title: The NAC transcription factor FaRIF controls fruit ripening in strawberry

status: Public on Feb 20 2021

city: Málaga

first: David

last: Posé

address: Avenida Louis Pasteur, 49

country: Spain

institute: Instituto de Hortofruticultura Subtropical y Mediterránea

summary: In contrast to climacteric fruits such as tomato, the knowledge on key regulatory genes controlling the ripening of strawberry, a non-climacteric fruit, is still limited. NAC transcription factors mediate different developmental processes in plants. Here, we identified and characterized FaRIF (Ripening Inducing Factor), a NAC transcription factor that is highly expressed and induced in strawberry receptacles during ripening. Functional analyses based on stable transgenic lines aimed at silencing FaRIF by RNA interference, either from a constitutive promoter or the ripe receptacle-specific EXP2 promoter, as well as overexpression lines showed that FaRIF controls critical ripening-related processes such as fruit softening and pigment and sugar accumulation. Physiological, metabolome and transcriptome analyses of receptacles of FaRIF-silenced and overexpression lines point to FaRIF as a key regulator of strawberry fruit ripening from early developmental stages, controlling abscisic acid (ABA) biosynthesis and signaling, cell wall degradation and modification, the phenylpropanoid pathway, volatiles production, and the balance of the aerobic/anaerobic metabolism. FaRIF is therefore a target to be modified/edited to control the quality of strawberry fruits.

overall_design: Transcriptome analysis from strawberry receptacles from control and 35Spro:FaRIF-RNAi #3 and 35Spro:FaRIF-RNAi #11 transgenic lines at the white and red stages or ripening, and from receptacles of control and EXP2pro:FaRIF-RNAi #1, EXP2pro:FaRIF-RNAi #7 and 35Spro:FaRIF #1 at the red stage. Three biological replicates of each sample was analyzed.

first: Carmen

last: Martín-Pizarro

first: José

middle: G

last: Vallariino

first: Sonia

last: Osorio

first: Victoriano

last: Meco

first: María

last: Urrrutia

first: Jeremy

last: Pillet

first: Ana

last: Casañal

first: Catharina

last: Merchante

first: Iraida

last: Amaya

first: Lothar

last: Willmitzer

first: Alisdair

last: Fernie

first: James

middle: J

last: Giovannoni

first: Miguel

last: Botella

last: Valpuesta


title: The Rhesus Macaque serves a model for Human Lateral Branching Nephrogenesis

status: Public on Feb 18 2021

city: Cincinnati

first: Nathan

last: Salomonis

state: OH

address: 3333 Burnet Avenue

department: Biomedical Informatics

country: USA

institute: Cincinnati Children's Hospital

type: Expression profiling by high throughput sequencing

summary: Infants born prematurely are at increased risk for chronic kidney disease and end stage renal disease later in life due to low nephron number. The mechanism of how nephrons are formed during late-gestation human kidney development is not known, and direct study of human fetal kidney development is fraught with moral and technical difficulties. In this study, the rhesus macaque kidney was identified to be morphologically similar to the human kidney during late-gestation. The preliminary findings support that kidney progenitor cells age over time and are different from the progenitor cells early in gestation. The non-human primate model could bridge the gap for molecular study of late-gestation human kidney development to ultimately improve nephron numbers in preterm infants.

overall_design: The morphology of third trimester rhesus kidneys was assessed by immunostaining, clearing, and 3D rendering. Single-cell RNA sequencing (scRNA-seq) and single-nucleus RNA sequencing (snRNA-seq) were performed on four cortically enriched fetal rhesus kidneys 129-131 days gestational age (GA) using cold protease digestion and 10xGenomics platform.

first: Meredith

middle: P

last: Schuh

first: Andrew

last: Potter

first: Lyan

last: Alkhudairy

first: Thakkar

last: Kairavee

first: Kashish

last: Chetal

first: Steven

first: Raphael

last: Kopan


title: Genome-wide open chromatin analysis of liver sinusoidal endothelial cells in the pathogenesis of NASH

status: Public on Feb 01 2021

city: Rochester

first: Mrunal

middle: Kishor

last: Dehankar

state: MN

address: 200 First St. SW

department: Computational genomics

institute: Mayo Clinic

type: Genome binding/occupancy profiling by high throughput sequencing

summary: We isolated liver sinusoidal endothelial cells (LSEC) from mice fed control chow (Chow) or the nonalcoholic steatohepatitis (NASH)-inducing high fat, fructose and cholesterol (FFC) diet, and subjected the cells to Omni-ATAC-seq. Out of the top 500 differentially abundant open chromatin regions between the two groups, 498 were more robust in FFC-fed mice compared with Chow-fed mice, suggesting a genome-wide active epigenetic regulation in LSEC during NASH development. Furthermore, in combination with RNA-seq, we demonstrated a robust transcriptional upregulation of the adhesion molecule VCAM-1 in LSEC in NASH pathogenesis.

overall_design: Liver sinusodial endothelial cells from NASH and control mice were subjected to Omni-ATAC-seq analysis.

first: Samar

middle: H

last: Ibrahim

first: Kunimaro

last: Furuta

first: Qianqian

last: Guo


title: Genome-wide transcriptome analysis of liver sinusoidal endothelial cells in the pathogenesis of NASH

summary: We isolated liver sinusoidal endothelial cells (LSEC) from mice fed control chow (Chow) or the nonalcoholic steatohepatitis (NASH)-inducing high fat, fructose and cholesterol (FFC) diet, and subjected the cells to bulk RNA-seq. Out of 13993 transcripts detected, the adhesion molecule Vcam1 was significantly upregulated in LSEC from FFC-fed mice compared to Chow-fed mice (Log2FC: 0.925, p: 3.6x10E-18), whereas the upregulation of another adhesion molecule Icam1 (Log2FC: 0.416, p: 0.014) was not as striking as Vcam1.

overall_design: Liver sinusoidial endothelial cells from NASH and control mice were subjected to bulk RNA-seq analysis.

first: Petra

last: Hirsova


title: Human Pluripotent Stem Cell-Derived Kidney Organoids for Modeling Epithelial Transport and Injury

status: Public on Dec 15 2020

city: St. Louis

first: Haojia

last: Wu

state: MO

address: 4523 Clayton Ave, MSB Rm 820

institute: Washington University in St Louis

summary: Maximizing the potential of human kidney organoids for drug testing, regenerative medicine and to model development and disease requires addressing cell immaturity, the lack of a branching collecting system and the off target cell types. Here we establish methods to independently generate the two kidney progenitor cell populations – metanephric mesenchyme and ureteric bud. Combining these two progenitor cell types results in organoids with an improved branched collecting system. We also identified the hormones aldosterone and arginine vasopressin as critical to promote maturation of collecting duct cell types. The resulting organoids contain the full range of epithelial cells in the nephron, including principal and intercalated cells. By scRNA-seq, we demonstrate superior proximal tubule maturation and reduced off-target cell populations using this protocol.

overall_design: Single cell profiling of kidney organoids using 10x Chromium

first: Benjamin

middle: D

last: Humphreys


title: SCL15 is a critical regulator for plant development, germination, seed dormancy and seed vigor in Arabidopsis thaliana

status: Public on Nov 04 2020

city: Saskatoon

first: Dwayne

last: Hegedus

state: SK

address: 107 Science Place

country: Canada

institute: Agriculture and Agri-Food Canada

summary: Seed maturation, dormancy and germination are distinct physiological processes. Transition from maturation to dormancy, and from dormancy into germination are not only critical developmental phases in the plant life cycle but are also important agricultural traits. These developmental processes and their phase transitions are fine determined and coordinately regulated by genetic makeup and environmental cues. SCARECROW-LIKE15 (SCL15) has been demonstrated to be essential for repressing the seed maturation programme in vegetative tissues (Gao et al., Nat Commun, 2015, 6:7243). Here we report that SCL15 is also important for seed dormancy maintenance, germination timing and seed vigor performance based on the effects of SCL15 mutation on plant germination, growth and reproduction when compared with wild type Arabidopsis and over-expression lines 35S:SCL15 and Napin:SCL15. Seed dormancy is enhanced by the mutation of SCL15 in a GA signaling dependent way, indicating that SCL15 plays a negative role for primary dormancy release. Seed germination is positively regulated by SCL15 through interaction with ABA, GA and auxin signaling. SCL15 acts as positive regulator of seed vigor and effect of SCL15 mRNA abundance on seed reserve accumulation and seed development during late embryogenesis may contribute to the seed vigor performance.

overall_design: We compared gene expression in three plant lines:  Wild type, Scl15 knockout, and Scl15 seed-specific overexpression.  For each line we sequenced 3 biological replicates.

first: Ming-Jun

last: Gao

first: Cathy

last: Coutu


title: Single-cell temporal transcriptomics of the human cell cycle

status: Public on Dec 11 2020

city: Solna

first: Emma

last: Lundberg

address: Science for Life Laboratory, Tomtebodavägen 23A

country: Sweden

institute: KTH Royal Institute of Technology

summary: We present the first comprehensive map of spatiotemporal heterogeneity of the human proteome by integrating proteomics at subcellular resolution, single-cell transcriptomics, and pseudotime measurements of each cell within the cell cycle. The cell cycle transcriptomic data in this series provide context for single-cell proteomic measurements of the cell cycle, and this subsequent single-cell proteogenomic analysis that can be found in this code repository: https://github.com/CellProfiling/SingleCellProteogenomics .

overall_design: A total of 1,152 single U2OS FUCCI cells were sorted by FACS, and RNA-Seq was collected for each cell using SMART-seq2 chemistry.

first: Diana

last: Mahdessian

first: Anthony

last: Cesnik

first: Christian

last: Gnann

first: Frida

last: Danielsson

first: Lovisa

last: Stenström

first: Muhammad

last: Arif

first: Cheng

last: Zhang

first: Trang

last: Le

first: Fredric

last: Johansson

first: Rutger

last: Shutten

first: Anna

last: Bäckström

first: Ulrika

last: Axelsson

first: Peter

last: Thul

first: Nathan

last: Cho

first: Oana

last: Carja

first: Mathias

last: Uhlén

first: Adil

last: Mardinoglu

first: Charlotte

last: Stadler

first: Cecilia

last: Lindskog

first: Burcu

last: Ayoglu

first: Manuel

last: Leonetti

first: Fredrik

last: Pontén

first: Devin

last: Sullivan


title: Lung transplantation for patients with severe COVID-19

status: Public on Oct 28 2020

city: Chicago

first: Alexander

middle: V

last: Misharin

state: Illinois

address: 303 E Superior

institute: Northwestern University

summary: Lung transplantation can potentially be a life-saving treatment for patients with non-resolving COVID-19-associated respiratory failure. Concerns limiting transplant include recurrence of SARS-CoV-2 infection in the allograft, technical challenges imposed by viral-mediated injury to the native lung, and potential risk for allograft infection by pathogens associated with ventilator-associated pneumonia in the native lung. Most importantly, the native lung might recover, resulting in long-term outcomes preferable to transplant. Here, we report results of the first successful lung transplantation procedures in patients with non-resolving COVID-19-associated respiratory failure in the United States. We performed sm-FISH to detect both positive and negative strands of SARS-CoV-2 RNA in the explanted lung tissue, extracellular matrix imaging using SHIELD tissue clearance, and single cell RNA-Seq on explant and warm post-mortem lung biopsies from patients who died from severe COVID-19 pneumonia. Lungs from patients with prolonged COVID-19 were free of virus but pathology showed extensive evidence of injury and fibrosis which resembled end-stage pulmonary fibrosis. We used a machine learning approach to project single cell RNA-Seq data from patients with late stage COVID-19 onto a single cell atlas of pulmonary fibrosis, revealing similarities across cell lineages. There was no recurrence of SARS-CoV-2 or pathogens associated with pre-transplant ventilator associated pneumonias following transplantation. Our findings suggest that some patients with severe COVID-19 develop fibrotic lung disease for which lung transplantation is the only option for survival.

overall_design:
Distal lung biopsies were obtained from the explanted lung and donor lung from Case 1, and the two post-mortem biopsies. In addition, a biopsy that included the main left bronchus and distal parenchyma from the upper lobe was obtained from another donor lung that was not placed for transplant. Single-cell suspensions from the biopsies were incubated with CD31 beads, and the positive fraction was selected for single-cell. The negative fraction was FACS-sorted for macrophages, epithelial and stromal cells. Single-cell libraries were prepared with 10x Genomics 3' V3 chemistry. Libraries were pooled and sequenced on Illumina HiSeq 4000 or NovaSeq 6000. Gene expression matrices were generated with 10x cellranger v3.1.0 software using custom reference genome of GRCh38.93 and SARS-CoV-2 (NC_045512.2).
****RNA-Seq raw data will be made available through dbGaP (controlled access) due to patient privacy concerns.

first: Ankit

last: Bharat

first: Melissa

last: Querrey

first: Nikolay

middle: S

last: Markov

first: Samuel

last: Kim

first: Chitaru

last: Kurihara

first: Rafael

last: Garza-Castillon

first: Adwaiy

last: Manerikar

first: Ali

last: Shilatifard

first: Rade

last: Tomic

first: Yuliya

last: Politanska

first: Hiam

last: Abdala-Valencia

first: Anjana

last: Yeldandi

first: Jon

middle: W

last: Lomasney

first: GR

last: Budinger


title: A Phase 2 Randomized Sequence Open Label Expanded Safety and Acceptability Study of Oral Emtricitabine/Tenofovir Disoproxil Fumarate Tablet and Rectally-Applied Tenofovir Reduced-Glycerin 1% Gel

status: Public on Jul 07 2020

city: Seattle

first: Florian

last: Hladik

state: WA

address: 850 Republican Street

department: Obstetrics and Gynecology

institute: University of Washington

summary: Human immunodeficiency virus (HIV) disproportionately affects men who have sex with men (MSM) and transgender women (TGW). Safe and acceptable topical HIV prevention methods that target the rectum are needed. MTN-017 was a phase 2, 3-period, randomized sequence, open-label, expanded safety and acceptability crossover study comparing rectally applied reduced-glycerin (RG) 1% tenofovir (TFV) and oral emtricitabine/TFV disoproxil fumarate (FTC/TDF). In each 8-week study period participants were randomized to RG-TFV rectal gel daily, or RG-TFV rectal gel before and after receptive anal intercourse (RAI; or at least twice weekly in the event of no RAI), or daily oral FTC/TDF. MSM and TGW (n = 195) were enrolled from 8 sites in the United States, Thailand, Peru, and South Africa with mean age of 31.1 years (range 18-64). The clinical results were reported here https://www.ncbi.nlm.nih.gov/pubmed/27986684. For the gene expression study, rectal biopsies were obtained from a subset of participants (n = 36) in the United States (Pittsburgh) and Thailand (Bangkok). Biopsies were provided at baseline and after each study period.

overall_design: MTN-017 was a phase 2, multi-site, randomized, six-sequence, three-period, open-label crossover study. The two products were rectally applied reduced-glycerin (RG) 1% tenofovir (TFV) and oral emtricitabine/TFV disoproxil fumarate (FTC/TDF). The three treatments were RG-TFV gel daily, RG-TFV gel pericoitally, and oral TDF/FTC daily. Rectal biopsies were obtained at baseline and after each treatment period. There were 36 participants and each participant's baseline (pre-treatment) sample was used as a control. Samples were not replicated on the array.

first: Sean

middle: M

last: Hughes

first: Claire

middle: N

last: Levy


title: Cortical RORb is required for layer 4 transcriptional identity and barrel integrity

status: Public on Sep 15 2020

city: Waltham

first: Erin

middle: Amelia

last: Clark

state: MA

address: 415 South St

department: Biology

institute: Brandeis University

summary: RNA-seq and ATAC-seq from layer 4 cortical neurons expressing RORb-gfp or GFP in an RORb KO.

overall_design: RNA-seq and ATAC-seq from FACS isolated neruons. RNA-seq was carried out on ~1000 L4 S1 neurons from mice of different ages (P2, P7, and P30). ATAC-seq was carred out on ~40,000 L4 neurons from P28-P30 mice. All samples were collected from a pool of cells taken from at least 1 male and 1 female.

first: Sacha

last: Nelson

first: Emma

last: Myers

first: Anton

last: Schulmann


title: Whole transcriptome sequencing of 57 laryngeal squamous cell carcinoma and paired adjacent normal tissues

status: Public on Jun 17 2020

city: Taiyuan

first: Yongyan

last: Wu

state: Shanxi

address: No.85 South Jiefang Road, Taiyuan, Shanxi, China

department: Department of Otolaryngology Head & Neck Surgery, The First Hospital

country: China

institute: Shanxi Medical University

summary: Laryngeal squamous cell carcinoma (LSCC) is a common form of head and neck cancer with poor prognosis. However, the mechanism underlying the pathogenesis of LSCC remains unclear. We performed high throughout transcriptome sequencing to identify lncRNA and mRNA that associated with LSCC progression.Transcriptome sequencing were performed on a cohort of LSCC tissues (57 samples) and paired adjacent normal mucosa tissues (57 samples).

overall_design: Expression of lncRNA and mRNA in 57 LSCC and 57 paired adjacent normal mucosa tissues was examination by high throughout sequencing.

first: Wei

last: Gao

first: Binquan

last: Wang

first: Qinli

last: Zhao


title: Single-cell RNA-sequencing of adult human prostates and urethra (normal and diseased)

status: Public on Apr 30 2020

city: Dallas

first: Gervaise

middle: H.

last: Henry

state: Texas

address: 5323 Harry Hines Blvd, Mail Code:9110

department: Urology

institute: UT Southwestern Medical Center

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

overall_design: Refer to individual Series


title: Single-cell RNA-sequencing of adult human prostates from organ donors

status: Public on Apr 28 2020

summary: Single-cell RNA-sequencing was conducted on heterogeneous human prostates FACS sorted for viability from organ donors (with no known prostatic diseases) on the 10x Genomics platform.

overall_design: Fresh human prostate specimens were digested into single-cell suspensions, cells were subject to single-cell RNA-sequencing using the 10x Genomics platform.

first: Douglas

last: Strand


title: Characterizing pancreatic β-cell heterogeneity in the streptozotocin model by single-cell transcriptomic analysis

status: Public on Apr 23 2020

city: Beijing

first: Cheng-ran

last: Xu

address: NO.5 YIHEYUAN ROAD HAIDIAN DISTRICT, BEIJING, P.R.CHINA

department: School of Basic Medical Sciences

institute: Peking University

summary:
Objectives
The streptozotocin (STZ) model is widely used in diabetes research. However, the cellular and molecular states of pancreatic endocrine cells in this model remain unclear. This study explored the molecular characteristics of islet cells treated with STZ and re-evaluated β-cell dysfunction and regeneration in the STZ model.

Methods
We performed single-cell RNA sequencing of pancreatic endocrine cells from STZ-treated mice. High-quality sequencing data from 2,999 cells were used to identify clusters via Louvain clustering analysis. Principal component analysis (PCA), t-distributed stochastic neighbor embedding (t-SNE), uniform manifold approximation and projection (UMAP), force-directed layout (FDL), and differential expression analysis were used to define the heterogeneity and transcriptomic changes in islet cells. In addition, qPCR and immunofluorescence staining were used to confirm findings from the sequencing data.

Results
Untreated β-cells were divided into two populations at the transcriptomic level, a large high-Glut2 expression (Glut2high) population and a small low-Glut2 expression (Glut2low) population. At the transcriptomic level, Glut2low β-cells in adult mice did not represent a developmentally immature state, although a fraction of genes associated with β-cell maturation and function were downregulated in Glut2low cells. After a single high-dose STZ treatment, most Glut2high cells were killed, but Glut2low cells survived and over time changed to a distinct cell state. We did not observe conversion of Glut2low to Glut2high β-cells up to 9 months after STZ treatment. In addition, we did not detect transcriptomic changes in the non-β endocrine cells or a direct trans-differentiation pathway from the α-cell lineage to the β-cell lineage in the STZ model.

Conclusions
We identified the heterogeneity of β-cells in both physiological and pathological conditions. However, we did not observe conversion of Glut2low to Glut2high β-cells, transcriptomic changes in the non-β endocrine cells, or direct trans-differentiation from the α-cell lineage to the β-cell lineage in the STZ model. Our results clearly define the states of islet cells treated with STZ and allow us to re-evaluate the STZ model widely used in diabetes studies.

overall_design: To explore the transcriptomic status of individual pancreatic endocrine cells in STZ-treated mice, we isolated cells from STZ-treated mice by fluorescence-activated cell sorting (FACS) and performed single-cell RNA sequencing (scRNA-seq) using a modified STRT-seq (mSTRT-seq) approach. To enrich endocrine cells, RFP+ cells were collected from Ngn3-Cre; Rosa-RFP mice. Mice were treated with a single high dose (200 mg/kg) of STZ and were assessed from day 1 (D6) to month 9 (M9). Additionally, to evaluate the maturation status of β-cells, we performed mSTRT-seq on Ngn3-Cre; Rosa-RFP+ cells from postnatal day (P) 3, P12, and P21 mice.

first: Ye

last: Feng

first: Wei-Lin

last: Qiu

first: Xin-Xin

last: Yu

first: Yu

last: Zhang

first: Mao-Yang

last: He

first: Lin-Chen

last: Li

first: Li

last: Yang

first: Weiyi

first: Michael

last: Franti

first: Junqing

last: Ye

first: Joerg

last: Hoeck

first: Cheng-Ran


title: Kentucky assay: 1-pentanethiol

status: Public on Apr 20 2020

city: Lexington

first: Timothy

last: McClintock

state: Kentucky

address: 508 Medical Science Buildi

department: Physiology

institute: University of kentucky

summary:
Mice have 1,100 odorant receptors.  Nearly all are orphan receptors.  The pattern of receptor responses to odors is the input that allows the brain to detect and discriminate odors
The Kentucky assay measures the function of each of the 1,100 odorant receptors and 14 TAARs  in vivo.

overall_design: FACS samples from S100a5-tauGFP mice (in groups of 3) simultaneously exposed to clean air (vehicle) or bourgeonal were subjected to microarray analysis using Clariom S arrays


title: Kentucky assay

status: Public on Mar 06 2020


title: Kentucky assay: artificial cigarette smoke odor


title: Kentucky assay: Citrus accord, 100%

summary:
Mice have 1,100 odorant receptors.  Nearly all are orphan receptors.  The pattern of receptor responses to odorants is the input that allows the brain to detect and discriminate odors
The Kentucky assay measures the function of each of the 1,100 odorant receptors and 14 TAARs  in vivo.

overall_design: FACS samples from S100a5-tauGFP mice (in groups of 3) simultaneously exposed to clean air (vehicle) or odorant were subjected to microarray analysis using Clariom S arrays

first: William

last: Titlow


title: Kentucky assay: Citrus accord, 5%

overall_design: FACS samples from S100a5-tauGFP mice (in groups of 3) simultaneously exposed to clean air (vehicle) or odorant were subjected to microarray analysis using Mouse Gene 1.0 ST arrays


title: Kentucky assay: Indole/ionone


title: Kentucky assay: Indole


title: Gene expression profiling identifies a gene signature that predicts progression to active tuberculosis several years before disease onset

status: Public on Feb 25 2020

city: Newark

first: Padmini

last: Salgame

state: NJ

address: 185 South Orange Ave

department: Medicine

institute: Rutgers New Jersey Medical School

summary: We evaluated the predictive ability of various gene signatures in baseline peripheral blood mononuclear cell samples to distinguish Mtb-infected individuals who eventually progress to TB disease (progressors) or who remain asymptomatic (non-progressors) during clinical follow-up; we also compare long-term Mtb-infected non-progressors from patients with TB disease

overall_design: Transcriptome profiles via RNAseq of progressors, non-progressors, and TB patients in a Brazilian household contact cohort were used to identify a gene signature predictive of progression to TB

first: W

middle: E

last: Johnson

first: Samantha

last: Leong

first: Yue


title: Transcriptome-wide Profile of Cerebral Cavernous Malformations Patients Reveal Important Long noncoding RNA molecular signatures

status: Public on Dec 03 2019

city: Jammu

first: Santhilal

last: Subhash

state: Jammu and Kashmir

address: Jagti, NH-44, PO Nagrota

department: Biosciences and Bioengineering

country: India

institute: Indian Institite of Technology Jammu

summary: In this study, by transcriptome-wide approach we demonstrate that lncRNAs are prevalent in CCMs disease and are likely to play critical roles in regulating important signaling pathways involved in the disease progression. We believe, that detailed future investigations on these set of identified lncRNAs can provide useful insights into the biology and, ultimately, in preventing this debilitating disease.

overall_design: Next Generation Sequencing analyses of transcriptome profiles from CCM patients

first: Souvik

last: Kar

first: Chandrasekhar

last: Kanduri


title: Small RNA sequencing of 57 laryngeal squamous cell carcinoma and paired adjacent normal tissues

first: Yongyan

last: Wu

type: Non-coding RNA profiling by high throughput sequencing

summary: Laryngeal squamous cell carcinoma (LSCC) is a common form of head and neck cancer with poor prognosis. However, the mechanism underlying the pathogenesis of LSCC remains unclear. We performed high throughout sequencing to identify miRNA that associated with LSCC progression.Small RNA libraries were constructed followed by sequencing on a cohort of LSCC tissues (57 samples) and paired adjacent normal mucosa tissues (57 samples).

overall_design: Expression of miRNA in 57 LSCC and 57 paired adjacent normal mucosa tissues was examination by high throughout sequencing.

first: Wei

last: Gao

first: Binquan

last: Wang

first: Xiwang

last: Zheng


title: The intestinal microbiota programs diurnal rhythms in host metabolism through histone deacetylase 3

status: Public on Sep 26 2019

city: Pittsburgh

first: Zheng

last: Kuang

state: PA

address: 4400 Fifth Avenue

department: Biological Sciences

institute: Carnegie Mellon University

summary: Circadian rhythmicity is a defining feature of mammalian metabolism that synchronizes metabolic processes to day-night light cycles. Here, we show that the intestinal microbiota programs diurnal metabolic rhythms in the mouse small intestine through histone deacetylase 3 (HDAC3).  The microbiota induced expression of intestinal epithelial HDAC3, which was recruited rhythmically to chromatin and produced synchronized diurnal oscillations in histone acetylation, metabolic gene expression, and nutrient uptake. HDAC3 also functioned non-canonically to coactivate estrogen related receptor a (ERRa), inducing microbiota-dependent rhythmic transcription of the lipid transporter gene Cd36 and promoting lipid absorption and diet-induced obesity. Our findings reveal that HDAC3 integrates microbial and circadian cues to regulate diurnal metabolic rhythms, and pinpoint a key mechanism by which the microbiota controls host metabolism.

overall_design: 1. RNAseq analysis of epithelial cell transcripts in Germ-free WT mice and conventional HDAC3fl/fl and HDAC3ΔIEC mice at 4 time points across a circadian cycle. Laser captured epithelial cells from 3 mice were pooled together for RNAseq at each time point. 2. ChIPseq analysis of epithelial cell H3K9ac and H3K27ac in Germ-free and conventional WT mice and conventional HDAC3fl/fl and HDAC3ΔIEC mice across a circadian cycle. Epithelial cells from 3 mice were pooled together for ChIPseq at each time point. 3. 16s sequencing analysis of fecal bacterial composition in HDAC3fl/fl and HDAC3ΔIEC mice before and after switching from chow diet to high-fat diet.

first: Yuhao

first: Yun

last: Li

first: Cunqi

first: Kelly

middle: A

last: Ruhn

first: Cassie

middle: L

last: Behrendt

first: Eric

last: Olson

first: Lora

last: Hooper


title: Translational profiling of proximal tubule in fibrotic kidney

status: Public on Sep 21 2019

first: Haojia

summary: Injury to the proximal tubule plays a central role in the initiation and progression of kidney fibrosis, and rates of chronic kidney disease progresses approximately 50% faster in males compared to females. We applied Translating Ribosome Affinity Purification (TRAP) followed by RNA-sequencing to characterize the cell-specific proximal tubule transcriptional landscape during fibrosis in male vs. female mice.

overall_design: Promixal tubule was profiled by Translating Ribosome Affinity Purification (TRAP)

first: Benjamin

last: Humphreys


title: Cytosolic Proteostatic Adaptation to Mitochondrial Stress Causes Progressive Muscle Wasting

status: Public on Aug 09 2019

city: Syracuse

first: Frank

last: Middleton

state: NY

address: 505 Irving Avenue

department: Neuroscience and Physiology

institute: SUNY Upstate Medical Univ

summary:
Purpose: Muscle wasting (or atrophy) occurs in primary neuromuscular diseases and during aging, with sarcopenia affecting 35.4% and 75.5% of women and man over 60 years of age. Mitochondrial dysfunction is proposed to contribute to muscle wasting. Here, we show that chronic adaptation to mitochondrial Precursor Over-accumulation Stress (mPOS) causes muscle wasting. mPOS is a newly discovered cell stress mechanism caused by the saturation or damage of the mitochondrial protein import machinery, which consequently leads to the toxic accumulation of precursor proteins in the cytosol.
Methods: We generated transgenic mice with a two-fold increase of Ant1, an adenine nucleotide translocase involved in ATP/ADP exchange on the inner mitochondrial membrane (IMM). We found that these animals progressively lose muscle mass. At two years of age, the skeletal muscle becomes barely quantifiable, without affecting the overall lifespan. We then performed whole-transcriptome RNA-sequencing on skeletal muscle samples of male and female mice at 6 months of age.
Results: After alignment and quantification, we show that the ANT1-transgenic muscles have a drastically remodeled transcriptome that represses protein synthesis, and stimulates proteasomal function, autophagy, lysosomal amplification and Gadd45a-signaling. These four processes are all known to promote muscle wasting.
Conclusions: These results suggest that chronic proteostatic adaptation to mPOS is a robust mechanism of muscle wasting, and it leads to or depends in part on a robust set of transcriptional adaptations. This finding may help the understanding of how mitochondria contribute to muscle wasting during aging. It may also have implications for diseases that are associated with ANT1 overexpression.

overall_design: Skeletal muscle mRNA profiles of 6-month old wild type (WT) and Ant1 transgenic overexpressing mice were generated by stranded paired-end RNA sequencing, in quadruplicate, using Illumina NextSeq500.

first: XinJie

last: Chen


title: FAK activity sustains intrinsic and acquired ovarian cancer resistance to platinum chemotherapy

status: Public on Jul 01 2019

city: La Jolla

first: David

last: Schlaepfer

state: CA

address: 3855 Health Sciences Dr.

department: Moores Cancer Center

institute: UCSD


title: Kentucky assay: cigarette smoke

first: Timothy

last: McClintock


title: FAK activity sustains intrinsic and acquired ovarian cancer resistance to platinum chemotherapy [KMF parental, KMF clone KT13 (FAK-/-), KT13 + GFP-FAK, KT13 + GFP-FAK R454, and KT13 + deltaGSK beta-catenin]

summary: Gene copy number changes, cancer stem cell (CSC) increases, and platinum chemotherapy resistance contribute to poor prognosis in patients with recurrent high grade serous ovarian cancer (HGSOC). CSC phenotypes involving Wnt-b-catenin and aldehyde dehydrogenase activities, platinum resistance, and tumor initiating frequency are here associated with spontaneous genetic gains, including genes encoding KRAS, MYC and FAK, in a new murine model of ovarian cancer (KMF). Noncanonical FAK signaling was sufficient to sustain human and KMF tumorsphere proliferation, CSC survival, and platinum resistance. Increased FAK tyrosine phosphorylation occurred in HGSOC patient tumors surviving neo-adjuvant platinum and paclitaxel chemotherapy and platinum resistant tumorspheres acquired FAK dependence for growth. Importantly, combining a pharmacologic FAK inhibitor with platinum overcame chemoresistance and triggered apoptosis in vitro and in vivo. Knockout, rescue, genomic and transcriptomic analyses collectively identified more than 400 genes regulated along a FAK/b-catenin/Myc axis impacting stemness and DNA repair in HGSOC, with 66 genes gained in a majority of Cancer Genome Atlas samples. Together, these results support combinatorial testing of FAK inhibitors for the treatment of recurrent ovarian cancer.

overall_design: mRNA profiles of KMF parental, KMF clone KT13 (FAK-/-), KT13 + GFP-FAK, KT13 + GFP-FAK R454, and KT13 + deltaGSK beta-catenin cells were generated in triplicate using an Illumina NovaSeq 6000 Sequencing System

first: Carlos

last: Díaz Osterman

first: Duygu

last: Ozmadenci

first: Elizabeth

last: Kleinschmidt

first: Kristin

last: Taylor

first: Allison

last: Barrie

first: Shulin

last: Jiang

first: Lisa

last: Bean

first: Florian

last: Sulzmaier

first: Christine

last: Jean

first: Isabelle

last: Tancioni

first: Kristen

last: Anderson

first: Sean

last: Uryu

first: Edward

last: Cordasco

first: Jian

first: Xiao

first: Guo

last: Fu

first: Marjaana

last: Ojalill

first: Pekka

last: Rappu

first: Jyrki

last: Heino

first: Adam

last: Mark

first: Guorong

last: Xu

first: Kathleen

last: Fisch

first: Vihren

last: Kolev

middle: T

last: Weaver

first: Jonathan

last: Pachter

first: Balázs

last: Győrffy

first: Michael

last: McHale

first: Denise

middle: C

last: Connolly

first: Alfredo

last: Molinolo

first: Dwayne

last: Stupack


title: FAK activity sustains intrinsic and acquired ovarian cancer resistance to platinum chemotherapy [ID8 and ID8-IP / KMF cells]

first: David

last: Schlaepfer

overall_design: mRNA profiles of ID8 and ID8-IP / KMF cells were generated in triplicate using an Illumina NovaSeq 6000 Sequencing System

first: Carlos

middle: J

last: Díaz Osterman

first: Duygu

last: Ozmadenci

first: Elizabeth

middle: G

last: Kleinschmidt

first: Kristin

last: Taylor

first: Allison

last: Barrie

first: Shulin

last: Jiang

first: Lisa

last: Bean

first: Florian

last: Sulzmaier

first: Christine

last: Jean

first: Isabelle

last: Tancioni

first: Kristen

last: Anderson

first: Sean

last: Uryu

first: Edward

last: Li

last: Chen


title: A conditionally immortalized Gli1-positive kidney mesenchymal cell line models myofibroblast transition

status: Public on Jun 27 2019

first: Haojia

last: Wu

summary: Glioma-associated oncogene homolog-1 (Gli1)-positive resident mesenchymal stem cell-like cells are the predominant source of kidney myofibroblasts in fibrosis, but investigating Gli1-positive myofibroblast progenitor activation is hampered by the difficulty of isolating and propagating primary cultures of these cells. Using a genetic strategy with positive and negative selection, we isolated Kidney-Gli1 (KGli1) cells that maintain expression of appropriate mesenchymal stem cell-like cell markers, respond to hedgehog pathway activation, and display robust myofibroblast differentiation upon treatment with transforming growth factor-β (TGF-β). Coculture of KGli1 cells with endothelium stabilizes capillary formation. Single-cell RNA sequencing (scRNA-seq) analysis during differentiation identified autocrine ligand-receptor pair upregulation and a strong focal adhesion pathway signal. This led us to test the serum response factor inhibitor CCG-203971 that potently inhibited TGF-β-induced pericyte-to-myofibroblast transition. scRNA-seq also identified the unexpected upregulation of nerve growth factor (NGF), which we confirmed in two mouse kidney fibrosis models. The Ngf receptor Ntrk1 is expressed in tubular epithelium in vivo, suggesting a novel interstitial-to-tubule paracrine signaling axis. Thus, KGli1 cells accurately model myofibroblast activation in vitro, and the development of this cell line provides a new tool to study resident mesenchymal stem cell-like progenitors in health and disease.

overall_design: DropSeq on primary culture kidney Gli1+ cells harvasted from 0, 6, 12, and 24 hrs after TGF-beta treatment

first: Benjamin

last: Humphreys


title: Coprophagia of rabbit puppies stimulate Immune System Development

status: Public on May 02 2019

city: Castanet-Tolosan

first: Laurent

last: Cauquil

address: 24 chemin de Borde Rouge

country: France

institute: INRA

summary: The rabbits ingest the mother's droppings at the nest. This behaviour contributes to the transmission of the maternal microbiota to its progeny, it is involved in the maturation of the digestive ecosystem of the rabbits and reduces mortality. In view of these observations, it is possible to assume that the digestive system is involved. To support this hypothesis, gene expression is measured using an expression chip. The aim is to detect over- or under-expressed genes under certain conditions and to link them in particular to immunity.

overall_design: Ileum gene expression of 57 rabbits was measured at 2 different times (35d and 49d old) and for 3 different conditions of breeding (FF: fecal pellets add to the net; NF: no fecal pellets add to the net; FFab: fecal pellets from doe under antibiotics add to the net).

first: Véronique

last: Duranthon

first: Sylvie

last: Combes


title: Conserved Transcriptomic Profiles Underpin Monogamy across Vertebrates

status: Public on Dec 18 2018

city: Austin

first: Rebecca

last: Young

state: TX

address: 2415 Speedway #C0930, Patterson Lab 607A

institute: University of Texas at Austin

summary: We compare fore- and mid-brain transcriptomes of reproductive males in monogamous and non-monogamous species pairs of Peromyscus mice, Microtus voles, parid songbirds, dendrobatid frogs, and Xenotilapia species of cichlid fishes. Our study provides evidence of a universal transcriptomic mechanism underlying the evolution of monogamy in vertebrates.

sample_organism:
Peromyscus maniculatus
Microtus pennsylvanicus
Peromyscus californicus
Anthus spinoletta
Oophaga pumilio
Microtus ochrogaster
Ranitomeya imitator
Xenotilapia ornatipinnis
Prunella modularis
Xenotilapia spiloptera

overall_design: Fore- and mid-brain mRNA of  reproductive males samples (n=3) were pooled and sequenced using an Illuma HiSeq platform.

first: Michael

last: Ferkin

first: Nina

middle: F

last: Ockendon

first: Veronica

last: Orr

first: Steven

last: Phelps

first: Ákos

last: Pogány

first: Corinne

last: Richards-Zawacki

first: Kyle

last: Summers

first: Tamás

last: Székely

first: Brian

last: Trainor

first: Araxi

middle: O

last: Urrutia

first: Gergely

last: Zachar

first: Lauren

last: O'Connell

first: Hans

last: Hofmann


title: Advantages of single nucleus over single cell RNA-seq in adult kidney

status: Public on Oct 13 2018

city: St. Louis

first: Haojia

last: Wu

address: 4523 Clayton Ave, MSB Rm 820

institute: Washington University in St Louis

summary: A key limitation in single cell genomics is generating a high-quality single cell suspension that contains rare or difficult to dissociate cell types and is free of RNA degradation or transcriptional stress responses. Samples with unpredictable availability or that must be collected at several timepoints present additional challenges. Using adult mouse kidney, we compared single-cell RNA sequencing (scRNA-seq) data generated using DropSeq with snRNA-seq data generated from nuclei using sNuc-DropSeq, DroNc-seq and 10X Chromium. We validated snRNA-seq on fibrotic kidney from day 14 unilateral ureteral obstruction (UUO).

overall_design: Dropseq, sNucDropseq, DroNcSeq and 10X Chromium were used to profile mouse healthy and fibrotic kidneys

first: Benjamin

middle: D

last: Humphreys


title: Cytoplasmic Location of Translation Controls Protein Output [CLIP-seq]

status: Public on Nov 15 2022

city: New York

first: Christine

last: Mayr

address: 417 E 68th Street

department: Cancer Biology and Genetics

institute: MSKCC

summary: The cytoplasm contains membrane-bound organelles and membraneless compartments. The TIS granule network is formed through assembly of the RNA-binding protein TIS11B together with its bound mRNAs and associates with a portion of the rough endoplasmic reticulum (ER) – one of the major sites of protein synthesis. Subcellular mRNA localization is widespread in polarized cells. However, it is largely unknown if mRNA localization is also widespread in non-polarized cells and if the location of protein synthesis has biological consequences. To identify compartment-specific cellular functions, we used fluorescent particle sorting to isolate TIS granules, the ER surface, and the cytosol and determined their mRNA contents.

overall_design: iCLIP-sequencing in HEK293T cells transfected with GFP-TIS11B, three biological replicates.

first: Ellen

last: Horste

first: Mervin

last: Fansler

first: Ting

last: Cai

first: Xiuzhen

last: Chen

first: Sibylle

last: Mitschka

first: Gang

last: Zhen

first: Flora

middle: Y

last: Lee

first: Jernej

last: Ule


title: mRNA Expression Data from Murine Hearts of Shiftwork MI, Normal MI and Sham Wildtype Mice at 24-hours Post-MI

status: Public on Nov 30 2018

city: Guelph

first: Tami

last: Martino

address: 50 Stone Road

department: Biomedical Sciences

institute: University of Guelph

summary:
Male C57Bl/6 mice were randomized to undergo 5 days of i) a shiftwork protocol (10-hour light: 10-hour dark cycle) before myocardial infarction (MI) surgery, ii) a normal 12-hour light: 12-hour dark environment before MI surgery, iii) a normal 12-hour light: 12-hour dark environment and used as sham controls, or iv) a shiftwork protocol (10-hour light: 10-hour dark cycle) and used as sham controls. MI surgery was performed on the 5th day, after which all mice were returned to a normal 12-hour light: 12-hour dark cycle. Hearts were collected 24-hours post-MI at ZT06.
The microarray approach allows the investigation of transcriptome-wide gene expression changes in hearts from mice on a shiftwork cycle or on a regular light:dark cycle before MI.

overall_design: There are a total of 16 samples, 3 from wildtype mice shiftworked for 5 days before MI, 3 from wildtype mice on a normal light:dark cycle before MI, 5 sham controls on a normal light:dark cycle, and 5 sham controls shiftworked for 5 days. Animals were sacrificed at 6 hours into the light phase.


title: Comparative analysis of kidney organoid and adult human kidney single cell and single nucleus transcriptomes

summary: We analyzed single cell transcriptomes over 80,000 cells isolated from 65 organoids differentiated from iPSCs and ESCs using two different protocols. We find that both protocols generate kidney organoids that contain a diverse range of kidney cells at differing ratios as well as non-renal cell types. We reconstructed lineage relationships during organoid differentiation through pseudotemporal ordering, and identified transcription factor networks associated with fate decisions. When comparing to adult human kidney, we  reveal immaturity of all kidney organoid cell types. These results define impressive kidney organoid cell diversity, identify incomplete differentiation as a major roadblock for current directed differentiation protocols and provide a human adult kidney snRNA-seq dataset against which to benchmark future progress.

overall_design: Dropseq and 10X Chromium were used to profile organoid cells and adult kidney nuclei


title: Cytoplasmic Location of Translation Controls Protein Output [RNA-seq]

overall_design: RNA-seq of different compartments from HEK293T cells


title: Gene expression and whole-transcriptome analysis of heart tissue isolated from mutant transgenic mice after 16 weeks of treatment with AAV9-M7.8L shRNA

status: Public on Jan 01 2020

city: San Diego, California

first: Kathia

last: Zaleta-Rivera

address: 9500 Gilman Drive, MC 0412

summary:
Purpose: Assess the effects of the myocardial transcriptional program and off-target delivery or endogenous RNA interference pathways by AAV9-M7.8L shRNA
Results: RNA sequencing including small RNA profiling was used to assess i) the presence of delivered therapeutic, ii) effects on the mutant and wild type alleles, iii) gene expression network effects of disease and silencing, and iv) disruption of the native small RNA processing apparatus and microRNA function. Transcriptome analysis showed that M7.8L shRNA and CFP was highly expressed in the hearts of humanized mutant transgenic mice treated at 3 days old of age and allele specific silencing  27% of the human MYL2-47K (RLC-47K) mutation without affecting the mouse endogenous myl2 gene.  miRNA profiling showed a pathological signature in untreated and control RLC-47K mice, with the upregulation of mir208a, and mir208b and downregulation of mir-499, which is a common response to cardiac injury, however no significant changes were observed for mir208a and mir-499 in the M7.8L treated group compared to the untreated and control groups. On the other hand, the expression of  mir208b was significantly downregulated in the treated group, which was consistent with a positive therapeutic benefit. This emphasizes the complexity of cardiac remodeling and the time-dependent nature of the changes in different signaling networks. To assess downstream broader transcriptional effects of the treatment, we adopted a network approach similar to those we have previously published.We obtained the top 30 differentially expressed genes between treated and control groups and extracted interacting genes and relationships from the STRING database. We then plotted the resulting interaction network with each gene's expression fold change . This visualization revealed reversal of the stress/remodeling myocardial gene program and related markers (including Myh7, Nppa, Nppb, Acta1) as well as up-regulation of gene networks that included acetyl-CoA transferases (Ech1, Ecl1, Acaa1), indicating a wide, systemic, transcriptional effect of the treatment in reverting the disease gene expression program. We also observed minimal impact of off-target delivery or endogenous RNA interference pathways. Thus, we assessed the expression level of the enzymes argonaute and dicer and found a slight increase of argonaute and no significant changes in the expression of dicer in the 3 days old treated mutant transgenic mice as compared to the untreated and control animals suggesting that shRNA/miRNA-shared pathways were modestly affected during four months of constitutive expression of M7.8L shRNA in the hearts of adult mice. These effects and the lack of in vivo cytotoxicity in RLC-4K treated mice are consistent with the effects of the H1 promoter that drives M7.8L shRNA expression in a more restrained manner than the U6 promoter. Similar findings have been observed in mouse liver after knockdown of hepatitis B virus with shRNA driven by weak promoters.
Conclusions: in vivo allele-knockdown of MYL2-47K at 4 months was 27% by RNA sequencing. This sustained but modest reduction appeared sufficient to revert the disease phenotype during four months of observation without affecting the normal allele. In addition, we observed that shRNA expression declined after four months of treatment, however this course of treatment was sufficient to ameliorate the disease with minimal off-target effects, while efficacy when mice were treated at older age was reduced. In humans, there is often progression of disease seen during adolescence. Based on this observation it would seem that RNAi therapies should target early disease.

overall_design:
Methods: RLC transgenic mice were injected via the jugular vein at three days old of age with AAV9 H1-M7.8L RSVp-Cerulean. For the neonatal group, 25ul of virus were injected (3x10^11 viral particles). Echocardiography and treadmill studies were done at 2 and 3.5 months of age. At 4 months of age, animals were sacrificed and hearts were isolated for hyperttophic biomarker quatification, collagene deposited and microRNAseq and mRNAseq. Two illumina RNA libraries were prepared: one Small RNA library ran in MiSeq Rapid Mode 50 nt-single end and an Poly A library  in HiSeq Rapid mode 100 nt -pair end
Heart_wtTg= Heart tissue isolated from wild type transgenic mice (wtTg) carrying the normal human allele of the MYL2 gene.
Heart_mutTg=Heart tissue isolated from mutant transgenic mice (mutTg) carrying the mutated human allele of the MYL2 gene.
Control virus= AAV9 virus non-expressing M7.8L shRNA.


title: Mapping the Single Cell Transcriptomic Response of Murine Diabetic Kidney Disease to Therapies

status: Public on Jun 14 2022

summary: In this study, we utilized the db/db, uninephrectomy and renin-hypertension mouse model. We compared vehicle to ACE inhibitor, Rosiglitizone, SGLT2 inhibitor, ACEi + Rosiglitizone and ACEi + SGLT2i at two time points (2 days and 2 weeks). We generated snRNA-seq datasets from all groups comprising nearly 1 million cells. Analysis of the resulting atlas revealed that the different medications affected strikingly different cell types. Combination therapy had the largest effects, but these effects were also largely non-overlapping. This study highlights the cellular complexity of diabetic nephropathy and the effects of different classes of therapy. The results support the development of combination therapies since different drug classes target different cell types in kidney.

overall_design: We employed single nucleus RNA-sequencing (snRNA-seq) to a model of murine DKD and five treatment regimens. We profiled a total of 70 mice from 14 groups, with N=4-6 mice per group.


title: Bulk RNA-seq on mouse model of diabetic nephropathy and in vitro model of SRSF7 knockdown

summary: In this dataset, we utilized the db/db, uninephrectomy and renin-hypertension mouse model. We performed bulk RNA-seq and compared vehicle to ACE inhibitor, Rosiglitizone, SGLT2 inhibitor, ACEi + Rosiglitizone and ACEi + SGLT2i at two time points (2 days and 2 weeks). To study the mechanism, we also performed bulk RNA-seq on human primary tubular epithelial cells with or without SRSF7 siRNA knockdown.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: We performed bulk RNA-seq to a model of murine DKD and in vitro model of SRSF7 siRNA knockdown.


title: Transcriptional Basis of Neuronal Diversity in the Mammalian Brain

status: Public on Jul 20 2018

city: Ashburn

first: Ken

last: Sugino

state: VA

address: 19700 Helix Dr

institute: Janelia Research Campus

summary: Neuronal diversity is a defining feature of the mammalian brain deemed necessary for realizing the complex function of the nervous system. In order to begin to understand the transcriptional basis of this diversity, we collected more than 170 neuronal and non-neuronal cell type-specific transcriptomes defined operationally by transgenic mouse lines and anatomical regions. The dataset indicates that the genes specifically expressed in neuronal cell types are biased toward long genes. We revealed that these long genes have higher capacities to be differentially expressed between cell types and thus assume an important role in diversification of the neuronal transcriptomes. Since mobile element insertions are the main cause of the gene elongations, we propose that exaptation of the inserted mobile elements significantly contributed to the neuronal diversity.

overall_design: Examination of whole cell transcriptomes in 174 cell types.

first: Lihua

last: Wang

first: Yasuyuki

last: Shima

first: David

last: Hunt

first: Andrew

last: Lemire

first: Erina

last: Hara

first: Mac

last: Hooks

first: Dimitri

last: Tränkner

first: Jayaram

last: Chandrashekar

first: Adam

last: Hantman

first: Sacha

last: Nelson


title: Skeletal muscle satellite cells, endothelial cells and single muscle fibers

status: Public on Jul 01 2018

city: Minneapolis

first: Mayank

last: Verma

address: 2001 6th st se

department: Stem Cell Institute

institute: University of Minnesota

summary: There is considerable crosstalk between satellite cells, endothelilal cells and muscle fibers. Transcriptome analysis from freshly isolated cells from each compartment should help elucidate these pathways.

overall_design: 2-3 replicates for each group are provided

first: Atsushi

last: Asakura


title: Single nucleus inDrops to profile adult human kidney

status: Public on Jun 19 2018

first: Haojia

last: Wu

overall_design: Single nuclei were isolated from adult human kidney and subjected to inDrops single cell RNA-seq

first: Benjamin

last: Humphreys


title: Inflammatory Response and Host-Donor Chimerism Defined by Single Cell RNA-Seq of Allograft Biopsy

summary: Kidney transplantation offers the best survival and quality of life for patients’ with end-stage kidney disease. The major barrier to successful long-term transplantation is the host’s immune response to alloantigens’ causing rejection of the transplant. The complexity of this immune response in kidney transplantation is still not fully understood and effective treatment strategies are needed. To better understand rejection at the molecular and cellular level we characterized 4,487 cells from a single biopsy core from a kidney transplant undergoing mixed rejection using single cell RNA sequencing.

overall_design: InDrop was used to generate single cell profiles from a allograft kidney biopsy


title: Single cell multi-omic sequencing (CITEseq) of human peripheral blood mononuclear cells (PBMCs)

status: Public on Feb 02 2022

first: Vasantika

last: Suryawanshi

state: CALIFORNIA

address: 9420 Athena Circle

institute: La Jolla Institute of Immunology

summary: We utilized CITESeq to investigate changes in immune cell frequencies and their transcriptomic signatures in PBMCs obtained from subjects with low and high coronary artery disease (CAD) severity quantified using gensini scoring system as well as subjects with and without IgE to alpha-gal sensitization

overall_design:
We compared changes in immune cell subtypes between subjects with low and high CAD severity or with and without IgE to alpha-gal sensitization
Raw data files include reads for both gene expression and antibody-derived tags

first: Coleen

last: McNamara

first: Klaus

last: Ley

first: Catherine

last: Hedrick

first: Yury

last: Miller


title: Parabiosis and single-cell RNA-Sequencing reveal a limited contribution of monocytes to myofibroblasts in kidney fibrosis

status: Public on Apr 24 2018

summary: Fibrosis is the common final pathway of virtually all chronic injury to the kidney. While it is well accepted that myofibroblasts are the scar-producing cells in the kidney, their cellular origin is still hotly debated. The relative contribution of proximal tubular epithelium and circulating cells including mesenchymal stem cells, macrophages and fibrocytes to the myofibroblast pool remains highly controversial. Using inducible genetic fate tracing of proximal tubular epithelium we confirm that proximal tubule does not contribute to the myofibroblast pool. However, in parabiosis models in which one parabiont is genetically labeled and the other is unlabeled and undergoes kidney fibrosis, we demonstrate that a small fraction of genetically labeled renal myofibroblasts derive from the circulation. Single cell RNA-Sequencing confirms this finding but indicates that these cells are circulating monocytes, express few extracellular matrix or other myofibroblast genes and do express many proinflammatory cytokines. We conclude that this small circulating myofibroblast progenitor population contributes to renal fibrosis by paracrine rather than direct mechanisms.

overall_design: Single cell RNA-seq was performed on FACS-sorted PDGFRB+CD45- and PDGFRB+CD45+ cell populations

first: Rafael

last: Kramann


title: Cleavage of histone H2A during embryonic stem cell differentiation destabilizes nucleosomes to counteract gene activation

status: Public on Dec 31 2021

city: Philadelphia

first: Yemin

last: Lan

address: 3400 Civic Center Blvd

institute: University of Pennsylvania

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

overall_design: Refer to individual Series


title: Different expression profiles of lncRNAs, mRNAs and circRNAs in preeclampsia and normal placenta  None

status: Public on Mar 01 2018

first: Zhenyu

last: Zhang

address: Gongtinanlu 8hao

institute: Beijing Chao-Yang Hospital,Capital Medical University

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


title: Different expression profiles of miRNAs in preeclampsia and normal placenta (miRNA)

summary: Preeclampsia is usually considered as a placental basis of diseases, as there are many differently expressed proteins or pathogenic proteins expressed in the placenta. Owing to the important role of post-transcriptional gene regulation in phenotypes and functions of cells, non-coding ribonucleic acid (ncRNA) molecules contributed to the regulation. We collected 7 placental samples from 3 preeclampsia patients and 4 normal women, focused on the basal plate of placenta, as it is the direct connection of mother and fetal, and adopted SBC human ceRNA array V1.0（4×180K）and human miRNA microarray (8*60 K). The results revealed that expressions of 2840 lncRNAs, 1093 mRNAs, 4282 circRNAs and 4 miRNAs were different between preeclampsia and normal placentas. The functions of differentially expressed lncRNAs and co-expressed potential targeting genes were predicted by analyzing Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) biological pathway analysis. Furthermore, we analyzed and find the co-expression and interaction patterns of different RNAs and possible ceRNA mechanism. The present study provided a systematic perspective on the potential function of non-coding RNAs (ncRNAs) in the pathogenesis of preeclampsia.

overall_design: 7 placental samples from 3 preeclampsia patients and 4 normal women were enrolled in. there were no replicates, control and/or reference Samples or dye-swaps.


title: Different expression profiles of lncRNAs, mRNAs and circRNAs in preeclampsia and normal placenta (ceRNA)

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

first: Qiushi

last: Wang

first: Chongdong

last: Liu


title: Triplet nucleotide repeat-based siRNAs are highly toxic to cancer cells

status: Public on Jan 12 2018

city: Chicago

first: Marcus

last: Peter

state: IL

address: 303 East Superior Street, Lurie 6-123

institute: Northwestern University Feinberg School of Medicine

summary: Triplet repeat siRNAs as found amplified in diseases such as Huntingtons disease can be used to kill cancer cells

overall_design: RNA isolated from HeyA8 cells 48 hrs after transfection with either a nontargeting siRNA (siScr), siCAG/CUG or siCGA/UCG were subjected to deep sequencing, using Illumina HiSeq4000.

first: Andrea

last: Murmann

first: Elizabeth

last: Bartom


title: Comparing gene expression timing and amplitude to delineate the unique pathways of brown and white rot wood-degrading fungi

status: Public on Jan 05 2018

city: saint paul

first: Jonathan

last: Schilling

state: minnesota

address: 2004 folwell ave

summary: Wood-degrading fungi play a critical role in global carbon cycling, and their varied mechanisms for deconstruction offer pathways for industrial bioconversion. In this study, we used comparative genomics to isolate upregulation patterns among fungi with brown rot (carbohydrate-selective) or white rot (lignin-degrading) nutritional modes. Specifically, we used whole-transcriptome profiling to compare early, middle, and late decay stages on wood wafers, matching differentially-expressed gene (DEG) patterns with fungal growth and enzyme activities. This approach highlighted 34 genes uniquely upregulated in early brown rot stages, with notable candidates involved in generating reactive oxygen species (ROS) as a pretreatment mechanism during brown rot. This approach further isolated 18 genes in late brown rot stages that may be adapted to handle oxidatively-reacted lignocellulose components. By summing gene expression levels in functional classes, we also identified a broad and reliable distinction in glycoside hydrolase (GH) versus lignocellulose oxidative (LOX) transcript counts that may reflect the energy investment burden of lignin-degrading machinery among white rot fungi.

sample_organism:
Pleurotus ostreatus
Trametes versicolor
Rhodonia placenta
Gloeophyllum trabeum

overall_design: We sequenced mRNA from 36 samples, including two brown rot and two white rot fungi, to compare the gene regulations of these two typical wood decay strategies. Each specie was used to colonize wood wafer directionally, a space for time experimental design for study wood decay successions. Then, 3 wood sections on wood wafer were sampled for RNA extraction, representing early to late decay stages, with 3 bioreplicates for each wood section for each specie.

first: Jiwei

first: Kevin

last: Silverstein

first: Melania

last: Figueroa

middle: S


title: Profiling of Human milk cell and lipid microRNAs from healthy and during naturally occurring infection breastfeeding mothers

status: Public on Dec 22 2017

city: Crawley

first: Mohammed

last: Alsaweed

address: 35 stirling hwy

department: Biochemistry

country: Australia

institute: UWA

summary: Human milk is highly recommended for infant during the first six month of life by World Healthy Organisation (WHO). Human milk is not only rich in macro-nutritional components, but also rich in cells and molecules. MicroRNAs are small non-coding RNAs, which enriched in human milk. These molecules are vital in enormous biological and cellular functions including immune system and in response to infections. By using deep sequencing method, 770,374,554 raw reads were generated from all samples (n=26). Then, filter analysis was done to remove 81,091,772 (10.5%), and 689,282,782 clean reads (89.5%) were considered as clean reads, which was retained for the subsequent bioinformatics analysis. Annotation and matching reads to miRBase revealed1780 mature known microRNAs identified in human milk cells and lipids derived from healthy, cold and other infection types mothers. In particular, 1680 known microRNAs were determined in infected mothers (n=14), while 1,606 known microRNAs in healthy mothers (n=12). Of these known microRNAs, 453 microRNAs were differentially expressed (p<0.05) between healthy and infected samples. The majority of the highly expressed miRNAs in all samples, in particular top 20 microRNAs, were also differentially expressed between healthy and infections. Further, 592 novel mature microRNA sequences were predicted, with only 65,878 total reads. Amongst the total reads of the novel microRNAs, top 20 novel miRNAs were found to contributed in 73.3% (total reads 48,295) of the total reads (65,878).

overall_design: Human milk samples were collected from 11 mothers in healthy (n=6) and in infection (n7) conditions. Human milk samples were fractionated to obtain cell and lipid fractions. Total RNA and miRNA were extracted and quantified from cell and lipid fractions. Next generation sequencing using illumina HiSeq 2000 was used to profile microRNAs in 26 samples, where 13 cells and 13 lipids. Filtered (clean) reads were aligned to the latest version of miRBase 21.0. Also, mirdeep software was used to predict novel miRNAs.  DESeq and Linear mixed effect models and ANOVA were used to compare miRNA expression levels between samples and conditions

first: Foteini

last: Kakulas

first: Donna

last: Geddes

first: Mezyndra

last: Badsha


title: CARS2HA

status: Public on Mar 15 2021

city: Ottawa

first: Anh-Thu

last: Dang

state: ON

address: 40 Ruskin St

institute: University of Ottawa Heart Institute

summary: Transfection experiments to investigate the role of CARS2 in macrophages.

overall_design: PMA differentiated THP-1 macrophages were transfected for 72 hours with CARS2 siRNA and NT2 control siRNA. RNA was harvested and the transcriptome was analyzed by transcription array. The experiment was repeated 3 times.

first: Anh

first: Ruth

last: McPherson


title: The HIF target MAFF promotes tumor invasion and metastasis through IL11 and STAT3 signaling

status: Public on Apr 30 2021

city: Headington

first: Eui Jung

last: Moon

address: Old Road Campus Research Building, Roosevelt Drive

department: Department of Oncology

country: United Kingdom

institute: University of Oxford

summary: Using RNA-sequencing and ChIP-sequencing, we identified direct target genes of the transcription factor MAFF in MDA-MB-231 under normoxia and hypoxia.

overall_design: MDA-MB-231, a human breast cancer cell line, was treated either under normoxia or hypoxia. After ChIP or RNA extraction, sequencing was performed. After knocking down endogenous MAFF in MDA-MB-231, we overexpressed V5-tagged MAFF with mutations on shRNA target sites. Then nuclei was extracted and we proceeded to ChIP procedures using V5 antibody to further determine direct targets of MAFF.

first: Eui

first: Stephano

last: Mello

first: Jake

last: Kirkland

first: Amato

last: Giaccia


title: CometChip® and TempO-Seq®: A high-throughput 96-well platform to measure and classify DNA damaging agents in human HepaRG™ Cells [HCC3]

status: Public on Jul 21 2021

first: Matthew

last: Meier

state: Ontario

address: 251 Sir Frederick Banting Driveway

department: Health Canada

institute: Government of Canada

summary:
Introduction: Higher-throughput mode-of-action-based assays provide a valuable approach to expedite chemical evaluation for human health risk assessment. In this study, we combined the high-throughput alkaline CometChip® assay with the TGx-DDI transcriptomic biomarker (DDI = DNA damage-inducing) using high-throughput TempO-Seq® as an integrated genotoxicity testing approach.
Objective: To determine if the high-throughput CometChip® assay and TGx-DDI biomarker analysis can be combined using human HepaRG™ cells to provide an efficient next-generation genotoxicity screening approach to identify DNA damage-inducing (DDI) chemicals.
Methods: Metabolically competent human HepaRG™ cell cultures were exposed to increasing concentrations of 12 chemicals (9 DDI and 3 non-DDI) using a repeat exposure design (0 hr, 24 hr, 48 hr) in 96-well plates to measure and classify chemicals based on their ability to damage DNA. After a 4 hr recovery period, exposed cells were used to perform the Trevigen CometChip assay to assess DNA damage or used for TempO-Seq® S1500+ Targeted  Transcriptome Sequencing for TGx-DDI classification purposes. Bioinformatics and statistical tools were used to classify chemicals as DDI or non-DDI using three separate analyses. Benchmark concentration analysis was also conducted for both assays for the purposes of potency ranking.
Results: In combination, the CometChip® assay and the TGx-DDI were 100% accurate in identifying chemicals that induce DNA damage. Quantitative benchmark concentration (BMC) modeling was applied to evaluate chemical potencies for both assays. The BMCs for the CometChip® assay and the TGx-DDI for all 12 chemicals were highly concordant (within four-fold) and resulted in identical potency rankings.
Conclusions: These results suggest that these two assays can be integrated for efficient, high-throughput identification of DNA damage in HepaRG™ cells. This study provides evidence for the complementarity of the high-throughput CometChip® assay with TGx-DDI biomarker analysis. Integration of these two tests provides an effective and high-throughput approach to identify DDI agents. This work is a first step in accomplishing a more integrated genotoxicity testing strategy to derive mechanistic information to better inform human health risk assessment in a high-throughput manner.

overall_design: Examination of the complementarity of two high-throughput genotoxicity tests, the CometChip assay to assess DNA damage and TGx-DDI biomarker analysis for chemical classification, following exposure to 9 DNA-damage inducing (DDI) chemicals and 3 non-DDI chemicals  in human HepaRG ™ cells.

first: Julie

middle: K

last: Buick

first: Andrew

last: Williams

first: Carol

last: Swartz

first: Leslie

last: Recio

first: Rémi

last: Gagné

first: Stephen

last: Ferguson

first: Bevin

middle: P

last: Engelward

first: Carole

last: Yauk


title: Small RNA-seq analysis of circulating miRNAs to identify phenotypic variability in Friedreich's ataxia patients

status: Public on Oct 18 2017

city: Valencia

first: Marta

last: Seco-Cervera

address: Av Blasco Ibañez, 15

institute: University of Valencia

summary: Friedreich’s ataxia (FRDA; OMIM 229300), an autosomal recessive neurodegenerative mitochondrial disease, is the most prevalent hereditary ataxia. In addition, FRDA patients showed additional non-neurological features such as scoliosis, diabetes and cardiac complications. Hypertrophic cardiomyopathy, which is found in two thirds of patients at the time of diagnosis, is the primary cause of death in these patients. In this data set, using small RNA-sequencing of small RNA purified from plasma samples of FRDA patients and controls we identified differential expression of miRNAs (hsa-miR-128-3p, hsa-miR-625-3p, hsa-miR-130b-5p, hsa-miR-151a-5p, hsa-miR-330-3p, hsa-miR-323a-3p, and hsa-miR-142-3p) between both groups. In addition, we found that miR-323a-3p can be used as a biomarker for differentiation of FRDA patients with cardiac problems. Identification of miRNA signatures could therefore provide new molecular explanation for pathological mechanisms occurring during the natural history of the FRDA. Since miRNA levels change with disease progression and pharmacological interventions, miRNAs will contribute to design new therapeutic strategies and improve clinical decisions.

overall_design: Plama miRNA profiles of 25 Friedreich's ataxia patients and 17 healthy subjects were generated by deep sequencing using Illumina HiScan SQ.

first: Dayme

last: González-Rodríguez


title: Genome-wide transcriptional analysis of gene expression in leukemic cells exposed to histamine dihydrochloride

status: Public on Jun 30 2017

city: Gothenburg

first: Roberta

last: Kiffin

address: Medicinaregatan 1F

department: Sahlgrenska Cancer Center

institute: University of Gothenburg

summary: Analysis of the effect on histamine dihydrochloride on the gene expression of  WT and NOX2-/- PLB cells

overall_design: Total RNA extracted from WT and NOX2-/-  PLB-985 cells cultured with or without histamine-dihydrochloride and DMSO.

first: Anna

last: Martner


title: MiRNA23B REGULATES SELF-RENEWAL AND CHEMORESISTANCE PROPERTIES OF COLON CANCER STEM CELLS

status: Public on Feb 28 2015

city: Newark

first: Bruce

last: Boman

state: DE

address: 4701, ogletown-stanton road

department: CTCR

institute: Helen F Graham Cancer Center and Research Institute

summary: MiRNAs have been identfied to play an important role in cancer stem cells. MiR23b is differentially expressed in various forms of cancer including colorectal cancer as compared to their normal counterparts. MiR23b regulates various aspects of cell behaviour such as differentiation, apoptosis and motility. The goal of the study was to identify the novel role of miR23b in self-renewal property of colon cancer stem cells via regulation of its candidate target mRNAs. To address this aim, HT29 colon cancer cells were transfected with miR23b Precursor, Antimir and their respective controls. RNA SEQ analysis of the cells with altered levels of miR23b assisted in the identification of interesting mRNA targets influenced by miR23b expression and involved self-renewal pathways.

overall_design: HT29 cells with altered levels of miR23b was subjected to RNA SEQ analysis to identify differential expresssion of mRNA targets of mIR23b

middle: M

first: Vignesh

last: Viswanathan

first: Monica

last: Accerbi

first: Skye

last: Schmidt


title: Epigenetic signature of birth-weight discordance in Danish twins

status: Public on Dec 15 2014

city: Denmark

first: Qihua

last: Tan

address: J. B. Winsløws Vej 9B

country: Denmark

institute: University of Southern Denmark

type: Methylation profiling by genome tiling array

summary: Epigenetic profiling of birth-weight discordant twins using Illumina's 450K Human DNA methylation BeadChip

overall_design: Comparing DNA methylation difference in birth-weight discordant twin pairs

first: Lene

last: Christiansen

first: Morten

last: Frost


title: Fibroblast cells immediate-early after human cytomegalovirus infection

status: Public on Jul 16 2003

city: Bern

first: Marc

last: Kenzelmann

address: Friedbuhlstrasse 51

department: Molecular Genome Analysis

country: Switzerland

institute: Institute of Medical Microbiology, University of Bern

summary:
Human cytomegalovirus (HCMV) has been shown to have the potential to alter cellular gene expression early after infection. However, one-gene approaches and the use of closed system gene expression technologies have identified only few cellular genes whose activity changed immediate-early. We therefore used serial analysis of gene expression (SAGE) to investigate the transcriptional program of human fibroblasts in response to HCMV in the immediate-early phase of infection. Differential expression of various cellular genes was monitored. Transcriptional expression changes of genes coding for ribosomal proteins reflected a general cellular response to starvation and stress. But differential regulation of genes coding for transcription factors and proteins associated with cellular metabolism, homeostasis and cell structure may represent transcriptional alterations in response to HCMV infection. Expression kinetics by 5' nuclease fluorigenic real-time PCR of selected genes revealed partial protection of infected cells against initial stress-associated alterations of gene expression and indicated fluctuations of transcriptional levels over time. Additionally, agreement with the quantitative results obtained by SAGE was observed only for genes up-regulated in HCMV-infected cells. This finding pointed to various technical and statistical parameters that all may be critical for quantitative transcriptome studies using global approaches, especially when exploring biological systems in a critical phase of cellular physiology.
Keywords: other

first: M

first: K

last: Muhlemann


title: Analysis of transcription in the Drosophila melanogaster testis

city: Bethesda

first: Brian

last: Oliver

state: MD

address: 50 South Drive

department: LBG

institute: NIDDK, NIH

summary:
Identification and annotation of all the genes in the sequenced Drosophila genome is a work in progress. Wild-type testis function requires many genes and is thus of potentially high value for the identification of transcription units. We therefore undertook a survey of the repertoire of genes expressed in the Drosophila testis by computational and microarray analysis. We generated 3141 high-quality testis expressed sequence tags (ESTs). Testis ESTs computationally collapsed into 1560 cDNA set used for further analysis. Of those, 11% correspond to named genes, and 33% provide biological evidence for a predicted gene. A surprising 47% fail to align with existing ESTs and 16% with predicted genes in the current genome release. EST frequency and microarray expression profiles indicate that the testis mRNA population is highly complex and shows an extended range of transcript abundance. Furthermore, >80% of the genes expressed in the testis showed onefold overexpression relative to ovaries, or gonadectomized flies. Additionally, >3% showed more than threefold overexpression at p <0.05. Surprisingly, 22% of the genes most highly overexpressed in testis match Drosophila genomic sequence, but not predicted genes. These data strongly support the idea that sequencing additional cDNA libraries from defined tissues, such as testis, will be important tools for refined annotation of the Drosophila genome. Additionally, these data suggest that the number of genes in Drosophila will significantly exceed the conservative estimate of 13,601.
Keywords: other

first: Justen

last: Andrews

first: Gerard

last: Bouffard

first: Chris

last: Cheadle

first: Jining

last: Lü

first: Kevin

last: Becker


title: NASH pathogenesis

status: Public on Feb 01 2021

city: Rochester

first: Mrunal

middle: Kishor

last: Dehankar

state: MN

address: 200 First St. SW

department: Computational genomics

institute: Mayo Clinic


title: RNA secondary structome of different cell lines

status: Public on Feb 05 2021

city: Qingdao

first: Lei

last: Sun

state: Shandong

address: Shandong street

institute: Shandong University

summary: we resolved the RNA secondary structure of human (HEK293,  HeLa, K562, HepG2, H9) and mouse (mES) cells based on optimized in vivo click selective 2'-hydroxyl acylation and profiling experiment (icSHAPE). we describe a deep discriminative neural network (PrismNet) that integrates big data of RBP binding and RNA secondary structure from matched living cells and accurately models the RNA sequence and structural preferences of protein-RNA interactions in vivo, enabling precise prediction of the perturbation effects of genetic variants.

overall_design: Libraries of 7 cell lines (human: HEK293, HeLa, K562, HepG2, H9 and mouse : mES) were constructed as the optimized icSHAPE protocol. The RNA structure in vivo was calculated based on DMSO samples (D), in vivo NAI-N3 treatment samples (N) by the new protocol icSHAPE-pipe.

first: Qiangfeng

last: Zhang


title: Antigen-reactive CD4 T cells after SARS-CoV-2 vaccination show divergent phenotypic states with or without restimulation [mixed samples]

status: Public on Nov 19 2025

city: Erlangen

first: Kilian

last: Schober

state: Bavaria

address: Maximiliansplatz 2

department: Mikrobiologisches Institut – Klinische Mikrobiologie, Immunologie und Hygiene

country: Germany

institute: Universitätsklinikum Erlangen

summary: Understanding T cell fate requires precise knowledge of antigen reactivity. For CD4+ T cells, conventional identification of antigen reactivity by peptide restimulation relies on cellular activation, but thereby also introduces a phenotypic bias. However, by performing single-cell RNA and TCR sequencing on both antigen-stimulated and unstimulated samples, clonotypes can be tracked across conditions to identify antigen-reactive CD4+ T cells and simultaneously assess their phenotypes in the unperturbed state. Using this “reverse phenotyping” strategy, complemented by DNA-barcoded peptide–HLA class II multimers, we here investigated the longitudinal phenotypic evolution of SARS-CoV-2 spike–reactive CD4+ T cells after repeated mRNA vaccination. Without stimulation, reactive clones showed more Th-neutral features and less of an activated Th1-like state than would be assessed after antigen restimulation, yet retained a distinct transcriptional state into the memory phase. These results uncover durable imprints in antigen-reactive CD4+ T cells and highlight that cell state classification can differ fundamentally when judged by phenotype versus function.

overall_design: Antigen-specific T cells after SARS-CoV-2 mRNA vaccination were identified by in vitro-restimulation using a peptide mix spanning the full-length SARS-CoV-2 spike glycoprotein. In vitro re-stimulated and unstimulated cells (non-naive CD4 and CD8 T cells) were sorted by FACS and subjected to 5' scRNAseq on a 10x Genomics platform

first: Katharina

last: Kocher

first: Felix

last: Drost

first: Christine

last: Schülein

first: Bernd

last: Spriewald

first: Benjamin

last: Schubert


title: Complex DNA Structural Variant on Chromosome 2 in a Pediatric Patient with  Development Delay and Congenital Malformation

status: Public on Oct 30 2025

city: Seattle

first: Jesse

last: Bengtsson

state: WA

address: 720 Broadway

institute: Pacific Northwest Research Institute

summary: The 2q31 region is commonly associated with pathogenic alleles of the HOXD cluster leading to various clinical phenotypes related to skeletal development. We present a patient with short stature, tetralogy of Fallot, and multiple congenital anomalies. Initial array comparative genomic hybridization (aCGH) revealed a de novo complex genomic rearrangement (CGR) spanning 2q31 in proband characterized as a triplication (TRP)-duplication (DUP)-triplication (TRP). Subsequent analysis applying combined next-generation sequencing methodologies including whole-genome sequencing (WGS) short-reads, PacBio WGS long-reads, and optical genome mapping (OGM) indicated two additional duplications on each end of the rearrangement, consisting of DUP-TRP-DUP-TRP-DUP. This involves three breakpoint junctions, of which each were resolved down to a nucleotide level. This genomic catastrophic event includes many disease-causing genes, and analysis of each gene and its known disorders was required in order to connect genotype to phenotype in a unique CNV.

overall_design: This work was designed to determine the structure of copy number variants on chr2

first: Ming Yin

last: Lun

first: Claudia M.B.

last: Carvalho


title: Tissue-specific iron levels modulate lipid peroxidation and the FLASH radiotherapy effect

status: Public on Oct 16 2025

first: Eui Jung

last: Moon

summary: In this study, we investigated how irradiation changes global transcriptomic changes in MDA-MB-231 cells. Cells were treated either at 0Gy or 10Gy and RNA was extracted to perform RNA sequencing.

overall_design: MDA-MB-231 cells were treated with 0Gy or 10 Gy irradiatio using Cs irradiator. 24 hours after the treatment RNA was collected by using Rneasy kit (Qiagen). RNA samples were sent to Novogene (Cambridge, UK) for library preparation and sequencing. Sequencing was performed by Novoseq 6000.

first: Nuria

last: Vilaplana Lopera

first: Jiyoung

last: Kim


title: Gene expression profiling of human prostate tumors identifies chromatin remodeling as a molecular link between obesity and lethal prostate cancer

status: Public on Mar 01 2017

city: Boston

first: Ericka

last: Ebot

state: MA

address: 677 Huntington Avenue

department: Epidemiology

institute: Harvard T.H. Chan School of Public Health

type:
Expression profiling by array
Third-party reanalysis

summary: Obese men are at higher risk of developing advanced prostate cancer and have higher rates of cancer-specific mortality. However, the biological mechanisms explaining these associations are unknown. Using gene expression data, we aimed to identify molecular alterations in prostate cancer tissue associated with obesity. Gene Set Enrichment Analysis identified fifteen gene sets up-regulated in the tumor tissue of obese prostate cancer patients (N=84) compared to healthy weight patients (N=192), five of which were related to chromatin remodeling. These gene sets were not identified in an analysis of adjacent normal tissue. Patients with tumors with high expression of chromatin remodeling genes had worse clinical characteristics (Gleason grade >7, 41% versus 17%, p-trend = 3.21 x 10-4) and poorer prostate cancer-specific survival independent of Gleason grade (lethal outcome, OR = 5.01, 95% CI = 2.31 to 11.38). Mediation analysis further supported a role for chromatin remodeling in the obesity-lethal prostate cancer relationship.

overall_design: Gene expression profiling was performed on 602 prostate tissue samples (402 tumor and 200 normal) from the Health Professionals Follow-up Study and Physicians' Health Study Prostate Tumor Cohort. This study includes analysis of 400 samples in GSE62872.

first: Lorelei

last: Mucci


title: 5-hydroxymethylcytosine deposition mediates Polycomb Repressive Complex 2 function in MYCN-amplified neuroblastoma [RNA-seq]

status: Public on May 12 2026

first: Mark

last: Applebaum

address: 900 E 57th St

department: Pediatrics, Section of Hematology/Oncology

institute: University of Chicago

summary: MYCN-amplification is a strong predictor of poor prognosis in neuroblastoma, an embryonal malignancy that accounts for 15% of pediatric cancer deaths. Here, we found that MYCN-amplified neuroblastoma tumors have increased 5-hydroxymethylcytosine (5-hmC) deposition on Polycomb Repressive Complex 2 (PRC2) target genes. 5-hmC and H3K27me3, a catalytic product of PRC2, directly co-localize at the nucleosomal level in MYCN-amplified neuroblastoma. Genes with co-localization of 5-hmC/H3K27me3 are involved in development related pathways and are transcriptionally repressed in MYCN-amplified neuroblastoma. Chemical and genetic inhibition of 5-hmC deposition results in a loss of H3K27me3 deposition on protein-coding genes. Furthermore, 5-hmC deposition predisposes H3K27me3 marked genes to transcriptional activation upon PRC2 inhibition with tazemetostat. Low expression of genes marked by 5-hmC/H3K27me3 is associated with poor clinical outcome. Our results suggest that 5-hmC/H3K27me3 co-operate to repress mediators of development highlighting a novel link between DNA modifications and chromatin modifications with potential therapeutic implications in MYCN-amplified neuroblastoma.

overall_design: CUT&RUN, nano-HMC-seal, and RNA-Seq performed under various conditions in neuroblastoma cell lines

first: Mohansrinivas

last: Chennakesavalu

first: Gabriel L.

last: Lopez

first: Varsha

last: Gupta

first: Kelley

last: Moore

first: Yuxing

last: Xue

first: Josie

last: Majowka

first: Sahil

last: Veeravalli

first: Ryan

last: Borchert

first: Monica

last: Pomaville

first: Alexandre

last: Chlenski

first: Chuan

last: He

first: Andrea

last: Piunti

first: Mark A.


title: Deficiency of JAG2, a muscular dystrophy-related gene, causes Notch signaling dysfunction in muscle stem cells

status: Public on May 11 2026

city: Minneapolis

first: Peter

middle: B

last: Kang

address: 2101 6th Street SE

department: Neurology

institute: University of Minnesota

summary: We previously identified a muscular dystrophy caused by biallelic variants in JAG2, whose protein product Jagged2 is a canonical Notch ligand. However, the disease mechanism remains unclear, particularly with respect to muscle stem cell (MuSC) function and muscle regeneration. We examined the consequences of JAG2 deficiency and modeled pathogenic JAG2 variants in vitro and in vivo, the latter in mouse and fly models and with particular attention to the MuSC-muscle endothelial cell (MuEC) niche. We found that both Jag2 deficiency and overexpression of pathogenic JAG2 variants impaired Notch signaling and myogenic self-renewal and differentiation. Hypomorphic Jag2 mutant (Jag2sm) mice display depleted MuSCs, corresponding with impaired muscle regeneration in those mice. Co-culture experiments and the examination of cell-type-specific Jag2 conditional knockout mice demonstrated that MuEC-specific Jag2 knockout resulted in reduced MuSC self-renewal, while MuSC-specific Jag2 knockout resulted in reduced myogenic differentiation. Human reference JAG2, but not human pathogenic variants of JAG2, rescued the deficiency of Serrate (Ser), the Drosophila ortholog of JAG2. Therefore, pathogenic variants in JAG2 impair muscle development and regeneration through disrupted cell-autonomous cis-inhibition and non-autonomous trans-activation involving Notch signaling dysfunction. Our findings indicate that optimizing JAG2-mediated Notch signaling is a potential therapeutic approach for JAG2-related muscular dystrophy.

overall_design: cDNA-seq profiling of Jag2 deficient mouse muscle stem cells (MuSCs) from 4 samples compared to the cDNA-seq profile of 3 of their WT counterparts, generated using Nanopore sequencing.

first: Minoru

last: Tanaka

first: Nam Chul

first: Isabelle

last: Draper

first: Hannah

middle: R

last: Littel

first: Mekala

last: Gunasekaran

first: Johnnie

last: Turner

first: Natalya

last: Wells

first: Qasim

last: Mujteba

first: Yoko

last: Asakura

first: Atsushi


title: Fif1/2/3 and Rsc1 regulates the development of Penicillium oxalicum fungi and the expression of cellulolytic genes

status: Public on Feb 19 2025

city: Qingdao 266237

first: Kexuan

last: Ma

state: China

address: No. 72 Binhai Road

department: State Key Laboratory of Microbial Technology

summary: The goals of this study are to compare different gene expressions for Penicillium oxalicum wild type strain (WT), Fif1/2/3 and Rsc1 deletion strain (Δfif1/2/3 and Δrsc1) under conditions of 2% glucose or 1% bran + 1% microcrystalline cellulose as carbon source. The results of correlation analysis between each sample showed that the gene expression level of Δfif1/2/3 and Δrsc1 was significantly different from that of the WT strain. The deletion of Fif1/2/3 and Rsc1 significantly down-regulates the expression levels of sporulation process genes. And the absence of Fif1/2/3 and Rsc1 can affect the expression of cellulase-encoding genes.

overall_design: Examination of differential gene expressions by digital gene expression tag profiling in Penicillium oxalicum wild type strain, Fif1/2/3 and Rsc1 deletion mutant strains in 18h in modifeid Mendal’s medium with 2% glucose or 1% bran + 1% microcrystalline cellulose as carbon sources. Three replicates were included for each samples.

first: Yuqi

last: Qin


title: Laser Interstitial Thermal Therapy Enhances Bidirectional Blood-Brain Barrier Permeability in Glioblastoma

status: Public on May 04 2026

city: St. Louis

first: Jason

last: Wong

state: MO

address: Neuroscience Research Building

department: Neurosurgery

institute: Washington University in St. Louis

summary: Laser interstitial thermal therapy (LITT) is a minimally invasive treatment for glioblastoma that increases blood-brain barrier (BBB) permeability. However, the mechanisms and spatiotemporal features of this effect remain unclear. It is also unknown whether LITT promotes release of circulating tumor DNA (ctDNA).Using our previously developed LITT mouse model, we employed single-cell RNA sequencing (scRNAseq) to investigate gene expression changes in endothelial cells following LITT in naïve mouse brain. Brains were also harvested at multiple time points to assess LITT effects on tight junction (TJ) integrity and transcytosis via immunofluorescence and transmission electron microscopy. Human glioblastoma tissues were analyzed to monitor ambient caveolae-mediated transcytosis in tumor regions. Finally, ctDNA levels in mouse plasma were quantified using digital droplet PCR following LITT.LITT triggered downregulation of pathways related to cell-cell junctions and upregulation of transcytosis. LITT transiently disrupted TJ integrity for 7 days up to 100 µm away from the ablation zone. Further, LITT increased caveolae-mediated transcytosis in endothelial cells for 21 days, peaking at 14 days, in part due to suppression of the transcytosis inhibitor Mfsd2a. LITT facilitated ctDNA detection in mouse plasma at 1 hour, 3 days, 7 days, and 14 days post-procedure.Our study demonstrates that LITT transiently disrupts the BBB in the periphery of the ablation with endothelial TJ disruption and transcytosis upregulation following distinct time courses. LITT effects on the BBB are bidirectional and enhance ctDNA release in addition to enabling brain entry of agents.

overall_design: Cell lysis, first-strand, and cDNA synthesis were performed using the Smart-seq-2 protocol in 96-well formats. After cDNA amplification (23 cycles), cDNA concentrations were measured with a dye-fluorescence assay (Quant-iT dsDNA High Sensitivity kit; Thermo Fisher) on a SpectraMax i3x microplate reader (Molecular Devices). Sample plates were selected for downstream processing if the mean concentration of blanks (ERCC-containing, non-cell wells) was greater than 0 ng/µL, and, after linear regression of the values obtained from the Quant-iT dsDNA standard curve, the R2 value was greater than 0.98. Sample wells were then selected if their cDNA concentrations were at least one standard deviation greater than the mean concentration of the blanks. These wells were reformatted to a new 384-well plate at a concentration of 0.3 ng/µL and a final volume of 0.4 µL using an Echo 550 acoustic liquid dispenser (Labcyte). Libraries were prepared and pooled using the Illumina Nextera XT Library Sample Preparation kit. Libraries were then sequenced on the NovaSeq 6000 Sequencing System (Illumina) using 2 × 100 bp paired-end reads and 2 × 8 bp index reads with a 200-cycle kit (Illumina, 20012861). Samples were sequenced at an average of 7.5M reads per cell.

first: Ryan

last: Cleary

first: Yiwei

last: Fu

first: David

last: Giles

first: Albert

last: Kim


title: Identify proinsulin regulators using CRISPR screen and mouse genetics [CRISPR screen]

status: Public on Nov 15 2023

city: Cleveland

first: Sisi

last: Lai

state: Ohio

address: 10900 Euclid Avenue, BRB 609A

department: Genetics and Genome Sciences

institute: Case Western Reserve University

summary: Proinsulin is the precursor of insulin in pancreatic beta cells. Altered proinsulin and proinsulin to insulin ratio mark beta cell dysfunction, predictuing disease progression into type 1 and type 2 diabetes. Of essential role for beta cell function, knowledge about proinsulin production and its role in disease are currently very limited. Using genome wide CRISPR screen, we identified 84 proinsulin regulators including classical protein convertases Pcsk1 and Cpe, and novel factors like Pdia6. Among the list 29 proinsulin regulators were trajectory genes involved in disease progression in obesity and type 2 diabetes in humans. In vivo mouse genetics study revealed unique genetic architecture and quantitative trait loci (QTLs) modulating plasma proinsulin levels. Integrative analyzing and mapping of the QTL signals directly pinpointed to proinsulin regulators identified from the CRISPR screen, which in return greatly improved resolution of the mouse genetic study. 4 out of 5 overlapped genes can be individually validated. Knocking down the leading hits Pdia6 leads to decreased proinsulin content and remarkable loss of proinsulin granules in beta cells. Consequently, proinsulin secretion was greatly decreased. Mechanistically, protein translation rate was greatly impaired after knocking down Pdia6. Our study demonstrated the power of combining in vitro functional genomics with in vivo mouse genetics study to identify proinsulin regulatory network in pancreatic beta cells.

overall_design: MIN6 cells transfected with the GeCKOv2 library were stained with proinsulin and insulin antibodies. Cells were assigned and sorted into "proinsulin high" and "proinsulin low" populations. Genomic DNA of each cell population were extracted using the Dneasy Blood & Tissue kit (Qiagen) and the sgRNA regions were PCR amplified by Herculase II (Agilent) polymerase using indicated primers. The PCR products were purified with Aline PCR Clean DX magnetic beads and processed into Truseq libraries followed by NGS analysis.

first: Chen

last: Weng

first: Yan

last: Li


title: PARP inhibition induces cytotoxicity in mESCs by activating endogenous retroviruses.

status: Public on Nov 08 2023

city: Basel

first: DBM Bioinformatics

last: Core Facility

state: BS

address: Hebelstrasse 20

department: Departement of Biomedicine

institute: University of Basel

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

overall_design: Refer to individual Series


title: Dosage compensation defects due to roX RNA deletion are rescued by recalibration of X/autosome stoichiometry [RNA-seq]

status: Public on Feb 26 2026

city: Planegg-Martinsried

first: Fotios

last: Gkountromichos

address: Großhaderner Strasse 9

department: Molecular Biology

institute: Biomedical Center, Ludwig-Maximilians-Universität München

summary: Metazoa evolved regulatory networks to balance the expression of their sex chromosomes. In Drosophila, males have a single gene-rich X chromosome, whereas females have two. Balanced X/autosome expression is essential for viability, and in male flies is achieved by activation of genes on the X through the male-specific-lethal (MSL) dosage compensation complex (DCC). This ribonucleoprotein assembly contains long, non-coding roX RNAs. To dissect the functional requirements of roX in a cell-based system, we deleted the roX2 gene in male S2 cells and selected two independent lines lacking detectable roX RNA. In the absence of roX, the remaining MSL protein complex was unable to associate with known or newly identified binding sites and thus failed to activate transcription. Surprisingly, the X/autosome expression ratio appeared nevertheless compensated. Cytogenetic and genomic analyses revealed that both roX-deficient cell populations had acquired additional X chromosomes. Apparently, chromosome gains due to mis-segregation made up for the loss of DCC-mediated dosage compensation. Interestingly, ectopic expression of full-length roX2, but not of shortened derivatives, fully restored DCC binding and normalized the karyotype. These findings illustrate that X chromosome dosage compensation is critical for viability even in cultured cells and provide a striking example of rapid evolution under stringent selection.

overall_design: ChIP-seq and CUT&RUN of MSL2 and H4K16ac and RNA-seq profiling of wild-type and roX2-KO Drosophila Schneider S2 cells.

first: George

last: Yankson

first: Muhunden

last: Jayakrishnan

first: Aline

last: Campos Sparr

first: Marisa

last: Müller

first: Patrick

last: Heun

first: Peter

last: Becker