title: Assessment of the dormant and proliferative vascular metastatic niche

summary: During metastasis, cancer cells travel the circulation to colonise distant sites. Due to the rarity of these events, the immediate cell fate decisions of metastasising tumour cells (mTC)  are poorly understood and the role of the endothelium, as dissemination interface, remains elusive. Using a novel combinatorial mTC enrichment approach, we provide a first transcriptional blueprint of the early colonisation process

overall_design: Mice were injected with niche-labeling dormant (D20R) or proliferative (4T1) breast cancer cell lines and labeled, as well as matched unlabeled lung endothelial cells were sampled 3.5 days post-injection. Comparative gene expression profiling analysis of RNAseq data for lung endothelial cells from the different conditions.


title: CUX1 regulates human hematopoietic stem cell chromatin accessibility via the BAF complex [CUT&RUN]

status: Public on Oct 01 2023

city: Chicago

first: Megan

last: McNerney

state: IL

address: 5128 Knapp Center for Biomedical Discovery 900 East 57th Street

department: Dept. of Pathology and Dept. of Pediatrics, Hematology/Oncology

country: USA

institute: University of Chicago

type: Genome binding/occupancy profiling by high throughput sequencing

summary: CUX1 is a HOX-family transcription factor that is essential for development and differentiation of multiple tissues.  CUX1 is recurrently mutated or deleted in cancer, particularly in myeloid malignancies. However, the mechanism by which CUX1 regulates gene expression and differentiation remains poorly understood, creating a barrier to understanding the tumor suppressive functions of CUX1.  Herein, we demonstrate that CUX1 directs the BAF chromatin remodeling complex to DNA to increase chromatin accessibility in hematopoietic cells. CUX1 preferentially regulates lineage-specific enhancers, and CUX1 target genes are predictive of cell fate in vivo. These data indicate that CUX1 functions as a pioneer factor to epigenetically regulate hematopoietic lineage commitment and homeostasis, and CUX1 deficiency disrupts these processes in stem and progenitor cells, facilitating transformation.

overall_design: CUT&RUN for transcription factor CUX1, GATA1, and BAF complex subunit SMARCA4 in primary human CD34+ HSPCs

first: Weihan

last: Liu

first: Jefferey

last: Kurkewich

first: Saira

last: Khan

first: Dhivyaa

last: Anandan


title: CUX1 regulates human hematopoietic stem cell chromatin accessibility via the BAF complex [ChIP-seq]

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for transcription factor CUX1, BAF complex subunit SMARCA4, and histone modification H3K27ac in K562 cells. ChIP-seqs for SMARCA4 and H3K27ac include samples transfected with CRISPR gRNAs gHPRT (control) and gCUX1.


title: CUX1 regulates human hematopoietic stem cell chromatin accessibility via the BAF complex [ATAC-seq]

overall_design: ATAC-seq in K562 cell line and primary human CD34+ HSPCs transfected with CRISPR gRNAs including gHPRT (control) and gCUX1


title: Methylation state of latent and proliferative metastatic tumor cells

status: Public on Oct 02 2023

city: Heidelberg

first: Moritz

last: Jakab

address: Im Neuenheimer Feld

country: Germany

institute: German Cancer Research Center

type: Methylation profiling by high throughput sequencing

overall_design: Mice were injected intravenously with 4T1 breast cancer tumor cells. 3.5 days post-injection, latent and proliferative tumor cells were extracted from the lungs and subjected to WGBS. Comparative analysis of DNA methylation of latent vs. proliferative metastatic tumor cells.

first: Hellmut

middle: G

last: Augustin


title: CUX1 regulates human hematopoietic stem cell chromatin accessibility via the BAF complex

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

overall_design: Refer to individual Series


title: Tryptophan restriction blocks MYC-driven tumorigenesis and reprograms cancer cells to rely on lipolysis

status: Public on Sep 30 2023

city: Dallas

first: Jiwoong

last: Kim

state: Texas

address: 5323 Harry Hines Blvd.

institute: UT Southwestern Medical Center

type: Expression profiling by high throughput sequencing

summary: Cancer cells vary in their nutritional dependencies, thus characterization of nutrient demand of each tumor type is needed to uncover specific vulnerabilities. We demonstrate that MYC-driven liver tumors rely on increased tryptophan (Trp) uptake to grow. By following 13C-Trp in vivo-labeling, we found that Trp catabolism is reduced while its incorporation into proteins is increased in tumors. Trp deprivation prevents MYC-driven tumors from arising, as well as the growth of xenografted cells while minimally affecting normal cells. Trp starvation causes a reduction in the expression of growth-related and ribosome biogenesis genes while enhancing regulators of lipid metabolism, including PPAR, and enzymes involved in -oxidation and ketosis. Under Trp starvation, surviving cancer cells are reprogramed to utilize lipids; thus, providing a high-fat diet rescued the growth of tumors starved of Trp. We shows that Trp deprivation may be a powerful tool to treat liver tumors if dietary fat intake is low.

overall_design: MYC-driven liver tumor model was generated by crossing TRE-MYC with LAP-tTA mouse. Male breeders with 2 copies of LAP-tTA and single copy of TRE-MYC was crossed with WT FVB females to generate LAP-tTA/TRE-MYC mice used for experiments. The breeders were maintained on doxycycline water (1 mg/mL). The females with the litters were transferred to a fresh cage on the day of birth to activate MYC overexpression. Animals were maintained on a regular chow diet. For comparison between WT and MYC overexpression, FVB WT males were used. Both the WT males and MYC overexpression males were 45 days old. For the experiments with different Trp diet, the mice were transferred to either the control diet, Low-Trp diet or No-Trp diet at the time points indicated

first: Maralice

last: Conacci Sorrell


title: MoTrPAC- Endurance Exercise Training Study In 6 Months Old Rats [RNA-seq]

city: Stanford

first: Euan

last: Ashley

state: CA

address: 870 Quarry Road

institute: Stanford University

summary: The goal of the endurance exercise training study in young adult rats was to perform exercise training studies in young adult (6-month-old month) F344 rats, and from these rats collect multiple tissues in order to provide high quality samples for detailed analysis by chemical analysis sites.  Tissues were collected from 10-12 rats sedentary control rats concurrent with the collection of the 8-week training groups.  The 8-week training group and controls were from the same cohort and same age at euthanasia. For the older age group, an additional set of controls (n=5-6) were collected with the 1-2 week training group. Rats were either sedentary or underwent an exercise training program.  Rats were exercised on the rodent treadmill 5 days per week using a progressive training protocol designed to exercise the rats at approximately 70% of VO2max and training was performed no earlier than 10:00 am and no later than 5:00 pm over 5 consecutive days per week. Training was initiated with the treadmill set at 70% of VO2 max and 5 degrees grade for 20 minutes. The duration of exercise was increased by one minute each day until day 31 of training (start of week 7), when a duration of 50 min was reached. Speed and grade of each training session increased in larger increments due to treadmill parameters. The highest intensity and duration of training began on day 31.  This intensity was maintained for the final 10 days of the protocol to ensure steady state had been achieved.  If any rats were unable to perform at least 4 days of training per week they were removed from the study and euthanized.  It is important to note that the starting treadmill speed varied depending on the sex and age of the rat.  The initial and maximum speeds were based on VO2max measurements obtained during the pre-training testing of the compliant rats.  Rats assigned to the control group followed a schedule similar to the training group. They were placed in one lane on the treadmill for 15 minutes/day, 5 days per week. The treadmill was set at 0 m/min at an incline that corresponded to the incline being used by the training group.

overall_design:
Regular exercise promotes whole-body health and prevents disease, yet the underlying molecular mechanisms throughout a whole organism are incompletely understood. Here, the Molecular Transducers of Physical Activity Consortium (MoTrPAC) profiled the temporal transcriptome, proteome, metabolome, lipidome, phosphoproteome, acetylproteome, ubiquitylproteome, epigenome, and immunome in whole blood, plasma, and 18 solid tissues in Rattus norvegicus over 8 weeks of endurance exercise training. The resulting data compendium encompasses 9466 assays across 19 tissues, 25 molecular platforms, and 4 training time points in young adult male and female rats.

Contributor: Molecular Transducers of Physical Activity Consortium (MoTrPAC)


title: MoTrPAC: Endurance Exercise Training Study In 6 Months Old Rats

summary:
MoTrPAC endurance exercise training study targets young adult (6-month-old) rats. Specifically, male and female Fischer 344 rats (n = 12) were subjected to progressive treadmill endurance exercise training for 1, 2, 4, or 8 weeks, with tissues collected 48 hours after the last exercise bout. Sex-matched sedentary, untrained rats were used as controls.
This study contributes to MoTrPAC's broader mission, which is to identify molecular changes occurring due to exercise. The ultimate goal is to understand how physical activity can improve and sustain health across various ages and fitness levels.
The program is supported by the NIH Common Fund. For additional information, visit the MoTrPAC Data Hub at https://motrpac-data.org/.

This SuperSeries is composed of the SubSeries listed below.

relation:
SuperSeries of: GSE242354
SuperSeries of: GSE242355
SuperSeries of: GSE242357

overall_design: 6-month-old young adult rats (Fischer 344) were subjected to progressive endurance exercise training for 1, 2, 4, or 8 weeks, with tissues collected 48 hours after the last training bout. Sex-matched sedentary, untrained rats were used as controls. Whole blood, plasma, and 19 solid tissues were analyzed using genomics, proteomics, metabolomics, and protein immunoassay technologies, with most assays performed in a subset of these tissues. Depending on the assay, between 3 and 6 replicates per sex per time point were analyzed.


title: Autophagy contributes to homeostasis in esophageal epithelium where high autophagic vesicle content marks basal cells with limited proliferation and enchanced self-renewal potential

status: Public on Sep 20 2023

city: Philadelphia

first: Kelly

middle: A

last: Whelan

state: PA

address: 3307 N Broad St. PAHB Rm 203

department: Fels Institute

institute: Temple University


title: An Innovative Single-Cell Approach for Phenotyping and Functional Genotyping of CAR NK Cells

status: Public on Sep 26 2023

city: Boston

first: Matthew

middle: Ryan

last: Sullivan

state: Massachusetts

address: 140 The Fenway

department: Pharmaceutical Sciences

institute: Northeastern University

summary: To expedite immunotherapy development, better analysis of treatment efficacy at early in vitro stages is needed. Using a droplet-based microfluidic platform, we have established a method for multi-parameter quantifiable phenotypic and genomic observations of immunotherapies. Chimeric antigen receptor (CAR) NK cells provide treatment of interest in the current immunotherapy landscape and provide an optimal model for evaluating our novel methodology.  For this approach, NK cells transduced with a CD19 CAR were compared to non-transduced NK cells in their ability to kill a lymphoma cell line. Using our novel single-cell droplet array platform, we quantified the increase in cytotoxicity and synaptic contact formation of CAR-NK cells over non-transduced NK cells. With our droplet sorter, we separated NK cells based on target cell killing for transcriptomic sequencing. Our data revealed expected improvement in cytotoxicity with the CD19 CAR but more importantly, provided unique insights into the factors involved in the cytotoxic mechanisms of CAR NK cells. This demonstrates a novel, improved system for immunotherapy screening.

overall_design: CAR and non-transduced NK cells were co-encapsulated In droplets in Raji lymphoma cells. Droplets were sorted based on NK cell killing of target cells, and the collected cell populations were submited to Novogene for sequencing.

middle: R

first: Michael

last: Finnochiaro

first: Yichao

last: Yang

first: Judene

last: Thomas

first: Alaa

last: Ali

first: Isabel

last: Kaplan

first: Yasmin

last: Abdulhamid

first: Eden

last: Bobilev

first: Michal

last: Sheffer

first: Rizwan

last: Romee

first: Tania

last: Konry


title: Autophagy contributes to homeostasis in esophageal epithelium where high autophagic vesicle content marks basal cells with limited proliferation and enchanced self-renewal potential [scRNA-Seq]

summary: We used scRNA-seq to examine the cellular and molecular alterations between 3D organoids generated from esophageal epithelial cells with low and high autophagic vesicle content.

overall_design: Esophageal epithelial cells were isolated from C57B6 animals, stained for integrin-b1, DAPI and Cyto-ID amd sorted into two populations: (1) Integrin-b1 positive, DAPI negative, Cyto-ID Low and (2) Integrin-b1 positive, DAPI negative, Cyto-ID High. Then, 500-1000 of sorted cells  were seeded per well in 50 μl Matrigel and cultured with mouse organoids media for 15 days. Single cells were isolated from organoids and analyzed via scRNA-Seq.

first: Adam

middle: L

last: Karami

first: Annie

middle: D

last: Fuller

first: Alena

last: Klochkova


title: Blockade of C5a receptor unleashes tumor-associated macrophage antitumor response and enhances CXCL9-dependent CD8+ T cell activity

status: Public on Sep 19 2023

city: Chongqing

first: Xiaojin

last: Luan

address: yuzhong road

country: China

institute: Chongqing medical university

summary: Macrophages play a crucial role in shaping the immune state within tumor microenvironment (TME) and are often influenced by tumors to hinder antitumor immunity. However, the underlying mechanisms are still elusive. Here, we observed abnormal expression of complement 5a receptor (C5aR) in human ovarian cancer (OC), and identified high levels of C5aR expression on tumor-associated macrophages (TAMs), which led to the polarization of TAMs towards an immunosuppressive phenotype. C5aR knockout or inhibitor treatment restored TAM antitumor response and attenuated tumor progression. Mechanistically, C5aR deficiency reprogrammed macrophages from a protumor state to an antitumor state, associating with the upregulation of immune response and stimulation pathways, which in turn resulted in the enhanced antitumor response of cytotoxic T cells in a manner dependent on chemokine (C-X-C motif) ligand 9 (CXCL9). The pharmacological inhibition of C5aR also improved the efficacy of immune checkpoint blockade therapy. In patients, C5aR expression associated with CXCL9 production and infiltration of CD8+ T cells, and high C5aR level predicted poor clinical outcomes and worse benefits from anti-PD-1 therapy. Thus, our study sheds light on the mechanisms underlying the modulation of TAM antitumor immune response by the C5a-C5aR axis and highlights the potential of targeting C5aR for clinical applications.

overall_design: We injected ID8 ovarian cancer cell line into WT and C5aR knockout mice, and after 2 months, tumor tissues in the abdominal cavity of the mice were isolated and TAM were obtained by flow sorting to explore the differences in TAM function and gene expression between the two groups.

first: Yong

last: Fu


title: H1 restricts euchromatin-associated methylation pathways from heterochromatic encroachment

status: Public on Sep 12 2023

city: Los Angeles

first: Zhenhui

last: Zhong

address: 610 Charles E Young Dr East

department: Department of Molecular, Cell and Developmental Biology

institute: University of California, Los Angeles

summary: Silencing pathways prevent transposable element (TE) proliferation and help to maintain genome integrity through cell division. Silenced genomic regions can be classified as either euchromatic or heterochromatic, and are targeted by genetically separable epigenetic pathways. In plants, the RNA-directed DNA methylation (RdDM) pathway targets mostly euchromatic regions, while CMT methyltransferases are mainly associated with heterochromatin. However, many epigenetic features - including DNA methylation patterning - are largely indistinguishable between these regions, so how the functional separation is maintained is unclear. The linker histone H1 is preferentially localised to heterochromatin and has been proposed to restrict RdDM from encroachment. To test this hypothesis, we followed RdDM genomic localisation in an H1 mutant by performing ChIP-seq on the largest subunit, NRPE1, of the central RdDM polymerase (Pol V). Loss of H1 resulted in heterochromatic TE enrichment of NPRE1. Increased NRPE1 binding was associated with increased chromatin accessibility in h1, suggesting that H1 restricts NRPE1 occupancy by compacting chromatin. However, RdDM occupancy did not impact H1 localization, demonstrating that H1 hierarchically restricts RdDM positioning. H1 mutants experience major symmetric (CG and CHG) DNA methylation gains, and by generating an h1/nrpe1 double mutant, we demonstrate these gains are largely independent of RdDM. However, loss of NRPE1 occupancy from a subset of euchromatic regions in h1 experienced corresponding loss of methylation in all sequence contexts, while at ectopically bound heterochromatic loci, NRPE1 deposited methylation specifically in the CHH context. Additionally, we found that H1 restricts the occupancy of the methylation reader and activator complex component, SUVH1, indicating that H1’s regulatory control of methylation pathways is not limited to RdDM. Together, the results support a model whereby H1 helps maintain the exclusivity of heterochromatin by preventing encroachment from other competing pathways.

overall_design: Use WGBS and ChIP-seq to study function of H1 in RdDM distribution.

first: C

middle: J

last: Harris


title: Functional and molecular analysis of LMNA mutations related muscular dystrophy in zebrafish

status: Public on Sep 08 2023

city: Zhunan

first: Chiou Hwa

last: Yuh

address: 35, Keyan Road

department: Institute of Molecular and Genomic Medicine

country: Taiwan

institute: National Health Research Institutes

summary: LMNA mutations cause laminopathies, a group of rare genetic diseases with no known cure, only symptomatic treatment and supportive care. In this study, we characterized five LMNA mutations (LMNA(L35P), LMNA(A539V), LMNA(W520G), LMNA(E358K), and LMNA(R453W)) identified from patients diagnosed with muscular laminopathy in the zebrafish model.

overall_design: We established transgenic fish overexpressing wild-type LMNA and each of the five LMNA mutants in the skeletal muscle and monitored swimming behavior, muscle endurance, and histopathological changes. We also used the LMNA zebrafish models for drug screening. Gene expression profiles of the muscle from the transgenic fish were studied through RNAseq.

first: Shao-Wei

last: Pan

first: Chiou-Hwa


title: MoTrPAC - Endurance Exercise Training Study In 6 Months Old Rats [RRBS]

first: Euan

last: Ashley

summary: The goal of the endurance exercise training study in young adult rats was to perform exercise training studies in young adult (6-month-old) F344 rats, and from these rats collect multiple tissues in order to provide high quality samples for detailed analysis by chemical analysis sites.  Tissues were collected from 10-12 rats sedentary control rats concurrent with the collection of the 8-week training groups.  The 8-week training group and controls were from the same cohort and same age at euthanasia. For the older age group, an additional set of controls (n=5-6) were collected with the 1-2 week training group. Rats were either sedentary or underwent an exercise training program.  Rats were exercised on the rodent treadmill 5 days per week using a progressive training protocol designed to exercise the rats at approximately 70% of VO2max and training was performed no earlier than 10:00 am and no later than 5:00 pm over 5 consecutive days per week. Training was initiated with the treadmill set at 70% of VO2 max and 5 degrees grade for 20 minutes. The duration of exercise was increased by one minute each day until day 31 of training (start of week 7), when a duration of 50 min was reached. Speed and grade of each training session increased in larger increments due to treadmill parameters. The highest intensity and duration of training began on day 31.  This intensity was maintained for the final 10 days of the protocol to ensure steady state had been achieved.  If any rats were unable to perform at least 4 days of training per week they were removed from the study and euthanized.  It is important to note that the starting treadmill speed varied depending on the sex and age of the rat.  The initial and maximum speeds were based on VO2max measurements obtained during the pre-training testing of the compliant rats.  Rats assigned to the control group followed a schedule similar to the training group. They were placed in one lane on the treadmill for 15 minutes/day, 5 days per week. The treadmill was set at 0 m/min at an incline that corresponded to the incline being used by the training group.


title: Whole genome transcriptomics of upper extremity veins from end-stage kidney disease patients and non-kidney disease organ donors

status: Public on Sep 07 2023

city: Miami

first: Anthony

last: Griswold

state: FL

address: 1501 NW 10th Ave, BRB 318

institute: University of Miami

summary: We report the RNA expression profiles of native veins used for AVF creation and of non-kidney disease veins obtained from organ donors.

overall_design: This study was designed to evaluate vascular changes in gene expression associated with chronic kidney disease. Additional ESKD patients are found in GSE119296 and GSE220796.

first: Roberto

middle: I

last: Vazquez-Padron

first: Laisel

last: Martinez


title: DNA Methylation-Based High-Resolution Mapping of Long-Distance Chromosomal Interactions in Nucleosome-Depleted Regions (RNA)

status: Public on Sep 05 2023

city: UNIVERSITY PARK

first: Lu

last: Bai

state: PENNSYLVANIA

address: 406 SOUTH FREAR, UNIVERSITY PARK

department: BMB

institute: Penn State University

summary: Here, we present Methyltransferase Targeting-based chromosome Architecture Capture (MTAC), a method that maps the contacts between a target site (viewpoint) and the rest of the genome with high resolution and sensitivity. By targeting M.CviPI DNA methyltransferase to the viewpoint and by detecting differentially methylated regions, MTAC detects hundreds of intra- and inter-chromosomal interactions in the budding yeast genome that cannot be captured by  4C, Hi-C, or Micro-C.

overall_design: MeDIP-seq data of targeted S. cerevisiae strains (LacO array inserted into the corresponding viewpoints) and control strains (No LacO insertion) under different conditions (growth condition, M.CviPI induction time, LacO copy numbers etc.). 4C-seq data of different viewpoints and Hi-C data for chromosome conformation capture in S. cerevisiae. ChIP-seq data for Met4. RNA-seq data of S. cerevisiae cells in -met condition.

first: Yi

last: Li

first: James

last: Lee


title: DNA Methylation-Based High-Resolution Mapping of Long-Distance Chromosomal Interactions in Nucleosome-Depleted Regions (HiC)


title: DNA-PKcs suppress chromosome translocation in human cells

status: Public on Sep 01 2023

first: Jinglong

last: Wang

state: California

address: 269 Campus Drive

department: Radiation Oncology

institute: Stanford Medicine

summary: DNA-PKcs is a crucial component of the non-homologous end joining (NHEJ) repair machinery. To investigate its function in human cell lines, we conducted a study using K562 and HEK293T cell lines. We introduced twinned DNA double-strand breaks (DSBs) or genome-wide DSBs into these cell lines via nucleofection and transfection, respectively. Subsequently, we employed high-throughput genome translocation sequencing (HTGTS) to capture the translocation events (i.e., ligation between "prey(s)" and "bait") and the rejoining events (i.e., direct repair within the "bait" locus) under different conditions, including with or without DNA-PKcs inhibition or deletion. We quantified the number of translocation events by normalizing them to the number of rejoining events, denoted as TL. Interestingly, DNA-PKcs inhibition led to an increase in TL, indicating a higher frequency of translocations. However, it is important to note that chromosomal translocations still predominantly relied on NHEJ despite DNA-PKcs inhibition. Furthermore, we observed that DNA-PKcs deletion resulted in an elevated utilization of microhomology in translocation formation. Nevertheless, NHEJ remained the primary mechanism driving translocation events.These findings provide valuable insights into the role of DNA-PKcs in the repair pathways involved in translocation events in human cell lines. The utilization of HTGTS allowed us to comprehensively analyze the effects of DNA-PKcs inhibition and deletion, shedding light on the interplay between NHEJ and alternative repair mechanisms in translocation formation.

overall_design: We induced DNA double-strand breaks (DSBs) using CRISPR-Cas9 technology in various cell lines, including K562-derived cell lines (K562-Bcl2, K562-Bcl2-PKcs-/-, and K562-iCas9) and the HEK293T-derived cell line HEK293T-iCas9. These cell lines were subjected to different treatment conditions, including DMSO, DPKi #1 (Nu7441), DPKi #2 (Nu7026), and ATMi. To capture translocation events, we utilized one of the DSB sites, either RAG1L or HBB, as a bait, which allowed us to detect its ligation with the remaining DSB site(s) using high-throughput genome translocation sequencing (HTGTS).

first: Cheyenne

last: Sadeghi

first: Richard

last: Frock


title: Verapamil treatment of β-cells

status: Public on Aug 30 2023

city: Dasman

first: Fahd

last: Almulla

address: Jasim Mohamad Al Bahar St

country: Kuwait

institute: Dasman Diabetes Institute

summary: In this study, we investigated the molecular and cellular mechanisms of verapamil treatment on β-cell function and survival using MIN6 cells. Verapamil's molecular processes were studied using transcriptomic data. MTT, cell count, and flow cytometry assessed cell proliferation, growth, and cycle. MIN6 cell function was assessed by glucose-stimulated insulin release and total insulin content. Seahorse and metabolic stress kits examined metabolic activity and oxygen consumption rate. The protective impact of verapamil on MIN6 cells was evaluated by challenging the verapamil treated cell with streptozotocin, T1D-cytomix, or T2D-cytomix cocktail. Our results demonstrate that verapamil treatment induced higher proliferation of MIN6 cells, altered expression of various proteins and genes, improved insulin secretion in hyperglycemic conditions, increased basal and maximal respiration levels, along with β-cell survival against streptozotocin, T1D-, or T2D-cytomix-induced toxicity, and rendered a protective effect.

overall_design:
Min6 cells were cultured in DMEM media with 5.6 mM glucose supplemented with 15% heat-inactivated fetal bovine serum (FBS), 2 mM l-glutamine, 1 mM sodium pyruvate, 10 mM HEPES, 50 μg/mL penicillin, 100 μg/mL streptomycin, and 70 mM β-mercaptoethanol at 37.0 °C, with 5% CO2. After 24 hours, cells were treated with 50 μM verapamil for another 24 hours. MIN6 cells at a passage of <25 were used in this study.
RNA isolation was performed from the verapamil treated and untreated MIN6 cells (12 independent experiments) using the RNeasy kit (Qiagen, Hilden, Germany), following standard protocol. 40 ng of purified RNA was used for whole transcriptome sequencing. Transcriptome libraries were produced using Truseq stranded mRNA kit (Illumina Inc. USA), following the manufacturer’s protocol, and were validated and quantified using bioanalyzer (Agilent, California, United States) and qubit fluorometer (Thermofisher Scientific, Massachusetts, United States), respectively. Then paired-end sequencing on Novaseq 6000 system (Illumina Inc. USA) was carried on. The resulting BCL files were concerted to Fastq using the bcl2fastq v.2.20 tool and qualified ty control of Fastq files using FastQC (v0.11.9). Trimmomatic (v0.39) was used for adaptor and quality trimming, and for the removal of extremely short reads. HISAT2 (v2.1.0) was used for data alignment. To enumerate the number of reads that are associated with the genes, htseq-count tool in HTSeq (v 0.9.1) was used. Differential gene expression analysis was conducted using Bioconductor package edgeR, by adopting the default setting.

first: Almulla

last: Fahd

first: Arefanian

last: Hossein

first: John

last: Sumi

first: Alhusayan

last: Mohammed


title: Developing a novel human adult kidney organoid model to recapitulate injury-associated regeneration and polycystic kidney disease [scRNA-Seq]

status: Public on Aug 31 2023

city: Jinan

first: liqiang

last: guo

state: Shandong

address: No. 107, Wenhua West Road

department: Shandong University

institute: Qilu Hospital

summary: Current renal organoid models derived from embryonic or induced pluripotent stem cells mimic development. Yet, few studies have attempted to generate organoids from human adult kidney to recapitulate regeneration or pathological dysregulation in vitro. Here, we report a novel expanding regenerative organoids culture system from renal cortex and medulla. Transcriptomic sequencing and immunostaining identified that these organoids share similar molecular features with kidney injury-responsive regeneration. Heterogeneous populations in organoids including cycling epithelial progenitors and differentiated cell types were identified by single cell sequencing including proximal tubules, principal cells and collecting duct (CD) progenitors that can be induced into functional CD system. Furthermore, we established polycystic organoids derived from patients that represent an advanced platform for polycystic kidney disease (PKD) modeling. By drug screening, QNZ, GSK2193874 and AMPK activators were shown to significantly reduce polycystic growth. Our results demonstrated a novel in vitro renal organoid model to study regenerating adult renal cells and PKD mechanism, providing tools for discovery of therapeutic targets.

overall_design: Comparative gene expression profiling analysis of scRNA-seq data for kidney organoids.

first: Liqiang

last: Guo

first: Yujia

last: Fan

first: Haoran

last: Du

first: Xinyan

last: Zhang

first: Shan

last: Jiang

first: Yong

last: Guan

first: Lingtong

last: Ren

first: Yachun

last: An

first: Xiaohui

first: Huixian

last: Sun

first: Feng

last: Kong

first: Benkang

last: Shi

first: Fan

last: Yi

first: Huili

last: Hu

first: Shengtian

last: Zhao


title: Xbp1 knockdown in CHO cells stably expressing Cdh13 (RNA-Seq)

status: Public on Sep 06 2023

city: Suita

first: Daisuke

last: Motooka

state: Osaka

address: 3-1, Yamadaoka

country: Japan

institute: NGS core facility, Research Institute for Microbial Diseases, Osaka University

summary: RNA expressions of CHO cells stably expressing Cdh13 were compared between cells transfected with negative control siRNA and with Xbp1 siRNA for 48 hours.

overall_design: Ctrl (n=3) and XBP1 KD (n=3)

first: Shunbun

last: Kita

first: Keita

last: Fukuoka


title: DNA Methylation-Based High-Resolution Mapping of Long-Distance Chromosomal Interactions in Nucleosome-Depleted Regions

first: Lu

last: Bai


title: PRC1.6 molecule L3MBTL2 protects MYCN-amplified neuroblastoma cells via epigenetic gene suppression

city: Kitaadachi-gun

first: Hisanori

last: Takenobu

state: Saitama

address: 818, Komuro, Ina-machi

department: Research Institute for Clinical Oncology

institute: Saitama Cancer Center

summary: Polycomb-group complexes are evolutionarily conserved epigenetic machineries that regulate stem cell fate decisions/development and are also implicated in tumorigenesis mainly by histone modification. PRC1 complexes mediates ubiquitylation of histone H2A on lysine 119 and consists of PRC1.1 to PRC1.6 complexes. Here, we studied the functional roles of a PRC1.6 molecule L3MBTL2 in neuroblastoma (NB) cells. L3MBTL2 knockout- and knockdown-experiments elucidated that L3MBTL2 depletion suppressed NB cell proliferation according with cell cycle arrest and gamma-H2A up-regulation. L3MBTL2 knockout profoundly suppressed xenograft tumor formation. Transcriptome analysis detected the suppressed cell cycle-related pathways and the activated the differentiation-related pathways. The remarkable de-repressed genes by the L3MBTL2 knockout were BRME1 and NRIP3. ChIP experiments showed co-localization of the PRC1.6 components PCGF6/E2F6/L3MBTL2 and MYCN at the transcription start sites (TSS) of these genes. L3MBTL2 knockout reduced H2AK119ub marks at the TSS regions but PCGF6 binding was heterogeneously changed. This study clarified the significance of PRC1.6 molecule L3MBTL2 in NB cell homeostasis and the epigenetic mechanism of the L3MBTL2-mediated gene suppression in NB that regulates the PRC1.6 complex localization and H2AK119 mono-ubiquitination in a gene locus-specific manner.

overall_design: Total RNA was extracted from L3MBTL2 KO NB cells, and a microarray analysis was performed using the Agilent platform of 8 × 60 K design ID G4851B (Agilent Single Color. 39494, Agilent Technologies, Santa Clara, CA, USA). Total RNA 200 ng was labeled with Cyanine3 using a Low Input Quick-Amp Labeling Kit (one color, Agilent Technologies) according to the manufacturer’s manuals.

first: Ryu

last: Okada

first: Shunpei

last: Satoh

first: Ryuichi

middle: P

last: Sugino

first: Masayuki

last: Haruta

first: Kyosuke

last: Mukae

first: Atsuko

last: Nakazawa

first: Jesmin

last: Akter

first: Miki

last: Ohira


title: Developing a novel human adult kidney organoid model to recapitulate injury-associated regeneration and polycystic kidney disease

first: liqiang

last: guo

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


title: The Role of Vitamin D in Emiliania huxleyi: A Microalgal Perspective on UV-B Exposure

status: Public on Sep 25 2023

city: Rehovot

first: Or

last: Eliason

address: 234 Hertzk

country: Israel

institute: The Weizmann Institute of Science

summary: An essential interaction between sunlight and eukaryotes involves the production of vitamin D through exposure to ultraviolet (UV) radiation. While extensively studied in vertebrates, the role of vitamin D in non-animal eukaryotes like microalgae remains unclear. To investigate the potential involvement of vitamin D in the response of microalgae to UV, we focus on Emiliania huxleyi, a microalga found in shallow ocean depths that are exposed to UV radiation. Our results show that E. huxleyi algae produce vitamin D2 and D3 in response to UV irradiation. We further demonstrate that E. huxleyi algae respond to external administration of vitamin D at the transcriptional level, regulating the expression of protective mechanisms that are also regulated in response to UV. Our data reveal that addition of vitamin D enhances the algal photosynthetic performance while reducing harmful reactive oxygen species buildup. This study contributes to understanding the function of vitamin D in E. huxleyi and sheds light on its role in non-animal eukaryotes, as well as its potential importance in marine ecosystems.

overall_design: In order to investigate the effect of weak UV radiation on the transcriptomic landscape of the algae E. huxleyi. Transcriptomic analysis was conducted using RNA extracted from E. huxleyi cultures grown in artificial sea water supplemented with L1-Si nutrients, under weak UV radiation or under regular growing light as control, using triplicates.

first: Sergey

last: Malitsky

first: Irina

last: Panizel

first: Ester

last: Feldmesser

first: Ziv

last: Porat

first: Martin

last: Sperfeld

first: Einat

last: Segev


title: Single-cell and spatial transcriptomics characterisation of the immunological landscape in the healthy and PSC human liver

city: Toronto

first: Diana

last: Nakib

state: ON

address: 101 College Street

country: Canada

institute: University of Toronto

overall_design: Refer to individual Series


title: A genetic-metabolic axis for metastatic liver organotropism

status: Public on Aug 29 2023

city: New York

first: Meri

last: Rogava

state: New York

address: 650 W 168th St, New York, NY 10032

department: Hematology Oncology

institute: Columbia University

summary:
To generate CRISPR/Cas9 knockout screen, we used mouse Kinome CRISPR Knockout Library (Brie) (Addgene # 75316) purchased from addgene. The mouse kinase sgRNA pool includes 2,852 sgRNAs targeting 713 kinase genes and 100 control non-targeting sgRNAs. Cas9 expressing HCmel12 melanoma cells were edited for 14 days, and tumor cells were injected for metastasis screening studies.   RNA-seq data: HCmel12 melanoma cells and CRISPR knockout HCmel12 melanoma cells - Pip4k2c KO were treated for 4 hours with insulin. Then cells were lysed in RLT buffer and used to perform mRNA profiling.
We performed single-cell RNA-sequencing (scRNA-seq) of eight mice with concurrent liver and lung metastasis. A total of 95,606 cells expressing 19,624 genes were included for downstream analyses.
Bulk RNA-sequencing analysis of 15 human melanoma liver metastasis samples from FFPE sample. Tumor areas were macro-dissected and RNA was extracted using Qiagen kit All Prep DNA/RNA FFPE Kit (Catalog Number 80234), concentration was quantified using Qu-bit and stored at-80 °C until use.

sample_organism:
Homo sapiens
Mus musculus
blank sample

platform_organism:
Homo sapiens
Mus musculus
blank sample

overall_design:
In vitro and in vivo CRISPR knockout screen of HCmel12 melanoma cells, and identification of drivers of site-specific metastasis.    mRNA profiles following of Parental and Pip4k2c KO HCmel12 melanoma cells with and without insulin treatment for 4hours.
C57/BL6 mice were injected 5x10^5 HCmel12 melanoma cells of indicated genotypes via lateral tail vein and after 21 days mice were euthanized and organs harvested. Around 10,000 cells per channel were loaded on a Chromium controller (10x genomics, Pasadena, CA). Sequencing libraries were prepared using standard parameters, and libraries were sequenced on a NovaSeq with S4 flow cell (Illumina, San Diego, CA) and 2x100 bp paired end reads. For downstream analyses, we include single-cell RNA sequencing of 95,606 cells from 16 samples (MR1-MR16), with matched liver and lung metastasis from HCmel12 mouse melanoma model of indicated genotypes. MR1-MR4 are from HCmel12 melanoma cells with Pip4k2c knockout; MR5-MR10 are from HCmel12 melanoma cells with Pten knockout; MR11-MR16 are from HCmel12 melanoma cells with Pip4k2c and Pten double knockouts.
Bulk RNA-sequencing of 15 independent human melanoma liver metastasis samples were taken from FFPE samples. 5 patients were primary type cutaneous melanoma, 10 were primary type uveal melanoma. Raw counts for each transcript were quantified with kallisto using human reference GRCh38. Raw count data was normalized to transcript per million (TPM).

>>>Submitter states raw data can not be provided for Human samples due to patient privacy concerns<<<

first: Clemens

last: Hug

first: Benjamin

last: Izar


title: Differential roles of RUBCN isoforms in autophagy and memory B-cell generation

first: Daisuke

last: Motooka

summary: RUBCN/Rubicon was originally identified as a negative regulator of canonical autophagy. However, its function remains controversial. Here we show that RUBCN is expressed as two isoforms of different sizes, RUBCN130 and RUBCN100, that are translated from alternative translation initiation sites. Selective RUBCN130 deficiency in B cells enhances autophagy and memory B-cell generation. Autophagy suppression by ATG7 deficiency reverses the enhancement of memory B-cell generation in B-cell–specific RUBCN130-deficient mice. While RUBCN130 is intracellularly localized in late endosomes and lysosomes, RUBCN100 is preferentially located in early endosomes and enhances the enzymatic activity of class III PI(3)K VPS34. Additionally, RUBCN100 plays a positive regulatory role in autophagy since its expression promotes autophagy and suppresses mTORC1 activation. Our findings reveal the critical role of functional interaction between RUBCN isoforms in autophagy regulation and also provide clues for developing a new vaccine strategy to induce efficient B-cell memory.

overall_design: Germinal center (GC) B cell mRNA profiles of CD19-Cre+/- and CD19-Cre+/-rubcnflox/flox mice 7 days or 14 days after NP-KLH-Alum immunization

first: Chao-Yuan

last: Tsai

first: Hitoshi

last: Kikutani


title: Autophagy contributes to homeostasis in esophageal epithelium where high autophagic vesicle content marks basal cells with limited proliferation and enchanced self-renewal potential [RNA-Seq]

first: Kelly

last: Whelan

summary: We used bulk RNA-seq to examine the  molecular alterations between esophageal epithelial cells with low and high autophagic vesicle content.

overall_design: Esophageal epithelial cells were isolated from C57B6 animals, stained for integrin-b1, DAPI and Cyto-ID and sorted into two populations: (1) Integrin-b1 positive, DAPI negative, Cyto-ID Low and (2) Integrin-b1 positive, DAPI negative, Cyto-ID High. RNA was isolated and analyzed via bulk-Seq.

first: Adam

last: Karami

first: Annie

last: Fuller

first: Alena

last: Klochkova


title: Gene expression profiles in the ileal and colonic epithelial cells from Interleukin (IL)-23-deficient mice and IL-22-deficient mice

summary: To investigate the function of IL-23 and IL-22 on the intestinal epithelial cells, we analyzed the gene expression profiles in ileal and colonic epithelial cells of mice deficient in IL-23 and IL-22.

overall_design: Intestinal epithelial cells from the ileum and colon of Il23-/- and Il22-/- mice

first: Ryu

last: Okumura

first: Ayaka

last: Nakatani

first: Kiyoshi

last: Takeda

last: Okuzaki


title: Transcriptional blueprint of the early colonisation process

city: Heidelberg

first: Moritz

last: Jakab

address: Im Neuenheimer Feld

institute: German Cancer Research Center


title: Illuminating the functions of understudied Fructosamine-3-kinase (FN3K) using a multi-omics approach reveals new links to nicotinamide adenine dinucleotides (NAD)

city: Athens

first: Natarajan

last: Kannan

address: 120 E. Green Street

department: Department of biochemistry and molecular biology

institute: University of Georgia

summary: Fructosamine-3-kinases (FN3Ks) are a conserved family of repair enzymes that phosphorylate reactive sugars attached to lysine residues in peptides and proteins. Although FN3Ks are present across the tree of life and share detectable sequence similarity to eukaryotic protein kinases, the biological processes regulated by these kinases are largely unknown. To address this knowledge gap, we leveraged the FN3K CRISPR Knock-Out (KO) cell line alongside an integrative multi-omics study combining transcriptomics, interactomics, metabolomics, and genomics to place these enzymes in a pathway context. The integrative analyses revealed the enrichment of pathways related to oxidative stress response, lipid biosynthesis (cholesterol and fatty acids), carbon and co-factor metabolism, and protein translational machinery. Moreover, statistically significant enrichment of metallothioneins and nicotinamide adenine dinucleotide (NAD) binding proteins suggest potential links between FN3Ks and NAD-mediated energy metabolism and redox balance. We report specific binding of human FN3K to NAD compounds in a metal and concentration-dependent manner and provide insight into their binding mode using modeling and experimental site-directed mutagenesis. By identifying a potential link between FN3Ks, redox regulation, and NAD-dependent metabolic processes, our studies provide a framework for targeting these understudied kinases in diabetic complications and other metabolic disorders.

overall_design: To investigate the pathways related to FN3K we Knocked out FN3K gene in HepG2 cells using Crispr-cas. We then performed gene expression profiling analysis obtained from RNA-seq of 3 different samples from the WT and the KO HepG2 cells

first: Samiksha

last: Katiyar

first: Rahil

last: Taujale

first: Safal

last: Shrestha


title: mESC-derived 6wk Lung Transplant

status: Public on Aug 24 2023

first: Feiya

last: Wang

state: MA

address: 670 Albany street, 2nd floor

institute: Center for Regenerative Medicine, Boston University

summary: The goal of this experiment was to compare the transcriptome of transplanted mouse ESC-derived cells and endogenous epithelial cells at 6 weeks post transplantation into a syngeneic wild type recipient. These cells were also compared to endogenous epithelial cells from an uninjured control.

overall_design: A 9 week old wild type 129X1/S1 mouse was given 1.5U/kg bleomycin intratracheally. 10 days later 6e5 ESC-derived tip-like cells were transplanted intratracheally into the same mouse. At 6 weeks post transplantation the lungs of this mouse were digested and sorted using FACS. We collected both endogenous and donor-derived epithelial cells from the same lung. In parallel an 11 week old uninjured control 129X1/S1 mouse was similarly dissected and lung epithelial cells were collected.

first: Michael

last: Herriges

first: Jonathan

last: Lindstrom-Vautrin

first: Carlos

last: Villacorta-Martin

first: Darrell

last: Kotton


title: Lung transplant


title: DNA Methylation-Based High-Resolution Mapping of Long-Distance Chromosomal Interactions in Nucleosome-Depleted Regions (MeDIP)

first: Lu

last: Bai

first: Yi

last: Li

first: James

last: Lee


title: DNA Methylation-Based High-Resolution Mapping of Long-Distance Chromosomal Interactions in Nucleosome-Depleted Regions (ChIP)


title: DNA Methylation-Based High-Resolution Mapping of Long-Distance Chromosomal Interactions in Nucleosome-Depleted Regions (4C)


title: shRNA-based miRNA overexpression results in significant off-target effects caused by isomiR production [miRNA-seq]

status: Public on Aug 22 2023

city: Moscow

first: Anton

last: Zhiyanov

address: 20 Myasnitskaya ulitsa

department: Faculty of Biology and Biotechnology

country: Russia

institute: HSE University

type: Non-coding RNA profiling by high throughput sequencing

summary: miRNA overexpression strategy based on RNA Polymerase (Pol) III mediated expression of short hairpin RNA (shRNA) coding particular miRNA is widely used for miRNA functional studies. For some miRNAs, e.g., encoded in the genome as a part of a polycistronic miRNA cluster, it is most likely the only way for their individual stable overexpression. Here we have revealed that extra \texttt{U} residues (up to five) added Pol III at the 3$'$-end of the transcribed shRNA associated with a shift in the Dicer cleavage position of the shRNA. This results in the undesirable formation of 5$'$-end miRNA isoforms (5$'$-isomiRs), which have a significantly altered seed region compared to the initially encoded canonical hsa-miR-93-5p. The predominant expression of 5$'$-isomiRs without three or four first nucleotides instead of the canonical isoform could be disclosed based on miRNA-Seq analysis. Moreover, mRNA sequencing data showed that the 5$'$-isomiRs of hsa-miR-93-5p presumably regulate their own mRNA targets. Thus, omitting miRNA-Seq analysis may lead to erroneous conclusions regarding revealed mRNA targets and possible molecular mechanisms in which studied miRNA is involved.

overall_design:
PC-3 (prostate cancer) cell line was transduced by lentiviral particles coding one of the three types of shRNA to achieve stable overexpression of hsa-miR-93-5p.
All shRNA constructs contained the sequence of the canonical hsa-miR-93-5p and differed in their loop sequence only (5'-CUACCUGCACGAACAGCACUUUG-3' -- upper stem; 5'-CUCGAG-3', 5'-UUCAAGAGA-3', 5'-UUCUAAAA-3' -- stem loops; 3'-...UUGAUGGACGUGCUUGUCGUGAAAC-5' -- lower stem).
To comprehensively understand the overexpressed isoforms of hsa-miR-93-5p and their impact on the cellular transcriptome profile, we conducted sequencing of both miRNAs (3 repeats for the control, 3 repeats for the first loop and 2 repeats for other ones) and mRNAs (3 repeats for control and all loops).

first: Diana

last: Maltseva

first: Ivan

last: Kirillov

first: Roman

last: Suvorov

first: Daria

last: Gubani

first: Anna

last: Kudriaeva

first: Alexey

last: Belogurov

first: Alexander

last: Tonevitsky


title: Deep sequencing of Phox2a nuclei reveals five classes of anterolateral system neurons

status: Public on Aug 21 2023

city: London

first: Franziska

last: Denk

address: Guy's Campus

department: Wolfson SPaRC

country: United Kingdom

institute: King's College London

summary: The anterolateral system (ALS) is a major ascending pathway from the spinal cord that projects to multiple brain areas and underlies the perception of pain, itch and skin temperature. Despite its importance, our understanding of this system has been hampered by the considerable functional and molecular diversity of its constituent cells. Here we use fluorescence-activated cell sorting to isolate ALS neurons belonging to the Phox2a-lineage for single-nucleus RNA sequencing. We reveal five distinct clusters of ALS neurons (ALS1-5) and document their laminar distribution in the spinal cord using in situ hybridization. We identify 3 clusters of neurons located predominantly in laminae I-III of the dorsal horn (ALS1-3) and two clusters with cell bodies located in deeper laminae (ALS4 & ALS5). Our findings reveal the transcriptional logic that underlies ALS neuronal diversity in the adult mouse and uncover the molecular identity of two previously identified classes of projection neurons. We also show that these molecular signatures can be used to target groups of ALS neurons using retrograde viral tracing. Overall, our findings provide a valuable resource for studying somatosensory biology and targeting subclasses of ALS neurons.

overall_design: Mouse spinal cord projection neurons in the anterolateral system were enriched by FACS using Phox2a-Sun1GFP mice and sequenced at single cell level using a plate-based approach (SMART-seq with UMIs)

first: Andrew

last: Bell


title: Gene comparison between flat and round shaped chondrocytes in cranial base synchondrosis

status: Public on Aug 14 2023

first: Daisuke

last: Motooka

summary: The aim of this study is to characterize each zones of chondrocytes and identify the associated unique molecules.

overall_design: Each layer of flat and round chondrocytes in sphenooccipital synchondrosis was excised using laser microdissection. RNA was extracted and subjected to RNA-Seq analyses.

first: Katsuhiko

last: Amano

first: Soma

last: Kato

last: Okuzaki


title: A comparative analysis of microglial inducible Cre lines

first: Riki

last: Kawaguchi

address: 760 Westwood Plaza, Room 37-420

department: Department of Psychiatry and Neurology Department of Psychiatry

institute: University of California, Los Angeles

summary: We investigated the effects of tamoxifen, CreER recombination, and genetic manipulations to genes whose promoters are used to driving CreER expression on microglial gene expression across 4 different microglial inducible Cre lines.

overall_design: CreER-expressing mice were injected with tamoxifen (100 mg/kg) or oil i.p. once daily from P28 to P31. 4 weeks later, at P56, microglia were isolated by FACS from the brains of the mice. RNA was isolated from the collected microglia used for RNA sequencing.

first: Schafer

last: Dorothy


title: Single cell RNA sequencing profiles of human iPSC-derived AT1-like cells in 3D cultures [SPC2B2_LDCI]

status: Public on Aug 08 2023

city: Boston

first: Pushpinder

last: Bawa

address: 670 Albany St

department: Boston University Medical Campus

institute: Center for Regenerative Medicine

summary: Comparison of differentiation of human iPSC derived alveolar epitheilal type 2 cells (iAT2s) into AT1-like cells (iAT1s) using a defined "LDCI" medium vs. lentiviral forced over-expression of activated nuclear YAP (YAP5SA)

overall_design:
Global transcriptomic profiling at single cell resolution of human induced pluripotent stem cell (iPSC)-derived alveolar epithelial type 2 cells (iAT2s), iAT1-YAP5SA cells transduced with constitutively active nuclear YAP (YAP5SA) lentivirus, and iAT1s differentiated using a defined, serum-free "LDCI" medium. The SPC2-ST-B2 clone of human iPSCs was used for these studies.

[UPDATE] 05-20-2024: The titles of Samples GSM6858854 and GSM6858856 were corrected. The file names of the associated processed data files (.h5) were corrected.

first: Claire

last: Burgess

first: Darrell

last: Kotton


title: Clinical significance of MSP-RON signaling based on mRNA-microRNA integration analyses in acute severe ischemic stroke patients (micro RNA data)

status: Public on Aug 11 2023

summary: The roles of mRNA and microRNA (miRNA) are widely known in many diseases including acute ischemic stroke. About 60 % of all human messenger RNAs (mRNAs) are regulated by microRNAs. Integration analysis using mRNA and miRNA are important to elucidate pathogenesis. But the contribution of mRNA and miRNA, especially miRNA targeted mRNA, related with severity of acute ischemic stroke is not remain understood. To clarify the pathway related with the severity of acute ischemic stroke, we examined mRNA and miRNA integration analysis targeted for acute ischemic stroke.

overall_design: We corrected RNA extracted from whole blood of 6 acute minor ischemic stroke patients (National Institutes of Health Stroke Scale [NIHSS] < 8) and 6 acute severe ischemic stroke patients (NIHSS ≥ 8) on admission. mRNA and miRNA were measured by RNA sequencing.

first: Hideaki

last: Kanki

first: Hisatake

last: Matsumoto


title: Streptococcus gordonii intraoral infection and periodontitis in C57BL/6J mice

status: Public on Aug 15 2023

city: gainesville

first: Kesavalu

middle: Lakshmyya

last: Naidu

state: Florida

address: 1600 SW Archer Road

department: Dentistry

institute: University of Florida

summary: Individual miRNA analyzed were successfully constructed through nanostring technology of a total of 577 mouse miRNAs in 20 number of SHAM mice and 20 number of Streptococcus gordonii infected mice, which have been euthanized on the end of 16 weeks infection study.

overall_design: The study depicted here, is a 16 weeks of total, 10 mice/group, Sham infected and Streptococcus gordonii infected groups both in 8 weeks and 16 weeks, followed 16 weeks, euthanized and extracted left mandibles for miRNA expression profiles, of a total of 577 unique Nanostring miRNA panels. This leading to successful construction of supervised.

first: Aravindraja

last: Chairmandurai

first: Lakshmyya

last: Kesavalu


title: Clinical significance of MSP-RON signaling based on mRNA-microRNA integration analyses in acute severe ischemic stroke patients

status: Public on Aug 13 2023


title: mESC-derived donor cells in culture and 15 weeks after transplantation

first: Feiya

last: Wang

summary: The goal of this experiment was to compare the transcriptome of transplanted mouse ESC-derived cells and endogenous epithelial cells at 15 weeks post transplantation into a syngeneic wild type recipient. In addition these cells were compared to ESC-derived and primary mouse tip-like cells grown in culture, to determine how cultured cells changed followeing transplantation.

overall_design: A 9 week old wild type 129X1/S1 mouse was given 1.5U/kg bleomycin intratracheally. 10 days later 5e5 ESC-derived tip-like cells were transplanted intratracheally into the same mouse. At 15 weeks post-transplantation the lungs of this mouse were digested and sorted using FACS. We collected both endogenous and donor-derived epithelial cells from the same lung. To analyze pre-transplantation donor populations, we collected passage 4 ESC-derived and passage 3 primary tip-like cells grown in Lung progenitor media for 6 days since passaging. Finally, we collected D13 ESC-derived epithelial cells from the WBRF lung specification protocol as outlined in Herriges et al., 2022.

first: Michael

last: Herriges

first: Jonathan

last: Lindstrom-Vautrin

first: Carlos

last: Villacorta-Martin


title: Stress-related transcriptomic changes associated with GFP transgene overexpression and active transgene silencing in plants

status: Public on Aug 25 2023

city: Heraklion

first: Kriton

last: Kalantidis

state: Crete

address: Voutes University Campus

department: Biology

country: Greece

institute: University of Crete

summary: We performed gene expression analysis using RNA-seq data of four plant samples for each of the following groups: Wild Type (WT) plants and transgenic GFP6.4 Non-Silenced (NS), Ongoing Spreading (OS) post-transcriptional gene silencing, and  Systemically Spread (SS) post-transcriptional gene silencing.

overall_design: The analysis reveals that spreading and maintenance of GFP-PTGS are associated with transcriptional reprogramming of genes that are involved in abiotic stress responses and pattern- or effector-triggered immunity-based stress responses.

first: Kallemi

last: Paraskevi

first: Verret

last: Frederic

first: Andronis

last: Christos

first: Ioannidis

last: Nikolaos

first: Glampedakis

first: Kotzabasis

last: Kiriakos

first: Kalantidis

last: Kriton


title: Gene body DNA hydroxymethylation restricts magnitude of transcriptional changes during aging [RNA-seq]

city: Baltimore

first: Supriyo

last: De

state: Maryland

address: 251 Bayview Blvd

department: Laboratory of Genetics and Genomics

institute: NIA-IRP, NIH

summary: DNA hydroxymethylation (5hmC), the most abundant oxidative derivative of DNA methylation, is typically enriched at enhancers and gene bodies of transcriptionally active and tissue-specific genes. Although aberrant genomic 5hmC has been implicated in age-related diseases, its functional role in aging remains unknown. Here, using mouse liver and cerebellum as model organs, we show that 5hmC accumulates in gene bodies associated with tissue-specific function and restricts the magnitude of gene expression changes with age. Mechanistically, 5hmC decreases the binding of splicing associated factors and correlates with age-related alternative splicing events. We found that various age-related contexts, such as prolonged quiescence and senescence, drive the accumulation of 5hmC with age. We provide evidence that this age-related transcriptionally restrictive function is conserved in mouse and human tissues. Our findings reveal that 5hmC regulates tissue-specific function and may play a role in longevity.

overall_design: RNA-seq using young (2-4 months) and old (18-20 months) mouse liver (four biological replicates per group).

first: James

last: Occean

first: Payel

last: Sen


title: Epigenetic selectivity of TopoIIα redistribution and histone eviction of anthracyclines

city: Leiden

first: Minkang

last: Tan

address: Einthovenweg 20

department: Department of Cell and Chemical Biology

country: Netherlands

institute: Leiden University Medical Center

summary: Anthracyclines act by disrupting the interface of TopoII and DNA and by evicting histones. The anthracycline-specific redistribution of TopoII and its association with histone eviction were addressed in K562 cells. Chromatin immunoprecipitation, followed by deep sequencing (ChIP-seq) against endogenously tagged TopoIIα, and transposase-accessible chromatin with sequencing (ATAC-seq) was performed 4 hours after anthracycline exposure.

overall_design: For ChIP-seq: Endogenous tagged 3×Flag-TopoIIα K562 cells were treated with 10 µM of indicated drug for 4 hours. Then cells were fixed in 1% formaldehyde and processed as dessscribed in PMID 19275939, 25961671 for ChIP against anti-Flag M2 (F3165, Sigma) . For ATAC-seq: K562 cells were treated with 10 µM of indicated drug for 4 hours. Then cells were processed as desscribed in PMID 24097267 and 28846090.

first: Baoxu

last: Pang

first: Feija

last: Hamoen

first: Sabina

middle: Y

last: van der Zanden


title: Adult mouse lung digestion test

first: Feiya

last: Wang

summary: This experiment was performed to help optimize a digestion protocol for FACS of adult mouse lung cells. The sample JH2 was used to help generate lung epithelial cell signatures.

overall_design: The goal of this experiment was to compare the various lung cell types yielded from two enzymatic digestion protocols: Morrisey Lab protocol (collagenase and dispase) and Jessie Huang's optimized protocol (a combination of Nan Tang and Jay Mizgerd's protocols: collagenase, dispase, elastase, with agarose instillation in the lungs) The four samples and their target cell recovery are the following: JH1 (non-EpCAM), 4000 cells, JH2 (EpCAM), 1000 cells, EM1 (non-EpCAM), 4000 cells, EM2 (EpCAM), 1000 cells I'll be adding 2 extra lanes this time to include cells digested through Ed Morrisey's lung digestion protocol. The other change is that I'm sorting the immune/endothelial cells separately from the mesenchymal population, and recombining them 1:1 in my non-EpCAM lanes (so that the former population doesn't overwhelm the latter in terms of cell numbers).

first: Michael

last: Herriges

first: Jessie

last: Huang

first: Darrell

last: Kotton


title: Gene body DNA hydroxymethylation restricts magnitude of transcriptional changes during aging.

summary:
DNA hydroxymethylation (5hmC), the most abundant oxidative derivative of DNA methylation, is typically enriched at enhancers and gene bodies of transcriptionally active and tissue-specific genes. Although aberrant genomic 5hmC has been implicated in age-related diseases, its functional role in aging remains unknown. Here, using mouse liver and cerebellum as model organs, we show that 5hmC accumulates in gene bodies associated with tissue-specific function and restricts the magnitude of gene expression changes with age. Mechanistically, 5hmC decreases the binding of splicing associated factors and correlates with age-related alternative splicing events. We found that various age-related contexts, such as prolonged quiescence and senescence, drive the accumulation of 5hmC with age. We provide evidence that this age-related transcriptionally restrictive function is conserved in mouse and human tissues. Our findings reveal that 5hmC regulates tissue-specific function and may play a role in longevity.

This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: Whole-genome bisulfite sequencing of Infectious spleen and kidney necrosis virus

status: Public on Aug 23 2023

city: Zhuhai

first: Mincong

last: Liang

state: Guangdong

address: No. 2 Daxue Road

department: School of Marine Sciences

institute: Sun Yat-sen University

summary: To obtain the site-by-site methylation landscape of the infectious spleen and kidney necrosis virus (ISKNV) genome, whole-genome bisulfite sequencing (WGBS) was performed on an ISKNV strain from 3 duplicate samples.

overall_design: After infecting Mandarin fish fry (MFF-1) cells for 7 days with ISKNV (OP896201.1) at 27 °C and 5% carbon dioxide using Dulbecco’s modified Eagle medium (DMEM), samples collected by repeated freezing and thawing were centrifuged. The total DNA of virion was extracted following to the manufacturer's protocol (Vazyme) and WGBS was performed.

first: Weiqiang

last: Pan

first: Shaoping

last: Weng

first: Jianguo

last: He

first: Changjun

last: Guo


title: 3D and Air Liquid Interface culture of human iPSC-derived alveoar epithelial type I-like cells (iAT1s) [NGAT LDCI]

first: Pushpinder

last: Bawa

summary: The goal of this study is to understand transcriptomic differences of human iPSC derived alveolar epithelial type I-like cells cultured in 3D and at Air Liquid Interface (ALI).

overall_design: BU3 NGAT iPSCs were differentiated into iPSC derived alveolar epithelial type 2 cells (iAT2s). Cells were either maintained as iAT2s in 3D Matrigel in CKDCI medium or differentiated into iAT1s using LDCI medium. ALI versions of iAT1 cultures were prepared as follows: to prepare “iAT1 ALI p0” cultures, first a single cell suspension of iAT2s was passaged onto 6.5mm transwell inserts (Corning) coated with hESC qualified Matrigel (Corning, 8774552), while switching CKDCI medium to LDCI at the time of plating. To prepare “iAT1 ALI p1” cultures, iAT2s in 3D Matrigel culture were first switched to LDCI medium in 3D for 9 days before being passaged as single cells onto Matrigel coated transwells for continued LDCI culture. All ALI cultures were continued for 10 days after transwell plating.

first: Claire

last: Burgess


title: Pathological effects of SARS-CoV-2 and α-synuclein preformed fibril in hESC-derived dopaminergic neurons

city: Seoul

first: Yong Jun

last: Kim

address: 26 Kyungheedaero

department: Department of Pathology

country: South Korea

institute: Kyung Hee University

summary: Progression Parkinson’s disease (PD) has been strongly correlated to concurrent virus infection such as herpes virus, Helicobacter pylori, hepatitis C, and pneumococcus and the concurrent immune response in the brain. However, the effect of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) on the onset and progression of PD is yet to be investigated. As the pandemic is getting closer to being under control and majority of the population in the world will have been infected with SARS-CoV-2, there will be a huge need for uncovering the unknown, possible neurological sequelae of SARS-CoV-2 infection. Here we report that SARS-CoV-2 infection increased the susceptibility of DA neurons to PFF-induced cell death while PFF or SARS-CoV-2 alone did not exert a cytotoxic effect on dopaminergic (DA) neurons. RNA sequencing data revealed mechanistic investigations that SARS-CoV-2, in vitro, increased susceptibility to PFF-induced PD-like pathology including changes in expression of signaling molecules in apoptosis, autophagy, oxidative stress, and mitochondrial function. Thus, our study provides a previously unappreciated paradigm that SARS-CoV-2 infection persists in the brain and increases susceptibility to neurodegenerative diseases such as PD via continuous inflammatory response as a long-term sequela.

overall_design: Biological replicates of hESC-derived dopaminergic neurons prepared under thoroughly isolated conditions were infected with SARS-CoV-2 along with treatment of α-synuclein preformed fibril, and each subset was analyzed.

first: Seung Pil

last: Yun


title: Gene body DNA hydroxymethylation restricts magnitude of transcriptional changes during aging [hMeDIP]

first: Supriyo

last: De

overall_design: hMeDIP-seq using young (2-4 months) and old (18-20 months) mouse liver. n=4 biological replicates per group.

first: James

last: Occean

last: Yang

first: Payel

last: Sen


title: Aging impairs cold-induced beige adipogenesis and adipocyte metabolic reprogramming

status: Public on Aug 07 2023

city: Philadelphia

first: Patrick

last: Seale

address: 3400 Civic Center Blvd., SCTR 12th Floor

institute: University of Pennsylvania

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


title: Aging impairs cold-induced beige adipogenesis and adipocyte metabolic reprogramming [single-nucleus RNA-seq]

summary: The energy-burning capability of beige adipose tissue is a potential therapeutic tool for reducing obesity and metabolic disease, but this capacity is decreased by aging. Here, we evaluate the impact of aging on the profile and activity of adipocytes during the beiging process through single nucleus gene expression analysis of inguinal white adipose tissue of young and aged mice in response to cold exposure.

overall_design: Inguinal white adipose tissue nuclei from Young (9 weeks) and Aged (57 weeks) C57BL/6 mice previously acclimated to 30°C for 3 weeks and either: maintained at 30°C for 2 weeks (TN); kept at 30°C for 11 more days before moving to 6°C for 3 days (3D cold), or moved to 6°C for 14 days (14D cold).

first: Corey

last: Holman

first: Ryan

last: Calhoun

first: Ethan

last: Fein

first: Christopher

last: Jacobs

first: Linus

last: Tsai

first: Evan

last: Rosen


title: Gene body DNA hydroxymethylation restricts magnitude of transcriptional changes during aging [direct RNA-seq]

overall_design: Long-read RNA-seq using young (~2 months) and old (~18 months) mouse liver (four biological replicates per group).

first: Cedric

last: Belair

first: Showkat

last: Dar

first: Manolis

last: Maragkakis


title: shRNA-based miRNA overexpression results in significant off-target effects caused by isomiR production [mRNA-seq]

first: Anton

last: Zhiyanov

summary: miRNA overexpression strategy based on RNA Polymerase (Pol) III mediated expression of short hairpin RNA (shRNA) coding particular miRNA is widely used for miRNA functional studies. For some miRNAs, e.g., encoded in the genome as a part of a polycistronic miRNA cluster, it is most likely the only way for their individual stable overexpression. Here we have revealed that extra \texttt{U} residues (up to five) added Pol III at the 3$'$-end of the transcribed shRNA associated with a shift in the Dicer cleavage position of the shRNA. This results in the undesirable formation of 5$'$-end miRNA isoforms (5$'$-isomiRs), which have a significantly altered seed region compared to the initially encoded canonical hsa-miR-93-5p. The predominant expression of 5$'$-isomiRs without three or four first nucleotides instead of the canonical isoform could be disclosed based on miRNA-Seq analysis. Moreover, mRNA sequencing data showed that the 5$'$-isomiRs of hsa-miR-93-5p presumably regulate their own mRNA targets. Thus, omitting miRNA-Seq analysis may lead to erroneous conclusions regarding revealed mRNA targets and possible molecular mechanisms in which studied miRNA is involved.

overall_design:
PC-3 (prostate cancer) cell line was transduced by lentiviral particles coding one of the three types of shRNA to achieve stable overexpression of hsa-miR-93-5p.
All shRNA constructs contained the sequence of the canonical hsa-miR-93-5p and differed in their loop sequence only (5'-CUACCUGCACGAACAGCACUUUG-3' -- upper stem; 5'-CUCGAG-3', 5'-UUCAAGAGA-3', 5'-UUCUAAAA-3' -- stem loops; 3'-...UUGAUGGACGUGCUUGUCGUGAAAC-5' -- lower stem).
To comprehensively understand the overexpressed isoforms of hsa-miR-93-5p and their impact on the cellular transcriptome profile, we conducted sequencing of both mRNAs (3 repeats for control and all loops) and miRNAs (3 repeats for the control, 3 repeats for the first loop and 2 repeats for other ones).

first: Diana

last: Maltseva

first: Ivan

last: Kirillov

first: Roman

last: Suvorov

first: Daria

last: Gubani

first: Anna

last: Kudriaeva

first: Alexey

last: Belogurov

first: Alexander

last: Tonevitsky


title: shRNA-based miRNA overexpression results in significant off-target effects caused by isomiR production


title: P31.Dataset

city: Los Angeles

first: Steve

last: Horvath

address: 695 Charles E. Young Drive South, Box 708822

department: Human Genetics

type: Methylation profiling by genome tiling array

summary: Cytosine methylation data generated on mammalian methylation platform

platform_organism:
Macaca mulatta
Homo sapiens
Mus musculus
Rattus

overall_design: The data includes 16 Blood, 16 Cortex, 16 Kidney, 16 Liver, 16 Spleen, 16 Tail of Mus musculus


title: P30.Dataset

overall_design: The data includes 16 Blood, 15 Cortex, 16 Kidney, 16 Liver, 16 Spleen, 16 Tail of Mus musculus


title: Nuclear YAP overexpression drives the human alveolar type 1 cell (AT1) cprogram in a cell autonomous manner in lentiviral transduced iPSC-derived alveolar type 2 cells (iAT2s)

first: Pushpinder

last: Bawa

summary: SPC2B2 iAT2s were transduced with either control WT YAP or constitutively active nuclear YAP (YAP5SA) lentivirus in a single cell suspension and were then grown in iAT2 media (CK + DCI) in 3D matrigel for 7 days.

overall_design: iPSCs (clone SPC2-ST-B2) underwent directed differentiation to produce lung alveolar epithelial type 2 cells (iAT2s), maintained in CK+DCI medium in 3D cultures. The iAT2s were then lentivirally transduced in a single cell suspension with either control WTYAP or constitutively active nuclear YAP (YAP5SA) lentivirus ((each vector also carrying a TagBFP reporter cassette), and the resulting cells grown out in 3D CK+DCI cultures were captured for profiling by scRNA-seq.

first: Claire

last: Burgess

first: Darrell

last: Kotton

first: Carlos

last: Villacorta-Martin


title: Aberrant histone H3 serotonylation dynamics in dorsal raphe nucleus contribute to maladaptive stress-induced gene expression programs and behavior

first: Aarthi

last: Ramakrishnan

address: 1425 Madison Avenue

department: Neuroscience

institute: Icahn School of Medicine at Mount Sinai

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: Clinical significance of MSP-RON signaling based on mRNA-microRNA integration analyses in acute severe ischemic stroke patients (mRNA data)

city: Suita

first: Daisuke

last: Motooka

address: 3-1, Yamadaoka

institute: NGS core facility, Research Institute for Microbial Diseases, Osaka University

overall_design: We corrected RNA extracted from whole blood of 6 acute minor ischemic stroke patients (National Institutes of Health Stroke Scale [NIHSS] < 8) and 6 acute severe ischemic stroke patients (NIHSS ≥ 8) on admission. mRNA and miRNA were measured by RNA sequencing.

first: Hideaki

last: Kanki

first: Hisatake

last: Matsumoto


title: Multi-omics in nasal epithelium reveals three axes of dysregulation for asthma risk in the African Diaspora populations

status: Public on Aug 16 2023

first: Rasika

middle: M

last: Mathias

state: MD

address: 5501 Bayview Cir

department: Allergy and Clinical Immunology

institute: Johns Hopkins University

summary: Background: Asthma, a complex chronic lung disease affecting the airways, has striking disparities across ancestral groups, but the molecular underpinning of these differences is poorly understood and minimally studied. A major goal of the Consortium on Asthma among African-ancestry Populations in the Americas (CAAPA) is to understand multi-omics signatures of asthma risk in the nasal epithelium focusing on populations of African ancestry.  Methods: RNASeq data were generated from nasal epithelium in subjects recruited from up to 7 sites (Baltimore, Washington DC, Chicago, Denver, Salvador Brazil, Barbados, and Nigeria). Current asthma cases (N=253) were compared to never-asthma controls (N=283) to identify differentially expressed genes (DEGs; q <0.05). Network analyses were performed with Ingenuity Pathway Analysis (IPA; DEGs with q<0.05) and weighted gene co-expression network analysis (WGCNA; DEGs with q<0.15). All models were fully adjusted for ancestry, sampling site, and appropriate latent factors.  Findings: CAAPA represents diversity across the African Diaspora with a wide range of continental African ancestry (9%-100%). We identified 389 DEGs; the top DEG, FN1, was downregulated in asthma cases (q=3.26x10-9) and encodes fibronectin which plays a role in wound healing. Others in the top 10 DEGs have high relevance for asthma: SNTG2 (q = 1.12x10-4) is the target of multiple miRNAs related to asthma; PPP1R9A expression (q=7.60x10-5) was previously determined to be influenced by IL-13 in mouse lung; and SPTBN1 (q=1.12x10-4) plays a key role in mediating TGFβ signaling. IPA revealed networks with upstream regulators relevant for immune response (IL4; p=7.25x10-10 and TGFβ1; p=5.47x10-8) and drug response (dexamethasone; p=4.31x10-10 and fluticasone propionate; p=9.42x10-8). Among asthma cases, genes regulated by dexamethasone and fluticasone propionate were not associated with inhaled corticosteroid medication use. The top three WGCNA modules implicate networks related to immune response (CEACAM5; p=9.62x10-16 and CPA3; p=2.39x10-14) and wound healing (FN1; p=7.63x10-9). Multi-omic analysis identified FKBP5 as a key contributor to asthma risk, whereby the association between nasal epithelium gene expression is mediated through methylation and is associated with increased use of inhaled corticosteroids. FKBP5 is a co-chaperone of glucocorticoid receptor signaling and known to be involved in drug response in asthma.   Interpretation: Our analyses reveal genes and networks in asthma that are differentially expressed in nasal epithelium of asthma cases of African ancestry in CAAPA. Importantly, this work reveals molecular dysregulation on three axes – increased Th2 inflammation, decreased capacity for wound healing, and impaired drug response – that may play a critical role in asthma within the African Diaspora.

overall_design: RNA sequencing data was generated from nasal epithelium samples in newly recruited subjects representing 7 locations across the African Diaspora: Baltimore, Washington DC, Chicago and Denver in the United States; Salvador, Brazil; Barbados in the Caribbean; and Nigeria in West Africa. We examined transcriptomic differences between asthma cases and never-asthma controls to identify differentially expressed individual genes and networks of co-expressed genes.

first: Kathleen

last: Barnes


title: Methylation studies in prairie voles

state: CA

summary:
An Infinium microarray platform (GPL28271, HorvathMammalMethylChip40) was used to generate DNA methylation data from several tissues from prairie voles (Microtus ochrogaster). Ear, liver, and brain samples from the Cornell University prairie vole colony were collected from 48 male and female prairie voles at various life stages: neonatal (<1 month old), sub-adult (2-4 months old), mature adult (4-10 months old), and middle aged/old adult (>10 months old). The pair bonded male and female prairie voles used in our study cohabitated with their partners for several months and produced at least three generations of litters. Animals were euthanized via rapid decapitation, their tissues rapidly extracted and frozen on dry ice before being stored at -80C until further processing for genomic DNA extraction. Brains were coronally sectioned and brain regions from the pair bonding circuit (PBC) were micro-dissected and pooled for each animal. The PBC brain regions included the prefrontal cortex, nucleus accumbens, lateral septum, ventral pallidum, and medial amygdala, and ventral tegmental area. Genomic DNA was isolated and purified using the phenol-chloroform extraction and ethanol precipitation method. A total of 144 tissue samples were collected and processed for DNA methylation analysis.
Tissues: Brain,  Ear, Liver

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus

overall_design: N=144 tissue samples from prairie voles (Microtus ochrogaster). Genome annotations of the array can be downloaded from https://github.com/shorvath/MammalianMethylationConsortium

last: Ophir


title: Aberrant histone H3 serotonylation dynamics in dorsal raphe nucleus contribute to maladaptive stress-induced gene expression programs and behavior [ChIP-seq]

summary: Major depressive disorder (MDD) is a debilitating illness that affects millions of individuals worldwide. While chronic stress increases incidence levels of MDD, stress-mediated disruptions in brain function that precipitate the disorder remain elusive. Serotonin-associated antidepressants (ADs) remain the first line of therapy for many with MDD, yet low remission rates and delays between treatment and symptomatic alleviation have prompted skepticism regarding precise roles for serotonin in the precipitation of MDD. Our group recently demonstrated that serotonin epigenetically modifies histone proteins (H3K4me3Q5ser) to regulate transcriptional permissiveness in brain. However, this phenomenon has not yet been explored following stress and/or AD exposures. Here, we employed a combination of genome-wide (ChIP-seq, RNA-seq) and western blotting analyses in dorsal raphe nucleus (DRN) of male and female mice exposed to chronic social defeat stress to examine the impact of stress exposures on H3K4me3Q5ser dynamics in DRN, as well as associations between the mark and stress-induced gene expression. Stress-induced regulation of H3K4me3Q5ser levels were also assessed in the context of AD exposures, and viralmediated gene therapy was employed to manipulate H3K4me3Q5ser levels to examine the impact of reducing the mark in DRN on stress-associated gene expression and behavior. We found that H3K4me3Q5ser plays important roles in stress-mediated transcriptional plasticity in DRN. Mice exposed to chronic stress displayed dysregulated dynamics of These findings establish a neurotransmission-independent role for serotonin in stress-associated transcriptional and behavioral plasticity in DRN.

overall_design: To investigate the effects of chronic stress on gene expression in the mouse DRN, we performed CSDS in a cohort of male and female mice. We then performed gene expression profiling analysis using data obtained from RNA-seq of male and female mice that had underwent CSDS and handled control mice. To assess whether alterations in the genomic enrichment of H3K4me3Q5ser correspond with meaningful patterns of genomic regulation following chronic stress exposures, we performed CSDS in separate cohorts of male and female mice. We then performed Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for histone variants H3K4me3Q5ser and H3K4me3 (H3K4me3 was only used for the male cohort). Finally, to investigate the effect of depletion of H3K4me3Q5ser on chronic stress-induced gene expression, we performed gene expression profiling analysis using data obtained from RNA-seq of a separate cohort of stressed mice (and handled controls) injected with 3 different viruses (H3.3Q5A, H3.3 WT, and an empty vector control).

first: Amni

last: Al-Kachak

first: Sasha

last: Fulton

first: Ian

last: Maze


title: Methylation studies in rhesus macaque

status: Public on Aug 05 2023

summary:
DNA methylation data from rhesus macaque (Macaca mulatta) profiled on the mammalian methylation array (HorvathMammalMethylChip40) which focuses on highly conserved CpGs across mammalian species.
We profiled n = 283 tissue samples (blood, skin, adipose, kidney, liver, lung, muscle, and cerebral cortex)

overall_design: n=283 samples/arrays. Genome annotations of the array can be downloaded from https://github.com/shorvath/MammalianMethylationConsortium

first: Julie

last: Mattison


title: Methylation studies in common marmoset

summary:
DNA methylation data from common marmosets (Callithrix jacchus) profiled on the mammalian methylation array (HorvathMammalMethylChip40) which focuses on highly conserved CpGs across mammalian species.
Rapamycin study in a subset of animals.

overall_design: n=96 blood samples/arrays. Genome annotations of the array can be downloaded from https://github.com/shorvath/MammalianMethylationConsortium

first: Adam

middle: B

last: Salmon


title: Methylation studies in strepsirrhini primates

last: Horvath

summary:
DNA methylation data from several primate species profiled on the mammalian methylation array (HorvathMammalMethylChip40) which focuses on highly conserved CpGs across mammalian species. We selected a total of 91 samples from animals representing 26 strepsirrhine species, in most cases, the entire lifespan, from immature (infant or juvenile) to senile stages: 68 samples from peripheral blood, 23 samples from skin
Blood and skin samples from many different primates. We profiled the following species: Cheirogaleus medius (Fat-tailed dwarf lemur), Daubentonia madagascariensis (Aye-aye), Eulemur albifrons (White-headed lemur), Eulemur collaris (Collared brown lemur), Eulemur coronatus (Crowned lemur), Eulemur flavifrons (Blue-eyed black lemur), Eulemur fulvus (Brown lemur), Eulemur macaco (Black lemur), Eulemur mongoz (Mongoose lemur), Eulemur rubriventer (Red-bellied lemur), Eulemur rufus (Red-fronted lemur), Eulemur sanfordi (Sanford's brown lemur), Galago moholi (South African galago), Hapalemur griseus (Bamboo lemur), Lemur catta (Ring-tailed lemur), Loris tardigradus (Slender loris), Microcebus murinus (Gray mouse lemur), Mirza zaza (Northern giant mouse lemur), Nycticebus coucang (Slow loris), Otolemur crassicaudatus (Greater galago), Perodicticus potto (Potto), Propithecus diadema (Diademed sifaka), Propithecus tattersalli (Golden-crowned sifaka), Varecia rubra (Red ruffed lemur). Peripheral blood was collected through venipuncture with standard procedures, either during a routine veterinary procedure or at time of necropsy. Skin tissues were collected during necropsies.

sample_organism:
Lemur catta
Cheirogaleus medius
Otolemur crassicaudatus
Loris tardigradus
Nycticebus coucang
Perodicticus potto
Eulemur coronatus
Eulemur fulvus
Hapalemur griseus
Propithecus tattersalli
Eulemur macaco
Microcebus murinus
Galago moholi
Daubentonia madagascariensis
Eulemur mongoz
Eulemur rubriventer
Eulemur fulvus collaris
Propithecus diadema
Eulemur flavifrons
Xanthonycticebus pygmaeus
Eulemur sanfordi
Mirza zaza
Propithecus coquereli
Varecia rubra
Eulemur rufus
Eulemur albifrons

overall_design: n=91 samples/arrays. Genome annotations of the array can be downloaded from https://github.com/shorvath/MammalianMethylationConsortium

first: Erin

middle: E

last: Ehmke


title: Methylation studies in baboons.

first: Steve

summary:
DNA methylation data from Papio hamadryas (baboons) profiled on the mammalian methylation array (HorvathMammalMethylChip40) which focuses on highly conserved CpGs across mammalian species.
Seven tissue types (fetal cerebral cortex, adult cerebral cortex, cerebellum, adipose, heart, liver, and skeletal muscle) with ages ranging from late fetal life to 22.8 years of age.

overall_design: n=325 samples/arrays. Genome annotations of the array can be downloaded from https://github.com/shorvath/MammalianMethylationConsortium

first: Peter

middle: W

last: Nathanielsz


title: Aberrant histone H3 serotonylation dynamics in dorsal raphe nucleus contribute to maladaptive stress-induced gene expression programs and behavior [RNA-seq]


title: Methylation studies in human cells N76

summary:
An Infinium microarray platform (GPL28271, HorvathMammalMethylChip40) was used to generate DNA methylation data from human cell types.
n=17 human DNA samples from endothelial cells (n=13), embryonic stem cells (n=2) and skin (n=2).

overall_design: Genome annotations of the array can be downloaded from https://github.com/shorvath/MammalianMethylationConsortium

first: Ken

last: Raj


title: Methylation studies in the vervet monkey

summary:
DNA methylation data from vervet cerebral cortex, blood, and liver using highly conserved mammalian CpGs represented on the mammalian methylation array (HorvathMammalMethylChip40).
We selected a total of 240 samples representing the entire vervet lifespan, from neonatal to senile stages: 144 samples from the peripheral blood, 48 samples from the liver, and 48 samples from the cortical brain area BA10.

overall_design: n=240 samples/arrays. Genome annotations of the array can be downloaded from https://github.com/shorvath/MammalianMethylationConsortium

first: Anna

last: Jasinska


title: Methylation studies in human and mouse placenta

summary:
An Infinium microarray platform (GPL28271, HorvathMammalMethylChip40) was used to generate DNA methylation data from placental samples from two species: human and mouse.
n=47 samples (n=24 placental samples from humans, 23 placental samples from mice).

first: Mary

middle: C

last: Wallingford


title: Methylation studies in multiple human tissues N66

summary:
An Infinium microarray platform (GPL28271, HorvathMammalMethylChip40) was used to generate DNA methylation data from human blood samples.
n=92 brain samples (n=46 samples from cerebellum, n=46 from cerebral cortex).

first: Harry

middle: V

last: Vinters


title: Methylation studies in human blood N94 N68

summary:
An Infinium microarray platform (GPL28271, HorvathMammalMethylChip40) was used to generate DNA methylation data from human tissue samples.
n=144 EDTA blood samples and n=240 blood samples

overall_design: Genome annotations of the array can be downloaded from https://github.com/shorvath/MammalianMethylationConsortium. Authors state the following for some samples: I cannot share the idat files, i.e. the raw data. I cannot share the raw data because of issues of IRB/consent forms.

first: Beate

last: Ritz


title: Aging impairs cold-induced beige adipogenesis and adipocyte metabolic reprogramming [single-cell RNA-seq]

first: Patrick

last: Seale

state: PA

summary: The energy-burning capability of beige adipose tissue is a potential therapeutic tool for reducing obesity and metabolic disease, but this capacity is decreased by aging. Here, we evaluate the impact of aging on the profile and activity of adipogenic precursor cells (APCs) through single cell gene expression analysis of inguinal white adipose tissue of young and aged mice through in response to cold exposure.

overall_design: Stromal vascular cells depleted of CD45+ immune cells from Young (9 weeks) and Aged (57 weeks) C57BL/6 mice previously acclimated to 30°C for 3 weeks and either: maintained at 30°C for 2 weeks (TN); kept at 30°C for 11 more days before moving to 6°C for 3 days (3D cold), or moved to 6°C for 14 days (14D cold).

first: Corey

last: Holman

first: Alexander

last: Sakers

first: Ryan

last: Calhoun


title: Methylation studies in multiple human tissues N47

summary:
An Infinium microarray platform (GPL28271, HorvathMammalMethylChip40) was used to generate DNA methylation data from human blood samples.
n=95 blood samples.

first: Andrew

last: Levine

first: Jacqueline

last: Hoare


title: Methylation studies in multiple human tissues N36

summary:
An Infinium microarray platform (GPL28271, HorvathMammalMethylChip40) was used to generate DNA methylation data from human tissue samples.
n=96 tissues. Skin (n=72), keratinocyte (n=20), fibroblast (1), epidermis (2), dermis (1)


title: Multi-cell type deconvolution using a probabilistic model of single-molecule DNA methylation haplotypes

status: Public on Aug 02 2023

city: Jerusalem

first: Benjamin

last: Berman

address: Ein Kerem campus

department: Developmental Biology and Cancer Research

institute: The Hebrew University

summary: Deconvolution methods infer quantitative cell type estimates from bulk measurement of mixed samples including blood and tissue. DNA methylation sequencing measures multiple CpGs per read, but few existing deconvolution methods leverage this within-read information. We develop CelFiE-ISH, which extends an existing method (CelFiE) to use within-read haplotype information. CelFiE-ISH outperforms CelFiE and other existing methods, achieving 30% better accuracy and more sensitive detection of rare cell types. We also demonstrate the importance of marker selection and tailoring markers for haplotype-aware methods. While here we use gold-standard short-read sequencing data, haplotype-aware methods will be well-suited for long-read sequencing.

overall_design: This is a reanalysis of GSE186458. Refer to GSE186458 for overall design and sample details. Raw fastq files are available at the European Genome-phenome Archive (EGA) under study accession number: EGAS00001006791.

first: Irene

last: Unterman

first: Dana

last: Avrahami

first: Efrat

last: Katsman

first: Timothy

last: Triche

last: Glaser


title: Single Cell Analysis Identifies Conserved Features of Immune Dysfunction in Simulated Microgravity and Spaceflight

status: Public on Aug 01 2023

city: Novato

first: Fei

last: Wu

address: 8001 Redwood Blvd

institute: Buck Institute for Research on Aging

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

overall_design: Refer to individual Series


title: Surprising mechanisms and regulatory roles of yeast transcription factors [RNA-seq]

city: SEATTLE

first: Lakshmi

last: Mahendrawada

state: WA

address: 1100 FAIRVIEW AVE N

department: Basic Sciences Division

institute: Fred Hutchinson Cancer Center

summary: DNA sequence-specific transcription factors (TFs) modulate transcription and chromatin architecture, acting from regulatory sites in enhancers and promoters of eukaryotic genes. How multiple TFs cooperate to regulate individual genes is still unclear. Most yeast TFs are thought to regulate transcription via binding to Upstream Activating Sequences, situated within a few hundred base pairs upstream of the regulated gene1. While this model has been validated for individual TFs and specific genes, it has not been tested in a systematic way. We integrated information on the binding and expression targets for the near-complete set of yeast TFs. Here we show that, contrary to expectations, there are few TFs with dedicated activator or repressor functions with most TFs having a dual role. While nearly all protein coding genes are regulated by one or more TFs, our analysis revealed limited overlap between TF binding and gene regulation. Rapid depletion of many TFs also revealed numerous regulatory targets distant from detectable TF binding sites, suggesting unexpected regulatory mechanisms. Our study provides a comprehensive survey of TF functions, offering insights into interactions between the set of TFs expressed in a single cell type and how they contribute to the complex program of gene regulation.

overall_design: Newly synthesized RNAs were labeled with 4TU, purified and analyzed with RNA-seq. Depletion of TFs was achieved through targeted degradation (auxin-degron system). Control and treatment sample files are labeled DMSO and 3IAA (3-indole acetic acid), respectively. All experiments were done in three replicates (A,B,C).

first: Linda

last: Warfiled

first: Rafal

last: Donczew

first: Steven

last: Hahn


title: Surprising mechanisms and regulatory roles of yeast transcription factors [ChEC-seq]

overall_design: ChEC-seq method was used to map genome-wide binidng of transcription factors. Experiments were done in two, three (A,B,C) replicates


title: Surprising mechanisms and regulatory roles of yeast transcription factors [ChIP-seq]

overall_design: Standard ChIP-seq approach including crosslinking, chromatin extraction, DNA fragmentation and immunoprecipitation. All experiments were done in triplicates.


title: 3D chromatin structure in colon cancer

status: Public on Jul 27 2023

city: Daejeon

first: Inkyung

last: Jung

address: KAIST, 291 Daehak-ro, Yuseong-gu

department: Biological Sciences

institute: KAIST

summary: We report the application of in situ Hi-C technology to 40 colorectal cancer patients and 10 paired-normal tissue to identify CRC specific changes in 3D chromatin structure. The chromatin contact matrices were generated by the sequencing data and image processing/deep learning-based algorithm was proposed to identify long-range abnormal chromatin interaction patterns in the contact matrices. The tumor specific 3D chromatin structure changes and the enhancer-promoter rewiring mediated by the identified chromatin structure changes were analyzed. The complex chromosome-wide rearrangements such as chromothripsis and its effect to 3D chromatin structure were also observed.

overall_design:
This study contains in situ Hi-C data for colorectal cancer patient samples.

Additional processed data is available at: http://junglab.kaist.ac.kr/Dataset/Kim_et_al_2023
Online tissue slide data repository is available at: http://junglab.kaist.ac.kr/Dataset/CellReports_tissueData.html

first: Kyukwang

last: Kim

last: Lee

first: Junghyun

last: Eom

first: Mooyoung


title: Single Cell Analysis Identifies Conserved Features of Immune Dysfunction in Simulated Microgravity and Spaceflight [scRNA-Seq]

summary: Microgravity is associated with immunological dysfunction, though the underlying mechanisms are poorly understood. Here, using single cell analysis of human peripheral blood mononuclear cells (PBMC)s exposed to short term (25 hours) simulated microgravity, we characterize altered genes and pathways across immune cells under basal and stimulated states with a Toll like Receptor-7/8 agonist. At basal state, simulated microgravity altered the transcriptional landscape across immune cells, with monocyte subsets showing most pathway changes. Remarkably, short term simulated microgravity was sufficient to increase endogenous retroviral and mycobacterial transcripts. Under stimulation in simulated microgravity, nearly all immune cells demonstrated differences in functional pathways. Results from single cell analysis were validated against additional PBMC samples, including by RNA sequencing and super-resolution microscopy, and against data from the Inspiration-4 (i4) mission, JAXA6 mission, Twins study, and spleens from mice housed on the international space station. Combined results show significant impacts of microgravity on pathways essential for optimal immunity, including the cytoskeleton, interferon signaling, pyroptosis, temperature-shock, nuclear receptors, IL-6 signaling, HIF1α, and sirtuin signaling. Using machine learning, we identified numerous compounds linking microgravity to immune cell transcription, and demonstrate that the flavonol, quercetin, can reverse most abnormal pathways. These results offer insight into maladaptation of the immune system in microgravity, and provide opportunities to develop countermeasures that maintain normal immunity in space.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for PBMCs under basal and stimulated states with a Toll like Receptor-7/8 agonist in simulated microgravity and normal gravity.

first: Zoe

last: Du

first: David

last: Furman

first: Dan

last: Winer


title: Single Cell Analysis Identifies Conserved Features of Immune Dysfunction in Simulated Microgravity and Spaceflight [RNA-Seq]

overall_design: Comparative gene expression profiling analysis of RNA-seq data for PBMCs under basal and quercetin treatment in simulated microgravity and normal gravity.