title: Gene expression changes in different stages of Laccaria bicolor basidiocarps

summary: Illumina  technology was used to generate mRNA profiles of three stages of L. bicolor basidiocarps.  Total RNA was extracted separately from cap and stipe.TruSeq mRNA Stranded libraries were constructed and   and 2 x 100 bp sequenced using Illumina HiSeq 2000 at the Genotoul sequencing facilities (Toulouse, France).    Raw reads were trimmed for low quality (quality score 0.05), Illumina adapters and sequences shorter than 15 nucleotides and   aligned to the L. bicolor v2 reference transcripts available at   the JGI database  https://mycocosm.jgi.doe.gov/Lacbi2/Lacbi2.home.html using CLC Genomics Workbench v8.

overall_design: mRNA profiles of cap and stipes of three stages of L.bicolor basidiocarps were generated  by Illumina HiSeq 2000 (2x100bp). Three biological replicates were sequenced.


title: The SON splicing factor is required for intracellular trafficking that promotes centriole assembly

status: Public on Dec 22 2021

city: Aurora

first: Ryan

last: Sheridan

state: CO

address: 12801 East 17th Avenue

country: USA

institute: University of Colorado Anschutz Medical Campus

type: Expression profiling by high throughput sequencing

summary: Control of the number of centrosomes is critical for cell division, trafficking and cilia. Regulation of centrosome number occurs through the precise duplication of centrioles that reside in the center of centrosomes. Here we explored transcriptional control of centriole assembly by focusing on alternative splicing factors in isolation from other cell cycle processes. Of five splicing factors originally identified as required for centriole assembly, only SON is specifically required. Procentriole assembly is severely disrupted when SON is reduced but early centriole assembly events still occur. Whole genome mRNA sequencing identified thousands of genes whose splicing and expression are affected by the reduction of SON, with an enrichment of genes involved in the microtubule cytoskeleton. SON is required for the proper splicing and expression of the centriolar satellite protein, CEP131. Fluorescence microscopy and electron tomography establish key differences to the trafficking and microtubule network around the centrosomes that contribute to the centriole assembly defects. This establishes SON as required for centriole assembly, partially through its activity in splicing CEP131 and through control of microtubules organized by the centrosome.

overall_design: Analysis of changes in mRNA abundance and alternative splicing after knockdown of the human splicing factor SON.

first: Alexander

middle: J

last: Stemm-Wolf

first: Eileen

middle: T

last: O’Toole

middle: M

first: Jacob

last: Morgan

first: Chad

middle: G

last: Pearson


title: Transcriptional profile of tumor associated macrophages in Ptenpc-/- and Ptenpc-/; Smad4pc-/- tumors

status: Public on Feb 16 2022

city: Pieve Emanuele (MI)

first: Bioinformatics

last: Unit

address: Via Rita Levi Montalcini 4

country: Italy

institute: IRCCS Humanitas Research Hospital

summary: Tumor associated macrophages (TAMs) are correlated with the progression of prostatic adenocarcinoma (PCa) but are still poorly described in this context. Here we applied high dimensional single-cell RNA-seq to profile the transcriptional landscape of TAMs in PCa. We identified a subset of tumor infiltrating macrophages that shows a dysregulation in transcriptional pathways associated with lipid metabolism. In human and mouse models of PCa this subset of macrophages expresses the scavenger receptor MARCO and is characterized by accumulation of lipid droplets. We identified a gene signature derived from MARCO-expressing TAMs that correlates with PCa progression and is associated with shorter disease-free survival.  Mechanistically, we observed that lipid accumulation in TAMs is promoted by the secretome of cancer cells. Lipid-loading confers on tumor-conditioned macrophages the capability to promote cancer cell migration mediated by CCL6. Importantly, administration of high fat diet to tumor-bearing mice raises lipid accumulation in TAMs and affects their transcriptional profile. Finally, we demonstrate that the accumulation of lipids in macrophages is dependent on MARCO expression and we show that MARCO blockade hinders tumor growth and invasiveness in models of advanced PCa. Our findings provide evidence that lipid-loaded TAMs represent a new therapeutic target in PCa.

overall_design: 3'mRNA-seq of tumor associated macrophage sorted by Ptenpc-/- and Ptenpc-/; Smad4pc-/-  mouse models

first: R

last: Carriero

first: M

last: Masetti

first: D

last: Di Mitri


title: Placental methylome reveals a 22q13.33 brain regulatory gene locus associated with autism.

status: Public on Jan 13 2022

city: Davis

first: Janine

last: LaSalle

state: CA

address: Medical Microbiology and Immunology

institute: UC Davis

type: Methylation profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Pathologically stabilized GLI3 promotes androgen-independent growth of SPOP mutant prostate cancer cells through reactivation of an AR signaling axis

status: Public on Jul 12 2022

city: SAN ANTONIO

first: YI

last: ZOU

state: TX

address: 8403 Floyd Curl Drive

institute: UTHSA-GCCRI

summary: Although androgen deprivation therapy triggers a rapid response in men with metastatic prostate cancer, most patients eventually progress to lethal castration resistant prostate cancer (CRPC) characterized by androgen receptor (AR)-dependent tumor growth despite castrate levels of circulating androgens. Current treatment options for CRPC remain limited and non-curative, rendering improved outcomes dependent on deeper mechanistic insight and new therapeutic targets. In this RNA sequencing study we profiled the transcriptomes of SPOP WT and mutant LNCaP cells before and after androgen deprivation by RNA-sequencing. Using standard criteria (minimum 2-fold change), we identified 981 genes that were differentially expressed in SPOP mutant vs SPOP WT LNCaP cells grown in the absence of androgens . Strikingly, a significant fraction (595 or ~60%) of these genes overlapped with genes (3510 in number) differentially expressed as a function of androgen in WT LNCaP cells, indicating partial restoration of AR signaling in SPOP mutant cells following androgen withdrawal. To determine the contribution of GLI3 to this process, we performed RNA-sequencing following GLI3 knockdown in androgen-deprived SPOP mutant LNCaP cells. Among the 595 androgen-responsive genes in LNCaP cells whose hormone-independent expression is regulated by SPOP 187 (or ~31%) are also regulated by GLI3, thus revealing a prominent role for GLI3 in restoration of AR signaling in SPOP mutant cells following androgen withdrawal. Enrichment analysis using Gene Ontology Biological Processes revealed these 187 GLI3-regulated genes to be prominently linked with “chromosome segregation”, “DNA replication”, “transcriptional regulation of in G1/S transition”, “regulation of mitotic cell cycle”, and “chromatin silencing” among others, suggesting possible molecular genetic bases for androgen independent growth of SPOP mutant cells. Taken together, these findings indicate that SPOP mutant prostate cancer cells acquire robust androgen-independent growth through reestablishment of an AR signaling axis that involves functional crosstalk with the SHH/GLI3 pathway.

overall_design: SPOP WT and SPOP mutant LNCaP cells that were transduced either with or without GLI3-specific shRNA-expressing lentivirus were grown in androgen replete or androgen deprived media. Total RNA was harvested and subjected to RNA sequencing.

first: Marieke

last: Burleson

first: Thomas

last: Boyer

first: Lu-Zhe

last: Sun

first: Yi

last: Zou

first: Yidong

last: Chen


title: Immunoprofiling of prostate cancer infiltrate

status: Public on Jan 12 2022

summary: Tumor associated macrophages (TAMs) are correlated with the progression of prostatic adenocarcinoma (PCa) but are still poorly described in this context. Here we applied high dimensional single-cell RNA-seq to profile the transcriptional landscape of TAMs in PCa. We identified a subset of tumor infiltrating macrophages that shows a dysregulation in transcriptional pathways associated with lipid metabolism. In human and mouse models of PCa this subset of macrophages expresses the scavenger receptor MARCO and is characterized by accumulation of lipid droplets. We identified a gene signature derived from MARCO-expressing TAMs that correlates with PCa progression and is associated with shorter disease-free survival.  Mechanistically, we observed that lipid accumulation in TAMs is promoted by the secretome of cancer cells. Lipid-loading confers to tumor-conditioned macrophages the capability to promote cancer cell migration mediated by CCL6. Importantly, administration of high fat diet to tumor-bearing mice raises lipid accumulation in TAMs and affects their transcriptional profile. Finally, we demonstrate that the accumulation of lipids in macrophages is dependent on MARCO expression and we show that MARCO blockade hinders tumor growth and invasiveness in models of advanced PCa. Our findings provide evidence that lipid-loaded TAMs represent a new therapeutic target in PCa.

overall_design: A total of six samples; two conditions (normal and tumor) and three patients.


title: Time Course of Laccaria bicolor S238N and Populus tremula x alba 717-1B4 in vitro ectomycorrhizal development

status: Public on Dec 15 2021

city: Champenoux

first: Annegret

last: Kohler

address: Centre Grand Est Nancy

country: France

institute: INRAE

summary: Illumina  technology was used to generate mRNA profiles of a time course of Laccaria bicolor S238N and Populus tremula x alba 717-1B4 in vitro ectomycorrhizal development.  Total RNA was extracted, TruSeq mRNA Stranded libraries were constructed and   and sequenced in triplicates (2 x 150 bp Illumina HiSeq3000) at the Genotoul sequencing facilities (Toulouse, France).    Raw reads were trimmed for low quality (quality score 0.05), Illumina adapters and sequences shorter than 15 nucleotides and   aligned to the L. bicolor v2 reference transcripts available at   the JGI database  https://mycocosm.jgi.doe.gov/Lacbi2/Lacbi2.home.html using CLC Genomics Workbench v8.

overall_design: mRNA profiles of a time course of Laccaria bicolor S238N and Populus tremula x alba 717-1B4 in vitro ectomycorrhizal development were generated  by Illumina HiSeq 3000 (2x150bp). Three biological replicates were sequenced."

first: Joske

last: Ruytinx

first: Sebastian

last: Wittulsky

first: Maíra

last: de Freitas Pereira

first: Francis

last: Martin


title: Targeted inhibition of LIFR enhances therapeutic efficacy of HDAC inhibitors in triple negative breast cancer

status: Public on Dec 02 2021

summary: Here, we examined the therapeutic utility of EC359 in improving the therapeutic efficacy of HDACi in TNBC models. BT-549  cells were treated with vehicle (DMSO), EC359, HDACi(Vorinostat), EC359+HDACi and the RNA was isolated and utilized for RNA-seq analysis. Our results demonstrated that the beneficial effect of the EC359+HDACi involves regulation of multiple genes that involved in several pathways including apoptosis, metabolism and cell cycle.

overall_design: Total RNA was isolated from BT-549 cells. Illumina TruSeq RNA Sample Preparation was performed following manufacturer's protocol. Samples were run on an Illumina HiSeq 3000 in duplicate. The combined raw reads were aligned to UCSC hg19 by Tophat. Genes were annotated and quantified by HTSeq-DESeq pipeline.

first: Suryavathi

last: Viswanadhapalli

first: Ratna

middle: K

last: Vadlamudi


title: Epigenetic signature induced by prolonged culture may impact therapeutic function of Tregs used in adoptive cell therapy

status: Public on Oct 15 2021

city: Berlin

first: Julia

last: Polansky

address: Augustenburger Platz 1

country: Germany

institute: Berlin Institute of Health @ Charité Universitätsmedizin Berlin

type: Methylation profiling by genome tiling array

summary: Adoptive transfer of regulatory T cells (Treg) is a promising new therapeutic option to treat detrimental inflammatory conditions. To reach sufficient cell yield for treatment, ex vivo isolated autologous or allogenic Tregs need to be expanded extensively in vitro during manufacturing of the Treg product. However, repetitive cycles of restimulation and prolonged culture have been shown to impact T cell phenotypes, functionality and fitness. We performed genome-wide DNA methylation profiling of cells throughout the manufacturing process of a polyclonal Treg product, which may be informative for predicting the cellular state and function of the final Treg product.

overall_design: First generation (1st gen.) Treg products were generated from peripheral blood-derived starting material which is depleted of CD8+ cells and enriched for CD25-expressing cells using the CliniMACS system. The cells were expanded for 23 days with repetitive TCR stimulation (using antiCD3/CD28 microbeads, 8 stimulations in total) in the presence of IL2 and Rapamycin. Cells were harvested at multiple timepoints throughout expansion, and subjected to DNA methylation analysis with the Illumina MethylationEPIC Array.

first: Kristy

last: Ou

first: Anne

last: Schulze

first: Gilles

last: Gasparoni

first: Abdulrahman

last: Salhab

first: Jörn

last: Walter


title: Single-cell analysis of pathology in Klinefelter syndrome and idiopathic male infertility

status: Public on Sep 26 2021

city: Salt Lake City

first: Jingtao

last: Guo

state: UT

address: 2000 Circle of Hope

department: Department of Surgery Division of Urology

institute: University of Utah School of Medicine

summary: Klinefelter syndrome (KS), also known as 47,XXY,  is characterized by a distinct set of physiological abnormalities, commonly including infertility. The molecular basis for Klinefelter-related infertility is still unclear, largely due to the cellular complexity of the testis and the intricate endocrine and paracrine signaling that regulates spermatogenesis. Here, we demonstrate an analysis framework for dissecting human testis pathology that uses comparative analysis of single-cell RNA-sequencing data from the biopsies of 13 human donors. By comparing donors from a range of ages and forms of infertility, we generate gene expression signatures that characterize normal testicular function and distinguish clinically distinct forms of male infertility. Unexpectedly, we identified a subpopulation of Sertoli cells within multiple cases of KS that lack transcription from the XIST locus, with the consequence of increased X-linked gene expression compared to all other KS cell populations. By systematic assessment of known signaling pathways, we identify 72 pathways potentially active in testis, dozens of which appear upregulated in KS.  Altogether our data support a model of pathogenic changes in interstitial cells cascading from loss of X-inactivation in pubertal Sertoli cells, and nominate testicular GNRH1 as a dosage-sensitive factor secreted by Sertoli cells that may contribute to the process. Our findings demonstrate the value of comparative patient analysis in mapping genetic mechanisms of disease, and identify an epigenetic phenomenon in KS Sertoli cells that may prove important for understanding causes of infertility and sex chromosome evolution.

overall_design: To dissect the pathological biology in Klinefelter syndrome (KS) and idiopathic male infertility, we combined and analyzed 26300 single cell transcriptomes derived from the testis of 12 carefully selected donors, chosen to allow us to isolate expression changes that are attributes of the specific defects of KS, versus changes that are general hallmarks of defects in spermatogenesis, and endocrine dysfunction. Our primary analysis framework is called Sparse Decomposition of Arrays (SDA), a matrix factorization method that we find very useful for summarizing large, multi-donor scRNA-seq data into manageable sets of co-regulated genes, known as SDA components. We have recently shown the value of SDA in interpreting testis pathology in mice13 and herein we expand on its application by showing utility in humans.

first: Kenneth

last: Aston

first: Donald

last: Conrad


title: NOT proteins in co-translation decay

status: Public on Aug 18 2021

city: Geneve

first: George

last: Allen

state: Geneve

address: Rue Michel-Servet 1

country: Switzerland

institute: University of Geneva

summary: The goal is to compare role of Not1,4,5 in co-translational decay from soluble and total RNA pools using null and degron strains

overall_design: The cells are grown exponentially and total RNA is prepared by acid phenol extraction from cell pellets or from cell lysates prepared as for polysome profiling

first: Benjamin

last: Weiss

first: Susanne

last: Huch

first: Vicent

last: Pelechano

first: Martine

middle: A

last: Collart


title: Dietary enrichment of BCAA ameliorates cardiac metabolism and function in failing heart

status: Public on Sep 01 2021

first: Bioinformatics

last: Unit

summary: Here we show that a specific diet in which dietary protein content has been replaced with a defined-amino acid formula enriched with BCAA, has a remarkable effect in treating heart failure (HF). In particular, we demonstrate that our dietary intervention has a theraputic relevance in the setting of preestablished disease, providing a critical rationale for further development of dietary interventions for HF.

overall_design: Eight-week-old male C57BL/6N mice were fed with either a low fat diet (SFA) or a diet in which casein was almost completely (93.5 %) replaced by free essential amino acids (SFA-EAA) and were  subjected to transverse aortic constriction (TAC) to induce left ventricle (LV) pressure overload. 4 weeks after sham or TAC surgery, total RNA was extracted from the LV of mice fed the SFA or SFA-EAA diet.

first: Paolo

last: Kunderfranco

first: Carolina

last: Greco

first: Gianluigi

last: Condorelli


title: Heat shock-induced transcriptomic response in Chlamydia trachomatis

status: Public on Dec 08 2021

first: YI

last: ZOU

overall_design: Mouse L929 cells infected with Chlamydia trachomatis L2 434/BU were incubated at 37 ℃. At 15.5 h postinoculation, a set of cultures were incubated at 45 ℃ for 30 minutes. The remaining set of cultures were maintained at 37 ℃. All cultures were terminated at 16 h postinoculation, total RNAs were extracted and sequenced.

first: Yehong

last: Huang

first: Yi

last: Zou

first: Korri

last: Weldon

first: Zhao

last: Lai

first: Huizhou

last: Fan


title: Circulating miR-184 is a Potential Biomarker of Cardiac and Renal Damage in Anderson-Fabry Disease

status: Public on Nov 06 2021

type: Non-coding RNA profiling by high throughput sequencing

summary: The clinical symptoms of Fabry disease are caused by progressive accumulation of unprocessed globotriaosylceramide metabolite within cells, inducing multiple organ damage. Enzyme replacement therapy (ERT) is the only strategy to restore enzymatic activity, but a reliable biomarker to assess treatment response does not exist. Here, we identify circulating miR-184 as a sensitive marker of response to ERT and of clinical outcome for cardiac and kidney involvement.

overall_design: We profiled 4 healthy controls and 8 Anderson Fabry disease patients before commencing theraphy. We compared the pre-ERT data to controls in order to identified some candidate significantly modulated in AFD patients to validate in a large cohort of AFD patients.

first: Irene

last: Salamon


status: Public on Oct 13 2021

summary:
The miR-182-5p/FGF21/acetylcholine axis mediates the crosstalk between adipocytes and macrophages to promote beige fat thermogenesis
miR182 overexpression in primary cultured iWAT

overall_design: The effect of miR182 overexpression on gene expression profile in primary cultured iWAT

first: Meng

last: Wen

first: Ting

last: Xiao

first: Xiuci

last: Liang

first: Jie

first: Xinyi

last: Peng

first: Jing

last: Wang

first: Jiahao

last: Liu

first: Christie

last: Bialowas

first: Hairong

last: Luo

first: Yacheng

last: Zhang

first: Bilian

first: Jingjing

first: Fang

last: Hu

first: Meilian

first: Lily

middle: Q

last: Dong

first: Zhiguang

last: Zhou

first: Feng

first: Juli

last: Bai


title: BRD4 regulates N6-methyladenosine modification of ESPL1 mRNA via interaction with RNA demethylase ALKBH5 to modulate breast cancer progression

status: Public on Dec 11 2021

city: GuangZhou

first: YOU

last: Wu

address: Xiaoguwei

country: China

institute: SUN YAT-SEN UNIVERSITY

summary: N6-methyladenosine (m6A) is important for RNA metabolism including stability and translation of messenger RNA (mRNA). Recent studies indicate that m6A-methylated RNA can modulate dynamic chromatin accessibility and gene transcription, while the potential link of chromatin to mRNA m6A remains largely unknown. We found that targeted inhibition of bromodomain-containing protein 4 (BRD4) by siRNA or a small compound inhibitor (JQ1) significantly decreases mRNA m6A levels and suppresses the malignancy of breast cancer (BC) cells via increased expression of ALKBH5, a demethylase for mRNA methylation. Mechanistically, inhibition of BRD4 increases the mRNA stability of ALKBH5 via enhanced binding between ALKBH5 3’UTR with RNA-binding protein RALY. Further, BRD4 serves as a scaffold for ubiquitin enzymes TRIM21 and ALKBH5, resulting in the ubiquitination and degradation of ALKBH5 protein. JQ1-increased ALKBH5 then demethylates mRNA of ESPL1, a critical oncogenic driver for breast cancer, and reduces binding between ESPL1 mRNA and m6A reader IGF2BP3, leading to decay of ESPL1 mRNA. Animal and clinical studies confirm a critical role of the BRD4/ALKBH5/ESPL1 pathway in BC progression. Overall, our study sheds light on another layer of gene regulation involving crosstalks between histone modification and RNA methylation.

overall_design: Expression profiling by high throughput sequencing in human MDA-MB-231 cancer cells treated with（n=2） or without JQ1（n=2)

first: Hongsheng

first: Haisheng

first: Linlin

last: Lu

first: Jiexin

last: Li


title: Characterization of tumor associated macrophages (TAM) in the tumor microenvironment of human melanoma

status: Public on Aug 09 2021

city: Madrid

first: Rafael

last: Samaniego

address: Calle Dr Esquerdo 46

country: Spain

institute: Fundación para la Investigación Biomédica del Hospital Gregorio Marañón

summary: Tumor cells attract and dynamically interact with monocytes/macrophages to subvert their differentiation into tumor associated macrophages (TAMs), which mainly promote immunosuppression and neoplastic progression, but the pathways and microenvironmental cues governing their protumoral deviation are not completely understood. Thus, identifying molecular pathways responsible for TAM differentiation may provide new therapeutic targets to improve the efficacy of immunotherapy of cancer.

overall_design: mRNA profiles of TAM ex vivo and in vitro in human melanoma. Ex vivo TAM were isolated from human skin melanoma. Monocytes from patients with melanoma were also isolated. In vitro TAM were created by coculturing monocytes or macrophages (M-CSF or GM-CSF differentiated) with different melanoma cell lines (BLM, A375 and SKMEL103) for 24 hours. All samples have been processed in triplicates

first: Alba

last: Gutiérrez Seijo

last: Samaniego García

first: Paloma

last: Sánchez-Mateos

first: Celia

last: Barrio Alonso

first: Elena

last: García Martínez


title: Discrete regulatory modules instruct hematopoietic lineage commitment and differentiation [DNaseI-seq]

status: Public on Sep 30 2021

city: Seattle

first: Grigorios

last: Georgolopoulos

state: WA

address: 2211 Elliott Ave #400

institute: Altius Institute

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Lineage commitment and differentiation is driven by the concerted action of master transcriptional regulators at their target chromatin sites. Multiple efforts have characterized the key transcription factors (TFs) that determine the various hematopoietic lineages. However, the temporal interactions between individual TFs and their chromatin targets during differentiation and how these interactions dictate lineage commitment remains poorly understood. We performed dense, daily, temporal profiling of chromatin accessibility (DNase I-seq) and gene expression changes (total RNA-seq) along ex vivo human erythropoiesis to comprehensively define developmentally regulated DNase I hypersensitive sites (DHSs) and transcripts. We link both distal DHSs to their target gene promoters and individual TFs to their target DHSs, revealing that the regulatory landscape is organized in distinct sequential regulatory modules that regulate lineage restriction and maturation. Finally, direct comparison of transcriptional dynamics (bulk and single-cell) and lineage potential between erythropoiesis and megakaryopoiesis uncovers differential fate commitment dynamics between the two lineages as they exit the stem and progenitor stage. Collectively, these data provide novel insights into the global regulatory landscape during hematopoiesis.

overall_design: DNase I-seq from bulk ex vivo erythroid differentiation cultures starting from GCSF-mobilized PBMC-derived CD34+ cells from 3 healthy adult donors.

first: Nikoleta

last: Psatha

first: Mineo

last: Iwata

first: Andrew

last: Nishida

first: Tannishtha

last: Som

first: Minas

last: Yiangou

first: John

last: Stamatoyannopoulos

first: Jeff

last: Vierstra


title: Discrete regulatory modules instruct hematopoietic lineage commitment and differentiation

overall_design: Total RNA-seq from bulk ex vivo erythroid and megakaryocytic differentiation cultures starting from GCSF-mobilized PBMC-derived CD34+ cells from 3 healthy adult donors.


title: Chromatin accessibility underlies cell-type specific programs of amphetamine-regulated gene expression in Nucleus Accumbens interneurons [SingleNucleus-RNA-seq]

status: Public on Aug 06 2021

city: Durham

first: David

last: Gallegos

state: North Carolina

address: 311 Research Dr

department: Neurobiology

institute: Duke University

summary: Parvalbumin-expressing (PV+) interneurons of the nucleus accumbens (NAc) play an essential role in the addictive-like behaviors induced by psychostimulant exposure. To identify molecular mechanisms of PV+ neuron plasticity, we isolated interneuron nuclei from the NAc of male and female mice following acute or repeated exposure to amphetamine (AMPH) and sequenced for cell type-specific RNA expression and chromatin accessibility. AMPH regulated the transcription of hundreds of genes in PV+ interneurons, and this program was largely distinct from that regulated in other NAc GABAergic neurons. Chromatin accessibility at enhancers predicted cell-type specific gene regulation, identifying transcriptional mechanisms of differential AMPH responses. Finally, we observed dysregulation of multiple PV-specific, AMPH-regulated genes in an Mecp2 mutant mouse strain that shows heightened behavioral sensitivity to psychostimulants, suggesting the functional importance of this transcriptional program. Together these data provide novel insight into the cell-type specific programs of transcriptional plasticity in NAc neurons that underlie addictive-like behaviors.

overall_design: Single nucleus-RNAseq sample of FACS sorted PV+ Interneuron nuclei after 35 min of either Sal or AMPH. Libraries run alongside amplified Multi-seq barcodes across 4 lanes for sequencing. Tissue was mixed from 6 male and 3 female mice.

first: Melyssa

last: Minto

first: Luke

last: Bartelt

first: Anne

middle: E

last: West


title: L3-L5, T10-L1 dorsal root, nodose and trigeminal sensory neuron-selective gene expression

status: Public on Sep 15 2021

first: YI

last: ZOU

summary: Specific genes for these sensory neurons are identified

overall_design: Sensory neurons were FACS sorted from ganglia of Pirt/TdTomato reporter mice

first: Anahit

middle: H

last: Hovhannisyan

first: Jennifer

last: Mecklenburg

first: Yi

last: Zou

first: Shivani

last: Ruparel

first: Zhao

last: Lai

first: Yu

middle: S

last: Kim

first: Theodore

last: Price

first: Armen

middle: N

last: Akopian


title: Mutations of the histone linker H1-4 in neurodevelopmental disorders and functional characterization of neurons expressing C-terminus frameshift mutant H1.4

status: Public on Jul 26 2021

state: NC

summary: Rahman syndrome (RMNS) is a rare genetic disorder characterized by mild to severe intellectual disability, hypotonia, anxiety, autism spectrum disorder, vision problems, bone abnormalities, and dysmorphic facies. De novo heterozygous mutations in H1-4 encoding the linker histone H1.4 are found in individuals with RMNS; however, the underlying mechanisms causing significantly impaired neurodevelopment are not understood. So far, all neurodevelopmental associated mutations in H1-4 are small insertions or deletions that create a shared frameshift, resulting in a H1.4 protein that is both truncated and possessing an abnormal C-terminus frameshifted tail (H1.4 CFT). To expand understanding of mutations and phenotypes associated with mutant H1-4, we identified additional and new DNA variants at both the C- and N-terminus of H1.4. The clinical features of mutations identified at the C-terminus are consistent with other reports that strengthen the support of pathogenicity of H1.4 CFT.  However, the pathogenicity of disrupting variants at the N-terminus could not be determined. To understand how H1.4 CFT may disrupt brain function, we exogenously expressed wildtype or H1.4 CFT protein in primary rat hippocampal neurons and assessed neuronal structure and function. Genome-wide transcriptome analysis revealed ~400 genes altered specifically in the presence of H1.4 CFT. Neuronal genes downregulated by H1.4 CFT were enriched for functional categories involved in synaptic communication and neuropeptide signaling. Neurons expressing H1.4 CFT showed reduced activity on extracellular electrode arrays, indicating that these transcriptional changes were sufficient to disrupt physiological neuronal function. These data are the first to characterize the consequence of H1.4 CFT in neurons. Our data provide initial insights into causes of  neurodevelopmental impairments associated with these frameshift mutations in the C-terminus of H1.4 and highlight the need for future studies on the function of normal histone H1.4 in neurons.

overall_design: Bulk RNA-seq was performed on biological replicates of DIV7 rat hippocampal neuron cultures expressing WT H1.4, H1.4 mutant C-terminus Frameshift Tail (CFT), or GFP as a control (n=4 WT or mutant H1.4, n=3 GFP).

first: Martine

middle: W

last: Tremblay

first: Matthew

middle: V

last: Green

first: Benjamin

last: Goldstein

first: Andrew

middle: I

last: Aldridge

first: Jill

last: Rosenfeld

first: Haley

last: Streff

first: Wendy

middle: D

last: Tan

first: William

last: Craigen

first: Nasim

last: Bekheirnia

first: Saeed

last: Tala

first: Yong-Hui

last: Jiang


title: Single cell transcriptional profiling of cultured developing neurons upon inflammatory challenge

status: Public on Jul 20 2021

first: Bioinformatics

last: Unit

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

overall_design: Refer to individual Series


title: Single cell transcriptional profiling of cultured developing neurons upon inflammatory challenge [in vivo]

summary: The communication between immune and central nervous system represents an emerging field in neuroscience with many potential consequences both in basic and translational medicine. Among the plethora of mechanisms which might be involved, it is now clear that that immune molecules released upon inflammatory state can modulate different physiological aspects of brain development, resulting in long-lasting pathological consequences which may interfere with normal behavior during adulthood. A common aspect of this immune molecule is to promote deep transcriptional changes responsible for long-term effects. Single-cell RNA sequencing is now becoming a cutting-edge technology for studying the genomic rearrangement occurring at single cell level in different experimental models, thus opening a new frontier in medicine. Here, by using primary cultured neurons as a simplified model for studying neuronal development, we study the long-term consequences of the proinflammatory cytokine interleukine-6 (IL-6) on developing neurons through a single-cell sequencing approach. Based on the immuneprofiling of the analyzed cells, we identified different neuronal and non-neuronal cell clusters whose transcriptional profile changed specifically upon the inflammatory stimulation.

overall_design: Cultured hippocampal neurons from C57 BL/6 E16 embryos in control condition and upon IL6 treatment harvested in vivo

first: P

last: Kunderfranco

first: A

last: Termanini

first: D

last: Pozzi

first: S

last: Lodato

first: M

last: Matteoli


title: Determination of the regulons of 55 response regulators from P. aeruginosa by DAP-seq

status: Public on Jul 27 2021

city: Zurich

first: Julian

last: Trouillon

address: Otto-Stern-Weg 3

department: Institute of Molecular Systems Biology

institute: ETH Zurich

summary: Determination of the binding sites of 55 transcription factors (all response regulators) in Pseudomonas aeruginosa strains PAO1, PA14 and IHMA87.

overall_design: DAP-seq analysis of His-tagged proteins binding to sheared genomic DNA of Pseudomonas aeruginosa PAO1, PA14 or IHMA87.

first: Sylvie

last: Elsen


title: Chromatin accessibility underlies cell-type specific programs of amphetamine-regulated gene expression in Nucleus Accumbens interneurons [ATAC-Seq]

first: David

last: Gallegos

overall_design: ATAC-seq of Isolated Nac interneurons and surrounding Unbound Fraction nuclei following treatment with either Saling or 3mg/kg AMPH

first: Melyssa

last: Minto

first: Anne

last: West


title: Aging, inflammation and DNA damage in the somatic testicular niche with idiopathic germ cell aplasia

status: Public on Aug 04 2021

city: Milan

first: Anna Sofia

last: Tascini

address: Via Olgettina, 60

department: Center for Omics Science

institute: IRCCS, Ospedale San Raffaele

summary: Germ cell aplasia represents the most severe form of male infertility, and is associated with increased risk of early onset age-related chronic diseases and higher risk of death. Here we investigated the transcriptional landscape of 3880 somatic cells clustered in Sertoli, peritubular Myoid, Leydig, endothelial, stromal, T cells and macrophages from 3 human testis with idiopathic germ cell aplasia. Deregulated somatic pathways were associated with over-expression of paternally imprinted genes in immature Leydig cells, extracellular matrix composition and organization, hormonal milieu, chronic pro-inflammatory environments and early ageing, which were validated with an external cohort of 44 men with idiopathic germ cell aplasia compared to 102 age-matched fertile men. These 7 transcriptomic datasets unveil new insights into the germ cell aplasia, and prompts new thinking to better understand the pathogenesis of the idiopathic disease and the associated clinical manifestations of early ageing process.

overall_design: Droplet-based scRNAseq on freshly isolated human testis paranchyma from three men with idiopathic non-obstructive azoospermia and one man with obstructive azoospermia

first: Massimo

last: Alfano


title: Chromatin accessibility underlies cell-type specific programs of amphetamine-regulated gene expression in Nucleus Accumbens interneurons [Nuclear and Ribo-tag RNA-seq]

overall_design: Total Nuclear RNA-seq, ATAC-seq, Ribo-TAG, and Single-Nucleus RNA-seq Profiles from Specifically Isolated Nucleus Accumbens (NAc) Interneuron Types (IP) and Surrounding Cells (UF) in response to Saline or AMPH Administration


title: A GrgA-Euo-HrcA transcriptional regulatory network controls the growth and development of the obligate intracellular bacterium Chlamydia

status: Public on Jul 08 2021

first: YI

last: ZOU

summary: Effects of overexpression of Chlamydia trachomatis transcription factors GrgA, Euo and HrcA on the chlamydial transcriptome were determined.

overall_design: Mouse L929 cells were infected with Chlamydia trachomatis transformed with the transcription factors. Infected cells were cultured in medium with or without anhydrotetracycline, which induces overexpression of transcription factors. Total RNAs were extracted and sequenced .

first: Wurihan

last: Wurihan

first: Yi

last: Zou

first: Korri

last: Weldon

first: Zhao

last: Lai

first: Huizhou

last: Fan


title: Transcriptomic analysis of Oidiodendron maius free-living mycelium grown on varying carbon sources

status: Public on Jul 12 2021

first: Annegret

last: Kohler

summary: Illumina MiSeq technology was used in a pilote project to generate mRNA profiles from Oidiodendron maius free-living mycelium grown on varying carbon sources. 75bp single reads and 75bp paired reads were generated and aligned to the O.maius reference transcripts using CLC Genomics Workbench 9.

overall_design: To analyse the effect of varying carbon sources, total RNA from O. maius free-living mycelium grown on modified MMN supplemented with glucose, BSA or peat were generated and sequenced by Illumina MiSeq. For this pilote experiment one sample with 75bp paired-reads and one sample with 75bp single reads from each treatment were sequenced.

first: Erin

middle: C

last: Feldman

first: Elena

last: Martino

first: Melanie

last: Jones

first: Daniel

last: Durall


title: Decoupling Lineage-Associated Genes in Acute Myeloid Leukemia Reveals Inflammatory and Metabolic Signatures Associated with Outcomes

status: Public on Jul 18 2021

city: Houston

first: Hussein

middle: A.

last: Abbas

address: 1400 Holcombe Blvd

department: Leukemia and Genomic Medicine

institute: MD Anderson Cancer Center

summary: AML is a heterogeneous disease with current genomic and cytogenetic based classifications do not fully account for patient-to-patient variability. By decoupling lineage-related changes from transcriptomic signatures and integrating orthogonal genomic and proteomic based assays, we uncovered AML group of patients with inflammatory and metabolic signatures that inform outcomes.

overall_design: Assessment of newly diagnosed AML patients


title: Single Cell Immunophenotyping of Lyme Erythema Migrans (Bulk TCR Repertoire Sequencing)

status: Public on Jun 07 2021

city: New Haven

first: Steven

last: Kleinstein

state: Ct

address: 300 George St.

department: Pathology

institute: Yale University

summary: Erythema migrans (EM) is a skin lesion caused by the spirochete B. burgdorferi (Bb) and is a hallmark initial sign of Lyme disease. Previous studies have demonstrated that T cells and innate immune cells mediate local inflammatory cytokine production that promote the reaction. Despite the established importance of B cells and antibodies in preventing Bb infection and resolving disease, the role of B cells in the skin immune response to Bb is incompletely defined. In this study, we characterized the immunophenotype of EM lesions and used single cell RNA-Seq to investigate B cell receptor (BCR) and T cell receptor (TCR) repertoires in the EM skin lesions and peripheral blood of patients with Lyme disease. We hypothesized that B cells from the circulation, potentially primed by exposure to Bb antigens in regional draining lymph nodes, are recruited into EM lesions and play an active role in the local response to infection. We found that B cells are more abundant in the EM lesion in comparison to autologous uninvolved skin and possess distinct characteristics, including abundant expression of MHCII genes and preferential IgM isotype usage. A subset exhibited low levels of somatic hypermutation despite a gene expression profile more consistent with memory than naïve B cell subsets. Moreover, infiltrating B cells were clonally expanded and a large fraction could be directly traced to circulating relatives. By leveraging single cell gene expression with paired BCR and TCR repertoire sequencing, we demonstrate, for the first time, that B cells are recruited to the skin infection site in early Lyme disease and express a phenotype suggesting that they could play a role in local antigen presentation and antibody production.

overall_design: Bulk TCR sequencing was performed on PBMCs from six subjects, all with confirmed cases of Lyme disease.

first: Tony

last: Melillo

first: Ruoyi

last: Jiang

first: Hailong

last: Meng

first: Linda

last: Bockenstedt


title: Single Cell Immunophenotyping of Lyme Erythema Migrans [Single-Cell TCR Repertoire Sequencing]

overall_design: Six subjects were studied, all with confirmed cases of Lyme Disease. Five of six had samples from both EM rash and unaffected skin. One subject had sample only from EM rash. One subject had an additional PBMC sample. Sequencing of TCR was performed using the 10X Genomics platform.


title: Impaired stem cell differentiation and somatic cell reprogramming in DIDO3 mutants with altered RNA processing and increased R-loop levels

status: Public on Jun 18 2021

first: Tirso

last: Pons

state: Madrid

address: C/ Darwin 3

department: Inmunology and Oncology

institute: Centro Nacional de Biotecnologia

summary: Embryonic stem cell (ESC) differentiation and somatic cell reprogramming are biological processes governed by antagonistic expression or repression of a largely common set of genes. Accurate regulation of gene expression is thus essential for both processes, and alterations in RNA processing are predicted to negatively affect both. We show that truncation of the DIDO gene alters RNA splicing and transcription termination in ESC and mouse embryo fibroblasts (MEF), which affects genes involved in both differentiation and reprogramming. We combined transcriptomic, protein interaction, and cellular studies to identify the underlying molecular mechanism. We found that DIDO3 interacts with the helicase DHX9, which is involved in R-loop processing and transcription termination, and that DIDO3-exon16 deletion increases nuclear R-loop content and causes DNA replication stress. Overall, these defects result in failure of ESC to differentiate and of MEF to be reprogrammed. MEF immortalization restored impaired reprogramming capacity. We conclude that DIDO3 has essential functions in ESC differentiation and somatic cell reprogramming by supporting accurate RNA metabolism, with its exon16-encoded domain playing the main role.

overall_design: List of mESC mRNA profiles of DIDO3 wild type and mutants

first: Agnes

last: Fütterer

first: Jesus

last: de Celis

first: Carlos

last: Martinez-A


title: Single Cell Immunophenotyping of Lyme Erythema Migrans

relation:
SuperSeries of: GSE166796
SuperSeries of: GSE169437
SuperSeries of: GSE169438
SuperSeries of: GSE171087
SuperSeries of: GSE171215
SuperSeries of: GSE172225


title: Single cell RNAseq analysis of wildtype and Igfbpl1-/- retina microglia

status: Public on Jun 05 2021

city: Cambridge

first: Guangan

last: Hu

state: MA

address: 500 Main Street

department: Koch Institute

institute: MIT

summary: IGFBPL1 deficiency leads  to progressive retinal neuron loss and phosphorylated Tau accumulation in the brain. To investigate the role of IGFBL1 in retina microglia homestasis and function. Total immune cells were sorted from wildtype and Igfbpl1-/- mice applied for single cell RNAseq analysis by 10X genomics technology. To further investigate the role of IGFBL1 in retina microglia homestasis and function. Total immune cells were sorted from microbead (MB)-induced glaucoma mice and glucoma mice treated with recombinant Igfbpl1 protein for single cell RNAseq analysis by 10X genomics technology. The scRNAseq data about MB-induced glaucoma refers to https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE226456 .

overall_design: scRNA-seq was performed for microglia isolated from retinas of 10 KO and 10 sex-matched WT mice (at 8-10 months of age), or retinas of 10 MB and 10 Igfbpl1-treated MB mice (at 8-10 months of age), using FACS. Mice were transcardially perfused with saline, and digested into single cell suspension in a dissociation solution that included collagenase/dispase (1 mg/ml), papain (80 units), and Dnase (0.5mg/ml) in DMEM for 1 hour at 37oC.

first: Jianzhu

last: Chen


title: DYNAMICS OF REPLICATION ORIGIN OVER-ACTIVATION

status: Public on Jun 01 2021

city: Bethesda

first: Christophe

last: Redon

state: MD

address: 37 Convent Drive

institute: NIH

summary: Safeguards against excess DNA replication are often dysregulated in cancer, and driving cancer cells towards over-replication is a promising therapeutic strategy. We determined DNA synthesis patterns in cancer cells undergoing partial genome re-replication due to perturbed regulatory interactions ("re-replicating cells"). These cells exhibited slow replication, increased frequency of replication initiation events and a skewed initiation pattern that preferentially reactivated early-replicating origins. Unlike in cells exposed to replication stress, which activated a novel group of hitherto unutilized (”dormant”) replication origins, the preferred re-replicating origins arose from the same pool of potential origins as those activated during normal growth. Mechanistically, the skewed initiation pattern reflected a disproportionate distribution of pre-replication complexes on distinct regions of licensed chromatin prior to replication. This distinct pattern suggests that circumventing the strong inhibitory interactions that normally prevent excess DNA synthesis can occur via at least two pathways, each activating a distinct set of replication origins.

overall_design: Nascent strands were purified with the lambda exonuclease methods from HCT116  cells or U2OS. Re-replicated DNA was isolated by BrdU cesium chloride gradient. Chromatin from HCT116 cells was subjected to ChIP-Seq with antibody directed against CDT1 and pS139-MCM2.

first: Aladjem

last: MI


title: Chromatin accessibility underlies cell-type specific programs of amphetamine-regulated gene expression in Nucleus Accumbens interneurons

first: David

last: Gallegos


title: Single Cell Immunophenotyping of Lyme Erythema Migrans Identifies IgM-Switched Memory B Cells (10X Single-Cell Gene Expression)

overall_design:
Six subjects were studied, all with confirmed cases of Lyme Disease. Five of six had samples from both EM rash and unaffected skin. One subject had sample only from EM rash. One subject had an additional PBMC sample.

UPDATE [Apr-27-2025] The .rds file was replaced.


title: Integration of Feeding Behaviour by the Liver Circadian Clock Reveals Network Dependency of Metabolic Rhythms

city: Pieve Emanuele (MI)

first: Bioinformatics

last: Unit

address: Via Rita Levi Montalcini 4

institute: IRCCS Humanitas Research Hospital


title: Integration of Feeding Behaviour by the Liver Circadian Clock Reveals Network Dependency of Metabolic Rhythms [ChIP-seq]

summary: The mammalian circadian clock, expressed throughout the brain and body, controls daily metabolic homeostasis. Clock function in peripheral tissues is required, but not sufficient, for this task. Due to lack of specialized animal models, it is unclear how tissue clocks interact with extrinsic signals to drive molecular oscillations. Here, we present a model in which the interaction between feeding and the liver clock can be isolated in vivo by reconstituting Bmal1 exclusively in hepatocytes (Liver-RE) in otherwise clock-less mice. We found that the cooperative action of BMAL1 and the transcription factor CEBPB regulates daily liver metabolic transcriptional programs. Functionally, the liver clock and feeding rhythm are sufficient to drive temporal glucose homeostasis. By contrast, liver rhythms tied to redox and lipid metabolism required communication with the skeletal muscle clock, demonstrating peripheral clock cross-talk. Our results highlight how the inner workings of the clock system rely on communicating signals to maintain daily metabolism.

overall_design: WT, BMAL1 KO and BMAL1 Liver reconstituted mice (Liver-RE) were fed ad libitum (AL) or feeding was restricted to 12 hours during the night (night feeding, NF). ChIP for CEBPB was performed on livers  collected at two circadian time points (zeitgeber time ZT8 and ZT20).

first: Carolina

last: Greco

first: Kevin

last: Koronowski

first: Jacob

last: Smith

first: Paolo

last: Kunderfranco

first: Salvador

last: Benitah


title: Integration of Feeding Behaviour by the Liver Circadian Clock Reveals Network Dependency of Metabolic Rhythms [RNA-seq]

overall_design: To study how CEBPB affects circadian transcription we generated transient knock-down (KD) cells by using a siRNA targeting Cebpb. Cells were synchronized with dexamethasone and RNA extracted at specific circadian time points (CT12 and CT24). To study the muscle clock-liver connection, we collected serum from WT and muscle specific BMAL1 knock-out mice (mKO) at zeitgeber time (ZT16). Cultured primary hepatocytes were treated with the collected serum for 24 hours.


title: A method for cryopreservation and single nucleus RNA-sequencing of normal adult human interventricular septum heart tissue reveals cellular diversity and function

city: Boston

first: Michael

last: Chin

address: 15 Kneeland St

department: Molecular Cardiology Research Institute

institute: Tufts Medical Center

summary: We developed a method for cryopreserving human heart tissue for later snRNA-seq analysis.  We profiled four unused donor hearts to generate a representative snRNAseq dataset.  This is the first dataset that focuses on adult human interventricular septum tissue, and our results reveal extensive cellular diversity.  IVS cardiomyocytes and fibroblasts show divergent biological pathway activity.

overall_design: There are four unused donor hearts that were sampled.  Each sample was sequenced one time.  All samples were processed and sequencing libraries generated at the same time, and sequenced on the same sequencing run.

first: Amy

last: Larson


title: Gene expression profile of colonic goblet cells (GCs) from SpdefKO_RedMUC298trTg and RedMUC298trTg mice

status: Public on Apr 16 2021

city: Gothenburg

first: Malin

middle: E. V.

last: Johansson

address: Medicinaregatan 9A

department: Department of Medical Biochemistry and Cell Biology

country: Sweden

institute: University of Gothenburg

summary: Spdef is a transcription factor involved in differentiation of goblet cells. Goblet cells from RedMUC298trTg and Spdef -/-RedMUC298trTg were sorted to analyse the differential gene expression in the absence of Spdef.

overall_design: Colonic GCs and the remaining epithelial cells (ECs) of the RedMUC298trTg and Spdef -/-RedMUC298trTg mice were isolated by Fluorescence-activated cell sorting (FACS) according to the presence or absence of mCherry signal. Sorted GCs were analysed using RNA sequencing (RNAseq).

first: Beatriz

last: Martinez Abad

first: Elisabeth

last: Nyström


title: Single cell transcriptional profiling of cultured developing neurons upon inflammatory challenge [in vitro]

status: Public on May 13 2021

overall_design: Cultured hippocampal neurons from C57 BL/6 E18 embryos in control condition and upon IL6 treatment harvested at days in vitro 5 (DIV5)

first: P

first: A

last: Termanini

first: D

last: Pozzi

first: S

last: Lodato

first: M

last: Matteoli


title: Gene expression profile at single cell level of goblet cells (GCs) from the distal colon (DC) and the 8th portion of the small intestine (Si8)

summary: Goblet cells are considered as a homogeneous population in the intestinal epithelium. We used single cell RNA sequencing (scRNA-seq) to analyze the diversity of GCs in the intestine.

overall_design: Intestinal GCs of the RedMUC298trTg mice were isolated by Fluorescence-activated cell sorting (FACS) according to the presence or absence of mCherry signal and analyzed using scRNAseq.


title: Transcriptomic analysis of WT and POLG mutator macrophages

status: Public on Apr 13 2021

city: Bar Harbor

first: Phillip

last: West

state: ME

address: 600 Main St

institute: The Jackson Laboratory

summary: The goal of this study was to characterize gene expression profiles of wild-type (WT) and POLG D257A/D257A mutator (POLG mutator) macrophages at rest and 6 hours after lipopolysaccharide (LPS) challenge.

overall_design: Both bone marrow-derived (BMDM) and thioglycollate elicited, peritoneal macrophages (PerMac) were analyzed. After 7 days of differentiation for BMDMs or 4 days post interperitoneal thioglycollate injection, macrophages were plated and stimulated with 200ng/ml LPS for six hours. Total cellular RNA from WT and POLG BMDMs and PerMacs was prepared using the Quick-RNA microprep kit (Zymo Research) and subjected to library preparation and RNA sequencing at the Experimental Genomics Core of the Texas A&M Institute for Genome Sciences and Society. FASTQ files were normalized, processed, and analyzed using BaseSpace Sequence Hub (Illumina). In brief, the STAR algorithm of RNAseq Alignment V2.0.0 software was utilized to align the results to the Mus musculus/mm10 (RefSeq) reference genome, then RNA-seq Differential Expression V1.0.0 software was used to obtain differential gene expression values and determine statistically significant changes in POLG mutator macrophages relative to WT.


title: Gene expression profile of goblet cells (GCs) from the distal colon (DC) and the 8th portion of the small intestine (Si8)

summary: Goblet cells together other cell types make up the intestinal epithelium and are responsible for mucus production. The goal of this project is to fully characterize the gene expression profile of the GCs in the colon and small intestine.

overall_design: Intestinal GCs and the remaining epithelial cells (ECs) of the RedMUC298trTg mice were isolated by Fluorescence-activated cell sorting (FACS) according to the presence or absence of mCherry signal. Sorted GCs were analysed using RNA sequencing (RNAseq).


title: Murine macrophages: Peritoneal exudate macrophages (PECs) vs tumor-associated macrophages (TAMs)

status: Public on Apr 01 2021

first: Bioinformatics

summary: Transcriptional landscape of two different TAMs subsets (F4/80hi and F4/80lo) FACS-sorted from fibrosarcoma-bearing WT mice in comparison with control macrophages (PEC)

overall_design: Biological replicates: 3 control replicates, 3 F4/80hi TAMs replicates and 3 F4/80lo TAMs replicates.

first: Alberto


title: DRG (dorsal root ganglia) and TG (trigeminal ganglia) fractions enriched with sensory neurons

status: Public on Mar 19 2021

city: SAN ANTONIO

first: YI

last: ZOU

address: 8403 Floyd Curl Drive

institute: UTHSA-GCCRI

summary: Male and female sensory neuron enriched genes were identified.

overall_design: Sensory neuronal fractions from TG and DRG tissues from 3 naïve males and 3 naïve females are isolated, RNA is extracted and sequenced

first: Jennifer

last: Mecklenburg

first: Yi

last: Zou

first: Andi

last: Wangzhou

first: Dawn

last: Garcia

first: Zhao

last: Lai

first: Gregory

last: Dussor

first: Theodore

middle: J

last: Price

first: Armen

last: Akopian


title: Gene expression analysis of two strains of Trametes versicolor

status: Public on Jan 15 2021

city: Champenoux

first: Annegret

last: Kohler

address: Centre Grand Est Nancy

institute: INRAE

summary: Illumina HiSeq technology was used to generate mRNA profiles from two strains of Trametes versicolor.   Mycelium of Trametes versicolor BRFM1218 and Trametes versicolor 1956-1252 were harvested after 2 and 4 weeks of incubation on 4% malt agar medium and used for total RNA extraction.   Paired-end reads of 100 bp were generated and aligned to Trametes versicolor (https://mycocosm.jgi.doe.gov/Trave1/Trave1.home.html) reference transcripts using CLC Genomics Workbench 7.5.1.

overall_design: mRNA profiles from from two strains of Trametes versicolor (BRFM1218 and 1956-1252) were generated by Illumina HiSeq2000 sequencing (2x100bp). Three biological replicates were sequenced from mycelium grown for 2 or 4 weeks on 4% malt agar medium.

last: Deroy

first: E

last: Gelhaye


title: DRG (dorsal root ganglia) sensory neurons innervating paw and thigh muscle

overall_design: Sensory neurons of DRG tissues backtaced from paw skin and thigh muscle for 4 naïve males and 4 naïve females are isolated, RNA is extracted and sequenced

first: Korri

last: Weldon


title: Identification of new inhibitory molecules in T lymphocytes upon HCC development for new therapeutic targets

status: Public on Dec 31 2020

city: Braunschweig

first: Robert

last: Geffers

address: Inhoffenstr. 7

department: Dep. Molecular Bacteriology

institute: HCI - Helmholtz Centre for Infection Research

summary: Aim of the present study is the identification of new inhibitory targets on T lymphocytes which appear upon hepatocellular carcinoma (HCC) development and lead to a dysfunction of T cells by HCC microenvironment.

overall_design: Hepatocellular carcinoma was induced by intrahepatic administration of two oncogenes (c-Myc and NrasG12V, abbreviation in the list below CN). Two control groups were injected with a single oncogene each (control group C and control group N), that did not result in cancer development. CD4 and CD8 cells were isolated from 6 tumor-bearing (TB) mice and from two groups (each with 6 mice) of healthy tumor-free (TF) control mice. In particular, CD4 and CD8 T cells were isolated from liver, liver-draining lymph nodes (relLN), not liver-draining lymph nodes (irrLN) and spleen. Microarray was performed on CD4 and CD8 T cells cells. In total, 3 groups by first microarray replicate were created with 4 organs each and in total 24 samples (CD4 and CD8). For the second replicate new 6 tumor-bearing and 6+6 tumor-free animals were used. In total, two replicates of microarray have been performed and in total 48 samples were analysed.

first: T

last: Yevsa

first: I

last: Hochnadel

first: R


title: Gene expression analyses of four Pisolithus microcarpu strains: Si9, MW3, R4 and R10. Gene expression in Eucalyptus grandis mycorrhizal root tip was compared to gene expression in free-living mycelium for each strain.

status: Public on Nov 18 2020

summary: Illumina HiSeq technology was used to generate mRNA profiles from Pisolithus microcarpus Si9, MW3, R4 or R10 ectomycorrhizal root tips compared to their respective free-living mycelium.

sample_organism:
Eucalyptus grandis
Pisolithus microcarpus

overall_design: Ectomycorrhizal root tips and control mycelium were harvested after 4 weeks of contact and used for RNA extraction.

first: Krista

last: Plett

first: Jonathan

middle: M

first: Francis

last: Martin

first: Ian

last: Anderson


title: Genome-wide Profiling of RNA Binding Targets of hnRNP H

status: Public on Nov 03 2020

first: Camron

last: Bryant

address: 72 East Concord St

department: Pharmacology

institute: Boston University School of Medicine

summary: To inform the mechanism of hnRNP H dysfunction in methamphetamine-induced dopamine release and behavior, we surveyed mRNA targets of hnRNP H via cross-linking immunoprecipitation coupled with high-throughput sequencing (CLIP-seq) in striatal tissue at baseline and at 30 min post-MA (2 mg/kg, i.p.). To integrate identification of hnRNP H targets with the impact of methamphetamine on downstream gene expression and splicing, we analyzed the transcriptome of the parallel samples used in CLIP-seq.

overall_design:
Identification of mRNA transcripts bound by hnRNP H in the striata of C57BL/6J wild-type in response to acute methamphetamine versus saline. Transcriptomic analyses for differential gene expression an alternative splicing in the striata of C57BL/6J wild-type in response to acute methamphetamine versus saline. Striata from four mice were pooled per replicate (3 replicates per Treatment). Each replicate used for CLIP-seq and RNA-seq was generated by pooling striata from 4 wild type mice across multiple litters. Each pool consisted of samples from 2 females and 2 males.

UPDATE [May-02-2025] The mutant Samples were removed because of an inconsistency in the size of the mutation across samples and within pooled samples. Maintenance of a heterozygous colony led to an alteration in the original 16 bp deletion such that there were both shorter and longer deletions segregating in the colony and in the samples originally posted.

first: Qiu

last: Ruan


title: Neuron-Derived Estrogen is Critical for Astrocyte Activation and Neuroprotection of the Ischemic Brain

status: Public on Oct 13 2020

first: YI

last: ZOU

summary: We examined the transcriptional changes modulated in ischemic brain of fore brain specific aromatase knockout mice (FBN-ARO-KO) by performing global transcriptome analysis.Total RNA was isolated from FLOX and FBN-ARO-KO mice that underwent 20-minute CCA occlusion, followed by 24-hour reperfusion. The collected hippocampi samples were subjected to RNA isolation and Illumina TruSeq RNA sample preparation and sequencing was done using UT Health San Antonio genomics core facility protocol. We observed that some of the key pathways that regulate astrocyte reactivity, such as RhoA signaling, actin-based motility by Rho signaling, signaling by Rho family GTPases, and protein ubiquitination, NRF2-mediated oxidative stress response pathways were significantly altered in FBN-ARO-KO+GCI mice.

overall_design: Total RNA was isolated from female FLOX and FBN-ARO-KO mice that underwent 20-minute CCA occlusion, followed by 24-hour reperfusion. RNA was isolated from the hippocampi using the RNeasy mini kit. Illumina TruSeq RNA sample preparation was performed following manufacturer's protocol. Samples were run on an Illumina HiSeq 3000 in duplicate. The combined raw reads were aligned to UCSC mm9 and genes were annotated by Tophat. Genes were annotated and quantified by HTSeq-DESeq pipeline.

first: Gangadhara

middle: R

last: Sareddy

first: Yidong

last: Chen

first: Ratna

last: Vadlamudi


title: Helianthemum almeriense mycorrhizal symbiosis

status: Public on Oct 21 2020

first: Annegret

summary: Illumina HiSeq technology was used to generate mRNA profiles from Helianthemum almeriense in three different conditions: non-mycorrhizal plant, well-watered mycorrhizal plant and drought-stressed mycorrhizal plant. Paired-end reads of 75 bp were generated and aligned to a de novo transcriptome assembly from H. almeriense, which was performed using Megahit version 1.1.3 and transcripts from each condition were mapped onto the de novo transcriptome with Bowtie2 version 2.3.0.

sample_organism:
Terfezia claveryi
Helianthemum almeriense

overall_design:
mRNA profiles from Helianthemum almeriense in three different conditions: non-mycorrhizal plant, well-watered mycorrhizal plant and drought-stressed mycorrhizal plant. The technology used was Ilumina HiSeq 2x75bp. Three biological replicates per tretment were used.
Pleae note that raw data of the [re-analysis] samples have mix of plant and fungal reads sequenced. In the GSE154490 previous submission, the fungal reads were analyzed and the plant reads were used in the current study.

first: José

last: Marqués-Gálvez

first: Shingo

last: Miyauchi

first: Alfonso

last: Navarro-Ródenas

first: Francisco

last: Arenas

first: Manuela

last: Pérez-Gilabert

first: Emanuelle

last: Morin

first: Lucas

last: Auer

first: Asunción

last: Morte


title: Gene expression analysis of shUhrf1 cardiomyocytes (CMs) isolated from mice subjected to transverse aortic constriction (TAC) for 1 week

status: Public on Oct 10 2020

first: Bioinformatics

last: Unit

summary: To identify UHRF1-regulated genes in TAC mice we performed a  gene expression analysis of cardiomyocytes (CMs) isolated from mice infected with AVV9 - an adeno-associated viral vector that efficiently transduces cardiomyocytes in vivo-encoding either a scrambled shRNA (AAV9-scr, control group) or sh-Uhrf1 #1 (AAV9-sh-Uhrf1 #1), and subjected  to TAC for 1 week.

overall_design: 4 samples analyzed in triplicate

first: Carolina

last: Greco

first: Paolo

last: Kunderfranco

first: Roberto

last: Papait

first: Gianluigi

last: Condorelli


title: Intestinal goblet cells are a heterogeneous lineage with diverse funcional potential

first: Malin

last: Johansson

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

overall_design: Refer to individual Series


title: Cell-specific Characterization of the Placental Methylome

city: Vancouver

first: Wendy

last: Robinson

state: BC

address: 950 W 28th Ave

department: Medical Genetics

country: Canada

institute: University of British Columbia

summary: Background: DNA methylation (DNAm) profiling has emerged as a powerful tool for characterizing the placental methylome. However, previous studies have focused primarily on whole placental tissue, which is a mixture of epigenetically distinct cell populations. Here, we present the first methylome-wide analysis of first trimester (n=9) and term (n=19) human placental samples of four cell populations: trophoblasts, Hofbauer cells, endothelial cells, and stromal cells, using the Illumina EPIC methylation array, which quantifies DNAm at >850,000 CpGs.  Results: The most distinct DNAm profiles were those of placental trophoblasts, which are central to many pregnancy-essential functions, and Hofbauer cells, which are a rare fetal-derived macrophage population. Cell-specific DNAm occurs at functionally-relevant genes, including genes associated with placental development and preeclampsia. Known placental-specific methylation marks, such as those associated with genomic imprinting, repetitive element hypomethylation, and placental partially methylated domains, were found to be more pronounced in trophoblasts and often absent in Hofbauer cells. Lastly, we characterize the cell composition and cell-specific DNAm dynamics across gestation.  Conclusions: Our results provide a comprehensive analysis of DNAm in human placental cell types from first trimester and term pregnancies. This data will serve as a useful DNAm reference for future placental studies, and we provide access to this data via download from dbGAP (phs002013.v1.p1), through interactive exploration from the web browser (https://robinsonlab.shinyapps.io/Placental_Methylome_Browser/), and through the R package planet, which allows estimation of cell composition directly from placental DNAm data.

overall_design: Placental tissues were obtained with approval from the University of British Columbia / Children’s and Women’s Health Centre of British Columbia Research Ethics Board (H04-70488, H16-02280, H13-00640). Women for a scheduled C-section with a healthy term (>37 weeks) singleton pregnancy were recruited with written informed consent at BC Women’s Hospital, Vancouver Canada. In addition, first trimester samples from elective terminations were obtained in a deidentified manner. A total of 9 first trimester (6.4-13 weeks) and 19 term (36.4-40.4 weeks) placental samples were obtained; all were screened for large chromosome abnormalities using CNV calling on the EPIC array, and found to be normal. No gross pathologies were noted. CS refers to fluorescense-activated cell-sorted samples, and enz refers to enzymatically separated trophoblast samples.

first: Victor

last: Yuan

first: Desmond

last: Hui

first: Yifan

last: Yin

first: Maria

last: Peñaherrera

first: Alexander

middle: G

last: Beristain

middle: P


title: Altered Intercellular Communication and Extracellular Matrix Signaling as a Disease Mechanism in Human Hypertrophic Cardiomyopathy

status: Public on May 20 2021

first: Christina

last: Codden

address: 800 Washington Stree

summary: To understand the interplay between cardiomyocyte and nonmyocyte cell types in human hypertrophic cardiomyopathy, single nuclei RNA-sequencing was performed on 9 myectomy specimens from HCM patients

overall_design: Myectomy specimens (samples 5-13) were sampled for single nuclei transcriptomic sequencing. Sample 5 was generated and sequenced on its own with NextSeq 550. Samples 6-13 were generated and sequenced togheter on a NovaSeq S4 run.

first: Amy

last: Larson

first: Michael

middle: T

last: Chin


title: Genome-wide map of DNA methylation of cardiomyocytes isolated from 1 week pressure-overload mice

summary: We investigated the role of DNA methylation in hypertrophic cardiomyocytes by means of genome wide approach showing that this epigenetic mark governs the metabolic remodelling of the diseased heart

overall_design: Profiling of 5mC in Sham and pressure-overload (TAC) isolated cardiomyocytes


title: Terfezia claveryi mycorrhizal symbiosis

first: Annegret

last: Kohler

summary: Illumina HiSeq technology was used to generate mRNA profiles from Terfezia claveryi in three different conditions:  free living mycellium, well-watered mycorrhizal plant and drought-stressed mycorrhizal plant. Paired-end reads of 75 bp were generated and aligned to Terfezia claveryi reference transcripts using  CLC Genomics Workbench 11.

platform_organism:
Terfezia claveryi
Helianthemum almeriense

overall_design: mRNA profiles from Terfezia claveryi in three different conditions: free living mycellium, well-watered mycorrhizal plant and drought-stressed mycorrhizal plant. The technology used was Ilumina HiSeq 2x75bp. Three biological replicates per tretment were used.

first: José

middle: E

last: Marqués-Gálvez

first: Shingo

last: Miyauchi

first: Alfonso

last: Navarro-Ródenas

first: Francisco

last: Arenas

first: Manuela

last: Pérez-Gilabert

first: Emanuelle

last: Morin

first: Lucas

last: Auer

first: Francis

last: Martin


title: Identification of the transcription start site of transcribed sequences from the mouse Sry locus by CAGE-seq

status: Public on Oct 01 2020

city: Suita-shi, Osaka

first: Ryo

last: Maeda

address: Yamadaoka 1-3

country: Japan

institute: The University of Osaka

summary: The mammalian sex-determining gene Sry induces male development. Through analyzing transcriptome of pre-Sertoli cells, we identified a novel sequence transcribed within palindromic sequence surrounding Sry. To examine whether this sequence contains transcription start site, Cap analysis gene expression (CAGE) -seq analysis was performed, in which putative transcriptional start sites can be identified by sequencing the 3’ end of cDNA corresponding to 5’ end of RNA. CAGE seq revealed that Cap site was absent within the novel sequence, whereas Sry transcription start site found to locate in minus strand at chrY:2,663,800-2,663,900. Combining the result from long-read RNA seq, we concluded that this sequence is the second exon of mouse Sry.

overall_design: Samples from mouse embryonic gonad at E11.5.

last: Miyawaki

first: Makoto

last: Tachibana


title: Identification of a novel transcriptional variant in the mouse Sry locus by long-read RNA-seq and conventional RNA-seq

summary: The mammalian sex-determining gene Sry induces male development. Sry is exclusively expressed in Nr5a1-highly expressing gonadal supporting cell precursor, pre-Sertoli cells, with a peak at embryonic day 11.5 (E11.5). We developed a method to enrich pre-Sertoli cells from mouse embryonic gonads carrying Nr5a1-hCD271 (LNGFR) transgene. To examine mRNA expression in pre-Sertoli cells, pre-Sertoli cells were purified and introduced into long-read RNA-seq and conventional RNA seq analyses. Through analyzing those RNA-seq data, we discovered a second exon of mouse Sry.

first: Shunsuke

last: Kuroki


title: TRIM21 knockout mouse livers show enhanced antioxidant capacity and decreased compensatory proliferation

status: Public on Apr 14 2021

first: YI

last: ZOU

summary: Acute response to diethylnitrosamine treatment in TRIM21 wild-type and knockout mice were compared and differentially expressed genes were inendified at 48 hours

overall_design: TRIM21 wild-type and knockout mice were treated with one dose of 200 mg/kg diethylnitrosamine (DEN) dissolved in PBS or PBS only by intraperitoneal injection, 48 h after the treatment, liver tissue were harvested and total RNA is extracted and sequenced

first: Wei-Xing

last: Zong

first: Fang

last: Wang

first: Jianliang

last: Shen

first: Weiwei

last: Dai


title: TRANSCRIPTIONAL ANALYSIS OF MUSCLE FROM CATTLE WITH ALTERNATIVE NCAPG/LCORL GENOTYPES

status: Public on Sep 10 2020

city: Knoxville

first: Jonathan

last: Beever

state: Illinois

address: 2506 River Drive

department: Animal Sciences

institute: University of Tennessee

summary: The LCORL-NCAPG locus is a major quantitative trait locus (QTL) on bovine chromosome 6 (BTA6) that influences growth and carcass composition in cattle. To further understand the molecular mechanism responsible for the changes associated with this locus, twenty-four Charolais-sired calves were selected for muscle transcriptome analysis based on alternative homozygous LCORL-NCAPG haplotypes (i.e., 12 "QQ" and 12 "qq", where "Q" is a haplotype harboring variation associated with increased growth). At 300 days of age, a biopsy of the longissimus dorsi muscle was collected from each animal for RNA sequencing. Total RNA was isolated and used for NGS library construction and libraries were sequenced on a HiSeq2500 using single-end chemistry. Sequencing yielded 898 million reads (average of >37 million reads/sample) that were mapped to the bovine reference genome (ARS-UCD 2.0). Gene expression analysis identified 733 genes as differentially expressed between QQ and qq animals (q-value < 0.05). Notably, LCORL and genes known to be important regulators of growth such as IGF2 were upregulated in QQ individuals, while genes associated with adiposity such as FASN and LEP were downregulated, reflecting the increase in lean growth associated with this locus. Gene set enrichment analysis revealed an overall trend of downregulation of pathways associated with adipogenesis, and upregulation of ribosomal and mitochondrial-related transcripts in QQ individuals, molecular differences which imply increased muscle hypertrophy instead of accumulation of fat in animals with this haplotype. These findings suggest this haplotype could be linked to a difference in LCORL expression that potentially leads to the downstream transcriptional effects observed, though further research will be needed to confirm the molecular mechanisms underlying the associated changes in phenotype.

overall_design:
Use of RNA-Seq for the examination of differential gene expression profiles between muscle samples from cattle with alternative genotypes for the NCAPG/LCORL QTL.

UPDATE: [08-30-2024] The processed data and data processing description were updated.

first: Fernanda

last: Rodrigues


title: Gene expression profile of tumor-associated macrophages in human colorectal liver metastasis (CLM)

status: Public on Aug 05 2020

first: Bioinformatics

last: Unit

summary: The immune landscape impacts outcome and therapeutic response in many tumor types, including colorectal liver metastases (CLM). It has long been known that in vitro polarized macrophages differ in morphology. Here we tested the hypothesis that morphology of tumor-associated macrophages (TAMs) in CLM represents a correlate of function with prognostic significance. Density and morphological metrics (area and perimeter) of TAMs were measured and correlated with clinic-pathological prognostic variables. While density of TAMs did not correlate with survival of CLM patients, cell area identified small and large macrophages that associated with 5-year disease-free survival rate of 27.8% and 0.2% respectively (P<0.001). RNA sequencing of morphologically distinct macrophages identified LXR/RXR as the most enriched pathway in large macrophages and upregulation of genes involved in cholesterol metabolism, phagocytosis and downregulation of the inflammatory program. These results support that accurate, morphometric characterization can serve as a simple readout of TAM diversity with prognostic significance.

overall_design: RNA-sequencing of small and large tumor associated macrophages in a cohort of 5 patients

first: Roberta

last: Carriero

first: Federica

last: Marchesi

first: Nina

last: Cortese

first: Matteo

last: Donadon

first: Alberto

last: Mantovani


title: TGF-b and Eomesodermin coordinate to maintain CD8+ regulatory T cells and limit spontaneous germinal center reaction

status: Public on Sep 17 2020

summary: We are interested in CD8+ regulatory T cells that limit germinal center reactions. We have found that in conditional knockout mice lacking both Tgfbr2 and Eomes expression in mature T cells, CD8+ regulatory T cells are severely defective. RNA-seq analysis was employed to characterize the genome-wide transcriptional changes in CD8+ regulatory T cells.

overall_design: CD8+ regulatory T cells were FACS sorted from the spleens of 3-month old naïve WT and Tgfbr2-/-Eomes-/- mice. Total RNA was extracted and subjected to RNA-seq analysis.

first: Shruti

last: Mishra

first: Chaoyu

last: Ma

first: Yong

last: Liu

first: Wei

last: Liao

first: Zhao

last: Lai

first: Yi

last: Zou

first: Yidong

last: Chen

first: Nu

last: Zhang


title: SARS-CoV-2 infection in the lungs of human ACE2 transgenic mice causes severe inflammation and immune cell infiltration, and compromised respiratory function

status: Public on Jul 29 2020

city: St. Louis

first: Jinsheng

last: Yu

state: MO

address: 660 S. Euclid Ave.

department: Genetics

institute: Washington University School of Medicine

summary: We evaluate heterozygous transgenic mice expressing human ACE2 receptor driven by the epithelial cell promoter cytokeratin-18 promoter (K18-hACE2) as a model of SARS-CoV-2 infection. Intranasal inoculation of K18-hACE2 mice with SARS-CoV-2 results in high levels of infection in the lung parenchyma with spread to other organs.

overall_design: Eight-week-old mice of both sexes were infected with 2.5 x 10^4 PFU of SARS-CoV-2 via intranasally. Lung tissues from mice 2, 4, 7 days post-infection and mock-infected mice were used to extract total RNA for  RNA-seq analysis.

first: Emma

last: Winkler

first: Adam

middle: L

last: Bailey

first: Natasha

last: Kafai

first: Sharmila

last: Nair

first: Broc

last: McCune

first: Julie

last: Fox

first: Rita

first: James

last: Earnest

first: Shamus

last: Keeler

first: Jon

middle: H

last: Ritter

first: Liang

last: I-Kang

first: Sarah

last: Dort

first: Annette

last: Robichaud

first: Richard

last: Head

first: Michael

last: Holtzman

last: Diamond


title: Long noncoding RNA INCA1 regulates tumor interferon signaling [CLIP-seq]

first: Marco

last: Mineo

address: 60 Fenwood Rd, BTM 8016N

institute: Brigham and Women's Hospital

summary: Tumor interferon signaling regulates the expression of immunosuppressive molecules and promotes cancer immune evasion. Although the role of long noncoding RNAs (lncRNAs) in the regulation of gene expression is now emerging, their function in tumor interferon signaling remains unexplored.  We have identified the interferon-γ (IFNγ)-stimulated non-coding RNA 1 (INCA1) as a novel lncRNA expressed form the PD-L1 locus. INCA1 is expressed in multiple tumor types and its levels increase after IFNγ stimulation. Silencing INCA1 decreased the expression of several interferon-stimulated genes (ISGs). We discovered that the transcripts of some ISGs are negatively regulated by HNRNPH1. We demonstrate that binding of INCA1 to HNRNPH1 is required for ISG expression. Overall, our findings reveal a mechanism of tumor interferon signaling regulation mediated by the lncRNA INCA1.

overall_design: Melanoma cell line was stimulated with interferon gamma for 6 hours. RNAs bound to HNRNPH1 were identified by CLIP-seq using Illumina HiSeq4000.

first: E

middle: A

last: Chiocca


title: Loss-of-function maternal-effect mutations of PADI6 are associated with familial and sporadic Beckwith-Wiedemann Syndrome with multi-locus imprinting disturbance

status: Public on Oct 02 2020

city: Naples

first: Ankit

last: Verma

state: Naples

address: Via Pietro Castellino, 111

institute: Institute of Genetics and Biophysics "A. Buzzati Traverso" (IGB-ABT)

summary: PADI6 is a component of the subcortical maternal complex (SCMC) which is a group of proteins that are abundantly expressed in the oocyte cytoplasm and essential for the proper development of the early embryo. The mutation(s) in the components of the subcortical maternal complex have been associated with reproductive failures, including formation of hydatidiform mole, female infertility and imprinting disorders with multi-locus imprinting disturbance (MLIDs).In the current study by using whole-exome sequencing analysis, we identified four cases of Beckwith-Wiedemann Syndrome with multi-locus imprinting disturbance while their mothers were carriers of variants in PADI6 gene. Genome-wide methylation profiling using Methylation EPIC array depicted the loss of methylation specifically at several known imprinted loci in affected individuals as compared to healthy siblings, parents and controls. Our findings firmly establish the role of PADI6 in imprinting disorders.

overall_design: DNA samples extracted from peripheral blood were subjected to methylation profile analysis using Infinium MethylationEPIC 850K Bead Chip and pyrosequencing. We also included 12 individuals as control samples.  This series includes re-analyzed samples from GSE133774.

first: Maria

last: Cubellis

first: Laura

last: Pignata

first: Angela

last: Sparago

first: Rosita

last: Del Prete

last: Monticelli

first: Vincenzo

last: Antona

first: Daniela

last: Melis

first: Romano

last: Tenconi

first: Silvia

last: Russo

first: Flavia

last: Cerrato

first: Andrea

last: Riccio


title: Long noncoding RNA INCA1 regulates tumor interferon signaling.


title: Long noncoding RNA expression profiles analysis in GBM patient-derived cells stimulated with interferon gamma

summary: Long noncoding RNAs (lncRNAs) are key regulators of gene expression both in physiological and pathological conditions. Previous studies showed changes in lncRNA expression during tumorigenesis. To analyze the role of lncRNAs in tumor interferon signaling and cancer-mediated immunosuppression, we used RNA-seq technique to identify lncRNAs that are differentially expressed in GBM patient-derived cells stimulated with interferon gamma compared to unstimulated cells. 15,768 lncRNAs were surveyed in the analysis. RNA-seq data show upregulation of 113 lncRNAs upon interferon gamma treatment (p value < 0.01, fold change > 2). Our findings indicate that the expression of several lncRNAs is stimulated by interferon gamma suggesting a critical role of lncRNAs in tumor interferon signaling.

overall_design: Patient-derived GBM cells were stimulated with interferon gamma for 24 hours. Non stimulated cells were used as control. LncRNA expression profiles were generated by RNA-seq, in triplicate, using Illumina HiSeq 4000.


title: RNA-seq and H3K9me2 ChIP-seq of postnatal male germ cells

status: Public on Jun 08 2020

first: Ryo

last: Maeda


title: Time series data of chromatin occupancy and transcription under cadmium stress

status: Public on Jul 04 2020

city: Durham

first: David

last: MacAlpine

address: Duke University

department: Department of Pharmacology and Cancer Biology

institute: Duke University Medical Center

summary: Though the sequence of the genome within each eukaryotic cell is essentially fixed, it exists in a complex and changing chromatin state. This state is determined, in part, by the dynamic binding of proteins to the DNA. These proteins---including histones, transcription factors (TFs), and polymerases---interact with one another, the genome, and other molecules to allow the chromatin to adopt one of exceedingly many possible configurations. Understanding how changing chromatin configurations associate with transcription remains a fundamental research problem. We sought to characterize at high spatiotemporal resolution the dynamic interplay between transcription and chromatin in response to cadmium stress. While gene regulatory responses to environmental stress in yeast have been studied, how the chromatin state is modified and how those modifications connect to gene regulation remain unexplored. By combining MNase-seq and RNA-seq data, we found chromatin signatures of transcriptional activation and repression involving both nucleosomal and TF-sized DNA binding factors.

overall_design: Time course of cadmium treated yeast for T=0 min (prior to cadmium addition), 7.5 min, 15 min, 30 min, 60 min, and 120 min. 12 samples of MNase chromatin (2 technical replicates) and 6 samples of RNA

first: Trung

middle: Q

last: Tran

first: Vinay

last: Tripuraneni

first: Heather

middle: K

first: Sneha

last: Mitra

first: Alexander

last: Hartemink


title: Genome wide map of H3K9me2 in postnatal male germ cells

summary:
We report the H3K9me2 distribution profile with ChIP sequencing of  postnatal male germ cells.
Histone modification levels are dynamically controlled during mammalian spermatogenesis. We found that H3K9 demethylases, Jmjd1a and Jmjd1b catalyze H3K9 demethylation in prospermatogonia. Combined loss of Jmjd1 enzymes disturbed prospermatogonia to spermatogonia transition in mice. To examine a role of Jmjd1 in prospermatogonia to spermatogonia transition, we performed RNA-seq and ChIP-seq analyses using postnatal germ cells at P3 and P7.

overall_design: H3K9me2 profiles of  postnatal male germ cells isolated from testes of a series of Vasa-Cre; Jmjd1; Jmjd1b conditional knockout mice

first: Makoto

last: Tachibana


title: CDK6 is an essential direct transcriptional target of NUP98-fusion-protein-driven acute myeloid leukemia

status: Public on May 08 2020

city: Vienna

first: Thomas

last: Eder

address: Veterinaerplatz 1

department: Department for Biological Sciences and Pathobiology

country: Austria

institute: University of Veterinary Medicine, Vienna

summary: Fusion proteins involving Nucleoporin 98 (NUP98) are recurrently found in Acute Myeloid Leukemia (AML) with poor prognosis. Lack of mechanistic insight into NUP98-fusion-dependent oncogenic transformation has precluded the identification of efficient targeting strategies. We reasoned that shared transcriptional programs of direct NUP98-fusion-protein-mediated gene control converge on actionable targets. To study the transcriptional regulation mediated by NUP98 fusion proteins we developed mouse models for regulatable expression of NUP98/NSD1, NUP98/JARID1A and NUP98/DDX10. Integration of transcriptional changes after oncogene shutdown in vivo with ChIP-seq data identified a common core of direct NUP98-fusion target genes in AML. Among the direct targets of all NUP98-fusions, the CDK6 (cyclin-dependent kinase 6) gene was highly expressed in mouse and human AML samples. CDK6 loss severely attenuated NUP98-fusion-driven leukemogenesis, and NUP98-fusion AML was hypersensitive to pharmacologic CDK6 inhibition in vitro and in vivo. These findings identify CDK6 as a conserved, critical direct target of NUP98-fusion proteins, proposing approved CDK4/CDK6 inhibitors as a rationale treatment option for AML patients with NUP98-fusions.

overall_design: 3 different mouse models with regulatable expression and chromatin binding for one fusion

first: Johannes

last: Schmoellerl

first: Ines

last: Barbosa

first: Tania

last: Brandstoetter

first: Luisa

last: Schmidt

first: Barbara

last: Maurer

first: Selina

last: Troester

first: Ha

last: Pham

first: Mohanty

last: Sagarajit

first: Gabriele

last: Manhart

first: Ezgi

last: Aslan

first: Stefan

last: Terlecki-Zaniewicz

first: Christa

last: Van der Veen

first: Gregor

last: Hörmann

first: Nicolas

last: Duployez

first: Arnaud

last: Petit

first: Helene

last: Lapillonne

first: Alexandre

last: Puissant

first: Raphael

last: Itzykson

first: Richard

last: Moriggl

first: Michael

last: Heuser

first: Roland

last: Meisel

first: Peter

last: Valent

first: Veronika

last: Sexl

last: Zuber

first: Florian

last: Grebien


title: Total RNA sequencing of postnatal male germ cells

first: Ryo

last: Maeda

summary:
We report the whole-transcriptome profile with total RNA sequencing of postnatal male germ cells.
Histone modification levels are dynamically controlled during mammalian spermatogenesis. We found that H3K9 demethylases, Jmjd1a and Jmjd1b catalyze H3K9 demethylation in prospermatogonia. Combined loss of Jmjd1 enzymes disturbed prospermatogonia to spermatogonia transition in mice. To examine a role of Jmjd1 in prospermatogonia to spermatogonia transition, we performed RNA-seq and ChIP-seq analyses using postnatal germ cells at P3 and P7.

overall_design: mRNA profiles of postnatal male germ cells isolated from testes of a series of Vasa-Cre; Jmjd1; Jmjd1b conditional knockout mice

first: Shunsuke

last: Kuroki

first: Makoto

last: Tachibana


title: Proline Glutamic acid and Leucine rich Protein 1 (PELP1) promotes glioblastoma progression by enhancing Wnt/β-catenin signaling

status: Public on Apr 24 2020

first: YI

last: ZOU

summary: We examined the transcriptional changes modulated by Proline Glutamic acid and Leucine rich Protein 1 (PELP1) by performing global transcriptome analysis. U87 cells were transfected with control siRNA or PELP1 siRNA and the RNA was isolated and utilized for RNA-seq analysis. Our results demonstrated that PELP1 modulated genes were related to inhibition of matrix metalloproteases, glioma invasion signaling, Wnt/β-catenin signaling and other pathways related to invasion and GBM signaling.

overall_design: Total RNA was isolated from U87 cells transfected with control siRNA or PELP1 siRNA. Illumina TruSeq RNA Sample Preparation was performed following manufacturer's protocol. Samples were run on an Illumina HiSeq 2000 in duplicate. The combined raw reads were aligned to UCSC hg19 and genes were annotated by Tophat. Genes were annotated and quantified by HTSeq-DESeq pipeline.

first: Gangadhara

last: Sareddy

first: Yidong

last: Chen

first: Ratna

last: Vadlamudi


title: Identification of a novel transcriptional variant in the mouse Sry locus

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

overall_design: Refer to individual Series


title: Cord blood DNA methylome in newborns later diagnosed with autism spectrum disorder reflects early dysregulation of neurodevelopmental and X-linked genes

status: Public on Mar 24 2020

city: Davis

first: Charles

last: Mordaunt

address: 3318 Tupper Hall, One Shields Ave

department: Medical Microbiology and Immunology

institute: University of California, Davis

summary: Autism spectrum disorder (ASD) is a neurodevelopmental disorder with complex heritability and higher prevalence in males. The neonatal epigenome has the potential to reflect past interactions between genetic and environmental factors during early development and influence future health outcomes. We performed whole-genome bisulfite sequencing of 152 umbilical cord blood samples from the MARBLES and EARLI high-familial risk prospective cohorts to identify an epigenomic signature of ASD at birth. Samples were split into discovery and replication sets and stratified by sex, and their DNA methylation profiles were tested for differentially methylated regions (DMRs) between ASD and typically developing control cord blood samples. DMRs were mapped to genes and assessed for enrichment in gene function, tissue expression, chromosome location, and overlap with prior ASD studies. DMR coordinates were tested for enrichment in chromatin states and transcription factor binding motifs. Results were compared between discovery and replication sets and between males and females. We identified DMRs stratified by sex that discriminated ASD from control cord blood samples in discovery and replication sets. At a region level, 7 DMRs in males and 31 DMRs in females replicated across two independent groups of subjects, while 537 DMR genes in males and 1762 DMR genes in females replicated by gene association. These DMR genes were significantly enriched for brain and embryonic expression, X chromosome location, and identification in prior epigenetic studies of ASD in post-mortem brain. In males and females, autosomal ASD DMRs were significantly enriched for promoter and bivalent chromatin states across most cell types, while sex differences were observed for X-linked ASD DMRs. Lastly, these DMRs identified in cord blood were significantly enriched for binding sites of methyl-sensitive transcription factors relevant to fetal brain development. At birth, prior to the diagnosis of ASD, a distinct DNA methylation signature was detected in cord blood over regulatory regions and genes relevant to early fetal neurodevelopment. Differential cord methylation in ASD supports the developmental and sex-biased etiology of ASD and provides novel insights for early diagnosis and therapy.

overall_design: Investigation of DNA methylation with whole-genome bisulfite sequencing in umbilical cord blood from two high-risk cohorts of newborns diagnosed with autism spectrum disorder (ASD) or typical development (TD) at 36 months (TD n = 76, ASD n = 76).

first: Janine

last: LaSalle


title: Different RNA profiles in plasma derived small and large extracellular vesicles of Neurodegenerative diseases patients.

city: Pavia

first: Daisy

last: Sproviero

address: Via Mondino, 2

institute: IRCCS Mondino Foundation

summary: We detected different deregulated RNAs in LEVs and SEVs from patients with Alzheimer's, Parkinson's Disease, Amyotrophic Lateral Sclerosis,  ALS. MiRNAs resulted to be the most interesting subpopulation of transcripts transported by plasma derived SEVs since they appeared to discriminate all NDs disease from CTRLs and they can provide a signature for each NDs. Common enriched pathways for SEVs were mainly linked to ubiquitin mediated proteolysis and Toll-like receptor signaling pathways and for LEVs to neurotrophin signaling and Glycosphingolipid biosynthesis pathway.

overall_design: Whole coding and small transcriptome of large(MVs) and small(EXO) Extracellular Vesicles and 6 AD, 9 PD, 6 sporadic ALS (SALS), 9 FTD patients were used

first: Stella

last: Gagliardi

first: Susanna

last: Zucca

first: Maddalena

last: Arigoni

first: Marta

last: Giannini

first: Maria

last: Garofalo

first: Martina

last: Olivero

first: Michela

last: Dell'Orco

first: Orietta

last: Pansarasa

first: Stefano

last: Bernuzzi

first: Micol

last: Avenali

first: Matteo

last: Ramusino

first: Luca

last: Diamanti

first: Brigida

last: Minafra

first: Giulia

last: Perini

first: Roberta

last: Zangaglia

first: Alfredo

last: Costa

first: Mauro

last: Ceroni

first: Nora

middle: I

last: Perrone-Bizzozero

first: Raffaele

last: Calogero

first: Cristina

last: Cereda


title: Transcriptomic analysis of fungal  Cd-regulated genes in the ericoid mycorrhizal symbiosis

status: Public on Feb 12 2020

first: Annegret

last: Kohler

summary: Illumina HiSeq2000 technology  was used to generate mRNA profiles from Oidiodendron maius  free-living mycelium and Vaccinium myrtillus mycorrhizal roots with or without Cadmium treatment.  150bp reads were generated and aligned to the O.maius reference transcripts using CLC Genomics Workbench 8

sample_organism:
Vaccinium myrtillus
Oidiodendron maius Zn

overall_design: To analyse the effect of Cadmium, total RNA of O. maius free-living mycelium and V. myrtillus mycorrhizal roots with or without Cadmium treatment were generated and sequenced by Illumina HiSeq2000. Three biological replicates from each treatment were sequenced.

first: Salvatore

last: Casarrubia

first: Stefania

last: Daghino

first: Vasanth

last: Singan

first: Erika

last: Lindquist

first: Francis

last: Martin

first: Elena

last: Martino

first: Silvia

last: Perotto


title: RNA sequencing of single LN cells sorted from virus-activated CD4 T clusters

status: Public on Jan 01 2020

city: Rehovot

first: Ido

last: Amit

address: 234 Herzl st.

department: Immunology

country: Israel

institute: Weizmann Institute of Science

summary: PA-GFP mice were infected subcutaneously with either rVSV or rLCMV viruses. Two days upon infection, draining popliteal lymph nodes (LN) were photoactivated in areas containing Ag-specific CD4+ T cell clusters. Photoactivated cells were single-cell sorted and RNA sequencing performed to determine cell composition of activated CD4+ T cell clusters.

overall_design: CFP+ Ag-specific CD4 T cells were transfered into PA-GFP mice, which were then infected in the footpad with either rVSV or rLCMV viruses. Two days upon infection, draining popliteal lymph nodes (LN) were photoactivated in areas containing Ag-specific CD4+ T cell clusters. LN were processed and photoactivated GFP+ cells were single-cell sorted in 384-well capture plates containing 2 μL of lysis solution and 10 barcoded poly(T) reverse-transcription (RT) primers for single-cell RNA-seq

first: Marco

last: De Giovanni

first: Valeria

last: Cutillo

first: Amir

last: Giladi

first: Chiara

last: Medaglia

first: Mirela

last: Kuka

first: Matteo

last: Iannacone