title: The transcriptional equilibration between androgen receptor and MYC signatures during prostate cancer transition centralizes on a distal developmental super-enhancer circuitry (HiChIP)

city: TORONTO

first: Haiyang

last: Guo

state: Ontario

address: 101 College Street, 11-601D, TMDT, 11-601D, TMDT

department: Princess Margaret Cancer Centre

institute: UNIV HEALTH NETWORK

summary: We used RNA-Seq, ChIP-Seq, 4C-Seq and HiChIP to assess the role of MYC in the transcriptional repression induced by DHT in prostate cancer.

overall_design: RNA-Seq, ChIP-Seq, 4C-Seq and HiChIP in prostate cancer cells

first: Yiming

last: Wu

first: Housheng

last: He

first: Shaoyong

last: Chen

first: Steven

last: Balk


title: The transcriptional equilibration between androgen receptor and MYC signatures during prostate cancer transition centralizes on a distal developmental super-enhancer circuitry (4C-Seq)

status: Public on Oct 29 2021

country: Canada

summary: We used RNA-Seq, ChIP-Seq and 4C-Seq to assess the role of MYC in the transcriptional repression induced by DHT in prostate cancer.

overall_design: 4C-Seq in prostate cancer cells

middle: H

middle: P


title: The transcriptional equilibration between androgen receptor and MYC signatures during prostate cancer transition centralizes on a distal developmental super-enhancer circuitry

type: Expression profiling by high throughput sequencing

type: Genome binding/occupancy profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: The transcriptional equilibration between androgen receptor and MYC signatures during prostate cancer transition centralizes on a distal developmental super-enhancer circuitry (RNA-Seq)

overall_design: RNA-Seq in prostate cancer cells


title: The transcriptional equilibration between androgen receptor and MYC signatures during prostate cancer transition centralizes on a distal developmental super-enhancer circuitry (ChIP-Seq)

overall_design: ChIP-Seq in prostate cancer cells


title: Altered BAF53A (ACTL6A) Stoichiometry Drives Human Squamous Cell Carcinoma [ATAC-seq]

city: Stanford

first: Zohar

last: Shipony

state: CA

address: Beckman Center B-279A  279 Campus Drive West

country: USA

institute: Stanford University

summary: To identify accessible chromatin regions regulated BAF53A in squamous cell carcinomas (SCCs), we performed ATAC-seq in FaDu SCC cell lines after BAF53A knockdown by siRNA and in normal keratinocytes with BAF53A overexpression.

overall_design: The ATAC-seq experiments were conducted 72 hours after siRNA transfection or one week after lentivirus transduction and drug selection. Two samples for each condition.

first: Chiung-Ying

last: Chang

first: William

middle: J

last: Greenleaf

first: Gerald

middle: R

last: Crabtree


title: Altered BAF53A (ACTL6A) Stoichiometry Drives Human Squamous Cell Carcinoma [CnR]

summary: To determine whether the chromatin accessibility for YAP/TEADs in squamous cell carcinoma cells is directly regulated by BAF53A within BAF complexes, we performed CUT&RUN to profile the distribution of YAP, TEAD1, and BAF155 (a DNA binding subunit of BAF complexes) across the genome.

overall_design: The CUT&RUN experiments were conducted 72 hours after siRNA transfection or one week after lentivirus transduction and drug selection. Two samples for each condition.


title: Altered BAF53A (ACTL6A) Stoichiometry Drives Human Squamous Cell Carcinoma [RNA-seq]

summary: To identify genes regulated by BAF53A, we carried out RNA-seq analysis in three SCC cell lines after BAF53A knockdown by siRNA and in normal keratinocytes with BAF53A overexpression.

overall_design: The RNA-seq experiments were conducted 72 hours after siRNA transfection or one week after lentivirus transduction and drug selection. Two samples for each condition.


title: KDM6B promotes activation of the oncogenic CDK4/6-pRB-E2F pathway by maintaining enhancer activity in MYCN-amplified neuroblastoma

city: Memphis

first: Beisi

last: Xu

state: Tennessee

address: 262 Danny Thomas Pl

department: Center for Applied Bioinformatics

institute: St Jude Children's Research Hosipital


title: m6A MeRIP-Seq of liver in Mettl3flox/flox and hepatocyte-specific Mettl3 knockout (HKO) mice

city: Harbin

first: Zheng

state: Heilongjiang

address: 92 Xidazhijie  Harbin Institute of Technology

country: China

institute: Harbin Institute of Technology

summary:
Purpose: Through mRNA m6A-profiling, we aim to characterize the mRNA m6A changes in the liver obtained from Mettl3flox/flox and HKO mice.
Methods: Total RNA was extracted using Tripure Isolation Reagent (Roche, Mannheim, Germany) from liver of Mettl3 flox/flox and HKO mice at 8 weeks old. Each sample (300 μg total RNA) was pooled from 3 mice for each group. Poly(A)+ RNA was purified using Dynabeads™ mRNA Purification Kit (Invitrogen) following the manufacturer’s instructions. Chemically fragmented poly(A)+ RNA was incubated with m6A antibody (Synaptic System, 202003) for immunoprecipitation following the standard protocol of Magna MeRIPTM m6A Kit (MERCK, 17-10499). Enrichment of m6A mRNA was then analyzed by high-throughput sequencing using Illumina Hiseq X platform. The m6A peaks were detected by MACS2. The motif search was detected by MEME and DREME.
Conclusion: The mRNA m6A profiles in the liver of Mettl3flox/flox and HKO mice were characterized.

overall_design: To map the mRNA m6A modification caused by METTL3 in liver, MeRIP-seq was performed in liver obtained from Mettl3flox/flox and HKO mice.

first: Xinzhi

last: Li


title: KDM6B promotes activation of the oncogenic CDK4/6-pRB-E2F pathway by maintaining enhancer activity in MYCN-amplified neuroblastoma  [RNA-seq]

summary: The H3K27me2/me3 histone demethylase KDM6B is over-expressed in neuroblastoma and is essential to neuroblastoma cell survival. While the KDM6B inhibitor, GSK-J4, has shown activity in in vitro and in vivo preclinical models, the mechanism of action remains poorly defined. We demonstrate that genetic and pharmacologic inhibition of KDM6B downregulates the pRB-E2F transcriptome and MYCN expression. Chemical genetic analyses show that high expression of the E2F transcriptome is positively correlated with sensitivity of cancer cells to GSK-J4. Mechanistically, inhibition of KDM6B activity 1) reduces the chromatin accessibility of E2F target genes and MYCN, 2) selectively leads to an increase of H3K27me3 but a decrease of the enhancer mark H3K4me1 at the CTCF and BORIS binding sites, which may, consequently, disrupt the long-range chromatin interaction of MYCN and E2F target genes, and 3) phenocopies the transcriptome induced by the specific CDK4/6 inhibitor palbociclib. Overexpression of CDK4/6 or Rb1 knockout confers neuroblastoma cell resistance to both palbociclib and GSK-J4. A gene signature targeted by KDM6B inhibition is associated with poor survival of patients with neuroblastoma regardless of the MYCN status. These data indicate that KDM6B activity promotes an oncogenic CDK4/6-pRB-E2F pathway in neuroblastoma cells via H3K27me3-dependent enhancer-promoter interactions, providing a rationale to target KDM6B for high-risk neuroblastoma.

overall_design: Examination of chromatin accessibility, Histone modification in different GSKJ4 treatment time points and integrative with RNA-seq

first: Jie

last: Fang

first: Hongjian

last: Jin

first: Jun

last: Yang


title: KDM6B promotes activation of the oncogenic CDK4/6-pRB-E2F pathway by maintaining enhancer activity in MYCN-amplified neuroblastoma [ATAC-Seq]

summary: The H3K27me2/me3 histone demethylase KDM6B is over-expressed in neuroblastoma and is essential to neuroblastoma cell survival. While the KDM6B inhibitor, GSK-J4, has shown activity in in vitro and in vivo preclinical models, the mechanism of action remains poorly defined. We demonstrate that genetic and pharmacologic inhibition of KDM6B downregulates the pRB-E2F transcriptome and MYCN expression. Chemical genetic analyses show that high expression of the E2F transcriptome is positively correlated with sensitivity of cancer cells to GSK-J4. Mechanistically, inhibition of KDM6B activity 1) reduces the chromatin accessibility of E2F target genes and MYCN, 2) selectively leads to an increase of H3K27me3 but a decrease of the enhancer mark H3K4me1 at the CTCF and BORIS binding sites, which may, consequently, disrupt the long-range chromatin interaction of MYCN and E2F target genes, and 3) phenocopies the transcriptome induced by the specific CDK4/6 inhibitor palbociclib. Overexpression of CDK4/6 or Rb1 knockout confers neuroblastoma cell resistance to both palbociclib and GSK-J4. A gene signature targeted by KDM6B inhibition is associated with poor survival of patients with neuroblastoma regardless of the MYCN status. These data indicate that KDM6B activity  promotes an oncogenic CDK4/6-pRB-E2F pathway in neuroblastoma cells via H3K27me3-dependent enhancer-promoter interactions, providing a rationale to target KDM6B for high-risk neuroblastoma.


title: Type I CRISPR-Cas provides robust immunity but incomplete attenuation of phage-induced cellular stress

status: Public on Oct 28 2021

city: Dunedin

first: Peter

middle: Charles

last: Fineran

state: Otago

address: 720 Cumberland Street

department: Department of Microbiology and Immunology

country: New Zealand

institute: University of Otago

summary: During infection, phages manipulate bacteria to redirect metabolism towards viral proliferation. To counteract phages, some bacteria employ CRISPR-Cas systems that provide adaptive immunity. While CRISPR-Cas mechanisms have been studied extensively, their effects on both the phage and the host during phage infection remains poorly understood. Here, we analysed the infection of Serratia by a siphovirus (JS26) and the transcriptomic response with, or without type I-E or I-F CRISPR-Cas immunity. In non-immune Serratia, phage infection altered bacterial metabolism by upregulating anaerobic respiration and amino acid biosynthesis genes, while flagella production was suppressed. Furthermore, phage proliferation required a late-expressed viral Cas4, which did not influence CRISPR adaptation. While type I-E and I-F immunity provided robust defence against phage infection, phage development still impacted the bacterial host. Moreover, DNA repair and SOS response pathways were upregulated during type I immunity. We also discovered that the type I-F system is controlled by a positive autoregulatory feedback loop that is activated upon phage targeting during type I-F immunity, leading to a controlled anti-phage response. Overall, our results provide new insight into phage-host dynamics and the impact of CRISPR immunity within the infected cell.

overall_design: RNA-seq study perfomed of Serratia WT, Serratia I-F BIM and Serratia I-E BIM during infection with bacteriopage JS26 (moi=50). Samples were taken prior to infection (uninfected control) and 5, 20 and 40 minutes post infection. For each strain, trancriptomic changes were evaluated between each infection time point (5, 20 nd 40 minutes post infection) in comparison to the uninfected control using the DESeq2 R/Bioconductor package (3.5.2) with a Wald test, followed by a Benjamini and Hochberg procedure. The experiement was perfromed in biological triplicate (37 samples in total).

first: Lucia

middle: M

last: Malone

first: Hannah

middle: G

last: Hampton

first: Xochitl

middle: C

last: Morgan


title: Molecular characterization of type I IFN-induced cytotoxicity in bladder cancer cell lines reveals biomarkers of resistance II

city: San Diego

first: Robin

last: Osterhout

address: 4245 Sorrento Valley Rd

institute: Ferring Pharmaceuticals

summary: Although anti-tumor activities of type I interferons (IFNs) have been recognized for decades, the molecular mechanisms contributing to clinical response remain poorly understood. The complex functions of these pleiotropic cytokines include stimulation of innate and adaptive immune responses against tumors as well as direct inhibition of tumor cells. In high-grade, Bacillus Calmette-Guérin (BCG)-unresponsive non-muscle invasive bladder cancer, nadofaragene firadenovec, a non-replicating adenovirus administered locally to express the IFNα2b transgene, embodies a novel approach to deploy the therapeutic activity of type I IFNs while minimizing systemic toxicities. Deciphering which functions of type I IFN are required for clinical activity will bolster efforts to maximize the efficacy of nadofaragene firadenovec and other type I IFN-based therapies, and inform strategies to address resistance. As such, we characterized the phenotypic and molecular response of human bladder cancer cell lines to IFNα delivered in multiple contexts, including adenoviral delivery. We found that constitutive activation of the type I IFN signaling pathway is a biomarker for resistance to both transcriptional response and direct cytotoxic effects of IFNα. We present several genes that discriminate between sensitive and resistant tumor cells, suggesting they should be explored for utility as biomarkers in future clinical trials of interferon-based anti-tumor therapies.

overall_design: 13 bladder cancer cell lines were treated with varying doses of recombinant human IFN-alpha. The RT4 cell line was also treated with human IFN-beta or mouse IFN-alpha. All samples were collected at 24 hrs post-treatment.

middle: E


title: Molecular characterization of type I IFN-induced cytotoxicity in bladder cancer cell lines reveals biomarkers of resistance


title: Molecular characterization of type I IFN-induced cytotoxicity in bladder cancer cell lines reveals biomarkers of resistance I

overall_design: 2 bladder cancer cell lines (RT4, J82) treated with varying doses of recombinant human IFN-alpha, TRAIL or untreated. Samples were collected at 4, 8 or 24 hrs post-treatment.


title: RNA-sequencing of CCN2 knockout and wild type mice following 4 hours after IRI

city: Utrecht

first: Floris

last: Valentijn

address: Heidelberglaan 100

country: Netherlands

institute: University Medical Center Utrecht

summary: In order to identify major regulatory events in the immediate phase of renal IRI associated with CCN2, we performed full transcriptome RNA-sequencing on a cDNA library constructed from RNA extracted from samples of kidney cortex.

overall_design: Kidney cortex mRNA profiles of  WT SHAM (n=4) vs WT IRI (n=4) vs KO SHAM (n=4) vs KO IRI mice (n=5)

middle: A

first: Lucas

middle: L

last: Falke

first: Michal

last: Mokry


title: Transcriptional response to reverse-turn peptidomimetics in human colorectal cancer cells

city: Ottawa

first: Yannick

middle: D.

last: Benoit

address: 451 Smyth road

institute: University of Ottawa

summary: HT29 cells were exposed to EC50 doses of reverse-turn peptidomimetic molecules ICG-001, CWP232228, and YB-0158 (vs. vehicle control DMSO) over 48 hours. RNA sequencing profiling was performed for each experimental condition.

overall_design: Whole transcriptome profiling

first: Angelique

middle: N

last: Masibag

middle: D


title: Mitochondria are a critical metabolic control mechanism for orchestrating phase-specific repair behaviors in wound macrophages

city: Baltimore

first: Immunometabolism

last: Department

state: Maryland

address: 1650 Orleans Street

department: Immunometabolism

institute: Johns Hopkins University

summary: Here we demonstrate that skin injury induces different metabolic programs in wound macrophages by profiling their early versus late stages at both the transcriptional and functional levels. We show that glycolytic metabolism in early phase wound macrophages is not sufficient to ensure a productive repair response. Instead, combining conditional disruption of the electron transport chain in myeloid cells by deletion of mitochondrial aspartyl-tRNA synthetase (DARS2) with single cell sequencing analysis of wound macrophages, we found that at early stage a defined subpopulation of macrophages requires repurposing of mitochondrial activity to initiate a cascade of mitochondrial ROS production, HIF1a stabilization, ultimately driving an effective pro-angiogenic transcriptional program essential for timely healing. In contrast, to convey late phase wound macrophages into repair mode they depend on IL-4Ra-mediated mitochondrial respiration and so far unknown regulation of mitohormesis. Collectively, we identify mitochondria as critical metabolic control mechanism for wound macrophage effector functions.

overall_design: BMDMs form WT and Dars2 KO animals were seeded in 12-well plates (Sigma-Aldrich) in a density of 250,000 cells/cm2 in growth medium. Cells were stimulated with IL-4 + IL-13 (50 ng/mL each) or vehicle for 48 h. Cells were washed twice in PBS (4°C) and lysed in RLT lysis buffer (Qiagen). Total RNA was isolated using the RNeasy Plus Mini Kit (Qiagen) according to the manufacturer’s instructions. Libraries were prepared using the Illumina® Stranded TruSeq® RNA sample preparation Kit.

first: Sebastian

last: Willenborg

first: David

last: Sanin

first: Alexander

last: Jais

first: Xiaolei

last: Ding

first: Thomas

last: Ulas

first: Julian

last: Nüchel

first: Milica

last: Popović

last: MacVicar

last: Langer

first: Joachim

last: Schultze

last: Gerbaulet

first: Axel

last: Roers

first: Edward

last: Pearce

first: Jens

last: Brüning

first: Aleksandra

last: Trifunovic

first: Sabine

last: Eming


title: Spatial transcriptomics of healing and non-healing diabetic foot ulcers

city: Boston

first: Aristidis

last: Veves

state: MA

address: 330 Brookline Ave

institute: Beth Israel Deaconess Medical Center

summary: Diabetic foot ulcers (DFUs) are a devastating complication of diabetes. To better understand the molecular mechanisms and cell types implicated in DFU healing, we used NanoString’s GeoMx Digital Spatial profiling platform on DFU tissue sections and compared gene expression of areas within the same ulcer as well as between patients who in 12 weeks following surgery healed their DFU (Healers, N=2) vs those who did not (Non-Healers, N=2).

overall_design: The spatial transcriptome profiling was performed using NanoString’s GeoMx Digital Spatial profiling platform on unfixed frozen 5 μm tissue sections. Samples were  processed as  follows: 1) 10% neutral buffered formalin fixation overnight, 2) target retrieval (1X Tris EDTA, pH 9.0 for 20 min), 3) proteinase K digestion (1 µg/mL for 15 min), 4) post-fixation (10% NBF, Tris-glycine stop buffer), 5) in-situ hybridization overnight with the GeoMx Cancer Transcriptome Atlas probe panel (1800-plex), 6) stringent washes (50:50 formamide/4X SSC), and 7) fluorescent antibody/marker (aSMA, Clone: 1A4, Abcam; CD45, Clone: 2B11+PD7/26, Novus; PanCK, Clone: AE1/AE3, Novus) incubation, 1 hour at room temperature. Sections were then loaded onto the GeoMx® Digital Spatial Profiler. For profiling, circular regions of interest (ROIs), approximately 500 μm in diameter, located within the ulcers or in neighboring non-ulcerated tissue were selected to include high concentrations of CD45+ immune cells in close proximity to vessels (aSMA+ structures). After ROI selection, the GeoMx instrument illuminated each ROI separately with UV light to cleave, aspirate, and deposit the oligonucleotides from the hybridized ISH probes for downstream sequencing into a 96-well plate.

first: Georgios

last: Theocharidis


title: Involvement of UBA2C in ambient temperature-dependent flowering by promoting FLM transcription

city: Beijing

first: xinjian

last: He

address: No. 7, zhongguancun life science park road, changping district

institute: National Institute of Biological Sciences


title: Involvement of UBA2C in ambient temperature-dependent flowering by promoting FLM transcription [RNA-seq]

summary: Ambient temperature dependent flowering time is an important feature that is required for plants to reproduce in various environmental conditions. The rising global temperature poses a significant challenge to the growth and reproduction of plants. In Arabidopsis thaliana, FLM-β, a major splicing isoform of the flowering repressor gene FLOWERING LOCUS M, is down-regulated in response to increasing temperature and represents a critical mechanism for plants to respond to temperature changes. However, it is unknown how the transcript level of FLM-β is down-regulated. Here we identify an RRM domain-containing protein, UBA2C, as a previously uncharacterized flowering repressor by forward genetic screening. We demonstrate that UBA2C directly binds to FLM chromatin and facilitates FLM transcription predominantly by inhibiting the histone H3K27 trimethylation, a histone mark related to transcriptional repression. At FLM chromatin, the histone H3K27 trimethylation is enhanced in response to increasing temperatures. Depletion of UBA2C weakens the response of FLM transcription and H3K27 trimethylation to temperature changes. UBA2C forms multiple puncta in the nucleus and the number of puncta increases with increasing temperatures. UBA2C contains a prion-like domain (PrLD) that is responsible for forming puncta in the nucleus in vivo. These results not only identify a previously unknown flowering-time regulator but also reveal the mechanism by which the regulator controls flowering time in response to temperature changes.

overall_design: Examination of the mRNA expression of wild type and uba2c mutant grown under long day conditions.

first: Xin-Jian


title: Involvement of UBA2C in ambient temperature-dependent flowering by promoting FLM transcription [ChIP-seq]

overall_design: Examination of H3K27me3 levels in wild type and uba2c mutant grown under long day.


title: TET deficiency promotes oncogenesis and DNA damage in B cells by increasing the levels of G-quadruplexes and R-loops [HTGTS]

city: La Jolla

first: Anjana

last: Rao

state: California

address: 9420 Athena Cir

department: Signaling and Gene Expression

institute: La Jolla Institute for Allergy and Immunology

summary: Enzymes of the TET family are methylcytosine dioxygenases that undergo frequent mutational or functional inactivation in both hematological and solid cancers. Recent studies have identified recurrent loss-of-function mutations in TET proteins in human patients with Diffuse Large B-Cell Lymphoma (DLBCL). Here we investigate the role of TET proteins in the pathogenesis of DLBCL by deleting the Tet2 and Tet3 genes in mature B cells in mice. Tet deletion perturbs mature B-cell homeostasis and causes spontaneous development of Germinal Center-derived B cell lymphomas. We show that an increase in G-quadruplexes and R-loops a common feature of TET deficiency in B cells as well as other hematopoietic cells. Genome-wide analyses revealed that G-quadruplexes and R-loops accumulated primarily near transcription start sites in TET-deficient B cells, and their accumulation correlated with increased DNA double-strand breaks. Moreover, CRISPR-mediated depletion of nucleases and helicases that regulate G-quadruplexes and R-loops led to decreased viability of TET-deficient but not control primary B cells. Our studies elucidate a molecular mechanism by which TET loss-of-function might predispose to development of B cell-derived and other malignancies, and highlight novel therapeutic avenues that could be further explored.

overall_design: HTGTS mapping in CD19 Tet2/3 DKO B cells

first: Vipul

last: Shukla

first: Daniela

last: Samaniego-Castruita


title: TET deficiency promotes oncogenesis and DNA damage in B cells by increasing the levels of G-quadruplexes and R-loops [MAPR]

overall_design: R-loops mapping, MAPR, in CD19 Tet2/3 DKO B cells


title: TET deficiency perturbs mature B cell homeostasis and promotes oncogenesis associated with accumulation of G-quadruplex and R-loop structures

type: Methylation profiling by high throughput sequencing

overall_design: Refer to individual Series


title: TET deficiency promotes oncogenesis and DNA damage in B cells by increasing the levels of G-quadruplexes and R-loops [WGBS]

overall_design: WGBS mapping in CD19 Tet2/3 DKO B cells


title: Mitochondrial C5aR1 activity in macrophages controls IL-1b production underlying sterile inflammation

city: Bethesda

first: Jack

last: Bibby

address: 10 Center Drive

institute: National Institutes of Health

summary: While serum-circulating complement destroys invading pathogens, intracellularly active complement, termed the ‘complosome’, functions as a vital orchestrator of cell-metabolic events underlying T cell effector responses. Whether intracellular complement is also non-redundant for the activity of myeloid immune cells is currently unknown. Here, we show that monocytes and macrophages constitutively express complement component (C) 5 and can generate autocrine C5a via formation of an intracellular C5 convertase. Further, cholesterol crystal-sensing by macrophages induces C5aR1 signaling on mitochondrial membranes, which shifts ATP production via reverse electron chain flux towards reactive oxygen species (ROS) production and anaerobic glycolysis to favor IL-1 production. Consequently, atherosclerosis-prone mice lacking macrophage-specific C5ar1 had ameliorated cardiovascular disease on a high-cholesterol diet. Conversely, inflammatory gene signatures and IL-1 produced by cells in unstable atherosclerotic plaques of patients were normalized by a specific cell-permeable C5aR1 antagonist. Deficiency of the macrophage cell autonomous C5 system also protected mice from crystal nephropathy mediated by folic acid. These data demonstrate unexpected intracellular formation of a C5 convertase and identify C5aR1 as a direct modulator of mitochondrial function and inflammatory output from myeloid cells. Together, these findings suggest that the complosome is a novel contributor to the biologic processes underlying sterile inflammation and indicate that targeting this system could be beneficial in macrophage-dependent diseases, such as atherosclerosis.

overall_design: Monocytes/macrophages were isolated from the kidney of control and mC5–/– mice at day 14 post folic acid injection, each group pooled and eclls subjevcted to mRNA sequencing

first: Claudia

last: Kemper


title: Single-cell reconstruction with spatial context of migrating neural crest cells and their microenvironments during vertebrate head and neck formation

city: Kansas City

first: Madelaine

last: Gogol

state: MO

address: 1000 E. 50th Street

department: Computational Biology Core

institute: Stowers Institute

summary:
The dynamics of multipotent neural crest cell differentiation and
invasion as cells travel throughout the vertebrate embryo remain
unclear. Here, we preserve spatial information to derive the
transcriptional states of migrating neural crest cells and the cellular
landscape of the first four chick cranial to cardiac branchial arches
(BA1-4) using label-free, unsorted single-cell RNA sequencing. The
faithful capture of branchial arch-specific genes led to identification
of novel markers of migrating neural crest cells and 266 invasion
genes common to all BA1-4 streams. Perturbation analysis of a small
subset of invasion genes and time-lapse imaging identified their
functional role to regulate neural crest cell behaviors. Comparison of
the neural crest invasion signature to other cell invasion phenomena
revealed a shared set of 45 genes, a subset of which showed direct
relevance to human neuroblastoma cell lines analyzed after exposure
to the in vivo chick embryonic neural crest microenvironment. Our
data define an important spatio-temporal reference resource to
address patterning of the vertebrate head and neck, and previously
AQ1 unidentified cell invasion genes with the potential for broad impact.

overall_design: Eight spatially and temporally distinct samples from chicken branchial arches 1-4 analyzed by 10X Genomics Chromiun scRNA-seq totaling 95,109 cells

first: Jason

last: Morrison

first: Rebecca

last: McLennan

first: Jessica

last: Teddy

first: Allison

last: Scott

first: Jennifer

last: Kasemeier-Kulesa

first: Paul

last: Kulesa


title: TET deficiency promotes oncogenesis and DNA damage in B cells by increasing the levels of G-quadruplexes and R-loops [RNA-seq]

overall_design: Transcriptomic analysis in CD19 Tet2/3 DKO B cells


title: Krüppel-like factor 5 regulates stemness, lineage specification, and regeneration of intestinal epithelial stem cells

city: Stony Brook

first: Vincent

last: Yang

state: New York

address: 101 Nicolls Rd., HSC T17-090

department: Medicine

institute: Stony Brook University

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


title: Epigenomics analysis of ESCC

city: Shantou

first: Yang

last: Chen

address: Department of Biochemistry and Molecular Biology, Shantou University Medical College, 22 Xinling Road, Shantou

institute: Shantou University Medical College

summary: We detected DNA methylation of 15 ESCC samples' tumor tissues and their pericarcinomatous tissues to identify the aberrant DNA methylation status in ESCC.

overall_design: Bisulphite converted DNA from the 15 samples were hybridised to the Illumina Infinium 450k Human Methylation Beadchip

first: En-Min

last: Li

first: Li-Yan

last: Xu


title: Transcriptomic profiling of KPM cell lines through RNA-Seq

city: Munich

first: Georgios

middle: T

last: Stathopoulos

state: Bayern

address: Max-Lebsche-Platz

department: Comprehensive Pneumology Center

country: Germany

institute: Helmholz Zentrum Munich

summary: Conditional mutant KRAS-expressing (LSL.KRASG12D; K) and TRP53-deleted (Trp53f/f; P) mice were intercrossed in all possible combinations, followed by intrapleural adenovirus-Cre injection. KRAS G12D; TRP53 f/f mice (KP mice) developed multifocal, lethal Malignant Pleural Mesothelioma that invaded the lungs, the chest wall and the mediastinal structures with a median overall survival of 41 days. Multiple cell lines were derived from primary MPM from KP mice. This was done by isolating, in sterile conditions, cells from the tumors of the KP mice and culturing them in minimum supplemented medium (DMEM+10% FBS + 1% PEN/STREP) for over 6 months, for over 30 passages.The WT mesothelial cells were isolated through a lavage procedure at the pleural space. Wt C57BL/6 mice were sacrificed. In order to wash the pleural space 1ml of sterile saline was injected and immediately withdrawn through the diaphragm. Subsequently 1ml of trypsin 1% was injected to the pleural space. We incubated for 8 minutes and withdrew the trypsin which contained the mesothelial cells. The cells were pelleted by centrifugation at 500g for 5 minutes.

overall_design: Compare differential gene expression between naïve mouse mesothelial cells and mouse malignant pleural mesothelioma cells.Alignment of sequencing traces for visual exploration and visualizzation of trascripts alteration.

first: Nikolaos

middle: I

last: Kanellakis

first: Mario

last: Pepe


title: Krüppel-like factor 5 regulates stemness, lineage specification, and regeneration of intestinal epithelial stem cells [RNA-seq]

summary: The essential functions of intestinal stem cells (ISCs) are to self-renew and give rise to progenitors that subsequently differentiate to absorptive or secretory cells, thus maintaining homeostasis in the intestinal epithelium. In this study, we analyzed the transcriptomic and epigenetic changes of ISCs with Klf5 deletion to understand the role of KLF5 in ISC identity and functions.

overall_design: RNA-sequencing and ChIP-seq analysis of control mouse intestinal stem cells and Klf5-deleted intestinal stem cells.

first: Chang-Kyung

last: Kim

first: Agnieszka

middle: B

last: Bialkowska

first: Madhurima

last: Saxena

first: Ramesh

last: Shivdasani

middle: W


title: RNA-Seq analysis of different tissue-types of developing rice seed

city: Mohali

first: Hasthi

last: Ram

address: Sector 81

department: Agriculture biotechnology

country: India

institute: NABI (National Agri-Food Biotechnology Institute)

summary: Aleurone layer differentiation completes by 9 DAF, and most of the nutrient filling occurs between 6-21 DAF, (Wu et al., 2016a, 2016b), so we decided to use 10 DAF time point for collection of pericarp, aleurone, embryo and endosperm tissues for RNA-Seq analysis. Since aleurone is mostly single layer, and it’s almost impossible to separately collect pure pericarp and aleurone layers manually, so firstly we developed a method to collect different tissue types of developing grain through LCM and RNA extraction and Sequencing

overall_design: 10 ng of total RNA was used for library preparation and sequencing using Illumina HiSeq2500 platform. 3 biological replicates for each of the tissue type (pericarp, aleurone, embryo, endosperm) were used. For each sample, we obtained in between of 17-32 million reads.


title: TET deficiency promotes oncogenesis and DNA damage in B cells by increasing the levels of G-quadruplexes and R-loops [HMCP]

first: Anjana

last: Rao

overall_design: HMCP mapping in CD19 Tet2/3 DKO B cells

first: Vipul

last: Shukla

first: Daniela

last: Samaniego-Castruita


title: RNA-seq profiling in eWAT, iWAT, and BAT-derived adipocytes

status: Public on Oct 27 2021

city: Odense M

first: Anne

last: Loft

address: Campusvej 55

department: Biochemistry & Molecular Biology

country: Denmark

institute: University of Southern Denmark

summary: Here we have employed RNA-seq to profile the transcriptional landscapes of in vitro differentiated primary mouse adipocytes isolated from epididymal and inguinal white adipose tissus as well as brown adipose tissue.

overall_design: RNA-seq profiling of in vitro differentiatied adipocytes isolated from three different adipose depots.

first: Susanne

last: Mandrup


title: Shexiang Tongxin Dropping Pill Protects against Chronic Heart Failure in Mice via Inhibiting the ERK/MAPK and TGF-β Signaling Pathways

city: Hangzhou

first: penghui

last: Yang

state: Zhejiang

address: 866 Yuhangtang Road

institute: Pharmaceutical Informatics Institute

summary:
Background: Chronic heart failure (CHF) is a major public health problem with high mortality and morbidity worldwide. Shexiang Tongxin Dropping Pill (STDP) is a widely used traditional Chinese medicine preparation for coronary heart disease and growing evidence proves that STDP exerts beneficial effects on CHF in the clinic. However, the mechanism of its effect on CHF still yet to be deciphered.
Objective: This study aimed to elucidate the potential pharmacological mechanism of STDP against CHF by integrating network pharmacology analysis and whole-transcriptome sequencing.
Methods: First, the mouse model of CHF was established by the transverse aortic constriction (TAC) surgery, and the efficacy of STDP against CHF was evaluated by assessing the alterations in cardiac function, myocardial fibrosis, and cardiomyocyte hypertrophy with echocardiography, Masson's trichrome staining, and wheat germ agglutinin staining. Next, a CHF disease network was constructed by integrating cardiovascular disease-related genes and the transcriptome sequencing data of mouse heart tissue, which was used to explore the underlying mechanism of action of STDP in CHF. Then, the key targets involved in the effects of STDP on CFH were determined by network analysis algorithms, and pathway enrichment analysis was performed to these key genes. Finally, important targets in the critical pathway were verified in vivo.
Results: STDP administration (86 mg/kg/d) obviously improved cardiac function, relieved cardiomyocyte hypertrophy, and ameliorated myocardial fibrosis in CFH mice. Moreover, STDP significantly reversed the imbalanced genes that belong to the disease network of CHF in mice with TAC, and the number of genes with the reverse effect was 395. Pathway analysis of the crucial genes with recovery efficiency revealed that pathways related to fibrosis and energy metabolism were highly enriched, while TGF-β pathway and ERK/MAPK pathway were predicted to be significantly affected. Consistently, validation experiments confirmed that inhibiting ERK/MAPK and TGF-β signaling pathways via reduction of the phosphorylation level of Samd3 and ERK1/2 is the important mechanism of STDP against CHF.
Conclusion: Our data provided strong evidence that STDP has great potential for the treatment of CHF and the mechanisms are mainly related to inhibition of ERK/MAPK and TGF-β signaling pathways.

overall_design:
First, the mouse model of CHF was established by the transverse aortic constriction (TAC) surgery. Next, a CHF disease network was constructed by integrating cardiovascular disease-related genes and the transcriptome sequencing data of mouse heart tissue, which was used to explore the underlying mechanism of action of STDP in CHF.
3 experimental condtions, 1 time point

first: Shuying

last: Zhang

first: Hanbing

last: Liu


title: Sox6 expression distinguishes dorsally and ventrally biased dopamine neurons in the substantia nigra with distinctive properties and embryonic origins

city: Chicago

first: Rajeshwar

last: Awatramani

state: Illinois

address: 320 E Searle

department: Neurology

institute: Northwestern University

summary: To determine the molecular differences between ventral Sox6+ and dorsal Sox6- DA neurons, we performed bulk RNA-sequencing in sorted mCherry+ and GFP+ cells from the SNc of adult Sox6-FSF-Cre, Th-2A-Flpo, RC-Frepe mice. Our analysis revealed large and significant differential gene expression between these two populations.

overall_design: mRNA profiling of two dopaminergic populations (Sox6+ and Sox6-) in the SNc of adult mice brains.

first: Milagros

last: Pereira Luppi

first: Maite

last: Azcorra

first: Giuliana

last: Caronia-Brown

first: Jean

middle: F

last: Poulin

first: Zachary

last: Gaertner

first: Serafin

last: Gatica

first: Oscar

last: Moreno-Ramos

first: Navid

last: Nouri

first: Marilyn

last: Dubois

first: Yongchao

last: Ma

first: Charu

last: Ramakrishnan

first: Lief

last: Fenno

first: Yoon

last: Seok Kim

first: Karl

last: Deisseroth

first: Francesca

last: Cicchetti

first: Daniel

last: Dombeck


title: ActD timecourse in HeLa cells, HeLa RNF219 KO cells, HeLa RNF219 KO cells overexpressing 3xFLAG-SBP-RNF219-WT or 3xFLAG-SBP-RNF219-mut

city: Mannheim

first: Johanna

middle: Daniela

last: Schott

address: Franz-Volhard-Straße 6

department: Mannheim Institute for Innate Immunoscience

institute: Heidelberg University

summary: The evolutionarily conserved CCR4-NOT complex acts as a central player in the control of mRNA turnover and mediates accelerated mRNA degradation upon histone deacetylase (HDAC) inhibition. Here, we explored acetylation-induced changes in the composition of the CCR4-NOT complex by purification of the endogenously tagged scaffold subunit NOT1 and identified ring finger protein 219 (RNF219) as an acetylation-regulated cofactor. We provide evidence that RNF219 is an active RING-type E3 ubiquitin ligase which stably associates with the CCR4-NOT complex via the NOT9 module through a short linear motif located in the C-terminal low-complexity region of RNF219. Using a reconstituted six-subunit human CCR4-NOT complex, we demonstrate that RNF219 acts as an inhibitor of deadenylation. Accordingly, our transcriptome-wide mRNA half-life measurements reveal that RNF219 attenuates global mRNA turnover in cells, independently of its E3 ligase activity. Our results establish RNF219 as a negative regulator of CCR4-NOT-mediated mRNA deadenylation, whose loss upon HDAC inhibition contributes to accelerated mRNA turnover.

overall_design: Transcriptional shut-off with ActD followed by RNA-Seq to determine mRNA half-lives on a transcriptome-wide scale in HeLa cells, HeLa RNF219 KO cells, HeLa RNF219 KO cells overexpressing 3xFLAG-SBP-RNF219-WT or 3xFLAG-SBP-RNF219-mut in two biological replicates

first: Fabian

last: Poetz

first: Doris

last: Lindner

first: Georg

last: Stoecklin


title: RNA-Seq on E12.5 WT and LncBAR-KO (KO) neurospheres (passage 3)

city: Wuhan

first: Andi

last: Wang

address: Luojiashan Road

institute: Wuhan University

summary: Neocortical projection neurons of mammalian brains are largely direct daughters of intermediate progenitors (IP), which are progenies of radial glial cells (RG). The maintenance of the RG pool, production and expansion of IPs are essential for neocortical formation during development, as well as neocortical expansion during evolution. Here we characterized an epigenetic circuit that controls precise neurogenic programming of the neocortex. The circuit comprises a long non-coding RNA – LncBAR and the SWI/SNF (BAF) chromatin-remodeling complex, which transcriptionally maintains the expression of Zbtb20. LncBAR knockout neocortex contains fewer upper-layer projection neurons. Intriguingly, loss of LncBAR promotes IP production of RGCs, but hampers neurogenic division and lengthens the cell-cycle durations of IPs during mid-later cortical neurogenesis. Moreover, in LncBAR knockout mice, depletion of the neural progenitor pool at embryonic stage causes fewer adult neural stem cells at the subventricular zone, leading to compromised adult neurogenesis to replenish the olfactory bulb. LncBAR binds to BRG1, the core enzymatic component of the SWI/SNF (BAF) chromatin-remodeling complex. LncBAR depletion enhances association of BRG1 with and the genomic locus of, and suppresses the expression of Zbtb20, a transcription factor gene known to regulate both embryonic and adult neurogenesis. ZBTB20 re-expression in LncBAR-knockout neural precursors reversed compromised neurogenic divisions of IPCs. Together, we revealed a previously unidentified epigenetic machinery to control neurogenesis of neural precursors.

overall_design: Neurospheres mRNA profiles of E12.5  WT and KO mice were generated by deep sequencing, in duplicate, using Illumina NovaSeq 6000.

first: Kuan

last: Tian

first: Junbao

first: Yan

last: Zhou


title: Xist-seeded nucleation sites form local concentration gradients of silencing proteins to inactivate the X-chromosome [II]

city: Los Angeles

first: Kathrin

last: Plath

address: 615 Charles E Young Dr S

institute: University of California, Los Angeles

summary: The long non-coding RNA Xist exploits numerous effector proteins to gradually induce gene silencing across the X chromosome. Here, we show that formation of the inactive X (Xi)-compartment is induced by ~50 locally confined granules, where two Xist RNA molecules nucleate supra-molecular complexes (SMCs) of interacting proteins. Xist-SMCs are dynamic structures that concentrate rapidly recycling proteins on the X by increasing their binding affinity, thereby facilitating their access to the entire chromosome. We find that gene silencing originates at Xist-SMCs and propagates across the entire X chromosome over time. The propagation of silencing is achieved by Polycomb-mediated coalescence of chromatin regions and aggregation of the critical silencing enzyme SPEN, via its intrinsically disordered domains. Our observations suggest a new model for X Chromosome Inactivation, whereby Xist RNA triggers macromolecular crowding of heterochromatinizing proteins at distinct sites to ultimately increase their occupancy throughout the X chromosome. This mechanism enables deterministic gene silencing across an entire chromosome without the need for Xist ribonucleoprotein complex-chromatin interactions at each target gene. Our findings uncover a spatial organization mechanism by which few RNA molecules can regulate a broad nuclear compartment through the recruitment and local concentration of dynamic effector proteins, and provide a quantitative framework for studying such compartments.

sample_organism: Mus musculus musculus x Mus musculus castaneus

overall_design: Single-cell and bulk RNA-seq of ESCs expressing mutant or WT SPEN. Single-cell RNA-seq of ESCs expressing deltaB or WT Xist. CLAP-seq on ESCs expressing WT and mutant SPEN forms.

first: Yolanda

last: Markaki

first: Elsie

last: Jacobson

first: Johnny

last: Chong

first: Yuying


title: BRG1 ChIP-Seq and RNA-Seq on E12.5 WT and LncBAR-KO (KO) neurospheres


title: BRG1 ChIP-Seq on E12.5 WT and LncBAR-KO (KO) neurospheres  (passage 3)

overall_design: Examination of BRG1-binding sites in E12.5 WT and KO neurospheres


title: Xist-seeded nucleation sites form local concentration gradients of silencing proteins to inactivate the X-chromosome [I]

summary: The long non-coding RNA Xist exploits numerous effector proteins to gradually induce gene silencing across the X chromosome. Here, we show that formation of the inactive X (Xi)-compartment is induced by ~50 locally confined granules, where two Xist RNA molecules nucleate supra-molecular complexes (SMCs) of interacting proteins. Xist-SMCs are dynamic structures that concentrate rapidly recycling proteins on the X by increasing their binding affinity, thereby facilitating their access to the entire chromosome. We find that gene silencing originates at Xist-SMCs and propagates across the entire X chromosome over time. The propagation of silencing is achieved by Polycomb-mediated coalescence of chromatin regions and aggregation of the critical silencing enzyme SPEN, via its intrinsically disordered domains. Our observations suggest a new model for X Chromosome Inactivation, whereby Xist RNA triggers macromolecular crowding of heterochromatinizing proteins at distinct sites to ultimately increase their occupancy throughout the X chromosome . This mechanism enables deterministic gene silencing across an entire chromosome without the need for Xist ribonucleoprotein complex-chromatin interactions at each target gene. Our findings uncover a spatial organization mechanism by which few RNA molecules can regulate a broad nuclear compartment through the recruitment and local concentration of dynamic effector proteins, and provide a quantitative framework for studying such compartments.

overall_design: Xist binding profiles at day 2 and day 4 of female ESC differentiation

first: Shawn

last: Tan

first: Iris

last: Dror


title: A transcriptional and open chromatin landscape and the role of ONECUT1 in  human pancreas differentiation [ATAC-seq]

city: Aachen

first: Ivan

last: Costa

address: Pauwelsstraße 19

institute: Unikilink RWTH Aachen

summary: Pancreatic differentiation and specification of lineages is a tightly controlled process involving a interconnected network of transcriptional regulation. Although more knowledge on human pancreatic development is accumulating, the precise role of many transcription factors is only described in mouse. Therefore, it is of great interest to expand our knowledge using alternative model systems such as pancreatic in vitro differentiation of human pluripotent stem cells. Here, we provide stage-specific data from RNA-, ChIP-, and ATAC-sequencing to dissect transcriptional and regulatory mechanisms during pancreatic development. Transcriptome and open chromatin maps of pancreas differentiation from human pluripotent stem cells provide a stage-specific pattern of known pancreas transcription factors and determine ONECUT1 as a crucial regulator in pancreas progenitors. Moreover, our data suggest that ONECUT1 is also involved in preparing pancreatic progenitors for later endocrine specification.Our approach of dissecting the transcriptional and regulatory mechanisms revealed an important role for the specific key player ONECUT1 and will help to better understand human development and disease.

overall_design: The human embryonic stem cell line HUES8 differentiated to definitive endoderm, gut tube,  pancreatic endoderm and pancreatic progenitor cells was used for ATAC sequencing.

first: Zhijian

last: Li

first: Alexander

last: Kleger

first: Sandra

last: Heller


title: Genome-wide fitness gene identification reveals Roquin as a potent suppressor of CD8 T cell expansion and anti-tumor immunity

first: Hanfei

last: Zhao

state: Beijing

address: Haidian District

department: School of Medicine

institute: Tsinghua University

summary: Robust expansion of adoptively transferred T cells is a prerequisite for effective cancer immunotherapy, but how many genes in the genome modulate T cell expansion remains unknown. Here, we performed in vivo and in vitro CRISPR screens to systematically identify genes influencing CD8 T cell expansion. In the mouse genome, ~ 2,600 and ~ 1,500 genes were required for optimal CD8 T cell expansion in vivo and in vitro, respectively. In vivo-specific CD8 T cell essential genes were enriched in metabolic pathways including mitochondrial metabolism. The strongest repressor of CD8 T cell expansion was Roquin, ablation of which drastically boosted T cell proliferation by enhancing cell cycle progression and upregulation of IRF4. Roquin-deficiency or IRF4 overexpression potently enhanced anti-tumor immunity. These data provide a functional catalog of CD8 T cell fitness genes, and suggest targeting Roquin-IRF4 axis is an effective strategy to enhance efficacy of adoptive transfer therapy for cancer.

overall_design: RNA sequencing: mRNA of 2 sgControl samples and 2 sgRc3h1 samples were analysed by NGS.


title: Role of transcription factor ONECUT1 (HNF6) during in vitro pancreatic differentiation of human pluripotent stem cells [RNA-seq]

summary: We have identified HNF6 as an essential transcription factor for endocrine pancreatic development. HNF6 binds to and possibly regulates other isletogenesis transcription factors, driving endocrine differentiation. RNA sequencing of control and HNF6-depleted hESC during in vitro pancreatic differentiation will help to understand the regulatory mechanisms during cell fate decisions.

overall_design: The human embryonic stem cell line HUES8 differentiated to definitive endoderm, pancreatic endoderm and pancreatic progenitor cells was used for RNA sequencing.

first: Gino

last: Kwon


title: C/EBPb cooperates with BLNK mutation in preB leukemogenesis

city: Tokyo

first: Takuro

last: Nakamura

address: 3-8-31 Ariake, Koto-ku

department: The Cancer Institute

country: Japan

institute: Japanese Foundation for Cancer Research

overall_design: Refer to individual Series


title: C/EBPb cooperates with BLNK mutation in preB leukemogenesis (BLNK2)

summary:
BLNK (BASH/SLP-65) encodes an adaptor protein within the B-cell receptor signaling. Loss-of-function mutations of BLNK are observed in human preB-ALL, and a subset of Blnk knock-out mice develop preB-ALL. To understand the molecular mechanism of preB-ALL development associated with the Blnk mutation, retroviral tagging was applied on Blnk KO mice using Moloney murine leukemia virus (MoMLV). The Blnk mutation significantly accelerated the disease onset of MoMLV-induced leukemia and increased the incidence of preB-ALL. Cebpb was identified as the most frequent common retroviral integration site, suggesting that Cebpb upregulation cooperates with Blnk mutation. Transgenic expression of the LAP (liver-enriched activator protein) isoform of C/EBP-beta significantly accelerated preB-ALL development of Blnk ko mice.
We used microarrays to detail the global program of gene expression in mouse preB-ALL

overall_design: Murine preB-ALL cell line LB31 and non-neoplastic bone marrow B-lymphocytes derived from wild type, Blnk KO, Cebpb LAP transgenic and Blnk KO/LAP tg mice were examined.

first: Morito

last: Kurata


title: C/EBPb cooperates with BLNK mutation in preB leukemogenesis (BLNK1)

overall_design: Murine preB-ALL cell line BKO408 and primary tumors developed in Blnk KO mice and/or Cebpb LAP transgenic mice were examined.


title: Interactions between different maturation states of oocytes and granulosa cells in human antral follicles identified by single-cell transcriptomics

status: Public on Oct 26 2021

city: Leiden

first: Susana

last: Chuva de Sousa Lopes

address: Einthovenweg 20

department: Anatomy and Embryology

institute: Leiden University Medical Center

summary: Human ovarian folliculogenesis is an highly regulated and complex process. Characterization of follicular cell signatures during this dynamic process is important to understand follicle fate (to grow, become dominant or undergo atresia). The transcriptional signature of human oocytes and granulosa cells (GC) in early-growing and ovulatory follicles have been previously described, however that of oocytes with surrounding GCs in small antral follicles have not been studied yet. Here, we have generated a unique dataset of single-cell transcriptomics (SmartSeq2) consisting of the oocyte with surrounding GCs from several individual (non-dominant) small antral follicles isolated from adult human ovaries. We have identified two main types of (healthy) follicles, with a distinct oocyte and GC signature. Using the CellphoneDB algorithm, we then investigated the bi-directional ligand-receptor interactions regarding the TGFβ/BMP, WNT, NOTCH, and receptor tyrosine kinases (RTK) signaling pathways between oocyte and GCs within each antral follicle type. Our work not only revealed the diversity of small antral follicles but also contributes to fill the gap in mapping the molecular landscape of human folliculogenesis and oogenesis.

overall_design: 141 cells from 14 individual antral follicles from 3 donor ovaries

first: S

first: I

last: Moustakas

first: X

last: Fan


title: Transcriptome analysis of LRRK2 knock-out microglia cells reveals T alterations of inflammatory- and oxidative stress-related pathways upon treatment with α-synuclein fibrils

first: Mark

middle: R

last: Cookson

state: MD

address: NIHBC 35 - PNRC I BG RM 1A-116

institute: National Institutue on Aging, NIH

summary:
We used the RNA-Sequencing to obtain transcriptomic profiles of LRRK2 wild-type (WT) and knock-out (KO) microglia cells treated with α-synuclein pre-formed fibrils (PFFs) or lipopolysaccharide (LPS) as a general inflammatory insult.
Conclusion: overall, the results suggest that microglial LRRK2 may contribute to the pathogenesis of PD via altered oxidative stress signaling.

overall_design: Primary mouse microglia cultures were incubated with LPS or α-synuclein fibrils and transcriptomic profiles were analyzed by bulkRNA Seq.

first: Isabella

last: Russo

first: Alice

last: Kaganovich

first: Jinhui

last: Ding

first: Natalie

last: Landeck

first: Adamantios

last: Mamais

first: Tatiana

last: Varanita

last: Biosa

last: Tessari

first: Luigi

last: Bubacco

first: Elisa

last: Greggio


title: Differential gene expression induced by Leukemia inhibitory factor in bovine aortic endothelial cells (BAE) vs choroidal endothelial (BCE) cells

city: San Diego

first: Pin

last: Li

address: 4350 Vision Dr

institute: Moores Cancer Center, UCSD

summary: To characterize the differential effects of LIF in BAE vs BCE cells, genes induced/suppressed by LIF were analyzed by RNA-seq following incubation with LIF. Remarkably, LIF treatment led to distinct gene expression patterns in these two cell types.

overall_design: Differential gene expression in mRNA of BAE and BCE cells after LIF treatment

first: Qin

first: Napoleone

last: Ferrara


title: Transcriptomic and physiological response of durum wheat grain to short period of heat stress at the early grain-filling stage

city: Valdivia

first: Javier

last: Canales

state: Los Ríos

address: Campus Isla Teja s/n

department: Instituto de Bioquimica y Microbiologia

country: Chile

institute: Universidad Austral de Chile

summary: Wheat is one of the most significant crops in terms of human consumption in the world. In a climate change scenario, extreme weather event such as heatwaves will be more frequent especially during the grain-filling (GF) stage and could affect grain weight and quality of crops. Molecular mechanisms underlying the response to short heat stress (HS) have been widely reported for the hexaploid wheat (Triticum aestivum) but the regulatory heat stress mechanisms in tetraploid durum wheat (Triticum turgidum ssp. durum) remain partially understood. In this work, we performed a transcriptomic analysis of durum wheat grains to HS during early GF to identify key HS response genes and their predicted regulatory networks under glasshouse conditions.

overall_design: Tetraploid wheat (Triticum turgidum spp. durum) genotype Queule-INIA was grown under standard glasshouse conditions. Three seeds per pots were sowing. At flowering (Zadok 65), three principal spikes/pot with similar development and size were tagged. Two thermal treatments were performed: control treatment (ambient air temperature on glasshouse) and short HS treatment, which consisted of increasing the air temperature in a range of moderately high temperatures (20 to 32 ºC). The grain samples (complete caryopsis) at 10 days after flowering were collected after three hours of HS from four pot per replicate (two basal grains of four central spikelest from 12 spikes were polled for each replicate). Three replicates for each thermal treatments were done.

first: Anita

last: Arenas-M


title: RNA-seq transcriptomic comparison between PyVmT-driven mammary tumours either expressing or lacking epithelial beta 1 integrin (Itgb1)

city: Montreal

first: Tung

last: Bui

state: Quebec

address: 1160 Pine Ave. W, R507

department: Biochemistry

institute: McGill University

summary: Using inducible oncogene (PyVmT) and conditional knockout transgenic systems, we generated mammary tumours lacking expression of beta 1 integrin specifically in epithelial cells. By RNA-sequencing profiling of the tumours, we identified transcripts and gene fusions that were differential between beta 1 integrin-proficient and -deficient tumours.

overall_design: Total RNA was extracted from mammary tumours at similar clinical burdens and subjected to RNA sequencing.

first: Yu

last: Gu

first: William

last: Muller


title: SOX1OT V1 Acts as a Decoy of HDAC10 to Promote SOX1-dependent hESC Neuronal Differentiation

city: Shanghai

first: Li

last: Jianguo

address: 1239 Siping Road

institute: Tongji University

summary: To investigate the mechanism by which SOX1-OT V1 regulates neural differentiation, The sample from d0, d4, d10, d16D (dorsal) and d16V (ventral) of neural differentiation were collected to perform RNA-seq assays to quantitate gene expression in control group and SOX1-OT V1-PAKI group.

overall_design: Examination of gene expression in Ctrl group and SOX1-OT V1-PAKI group during d0, d4, d10 and d16 in hESC neural differentiation.

first: Jiajie

last: Xi

first: Yanxin

last: Xu

first: Jianguo

first: Jiuhong

last: Kang


title: Xist-seeded nucleation sites form local concentration gradients of silencing proteins to inactivate the X-chromosome

first: Kathrin

last: Plath

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

platform_organism: Mus musculus musculus x Mus musculus castaneus


title: Transcription-wide distribution of dihydrouridine (D) into mRNAs reveals its requirement for meiotic chromosome segregation [Ribo/RNA-seq]

city: Namur

first: Carlo

last: Yague-Sanz

address: 61 rue de Bruxelles

department: Medecine

country: Belgium

institute: Namur University

summary: Here we have developed Rho-seq, an integrated pipeline detecting a range of modifications through differential modification-dependent Rhodamine labeling. Using Rho-seq, we report that the reduction of uridine to dihydrouridine by the Dus reductase family targets tRNAs in E. coli but expands to mRNAs is yeast. The modified mRNAs are enriched for cytoskeleton related encoded protein. We show that the a-tubulin encoding mRNA nda2 undergoes dihydrouridination, which affects its protein expression level. The absence of the modification onto the nda2 mRNA strongly impacts meiosis by inducing a metaphase delay or by completely preventing the formation of spindles during meiosis I and meiosis II, eventually resulting in low gamete viability. Collectively these data show that the codon specific reduction of uridine within mRNA is required for proper meiotic chromosome segregation and gamete viability.

overall_design: Ribo-seq and total RNA-seq for matching samples of wild-type and delta4dus S. pombe cells

first: Felix

last: Ernst

first: Denis

last: Lafontaine

first: Damien

last: Hermand


title: Transcription-wide distribution of dihydrouridine (D) into mRNAs reveals its requirement for meiotic chromosome segregation. [RNA-Seq]

overall_design: RNA-seq in wild-type and delta4dus strain, a strain where all 4 genes encoding for dus enzymes are deleted.

first: Olivier

last: Finet

first: Maxime

last: Wéry

first: Antonin

last: Morillon


title: Genome-wide cancer-specific chromatin accessibility patterns derived from archival processed xenograft tumors

city: Chapel Hill

first: Ian

middle: Jonathan

last: Davis

state: NC

address: 450 West Drive

institute: University of North Carolina-Chapel Hill

summary: This study introduces the identification of genome-wide cancer-specific chromatin signatures from archival tissues using nanodroplet-assisted FAIRE-seq. Our enhanced cavitation method, a nanodroplet reagent consisting of a lipid shell with a liquid perfluorocarbon core, facilitated the extraction of intact chromatin from FFPE xenograft tissues across 3 cancer types, encompassing 10 cell lines. Chromatin states that influence gene expression and other nuclear processes can be altered in disease. Studying these patterns in tissues has been limited since existing chromatin accessibility assays are ineffective for archival formalin-fixed, paraffin embedded (FFPE) tissues. Inclusion of nanodroplets during the extraction of chromatin from FFPE tissues enhances the recovery of intact accessible and nucleosome-bound chromatin. We demonstrate that the addition of nanodroplets to the chromatin accessibility assay FAIRE (formaldehyde-assisted isolation of regulatory elements), does not affect the accessible chromatin signal. Applying the technique to FFPE human tumor xenografts, we identified tumor-relevant regions of accessible chromatin shared with those identified in primary tumors. Further, we deconvoluted non-tumor signal to identify cellular components of the tumor microenvironment. Incorporation of this method of enhanced cavitation into FAIRE offers the potential for extending chromatin accessibility to clinical diagnosis and personalized medicine, while also enabling the exploration of gene regulatory mechanisms is archival samples.

overall_design: Analysis of Chromatin Signal Via FAIRE: in cells, with and without nanodroplets (2 replicates per treatment in EWS894, one replicate per treatment in HUVEC [control]), and in FFPE xenograft tissue using nanodroplet cavitation (10 cell line-derived xenograft tissue types)

first: Shelsa

middle: S

last: Marcel

first: Austin

last: Quimby

first: Melodie

middle: P

last: Noel

first: Oscar

last: Jaimes

first: Marjan

last: Mehrab-Mohseni

first: Suud

last: Ashur

first: Brian

last: Velasco

first: James

middle: K

last: Tsuruta

first: Sandeep

last: Kasoji

first: Charlene

last: Santos

first: Paul

last: Dayton

first: Joel

last: Parker

middle: J

first: Samantha

last: Pattenden


title: Cell‐intrinsic functions of Bhlhe40 in activated B cells and TFH cells restrain the GC reaction and prevent lymphomagenesis

status: Public on Oct 25 2021

city: Solna

first: Taras

last: Kreslavsky

address: Nks Bioclinicum, J7:30, Visionsgatan 4

department: Department of Medicine, Solna (MedS)

country: Sweden

institute: Karolinska Institutet

summary: The generation of high-affinity antibodies against pathogens and vaccines requires the germinal center (GC) reaction – a process that relies on a complex interplay between specialized effector subsets of B and CD4 T lymphocytes – GC B cells and T follicular helper (TFH) cells. Intriguingly, several key positive regulators of the GC reaction are common for both cell types. Here, we report that the transcription factor Bhlhe40 is a crucial cell-intrinsic negative regulator affecting both the B and T cell sides of the GC reaction. In activated CD4 T cells, Bhlhe40 was required to restrain proliferation thus limiting the number of TFH cells. In B cells, Bhlhe40 executed its function in the first days after immunization by selectively restricting the generation of the earliest GC B cells but not of early memory B cells or plasmablasts. Conditional Bhlhe40 inactivation confirmed cell-autonomous functions of Bhlhe40 in both GC B and TFH cells, while the GC phenotype was further enhanced upon loss of Bhlhe40 in both cell types. This negative regulation of the GC reaction by Bhlhe40 was of crucial importance, as Bhlhe40-deficient mice with progressing age succumbed to a B cell lymphoma characterized by the accumulation of monoclonal GC B-like cells and polyclonal TFH cells in various tissues.

overall_design:
5 samples from 5 mice:
Bhlhe40-/- lymphoma cells sorted from a sick Bhlhe40-/- mouse
Bhlhe40-/- lymphoma cells sorted from a sick Bhlhe40-/- mouse
Bhlhe40-/- lymphoma cells sorted from a sick Bhlhe40-/- mouse
Bhlhe40-/- lymphoma cells sorted from a sick Bhlhe40-/- mouse
Bhlhe40-/- lymphoma cells sorted from sick secondary recipient mouse (Rag2-/-)

first: René

last: Rauschmeier

first: Annika

last: Reinhardt

first: Charlotte

last: Gustafsson

first: Vassilis

last: Glaros

first: Josefine

last: Dunst

first: Artem

middle: V

last: Artemov

first: Reshma

last: Taneja

first: Igor

last: Adameyko

first: Robert

last: Månsson

first: Meinrad

last: Busslinger


title: Gene expression profile of HSCs from Angptl2fl/fl or Cdh5-Cre;Angptl2fl/fl mice

city: shanghai

first: wenqian

last: yang

address: 280 South Chongqing Road

institute: Shanghai Jiaotong University School of Medicine

summary: To identify the intracellular targets of endothelial cell-specific ANGPTL2 that control HSC stemness, HSCs from Angptl2fl/fl or Cdh5-Cre;Angptl2fl/fl  were sorted, followed by the extraction of total RNA and subjected to the RNA-sequencing.

overall_design: HSCs from Angptl2fl/fl or Cdh5-Cre;Angptl2fl/fl  were sorted to measure gene expression

first: J

last: Zheng

first: Z

last: Yu

first: W

last: Yang


title: Biliary organoids uncover delayed epithelial development and barrier function in biliary atresia.

city: Cincinnati

first: Jorge

middle: A

last: Bezerra

state: OH

address: 3333 Burnet Ave.

department: Gastroenterology, Hepatology & Nutrition

institute: Cincinnati Children's Hospital Medical Center

summary:
Background: RNASeq was performed on organoids derived from livers of normal healthy donors and patients with biliary atresia to characterize transcriptomic signatures.
Methods: Organoids generated from livers of normal healthy donors and patients with biliary atresia were cultured either in expansion (undifferentiated: 3 NCOs and 11 BACOs) or differentiation medium (differentiated: 3 BACOs). Liver tissues obtained from deceased-donor subjects served as normal controls (N=3). Total RNA was isolated from organoids and liver biopsy tissue specimens.
Results: Organoids from patients with biliary atresia showed abnormal cell polarity, loss of tight junctions, increased permeability and decreased expression of genes related to epidermal growth factor (EGF)- and fibroblast growth factor 2 (FGF2)-signaling. When treated with EGF+FGF2, biliary atresia organoids expressed differentiation and functional markers with restored cell polarity.
Conclusion: Organoids from biliary atresia are viable and have evidence of halted epithelial development. The induction of developmental markers, improved cell‐cell junction, and decreased epithelial permeability by EGF and FGF2 identifies potential strategies to promote epithelial maturation and function.

overall_design: RNA-seq was performed using organoids derived from livers of normal donors and patients with biliary atresia. Liver tissues from normal donors were also subjected to RNA-sequencing.

first: Surya

last: Amarachintha

first: Reena

last: Mourya

first: Hiroaki

last: Ayabe

first: Li

first: Zhenhua

last: Luo

first: Xiaofeng

last: Li

first: Unmesha

last: Thanekar

first: Pranavkumar

last: Shivakumar


title: K27M and K36M mutations on non canonical Histone 3.3 promote redistribution of antagonistic chromatin marks, disrupted development, and tumorigenesis

city: Montréal

first: Claudia

middle: L

last: Kleinman

state: Québec

address: 3999 Côte Ste-Catherine Road

department: Human Genetics

institute: Lady Davis Institute for Medical Research

type: Non-coding RNA profiling by high throughput sequencing

summary: We conducted RNA-seq analysis to identify genes that are differentially expressed in H3K27M and H3K36M oncohistones compared to wt and control eye tissue (eye discs), followed by smRNA-seq profiling based on our results and to confirm upregulation of piRNAs

overall_design: 3 data types (RNA-seq, smRNA-seq and ChIP-seq data). RNA-seq and smRNA-seq experiments has 12 samples, which is composed of 3 replicates of 4 genotypes (H3K27M, H3K36M, histone WT and control eye tissue (Yw)). Additional RNA-seq RNAi experiments has been performed on 10 sets (3 replicates each, 30 samples total). H3K27me3 and H3K36me2 ChIP-seq was also performed (14 samples)

first: Amel

last: Chaouch

first: Johannes

last: Berlandi

first: Felice

last: Frey

first: Carol

middle: C

last: Chen

first: Shireen

last: Badini

first: Dylan

last: Marchione

first: Benjamin

last: Garcia

first: Ashot

last: Harutyunyan

first: Brian

last: Krug

first: Haifen

first: Jacek

last: Majewski

first: Steven

last: Hébert

first: Astrid

last: Jeibmann

first: Martin

last: Hasselblatt

first: Paul

last: Lasko

first: Margret

last: Shirinian

first: Nada

last: Jabado


title: ChIP-sequence analysis of H3K27ac, H3K4me1, and SETD5 in 3T3-L1 preadipocytes.

city: Akita

first: Yoshihiro

last: Matsumura

state: Akita

address: Hondo 1-1-1

department: Biochemistry and Metabolic Science

institute: Akita University Graduate School of Medicine

summary: Enhancer activation is essential for cell-type specific gene expression during cellular differentiation, however, how enhancers transition from a hypoacetylated “primed” state to a hyperacetylated-active state is incompletely understood. Here, we show SET domain-containing 5 (SETD5) forms a complex with NCoR-HDAC3 co-repressor that prevents histone acetylation of enhancers for two master adipogenic regulatory genes Cebpa and Pparg early during adipogenesis. The loss of SETD5 from the complex is followed by enhancer hyperacetylation. SETD5 protein levels were transiently increased and rapidly degraded prior to enhancer activation providing a mechanism for the loss of SETD5 during the transition. We show that induction of the CDC20 co-activator of the ubiquitin ligase leads to APC/C mediated degradation of SETD5 during the transition and this operates as a molecular switch that facilitates adipogenesis.

overall_design: ChIP using anti-H3K27ac, anti-V5, anti-H3K27ac, or anti-SETD5 antibody followed by next-generation sequencing.


title: Gene expression data from human breast cancer MCF-7 cells treated with siRNA targeting OCT1

first: Kotaro

last: Azuma

address: 7-3-1, Hongo, Bunkyo-ku

institute: University of Tokyo

summary: To evaluate the effect of OCT1 in breast cancer cells, expression of OCT1 was knocked down in MCF-7 cells by small interfering RNA (siRNA). Microarray analysis was performed to analyze gene expression profiles of these cells.

overall_design: MCF-7 cells were treated with two specific siRNAs targeting OCT1 (siOCT1 #1 and siOCT1 #2) and a control siRNA targeting firefly luciferase (siControl). Total RNA was extracted from the cells for gene profiling 48 h after transfection of siRNA. RNA integrity number (RIN) was measured by Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA). It was confirmed that RINs of all RNAs were above 8.6. RNAs extracted from biological triplicates treated with the same siRNA were combined, and subjected to the microarray analysis using Clariom S Array, Human (Affymetrix/Thermo Fisher Scientific, Walthan, MA, USA).


title: Expression data from SETD5-expressing 3T3-L1 cells; ChIP-seq of H3K27ac, H3K4me1, and SETD5 in 3T3-L1 preadipocytes.

overall_design: Refer to individual Series


title: Sutural fibroblasts exhibit the function of vascular endothelial cell upon mechanical strain

city: Beijing

first: Guan

last: Li

email: umemaro@163.com, zzmbysy@sina.com

address: 49 North Garden Road

institute: Peking University Third Hospital

summary: Midfacial hypoplasia is a kind of facial dysplasia. The technique of trans-sutural distraction osteogenesis(TSDO) can promote midface growth so as to ameliorate this symptom.  Here, we used single-cell RNA sequencing to define the rat's cell classification of zygomatic maxillary suture and the changes of cell clusters in the suture before and after seven-day distraction.

overall_design: one sample is from the 7-day-distracted zygomatic maxillary suture (experimental group, distraction osteogenesis group, DO), another sample is from the sham operation zygomatic maxillary suture (controlled group, sham operation controlled group, SC)

first: Zhenmin

last: Zhao

first: Luosha

last: Gu

first: Wei

last: Liang


title: Impact of anti-CD40 treatment on mouse livers

city: Adelaide

first: Feargal

last: Ryan

state: Adelaide

address: North Terrace

country: Australia

institute: SAHMRI

summary: Treating samples with anti-CD40, and antibiotics to establish what transcriptional impact antibiotics is having. Anti-CD40 was found to induce a strong inflammatory signature. Antibiotics in combination with anti-CD40 attenuated this resulting in a much improved phenotype. However the detectable transcriptional differences were somewhat modest.

overall_design: 20 samples in total. 5 per group. 4 groups, which are Control. Contorl + ABX. Anti-CD40, Anti-CD40 + ABX. All are from individual mice. No longitudinal measurements.

first: David

last: Lynn

first: Stephen

last: Blake


title: Genome-wide expression analysis of C. elegans nematodes overexpressing the transcription factor grh-1

status: Public on Oct 24 2021

city: Schwerzenbach

first: Fabian

last: Fischer

address: Schorenstrasse 16

department: Department of Health Sciences and Technology

country: Switzerland

institute: ETH Zurich

summary: We report identification of possible GRH-1 target genes in C. elegans, by analyzing changes in overall transcriptome following stable overexpression of this transcription factor.

overall_design:
In total six samples (independent biological replicates) were analysed. Three samples were derived from wild-type N2 nematodes and three from a strain stably overexpressing grh-1.
contributor: Functional Genomics Center Zurich (FGCZ)

first: Giovanna

last: Grigolon

first: Michael

last: Ristow


title: RNA-seq analysis in young and senescent endothelial cells

city: Bunkyo-ku

first: Goro

last: Katsuumi

state: Tokyo

address: Hongo 2-1-1

institute: Juntendo University

summary: To investigate how the pattern of gene expression is changed in endothelial cells by cellular senescence, RNA-seq analysis was carried out with human umbilical vein endothelial cells(HUVECs)

overall_design: RNA-seq

first: Masayoshi

last: Suda

first: Tohru

last: Minamino


title: Low responders to endurance training exhibit greater atrophy

city: Robina

first: Jamie-Lee

middle: May

last: Thompson

state: QLD

address: 14 University Drive

department: Health Sciences and Medicine

institute: Bond University

summary: Divergent skeletal muscle phenotypes result from chronic resistance-type versus endurance-type contraction, reflecting the principle of training specificity. However, it is unclear whether there is a common set of genetic factors that influence skeletal muscle adaptation to disuse. Female rats were obtained from out-bred lines selectively bred from high responders to endurance training (HRT) or low responders to endurance training (LRT; n=6/group; generation 19). Both groups underwent 3 d of hindlimb immobilization to induce atrophy of the plantaris and soleus muscles prior to comparison to non-immobilization controls of the same genotype. RNA sequencing was performed to identify Gene Ontology Biological Processes with differential (LRT vs HRT) gene set enrichment. Running distance, determined well in advance of hindlimb immobilization, increased in response to aerobic training in HRT but not LRT. The atrophy response to hindlimb immobilization was exaggerated in LRT versus HRT. There were between-group differences for 140 processes in plantaris muscle and 118 processes in soleus muscle. In conclusion, low responders to aerobic endurance training exhibited exaggerated atrophy, and this was associated with differential gene expression. Thus, our findings suggest that genetic factors that underpin aerobic training maladaptation may also dysregulate the transcriptional activity of biological processes that contribute to adaptation to hindlimb immobilization.

overall_design: RNA-seq of 14-month old female LRT/HRT rats (generation 19) following 3 days atrophy of plantaris and soleus compared to controls (total=24 samples; n=6/group)

first: Kevin

last: Ashton

first: Vernon

middle: G

last: Coffey

first: Daniel

last: West

middle: M


title: RNA-sequencing Analysis of GBM Neurosphere Cells with Fluoxetine or DMSO treatment

city: La Jolla

first: Paul

last: Mischel

state: CA

address: 9500 Gilman Drive, CMME-2021

institute: University of California, San Diego

summary: To determine fluoxetine-induced transcriptional signatures in GBM cancer cells, we performed RNA-sequencing analysis of three GBM patient-derived neurosphere cancer cell lines after fluoxetine or DMSO treatment. Genes with differential expression and associated transcriptional signatures were analyzed and identified in three cancer cell lines.

overall_design: mRNA profiles of three GBM neurosphere lines with 5 µM fluoxetine or DMSO treatment for 42 hours

first: Junfeng

last: Bi


title: Expression data from SETD5-expressing 3T3-L1 cells.

first: Yoshihiro

last: Matsumura

summary: SETD5 target genes in 3T3-L1 cells were analyzed.

overall_design: timecourse


title: Dirty mice as an alternative for preclinical vaccine testing

status: Public on Oct 23 2021

city: Minneapolis

first: Ingunn

last: Stromnes

state: Minnesota

address: 2-186 Wallin Medical Biosciences Building, 2101 6th St SE

department: Medical School

institute: University of Minnesota

summary: Laboratory mice comprise an inexpensive and expeditious model organism for preclinical vaccine testing; however, vaccine immunogenicity often fails to adequately translate to humans. Recent reports indicate that reconstituting physiologic microbial experience to specific pathogen free (SPF) mice induces durable immunological changes that better recapitulate the human immune system. We examined the impact of microbial experience on responses to vaccination after cohousing laboratory mice with pet store mice. We demonstrate that human transcriptional responses to influenza vaccination are better recapitulated in cohoused mice. Induction of humoral responses by vaccination was dampened in cohoused mice and resulted in poor control upon challenge. Additionally, the establishment of protective heterosubtypic T cell immunity was compromised in cohoused mice. In summary, SPF mice exaggerated both humoral and T cell protection induced by influenza vaccines compared to cohoused mice, suggesting that reconstituting microbial experience in laboratory mice through cohousing may better inform preclinical vaccine testing.

overall_design:
SAMPLE GROUP 1: Pet store mice were purchased from various Twin Cities area pet stores. Pet store mice were cohoused with 8-week-old female C57BL/6 (The Jackson Laboratory). Cohousing occurred within a BSL-3 facility. C57BL/6 mice were cohoused for 60 days, bled for flow cytometry analysis and screened for infectious agents using EZ-spot and PCR Rodent Infections Agent (PRIA) array methods (Charles River Laboratories). Age-matched mice were maintained in SPF facilities.
SAMPLE GROUP 2: For IAV infections, mice were anesthetized using a weight-based dose of ketamine/xylazine delivered intraperitoneally (i.p.). Mice were vaccinated intranasally (i.n.) with 1000 PFU of X31 or vaccinated intramuscularly (i.m.) with 180 ug of 2019-2020 seasonal quadrivalent influenza vaccine (Sanofi Pasteur) with or without 25 uL AddaVax (InvivoGen). For challenge, mice were infected i.n. with 1000 PFU of PR8.
Whole lungs were harvested and RNA was extracted using AllPrep DNA/RNA kit (Qiagen). The cDNA library was prepared using strand-specific RNA-sequencing protocols. Samples were run on an Illumina NovaSeq (50 bp paired-end). We obtained an average of 27 million read pairs per sample. Sequencing reads were mapped to the mouse genome (GRCm38) using Bowtie aligner (bowtie2 version 2.3.4.1) with local mode, -L 22 and -N 1 parameters (Langmead and Salzberg, 2012). Reads were assigned to Ensembl gene models (Mus_musculus.GRCm38.87.gtf) with featureCounts of the Subread software package (version 1.5.1) (Liao et al., 2014). The reads count matrices were organized corresponding to experimental design and used for subsequent statistical analysis using the bioconductor package edgeR (version 3.24.3) (McCarthy et al., 2012; Robinson et al., 2010). The raw reads count table were normalized by using default method in the package prior to generating statistics. Multidimensional scaling was performed with edgeR using the top 500 differentially expressed genes across samples. The regression model in the edgeR package with block design and interaction model was used for statistical analysis to select the corresponding significant genes. Gene ontology analysis was performed using Panther on genes in each cluster with an adjusted p value <0.01 and LogFC >0.5.
Mouse PBMCs were isolated using Ficol-Paque PREMIUM (Millipore Sigma) and RNA was extracted using RNeasy Micro Plus Kit (Qiagen). The cDNA library was prepared using strand-specific RNA-sequencing protocols. Samples were run on an Illumina NovaSeq (150 bp paired-end). We obtained an average of 35 million read pairs per sample. Sequence processing and mapping was performed as described above. The normalized reads table of mouse blood samples were reformatted to meet the requirements for the subsequent GSEA analysis (Mootha et al., 2003; Subramanian et al., 2005). The gene lists were prepared from human vaccination data and merged into an immune geneset (c7.immune.datasets.gmt) to generate a customized geneset (c7.custom.immune.datasets.gmt) (Mootha et al., 2003; Subramanian et al., 2005). The mouse datasets originated from either SPF or dirty mouse models were computed against the customized geneset by using desktop GSEA analysis engine with default parameters except the enrichment plot generation.

first: Jessica

last: Fiege

first: Katherine

middle: E

last: Block

first: Mark

last: Pierson

first: Hezkiel

last: Nanda

first: Frances

last: Shepherd

first: Clayton

last: Mickelson

first: J

last: Stolley

first: William

last: Matchett

first: Sathi

last: Wijeyesinghe

last: Meyerholz

first: Vaiva

last: Vezys

first: Steven

last: Shen

first: Sara

last: Hamilton

last: Masopust

first: Ryan

last: Langlois


title: Expression data from rice inflorescences of the sro mutant and wild type

first: Xu

last: wei

state: Shanghai

address: 800 Dong Chuan Road

department: Life Science

institute: SJTU

summary:
Plant organ primordia develop into final size through accelerated cell proliferation and cell expansion. During the early flower development, the size of plant reproductive organs is precisely regulated by numerous genes influencing either or both of these two processes.
SRO, a C2H2 Zinc finger transcription factor orthologous to Arabidopsis SUPERMAN in rice, plays a critical role in regulating the reproductive organ size.We used microarrays to detail the expression of genes that were under the control of SRO during reproductive organ development in rice

overall_design: SRO expression reaches a peak at stage Sp7 (inflorescence length 4-5 mm) when stamen and carpel were initiated in most spikelets. We collected 4-5mm inflorescence of sro and wild type (Japonica variety 9522) in the paddy field, three biological replicates each. Total RNA were extracted using Trizol method and hybridized on Affymetrix microarrays.

last: Wei


title: CDC42 controlled apical-basal polarity regulates intestinal stem cell to transit amplifying cell fate transition via YAP-EGF-mTOR signaling

first: Zheng

last: Zhang

address: 8760 Sturbridge Dr

department: Division of Experimental Hematology and Cancer Biology

summary: Epithelial polarity is controlled by a polarity machinery including the Rho GTPase CDC42 and Scribble/PAR. By using intestinal stem cell (ISC)-specific deletion of CDC42 in Olfm4-IRES-eGFPCreERT2;CDC42flox/flox mice, we found that ISC-initiated CDC42 loss caused a drastic hyper-proliferation of transit amplifying (TA) cells and disrupted epithelial polarity. CDC42-null crypts displayed expanded TA cell and diminished ISC populations, accompanied by elevated hippo signaling via YAP/TAZ - Ereg and mTOR activation, independent from canonical Wnt signaling. YAP/TAZ conditional knockout restored the balance of ISC/TA cell populations and crypt proliferation but did not rescue the polarity in CDC42-null small intestine. mTOR or EGFR inhibitor treatment of CDC42 KO mice exhibited similar rescuing effects without affecting YAP/TAZ signaling. Inducible ablation of Scribble in intestinal epithelial cells mimics that of CDC42 KO defects including crypt hyperplasia and hippo signaling activation. Mammalian epithelial polarity regulates ISC and TA cell fate and proliferation via a hippo-Ereg-mTOR cascade.

overall_design: 1 control, 1 mutant, 1 rescue

first: Yi

last: Zheng


title: NatB impacts growth and the response to osmotic stress in Arabidopsis

status: Public on Oct 22 2021

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

department: ZMF

institute: University Heidelberg

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


title: Multi-omics analysis of spatially distinct stromal cells reveals tumor-induced O-glycosylation of the CDK4-pRB axis in fibroblasts at the invasive tumor edge

city: Stanford

first: Gina

last: Bouchard

address: 318 Campus Drive, Clark Center, W-250

institute: STANFORD UNIVERSITY

summary: The invasive leading edge represents a potential gateway for tumor metastasis. The role of fibroblasts from the tumor edge in promoting cancer invasion and metastasis has not been comprehensively elucidated. We hypothesize that crosstalk between tumor and stromal cells within the tumor microenvironment (TME) results in activation of key biological pathways depending on their position in the tumor (edge vs core). Here we highlight phenotypic differences between tumor-adjacent-fibroblasts (TAF) from the invasive edge and tumor core fibroblasts (TCF) from the tumor core, established from human lung adenocarcinomas. A multi-omics approach that includes genomics, proteomics, and O-glycoproteomics was used to characterize crosstalk between TAFs and cancer cells. These analyses showed that O-glycosylation, an essential post-translational modification resulting from sugar metabolism, alters key biological pathways including the cyclin-dependent kinase 4 and phosphorylated retinoblastoma protein (CDK4-pRB) axis in the stroma and indirectly modulates pro-invasive features of cancer cells. In summary, the O-glycoproteome represents a new consideration for important biological processes involved in tumor-stroma crosstalk and a potential avenue to improve the anti-cancer efficacy of CDK4 inhibitors.

overall_design:
mRNA profiles of human LUAD cell line HCC827 and primary fibroblasts isolated from different tumor regions, normal fibroblasts (NFs) >5cm away from the tumor, Tumor-Adjacent Fibroblasts from the tumor edge and Tumor Core Fibroblasts (TCFs)  from the tumor core. Monocultures of each group are used as the experimental control with each group having 3 independent biological replicates.
**RAW DATA not provided**

first: Fernando

last: Marques

first: Loukia

last: Karacosta

first: Weiruo

first: Abel

last: Bermudez

first: Nicholas

last: Riley

first: Sushama

last: Varma

first: Lindsey

last: Mehl

first: Jalen

last: Benson

first: Joseph

middle: B

last: Shrager

first: Carolyn

last: Bertozzi

first: Sharon

last: Pitteri

first: Amato

last: Giaccia

first: Sylvia

last: Plevritis


title: Transcriptomic profilling of cisplatin sensitive and  resistance in signet ring KATOIII gastric cancer cells

city: Chiangmai

first: Supachai

last: Yodkeeree

state: Chiangmai

address: 110 Intrawarorote

country: Thailand

institute: Chiangmai University

summary:
Purpose: The goal of our study is to identify the differentially expressed genes between cispaltin sensitive and cisplatin resistance gastric cancer cell line.
Methods: Transcriptome sequencing of cisplatin sensitive and cisplatin resistance KATOIII cells were generated by  Illumina HiSeq TM, for triplicates
Results : Using an optimized data analyzed workflow, we mapped 57773 genes and were found 5966 differentially expressed genes between cisplatin sensitive KATOIII and cisplatin resistance KATO/DDP cell lines.

overall_design: Acquired cisplatin resistance KATO/DDP cell line was established from parental cell line KATOIII by step wise treated with cispaltin over 6months. KATO/DDP cells were maintained in low dose cisplatin. KATO/DDP cells were allowed to grow in drug free media for at least two passages and transcriptomic sequencing was conducted.

first: Nang

last: Phoo


title: anti-TAF7 RIP-Seq identifies RNA species bound by cytoplasmic TAF7 in HeLa TAF7 (WT) cells

city: Bethesda

first: Dinah

middle: S.

last: Singer

address: Building 10, Room 4B-17

department: Division of Cancer Biology

institute: National Cancer Institute

summary: We perform TAF7 RIP-Seq to generate a transcriptome-view of RNA targets bound by TAF7

overall_design: We immunoprecipitated cytoplasmic RNA from HeLa TAF7 (WT) cells, with an anti-TAF7 antibody, followed by high-throughput RNA-Seq (TAF7 RIP-Seq).

first: Dan

last: Cheng


title: Characterization of nucleocapsid-RNA interactions in Rift Valley fever virus infected cells

city: Missoula

first: J. Stephen

last: Lodmell

state: MT

address: 32 Campus Drive

department: Division of Biological Sciences

institute: University of Montana

summary: Crosslinking immunoprecipitation and sequencing was used to characterize nucleocapsid-RNA interactions in Rift Valley fever virus infection. This data set includes illumina HiSeq paired-end reads of Rift Valley fever virus infected HEK293 cells. The sequencing libraries were generated from nucleocapsid-bound RNAs.

overall_design: Samples are prepared at 12-, 24-, and 36-hour post-infection. Each timepoint included two biological replicates of experimental treatment and one size-matched control.

first: Miyuki

last: Hayashi

first: Jean-Marc

last: Lanchy

first: J


title: Reactive astrocytes in ALS models display dysregulated intron retention

city: London

first: Oliver

last: Ziff

state: London

address: 1 Midland Road

country: United Kingdom

institute: Francis Crick Institute

summary: Reactive astrocytes are implicated in Amyotrophic Lateral Sclerosis (ALS), although the mechanisms controlling reactive transformation are unknown. We show that decreased intron retention (IR) is common to human induced pluripotent stem cell (hiPSC)-derived astrocytes carrying VCP, C9orf72 and SOD1 ALS-causing mutations as well as astrocytes stimulated to undergo reactive transformation. Notably, transcripts with decreased IR and increased expression are overrepresented in reactivity processes including cell-adhesion, stress-response, and immune-activation. We examined astrocyte translatome sequencing (TRAP-seq) from a SOD1 mouse model, which revealed a significant number of transcripts with reduced IR in ALS are upregulated in translation. Using nucleo-cytoplasmic fractionation of VCP astrocytes coupled with mRNA sequencing and proteomics, we identify that decreased IR in nuclear-detained transcripts is associated with increased cytoplasmic expression of genes and proteins encoding regulators of reactivity - indicating nuclear-to-cytoplasmic translocation and translation of spliced reactivity-related transcripts. These results provide novel insights into the molecular factors controlling the reactive transformation of ALS astrocytes.

overall_design: iPSC-derived astrocyte mRNA profiles of 2 control and 2 VCP mutant lines

first: Taha

last: Doaa

first: Crerar

last: Hamish

first: Clarke

last: Benjamin

first: Charkrabarti

last: Anob

first: Kelly

last: Gavin

first: Nicholas

last: Luscombe

first: Rickie

last: Patani

first: Jacob

last: Neeves

first: Guilia

last: Tyzack


title: The Nuclear Transcription factor TAF7 is a Cytoplasmic RNA Chaperone


title: FLAG RIP-Seq identifies RNA species bound by cytoplasmic TAF7 in HeLa TAF7 (WT) cells

summary: We perform FLAG RIP-Seq to generate a transcriptome-view of RNA targets bound by TAF7

overall_design: We immunoprecipitated cytoplasmic RNA from HeLa TAF7 (WT) cells, with an anti-FLAG antibody, followed by high-throughput RNA-Seq (FLAG RIP-Seq).


title: SUMOylation of Linker Histone H1 Drives Chromatin Condensation and Restriction of Embryonic Cell Fate Identity [RNA-seq]

city: Rehovot

first: Noa

last: Novershtern

address: Weizmann Institute

department: Molecular Genetics

country: Israel

institute: Weizmann Institute of Science

summary: The fidelity of the early embryonic program is underlined by tight regulation of the chromatin. Yet, our understanding of how the chromatin is organized to prohibit the reversal of the developmental program remains limited. Specifically, the totipotency to pluripotency transition marks one of the most dramatic events to the chromatin, yet the nature of histone changes and regulation underlying this process are only partly characterized. Here we show that linker histone H1 is post-translationally modulated by SUMO2/3, which facilitates its fixation onto ultra-condensed heterochromatin in embryonic stem cells (ESCs). Upon SUMOylation depletion, the chromatin becomes de-compacted and H1 is evicted, leading to totipotency reactivation. Further, we show that H1 and SUMO2/3 jointly mediate the repression of totipotent elements. Lastly, we demonstrate that preventing SUMOylation on H1 abrogates its ability to repress totipotency in ESCs. Collectively, our findings unravel a critical role for SUMOylation of H1 in mediating chromatin repression and desolation of the totipotent identity.

overall_design: RNA-seq was performed to measure changes in mRNA expression in DOX-induced Ubc9 depleted mESCs and their control, and in histone H1 TKO (H1.2, H1.3, H1.4) mESCs and their control.

first: Daoud

last: Sheban

first: Tom

last: Shani

first: Yifat

last: Merbl

last: Hanna


title: SUMOylation of Linker Histone H1 Drives Chromatin Condensation and Restriction of Embryonic Cell Fate Identity [ATAC-seq]

overall_design:
ATAC-seq was measured in Ubc9-depleted mESCs and their isogenic control, and in H1-Triple- KO mESCs (H1.2, H1.3, H1.4)  and their control. Two replicates were generated from each condition.
Please note that each processed data file was generated from both replicates and is linked to the corresponding *replicate 1 sample records.

middle: H


title: HSF1 facilitates lymphatic metastasis of bladder cancer via a novel PRMT5-WDR5-dependent transcriptional program

city: Guangzhou

first: Ming

last: Huang

address: Yanjiang West Road

institute: Sun Yat-sen Memorial Hospital

summary:
To further identify the underlying mechanisms of HSF1 in LN metastasis, we performed genome-wide RNA expression profile screening in which we compared gene expression profiles in HSF1-knockdown and control T24 cells
To further identify the underlying mechanisms of HSF1 in LN metastasis, we performed genome-wide RNA expression profile screening in which we compared gene expression profiles in HSF1-knockdown and control UM-UC-3 cells

overall_design:
Bladder cancer cells T24 were treated with SiRNA or control  for 48h, respectively. The RNA of the treated cells was extracted and sequenced on Illumina platform and 100-bp paired-end reads were generated.
Bladder cancer cells UM-UC-3 were treated with SiRNA or control  for 48h, respectively. The RNA of the treated cells was extracted and sequenced on Illumina platform and 100-bp paired-end reads were generated.

first: Wen

last: Dong

first: Xu

last: Chen

first: Tianxin

last: Lin


title: Integrated Analysis of Hub Genes and MicroRNAs in Human Placental Tissues from In Vitro Fertilization-Embryo Transfer

status: Public on Oct 21 2021

city: Zhengzhou

first: Shuheng

last: Yang

state: Henan

address: Zhengzhou, No. 7 Kangfuqian Street, Erqi

institute: Third Affiliated Hospital of Zhengzhou University

overall_design: Refer to individual Series


title: SUMOylation of Linker Histone H1 Drives Chromatin Condensation and Restriction of Embryonic Cell Fate Identity


title: Integrated Analysis of Hub Genes and MicroRNAs in Human Placental Tissues from In Vitro Fertilization-Embryo Transfer [RNA-seq]

summary: Next generation sequencing was perfomed to identify differentially expressed gene in Placental tissue samples from IVF-ET assisted or natural conceived pregnancies

overall_design: Placental tissue samples were collected from women who underwent caesarean deliveries after IVF-ET assisted or natural conceived pregnancies

first: Wei

last: Zheng

first: Cheng

first: Ruowen

last: Zu


title: Integrated Analysis of Hub Genes and MicroRNAs in Human Placental Tissues from In Vitro Fertilization-Embryo Transfer [miRNA-seq]

summary: Next generation sequencing was perfomed to identify differentially expressed micro-RNA in Placental tissue samples from IVF-ET assisted or natural conceived pregnancies


title: gene expression of aorta of ApoE KO mice after Gpnmb vaccine treatment

city: Niigata

first: Masayoshi

last: Suda

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

department: Department of Cardiovascular Biology and Medicine

institute: Niigata University

summary: Accumulation of senescent cells in various tissues has been reported to have a pathological role in age-associated diseases. Inhibition of cellular aging signals prevents the onset of age-associated pathology, but there is a risk of promoting carcinogenesis. Elimination of senescent cells (senolysis) was recently reported to reversibly improve pathological changes related to aging in aged mice without increasing the development of cancer. Here we report that glycoprotein nonmetastatic melanoma protein B (Gpnmb) could be a molecular target for senolytic therapy. Elimination of Gpnmb-positive cells by vaccination improved atherosclerosis.

overall_design: We fed the HFD to ApoE KO mice from 4 weeks of age, administered Gpnmb vaccine or control vaccine at 8 weeks of age, and analyzed these mice at 16 weeks.

first: Goro

last: Katsuumi

first: Tohru

last: Minamino