title: Transcriptomic Analysis of the Innate Immune Response to Plasmid DNA in vitro

status: Public on Feb 12 2021

city: Villanova

first: Jacob

last: Elmer

state: PA

address: 800 E Lancaster Ave

department: Chemical & Biological Engineering

institute: Villanova University

summary: The innate immune response to cytosolic DNA is intended to protect the host from viral infections, but it can also inhibit the delivery and expression of therapeutic transgenes in gene and cell therapies. The goal of this work was to use mRNA-sequencing to reveal correlations between the transfection efficiencies of four cell types (PC-3, Jurkat, HEK-293T, and primary CD3+ T cells) and their innate immune responses to Lipofection in serum-free media (SFM). Overall, the highest transfection efficiency was observed in HEK-293T cells, which upregulated only 142 genes with no known anti-viral functions. Lipofection upregulated a much larger number (n = 1,057) of cytokine-stimulated genes (CSGs) in PC-3 cells, which exhibited a significantly lower transfection efficiency. However, the addition of serum during Lipofection and electroporation provided much higher transfection efficiencies and lower number of upregulated genes. This inverse correlation between transfection efficiency and the number of differentially expressed genes was contradicted by the T cell lines that achieved lower transfection efficiencies and only upregulated a few upregulated genes following Lipofection. However, several of the CSGs that were absent in HEK and upregulated in PC-3 cells were constitutively expressed in T cells, suggesting that T cells constitutively express CSGs to prevent infection.

overall_design: 3 cell lines transfected with Lipofectamine in serum-free media (SFM), 6 samples per cell line with (3) untransfected and (3) transfected samples; plus 12 PC-3 samples that were either Lipofected or electroporated in SCM (30 samples overall)

first: Eric

last: Warga

first: Emily

last: Harris

last: Tucker


title: JAK inhibitors dampen activation of interferon-activated transcriptomes and the SARS-CoV-2 receptor ACE2 in human renal proximal tubules

status: Public on Feb 03 2021

city: Bethesda

first: Hye Kyung

last: Lee

state: MD

address: 8 CENTER DR RM 107

department: National Institute of Diabetes and Digestive and Kidney (NIDDK)

country: USA

institute: National Institutes of Health (NIH)

type: Expression profiling by high throughput sequencing

type: Genome binding/occupancy profiling by high throughput sequencing

summary: SARS-CoV-2 infections initiate cytokine storms and activate genetic programs leading to progressive hyperinflammation in multiple organs of patients with COVID-19. While it is known that COVID-19 impacts kidney function, leading to increased mortality, cytokine response of renal epithelium has not been studied in detail. Here, we report on the genetic programs activated in human primary proximal tubule (HPPT) cells by interferons and their suppression by ruxolitinib, a Janus kinase (JAK) inhibitor used in COVID-19 treatment. Integration of our data with those from patients with acute kidney injury and COVID-19, as well as other tissues, permitted the identification of kidney-specific interferon responses. Additionally, we investigated the regulation of the recently discovered isoform (dACE2) of the angiotensin-converting enzyme 2 (ACE2), the SARS-CoV-2 receptor. Using ChIP-seq, we identified candidate interferon-activated enhancers controlling the ACE2 locus, including the intronic dACE2 promoter. Taken together, our study provides an in-depth understanding of genetic programs activated in kidney cells.

overall_design: Refer to individual Series


title: Single cell RNA-seq analysis of young (2 months) and old (18 months) mouse hematopoietic stem and progenitor cells

status: Public on Feb 02 2021

city: Marseille

first: Estelle

last: Duprez

state: région Sud - Provence-Alpes-Côte d'Azur

address: 27 Bd Leï Roure, CS 30059

country: France

institute: Inserm

summary: Hematopoietic stem cells (HSCs) represent a rare population of cells residing in the Bone Marrow (BM) at the top of hematopoietic hierarchy. A critical balance is maintained between self-renewal and lineage differentiation of HSCs to maintain hematopoietic homeostasis. With aging, this balance is altered with an increase of self-renewal long term HSCs and a myeloid biased differentiation, which favors the appearance of myeloid leukemias and anemias. This experiment aims to understand molecular mechanisms that cause this aged-related disequilibrium in the mouse. To this end, we generated single cell RNA-seq data from pools of young and old hematopoietic stem and progenitor cells (HSPCs), isolated from mouse BMs.

overall_design: Mice at young age (2 months) or at old age (17-18 months) were sacrified and bone marrow (BM) harvested. Pools of 2 or 3 BMs of the age-matched mice were formed to obtain 2 samples of young mice (young_A and young_B) and 2 samples of old mice (old_A and old_B). For each sample, cells were lineage depleted by using the Lineage Cell Depletion Kit (Miltenyi) and labelled with the following antibody cocktail: anti-cKit, anti Sca-1 anti CD34, anti CD150, anti CD48 and anti Flt3 antibodies to purify Lin-Sca1+cKit+ Flt3- cells (HSPCs) by multi-parameter fluorescence-activated cell sorting (FACS). We used the 10x Genomics platform and FACS purified HSPCs were loaded 30 min after the sorting onto a Chromium Single Cell Chip and processed with the Chromium Controller (10x Genomics) according to the manufacturer’s instructions for single cell barcoding at a target capture rate of 4000 individual cells per sample. Libraries were prepared using Chromium Single-Cell 3′ Reagent Kits v2 (10x Genomics) and were sequenced using an Illumina NextSeq500 sequencer to an average depth of about 45,000 reads per cell for Young_A and Old_B samples -and about 130,000 reads per cell for Old_A and Young_B samples.


title: Interleukin-17 governs hypoxic adaptation of injured epithelium

status: Public on Feb 18 2021

city: New York

first: Shruti

last: Naik

state: NY

address: 435 East 30th Street

department: Pathology

institute: NYU Langone Health

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


title: Transcriptome and chromatin accessiblity analysis of mice soft palate to unreveal the role of Runx2 in regulating palate muscle development.

status: Public on Jan 27 2021

city: LA

first: Xia

last: Han

state: CA

address: 2250 Alcazar Street

institute: University of Southern California

summary: We report the application of single cell transcriptome, bulk transcriptome, and chromatin accessibility analysis for investigating the role of Runx2 in regulating soft palate muscle development. By isolating single cells from soft palate tissue of wild type embryos at E13.5, E14.5 and E15.5, we describe the heterogeneity of soft palate mesenchyme during development by analyzing single cell transcriptome. Combined analysis of bulk and single cell transcriptome of soft palate from wild type and Runx2 mutant suggests Runx2 activate expression of perimysial markers. Finally, we show that Runx2 activates expression of perimysial markers probably by repressing Twist1 through chromatin accessibility analysis. This study provides the first single cell level heterogeneity analysis of developing soft palate and shows the important role of Runx2 in regulating soft palate muscle development.

overall_design: Transcriptome and chromatin accessiblity profiling of developing mouse soft palate

first: Yang

last: Chai


title: Conjoint Analysis of Metabolome and Transcriptome Reveals the Difference in Flavonoid Biosynthesis in Two Pomelo Cultivars

status: Public on Feb 01 2021

city: xuzhou

first: chenxu

last: zhao

state: jiangsu

address: No.101, Shanghai road,  Tongshan District

country: China

institute: jiangsu normal university

summary: Our study demonstrated the fluctuation of flavonoid biosynthesis in the two pomelo cultivars and laid a theoretical foundation for pomelo breeding to generate fruits with high flavonoid content.

overall_design: De novo transcriptome sequencing was performed on ripe fruits of two pomelo cultivars, each cultivar contained 3 biological repeats.

first: Chenxu

last: Zhao


title: Reprogramming an endogenous small RNA pathway for multiplexed and transgenerational gene silencing in C. elegans

status: Public on Jan 21 2021

city: Piscataway

first: Sam

middle: Guoping

last: Gu

state: New Jersey

address: 604 Allison Road

department: Molecular Biology and Biochemistry

institute: Rutgers University

type: Non-coding RNA profiling by high throughput sequencing

summary: High-throughput sequencing analysis of C. elegans strains that were subject to piRNA-mediated RNA interference ("piRNAi"), a method developed in this study. The relative ease of targeting exogenous CRISPR/Cas proteins to specific DNA or RNA sequences using short guide RNAs has enabled the development of a wealth of tools in genetically tractable systems. Here, we demonstrate that an endogenous pathway can similarly be repurposed for gene silencing by expression of short guide piRNAs (21 nucleotides) in C. elegans. The cloning-free method, piRNA-mediated RNA interference ("piRNAi"), is specific, allows multiplexed gene silencing, and can silence genes in the female and male germline that are otherwise refractory to RNA interference (RNAi). Silencing requires several piRNAs expressed from extra-chromosomal DNA and tolerates up to four mismatches. Targeting decreases mRNA levels, increases secondary small interfering RNAs (22G), and results in repressive chromatin modifications at the target locus, indicating transcriptional and post-transcriptional silencing. We use piRNAi to induce transgenerational silencing of two canonical targets (gfp and oma-1) and identify two novel genes (him-5 and him-8) that inherit epigenetic silencing for four and six generations, respectively.

overall_design: small RNA-seq, mRNA-seq, and ChIP-seq of C. elegans that underwent piRNAi against different genes or control piRNAi

first: Monika

last: Priyadarshini

first: Julie

middle: Z

last: Ni

first: Amhed

middle: M

last: Vargas-Velazquez

middle: G

first: Christian

last: Frøkjær-Jensen


title: Interleukin-17 governs hypoxic adaptation of injured epithelium [spatial transcriptomics]

summary: To define the gene signature and spatial architecture of the skin after injury, we performed spatial transcriptomics from mouse unwounded and wounded skin.

overall_design: Wild type (unwounded, wounded) and GFP-KI (wounded) skin were fresh frozen and sectioned at 10um thickness onto spatial transcriptomics (ST) slides for mRNA capture, followed by library preparation and sequencing. The GFP-KI genotype disrupts the Rorc gene.

first: Piotr

last: Konieczny

first: Xing

last: Yue

first: Ikjot

last: Sidhu


title: Samples from exacerbating COPD subjects before and after treatment with nemiralisib

status: Public on Dec 31 2020

city: Stevenage

first: Glyn

last: Bradley

address: Medicines Research Centre

department: Computational Biology

country: United Kingdom

institute: GSK

summary: To study the effects of treatment with an inhaled PI3Kδ inhibitor during recovery from an exacerbation of Chronic Obstructive Pulmonary Disease (COPD) due to corrective effects on neutrophils that display dysregulated migration characteristics. We aimed to develop novel induced sputum endpoints to demonstrate changes in neutrophil phenotype and proof of mechanism of action in the lung.

overall_design: Matched Sputum and Whole Blood samples  were taken at baseline in  28 COPD subjects pre and post treatment


title: Transcriptome analysis of melanoma cells stably expressing BMP6

status: Public on Jan 10 2021

city: NUTLEY

first: EUN JOON

last: LEE

state: NJ

address: 200 METRO BLVD

department: CDI CENTER

institute: HACKENSACK MERIDIAN

summary: Molecular function of BMPs in metastatic melanoma progression is undefined. The goal of this study is to identify BMP6-activated gene signaturs associated with metastatic progresses in human cutaneous melanoma. Transcriptome profiles (RNA-seq) of three melanoma cell lines (WM1341D, WM983B, and 1205Lu) stably expressing BMP6 and coressponding control cells were generated by deep sequencing using illumona HiSeq and mapped more than 30 million sequencing reads per sample to the human genome (build Hg19). Gene signatures down-regulated by BMP6 are mostly associated with extracellular matrix organization and growth factor binding, suggesting a metastasis-suppressive role of BMP6 in melanoma.

overall_design: Genome-wide RNA profiles of BMP6-overexpressing human cutaneous melanoma cell lines and corresponding control cells

first: B

last: Ryu

first: D

last: Min


title: Samples from stable COPD subjects before and after treatment with nemiralisib


title: Integrative analysis of intrinsic and adaptive resistance to KRASG12C inhibitors in lung adenocarcinoma models

status: Public on Jan 06 2021

city: nantong

first: mangze

last: hu

address: qixiu street 19

institute: nantong university

summary: KRASG12C inhibitors have been widely reported and studied in recent years. Some of the inhibitors, such as AMG510 and ARS1620, have been reported in clinical studies to be effective in treating patients with non-small cell lung cancer (NSCLC). However, the rapid development of drug resistance in tumor cells will delay the clinical application of these drugs. Therefore, how to block the resistance to these inhibitors in tumor cells with KRASG12C mutations is crucial. We report the alteration in transcriptomics of NSCLC cell line H358 after long-term ARS1620 treatment to explore the mechanism of H358 resistance.

overall_design:
mRNA profiles of H358-P (H358 cell treated with ARS-1620 for 0 hour), ARS-24H (H358 cell treated with ARS-1620 for 24 hours), ARS-48H (H358 cell treated with ARS-1620 for 48 hours), and H358-R (H358 cell treated with ARS-1620 for long period until it is resistant to ARS1620).

mRNA profiles of H358_P (H358 cell treated with ARS-1620 for 0 hour), H358_ARS (H358 cell treated with ARS-1620 for 24 hours), H358_M1 (H358 cell treated with ARS-1620 for 24 hours with M1-type macrophage conditional medium), H358_M2 (H358 cell treated with ARS-1620 for 24 hours with M1-type macrophage conditional medium)

first: Hu

last: Mangze

first: Wu

last: En

first: Liu

last: Ying


title: Single-Cell Trajectories of Melanoma Cell Resistance to Targeted Treatment

status: Public on Jan 16 2021

city: Leipzig

first: Maria

last: Schmidt

address: Haertelstraße 16-18

country: Germany

institute: IZBI

summary: In order to identify mechanisms of melanoma treatment resistance, we applied micorofluidic scRNA-Seq to the transcripomes of a total of about 31,000 single cells obtained form A375 melanoma cell line untreated/sensitive or treated with BRAF inhibitor vemurafenib, either alone or in combination with MEK1 inihibitor cobimetinib or trametinib. Analysis by dimensionality reduction software tSNE and SOM identified a clonal heterogeneity clearly seperating all 4 possible treatment conditions.

overall_design: scRNA-Seq of BRAF-mutant A375 cells in 4 treatment conditions: untreated/sensitive cells, cells resistant to vemurafenib, cells double-resistant to vemurafenib and cobimetinib, cells double-resistant to vemurafenib and trametinib

first: Sünke

last: Mortensen

first: Henry

last: Loeffler-Wirth

first: Corinna

last: Kosnopfel

first: Knut

last: Krohn

first: Hans

last: Binder

first: Manfred

last: Kunz


title: Identification of m6A residues at single nucleotide resolution using eCLIP and an accessible custom analysis pipeline

city: Mobile

first: Justin

last: Roberts

state: AL

address: 5851 USA Drive North, MSB 3370

department: Pharmacology

institute: University of South Alabama

summary: We have developed a modified eCLIP-based method (meCLIP) to identify m6A residues at single-nucleotide resolution. By coupling the improvements of eCLIP with an easy-to-use computational pipeline, we have successfully identified over 50,000 unique m6A residues in the two breast cancer cell lines that were analyzed (MCF-7 and MDA-MB-231) and over 8,000 unique residues in HEK-293 cells.  We compared these residues to the sites called using the currently most utilized m6A identification method (miCLIP).

overall_design: m6A identification in 3 cell lines (MCF-7, MDA-MB-231, and HEK-293) using modified eCLIP-based library preparation and custom analysis pipeline

middle: T

first: Aaron

last: Johnson


title: Epistatic transcriptional interations underlying oncogenic genetic interactions (GI) via combinatorial CROP-seq

status: Public on Jan 31 2021

city: Stony Brook

first: Robert

middle: Scott

last: Powers

address: 100 Nicolls Rd

institute: Stony Brook University

summary: In our combinatorial CRISPR screenings, we screened for tumor/growth promoting GIs between 52 tumor suppressor genes (TSGs). In this part, we systematically profiled single-cell transcriptomes of double knocking-out (DKO) and single knocking-out (SKO) cells of GI pairs identified in our GI screenings, and tried to decipher the role of transcription in the phenotypic effects of GIs.

overall_design: Cell library expressing dual CROPseq-sgRNAs was constructed by infection of CROPseqGuide-Puro-sgRNAs viruses and CROPseqGuide-Blasti-sgRNAs viruses sequentially. MCF10A-Cas9-Venus-vector cells were infected with 15 different CROPseqGuide-Puro-sgRNA viruses individually. CROPseqGuide-puro-(NF1_1, PTEN_5, SMAD4_5, CASP8_5, CBFB_2, CDH1_5, RB1_3, TP53_3, NF2_2, TBX3_3, USP9X_3, TP53_4, TP53_5, hRosa26_2, CTRL0002), and selected in 1.5 µg/ml puromycin for 4 days. Cells were then frozen, and passed for the next infection of CROPseqGuide-Blasti viruses. After 24 h of infection, Blasticidin (15 ng/µl) was added for selection. 72 of different pair-wised sgRNA combinations in total were included in the CROPseq cell library. Cell library was then cultured in different media and harvested for single cell transcriptome profiling. Single cells contain different perturbations that generating single knocking-out (SKO) and double knocking_out (DKO) and Control cells.

first: Xiaoyu

last: Zhao

first: Scott


title: Atypical chromatin structure of immune-related genes expressed in chicken erythrocytes

city: Winnipeg

first: James

middle: Ronald

last: Davie

state: Manitoba

address: 745 Bannatyne Avenue, RM 333A

department: Biochemistry and Medical Genetics

country: Canada

institute: University of Manitoba


title: Atypical chromatin structure of immune-related genes expressed in chicken erythrocytes [RNA-seq]

summary: Transcriptional regulation is impacted by multiple layers of genome organization. Here, we report that immune genes were associated with H3K4me3 and H3K27ac. In conjunction with next-generation DNA, RNA sequencing, chromatin immunoprecipitation-DNA sequencing and FAIRE sequencing, we identified the active chromosomal compartments and determined their structural signatures in relation to expression levels.

overall_design: Examination of gene expression in 6C2 line (a transformed chicken erythrocyte precursor cell line).

first: Sanzida

last: Jahan

first: Wayne

last: Xu

first: Tasnim

middle: H

last: Beacon

first: Aleksander

last: Ilic

middle: R


title: Genetic and transcriptomic basis of copper tolerance across natural European Drosophila melanogaster populations

city: Barcelona

first: Gabriel

middle: Eduardo

last: Rech

address: Passeig Marítim de la Barceloneta 37-49

country: Spain

institute: Consejo Superior de Investigaciones Cientificas - Institute of Evolutionary Biology (CSIC-UPF)

summary: Resistance to oxidative stress plays a vital role in animal physiology, where it influences both life history traits and the ability to tolerate the effects of a myriad of environmental stressors. While stress resistance has previously been shown to share a role in shaping an organism's response to traits as varied as desiccation, thermal tolerance and xenobiotic resistance, heavy metal tolerance presents a particular challenge with regards to adaptation to stress. Heavy metals contamination can result in robust and persistent selection pressure: not only is acute exposure highly toxic, but metals can accumulate in the environment over long periods, prolonging this exposure. However, many heavy metals, such as copper and zinc, are also essential micronutrients, which may constrain adaption in high copper conditions. To determine the genetic basis of copper tolerance in European Drosophila melanogaster, we phenotyped 76 inbred lines sampled from nine locations across Western Europe on copper sulphate, demonstrating that that copper tolerance is a highly variable trait. A combination of long-read nanopore sequencing and high-throughput RNA-seq analysis carried out before and after copper exposure shows that while copper tolerance is a highly heterogenous trait, affected by changes in expression across multiple loci, the greatest changes in expression a seen in the digestive tract. In addition, a large proportion of genes found differentially expressed upon copper exposure have previously shown to be regulated by a number of transcription factors with known roles in a broad range of metabolic processes, indicating that while the initial response may be tissue restricted, long term affects of copper expose are more likely to be systemic.

overall_design: Of 76 lines phenotyped, three for the more sensitive tail of the distribution (COR-018, JUT-008, AKA-018) and three from the more resistant end (MUN-008, GIM-012, MUN-020) were selected for further analysis. Briefly, 3- to 7-day-old females from the six lines were exposed to 20mM copper sulfate in a 5% solution for 24 hours. Exposure involved both contact and ingestion. 20 females were used in each biological repeat, for a total of three repeats. Controls were conducted under the same conditions, without the use of copper.

first: Llewellyn

last: Green

first: Judit

last: Salces-Ortiz

middle: E

first: Santiago

last: Radío

first: Josefa

last: González


title: Atypical chromatin structure of immune-related genes expressed in chicken erythrocytes [ChIP-seq]

summary: Transcriptional regulation is impacted by multiple layers of genome organization. Here, we report that immune genes were associated with H3K4me3 and H3K27ac.Our data provide a genome-wide profile of chromatin signatures for immune genes in chicken polychromatic erythrocytes.

overall_design:
Epigenomic landscape of immune genes in chicken erythrocytes
Examination of two different histone modification in Chicken polychromatic erythrocyte cells.

last: RDavie


title: ALI1 interacts with N-acyl homoserine lactone and is involved in the perception of the quorum sensing molecule

status: Public on Dec 20 2020

city: Braunschweig

first: Abhishek

last: Shrestha

address: Messeweg 11/12

institute: Julius-Kuehn Institute

summary: In this report, we investigated oxo-C14-HSL-interacting proteins in plants. We propose the AHL-Interacting Protein 1 (ALI1) (previously known as AtGalk2) as interacting protein for oxo-C14-HSL in Arabidopsis. We present here several levels of confirmation and suggest that ALI1 is required for the perception of oxo-C14-HSL in Arabidopsis. This is the first direct evidence of a plant protein interacting with a bacterial quorum sensing molecule.

overall_design: Examination of Col-0 and ali1 mutant seedlings pretreated for three days with 6 µM oxo-C14-HSL or acetone control and subsequently elicited with 100 nM flg22. All treatments were performed in triplicates.

first: Maja

last: Grimm

first: Adam

last: Schikora


title: A Lysosome independent role for TFEB in activating DNA repair and inhibiting apoptosis in breast cancer cells

status: Public on Dec 22 2020

city: Saint John

first: Thomas

last: Pulinilkunnil

state: New Brunswick

address: 100 Tucker park road

department: Biochemistry and Molecular Biology

institute: Dalhousie University

summary: Transcription factor EB (TFEB) is a master regulator of lysosomal biogenesis and autophagy with critical roles in several cancers. Lysosomal autophagy promotes cancer survival through degradation of toxic molecules and maintenance of adequate nutrient supply. Doxorubicin (DOX) is the standard of care treatment for triple-negative breast cancer (TNBC); however, chemoresistance at lower doses and toxicity at higher doses limit its usefulness. By targeting pathways of survival, DOX can become an effective antitumor agent. In this study, we examined the role of TFEB in TNBC and its relationship with autophagy and DNA damage induced by DOX. In TNBC cells, TFEB was hypo-phosphorylated and localized to the nucleus upon DOX treatment. TFEB knockdown decreased the viability of TNBC cells while increasing caspase-3 dependent apoptosis. Additionally, inhibition of TFEB-phosphatase calcineurin sensitized cells to DOX-induced apoptosis in a TFEB dependent fashion. Regulation of apoptosis by TFEB was not a consequence of altered lysosomal function, as TFEB continued to protect against apoptosis in the presence of lysosomal inhibitors. RNA-Seq analysis of TFEB knockdown MDA-MB-231 cells identified a significant downregulation in cell cycle and homologous recombination while genes involved in interferon-γ and TNFα signaling were upregulated. In consequence, knockdown of TFEB was found to disrupt DNA repair following DOX, as evidenced by persistent γH2A.X detection. Together, these findings describe in TNBC a novel lysosomal independent function for TFEB in responding to DNA damage.

overall_design: MDA-MB-231 cells were transfected with either of two siRNA’s targeting TFEB (n=3 for each siRNA) or a non-targeting control (n=4) and cultured for 48 h before cells were harvested and RNA extracted using the Qiagen RNeasy mini kit according to the manufacturer’s instructions.

first: Logan

last: Slade

first: Dipsikha

last: Biswas

first: Francis

last: Ihionu

first: Yassine

last: El Hiani

first: Petra

middle: C

last: Kienesberger


title: Antifibrogenic activities of CYP11A1-derived vitamin D3-hydroxyderivatives are modified by RORγ expression [I]

city: Birmingham

first: Andrzej

last: Slominski

address: 1720 2nd Avenue South

department: Dermatology

institute: UAB

summary: The aim of this study was to test the role of RORγ in the action of the above analogs using murine fibroblasts isolated from the skin of wild type (RORg+/+) and knock out (RORg-/-) mice.

overall_design: mRNA profiles of fibroblasts isolated from  the skin of the wild type (WT) and RORg-/- mice treated with CYP11A1- derived vitamin D3 derivatives: 20(OH)D3 and 1,20(OH)2D3 were generated by sequencing. We utilized RNA-sequencing in order to compare the gene expression profiles in wild type and RORγ-/- fibroblasts. Utilizing analysis we compared the gene expression profile of ethanol only treated RORγ-/- fibroblasts with ethanol treated RORγ+/+ fibroblasts. Analysis showed changes in five top canonical pathways including: role of BRCA1 in DNA damage response; Cell cycle: G2/M DNA damage checkpoint regulation; cell cycle control of chromosomal replication; mitotic roles of polo-like kinase; and hepatic fibrosis/ hepatic stellate cell activation. Among ingenuity’s  biological functions and diseases and disorders, cancer, gastrointestinal diseases, organismal injury and abnormalities, reproductive system diseases, and hematological diseases are significantly affected. The main cellular functions that are affected are pertinent to liver and kidney inducing hepatotoxicity, renal toxicity, as well as cardiotoxicity.

first: Zorica

last: Janjetovic


title: Bulk RNA-seq of mouse cells from the dorsal cerebral cortex during its formation

city: Basel

first: Verdon

last: Taylor

address: Mattenstrasse 28

department: Department of Biomedizin

country: Switzerland

institute: University of Basel

summary: Dorsal cortices from embryonic day (E10.5) to postnatal day 1 (PN) were micro-dissected and dissociated into single cell suspensions using Papain and Ovo-mucoid mix. Cells were washed with L15 medium and FAC-sorted for GFP positive NSCs using FACSariaIII (BD Biosciences) derived from Hes5::GFP transgenic embryos for NSCs and Tbr2::GFP transgenic embryos for BPs and NBNs.

overall_design: 70 samples of neural stem cells, basal progenitors and newborn neurons, daily from embryonic day 10.5 to first post-natal day.

first: Tanzila

last: Mukhtar

first: Alice

last: Grison

first: Zahra

last: Karimaddini

first: Marcello

last: Boareto do Amaral

first: Jeremie

last: Breda

first: Pascal

last: Grobecker

first: Katja

last: Eschbach

first: Christian

last: Beisel

first: Dagmar

last: Iber

first: Erik

last: van Nimwegen

first: Suzana

last: Atanasoski


title: RNA-seq of longissimus dorsi muscles in Japanese black (Wagyu) and Chinese Red Steppes cattle

status: Public on Nov 28 2020

city: Changchun

first: Xibi

last: Fang

address: No. 5333 Xian Road

institute: Jilin University

summary: Comparative transcriptome profile of genes differentially expressed in longissimus dorsi muscles between Japanese black (Wagyu) and Chinese Red Steppes cattle by RNA-seq

overall_design: RNA-seq analysis were performed in longissimus dorsi muscles samples between Wagyu and Chinese Red Steppes cattle using sequencing platform of the Illumina HiSeq2000, respectively.

first: Zhihui

last: Zhao


title: Epigenetic biomarkers for EZH2 inhibitor sensitivity in neuroblastoma

status: Public on Nov 25 2020

city: Kitaadachi-gun

first: Hisanori

last: Takenobu

state: Saitama

address: 818, Komuro, Ina-machi

department: Research Institute for Clinical Oncology

country: Japan

institute: Saitama Cancer Center

type: Methylation profiling by genome tiling array

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

overall_design: Refer to individual Series


title: The Genomic Research in Alpha-1 Antitrypsin Deficiency and Sarcoidosis Study (GRADS)  Sarcoidosis study [Sarc]

status: Public on Dec 08 2020

city: New Haven

first: Jen-hwa

last: Chu

state: CT

department: Pulmonary, Critical Care and Sleep Medicine

institute: Yale University School of Medicine

summary: Whole genome mRNA and microRNA profiling of bronchoalveolar lavage (BAL) and peripheral blood mononuclear cell (PBMC) in Sarcoidosis patients

overall_design: 199 Sarcoidosis patients were enrolled in the Genomic Research in Alpha-1 Antitrypsin Deficiency and Sarcoidosis study (GRADS) following the GRADS study protocol (Moller et al., Ann Am Thorac Soc, 2015 PMID: 26193069), including 24 stage I, 33 stage II-III treated, 40 stage II-III untreated, 17 stage IV treated, and 12 stage IV untreated.

first: Xiting

last: Yan

first: Naftali

last: Kaminski


title: Epigenomic profiling of neuroendocrine prostate cancer and prostate adenocarcinoma xenografts

status: Public on Nov 22 2020

city: Boston

first: Sylvan

last: Baca

state: MA

address: 450 Brookline Ave

institute: Dana–Farber Cancer Institute

summary: We profiled the epigenomes of neuroendocrine prostate cancer and prostate adenocarcinoma patient-derived xenografts using ChIP-seq for transcription factors and histone modifications.

overall_design: ChIP-seq for H3K27ac, H3K4me3, H3K27me3, and FOXA1

first: M

middle: L

last: Freedman

first: E

last: Corey


title: A Renal CpG Island Methylator Phenotype (R-CIMP) in Kidney Tumors Associated with Germline Mutations of FH and SDHB

status: Public on Oct 31 2020

city: Bethesda

first: Christopher

middle: James

last: Ricketts

state: Maryland

address: Building 10

department: Urologic Oncology Branch

institute: National Cancer Institute

summary: Germline mutations within the Krebs cycle enzyme genes fumarate hydratase (FH) or succinate dehydrogenase (SDHB, SDHC, SDHD) have been associated with an increased risk of renal cell carcinoma (RCC).  These RCCs are characterized by loss of enzyme activity and significantly increased levels of intracellular fumarate or succinate that are predicted to inhibit 2-oxoglutarate-dependent dioxygenases, such as the TET enzymes that regulate DNA methylation.  These tumors represent aggressive forms of RCC that can metastasize early and require specific patient management and treatment.  Therefore, identifying effective and accurate methods for diagnosing these tumors is very beneficial.  This study evaluated and compared the genome-wide methylation profiles of 33 RCCs from patients with RCC susceptibility syndromes, 10 associated normal samples and 13 cell-line models using the Illumina HumanMethylation450 BeadChip assay.  Fifteen tumors derived from patients with germline FH (n=9) or SDHB (n=6) mutations demonstrated a distinct pattern of hypermethylation (R-CIMP) with enrichment for hypermethylation within the CpG island regions.  A small, selected panel of probes was characterized that could identify R-CIMP and distinguish between FH and SDHB tumors.  Cell-line models derived from HLRCC (n=3) or SDHB (n=1) kidney tumors demonstrated similar patterns of hypermethylation to the tumors, yet re-expression of either wild-type FH or SDHB did not alter the hypermethylation pattern.  Treatment of the cell line models with 5-aza-2′-deoxycytidine resulted in reduced rates of invasion.

overall_design: Bisulphite converted DNA from the 33 primary renal tumors, 10 associated normal kidney samples, 2 control renal cell lines were hybridised to the Illumina Infinium HumanMethylation450 BeadChips

middle: J

first: W

last: Linehan


title: Epigenetic biomarkers for EZH2 inhibitor sensitivity in neuroblastoma [ChIP-seq]

summary: EZH2 is a H3K27 methylase and a target of cancer epigenetic treatments. We recently reported the oncogenic roles and NTRK1 (TRKA) epigenetic regulation by EZH2 in the MYCN-amplified aggressive neuroblastomas (NB) (L. Here, we investigated the effects and function of small molecule EZH2 inhibitor (EZH2i) on aggressive NB model cell lines. We examined the antitumor effects of EZH2i using WST assay and colony formation assay. By EZH2i treatments, suppression of proliferation, G0/G1 cell cycle arrest, and apoptosis were observed in sensitive NB cells dose-dependently, whereas they were not observed in resistant NB cells. Transcriptome analysis and GSEA indicated significant changes were observed in the gene set related to differentiation and cell cycle arrest in the sensitive cells. We selected genes induced at mRNA level by EZH2i only in the sensitive cells and confirmed tumor suppressor function in NB cells. Almost of the EZH2i-induced gene promoters were marked by H3K27me3 in the sensitive NB cell line. Interestingly, a part of the EZH2i-induced gene promoters have CpG islands and methylated in NB tumor samples registered in databases and the EZH2i-resistant NB cells. Further, combination of EPZ-6438 and 5-aza-deoxycitide, resulted in effective suppression of proliferation in the EPZ-6438-resistant 3 NB cell lines. Transcriptome/methylome analysis of the EPZ-6438 and 5-aza-deoxycitide-treated NB cells revealed the combinational epigenetic regulation of the tumor suppressors and oncogene expression. Finally, we found that methylome analysis of the promoter regions, e.g. VSTM2L, GPNMB, and TIMP3 CpG islands can be biomarkers of EPZ-6438-registancy in unfavorable NB patients. These responsible CpG island methylation appears to be biomarkers for the application of EZH2i/DNMTi combination therapy.

overall_design: We performed EZH2, H3K3me3, H3K27ac, H3K27me3 and MYCN for neuroblastoma cell, IMR32.

first: Yuki

last: Endo

first: Takehiko

last: Kamijo


title: Gene expression profiles of non-recurrent human glioblastoma tumorspheres

status: Public on Oct 06 2020

city: Seoul

first: Junseong

last: Park

address: 222 Banpo-daero, Seocho-gu

department: Cancer Evolution Research Center

country: South Korea

institute: The Catholic University of Korea

summary: Samples were obtained from 23 non-recurrent GBM patients treated at Severance Hospital

first: Seok-Gu

last: Kang


title: IL6R is a target of miR-197 in human keratinocytes

status: Public on Aug 25 2020

city: Jerusalem

first: Iddo

middle: Z.

last: Ben-Dov

address: Ein Kerem

department: Nephrology and Hypertension

country: Israel

institute: Hadassah Medical Center

summary: Background: Psoriasis is a chronic inflammatory disorder with cutaneous and systemic manifestations and substantial negative effects on patients' life quality. MicroRNAs (miRNAs) are post-transcriptional regulators of gene expression. Evidence suggests that miRNAs play a role in the pathogenesis of psoriasis. Previously studies, from others and by us, show-specific miRNAs that are differentially expressed between the psoriasis lesion and healthy skin. One of those miRNAs is miR-197-3p whose expression is down-regulated in the psoriatic lesions compared to normal or uninvolved psoriatic skin. In order to understand miR-197's role in psoriasis, we found that it could modulate IL-22 and IL-17 signaling. Objectives: We aimed to identify additional biochemical targets of miR-197 in psoriasis. Methods: We have chosen to apply a transcriptome-wide biochemical approach (PAR-CLIP) to search for new targets of miR-197 in keratinocytes. Results: in this work, using PAR-CLIP, we found an additional biochemical target of miR-197, one of the subunits of the receptor to IL-6. IL-6R is known to be up-regulated in psoriasis and even was considered as a possible therapeutic target. Conclusions: From the present data and our previous studies it appears that miR-197 is a major regulator of the interaction between immune system cells and keratinocytes.

overall_design: AGO2 PAR-CLIP experiments in wild-type and miRNA-transfected skin cells in culture to identify miRNA targets

first: Moamen

last: Masalha

first: Devorah

last: Gur-Wahnon

first: Dror

last: Avni

first: Yechezkel

last: Sidi


title: Single Cell Transcriptomics reveals renal myeloid dynamics post reversable unilateral ureteric injury

status: Public on Sep 27 2020

city: Edinburgh

first: Eoin

middle: D

last: O'Sullivan

address: 47 Little France Crescent

department: Centre for Inflammation Research

institute: University of Edinburgh

summary: The kidney has limited capacity to regenerate following injury and preferentially repairs chronic injury with secreted extracellular matrix proteins.  This can be a progressive process with functioning kidney tissue being replaced detrimentally with fibrotic scar tissue, ultimately leading to kidney failure.  Whilst the renal response to injury has been well described it has been examined at whole organ resolution and there has been very limited description of the contribution of individual cells to the kidney’s reparative ability.  Using the reversible unilateral ureteric obstruction model, a model of reversable injury, we describe the transcriptomic changes that occur during obstructive renal injury and subsequent repair at a single cell resolution and describe the altered myeloid cell populations and kinetics likely involved in ongoing tissue repair.

overall_design: 5 single cell libraries, (4*10x workflows and 1*smartseq2), 3 mice pooled per library, deep sequencing on Nextseq 550

first: Bryan

last: Conway

first: Daniel

last: Simpson

first: Neil

last: Henderson

first: Carolynn

last: Cairns

first: Tamir

last: Chandra

first: Laura

last: Denby


title: Massively parallel functional testing of MSH2 missense variants conferring Lynch Syndrome risk

status: Public on Dec 23 2020

city: Ann Arbor

first: Jacob

last: Kitzman

state: MI

address: 4811 Med Sci II, 1241 E Catherine St

department: Department of Human Genetics

institute: University of Michigan

summary: We performed a massively parallel screen in human HAP1 cells to identify loss-of-function missense variants in the key DNA mismatch repair factor MSH2. Resulting variant loss-of-function (LOF) scores are strongly concordant with previous functional evidence and available variant classification.

overall_design: Single amino-acid saturation mutagenesis was used to generate libraries comprising every possible missense, synonymous and nonsense variant within each of 21 tiles across MSH2 cDNA, which were tagged with degenerate barcodes, and pacakged into lentivirus and used to transduce HAP1 MSH2 KO cells were transduced at low multiplicity (<0.1). Genomic DNA was harvested at baseline ('P0') and after two rounds of functional selection by 6-TG ('DB6') or mock treatemnt ('DB').  Integrated MSH2 constructs were sequenced within each mutant tile to identify and quantify loss-of-function alelles enriched by 6-TG selection.

middle: O


title: Transplantation of cranial neural crest-derived pericytes from human pluripotent stem cells promotes functional recovery in a murine model of ischemic stroke

status: Public on Aug 14 2020

city: Guangzhou

first: Weiqiang

last: Li

address: Zhongshan Road 2

institute: Sun Yat-sen university

summary: Here, human pluripotent stem cells (including hiPSC and hESC) were induced to differentiate to pericytes (PCs) through the intermediate stage of cranial neural crest stem cells (NCSCs). We sequenced mRNA samples at different stages during NCSC-PCs differentiation of human pluripotent stem cells to generate the gene expression profiles of these cells.

overall_design: 9 samples, including undifferentiated hPSC (hiPSC, H1, and H9), hPSC-NMP-derived paraxial mesoderm (hPSC-NMP-PM; including hiPSC-NMP-PM, H1-NMP-PM, and H9-NMP-PM), hPSC-NMP-MSC (Passage 5; including hiPSC-NMP-MSC, H1-NMP-MSC, H9-NMP-MSC1, and H9-NMP-MSC2), BMSC1 (Passage 5), and BMSC2 (Passage 5), were analyzed.

first: Jiaqi

last: Sun

first: Jin

last: Gong

first: Yinong

last: Huang

first: Andy

middle: P

last: Xiang


title: Control of osteoblast regeneration by a train of Erk activity waves

status: Public on Sep 23 2020

city: Madison

first: jianhong

last: ou

state: WI

address: 330 N Orchard Street

institute: Morgridge institute for research

summary: We report here a dataset regarding the transcriptome of Erk active osteoblasts in regenerating zebrafish scales. We recently discovered that the marker osx:Venus-hGeminin anti-correlates with Erk activity in those cells. Thus, by sorting (using FACS) cells based on both the expression of an osteoblast marker (osx::H2A-mCherry) and the levels of hGeminin, we could sort osteoblasts into separate Erk+ and Erk- populations and perform RNAsequence (in triplicates). We found that dusp and sprouty transcripts are elevated in osteoblasts with high Erk activity. Specifically, dusp2, dusp5 and spry4 transcripts are predominant in scales and consistently present at higher levels in the population enriched for Erk+ cells.

overall_design: Comparison of the transcriptome of osteoblasts of regenerating zebrafish scales with high and low Erk activity. Cells are sorted on the basis of their osx:Venus-hGeminin signal, which anti-correlates with Erk activity.

first: Alessandro

last: De Simone

first: Stefano

last: Di Talia


title: mRNA expression data of Tumor budding cells and Tumor center cells

status: Public on Sep 09 2020

city: Tianjin

first: Yanrong

last: Liu

address: No.220, Tongyan Road

institute: Tianjin international biomedical joint research institute

summary: The gene expression in  Tumor budding cells was substantially different from that in the cells of tumor center areas.We used microarray to explore the difference of mRNA expression between budding cells and primary tumor cells in patients with colorectal cancer, and then explored the mechanism of tumor budding

overall_design: LCM technique was used to dissect and capture the bud cells and tumor mass cells of CRC tissues. 6 µm-thick sections of the CRC tissues were cut from paraffin embedded tissues and mounted onto cross-linked polyethylene foil attached to a glass slid to facilitate the removal of the selected specimen from the slide to the PCR tube. The slides were further processed for H&E staining. We precisely captured single or clusters of TB cells and the tumor mass cells by using a LCM microscope. The samples were lysed with TRIzol to isolate the total RNA. After amplification, the cDNA was analyzed via expression profile microarrays by Genergy Bio-technology . Data analysis was performed to determine the differentially expressed genes. Gene set enrichment was conducted to detect the genes involved in molecular functions, biological processes, and cellular components. KEGG pathway analysis was also performed to reveal the molecular signaling pathways.

first: Tao


title: Gcn2 eIF2a kinase mediates combinatorial translational regulation through nucleotide motifs and uORFs in the mRNA 5’ leader regions

city: Kobe

first: Atsushi

last: Matsuda

address: 588-2, Iwaoka, Iwaoka-cho, Nishi-ku

institute: National Institute of Information and Communications Technology

summary: Cellular signaling controls translation through  cis regulatory elements found in mRNAs. Gcn2 is the master regulator of translation during nutrient limitation in normal and cancer cells. Activated Gcn2 phosphorylates eIF2a, thereby repressing general translation while activating translation of specific mRNAs with upstream ORFs (uORFs) in its leader regions. Here we performed genome-wide measurement of mRNA translation during histidine starvation in  fission yeast Schizosaccharomyces pombe. Polysomal microarray hybridization experiments identified a group of 1779 genes whose translation is up-regulated in Gcn2-dependent manner. We find that translation is reprogrammed to enhance organellar synthesis and transcription and repress ribosome synthesis. The 1779 genes included gcn5 and hri2 shown to promote growth under histidine starvation. They encode histone acetyl transferase and heme-binding eIF2a kinase activated by oxidative stress, and their 5’-leader contains 3 or 4 uORFs, respectively. Our reporter studies show that uORFs in gcn5 and hri2 operate similarly to those found in S. cerevisiae GCN4, the founding case for uORF-dependent regulation. Moreover, motif analysis identified 5’-UGA(C/G)GG-3’ as a motif promoting translation during starvation. Using hrd1 5’UTR with such a motif, we demonstrated its requirement in Gcn2-dependent translational control. To our knowledge, this is the first nucleotide motif found to be responsible for translational control by Gcn2. We propose that Gcn2 mediates translational control of more specific mRNAs than previously anticipated

overall_design: Polysome profile at exponentially-growing phase in the fission yeast with and without 3AT.

first: Yuji

last: Chikashige

first: Hiroaki

last: Kato

first: Mackenzie

last: Thornton

first: Whitney

last: Pepper

first: Thomas

last: Baird

first: Madelyn

last: Hilgers

first: Ariana

last: Cecil

first: Izumi

last: Asano

first: Haana

last: Yamada

first: Cheyenne

last: Brunkow

first: Carter

last: Moravek

first: Chie

last: Mori

first: Takeshi

last: Urano

first: Chingakham

last: Singh

first: Ronald

last: Wek

first: Katsura


title: Tp53 suppression promotes cardiomyocyte proliferation during zebrafish heart regeneration

status: Public on Sep 21 2020

first: jianhong

last: ou

summary: Transcriptome sequencing of uninjured and regenerating (7dpi) tp53M214K and tp53WT ventricles.

overall_design: 4 experimental groups were analyzed in triplicates: 1) uninjured ventricle of tp53 mutant fish; 2) injured ventricle of tp53 mutant fish; 3) uninjured ventricle of tp53 wild type fish; 4) injured ventricle of tp53 wild type fish.

first: V

last: Cigliola

first: A

last: Shoffner

first: K

last: Poss


title: β-catenin associated protein complex maintains ground state mouse embryonic stem cell by regulating lineage development

status: Public on Aug 20 2020

city: Kansas City

first: Shiyuan

middle: (Cynthia)

last: Chen

state: MO

institute: Stowers Institute for Medical Research

summary: Mouse embryonic stem (ES) cells cultured in defined medium with MEK and GSK3 inhibitors (2i) resemble the pre-implantation epiblast in the ground state, with full development capacity including the somatic lineages and the germline. Although β-catenin is known to be crucial for naive pluripotency of ES cells, the mechanism is not fully understood. Here we showed that β-catenin interacted with a repressive protein complex to maintain the ground state of ES cells by fine-tuning their lineage development potential. Absence of β-catenin impaired ES cell self-renewal without affecting the core self-renewal circuitry of Oct4, Sox2 and Nanog as well as other pluripotency factors. However, β-catenin-deficient cells showed a primed state transcriptional signature with perturbed expression of germline and neuronal lineage genes. Knockdown of Tcf7l1, the repressor in canonical Wnt signaling pathway, did not completely rescue the β-catenin-deficient phenotype of ES cells. Mechanistically, β-catenin formed a novel biochemical complex with E2F6, HP1γ and HMGA2 to restrain ES cells from differentiation by co-occupying the promoters of germline and neuronal lineage regulators independent of TCF7L1. Overall, out work showed that β-catenin maintained ground state ES cells by orchestrating their development plasticity through a repressive protein complex with E2F6, HP1γ and HMGA2.

overall_design: Analyzing developmental genes regulated by β-catenin and associated protein complex

first: Fang

last: Tao

first: Linheng

last: Li


title: Cellular and molecular basis of increased renal ammonia excretion in hyperammonemic conditions

status: Public on Aug 01 2020

city: Maastricht

first: Zita

last: Soons

state: Netherlands

address: Postbus 616

department: General Surgery

country: Netherlands

institute: Maastricht University

summary: First, to characterize experimentally the changes in metabolic processes and gene expression associated with systemic hyperammonemia, in order to better understand the mechanisms responsible for this pathology; second, to construct a predictive a metabolic model of the pathways involved in order to investigate how the development of hyperammonemia can be explained by fundamental shifts in cellular metabolic objectives and gene expression.

overall_design: Examination of a hyperammonemic vs normal diet in rodents

first: Liliane

last: Mpabanzi

first: Jessica

last: Wainwright

first: Dipok

last: Dhar

first: Cees

last: Dejong

first: Rajif

last: Jalan

first: Jean-Marc

last: Schwartz

first: Steven

last: Olde Damink


title: RNA-seq of mouse cells from the dorsal cerebral cortex during its formation

status: Public on Dec 31 2020

first: Verdon

last: Taylor


title: Benchmarking full-length transcript single cell mRNA sequencing protocols

city: København Ø

first: Victoria

last: Probst

address: Genomic Medicine, Blegdamsvej 9

country: Denmark

institute: Rigshospitalet, state hospital

summary: Here we present a performance evaluation of three different plate-based scRNA-seq protocols. Two commercially available kits; NEBNext Single Cell/ Low Input RNA Library Prep Kit (NEB), SMART-seq HT kit (Takara), and non-commercially available protocol Genome & transcriptome sequencing (G&T). We evaluated each kit based upon sensitivity, reproducibility, ease of use and price point per cell. This evaluation is specifically relevant for implementation of scRNA-seq in e.g. diagnostics, requiring high sensitivity in regards of gene detection, high reproducibility between samples, minimum hands on time and smooth sample preparation for technicians, as well as keeping a reasonable price point per patient. G&T protocol delivered the highest detection of genes per single cell, at the absolute lowest price point. Takara's kit delivered likewise high gene detection per single cell, and high reproducibility between sample, however at the absolute highest price points. Here we present pros and cons of each protocol, sequencing breast cancer cell line T47D.

overall_design: Assessment of three plate-based full-length scRNA-seq protocols on T47D breast cancer cells.

first: Frederik

last: Otzen Bagger


title: A new hypomethylating agent, OR-2100, resists degradation by cytidine deaminase, leading to favourable oral absorbability and ant-leukaemia effects

status: Public on Jun 30 2020

city: Saga

first: Shinya

last: Kimura

address: 5-1-1 Nabeshima

department: Drug Discovery and Biomedical Sciences, Faculty of Medicine

institute: Saga University

summary: DNA methyltransferase inhibitors have improved the prognosis of myelodysplastic syndrome (MDS) and acute myeloid leukaemia (AML). However, these agents must be administered intravenously or subcutaneously because they are degraded easily by cytidine deaminase (CDA). OR2100 (OR21), an oligonucleotide comprising decitabine nucleoside 5'-O-trisilylate, resists degradation by CDA. Direct duodenal administration led to high plasma concentrations of OR21 in a cynomolgus monkey model. Microarray analysis of MDS and AML cell lines revealed that OR21 enriched expression of genes associated with tumour suppression, cell differentiation, and immune system processes. Conversely, immune system process pathways were downregulated in azacytidine-resistant AML cells, indicating that these pathways play a pivotal role in the action of hypomethylating agents. Both in vivo and in vitro, OR21 showed anti-leukaemia effects against MDS and AML cells, and a better safety profile than decitabine. These results suggest that OR21 is a candidate drug for a phase 1 study as an alternative to DAC.

overall_design: To investigate the effect of OR2100,  comparing the gene expressions between OR21 treated cells and untreated cells.

first: Hiroshi

last: Ureshino

first: Yuki

last: Kurahashi

first: Tatsuro

last: Watanabe

first: Kazuharu

last: Kamachi

last: Fukuda-Kurahashi

first: Nao

last: Yoshida

first: Naoko

last: Hattori

first: Yoshihiro

last: Hayashi

first: Kaoru

last: Tohyama

first: Seiji

last: Okada

first: Hironori

last: Harada

first: Toshikazu

last: Ushijima


title: Tissue Regeneration Enhancer Element Discovery by Chromatin Accessibility Profiling of Regenerating Zebrafish Fins

status: Public on Jul 19 2020

first: jianhong

last: ou

summary: Mammalian genomes likely encode all gene products required to regenerate an amputated limb, yet they lack the correct instructions for strategically modulating those gene products to accomplish limb regeneration. Zebrafish and many other non-mammalian vertebrates possess these instructions, which exist as gene cis-regulatory elements. Here, to identify candidate tissue regeneration enhancer elements (TREEs) important for zebrafish fin regeneration, we performed ATAC-seq from bulk tissue or purified fibroblasts of uninjured and regenerating caudal fins.  We identified thousands of DNA regions from each tissue type with dynamic accessibility during regeneration, and assigned these regions to proximal genes with corresponding changes in RNA levels. To determine whether these profiles revealed bona fide TREEs, we tested the sufficiency of several sequences in stable transgenic and mutant lines. These experiments identified new regulatory sequences near several induced and/or required genes, including fgf20a, cx43, and mdka, with unique expression domains for each confirmed TREE.  Deletion of TREE sequences from the zebrafish genome revealed requirements and redundancies surrounding cis-regulatory regions. Our study generates a novel resource for dissecting the regulatory mechanisms of appendage regeneration.

overall_design: Samples were enzymatically dissociated with Liberase and collected in biological triplicates for RNA and ATAC library preparation. Corresponding sample pools include: whole fin 0 dpa and whole fin 4 dpa whole fin 0 dpa and whole fin 1 dpa, and fibroblast 0 dpa and fibroblast 4 dpa.

first: John

last: Thompson

first: Jianhong

last: Ou

first: Kenneth

last: Poss


title: Single-cell RNA-seq of mouse cells from the dorsal cerebral cortex during its formation

city: Basel

first: Verdon

last: Taylor

institute: University of Basel

summary: Dorsal cortices from embryonic day (E10.5) to postnatal day 3 (P3) were micro-dissected and dissociated into single cell suspensions using Papain and Ovo-mucoid mix. Cells were washed with L15 medium and FAC-sorted for GFP positive NSCs using FACSariaIII (BD Biosciences) derived from Hes5::GFP transgenic embryos for NSCs and Tbr2::GFP transgenic embryos for BPs and NBNs.

overall_design: 1094 cells, either neural stem cells, basal progenitors and newborn neurons, daily from embryonic day 10.5 to third post-natal day.

first: Tanzila

last: Mukhtar

first: Alice

last: Grison

first: Zahra

last: Karimaddini

first: Marcello

last: Boareto do Amaral

first: Jeremie

last: Breda

first: Pascal

last: Grobecker

first: Katja

last: Eschbach

first: Christian

last: Beisel

first: Dagmar

last: Iber

first: Erik

last: van Nimwegen

first: Suzana

last: Atanasoski


title: A cord blood multi-omic analysis of birthweight reveals new underlying mechanisms related to cholesterol metabolism [gene expression]

status: Public on Jun 22 2020

city: Diepenbeek

first: Michelle

last: Plusquin

address: Campus Diepenbeek Agoralaan Gebouw D

country: Belgium

institute: Hasselt University

summary:
Birthweight reflects in utero exposures and later health evolution. Despite existing studies employing high-dimensional molecular measurements, the understanding of underlying mechanisms of birthweight remains limited.   To investigate the systems biology of birthweight, we cross-sectionally integrated the methylome, the transcriptome, the metabolome and a set of inflammatory proteins measured in cord blood samples, collected from four birth-cohorts (n=489). We focused on two sets of 68 metabolites and 903 CpGs previously related to birthweight and investigated the correlation structures existing between these two sets and all other omic features via bipartite Pearson correlations.
This dataset revealed that the set of metabolome and methylome signatures of birthweight have seven signals in common, including three metabolites [PC(34:2), plasmalogen PC(36:4)/PC(O-36:5), and a compound with m/z of 781.0545], two CpGs (on the DHCR24 and SC4MOL gene), and two proteins (periostin and CCL22). CCL22, a macrophage-derived chemokine has not been previously identified in relation to birthweight. Since the results of the omics integration indicated the central role of cholesterol metabolism, we explored the association of cholesterol levels in cord blood with birthweight in the ENVIRONAGE cohort (n=1,097), finding that higher birthweight was associated with increased high-density lipoprotein cholesterol and that high-density lipoprotein cholesterol was lower in small versus large for gestational age newborns.  Our data suggests that an integration of different omic-layers in addition to single omics studies is a useful approach to generate new hypotheses regarding biological mechanisms. CCL22 and cholesterol metabolism in cord blood play a mechanistic role in birthweight.

overall_design: epidemiologic study (200 cord blood samples).  165 samples were analyzed. 35 samples were excluded due to failed RNA extraction, processing or missing covariates.  Raw data for all samples are included in this series.

first: Rossella

last: Alfano

first: Marc

last: Chadeau-Hyam

first: Akram

last: Ghantous

first: Pekka

last: Keski-Rahkonen

first: Leda

last: Chatzi

first: Almudena

last: Perez

first: Zdenko

last: Herceg

first: Manolis

last: Kogevinas

first: Theo

middle: M

last: de Kok

first: Tim

middle: S

last: Nawrot

first: Alexei

last: Novoloaca

first: Chirag

last: Patel

first: Costanza

last: Pizzi

first: Nivonirina

last: Robinot

first: Franca

last: Rusconi

first: Augustin

last: Scalbert

first: Jordi

last: Sunyer

first: Roel

last: Vermeulen

first: Martine

last: Vrijheid

first: Paolo

last: Vineis

first: Oliver

last: Robinson


title: Generation of highly diverse peptide library by linear-double-stranded DNA based AND gate genetic circuit in mammalian cells

first: Shuai

last: Li

state: Tianjin

address: Huanhuxi Road

institute: Tianjin Tumor Hospital

summary: Display technologies, e.g., phage, ribosome, mRNA, bacterial, and yeast-display, combine high content peptide libraries with appropriate screening strategies to identify functional peptide sequences. Construction of large peptide library and display-screen system in intact mammalian cells will facilitate the development of peptide therapeutics targeting transmembrane proteins. Our previous work established linear-double-stranded DNAs (ldsDNAs) as innovative biological parts to implement AND gate genetic circuits in mammalian cell line. In the current study, we employ ldsDNA with terminal NNK degenerate codons as AND gate input to build highly diverse peptide library in mammalian cells. Only PCR reaction and cell transfection experiments are needed to construct the library. High-throughput sequencing (HTS) results reveal that our new strategy could generate peptide library with both amino acid sequence and peptide length diversities. Our work establishes ldsDNA as biological parts for building highly diverse peptide library in mammalian cells, which shows great application potential in developing therapeutic peptides targeting transmembrane proteins.

overall_design: We apply ldsDNA-based AND gate calculation to generate highly diverse peptide library in mammalian cells; Six different combinations of these two subgroup ldsDNAs were introduced into HEK293T cells to construct the AND-gate genetic circuits.


title: mRNA sequencing of human osteoarthritis chondrocytes treated with or without autotaxin inhibitor

status: Public on Jun 18 2020

city: Toronto

first: Mohit

last: Kapoor

state: Ontario

address: 60 Leonard Ave

institute: Schroeder Arthritis Institute

summary: OBJECTIVE: To identify the changes in gene expression elicted by ATX inhibition in human OA primary chondrocytes. Chondrocytes were obtained from patients undergoing knee artheroplasty, cultured, and treated for 24 h with ATX inhibitor or control (without inhibitor). Total RNA was then extracted, and mRNA libraries were prepared using Illumina's TruSEQ stranded mRNA library preparation kit, pooled together, and sequenced on Illumina's NextSeq550.

overall_design: Differential expression analysis was performed on the mRNA-SEQ data obtained from 6 prepared libraries, where 3 were treated with the ATX inhibitor. Subsequent pathway analysis identified pathways related to cholesterol analogue metabolism and cell-cycle that could be modulated by ATX inhibition in human OA chondrocytes.

first: Poulami

last: Datta

first: Rajiv

last: Gandhi

first: Sayaka

last: Nakamura

first: Starlee

last: Lively

first: Evgeny

last: Rossomacha

first: Pratibha

last: Potla

first: Konstantin

last: Shestopaloff

first: Helal

last: Endisha

first: Chiara

last: Pastrello

first: Igor

last: Jurisica

first: Jason

last: Rockel


title: Comparison of Methylation Capture Sequencing and Infinium EPIC Methylation Array in Peripheral Blood Mononuclear Cells

status: Public on Jun 21 2020

city: New Haven

first: Ke

last: Xu

institute: Yale University

type: Methylation profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Single Cell sequencing of human Sputum cells in cystic fibrosis and healthy controls

status: Public on Jul 01 2020

first: Jonas

last: Schupp

address: 300 Cedar Street

department: PCCSM

institute: YALE UNIVERSITY

summary: The study aimed to compare the gene expression profiles at a single cell level in Sputum cells between patients with cystic fibrosis (CF) and disease controls (CTRL).

overall_design:
Single-cell RNA sequencing data was generated from Sputum of 9 CF patients (10 libraries) and 5 CTRL
Raw data to be made available through dbGaP

first: Clemente

last: Britto

first: Naftali

last: Kaminski


title: Comparison of Methylation Capture Sequencing and Infinium EPIC Methylation Array in Peripheral Blood Mononuclear Cells [MC-seq]

summary:
Background: Epigenome-wide association studies (EWAS) have been widely applied to identify methylation CpG sites associated with human disease. To date, the Infinium Methylation EPIC array (EPIC) is commonly used for high-throughput DNA methylation profiling. However, the EPIC array covers only 30% of the human methylome. Methylation Capture bisulfite sequencing (MC-seq) captures target regions of methylome and has advantages of extensive coverage in the methylome at an affordable price.
Methods: Epigenome-wide DNA methylation in four peripheral blood mononuclear cell samples was profiled by using SureSelectXT Methyl-Seq for MC-seq and EPIC platforms separately. CpG site-based reproducibility of MC-seq was assessed with DNA sample inputs ranging in quantity of high (> 1000ng), medium (300-1000ng), and low (150ng-300ng). To compare the performance of MC-seq and the EPIC arrays, we conducted a Pearson correlation and methylation value difference at each CpG site that was detected by both MC-seq and EPIC. We compared the percentage and counts in each CpG island and gene annotation between MC-seq and the EPIC array.
Results: After quality control, an average of 3,708,550 CpG sites per sample was detected by MC-seq with DNA quantity >1000ng. Reproducibility of MC-seq detected CpG sites was high with strong correlation estimates for CpG methylation among samples with high, medium, and low DNA inputs (r > 0.96). The EPIC array captured an average of 846,464 CpG sites per sample. Compared with the EPIC array, MC-seq detected more CpGs in coding regions and CpG islands. Among the 472,540 CpG sites captured by both platforms, methylation of a majority of CpG sites was highly correlated in the same sample (r: 0.98~0.99). However, methylation for a small proportion of CpGs (N=235) differed significantly between the two platforms, with differences in beta values of greater than 0.5.
Conclusions: Our results show that MC-seq is an efficient and reliable platform for methylome profiling with a broader coverage of the methylome than the array-based platform. Although methylation measurements in majority of CpGs are highly correlated, a number of CpG sites show large discrepancy between the two platforms, which warrants further investigation and needs cautious interpretation.

overall_design: 12 MC-seq samples from 4 subjects.

first: Bradley

last: Aouizerat

first: Xinyu

last: Zhang

first: Chang

last: Shu


title: A cord blood multi-omic analysis of birthweight reveals new underlying mechanisms related to cholesterol metabolism

status: Public on Jun 19 2020

first: Michelle

last: Plusquin

overall_design: epidemiologic study (500 cord blood samples)

first: Rossella

last: Alfano

first: Marc

last: Chadeau-Hyam

first: Akram

last: Ghantous

first: Pekka

last: Keski-Rahkonen

first: Leda

last: Chatzi

first: Almudena

last: Perez

first: Zdenko

last: Herceg

first: Manolis

last: Kogevinas

first: Theo

last: de Kok

first: Tim

last: Nawrot

first: Alexei

last: Novoloaca

first: Chirag

last: Patel

first: Costanza

last: Pizzi

first: Nivonirina

last: Robinot

first: Franca

last: Rusconi

first: Augustin

last: Scalbert

first: Jordi

last: Sunyer

first: Roel

last: Vermeulen

first: Martine

last: Vrijheid

first: Paolo

last: Vineis

first: Oliver

last: Robinson


title: Charting the prostate epigenomic landscape from transformation to progression

status: Public on Jun 16 2020

city: Boston

first: Matthew

last: Freedman

state: Massachusetts

address: 450 Brookline Avenue

institute: Dana Faber Cancer Institute

summary: We generate transcription factor, histone modification and ATAC cistromes in nomal prostate epithelium, primary prostate tumor and metastatic prostate cancer human specimens

overall_design: ChIP-seq for AR, FOXA1, HOXB13, H3K27Ac, H3K4me2, H3K4me3, H3K27me3 and ATAC-seq

first: Mark

last: Pomerantz

first: Wilbert

last: Zwart

first: Eva

last: Corey


title: Comparison of Methylation Capture Sequencing and Infinium EPIC Methylation Array in Peripheral Blood Mononuclear Cells [EPIC array]

status: Public on Jun 11 2020

first: Ke

last: Xu

overall_design: Bisulphite converted DNA from the 4 samples were hybridised to the Illumina Infinium EPIC Human Methylation BeadChip.

first: Bradley

last: Aouizerat

first: Xinyu

last: Zhang

first: Chang

last: Shu


title: Driver mutations of the adenoma-carcinoma sequence govern the intestinal epithelial global translational capacity.

status: Public on May 31 2020

city: Amsterdam

first: Sander

last: Meisner

state: NH

address: Meibergdreef 69-71

department: Tytgat institute

institute: AMC

summary: In colorectal cancer, the role of the most common driver mutations in APC, KRAS, SMAD4 and TP53, on global mRNA translation are incompletely understood. To adress this, we generated and characterised mouse intestinal organoid models with oncogenic mutations in each of these genes using Cre-Lox recombination in ex vivo organoid cultures combined with stable expression of short hairpin RNAs. Microarray analysis was used to characterise transcriptomic reprogramming that supports altered global translation rates in mutant cells.

overall_design: Using genetically modified organoid models we compared intestinal epithelial cells with the following genotypes: 1) wildtype 2) Apc loss 3) Apc loss and oncogenic KrasG12D 4) Apc loss, oncogenic KrasG12D and Smad4 loss 4) Apc loss, oncogenic KrasG12D, Smad4 loss and p53 loss.

first: Wouter

last: Smit

first: Jarom

last: Heijmans


title: Transcriptomic profiling identifies unique and shared functions of oncogenic KRAS and RIT1

status: Public on Mar 06 2020

city: Seattle

first: Alice

last: Berger

state: WA

address: 1100 Fairview Ave N

institute: Fred Hutchinson Cancer Center

summary: Aberrant activation of RAS oncogenes is a prevalent event in lung adenocarcinoma, with somatic mutation of KRAS occurring in ~30% of tumors. Recently, we identified somatic mutation of the RAS-family GTPase RIT1 in lung adenocarcinoma, but relatively little is known about the biological pathways regulated by RIT1 and how these relate to the oncogenic KRAS network. Here we present (quantitative proteomic and) transcriptomic profiles from KRAS-mutant and RIT1-mutant isogenic lung epithelial cells and globally characterize the signaling networks regulated by each oncogene.

overall_design: Whole transcriptome (mRNA) profiles of 18 samples, encompassing five genetic perturbations through lentiviral transduction of wild-type or variant vectors (KRAS WT, KRAS G12V, KRAS Q61H, RIT1 WT, RIT1 M90I), as well as one control plasmid vector (Renilla). Sequenced in triplicate on Illumina NovaSeq.

first: April

last: Lo


title: Identification of bicyclomycin-sensitive transcripts in Vibrio cholerae

status: Public on May 07 2020

city: Jena

first: Mona

last: Hoyos

address: Winzerlaer Straße 2

department: Institute for General Microbiology

institute: FSU Jena

summary: In this study we used BCM, inhibitor of Rho activity, to determine Rho-dependent transcription termination sites in V. cholerae.

overall_design: V. cholerae oppA::3xFLAG oppB::3xFLAG strains with wild-type oppB or the oppB start codon mutated to ATC were grown to early stationary phase (OD600 of 1.5). Cultures were divided in half and treated with either H2O (mock treatment) or BCM (25 µg/ml final conc.) for 2h before RNA samples were collected.  The experiment was performed with three independent biological replicates.

first: Michaela

last: Huber

first: Konrad

last: Förstner

first: Kai

last: Papenfort


title: Cell Type-Specific Transcriptomics Reveals that Mutant Huntingtin Leads to Mitochondrial RNA Release and Neuronal Innate Immune Activation

status: Public on Jul 17 2020

city: Cambridge

first: Myriam

last: Heiman

address: 77 Massachusetts Ave., Bldg 46-4285

department: Brain and Cognitive Sciences

institute: Massachusetts Institute of Technology

summary: The mechanisms by which mutant Huntingtin leads to neuronal cell death in Huntington’s disease are not fully understood. To gain new molecular insights, we used snRNA-Seq and TRAP to conduct transcriptomic analyses of striatal cell type-specific gene expression changes in human HD and mouse models of HD.  In striatal spiny projection neurons we observe a release of mitochondrial RNA and a concomitant upregulation of innate immune signaling in spiny projection neurons. We observe that the released mtRNAs can directly bind to the innate immune sensor PKR.  We highlight the importance of studying cell type-specific gene expression dysregulation in HD pathogenesis, and reveal that the activation of innate immune signaling in the most vulnerable HD neurons provides a novel framework to understand the basis of mHTT toxicity and raises new therapeutic opportunities.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design:
Cell type-specific profiling of human HD and HD mouse model striatal and corticostriatal cell types.

Please note that the additional counts.mtx, coldata.tsv and rowdata.tsv files containing metadata and sample information were provided on Oct 22, 2020.

first: Sergio

last: Pineda

first: Hyeseung

last: Lee


title: A new hypomethylating agent, OR-2100, resists degradation by cytidine deaminase, leading to favorable oral absorbability and anti-leukemia effects

status: Public on Apr 09 2020

first: Shinya

last: Kimura

summary: DNA methyltransferase inhibitors have improved the prognosis of myelodysplastic syndrome (MDS) and acute myeloid leukaemia (AML). However, these agents must be administered intravenously or subcutaneously because they are degraded easily by cytidine deaminase (CDA). OR2100 (OR21), an oligonucleotide comprising decitabine nucleoside 5'-O-trisilylate, resists degradation by CDA. Direct duodenal administration led to high plasma concentrations of OR21 in a cynomolgus monkey model. Transcriptome and methylome analysis of MDS and AML cell lines revealed that OR21 enriched expression of genes associated with tumour suppression, cell differentiation, and immune system processes via alteration of regional promoter methylation. Conversely, immune system process pathways were downregulated in azacytidine-resistant AML cells, indicating that these pathways play a pivotal role in the action of hypomethylating agents. Both in vivo and in vitro, OR21 showed anti-leukaemia effects against MDS and AML cells (including AZA-resistant), and a better safety profile than decitabine. These results suggest that OR21 is a candidate drug for a phase 1 study as an alternative to DAC.

overall_design: To investigate the effect of OR2100,  comparing the gene expressions between OR2100 treated cells and untreated cells.

first: Hiroshi

last: Ureshino

first: Yuki

last: Kurahashi

first: Tatsuro

last: Watanabe

first: Satoshi

last: Yamashita

first: Kazuharu

last: Kamachi

last: Fukuda-Kurahashi

first: Nao

last: Yoshida

first: Naoko

last: Hattori

first: Yoshihiro

last: Hayashi

first: Kaoru

last: Tohyama

first: Seiji

last: Okada

first: Hironori

last: Harada

first: Toshikazu

last: Ushijima


title: Early commitment genes drive fast, irreversible commitment to human embryonic stem cell differentiation [scRNA-seq]

status: Public on Apr 19 2020

city: London

first: Silvia

middle: DM

last: Santos

address: 1 Midland Road

institute: The Francis Crick Institute

summary:
The goal of this study was to characterise transcriptional changes in single hESCs grown in a colony and treated with BMP4 to induce differentiation
The goal of this study was to characterise transcriptional changes in single GATA3-/- hESCs grown in a colony and treated with BMP4 to induce differentiation

overall_design:
scRNA-Seq was performed on cultured hESCs grown in mTeSR1 with BMP4 for 48 hours.
scRNA-Seq was performed on a cultured hESC GATA3-/- monoclonal cell line grown in mTeSR1 with BMP4 for 48 hours.

first: Santos

last: Silvia


title: Genomic location of H4R3me2a and H3R2me2s in chicken polychromatic erythrocytes

status: Public on Mar 09 2020

city: Winnipeg

first: James

middle: Ronald

last: Davie

address: 745 Bannatyne Avenue, RM 333A

department: Biochemistry and Medical Genetics

institute: University of Manitoba

summary: H4R3me2a and H3R2me2s often track together, locate to transcriptionally active DNA and are at regulatory regions of expressed genes.

overall_design: Two biological replicates of ChIP DNA immunoprecipitated with H4R3me2a and H3R2me2s antibodies and one input sample were sequenced to find their genomic location

first: Tasnim

last: Beacon

first: Wayne

last: Xu


title: Musashi-1 is a master regulator of aberrant translation in Group 3 medulloblastoma

status: Public on Feb 01 2020

city: Hamilton

first: Sheila

last: Singh

state: ON

address: 1280 Main Street West

department: Biochemistry and Biomedical Sciences

institute: McMaster University

summary: Transcripts regulated by Musashi-1 (MSI1) are explored through shRNA-mediated knockdown of MSI1 in SU_MB002 medulloblastoma cells.

overall_design: SU_MB002, a treatment refractory pediatric medulloblastoma cell line is transduced with either a scrambled control or shMsi1 knockdown construct. The changes in transcriptomic profile is identified through RNA-sequencing

first: Michelle

last: Kameda

first: Kevin

last: Brown


title: Tomato fruit susceptibility to fungal disease is not an inevitable outcome of ripening and can be uncoupled by targeting susceptibility factors

status: Public on Apr 08 2020

city: Davis

first: Barbara

last: Blanco-Ulate

state: CA

address: One Shields Avenue

department: Plant Sciences

institute: University of California, Davis

summary: The increased susceptibility of ripe fruit to fungal pathogens poses a substantial threat to crop production and marketability. Here, we coupled transcriptomic analyses with mutant studies to uncover critical genes and processes governing ripening-associated susceptibility in tomato (Solanum lycopersicum) fruit. Using wild-type unripe and ripe fruit inoculated with three fungal pathogens—Botrytis cinerea, Fusarium acuminatum, and Rhizopus stolonifer—we identified common pathogen response genes reliant on chitinases, WRKY transcription factors, and reactive oxygen species detoxification. Interestingly, susceptible ripe fruit demonstrated a more extensive defense response than resistant unripe fruit, indicating that the magnitude and diversity of defense response does not significantly impact the interaction. To tease apart individual features of ripening that may be responsible for susceptibility, we utilized three tomato non-ripening mutants: Cnr, rin and nor. Fruit from these mutants displayed different patterns of susceptibility to fungal infection. Functional analysis of the genes altered during ripening in the susceptible genotypes revealed losses in the maintenance of cellular redox homeostasis. Moreover, jasmonic acid accumulation and signaling coincided with the activation of defenses in resistant fruit. Lastly, based on high gene expression in susceptible fruit, we identified and tested two candidate susceptibility factors, pectate lyase (PL) and polygalacturonase (PG2a). CRISPR-based knockouts of PL, but not PG2a, resulted in more than 50% decrease in the susceptibility of ripe fruit, demonstrating that PL is a major susceptibility factor. Ultimately, this study demonstrates that targeting specific genes that drive susceptibility is a viable strategy to improve resistance of tomato fruit against fungal pathogens.

sample_organism:
Solanum lycopersicum
Rhizopus stolonifer
Fusarium acuminatum
Botrytis cinerea

overall_design: wild-type unripe/ripe fruit and three tomato non-ripening mutants (Cnr, rin and nor) inoculated with three fungal pathogens - Botrytis cinerea, Fusarium acuminatum, and Rhizopus stolonifer. At 1 dpi, fruit pericarp and epidermal tissue of the blossom end halves of healthy, wounded, and infected fruit were collected

first: Christian

last: Silva

first: Casper

last: van den Abeele

first: Isabel

last: Ortega-Salazar

first: Victor

last: Papin

first: Jaclyn

last: Adaskaveg

first: Duoduo

last: Wang

first: Clare

last: Casteel

first: Graham

middle: B

last: Seymour


title: LncRNA expression profile between prenatal and adult mouse liver [microarray]

status: Public on Mar 01 2020

city: Shanghai

first: Youqiong

last: Ye

address: 280 Chongqing south road

institute: Shanghai Jiao Tong University School of Medicine

summary: We have employed Arraystar Mouse LncRNA Microarray V3.0 as a discovery platform to identify LncRNA and mRNA profile between prenatal and adult mouse liver tissues.  Mouse E18 and 2-month old liver total RNA were commercially purchased.

overall_design: Prenatal E18 and 2-month adult mice liver total RNA were isolated from 3 different animals.

first: Yajuan

last: Li

first: Chunru

last: Lin

first: Liuqing

last: Yang


title: Molecular Pathology of Human Knee Arthrofibrosis Defined by RNA Sequencing

status: Public on Jan 01 2020

city: Rochester

first: Daniel

middle: Rothschild

last: OBrien

state: MN

address: 200 First St. SW

institute: The Mayo Clinic

summary: This study aims to compare the genetic profile of fibrotic and non-fibrotic human knee capsular tissue in an effort to identify possible molecular pathways responsible for the development of AF. RNA sequencing (RNA-seq) and bioinformatics were used to define differentially expressed genes (DEGs) and molecular pathways linked to joint stiffening.  Gene expression profiling revealed a distinct clustering of each patient group by principal component analysis, hierarchical clustering and similarity matrix analysis. Three prospectively-collected, matched patient cohorts were used to formally describe gene expression signatures of AF patients. The findings define molecular and pathological markers of AF, as well as novel potential targets for pre-diagnosis and pharmacological treatment of AF patients.

overall_design: Examination of pTKA (n=4), rTKA-A (n=4) and rTKA-NA (n=4) tissues for molecular markers.

first: Banu

last: Bayram

first: Andre

last: van Wijnen

first: Matthew

last: Abdel


title: Transcriptome profiling of the HVC of the young and adult zebra finch brain by RNA-Seq

city: New Orleans

first: XiaoChing

state: LA

address: 2020 Gravier St.

department: Neuroscience Center

institute: LSU School of Medicine

summary: Abstract: Juvenile zebra finches learn to sing by imitating songs of adult males early in life. The development of the song control circuit and the song learning and maturation processes are highly intertwined, involving gene expression, neurogenesis, circuit formation, synaptic modification, and sensory-motor learning, which eventually lead to a mature song. To better understand the genetic mechanisms underlying these events, we used RNA-sequencing (RNA-Seq) to profile genome-wide transcriptomes in the HVC, a brain nucleus controlling song behavior, in juvenile and adult zebra finches. We found that gene expression programs related to axon guidance, RNA metabolism, lipid metabolism, and ATP synthesis were enriched in the HVC relative to the rest of the brain in juveniles. As juveniles matured into adults, massive gene expression changes occurred in the HVC. Gene expression shifted from amino acid metabolism, laminin interaction, cell proliferation, and mitochondrial protein translation to synaptic functions; genes associated with G protein coupled-receptors, GTPase signaling, ion channels, and inhibitory transmission increased expression. Unexpectedly, a group of genes known for their functions in the immune system was also developmentally regulated in the HVC. These data will serve as a rich resource for further analysis of development and function of a neural circuit that controls vocal behavior.

overall_design: Sequencing cDNA libraries from HVC and whole brain tissues at 45 and 100 days of age

first: Zhimin

last: Shi

first: Lana

last: Schaffer

first: Steven

last: Head

first: Terry

last: Gassterland


title: 3D vs . 2D culture of HUASMC

status: Public on Dec 16 2019

city: Mannheim

first: Carolina

last: Delatorre

address: Theodor-Kutzer-Ufer 1-3

institute: University Heidelberg

summary: To study the impact of the organotypic assembly of vascular smooth muscle cells on their transcriptome, we cultured human umbilical artery smooth muscle cells under 2D conditions and as aggregates in hanging drops under 3D conditions. After 48 hours, RNA was isolated from both groups

overall_design: 3 samples of 3D cultured HUASMCs and 3 samples of 2D cultured HUASMCs were processed for RNA extraction

first: Thomas

last: Korff


title: Single-cell transcriptomic profiling of mouse lung tumor in response to CDK7 inhibitor, anti-PD-1 and combination treatment

status: Public on Dec 27 2019

first: Ruben

last: Dries

address: 360 Longwood Ave

department: Computational Biology

institute: DFCI

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

overall_design: Refer to individual Series


title: CHD8 and ELK1 cooperativity regulate cellular sensitivity to MAPK/ERK pathway

status: Public on Nov 27 2019

city: STANFORD

first: BAHAREH

last: HADDADDERAFSHI

address: 736 ESCONDIDO RD, APT 204

institute: Ms.

summary: The chromodomain helicase DNA binding protein CHD8 is among the most frequently found de-novo mutations in autism. Unlike other autism-risk genes, CHD8 mutations appear to be fully penetrant. Despite this prominent disease involvement, relatively little is known about its molecular function. Based on sequence homology, CHD8 is believed to be a chromatin regulator but mechanisms for its genomic targeting and its function on chromatin are unclear. Here, we developed a human cell model carrying conditional CHD8 loss-of-function alleles. Remarkably, while undifferentiated human embryonic stem (ES) cells required CHD8 for survival, postmitotic neurons survived following CHD8 depletion. Chromatin accessibility revealed that CHD8 is a highly potent and general chromatin activator, enhancing transcription of its direct target genes. We also found that CHD8 genomic binding in human neurons was significantly enriched at ELK1 DNA binding motifs as previously found in other cell types. Given its prominent role as effector molecule of the MAPK/ERK pathway, we decided to further explore its relationship with CHD8. ELK1 motif-containing CHD8 binding sites showed a higher degree of chromatin opening function of CHD8 than other CHD8 binding sites. Moreover, ELK1 was required for CHD8 binding to Elk1-containing sites, but not other sites. Finally, the anti-apoptotic function of CHD8 in human ES cells could be rescued by depletion of ELK1 and the enhancement of neurogenesis by ELK1 was dependent on presence of CHD8. In summary, our results establish a clear role of CHD8 for chromatin opening and transcriptional activation and a molecular and functional interdependence of CHD8 and ELK1. These data imply the involvement of the MAPK/ERK pathway effector ELK1 in the pathogenesis of autism caused by CHD8 mutations.

overall_design: The overall experiment is as follows: the ChIP-seq of CHD8 in human excitatory neurons using two antibodies, and the ATAC-seq results of CHD8 homozygous KO and control cells and the RNA-seq of CHD8 homozygous KO.

first: Bahareh

last: Haddad Derafshi


title: Pregnancy has a minimal impact on the acute transcriptional signature to vaccination

status: Public on Jan 31 2020

city: Berlin

first: January

last: Weiner

address: Charitéplatz 1

department: CUBI

institute: Berlin Institute of Health, Charité Medical University of Berlin


title: Early commitment genes drive fast, irreversible commitment to human embryonic stem cell differentiation

first: Silvia

last: Santos


title: Transcriptional profiles in pregnant women in response to vaccination

summary: Vaccination in pregnancy is an effective tool to protect both the mother and infant. Vaccines against tetanus, pertussis and influenza are recommended for use in pregnancy and new vaccines with specific indications for pregnancy are in the clinical trials pipeline. However our understanding of the immune response to vaccination in pregnancy is incomplete. We compared the effect of pregnancy on early (24 hours) transcriptional responses to vaccination. Pregnant mice and women were immunised with Boostrix-IPV, a vaccine containing pertussis antigens.

overall_design: Pregnant women and mice were immunised with Boostrix-IPV, a multivalent vaccine, which containing three pertussis antigens. Blood was collected from women before and after vaccination and RNA extracted for analysis by microarray.

first: John

last: Tregoning


title: RNA-seq analysis of Pten's function in regulating embryonic stem cell transition from naïve to primed pluripotent state

status: Public on Feb 16 2020

city: Hong Kong

first: Wuming

last: Wang

address: Sha Tin

institute: The Chinese University of Hong Kong

summary: The goals of this study are to explore the function of Pten in regulating the pluripotency transition of mouse embryonic stem cells through Pten knockout and mutation.

overall_design: we generated Pten−/− and Pten-A3 mutant mouse ESCs with the CRISPR-Cas9 system and explored the effects on the pluripotency transition of mouse embryonic stem cells. We used a series of biological technologies such as Western blot, quantitative real time PCR, and cell culture to verity the conclusions.

first: Gang

last: Lu

first: Wai-Yee

last: Chan

first: Zi-Jiang

last: Chen


title: Sirena1: The most abundant lncRNA in mouse oocytes brings together post-transcriptional regulations and mitochondrial distribution

status: Public on Sep 30 2019

city: Prague

first: Filip

last: Horvat

address: Videnska 1083

country: Czech Republic

institute: Institute of Molecular Genetics of the ASCR

sample_organism:
Mus musculus
Rattus norvegicus

platform_organism:
Mus musculus
Rattus norvegicus


title: Uncovering the role admixture in health disparities: Association of hepatocyte gene expression and DNA methylation to African Ancestry in African-Americans

status: Public on Oct 31 2019

city: Chicago

first: Minoli

last: Perera

state: IL

address: 303 E Chicago Ave.

department: Pharmacology

institute: Northwestern Univeristy


title: Simultaneous lineage and transcriptome analysis of hematopoietic stem cell fates

status: Public on Mar 23 2020

city: Boston

first: Alejo

last: Rodriguez-Fraticelli

address: 1 Blackfan Circle

department: Hematology-Oncology

institute: Boston Children's Hospital

summary: Bone marrow transplantation therapy relies on the life-long regenerative capacity of hematopoietic stem cells (HSCs). HSCs present a wide complexity of regenerating behaviours at the clonal level, but the mechanisms underlying this diversity are still unclear. Recent advances in single cell sequencing have described transcriptional differences amongst HSCs, providing a possible explanation for their functional heterogeneity. However, the destructive nature of sequencing assays prevents simultaneous observation of stem cell functions. Thus, it is unclear to what extent transcriptome states carry information about stem cell outcomes. Here, we applied expressible barcodes to simultaneously recover lineages and transcriptomes from single adult HSCs, and investigated their clonal trajectories during bone marrow reconstitution in vivo. Using clonal readouts, we unveiled a previously underappreciated subset of quiescent HSCs that cell-autonomously retains native-like behaviours. Transcriptome enrichment using clonal information identified a distinct molecular signature that characterizes functional long-term repopulating HSCs. Probing this signature through in vivo CRISPR screening, we described the transcription factor Tcf15 to be required, and sufficient, to drive HSC quiescence and long-term self-renewal. In situ, Tcf15 labels the subset of native multipotent HSCs and its expression is inherited in a hierarchical fashion. In conclusion, our work elucidates molecular programs associated with stem cell function, and identifies a mechanism for the maintenance of the native-like quiescent state.

overall_design: Single-cell mRNA sequencing of barcoded hematopoietic stem cells (HSC libraries) and progenitor cells (KIT libraries) using the inDrop (v3) pipeline. Sample 1: single cell mRNA sequencing libraries from 2 primary recipients (recipient 1 and 2). Sample 2: single cell mRNA sequencing libraries from 2 primary recipients (recipient 3 and 4). Sample 3:single cell mRNA sequencing libraries from 1 primary recipient (recipient 5). Sample 4: single cell mRNA sequencing libraries from secondary recipients. Sample 5: single cell mRNA sequencing libraries from CROPseq experiment replicate A and replicate B. Sample 6: single cell mRNA sequencing library from TetO-Tcf15 experiment (wt vs. TetO-Tcf15 KIT cells).


title: Gene expression profile of podocalyxin-like protein 1(PODXL) overexpressing and  GFP overexpressing control embryonic stem cells

status: Public on Dec 01 2019

city: Nankang

first: Jean

state: Taipei

address: 128 Academia Road, Section 2, IBMS, N401F

department: Genomics Research Center

country: Taiwan

institute: Academia Sinica

summary: The transmembrane signals maintain the pluripotency of human pluripotent stem cells (hPSCs) are rarely investigated. A transmembrane glycoprotein, podocalyxin-like protein 1 (PODXL, also called podocalyxin like protein-1, PCLP1, Gp200/GCTM-2, MEP21, and Thrombomucin), aside from its well-known role in tumor malignancy, very little is known about its functions in hPSCs. In order to map the early signals triggered by PODXL, after 3 days of PODXL overexpression, a comprehensive gene expression profile changes were analyzed by cDNA microarray.

overall_design: PODXL overexpressing and GFP overexpressing HUES6 cells by lentivirus transduction for 3 days and were used for gene expression analysis using GeneChip® Human Genome U133 Plus 2.0 Array.

first: Wei-Ju


title: Transcriptional responses in muscle of pregnant mouse upon immunization

status: Public on Jan 25 2020

overall_design:
Twenty mice (10 pregnant and 10 controls) were immunised intramuscularly with Boostrix-IPV® (produced by GlaxoSmithKline containing diphtheria toxoid, tetanus toxoid, inactivated polio virus and three Bordetella pertussis antigens) or saline as an injection control. Muscle samples were collected 24 hours after immunisation and the extracted RNA was analysed by murine microarray analysis.
John S. Tregoning, Department of Infectious Disease, St Mary’s Campus, Imperial College London, W2 1PG.
January Weiner 3rd, Core Unit Bioinformatics, Berlin Institute of Health, Berlin, Germany

last: Weiner 3rd


title: Sirena1: The most abundant lncRNA in mouse oocytes brings together post-transcriptional regulations and mitochondrial distribution (rat wild-type GV oocytes)

summary: Long non-coding RNAs (lncRNAs) are a large group of rapidly evolving non-coding RNAs. Tens of thousands of lncRNAs were identified but function has been assigned to relatively few. LncRNAs expressed in mouse oocytes have been annotated but their contribution to oocyte development and early development remains unknown. Here, we report evolutionary history and functional analysis of Sirena1, maternal lncRNA that is the most expressed maternal lncRNA and 10th most abundant Pol II transcript in mouse oocytes.

overall_design: Bulk RNA-seq of rat GV oocyte - 4 replicates

first: Petr

last: Svoboda

first: Radek

last: Malik

first: Sravya

last: Ganesh


title: Variant and cell-context specific H3K27M reprogramming results in distinct enhancer architecture and oncogenic states

status: Public on Oct 03 2019

city: Stanford

first: Michelle

last: Monje

address: 265 Campus Drive, SIM1 G3035

institute: Stanford University

summary: Diffuse intrinsic pontine glioma (DIPG) is a fatal malignancy of the childhood pons characterized by a unique lysine-to-methionine substitution in histone-3 at lysine 27 (H3K27M). We show here that the specific Polycomb targets disrupted by H3K27M and resultant oncogenic state is dependent on both the variant of histone-3 and the cell- context in which the mutation occurs. Through primary DIPG tumor characterization and isogenic expression, we show that the same H3K27M mutation displays distinct modes of oncogenic reprogramming and establishes distinct enhancer architecture depending on whether it occurs in genes encoding H3.3 or H3.1. By comparison to non-malignant pediatric pontine tissue, we create a molecular map for DIPG, identifying and functionally validating both shared and subgroup-specific pathophysiology. Directly comparing the earliest events of H3K27M tumor initiation in putative cells-of-origin demonstrates that DIPG arises only from an oligodendrocyte precursor cell state.

overall_design:
H3K27Ac profiling of 30 primary DIPG and normal pontine tissue samples. Omni-ATAC profiling of 9 primary samples. RNA-seq profiling of 10 primary samples. ChIP-seq profiling of 12 patient-derived DIPG cultures. Multiple histone and TF ChIP-seq profiling of 5 stages of iPSC differentiation in the presence or absence of H3K27M. There are no restrictions or privacy issues. They were obtained under informed consent under an IRB protocol and have been fully deidentified.

Gene expression was quantified in "cnmc842t" primary human DIPG tumor sample and "pons02" primary human non-tumor pontine sample. RNA was sequenced on the Illumina NextSeq 500 and tpm values were quantified using featureCounts (Liao et al, 2014). Due to patient privacy concerns, we are witholding raw sequencing files at this time.

first: Surya

last: Nagaraja

first: Michael

last: Quezada

first: Rebecca

last: Mancusi