) and only one gene related to the immune system. This data supports the main findings of the paper, which state that both spaceflight and low-shear modeled microgravity conditions increase the virulence of this pathogen, independent of the host immune system. This data, which shows that there are no significant immune-related changes to the host when infected with space-grown sample compared to ground-grown sample, provides further evidence that there are likely phenotypic changes to the pathogen itself that is causing increased virulence in spaceflight and in low-shear modeled microgravity.

overall_design: RNA was extracted in triplicate from 2 pooled adult (2-3 day old female) Drosophila melanogaster (w1118) per treatment, with 4 total treatment groups (no injection control, sham injection with PBS, ground bacteria-injected, and space bacteria-injected) with poly(A)+ RNA libraries. Samples were multiplexed and sequenced 100bp paired-end ready were sequenced on one lane of the Illumina HiSeq-4000.

first: Medaya

last: Torres

last: Clemens

first: Shannon

last: Hateley

first: Ravikumar

last: Hosamani

first: William

last: Wade

first: Sharmila

last: Bhattacharya

first: Lior

last: Pachter


title: Hippocampal Subregions Express Distinct Dendritic Transcriptomes that Reveal Differences in Mitochondrial Function in CA2 [array]

last: Farris

overall_design: Hippocampal cell-type and compartment specific transcriptomes were generated using laser capture microdissection on three adult male Amigo2-EGFP mice. The cell body (stratum pyramidale) and dendritic layers (stratum radiatum) from CA1 and CA2 were individually captured and expression was measured using the affymetrix whole transcriptome array. This was a pilot study for the accompanying RNA-Seq dataset from all subregions (CA1,CA2, CA3 and DG).

first: Farris

last: Shannon

first: Ward

last: James M.


title: Dynamic Lineage Priming by ERK is Driven by Transcription Factor-Independent Enhancer Regulation [TBP]

status: Public on Aug 08 2019

city: Copenhagen

first: Josh

last: Brickman

address: 3B Blegdamsvej

department: reNEW

institute: Copenhagen University

summary: Extensive analysis if the means by which ERK affects transcription via enhancer regulation in mouse embryonic stem cells. This study combines analysis of mRNA, and nascent RNA dynamics and correlates this with changes in transcription factor, co-factor, and RNAPII binding and activity.

overall_design: Mouse embryonic stem cells, stably expressing a cRAF-ErT2 expression cassette, were treated with 4OHT for 2hrs to activate ERK signalling via cRAF-ErT2

first: Joshua

last: Hamilton


title: Etv1 controls the establishment of non-overlapping motor innervation of neighboring facial muscles during development

city: Boston

first: Alan

middle: Peter

last: Tenney

address: 3 Blackfan Circle

department: Kirby Center for Neuroscience

institute: Boston Children's Hospital

summary:
The motor neurons innervating the muscles of facial expression are organized into somatotopic hindbrain clusters termed subnuclei.  Each of the medial, intermediate, dorsolateral, and lateral subnuclei gives rise to a specific branch of the facial motor nerve (cranial nerve VII).  How subnucleus-specific gene expression could mediate the accurate development of facial nerve projections was not well understood.
We isolated specific facial motor subnuclei from E16.5 hindbrain cryosections using laser capture microdissection, purified the total RNA and analyzed it on Affymetrix Mouse Genome 430 2.0 arrays.

overall_design: E16.5 mouse hindbrains were fresh frozen in optimal cutting compound (OCT), cryosectioned onto PEN-foil covered glass slides, stained with cresyl violet to identify facial motor neuron cell bodies, and individual subnuclei were isolated on a Zeiss Palm Microbeam system.  cDNA libraries were prepared using Nugen WT-Ovation Pico RNA amplification system and analyzed using an Affymetrix Mouse Genome 430 2.0 array

first: Chris

last: Henderson


title: Long-term culture of alveolospheres

first: Carlos

last: Villacorta-Martin

address: 670 Albany St

institute: Center for Regenerative Medicine at Boston University

summary: iPSC derived AEC2 cells for independent validation of stable SFTPCtdTomato+ outgrowth by scRNA-seq using iPSCs

overall_design: Cells sorted at day 51 for SFTPCtdTomato were replated as alveolospheres in 3D conditions in CK+DCI media. They were subsequently passaged as single cells 4 times on the days indicated, without further cell sorting. At day 115 all live cells were encapsulated for scRNA-seq using the 10X Chromium System

first: Konstantinos

last: Alysandratos

first: Killian

last: Hurley

first: Darrell

last: Kotton


title: Dynamic Lineage Priming by ERK is Driven by Transcription Factor-Independent Enhancer Regulation [ESRRB_SOX2]


title: Dynamic Lineage Priming by ERK is Driven by Transcription Factor-Independent Enhancer Regulation [Med24]


title: Gene profile in ovarian cancer cell spheroids

status: Public on Sep 06 2019

city: Seongnam-si

first: Hyun

last: Park

address: Bundang-gu, Yatap-dong

department: Obstetrics and Gynecology

country: South Korea

institute: CHA university, CHA Bundang Medical Center

summary: Cancer stem cells can self-renew, proliferate into differentiated cells, or enter a quiescent state and are regarded to cause chemoresistance and recurrence. Fresh tumor cells from three ovarian cancer patients were cultured to isolated spheroid-forming cells (SFC; cancer stem-like cells). The miRNAs that exhibited significant differential expression between SFCs and adherent cells were identified using miRNAs microarrays.

overall_design: Total RNA obtained from four different spheroid-forming cell (sp1, sp2, sp3, and sp5) compared to corresponding parent cancer cell (pr1, pr2, pr3 and pr4) by cDNA microarray.

first: Heejung

last: An

first: So-hyun

last: Hwang

first: Ju-Yeon

last: Jeong


title: microRNAs in ovarian cancer cell spheroids

overall_design: total RNA obtained from four different spheroid-forming cells (sp1, sp2, sp3, and sp4) compared to corresponding parent cancer cells (pr1, pr2, pr3 and pr4) by miRNA microarray.


title: Dynamic Lineage Priming by ERK is Driven by Transcription Factor-Independent Enhancer Regulation [EP300]

first: William


title: Dynamic Lineage Priming by ERK is Driven by Transcription Factor-Independent Enhancer Regulation [Mediator ChIP-seq]


title: Improved expansion, functionality and tumor targeting of adoptively transferred T cells with kinetically engineered IL-2

status: Public on Aug 07 2019

city: Los Angeles

first: Jennifer

last: Tsoi

address: 570 Westwood Blvd, CNSI 4338

department: University of California, Los Angeles

institute: UCLA

summary: The adoptive transfer of cancer-specific T cells in combination with high dose interleukin-2 (IL-2) is able to induce effective anti-tumor responses. However, tumors frequently relapse after an initial response and the known toxicities of IL-2 further limit the use of this therapy. NKTR-214 is a CD122-biased polyethylene glycol (PEG)-genetically engineered IL-2 designed to provide sustained signaling through the heterodimeric IL-2 receptor pathway (IL-2Rβγ) to preferentially activate and expand CD8 T and natural killer (NK) cells over T regulatory cells (Tregs) in the tumor. We report that combination of adoptive T cell transfer (ACT) and NKTR-214 markedly increases the proliferation, homing and polyfunctionality of antitumor T cells into the tumor. The treatment is well tolerated and leads to robust anti-tumor response in the aggressive B16F10 model. These results suggest that NKTR-214 could improve the efficacy of ACT protocols tested in humans.

overall_design: C57/BL6 mice were implanted subcutaneously with B16F10 syngeneic murine melanoma cell line. When the tumors reached the volume of at least 150mm3, mice received adoptive cell transfer of pmel-1 T cells with NKTR-214 or IL-2. Tumors from three biological replicates were harvested at day 12 after treatment .

first: Giulia

last: Parisi

first: Justin

last: Saco

first: Felix

last: Bergara

first: Paige

last: Krystofinski

first: Cristina

last: Puig-Saus

first: Ruixue

last: Zhang

first: Jing

last: Zhou

first: Gardenia

last: Cheung-Lau

first: Catherine

middle: S

last: Grasso

first: Siwen

last: Hu-Lieskovan

first: Anna

last: Wu

first: Begonya

last: Comin-Anduix

first: Deborah

middle: H

last: Charych

first: Antoni

last: Ribas


title: Gene expression profiling of leukemia cells following asparagine depletion

status: Public on Aug 06 2019

city: Indianapolis

first: Chi

state: IN

institute: INDIANA UNIVERSITY

summary: We will report the gene expression changes following asparagine depletion in human ALL cell line, RS4;11

overall_design: RNA was extracted from cells 16 hours post asparagine withdrawal from the tissue-culturing medium

first: Ji


title: Inverse data-driven modelling and multiomics analysis reveals PHGDH as a metabolic signature of M2 macrophages

status: Public on Aug 04 2019

city: Vienna

first: Thomas

last: Weichhart

address: Waehringerstraße 10

department: Center for Pathobiochemistry and Genetics

country: Austria

institute: Medical University of Vienna

summary: RNAseq data from C57BL/6 bone marrow-derived macrophages that were stimulated with IL-4 in the presence or absence of the PHGDH inhibitor CBR-5884.

overall_design: BMDM were pre-treated with either 30 µM CBR-5884 (AxonMedchem) or solvent. Thereafter, 10 ng/ml IL-4 (Peprotech) was added and cells were harvested 24h later for RNA isolation.

first: Jayne

middle: L

last: Wilson

first: Monika

last: Linke


title: rDNA chromatin interactions in the MYC-driven Eμ-Myc transgenic mouse model of B-cell lymphoma [ChIP-seq]

status: Public on Aug 01 2019

city: Badalona

first: Jeannine

last: Diesch

state: Barcelona

address: Ctra de Can Ruti, Camí de les Escoles s/n

department: Research

institute: Josep Carreras Leukaemia Research Institute

summary: Analysis of PolI and H3K27me3 binding patterns by ChIP-seq in mouse wildtype, premalignant and malignant Eμ-Myc cells.

overall_design: ChIP-seq using anti-PolI or -H3K27me3 antibodies in mouse wildtype, premalignant and malignant primary preB Eμ-Myc cells

first: Gretchen

last: Poortinga


title: Epigenetic Transgenerational Inheritance of Parent-of-Origin Allelic Transmission of Outcross Pathology and Sperm Epimutations Following Ancestral Toxicant Exposures

status: Public on Jul 23 2019

city: Pullman

first: Michael

last: Skinner

state: WA

address: Abelson 507

department: SBS

institute: WSU

summary: Previous observations have demonstrated that the agricultural fungicide vinclozolin and the pesticide DDT (dichlorodiphenyltrichloroethane) induce transgenerational sperm epimutations involving DNA methylation. These two environmental toxicants were used to investigate the impacts of parent-of-origin outcross on the epigenetic transgenerational inheritance of disease. Male and female rats were collected from a paternal outcross (POC) or a maternal outcross (MOC) F4 generation control and exposure lineages for pathology and epigenetic analysis. This model allows the parental allelic transmission of disease and epimutations to be investigated. There was increased pathology incidence in MOC outcross F4 generation male prostate, kidney, obesity and multiple diseases through a maternal allelic transmission. The POC outcross F4 generation female offspring had increase pathology incidence for kidney, obesity and multiple diseases through the paternal allelic transmission. Some disease such as testis or ovarian pathology appear to be transmitted through the combined actions of both male and female alleles. Analysis of the F4 generation sperm epigenomes identified differential DNA methylated regions (DMRs) in a genome-wide analysis. Observations demonstrate that DDT and vinclozolin have the potential to promote the epigenetic transgenerational inheritance of disease and sperm epimutations to the outcross F4 generation in a sex specific and exposure specific manner.

overall_design: The experimental design involved a daily transient exposure of gestating female F0 generation rats during embryonic days E8–E14 to 100 mg/kg per day of vinclozolin or 25 mg/kg body weight of DDT in dimethylsulfoxide (DMSO) using intraperitoneal injection. A separate control generation lineage was exposed during days E8–E14 of gestation to vehicle DMSO alone. Six different gestating females from different litters for each control, vinclozolin or DDT lineage were used. The F1 generation offspring were obtained and aged to postnatal 90-day of age and randomly selected males and females from different litters bred within the specific lineage. The F2 generation offspring were obtained and aged to 90 days and similarly bred to unrelated males and females from different litters within the same lineage to generate the F3 generation. The F3 generation offspring were aged to 90 days and males and females from different litters were selected to be outbred with either wild type males or wild type females to generate the F4 paternal outcross (POC) generation and the F4 maternal outcross (MOC) generation. No sibling or cousin breeding was used to avoid any inbreeding artifacts. All the animals were sacrificed at 1 year of age for epididymal sperm collection and histopathology analysis of different tissues. The differential DNA methylated regions (DMRs) between the control versus vinclozolin or DDT lineage male sperm were identified using a methylated DNA immunoprecipitation (MeDIP) followed by DNA next-generation sequencing.

first: Millissia

last: Maamar

first: Stephanie

middle: E

last: King

first: Eric

last: Nilsson

first: Daniel

last: Beck


title: Transcriptomic analysis of Verbena bonariensis leaves in response to low temperature

status: Public on Jul 25 2019

city: Chengdu

first: Meng-qi

last: Wang

address: Huimin street 211

institute: Sichuan Agricultural University

summary: The samples were respectively from three replicates of the cold-stress treatment and the control, then we obtained six cDNA libraries. 271,920 unigenes were produced from 406,641 assembled transcripts. Of these, 42,490 significantly differential expression genes (Corrected P-value <0.05) were obtained, including 20,412 up- and 23,078 down-regulated genes.

overall_design: Verbena bonariensis seeds were available from Benary Manufacturer and grown in the greenhouse (16 h photoperiod, 25℃/16℃ day/night temperature). 3 months old seedlings were transferred to the following temperature treatment conditions: 4℃ for 24 h, followed by -4℃ for 4 h (wilting symptoms began to appear). Control seedlings remains unchanged. leaves mRNA profiles of the development were generated by deep sequencing, in  triplicate, using Illumina HiSeq.


title: Error-free and error-prone DNA repair gene expression through reprogramming and passage in human iPS cells

status: Public on Jul 21 2019

city: Suita

first: Daisuke

last: Okuzaki

state: Osaka

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

institute: Osaka univ.

summary: Medical applications of human iPS cells(hiPSC) are evolving, but detailed elucidation of the mechanisms of reprogramming remains to be elucidated. Reprogramming is accompanied by an increase in the expression of related genes that maintain pluripotency, such as OCT3 /4 and NANOG. Also, through reprogramming, many CNVs and point mutation arise in genomes, which constitute a major barrier to the use of hiPSC for regenerative medicine. On the other hand, we recently found that DNA repair-related genes expression are altered through reprogramming, elevated expression of genes that accurately convey genomic information, such as homologous recombination (HR) and mismatch repair(MMR), and decreased expression of error-prone translesion Synthesis polymerase(TLS). Here, we confirmed this expression change in another cell-line, and further found that this expression change was maintained by overlapping passages as well as OCT3 /4 and NANOG. This suggests that changes in the expression of DNA repair-related genes associated with reprogramming and their maintenance may be new indicators of the quality control of cells exhibiting pluripotency.

overall_design: RNA-sequencing analyses were performed in two fibroblast cells and five its-derived induced pluripotent stem cells.

first: Yasuhide

last: Yoshimura


title: VDR ChIP-Seq on colonic human organoids

city: madrid

first: Alba

last: Costales

state: madrid

address: Arturo Duperier, 4

department: cancer genetics

institute: IIB

summary: Genome-wide maps of VDR binding sites in colonic organoids estimulated with calcitriol

overall_design: Three independent VDR ChIP-Seq analysis of 3D stem cell enriched cultures of two different patients each stimulated with calcitriol/vehicle.

first: Asunción

last: Fernández-Barral

first: Antonio

last: Barbáchano

first: Alberto

last: Muñoz

last: Costales-Carrera


title: Genome-wide CRISPR screening identifies new regulators of glycoprotein secretion

city: Cambridge

first: Brian

middle: Yee Hong

last: Lam

address: Box 289 Addenbookes Hospital, Hills Road

department: Metabolic Research Laboratories

country: United Kingdom

institute: University of Cambridge

summary:
Background: The fundamental process of protein secretion from eukaryotic cells has been well described for many years, yet gaps in our understanding of how this process is regulated remain.
Methods: With the aim of identifying novel genes involved in the secretion of glycoproteins, we used a screening pipeline consisting of a pooled genome-wide CRISPR screen, followed by secondary siRNA screening of the hits to identify and validate several novel regulators of protein secretion.
Results: We present approximately 50 novel genes not previously associated with protein secretion, many of which also had an effect on the structure of the Golgi apparatus. We further studied a small selection of hits to investigate their subcellular localization. One of these, GPR161, is a novel Golgi-resident protein that we propose maintains Golgi structure via an interaction with golgin A5.
Conclusions: This study has identified new factors for protein secretion involved in Golgi homeostasis.

overall_design: Genome-wide CRISPR screening

middle: J

last: Popa

first: Julien

last: Villeneuve

first: Sarah

last: Stewart

first: Esther

last: Garcia

first: Anna

last: Harrison

first: Kevin

last: Moreau


title: Gestational and lactational exposure to gossypol alters the testis transcriptome

status: Public on Jul 04 2019

city: Madison

first: Francisco

last: Peñagaricano

state: Wisconsin

address: 1675 Observatory Drive

department: Animal and Dairy Sciences

institute: University of Wisconsin-Madison

summary: Reproductive capacity can be altered by challenges experienced during critical periods of development, including fetal development and early neonatal life. Gossypol is a polyphenolic compound, commonly found in seeds of cotton plants, that impairs male reproduction. In this study, we investigated whether the exposure to gossypol in utero and during lactation alters testis development and testis gene expression in sheep.

overall_design: From conception until 60 days postpartum, Santa Inês ewes were randomly assigned to a control diet or a gossypol-rich diet based on cottonseed. A total of eighteen male lambs, 9 from control and 9 from cottonseed maternal diets, were used in this study. Lamb testicles were removed at 60 days of age and subjected to RNA-sequencing.

first: Helder

last: Louvandini

last: Peñagaicano


title: MELOHOSTRACE: Whole genome polymorphism across Meloidogyne incognita isolates showing different biological traits

status: Public on Jul 10 2019

city: Valbonne - Sophia-Antipolis

last: Lebrigand

address: 660 route des lucioles

country: France

institute: IPMC/CNRS

summary: High-coverage whole genome sequencing of 11 Brazilian isolates of the root-knot nematode Meloidogyne incognita, presenting different host plant preferences and different geographical origins. Four M. incognita host races had been proposed in the past, based on host (in)compatibility on four different plant strains. The objective was to assess whether genomic variations (SNP) correlate with host range compatibility, geographical origin and host plant of origin.

overall_design: 11 M. incognita Brazilian geographical isolates that represent the four described host races in replicates were collected. For each isolate, the offspring of one single female was retrived and multiplied on tomato plants for tens of generations. Pools of individuals where then collected for each isolate and the genome of the 12 pools of individuals were sequenced at high coverage (>100X)

first: Erika

last: Albuquerke

first: Regina

middle: M

last: Carneiro

first: Marie-Jeanne

last: Arguel

first: Georgios

last: Koutsovoulos

first: Eder

last: Marques

first: Andressa

last: Machado

first: Philippe

last: Castagnone-Sereno

first: Etienne

last: Danchin


title: High-throughput RNA sequencing on circular RNA profiles of human pancreatic cancer cell lines and gemcitabine resistant pancreatic cancer cell lines.

status: Public on Jul 07 2019

city: HeFei

first: Mei

last: Huang

state: An Hui

address: 17#Lu Jiang Road

department: General surgery

institute: Anhui Provincial Hospital

summary: Gemcitabine resistance is currently the main problem of chemotherapy for advanced pancreatic cancer patients. The resistance is thought to be caused by altered drug metabolism or reduced apoptosis of cancer cells. However, the underlying mechanism of Gemcitabine resistance in pancreatic cancer remains unclear. In this study, we established Gemcitabine resistant PANC-1 (PANC-1-GR) cell lines and compared the circular RNAs (circRNAs) profiles between PANC-1 cells and PANC-1-GR cells by RNA sequencing.

overall_design: Examing 2 conditions, each with 3 replicates

first: Feng

last: Shao


title: Ulcerative colitis gene expressions file

city: Guangzhou

first: Jin

last: Tao

state: Guangdong

address: 600 Tianhe Road, Guangzhou

department: Department of Gastroenterology

institute: The Third Affiliated Hospital of Sun Yat-Sen University

summary: Ulcerative colitis related gene expressions analysis in colonic biopsy samples from control and ulcerative colitis patients

overall_design: Three paired colonic mucosal samples from colitis patients and control individuals were collected. Total RNA of each one was extracted and reverse transcribed into cDNA. The cDNA then processed for gene expression microanalysis.


title: Gene expression changes in rat islets with glucolipotoxic conditions with or without protective compound

status: Public on Jul 16 2019

first: Faye

last: Zhao

address: 250 Massachusetts Ave

institute: NIBR

summary: To determine which GLT-regulated genes might be affected by compound D, we performed an RNA-sequencing analysis of rat islets treated ex-vivo with or without GLT and compound D for 3 hours and 24 hours. Compound E (related inactive compound) was used to account for non-specific scaffold effects.

overall_design: Islets from 8 rats were pooled together and divided into 8 groups: 3hr GLT (27mM glucose, 300uM PA); 3hr control (11mM glucose, no PA); 24hr GLT;24hr control; 3hr GLT + cpd D 300nM; 24hr GLT + cpd D 300nM; 3hr GLT + cpd E 300nM; 24hr GLT + cpd E 300nM. After treatment islets were collected for RNA prep; Experiments were repeated 3 times (3 separate isolations)

first: Heming

last: Xing

first: Jianning

last: Yin

first: Alina

last: Berdichevsky


title: Spatiotemporal single-cell analysis of gene expression in the mouse suprachiasmatic nucleus

status: Public on Jun 19 2019

city: Shanghai

first: shaoang

last: wen

state: Shanghai

address: NO.320 Yueyang Road Shanghai, China

institute: institute of neuroscience

summary: Mammalian circadian behaviors are orchestrated by suprachiasmatic nucleus (SCN) in the hypothalamus. Yet basic SCN cell types and their roles in circadian pacemaking are still unclear. In this study, we comprehensively characterized the basic cell types of SCN and their circadian and light-induced gene expression. In SCN, we identified seven major cell types among which neurons, astrocytes, ependymocytes and endothelial cells display cell-type specific circadian gene expression. We found that five SCN neuron subtypes, Avp+/Nms+, Vip+/Nms+, Vip+/Grp+, Cck+/C1ql3+ and Cck+/Bdnf+, differ in their spatial distribution, circadian rhythmicity and light responsiveness. Among the rhythmic neuron subtypes, we observed a wave of circadian gene expression propagating from the subtypes in posterior SCN  to the subtypes in anterior SCN. Such wave can be explained by the neuropeptide-receptor signaling network in which Avp+/Nms+ subtype is the leader of circadian oscillations. Our study provides insights into the basic neural mechanism of circadian pacemaking in mammals.

overall_design: 10X geomics single cell trascriptome sequencing of mice SCN

first: Shao'ang

last: Wen

first: Meng


title: Characterization of Slfn3KO mice

status: Public on Jun 24 2019

city: Grand Forks

first: Danielle

last: Perley

state: North Dakota

address: 1301 N Columbia Rd

institute: University of North Dakota Genomics Core

summary: RNA sequencing was performed on intestinal mucosa from male and female Slfn3KO mice to determine gene expression changes related to decreased weight gain in the Slfn3KO mice

overall_design: 4 sample groups: Male wildtype and Slfn3KO, Female wildtype and Slfn3KO

first: Marc

last: Basson

first: Emilie

last: Vomhof-DeKrey


overall_design: Drop-seq of mice SCN at 12 circadian time points and 1 flash stimulate time point


title: Single-cell RNA-sequencing of skin, fresh blood, and cultured peripheral blood mononuclear cells from a patient with drug-induced hypersensitivity syndrome and healthy volunteers

status: Public on Jun 17 2019

city: Seoul

first: Doyoung

last: Kim

address: 50-1 Yonsei-ro Seodaemun-gu

department: Dermatology

institute: Yonsei University College of Medicine

summary:
Purpose: Determine new therapeutic targets for a refractory drug-induced hypersensitivity syndrome/DRESS using single cell transcriptomic analysis.
Methods: Skin cells were dissociated from skin biopsies of a patient with DRESS and 5 healthy volunteers using enzymatic digestion, then viable skin cells were sorted using flow cytometry. Peripheral blood mononuclear cells (PBMCs) were isolated from peripheral blood using Ficoll-paque density separation. PBMCs were cultured with or without medications for 4 days. In detail, 200,000 PBMCs were cultivated in 200ul of RPMI-1640 supplemented with 10% human AB serum with (PBMC_T4_BACT) or without (PBMC_T4_CTRL) 48 ug/mL sulfamethoxazole/trimethoprim (SMX-TMP). For the in vitro therapeutic experiments, PBMCs were cultured in the presence of SMX-TMP with (DRESS_Day4_TOFA) or without (DRESS_Day4_BACT) tofacitinib. The patient was treated with 10mg/d of tofacitinib, a JAK3 inhibitor. The freshly isolated PBMCs were collected again two weeks after initiation of intervention (PBMC_POST2W). Single cells from the skin, freshly isolated PBMCs, and culture PBMCs were captured using droplet based single-cell approach (10x Genomics) and library were prepared.
Results: The lymphocytes in skin and PBMCs exhibited upregulation of skin-homing chemokine receptors, CCR4 and CCR10, and JAK3 and STAT1. Treatment with tofacitinib dramatically extinguished skin inflammation in a chronic refractory case of DiHS/DRESS.
Conclusions: A successful intervention with tofacitinib in a refractory case of DiHS/DRESS was guided by the use of scRNAseq, which demonstrated aberrant activity in the JAK-STAT pathway.

overall_design: Transcriptome profiles of skin, blood, and cultured PBMCs were generated by droplet-based single cell RNA-seq.

first: Benjamin

last: Voisin

first: Keisuke

last: Nagao


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

overall_design: Refer to individual Series


title: Gene expression profile in patient-derived ameloblastoma tumor

status: Public on Jun 11 2019

city: Nagoya

first: Akinobu

last: Ota

address: 1-1 Yazakokarimata

department: Food and Nutritional Environment

institute: Kinjo Gakuin University

summary: We have employed whole genome microarray expression profiling as a discovery platform to identify genes that are associated with pathogenesis of ameloblastoma using ameloblastoma tumor and corresponding normal counterpart from patients.

overall_design: Total RNA were isolated from freshly-excised tumor and normal oral tissues with Dnase treatment.

first: Sayuri

last: Kondo

first: Takayuki

last: Ono


title: Impact of genome architecture upon the functional activation and repression of Hox regulatory landscapes

status: Public on Jun 12 2019

city: Geneva

first: Eddie

last: Rodríguez-Carballo

address: 4, Boulevard d'Yvoy

department: Department of Genetics and Evolution

country: Switzerland

institute: Université de Genève


title: Impact of genome architecture upon the functional activation and repression of Hox regulatory landscapes [ChIP-seq]

summary: The spatial organization of the mammalian genome is complex and relies upon the formation of chromatin domains of various scales. At the level of gene regulation in cis, collections of enhancer sequences define large regulatory landscapes that usually match with the presence of topologically associating domains (TADs). These domains are largely determined by bound CTCF molecules and often contain ranges of enhancers displaying similar or related tissue specificity, suggesting that in some cases such domains may act as coherent regulatory units, with a global on or off state. By using the HoxD gene cluster as a paradigm, we investigated the effect of large genomic rearrangements affecting the two TADs flanking this locus, including their fusion into a single chromatin domain. We show that, within a single hybrid TAD, the activation of both proximal and distal limb enhancers initially positioned in either TADs globally occurred as when both TADs are intact. We also show that the timely implementation of distal limb enhancers depends on whether or not target genes had previously responded to proximal enhancers, due to the presence or absence of H3K27me3 marks. From this work, we conclude that antagonistic limb proximal and distal enhancers can exert their specificities when positioned into the same TAD and in the absence of their genuine target genes. We also conclude that removing these target genes reduced the coverage of a regulatory landscape by chromatin marks associated with silencing and thus prolonged its activity in time. Since Polycomb group proteins are mainly recruited at the Hox gene cluster, our results suggest that Polycomb Repressive Complex 2 (PRC2) can extend its coverage to far-cis regulatory sequences as long as confined to the neighboring TAD structure.

overall_design: ChIP analysis of H3K27ac, H3K27me3, EZH2 and RING1B from mouse Wt and mutant forelimb tissues

first: E

last: Rodriguez-Carballo

first: N

last: Yakushiji-Kaminatsui

first: L

last: Lopez-Delisle

first: D

last: Duboule


title: Gene expression in gastric Mist1+ cells.

status: Public on Jun 25 2019

city: Tokyo

first: Yoku

last: Hayakawa

state: TOKYO

address: 7-3-1, Hongo, Bunkyo-ku, Clinical Research Center 4F, Room 425

institute: University of Tokyo

summary:
Mist1+ cells and parietal cells in mouse stomach were separatedly sorted, and RNAs were isolated.
Mist1 (also known as Bhlha15) is expressed in gastric chief cells and gastric stem cells in mice. However, more specific genes for each population needs to be identified to better understand the precise biology in these cell populations. In order to address cell specific gene signature, we separately sorted Mist1+ gastric chief cells and Mist1+ gastric stem cells by FACS, and performed microarray analysis.  Mist1+ gastric chief cells were sorted by using Mist1-CreERT; R26-TdTomato mouse stomach, immediately after tamoxifen administration. Mist1+ gastric stem cells were sorted by chief cell-ablated Mist1-CreERT; R26-TdTomato mouse stomach, combining with Lgr5-DTR mice. Lgr5-expressing chief cells were ablated by giving DT into these mice. As a control, acid-secreting gastric parietal cell samples were used.
Mice were treated with or without Lgr5-DT ablation before sorting.

overall_design: Mist1+TdTomato+ cells were sorted by FACS. Each group has 3 replicates. Groups contain parietal cell samples, Mist1+ cell samples, Mist1+ cell after Lgr5-ablation samples.

first: Masahiro

last: Hata

first: Hiroto

last: Kinoshita

first: Mitsuru

last: Konishi

first: Mayo

last: Tsuboi

first: Yukiko

last: Oya

first: Hayato

last: Nakagawa

first: Hiroaki

last: Fujiwara

first: Samuel

last: Asfaha

first: Daniel

last: Worthley

first: Yuki

last: Muranishi

first: Takahisa

last: Furukawa

first: Shunsuke

last: Kon

first: Hiroyuki

last: Tomita

first: Timothy

last: Wang

first: Kazuhiko

last: Koike


title: Whole lung transcriptomics of a house dust mite model of mild/moderate asthma

status: Public on Jun 06 2019

city: Reno

first: William

middle: T

last: Gerthoffer

state: Nevada

address: 1440 N Virginia St

department: Pharmacology

institute: University of Nevada, Reno

type: Non-coding RNA profiling by high throughput sequencing

summary:
Purpose:  Identify whole lung gene expression patterns in a house dust mite model of mild/moderate asthma
Methods: Lung gene expression profiles of 10 week old BALB/c female mice were generated by ribosome-depleted, 150 nt, paired-end, stranded RNA-seq with Illumina HiSeq v4.  Sequence reads that passed quality filters after trimming were analyzed  with Sailfish-cir to identify linear RNAs and circular RNAs. Differential expression of linear RNAs was assessed with Deseq2 . QRT–PCR validation was performed using TaqMan and SYBR Green methods.
Results: 100 million sequence reads per sample were mapped to the mouse genome (build mm10) using Sailfish-cir to identify linear and circular RNA transcripts. Pathway analysis of differentially expressed genes identified upregulation of gene sets for human asthma, mouse lung allergic inflammation, Muc5ac regulated genes and smooth muscle genes after allergic sensitization. Gene level exppression in each asthma-related pathway was reduced by the miR-145 antagonist. The miR-145 antagonist and several nontargeting oligos also upregulated interferon signaling pathways suggesting a general antiinflammatory effect of LNA/DNA oligos in the lung.
Conclusions: Lung-directed delivery of LNA/DNA oligonucleotides with cationic lipid nanoparticles is an efffective means to prevent inflammatory gene expression in a house dust mite model of mild/moderate asthma.

overall_design: Linear and circular RNA transcript expression was compared in whole lung tissue from unsensitized, house dust mite sensitzed, antimiR-145 treated treated mice

first: Sabrina

last: Ramelli

first: Tong

last: Zhou


title: Effects of siRNA gene silencing on transcriptional responses of human synovial fibroblasts to TNF and IL-17A (RNA-seq Data 2)

status: Public on Jun 01 2019

city: Charlestown

first: Kamil

last: Slowikowski

state: Massachusetts

address: Mailstop CNY 149-8, 149 13th Street

institute: Massachusetts General Brigham

summary: TNF and IL-17A synergistic effects on gene expression after silencing CUX1, LIFR, STAT3, STAT4, ELF3

overall_design:
Human fibroblasts were transfected with siRNAs and then stimulated with TNF or TNF and IL-17A.

RNA-seq Data 2 (n=192): 4 synovial fibroblast cell lines from patient tissues, 4 time points (0, 1, 6 and 16 hours), 2 stimulations (TNF (0.1 ng/mL); TNF (0.1 ng/mL) and IL-17A (1 ng/mL)), and 5 siRNAs (CUX1, LIFR, STAT3, STAT4, ELF3)

---------------------------------------------------------
Authors state "We don't have the required patient consents to deposit the raw sequencing reads."
Thus, this dataset is incomplete.

first: Hung

middle: N

last: Nguyen

first: Erika

last: Noss

first: Daimon

last: Simmons

first: Fumitaka

last: Mizoguchi

first: Gerald

last: Watts

first: Michael

last: Gurish

last: Brenner

first: Soumya

last: Raychaudhuri


title: Breast cancer cell line panel stimulated with estradiol

city: Eindhoven

first: Marcia

middle: Alves de

last: Inda

address: High Tech Campus 11

department: PDx

country: Netherlands

institute: Philips Research

summary: A panel of twelve breast cancer cell lines (ATCC) were exposed to 0, 1 or 10 nM 17β-estradiol (E2) for 16 hours. Cells were maintained in DMEM/F12 1:1 (DF) supplemented with 10% or 20% fetal calf serum (FCS) or 20% FCS and 0.01 mg/ml insulin. Two days before experiments, cells were seeded in 60 mm plates in DF with charcoal stripped phenol red-free serum supplemented with non-essential amino-acids and pen/strep, at a density such that 75%-90% confluence was obtained by the time of harvesting. Medium was refreshed 24 hours before exposure to 1 nM E2, 10 nM E2 or DMSO (control) for 16h. Subsequently cells were harvested and RNA was extracted using the Nucleospin RNA isolation kit (Macherey-Nagel).

overall_design: A panel of twelve breast cancer cell lines were exposed with 0, 1 or 10 nM 17β-estradiol (E2) for 16 hours.

first: Márcia

middle: A

first: Anne

last: van Brussel

first: Eveline

last: den Biezen

first: Bart

last: van den Burg

first: Hai

last: Man

first: Irene

last: Middelhof

first: Wim

last: Verhaegh

first: Anja

last: van de Stolpe


title: Tissue-resident PDGFRα stromal cells modulate both fibrosis and tissue revascularization during wound repair

status: Public on Jul 01 2019

city: New York

first: Gabriel

last: Hofman

state: New York

address: 1 Gustave L Levy Plaza

department: Department of Genetics and Genomics Sciences

country: USA

institute: Icahn School of Medicine at Mount Sinai

summary: PDGFRα+ cells are interstitial/perivascular mesenchymal progenitor cells that have been associated with fibro-adipogenic processes. However, their function during tissue homeostasis or in response to revascularization and regeneration stimuli remains to be fully defined. Here, by high-throughput transcriptomic analysis, adoptive transfer and multicolor lineage tracking we showed that PDGFRα+ cells from skeletal muscle cluster as a population that is transcriptionally distinct from other mesenchymal stromal cells and with an essential role in tissue revascularization and restructuring of ischemic areas. We further showed that tissue regeneration involves the removal of differentiated PDGFRα+-derived cells, while pathological healing occurred if PDGFRα+-derived cells persisted as terminally differentiated mesenchymal cells (e.g. myofibroblasts). From the perspective of tissue regeneration, these studies support a context-dependent 'yin-yang' biology of PDGFRα+ cells, that possess an innate ability to stabilize newly formed blood vessels and concurrently limit injury expansion after ischemia, while also being capable of promoting fibrosis in an unfavorable environment.

overall_design: RNA-seq on mouse tissues

last: Hoffman

first: Jason

last: Kovacic