title: Stromal upregulation of SOX2 promotes tumorigenesis through the generation of a SFRP1/2-expressing cancer-associated fibroblast population [scRNA-seq II]

first: Jorge

last: Moscat

summary: Although how CAFs impact the tumor epithelium is being progressively unveiled,  transcriptional processes of lineage plasticity in fibroblasts govern the acquisition of the CAF phenotype are much less understood. Here we show that the upregulation of SOX2 is a critical step in this process, which is negatively regulated by the atypical protein kinase (aPKC) PKCz. We demonstrate that the loss of PKCz is essential for the acquisition of the CAF phenotype and for the induction of the desmoplastic and more aggressive phenotype of intestinal tumors in a SOX2-dependent manner. Furthermore, we show here that the loss of PKCz drives the reprogramming of colon stromal fibroblasts into two different subpopulations that express either the Wnt regulators Sfrp1/2 or osteopontin, both ligands positively impinging into the mesenchymal and stem cell activation programs.

overall_design: Orthotopic tumors of Mouse tumor organoids (MTOs) with WT sgScr, Prkcz-/- sgScr or Prkcz-/- sgSfrp2 colon fibroblasts in cecum were harvested and digested into single cells.

first: Hiroaki

last: Kasashima

first: Angeles

last: Duran

first: Yuki

last: Nakanishi

first: Anxo

last: Martinez-Ordoñez

first: Hiroto

last: Kinoshita

first: Juan

last: Linares

first: Miguel

last: Reina-Campos

first: Yotaro

last: Kudo

first: Antoine

last: L'Hermitte

first: Masakazu

last: Yahiro

first: Masaichi

last: Ohira

first: Daniele

last: Tauriello

first: Eduard

last: Batlle

first: Maria

last: Diaz-Meco


title: Global gene networks of canine monocyte-derived macrophages infected with Mycobacterium intracellulare

status: Public on Sep 24 2020

city: Seoul

first: Suji

last: Kim

state: Gwanak-gu

address: 1, Gwanak-ro

department: Veterinary Medicine

country: South Korea

institute: Seoul National University

type: Expression profiling by high throughput sequencing

summary: An opportunistic intracellular pathogen Mycobacterium intracellulare, a member of the nontuberculous mycobacteria (NTM) cluster, causes respiratory disease in immunosuppressed hosts, including companion dogs. The purpose of this study is to investigate a host-M.intracellulare interactome in canine monocyte-derived macrophages during the infection.

overall_design: Monocyte-derived macrophges (MDMs) were isolated from buffy coats of ten healthy beagle dogs by density gradient centrifugation. MDMs were stimulated with M. intracellulare. Total RNAs were extracted from the cells at 0, 6, 24, and 72h after infection. The construction of library was performed using QuantSeq 3’mRNA-Seq Library Prep Kit. High-throughput sequencing was performed as single-end 75 sequencing using NextSeq 500.

first: Han

middle: S

last: Yoo


title: Identification of genes with different expression in wild- and half-size Xenopus laevis embryos by transcriptome comparison

status: Public on Sep 29 2020

city: Moscow

first: Evgeny

middle: E

last: Orlov

address: Miklukho-Maklaya 16/10

department: Department of Genomics and Postgenomic Technologies

country: Russia

institute: Shemyakin-Ovchinnikov Institute of Bioorganic Chemstry, RAS

summary: To identify genes with different expression levels in Xenopus laevis embryos of different sizes, RNAseq of middle gastrula RNA of the wild-size and artificially prepared half-size embryos was done. As a result, several genes with drastically different expression between these two types of embryos were found.

overall_design: Three biological replicates were analyzed for 2 conditions (intact embryos vs their siblings divided at two-blastomere stage)

first: Eugeny

first: Andrey

last: Zaraisky


title: Myeloid specific ASXL2 deletion limits diet induced obesity by regulating energy expenditure

status: Public on Jan 23 2021

city: St Louis

first: nidhi

last: rohatgi

state: MO

address: 660 S Euclid Ave

department: pathology and immunology

country: USA

institute: washington university in st. louis

summary: We previously reported that global deletion of the Enhancer of Trithorax and Polycomb (ETP) gene, Asxl2, attenuates osteoclast differentiation and also completely protects mice from HFD-induced weight gain.  To determine role of this gene specifically in myeloid compartment, ASXL2flox mice were bred with LysM cre (Asxl2LysM).   Bone marrow-derived macrophages (BMM) were cultured for 2 days with or without Rank-ligand (RANKL). We characterized the transcriptomic profiles of BMMs and  osteoclast by performing unbiased RNA-sequencing. The expression profiles of both macrophages and osteoclast was significantly distinct between two genotypes. In particular, Enrichr analysis of differentially expressed genes (DEG) reveals substantial downregulation of those associated with extracellular matrix (ECM) organization, collagen formation, cytokine-cytokine interaction and inflammatory response including genes encoding TNFα, MMPs and CXCLs, in Asxl2LysM BMMs. In contrast, cell cycle and mitosis related genes are upregulated. The fact that most of the dominant downregulated genes are also implicated in modulating adipose tissue inflammation and fibrosis, supports the concept that genetic deletion of ASXL2, in myeloid cells, may modify obesity.

overall_design: Examination of transcriptional profiles of macrophages and osteoclast derived from ASXL2flox and ASXL2LysM mice

first: Nidhi

last: Rohatgi

first: Wei

last: Zou

first: Steven

middle: L

last: Teitelbaum


title: Description of transcriptome in non-small cell lung cancer cell lines without KEAP1/NRF2 mutations in response to an electrophilic reagent dimethylmaleate (DEM)

status: Public on Sep 23 2020

city: Sendai

first: Hozumi

last: Motohashi

address: 2-1 Seiryo-machi, Aoba-ku

department: Medical Biochemistry

country: Japan

institute: Tohoku University

summary: We report DEM-induced changes in the transcriptome of ABC1 and HCC4006 cell lines.

overall_design: RNA-seq analysis in 2 cell types (ABC1 and HCC4006) after treatment with DEM or vehicle (DMSO).

first: Keito

last: Okazaki

first: Hayato

last: Anzawa

first: Fumiki

last: Katsuoka

first: Hiroki

last: Sekine

first: Ikuko

last: Motoike

first: Shu

last: Tadaka

first: Kengo

last: Kinoshita


title: NRF2-dependent transcriptome and H3K27ac distribution in non-small cell lung cancer

type: Genome binding/occupancy profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Single-cell transcriptomic sequencing of BCMA CAR-T cells during CAR-T therapy in refractory primary plasma cell leukemia

status: Public on Oct 01 2020

city: Hangzhou

first: Xue

last: Li

state: Zhejiang

address: yuhangtang road

country: China

institute: zhejiang University

summary: Chimeric antigen receptor T-cell (CAR-T) therapy has revolutionized the clinical treatment of hematological malignancies due to the prominent anti-tumor effects. B-cell maturation antigen (BCMA) CAR-T cells have demonstrated promising effects in patients with relapsed/refractory multiple myeloma. However, the dynamics of CAR-T cell proliferation and cytotoxicity in a patient remains largely unexplored. Single-cell RNA sequencing samples were collected at three phases: CAR-T products before infusion, CAR-T on day 8 after infusion, and CAR-T on day 15 after infusion. After obtaining the PBMCs for each phase, CAR-T and endogenous T cells were collected by fluorescence-activated cell sorting with anti-Mouse IgG Biotin, FITC Streptavidin, and anti-human CD3 APC.

overall_design: ScRNA-seq libraries were generated from the 10X Chromium Single Cell 3 Reagent Kits v2 (PN-120237) according to the manufacturer’s protocol (10x Genomics). Libraries were sequenced on the Illumina Hiseq X10 platform according to the manufacturer’s instructions (Illumina). Read 1 and Read 2 (paired end) were 150 bp, and the index primer was 8 bp.

first: Xin

last: Guo

first: Yongxian

last: Hu

first: He

last: Huang


title: Regulation of cholesterol biogenesis by the glucose-sensing transcription factor MondoA is required for zebrafish epiboly

status: Public on Sep 11 2020

city: Lausanne

first: Benjamin

middle: D

last: Weger

state: VD

address: Station 15

department: SV

country: Germany

institute: EPFL


title: Contribution of NRF2 to genome-wide distribution of H3K27ac deposition in A549 cells, a non-small cell lung cancer cell line with KEAP1 mutation

summary: We report NRF2-dependent and -independent enhancers by comparing H3K27ac deposition in A549 cells with and without NRF2 knockdown.

overall_design: ChIP-seq analysis of A549 cells treated with NRF2 siRNA or control siRNA with anti-H3K27ac antibody.


title: Description of NRF2-dependent transcriptome in non-small cell lung cancer cell lines with KEAP1 mutations

summary: We report NRF2-dependent changes in the transcriptome of A549, H460 and H2023 cell lines.

overall_design: RNA-seq analysis in 3 cell types (A549, H460 and H2023) after introduction of NRF2 siRNA or control siRNA.


title: Transcriptional profiling of the prefontal cortex and nucleus accumbens of mice upon chronic stress

status: Public on Sep 20 2020

summary: Mitochondrial dysfunction was highlighted as a crucial vulnerability factor for the development of depression. However, systemic studies assessing stress-induced changes in mitochondria-associated genes in brain regions relevant to depression symptomatology remain scarce. Here, we performed a genome-wide transcriptomic study to examine mitochondrial gene expression in the prefrontal cortex (PFC) and nucleus accumbens (NAc) of mice exposed to multimodal chronic restraint stress. We identified mitochondria-associated gene pathways as most prominently affected in the PFC and with lesser significance in the NAc. A more detailed mitochondrial gene expression analysis revealed that in particular mitochondrial DNA-encoded subunits of the oxidative phosphorylation complexes were altered in the PFC. The comparison of our data with a reanalyzed transcriptome data set of chronic variable stress mice and major depression disorder subjects showed that the changes in mitochondrial DNA-encoded genes are a feature generalizing to other chronic stress-protocols as well and might have translational relevance. Finally, we provide evidence for changes in mitochondrial outputs in the PFC following chronic stress that are indicative of mitochondrial dysfunction. Collectively, our work reinforces the idea that changes in mitochondrial gene expression are key players in the prefrontal adaptations observed in individuals with high behavioral susceptibility and resilience to chronic stress.

overall_design: Mitochondrial gene signature in the prefrontal cortex for differential susceptibility to chronic stress

first: Meltem

first: Daniel

last: Alpern

first: Antoine

last: Cherix

first: Sriparna

last: Ghosal

first: Jocelyn

last: Grosse

first: Julie

last: Russeil

first: Rolf

last: Gruetter

first: E

middle: R

last: de Kloet

first: Bart

last: Deplancke

first: Carmen

last: Sandi


title: RNA-seq of mondoa zebrafish morphants

summary: The glucose-sensing Mondo pathway regulates expression of metabolic genes in mammals. Here, we have revealed an unexpected role of this pathway in vertebrate embryonic development. We characterized Mondo pathway function in the zebrafish and showed that knock-down of mondoa impaired the early morphogenetic movement of epiboly in zebrafish embryos. Expression of nsdhl , an enzyme of cholesterol and pregnenolone synthesis, was strongly reduced in these embryos. Loss of Nsdhl function likewise impaired epiboly and led to microtubule cytoskeleton defects in the embryo, similar to MondoA loss of function. Both epiboly and microtubule cytoskeleton defects were partially restored by pregnenolone treatment. Gene disruption of mondoa perturbed epiboly with only partial penetrance, likely due to compensatory changes in the expression of cholesterol/steroid metabolism genes. Collectively, our results show a novel role for MondoA in the regulation of early vertebrate development, connecting glucose, cholesterol and steroid hormone metabolism with early embryonic cell movements.

overall_design: RNA-seq in mondoa zebrafish morphants

first: M

first: B

first: A

last: Schink

last: Takamiya

first: J

last: Stegmaier

first: C

last: Gobet

last: Parisi

middle: Y

last: Kobitski

last: Mertes

first: N

last: Krone

first: U

last: Straehle

first: G

middle: U

last: Nienhaus

first: R

last: Mikut

first: P

last: Gut

first: T

last: Dickmeis


title: Stromal upregulation of SOX2 promotes tumorigenesis through the generation of a SFRP1/2-expressing cancer-associated fibroblast population [Quant-seq]

status: Public on Nov 17 2020

city: New York

first: Jorge

last: Moscat

state: NY

address: 1188 York Avenue

department: Pathology and Laboratory Medicine

institute: WEILL CORNELL MEDICINE

overall_design: WT sgScr, Prkcz-/- sgScr and Prkcz-/- sgSox2 colon fibroblasts were profiled in four biological replicates under normal conditions.

first: Hiroaki

last: Kasashima

first: Angeles

last: Duran

first: Yuki

last: Nakanishi

first: Anxo

last: Martinez-Ordoñez

first: Hiroto

last: Kinoshita

first: Juan

middle: F

last: Linares

first: Miguel

last: Reina-Campos

first: Yotaro

last: Kudo

first: Antoine

last: L'Hermitte

first: Masakazu

last: Yahiro

first: Masaichi

last: Ohira

first: Daniele

middle: V

last: Tauriello

first: Eduard

last: Batlle

first: Maria

middle: T

last: Diaz-Meco


title: DNA methylation signatures of adolescent victimization: Analysis of a longitudinal monozygotic twin sample.

status: Public on Dec 15 2020

city: London

first: Chloe

last: Wong

state: Select a State or Province

address: MRC SGDP Centre, Institute of Psychiatry,

country: United Kingdom

institute: King's College London

summary: Genome-wide patterns of DNA methylation were quantified using the Illumina Infinium EPIC array (“EPIC array”) in DNA samples isolated from buccal swabs collected at ages 5, 10 and 18 and whole blood samples collected at age 18 from 118 Monozygotic twin pairs from the Environmental Risk (E-Risk) Longitudinal Twin Study. Comparison of DNA methylation profiles of 233 age 18 blood samples with data on EPIC and Illumina 450K methylation arrays.

overall_design: Bisulphite converted DNA from the 944 samples were hybridised to the Illumina Infinium HumanMethylation850 BeadChip; raw data (preQC folder->raw idats folder; Phenotype_file_944preQC.csv), processed files (betas_normalised.csv, pheno.csv). Overlapping samples (N=233) had methylation data on two DNA methylation arrays -EPIC and 450K, we compared the methylation profiles of these samples to assess the correlation between the two arrays using two strategies: -(1)When these samples were normalized together (raw files for EPIC array data are in  preQC folder->raw idats folder; Overlaping_probes_normalised_together_450K_EPIC_pheno.csv, raw idats for 450K are in folder raw_idats_450k, processed betas for both arrays file (Overlaping_probes_normalised_together_450K_EPIC_betas.csv) (2) When these samples were normalized separately - only overlapping probes on both arrays for the common samples were analysed - processed betas file for 450K array (Overlaping_probes_normalised_seperately_450K_betas.csv, Overlaping_probes_normalised_seperately_450K_pheno.csv) and EPIC array (Overlaping_probes_normalised_seperately_EPIC_betas.csv, Overlaping_probes_normalised_seperately_EPIC_pheno.csv). Categories description: 1 - MZ discordant twins exposed to adolescence victimisation, 2 - MZ concordant twins unexposed to adolescence victimisation, and 3 - MZ concordant twins exposed to adolescent victimisation

first: Radhika

last: Kandaswamy

middle: C


title: Gene expression analysis of dissociated and FDG FACS-sorted mammary glands of 16 week old nulliparous AXL +/LacZ  and AXL LacZ/LacZ  mice (B6.129P2-AXLtm1Dgen  strain, Jackson Labs)

status: Public on Aug 25 2020

city: Bergen

first: Pouda

middle: Panahandeh

last: Strømland

address: Jonas Lies Vei 91

country: Norway

institute: University of Bergen

summary: The receptor tyrosine kinase AXL is associated with epithelial plasticity in several solid tumors including breast cancer and AXL-targeting agents are currently in clinical trials. We hypothesized that AXL is a driver of stemness traits in cancer by co-option of a regulatory function normally reserved for stem cells. AXL-expressing cells in human mammary epithelial ducts co-expressed markers associated with multipotency, and AXL inhibition abolished colony-formation and self-maintenance activities while promoting terminal differentiation in vitro. Axl-null mice did not exhibit a strong developmental phenotype, but enrichment of Axl+ cells was required for mouse mammary gland reconstitution upon transplantation, and Axl-null mice had reduced incidence of Wnt1-driven mammary tumors. An AXL-dependent gene signature is a feature of transcriptomes in basal breast cancers, and reduced patient survival irrespective of subtype. Our interpretation is that AXL regulates access to epithelial plasticity programs in MaSCs and, when coopted, maintains acquired stemness in breast cancer cells.

overall_design:
Gene expression analysis of FDG FACS-sorted 16 week old nulliparous AXL +/LacZ  and AXL LacZ/LacZ  (B6.129P2-AXLtm1Dgen  strain, Jackson Labs) was conducted using the Illumina MouseWG-6 v2.0 Expression BeadChip (BD-201-0202, BD-201-0602).

AXL-expressing cells were enriched from dissociated mammary glands by FACS using the fluorogenic β -galactosidase substrate fluorescein Di-β-D-galactopyranoside (FDG; FluoReporter® lacZ Flow Cytometry Kit, Molecular Probes F-1930). All samples are pooled mammary glands from several individuals of the same genotype. The following sorting strategy were used: freshly dissociated, labelled cells were discriminated from the debris and gated in the forward scatter (FSC-A) and side scatter (SSC-A) plots. Subsequently, the forward scatter Width (FSC-W) versus FSC-A plots were used for doublet cell exclusion. Propidium iodide (PI) staining was used for dead cell discrimination and the APC channel was used as a dump channel for the APC conjugated lineage markers used. Thus, only single, viable, PI-negative, and APC-negative (CD45-, CD31-, CD11b-) cells were included in the final sort of FDG-high and FDG-low cells used for subsequent experiments. An FDG high gate (highest 5%) was used to enrich for AXL-expressing cells, while AXL-negative cells were sorted using an FDG low gate (lowest 65%). A post-sort analysis was performed to verify purity of the sorted cells.
Log2 quantile normalized of the gene expression data were used for unsupervised hierarchical clustering, gene signature analysis and differentially expressed genes. Hierarchical clustering was performed using Pearson’s correlation as distance measurement. Gene signatures among cell population were determined by comparing the gene expression levels and available molecular signatures of the mammary cell subpopulations (Lim et al., 2009) using GSEA software package (Subramanian et al., 2005). Differentially expressed genes between AXL +/LacZ  FDG high  and AXL LacZ/LacZ  FDG high  cell groups were identified using Rank Product method. The genes with a p-value <0.01 and fold change >= 1.5 were considered as differentially expressed genes.

first: Agenete S.T.

last: Egelsen

first: Katarzyna

last: Wnuk-Lipinska

first: Sebastian

last: Bougnaud

first: Noëlly

last: Madeleine

first: Fanny A

last: Pelissier Vatter

first: Crina

last: Tiron

first: Rene

last: Villadsen

first: Masaru

last: Miyano

first: Maria L

last: Lotsberg

last: Panahandeh

first: James

last: Lorens

first: Nils

last: Halberg

first: Mark

last: LaBarge


title: α-ketogluatrate inhibits osteoclastogenesis

status: Public on Aug 04 2020

city: seoul

first: Jueng Soo

last: You

address: 120 Neungdong-ro

institute: Konkuk University

summary: Transcriptome analysis after treating dimethyl α-ketogluatrate during osteoclastogenesis

overall_design: Treating 1mM dimethyl α-ketogluatrate to mouse bone marrow derived macrophages during their differentiation to osteoclasts

first: Juen

first: Sangyong

last: Lee


title: Protein Kinase 𝜆/𝜄 suppresses liver cancer by repressing autophagy and oxidative phosphorylation in hepatocytes [DH]

status: Public on Jun 30 2020

first: Jorge

last: Moscat

summary: Oxidative stress plays a critical role in liver tissue damage and in hepatocellular carcinoma (HCC) initiation and progression. However, the mechanisms that regulate autophagy and metabolic reprogramming during the generation of reactive oxygen species (ROS), and how ROS promotes tumorigenesis, still need to be fully understood. We show that protein kinase C (PKC) 𝜆/𝜄 loss in hepatocytes promotes autophagy and oxidative phosphorylation. This results in ROS generation, which through NRF2 drives HCC cell autonomously and non-autonomously. Although PKC𝜆/𝜄 promotes tumorigenesis in oncogene-driven cancer models, emerging evidence demonstrate that it is a tumor suppressor in more complex carcinogenic processes. Consistently, PKC𝜆/𝜄 levels negatively correlate with HCC histological tumor grade, establishing this kinase as a tumor suppressor in liver cancer.

overall_design: Hepatic mRNA profiles of 36-week old wild-type (Prkcif/f) and hepatocyte-specific Protein Kinase  𝜆/𝜄-KO (Prkcif/fAlbCre) mice with diethylnitrosamine (DEN, 25 mg/kg) injection (i.p.) at 2 weeks of age followed by 60% fat diet (HFD) feeding from 4 to 36 weeks of age.

first: Yotaro

last: Kudo

first: Angeles

last: Duran

first: Maria

last: Diaz-Meco


title: Protein Kinase 𝜆/𝜄 suppresses liver cancer by repressing autophagy and oxidative phosphorylation in hepatocytes.


title: Trancriptome profiling of human OCI-AML3 AML cell line stably transfected by pMEP4-Empty or pMEP4-RhoH plasmids, respectively.

status: Public on Aug 03 2020

city: lille

first: frédéric

last: leprêtre

address: Boulevard du Pr Leclercq

department: CHU of Lille, CBP

country: France

institute: Lille University

summary: Transcriptome profiling of Human OCI-AML3 cell line with low RhoH expression, stably transfected either by Empty or by RhoH sur-expressing vectors.

first: Carl

last: Shelley

first: Sylvie

last: Galiègue-Zouitina


title: Integrating single-cell RNA-seq and imaging with SCOPE-seq2

status: Public on Jun 28 2020

first: Peter

last: Sims

address: 3960 Broadway

institute: Columbia University

summary: Live cell imaging allows direct observation and monitoring of phenotypes that are difficult to infer from the transcriptome. However, existing methods for linking microscopy and single-cell RNA-seq (scRNA-seq) have limited scalability. Here, we describe an upgraded version of Single Cell Optical Phenotyping and Expression (SCOPE-seq2), which builds on our earlier efforts to combine single-cell imaging and expression profiling, with substantial improvements in throughput, molecular capture efficiency, linking accuracy, and compatibility with standard microscopy instrumentation. We introduce improved optically decodable mRNA capture beads and implement a more scalable and simplified optical decoding process. We demonstrated the utility of SCOPE-seq2 for fluorescence, morphological, and expression profiling of individual primary cells from a human glioblastoma (GBM) surgical sample, revealing relationships between simple imaging features and cellular identity, particularly among malignantly transformed tumor cells.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Perfromed SCOPE-seq v2 on mixed human (U87) and mouse (3T3) cells, and cells collected from human glioblastoma.

first: Jinzhou

last: Yuan

first: Zhouzerui

last: Liu


title: Transcriptomic changes of sigmoidal gut biopsies in psoriasis patients and healthy subjects

city: San Francisco

first: Hsin-Wen

last: Chang

state: CA

address: 2340 Sutter Street

department: Dermatology

institute: UCSF

summary: This study aims to understand the systemic component of psoriasis pathogenesis since psoriasis patients have higher risk of developing diesases beyond skin inflammation. In this study, we collected sigmoidal gut biopsies to profile host transcriptomic changes associated with psoriasis patients and healthy subjects. This exepriment provided transcriptomic dataset of host response and is integrated  with fecal metagenomic data and flow cytometry dataset as part of the multi-omic study.

overall_design: Total RNA isolated from snip biopsies of sigmoidal colon and used for whold transcriptome RNAseq. The RNAseq analysis was done with 16 healthy subjects and 26 psoriasis patients.

first: Wilson

last: Liao


title: Methylation data from stored peripheral blood leukocytes from African American participants in the GENOA study

status: Public on Aug 31 2020

city: Ann Arbor

first: Minjung

last: Kho

state: Michigan

address: School of Public Health University of Michigan 1415 Washington Heights

institute: University of Michigan

summary: African-American individuals of the GENOA cohort

overall_design: Participants in this study are drawn from the GENOA study, a population-based study from Jackson, Mississippi

first: Sharon

last: Kardia

first: Jennifer

middle: A

last: Smith


title: Gene expression analysis from placenta of Cornelia de Lange Syndrome (CdLS) mouse models

status: Public on Jul 27 2020

city: Kansas City

first: Madelaine

last: Gogol

address: 1000 E. 50th Street

department: Computational Biology Core

institute: Stowers Institute

summary: CdLS is caused by mutaion in cohesin and associated proteins, such as Nipbl and Hdac8. We performed RNA seq analysis from Nipbl+/- and Hdac8-/0 placenta with their respective wild type control at 14.5 dpc, to identify molecular pathways affected. To understand the effect of protein kinase R (PKR) on gene expression we also performed RNA seq analysis from Nipbl+/- and Hdac8-/0 placenta lacking PKR.

overall_design: Total RNA was isolated using Trizol method and cDNA was prepatred using TruSeq Stranded Total RNA LT kit (RS-122-2302) for Illumina sequencing.

first: Vijay

middle: P

last: Singh

last: Gerton


title: Protein Kinase 𝜆/𝜄 suppresses liver cancer by repressing autophagy and oxidative phosphorylation in hepatocytes [RD]

first: Jorge

last: Moscat

summary: Oxidative stress plays a critical role in liver tissue damage and in hepatocellular carcinoma (HCC) initiation and progression. However, the mechanisms that regulate autophagy and metabolic reprogramming during the generation of reactive oxygen species (ROS), and how ROS promotes tumorigenesis, still need to be fully understood. We show that protein kinase C (PKC) 𝜆/𝜄 loss in hepatocytes promotes autophagy and oxidative phosphorylation. This results in ROS generation, which through NRF2 drives HCC cell autonomously and non-autonomously. Although PKC/ promotes tumorigenesis in oncogene-driven cancer models, emerging evidence demonstrate that it is a tumor suppressor in more complex carcinogenic processes. Consistently, PKC𝜆/𝜄 levels negatively correlate with HCC histological tumor grade, establishing this kinase as a tumor suppressor in liver cancer.

overall_design: Hepatic mRNA profiles of 28-week old wild-type (Prkcif/f) and hepatocyte-specific Protein Kinase  𝜆/𝜄-KO (Prkcif/fAlbCre) mice fed with regular chow

last: Kudo


title: Identification of 3 Endotypes In Pediatric ARDS Using Nasal Transcriptomics-Low Input

status: Public on Jun 23 2020

city: Cincinnati

first: Brian

middle: Michael

last: Varisco

state: OH

address: 3333 Burnet Avenue, MLC 7006

department: Critical Care Medicine

institute: Cincinnati Children's Hospital Medical Center

summary: This study used nasal transcriptomic profiling of the inferior turbinate in control and pediatric ARDS subjects to identify endotypes. This data set is for amplified specimens. The study identfied three pediatric ARDS endotypes.

overall_design:
Prospective, observational clinical trial of gene expression of in nasal brushings in control and pediatric ARDS subjects
Endotype definitions:
A1 and A2 are both baseline endotypes
B is an innate inflammatory endotype
C is ciliary and microtubule dysfunction endotype


title: Identification of 3 Endotypes In Pediatric ARDS Using Nasal Transcriptomics-Standard Input

summary: This study used nasal transcriptomic profiling of the inferior turbinate in control and pediatric ARDS subjects to identify endotypes. This data set is for non-amplified specimens. The study identfied three pediatric ARDS endotypes.

overall_design:
Prospective, observational clinical trial of gene expression of in nasal brushings in control and pediatric ARDS subjects
Endotype definitions:
A is baseline endotype
B is an innate inflammatory endotype
C is ciliary and microtubule dysfunction endotype


title: NRF2 Activates Growth Factor Genes and Downstream AKT Signaling to Induce Mouse and Human Hepatomegaly (RNA-seq dataset 2)

status: Public on Apr 28 2020

summary: The goal of this study is to provide the liver metabolic changes in the liver specific constitutively NRF2 activated (Nrf2Act-hep) mice

overall_design: RNAs were extracted from livers of 6 week-old Wild Type (WT) B6 and Nrf2Act-hep mice for RNA-seq analysis.

first: Feng

last: He

first: Miguel

last: Reina-Campos

first: Angeles

last: Duran Molina

last: Diaz-Meco

first: Michael

last: Karin


title: Identification of 3 Endotypes In Pediatric ARDS Using Nasal Transcriptomics

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

overall_design: Refer to individual Series


title: NRF2 Activates Growth Factor Genes and Downstream AKT Signaling to Induce Mouse and Human Hepatomegaly


title: RNA-seq of mondoa zebrafish mutants

first: Benjamin

last: Weger

overall_design: RNA-seq  in mondoa zebrafish mutants

first: Meltem

first: Andrea

last: Schink

first: Masanari

last: Takamiya

first: Johannes

last: Stegmaier

first: Cedric

last: Gobet

first: Alice

last: Parisi

first: Anrei

last: Kobitski

first: Jonas

last: Mertes

first: Nils

last: Krone

first: Uwe

last: Straehle

first: G

last: Nienhaus

first: Ralf

last: Mikut

first: Philipp

last: Gut

first: Thomas

last: Dickmeis


title: Hippocampal Subregion Transcriptomic Profiles Associated with Age-Related Changes in Spatial Pattern Separation

status: Public on May 22 2020

city: Gainesville

first: Tom

last: Foster

state: FL

address: 1149 Newell Drive

institute: University of Florida

summary: Previous studies of age-related transcriptional changes indicate that cognitive impairments are associated with differentially expressed genes DEGs linked to defined neural systems; however, studies that examine multiple regions of the hippocampus fail to find major links between behavior and transcription in the dentate gyrus DG. The DG is implicated in pattern separation PS and exhibits multiple age-related changes that may affect PS performance. We hypothesize that an age-related decline in PS performance is associated with distinct changes in transcriptional profile, most strongly within the DG compared to other hippocampal subregions. We used a water maze beacon discrimination task to characterize PS in young 5 mo and middle-age 12 mo male F344 rats, followed by a spatial reference memory test. Middle-age rats showed consistent deficits in discriminating two identical beacons compared to young. Reference memory was not different between these two age groups. Interestingly, with increasing spatial overlap between the cues, older animals appeared to compensate for impaired PS performance though greater reliance on spatial reference memory. mRNA sequencing of hippocampal subregions DG, CA1, and CA3 indicated that the DG of middle-age rats expressed more genes correlated with PS performance. In contrast, reliance on a spatial reference memory was associated with differential expression of genes in regions CA1 and CA3. These results indicate that the beacon task is sensitive to PS impairment as early as middle-age, and distinct gene profiles are observed in neural circuits that underlie different strategies used to solve the task.

overall_design: Transcription was performed on young and middle-age F344 male rats in individual hippocampal subregions DG, CA1 and CA3. There were 84 samples 28 per brain region x 3 brain regions total for both age groups.

first: Garrett

last: Smith

first: Asha

last: Rani

first: Ashok

last: Kumar

first: Jolie

last: Barter


title: Decoding drought tolerance mechanisms in Holm oak (Quercus ilex) throught a combined transcriptomics and proteomics analysis

status: Public on Apr 03 2020

city: Cordoba

first: Victor

middle: Manuel

last: Guerrero-Sanchez

state: Spain

address: Medina Azahara

department: Biochemistry and Molecular Biology

country: Spain

institute: University of Cordoba

summary: Transcript profiling of leaves from Quercus ilex seedlings subjected to well-watering and drought-stress (irrigation withdrawal) conditions

overall_design: Leaf mRNA from 6 month seedlings control and after 17 and 24 days of drought imposed by irrigation withdrawal were generated by deep sequencing, using Illumina HiSeq 4000

middle: M


title: Genome-wide roles of DNA methyltransferases in mouse embryos

status: Public on May 20 2020

city: Illkirch

first: Michael

last: Weber

address: 300 Bd Sebastien Brant

department: UMR7242 Biotechnology and Cell Signalling

institute: CNRS

type: Methylation profiling by high throughput sequencing

summary: Mouse embryos acquire global DNA methylation of their genome during implantation. However the exact roles of DNA methyltransferases (DNMTs) in embryognesis have not been studied comprehensively. Here we systematically analyze the consequences of genetic inactivation of Dnmt1, Dnmt3a and Dnmt3b on the methylome and transcriptome of mouse embryos and fibroblasts.

overall_design:
We mapped DNA methylation by Whole Genome Bisulfite Sequencing (WGBS) in two independent WT, Dnmt1-/- and Dnmt3a-/- Dnmt3b-/- (DKO) E8.5 embryos. We also sequenced RRBS libraries from three Dnmt1-/- (D1KO_Rep1-3) and WT (D1WT_Rep1-3) littermate E8.5 embryos, as well as three Dnmt3a-/- Dnmt3b-/- (DKO_Rep1-3) together with two WT (D3abWT_Rep1-2), three Dnmt3a-/+ (D3aHet_Rep1-3), three Dnmt3a-/+ Dnmt3b-/+ (D3abHet_Rep1-3) littermate E8.5 embryos.

To study the role of DNMT3A/B and DNMT1 in maintenance methylation, we generated Dnmt3aL2/L2; Dnmt3bL2/L2; CreERT2 and Dnmt1L2/L2; CreERT2 immortalized mouse embryonic fibroblasts (MEFs). The CreERT2 recombinase is activated by tamoxifen treatment to generate Dnmt3a Dnmt3b double conditional knockout (cDKO) and Dnmt1 conditional knockout (D1cKO) MEFs. We performed three independent tamoxifen induction experiments and profiled DNA methylation by RRBS in cells treated with Tamoxifen (Tam_Rep1-3) or not treated with Tamoxifen (noTam_Rep1-3) at various time points of culture (day 23 and day 69 for cDKO MEFs, day 5 and day 7 for D1cKO MEFs).

The transcriptome of Dnmt mutant embryos was analyzed by RNA-seq. We sequenced RNA-seq libraries from three Dnmt1-/- (D1KO_Rep1-3) and three WT (D1WT_Rep1-3) littermate E8.5 embryos, as well as six Dnmt3a-/- Dnmt3b-/- E8.5 embryos (DKO_Rep1-6) together with two WT (D3abWT_Rep1-2) and four Dnmt3a-/+ (D3aHet_Rep1-4) littermate controls.

last: Dahlet


title: Substrate stiffness effects on mRNA and lncRNA expression in mouse embryonic cardiomyocytes

status: Public on Apr 18 2020

city: Boulder

first: Corey

last: Neu

state: Colorado

address: 427 UCB - Mechanical Engineering, 1111 Engineering Drive

department: Mechanical Engineering

institute: University of Colorado, Boulder

type: Non-coding RNA profiling by high throughput sequencing

summary: Cardiomyocytes develop abnormal beating patterns and dedifferentiate on substrate with stiffness other than the physiological heart properties. This effect can be replicated in vitro with primary cardiomyocyte. To get a better idea of pathways involved and to identify new target genes, we aimed to compare mRNA and lncRNA of embryonic cardiomyocytes plated on either soft or stiff substrates

overall_design: Primary embryonic cardiomyocytes were harvested from H2b-eGFP carrying mouse embryos at E18.5 and plated on either physiological soft (~10 kPa) or stiff (~150kPa) PDMS substrates (see puplication for accurate stiffness values)

first: Benjamin

last: Seelbinder


title: NRF2 Activates Growth Factor Genes and Downstream AKT Signaling to Induce Mouse and Human Hepatomegaly (RNA-seq dataset 1)

first: Jorge

last: Moscat

summary: Transcriptional changes induced by adenovirus p62 induced NRF2 activation in the mouse liver.

overall_design: 7 days after the liver-specific p62 knock out mice were injected with adenovirus-GFP, p62 wild type, or p62KIR mutant. Liver samples were collected from the adenovirus infected livers or uninfected control livers.

first: Shinichiro

last: Yamachika

first: Miguel

last: Reina-Campos

first: Angeles

last: Molina

first: Maria

last: Diaz-Meco


title: Ectonucleotidase CD39 is highly expressed on ATLL cells and is responsible for their immunosuppressive function.

status: Public on Apr 16 2020

city: Suita

first: Daisuke

last: Okuzaki

state: Osaka

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

institute: Osaka univ.

summary: Adult T-cell leukemia/lymphoma (ATLL) patients are in severely poor prognosis partially because of their immunosuppressive state. As majority of patients have leukemic cells with the similar phenotype with Tregs, some reports have suggested that ATLL cells themselves have immunosuppressive functions. However, hitherto, there are controvertial discussions. In this study, we found that CD39 is expressed on some of ATLL cells, especially highly on those of aggressive subtypes.

overall_design: We compared whole transcriptome of leukemic cells and that of normal CD4+ cells, using RNA-seq technologies.

first: Yasuhiro

last: Nagate


title: Global changes in human neutrophil transcriptome profile during Filifactor alocis challenge

status: Public on Apr 06 2020

city: Louisville

first: Eric

middle: Christian

last: Rouchka

state: Kentucky

address: 522 East Gray Street

department: Biochemistry and Molecular Genetics

institute: University of Louisville

summary: Periodontitis is a multifactorial chronic inflammatory infectious disease with a high prevalence in the adult population in the USA. Until recently, research into periodontitis focused primarily on putative pathogens such as Porphyromonas gingivalis. However, a reappraisal of microbial etiology has marked a turning point in the field due to the development of culture-independent techniques that allow the identification of bacterial species directly from nucleic acids. Filifactor alocis, a Gram positive anaerobic oral bacterium, has emerged as an important periodontal pathogen. Neutrophils are recruited in high numbers to the gingival tissue, where they are linked with protection against periodontal disease. However, periodontal pathogens evolved different strategies to resist neutrophil microbicidal mechanisms while propagating inflammation, which affords a source of nutrients. The goal of this study was to determine the global changes in human neutrophil gene expression induced by F. alocis challenge.  RNA-sequencing analysis shows that F. alocis-challenge alters human neutrophil transcriptome including expression of genes associated with regulation of Toll-Like Receptor signaling pathway, MAPK signaling pathway, apoptosis, cytokines and chemokines, among other neutrophil effector functions.

overall_design: A total of 16 samples were submitted for RNA-sequencing analysis. Those 16 samples corresponded to four independent donors, with four experimental conditions, as outlined on the treatment protocol section, per donor. Unstimulated neutrophils were used as negative controls.

first: Aruna

last: Vashishta

first: Richard

middle: J

last: Lamont

first: Xiaohong

last: Li

first: Silvia

last: Uriarte


title: MYC Dysregulates Mitotic Spindle Function Creating a Dependency on TPX2

status: Public on Mar 30 2020

first: Andrei

last: Goga

address: 513 Parnassus Ave

department: Cell & Tissue Biology


title: Gene expression analysis of EuMyc lymphoma cells after MYC inactivation

summary: Tumors that overexpress the MYC oncogene frequently demonstrate aneuploidy, numerical chromosome alterations associated with highly aggressive cancers, rapid tumor evolution, and poor patient outcome. Here, we identify that MYC overexpression induces defects in microtubule nucleation and mitotic spindle assembly, promoting chromosome segregation defects, micronuclei and chromosomal instability (CIN). High TPX2 expression is permissive for mitotic spindle assembly and chromosome segregation in cells with MYC overexpression; whereas TPX2 depletion blocks mitotic progression, induces cell death and prevents tumor growth. Attenuating MYC expression reverses mitotic defects, even in established tumor cell lines, implicating an ongoing role for high MYC in the persistence of CIN in tumors. Our studies implicate the MYC oncogene as a regulator of spindle assembly and identify a new MYC-TPX2 synthetic-lethal interaction that could represent a future therapeutic strategy in MYC-overexpressing cancers. Moreover, our studies suggest that blocking MYC activity can attenuate the emergence of CIN and tumor evolution.

overall_design: Cells were grown in the absence (MYC ON, reference samples) of doxycycline and presence of doxycycline for three days (MYC OFF). Three biological replicates of each condition were performed.

first: Julia

last: Rohrberg

first: Aaron

middle: N

last: Chang


title: Gene expression analysis of MTBTOM tumors

overall_design: MTB-TOM (MMTV-rtTA/TetO-MYC) mice were bred and maintained off of doxycycline. At 12-15 weeks of age, female mice were put on doxycycline to induce MYC expression and tumorigenesis. Tumors at 1 cm at any single dimension were flash frozen in liquid nitrogen. Mice were put off doxycycline when tumors reached 1 cm for three days to switch off MYC expression (regressed tumor). Mammary glands from mice that were never on doxycycline were taken as control tissue.

first: Sanjeev

last: Balakrishnan

first: Alicia

last: Zhou


title: Gene expression in islets from βUCP2Tg mice and WT mice

status: Public on Mar 21 2020

city: yokohama

first: Ryota

last: Inoue

address: Fukuura 3-9, Kanazawa-ku

department: Endcriology and Metabolism

institute: Yokohama City University

summary: To investigate a role of UCP2 in pancreatic β-cells, we  performed whole genome microarray in islets from βUCP2Tg mice, which overexpressed UCP2 in specifically β-cells.

overall_design: Isolated islets from βUCP2Tg mice or WT mice were incubated at 200 mg/dL glucose for 8 hours.

first: Jun

last: Shirakawa

first: Yu

last: Togashi


title: Expression analysis of Wild-type and circKcnt2-deficient ILC3s from DSS-treated mice

status: Public on Dec 31 2019

city: Beijing

first: Benyu

last: Liu

state: Beijing

address: 15, Datun Road, Chaoyang district

department: The CAS key Laboratory of Infection and Immunity, Institute of Biophysics

institute: Institute of Biophysics, CAS

summary: Investigation of differentially expressed genes in  circKcnt2-deficient ILC3s

overall_design: Gene expression profiling using LinCD90highCD45low ILCs from DSS-treated circKcnt2-deficient mice or WT littermates. Total RNA from each sample was quantified using the NanoDrop ND-1000. The sample preparation and microarray were performed in accordance with the Affymetrix Mouse Gene2.0 analysis protocol (Affymetrix).

first: Zusen

last: Fan


title: A transcriptomics investigation into embryo development and dormancy in Ginkgo biloba

status: Public on Jan 17 2020

city: Yangzhou

first: Biao

last: Jin

state: Jiangsu

address: Wenhui east road no. 48

department: College of Horticulture and Plant Protection

institute: Yangzhou University

summary: We sequenced mRNA from the different development stage of G. biloba embryo using the Illumina HiSeq 4000 platform to generate the transcriptome dynamics to explore ginkgo embryo development mechanism of post-maturation and lay the foundation for revealing the molecular mechanisms of seed dormancy and germination of G. biloba seed.

overall_design: Transcriptome sequencing in different development stage of G. biloba embryo.

first: Li

last: Wang

first: Zhichao

last: Jia


title: Single-cell transcriptomic atlas of FACS-sorted mouse muscle tissue cells

status: Public on Jan 11 2020

city: Ithaca

first: Andrea

last: De Micheli

address: 161 Weill Hall

department: Biomedical Engineering

institute: Cornell University

summary: We report a series of single-cell transcriptomic datasets of FACS-sorted mouse muscle tissue cells from injured muscle produced using the Chromium 10X technology.

overall_design: The overall objective of the study was to generate a transcriptomic atlas of FACS-sorted mouse muscle cell populations at different timepoints post notexin-injury using single-cell RNA-sequencing.

first: Benjamin

middle: D

last: Cosgrove


title: Human cytomegalovirus IE2 drives transcription initiation from a select subset of late infection viral promoters by host RNA polymerase II

status: Public on Mar 05 2020

city: Iowa City

first: David

middle: H

last: Price

state: IA

address: 431 Newton Road

department: Department of Biochemistry and Molecular Biology

institute: University of Iowa

summary: Herpesvirus late promoters activate gene expression after viral DNA synthesis has begun. Alphaherpesviruses utilize a viral immediate-early protein to do this, whereas beta- and gammaherpesviruses primarily use a 6-member set of viral late-acting transcription factors (LTF) that are drawn to a TATT sequence in the late promoter. The betaherpesvirus, human cytomegalovirus (HCMV), produces three immediate-early 2 protein isoforms, IE2-86, IE2-60, IE2-40, in late infection, but whether they activate late viral promoters is unknown. Here, we quickly degrade the IE2 proteins in late infection and analyze effects on transcription using customized PRO-Seq and computational methods combined with multiple validation methods. We discover that the IE2 proteins selectively drive RNA Pol II transcription initiation at a subset of viral early-late and late promoters common to different HCMV strains, but do not substantially affect Pol II transcription of the 9,942 expressed host genes. Most of the IE2-activated viral late infection promoters lack the TATT sequence bound by the HCMV UL87-encoded LTF. The HCMV TATT-binding protein is not mechanistically involved in late RNA expression from the IE2-activated TATT-less UL83 (pp65) promoter, as it is for the TATT-containing UL82 (pp71) promoter. While antecedent viral DNA synthesis is necessary for transcription from the late infection viral promoters, continued viral DNA synthesis is unnecessary. We conclude that the IE2 proteins target a distinct subset of late infection HCMV promoters for transcription initiation by RNA Pol II. Commencement of viral DNA replication renders the HCMV genome late promoters susceptible to late-acting viral transcription factors, which do not appreciably affect host transcription during this late time.

overall_design: In this study, we assessed the effects of IE2 depletion late in HCMV infection. We analyzed 19 PRO-Seq datasets from HFF that were infected with HCMV strains Towne or TB40. We show that the effects of IE2 depletion on viral gene transcription are reproduced in the context of infection with different HCMV strains. Replicate analyses of the effects of IE2 depletion in the context fo TB40 infection were performed.  This series includes re-analysis of GSM3104912, an uninfected HFF PRO-seq sample.  The re-analyzed processed data .bw files are available at the foot of this record.

first: Ming

last: Li

first: Christopher

middle: B

last: Ball

first: Geoff

last: Collins

first: Qiaolin

last: Hu

first: Donal

middle: S

last: Luse

first: Jeffery

middle: L

last: Meier


title: A single-cell RNA-seq atlas of the pathogenic stage of Schistosoma mansoni identifies a key regulator of blood feeding [scRNA-Seq]

status: Public on Mar 11 2020

city: Dallas

first: George

last: Wendt

state: TX

address: 6001 Forest Park Road, ND7.300

department: Pharmacology

institute: University of Texas Southwestern Medical Center

summary: In order to better understand  the biology of adult schistosomes, we performed single-cell RNAseq on adult male, adult sexually-mature female, and adult virgin female parasites.

overall_design: Adult parasites were dissociated then live, single cells were sorted by FACS. Single-cell RNAseq libraries were generated from these cells, then these libraries were sequenced. Further data processing was carried out in Seurat as desribed in the associated manuscript.

middle: R

first: Lu

last: Zhao

first: James


title: circRNA expression files in ILC3s after DSS treatment

status: Public on Dec 17 2019

first: Benyu

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

summary: To explore the role of circRNAs during ILC3-driven colitis, we isolated ILC3s from DSS treated or control Rag1-/- mice. Then circRNA microArray analysis were performed and differentially expressed circRNAs were identified.

overall_design: Total RNAs from ILC3s were isolated and used for microarray through Arraystar Mouse circRNA Array V2 (8x15K, Arraystar).


title: Selective Translation Complex Profiling in yeast and human Reveals Staged Initiation and Co-translational Assembly of Initiation Factor Complexes

status: Public on Jun 25 2020

city: Canberra

first: Susan

last: Wagner

state: ACT

address: 131 Garran Road

department: The John Curtin School of Medical Research

country: Australia

institute: Australian National University

sample_organism:
Saccharomyces cerevisiae
Homo sapiens

platform_organism:
Saccharomyces cerevisiae
Homo sapiens

overall_design: Refer to individual Series


title: Peripheral clonal expansion of T lymphocytes associates with tumour infiltration and response to cancer immunotherapy

status: Public on Dec 09 2019

city: South San Francisco

first: Thomas

middle: D.

last: Wu

address: 1 DNA Way

institute: Genentech, Inc.

summary: We performed single-cell RNA sequencing (scRNA-seq) and deep analysis of T cell receptor (TCR) clonotypes (scTCR-seq) in cancer patients across several indications, assessing the profiles of TCRs in the various populations of T cells in tumours, normal adjacent tissue (NAT), and peripheral blood.  In a subset of patients, we find clear evidence of clonotypic expansion of T effector-like cells not only within the tumour but also in NAT.

overall_design:
Single-cell RNA-seq and single-cell TCR-seq of pretreatment samples from 14 cancer patients, taken from tumor, normal adjacent tissue, and peripheral blood
------------------------------------------------------
The authors have submitted the raw data to EGA: EGAS00001003993 (scRNA-seq) and and EGAS00001003994 (scTCR-seq)

first: Shravan

last: Madireddi

first: Patricia

middle: E

last: de Almeida

first: Romain

last: Banchereau

first: Ying-Jiun

last: Chen

first: Avantika

last: Chitre

first: Eugene

middle: Y

last: Chiang

first: Hina

last: Iftikhar

first: William

last: O'Gorman

first: Amelia

last: Au-Yeung

first: Chikara

last: Takahashi

first: Leonard

last: Goldstein

first: Chungkee

last: Poon

first: Shilpa

last: Keerthivasan

first: Denise

last: de Almeida Nagata

first: Xiangnan

last: Du

first: Hyang-Mi

last: Lee

first: Karl

last: Banta

first: Sanjeev

last: Mariathasan

first: Meghna

last: Das Thakur

first: Mahrukh

last: Huseni

first: Marcus

last: Ballinger

first: Ivette

last: Estay

first: Patrick

last: Caplazi

first: Zora

last: Modrusan

first: Lelia

last: Delamarre

first: Ira

last: Mellman

first: Richard

last: Bourgon

first: Jane

last: Grogan


title: Genome-wide occupancy of chromatin remodeller SMARCAL1 and BRG1 in human cells

status: Public on Sep 12 2019

city: New Delhi

first: Rohini

last: Muthuswami

address: Room# 333, School of Life Sciences, JNU

department: School of Life Sciences

country: India

institute: Jawaharlal Nehru University

summary: In this study we report genome wide occupancy of SMARCAL1 and BRG1 in control HeLa cells. Our analysis showed binding of these two remodellers on DNA damage response gene, chromatin remodellers, cell cycle and apoptosis regulating genes.

overall_design: Chromatin immunoprecipitation of SMARCAL1 and BRG1 was done using polyclonal and monoclonal antibodies respectively and subjected to high-throughput next generation sequencing on illumine platform.

first: R

last: Rakesh

first: Saddam

last: Hussain

first: Deepa

last: Bisht

first: Upasna

last: Chanana


title: Transcriptomic comparison of young and aged choroid at the bulk and single-cell levels (single cells)

status: Public on Apr 23 2020

first: Andrew

last: Voigt

state: Iowa

address: 375 Newton Road

summary:
Purpose: The goals of this study were to identify cell specific expression patterns from infant and aged choroid, with a particular emphasis on how endothelial gene expression changes with age.
Methods: Independent libraries were prepared for infant and adult choroidal cells from four human donors. Macular and peripheral samples from single-cell donors 18-21 were acquired, analyzed, and uploaded in a previous experiment (GSE135922). In single-cell donors 22-25, new reads were acquired from a 12-mm macula-centered punch. Choroidal punches gently dissociated in collagenase II for 1 hours before cryopreservation. Thawed cells were enriched endothelial cells by incubating with anti-CD31-microbeads. Both CD31-positive and CD31-negative libraries from single-cell donors 22-25 were sequenced on an Illumina NovaSeq system. Sequenced reads were mapped to the human genome build hg19 with CellRanger(v3.0.1) and filtered to remove cells likely to be doublets or cells with a high proportion of mitochondrial reads. Libraries from single-cell donors 22-25 were aggregated with donors 18-21 using canonical correlation analysis. Feature selection was performed with the variance stabilizing transformation before integration was performed with Seurat (v3.0.1).
Results: A total of 37,070 cells were recovered after filtering with 415,740,738 corresponding reads. A total of 17,229 cells were recovered from infant libraries while 19,841 cells were recovered from the adult libraries. Clusters were assigned to known choroidal cell types based on expression of distinguishing marker genes. Differential expression analysis identified genes enriched in each population of cells originating from infant versus adult libraries. Particular emphasis was given to genes enriched in infant choriocapillaris endothelial cells.
Conclusions: This study provides a transcriptomic comparison of infant and aged human donor choroid at the bulk and single-cell levels. The aged choroid, in particular the aged vasculature, is enriched in pro-inflammatory genes.

overall_design: mRNA profiles for thousands of cells from infant and adult choroidal isolates were generated from four donor eyes (single-cell donors 22-25) using 10X Genomics Chromium single-cell system followed by sequencing on an Illumina NovaSeq.

first: Todd

last: Scheetz

first: Robert

middle: F

last: Mullins


title: small RNA Seq of Subcutaneous adipose tissue from endothelial-AGO1-knockout (EC-AGO1-KO) mice and wild-type (WT) littermates fed 16 week of high fat high sucrose diet

status: Public on Sep 06 2019

city: La Jolla

first: Sheng

last: Zhong

state: California

address: 9500 Gilman Drive, MC 0412

department: Department of Bioengineering

institute: University of California, San Diego

summary:
Purpose:to reveal the changes in small RNA, esp. microRNA to correlate with transcriptome changes occuring due to EC-AGO1-KO and further explain the observed phenotype.
Methods: Subcutaneous adipose tissue were harvested.Small RNA library was prepared and for sequencing.
Results: We found substantial changes in miRNA due to EC-AGO1-KO.
Conclusions: Our study represents the detailed analysis of Ago1 regulated small RNA transcriptomes in subcutaneous adipose tissue between WT and KO mice. We conclude that small RNA-seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions.

overall_design: Three biological replica, each collected from an individual mice, per genotype were processed.

first: Zhen

last: Chen

first: Zhijie

last: Qi


title: Endothelial-AGO1-knockout (EC-AGO1-KO) mice and wild-type (WT) littermates

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


title: RNA Seq of Subcutaneous adipose tissue from endothelial-AGO1-knockout (EC-AGO1-KO) mice and wild-type (WT) littermates

summary:
Purpose: to profile transcriptome changes due to EC-AGO1-deficiency
Methods: Subcutaneous adipose tissue were harvested. RNA was extracted using TRIzol and library was prepared for sequencing.
Results: We found genes involved in pathways promoting angiogenesis, browning, insulin sensitivity to be upregulated, and those promoting inflammation and fibrosis to be decreased in KO compared with WT mice.
Conclusions:Our study represents the detailed analysis of Ago1 regulate transcriptomes in SAT between WT and KO mice. We conclude that RNA-seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions.

overall_design: To elucidate the molecular changes underlying the observed metabolic phenotype in EC-AGO1-KO mice.


title: Double-stranded Alu RNAs, type 1 IFN responses, and relapsing remitting multiple sclerosis

status: Public on Feb 10 2020

city: Nashville

first: Jeff

last: Rathmell

state: TN

address: 1211 Medical Center Drive

department: PMI

institute: Vanderbilt University Medical Center

summary: We report here an double stranded RNA sequencing from multiple sclerosis patient blood samples

overall_design: Whole blood samples (~2.5 ml) were collected in PAXGENE tubes to immediately stabilize endogenous RNA from the following patient groups: 1) patients at the indicated times after their first clinical event suggestive of presence of RRMS commonly referred to as a clinically isolated event or CIS (MS-C) who later went on to receive a diagnosis of RRMS, files labeled as sample 1, sample 2, sample 3 or MS-C 1, MS-C 2, MS-C 3, and healthy controls, sample 4, sample 5, sample 6 or HC 1, HC 2, HC 3.

first: Thomas

last: Aune

first: John

last: Karijolich


title: Transcriptomic analysis of response of Pseudomonas aeruginosa AG1 after exposure to Ciprofloxacin

status: Public on Jan 01 2020

city: Montes de Oca

first: Jose

middle: Arturo

last: Molina-Mora

state: San Jose

address: Sede Universitaria Rodrigo Facio

department: Facultad de Microbiología

country: Costa Rica

institute: Universidad de Costa Rica

summary: We report the transcriptomic analysis of the response of P. aeruginosa AG1 to Ciprofloxacin to identify molecular determinants related to its tolerance to the antibiotic and the enriched pathways along time

overall_design: Examination of three times after exposure to Ciprofloxacin, times 0, 2.5 and 5 hours in P. aeruginosa AG1, 3 replicates in each case. Time 0h was taken as control.

middle: A

first: Fernando

last: Garcia-Santamaria


title: Exon Level Expression Profiling: a Novel Unbiased Transcriptome

status: Public on Feb 18 2020

city: Tsukuba

first: Fuminori

last: Tsuruta

address: 1-1-1 Tennodai

institute: University of Tsukuba

summary:
Transcriptome analysis of usp15 deficient mice
RNA metabolism plays an important for regulating protein diversity. USP15, which is a deubiquitinating enzyme, is known to be a responsible gene for developmental disorders and neurodegenerative disorders. Although USP15 is implicated in RNA processing, the downstream targets regulated by USP15 have not been elucidated. Here, we performed exon array screening to identify the target of USP15 using Usp15 deficient mice. We were able to found a lot of candidate genes and several genes are associated with some diseases as described above.

overall_design: The tissues in both wild type and USP15 deficient mice (one-month-old) were collected for RNA extraction and hybridization on Affymetrix exon array.

first: Jaehyun

last: Kim


title: Transcriptome-wide m6A Methylation Profiling of Wild Type and ALKBH5-/- Peritoneal Macrophages by m6A-seq

status: Public on Aug 22 2019

first: Yang

last: Liu

address: Dongdan Santiao 5

department: Immunology

institute: Peking Union Medical College&Chinese Academy of Medical Sciences

summary: By performing m6A-seq analysis on the peritoneal macrophages that derived from ALKBH5-/- mice and littermate mice infected with or without vesicular stomatitis virus (VSV), we want to investigate whether ALKBH5 deficiency-mediated m6A RNA methylation contributes to the regulation of its target genes expression. m6A-seq analysis revealed enriched and specific m6A peaks on the transcript of ALKBH5-targeted gene, which were substantially increased in ALKBH5-deficient peritoneal macrophages than that in wild-type cells whatever infected with or without VSV.  Meanwhile we didn’t observe up-regulation of m6A signal on VSV in ALKBH5-deficient cells; and also didn't find significant difference of m6A signals on IFN-β mRNA between ALKBH5-deficient and wild type cells whatever infected with or without VSV. These demonstrated that deficiency of ALKBH5 controls viral replication by increasing the m6A modification of ALKBH5 target gene to regulate its expression.

overall_design: Examination of m6A RNA modifications in wild type and ALKBH5-/- peritoneal macrophages infected with or without VSV, two biological replicates.


title: Gene expression in WT and Thpok-deficient LCMV-specific effector T cells

status: Public on Aug 15 2019

last: Ciucci

summary: Gene expression of effector CD4+ and CD8+ T cells determined by RNAseq 7 days after LCMV Armstrong infection

overall_design: 7 days post-infection with LCMV Arm spleen GP66:I-Ab+ T cells from Zbtb7bAD (CD4 Zbtb7b KO) or Tnfrsf4-Cre– (CD4 Ctrl) mice and of spleen GP33:H-2Db+ T cells from Tnfrsf4-Cre– animals (CD8 Ctrl) were sorted and gene expression was determined by RNAseq

first: Remy

last: Bosselut


title: A conserved noncoding locus modulates random monoallelic Xist expression across a TAD boundary

status: Public on Dec 01 2019

city: Paris Cedex 05

first: Nicolas

last: Servant

address: 26 rue d'ulm

institute: Institut Curie

summary: Topologically associating domains (TADs) are thought to restrict the action of distal cis-regulatory elements, such as enhancers, to target gene promoters within the same TAD. Here we discover that a cis-regulatory element of Xist is located almost 200kb away from its promoter and across a TAD boundary. This element, the promoter of a noncoding RNA, Linx, opposes Xist up-regulation in cis and influences the choice of X chromosome to be inactivated. Even though Linx lies in the same TAD as Xist’s antisense Tsix locus, we show that the repressive action of Linx on Xist is independent of Tsix. Furthermore, this Xist regulatory action is independent of Linx transcript or of its transcription. Finally, we demonstrate that Linx cis-regulatory repressive element is well conserved in mammals, unlike Tsix, suggesting that it represents an ancestral mechanism for random monoallelic Xist expression. Our study uncovers a novel regulatory axis for X-chromosome inactivation and a new class of cis-regulatory effects that rely on TAD partitioning to modulate developmental decisions.

overall_design: Our dataset includes 8 RNA-seq samples, 22 5C-samples, 20 Capture-C samples and 6 ATAC-seq samples. These include at least two biological replicates for each condition. Control/reference samples were included and processed in parallel: "wildtype" genotype to compare with deletions/inversions, and "day 0 (undifferentiated)" to compare with differentiated samples.

first: Rafael

last: Galupa

first: Elphege

middle: P

last: Nora

first: Rebecca

last: Worsley-Hunt

first: Christel

last: Picard

first: Chris

last: Gard

first: Joke

middle: G

last: vanBemmel

first: Yinxiu

last: Zhan

first: Fatima

last: ElMarjou

first: Colin

last: Johanneau

first: Patricia

last: Diabangouaya

first: Agnes

last: LeSaux

first: Sonia

last: Lameiras

first: Juliana

last: Fonseca

first: Friedemann

last: Loos

first: Joost

last: Gribnau

first: Sylvain

last: Baulande

first: Uwe

last: Ohler

first: Luca

last: Giorgetti

first: Edith

last: Heard


title: A ribosome assembly stress response regulates transcription to maintain proteome homeostasis

status: Public on Jun 24 2019

city: GENEVA

first: Benjamin

last: Albert

address: 30, quai Ernest-Ansermet

department: Bimol

country: Switzerland

institute: University of Genevea

summary: Ribosome biogenesis is a complex and energy-demanding process requiring tight coordination of ribosomal RNA (rRNA) and ribosomal protein (RP) production.  Alteration of any step in this process may impact growth by leading to proteotoxic stress.  Although the transcription factor Hsf1 has emerged as a central regulator of proteostasis, how its activity is coordinated with ribosome biogenesis is unknown.  Here we show that arrest of ribosome biogenesis in the budding yeast S. cerevisiae triggers rapid activation of a highly specific stress pathway that coordinately up-regulates Hsf1 target genes and down-regulates RP genes.  Activation of Hsf1 target genes requires neo-synthesis of RPs, which accumulate in an insoluble fraction, leading to sequestration of the RP transcriptional activator Ifh1.  Our data suggest that levels of newly-synthetized RPs, imported into the nucleus but not yet assembled into ribosomes, work to continuously balance Hsf1 and Ifh1 activity, thus guarding against proteotoxic stress during ribosome assembly.

overall_design: RNA Polymerase II binding was measured upon nuclear depletion of topoisomerase 1, 2 or both and/or following cycloheximide, diazaborine or rapamycin treatment.

first: David

last: Shore


title: Human models of NUP98-KDM5A megakaryocytic leukemia contribute to uncover new biomarkers and therapeutic vulnerabilities

status: Public on Nov 25 2019

city: Montreal

last: Cellot

state: Quebec

address: 3175 Côte-Sainte-Catherine

country: Canada

institute: Centre Hospitalier Universitaire (CHU) Sainte-Justine Research Center

summary: We generated human synthetic models of NUP98-KDM5A leukemia and compared gene expression profiles to  primary pediatric samples.

overall_design: RNA sequencing of synthetic human model and primary pediatric leukemias. CD34+cord blood hematopoietic stem/progenitor cells were used as control.

first: Sophie

last: Cardin

first: Mélanie

last: Bilodeau

first: Mathieu

last: Roussy

first: Léo

last: Aubert

first: Thomas

last: Milan

first: Loubna

last: Jouan

first: Alexandre

last: Rouette

first: Louise

last: Laramée

first: Patrick

last: Gendron

first: Jean

last: Duchaine

first: Hélène

last: Decaluwe

first: Jean-François

last: Spinella

first: Stéphanie

last: Mourad

first: Françoise

last: Couture

first: Daniel

last: Sinnett

first: Élie

last: Haddad

first: Josette-Renée

last: Landry

first: Jing

last: Ma

first: Keith

last: Humphries

first: Philippe

last: Roux

first: Josée

last: Hébert

first: Tanja

last: Gruber

first: Brian

middle: T

last: Wilhelm


title: Single-cell transcriptomics of the human retinal pigment epithelium and choroid in health and macular degeneration

status: Public on Oct 30 2019

first: Todd

last: Scheetz

address: 3181B MERF

institute: UNIVERSITY OF IOWA

summary:
Purpose: The goals of this study were to identify cell specific expression patterns of the retinal pigment epithelium (RPE) and a variety of choroidal cell types originating from the macula and the periphery of human donor eyes, with a particular emphasis on identifying expression signatures of choroidal endothelial cells.
Methods: Independent libraries were prepared for macular and peripheral samples of combined RPE/choroid from seven donors in two single cell sequencing experiments. In the first experiment, 8-mm macular and peripheral punches of RPE/choroid from Donors 1-3 were digested in papain prior to cryopreservation and subsequent GEM barcoding/library construction. Donors 1-2 had no noted ophthalmologic disease documented, while Donor 3 was diagnosed with age-related macular degeneration. In the second experiment, 12-mm macular and peripheral punches of RPE/choroid from Donors 4-7 were digested in collagenase II prior to cryopreservation, CD31-magentic bead enrichment and subsequent GEM barcoding/library construction. Donors 5-7 had no noted ophthalmologic disease documented, while Donor 4 was diagnosed with age-related macular degeneration. In both experiments, libraries were sequenced on a HiSeq4000. Sequenced reads were mapped to the human genome build hg19 will CellRanger(v3.0.1) and filters removed cells likely to be doublets or cells with a high proportion of mitochondrial reads. Clustering of cells with similar expression profiles was performed with Seurat (v3.0.2).
Results: In the first experiment with unenriched RPE/choroid from donors 1-3, we recovered 4,355 cells post filtering with 40,177,477 corresponding reads. A total of 2,167 cells originated from the macula and 2,168 cells originated from the periphery. A total of 11 clusters were identified, and highly enriched genes in each cluster were used to classify clusters into their presumed dominant cell type. Differential expression analysis was performed between cells of macular and peripheral origin in each cluster and between donors with and without a history of age-related macular degeneration.
Results: In the second experiment with CD31-enriched RPE/choroid from donors 4-7, we recovered 14,234 cells post filtering with 135,742,297 corresponding reads. A total of 7,647 cells originated from the macula and 6,587 cells originated from the periphery. A total of 8,521 of these cells were presumed endothelial cells. A total of 13 clusters were identified, and highly enriched genes in each cluster were used to classify clusters into their presumed dominant cell type(s). Differential expression analysis was performed between cells of macular and peripheral origin in each cluster and between donors with and without a history of age-related macular degeneration. Within each of the endothelial clusters (Clusters 5-8), differential expression analysis was performed between each cluster and the remaining endothelial cells.
Conclusions: This study provides a large atlas of single-cell level gene expression patterns of the human retinal pigment epithelium and choroidal cell types. We identify expression patterns of most expected choroidal cell populations and describe macular versus peripheral regional differences. We additionally identify enriched transcripts in specific cell populations in age-related macular degeneration. We characterize gene expression patterns along the choroidal vascular tree, and identify populations of arterial, capillary, and venous endothelial cells. Our results show that single-cell sequencing can be performed on human RPE/choroid after cryopreservation, and that CD31 magnetic bead enrichment can be employed to enrich for endothelial cells for single-cell sequencing.

overall_design: mRNA profiles for thousands of cells from macular and peripheral RPE/choroid isolates were generated from seven human donor eyes using 10X Genomics Chromium single-cell system followed by sequencing on an Illumina HiSeq 4000.

first: Robert

last: Mullins


title: ZmNF-YB16-YC17-YA1 complex participates in the regulation of plant growth and drought resistance in maize

status: Public on Sep 21 2019

city: qingdao

first: wang

last: baomei

state: shandong

address: school of life science，shandong university，72 binhai road， aoshanwei town， jimo city

department: school of  life science

institute: zea maize

summary: This was a comparative transcriptome analysis by using high throughput sequencing. To assess the effects of drought stress and NF-Y transcription factors ZmNF-YA1 and ZmNF-YB16 on maize, leaves from wild-type (W22), zmnf-ya1 (m67) mutant, wild-type (B104) and ZmNF-YB16 overexpression (OE) plants grow under well-watered and drought stress conditions were collected and RNAseq was performed. We tracked the gene expression events of inbred maize lines W22 or B104 seedlings in response to drought stress to evaluate how drought stress affects the gene expression program in maize. At the same time, we analyzed the effects of drought stress on gene expression in zmnf-ya1 and ZmNF-YB16 OE plants to investigate whether and how ZmNF-YA1 and ZmNF-YB16 confer drought stress tolerance in maize. Maize plants were grown under well-watered conditions until the V4 stage (zmnf-ya1 and W22) or V9 stage (ZmNF-YB16 OE and B104), and then half of them were exposed to drought stress treatment. Water loss in the soil and the electrolyte leakage from leaf cells were used to assess drought stress in plants. Leaves from 3-4 plants were pooled for each sample, and two replicates were used. RNA was extracted from small strips of leaf lamina excised from the first fully expanded leaf of the plants.

overall_design: Examination of 6 different materials (B104, ZmNF-YB16 OE, DH4866, ZmNF-YA1 OE, W22, zmnf-ya1 mutant ) under normal and drought conditions

first: Baomei

last: Wang

first: Jieming

first: Chunmei

last: He

first: Dengfeng

last: Zhang

first: Peng

last: Li

first: Juren

first: Zhaoxia


title: RNA Seq of HMVEC under hypoxia

first: Sheng

last: Zhong

summary:
Purpose: to profile transcriptome changes due to EC-AGO1-deficiency
Methods: We had HMVECs subjected to normoxia (20%) or hypoxia (2%) for 0, 12, 24, and 48 hr in biological replicates. Total RNA was extracted with mirVana total RNA isolation kit (Life Technologies). RNA-seq was performed.
Results: We found genes involved in pathways promoting angiogenesis, browning, insulin sensitivity to be upregulated, and those promoting inflammation and fibrosis to be decreased in KO compared with WT mice.
Conclusions:Our study represents the detailed analysis of Ago1 regulate transcriptomes in HMVEC under Hx. We conclude that RNA-seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions.
To elucidate the molecular changes underlying the observed metabolic phenotype in EC-AGO1-KO mice.

overall_design: Biological replicates for each condition

first: Zhijie

last: Qi


title: Individual nucleotide resolution Crosslinking Immunoprecipitation (iCLIP)-seq

summary:
Purpose: to identify the AGO1-bound miRNAs and mRNAs in human endothelial cells subject to hypoxic condition (2% oxygen)
Methods: human microvascular endothelial cells was cultured under normoxia (20% oxygen) or hypoxia (2%) oxygen for 24 hours. Total RNA was extracted and RNA and small RNA libraries were prepared for Seq.
Results: We found substantial changes in AGO1-bound mRNAs due to hypoxia. A portion of CLIP-seq reads also reveal direct binding to miRNA to mRNA.
Conclusions: hypoxia induces profound changes in mRNAs associated with AGO1.

first: Zhen

last: Chen


title: Development of gene expression signatures of CAL-27 cells for treatment of shXBP-1s.

status: Public on Aug 06 2019

city: New York

first: Xinyuan

last: Lei

state: New York

address: E5310 Melville library

department: Molecular and Cellular Biology

institute: Stony Brook University

summary: We have employed mRNA microarray expression profiling as a discovery platform to identify genes with the potential to explain how knockdown of XBP-1s upregulated the cell membrane expression of HLA of CAL-27 cells. Both knockdown group and control group were comfirmed to be stable transfected.

overall_design: Three samples for shXBP-1s group and three samples for shCtrl group.

first: Fan

last: Song


title: Circadian regulation of cochlear sensitivity to noise by circulating glucocorticoids

status: Public on Jun 15 2019

city: Lausanne

first: Benjamin

last: Weger

state: VD

address: Station 15

department: SV

institute: EPFL

overall_design: Refer to individual Series


title: Gene expression in WT and Thpok-deficient LCMV-specific effector T cells after retroviral transduction

first: Thomas

last: Ciucci

summary: Gene expression of transduced effector CD4+ T cells determined by RNAseq 7 days after LCMV Armstrong infection

overall_design: SMARTA cell from Zbtb7bAD (CD4 Zbtb7b KO) or Tnfrsf4-Cre– (CD4 Ctrl) mice were transduced with Bcl6 or Thpok retrovirus and transfered into WT recipients. 7 days post-infection with LCMV Arm transduced spleen SMARTA cells were sorted and gene expression was determined by RNAseq

first: Remy

last: Bosselut


title: Comparative transcriptomics analyses of fruiting body development in Fusarium species

status: Public on Jun 20 2019

city: East Lansing

first: Wonyong

last: Kim

state: Michigan

address: 612 Wilson Road, Room 166

department: Plant Biology

institute: Michigan State University

summary: Fusarium neocosmosporiellum (formerly Neocosmospora vasinfecta) has been reported as a fruit- and root-rot pathogen of numerous field crops, although it is not known to cause significant losses on any crop. This cosmopolitan species has also been reported as an opportunistic human pathogen, from infected soybean cyst nematodes, deer dung, and soil, and it possesses a highly active CO2 fixation mechanism. To better understand the metabolic potential of this fungus, we sequenced the genome of one isolate of F. neocosmosporiellum and compared its gene content with previously published Fusarium genomes. The predicted gene numbers were similar to F. graminearum, but the F. neocosmosporiellum genome contained more carbohydrate metabolism-related and transmembrane transport genes, and it appears to have a greater ability to utilize resources in the environment as a cosmopolitan saprotroph. Transcriptome data during perithecium development was compared with that of the model plant pathogen F. graminearum. The F. neocosmosporiellum genome included both MAT1-1 and MAT1-2 idiomorphs, as in the homothallic F. graminearum, however MAT gene organization and their expression patterns during perithecium development differed in these species. We also found that many transmembrane transport genes were differentially expressed during perithecium development, which may account for the larger perithecia of F. neocosmosporiellum. Finally, comparative analysis of the secondary metabolite gene clusters identified several polyketide synthase genes that were induced during perithecium development. Deletion of a novel polyketide synthase gene in F. neocosmosporiellum resulted in a defective perithecium phenotype. In summary, comparative analysis of the transcriptional programs during perithecium development has provided novel insights into morphological and physiological diversification in F. neocosmosporiellum.

sample_organism:
Fusarium graminearum
Fusarium neocosmosporiellum

overall_design: Time-series mRNA profiles during the perithecial development for the Fusarium neocosmosporiellum strain NRRL_22166 were generated by deep sequencing, in triplicate, using the Illumina HiSeq 2500 system.


title: Single-cell methylation and accessibility of mouse embryos E4.5 to E7.5. First batch.

status: Public on Sep 30 2019

city: Cambridge

first: Felix

last: Krueger

address: Granta Park

department: Bioinformatics

institute: Altos Labs

summary:
Formation of the three primary germ layers during gastrulation is an essential step in the establishment of the vertebrate body plan. Recent studies employing single cell RNA-sequencing have identified major transcriptional changes associated with germ layer specification. Global epigenetic reprogramming accompanies these changes, but the role of the epigenome in regulating early cell fate choice remains unresolved, and the coordination between different epigenetic layers is unclear. Here we describe the first single cell triple-omics map of chromatin accessibility, DNA methylation and RNA expression during the exit from pluripotency and the onset of gastrulation in mouse embryos. We find dynamic dependencies between the different molecular layers, with evidence for distinct modes of epigenetic regulation. The initial exit from pluripotency coincides with the establishment of a global repressive epigenetic landscape, followed by the emergence of local lineage-specific epigenetic patterns during gastrulation. Notably, cells committed to mesoderm and endoderm undergo widespread coordinated epigenetic rearrangements, driven by loss of methylation in enhancer marks and a concomitant increase of chromatin accessibility. In striking contrast, the epigenetic landscape of ectodermal cells is already established in the early epiblast. Hence, regulatory elements associated with each germ layer are either epigenetically primed or epigenetically remodelled prior to overt cell fate decisions during gastrulation, providing the molecular logic for a hierarchical emergence of the primary germ layers.

We strongly encourage anyone wanting to use these data to first try the parsed data in the link below together with the scripts we used in the paper which can be found in the GitHub repository.

Useful links:
Parsed data: (ftp://ftp.ebi.ac.uk/pub/databases/scnmt_gastrulation)
Github repository: (https://github.com/rargelaguet/scnmt_gastrulation)

overall_design: 758 single cells isolated from mouse embryos at E4.5, E5.5, E6.5 and E7.5 and processed using scNMT-seq (Clark et al 2018)

first: Ricard

last: Argelaguet

first: Hisham

last: Mohammed

first: Stephen

middle: J

last: Clark

first: L

middle: C

last: Stapel

first: Christel

first: Chantriolnt-Andreas

last: Kapourani

first: Yunlong

last: Xiang

first: Courtney

last: Hanna

first: Sebastien

last: Smallwood

first: Ximena

last: Ibarra-Soria

first: Florian

last: Buettner

first: Guido

last: Sanguinetti

first: Wei

last: Xie

first: Peter

last: Rugg-Gunn

first: Gavin

last: Kelsey

first: Wendy

last: Dean

first: Jennifer

last: Nichols

first: Oliver

last: Stegle

first: John

last: Marioni

first: Wolf

last: Reik


title: AKIRIN1 is a suitable reference gene in natural killer cells and granulocytes from patients with SIRS and septic shock [NK cells]

status: Public on Jun 10 2019

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

department: ZMF

institute: University Heidelberg

summary: Timely and reliable distinction of non-infectious systemic inflammatory response syndrome (SIRS), common in critically ill patients, from sepsis to support adequate antimicrobial therapy safes lives but is clinically challenging. Expeditious sepsis biomarkers are thus urgently sought. Blood transcriptional profiling provides insights into sepsis pathophysiology, but variability in leukocyte subtype composition complicates profile interpretation, and reliable reference genes to normalize gene expression in sepsis are lacking. Here, we identified AKIRIN1 as a reference gene, specifically, in peripheral NK cells and granulocytes for differential gene expression analysis between patients with SIRS and septic shock on intensive care unit admission. Discovery by a two-step probabilistic selection from microarray data followed by validation through branched DNA assays in independent patients revealed several candidate reference genes in NK cells, namely, AKIRIN1, PPP6R3, TAX1BP1, and ADRBK1. For in vitro priming of NK cells, GUSB however was confirmed as reference gene of choice. Initially, no candidate genes could be validated in granulocytes, an additional rescreen of known reference genes by RT-PCR included. By serendipity, we could determine equal AKIRIN1 expression levels also in SIRS and septic shock granulocytes and no change by in vitro challenge of granulocytes with LPS. Inspection of four external neutrophil transcriptome datasets further support unchanged AKIRIN1 expression in human systemic inflammation. Invariable AKIRIN1 expression in peripheral NK cells and granulocytes needs further validation in sepsis and other infectious and inflammatory diseases. As a reference gene in these cells and conditions, AKIRIN1 may further our understanding of innate immunity and lead to new biomarkers.

overall_design: We enrolled critically ill patients and collected blood on admission to our surgical intensive care unit if, within the preceding 24 hours, they had a diagnosis of post-traumatic systemic inflammatory response syndrome (SIRS) or septic shock. Hospitalized noncritically ill control patients were recruited on presurgical examination. To transcriptionally characterize the innate immune response to sterile (SIRS) and infectious (septic shock) systemic inflammation, natural killer (NK) cells were isolated from patient blood for RNA extraction and hybridization on Affymetrix microarrays.

first: Anna

last: Coulibaly

first: Holger

last: Lindner


title: Identification of Fcmr-dependent heterogeneity in tumor associated mononuclear phagocytes

status: Public on Jun 18 2019

city: Toronto

first: Tak

last: Mak

state: ON

address: 610 University Ave

department: The Campbell Family Institute for Breast Cancer Research

institute: Princess Margaret Cancer Centre, University Health Network

summary: The mononuclear phagocytic system (MPS) is characterized by functional diversity and plasticity, including within the tumor microenvironment (TME). Tumor-associated mononuclear phagocytes (TMPs) within the TME come from various ontological origins. To determine how Fcmr deficiency might impact the functional heterogeneity of mature mononuclear phagocytes (MPs) within the TME, we performed single-cell RNA sequencing (scRNAseq) on MPs isolated from B16 tumors resected from Fcmr-/- and Fcmr+/+ mice. To evaluate a homogenous population of MPs within the TME we chose to examine cells harboring expression of markers found in more mature, differentiated MPs. Therefore, we then sorted MerTk+ CD64+ TMPs by FACS and subjected these cells to single-cell transcriptomic analyses using the Chromium 10X Genomics platform. We obtained RNAseq profiles from 6352 Fcmr+/+ and 7999 Fcmr-/- TMPs.

overall_design: Comparison of tumor mononuclear phagocytes from Fcmr+/+ and Fcmr-/- mice

first: Shawn

last: Kubli

first: Parameswaran

last: Ramachandran

middle: W


title: Adipocyte p62/SQSTM1 suppresses tumorigenesis through the opposite regulation of metabolism in fat and tumor

status: Public on Jun 26 2019

first: Jorge

last: Moscat

state: NY

address: 1188 York Avenue

department: Pathology and Laboratory Medicine

institute: WEILL CORNELL MEDICINE

summary: Obesity is a leading risk factor for tumorigenesis and there is emerging support for a positive association between obesity and a more aggressive fatal prostate cancer. However, a complete understanding of the specific cross-talk between adipocytes and tumor cells in vivo and independently of dietary contributions is a major gap in the field. Here we interrogated human cancer data sets and used a TRAMP+ mouse line in which the signaling adaptor p62/Sqstm1is selectively inactivated in the adipose tissue. Our data demonstrate that p62 loss in adipocytes promotes an aggressive metastatic prostate cancer (PCa) phenotype with marked enrichment in fatty acid oxidation genes. Reciprocally, p62-deficiency in adipocytes promotes a general shutdown of energy utilizing pathways through mTORC1 inhibition trigger by the tumor in vivo. This reveals a central role of adipose p62 in the symbiotic adipocyte-tumor collaboration to promote the tumor metabolic fitness by enhancing its metabolism at expenses of that of the adipocyte.

overall_design: Epidydimal adipose tissues and prostate tumors from TRAMP+/p62Adipo and TRAMP+/p62WT mice

first: Jianfeng

last: Huang

first: Angeles

last: Duran

first: Miguel

last: Reina-Campos

first: Maria

last: Diaz-Meco


title: Identification of glucocorticoid-dependent circadian genes in the cochlea

first: Benjamin

middle: D

last: Weger

summary: The cochlea possesses a robust circadian clock machinery that regulates auditory function. How the cochlear clock is influenced by the circadian system remains unknown. Here we show that cochlear rhythms are system-driven and require local Bmal1 as well as central input from the suprachiasmatic nuclei (SCN). SCN ablations disrupted the circadian expression of the core clock genes in the cochlea. Since the circadian secretion of glucocorticoids (GCs) is controlled by the SCN and that GCs are known to modulate auditory function, we assessed their influence on circadian gene expression. Removal of circulating GCs by adrenalectomy (ADX) did not have a major impact on core clock gene expression in the cochlea. Rather it abolished the transcription of clock-controlled genes involved in inflammation. ADX abolished the known differential auditory sensitivity to day and night noise trauma and prevented the induction of GABA-ergic and glutamate receptors mRNA transcripts. However, these improvements were unrelated to changes at the synaptic level suggesting other cochlear functions may be involved. Due to this circadian regulation of noise sensitivity by GCs, we evaluated the actions of the synthetic glucocorticoid dexamethasone (DEX) at different times of the day. DEX was effective in protecting from acute noise trauma only when administered during daytime, when circulating glucocorticoids are low, indicating that chronopharmacological approaches are important for obtaining optimal treatment strategies for hearing loss. GCs appear as a major regulator of the differential sensitivity to day or night noise trauma, a mechanism likely involving the circadian control of inflammatory responses.

overall_design: Cochlear samples from sham operated or adrenalectomized (ADX) CBA/Sca mice were collected every 4th hour during a 24h period and subjected to RNAseq (n=3 per time point, corresponding to a total of 36 samples).

first: Christopher

last: Cederroth

first: Jung-sub

last: Park

first: Vasiliki

last: Basinou

first: Evangelia

last: Tserga

first: Heela

last: Sarlus

middle: K

last: Magnusson

first: Nadir

last: Kadri

first: Frédéric

last: Gachon

first: Barbara

last: Canlon


title: AKIRIN1 is a suitable reference gene in natural killer cells and granulocytes from patients with SIRS and septic shock [granulocytes]

first: Carsten

last: Sticht

overall_design: We enrolled critically ill patients and collected blood on admission to our surgical intensive care unit if, within the preceding 24 hours, they had a diagnosis of post-traumatic systemic inflammatory response syndrome (SIRS) or septic shock. Hospitalized noncritically ill control patients were recruited on presurgical examination. To transcriptionally characterize the innate immune response to sterile (SIRS) and infectious (septic shock) systemic inflammation, granulocytes were isolated from patient blood for RNA extraction and hybridization on Affymetrix microarrays.

first: Anna

last: Coulibaly

first: Holger

last: Lindner


title: Reconstituting the transcriptome and DNA methylome landscapes of human implantation

status: Public on Jul 11 2019

city: Beijing

first: Rui

last: WANG

address: No.5 Yiheyuan Road, Haidian District

department: Biodynamics Optical Imaging Center (BIOPIC)

institute: Peking University

summary: Implantation is a milestone event during mammalian embryogenesis. Implantation failure is a nonnegligible cause of human early pregnancy loss. Due to the extreme difficulty of obtaining in vivo human early post-implantation embryos, it remains elusive how the gene regulatory network and epigenetic mechanisms control human embryo implantation. Here, combining an in vitro culture system for human post-implantation development and single-cell omics sequencing technologies, over 8,000 individual cells from 65 human peri-implantation embryos were systematically analyzed. Unsupervised dimensionality reduction and clustering algorithm of the transcriptome data show stepwise implantation routes for the epiblast (EPI), primitive endoderm (PE), and trophectoderm (TE) lineages, suggesting robust preparation for the proper establishment of a mother-to-offspring connection during implantation. Female embryos showed initiation of random X chromosome inactivation based on analysis of parental allele-specific expression of X chromosome-linked genes during implantation. Surprisingly, by the single-cell Trio-Seq (scTrio-Seq) analysis, the genome re-methylation of PE lineage was shown to be much slower than those of both EPI and TE lineages during implantation process, indicating distinct DNA methylome re-establishment features between EPI and PE although both of which were derived from inner cell mass (ICM). Collectively, our work paves the way for understanding the complex molecular mechanisms that regulate human embryo implantation, offering new insights and future efforts in early embryonic development and reproductive medicine.

overall_design:
Single cell transcriptome profiles of human post-implantation embryos were generated by next generation sequencing using Illumina HiSeq 4000. And the transcriptome part of the single-cell Trio-seq2 were sequenced on the platform of Illumina HiSeq 4000 as well.
Please note that the *txt files (linked to each sample records) provide the barcode sequence and corrsponding samples. For example, the file 'ha_170710A.txt' includes the barcode sequence and sample names for the 'ha_170710A' sample.

first: Fan

last: Zhou

last: Wang


title: AKIRIN1 is a suitable reference gene in natural killer cells and granulocytes from patients with SIRS and septic shock

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


title: Coordination of hunger and sleep through circadian regulation of transcription in energy-sensing neurons

status: Public on Mar 04 2019

city: Chicago

first: Nathan

last: Waldeck

state: IL

address: 303 E Superior St, Lurie 7-220

institute: Northwestern University

summary: Alignment of fasting and feeding with the sleep/wake cycle is coordinated by hypothalamic neurons, though the underlying molecular programs remain incompletely understood. Here we demonstrate that the clock transcription pathway maximizes eating during wakefulness and glucose production during sleep through transcription pathway maximizes eating during autonomous circadian regulation of NPY/AgRP neurons. Tandem profiling of whole cell and ribosome-bound mRNAs in morning and evening under dynamic fasting and fed conditions identified temporal control of activity-dependent gene repertoires in AgRP neurons central to synaptogenesis, bioenergetics, and neurotransmitter and peptidergic signaling. Synaptic and circadian pathways were specific to whole cell RNA analyses, while bioenergetic pathways were selectively enriched in the ribosome-bound transcriptome. Finally, we demonstrate that the AgRP clock mediates the transcriptional food acquisition with sleep/wake state. response to leptin. Our results reveal that time-of-day restriction in transcriptional control of energy-sensing neurons underlies the alignment of hunger and day restriction in transcriptional control of energy-sensing neurons underlies the alignment of hunger and food acquisition with sleep/wake state.

overall_design: Examination of AGRP neurons including BMAL1-KO, under 3 different nutrient states, leptin adiministration, and time of day collection points.

first: Jonathan

last: Cedernaes

first: Joseph

last: Bass


title: Endogenous glucocorticoid rhythms regulate the circadian sensitivity to noise

first: Benjamin

last: Weger

overall_design: To explore the influence of GCs on time-dependent auditory function, we exposed animals to noise (6-12 kHz, 100 dB SPL for 1 h) during daytime (ZT3)  or nighttime (ZT15). on whole cochleae collected 2 hours post-day or night noise trauma

last: Cederroth

last: Park


title: Increased Serine and One Carbon Pathway Metabolism by PKCl/i Deficiency Promotes Neuroendocrine Prostate Cancer

status: Public on Mar 05 2019

first: Jorge

last: Moscat

summary:
Increasingly effective therapies targeting the androgen receptor have paradoxically promoted the incidence of neuroendocrine prostate cancer (NEPC), the most lethal subtype of castration-resistant prostate cancer (PCa), for which there is no effective therapy. Here we report that protein kinase C (PKC)l/i is downregulated in de novo and during therapy-induced NEPC, which results in the upregulation of serine biosynthesis through an mTORC1/ATF4-driven pathway. This metabolic reprogramming increases intracellular SAM levels to support cell proliferation and epigenetic changes that favor the development of NEPC characteristics. Altogether, we have uncovered a metabolic vulnerability triggered by PKCl/i deficiency in NEPC, which offers potentially actionable targets to prevent therapy resistance in PCa.

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