title: Single nuclei RNAseq of rat area postrema and nucleus tractus solitarius after GDF15 treatment

status: Public on Jan 05 2022

city: Philadelphia

first: Benjamin

middle: C.

last: Reiner

state: PA

address: 125 S 31st St

institute: University of Pennsylvania

summary: We performed single-nuclei RNAseq of Sprague Dawley rat area postrema and nucleus tractus solitarius brain samples from animals treated with GDF-15 to identify cellular subtype specific changes in the neural transcriptome.

overall_design: We performed the 10x Genomics 3' gene expression assay (v3.1) on nuclei isolated from frozen Sprague Dawley rat area postrema and nucleus tractus solitarius combined brain punches. At the onset of the dark cycle, rats (~400 g) were injected with GDF15 (100 μg/kg, n=4) (i.p.). After six hours, rats were deeply anesthetized with a triple cocktail of ketamine, xylazine and acepromazine (180 mg/kg, 5.4 mg/kg and 1.28 mg/kg, respectively; i.p.) in the middle of the dark phase. Brains were removed and snap-frozen in dry ice-cold hexane. Three adjacent micro-punch samples (each ~1 cubic mm) containing the AP and left and right NTS were collected from coronally-prepared brains on a cryostat, pooled together, and stored at -80°C until further processing. Nuclei were isolated by differential centrifugation and microfluidically captured using the 10x Genomics Chromium controller. Sequencing libraries were constructed and sequenced on an Illumina NovaSeq 6000.

middle: C

first: Richard

last: Crist

first: Matthew

last: Hayes

first: Bart

last: De Jonghe

first: Tito

last: Borner


title: The ATP-hydrolyzing ectoenzyme E-NTPD8 attenuates colonic inflammation through regulation of P2X4 receptor-dependent metabolism in myeloid cells [F0536]

status: Public on Sep 23 2021

city: Suita

first: Daisuke

last: Okuzaki

state: Osaka

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

country: Japan

institute: Osaka univ.

type: Expression profiling by high throughput sequencing

summary: Extracellular adenosine triphosphate (ATP) released by mucosal immune cells and by microbiota in the intestinal lumen elicits diverse immune responses that mediate the intestinal homeostasis via P2 purinergic receptors, while overactivation of the ATP signaling leads to disruption of mucosal immune system linked to pathogenesis of intestinal inflammation. In the small intestine, hydrolysis of luminal ATP by E-NTPD7 in epithelial cells is essential for control of the number of Th17 cells. However, the molecular mechanism underlying regulation of microbiota-derived ATP in the colon is poorly understood. Here, we show that E-NTPD8 is highly expressed in large intestinal epithelial cells and hydrolyzes microbiota-derived luminal ATP. Compared to wild-type mice, Entpd8-/- mice develop more severe DSS-induced colitis. In this context, either depletion of neutrophils and monocytes by injecting with anti-Gr-1 antibody or introduction of P2rx4 deficiency into hematopoietic cells ameliorates colitis in Entpd8-/- mice. Increased level of luminal ATP in the colon of Entpd8-/- mice promotes glycolysis in neutrophils and monocytes through P2X4 receptor-dependent Ca2+ influx, which links to prolonged survival and elevated ROS production in these cells. Together, these results indicate that E-NTPD8 limits intestinal inflammation by controlling metabolic alteration toward glycolysis via P2X4 receptor in myeloid cells.

overall_design: We comprehensively analyzed small and large intestinal epithelial cells by performing RNA-seq analysis.

first: Ryu

last: Okumura


title: KMT2C/KMT2D (MLL3/MLL4) Histone Methyltranferase Activity Dependent Chromatin Organization at Enhancers during Embryonic Stem Cell Differentiation [ChIP-seq]

status: Public on Feb 28 2022

city: La Jolla

first: Bing

last: Ren

state: CA

address: 9500 Gilman Dr., CMM-East, Admin Area/Rm 2071

country: USA

institute: University of California, San Diego School of Medicine

type: Genome binding/occupancy profiling by high throughput sequencing

summary: PLAC-seq, mRNA-seq, and ChIP-seq experiments in mouse embryonic stem cells and neural progenitor cells in the presence or absence of  MLL3/4 catalytic activity and MLL2.

first: Naoki

last: Kubo


title: Identification of recurrence biomarkers in over 40 year’s women with lymph-node-positive primary breast cancer

status: Public on Sep 04 2021

city: Shanghai

first: Enuo

last: Liu

address: 2140 Xietu Road

country: China

institute: Shanghai Institute for Biomedical and Pharmaceutical Technologies

summary: Several studies provide genes expression characteristic correlated to recurrence in breast cancer patients with lymph node negative. However few reports mentioned about the gene expression file in patients with lymph node metastasis confirmed during surgery, of which the cumulative incidences of relapse are more than 50%.

overall_design: A total of 37 patients were followed up for more than 5 years. Sections of formalin-fixed paraffin embedded (FFPE) were prepared from breast tumors and well preserved. Twenty-five FFPE samples of ductual breast cancer patients with recurrent cancer and 12 FFPE samples of ductal breast cancer patients with no recurrence were analyzed the gene expression difference. Cancer tissues with ER positive or negative status were determined by immunohistochemistry method. All patients had positive lymph nodes confirmed during surgery and accompanied with lymphocytic invasion. All patients began to take Tamoxifen medicine after surgery and continued for more than 5 years or until cancer recurrence. All patients in this analysis had received chemotherapy treatment.

first: Luyi

last: Ye

first: Sean

middle: S

last: Ma

first: Fan

last: Zhang

first: Tiansheng

last: Xu

first: Zai-Si

last: Ji


title: Methylation array profiling of small B-cell lymphomas

status: Public on Sep 02 2021

city: Toronto

first: Daniel

last: Xia

address: 200 Elizabeth Street

country: Canada

institute: University Health Network

type: Methylation profiling by genome tiling array

summary: This dataset includes chronic lymphocytic leukemia/small lymphocytic lymphoma (CLL/SLL), follicular lymphoma (FL), mantle cell lymphoma (MCL), and marginal zone lymphoma (MZL) cases reviewed for pathology consensus at the University Health Network.  Also included are challenging cases of small B-cell lymphomas without pathology consensus.  Methylation array profiling was performed using the Infinium MethylationEPIC array platform.  Unprocessed IDAT files and matrix with beta values (beta_TGL51_illumina_annot_geo.txt) are provided.

overall_design: Bisulphite converted DNA from the 37 formalin-fixed paraffin embedded (FFPE) samples were hybridised to the Illumina Infinium MethylationEPIC Beadchip

first: Alberto

middle: J

last: Leon


title: Fibroblast Growth Factor Receptor 3 Alterations and Response to Immune Checkpoint Inhibition in Metastatic Urothelial Cancer: A Real World Experience

status: Public on Jun 08 2021

city: Chapel Hill

first: Kim Lab

last: UNC

state: NC

address: 450 West Drive, Room 21-209

institute: UNC-CH LCCC

summary:
Purpose: We evaluated clinical outcomes of patients with FGFR3-altered metastatic UC treated with ICB and investigate the underlying immunogenomic mechanisms of response and resistance
Methods: 103 patients with metastatic UC treated with ICB at a single academic medical center from 2014-2018 were identified. Clinical annotation for demographics and cancer outcomes, as well as somatic DNA and RNA sequencing were performed. Objective response rate to ICB, progression-free survival, and overall survival was compared between patients with FGFR3 alterations and those without. RNA expression, including molecular subtyping and T cell receptor clonality, was also compared between FGFR3-altered and non-altered patients
Results: Our findings from this dataset confirm that FGFR3-altered (n=17) and wild type (n=86) bladder cancers are equally responsive to ICB (12 vs 19%, p=0.73).  Moreover, we demonstrate that despite being less inflamed, FGFR3-altered tumors have equivalent T cell receptor (TCR) diversity and that the balance of a CD8 T cell gene expression signature to immune suppressive features is an important determinant of ICB response
Conclusions: Our work in a real world dataset validates prior observations from clinical trials but also extends this prior work to demonstrate that FGFR3-altered and wild type tumors have equivalent TCR diversity and that the balance of effector T cell to immune suppression signals are an important determinant of ICB response.

overall_design:
RNA sequencing of patients with advanced UC. Sample BACI165 was sequenced twice.

>>>Submitter states that raw data are unavailable due to patient privacy concerns<<<

Update: [07-12-2023] GSE176307_salmon_tpm_gene.matrix.tsv replaced GSE176307_BACI_tpm_gene.matrix.tsv.

first: William

middle: Y

last: Kim

first: Tracy

middle: L

last: Rose

middle: H

last: Weir


title: Effect of epigenotoxic chemicals on DNA methylation profiles of human induced pluripotent stem cells [methylation]

status: Public on Jul 23 2021

city: Yokohama

first: Xian-Yang

last: Qin

state: Kanagawa

address: 1-7-22 Suehiro, Tsurumi

institute: RIKEN Center for Integrative Medical Sciences

summary: We studied the effects of chemical exposure on global DNA methylation by using mCherry-methyl-CpG-binding domain (MBD)-nls human induced pluripotent stem cells (iPSCs). According to the fluorescent MBD parameters, we divided the effects of 135 chemical on global DNA methylation into 3 categories; reduction (hypomethylation), increase (hypermethylation) and little/no effect. We performed DNA methylome assay to examine the effects of 6 epigenotoxic chemicals on genome-wide DNA methylation patterns in human iPSCs. Our results indicated that hypermethylation agents increased DNA methylation and downregulated the expression of genes involved in cell cycle or development.

overall_design: Human iPSCs were exposed to DMSO, biotin, etoposide, propyl gallate, theophylline, bisphenol A, and thalidomide for 48 hours and then total genomic DNA was isolated for DNA methylome assay.

first: Satoshi

last: Otsuka

first: Tomohiro

last: Ito

first: Hideko

last: Sone


title: Differential RNA expression in human neck and squamous cell carcinoma cell lines (T-HEp3 and D-HEp3).

status: Public on Nov 18 2021

city: Bronx

first: Julio

middle: A

last: Aguirre-Ghiso

state: NY

address: 1301 Morris Park Ave

department: Cell Biology

institute: Albert Einstein College of Medicine

summary: We report the RNA expression profile in the tumorigenic (T-HEp3) and dormant (D-HEp3) HNSCC cell lines. T-HEp3 is a human epidermoid carcinoma, which grows on chorioallantoic membreane and metastasizes with high efficency into the organs of chick embryo. Upon serial paasage for more than 50 times in vitro , T-HEp3 loses tumorigenic and metastatic potential and termed as D-HEp3. This is an ideal cell line model system to study cancer dormancy.

overall_design: RNA sequencing was performed in T-HEp3 (P0, primary cells extracted from tumor grown on chicken CAM and plated on dish) and D-HEp3 grown in vitro (passage later than 130).

first: Deepak

middle: K

last: Singh


title: Effect of epigenotoxic chemicals on transcriptomic profiles of human induced pluripotent stem cells [RNA-seq]

summary: We studied the effects of chemical exposure on global DNA methylation by using mCherry-methyl-CpG-binding domain (MBD)-nls human induced pluripotent stem cells (iPSCs). According to the fluorescent MBD parameters, we divided the effects of 135 chemical on global DNA methylation into 3 categories; reduction (hypomethylation), increase (hypermethylation) and little/no effect. We performed RNA-seq analysis to examine the effects of chemicals on the expression of 100 stemness-related genes. In this series of experiment, we selected 5 compounds for genome-wide analyses. Etoposide, propyl gallate, and biotin were selected as representative chemicals of hypermethylation agents. Theophylline and bisphenol A were selected as representative chemicals of hypomethylation agents and undefined-epigenetic agents, respectively. Our results indicated that hypermethylation agents increased DNA methylation and downregulated the expression of genes involved in cell cycle or development.

overall_design: Human iPSCs cells were exposured to DMSO, biotin, etoposide, propyl gallate, theophylline, or bisphenol A for 48 hrs and then total RNA was isolated for RNA-seq analysis.


title: Next Generation Sequencing Facilitates Quantitative Analysis of Transcriptome profile in IEC 4.1-WT and IEC4.1-Ifnar1-/- KO cells (C12 KO) in response to Cryptosporidium parvum

status: Public on Oct 20 2021

city: Omaha

first: Xianming

last: Chen

state: NE

address: 2500 california plaza

institute: creighton university

summary: This study aims to measure the impact of Ifnar1-/- knockdown (KO) on the transcriptome profile in cultured IEC 4.1 cell in response to C. parvum infection.  IEC4.1-WT cells and IEC4.1-Ifnar1-/- cells (stably CRISPR/Cas9 knockout; C12 KO cells) were exposed to C. parvum infection. Cells treated with a scrambled non-specific siRNA were used as the control. Total RNA was collected for the genome-wide analysis.

overall_design: The murine intestinal epithelial cells were grown to 80% confluence for four groups: IEC4.1 control (Group A, A1-A3), IEC4.1 + C. parvum 24h (Group E, E1-E3, IEC 4.1 cells exposed to C. parvum infection for 24h), C12 control (Group C, C1-C3), C12 + C. parvum 24h (Group F, F1-F3, C12 cells exposed to C. parvum infection for 24h).  After treatment, total RNAs were prepared with the RNeasy Mini kit (Qiagen) according to the manufacturer’s instruction.


title: MicroRNA expression profiling in acute kidney injury

status: Public on May 14 2021

city: Saitama

first: Akinori

last: Aomatsu

address: 1-847 Amanuma-cho, Omiya-ku

department: Nephrology

institute: Saitama Medical Center, Jichi Medical University

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

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

overall_design: Refer to individual Series


title: Identification of circular RNA hsa_circ_001879 and hsa_circ_004104 as novel biomarkers for coronary artery disease

status: Public on Jun 07 2021

city: Beijing

first: Laiyuan

last: Wang

state: Beijing

address: Xicheng District, No.167 Beilishi Road

department: Department of Epidemiology

institute: Department of Epidemiology, State Key Laboratory of Cardiovascular Disease

summary: The circRNA profiles of 24 CAD patients and 7 controls were performed by microarray. Six classifiers were used to evaluate potential circRNAs biomarkers. The expression levels of candidate circRNAs were further verified by qRT-PCR in large cohorts. Logistic regression analysis and receiver operating characteristic were conducted to assess the diagnostic value. A total of 624 circRNAs and 171 circRNAs were significantly upregulated and downregulated, respectively, in CAD patients relative to controls. A four-circRNA signature was identified using six different classifiers. Among these four circRNAs, hsa_circ_001879 and hsa_circ_004104 were found significantly upregulated in validation cohorts. We offered a transcriptome-wide overview of aberrantly expressed circRNAs in CAD patients, and Hsa_circ_001879 and hsa_circ_004104 were replicated and identified to be significantly upregulated in CAD patients. Our results suggested that hsa_circ_001879 and hsa_circ_004104 might serve as diagnostic biomarkers for CAD.

overall_design: 24 CAD patients and 7 controls

first: Tianyu

last: Zou


title: Overexpression of miRNA-5100 with PEI-NPs led to change in expression of many mRNAs

summary: The aim of this study was to identify miRNAs that regulate AKI and develop their applications as diagnostic biomarkers and therapeutic agents. First, kidney tissues from two different AKI mouse models, namely, AKI induced by the administration of lipopolysaccharide (LPS) causing sepsis (LPS-AKI mice) and AKI induced by renal ischemia–reperfusion injury (IRI-AKI mice), were exhaustively screened for their changes of miRNA expression compared with that of control mice by microarray analysis followed by quantitative RT-PCR. The initial profiling newly identified miRNA-5100, whose expression levels significantly decreased in kidneys in both LPS-AKI mice and IRI-AKI mice. Next, the administration of miRNA-5100-mimic conjugated with a nonviral vector, polyethylenimine nanoparticles (PEI-NPs), via the tail vein significantly induced miRNA-5100 overexpression in the kidney and prevented the development of IRI-AKI mice by inhibiting apoptosis and inflammation in vivo. Furthermore, serum levels of miRNA-5100 in patients with AKI were identified as significantly lower than those of healthy subjects. ROC analysis showed that the serum expression level of miRNA-5100 can identify AKI (cut-off value 0.14, AUC 0.96, sensitivity 1.00, specificity 0.833, p<0.05). These results suggest that miRNA-5100 regulates AKI and may be useful as a novel diagnostic biomarker and therapeutic target for AKI.

overall_design: The effect of miRNA-5100-mimic treatment was investigated by an in vivo, nonviral vector gene transfection method 38. Polyethyleneimine is a crude nonlipid polycationic polymer with a positive charge on its surface. miRNAs are mixed with a negative charge to create a complex by mixing them. miRNAs with PEI-NPs have high biocompatibility, stability, and transfection ability. The sequence of the miRNA-5100 mimic used was 5-UCGAAUCCCAGCGGUGCCUCU-3. Complexes of miRNA-5100 mimics and PEI-NPs were formed at an N/P ratio of 6 with miRNA-5100 at a concentration of 5 nmol in a volume of 200 μl (GeneDesign). Complexes of control miRNA and PEI-NPs were similarly formed with control miRNA and an N/P ratio of 6 at a concentration of 5 nmol in a volume of 200 μl. miRNA with PEI-NPs was administered by tail vein injection in all mouse models. The sequence of control miRNA was 5-GGUUCGUACGUACACUGUUCA-3(GeneDesign). Four different protocols for preventing AKI were used in this study for comparison (sham model, IRI-AKI model, IRI-AKI+miRNA-5100-mimic-PEI-NPs model, IRI-AKI+control-miRNA-PEI-NPs model). In the sham model, a midline incision was made in the abdominal skin, muscle, and peritoneal membrane. In the IRI-AKI mouse model, an operation involving right nephrectomy and left renal clamp and reperfusion (for 45 min) was performed. In the IRI-AKI+miRNA-5100-mimic-PEI-NPs model, miRNA-5100-mimic with PEI-NPs was injected via the tail vein 2 days before the IRI procedure. The mixture was adjusted to be 5 nmol miRNA-5100-mimic with PEI-NPs in a volume of 200 μl. In the IRI-AKI+control-miRNA-PEI-NPs model, control miRNA with PEI-NPs was injected via the tail vein 2 days before the IRI procedure. The mixture was adjusted to be 5 nmol control miRNA with PEI-NPs in a volume of 200 μl. All mouse models underwent blood sampling and removal of the left kidney 24 h after the operation. A blood sample was extracted from the vena cava from each animal.

first: Yoshiyuki

last: Morishita


title: Gene-expression profiles of whole blood cells from a Han Chinese population with or without Type-2 Diabetes Mellitus or/and its complications in nephropathy and retinopathy

status: Public on Nov 17 2021

city: Taichung

first: Fuu-Jen

last: Tsai

address: No.2, Yude Rd., North Dist.

department: Department of Medical Research

country: Taiwan

institute: China Medical University Hospital

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

platform_organism:
Homo sapiens
synthetic construct


title: Transcriptomic profile of Tfh cells during intestinal helminth infection

city: CLAYTON

first: Aidil

last: Zaini

state: VICTORIA

address: LEVEL 3, BUILDING 77, MONASH UNIVERSITY

department: BIOCHEMISTRY AND MOLECULAR BIOLOGY

country: Australia

institute: MONASH UNIVERSITY

summary: The goal of this study was to define the regulation of Tfh cell response during intestinal helminth infection. Using the helminth Trichuris muris, we performed RNA-seq analysis on Tfh cells that develop during acute vs chronic helminth infection. We found that the transcriptomic profile of acute vs chronic induced Tfh cells are distinct and they express Th2/Th1-associated genes, respectively.

overall_design: Mice were infected with acute (high dose, HD) and chronic (low dose, LD) Trichuris muris. At d21 post infection, messentric lymph node (mLN)-derived Tfh cells (CD4+ CD44hi FOXP3- Ly6C- CD162- PD-1+ CXCR5+), as well as naive Th cells (CD4+ FOXP3- CD44lo CD62Lhi ) from uninfected mice were sorted and purified, followed by RNA extraction for RNA-seq analysis. 2 replicates were included for each group (acute & chronic Tfh cells, as well as naive CD4 T cells).

first: Deanna

middle: D

last: Lucas


title: Comparative analyses of gibbon centromeres reveal dynamic species-specific shifts in repeat composition [RNA-seq]

status: Public on May 24 2021

city: Portland

first: Mariam

last: Okhovat

state: Oregon

address: 3030 S Moody Ave.

department: Medicine

institute: Oregon Health and Science University

summary: Centromeres are functionally conserved chromosomal loci essential for proper chromosome segregation during cell division, yet they show high sequence diversity across species. A near universal feature of centromeres is the presence of repetitive sequences, such as satellites and transposable elements (TEs). Because of their rapidly evolving karyotypes, gibbons represent a compelling model to investigate divergence of functional centromere sequences across short evolutionary timescales. Previously, we identified a novel composite retrotransposon, LAVA, that is exclusive to gibbons and expanded within the centromere regions of one gibbon genus, Hoolock. In this study, we use ChIP-seq, RNA-seq and fluorescence in situ hybridization to comprehensively investigate the repeat content of centromeres of the four extant gibbon genera (Hoolock, Hylobates, Nomascus and Siamang). We find that CENP-A nucleosomes and the DNA-protein interface with the inner kinetochore are enriched in retroelements in all gibbon genera, rather than satellite DNA. We find that LAVA in Hoolock is enriched in the centromeres of most chromosomes and shows centromere- and species-specific sequence and structural differences compared to other genera, potentially as a result of its co-option to a centromeric function. In contrast, we found that a centromeric retroelement-derived macrosatellite, SST1, corresponds with chromosome breakpoint reuse across gibbons and shows high sequence conservation across genera. Finally, using de novo assembly of centromere-specific sequences, we determine that transcripts originating from gibbon centromeres recapitulate species-specific TE diversity. Combined, our data reveals dynamic, species-specific shifts in repeat content that define gibbon centromeres and coincide with the extensive karyotypic diversity observed within this lineage.

sample_organism:
Symphalangus syndactylus
Nomascus leucogenys
Hylobates moloch
Hoolock leuconedys

overall_design: Total RNA-sequencing was carried out on four gibbon species, representing the four extant gibbon genera (Siamang, Hylobates, Hoolock and Nomascus).

first: Gabrielle

last: Hartley

first: Rachel

last: O'Neill

first: Lucia

last: Carbone


title: Border-associated macrophages mediate the neuroinflammatory response in an alpha-synuclein model of Parkinson disease

status: Public on Jun 20 2021

city: Birmingham

first: David

last: Figge

state: AL

address: 1719 6th Ave. S, CIRC 520

department: Neurology

institute: University of Alabama-Birmingham

summary: Neuroinflammation and accumulation of alphα-synuclein (α-syn) are core features of Parkinson disease (PD). We found that α-syn-induced neuroinflammation is driven by antigen presentation from CNS resident macrophages. A subset of these, border-associated macrophages (BAMs), expand and express genes and proteins necessary for immune cell recruitment, infiltration, and antigen presentation, whereas depletion of BAMs prevents neuroinflammation and neurodegeneration. These results point to a critical role for BAMs in initiating PD pathogenesis.

overall_design: Mononuclear cells from 3-4 ventral midbrains pooled per sample, and sorted for CD45+ CD11b+ CX3CR1+ Ly6C- Ly6G- 301 and NK1.1- 302 cells on a BD FACsAria. Sorted cells were loaded onto the 10X Chromium 303 platform (10X genomics), and libraries were constructed using the Single Cell 3′ 304 Reagent Kit V2 according to the manufacturer’s instructions. Two biological replicates for each group were processed separately.

first: Ashley

last: Harms


title: Microarray-based clustering analysis of miRNAs altered in LPS-AKI mouse kidney

summary: The aim of this study was to identify miRNAs that regulate AKI and develop their applications as diagnostic biomarkers and therapeutic agents. First, kidney tissues from two different AKI mouse models, namely, AKI induced by the administration of lipopolysaccharide (LPS) causing sepsis (LPS-AKI mice) and AKI induced by renal ischemia–reperfusion injury (IRI-AKI mice), were exhaustively screened for their changes of miRNA expression compared with that of control mice by microarray analysis.

overall_design: A septic acute kidney injury model, with AKI induced by the intraperitoneal administration of lipopolysaccharide (LPS-AKI model), was created in accordance with a previously reported method . For the LPS model mice, LPS was injected into the peritoneal cavity as a body weight-based dose of 10 μg/g (Sigma-Aldrich, St. Louis, MO). The kidneys were collected 24 h later. A blood sample was obtained from the vena cava from each animal. The sham model of LPS was injected with the same dose of normal saline.


title: Comparative analyses of gibbon centromeres reveal dynamic species-specific shifts in repeat composition

relation:
SuperSeries of: GSE161191
SuperSeries of: GSE161308

platform_organism:
Symphalangus syndactylus
Nomascus leucogenys
Hylobates moloch
Hoolock leuconedys


title: A dataset of sequential DNA methylation profiles (2 timepoints) of 10 patients with chronic lymphocytic leukemia

status: Public on Mar 15 2021

city: Ulm

first: Deyan

middle: Yordanov

last: Yosifov

address: Albert-Einstein-Allee 23

department: Internal Medicine III

country: Germany

institute: University Hospital Ulm

summary: Clonal and subclonal evolution is involved in the progression of chronic lymphocytic leukemia (CLL). Evolution can work to select not only genetic mutations, but also epigenetic states. Here we performed a long-term longitudinal DNA methylation profiling study of CLL patients to look for associations of epigenetic evolution to different disease courses. In line with the genetic data, large-scale methylation evolution was not present in any of the evaluated long-term untreated (n = 3) and relapsed (n = 2) patients displaying clonal changes of linear type while 3 of the 5 examined refractory patients featured profound changes in DNA methylation.

overall_design: 20 paired samples of CLL patients (10 patients x 2 timepoints) were analyzed by Illumina Infinium HumanMethylation450 BeadChips. Three patients were long-term untreated at both timepoints, 2 relapsed between the timepoints and 5 developed/maintained refractory disease. Time between consecutive samples ranged from 20 to 108 months.

first: Eugen

last: Tausch

first: Daniel

last: Mertens


title: Human nasal epithelial and immune cell responses to SARS-CoV-2 versus influenza A virus

status: Public on Sep 29 2021

city: Worcester

first: Alan

middle: G

last: Derr

state: Massachusetts

address: 55 Lake Ave North

department: Program in Bioinformatics and Integrative Biology

institute: University of Massachusetts Medical School

summary: We performed single-cell RNA sequencing (scRNA-Seq) on nasal wash cells freshly collected from adults with COVID-19, influenza A, or no disease (healthy). Major cell types and subtypes were defined using cluster analysis and classic transcriptional markers.

overall_design: Seq-Well single-cell RNA-Seq analysis of cells taken from nasal wash samples from healthy donors and patients diagnosed with either COVID-19 or influenza A

first: Jennifer

middle: P

first: Kevin

last: Gao

first: Kerstin

last: Nundel

first: Ann

last: Marshak-Rothstein

first: Robert

middle: W

last: Finberg


title: Human MSI colon cancer

status: Public on Mar 03 2021

city: Nashville

first: Ken

last: Lau

state: TN

address: 2215 Garland Ave. MRBIV10475

department: Cell and Developmental Biology

institute: Vanderbilt University

summary: CRC with adjacent normal

overall_design: single-cell RNA-seq of single fraction of cancer tissue and adjacent normal

last: Simmons


title: Human MSI colon cancer study


title: Impact of in vivo acute and chronic interleukin-1 beta treatment on hematopoietic stem cell gene expression

status: Public on Apr 09 2021

city: AURORA

first: Etienne

last: Danis

state: CO

department: Cancer Center

institute: University of Colorado, Denver - Anschutz Medical Campus

summary: This study identifies molecular changes in hematopoietic stem cells harvested from wild-type C57BL/6 mice following acute or chronic IL-1 exposure in vivo.

overall_design: RNA-sequencing analysis of pooled mouse SLAM cells (HSC enriched fraction, defined here as LSK/Flk2-/CD48-/CD150+). Each datafile represents a biological replicate derived from SLAM cells sorted from pools of 3-5 mice.

first: Giovanny

last: Hernandez

first: Eric

middle: M

last: Pietras


title: CPEB3-dowregulated Nr3c1 mRNA translation confers resilience to developing posttraumatic stress disorder-like behavior in fear-conditioned mice

status: Public on Apr 26 2021

city: Taipei

first: Yi-Shuian

last: Huang

address: 128 Sec. 2, Academia Rd. Nankang

institute: Institute of Biomedical Sciences, Academia Sinica

summary: Susceptibility or resilience to posttraumatic stress disorder (PTSD) depends on one’s ability to appropriately adjust synaptic plasticity for coping with the traumatic experience. Activity-regulated mRNA translation synthesizes plasticity-related proteins to support long-term synaptic changes and memory. Hence, cytoplasmic polyadenylation element-binding protein 3-knockout (CPEB3-KO) mice, showing dysregulated translation-associated synaptic rigidity, may be susceptible to PTSD-like behavior. Here, using a context-dependent auditory fear conditioning and extinction paradigm, we found that CPEB3-KO mice exhibited traumatic intensity-dependent PTSD-like fear memory. A genome-wide screen of CPEB3-bound transcripts revealed that Nr3c1, encoding glucocorticoid receptor (GR), was translationally suppressed by CPEB3. Thus, CPEB3-KO neurons with elevated GR expression exhibited increased corticosterone-induced calcium influx and decreased mRNA and protein levels of brain-derived neurotrophic factor (Bdnf). Moreover, the reduced expression of BDNF was associated with increased GR level during fear extinction in CPEB3-KO hippocampi. Intracerebroventricular delivery of BDNF before extinction training mitigated spontaneous fear intrusion in CPEB3-KO mice during extinction recall. Analysis of two GEO datasets revealed decreased transcriptomic expression of CPEB3 but not NR3C1 in peripheral blood mononuclear cells of humans with PTSD. Collectively, this study reveals that CPEB3, as a potential PTSD-risk gene, downregulates Nr3c1 translation to maintain proper GR-BDNF signaling for fear extinction.

overall_design: RNAs precipitated by CPEB3 IgG and control IgG

first: Wen-Hsin

last: Lu

first: Hsiu-Chen

last: Lin


title: Insights into Epithelial Cell Senescence from Transcriptome and Secretome Analysis of Human Oral Keratinocytes

status: Public on Mar 18 2021

city: San Diego

first: April

middle: Elizabeth

last: Williams

state: California

address: 10010 N Torrey Pines Rd

department: IGC

institute: Salk Institute for Biological Studies


title: Interpreting type 1 diabetes risk with genetics and single cell epigenomics

city: La Jolla

first: Kyle

last: Gaulton

address: 9500 Gilman Drive

department: Pediatrics

institute: University of California, San Diego

summary: Genetic risk variants identified in genome-wide association studies (GWAS) of complex disease are primarily non-coding, and translating risk variants into mechanistic insight requires detailed gene regulatory maps in disease-relevant cell types. Here, we combined a GWAS of type 1 diabetes (T1D) in 520,580 samples with candidate cis-regulatory elements (cCREs) in pancreas and peripheral blood mononuclear cell types defined using single nucleus ATAC-seq (snATAC-seq) of 131,554 nuclei. T1D risk variants were enriched in cCREs active in T cells and additional cell types, including acinar and ductal cells of the exocrine pancreas. Risk variants at multiple T1D signals overlapped exocrine-specific cCREs linked to genes with exocrine-specific expression. At the CFTR locus, T1D risk variant rs7795896 mapped in a ductal-specific cCRE which regulated CFTR, and the risk allele reduced transcription factor binding, enhancer activity and CFTR expression in ductal cells. These findings support a role for the exocrine pancreas in T1D pathogenesis and highlight the power of large-scale GWAS and single cell epigenomics for understanding the cellular origins of complex disease.

overall_design: Single nucleus ATAC-seq of purified pancreatic islets, whole pancreas, and peripheral mononuclear blood cells from human donors.

first: Joshua

last: Chiou


title: Microarray-based clustering analysis of miRNAs altered in IRI-AKI mouse kidney

first: Akinori

last: Aomatsu

overall_design: A model with ischemia–reperfusion injury-induced acute kidney injury (IRI-AKI) was created in accordance with a previously reported method. This IRI model was generated using male C57BL/6 mice (9 weeks old; 20–25 g) housed in a room with controlled temperature, humidity, and a 12 h light–dark cycle. The mice were anesthetized using isoflurane as follows: anesthesia induction concentration 3.0%–5.0%, maintenance concentration 2.0%–3.0%, and concentration during clamping 1.0%–1.5%. In the IRI model described here, single midline abdominal surgery was used both to perform right nephrectomy and to induce ischemia–reperfusion of the left kidney. Successful ischemia could be visually confirmed by gradual uniform darkening of the kidney. This IRI model had a 25- or 45-min clamping time, with the kidneys being collected 12 or 24 h later. A blood sample was obtained from the vena cava of each animal. For the sham model of IRI, only a midline incision was made.

first: Yoshiyuki

last: Morishita


title: Epigenetic blueprint identifies poor outcome and hypomethylating agent-responsive T-ALL subgroup

status: Public on Mar 01 2021

city: Paris

first: Vahid

last: Asnafi

address: 149 rue de Sèvres

country: France

institute: Universite de Paris (Descartes)

summary: Adult T-cell acute lymphoblastic leukemia (T-ALL) is an aggressive hematological malignancy still associated with poor outcome calling for new therapeutic options. DNA methylation landscapes of adult T-ALL remain largely uncharacterized. Here, we systematically analyzed the DNA methylation profiles of normal thymic sorted T-cell subpopulations and 143 primary adult T-ALLs as part of French GRAALL 2003-2005 trial. Our results indicated that T-ALL is epigenetically distinct from normal T-cell subpopulations and consisted of five major subtypes (C1-C5) which were either associating with co-occurring DNMT3A/IDH2 mutations (C1), TAL1 deregulation (C2), TLX3 (C3), TLX1/in cis-HOXA9 (C4) or in trans-HOXA9 (C5) overexpression. Importantly, our data identified an unexpected subset of hypermethylated T-ALL associated with poor outcome and primary therapeutic response. Using mouse xenografts, we showed that hypermethylated T-ALL samples displayed therapeutic response to the DNA hypomethylating agent, 5-Azacitidine, which significantly delayed tumor progression suggesting epigenetic-based therapies as a novel treatment option in hypermethylated T-ALL.

overall_design: To assess the heterogenity among adult T-ALLs, DNA methylation landscape of 143 primary adult T-ALL samples along with 6 distinct sorted normal thymic cell types were analysed using Illumina Methylation EPIC arrays.

first: Aurore

last: Touzart

first: Anand

last: Mayakonda

first: Christoph

last: Plass


title: Expression data from Plasmodium falciparum

status: Public on Nov 30 2020

city: Yokohama

first: Hiroko

last: Asahi

address: 1-7-22, Suehiro-cho, Tsurumi-ku

institute: RIKEN Center for Biosystems Dynamics Research

summary:
Artemisinin and its derivatives exert the potent, antimalarial action, although the mechanisms by which these drugs inhibit the growth of mararia parasites is not fully understood.
We used microarrays to detail the global gene expression change in early erythrocytic P. falciparum, and identified molecules that may contribute to the activity of dihydroartemisinin.

platform_organism:
Plasmodium falciparum
Anopheles gambiae

overall_design: To identify genes differentially expressed in P. falciparum exposed to dihydroartemisinin other drugs 7-benzylidenealtrexone and rimonaband were also analyzed.

first: Akira

last: Wada


title: Transcriptional effects of MAF- and MAFB-siRNAs on M-CSF-derived macrophages

status: Public on Dec 09 2020

city: Madrid

first: Miguel

last: Vega

address: Ramiro de Maeztu 9

country: Spain

institute: CIB (CSIC)

summary: Analysis of the role of transcriptions factors MAF and MAFB on the phenotypic profles of human M-CSF-derived macrophages. Methods: Human Peripheral Blood Mononuclear Cells (PBMC) were isolated from buffy coats from donors over a Lymphoprep gradient according to standard procedures. Monocytes were purified from PBMC by magnetic cell sorting using anti-CD14 microbeads (>95% CD14+ cells). Monocytes (0.5 x 106 cells/ml, >95% CD14+ cells) were cultured  in RPMI 1640 supplemented with 10% fetal bovine serum (FBS) for 7 days in the presence of 10 ng/ml M-CSF to generate M-CSF-polarized macrophages (M-MØ). Macrophages were differentiated from peripheral blood monocytes from 3 healthy donors with M-CSF (M-MØ) to generate anti-inflammatory M-MØ. Macrophages were transfected with either Control siRNA or MAFB-specific siRNA or MAF-specific siRNA for 24h and global gene expression was analysed by RNA-Seq.

overall_design: mRNA profiles of human M-CSF-derived macrophages treated with siRNA-MAF or siRNA-MAFB

first: Angeles

last: Dominguez-Soto

first: Angel

last: Corbí


title: RNA-seq of mouse primary keratinocytes treated with recombinant IL-33

status: Public on Feb 22 2021

city: Wuhan

first: Fanfan

last: Zeng

state: Hubei

address: No.13, Hangkong Road

department: Department of Immunology

institute: Tongji Medical College, Huazhong University of Science and Technology

summary: Mouse primary keratinocytes were treated with recombinant IL-33 to elucidate the effect of IL-33 signaling on keratinocytes

overall_design: Primary keratinocytes from neonatal mice were cultured in vitro for 2 days, then treated   with or without recombinant IL-33 for 12 h. Total RNA were then extracted and subjected to RNA-seq analysis

first: Zeng

last: Fanfan

first: Zheng

last: Fang


title: Single-cell RNA-seq of total cells from testes of adult WT and miR-202-/- mice

status: Public on May 21 2021

first: Chunsheng

last: Han

address: 1-5 Beichen West Road, Chaoyang District

department: Institute of Zoology

institute: Chinese Academy of Sciences

summary: We report to investigate the changes in cellular composition and gene expression upon miR-202 KO. One testis from each of three adult WT mice and three adult KO mice was collected, and the KO and WT testes were pooled respectively for subsequent analysis. A total of 15,310 WT and 12,935 KO cells passed standard quality control and were used for subsequent analysis.

overall_design: Examination of changes in cellular composition and gene expression in adult wildtype and miR-202-/- mouse testes by single-cell RNA-seq.

first: Jian

last: Chen

first: Chenxu

last: Gao

first: Xinwen

last: Lin


title: Transcriptional effects of activation stimuli on M-CSF-derived macrophages

summary:
Analysis of the effect of various activation stimuli on the transcriptional signature of human M-CSF-dependent monocyte-derived macrophages.
Methods: Human Peripheral Blood Mononuclear Cells (PBMC) were isolated from buffy coats from donors over a Lymphoprep gradient according to standard procedures. Monocytes were purified from PBMC by magnetic cell sorting using anti-CD14 microbeads (>95% CD14+ cells). Monocytes from three independent donors (0.5 x 106 cells/ml, >95% CD14+ cells) were cultured  in RPMI 1640 supplemented with 10% fetal bovine serum (FBS) at 37°C in a humidified atmosphere with 5% CO2 and 21% O2 for 7 days in the presence of 10 ng/ml M-CSF, with cytokine addition every two days. After 7 days, macrophages were either untreated (CNT) or treated with 10 ng/ml E. coli 055:B5 lipopolysaccharide (LPS), 100 ng/ml of the TLR7 agonist CL264 (CL), BSA or 200 mM palmitate (PAL) for 0.5h, 2h, 4h or 12h.

overall_design: mRNA profiles of human M-CSF-derived macrophages exposed to different activation stimuli at various time points

first: Victor

last: Cuevas

first: Marta

last: Riera Borrull


title: A methylation signature at diagnosis in patients with high-risk Myelodysplastic Syndromes and secondary Acute Myeloid Leukemia predicts azacitidine response but not relapse

status: Public on Jan 27 2021

city: Badalona

first: Roberto

last: Malinverni

state: Barcelona

address: Josep Carreras Building, Ctra de Can Ruti,

institute: Josep Carreras Leukaemia Research Institute

summary: Epigenetic therapy, using hypomethylating agents (HMA), is known to be effective in the treatment of high-risk myelodysplastic syndromes (MDS) and acute myeloid leukemia (AML) patients who are not suitable for intensive chemotherapy or allogeneic stem cell transplantation. However, response rates to HMA are low and there is an unmet need in finding prognostic and predictive biomarkers of treatment response. We performed global methylation analysis of 75 patients with high risk MDS and secondary AML (sAML) who were included in CETLAM MDS-09 protocol, in which patients received HMA or intensive treatment according to age, comorbidities and cytogenetics. At diagnosis, no global methylation pattern allowed us to differentiate patients according to the cytological subtype, cytogenetics or treatment response. But we found a methylation signature defined by 200 probes, which allowed us to distinguish between responding and non-responding patients to azacitidine (AZA) treatment. Studying follow-up samples, we have confirmed that AZA decreases global DNA methylation, but in our cohort the degree of methylation decrease did not correlate with the type of response. The methylation signature detected at diagnosis was not useful in treated samples to determine a methylation pattern predictive of progression or relapse. In conclusion, altered DNA methylation patterns at diagnosis, in a subset of determined CpGs, may serve as biomarker for predicting AZA response.

overall_design:
Bisulphite converted DNA from the 202 samples were hybridised to the Illumina Infinium 450k Human Methylation Beadchip

Definitions:

DX = at Diagnosis
CTR = Control (Healthy Donor)
POST TPH = Post Transplant

first: M

last: Cabezón

first: R

first: J

last: Bargay

first: B

last: Xicoy

first: S

last: Marcé

first: A

last: Garrido

last: Tormo

first: L

last: Arenillas

last: Borras

first: MJ

last: Jiménez

last: Hoyos

first: D

last: Valcárcel

last: Escoda

first: F

last: Vall

last: Garcia

first: X

last: Font

first: E

last: Rámila

last: Feliu

last: Buschbeck

last: Zamora


title: The order and stochasticity in the Drosophila genome folding revealed by single-nucleus Hi-C

status: Public on Oct 22 2020

city: Cambridge

first: Aleksandra

last: Galitsyna

address: 77 Massachusetts Avenue

department: IMES

institute: Massachusetts Institute of Technology

summary:
We generated and analyzed single-cell Hi-C libraries from cultrured Drosophila cells. The data obtained allowed us to explore cell-to-cell variability in TAD profiles and inter-TAD interactions showing that strong TAD boundaries are determined by high levels of active chromatin. DPD polymer simulations were utilized to reconstruct 3D structures of haploid X chromosomes. These structures showed marked cell-to-cell variabilty in the overall shape of the chromosome territory and relatively conserved chromatin chain path inside TADs.
DPD polymer simulations were utilized to reconstruct 3D structures of haploid X chromosomes.
These structures showed marked cell-to-cell variabilty in the overall shape of the chromosome territory and relatively conserved chromatin chain path inside TADs.

overall_design: We generated bulk and single-cell Hi-C libraries for Drosophila melanogaster for 88 ML-DmBG3-c2 cells

first: Vlada

last: Zakharova


title: Regional specificity of gene expression in dopaminoceptive neurons

status: Public on Sep 09 2020

city: Great Chesterford

first: Nicolas

last: Gambardella

state: Essex

address: Lewis House, Great Chesterford Court

country: United Kingdom

institute: aSciStance Ltd

summary: Cell types are defined by their patterns of gene expression. Forebrain dopaminoceptive neurons play a key role in movement, action selection, and motivation, and are dysregulated in addiction, Parkinson’s disease, and many other medical conditions. To investigate similarities and differences between the main types of dopamine-sensitive neurons we compared the full ensemble of translated mRNAs in neurons expressing D1 or D2 dopamine receptors in the dorsal striatum and nucleus accumbens, and in D1 receptor-expressing neurons of the prefrontal cortex. We identified marked differences in mRNA profiles between these populations and distinct sets of genes that establish D1, D2, dorsal and ventral identities. Network analysis revealed transcription factors with known or putative role in these differences. Prostaglandin E2 appeared as a candidate upstream regulator of dorsal striatum and pharmacological experiments supported this hypothesis. Our study provides a powerful resource for the molecular studies of the striatum and new clues about its regional gene expression pattern.

overall_design: BAC (bacterial artificial chromosome) transgenic mice were generated, expressing eGFP fused to the N-terminus of the large subunit ribosomal protein L10a under the control of dopamine D1a or D2 receptor promoter. Brain tissue was punched from thick slices of prefrontal cortex, dorsal and ventral striatum. Each sample was generated by pooling together tissues from 3 mice, with at least one male and one female. 14 to 19 samples were created for each of the region/receptor combination.

first: Enrica

last: Montalban

first: Lieng

last: Taing

last: Le Novère

first: Jean-Pierre

last: Roussarie

first: Jean-Antoine

last: Girault


title: Genome-wide integration of microRNA and the transcriptome during human alveolar epithelial cell transdifferentiation identifies SGK1 as novel target of miR- 424/503 [RNA-Seq]

status: Public on Jul 01 2020

city: Duarte

first: Crystal

middle: N

last: Marconett

email: cmarcone@usc.edu, cmarconett@coh.org

address: 1500 E Duarte Rd

department: Integrative Translational Sciences

institute: City of Hope

summary: The alveolar epithelium is comprised of two cell types, alveolar type 1 (AT1) and type 2 (AT2) cells, the latter being capable of self-renewal and transdifferentiation into AT1 fate to establish alveolar function. Micro-RNAs (miRNAs) re critical regulators of developmental pathways, including branching morphogenesis. To determine if miRNAs also play a crucial role in establishment/maintenance of cellular identity within the alveolar epithelium, we performed genome-wide analysis of miRNAs alongside transcriptomic alterations during transdifferentiation of human AT2 (hAT2) into AT1-like cells in vitro . Our results indicated that miRNAs are tightly correlated to known gene expression pattern changes during AEC differentiation. We were able to define three phases of miRNA expression during the trans differentiation process, “early”, “late” and “consistently” changed, which further sub-classified as up- or downregulated. miRNAs with altered expression at all time points during AT1-like differentiation were the largest subgroup, suggesting the need for consistent regulation of signaling pathways to mediate transdifferentiation .  Target prediction analysis and integration with previously published gene expression data identified glucocorticoid signaling as the top pathway regulated by miRNAs. Serum/glucocorticoid kinase 1 (SGK1) emerged as a central regulatory factor with temporally-correlated loss of expression and gain of hsa-miR-424 and hsa-miR-503 expression. Functional validation demonstrated specific targeting of these miRNAs to the 3’UTR of SGK1. Taken together, our data show the time-related contribution of miRNAs to the alveolar transdifferentiation process and suggest the need for inhibition of glucocorticoid pathway signaling to achieve the AT1-like cell phenotype in vitro. The miRNA-mRNA interactions identified herein may help to establish AT2 to AT1 cell differentiation in vivo.

overall_design: Total RNA was isolated from primary alveolar epithelial cells taken from human remnant transplant lung and purified as described previously (Marconett et al., 2013).

first: Alessandra

last: Castaldi

first: Masafumie

last: Horie

first: Megan

middle: E

last: Rieger

first: Mickael

last: Dubourd

first: Mitsuhiro

last: Sunohara

first: Kusum

last: Pandit

first: Naftali

last: Kaminski

first: Beiyun

last: Zhou

first: Ite

last: Offringa

first: Zea

last: Borok


title: Genome-wide integration of microRNA and the transcriptome during human alveolar epithelial cell transdifferentiation identifies SGK1 as novel target of miR- 424/503

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

overall_design: Refer to individual Series


title: Human adjacent normal colon downsampled related to GSE158636

first: Ken

last: Lau

summary: Adjacent normal to crc

overall_design: single fraction of  normal

first: Alan

last: Simmons

first: Bob

last: Chen


title: Breast Cancer Stem Cells Regulated Phenotypic Equilibrium Drives Tamoxifen Resistance

status: Public on Aug 20 2020

city: Heifei

first: Mingming

last: Wu

state: Anhui

address: inZhai Road Baohe District

institute: University of Science and Technology of China

summary: Breast cancers consist of heterogeneous cellular subpopulations that differ in molecular properties and functional attributes. Cancer cells display phenotypic equilibrium between the stem-like and differentiated states during neoplastic homeostasis. The mechanism and functional implications of the subpopulation equilibrium in cancer progression remain largely unknown. Herein, we report that BCSCs secretome conditioned bulk tumor cells developed resistance to anti-endocrine therapy both in vitro and in vivo. IL8 was significantly enriched in BCSCs secretome and blockade of IL8 signaling reversed the tamoxifen resistance induced by BCSCs. The enhanced Wnt/β-catenin signal simultaneously increased the secretion of IL8 in BCSCs, which leads to the seemingly contradictory behaviors of bulk tumor cells. Collectively, our study characterizes the paracrine effects and identifies key molecules secreted by BCSCs, which may become therapeutic vulnerabilities to overcome tamoxifen resistance.

overall_design: The BCSCs isolated from flow cytometry sorting or mammospheres culturing were seeded with the regular medium in monolayer culture for 48 hours. The medium from parallelly cultured parental cells was used as the control medium. The conditioned medium was centrifuged at 4,000 g for 3 minutes and filtered with a 0.22 μm filter unit (Millipore) to deplete any cell debris.the BCSCs isolated from flow cytometry sorting or mammospheres culturing were seeded with the regular medium in monolayer culture for 48 hours. The medium from parallelly cultured parental cells was used as the control medium. The conditioned medium was centrifuged at 4,000 g for 3 minutes and filtered with a 0.22 μm filter unit (Millipore) to deplete any cell debris. The MCF-7 cells were cultured with the CM derived from BCSCs or parental cells for 48 hours, and the RNA was isolated and sequenced.

first: Xiao

last: Zhang

first: Tao

last: Zhu


title: Genome-wide integration of microRNA and the transcriptome during human alveolar epithelial cell transdifferentiation identifies SGK1 as novel target of miR- 424/503 [miRNA-array]

first: Crystal

last: Marconett

state: CA

overall_design: human alveolar epithelial type 2 (hAT2) cells were isolated from remnant transplant lungs and differentiated into alveolar type 1 (AT1-lik cells over the course of 8 days in culture. miRNA was isolated and profiled on the Agilent miRNA and normalized using the AgiMicroRNA package in R.


title: MC-LR induced ncRNA and mRNAs changes in mouse testis

status: Public on Aug 31 2020

city: Nanjing

first: Xiannan

last: Meng

address: Hankou Road 22

institute: Nanjing University

summary: We have builded a network including mRNA, miRNA, piRNA, lncRNA and circRNA after exposure to MC-LR for 6 months in testicular tissue. And we find MC-LR could induce testicular toxicity and apoptosis by disturbing the netwok.

overall_design: Examination of 2 different doses of MC-LR exposure to testis

first: Ling


title: Mutations in homologous recombination genes BRCA1 and BRCA2 differentially affect the tumor microenvironment and response to checkpoint blockade immunotherapy

status: Public on Aug 27 2020

city: Cleveland

first: Vladimir

last: Makarov

state: OH

address: 9500 Euclid Ave

department: LRI

institute: Cleveland Clinic

summary: We report differential effects of mutations in genes of the homologous recombination (HR) pathway on response after ICB administration in mouse and human tumors, and show that truncating mutations in BRCA2 are associated with superior response to ICB compared to BRCA1-deficient tumors.  Immunogenomic analyses demonstrated that mutations in BRCA1 and BRCA2 differentially modulate the tumor-immune microenvironment, with gene expression programs related to both adaptive and innate immune pathways enriched in BRCA2-deficient tumors.  Single-cell RNA sequencing further revealed distinct T cell, NK, macrophage, and dendritic cell populations enriched in BRCA2 mutant tumors relative to BRCA1-deficient tumors.

overall_design: Bulk RNA-sequencing from immunotherapy-naïve and immunotherapy-treated mouse 4T1 parental, Brca1 mutant, and Brca2 mutant tumors.  Single cell RNA-sequencing from immunotherapy-naïve 4T1 parental, Brca1 mutant, and Brca2 mutant tumors

first: Nadeem

last: Riaz

first: Timothy

last: Chan

first: Robert

last: Samstein

first: Chirag

last: Krishna


title: Aging of preleukemic thymocytes drives CpG island hypermethylation in T-cell acute lymphoblastic leukemia

status: Public on Sep 24 2020

city: South San Francisco

first: Juliette

last: Roels

address: 1 DNA Way

institute: Genentech

type: Methylation profiling by high throughput sequencing

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: Circuits between infected macrophages and T cells in SARS-CoV-2 pneumonia

status: Public on Aug 05 2020

city: Chicago

first: Alexander

middle: V

last: Misharin

state: Illinois

address: 303 E Superior

institute: Northwestern University

summary: Some patients infected with Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) develop severe pneumonia and the acute respiratory distress syndrome (ARDS). Distinct clinical features in these patients have led to speculation that the immune response to virus in the SARS-CoV-2-infected alveolus differs from other types of pneumonia. We collected bronchoalveolar lavage fluid samples from 88 patients with SARS-CoV-2-induced respiratory failure and 211 patients with known or suspected pneumonia from other pathogens and subjected them to flow cytometry and bulk transcriptomic profiling. We performed single-cell RNA-seq on 10 bronchoalveolar lavage fluid samples collected from patients with severe COVID-19 within 48 hours of intubation. In the majority of patients with SARS-CoV-2 infection, the alveolar space was persistently enriched in T cells and monocytes. Bulk and single-cell transcriptomic profiling suggested that SARS-CoV-2 infects alveolar macrophages, which in turn respond by producing T cell chemoattractants. These T cells produce interferon-gamma to induce inflammatory cytokine release from alveolar macrophages and further promote T cell activation. Collectively, our results suggest that SARS-CoV-2 causes a slowly-unfolding, spatially-limited alveolitis in which alveolar macrophages harboring SARS-CoV-2 and T cells form a positive feedback loop that drives persistent alveolar inflammation.

overall_design:
Bronchoalveolar lavage (BAL) fluid from 12 patients (10 COVID-19 positive, 1 COVID-19 negative with bacterial pneumonia secondary to infection with Pseudomonas aeruginosa and Acinetobacter baumannii,  1 COVID-19 negative, intubated for airway protection to facilitate endoscopy for severe gastrointestinal bleeding without pneumonia) was obtained within 48 hours of intubation at Northwestern Memorial ICU. BAL fluid was flow-sorted for macrophages and T cells and single-cell libraries were prepared with 10x 5' gene expression kit. Libraries were sequenced on Illumina NovaSeq 6000. Gene expression matrices were generated with 10x cellranger v3.1.0 software. Matrices were combined together and processed with scanpy to create an integrated object with COVID-19-only samples (main.h5ad; 10 COVID-19-positive patients) and a supplemental object with all samples (supplement.h5ad; 10 COVID-19-positive patients and 2 COVID-19-negative patients).
[contributor]  The NU SCRIPT Study Investigators

Please note that the following files have been corrected on July 17, 2023:
main-metadata.csv.gz
main.h5ad.gz
supplement-metadata.csv.gz
supplement.h5ad.gz

***Due to patient privacy concerns, the submitter declares that patient data will be submitted to dbGaP.***

first: Rogan

last: Grant

first: Luisa

last: Morales-Nebreda

first: Nikolay

last: Markov

first: Suchitra

last: Swaminathan

first: Melissa

last: Querrey

first: Estefany

middle: R

last: Guzman

first: Darryl

last: Abbott

first: Helen

last: Donnelly

first: Alvaro

last: Donayre

first: Isaac

last: Goldberg

first: Zasu

last: Klug

first: Nicole

last: Borkowski

first: Ziyan

last: Lu

first: Hermon

last: Kihshen

first: Yuliya

last: Politanska

first: Lango

last: Sichizya

first: Mengjia

last: Kang

first: Ali

last: Shilatifard

first: Chao

last: Qi

first: Jon

last: Lomasney

first: A

middle: C

last: Argento

first: Jacqueline

last: Kruser

first: Elizabeth

last: Malsin

first: Chiagozie

middle: O

last: Pickens

first: Sean

middle: B

last: Smith

first: James

last: Walter

first: Anna

last: Pawlowski

first: Daniel

last: Schneider

first: Prasanth

last: Nannapaneni

first: Hiam

last: Abdala-Valencia

first: Ankit

last: Bharat

first: Cara

last: Gottardi

first: G

last: Budinger

first: Benjamin

last: Singer

first: Richard


title: Comparison of C. glutamicum growing with GABA as carbon source in the presence or absence of (NH4)2SO4.

status: Public on Mar 25 2020

city: Juelich

first: Tino

last: Polen

state: NRW

address: Wilhelm-Johnen-Str 1

department: IBG-1: Biotechnology

institute: Forschungszentrum Jülich GmbH

summary: γ-Aminobutyric acid (GABA) is a non-proteinogenic amino acid and widespread in nature from microorganisms to plants and animals. DNA microarray analysis revealed that the transcription of gabTDP was strongly increased in C. glutamicum wild type grown with GABA and urea compared to the same strain cultivated with glucose and urea. Remarkably, the presence of ammonia partially inhibited growth on GABA, and the reasons for it were also investigated in this study.

platform_organism: Bacillus subtilis subsp. subtilis str. 168

overall_design: The aim was to identify genes differentially expressed in Corynebacterium glutamicum ATCC13032 cultivated in CGXII minimal medium with GABA as carbon source either with or without ammonium because addition of ammonium caused a growth defect under these conditions. C. glutamicum ATCC 13032 was cultivated inCGXII medium with GABA as carbon source and either (NH4)2SO4 or K2SO4. The cells were harvested in the exponential growth phase at an OD600 of 5.

first: Lingfeng

last: Zhu


title: Methylation profiles of PMF with and without progression to myelofibrosis

status: Public on Feb 08 2021

city: Hannover

first: Helge

last: Stark

address: Carl-Neuberg-Straße 1

department: Institute of Pathology

institute: Medical School Hannover

summary: Patients with prefibrotic PMF have a heterogeneous risk for progression to myelofibrosis. This projects evaluates the potential of comprehensive DNA methylation profiling for predicting fibrotic progress.

overall_design: DNA methylation patterns were studied in a cohort PMF patients with and without progress to myelofibrosis

first: Ulrich

last: Lehmann

first: Stephan

last: Bartels

first: Hans

last: Kreipe


title: Movement of Arabidopsis thaliana inverted repeat small RNA between leaves vascular and epidermis tissues

status: Public on Apr 06 2020

city: Zürich

first: Alexis

last: Sarazin

address: Universitätstrasse 2

country: Switzerland

institute: ETH

type: Non-coding RNA profiling by high throughput sequencing

summary: We aimed at characterizing the identity of the silencing signal i.e. siRNA or longer dsRNA precursor thereof. We used transgenic dsRNA, endogenous dsRNA or virus infection as sources of siRNAs combined to sophisticated immunoprecipitation-based procedures coupled to deep-sequencing. We found that siRNAs populations are highly similar between incipient and recipient cells in the three systems. Additionally, a significant depletion of 5’U and 5’A content in the recipient cells suggested Argonaute-loading dependent depletion of these siRNAs during their movement over multiple cell layers. Using the PAZ-domain mutants ago1-18 and ago1-42 confirmed that the observed depletion of mobile siRNAs is the result of RISC loading. The results advocate movement of individual siRNA duplexes as opposed to their precursors and that loading into Argonaut proteins renders those small RNAs cell-autonomous.

overall_design: small RNA from vasculature and epidermis tissus from Arabidopsis thaliana Col0 leaves (2 replicates for each) . RNA-seq from Arabidopsis thaliana epidermis in Col0 WT plants or ir71 mutant (2 replicates for each).

first: Emanuel

last: Devers

first: Christopher

last: Brosnan

first: Daniele

last: Albertini

first: Andrea

last: Amsler

first: Florian

last: Brioudes

first: Pauline

last: Jullien

first: Peiqi

last: Lim

first: Gregory

last: Schott

first: Olivier

last: Voinnet


title: Epigenome analysis of relapse and relapse-free T-cell lymphoblastic lymphoma

status: Public on May 04 2020

city: Guangzhou

first: Xiao-Peng

last: Tian

address: 651 Dong Feng RD East

department: Department of Medical Oncology

institute: Sun Yat-sen University Cancer Center

summary: Genome-wide DNA methylation profiling of relapse and relapse-free T-cell lymphoblastic lymphoma (T-LBL) samples. The Illumina 850k Human DNA methylation EPIC BeadChip was used to obtain DNA methylation profiles across approximately 850,000 CpGs in T-LBL samples. Samples included 21 relapse T-LBL samples, and 28 relapse-free T-LBL samples.

overall_design: Bisulphite-converted DNA from the 49 samples were hybridised to the Illumina 850k Human Methylation EPIC BeadChip.

first: Xiao

first: Qing

middle: Q

last: Cai


title: Comparison of Corynebacterium glutamicum

status: Public on Mar 24 2020

first: Tino

last: Polen


title: Comparison of Corynebacterium glutamicum with GABA or glucose as carbon source

overall_design: The aim was to identify genes differentially expressed in Corynebacterium glutamicum during growth with glucose or with GABA as carbon source. For this purpose, C. glutamicum ATCC13032 was cultivated in CGXII medium with K2SO4 (20 mM) instead of (NH4)2SO4, with urea (151mM) and with either  glucose  or GABA as carbon source (250 mM carbon each ). The cells were harvested in the exponential growth phase at an OD600 of 5.

first: Lingfeng

last: Zhu


title: Analysis of methylation In childhood acute myeloid leukemia (AML)

status: Public on Jan 01 2020

city: Little Rock

first: Jason

middle: Eli

last: Farrar

state: AR

address: 1 Children's Way, #512-10

department: Pediatrics/Hematology-Oncology

institute: University of Arkansas for Medical Sciences

summary: The Illumina Human Methylation EPIC array was used to assess methylation status at initial diagnosis in bone marrow or peripheral blood specimens from children with acute myeloid leukemia.

overall_design: Disease state design

first: Timothy

middle: J

last: Triche


title: AP-1 imprints a reversible transcriptional programme of senescent cells

status: Public on Jan 28 2020

city: Paris Cedex 15

first: Oliver

last: Bischof

address: 28 rue du Docteur Roux

department: Cell Biology & Infection

institute: Institut Pasteur

summary: Senescent cells affect many physiological and pathophysiological processes. While select genetic and epigenetic elements for senescence induction have been identified, the dynamics, epigenetic mechanisms and regulatory networks defining senescence competence, induction and maintenance remain poorly understood, precluding the deliberate therapeutic targeting of senescence for health benefits. Here, we examined the possibility that the epigenetic state of enhancers determines senescent cell fate. We explored this by generating time-resolved transcriptomes and epigenome profiles during oncogenic RAS-induced senescence and validating central findings in different cell biology and disease models of senescence. Through integrative analysis and functional validation, we reveal links between enhancer chromatin, transcription factor recruitment and senescence competence. We demonstrate that activator protein 1 (AP-1) ‘pioneers’ the senescence enhancer landscape and defines the organizational principles of the transcription factor network that drives the transcriptional programme of senescent cells. Together, our findings enabled us to manipulate the senescence phenotype with potential therapeutic implications.


title: RETRACTED: Decoding aging and maturation related transcriptome and methylome dynamics in mouse oocytes by single cell parellel sequencing technology

status: Public on Aug 01 2019

first: Thomas

last: Chan

address: Room623, Area 39, CUHK, Shatin

department: School of Biomedical Sciences

country: Hong Kong

institute: The Chinese University of Hong Kong

summary: The GSE119906 raw data have been removed due to retraction of the associated publication and at the request of the submitter.

overall_design: Retracted.

first: Yan

last: Qian

first: Qin

last: Cao

first: Jinyue

last: Liao

first: Alfred

last: Luk

first: Annie

last: Lee

first: Ashley

middle: H

last: Suen

first: Nelson

middle: L

last: Tang

first: Ling

last: Chi

first: Hoi

middle: S

last: Chung

first: Tak

middle: Y

last: Leung

first: Kevin

last: Yip

first: Wai-Yee

first: David

first: Tin

last: Li

first: Tin-Lap


title: AP-1 Imprints a Reversible Transcriptional Programme of Senescent Cells

status: Public on Jun 14 2019

first: Oliver

summary: Senescent cells affect many physiological and pathophysiological processes. While select genetic and epigenetic elements for senescence induction have been identified, the dynamics, epigenetic mechanisms and regulatory networks defining senescence competence, induction and maintenance remain poorly understood, precluding the deliberate therapeutic targeting of senescence for health benefits. Here, we examined the possibility that the epigenetic state of enhancers determines senescent cell fate. We explored this by generating time-resolved transcriptomes and epigenome profiles during oncogenic RAS-induced senescence and validating central findings in different cell biology and disease models of senescence. Through integrative analysis and functional validation, we reveal links between enhancer chromatin, transcription factor recruitment and senescence competence. We demonstrate that activator protein 1 (AP-1) 'pioneers' the senescence enhancer landscape and defines the organizational principles of the transcription factor network that drives the transcriptional programme of senescent cells. Together, our findings enabled us to manipulate the senescence phenotype with potential therapeutic implications.

overall_design: We performed time-series experiments on ER:RASv12-transduced WI38 fibroblasts treated with 4-hydroxytamoxifen (4OHT) for 144 hours to induce OIS. Small interfering RNAs (20 µM) targeting JUN, ETS1, and RELA as well as non-targeting controls were transfected into WI-38-ER:RASv12 either before the OIS induction (T0), or 72 h or 144 h after induction.

first: Ricardo

middle: I

last: Martínez Zamudio

first: Pierre-François

last: Roux

first: Gregory

last: Doré


title: Functional and Topographic Effects on DNA Methylation Across IDH1/2 Mutant Cancers

status: Public on Jan 15 2020

city: New York City

first: Matija

last: Snuderl

state: NY

address: 240 E 38th St

department: Pathology

summary:
Background: IDH1/2 mutations are present in cancer arising from various tissues; however, common and disease specific effects on DNA methylation across IDH mutant cancers remain unknown.
Results: We analyzed DNA methylation data from IDH1/2 mutant acute myeloid leukemia (AML), oligodendroglioma, astrocytoma, breast carcinoma, sinonasal undifferentiated carcinoma (SNUC) and cholangiocarcinoma. We show that only a small fraction of differentially methylated probes is disease specific and that hypermethylation affects predominantly gene bodies and enhancers while gene promoters in IDH1/2 mutant cancers remain profoundly unmethylated. Commonly hypomethylated enhancers were associated with tissue differentiation and cell fate determination. We also show that some chromosomes and chromosomal regions are more affected by IDH mutation. In particular we show that regions of dense heterochromatin on several chromosomes do not appear to be affected by IDH mutation induced hypermethylation.
Conclusions: We show that there are gene region and chromosome specific areas that are preferentially affected or spared by changes in DNA methylation across IDH mutant cancers. This suggests that while IDH mutation causes the same biochemical change in all cancers, the effect may vary in tissue specific fashion. Hypomethylation of enhancers associated with cell differentiation may mediate lack of differentiation in IDH1/2mutant cancers.

overall_design: Methylation data from isocitrate dehydrogenase (IDH)-mutated acute myeloid leukemia (AML, N=21) and cholangiocarcinoma (N=9) were obtained from The Cancer Genome Atlas (TCGA). DNA methylation data from IDH mutated breast carcinoma (N=5) with altered nuclear polarity and sinonasal undifferentiated carcinomas (N=8) were obtained from our previously published cohorts. In addition, DNA was extracted from the tumors of 20 patients with IDH mutated oligodendroglioma and 31 patients with IDH mutated astrocytoma who had been treated at the New York University Langone Medical Center (NYULMC). DNA was extracted from archival formalin-fixed paraffin-embedded (FFPE) tissue from tumor biopsies using automated Maxwell Promega system, and methylation profiling was performed at the NYU Department of Molecular Pathology using the Illumina Infinium Human Methylation 450 Bead-Chip (450 K array) or Illumina EPIC array according to the manufacturer’s instructions. Samples were not analyzed in replicates and there are no other samples aside from what are listed here.

first: Ramona

last: Bledea

first: Varshini

last: Vasudevaraja

first: Seema

last: Patel

first: James

last: Stafford

first: Jonathan

last: Serrano

first: Gianna

last: Esposito

first: Andreas

last: Kloetgen

first: John

middle: G

last: Golfinos

last: Zagzag

first: Britta

last: Weigelt

first: Snjezana

last: Dogan

first: Jorge

last: Reis-Filho

first: Sarah

last: Chiang

first: Dimitris

last: Placantonakis

first: Aristotelis

last: Tsirigos


title: Cutaneous Immunoprofile of Three Spotted Fever Group Rickettsiosis

status: Public on Dec 03 2019

city: Beijing

first: guo

last: wenbin

address: No. 20, East Street, Fengtai District, Beijing

institute: Beijing Institute of Microbiology and Epidemiology

summary: Spotted Fever Group Rickettsiae (SFGR) can cause mild to fatal illness. The early interaction between the host and rickettsia in skin is largely unknown, and the pathogenesis of severe rickettsiosis remains an important topic. A surveillance of SFGR infection by PCR of blood and skin biopsies followed by sequencing, and immunohistochemical detection was performed on patients with a recent tick bite from 2013–2016. Humoral and cutaneous immune profiles were evaluated for different SFGR cases by serum cytokine and chemokine detection, skin immunohistochemical (IHC) staining, and transcriptome sequencing (RNA-seq). A total of 111 SFGR cases were identified, including 79 Candidatus Rickettsia tarasevichiae (CRT), 22 R. raoultii, 8 R. sibirica, and 2 R. heilongjiangensis. The sensitivity to detect SFGR in skin biopsies (9/24, 37.5 %) was significantly higher than in blood samples (105/2671, 3.9 %) (p<0.05). As early as one day after the tick bite, rickettsia could be detected in the skin. R. sibirica infection was more severe than CRT and R. raoultii. Increased levels of serum IL18, IP10, and MIG, and decreased IL2 in R. sibirica febrile patients were observed compared to CRT febrile infections. RNA-seq and IHC staining could not discriminate SFGR infected and uninfected tick-fed skin lesions. The type I interferon (IFN) response was differently expressed between R. sibirica and R. raoultii infection at the cutaneous interface. Severe rickettsiosis might be inclined to induce an increased type I IFN response on the infected skin but which were complicated by the bite of a tick eliciting immune cell infiltration.

overall_design: Skin biopsies were assessed for the presence of rickettsial infection by PCR and immunohistochemical (IHC) staining, for transcriptomic profiles by RNA-seq

last: Jia

first: Hong-Bo

last: Liu

first: Wen-Qiang

last: Shi

first: Wu-Chun

last: Cao


title: Investigating the genetic interaction between Pkhd1 and Pkd1

status: Public on Sep 01 2019

city: Rochester

first: Rory

last: Olson

state: MN

address: 200 1st St SW

institute: Mayo Clinic

summary: The lack of rapidly progressive murine models reflecting the classical infantile disease in ARPKD inhibits progress to understanding pathogenesis. The role that primary cilia play in PKD is also controversial. Here new mouse and rat models, generated by interbreeding appropriate ARPKD and ADPKD strains are characterized; better reflecting the severe human disease. Analysis of mRNA expression in the individual ARPKD and ADPKD models, and the combined mice highlighted different disrupted pathways but with a commonality of dysregulated mechanisms associated with primary cilia. These models will help understand ARPKD and improve preclinical testing for this disease. The study also, in unbiased way, reinforces that cilia are important for pathogenesis in both disorders.

overall_design: Methods: Transcriptome profiles from whole kidney tissue extracted from post-natal day 0, 3 and 12 aged mice extracted from single homozygous (Pkhd1-/- and Pkd1RC/RC), digenic (Pkhd1-/-;Pkd1RC/RC) and WT controls were generated, in triplicate, using Illumina HiSeq4000 platform. The sequence reads that passed quality filters were processed through Mayo Clinic's MAP-RSeq (v2.1.0) pipeline using TopHat2 with the bowtie option. Gene set enrichment analysis was performed to reveal common biological processes between mutant datasets compared to WT controls.

first: Peter

last: Harris


title: Transcriptomic comparison between nickel hyperaccumulator and non-accumulator plant species from the Homalium  genus (Salicaceae) endemic from New Caledonia

status: Public on Jun 05 2019

city: Auzeville Tolosane

first: Sylvain

last: MERLOT

address: 24, chemin de Borde Rouge

department: Biological Sciences

institute: CNRS

summary: The leaf transcriptome of the nickel hyperaccumulator species Homalium kanaliense (Salicaceae) endemic from  New caledonia were compared to the closely related non-accumulator Homalium betulifolium, living on Gallery forest or maquis on serpentine soil, to identity differentially expressed genes potentially involved in Ni hyperaccumulation.

sample_organism:
Homalium kanaliense
Homalium betulifolium

overall_design: Leaves from 3 independant individual plants of Homalium kanaliense and Homalium betulifolium were collected in their natural environment. RNA of the 6 independant samples were extracted and sequenced using the Illumina paired-end sequencing technology. Reads from one individual plant per species were assembled de novo to generate transcriptome sequences. The transcriptome of H. kanaliense was used as a reference to compare the expression of genes in both species.

first: Vanesa

last: Garcia de la Torre

first: Clarisse

last: Majorel-Loulergue

first: Louis-Charles

last: Brinon

first: Stéphanie

last: Huguet

first: Valérie

last: Burtet-Sarramegna

first: Bruno

last: Fogliani

last: Merlot


title: Studying RNA-DNA interactome by Red-C identifies noncoding RNAs associated with various chromatin types and reveals transcription dynamics

status: Public on May 15 2020

city: Cambridge

first: Aleksandra

last: Galitsyna

address: 77 Massachusetts Avenue

institute: Massachusetts Institute of Technology

summary: Noncoding RNAs (ncRNAs) participate in various biological processes, including regulation of transcription and sustaining genome 3D organization. Here, we present a method called Red-C, which exploits proximity ligation to identify contacts with the genome for all RNA molecules present in the nucleus. Using Red-C, we uncover RNA-DNA interactome of human K562 cells and identify hundreds of ncRNAs enriched in active or repressed chromatin. We found two miRNAs, MIR3648 and MIR3867 transcribed from rRNA locus, that are associated with inactive chromatin genome-wide. These miRNAs favor bulk heterochromatin over Polycomb repressed one and interact preferentially with late-replicating genomic regions. Analysis of RNA-DNA interactome also allowed us to trace the kinetics of mRNA production. Our data support the model of co-transcriptional intron splicing, however, surprisingly, contradict the hypothesis of circularization of actively transcribed genes.

overall_design: The Red-C experimental procedure for mapping RNA-DNA interactome is based on adapter-mediated RNA-DNA ligation in fixed nuclei followed by high-throughput sequencing of the chimeric RNA-DNA molecules. We applied Red-C protocol to asynchronous cell cultures (K562, normal human skin fibroblasts). The specificity of Red-C protocol was verified in control experiments with the omission of the DNA ligation step or treatment of RNA-DNA chimeras with RNase A. We also performed RNA-seq analysis of rRNA-depleted total cellular RNA from K562 cells.

first: Alexey

middle: A

last: Gavrilov

first: Anastasiya

last: Zharikova


first: Oliver

last: Bischof

overall_design: We performed time-series experiments on ER:RASv12-transduced WI38 fibroblasts treated with 4-hydroxytamoxifen (4OHT) for 144 hours to induce OIS. Total RNA was collected at 6 time points (0, 24, 48, 72, 96 and 144 h, 2 biological replicates), which encompass the basal proliferative (0 h), hyperproliferative (24-48 h), initiation (72-96 h) and establishment (144 h) stages of OIS, and global gene expression levels were determined using Affymetrix HTA2.0 microarrays. We reasoned that inclusion of the more physiologically prevalent cell state of Quiescence in our experimental strategy would allow us to identify the OIS-specific transcriptome profile. Accordingly, WI38 fibroblasts were induced into Quiescence by serum deprivation for 96 hours. Total RNA was collected at 6 time points (0, 12, 24, 48, 72, and 96 h, 2 biological replicates) and processed in parallel with the OIS time-series.

first: Ricardo

last: Zamudio

first: Pierre-François

last: Roux

first: Gregory

last: Doré


title: Genomic decoding of neuronal depolarization by stimulus-specific NPAS4 heterodimers, RNA sequencing

status: Public on Oct 02 2019

city: La Jolla

first: Nathaniel

last: Delos Santos

address: 9500 Gilman Drive MC 0640

institute: University of California San Diego

summary: Cells regulate gene expression in response to salient external stimuli. In neurons, depolarization leads to the expression of inducible transcription factors (ITFs) that direct subsequent gene regulation. Depolarization encodes both a neuron’s action potential (AP) output and synaptic inputs, via excitatory postsynaptic potentials (EPSPs). However, it is unclear if distinct types of electrical activity can be transformed by an ITF into distinct modes of genomic regulation. Here, we show that APs and EPSPs in mouse hippocampal neurons trigger two spatially segregated and molecularly distinct induction mechanisms that lead to the expression of the ITF NPAS4. These two pathways culminate with the formation of stimulus-specific NPAS4 heterodimers that exhibit distinct DNA binding patterns. Thus, NPAS4 differentially communicates increases in a neuron’s spiking output and synaptic inputs to the nucleus, enabling gene regulation to be tailored to the type of depolarizing activity along the somato-dendritic axis of a neuron.

overall_design: To augment neuronal activity, cells were incubated in the indicated drugs reconstituted in dimethyl sulfoxide (DMSO) or water, and diluted in maintenance media for 2 h (ChIP-seq and RNA-seq experiments). To silence neuronal activity for ChIP-seq and RNA-seq experiments, twenty seven DIV rat hippocampal neurons were incubated in (µM): 1 tetrodotoxin citrate (TTX), 10 3-((R)-2-Carboxypiperazin-4-yl)-propyl-1-phosphonic acid (CPP), and 10 2,3-Dioxo-6-nitro-1,2,3,4-tetrahydrobenzo[f]quinoxaline-7-sulfonamide disodium salt (NBQX) reconstituted in water and diluted in maintenance media for 24 h prior to harvesting on day of experiment. The next day, media was then replaced with the same (silenced, – Stim) or media with 50 µM PTX (stimulated, + Stim), media with PTX plus Nimodipine (Nim; 20 µM reconstituted in DMSO), or media with PTX plus CPP (10 µM, reconstituted in water), and incubated for 2 h at 37°C. Neurons were continuously maintained at 37°C and 5% CO2 until harvesting or fixation. Cells were lysed in TRI-reagent and RNA was extracted using a Direct-zol kit (Zymo Research Cat#R2051) with on-column DNase treatment, following the manufacturer’s instructions. Strand-specific total RNA-seq libraries from ribosomal RNA-depleted RNA were prepared using the TruSeq kit Stranded Total RNA Library kit (Illumina) according to the manufacturer-supplied protocol. Library construction was performed by the IGM Genomics Center, University of California, San Diego, La Jolla, CA. Libraries were sequenced 76bp single-end on an Illumina NextSeq 500 instrument.

first: G

last: Brigidi

first: Michael

last: Hayes

middle: P

first: Andrea

last: Hartzell

first: Lorane

last: Texari

first: Pei

last: Lin

first: Anna

last: Bartlett

first: Joseph

last: Ecker

first: Christopher

last: Benner

first: Sven

last: Heinz

first: Brenda

last: Bloodgood


title: C19ORF66 broadly escapes viral-induced endonuclease cleavage and restricts Kaposi’s Sarcoma Associated Herpesvirus (KSHV)

status: Public on Mar 27 2019

city: Amherst

first: Mandy

last: Muller

state: MA

address: 639 North Pleasant Street, 101 Morrill IVN

department: Microbiology

institute: University of Massachusetts, Amherst

summary: We report the application of RNA-seq to identify the mRNA targets of 4 herpesviral endonucleases and uncovered a cluster of transcripts escaping degradation from all tested endonucleases.

overall_design: mRNA profiles were obtained from HEK-293T cells that were transfected with 4 herpesviral endonuclease, cells sorted and total mRNA extracted, polyA enriched and after library prep were sequences on a HiSeq 4000

first: William

last: Rodriguez


title: Transcriptomic comparison between nickel hyperaccumulator and non-accumulator plant species from diverse genera and geographic locations

first: Sylvain

last: MERLOT

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

sample_organism: [Phyllanthus] conjugatus var. ducosensis

overall_design: Refer to individual Series


title: Identification of Functional Lung Adenocarcinoma Susceptibility Loci through Positional Integration with Human Alveolar Cell Epigenomes

status: Public on Mar 18 2019

city: Duarte

first: Crystal

middle: N

last: Marconett

address: 1500 E Duarte Rd

institute: City of Hope

summary: Lung adenocarcinoma (LUAD) is the predominant lung cancer subtype. To date, 15 single nucleotide polymorphisms (SNPs) have been reproducibly associated with LUAD susceptibility. However, as most SNPs identified in genome-wide association studies (GWAS) are not located in the coding regions of genes and are co-inherited with hundreds of SNPs in linkage disequilibrium (LD), mechanistic links to disease outcomes remain largely unexplored. We hypothesized that some SNPs increase LUAD risk by affecting enhancers of gene transcription in alveolar epithelial cells (AECs), the purported cells of origin for LUAD.  Forty-six LUAD risk-associated SNPs mapped to putative AEC enhancers, and 11 of these were located in FAIRE peaks. Of those, seven were predicted to form transcription factor binding motifs. For four of these, ChIPseq data confirmed the binding of the predicted transcription factors. We chose rs452384, rs6942067 and rs11364096 for functional validation. The reference (risk) allele for rs452384 forms an NKX2-1 binding site that is disrupted by the alternate allele, elicited a 42% increase in activity in H1648 LUAD cells relative to the alternative allele (P = 6.7 x 10-3), and was associated with elevated TERT levels in esophageal tissue (P = 6 x 10-8). The reference (risk) allele for rs6942067 forms an EP300 binding site disrupted by the alternate allele, elicits a 94% increase in enhancer activity relative to the alternative allele in H1648 LUAD cells (P = 2.7 x 10-2), and was associated with higher expression of potential oncogene DCBLD1 in blood (P = 5.2 x 10-16). Lastly, the alternate (risk) allele for rs11364096 disrupts binding sites for FOXA1, HDAC2 and SP1, elicits a 32% decrease in enhancer activity in A549 LUAD cells relative to the reference allele (P = 5.7 x 10-3), and LUAD data from The Cancer Genome Atlas indicates that this SNP is associated with altered expression in LUAD of four genes on other chromosomes. Our analyses provide possible mechanisms for the genetic susceptibility to LUAD, with the identification of three strong functional SNP candidates that appear to affect AEC enhancers. Further investigation of these enhancers and their target genes may ultimately yield more effective and personalized strategies for LUAD risk assessment, prevention and treatment.

overall_design: To test this hypothesis, we performed ChIP-seq for enhancer histone marks using purified primary human AECs, and carried out formaldehyde-assisted identification of regulatory elements (FAIRE) to identify transcription factor accessible DNA. We integrated this data with LUAD index SNPs and SNPs in high LD (r^2≥0.5). We performed transcription factor binding site predictions to identify SNPs likely to affect transcription factor binding. Next, we used luciferase reporter assays to test whether selected SNPs confer allele-specific enhancer activity in LUAD cell lines. Lastly, we performed expression quantitative trait locus (eQTL) analysis to identify potential target genes affected by selected SNPs.

first: Chenchen

last: Yang

first: Theresa

last: Steuve

first: Suhn

middle: K

last: Rhie

first: Jiao

last: Luo

first: Kim

last: Siegmund

first: Beiyun

last: Zhou

first: Zea

last: Borok

first: Ite

last: Offringa


title: LINC00261 is an epigenetically-regulated tumor suppressor that is essential for activation of the DNA damage response [H522-LINC00261 RNA-seq data set]

status: Public on Mar 01 2019

summary: Lung cancer is the leading cause of cancer-related death in the United States. Long non-coding RNAs (lncRNAs) are a class of regulatory molecules whose role in lung carcinogenesis is poorly understood. In this study, we profiled lncRNA expression in lung adenocarcinoma (LUAD) cell lines, compared their expression to that of purified alveolar epithelial type II cells (the purported cell of origin for LUAD), cross-referenced these with lncRNAs altered in primary human tumors, and interrogated for lncRNA whose expression correlated with patient survival. We identified LINC00261, a lncRNA with unknown function in LUAD, adjacent to the pioneering transcription factor FOXA2. Loss of LINC00261 was observed in multiple tumor types, including liver, breast, and gastric cancer. Reintroduction of LINC00261 into human LUAD cell lines inhibited cell migration and slowed proliferation by inducing a G2/M cell cycle arrest while upregulating DNA damage pathway genes and inducing phosphorylation-mediated activation of components of the DNA damage pathway. FOXA2 was able to induce LINC00261 expression, and the entire locus underwent hypermethylation in LUAD, leading to loss of expression. We have thus identified an epigenetically deregulated lncRNA, whose loss of expression in LUAD promotes the malignant phenotype and blocks activation of the DNA damage machinery, predisposing lung cells to cancer development.

overall_design: H522 lung adenocarcinoma cell lines were stably transfected with either CMV-LINC00261 expression vector or CMV-NEO control.

first: Shandy

last: Shahabi

first: Vishaly

last: Kumaran

first: Jonathan

last: Castillo

first: Zhengmin

last: Cong

first: Gopika

last: Nandagopal

first: Daniel

last: Mullen

first: Alexander

last: Alvarado

first: Michele

middle: R

last: Correa

first: Autumn

last: Saizan

first: Riya

last: Goal

first: Amrita

last: Bhat

first: Sean

last: Lynch


title: Transcriptomic characterization of human innate T cells

status: Public on Jan 08 2019

city: Boston

first: Maria

last: Gutierrez-Arcelus

address: 77 Avenue Louis Pasteur

department: Medicine

institute: Brigham and Women's Hospital, Harvard Medical School

summary: We performed low input RNA-seq and single-cell RNA-seq to transcriptionally characterize four human innate T cell (ITCs) subsets, namely iNKT, MAIT, Vδ1 expressing γδ T cells, and Vδ2 expressing γδ T cells. We compared ITCs to CD4+ T and CD8+ T cells, representing the adaptive compartment, and to Natural Killer (NK) cells, representing the innate compartment.

overall_design:
Low input RNA-seq was performed for 6 healthy individuals, with two replicates per cell type. Single-cell RNA-seq was performed for 2 healthy individuals, obtaining a total of 2,036 high quality cells.
Submitter note: Because these are human data, our raw data is available in dbGAP with accession number phs002007.v1.p1 (https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs002007.v1.p1).

first: Patrick

last: Brennan

first: Soumya

last: Raychaudhuri


title: Plasma Adiponectin Levels are Associated with Circulating Inflammatory Cytokines in Autoantibody Positive First-Degree Relatives of Rheumatoid Arthritis Patients

status: Public on Jul 01 2018

first: Jan

middle: M

last: Hughes-Austin

address: 9500 Gilman Drive

department: Orthopaedic Surgery

institute: University of California, San Diego

summary:
Background: Extra-articular manifestations of rheumatoid arthritis (RA), potentially due to systemic inflammation, include cardiovascular disease and sarcopenic obesity. Adiponectin, an adipose-derived cytokine, has been implicated in inflammatory processes in RA, but little is known regarding its association with inflammation in a pre-clinical period. Therefore, we investigated whether adiponectin was associated with inflammatory markers in individuals at risk for RA, and whether RA-related autoimmunity modifies these associations.

Methods: We analyzed samples from 144 first-degree relatives (FDRs) of RA probands, of whom 23 were positive for anti-cyclic citrullinated peptide antibody and/or ≥ 2 rheumatoid factor isotypes (IgM, IgG or IgA). We called this phenotype the ‘high risk autoantibody profile (HRP)’ as it has been shown in prior work to be >96% specific for future RA. We measured adiponectin, cytokines/chemokines, and high-sensitivity C-reactive protein (hsCRP). Using linear mixed effects models, we evaluated interaction between HRP positivity and adiponectin on inflammatory markers, adjusting for age, sex, ethnicity, body mass index, pack-years smoking, and use of cholesterol-lowering medications.

Results: In everyone, adiponectin concentration was inversely associated with hsCRP and IL-1b in adjusted models, where a 1% higher adiponectin was associated with a 26% lower hsCRP (p=0.04) and a 26% lower IL-1b (p=0.04). Significant interactions between HRP and adiponectin for associations with GM-CSF, IL-6, and IL-9 were detected in fully adjusted models (p=0.0006, p=0.006, p=0.01, respectively). In HRP positive FDRs but not HRP negative FDRs, a 1% higher adiponectin was associated with 97% higher GM-CSF, 73% higher IL-6, and 54% higher IL-9 concentrations.

Conclusions: Adiponectin associates with inflammatory markers, and these associations differ in individuals with a high-risk autoantibody profile compared with those without. The interaction between adiponectin and autoimmunity may occur systemically, rather than at the joint, which may provide insight into the systemic effects of RA-related autoantibodies and inflammation in the absence of clinically apparent RA.

first: Kevin

middle: D

last: Deane

first: Jon

middle: T

last: Giles

first: Lezlie

last: Derber

first: Gary

last: Zerbe

first: Dana

last: Dabelea

first: Jeremy

last: Sokolove

first: William

last: Robinson

first: V

last: Holers

first: Jill

last: Norris


title: LINC00261 is an epigenetically-regulated tumor suppressor that is essential for activation of the DNA damage response (AEC/LUAD RNA-seq data set)

first: Crystal

last: Marconett

overall_design: Primary AEC isolated from three human donor remnant transplant lungs and sixteen (16) lung adenocarcinoma cell lines. Note that PC3 and PC9 are lung adenocarcinoma cell lines from Japan, NOT prostate cancer cell lines

first: Shandy

last: Shahabi

first: Vishaly

last: Kumaran

first: Jonathan

last: Castillo

first: Zhengmin

last: Cong

first: Gopika

last: Nandagopal

first: Daniel

last: Mullen

first: Alexander

last: Alvarado

first: Michele

last: Correa

first: Autumn

last: Saizan

last: Goel

first: Beiyun

last: Zhou

first: Zea

last: Borok


title: LINC00261 is an epigenetically-regulated tumor suppressor that is essential for activation of the DNA damage response


title: Epigenome-wide analysis of DNA methylation in lung tissue shows concordance with blood studies and identifies tobacco smoke-inducible enhancers

status: Public on Feb 07 2018

summary: Smoking-associated DNA hypomethylation has been observed in blood cells and linked to lung cancer risk. However, its cause and mechanistic relationship to lung cancer remain unclear. We studied the association between tobacco smoking and epigenome-wide methylation in non-tumor lung (NTL) tissue from 237 lung cancer cases in the Environment And Genetics in Lung cancer Etiology study, using the Infinium HumanMethylation450 BeadChip. We identified seven smoking-associated hypomethylated CpGs (P < 1.0 × 10-7), which were replicated in NTL data from The Cancer Genome Atlas. Five of these loci were previously reported as hypomethylated in smokers' blood, suggesting that blood-based biomarkers can reflect changes in the target tissue for these loci. Four CpGs border sequences carrying aryl hydrocarbon receptor binding sites and enhancer-specific histone modifications in primary alveolar epithelium and A549 lung adenocarcinoma cells. A549 cell exposure to cigarette smoke condensate increased these enhancer marks significantly and stimulated expression of predicted target xenobiotic response-related genes AHRR (P = 1.13 × 10-62) and CYP1B1 (P < 2.49 × 10-61). Expression of both genes was linked to smoking-related transversion mutations in lung tumors. Thus, smoking-associated hypomethylation may be a consequence of enhancer activation, revealing environmentally-induced regulatory elements implicated in lung carcinogenesis

overall_design: NGS data from purified alveolar epithelial type 2 (AT2) cells originating from 2 donor lungs, including whole genome bisulfite sequencing (WGBS) and Chromatin immunoprecipitation (ChIPseq)

first: T

last: Stueve

first: Wen

middle: Q

last: Li

first: Jianxin

last: Shi

first: C

last: Zhang

last: Yang

first: D

first: W

last: Wheeler

first: Xing

last: Hua

first: B

first: Z

first: N

last: Caporaso

first: A

middle: C

last: Pesatori

first: J

last: Duan

first: I

last: Laird-Offringa

first: M

last: Landi