title: Hypoxia-inducible factor 1 signaling drives placental aging and can elicit inflammatory changes in uterine myocytes

status: Public on Mar 29 2022

city: Boston

first: Erin

last: Ciampa

address: 99 Brookline Avenue, RN-345

institute: Beth Israel Deaconess Medical Center

summary: Placental aging has been proposed to promote labor onset, but specific mechanisms remain elusive. An unbiased transcriptomic analysis of healthy mouse placenta revealed that hypoxia-inducible factor 1 (HIF-1) stabilization is a hallmark of advanced gestational timepoints, accompanied by mitochondrial dysfunction and cellular senescence. We validated these gestational age-associated changes through similar findings in human placenta. In parallel in primary mouse trophoblasts and human choriocarcinoma JAR cells, we modeled HIF-1 induction using prolyl hydroxylase inhibitors cobalt chloride (CoCl2) and dimethyloxalylglycine (DMOG), and demonstrated that mitochondrial dysfunction and cellular senescence occur secondary to HIF-1 stabilization. Whole transcriptome analysis revealed that HIF-1 stabilization in JAR cells recapitulated the dysregulation of several pathways observed in aged placenta. Further, conditioned media from cultured trophoblasts following HIF-1 induction is sufficient to induce a contractile phenotype in immortalized uterine myocytes, suggesting a mechanism by which the aging placenta may help drive the transition from uterine quiescence to contractility at the onset of labor.

overall_design: RNA was isolated from JAR choriocarcinoma cells following six days of culture with 100µM CoCl2 versus control conditions (six replicates each) for expression profiling by high-throughput sequencing

first: Samir

last: Parikh


title: Transcriptional Effects of Melatonin of the Gut Commensal Bacterium Klebsiella aerogenes

status: Public on Mar 23 2022

city: Lexington

first: Kinga

middle: B.

last: Graniczkowska

state: KY

address: 675 Rose St

department: Biology

country: USA

institute: University of Kentucky

type: Expression profiling by high throughput sequencing

summary: In this study, we implemented RNA sequencing to identify melatonin sensitive transcripts during culture maturation. This work demonstrates that majority of melatonin sensitive genes are growth stage specific. Melatonin caused differential gene expression of 81 transcripts during the exponential growth and 30 during early stationary phase. This indole molecule affects genes related to the biofilm formation, fimbria biogenesis, transcriptional regulators, carbohydrate transport and metabolism, phosphotransferase system (PTS), stress response, metal ion binding and transport. It is likely that differential expression of biofilm and fimbria related genes is responsible for differences in macrocolony area. Additionally, melatonin potentially helps Klebsiella aerogenes in host colonization.

overall_design: K. aerogenes mRNA profiles of exponential cells grown with 0nM or 1nM melatonin and early stationary cells incubated with 0nM or 1nM melatonin

middle: B

first: Vincent

middle: M

last: Cassone


title: Pathogen-specific innate immune response patterns are distinctly affected by genetic diversity

status: Public on Mar 03 2022

city: Jena

first: Sascha

last: Schäuble

address: Beutenbergstraße 11a

country: Germany

institute: Leibniz Institute for Natural Product Research and Infection Biology

summary: Innate immune responses vary by pathogen and host genetics. We generated transcriptomes of monocytes from 215 individuals, with and without stimulation (3h or 6h) by fungal, Gram-negative or Gram-positive bacterial pathogens. Monocytes showed a conserved response to bacterial pathogens and a distinct antifungal response. Mapping expression quantitative trait loci (eQTLs) identified 745 response eQTLs (reQTLs) and corresponding genes showing pathogen-specific effects. Compared to all differentially expressed genes, reQTL-regulated genes were more frequently upregulated, indicating cell-activating gene regulation. ReQTL-regulated gene products are essential in NOD-like, C-type lectin, Toll-like and complement receptor-signaling pathways. ReQTLs functionally characterize risk variants identified through genome-wide association studies for autoimmunity, inflammatory or infectious diseases and cancer. Thus, in addition to the transcriptional response of monocytes, their genetic regulation differs for bacterial and fungal pathogens. ReQTLs help explain interindividual variation in immune response to infection and provide candidate genes for variants associated with a range of diseases.

overall_design: 3’-mRNA-sequencing of human monocytes from 215 healthy male blood donors after stimulation wit Aspergillus fumigatus, Neisseria meningitidis, Staphylococcus aureus or left unstimulated for 3h and 6h.

first: Antje

last: Häder

last: Schaeuble

first: Benedikt

middle: C

last: Buerfent

first: Jan

last: Gehlen

first: Vitalia

last: Schüller

first: Timo

last: Hess

first: Thomas

last: Wolf

first: Julia

last: Schröder

first: Michael

last: Weber

first: Kerstin

last: Hünniger

first: Jürgen

last: Löffler

first: Slavena

last: Vylkova

first: Gianni

last: Panagiotou

first: Johannes

last: Schumacher

first: Oliver

last: Kurzai


title: Single cell RNA sequencing from stroma in the E16 salivary gland

status: Public on Mar 01 2022

city: Albany

first: Nicholas

last: Moskwa

state: New York

address: 1400 Washington Avenue

institute: University at Albany

summary:
Purpose: Use scRNA Seq to find B10stromal subpopulations and define how these subpopulations contribute to salivary gland proacinar differentiation.
Method: scRNA Seq on stromal enriched cells from E16 salivary glands. Model closely related cells using PCA and UMAP regressions. Find genes that broadly and specifically define cell subpopulations.
Results: The epithelium and stromal fibroblasts have multiple subpopulations. Stromal cells can be subdivided by their expression of Pdgfra, Pdgfrb, Thy1, Wnt2, and Acta2.
Conclusions: Pdgfra expressing stroma specifically use BMP7 to promote proacinar differentiation.

overall_design: Transcriptome analysis of stromal cell subpopulations

first: Deirdre

middle: A

last: Nelson

first: Paolo

last: Forni

first: Melinda

last: Larsen


title: mRNA and miRNA expression profiles of murine macrophages (cell line: RAW264.7)

city: Halle (Saale)

last: Schumann

address: Franzosenweg 1a

institute: University Medicine Halle (Saale)

type: Non-coding RNA profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Spatial transcriptomic maps of whole mouse embryos

status: Public on Feb 28 2022

city: Cambridge

first: Luyi

last: Tian

state: MA

address: 415 main st Cambridge

institute: Broad institute

summary: Precise spatiotemporal orchestration of gene expression is required for proper embryonic development. The application of high throughput single-cell technologies have provided comprehensive transcriptomic definitions of cell states within the embryo, but our knowledge of their spatial localization remains elusive. To explore early mouse organogenesis, we used Slide-seq to generate high-resolution maps of whole E8.5 and E9.5 mouse embryos. We developed sc3D, a tool for creating a three-dimensional (3D) 'digital embryo,' which allowed us to quantitatively decipher regionalized gene expression across multiple tissues. Our transcriptomic atlas facilitated us to characterize gene expression patterns along the anteroposterior and dorsoventral axes, with a particular emphasis on neural tube development. We nominated and functionally characterized Prdm8, a histone methyltransferase, as a neural tube patterning gene. Furthermore, we were able to determine the transcriptional identity of ectopic neural tubes in a classical Tbx6 mutant, which provided us with additional insights into neural tube patterning. Taken together, we combined computational and experimental tools to generate a framework that enables systematic spatiotemporal dissection of complex embryonic structures via high-throughput profiling of molecular phenotypes, thereby paving the way for the investigation of congenital and developmental abnormalities.

overall_design: Slide-seq v2 on whole mouse embryos E8.5 and E9.5 stage

first: Abhishek

last: Sampath Kumar

first: Alexander

last: Meissner

first: Fei

last: Chen


title: mRNA expression profiles (transcriptome) of murine macrophages (cell line: RAW264.7)

summary: We report the transcriptome of murine macrophages (cell line: RAW264.7) after supplementation with polyunsaturated fatty acids (PUFA) and stimulation with LPS. The fatty acids docosahexaenoic acid (DHA, C22:6n3) or arachidonic acid (AA, C20:4n6) were included in the culture medium in concentrations of 15 µmol/L using ethanol as a vehicle (0.2 % v/v final ethanol concentration). Cells were cultured in the enriched media totaling 72 h. Stimulation of cells was performed in the last 24 h of fatty acid supplementation by addition of LPS (1 µg/mL; from E. coli serotype 0111:B4).

overall_design: mRNA profiles of murine macrophages (cell line: RAW264.7) supplemented with unsaturated fatty acids and/or exposed to an inflammatory milieu were generated by deep sequencing, in triplicate, using Illumina HiSeq2500.

first: Claudia

last: Roessler


title: Single-cell sequencing reveals PDFGRα+ stromal cell subpopulations that promote proacinar differentiation in embryonic salivary gland organoids


title: miRNA expression profiles of murine macrophages (cell line: RAW264.7)

first: Julia

summary: We report the miRNA profile of murine macrophages (cell line: RAW264.7) after supplementation with polyunsaturated fatty acids (PUFA) and stimulation with LTA. The fatty acids docosahexaenoic acid (DHA, C22:6n3) or arachidonic acid (AA, C20:4n6) were included in the culture medium in concentrations of 15 µmol/L using ethanol as a vehicle (0.2 % v/v final ethanol concentration). Cells were cultured in the enriched media totaling 72 h. Stimulation of cells was performed in the last 24 h of fatty acid supplementation by addition of LTA (0.5 µg/mL; from Staphylococcus aureus).

overall_design: miRNA profiles of murine macrophages (cell line: RAW264.7) supplemented with unsaturated fatty acids and/or exposed to an inflammatory milieu were generated by deep sequencing, in triplicate, using Illumina sequencing.


title: mRNA expression analysis of the hippocampus in a vervet monkey model of fetal alcohol spectrum disorder

status: Public on Feb 23 2022

city: Montreal

first: Roberta

last: Palmour

state: Quebec

address: 1033 Pine West

department: Psychiatry

country: Canada

institute: McGill

summary:
Alcohol preferring vervet dams were permitted to ingest alcohol 4 days/week during the second half of gestation (e90-e165) and paired with sucrose matched controls. Cases and controls were sacrificed with subsequent hippocampal extraction at 5 months and 2 years. RNA was extracted according to the manufacturer's protocol and hybridized to the Affymetrix Rhesus Genechip microarray.
We sought to identify pathways and genes involved in the development of fetal alcohol spectrum disorder in a non-human primate in order to develop an understanding of how this disorder may develop in humans.

overall_design: 2x2 ANOVA, main effect=alcohol, main effect=age, main effect=interaction. Six replicates/group

first: Rob

middle: F

last: Gillis


title: H3K27me3 conditions chemotolerance in triple-negative breast cancer [WES]

status: Public on Feb 16 2022

city: Paris

first: Céline

last: Vallot

address: 26 Rue D'Ulm

country: France

institute: Institut Curie

summary: Triple-negative breast cancer is associated with the worst prognosis and the highest risk of recurrence among all breast cancer subtypes1. Residual disease, formed by cancer cells persistent to chemotherapy, remains the major clinical challenge towards full cure2,3. There is now consensus that non-genetic processes contribute to chemoresistance in various tumor types, notably through the initial emergence of a reversible chemotolerant state4–6. Understanding non-genetic tumor evolution stands now as a prerequisite for the design of relevant combinatorial approaches to delay recurrence. Here we show that the repressive histone mark H3K27me3 is a determinant of cell fate under chemotherapy exposure, monitoring epigenomes, transcriptomes and lineage with single-cell resolution. We identify a reservoir of persister basal cells with EMT markers and activated TGF-? pathway leading to multiple chemoresistance phenotypes. We demonstrate that, in unchallenged cells, H3K27 methylation is a lock to the expression program of persister cells. Promoters are primed with both H3K4me3 and H3K27me3, and removing H3K27me3 is sufficient for their transcriptional activation. Leveraging lineage barcoding, we show that depleting H3K27me3 alters tumor cell fate under chemotherapy insult - a wider variety of tumor cells tolerate chemotherapy. Our results highlight how chromatin landscapes shape the potential of unchallenged cancer cells to respond to therapeutic stress and pave the way for combinatorial therapy with modulators of chromatin

overall_design: whole exome sequencing data for MDA-MB-468 cells treated with 5-FU or DMSO

first: Marsolier

last: Justine

first: Prompsy

last: Pacôme

first: Durand

last: Adeline

first: Vallot

last: Céline


title: H3K27me3 conditions chemotolerance  in triple-negative breast cancer [CUT&TAG]

status: Public on Feb 15 2022

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Triple-negative breast cancer is associated with the worst prognosis and the highest risk of recurrence among all breast cancer subtypes1. Residual disease, formed by cancer cells persistent to chemotherapy, remains the major clinical challenge towards full cure2,3. There is now consensus that non-genetic processes contribute to chemoresistance in various tumor types, notably through the initial emergence of a reversible chemotolerant state4–6. Understanding non-genetic tumor evolution stands now as a prerequisite for the design of relevant combinatorial approaches to delay recurrence. Here we show that the repressive histone mark H3K27me3 is a determinant of cell fate under chemotherapy exposure, monitoring epigenomes, transcriptomes and lineage with single-cell resolution. We identify a reservoir of persister basal cells with EMT markers and activated TGF-β pathway leading to multiple chemoresistance phenotypes. We demonstrate that, in unchallenged cells, H3K27 methylation is a lock to the expression program of persister cells. Promoters are primed with both H3K4me3 and H3K27me3, and removing H3K27me3 is sufficient for their transcriptional activation. Leveraging lineage barcoding, we show that depleting H3K27me3 alters tumor cell fate under chemotherapy insult - a wider variety of tumor cells tolerate chemotherapy. Our results highlight how chromatin landscapes shape the potential of unchallenged cancer cells to respond to therapeutic stress and pave the way for combinatorial therapy with modulators of chromatin.

overall_design:
Single-cell ChIP-seq, bulk ChIP-seq and Chromatin Indexing of MDA-MB-468 Triple Negative Breast Cancer (TNBC) cell line in responset to 5FU treatment. Single-cell ChIP-seq of PDX Triple Negative Breast Cancer (TNBC) samples untreated.

>>>Submitter states that raw data are unavailable due to patient privacy concerns<<<

first: Justine

last: Marsolier

first: Pacôme

last: Prompsy

first: Adeline

last: Durand


title: Time series transcriptome of Venturia inaequalis (apple scab) infecting Malus domestica (apple)

status: Public on Mar 14 2022

city: palmerston north

first: Carl

last: Mesarich

state: Manawatu-Wanganui

address: Tennent Drive

country: New Zealand

institute: Massey University

summary: V. inaequalis causes apple scab disease, the most economically important disease of apples. In this study, we generated a comprehensive RNA-seq transcriptome of V. inaequalis during host colonization of apple, with six in planta time points (12hpi, 24hpi, 2dpi, 3dpi, 5dpi, 7dpi) and one in culture reference (fungus grown on cellophane membranes overlaying potato dextrose agar). Analysis of this transcriptome identified five in planta gene expression clusters or waves corresponding to three specific infection stages: early, mid and mid-late infection of subcuticular biotrophic host-colonization. In our analysis we focus on general fungal nutrition (plant cell wall degrading enzymes and transporters) as well as effectors (proteinaceous effectors and secondary metabolites). Early infection was characterized by the expression of genes that encode plant cell wall-degrading enzymes (PCWDEs) and proteins associated with oxidative stress responses. Mid-late infection was characterized by genes that encode PCWDEs and effector candidates (ECs).

sample_organism:
Malus domestica
Venturia inaequalis

platform_organism:
Malus domestica
Venturia inaequalis

overall_design: Deatached apple leaves were infected with V. inaequalis MNH120 (also known as ICMP 13258 and Vi1)  spores. Infected leaves were collected at 12hpi, 24hpi, 2dpi, 3dpi, 5dpi, 7dpi. As in culture reference, V. inaequalis spores were added to a cellophane membrane overlaying potato dextrose agar and mycelia grown on the cellophane membrane surface was collected at 7 dpi.  Four biological replicates per time point were collected for each sample.

first: Mercedes

last: Rocafort

first: Joanna

middle: K

last: Bowen

first: Berit

last: Hassing

first: Murray

middle: P

last: Cox

first: Brogan

last: McGreal

first: Silvia

last: de la Rosa

first: Kim

last: Plummer

first: Rosie

middle: E

last: Bradshaw

middle: H


title: A unique epigenomic landscape defines CD8+ tissue-resident memory T cells

status: Public on Apr 02 2022

city: Stanford

first: Julia

last: Belk

state: California

address: 450 Serra Mall

institute: Stanford University

summary: Memory T cells provide rapid and long-term protection against infection and tumors. The memory CD8+ T cell repertoire contains phenotypically and transcriptionally heterogeneous subsets with specialized functions and recirculation patterns. While these T cell populations have been well characterized in terms of differentiation potential and function, the epigenetic changes underlying memory T cell fate determination and tissue-residency remain largely unexplored. Here, we examined the single-cell chromatin landscape of CD8+ T cells over the course of acute viral infection. We reveal an early bifurcation of memory precursors displaying distinct chromatin accessibility and define epigenetic trajectories that lead to a circulating (TCIRC) or tissue-resident memory T (TRM) cell fate. While TRM cells displayed a conserved epigenetic signature across organs, we demonstrate that these cells exhibit tissue-specific signatures and identify transcription factors that regulate TRM cell populations in a site-specific manner. Moreover, we demonstrate that TRM cells and exhausted T (TEX) cells are distinct epigenetic lineages that are distinguishable early in their differentiation. Together, these findings show that TRM cell development is accompanied by dynamic alterations in chromatin accessibility that direct a unique transcriptional program resulting in a tissue-adapted and functionally distinct T cell state.

overall_design: scATAC-seq datasets of CD8+ T cells in LCMV and HSV infections

first: Frank

last: Buquicchio

first: Raissa

last: Fonseca

first: Ansuman

middle: T

last: Satpathy

first: Laura

last: Mackay


title: H3K27me3 conditions chemotolerance in triple-negative breast cancer  [ChIP-seq]

first: Céline

last: Vallot

overall_design: Two sequential ChIP-seq samples on untreated MDA-MB-468 cells of H3K27me3 followed byH3K4me3 or H3K27me3 followed by IgG negative control. The ‘primary’ ChIP containing part of the tube before the second immuno-precipation was also sequenced for each sample in order to eliminate background noise. BigWigs of the sequencing ChIPs compared to their respective ‘primary’ ChIP are also present.  8 bulk ChIP-seq MDA-MB-468 cells against H3K27me3 mark treated or not with 5-FU (‘persister’ or ‘DMSO’).   5 demultiplexed chromatin indexing samples from the same pool agaisnt H3K4me3 mark, treated or not with 5-FU.

first: Justine

last: Marsolier


title: H3K27me3 conditions chemotolerance in triple-negative breast cancer [scChIP-seq]

overall_design:
Single-cell ChIP-seq, bulk ChIP-seq and Chromatin Indexing of MDA-MB-468 Triple Negative Breast Cancer (TNBC) cell line in responset to 5FU treatment. Single-cell ChIP-seq of PDX Triple Negative Breast Cancer (TNBC) samples untreated.
>>> Raw data not provided due to patient privacy concerns: GSM5008865-GSM5008866. <<<

first: Pacôme

last: Prompsy

first: Adeline

last: Durand


title: miRNA expression analysis of the hippocampus in a vervet monkey model of fetal alcohol spectrum disorder

status: Public on Jan 24 2022

first: Roberta

last: Palmour

summary:
Alcohol preferring vervet dams were permitted to ingest alcohol 4 days/week during the second half of gestation (e90-e165) and paired with sucrose matched controls. Cases and controls were sacrificed with subsequent hippocampal extraction at 5 months and 2 years. RNA was extracted according to the manufacturer's protocol and hybridized to the Affymetrix Rhesus Genechip microarray.
We sought to identify whether global downregulation in mRNA dataset was related to miRNA expression in a non-human primate model of FASD in order to develop an understanding of how this disorder may develop in humans.

first: Rob

last: Gillis


title: Human native bone marrow CD200 positive mesenchymal stromal cells exhibit characteristics of cells forming the hematopoietic stem cell niche

status: Public on Mar 08 2022

city: TOULOUSE

first: Frederic

last: Deschaseaux

state: HAUTE-GARONNE

address: 4 BIS AVENUE HUBERT CURIEN, BATIMENT INCERE

department: Research

institute: EFS-Occitanie, Inserm U1031

summary: Bone marrow (BM) mesenchymal stem/stromal cells are non-hematopoietic (CD45-), non-endothelial (CD31-) multipotential cells capable to differentiate into osteoblastes, chondrocytes and adipocytes. In addition, different subpopulations of MSCs and some of their derivatives (early osteoblastic lineage cells) were shown to form HSC-niche. This makes a complex picture of the relationship between MSCs and HSCs. Despite growing data in mice model, few describe the human counterpart. The BM CD200+ and CD271+ fractions were previously shown to be enriched in native MSCs in human. Herein, we found heterogeneity in expression of CD200 within CD45-/CD31-/CD271+ human BM fraction. We thus selected CD200+ and CD200- cells from CD45-/CD31-/CD271+ BM samples and we analyzed their transcriptome. The differential display of gene expression between these two types of BM fractions will give new insights in the identification of native human MSCs.

overall_design: Several human BM samples  (n=6) were performed in order to specifically select CD271positive non-hematopoietic (CD45negative)/non-endothelial (CD31negative) cells expressing CD200 molecule and compared to those which were negative for CD200. This was perfomed through the use of flow cytometer. Then, the whole mRNA transcriptome of CD45neg/CD31neg/CD271pos/CD200pos was determined. Included patients were named in the protocol as (13_14) ; (17_18) ; (21_22) ; (23_24) ; (25_26 ); (27_28).

first: Nicolas

last: Espagnolle

first: Loïc

last: Fiévet

first: Sophie

last: Dupuis

first: Jean-Christophe

last: Pagès


title: Transcriptome profiling of local Kashmiri Vs commercial poultry for disease resistance against salmonellosis

status: Public on Feb 01 2022

city: Gandarbal

first: Basharat

middle: Ahmad

last: Bhat

state: Kashmir

address: Shuhama

department: Animal Biotechnology

country: India

institute: Sher-e-Kashmir University of Agricultural Sciences and Technology

summary: Salmonella being one of the major infectious diseases in poultry causes considerable economical losses in terms of mortality and morbidity especially in countries which lack effective vaccination programs. Salmonellosis is considered to be most important zoonotic disease which causes considerable foodborne illness that leads to enormous economic loses. To minimize such losses, enhancing disease resistance to different pathogens seems to be a promising strategy. The indigenous chicken, evolved through thousands of years of natural selection, are well adapted to the local climatic conditions with better resistance to diseases. In the present study we investigated liver and spleen transcriptome profile of indigenous (Kashmir faverolla) breed and commercial broiler poultry at day 5 post-inoculation with Salmonella typhimurium using RNA sequencing. The DEGs and pathways identified shall provide potential targets to enhance disease resistance in poultry through successful breeding programmes.

overall_design: Two tissues (liver and spleen) from two chicken breeds i.e. Kashmir faverolla and commercial broiler were taken following infection with Salmonella typhimurium. The samples were taken in replicates with respective controls aswell.

first: Syed

last: Andrabi

first: Mashooq

last: Dar


title: Microarray analysis of Replicative senescence and TNF-α induced senescence in Human umbilical vein endothelial cells (HUVECs)

status: Public on Jan 27 2022

city: Redmond

first: Renuka

last: Kandhaya Pillai

state: WA

department: aging

institute: university of washington

summary: Cellular senescence is a dynamic tumor suppression mechanism that limits the proliferation of impaired cells, by executing a stable cell cycle arrest. Understanding the molecular pathways and regulatory circuits that are involved in the process of senescence is presently incomplete. In this study, we determined the changes in gene expression during the establishment of replicative senescence, by comparing the expression profiles of young and senescent human umbilical vein endothelial cells (HUVECs). Exploration of array data using ingenuity pathway analysis showed that genes involved in cell cycle regulation, cellular assembly and organization, DNA replication, recombination and repair were significantly down regulated during senescence.

overall_design:
Human umbilical vein endothelial cells (HUVECs) were cultured continously until cells exhibit senescent morphology or reached proliferative arrest (Replicative senescence) or cells were untreated or treated TNFα (5ng/ml) continously for 26 days or (Passage 2 -Passage 8/ Passage 3- Passage9)//until cells exhibit senescent morphology. Gene expression of young  cells were compared to corresponding old passage or replicative senescence cell or with cells underwent senescence with inflammatory cytokine TNF-α
Some samples are missing CEL files due to storage failure.

last: Kadhaya-Pillai

first: Francesc

last: Miro-Mur

first: Simo

last: Schwartz Jr


title: Aging-related olfactory loss is associated with olfactory stem cell transcriptional alterations in humans

status: Public on Jan 21 2022

city: Durham

first: Bradley

last: Goldstein

state: NC

address: 203 Research Dr.

department: Department of Head and Neck Surgery & Communication Sciences

institute: Duke University School of Medicine

summary: Single cell analysis of older, hyposmic adult and normosmic adult olfactory epithelium yields evidence for inflammation-associated changes in the OE stem cells of presbyosmic patients

overall_design: Single cell 3' RNAseq of olfactory epithelium from 6 adult human patients (3 normosmic subjects, based on psychophysical olfactory assessment, with SIT scores 34 – 37; 3 presbyosmic subjects, SIT scores 11 - 29 and age  >65 years) using the 10X Genomics Chromium platform and sequenced on Illumina Nextseq 500.

first: Allison

last: Oliva


title: Antimalarial genetic screens of Plasmodium falciparum show peculiarities between the DHA and BTZ responses

status: Public on Jan 31 2022

city: TAMPA

first: Camilla

middle: Valente

last: Pires

address: 3720 Spectrum Blvd, 404

institute: University of South Florida

summary: RNAseq data profiling antimalarial-sensitive P. falciparum piggyBac mutants with and without exposure to low dose of DHA and BTZ.

overall_design: Each sample contains paired-end fastq data for two complete bioreps (rep1 and rep2) of the two parasite lines (NF54 wild-type control; antimalarial-sensitive mutant referred to in sample-name as PB104) collected after 3-cycles-growth with or without exposure to dihydroartemisin-DHA or Bortezomib-BTZ . Each sample was run on Illumina Nextseq

middle: V

first: Jenna

last: Oberstaller

first: Min

last: Zhang

first: Chengqi

last: Wang

first: John

last: Adams


title: mRNA expression profiles of murine macrophages (cell line: RAW264.7)

first: Julia

last: Schumann

summary: We report the transcriptome profile of murine macrophages (cell line: RAW264.7) after supplementation with polyunsaturated fatty acids (PUFA) and stimulation with LTA. The fatty acids docosahexaenoic acid (DHA, C22:6n3) or arachidonic acid (AA, C20:4n6) were included in the culture medium in concentrations of 15 µmol/L using ethanol as a vehicle (0.2 % v/v final ethanol concentration). Cells were cultured in the enriched media totaling 72 h. Stimulation of cells was performed in the last 24 h of fatty acid supplementation by addition of LTA (0.5 µg/mL; from Staphylococcus aureus).

overall_design: mRNA profiles of murine macrophages (cell line: RAW264.7) supplemented with unsaturated fatty acids and/or exposed to an inflammatory milieu were generated by deep sequencing, in triplicate, using Illumina sequencing.

first: Claudia

last: Roessler


title: H3K27me3 conditions chemotolerance in triple-negative breast cancer [scRNA-seq]

first: Céline

last: Vallot

overall_design:
Single-cell RNA-seq of MDA-MB-468 Triple Negative Breast Cancer (TNBC) cell line in response to 5FU treatment in or without addition of GSKJ4 or UNC. Single-cell RNA-seq of HBCx95 Patient Derived Xenographt (PDX) of  Triple Negative Breast Cancer (TNBC) in response to 5FU treatment (Capecitabine).

>>> Raw data not provided due to patient privacy concerns: GSM5017696-GSM5017700 and GSM5662564-GSM5662567. <<<

first: Justine

last: Marsolier

first: Pacôme

last: Prompsy

first: Adeline

last: Durand


title: Determination of the WWOX gene function in modulating cellular pathways activated by AP-2α and AP-2γ transcription factors in bladder cancer

status: Public on Jan 17 2022

city: Lodz

first: Damian

last: Kołat

address: Zeligowskiego St. 7/9

department: Department of Molecular Carcinogenesis

country: Poland

institute: Medical University of Lodz

summary: The aim of the current study was to investigate how various levels of WWOX, AP-2α and AP-2γ affect signaling pathways in bladder cancer cell lines. Global transcriptome analysis using CAGE-seq was conducted.

overall_design: The study was based on three bladder cancer cell lines i.e. RT-112, HT-1376 and CAL-29 for which overexpression of genes encoding WWOX, AP-2α and AP-2γ was induced by lentiviral transduction. Investigated variants included: Control (treated with lentrivirus blank controls); native WWOX with AP-2α overexpression; native WWOX with AP-2γ overexpression; WWOX overexpression with native AP-2α/γ; WWOX and AP-2α overexpression; WWOX and AP-2γ overexpression.

first: Żaneta

last: Kałuzińska-Kołat

first: Elżbieta

last: Płuciennik

first: Andrzej

last: Bednarek


title: Genome-wide DNA methylation profiles of hepatocellular carcinoma

city: Shinjuku-ku

first: Yae

last: Kanai

state: Tokyo

address: 35 shinanomachi

department: Pathology

country: Japan

institute: Keio University School of Medicine

type: Methylation profiling by genome tiling array

summary: Genome-wide DNA methylation profiling was performed in samples of cancerous tissue obtained from patients with hepatocellular carcinomas using the Illumina Infinium HumanMethylation450 Beadchip.

overall_design: Genomic DNA was extracted form fresh-frozen tissue specimens obtained from partial hepatectomy materials of 22 patients, who had provided written informed consent, and was subjected to bisulfite conversion followed by Infinium assay.

first: Eri

last: Arai

first: Junko

last: Kuramoto


title: Single-nuclei isoform RNA sequencing reveals combination patterns of transcript elements across human brain cell types

status: Public on Jan 16 2022

city: New York

first: Anoushka

last: Joglekar

state: NY

address: 413 E 69th St

department: Dept. of Neurogenetics

institute: Weill Cornell Medicine

summary: Single-nuclei RNA-Seq is widely employed to investigate cell types, especially of human brain and frozen samples. In contrast to single-cell approaches, many single-nuclei reads are purely intronic. Here, using microfluidics, PCR-based artifact removal, target enrichment, and long-read sequencing, we developed single-nuclei isoform RNA-sequencing (‘SnISOr-Seq’), and applied it to human adult frontal cortex. SnISOr-Seq dramatically increased the fraction of informative reads. We found that exons associated with autism exhibit coordinated and highly cell-type specific inclusion. We discovered two distinct combination patterns: first, those distinguishing neural cell types, enriched in TSS-exon, exon-polyA-site, and non-adjacent exon pairs. Second, those with multiple configurations within one cell type, enriched in adjacent exon pairs. Furthermore, adjacent exons are predominantly mutually-associated, while distant exons are frequently mutually-exclusive. Finally, we observed that human-specific exons are almost as tightly coordinated as conserved exons. SnISOr-Seq enables single-nuclei long-read isoform analysis in human brain, and in any frozen or hard-to-dissociate sample.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: 10X single-nuclear RNA sequencing done on two replicates of human Frontal Cortex samples. PacBio done on the same cDNA, after linear PCR. 10X single-cell RNA sequencing followed by Oxford Nanopore long read sequencing as a control sample. FACS sorted nuclei obtained from Human prefrontal cortex samples for bulk RNA sequencing on Illumina, also used as control.

first: Simon

last: Hardwick

first: Wen

last: Hu

first: Hagen

last: Tilgner


title: H3K27me3 conditions chemotolerance  in triple-negative breast cancer [ChIP-reChIP]

overall_design:
Two sequential ChIP-seq samples on untreated MDA-MB-468 cells of H3K27me3 followed byH3K4me3 or H3K27me3 followed by IgG negative control. The ‘primary’ ChIP containing part of the tube before the second immuno-precipation was also sequenced for each sample in order to eliminate background noise. BigWigs of the sequencing ChIPs compared to their respective ‘primary’ ChIP are also present.  8 bulk ChIP-seq MDA-MB-468 cells against H3K27me3 mark treated or not with 5-FU (‘persister’ or ‘DMSO’).   5 demultiplexed chromatin indexing samples from the same pool agaisnt H3K4me3 mark, treated or not with 5-FU.

>>>Raw data not available for patient-derived PDX samples due to privacy concerns<<<


title: H3K27me3 conditions chemotolerance in triple-negative breast cancer

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

overall_design: Refer to individual Series


title: Fibrotic signatures in Crohn's disease patients

status: Public on Jan 02 2022

city: Milano

first: Luca

last: Massimino

state: MI

address: Via Olgettina, 58

department: Gastroenterology

country: Italy

institute: Ospedale San Raffaele

summary: This study investigates the presence of specific fibrosis-associated gene expression signatures in Crohn's disease patient biopsies.

overall_design: n=40 CD biopsies: n=19 fibrotic biopsies, n=21 not fibrotic biopsies

first: Federica

last: Ungaro

first: Luigi

last: Lamparelli

first: Silvio

last: Danese


title: circZFR promote lung carcinogenesis and oxidative phosphorylation by modulating alternative splicing

status: Public on Jan 08 2022

city: Nanjing

first: Keith

last: Ma

address: No.44 Baiziting Road

country: China

institute: Nanjing Medical University

summary: Our study suggested that circZFR was a potential oncogene in lung adenocarcinoma. To investigate the function of circZFR, we performed high-thoughput RNA sequencing (RNA-Seq) assays after the silence of circZFR in A549 cell lines.

overall_design: In human lung adenocarcinoma A549 cells, we downregulated the expression of circZFR utilizing small interference RNA (siRNA) and used scrumble as negative control. Then we used RNA-Seq to reveal the change of mRNA profiles after the silence of circZFR.

first: Z

first: H

last: Chen

first: Y

last: Xu

first: S

last: Wang

first: C

last: Han

first: W

last: Xia

first: R

last: Yin

first: L


title: Regulation of chromatin accessibility in early zebrafish embryos by Pou5f3 and Sox19b transcription factors.

status: Public on Jan 07 2022

city: Freiburg

first: Daria

last: Onichtchouk

address: Hauptstrasse 1

institute: University of Freiburg

summary: Pou5f3 and Sox19b transcription factors promote chromatin accessibility and activate zygotic transcription in zebrafish embryos. It is poorly understood how two transcription factors act together on chromatin. To answer this question, we performed  Omni-ATAC-seq on the zebrafish embryos, single and double mutants by Pou5f3 and Sox19b, as well as the wild-type, at two blastula developmental stages, oblong and dome. We report, that chromatin accessibility on 48% of all putative enhancers depends on Pou5f3 and Sox19b.  Out of them, accessibility on 33% enhancers is reduced in the double mutant and of 15% is increased.  Enhancers with reduced and increased chromatin accessibility differ in GC content and  transcription factors binding motif frequency, and are linked to early and late developmental regulatory genes, respectively. Our results indicate that Pou5f3 and Sox19b  not only activate early zygotic genes, but also prevent premature activation of  late developmental enhancers.

overall_design: Omni-ATAC-seq on whole embryos

first: Aileen

last: Riesle


title: A comprehensive series of temporal transcription factors in the fly visual system

status: Public on Jan 01 2022

first: NIKOLAOS

last: KONSTANTINIDES

address: 15 rue Helene Brion

institute: Institut Jacques Monod

summary: The brain consists of hundreds or thousands of different neuronal types that are generated through multiple divisions of neuronal stem cells. These stem cells have the capacity to generate different neuronal types at different stages of their development. In Drosophila,  this temporal patterning is driven by the successive expression of temporal transcription factors (tTFs). While a number of tTFs are known in different animals and across various parts of the nervous system, these have been mostly identified by informed guesses and antibody availability. We used single-cell mRNA sequencing to identify the likely complete series of tTFs that specify most Drosophila medulla neurons in the optic lobe. We tested the genetic interactions among these tTFs. While we verify the general principle that tTFs regulate the progression of the series by activating the next tTFs in the series and repressing the previous ones, we also identify more complex regulations. Two of the tTFs, Eyeless and Dichaete, act as hubs integrating the input of several upstream tTFs before allowing the series to progress and in turn regulating the expression of several tTFs. Moreover, we show that tTFs not only specify neuronal identity but also control subsequent neuronal differentiation. We find that terminal differentiation genes, such as neurotransmitter-related genes, are present as transcripts, but not as proteins, in immature larval neurons days before they are being used in functioning neurons; we show that these mechanisms are conserved in humans. Our results offer a comprehensive description of a temporal series of tTFs in a neuronal system, offering mechanistic insights into the regulation of the progression of the series and the regulation of neuronal diversity. This represents a proof-of-principle for the use of single-cell mRNA sequencing for the comparison of temporal patterning across phyla that can lead to an understanding of how the human brain develops and how it has evolved.

overall_design: 49,893 single-cell transcriptomes from 40 L3 optic lobes were analyzed using 10XGenomics single-cell sequencing in 10 different experiments

first: Nikos

last: Konstantinides

first: Claude

last: Desplan


title: Mesenchymal-epithelial crosstalk shapes intestinal regionalisation via Wnt and Shh signalling

status: Public on Dec 11 2021

city: Copenhagen N

first: Marianne

middle: Terndrup

last: Pedersen

address: Ole Maaloes Vej 5

department: University of Copenhagen

country: Denmark

institute: BRIC


title: Advanced genomics identifies growth effectors for proteotoxic ER stress recovery in Arabidopsis thaliana

status: Public on Dec 20 2021

city: East Lansing

first: Dae Kwan

last: Ko

address: 612 Wilson Rd.  Plant Biology RM 122

department: Plant Research Laboratories

institute: Michigan State University

summary: Adverse environmental and pathophysiological situations can overwhelm the biosynthetic capacity of the endoplasmic reticulum (ER), igniting a potentially lethal condition known as ER stress. ER stress results in growth reduction and the activation of a conserved cytoprotective signaling cascade, the unfolded protein response (UPR), to mitigate ER stress. As ER stress subsides, growth is resumed; however, despite a pivotal role of the UPR in growth restoration, the underlying mechanisms are yet unknown. To discover these, we undertook a genomics approach and mined the gene reprogramming roles of the two critical and conserved UPR modulators, basic leucine zipper28 (bZIP28) and bZIP60 in ER stress resolution. Through a coexpression-based network modeling and experimental validation, we identified key responsive genes acting downstream of the UPR bZIP-transcription factors (bZIP-TF), and demonstrated their roles in organ growth during recovery from ER stress. Our analyses have also set up a novel pipeline for functional gene discovery in ER stress resolution with broad applicability across multicellular eukaryotes.

overall_design: For RNA-seq analysis, a total of 54 samples, which consists of 3 genotypes under 2 treatments at 3 time-points in 3 biological replicates, were processed. For ChIP-seq analysis, a total of 48 samples, which consists of 2 proteins with 2 treatment at 3 time-points in 2 biological replicates, were processed.

first: Federeica

last: Brandizzi


title: Ret loss-of-function decreases neural crest progenitor proliferation and restricts developmental fate potential during enteric nervous system development

status: Public on Dec 30 2021

city: Baltimore

first: Loyal

last: Goff

state: MD

address: 733 N. Broadway Avenue

department: Institute of Genetic Medicine

institute: Johns Hopkins University

summary: The receptor tyrosine kinase gene RET plays a critical role in the fate specification of enteric neural crest cells (ENCCs) during enteric nervous system (ENS) development. Pathogenic RET loss of function (LoF) alleles are associated with Hirschsprung disease (HSCR), which is marked by aganglionosis of the gastrointestinal (GI) tract. ENCCs invade the developing GI tract, proliferate, migrate caudally, and differentiate into all of the major ENS cell types. Although the major phenotypic consequences, and the underlying transcriptional changes from Ret LoF in the developing ENS have been described, its cell type and state-specific effects are unknown. Consequently, we performed single-cell RNA sequencing (scRNA-seq) on an enriched population of ENCCs isolated from the developing GI tract of Ret null heterozygous and homozygous mouse embryos at embryonic day (E)12.5 and E14.5. We demonstrate four significant findings: (1) Ret-expressing ENCCs are a heterogeneous population composed of ENS progenitors as well as glial and neuronal committed cells; (2) neurons committed to a predominantly inhibitory motor neuron developmental trajectory are not produced under Ret LoF, leaving behind a mostly excitatory motor neuron developmental program; (3) HSCR-associated and Ret gene regulatory network genes exhibit distinct expression patterns across Ret-expressing ENCC cells with their expression impacted by Ret LoF; and (4) Ret deficiency leads to precocious differentiation and reduction in the number of proliferating ENS precursors. Our results support a model in which Ret contributes to multiple distinct cellular phenotypes and that Ret LoF contributes to GI aganglionosis in multiple independent ways.

overall_design: Modified Smart-Seq2 single-cell RNA-Seq of 1,003 cells from the developing mouse gut (E12.5 & E14.5) in both male and female wild type and Ret homozygous null animals. N=2 replicate animals  for each condition. Varying number of cells passing QC for each condition.

first: Elizabeth

last: Vincent

first: Sumantra

last: Chatterjee

first: Gabrielle

last: Cannon

first: Dallas

last: Auer

first: Holly

last: Ross

first: Aravinda

last: Chakravarti


title: Mesenchymal-epithelial crosstalk shapes intestinal regionalisation via Wnt and Shh signalling [RNA-seq]

summary:
In the small intestine (SI), regionalisation enables sequential processing of food and nutrient absorption. To characterise the basis for region-specific mesenchymal-epithelial crosstalks during late small intestinal morphogenesis, we combined transcriptional profiling of epithelial and mesenchymal cell populations isolated from different intestinal regions with ChIP-seq, 3D imaging and functional ex vivo and organoid studies.
We find that a mesenchymal PDGFRA-high population located in close proximity to the developing epithelium is enriched for genes involved in signalling and support the epithelium in a region-specific manner via the establishment of a proximal to distal gradient of epithelial Wnt activity. Furthermore, we provide evidence that Wnt signalling in the distal SI directly regulates epithelial expression of Sonic Hedgehog (SHH), which in turn acts on mesenchymal cells driving villi formation. Our results therefore uncover a mechanistic link between Wnt and Hedgehog signalling across different cellular compartments central for anterior-posterior regionalisation and correct organ formation.

overall_design:
RNA-seq of epithelial - EpCAM+ - and mesenchymal - PDGFRA-HIGH (PDGFRA-high/CD29-med), PDGFRA-MED (PDGFRA-med/CD29-med) and CD29-HIGH (CD29-high/PDGFRA-med) - cell populations isolated from proximal, mid and distal parts of the mouse intestine at embryonic day 16.5 (E16.5).
RNA-seq of epithelial cells isolated from different regions of the mouse E16.5 intestine upon treatment with PORCN inhibitor from E12.5 to E16.5.
RNA-seq data of intestinal epithelial cells isolated from proximal and distal parts of the mouse intestine at embryonic day 13.5 (E13.5).

first: Martti

last: Maimets

first: Malte

last: Thodberg

first: Kim

last: Jensen


title: ChIP-seq for TCF7L2/TCF4 in E16.5 intestinal epithelial cells

summary: As part of our comprehensive characterization of intestinal development, we performed ChIP-seq for TCF7L2/TCF4 in mouse E16.5 intestinal epithelial cells. We identified more than 6000 regions bound by TCF7L2/TCF4 including a binding site in an enhancer driving Shh expression. Combined with transcriptional and functional analyses, our data reveal a novel cross-talk between WNT and Hedgehog signaling pathways.


title: FOXC1 and FOXC2 promote endothelial-derived R-spondin 3 and CXCL12 signals in intestinal regeneration after ischemia-reperfusion injury

status: Public on Dec 13 2021

city: Chicago

first: Matthew

middle: J.

last: Schipma

state: IL

address: 750 N. Lake Shore Drive

department: Biochemistry and Molecular Genetics

institute: Northwestern University

summary: Intestinal ischemia induces mucosal damage while simultaneously activating intestinal stem cells (ISCs), which subsequently regenerate the damaged intestinal epithelium. However, whether angiocrine factors secreted from vascular endothelial cells (ECs) - blood and lymphatic ECs (BECs and LECs, respectively) – regulate ISC-mediated regeneration have yet to be elucidated. Here, we identify FOXC1 and FOXC2 as essential regulators of angiocrine signaling in regeneration of the small intestine after ischemia-reperfusion (I/R) injury. EC- and LEC-specific deletions of Foxc1, Foxc2, or both in mice augment I/R-induced intestinal damage by causing defects in vascular regrowth, expression of the chemokine CXCL12 and the Wnt activator R-spondin 3 in BECs and LECs, respectively, and activation of Wnt signaling in ISCs. Treatment with CXCL12 and R-spondin 3 rescues the I/R-induced intestinal damage in EC- and LEC-Foxc mutant mice, respectively. This study provides evidence that FOXC1 and FOXC2 are required for intestinal regeneration by stimulating angiocrine CXCL12 and Wnt signaling.

overall_design: The 10X Genomics Chromium platform was used to obtain single cell transcriptomes from the distal jejuna of two control mice and two endothelial cell-specific Foxc1 and Foxc2 compound knockout mice 18.5 hours after small intestinal ischemia and reperfusion injury.

first: Can

last: Tan

first: Pieter

middle: R

last: Norden

first: Ting

last: Liu

first: Naoto

last: Ujiie

first: Xiaocai

last: Yan

first: Kazushi

last: Aoto

first: Sagrario

last: Ortega

first: Isabelle

middle: G

last: De Plaen

first: Tsutomu

last: Kume


title: Transcriptional Responses of Human Intestinal Organoids to Interferon Types I, II, and III

status: Public on Dec 21 2021

city: Portland

first: Timothy

middle: J

last: Nice

state: OR

address: 3181 SW Sam Jackson Park Rd

department: Molecular Microbiology and Immunology

institute: Oregon Health & Science University

summary: RNAseq of intestinal epithelial cell (IEC) organoids derived from biopsy of ileum or colon from healthy subjects and treated with type I interferon (IFN beta), type II interferon (IFN gamma), or type III interferon (IFN lambda 2).

overall_design: Treatments were added to IEC organoids in culture media. RNA was isolated four hours after treatments. Samples were collected in biological triplicate (IEC organoid).

first: David

last: Constant


title: Competing endogenous RNA analysis reveals the regulatory potency of CKAP5 in HPV+ HNSCC based on high throughput sequencing technology and clinical validation [miRNA]

status: Public on Dec 08 2021

city: binzhou

first: Yue

last: Wang

state: shandong

address: NO.661 Huanghe Er Road, Binzhou City

institute: binzhou medical university

summary: Purpose: The current study used high-throughput sequencing technology and related basic experimental verification assays to evaluate new pathogenic mechanisms of Human papilloma virus HPV+ Head and neck squamous cell carcinoma (HNSCC) as well as to determine the potential therapeutic targets.  Materials and methods: In this study 3 pairs of tissues were collected from patient with HPV+ and HPV- HNSCC for high-throughput sequencing analysis. After mRNA sequencing and analysis, multiple bioinformatics methods, real-time quantitative reverse transcription-quantitative polymerase chain reaction (qRT-PCR) and immunehistochemical verification assays were carried out to evaluate the potential therapeutic targets of HNSCC (CKAP5). The CKAP5 was then used to further predict the circular RNA (circRNA), long non-coding RNA (lncRNA), and microRNA (miRNA). Sequencing analysis was also performed to further evaluate the potential carcinogenic pathway. Human papilloma virus detection was carried out through Enzyme-Linked Immune Sorbent Assay (ELISA) and the RT-PCR.  Results: Results of high-throughput sequencing analysis, related databases, and verification of qRT-PCR at the cell and tissue level, revealed that the expression level of CKAP5 in HPV+HNSCC was significantly higher than that in HPV-HNSCC. Further, a competitive endogenous RNA (ceRNA) network was also constructed through the analysis of Miranda, multiMiR, lncBase prediction, and sequencing technology. The constructed ceRNA consisted of 1 mRNA, 2 miRNAs, and 1 lncRNA, and 6 CircRNAs. This was verified by RNA22, whereby the relationship between miR-155-5p and CKAP5 was found to be important whereas the hsa_circ_00058495 was a key circRNA according to the binding site scores.   Conclusion: In conclusion it was evident that Hsa_circ_00058495/miR-155-5p CKAP5 may be an important pathway which is involved in the occurrence and development of HPV+ HNSCC.

first: Xiangrui

last: Ma

first: Shuhan

first: Legang

last: Sun

first: Wenlong


title: Effect of benzo(a)pyrene on the replication of vesicular stomatitis virus and transcriptomic analysis.

status: Public on Dec 26 2021

city: Nangjing

first: Jing

last: Wu

address: Medical School, Nanjing University, 22# Hankou Road, Nanjing, Jiangsu Province

institute: Nanjing University

summary: Benzo(a)pyrene (Bap), a key component of cigarette smoke (CS), is a pollutant and widely present in our daily life. The roles of Bap on viral replication have been amply discussed and controversial. In our present study, we investigated the effect and mechanism of Bap on the replication of vesicular stomatitis virus (VSV) and respiratory syncytial virus (RSV) in vitro. HeLa cells were pre-exposed to Bap at 10 μM for 48 h and then infected with VSV (MOI=1) for 24 h. RNA sequencing analysis was conducted to identify Bap-dysregulated genes and qPCR analysis was used to identify the result. Chronic exposed to Bap significantly inhibited the replication of VSV and RSV in vitro and in vivo.

overall_design: HeLa cells were pre-exposed to 10 μM Bap for 48 h and then infected with VSV (MOI=1) for 24 h with continuous exposure to Bap.

first: Deyan

last: Chen

first: Zhiwei


title: Competing endogenous RNA analysis reveals the regulatory potency of CKAP5 in HPV+ HNSCC based on high throughput sequencing technology and clinical validation [mRNA]

overall_design: The current study used high-throughput sequencing technology and related basic experimental verification assays to evaluate new pathogenic mechanisms of Human papilloma virus HPV+ Head and neck squamous cell carcinoma (HNSCC) as well as to determine the potential therapeutic targets.


title: Competing endogenous RNA analysis reveals the regulatory potency of CKAP5 in HPV+ HNSCC based on high throughput sequencing technology and clinical validation


title: RNA-seq of C18-4 cells,F0/F1 mouse testis from different lncRNA5251 modification groups

status: Public on Dec 01 2021

city: Qingdao

first: Yong

last: Zhao

state: Shandong

address: 700 Changcheng Road

department: College of Life Sciences

institute: Qingdao Agricultural University


title: RNA-seq of F1 mouse testis samples from differentlncRNA5251 modification groups

summary: The goat of this project is to explore lncRNA5251  regulation spermatogenesis. We tried to search the mechanism oflncRNA5251 regulation spermatogenesis. RNA-seq of F1 mouse testis samples from different groups: 5NC,  lncRNA5251 overexpression, 3NC, lncRNA5251 knockdown.  The testes of mouse were transfected with virus with 5NC, lncRNA5251 overexpression, 3NC, lncRNA5251 knocdown letivirus.

overall_design: RNA-seq of F1 mouse testes samples from different groups: 5NC,  lncRNA5251 overexpression, 3NC,  lncRNA5251 knockdown. The F1 mouse testes  were transfected with virus with overexpression or  inhibition of  lncRNA5251.

first: Xiao

last: Han


title: RNA-seq of F0 mouse testis samples from differentlncRNA5251 modification groups

summary: The goat of this project is to explore lncRNA5251  regulation spermatogenesis. We tried to search the mechanism oflncRNA5251 regulation spermatogenesis. RNA-seq of F0 mouse testis samples from different groups: 5NC,  lncRNA5251 overexpression, 3NC, lncRNA5251 knockdown.  The testes of mouse were transfected with virus with 5NC, lncRNA5251 overexpression, 3NC, lncRNA5251 knocdown letivirus.

overall_design: RNA-seq of F0 mouse testes samples from different groups: 5NC,  lncRNA5251 overexpression, 3NC,  lncRNA5251 knockdown. The F0 mouse testes  were transfected with virus with overexpression or  inhibition of  lncRNA5251.


title: mRNA expression profiles (transcriptome) of TIME and RAW264.7

city: Halle (Saale)

first: Julia

last: Schumann

address: Franzosenweg 1a

institute: University Medicine Halle (Saale)


title: RNA-seq of C18-4  cells samples from differentlncRNA5251 modification groups

summary: The goat of this project is to explore lncRNA5251  regulation spermatogenesis. We tried to search the mechanism of lncRNA5251 regulation spermatogenesis. RNA-seq of C18-4  cells samples from different groups: 5NC,  lncRNA5251 overexpression, 3NC, lncRNA5251 knockdown.  The cell were transfected with virus with 5NC, lncRNA5251 overexpression, 3NC, lncRNA5251 knocdown letivirus.

overall_design: RNA-seq of C18-4  cells samples from different groups: 5NC,  lncRNA5251 overexpression, 3NC,  lncRNA5251 knockdown. The C18-4 cells  were transfected with virus with overexpression or  inhibition of  lncRNA5251.

first: Cong

last: Zhang


title: mRNA expression profiles (transcriptome) of human endothelial cells (cell line: TIME)

summary: We report the transcriptome of human endothelial cells (cell line: TIME) after supplementation with polyunsaturated fatty acids (PUFA) and/or stimulation with pro-inflammatory cytokines. The fatty acids docosahexaenoic acid (DHA, C22:6n3) or arachidonic acid (AA, C20:4n6) were included in the culture medium in concentrations of 15 µmol/L using ethanol as a vehicle (0.2 % v/v final ethanol concentration). Cells were cultured in the enriched media totaling 144 h. Stimulation of cells was performed in the last 24 h of fatty acid supplementation by addition of the cytokines IL-1β, TNF-α, and IFN-γ each in a concentration of 5 ng/ml.

overall_design: mRNA profiles of human endothelial cells (cell line: TIME) supplemented with unsaturated fatty acids and exposed to an inflammatory milieu were generated by deep sequencing, in triplicate, using Illumina HiSeq2500.

first: Claudia

last: Roessler


title: Library comparison between TruSeq, SMARTer and TeloPrime

status: Public on Dec 03 2021

city: Uchinada

first: Hiroki

last: Ura

state: Ishikawa

address: 1-1 Daigaku

institute: Kanazawa Medical University Hospital

summary: We comparison the performance of three different library for transcriptome analysis.

overall_design: mRNA profile of 3 different library samples were generated from 2 different patient's peripheral blood mononuclear cells (PBMCs).

first: Yo

last: Niida


title: Enhancing CDK4/6 inhibitor therapy for medulloblastoma using nanoparticle delivery and scRNA-seq-guided combination with sapanisertib

status: Public on Nov 16 2021

city: Atanta

first: Tim

last: Gershon

state: GA

address: Emory University School of Medicine

department: Pediatrics

institute: Emory University

summary: We report scRNA-seq data showing the effect of palbociclib treatment on medulloblastomas that form in Smo-mutant mice. We generate tumor-bearing mice by breeding hGFAP-Cre and SmoM2 mouse lines to prodce tumor-prone progeny heterozygous for both transgenes (G-Smo mice). We compare tumors from untreated G-Smo mice to  tumors from G-Smo ice treated with nanoparticle--delievered palbociclib, using Drop-seq-based scRNA-seq.

overall_design: scRNA-seq comparison of tumors in replicate drug-treated mice and untreated controls previously uploaded in accession number GSE150579.

first: Taylor

last: Dismuke

first: Chaemin

last: Lim

first: Daniel

last: Malawsky

first: Timothy

first: Marina

last: Sokosky


title: Maternal diet disrupts the placenta-brain axis in a sex-specific manner

status: Public on Nov 18 2021

city: Durham

first: Benjamin

last: Devlin

state: North Carolina

address: 210 Research Drive

department: Psychology and Neuroscience

institute: Duke University

summary:
Purpose: Next generation bulk RNA sequencing of a large group (37 individuals) of matched tissues (fetal brain and fetal placenta) from human fetuses collected via elective termination at 72-82 days post conception (d.p.c.), a timeframe that closely matches the embryonic developmental window used in our mouse studies (14.5-16.5)
Methods: Human placenta (maternal decidua separated from fetal placenta) and fetal brain tissues were obtained from the NIH-supported Laboratory of Developmental Biology at the University of Washington between the years 1999 and 2010 and used under a protocol approved by the Duke University Institutional Review Board (Pro00014066). Tissue specimens were stored at -80°C until required for RNA or protein extraction. Prior to collection, informed consent was obtained from all individuals undergoing the elective termination. RNA from human tissue was prepared for sequencing using an Illumina TrueSeq RNA Exome kit and sequenced on an Illumina NovaSeq 6000 configured for a S2 flow cell at 50bp PE.
Results: PCR for the Y chromosome (SRY) identified 17 male and 20 female fetal tissue sets, with the average age of 78.2 d.p.c. for both sexes. No maternal data were available, so we assessed decidual triglyceride accumulation to use as a proxy for maternal weight, given that women with overweight/obesity exhibit triglyceride accumulation in the placenta. Triglyceride levels trended higher in pregnancies with female fetuses, but there was no significant difference between triglyceride accumulation in decidua associated with male or female pregnancies. Pearson's Correlation of gene expression with maternal triglyceride accumulation from bulk RNA-seq from 16 matched male and 19 matched female brain and placenta samples revealed a strong dimorphic trend in gene expression. In male pregnancies, differentially correlated genes were predominantly over-expressed with increasing maternal weight (i.e. gene expression increased as maternal triglycerides increased); the opposite effect was seen in female pregnancies. In the male brain, only 45 genes significantly correlated with maternal triglyceride accumulation (either positive or negative), whereas 781 genes were significantly correlated in females.

overall_design: bulk RNA-seq from 16 matched male and 19 matched female human fetal brain and placenta samples (72-82 days post conception). Triglyceride accumulation in maternal placenta (decidua) was used as a proxy for maternal dietary fat consumption, given no available patient characteristics. Correlations were performed to understand which genes change in response to increasing maternal fat intake.

first: Alexis

middle: M

last: Ceasrine

first: Susan

last: Murphy

first: Staci

middle: D

last: Bilbo


title: Transcriptomic Analysis of Wound Healing and Skin Rejuvenation Following Ablative Fractional Laser Treatment of Human Skin

status: Public on Nov 07 2021

city: Mason

first: Joe

last: Sherrill

state: Ohio

address: 8700 Mason-Montgomery Rd

institute: Procter and Gamble

summary: Ablative fractional laser treatment is considered the gold standard for skin rejuvenation. In order to understand how fractional laser works to rejuvenate skin, we performed microarray profiling on skin biopsies to identify temporal and dose-response changes in gene expression following fractional laser treatment.

overall_design: The backs of 14 women received ablative fractional laser (Fraxel) treatments and  4 mm punch biopsies were collected at baseline (day 0) and days 1, 3, 7, 14, 21 and 28 days after a single treatment (in addition to an untreated site).  In addition, in order to understand the effect that multiple fractional laser treatments have on skin rejuvenation, several sites received  either 1, 2, 3, or 4 treatments (with 28 days between treatments) and  4 mm punch biopsies were also collected from these sites.  RNA was extracted from the biopsies and gene expression was analyzed using Affymetrix U219 gene chips and gene expression was compared between untreated and treated sites.

first: Robert

last: Isfort

first: Charles

middle: C

last: Bascom


title: Small molecule RBI2 disrupts ribosome biogenesis through pre-rRNA depletion

status: Public on Nov 08 2021

city: Birmingham

first: David

middle: A

last: Schneider

state: Alabama

address: 705 20th Street South

institute: University of Alabama at Birmingham

summary: In all domains of life, the rate of protein synthesis is directly linked to the rates of cell growth and proliferation. Consequently, highly proliferative cancer cells are especially sensitive to perturbations in ribosome biogenesis. While ribosome synthesis and cancer have a well-established relationship, only recently has ribosome biogenesis drawn interest as a cancer therapeutic target. Here, we have exploited the relationship between ribosome biogenesis and cancer cell proliferation by using a potent ribosome biogenesis inhibitor: RBI2 (Ribosome Biogenesis Inhibitor 2) to perturb cancer cell growth and viability.  We demonstrate that RBI2 significantly decreases cell viability in malignant melanoma cells and breast cancer cell lines. Treatment with RBI2 dramatically and rapidly decreases ribosomal RNA (rRNA) synthesis, without affecting the occupancy of RNA polymerase I (Pol I) on the ribosomal DNA template. Next-generation RNA sequencing (RNA-seq) reveals that RBI2 and previously described ribosome biogenesis inhibitor CX-5461 induce distinct changes in the transcriptome. Investigation of the content of the pre-rRNAs through RT-qPCR reveals an increase in polyadenylation of cellular rRNA after treatment with RBI2, a known pathway by which rRNA degradation occurs. Northern blotting revealed that RBI2 does not appear to impair or alter rRNA processing.  Collectively, these data suggest that RBI2 inhibits rRNA synthesis distinctly from other previously described ribosome biogenesis inhibitors, potentially through a novel pathway that upregulates turnover of premature rRNAs.

overall_design: MDA-MB-231 cells treated with 5 µM of RBI2 or CX-5461 as a function of time (10 minutes, 30 minutes, and 120 minutes). Two replicates were included for each time point. Another two samples were not treated and served as untreated controls

first: Catherine

last: Scull

first: Yinfeng

first: Guy

last: Twa

first: Naiheng

last: Yang

middle: N

last: Hunter III

first: Corinne

last: Augelli-Szafran


title: TF ChIP-seq from middle frontal area 46 (ENCSR666JEF)

status: Public on Nov 04 2021

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

institute: ENCODE DCC

summary:
CTCF TF ChIP-seq on middle frontal area 46 tissue female adult (85 years) with Alzheimer's disease.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: TF ChIP-seq from middle frontal area 46 (ENCSR913SEI)

summary:
CTCF TF ChIP-seq on middle frontal area 46 tissue female adult (86 years) with Alzheimer's disease.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Histone ChIP-seq from middle frontal area 46 (ENCSR723RUM)

summary:
H3K27ac ChIP-seq on middle frontal area 46 tissue female adult (90 or above years) with Alzheimer's disease.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Histone ChIP-seq from middle frontal area 46 (ENCSR449AUD)

summary:
H3K27ac ChIP-seq on middle frontal area 46 tissue female adult (89 years) with Alzheimer's disease

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: TF ChIP-seq from middle frontal area 46 (ENCSR575WYM)

summary:
CTCF ChIP-seq on middle frontal area 46 tissue female adult (87 years)

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: TF ChIP-seq from middle frontal area 46 (ENCSR779YTI)

summary:
CTCF TF ChIP-seq on middle frontal area 46 tissue female adult (90 or above years).

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Histone ChIP-seq from middle frontal area 46 (ENCSR597RXN)

summary:
H3K27ac ChIP-seq on middle frontal area 46 tissue female adult (87 years)

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Histone ChIP-seq from middle frontal area 46 (ENCSR549ZDH)

summary:
H3K27ac ChIP-seq on middle frontal area 46 tissue female adult (88 years) with Alzheimer's disease.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: TF ChIP-seq from middle frontal area 46 (ENCSR610UDC)


title: TF ChIP-seq from middle frontal area 46 (ENCSR445NJB)

summary:
CTCF ChIP-seq on dorsolateral prefrontal cortex tissue female adult (78 years) originated from dorsolateral prefrontal cortex

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: scChIX-seq infers dynamic relationships between histone modifications in single cells

status: Public on Nov 30 2021

city: Utrecht

first: Jake

last: Yeung

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute

summary: Regulation of chromatin states involves the dynamic interplay between different histone modifications to control gene expression. Recent advances have enabled mapping of histone marks in single cells, but most methods are constrained to profile only one histone mark per cell. Here we present an integrated experimental and computational framework, scChIX-seq (single-cell chromatin immunocleavage and unmixing), to map multiple histone marks in single cells. scChIX-seq multiplexes two histone marks together in single cells, then computationally deconvolves the signal using training data from respective histone mark profiles. This framework learns the cell type-specific correlation structure between histone marks, and therefore does not require a priori assumptions of their genomic distributions. Using scChIX-seq, we demonstrate multimodal analysis of histone marks in single cells across a range of mark combinations: two repressive marks, two active marks, and an active plus a repressive mark. In mouse gastrulation, we find that cell type-specific regulation in active chromatin can be accompanied by stable heterochromatin landscapes that are shared across cell types. Applying scChIX-seq to two active marks during macrophage differentiation, we find H3K4me1 dynamics preceding H3K36me3. Modeling these dynamics enables integrated analysis of chromatin velocity during differentiation. Overall, scChIX-seq unlocks systematic interrogation of the interplay between histone modifications in single cells.

overall_design: single-cell ChIC-seq data on bone marrow, mouse gastrulation, and macrophage in vitro differentiation

first: Maria

last: Florescu

first: Peter

last: Zeller

first: Buys

last: de Barbanson

first: Max

last: Wellenstein

first: Alexander

last: van Oudenaarden


title: TF ChIP-seq from middle frontal area 46 (ENCSR676LDQ)

summary:
CTCF TF ChIP-seq on middle frontal area 46 tissue female adult (90 or above years) with Alzheimer's disease.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: TF ChIP-seq from middle frontal area 46 (ENCSR369RRE)

summary:
CTCF ChIP-seq on dorsolateral prefrontal cortex tissue female adult (74 years) originated from dorsolateral prefrontal cortex

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: TF ChIP-seq from middle frontal area 46 (ENCSR525VXD)

summary:
CTCF ChIP-seq on middle frontal area 46 tissue female adult (90 or above years)

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Histone ChIP-seq from middle frontal area 46 (ENCSR860TEJ)

summary:
H3K27ac ChIP-seq on middle frontal area 46 tissue female adult (90 or above years)

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: TF ChIP-seq from middle frontal area 46 (ENCSR957UPE)

summary:
CTCF ChIP-seq on middle frontal area 46 tissue female adult (89 years) with Alzheimer's disease

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: TF ChIP-seq from middle frontal area 46 (ENCSR094PSL)

summary:
CTCF ChIP-seq on dorsolateral prefrontal cortex tissue female adult (88 years) originated from dorsolateral prefrontal cortex

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: TF ChIP-seq from middle frontal area 46 (ENCSR168KQC)

summary:
CTCF ChIP-seq on dorsolateral prefrontal cortex tissue female adult (84 years) originated from dorsolateral prefrontal cortex

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: TF ChIP-seq from middle frontal area 46 (ENCSR259PNW)

summary:
CTCF TF ChIP-seq on middle frontal area 46 tissue female adult (88 years) with Alzheimer's disease.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Histone ChIP-seq from middle frontal area 46 (ENCSR152MAZ)

summary:
H3K27ac ChIP-seq on middle frontal area 46 tissue female adult (86 years) with Alzheimer's disease.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Histone ChIP-seq from middle frontal area 46 (ENCSR004HIE)

summary:
H3K27ac ChIP-seq on middle frontal area 46 tissue female adult (90 or above years).

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: TF ChIP-seq from middle frontal area 46 (ENCSR332WTG)


title: Histone ChIP-seq from middle frontal area 46 (ENCSR520KVD)


title: TF ChIP-seq from middle frontal area 46 (ENCSR230RQK)


title: TF ChIP-seq from middle frontal area 46 (ENCSR092VKJ)

summary:
CTCF ChIP-seq on dorsolateral prefrontal cortex tissue female adult (90 or above years) originated from dorsolateral prefrontal cortex

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Histone ChIP-seq from middle frontal area 46 (ENCSR498NGT)

summary:
H3K27ac ChIP-seq on middle frontal area 46 tissue female adult (85 years) with Alzheimer's disease.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: TF ChIP-seq from middle frontal area 46 (ENCSR329KRE)

summary:
CTCF ChIP-seq on dorsolateral prefrontal cortex tissue female adult (89 years) originated from dorsolateral prefrontal cortex

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Histone ChIP-seq from middle frontal area 46 (ENCSR004YQD)

summary:
H3K27ac ChIP-seq on middle frontal area 46 tissue female adult (87 years)

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Specification of human immune cell epigenetic identity by combinations of transcription factors (MethylationEPIC)

status: Public on Nov 02 2021

first: Supriyo

last: De

state: Maryland

address: 251 Bayview Blvd

department: Laboratory of Genetics and Genomics

institute: NIA-IRP, NIH

summary: Lineage-specific methylation and transcriptomic patterns were identified in 6 primary immune cells from 24 healthy donors. We also look into the association of B cell-specific methylated sites with EBF1 ChIP-Seq binding patterns

overall_design: Human blood was fractionated into 11 subsets using a combination of magnetic beads and flow cytometry, and DNA isolated from 1 – 2 million cells. A total of 300 ng genomic DNA was treated with sodium bisulfite using Zymo EZ-96 DNA Methylation  Kit per the manufacturer's protocol, and  each sample  then hybridized to Illumina Infinium Human MethylationEPIC BeadChip arrays followed by processing and quantitation of methylation ( β ranging from 0-1) for each probe. Data from the Illumina Infinium MethylationEPIC array was analyzed in R using minfi package. noob-BMIQ normalization of the probes was performed after removing low quality probes (detection p values cutoff 0.01).

first: Mary

last: Kaileh

first: Roshni

last: Roy

first: Senthilkumar

last: Ramamoorthy

first: Sören

last: Boller

first: Rudolf

last: Grosschedl

first: Supriy

first: Luigi

last: Ferrucci

first: Ranjan

last: Sen


title: Histone ChIP-seq from middle frontal area 46 (ENCSR315UUP)

summary:
H3K27ac ChIP-seq on middle frontal area 46 tissue female adult (90 or above years) with Alzheimer's disease.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: TF ChIP-seq from middle frontal area 46 (ENCSR237BTA)

summary:
CTCF ChIP-seq on dorsolateral prefrontal cortex tissue female adult (81 years) originated from dorsolateral prefrontal cortex

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: USP29 coordinates MYC and HIF1α stabilization to promote tumor metabolism and progression

status: Public on Oct 11 2021

city: Wuhan

first: Rongfu

last: Tu

address: Donghu Road, No. 115, Wuchang District, Wuhan, Hubei Province, P.R. China

institute: Wuhan University

summary: Deleption of USP29 significantly inhibits aerobic glycolysis, glutamine catabolism and proliferation of cancer cells. To test the underlying mechanisms, RNA-seq was performed using USP29 or control depleted SK-N-BE2 and Ramos cells.

overall_design: Tumor cells were infected with control sgRNA or USP29 sgRNA, respectively.

first: Wenqian

last: Kang

first: Hudan

last: Liu

first: Guoliang

last: Qing


title: Initiation of organ maturation and fruit ripening in grapevine is controlled by the CARPO-NAC transcription factor [Syrah]

status: Public on Oct 07 2021

city: Verona

first: Sara

last: Zenoni

address: Strada Le Grazie 15

institute: Università degli Studi di Verona

summary: In this study we identified the NAC family member VviCARPO (Controlled Adjustment of Ripening and maturation of Plant Organs) as a key regulator of grapevine maturation. We explored CARPO binding landscapes through DAP-seq and overlapped its bound genes with transcriptomics datasets from stable and transient CARPO overexpressing grapevine plants to narrow a set of high-confidence targets. Among these, we identified key molecular ripening markers. Physiological, metabolic and promoter activation analyses showed that CARPO induces chlorophyll degradation and anthocyanin accumulation through the up regulation of VviSGR1 and VviMYBA1, respectively, with the latter being up-regulated by a VviCARPO-VviNAC03 regulatory complex. CARPO complemented the nor mutant phenotype in tomato, suggesting it may have acquired a dual role as an orchestrator of both ripening- and senescence-related processes. Our results evidenced that CARPO is a master regulator of the grapevine vegetative-to-mature phase organ transition and therefore an essential target for insuring fruit quality and environmental resilience.

overall_design: Transcriptomic changes caused by the VviCARPO overexpression were inspected by a microarray analysis performed on leaf RNA of selected transgenic lines and control plants. Three biological replicates of fully expanded leaves were collected.

first: Erica

last: D'Incà

first: Chiara

last: Foresti

first: Luis

last: Orduña

first: Alessandra

last: Amato

first: Elodie

last: Vandelle

first: Antonio

middle: S

last: Pajuelo

first: Alessandro

last: Botton

first: Stefano

last: Cazzaniga

first: Edoardo

last: Bertini

first: Mario

last: Pezzotti

first: James

last: Giovannoni

first: Julia

last: Vrebalov

first: Jose

last: Matus

first: Giovanni

middle: B

last: Tornielli


title: Initiation of organ maturation and fruit ripening in grapevine is controlled by the CARPO-NAC transcription factor

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

overall_design: Refer to individual Series


title: Transcriptomes of 8 radiosensitive and 8 radioresistant colorectal cancer (CRC) patients

city: Changzhou

first: You

last: Zhou

state: Jiangsu

address: Juqian Rd No.185

institute: The Third Affiliated Hospital of Soochow University

summary: Radiotherapy is essential to treat colorectal cancer (CRC) although the tolerance of which is of quite common occurrence in clinic. Long noncoding RNA (lncRNA) and circular RNA (circRNAs) have an important role in the radio-resistance of CRC through regulating targeted genes or proteins expression at either transcriptional or post-translational levels. In this study, we aimed to seek out novel lncRNAs and circRNAs involved in radio-resistance by RNA-seq analysis of 8 radiosensitive and 8 radioresistant CRC patients.

overall_design:
Total RNA from 8 radiosensitive and 8 radioresistant CRC patients was generated by deep sequencing, in triplicate, using Illumina HiSeq 4000.

Please note that the Series summary was updated and the *circRNA.txt files were added on May 11, 2022.

first: Yingjie

last: Shao

first: Wendong

last: Gu

first: Jingting

last: Jiang


title: Identification of m6A-mediated transcriptome changes in mouse liver after exposure to  HFD, PCB126 and Aroclor mixtures

status: Public on Sep 29 2021

city: Louisville

first: Eric

middle: Christian

last: Rouchka

state: Kentucky

address: 522 East Gray Street

institute: University of Louisville

summary: Exposure to polychlorinated biphenyls (PCBs) and high fat diet (HFD) results in nonalcoholic steatohepatitis (NASH) in mice by altering intracellular signaling and inhibiting epidermal growth factor receptor (EGFR) signaling. Post-transcriptional chemical modification (PTM) of RNA regulates biological processes. This study tested the hypothesis that PCB exposure alters the global RNA epitranscriptome in HFD-fed male mouse liver.  C57BL/6J male mice were fed a 42% milk fat diet (HFD) and exposed to Aroclor 1260 (20mg/kg), PCB 126 (20 µg/kg), both Aroclor 1260 and PCB 126, or vehicle control for 12 weeks.  RNA modifications altered by PCB exposure were analyzed in comparison to the readers, writers, and erasers of these marks in the RNA transcriptome.

overall_design: Male C57Bl/6J mice were fed a HFD (42% kCal from fat) and treated with Aroclor 1260, PCB 126, and the combination of Aroclor 1260 + PCB 126 for 12 weeks.  A total of four sample groups with five replicates each were sequenced (high fat diet alone; high fat diet with Aroclor 1260 treament; high fat diet with PCB 126 treatment; and high fat diet with Aroclor 1260 + PCB 126 treatment).

first: Carolyn

last: Klinge

first: Kellianne

last: Piell

first: Belinda

last: Petri

first: Liqing

last: He

first: Xiang

last: Zhang

first: Jianmin

last: Pan

first: Shesh

last: Rai

first: Kalina

last: Andreeva

first: Banrida

last: Wahlang

first: Matthew

last: Cave


title: Aspergillus fumigatus ZnfA, a novel zinc finger transcription factor involved in calcium metabolism and caspofungin tolerance

status: Public on Oct 04 2021

city: Ribeirao Preto

first: Gustavo

middle: Henrique

last: Goldman

state: Sao Paulo

address: Avenida do Cafe

country: Brazil

institute: Sao Paulo University

summary: Invasive Pulmonary Aspergillosis (IPA) is a life-threatening fungal infection especially in immunocompromised population. The low availability of antifungal drugs coupled with the emergence of antifungal resistance has become an important clinical concern. Caspofungin (CSP) is recommended as second-line therapy but resistance and tolerance mechanisms have been reported. However, how the fungal cell articulates the response to CSP is not completely understood. In this work we have characterized ZnfA, a new transcription factor (TF) identified in previous screening studies that is involved in calcium and CSP A. fumigatus response. This TF plays an important role in iron homeostasis and cell wall organization in response to high CSP concentrations as revealed by Chromatin Immunoprecipitation coupled to DNA sequencing (ChIP-seq) analysis. Furthermore, ZnfA acts collaboratively with the key TF CrzA in the response to calcium, cell wall and osmotic stresses. Thus, this study increases our knowledge about the link between calcium signaling and the CSP cellular response and exposes the complex connections among different pathways that govern stress sensing in A. fumigatus.

overall_design: RNApolll and ChIPseq analysis of 8 and 4 samples, respectively, two replicates for each condition

first: Clara

last: Valero

first: Ana

last: Colabardini

first: Patrícia

last: de Castro

first: Lilian

middle: P

last: Silva

first: Laure

last: Ries

first: Lakhansing

last: Pardeshi

first: Fang

last: Wang

first: Roberto

first: Celso

last: Martins

first: Cristina

last: Pereira

first: Michael

last: Bromley

first: Koon

middle: H

last: Wong


title: RNASeq analysis of endothelial cells isolated from B16F0 tumours treated with IgG/ 15C4.

status: Public on Sep 27 2021

city: London

first: Athina

last: Dritsoula

address: UCL Institute of Ophthalmology 11-43 Bat

country: United Kingdom

institute: University College London

summary: LRG1 is a novel proangiogenic and profibrotic molecule that is upregulated in pathologies characterised by abnormal angiogenesis such as AMD and cancer. Blocking LRG1 by genetic models or by our in-house developed function blocking antibody leads to vascular normalsation. In this study, we have treated B16F0 melanoma tumours with 15C4, our function blocking antibody, or with IgG as a control. The tumours were collected at day 17 and the endothelial cell population was isolated by FACS sorting the CD31 positive cells. RNA was isolated and used for the preparation of cDNA libraries. Expression profile of the endothelial cell population was assessed by Illumina sequencing. Differenital expression analysis was conducted using the DESeq2 package in R.

overall_design: Examination of the expression profile of the FACS-sorted endothelial population of the IgG-/15C4-treated B16F0 melanoma tumours.

first: John

last: Greenwood


title: Initiation of organ maturation and fruit ripening in grapevine is controlled by the CARPO-NAC transcription factor [Sultana]

first: Sara

last: Zenoni

overall_design: For transient transformation of Vitis vinifera cv. Sultana, the 35S:VviCARPO construct was transferred to Agrobacterium tumefaciens strain C58C1 by electroporation. As control, Agrobacterium was also transformed with an empty pK7WG2 containing a non-coding sequence. Seven in vitro six-week-old plants of grapevine cv. Sultana for overexpression and five for the control were immersed in each bacterial suspension and vacuum infiltrated (2 X 2 min at 90kPa). After agroinfiltration, plantlets were allowed to recover in vitro for seven days before collecting material for RNA extraction and transcriptomic analysis.

first: Erica

last: D'Incà

first: Chiara

last: Foresti

first: Luis

last: Orduña

first: Alessandra

last: Amato

first: Elodie

last: Vandelle

first: Antonio

last: Pajuelo

first: Alessandro

last: Botton

first: Stefano

last: Cazzaniga

first: Edoardo

last: Bertini

first: Mario

last: Pezzotti

first: James

last: Giovannoni

first: Julia

last: Vrebalov

first: Jose

middle: T

last: Matus

first: Giovanni

last: Tornielli


title: Dynamic CD4 T cell heterogeneity defines subset-specific suppression and PDL1-blockade driven functional restoration in chronic infection

status: Public on Sep 20 2021

city: Toronto

first: Ramanandan

last: Prabhakaran

state: Ontario

address: 610 University Avenue

institute: University Health Network-Princess Margaret Cancer Center


title: Adipose tissue immunology, inflammation and exosomes in regulating insulin sensitivity in people with obesity and nonalcoholic fatty liver disease

status: Public on Oct 01 2021

city: Izumo

first: Jun

last: Yoshino

state: Shimane

address: 89-1 Enya-cho

institute: Faculty of Medicine, Shimane University

summary:
Background and Aims: Insulin resistance is a key factor in the pathogenesis of NAFLD. We evaluated the importance of subcutaneous abdominal adipose tissue (SAAT) inflammation and both plasma and SAAT-derived exosomes in regulating insulin sensitivity in people with obesity and NAFLD.
Methods: Adipose tissue inflammation (macrophage and T cell content and gene expression of proinflammatory cytokines), liver and whole-body insulin sensitivity (assessed by a hyperinsulinemic-euglycemic clamp and glucose tracer infusion), and 24-hour serial plasma cytokine concentrations were evaluated in three groups stratified by adiposity, insulin sensitivity and intrahepatic triglyceride (IHTG) content: 1) metabolically-healthy lean (LEAN; n=14); 2) metabolically-healthy obese with normal IHTG content (OB-NL; n=28); and 3) metabolically-unhealthy obese with NAFLD (OB-NAFLD; n=28). The effect of plasma and SAAT-derived exosomes on insulin action (insulin-stimulated Akt phosphorylation) in human skeletal muscle myotubes was assessed in a subset of participants.
Results: Proinflammatory macrophages, proinflammatory CD4 and CD8 T cell populations, and gene expression of several cytokines in SAAT were greater in the OB-NAFLD than the OB-NL and LEAN groups. However, with the exception of PAI-1, which was greater in the OB-NAFLD than the LEAN and OB-NL groups, 24-hour plasma cytokine concentration areas-under-the-curve (AUC) were not different between groups. The percentage of proinflammatory macrophages and plasma PAI-1 concentration AUC were inversely correlated with both hepatic and whole-body insulin sensitivity. Compared with exosomes from OB-NL participants, plasma and SAAT-derived exosomes obtained from the OB-NAFLD group impaired insulin action in myotubes.
Conclusion: These results suggest SAAT-derived exosomes and PAI-1 are involved in the pathogenesis of systemic insulin resistance in people with obesity and NAFLD. ClinicalTrials.gov number: NCT02706262.

overall_design: We obtained subcutaneous adipose tissue samples from people who were metabolically-healthy lean (MHL), metabolically-healthy obese (MHO), and metabolically-unhealthy obese (MUO) n=66).

first: Anja

last: Fuchs

first: Gordon

middle: I

last: Smith

first: Bruce

middle: W

last: Patterson

first: Samuel

last: Klein

first: Dmitri

last: Samovski

first: Vincenza

last: Cifarelli

first: Sarah

last: Farabi

first: Shin-Wen

last: Chang

first: Terence

last: Myckatyn

first: Terri

last: Pietka


title: Dynamic CD4 T cell heterogeneity defines subset-specific suppression and PDL1-blockade driven functional restoration in chronic infection [scRNA-seq]

summary: Inhibiting PD1:PDL1 signaling has transformed therapeutic immune restoration. CD4 T cells are critical to sustain immunity in chronic infections and cancer, yet little is known about how PD1/L1 modulates CD4 T helper (Th) responses or the ability to restore CD4 Th-mediated immunity by inhibiting PD1/L1 signaling. We demonstrate that PD1/L1 specifically suppresses CD4 Th1 cell amplification, prevents CD4 Th1 cytokine production, and abolishes CD4 CTL killing capacity during chronic infection. Inhibiting PDL1 during chronic infection rapidly restored these functions, while simultaneously enhancing Th1-like Treg amplification and activation, indicating a system-wide CD4-Th1 recalibration. Paradoxically, PDL1-blockade decreased TCR signaling, while re-directing intrinsically-suppressive type I interferon networks towards dominant IFNγ-mediated responses. Mechanistically, PDL1-blockade specifically targeted defined populations with pre-established, but actively-suppressed proliferative potential, with limited impact on minimally-cycling TCF1+ Tfh, despite high PD1 expression. Thus, CD4 T cells require unique differentiation and functional states to be targets of PDL1-directed suppression and therapeutic restoration.

overall_design: Single cell RNA-seq of isotype vs anti-PDL1 treated virus-specific CD4 T cells

first: Brooks

last: David


title: Increased adipose tissue fibrogenesis, not impaired expandability, is associated with nonalcoholic fatty liver disease

summary:
BACKGROUND AND AIMS: It is proposed that impaired expansion of subcutaneous adipose tissue (SAT), caused in part by an increase in adipose tissue fibrosis, redirects fatty acids to the liver and other organs, leading to ectopic lipid accumulation and insulin resistance. We therefore evaluated whether a decrease in SAT expandability, assessed by measuring SAT lipogenesis (triglyceride production), and an increase in SAT fibrogenesis (collagen production) are associated with nonalcoholic fatty liver disease (NAFLD) and insulin resistance in people with obesity.
APPROACH AND RESULTS: In vivo SAT lipogenesis and fibrogenesis, the expression of SAT genes involved in extracellular matrix (ECM) formation, and insulin sensitivity were assessed in three groups stratified by adiposity, insulin sensitivity and intrahepatic triglyceride (IHTG) content: 1) healthy lean (Lean-NL; n=12); 2) obese with normal IHTG content and normal glucose tolerance (Ob-NL; n=25); and 3) obese with NAFLD and abnormal glucose metabolism (Ob-NAFLD; n=25). Abdominal SAT total triglyceride synthesis rates were greater in the Ob-NL (65.9±4.6 g/wk) and Ob-NAFLD (71.1±6.7 g/wk) than the Lean-NL group (16.2±2.8 g/wk), without a difference between the obese groups. Abdominal SAT collagen synthesis rate and the composite expression of collagen genes progressively increased from Lean-NL to Ob-NL to Ob-NAFLD and were greater in the Ob-NAFLD than the Ob-NL group (P<0.05). Collagen synthesis rate and the composite expression of collagen genes correlated with factors that regulate collagen production, including circulating insulin and fibrogenic factors in SAT (all P<0.001).
CONCLUSIONS: Adipose tissue lipogenesis and expandability are not impaired in people with obesity and NAFLD. However, SAT fibrogenesis and extracellular matrix remodeling are greater in people with obesity and NAFLD than in those with obesity and normal IHTG content.
ClinicalTrials.gov number: NCT02706262.

overall_design: In this study, we evaluated gene expression of proteins involved in regulating adipose tissue remodeling in subcutaneous adipose tissue obtained from 1) lean with normal IHTG content and glucose tolerance (Lean-NL, n=12); ii) obese with normal IHTG content and glucose tolerance (Ob-NL, n=21); and iii) obese with NAFLD and prediabetes (Ob-NAFLD, n=24).

first: Joseph

last: Beals

first: Mahalakshmi

last: Shankaran

first: Tyler

last: Field

first: George

last: Schweitzer

first: Marc

middle: K

last: Hellerstein


title: MARCO+ lymphatic endothelial cells sequester arthritogenic alphaviruses in the draining lymph node and limit viral dissemination

status: Public on Sep 10 2021

city: Aurora

first: Jay

middle: R.

last: Hesselberth

state: CO

department: Biochemistry and Molecular Gentetics

institute: University of Colorado School of Medicine

summary: While viremia in the vertebrate host is a critical determinant of arboviral reservoir competency, transmission efficiency, and disease severity, immune mechanisms that control arboviral viremia are poorly defined. Here, we identify critical roles for the scavenger receptor MARCO in controlling viremia during arthritogenic alphavirus infections in mice. Following subcutaneous inoculation, alphavirus particles drain via the lymph and are rapidly captured by MARCO+ lymphatic endothelial cells (LECs) in the draining lymph node (dLN), limiting viral spread to the bloodstream. Upon reaching the bloodstream, MARCO-expressing Kupffer cells in the liver remove circulating alphavirus particles, limiting viremia and further viral dissemination. MARCO-mediated accumulation of alphavirus particles in the lymph node and liver has important implications as viremia and viral tissue burdens are elevated in MARCO-/- mice and disease outcomes are more severe. These findings uncover a previously unrecognized pathogen scavenging role for LECs and improve our mechanistic understanding of viremia control during arboviral infections.

overall_design: Identification of cells harboring CHIKV RNA using single-cell RNA sequencing.

first: Kathryn

last: Carpentier

first: Ryan

last: Sheridan

first: Cormac

last: Lucas

middle: R

first: Thomas

middle: E

last: Morrison