title: RNA sequencing of T helper type 1 differentiated cultures in polyarticular juvenile idiopathic arthritis and healthy controls

status: Public on Oct 04 2021

city: Nashville

first: Anna

last: Patrick

state: TN

address: 2141 Blakemore Avenue

institute: Vanderbilt University Medical Center

summary: Biologic pathway differences in polyarticular JIA and healthy control Th1 culture cells were determined by RNA sequencing and pathway analysis. RNA from 3 JIA and 3 pediatric healthy control Th1 cultures were analyzed for differential gene expression using DESeq2.

overall_design: Examination of RNA sequencing in 3 JIA Th1 cultures and 3 healthy control Th1 cultures.

first: Thomas

last: Aune

first: Philip

middle: S

last: Crooke


title: WGBS of 169 ddm1-derived epiRILs

status: Public on Oct 07 2021

city: Freising

first: Frank

last: Johannes

state: Bavaria

address: Emil-Ramann str. 4

department: Department of Molecular Life Sciences

country: Germany

institute: Technical University of Munich

type: Methylation profiling by high throughput sequencing

summary: 169 ddm1-derived epigenetic recombinant inbred lines (epiRILs) were obtained from the Versailles Arabidopsis Stock center of INRA (http://publiclines.versailles.inra.fr/) and they were propagated in a fully automatic phenotyping facility for small plants at the Leibniz Institute of Plant Genetics and Crop Plant Research (IPK). Whole Genome Bisulphite Sequencing was performed at the Beijing Genome Institute.

overall_design: 169 ddm1-derived epiRILs

first: Ioanna

last: Kakoulidou

last: Altmann

first: Rhonda

middle: C

last: Meyer


title: Expression analysis of altered neutrophils from septic mice

status: Public on Oct 01 2021

city: London

first: Venizelos

last: Papayannopoulos

address: 1 Midland Road

country: United Kingdom

institute: The Francis Crick Institute

type: Expression profiling by high throughput sequencing

summary: Neutrophils are critical for effective anti-fungal immune responses. However, in fungal sepsis neutrophils undergo a phenotypical (Ly6G downregulation) and functional alteration (defective ROS production), impairing their anti-fungal capacity. Therefore we wish to characterize the neutrophils in septic mice transcriptionally to describe their role in driving sepsis. We included several control groups. Mice that lack T cells (TCRaKO mice) have increased resistance to the infection and their neutrophils appear unaltered. We identified G-CSF and DNA/histones to be responsible for affecting granulopoiesis, as rG-CSF and Clodronate liposomes combined expand Ly6Glow neutrohils in naive mice.

overall_design:
The spleens were gently meshed and filtered to obtain a single cell suspension. ACK treatment was performed to lyse erythrocytes. A neutrophil enrichment was performed using a commercially available kit (StemCell), to obtain a semi-pure neutrophil suspension. These cells were stained with fluorescently labeled antibodies and DAPI, and live neutrophils were sorted as CD3/CD19-, CD11b+ and either high or low expression of Ly6G. 20.000-100.000 cells were sorted per condition. Sorted neutrophils were washed and resuspended in 300ul RLT. RNA extraction was performed using the Qiagen RNeasy mini-kit, and the Nugen cDNA synthesis kit was used for library prep.

GCSFCLODRONATE treatment: Mice were injected intravenously with 1mg of clodronate liposomes (Liposoma) and the subsequent day intraperitoneally with 2.5ug recombinant G-CSF (rG-CSF; BioLegend). Splenic neutrophils were collected for RNA extraction two days after rG-CSF injection.

first: Dennis

last: Hoving

first: Stefan

last: Boeing


title: Investigating the role of aging and lung fibrosis in Endothelial Cells with RNA sequencing

status: Public on Sep 30 2021

city: Rochester

first: Mrunal

middle: Kishor

last: Dehankar

state: MN

address: 200 First St. SW

department: Computational genomics

country: USA

institute: Mayo Clinic

summary: In order to elucidate the contribute of the pulmonary vasculature to lung fibrosis, we injured young and aged mice with bleomycine, to create a model of resolving versus persistent lung fibrosis. The animals were sacrificed 30 days after the injury (time point in which we observed a divergent resolving vs persistent lung fibrosis in young vs aged mice). We found that lung fibrosis resolution in young mice was accompained by the activation of transcriptional programs promoting vascular repair and lung fibrosis resolution. Lung endothelial cells from aged mice after injury failed to activate these programs, leading to dysrepair and progressive fibrosis.

overall_design: Freshly isolated lung endothelial cells from young and aged mice either sham or after bleomycin were subjected to ATACseq analysis. A widespresd reduction in chromatin accessibility was found in aged lung endothelial cells, either sham or after bleomycin administration, compared to young endothelial cells.

first: Nunzia

last: Caporarello

first: Giovanni

last: Ligresti

first: Daniel

middle: J

last: Tschumperlin


title: Temporal analysis of enhancers during mouse brain development reveals dynamic regulatory function and identifies novel regulators of cerebellar development.

status: Public on Sep 15 2021

city: Vancouver

first: Miguel

last: Ramirez

state: BC

address: 950 W 28th Ave

department: Centre for Molecular Medicine and Therapeutics

country: Canada

institute: BC Children's Hospital Research Institute

type: Genome binding/occupancy profiling by high throughput sequencing

summary: In this study, we identified active enhancers in the mouse cerebellum at embryonic and postnatal stages establishing the first catalog of enhancers active during embryonic cerebellum development. The majority of cerebellar enhancers have dynamic activity between embryonic and postnatal development. Cerebellar enhancers were enriched for neural transcription factor binding sites with temporally specific expression. Putative gene targets displayed spatially restricted expression patterns, indicating cell-type specific expression regulation. Functional analysis of target genes indicated that enhancers regulate processes spanning several developmental epochs such as specification, differentiation and maturation. We use these analyses to discover one novel regulator and one novel marker of cerebellar development: Bhlhe22 and Pax3, respectively. We identified an enrichment of de novo mutations and variants associated with autism spectrum disorder in cerebellar enhancers. Our study provides insight into the dynamics of gene expression regulation by enhancers in the developing brain and delivers a rich resource of novel gene-enhancer associations providing a basis for future in-depth studies in the cerebellum.

overall_design: We utilize chromatin immunoprecipitation followed by sequencing (ChIP-seq) of enhancer associated histone marks H3K4me1 and H3K27ac at 3 stages of embryonic and early postnatal cerebellar development.

last: Goldowitz


title: Host Induced Gene Silencing of the Sclerotinia sclerotiorum ABHYDROLASE-3 gene reduces disease severity in Brassica napus

status: Public on Sep 29 2021

city: Winnipeg

first: Nick

last: Wytinck

state: MB

address: 50 Sifton Road

department: Department of Biological Sciences

institute: University of Manitoba

summary: Sclerotinia sclerotiorum is a pathogenic fungus that infects hundreds of crop species, causing extensive yield loss every year. Chemical fungicides are used to control this phytopathogen, but with concerns about increasing resistance and impacts on non-target species, there is a need to develop alternative control measures. In the present study, we engineered Brassica napus to constitutively express a hairpin (hp)RNA molecule to silence ABHYRDOLASE-3 in S. sclerotiorum. We demonstrate the potential for Host Induced Gene Silencing (HIGS) to protect B. napus from S. sclerotiorum using leaf, stem and whole plant infection assays. The interaction between the transgenic host plant and invading pathogen was further characterized at the molecular level using dual-RNA sequencing and at the anatomical level through microscopy to understand the processes and possible mechanisms leading to increased tolerance to this damaging necrotroph. We observed significant shifts in the expression of genes relating to plant defense as well as cellular differences in the form of structural barriers around the site of infection in the HIGS-protected plants. Our results provide proof-of-concept that HIGS is an effective means of limiting damage caused by S. sclerotiorum to the plant and demonstrates the utility of this biotechnology in the development of resistance against fungal pathogens.

overall_design: Examination of infected stem tissue from untransformed and RNAi canola, 0, 1 and 7 days post infection.

first: Dylan

last: Ziegler

last: Walker

last: Sullivan

first: Kirsten

last: Biggar

first: Deirdre

last: Khan

first: Solihu

middle: K

last: Sakariyahu

first: Olivia

last: Wilkins

first: Steve

last: Whyard

first: Mark

last: Belmonte


title: An integrative multi-omic analysis reveals a major metabolic rewiring between keratinocytes from babies and adults.

status: Public on Sep 12 2021

city: Val-de-Reuil

first: Cécilia

last: Brun

address: Campus de Maigremont

department: Translational Science - Essential Health

country: France

institute: Johnson & Johnson Santé Beauté France

summary: Even though its development starts early in utero, neonatal skin is still immature at birth relative to adult and undergoes a maturation process extending to the first years of life. It is now established that stratum corneum is thinner and dryer, and that skin contains less natural moisturizing factors and lipids in newborns compared to children and adults. Moreover, it has been shown that skin surface area expansion is not linear throughout life and is peaking perinatally, suggesting that baby skin has a higher epidermal cellular turnover. Despite growing resources showing differences between adult and infant skin physiology, molecular and metabolic specificities of baby skin are still poorly understood. To address this critical knowledge gap, we performed an integrative transcriptomic and metabolomic study comparing human primary keratinocytes from babies and adults. Based on state-of-the-art integrative frameworks, our analyses revealed a major shift in the global energetic metabolism in baby keratinocytes compared to adults, highlighting increased amino acid metabolism and mitochondrial oxidative phosphorylation in baby cells to fuel TCA cycle, while showing glycolysis as the major cell energy source in adult cells.

overall_design: Human primary keratinocytes were provided by Sterlab (Sophia Antipolis, France) from 6 baby and 6 adult volunteers. Briefly, keratinocytes were isolated from foreskin and from abdominoplasty, for babies and adults respectively. Then, Keratinocytes were cultured in KGM gold basal medium supplemented with KGM-Gold Keratinocyte SingleQuots Kit (Lonza). One passage after thawing, RNAs were extracted using RNeasy 96 QIAcube HT Kit (Qiagen) and supernatants were collected. Samples were finally sent to Genex (Longjumeau, France) for transcriptomic analysis and Metabolon (Morrisville, USA) for metabolomic profiling.

first: Claire

last: Mangez

first: Pierre-François

last: Roux

first: Georgios

last: Stamatas

first: Thierry

last: Oddos


title: Understanding the role of myoglobin content in Iberian pigs fattened in an extensive system through analysis of the transcriptome profile

city: Zafra

first: María

middle: Muñoz

last: Muñoz

state: Badajoz

address: Centro I+D en Cerdo Ibérico, carretera Ex-101, km 4.7

country: Spain

institute: INIA

summary: Meat color is the first perceived sensory feature and one of the most important quality traits. Myoglobin is the main pigment in meat, giving its characteristic cherry-red color which is highly appreciated by consumers. In the current study, we used the RNA-seq technique to characterize the longissimus dorsi muscle transcriptome in two groups of Iberian pigs with divergent breeding values for myoglobin content. As a result, we identified 57 differentially expressed genes and transcripts (DEG). Moreover, we have validated the RNA-seq expression of a set of genes by qPCR. Functional analyses revealed an enrichment of DEGs in biological process related to oxidation (HBA1), lipid metabolism (ECH1, PLA2G10, PLD2), inflammation (CHST1, CD209, PLA2G10), and immune system (CD209, MX2, LGALS3, LGALS9). The upstream analysis showed a total of five transcription regulatory factors and eight master regulators that could regulate the expression of some DEGs, highlighting SPI1 and MAPK1, since they regulate the expression of DEGs involved in immune defence and inflammatory processes. Iberian pigs with high myoglobin content also showed higher expression of the HBA1 gene and it has been described that both molecules have a protective effect against oxidative and inflammatory processes. Therefore, the HBA1 gene is a very promising candidate gene to harbour polymorphisms underlying the myoglobin content, whereby, further studies should be carried out for its potential use in an Iberian pig selection program.

overall_design: Twelve Iberian individuals with divergent breeding values for myoglobin content were selected (six per group), samples of Longissimus dorsi were collected after the slaughter, RNA from these samples was extracted, pair-end libraries of 150 bp  were constructed

middle: A

last: Fernández-Barroso

first: Yolanda

last: Núñez

first: Luisa

last: Ramírez-Hidalgo

first: Gema

last: Matos

first: Juan

middle: M

last: García-Casco


title: Single-cell gene expression of virus-specific CD4  T cells in response to acute and chronic infection

status: Public on Sep 21 2021

first: Thomas

last: Ciucci

summary: Single-cell gene expression of GP66 CD4+ T cells  was determined by scRNAseq after LCMV Armstrong  and Clone 13 infection

overall_design: C57Bl6 were infected with LCMV Armstrong or Clone 13. Spleen GP66+ CD4+ T cells were sorted 7 , 21 and 80 days post-infection and gene expression was determined by scRNAseq + scTCR

first: Santiago

last: Carmona


title: Transcriptome analysis reveals the roles of long non-coding RNA and mRNA in bursa of Fabricius during pigeon (Columba livia) development

city: Chengdu

first: Xun

last: Wang

state: China

address: Huimin road 211#, Wenjiang district

country: China

institute: Sichuan agricultural university

type: Non-coding RNA profiling by high throughput sequencing

summary: We identified 13,072 mRNAs and 19,129 lncRNAs, of which 2,977 mRNAs and 1,527 lncRNAs were differential expressed in pigeon BFs over three developmental stages.

overall_design: we analyzed the three stages (1 day, 13 days and 26 days) of bursa of Fabricius in White-King pigeon using transcriptome sequencing

first: Jie

last: Wu


title: Single-cell transcriptomes of the mouse retinal pigment epithelium response to low dose of doxorubicin

status: Public on Sep 08 2021

city: Daejeon

first: Ho-yeon

last: Lee

address: 125, Gwahak-ro, Yuseong-gu

country: South Korea

institute: KRIBB

summary:
Purpose : Address heterogeneous composition in RPE cells and identify what subpopulation might be changed when cellular senescence is induced
Methods: Mouse RPE cells (Control and Doxorubicin treatment) were isolated and sequenced using Chromium Next GEM Single Cell 5p RNA library v1.1. Alignment and quantification of raw data was performed through CellRanger v4.0.0 (10X Genomics) with reference to mm10 genome (FASTA).
Results : As a result of mapping sequence reads to the reference genome (mm10) using the CellRanger count function, we obtained count data of 36030 filtered cells for 32285 features. R package Seurat (v 3.2.3) was used to perform additional analysis of filtered data including clustering. After classifying the clusters with the cell type marker from the clustering results of the entire cell data, the clusters showing the high expression level (log2FC >2) of RPE65, a marker gene for RPE cells, were isolated. In the isolated 3355 cells, 5 clusters and their marker genes were identified.
Conclusion : In this study, we could find changes in heterogeneous composition and senescence in mouse RPE cells. RPE cells were classified into clusters according to their heterogeneity, and anti-apoptotic and senescent changes were confirmed through changes in gene expression in the Dox-treated in vivo mouse model. Some of the DEGs of Con vs Dox contained genes that have not yet been identified related to senescence. The RPE-specific transcriptome in this study enhances the understanding of the role of RPE senescence in AMD and will therefore be useful for developing treatments targeting RPE senescence and testing their effectiveness.

overall_design: mRNA profiles of mouse RPE cells in senescence model

first: Hyungwoo

first: Ho-Yeon

first: Jae-Byoung

last: Chae


title: Genome-wide occupancy profiling of H3K4me3, H3K27ac and H2AZ in glioblastoma stem cell specimens (TS-543) [ChIP-Seq]

status: Public on Sep 05 2021

city: Singapore

first: Roberto

last: Tirado-Magallanes

email: e0056363@nus.edu.sg, rtmag4@gmail.com

state: Singapore

address: 14 Medical Dr

country: Singapore

institute: Cancer Science Institute of Singapore

summary: Glioblastoma stem cells (TS-543) were harvested and cross-linked with 1% formaldehyde for 10 mins at room temperature. The cells were lysed using SDS Lysis buffer for ChIP (1% SDS, 10 mM EDTA, 50 mM Tris-HCl pH 8). The lysate was then sonicated for 25 cycles at 30% amplitude (15 s ON and 45 s OFF). The sonicated samples were then diluted in ChIP dilution buffer (0.01% SDS, 1% Triton-X-100, 1.2 mM EDTA, 16.7 mM Tris–HCl pH 8, 167 mM NaCl) and used for the immunoprecipitation with H3K27ac (Abcam, Ab4729), H2AZ (Active motive, cat#39113) and H3K27ac (Abcam cat#ab8580). After an over-night incubation with antibody, the bound DNA was washed sequentially with low salt wash buffer (0.1% SDS, 1% Triton X 100, 2 mM EDTA, 20 mM Tris–HCl pH 8, 150 mM NaCl), high salt wash buffer (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris–HCl pH 8, 500 mM NaCl), LiCl wash buffer (0.25 M LiCl, 1% NP40, 1%deoxycholate, 1 mM EDTA, 10 mM Tris–HCl pH 8) and TE wash buffer (10 mM Tris–HCl pH 8, 1 mM EDTA) to remove non-specific sequences and eluted in the elution buffer (84 mg NaHCO3, 1 ml 10% SDS, 9 ml H2O). Then the samples were reverse cross-linked using NaCl at 65°C overnight. The eluted DNA was purified and used for library preparation. Library preparation was performed as previously described as described in Bowman et al. BMC Genomics 2013. Briefly, end repair with NEBNext End Repair enzyme (NEB, E6050) and clean-up with 2.4x volume AMPure XP beads (Beckman Coulter, A63880). A-tailing with Klenow Fragment (NEB, M0212) and purified with 2.4x volume AMPure XP beads. Adapter ligation reactions contained annealed universal adapter and T4 rapid ligase (NEB, B0202) and clean-up with 1.8x volume AMPure XP beads. Chromatin was amplified using KAPA Real-time Library Amplification Kit (KAPABIOSYSTEMS, KK2701) with universal primer and barcoded primer. Amplified chromatin was purified with QIAquick Gel Extraction Kit (Qiagen) and sequenced paired-end with Illumina NextSeq 500.

overall_design: ChIP-seq from glioblastoma stem cell specimens (TS-543).

first: Yoon

last: Jeehyun

first: Oleg

last: Grinchuk

first: Derrick

last: Ong

middle: T

last: Magallanes


title: Transcriptomic study with knock-in of PIK3CD in tumoral experimental mouse model

city: VILLEJUIF

first: christophe

last: desterke

address: 14-16 avenue Paul Vaillant Couturier

department: UFR medecine institute Andre Lwoff

institute: university Paris Sud11

summary:
The isoform delta of class I Phosphoinositide 3-kinase (PI3Kdelta) is expressed primarily in hematopoietic cells, and its inhibitor, idelalisib, is approved for the treatment of leukemia and lymphoma. PI3Kdelta orients the apicobasal axis and regulates lumen formation through assembly of the extracellular matrix. PI3Kdelta overexpression in hepatocellular carcinoma (HCC) cells (Huh7) leads to profound changes in cell morphogenesis and is associated to the up-regulation of stem cell markers.
With tumoral experimental mouse model, investigations on PI3Kdelta implication were performed after knock-in transfection

overall_design: RNA from tumors were used to perform transcriptome Clariom S mouse experiments in triplicates for three individual samples in each experimental condition: transfection with empty vector (AAV) and transfection with PIK3CD vector.

first: Jean

last: Agnetti

first: Christophe

last: Desterke

first: Didier

last: Samuel

first: Ama

last: Gassama-Diagne


title: RNA sequencing of endometrial glands during the implantation window in women with recurrent pregnancy loss

status: Public on Sep 23 2021

city: Southampton

first: Jennifer

middle: Elizabeth

last: Pearson-Farr

address: MP887, Southampton General Hospital

department: Human Development and Health

institute: University of Southampton

summary: This study sought to determine whether an endometrial gland specific transcriptome and splicing profile are altered in the window of implantation (days 21-23 of the menstrual cycle) in women with recurrent pregnancy loss. Our data provide a comprehensive catalogue of gene isoforms and relative exon usage in endometrial glands. The endometrial gland targets identified in this study could be used to identify a perturbed endometrium, isolate causes of recurrent pregnancy loss and develop targeted therapies in personalised medicine.

overall_design: RNA sequencing comparing endometrial glands at the window of implantation from women with recurrent pregnancy loss and controls.

first: Gabrielle

last: Wheway

first: Maaike

last: Jongen

first: Rohan

last: Lewis

first: Ying

last: Cheong

first: Jane

last: Cleal


title: Distinct Functional Properties of Perinatal vs. Adult Adipose Progenitors

status: Public on Aug 23 2021

city: Durham

first: Rana

last: Gupta

state: North Carolina

address: Carmichael Building, 300 North Duke St.

department: Duke Molecular Physiology Institute

institute: Duke University

summary: We previously identified functional distinct sub-populations in adult male gWAT Pdgfrb+ cells utilizing the MuralChaser lineage tracking system and single-cell RNA-seq. Later in this related submission, we performed single-cell RNA-seqs on different developing stage of gWAT (P3, P7 and 5-week). We identified 4 sub-populations of Pdgfrb+ cells. Bulk-mRNA were conducted to these sub-populations in order to understand their transcriptomic profiles.

overall_design: Bulk mRNA-seq was done on freshly isolated Pdgfrb+ sub-populations (adipocyte precursor cells, fibro-inflammatory progenitors, mesothelial-like cells, smooth muscle cells) by FACS.

first: Qianbin

last: Zhang


title: RNAseq analysis of gene expression profiles in a mouse model of tuberous sclerosis

status: Public on Aug 31 2021

city: New York

first: GUOMEI

last: TANG

state: New York

department: Neurology

institute: Columbia University

summary: We have generated a tuberous sclerosis complex (TSC) mouse model through mouse Gfap-Cre mediated conditional knockout of Tsc1 gene. Tsc1 depletion occurs in most astrocytes and a fraction of upper cortical and hippocampal neurons. The mice develop spontaneous seizures after 10 weeks of age. To determine the effect of Tsc1 deficiency on astrocytes, we compared astrocyte gene expressio profiles between mGfap-Cre:Tsc1CKO and littermate control mice at 4 weeks and 15 weeks of age. At 4 weeks, mGfap-Cre:Tsc1CKO mice showed increased transcription of a few astrocyte genes, including Vim, Amigo2, Thbs4, Slc7a11, Gjb6 and ALDH1L1, and there were not changes in protein products of these genes.  At 15 Weeks, mGfap-Cre:Tsc1CKO mice with seizures showed increased transcription of reactive astrocyte genes, including Gfap, Vim, CD44, Sparc, Serpina3n and many others. The transcriptional changes were consistent with enhanced protein levels.

overall_design: Total RNA (RIN>=9.8) was extracted from upper half cortex of somatosensory and parietal cortices of mGfap-Cre+:Tsc1CKO and control mice. mRNAs were enriched using poly-A-pull-down. Library was prepared using the Illumina TruSeq RNA prep kit, and sequenced using an Illumina HiSeq 2000 system with a read length of 100 bases. RTA (Illumina) was used for base calling and bcl2fastq (1.8.4) was applied to covert BCL to fastaq format. The reads were mapped to a mouse reference genome mm9 using Tophat (2.0.4). Differential gene experssion analysis was conducted using DESeq2 pipeline, with a FDR of 0.1, and an adjusted p value cutoff 0.05.

first: Osama

last: AI Dalahmah

first: Guomei

last: Tang


title: Profiling of transcriptomic changes using seq in postmortem brains of subjects with alcohol use disorder

status: Public on Oct 13 2021

city: Boston

first: Huiping

state: Massachusetts

address: 72 East Concord Street

department: Psychiatry

institute: Boston University School of Medicine

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

overall_design: Refer to individual Series


title: Cardiac Sex Differences in the Transcriptome of C57 Male and Female Adult Hearts

status: Public on Aug 25 2021

city: Chapel Hill

first: Wei

last: Shi

state: NC

address: 221 Fordham Hall

department: Biology

institute: UNC-Chapel Hill

summary:
Purpose: The goals of this study are to compare adult male and female C57 mouse hearts  transcriptome profiling (RNA-seq) to conclude cardiac sex differences at the mRNA level.
Methods: mRNA profiles of adult male and female C57 mouse hearts were generated by deep sequencing, n=4 for each sex, using Illumina HiSeq2500. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks.
Results: Using an optimized data analysis workflow, we mapped about 50 million sequence reads per sample to the mouse genome (build mm10) and identified 16,160 transcripts in the mouse hearts.

overall_design: Adult male and female C57 mouse hearts RNAseq

first: Frank

last: Conlon


title: Cardiac Sex Differences in the Transcriptome of C57 Male and Female E9.5 Hearts

summary:
Purpose: The goals of this study are to compare E9.5 male and female C57 mouse embryonic hearts  transcriptome profiling (RNA-seq) to conclude cardiac sex differences at the mRNA level.
Methods: mRNA profiles of E9.5 male and female C57 mouse embryonic hearts were generated by deep sequencing, n=4 for each sex, using Illumina HiSeq2500. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks.
Results: Using an optimized data analysis workflow, we mapped about 30 million sequence reads per sample to the mouse genome (build mm10) and identified 16,460 transcripts in the mouse hearts.

overall_design: E9.5 male and female C57 mouse embryonic hearts RNAseq

first: Kerry

last: Dorr


title: Yap/Taz inhibit goblet cell fate to maintain lung epithelial homeostasis (ChIP-seq)

status: Public on Aug 19 2021

city: BOSTON

first: Boting

last: Ning

address: 72 E Concord St

institute: BOSTON UNIVERSITY

summary: Proper lung function relies on precisely balanced numbers of specialized epithelial cell types that work together and are maintained in homeostasis. In this study we have described essential roles for the transcriptional regulators YAP and TAZ, which are key effectors of Hippo pathway signaling, in maintaining lung epithelial homeostasis. Phenotypes associated with Yap/Taz deletion include alveolar defects and a striking development of goblet cell metaplasia throughout the airways. Knockdown of YAP and TAZ in HBECs similarly drives mucin expression. The TEAD family of transcription factors are well characterized partners of the YAP/TAZ transcriptional effectors, and we have found that knockdown of TEAD1-4 similarly drives elevated mucin expression. In order to further understand the role of the TEAD transcription factors in human lung epithelial cell fate, we conducted TEAD Chromatin Immunopreciptitation (ChIP)-Sequencing.

overall_design: Examination of TEAD chromatin binding profiles in human bronchial epithelial cells. HBECs were cultured to high density in Pneumacult EX plus before ChIP Seq analysis. Cells were crosslinked via ethylene glycol bis (succinimidyl succinate) (EGS) and formaldehyde. Chromatin was sheared by sonication and immunoprecipitated with TEAD antibody (AvivaSystemsBiology).

first: Julia

last: Berthet

first: Xaralabos

last: Varelas


title: RNAseq analysis of silica coated magnetic nanoparticles treated BV2 cells

status: Public on Aug 18 2021

city: Suwon

first: Gwang

last: Lee

state: Yeongtong-gu

address: 206 Worldcup-ro

department: Department of Physiology and Department of Biomedical Sciences

institute: Ajou University

summary: We report the gene expression profile in BV2 murine microglia cell line after treatment of silica coated magnetic nanoparticles with low dose (0.01 µg/µl) and high dose (0.1 µg/µl) for 12 h.

overall_design: To analyze the changes of gene expression after treatment with silica-coated-magnetic nanoparticles containing the rhodamine B isothiocyanate dye [MNPs@SiO2(RITC)] in BV2 cells, BV2 cells were treated with 0.01 and 0.1 µg/µl of MNPs@SiO2(RITC) for 12 h, lysed, and total RNA was isolated with TruSeq Stranded Total RNA Library Prep Kit (Illumina, CA). RNA quality was analyzed by rRNA band integrity on an Agilent RNA 6000 Nano kit (Agilent Technologies, CA). cDNA library was constructed from 1 µg of total RNA. Magnetic beads conjugated with Oligo (dT) were used to enrich poly A tailed mRNA. Purified mRNAs were fragmented into short fragments, and double-stranded cDNAs were synthesized. The cDNAs were modified with end-repair, poly (A) addition, and connected with sequencing adapters using the TruSeq RNA sample prep Kit (Illumina, CA). cDNA fragments were purified with BluePippin (Sage Science, MA) and amplified by PCR. The cDNA library size and quality were determined with an Agilent High Sensitivity DNA kit (Agilent Technologies, CA). The library was sequenced using an Illumina HiSeq2500 sequencer (Illumina, CA).

first: Tae

middle: H

last: Shin


title: Decoding the origin of neuronal diversity in hypothalamus by single-cell RNA-seq

status: Public on Aug 05 2021

city: Beijing

first: yuhong

address: No.1 West Beichen Road

department: Institute of Genetics and Developmental Biology (IGDB)

institute: Chinese Academy of Sciences (CAS)

summary: The hypothalamus is one of the most complex brain structures whose development involves a plastic process of neuronal fate specification. Progress has been made to decipher the gene regulatory programs that are responsible for hypothalamus development; however, the molecular developmetal trajectory of hyothalamus is largely unknown. To understand how pre- and postmitotic transcriptional programs interact and coordinate to endow neuronal cell subtypes with their characteristic properties during hypothalamic development, we performed single-cell RNA sequencing (scRNA-seq) on single cells derived from Rax+ hypothalamic neuroepithelium at four critical developmental points during hypothalamic development. Our single-cell analysis provides a developmental landscape of mouse hypothalamus. We show that while the fate of radial glial cells (RGCs) is predetermined before differentiation but lack spatial code to distinguish from each other, different clusters of intermediate progenitors (IPCs) emerge to display diversifying fates and subdivide hypothalamic primordium into distinct spatially-restricted progenitor domains. We further characterize the maturation dynamics of hypothalamic neurons and suggest that immature neurons could evolve into multiple peptidergic neuronal subtypes. Finally, we identify sets of transcription factors (TFs) serving as regulons to determine the fate of diverse GABAergic and Glutamatergic neurons in hypothalamus. Together, our study offers a single-cell transcriptional framework for the hypothalamus developmental trajectory and propose a cascade diversifying model to deconstruct the origin of neuronal diversity in hypothalamus.

overall_design: To infer the lineage progression underlying hypothalamus development, we first labeled hypothalamic neuroepithelium by applying a single dose of tamoxifen in Rax-CreERT2::Ai14 mice at embryonic day 9 (E9) and performed lineage tracing for cell collection. Next, we microdissected hypothalamus from induced Rax-CreERT2::Ai14 mice across 4 different time points that cover the process of neurogenesis and early maturation for hypothalamic neurons [E11, E14, postnatal days 0 (P0) and P7], and collected live tdTomato+ cells by fluorescent-activated cell sorting for single-cell transcriptomic sequencing

first: Mingrui

last: Xu

first: Yu-Hong

first: Xiang

first: Qing-Feng

last: Wu


title: Col-0 anthers, control and iron-deficient

status: Public on Jul 31 2021

city: Taipei

first: Der-Fen

last: Suen

address: No. 128, Sec. 2, Academia Road, Nankang

department: Agricultural Biotechnology Research Center

country: Taiwan

institute: Academia Sinica

summary: RNAseq transcriptome of anthers of Arabidopsis thaliana Columbia-0 grown under control (1/2 Hoagland) and Fe deficiency conditions.

overall_design: Control Col-0 anthers compared to Fe-deficient anthers.

first: Tzu

last: Huang

first: Der

middle: F


title: Rapid redistribution and extensive co-binding of NANOG and GATA6 at shared regulatory elements underlie specification of divergent cell fates [CUT&TAG, CUT&RUN]

status: Public on Jul 30 2021

city: Bethesda

first: Pedro

middle: P

last: Rocha

state: Maryland

address: 6 Center Drive Building 6B 2B220

department: NICHD

institute: National Institutes of Health

summary: Establishment of divergent cell types from a common progenitor requires transcription factors (TFs) to promote lineage-restricted transcriptional programs while suppressing alternative fates. In the mouse blastocyst, cells of the inner cell mass (ICM) coexpress NANOG and GATA6, two TFs that drive the bifurcation of these progenitors into either the epiblast (Epi) or the primitive endoderm (PrE), respectively. Here, using in vitro differentiation, we describe the molecular mechanisms of how GATA6 quickly induces the PrE fate while repressing the Epi lineage. GATA6 functions as a pioneer TF by inducing nucleosome repositioning at regulatory elements controlling PrE genes, making them accessible for deposition of active histone marks and leading to rewiring of chromatin interactions and ultimately transcriptional activation. GATA6 also binds most regulatory elements of Epi genes followed by eviction of the Epi-specific TFs NANOG and SOX2, loss of active histone marks, and reduction in chromatin accessibility that culminates in transcriptional repression. Unexpectedly, evicted NANOG and SOX2 transiently bind PrE regulatory elements occupied by GATA6. Our study shows that GATA6 binds and modulate the same regulatory elements as Epi TFs, a phenomenon we also validated in blastocysts. We propose that the ability of PrE and Epi-specific TFs to extensively bind and regulate the same gene networks contributes to ICM plasticity and allows rapid cell lineage specification by coordinating both activation and repression of divergent transcriptional programs.

overall_design:
Mapping transcription factor binding and histone distribution changes during primitive endoderm differentiation.

Please note that the records have been updated with additional processed data *peaks.narrowPeak files on June 16th, 2022.

first: Joyce

last: Thompson


title: Rapid redistribution and extensive co-binding of NANOG and GATA6 at shared regulatory elements underlie specification of divergent cell fates [Hi-C]

overall_design: Assaying 3D-chromatin structure during in vitro differentiation of mouse embryonic stem cells into primitive endoderm.


title: Rapid redistribution and extensive co-binding of NANOG and GATA6 at shared regulatory elements underlie specification of divergent cell fates [ChIP-seq]

overall_design: Mapping changes in Nanog binding during in vitro differentiation of mouse embryonic stem cells into primitive endoderm.


title: Effects of prenatal valproic acid exposure on hippocampal gene expression after birth

status: Public on Jul 23 2021

city: Higashi-Hiroshima

first: Yasuhiro

last: Ishihara

state: Hiroshima

address: 1-7-1 Kagamiyama

department: Graduate School of Integrated Sciences for Life

country: Japan

institute: Hiroshima University

summary: Valproic acid (VPA) is a clinically used antiepileptic drug, but it has significant risks for low verbal intelligence quotient scores, attention deficit hyperactivity disorder and autism spectrum disorder in children when it is administered during pregnancy. Prenatal VPA exposure is reported to affect neurogenesis and neuronal migration and differentiation. In addition, growing evidence showed that a brain immune cell, microglia are activated by VPA treatment. However, a role of activated microglia by VPA remains unclear. The purpose of this study is identify a candidate gene which is responsible for VPA-induced behavioral disorders.

overall_design: Hippocampus of P5 mice exposed to vehicle or valproate at E11.5.

first: Tatsuya

last: Honda


title: Cisplatin-induced decrease of mRNA length reveals functional and translated intronic-polyadenylation isoforms in the annotated 5’-untranslated region of genes

status: Public on Jul 28 2021

city: Orsay

first: Céline

middle: M.

last: Labbé

address: Rue Henri Becquerel

institute: Institut Curie


title: Differentially expressed genes in HSCC tissues, Normal hypopharyngeal tissue and Cervical lymph nodes

status: Public on Jul 18 2021

city: chiba

first: sachi

last: oshima

state: chiba

address: 1-8-1 inohana chuo-ku

department: Grad. Sch. Med

institute: Chiba Univ

summary: To identify differentially expressed genes by HSCC tissues, Normal hypopharyngeal tissues and Cervical lymph nodes were subjected to Agilent whole genome microarrays.

overall_design: All specimens used in the study were obtained by surgical resection at Chiba University Hospital.

first: Naohiko

last: Seki

first: Sachi

last: Oshima


title: Sex-biased expression of microRNAs in Drosophila pseudoobscura

status: Public on Jul 14 2021

city: Colchester

first: Antonio

last: Marco

address: Wivenhoe Park

department: School of Life Sciences

institute: University of Essex

summary: Small RNA sequencing from Drosophila pseudoobscura males and virgin females.

overall_design: All flies were kept at 18ºC on cornmeal based media, with 12 hours light/dark cycles. Adult males and females were collected at age 7 days. We extracted total RNA form samples using TRIzol (Life Technologies) as recommended by the manufacturer. RNA was dissolved in RNase-free water. For small RNA sequencing we used the TruSeq Small RNA Sample Preparation Kit (Illumina) to generate the cDNA library and we selected constructs of sizes 145 to 160 bp in a 6% PAGE gel, and precipitated in ethanol. DNA integrity was checked with TapeStation (Agilent). Samples were sequenced in-house with an Illumina MiSeq sequencing machine.


title: Rapid redistribution and extensive co-binding of NANOG and GATA6 at shared regulatory elements underlie specification of divergent cell fates [RNA-seq]

overall_design: Mapping transcription changes during in vitro differentiation of mouse embryonic stem cells into primitive endoderm.


title: Bulk RNA-seq, scRNA-seq, and TCR-seq to study features of the transcriptome and TCR repertoire of a stably persisting population of regulatory T cells generated in mice with autoimmune inflammation by conversion from Treg "wannabes"

status: Public on Jul 09 2021

first: Michail

last: Schizas

address: 1275 York ave

institute: Memorial sloan Kettering

relation:
SuperSeries of: GSE179706
SuperSeries of: GSE179707
SuperSeries of: GSE179708


title: TCR-seq to study features of the transcriptome and TCR repertoire of a stably persisting population of regulatory T cells generated in mice with autoimmune inflammation by conversion from Treg "wannabes"

summary: The immunosuppressive function of regulatory T (Treg) cells is dependent on continuous expression of the transcription factor Foxp3. Foxp3 loss-of-function or induced ablation of Treg cells results in a fatal autoimmune disease featuring all known types of inflammatory responses with every manifestation stemming from Treg cell paucity, highlighting a vital function of Treg cells in preventing fatal autoimmune inflammation.  However, a major question remains whether Treg cells can persist and effectively exert their function in a disease state, where a broad spectrum of inflammatory mediators can either inactivate Treg cells or render innate and adaptive pro-inflammatory effector cells insensitive to suppression.  By reinstating Foxp3 protein expression and suppressor function in cells expressing a reversible Foxp3 null allele in severely diseased mice, we found that the resulting single pool of “redeemed” Treg cells normalized immune activation, quelled severe tissue inflammation, reversed fatal autoimmune disease, and provided long-term protection against them. Thus, Treg cells are functional in settings of established broad spectrum systemic inflammation and are capable of affording sustained reset of immune homeostasis.

overall_design: TCR-seq of Treg cells isolated from rescued Foxp3LSL mice harvested 1.5 (2 replicates), 3 (4 replicates), 5 (2 replicates), and 7 (5 replicates) months after 4-OHT treatment.

first: W

last: Hu

first: Z

last: Wang

first: M

first: A

middle: Y

last: Rudensky


title: Comparison between blue and green Spanish firs

status: Public on Nov 20 2021

city: Malaga

first: Rafael

last: Cañas

address: Facultad de Ciencias, Campus de Teatinos

department: Biología Molecular y Bioquímica

institute: Universidad de Málaga

summary: Spanish fir (Abies pinsapo) is a relict tree that is found in southern Spain mountains. In natural conditions two phenotypes can be observed, trees with blue needles and trees with green needles. The aim of the present work is to elucidate at transcriptomic levels the possible causes of the differences between these phenotypes.

overall_design: Needle samles from 6 trees were harvested for each of the considered phenotypes. The samples were isolated from field-grown adult trees in Sierra de las Nieves (Yunquera, Spain) in spring (april 2021)

first: Francisco

last: Ortigosa

first: César

last: Lobato-Fernández

first: Concepción

last: Ávila

last: Cánovas


title: scRNA-seq to study features of the transcriptome and TCR repertoire of a stably persisting population of regulatory T cells generated in mice with autoimmune inflammation by conversion from Treg "wannabes"

overall_design: scRNA-seq of Treg cells isolated from 7-month-old rescued Foxp3LSL (cells pooled from 4 mice) and control Foxp3DTR-GFP (cells pooled from 5 mice) mice.


title: Rapid redistribution and extensive co-binding of NANOG and GATA6 at shared regulatory elements underlie specification of divergent cell fates [ATAC-seq]

first: Pedro

last: Rocha

overall_design:
Mapping changes in chromatin accessibility using ATAC-seq during in vitro differentiation of mouse embryonic stem cells into primitive endoderm.

Please note that the records have been updated with additional processed data *bfilt.bed files on June 16th, 2022.

first: Joyce

last: Thompson


title: Exposure of meiosis-to-microspore-stage tomato flowers to long-term mild heat results in pollen failure after mitosis.

status: Public on Jul 17 2021

city: Nijmegen

first: Ivo

last: Rieu

address: Heyendaalseweg 135

department: Radboud Institute for Biological and Environmental Sciences

country: Netherlands

institute: Radboud University

summary: Crop reproductive success is significantly challenged by heatwaves, which are increasing in frequency globally. The main reason is reduced male fertility due to abnormal pollen development, but the mechanism behind the developmental deviation is not well understood. Here, long-term mild heat (LTMH) treatment, mimicking a heatwave, was applied to flowers or whole plants and followed up by cytological, transcriptomic and biochemical analyses. LTMH was shown to act directly on the flowers and not via a systemic effect on other plant tissue. The meiosis to early microspore stage was the most to LTMH and three to four days of LTMH exposure around this period was sufficient to significantly reduce pollen viability. Extensive cytological analysis showed that abnormalities in pollen development could first be observed after pollen mitosis I and tapetum development appeared unaffected. Transcriptomic and biochemical analyses suggested that pollen development suffers from tapetal ER stress, with a limited role for oxidative stress. These characteristics differentiate the response of developing anthers and pollen to LTMH from that to severe heat stress.

overall_design: 12 samples in total, consisting of 3 sample types with 4 replicates each. Sample types: 1) control temperature (CT), 2) 1 day long-term mild heat (1D-LTMH), 3) 4 days long-term mild heat (4D-LTMH).

first: Jiemeng

last: Xu

first: Stuart

last: Jansma

first: Mieke

last: Wolters-Arts

first: Peter

last: de Groot


title: Bulk RNA-seq to study features of the transcriptome and TCR repertoire of a stably persisting population of regulatory T cells generated in mice with autoimmune inflammation by conversion from Treg "wannabes"

summary: The immunosuppressive function of regulatory T (Treg) cells is dependent on continuous expression of the transcription factor Foxp3. Foxp3 loss-of-function or induced ablation of Treg cells results in a fatal autoimmune disease featuring all known types of inflammatory responses with every manifestation stemming from Treg cell paucity, highlighting a vital function of Treg cells in preventing fatal autoimmune inflammation. However, a major question remains whether Treg cells can persist and effectively exert their function in a disease state, where a broad spectrum of inflammatory mediators can either inactivate Treg cells or render innate and adaptive pro-inflammatory effector cells insensitive to suppression. By reinstating Foxp3 protein expression and suppressor function in cells expressing a reversible Foxp3 null allele in severely diseased mice, we found that the resulting single pool of “redeemed” Treg cells normalized immune activation, quelled severe tissue inflammation, reversed fatal autoimmune disease, and provided long-term protection against them. Thus, Treg cells are functional in settings of established broad spectrum systemic inflammation and are capable of affording sustained reset of immune homeostasis.

overall_design: Bulk RNA-seq of Treg cells isolated on day 7 post treatment from 4-hydroxytamoxifen (4-OHT)-treated experimental (Foxp3LSLCd4creERT2, 3 replicates) and healthy control (Foxp3DTR-GFP, 3 replicates) mice, and Treg "wannabes" from similarly treated sick control (Foxp3LSLCd4wt, 2 replicates) mice. Bulk RNA-seq of activated vs resting Treg "wannabes" isolated from diphtheria toxin-reated Foxp3LSL/DTR-GFP (3 replicates) and Foxp3LSL/WT (2 replicates) mice, respectively.


title: RNA-seq of seven altitude-adapted female speed skaters before and after exercise

status: Public on Jul 12 2021

city: Hinxton

first: Alexander

last: Predeus

address: Wellcome Trust Genome Campus

institute: Wellcome Sanger Institute

summary: Whole blood samples were collected from seven elite female skaters on the peak of altitude adaptation (day 18), before and after ~ 1h long exercise. Samples were globin-depleted and polyA-selected, converted to cDNA, and sequenced using Illumina paired-end reads (12-40M reads).

overall_design: We performed a whole transcriptome sequencing analysis of peripheral blood in seven altitude-adapted elite speed skaters, before and after ~ 1h long exercise. Reads were aligned to genome and transcriptome using STAR, and quantified using RSEM. Gene expression and enrichment was analyzed in R using DESeq2. Pathway analysis was done using the Molecular Signatures Database (MsigDB) via MsigDB website.

first: Andrey

last: Glotov

first: Irina

middle: E

last: Zelenkova

first: Elena

last: Vashukova

first: Anna

middle: R

last: Shuvalova

first: Alexandra

middle: D

last: Zolotareva

first: Dmitrii

last: Polev

first: Yury

last: Barbitoff

first: Oleg

last: Sarana

first: Sergey

middle: G

last: Scherbak

first: Petr

middle: I

last: Lidov

first: Mariya

last: Rozina

first: Victoria

middle: L

last: Gogotova

middle: V


title: Rapid redistribution and extensive co-binding of NANOG and GATA6 at shared regulatory elements underlie specification of divergent cell fates

status: Public on Jul 29 2021

first: Pedro

last: Rocha

overall_design: Refer to individual Series


title: Diet and exercise reduce pre-existing NASH and fibrosis and have additional beneficial effects on the vasculature#adipose tissue and skeletal muscle via organ-crosstalk

status: Public on Jul 10 2021

city: Leiden

first: Anita

last: van den Hoek

state: Zuid-Holland

address: Zernikedreef 9

department: MHR

institute: TNO

summary: Background: Non-alcoholic steatohepatitis (NASH) has become one of the most common liver diseases and is still without approved pharmacotherapy. Lifestyle interventions using exercise and diet change remain the current treatment of choice and even a small weight loss (5-7%) can already have a beneficial effect on NASH. However#the underlying molecular mechanisms of exercise and diet interventions remain largely elusive#and it is unclear whether they exert their health effects via similar or different pathways.  Methods: Ldlr-/-.Leiden mice received a high fat diet (HFD) for 30 weeks to establish an advanced state of NASH/fibrosis with simultaneous atherosclerosis development. Groups of mice were then either left untreated (control group) or were treated for 20 weeks with exercise (running wheel)#diet change (switch to a low fat chow diet) or the combination thereof. The liver and distant organs including heart#white adipose tissue (WAT) and muscle were histologically examined. Comprehensive transcriptome analysis of liver#WAT and muscle revealed the organ-specific effects of exercise and diet and defined the underlying pathways.  Results: Exercise and dietary change significantly reduced body weight#fat mass#adipocyte size and improved myosteatosis and muscle function with additive effects of combination treatment. WAT inflammation was significantly improved by diet change#tended to be reduced with exercise#and combination therapy had no additive effect. Hepatic steatosis and inflammation were almost fully reversed by exercise and diet change#while hepatic fibrosis tended to be improved with exercise and was significantly improved with diet change. Additive effects for the combination therapy were shown for liver steatosis and associated liver lipids#and atherosclerosis#but not for hepatic inflammation and fibrosis. Pathway analysis revealed complementary effects on metabolic pathways and lipid handling processes#thereby substantiating the added value of combined lifestyle treatment.  Conclusions: Exercise#diet change and the combination thereof can reverse established NASH/fibrosis in obese Ldlr-/-.Leiden mice. In addition#the lifestyle interventions had beneficial effects on atherosclerosis#WAT inflammation and muscle function. For steatosis and other parameters related to adiposity or lipid metabolism#exercise and dietary change affected more distinct pathways that acted complementary when the interventions were combined resulting in an additive effect for the combination therapy on important endpoints including NASH and atherosclerosis. For inflammation#exercise and diet change shared several underlying pathways resulting in a net similar effect when the interventions were combined.

first: Jelle

middle: C

last: de Jong

first: Nicole

last: Worms

last: van Nieuwkoop

first: Marijke

last: Voskuilen

first: Aswin

last: Menke

first: Serene

last: Lek

first: Martien

last: Caspers

first: Lars

last: Verschuren

first: Robert

last: Kleemann


title: Examine the impact of insulin suppression on embryo

status: Public on Jul 01 2021

city: Dallas

first: Matt

last: Sieber

state: Texas

address: 5323 Harry Hines blvd, MC 9040 ND12.214

institute: UT Southwestern Medical Center

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


title: Examine the impact of insulin suppression on embryo H3K9m-me3

summary: These expeirments compare the H3K9m-me3 ChIP profiles for embryonic progeny of  GFP expressing (control) and InR-DN expressing stage 14 oocytes.

overall_design: In this experiment we collected 16 hr embryonic progeny of GFP expressing oocytes and InR-DN expressing oocytes and conducted  H3K9-me3 sequencing analysis

first: Matthew


title: Using Auxin-inducible-degradation System to Interrogate Tissue-specific Transcriptional Programs of HSF-1 in Reproduction, Lifespan Assurance and Heat Shock Response.

city: Valhalla

first: Jian

last: Li

state: NY

address: 15 Dana Road

institute: New York Medical College


title: SARS-CoV-2 infected and uninfected VeroE6 and A549-ACE2: Bemcentinib and liposome treatments

status: Public on Jun 26 2021

city: Iowa City

first: Wendy

last: Maury

state: Iowa

address: 51 Newton Rd, Bowen Science Building 3-615

department: Microbiology and Immunology

institute: University of Iowa

summary: VeroE6 or A549-ACE2 cells were treated with inhibitors of phosphatidylserine receptors and infected with SARS-CoV-2.

sample_organism: Severe acute respiratory syndrome coronavirus 2

overall_design: VeroE6 or A549-ACE2 (lentiviral overexpression) were left untreated or treated with 1 micromolar bemcentinib for 1 hour, then challenged with a SARS-CoV-2 MOI of 0.01 (VeroE6) or 0.5 for either 18 hours (VeroE6) or 24 hours (A549-ACE2). Cells are lysed and mRNA isolated according to RNEasy miniprep protocol. Additional treatments are included, such as phsphatidylserine liposomes, phosphatidylcholine liposomes. 100000 reads were collected from each sample.

first: Dana

last: Bohan


title: Next-generation sequencing of human monocyte-derived dendritic cells stimulated with sialic acid glycodendrimers in the absence or presence of LPS

status: Public on Jun 23 2021

city: Amsterdam

first: Joyce

last: Lubbers

state: Noord-Holland

address: De Boelelaan 1108

department: Molecular Cell Biology and Immunology

institute: Amsterdam UMC

summary: To investigate whether a2-3 sialic acid dendrimers that bind to Siglec-9 would alter signalling and reprogramming of human monocyte-derived dendritic cells with and without LPS.

overall_design: 24 samples were included in next-generation sequencing, including triplicates for control moDCs, control glycodendrimer, alpha2-3 sialic acid glycodendrimer and a2-6 sialic acid glycodendrimers, all-in the absence or presence of LPS. The control dendrimers and control dendrimers in the presence of LPS serve as reference samples.

last: Lübbers

first: Eveline

first: Sandra

middle: J

last: van Vliet

first: Yvette

last: van Kooyk


title: Using Auxin-inducible-degradation System to Interrogate Tissue-specific Transcriptional Programs of HSF-1 in Reproduction and Heat Shock Response. [Germline - Timecourse]

summary: To understand the roles of HSF-1 and its regulation in reproduction and heat shock response in a tissue-specific manner, we coupled tissue-specific HSF-1 depletion in C. elegans by auxin-inducible degron (AID) with genome-wide transcriptional analyses in whole animals. We used ChIP-seq to analyze the occupancy of HSF-1 (tagged with AID::GFP) and RNA Pol II in young adult (YA) animals grown at 20°C or upon heat shock (HS) at 34°C for 30 min following an acute depletion of HSF-1 by AID for 2 hours either in the somatic or in the germline cells. Depletion by AID was performed by transferring worms expressing the E3 ligase TIR1 and carrying AID insertion to endogenous HSF-1 (JTL611 or JTL621) to NGM plates containing 1mM auxin (indole- 3-acetic acid, Sigma). The mock treatment was done by transferring worms to plates only containing the vehicle ethanol (EtOH). In parallel, we used RNA-seq to analyze the heat shock respnse upon depletion of HSF-1 in the soma or the germline for 2 hours. In addition, we also analyzed the transcriptomic changes by RNA-seq upon tissue-specific depletion of HSF-1 initiated at young adult stage for different length of time. In all RNA-seq analyses, we included the strains that only express TIR1 but do not have degron insertion at HSF-1 (CA1200 and CA1199) to control for the effects of auxin treatment and AID insertion into HSF-1.

overall_design: Experiment type: ChIP-seq, RNA-seq. Biological Source: strain: JTL611, JTL621, CA1200 and CA1199. Developmental dtage: young adult. Experimental Factors: temperature: 20 degree celsius (non-heat-shock, NHS), 34 degree celsius (heat-shock, HS); antibodies: anti-GFP (clontech, polyclonal), anti-Pol II (8WG16, BioLegend).


title: Using Auxin-inducible-degradation System to Interrogate Tissue-specific Transcriptional Programs of HSF-1 in Reproduction and Heat Shock Response. [HS response]


title: Comparative regulatory analysis of single cell data reveals a novel B cell subpopulation in chronic lymphocytic leukemia

status: Public on Jun 29 2021

city: Pleasanton

first: Joseph

last: Arthur

state: CA

address: 6230 Stoneridge Mall Road

institute: 10x Genomics

summary: We propose a computational method for single cell comparative regulatory analysis based on single cell gene expression (scRNA-seq) and single cell chromatin accessibility data (scATAC-seq) from two different conditions. Our software sc-compReg provides joint clustering and embedding of the cells from both scRNA-seq and scATAC-seq, and construction of differential regulatory networks across two conditions. We apply the method to compare gene regulatory networks in bone marrow mononuclear cells (BMMCs) obtained from a healthy donor and one with chronic lymphocytic leukemia (CLL). The analysis reveals a tumor-specific B cell subpopulation and identifies TOX2 as a novel regulator of this subpopulation.

overall_design:
Single cell RNA and single cell ATAC-seq profiles of BMMCs from two donors (CLL, Healthy)

***Raw sequence data is not submitted to a repository to protect the privacy of the anonymous human donors recruited by AllCells***

first: Zhana

last: Duren

first: Sophia

last: Lu

first: Francesca

last: Meschi

first: Corey

middle: M

last: Nemec

first: Wing

last: Wong

first: Yifeng

last: Yin


title: Alternative splicing regulates the physiological adaptation of the mouse hind limb postural and phasic muscles to microgravity

status: Public on Jun 25 2021

city: Philadelphia

first: Yuanyuan

last: Wang

state: PA

address: 3720 Chestnut St, Apt 709

institute: UCLA

summary: We sought to comprehensively elucidate the transcriptomic underpinnings of microgravity-induced muscle phenotypes in mice by evaluating both differential gene expression (DGE) and changes in alternative splicing (AS) due to extended spaceflight. Total RNA was isolated from the gastrocnemius and quadriceps, postural and phasic muscles of the hind limb, respectively, of 32-week-old female BALB/c mice exposed to microgravity or ground control conditions for nine weeks. RNA sequencing revealed that DGE and AS varied across postural and phasic muscle types with preferential employment of DGE in the gastrocnemius and AS in the quadriceps. Gene ontology analysis indicated that DGE and AS regulate distinct molecular processes. Various non-differentially expressed transcripts encoding musculoskeletal proteins (Tnnt3, Tnnt1, Neb, Ryr1, and Ttn) and muscle-specific RNA binding splicing regulators (Mbnl1 and Rbfox1) were found to have significant changes in AS that altered critical functional domains of their protein products. In striking contrast, microgravity-induced differentially expressed genes were associated with translation/ribosomal function and lipid metabolism. Our work serves as the first comprehensive investigation of coordinate changes in DGE and AS in large limb muscles across spaceflight. We propose that substantial remodeling of pre-mRNA by AS is a major component of transcriptomic adaptation of skeletal muscle to microgravity. The alternatively spliced genes identified here could be targeted by small molecule splicing regulator therapies to address microgravity-induced changes in muscle during spaceflight.

overall_design: Evaluate DGE and AS in hindlimb muscles of mice exposed to microgravity.

first: Henrich

last: Mason

first: Wang

last: Yuanyuan


title: Control of nitrogen remobilization and senescence in Arabidopsis thaliana by DNA methylation dynamics

status: Public on Jun 10 2021

city: Stuttgart

first: Emil

last: Vatov

address: Schloß Hohenheim 1

institute: University of Hohenheim

summary: Senescence is altered in mutants that are defective in DNA methylation; in leaves the process of senescence is associated with very moderate initial decline in chromosomal methylation that reversed at later stages. Methylation changes were not specifically associated with senescence-associated genes and potential regulation of transcription factor binding is suggested.

overall_design: Examination of cytosine methylation at four distinct timepoints after flower induction in A. thaliana

first: Ulrike

last: Zentgraf

first: Uwe

last: Ludewig


title: Using Auxin-inducible-degradation System to Interrogate Tissue-specific Transcriptional Programs of HSF-1 in Reproduction and Heat Shock Response. [ChIP-Seq]

first: Jian

last: Li


title: The timing of differentiation and potency of CD8 effector function is set by RNA binding proteins

status: Public on Jun 09 2021

city: Cambridge

first: Louise

last: Matheson

address: Babraham Research Campus

department: Laboratory of Lymphocyte Signalling and Development

institute: The Babraham Institute

summary: CD8 T cell differentiation into effector cells is initiated early after antigen encounter by signals from the T cell antigen receptor and costimulatory molecules.  The molecular mechanisms that determine the timing and rate of differentiation however are not defined. Here we show that the RNA binding proteins (RBP) ZFP36 and ZFP36L1 limit the rate of differentiation of activated naïve CD8 T cells and the potency of the resulting cytotoxic lymphocytes. The RBP act in an early and short temporal window to enforce dependency on costimulation via CD28 for full T cell activation and effector differentiation by directly binding mRNA of NF-kB, IRF8 and NOTCH1 transcription factors and IL2. Their absence in T cells, or the adoptive transfer of a small numbers of CD8 T cells lacking the RBP, promotes resilience to influenza A virus infection without immunopathology. These findings highlight ZFP36 and ZFP36L1 as nodes for the integration of the early T cell activation signals determining the speed and quality of the CD8 response.

overall_design: ZFP36L1 iCLIP libraries were prepared from OT-I transgenic cytotoxic T lymphocytes, with three biological replicates in control cells, and three biological replicates in Zfp36/Zfp36l1 conditional knockout cells as a negative control.

first: Twm

last: Mitchell

first: Georg

last: Petkau

middle: S

first: Martin

last: Turner


title: RNA sequencing analysis of covR-deficient Streptococcus agalactiae during Zn intoxication

status: Public on Jun 01 2021

city: Gold Coast

first: Glen

last: Ulett

state: QLD

address: Parklands Drive

department: School of Medical Science

country: Australia

institute: Griffith University

summary: Total RNA was isolated from mid-log phase Streptococcus agalactiae cells deficient in CovR (∆covR strain GU2400), grown in Todd-Hewitt broth (THB) medium, supplemented with 0.25 mM Zn and sequenced using Illumina NextSeq500

overall_design: Four biological replicate cultures of S. agalactiae deficient in CovR (∆covR strain GU2400) were grown in THB + 0.25 mM Zn.


title: Gene Expression Profiling of Mismatch Repair Deficient Intestinal Stem Cells

city: Houston

first: Eduardo

last: Vilar-Sanchez

address: 1515 Holcombe Blvd, Unit 1360

institute: UT MD Anderson Cancer Center

summary: We have generated a gene signature of mismatch repair (MMR) deficient intestinal stem cells (ISCs) using whole-genome transcriptomics and proteomics from murine intestinal stem cells and epithelial non-stem cells in a Lynch syndrome mouse model (Msh2-fl/fl;Villin-Cre). Then we have validated this signature in RNA-seq data from LS normal unaffected mucosa (UM), adenomas (AD) and adenomas with high-grade dsyplasia (AD-HGD) and tumors (T). MMR status for LS tumors and adenomas with high-grade dysplasia was categorized as KO, for unaffected mucosa as HET and FAP samples as WT.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: We have performed mRNAseq using Illumina Hi-Seq in 3 mouse per genotype (9 total) and sequenced them in triplicated (total number of samples 18). 17 patients with FAP as controls (7 paired adenoma/mucosa samples and 10 unmatched normal mucosas) and 30 patients with LS (7 macthed tumor/adenomas with high-grade dysplasia and normal mucosa and 23 with normal mucosa only).

last: Vilar


title: Riluzole administration to rats with levodopa-induced dyskinesia analyzed by RRBS

status: Public on Jun 03 2021

city: Budapest

first: Ábel

last: Fóthi

state: Please Select

address: Magyar Tudosok korutja 2.

country: Hungary

institute: Institute of Enzymology, RCNS

summary: Dyskinesias are characterized by abnormal repetitive involuntary movements due to dysfunctional neuronal activity. Although levodopa-induced dyskinesia, characterized by tic-like abnormal involuntary movements, has no clinical treatment for Parkinson’s disease patients, animal studies indicate that Riluzole, which interferes with glutamatergic neurotransmission, can improve the phenotype. The rat model of levodopa-induced dyskinesia is a unilateral lesion with 6-hydroxydopamine in the medial forebrain bundle, followed by the repeated administration of levodopa. The molecular pathomechanism of levodopa-induced dyskinesia is still not deciphered, however implication of epigenetic mechanisms was suggested. In this study, we investigated the striatum for DNA methylation alterations under chronic levodopa treatment with or without co-treatment with Riluzole. Our data show that the lesioned and contralateral striata have nearly identical DNA methylation profiles. Chronic levodopa and levodopa+Riluzole treatments led to DNA methylation loss, particularly outside of promoters, in gene bodies and CpG poor regions. We observed that several genes involved in the levodopa-induced dyskinesia underwent methylation changes. Furthermore, the Riluzole co-treatment, which improved the phenotype, pinpointed specific methylation targets, with more than 20% methylation difference relative to levodopa treatment alone. These findings indicate potential new druggable targets for levodopa-induced dyskinesia.

overall_design: 3 groups of 3 rats after unilateral 6-OHDA lesion and no treatment or L-DOPA treatment or L-DOPA + Riluzole treatment for 2 weeks. Analysis of both striata from each animal.

first: Luca

last: Pagliaroli

first: Abel

last: Fothi

first: Tamas

last: Aranyi


title: RNA sequencing analysis of covR-deficient Streptococcus agalactiae

summary: Total RNA was isolated from mid-log phase Streptococcus agalactiae cells deficient in CovR (∆covR strain GU2400), grown in Todd-Hewitt broth (THB) medium and sequenced using Illumina NextSeq500

overall_design: Four biological replicate cultures of S. agalactiae deficient in CovR (∆covR strain GU2400) were grown in THB.


title: Maternal EHMT2 is essential for homologous chromosome segregation by regulating Cyclin B3 in mouse oocytes

city: Beijing

first: Qingyuan

last: Sun

state: Beijing

address: Beichen West Rd., Chaoyang

department: State Key Laboratory of Stem Cell and Reproductive Biology

institute: Institute of Zoology, Chinese Academy of Sciences

summary: During oocyte growth, various epigenetic modifications gradually establish, accompanying by large amounts of mRNAs and proteins accumulate. However, progress has been slow regarding the relationship between epigenetic modification and meiosis. Here, using Gdf9-Cre to achieve oocyte-specific ablation of Ehmt2 (Euchromatic Histone Lysine Methyltransferase 2) from primordial follicle stage, we found that female mutant mice were infertile and oocyte-specific knockout of Ehmt2 caused the failure of homologous chromosome separation independent of persistently activated SAC during the first meiosis. Further studies revealed that lacking maternal Ehmt2 affected the transcriptional level of Ccnb3, and microinjection of exogenous Ccnb3 mRNA could partly rescue the failure of homologous chromosomes segregation. Of particular importance was that EHMT2 could directly interact with CCNB3, despite truncated the SET domain. Therefore, our findings highlight the novel function of maternal EHMT2 on the metaphase I-to-anaphase I transition in mouse oocyte: directly interacting with CCNB3 apart from regulating the transcription of Ccnb3.

overall_design: DNA methylation sequencing and RNA-sequencing were performed on the Ehmt2 Gdf9-cre deleted  and control group oocytes.

first: Tie-Gang

last: Meng

first: Qing-Yuan


title: KLF4 Recruits SWI/SNF to Increase Chromatin Accessibility and Reprogram the Endothelial Enhancer Landscape under Laminar Shear Stress [RNA-seq siDUSP5]

status: Public on May 28 2021

city: Stanford

first: Jan-Renier

last: Moonen

address: 269 Campus Drive, CCSR 1220

department: Pediatrics

institute: Stanford University

summary: Physiologic laminar shear stress (LSS) induces an endothelial gene expression profile that is vasculo-protective. In this report, we delineate how LSS mediates changes in the epigenetic landscape to promote this beneficial response. We show that under LSS, KLF4 interacts with the SWI/SNF nucleosome remodeling complex to increase accessibility at enhancer sites that promote expression of homeostatic endothelial genes. By combining molecular and computational approaches we discovered enhancers that loop to promoters of known and novel KLF4- and LSS-responsive genes that stabilize endothelial cells and suppress inflammation, such as BMPR2 and DUSP5. By linking enhancers to genes that they regulate under physiologic LSS, our work establishes a foundation for interpreting how non-coding DNA variants in these regions might disrupt protective gene expression to influence vascular disease.

overall_design: For DUSP5 loss-of-function,  pulmonary artery endothelial cells (PAEC) were treated with siRNA targeting DUSP5 (siDUSP5), or non-targeting controls (siC). 24 h post transfection, cells were exposed to 15 dyn/cm2 of LSS.

first: James

last: Chappell

first: Michael

last: Snyder

first: Marlene

last: Rabinovitch


title: Microbes Malnutrition Microglia

status: Public on May 31 2021

city: Vancouver

first: Kylynda

last: Bauer

state: BC

address: #301 – 2185 East Mall

institute: Michael Smith Laboratories

summary: This study examines the role of early exposure to gut microbes and poor diet on microglial function in mice. Groups = control (CON), malnourished (MAL), and malnourished + microbial exposure (E/MALBG).  CD11b+ cells (microglial enrichment) were isolated from whole mouse brains (Adult Brain Disruption Kit, Miltenyi Biotec). After sample quality control (Agilent 2100 Bioanalyzer), qualifying samples were sent for RNA-Seq (Illumina NextSeq 500 with Paired End 42bp × 42bp reads; demultiplexed: Illumina's bcl2fastq2). Following alignment against mouse reference genes (STAR aligner), DEG analyses was conducted using the DESeq2 pipeline.

overall_design: RNA-Seq from Cd11b+ brain cells

first: B

middle: B

last: Finlay

first: Amy

last: Lee

first: Robert

last: Hancock


title: KLF4 Recruits SWI/SNF to Increase Chromatin Accessibility and Reprogram the Endothelial Enhancer Landscape under Laminar Shear Stress [RNA-seq caMEK5]

overall_design: For KLF gain-of-function, pulmonary artery endothelial cells (PAEC) were transduced with adenoviral vectors encoding a constitutively active mutant of MEK5, or GFP as control (n=3 experimental replicates). 90h post-transduction cells were washed with PBS and lysed for RNA extraction.


title: Bidirectional genome-wide CRISPR screens reveal host factors regulating SARS-CoV-2,  MERS-CoV and seasonal HCoVs

first: John

last: Doench

state: MA

address: 75 Ames St.

department: Genetic Perturbation Platform

institute: Broad Institute

type:
Other
Third-party reanalysis

summary: Several genome-wide CRISPR knockout screens have been conducted to identify host factors regulating SARS-CoV-2 replication, but the models used have often relied on overexpression of ACE2 receptor and didn’t express TMPRSS2 protease, known to be important for viral entry at the plasma membrane. Here, we conducted a meta-analysis of these screens and showed a high level of cell-type specificity of the identified hits, arguing for the necessity to pursue efforts to uncover the full landscape of SARS-CoV-2 regulators. We performed genome-wide, bidirectional CRISPR screens in Calu-3 lung epithelial cells, as well as knockout screens in Caco-2 intestinal cells. As well as identifying ACE2 and TMPRSS2 as top hits, our study reveals a series of so far unidentified and critical host-dependency factors, including the Adaptins AP1G1 and AP1B1 and the flippase ATP8B1. Additionally, new anti-SARS-CoV-2 proteins with potent activity, including several membrane-associated Mucins (MUC1, MUC4 and MUC21), IL6R and CD44 were identified . We further observed that these genes mostly acted at the critical step of viral entry, with the notable exception of ATP8B1, the knockout of which prevented late stages of viral replication. Exploring the pro- and anti-viral breadth of these genes using highly pathogenic MERS-CoV, seasonal HCoV-NL63 and -229E and influenza A virus, we reveal that some genes such as AP1G1 and ATP8B1 are general coronavirus cofactors. In contrast, Mucins recapitulated their known role as a general antiviral defense mechanism. These results demonstrate the value of considering multiple cell models and perturbational modalities for understanding SARS-CoV-2 replication and provide a list of potential new targets for therapeutic interventions.

sample_organism:
Homo sapiens
Chlorocebus sabaeus

platform_organism:
Homo sapiens
Chlorocebus sabaeus

overall_design:
32 samples analyzed (24 generated by this study (raw+processed data) and 8 by the other studies mentioned (only processed data), Control named: initial population, Selected population named: resistant population, replicates are included and mentionned below
We re-analyzed 8 genome-wide CRISPR screens using SARS-CoV-2 conducted by groups outside of ours for comparison purposes. 6 of these 8 screens are published, while the 2 screens from the Hsu lab have been released as a pre-print.  The authors of the corresponding manuscripts generously provided raw read count data for this meta-analysis, and we will refer to screens by the senior author of the manuscript. The same data processing pipeline was applied to each screen, which has been detailed in the "Data Processing" section below. For each screen, the control population refers to the uninfected population, while the experimental population refers to the samples infected with SARS-CoV-2. If there were multiple replicates of infected populations, they were averaged for the final processed z-score.

Reanalyzed datasets:
Wei et al., 2021: (Senior author: Wilen) ;  Title: Genome-wide CRISPR Screens Reveal Host Factors Critical for SARS-CoV-2 Infection;  Cell line: Vero E6;  Screen type: Knockout (KO);  SARS-CoV-2 strain: USA-WA1/2020;  Library: C. sabeus;  CRISPR screen raw data location: available with paper
Daniloski et al., 2021: (Senior author: Sanjana) ;  Title: Identification of Required Host Factors for SARSCoV-2 Infection in Human Cells;  Cell line: A549 (ACE2);  Screen type: Knockout (KO);  SARS-CoV-2 strain: USA-WA1/2020;  Library: GeCKOv2;  CRISPR screen raw data location: GEO (GSE158298)
Zhu et al., 2021: (Senior author: Zhang) ;  Title: A genome-wide CRISPR screen identifies host factors that regulate SARS-CoV-2 entry;  Cell line: A549  (ACE2);  Screen type: Knockout (KO);  SARS-CoV-2 strain: nCoV-SH01;  Library: Brunello;  CRISPR screen raw data location: available with paper
Wang et al., 2021: (Senior author: Puschnik)   Title: Genetic Screens Identify Host Factors for SARSCoV-2 and Common Cold Coronaviruses  Cell line: Huh-7.5.1-ACE2-TMPRSS2  Screen type: Knockout (KO)  SARS-CoV-2 strain: USA-WA1/2020  Library: GeCKOv2  CRISPR screen raw data location: EMBL-EBI ArrayExpress (E-MTAB-9638)
Schneider et al., 2021: (Senior author: Poirier)   Title: Genome-Scale Identification of SARS-CoV-2 and Pan-coronavirus Host Factor Networks  Cell line: Huh-7.5  Screen type: Knockout (KO)  SARS-CoV-2 strain: USA-WA1/2020  Library: Brunello  CRISPR screen raw data location: GEO (GSE162038)
Baggen et al., 2021: (Senior author: Daelemans)   Title: Genome-wide CRISPR screening identifies TMEM106B as a proviral host factor for SARS-CoV-2  Cell line: Huh-7  Screen type: Knockout (KO)  SARS-CoV-2 strain: Belgium/GHB-  03021/2020  Library: Brunello  CRISPR screen raw data location: SRA (SRR13255539, SRR13255540, SRR13255541, SRR13255542, SRR13255543, SRR13255544, SRR13255545, SRR13255546, SRR13255547)
Biering et al., 2021: (Senior author: Hsu) ;  Title: Genome-wide, bidirectional CRISPR screens identify mucins as critical host factors modulating SARS-CoV-2 infection;  Cell line: Calu-3;  Screen type: Knockout (KO);  SARS-CoV-2 strain: USA-WA1/2020;  Library: Brunello;  CRISPR screen raw data location: not yet published
Biering et al., 2021: (Senior author: Hsu) ;  Title: Genome-wide, bidirectional CRISPR screens identify mucins as critical host factors modulating SARS-CoV-2 infection;  Cell line: Calu-3;  Screen type: Activation;  SARS-CoV-2 strain: USA-WA1/2020;  Library: Calabrese Set A;  CRISPR screen raw data location: not yet published

first: Antoine

last: Rebendenne

first: Priyanka

last: Roy

first: Ana

last: Valadao

first: Yenarae

first: Peter

last: DeWeirdt

first: Mudra

last: Hegde

first: Caroline

last: Goujon


title: KLF4 Recruits SWI/SNF to Increase Chromatin Accessibility and Reprogram the Endothelial Enhancer Landscape under Laminar Shear Stress [HiCHIP]

overall_design: PAEC were exposed to 15 dyn/cm2 of LSS for 24h and compared to PAEC cultured under static conditions. HiChIP was performed as previously described (Mumbach et al. Nat Methods. 2016) using 1000,000 cells.


title: The LysR-type transcriptional regulator BsrA (PA2121) is engaged in the control of vital metabolic pathways in Pseudomonas aeruginosa (RNA-seq)

status: Public on Jun 17 2021

city: Warszawa

first: Adam

last: Kawałek

address: Pawinskiego 5A

department: Department of Microbial Biochemistry

country: Poland

institute: Institute of Biochemistry and Biophysics, PAS

summary: Pseudomonas aeruginosa, a facultative human pathogen causing nosocomial infections, has complex regulatory systems involving many transcriptional regulators. The LTTR family (LysR-Type Transcriptional Regulators) consists of proteins involved in regulation of various processes including stress response, motility, virulence or amino acid metabolism. The aim of this study was characterization of the LysR-type regulator BsrA (PA2121), identified previously as a negative regulator of biofilm formation in P. aeruginosa. To identify the BsrA binding sites in P. aeruginosa the ChIP-seq analysis was performed. It revealed 765 BsrA binding sites in P. aeruginosa PAO1161 genome, among them 367 was localized in the intergenic regions. Parallel transcriptomic analysis identified altered expression of 157 genes in response to BsrA excess, among them 35 had a BsrA binding site in the corresponding promoter regions, indicating direct influence of BsrA on expression of these genes. BsrA-repressed loci encompass genes encoding proteins engaged in key metabolic pathways including the tricarboxylic acid cycle. A group of directly activated genes by BsrA, consists of several loci encoding proteins involved in pili/fimbriae assembly as well as secretion and transport systems. Results also confirmed that BsrA acts as an autorepressor. Presented data uncover the regulon of BsrA protein with its role as transcriptional regulator of genes engaged in vital cellular processes in P. aeruginosa.

overall_design: Pseudomonas aeruginosa PAO1161 (leu-, r-, RifR) derivative of PAO1 was used in the experiment (Kawalek et al., 2020; BMC Genomics, 21:14). To determine the impact of an increased BsrA level on the transcriptome, the RNA-seq analysis was performed on RNA isolated from Pseudomonas aeruginosa PAO1161/pMEB63 (lacIQ-tacp-bsrA) cultures grown under selection in L broth with 0.05 mM IPTG (hereafter referred to as BsrA) as well as from Pseudomonas aeruginosa PAO1161 carrying pAMB9.37 (lacIQ-tacp) cells grown under selection in L broth with 0.05 mM IPTG (empty vector control, hereafter called EV). The RNA was isolated from exponentially growing cultures (OD600 0.5). Three independent biological replicates of total RNA were isolated for each strain.

first: Magdalena

last: Modrzejewska

last: Kawalek

first: Aneta

middle: A

last: Bartosik


title: KLF4 Recruits SWI/SNF to Increase Chromatin Accessibility and Reprogram the Endothelial Enhancer Landscape under Laminar Shear Stress [RNA-seq LSS]

first: Jan-Renier

last: Moonen

overall_design: PAEC were exposed to 15 dyn/cm2 of LSS, or static conditions, for 24 h. Gene expression was analyzed by RNA-Seq.

first: James

last: Chappell

first: Michael

last: Snyder


title: KLF4 Recruits SWI/SNF to Increase Chromatin Accessibility and Reprogram the Endothelial Enhancer Landscape under Laminar Shear Stress [ChIP-seq KLF & histone marks]

overall_design: For KLF gain-of-function, pulmonary artery endothelial cells (PAEC) were transduced with adenoviral vectors encoding a constitutively active mutant of MEK5, or GFP as control, (n=2 experimental replicates), 90h post-transduction, cells were fixed and prepared for ChIP-Seq for H3K4me1, H3K27ac, KLF4 and BRG1.

first: Marlene

last: Rabinovitch


title: KLF4 Recruits SWI/SNF to Increase Chromatin Accessibility and Reprogram the Endothelial Enhancer Landscape under Laminar Shear Stress [RNA-seq siKLF]

overall_design: For KLF loss-of-function, pulmonary artery endothelial cells (PAEC) were treated with siRNA targeting KLF2 and KLF4 (siKLF), or non-targeting controls (siC). 24 h post transfection, cells were exposed to 15 dyn/cm2 of LSS for 24h.


title: KLF4 Recruits SWI/SNF to Increase Chromatin Accessibility and Reprogram the Endothelial Enhancer Landscape under Laminar Shear Stress [ATAC-seq caMEK5]

overall_design: For KLF gain-of-function, pulmonary artery endothelial cells (PAEC) were transduced with adenoviral vectors encoding a constitutively active mutant of MEK5, or GFP as control (n=3 experimental replicates). ATAC-seq was performed as previously described (Buenrostro et al. Nat Methods. 2013) using 100,000 cells and 5 ul of TDE1 (Nextera Tn5 transposase, Illumina).


title: KLF4 Recruits SWI/SNF to Increase Chromatin Accessibility and Reprogram the Endothelial Enhancer Landscape under Laminar Shear Stress

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

overall_design: Refer to individual Series


title: KLF4 Recruits SWI/SNF to Increase Chromatin Accessibility and Reprogram the Endothelial Enhancer Landscape under Laminar Shear Stress [ATAC siKLF]

overall_design: For KLF loss-of-function,  pulmonary artery endothelial cells (PAEC) were treated with siRNA targeting KLF2 and KLF4 (siKLF), or non-targeting controls (siC). 24 h post transfection, cells were exposed to 15 dyn/cm2 of LSS for 24h.


title: KLF4 Recruits SWI/SNF to Increase Chromatin Accessibility and Reprogram the Endothelial Enhancer Landscape under Laminar Shear Stress [ATAC-seq LSS]

overall_design: PAEC were exposed to 15 dyn/cm2 of LSS for 24h and compared to PAEC cultured under static conditions. ATAC-seq was performed as previously described (Buenrostro et al. Nat Methods. 2013) using 100,000 cells and 5 ul of TDE1 (Nextera Tn5 transposase, Illumina).


title: RNA sequencing analysis of CopY-deficient Streptococcus agalactiae

first: Glen

last: Ulett

summary: Total RNA was isolated from mid-log phase Streptococcus agalactiae cells deficient in CopY (∆copY strain GU2857), grown in Todd-Hewitt broth (THB) medium and sequenced using Illumina NextSeq500.

overall_design: Four biological replicate cultures of S. agalactiae deficient in CopY (∆copY strain GU2857) were grown in THB.


title: KLF4 Recruits SWI/SNF to Increase Chromatin Accessibility and Reprogram the Endothelial Enhancer Landscape under Laminar Shear Stress [ChIP-seq BRG1]


title: RNA sequencing analysis of Streptococcus agalactiae 874391 (wild-type) during Zn intoxication

status: Public on May 11 2021

summary: Total RNA was isolated from mid-log phase Streptococcus agalactiae 874391 wild-type cells grown in Todd-Hewitt broth (THB) medium supplemented with 0.25 mM Zn and sequenced using Illumina NextSeq500.

overall_design: Four biological replicate cultures of S. agalactiae 874391 (wild type) were grown in THB + 0.25 mM Zn.


title: Adaptation to chronic ER stress enforces pancreatic beta-cell plasticity

status: Public on May 20 2021

city: Cleveland

first: Chien-Wen

last: Chen

state: OH

address: 2109 Adelbert Road

department: Genetics and Genome Sciences

institute: Case Western Reserve University

summary: The next-generation-sequencing (NGS) of ribosome footprintings and poly(A) enriched RNA-seq have been proformed to examine transcriptional and translational changes in an mouse insulinoma cell MIN6 under acute and chronic endoplasmic reticular stresses.

overall_design: Mouse insulinoma cell MIN6 treated with 200uM of Cyclopiazonic acid for 1 (CPA1) and 18 hours (CPA18). An 18 hour DMSO treatment served as the control (CPA0). Ribo-seq and poly(A) enriched RNA-seq (mRNA-seq) have been proformed. Three independent biological replications were proformed.

first: Maria

last: Hatzoglou


title: Mapping Transcription Factor Nucleosome Dynamics in Plasma

status: Public on May 24 2021

city: Aurora

first: Satyanarayan

last: Rao

state: CO

address: 12801 E 17th Ave, RC1 South

department: Biochemistry and Molecular Genetics

institute: University of Colorado, Denver | Anschutz Medical Campus

summary: Cell-free DNA (cfDNA) contains a composite map of the epigenomes of its cells-of-origin. Tissue-specific TF binding inferred from cfDNA could enable us to track disease states in humans in a non-invasive manner. Here, we present a method to identify the subset of genome-wide transcription factor binding sites that are protected in plasma. We map binding at tissue-specific sites of constitutive factor CTCF and tissue-specific factors PU.1, LYL1, ER, and FOXA1 in plasma cfDNA. Our method also captures the chromatin structure around the factor-bound sites in their cells-of-origin. We define pure tumor TF signatures in an in vivo model by applying our method to estrogen receptor-positive (ER+) breast cancer xenografts. The tumor-specific cfDNA protections of ER-α and FOXA1 reflect TF-specific accessibility across human breast tumors, demonstrating our ability to capture tumor TF binding in plasma. By modeling cfDNA from cancer donors as a mixture of healthy plasma and pure tumor signatures, we can identify tumor TF binding in humans. Thus, our method enables non-invasive mapping of the regulatory phenotype of cancer in humans.

overall_design: sequencing of cell-free DNA extracted from plasma

first: Alexis

last: Zukowski

first: Amy

last: Han

first: Etatna

last: Kopin

first: Carol

last: Sartorius

last: Kabos

first: Srinivas

last: Ramachandran


title: A diet-induced type 2 diabetes model in Drosophila

status: Public on May 17 2021

city: Hangzhou

first: Danping

state: Zhejiang

address: 866 Yuhangtang Rd

institute: Zhejiang Univerisity

summary: We showed in this present study that HSD feeding could induce type 2 diabetes-like phenotype in fruit flies, resembling the key disease features including hyperglycemia, glucosuria, increased hunger and thirsty, unexplained weight loss, and reduced female fecundity. We also showed that HSD-fed flies shared similar molecular mechanisms underlying type 2 diabetes patients, including both insulin deficiency and insulin resistance. Last but not least, disrupting insulin signaling in fruit flies could mimic the effect of HSD feeding to induce type 2 diabetes-like phenotype, further confirming that these phenotypes were a result of compromised insulin signaling upon HSD feeding. Taken together, we demonstrated that this diet-induced type 2 diabetes model in fruit flies rightly and comprehensively recapitulated the physiological, metabolic, behavioral, and molecular features of human type 2 diabetes, offering a valid and accessible model to study the underlying mechanism of this disease and to validate potential diagnostics and therapeutic tools. Given the highly conserved regulatory framework of physiology and metabolism between flies and human, our work has paved a way to generate novel insights into type 2 diabetes, a common, severe, and yet poorly understood disease in human.

overall_design: Total RNA from fly brains or fat body was extracted from 5-day-old female flies using the RNeasy Mini kit (Qiagen, Germany), subjected to poly(A) mRNA isolation, cDNA synthesization, library preparation (NEBNext Ultra RNA Library Prep Kit, NEB), and sequencing (Illumina Hiseq X Ten). Sequence data were subsequently mapped to Drosophila genome and uniquely mapped reads were collected for further analysis. Gene expression was calculated by the RPKM (Reads Per Kilobase of exon per Million reads mapped). The genes with p-value less 0.05 and fold change more than 1 were considered as the differentially expressed gene.

first: Chen

last: Danping

first: Wang

last: Liming


title: Integrated chromatin accessibility and transcriptome landscapes of doxorubicin-resistant breast cancer cells

status: Public on May 12 2021

city: Shanghai

first: Xuelong

last: Wang

address: No. 100 Banxia Road

institute: Chinese Academy of Sciences

summary: Doxorubicin is considered to be the most effective chemotherapeutic drug used to treat breast cancer. Unfortunately, resistance to this drug is common, resulting in poor patient prognosis and survival. Dynamically reorganized chromatin allows rapid access of the gene regulatory machinery to open genomic regions facilitating subsequent gene expression through direct transcription factor (TF) activation and regulatory element binding. To better understand the regulatory network underlying doxorubicin resistance in breast cancer cells, we explored the systematic alterations of chromatin accessibility and gene expression by the assay for transposase-accessible chromatin using sequencing (ATAC-seq) in combination with RNA sequencing, followed by integrative analysis to identify potential regulators and their targets associated with differentially accessible regions (DARs) in doxorubicin-resistant MCF7 (MCF7-DR) cells. A total of 3963 differentially expressed genes (DEGs) related to doxorubicin resistance were identified, including dramatically up-regulated MT1E, GSTP1, LDHB, significantly down-regulated TFF1, UBB, DSCAM-AS1, and histone-modifying enzyme coding genes HDAC2, EZH2, PRMT5, etc. By integrating with transcriptomic datasets, we identified 18,228 DARs in MCF7-DR cells compared to control, which were positively (r = 0.6) correlated with their nearest DEGs. There were 11,686 increased chromatin-accessible regions, which were enriched in up-regulated genes related to diverse KEGG pathways, such as the cell cycle, regulation of actin cytoskeleton, signaling pathways of MAPK, PI3K/Akt and Hippo, which play essential roles in regulating cell apoptosis, proliferation, metabolism, and inflammatory responses. The 6,542 decreased chromatin-accessible regions were considered to be related to declined doxorubicin-associated biological processes, for instance, endocrine and insulin resistance, central carbon metabolism, signaling pathways of TGF-beta and P53. Analyses of the DAR sequences showed that, besides the AP-1 family, TEAD and FOX family TF DNA-binding motifs were highly enriched in hyper- and hypo-accessible regions respectively. Moreover, critical TFs and their potential targets associated with DARs were identified, such as TEAD1, RUNX1, GRHL2 and FOXA1. In addition, we put forward that the loss of FOXA1/GRHL2 collaboration might be responsible for acquired resistance to doxorubicin in breast cancer. These data provided clear insights and resources for an improved understanding of the non-genetic landscape of doxorubicin-resistant breast cancer cells based on chromatin accessibility and transcript levels, which allowed for detection of critical TFs, potential cis-regulatory elements, and therapeutic targets.

overall_design: Genome-wide profiling of chromatin accessibility and gene expression in parental and doxorubicin-resistant breast cancer cells. In total, 8 samples were analyzed. RNA-seq_MCF7_1 and RNA-seq_MCF7_2 were two biological replicates and served as the control group. RNA-seq_MCF7-DR_1 and RNA-seq_MCF7-DR_2 were two biological replicates and served as the treatment group. ATAC-seq_MCF7_1 and ATAC-seq _MCF7_2 were two biological replicates and served as the control group. ATAC-seq_MCF7-DR_1 and ATAC-seq_MCF7-DR_2 were two biological replicates and served as the treatment group.


title: RNA sequencing analysis of Streptococcus agalactiae 874391 (wild-type)

summary: Total RNA was isolated from mid-log phase Streptococcus agalactiae 874391 wild-type cells grown in Todd-Hewitt broth (THB) medium and sequenced using Illumina NextSeq500

overall_design: Four biological replicate cultures of S. agalactiae 874391 (wild type) were grown in THB.


title: RNA-seq analysis of archived blood from common bottlenose dolphin health assessments in the northern Gulf of Mexico

status: Public on May 04 2021

city: Johns Island

first: Jeanine

last: Morey

state: SC

address: 3419 Maybank Hwy, Ste B

department: Conservation Medicine

institute: National Marine Mammal Foundation

summary: Archived blood samples collected during common bottlenose dolphin health assessments in the northern Gulf of Mexico from 2013 to 2018 were analyzed by RNA-seq to support and enhance the assessment of animal health.  The transcriptomic data were analyzed in conjunction with the substantial pool of health and environmental data collected during health assessments to investigate the utility of transcriptomic data in overall assessment of dolphin health and/or as markers of specific health concerns.

overall_design: Illumina based RNA-seq analyses were carried out on RNA extracts of whole blood from 76 archived samples using the Tursiops truncatus NIST Tur_tru v1 genome as a guide.  Samples were collected in Barataria Bay, LA (n=60) or Sarasota Bay, FL (n=16) from 2013-2018.   Samples from Sarasota Bay served as a reference population that had not been exposed to substantial oil, whereas the samples from Barataria Bay come from a population directly impacted by the Deepwater Horizon oil spill.

first: Lori

middle: H

last: Schwacke

first: Randy

last: Wells


title: Effect of Disease and Exercise in Skeletal Muscle of Patients with Peripheral Artery Disease

status: Public on Apr 30 2021

city: Boston

first: Grace

last: Daher

address: 1 Joslin Place

institute: Joslin Diabetes Center

summary: PAD is associated with reduced uptake of glucose and insulin resistance in skeletal muscle. In this study, we look at the effect of exercise on gene expression in patients with PAD.

overall_design: Two types of patients were recruited for this study: patients with peripheral arterial disease (PAD) and healthy patients without the disease. Healthy patients were measured only once. PAD patients were measured twice: once at baseline, then a second time after each patient was randomly administered one of two treatments, exercise or control.  The age of healthy patients was also recorded, as greater than or less than 50 year of age.

first: Caitlin

last: Parmer

first: Ana

last: De Sousa-Coelho

first: Alison

last: Burkart

first: Jonathan

last: Dreyfuss

first: Hui

last: Pan

first: Joshua

last: Prenner

first: Jessica

last: Milian

first: Reena

last: Pande

first: Mary

last: Patti

first: Mark

last: Creager


title: Induction of a colitogenic phenotype in Th1-like cells depends on interleukin-23 receptor signaling [in vivo]

status: Public on May 01 2021

city: Berkeley

first: David

last: DeTomaso

address: Stanley Hall

department: Computational Biology

institute: UC Berkeley

summary: Th1 cells were adoptively transferred into RAG1 KO mice from either wildtype (Il23rwt/eGFP) or KO (Il23reGFP/eGFP) donors. At the peak of disease in recipients of wildtype cells, the animals were euthanized and intestinal T cells were isolated from the chosen recipients of both wildtype and KO cells for 10x massively parallel single-cell RNA-sequencing.

overall_design: From both recipients of wildtype (Il23rwt/eGFP) or KO (Il23reGFP/eGFP) Th1 cells the following tissues were isolated for single-cell RNA sequencing: spleen, small intestine lamina propria (LPL), colon LPL and colon intraepithelial lymphocytes (IEL).

first: Mathias

last: Pawlak

first: Gerd

last: Meyer zur Hoerste

first: Jackson

last: Nyman

first: Danielle

last: Dionne

first: Chao

first: Antonia

last: Wallrapp

first: Patrick

last: Burkett

first: Samantha

last: Riesenfeld

first: Anna

last: Kohl

first: Ramnik

last: Xavier

last: Anderson

first: Aviv

last: Regev

first: Nir

last: Yosef

first: Vijay

middle: K

last: Kuchroo


title: Induction of a colitogenic phenotype in Th1-like cells depends on interleukin-23 receptor signaling