title: Adipogenic differentiation of gluteal and abdominal adipose stem cells

status: Public on Jun 17 2022

city: Oslo

first: Philippe

last: Collas

address: PO Box 1112 Blindern

department: Institute of Basic Medical Sciences

country: Norway

institute: University of Oslo

summary: Obesity and associated metabolic outcomes define the metabolic syndrome. Interestingly, an under-appreciated fact is that body fat distribution, rather than total body fat amount, is a key determinant of metabolic disease. Indeed, in contrast to upper-body obesity, lower-body fat accumulation inversely correlates with metabolic risks. Understanding processes regulating upper- vs. lower-body fat expansion is paramount to predict (and prevent) these risks. We combine functional, proteomics, transcriptomics and epigenomics analyses to identify chromatin-associated mechanisms of adipose depot-specific fat expansion. Here, we analyze by RNA-seq the transcriptome of adipose stem cells (ASCs) from gluteal (lower-body) and abdominal subcutaneous (upper-body) depots induced to differentiate in vitro towards the adipogenic lineage. We aim to identify adipose depot-specific and temporal differences in the up- or down-regulation of gene expression, and a later stage relate these differences to changes in chromatin states.

overall_design: Analysis of the transcriptome by RNA-seq in adipose tissue-derived stem cells (ASCs) induced to differentiate in vitro into the adipocyte lineage. ASCs were collected on day -2 (proliferating stage), day 0 (confluent, cell cycle-arrested stage, time of differentiation induction), and on days 1, 3 and 9 of differentiation. ASCs were isolated from two donors (1 from gluteofemoral subcutaneous adipose tisse, 1 from abdominal subcutaneous adipose tissue), cultured and subjected to three independent differentiation experiments for each donor. Cells were collected at indicated time points and processed for RNA-seq analysis. The transcriptome of gluteofemoral ASCs upon knockdown of the lncRNA HOTAIR was also investigated via stable shRNA knockdown.

first: Evdokiia

last: Potolitsyna

first: Sarah

last: Hazell Pickering

first: Nolwenn

last: Briand


title: circular RNA expression in the rat orbitofrontal cortex after self-administration of heroin or sucrose

status: Public on Feb 16 2022

city: Philadelphia

first: Stephanie

last: Daws

state: PA

address: 3500 N Broad St

country: USA

institute: Temple University

summary: In this study we identified circular RNAs that are regulated in the orbitofrontal cortex after chronic heroin self-administration of a dosage of 0.03mg/kg/infusion or sucrose self-administration.

overall_design: We performed a microarray with 3 biological replicates each of orbitofrontal cortex tissue from male saline or male heroin self-administration animals, and male sucrose self-administration or male naive animals, collected immediately after the last self-administration session.

last: Sillivan


title: Gene expression data in A172 cell line transfected with MED12 siRNA or its control

status: Public on Jan 01 2022

city: New Delhi

first: Dr. Ritu

last: Kulshreshtha

state: New Delhi

address: Room 134, Block I

department: Dept of Biochemical Engineering and Biotechnology

country: India

institute: Indian Institute of Technology

summary:
This study identifies the genes differentially expressed upon MED12 knockdown in A172 glioblastoma cell line.
Clariom_S_Human Array was used to assess mRNA expression profile in response to MED12 Knockdown in A172 cells.

overall_design: A172 cells were transfected with either MED12 specific siRNA or scrambled control. The cells were harvested for RNA isolation 48 hours post-transfection. RNA was used for the gene expression analysis using Clariom S Array system.

first: Srishti

last: Srivastava

first: Ritu


title: Kidney cell type specific changes in the chromatin and transcriptome landscapes following epithelial Hdac1 and Hdac2 knockdown

status: Public on Dec 27 2021

city: Birmingham

first: Kelly

middle: Anne

last: Hyndman

state: Al

address: 1918 University BLVD

department: Medicine

institute: University of Alabama at Birmingham

type: Genome binding/occupancy profiling by high throughput sequencing

summary: We report the chromatin accessibility  with knock down of HDAC1 and HDAC2 from the epithelium of the adult mouse kidney

overall_design: Single nucleus sequencing of a male control mouse, female control mouse, male, inducible, nephron epithelium HDAC1 and HDAC2 knockout mouse, and a female, inducible, nephron epithelium HDAC1 and HDAC2 knockout mouse

middle: A

first: David

middle: K

last: Crossman


title: Azospirillum brasilense alters root system architecture through both auxin-dependent and -independent pathways

status: Public on Dec 24 2021

city: Winnipeg

first: Olivia

last: Wilkins

state: Manitoba

address: 66 Chancellors Cir

department: Biological Sciences

country: Canada

institute: University of Manitoba

type: Expression profiling by high throughput sequencing

summary: Azospirillum is a plant growth promoting rhizobacteria (PGPR) with ability to produce several phytohormones such as auxins, mainly indole-3-acetic acid (IAA).  The positive interaction of Azospirillum with plants has been simplified and explained through the bacterial capacity to produce IAA. Typical changes on root architecture by promoting the number of lateral roots and hair formation, and reducing the primary root length were established in inoculated plants. These changes increase the root surface improving the water and nutrients acquisition, and thus the growth of the whole plant. The mechanisms by which Azospirillum induces such changes fails to be explained only by the bacterial capacity to produce IAA. In this work, we have evaluated the root architecture and gene expression changes occurred in Arabidopsis thaliana inoculated with A. brasilense Az39 and the IAA-deficient mutant (Az39 ipdC-), or treated with exogenous IAA solution to confirm both, the IAA-dependent and IAA-independent Azospirillum´s pathways to promote the root growth. Our results demonstrate the ability of Az39 to modify the primary root development through IAA biosynthesis, while other IAA-independent mechanisms were related to an increase in the lateral roots development and the root hairs number. Jasmonates, ethylene and salicylic acid were increased in the IAA-deficient bacterial treatments, as the ipdC mutant significantly up-regulated transcription of genes enriched of these phytohormones signaling after 7 days. Further, the physical presence of the inactive bacteria (Az39φ) seems to mediate the development of root hairs, a mechanism common to other non-PGPR as E. coli DH5α. Our results suggest that Az39 inoculation induces morphological changes in root architecture through both IAA-dependent and independent mechanism. The IAA biosynthesis by Az39 reduces the primary root length; while the cells contact with the roots increases the root hairs production. Both the synthesis of active IAA and the presence of metabolically active Az39 cells increase the growth and development of lateral roots.

overall_design: 2 strains of Azospirillum rhizobacteria (Az39 and -ipdc mutant) and an NaCl control were applied to the roots of Arabidopsis thaliana seedlings for transcriptomic analysis at 24 hours and 7 days post treatment; 2 replicates each, of at least 50 root systems per rep

first: Verónica

last: Mora

first: Gastón

last: López

first: Romina

last: Molina

first: Nuria

last: De Diego

first: Sanja

middle: C

last: Zeljković

first: Sara

middle: S

last: Sarmiento

first: Lukáš

last: Spíchal

first: Sean

middle: M

last: Robertson

first: Mark

middle: F

last: Belmonte

first: Fabricio

last: Cassán


title: Transcriptome analysis of myeloid cells (CD11b) and astrocytes (ACSA2) from the striatum and midbrain of control and parkinsonian animals

status: Public on Dec 19 2021

city: Pamplona

first: Maria S.

last: Aymerich

state: Navarra

address: Calle Irunlarrea, 1

department: Biochemistry and Genetics

country: Spain

institute: Universidad de Navarra

summary: Inflammation is a common feature in neurodegenerative diseases that participates in the process of neuronal loss. Here, we questioned whether the inflammatory reaction generated in Parkinson´s disease (PD) by dopaminergic neuron degeneration would trigger specific inflammatory reactions in the midbrain and in the striatum that could modify the course of neuronal death. Experimental parkinsonism was induced by overexpressing α-synuclein in the substantia nigra with a viral vector. Bulk RNA sequencing of purified midbrain microglia/myeloid cells showed a phagocytic and anti-inflammatory M2 phenotype, while midbrain astrocytes presented a pro-inflammatory state. In the striatum, microglia but not astrocytes presented a pro-inflammatory state.

overall_design: Control mice were injected with an AAV9-Control (AAV9-IRES-mCherry) and Syn mice were injected with an AAV9-Syn (AAV9-Syn-IRES-mCherry) into the substantia nigra by stereotaxic surgery. Mice were sacrifized 2 weeks after surgery, and CD11b+ and ACSA2+ cells were purified from the striatum and the midbrain to perform RNA sequencing.

first: M


title: Effect of volume overload on right ventricular remodeling in neonatal SD rats

status: Public on Dec 08 2021

city: Shanghai

first: Qing

last: Cui

state: Shanghai

address: Dongfang Lu No.1678

country: China

institute: Shanghai Children′s Medical Center Affiliated to Shanghai Jiaotong University School of Medicine

summary: We reported the RNAseq analyses of right ventricualr free wall myocardium in neonatal volume overload (VO) SD rat. VO was induced by the fistula between abdominal aorta and inferior vena cava (AVF) within 24 hours postnatally (P1). RNAseq analyses of RV free wall at P7 from VO and sham-operated rat revealed that there were 454 differentially expressed genes between VO and sham group at P7. GO analysis showed that in the VO and sham comparison, the upregulated genes mainly mediated immune system response and the downregulated genes mainly mediated apoptotic process at P7. VO has no effect to neonatal right ventricular cardiomyocyte proliferation.

overall_design: RNAseq analyses of right ventricular free wall myocardium in neonatal volume overload and sham-operated SD rat

first: Sijuan

last: Sun

first: Lincai

last: Ye

first: Jie

last: Shen


title: Transcriptional analysis of the effects of early life exposure to fluoxetine on telencephalon and hypothalamus in SR4G transgenic zebrafish larvae and adults

status: Public on Apr 26 2022

city: Ottawa

first: Matthew

last: Meier

state: Ontario

address: 251 Sir Frederick Banting Driveway

department: Health Canada

institute: Government of Canada

summary: Our previous study suggested persistent transgenerational effects of fluoxetine (FLX) exposure, in both environmental and therapeutic concentrations, on stress response and behaviour up to 3 generation withdrawn from exposure in larvae and adult zebrafish. To lay the foundations of the mechanistic of such transgenerational effects, we studied the effect of FLX on stress response in brain tissues (telencephalon and hypothalamus) of larvae and adult zebrafish using differentially expressed genes at the transcriptome level. To monitor the stress response, we used a transgenic zebrafish line (SR4G) which are expressing green fluorescence protein (GFP) in response to endogenous and exogenous glucocorticoids. The transcriptome analysis of GFP RNA as an internal control, provided us with an invaluable tool to clearly visualize and differentiate between stressed and unstressed groups as per treatments. To stimulate stress in both larvae and adult zebrafish we used a modified net stressing technique consisting of consecutive sequence of air exposure and incubation intervals. A pool of 22 larvae heads and a pool of 5 telencephalon and 5 hypothalamus dissected tissues were used as the target tissues for RNA extraction. All experiments were replicated in n=6 per 4 different groups including Control-Unstressed (Cnt-U), Control-Stressed (Cnt-S), Fluoxetine-Unstressed (FLX-U), and Fluoxetine-Stressed (FLX-S) using pools of larvae heads, telencephalon, and hypothalamus. After total RNA extraction, using Illumina technology all samples were sequence and the list of differentially expressed genes (DEGs) were produced using DSEQ pipeline in R.

overall_design: Three different target tissue, two from 6 months old adults (Telencephalon and Hypothalamus) and one from 6 days post fertilization larvae (dissected heads). One treatment, Fluoxetine, One control (ethanol as vehicle), two condition (Stressed, Unstressed)

first: Amin

last: Nozari

first: Remi

last: Gagne

first: Carole

last: Yauk

first: Vance

middle: L

last: Trudeau


title: miRNA-seq and RNA-seq data from pharmacological inhibition of the G9a histone methyltransferase with UNC0642 in SAMP8 mice

status: Public on Nov 24 2021

city: Barcelona

first: Christian

middle: Griñán

last: Ferré

state: Barcelona

address: Joan XIII, s/n

department: Pharmacology, Toxicology and Therapeutic Chemistry

institute: University of Barcelona

type: Non-coding RNA profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: RNA-seq data from pharmacological inhibition of the G9a histone methyltransferase with UNC0642 in SAMP8 mice

summary:
Purpose: The aim of this study is to compare brain transcriptome profile (RNA-seq) after G9a inhibition.
Methods: Hippocampus profiles of 7-month-old SAMP8 Control and SAMP8 Treated mice groups were generated by deep sequencing, pooled using Ilumnia Hiseq.
Results: G9a inhibition with UNC0642 induces a transcriptional profile that allows beneficial effects on cognitive performance. Differential expression analysis identified 697 differentially expressed genes (DEG) (fold change cutoff of ≥1.3, p-value<0.05). Of which 217 are reduced, and 480 are increased in SAMP8 UNC0642.
Conclusions: Our study showed the first transcriptome analysis of whole brain after G9a inhibition, generated by RNA-seq technology, demonstrating transcriptomic changes.

overall_design: Hippocampus mRNA profiles after G9a inhibition in SAMP8 mice

last: Griñán-Ferré

first: Aina

last: Bellver-Sanchis

first: Mercè

last: Pallàs

first: Pedro

last: López


title: Multi-omic analysis of microRNA-mediated regulation reveals a proliferative axis involving miR-10b in fibrolamellar carcinoma

status: Public on Nov 03 2021

city: Ithica

first: Praveen

last: Sethupathy

state: NY

address: Cornell University College of Veterinary Medicine, Box 17

institute: Cornell University

summary: Fibrolamellar carcinoma (FLC) is an aggressive liver cancer with low survival rates and no standard-of-care. The vast majority of FLC patients carry a causative somatic mutation that leads to the gene fusion, DNAJB1-PRKACA. To work toward novel therapeutic strategies, it is important to understand the mechanisms underlying FLC etiology and progression. To that end, in this study, we analyzed a large sample cohort (52 patients) using multiple genome-scale assays to define genes subject primarily to post-transcriptional regulation by microRNAs. These studies revealed a candidate master microRNA regulator in FLC, miR-10b. Functional experiments in cells established from a patient-derived xenograft model revealed that miR-10b contributes to FLC cell metabolic health and proliferation.

overall_design: Multi-omic comparison of small RNAseq, RNAseq, and ChROseq data from liver tissue from fibrolamellar carcinoma patients.

first: Matt

last: Kanke


title: Checkpoint blockade induced CD8+ T cell differentiation in responders in head and neck cancers

status: Public on Dec 01 2021

city: Boston

first: Ravindra

last: Uppaluri

state: Massachusetts

address: 450 Brookline Avenue

institute: Dana-Farber Cancer Institute

summary:
Background: Outcomes for locally advanced or recurrent/ metastatic head and neck squamous cell carcinomas (HNSCCs) remain unfavorable despite recent advances with immune checkpoint blockade (ICB). Preclinical studies using model antigens identified a critical role of CD8+TCF7+PD1+ T cells in anti-PD1 response. Studies on the heterogeneity and clonal dynamics of global tumor infiltrating T lymphocytes (TILs) in the HNSCC anti-PD1 and anti-CTLA4 response have not been explored.
Results: In this study, we generated isogenic HNSCC anti-PD1 sensitive/resistant models that bore distinct cancer cell intrinsic transcriptomic programs. Tumor microenvironment characterization using mass cytometry and targeted depletion revealed the contribution of Tregs and M2-like macrophages in anti-PD1 resistance. Paired single-cell RNA and TCR sequencing on tumor infiltrating immune cells from ICB responsive and resistant HNSCC models identified a spectrum of CD8+ TIL subsets including TCF7+PD1- (naïve/memory-like), TCF7+PD1+ (progenitor exhausted), and TCF7-PD1+ (terminally exhausted). Mapping TCR shared fractions between these subsets identified that successful anti-PD1 or anti-CTLA4 therapy induced higher post-treatment T cell lineage transitions. A TIL differentiation gene signature was associated with better responses in multiple ICB clinical trials.
Conclusions: Together, analyses integrating scRNAseq and TCRseq demonstrate distinct differentiation dynamics of CD8+ TILs in novel ICB responsive and resistant HNSCC models, highlighting critical aspects of CD8+ TIL differentiation in response to ICB.

overall_design: profiling tumor infiltrating T cells scRNA and TCR-seq in responding and resistance conditions, as well as bulk RNAseq of bulk tumors and cell lines


title: Single-cell sequencing of tumor ecosystems in papillary thyroid carcinoma

status: Public on Sep 19 2021

first: Yulong

last: Wang

address: 270 Dongan Road, Shanghai

department: Department of Head and Neck Surgery

institute: Fudan University Shanghai Cancer Center

summary: The tumor ecosystem of papillary thyroid carcinoma (PTC) is poorly characterized. Using single-cell RNA sequencing, we profiled transcriptomes of 158,577 cells from 11 patients’ paratumors, localized/advanced tumors, initially-treated/recurrent lymph nodes and radioactive iodine (RAI)-refractory distant metastases, covering comprehensive clinical courses of PTC.Our study illuminates a comprehensive landscape of PTC ecosystem that suggests potential prognostic and therapeutic implications. Our work not only adds dimensions to the biological underpinnings of PTC heterogeneity, but also provides a benchmark dataset for this malignancy.

overall_design:
In total, 23 fresh surgical specimens (7 primary tumors, 6 para-tumors, 8 metastatic LNs and 2 subcutaneous metastatic loci) were collected and subjected to scRNA-seq with 10X Genomics.
**Submitter declares that the raw data have been deposited in the Genome Sequence Archive (https://ngdc.cncb.ac.cn/gsa/) under submission number HRA001107.**

first: Weilin

last: Pu

first: Xiao

last: Shi

first: Pengcheng

last: Yu

first: Meiying

last: Zhang

first: Xiaoming


title: RNA sequencing analysis of gene expression in the prefrontal cortex of mice treated with antidepressant drugs

status: Public on Jan 17 2022

city: Kyoto

first: Shusaku

last: Uchida

state: Kyoto

address: 53 Kawaharamachi, Sakyo-ku

country: Japan

institute: Kyoto University

summary: We performed high-throughput profiling of gene expression in mouse prefrontal cortex in response to antidepressant treatment. BALB/c mice were treated with sertraline, duloxetine, or water for three weeks. Then we performed forced swim test to check their antidepressant-like behavior. We divided these animals to responder and non-responder based on their behavior in the forced swim test. We then conducted the transcriptomics analysis and found specific and distinct genes in responder and non-responder mice. Our study provided deep insights into the understanding of the molecular mechanisms underlying the behavioral response to antidepressants.

overall_design: BALB/c mice were treated with sertraline, duloxetine, or water for three weeks. Total 5 groups were set up: mice received water (E), sertraline for responder (F) and non-responder (G), duloxetine for responser (H) and non-responder (I). Three replicates were used for each group.


title: Maternally infection promotes offspring tissue-specific immune fitness

status: Public on Sep 24 2021

city: Bethesda

first: Verena

last: Link

address: 4 Memorial Drive

department: NIAID

institute: NIH

summary: Mammals evolved in the face of pathogen exposure, the vast majority of these encounters resulting in asymptomatic or mild infections. How these constitutive exposures at specific developmental stages impact the host immune system for the long term remains poorly understood. Here we show that maternally restricted, mild infections, can have a permanent and tissue-specific impact on the offspring immunity. This imprinting is associated with a selective increase of Th17 cells within the gut, but not other compartment, and results from enhanced tonic responses to the microbiota. Mechanistically, we found that IL-6 produced by the mother during infection can directly act on fetus intestinal epithelial cells, leading to long-term alteration in chromatin and transcriptomic profiles in intestinal epithelial cells. As such at the adult stage, offspring display enhanced protective responses to oral infections. Together this work proposes that maternal infections can be coopted during fetal development as a mean to promote long-term tissue-specific immune fitness in offspring.

overall_design: Examiniation of epithelial cells and whole tissue through RNA-seq, ATAC-seq and single cell RNA-seq in mice born to mothers treated with control, YopM or IL-6.

first: Ai

middle: I

last: Lim

first: Yasmine

last: Belkaid


title: Antipsychotic-induced epigenomic reorganization in frontal cortex samples from individuals with schizophrenia

status: Public on Nov 05 2021

city: Blacksburg

first: Chang

last: Lu

state: VA

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

department: Chemical Engineering

institute: Virginia Tech

summary: We examined the effects of antipsychotic medications on the cell-specific epigenomics and transcriptomics in the frontal cortex of schizophrenic subjects.

overall_design:
We performed ChIP-seq (H3K4me3 and H3K27ac) and RNA-seq on neuronal and glial nuclei of frontal cortex samples from two cohorts of postmortem schizophrenic subjects that were treated or untreated with antipsychotic medications and their controls with individually matched sex and age. In total, we tested 29 schizophrenics (15 untreated and 14 treated) and their matched control samples. Two replicates were produced on each brain sample for each assay. ChIP-seq data were generated using MOWChIP-seq (Zhu et al., Nature Protocols 14 (2019) 3366-3394.) and RNA-seq data were produced using the combination of SMART-seq2 (Picelli et al., Nature Protocols 9 (2014) 171–181.) and a Nextera XT DNA library preparation kit. The filename contains the information on the experimental group, the number of the sample within the group, the type of the brain nuclei, the epigenomic/transcriptomic data set (either H3K27ac or mRNA), and the number of replicate. For example, "SCZ_1_untreated_NeuN+_H3K4me3_R1" refers untreated schizophrenic sample #1, replicate 1 ChIP-seq data on H3K4me3.

>>> Submitter declares that the raw data will be deposited in dbGaP due to patient privacy concerns. <<<

first: Bohan

last: Zhu

first: Chengyu

last: Deng


title: The NK cell stress response status modulates anti-tumor immunity [ChIP-seq]

status: Public on Jan 26 2022

city: New York

first: Kathryn

middle: Grace

last: Hockemeyer

state: New York

address: 550 1st Avenue

department: Pathology

institute: NYU Langone Health

summary: The tumor microenvironment (TME) harbors numerous types of cellular stress that can activate Heat Shock Factor 1 (HSF1), a central regulator of stress response. HSF1 has been shown to directly regulate diverse gene programs beyond the classical heat shock response in a cell-type- and context-specific manner. Here, we uncover significant variability in HSF1 levels and activity between immune populations in patient tumors, with the lowest in natural killer (NK) cells. We demonstrate that accumulation of activated HSF1 in the TME dampens anti-tumor immunity through impairing NK cell cytotoxicity, which could be rescued by NK cells with homeostatic levels of HSF1. HSF1 stabilization results in altered chromatin accessibility and expression of surface receptors and signaling proteins involved in NK cell activation. We further reveal direct occupancy of HSF1 at promoters of genes encoding mediators of NK cell cytotoxicity. Single-cell transcriptional profiling of the TME in the context of elevated HSF1 revealed an inverse relationship between the stress response status and NK cell effector function. Collectively, this work identifies a novel role of HSF1 in regulating the NK cell activation state and subsequent anti-tumor functionality.

overall_design: Chromatin immunoprecipitation (ChIP) for HSF1 was performed in the NK cell line NK-92 MI (10 x 10^6 cells). HSF1 ChIP and input subsequently were sequenced using Novaseq 6000.

first: Elena

last: Battistello

first: Iannis

last: Aifantis


title: Simple oligonucleotide-based multiplexing of single-cell chromatin accessibility

status: Public on Oct 20 2021

city: Houston

first: Anil

last: Sood

state: TX

address: 6767 Bertner Ave

department: genetics

institute: MDACC

summary: we reported the development of an accurate, easy-to-use and scalable system (SNuBar) for multiplexing single cell ATAC or multi-omics (ATAC&RNA) assays, and applied this method to multiplex therapy combinations in a lung cancer mouse model and macro-spatial regions of normal breast tissues and samples.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: SNuBar multiplexes scATAC-seq and scATAC&RNA-seq with unmodified oligonucleotides, identfies treatment-induced chromatin dynamics in 28 mice with lung tumors, profiles epigenetic heterogeneity of 32 spatial regions in normal breast tissues, identifies TFs that regulated breast cell type identities.

first: Kaile

first: Zhenna

last: Xiao

first: Yun

last: Yan

first: Nicholas

last: Navin


title: Maternally infection promotes offspring tissue-specific immune fitness [scRNA-seq]

overall_design: Examiniation of epithelial stem cells by single cell RNA-seq (10X 3' kit) in the gut of mice born to mothers treated with control, YopM or IL-6.


title: Single-cell transcriptomics of human iPSC differentiation dynamics reveal a core molecular network of Parkinson’s disease

status: Public on Sep 04 2021

city: Esch-sur-Alzette

first: Kamil

last: Grzyb

email: kamilgen@gmail.com, kamil.grzyb@uni.lu

address: 2, avenue de l'Université

country: Luxembourg

institute: University of Luxembourg - LCSB

summary: Gabriela Novak et al. utilize scRNA-seq to investigate expression profiles in iPSC-derived midbrain dopaminergic neurons from Parkinson's disease patients or healthy controls. Their results suggest a core molecular network associated with Parkinson's disease pathology, and provide a future resource for investigation of this critical disorder.

overall_design: Single-cell RNA-Sequencing experiments were performed on a total of 12 samples.

first: Gabriela

last: Novak

first: Dimitrios

last: Kyriakis

first: Michela

last: Bernini

first: Sophie

last: Rodius

first: Gunnar

last: Dittmar

first: Steven

last: Finkbeiner

first: Alexander

last: Skupin


title: myotis bat morbillivirus

status: Public on Jul 31 2021

city: new york

first: satoshi

last: ikegame

state: new york

address: 1468 madison avenue, Annenbergbuilding 17-24

department: microbiology

institute: Icahn school of medicine at Mount Sinai

summary: We report myotis bat morbillivirus sequence indentification from myotis riparius

overall_design: single experiment

first: Satoshi

last: Ikegame

first: Simon

last: Anthony

first: Heather

last: Wells

first: Edison

last: Durigon


title: Maternal plasma cell-free RNA sequencing for preeclamptic and normotensive mothers

status: Public on Jan 03 2022

city: Stanford

first: Mira

middle: Noura

last: Moufarrej

state: CA

address: 318 Campus Drive, E300

department: Bioengineering

institute: Stanford University

summary: Liquid biopsies that measure circulating cell-free RNA (cfRNA) offer an unprecedented opportunity to noninvasively study the development of pregnancy-related complications and to bridge gaps in clinical care. Here, we sequenced cfRNA from 404 blood plasma samples (199 pregnant mothers) to identify and validate cfRNA transcriptomic changes that are associated with preeclampsia (PE), a multi-organ syndrome which is the second largest cause of maternal death globally. For each individual, samples were collected at one or more timepoints across gestation. For some, samples were also collected at least once post-partum.

middle: N

first: Stephen

middle: R

last: Quake

first: David

last: Stevenson


title: Evaluation of viral mRNA modification

summary: We report viral mRNA modification in bat morbillivirus infection

overall_design: three replicate experiment

first: Bebhur

last: Lee


title: Evaluation of viral transcriptome

summary: We report transcriptome of bat morbillivirus

overall_design: single replicate experiment


title: High-throughput Sequencing of exosomal lncRNAs and circRNAs in large artery atherosclerosis stroke

status: Public on Jun 08 2021

city: Shandong

first: Shuai

last: Zhang

address: Qingdao, Shandong,China

institute: he Affiliated Hospital of Qingdao University

summary: Purpose: This study aimed to explore the differential expression profiles of exosomal lncRNAs and evaluated their potential utility in the accurate diagnosis of LAA stroke. Methods: LncRNA profiles of exosomes in large artery atherosclerosis stroke and controls were generated by high-throughput sequencing. The sequence reads that passed quality filters were analyzed at the transcript isoform level with Hisat2, Trapnell, STAR. qRT–PCR validation was performed using TaqMan and SYBR Green assays. Results: A total of 1020 differentially expressed lncRNAs were identified in LAA stroke patients. GO and KEGG pathway analyses indicated that their target genes are involved in atherosclerosis-related pathways, including inflammation, cell adhesion, and cell migration. 8 exosomal lncRNAs were confirmed with qRT–PCR.The result showed that the expression trend of differential expressed lncRNAs in validation was consistent with RNA-seq.Conclusion: Our study showed the differential expression of lncRNAs in plasma exosomes and presented related diagnostic potential for LAA stroke for the first time. The results suggested that exosomal lncRNA could be potential diagnostic tools in LAA stroke. Circular RNAs (circRNAs), novel endogenous noncoding RNAs, play diverse roles in ischemic stroke. Recently, the abundance and stability of circRNAs in exosomes have been identified. However, a comprehensive analysis of exosomal circRNAs in large artery atherosclerotic (LAA) stroke has not yet been reported. We performed RNA sequencing (RNA-Seq) to comprehensively identify differentially expressed exosomal circRNAs in five paired LAA and normal controls. RNA-Seq identified a total of 462 circRNAs in peripheral exosomes; there were 25 differentially expressed circRNAs among them. Additionally, circRNA competing endogenous RNA (ceRNA) network and translatable analysis revealed the potential functions of the exosomal circRNAs in LAA progression. Two ceRNA pathways involving 5 circRNAs, 2 miRNAs, and 3 mRNAs were confirmed by qRT-PCR. In the validation cohort, receiver operating characteristic (ROC) curve analysis identified two circRNAs as possible novel biomarkers, and a logistic model combining two and four circRNAs increased the area under the curve compared with the individual circRNAs.

overall_design: Plasma exosomal lncRNA and circRNA profiles of large artery atherosclerosis stroke and healthy controls

first: Xudong

last: Pan

first: Xiaoyan

last: Zhu

first: Aijun

last: Ma


title: DNA hypohydroxymethylation in pediatric brain tumors is associated with CTCF binding sites and reduced survival

status: Public on Jun 01 2021

city: Hanover

first: Nasim

last: Azizgolshani

state: NH

address: Dartmouth College

department: Christensen Lab

institute: Dartmouth College

type: Methylation profiling by genome tiling array

summary: We measured genome-scale 5hmC in glioma, ependymoma, and embryonal tumors from children, as well as control pediatric brain tissues using oxidative and bisulfite treatments. Tumor 5hmC localized to regulatory elements crucial to cell identity, including transcription factor binding sites and super-enhancers. A linear model tested the CpG-specific differences in 5hmC between tumor and non-tumor samples, as well as between tumor subtypes. Compared to non-tumor samples, tumors were hypohydroxymethylated across the epigenome. Differentially hydroxymethylated loci among tumor subtypes tended to be hypermethylated and disproportionally found in CTCF binding sites and genes related to posttranscriptional RNA regulation, such as DICER1.  Model-based clustering results indicated that patients with low 5hmC patterns have poorer overall survival and increased risk of recurrence.

overall_design: BS and oxBS conversions were performed with 1.2 -1.4 _g of DNA according to the TrueMethyl protocol. ssDNA was recovered and quantified with Qubit and were hybridised to the Illumina Infinium HumanMethylationEPIC Beadchip v1.0_B4  using standard Illumina protocol.

first: Curtis

last: Petersen

first: Youdinghuan

last: Chen

first: Lucas

last: Salas

first: Laurent

last: Perreard

first: Lananh

last: Nguyen

first: Brock

last: Christensen


title: Megakaryocyte Progenitor Cell Function is Enhanced Upon Aging Despite the Functional Decline of Aged Hematopoietic Stem Cells

city: Santa Cruz

first: Camilla

last: Forsberg

state: California

address: 1156 High Street

institute: Institute for the Biology of Stem Cells, University of California Santa Cruz

summary: We sequenced mRNA from young or old MkP populations identified in the mouse in order to determine novel molecular regulators of their unique functional properties.

overall_design: mRNA levels were examined in bulk Young or Old Lin-cKit+Sca1-CD150+CD41+ cells  isolated from the bone marrow of Young or Old WT mice

first: D

last: Poscablo

first: A

last: Worthington

first: S

last: Smith-Berdan

first: E


title: miRNA-seq data from pharmacological inhibition of the G9a histone methyltransferase with UNC0642 in SAMP8 mice

first: Christian

last: Ferré

summary:
Purpose: The aim of this study is to compare brain transcriptome profile (RNA-seq) after G9a inhibition.
Methods: Hippocampus profiles of 7-month-old SAMP8 Control and SAMP8 Treated mice groups were generated by deep sequencing, pooled using Ilumnia Hiseq.
Results: G9a inhibition with UNC0642 induces a transcriptional profile that allows beneficial effects on cognitive performance. Differential expression analysis identified 697 differentially expressed genes (DEG) (fold change cutoff of ≥1.3, p-value<0.05). Of which 217 are reduced, and 480 are increased in SAMP8 UNC0642.
Conclusions: Our study showed the first transcriptome analysis of whole brain after G9a inhibition, generated by RNA-seq technology, demonstrating transcriptomic changes.

overall_design: Hippocampus miRNA profiles after G9a inhibition in SAMP8 mice

last: Griñán-Ferré

first: Aina

last: Bellver-Sanchis

first: Mercè

last: Pallàs

first: Pedro

last: López


title: Single-cell atlas of human oral mucosa reveals a stromal-neutrophil axis in tissue immunity regulation

status: Public on Apr 21 2021

first: Niki

last: Moutsopoulos

address: 30 convent Dr

institute: NIDCR

summary: The oral mucosa remains an understudied barrier tissue rich in exposure to antigens, commensals and pathogens. Moreover, it is the tissue where one of the most prevalent human microbe-triggered inflammatory diseases, periodontitis, occurs. To understand this complex environment at the cellular level, we assemble herein a human single-cell transcriptome atlas of oral mucosal tissues in health and periodontitis. Our work reveals transcriptional diversity of stromal and immune cell populations, predicts intercellular communication and uncovers an altered immune responsiveness of stromal cells participating in tissue homeostasis and disease at the gingival mucosa. In health, we define unique populations of CXCL1,2,8- expressing epithelial cells and fibroblasts mediating immune homeostasis primarily through the recruitment of neutrophils. In disease, we further observe stromal, particularly fibroblast hyper-responsiveness linked to recruitment of leukocytes and neutrophil populations. Our work suggests a stromal-neutrophil axis as a key regulator of mucosal immunity. Pursuant to these findings, most Mendelian forms of periodontitis were shown to be linked to genetic mutations in neutrophil-expressed genes. Moreover, we document previously unappreciated expression of known pattern- and damage- recognition receptors on stromal cell populations in the setting of periodontitis, suggesting avenues for triggering of stromal responsiveness. This comprehensive atlas offers an important reference for in-depth understanding of oral mucosal homeostasis and inflammation and reveals unique stromal–immune interactions implicated in tissue immunity.

overall_design: Examination of human oral mucosa including healthy and diseased gingival mucosa and healthy buccal mucosa.

first: Drake

middle: W

last: Williams


title: Neutrophil Subtypes Shape HIV-specific CD8 T Cell Responses After Vaccinia Virus Infection.

status: Public on Apr 12 2021

city: New Haven

first: Andrés

last: Hidalgo

address: 10 Amistad Street

institute: Yale University

summary: Neutrophils are innate immune cells involved in the elimination of pathogens. Recent studies showed that neutrophils can also act as antigen presenting cells (APC) to induce adaptive immune responses. Specific neutrophil populations (Na and Nb) with different levels of APC markers and in vitro distinct capacity to generate vaccinia virus (VACV)-specific CD8 T cell responses have been shown. However, how these neutrophil subtypes exert their role in vivo and how manipulation of Nb/Na ratio can influence vaccine-mediated immune responses are not known. In the context of VACV infection, we characterized HIV-specific CD8 T cell responses, delineated neutrophil transcriptomic profiles and described neutrophil dynamic behaviors in the spleen. By splenic multiphoton intravital microscopy (MV-IVM), we could distinguish both neutrophil subtypes and found that they showed distinct migratory and motility patterns and different ability to interact with CD8 T cells and move towards them. After analysis of adhesion, inflammatory and migration receptors from peritoneal cavity, blood and spleen, we defined that Nb neutrophils overexpressed the trans-endothelial migration marker a4b1integrin compared to Na subtype. Finally, by inhibiting a4b1integrin, we increased the Nb/Na ratio in peritoneal cavity and spleen, and in turn enhanced CD8 T cell responses to HIV-antigens. These findings provide significant advancements in the comprehension of neutrophil-based control of adaptive immune system. These results are relevant in vaccine vector design that could induce distinct neutrophil subtypes and, in consequence modulate antigen-specific T cell responses.

overall_design: Bulk RNA-seq of Nα and Nβ shorted from pertinoneal washes of three mice immunized with 10^7 pfu of NYVAC-C Δ3

first: Mauro

last: Di Pilato

first: Miguel

last: Palomino-Segura

first: Andrea

last: Rubio-Ponce

first: Ernesto

last: Mejías-Pérez

first: Alberto

middle: B

last: Filippini


title: Single cell transcriptomic analysis of diffuse large B cells in cerebrospinal fluid of central nervous system lymphoma

status: Public on Aug 25 2021

city: Shanghai

first: Zhe

last: Wang

address: Siping Road, Shanghai

institute: Tongji university

summary: Diffuse large B-cell lymphoma (DLBCL) is the predominant type in central nervous system lymphoma (CNSL) including primary CNSL and secondary CNSL. Diffuse large B cells in cerebrospinal fluid (CSF-DLBCs) have offered great promise for the diagnostics and therapeutics of CNSL leptomeningeal involvement. To explore the distinct phenotypic states of CSF-DLBCs, we analyzed the transcriptomes of CSF-DLBCs from seven CNSL-DLBCL patients using single-cell RNA sequencing technology. We defined CSF-DLBCs based on abundant expression of B-cell markers, as well as the enrichment of cell proliferation and energy metabolism pathway. CSF-DLBCs within individual patient have monoclonality with similar variable region of light chains (VL) expression. It is interesting to find some CSF-DLBCs have double classes of VL (lambda and kappa) transcripts. We identified substantial heterogeneity in CSF-DLBCs, and found significantly greater among-patient heterogeneity compared to among-cell heterogeneity within patient. The transcriptional heterogeneity across CSF-DLBCs are manifested in cell cycle state and cancer-testis antigens expression. Our results will provide insight into the mechanism research and new diagnostic direction of CNSL-DLBCL leptomeningeal involvement.

overall_design: We analyzed the transcriptomes of CSF-DLBCs from seven CNSL-DLBCL patients using single-cell RNA sequencing technology

first: Haoyu

last: Ruan


title: Small RNA analysis of human erythropoiesis

status: Public on Oct 14 2021

city: Vellore

first: Shaji

last: Velayudhan

state: Tamil Nadu

address: Centre for Stem Cell Research, Christian Medical College, Bagayam

institute: Christian Medical College

summary: Small RNAs including microRNAs play a critical role at different stages of haematopoiesis. The study was designed to profile miRNA expression during human erythropoiesis.

overall_design: The CD34+ haematopoietic progenitors obtained from a normal donor were expanded for 5 days in the phase I medium and then differentiated using erythroid culture medium to obtain erythroid progenitors at different stages of erythropoiesis. RNA was extracted from the cells from day 3 of phase I of the culture and from the cells from day 9, day 11 and day 14 of phase II of the culture. Small RNAs were analyzed by Next Generation Sequencing.


title: Endotype of Allergic Asthma with Airway Obstruction in Urban Children

status: Public on Apr 01 2021

city: Seattle,

first: Stephanie

last: Osmond

state: WA

address: 1201 9th Ave

institute: Benaroya Research Institute

summary: In the first decade of life, high-asthma risk urban children develop stable phenotypes of respiratory health versus disease that link early life environmental exposures to childhood allergic sensitization and asthma. Moreover, unique patterns of nasal gene expression demonstrate how specific molecular pathways underlie distinct respiratory phenotypes, including allergic and non-allergic asthma.

overall_design: URECA is a high risk asthma birth cohort study. These samples are nasal brush samples taken at age 11. They were used to identify airway gene expression patterns that associate with clinical phenotypes over time.

first: Matthew

last: Altman

first: Sima

last: Ramratnam

first: Daniel

middle: J

last: Jackson

first: Scott

last: Presnell

first: Peter

last: Gergen

first: Leonard

last: Bacharier

first: George

middle: T

last: O'Connor

first: Meyer

last: Kattan

first: Robert

last: Wood

first: Agustin

last: Calatroni

first: Cynthia

last: Visness

first: James

middle: E

last: Gern


title: Differential chromatin binding of the lung lineage transcription factor NKX2-1 resolves opposing murine alveolar cell fates in vivo [ChIP-seq]

status: Public on Mar 08 2021

city: Memphis

first: Danielle

middle: R.

last: Little

state: Tennessee

address: 262 Danny Thomas Pl Rm D2031

department: Developmental Neurobiology

institute: St. Jude Children's Research Hospital

summary: Differential use of identical DNA sequences leads to distinct tissue lineages and then multiple cell types within a lineage, an epigenetic process central to progenitor and stem cell biology. The associated genomic changes, especially in native tissues, remain insufficiently understood, and are hereby addressed in the mouse lung, where the same lineage transcription factor NKX2-1 promotes the diametrically opposed alveolar type 1 (AT1) versus AT2 cell fate. We show that the cell-type-specific function of NKX2-1 is attributed to its differential chromatin binding that is acquired or retained during development in coordination with partner transcriptional factors. Loss of YAP/TAZ redirects NKX2-1 from its AT1-specific to AT2-specific binding sites, leading to transcriptionally exaggerated AT2 cells when deleted in progenitors or AT1-to-AT2 conversion when deleted after fate commitment. Nkx2-1 mutant AT1 and AT2 cells gain distinct accessible sites including those of the opposite fate while adopting the gastrointestinal fate, suggesting an epigenetic plasticity larger than a transcriptional one. Our genomic analysis of single or purified cells, coupled with precision genetics, provides an epigenetic roadmap of alveolar cell fate and potential, and introduces an experimental benchmark for unraveling the in vivo function of lineage transcription factors.

overall_design: ChIP-seq on Chromatin obtained from nuclei of either whole lungs,  AT1, or AT2 cells. If AT1 or AT2 cells, then nuclei were sorted for GFP expression as a result of recombination of RosaSun1GFP undercontrol of a cell type specific driver.

first: Jichao

last: Chen


title: Comprehensive characterization of tumor immune landscape following oncolytic virotherapy by single-cell RNA sequencing

status: Public on Nov 01 2021

first: Guangsheng

last: Pei

state: Texas

address: 7000 Fanin

institute: UTHealth

summary: single-cell RNA sequencing analysis on carcinomas treated with an HSV-2-based oncolytic virus to characterize the immunogenic changes in the TME

overall_design: Carcinomas treated with an HSV-2-based oncolytic virus

first: Divya

last: Ravirala

first: Zhongming

last: Zhao

first: Shaun

last: Zhang


title: Localized skin inflammation during cutaneous leishmaniasis drives a chronic, systemic IFN-g signature

status: Public on Mar 23 2021

city: Philadelphia

first: Camila

last: Farias Amorim

state: United States

address: 380 S University Ave

department: Pathobiology

institute: University of Pennsylvania

summary: Cutaneous leishmaniasis is a localized infection controlled by CD4+ T cells that produce IFN-g within lesions. Phagocytic cells recruited to lesions, such as monocytes, are then exposed to IFN-g which triggers their ability to kill the intracellular parasites. Consistent with this, a transcriptional analysis of lesions from patients identified the presence of a strong interferon stimulated gene (ISG) signature. To determine what systemic responses are occurring that might influence the disease, we performed RNA sequencing (RNA-seq) on the blood of L. braziliensis-infected patients, as well as healthy controls. Functional enrichment analysis identified a transcriptional ISG signature as the dominant response in the blood of patients. An increase in monocytes and macrophages in the blood, estimated from our RNA-seq dataset, was positively correlated with this ISG signature. Consistent with this result, patients had circulating IFN-g in their serum. A cytotoxicity signature, which is a dominant feature in the lesions, was also found in the blood and correlated with an increased abundance of cytolytic cells. Thus, two transcriptional signatures present in lesions were found systemically, although with a substantially reduced number of differentially expressed genes (DEGs). Finally, we found that the number of DEGs and ISGs in leishmaniasis was similar to tuberculosis – another localized infection – but significantly less than observed in malaria. In contrast, the cytolytic signature and increased cytolytic cell abundance was not found in tuberculosis or malaria.  Our results indicate that systemic signatures can reflect what is occurring in leishmanial lesions. Furthermore, the presence of an ISG signature in blood monocytes and macrophages suggests that when these cells enter lesions they may already be primed to control the parasites.

overall_design: Whole blood samples from patients infected with Leishmania braziliensis (n=50) and from not-infected individuals (n=14)

first: Phillip

last: Scott

last: Beiting


title: Single-cell RNA sequencing of human osteosarcoma

status: Public on Aug 19 2021

city: Nanning

first: Wenyu

last: Feng

state: Guangxi

address: Shuangyong road 22

department: Center for Genomic and Personalized Medicine

institute: Guangxi Medical University

summary: We performed the scRNA-seq analysis of 6 osteosarcoma tissues based on the 10X Genomics.

overall_design: Primary osteosarcoma tissues from 6 patients were used for single cell RNA sequencing by 10X Genomics

first: Yun

last: Liu

first: Yan

last: Dai

first: Mengying

last: Bao

first: Zhenchao

last: Yuan

first: Yu

last: Ye

first: Mingwei

last: He

first: Zhaojie

last: Qin

first: Shijie

last: Liao

first: Juliang

first: Qian

last: Huang

first: Zhenyuan

last: Yu

first: Yonghua

last: Jiang

first: Jinling

first: Jie

last: Ma

first: Zengnan

last: Mo

first: Qingjun

last: Wei


title: Differential chromatin binding of the lung lineage transcription factor NKX2-1 resolves opposing murine alveolar cell fates in vivo

first: Danielle

last: Little

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

overall_design: Refer to individual Series


title: Chili pepper RNA-Seq data for fruit development in a set of accessions

status: Public on Mar 16 2021

city: Irapuato

first: Octavio

last: Martinez de la Vega

state: Guanajuato

address: km 9.6 Libramiento Norte

department: Unidad de Genómica Avanzada (Langebio)

country: Mexico

institute: Cinvestav

summary: Twelve chili pepper accessions, six domesticated, four wild and two F1 crosses were studied. RNA-Seq experiments were performed with fruits from each accession at 7 different times after anthesis. Additionally, samples of seedlings from two accessions were evaluated. The data set is comprised by 179 samples, that in total have more than 3 billion reads map to the Capsicum annuum genome.

overall_design: Complete factorial design with 2 factors: accessions (12 levels) and time of fruit development (7 levels) with two replicates per factor combination.

last: Martínez

first: Magda

last: Arce-Rodríguez

first: Fernando

last: Hernández-Godínez

first: Christian

last: Escoto-Sandoval

first: Felipe

last: Cervantes-Hernández

first: Corina

last: Hayano-Kanashiro

first: José

last: Ordaz-Ortiz

first: M

middle: H

last: Reyes-Valdés

middle: G

last: Razo-Mendivil

first: Ana

last: Garcés-Claver

first: Neftalí

last: Ochoa-Alejo


title: Differential chromatin binding of the lung lineage transcription factor NKX2-1 resolves opposing murine alveolar cell fates in vivo [scATAC-Seq]

overall_design: FACS-purified lung epithelial, immune, endothelial, and mesenchymal cells were processed through the Chromium Single Cell Gene Expression Solution Platform (10X Genomics)

first: Jichao

last: Chen


title: Deciphering isoform switching and specific isoform usage during biofilm lifestyle by Candida glabrata analysed through global transcriptomic approach

status: Public on Jun 09 2021

city: CHANDIGARH

first: KHEM

last: RAJ

state: Chandigarh

address: Deparment of Microbiology, BMS Block-I, PANJAB UNI, PANJAB UNIVERSITY, SECTOR -25

department: Microbiology

institute: PANJAB UNIVERSITY

summary:
Methodology: RNA was extracted using Hi-PurA yeast RNA purification kit from biofilm and planktonic growth phase and sequenced by Illumina Hi-Seq 2500 and  platform with 250bp paired chemistry and analysed by IsoformSwitchAnalyseR tool of bioconductor
Results: Differential transcript expression (DTE) and differential transcript utilization (DTU) of C. glabrata showed that it utilized 292 significant transcripts isoforms during biofilm formation via isoform switching process.
Conclusion: Investigation of the present study elucidated that the switched isoform and predicted proteins encoded in biofilm growth mode of this pathogen could be used as a potential target for the development of novel antifungal targets.

overall_design:
mRNA of 24h grown biofilm growth phase from 3 biological replicates and similarly 3 biological replicates were taken from  planktonic growth phase
**Please note that  duplicated sample records of GSE152789 samples were created for the convenient retrieval of the complete raw data from SRA.

first: Khem

last: Raj

first: Geeta

last: Shukla

first: Praveen

last: Rishi

first: Amrita

last: Kaur

first: Shivaprakash

middle: M

last: Rudramurhty

first: Dattatray

middle: S

last: Mongad


title: Differential chromatin binding of the lung lineage transcription factor NKX2-1 resolves opposing murine alveolar cell fates in vivo [scRNA-Seq]

first: Danielle

last: Little


title: Differential chromatin binding of the lung lineage transcription factor NKX2-1 resolves opposing murine alveolar cell fates in vivo [ATAC-seq]


title: Divergent immunometabolic changes in adipose tissue and skeletal muscle with ageing in healthy humans

status: Public on May 26 2021

city: Boston

first: William

middle: V

last: Trim

state: MA

address: 25 Shuttack Street

department: Systems Biology

institute: Harvard Medical School

summary: RNA-sequencing from 12 young (20-35 years old) and 12 older (60-85 years old) participants' skeletal muscle and adipose tissue. Biopsies were taken at rest following an overnight fast, and following alcohol/caffeine restriction for 24 hours, and no strenuous physical activity for 48 hours. Skeletal muscle was taken by the Bergstrom technique under local anaesthesia (Lidocaine hydrochloride) from the dominant leg Vastus Lateralis, and adipose tissue was taken by needle aspiration 5cm lateral to the umbilicus.

overall_design: Examination of the effect of ageing on adipose tissue and skeletal muscle transcriptomes in healthy, active younger and older men

first: Jean-Philippe

last: Walhin

first: Francoise

last: Koumanov

first: Anne

last: Bouloumie

first: Mark

middle: A

last: Lindsay

first: Yung

middle: C

first: Rebecca

middle: L

last: Travers

first: James

last: Turner

first: Dylan

last: Thompson


title: Identification of transcriptional targets of TBX3 in PTC cells and mPTC by RNA sequencing

status: Public on Apr 30 2021

city: Tianjin

first: Peitao

last: Zhang

address: Qixiangtai Road 22

institute: Tianjin Medical University

summary: The purposes of this study were to compare and analyze the expression differences of  mouse papillary thyroid carcinoma (mPTC) induced by BrafV600E after Tbx3 deletion. And in order to gain insights into global gene expression regulated by TBX3 in human PTC cells, RNA-Seq experiments were performed in K1 cells with knockdown of TBX3.

overall_design: mRNA profiles of K1-shctrl and K1-shTBX3 were generated by deep sequencing, in duplicate, using Illumina novaseq6000 . And mRNA profiles of mouse papillary thyroid carcinoma (mPTC) control and Tbx3 knockout were generated by deep sequencing, in triplicate, using Illumina novaseq6000.

first: Li

last: Zhao


status: Public on Jan 31 2021

city: Dummerstorf

first: Jens

last: Vanselow

address: Wilhelm-Stahl-Allee 2

department: Reproductive Biology

country: Germany

institute: Leibniz Institute for Farm Animal Biology

summary: Expression profiling of bovine granulosa cells after oleic acid (OA) treatment vs. control (C) conditions after 8 days in culture.

first: Vengala

last: Yenuganti

first: Dirk

last: Koczan


title: MUC1-C integrates activation of the IFN-γ pathway with suppression of the tumor immune microenvironment in triple-negative breast cancer

status: Public on Feb 03 2021

city: Buffalo

first: Qiang

last: Hu

state: NY

address: Elm & Carlton Streets

institute: Roswell Park Cancer Institute

summary: Immune checkpoint inhibitors (ICIs) have had a profound impact on the treatment of many tumors; however, their effectiveness against triple-negative breast cancers (TNBCs) has been limited. One factor limiting responsiveness of TNBCs to ICIs is a lack of functional tumor i-infiltrating lymphocytes (TILs) in ‘“non-inflamed’” or ‘“cold’” tumor immune microenvironments (TIMEs), albeitalthough by unknown mechanisms. Targeting MUC1-C in a mouse transgenic TNBC tumor model increases cytotoxic tumor -infiltrating CD8 + T cells (CTLs), supporting a role for MUC1-C in immune evasion. The basis for these findings and whether they extend to human TNBCs are not known.

overall_design: Human TNBC cells (BT-549) silenced for MUC1-C using doxycycline inducible shRNAs were analyzed for the effects of MUC1-C on global transcriptional profiles.

first: Donald

last: Kufe

first: Song

last: Liu

first: Nami

last: Yamashita

middle: D

last: Long


title: G2/M DNA synthesis at transcription start sites because of RNA transcription persistence during DNA replication

status: Public on Feb 17 2021

city: Birmingham

first: Marco

last: Saponaro

address: Vincent Drive

department: Institute of Cancer and Genomic Sciences

country: United Kingdom

institute: University of Birmingham


title: Dual detection of chromatin accessibility and DNA methylation using ATAC-Me

status: Public on Mar 02 2021

city: Nashville

first: Emily

last: Hodges

state: TN

address: 2215 Garland Ave

department: Department of Biochemistry

institute: Vanderbilt University

type: Methylation profiling by high throughput sequencing

summary: We provide a detailed protocol for the generation of ATAC-Me libraries in a variety of cell types including H9 ESCs. We also display anticipated results that may be generated from application of the protocol to different model systems.

overall_design: Generation of ATAC-Me libraries and displays of potential analysis.

first: Lindsey

middle: N

last: Guerin

first: Kelly

last: Barnett


title: Genomic features and virulence characteristics of a rare Burkholderia thailandensis strain causing human infection

status: Public on Feb 15 2021

city: Chongqing,

first: Qiu

last: Zhong

address: Daping Changjiang street 10#

department: Department of Clinical Laboratory

institute: Third Military Medical University

summary: Introduction. Burkholderia thailandensis is a clinically rare opportunistic pathogen in the genus Burkholderia, and the genomic features and virulence characteristics of B. thailandensis strains that cause human infection remain unclear.Gap Statement. B. thailandensis strains with different virulence induce different host innate immune responses in vitro.Aim. This work aimed to understand the sequence diversity, phylogenetic relationship, and virulence of B. thailandensis BPM causing human infection.Methodology. The comparative molecular and genomic analyses, and mouse infection studies were applied to analyse the virulence and genomic features of B. thailandensis BPM originating from China.Results. The whole genome sequence analysis showed that the genomes of BPM and other avirulent B. thailandensis strains were broadly similar, comprising two highly syntenic chromosomes with comparable numbers of coding regions (CDs), protein family distributions, and horizontally acquired genomic islands. By examining species-specific genomic regions, we obtained molecular explanations for previously known differences in virulence and discovered the potential specific virulence-associated genes of BPM, which likely work together to confer the virulence of BPM. Significantly reduced LD50 and survival rates during mouse infection experiments were found in BPM compared to the avirulent B. thailandensis E264 (BtE264).Conclusion. Taken together, the results of this study provide basic information on the genomic features and virulence characteristics of the virulent B. thailandensis strain BPM, which is helpful for understanding its evolution as it relates to pathogenesis and environmental adaptability.

overall_design: Samples were taken from Burkholderia thailandensis E264 and Burkholderia thailandensis BPM respectively . Three independent experiments were performed

first: Jin

last: LI

first: Jian

last: Li

first: Hui-Min

last: Chong

first: Li-Xin

last: Wang

first: Yun

last: Xing

first: Wei-Ping

last: Lu


title: BRD9 is a regulator of androgen receptor signaling and prostate cancer progression

status: Public on Dec 28 2020

city: West Lafayette

last: Dykhuizen

state: IN

address: 201 S. University

department: medicinal chemistry and molecular pharmacology

institute: Purdue University


title: BRD9 is a critical regulator of androgen receptor signaling and prostate cancer progression - RNA-Seq

summary: Standard RNA-Seq analysis from LNCaP cells treated with shBRD9 for 3d, shBRD9 for 11d, or 3 µM IBRD9 for 3d.

overall_design: mRNA profiles of LNCaP cells with lentiviral mediated knockdown (shRNA) or knckout (CRISPR-Cas9). Performed as three separate experiments with each condition in triplicate: shSCR vs shBRD9 for 3d, shSCR vs shBRD9 for 11d, and 3 µM IBRD9 vs DMSO for 3d.

first: Sagar

last: Utturkar


title: Effects of losmapimod on antigen-specific response in aged skin

status: Public on Nov 14 2020

city: Lancaster

first: Barbara

middle: Bo-Ju

last: Shih

address: Bailrigg

department: Biomedical and Life Sciences

institute: Lancaster University

summary: Older humans are more susceptible to infections, even those to which they were immune to in their youth. Vaccination against many different infectious agents is also sub-optimal in these individuals. To investigate the mechanisms involved in the decline in immunity during ageing we inject safe derivatives of microorganisms into the skin of old and young volunteers.  After injection of the agent, we can extract the white cells (leucocytes) that accumulate at the site of the immune response to test for their function.  One of the responses we have been investigating is that to the varicella zoster virus (VZV) that induces chickenpox mainly in young individuals. Infected subjects control this persistent virus until an older age where reduced immunity leads to viral re-activation to cause shingles.  We have found that this defective response is associated with increased baseline inflammation in this tissue. Although inflammatory responses are required to clear infections, excessive inflammation has previously been shown to interfere with the generation of specific immunity.  We will therefore investigate ways of enhancing the immune response of older humans by blocking basal inflammation.     To extend our initial observations of high background inflammation in the skin, we will investigate which cells in this tissue are responsible for the production of inflammatory mediators by using a second human experimental system that tests the response to a skin irritant known as cantharadin. Next we will block inflammation in the skin to determine whether this can lead to improved responses upon challenge with antigens. This will be achieved by pre-treating old subjects with a drug that has already been developed by GSK (Losmapimod, p38MAPkinase inhibitor) and another that is available off the shelf (vitamin D3). The GSK p38 inhibitors are currently being tested to prevent unwanted inflammation. A surprising observation we made was that p38 inhibition could also rejuvenate human T lymphocytes and enhance their ability to proliferate in vitro. Therefore the inhibition of p38 may block unwanted inflammatory response as well as enhance T lymphocyte reactivity. Vitamin D3 has also been shown to have anti-inflammatory effects and works in part by inhibiting p38MAPkinase activation. The use of 2 separate interventions in this project increases the likelihood of success in this study. While Losmapimod may be more specific in its anti-inflammatory action, the use of vitamin D3 is more cost effective as it is a cheap compound that is readily available.     The desirable outcome of this study is that either one or other of these compounds, that older volunteers will be treated with, will boost their response to microbial antigen challenge in the skin. This will provide proof of concept data that will lead to the exciting possibility of enhancing immunity by inhibiting the increased baseline inflammatory responses that are found during ageing. This may be a strategy to enhance immune responses in general and specifically to enhance vaccination efficacy to various diseases that is less effective in older subjects.

overall_design: A total of 126 samples were analysed, including normal skin (n=30), saline (6 hour; n=30), VZV (6 hour; n=32), and VZV (day2; n=34).

first: Arne

last: Akbar

first: Milica

last: Vukmanovic-Stejic


title: Effects of vitamin D on non-specific inflammatory response in aged skin.

status: Public on Nov 17 2020

summary: We have previously demonstrated older skin exhibits increased sterile inflammation 6 hours after saline-injection. In this work, we examined whether vitamin D in vivo would attenuate this non-specific inflammatory response towards saline in elder individuals (≥65 years).

overall_design: Skin mRNA profiles 6 hours after saline injection were studied before and after vitamin D supplementation.


title: A human tissue screen identifies a regulator of ER secretion as a brain size determinant [organoid - screen]

status: Public on Nov 01 2020

city: Vienna

first: Christopher

last: Esk

address: Dr. Bohr-Gasse 3

country: Austria

institute: IMBA - Institute of Molecular Biotechnology GmbH

summary: A screen in human organoids reveals IER3IP1 function

overall_design: PCR amplicon, CRISPR-LICHT screen

first: Dominik

last: Lindenhofer

first: Juergen

last: Knoblich


title: A human tissue screen identifies a regulator of ER secretion as a brain size determinant


title: A human tissue screen identifies a regulator of ER secretion as a brain size determinant [scRNA-Seq]

overall_design: scRNAseq of organoids, day40, 10x Chromium


title: Intermittent short-duration reoxygenation protects against simulated high altitude-induced pulmonary hypertension in rats

status: Public on Nov 06 2020

city: Xi'an

first: Qiang

last: Lyu

address: No169 Changle Road

department: Department of Aerospace Physiology

institute: Fourth Military Medical University

summary: High-altitude pulmonary hypertension (HAPH) is a severe and progressive disease caused by chronic hypoxia and subsequent pulmonary vascular remodeling. No cure is currently available owing to an incomplete understanding about vascular remodeling. It is believed that hypoxia-induced diseases can be prevented by treating hypoxia. Thus, this study aimed to determine whether daily short-duration reoxygenation at sea level attenuates pulmonary hypertension under high-altitude hypoxia. To this end, a simulated 5,000-m hypoxia rat model was used to evaluate the effect of short-duration reoxygenation. Results show that intermittent, not continuous, short-duration reoxygenation effectively attenuates hypoxia-induced pulmonary hypertension. The mechanisms underlining the protective effects involved that intermittent, short-duration reoxygenation prevented functional and structural remodeling of pulmonary arteries and proliferation, migration, and phenotypic conversion of pulmonary artery smooth muscle cells under hypoxia. The specific genes or potential molecular pathways responsible for mediating the protective effects were also characterised by RNA sequencing.This study is novel in revealing a new potential method in preventing high-altitude pulmonary hypertension. It gives insights into the selection and optimisation of oxygen supply schemes in high-altitude areas.

overall_design: In order to investigate whether intermittent short-duration reoxygenation  can prevent HAPH, rats were randomly assigned into four groups and subjected to different oxygenation treatments each day. For the normoxia (N) group, rats were exposed to 400 m (laboratory altitude, gas composition: 21% O2–79% N2) for 24 h each day. For the hypoxia (H) group, rats were exposed to a hypobaric chamber with a pressure of 405 mmHg to simulate hypoxia at about 5000 m for 24 h each day. For the hypoxia + continuous 3-h reoxygenation (C3) group, rats were exposed to a hypobaric chamber similar to group H as well as to 42% O2–58% N2 continuously for 3 h each day. For the hypoxia + intermittent 3-h reoxygenation (I3) group, rats were treated similarly as group H, with 42% O2–58% N2 intermittently for 3 h each day. when the inspired oxygen concentration is 42% at 5000 m, the physiological equivalent altitude is about sea level. After 2-week treatment,whole lung RNA-seq was detected in the N, H, C3, and I3 groups (n=3 for each group).

last: Ma


title: Single cell RNA-seq analysis reveals the crucial role of Collagen triple helix repeat containing 1 (Cthrc1) cardiac fibroblasts for ventricular remodeling after myocardial infarction [ATAC-seq]

status: Public on Sep 29 2020

city: New York

first: Silvia

last: Hernandez

state: New York

address: 1300 Morris park avenue

department: Medicine- Cardiology

institute: Albert Einstein College of Medicine

summary: Cardiac fibroblasts have a central role during the ventricular remodeling process associated to different types of cardiac injury. Recent studies have shown that fibroblasts do not respond homogeneously to heart damage, suggesting that the adult myocardium may contain specialized fibroblast subgroups with specific functions. Due to the limited set of bona fide fibroblast markers, a proper characterization of fibroblast population dynamics in response to cardiac damage is still missing. Using single cell RNA-seq we have identified and characterized a fibroblast subpopulation that emerges in response to myocardial infarction (MI) in a murine model. These activated fibroblasts exhibit a clear pro-fibrotic signature, express high levels of the hormone CTHRC1 and of the immunomodulatory co-receptor CD200, and localize to the wounded myocardium. Combining epigenomic profiling with functional assays, we unveil important candidate regulators mediating their response to cardiac damage. We show that the absence of CTHRC1, a top marker of this activated fibroblast subpopulation, results in pronounced lethality due to ventricular rupture within the first week post-myocardial infarction. Finally, we find evidence for the existence of similar mechanisms in a pig pre-clinical model of MI and establish a positive correlation between Cthrc1 levels and cardiac function after MI.

overall_design: Time-course of study of cardiac fibroblasts after myocardial infarction. Samples include Healthy Myocardium (Control) and 7, 14, 30 days post-infarction. Cardiac fibroblasts were also selected (mEFSK4) from Cthrc1-KO mice 7 days post-infarction.

first: Adrian

last: Ruiz-Villalba

first: Juan

middle: P

last: Romero

first: Amaia

last: Vilas-Zornoza

first: Nikolaus

last: Fortelny

first: Laura

last: Castro

first: Patxi

last: San Martin-Uriz

first: Erika

last: Lorenzo-Vivas

first: Paula

last: Garcia-Olloqui

first: Marcel

last: Palacios

last: Gavira

first: Gorka

last: Bastarrika

first: Stefan

last: Janssens

first: Elena

last: Iglesias

first: Gloria

last: Abizanda

first: Xabier

last: Martinez de Morentin

first: Christoph

last: Bock

first: Diego

last: Alignani

first: Gema

last: Medal

first: David

last: Gomez-Cabrero

first: Igor

last: Prudovsky

first: Yong

last: Ri-Jin

first: Sergey

last: Ryzhov

first: Haifeng

last: Yin

first: Beatriz

last: Pelacho

first: Volkhard

last: Lindner

last: Lara-Astiaso

first: Felipe

last: Prosper


title: G2/M DNA synthesis at transcription start sites because of RNA transcription persistence during DNA replication [BrdU-Seq]

first: Marco

last: Saponaro

summary: RNA transcription and DNA replication both use DNA as a substrate, that however can be engaged only by one of them at any given time. Consequently, conflicts between transcription and replication significantly affect genome stability and human health. To understand the reciprocal interplay between transcription and replication in human cells, we performed a genome-wide analysis of the two processes throughout S-phase. We found that transcription persists during replication, with direct consequences for replication progression through genes and sites of DNA damage. Importantly however, we also found that transcription start sites will not be replicated together with the surrounding regions, and remain under-replicated throughout S-phase. DNA synthesis across transcription start sites occurs specifically when cells enter mitosis, because the RNA Polymerase II is removed at that point from the majority of the genes. Intriguingly, this G2/M DNA synthesis is not associated with increased DNA damage and occurs at very high frequency.

overall_design: Genome-wide DNA replication profile of BJ-hTERT cells throughout S phase with or without indicated treatments generated by NEXT-seq in one or two biological repeats

first: Jianming

last: Wang

first: Patricia

last: Rojas


title: Bulk and single RNA sequencing on the role of Igf2bp2 in myeloid-biased HSC

status: Public on Feb 05 2021

city: San Diego

first: Pura

last: Muñoz-Cánoves

address: 5510 Morehouse Dr

institute: Altos Labs

summary: Using RNA sequencing analysis on myeloid biased HSC, we compared gene expression profiles between WT and Igf2bp2 knock-out mice at young and old age. 1421 differentially expressed genes were identified in young myeloid biased HSC from Igf2bp2 knock-out mice compared to young WT; however, only 26 differentially expressed genes were identified in old myeloid biased HSC from Igf2bp2 knock-out mice compared to old WT. Compared to young WT myeloid biased HSC, myeloid biased HSC from young Igf2bp2 knock-out exhibits reduced expression of genes involved in metabolism and translation. In addition, single cell RNA sequencing analysis of myeloid biased HSC in young wildtype mice identified nine sub-clusters. HSCs from a sub-cluster with high expression of Igf2bp2 exhibit up-regulated IGF/PI3K/AKT signaling and increased expression of genes involved in HSC quiescence and maintenance. Altogether, the study provides a correlation and mechanism to understand the role of Igf2bp2 in HSC function and aging.

overall_design: RNA sequencing of myeloid-biased HSC from Wild Type and Igf2bp2-/- mice at young and old; single cell RNA sequencing of myeloid-biased HSC from Wild Type at 6 week old

first: MiaoMiao

last: Suo

first: Martin

last: Bens

first: Ivonne

last: Görlich


title: Profiling chromatin accessibility in pediatric acute lymphoblastic leukemia identifies subtype-specific chromatin landscapes and gene regulatory networks

status: Public on Feb 02 2021

city: Memphis

first: Daniel

last: Savic

address: 262 Danny Thomas Pl

department: Pharmaceutical Sciences

institute: St. Jude Children's Research Hospital

summary: ATACseq and RNAseq were performed on a variety of ALL Patient Samples

overall_design:
Examination of open chromatin and gene expression in 24 different ALL patients.

UPDATE: [08-25-2023] The Sample titles were updated. The bigWig file names were updated, but the data did not change. The column headers in the GSE161501_ALL_cell_RNAseq_read_counts.txt file were updated, but the data did not change.

first: Jonathan

last: Diedrich


title: Transcriptional responses of GII.4 human norovirus infection in jejunal human intestinal enteroids

city: Houston

first: Mary

last: Estes

state: TX

address: 1 Baylor Plaza

department: Microbiology and Virology

institute: Baylor College of Medicine

summary: The goal of this project was to evaluate intestinal epithelial responses to GII.4 human norovirus infection.

overall_design: Jejunal (J2 and J11) human intestinal enteroid cultures infected with GII.4 human norovirus. Mock- and gamma-irradiated GII.4 (gGII.4) inoculated cultures were used as controls. We performed RNA sequencing (RNA-Seq) to determine transcriptional responses to GII.4 at 6, 10 and 24 hours post-inoculation (hpi) in comparison to mock-inoculated cultures (3 hpi) or inoculation with gGII.4 HuNoV (6, 10 and 24 hpi).

first: Sasirekha

last: Ramani

first: Cristian

last: Coarfa


title: Single cell RNA-seq analysis reveals the crucial role of Collagen triple helix repeat containing 1 (Cthrc1) cardiac fibroblasts for ventricular remodeling after myocardial infarction

first: Silvia

last: Hernandez

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

sample_organism:
Homo sapiens
Sus scrofa
Mus musculus

platform_organism:
Homo sapiens
Sus scrofa
Mus musculus

overall_design: Refer to individual Series


title: Single cell RNA-seq analysis reveals the crucial role of Collagen triple helix repeat containing 1 (Cthrc1) cardiac fibroblasts for ventricular remodeling after myocardial infarction [RNA-seq]

overall_design: Time-course study of cardiac fibroblasts after myocardial infarction. Samples include Healthy Myocardium (Control) and 7, 14 and 30 days post-infarction. Cardiac fibroblasts were also selected (mEFSK4) from Cthrc1-KO mice 7 days post-infarction.

first: Adrian

last: Ruiz-Villalba

first: Juan

last: Romero

first: Amaia

last: Vilas-Zornoza

first: Nikolaus

last: Fortelny

first: Laura

last: Castro

first: Patxi

last: San Martin-Uriz

first: Erika

last: Lorenzo-Vivas

first: Paula

last: Garcia-Olloqui

first: Marcel

last: Palacios

last: Gavira

first: Gorka

last: Bastarrika

first: Stefan

last: Janssens

first: Elena

last: Iglesias

first: Gloria

last: Abizanda

first: Xabier

last: Martinez de Morentin

first: Christoph

last: Bock

first: Diego

last: Alignani

first: Gema

last: Medal

first: David

last: Gomez-Cabrero

first: Igor

last: Prudovsky

first: Yong

last: Ri-Jin

first: Sergey

last: Ryzhov

first: Haifeng

last: Yin

last: Pelacho


title: Co-option of neutrophil fates by tissue environments

status: Public on Sep 08 2020

city: New Haven

first: Andrés

last: Hidalgo

address: 10 Amistad Street

institute: Yale University


title: Expression analysis of microRNAs in INT-HA-induced M2-like macrophages and untreated macrophages (M0)

status: Public on Feb 08 2021

city: shanghai

first: boke

last: zhang

address: 600 Yishan Road

institute: Shanghai Jiao Tong University Affiliated Sixth People's hospital

summary: Using the highly sensitive miRNA microarray, we screened 107 up-regulated microRNAs and 33 down-regulated microRNAs in the INT-HA-induced M2-like macrophages and we explored the functions of these miRNAs in macrophage polarization. The enrichment results indicated that these miRNAs might participate in the process of macrophage polarization. Furthermore, the quantitative real-time polymerase chain reaction results showed that miR-935 may play an important role in M2 macrophage polarization which was activated by INT-HA.

platform_organism:
Homo sapiens
Human alphaherpesvirus 2
Herpesvirus saimiri (strain 11)
JC polyomavirus
Human immunodeficiency virus 1
Human betaherpesvirus 6B
Merkel cell polyomavirus
Betapolyomavirus hominis
Betapolyomavirus macacae

overall_design: In this study, primary human macrophages derived from peripheral blood monocytes (n=3) were treated with 50 μg/ml INT-HA for 72 h. The miRNA expression profiling was acquired and the function of the abudant miRNAs in INT-HA-induced M2-like macrophages were analyzed by bioinformatic methods,finally,miR-935 might be involved in the regulation of macrophage polarization, a potential therapeutic target for antitumor treatment.

first: Boke

last: Zhang

first: Yan

last: Du

first: Yiqing

last: He

first: Yiwen

last: Liu

first: Guoliang

first: Cuixia

last: Yang

first: Feng

last: Gao


title: SAMMY-seq, H3K9me3 and H3K27me3 ChIP-seq and RNA-seq of control and progeria fibroblasts

status: Public on Sep 05 2020

city: Milan

first: Chiara

last: Lanzuolo

address: Via Francesco Sforza 35

country: Italy

institute: CNR and Istituto Nazionale Genetica Molecolare

summary: We present a new high-throughput sequencing-based technique, named Sequential Analysis of MacroMolecules accessibilitY (SAMMY-seq), for the genome-wide mapping of chromatin regions separated by differential accessibility. The method is based on the sequential extraction of multiple chromatin fractions, corresponding to increasingly compacted and less accessible chromatin regions, which are mapped along the genome using high-throughput sequencing. Using SAMMY-seq we analyzed Hutchinson-Gilford progeria syndrome (HGPS) skin fibroblasts and normal control fibroblasts. Additionally we carried out ChIP-seq for the H3K9me3 and H3K27me3 histone modifications and RNA-seq for the characterization of transcriptome changes on the same HGPS and control fibroblasts.

overall_design:
Using SAMMY-seq we analyzed Hutchinson-Gilford progeria syndrome (HGPS) skin fibroblasts and normal control fibroblasts. Additionally we carried out ChIP-seq for the H3K9me3 and H3K27me3 histone modifications and RNA-seq for the characterization of transcriptome changes on the same HGPS and control fibroblasts.

Human raw data will be uploaded to dbGaP

first: Endre

last: Sebestyén

first: Fabrizia

last: Marullo

first: Cristiano

last: Petrini

first: Federica

last: Lucini

first: Andrea

last: Bianchi

first: Sara

last: Valsoni

first: Ilaria

last: Olivieri

first: Laura

last: Antonelli

first: Francesco

last: Gregoretti

first: Gennaro

last: Oliva

last: Ferrari


title: Molecular Transducers of Human Skeletal Muscle Remodeling under Different Loading States [CDF: GC_M_HTA_3utr_Grch38,binary.cdf]

status: Public on Aug 11 2020

city: Stirling

first: James

last: Timmons

address: Bridge of Allan

institute: Augur Precision Medicine LTD

summary:
The annotation of the Affymetrix HTA 2.0 array was updated to optimise the detection of RNA in human skeletal muscle biopsy samples by removing invalid and low signal-high-variance probes (as for CDF GPL24047). The probes were then summarized into groups (probe-sets) reflecting either an ensembl full transcript identifier (FL-ENST, GPL24047) or just the probes targeting the 3' UTR or the 5' UTR of that particular ENST.  Therefore, 3 different CDF were used to process the HTA 2.0 arrays in this study. Note that each CEL file was GC adjusted using APT while our custom CDF pipeline removes any probe that has >80% or <20% GC content (~50,000). The analysis was carried out only on the pairs of probe-sets i.e. FL-ENST vs 3'UTR or FL-ENST vs 5'UTR or 3'UTR vs 5'UTR.
Dynamic muscle loading alters tissue phenotype reflecting altered metabolic and functional demands. In humans, heterogeneous adaptation to loading complicates identification of the underpinning molecular regulators. We present a within-person analysis strategy that reduced heterogeneity for changes in muscle mass by ~40% and employed a genome-wide transcriptome method that modeled each mRNA from coding exons and 3’/5’ untranslated (UTR) regions. Our strategy detected ~3-4 times more regulated genes than similarly sized studies, including substantial UTR-selective regulation that other methods would not detect. We discovered a core of 141 genes correlated to muscle growth validated from newly analyzed independent samples (n=100). Further validating these identified genes, via RNAi in primary muscle cells, we demonstrate that members of the core genes were regulators of protein synthesis e.g. Molecular Transducers of Physical Activity in Humans MoTrPAC. Employing proteome-constrained networks and pathway analysis revealed notable relationships with the molecular characteristics of human muscle aging and insulin sensitivity, as well as potential drug-therapies. https://doi.org/10.1016/j.celrep.2020.107980

overall_design: human muscle profiles from men and women before and after muscle resistance training and/or unloading

first: Stuart

last: Phillips


title: Tissue neutrophil heterogeneity in germ free mice

first: Andrés

last: Hidalgo

summary:
Purpose: The goals of this study are to compare bulk RNAseq profiles of tissue neutrophils in germ free mice.
Methods: Bulk RNAseq of sorted neutrophils from spleen, blood, lung from spf and germ free mice, using Illumina. The sequence reads that passed quality filters were analyzed at the gene level with RSEM.

overall_design: Examination of different transcriptomic profiles in neutrophils from germ free mice from 3 different tissues.

first: Iván

last: Ballesteros

last: Rubio-Ponce


title: Pressure overload greatly promotes neonatal right ventricular cardiomyocyte proliferation - a new model for heart regeneration study

status: Public on Aug 19 2020

city: Shanghai

first: Lincai

last: Ye

state: China

address: Heart Center 7003, 1678 Dongfang Road

department: Shanghai Institute For Pediatric Congenital Heart Disease

institute: Shanghai Children's Medical Center

summary:
Background: Current mammalian model for heart regeneration research is limited in apex amputation or myocardium infarction, both of which are controversy. Moreover, RNAseq demonstrated there were a very limited set of differential expressed genes between sham and operation heart in the myocardium infarction model. Here we investigated whether pressure overload in the right ventricle(RV), a common phenomenon in congenital heart disease children, could be a better animal model for heart regeneration study when consider cardiomyocyte(CM) proliferation as the most important index.
Methods and results: Pressure overload was induced by pulmonary artery banding (PAB) on day1 and confirmed by echocardiography and hemodynamic measurements at postnatal day 7(P7). RNAseq analyses of purified RVCM at P7 from PAB and sham-operated rats revealed there were 5469 differential expressed genes between these two groups. GO and KEGG analysis showed that these genes mainly mediated mitosis and cell division. Cell proliferation assay indicates a continuous over-proliferation of RVCM after PAB, in particular for P3. In addition, there were ~2 times-fold increase of Ki67/Phh3 -positive CM in human overload RV compared to non-overload RV. Other features about this model included CM hypotrophy and no fibrosis..
Conclusions: Pressure overload profoundly promotes RVCM proliferation in the neonatal stage both in rats and human beings, activated a regeneration-specific gene program, and may offer a better alternative animal model for heart regeneration research..

overall_design: Purified rat right ventricular cardiomyocytes from Sham and PAB group were generated by deep sequencing, each group contains 6 samples,    using Illumina HiSeq 2500.

first: Haifa

last: Hong

first: Jinfen

last: Liu

first: Yanhui

last: Huang

first: Hao

last: Zhang

first: Haibo

first: Huiwen

last: Chen

first: Huang

last: Yanhui

first: Yinyin

last: Xiao

first: Chuan

last: Jiang


title: Molecular Transducers of Human Skeletal Muscle Remodeling under Different Loading States [CDF: GC_M_HTA_5utr_Grch38,binary.cdf]


title: Determine the effects on the transcriptome of depleting STAG2 in RT112, a bladder cancer cell line.

status: Public on Jul 23 2020

city: Madrid

first: Jaime

last: Martinez de Villarreal

state: Madrid

address: Melchor Fernández Almagro, 3

department: Molecular Oncology Programme

institute: CNIO

overall_design: One control and two STAG2-silenced conditions were evaluated. Three replicates per condition were generated.

first: Richart

last: Laia

first: Lapi

last: Eleonora

first: Pancaldi

last: Vera

first: Cuenca

last: Mirabai

first: Carrillo-de-Santa-Pau

last: Enrique

first: Madrid-Mencia

last: Miguel

first: Neyret-Kahn

last: Helene

first: Radvanyi

last: François

first: Rodríguez

last: Juan A.

first: Cuartero

last: Yasmina

first: Serra

first: Valencia

last: Alfonso

first: Marti-Renom

last: Marc A.

first: Real

last: Francisco X.


title: A topological atlas reveals layers of genome reorganization in colorectal cancer

status: Public on Aug 24 2020

city: Basel

first: Alejandro

last: Reyes

address: Fabrikstrasse 22

department: Data Sciences

country: Switzerland

institute: Novartis Institutes For BioMedical Research

summary: To understand how nuclear architecture is altered in cancer, we profiled genome topology along with DNA methylation, chromatin modifications and the DNA binding factors CTCF in primary colon tumors, normal colon and colon cancer cell lines.

overall_design:
Samples include colon cancer cell lines (HCT116, SW480, RKO, LS-174T), a line derived from normal colon (FHC) and patient biopsies.

The raw data from the in vitro models can be found through SRA. Due to patient privacy concerns, raw data for patient samples have been submitted to dbGAP (accession phs002288.v1.p1).

first: Sarah

last: Johnstone

first: Martin

last: Aryee

first: Bradley

last: Bernstein


title: A human tissue screen identifies a regulator of ER secretion as a brain size determinant [organoid - lineage tracing]

first: Christopher

last: Esk

overall_design: PCR amplicon sequencing, lineage tracing

first: Dominik

last: Lindenhofer

first: Juergen

last: Knoblich


title: Tissue neutrophil heterogeneity

first: Andrés

last: Hidalgo

summary:
Purpose: The goals of this study are to compare bulk RNAseq profiles of tissue neutrophils.
Methods: Bulk RNAseq of sorted neutrophils from bone marrow, spleen, blood, lung, peripheral blood, skin and intestine from wild-type (WT) mice, in triplicate, using Illumina. The sequence reads that passed quality filters were analyzed at the gene level with RSEM which mapped about 26 million sequence reads per sample to the mouse genome (build mm10/GRCm38) and identified 32328 genes.

overall_design: Examination of different transcriptomic profiles in neutrophils from 6 different tissues.

first: Iván

last: Ballesteros

first: Andrea

last: Rubio-Ponce


title: A human tissue screen identifies a regulator of ER secretion as a brain size determinant [RNA-Seq]

overall_design: mRNA sequencing of H9 WT and IER3IP1 cerebral organoids using Quantseq.


title: Single cell RNA-seq analysis reveals the crucial role of Collagen triple helix repeat containing 1 (Cthrc1) cardiac fibroblasts for ventricular remodeling after myocardial infarction [scRNA-seq]

first: Silvia

last: Hernandez

first: Adrian

last: Ruiz-Villalba

first: Juan

last: Romero

first: Amaia

last: Vilas-Zornoza

first: Nikolaus

last: Fortelny

first: Laura

last: Castro

first: Patxi

last: San Martin-Uriz

first: Erika

last: Lorenzo-Vivas

first: Paula

last: Garcia-Olloqui

first: Marcel

last: Palacios

last: Gavira

first: Gorka

last: Bastarrika

first: Stefan

last: Janssens

first: Elena

last: Iglesias

first: Gloria

last: Abizanda

first: Xabier

last: Martinez de Morentin

first: Christoph

last: Bock

first: Diego

last: Alignani

first: Gema

last: Medal

first: David

last: Gomez-Cabrero

first: Igor

last: Prudovsky

first: Yong

last: Ri-Jin

first: Sergey

last: Ryzhov

first: Haifeng

last: Yin

first: Beatriz

last: Pelacho

first: Volkhard

last: Lindner

last: Lara-Astiaso

first: Felipe

last: Prosper


title: Cellular repertoires of the song motor pathway of songbirds

status: Public on May 14 2020

city: San Francisco

first: Michael

last: Brainard

state: CA

address: 675 Nelson Rising Ln

institute: University of California, San Francisco

summary: Birdsong is powerful model for the neural mechanisms underlying motor skill learning. The success of this model is in part due to the experimental advantages of the song system, the anatomically and functionally discrete neural circuit dedicated to song. Despite a detailed understanding of the physiological and systems levels properties of this circuit, we still lack a comprehensive understanding of what cell types are present in each region of the song system and how these cell types compare to those found in the brains of other vertebrates. Here, we characterize the cellular repertoire of the song motor pathway using single-cell RNA-sequencing.

overall_design: Two song premotor pathway regions, HVC and RA, were dissected from three adult (~200 dph) male Bengalese finches and prepared for single-cell RNA-seq using 10x 3’ v2 RNA-sequencing

first: Bradley

last: Colquitt


title: Human placenta-derived mesenchymal stem cells ameliorate diabetic nephropathy

status: Public on Jun 26 2020

city: Nanchang

first: Jixiong

last: Xu

state: Jiangxi Province

address: No.17 Yongwaizheng St.

department: Department of Endocrinology and Metabolism

institute: The first hospital of nanchang university

summary: The aim of this study is to compare renal transcriptome profiling between diabetic nephropathy (DN) and DN treated with human placenta-derived mesenchymal stem cells (PMSCs) groups. Twelve renal cortex samples (n=6 for each DN and treatment group) were sequenced using Illumina Hiseq 4000. We identified 90 differentially expressed genes between DN and treatment griups with |og2 FoldChange| ≥1 and p value <0.05. Our study represents the first detailed analysis of renal transcriptomes, with biologic replicates, generated by RNA-seq technology.

overall_design: Renal transcriptome  profiles of diabetic nephropathy rats

first: Jiao

last: Wang

first: Honghong

last: Liu


title: 22-nucleotide siRNAs mediate translational repression and trigger a silencing storm [es]

status: Public on Apr 13 2020

city: Shenzhen

first: Bosheng

last: Li

state: Guangdong

address: SUStech Huiyuan #1 406

department: MCDB

institute: SUSTC (current, may different with previous institution )

summary: Small interfering RNAs (siRNAs) are critical for proper development and immunity in eukaryotes1. Plants produce siRNAs with lengths of 21-, 22-, or 24- nucleotides (nt), wherein the 21- and 24-nt siRNAs mediate mRNA cleavage and DNA methylation2,3, respectively. However, the biological functions of 22-nt siRNAs remain elusive. Here we report the identification and characterization of a group of endogenous 22-nt siRNAs generated from the action of DICER-LIKE 2 (DCL2). When cytoplasmic RNA decay and DCL4 are deficient, the massive accumulation of 22-nt siRNAs causes pleiotropic growth disorders, including severe dwarfism, meristem defect, and pigmentation. Notably, two genes that encode nitrate reductases, NIA1 and NIA2, produce nearly half of the total of 22-nt siRNAs. Production of 22-nt siRNA triggers explosive self-amplification that leads to a small RNA storm, and induces dramatic translational repression both gene-specifically and globally. 22-nt siRNAs are also found to preferentially accumulate upon nitrogen deficiency, which acts to restrain plant growth and promote stress responses. Thus, our research uncovers the unique properties of 22-nt siRNAs, a previously unexplored class of plant siRNAs, and highlights the length of small RNA as a major functional determinant.

overall_design: ein5-1 ski2-3 and ein5-1 ski2-3 dcl4-2 dcl2-1 were grown on the MS medium for 6 days and then were transferred to the soil for another 14 days. Aerial parts were collected for small RNA extraction. Three or four biological replicates were prepared for each genotype. Library preparation and high-throughput sequencing were conducted in accordance with the manufacturers’ instructions. Total small RNA was extracted using the miRNeasy Mini Kit (Qiagen). Sequencing libraries were prepared using the NEBNext® Small RNA Library Prep Set for Illumina. RNA quality and library quality were examined by a Bioanalyzer 2100 instrument (Agilent), and single-end, 50-bp deep sequencing was performed on an Illumina HiSeq 4000 platform.

first: Huihui

last: Wu

first: Hongwei

last: Guo


title: 22-nucleotide siRNAs mediate translational repression and trigger a silencing storm

overall_design: Col-0, dcl4-2 and dcl4-2 dcl2-1 were grown on the MS or 1μM ABA medium for 14 days and seedlings were collected for small RNA extraction. Three biological replicates were prepared for each genotype. Library preparation and high-throughput sequencing were conducted in accordance with the manufacturers’ instructions. Total small RNA was extracted using the miRNeasy Mini Kit (Qiagen). Sequencing libraries were prepared using the NEBNext® Small RNA Library Prep Set for Illumina. RNA quality and library quality were examined by a Bioanalyzer 2100 instrument (Agilent), and paired-end, 150-bp deep sequencing was performed on an Noveseq6000 platform. Only read1 was used for downstream analysis


title: NIH-3T3 cell line response to proteasome inhibitor

status: Public on May 21 2020

city: Richmond

first: Senthil

last: Radhakrishnan

state: VA

address: 1101 E Marshall St

institute: Virginia Commonwealth University

summary: In this study, we compared the transcriptional profile of NIH-3T3 cells that are either wild-type (WT) or Nrf1 knockout (Nrf1-KO).  We treated these cells with carfilzomib for 6 hours or 24 hours and performed RNA-sequencing with these samples.

overall_design: The samples are from 3 biological replicates

middle: K