title: Analysis of the eIF4E3-dependent translatome after Torin1-induced stress in N2a cells ctrl and eIF4E3 KO

city: Rehovot

first: Benjamin

last: Weiss

address: 234 Herzl Street

institute: Weizmann Institute of Science

summary: The eIF4E are a family of initiation factors that bind the mRNA 5’ cap, regulating the proteome and the cellular phenotype. eIF4E1 mediates global translation and its activity is controlled via the PI3K/AKT/mTOR pathway. mTOR down-regulation results in eIF4E1 sequestration into an inactive complex with the 4E binding proteins (4EBPs). The second member, eIF4E2, regulates the translatome during hypoxia. However, the exact function of the third member, eIF4E3, has remained elusive. We have dissected its function using a range of techniques. Starting from the observation that it does not interact with 4EBP1, we demonstrate that eIF4E3 recruitment into an eIF4F complex occurs when Torin1 inhibits the mTOR pathway. Ribo-seq studies demonstrate that this complex (eIF4FS) is translationally active only during stress and that it selects specific mRNA populations based on 5’ TL (UTR) length. The interactome reveals that it associates with cellular proteins beyond the cognate initiation factors, suggesting that it may have “moon-lighting” functions. Finally, we provide evidence that cellular metabolism is altered in an eIF4E3 KO background but only upon Torin1 treatment. We propose that eIF4E3 acts as a second branch of the integrated stress response, re-programming the translatome to promote “stress resistance” and adaptation.

overall_design: 3 biological replicates for each of the four conditions tested: N2a WT cells +/- Torin1, N2a KO cells +- Torin1

first: George

last: Allen

first: Pascale

last: Jaquier-Gubler

first: Joseph

last: Curran


status: Public on Feb 25 2021

city: Ningbo

first: Xinyang

last: Wu

state: Zhejiang

address: 818# Fenghua Road

country: China

institute: Ningbo University

type: Expression profiling by high throughput sequencing

summary: Transcriptome sequencing from Nicotiana benthamiana leaves non-infected and infected with Turnip mosaic virus at 6 days post inoculation.

overall_design: Transcriptome sequencing from Nicotiana benthamiana leaves non-infected and infected with Turnip mosaic virus (TuMV). 6 days post inoculation, total RNA of leaves were used for transcriptome sequencing.

first: Fei

last: Yan

first: Hongying

last: Zheng


title: Epigenetic profiling to identify a human effector regulatory T cell core signature [H3K27ac]

status: Public on Feb 23 2021

city: Utrecht

first: Lisanne

last: Lutter

address: Lundlaan 6

country: Netherlands

institute: University Medical Center Utrecht

type: Genome binding/occupancy profiling by high throughput sequencing

summary: We investigated the active enhancer landscape of human Treg in an autoimmune-associated inflammatory environment, i.e. synovial fluid (SF) from inflamed joints of Juvenile Idiopathic Arthritis (JIA) to improve our understanding of human effector Treg programming.

overall_design: Examination of H3K27acmodifications in 3 biological replicates of each healthy adult peripheral blood and Juvenile Idiopathic Arthritis patient synovial fluid regulatory T cells.

first: Femke

last: van Wijk

first: Jorg

last: van Loosdregt

first: Michal

last: Mokry


title: IL-21 and IFNalpha therapy rescues terminally-differentiated NK cells and limit SIV reservoir in ART-treated macaques [cohort2]

status: Public on Feb 22 2021

city: Atlanta

first: Gregory

middle: K

last: Tharp

state: GA

address: 954 Gatewood Dr

department: Developmental and Cognitive Neuroscience

country: USA

institute: Yerkes National Primate Research Center

summary: Unlike HIV infection, which progresses to AIDS absent suppressive anti-retroviral therapy (ART), nonpathogenic infections in natural hosts, such African green monkeys (AGMs), are characterized by a lack of gut microbial translocation and robust secondary lymphoid Natural Killer (NK) cell responses resulting in absence of chronic inflammation and limited SIV dissemination in lymph nodes (LN) B-cell-follicles, respectively. In a pathogenic infection model (i.e. ART-treated, SIVmac239-infected rhesus macaques; RMs), sequential Interleukin (IL)-21 and interferon (IFN)-alpha therapy generated terminally-differentiated blood NK cells (NKG2a/clowCD16+) with potent HLA-E-restricted activity in response to SIV-ENV peptides in contrast to control RMs, where less differentiated, IFN-gamma+ NK cells predominated. The frequency and cytolytic activity of NKG2a/clowCD16+ NK cells correlated with a reduction of replication-competent SIV in LN during ART and viral rebound delay following analytical treatment interruption. These data demonstrate that AGM-like NK cell differentiation profiles can be rescued in RMs to promote viral clearance in tissues.

overall_design: 13 SIV infected and ART-treated rhesus macaques were used. 8 were treated with IL-21 and IFN-alpha and PEGylated-IFN-alpha and 5 were untreated controls. Blood was sampled longitudinally post-treatment.

first: Justin

last: Harper

first: Nicolas

last: Huot

first: Luca

last: Micci

first: Colin

last: King

first: Philippe

last: Rascle

first: Neeta

last: Shenvi

first: Hong

last: Wang

first: Cristin

last: Galardi

first: Amit

middle: A

last: Upadhyay

first: Francois

last: Villinger

first: Jeffrey

last: Lifson

first: Kirk

last: Easley

first: Beatrice

last: Jacquelin

first: Richard

middle: M

last: Dunham

first: Steven

last: Bosinger

first: Michaela

last: Müller-Trutwin

first: Mirko

last: Paiardini


title: Epigenetic profiling to identify a human effector regulatory T cell core signature

first: Lisanne

last: Lutter

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

overall_design: Refer to individual Series


title: Epigenetic regulation of metabolic adaptation predicts response to Inositol hexakisphosphate (IP6) treatment in Group 4 medulloblastoma (RNA-seq, ChIP-seq)

status: Public on Mar 04 2021

city: London

first: Silvia

last: Marino

address: 4, Newark St

country: United Kingdom

institute: Queen Mary University of London

summary: Deregulation of chromatin modifiers plays an essential role in the pathogenesis of medulloblastoma (MB), the most common paediatric malignant brain tumour. Here, we identify a BMI1-dependent sensitivity to deregulation of inositol metabolism in a proportion of medulloblastoma. We demonstrate mTOR pathway activation and metabolic adaptation specifically in medulloblastoma of the molecular subgroup G4 characterised by a BMI1High;CHD7Low signature and show this can be counteracted by IP6 treatment. Finally, we demonstrate that IP6 synergises with cisplatin to enhance its cytotoxicity in vitro and extends survival in a pre-clinical BMI1High;CHD7Low xenograft model.

overall_design: ChIP-Seq and RNA-Seq of medulloblastoma cell lines

first: Sara

last: Badodi

first: Nicola

last: Pomella


title: IL-21 and IFNalpha therapy rescues terminally-differentiated NK cells and limit SIV reservoir in ART-treated macaques [cohort3]

first: Gregory

last: Tharp

overall_design: 6  rhesus macaques were used infected with SIV and then ART-treated. RNASeq was performed on blood longitudinaly, pre-infection, pre-ART, and at 2 post-ART timepoints.

first: Justin

last: Harper

first: Nicolas

last: Huot

first: Luca

last: Micci

first: Colin

last: King

first: Philippe

last: Rascle


title: Detection of gene cis-regulatory element perturbations in single-cell transcriptomes

status: Public on Feb 24 2021

city: Boston

middle: I

last: Sherwood

state: MA

address: 77 Avenue Louis Pasteur

department: Division of Genetics, Department of Medicine

institute: Brighan and Women's Hospital and Harvard Medical School

summary: We introduce poly-adenine CRISPR gRNA-based single cell RNA-sequencing (pAC-Seq), a method enabling simultaneous observation of mutagenic guide RNAs (gRNAs) and their transcriptional consequences in single cell RNA sequencing (scRNA-seq) data. We have made gRNAs robustly visible in scRNA-seq data while maintaining full activity by modifying them with a hardcoded poly-adenine tract. We apply pAC-Seq to study the transcriptomic effects of non-coding CRISPR/Cas9-induced mutations in a pooled screening format. pAC-Seq is a simple, robust, and broadly applicable method of measuring the global effects of genomic mutation.

overall_design: Pooled screening of transcriptomic effects of CRISPR/Cas9-induced non-coding mutations

first: Grace Hui Ting

last: Yeo

first: Oscar

last: Juez

first: Qing

last: Chen

first: Budhaditya

last: Banerjee

first: Lendy

last: Chu

first: Max

middle: W

last: Shen

first: May

last: Sabry

first: Ive

last: Logister

first: David

last: Gifford


title: Ultra-low RNA Sequencing of Live+CD3+CD8+CD44+ T cells from Flu-infected and Non-infected Lean and Obese Lungs

status: Public on Feb 20 2021

city: Chapel Hill

first: Abrar

middle: E

last: Al-Shaer

state: NC

address: 135 Dauer Dr

department: Nutrition

institute: University of North Carolina Chapel Hill

summary: Live+CD3+CD8+CD44+ T cells were sorted on the FACSAria II from lungs of lean and obese C57BL/6J mice (fed high fat diet 60% kcal), either on day 0 of infection (non-infected) or day 10 post-infection (H1N1 influenza A/PR/8/34 virus). The sorted T cells were sequenced on an Illumina HiSeq 4000 using a 2x150bp Paired End configuration.

overall_design: Sorted T cells came from 4 different groups: (1) Lean (fed low fat diet 10% kcal) C57BL/6J mice, non-infected day 0 lung tissue harvested (2) Lean C57BL/6J mice, infected day 10 lung tissues harvested (H1N1 influenza A/PR/8/34 virus) (3) Obese (fed high fat diet 60% kcal) C57BL/6J mice, non-infected day 0 lung tissue harvested (4) Obese C57BL/6J mice, infected day 10 lung tissues harvested (H1N1 influenza A/PR/8/34 virus)

first: William

middle: D

last: Green

last: Shi

first: J

middle: J

last: Milner

first: Kymberly

last: Gowdy

first: Nancie

last: MacIver

first: Melinda

last: Beck

first: Saame

middle: R

last: Shaikh


title: IL-21 and IFNalpha therapy rescues terminally-differentiated NK cells and limit SIV reservoir in ART-treated macaques [cohort1]

first: Gregory

last: Tharp

overall_design: 11 SIV infected and ART-treated rhesus macaques were used. 6 were treated with IL-21 and IFN-alpha and 5 were untreated controls.

first: Justin

last: Harper

first: Nicolas

last: Huot

first: Luca

last: Micci

first: Colin

last: King

first: Philippe

last: Rascle

first: Neeta

last: Shenvi

first: Hong

last: Wang

first: Cristin

last: Galardi

first: Amit

last: Upadhyay

first: Francois

last: Villinger

first: Jeffrey

last: Lifson

first: Kirk

last: Easley

first: Beatrice

last: Jacquelin

first: Richard

last: Dunham

first: Steven

last: Bosinger

first: Michaela

last: Müller-Trutwin

first: Mirko

last: Paiardini


title: Epigenetic profiling to identify a human effector regulatory T cell core signature [H3K4me1]

first: Lisanne

last: Lutter

summary: We investigated the gene expression profile and active enhancer landscape of human Treg in an autoimmune-associated inflammatory environment, i.e. synovial fluid (SF) from inflamed joints of Juvenile Idiopathic Arthritis (JIA) to improve our understanding of human effector Treg programming.

overall_design: Examination of H3K4me1 modifications in 3 biological replicates of each healthy adult peripheral blood and Juvenile Idiopathic Arthritis patient synovial fluid regulatory T cells.

first: Femke

last: van Wijk

first: Jorg

last: van Loosdregt

first: Michal

last: Mokry


title: IL-21 and IFNalpha therapy rescues terminally-differentiated NK cells and limit SIV reservoir in ART-treated macaques

first: Gregory

last: Tharp


title: Analysis of the transcriptome and DNA methylome in response to acute and recurrent low glucose in human primary astrocytes (RNA-Seq)

status: Public on Feb 17 2021

city: Exeter

first: Emma

last: Walker

address: RILD Barrack Rd

institute: University of Exeter

summary: Aims/hypothesis: Recurrent hypoglycaemia (RH) is a major side-effect of intensive insulin therapy for people with diabetes. Changes in hypoglycaemia sensing by the brain contribute to the development of impaired counterregulatory responses to and awareness of hypoglycaemia. Little is known about the intrinsic changes in human astrocytes in response to acute and recurrent low glucose (RLG) exposure.  Methods: Human primary astrocytes (HPA) were exposed to zero, one, three or four bouts of low glucose (0.1 mmol/l) for three hours per day for four days to mimic RH.  On the fourth day, DNA and RNA were collected. Differential gene expression and ontology analyses were performed using DESeq2 and GOseq respectively. DNA methylation was assessed using the Infinium MethylationEPIC BeadChip platform.  Results: 24 differentially expressed genes (DEGs) were detected (after correction for multiple comparisons). One bout of low glucose exposure had the largest effect on gene expression. Pathway analyses revealed that endoplasmic-reticulum (ER) stress-related genes such as HSPA5, XBP1, and MANF, involved in the unfolded protein response (UPR), were all significantly increased following LG exposure, which was diminished following RLG. There was little correlation between differentially methylated positions and changes in gene expression yet the number of bouts of LG exposure produced distinct methylation signatures.  Conclusions/interpretation: These data suggest that exposure of human astrocytes to transient LG triggers activation of genes involved in the UPR linked to endoplasmic reticulum (ER) stress. Following RLG, the activation of UPR related genes was diminished, suggesting attenuated ER stress. This may be mediated by metabolic adaptations to better preserve intracellular and/or ER ATP levels, but this requires further investigation.

middle: L

last: Dempster

first: Craig

last: Beall

first: Paul

middle: G

last: WeightmanPotter

first: Sam

last: Washer


title: Therapeutic Targeting of Protein Disulfide Isomerase PDIA1 in Multiple Myeloma

city: Cleveland

first: Babal

last: Jha

state: Ohio

address: 9500 Euclid Ave, NE6-253

department: Translational Hematology and Oncology

institute: Cleveland Clinic

summary: Patients with multiple myeloma refractory to standard treatments have short survival. High PDIA1 expression confers resistance to proteasome inhibitors and other stressors due to the gain in ER-function, while maintaining or increasing vulnerability to PDIA1 inhibition. In this study we report the identification and characterization of an orally bioavailable novel PDIA1 inhibitor CCF642-34 that is effective against multiple myeloma in pre-clinical models.

overall_design: MM1.S cells were treated with 3µM of either CCF642 or CCF642-34 for 6 hours and gene expression analysis was performed by RNA sequencing.

first: Frederic

last: Reu

first: Metis

last: Hasipek


title: Single Cell RNA-Seq of PBMC from COVID-19 patients and Control subjects

city: Baltimore

first: Srinivasan

last: Yegnasubramanian

state: MD

address: 1661 Orleans St

institute: Johns Hopkins SOM

summary: Single Cell RNA-Seq of PBMC from COVID-19 patients and control patients using 10x genomics 5' DGE

overall_design: 3 Healthy Control PBMC and 6 COVID-19 patient's PBMC

first: Jonathan

last: Powell

first: Andrea

last: Cox

first: Ajay

last: Vaghasia


title: Analysis of the transcriptome and DNA methylome in response to acute and recurrent low glucose in human primary astrocytes (BeadChip)

overall_design: Human primary astrocytes (HPA) were exposed to zero, one, three or four bouts of low glucose (0.1 mmol/l) for three hours per day for four days to mimic RH.  On the fourth day, DNA and RNA were collected. Differential gene expression and ontology analyses were performed using DESeq2 and GOseq respectively. DNA methylation was assessed using the Infinium MethylationEPIC BeadChip platform.


title: Human Naïve Epiblast Cells Possess Unrestricted Lineage Potential II

city: Cambridge

first: Giuliano

middle: Giuseppe

last: Stirparo

state: Cambridgeshire

address: 418 Cambridge Science Park Milton Rd

institute: Cerevance ltd

summary: Transcriptomic analysis confirms the trophoblast identity of the naïve pluripotent stem cell derived TSC cultures by comparing to the placenta derived TSC culture.

overall_design: The deposited data are RNAsequencing data of human trophoblast stem cells. The study comprises six human naive pluripotent stem cell derived trophoblast stem cell cultures (HNES1, niPSC2, niPSC4)  and one placenta derived trophoblast stem cell culture (CT27).   Each culture has two biological dupicates.

first: Ge

last: Guo


title: Analysis of the transcriptome and DNA methylome in response to acute and recurrent low glucose in human primary astrocytes


title: RSC primes the quiescent genome for hypertranscription upon cell cycle re-entry

status: Public on Feb 16 2021

city: Seattle

first: Christine

last: Cucinotta

state: Washington

address: 1100 Fairview Ave N

department: Basic Sciences

institute: Fred Hutchinson Cancer Research Center

summary: We report gene expression patterns and chromatin architecture changes as yeast re-enter the cell cycle from quiescence

overall_design: Examination of RNA levels, chromatin profiling, and nucleosome positions in yeast with and without the chromatin remodeler RSC


title: Microarray Analyses of mRNA and lncRNA in TAMs isolated from breast tumor of PyMT mice with or without chemotherapy

city: Guangzhou

first: Jiang

last: Liu

address: 107 Yanjiang West Road

institute: Sun Yat-sen Memorial Hospital, Sun Yat-sen University

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

summary:
Chemotherapies have been shown to enhance anti-tumor immunity, but whether chemotherapies affect tumor-associated macrophages (TAMs) is still uclear.
We found TAMs is different with or without chemotherapy by comparing RNA profile of TAMs with or without chemotherapy.

overall_design: We comparied mRNA and lncRNA expression profile of TAMs isolated from breast tumor of PyMT mice with or without chemotherapy to ensure difference. This array contained lncRNA and mRNA of mouse.


title: Transcriptome Analysis of Basal NK Cells and Different NKAE Cell Products

city: Madrid

first: Nerea

last: Matamala

address: Calle de Pedro Rico, 6

country: Spain

institute: IDIPAZ

summary: Natural killer (NK) cells represent promising tools for cancer immunotherapy. We report the optimization of an NK cell activation–expansion process and its validation on clinical-scale. Activated and expanded NK cells (NKAE) were obtained by coculturing total peripheral blood mononuclear cells (PBMC) or CD45RA+ cells with irradiated K562mbIL15-41BBL or K562mbIL21-41BBL. Transcriptome profile showed to be different between basal NK cells and NKAE cells expanded with K562mbIL21-41BBL or K562mbIL15-41BBL

overall_design: NK cells from two representative donors were obtained pre and post-expansion. Activated and expanded NK cells (NKAE) were obtained by coculturing total peripheral blood mononuclear cells (PBMC) or CD45RA+ cells with irradiated K562mbIL15-41BBL or K562mbIL21-41BBL. Library preparation and RNA sequencing were performed.

first: Beatriz

last: Ruz-Caracuel

first: Adela

last: Escudero

first: Antonio

last: Pérez-Martínez


title: Microarray Analyses of lncRNA and mRNA in TAMs from breast cancer patient before or after chemotherapy

summary:
Chemotherapies have been shown to enhance anti-tumor immunity, but whether chemotherapies affect tumor-associated macrophages (TAMs) is still uclear.
We found TAMs is different before and after chemotherapy by comparing RNA profile of TAMs before and after chemotherapy.

overall_design: We comparied mRNA and lncRNA expression profile of TAMs isolated from tumor samples before and after chemotherapy to ensure difference. This array contained lncRNA and mRNA of human.


title: Human Naïve Epiblast Cells Possess Unrestricted Lineage Potential

status: Public on Feb 10 2021

first: Daniel

last: Spindlow

state: Devon

address: Stocker Road

department: Living Systems Institute

summary: Classical mouse embryology has established a paradigm of early development drivenby sequential lineage bifurcations. Accordingly, mouse embryonic stem cells derivedfrom early epiblast have lost the potency to produce extraembryonic trophectoderm.We show in contrast that human naive epiblast cells readily make trophectoderm.Inhibition of ERK signalling, instrumental in naive stem cell propagation, unexpectedlypotentiates trophectoderm formation, an effect enhanced by Nodal inhibition.Transcriptome analyses authenticate conversion into trophectoderm with subsequentproduction of syncitiotrophoblast, cytotrophoblast and trophoblast stem cells. Geneticperturbations indicate that NANOG suppresses and TFAP2C enables trophectoderminduction. Consistent with post-implantation progression, trophectoderm potential isextinguished in conventional human pluripotent stem cells, which instead makeamnion. Finally, human embryo epiblasts from late blastocysts efficiently generatetrophectoderm and differentiated trophoblast. Thus, pluripotent cells in the humanembryo retain extraembryonic lineage plasticity and regenerative potential untilimplantation. Harnessing this unanticipated regulative capacity may be beneficial forassisted reproduction technology.

overall_design: Human naive pluripotent stem cells (HNES1) were differentiated to trophectoderm in N2B27 basal medium supplementated with PD0325902(PD03) and PD03+A1(PDA83).  RNA samples were collected in a time course.


status: Public on Feb 09 2021

overall_design: The deposited data are RNAsequencing data for studying human naïve stem cells to trophectoderm differentiation. The study comprises two human naïve pluripotency cell lines, HNES1 and cR-H9. The two cell lines were treated in four different medium, N2B27 basal medium or  N2B27 basal mudium supplementated with PD0325902(PD03),  A8301 or PD03+A8301(PDA83).  RNA samples were collected in a time course.


title: Transcriptomic response of Tigriopus californicus populations to a fluctuation in salinity

status: Public on Feb 12 2021

first: Jeeyun

last: Lee

address: Coker Hall, room 418

department: Biology

institute: University of North Carolina at Chapel Hill

summary: Populations that tolerate extreme environmental conditions with frequent fluctuations can give valuable insights into physiological limits and adaptation. In some estuarine and marine ecosystems, organisms must adapt to extreme and fluctuating salinities, but not much is known how varying salinities impact local adaptation across a wide geographic range. We used eight geographically and genetically divergent populations of the intertidal copepod Tigriopus californicus to test if northern populations have greater tolerance to low salinity stresses, as they experience greater precipitation and less evaporation. We used a common garden experiment approach and exposed all populations to acute low (1, 3ppt) and high (110, 130ppt) salinities for 24 hours, and a fluctuation between baseline salinity and moderate low (7ppt) and high (80ppt) salinities over 49 hours. We also performed RNA-sequencing at several time points during the fluctuation between baseline and 7ppt to understand the molecular basis of divergence between two populations with differing physiological responses. We present these novel findings: 1) acute low salinity conditions caused more deaths than high salinity, 2) molecular processes that elevate proline levels increased in 7ppt, which contrasts with other T. californicus studies that mainly associated accumulation of proline with hyperosmotic stress. We also find that 3) tolerance to a salinity fluctuation did not follow a latitudinal trend, but was instead governed by a complex interplay of factors including population and the duration of salinity stress. This highlights the importance of including a wider variety of environmental conditions in empirical studies to understand local adaptation.

overall_design: 1. Population AB at 35ppt control, 2. AB at 7ppt, 3. AB at 35ppt recovery, 4. Population SD at 35ppt control, 5. SD at 7ppt, 6. SD at 35ppt recovery. There were 2 replicates for each number, totalling 12 Samples (libraries)

first: Marshall

middle: C

last: Phillips

first: Monica

last: Lobo

first: Christopher

middle: S

last: Willett


city: Los Angeles

first: Feiyang

last: Ma

state: CA

address: 610, Charles Young Dr East, TLSB 3000C

department: Molecular Biology Institute

institute: UCLA

overall_design: Examination of mouse tumor infiltrating immune cell expression changes after Maoa gene knock out, scRNA-seq

first: Xi

last: Wang

first: Yuchen

first: Matteo

last: Pellegrini

first: Lili

last: Yang


title: Single-cell RNA sequencing of healthy and inflamed murine neutrophils

first: CBDM

last: Lab

department: Microbiology and Immunobiology

institute: Harvard Medical School

summary: Dataset containing single-cell RNA sequencing data of >17,000 healthy and perturbed murine neutrophils across biological tissues. This study contains expression data from healthy tissues (bone marrow, spleen, peripheral blood) as well as models of experimental (K/BxN serum transfer arthritis: peripheral blood and joint, IL-1β peritonitis and IL-1β pneumonitis). Single cell RNA-sequencing was performed on the 10X platform

overall_design: CD11b+ Ly6G+ PI-negative live neutrophils were sorted from healthy tissues (bone marrow, spleen, peripheral blood) and models of experimental inflammation (K/BxN serum transfer arthritis: peripheral blood and joint, IL-1β peritonitis and IL-1β pneumonitis) and single cell RNA-sequencing was performed on the 10X platform.

first: Ricardo

last: Grieshaber-Bouyer

first: Peter

last: Nigrovic


title: Integrative genomic analysis of early neurogenesis reveals a temporal genetic program for differentiation and specification of preplate and Cajal-Retzius neurons [RNA-Seq]

status: Public on Feb 05 2021

city: Shanghai

first: Jia

last: Li

address: No.67 chifeng road, yangpu district

institute: Tongji University

type: Non-coding RNA profiling by high throughput sequencing

summary: Neurogenesis in the developing neocortex begins with the generation of the preplate, which consists of early-born neurons including Cajal-Retzius (CR) cells and subplate neurons. Here, utilizing the Ebf2-EGFP transgenic mouse in which EGFP initially labels the preplate neurons then persists in CR cells, we reveal the dynamic transcriptome profiles of early neurogenesis and CR cell differentiation. Genome-wide RNA-seq and ChIP-seq analyses at multiple early neurogenic stages have revealed the temporal gene expression dynamics of early neurogenesis and distinct histone modification patterns in early differentiating neurons. We have identified a new set of coding genes and lncRNAs involved in early neuronal differentiation and validated with functional assays in vitro and in vivo. In addition, at E15.5 when Ebf2-EGFP+ cells are mostly CR neurons, single-cell sequencing analysis of purified Ebf2-EGFP+ cells uncovers molecular heterogeneity in CR neurons, but without apparent clustering of cells with distinct regional origins. Along a pseudotemporal trajectory these cells are classified into three different developing states, revealing genetic cascades from early generic neuronal differentiation to late fate specification during the establishment of CR neuron identity and function. Our findings shed light on the molecular mechanisms governing the early differentiation steps during cortical development, especially CR neuron differentiation.

overall_design: mRNA profile of cortical Ebf2-EGFP+ and Ebf2-EGFP- cells at mouse embryonic stage E11.5, E13.5 and E15.5

first: Lei

last: Sun

first: Zhi

last: Lu

first: Qin

last: Shen


title: Integrative genomic analysis of early neurogenesis reveals a temporal genetic program for differentiation and specification of preplate and Cajal-Retzius neurons

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

overall_design: Refer to individual Series


title: Single-nucleotide–level mapping of DNA regulatory elements that control fetal hemoglobin expression (RNA-Seq)

status: Public on Feb 04 2021

city: Memphis

first: Yong

last: Cheng

state: Tennessee

address: 262 Danny Thomas Place

department: Department of Hematology

institute: St. Jude Children’s Research Hospital

summary: gRNA screening for HbF+ and HbF- samples were performed to identify candidate cis-regulatory elements.

overall_design: CRISPR pooled gRNA screening, RNA-seq, ChIP-seq and ATAC-seq were performed

first: Li

first: Yichao


title: Single-nucleotide–level mapping of DNA regulatory elements that control fetal hemoglobin expression (histone ChIP-Seq)


title: Single-nucleotide–level mapping of DNA regulatory elements that control fetal hemoglobin expression (TF ChIP-Seq)


title: RAL GTPases mediate EGFR/MAPK signalling-driven intestinal stem cell proliferation and tumourigenesis upstream of RAS activation.

status: Public on Feb 01 2021

city: Glasgow

first: Mate

last: Naszai

address: Wolfson Wohl Cancer Research Centre

institute: University of Glasgow

summary: Abstract: RAS-like (RAL) GTPases function in Wnt signalling-dependent intestinal stem cell proliferation and regeneration. Whether RAL proteins work as canonical RAS effectors in the intestine, and the mechanisms of how they contribute to tumorigenesis remain unclear. Here, we show that RAL GTPases are necessary and sufficient to activate EGFR/MAPK signalling in the intestine. We identify non-canonical roles of RAL GTPases not as RAS effectors, but rather by acting upstream of RAS activation via induction of EGFR internalisation . Knocking down Drosophila RalA from intestinal stem and progenitor cells leads to increased levels of plasma membrane-associated EGFR and decreased MAPK pathway activation. Importantly, in addition to impacting stem cell proliferation and damage-induced intestinal regeneration, this function of RAL GTPases drives EGFR-dependent tumorigenic growth in the intestine and in human mammary epithelium. Altogether, our results reveal previously unrecognised cellular and molecular contexts where RAL GTPases become essential mediators of EGFR-driven tissue homeostasis and malignant transformation. Results: RalA is required within ISCs to induce midgut  adult midgut regeneration following damage by oral infection with Erwinia carotovora carotovora 15 (Ecc15) (Johansson et al., 2019). To achieve a global view of intestinal pathways affected by RalA, we performed a transcriptomic analysis by RNAseq of whole midguts from vehicle treated (Mock) or damaged (Ecc15 fed) control animals or following RalA knockdown in intestinal stem and progenitor cells using the escargot-gal4 driver (ISC/EB>) (Micchelli and Perrimon, 2006). Consistent with its effect on ISC proliferation (Johansson et al., 2019), RalA knockdown significantly impaired damage-induced upregulation of cell cycle genes in the midgut. Additionally, levels of multiple transcriptional targets of the EGFR/MAPK pathway (Golembo et al., 1996; Hsu et al., 2001; Jin et al., 2015; Meng and Biteau, 2015), such as argos (aos), rhomboid (rho), Sox21a and string (stg) were increased following Ecc15 infection in control midguts. The upregulation of these target genes was significantly impaired upon RalA knockdown.

overall_design: Methods: Total RNA from a minimum of 25 midguts was extracted using QIAGEN RNAeasy kit, following the manufacturer’s instructions, including the on-column DNase digestion step. For RNA-seq an RNA integrity score was determined (average = 9.4, SD = 0.6, lowest score used = 8.2; Agilent technologies 2200 Tapestation, RNA Screen Tape). Libraries for cluster generation and DNA sequencing were prepared following (Fisher et al., 2011), using Illumina TruSeq RNA library Preparation Kit v2. Libraries were run on the Next Seq 500 platform (Illumina) using the High Output 75 cycles kit (2x36 cycles, paired end reads, single index).

first: Julia

middle: B

last: Cordero


title: Human FKRP Deficient Patient Study

city: Melbourne

first: Fernando

last: Rossello

state: VIC

address: L 10, 305 Grattan Street

country: Australia

institute: The University of Melbourne

summary: This study evaluates muscle cell RNA seq of FKRP deffiecient patients from the the European Biobank.

overall_design: Myoblast RNA seq analysis

first: Sara

last: Alei

first: Alasdair

last: Wood

last: Currie


title: Integrative genomic analysis of early neurogenesis reveals a temporal genetic program for differentiation and specification of preplate and Cajal-Retzius neurons [ChIP-Seq]

overall_design: Examination of 2 different histone modifications (H3K27ac, H3K27me3) in early differentiated neurons and neural progenitor cells.

first: Xiao-Ming

last: Yu

first: Jing-Dong

last: Han


title: RNA-seq analysis of canine samples

status: Public on Feb 19 2021

city: Nashville

first: Justin

last: Gregory

state: TN

address: 1211 Medical Center Drive

department: Dept of Pediatrics

institute: Vanderbilt University Medical Center

summary:
Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare NGS-derived retinal transcriptome profiling (RNA-seq) to microarray and quantitative reverse transcription polymerase chain reaction (qRT–PCR) methods and to evaluate protocols for optimal high-throughput data analysis
Methods: Retinal mRNA profiles of 21-day-old wild-type (WT) and neural retina leucine zipper knockout (Nrl−/−) mice were generated by deep sequencing, in triplicate, using Illumina GAIIx. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks. qRT–PCR validation was performed using TaqMan and SYBR Green assays
Results: Using an optimized data analysis workflow, we mapped about 30 million sequence reads per sample to the mouse genome (build mm9) and identified 16,014 transcripts in the retinas of WT and Nrl−/− mice with BWA workflow and 34,115 transcripts with TopHat workflow. RNA-seq data confirmed stable expression of 25 known housekeeping genes, and 12 of these were validated with qRT–PCR. RNA-seq data had a linear relationship with qRT–PCR for more than four orders of magnitude and a goodness of fit (R2) of 0.8798. Approximately 10% of the transcripts showed differential expression between the WT and Nrl−/− retina, with a fold change ≥1.5 and p value <0.05. Altered expression of 25 genes was confirmed with qRT–PCR, demonstrating the high degree of sensitivity of the RNA-seq method. Hierarchical clustering of differentially expressed genes uncovered several as yet uncharacterized genes that may contribute to retinal function. Data analysis with BWA and TopHat workflows revealed a significant overlap yet provided complementary insights in transcriptome profiling.
Conclusions: Our study represents the first detailed analysis of retinal transcriptomes, with biologic replicates, generated by RNA-seq technology. The optimized data analysis workflows reported here should provide a framework for comparative investigations of expression profiles. Our results show that NGS offers a comprehensive and more accurate quantitative and qualitative evaluation of mRNA content within a cell or tissue. We conclude that RNA-seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions.

overall_design: Retinal mRNA profiles of 21-day old wild type (WT) and Nrl-/- mice

first: Kushal

last: Suryamohan


title: Large-scale single-cell analysis reveals critical immune characteristics of COVID-19 patients

city: Beijing

first: Zemin

last: Zhang

address: No. 5 Yiheyuan Road, Haidian District

department: Biomedical Pioneering Innovation Center

institute: Peking University

summary: We profiled scRNA-seq of 284 samples collected from 196 individuals, including 22 patients with mild/moderate symptoms, 54 hospitalized patients with severe symptoms, and 95 recovered convalescent persons, as well as 25 healthy controls. The samples were obtained from various tissue types, including human peripheral blood mononuclear cells (249), bronchoalveolar lavage fluid (12) and pleural pleural effusion (1)/sputum (22).

overall_design:
Multiple types of tissues from healthy individuals and COVID-19 patients were collected to obtain single cells and were subjected to sequencing.

***The GEO records contain only processed data (raw counts in sparse matrix format) as raw data is unavailable due to patient privacy concerns.

[Web link]:  This integrated h5 file includes raw counts, normalized data, dimension reduction matrix, et al. which would be convenient for other researchers.


title: Alteration in porcine testicular gene expression in response to reduced testicular estradiol synthesis

status: Public on Jan 31 2021

city: Davis

first: Trish

last: Berger

address: One Shields Avenue

department: Animal Science

institute: University of California

summary: Early reduction of testicular estrogen synthesis induces increased Sertoli cell proliferation.  This experiment was an initial analysis of potential changes in gene expression and included four litters with six  boars in each litter.Boars were derived from PIC genetic lines. Half of the boars in each litter were orally treated with the aromatase inhibitor letrozole (0.1 mg/kg) once per week, a teatment that inhibits aromatase by greateer than 90% at this age. the remaining boars in each litter were treted with the canola oil vehicle. Testis samples were collected from vehicle-treated and letrozole-treated boars in each litter at each age (2 weeks, 3 weeks, and 5 weeks). Testis tissue was collected at euthanasia, flash frozen on dry ice, and stored at -80o C prior to library preparation. Libraries were prepared for RNAseq analysis and the results analyzed with the CLC Genomics Workbench

overall_design: Boars were randomly assigned to treatment at 1 week of age with three littermates in each replicate receiving weekly dosing with 0.1 mg/kg of letrozole through 1 week before tissue collection and three additional littermates receiving weekly dosing with the canola oil vehicle. The experiment comprised a total of 4 replicates (24 boars). In each replicate, one vehicle-treated and one letrozole-treated boar donated tiissue at 2 weeks of age,  one vehicle-treated and one letrozole-treated boar donated tiissue at 3 weeks of age and the remaining two boars donated tissue at 5 weeks of age.Testis tissue was collected at euthanasia, flash frozen on dry ice, and stored at -80o C prior to library preparation. Libraries were prepared for RNAseq analysis and the results analyzed with the CLC Genomics Workbench

first: Barbara

last: Nitta-Oda


title: Non-viral derivation of a transgene-free induced pluripotent stem cell line from a male beagle dog

status: Public on Jan 28 2021

city: Shinjuku

first: Sho

last: Yoshimatsu

state: Tokyo

address: 35 Shinanomachi

department: Physiology

country: Japan

institute: Keio University School of Medicine

summary: We previously reported the non-viral derivation of transgene-free induced pluripotent stem cells (iPSCs) from somatic fibroblasts of a female beagle dog using an optimized induction medium and non-transgene-integrating episomal vectors. Here, we report derivation of an induced pluripotent stem cell line OF35Y-iPS from a male beagle dog, which showed standard characteristics of pluripotency such as a strong gene expression profile of pluripotency markers, differentiation potential into all three germ layers, and normal karyotype (78XY). Furthermore, we demonstrated the iPSC line was suitable for genome editing technology. The novel iPSC line would be a useful foothold for stem cell research and regenerative veterinary medicine

overall_design: RNA seq of canine iPSCs

first: Yumi

last: Yoshii

first: Kazuya

last: Edamura

first: Hideyuki

last: Okano


title: Exploring specific microRNAs in amniotic fluid for chorioamnionitis

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

institute: Toray Industries,Inc.

summary: To identify candidate miRNAs in amniotic fluids as biomarkers for chorioamnionitis, we compared miRNA array data in amniotic fluids between pregnant women with the absence and presence of histological chorioamnionitis.

overall_design: Amniotic fluid samples were collected from 15 pregnant women. Twelve patients were the concurrent infection group and three early pregnant patients were control.

first: Chihiro

last: Kiyoshima

first: Shingo

last: Miyamoto


title: Skin response to urban pollution in an ex vivo model

city: LONGJUMEAU

first: Angela

last: PATATIAN

address: 1CHEMIN DE SAULXIER

department: ESSONNE

country: France

institute: GENEX

summary: A vast range of pollutants (polycyclic aromatic hydrocarbons, heavy metals, particulate matters) are generated by increasing urbanization. The skin epidermis, as the outermost line of defense of the body, is continuously exposed to external aggressions, including environmental pollution.  To study the effects of air pollutant exposure on skin physiology, the first challenge was to define a model that mimics as close as possible the in vivo skin exposure to atmospheric pollution. In the present study, the pollutant mixture was designed on the basis of the French non-profit organization ‘Air Parif’ database and nebulized on human skin explants using the Pollubox® device. Cellular and molecular modifications in skin explants were investigated from several donors exposed to a pollutant mix (P) or an organic solvent (OS). Transcriptomic analyses coupled to immunolabelling showed that P exposure induced the expression of detoxifying enzymes notably in the stratum granulosum. Interestingly, transmission electron microscopy observations demonstrated that, in our model, diesel particles smaller than 300 nm could penetrate the skin up to the granular layer. This may cause local alterations of the microenvironment which alter the skin physiology. Therefore, the response of the epidermis to pollutant exposure is likely to be layer-specific.

overall_design: The study was approved by an ethics committee and performed in accordance with the Declaration of Helsinki after the patient had given informed consent.Full-thickness human skin biopsies were obtained from abdomen of healthy female donors who had undergone plastic surgery. The hypodermis was removed from the skin and circular explants were excised using a sample punch. The samples were placed immediately in BIO-EC’s Explant Medium (BEM) for 5 days and were cultured under classical cell culture conditions (37°C in 5% CO2). On day 5 (D5), the explants of the concerned batches were placed in the exposure system Pollubox® and treated with a solution containing heavy metals, hydrocarbons and fine particulate matters for 1h30 min. Some of these compounds were solubilized in an organic solvent (OS) which was also evaluated on the skin explants. On D6 and D7 respectively 24 and 48 hours after pollutants exposure, skin explants were harvested and were cut in half for storage in RNAlater (Qiagen) or fixation in buffered formol. Total RNAs were extracted using the ReliaPrep Tissue Miniprep kit  from Promega after disruption and homogenization using the TissueLyser Kit. RNAs (70ng) of each explant from 4 donors (V1 to V4) were used for reverse transcription, amplification and Cy3 labeling, using the Low Input Labeling kit, one-color (Agilent Technologies). All cRNAs were hybridized to human whole genome oligo microarrays (Agilent Technologies V3 AMADID072363) which contains 60.000 probes, derived from the National Center for Biotechnology Information Reference Sequence (NCBI) RefSeq. Microarray data were quantified (GeneExtraction Feature V10.7) and normalized with R tools (Bioconductor). The different experiments completed during our study on the human skin explants from various volunteers in the context of the URBASKIN project supported by french FUI (Fonds Unique Interministeriel).

first: A

last: Patatian

first: C

last: Delestre-Delacour

first: G

last: Percoco

first: Y

last: Ramdani

first: M

last: DiGiovanni

last: Chamarat

last: Durand

first: L

last: Peno-Mazzarino

first: T

last: Bader

last: Fays

last: Judith

last: Bénard

last: Driouich

first: E

last: Lati

first: P

last: Benech

last: Follet-Gueye


title: Microarray Analyses of mRNA in lncRNA IRENA overexpressed macrophages

first: Jiang

last: Liu

summary:
LncRNAs play a critical role in both innate and adaptive immunity by regulating survival, differentiation, migration and cytokine production of the immune cells
We found a cytoplasmic lncRNA IRENA in the TAMs, which triggered the NF-κB signaling and increased the production of pro-tumor inflammatory cytokines.

overall_design: We comparied mRNA expression profile of IRENA overexpressed macrophages with vector group.


title: Comparative host transcriptome in response to pathogenic fungi identifies common and species-specific transcriptional antifungal host response pathways

city: Nijmegen

first: Mariolina

last: Bruno

address: Geert Grooteplein Zuid 10

department: Experimental Internal Medicine

institute: Radboudumc

summary: Candidiasis, aspergillosis, and mucormycosis cause the majority of nosocomial fungal infections in immunocompromised patients. Using an unbiased transcriptional profiling in PBMCs exposed to the fungal species causing these infections, we found a core host response in healthy individuals that governs effective fungal clearance: it consists of 156 transcripts, involving canonical and non-canonical immune pathways. Systematic investigation of key steps in antifungal host defense revealed fungal-specific signatures. As previously demonstrated, C. albicans induced interferon-related pathways. In contrast, PRRs, ROS production and host glycolytic pathways were down-regulated in response to R. oryzae, and their modulation is associated with ER-stress response. TLR5 was surprisingly identified to be uniquely regulated by A. fumigatus and to control its-induced cytokine release. In conclusion, our data reveals the transcriptional profiles induced by C. albicans, A. fumigatus, and R. oryzae, and describes both the common and specific antifungal host responses that could be exploited for novel therapeutic strategies.

overall_design: RNA sequencing profiles of human PBMCs stimulated for 4h and 24h with A. fumigatus, C. albicans and R. oryzae

first: Yang

last: Li

first: Vinod

last: Kumar

first: Mark

last: Gresnigt

first: Frank

last: van der Veerdonk


title: Candidate gene screening for lipid deposition combining transcriptomic and proteomic data in Nanyang Black pig

city: BeiJing

first: zhong

last: ann

address: Haidian Yuanmingyuan west road 2

institute: China Agricurltural University

summary: Lower selection intensity resulted in obvious genetically and phenotypically divergences in China indigenous breeds. Nanyang black pig, a China indigenous breed, was famous for its high lipid deposition and high genetic divergence, which made it an ideal model investigating mechanism of lipid position traits in pig. Here, transcriptome and TMT-based proteome analyses were carried out in longissimus dorsi (LD) tissue of high genetic variation individual Nanyang black pigs. After phenotyping in a big population with multi-production traits indexes, six Nanyang black pigs were selected and divided into relatively high and low lipid deposition groups. Combining analyses of transcriptomic and proteomic data identified 15 candidate genes determining lipid deposition genetic divergence in Nanyang black pig. Among them, FASN, CAT, and SLC25A20 were main causal candidate genes. The other genes could be divided as lipid deposition related gene (BDH2, FASN, CAT, DHCR24, ACACA, GK, SQLE, ACSL4, SCD), PPARA-centered fat metabolism regulatory factors (PPARA, UCP3), transcription or translation regulators (SLC25A20, PDK4, CEBPA), and integrin, structural proteins, signal transduction-related genes (EGFR). The multi-omics data set provided a valuable resource for analyses on lipid deposition-traits in pig, especially in Nanyang black pig.

overall_design: Transcriptome of six longissimus dorsi (LD) tissues of high genetic variation individual Nanyang black pigs.

first: Liyuan

last: Wang

first: Hao

last: Zhang

first: Yunfeng

last: Lu


title: Oncostatin M maintains naïve pluripotency of mESCs by tetraploid embryo complementation (TEC) assay

status: Public on Jan 23 2021

city: Tianjin

first: Xiaoying

last: Ye

address: 94 Weijin Road

department: Cell Biology and Genetics

institute: Nankai University

summary: It has been well established that (LIF) is essential for maintaining naive pluripotency of ESCs. Oncostatin M (OSM) is a member of the IL-6 family of cytokines which share gp130 as a receptor subunit, and the OSM-gp130 complex can recruit either LIF receptor β or OSM receptor β. Here we show that OSM can completely replace LIF to maintain naive pluripotency of mouse ESCs. Mouse ESCs cultured in the presence of LIF or OSM not only express pluripotency genes at similar levels but also exhibit the same developmental pluripotency as evidenced by generation of germline competent chimeras, supporting previous findings. Moreover, we demonstrate that mESCs cultured in OSM produce viable all-ESC pups by tetraploid embryo complementation (TEC) assay, the most stringent functional test of authentic pluripotency. Furthermore, the telomere length and telomerase activity also are crucial for unlimited self-renewal and genomic stability of mESCs, and these do not differ in mESCs cultured under OSM or LIF. The transcriptome of mESCs cultured in OSM overall is very similar to that of LIF, and OSM activates Stat3 signaling pathway, like LIF. Additionally, OSM upregulates pentose and glucuronate interconversions, ascorbate and aldarate metabolism, steroid and retinol metabolism pathways. Although the significance of these pathways remains to be determined, our data shows that OSM can maintain the naive pluripotent stem cells in the absence of LIF.

overall_design: Examination of gene expression profile of mouse ESCs in 3 different culture condition and each with two replicates.

first: Chenglei

last: Tian

first: Linlin

first: Guofeng

last: Feng

first: Kairang

last: Jin

first: Lin


title: Murine blastocysts release mature microRNAs into culture media that reflect developmental status

status: Public on Jan 16 2021

city: London

first: Dean

middle: Harvey

last: Betts

state: Ontario

address: 1151 Richmond St.

department: Department of Physiology and Pharmacology

country: Canada

institute: Western University

summary: Extracellular microRNA sequences have attracted interest for their potential use as accessible biomarkers that may be non-invasively collected from a wide range of biological fluids, including spent culture media. The ongoing milieu between the late-stage preimplantation embryo and the receptive uterus remains an actively investigated area of research and the physiological role of secreted microRNA sequences remains to be determined. Spent culture media used to culture late stage E4.0 murine blastocysts was screened for 641 mature microRNA sequences using a qPCR-based array. We report here the 39 sequences that were exclusively detected in the conditioned media using this approach. The embryonic miR-290 family were among the most abundant extracellular sequences. Notably, implantation-relevant members miR-126a, miR-101a, miR-143 and miR-320 were also detected.

sample_organism:
Mus musculus
other sequences

platform_organism:
Mus musculus
Rattus norvegicus

overall_design: Spent murine blastocyst culture was analyzed for mature microRNA using TaqMan Rodent MicroRNA Array v3.0 A + B Cards after RT using a TaqMan MicroRNA Reverse Transcription Kit with Megaplex RT Primers and preamplification using Megaplex PreAmp Primer Pools, Rodent Pools Set v3.0. 2 samples were analyzed: 1) a 6 µL sample of 8 µL culture media conditioned with 25 murine CD1 blastocysts from 99 h to 116 h post-hCG injection, 2) a negative control and contains an equivalent volume of blank culture media.

first: David

last: Hawke

middle: H

first: Andrew

last: Watson


title: HNRNPU regulates lncRNAs nuclear localization

city: Sha Tin

first: Yile

last: Huang

state: Hong Kong

address: Room 503, Li Ka Shing Health and Science Buiding, Prince of Wales Hospital, Sha Tin

department: Chemical Pathology

institute: The Chinese University of HongKong

summary: To elucidate the role of HNRNPU in regulation of lncRNAs nuclear localization, we knocked down HNRNPU in K562 cells using short interfering RNAs and performed subcellular RNA-seq using nuclear or cytosolic RNAs

overall_design: Examine lncRNA subcellular localization in HNRNPU-KD and Control K562 cell lines

first: Yu

last: Zhao


title: Gene expression analysis after miR-125a-3p over-expression in oligodendrocyte precursor cells (OPCs)

status: Public on Jan 21 2021

city: Milano

first: Davide

last: Marangon

state: MI

address: Via Giuseppe Balzaretti 9

country: Italy

institute: Università degli studi di Milano

summary: MiR-125a-3p over-expression in OPCs impairs their differentiation into fully mature oligodendrocytes. We performed a whole microarray profiling to identify new miR-125a-3p direct targets and altered signaling pathways responsible for its the detrimental effect on oligodendrocyte maturation.

overall_design: Gene expression was measured in OPCs 48h after miR-125a-3p (or negative control) over-expression. 2 indipendent samples were used for each condition.

last: Lecca

first: Maria

middle: P

last: Abbracchio


title: Integrative genomic analysis of early neurogenesis reveals a temporal genetic program for differentiation and specification of preplate and Cajal-Retzius neurons [scRNA-Seq]

first: Jia

last: Li

summary: Neurogenesis in the developing neocortex begins with the generation of the preplate, which consists of early-born neurons including Cajal-Retzius (CR) cells and subplate neurons. Here, utilizing the Ebf2-EGFP transgenic mouse in which EGFP initially labels the preplate neurons then persists in CR cells, we reveal the dynamic transcriptome profiles of early neurogenesis and CR cell differentiation. Genome-wide RNA-seq and ChIP-seq analyses at multiple early neurogenic stages have revealed the temporal gene expression dynamics of early neurogenesis and distinct histone modification patterns in early differentiating neurons. We have identified a new set of coding genes and lncRNAs involved in early neuronal differentiation and validated with functional assays in vitro and in vivo. In addition, at E15.5 when Ebf2-EGFP+ cells are mostly CR neurons, single-cell sequencing analysis of purified Ebf2-EGFP+ cells uncovers molecular heterogeneity in CR neurons, but without apparent clustering of cells with distinct regional origins. Along a pseudotemporal trajectory these cells are classified into three different developing states, revealing genetic cascades from early generic neuronal differentiation to late fate specification during the establishment of CR neuron identity and function. Our findings shed light on the molecular mechanisms governing the early differentiation steps during cortical development, especially CR neuron differentiation.

overall_design: single cell mRNA profile of cortical Ebf2-EGFP+ cells at mouse embryonic stage E15.5

first: Lei

last: Sun

first: Qin

last: Shen


title: Establishing a common marmoset induced pluripotent stem cell line NM-iPS by an all-in-one episomal vector approach

status: Public on Jan 10 2021

first: Sho

last: Yoshimatsu

summary: Epstein-Barr virus (EBV)-based episomal vector system enables persistent transgene expression, which is advantageous for efficient derivation of transgene-free induced pluripotent stem cells (iPSCs) without viral transduction. Here, we report establishment of an iPSC line from somatic fibroblasts of a neonatal common marmoset monkey (marmoset; Callithrix jacchus) using an all-in-one episomal vector that we newly developed. The established iPSC line, named NM-iPS, showed standard characteristics of pluripotency such as pluripotency-related marker expression, three germ layer differentiation, and normal karyotype (2n = 46). The novel iPSC line would be a useful resource for stem cell research using non-human primates.

overall_design: RNA seq of marmoset iPSCs

first: Mayutaka

last: Nakajima

first: Hideyuki

last: Okano


title: Gene expression changes during senenscence in primary dermal human fibroblasts

status: Public on Jan 09 2021

city: Saskatoon

first: Christopher

middle: H.

last: Eskiw

state: SK

address: 51 Campus Drive

department: Food and Bioproduct Science

institute: University of Saskatchewan

summary: Analysis of gene expression changes following replicative senescnce  Here we induced normal (primary) human diploid fibroblasts into senescence using serial passaging to determine which genes changed expression as a function of exit from the cell cycle.

overall_design: Microarray analysis of transcrpts from senescent priamry dermal fibroblasts compared to those prolfierative primary dermal fibroblasts as base line. 4 independent arrays were used with dye swaps to make direct comparisions between senescent and prolfierative gene expression levels.

first: C


title: Potential MDDC reprogramming when exposed to BKPyV

status: Public on Jan 14 2021

city: Nantes

first: Matthieu

last: Giraud

address: 30 bd Jean Monnet

department: CRTI

institute: INSERM _ Université de Nantes

summary: Absence of significant mRNA profile modifications upon BKPyV co-culture in human MDDC suggesting no cell reprogramming.

overall_design: MDDC from four distinct blood donors were analyzed by 3′ digital gene expression (DGE) RNAseq. The libraries were prepared from 10 ng of total RNA. The mRNA poly(A) tails were tagged with universal adapters, specific barcodes and unique molecular identifiers (UMIs) during template switching reverse transcriptase. Barcoded cDNAs from multiple samples were  pooled, amplified and tagmented using a transposon-fragmentation. The obtained library was on an Illumina HiSeq 2500. After read counting, DESeq 2 was used to normalize expression.

first: Franck

last: Halary


title: αSMA+ fibroblasts suppress differentiation of Lgr5+ cancer stem cells via BMP4 and restrain progression of colorectal cancer

status: Public on Jan 06 2021

city: Houston

first: Karina

last: Vazquez-Arreguin

state: TX

address: 1881 East Rd

department: Cancer Biology

institute: MD Anderson Cancer Center

summary:
Purpose: This study interrogated the role of αSMA+ CAFs in a genetic moue model of metastatic colorectal cancer.
Methods: αSMA+ CAFs  were selectively depleted in mouse CRC model. RNA was isolated from tumors from control and depleted mice, as well as from the colon of WT mice and sequenced.
Results: Mice with αSMA+ CAF-depletion exhibited increased inflammation and immunosuppressive phenotype in tumors. Depleted mice also had an increased incidence of Lgr5+ CSCs. BMP4 and TGFβ1 was increased in depleted tumors compared to control.
Conclusion: αSMA+ CAFs  have a tumor restraining function in CRC, via BMP4/TGFβ1 signaling.

overall_design: Total RNA sequenced from tumors from 3 control and 3 depleted mice, as well as normal colon epithelium from 3 WT mice.

last: Vázquez-Arreguín

first: Changsoo

last: Kwak

first: Hikaru

last: Sugimoto

first: Bingrui

first: Valerie

last: LeBleu

first: Raghu

last: Kalluri


title: Native single molecule sequencing and de novo assembly of Hepatitis B Virus to detect 5mCpG

status: Public on Jan 05 2021

city: Lyon Cedex 08

first: Chloe

middle: Desiree

last: Goldsmith

address: 28 Rue Laennec

department: Cancer Research Center of Lyon

institute: INSERM

type: Methylation profiling by high throughput sequencing

summary: Methylation of Hepatitis B Virus (HBV) DNA in a CpG context (5mCpG) can alter the expression patterns of viral genes related to infection and cellular transformation. Moreover, it may also provide clues to why certain infections are cleared, or persist with or without progression to cancer. The detection of 5mCpG often requires techniques that damage DNA or introduce bias through a myriad of limitations. Therefore, we developed a method for the detection of 5mCpG on the HBV genome that does not rely on bisulfite conversion or PCR. Moreover, using the developed technique, we have provided the first de novo assembly of native HBV DNA, as well as the first landscape of 5mCpG from native HBV sequences

overall_design: PHH were isolated from halthy liver tissue and plated before HBV infection with different genotypes. Also investigated fine needle biopsys for HBV DNA.

first: Hector

last: Hernandez-Vargas


title: Feeding differentially regulates clocks and rhythmicity of peripheral tissues through the liver-clock

status: Public on Jan 29 2021

city: Rehovot

first: Gal

last: Manella

state: Israel

address: 234 Herzel St.

country: Israel

institute: Weizmann Institute of Science

summary: The mammalian circadian system consists of a central clock in the brain that synchronizes clocks in peripheral tissues. While the hierarchy between the central and peripheral clocks is well established, peripheral clocks are largely viewed as a group and little is known regarding their specificity and functional organization. We employed feeding paradigms in conjunction with liver-specific clock-deficient murine model to map disparities and potential interactions between peripheral clocks. We found that peripheral clocks largely differ in their response to feeding-time. In view of its prominent role in nutrient processing, we hypothesized that the liver-clock instigate the response of peripheral clocks to feeding. Although the liver-clock did not affect the rhythmicity of clocks in other peripheral tissues, it strongly modulated their transcriptional rhythmicity upon daytime feeding. Overall, our findings suggest a role for the liver-clock in buffering feeding-related signals that affect rhythmicity of other peripheral tissues upon nutrient challenge, irrespective of their clocks.

overall_design: Mice of either Alb-Cre+ (control) or Bmal1 fl/fl Alb-Cre+ (aka BLKO), where fed either Ad Libitum (AL) or only during the light-phase (Daytime-feeding, DF)

first: Gad

last: Asher

first: Marina

last: Golik

first: Elizabeth

last: Sabbath


title: Elucidating The Role Of ∆9-Tetrahydrocannabinol (Thc) And Cannabidiol (Cbd) In Developmental Toxicity

status: Public on Jan 01 2021

city: Woods Hole

first: Neelakanteswar

last: Aluru

state: MA

address: 45 Water Street

department: Biology

institute: Woods Hole Oceanographic Institution

summary: Increased availability of cannabis and cannabinoid-containing products necessitates the need for understanding how exposure to these compounds can affect development. Using cannabinoid receptor-null zebrafish (cnr1-/- and cnr2-/-), we conducted experiments to assess the roles of these receptors in ∆9-tetrahydrocannabinol (THC) and cannabidiol (CBD) developmental and behavioral toxicity. THC increased mortality and deformities (pericardial and yolk sac edemas, a reduction in size) in cnr1-/- and cnr2-/- fish. Conversely, CBD-induced malformations and mortality were significantly reduced in the cnr1-/- and cnr2-/- larvae. THC and CBD exposure caused significantly decreased larval behavior (96 hpf), however, decreased distance travelled was protected in the cnr1-/- and cnr2-/- fish, suggesting these receptors are responsible for mediating behavioral toxicity. Transcriptomic profiling in cnr+/+ embryos developmentally exposed to 4 μM THC or 0.5 μM CBD revealed that a significant portion of differentially expressed genes were targets of PPARγ, a predicted upstream regulator. In Cnr-positive embryos, co-exposure to the PPARγ inhibitor GW9662 and THC or CBD, there was increased toxicity compared to exposure with THC or CBD alone. Co-treatment in the cnr2-/- fish with GW9662 did not alter the CBD-induced decrease in activity. However, co-treatment with GW9662 did remove the protective effect observed in cnr1-/- fish treated to CBD alone. Collectively, these results indicate that PPARγ, Cnr1, and Cnr2 all play crucial roles in the developmental toxicity of THC and CBD.

overall_design: Tg(fli1:egfp) strain of zebrafish embryos was exposed to either DMSO, THC or CBD. We sequenced 4 biological replicates per treatment condition.

first: Zacharias

last: Pandelides

first: Cammi

last: Thornton

first: Kristie

last: Willett


title: AGO2 protects Drosophila siRNAs and microRNAs from target-directed degradation, even in the absence of 2′-O-methylation

city: Cambridge

first: Elena

last: Kingston

state: Massachusetts

address: Nine Cambridge Center

institute: Whitehead Institute MIT

summary: Target-directed degradation (TDD) of microRNAs (miRNAs) plays an important role in shaping miRNA abundances across bilateria. Some endogenous small interfering RNAs (siRNAs) of Drosophila cells have target sites resembling those that trigger miRNA TDD, raising the question as to whether they too might undergo such regulation. Here, we find that at least seven of these siRNAs are indeed sensitive to TDD when loaded into AGO1, the Argonaute paralog that preferentially associates with miRNAs. Despite this sensitivity when loaded into AGO1, these siRNAs are not detectably regulated by TDD because most molecules are loaded into AGO2, the Argonaute paralog that preferentially associates with siRNAs, and we find that siRNAs and miRNAs loaded into AGO2 are insensitive to TDD. One explanation for the protection of these small RNAs loaded into AGO2 is that these small RNAs are 2′-O-methylated at their 3′ termini.  However, contrary to previous proposals, 2′-O-methylation does not protect these RNAs from TDD, which indicates that their protection is instead conferred by features of the AGO2 protein itself. Together, these observations clarify the requirements for regulation by TDD and revise our understanding of the role of 2′-O-methylation in small-RNA biology.

overall_design: Measurement of miRNA and siRNA abundances in AGO1 and/or AGO2 in wild-type, dora, hen1, or hen1/dora Drosophila S2 cell lines

first: David

last: Bartel


title: The effect of age on interstitial cells following renal ischemia reperfusion injury

city: Edinburgh

first: Eoin

last: O'Sullivan

address: 47 Little France Crescent

department: Centre for Inflammation Research

institute: University of Edinburgh

summary: Single Cell RNA-SEQ of Murine Kidney post Ischemia Reperfusion Injury demonstrates heterogeneous mesencymal cells post injury and recapitulates novel markers with transcipts

overall_design: Unbiased examination of single cell RNA-seq of injured murine kidney

first: Isaac

last: Shaw

last: Ferenbach


title: Whole leaf vs. Leaf protoplst bulk RNA sequencing dataset

status: Public on Dec 31 2020

city: Düsseldorf

first: Jiyun

last: Kim

address: Universitätsstr. 1

country: Germany

institute: HHU

summary: The leaf vasculature plays a key role in solute translocation. Veins consist of at least seven distinct cell types, with specific roles in transport, metabolism, and signaling. Little is known about the vascular cells in leaves, in particular the phloem parenchyma (PP). PP effluxes sucrose into the apoplasm as a basis for phloem loading; yet PP has only been characterized microscopically. Here, we enriched vascular cells from Arabidopsis leaves to generate a single-cell transcriptome atlas of leaf vasculature. We identified ?19 cell clusters, encompassing epidermis, guard cells, hydathodes, mesophyll, and all vascular cell types, and used metabolic pathway analysis to define their roles. Clusters comprising PP cells were enriched for transporters, including SWEET11 and SWEET12 sucrose and UmamiT amino acid efflux carriers. PP development occurs independently from APL, a transcription factor required for phloem differentiation. PP cells have a unique pattern of amino acid metabolism activity distinct from companion cells (CC), explaining differential distribution/metabolism of amino acids in veins. The kinship relation of the vascular clusters is strikingly similar to the vein morphology, except for a clear separation of CC from the other vascular cells including PP. In summary, our scRNA-seq analysis provides a wide range of information into the leaf vasculature and the role and relationship of the leaf cell types.

overall_design:
mRNA profiles of whole leaf and protoplasts from Col-0 plants grown in short day (8hr light/16hr dark) condition
Total RNA was extracted from leaves (not protoplasted) and leaf protoplasts isolated using the same method for the single cell sequencing using the RNeasy Kit. Two biological replicates were made for leaf and leaf protoplast samples. Libraries were constructed using the ULTRA II directional library kit and size selection was done using SPRI beads. QC-tested libraries were sequenced on an Illumina HiSeq 2500 lane with 150 bp paired-end.

first: Ji-Yun

first: Efthymia

last: Symeonidi

first: Tin

middle: Y

last: Pang

first: Tom

last: Denyer

first: Diana

last: Weidauer

first: Margaret

last: Bezrutczyk

first: Manuel

last: Miras

first: Nora

last: Zöllner

first: Michael

middle: M

last: Wudick

first: Thomas

last: Hartwig

first: Martin

last: Lercher

first: Li-Qing

last: Chen

first: Marja

last: Timmermans

first: Wolf

last: Frommer


title: scRNAseq of mock, HSV-1 or HSV-2 infected C57BL/6 Vaginal tissue at 5 days post infection

first: Maxim

middle: N.

last: Artyomov

state: MO

address: 660 S. Euclid Avenue, Campus Box 8118

department: Immunology&Pathology

institute: Washington University in St.Louis

summary:
Purpose: To compare single cell transcriptional profiling (scRNAseq) of different murine genital herpes infection models with HSV1-McKrae and HSV2-186.
Method: DMPA-treated WT C57BL/6 mice were infected with HSV1-McKrae, HSV2-186 or PBS intravaginally. Vaginal tissues were harvested  at 5 days post infection, live cells were sorted, a minimum of 16,000 cells were used for scRNAseq.
Results: By tSNE visualization of 21,633 cells across all samples, 17 distinct clusters were resolved. We found significantly increased levels of Interferons-Stimulated-Genes (ISGs) in the neutrophils potentially contributing to disease onset and progression in HSV2 genital infections.
Conclusion: Our study is the first comparison between the transcriptional signature of two genital herpes model- namely HSV1 and HSV2. Generated by scRNAseq, this study would provide researchers with gene candidates associated with the disease progression and inflammation induced by genital infections with HSV1 and HSV2.

overall_design: Examination of distinct gene transcriptional signatures between mock, HSV1 or HSV2 infected WT C57BL/6 mice using scRNAseq.

first: Maria

last: Fabbrizi

first: Ying

last: Lim

first: Prabhakar

last: Andhey

first: Haina

last: Shin


title: RNA sequence from sciatic nerve of HSF WT and V30M TTR mice

status: Public on Jan 20 2021

city: Porto

first: João

last: Moreira

address: Rua Alfredo Allen, 208

country: Portugal

summary: RNA from sciatic nerves was isolated from HSF WT and HSF V30M mice with RNeasy Mini columns and first-strand complementary DNA (cDNA) was synthesized using the SuperScript double-stranded cDNA Kit.

overall_design: RNA sequence profile of 6 month old mice

last: Saraiva


title: Single cell transcriptome analysis of proprioceptive muscle afferents

city: New York

first: Vilas

last: Menon

state: NY

department: Neurology

institute: Columbia University Medical Center

summary: We report on the single cell RNA sequencing of genetically identified adult, neonatal, and embryonic proprioceptors. High depth sequencing data was acquired for all developmental time points using plate-seq. For adult proprioceptors, bioinformatics analysis identified five molecularly distinct subsets. At least two of these subsets have been validated to correspond to group Ia muscle spindle afferents and group Ib GTO afferents, respectively.

overall_design: Proprioceptors were labeled using intersectional genetic tools and fluorescently labeled neurons were isolated using fluorescence activated cell sorting (FACS). Neurons were directly deposited in lysis buffer in 96-well plates and subjected to RNA isolation, cDNA generation, library preparation and single cell sequencing. Single proprioceptor transcriptomes were filtered for high quality cells (>2000 UMI's), and limited satellite cell contamination (<10% Apoe).

first: Joriene

last: de Nooij


title: Single cell RNA sequencing of Col-0 leaf cell

first: Jiyun

last: Kim

overall_design:
We enriched vascular cells from Arabidopsis leaves to generate a single-cell transcriptome atlas of leaf vasculature.
Two biological replicates were performed with the aim of capturing ~7,000 leaf protoplasts for each replicate. Freshly isolated protoplasts were loaded into the 10X Genomics Chromium single cell microfluidics device according to the Single Cell 3’ Reagent Kit v2 protocol. scRNA-seq library sequencing was performed on a NextSeq platform.

first: Ji-Yun

first: Efthymia

last: Symeonidi

first: Tin

last: Pang

first: Tom

last: Denyer

first: Diana

last: Weidauer

first: Margaret

last: Bezrutczyk

last: Miras


title: Breast cancer hybrid cells after spontaneous cell fusion with MSC display tumor dorming-like properties

city: Hannover

first: Ralf

last: Hass

state: Germany

address: Carl-Neuberg-Str. 1

department: Gynecology

institute: Hannover Medical School

summary: Functional changes were investigated in vitro and in vivo following spontaneous fusion and hybrid cell formation in co-cultures of primary human mesenchymal stroma/stem-like cells (MSC) with human MDA-MB-231 breast cancer cells. Lentiviral fluorescence-labeled MSC with eGFP and breast cancer cells labeled with mcherry resulted in dual-fluorescing hybrid cells. Double FACS sorting and single cell cloning revealed  different aneuploid hybrid populations (MDA-hyb1 MDA-hyb3, MDA-hyb5)

overall_design: A total of 4 different total RNA samples was subjected to microarray analysis according to a single-color design.


title: Features of repertoire diversity and heterogeneity in gene expression of CMV-specific CTL following allogeneic HCT

city: Saitama

first: Hideki

last: Nakasone

address: 1-847, Amanuma-cho, Omiya-ku

department: Hematology

institute: Jichi Medical University Saitama Medical Center

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

overall_design: Refer to individual Series


title: Transcriptional dynamics of transposable elements when converting fibroblast cells of Macaca mulatta to neuroepithelial stem cells [mmu-14-samples]

city: Kunming

first: Yun

last: Zheng

state: Yunnan

address: 452 Fengyuan Road

institute: Yunnan Agricultural University

summary: Transposable elements (TE) account for more than 50% of human genome. It has been reported that some types of TEs are dynamically regulated in the reprogramming of human cell lines. However, it is largely unknown whether some TEs in Macaca mulatta are also regulated during the reprogramming of cell lines of monkey. Here, we systematically examined the transcriptional activities of TEs during the conversion of Macaca mulatta fibroblast cells to neuroepithelial stem cells (NESCs). Hundreds of TEs were dynamically regulated during the reprogramming of Macaca mulatta fibroblast cells. Furthermore, 60 Long Terminal Repeats (LTRs), as well as some integrase elements, of MacERV3 were transiently activated during the early stages of the conversion process. These LTRs were potentially bound by critical transcription factors for reprogramming, such as KLF4 and ETV5. These results suggest that the transcription of TEs are delicately regulated during the reprogramming of Macaca mulatta fibroblast cells. Although the family of ERVs activated during the reprogramming of fibroblast cells in Macaca mulatta are different from those in the reprogramming of human fibroblast cells, our results suggest that the activation of some ERVs is a conserved mechanism in primates for converting fibroblast cells to stem cells.

overall_design: The fibroblast cells of Macaca mulatta were induced to neuroepithelial stem cells to identify critical transposable elements (TEs) that may contribute to the reprogramming procedure. During the conversion procedure, cells were collected at 7 different stages and were sequenced with RNA-seq to obtain the expression levels of genes and TEs. The enriched cis-regulatory motifs in LTRs of MacERV3 were analyzed to find putative transcription factors of the LTRs. Then, the correlation coefficient values of TFs and LTRs were analyzed to further support the regulatory relations between the identified TFs and LTRs.


title: Environmental enrichment restores a young DNA methylation landscape in the aged mouse hippocampus

city: Dresden

first: Gerd

last: Kempermann

state: Saxony

address: Tatzberg 41

institute: German Center for Neurodegenerative Diseases (DZNE)

summary: The decline of brain function during aging is associated with epigenetic changes, including DNA methylation. Lifestyle interventions can improve brain function during aging, but their influence on age-related epigenetic changes is unknown. Using genome-wide DNA methylation sequencing, we here show that environmental enrichment counteracted age-related DNA methylation changes in the hippocampal dentate gyrus of mice. Specifically, environmental enrichment prevented the aging-induced CpG hypomethylation at target sites of the methyl-CpG-binding protein Mecp2, which is known to control neuronal functions. The genes at which environmental enrichment counteracted aging effects have described roles in neuronal plasticity, neuronal cell communication and adult hippocampal neurogenesis and are dysregulated with age-related cognitive decline in the human brain. Our results highlight the rejuvenating effects of environmental enrichment at the level of DNA methylation and give molecular insights into the specific aspects of brain aging that can be counteracted by lifestyle interventions.

overall_design: Mice of different ages were housed in standard housing conditions or in environmental enrichment. DNA methylation profiling was performed by Reduced Representation BIsulfite Sequencing on micro-dissected dentate gyrus tissue. Reduced representation bisulfite sequencing was performed on a total of 30 samples.

first: Sara

last: Zocher

first: Rupert

middle: W

last: Overall


title: Transcriptome profiling of human lung cancer cell lines with synthetic "sequin" controls

status: Public on Jan 12 2021

city: PARKVILLE

first: Xueyi

last: Dong

state: VIC

address: 1G ROYAL PARADE

institute: Walter and Eliza Hall Institute of Medical Research

summary:
Purpose: The aim of this study is to build up a transcriptomic data analysis pipeline and test its performance using synthetic "sequins" controls and lung cancer cell lines.
Methods - Cell Culture: Lung adenocarcinoma cell lines NCI-H1975 and HCC827 from a range of passages (2-4) were grown on 3 separate occasions in Roswell Park Memorial Institute (RPMI) 1640 medium with 10% fetal calf serum and 1% penicillin-streptomycin.
Methods - RNA preparation: Total RNA was extracted using the TRIzol reagent. 6 ng of sequins were added to 1 ug of total RNA (mix  A with H1975, mix B with HCC827).
Methods - Library prep: the sequin+total RNA mixtures were subjected to polyA selection (NEBNext PolyA E7490) and library prep (NEBNext Ultra II Directional RNA Library Prep Kit for Illumina) following manufacturer's instructions; we performed 9 PCR cycles

overall_design:
Total RNA was extracted from lung adenocarcinoma cell lines NCI-H1975 and HCC827 (2 independent samples for each cell line). Both mRNA and Total RNA transcriptomes from these samples were profiled by RNA-Seq (Illumina short-read, Oxford Nanopore Technologies PromethION and PacBio Sequel II)
The processed data are the raw counts of all Sequin genes. Although there are some reads from human cell lines in this dataset, by mapping all of the reads to the Sequin decoy chromosome, we can get a mapping rate around 80%, and we only analysed the Sequins genes in our study.

first: Luyi

last: Tian

first: Quentin

last: Gouil

first: Matthew

middle: E

last: Ritchie


title: Differential expression profiles of plasma tsRNAs in children with fulminant myocarditis

status: Public on Dec 29 2020

city: Jinan

first: Jing

last: Wang

address: No. 324, jingwuweiqi road, huaiyin district

institute: Shandong Provincial Hospital

summary: We report the application of high-throughput RNA sequencing technology to examine expression profiling of plasma transfer RNA (tRNA)-derived small RNAs (tsRNAs) in children with fulminant myocarditis during acute phase (FM-A group), children with fulminant myocarditis during convalescent phase (FM-C group), and healthy volunteers (Con group). A total of 750 precisely matched tsRNAs were identified in the plasma from the three groups. We find that  a total of 13 tsRNAs were differentially expressed in FM-A and CON samples, of which 11 tsRNAs were upregulated and 2 were downregulated, and 694 tsRNAs were excluded ; a total of 8 tsRNAs were differentially expressed in paired FM-C and CON samples, of which 2 tsRNAs were upregulated and 6 were downregulated  and 703 tsRNAs were excluded . This study provides new ideas for future research on elucidating the mechanisms of myocarditis through regulating tsRNAs levels.

overall_design: Examination of different expression profiling of tsRNAs in children with fulminant myocarditis.

first: Bo

last: Han

first: Li

last: Zhang

first: Jianli

last: Lv

first: Yan

first: Xiaofei

last: Yang

first: Diandong

last: Jiang

first: Yingchun

last: Yi

first: Jianjun


title: Transcriptome Analysis of Bladder Cancer Cell Persistently Infected by Newcastle disease virus (NDV)

status: Public on Dec 28 2020

city: Serdang

first: Lee Chin

last: Chan

state: Selangor

address: Jalan Sapucaya

department: Microbiology

country: Malaysia

institute: Universiti Putra Malaysia

summary: This project seeks to determine if there is a difference in expression between  bladder cancer cells vs NDV-resistant bladder cancer cells.This result provides insight of the orchestrated transcriptomic changes that occur in the development and maintenance of NDV persistency of infection, which can be an useful resource for future downstream analysis of the identified targets.

overall_design: NDV resistant bladder cancer cell EJ28 compared to parental EJ28

first: Lee-Chin


title: Microarray expression data from follicular lymphoma patients' lymph node biopsies (frozen)

city: TOULOUSE

first: Pauline

last: Gravelle

address: 1 Avenue Irène Joliot Curie

department: Anatomy-Pathology

institute: IUCT-ONCOPOLE

summary:
Abstract from the associated publication:
Although PET allows an accurate staging of disease in follicular lymphoma (FL) patients, the impact of pre-treatment maximum standardized uptake  (SUVmax) value in this population remains elusive as well as its real biological significance. A training cohort of 48 FL patients and a validation cohort of 84 patients unpreviously treated were included retrospectively. SUVmax of 18-FDG PET was evaluated by centrally expert review and the optimum threshold of SUVmax value was determined in the training cohort to predict progression free survival (PFS). To explore the biologic meaning of PET results, tumor samples were analyzed from the two cohorts independantly :- the tumor microenvironment immune cartography by immunochemistry , - the cell gene-expression profiles assessed using Sample enrichment score  combined to CIBERSORT method and - the tumor cell mutational profile determined by targeted Next Generation Sequencing (t-NGS). At baseline, patients with a SUVmax >14.5 had a significantly lower PFS compared to patients with SUVmax ≤14.5 (2y PFS: 40% vs 86%, HR = 0.16, p = 0.0009). The prognostic value of SUVmax was confirmed in the validation cohort (p= 0.006). Neither immune cell infiltration nor immune checkpoint expression were related to the baseline PET metrics including SUVmax. By constrast, high tumor cell proliferation (assessed by Ki67 staining)  was significantly related to high SUVmax level ( p= 0.007). Interestingly FOXO1 mutated patients harbored high SUVmax and high tumor proliferation, that is why FOXO1 status could reflect to proliferation of FL tumor cells through SUVmax and Ki67 staining. So, FL patients with high baseline SUVmax related to high tumor cell proliferation  have a poorer PFS despite absence of  lymphoma transformation.

overall_design:
We produced and analyzed the transcriptomic profiles in a representative cohort of 40 follicular lymphomas patients to analyze the cellular composition in the tumor microenvironment through CIBERSORT method, and  to characterize the cell gene-expression profiles in this disease.  We used microarrays to compare the global gene expression profile between groups of FL patients whom the PET (positon emission tomography) show high fluorodeoxy glucose (FDG) uptake reflecting high maximum standardized uptake  (SUVmax) value as compared with low FDG uptake. The optimum treshold to divide into these two groups is the SUVmax of 14.5 This analysis unveiled activated gene signature for tumor cell proliferation and DNA repair pathways in SUVmax >14.5 group.
Frozen biopsies of diagnosed follicular lymphomas were selected for RNA extraction, amplification on GeneChip® WT PLUS and hybridization on Human Transcriptome Array 2.0 microarrays ( HTA 2.0 ; Affymetrix).

first: Cédric

last: Rossi

first: Camille

last: Laurent


title: Gene expression analyses of palbociclib treated ER+ breast cancer cell lines as assessed by RNA-seq

city: Pearl River

first: Reeja

last: Maskey

address: 401 N Middletown Rd

department: Oncology Research & Development

institute: PFIZER INC.

summary: The goal of this study is to measure gene expression changes resulting over time of palbociclib treatment of T47D, MCF7, and CAMA1 ER+ breast cancer cell lines.

overall_design: Examination of gene expression changes in ER+ breast cancer cell lines (T47D, MCF7 and CAMA1) treated with palbociclib for 2, 7, 10 and 14 days.  As a control, each of the three cell lines has vehicle treated sub-confluent log phase growing cells for comparison with palbociclib treated cells.

first: Anthony

last: Mazurek

first: Wenyan

last: Zhong


title: RNA-seq analysis of transcriptome profiling in Apis cerana

status: Public on Jan 07 2021

city: Seoul

first: Igojo

last: Kang

state: Seoul

address: Gwanak_1 Gwanak-ro, Gwanak-gu

department: Applied Biology and Chemistry

country: South Korea

institute: Seoul National University

summary: High-throughput RNA sequencing was carried out for understanding of caste and organs of Asian honeybees.

overall_design: Examination of 11 different organs in Apis cerana

first: Woojin

last: Kim

first: Jae

last: Lim

first: Chanseok

last: Shin


title: Blood based expression of colorectal cancer and healthy controls

city: Shanghai

first: changming

last: cheng

address: No. 151, Libing Road

institute: National Engineering Center for Biochip at Shanghai China

summary:
The immune system is crucial in regulating colorectal cancer tumorigenesis. Identification of immune-related transcriptomic signatures derived from the peripheral blood of colorectal cancer patients will provide insights into colorectal cancer pathogenesis and suggest novel clues to potential colorectal cancer immunotherapy strategies.
We used microarrays to detail the blood-based gene expression of colorectal cancer patients and healthy controls to identify the colorectal cancer-specific immune genes potentially diagnostic for colorectal cancer.

overall_design: We collected blood samples from 59 colorectal cancer patients and 62 healthy controls and carried out whole blood gene expression profiling using affymetrix microarray hybridization. Immune-related gene expression signatures for colorectal cancer were identified from immune gene datasets, and an algorithmic predictive model was constructed for distinguishing colorectal cancer from controls.

first: Guang

last: Cheng

first: Wei

last: Xia


title: Setd2 Epidermal Deficiency Promotes Cutaneous Wound Healing via Activation of AKT/mTOR Signaling

status: Public on Dec 25 2020

city: shanghai

first: xiaoxue

last: li

address: huashan road

institute: shanghai jiaotong university


title: Setd2 Epidermal Deficiency Promotes Cutaneous Wound Healing via Activation of AKT/mTOR Signaling (ChIP-Seq)

summary: Skin wound healing is one of the major prevalent medical problems in the worldwide. Wound healing involves multi-process synergy and re-epithelialization is an essential part of wound healing. Histone H3K36 tri-methylase Setd2 has been extensively studied in different biological processes and diseases. However, the function of Setd2 in the wound healing remains unclear. To elucidate the biological role of Setd2 in the skin wound healing, conditional gene targeting was employed to establish epidermis-specific Setd2-deficient mice. We found that Setd2 deficiency resulted in accelerated re-epithelialization during cutaneous wound healing by promoting keratinocytes proliferation and migration. Furthermore, we demonstrated that loss of Setd2 activated the AKT/mTOR pathway, and pharmacological inhibitions of AKT and mTOR with MK2206 and rapamycin delayed wound closure, respectively. In conclusion, our results reveal the essential role of Setd2 in skin wound healing that is Setd2 loss promotes cutaneous wound healing via activation of AKT/mTOR signaling.

overall_design: ChIP assays of  Setd2fl/fl mouse skin primary keratinocytes were generated by deep sequencing

first: Xiaoxue

last: Li


title: SARSeq, a robust and highly multiplexed NGS assay for parallel detection of SRAS-CoV2 and other respiratory infections

status: Public on Dec 23 2020

city: Vienna

first: Alexander

last: Stark

address: Campus-Vienna-Biocenter 1

country: Austria

institute: The Research Institute of Molecular Pathology (IMP)

summary: During a pandemic, mitigation as well as protection of system-critical or vulnerable institutions requires massively parallel, yet cost-effective testing to monitor the spread of agents such as the current SARS-CoV2 virus. Here we present SARSeq, saliva analysis by RNA sequencing, as an approach to monitor presence of SARS-CoV2 and other respiratory viruses performed on tens of thousands of samples in parallel. SARSeq is based on next generation sequencing of multiple amplicons generated in parallel in a multiplexed RT-PCR reaction. It relies on a two-dimensional unique dual indexing strategy using four indices in total, for unambiguous and scalable assignment of reads to individual samples. We calibrated this method using dilutions of synthetic RNA and virions to show sensitivity down to a few molecules, and applied it to hundreds of patient samples validating robust performance across various sample types. Double blinded benchmarking to gold-standard quantitative RT-PCR performed in a clinical setting and a human diagnostics laboratory showed robust performance up to a Ct of 36. The false positive rate, likely due to cross contamination during sample pipetting, was estimated at 0.04-0.1%. In addition to SARS-CoV2, SARSeq detects Influenza A and B viruses as well as human rhinovirus and can be easily expanded to include detection of other pathogens. In sum, SARSeq is an ideal platform for differential diagnostic of respiratory diseases at a scale, as is required during a pandemic.

overall_design:
Massively parallel, cost-effective detection of SARS-CoV2 using saliva analysis by RNA sequencing (SARSeq). Study includes left-over patient samples.
[contributor] Vienna Covid-19 Detection Initiative Members

first: Ramesh

last: Yelagandula

first: Aleksandr

last: Bykov

last: Vogt

first: Robert

last: Heinen

first: Ezgi

last: O?zkan

first: Marcus

last: Strobl

first: Juliane

last: Baar

first: Kristina

last: Uzunova

first: Bence

last: Hajdusits

first: Darja

last: Kordic

first: Erna

last: Suljic

first: Amina

last: Kurtovic-Kozaric

first: Sebija

last: Izetbegovic

first: Justine

last: Schaefer

first: Peter

last: Hufnagl

last: Zoufaly

first: Tamara

last: Seitz

first: Manuela

last: Födinger

first: Franz

last: Allerberger

first: Luisa

last: Cochella

first: Ulrich

last: Elling


title: Unique and distinct identities and functions of leaf phloem cells revealed by single cell transcriptomics

first: Jiyun

last: Kim


title: Schistosoma mansoni infection metabolically reprograms the myeloid lineage in a mouse model of metabolic disease

status: Public on Dec 21 2020

city: Salt Lake City

first: Keke

middle: Celeste

last: Fairfax

state: UT

address: 15 N Medical Drive East

department: Pathology

institute: University of Utah

summary:
We studied the effects of helminth infection and cytokine activation in the metabolic signatures of bone marrow derived macrophages using an approach that integrated transcriptomics, metabolomics, and lipidomics in a metabolic disease prone mouse model. We demonstrate that bone marrow derived macrophages (BMDM) from S. mansoni infected male ApoE-/- mice have dramatically increased mitochondrial respiration compared to those from uninfected mice. This change is associated with increased glucose and palmitate shuttling into TCA cycle intermediates, increased accumulation of free fatty acids, and decreased accumulation of cellular cholesterol esters, tri and diglycerides. Systemic injection of IL-4 complexes is unable to recapitulate either reductions in systemic glucose AUC or the re-programing of BMDM mitochondrial respiration seen in infected males. Finally, the metabolic reprogramming of male myeloid cells is transferrable via bone marrow transplantation to an uninfected host, indicating maintenance of reprogramming in the absence of sustained antigen exposure.
Conclusions: Our findings identify a transferable and long-lasting reprograming of the metabolic signature of macrophages by helminth infection that is sufficient to improve systemic glucose metabolism thus providing a mechanistic insight into the factors regulating the beneficial roles of infection in metabolic disease

overall_design: RNA-seq of bone marrow derived macrophages from uninfected, S. mansoni infected or IL-4c treated male mice.

first: Diana

last: Cortes-Selva


title: IL-6-induced gene expression in HUVEC

status: Public on Dec 22 2020

city: Albany

first: Alejandro

middle: Pablo

last: Adam

address: 43 New Scotland Ave

department: Molecular and Cellular Physiology

institute: Albany Medical College

summary: Cells were treated for thirty minutes with ruxolitinib or DMSO as vehicle control prior to exposure for three hours with 400 ng/ml IL-6 and 200 ng/ml sIL6Ra.

overall_design: Three independent replicates per group, DMSO, DMSO+IL-6, or Rux+IL-6


title: Profiling of RNA Pol II occupancy in adult Drosophila terminal tracheal cell using TaDa (Targeted DamID) in context of homeostasis or damaged intestine

city: London

first: Tony

middle: David

last: Southall

address: South Kensington Campus

department: Life Sciences

institute: Imperial College London

summary: Cell-type specific transcriptional profiling is key to understanding cell fate specification, function and adaptation. This is particularly advantageous for studying specific cell types from complex tissues. In this study, we have used ‘TaDa’ (Targeted DamID), a technique that enables profiling of rare cell populations or cells difficult to isolate by conventional methods. Furthermore, TaDa profiling occurs in vivo and isn’t subject to artefacts arising from disruption of the tissues and cell sorting. Here, we profile the genome-wide binding of RNA polymerase II (Pol II) in terminal tracheal cells (TTCs) that are tightly associated with intestinal tissue from adult Drosophila. We compare terminal tracheal transcriptome from control to regenerative intestine in adult fly.  Our data reveal new tracheal intrinsic mechanisms that are essential, in this gut-trachea communication, for regulating intestinal stem cell proliferative activity in context of damage. Our study represents the first analysis of terminal tracheal cell transcriptional profiling in context of homeostasis and regenerative adult intestine and provide new insight into the regulatory programs that underlie the complex interactions between gut-neighbourhood.

overall_design: Animals were raised and aged at 18 degrees and shifted to 29 degrees 7 days after eclosion. 24 hours after temperature shift, tissues were collected and frozen. Of to note, during the last 16 hrs at 29°C, flies were fed a Sucrose or Sucrose + Pe solution.Then, Genomic DNA was isolated, RNAseA treated and DpnI digested. Adaptors were ligated to DpnI digested DNA followed by DpnII digestion PCR amplification, sonication and removal of adaptors. Libraries were generated using the NEBNext® Ultra™ II DNA Library Prep Kit for Illumina. NextSeq™ 500 platform was used. We analysed 8 samples in total. 2 biological replicates were performed for adult terminal tracheal cells  in control condition (Suc) and in test condition (Pe).

first: Jessica

last: Perochon

first: Yachuan

last: Yu

first: Gabriel

middle: N

last: Aughey

middle: D

first: Julia

last: Cordero


title: Developmental programs in neuroblastoma [scRNA-seq IMR575-shMYCN]

status: Public on Dec 18 2020

city: Heidelberg

first: Frank

last: Westermann

address: Im Neuenheimer Feld 280

institute: Hopp Children's Cancer Center (KiTZ) and German Cancer Research Center (DKFZ)

summary: Neuroblastoma is a pediatric tumor of the developing sympathetic nervous system. We investigate developmental origins of neuroblastoma, the role of oncogenic MYCN in blocking normal differentiation and evaluate therapeutic interventions to overcome differentiation blocks. Here, we provide single cell expression profiles of IMR5/75-shMYCN cells upon knockdown of MYCN and control.

overall_design: single-cell RNA-seq in cell line IMR5/75-shMYCN after knockdown of MYCN and control