title: Biopsy expression profiling of an adult inflammatory bowel disease cohort

first: Carmen

last: argmann

summary: Inflammatory Bowel Disease (IBD) is a progressive disease of the gut and consists of two types, Crohn’s Disease (CD) and Ulcerative Colitis (UC). It is a complex disease involving genetic, microbial, and environmental factors. The incidence of IBD is steadily increasing and current therapeutic options are plateauing. Thus treatments are evolving to 1. deeper levels of remission from clinical to endoscopic and histologic normalization and 2. Embrace novel targets or drug combinations. We explored whole transcriptome data generated in biopsy specimens sampled from a large cohort of adult IBD and control subjects to provide 1. a granular, objective and sensitive molecular measures of disease activity in the gut and 2. Novel molecular mechanisms and biomarkers underlying IBD pathology.

overall_design: The Mount Sinai Crohn's and Colitis registry (MSCCR) is a prospective cross-sectional cohort consisting of adult IBD patients and controls. Biopsy RNA sequencing (RNA-Seq) data were generated on whole blood sampled at the time of the participant’s endoscopy visit which also included detailed clinical, histological and endoscopic assessments.

last: Argmann

first: Mayte

last: Suárez-Fariñas

first: Ruixue

last: Hou

first: Aritz

last: Irizar


title: Epigenome wide DNA methylation profile of neonatal blood spots from the Archives for Research on Child Health (ARCH) cohort

status: Public on Jan 31 2022

city: Ann Arbor

first: Maureen

last: Sartor

state: MI

address: 100 Washtenaw Ave

department: Computational Medicine and Bioinformatics

country: USA

institute: University of Michigan

summary: Genome wide DNA methylation profiling of human samples from dried neonatal blood spots taken at birth from a cohort of pregnant people and their infants in Michigan. The Illumina MethylationEPIC Beadchip array was used to obtain DNA methylation profiles across over 850,000 CpGs in dried neonatal blood spot samples. Samples were collected from 166 infants at birth.

overall_design: Bisulphite converted DNA from the 166 samples were hybridised to the Illumina MethylationEPIC Beadchip

first: Rebekah

last: Petroff


title: LncRNAs expression profiling in small extracellular vesicles derived from brown adipose tissue

status: Public on Feb 12 2022

city: Chengdu

first: Pengyu

last: Hong

address: No.14, Section 3, Renmin South Road

country: China

institute: West China School of Stomatology, Sichuan University

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

summary: Brown adipose tissue (BAT) is considered as a main site of adaptive thermogenesis and the thermogenic activities of brown and beige adipocytes are also linked to generating heat and counteracting obesity. Recent studies revealed that BAT could secrete certain batokines-like factors especially small extracellular vesicles (sEV), which contributed to the systemic consequences of BAT activities. As a newly emerging class of mediators, some long non-coding RNAs (lncRNAs) have exhibited metabolic regulatory effects in adipocyte development. However, besides the well-studied lncRNAs, the lncRNAs carried by sEV derived from brown adipose tissue (sEV-BAT) have not been characterized yet. In this study, we conducted a lncRNA microarray assay on sEV-WAT and sEV-BAT. A total of 563 types of known lncRNAs were identified to be differentially expressed, among which 232 lncRNAs were upregulated and 331 lncRNAs were downregulated in sEV-BAT. Three novel candidates (AK029592, humanlincRNA1030 and ENSMUST00000152284) were selected for further validation. LncRNA–mRNA network analysis revealed candidate lncRNAs were largely embedded in cellular metabolic pathways. During adipogenic and thermogenic phenotype differentiation in ASCs and 3T3-L1 cells, only the expressions of AK029592 were upregulated. The three lncRNAs were all relatively enriched in brown adipose tissues and brown adipocytes. In different adipocytes, sEV and adipose tissue, the expression of AK029592 and ENSMUST00000152284 were significantly decreased in obese mice compared to lean controls, while obesity could not alter the expression of humanlincRNA1030.

overall_design: LncRNAs expression were measured in sEV-BAT and sEV-WAT from C57BL/6 male mice with three replicates using Arraystar Mouse LncRNA Arrays V4.0

first: Yue

last: Wu

first: Mei

last: Yu

first: Weidong

last: Tian


title: Deeply hidden genome organization mediated by base-unpairing regions (BURs) directly bound by SATB1 linked to transcription

status: Public on Dec 28 2021

city: San Francisco

first: Terumi

last: Kohwi-Shigematsu

state: CA

address: 513 Parnassus Ave (HSW810)

department: Department of Orofacial Sciences

institute: UCSF

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Mammalian genomes are organized by multi-layered chromatin folding. How three-dimensional genome organization contributes to cell-type specific transcription remains unclear. We uncover genomic elements termed base-unpairing regions (BURs), distributed genome-wide, as the sole and direct targets of cell-type specific SATB1 protein in vivo. The SATB1 direct-binding profile was generated by analyzing stringently-purified genomic DNA crosslinked to its directly-bound proteins only (ureaChIP-seq). Furthermore, a SATB1-bound BUR interacts extensively and frequently over the entire 5.7 megabase gene-rich region within many regulatory regions, including those near SATB1-dependent Rag1/Rag2 genes. SATB1 depletion leads to major loss of these interactions with greatly reduced Rag1/Rag2 expression. Most BURs reside within lamina associated domains (LADs), among which SATB1 binds to cell-type specific groups of BURs. Genome organization mediated by CTCF and SATB1 are distinct as these proteins do not co-bind chromatin in vivo and their direct binding sites are mutually exclusive genome-wide. These results revealed a previously undetected chromatin organization mediated by SATB1 direct binding to selected BURs genome-wide and suggest that chromatin interactions from some of these BURs provide a regulatory network underlying cell-type specific gene expression.

overall_design: Studying genome-wide binding and chromatin interaction profiles of SATB1 using urea-purified crosslinked chromatin

first: Yoshinori

last: Kohwi

first: Xianrong

last: Wong

first: Mari

last: Grange

first: Thomas

last: Sexton

first: Hunter

middle: W

last: Richards

first: Ya-Chen

last: Liang

first: Chen-Ming

last: Chuong

first: Yohko

last: Kitagawa

first: Shimon

last: Sakaguchi

first: Vladimir

middle: A

last: Botchkarev

first: Ichiro

last: Taniuchi

first: Karen

middle: L

last: Reddy


title: A human Y334C mutation in selenocysteine synthase causes cardio-respiratory failure and perinatal death in mice which can be rescued by selenium-independent GPX4

status: Public on Nov 24 2021

city: Bonn

first: Ulrich

last: Schweizer

state: NRW

address: Nussallee 11

department: Institut für Biochemie und Molekularbiologie

country: Germany

institute: Universitätsklinikum Bonn

type: Expression profiling by high throughput sequencing

summary: Selenoproteins are a small family of proteins containing the trace element selenium in form of the rare amino acid selenocysteine (Sec), which is decoded by the UGA codon. In humans, a number of pathogenic mutations in genes encoding distinct selenoproteins or selenoprotein biosynthesis factors have been identified. Pathogenic mutations in selenocysteine synthase (SEPSECS), which catalyzes the last step in Sec-tRNA[Ser]Sec biosynthesis, were reported in children suffering from progressive cerebello-cerebral atrophy. To understand the underlying mechanisms of SEPSECS mutations, we generated a novel mouse model recapitulating the respective human pathogenic Y334C mutation in the murine Sepsecs gene (SepsecsY334C). Unlike in patients,  homozygous mutant pups died perinatally with signs of cardio-respiratory failure. Perinatal death is reminiscent of the Sedaghatian spondylometaphyseal dysplasia disorder in humans, which is caused by inactivating mutations of the gene encoding the selenoprotein and key ferroptosis regulator glutathione peroxidase 4 (GPX4). Protein expression levels of distinct selenoproteins in SepsecsY334C/Y334C mice were found to be generally reduced in brain and isolated cortical neurons, while  transcriptomics analysis uncovered an upregulation of NRF2-regulated genes. Crossbreeding of SepsecsY334C/Y334C mice with mice harboring a targeted mutation of the catalytically active site Sec to Cys in GPX4 surprisingly rescued perinatal death of SepsecsY334C/Y334C mice, showing that the cardio-respiratory defects of Sepsecs-mutant mice were caused by the lack of GPX4. Like in SepsecsY334C/Y334C mice, selenoprotein expression levels remained low and NRF2-regulated genes remained highly expressed in these compound mutant mice, indicating that  selenium-independent GPX4, along with a sustained antioxidant response are sufficient to compensate for dysfunctional Sec-tRNA[Ser]Sec biosynthesis. Our findings imply that children with mutations in SEPSECS or GPX4 may benefit from treatments partially compensating for impaired GPX4 activity.

overall_design: 3' Poly(A) RNA-sequencing of cortex and heart from N = 3 Ctl and Sepsecs Y334C MT mice and N = 3 Ctl and N = 5 Sepsecs Y334C Gpx4 U/C MT mice

first: Noelia

last: Fradejas-Villar

first: Simon

last: Bohleber


title: Gastric Myofibroblasts Control Chief Cell differentiation, and their recovery from SPEM

status: Public on Jan 01 2022

city: Berlin

first: Hans-Joachim

last: Mollenkopf

address: Charitéplatz 1

institute: Max-Planck-Institute for Infection Biology

summary: Chief cells expressing Wnt/R-spondin target genes are located in the stomach corpus gland base. These cells can act as reserve stem cells and their transdifferentiation is a hallmark of spasmolytic polypeptide expressing metaplasia (SPEM). Mechanisms that control their differentiation, transdifferentiation and re-differenitiation are not fully understood. We investigated the function of R-spondin 3, a Wnt signaling activator and Lgr5 ligand, by using conditional mouse models that enable manipulation of R-spondin 3 gene expression in gastric myofibroblasts.The effect and the physiological function of R-spondin 3 was analyzed in the corpus and colon with R-spondin 3 gene knock-out mice  in Myh11+ myofibroblasts (Myh11-CreERT2; Rspo3fl/fl (RSPO3 KO) or R-spondin 3 gene knock-in overexpressiong myofibroblasts ( Myh11-CreERT2/Rosa26Sor6(CAG–Rspo3) ( RSPO3 KI)).

overall_design: Microarray experiments were performed as dual-color hybridizations on Agilent whole mouse catalog 4x44K (Agilent-014868) and 8x60K (Agilent-074809) arrays. To compensate for dye-specific effects, a dye-reversal color-swap was applied.

first: Michael

last: Sigal

first: Anne-Sophie

last: Fischer

first: Stefanie

last: Müllerke

first: Hilmar

last: Berger


title: Effects of tRNA[Ser]Sec anticodon stem loop modifications on selenoprotein expression

status: Public on Nov 17 2021

summary: Expression of selenoproteins requires the co-translational incorporation of selenocysteine (Sec) in response to an in-frame UGA codon. The machinery of UGA/Sec re-coding is complex and many factors affect the hierarchy of expression among selenoproteins, including modification of tRNA[Ser]Sec. Its hyper-modification in the anticodon stem loop is influenced by selenium bioavailability, and a mutation in adenosine 37 (A37) that abrogates isopentenylation, has a profound effect on selenoprotein expression in mice. Patients with mutations in tRNA-isopentenyl-transferase (TRIT1) show a severe neurological disorder and hence we wondered whether mutations in TRIT1 negatively affected the expression of selenoproteins. Fibroblasts from a patient carrying a pathogenic R323Q mutation in TRIT1 in homozygosity did not show decreased selenoprotein expression, although recombinant TRIT1R323Q had significantly reduced activity in vitro towards anticodon stem-loop substrates. We thus engineered mice conditionally deficient in Trit1 in hepatocytes and neurons. Selenoprotein expression as assessed by western blotting, 75Se metabolic labeling, and ribosomal profiling was not decreased despite the general reduction of N6-isopentenyl-adenosine in tRNAs. We show that 5-methylcarboxymethylation and 2’O-methylation of U34 occur independently of isopentenylation of A37 in tRNA[Ser]Sec. Reanalyzing previously published ribosomal profiling datasets, we demonstrate that (i) failure of 5-carboxymethylation at U34 is associated with reduced expression of GPX1, but not GPX4, and that (ii) FTSJ1 is not the elusive U34-2’O-methyltransferase involved in the methylation of tRNA[Ser]Sec.

overall_design: Ribosome profiling of liver samples from 3 Trit1-deficient mice and 3 control mice


title: Mammalian PERIOD2 regulates H2A.Z incorporation into chromatin to orchestrate circadian negative feedback [RNA-Seq]

status: Public on Feb 17 2022

city: Lyon

first: Kiran

last: Padmanabhan

address: 32-34 avenue Tony Garnier

department: IGFL

country: France

institute: ENS-Lyon

summary: We report the interdependance of PERIOD and H2A.Z to orchestrated the circadian negative feedback. H2A.Z is required for the circadian rhythm, it allows the binding of Bmal1 and PERIOD2 to the chromatin. And reciprocally, PERIOD2 aid H2A.Z deposition by interacting with the specific chaperone YL1.

overall_design: RNA-seq between wildtype and period triple KO or H2A.Z double KO MEF cells

first: Kevin

last: Tartour

first: Francesca

last: Andriani

first: Eric

middle: J

last: Folco


title: Mechanisms of failing erythropoiesis in Diamond-Blackfan anemia revealed by single cell profiling of human bone marrow progenitors

status: Public on Aug 31 2021

city: Bethesda

first: Jens

last: Lichtenberg

state: MD

address: 49 Convent Dr 3A19

department: National Human Genome Research Institute

institute: National Institutes of Health

summary: Single-cell RNAseq of CD34+Lineage negative hematopoietic stem and progenitor healthy control and DBA was performed to elucidate the transcriptional features of DBA haematopoiesis.

overall_design: Single cell transcriptional profiling using the 10x Genomics platform was performed on 45888 CD34+ Lineage- hematopoietic stem and progenitor cells FACS- isolated from 3 RPS-DBA samples, 3 RPL-DBA samples, and 3 healthy donor controls.

first: Deena

last: Iskander

first: Guanlin

last: Wang

first: Elisabeth

middle: F

last: Heuston


title: Jpx RNA regulates CTCF anchor site selection and formation of chromosome loops

status: Public on Dec 01 2021

city: Boston

first: Hyun Jung

last: Oh

state: MA

address: 185 Cambridge St.

institute: MGH

summary: Chromosome loops shift dynamically during development, homeostasis, and disease. CTCF is known to anchor loops and construct 3D genomes, but how anchor sites are selected is not yet understood. Here we unveil Jpx RNA as a determinant of anchor selectivity. Jpx RNA targets thousands of genomic sites, preferentially binding promoters of active genes. Depleting Jpx RNA causes ectopic CTCF binding, massive shifts in chromosome looping, and downregulation of >700 Jpx target genes. Without Jpx, thousands of lost loops are replaced by de novo loops anchored by ectopic CTCF sites. Although Jpx controls CTCF binding on a genome-wide basis, it acts selectively at the subset of developmentally sensitive CTCF sites. Specifically, Jpx targets low-affinity CTCF motifs and displaces CTCF protein through competitive inhibition. We conclude that Jpx acts as a CTCF release factor and shapes the 3D genome by regulating anchor site usage.

overall_design: We performed Jpx CHART-seq in undifferentiated (d0) and differentiating (days 4 and 7 of differentiation) mouse ES cells. Jpx antisense (AS) CHART and no-RNase H CHART served as negative control experiments. We conducted RNA-seq, CTCF ChIP-seq, and RAD21 ChIP-seq in control or Jpx-depleted d7 mouse ES cells. In situ Hi-C experiments were performed in d7 (control and Jpx-depleted) mouse ES cells.

first: Rodrigo

last: Aguilar

first: Barry

last: Kesner

first: Hun-Goo

last: Lee

first: Andrea

last: Kriz

first: Hsueh-Ping

last: Chu

first: Jeannie

middle: T


title: Intramolecular ligation method (iLIME) for pre-miRNA quantification and sequencing

status: Public on Oct 11 2021

city: Hong Kong SAR

first: Truc

middle: Cong

last: LE

address: Clearwater Bay, Kowloon

department: Life Science

country: Hong Kong

institute: The Hong Kong University of Science and Technology

type: Non-coding RNA profiling by high throughput sequencing

summary: Hairpin-containing pre-miRNAs are precursors of microRNAs (miRNAs) that play important roles in cellular processes and various human diseases. Pre-miRNAs are produced from longer primary transcripts (pri-miRNAs). The falsity in cellular expression and sequences of pre-miRNAs might cause cellular defects or human diseases. However, the current pre-miRNA quantification methods by qPCR cannot discriminate between pre-miRNAs and their parental pri-miRNAs. In addition, the ligation of the sequencing adapter to 5’-end of pre-miRNAs is inefficient, therefore, pre-miRNA sequencing is highly impractical. Here, we developed a method, called the intramolecular ligation method (iLIME) for pre-miRNA quantification and sequencing. This method utilized T4 RNA ligase 1 to convert hairpin-pre-miRNAs into circularized RNAs that do not naturally exist in cells. The resulting circuliarized RNAs allow us to design unique primers to quantify pre-miRNAs by qPCR specicially, and thus this qPCR can distinguish pre-miRNA from pri-miRNAs. In addition, the iLIME also allows us to sequence pre-miRNAs using next-generation sequencing. The iLIME method offers a simple and effective way to quantify and sequence pre-miRNAs. This will be useful in investigating pre-miRNAs for addressing research questions for medical applications. The iLIME can be potentially extended to other hairpin-containing RNAs, such as tRNAs and snRNAs.

sample_organism:
Homo sapiens
synthetic construct

platform_organism:
Homo sapiens
synthetic construct

overall_design: Cloning of synthesized precursor miRNAs (pre-miRNAs) and endogenous pre-miRNAs from human cell lines, HCT116 and HEK293T

first: Le

middle: M

last: Ngoc

middle: C

last: Truc

first: Nguyen

last: Anh


title: Reactivation of multiple fetal miRNAs in lung adenocarcinoma

status: Public on May 29 2021

city: Vancouver

first: Wan

last: Lam

address: 675 West 10th Ave

country: Canada

institute: BC Cancer Research Centre

summary: MicroRNAs (miRNAs) play vital roles in the regulation of normal developmental pathways. However, cancer cells can co-opt these miRNAs, and the pathways that they regulate, to drive pro-tumourigenic phenotypes. Characterization of the miRNA transcriptomes of fetal organs is essential for identifying these oncofetal miRNAs, but it has been limited by fetal sample availability. As oncofetal miRNAs are absent from healthy adult lungs, they represent ideal targets for developing diagnostic and therapeutic strategies. We conducted small RNA sequencing of a rare collection of 25 human fetal lung (FL) samples, and compared them to two independent cohorts (n = 140, n = 427), each comprised of adult non-neoplastic lung (ANL) and lung adenocarcinoma (LUAD) samples. We identified 13 oncofetal miRNAs that were expressed in FL and LUAD but not in ANL. These oncofetal miRNAs are potential biomarkers for LUAD detection (AUC = 0.963). Five of these miRNAs are derived from the imprinted C14MC miRNA cluster at the 14q32 locus, which has been associated with cancer development and abnormal fetal and placental development. Additionally, we observed the pulmonary expression of 44 previously unannotated miRNAs. The sequencing of these fetal lung samples also provides a baseline resource against which aberrant samples can be compared.

overall_design: We used a sequencing-based approach to profile the miRNA transcriptomes of a group of 165 samples, consisting of 25 fetal lung (FL) samples, 77 adult non-malignant lung (ANL) samples, and 63 lung adenocarcinoma (LUAD) samples, in order to identify lung oncofetal miRNAs. The miRNA expression of 73/77 ANL and 59/63 LUAD samples in this study was previously analyzed using different methods, and that resulting data was deposited in GEO (GSE62182). Sample titles for these samples directly correspond to those used in GSE62182. Samples from GSE62182 that yielded less than 5 million sequencing reads were excluded from this study.


title: Mis-splicing of Mdm2 leads to Increased P53-Activity and Craniofacial Defects in a MFDM Eftud2 Mutant Mouse Model

status: Public on Sep 03 2021

city: Montreal

first: Loydie

last: Jerome-Majewska

state: QC

address: 1001 Decarie Blvd EM0.2210

department: Pediatrics

institute: McGill University Health Centre Glen Site

summary:
Purpose: EFTUD2, a GTPase and core component of the splicesome, is known to be mutated in patients with mandibulofacial dysostosis with microcephaly (MFDM).   In this study, we examine the role of this gene in neural crest cells, the precursors of bones and cartilages affected in MFDM patients.
Methods: We generated a mutant mouse line with conditional mutation in Eftud2 and used Wnt1-Cre2 to delete it in neural crest cells.
Results: We show that homozygous deletion of Eftud2 leads to neural crest cell death and malformations in the brain and craniofacial region of embryos. RNAseq analysis of embryonic heads revealed a significant increase in exon skipping and retained introns in mutants and enriched levels of Mdm2 transcripts lacking exon 3. Mutants also had increased nuclear P53, higher expression of P53-target genes, and increased cell death. Craniofacial development was significantly improved when mutant embryos were treated with Pifithrin-alpha, an inihibitor of P53.
Conclusion: We propose that craniofacial defects caused by mutations of EFTUD2 are a result of mis-splicing of Mdm2 and P53-associated cell death. Hence, drugs that reduce P53 activity may help prevent craniofacial defects associated with spliceosomopathies.

overall_design: Neural crest cell-specific Eftud2 embryos mRNA profiles of E9.0 and E9.5 heterozygous (Eftud2+/-) and homozygous (Eftud2-/-) mice

first: Marie-Claude

last: Beauchamp

first: Anissa

last: Djedid

last: Bareke

first: Fjodor

last: Merkuri

first: Rachel

last: Aber

first: Annie

last: Tam

first: Peter

last: Stirling

first: Jennifer

last: Fish

first: Jacek

last: Majewski


title: The impact of c-di-AMP levels on gene expression in Enterococcus faecalis

status: Public on May 14 2021

city: Gainesville

first: Jessica

middle: K

last: Kajfasz

state: FL

address: 1395 Center Drive

department: Oral Biology

institute: University of Florida

summary: Second messenger nucleotides such as c-di-AMP are produced by bacteria in response to environmental stimuli and can contribute to the regulation of a number of cellular processes including osmoregulation, envelope homeostasis, central metabolism, and biofilm formation.  Here, as part of an effort to uncover the biological significance of c-di-AMP in the opportunistic pathogen Enterococcus faecalis, we utilized high-throughout RNA Sequencing analysis to explore the impact of deletion of genes responsible for c-di-AMP synthesis (cdaA) and degradation (dhhP and gdpP).

overall_design: Enterococcus faecalis OG1RF and isogenic mutant strains ∆cdaA, ∆dhhP, and ∆gdpP∆dhhP were grown in the chemically defined medium CDM.  Cultures were grown to mid-exponential phase (OD600 = 0.35), at which point these samples were harvested for transcriptional profiling.

first: Ling

middle: N

first: Shivani

last: Kundra

first: Jose

last: Lemos


title: Transcriptomic and epigenetic profiling of fibroblasts in Idiopathic Pulmonary Fibrosis (IPF)

status: Public on Jul 20 2021

city: Houston

first: Lisha

last: Zhu

state: TX

address: 7000 fannin st

institute: UT Health Science Center at Houston

summary: ATAC-Seq was applied to identify differentially accessible regions within the genome between healthy and IPF fibroblasts.

overall_design: We have used ATAC-Seq on upper lobe cultured fibroblasts from 3 healthy controls and 3 IPF patients to identify differentially accessible regions and transcription factor binding sites within the genome of these cells

first: Harry

last: Karmouty-Quintana


title: Transcriptomic, proteomic, and metabolomic analyses identify candidate pathways linking maternal cadmium exposure to altered neurodevelopment and behavior

status: Public on Aug 18 2021

city: RALEIGH

first: Dereje

last: Jima

state: NC

address: 850 Main Campus Drive

department: CHHE

institute: NCSU

summary:
Purpose: Identify gene expression changes in whole brains of newborn pups whose mothers were exposed to Cd during pregnancy (50ppm CdCl2) compared to unexposed controls (0ppm CdCl2).
Methods: 5- to 7-week-old C57BL/6J (‘B’) and CAST/EiJ (‘C’) females (the F0 generation) were exposed through their drinking water to 0 ppm or 50 ppm Cd in the form of CdCl2 (Sigma-Aldrich, catalog number 202908) for a period of 5 weeks, then mated with a male of the opposite strain. Cd exposure continued throughout pregnancy and was discontinued at litter birth. A hybrid mating scheme (the F1 generation) was employed to enable analyses of allele-specific gene expression and DNA methylation for a separate study (Hudson & Cowley, manuscript in preparation). The genotypes of F1 mice are referred to as ‘BxC’ (B mother x C father). F1 animals were sacrificed and dissected within 24 hours of birth; sample sizes can be found in supplementary tables associated with the publication. F1 mice were dissected within 24 hours of birth. All animal work was approved by the North Carolina State University (NCSU) Institutional Animal Care and Use Committee, under protocol 16-045-B. All experiments were conducted in accordance with the Guiding Principles in the Use of Animals in Toxicology. Frozen whole brains obtained from four 0 ppm and four 50 ppm newborn female BxC pups representing four litters per exposure group were pulverized using a hammer and liquid nitrogen. 7-10 mg of tissue was then used to extract DNA and RNA simultaneously using the AllPrep DNA/RNA/miRNA kit (Qiagen, 80204). RNA was extracted using the recommended protocol for fatty tissues. RNA and DNA were quantified using a Nanodrop 2000. RNA purity and size integrity were determined at the NCSU Genomic Sciences Laboratory (GSL) using an Agilent 2100 Bioanalyzer with an RNA 6000 Nano Chip (Agilent Technologies).
Results: We identified 15 significantly differentially expressed genes (DEGs) that aligned to both the B and C genomes.
Conclusions: These 15 DEGs (and subsequent confirmatory qRT-PCRs on the 8 samples sequenced here plus an additional Cd dose and samples) suggest altered onset of myelination throughout the whole brain, as well as aberrant Hox gene expression due to maternal Cd exposure.

overall_design: Maternal cadmium (Cd) -exposed mRNA profiles from whole brains of 1-day-old F1 0ppm (control) and F1 50ppm (exposed) pups from C57BL/6J (‘B’, mother) and CAST/EiJ (‘C’, father) inbred mouse strains.

first: Kathleen

last: Hudson

first: Emily

last: Shiver

first: Jianshi

last: Yu

first: Sanya

last: Mehta

middle: D

first: Maureen

last: Kane

first: Heather

middle: B

last: Patisaul

first: Michael

last: Cowley


title: Growth media conditions influence the secretion route and release levels of engineered extracellular vesicles

status: Public on Apr 29 2021

city: Stockholm

first: Daniel

middle: Wesley

last: Hagey

address: Nobels vag 3

country: Sweden

institute: Karolinska Institutet

summary: Extracellular vesicles (EVs) are nanosized cell-derived vesicles found in all bodily fluids which provide a route of intercellular communication by transmitting biological cargo. While EVs offer promise as therapeutic agents, the molecular mechanisms of EV biogenesis are not yet fully elucidated, in part due to the concurrence of numerous interwoven pathways which give rise to heterogenous EV populations in vitro. The effects of conditions in the cellular environment on EV production are of particular interest. In this study, we utilize a quantifiable EV-engineering approach to investigate how various cell media conditions alter EV production. The presence of serum, exogenous EVs, and other signaling factors in cell media alters EV production on physical, molecular, and transcriptional levels. Further, we demonstrate that exosome biogenesis pathways are the major factors contributing to EV production under optimized conditions. Our findings suggest a novel understanding to the mechanisms underlying EV production in cell culture which can be applied to develop advanced EV production methods.

overall_design: Sequencing of  HEK293 cells in different media conditions


title: Epigenetic modification of the COX-2/PGE2 pathway modulates macrophage phenotype and cell-targeted manipulation improves diabetic tissue repair

status: Public on Oct 07 2020

first: Lam

last: Tsoi

address: Medical Sciences 1 Bldg. 1301 E. Catherine

summary: RNA-sequencing techniques to profile the transcriptomes of lesional skin of diabetic patients

overall_design: Comparison between lesional skin from diabetic patients to normal skin

first: Frank

last: Davis

first: Katherine

last: Gallagher


title: Targeting the histone demethylase LSD1 prevents cardiomyopathy in a mouse model of laminopathy

status: Public on Dec 21 2020

city: Marseille

first: michel

last: PUCEAT

address: 27 bd Jean moulin

department: University aix marseille

institute: INSERM

summary:
LMNA mutations in patients are responsible for a dilated cardiomyopathy. Molecular mechanisms underlying both the origin and development of the pathology are still unknown. Herein, using mouse pluripotent stem cells (ESC) as well as a mouse model, both harbouring p.H222P Lmna mutation, we found early defects in cardiac differentiation of mutated ESCs and dilatation of mutated embryonic hearts at E13.5 pointing to a developmental origin of the disease.
Using mouse ESC, we demonstrate that cardiac differentiation of LmnaH222P/+ was impaired at the mesodermal stage. Expression of Mesp1, a mesodermal cardiogenic gene involved in epithelial-mesenchymal transition (EMT) of epiblast cells as well as Snai1 and Twist, was decreased in LmnaH222P/+ cells when compared to wild type in the course of differentiation. In turn, cardiomyocyte differentiation was impaired.
Chromatin immunoprecipitation assay of H3K4me1 in differentiating cells revealed a specific decrease of this histone mark on regulatory regions of Mesp1 and Twist in LmnaH222P/+ cells. Downregulation or inhibition of LSD1 that specifically demethylates H3K4me1 rescued the epigenetic landscape of mesodermal LmnaH222P/+ cells and in turn contraction of cardiomyocytes. Inhibition of LSD1 in pregnant mice or neonatal mice prevented cardiomyopathy in E13.5 LmnaH222P/H222P offsprings and adults, respectively.
Thus LSD1 turns out to be a therapeutic target to prevent or cure dilated cardiomyopathy associated laminopathy.

overall_design: 2 samples E13.5 mouse embryonic hearts

first: Anne-Claire

last: Guénantin

first: Imen

last: Jébéniani

first: Julia

last: Leschick

first: Erwan

last: Watrin

first: Gisèle

last: Bonne

first: Nicolas

last: Vignier

last: Pucéat


title: Maastricht Human Plaque Study (MaasHPS)

status: Public on Dec 15 2020

city: Maastricht

first: Han

last: Jin

address: P. Debyelaan 25

country: Netherlands

institute: Maastricht University

summary: Microarray transcriptional profiling of carotid atherosclerotic plaques taken from symptomatic patients undergoing carotid endarterectomy surgery.

overall_design: In order to better identify processes associated with intraplaque haemorrhage (IPH) and plaque instability, in this study we compared gene makeup of low- vs high-risk atherosclerotic lesion segments from carotid endarterectomy patients, as judged from absence or presence of intraplaque haemorrhage, respectively.

first: Erik

last: Biessen


title: Single keratinocyte analysis uncovers Foxm1 as a Yap-dependent regulator of human epidermal stem cells

status: Public on Mar 18 2021

city: Padova

first: Mattia

last: Forcato

address: Via Ugo Bassi, 58/B

country: Italy

institute: University of Padova

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

overall_design: Refer to individual Series


title: Single keratinocyte analysis uncovers Foxm1 as a Yap-dependent regulator of human epidermal stem cells (microarray)

summary: Autologous epidermal cultures can permanently restore a functional epidermis on severely burned patients. Transgenic epidermal grafts do so also in genetic skin diseases as Junctional Epidermolysis Bullosa. Clinical success strictly requires an adequate number of epidermal stem cells, detected as holoclone-forming cells. To date, such cells can be only partially distinguished from the other transient amplifying clonogenic keratinocytes and cannot be prospectively isolated.  Here we show that genome-wide single-cell transcriptome analysis performed on primary human epidermal keratinocyte cultures identified categories of genes clearly distinguishing the different clonal types, unveiled that holoclone-forming cells are enriched in genes regulating cell cycle, DNA repair (including telomerase), chromosome segregation and spindle organization, confirmed that human epidermal keratinocytes are hierarchically organized along a continuous, mainly linear trajectory showing that stem cells sequentially generate progenitors producing terminally differentiated cells and uncovered the role of FOXM1 as a YAP-dependent key regulator of normal and adhesion-defective epidermal stem cells.

overall_design: To explore whether holoclones, meroclones and paraclones activate different transcriptional programs, we performed genome-wide microarray gene expression profiling of 62 clones (22 holoclones, 29 meroclones and 11 paraclones) isolated from 6 different primary cultures (K5, K18, K22, K38, K42 and K49). Sub-confluent epidermal cultures were trypsinized, serially diluted and plated in 96-well plates (0.5-1 cells per well). After 7 days of cultivation, single clones were identified under an inverted microscope and trypsinized. One-quarter of the clone was cultured for 12 days onto an indicator dish, which was then fixed and stained with rhodamine B for the classification of clonal type 12-d after. The remaining three-quarters of the clone was cultivated on 6-well plates for 4–5 days and then used to collect mRNA.

first: Elena

last: Enzo

first: Alessia

last: Secone Seconetti

first: Roberta

last: Contin

first: Sonia

last: Carulli

last: Tenedini

first: Enrico

last: Tagliafico

first: Silvio

last: Bicciato

first: Michele

last: De Luca


title: Transcriptome-wide Analysis of Intracranial Artery in Patients with Moyamoya Disease Showing Up-regulation of Immune Response, and Down-regulation of Oxidative Phosphorylation and DNA Repair

status: Public on Oct 02 2020

city: Showa-ku, Nagoya

first: Kinya

last: Yokoyama

state: Aichi

address: Tsurumai 65

department: Neurosurgery

country: Japan

institute: Nagoya University Hospital

summary: Micro-samples of the middle cerebral artery (MCA) were collected from patients with MMD (n=11) and those with control (n=9). Using microarray techniques, transcriptome-wide analysis was performed. Comparison of the MCA gene expression between patients with MMD and control detected 62 and 26 genes whose expression was significantly (P<0.001, fold change>2) up- or down-regulated in the MCA of MMD. Gene set enrichment analysis of genes expressed in the MCA of MMD revealed positive correlations with genes involved in antigen processing and presentation, dendric cells pathway, cytokine pathway, and interleukin 12 pathway, whereas negative correlations with genes involved in oxidative phosphorylation and DNA repair. In addition, quantitative polymerase chain reaction analysis confirmed decreased gene expressions of tetraspanin 2 and ras homolog family member Q in MCA of MMD (P<0.05).

overall_design:
Micro-samples of the middle cerebral artery (MCA) were collected from patients with MMD (n=11) and those with control (n=9).

GSE157628 includes re-used Samples from GSE141022. The GSE157628 Samples were re-used in GSE189993.

first: Fumiaki

last: Kanamori


title: Single Cell RNA sequencing of mouse SQ tumor from C57BL/6 with or with liver tumor.

status: Public on Sep 09 2020

city: San Francisco

first: Jennifer

middle: Anne

last: Smith

address: 513 Parnassus Ave HS1102

department: Diabetes Center

institute: University of California, San Francisco

summary: The presence of liver tumor changes the transcriptome of SQ tumor-infiltrating adaptive and innate immune cells.  We report differential transcriptomic changes within in the SQ tumor immune infiltrate of mice with and without concurrent liver tumor implantation within their livers.  We show heatmap displaying the top 20 differentially expressed genes by SQ MDSC and Tregs between the two groups via scRNAseq. Violin plots showing the top 2 differentially upregulated genes by SQ Tregs from mice with liver tumor.  Heatmap displaying the top 20 differentially upregulated genes by SQ CD8 T cells between the two groups. Violin plots showing differential expression of ICOS and CTLA-4 by SQ CD8 T cells between the two groups. Unbiased re clustering (UMAP) and stacked bar graph of relative frequencies of monocyte/myeloid cells showing 9 distinct scRNAseq subclusters. Violin plots showing relative MDSC score ordered by monocyte/myeloid cell subclusters.  Our data suggests that mice with liver tumors have increased activation of Tregs, decreased activation of CD8 T cells and transcriptomic modifications within the MDSC compartment within their SQ tumors.

overall_design: FACS-sorted live CD45+ tumor infiltrating cells from the subcutaneous tumor 14 days post implantation from SQ and SQ+Liver from 3 pooled mice.  2 independent experiments.

first: James

last: Lee


title: Peroxisome import stress induces eIF2α phosphorylation and impairs ribosome biogenesis

status: Public on Feb 23 2021

city: Ames

first: Kerui

last: Huang

state: IA

address: 2437 Pammel Drive

department: Genetics and Genomics

institute: Iowa State University

summary: Peroxisome biogenesis diseases (PBDs) are characterized by global defects in peroxisomal function and can result in severe brain, liver, kidney, and bone malfunctions. PBDs are due to mutations in peroxisome biogenesis factors (PEX genes) that are responsible for peroxisome assembly and function. Increasing evidence suggests that peroxisome import functions decline during aging. However, the transcriptome profiling of peroxisome import defects and how they affect disease development are still lacking. PEX5 encodes the cytoplasmic receptors for peroxisome-targeting signal types 1. We generate knock-in human HEK293 cells mutant using CRISPR to transiently express PEX5 cysteine 11 to alanine mutant (PEX5C11A), which blocks PEX5 recycling and exerts dominant negative effect on PEX5 mediated peroxisome import. To identify conserved responses, we perform transcriptomic analysis on Drosophila oenocyte-specific Pex1, Pex12 and Pex5 knockdowns and on human cells with impaired peroxisome import (through expressing PEX5C11A and applying PEX5 siRNA respectively). PEX5C11A induction triggers vast transcriptomic changes, including decreased oxidative phosphorylation, increased MAPK signaling and HIPPO signaling. PEX5 siRNA specifically decreases spliceosome activity and increases cholesterol metabolism. Using gene set enrichment analysis (GSEA), we identify protein processing in endoplasmic reticulum pathway, specifically ER-associated protein degradation (ERAD) pathway is induced in all PEX knockdowns in Drosophila. Peroxisome dysfunction elevates eIF2α phosphorylation in both Drosophila and human cell culture independent of XBP1 activation, suggesting increased integrative stress response (ISR). Moreover, peroxisome stress decreases ribosome biogenesis genes and impairs ribosome biogenesis in flies and human cells. Specifically, peroxisome stress impairs the 5'-ETS cleavage activity during the ribosome biogenesis and dampens 40S small ribosomal export in both flies and human. Our results suggest that reduced ribosome biogenesis and elevated ISR could be conserved cellular response to peroxisome import stress.

sample_organism:
Drosophila melanogaster
Homo sapiens

platform_organism:
Drosophila melanogaster
Homo sapiens

overall_design: We analyzed Drosophila oenocyte-specific Pex1, Pex5 and Pex12 knockdown (PromE-Gal4 > RNAi) samples. RNAi is induced upon mifepristone feeding (+RU), thus, no RU feeding is included as control (-RU). We also included oenocyte control samples (PromE-Gal4 > wild type), treated with or without RU. We included human cell lines with inducible PEX5C11A mutant protein (treated with or without Doxycycline) and human cells treated with or without PEX5 siRNA. 3 replicates in each group and a total of 36 samples are analyzed.

first: Jinoh

last: Kim

first: Pham

last: Vo

first: Ting

last: Miao

first: Mirre

last: Simons

first: Hua

last: Bai


title: Affymetrix CytoScan HD and OncoScan array data for malignant melanoma samples

status: Public on Dec 15 2021

city: Budapest

first: Laura

last: Vizkeleti

address: Üllői str. 93.

department: 2nd Deptartment of Pathology

country: Hungary

institute: Semmelweis University

type:
Genome variation profiling by SNP array
SNP genotyping by SNP array

summary: Malignant melanoma is a highly metastatic disease disseminating to several distant sites. This potential is also of great clinical impact for patient survival and therapeutic success. Knowledge about melanoma genomics is mainly based on lymphatic or skin metastases derived data, whereas data from distant sites is rather limited. Therefore, an autopsy-based visceral metastasis biobank was established and an array-based CNV analysis was performed focusing primarily on major organs (brain, lung and liver) on a total of 38 samples (10 primary and 28 organ metastasse). A unique picture emerged about organ specific CNV type distributions or gene alterations including the frequent loss of DNA damage error genes in brain metastases, the presence of HGF/MET autocrine loop in brain and lung metastases, the traces of immunogenic mimicry exclusive for lung metastases or the correlation of BRAF copy number and mutant allele frequency especially in lung metastases. All these above phenomena have a great influence on therapy efficacy or resistance.

overall_design:
Affymetrix CytoScan HD or OncoScan arrays were performed according to the manufacturer's directions on DNA extracted from cryopreserved or FFPE archived diagnostic and/or autopsy cutaneous melanoma samples.
Copy number analysis of Affymetrix CytoScan and OncoScan arrays was performed for 38 malignant melanoma of the skin.

first: Orsolya

last: Papp

first: Viktória

last: Doma

first: Valdés

last: Gil

first: György

last: Markó-Varga

first: Sarolta

last: Kárpáti

first: József

last: Tímár

last: Vízkeleti


title: Single-cell analyses reveal aberrant pathways for megakaryocyte-biased hematopoiesis in myelofibrosis and identify mutant clone-specific targets

status: Public on Jun 30 2020

first: Jens

last: Lichtenberg

address: 49 Convent Dr 3A19

summary: Myelofibrosis is a severe myeloproliferative neoplasm characterised by increased numbers of abnormal bone marrow megakaryocytes that induce progressive fibrosis, destroying the hematopoietic microenvironment. To determine the cellular and molecular basis for aberrant megakaryopoiesis in myelofibrosis, we performed high-throughput single-cell transcriptome profiling of 50,702 hematopoietic stem/progenitor cells (HSPCs), and single-cell proteomics, genomics and functional assays. We identified an aberrant pathway for direct megakaryocyte differentiation from the earliest stages of hematopoiesis in myelofibrosis and associated aberrant molecular signatures, including surface antigens selectively expressed by JAK2-mutant HSPCs. Myelofibrosis megakaryocyte progenitors were heterogeneous, with distinct expression of fibrosis and proliferation-associated genes and putative therapy targets. We validated the integrin G6B as a promising JAK2-mutant clone-specific surface antigen, warranting further development as an immunotherapeutic target. Our study paves the way for selective immunotherapeutic targeting in myelofibrosis and more broadly illustrates the power of single-cell multi-omics to discover tumor-specific therapeutic targets and mediators of tissue fibrosis.

overall_design: Examination of 3 human myelofibrosis tissue samples and 2 controls

first: Bethan

last: Psaila

first: Elisabeth

last: Heuston


title: Cytokine-sensing primary enhancer cluster launches secondary enhancers to activate multi-gene locus

status: Public on Jun 06 2020

first: Michaela

last: Willi

address: 9000 Rockville Pike

department: NIDDK

institute: NIH


title: Single-cell landscape of bronchoalveolar immune cells in COVID-19 patients

status: Public on Apr 22 2020

city: Shenzhen

first: Zheng

last: Zhang

state: Guangdong

address: No. 29, Bulan Road

institute: Shenzhen 3rd People's Hospital

summary: Immune characteristics associated with Coronavirus Disease-2019 (COVID-19) severity are currently unclear. We characterized bronchoalveolar lavage fluid (BALF) immune cells from patients with varying severity of COVID-19 disease and from healthy subjects using single-cell RNA-sequencing. Proinflammatory monocyte-derived macrophages were abundant in the BALF from severe COVID-9 patients. Moderate cases were characterized by the presence of highly clonally expanded tissue-resident CD8+ T cells. This atlas of the bronchoalveolar immune-microenvironment suggests potential mechanisms underlying pathogenesis and recovery in COVID-19.

overall_design: Using 10x genomics to measure single-cell RNA sequence (scRNA-seq)/TCR-seq to comprehensively characterize the lung immune microenvironment in the bronchoalveolar lavage fluid (BALF) from 6 severe and 3 moderate COVID-19 patients and 3 healthy control.

first: Mingfeng

last: Liao

first: Yang

last: Liu

first: Jing

last: Yuan

first: Yanling

last: Wen

first: Gang

last: Xu

first: Juanjuan

last: Zhao

first: Lin

last: Cheng

first: Jinxiu

last: Li

first: Xin

last: Wang

first: Fuxiang

first: Lei

first: Ido

last: Amit

first: Shuye


title: Transcriptome-wide Analysis of Intracranial Artery of Moyamoya Disease Showing Up-regulation of Inflammatory Response with Increased Expression of TLR2 and SYK, and Down-Regulation of Collagen Formation with Decreased Expression of COL15A1 [MCA]

status: Public on Feb 29 2020

first: Kinya

last: Yokoyama

summary: During superficial temporal artery (STA)-middle cerebral artery (MCA) anastomoses, micro-samples of both MCA and STA from the patients with MMD (n=4) and internal carotid artery aneurysm (IA) (n=4) were collected. Using microarray technique, transcriptome-wide analyses were performed. Comparing MCA gene expression profile between MMD and IA, we detected 39 up-regulated and 12 down-regulated genes in MMD, showing over 15-fold change with significant difference (P<0.05). Gene set enrichment analysis revealed positive correlation of inflammatory response and negative correlation of collagen formation with MCA of MMD. In addition, by quantitative polymerase chain reaction, significant increased gene expression of TLR2 (P=0.009) and SYK (P=0.04), and decreased gene expression of COL15A1 (P=0.0001) in MCA of MMD were confirmed. While in STA transcriptome analysis, no gene showed significant difference.

overall_design:
During superficial temporal artery (STA)-middle cerebral artery (MCA) anastomoses, micro-samples of both MCA and STA from the patients with MMD (n=4) and internal carotid artery aneurysm (IA) (n=4) were collected.

The GSE141022 Samples were re-used in GSE157628 and GSE189993.

first: Humiaki

last: Kanamori


title: Genotyping analysis employing Illumina Infinium ImmunoArray-24 v2.0 BeadChip

status: Public on Jan 29 2020

city: Cork

first: Marcus

last: Claesson

address: College Road

country: Ireland

institute: University College Cork

summary: Mucosal host DNA methylation was associated  with the presence of inflammation suggesting epigenetic changes in response to the microbiota. Hierarchical clustering of the microbiota indicated ten subgroups, whereas some were driven by certain Enterbacteriacae and Bacteroides keystone species, and which were associated with host  genotype and DNA methylation profiles, but with little influence from the habitual  diet.

overall_design: Genetic samples from 170 patients were genotyped and analysed for correlation with condition, status and assocation to micobiota clustered subgroups.

first: F

last: Ryan

first: E

last: Laserna-Mendieta

last: Power

first: A

middle: G

last: Clooney

first: P

last: McMurdie

first: S

last: Iwai

last: Ahern

first: B

last: Flemer

last: Zomer

last: Fanning

first: J

last: O'Callahgan

last: Walton

last: Temko

first: D

last: Sheehan

first: C

last: Moran

first: L

last: Jackson

first: W

last: Stack

last: Bell

first: T

middle: Z

last: DeSantis

last: Shanahan

first: M

last: Clesson


title: Effects of Prenatal Exposure to a Mixture of Organophosphate Flame Retardants on Placental Gene Expression and Serotonergic Innervation in the Developing Rat Brain

status: Public on Apr 08 2020

first: Dereje

last: Jima

summary: There is a growing need to understand the potential neurotoxicity of organophosphate ester flame retardants (OPFRs) and plasticizers because use and, consequently, human exposure, is rapidly expanding.  We have previously shown in rats that developmental exposure to the commercial FR mixture Firemaster® 550 (FM 550), which contains OPFRs, results in sex-specific behavioral effects, and identified the placenta as a potential target of toxicity. The placenta is a critical coordinator of fetal growth and neurodevelopment, and a source of neurotransmitters (NTs) for the developing brain. We have shown in rats and humans that FRs accumulate in placental tissue, and induce functional changes, including altered neurotransmitter (NT) production.  Here we sought to establish if OPFRs (triphenyl phosphate, TPHP, and a mixture of isopropylated triarylphosphate isomers, ITPs) alter placental function and fetal forebrain development, with disruption of tryptophan (Trp) metabolism as a primary pathway of interest. Wistar rat dams were orally exposed to OPFRs (0, 500, 1,000, or 2,000 μg/day) or a serotonin (5-HT) agonist (5-MT) for 14 days during gestation and placenta and fetal forebrain tissues collected for analysis by transcriptomics and metabolomics. Relative abundance of genes responsible for the transport and synthesis of placental 5-HT were disrupted, and multiple neuroactive metabolites in the 5-HT and kynurenine (Kyn) metabolic pathways were upregulated. Additionally, 5-HTergic projections were significantly longer in the fetal forebrains of exposed males. These findings suggest that OPFRs have the potential to impact the 5-HTergic system in the fetal forebrain by disrupting placental Trp metabolism.

overall_design: As an initial hypothesis-generating approach, placental punches from the fetal side (5 per sex per group, from vehicle and 8mg/kg OPFRs) underwent RNA sequencing (RNA-seq), a total of 10 control and 10 with high dose treatment. RNA extraction was performed with the Qiagen RNEasy Miniprep kit according to the manufacturer protocol (Qiagen, Cat. 74134).  RNA quality was determined using an Agilent 2100 Bioanalyzer and all samples, for both tissue types, had an RNA integrity number (RIN) = 10.  Sequencing libraries were prepared as described previously (Puzianowska-Kuznicka et al. 2006), using NEBNext Ultra Directional RNA Library Prep kit and NEBNext Poly(A) mRNA Magnetic Isolation Module (catalogs E7420 and E7490; New England Biolabs), to be compatible with Illumina sequencing.  Isolation, heat fragmentation, and priming was performed according to manufacturer’s instructions.  cDNA synthesis was followed by purification and size selection.  Finally, library clean-up was performed used AMPure XP beads (Beckman Coulter Genomics, Cat. A63881) and quality was assessed using the Agilent 2100 Bioanalyzer.  Sequencing was performed using a 125-bp single-end protocol on a single lane of an Illumina HiSeq2500 sequencer.  Approximately, 33 million uniquely mapped reads were generated per placental library.

first: Kylie

last: Rock

first: Genevieve

last: St Armour

first: Brian

last: Horman

first: Allison

last: Phillips

first: Matthew

last: Ruis

last: Stewart

first: David

last: Muddiman

first: Heather

last: Stapleton

last: Patisaul


title: Genome wide blood DNA methylation measured at birth and age 7 on the EPIC array

status: Public on Jun 04 2020

city: Chicago

first: Carole

last: Ober

state: IL

address: 920 E 58TH ST

department: Human Genetics

institute: The University of Chicago

type: Methylation profiling by genome tiling array

summary: We measured the DNA methylation levels at ~800,000 CpG sites from ethnically admixed children in CBMCs at birth and PBMCs age 7 to study the longitudinal dynamics of methylation marks. We found that self-reported race-dependent methylation levels were conserved over time, which helped to suggest that blood methylation levels are robust to environmental exposures during the first 7 years of life.

overall_design: DNA methylation measured on the EPIC array in CBMCs at birth and PBMCs at age 7 from 196 children.

first: Chris

last: McKennan


title: Gene expression changes following Knock-down of eRNA_06347 in post-stroke mouse cortex

status: Public on Nov 12 2020

city: Edison

first: Ashutosh

last: Dharap

state: NJ

address: 65 James st

department: Neuroscience

institute: HackensackMeridian Health JFK Medical Center

summary: RNA-sequencing was conducted to profile the transcriptome of the eRNA_06347 knockdown post-stroke mouse cortices ( knockdown achieved by intracerebroventricular injection of oligos against eRNA_06347).  RNA was isolated from sham, Negative control oligo injected post-stroke cortices and eRNA_06347 knockown post-stroke cortices (three independent biological replicates per group),converted into cDNA libraries,  and used for Illumina deep sequencing.The sequencing reads were aligned to the mouse reference genome GRCm38 using HISAT2. Stringtie was used to assemble the aligned sequences into transcript isoforms using mouse transcript annotations from Ensembl 81 as a guide, then merged to reconstruct a comprehensive transcriptome using perl scripts and gffcompare. After the ﬁnal transcriptome was generated, StringTie and Ballgown were used to estimate the expression levels of all the transcripts. StringTie was used to evaluate expression levels for mRNAs by calculating the FPKMs. The differentially expressed mRNAs were identified as log2 fold change >1 or log2 fold change <-1 and with statistical significance p<0.05 using Ballgown.Doing so, We found that 106 genes were significantly upregulated and 49 genes were significantly downregulated in the eRNA_06347 knockdown group as compared to the negative control.

overall_design: Genome-wide transcriptomic profiles of eRNA_06347 knockdown post-stroke mouse cortices compared to sham cortices and negative control post-stroke mouse cortices

first: Sunil

last: Bhattarai

first: Aparna

last: Akella


title: Decreased epithelial Progesterone Receptor A at the window of receptivity is required for preparation of the endometrium for embryo attachment

status: Public on Aug 29 2019

city: RTP

first: Franco

last: Demayo

address: 111 TW Alexander Drive

institute: NIEHS

summary: The progesterone receptor A (PGRA) isoform is the dominantly expressed isoform within the mouse uterus and is indispensable for uterine function and fertility in the murine reproductive tract. During early pregnancy, the PGRA isoform is spatiotemporally expressed in the uterine epithelium. At days 2-3 of pregnancy, PGRA is upregulated within the epithelium and then decreases before day 4, the day of embryo implantation. This decrease of PGRA has been recognized as a marker to initiate the time in which the uterus is receptive to the embryo, yet this has never been functionally tested. We hypothesized the decrease of PGRA at the window of receptivity is required for successful embryo implantation. In order to test this hypothesis, we generated a PGRA conditional expression allele initiated by Cre recombinase present in the uterine epithelial compartment. The PGRA expressing mice exhibited infertility with the inability to undergo embryo implantation or decidualization. RNA microarray and ChIP-Seq analyses were utilized to identify the differentially regulated pathways controlled by PGRA at the time of implantation.

overall_design: Mice exhibiting overexpression of PGRA in the uterine epithelium and littermate controls were mated to vasectomized male mice. Upon the presence of the post-coital plug, mice were sacrificed 4 days later and uterine horns were harvested and frozen. RNA was isolated from the uterus and pooled. An Agilent RNA microarray was performed on samples individually consisting of 3 pooled samples. Therefore, 9 mice are represented in total per genotype.

last: Wetendorf

first: S

last: Wu

first: X

last: Wang

first: C

last: Creighton

first: R

last: Lanz

first: L

last: Blok

last: Tsai

first: J

middle: P

last: Lydon

first: F

last: DeMayo


title: Human Single Cell Transcriptional Profiling Identifies Epigenetically Altered PGE2 Pathway that Modulates Diabetic Macrophage Phenotype and Wound Repair

status: Public on Oct 07 2020

city: Ann Arbor

first: Lam

last: Tsoi

institute: University of Michigan

summary: single cell RNA-sequencing to profile the transcriptomes of lesional skin of diabetic patients at the cellular level.

overall_design: Comparison between lesional skin from diabetic patients to normal skin

first: Frank

last: Davis

first: Katherine

middle: A

last: Gallagher


title: Reconstruction of the decidual pathway in human endometrial cells using single-cell RNA-Seq

status: Public on Jan 06 2020

city: Coventry

first: Jan

last: Brosens

address: University Hospital Coventry and Warwickshire

department: Warwick Medical School

country: United Kingdom

institute: University of Warwick

summary: The fate of the human endometrium is determined during the mid-luteal window of implantation, coinciding with differentiation of endometrial stromal cells (EnSCs) into specialized decidual cells. Upon embryo implantation, differentiating EnSCs transform the endometrium into the decidua of pregnancy; whereas falling progesterone levels in the absence of pregnancy lead to tissue breakdown and menstruation. We used single-cell RNA sequencing to map the transcriptomic changes in primary EnSCs along a decidual time-course and in response to withdrawal of differentiation signals. We demonstrate that decidual transformation starts with a precipitous transcriptional response, which is followed by synchronous transition of EnSCs through intermediate states before emerging as divergent subpopulations, representing decidual cells and senescent decidual cells. Single-cell analysis of timed luteal phase biopsies identified multiple endometrial epithelial subpopulations and immune cells, most prominently uterine NK cells. In the stroma, transition from receptive to post-receptive endometrial state was marked by progression of EnSCs along diverging transcriptional trajectories, involving genes with conserved branching dynamics in vivo and in vitro. Our findings indicate that specification of EnSCs into distinct decidual subpopulations underpins endometrial fate decisions during the window of implantation.

overall_design: Endometrial mid-luteal phase biopsies or timecourse of primary endometrial stromal cells decidualized in culture were recovered and subjected to single-cell analysis using nanoliter droplet barcoding and high throughput sequencing of RNA (Drop-Seq)

first: Emma

middle: S

last: Lucas

first: Pavle

last: Vrljicak

first: Maria

last: Diniz-da-Costa

first: Sascha

last: Ott


title: Evaluation of gene expression between ALDH-high and ALDH-low cells in endometrial cancer-derived spheroids

status: Public on Dec 25 2018

city: Niigata

first: Tatsuya

last: Ishiguro

address: 1-757, Asahimachi-dori, Chuo-ku

institute: Niigata university

summary: To identify genes that are differentially expressed between ALDH-high and ALDH-low cells in endometrial cancer-derived spheroids, we performed whole genome microarray expression profiling as a discovery platform. Human endometrial cancer stem spheroid cells from three patients were sorted into ALDH-high and ALDH-low cells using the FACS Aria II Cell Sorter. Total RNA extracted from the cells were labeled with Cy3 and used for microarray analyses with Agilent Whole Human Genome Oligo Microarrays.

overall_design: Gene expression in fluorescence-activated cell-sorted ALDH-high and ALDH-low cells derived from three endometrial cancer patients was measured.

first: Yutaro

last: Mori


title: Single keratinocyte analysis uncovers Foxm1 as a Yap-dependent regulator of human epidermal stem cells (scRNA-Seq)

status: Public on Mar 18 2021

first: Mattia

last: Forcato

overall_design: The purpose of this study is to define, at single-cell levels, transcriptional profile of keratinocytes stem cells and transient amplifying progenitors. Single-cell RNA seq data from two human primary keratinocyte cultures (K82 and K86) harvest at early passsages (t1, profiled 3.367 and 3.978 cells respectively) and after serial cultivation (t2, profiled 4292 and 3576 cells respectively) were obtained with 10X Genomics Chromium Technology.

first: Elena

last: Enzo

first: Alessia

last: Secone Seconetti

first: Sergio

last: Bondanza

first: Clelia

last: Peano

first: Silvio

last: Bicciato

first: Michele

last: De Luca


title: Transcriptome-wide Analysis of Intracranial Artery of Moyamoya Disease Showing Up-regulation of Inflammatory Response with Increased Expression of TLR2 and SYK, and Down-Regulation of Collagen Formation with Decreased Expression of COL15A1

first: Kinya

last: Yokoyama

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

overall_design: Refer to individual Series


title: Effects of Cadmium Exposure on DNA Methylation at Imprinting Control Regions and Genome-Wide in Mothers and Newborn Children.

status: Public on Dec 04 2018

city: RALEIGH

first: Dereje

last: Jima

address: 850 Main Campus Drive

institute: NCSU

type: Methylation profiling by high throughput sequencing

summary: Background: Imprinted genes are defined by their preferential expression from one of the two parental alleles. This unique mode of gene expression is dependent on allele-specific DNA methylation profiles established at regulatory sequences called imprinting control regions. These loci are frequently used as biosensors to study how environmental exposures affect methylation and transcription. However, a critical unanswered question is whether they are more, less or equally sensitive to environmental stressors as the rest of the genome. Objectives: Using cadmium exposure in humans as a model, we determined the relative sensitivity of imprinting control regions to perturbation of methylation compared to similar, non-imprinted loci in the genome. Methods: We assayed DNA methylation genome-wide using bisulfite sequencing of newborn cord blood and maternal blood samples selected on the basis of maternal blood cadmium levels. Differentially methylated regions associated with cadmium exposure were identified. Results: In newborn cord blood and maternal blood, 641 and 1945 cadmium-associated differentially methylated regions were identified, respectively. These were strongly enriched at maternally-methylated imprinting control regions when compared to similar loci in newborn cord blood (P = 5.64E-8) and maternal blood (P = 6.22E-14), suggesting an increased sensitivity for imprinting control regions to cadmium. Genome-wide, methylation changes were enriched in maternal blood at genes implicated in body mass index (P = 2.0E-5), blood pressure (P = 3.8E-5) and body weight (P = 1.4E-3), with similar trends for metabolic and cardiovascular functions in cord blood, suggesting that epigenetic changes may contribute to the etiology of cadmium-associated diseases. Conclusions: We present the first global nucleotide-resolution DNA methylation profile associated with cadmium exposure in humans. We identify imprinting control regions as hotspots for perturbation by cadmium, possibly due to their unique modes of regulation, motivating further study of these loci to provide insight into the mechanisms of cadmium action.

overall_design: We analyzed specimens from 20 pregnant women and 19 of their offspring. We selected 10 women with the highest blood Cd concentrations in the first trimester of pregnancy and 10 from the majority of women with blood concentrations close to zero.

first: Michael

last: Cowley

first: David

last: Skaar

first: Rachel

last: Maguire

first: Kathleen

last: Hudson

first: Sarah

last: Park

first: Patricia

last: Sorrow

first: Cathrine

last: Hoyo


title: Ribosome profiling of selenoproteins in vivo reveals consequences of pathogenic Secisbp2 missense mutations

status: Public on Jul 26 2019

city: Bonn

first: Ulrich

last: Schweizer

address: Nussallee 11

institute: Universitätsklinikum Bonn

summary: Re-coding of UGA codons as selenocysteine (Sec) codons in selenoproteins depends on a selenocysteine insertion sequence (SECIS) in the 3’ UTR of mRNAs of eukaryotic selenoproteins. SECIS-binding protein 2 (SECISBP2) increases the efficiency of this process. Pathogenic mutations in SECISBP2 reduce selenoprotein expression and lead to phenotypes associated with the reduction of deiodinase activities and selenoprotein N expression in humans. Two functions have been ascribed to SECISBP2: binding of SECIS elements in selenoprotein mRNAs and facilitation of co-translational Sec insertion. To separately probe both functions, we established here two mouse models carrying two pathogenic missense mutations in Secisbp2 previously identified in patients. We found that the C696R substitution in the RNAbinding domain abrogates SECIS binding and does not support selenoprotein translation above the level of a complete Secisbp2 null mutation. The R543Q missense substitution located in the selenocysteine insertion domain resulted in residual activity and caused reduced selenoprotein translation, as demonstrated by ribosomal profiling to determine the impact on UGA re-coding in individual selenoproteins. We found, however, that the R543Q variant is thermally unstable in vitro and completely degraded in the mouse liver in vivo, while being partially functional in the brain. The moderate impairment of selenoprotein expression in neurons led to astrogliosis and transcriptional induction of genes associated with immune responses. We conclude that differential SECISBP2 protein stability in individual cell types may dictate clinical phenotypes to a much greater extent than molecular interactions involving a mutated amino acid in SECISBP2 .

overall_design: Ribosome profiling and RNA-sequencing of cortex samples from 2 Secisbp2 R543Q/fl; Camk-Cre pos mice and 2 control mice.

first: Simon

last: Bohleber

last: Howard


title: An essential role for Abscisic acid in the regulation of xylem fibre differentiation

status: Public on May 23 2018

city: Manchester

middle: Roy

last: Turner

address: Oxford Road

department: Faculty of Biology, Medicine and Health Science, School of Biological Science

institute: University of Manchester

summary: The Arabidopsis hypocotyl is an excellent model for understanding radial growth in plants. Division of the cambial cells and their subsequent differentiation into xylem and phloem drives radial expansion of the hypocotyl. Following the transition to reproductive growth, a phase change occurs in the Arabidopsis hypocotyl. During this second phase, the relative rate of xylem production is dramatically increased compared to that of phloem and xylem fibres containing thick secondary cell walls also form, which results in the production of xylem tissue comparable to the wood of trees. Abscisic acid (ABA) is a phytohormone known to have a major role in various plant processes, including in the response to changes in environmental conditions and in the promotion of seed dormancy. Using two different genetic backgrounds and different environmental conditions, we identified a set of core of transcriptional changes associated with the switch to the second phase of growth in the hypocotyl. ABA signalling pathways were identified as being as significantly over-represented in this set of core genes. Reverse genetic analysis demonstrated that mutants defective in ABA-biosynthesis enzymes exhibited significantly delayed fibre production without affecting the xylem:phloem ratio. The altered morphology is also reflected at the transcript level, with a reduced expression of marker genes associated with fibre formation in aba1 mutants. The application of exogenous ABA to the mutant rescued the phenotype, restoring fibre differentiation to wild-type levels. Taken together the data reveals an essential role for ABA in the regulation of fibre formation.

overall_design: We used RNA-seq to probe transcripome changes in Arabidopsis thaliana transgenic line 35S::CO:GR co-2 tt4 during dexamethasone treatment to follow xylem transition from phase I to phase II

first: Matthew

last: Cooper

first: Liam

last: Campbell

first: J

last: Etchells

first: Manoj

last: Kumar

middle: R


title: Next Generation Sequencing for Genome-wide Maps of DNA Methylation, ChIP-seq and RNA-seq in Liver Cells

status: Public on Dec 17 2018

city: Shanghai

first: Jin

last: Li

state: Shanghai

address: 130 Dong-An Road

department: Institutes of Biomedical Sciences (IBS)

institute: Fudan University

summary: Aberrant DNA methylation is a distinguished feature of cancer. We introduce a novel method of Guide Positioning Sequencing (GPS) for precisely detecting whole genome DNA methylation and applied GPS as well as ChIP-seq and RNA-seq in normal liver cells and hepatoma cell lines to find how abberant DNA-methylation affect gene expression and cell identity during tumorigenesis and metastasis. We systematically found that the methylation difference between genebody and promoter is an effective predictor for gene expression with a correlation coefficient of 0.7. Moreover, Methylation boundary shift (MBS) in the promoter or enhancer is also capable of modulating the expression categorized within immune response process and tumor metabolism. Furthermore, aberrant DNA methylation is related to the gain or loss of tissue specific enhancer which is responsible for altering cell identity during liver cancer development and metastasis prone to the lung.

overall_design: Epigenetic information of normal liver cells and hepatoma cell lines.

first: Wenqiang

last: Yu

first: Yan

first: Wei

first: Ming

last: Gao

first: Huaibing

last: Luo

first: Shihua

last: Dong


title: A Pipeline for High Throughput Concentration Response Modeling of Gene Expression for Toxicogenomics

status: Public on Feb 22 2018

first: Dereje

last: Jima

summary: Concentration Response Modeling on targeted RNAseq (TempOSeq) transcripts from the s1500+ panel utilizing iPSC-Cardiomyocytes treated with four chemicals

overall_design: Fully induced beating cardiomyocytes from the standard donor (Cellular Dynamics) were treated with either Media, DMSO+Media or 3 doses of 4 chemicals. Following 24 hours of incubation, the cell medium was discarded, and cardiomyocytes were lysed with 10μl 1x lysis buffer provided in the TempOSeq assay kit (BioSpyder Technologies, Carlsbad, CA).

first: John

first: Fabian

last: Grimm

first: Yi-Hui

last: Zhou

first: Ivan

last: Rusyn

first: Fred

last: Wright


title: The REMBRANDT study – a large collection of genomic data from brain cancer patients [gene expression]

status: Public on May 25 2018

city: Washington

first: Krithika

last: Bhuvaneshwar

state: DC

address: 2115 Wisconsin Ave NW

institute: Georgetown University

summary:
The Rembrandt brain cancer dataset and includes clinical and biospecimen data from this study for 671 patients collected from 14 contributing institutions in 2005. Such combined datasets would provide researchers with a unique opportunity to conduct integrative analysis of gene expression and copy number changes alongside clinical outcomes (overall survival) in this large brain cancer study.
In 2015, the NCI retired the REMBRANDT data portal, and all molecular data including microarray gene expression, copy number, and clinical data, was migrated to the Georgetown Database of Cancer  (G-DOC). The G-DOC platform can be accessed at: https://gdoc.georgetown.edu. G-DOC is a data integration platform that offers advanced computational tools to handle a variety of biomedical BIG DATA including gene expression arrays, NGS and medical images so that they can be analyzed in the full context of other omics and clinical information. After migration of the REMBRANDT dataset into G-DOC, we applied our novel algorithm for copy number data analysis called Chromosomal Instability Index (CINdex), published as an open source Bioconductor package . This submission includes the copy number data, processed on two Affymetrix 50K copy number arrays and gene expression data processed on the Affymetrix U133 Plus2 array. It also includes the Chromosome and Cytoband CINdex matrices.

overall_design:
Total RNA was extracted from the tumor tissue (50-80 mg) using the Trizol reagent (Invitrogen) and following the manufacturer's instructions. The quality of RNA extracted was verified using Agilent’s Bioanalyzer System with the help of RNA Pico Chips. 5 μg RNA extracted from each sample was processed using the Affymetrix U1332 Plus gene expression microarray chips

This series represents a different subset of REMBRANDT samples from those contained in GSE68848.

first: Yuriy

last: Gusev

first: Subha

last: Madhavan


title: Discovery of Methylated Circulating DNA Biomarkers For Comprehensive Non-Invasive Monitoring Of Treatment Response In Metastatic Colorectal Cancer.

status: Public on Oct 10 2017

city: Candiolo

first: Ludovic

last: Barault

state: Torino

address: IRCC Candiolo

department: Department of Oncology

institute: University of Torino

summary:
Evaluation of cell free circulating DNA (cfDNA) has recently been proposed for tracking disease relapse in colorectal cancer (CRC). Such assays could overcome the issues of classical monitoring, but requires personalized assay design due to absence of common alteration. On the contrary, early methylation alterations are restricted to delimited genomic loci allowing comprehensive assay design for population study. Our objective was to identify new cancer specific methylation biomarkers fitted to assess cfDNA over treatment, thus monitoring response in the metastatic CRC (mCRC) setup. Genome wide methylation profiling of colorectal cancer cell lines (surrogate to pure tumor tissue) was carried out and compared to publically available normal healthy colon mucosa (cancer unrelated). Identified loci were validated in additional publically available cohorts. Digital PCR assays were designed for selected markers and assessed in cfDNA of self-declared healthy donors (>40 years old), and of mCRC patients. Longitudinal assessment was performed in a subset of colorectal cancer patients treated with different therapy regimen (chemotherapy or targeted agents).
Samples from the current GEOset were extracted by Wizard SV Genomic DNA Purification System (Promega). DNA samples were checked for integrity by 1% agarose gel, and quantity via Picogreen quantification. All samples were bisulfite converted using the EZ DNA methylation Gold kit (Zymo Research) with a minimum input of 500ng and following manufacturer’s instructions. Infinium HumanMethylation450 BeadChip arrays were carried out according to the Illumina Infinium HD methylation protocol.

overall_design: All raw data (IDAT files) were imported in R Bioconductor using the minfi package. Matrix signal intensities data correspond to Methylated and unmethylated signal obtained through getMeth and getUnmeth function after preprocessRaw. Processed data were obtained via preprocessIllumina function (using background correction and control normalization) to achieve similar normalized data than GEO downloaded datasets.

first: Sebastian

last: Moran

first: Manel

last: Esteller

first: Federica

last: Di Nicolantonio


title: The REMBRANDT study – a large collection of genomic data from brain cancer patients [SNP]

summary:
The Rembrandt brain cancer dataset and includes clinical and biospecimen data from this study for 671 patients collected from 14 contributing institutions in 2005. Such combined datasets would provide researchers with a unique opportunity to conduct integrative analysis of gene expression and copy number changes alongside clinical outcomes this large brain cancer study.
In 2015, the NCI retired the REMBRANDT data portal, and all molecular data including microarray gene expression, copy number, and clinical data, was migrated to the Georgetown Database of Cancer  (G-DOC). The G-DOC platform can be accessed at: https://gdoc.georgetown.edu. G-DOC is a data integration platform that offers advanced computational tools to handle a variety of biomedical BIG DATA including gene expression arrays, NGS and medical images so that they can be analyzed in the full context of other omics and clinical information.
After migration of the REMBRANDT dataset into G-DOC, we applied our novel algorithm for copy number data analysis called Chromosomal Instability Index (CINdex), published as an open source Bioconductor package . This submission includes the copy number data, processed on two Affymetrix 50K copy number arrays and gene expression data processed on the Affymetrix U133 Plus 2 array. It also includes the Chromsome and Cytoband CINdex matrices.

overall_design:
Tissue (Approximately 10 μg from each tumor) was used to extract high molecular weight, genomic DNA using QIAamp DNA Micro DNA extraction kit (Qiagen) following the manufacturer's instructions. The quality of DNA was checked by electrophoresis run in a 2% agarose gel. Genomic DNA (250 ng) from samples received were hybridized to Affymetrix 100K single nucleotide polymorphism (SNP) chips, which covers 116,204 single nucleotide polymorphism loci in the human genome with a mean intermarker distance of 23.6 kb. The 100K arrays were a set of 2 chips, 50K each, designed for different restriction enzyme - XbaI and HindIII. These arrays were processed separately and looked for their concordance. It give two simultaneous data type outputs: allelic calls and signal intensity, allowing for the determination of both copy number alterations and regions of allelic imbalances (loss of heterozygosity). Calls were determined by the GTYPE software version 3.0 with 25% level of confidence.

The CINdex package uses the segment level data (obtained from the CN4.cnchp files) to calculate the genomic instability in terms of copy number gains and losses separately at the chromosome and cytoband level. The genomic instability across a chromosome offers a global view (referred to asChromosome CIN), and the genomic instability across cytobands regions provides higher resolution (referred to as Cytobands CIN) view of instability. This allows assessing the impacts of copy number alternations on various biological events or clinical outcomes by studying the association of CIN indices with those events. The CINdex algorithm was applied on both the XbaI and HindIII Rembrandt copy number arrays.

>>>CEL files are available only for 16 samples due to a corrupted archive. All samples contain processed data as either .CHP or CNCHP files.<<<


title: Rexinoid signalling during early myogenic differentiation

status: Public on Sep 13 2017

city: Ottawa

first: Qiao

last: Li

state: Ontario

address: 451 smyth road

department: Cellular and Molecular Medicine

institute: University of Ottawa


title: Overlap in signaling between constitutively active forms of Smoothened and the α subunit of the heterotrimeric G protein G13

status: Public on May 05 2018

city: Philadelphia

first: David

last: Manning

state: PA

address: 3620 Hamilton Walk

institute: University of Pennsylvania

summary: RNA sequencing was used to evaluate genes regulated in C3H10T1/2 cells by the Smo agonist purmorphamine

overall_design: Cells were treated with an optimized concentration (2 micromolar) of purmorphamine for 48 hours, at which time RNA was isolated and sequenced

first: Xueshui

last: Guo

first: Natalia

last: Riobo-Del Galdo

first: Eun

middle: J

last: Kim

first: Gregory

last: Grant


title: Arabidopsis seedling hydroponic treatment with Streptomyces AGN23 culture supernatants

status: Public on Sep 15 2018

city: CASTANET TOLOSAN

first: Thomas

last: Rey

address: 24 chemin de borde rouge, BP42617

institute: DE SANGOSSE

summary: The objective of this study was to evaluate the effect of extracellular culture medium of Streptomyces AGN23, a strain inducing disease resistance in plants, on the Arabidopsis transcriptome.

overall_design: A total of 17 samples were analysed comprising 3 biological replicates for each of the 3 timepoints of the kinetic (1 hour, 6 hour, 24 hour) for both treated (AGN) and control actilande (ACT) treatments.

first: Bernard

last: Dumas

first: Sophie

last: Vergnes

first: Marine

last: Veyssière


status: Public on May 19 2018

first: Manoj

last: Kumar

state: Lancashire

department: Faculty of Biology, Medicine and Health

summary:
The Arabidopsis hypocotyl is an excellent model for understanding radial growth in plants. Division of the cambial cells and their subsequent differentiation into xylem and phloem drives radial expansion of the hypocotyl. Following the transition to reproductive growth, a phase change occurs in the Arabidopsis hypocotyl. During this second phase, the relative rate of xylem production is dramatically increased compared to that of phloem and xylem fibres containing thick secondary cell walls also form, which results in the production of xylem tissue comparable to the wood of trees. Abscisic acid (ABA) is a phytohormone known to have a major role in various plant processes, including in the response to changes in environmental conditions and in the promotion of seed dormancy. Using two different genetic backgrounds and different environmental conditions, we identified a set of core of transcriptional changes associated with the switch to the second phase of growth in the hypocotyl. ABA signalling pathways were identified as being as significantly over-represented in this set of core genes. Reverse genetic analysis demonstrated that mutants defective in ABA-biosynthesis enzymes exhibited significantly delayed fibre production without affecting the xylem:phloem ratio. The altered morphology is also reflected at the transcript level, with a reduced expression of marker genes associated with fibre formation in aba1 mutants. The application of exogenous ABA to the mutant rescued the phenotype, restoring fibre differentiation to wild-type levels. Taken together the data reveals an essential role for ABA in the regulation of fibre formation.
We used microarrays to probe transcripome changes I Arabidopsis hypocotyls following transition from phase I to phase II

overall_design: Arabidopsis thaliana, Col-0 plants were grown under short day conditions for 6 weeks and switched to long days to induce flowering. RNA was extracted in triplicates from the hypocotyls of plants 0, 1, 2, 4 and 10 days following the day length switch, with 8 individual plants pooled per replicate

first: Liam

last: Campbell

first: J

last: Etchells

first: Matthew

last: Cooper

first: Simon

last: Turner


title: Disruption of Trim9 function abrogates macrophage motility in vivo

status: Public on Sep 26 2017

first: Dereje

last: Jima

summary: The vertebrate immune response is comprised of multiple molecular and cellular components that interface to provide an adequate defense against pathogens.  Although much is known on how individual molecules or cells respond to infection, an understanding of the whole-organism response to pathogen exposure remains unresolved, due to the dynamic complexity of the immune system and its interdependent innate and adaptive functionality.  Zebrafish larvae provide a unique model for overcoming this obstacle as larvae can successfully defends themselves from pathogens while lacking a functional adaptive immune system during the first few weeks of life, making it possible to examine exclusively the innate immune response in a whole-organism context. It was hypothesized that the transcriptional response of zebrafish larvae to immune agonists would identify known immune-response genes as well as reveal genes that mediate innate immunity in novel ways.  In order to test this hypothesis, zebrafish larvae were exposure to the chemically diverse immune agonists, polyinosine-polycytidylic acid (PolyIC) and synthetic triacylated lipoprotein (Pam3CSK4) and transcriptome analyses completed using microarray analyses.  This strategy successfully identified known immune response genes, as well as genes that had not been implicated in immune function, including the E3 ubiquitin ligase, tripartite motif 9 (trim9). Although Trim9 expression has been described as “brain specific”, here we demonstrate elevated levels of trim9 transcripts in macrophages after immune stimulation. As Trim9 has been implicated in axonal migration, we investigated and demonstrate that disruption of Trim9 function impairs macrophage chemotaxis and cellular architecture in vivo. These results demonstrate that Trim9 mediates cellular movement and migration in macrophages as well as neurons.

overall_design: Zebrafish larvae were exposed to the chemically diverse immune agonists, polyinosine-polycytidylic acid (PolyIC) and synthetic triacylated lipoprotein (Pam3CSK4) and transcriptome analyses completed using microarray analyses. RNA were extracted at 4, 8, 12, 24 and 36 time points after exposure to PolyIC and Pam3CSK4. At each timepoint we  have a untreated controls.

first: Debra

last: Tokarz

first: Heffelinger

last: Amy

first: Jima

last: Dereje

first: Gerlach

last: Jamie

first: Shah

last: Radhika

first: Rodriguez-Nunez

last: Ivan

first: Fletcher

last: Ashley

first: Nordone

last: Shila

first: Law

first: Heber

last: Steffen

first: Yoder

last: Jeffrey


title: Comprehensive microRNA-sequencing of small extracellular vesicles derived from head and neck carcinoma cells reveals common secretion profiles

status: Public on Jul 11 2017

city: Cincinnati

first: Scott

last: Langevin

state: OH

address: 160 Panzeca Way, ML0056

department: Department of Environmental Health

institute: University of Cincinnati College of Medicine

summary: Exosomes are nano-sized (40-150 nm), membrane encapsulated vesicles that are released by cells into the extracellular space and function as intercellular signaling vectors through the horizontal transfer of biologic molecules, including microRNA (miRNA). Although secreted by both normal and malignant cells, there is evidence that cancer-derived exosomes enable the tumor to manipulate its microenvironment, contributing to the capacity of the tumor for immune evasion, growth, invasion, and metastatic spread.

overall_design: The purpose of this study was to apply miRNA-sequencing to exosomes isolated from conditioned culture media to comprehensively characterize miRNA secreted in exosomes from 4 distinct head and neck squamous cell carcinoma (HNSCC) cell lines and normal oral epithelial cells.

first: Mario

last: Medvedovic


title: The REMBRANDT study – a large collection of genomic data from brain cancer patients

first: Krithika

last: Bhuvaneshwar

type:
Expression profiling by array
Genome variation profiling by SNP array


title: Molecular Effects of Developmental FM 550 Exposure in Wistar Rat Fetal Forebrain

status: Public on Feb 28 2018

summary: Firemaster® 550 (FM 550) is a flame retardant (FR) mixture that has become one of the most commonly used FRs in foam-based furniture and baby products.  Human exposure to this commercial mixture, comprised of brominated and organophosphate components, is widespread.  We have repeatedly shown that developmental exposure can lead to sex-specific behavioral effects in rats.  Accruing evidence of endocrine disruption and potential neurotoxicity have raised concerns regarding the neurodevelopmental effects of FM 550 exposure, but the specific mechanisms of action remains unclear.  Additionally, we observed significant, and in some cases sex-specific, accumulation of FM 550 in placental tissue following gestational exposure.  Because the placenta is an important source of hormones and neurotransmitters for the developing brain, it may be a critical target of toxicity to consider in the context of developmental neurotoxicity.  Using a mixture of targeted and exploratory approaches, the goal of the present study was to identify possible mechanisms of action in the developing forebrain and placenta. Wistar rat dams were orally exposed to FM 550 (0, 300, or 1,000 µg/day;) for 10 days during gestation and placenta and fetal forebrain tissue collected for analysis.  In placenta, evidence of endocrine, inflammatory, and neurotransmitter signaling pathway disruption was identified.  Notably, 5-HT turnover was reduced in placental tissue and fetal forebrains indicating that 5-HT signaling between the placenta and the embryonic brain may be disrupted.  These findings demonstrate that environmental contaminants, like FM 550, have the potential to impact the developing brain by disrupting normal placental functions.

overall_design: RNA-seq of FM550 and control-treated fetal forebrain.

first: Kylie

last: Rock

first: Brian

last: Horman

first: Allison

middle: L

last: Phillips

first: Susan

last: McRitchie

last: Watson

first: Jocelin

last: Deese-Spruill

last: Sumner

first: Heather

last: Stapleton

last: Patisaul


title: Concurrent single cell RNA and targeted DNA sequencing on a microfluidics device allows high-throughput identification of transcriptome and genome alterations during the development of tyrosine kinase inhibitor resistance in EGFR-mutant lung cancer cells

status: Public on Mar 23 2019

city: Singapore

first: Huipeng

last: Li

address: 60 Biopolis St, #02-01

department: Computational and Systems Biology

country: Singapore

institute: Genome Institute of Singapore

summary: Within the clonal heterogeneity of a tumor, the co-measurement of both genomic and transcriptomic signatures in single cells is of fundamental importance to accurately assess how the genetic information, for instance a somatic mutation, is correlated with a transcriptomic and cancer-related phenotype. However, there is currently no microfluidics-based high-throughput assay available that allows this analysis. To resolve this, we developed a new method for concurrent sequencing of the transcriptome and targeted genomic regions (CORTAD-seq) within the same single cell on a microfluidic high-throughput platform. Its operation is simple, at moderate reagent cost, with excellent data quality and good accessibility for a broad scientific community. We implemented this new method to dissect the cellular consequences of mutations that result in resistance to targeted therapy. Using different tyrosine kinase inhibitor (TKI) resistant PC9 lung cancer cell lines as our study model, we detected signatures of TKI resistant genes as well as expansion of T790M mutation and EGFR amplification in the resistant cells. Interestingly, we identify transcriptomic characteristics for resistance that are not dependent on the presence of T790M, the most common resistance mutation in EGFR, indicating that phenotypically similar resistance scenarios can emerge without T790M mutation and other genomic alterations or epigenetic modifications are required for the manifestation of the resistance phenotype. Cumulatively, the application of this method allows accurate evaluation of the genomic and transcriptomic changes in cancer during development of drug resistance at single cell level in uncovering potential new biomarker and therapeutic targets in resistant cancer.

overall_design:
A new method has been developed for concurrent single cell transcriptome and targeted genomic sequencing on a microfluidic platform. We utilized three PC9 lines that are responsive or resistant to TKI treatment as our study model. We implemented analysis pipeline for single cell RNAseq and targeted DNAseq studies.
546 single cells of PC9 cells were sequenced using the CoRTAD protocol. 507 cells with both the scRNAseq data and targeted DNA data passing the QC were selected for downstream analysis (20 cells in DMSO condition were also excluded from the downstream analysis).

first: Say

last: Kong


title: Molecular architecture underlying fluid absorption by the developing inner ear

status: Public on Sep 11 2017

city: Bethesda

first: Robert

last: Morell

state: MD

address: 35A Convent Drive, Room 1F-103

institute: National Institute on Deafness and Other Communication Disorders

summary: Single-cell RNA-seq analysis of pre- and postnatal mouse endolymphatic sac demonstrates two types of differentiated cells distinguished by their mRNA expression signatures.

overall_design: mRNA-seq profiles from 213 single cells from embryonic day 12.5, 16.5, postnatal day 5 and 30 mouse endolymphatic sac were analyzed

first: Keiji

last: Honda

first: Michael

last: Kelly

first: Joseph

last: Burns

last: Hoa

first: Matthew

middle: W

last: Kelley

first: Andrew

last: Griffith


title: DNA methylation in lung cells is a key modulator of asthma endotypes and genetic risk [DNA methylation]

status: Public on Jan 06 2017

city: Chicago

first: Carole

last: Ober

address: 920 E 58TH ST

institute: The University of Chicago

summary: We generated genome-wide methylation data using the 450K from freshly isolated airway epithelial cells of asthmatics and non-asthmatics. This data was paired with genome-wide genetic and gene expression data from the same individuals allowing for an integrated analysis of genetic, transcriptional, and epigenetic signatures in asthma.

overall_design:
Examination of genome-wide methylation levels and comparison to phenotypes

Please note that the 'metadata__UPDATED.txt.gz' is an updated version (April 9th, 2021), replacing the previous file.

first: Jessie

last: Nicodemus-Johnson

first: William

last: Wentworth-Sheilds


title: Genomic binding of PAX8-PPARG fusion protein regulates cancer-related pathways and alters the immune landscape of thyroid cancer

status: Public on Dec 21 2016

first: Maureen

last: Sartor

state: MI

address: 2017 Palmer Commons Bldg., 100 Washtenaw Ave

department: Department of Computational Medicine and Bioinformatics

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

overall_design: Refer to individual Series


title: Bisphenol A-associated alterations in genome-wide DNA methylation and gene expression patterns reveal sequence-dependent and non-monotonic effects in human fetal liver

status: Public on Aug 01 2017

summary: Here, we undertake the first epigenome-wide analysis of the effect of BPA concentration on human fetal liver DNA methylation. Enzymatic enrichment of genomic DNA for high CG density and methylation followed by next-generation sequencing yielded data for positional methylation across the genome. Comparing three groups of BPA-exposed subjects (n = 18; 6 per group), high (35.44–96.76 ng/g), low (3.50 to 5.79 ng/g), and non-detect (<0.83 ng/g), revealed regions of altered methylation. Similar numbers of regions of altered methylations were detected in pairwise comparisons; however, their genomic locations were distinct between the non-detect and low or high BPA groups. In general, BPA levels were positively associated with methylation in CpG islands and negatively associated with methylation in CpG shores, shelves, and repetitive regions. DNA methylation at the SNORD imprinted cluster (15q11q13) illustrated both linear and non-monotonic associations with BPA levels. BPA levels in human fetal liver tissue are associated with complex linear and non-monotonic as well as sequence-dependent alterations in DNA methylation.

overall_design: Differential methylation as determined by read-count of methylation senstive enzyme treated samples of human fetal liver stratified by BPA exposure.

first: Christopher

last: Faulk

first: Jung

middle: H

last: Kim

first: Tamara

last: Jones

first: Richard

middle: C

last: McEachin

first: Muna

last: Nahar

first: Dana

last: Dolinoy


title: Blastomyces dermatitidis: SREB null mutant versus wild type at 37oC and 6, 24, and 48-hrs 22oC

status: Public on Jun 01 2015

city: Madison

first: Gregory

middle: M

last: Gauthier

state: WI

address: 1550 Linden Drive

department: Medicine

institute: University of Wisconsin - Madison

summary:
The goal of this study was to capture the transcriptional response regulated by the GATA transcription factor encoded by SREB during the first 48-hours of the temperature-dependent shift from yeast (37oC) to mycelia (22oC).
Gene expression microarrays were used to compare an SREB null mutant (SREBΔ) to an isogenic wild type strain (ATCC 26199).  SREB null mutants fail to fully complete the conversion from yeast to sporulating mycelia after a drop in temperature from 37oC to 22oC, and under iron-replete conditions cannot properly repress siderophore biosynthesis. Deletion of SREB in ATCC 26199 produced SREBΔ.  The isogenic wild-type strain is ATCC 26199.

overall_design: Total RNA was isolated from 3 biological replicates of SREBΔ and the isogenic wild-type control (ATCC 26199) at 37oC and 6, 24, and 48-hrs at 22oC (24 total samples).  All cultures were grown in liquid HMM (Histoplasma macrophage media) under iron replete conditions (10 uM FeSO4).  All glassware was pre-treated with 2N HCl and extensively washed with ddH2O.

first: Amber

last: Marty

first: Aimee

middle: T

last: Broman

first: Christina

last: Kendziorski