title: Time-course analysis of transcriptome changes induced by ex vivo culture in human cord blood hematopoietic stem cell at single cell resolution [CB]

status: Public on Nov 19 2022

city: Cambridge

first: Elisa

last: Laurenti

address: Jeffrey Cheah Biomedical Centre

department: Haematology

institute: University of Cambridge

summary: Here we present the single cell transcriptomes of human cord blood (CB) long-term hematopoietic stem cells (LT-HSCs) cultured in differentiation promoting medium over a time-course of 0, 6 24 or 72 h. A condition was included for LT-HSCs cultured with the CDK6 inhibitor Palbociclib for durations of 24 or 72 h. Palbociclib causes reversible cell cycle arrest in early G1 in these culture conditions. The objectives of this study were to understand the impact of cell culture on CB LT-HSCs in a time resolved manner and to investigate the role of cell cycle progression in driving this transcriptional change. In the present study we report that 72 h of culture causes extensive rewiring of the CB LT-HSC transcriptome and that changes are dynamically acquired over the time-course. We also report that cell cycle progression is not the main driver of transcriptional change in tested culture conditions.

overall_design: Independent CB donor samples (all male) were pooled (n=2 independent donors in pool 1 and n=3 independent donors in pool 2) and LT-HSCs (CD34+/CD38-/CD45RA-/CD90+/CD49f+) were single cell sorted at the 0 h timepoint or bulk sorted and these bulks were cultured for 6, 24 h or 72 h in media promoting HSC differentiation before single cell sorting for scRNAseq (Live cells sorted after exclusion of dead cells with Zombie Aqua) . For 24 or 72 h culture durations a separate condition was included where LT-HSCs were cultured in differentiation facilitating media with 200nM Palbociclib (PD033299). Palbociclib is a CDK6 inhibitor which reversibly arrests cell cycle progression past early G1 in tested culture conditions. scRNA-Seq plates were processed and libraries generated using an adapted version of the Smart-Seq2 protocol. Paired-end sequenced of 50 bp fragments was performed by NovaSeq.

first: Carys

last: Johnson

first: Kendig

last: Sham

first: Serena

last: Belluschi


title: In vivo CRISPR screens identify a dual function of MEN1 in regulating tumor-microenvironment interactions.

status: Public on Nov 03 2022

city: Shanghai

first: Yin

last: Liu

state: Shanghai

address: Building #2, 507 Zhengmin Road

department: Department of Laboratory Medicine

country: China

institute: Shanghai Pulmonary Hospital, Tongji University School of Medicine

type: Expression profiling by high throughput sequencing

type: Genome binding/occupancy profiling by high throughput sequencing

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: Effect of Nanoemulsion Targeting on the activation state of neutrophils and monocytes

status: Public on Dec 20 2022

city: Düsseldorf

first: Pascal

last: Bouvain

address: Universitätsstr. 1

department: molekulare Kardiologie

country: Germany

institute: Uniklinik Düsseldorf

summary: To exclude any activation of neutrophils and monocytes by our targeting emulsions (mNPPFCs) we incubated murine and human neutrophils with them followed by RNA isolation and sequencing to look for possible upregulation

overall_design: Comparative gene expression profiling analysis of RNA-seq data for neutrophils and monocytes from mice and men treated with mNPPFCs, ConPFCs or left untreated

first: Ulrich

last: Flögel

first: Patrick

last: Petzsch

first: Thorsten

last: Wachtmeister


title: mRNA sequencing data of inguinal adipose tissue (iAT) of mice at postnatal day 6 (P6) and 56 (P56)

status: Public on Sep 22 2022

city: Ulm

first: Tamás

last: Röszer

address: Albert-Einstein-Allee 11

department: Institute of Neurobiology

institute: University of Ulm

summary: Non-treated, C57Black/6 male mice were used.

overall_design: Gene expression levels compared between P6 and P56.


title: Loss of PRC2 enforces a mesenchymal neural crest stem cell phenotype in NF1-deficient cancer through activation of core transcription factors [CUT&RUN]

status: Public on Sep 20 2022

city: New Brunswick

first: Xiyuan

last: Zhang

state: NJ

address: 195 Little Albany St.

department: Pediatric Hematology/Oncology

country: USA

institute: Rutgers Cancer Institute

summary: Genetic alterations that result in the dysregulation of polycomb repressive complex 2 (PRC2) are common features of multiple cancer types. Loss-of-function mutations in the PRC2 genes, SUZ12 or EED, occur at high frequency in malignant peripheral nerve sheath tumors (MPNST), a clinically aggressive sarcoma that arises from NF1-deficient Schwann cells. To define the oncogenic mechanisms mediated by PRC2 loss, we used engineered MPNST model systems that dynamically reassemble a competent PRC2 coupled with single cell sequencing from clinical samples to evaluate the transcriptomic and epigenetic consequences of PRC2 loss. We discovered a two-pronged oncogenic process; first, PRC2 loss leads to remodeling of bivalent chromatin and the enhancer landscape of the tumor cell. These epigenetic changes result in the upregulation of developmentally regulated transcription factors, including FOXC1, which enforce a transcriptional circuit that is a core vulnerability of the cell. Second, PRC2 loss reduces type I interferon signaling and antigen presentation as a downstream consequence of hyperactivated Ras signaling and its crosstalk with STAT and IRF transcription factors. Mapping of the transcriptional program of these PRC2-deficient tumor cells onto a constructed developmental trajectory of the developing neural crest stem cell revealed that changes induced by PRC2 loss enforced a cellular profile characteristic of a primitive mesenchymal neural crest stem cell.

overall_design: Epigenetic and transcriptomic profiling of doxycycline-inducible restoration of a functional PRC2 in human MPNST cells.

first: Jack

middle: F

last: Shern


title: Distinct Circulating Expression Profiles of Long Non-coding RNAs in Heart Failure Patients with Ischemic and Non- ischemic Dilated Cardiomyopathy

status: Public on Oct 08 2022

first: Xiaohui

last: Zhou

address: No.150 Jimo Road,Pudong district

department: Shanghai Heart Failure Research Center

institute: Shanghai East Hospital, Tongji University School of Medicine, Shanghai

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

summary: Ischemic cardiomyopathy(ICM) and dilated cardiomyopathy(DCM), with distinct long-term prognosis and responses to treatment, are two major problems that lead to heart failure(HF) ultimately. In this study, we investigated the lncRNA and mRNA expressions in the plasma of patients with DCM and ICM and analyzed the different lncRNA profile between the two groups. These findings revealed for the first time the specific expression pattern of both protein-coding RNAs and lncRNAs in plasma of HF patients due to DCM and ICM which may provide some important evidence to conveniently identify the etiology of myocardial dysfunctions and help to explore a better strategy for future HF prognosis evaluation.

overall_design: 20 peripheral fasting blood samples were donated by chronic heart failure patients with DCM (n=11) and ICM (n=9). Plasmas were analyzed by RNA microarray (Arraystar Human LncRNA microarray, v4.0, containing 40173 lncRNAs and 20730 coding transcripts). Inclusion criteria were as follow: (1)All patients had ventricular dilation and LVEF<50%. (2)Patients with ICM were diagnosed by coronary angiogram(CAG) or suffered from myocardial infarction before. (3)All patients with DCM were proved non-ischemic by CAG or coronary CTA and in the absence of hypertensive, valvular or congenital heart diseases. Patients with the following conditions were excluded from the study: (1)Cardiac resynchronisation/modulation therapy in 3 months, (2)Acute myocardial infarction in 3 months, (3)coronary artery bypass grafting in 3 months, (4)malignant tumor or immune diseases were excluded.

first: Huimin

last: Fan

first: Fang

last: Lin

first: Xin

last: Gong


title: Loss of PRC2 enforces a mesenchymal neural crest stem cell phenotype in NF1-deficient cancer through activation of core transcription factors [single-cell RNA-seq]

overall_design:
Transcriptomic profiling of human MPNST samples.

>>>Raw data are not available for these samples due to patient privacy concerns<<<


title: CEBPD suppresses motility-associated gene signatures and reduces pancreatic ductal adenocarcinoma cell migration

status: Public on Sep 26 2022

city: Amsterdam

first: C.

middle: Arnold

last: Spek

address: Meibergdreef 9

department: CEMM

country: Netherlands

institute: Amsterdam UMC

summary:
To investigate the effects of CEBPD on pancreatic ductal cell tumorigenicity, we established doxycycline-inducible MIA PaCa-2 cells for CEBPD over-expression, as well as non-control cells with an empty inducible construct.
RNAseq was performed on these cells in the presence and absence of doxycycline and we showed that CEBPD activates gene signatures associated with cell motility.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for CEBPD-inducible and control cells (CTRL) in the presence and absence of doxycycline after 0, 8, 24 and 48 hours.

first: Leonie

last: Hartl

first: Pien

middle: A

last: Maarschalkerweerd

first: Joe

middle: M

last: Butler

first: Manz

last: Xue

first: Frances

middle: S

last: de Man

first: Victor

last: Thijssen

first: Maarten

last: Bijlsma

first: JanWillem

last: Duitman

first: C


title: Loss of PRC2 enforces a mesenchymal neural crest stem cell phenotype in NF1-deficient cancer through activation of core transcription factors [ATAC-seq]


title: Loss of PRC2 enforces a mesenchymal neural crest stem cell phenotype in NF1-deficient cancer through activation of core transcription factors [RNA-seq]


title: Anti-GD2 antibodies conjugated to IL15 and IL21 mediate potent anti-tumor cytotoxicity against neuroblastoma

status: Public on Sep 01 2022

summary: Half of the patients with high-risk neuroblastoma (NB) who receive GD2-targeted monoclonal antibody do not achieve long-term remissions. Recently, the antibody hu14.18 has been linked to interleukin (IL)2 (hu14.18-IL2) to enhance its efficacy and shown promising preclinical and clinical activity. We developed two new immunocytokines (ICs) by linking two other γc cytokines, IL15 and IL21, to hu14.18. The purpose of this study was to compare hu14.18-IL15 and -IL21 to hu14.18-IL2 in their ability to induce antibody-dependent cell-mediated cytotoxicity (ADCC) against NB. We assessed ADCC of hu14.18-IL15 and -IL2 (human cytokines, cross-reactive to mouse) against GD2low and GD2high NB cell lines in vitro. T-cell deficient mice with orthotopic patient-derived xenografts (PDXs) and immunocompetent mice with transplantable orthotopic NB were used to test all three ICs, including hu14.18-IL21 (murine IL21, not cross-reactive to human). Mechanistic studies were performed using single-cell RNA-sequencing (scRNA-seq). Hu14.18-IL15 and hu14.18-IL2 mediated equivalent in vitro ADCC by human NK cells. When combined with chemotherapy, all three ICs similarly controlled the growth of PDXs in nude mice with murine NK effector cells. However, hu14.18-IL15 and -IL21 outperformed hu14.18-IL2 in immunocompetent mice with syngeneic NB, inducing complete tumor regressions and extending survival. scRNA-seq data revealed an increase in CD8+ T cells and M1 tumor-associated macrophages and decreased regulatory T cells and myeloid-derived suppressor cells in the tumor microenvironment. Hu14.18-IL15 and Hu14.18-IL21 exhibit robust preclinical activity, warranting further consideration for clinical testing in patients with GD2-expressing NB.

overall_design: A/J mice were injected orthotopically with NXS-2 cells (5×105). Three weeks later, mice were randomly stratified into four different groups to receive 1) Vehicle, 2) hu14.18-IL2, 3) hu14.18-IL15, 4) hu14.18-IL21. ICs were administered IV as one dose of 25 µg. About 48 hours later, tumors were processed into sc suspensions and enriched via CD45 magnetic bead positive selection (Stem Cell Technologies). The viability of samples was confirmed to be >80% prior to further processing. Three individual mouse samples per treatment group were pooled. About 10,000 cells from each treatment group were loaded with the goal of capturing 6,000 cells using the 10X Genomics 3’ v3.1 chemistry.

first: Rosa

last: Nguyen


title: Characterization of transcriptomic changes induced by a gene therapy cell culture protocol to single human bone marrow and mobilized peripheral blood hematopoietic stem and progenitor cells [BM_MPB]

first: Elisa

last: Laurenti

country: United Kingdom

summary: Here we present the single cell transcriptomes of human adult mobilized peripheral blood (mPB) and bone marrow (BM) hematopoietic stem and progenitor cell (HSPC) subsets,: long-term haematopoietic stem cells (LT-HSCs), short-term HSCs (ST-HSCs) and CD34+ cells before (0 h) and after 62 hours (62 h) of culture in a conditions mimicking gene therapy protocols. The culture protocol includes two hits of lentiviral transduction (lentiviral vector contains a GFP construct) and media as previously published . The objectives of this study are to investigate the effects of lentiviral transduction and cell culture in gene therapy protocol conditions on human mPB and BM haematopoietic stem and progenitor cell (HSPC) subsets. In the present study we report that 62 h of culture in gene therapy media significantly alters the transcriptome of BM and mPB subsets. In contrast, lentiviral transduction alone has a minimal effect on the transcriptome of all tested subsets. T=transduced GFP+; NT=non transduced; GFP-= transduced GFP-

overall_design: 4 independent healthy male mPB donors (aged 25-28) and 3 independent healthy male BM donors (aged 27-32) were used for the present study. CD34+ enriched cells were single cell sorted for scRNA-Seq at the 0 h timepoint or bulk sorted from the following populations: LT-HSCs (CD19-/CD34+/CD38-/CD45RA-/CD90+/CD49f+), ST-HSCs (CD19-/CD34+/CD38-/CD45RA-/CD90-/CD49f-) and CD34+ (CD19-/CD34). Bulk subsets were cultured in a 62 h ex vivo gene therapy protocol and either exposed to a lentiviral vector containing a GFP construct (GFP+ or GFP-) or non transduced (NT). A separate condition was also included where mPB LT-HSCs were transduced and cultured for 62 h in the presence of 200nM Palbociclib (PD033299). Palbociclib is a CDK6 inhibitor which reversibly arrests cell cycle progression past early G1 in tested culture conditions. At 62 h, Live cells (isolated as Zombie Aqua negative) from LT-HSC, ST-HSC and CD34+ subsets were single cell sorted for scRNA-Seq. scRNA-Seq plates were processed and libraries generated using an adapted version of the Smart-Seq2 protocol. Paired-end sequenced of 50 bp fragments was performed by Illumina HiSeq 4000.  The human biological samples were sourced ethically and their research use was in accord with the terms of the informed consents under an IRB/EC approved protocol.

first: Carys

last: Johnson

first: Kendig

last: Sham

first: Natalie

last: Francis


title: Sex-determining 3D regulatory hubs revealed by genome spatial auto-correlation analysis [RNA-seq]

status: Public on Nov 21 2022

city: Berlin

first: Irene

last: Mota-Gomez

address: Hannoversche strasse 28

institute: Max Delbruck Center

summary: Mammalian sex is determined by a network of antagonistic genes that are well characterized. However, its non-coding regulation is still largely unknown. Here we explore the 3D chromatin landscape of sex determination in vivo. We integrate Hi-C with ChIP-seq experiments using METALoci, a novel genome spatial auto-correlation analysis approach that identifies 3D regulatory hubs across the genome. We uncover a prominent rewiring of chromatin interactions during sex determination. By combining predictive approaches and validations in transgenic mice we identify a novel Fgf9 regulatory hub, which deletion results in male-to-female sex reversal.

overall_design: RNA-seq experiments in E13.5 XY WT and E13.5 XY Fgf9 Δ306 mouse gonads.

first: Juan

last: Rodriguez

first: Shannon

last: Dupont

first: Oscar

last: Lao

first: Johanna

last: Jedamzick

first: Ralf

last: Kühn

first: Scott

last: Lacadie

first: Sara

last: Garcia-Moreno

first: Alicia

last: Hurtado

first: Rafael

middle: D

last: Acemel

first: Blanche

last: Capel

first: Marc

last: Marti-Renom

first: Dario

middle: G

last: Lupianez


title: Loss of PRC2 enforces a mesenchymal neural crest stem cell phenotype in NF1-deficient cancer through activation of core transcription factors

first: Xiyuan

last: Zhang


title: A cryptic transactivation domain of EZH2 binds AR and AR’s splice variant promoting oncogene activation and prostate tumorigenesis [RNA-Seq]

status: Public on Aug 29 2022

city: Nanjing

first: jun

last: wang

state: Jiangsu

address: No. 163 Xianlin Avenue, Qixia District

department: IMB

institute: Nanjing University

summary: Enhancer of Zeste Homolog 2 (EZH2) and androgen receptor (AR) are both crucial for the development and progression of prostate tumor, including advanced castration-resistant prostate cancer (CRPC). Previously, it was reported that, in order to sustain tumorigenicity of prostate cancer, EZH2 has noncanonical functions in interaction with AR for mediating gene activation, in addition to its canonical role as a transcriptional repressor and enzymatic subunit of Polycomb Repressive Complex 2 (PRC2). However, the molecular basis underlying non-canonical activities of EZH2 in prostate cancer remains far from clear, and therapeutic strategies for targeting EZH2:AR-mediated gene-activation activities are also lacking.  Here, we report that a hidden transactivation domain of EZH2 (EZH2TAD) binds both AR and AR’s variants enriched in CRPCs, notably AR splice variant 7 (AR-V7), mediating the assembly and/or recruitment of a gene-activation-related complex at genomic sites that lack PRC2 binding. Such noncanonical targets of EZH2:AR/AR-V7:(co)activators are enriched for the clinically-relevant prostate oncogenes. EZH2TAD is crucial for EZH2-mediated transactivation of oncogenes and for CRPC growth in vitro and in vivo. To completely block EZH2’s multifaceted oncogenic activities in prostate cancer, we employed MS177, a recently developed proteolysis targeting chimera (PROTAC) of EZH2.  MS177 achieved on-target depletion of both EZH2’s canonical (EZH2:PRC2) and noncanonical (EZH2TAD:AR/AR-V7:coactivators) complexes in prostate tumor, eliciting much more potent antitumor effects than the existing catalytic inhibitors of EZH2. Overall, this study reports previously unappreciated requirements of EZH2TAD for mediating EZH2’s noncanonical recruitment and gene-activation functions in prostate tumor and suggests EZH2-targeting PROTACs as potentially attractive therapeutics for the treatment of aggressive prostate tumors that reply on circuits wired by EZH2 and AR.

overall_design: We used RNA-seq to examine transcriptomic profiles of 22Rv1 cells after depletion of EZH2 (shEZH2) versus control (shEV); also, transcriptomic profiling was conducted in 22Rv1 cells after the treatment with either MS177, C24 or MS177N1, compared DMSO.

first: Jun

last: Wang

first: Greg

first: Ling

last: Cai


title: Adaptation to ex vivo culture drives human haematopoietic stem cell loss of repopulation capacity in a cell cycle independent manner

status: Public on Nov 17 2022

first: Elisa

last: Laurenti


title: The genomic and immune landscape of long-term survivors of high-grade serous ovarian cancer [RNAseq]

status: Public on Aug 26 2022

city: Melbourne

first: Dale

middle: W

last: Garsed

state: VIC

address: 305 Grattan St

country: Australia

institute: Peter MacCallum Cancer Centre

summary: Less than half of all patients with advanced-stage high-grade serous ovarian cancers (HGSC) survive more than five years post-diagnosis but those who have an exceptionally long survival could provide new insights into tumor biology and therapeutic approaches. We analyzed 60 patients with advanced-stage, HGSC who survived more than 10 years after diagnosis using whole-genome sequencing, transcriptome, and methylome profiling of their primary tumor samples, comparing this data to 66 short- or moderate-term survivors. Tumors of long-term survivors were more likely to have multiple alterations in genes associated with DNA repair, and more frequent somatic variants resulting in an increased predicted neoantigen load. Patients clustered into survival groups based on genomic and immune cell signatures, including three subsets of patients with BRCA1 alterations with distinctly different outcomes. Specific combinations of germline and somatic gene alterations, tumor cell phenotypes, and differential immune responses appear to contribute to long-term survival in HGSC.

overall_design:
Transcriptomic profiling was done on 56 high grade serous ovarian cancer samples, 53 of which were primary tumors and 3 were relapse tumors. 75 samples from GSE209964 were also used as part of the cohort.
**Raw data uploaded to European Genome-phenome Archive (EGA) repository under the accession codes EGAD00001000877 and EGAD00001008537**

first: Ahwan

last: Pandey

first: David

last: Bowtell


title: Gemin5-dependent RNA association to polysomes supports selective translation of mRNA subsets

status: Public on Aug 24 2022

city: Madrid

first: Encarnacion

last: Martinez-Salas

state: Madrid

address: Nicolás Cabrera 1

country: Spain

institute: Centro de Biologia Molecular Severo Ochoa, CSIC-UAM

summary: Here we report the identification at a genome-wide scale of the mRNAs associated to polysomes in Gemin5-depleted cells relative to control cells. Among the polysomal Gemin5-enhanced mRNAs, we identified numerous transcripts belonging to two distinct families, which encode ribosomal proteins and histones.

overall_design: Examination of the mRNAs differentially associated to polysomes following Gemin5 silencing revealed the presence of  unique cis-acting regulatory elements, the TOP element at the 5´end and the hSL hairpin at the 3´end, respectively.

first: Azman

last: Embarc-Buh

first: Rosario

last: Francisco-Velilla

first: Juan Antonio

last: Garcia-Martin

first: Salvador

last: Abellan

first: Jorge

last: Ramajo


title: 3D-hUMSCs exosomes enriched with miR-125b-5p and miR-132-3p ameliorate vitiligo by simultaneously suppressing oxidative stress-induced melanocyte damage and potentiating Treg cells-mediated immunosuppression

status: Public on Aug 14 2022

city: Beijing

first: Shuang

last: Li

state: Beijing

address: Biomedical engineering

department: Biomedical engineering

institute: Beihang university

type: Non-coding RNA profiling by high throughput sequencing

summary: As a crucial component of exosome cargo, miRNAs have been reported to be deeply involved in regulating intercellular communication and multiple biological functions. Based on the results above, we performed high-throughput miRNA sequencing of 2D-Exo and 3D-Exo to identify the potential miRNAs.

overall_design: Exosomes extracted from 2D and 3D cultured human umbilical cord mesenchymal stem cells supernatants were sequenced

first: Qi

first: Yuqi

last: Zhou

first: Liaoran

last: Niu

first: Weinan

last: Guo


title: Histone H3 proline 16 hydroxylation regulates mammalian gene expression [CUT&RUN]

status: Public on Aug 02 2022

first: jun

last: wang

summary: Histone posttranslational modifications (PTMs) are important for regulating various DNA-templated processes. Emerging evidence suggests a critical involvement of the previously less-explored histone PTMs in gene activity regulation. Here, we report the existence of a new histone PTM in the mammalian cells, hydroxylation of H3 proline 16 (H3P16-OH) catalyzed by EglN2, a proline hydroxylase. We show that EglN2-mediated H3P16-OH enhances direct binding of Lysine-Specific Demethylase 5A (KDM5A) with its substrate, H3 lysine 4 trimethylation (H3K4me3), resulting in enhanced chromatin recruitment of KDM5A and decrease of H3K4me3 at target genes. Genome-wide mapping by CUT&RUN in multiple mammalian cell models reveals a functional connection between EglN2, H3P16-OH, KDM5A and H3K4me3. Integrated analysis with RNA-Seq also identifies distinct subsets of genes that are regulated through H3P16-OH in different cell lines. This study therefore demonstrates a new player of the “histone code” by revealing a role of H3P16-OH in regulating gene expression in mammalian cells.

overall_design: Genome-wide mapping by CUT&RUN or spike-in CUT&RUN in multiple mammalian cell models reveals a functional connection between EglN2, H3P16-OH, KDM5A and H3K4me3. A faction of Drosophila chromatin was added to these human cells as spike-in controls.

first: Xijuan

last: Liu

first: Qing

last: Zhang


title: Histone H3 proline 16 hydroxylation regulates mammalian gene expression


title: Histone H3 proline 16 hydroxylation regulates mammalian gene expression [RNA-Seq]

overall_design: Genome-wide mapping by CUT&RUN in multiple mammalian cell models reveals a functional connection between EglN2, H3P16-OH, KDM5A and H3K4me3


title: Three-dimensional morphologic and molecular atlases of murine nasal vasculatures [Mouse_Nasal_10X]

status: Public on Jul 12 2022

city: Daejeon

first: Myung Jin

last: Yang

country: South Korea

institute: Institute for Basic Science

summary: To investigate heterogeneity of nasal environments and vasculatures, and their changes in allergic rhinitis (AR) model, nasal cells and endothelial cells (EC)s from Ctrl and AR model mouse were FACS sorted and single-cell RNA seqs were performed

overall_design: Nasal cells or ECs from Ctrl and AR model mouse were sorted and single-cell libraries were made

first: GouYoung

last: Koh

first: SeonPyo

last: Hong

first: MyungJin


title: Histone deacetylation primes chromatin to preserve epigenetic memory for self-propagation of heterochromatin domain [ChIP-seq]

city: Bethesda

first: Shiv

last: Grewal

state: MD

address: NCI bldg 37 Rm 6068 9000 Rockville Pike

department: LBMB

institute: NCI

summary: Clr3-Myc occupancy along fission yeast chromosomes.

overall_design: Genome wide occupancy of Clr3-MYC profiled by next generation sequencing of DNA co-purifying with Clr3-MYC chromatin.

first: Martin

last: Zofall

first: Rima

last: Sandhu

first: Sahana

last: Holla

first: David

last: Wheeler

middle: I


title: RHINOVIRUS INFECTION OF THE AIRWAY EPITHELIUM ENHANCES MAST CELL IMMUNE RESPONSES VIA EPITHELIAL-DERIVED INTERFERONS

status: Public on Jun 22 2022

city: Seattle,

first: Stephanie

last: Osmond

state: WA

address: 1201 9th Ave

institute: Benaroya Research Institute

summary: Rationale: Mast cells (MCs) within the airway epithelium in asthma are closely related to airway dysfunction, but crosstalk between airway epithelial cells (AECs) and MCs in asthma remains incompletely understood. Human rhinovirus (HRV) infections are key triggers for asthma progression and AECs from individuals with asthma may have dysregulated anti-viral responses.   Objectives: We utilize primary phenotyped AECs in an ex vivo coculture model system to examine crosstalk between AECs and MCs following epithelial HRV infection.  Methods: Primary AECs were obtained from children with asthma (n=11) and healthy children (n=10), differentiated at air-liquid interface, and cultured in the presence of laboratory of allergic diseases-2 (LAD2) MCs. AECs were infected with HRV serogroup A 16 (HRV16) for 48 hours. RNA isolated from both AECs and MCs underwent RNA-sequencing (RNAseq) analysis. Direct effects of epithelial-derived interferons on LAD2 MCs were examined by qPCR.  Results: MCs increased expression of pro-inflammatory and anti-viral genes in AECs. AECs demonstrated a robust antiviral response following HRV16 infection that resulted in significant changes in MC gene expression, including upregulation of genes involved in anti-viral responses, leukocyte activation, and type-2 (T2) inflammation. Subsequent ex vivo modeling demonstrated that IFN-β induces MC IL13 expression. The effects of AEC phenotype were small relative to the effects of viral infection and the presence of MCs.  Conclusions: There is significant crosstalk between AECs and MCs, which are present in the epithelium in asthma. Epithelial-derived interferons not only play a role in viral suppression, but further alter MC immune responses including specific T2 genes.

overall_design: Primary AECs obtained from children with asthma (n=11) and healthy children (n=10) and differentiated at air-liquid interface were cultured in the presence and absence of laboratory of allergic diseases-2 (LAD2) MCs. AECs were infected with HRV serogroup A 16 (HRV16) or vehicle control for 48 hours. RNA isolated from both AECs and MCs underwent bulk RNA-sequencing (RNAseq) analysis.

first: Ryan

middle: C

last: Murphy


title: Histone deacetylation primes chromatin to preserve epigenetic memory for self-propagation of heterochromatin domains

type: Genome binding/occupancy profiling by genome tiling array

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

overall_design: Refer to individual Series


title: Three-dimensional morphologic and molecular atlases of murine nasal vasculatures [Mouse_Nasal_SmartSeq]

summary: To investigate heterogeneity of murine nasal  Prox1+ vasculatures,  GFP+ cells from Prox1-GFP mouse nasal tissue were FACS sorted and single-cell RNA seq was performed

overall_design: Nasal Prox1+ cells were FACS sorted and single-cell libraries were made


title: Single cell RNA sequencing of left ventricular endothelial cells after sham or acute myocardial infarction surgery in C57BL/6N wild-type mice.

status: Public on Jun 20 2022

city: Hannover

first: Marc

middle: R.

last: Reboll

state: NDS

address: Carl-Neuberg-Str. 1

department: Molecular and Translational Cardiology, Department of Cardiology and Angiology

institute: Hannover Medical School

summary: Endothelial cells were isolated from the infarct region (anteroapical wall distal to the coronary artery ligation site representing the infarct core and border zone) 3 days after sham or acute myocardial infarction (AMI) surgery. AMI was induced by 60 min coronary ligation followed by reperfusion. Endothelial cells were subjected to single cell RNA sequencing.

overall_design: 11,200 cells were analyzed per condition.

first: Kai

last: Wollert

middle: R


title: Medulloblastoma is a differentiation disorder of the human rhombic lip

status: Public on Jun 15 2022

city: Winnipeg

first: Tamra

last: Werbowetski-Ogilvie

state: Manitoba

address: 611-745 Bannatyne Avenue

department: Biochemistry & Medical Genetics

country: Canada

institute: University of Manitoba

summary: RNA sequencing was performed on Group 3 medulloblastoma tumorspheres expressing high vs. low levels of OTX2.

overall_design: OTX2 levels were knocked down in HDMB03 and MB3W1 Group 3 MB cells (2X10^5 cells/well) as previously described (Zagozewski et al., Nature Comm, 2020; Stromecki et al., Molecular Oncology, 2018). Briefly, OTX2 was silenced using Silencer Select siRNAs 9931 or 9932 (Life Technologies) at a concentration of 30 nM. A non-silencing (scramble) served as the negative control. Samples were collected at 72 hours for RNA extraction and sequencing.


title: Acinetobacter baumannii response to cefiderocol challenge in human urine

status: Public on Jun 01 2022

city: Fullerton

first: M. S.

last: Ramirez

state: CA

address: 800 N. State College Blvd

institute: California State University Fullerton

summary: Cefiderocol (CFDC) is a novel chlorocatechol-substituted siderophore approved to treat complicated urinary tract infections and for hospital-acquired and ventilator-acquired pneumonia. In previous work, human fluids, were shown to increase the minimum inhibitory concentration (MICs) of Acinetobacter baumannii against CFDC and  reduce  the expression of genes related to iron uptake systems, which could explain the need for higher concentrations of CFDC to exert inhibitory action. Herein, we analyzed the impact of human urine (HU), which contains low albumin concentrations, on the expression of iron-uptake related genes and MIC values of two carbapenem-resistant A. baumannii. Levels of resistance to CFDC were not modified by HU in strain AMA40 but were reduced in the case of strain AB5075. Testing other carbapenem-resistant A. baumannii isolates showed that the CFDC MICs were unmodified or reduced in the presence of HU. The expression of piuA, pirA, bauA, and bfnH determined by qRT-PCR was enhanced in both strains when HU was present in the culture medium. All four tested genes are involved in recognizing ferric siderophore complexes or internalization into the cell’s cytosol. In contrast, the effect of HU on genes associated with resistance to β-lactams, antibiotics commonly used to treat urinary tract infections caused by A. baumannii, was variable; the transcriptional analysis of pbp1, pbp3, blaOXA-51-like, blaADC, and blaNDM-1 showed significant variation. In summary, HU, probably due to the albumin and free iron content, does not adversely impact or slightly improves the activity of CFDC when tested against A. baumannii in urine in contrast to other human bodily fluids.

overall_design: Total mRNA of Acinetobacter baumanii AB5075 or Acinetobacter baumannii AMA40 was isolated from bacteria incubated in Mueller Hinton medium with or without 50% human urine

first: Maria

first: Rodrigo

last: Sieira


title: Cellular scRNA-seq of human umbilical cord mesenchymal stem cell (HUCMSC) and human umbilical vein endothelial cells (HUVEC)

status: Public on May 04 2022

first: Georg

last: Hansmann

address: Carl-Neuberg-Strasse 1

summary: We report the first application of human umbilical cord mesenchymal stem cell (HUCMSC)-derived therapy for pulmonary arterial hypertension (PAH). A 3-year-old female presented with heritable PAH (ACVLR1 missense mutation) associated with hereditary hemorrhagic telangiectasia (HHT). Serial intra-pulmonary arterial and centrally intravenous infusions of conditioned media (CM) from allogenic HUCMSCs resulted in marked clinical and hemodynamic improvement after six months. A consecutive multiple cord single-cell RNA-seq integrated analysis (HUCMSC and HUVEC control) revealed eight common cell clusters, of which two (overrepresented by HUCMSCs) had regenerative potential.

overall_design: scRNA profiles of HUCMSC and HUVEC.


title: Transcriptome analysis of hepatocellular carcinoma and adjacent non-tumor liver tissues [I]

status: Public on May 18 2022

city: San Antonio

first: Yidong

last: Chen

state: Texas

address: 8403 Floyd Curl Drive, MSC 7784

department: Population Health Sciences

institute: UT Health Science Center at San Antonio

summary: Integrin alpha 6 (ITGA6) forms integrin receptors with either integrin β1 (ITGB1) or integrin beta 4 (ITGB4). To study its expression and regulatory functions in hepatocellular carcinoma (HCC) progression, whole transcriptome RNA sequencing in paired HCC tumor and adjacent non-tumor liver tissue samples from ten local Hispanic patients was performed. The average expression of ITGA6 was found increased by over 3.5-fold in HCC tumor tissues in comparison with their adjacent non-tumor tissues. The study indicates integrin alpha6-beta4 complex as a potential therapeutic target for treating patients in HCC.

overall_design: 10 tumor-normal pairs of HCC samples were profiled using high-throughput RNA sequencing techniques and their relative gene expression levels were compared.

first: Lu-Zhe

last: Sun

first: Francisco

last: Cigarroa

first: Hakim

last: Bouamar

first: Zhao

last: Lai


title: Single-cell RNA sequencing of human peripheral blood progenitors captures early mast cell differentiation

status: Public on May 03 2022

city: Solna

first: Joakim

last: Dahlin

address: CMM, Visionsgatan 18

department: Department of Medicine, Solna

country: Sweden

institute: Karolinska Institutet

summary: Activation of mast cells through FcεRI can result in allergic responses. The identity of mast cells progenitors is controversial, in particular whether these cells express FcεRI. Here, we performed single-cell RNA sequencing of human peripheral blood progenitors to study the appearance of FcεRI during hematopoietic progenitor differentiation.

overall_design:
We performed single-cell RNA sequencing of FACS isolated human hematopoietic progenitor cells. The first dataset constitutes Lin− c-Kit+ cells sorted from a peripheral blood sample. The second dataset constitutes Lin− CD34+ c-Kit+ cells with spike-in Lin− CD34+ c-Kit+ FcεRI+ cells. Briefly, to generate the latter dataset peripheral blood cells from a donor were divided into two fractions. Cells from one fraction was labeled with phycoerythrin (PE)-hashtag-oligonucleotides. Lin− CD34+ c-Kit+ cells were sorted from the unlabeled fraction and Lin− CD34+ c-Kit+ FcεRI+ cells were sorted from the PE-hashtag-oligonucleotide-labeled fraction. The two sorted cell fractions were pooled and single-cell transcriptomics was performed.

**As Swedish legislation and GDPR prevent unrestricted distribution of raw sequencing data, raw sequence data cannot be provided, including through controlled access databases.

first: Daryl

last: Boey

first: Chenyan

last: Wu


title: Community assessment of methods to deconvolve cellular composition from bulk gene expression

status: Public on Jun 06 2022

city: Stanford

first: Andrew

last: Gentles

address: 291 Campus Drive

institute: Stanford University

summary: We generated in vitro and in silico admixtures of tumor, immune, and stromal cells and sequenced them along with the purified populations from which they were derived. We used the admixtures as ground truth in a community-wide DREAM Challenge aimed at providing an objective, unbiased assessment of published deconvolution methods and at promoting development of new approaches. We benchmarked seven published methods and found that they could predict most cell types well, though dissecting functional states of T cells remains difficult: few methods predict memory CD4+ T cells or the memory versus naïve compartments of CD8T+ cells and, those that do, show large performance gaps relative to other cell types. We spurred development of 21 novel methods, some of which were able to reliably infer these cellular functional states.

overall_design: RNA-seq profiling of 11 purified immune cell populations, 2 purified stromal cell populations, 2 cancer cell lines, and in vitro admixtures of these purified populations.

first: Brian

last: White

middle: J


title: Three-dimensional morphologic and molecular atlases of human nasal vasculatures [Human_Nasal_10X]

first: Myung Jin

last: Yang

summary: To investigate heterogeneity of human nasal vasculaturesendothelial cells (EC)s from human donors (2 male and 2 female) were FACS sorted and single-cell RNA seqs were performed

overall_design: Nasal ECs from human donors were sorted and single-cell libraries were made

first: GouYoung

last: Koh

first: SeonPyo

last: Hong

first: MyungJin


title: Anti-tumor efficacy of a potent and selective non-covalent KRASG12D inhibitor

status: Public on Apr 28 2022

city: San Diego

first: Peter

last: Olson

state: California

address: 3545 Cray Court

institute: Mirati Therapeutics

summary: We report the expression result for the invivo and invitro cell lines treated with MRTX1133

first: Jill

last: Hallin

first: Lars

last: Engstrom


title: Three-dimensional morphologic and molecular atlases of human/mouse nasal vasculatures


title: Regulation of brain aging by neutral sphingomyelinase 2

status: Public on Apr 27 2022

city: Lexington

first: Erhard

last: Bieberich

state: KY

address: 800 Rose Str

department: Physiology

institute: University of Kentucky

summary:
Purpose:  The goals of this study are to compare next generation sequencing-derived brain cortex transcriptome profiling (RNA-seq) to study the  role of neutral sphingomyelinase 2 (smpd3) in brain aging.
Methods: Brain cortex mRNA profiles of 10 month old  (fro/+) and smpd3 total knockout (fro/fro) mice were generated by deep sequencing, in duplicate, using Illumina NovaSeq 6000. (https://en.novogene.com)
Results:A total of 1462 transcripts differed between genotypes, with 891 transcripts increased and 571 transcripts decreased.
Conclusions: Transcriptome differences link decreased oxidative stress and astrocyte activation in brain cortex to nSMase2 deficiency, while synaptic signaling transcripts increased in ways consistent with increased cognitive function previously demonstrated in nSMase2-deficient mice.

overall_design: Brain cortex mRNA profiles of 10 months old smpd3 heterozygous (fro/+) and total knockout (fro/fro) mice

first: Zhihui

last: Zhu

first: Bieberich

last: Erhard


title: Gene expression analysis in canine discoid/chronic lupus erythematosus, mucocutaneous lupus erythematosus and pyoderma

status: Public on Mar 23 2022

city: North Grafton

first: Jillian

last: Richmond

state: Massachusetts

address: 200 Westboro Road

department: Comparative Pathobiology

institute: Tufts Cummings School of Veterinary Medicine

summary: We performed a comparative immunology case study of client-owned dogs to determine if immune and skin gene expression profiles in spontaneous canine cutaneous lupus erythematosus mirror those observed in human cutaneous lupus.

overall_design:
Gene expression was analyzed using 160 custom Nanostring probes to analyze 7 canines with DLE, 1 canine with CCLE, 1 canine with MLE and 1 canine with pyoderma compared to 5 healthy controls (leg margin excisions).

UPDATE: [09-11-2024] For Sample GSM4869949, the title was changed from "Skin_biopsy_DICLE_case1" to "Skin_biopsy_Control/Pyoderma_case3", and the disease status was changed from "DICLE" to "Control/Pyoderma".

first: Nicholas

last: Robinson


title: The Regulatory Evolution of the Primate Fine-Motor System

status: Public on Mar 07 2022

city: Pittsburgh

first: Morgan

last: Wirthlin

state: Pennsylvania

address: 4400 Fifth Ave

department: Computational Biology

institute: Carnegie Mellon University

summary: In mammals, fine motor control is essential for skilled behavior, and is subserved by specialized subdivisions of the primary motor cortex (M1) and other components of the brain’s motor circuitry. We profiled the epigenomic state of several components of the Rhesus macaque motor system, including subdivisions of M1 corresponding to hand and orofacial control. We compared this to open chromatin data from M1 in rat, mouse, and human. We found broad similarities as well as unique specializations in open chromatin regions (OCRs) between M1 subdivisions and other brain regions, as well as species- and lineage-specific differences reflecting their evolutionary histories. By distinguishing shared mammalian M1 OCRs from primate- and human-specific specializations, we highlight gene regulatory programs that could subserve the evolution of skilled motor behaviors such as speech and tool use. Further, in order to predict candidate enhancers in additional species for which primary data was not available, we developed machine learning models trained on genome sequence across species.

sample_organism:
Macaca mulatta
Mus musculus
Rattus norvegicus

overall_design: To supplement publicly available open chromatin datasets, we generated bulk tissue ATAC-seq data from fresh mouse liver tissue (one male and one female replicate), fresh rat tissues (two male and one female replicate), and fresh macaque tissue (one male and one female replicate).  Our data includes cortex, striatum, and liver from all three species, and the cortex and striatum data from macaque consists of multiple sub-regions of these brain regions.

middle: E

first: Irene

last: Kaplow

first: Alyssa

last: Lawler

first: Ashley

last: Brown

first: Jing

last: He

first: Michael

last: Kleyman

first: BaDoi

middle: N

last: Phan

first: William

last: Stauffer

first: Andreas

last: Pfenning


title: Schwann cell precursors represent a neural crest-like hub state with biased multipotency

city: New York

first: Louis

last: Faure

state: NY

address: 321 E 61st Street

institute: Memorial Sloan Kettering Cancer Center

summary: Schwann cell precursors (SCPs) are nerve-associated progenitors that not only can generate myelinating and non-myelinating Schwann cells but also are multipotent like the neural crest cells from which they originate. SCPs are omnipresent along outgrowing peripheral nerves throughout the body of vertebrate embryos. By using single-cell transcriptomics to generate the atlas of the entire neural crest lineage, we show that early SCPs and late migratory crest have similar transcriptional profiles characterized by a multipotent “hub” state containing cells biased towards traditional neural crest fates.  SCPs keep diverging from the neural crest after being primed towards terminal Schwann cell and other fates, with different subtypes residing in distinct anatomical locations. Functional experiments using CRISPR-Cas9 loss-of-function further show that knock-out of the hub gene Sox8 causes defects in neural crest-derived cells along peripheral nerves by facilitating differentiation of SCPs towards sympathoadrenal fates. Finally, specific tumour populations found in melanoma, neurofibroma and neuroblastoma map to different stages of SCP/Schwann cell development.  Overall, SCPs resemble migrating neural crest cells that maintain multipotency and become transcriptionally primed toward distinct lineages.

overall_design: Smart-Seq2 protocol was performed on single isolated cells by Eukaryotic Single Cell Genomics Facility at SciLifeLab, Stockholm. Single TOMATO+ cells were sorted into 384-well plates prefilled with lysis buffer according to the previously published SmartSeq2 protocol (Picelli, Faridani et al. 2014) using a BD FACSAria Fusion Cell Sorter B5/R3/V3 system with a three-laser configuration (488nm, 633nm, and 405nm) and 16 fluorescence detectors. Single-cell transcriptomic sequencing was performed as previously described (Picelli, Faridani et al. 2014).

first: Kastriti

last: Eleni

first: Dorothea

last: von Ahsen

first: Thibault

last: Bouderlique

first: Johan

last: Boström

first: Tatiana

last: Solovieva

first: Cameron

last: Jackson

first: Marianne

last: Bronner

first: Dies

last: Meijer

first: Saida

last: Hadjab

first: Francois

last: Lallemend

first: Alek

last: Erickson

first: Marketa

last: Kaucka

first: Viacheslav

last: Dyachuk

first: Thomas

last: Perlmann

first: Laura

last: Lahti

first: Jan

last: Krivanek

last: Brunet

first: Kaj

last: Fried

first: Igor

last: Adameyko


title: A preliminary, observational study using whole-blood RNA sequencing reveals differential expression of inflammatory and bone markers post-implantation of percutaneous osseointegrated prostheses

status: Public on Apr 04 2022

city: Salt Lake City

first: Sujee

last: Jeyapalina

state: Utah

address: 500 Foothill Dr

institute: Department of Veteran Affairs

summary: While the benefits of direct skeletal attachment of artificial limbs are well recognized, device failure due to infection and insufficient osseointegration remain obstacles to obtaining consistent, successful outcomes. Currently, the potential for device failure is assessed by clinical, radiographic evidence of bone atrophy, the presence of radiolucent lines at the bone-implant interface, and subjective pain and function scores. Our hypothesis is that measurable biological indices might add an objective means to assess trends toward bone and stomal healing. This longitudinal cohort study was undertaken to identify potential serological biomarkers suggestive of bone remodeling and the presence of stomal tissue inflammation. Ten unilateral transfemoral amputee Veterans, who were implanted with a percutaneous osseointegration (OI) system, were recruited to participate in this IRB-approved study. Venous blood samples were obtained from before the Stage 1 Surgery up to 1 year following the Stage 2 Surgery. Whole-blood RNA was extracted, sequenced, mapped, and analyzed. Of the significant differentially expressed (DEGs) genes (p<0.05) identified, four genes (IL12B, IL33, COL2A1, and SOST) were validated using qPCR. Enrichment analysis was performed to identify significant (p<0.01) Gene Ontology (GO) terms. Most DEGs were only detected at PoS1 immediately after the first surgery. Four significant genes identified, IL12B and IL33, related to inflammation, and COL2A1 and SOST associated with bone remodeling were identified with greater than 20 log fold-change. Whole-blood RNA-seq data from 10 patients who previously underwent percutaneous osseointegrated lower limb implantation revealed four genes of interest that are known to be involved in inflammation or bone remodeling. If verified in future studies, these genes may serve as markers for predicting optimal bone remodeling and stomal tissue healing following OI implantation.

overall_design:
Whole-blood samples were collected from patients before their first surgery and up to 12 months after their second surgery. A total of 97 samples were collected.

Please note that the values in the 'characteristics: time point' represent:
PrS: pre-surgery
PoS: post-surgery
W: week
M: month
For example, PoS2-W2 means post-surgery 2 week 2.


title: Cortex DNA methylation profiles for the Brains for Dementia research cohort

status: Public on Jun 27 2022

city: Exeter

first: Eilis

last: Hannon

address: RILD building

institute: University of Exeter

summary: Genome-wide patterns of DNA methylation were quantified using the Illumina Infinium HumanMethylationEPIC BeadChip (“EPIC array”) in DNA samples isolated from cortex (dorsolateral prefrontal cortex and occipital cortex) for individuals with various amounts of dementia neuropathology.

overall_design: This data includes 1221 adult samples profiled as part of the Brains for Dementia research (BDR) cohort. It includes data for 610 dorsolateral prefrontal cortex samples and 611 occipital cortex samples.

first: G

last: Shireby

first: E

first: J

last: Mill


title: ANKRA2-regulated transcriptome in U2OS

status: Public on Mar 04 2022

city: Jena

first: Martin

last: Fischer

state: Thuringia

address: Beutenbergstraße 11

institute: Leibniz Institute on Aging - Fritz Lipmann Institute (FLI)

summary: Identification of the ANKRA2-regulated transcriptome in Nutlin-3a and DMSO control treated U2OS cells

overall_design: RNA-seq (PolyA) from Nutlin-3a and DMSO control treated U2OS cells transfected with siControl or siANKRA2

first: Konstantin

last: Riege

first: Steve

last: Hoffmann


title: Analysis of gastrocnemius muscle transcriptome from chow-fed WT-control and UCP1 knockout female rats at room temerature and after exposure to 4 degrees Celsius

status: Public on Mar 01 2022

city: Baton Rouge

first: Jaycob

last: Warfel

state: Louisiana

address: 6400 Perkins Road

department: RNA Homeostasis

institute: PBRC

summary: To determine the effects of cold exposure on skeletal muscle gene expression in rats with and without UCP1, we assessed gastrocnemius muscle in chow-fed control and whole body UCP1 knockout rats using RNA-seq.

overall_design: Examination of gastroc mRNA profiles in 2 different temperature condition in control and Ucp1 KO female rats

first: Randall

last: Mynatt

first: Sujoy

last: Ghosh

first: Susan

last: Newman

first: Richard

middle: P

last: Carmouche

first: Jasleen

last: Kaur

first: Sara

last: Webb


title: Histone deacetylation primes chromatin to preserve epigenetic memory for self-propagation of heterochromatin domains [Clr3-CDx2]

status: Public on Jul 12 2022

city: Bethesda

first: Shiv

last: Grewal

address: NCI bldg 37 Rm 6068 9000 Rockville Pike

institute: NCI

summary:
Clr3-CDx2 occupancy along fission yeast chromosomes.
Chromodomain-mediated  loading targets  Clr3-CDx2  to heterochromatin domains.

overall_design: DNA co-purified with Clr3-CDx2 chromatin was random-prime PCR amplified and analyzed using custom 60mer Agilent array that tiles Schizosaccharomyces pombe genome in 300bp intervals.

last: Zofall

first: Rima

last: Sandhu

first: Sahana

last: Holla

first: David

last: Wheeler


title: The molecular phenotypes of injury, steatohepatitis, and fibrosis in liver transplant biopsies in the INTERLIVER study

status: Public on Jan 09 2022

city: Edmonton

first: Jessica

last: Chang

address: 250 Heritage Medical Research Centre

department: Medicine

institute: University of Alberta

summary: To extend previous molecular analyses of rejection in liver transplant biopsies in the INTERLIVER study (ClinicalTrials.gov #NCT03193151), the present study aimed to define the gene expression selective for parenchymal injury, fibrosis, and steatohepatitis. PC1 reflected parenchymal injury and related inflammation in the early posttransplant period, slowly regressing over many months. PC2 separated early injury from late fibrosis. Positive PC3 identified a distinct mildly inflamed state correlating with histologic steatohepatitis. Injury PCs correlated with liver function and histologic abnormalities. A classifier trained on histologic steatohepatitis predicted histologic steatohepatitis with cross-validated AUC=0.83, and was associated with pathways reflecting metabolic abnormalities distinct from fibrosis. PC2 predicted histologic fibrosis (AUC=0.80), as did a molecular fibrosis classifier (AUC=0.74). The fibrosis classifier correlated with matrix remodeling pathways with minimal overlap with those selective for steatohepatitis, although some biopsies had both. Genome-wide assessment of liver transplant biopsies can not only detect molecular changes induced by rejection but also those correlating with parenchymal injury, steatohepatitis, and fibrosis, offering potential insights into disease mechanisms for primary diseases.

overall_design: We analyzed genome-wide microarray measurements from 337 liver transplant biopsies from 13 centers. We examined expression of genes previously annotated as increased in injury and fibrosis using principal component analysis (PCA).


title: single cell transcriptome profiling for palm and hip skin

status: Public on Feb 09 2022

city: Ann Arbor

first: Lam

last: Tsoi

state: MI

address: Medical Sciences 1 Bldg. 1301 E. Catherine

institute: University of Michigan

summary: single cell RNA-seq profiling of palm and hip

overall_design: We conducted scRNA-seq of the epidermal and dermal layers of skin from palm and hip

first: Johann

last: Gudjonsson


title: Vocal learning-associated convergent evolution in mammalian regulatory elements and proteins

status: Public on May 24 2022

first: Morgan

last: Wirthlin

summary: This represents the first transcriptomic and epigenomic characterization of the vocalization-associated brain circuits of a non-human mammalian vocal learner (Egyptian fruit bat), yielding fundamental insights into the regulatory and molecular pathways underlying the evolution of complex vocal behavior in mammals.

overall_design: We generated ATAC-seq and RNAseq from a range of adult Egyptian fruit bat (Rousettus aegyptiacus) tissues, including 7 brain regions and 3 non-brain tissues.

first: Xiaomeng

last: Zhang

first: Irene

last: Kaplow

first: Andreas

last: Pfenning


title: ImmGen cytokines: Signatures of “common γ-chain” family cytokines

status: Public on Jan 01 2022

city: Boston

first: Liang

last: Yang

state: MA

address: 77 Avenue Louis Pasteur

department: Pathology

institute: Harvard Medical School

summary: Profiling of early in-vivo responses to the 6 common gamma-chain family cytokines, in 14 immunologic cell-types.

overall_design:
5-8 week old C57Bl/6J mice from the Jackson Laboratory were injected intravenously with free cytokine or a cytokine-antibody complex (10ug mIL2; 5 μg IL4 with 25 μg 11B11 anti-IL4 mAb; 0.75ug mIL7 with 15ug anti-IL7 M25 mAb; 5ug mIL9; 2.5ug mIL15 with 15ug mIL15Ra-Fc; 20ug mIL21. After 2 hours, spleen and peritoneal cavity cells were harvested, and 14 myeloid and lymphoid cell-types were sorted (double-sorted per ImmGen SOP) and processed for RNA-seq.
- Mast Cell	Perit. Cavity	MC	CD45+[CD11b-CD11c-][CD19-CD4-CD8-]CD117+FcEr1a+
- Large PC Macrophage 	Peritoneal Cavity	MF.PC	ICAM2+F4/80
- Treg Cell	Spleen	Treg	CD19-CD8-TER119-GR1-TCRB+CD4+CD25hi
- Tgd Cell	Spleen	Tgd	CD19-CD8-TER119-GR1-TCRB-TCRgd+
- NK Cell	Spleen	NK	CD19-CD8-TER119-GR1-TCRB-NK1.1+
- CD8+ Dendritic Cell	Spleen	DC8	TCRB-CD11chiCD8a+
- Classical Monocytes	Spleen	Mo	CD115+Ly6C+
- Plasmacytoid Dendritic Cell	Spleen	pDC	CD11cintB220+SiglecH+
- Neutrophil	Spleen	GN	TCRB-B220-Ly6G+(clone 1ab)
- Red Pulp Macrophage	Spleen	MF.RP	TCRB-MHCIIint-F4/80hi
- Follicular B Cell	Spleen	Bfo	CD19+TCRB-CD93-CD23+CD43-CD5-
- MZB Cell	Spleen	MZB	CD19+TCRB-CD93-CD23-CD21hi
- Naïve CD4+ Tab cell	Spleen	T4n	CD19-TCRB+CD4+CD8-CD62Lhi
- Effector/Mem CD8+ Tab cell	Spleen	T8em	CD19-TCRB+CD4-CD8+CD62L-

first: Alev

last: Baysoy

first: Kumba

last: Seddu

first: Felicia

last: Chen

first: Christophe

last: Benoist


title: Single cell transcriptical changes in major trauma patient

status: Public on Feb 26 2022

city: Wuhan

first: Zhaohui

last: Tang

state: Hubei

address: no.1095 Jiefang Avenue

department: Division of Trauma & Surgical Critical Care, Department of Surgery

institute: Tongji Hospital

summary: The mortality rate for patients with trauma is 5.8 million per year. For people aged 15-49, trauma is one of the three leading causes of death. Activation of the coagulation system, intractable hypoxemia, infections and acidosis accompanying post-traumatic patients cannot be separated from trauma immunization. The purpose of this research is to understand the expression of immune cells in patients after trauma, especially severe multiple injuries, and to construct an immune cell profile of patients with multiple injuries.

overall_design:
The inclusion criteria for trauma patients are:
1) male trauma patients (manual laborers with ISS score > 25)
2) Patients between the ages of 18 and 50 years.
3) No blood transfusion and no hormonal therapy prior to specimen collection
4) No significant immunosuppression.
5) About 8-16 h after the injury.
This research studied the early immunity of patients with multiple injuries, and collected single cell information from three patients with multiple injuries and three control patients to clarify the early immunity of patients with multiple injuries and to understand the initiating factors of immunity in patients with multiple injuries.

first: Jingzhi

first: Teding

first: Liangsheng

first: Hai

last: Deng

first: Deng

first: Jialiu

last: Luo

first: Cong

first: Zhenwen

last: Li

first: Han

last: Wu

first: Tingxuan

first: Liming

last: Dong


title: EZH2 non-canonically binds cMyc and p300 through a cryptic transactivation domain to mediate gene activation and promote oncogenesis [RNA-seq]

status: Public on Dec 29 2021

city: Nanjing

first: jun

last: wang

state: Jiangsu

address: No. 163 Xianlin Avenue, Qixia District

institute: Nanjing University

summary: Canonically, Enhancer of Zeste Homolog 2 (EZH2) serves as the main catalytic subunit of Polycomb Repressive Complex 2 (PRC2), mediating H3K27me3 deposition and transcriptional repression. Here, we report that, in MLL1-rearranged acute leukemias, EZH2 has additional noncanonical functions by binding the oncoprotein cMyc at its non-PRC2 target sites where EZH2 uses a hidden transactivation domain (TAD) for (co)activator recruitment and gene activation. Canonical (EZH2:PRC2) and noncanonical (EZH2-TAD:cMyc) activities of EZH2 both promote oncogenesis, thus explaining the slow and often ineffective antitumor effects by current catalytic inhibitors of EZH2. To suppress EZH2’s multifaceted activities in cancer, we employed the Proteolysis Targeting Chimera (PROTAC) technology and developed a small-molecule degrader, MS177, which achieved effective, on-target depletion of EZH2 and its interacting partners (i.e., both canonical EZH2:PRC2 and noncanonical EZH2:cMyc complexes). MS177-mediated onco-target degradation is cereblon- and proteasome-dependent. Compared to EZH2 enzymatic inhibitors, MS177 is fast-acting and much more potent in suppressing cancer growth. Overall, this study reveals noncanonical oncogenic functions of EZH2, and presents a highly effective PROTAC for targeting EZH2’s multifaceted tumorigenic actions and a novel and attractive therapeutic strategy for the treatment of EZH2-depdendent cancers.

overall_design: Examination of transcriptome profiles in MV4;11 cells with depletion of either EZH2 (shEZH2) or cMyc (knockout by independent sgRNAs, sg1 or sg5) or EOL-1 cells with depletion of EZH2 (sgEZH2)

first: Jun

last: Wang

first: Greg


title: EZH2 non-canonically binds cMyc and p300 through a cryptic transactivation domain to mediate gene activation and promote oncogenesis [CUT&RUN]

overall_design: Use CUT&RUN to examine the genome-wide binding of HA-tagged EZH2 and cMyc in EOL-1 and MV4;11 cells, as well as EZH2, H3K27me3, H3K27ac and cMyc in the acute myeloid leukemia (AML) patient-derived xenograft (PDX) cells carrying MLL-AF9 fusion (from PRoXe; DFAM-68555).


title: EZH2 non-canonically binds cMyc and p300 through a cryptic transactivation domain to mediate gene activation and promote oncogenesis

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

overall_design: Refer to individual Series


title: EZH2 non-canonically binds cMyc and p300 through a cryptic transactivation domain to mediate gene activation and promote oncogenesis [RNA-Seq]

overall_design: Use RNA-seq to examine the transcriptome profiles of EOL-1, MV4;11, and MOLM13 cells, treated with either DMSO, C24 (an EZH2 inhibitor), MS177 (a C24-based CRBN-dependent PROTAC of EZH2), or MS177N1 (an MS177-related analog compound incapable of binding to CRBN E3 ligase).


title: EZH2 non-canonically binds cMyc and p300 through a cryptic transactivation domain to mediate gene activation and promote oncogenesis [ChIP-Seq]

overall_design: Use ChIP-seq to examine the genome-wide binding of EZH2 or H3K27me3 in EOL-1 or MV4;11 cells, treated with either DMSO, C24 (an EZH2 inhibitor) or MS177 (the EZH2 PROTAC/degrader); a fraction of Drosophila chromatin was added as spike-in control, probed with the Drosophila specific H2Av antibody, for accessing relative binding of EZH2 or H3K27me3 post-treatment of different compounds.


title: Gene expression profiling of  mycosis fungoides with and without LCT as well as CTCL cell lines via PEG10 knockdown and overexpression by RNA-seq

status: Public on Dec 25 2021

city: Beijing

first: Fengjie

last: Liu

address: No.8 Xishiku Street, Xi Cheng District

department: Dermatology and Venereology

institute: Peking University First Hospital

summary: Mycosis fungoides (MF), the most common subtype of cutaneous T-cell lymphoma (CTCL), may undergo large-cell transformation (LCT), which is related to aggressive clinical courses and resistance to conventional treatments. However, the mechanisms of LCT remain largely unknown.We performed RNA-seq on biopsied specimens isolated from 26 MF-LCT patients and 23 MF-NLCT patients to decipher the mechanisms underlying LCT. We found PEG10 was overexpressed in MF-LCT compared with MF -NLCT cases. In order to explore the function of PEG10 in the pathogenesis of MF, transcriptome sequencing  was performed  among  HH cells transfected with shRNAs targeting PEG10 (shPEG10) and scrambled shRNA(sh0) , Myla cells transfected with empty vetors(vec) and PEG10 expression vectors ( RF1b, RF1b/2, RF1b/2+CNF) to investigate genes regulated by PEG10 in CTCL cells .

overall_design:
Two-condition experiment  1) MF skin-biopsy samples: 26 MF-LCT vs 23 MF-NLCT; 2) CTCL cell line HH: sh0 vs shPEG10. Biological replicates: 3 sh0 replicates, 3 shPEG10 replicates; 3) CTCL cell line Myla: vec vs PEG10. Biological replicates: 3 vec replicates, 5 PEG10 replicates (containing 2 PEG10-RF1b replicates (sPEG10_OE1， sPEG10_OE2), 2 PEG10-RF1b/2 replicates (lPEG10_OE1，lPEG10_OE2), 1 PEG10-RF1b/2+CNF(lPEG10_OE3))

**Please note that the records have been updated with additional sample characteristics information on Sep 18, 2024.

first: Yang


title: RNA sequencing data of TCam-2, 2102EP, JAR, JEG-3, NCCIT, and MPAF fibroblast cells treated with palbociclib and H2O pH3 as solvent control

status: Public on Dec 15 2021

city: Düsseldorf

first: Daniel

last: Nettersheim

state: NRW

address: Moorenstr. 5

department: Dep. of Urology

institute: Medical Faculty and University Hospital Düsseldorf, Heinrich Heine University

overall_design: Single end 3' RNA sequencing of  cell lines (TCam-2, 2102EP, JAR, JEG-3, NCCIT, and MPAF fibroblasts) treated with the CDK4/6 inhibitor 10 μM palbociclib for 16 h. H2O pH3 was used as a solvent control.


title: Expression data of mouse calvarial stem cells from p75 floxed mice (p75fl/fl) stimulated with Adenovirus encoding Cre recombinase (Ad-Cre) or control (Ad-GFP) [RNA-seq]

status: Public on Dec 22 2021

city: Baltimore

first: Aaron

last: James

state: MD

address: 600 North Wolfe Street

institute: Johns Hopkins University School of Medicine

summary: The cranial sutures are fibrous joints containing skeletal progenitor cells, which maintain homeostasis of the uninjured skull or participate in healing the skull after injury. Nerve growth factor (NGF) via its high-affinity receptor tropomyosin receptor kinase A (TrkA) regulates skeletal re-innervation, which is essential for later elements of bone repair, including revascularization and bone matrix deposition. However, emerging evidence suggests that NGF signaling may have more pleiotropic effects in bone repair than previously considered. In addition to induction of nerve ingrowth and promotion of nerve survival, pro-NGF may bind to its low-affinity receptor Ngfr (p75, Cd271), which is present in a variety of mesenchymal cells. p75 expression has been correlated to cell migration and invasion in multiple cell types. NGF binding to the p75 receptor stimulates migration and initiates recruitment of various adaptors, which activate NF-κB, RhoA, and c-Jun N-terminal kinase (JNK) signaling. In this study, changes in the transcriptome of calvarial stem cells after p75 knockout were evaluated by RNA sequencing.

overall_design: 6 Total samples were analyzed, 3 Adenovirus-Cre treated versus 3 Avenovirus-Vector controls.

first: Jiajia

last: Xu

first: Zhao


title: Myeloid-to-mesenchymal NGF-p75 signaling coordinates cell migration during repair.


title: Myeloid-to-mesenchymal NGF-p75 signaling coordinates cell migration during bone repair [scRNA-seq]

summary: The cranial sutures are fibrous joints containing skeletal progenitor cells, which maintain homeostasis of the uninjured skull or participate in healing the skull after injury. Nerve growth factor (NGF) via its high-affinity receptor tropomyosin receptor kinase A (TrkA) regulates skeletal re-innervation, which is essential for later elements of bone repair, including revascularization and bone matrix deposition. However, emerging evidence suggests that NGF signaling may have more pleiotropic effects in bone repair than previously considered. In addition to induction of nerve ingrowth and promotion of nerve survival, pro-NGF may bind to its low-affinity receptor Ngfr (p75, Cd271), which is present in a variety of mesenchymal cells. p75 expression has been correlated to cell migration and invasion in multiple cell types. NGF binding to the p75 receptor stimulates migration and initiates recruitment of various adaptors, which activate NF-κB, RhoA, and c-Jun N-terminal kinase (JNK) signaling. In this study, single cell transcriptomics highlights altered signaling pathway activation and impaired cellular migration with p75 conditional gene deletion in PDGFRα-expressing cells.

overall_design: 2 Total samples were analyzed comparing mRNA from p75 floxed mice (p75fl/fl) and p75 conditional knockout mice (p75PDGFRα).


title: The MYCN oncoprotein resolves conflicts of stalling RNA Polymerase with the replication fork

status: Public on Dec 10 2021

city: Wuerzburg

first: Martin

last: Eilers

address: Am Hubland

department: Chair for Biochemistry and Molecular Biology

institute: University of Wuerzburg


title: The MYCN oncoprotein resolves conflicts of stalling RNA Polymerase with the replication fork [DP_EXOSC10_Screen]

summary: During the S-phase, conflicts of replication forks with RNA Polymerase II (RNAPII) threaten genomic stability. While the PAF complex can resolve such conflicts during elongation, the particularly deleterious conflicts with stalling RNAPII are resolved by an as of yet unknown mechanism. Here we show that the MYCN oncoprotein forms a ternary complex with RNAPII and the nuclear RNA exosome, a 3’‑5’ exoribonuclease complex. Together with TFIIS, this complex restarts promoter‑proximal RNAPII, allows escape from co-directional transcription-replication conflicts and prevents double‑strand break accumulation. In cells lacking RNA exosome function, MYCN globally terminates transcription. MYCN-mediated termination is triggered by ATM‑dependent recruitment of BRCA1, which then stabilizes nuclear mRNA decapping complexes. Disruption of mRNA decapping activates ATR, indicative of head-on transcription-replication conflicts, and inhibits DNA replication. We propose that MYCN resolves transcription-replication conflicts via this two-step mechanism to sustain the rapid proliferation of neuroendocrine tumor cells.

overall_design: Drop-out screen using pooled doxycycline (Dox)-inducible shRNAs in SH-EP-MYCNER cells, that allow MYCN activation by addition of 4-hydroxytamoxifen (4-OHT). Two biological replicates, all conditions done in triplicate.

first: Dimitrios

last: Papadopoulos

first: Jacqueline

last: Kalb

last: Solvie

first: Apoorva

last: Baluapuri

first: Steffi

last: Herold

first: Theresa

last: Endres

first: Celeste

last: Giansanti

first: Christina

last: Schülein-Völk

first: Carsten

last: Ade

first: Cornelius

last: Schneider

first: Utz

last: Fischer

first: Matthias

last: Dobbelstein

first: Elmar

last: Wolf


title: The MYCN oncoprotein resolves conflicts of stalling RNA Polymerase with the replication fork [DP_EXOSC10_BLISS]

overall_design: BLISS after EXOSC10 depletion with doxycycline (Dox)-inducible shRNAs in SHEP-MYCNER cells, which allow MYCN activation by addition of 4-hydroxytamoxifen (4-OHT). Replicates indicated by R.

first: Daniel


title: The MYCN oncoprotein resolves conflicts of stalling RNA Polymerase with the replication fork [DP_EXOSC10_ChIP_4sUseq]

overall_design: ChIPRX and 4sUseq experiments after ATM inhibition or after knock-down of EXOSC10, TCEA1, or DCP1A via Dox-inducible shRNAs in SH-EP-MYCNER cells, which allow MYCN activation via 4-OHT addition . Replicates indicated by R, all ChIPRX experiments normalized to mouse NIH3T3 spike-in, except for MYCN ChIPseq. No chase 4sU experiment normalized to 4sU-labelled mouse T-cell spike-in, all other 4sUseq experiments read normalized.


title: RIOK2-dependent transcriptional changes in primary human hematopoietic stem and progenitor cells (HSPCs)

status: Public on Dec 02 2021

first: Shrestha

last: Ghosh

address: SM 752, Smith building, 1 Jimmy Fund Way

institute: Dana Farber Cancer Institute, Boston

summary: Purpose: Illumina next-generation sequencing (NGS) has been used to interrogate the transcriptome profiling (bulk RNA-seq) of primary human HSPCs in the presence and absence of RIOK2. Primary human hematopoietic stem and progenitor cells (HSPCs) isolated from 3 different donors were genome edited to obtain knockdown (KD) and knockout (KO) of RIOK2. The genome edited HSPCs were then differentiated for 48 hours and their total RNA was isolated to perform cDNA synthesis and bulk RNA sequencing. The overall goal of this study was to investigate the global alterations in gene expressions with dose-dependent loss of RIOK2 in primary human HSPCs, that would expand our understanding of RIOK2-dependent transcriptomic changes involved in hematopoietic differentiation.

overall_design: Primary human HSPCs isolated from 3 different donors were subjected to genome-editing using CRISPR-Cas9 to generate knockdown (KD) and knockout (KO) of RIOK2. The cells were placed in differentiation media for 48 hours followed by RNA extraction. RNA sequencing libraries were prepared using the NEBNext Ultra RNA Library Prep Kit for Illumina following manufacturer’s instructions (NEB, Ipswich, MA, USA). Briefly, mRNAs were first enriched with Oligo(dT) beads. Enriched mRNAs were fragmented for 15 minutes at 94 °C. First strand and second strand cDNAs were subsequently synthesized. cDNA fragments were end repaired and adenylated at 3’ends, and universal adapters were ligated to cDNA fragments, followed by index addition and library enrichment by limited-cycle PCR. The sequencing libraries were validated on the Agilent TapeStation (Agilent Technologies, Palo Alto, CA, USA), and quantified by using Qubit 2.0 Fluorometer (Invitrogen, Carlsbad, CA) as well as by quantitative PCR (KAPA Biosystems, Wilmington, MA, USA). The sequencing libraries were clustered on 1 lane of a flowcell. After clustering, the flowcell was loaded on the Illumina HiSeq instrument (4000 or equivalent) according to manufacturer’s instructions. The samples were sequenced using a 2x150bp Paired End (PE) configuration. Image analysis and base calling were conducted by the HiSeq Control Software (HCS). Raw sequence data (.bcl files) generated from Illumina HiSeq was converted into fastq files and de-multiplexed using Illumina's bcl2fastq 2.17 software.

first: Laurie

middle: H

last: Glimcher


title: Comprehensive profiling of myxopapillary ependymomas identifies a distinct molecular subtype with relapsing disease

status: Public on Apr 25 2022

city: Hamburg

first: Michael

last: Bockmayr

address: Martinistr. 52

department: Pediatric Hematology and Oncology

institute: University Medical Center Hamburg-Eppendorf

type: Methylation profiling by genome tiling array

summary: Myxopapillary ependymoma is a heterogeneous disease with respect to histopathology and clinical outcome. However, there are no diagnostic markers or clinical parameters that reliably predict the progression-free survival of the respective patients. We analyzed 185 tumors that classified as myxopapillary ependymoma based on global DNA methylation. Of these, 46 samples have been previously analyzed in GSE65362, GSE90496 or GSE109381. Using k-means clustering, our series split up into two distinct subtypes: MPE-A occurred in younger patients (median age 27 years) and were significantly enriched with tumors demonstrating papillary morphology and MGMT promoter methylation. Half of these tumors could not be totally resected, and 85% relapsed within 10 years. On the other hand, MPE-B occurred at a median age of 45 years. They included a significantly higher number of tumors with an initial diagnosis of WHO grade II and tanycytic morphology. Importantly, patients within this subgroup had a significantly better outcome with a relapse rate of only 33% in 10 years.

overall_design: 185 specimens were analyzed using the Illumina Infinium HumanMethylation450 or the MethylationEPIC BeadChip.

first: Ulrich

last: Schüller


title: Genome wide maps of chromatin accessibility in primary human CD34+ stem and progenitor cells

summary: We report that loss of RIOK2 leads to global alterations in chromatin accessibility in primary human hematopoietic stem and progenitor cells.

overall_design: ATAC-sequencing analysis performed in the presence and absence of RIOK2 in differentiating primary human CD34+ stem and progenitor cells.


title: RNA-Sequencing of Xenopus tail regeneration using small molecule antagonists of Hif1a or Wnt signaling

status: Public on Dec 01 2021

city: Seattle

first: Jeet

last: Patel

state: WA

address: HSB J-Wing, J405

department: Biochemistry

institute: University of Washington

summary: Regeneration of complex tissues is initiated by an injury-induced stress response, eventually leading to activation of developmental signaling pathways, such as Wnt signaling. How early injury cues are interpreted and coupled to activation of these developmental signals and their targets is not well understood. Here, we show that Hif1α, a stress induced transcription factor, is required for tail regeneration in Xenopus tropicalis. We find that Hif1α is required for regeneration of differentiated axial tissues, including axons and muscle. Using RNA-sequencing, we find that Hif1α and Wnt converge on a broad set of genes required for posterior specification and differentiation, including the posterior hox genes. We further show that Hif1α is required for transcription via a Wnt-responsive element, a function that is conserved in both regeneration and early neural patterning. Our findings indicate a regulatory role for Hif1α in Wnt mediated gene expression across multiple tissue contexts.

overall_design: Tail tissue proximal to the amputation site (for 0hpa) or regenerating tissue (24hpa following treatment with DMSO, 2-methoxyestradiol, echinomycin, or IWR-1) was collected for RNA extraction. Paired end sequencing was performed on prepared libraries via an Illumina HiSeq instrument.

first: Andrea

last: Wills


title: Ultra-Deep Single-Cell Analyses Reveals Novel Mechanisms of Gut Enteroendocrine Cell Sensing Dysfunction in Human Obesity

status: Public on Nov 30 2021

city: Rochester

first: Maria

middle: Laura

last: Ricardo Silgado

state: Minnesota

address: 222 3rd Ave SW

department: Gastroenterology and Hepatology

institute: Mayo Clinic

summary: We sought to investigate the transcriptomic profile of native human EECs at an ultra-deep single-cell level from endoscopic biopsies of patients with normal weight, and obesity with and without abnormal satiety. EECs transcriptomic revealed several molecular signatures of obesity in the form of both single-gene and pathway level alterations, including terminal differentiation, hormone processing, negative feedback circuits, and GPCR-signaling. The aberrant GPCR-signal is mediated by over-expression of the regulator of G-protein receptor signaling (RGS) pathway, a global negative regulator of GPCRs signaling. We confirmed co-expression of RGS9 in human EECs, and its expression is negatively correlated postprandial PYY blood levels. Furthermore inhibition of RGS9 in primary culture of human colonic tissue increased GLP-1 and PYY release from EECs ex vivo. Our study provides a rich data source and describes a novel aberrant pathway in EEC-signaling in human obesity.

overall_design: Single cell RNA-Sequencing from thirteen sigmoid mucosal biopsies of patients with obesity and lean

first: Alison

last: McRae

middle: L

last: Ricardo-Silgado

first: Yuanhang

last: Liu

first: Gerardo

last: Calderon

last: Gonzalez

first: Fariborz

last: Rohakhtar

first: Cadman

last: Leggett

first: Vernadette

last: Simon

first: Ying

last: Li

first: Fiona

last: Gribble

first: Andres

last: Acosta


title: Distinct Transcriptosomes of Kidneys of Chronic Kidney Disease Mice with Time Restricted Feeding

status: Public on Nov 24 2021

city: Seoul

first: Yina

last: Fang

address: 64, Goryeodae-ro 17ga-gil, Seongbuk-gu

institute: Korea University Anam Hospital

summary: To further character the significant changes in renal gene expression after time restricted feeding (TRF) treatment in CKD mice,RNA-sequencing was performed in the kidneys.

overall_design: The RNAs from kidney of control, CKD and CKD TRF mice was extracted and sent to E-Biogen Inc for QuantSeq 3` mRNA-Seq

first: Myung-Gyu

last: Kim


title: Ischemic heart disease selectively modifies the right atrial appendage transcriptome

status: Public on Nov 15 2021

city: Ankara

first: Arda

last: Eskin

state: Cankaya

address: Universiteler Mah.

department: Informatics Institute

country: Turkey

institute: Middle East Technical University

summary:
Purpose: This study aims to identify IHD-associated signature RNAs from the atrial myocardium and evaluate their ability to reflect disease severity or cardiac surgery outcomes.
Methods: We collected right atrial appendage (RAA) biopsies from 40 patients with invasive coronary angiography (ICA)-positive IHD undergoing coronary artery bypass surgery and from 8 patients ICA-negative for IHD (non-IHD) undergoing valvular surgery. Following RNA sequencing, RAA transcriptomes were analyzed against those 429 donors from the GTEx project without cardiac background.
Results: The IHD transcriptome was characterized using repressed RNA expressions in pathways for cell–cell contacts and mitochondrial dysfunction. Specifically, we identified the increased expressions of the CSRNP3, FUT10, SHD, NAV2-AS4, and hsa-mir-181 genes to correlate with the complexity of coronary artery obstructions or with a functional cardiac benefit from bypass surgery.
Conclusions: Our results provide an atrial myocardium–focused insight into IHD signature RNAs. The specific gene expression changes we characterized here pave the way for disease mechanism–based identification of biomarkers allowing for the early detection and treatment of IHD.

overall_design: Atrial appendage mRNA profiles of invasive coronary angiography (ICA)-positive IHD undergoing coronary artery bypass surgery and ICA-negative for IHD (non-IHD) undergoing valvular surgery.

first: Severi

last: Mulari

first: Milla

last: Lampinen

first: Annu

last: Nummi

first: Tuomo

last: Nieminen

first: Kari

last: Teittinen

first: Teija

last: Ojala

first: Matti

last: Kankainen

first: Antti

last: Vento

first: Jari

last: Laurikka

first: Markku

last: Kupari

first: Ari

last: Harjula

first: Nurcan

last: Tuncbag

first: Esko

last: Kankuri


title: Endogenous retroviruses mediate transcriptional rewiring in response to oncogenic signaling in colorectal cancer [CUT&RUN]

status: Public on Oct 31 2021

city: Boulder

first: Edward

middle: Boyi

last: Chuong

state: CO

address: JSC Biotech Building, 3415 Colorado Ave

department: BioFrontiers Institute and Molecular, Cellular & Developmental Biology Department

institute: University of Colorado Boulder

summary: Cancer cells exhibit rewired transcriptional regulatory networks that promote tumor growth and survival. However, the processes that configure these pathological networks remain poorly understood. Through a pan-cancer epigenomic analysis, we found that primate-specific endogenous retroviruses (ERVs) are an abundant source of enhancers that mediate transcriptional dysregulation in cancer. In colorectal cancer and other epithelial tumors, AP1 signaling drives aberrant activation of enhancers derived from the primate-specific ERV family LTR10. CRISPR studies revealed that LTR10 elements control colorectal cancer-specific gene expression at multiple loci associated with tumorigenesis. Within the human population, individual LTR10 elements show extensive structural variation due to repeat instability of an internal variable number tandem repeat (VNTR) region that affects AP1 binding. Our findings reveal that ERV-derived enhancers link oncogenic signaling to transcriptional dysregulation and shape the evolution of cancer-specific regulatory networks.

overall_design: Epigenomic (CUT&RUN) profiling of a colorectal cancer cell line (HCT116) that was either untreated or treated with 1 uM Cobimetinib or 100 ng/mL TNF-alpha for 24hr.

first: Atma

last: Ivancevic

first: David

last: Simpson

first: Olivia

last: Joyner

first: Stacey

last: Bagby

first: Lily

last: Nguyen

first: Ben

last: Bitler

first: Todd

last: Pitts

middle: B


title: Endogenous retroviruses mediate transcriptional rewiring in response to oncogenic signaling in colorectal cancer

overall_design: Refer to individual Series


title: The Role of Circadian Clock System in Chronic Kidney Disease.

first: Yina

last: Fang

summary: To better elucidate underlying mechanisms of circadian gene disruption on chronic kidney disease, we compared whole kidney transcriptome profiles between kidneys of  WT and Bmal1 KO mice.

overall_design: The RNAs from kidney of wild type (WT) and Bmal1 KO mice was extracted and sent to E-Biogen Inc for QuantSeq 3` mRNA-Seq

first: Myung-Gyu

last: Kim


title: Orosomucoid 2 maintains hepatic lipid homeostasis through suppression of de novo lipogenesis

status: Public on Oct 19 2021

city: Shanghai

first: Yunchen

last: Luo

address: shanghai hongkou

institute: Shanghai Jiao Tong University School of Medicine

summary: Non-alcoholic fatty liver disease (NAFLD) is caused by imbalance in lipid metabolism. In this study, we show that the hepatokine Orosomucoid 2 (ORM2) is a key regulator of de novo lipogenesis in the liver. Hepatic and plasma ORM2 levels are markedly decreased in obese murine models and NAFLD patients. Through multiple loss- and gain-of function studies, we demonstrate that ORM2 is essential to maintain hepatic and systemic lipid homeostasis. At the mechanistic level, ORM2 binds to inositol 1, 4, 5-trisphosphate receptor type 2 (ITPR2) to activate AMP-activated protein kinase (AMPK) signaling, thereby inhibiting sterol regulatory element binding protein 1c (SREBP-1c)-mediated lipogenic gene program. Notably, intraperitoneal injections of recombinant ORM2 protein or stabilized ORM2-FC fusion protein markedly improved liver steatosis, steatohepatitis and atherosclerosis in preclinical mouse models, without adverse effects on body weight or food intake. Thus, these findings suggest that ORM2 may serve as a potential target for therapeutic intervention in NAFLD, NASH and related lipid disorders.

overall_design: Male ob/ob mice were purchased from GemPharmatech Company (Nanjing, China). Mice were randomly divided into two groups and administered with adenovirus containing GFP or ORM2 (1×10E9 plaque-forming units/mouse) through tail vein injection, respectively. 12 days later, mice were sacrificed and liver tissues were harvested for RNA-Seq analysis and other experiments. The objective of RNA-Seq is to identify potential target genes of ORM2 in improving liver steatosis. In our datasets, Ad-GFP means ob/ob mice transduced with adenovirus containing GFP. Ad-ORM2 means ob/ob mice transduced with adenovirus containing ORM2. n=4 in each group.

first: Bing

last: Zhou

first: Yan

last: Lu


title: Endogenous retroviruses mediate transcriptional rewiring in response to oncogenic signaling in colorectal cancer [RNA-seq]

overall_design: Transcriptional profiling (RNA-seq) of a colorectal cancer cell line (HCT116) that was either untreated or treated with 100 ng/mL Cobimetinib or TNF-alpha for 24 hr. RNA-seq is also provided from clonal HCT116 lines that stably express Cas9 and pairs of gRNAs targeting LTR10 elements near genes: ATG12, XRCC4, MEF2D, FGF2, MCPH1. As well as silencing of the TSS of the following genes: FOSL1 and cJUN and ATG12; and CRISPR knockout of an LTR10 element within gene KDM6A. Finally, RNA-seq is also provided for HCT116 cell line-based xenografts (CDXs) that were either treated with trametinib or a vehicle control. CDX samples were established from HCT116 cells that were engrafted into two immunodeficient mice. Trametinib was purchased from Selleck Chemicals and dissolved in 10% Cremophor EL+5% PEG400 in water. The drug was dosed at 0.125 mg/kg by oral gavage daily for 21 days. Replicates are derived from the left and right flanks of mouse 0 (trametinib-treated) and mouse 95 (treated with a vehicle).

middle: M


title: JAK/STAT blockade in cHL

status: Public on Oct 15 2021

city: Madrid

first: Sara

last: Fernández Robledo

state: Madrid

address: C/ Arturo Soria, 270

institute: Fundación MD Anderson

summary: Here we investigated the effects of JAK/STAT pharmacological inhibition on cHL cell models using ruxolitinib, a JAK 1/2 inhibitor. We use five classical Hodgkin lymphoma cell lines: L428, L1236, L540, KMH2, L591

overall_design: Total RNA was isolated from all the untreated cell lines and after 6, 12, 24 and 48 h of drug incubation with ruxolitinib at the IC50 doses

first: S

last: Fernandez


title: Transcriptome analysis of hair follcile stem cell quiescence

status: Public on Sep 30 2021

first: Chi

last: Zhang

state: Colorado

address: 347 UCB

department: MCDB

summary: Hair follicle stem cells(HFSCs) can transition between active and quiescent stages during normal hair cycle or would healing.  Transcriptional regulation has been show to regulate the transition. Previous studies have shown that two transcription factor, Foxc1 and Nfatc1, can help maintain the stem cells in quiescent state, the deletion of either one could lead to precocious activation. Here, we collect the hair follicle stem cell at postnatal day 30 from both control mice, Nfatc1 knockout mice, Foxc1 knockout mice(downloaded) and Foxc1/Nfatc1 double knockout mice to study the transcriptional regulation network of HFSCs quiescence.

overall_design: Poly(A)-enriched transcriptome RNA-seq on HFSCs isolated at anagen stage(P30) of hair cycle. For K14Cre Nfatc1 control and cKO mice ,HFSCs were isolated using FACS sorting enriching DAPIneg, K14-H2BGFPhi, Sca1lo, α6hi and CD34hi cells. For K15CrePR mouse line, mice were treated with tomaxifen for 6days for induction and  dKO HFSCs were sorted enriching DAPIneg, K14-H2BGFPhi ,  tdtomatohi, Sca1lo and CD34hi cells, control HFSCs were sorted enriching DAPIneg, K14-H2BGFPhi, Sca1low and CD34hi cells.


title: Single cell transcriptomic analysis of aging hair follicles

summary: Tissue stem cells are required for homeostasis and wound repair throughout the entire lifespan.  Multiple mechanisms have been extensively studied for the maintenance of stem cell. Here we use single cell RNAseq to study the stem cell maintenance during aging. We sought out to compare the gene expression changes in different cell lineages between control, Foxc1/Nfatc1 double knockout mice and aging mice.

overall_design: For single cell RNAseq, the epidermal cells were sorted such that the interfollicular epidermis and hair follicle cells were at the ratio of 1:3. Around 5k cells were collected and used for the assay. We followed the 10xgenomics single cell RNAseq protocol version3.


title: Open chromatin analysis of hair follcile stem cell quiescence

summary: Tissue stem cells are required for homeostasis and wound repair throughout the entire lifespan.  Multiple mechanisms have been extensively studied for the maintenance of stem cell quiescence. Here we use Omini-ATACseq and single cell ATACseq to study the stem cell quiescence at epigenetic level. We sought out to compare the open chromatin state in different cell lineages between control and Foxc1/Nfatc1 double knockout mice. The single cell ATACseq could further help infer the transcription regulation between enhancers and promoters interaction.

overall_design: For the bulk omini ATACseq, all the hair follicle stem cells(HFSCs) were FACS sorted and used to perform omini-ATACseq assay. For single cell ATACseq, the epidermal cells were sorted such that the interfollicular epidermis and hair follicle cells were at the ratio of 1:3. A total of 10k cells were collected and used for the assay. We followed the 10xgenomics single cell ATACseq protocol.


title: Escape of hair follicle stem cells from a defective niche

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


title: Altered Human Alveolar Bone Gene Expression in Type 2 Diabetes

status: Public on Oct 01 2021

city: Houston

first: Gena

last: Tribble

state: Texas

address: 1941 East Road, BBS 5324

institute: UTHealth

summary: The objective of this study is to investigate alveolar bone gene expression in health and diabetes through RNA-sequencing and bioinformatics analysis.

overall_design: Cross-sectional, no replicates, 10 healthy, 8 diabetic

first: Srinivas

last: Ayilavarapu

first: Abbas

last: Doctor

first: Chun-Teh

last: Lee

middle: D

first: Robin

last: Weltman

first: Nikola

last: Angelov


title: Comparative analysis of gene expression in brown adipose tissue, beige adipose tissue and white adipose tissue

status: Public on Sep 09 2021

city: Ulm

first: Tamás

last: Röszer

address: Albert-Einstein-Allee 11

department: Institute of Neurobiology

institute: University of Ulm

summary:
We isolated fat depots from mice, and compared their transcriptome.
Hoang, Anh C., Haidong Yu, and Tamás Röszer. 2021. "Transcriptional Landscaping
 Identifies a Beige Adipocyte Depot in the Newborn Mouse" Cells 10, no. 9: 2368.

overall_design: Adult samples: C57Black/6 male mice at age week 8. Infant samples: C57Black/6 mice at postnatal day 6. Tissue samples: WAT=inguinal white adipose tissue, BAT=brown adipose tissue (from interscapular region). The beige adipose tissue is represented by infant WAT.


title: Single-cell RNA-seq reveals the transcriptional landscape in ischemic stroke

status: Public on Sep 24 2021

city: Tianjin

first: Kai

last: Zheng

address: No.154 Anshan Road, Heping District

institute: Tianjin Medical University General Hospital

summary: Here, we employed single-cell RNA sequencing (scRNA-seq) to comprehensively map the cell populations in the mouse model of MCAO (middle cerebral artery occlusion).

overall_design: Single cell suspension was prepared from mouse brain tissues at 24 h after MCAO or sham-operations.

first: Junwei

last: Hao


title: test1

status: Public on Sep 28 2021

city: qq

first: Pierre

middle: X

last: Ledoux

address: qq

institute: werty


title: High Glucose Macrophage Exosomes Enhance Atherosclerosis by Driving Cellular Proliferation & Hematopoiesis [RNA-Seq]

status: Public on Aug 18 2021

city: Phoenix

first: Eric

last: Alsop

state: AZ

address: 445 N 5th St

institute: TGen

summary: Hyperglycemia is a recognized risk factor for cardiovascular complications in diabetes. While hyperglycemia is known to cause microRNA dysregulation that contributes to cellular activation, whether it can do so through intercellular communication via extracellular vesicles (EVs) is not known. We investigated whether EVs produced under hyperglycemic conditions could communicate signaling to drive atherosclerosis. We did so by treating Apoe−/−mice with exosomes produced by bone marrow‐derived macrophages (BMDM) exposed to high glucose (BMDM–HG-exo) or control. Repeated infusion of BMDM–HG-exo led to a robust increase in hematopoiesis leading to augmented circulating myeloid cell numbers. Four weeks of BMDM–HG-exo infusions increased atherosclerotic lesion sizes with an accumulation of macrophage and apoptotic cells in the aortic root. Transcriptome-wide analysis of naïve cultured macrophages treated with BMDM–HG-exo showed an upregulation of genes associated with cell proliferation. Furthermore, BMDM–HG-exo reprogramed energy metabolism in recipient macrophages with an upregulation of glycolytic activity. Plasma EVs isolated from human subjects with type II diabetes exerted similar cell signaling when incubated with cultured human macrophages. Lastly, profiling microRNA in BMDM–HG-exo and human diabetic plasma EVs converged on miR-486 as commonly enriched. In conclusion, our findings show that EVs serve to communicate detrimental

overall_design: RNA-Seq

first: Bouchareychas

last: Laura

first: Alsop

last: Eric

first: Jensen

last: Kendall

first: Raffai

last: Robert


title: High Glucose Macrophage Exosomes Enhance Atherosclerosis by Driving Cellular Proliferation & Hematopoiesis


title: Single cell RNA sequencing of healthy donor human CAR-T cells and adjacent tumor tissue from NSG mice bearing ASPC-1 tumors that are treated with CAR-T cells

status: Public on Sep 01 2021

city: Philadelphia

first: Lexus

last: Johnson

state: Pennsylvania

address: 421 Curie Blvd, 532

department: Radiation Oncology

institute: University of Pennsylvania

summary: The goal of this study was to assess the consequences of RN7SL1 production on CAR-T cell gene expression cells within the ASCP-1 tumor microenvironment. RN7SL1 RNA-producing CAR-T cells are the relevant experimental condition, while control M5BBz CAR-T cells are also collected.

overall_design: Single-cell mRNA profiles. 10X 3' v3.1 chemistry utilized.

first: Andy

last: Minn


title: High Glucose Macrophage Exosomes Enhance Atherosclerosis by Driving Cellular Proliferation & Hematopoiesis [miRNA-Seq]

overall_design: miRNA-Seq


title: Whole embryo depletion of Taf15 in gastrula and neurula stage Xenopus tropicalis embryos

status: Public on Jul 24 2021

city: Berkeley

first: Richard

last: Harland

state: CA

address: 571 Life Sciences Addition #3200

department: Department of Molecular and Cell Biology

institute: UC Berkeley

summary: We examined the role of Taf15 in in gastrula and neurula stage Xenopus tropicalis embryos.

overall_design: To determine the role of Taf15 in early Xenopus development, we used RNA-sequencing (RNA-seq) from single embryos depleted of M- and Z-Taf15, using reagents that targeted either all mRNA by inhibiting translation with Morpholino antisense and mismatch oligonucleotides (MOs) or only zygotic function using splice-blocking MOs or CRISPR-mediated mutagenesis.

first: Caitlin

middle: S

last: DeJong

first: Darwin

last: Dichmann

first: Cameron

last: Exner

first: Yuxiao

last: Xu