title: A novel lncRNA XLOC_032768 rescues cisplatin-induced apoptosis of renal tubular cells and acute kidney injury by repressing TNF-α expression in trans-manner [mouse]

summary: The cellular and molecular mechanisms by which cisplatin induces nephrotoxicity have been investigated extensively. However, the role of long non-coding RNAs (lncRNAs) in cisplatin-induced nephrotoxicity has not been received much attention. Here, we explore the functions and underlying mechanisms of a novel lncRNA XLOC_032768 in cisplatin-induced nephrotoxicity. Cisplatin treatment resulted in the apoptosis of renal epithelial cells in a mouse model and human renal proximal tubular epithelial cells (HK-2). By performing differentially expressed genes (DEGs) of the transcriptome data, we found the expression of lncRNA XLOC_032768 was significantly repressed by cisplatin treatment, which was also validated by RT-qPCR experiment of in vivo and in vitro model. Overexpression of lncRNA XLOC_032768 significantly inhibited the cisplatin-induced apoptosis of HK-2 and the expression of biomarkers for cisplatin-induced nephrotoxicity. Results from XLOC_032768 overexpression experiment revealed that XLOC_032768 target the tumor necrosis factor (TNF)-α in trans in HK-2 cells and mouse exposed to cisplatin. The administration of lncRNA XLOC_032768 attenuated renal dysfunction, morphological damage, and renal tubular cell injury, which was accompanied by TNF-α preservation, in a mouse model of cisplatin nephrotoxicity. These data indicate that XLOC_032768 suppressed cisplatin-induced apoptosis of tubular epithelial cells and acute kidney injury via a TNF mechanism. LncRNA XLOC_032768 would be a novel agent to reduce cisplatin-induced nephrotoxicity.

overall_design: The C57 mouse for separated into two groups. The two groups were injected with either physiological saline (control) or cisplatin, respectively. The mouse kindey from the two group were extracted and prepared for the following experiments with two biological replicates.

first: Xiangjun

last: Zhou

first: Fan

last: Cheng


title: Transcriptomic in silico screens identify niclosamide for protection against cisplatin- and noise-induced hearing loss in zebrafish and mice through Nrf2 activation

status: Public on Jul 16 2021

city: Omaha

first: Marisa

last: Zallocchi

state: NE

address: 2500 California Plaza

department: Biomedical Sciences

country: USA

institute: Creighton University

type: Expression profiling by high throughput sequencing

summary: We report the RNA expression of the House Ear Institute-Organ of Corti (HEI-OC1) cells with and without cisplatin exposure to identify differencialyy expressed genes. The results of RNA-seq analysis showed 2732 downregulated, and 1639 upregulated genes above 1-fold change in cisplatin threated cells compared to non-treated controls.

overall_design: RNA-seq analysis of HEI-OC1 cells following 15-hour exposure to cisplatin (70 µM)

first: Zuo

last: Jian

first: Salehi

last: Pezhman

first: Zallocchi

last: Marisa

first: Sarath

last: Vijayakumar

first: Madeleine

last: Urbanek

first: Kimberlee

middle: P

last: Giffen

first: Yuju

last: Li

first: Santanu

last: Hati


title: Characterization of the coding and noncoding transcriptome in undifferentiated and differentiated WT and Carma-3XpA/+ mouse embryonic stem cells

status: Public on Aug 02 2021

city: Lausanne

first: Mohamed

last: Nemir

state: Vaud

address: Bugnon 27

department: Cœur et Vaisseau

country: Switzerland

institute: Lausanne University Hospital

summary: RNA (poly(A)+ fraction) was isolated from WT and Carma-3XpA mouse embryonic stem cells at the undifferetiated and differentiated (d3, d6 and d96 days; using the hanging drop model) state. Profiling of the transcritome at these stages of differentiation using deep RNA sequencing allows identifying modulated coding and noncoding transcripts upon induction of differentiation.

overall_design: RNA profiling of mouse embryonic stem cells at undifferentiated and differentiated state. The analysis was performed on WT and Carma-3XpA/+ embryonic stem cells at undifferentiated (d0) and differentiated state (d3, d6 and d10). For each, three biological replicates were used.

first: Maryam

last: Kay

first: Bahram

middle: M

last: Soltani

first: Panagiotis

last: Chauvadras

first: Hassan

last: Ansari

first: Hussein

last: Baharvand

first: Thierry

last: Pedrazzini


title: Small RNA next-generation sequencing of cardiac fibroblasts isolated from young and old mice

status: Public on Jul 14 2021

city: Vienna

first: Matthias

last: Hackl

state: Austria

address: Leberstrasse 20

country: Austria

institute: TAmiRNA GmbH

type: Non-coding RNA profiling by high throughput sequencing

summary: MiRNA expression profile was assessed in cardiac fibroblasts isolated from young (2 months old) and aged (16 months old) mice, by next generation sequencing of small RNA. Bioinformatic analysis of next-generation sequencing output demonstrated 88 differentially expressed miRNAs in aged mice - derived cardiac fibroblasts versus young mice-derived cells, of which two thirds were downregulated and one third were upregulated. The majority of downregulated miRNAs were mapped to chromosome 12, as part of Meg3-Mirg locus, while the remaining were spread on all chromosomes. Almost 90% of miRNA genes within Meg3-Mirg locus were expressed over a wide range in cardiac fibroblasts and had a decreasing trend in the aged group, the majority being significantly downregulated. This study provides evidence that aging is associated to significant alterations in miRNA expression profile in cardiac fibroblasts, a predominant feature being the downregulation of miRNAs within Meg3-Mirg locus.

overall_design: MicroRNA profiles of cardiac fibroblasts isolated from young (2 months old, i.e.reference sample) and old (16-17 months old) C57Bl/6J mice were generated by next-generation sequensing, in 6 biological replicates per each group, using Illumina HiSeq 2500.

first: Ana-Mihaela

last: Lupan

first: Evelyn

middle: G

last: Rusu

first: Alexandrina

last: Burlacu


title: Direct reprogramming of fibroblasts into a cardiovascular tissue

status: Public on Jul 08 2021

city: seoul

first: Jaeyeaon

last: Cho

address: Yonsei-ro 50

country: South Korea

institute: Yonsei University College of Medicine

summary:
Purpose: To explore detailed transcriptome changes during the transition from fibroblasts toward cardiac cells
Methods: We performed single-cell RNA-seq on MTTFs (11,580 cells) and MTTFs treated with MAB for 6 days (12,261 cells). In MTTFs, the mean reads and mediam genes per cell were 53,107 and 5,096, respectively; In reprogrammed cells, the mean reads and medium genes per cell were 100,515 and 6,164, respectively.
Result & Conclusion: Single-cell RNA-seq studies demonstrate a simultaneous reprogramming of mouse tail-tip fibroblasts (MTTFs) by MAB into CMs, Ecs and SMCs.

first: Young-sup

last: Yoon


title: Expression data from lateral and paraxial mesodermal cells differentiated from mouse Embryonic Stem Cells

status: Public on Jul 07 2021

city: Istanbul

first: Emre Can

last: Tüysüz

address: Ibrahimaga Mah.

country: Turkey

institute: Yeditepe University

summary: Mouse Embryonic Stem Cells (mESCs) were differentiated with EB formation and characterized with Flk1 and PDGFαR specific antibodies. miRNA profile of lateral mesodermal cells, paraxial mesodermal cells, DN (Double negative) and DP (Double positive) populations were firstly determined and effects of differentially expressed miRNAs transfected transiently on EB formation, and myogenic and hematopoietic differentiation potential were assessed.

overall_design: ES-E14TG2a cells were differentiated to with EB formation and four different subgroups including lateral mesodermal cells, paraxial mesodermal cells, DN cells and DP cells were sorted on day 5. miRNA profile of these subgroups were detected.

first: Emre

middle: C

last: Tuysuz

first: Sukru

last: Gulluoglu

first: Omer

middle: F

last: Bayrak


title: Vitamin A deficiency affects gene expression in the Drosophila melanogaster head

status: Public on Jul 26 2021

city: Boston

first: Jens

last: Rister

state: MASSACHUSETTS

address: 100 Morrissey Boulevard

department: Biology

institute: University of Massachusetts Boston

summary: We report genes and molecular pathways that respond to vitamin A deficiency.

overall_design: Comparing total RNA from heads of vitA deficient or vitA replete four-day old wild type female Canton S.

first: Deepshe

last: Dewett

last: Labaf

first: Kourosh

last: Zarringhalam


title: Gene expression analysis of Eu-TCL1 CLL cells with Zap70 expression

city: New Haven

first: Mark

last: Robinson

state: CT

address: 300 George St

department: Center of Molecular and Cellular Oncology

institute: Yale University

summary: RNA-sequencing was used to determine gene expression of 4  Eµ-TCL1 (control) and 4 Eµ-TCL1 Zap70-ki mice which developed CLL.

overall_design: 4 biological replicates of WT and knock-in conditions.

first: Markus

last: Muschen

first: Teresa

last: Sadras


title: Transcript profiling of putative NF-kB activators in wild-type and NFKB1-null HeLa cells

status: Public on Jul 01 2021

city: Research Triangle Park

first: Christopher

last: Corton

state: NC

address: 109 TW Alexander Dr.

institute: US-EPA

summary: In future high-throughput transcriptomic studies, we propose that the use of cell lines nullizygous for important target genes of environmental chemicals will greatly facilitate the interpretation of gene expression profiles. To provide support for this concept, we generated transcript profiles of known or putative NF-kB activators in wild-type and NFKB1-null HeLa cells. Both cell lines were treated with interleukin 1 (IL1beta), tumor necrosis alpha (TNFalpha) or one of two chemicals identified in high throughput assays for NF-kB activity (chlorhexidine diacetate and carbocyanine). The profiles were generated using TempO-Seq targeted sequencing of ~3000 human genes. Almost all of the genes regulated by IL1beta and TNFalpha in wild-type cells were no longer altered in the NFKB1-null cells and approximately half of the genes regulated by Chlorhexidine diacetate and carbocyanine were dependent on NFKB1 for expression changes.  These studies demonstrate that many of the changes in gene expression after exposure to the putative NF-kB activators were NFKB1-dependent.

overall_design: An initial range finding experiment was conducted in wild-type and the NFKB1-null HeLa cells, to determine the optimal concentration of the tested chemicals. Cells were plated in 12-well plates and incubated 20 hours. The media was replaced with dosing solutions containing DMSO (0.05%) or IL1beta (1 ng/mL), TNFalpha (5 ng/mL), chlorhexidine diacetate (50 µM), or carbocyanine (50 µM) in DMSO (0.05%).  After 6 hours of exposure, media was removed and cells were lysed in 0.3 mL Trizol, followed by RNA extraction. Gene expression changes in wild-type and NFKB1-null cells were evaluated using the human 1500+ Tempo-Seq platform (BioSpyder, Inc, Carlsbad, CA).

first: J

last: Liu


title: PPM1D mutations are oncogenic drivers of Diffuse Midline Gliomas and are sufficient to enhance glioma formation

status: Public on Jul 11 2021

first: Prasidda

last: Khadka

address: 450 Brookline Ave

institute: Dana Farber Cancer Institute

summary: The role of PPM1D mutations in de novo gliomagenesis has not been systematically explored. Here we analyze whole genomes sequences of 170 pediatric high-grade gliomas and find that truncating mutations in PPM1D that increase the stability of its phosphatase are clonal driver events in 11% of DMGs and are enriched in primary pontine tumors. Through the development of novel DMG mouse models, we show that PPM1D mutations potentiate gliomagenesis and that PPM1D activity is required for in vivo oncogenesis. Finally, we applied integrative phosphoproteomic and functional genomics assays and found that the oncogenic effects of PPM1D truncation converge on regulators of cell cycle, DNA damage response, and p53 pathways, revealing therapeutic vulnerabilities including MDM2 inhibition. Together, these findings highlight PPM1D mutations to represent a targetable driver of pediatric gliomas.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Examination of PPM1D truncating mutations in tumor cells from mouse models of DIPG and patient-derived DIPG cell lines

first: Timothy

last: Phoenix

first: Pratiti

last: Bandopadhayay


title: Whole transcriptome analysis of resveratrol and metformin improving high fat diet induced insulin resistance in liver and muscle

status: Public on Jun 18 2021

city: Shijiazhuang

first: Linyi

last: Shu

state: Hebei

address: 348 Heping West Road

department: Department of Endocrinology

country: China

institute: Hebei General Hospital

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

overall_design: Refer to individual Series


title: Identifying High-Risk Triple-Negative Breast Cancer Patients by Molecular Subtyping

status: Public on Jul 31 2021

city: Halle (Saale)

first: Martina

last: Vetter

address: Ernst-Grube-Str. 40

department: Dept. of Gynaecology

country: Germany

summary:
Triple-negative breast cancer (TNBC) is considered the most aggressive type of breast cancer with limited options for therapy. TNBC is a heterogeneous disease and tumours has been classified into TNBC subtypes using gene expression profiling to distinguish basal-like1 (BL1), basal-like2 (BL2), immunomodulatory (IM), mesenchymal (M), mesenchymal/stem-like (MSL), luminal androgen receptor (LAR) and one non-classifiable group (called unstable, UNS).
The aim of this study was to verify the clinical relevance of molecular subtyping of TNBCs by expression analysis to improve the individual indication of systemic therapy.

overall_design: Molecular subtyping was performed in 124 TNBC tumours that were obtained from a prospective, multicentre cohort including 1,270 histopathologically confirmed invasive, non-metastatic breast cancers (NCT 01592825).

first: Carolin

last: Hartung

first: Martin

last: Porsch

first: Kathrin

last: Stückrath

first: Sandy

last: Kaufhold

middle: S

last: Staege

first: Volker

last: Hanf

first: Tilmann

last: Lantzsch

first: Christoph

last: Uleer

first: Susanne

last: Peschel

first: Jutta

last: John

first: Marleen

last: Pöhler

first: Edith

last: Weigert

first: Jörg

last: Buchmann

first: Karl-Friedrich

last: Bürrig

first: Kathleen

last: Schüler

first: Daniel

last: Bethmann

first: Ivo

last: Große

first: Eva

middle: J

last: Kantelhardt

last: Thomssen


title: Whole transcriptome analysis of resveratrol and metformin improving high fat diet induced insulin resistance

first: Linlin

last: Yang

address: 348, Heping west road

summary: Long non-coding RNAs (lncRNAs) play key roles in various diseases; however, their functions in insulin resistance are unclear. This study aimed to determine whether resveratrol or metformin could influence the expression of lncRNA and to elucidate the underlying mechanism. We conducted a high-throughput sequencing analysis to detect lncRNA and mRNA expression signatures of mice that were fed with HFD to induce IR.

overall_design: Mice were assigned into 4 groups, skeletal muscle were collected, snap frozen on dry ice. Total RNA was harvested using Trizol reagent and then sequenced through Illumina NovaSeq 6000.

first: Guangyao

last: Song

first: Chao

last: Wang

first: Huijuan

last: Ma


title: Transcriptional regulator AflR on the overall regulation mechanism of Aspergillus flavus

city: Qingdao

first: peng

last: wang

address: Ocean University of China, No.5 Yushan Road, Shinan District

institute: Ocean University of China

summary:
Objective: Aspergillus flavus aflR, a gene encoding a Zn(II)2Cys6 DNA-binding domain, is an important transcriptional regulator of the aflatoxin biosynthesis gene cluster. Our previous results of GO analysis for the binding sites of AflR in A. flavus suggest that AflR may play an integrative regulatory role. This study aimed to investigate the integrative function of the aflR gene in A. flavus.
Design: In this study, we used Aspergillus flavus NRRL3357 as a wild-type strain (WT) and constructed a knockout strain of A. flavus ΔaflR by homologous recombination. Based on the transcriptomics technology, we investigated the metabolic effects of aflR gene on growth, development and toxin synthesis of A. flavus, and discussed the overall regulation mechanism of aflR gene on A. flavus at the transcriptional level.
Results: The disruption of aflR severely affected the aflatoxin biosynthetic pathway, resulting in a significant decrease in aflatoxin production. In addition, disrupted strains of the aflR gene produced relatively sparse conidia and a very small number of sclerotia. However, the biosynthesis of cyclopiazonic acid (CPA) was not affected by aflR gene disruption. Transcriptomic analysis of the ΔaflR strain grown on potato dextrose agar (PDA) plates at 0 h, 24 h, and 72 h showed that expression of clustering genes involved in the biosynthesis of aflatoxin was significantly down-regulated. Meanwhile, the ΔaflR strain showed significant expression differences in genes involved in spore germination, sclerotial development, and carbohydrate metabolism compared to the WT strain.
Conclusions: The results showed that the A. flavus aflR gene also played a positive role in the growth and development of fungi.

overall_design: mRNA profiles of wild-type (WT) and aflR knockout A. flavus at 0 h, 24 h and 72 h

first: Qing

last: Kong

first: Peng

first: Jia

last: Xu

first: Perng-Kuang

last: Chang

first: Zhemin

last: Liu


title: Differential miRNA and mRNA Expression in Immortalized Human Keratinocytes (HaCaT) after Low Arsenic Exposure (RNA-Seq)

city: Louisville

first: J.

middle: Christopher

last: States

state: KY

address: 505 S. Hancock St., Rm 304

department: Department of Pharmacology & Toxicology

institute: University of Louisville

summary: Determining the miRNA and mRNA expression profiles in HaCaT cells at early and late stages of arsenite exposure to reveal early and late changes in the HaCaT cells transformation process.

overall_design: 4 biological replicates of HaCaT cells exposed to 100 nM sodium arsenite and unexposed HaCaT cells (Control)

first: Laila

last: Al-Eryani

first: Samantha

last: Jenkins

first: Elizabeth

last: Hudson

first: Theodore

last: Kalbfleisch

first: J


title: Retinoblastoma genome variation profiling by genome tiling array

status: Public on Jul 06 2021

city: paris

first: Elodie

last: chapeaublanc

address: 26 rue d'ulm

department: UMR 144

country: France

institute: Institut Curie

type: Genome variation profiling by genome tiling array

summary: Retinoblastoma is the most common intraocular cancer of infancy and childhood, with an incidence of one case per 15,000 - 20,000 live births. An early event in retinoblastoma genesis is a functional loss of both alleles of the RB1 gene. However, other genes are likely to be involved in the development of this cancer. In this study we sought to build a comprehensive molecular portrait of this cancer by performing transcriptomic, methylomic, genomic  profiling of primary retinoblastoma samples. Most of the patients whose tumors were studied had received no treatment prior to surgical enucleation.

overall_design:
Immediately following enucleation, a needle was inserted through the eye's anterior chamber to extract a tumor sample by aspiration; the tumor specimen was then snap frozen. For these arrays, DNA was extracted from these snap frozen samples.
We used 5.3K BAC-CGH arrays to study the genome alteration patterns of 26 primary retinoblastoma tumors.
We used 3.5K BAC-CGH arrays to study the genome alteration patterns of 52 primary retinoblastoma tumors.

first: François

last: Radvanyi

first: Meriem

last: Sefta

last: Chapeaublanc

first: Céline

last: Brulard


title: Effects and role(s) of the noncoding subgenomic RNA of red clover necrotic mosaic virus in virus infection

status: Public on Jun 26 2021

city: Ames

first: Wyatt

middle: Allen

last: Miller

state: IA

address: 2213 Pammel Dr

department: Plant Pathology & Microbiology

institute: Iowa State University

summary: In recent years, a new class of viral noncoding subgenomic (ncsg)RNA has been identified that is generated as a stable degradation product formed via an exonuclease-resistant (xr) RNA structure that blocks the progression of 5’-3’ exonuclease that degrades viral RNAs in infected cells.  The xrRNA-derived ncsgRNAs have been implicated in virus pathogenicity, virus movement and transmission, and suppressing antiviral defense responses.  Although ncsgRNAs of animal viruses have been studied extensively, research on the role of xrRNA-derived plant viral ncsgRNAs remain scarce.  In this study, we assess the effects of the ncsgRNA of red clover necrotic mosaic virus (RCNMV), called SR1f, in infected plants.  We demonstrate that the presence of SR1f leads to severe symptoms and increased viral RNA accumulation in Nicotiana benthamiana and Arabidopsis thaliana.  We also provide evidence that suppression of RNA silencing is not the primary function of SR1f.  Additionally, a comparative transcriptomic analysis in N. benthamiana infected with wildtype RCNMV and an SR1f-deficient mutant RCNMV reveal that wt RCNMV infection that produces SR1f has a greater and significant impact on cellular gene expression resulting in deregulation of several cellular pathways with upregulation of genes mainly involved in plant hormone signaling, plant-pathogen interaction, MAPK signaling, and several metabolic pathways and downregulation of genes involved mainly in photosynthesis.

overall_design: Comparative transcriptomic analysis of non-inoculated systemic leaves of Nicotiana benthamiana plants that were mechanically inoculated with either (1) wildtype redclover necrotic mosaic virus (wt RCNMV RNA1 + RNA2, 4 biological replicates), (2) RCNMV∆SR1f (mutant RCNMV RNA1-m1 + RNA2, 4 biological replicates), or (3) 10 mM sodium phosphate buffer (Mock-inoculation, 3 biological replicates)

first: Pulkit

last: Kanodia

first: W

middle: A


title: Transcriptomes of AGS cells with and without FTO depletion

status: Public on Jun 23 2021

city: Changzhou

first: You

last: Zhou

state: Jiangsu

address: Juqian Rd No.185

institute: The Third Affiliated Hospital of Soochow University

summary: RNA sequencing of AGS cells with and without FTO depletion to identify FTO-regulated genes

overall_design: Total RNA from AGS cells with and without FTO depletion was generated by deep sequencing, in triplicate, using Illumina HiSeq 4000.

first: Jingting

last: Jiang


title: CRISPR gene editing and inducible pluripotent stem cell neuronal disease modelling for rare disease diagnosis: EMHM1 genetic variant analysis in Kleefstra Syndrome

city: North Coogee

first: Denise

last: Anderson

state: WA

address: 71 Caledonia Loop

country: Australia

institute: INSiGENe Pty Ltd

summary: Over 400 million people worldwide are living with a rare disease, with genetic variants determining 80% of cases. Next Generation Sequencing identifies potential disease causative genetic variants, however many of these are classified as variants of uncertain significance (VUS). Each VUS requires functional validation as pathogenic or benign in disease pathology in specialist laboratories creating major delays in patient diagnosis. In this study we test a rapid genetic variant assessment pipeline using an EHMT1 (Euchromatin histone methyltransferase 1; EHMT1 p.Gln1144Ter)  genetic variant that is pathogenic for Kleefstra Syndrome. Precise CRISPR homology directed (HDR) gene editing introduced the single nucleotide genetic variant in iPS cells and EHMT1_SNV cell clones were rapidly identified with amplicon sequencing. Induction of neural differentiation and RNA sequencing determined differences in differentiation at the gene and transcription factor level. The applied CRISPR HDR methodology was rapid and reliable for the introduction of SNVs in iPSCs for subsequent neuronal cell differentiation. Key features of Kleefstra Syndrome were identified, with involvement of key transcription factors REST and SP1 in disease mechanisms. This study indicates that precise iPSC gene editing and changes in disease modelling pathways can contribute to disease diagnosis and understanding of mechanisms.

overall_design: Comparison of CRISPR edited EHMT1_SNV and EHMT1_WT iPSCs via RNA sequending before and after induction of neural differentiation

first: Vanessa

last: Fear


title: Sparcl1 promotes nonalcoholic steatohepatitis progression through upregulation of CCL2

status: Public on Jun 10 2021

city: Lianyungang City

first: bin

last: liu

state: Jiangsu Province

institute: Jiangsu Ocean University

summary: 1. White adipose tissues (WAT) are capable of secreting not only fatty acids but also a class of secretory proteins that modulate the homeostasis of distant organs, including the liver. To identify potential WAT-enriched secretory factors involved in NASH progression, C57BL/6 male mice were fed with a normal chow diet or HFHC diet for two different periods: 12 weeks and 28 weeks. Then, we compared the expression profile of epididymal WAT (eWAT) from mouse models of NAFL and NASH above mentioned by RNA-Sequencing analysis.    2.  To investigate the contribution of Sparcl1 in the pathogenesis of NASH, male C57BL/6J mice were fed a HFHC diet for 12 weeks, and then intraperitoneal injected with saline or recombinant Sparcl1 protein (0.2mg/kg) every other day for 3 weeks. To elucidate the molecular basis of Sparcl1-mediated NASH progression, we conducted RNA-Sequencing analysis for differentially expressed genes using the livers of chronic recombinant Sparcl1 protein or saline- treated mice.

overall_design: Male C57BL/6J mice aged 6 weeks were purchased from the Shanghai Laboratory Animal Company (SLAC, Shanghai, China). For NAFL or NASH diet feeding, C57BL/6J mice were fed a diet containing 40% fat, 22% fructose, and 2% cholesterol (D09100310, Research Diets Inc.) for 12 or 28 weeks. Mice were intraperitoneal injected with saline or recombinant Sparcl1 protein (0.2mg/kg) every other day for 3 weeks. RNA high throughput sequencing was performed by Cloud-Seq Biotech (Shanghai, China). Briefly, total RNA was used for removing the rRNAs with NEBNext rRNA Depletion Kit (New England Biolabs, Inc., Massachusetts, USA) following the manufacturer's instructions. RNA libraries were constructed by using NEBNext® Ultra™ II Directional RNA Library Prep Kit (New England Biolabs, Inc., Massachusetts,USA) according to the manufacturer’s instructions. Libraries were controlled for quality and quantified using the BioAnalyzer 2100 system (Agilent Technologies, Inc., USA). Library sequencing was performed on an illumina Hiseq instrument with 150bp paired end reads. Paired-end reads were harvested from Illumina HiSeq 4000 sequencer, and were quality controlled by Q30. After 3’ adaptor-trimming and low quality reads removing by cutadapt software (v1.9.3), the high quality clean reads were aligned to the reference genome (UCSC mm10) with hisat2 software (v2.0.4). Then, guided by the Ensembl gtf gene annotation file, cuffdiff software (part of cufflinks) was used to get the gene level FPKM as the expression profiles of mRNA, and fold change and P value were calculated based on FPKM, differentially expressed mRNA were identified.

first: Yan

last: Lu

first: Bin

last: Liu


title: A novel lncRNA XLOC_032768 rescues cisplatin-induced apoptosis of renal tubular cells and acute kidney injury by repressing TNF-α expression in trans-manner [human]

status: Public on Jul 27 2021

city: Wuhan

first: Dong

last: Chen

state: Hubei

address: 388 GaoXin 2nd Road, East Lake Hi-Tech Development Zone

department: Center for Genome Analysis

institute: ABLife, Inc.

summary: The cellular and molecular mechanisms by which cisplatin induces nephrotoxicity have been investigated extensively. However, the role of long non-coding RNAs (lncRNAs) in cisplatin-induced nephrotoxicity has not been received much attention. Here, we explore the functions and underlying mechanisms of a novel lncRNA XLOC_032768 in cisplatin-induced nephrotoxicity. Cisplatin treatment resulted in the apoptosis of renal epithelial cells in a mouse model and human renal proximal tubular epithelial cells (HK-2). By performing differentially expressed genes (DEGs) of the transcriptome data, we found the expression of lncRNA XLOC_032768 was significantly repressed by cisplatin treatment, which was also validated by RT-qPCR experiment of in vivo and in vitro model. Overexpression of lncRNA XLOC_032768 significantly inhibited the cisplatin-induced apoptosis of HK-2 and the expression of biomarkers for cisplatin-induced nephrotoxicity. Results from XLOC_032768 overexpression experiment revealed that XLOC_032768 target the tumor necrosis factor (TNF)-α in trans in HK-2 cells and mouse exposed to cisplatin. The administration of lncRNA XLOC_032768 attenuated renal dysfunction, morphological damage, and renal tubular cell injury, which was accompanied by TNF-α preservation, in a mouse model of cisplatin nephrotoxicity. These data indicate that XLOC_032768 suppressed cisplatin-induced apoptosis of tubular epithelial cells and acute kidney injury via a TNF mechanism. LncRNA XLOC_032768 would be a novel agent to reduce cisplatin-induced nephrotoxicity.

overall_design: We prepraed human HK-2 cells to perform the experiment. LncRNA overexpression plasmid and negative control were transferred into the cells, respectively. The cells were exposed to cisplatin for 24h. We then captured the RNAs after removing the rRNAs in the cells. Two biological replicates were prepared for each treatment.

first: Xiangjun

first: Fan

last: Cheng


title: GeoMx Cancer Transcriptome Atlas (CTA) mRNA assay on 191 ROIs from a NSCLC tumor. [NSCLC_191_grid]

city: Seattle

first: Patrick

last: Danaher

address: 530 Fairview Ave N

institute: NanoString Technologies, Inc.

summary: Dense spatial gene expression profiling of a NSCLC tumor. This study was part of Danaher & Kim et al., "Advances in mixed cell deconvolution enable quantification of cell types in spatially resolved gene expression data"

overall_design: One NSCLC tumor was profiled with the GeoMx Cancer Transcriptome Altas RNA assay. 191 ROIs were chosen, and tumor (PanCK+) and microenvironment (PanCK-) AOIs were collected from each ROI.

first: Youngmi

last: Kim

first: Brenn

last: Nelson

first: Griswold

last: Maddy

first: Zhi

last: Yang

first: Erin

last: Piazza

first: Joseph

last: Beechem


title: GeoMx Cancer Transcriptome Atlas (CTA) mRNA assay on 191 ROIs from a NSCLC tumor.

overall_design: Five NSCLC tumors were profiled with the GeoMx Cancer Transcriptome Atlas RNA assay. 20-24 ROIs were chosen from each tissue, and tumor (PanCK+) and microenvironment (PanCK-) AOIs were collected from each ROI. Matching GeoMx protein data was collected on the same tissues and ROIs.


title: GeoMx Cancer Transcriptome Atlas (CTA) mRNA assay on an FFPE cell pellet array of mixed HEK293T and CCRF-CEM cell lines.

summary: Gene expression profiling of mixed cell lines, used to evaluate the performance of deconvolution methods. This study was part of Danaher & Kim et al., "Advances in mixed cell deconvolution enable quantification of cell types in spatially resolved gene expression data"

overall_design: The cell lines HEK293T and CCRF-CEM were mixed in a dilution series and made into an FFPE cell pellet array. Using the GeoMx NGS RNA assay, a single AOI was profiled from each pellet.


title: Diversity of satellite glia in sympathetic and sensory ganglia

status: Public on Jun 01 2021

city: Baltimore

first: Rejji

last: Kuruvilla

state: MD

address: 3400 N. Charles St.

institute: Johns Hopkins University

summary: Satellite glia are the major glial type found in ganglia of the peripheral nervous system that wrap around cell bodies of sympathetic and sensory neurons that are very diverse. Other than their close physical association with peripheral neurons, little is known about this glial population. Here, we performed single cell RNA sequencing analysis and identified five different populations of satellite glia from sympathetic and sensory ganglia. We identify three shared populations of satellite glia enriched in immune-response genes, immediate-early genes and ion channels/ECM-interactors, respectively. Sensory- and sympathetic-specific satellite glia are differentially enriched for modulators of lipid metabolism. Sensory glia are also specifically enriched for genes involved in glutamate turnover. Further, satellite glia and Schwann cells can be distinguished by unique transcriptional signatures. This study reveals remarkable heterogeneity of satellite glia in the peripheral nervous system.

overall_design: Single cell gene expression profiling of sympathetic (SCG) and sensory (DRG) ganglia using the Drop-Seq protocol

first: Michael

middle: B

last: Thomsen

first: Aurelia

last: Mapps


title: CITE-seq of 6 patients treated with the Pfizer BioNTech BNT162b2 mRNA vaccine

status: Public on Jun 25 2021

city: Stanford

first: Madeleine

last: Scott

state: CA

address: 729 Lagunita Dr

institute: Stanford

summary: Purpose: To understand the single cell landscape of patients treated with the BNT162b2 mRNA vaccine

overall_design: Methods: peripheral blood was isolated from 6 volunteers before, 24 or 48 hours, and 7 days after the primary and secondary immunization

middle: K

first: Prabhu

last: Arunachalam

first: Thomas

last: Hagan


title: Impact of the aryl hydrocarbon receptor on Aurora A kinase and the G2/M phase pathway in hematopoietic stem and progenitor cells

status: Public on Jun 07 2021

city: Rochester

first: Anthony

last: Franchini

state: NY

address: 601 Elmwood Ave

institute: University of Rochester

summary: Analysis of gene expression changes to HSCs and MPPs following loss of aryl hydrocarbon receptor activation

overall_design: To determine role of aryl hydrocarbon receptor gene targets that control HSC function and proliferation.

first: Keegan

last: Vaughn

first: Kameshwar

last: Singh

first: Soumyaroop

last: Bhattacharya

last: Gasiewicz

first: B

last: Lawrence


title: High-resolution mapping of regulatory element interactions and genome architecture using ARC-C [RNA-Seq]

city: Cambridge

first: Julie

last: Ahringer

address: Tennis Court Road

department: The Gurdon Institute

country: United Kingdom

institute: University of Cambridge

summary: Interactions between cis-regulatory elements such as promoters and enhancers are important for transcription but global identification of these interactions remains a major challenge. Leveraging the chromatin accessiblity of regulatory elements, we developed ARC-C (accessible region chromosome conformation capture), which profiles chromatin regulatory interactions genome-wide at high resolution. Applying ARC-C to C. elegans, we identify ~15,000 significant interactions at 500bp resolution. Regions bound by transcription factors and chromatin regulators such as cohesin and condensin II are enriched for interactions, and we use ARC-C to show that the BLMP-1 transcription factor mediates interactions between its targets. Investigating domain level architecture, we find that C. elegans chromatin domains defined by either active or repressive modifications form topologically associating domains (TADs) and that these domains interact to form A/B (active/inactive) compartment structure. ARC-C is a powerful new tool to interrogate genome architecture and regulatory interactions at high resolution.

overall_design: We performed RNA-seq replicates measuring polyA mRNA expression in wildtype and met2set25 C elegans L3 larvae.

first: Ni

last: Huang

first: Wei

middle: Q

last: Seow


title: RNA-seq analysis of Mycobacterium Smegmatis ΔF6 vs. Wild type

status: Public on May 31 2021

city: Moscow

first: Artem

last: Grigorov

address: Ulitsa Miklukho-Maklaya, 16/10

department: Genomics and Postgenomic Technologies

country: Russia

institute: Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry

summary: The study was conducted to understand the role of F6 small non-coding RNA in M.smegmatis. The results are a description of transcriptome changes in M. smegmaits strain with deletion of a gene of small RNA F6 relative to wild type strain.

overall_design: Trancriprtome profiles of wild type and ΔF6 strains of M.smegmatis in logarithmic phase were generated by deep sequencing, in triplicate, using IlluminaHiSeq2500

first: Elena

last: Salina

first: Oksana

last: Bychenko

first: Yulia

last: Skvortsova

first: Tatyana

last: Azhikina


title: High-resolution mapping of regulatory element interactions and genome architecture using ARC-C

type: Genome binding/occupancy profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: High-resolution mapping of regulatory element interactions and genome architecture using ARC-C [ARC-C]

overall_design: We performed ARC-C in wildtype, blmp-1 and met2set25 C elegans L3 larvae.


title: Effect of enforced expression of ZAP70 in development of naïve B-cell repertoire

city: New Haven

first: Mark

last: Robinson

address: 300 George St

institute: Yale University

summary: We investigate the effect of altered kinase levels (ZAP70) in the VDJ usage of B-cell receptors in humanized mice

overall_design: Human cord blood derived CD34+ progenitor cells were transduced with a GFP vector control, or GFP-labelled ZAP70 lentivirus and injected into NOD/Scid/Il-2rg/Kit-W41J/Tyr mice. GFP positive and negative naïve B-cells (CD19+CD27-CD10-) were isolated from 6-month old mice by FACS. 10,000 cells pooled from 3 independent mice per group were subjected to single cell BCR VDJ sequencing (10X).

first: Markus

last: Muschen

first: Teresa

last: Sadras


title: Transcriptional profiling to elucidate processes regulated by 2',3'-cyclic nucleotide monophosphates in Escherichia coli

status: Public on May 23 2021

city: Atlanta

first: Gregory

last: Tharp

state: GA

address: 954 Gatewood Dr

department: Developmental and Cognitive Neuroscience

institute: Yerkes National Primate Research Center

summary: The impact of 2',3'-cyclic nucleotide monophosphates (2',3'-cNMPs) on global gene expression in E. coli was investigated by heterologous expression of a 2',3'-cyclic nucleotide phosphodiesterase (CNPase), which reduces intracellular 2',3'-cNMP levels.

overall_design: Global transcript levels in E. coli expressing CNPase were compared to levels in control cells expressing a catalytically inactive variant of the enzyme to identify cellular processes modulated by 2',3'-cNMPs.

first: Emily

middle: E

last: Weinert

first: Benjamin

last: Fontaine

first: Nirav

last: Patel


title: lncRNA-CR46018 as a positive regulator controls Drosophila Toll immune response by interacting with Dif/Dorsal

status: Public on May 20 2021

city: Nanjing

first: Hongjian

last: Zhou

address: No.1 Wenyuan Road, Xianlin University Town, Nanjing

institute: Nanjing Normal University

summary: The Toll signaling pathway is highly conserved from insects to mammals. Drosophila is a model species that is commonly used to study innate immunity. Although many studies have assessed protein-coding genes that regulate the Toll pathway, it is unclear whether long noncoding RNAs (lncRNAs) play regulatory roles in the Toll pathway. Here, we evaluated the expression of the lncRNA CR46018 in Drosophila. Our results showed that this lncRNA was significantly overexpressed after infection of Drosophila with Micrococcus luteus. A CR46018-overexpressing Drosophila strain was then constructed; we expected that CR46018 overexpression would enhance the expression of various antimicrobial peptides downstream of the Toll pathway, regardless of infection with M. luteus. RNA-seq analysis of CR46018-overexpressing Drosophila after infection with M. luteus showed that upregulated genes were mainly enriched in Toll and Imd signaling pathways. Moreover, bioinformatics predictions and RNA-immunoprecipitation experiments showed that CR46018 interacted with the transcription factors Dif and Dorsal to enhance the Toll pathway. During gram-positive bacterial infection, flies overexpressing CR46018 showed favorable survival compared with flies in the control group. Based on these findings, we renamed CR46018 as lncRNA-RDIP. Overall, our current work not only reveals a new immune regulatory factor, lncRNA-RDIP, and explores its potential regulatory model, but also provides a new perspective for the effect of immune disorders on the survival of Drosophila melanogaster.

overall_design: the infected M. luteus male adult CR46018-overexpressing and control flies were collected at 12 h post-infection for subsequently RNA-seq

first: Shengjie

last: Li

first: Fei

last: Ma

first: Ping

last: Jin


title: CRISPR activation and interference screens decode stimulation responses in primary human T cells [CRISPR]

status: Public on May 13 2021

city: San Francisco

first: Zachary

last: Steinhart

address: 1650 Owens St

department: Gladstone-UCSF Institute of Genomic Immunology

institute: J. David Gladstone Institutes

summary: Regulation of cytokine production in stimulated T cells can be disrupted in autoimmunity, immunodeficiencies, and cancer. Systematic discovery of stimulation-dependent cytokine regulators requires both loss-of-function and gain-of-function studies, which have been challenging in primary human cells. We now report genome-wide CRISPR activation (CRISPRa) and interference (CRISPRi) screens in primary human T cells to identify gene networks controlling interleukin 2 and interferon gamma production. Arrayed CRISPRa confirmed key hits and enabled multiplexed secretome characterization, revealing reshaped cytokine responses. Coupling CRISPRa screening with single-cell RNA-seq enabled deep molecular characterization of screen hits, revealing how perturbations tuned T cell activation and promoted cell states characterized by distinct cytokine expression profiles. Together, these screens reveal genes that reprogram critical immune cell functions, which could inform the design of immunotherapies.

sample_organism:
Homo sapiens
unidentified plasmid

platform_organism:
Homo sapiens
unidentified plasmid

overall_design: Pooled CRISPRa and CRISPRi screens followed by sorting for IL-2 and IFN-g high or low expressing bins

first: Ralf

last: Schmidt

first: Madeline

last: Layeghi

first: Jacob

middle: W

last: Freimer

first: Vinh

last: Nguyen

first: Franziska

last: Blaeschke

first: Alexander

last: Marson


title: Mapping N6-methyladenosine (m6A) peaks in wild-type and METTL5 knockout (KO) HeLa cells

status: Public on May 19 2021

city: Chicago

first: Caraline

last: Sepich

state: IL

address: 929 E 57th Street

department: Chemistry

institute: University of Chicago

summary: We report the application of MeRIP-seq to map m6A peaks in wild type and METTL5 KO HeLa cells to investigate targets of the m6A methyltransferase METTL5.

overall_design: Comparing RNA-seq of m6A-immunoprecipitate samples to reference input samples to map m6A peaks followed by comparison of peaks between wild type and METTL5 KO cells.

last: Sepich-Poore

first: Sigrid

last: Nachtergaele

first: Chuan

last: He


title: Identification of candidate genes simultaneously shared by adipogenesis and osteoblastogenesis from human mesenchymal stem cells

status: Public on May 21 2021

city: Jiujiang

first: Jianjun

last: Xiong

address: 17 Lufeng Road

institute: Jiujiang University

summary: we aimed to screen candidate genes of adipocyte/osteoblastogenesis using human mesenchymal stem cells (hMSCs) at 3, 5, and 7 days through RNA-Seq technique. The 275 significantly differentially expressed genes (DEGs) were identified simultaneously shared by two anecdotes. Furthermore, we confirmed that ANKRD1 (ankyrin repeat domain 1) facilitated adipogenesis and weaked osteoblastogenesis  via RNA interference (RNAi), and IGF1 (insulin like growth factor 1) simultaneously enhancted adipo-osteoblastogenesis. This study would provide the potential molecular switches for the study of the balance of adipo-osteoblastogenesis and therapy of metabolic bone disease osteoporosis.

overall_design: Examination of 4 different sampling time in human mesenchymal stem cells.

first: Weidong

first: Shan

last: Wu

first: Jianyun

last: Liu


title: GeoMx Cancer Transcriptome Atlas (CTA) mRNA assay

first: Patrick

last: Danaher


title: Differential transcriptome analysis reveals genes related to low- and high-temperature stress in the fall armyworm (Spodoptera frugiperda)

status: Public on May 26 2021

city: Gimcheon

first: Mohammad

last: Vatanparast

address: 167, Yongjeon-ro

department: Plant quarantine technology center

institute: Animal and Plant Quarantine Agency

summary:
Purpose: We aimed to use RNA-Seq and de novo transcriptome assembly to produce transcriptomes and analyze the changes in transcription regulation associated with cold and heat treatment in Spodoptera frugiperda. A detailed differential expression analysis revealed a number of candidate genes that may be associated with FAW cold and heat tolerance. To validate the RNA-seq results, we used qRT-PCR. We hoped to provide a foundation for the adaptive mechanism as well as a rich resource for the discovery and detection of novel genes involved in cold and heat stress responses of Spodoptera frugiperda.
Methods: Spodoptera frugiperda was reared at lab condition, and incubated at 2 different temperature( 4 and 40°C) for 16 hours as temperature treatment groups. RNA was extracted using Trizol reagent and Illumina sequencing was performed at Macrogen. Illumina short reads were quality-filtered and Illumina-based de novo transcriptome assembly was performed. Differential Gene Expression Analysis was studied for different tempearture conditions.
Results: A total of 211,967 unigenes were collected, at least 14,338 of which were annotated with gene descriptions, gene ontology terms, and metabolic pathways. There were 50 GO functional sub-groups and 21 EggNOG words as a result. DEGs with log2FC≥2 were identified and compared at various temperatures. In comparison to the 25°C treated group, we discovered 199 and 1248 individual DEGs co-regulated at 4 and 40°C, respectively. Comparing transcriptome profiles for differential gene expression revealed a number of DE genes, including cytochrome P450, odorant binding proteins (OBP), and immune system genes previously implicated in cold and high temperature resistance. The enrichment pathways were identified using KEGG analysis, and heatmaps of similar unigenes from both treatment groups (T4 and T40) were plotted. We used qPCR to confirm the RNA-seq data on 10 up- and down-regulated DEGs.
Conclusions: In conclusion, we used RNA-Seq technology focused on high-throughput sequencing to compare the transcriptomes of Spodoptera frugiperda under high- and low-temperature stresses. This research was the first to identify a large number of genes that were significantly up-regulated at high and low temperatures. Many genes were discovered through comparative transcriptome analysis, and a significant number of improvements in metabolic pathways were discovered through GO and KEGG enrichment analysis. Our findings will help future molecular research and genomic studies. These newly found genes may be important and necessary to FAW harsh environment tolerance and its behavior for adaptation in new environment as well as quarantine area.

overall_design: Total RNA of Spodoptera frugiperda for two different treated temperatures was extracted. The control group consisted of larvae incubated at 25°C

first: Youngjin

last: Park


title: Human embryoid bodies as a novel system for genomic studies of functionally diverse cell types

status: Public on Jun 16 2021

first: Katherine

last: Rhodes

address: 5841 South Maryland Avenue, MC 6092

department: Genetic Medicine

summary: Embryoid bodies, 3D aggregates of spontaneously differentiating iPSCs, have the potential to be a useful model system for genomic studies of diverse cell types. We first collected single-cell RNA-sequencing data from embryoid bodies (EBs) generated from 3 Yoruba individuals (18858, 18511, and 19160) in 3 replicates. We classify functional heterogeneity in EB cells using unsupervised clustering, differential expression analysis, reference annotation, and topic modelling. We then inferred differentiation trajectories that recapitulate known developmental patterns of gene expression. We later collected Day 21 EBs from a single replicate of 5 additional Yoruba iPSC lines (18856, 18912, 19140,19159, and 19210) and use this data to demonstrate robustness of EB cell type composition across iPSC lines. Our results establish EBs as a powerful model system to facilitate discovery of QTLs for cell type composition, as well as eQTLs and dynamic eQTLs across a multitude of human cell types and developmental trajectories.

overall_design: We differentiated iPSCs from 3 Yoruba individuals to Embryoid Bodies in 3 replicates. On day 21 of differentiation, EB cells from all 3 individuals were pooled and single-cell RNA-seq data was collected using the 10x Genomics V3.0 kit.  We then differentiated iPSCs from an additional 5 Yoruba individuals. On day 21 of differentiation, EB cells from all 5 individuals were pooled and single-cell RNA-seq data was collected using the 10x Genomics V3.1 kit.

first: Kenneth

last: Barr

first: Joshua

last: Popp

first: Benjamin

last: Strober

first: Alexis

last: Battle

first: Yoav

last: Gilad


title: Next-Generation Sequencing Transcriptome Quantitative Analysis of Hearts of Male Fetuses From Obese Female Mice

status: Public on Jun 05 2021

first: Lucas

last: Pantaleao

address: 11A Glisson Road

summary: Obesity during pregnancy increase the risk for cardiac in the offspring. We used RNA next-generation sequencing analysis to have a snapshot of the heart transcriptome in male offspring exposed to maternal obesity and weaned onto an obesogenic diet.

overall_design: Female C57BL/6J mice received either commercial standard (RM1) or a high-fat diet [20% lipids (Special Dietary Services)] plus sweetened condensed milk [55% simple carbohydrates/8% lipids (Nestle, UK)] from weaning. After around 6 weeks on their respective diets, mice were mated with male counterparts and went through a first pregnancy and lactation to ensure their breeding competence. Mice were mated a second time, and first day of pregnancy was marked by the detection of a vaginal plug. On day 18.5 of gestation, pregnant mice were killed by raising CO2 concentrations or cervical dislocation. Fetuses were surgically removed and immediately killed by laying in cold buffer. Fetal heart ventricles were dissected, weighed, snap frozen and stored at −80 °C. Cardiac RNA from male offspring was extracted using a Qiazol/miRNeasy mini kit protocol (Qiagen, Hilden, Germany). Library preparation for mRNA sequencing followed manufacturer protocol of TruSeq RNA Library Preparation kit (Illumina, Cambridge, UK).

first: Elena

last: Loche

first: Susa

last: Ozanne

first: Ania

last: Wilczynska


title: Complement activation induces excessive T cell cytotoxicity in severe COVID-19

status: Public on Jun 08 2021

city: Berlin

first: Nils

last: Blüthgen

address: Chariteplatz 1

department: Institute of Pathology

institute: Charite Universitätsmedizin Berlin

summary: We performed single cell transcriptomics in 13 acute and convalescent mild versus severe COVID-19 subjects, in healthy controls and in sujects with flu-like-illness and HBV infection  to assess COVID-19-specific T cell populations und function.

overall_design:
Blood from 19 COVID-19 patients at acute and convalescent (for 13 patients) phases for mild-moderate (9 patients) and severe (10 patients), from 6 healthy controls as well as from 8 patients with flu-like disease and 4 patients with chronic HBV infection was collected and PBMC prepared. From part of the PBMC CD38+ CD4+ an CD8+ were purified and both, total PBMC and enriched CD38+ T cells were subjected to 5' GEX scRNA- and 5'-VDJ library preparation. For many samples, both all PBMCs and enriched CD38+ T-cells were sequenced. Samples were pooled with Antibody-based Hashtags and demultiplexed. based on both Hashtags and SNPs.

>>> Submitter declares raw data not available due to patient privacy concerns <<<

first: Birgit

last: Sawitzki

first: Rosario

last: Astaburuaga-García

first: Benedikt

last: Obermayer-Wasserscheid

first: Dieter

last: Beule

first: Emanuel

last: Wyler

first: Sophia

last: Brumhard

first: Philipp

last: Georg


title: The SCP4-STK35/PDIK1L complex is a dual phospho-catalytic signaling dependency in acute myeloid leukemia (RNA-Seq)

status: Public on May 12 2021

city: Cold Spring Harbor

first: Sofya

last: Polyanskaya

address: 1 Bungtown Road

department: Cancer Center

institute: Cold Spring Harbor Laboratory

summary: Transcriptome analysis by high throughput sequencing

overall_design: Gene expression profiles in MOLM-13/Cas9+ cells with guideRNA-mediated gene knockouts

first: Osama

last: Demerdash

first: Olaf

last: Klingbeil

first: Christopher

middle: R

last: Vakoc


title: RNA Sequencing of WT Aged Vehicle vs. HPBCD Peri-Infarct Regions

status: Public on May 03 2021

city: Tucson

first: Danielle

last: Becktel

state: AZ

address: 1656 E Mabel Street, Rm 214

department: Immunobiology

institute: University of Arizona

summary: Prior to assessing the impact of repeated HPβCD administration on the peri-infarct region of the brain, we first compared the transcriptome of the peri-infarct region to the equivalent region of the contralateral hemisphere in aged (18-month-old) mice at 7 weeks after distal middle cerebral artery occlusion + hypoxia (DH) stroke. The peri-infarct region was characterized by 3,910 differentially expressed genes. Of these, 2,123 were upregulated, many of which were also upregulated in infarcts at 7 weeks after stroke. For instance, the infarct and peri-infarct regions were both defined by the upregulation of degradative enzymes, TLRs, and scavenger receptors. In addition, the upregulation of Lpl, Lrp2, Ch25h, Apoe, Trem2, and Abca1 signified a divergence from lipid homeostasis. These alterations in innate immunity coincided with corresponding perturbations in adaptive immunity. The upregulation of Cd3d, Cd3e, Cd3g, Blnk, Sdc1 and Jchain suggests that chronic inflammation persists in peri-infarct regions for at least 7 weeks after stroke. Conversely, the DE analysis revealed that 1,787 genes were downregulated in peri-infarct regions compared to equivalent regions of the contralateral hemisphere. These genes were primarily involved in mitochondrial respiration and neuronal function. Together, these results demonstrate that the transcriptome of the peri-infarct region is characterized by the upregulation of genes involved in inflammation and lipid metabolism and the downregulation of genes involved in mitochondrial respiration and neuronal function. To evaluate the impact of HPβCD treatment on the transcriptome of the peri-infarct region, we also performed bulk RNA-Seq on brain tissue collected 7 weeks after DH stroke. For this analysis, we compared the peri-infarct regions of vehicle- and HPβCD-treated aged mice. The peri-infarct region of HPβCD-treated mice was characterized by 5,385 differentially expressed genes. The DE analysis revealed that peri-infarct regions of HPβCD-treated mice were characterized by the downregulation of multiple degradative enzymes, chemokine receptors, and scavenger receptors. In addition, the transcriptomic analysis demonstrated a restoration of lipid homeostasis in peri-infarct regions of HPβCD-treated mice compared to vehicle-injected mice, as evidenced by the downregulation of Lipa, Apoe, Lamp1, Npc1, and Npc2 and upregulation of Nceh1 and Ldlr. Reductions in innate and adaptive immune responses characterized peri-infarct regions of HPβCD-treated mice; these alterations are consistent with the attenuated chronic inflammation that characterized infarcts of the HPβCD-treated aged mice. These results demonstrate that HPβCD treatment after stroke attenuates chronic inflammation and promotes lipid metabolism in peri-infarct regions of aged mice. Additionally, the DE analysis revealed an upregulation of genes involved in myelin sheath structural integrity, such as Ina, Omg, and Nefl, and synaptic plasticity and neuroplasticity, such as Syn1, Bdnf, Nrg1, Negr1, and Nsg1. These results suggest that HPβCD treatment improves the structure and function of neurons in peri-infarct regions of aged mice after stroke.

overall_design: Bulk RNA sequencing was performed on peri-infarct regions and contralateral hemispheres of vehicle- and HPBCD-treated aged mice at 7 weeks after stroke to assess transcriptional changes that occur following repeated subcutaneous administration of HPBCD.

first: Kristian

last: Doyle


title: RNA Sequencing of WT Aged Vehicle vs. HPBCD Infarcts

summary: We systematically characterized the transcriptomes of stroke infarcts in vehicle- and HPβCD-treated aged (18-month-old) mice by performing bulk RNA-Seq on infarcted brain tissue collected 7 weeks after distal middle cerebral artery occlusion + hypoxia (DH) stroke. The DE analysis revealed 991 upregulated genes and 1,876 downregulated genes. HPβCD treatment upregulated intracellular cholesterol transporters, lipoproteins, and lipoprotein receptors, such as Npc1, Npc2, Apoe, Trem2, Abca1, Vldlr, and Hdlbp, and downregulated Ffar1, Lrpb1, and Dgkb. These alterations in lipid metabolism suggest that HPβCD aids in the restoration of lipid homeostasis by 7 weeks after stroke. In addition, the DE analysis revealed a downregulation of genes involved in chemotaxis, including Cx3cr1, Cxcl5, and Ccr6, and innate and adaptive immune responses, including Mmd2, Mzb1, Btla, Jchain, and Igkv5-48. Correspondingly, there was an upregulation of anti-inflammatory genes, such as Tgfb1, Tgfb2, P2ry2, and Il18bp. Next, we performed genome-wide expression analysis of the RNA-Seq data using GSEA, which revealed significant enrichment of various biological processes in infarcts of HPβCD-treated aged mice, including (i) collagen formation, (ii) regulation of angiogenesis, (iii) lipid catabolic process, (iv) regulation of autophagy, and (v) regulation of apoptotic process. These results indicate that HPβCD treatment promotes lipid metabolism and angiogenesis and dampens chronic inflammation in infarcts of aged mice at 7 weeks after stroke.

overall_design: Bulk RNA sequencing was performed on chronic stroke infarcts of vehicle- and HPBCD-treated aged mice to assess transcriptional changes that occur following repeated subcutaneous administration of HPBCD.


title: RNA Sequencing of WT Chronic Stroke Infarcts vs. Contralateral Cortices

status: Public on Apr 30 2021

summary: We conducted bulk RNA sequencing on infarcts collected from young adult (3-month-old) mice at 7 weeks after the distal middle cerebral artery occlusion + hypoxia stroke model and compared them to contralateral cortices. As expected, differential expression (DE) analysis revealed marked differences between infarcts and contralateral cortices: 3,930 upregulated and 2,869 downregulated genes. The most significantly upregulated genes, including Lpl, Spp1, Cd36, Mmp2, and Mmp19, and the most highly enriched genes, including Cd5l, Mmp3, Mmp12, and Mmp13, indicate a pronounced disturbance in lipid homeostasis in infarcts at 7 weeks after stroke. In addition to alterations in lipid metabolic processes, the transcriptome also revealed a signature of chronic inflammation at 7 weeks after stroke. We then used IPA software to define upstream regulators and identify altered biological processes based on DE analysis. Differentially expressed genes were associated with the following upregulated biological processes: (i) atherosclerosis signaling, (ii) IL-1 signaling, (iii) inflammasome pathway, (iv) eicosanoid signaling, (v) B cell receptor (BCR) signaling, and (vi) phospholipases, along with others. IPA also identified lipid metabolic upstream regulators such as cholesterol, phospholipids, and LDL, as well as immunological upstream regulators such as MYD88, IL18, CD3, IL1B, TLR4, and TNF. These altered biological processes indicate that the stroke infarct transcriptome is characterized by chronic inflammation, dysregulated lipid metabolism, and impaired or absent neuronal function at 7 weeks after stroke.

overall_design: Bulk RNA sequencing was performed on chronic stroke infarcts and equivalent regions of the contralateral cortex to assess transcriptional changes that occur following ischemic stroke.


title: Integrated Genome and Transcriptome Analyses Reveal the Mechanism of Genome Instability in Ataxia with Oculomotor Apraxia 2 [MeDIP-Seq]

status: Public on Apr 29 2021

city: London

first: Steve

last: West

address: 1 Midland Road

institute: The Francis Crick Institute

type: Methylation profiling by high throughput sequencing

summary: Mutations in the SETX gene, which encodes Senataxin, are associated with the progressive neurodegenerative diseases Ataxia with Oculomotor Apraxia 2 (AOA2) and Amyotrophic Lateral Sclerosis 4 (ALS4). To identify the causal defect in AOA2, patient-derived cells and SETX knockouts (human and mouse) were analyzed using integrated genomic and transcriptomic approaches. We observed a genome-wide increase in chromosome instability (gains and losses) within genes and at chromosome fragile sites, resulting in changes to gene expression profiles. Senataxin loss caused increased RNA polymerase II pausing events (transcription stress) near promoters that correlated with high GCskew and R-loop accumulation at promoter-proximal regions. Notably, the chromosomal regions with gains and losses overlapped with regions of elevated transcription stress. Aberrant R-loops were resolved by transcription-coupled repair (TCR), in reactions dependent upon the Cockayne Syndrome protein CSB. We found that CSB was required for the recruitment of the TCR endonucleases XPG and XPF, and recombination factors to target and resolve transcription bubbles containing R-loops and promote genomic instability. These results show that cells derived from individuals with Ataxia with Oculomotor Apraxia 2 exhibit transcription stress giving rise to genome-wide chromosomal fragility, termed transcription stress-induced fragile sites (TSFS), in transcribed regions of the mammalian genome.

overall_design: Examination of differential DNA methylation in human HAP1 WT and SETX knockout cells by 5-methylcytosine (5meC) DNA immunoprecipitation sequencing. Input DNA was used as a control.

first: Radhakrishnan

last: Kanagaraj

first: Richard

last: Mitter

first: Stephen


title: LCDR maintains the integrity of lysosomal membrane by hnRNP K-stabilized LAPTM5 transcript and promotes cell survival

status: Public on May 05 2021

first: Shan

last: Gao

address: No. 2 Sipailou, Xuanwu District

institute: Southeast University

summary: Lysosome plays important roles in cellular homeostasis and its dysregulation is associated with cancer. However, the regulation and underlying mechanism of lysosome in cancer survival remain incompletely understood. Here, we reveal a role for a histone acetylation-regulated long non-coding RNA termed as lysosome cell death regulator (LCDR) in lung cancer cell survival, knockdown of which promotes apoptosis. Mechanistically, LCDR binds to heterogenous nuclear ribonucleoprotein K (hnRNP K) to regulate the stability of lysosomal-associated protein transmembrane 5 (LAPTM5) transcript that maintain integrity of lysosomal membrane. Consequently, knockdown of LCDR, hnRNP K or LAPTM5 promotes lysosomal membrane permeabilization and lysosomal cell death-mediated apoptosis. LAPTM5 overexpression or cathepsin B inhibitor partially restores the effects of this axis on lysosomal cell death. Clinically, LCDR/hnRNP K/LAPTM5 are upregulated in lung cancer tissues and coexpression of this axis shows the increased diagnostic value for lung cancer. These findings shed light on LCDR/hnRNP K/LAPTM5 as potential therapeutic targets and targeting lysosome is a promising strategy in cancer treatment.

overall_design: We conducted total RNA sequencing after the BEAS-2B and NCI-H1299 were treated with DMSO and TSA for 24 hours, LCDR and hnRNPK genes were knocked down in NCI-H1299 cell lines. Totally 22 samples were generated.

first: Xiwang

last: Yang

first: Ya

last: Wen

first: Shaomin

last: Liu

first: Liqiang

last: Duan

first: Tongfeng

first: Zhuo

last: Wang

first: Yinmin

last: Gu

first: Yibo

last: Xi

first: Xiaodong

first: Dingshan

last: Luo

first: Ruobing

last: Zhang

first: Yajuan

first: Yang

first: Tianyou

last: Cheng

first: Siyuan

last: Jiang

first: Xiaofeng

last: Zhu

first: Xiaohui

first: Yongbo

last: Pan

first: Shuwen

last: Chen

first: Jinfei

first: Xiaoding

last: Xu


title: High-resolution mapping of regulatory element interactions and genome architecture using ARC-C [ChIP-Seq]

status: Public on Jun 01 2021

first: Julie

last: Ahringer

summary: Interactions between cis-regulatory elements such as promoters and enhancers are important for transcription but global identification of these interactions remains a major challenge. Leveraging the chromatin accessiblity of regulatory elements, we developed ARC-C (accessible region chromosome conformation capture), which profiles chromatin regulatory interactions genome-wide at high resolution. Applying ARC-C to C. elegans, we identify ~15,000 significant interactions at 500bp resolution. Regions bound by transcription factors and chromatin regulators such as cohesin and condensin II are enriched for interactions, and we use ARC-C to show that the BLMP-1 transcription factor mediates interactions between its targets. Investigating domain level architecture, we find that C. elegans chromatin domains defined by either active or repressive modifications form topologically associating domains (TADs) and that these domains interact to form A/B (active/inactive) compartment structure. ARC-C is a powerful new tool to interrogate genome architecture and regulatory interactions at high resolution.

overall_design: We performed ChIP-Seq replicates targetting BLMP-1, JMJD-2, SCC-1, SIN-3, TOP-2 and ZFP-1 in wildtype C elegans L3 larvae.

first: Ni

last: Huang

first: Wei

last: Seow


title: A baseline transcriptional signature associates with clinical malaria risk in RTS,S/AS01-vaccinated African children

city: Barcelona

first: Carlota

last: Dobaño

address: Rosselló 153

country: Spain

institute: ISGlobal, Hospital Clínic - Universitat de Barcelona

summary: In a phase 3 trial in African infants/children, the RTS,S/AS01 (GSK) vaccine showed moderate efficacy against clinical malaria. We aimed to identify RTS,S/AS01-induced signatures associated with clinical malaria by analyzing antigen-stimulated peripheral blood mononuclear cells sampled from a subset of trial participants at baseline and month 3 (one month post-final dose). RTS,S/AS01 vaccination was associated with downregulation of B-cell and monocyte-related blood transcriptional modules (BTMs) and upregulation of T-cell related BTMs, as well as higher month 3 (vs baseline) (CSP)-specific CD4+ T-cell responses. For some RTS,S/AS01-associated BTMs, month 3 levels correlated with anti-circumsporozoite protein (CSP) IgM and inversely with anti-CSP IgG responses. There were few RTS,S/AS01-associated BTMs whose month 3 levels correlated with malaria risk. In contrast, baseline levels of dendritic cell and monocyte RTS,S/AS01-associated BTMs correlated with malaria risk. A cross-study analysis supported generalizability of these correlations to healthy, malaria-naïve adults, suggesting inflammatory monocytes may inhibit protective RTS,S/AS01-induced responses.

sample_organism:
Homo sapiens
blank sample

platform_organism:
Homo sapiens
blank sample

overall_design: 1,900 samples were sequenced in 5 batches of 384-well plates. Two positive (human universal reference) and two negative (water) controls were included in each plate. No replicates of samples were performed.

first: Jason

last: Carnes

first: Gemma

last: Moncunill

first: William

last: Young

first: Lindsay

middle: N

last: Carpp

first: Stephen

middle: D

last: Rosa

first: Joseph

last: Campo

first: Augusto

last: Nhabomba

first: Maxmillian

last: Mpina

first: Chenjerai

last: Jairoce

first: Greg

last: Finak

first: Paige

last: Haas

first: Carl

last: Murie

first: Phu

last: Van

first: Héctor

last: Sanz

first: Sheetij

last: Dutta

first: Benjamin

last: Mordmüller

first: Selidji

middle: T

last: Agnandji

first: Núria

last: Díez-Padrisa

first: Nana

last: Williams

first: John

last: Aponte

first: Clarissa

last: Valim

first: Daniel

last: Neafsey

first: Claudia

last: Daubenberger

first: Juliana

last: McElrath

first: Ken

last: Stuart

first: Raphael

last: Gottardo


title: CRISPR activation and interference screens decode stimulation responses in primary human T cells [Bulk RNA-seq]

first: Zachary

last: Steinhart

overall_design: RNA-seq of CD4+ human T cells after CRISPR activation of FOXQ1 in restimulated and resting conditions

first: Ralf

last: Schmidt

first: Madeline

last: Layeghi

first: Jacob

last: Freimer

first: Vinh

last: Nguyen

first: Franziska

last: Blaeschke

first: Alexander

last: Marson


title: Single cell RNA-seq of the developing mouse hypothalamus

status: Public on May 14 2021

city: Ann Arbor

first: Malcolm

last: Low

state: MI

address: 1000 wall street

department: Molecular & Integrative Physiology

institute: University of Michigan

summary: Neurons in the hypothalamic arcuate nucleus (ARC) are fundamental regulators of energy homeostasis, growth and reproduction. Spatially overlapping subpopulations of ARC neurons produce specific neuropeptides including melanocortins, opioids, neuropeptide Y, growth hormone releasing hormone and kisspeptin. However, the developmental pathways controlling ARC neuron specification, differentiation and maturation remain poorly understood relative to more structurally ordered brain regions. Here, we analyzed the transcriptomes of individual mouse ARC neurons sorted for expression of a Proopiomelanocortin-Td-dsRed transgene at four embryonic (E11.5, E13.5, E15.5 and E17.5) and two postnatal (P5 and P12) ages. There was an unanticipated complexity of neurochemical subpopulations in the developing ARC characterized by low, medium or high levels of Pomc transcripts and distinct temporal patterns of transcription factor expression. Moreover, sizeable fractions of Pomc-positive neural progenitors differentiated into non-POMC neurons by P12. We conclude that ARC neuronal development is highly dynamic with plasticity that may be susceptible to environmental programming.

overall_design: Embryonic hypothalami were dissected at E11.5, E13.5, E15.5, and E17.5. Postnatal hypothalami were isolated from pups at postnatal day 6 (P6) and P12. In each dissection, hypothalami from at least 6 pups were pooled together to acquire enough cells for fluorescence-activated cell sorting (FACS). After FACS, cells were counted and subjected to scRNA-seq library preparation and sequencing (10x Genomics).

first: Hui

last: Yu

first: Marcelo

last: Rubinstein


title: Analysis of wild-type and METTL5 knockout cells

status: Public on May 18 2021

first: Caraline

last: Sepich

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

overall_design: Refer to individual Series


title: CRISPR activation and interference screens decode stimulation responses in primary human T cells


title: Transcriptomic analysis of wild-type (WT) and METTL5 knockout (KO) mice

summary: We report the application of next-generation sequencing to analyze the transcriptomes of brains and livers of WT and METTL5 KO mice to understand the role(s) of METTL5 in these organs.

overall_design: Gene expression analysis to compare WT and KO mice (liver and brain).

last: Sepich-Poore

first: Sigrid

last: Nachtergaele

first: Chuan

last: He


title: Integrated Genome and Transcriptome Analyses Reveal the Mechanism of Genome Instability in Ataxia with Oculomotor Apraxia 2

first: Steve

last: West


title: DDX17 is involved in DNA damage repair and modifies FUS toxicity in an RGG-domain dependent manner

city: Pittsburgh

first: Bernhard

last: Kuhn

state: Pennsylvania

address: 4401 Penn Ave

institute: Children's Hospital of Pittsburgh

summary: Mutations in the RNA binding protein, Fused in Sarcoma (FUS), lead to amyotrophic lateral sclerosis (ALS), the most frequent form of motor neuron disease. Cytoplasmic aggregation and defective DNA repair machinery are etiologically linked to mutant FUS-associated ALS. Although FUS is involved in numerous aspects of RNA processing, little is understood about the pathophysiological mechanisms of mutant FUS. Here, we employed RNA-sequencing technology in Drosophila brains expressing FUS to identify significantly altered genes and pathways involved in FUS-mediated neurodegeneration.

overall_design: Examination of the transcriptomic profile of wild-type and mutant FUS expressing Drosophila neurons compared to control Drosophila.

first: Tyler

last: Fortuna

first: Udai

last: Pandey

first: Dhivyaa

last: Rajasundaram


title: Integrated Genome and Transcriptome Analyses Reveal the Mechanism of Genome Instability in Ataxia with Oculomotor Apraxia 2 [LCL RNA-seq]

overall_design: Examination of mRNA profiles in AOA2 and control (CTRL) lymphoblastoid cell lines by deep sequencing.

first: Radhakrishnan

last: Kanagaraj

first: Richard

last: Mitter

first: Stephen


title: Gene expression analysis of Japanese macaque reveals potential markers of lip vermillion epithelium

status: Public on Apr 27 2021

city: Niigata

first: Kenji

last: Izumi

state: Niigata

address: 2-5274, Gakkocho-dori, Chuo-ku

department: Dentistry

country: Japan

institute: Niigata University

summary: Our histological findings showed that vermillion is present in the lip of Japanese macaque. In addition, the immunostaining pattern of K10 and SPRR3 of the lip of Japanese macaque is similar to that of a human. Thus, the transcriptome analysis of Japanese monkey can provide several unique genes specific to vermillion keratinocytes, which is required to develop a human lip/vermillion in vitro model.

overall_design: We examined histological and immunohistochemical characteristics as well as gene expression pattern of the lip vermillion of Japanese macaque in comparison with epidermal and oral keratinocytes.

first: Hiroko

last: Kato

first: Ling

last: Yiwei

first: Emi

last: Hoshikawa

first: Ayako

last: Suzuki

first: Kenta

last: Haga

first: Eriko

last: Naito

first: Atsushi

last: Uenoyama

first: Shujiro

last: Okuda


title: RNA Sequencing of WT Aged Vehicle vs. HPBCD

first: Danielle

last: Becktel


title: RABID transcriptome from priming EAE astrocyte networks

status: Public on Apr 22 2021

city: Boston

first: Michael

last: Wheeler

state: MA

address: 60 Fenwood Rd.

department: Neurology

institute: Brigham and Women's Hospital

summary: Tracing astrocyte networks in EAE priming in B6 mice

overall_design: Mice harvested during EAE priming phase (n=3). Sorting of mCherry+ cells analyzed at 7-8 dpi of Rab-DG-mCherry-BC transduced at 7 days post-EAE induction.

first: Zhaorong

last: Li

first: Iain

last: Clark

first: Francisco

last: Quintana


title: A Variant in Human AIOLOS Impairs Adaptive Immunity by Interfering with IKAROS

status: Public on May 01 2021

city: Bunkyo

first: Motoi

last: Yamashita

state: Tokyo

address: 1-5-45, Yushima

institute: Tokyo Medical and Dental University

summary:
A missense mutation (G158R) in Aiolos, encoded by Ikzf3 gene,  resulted in defective generation of B cells in mice. Pre-B cells were profoundly decreased in homozygous mutant mice. Heterozygous mutant mice showed milder B cell developmental defects, and B cells in the secondary lymphoid organs decreased. Genome-wide binding of Aiolos and Ikaros were altered in the thymus of homozygous Ikzf3 G158R mice. Our findings indicate that Aiolos-G158R hinders B cell development by interfering Ikaros' function via formation of heterodimers.
A heterozygous missense variant (G159R) in AIOLOS, encoded by IKZF3 gene, resulted in impaired adaptive immunity, which predominantly manifested as profound B cell developmental defect. Genome-wide binding of wild-type AIOLOS and AIOLOS G159R mutant were examined in IKZF3 knock-out human pre-B cell line NALM-6, retrovirally transduced with doxycycline inducible wild-type AIOLOS or AIOLOS G159R. Changes in genome-wide binding and binding motif were observed for AIOLOS G159R mutant.

overall_design:
Sample 1-6: mRNA profiles of pre-B cells in wild-type and heterozygous Ikzf3 G158R mutant mice.
Sample 7-16: Genome-wide bindings of Ikaros and Aiolos in the thymocytes of wild-type and homozygous Ikzf3 G158R mutant mice.
Sample 17-26: Genome-wide bindings of WT AIOLOS and AIOLOS G159R mutant in IKZF3 knockout human pre-B cell line NALM6.

first: Kazuki

last: Okuyama


title: Transcriptional profiling of chemical Dot1L inhibition during reprogramming to induced pluripotent stem cells

city: Madison

first: Rupa

last: Sridharan

state: WI

address: 330 N. Orchard Street

department: Wisconsin Institute for Discovery

institute: University of Wisconsin

summary: Three independent transcriptional profiling experiments were performed to ascertain how Dot1L affects cell fate change. 1) In a timecoure ("Tc"), reprogramming mouse embryonic fibroblasts were treated with DMSO control or Dot1L inhibitor (Dot1Li -SGC0946) for 2 or 4 days. Surprisingly, despite the enrichment of H3K79me2 on thousands of actively transcribed genes, Dot1L inhibition (Dot1Li) results in few changes in steady state mRNA levels during reprogramming, the majority of which are spuriously upregulated. 2) To determine if Dot1Li increased reprogramming beyond the mesenchymal to epithelial transition (MET) that occurs early in reprogramming when starting from MEFs, reprogramming cells were sorted ("Sort") for surface CDH1 expression, and then treated with Dot1Li or control. Dot1Li increased reprogramming efficiency of both CDH1- and CDH1+ populations to a similar extent and few genes were DE. 3) To assess if Dot1Li increased pluripotency acquisition beyond CDH1 upregulation, CDH1 or empty vector was expressed ("Exp") in reprogramming cells. CDH1 expression did not initiate MET, or enhance reprogramming.

overall_design: mRNA profiles of MEFs, ESCs, and reprogramming cells with Dot1L chemical inhibition

first: Coral

last: Wille


title: Integrated Genome and Transcriptome Analyses Reveal the Mechanism of Genome Instability in Ataxia with Oculomotor Apraxia 2.

first: Steve

last: West

overall_design: Examination of gene expression profiles in AOA2 and control (CTRL) lymphoblastoid cell lines by Affymetrix Human Gene 1.0 ST microarrays.

first: Radhakrishnan

last: Kanagaraj

first: Probir

last: Chakravarty

first: Stephen


title: RABID barcodes from priming EAE astrocyte networks


title: Post-replicative nick translation occurs on the lagging strand during prolonged depletion of DNA ligase I in Saccharomyces cerevisiae

city: New York

first: Duncan

last: Smith

address: 1009 Silver Center, 100 Washington Sq E

department: Dept. of Biology/Center for Genomics and Systems Biology

institute: New York University

summary: During lagging-strand synthesis, strand-displacement synthesis by DNA polymerase delta (Pol ∂), coupled to nucleolytic cleavage of DNA flap structures, combine to produce a nick translation reaction that replaces the DNA at the 5’ end of the preceding Okazaki fragment. Previous work following depletion of DNA ligase I in Saccharomyces cerevisae suggests that DNA-bound proteins, principally nucleosomes and the transcription factors Abf1/Rap1/Reb1, pose a barrier to Pol ∂ synthesis and thereby limit the extent of nick translation in vivo. However, the extended ligase depletion required for these experiments could lead to ongoing, non-physiological nick translation. Here, we investigate nick translation by analyzing Okazaki fragments purified after transient nuclear depletion of DNA ligase I in synchronized or asynchronous S. cerevisiae cultures. We observe that, even with a short ligase depletion, Okazaki fragment termini are enriched around nucleosomes and Abf1/Reb1/Rap1 binding sites. However protracted ligase depletion leads to a global change in the location of these termini, moving them towards nucleosome dyads from a more upstream location and further enriching termini at Abf1/Reb1/Rap1 binding sites. Additionally, we observe an under-representation of DNA derived from DNA polymerase alpha – the polymerase that initiates Okazaki fragment synthesis – around the sites of Okazaki termini obtained from transient ligase depletion. Our data suggest that, while nucleosomes and transcription factors do limit strand-displacement synthesis by Pol ∂ in vivo, post-replicative nick translation can occur at unligated Okazaki fragment termini such that previous analyses represent an overestimate of the extent of nick translation occurring during normal lagging-strand synthesis.

overall_design: Okazaki fragments from a Cdc9 anchor away strain were sequenced from asynchronous and synchronous cultures after rapamycin treatment to deplete Cdc9 from the nucleus.

first: Natasha

last: Koussa


title: Microglial Semaphorin4D and astrocyte PlexinB1-B2 knockdown in EAE

summary: Identification of pathways regulated by semaphorin 4D-PlexinB1/B2 signaling in astrocytes during EAE

overall_design: Gfap-Cas9;sgScrmbl-targeted (n=3); Gfap-Cas9;sgPlxnb1-targeted (n=3); Gfap-Cas9;sgPlxnb2-targeted (n=3); Itgam-Cas9;sgScrmbl-targeted (n=3); Itgam-Cas9;sgSema4d-targeted (n=3)


title: RABID barcodes from peak EAE astrocyte networks

summary: Tracing astrocyte networks in experimental autoimmune encephalomyelitis (EAE)  in B6 mice

overall_design: Mice harvested during EAE peak phase (n=4). Sorting of mCherry+ cells analyzed at 7-8 dpi of Rab-DG-mCherry-BC transduced at 12 days post-EAE induction.


title: RABID barcodes from naive astrocyte networks

summary: Tracing astrocyte networks in naive B6 mice

overall_design: N=4 mice. Sorting of mCherry+ cells analyzed at 7-8 dpi of Rab-DG-mCherry-BC


title: RABID transcriptome from peak EAE astrocyte networks

summary: Tracing astrocyte networks in EAE in B6 mice


title: RABID transcriptome from naive astrocyte networks


title: RNA-seq for ESC-derived CPs in presence or absence of SUZ12, MTF2, or JARID2

status: Public on Apr 21 2021

city: Philadelphia

first: Roberto

last: Bonasio

state: PA

address: 3400 Civic Center Blvd - SCTR 9-111

department: Cell and Developmental Biology

institute: University of Pennsylvania

summary: We performed mRNA-seq after differentiation of embryonic stem cells (ESCs) into cardiac precursors (CPs) with with or without inducing degradation of PRC2 subunits MTF2, JARID2, or SUZ12 using the AID system

overall_design: We sequenced two biological replicates each for all samples

first: Ana

last: Petracovici


title: Integrated Genome and Transcriptome Analyses Reveal the Mechanism of Genome Instability in Ataxia with Oculomotor Apraxia 2 [MEF RNA-seq]

summary: Mutations in the SETX gene, which encodes Senataxin, are associated with the progressive neurodegenerative diseases Ataxia with Oculomotor Apraxia 2 (AOA2) and Amyotrophic Lateral Sclerosis 4 (ALS4). To identify the causal defect in AOA2, patient-derived cells and SETX knockouts (human and mouse) were analyzed using integrated genomic and transcriptomic approaches. We observed a genome-wide increase in chromosome instability (gains and losses) within genes and at chromosome fragile sites, resulting in changes to gene expression profiles. Senataxin loss caused increased RNA polymerase II pausing events (transcription stress) near promoters that correlated with high GCskew and R-loop accumulation at promoter-proximal regions. Notably, the chromosomal regions with gains and losses overlapped with regions of elevated transcription stress. Aberrant R-loops were resolved by transcription-coupled repair (TCR), in reactions dependent upon the Cockayne Syndrome protein CSB. We found that CSB was required for the recruitment of the TCR endonucleases XPG and XPF, and recombination factors to target and resolve transcription bubbles containing R-loops and promote genomic instability. These results show that cells derived from individuals with Ataxia with Oculomotor Apraxia 2 exhibit transcription stress giving rise to genome-wide chromosomal fragility, termed transcription stress-induced fragile sites (TSFS), in transcribed regions of the mammalian genome.

overall_design: Examination of mRNA profiles in wild-type (Setx+/+) and Setx knockout (Setx-/-) mouse embryonic fibroblasts by deep sequencing.

first: Richard

last: Mitter


title: Role of splicing factor SRSF1 during the late stages of T cell maturation in the thymus

city: Beijing

first: Shuyang

last: Yu

address: 2 Yuanmingyuan West Road

department: College of Biological Sciences

institute: China Agricultural University

summary: In thymus, the post-selection single positive thymocytes undergo further intrathymic maturation including down-regulation of CD69 and CD24, up-regulation of Qa-2, through which single positive thymocytes became equipped with emigration competency, then emigrate to periphery. Here we find that RNA binding protein Srsf1 is essential for the final maturation and survival of thymocytes.

overall_design: 5 RNA-Seq samples：3 WT replicates and 2 SRSF1 KO replicates; 4 CLIP-seq samples: 2 SRSF1 CLIP-seq replicates,  2 IgG CLIP-seq replicates

first: Zhihong

last: Qi


title: RNA-seq analysis of Arabidopsis ATAF2 loss- and gain-of-function mutants

status: Public on Apr 20 2021

city: Pullman

first: Hao

last: Peng

department: Crop and Soil Sciences

institute: Washington State University

summary: Four-day old seedlings of Arabidopsis wildtype Col-0, T-DNA insertional mutant ataf2-2, and overexpression line ATAF2ox-3 were collected for total RNA extraction. Three biological replicates were prepared for each genotype.

overall_design: Examination of differentially expressed genes in ataf2-2 and ATAF2ox-3 when compard to Col-0

first: Michael

middle: M

last: Neff


title: Transcriptional analysis of Coccidioides immitis mycelia and spherules by RNA sequencing

status: Public on Apr 01 2021

city: La Jolla

first: Theo

last: Kirkland

address: 9500 Gilman Drive

institute: UCSD

summary: Coccidioides immitis and posadasii are dimorphic fungi that transform from mycelia with internal arthroconidia in the soil to a tissue form known as a spherule.  Genes that were highly up-regulated in young spherules include a spherule surface protein and iron and copper membrane transporters.  Genes that are unique to Coccidioides spp. are also over-represented in this group, suggesting that they may be important for spherule differentiation.   Enriched GO terms in up-regulated genes in young spherules include oxidation/reduction, response to stress and membrane proteins.  Down-regulated genes are enriched for transcription factors, especially helix-loop-helix and C2H2 type zinc finger domain-containing proteins which is consistent with the dramatic change in transcriptional profile.  Almost all genes that are up-regulated in young spherules remain up-regulated in mature spherules, but a small number of genes are differentially expressed in those two stages of spherule development. Mature spherules express more Hsp31, and amylase than young spherules and less tyrosinase.  Some expression of transposons was detected and most of the differentially expressed transposons were up-regulated in spherules.

overall_design: RNA was harvested from C. immitis RS mycelia, young spherules or mature spherules grown in vitro.  rRNA was depeted and biological duplicate strand-specific, paired-end libraries were made and 100 bases sequenced from both ends using an Novaseq 6000 instrument according to the manufacturer's instructions (Illumina).  Paired reads were mapped to predicted CDS or transposons using Kallisto.  The count tables were normalized and  adjusted p values and fold change values were determined in DESeq2.

first: Aaron

last: Carlin

first: Sinem

last: Beyhan

first: Jesus

last: Pena

first: Jason

last: Stajich

first: Suganya

last: Viriyakosol

first: Joshual

last: Fierer


title: RNA-seq for ESC and NPC in presence or absence of SUZ12, MTF2, or JARID2

summary: We performed mRNA-seq before and after differentiation of embryonic stem cells (ESCs) into neural progenitor cells (NPCs) with with or without inducing degradation of PRC2 subunits MTF2, JARID2, or SUZ12 using the AID system

overall_design: We sequenced three biological replicates each for all samples except the RNA-seq of NPCs in SUZ12 degradation conditions, for which we only sequenced two replicates


title: Integrated Genome and Transcriptome Analyses Reveal the Mechanism of Genome Instability in Ataxia with Oculomotor Apraxia 2 [CML RNA-seq]

first: Steve

last: West

overall_design: Examination of mRNA profiles in human HAP1 wild-type and SETX knockout cells by deep sequencing.

first: Radhakrishnan

last: Kanagaraj

first: Stephen

middle: C


title: The biphasic and age-dependent impact of Klotho on hallmarks of aging and skeletal muscle function

first: Sruthi

last: Sivakumar

address: 450 Technology drive

institute: University of Pittsburgh

summary: Aging is accompanied by a disrupted information flow, which results from accumulation of molecular mistakes. These mistakes ultimately give rise to debilitating disorders such as skeletal muscle wasting, or sarcopenia. To estimate the growing “disorderliness” of the aging muscle system, we employed a statistical physics approach to estimate the state parameter, entropy, as a function of genes associated with hallmarks of aging. Although the most prominent structural and functional alterations were observed in the oldest old mice (27-29 months), we found that the escalating network entropy reached an inflection point at old age (22-24 months). To probe the potential for restoration of molecular “order” and reversal of the sarcopenic phenotype, we overexpressed the longevity protein, a-Klotho. Klotho overexpression modulated genes representing all hallmarks of aging in both old and oldest-old mice. However, whereas Klotho improved strength in old mice, intervention failed to induce a benefit beyond the entropic tipping point.

overall_design: RNA seq data from skeletal muscle from 3 age groups with and without Klotho intervention

first: Abish

last: Pius

first: Zachary

last: Clemens

first: Amrita

last: Sahu

first: Jian

last: Cui

last: Barchowsky

first: Fabrisia

last: Ambrosio


title: Integrated Genome and Transcriptome Analyses Reveal the Mechanism of Genome Instability in Ataxia with Oculomotor Apraxia 2 [ChIP-seq]

overall_design: Examination of RNAPII binding/occupancy in human HAP1 WT and SETX knockout cells. Input DNA was used as a control.

first: Richard

last: Mitter


title: PRC2 profile and chromatin marks in ESC and NPC

first: Roberto

last: Bonasio

summary: We performed CUT&RUN for SUZ12, JARID2, MTF2, H3K27me3, and H3K4me3 before and after differentiation of ESCs into NPCs

overall_design: We sequenced two biological replicates each for all CUT&RUN samples

first: Ana

last: Petracovici


title: MTF2 and JARID2 function in ESC differentiation

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

overall_design: Refer to individual Series


title: A disease-linked lncRNA mutation in RNase MRP inhibits ribosome synthesis [yeast]

status: Public on Mar 29 2021

city: Edinburgh

first: Nic

last: Robertson

address: Swann Building, Max Born Crescent

department: Tollervey Lab

institute: University of Edinburgh

summary: Mutations in the human RMRP gene cause Cartilage Hair Hypoplasia (CHH), an autosomal recessive disorder characterized by skeletal abnormalities and impaired T-cell activation. RMRP encodes a non-coding RNA, which forms the core of the RNase MRP ribonucleoprotein complex. In budding yeast, RMRP cleaves a specific site in the pre-ribosomal RNA (pre-rRNA) during ribosome synthesis. CRISPR-mediated disruption of RMRP in human cells lines caused growth arrest, with pre-rRNA accumulation. Here, we analyzed disease-relevant primary cells, showing that mutations in RMRP impair mouse T cell activation and delay pre-rRNA processing. Analysis of pre-rRNA processing in patient-derived human fibroblasts with CHH-linked mutations showed a similar pattern of processing delay. Human cells engineered with the most common CHH mutation (70AG in RMRP) show specifically impaired pre-rRNA processing, resulting in reduced mature rRNA and a reduced ratio of cytosolic to mitochondrial ribosomes. Moreover, the 70AG mutation caused a reduction in intact RNase MRP complexes. Together, these results indicate that CHH is a ribosomopathy, and the first human disorder of rRNA processing to be described.

overall_design: Yeast with HTP-tagged Pop1 were grown to log-phase, and RNA:protein interactions stabilised with UVC irradiation. RNAs interacting with Pop1 were purified by CRAC.

first: Vadim

last: Shchepachev

first: David

last: Wright

first: Tomasz

last: Turowski

first: Christos

last: Spanos

first: Aleksandra

last: Helwak

first: Rose

last: Zamoyska

last: Tollervey


title: A disease-linked lncRNA mutation in RNase MRP inhibits ribosome synthesis

sample_organism:
Saccharomyces cerevisiae
Homo sapiens

platform_organism:
Saccharomyces cerevisiae
Homo sapiens


title: Glial immune-related pathways as mediators of closed head TBI effects on behavior and lethality in Drosophila

status: Public on Mar 31 2021

city: Evanston

first: Ravi

last: Allada

address: 2205 Tech Drive

department: Neurobiology

institute: Northwestern University

summary: We applied TRAP-seq to adult flies expressing GFP tagged Rpl10 in the glial cells (with Repo-Gal4) to look for genes whose translation are affect at different time points after recieving TBI

overall_design: RNAs in glial cells undergoing translation are extracted by pruifing RNAs bond to GFP tagged Rpl10. Samplings were done with adult flies on the 3rd, 6th or 10th day at ZT0 after they recieved TBI at ZT0. Control flies were from the same parents, kept under the same condition and sampled in paralelle at the same time points except they did not recieve any real TBI.

first: Bart

last: van Alphen

first: Samuel

last: Stewart

first: Taichi

last: Itoh

first: Marta

last: Iwanaszko

first: Fangke

last: Xu


title: Gut Microbe-Targeted Choline Trimethylamine Lyase Inhibitors Improves Obesity Via Rewiring of Host Circadian Rhythms.

city: Cleveland

first: Chase

last: Neumann

state: OH

address: 99089 Carnegie Ave

institute: CCF

summary: The increasing prevalence of obesity and related metabolic disorders represents a growing  public health concern. Despite advances in other areas of medicine, a safe and effective drug  treatment for obesity has been elusive. Obesity has repeatedly been linked to reorganization of  the gut microbiome 1-4 , yet to this point obesity therapeutics have been targeted exclusively  toward the human host. Here we show that gut microbe-targeted inhibition of the  metaorganismal trimethylamine N-oxide (TMAO) pathway protects mice against the metabolic  disturbances associated with diet-induced obesity (DIO) or leptin deficiency (ob/ob). Selective  small molecule inhibition of the gut microbial enzyme choline TMA-lyase (CutC) does not  significantly reduce food intake, but instead is associated with beneficial remodeling of the gut  microbiome, improvement in glucose tolerance, and enhanced energy expenditure. Leveraging  untargeted metabolomics we discovered that CutC inhibition is associated with reorganization  of host circadian control of both phosphatidylcholine and energy metabolism. Collectively, this  study underscores the close relationship between microbe and host metabolism, and provides  evidence that gut microbe-derived trimethylamine (TMA) is a key regulator of the host  circadian clock. This work also demonstrates that gut microbe-targeted enzyme inhibitors can  have profound effects on host energy metabolism, and have untapped potential as anti-obesity  therapeutics.

overall_design: All animals were on a 60% high fat diet leading into the study. One group (n=5) was maintained as vehicle cohort. The other group (n=6) was maintained on IMC (specific inhibitor of choline conversion to TMA). We analyzed n = 6 per Vehicle group, however one of the control samples did not meet QC standards and was dropped from the study.

first: J

last: Brown

first: Rebecca

last: Schugar

first: Christie

last: Gliniak