title: Spatiotemporal single-cell profiling of gastrointestinal GVHD reveals invasive and tissue-resident memory T cell states

status: Public on Sep 02 2020

city: Boston

first: James

middle: John

last: Kaminski

address: 1 Blackfan Circle

department: Hematology / Oncology

institute: Boston Children's Hospital

summary: One of the major barriers to understanding the control of T cell infiltration into target tissues has been the inherent difficulty in capturing the key variable of time in this process. Time is a critical variable, given that T cells are actively homing towards and infiltrating into target organs, and are concordantly evolving a highly pathogenic transcriptional program. Without understanding the time-dependency of T cell infiltration, we cannot fully comprehend key drivers and their dynamics.  Here, we have been able to deconvolute time as a variable during T cell infiltration and tissue destruction during primate aGVHD by applying Serial Intravascular Staining (‘SIVS’) and pairing this with multiparameter flow cytotmetric and single-cell transcriptomic analysis. We also demonstrate significant overlap between NHP transcriptional signatures and those found in patients with active aGVHD, underscoring the clinical relevance of these findings.

overall_design: Bulk RNA-Seq examination of transcriptomes of patient samples receiving placebo from the ABA2 clinical trial (NCT01743131).

first: Victor

last: Tkachev


title: RNA-seq across 27 developmental stages in Sus scrofa skeletal muscle

status: Public on Sep 01 2020

city: Shenzhen

first: Zhonglin

last: Tang

state: GuangDong

address: No.7, Pengfei road, Dapeng District

department: Agricultural Genome Institute at Shenzhen

country: China

institute: Chinese Academy of Agricultural Sciences

type: Expression profiling by high throughput sequencing

summary: To obtain an overview of the transcriptome landscape in developing pig skeletal muscle, 81 high-quality transcriptome libraries that covered 27 developmental stages (3 biological replicates per stage) in pig skeletal muscle were produced by strand-specific rRNA-depleted total RNA sequencing (RNA-seq). We generated  8.59 billion paired-end reads (150 bp × 2) covering 1.24 Tb of sequence for RNA-seq.

overall_design: RNA-seq profiles of Sus scrofa skeletal muscles that covered 27 developmental stages.


title: Single cell gene expression analysis of stem cell-derived cerebral organoids treated with Methamphetamine

status: Public on Sep 11 2020

city: San Diego

first: Tariq

last: Rana

state: CA

address: 9500 Gilman Dr

department: Paediatrics

country: USA

institute: UCSD

summary: To study the effects of fetal brain exposure to methamphetamine, embryonic stem cell-derived cerebral organoids were treated with methamphetamine and cell type-specific gene expression was analysed using scRNA-seq.

overall_design: 8 cerebral organoids were mock treated and 6 cerebral organoids were treated with 5uM methamphetamine for 7 days before being enzymatically dissociated and analyzed by scRNA-seq using the 10x Genomics platform.

first: Jason

last: Dang


title: Whole-genome bisulfite sequencing across 27 developmental stages in Sus scrofa skeletal muscle

type: Methylation profiling by high throughput sequencing

summary: To obtain an overview of the methylome landscape in the developing pig skeletal muscle, 81 high-quality whole-genome bisulfite sequencing(WGBS) libraries that covered 27 developmental stages (3 biological replicates per stage) from embryonic day 33 (E33) to postnatal day 180 (D180) were produced by whole-genome bisulfite sequencing.

overall_design: WGBS profiles of Sus scrofa skeletal muscles that covered 27 developmental stages.


title: Cell-type-specific epigenomic variations associated with BRCA1 mutation in pre-cancer human breast tissues

status: Public on Aug 25 2020

city: Blacksburg

first: Chang

last: Lu

state: VA

address: 235 Goodwin Hall, 635 Prices Fork Road, Virginia Tech

department: Chemical Engineering

institute: Virginia Tech

type: Genome binding/occupancy profiling by high throughput sequencing

summary: BRCA1 germline mutation carriers are predisposed to breast cancers. Epigenomic regulations have been known to strongly interact with genetic variations and potentially mediate biochemical cascades involved in tumorigenesis. Due to the cell-type specificity of epigenomic features, profiling of individual cell types is critical for understanding the molecular events in various cellular compartments within complex breast tissue. Here we report cell-type specific profiling of genome-wide histone modifications, including H3K27ac and H3K4me3 in basal, luminal progenitor, mature luminal, and stromal cells, extracted from pre-cancer BRCA1 mutation carriers and non-carriers, using a low-input technology. We discover that basal and stromal cells present the most substantial epigenomic differences between mutation carriers and non-carriers while luminal progenitor and mature luminal cells are relatively unchanged with the mutation. Furthermore, the epigenomic changes in basal cells due to BRCA1 mutation appear to facilitate their transformation into luminal progenitor cells. Our findings shed light on the pre-cancer epigenomic dynamics due to BRCA1 mutation and how they may contribute to eventual development of basal-like breast cancer.

overall_design:
H3K27ac and H3K4me3 were profiled in four cell types from healthy breast tissues in women with and without the BRCA1 gene mutation. The cell types include basal cells (BCs), luminal progenitor cells (LPs), mature luminal cells (MLs), and stromal cells (SCs). We examined five non-carriers (BRCA1+/+: NC-1, NC-2, NC-3, NC-4, and NC-5) and three BRCA1 mutation carriers (BRCA1mut/+: MUT-1, MUT-2, and MUT-3). The profiling was conducted using MOWChIP-seq technology (Cao et al. Nature Methods, 12 (2015) 959-962; Zhu et al. Nature Protocols 14 (2019) 3366-3394).

**The submitter declares that the raw data will be made available in dbGaP due to patient privacy concerns.**

first: Lynette

last: Naler


title: 27 developmental stages in Sus scrofa skeletal muscle

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

overall_design: Refer to individual Series


title: Transcriptional Characterization of the Tumor Microenvironment and Prognostic Gene Signatures in Conjunctival Melanoma

status: Public on Aug 30 2020

city: Freiburg

first: Clemens

last: Lange

address: Kilianstraße 5

department: Klinik für Augenheilkunde

country: Germany

institute: Uniklinik Freiburg

summary:
Purpose: To characterize the transcriptome and cellular the tumor microenvi-ronment of conjunctival melanoma (CM) compared to healthy conjunctiva and to analyze the transcriptional differences between CM with good and poor clinical outcome.
Methods: Twelve formalin-fixed and paraffin-embedded (FFPE) CM of twelve patients were analyzed by Massive Analysis of cDNA Ends (MACE) RNA se-quencing. Six samples each with good and poor clinical outcome were exam-ined, the latter being defined by local recurrence or systemic metastases with a follow-up of at least 24 months. Eight age-matched healthy FFPE conjunctival specimens from eight patients who underwent retinal detachment surgery served as controls. Bioinformatic cell type enrichment analysis with xCell was used to characterize the tumor microenvironment (TME). Differentially expressed genes (DEG) and the associated biological processes were analyzed between CM and control conjunctiva. Additionally, a prognostic transcription profile was identified by comparing melanoma of good and poor clinical outcome.
Results: The TME of conjunctival melanoma was characterized by the enrich-ment of melanocytes, pericytes and especially several immune cell types. Among them, plasmacytoid dendritic cells (pDC), natural killer T cells (NKT), B cells and mast cells were most significantly increased in CM compared to healthy conjunc-tiva. DEG between CM and control were mainly involved in biological processes such as inhibition of apoptosis, proteolysis and response to growth factors. POU3F3, BIRC5 and 7 were among the top expressed genes associated with inhibition of apoptosis. Twenty genes, among them CENPK, INHA, USP33 and CASP3, were identified as prognostically relevant factors reaching high classifi-cation accuracy (AUC: 1.0).
Conclusions: The present study provides new insights into the TME and the transcriptional profile of CM and additionally identifies new prognostic bi-omarkers. These results might lead to new diagnostic and therapeutic options for CM.

overall_design: MACE RNA sequencing of 12 human conjunctival melanoma (six with poor and six with good clinical outcome), and 8 healthy conjunctival samples as controls.

first: Julian

last: Wolf

first: Claudia

last: Auw-Haedrich

first: Anja

last: Schlecht

first: Stefaniya

last: Boneva

first: Hans

last: Mittelviefhaus

first: Thabo

last: Lapp

first: Hansjürgen

last: Agostini

first: Thomas

last: Reinhard

first: Guenther

last: Schlunck


title: A chimpanzee adenovirus-vectored single dose therapeutic vaccine for post kala azar dermal leishmaniasis

status: Public on Aug 22 2020

city: Siena

first: Francesco

last: Santoro

state: SI

address: Viale Bracci, 16, V lotto, I piano

department: Department of Medical Biotechnologies

country: Italy

institute: University of Siena

summary: Purpose: The goals of this study were to identify molecular patterns activated by the vaccine and potential predictors of clinical success.

overall_design: Methods: Whole blood samples (2.5 ml) were collected into PAXGene tubes immediately prior to vaccination and at 1, 3 and 7 days post vaccination from 24 patients with persistent PKDL

first: Monica

last: Carraro


title: Transcriptomic comparison between nickel hyperaccumulator and non-accumulator plant species from the Phyllanthus genus (Phyllanthaceae) from New Caledonia.

status: Public on Aug 17 2020

city: Auzeville Tolosane

first: Sylvain

last: MERLOT

address: 24, chemin de Borde Rouge

department: Biological Sciences

country: France

institute: CNRS

summary: The leaf transcriptome of the nickel hyperaccumulator Phyllanthus luciliae (Phyllanthaceae) endemic from New Caledonia was compared to the related non-accumulator Phyllanthus conjugatus var. ducosensis, living respectively on ultramafic and sedimentary soil, to identity differentially expressed genes potentially involved in Ni hyperaccumulation.

sample_organism: [Phyllanthus] conjugatus var. ducosensis

overall_design: Leaves from 3 independant individual plants of Phyllanthus lucilia and Phyllanthus conjugatus were collected in their natural environment. RNA of the 6 independant samples were extracted and sequenced using the Illumina paired-end sequencing technology.

first: Vanesa

middle: S

last: Garcia de la Torre

first: Clarisse

last: Majorel-Loulergue

first: Alexandra

last: Launay-Avon

first: Valérie

last: Burtet-Sarramegna

first: Bruno

last: Fogliani

last: Merlot


title: Social reprogramming in ants induces longevity-associated glia remodeling

city: Philadelphia

first: Roberto

last: Bonasio

state: PA

address: 3400 Civic Center Blvd - SCTR 9-111

department: Cell and Developmental Biology

institute: University of Pennsylvania

sample_organism:
Drosophila melanogaster
Harpegnathos saltator


title: microRNA expression Data from cerebrospinal fluid of cancer patients

status: Public on Sep 29 2020

city: Goyang

first: Ho-Shin

last: Gwak

state: Non US

address: 323 Ilsan-ro, Ilsandong-gu

department: Dept. of Cancer Control

country: South Korea

institute: National Cancer Center Graduate School of Cancer Science and Policy

summary: Purpose: Leptomeningeal metastasis (LM) is a dismal terminal stage disease of solid cancer without definitive treatment. Both the limitation of cerebrospinal fluid (CSF) sample volume and a paucity of floating cancer cells are difficulties to study the genomic profiling of LM. As the profiling of microRNAs reflect the strategy and behavior of cancer cells to survive, and CSF is carrying micro-molecules from central nervous system (CNS), we evaluated the extracellular microRNA profiles of CSF from different CNS tumor status including LM.  Materials and Methods: We prospectively collected CSF from 65 patients of five groups of cancer control (CC), healthy control (HC), LM, brain metastasis (BM); and brain tumor (BT). Extracellular RNA was extracted from 2 mL of CSF after proper cell down, and preceded to small RNA microarray with Affymetrix miRNA 4.0 microarray chips.  Results: The mean RNA yield of LM patients was significantly higher compared to that of other patients groups (9.28 vs. 6.30 ㎍, p = 0.003). The small RNA (< 70 nucleotides) percentage was the highest in controls than that of other groups (53% vs. 26%, p < 0.001). Among 6,599 small RNA probes, mature microRNAs showed higher expression than that of pre-microRNAs and small nucleolar RNAs. The number of probes with the Present call in all samples is 22 mature microRNAs, 18 pre-mature microRNAs, and 27 small nucleolar RNAs. Expression value of mature microRNAs regarding their direction of 5 prime (5p) and 3 prime (3p), the expression of 3p microRNA is higher than those of 5p microRNA in both LM and BM samples (p < 0.001). Both supervised and unsupervised hierarchical clustering of 263 microRNAs, which showed more than 2 fold change at a significance level of p < 0.05, can differentiate LM from other CNS tumor patient groups. Prediction analysis of microarray (PAM) identified 13 microRNAs differentiate LM group from others including hsa-miR-335-5p and hsa-miR-466. MicroRNA profiling using significance of analysis of microarrays (SAM) analysis did not differentiate HC and CC. Whereas CSF samples from patients with LM showed the most number of 108 differentially expressed (more than 2 fold change) microRNAs compared to control group and also revealed 36 differentially expressed microRNAs between LM and BM including hsa-miR-466, hsa-miR-190a-3p, hsa-miR-98-3p, hsa-miR-34b-3p and so on. Representative discriminative microRNAs from microarray data were confirmed their expression level by digital droplet PCR in available CSF samples among the microarray samples. Gene Set Enrichment Analysis was performed using both 10 highly expressed and 6 suppressed microRNAs between LM and BM after normalization and 13 microRNAs from PAM analysis. The most targeted pathway was ‘positive-/ negative-transcription from RNA polymerase II promoter followed by ‘positive regulation of transcription, DNA-templated’ by discriminative microRNAs. When pathways were denoted by microRNAs from PAM, the most enriched pathway was inflammatory response and transcription relative to immune response.   Conclusion: We performed extracellular small RNA microarray successfully with small volume of CSF. Analysis of profiles of microRNA according to patients with various CNS tumor status suggested the unique profiles might responsible for leptomeningeal metastasis.

overall_design: Cerebrospinal fluids from various cancer patients were collected for total RNA extraction. The miRNA profiles of each CSF were detected using GeneChip miRNA 4.0 array (Affymetrix, Santa Clara, CA)

first: Kyue

middle: Y

last: Lee

first: Ji-Hye

last: Lim


title: Single-cell RNA sequencing of Harpegnathos saltator brains

summary: We used 10x Genomics and Drop-seq single-cell RNA-seq to identify the cell type composition of the Harpegnathos brain and  study how it changes during the process of adult caste transition (from worker to pseudo-queen), aging, and brain injury.

overall_design: Three experiments: caste transition (6 worker replicates, 5 gamergate replicates); aging (4 time points, ≥3 replicates each); injury (two time points, control and injury, ≥3 replicates each).

first: Emily

last: Shields


title: Extracellular vesicles from Pseudomonas aeruginosa suppress MHC-related molecules in human Lung Macrophages

status: Public on Aug 03 2020

city: Lebanon

first: David

middle: Alan

last: Armstrong

state: NH

address: 1 Medical Center Dr., Borwell 508E

institute: Dartmouth Hitchcock Medical Center

type: Methylation profiling by genome tiling array

summary: We investigate whether EVs secreted from P. aeruginosa alter MHC antigen expression in lung macrophages, thereby potentially contributing to decreased pathogen clearance.

overall_design: Primary lung macrophages from human subjects were collected via bronchoalveolar lavage (BAL) and exposed to EVs isolated from P. aeruginosa in vitro. Gene expression was measured with the NanoString nCounter gene expression assay and validated by examining total cellular protein. DNA methylation was measured with the EPIC array platform to assess changes in methylation at MHC-specific locations.

middle: A


title: Transcription analysis from the human embryonic kidney 293 cells (HEK293) were pre-treated with JIB-04, and then uninfected and infected with porcine rotavirus (PoRV)

status: Public on Aug 14 2020

city: Beijing

first: shimeng

last: Huang

address: No. 2 Yuanmingyuan West Road, Haidian District

department: College of Animal Science and Technology

institute: China Agricultural University

summary: Purpose: Investigation of whole genome gene expression level changes in HEK293 cells response to JIB-04 and porcine rotavirus (PoRV)

overall_design: Methods: HEK293A cells were pre-treated with JIB-04 (10 μM) for 12 hr, and then uninfected or infected with porcine rotavirus (PoRV) (MOI=0.01) for the 12 hpi. Total RNA from cells in duplicate was extracted using RNeasy Mini kit (Qiagen) according to manufacturer’s guidelines. RNA sample quality was measured by both NanoDrop spectrophotometer (Thermo Fisher Scientific) and Bioanalyzer 2100 (Agilent). Libraries were sequenced on the Illumina HiSeq 2500 platform. Then, differential gene expression analysis was performed using DESeq2.

first: Bin

last: Li

first: Siyuan

last: Ding

first: Shimeng


title: Single cell transcriptomes of pancreatic pre-invasive lesions and cancer reveal acinar metaplastic cells’ heterogeneity

status: Public on Jul 31 2020

city: Jerusalem

first: Oren

last: Parnas

address: Faculty of Medicine, Ein-Kerem medical center

department: Immunology

country: Israel

institute: Hebrew University

summary: In this project we have used single cell RNA-seq to profile pancreatic cancer development in a mouse model, from pre-invasive stage to cancer,  and in human PDAC sample. Using a reporter gene, we were able to dissect metaplastic acinar cell heterogeneity, profiled six different acinar metaplastic cell types and states, validated their localization to pre-invasive lesions and correlated findings with human PDAC. In addition, we detected transcription factors, Onecut2 and Foxq1, that strictly expressed in metaplastic cells.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Tamoxifen was injected into six-eight weeks old Ptf1a-CreER, LSL-Kras-G12D, LSL-tdTomato (PRT) mice, and the pancreas was collected for single cell purification from mice at six different time points post-tamoxifen injection (PTI)

first: Yehuda

last: Schlesinger

first: Oshri

last: Yosefov-Levi


title: An insulin-stimulated proteolytic mechanism links energy expenditure with glucose uptake

status: Public on Jul 23 2020

city: West Haven

first: Francesc

last: Lopez

state: CT

department: Department of Genetics

institute: Yale University

summary: Mechanisms to coordinately regulate oxidative metabolism and glucose transport into cells are not well described. In muscle and fat, insulin mobilizes GLUT4 glucose transporters to the cell surface in part by stimulating the site-specific endoproteolytic cleavage of TUG proteins. Here, we show that the TUG C-terminal cleavage product enters the nucleus, binds the transcriptional 30 regulators PGC-1a and PPARg, and increases oxidative metabolism, thermogenic protein expression, and energy expenditure. The PPARg2 Pro12Gly polymorphism, which confers reduced diabetes risk, enhances TUG binding. The TUG cleavage product stabilizes PGC-1a, so that both proteins are susceptible to an Ate1 arginyltransferase -dependent degradation mechanism. We conclude that TUG cleavage coordinates energy expenditure with glucose 35 uptake, and that alterations in this pathway may contribute to metabolic disease.

overall_design: Examination of gene expression differences between wiltype mice and transgenic mice with constitutive, insulin-independent TUG cleavage in muscle

first: Estifanos

middle: N

last: Habtemichael

first: Don

middle: T

first: João-Paulo

last: Camporez

first: Xavier

middle: O

last: Westergaard

first: Chloe

middle: I

last: Sales

first: Xinran

last: Liu

last: López-Giráldez

first: Stephen

middle: G

last: DeVries

first: Hanbing

first: Diana

last: Ruiz

first: Kenny

last: Wang

first: Sandro

last: Hirabara

first: Daniel

middle: F

last: Vatner

first: William

last: Philbrick

first: Gerald

last: Shulman

first: Jonathan

last: Bogan


title: RNA-seq in old and young Drosophila brains

first: Roberto

last: Bonasio

summary: We analyzed gene expression profiles from young and old Drosophila brains using polyA+ RNA-seq

overall_design: Three biological replicates for young flies and four biological replicates for old flies

first: Emily

last: Shields


title: Super-Enhancer-Associated Aortic Valve Stenosis Risk Locus 1p21.2 Alters NFATC2 Binding Site and Promotes Fibrogenesis [H3K27ac HiChIP]

status: Public on Jul 16 2020

city: Québec

first: Patrick

last: Mathieu

state: QC

address: 2725 Ch Ste-Foy

country: Canada

institute: Quebec Heart and Lung Institute

summary: Genome-wide association studies identified a strong signal for non coding variants at the 1p21.2 locus associated with calcific aortic valve stenosis (CAVS). Regulation at the locus and impact on the biology of the aortic valve is presently unknown. Integrative mapping of genetic association data was performed. The locus was evaluated by 3D genome mapping, analysis of atomic resolution data, DNA-binding assay and CRISPR activation (CRISPRa). Weighted gene co-expression network analysis (WGCNA) was performed to determine regulatory network in CAVS. The functional impact of the locus was assessed in isolated VICs. Fine-grained mapping at 1p21.2 risk locus identified rs6702619 as being located in open chromatin and a distant-acting super-enhancer including chromatin interaction with the promoter of PALMD in VICs. Atomic-level data showed that the risk variant modified base readout and DNA shape, which prevented the recruitment of NFATC2, a transcription factor involved in heart valve morphogenesis, and lowered the expression of PALMD. CRISPRa confirmed that rs6702619 exerts a control on the expression of PALMD. WGCNA performed in 233 calcified aortic valves identified a co-expression network encompassing PALMD, which was enriched in actin-based process. In LC-MS/MS and co-immunoprecipitation assay, actin was identified as a protein interacting with PALMD. Lower expression of PALMD in VICs promoted the polymerization of actin, the activation of myocardin-related transcription factor and fibrogenesis. Risk allele at rs6702619 disrupts a NFATC2 binding site and decreases enhancer-mediated expression of PALMD, which results in actin polymerization, a myofibroblast-like phenotype in VICs and fibrogenesis, a key underpinning process in the pathogenesis of CAVS.

overall_design: H3K27ac HiChIP in human aortic valve interstitial cells.

first: Arnaud

last: Chignon

first: Mickael

last: Rosa

first: Marie-Chloé

last: Boulanger

first: Déborah

last: Argaud

first: Romain

last: Devillers

first: Valentin

last: Bon-Baret

first: Ghada

last: Mkannez

first: Zhonglin

last: Li

first: Nathalie

last: Gaudreault

first: David

last: Gosselin

first: Sébastien

last: Thériault

first: Yohan

last: Bossé


title: Hi-C ES and neocortex from Bonev et al. 2017

status: Public on Nov 12 2020

city: Lausanne

first: Lucille

last: Lopez-Delisle

address: Station 19

country: Switzerland

institute: EPFL

type:
Other
Third-party reanalysis

summary: Reanalysis of some Hi-C from Bonev et al. 2017 with HiCUP version 0.6.1

relation:
Reanalysis of: GSM2533818
Reanalysis of: GSM2533819
Reanalysis of: GSM2533820
Reanalysis of: GSM2533821
Reanalysis of: GSM2533835
Reanalysis of: GSM2533836
Reanalysis of: GSM2533837
Reanalysis of: GSM2533838
Reanalysis of: GSM2533839
Reanalysis of: GSM2533840
Reanalysis of: GSM2533841
Reanalysis of: GSM2533842
Reanalysis of: GSE96107

overall_design:
This is a third-party reanalysis of some datasets of GSE96107 to provide a more friendly format
data processing: Fastq were retrieved from SRA. They were processed with HiCUP v0.6.1 specifying DpnII, ^GATC as enzyme. Pairs were extracted with custom python script. The 4 replicates were merged. Pairs were split by chromosome and sorted. All scripts are available at https://github.com/lldelisle/Hi-C_reanalysis_Bonev_2017 .
Genome build: mm10
Files: text file in juicebox format (<readname> <str1> <chr1> <pos1> <frag1> <str2> <chr2> <pos2><frag2> <mapq1> <mapq2> with str = strand (0 for forward, anything else for reverse), pos = middle of the fragment.)

first: Denis

last: Duboule


title: Super-Enhancer-Associated Aortic Valve Stenosis Risk Locus 1p21.2 Alters NFATC2 Binding Site and Promotes Fibrogenesis [ChIP-Seq]

overall_design: ChIP-seq (H3K4me1, H3K4me3, H3K27ac) in human aortic valve interstitial cells.


title: Genome-wide analysis of DNA replication and double strand breaks by TrAEL-seq

status: Public on Jul 27 2020

city: Cambridge

first: Felix

last: Krueger

address: Granta Park

department: Bioinformatics

country: United Kingdom

institute: Altos Labs

summary: We have designed a methodology for capture of DNA 3’ ends that allows mapping of resected DNA breaks, stalled replication forks and also normal replication fork progression. This Transferase-activated end ligation or TrAEL-seq method involves ligation of a functionalised linker to DNA 3’ ends followed by fragmentation, purification of adaptor ligated fragments, second adaptor ligation and library amplification. The major advantages of TrAEL-seq compared to other available methods are: i) an ability to map double strand breaks after resection, ii) excellent sensitivity and signal-to-noise in detecting replication fork stalling and iii) ability to map replication fork progression in unsynchronised, unlabelled populations of both yeast and mammalian cells. The samples provided here were selected to demonstrate different aspects of TrAEL-seq activity: the SfiI and dmc1 datasets shows capture of 3’ extended single strand DNA. The other yeast datasets show replication and replication fork stalling information. The RAF and RAF-GAL grown yeast samples show the effect transcriptional induction on replication fork progression. The hESC samples show the capacity to derive replication profiles from mammalian cells.

sample_organism:
Saccharomyces cerevisiae
Homo sapiens

platform_organism:
Saccharomyces cerevisiae
Homo sapiens

overall_design: TrAEL-seq libraries for a yeast wild-types and mutants, along with END-seq controls and TrAEL-seq libraries from hESCs

first: Neesha

last: Kara

first: Peter

last: Rugg-Gunn

first: Jonathan

last: Houseley


title: Super-Enhancer-Associated Aortic Valve Stenosis Risk Locus 1p21.2 Alters NFATC2 Binding Site and Promotes Fibrogenesis [ATAC-Seq]

first: Patrick

last: Mathieu

overall_design: ATAC-seq in human aortic valve interstitial cells.

first: Arnaud

last: Chignon

first: Mickael

last: Rosa


title: A Reservoir of Fibroblasts Promotes Recovery from Limb Ischemia

status: Public on Aug 08 2020

city: Memphis

first: JIE

last: Lv

state: TN

address: 262 Danny Thomas Place

department: Department of Computational Biology

institute: St Jude Children's Research Hospital

summary:
Background: The angiogenic response to ischemia restores perfusion so as to preserve tissue. A role for mesenchymal-to-endothelial transition in the angiogenic response is controversial. This study is to determine if resident fibroblasts contribute to angiogenesis.
Methods: We utilized the murine model of hindlimb ischemia, and in vivo matrigel plug assay together with lineage tracing studies and single cell RNA-sequencing (scRNA-seq) to examine the transcriptional and functional changes in fibroblasts in response to ischemia.
Results: Lineage tracing using Fsp1-Cre: R26R-EYFP mice revealed the emergence within the ischemic hindlimb of a small subset of YFP+ CD144+ CD11b- fibroblasts (E*cells) that expressed endothelial cell (EC) genes.  Subcutaneous administration of matrigel in Fsp1-Cre: R26R-EYFP mice generated a plug that became vascularized within 5 days.  Isolation of YFP+ CD11b- cells from the plug revealed a small subset of YFP+ CD144+ CD11b- E*cells which expressed EC genes.   Pharmacological or genetic suppression of innate immune signaling reduced vascularity of the matrigel plug and abrogated the generation of these E*cells.  These studies were repeated using human fibroblasts, with FACS analysis revealing that a small percentage of human fibroblasts that were induced to express EC markers in the matrigel plug assay. Pharmacological suppression or genetic knockout of inflammatory signaling abolished the generation of E*cells, impaired perfusion recovery and increased tissue injury after femoral artery ligation.  To further characterize these  E*cells, we performed scRNA-seq and revealed eight discrete clusters of cells expressing characteristic fibroblast genes, of which two clusters (C5 and C8) also expressed some EC genes.   Ischemia of the hindlimb induced expansion of clusters C5 and C8. The C8 cells did not express CD144, nor did they form networks in Matrigel, but did generate angiogenic cytokines. The C5 fibroblasts most resembled E* cells in their expression of CD144 and their ability to form EC-like networks in Matrigel.
Conclusion:  Together, these studies indicate the presence of subsets of tissue fibroblasts which seem poised to contribute to the angiogenic response. The expansion of these subsets with ischemia is dependent upon activation of innate immune signaling, and contributes to recovery of perfusion and preservation of ischemic tissue.

overall_design: YFP+CD11b- cells were FACS sorted from hindlimb muscle isolated from Fsp1-Cre: R26R-EYFP mice without ischemic surgery or 28 days after ischemic surgery. 5000 Cells were captured using 10X chromium system following manufacturer’s protocol. Each library was sequenced on one lane on an illumina Hi-seq 4000 system.

first: Shu

last: Meng

first: Jie

first: Kaifu

last: Chen

first: John

middle: P

last: Cooke


title: Targeted sequencing of localized and metastatic cutaneous squamous cell carcinoma

status: Public on Jul 15 2020

city: Omaha

first: Marissa

last: Lobl

state: NE

address: 4014 Leavenworth St.

institute: UNMC

type: Genome variation profiling by high throughput sequencing

summary: We report sequencing of 10 localized and 10 metastatic cutaneous squamous cell carcinomas from human subjects. Sequencing was done on an oncology targeted gene mutation panel consisting of 76 genes.

overall_design: Case-control study.

first: Ashley

last: Wysong


title: Super-Enhancer-Associated Aortic Valve Stenosis Risk Locus 1p21.2 Alters NFATC2 Binding Site and Promotes Fibrogenesis

overall_design: Refer to individual Series


title: Cr(VI) Promotes Differential Binding of CTCF to its Cognate Sites

status: Public on Jul 21 2020

city: Cincinnati

first: Mario

last: Medvedovic

state: OH

address: 3223 Eden Av. ML 56

department: Department of Environmental Health

institute: University of Cincinnati

summary: Using ChIP-seq, we characterize the differential binding of CTCF following 48 hours of low-dose, Cr(VI) treatment. Differentially-bound sites are enriched in regions near genes that are actively transcribed in the basal state and strength of initial binding may be a factor in determining the directionality of binding affinity fluctuations. CTCF and cohesin samples were used to predict intra-TAD chromatin loops in an effort to provide an initial characterization of how Cr(VI) potentially disrupts chromatin-chromatin contacts important for the regulation of transcription, serving as a foundation for future studies.

overall_design: Examination of CTCF, cohesin, and five histone modifications in control and Cr(VI)-treated (1 µM) Hepa-1c1c7 cells using ChIP-seq.

first: Andrew

last: VonHandorf

first: Hesbon

last: Zablon

first: Jacek

last: Biesiada

first: Xiang

last: Zhang

first: Alvaro

last: Puga


title: CTCF Mediates Dosage and Sequence-context-dependent Transcriptional Insulation through Formation of Local Chromatin Domains [ChIP-seq]

status: Public on Jul 06 2020

city: La Jolla

first: Bing

last: Ren

address: 9500 Gilman Dr., CMM-East, Admin Area/Rm 2071

institute: University of California, San Diego School of Medicine

summary: Insulators play a critical role in spatiotemporal gene expression in metazoans by separating active and repressive chromatin domains and preventing inappropriate enhancer-promoter contacts. The evolutionarily conserved CCCTC-binding factor (CTCF) is required for insulator function in mammals, but not all of its binding sites act as insulators. Here, we explore the sequence requirements of CTCF-mediated transcriptional insulation with the use of a sensitive insulator reporter assay in mouse embryonic stem cells. We find that potent insulation is provided by multiple CTCF binding sites. Furthermore, CTCF-mediated insulation is dependent on DNA sequences adjacent to its core binding motifs, and CTCF binding sites from topologically associating domains (TAD) boundaries are more likely to function as insulators than those outside TAD boundaries independent of binding strength. Using chromosomal conformation capture assays and high resolution chromatin imaging techniques, we demonstrate that insulators reduce enhancer-promoter contacts by forming local chromatin domains. Taken together, our results provide strong genetic, molecular and imaging evidence connecting chromatin topology to action of insulators in the mammalian genome.

overall_design:
Examination of insulator activity of CTCF binding seqences and their effects on chromatin topology in mouse embryonic cells

Chromosome coordinates of variants:
'4CBS' was inserted between chr3:34,726,762-34,727,258; mm10
'4CBS downstream' was inserted between chr3:34,794,087-34,794,154; mm10.

first: Huang

last: Hui

first: Ren

last: Bing


title: Analysis of lung transcriptomic changes following inhibition of LTβR-signalling in cigarette smoke exposed mice

status: Public on Jul 10 2020

city: Biberach

first: Meshal

last: Ansari

address: Birkendorfer Straße 65

institute: Boehringer Ingelheim

summary: How LTβR-signalling drives chronic tissue damage particularly in the lung, which mechanisms regulate this process, and whether LTβR-blockade might be of therapeutic value has remained unclear. To study the mechanisms underlying LTβR-inhibition, a transcriptional analysis was performed on lung tissue from B6 mice exposed to cigarette smoke for 6 months and treated therapeutically with LTβR-Ig from 4 to 6 months compared to mice exposed to cigarette smoke for 6 months and treated with control Ig from 4 to 6 months and filtered air control. Single-cell RNA-Seq identified 24 distinct cell populations across >20,000 cells in lungs with distinct changes occurring upon cigarette smoke exposure and LTβR-Ig treatment.

overall_design: Single-cell transcriptomics experiment after cigarette smoke exposure and drug treatment.

first: Thomas

middle: M

last: Conlon

first: Gerrit

last: John-Schuster

first: Maximilian

last: Strunz

first: Fabian

middle: J

last: Theis

first: Herbert

middle: B

last: Schiller

first: Mathias

last: Heikenwalder

first: Ali

last: Yildirim


title: Deconvoluting alloimmunity in time and space through Serial Intravascular Staining: Evidence for rapid donor tissue-resident memory T cell resident memory formation during gastrointestinal GVHD.

status: Public on Jul 01 2020

city: Boston

first: James

last: Kaminski

state: MA

address: 1 Blackfan Circle

institute: Boston Children's Hospital

summary: Here we have applied Serial Intravascular Staining (‘SIVS’), complemented by single cell transcriptomic analysis, to ascertain the time-, tissue- and donor-dependence of T cell infiltration-mediated immune pathology during aGVHD in a non-human primate (NHP) model. We demonstrate rapid differentiation of donor tissue-infiltrating CD8 T cells in situ into tissue-resident memory T cells (TRM), coincident with destruction of aGVHD target tissues. We also combined SIVS with single cell RNA Sequencing (scRNASeq) to identify the transcriptional programs controlling these actively infiltrating cells.

overall_design: Examination of transcriptomes of individual colon cells in non-human primate (NHP) model of aGVHD

first: Victor

last: Tkachev


title: Identified differentially expressed lncRNAs in type 2 diabetes patients

status: Public on Jun 30 2020

first: yihan

last: liu

address: No.10 Xitoutiao, Youanmen, Fengtai District

institute: Capital Medical University

type: Non-coding RNA profiling by high throughput sequencing

summary: Long noncoding RNAs (lncRNAs) is already evidently involved in a variety of biological functions and pathophysiological mechanisms underlying the diabetes. However, the role of lncRNAs in the type 2 diabetes (T2D) has not been explored clearly yet. The aim of this study was to determine the circulating lncRNA profile and confirmed the differentially expressed lncRNA between T2D patients.

overall_design: Leukocyte lncRNA profiles of T2D patients were generated by deep sequencing.

first: Xiaoyan

last: Du

first: Yihan

last: Liu


title: Transcriptional analyses of maize leaves in response to high‐density planting

status: Public on Jun 29 2020

city: Shenyang

first: Chenghao

last: Zhao

address: No.120 Dongling Road

institute: Shenyang Agricultural University

summary:
Maize (Zea mays L.) is one of the major cereal crops worldwide. Increasing planting density is an effective way to improve crop yield. However, plants grown under high-density conditions compete for water, nutrients, and light, which often leads to changes in productivity. To date, few studies have determined the transcriptomic differences in maize leaves in response to different planting densities. This study examined the whole-genome expression patterns in the leaves of maize planted under high and low densities to identify density-regulated genes. Leaves at upper, ear, and lower stem nodes were collected at the grain-filling stage of the maize hybrid Xianyu335 grown under low-density planting and high-density planting. In total, 72, 733, and 1,739 differentially expressed genes (DEGs) were identified in the respective upper, ear, and lower leaves under HDP. Upregulated and downregulated DEGs in the upper and lower leaves were similar in number, whereas upregulated DEGs in the ear leaves were significantly higher in number than the downregulated DEGs. Functional analysis indicated that genes responding to HDP-related stresses were mediated by pathways involving four phytohormones responsible for metabolism and signaling, osmoprotectant biosynthesis, transcription factors, and fatty acid biosynthesis and protein
kinases, which suggested that these pathways are affected by the adaptive responses mechanisms underlying the physiological and biochemical responses of the leaves of maize planted at high density.

overall_design: RNA-seq of leaves at different nodes of  maize hybrid Xianyu 335 under different plant densities were conducted to explore the mechanisms of responsing to high plant density

first: Lijun

last: Zhang

first: Shuwen

last: Ji

first: Chao

last: Ge

first: Zhongxian

last: Shi

first: Ao

first: Zhenhai

last: Cui

first: Zuoying

last: Wang

first: Yanye

last: Ruan


title: Single-cell transcriptomic analysis 30 hpf Zebrafish trunks

status: Public on Jun 23 2020

city: Tampa

first: Saulius

last: Sumanas

state: Florida

address: 560 Channelside Dr

institute: University of South Florida

summary: Here we performed single-cell RNAseq analysis of whole wildtype zebrafish trunks at 30hpf using 10x Genomics' Chromium platform. 22 distinct cell populations were identified, spanning all three embryonic germ layers.

overall_design: Whole trunks excised from 30 embryos at 30 hpf were dissociated using a cold protease dissociation protocol. Barcoding of cells and and cDNA library construction was carried out using 10X Genomics' Chromium platform.

first: Satish

last: Casie Chetty

first: Sanjeeva

last: Metikala


title: Gene expression signatures in human B lymphoma cell line VAL

status: Public on Jun 16 2020

city: Nagoya

first: Akinobu

last: Ota

state: Aichi

address: 1-1 Yazakokarimata

department: Food and Nutritional Environment

country: Japan

institute: Kinjo Gakuin University

summary: To investigate the effect of PD-1 expression on gene expression, we have employed whole genome microarray expression profiling as a discovery platform to identify genes related to the cell proliferation of human B-cell lymphoma (HBCL) cell line VAL in vitro.

overall_design: PD-1-wildtype or PD-1-knockout VAL cells were incubated for 24 h in vitro.

first: Hanamura

last: Ichiro

first: Sivasundaram

last: Karnan


title: CTCF Mediates Dosage and Sequence-context-dependent Transcriptional Insulation through Formation of Local Chromatin Domains

first: Bing

last: Ren

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


title: CTCF Mediates Dosage and Sequence-context-dependent Transcriptional Insulation through Formation of Local Chromatin Domains [Hi-C and PLAC-seq]

overall_design:
Examination of insulator activity of CTCF binding seqences and their effects on chromatin topology in mouse embryonic stem cells.

Chromosome coordinates of variants:
'4CBS' was inserted between chr3:34,726,762-34,727,258; mm10
'4CBS downstream' was inserted between chr3:34,794,087-34,794,154; mm10.

first: Huang

last: Hui

first: Ren

last: Bing


title: Genomic characterization of five commonly used endometrial cancer cell lines

status: Public on May 27 2020

city: Iowa City

first: Jesus

last: Gonzalez Bosquet

state: IA

address: 200 Hawkins Dr

institute: University of Iowa

summary: An in-depth examination of five endometrial cancer cell lines in which mutation profiles, copy number variation, micro-satellite instability and homolgous recombination repair ability were determined and assessed in the context of TCGA endometrial cancer groups.

overall_design: Five endometrial cancer cell lines; Ishikawa, ECC-1 Hec50co, KLE and RL95-2, were grown under optimized conditions, whole cell RNA was purified from each cell line and used for CODIS validation, RNA sequencing and MSI testing.

first: Eric

last: Devor

last: Gonzalez-Bosquet

first: Kristina

middle: W

last: Thiel

first: Kimberly

middle: K

last: Leslie


title: 3’ MACE RNA-Sequencing allows for Transcriptome Profiling in Long-Term Stored Human Tissue Samples

status: Public on Jun 15 2020

city: Freiburg

first: Clemens

last: Lange

address: Kilianstraße 5

institute: Uniklinik Freiburg

summary: This study aims to compare the potential of standard RNA-sequencing (RNA-Seq) and 3’ massive analysis of c-DNA ends (MACE) RNA-sequencing for the analysis of fresh tissue and describes transcriptome profiling of formalin-fixed paraffin-embedded (FFPE) archival human samples by MACE.

first: Stefaniya

last: Boneva

first: Anja

last: Schlecht

first: Daniel

last: Boehringer

first: Hans

last: Mittelviefhaus

first: Thomas

last: Reinhard

first: Hansjürgen

last: Agostini

first: Claudia

last: Auw-Haedrich

first: Guenther

last: Schlunck

first: Julian

last: Wolf


title: 131I exposured young and adult rat thyroid

status: Public on May 31 2020

city: Gothenburg

first: Malin

last: Larsson

address: Gula straket 2B

country: Sweden

institute: University of Gothenburg

summary: Transcriptional profiling of rat thyroid cells  comparing control untreated thyroid cells with 131I irradiated thyroid cells. Goal was to invesigate radiation induced gene expression profiles

overall_design: Two-condition experiment, irradiated vs non-irradiated samples. Biological replicates: 4 control replicates, 4 irradiated replicates. For four different doses and four ages

first: Nils

last: Rudqvist

first: Johan

last: Spetz

first: Toshima

middle: Z

last: Paris

first: Britta

last: Langen

first: Khalil

last: Helou

first: Eva

last: Forssell-Aronsson


title: Comprehensive genomic analysis of CD4 T cell subtypes infiltrating human triple-negative breast cancer

status: Public on May 20 2020

city: Zhengzhou

first: Sha

last: Zhu

state: Henan

institute: Zhengzhou University

summary: Triple-negative breast cancer is a typical molecular subtype of breast cancer that lacks the expression of estrogen receptor, progesterone receptor and human epidermal growth factor receptor 2 which is also well known for its aggressive and metastatic clinical characteristics. Currently, no specific targeted therapy is available for TNBC. CD4+ T cells are critical regulators of immune responses but their role in breast cancer is currently unknown. Therefore, we investigated the gene expression profile of tumor infiltrating CD4+ T cells and to predict their potential roles in modulating antitumor immune function. As a result, abundant Treg and exhausted lymphocytes were detected, accompanied by largely decreased of effector/memory and cytotoxic T cells.

overall_design: The study is composed of 2 groups, CD4 T cells from primary tumors and peripheral blood (n=2). All triple-negative breast cancer patients were treatment naive. Cells were flow sorted and purity of cells were at least 95%.

first: He

last: Zhang


title: Iron Responsive Element (IRE)-mediated responses to iron dyshomeostasis in Alzheimer’s disease

status: Public on May 06 2020

city: Adelaide

first: Nhi

last: Hin

address: North Terrace

country: Australia

institute: University of Adelaide

summary:
Background: Iron trafficking and accumulation has been associated with Alzheimer’s disease (AD) pathogenesis. However, the role of iron dyshomeostasis in early disease stages is uncertain. Currently, gene expression changes indicative of iron dyshomeostasis are not well characterised, making it difficult to explore these in existing datasets.

Results: We identified sets of genes predicted to contain Iron Responsive Elements (IREs), and used these to explore iron dyshomeostasis responses in transcript datasets involving (1) cultured cells under iron overload and deficiency treatments, (2) post-mortem brain tissues from AD and other neuropathologies, (3) 5XFAD transgenic mice modelling AD pathologies, and (4) a zebrafish knock-in model of early-onset, familial AD (fAD). IRE gene sets were sufficiently sensitive to distinguish not only between iron overload and deficiency in cultured cells, but also between AD and other pathological brain conditions. Notably, we see changes in 3’ IRE transcript abundance as amongst the earliest observable in zebrafish fAD-like brains and preceding other AD-typical pathologies such as inflammatory changes. Unexpectedly, while some 3’ IRE transcripts show significantly increased stability under iron deficiency in line with current assumptions, many such transcripts instead show decreased stability, indicating that this is not a generalizable paradigm.

Conclusions: Our results reveal iron dyshomeostasis as a likely early driver of fAD and as able to distinguish AD from other brain pathologies. Our work demonstrates how differences in the stability of IRE-containing transcripts can be used to explore and compare iron dyshomeostasis responses in different species, tissues, and conditions.

overall_design:
Whole-brain profiles from wild type (+/+) and heterozygous mutant fAD-like (psen1 Q96_K97del/+) zebrafish under hypoxia or normoxia. Brains were taken from zebrafish aged at 6 months and 24 months.
This series includes re-analysis of all samples in GSE126096.

first: Morgan

last: Newman

first: Stephen

last: Pederson

first: Michael

last: Lardelli


title: Molecular determinants and heterogeneity of circulating and tissue-resident memory CD8+ T lymphocytes revealed by single-cell RNA sequencing

status: Public on May 15 2020

first: John

last: Chang

address: 9500 Gilman Drive

department: School of Medicine

institute: UCSD

summary: We generated a single-cell transcriptomic resource dataset encompassing the gene-expression patterns of circulating and small intestine intraepithelial CD8+ T cells in response to viral infection. Our analyses revealed a core transcriptional program shared between circulating memory and tissue-resident memory (TRM) cells, along with key differences in the kinetics and magnitude of gene expression between these two memory CD8+ T lymphocyte subtypes. Moreover, we elucidated previously unappreciated heterogeneity within the small intestine intraepithelial CD8+ T cell pool at multiple time points following infection.

overall_design: Single cell RNA sequencing was performed on CD8 T cells isolated from the spleen or small intestinal intraepithelial compartment at 11 timepoints following infection with lymphocytic choriomeningitis virus

first: Zhaoren

last: He

first: Nadia

last: Kurd


title: Transcriptional Analysis of Lipid Metabolism Controlling Enzymes in Bovine Ovary

status: Public on Apr 23 2020

city: Nouzilly

first: Svetlana

last: UZBEKOVA

address: PRC INRA

institute: INRA

summary: Gene expression was analysed in bovine ovarian folliculr cells : theca, granulosa, cumulus and oocyte

overall_design: Transcriptomes of theca, granulosa, cumulus and oocytes from ovarian follicles 3-6 mm were compared

first: A

last: Vitorino Carvalho

first: V

last: Duranthon

first: P

last: Bertevello

first: S

last: Uzbekova


title: Muscle transcriptome response to 84-day bed rest with and without resistance exercise in men: the search for the residual signature of muscle atrophy

status: Public on Apr 07 2020

city: Stockholm

first: Eric

last: Rullman

address: C1:82 Karolinska University Hospital, Huddinge

department: Laboratory Medicine

institute: Karolinska Institutet

summary: The present study concerns the effects of 90 days of sustained recumbence (bedrest) on skeletal muscle gene expression with and without exercise countermeasures.

overall_design: Twenty-one healthy men (age range 26-41 yr) were randomized to performed 90-d bed rest with (BRE; n=9) or without (BR; n=12) concurrent iso-inertial resistance exercise targeting the quadriceps muscle group (i.e. supine squat; 4 sets of 7 maximal concentric-eccentric repetitions every third day) employing flywheel technology. Muscle biopsies from m. vastus lateralis were obtained from all subjects before and after 84 days of bed rest.


title: Microarray analysis of Polyoma Small T expressing U2OS cell lines

status: Public on Apr 29 2020

city: Srinagar

first: Shaida

last: Andrabi

state: Kashmir

address: Srinagar

department: Biochemistry

country: India

institute: University of Kashmir

summary:
In order to understand which pathways are involved and what genes are affected when small T is expressed in mammalian cells, we carried out microarray analaysis in these cell lines
Total cellulatr RNA was isolated at 20 hrs after doxycycline addition in samples 2,4 and 6 (+DOX), and was subjecyed to microarray analysis using  Affymetrix Human Genome U133 Plus 2.0 (HG-U133_Plus_2) chips.

overall_design: We had inducible Polyoma Small T cell lines. Docycyline was added to induce the expression of small T antigen. RNA was isolated from these cells and used for whole genome microarray analysis

first: Thomas

last: Robert


title: Transcriptional profiling of p53 mutants in KP LUAD cells

status: Public on Mar 18 2020

city: New York

first: Yu-Jui

last: Ho

state: New York

address: 417 E 68th St

department: Cancer Biology & Genetics Program

institute: Memorial Sloan Kettering Cancer Center

summary: Transcriptional profiling of KP LUAD cells expressing a panel of p53 mutant cDNAs.

overall_design: 1 million KP LUAD cells were seeded in 10cm plates and immediately transduced with retroviral supernatants and 8ug/mL polybrene. Cells were grown for 48hrs before purifying using fluorescence activated cell sorting (FACS). All transductions were done in triplicate. Following transduction, stable GFP+ populations were purified by FACS on a FACSAria (BD Biosciences). 120 hours post-transduction, total RNA was isolated using the RNeasy Mini Kit (Qiagen) following standard manufacturer protocols.

first: Francisco

last: Sánchez-Rivera


title: RNA-seq expression profiling of ductal macrophages and antigen presenting cells from virgin mouse mammary glands

status: Public on Apr 01 2020

city: Parkville

first: Gordon

last: Smyth

state: Vic

address: 1G Royal Pde

institute: Walter and Eliza Hall Institute of Medical Research

summary:
Macrophages are diverse immune cells that reside in all tissues to regulate development, function and homeostasis.  In the mammary gland, a highly dynamic organ that undergoes dramatic remodeling throughout life, macrophages have been implicated in development and breast tumorigenesis. Ductal macrophages, as opposed to their stromal counterparts, were found to promote ductal morphogenesis during puberty and efficiently phagocytose alveolar cells post-lactation. Within mammary tumors, only ductal macrophages expanded to form a network throughout the tumor, where they also contact intra-tumoral T cells. Furthermore, ductal macrophages accelerated the growth of tumor organoids. Thus, pro-remodeling mammary ductal macrophages represent the normal tissue counterpart of tumor macrophages in an organ that is highly susceptible to oncogenesis.

To gain insight into ductal macrophage function, we sorted all antigen presenting cell populations from mouse mammary glands and undertook RNA-seq expression profiling. This showed that ductal macrophages have a distinct expression profile from those of stromal macrophages or dendritic cells from the mammary gland. Results from this data series are presented in Figure 2 of Dawson et al (2020).

overall_design: Two biological replicates were prepared of each of ductal macrophages, stromal macrophages, CD11b-CD103+ dendritic cells, CD11b-CD103- dendritic cells and CD11b+ dendritic cells from the mammary glands of adult, female, virgin mice. Paired-end 80bp RNA-seq reads were generated on an Illumina NextSeq 500 sequencer.


title: Co-expression of calcium channels and delayed rectifier potassium channels protects the heart from proarrhythmic events [Figure 8 mRNA data]

status: Public on Mar 10 2020

city: Darlinghurst

first: Jamie

middle: Ian

last: Vandenberg

state: NSW

address: 405 Liverpool Street

department: Molecular Cardiology and Biophysics

institute: Victor Chang Cardiac Research Institute

summary:
Analysis of rhythmonome gene expression in cardiac myocytes derived from human induced pluripotent stem cells
Cardiac electrical activity is controlled by the carefully orchestrated activity of more than a dozen different ion conductances. Yet, there is considerable variability in cardiac ion channel expression levels both within and between subjects. In this study we tested the hypothesis that variations in ion channel expression between individuals are not random but rather there are modules of co-expressed genes and that these modules make electrical signaling in the heart more robust.
Meta-analysis of 3653 public RNA-Seq datasets identified a strong correlation between  expression of CACNA1C (L-type calcium current, ICaL) and KCNH2 (rapid delayed rectifier K+ current, IKr), which was verified in mRNA extracted from human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CM). In silico modeling, validated with functional measurements in hiPSC-CM, indicates that the co-expression of CACNA1C and KCNH2 limits the variability in action potential duration and reduces susceptibility to early afterdepolarizations, a surrogate marker for pro-arrhythmia.

overall_design: Duplicate samples (a,b) from 6 samples derived from iPS cells. Total RNA was obtained from 40,000 hiPSC-CMs lysed using QIAzol Lysis reagent (Qiagen). The RNA was purified using miRNeasy® Mini Kit (Qiagen), and all samples had RIN values >7.5, and were analysed using Agilent Bioanalyzer pico-chip. RNA samples were hybridised with probes designed to detect 35 known rhythmonome genes using nCounter (NanoString Technologies)

first: Melissa

last: Mangala

first: Matthew

last: Perry

first: Adam

last: Hill


title: Co-expression of calcium channels and delayed rectifier potassium channels protects the heart from proarrhythmic events [Figure 2 mRNA data]

overall_design: 10 samples derived from iPS cells derived from 10 control subjects. Total RNA was obtained from 40,000 hiPSC-CMs lysed using QIAzol Lysis reagent (Qiagen). The RNA was purified using miRNeasy® Mini Kit (Qiagen), and all samples had RIN values >7.5, and were analysed using Agilent Bioanalyzer pico-chip. RNA samples were hybridised with probes designed to detect 35 known rhythmonome genes using nCounter (NanoString Technologies)


title: Efficient Identification of Multiple Pathways: RNA-Seq Analysis of Livers from 56Fe Ion Irradiated Mice

status: Public on Mar 03 2020

city: Galveston

first: Anna

last: Nia

state: TX

address: 301 University Blvd

department: Biochemistry and Molecular Biology

institute: University of Texas Medical Branch

summary: Background: mRNA interactions with each other and other signaling molecules define different biological pathways and functions. Researchers have been investigating various tools to analyze these types of interactions. In particular, gene co-expression network methods have proved useful in finding and analyzing these molecular interactions. Many different analytical pipelines to identify these interactions networks have been proposed with the aim of identifying an optimal partition of the network where the individual modules are neither too small to make any general inference or too large to be biologically interpretable.   Results: In this study, we propose a new pipeline to perform gene co-expression network analysis. The proposed pipeline uses WGCNA, a widely used software to perform different aspects of gene co-expression network analysis and modularity maximization algorithm to analyze novel RNA-Seq data to understand the effects of low-dose 56Fe ion irradiation on the formation of hepatocellular carcinoma in mice. The network results along with experimental validation show that using WGCNA combined with Modularity provide a more biologically interpretable network in our dataset. Our pipeline showed better performance than the existing clustering algorithm in WGCNA in finding modules and identified a module with mitochondrial subunits that are supported by mitochondrial complex assay.   Conclusions: We present a pipeline that can reduce the problem of parameter selection with the existing algorithm in WGCNA for comparable RNA-Seq datasets which may assist in future research to discover novel mRNA interactions and their downstream molecular effects.

overall_design: C57BL16 males were placed into 2 treatment groups and received the following irradiation treatments at Brookhaven National Laboratories (Long Island, NY): 600 MeV/n 56Fe (0.2 Gy), and no irradiation. Left liver lobes were collected at 30, 60, 120, 270, and 360 days post-irradiation, flash frozen and stored at -80°C until they could be processed for RNA-Seq. Livers were sampled by taking two 40-micron thick slices using a cryotome at -20°C. This allowed multiple sampling of the tissue without the tissue going through multiple freeze/thaw cycles. Total RNA was isolated from the liver slices using RNAqueousTM Total RNA Isolation Kit (ThermoFisher Scientific, Waltham, MA) and rRNA was removed via Ribo-ZeroTM rRNA Removal Kit (Illumina, San Diego, CA) prior to library preparation with the Illumina TruSeq RNA Library kit. Samples were sequenced in a paired-end 50 base format on an Illumina HiSeq 1500. Reads were aligned to the mouse GRCm38 reference genome using the STAR alignment program, version 2.5.3a, with the recommended ENCODE options.[34] The -quantMode GeneCounts option was used to obtain read counts per gene based on the Gencode release M14 annotation file.[35] Total number of reads used in analysis varies between 23-35 millions of reads.

first: Brooke

middle: L

last: Barnette

first: Robert

last: Ullrich

first: Mark

middle: R

last: Emmett


title: Co-expression of calcium channels and delayed rectifier potassium channels protects the heart from proarrhythmic events

overall_design: Refer to individual Series


title: Direct Reprogramming of Fibroblasts into a Cardiomimetic Tissue

status: Public on Mar 13 2020

city: Seoul

first: Jaeyeaon

last: Cho

address: 50-1 Yonsei-ro, Seodaemoon-gu

department: Medicine

institute: Yonsei University

summary: Mouse tail-tip fibroblasts could be reprogrammed toward cardiomimetic tissue by combined treatments of miRNA, ascorbic acid and BMP4

overall_design: Total RNA was extracted in tail-tip mouse fibroblasts 0, 6 and 10 days after the reprogramming treatments, and the converted cDNAs from isolated RNAs and input were used to generate DNA libraries following the Illumina protocol.

first: Young-sup

last: Yoon


title: EP001: The interferon transcriptome in uterine NK cells is upregulated during the second trimester of pregnancy allowing extravillous trophoblast invasion

status: Public on Jan 30 2020

city: Utrecht

first: Marian

last: Groot Koerkamp

state: Utrecht

address: Heidelberglaan 25

department: Research

country: Netherlands

institute: Princess Maxima Center for Pediatric Oncology

summary: Uterine Natural Killer (uNK) cells regulate essential developmental processes at the maternal-fetal interface during early pregnancy. Uterine NK cell functions are tightly regulated during early placentation to stimulate trophoblast invasion and remodel uterine spiral arteries. Access to human 1st and 2nd trimester uterine tissues allowed us to investigate the transcriptional changes in uNK cells during the early stages of early human pregnancy. Microarray analysis identified 97 upregulated genes in 2nd compared to 1st trimester purified uNK cells of which the majority (61%) clustered as interferon-stimulated-genes (ISG), with ISG15 and ISG20 being upregulated profoundly. Type I interferons (IFNα/β), but not type II interferon (IFNɣ) increased expression of the identified interferon target genes ISG15 and ISG20 in uNK cells in vitro. Moreover, the cytokine-like protein ISG15 stimulated in vitro trophoblast invasion. Second trimester uNK cells promoted trophoblast invasion in vitro, whereas both 1st and 2nd trimester uNK cells stimulated endothelial tube formation. IFNα but not IFNβ stimulation of 1st trimester uNK cells enhanced their capacity to promote trophoblast invasion. In conclusion, the uNK cell interferon transcriptome is upregulated during the 2nd trimester allowing uNK cells to promote trophoblast invasion. Type I interferon signaling regulates uNK cell-induced trophoblast invasion via induction of effector molecules like ISG15. First trimester uNK cells can be induced to act like second trimester uNK cells by IFNα with respect to promotion of trophoblast invasion. Key words: Gene expression profiling ■ uterine natural killer cells ■ extravillous trophoblast invasion ■ interferon alpha ■ ISG15

overall_design: We performed microarray analysis on highly purified CD56brightCD16-CD3- uNK cells comparing decidual tissue from 1st and 2nd trimester pregnancy terminations. Each group consisted of 6 donors. Total RNA was amplified and labeled with cy5 and co-hybridized with cy3 labeled Stratagene Universal Reference RNA on Agilent human V2 arrays.

first: Emiel

middle: D

last: Post Uiterweer

first: Arie

last: Franx

first: Frank

last: Holstege

first: Niels

last: Eijkelkamp

first: Cobi

last: Heijnen


title: Purity Independent Subtyping of Tumors (PurIST), a clinically robust single sample classifier for tumor subtyping in pancreatic cancer

status: Public on Feb 21 2020

city: Chapel Hill

first: Xianlu

middle: Laura

last: Peng

state: NC

address: 450 West Dr.

institute: The University of North Carolina at Chapel Hill


title: Integrated analysis of ovarian cancer samples to facilitate precision medicine

status: Public on Jan 27 2020

city: Huntsville

first: Sara

last: Cooper

state: AL

address: 601 Genome Wau

institute: HudsonAlpha Institute

summary: RNA-sequencing and metabolomic analysis reveal pathways important to drug response and associated with formation of metastasis

overall_design: RNA-sequencing of patient ovarian cancer primary tissues, ascites and post-treatment tissue samples

first: Rebecca

middle: C

last: Arend


title: Single-cell transcriptome analysis revealed continuous changes in molecular phenotypes during epithelial-to-mesenchymal transition

status: Public on Jan 15 2020

city: Yokohama

first: Imad

last: Abugessaisa

address: 1-7-22 Suehiro-cho, Tsurumi-ku

department: IMS

institute: RIKEN

summary: Many genes involved in epithelial-to-mesenchymal transition (EMT) have been identified to date, but mechanisms contributing to the phenotypic diversity and those governing the coupling between the dynamics of epithelial genes and that of the mesenchymal genes are unclear. In this study, we employed single-cell transcriptome analysis to study the gene expression changes during dynamic E-to-M transition. Dose-dependent response to TGFbeta signal suggested that gene expression patterns between E and M states are rather continuous unlike binary switching between two discrete populations. E and M genes can be classified into several subclusters based on expression correlation and it turned out that some E and M genes are mutually exclusive but others are not. Our data suggests that complex and continuous changes in molecular phenotypes occur during EMT at a single-cell level.

overall_design:
10x Genomic Chromium data set was generated from the MCF10A cells (ATCC)
RNA-Seq library was prepared using 10x Chromium Single Cell 3' –end Reagent Kits User Guide (v2 Chemistry).  Libraries were sequenced using paired-end sequencing (26bp Read 1 and 98bp Read 2) with a single sample index (8bp) on the Illumina HiSeq 2500.

first: Kazuhide

last: Watanabe

first: Masataka

last: Takahashi

first: Harukazu

last: Suzuki

first: Takeya

last: Kasukawa


title: Muscle-type specific transcriptomic expression patterns in Drosophila

status: Public on Jan 11 2020

city: Kansas City

first: Maria

middle: Lynn

last: Spletter

state: MO

address: 5009 Rockhill Rd

department: Biological and Biomedical Systems

institute: University of Missouri Kansas City

summary: To complement our existing data on developmental gene expression changes in flight muscle (IFM) development in Drosophila (GSE107247, GSE63707), we performed mRNA-Seq on dissected leg samples at three stages during pupal development (30, 50 and 72h APF). We further sequenced an additional timepoint at 24h APF for RNAi knockdown of aret (Bru1) in flight muscle. Comparison of splicing and expression profiles of sarcomeric genes allowed us to identify muscle-type specific differences in gene and isoform expression between fibrillar flight muscle and tubular leg muscle. We can further trace the dynamics of exon usage in sarcomere genes across the developmental timecourse, allowing us to identify events the switch during muscle differentiation and maturation.

overall_design: Design 1: aret (Bru1) RNAi IFM at 24h APF (versus WT IFM at 24h APF from GSE107247); Design 2: timecourse of whole leg gene expression at imaginal disc (myoblast), 30h, 50h and 72h APF.

last: Schnorrer

first: Assa

last: Yeroslaviz

first: Bianca

last: Habermann

first: Alexander

last: Stark


title: Whole kidneys at embryonic day 16.5: wildtype (WT) vs. conditional Dot1-knockout (KO) from Six2-positive nephron progenitor cells (NPC)

status: Public on Dec 31 2019

city: New Orleans

first: Samir

middle: S

last: El-Dahr

state: LA

address: 1430 Tulane Ave

department: Pediatrics

institute: Tulane University School of Medicine

summary: Transcriptional profiling of whole kidneys from Six2CreEGFP mice without (WT) or with (KO) homozygously floxed DOT1 alleles at the age of embryonic day 16.5. This experiment aimed to uncover the genome-wide alternation in gene expression resulting from the removal of DOT1 gene in the nephron progenitor population (Six2 positive) and successive changes to the series of events in kidney development.

overall_design: Two-condition experiment, WT vs. KO kidneys. Biological replicates: 4 WTs and 4 KOs.

first: Yuwen

last: Li

first: Fenglin

last: Wang


title: DNase-seq profiling of Saos-2 and U2OS cell lines

status: Public on Jan 03 2020

first: Matthew

middle: T

last: Maurano

state: NY

address: 435 East 30th Street

department: Institute for Systems Genetics

institute: NYU School of Medicine

summary: We performed DNase-seq on two osteosarcoma cell lines, Saos-2 and U2OS. This was done to identify regulatory regions within the genomes of these cells. We performed hotspot calling on these data using Hotspot2 (https://github.com/Altius/hotspot2) to identify 51,556 DNaseI hypersensitive sites within Saos-2 cells and 63,388 within U2OS cells.

overall_design: A single replicate of each of Saos-2 and U2OS cell lines was profiled using DNase-seq

first: Megan

last: Hogan

first: Nicholas

middle: A

last: Vulpescu


title: Establishment of hTERT immortalized mouse cardiosphere derived cell line

first: zhenglong

last: guo

address: NO.7, Weiwu road

institute: Henan Provincial People's Hospital

summary: The analysis showed differences of transcriptomes between primary CDCs and immortalized CDCs as well as revealed TGF-β inhibitor-SB431542 treatment induced expression changes. We identified hTERT immortalization could result the cell proliferation and cell cycle related genes upregulation in iCDC. KEGG results demonstrated that TGF-β inhibitor SB431542 treatment could inhibit cardiomyopathy-related pathway which indicate TGF-β signaling pathway may serve as new target for cardiomyopathy therapy, and iCDC could be used as a heart-related chemicals screening.

overall_design: Primary CDCs, iCDCs and SB432542-treated iCDCs mRNA profiles were generated by deep sequencing, in triplicate, using Illumina HiSeq2000.

first: Zhenglong

last: Guo


title: FACS-sorted GFP-positive ureteric bud (UB) cells at postnatal day 0 (P0): wildtype (WT) vs. conditional Dot1-knockout (KO) from Hoxb7-positive cells

summary: Transcriptional profiling of GFP-positive UB cells from Hoxb7CreGFP mice without (WT) or with (KO) homozygously floxed DOT1 alleles at the age of postnatal 0. This experiment aimed to uncover the genome-wide alternation in gene expression resulting from the removal of DOT1 gene in the collecting duct cell population (Hoxb7 positive) and successive changes to the series of events in kidney development.

overall_design: Two-condition experiment, Dot1 WT vs. KO UB cells. Biological replicates: 4 WTs and 4 KOs.


title: Transcriptome-wide maps of m6A methylation in mouse embryonic and postnatal cerebral cortex

status: Public on Dec 13 2019

city: Fuzhou

first: Long-Bin

last: zhang

state: Fujian

address: Jianping Road

department: College of Biological Science and Engineering

institute: Fuzhou University

summary: We report the applicatin of Methylation RNA Immunoprecipitation with Next Generation Sequencing (MeRIP-seq) technology for high-throughput status of m6A methylation modifications in mouse embryonic and postnatal cerebral cortices. By data analysis, we provided the distinct status of m6A methylation between embryonic and postnatal cortices.

overall_design: m6A methylation status of wild-type (WT) mouse cerebral cortex at embryonic day 13 and postnatal day 14

first: L

last: Zhang

first: T

last: Sun


title: RNA-seq of P. aeruginosa clinical isolate collection under biofilm growth conditions

status: Public on Jan 21 2020

city: Hanover

first: Susanne

last: Häußler

address: Feodor-Lynen-Str. 7

department: Molecular Bacteriology

institute: Twincore

summary:
Purpose : The goal of this study was to use RNA-seq to compare transcriptional profiles under biofilm conditions with planktonic growth and explore the correlation of gene expression of a collection of clinical P. aeruginosa isolates to various phenotypes, such as biofilm structure or virulence.
Methods : mRNA profiles were generated for Pseudomonas aeruginosa clinical samples derived from various geographical locations by deep sequencing. The removal of ribosomal RNA was performed using the Ribo-Zero Bacteria Kit (Illumina) and cDNA libraries were generated with the ScriptSeq v2 Kit (Illumina). The samples were sequenced in single end mode on an Illumina HiSeq 2500 device or paired end mode on an Illumina Novaseq 6000. mRNA reads were trimmed and mapped to the NC_008463.1 (PA14) reference genome from NCBI using bowtie2 with default settings.

overall_design: mRNA profiles from Pseudomonas aeruginosa derived from static biofilm cultures grown for 12h to 48h in 96-well microtiter plates or planktonic LB cultures grown to an OD600 = 2 and deep sequenced using Illumina HiSeq 2500/NovaSeq 6000.

first: Janne

middle: G

last: Thöming

first: Jürgen

last: Tomasch

first: Sven

last: Willger


title: Identified  differentially expressed lncRNAs in Type 1 Diabetes Patients

city: Beijing

first: yihan

last: liu

address: No.10 Xitoutiao, Youanmen, Fengtai District

institute: Capital Medical University

summary: Long noncoding RNAs (lncRNAs) is already evidently involved in a variety of biological functions and pathophysiological mechanisms underlying the diabetes. However, the role of lncRNAs in the type 1 diabetes (T1D) has not been explored clearly yet. The aim of this study was to determine  the circulating lncRNA profile and confirmed the differentially expressed lncRNA between T1D patients and healthy control.

overall_design: Leukocyte lncRNA profiles of healthy control and T1D patients were generated by deep sequencing

first: Xiaoyan

last: Du

first: Yihan

last: Liu


title: Purity Independent Subtyping of Tumors (PurIST), a clinically robust single-sample classifier for tumor subtyping in pancreatic cancer (RNA-Seq)

status: Public on Dec 10 2019

first: Xianlu

last: Peng

summary:
Purpose: Molecular subtyping for pancreatic cancer has made substantial progress in recent years, facilitating the optimization of existing therapeutic approaches to improve clinical outcomes in pancreatic cancer. With advances in treatment combinations and choices, it is becoming increasingly important to determine ways to place patients on the best therapies upfront. Although various molecular subtyping systems for pancreatic cancer have been proposed, consensus regarding proposed subtypes, as well as their relative clinical utility, remains largely unknown and presents a natural barrier to wider clinical adoption.

Methods: We assess three major subtype classification schemas in the context of results from two clinical trials and by meta-analysis of publicly available expression data to assess statistical criteria of subtype robustness and overall clinical relevance. We then developed a single-sample classifier (SSC) using penalized logistic regression based on the most robust and replicable schema.

Results: We demonstrate that a tumor-intrinsic two-subtype schema is most robust, replicable, and clinically relevant. We developed Purity Independent Subtyping of Tumors (PurIST), a SSC with robust and highly replicable performance on a wide range of platforms and sample types. We show that PurIST subtypes have meaningful associations with patient prognosis and have significant implications for treatment response to FOLIFIRNOX.

Conclusions: The flexibility and utility of PurIST on low-input samples such as tumor biopsies allows it to be used at the time of diagnosis to facilitate the choice of effective therapies for patients with pancreatic ductal adenocarcinoma and should be considered in the context of future clinical trials.

overall_design:
Analysis of gene expression in pancreatic adenocarcinoma (PDAC).
Yeh_seq: For primary PDAC tumors, data include 47 flash frozen (FF), 5 formalin-fixed and paraffin embedded (FFPE) and 45 fine-needle aspiration (FNA) ; for patient derived xenograft (PDX), data include 18 FF, 7 FFPE and 3 FNA samples.
Linehan_seq: 66 PDAC biopsies were subjected to sequencing.

first: Jen Jen

last: Yeh

first: Naim

middle: U

last: Rashid


title: Bevacizumab may differentially improve ovarian cancer outcome in patients with proliferative and mesenchymal molecular subtypes

status: Public on Nov 08 2019

city: Rochester

first: Sean

last: Dowdy

state: Minnesota

address: 200 First St. SW

department: Obstetrics and Gynecology

institute: Mayo Clinic

overall_design:
DASL gene expression arrays were performed on FFPE tissue from patients enrolled on the ICON7 trial. Patients were stratified into four TCGA molecular subtypes. Associations between molecular subtype and the efficacy of randomly assigned therapy with bevacizumab were assessed.

Standard treatment: CARBOPLATIN PLUS PACLITAXEL CHEMOTHERAPY
Bevacizumab treatment: CARBOPLATIN PLUS PACLITAXEL CHEMOTHERAPY PLUS BEVACIZUMAB

The primary endpoints in the ICON7 trial used to measure treatment efficacy were OS and PFS.

OS: Overall survival was calculated from the date of randomization to the date of death from any cause; data for patients still alive were censored at the date the patient was last known to be alive.
final_ostm = time in days
final_osid = 1=dead, 0=alive

PFS: Progression-free survival was calculated from the date of randomization to the date of the first indication of disease progression or death, whichever occurred first; the data for patients who were alive without disease progression were censored as of the date of their last assessment.
final_pfstm = time in days
final_pfsid = 1=event, 0=no-event

first: Boris

last: Winterhoff

first: Stefan

last: Kommoss


title: Transcriptomic characterisation of phenotypic haematopoietic stem cells from human adult bone marrow, spleen and peripheral blood

status: Public on Jan 14 2020

city: Cambridge

first: Hugo

middle: P.

last: Bastos

address: Jeffrey Cheah Biomedical Centre, Puddicombe Way

department: Haematology

institute: Wellcome - MRC Cambridge Stem Cell Institute

summary: Haematopoietic stem cells (HSCs) and multipotent progenitors (MPPs), the precursors of all blood cells, reside predominantly in the bone marrow (BM). Recent evidence suggests that other anatomical sites may contribute significantly to blood production, but the cellular, molecular and functional composition of extramedullary HSC/MPP pools remains unexplored. Here, we have compared the transcriptomes of single cells sorted from the phenotypic HSC/MPP pool of adult bone marrows and spleens from the same donors.

overall_design: Examination of the genome-wide transcriptome of  single HSC/MPPs isolated from paired bone marrow (BM) and spleen (SPL) from 2 deceased organ donors.

first: Elisa

last: Laurenti

middle: P

first: Nicole

last: Mende

first: Kourosh

last: Saeb-Parsy

first: Krishnaa

last: Mahbubani

first: Abbie

last: Curd


title: p300 and CBP are essential for skeletal muscle homeostasis, contractile function and survival

status: Public on Dec 12 2019

city: La Jolla

first: Simon

last: Schenk

state: California

address: 9500 Gilman Drive #0863

department: Orthopaedic Surgery

institute: University of California San Diego

summary: Reversible ε-amino acetylation of lysine residues regulates transcription as well as metabolic flux; however, roles for specific lysine acetyltransferases in skeletal muscle physiology and function is unknown. In this study, we investigated the role of the related acetyltransferases p300 and CBP in skeletal muscle transcriptional homeostasis and physiology in adult mice. These data reveal that p300 and CBP are required for the control and maintenance of contractile function and transcriptional homeostasis in skeletal muscle, and ultimately, organism survival.

overall_design: Mice with skeletal muscle-specific and inducible knockout of p300 and CBP (PCKO) were treated with tamoxifen via oral gavage for 5 days, starting at 13-15 weeks of age. At the day after the last tamoxifen gavage, mice were sacrificed after a 4 hour fast, and tissues were excised and snap-frozen. RNA was profiled in Extensor digitorum longus muscles using Agilent SurePrint G3 Mouse GE 8x60K Microarrays according to the manufacturer's instructions. There were 4 mice each in the control (wildtype) and PCKO groups.

first: Kristoffer

last: Svensson

first: Andrew

last: Philp


title: Transcriptomic Analysis Of circRNAs/miRNAs/mRNAs upon Middle East Respiratory Syndrome Coronavirus (MERS-CoV) infection

status: Public on Nov 30 2019

city: Hong Kong

first: Hein Min

last: Tun

address: Prince of Wales Hospital, Shatin

country: Hong Kong

institute: CUHK

summary: Human circular RNAs can function in competing endogenous RNA (ceRNA) network by sponging miRNA and regulating gene expression. Viruses are evolved to regulate noncoding RNAs such as miRNAs and circRNAs to facilitate their propagation and pathogenesis. Studies on how host ceRNAs upon human coronavirus infection were scarce, and the functions of circRNAs during the infection of Middle East respiratory syndrome coronavirus (MERS-CoV)  has not been deeply revealed. Therefore, we conducted a whole transcriptional profile (RNA-seq) analysis to compare the expression of circRNAs, miRNAs and mRNAs between the mock-infected and MERS-CoV-infected human lung adenocarcinoma (Calu-3) cells. Integrated analysis of ceRNAs revealed putative viral pathogenic circRNAs induced by MERS-CoV and their interplay with miRNAs and genes. Our study offered new insights into the mechanisms of interplays of MERS-CoVs and hosts, and established a model promising to be applied to other coronavirus or other viruses for the identification of novel host factors.

overall_design: The expression of cirRNA, miRNA and mRNA were examined in triplicate samples of Middle east respiratory syndrome coronavirus (MERS-CoV) infected (6hpi and 24hpi) and mock infected human lung adenocarcinoma (Calu-3) cells. A mRNA library, a small RNA library and an Ribodepleted, RNase R treated circRNA library were constructed, followed by deep sequencing on Illumina Hiseq X-Ten platform.

first: Xi

last: Zhang

first: Hin

last: Chu

first: Jasper

middle: F

last: Chan

first: Kwok-Yung

last: Yuen


title: Reconstruction of the global neural crest gene regulatory network in vivo [single cell]

status: Public on Oct 09 2019

city: Oxford

first: Tatjana

last: Sauka-Spengler

state: Oxfordshire

address: Radcliffe Department of Medicine

department: University of Oxford

institute: MRC Weatherall Institute of Molecular Medicine

summary: Precise control of developmental processes is encoded in the genome in the form of gene regulatory networks (GRNs). Such multi-factorial systems are difficult to decode in vertebrates owing to their complex gene hierarchies and transient dynamic molecular interactions. Here we present a genome-wide in vivo reconstruction of the GRN underlying development of neural crest (NC), an emblematic embryonic multipotent cell population. By coupling NC-specific epigenomic and single-cell transcriptome profiling with genome/epigenome engineering in vivo, we identify multiple regulatory layers governing NC ontogeny, including NC-specific enhancers and super-enhancers, novel trans-factors and cis-signatures. Assembling the NC regulome has allowed the comprehensive reverse engineering of the NC-GRN at unprecedented resolution. Furthermore, identification and dissection of divergent upstream combinatorial regulatory codes has afforded new insights into opposing gene circuits t hat define canonical and neural NC fates. Our integrated approach, allowing dissection of cell-type-specific regulatory circuits in vivo, has broad implications for GRN discovery and investigation.

overall_design: Single cell transcriptional and epigenomic profilling of avian neural crest cells isolated from their in vivo context at 6ss and 7ss stages.

first: Ruth

middle: M

last: Williams

first: Ivan

last: Candido-Ferreira

first: Emmanouela

last: Repapi

first: Daria

last: Gavriouchkina

first: Upeka

last: Senanayake

first: Jelena

last: Telenius

first: Irving

last: Ling

first: Stephen

last: Taylor

first: Jim

last: Hughes


title: Comparative transcriptomic characterisation of canine prostate fine-needle-aspiration and tissue samples - from sampling to sequencing

status: Public on Oct 08 2019

city: Graz

first: Leila

last: Taher

address: Stremayrgasse 16/I

country: Austria

institute: Graz University of Technology

summary:
Ultrasound-guided fine-needle aspiration (US-FNA) biopsy is a widely used minimally invasive sampling procedure for cytological diagnosis. This study investigates the feasibility of using US-FNA samples for both cytological diagnosis and whole transcriptome RNA-sequencing analysis (RNA-Seq), with the ultimate aim of improving canine prostate cancer management.
The feasibility of the US-FNA procedure was evaluated intra vitam on 43 dogs. Additionally, aspirates from 31 euthanised dogs were collected for standardising the procedure. Each aspirate was separated into two subsamples: for cytology and RNA extraction. Additional prostate tissue samples served as control for RNA quantity and quality evaluation, and differential expression analysis. The US-FNA sampling procedure was feasible in 95% of dogs. RNA isolation of US-FNA samples was successfully performed using phenol-chloroform extraction. The extracted RNA of 56% of a subset of US-FNA samples met the quality requirements for RNA-seq. Expression analysis revealed that only 153 genes were exclusively differentially expressed between non-malignant US-FNAs and tissues. Moreover, only 36 differentially expressed genes were associated with the US-FNA sampling technique and unrelated to the diagnosis. Furthermore, the gene expression profiles clearly distinguished between non-malignant and malignant samples. This proves US-FNA to be useful for molecular profiling.

overall_design: Fine-needle aspirates of the canine prostate: non-malignant (n=5) and malignant (n=2); canine prostate tissues: non-malignant (n=9) and malignant (n=9). Aspirates and tissue samples of the canine prostate were used for RNA-sequencing. Non-malignant prostate tissue samples were used as control. Differentially expressed genes were used for evaluation of similarities and differences in aspirates and canine prostate tissues.

first: Hugo

last: Escobar

first: Ingo

last: Nolte

first: Heike

last: Thiemeyer

first: Jan

last: Schille

first: Julia

last: Beck

first: Ekkehard

last: Schütz

first: Bertram

last: Brenig

first: Marion

last: Hewicker-Trautwein

first: Reinhard

last: Mischke

first: Stephan

middle: O

last: Hungerbuehler

first: Lisa

last: Harder

first: Zdzislaw

last: Kielbowicz


title: A technique to detect native R-loops genome-wide without immunoprecipitation

status: Public on Oct 18 2019

city: Philadelphia

first: Roberto

last: Bonasio

state: PA

address: 3400 Civic Center Blvd - SCTR 9-111

department: Cell and Developmental Biology

institute: University of Pennsylvania

summary: We adapted the nuclease-targeting approach CUT&RUN (Skene & Henikoff, eLife 2017) to map R-loops in vivo. We show that this approach accurately identifies R-loops that are sensitive to both Actinomycin D and RNase H and largely overlap with previously identified regions containing R-loops. We also show that MapR can identify R-loops genome-wide from much smaller input material than existing techniques.

overall_design: DNA fragments from R-loop were relased by incubating nuclei with GST-RNAseH∆-Mnase in vitro (MapR), where ∆ indicates a mutation that kills the catalytic activity of RNase H. As a control, we incubated the nuclei with GST-Mnase lacking the RNase H moiety (MapR control). We also compared these results with those obtained by expressing a catalytically inactive RNase H fused to the FLAG epitope tag directly in cells and then performing a more conventional CUT&RUN assay (Skene & Henikoff, eLife 2017) using an anti-FLAG antibody. In that case the control is performing the CUT&RUN assay with a non-specific IgG control.

first: Qinqing

last: Yan

first: Emily

last: Shields

first: Kavitha

last: Sarma


title: The differentially long noncoding RNAs and mRNA in the hippocampus of Nrf2-knockout mice

status: Public on Aug 22 2019

city: Shijiazhuang

first: Lei

last: Wang

address: Hebei Medical University, No. 361, Zhongshan East Road, Chang'an District

country: China

institute: Heibei Medical University

type:
Non-coding RNA profiling by array
Expression profiling by array

summary: Non-coding long noncoding RNAs (lncRNAs)  and mRNA have displayed dysregulated expression in the hippocampus of Nrf2-knockout mice.

overall_design:
Arraystar Mouse LncRNA Microarray V3.0 (Rockville, MA, USA) is designed for the global profiling of mouse lncRNAs and protein-coding transcripts, which is updated from the previous Microarray V2.0. About 35,923 lncRNAs and 24,881 coding transcripts can be detected by the third-generation lncRNA microarray.
To compare the profile differences in the hippocampus tissues between Nrf2 (+/+) and Nrf2 (-/-) mice.

first: Shaoguang

last: Sun


title: Phospho-antibody microarray analyses for islets of control and  Mettl14 knock-out mice

status: Public on Aug 09 2019

city: Boston

first: Hui

last: Pan

address: 1 Joslin Place

department: Bioinformatics and Biostatistics Core

country: USA

institute: Joslin Diabetes Center

summary: β-cell specific Mettl14 knock-out mice display reduced N6-methyladenosine (m6A) levels and recapitulate human Type II diabetes (T2D) islet phenotype with early diabetes onset and mortality secondary to decreased β-cell proliferation and insulin degranulation. To gain insights into the role of m6A in regulating the IGF1/insulin -> AKT - > PDX1 pathway and to dissect the signaling networks modulating AKT phosphorylation,  we subjected freshly isolated islets from control and Mettl14 knock-out mice to phospho-antibody microarrays.

overall_design: Mettl14fl/fl mice on a C57BL/6N background was created and provided by Dr. Chuan He (University of Chicago). To obtain β-cell specific Mettl14 knock-out mice, Mettl14fl/fl mice were breed with B6(Cg)-Ins1tm1.1(cre)Thor/J (Jackson Labs, USA) and male mice wild-type for nicotinamide nucleotide transhydrogenase (Nnt) mutation were used. Mice were weaned at 3 weeks of age and maintained on a chow diet (PicoLab® mouse diet 20 – 5058). Islet isolations were performed in anesthetized mice and their pancreas infused with liberase (Roche, Germany). Following incubation at 37C for 17 min the digested pancreases were washed filtered through a 400µm filter and run on a Histopaque (Sigma, USA) gradient. The purified islets were handpicked, counted and cultured overnight in 7mM glucose RPMI media (Gibco, USA) containing 10% FBS and 1% PS (Gibco, USA). Islets were handpicked, washed 2 times with ice-cold DPBS by self-sedimentation.  Protein lysates from 200 size-matched islets from each sample (4 control pools and 2 Mettl14 knock-out pools) were used for Kinex™ KAM-1325 antibody microarray analyses.

first: Dario

last: De Jesus

first: Rohit

middle: N

last: Kulkarni


title: N6-methyladenosine (m6A) profiling of EndoC-bH1 cell line and RNA seq of Mettl14 knockout mice beta cell

city: CHICAGO

first: Zijie

last: Zhang

state: IL

department: Chemistry

institute: University of Chicago

summary: In type 2 diabetes, pancreatic beta-cells fail to compensate for the presence of insulin resistance in target tissues and represent a central player in the disease development. Identifying and studying innovative molecular mechanisms that lead to beta-cell failure in diabetes represent an interesting line of research and are necessary. N6-Methyladenosine (m6A) is the most abundant modification in mRNA and is found virtually in all mammals. Through m6A-profiling of m6A methyltransferase depleted animal model and human beta cell model, we aim to characterize the pathways affected by m6A methylation in the beta cells.

overall_design: Total RNA was extracted from the tissue by TRIzol. mRNA was enriched by polyT beads followed by fragmentation with Bioruptor ultrasonicator. m6A-immunoprecipitation were performed using EpiMark N6-Methyladenosine enrichment kit (NEB cat. E1610S). Kapa RNA hyper kit for Illumina was used to construct library from  mRNA for input RNA and eluted RNA from the  m6A-IP. The libraries were sequenced by the Hiseq4000 platform at SE50 mode.

last: DeJesus

first: Chuan

last: He


title: N6-methyladenosine (m6A) profiling of type II diabetes islets

summary: In type 2 diabetes, pancreatic beta-cells fail to compensate for the presence of insulin resistance in target tissues and represent a central player in the disease development. Identifying and studying innovative molecular mechanisms that lead to beta-cell failure in diabetes represent an interesting line of research and are necessary. N6-Methyladenosine (m6A) is the most abundant modification in mRNA and is found virtually in all mammals. Through m6A-profiling, we aim to characterize the dynamic RNA methylation changes in islets obtained from patients with type 2 diabetes.

overall_design: MeRIP-seq profiling of T2D islets


title: Human CD11b+ macrophages - Aging of hematopoietic stem cells is driven by regional specialization of marrow macrophages

status: Public on Jun 10 2019

first: Laura

last: Calvi

address: 601 Elmwood Ave

institute: University of Rochester Medical Center

summary: The human aged hematopoietic system is prone to dysfunction and clonal selection. Aged hematopoietic stem cells (HSCs) have well-defined characteristics, but the contribution of the bone marrow microenvironment (BMME) to HSC ageing is unclear. We identify age-dependent changes in bone-associated (BA) and marrow-associated (MA) cell populations in murine and human marrow, where only aged MA cells induce aged HSC characteristics. MA aged macrophages (Mφs) could impart aged characteristics to both HSC and BMME populations, and demonstrated decreased ability to engulf senescent neutrophils. Moreover, removal of Mφs from young mice rapidly induced aged HSC characteristics. Interleukin-1β (IL-1β), a cytokine that is restrained when Mφs engulf apoptotic cells, was a key mediator of microenvironmental HSC aging. These data define a previously unknown role for aged MA Mφs to orchestrate BMME and HSC changes. Mφs and IL-1β may therefore represent novel targets for preventing or reversing hematopoietic defects due to advanced age.

overall_design: mRNA profiles of human macrophages (CD45+, CD163+, CD11b+, Side-Scatter-Low) from central marrow (CM)  and spicule associated cells (SAC) isolated from the marrow aspirate of healthy human donors by Illumina HiSeq 2500 sequencing.

first: Corey

last: Hoffman

first: Sarah

last: Latchney

first: Mark

last: LaMere

first: Jason

last: Myers

first: John

last: Ashton

first: Allison

last: Li

first: Frank

last: Akwaa

first: Rakhil

last: Rubinova

first: Amanda

last: McCabe

first: Julianne

last: Smith

first: Jane

last: Liesveld

first: Benjamin

last: Frisch

first: Michael

last: Elliott

first: Katherine

last: MacNamara

last: Becker


title: Mouse CD11b+ macrophages - Aging of hematopoietic stem cells is driven by regional specialization of marrow macrophages

overall_design: mRNA profiles of CD11b+ macrophages from bone marrow  and bone associated cells were generated from three individual mice by Illumina HiSeq 2500 sequencing.


title: Cancer-Causing Mutations in SF3B1 Alter Splicing by Disrupting Interaction with SUGP1

status: Public on Jul 24 2019

city: NewYork

first: Zhaoqi

last: Liu

address: ICRC Building 8th Floor, Office 803B 1130 St. Nicholas Ave

department: Systems Biology

institute: Columbia university

summary: SF3B1, which encodes an essential spliceosomal protein, is frequently mutated in myelodysplastic syndromes (MDS) and many cancers. However, the defect of mutant SF3B1 is unknown. Here, we analyzed RNA-sequencing data from MDS patients and confirmed that SF3B1 mutants use aberrant 3' splice sites. To elucidate the underlying mechanism, we purified complexes containing either wild-type or the hotspot K700E mutant SF3B1, and found that levels of a poorly studied spliceosomal protein, SUGP1, were reduced in mutant spliceosomes. Strikingly, SUGP1 knockdown completely recapitulated the splicing errors, whereas SUGP1 overexpression drove the protein, which our data suggests plays an important role in branchsite recognition, into the mutant spliceosome and partially rescued splicing. Other hotspot SF3B1 mutants showed similar altered splicing and diminished interaction with SUGP1. Our study demonstrates that SUGP1 loss is the sole defect of mutant SF3B1 spliceosomes and, since this defect can be rescued, suggests possibilities for therapeutic intervention.

overall_design: 15 MDS samples with varying SF3B1 status

first: Abdullah

last: Ali