title: Role of TUT4 and TUT7 on the regulation of MHV poly(A) tail length and 3' end additions [17-CL1_Mutants]

first: ANKIT

last: GUPTA

summary: Terminal uridylation of mRNAs poly(A) tails by Terminal Uridylyl Transferases (TUTs) promote transcript decay. Here, we investigate the role of two functionally redundant mammalian TUTs, TUT4 and TUT7 (TUT4/7), in mouse hepatitis virus (MHV) RNA processing. We generated a TUT4/7 knock-down 17-CL1 cell line using lentivirus encoding shRNAs against Tut4 and Tut7 transcripts (shTUT4/7) and a control 17-CL1 cell line (shCTL) with a non-targeting shRNA. We then infected the shCTL and shTUT4/7 cells with MHV and isolated RNA at 24- and 48-hours post-infection (hpi). We found that viral RNA poly(A) tails of about 20 and 40 nucleotides are highly uridylated and that the uridylation of the 20 nucleotide long tails is dependent on TUT4/7. Depletion of TUT4/7 also resulted in an accumulation of the viral RNA.

overall_design: Direct RNAseq of RNA isolated from MHV-infected 17-CL1 shCTL and shTUT4/7 mutant cells at 24 and 48 hpi

first: Ankit

last: Gupta

first: Brian

middle: N

last: Papas

first: Marcos

last: Morgan


title: Skeletal muscle DNA methylation and mRNA responses to a bout of higher versus lower load resistance exercise in previously trained men

status: Public on Dec 14 2022

city: Oslo

first: Adam

middle: P

last: Sharples

address: 220 Sognsveien

country: Norway

institute: Norwegian School of Sport Sciences

type: Methylation profiling by genome tiling array

summary: We sought to determine the skeletal muscle genome-wide DNA methylation and mRNA respons-es to one bout of lower-load (LL) versus higher-load (HL) resistance exercise. Trained col-lege-aged males (n=11, 23±4 years old, 4±3 years self-reported training) performed LL or HL bouts to failure separated by one week. The HL bout (i.e., 80 Fail) consisted of four sets of back squats and four sets of leg extensions to failure using 80% of participants estimated one-repetition maximum (i.e., est. 1-RM). The LL bout (i.e., 30 Fail) implemented the same paradigm with 30% of est. 1-RM. Vastus lateralis muscle biopsies were collected before, 3 hours, and 6 hours after each bout. Muscle DNA and RNA were batch-isolated and analyzed using the 850k Illumina Methyl-ationEPIC array and Clariom S mRNA microarray, respectively. Performed repetitions were sig-nificantly greater during the 30 Fail versus 80 Fail (p<0.001), although total training volume (sets x reps x load) was not significantly different between bouts (p=0.571). Regardless of bout, more CpG site methylation changes were observed at 3- versus 6-hours post exercise (239,951 versus 12,419, respectively; p<0.01), and nuclear global ten-eleven translocation (TET) activity, but not global DNA methyltransferase activity, increased 3- and 6-hours following exercise regardless of bout. The percentage of genes significantly altered at the mRNA level that demonstrated opposite DNA methylation patterns was greater 3- versus 6-hours following exercise (~75% versus ~15%, respectively). Moreover, high percentages of genes that were up- or downregulated 6 hours fol-lowing exercise also demonstrated significantly inversed DNA methylation patterns across one or more CpG sites 3 hours following exercise (65% and 82%, respectively). While 30 Fail de-creased DNA methylation across various promoter regions versus 80 Fail, transcriptome-wide mRNA and bioinformatics indicated that gene expression signatures were largely similar be-tween bouts. Bioinformatics overlay of DNA methylation and mRNA expression data indicated that genes related to “Focal adhesion”, “MAPK signaling”, and “PI3K-Akt signaling” were sig-nificantly affected at the 3- and 6-hour time points, and again this was regardless of bout. In con-clusion, extensive molecular profiling suggests that post-exercise alterations in the skeletal muscle DNA methylome and mRNA transcriptome elicited by LL and HL training bouts to failure are largely similar, and this could be related to equal volumes performed between bouts.

overall_design: DNA methylation

first: Michael

middle: D

last: Roberts


title: Multi-omics gene regulatory network analysis of resting and stimulated PBMCs [PBMC isolate scRNA-seq]

status: Public on Jun 20 2022

city: Cambridge

first: Vinay

last: Kartha

state: MA

address: 7 Divinity Ave

country: USA

institute: Harvard University

type: Expression profiling by high throughput sequencing

summary: Cells require coordinated control over gene expression changes when responding to environmental stimuli. Recent advancements in single-cell technologies have enabled studies of regulatory dynamics associated with cellular perturbation response in immune cells. However, associating these changes to underlying differences in epigenetic regulation through integration of multi-omic data has not been achieved at single-cell resolution. Here, we apply single-cell ATAC-seq (scATAC-seq) and scRNA-seq to assay chromatin accessibility and gene expression in resting and stimulated human blood cells. Collectively, we generate ~91,000 high-coverage single-cell profiles, allowing us to probe the cis-regulatory landscape of immunological response across cell types, stimuli and time. Advancing tools to integrate multiomic data, we connect distal cis-regulatory elements to genes, identifying key regulatory hubs associated with immune signaling and stress response. Subsequently, we design FigR - a method to infer gene regulatory networks (GRNs) to identify candidate TF regulators across single cells. Importantly, construction of a GRN using stimulus response data identifies TF regulatory activity associated with  genetic variants in inflammatory diseases. Lastly, we assess the time-dependent regulatory dynamics of immune stimulation, where we find that cells alter chromatin accessibility prior to productive gene expression, a process occurring at time scales of minutes. Extending this concept of chromatin-mediated priming, and incorporating regulatory relationships defined by FigR, we detect a rare subpopulation of monocytes marked by a primed chromatin state predictive of enhanced immunological response. Overall, we build upon computational tools for GRN construction and demonstrate the utility of GRNs for analysis of multi-omic single cell data.

overall_design: Human isolated peripheral blood CD4+, CD8+, CD14+, CD19+ and CD56+ cells were processed using the BioRad SureCell single-cell RNA-seq platform across multiple channels in the instrument.

first: Fabiana

last: Duarte


title: Influence of vaccination and time on gene expression of healthy backgrounded beef cattle

status: Public on Aug 29 2022

city: Canyon

first: Matthew

middle: Adam

last: Scott

state: TX

address: 3201 Russell Long Blvd

department: Large Animal Clinical Sciences

institute: Texas A&M University

summary: Twelve clinically healthy backgrounded cattle (n=6 vaccinated, n=6 non-vaccinated), over four time points (median age in days: 107, 114, 183, 230) were selected for whole blood (Tempus Blood RNA Tubes) mRNA sequencing via NovaSeq 6000 S4 workflow. Sequenced raw reads (~35M/sample) were analyzed for the influence of time (immunological development) and vaccination with a commercial modified live viral multivalent vaccine on host gene expression.

overall_design:
Comparative time-course RNA-Seq analysis on lysed whole blood samples across four time points. Cattle (n=12) were evenly distributed based on vaccine administration at median day 107 and boostering at median day 183, or no vaccination.

Grant:
#2019-67015-29845
Title: "Impact of management decisions during the cow-calf, backgrounding, and feedlot phases of beef production on BRD morbidity and mortality risks"
Funding source: USDA National Institute of Food and Agriculture (NIFA) Agriculture and Food Research Initiative (AFRI).

middle: A


title: Multi-omics gene regulatory network analysis of resting and stimulated PBMCs [scATAC-seq]

type: Genome binding/occupancy profiling by high throughput sequencing

overall_design: Human peripheral blood mononuclear cells from 3-4 donors were stimulated with either Interferon gamma, LPS or PMA/ionomycin for 1 hour and 6 hours and then profiled using the BioRad SureCell single-cell ATAC-seq platform. Control samples (DMSO) are included for both the 1 hour and 6 hours time points. In addition, the 6 hours stimulations were performed in the presence of a Golgi inhibitor for all 3 stimulants and control.


title: The transcriptomic landscape of glutamatergic cortical neurons carrying Alzheimer’s disease PSEN1 mutations reveals alterations in structural components, signalling, and ncRNA regulation

status: Public on Jan 24 2023

city: Copenhagen

first: Christian

last: Anthon

address: Thorvaldsensvej 57

country: Denmark

institute: University of Copenhagen

summary: To investigate gene expression changes related to two fAD mutations (A79V and L150P) in the Presenilin-1 gene (PSEN1) we compared the transcriptomes (polyA and total) of glutamatergic cortical neurons derived from fAD-mutant human induced pluripotent stem cells and their individual isogenic controls generated via precision CRISPR/Cas9 genome editing.

overall_design: RNA-seq study on human induced pluripotent stem cells differentiated in glutamatergic cortical neurons carrying A79V and L150P mutations in PSEN1, compared to gene-corrected controls.

first: Giulia

middle: I

last: Corsi

first: Veerendra

last: Gadekar

first: Henriette

last: Haukedal

first: Nadezhda

middle: T

last: Doncheva

first: Sheetal

last: Ambardar

first: Dasaradhi

last: Palakodeti

first: Anja

middle: H

last: Simonsen

first: Troels

last: Nielsen

first: Jørgen

middle: E

first: Poul

last: Hyttel

first: Kristine

last: Freude

first: Stefan

last: Seemann

first: Jan

last: Gorodkin


title: HypoMap – a unified single cell gene expression atlas of the murine hypothalamus

status: Public on Oct 13 2022

city: Cologne

first: Jens

last: Brüning

address: Gleueler Str. 50

country: Germany

institute: Max Planck Institute for Metabolism Research

summary: The hypothalamus plays a key role in coordinating a plethora of fundamental body functions, such as energy homeostasis, social behavior and sleep. Despite recent progress in single-cell technologies, we still lack a unified catalogue and molecular characterization of the heterogeneous cell types and, specifically, neuronal subtypes in this brain region. Here, we combined 17 publicly available hypothalamic single cell sequencing datasets and in-house single-nuclear sequencing of 36,626 cells to create 'HypoMap', an integrated reference atlas of the murine hypothalamus of 384,925 cells. We have leveraged the power of this vast amount of available data by combining them in a single platform, which allows the future incorporation of additional experiments. We validated HypoMap by comparing data collected from SmartSeq2 and bulk RNA sequencing of selected neuronal cell types with different degrees of cellular heterogeneity. Finally, we identified novel classes of glucagon-like peptide-1 receptor (Glp1r)- and Prepronociceptin (Pnoc-) expressing neurons and validated them using single-molecule in situ hybridization. Collectively, HypoMap provides a unified framework for the systematic functional annotation of murine hypothalamic cell types, and will serve as an important platform for future studies to further unravel the functional organization of hypothalamic neurocircuits, as well as identifying novel druggable targets for treating metabolic disorders.

overall_design: We generated bacTRAP RNA-seq datasets of specific hypothalamic cell types, which have been shown to be of critical importance in control of energy and glucose homeostasis, but vary in their heterogeneity and anatomical distribution. To this end, we first crossed mice expressing Cre recombinase in either AgRP neurons, POMC neurons, Pnoc-expressing neurons or in Glp1r-expressing neurons with mice allowing for Cre-dependent expression of a fusion protein of the ribosomal protein L10a and GFP.

first: Lukas

last: Steuernagel


title: Transcriptomic impact of PrsA over-expression during fed-batch Bacillus subtilis alpha-amylase fermentation

status: Public on Jul 06 2022

summary: The production of alpha-amylase (AMY) enzyme in Bacillus subtilis at a high rate leads to accumulation of unfolded AMY, which causes secretion stress. The over-expression of the PrsA chaperon aids the enzyme folding and thus reduces stress. Stress pathways are complex and intertwined in regulation of a variety of cellular mechanism; for instance, PrsA over-expression leads to reduced cell growth. To capture an overview over the impacted mechanisms, we analyze the transcriptomic changes during fed-batch AMY fermentation between a PrsA over-expressing strain and a control in a time-series RNA-seq experiment (n=3, 6 timepoints). We found evidence of transcription in 542 previously un-annotated regions, of which 234 had significant changes in transcription levels (Overall FDR 0.01). The pairwise comparison of up-/downregulated genes and their over-representation in biological processes (FDR 0.01) suggest that the PrsA over-expression might alter ATP biosynthesis activity, amino acid metabolism, and cell wall stability. An additional investigation of the protein-protein association network highlights potential cell motility signaling. Overall, these highlighted mechanisms could potentially further reduce secretion stress or detrimental aspects of PrsA over-expression during AMY production.

sample_organism: Bacillus subtilis subsp. subtilis str. 168

overall_design: RNA-seq study of fed-batch AMY fermentation over time compared between a PrsA over-expressing strain and a control

first: Adrian

middle: S

last: Geissler

first: Line

last: Poulsen

first: Enrique

last: González-Tortuero

first: Anne

last: Breüner

first: Lars

middle: J

last: Jensen

first: Carsten

last: Hjort

first: Jeppe

last: Vinther


title: SmcHD1 underlies the formation of H3K9me3 blocks on the inactive X chromosome in mice

status: Public on Jul 20 2022

city: Toyonaka

first: Koji

last: Nagao

state: Osaka

address: 1-1 Machikaneyama

department: Graduate School of Science

country: Japan

institute: Osaka University

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

overall_design: Refer to individual Series


title: Integrative tissue analysis of men with prostate cancer VI [PCBN]

status: Public on Apr 27 2022

city: Bethesda

first: Adam

middle: G.

last: Sowalsky

state: MD

address: 37 Convent Drive Building 37 Room 1062B

department: Genitourinary Malignancies Branch

institute: National Cancer Institute

summary: Prostate cancer is readily curable if detected early. The overall goal of this study is to conduct integrative profiling of tumor and blood genomics and transcriptomics.

overall_design:
To identify potential genomic drivers of tumor aggressivity, we conducted whole transcriptome sequencing.
*** Submitter declares that the raw data are being submitted to dbGaP (accession ID phs001813, https://www.ncbi.nlm.nih.gov/gap) because of patient privacy concerns. ***

middle: G

first: Eytan

last: Ruppin

first: Kenneth

last: Aldape


title: Multi-omics gene regulatory network analysis of resting and stimulated PBMCs [stimulation scRNA-seq]

first: Vinay

last: Kartha

overall_design: Human peripheral blood mononuclear cells from 3-4 donors were stimulated with either Interferon gamma, LPS or PMA/ionomycin for 1 hour and 6 hours and then profiled either using the BioRad SureCell single-cell RNA-seq platform. Control samples (DMSO) are included for both the 1 hour and 6 hours time points. In addition, the 6 hours stimulations were performed in the presence of a Golgi inhibitor for all 3 stimulants and control.

first: Fabiana

last: Duarte


title: RNA sequencing of PC9 and four erlotinib-persister cells derived from PC9

status: Public on Apr 13 2022

city: Tampa

first: Eric

last: Haura

state: FL

address: 12902 Magnolia Drive

institute: H. Lee Moffitt Cancer Center and Research Institute, Inc

summary: Given the recent reports on the role of AXL in mediating resistance to EGFR-targeted therapy, we generated cell line models of Erlotinib-resistance to investigate the effect of AXL inhibitors on EGFR TKI resistance. For this, EGFR-mutant PC9 cells were passed through a persister bottleneck by applying strong drug selection pressure to generate drug-tolerant erlotinib persister cells. We created four Erlotinib-resistant clones from one parental population; S1-34, S2-10, S2-17 and S2-30. Whole exome and RNA sequencing analyses were performed to probe the differences in Erlotinib-resistance mechanisms present in these persister-derived Erlotinib-resistant cells.

overall_design: 5 samples were analyzed: PC9, S1_34, S2_10, S2_17, and S2_30. Each sample was run only once.

first: Matthew

last: Smith

first: Sina

last: Hosseinian

first: Anurima

last: Majumder

first: Paul

last: Stewart


title: CRISPRi screen for a-amylase yield improvements in Bacillus subtilis

status: Public on Feb 22 2023

first: Christian

last: Anthon

summary: Our study showed that optimizing ncRNA expression can increase or lower the yield of alpha-amylase enzyme production in Bacillus subtilis while revealing a range of potentially novel ncRNAs.

platform_organism: Bacillus subtilis subsp. subtilis str. 168

overall_design: RNA-seq data for bacterial amylase production in two strains (codon optimized v. control) with two fed-batch replicates on two days

first: Adrian

last: Geissler

first: Annaleigh

last: Ohrt Fehler

first: Line

last: Dahl Poulsen

first: Thomas

last: Beuchert Kallehauge

first: Ferhat

last: Alkan

first: Stefan

last: Seemann

first: Michael

last: Dolberg Rasmussen

first: Jan

last: Gorodkin


title: Prospective transcriptional landscape of ectocervix samples from Kenyan cohort

status: Public on Nov 03 2022

city: Stockholm

first: Kristina

last: Broliden

state: Solna

address: Visionsgatan 4, J7:20

department: Dept. of Medicine Solna

country: Sweden

institute: Karolinska Institutet


title: Multi-omics gene regulatory network analysis of resting and stimulated PBMCs

first: Vinay

last: Kartha


title: Whole-transcript expression data of native stromal cells from normal human tonsil samples

status: Public on Mar 01 2022

city: Rennes

first: Delphine

last: Rossille

address: 2 avenue du Pr. Léon Bernard

country: France

institute: INSERM U1236-MOBIDIC

summary: Despite recent advances in the characterization of lymphoid stromal cell origin, heterogeneity, and function in mice, little is known in human. Most of transcriptomics approaches in human was performed on cultured, and amplified stromal cells modifying their phenotype and function. We purified native stromal cells from fresh and healthy tonsil samples. Gene expression profiling based on three lymphoid stromal cell types provides new insights on the characterization of those cells in human.

overall_design: Tonsil tissues from 6 healthy donors were collected and enzymatically dissociated. After depletion of hematopoietic cells three stromal cell subsets were sorted by FACS based on their phenotype. DN: CD45[Neg] /CD11b[Neg] /CD235a[Neg] /CD31[Neg] /Podoplanin[Neg] /CD21[Neg] /CD49a[Pos] ; FDC: CD45[Neg] /CD11b[Neg] /CD235a[Neg] /CD31[Neg] /Podoplanin[Pos] /CD21[Pos] ; FRC: CD45[Neg] /CD11b[Neg] /CD235a[Neg] /CD31[Neg] /Podoplanin[Pos] /CD21[Neg] /CD49a[Pos]). RNA extraction was performed on 10 000 cells for each stromal cell subsets then amplified. Hybridization was performed onto Affymetrix GeneChip® Human Genome U133 Plus 2.0 oligonucleotide arrays (Affymetrix) according to manufacturer’s instructions.

first: Frédéric

last: Mourcin

first: Rada

last: Amin

first: Karin

last: Tarte


title: Chromatin accessibility mapping for GWAS risk loci reveals compound genetic effects of neurodevelopment and neurodegenerative disorders in human neurons

status: Public on Jan 23 2022

city: Evanston

first: Jubao

last: Duan

state: IL

address: 1001 University Place

department: Center for Psychiatric Genetics

institute: NorthShore University HealthSystem

summary: Here, in NEUROG2-induced human neurons, we identified 31 credible risk SNPs in 26 schizophrenia (SZ) risk loci that displayed allele-specific open chromatin (ASoC) and were likely to be functional. For the VPS45 locus showing the strongest ASoC, CRISPR/Cas9 editing of ASoC SNP (rs2027349) altered the local expression of VPS45 and AC244033.2 (a lncRNA), and a distal gene, C1orf54. Notably, the global expression changes in neurons correlated with post-mortem brain expression signatures of neuropsychiatric disorders. Neurons carrying risk allele exhibited increased dendritic complexity, synaptic puncta density and hyperactivity, which were partially reversed by knocking-down each cis-regulated gene (VPS45, AC244033.2, or C1orf54), suggesting phenotypic contribution from all three genes.

overall_design: In NEUROG2-induced human neurons, we identified 31 credible risk SNPs in 26 schizophrenia (SZ) risk loci that displayed allele-specific open chromatin (ASoC) and were likely to be functional. For the VPS45 locus showing the strongest ASoC, CRISPR/Cas9 editing of ASoC SNP (rs2027349) altered the local expression of VPS45 and AC244033.2 (a lncRNA), and a distal gene, C1orf54. Our study reveals a compound effect of multiple genes at a single SZ locus that impairs neurodevelopment and synaptic function, providing a mechanistic link between a noncoding SZ risk variant and disease-related cellular phenotypes.

first: Duan

last: Jubao

first: Zhang

last: Siwei


title: PDAP1 RIP in UV-crosslinked human T cells

status: Public on Jan 10 2022

city: Bellinzona

first: Cristina

last: Leoni

state: Ticino

address: Via F. Chiesa 5

department: Molecular Immunology

country: Switzerland

institute: Institute for Research in Biomedicine

summary: Human CD4+ Total memory cells (CD4+CD25-CD45RA-CCR7+/-) were activated for 5d with anti-CD3/anti-CD28 antibodies. About 40*10^6 cells were then irradiated twice with 254nm UV light at 0.2J and then lysed in RIPA buffer. 1mg of cell extract was incubated on a rotating wheel ~16 h at 4°C with anti-PDAP1 antibody. PDAP1:mRNA complexes were immunoprecipitated with protein-G dynabeads 4hrs at 4°C and then treated with proteinase K. RNA was then purified using TRI-reagent and RNA zymospin columns. Three independent donors were used for this experiment. Inputs were also sequenced. Total RNA was sequenced in paired-end mode. This experiment is assessing direct targets bound by PDAP1 in human T cells.

overall_design: Immunoprecipitation of PDAP1 protein with 1mg of human CD4 T cell extract and sequencing of the PDAP1-associated RNA.

first: Michele

last: Chirichella

first: Niccolò

last: Bianchi


title: Mechanism of nucleosome positioning, spacing and regularity in Saccharomyces cerevisiae

status: Public on Oct 20 2021

city: Paris

first: Ashish

middle: Kumar

last: Singh

state: Ile-de-France

address: 25-28 Rue du Dr Roux

department: Development and Stem Cell Biology

institute: Institute Pasteur

summary: Numerous nucleosome remodeling enzymes tightly regulate nucleosome positions in eukaryotic cells. Transcription and statistical positioning of nucleosomes may also contribute to proper nucleosome organization. Individual contributions remain controversial due to strong redundancy of processes acting on the nucleosome landscape. By incisive yeast genome engineering we radically decreased their redundancy. We find the transcriptional machinery to be disruptive of evenly spaced nucleosomes, and proper nucleosome density critical for their biogenesis. INO80 spaces nucleosomes in vivo and positions the first nucleosome covering genes. It requires its Arp8 and Ies2 subunits, but unexpectedly not the Nhp10 module, for spacing. Whereas H2A.Z stimulates INO80 in vitro, its presence is dispensable for INO80 +1 positioning function in vivo. DNA damage, recombination and transposon integration assays suggest that evenly spaced nucleosomes protect cells against genotoxic stress. We derive a unifying model of the biogenesis of the nucleosome landscape and suggest that it evolved not only to regulate but also to protect the genome.

overall_design: MNase digestion of yeast nuclei followed by paired-end sequencing on following strains: 1. RNA Polymerase II and INO80 depletion in all 3 possible combinations in W303 wild type yeast and a mutant yeast lacking Isw1, Isw2 and Chd1 (TKO) for different time points; 2. Deletion of several subunits of yeast INO80 complex in WT, TKO and TKO depleted with RNA Polymerase II; 3. Histone depletion via Gal1-10 promoter in WT and TKO; ATAC-seq of WT, TKO and arp8Δ strains; 4. Depletion of TBP in TKO cells; 5. Depletion of RNA Polymerase II in TKO cells after G1 arrest.

middle: K

first: Tamas

last: Schauer

first: Lena

last: Pfaller

first: Felix

last: Mueller-Planitz


title: Gene expression profiling in ninaE wild type and ninaE G69D/+ Drosophila photoreceptors

status: Public on Oct 02 2021

city: New York

first: Hyung Don

last: Ryoo

state: NY

address: 550 First Avenue, MSB 497

department: Cell Biology

institute: NYU School of Medicine

summary: Cell type specific gene expression profiling was performed with adult Drosophila photoreceptors. Two genotypes were compared: ninaE wild type control and ninaEG69D/+ mutants that have chronic endoplasmic reticulum stress. To specifically isolate RNAs from these cell types, we drove nuclear envelope-localized EGFP::Msp300KASH expression with the photoreceptor specific Rh1-Gal4 driver. Anti-GFP beads were used to isolate the nuclei from those adult fly photoreceptor cells. Novaseq was used to perform RNA-seq.

overall_design: For adult photoreceptor purification, we followed a published protocol by Vikki Weake and colleagues (Hall et al., (2017) Transcriptome profiling of aging Drosophila photoreceptors reveals gene expression trends that correlate with visual senescence. BMC Genomics 18(1): p. 894).

first: Huai-Wei

last: Huang

first: Hyung


title: The X-chromosome dosage compensation program during the development of cynomolgus monkeys

status: Public on Nov 19 2021

city: Kyoto

first: Yukihiro

last: Yabuta

state: Kyoto

address: Yoshida-Konoe-cho, Sakyo-ku

department: Anatomy and Cell Biology

institute: Kyoto University, Graduate school of medicine

summary: X-chromosome dosage compensation ensures balanced gene dosage between the X chromosome and autosomes and between the sexes, involving divergent mechanisms among mammals. We elucidated a distinct mechanism for X-chromosome inactivation (XCI) in cynomolgus monkeys, a model for human development. The trophectoderm and cytotrophoblast acquire XCI around implantation through an active intermediate bearing repressive modifications and compacted structure, whereas the amnion, epiblast, and hypoblast maintain such an intermediate protractedly, attaining XCI by a week after implantation. Males achieve X-chromosome up-regulation (XCU) progressively, whereas females show XCU coincidentally with XCI, both establishing the X:autosome dosage compensation by 1 week after implantation. Conversely, primordial germ cells undergo X-chromosome reactivation by reversing the XCI pathway early during their development. Our findings establish a foundation for clarifying the dosage compensation mechanisms in primates, including humans.

overall_design: Single cell transcriptome analysis of cynomolgus monkey embryo using SC3-seq technology.

first: Ikuhiro

last: Okamoto

first: Tomonori

last: Nakamura

first: Kotaro

last: Sasaki

first: Chiduru

last: Iwatani

first: Hideaki

last: Tsuchiya

first: Shin-ichiro

first: Masatsugu

last: Ema

first: Takuya

last: Yamamoto

first: Mitinori

last: Saitou


title: Impact of obesity on the molecular response to a single bout of exercise

status: Public on May 04 2022

city: Rochester

first: Yuanhang

last: Liu

state: MN

address: 200 1ST ST SW

institute: Mayo Clinic

summary: The health benefits of physical activity are well documented, but several exercise response parameters are attenuated in obese individuals.  The goal of this study was to identify molecular mechanisms that may influence exercise response in skeletal muscle of obese individuals.  We performed comparison of the transcriptome in muscle from lean and obese individuals before and after an acute exercise bout.

overall_design: Muscle samples from 4 lean and 4 obese adults were selected. RNA sequencing were used to interrogate the transcriptome from muscle biopsy tissue for the 8 subjects before and after exercise

first: Ian

middle: R

last: Lanza

first: Patrick

last: Vanderboom


title: An RFX/miR-150 axis restrains proliferation of primary human T lymphocytes

city: Milan

first: Francesco

last: Gualdrini

address: Via Adamello, 16

department: Department of Experimental Oncology

country: Italy

institute: European Institute of Oncology


title: Genomic and evolutionary classification of lung cancer in never smokers

status: Public on Jun 22 2021

city: Rockville

first: Tongwu

last: Zhang

address: 9609 Medical Center Drive

department: Division of Cancer Epidemiology & Genetics

summary: Lung cancer in never smokers (LCINS) is a common cause of cancer mortality, but is poorly characterized. Here we show, through high coverage whole genome sequencing of 232 tumors (Sherlock-Lung study), that LCINS can be separated into three subtypes, defined by somatic copy number aberrations. While the dominant subtype (‘piano’), rarely found in lung cancer from smokers, is characterized by quiet copy number profiles, the other subtypes are associated with specific arm-level amplifications and EGFR mutations (‘mezzo-forte’), and whole genome doubling (‘forte’). Piano tumors feature somatic UBA1 mutations, germline AR variants, and stem cell-like properties, including low mutational burden, infrequent TP53 alterations, high intra-tumor heterogeneity, long telomeres, and slow growth as suggested by the occurrence of cancer driver genes decades prior to tumor diagnosis. To assess the stem cell-like features in piano tumors, we performed bulk RNA-seq from our Sherlock-Lung study including 35 adenocarcinomas (16 Piano, 8 Mezzo-forte, 11 Forte) and 32 tumor-paired normal lung tissue. We compared expression of  gene sets included in differnt stem-cell signatures and and the finding suggests that less differentiated and a lineage infidelity in paino subtype, which could be the signs of stemness.

overall_design:
To analyzed the cell of origin and differentiation stages of lung cancer in never-smokers, we performed RNA-seq of 35 lung tumor samples and 32 paired normal lung tissue samples from 34 lung cancer patients. The tumor samples were classified into three subtypes using the somatic copy number aberrations (SCNA) detected by whole genome sequencing. We analyzed the gene expression signatures of relevant biolological processes and cell lineages across the three SCNA subtypes.
*******************************************************************
Raw data are available in dbGaP (accession number phs003955.v1.p1)
*******************************************************************

first: Maria

last: Landi

first: Wei

last: Zhao


title: Total RNA sequencing of FXN knockdown or RNA editing gene knockdown in pulmonary artery endothelial cells

status: Public on Apr 09 2021

city: Pittsburgh

first: Stephen

middle: Y

last: Chan

state: PA

address: 200 Lothrop Street

institute: University of Pittsburgh School of Medicine

summary: This data set provides different RNA expression data for primary human pulmonary endothelial cells with and without FXN deficiency or with and without RNA editing genes achieved by RNAi transfection in an effort to understand the endothelial-specific effects of acquired frataxin (FXN) deficiency and acquired RNA editing deficiency on pulmonary vascular disease.

overall_design: Comparison of differential gene expression in FXN-deficient vs FXN-replete or RNA editing-deficient vs RNA editing-replete pulmonary artery endothelial cells

first: Adam

last: Handen

first: Gil

last: Speyer

first: Seungchan

last: Kim

first: William

last: Horne


title: Intrachromosomal interactions across the intestinal crypt-villus axis and the imapct on chromatin looping upon HNF4 loss

status: Public on Jan 16 2021

city: Piscataway

first: Michael

last: Verzi

state: NJ

address: 145 Bevier Road

department: Genetics

institute: Rutgers, the State University of New Jersey

summary: This study provides a map of enhancer-promoter interactions in the intestinal epithelium. We find that key drivers of intestinal differentiation, HNF4 transcription factors, are required for enhancer-promoter interactions at their direct target genes. Depletion of HNF4 disrupts chromatin looping, nearby enhancer chromatin, and target gene expression.

overall_design: H3K4me3 HiChIP-seq, ATAC-seq and MNase ChIP-seq of active chromatin markers (H3K4me2 and H3K27ac) were employed to survey enhancer-promoter interactions in crypt and villus cells of the intestinal epithelium. By comparing H3K4me3 HiChIP-seq profiles of Hnf4DKO and their littermate controls, HNF4-dependent enhancer-promoter interactions in the mouse duodenal epithelium were also identified in this study.

first: Lei

last: Chen

first: Weihuan

last: Cao

first: Rohit

last: Aita

first: Dennis

last: Aldea

first: Christopher

last: Ellison


title: Nanoplastics and sunscreens contained in personal care products induce neurotoxicity in early zebrafish embryos

status: Public on Sep 12 2020

city: Nanjing

first: Yuxuan

last: Liu

address: NO1 Xikang Road

country: China

institute: HOHAI

summary: Nanoplastics with small particle size and high surface area/volume ratio make them easy to absorb environmental pollutants and affect their bioavailability. In this study, polystyrene nanoplastic beads (PS-NPBs) with a particle size of 100nm and sunscreen butyl methoxydibenzoylmethane (BMDBM) contained in personal care products were chosen as target pollutants to study their developmental toxicity and interactive effects on zebrafish embryo. The exposure period was 2-12 hours post fertilization (hpf). The BMDBM and PS-NPBs significantly upregulated the genes related to antioxidant enzymes and downregulated the gene expression of aromatase and DNA methyltransferases, but the influenced genes were not exactly the same, and the combined exposure reduced the adverse effects on the expression of all genes. With the help of single-cell RNA sequencing technology, the neural mid cells were identified as the target cells of both pollutants, and brain development, head development and notch signaling pathway were the functions they commonly altered. The key genes and functions that are specifically affected by BMDBM and/or PS-NPBs were identified. The BMDBM mainly affect the differentiation and fate of neurons in central nervous system through the regulation of her5, her6, her11, lfng, pax2a and fgfr4. The PS-NPBs regulated the expression of olig2, foxg1a, fzd8b, six3a, rx1, lhx2b, nkx2.1a and sfrp5 to alter nervous system development, retinal development, and stem cell differentiation. The phenotypic responses of zebrafish larvae at 120 hpf were tested, and significant inhibition of locomotor activity was found, indicating that early disrupting effect on central nervous system would have a sustained impact on the behavior of zebrafish.

overall_design: mRNA profiles of 12 hpf wild type zebrafish embryos


title: Induction of a timed metabolic collapse to overcome cancer chemoresistance

status: Public on Aug 05 2020

city: Cambridge

first: David

last: Scadden

address: 7 Divinity Ave, Sherman Fairchild Research Building #201

department: Stem Cell and Regenerative Biology

institute: Harvard University

summary: We identified a transient increase in metabolites involved in glutamine metabolism in chemoresistant acute myeloid leukemia (AML) cells. To further investigate this, we evaluated the transcriptome of AML cells from bone marrow of vehicle-treated mice and mice treated with induction chemotherapy (doxorubicin+cytarabine) at 3 days (iCT group) and 10 days (relapse group) after completion of the chemotherapy.

overall_design: We isolated GFP+ acute myeloid leukemia cells (MLL-AF9 transgenic) from bone marrow of vehicle-treated mice and mice treated with induction chemotherapy (doxorubicin+cytarabine) at 3 days (iCT group) and 10 days (relapse group) after completion of the chemotherapy by fluorescence-activated cell sorting, collected RNA, and ran RNA-seq.


title: Genome-wide chromatin accessibility mapping upon pharmacological LSD1 inhibition in MCC [ATACseq]

status: Public on Sep 04 2020

city: Vienna

first: Anna

middle: Christina

last: Obenauf

address: Campus-Vienna-Biocenter 1

country: Austria

institute: Research Institute of Molecular Pathology

summary: Merkel cell carcinoma (MCC) is a highly aggressive, neuroendocrine skin cancer that lacks actionable mutations, which could be utilized for targeted therapies. Epigenetic regulators governing cell identity may represent unexplored therapeutic entry points. Here, we targeted epigenetic regulators in a pharmacological screen and discovered that the lysine-specific histone demethylase 1A (LSD1/KDM1A) is required for MCC growth in vitro and in vivo. We show that LSD1 inhibition in MCC disrupts the LSD1-CoREST complex leading to displacement and degradation of HMG20B (BRAF35), a poorly characterized complex member that is essential for MCC proliferation. Inhibition of LSD1 causes derepression of transcriptional master regulators of the neuronal lineage, activates a gene expression signature resembling normal Merkel cells, and induces cell cycle arrest and cell death. Our study unveils the importance of LSD1 for proliferation and maintaining cell identity in MCC. There is growing evidence that cancer cells exploit cellular plasticity and dedifferentiation programs to evade destruction by the immune system. The combination of LSD1 inhibitors with checkpoint inhibitors may thus represent a promising treatment strategy for MCC patients.

overall_design: ATACseq profiling of PeTa cell line upon pharmacological LSD1 inhibitor treatment. PeTa cells were treated in duplicates for 6 days with 100nM GSK-LSD1 or DMSO. ATACseq was performed according to the Omni-ATACseq protocol (Corces et al, 2017).

first: Lukas

last: Leiendecker

first: Pauline

last: Jung

first: Izabela

last: Krecioch

first: Tobias

last: Neumann

first: Alexander

last: Schleiffer

first: Karl

last: Mechtler

first: Thomas

last: Wiesner

middle: C


title: Transcriptomic profiling of isolated mouse Merkel cells [SMARTseq]

overall_design: Gene expression profiling of mouse Merkel cells (NCAM/CD56+) and bulk mouse skin cells in triplicates.


title: Sex differences in neutrophil biology modulate response to type I Interferons and immunometabolism

status: Public on Jun 29 2020

city: Bethesda

first: Kan

last: Jiang

address: 9000 Rockville Pike

institute: NIAMS/NIH

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

overall_design: Refer to individual Series


title: Gene expression profiling study to identify distinct subtypes in diffuse type gastric cancer

status: Public on Mar 18 2020

city: Daejeon

first: Seon-Kyu

last: Kim

address: 125 Gwahak-ro, Yuseong-gu, Daejeon 305-806, Korea

department: Personalized Genomic Medicine Research Center

country: South Korea

institute: Korea Research Institutue of Bioscience & Biotechnology

summary: Although recent advances in high-throughput technology have provided many insights into gastric cancer (GC), few reliable biomarkers for handling diffuse type GC are identified. Here, we aim to identify a signature classifying high risk diffuse type GC. To identify molecular subtypes of diffuse type GC, we generated RNA-seq based transcriptome data, which were generated using normal mucosa and tumor cells from 140 fresh frozen tissues including diffuse type GCs (n = 107). Unsupervised hierarchical cluster analysis of the RNA-seq data revealed three distinct subgroups of GC. Based on these subtypes, we generated a signature reflecting the best characteristics of aggressive diffuse type GC. When estimating prognostic value, the signature showed a strong prediction ability and an independent clinical utility in diffuse type GC patients. Our signature represents a promising diagnostic tool for the identification of diffuse type GC patients that have a high risk of poor clinical behavior.

overall_design: RNA-seq data of 140 fresh-frozen tissues, including diffuse-type gastric cancer tissues (n = 107), intestinal-type gastric cancer tissues (n = 23), and normal gastric tissues (n = 10), were generated. Total RNA was extracted using the RNeasy Mini Kit (Qiagen, CA, USA) following the manufacturer’s instructions. RNA quality and integrity were confirmed by agarose-gel electrophoresis with ethidium-bromide staining and visual inspection under ultraviolet light. Sequencing libraries were prepared using the TruSeq Stranded Total RNA Sample Prep Kit (Illumina, CA, USA) according to the manufacturer’s protocol. Briefly, ribosomal RNA (rRNA) was depleted from total RNA, and the remaining RNA fragments were randomly primed and converted into strand-specific cDNA libraries. After end repair and adapter ligation, the libraries were amplified by PCR. Sequencing was performed in paired-end mode (2 × 75 bp) on the Illumina NextSeq 500 platform.

first: Jeong-Hwan

first: Hee-Jin

first: Hai-Jeong

last: Hur

first: Dong-Hyuck

last: Bae

first: Yong


title: Ribosome profiling and mRNA-seq of muscle skeletal muscle and DROSHA KO 293T cells

status: Public on Dec 31 2020

city: Tokorozawa

first: Hiroaki

last: Sako

institute: Waseda University

summary: We conducted ribosome profiling and mRNA-seq using mouse skeletal muscle tissues and 293T cells (NTC control and DROSHA KO) with Hiseq 2500

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Examination of translation status of mouse skeletal muscle and the differences between NTC and DROSHA KO in 293T cells

first: Katsuhiko

last: Suzuki

first: Tadashi

last: Yamamoto


title: Renal proximal tubule cell state and metabolism are coupled by nuclear receptors

status: Public on Dec 09 2020

city: Bukgu

first: Jihwan

last: Park

state: Gwangju

address: 123 Cheomdangwagi-ro

institute: GWANGJU INSTITUTE OF SCIENCE /TECHNOLOGY

summary: Kidney disease development is poorly understood due to the complex cellular interactions of more than 25 different cell types, each with specialized functions. Here, we used single cell RNA-sequencing to resolve cell type-specific and cell fraction changes in kidney disease.   Whole kidney RNA-sequencing results were strongly influenced by cell fraction changes, but minimally informative to detect cell type-specific gene expression changes. Cell type-specific differential expression analysis identified proximal tubule cells (PT cells) as the key vulnerable cell type in diseased kidneys. Through unbiased cell trajectory analyses, we show that PT cell differentiation state is altered in disease state. Metabolism (fatty acid oxidation and oxidative phosphorylation) in PT cells showed the strongest and reproducible association with PT cells state. The coupling of cell state and metabolism is established by nuclear receptors such as ESRRA that not only control cellular metabolism but also the expression of PT cell-specific genes in mice and patient samples.

overall_design: Single cell and bulk transcriptome analysis of folic acid-induced neprophathy kidneys

first: Poonam

last: Dhillon

first: Carmen

last: Hurtado

first: Lingzhi

last: Li

first: Shizheng

last: Huang

first: Juanjuan

last: Zhao

first: HyunMi

last: Kang

first: Rojesh

last: Shrestra

first: Michael

last: Balzer

first: Shatakshee

last: Chatterjee

first: Patricia

last: Prado

first: SeungYub

last: Han

first: Hongbo

last: Liu

first: Xin

last: Sheng

first: Kirill

last: Bartmanov

first: Juan

middle: P

last: Rojas

first: Felipe

last: Prósper

first: Mingyao

first: Liming

last: Pei

first: Junhyong

first: Nuria

last: Monserrat

first: Katalin

last: Suszták


title: Chromatin profiling upon pharmacological LSD1 inhibition in MCC [CUT&RUN]

first: Anna

last: Obenauf

overall_design:
CUT&RUN profiling of PeTa cell line upon pharmacological LSD1 inhibitor treatment.
Please note that each processed data file was generated from two replicates as indicated in the corresponding sample description field.

first: Lukas

last: Leiendecker

first: Pauline

last: Jung

first: Izabela

last: Krecioch

first: Tobias

last: Neumann

first: Alexander

last: Schleiffer

first: Karl

last: Mechtler

first: Thomas

last: Wiesner


title: Epigenetic and transcriptomic characterization of pure adipocyte fractions from obese pigs identifies candidate pathways controlling metabolism

status: Public on Dec 05 2019

city: Copenhagen

first: Christian

last: Anthon

address: Thorvaldsensvej 57

institute: University of Copenhagen

type: Methylation profiling by high throughput sequencing

summary: Reprogramming of adipocyte function in obesity is implicated in metabolic disorders like type 2 diabetes. Here, we used the pig, an animal model sharing many physiological and pathophysiological similarities with humans, to perform in depth epigenomic and transcriptomic characterization of pure adipocyte fractions. Using a combined DNA methylation capture sequencing and Reduced Representation bisulfite sequencing (RRBS) strategy, we identified 2479 differentially methylated regions (DMRs) located at close proximity to-, or within genes. By sequencing of the transcriptome from the same adipocyte cells, we identified 276 differentially expressed transcripts with at least one or more DMRs. These transcripts were over-represented in gene pathways related to MAPK, insulin and adipocytokine signaling. Using a candidate gene approach, we further characterized 13 genes potentially regulated by DNA methylation and identified putative transcription factor binding sites that could be affected by the differential methylation in obesity. Our data constitute a valuable resource for further investigations aiming to delineate the epigenetic etiology of metabolic disorders.

overall_design: MeDip-seq, RRBS-seq and RNA-seq of adipocytes from lean and obese pigs.

first: Mette

last: Jacobsen

first: Jakob

last: Havgaard

first: Caroline

middle: M

last: Junker Mentzel

first: Susanna

last: Cirera

first: Poula

last: Sørensen

first: Sachin

last: Pundhir

first: Peter

last: Karlskov-Mortensen

first: Camilla

last: Bruun

first: Philippe

last: Lesnik

first: Maryse

last: Guerin

first: Jan

last: Gorodkin

first: Claus

middle: B

last: Jørgensen

first: Merete

last: Fredholm

first: Romain

last: Barrès


title: Nrf2 and HIF1α merge to arsenic-induced metabolic reprogramming and formation of the cancer stem-like cells.

status: Public on Feb 25 2020

city: Detroit

first: Fei

last: Chen

state: Michigan

address: 4417 Second Ave APT 119

department: Department of Pharmaceutical Sciences

institute: wayne state university

summary: Arsenic (iAs) induces generation of the cancer stem-like cells (CSCs) through Nrf2-dependent HIF1α activation, and the subsequent metabolic reprogramming from mitochondrial oxdaive phosphorylation to glycolysis in epithelial cells.

overall_design: Genome-wide ChIP-seq analysis of the global binding of Nrf2 (sc-13032) and/or HIF1α (ab2185)  on the genome in the cells treated with iAs (1 μM for 6 hrs).

first: Zhuoyue

last: Bi


title: Induction of the Germ-Cell Fate from Pluripotent Stem Cells in Cynomolgus Monkeys

status: Public on Jan 29 2020

first: Yukihiro

last: Yabuta

sample_organism:
Macaca fascicularis
Mus musculus

platform_organism:
Macaca fascicularis
Mus musculus


title: Development of gene expression signatures for NSCLC

status: Public on Sep 14 2019

city: Shijiazhuang

first: Lingxiao

last: Xing

state: Hebei

address: No.361 East Zhongshan Road

institute: Hebei Medical University

summary: Eight frozen tissues of NSCLCs (4 SCCs and 4 ACs) and paired normal lung tissues were used to screen the global profiling of human long-noncoding RNAs (lncRNAs) and protein-coding transcripts.

overall_design: Transcriptomes of eight pairs of NSCLC and adjacent non-tumor tissue and identified  differentially expressed genes，and to address the potential pathological drivers of disease progression to better control this deadly cancer.


title: Tumor cell biodiversity drives microenvironmental reprogramming in liver cancer

status: Public on Oct 06 2019

first: Xin

middle: Wei

last: Wang

state: MARYLAND

address: 37 Convent Drive

department: Laboratory of Human Carcinogenesis

institute: National Cancer Institute

summary: Single-cell transcriptome profiling of liver cancer biospecimens from nine hepatocellular carcinoma and ten intrahepatic cholangiocarcinoma patients.

overall_design: A total of 19 tumors were profiled. Set 1 contains scRNA-seq data of twelve samples, i.e., S16_P10_LCP18, S02_P01_LCP21, S10_P05_LCP23, S09_P04_LCP25, S08_P03_LCP26, S07_P02_LCP28, S11_P06_LCP29, S12_P07_LCP30, S20_P12_LCP35, S21_P13_LCP37, S15_P09_LCP38, and S19_P11_LCP39. Set 2 includes scRNA-seq data of seven samples, i.e., S351_P10_LCP34, S355_P13_LCP42, S358_P16_LCP46, S305_P06_LCP56, S300_P02_LCP60, 364_P21_LCP65, and S365_P22_LCP66. Detailed information can be found in samples.txt file of each Set. The last two digits of the sample ID here correspond to the sample ID in the paper (PMID: 31588021), e.g., S16_P10_LCP18 matches with H18 and S02_P01_LCP21 matches with H21.

middle: W


title: Induction of the Germ-Cell Fate from Pluripotent Stem Cells in Cynomolgus Monkeys [scRNA-Seq]

summary: In vitro reconstitution of germ-cell development from pluripotent stem cells (PSCs) has created key opportunities to explore the fundamental mechanisms underlying germ-cell development, particularly in mice and humans. Importantly, such investigations have clarified critical species differences in the mechanisms regulating mouse and human germ-cell development, highlighting the necessity of establishing an in vitro germ-cell development system in other mammals, such as non-human primates. Here, we show that multiple lines of embryonic stem cells (ESCs) and induced pluripotent stem cells (iPSCs) in cynomolgus monkeys (Macaca fascicularis; cy) can be maintained stably in an undifferentiated state under a defined condition with an inhibitor for WNT signaling, and such PSCs are induced efficiently into primordial germ cell-like cells (PGCLCs) bearing a transcriptome similar to early cyPGCs. Interestingly, the induction kinetics of cyPGCLCs from cyPSCs is faster than that of human (h) PGCLCs from hPSCs, and while the transcriptome dynamics during cyPGCLC induction is relatively similar to that during hPGCLC induction, it is substantially divergent from that during mouse (m) PGCLC induction. Our findings delineate common as well as species-specific traits for PGC specification, creating a foundation for parallel investigations into the mechanism for germ-cell development in mice, monkeys and humans.

overall_design: RNAseq analysis during cynomolgus monkey PGCLC induction.

first: Yoshitake

last: Sakai

first: Tomonori

last: Nakamura

first: Ikuhiro

last: Okamoto

first: Sayuri

last: Gyobu-Motani

first: Hiroshi

last: Ohta

first: Tomoyuki

last: Tsukiyama

first: Chiduru

last: Iwatani

first: Hideaki

last: Tsuchiya

first: Masatsugu

last: Ema

first: Asuka

last: Morizane

first: Jun

last: Takahashi

first: Takuya

last: Yamamoto

first: Mitinori

last: Saitou


title: Sex differences in neutrophil biology modulate response to type I Interferons and immunometabolism (bulkRNA-seq)

first: Kan

last: Jiang

summary: Differences in female and male immunity may contribute to variations in response to infections and predisposition to autoimmunity. The characterization of the mechanisms that drive differential neutrophil phenotypes between genders has been investigated. This provides new insights that distinct sex difference in neutrophil biology related to responses to type I IFNs, immunometabolism and maturation status that may have prominent functional and pathogenic implications. The transcriptome of neutrophils from healthy adult males and females was characterized using bulk RNASeq. The transcriptome of whole blood leukocytes was elucidated using scRNASeq.

overall_design: The RNAseq dataset includes a total of 14 individual samples. The scRNASeq dataset includes a total of 7 individual samples. This study sought to characterize sex differences in neutrophil biology. Transcriptomic profiles of neutrophils from healthy adult males and females were characterized.

first: S

last: Gupta

last: Nakabo

first: L

last: O'Neil

first: G

last: Wigerblad

first: P

last: Mistry

first: K

last: Dell'Orso

first: H

last: Sun

first: M

last: Kaplan


title: Acquired resistance to targeted therapy confers cross-resistance to immunotherapy

status: Public on Jun 26 2021

first: Anna

last: Obenauf

summary:
We identify a profoundly remodelled TME in targeted therapy resistant (RTT) tumours. We provide bulk transcriptomic data of targeted therapy naive (NTT) and RTT tumours of 3 murine models. Additionally, we provide low-input sequencing of CD103+ dendritic cells and T cells from NTT and RTT Braf/Pten tumours.
We identified that in RTT cell lines the MAPK pathway is reactivated and provide SLAM-seq data to determine transcriptional targets of MAPK pathway inhibition in NTT and RTT cell lines.
We also provide ATAC-Seq data of NTT and RTT cell lines sorted from tumors of the Braf/Pten melanoma model.

overall_design:
RNA-Seq, SMART-seq and Quant-seq of bulk tumors in vivo, sorted tumor cells and sorted CD45 + cells seperately.
RNA-Seq and Quant-seq of NTT and RTT cell lines in vitro ± IFNy.
Smart-seq of sorted CD11c+ CD103+ DCs from tumors, Smart-seq of sorted CD3+ CD8+ T cells from tumours.
SLAM-Seq of targeted therapy naïve and RAFi resistant Braf/Pten melanoma ± MEKi.
ATAC-Seq of NTT and RTT cell lines sorted from Braf/Pten melanoma tumors.

first: Lisa

last: Haas

first: Tobias

last: Neumann

first: Maria

last: Novatchkova

first: Lukas

last: Leiendecker

first: Anais

last: Elewaut


title: DPPA2/4 and SUMO E3 ligase PIAS4 opposingly regulate the emergence of 2C-like cells and zygotic transcriptional program

status: Public on Mar 05 2019

city: Beijing

first: Yangming

last: Wang

address: 5 Yiheyuan Road

department: Institute of Molecular Medicine

institute: Peking University

summary: The accurate activation of ZGA transcriptome is important for understanding normal embryo development. However, only few factors are found to regulate this process. Here we identified Pias4-Dppa2 axis regulate the activation of ZGA transcriptome, Dppa2 can activate ZGA transcriptome, Pias4 inhibits it by catalyzing the sumoylation of DPPA2, turning Dppa2 from an activator into a repressor.

overall_design: Examination of differential expressed genes between WT and Pias4 knock down/Dppa2 over expression/Dppa2 knock down/Dppa4 knock down/Dppa2/4 knock down mouse embryonic stem cells grown in normal ES culture media by poly(A)+ RNA-Seq. Two biological replicates were completed for each groups.

first: Yao-Long

last: Yan

first: Chao

last: Zhang

first: Jing

last: Hao

first: Xue-Lian

first: Jia

last: Ming

first: Li

last: Mi

first: Jie

first: Xinli

last: Hu


title: Transcriptional and chromatin profiles of duodenum epithelium upon HNF4 loss in mice by RNA-seq and ChIP-seq

status: Public on Apr 08 2019

first: Michael

last: Verzi

summary: We find that HNF4G is an intestine-particular HNF4 paralog, and works redundantly with HNF4A for driving intestinal differentiation by controlling chromatin accessibility and regulating thousands of transcripts particular to differentiated cells. Without HNF4s, cells fail to achieve a differentiated state. A positive feedback loop between HNF4 transcriptional regulation and BMP/SMAD signaling stabilizes differentiation, and the two inputs cooperatively activate differentiation gene expression.

overall_design: Transcriptional profiling was employed to identify HNF4-dependent gene expression in the mouse duodenal epithelium. A series of ChIP-seq experiments (Hnf4alpha, Hnf4gamma and H3K27ac-MNase) identified the HNF4 binding regions in mouse duodenal epithelium and discovered and validated extensive co-binding with Smad4 in CaCO2 cells and mouse duodenal epithelium.

first: Lei

last: Chen

first: Perekatt

middle: O

last: Ansu


title: Integrative tissue analyses of men with prostate cancer [BI]

status: Public on Sep 30 2021

first: Adam

last: Sowalsky

address: 37 Convent Drive Building 37 Room 1062B


title: Efficacy and safety assessment of a TRAF6-targeted nanoimmunotherapy in atherosclerotic mice and non-human primates

status: Public on Oct 11 2017

city: New York

first: XIANXIAO

last: ZHOU

address: 1470 Madison AVE

department: Department of Genetics and Genomic Sciences

institute: Ichan School of Medicine at Mount Sinai

summary: In atherosclerosis, macrophage accumulation is directly linked to destabilization and rupture of plaque, causing acute atherothrombotic events. Circulating monocytes enter the plaque and differentiate into macrophages, where they are activated by CD4+ T-lymphocytes through CD40-CD40 ligand signaling. Here we show that interruption of this signaling pathway in monocyte / macrophage exerts rapid anti-inflammatory effects in an Apoe-/- mouse model of atherosclerosis. For this purpose we developed an infusible recombinant high-density lipoprotein nanoparticle carrying small molecule inhibitor of the interaction of CD40s and tumor necrosis factor receptor-associated factor 6. We show monocyte / macrophage specific targeting of our nanoimmunotherapy, which impairs their migratory capacity. Rapid induction of plaque inflammation by this therapy represents a novel strategy in the treatment of atherosclerosis, with high potential for clinical translation, as illustrated by the favorable toxicity profile in non-human primates.

overall_design: 39 atherosclerosis samples sequenced, 10 treated with TRAF6i-HDL, 10 treated with PBS as control, 10 treated with mTORi-HDL and another 9 treated with S6K1i-HDL.

first: Marnix

last: Lameijer

first: Mandy

last: van Leent

first: Xianxiao

last: Zhou

first: Joost

last: Malkus

first: Francois

last: Fay

first: Brenda

middle: L

last: Sanchez-Gaytan

first: Carlos

last: Pérez-Medina

first: Yuxiang

last: Ye

first: Gregory

last: Wojtkiewicz

first: Erik

last: Stroes

first: Esther

last: Lutgens

first: Edward

middle: A

last: Fischer

first: Mihai

last: Netea

first: Filip

last: Swirski

first: Matthias

last: Nahrendorf

first: Zahi

last: Fayad

first: Willem

last: Mulder

first: Bin

first: Raphaël

last: Duivenvoorden


title: RNA-Sequencing of carnosine treated wild-type BDF1 (WT) and transgenic Thy1-aSyn mice

status: Public on Dec 31 2018

city: Cincinnati

first: Mei-Ling

last: Bermudez

state: Ohio

address: 160 Panzeca Way

department: Environmental Health

institute: University of Cincinnati

summary: Mitochondrial dysfunction plays a central role in the pathogenesis of neurodegenerative diseases such as Parkinson’s disease (PD). This study tested the hypothesis that the dipeptide carnosine would exert a beneficial effect in the Thy1-aSyn mouse model of PD, which displays mitochondrial dysfunction. Mitochondrial function and gene expression were evaluated in the midbrain after two months of carnosine administration by intranasal (IN) or drinking water routes of exposure. IN carnosine attenuated transcriptional changes in the midbrain in Thy1-aSyn mice. Additionally, IN-carnosine increased expression of mitochondria complexes and enhanced mitochondrial function, suggesting a potential neuroprotective role for IN-carnosine in PD.

overall_design: 5 treatment groups, 3 replicates/group, 1 WT control group, 1 WT treated with 2 mg of carnosine intranasally, 1 TG control group, 1 TG treated with 2 mg of carnosine intranasally, 1 TG treated with 10 mM carnosine in drinking water.

first: Matthew

last: Skelton

first: Mary

last: Genter


title: Distinct macrophage populations upon physiological changes in adipose tissue

status: Public on Jun 04 2018

first: Hee-Woong

last: Lim

address: 3333 Burnet Ave. MLC 7024

department: Division of Biomedical Informatics

institute: Cincinnati Children's Hospital Medical Center


title: Distinct macrophage populations upon physiological changes in adipose tissue [RNA-seq]

summary: We report that obese fat tissue of mice contain multiple distinct populations of adipose tissue macrophage (ATM) with unique transcriptomes and chromatin landscapes. Mouse Ly6c ATMs express genes that are adipogenic, while CD9 ATMs express pro-inflammatory genes under the control of activating transcription factors. Adoptive transfer of Ly6c ATMs into lean mice activates gene programs typical of normal adipocyte physiology. By contrast, adoptive transfer of CD9 ATMs drives gene expression that is characteristic of obesity.

overall_design: ATM populations were sort-purified from murine obese eWAT and subjected to RNA-seq analysis. BMDMs were generated and subjected to polarization protocols. eWAT was isolated from mice injected with sort-purified ATM populations.

first: David

last: Hill

first: Yong

middle: H

last: Kim

first: Wesley

last: Ho

first: Yee

last: Foong

first: Victoria

last: Nelson

first: Hoang

last: Nguyen

first: Kavya

last: Chegireddy

first: Jihoon

first: Taku

last: Kambayashi

first: Kyoung-Jae

last: Won

first: Mitchell

last: Lazar


title: Combined TP53 and RB1 Loss Promotes Prostate Cancer Resistance to a Broad Spectrum of Cancer Therapeutics and Confers Vulnerability to Replication Stress

status: Public on Jun 01 2020

city: Seattle

first: Ilsa

last: Coleman

state: WA

address: 1100 Fairview Ave N, E2-112

department: Human Biology

institute: Fred Hutchinson Cancer Center

summary: Prostate cancers (PC) with loss of the potent tumor suppressors TP53 and RB1 exhibit poor outcomes that include resistance to androgen receptor (AR) pathway antagonists. TP53 and RB1 also influence cell plasticity and are frequently lost in PCs with neuroendocrine (NE) differentiation. Therapeutic strategies that address these aggressive variant PCs are urgently needed. Using deep genomic profiling of 410 metastatic biopsies, we determined the relationships between combined TP53 and RB1 loss and PC phenotypes. Notably, 40% of TP53/RB1 deficient tumors were classified as AR-active adenocarcinomas indicating that NE differentiation is not an obligate consequence of TP53/RB1 inactivation. A gene expression signature reflecting TP53/RB1 loss was associated with diminished responses to AR antagonists and reduced survival. These tumors exhibit high proliferation rates and evidence of elevated DNA repair processes. While tumor cells lacking TP53/RB1 were highly resistant to all single agent therapeutics, the combination of pharmacological PARP and ATR inhibition produced significant responses, reflecting a clinically-exploitable vulnerability resulting from replication stress.

overall_design: RNA sequencing of human prostate tumor cell lines and metastatic castration-resistant prostate cancer (mCRPC) tumors using Illumina TruSeq Stranded mRNA Library prep and sequenced on Illumina HiSeq 2500.

first: Michael

middle: D

last: Nyquist

first: Alexandra

last: Corella

first: Navonil

last: De Sarkar

first: Arja

last: Kaipainen

first: Gavin

last: Ha

first: Roman

last: Gulati

first: Lisa

last: Ang

first: Payel

last: Chatterjee

first: Jared

last: Lucas

first: Colin

last: Pritchard

first: Gail

last: Risbridger

first: John

last: Isaacs

first: Bruce

last: Montgomery

first: Colm

last: Morrissey

first: Eva

last: Corey

first: Peter

middle: S


title: Progesterone Regulation of Extracellular Vesicles in the Uterine Luminal Fluid of Sheep (RNA-Seq)

status: Public on Sep 08 2017

city: Columbia

first: Thomas

last: Spencer

state: MO

address: 920 East Campus Drive

department: Animal Sciences

institute: University of Missouri

summary: Progesterone (P4) acts via the endometrium to modify the uterine environment and promotes conceptus growth for elongation and pregnancy establishment. Ewes were ovariectomized and treated with P4 for 14 days or P4 for 14 days and RU486, a progesterone receptor antagonist, from days 8 to 14. Interrogation of the endometrial transcriptome resulted in 1,611 differentially abundant transcripts with 931 increased and 680 decreased in P4 as compared to P4+RU treated ewes.

overall_design: Endometrium from P4-treated (n=5) or P4+RU486-treated ewes (n=5)

first: Gregory

last: Burns

first: Kelsey

middle: E

last: Brooks

first: Eleanore

middle: V

last: O'Neil

first: Darren

last: Hagen

first: Susanta

last: Behura


title: eQTL analysis - Extracting genotype information of recombinant inbred lines from transcript profiles established with high-density oligonucleotide arrays

status: Public on Aug 21 2017

city: Stadt Seeland

first: Renate

middle: Hanna

last: Schmidt

state: Sachsen-Anhalt

address: Corrensstrasse 3

department: Breeding Research

institute: Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)

summary: In order to identify eQTL in developing seeds of Arabidopsis thaliana 116 Arabidopsis thaliana recombinant inbred lines (C24/Col 0 and Col 0/C24, Törjék et al. 2006) were analysed.

overall_design:
Expression data of 116 recombinant inbred lines (C24/Col 0 and Col 0/C24) that were established for developing seeds of the same stage (10-11 days after flower opening) provided the basis for an eQTL analysis. For each line one biological replicate was evaluated. The data were also used to develop a sequence feature polymorphism map. A sequence-based approach identified features on the array that showed sequence polymorphisms between A. thaliana accessions Col 0 and C24. Hybridisation intensities were retrieved for all probe sets consisting of one or several probes that were polymorphic in C24 (VM probes) and at least three probes that revealed perfect matches to the Col 0 and C24 genomes (IM probes). The mean hybridisation intensity of all IM probes of a particular probe set was divided by that of each VM probe. For each of the polymorphic probes the resulting ratios of all RILs were compiled and sorted in ascending order before they were subjected to a sliding window analysis in order to identify SFP markers. The genotypes of the recombinant inbred lines were determined with the SFP markers and a linkage map of the Col 0/C24 and C24/Col 0 recombinant inbred populations was generated.
Data for the parental lines Col-0 and C24 are also available (GSE94762).

first: Anastassia

last: Boudichevskaia


title: Self-patterning of rostral-caudal neuroectoderm requires dual role of Fgf signaling for localized Wnt antagonism [RNA-seq]

status: Public on Aug 05 2017

city: Chicago

first: NOZOMU

last: TAKATA

state: Illinois

address: 303 East Superior Street, 10-220

department: Center for Vascular and Developmental Biology

institute: Northwestern University Feinberg School of Medicine

summary: The neuroectoderm is patterned along a rostral-caudal axis in response to localized factors in the embryo, but exactly how these factors act as positional information for this patterning is not yet fully understood. Here, using the self-organizing properties of mouse embryonic stem cell (ESC), we report that ESC-derived neuroectoderm self-generates a Six3+ rostral and a Irx3+ caudal bipolarized patterning. In this instance, localized Fgf signaling performs dual roles, as it regulates Six3+ rostral polarization at an earlier stage and promotes Wnt signaling at a later stage. The Wnt signaling components are differentially expressed in the polarized tissues, leading to genome-wide Irx3+ caudal-polarization signals. Surprisingly, differentially expressed Wnt agonists and antagonists have essential roles in orchestrating the formation of a balanced rostral-caudal neuroectoderm pattern. Together, our findings provide key processes for dynamic self-patterning and evidence that a temporally and locally regulated interaction between Fgf and Wnt signaling controls self-patterning in ESC-derived neuroectoderm.

overall_design: The duplicated samples for each of Rax::GFP+ and Rax::GFP- cells during ESC (embryonic stem cell)-derived neural tissue development were analyzed.

first: Nozomu

last: Takata

first: Eriko

last: Sakakura

first: Mototsugu

last: Eiraku

first: Takeya

last: Kasukawa

first: Yoshiki

last: Sasai


title: Sex differences in neutrophil biology modulate response to type I Interferons and immunometabolism (scRNA-seq)

status: Public on Jun 29 2020

first: Kan

last: Jiang

state: MD

first: S

last: Gupta

last: Nakabo

first: L

first: G

last: Wigerblad

first: P

last: Mistry

first: K

last: Dell'Orso

first: H

last: Sun

first: M

middle: J

last: Kaplan


title: Establishment of Functional Genomics Pipeline in Mouse Epiblast-Like Tissue by Combining Transcriptomic Analysis and Gene Knockdown/Knockin/Knockout, Using RNA Interference and CRISPR/Cas9 [RNA-seq]

status: Public on Feb 01 2016

summary: The epiblast (foremost embryonic ectoderm) generates all three germ layers and therefore has crucial roles in the formation of all mammalian body cells. Regulation of epiblast gene expression is poorly understood due to the difficulty of manipulating epiblast tissues in vivo. In the present study, using the self-organizing properties of embryonic stem cells (ESCs), we generated and characterized epiblast-like tissue in three-dimensional (3D) culture. We identified significant genome-wide expression changes in this epiblast-like tissue. Additionally, we identified the significance of the Fgf/Erk and ectoderm formation pathways, using the bioinformatics resource IPA and DAVID. We first focused on Fgf5, which ranked in the top 10 among discovered genes. Toward functional analysis of Fgf5, we developed efficient methods of genome engineering (CRISPR/Cas9) and RNA interference (RNAi). Notably, we show one-step generation of an Fgf5 reporter line, null and in/del mutants. Furthermore, mutation types correlated well with CRISPR/Cas9 activity. For time- and dose-dependent depletion of Fgf5 over the course of development, we generated an ESC line harboring a drug-inducible short hairpin RNA cassette integrated by the Tol2 transposon system (pRNAi). Our methods provide a framework for a broad array of applications in the areas of mammalian genetics and molecular biology to understand development and to improve future therapeutics.

overall_design: The duplicated samples for each of at day0 (ESC) and day 3 (epiblast-like tissue) during SFEBq (serum-free floating culture of embryoid body-like aggregates with quick reaggregation) treatment were analyzed.

first: Tetsushi

last: Sakuma

first: Takashi

last: Yamamoto


title: Direct Isolation and Characterization of Human Nephron Progenitors.

status: Public on Sep 16 2016

city: Los Angeles

first: Brendan

last: Grubbs

state: CA

address: 4661 W. Sunset Blvd.

department: Obstetrics and Gynecology

institute: University of Southern California

summary: Mature nephrons originate from a small population of uninduced nephrogenic progenitor cells (NPs) within the cap mesenchyme. These cells are characterized by the coexpression of SIX2 and CITED1. Many studies on mouse models as well as on human pluripotent stem cells have advanced our knowledge of NPs, but very little is known about this population in humans, since it is exhausted before birth and strategies for its direct isolation are still limited. Here we report an efficient protocol for direct isolation of human NPs without genetic manipulation or stepwise induction procedures. With the use of RNA-labeling probes, we isolated SIX2+CITED1+ cells from human fetal kidney for the first time. We confirmed their nephrogenic state by gene profiling and evaluated their nephrogenic capabilities in giving rise to mature renal cells. We also evaluated the ability to culture these cells without complete loss of SIX2 and CITED1 expression over time. In addition to defining the gene profile of human NPs, this in vitro system facilitates studies of human renal development and provides a novel tool for renal regeneration and bioengineering purposes

overall_design:
Single cell suspensions from 3 freshly isolated human fetal kidneys ( 17 weeks of gestation) were labelled overnight with RNA probes for SIX2 and CITED1 and sorted to obtain a 1) double positive population and2)  a negative fraction. Long term goal is to investigate the transcription profile that differentiate positive versus negative selections.

***************************************************************
Raw files for human/patient samples were not submitted to GEO due to concerns about submitting personally identifiable sequence data for open access.
***************************************************************

first: Laura

last: Perin

first: Stefano

last: Da Sacco

first: Matthew

last: Thornton


title: Genetic analysis of Ikaros target genes and tumor suppressor function in BCR-ABL1+ pre-B ALL [RNA-seq]

status: Public on Feb 06 2017

city: Burlington

first: Seth

last: Frietze

state: VT

address: 149 Beaumont Avenue

department: Biomedical and Health Sciences

institute: University of Vermont

summary: RNA-seq was performed in human Ph+ pre-B ALL cells that harbor a deletion of the Ikaros DNA binding domain (Ik6) after doxycycline induction of exogenous expression of wild-type Ikaros (Ik1) or control empty vector over 0, 12, 24 and 48 hours. Biological replicates (n=2) using independent cultures and inductions were performed.

overall_design: RNA-Seq from human BCR-ABL+ pre-B ALL xenograft cell-line PDX2 following 24 h of DOX induction of IK1 or empty vector controls

first: Hilde

last: Schjerven


title: Genetic analysis of Ikaros target genes and tumor suppressor function in BCR-ABL1+ pre-B ALL

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

overall_design: Refer to individual Series


title: Study of Bacillus cereus spore germination and outgrowth in a vegetable food model by means of genome-wide transcriptome analysis

status: Public on Jan 26 2015

city: Cremona

first: Daniela

last: Bassi

state: CR

address: via Milano 24

department: Istituto di Microbiologia

institute: Università Cattolica del Sacro Cuore

summary: Pathogenic species belonging to Bacillus cereus sensu lato group possess a high evolutionary advantage in the environment and in food matrices thanks to their capacity to survive as silent spores to harsh environmental insults and grow at relatively low temperatures. Ready to re-heat products are at severe risk for contamination by members of Bacillus cereus s.l. group if not stored at proper conditions. In this work, the goal was to assess, by means of a genome-wide transcriptional assay, the isolated strain Bacillus cereus UC10070 gene expression behind the process of spore germination and consequent outgrowth in an artificially contaminated vegetable-based food model. A vegetable food model subjected to a heat treatment was determined to present favourable conditions for spores germination. Microscopic analyses together with OD measurements were applied to select the key steps of B. cereus cell cycle to be used for the microarray analysis. Using this approach we found a total of 1,646 probe sets differentially expressed and modulated during the entire B. cereus life cycle in the vegetable foodstuff.

platform_organism: [Bacillus thuringiensis] serovar konkukian str. 97-27

overall_design: RNA was isolated from the dormant spores (DS), germinating spores at 40 minutes (GSP), early-log phase at 2h (C2h) and late log phase cells at 12 hours (C12h) after thermal treatment of B. cereus UC10070 previously isolated froma biofilm on a spoiled vegetable-based puree. There were 3 biological replicates (independent cultures) for each condition. Complete genome sequence of B. thuringiensis sv konkukian str. 97-27 (NCBI Reference Sequence: NC_005957.1) was chosen for its high homology with B. cereus s.l. UC10070, to design probes corresponding to 5,197 genes spotted in duplicates onto ElectraSenseH 12K microarrays chip.

first: Francesca

last: Colla

first: Simona

last: Gazzola

first: Edoardo

last: Puglisi

first: Massimo

last: Delledonne

first: Pier

last: Cocconcelli


title: Leucegene: AML sequencing

status: Public on Jul 09 2015

city: Montreal

first: Guy

last: Sauvageau

state: QC

address: 2950, Chemin de Polytechnique

country: Canada

institute: Institute for Research in Immunology and Cancer


title: Leucegene: AML sequencing (part 5)

summary: RNA sequencing of human leukemia

overall_design: The goals of this project are to obtain a comprehensive study of mutations and gene expression in human acute myeloid leukemia (AML). Methods: AML cells were thawed. DNA and RNA (polyA) was extracted and sequences were obtained with an illumina HiSeq 2000 sequencer. Results are pending.

first: Vincent

last: Lavallée

first: Jana

last: Krosl

first: Brian

last: Wilhelm

first: Frédéric

last: Barabé

first: Patrick

last: Gendron

first: Geneviève

last: Boucher

first: Raphaëlle

last: Lambert

first: Claude

last: Rondeau

first: Annie

last: Bilodeau

first: Sylvie

first: Caroline

last: Pabst

first: Jonathan

last: Yeh

first: Bernhard

last: Lehnertz

first: Radia

last: Johnson

first: Clarisse

last: Thiollier

first: Giovanni

last: D'Angelo

first: Sébastien

last: Lemieux

first: Josée

last: Hébert


title: RNA-seq performed on either wild-type, p53 null, or p21 null MMTV-Wnt1 mouse mammary tumors treated with or without doxorubicin.

status: Public on Jul 03 2019

city: New Orleans

first: James

middle: G

last: Jackson

state: LA

address: 1430 Tulane

institute: Tulane

summary: The effects of doxorubicin on mammary tumors

overall_design: MMTV-Wnt1 transgenic mice formed spontaneous mammary tumors, and then were treated or not with doxorubicin. Genotypes of MMTV-Wnt1 mice were Trp53 wild-type (untreated n=6, doxorubicin n=6), Trp53 null (untreated n=6, doxorubicin n=6), Cdkn1a (p21) null (untreated n=6, doxorubicin n=10). Tumors were harvested 24hr following final doxorubicin treatment.


title: The complete methylome of hematopoietic stem cells and their immediate progeny

status: Public on Aug 25 2014

city: Heidelberg

first: Christoph

last: Plass

address: Im Neuenheimer Feld 280

institute: German Cancer Research Center

summary: Hematopoietic stem cells (HSCs) constitute a rare cell population in bone-marrow and are capable of live-long self-renewal and production of all mature blood cell types. Cell differentiation processes are governed by epigenetic mechanisms whose study during early differentiation steps will provide insights into stem cell function and differentiation. We performed whole-genome bisulfite sequencing on HSCs and their immediate progeny, namely three different multipotent progenitor subpopulations (MPP1, MPP2, and MPP).

overall_design: Whole-genome bisulfite sequencing of hematopoietic stem cells (HSCs) and 3 different multipotent progenitor subpopulations (MPP). Three independent biological replicates each were analyzed.

first: Daniel

last: Lipka

first: Qi

last: Wang

first: Amelie

last: Lier

first: Michael

last: Milsom