title: Gene expression profiling using tumor tissue grown in C57 mice exposed to 4 °C or 30 °C

city: STOCKHOLM

first: Kayoko

last: Hosaka

state: Solna

address: Solnavägen 9

department: MTC

institute: Karolinska institutet

summary: To study tumor and tumor microenvironment alteration in different temperature exposure, we performed gene expression profiling analysis using tumor tissues isolated from tumor-bearing mice housed at 30 °C or  4 °C.

overall_design: The tumor-bearing mice inoculated with MC38 mouse tumor cell lines were housed at 30 °C or  4 °C for two weeks. Removed tumor tissues were subjected to the RNA-seq. Differential expression analysis between three 30 °C and two 4 °C samples was compared.

first: Yunlong

last: Yang

first: Xiaoting

last: Sun


title: Bulk RNA-sequencing of FUS H517Q and healthy iPSC-derived motor neurons

status: Public on May 20 2022

city: Exeter

first: Akshay

last: Bhinge

address: Stocker Road

department: CBS

country: United Kingdom

institute: Living Systems Institute, University of Exeter

type: Expression profiling by high throughput sequencing

summary:
We sought to investigate changes in gene expression levels including changes in pri-microRNAs in FUS H517Q motor neurons
Motor neurons were differentiated from patient-derived FUS H517Q and healthy iPSCs, and harvested at day 30. We performed gene expression profiling analysis using data obtained from bulk RNA-seq.

overall_design: Comparative gene expression profiling using RNA-seq analysis of FUS H517Q and healthy motor neurons.

first: Sophie

last: Hawkins

first: Seema

last: Namboori


title: Effect of intervention with AAV8-scFv-E06 on FPC diet induced transcriptomic chnages in whole liver tissue

city: Charlottesville

first: Clint

last: Upchurch

email: cmu3yz@virginia.edu, nl2q@virginia.edu

state: VA

address: 1307 Lane Rd.

department: Pharmacology

country: USA

institute: University of Virginia

summary: To investigate genes regulated by expression scFv-E06 in the liver of mice fed FPC diet

overall_design: Mice were inncolated with AAV8-scFv-E06 or AAV8-GFP i.v. after 6 weeks on FPC diet. Mice were fed for an additional 14 weeks prior to extraction of RNA from whole liver tissue.

middle: M

first: Scott

last: Yeudall

first: Caitlin

last: Pavelec

first: Dennis

last: Merk

first: Jan

last: Greulich

first: Mohan

last: Manjegowda

first: Shyam

middle: S

last: Raghavan

first: Irina

last: Bochkis

first: Michael

last: Scott

first: Edward

last: Perez-Reyes

first: Norbert

last: Leitinger


title: Effect of truncated OxPAPC, full-length OxPAPC, and OxPAPC on AML12 hepatocytes.

summary: To investigagte the differnetial regultion of gene expression by truncated OxPAPC, full-length OxPAPC, or OxPAPC.

overall_design: AML12 hepatocytes were treated for four hours with either truncated OxPAPC, full-length OxPAPC, or OxPAPC (100 ug/mL).


title: Generation of functional human oligodendrocytes from dermal fibroblasts by direct lineage conversion

city: Stanford

first: Cheen Euong

last: Ang

state: CA

address: 265 Campus Drive, G3145

institute: Stanford University

summary: We report the generation of myelinating human oligodendrocytes from dermal fibroblasts using a direct lineage conversion technique.

overall_design: Examination of human oligodendrocytes from dermal fibroblasts generated with [OLIG2, SOX10, ASCL1, NKX2.2, NKX6.1], [OLIGX, SOX10, ASCL1, NKX2.2], [OLIGX, SOX10, ASCL1, NKX2.2, P53DD] in comparison to dermal fibroblasts, human primary oligodendrocytes, and human iPS cell-derived oligodendrocytes.

first: Hiroko

last: Nobuta

first: Marius

last: Wernig

first: Koji

last: Tanabe


title: Fibrillin-1 regulated miR-122 has a critical role in thoracic aortic aneurysm formation

city: Montreal

first: Rongmo

last: Zhang

state: QC

address: 3640 Rue university

department: Anatomy and Cell Biology

country: Canada

institute: McGill University

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

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

platform_organism:
Mus musculus
synthetic construct

overall_design: Refer to individual Series


title: scRNA-seq analysis of the effect IL20RB knock-out in esophageal immune cells of an eosinophilic esophagitis (EoE) mouse model

city: Basel

first: DBM Bioinformatics

last: Core Facility

state: BS

address: Hebelstrasse 20

department: Departement of Biomedicine

country: Switzerland

institute: University of Basel

summary: An EoE mouse model was induced by epicutaneous sensitization and oral challange with ovalbumin. Single-cell RNA-seq was performed to compare CD45+ immune cells from wild-type and IL20RB knock-out mice esophagus samples.

overall_design: Esophagus cell suspensions from five wild-type animals were labeled with BioLegend hashtaging antibodies TotalSeq-B0301 to B0305, while suspensions from five IL20RB knock-out animals were labeled with antibodies TotalSeq-B0306-B0310. All 10 cell suspensions were pooled and sorted for live CD45+ cells. The pooled single cell suspension was loaded on 2 wells from a cartridge of the 10X Genomics Chromium Single Cell Controller for cell capture and library preparation.

first: Tanay

last: Kaymak

last: Niess

first: Julien

last: Roux


title: A critical role of the mechanosensor PIEZO1 in glucose-induced insulin secretion in pancreatic β-cells

city: Malmö

first: Lena

last: Eliasson

address: Jan Waldenströms gata 35

country: Sweden

institute: Lund University Diabetes Centre

summary: PIEZO1 is a mechanosensitive ion channel involved in the regulation of a diverse range of physiological responses. We examined the role of the mechanosensor ion channel PIEZO1 in glucose-induced insulin secretion in pancreatic β-cells. PIEZO1 expression is elevated in β-cells from human donors with type-2 diabetes (T2D) and a rodent T2D model (db/db 48 mouse). Silencing of Piezo1 inhibits glucose-induced Ca2+ signaling and insulin secretion. PIEZO1 translocates from the cytosol and plasmalemma into the nucleus in cells cultured at high glucose, experimental conditions emulating diabetes. The translocation of PIEZO1 into the nucleus in response to hyperglycemia suggests that PIEZO1 might be involved in transcriptional control in addition to serving as a mechanosensor in the plasma membrane. To address this, we performed mRNA sequencing in INS-1 832/13 cells to determine which genes are regulated by Piezo channels. Overall, we found 3292, 1656, and 1920 genes were significantly differentially expressed after silencing Piezo1, Piezo2, or both genes (adj.p-value < 0.05). Among these, the expression of the gene encoding cocaine- and amphetamine-regulated transcript (Cartpt) was increased >15-fold. We confirmed this effect by qPCR, which indicated a corresponding stimulation of expression. In insulin-secreting INS-1 832/13 cells, Cart has been reported to influence the expression and release of insulin. Thus, the impact of PIEZO1 on β-cell function may not be limited to electrical excitability but these changes are likely to operate on a slower timescale than the acute/electrical effects.

overall_design: Examination of mRNA profiles of untreated, treated with non-targeting siRNA, Piezo1-silenced, Piezo2-silenced, Piezo1 and Piezo2 silenced INS-1 cells (4 replicates/5 conditions)

first: Alexandros

last: Karagiannopoulos

first: Yingying

last: Ye

first: Enming

first: Erik

last: Renström


title: Studying the transcriptomic effects of the IL-20 cytokine subfamily on the esophageal epithelium

summary: Esophagus organoids were subjected to a cytokine treatment, and the sample were studied with RNA-sequencing.

overall_design:
Esophagus biopsies were obtained from five healthy individuals and organoids were grown from them. The organoids were subjected to cytokine treatment (IL-20 cytokine subfamily cytokines: IL19, IL20 and IL24) for 24h after 11 days of culture.

>>> Raw data not provided due to patient privacy concerns. <<<

first: Jan


title: Epigenomic and transcriptomic features induced by silencing of ZNF280C in colon cancer cells and  knock-out of Zfp280c in mice [ChIP-Seq, ATAC-Seq]

city: Shenzhen

first: Xing-sheng

last: Shu

state: Guangdong

address: No 3688, Nanhai Avenue

department: Medical School

country: China

institute: Shenzhen University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Znic finger proteins play crucial roles in development and disease, including tumorigenesis. Here, we identifed ZNF280C as a novel oncogenic driver in colorectal cancer, and systematically studied the molecular mechanisms underlying ZNF280C-mediated malignant transformation and progression.

overall_design: RKO colon cancer cells stably expressing a ZNF280C-targeting shRNA controlled by a tetracycline-inducible promoter were treated with or without 1 ug/ml doxycycline for 72 hours, and the cells were harvested for analysis as described below. For transgenic mice experiments, Zfp280c knock-out or wild-type C57BL/6J mice were sacrificed at 12 weeks of age and colon tissues were havested for transriptomic analysis as described below.

first: Xingsheng


title: Epigenomic and transcriptomic features induced by silencing of ZNF280C in colon cancer cells and  knock-out of Zfp280c in mice [RNA-Seq]

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: Overexpression of DDX42 suppresses the altered RNA splicing associated with the K700E mutated SF3B1 in 293T cells

city: Chang Chun

first: Xin

last: Hu

address: 2699 Qianjin road,china

institute: Jilin university

summary: We report the bulk RNA-seq in HEK293T cells transfected with DExD/H ATPase and SF3B1

overall_design: RNA-seq in wild type SF3B1 transfected 293T cells (WT); SF3B1-K700E mutation transfected 293T cells (K700E); 293T cells transfected with SF3B1-K700E and DDX42 (K700E&DDX42);  293T cells transfected with SF3B1-K700E and DDX46 (K700E&DDX46). Each cell type have 5 biological replicates.

first: Bo

last: Zhao

first: Rui

last: Qian

first: Youzhong

last: Wan


title: Gene expression profiles of CD4+ T cells before and after methotrexate treatment in rheumatoid arthritis patients [Microarray]

city: Chiba

first: Shigeru

last: Tanaka

address: 1-8-1 Inohana

department: Allergy and Clinical Immunology

country: Japan

institute: Chiba University

summary: To understand the molecular mechanisms by which methotraxate improves the disease activity in rheumatoid arthritis, CD4+ T cells were obtained before and 3month after methotrexate treatment.

overall_design: 28 treatment naïve rheumatoid arthritis patients participated in the study. Blood samples were obtained before and 3 months after methotrexate treatment. CD4+ T cells were magnetically purified and subjected the DNA microarray analyses.

first: Hiroshi

last: Nakajima


title: RNA-sequencing analysis of db/db mice dorsal wounds treated with programmable mechanical stretch or control patches

city: Boston

first: Aristidis

last: Veves

state: MA

address: 330 Brookline Ave

institute: Beth Israel Deaconess Medical Center

summary: We utilized bulk RNA-seq to profile the mRNA expression in day 10 wounds of db/db mice treated with control no strain patches, strain patches or tegaderm only

overall_design: Full thickness 6mm punch biopsy wounds were inflicted on the back of 12-week old male db/db mice. Immediately after injury, ~30% strain inducing patches, no strain patches, or tegaderm (TD) only were applied onto the wounds. The tissue was collected on Day 10 post-wounding for downstream analyses. mRNA profiles from back skin wounds of TD treated db/db mice (n=5), strain (n=4) and no strain (n=3) were examined.

first: Georgios

last: Theocharidis

first: Xanthi

middle: L

last: Katopodi


title: Single-cell reconstitution reveals persistence of clonal heterogeneity in the murine hematopoietic system

first: Clara

middle: F

last: Alves-Pereira

address: 450 Brookline Avenue, SM958b

department: Cancer Biology

institute: Dana-Farber Cancer Institute


title: Single-cell reconstitution reveals persistence of clonal heterogeneity in the murine hematopoietic system [WES]

summary: We transplanted a single HSC into irradiated mice, creating a clonal hematopoietic system. This allowed us to study mitotically stable allelic imbalances at peripheral compartments (T cells, B cells).

overall_design: Whole exome sequencing (WES) analysis in B and T cells from clonal hematopietic system in vivo was performed to exclude cases of allelic imbalances produced by loss of heterozygosity

first: Nadiya

last: Kubasova

first: Alexander

last: Gimelbrant

first: Vasco

last: Barreto


title: RNA-sequencing analysis of db/db mice dorsal wounds treated with polarized macrophages conditioned media or control loaded bandages

summary: We utilized bulk RNA-seq to profile the mRNA expression in day 10 wounds of db/db mice treated with control alginate bandages or bandages containing conditioned media from M0, M1, M2a and M2c polarized macrophages

overall_design: Full thickness 6mm punch biopsy wounds were inflicted on the back of 16-week old male db/db mice. Immediately after injury, control alginate bandages or bandages containing conditioned media from M0 (CM0), M1 (CM1), M2a (CMA) or M2c (CMC) polarized primary macrophages were applied on the wounds. The bandages were replenished on Day 3 and tissue was collected on Day 10 post-wounding for downstream analyses. mRNA profiles from back skin wounds of control treated db/db mice (n=6), CM0 (n=4), CM1 (n=4), CMA (n=5) and CMC (n=5) were examined.


title: Macrophage response towards infection by the Leishmania-viral endosymbiont duo

status: Public on May 19 2022

city: Epalinges

first: Nicolas

last: Fasel

address: Chemin des Boveresses 155

department: Department of Biochemistry

institute: University of Lausanne

summary: Leishmania RNA virus 1 (LRV1) is a double stranded RNA (dsRNA) virus found in some strains of the human protozoan parasite Leishmania, the causative agent of leishmaniasis, a neglected tropical disease. Interestingly, the presence of LRV1 inside Leishmania constitutes an important virulence factor which worsens leishmaniasis outcome in a type I interferon (type I IFN) dependent manner and contributes to treatment failure. Understanding how macrophages respond towards Leishmania alone or in combination with LRV1 as well as the role that type I IFNs may play during infection is fundamental to oversee new therapeutic strategies. In order to dissect the macrophage response towards infection, RNA Sequencing (RNA-Seq) was performed on murine wild-type (WT) bone marrow derived macrophages infected with Leishmania guyanensis (Lgy) devoid or not of LRV1 (LgyLRV1- and LgyLRV1+ respectively) or co-infected with LgyLRV1- and Lymphocytic choriomeningitis virus (LCMV) for 8 and 24 hours. Additionally, macrophages were treated with type I IFN (IFNα or IFNβ) after 6 hours of infection.

overall_design: Transcriptomic analysis of WT bone marrow derived macrophages (BMDMs) under 5 different conditions and 2 time points. Total number of samples 30, each condition was done in triplicates.

first: Amel

last: Bekkar

first: Nathalie

last: Isorce

first: Tiia

last: Snäkä

first: Stéphanie

last: Claudinot

first: Chantal

last: Desponds

first: Dmitry

last: Kopelyanskiy

first: Florence

last: Prével

first: Marta

last: Reverte

first: Ioannis

last: Xenarios

first: Filipa

last: Teixeira

first: Matteo

last: Rossi


title: Single-cell reconstitution reveals persistence of clonal heterogeneity in the murine hematopoietic system [RNA-seq]

summary: We transplanted a single HSC into irradiated mice, creating a clonal hematopoietic system. Using RNA-Seq on the cDNA of the peripheral compartments (T cells, B cells), we studied mitotically stable transcriptional states of the alleles of the entire transcriptome on the differentiating HSC.

overall_design: Analysis of mitotically stable allelic transcriptional states of murine B and T cells from a clonal hematopietic system in vivo.


title: Lipid Accumulation Induced by APOE4 Impairs Microglial Surveillance of Neuronal-Network Activity

city: Cambridge

first: Hiruy

last: Meharena

address: 43 Vassar St

department: The Picower Institute for Learning and Memory

institute: Massachusetts Institute of Technology

summary: Apolipoprotein E4 (APOE4) is the greatest known genetic risk factor for developing late-onset Alzheimer’s disease and its expression in microglia is associated with pro-inflammatory states. How the interaction of APOE4 microglia with neurons differs from microglia expressing the disease-neutral allele APOE3 is currently unknown. Here, we employ CRISPR-edited induced pluripotent stem cells (iPSCs) to dissect the impact of APOE4 in neuron-microglia communication. Our results reveal that APOE4 induces a distinct metabolic program in microglia that is marked by the accumulation of intracellular neutral lipid stores through impaired lipid catabolism. Importantly, this altered lipid-accumulated state shifts microglia away from homeostatic surveillance and renders APOE4 microglia weakly responsive to neuronal activity. By examining the transcriptional signatures of APOE3 versus APOE4 microglia before and after exposure to neuronal conditioned media, we further established that neuronal soluble cues differentially induce a lipogenic program in APOE4 microglia that exacerbates pro-inflammatory signals. Pharmacological blockade of lipogenesis in APOE4 microglia is sufficient to diminish intracellular lipid accumulation and restore microglial homeostasis. Remarkably, unlike APOE3 microglia that support neuronal network activity, co-culture of APOE4 microglia with neurons disrupts the coordinated activity of neuronal ensembles. We identified that through decreased uptake of extracellular fatty acids and lipoproteins, APOE4 microglia disrupts the net flux of lipids which results in decreased neuronal activity via the potentiation of the lipid-gated K+ channel, GIRK3. These findings suggest that neurological diseases that exhibit abnormal neuronal network-level disturbances may in part be triggered by impairment in lipid homeostasis in non-neuronal cells, underscoring a novel therapeutic route to restore circuit function in the diseased brain.

overall_design: After 4 weeks in culture, APOE3 or APOE4 iMGLs pre-conditioned in unspent neuronal media for 24hrs were further incubated with spheroid conditioned neuronal media for 2 hours. Cells were lysed and harvested for RNA extraction, library preparation and bulk sequencing. Biological triplicates were analyzed for 4 groups: APOE3 vs APOE4 iMGLs with or without exposure to APOE3 spheroid conditioned media (+CM)

first: Matheus

middle: B

last: Victor

first: P

last: Bozzelli

first: Noelle

last: Leary

first: George

last: Samaan

first: Xochitl

last: Luna

first: Mitchell

middle: H

last: Murdock

first: Djuna

last: von Maydell

first: Audrey

last: Effenberger

first: Oyku

last: Cerit

first: Hsin-Lan

last: Wen

first: Liwang

last: Liu

first: Gwyneth

last: Welch

first: Maeve

last: Bonner

first: Li-Huei

last: Tsai


title: Single-Cell RNA Sequencing to Decipher the Immunogenicity of ChAdOx1 nCoV-19/AZD1222 and mRNA-1273 Vaccines in Patients with Autoimmune Rheumatic Diseases

city: Taichung City

first: thh

last: lab

address: 1650 Taiwan Boulevard Sect. 4, Taichung, Taiwan 40705, ROC

country: Taiwan

institute: TCVGH

summary: Objectives: To investigate the differences in efficacy and safety between the vector vaccine ChAdOx1 nCoV-19/AZD1222 (Oxford-AstraZeneca) and mRNA-based vaccine mRNA-1273 (Moderna), and evaluate the impact of anti-rheumatic medications on immunogenicity in patients with autoimmune rheumatic diseases (AIRD). Methods: From September 16 to November 15, 2021, we consecutively enrolled participants aged≥20 years with AIRD who received COVID-19 vaccination. The level of serum IgG antibodies to the SARS-Cov-2 receptor-binding domain on the spike protein S1 subunit was quantified by electrochemiluminescence immunoassay at 4-6 weeks after vaccination. The immunogenicity and adverse reactions between ChAdOx1 nCov-19/AZD1222 and mRNA-1273 were compared.  Results: Of the 243 rheumatic disease patients who received COVID-19 vaccines, 113 and 130 were immunized with AZD1222 and mRNA-1273, respectively. The anti-SARS-CoV-2 IgG seropositivity rate was 78.8% (89/113) for AZD1222 and 83.1% (108/130) for mRNA-1273. The level of anti-SARS-Cov-2 IgG was higher in patients who received mRNA-1273 than in those who received AZD1222. Prednisolone-equivalent dose >5 mg/day, methotrexate (MTX), non-anti-tumor necrosis factor (TNF)-a biologics, and Janus kinase (JAK) inhibitor use were associated with inferior immunogenicity. All reported adverse reactions were minor. More localized pain at the injection site and less fever and chills were observed in patients receiving mRNA-1273 compared with those receiving AZD1222. Rheumatic disease activities after vaccination remained stable in most patients. Conclusions: mRNA-1273 and AZD1222 vaccines exhibited differential immunogenicity and adverse reaction profiles. Our study findings support temporary discontinuation of daily prednisolone dose >5 mg, MTX, non-anti-TNF-a biologics, or JAK inhibitors after COVID-19 vaccination.

overall_design: Examination of 2 different clinical outcome in PBMC of patients with Autoimmune Rheumatic Diseases

first: Yen-Ju

last: Chen

first: Po-Liang

last: Cheng

first: Wen-Nan

last: Huang

first: Hsin-Hua

first: Hong-Wei

first: Jun-Peng

first: Ching-Tsa

last: i Lin

first: Kuo-Tung

last: Tang

first: Wei-Ting

last: Hung

first: Tsu-Yi

last: Hsieh

first: Yi-Hsing

first: Yi-Ming

first: TZU-HUNG

last: HSIAO


title: Using Auxin-inducible-degradation System to Interrogate Tissue-specific Transcriptional Programs of HSF-1 in Lifespan Assurance [HSF-1 transcriptome in the soma]

city: Valhalla

first: Jian

last: Li

state: NY

address: 15 Dana Road

institute: New York Medical College

summary: To determine the transcriptional program of HSF-1 in lifespan assurance in C. elegans, we coupled HSF-1 depletion specifically from the soma by auxin-inducible degron (AID) with RNA-seq analyses in whole animals. Depletion of HSF-1 from the soma was performed by transferring worms that express the E3 ligase TIR1 in somatic tissues and carry AID insertion to the endogenous HSF-1 onto NGM plates containing 1mM auxin (indole- 3-acetic acid, Sigma). The mock treatment was done by transferring worms to plates only containing the vehicle ethanol (EtOH). We analyzed the transcriptomic changes by RNA-seq upon soma-specific depletion of HSF-1 initiated at young adult stage for different length of time. We included the strains that only express TIR1 but do not have degron insertion at HSF-1 (CA1200) to control for the effects of auxin treatment and AID insertion into HSF-1. We performed analyses in the wild-type background (JTL611) as well as in the longlived, germline stem cell (GSC) arrested glp-1(e2141) mutant (JTL667). The AID model in fem-3(q20) mutant (JTL670) was included as a control for JTL667. JTL670 (fem-3) is sterile at 25°C as JTL667 (glp-1) but has normal lifespan.

overall_design: Experiment type: RNA-seq. Biological Source: strains: JTL611, CA1200, JTL667 and JTL670. Developmental stage: young adult. Experimental Factors: temperature: 20 degree celsius for JTL611 and CA1200, 25 degree celsius for the temperature-sensitive JTL667 (glp-1) and JTL670 (fem-3) mutants.


title: GRHL2 enhances phosphorylated estrogen receptor DNA binding and regulates ER-mediated transcriptional activation and repression[ChIP-seq]

city: Madison

first: Elaine

last: Alarid

state: WI

address: 1111 Highland Avenue

department: McArdle Laboratory for Cancer Research, Department of Oncology and Carbone Comprehensive Cancer Center

institute: University of Wisconsin - Madison

summary: Phosphorylation of estrogen receptor α (ER) at serine 118 (pS118-ER) is induced by estrogen and is the most abundant post-translational mark associated with a transcriptionally active receptor. Cistromic analysis of pS118-ER from our group found enrichment of the GRHL2 motif near pS118-ER binding sites. In this report we use cistromic and transcriptomic analyses to interrogate the relationship between GRHL2 and pS118-ER. We found that GRHL2 is bound to chromatin at pS118-ER/GRHL2 co-occupancy sites prior to ligand treatment, and GRHL2 binding is required for maximal pS118-ER recruitment. pS118-ER/GRHL2 co-occupancy sites were enriched at active enhancers marked by H3K27ac and H3K4me1, along with FOXA1 and p300. Transcriptomic analysis yielded four subsets of ER/GRHL2 co-regulated genes revealing that GRHL2 can both enhance and antagonize E2-mediated ER transcriptional activity. Gene ontology analysis identified several coregulated genes involved in cell migration. Accordingly, knockdown of GRHL2 combined with estrogen treatment resulted in increased cell migration but no change in proliferation. These results support a model in which GRHL2 binds to select enhancers and facilitates pS118-ER recruitment to chromatin which then results in differential activation and repression of genes that control ER-positive breast cancer cell migration.

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for GRHL2 in wild-type ER and ER-S118A mutant MCF7 cell lines treated with estrogen (E2).

first: Rebecca

last: Reese

middle: T


title: GRHL2 enhances phosphorylated estrogen receptor DNA binding and regulates ER-mediated transcriptional activation and repression [RNA-seq]

overall_design: RNA-seq of MCF7 and T47D cells depleted of GRHL2 with siRNA and treated with estrogen (E2).


title: FGFR3 is Expressed by Human Primordial Germ Cells and is Repressed after Meiotic Initiation to Form Primordial Oocytes

city: Los Angeles

first: Tsotne

last: Chitiashvili

address: 615 Charles E Young Dr S

institute: University of California - Los Angeles

summary: Human germ cell development is a highly regulated process beginning soon after embryo implantation with the specification of primordial germ cells (PGCs) and ending in adulthood with the differentiation of gametes. Here, we show that fibroblast growth factor receptor 3 (FGFR3) is expressed by human PGCs during the first and second trimester, becoming repressed as PGCs differentiate into primordial oocytes. Using fluorescence activated cell sorting (FACS) with antibodies that recognize FGFR3 followed by single cell RNA sequencing, we show that isolating FGFR3-positive cells enriches for human PGCs. Taken together, FGFR3 could be used in future studies as a strategy to identify maturing hPGCs.

overall_design: In our work, we performed single cell RNA-sequencing (scRNA-seq) with 10x Genomics on FGFR3 sorted ovarian cells from Week 8 and Week 13 human prenatal ovaries. We have also performed scRNA-seq of Day 4 PGCLC aggregate cells differentiated from UCLA1 human embryonic stem cells

first: Kathrin

last: Plath

first: Amander

last: Clark


title: GRHL2 enhances phosphorylated estrogen receptor DNA binding and regulates ER-mediated transcriptional activation and repression

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

overall_design: Refer to individual Series


title: Fetal growth restriction through parental and  fetal immune gene variation and intercellular communications cascade

city: Oxford

first: Gurman

last: Kaur

address: Headley Way

department: John Radcliffe Hospital

institute: University of Oxford

summary: Fetal growth restriction (FGR) affects 5-10% of pregnancies worldwide, and can have serious consequences for both mother and child. Both preventative and treatment strategies are currently largely lacking due to a poor understanding of the pathogenesis of FGR. There is strong genetic evidence for the involvement of KIR and HLA genes in FGR, however, the specific HLA and KIR risk alleles and their functional effects have been difficult to map due to linkage disequilibrium, maternal and paternal influence, and an inability to investigate pathological human pregnancies at critical early gestational stages. Here we demonstrate that the interaction between two defined genes, the maternal KIR2DL1 expressed on uterine natural killer (NK) cells, and the paternally-inherited HLA-C*0501, expressed on fetal trophoblast cells, leads to FGR in a humanised mouse model. We show that the initial KIR2DL1 and C*0501 interaction leads to pathogenic uterine arterial remodeling and a modulation of uterine NK cell function. We delineate how this initial effect cascades to changes in transcriptional expression and intercellular communication in a myriad of cell types and pathways at the maternal-fetal interface. These findings reveal new mechanistic insight into the importance of specific KIR and HLA risk alleles in FGR, and provide new avenues of prevention and treatment to reduce disease burden and improve long-term health outcomes of the child.

overall_design: We built a mouse single cell atlas of uterine NK cells at mid-gesttaion (gd9.5), using both full length scRNA-seq and 3’ droplet-based scRNA-Seq, from the three different mating groups: KIR x C*05 (FGR), WT x C*05 (control 1) and C*05/KIR x WT mice (control 2). In the full length scRNA-seq cohort, we had five replicates per mating group; in the 3' droplet-based scRNA-Seq cohort, we had four replicates for WT x C*05 (control 1) and three replicates each for KIR x C*05 (FGR) and C*05/KIR x WT (control 2). We also analysed all cell types at the maternal-fetal interface at mid-gestation using droplet-based scRNA-seq from the three different mating groups, with three replicates per mating group.

first: Caroline

last: Porter

first: Orr

last: Ashenberg

first: Jack

last: Lee

first: Samantha

middle: J

last: Riesenfeld

first: Matan

last: Hofree

first: Maria

last: Aggelakopoulou

first: Ayshwarya

last: Subramanian

first: Subita

last: Kuttikkatte

first: Kathrine

middle: E

last: Attfield

first: Christiane

last: Desel

first: Jessica

last: Davies

first: Hayley

middle: G

last: Evans

first: Inbal

last: Avraham-Davidi

first: Lan

last: Nguyen

first: Danielle

middle: A

last: Dionne

first: Anna

last: Neumann

first: Lise

last: Jensen

first: Thomas

middle: R

last: Barber

first: Elizabeth

last: Soilleux

first: Mary

last: Carrington

first: Gil

last: McVean

first: Orit

last: Rozenblatt-Rosen

first: Aviv

last: Regev

first: Lars

last: Fugger


title: Zinc finger protein 280C contributes to colorectal tumorigenesis by maintaining epigenetic repression at H3K27me3-marked loci

first: Xing-sheng

last: Shu


title: TLR3 overexpression induces invasion of prostate cancer cells, whereas its activation triggers apoptosis

city: Brno

first: Jirina

last: Prochazkova

address: Kralovopolska 135

department: Cytokinetics

country: Czech Republic

institute: Institute of Biophysics CAS

summary: Toll-like receptors are proteins that play an important role in the innate immune system. They are frequently detected in immune cells such as macrophages or dendritic cells. Their role has been in part studied in prostate cancer. However, in the present study we focus mostly on their functional significance at various types of cancer therapy resistance.

overall_design: Examination of differential gene expression analysis between control DU145 cells (clones A6, D7) and cells overexpressing TLR3 (clones B9, C12)

first: Ximena

last: Muresan

first: Jiřina

last: Procházková

first: Václav

last: Hejret

first: Karel

last: Souček


title: The long noncoding RNA Malat1 regulates CD8+ T cell differentiation by mediating epigenetic repression (CUT&RUN)

status: Public on May 18 2022

city: La Jolla

first: John

last: Chang

address: 9500 Gilman Drive

department: School of Medicine

institute: UC San Diego

summary: The long noncoding RNA Malat1 impacts the differentiation of effector and memory CD8+ T cell subsets by virtue of preferential epigenetic repression of memory-associated genes in terminal effector cells through an interaction with Ezh2

overall_design: Malat1 Knockdown and Nontarget P14 CD8+ T cells were sorted 7 days after LCMV infection

first: Jad

last: Kanbar


title: Next Generation Sequencing Facilitates Transcriptomes Quantitative Analysis of siRNA mediated ASGR1 knockdown

city: Wuhan

first: ju

middle: qiong

last: wang

address: Ba yi Road

department: College of Life Sciences

institute: Wuhan University

summary:
Purpose: The goal of this study is to demonstrate the gene profiles of ASGR1 knock down mediated by siRNA compared with siControl in Huh7 cells.
Methods: The Huh7 cells were transfected with small interference RNA (siRNA) targeting scramble (WT) or ASGR1 (AS2) for 8 hours, then cells were refreshed with Dulbecco's Modified Eagle Medium (DMEM) supplemented with 100 units ml-1 penicillin, 100 μg ml-1 streptomycin sulfate, and 10% fetal bovine serum (FBS). After 72 hours, the cells were harvested for RNA isolation and followed by high-throughput sequencing, in triplicate, using Illumina GAIIx. The sequence reads that passed quality filters were analyzed at the transcriptome with Hisat2(v2.0.1). qRT–PCR validation was performed using SYBR Green assays.
Results: Using an optimized data analysis workflow, we mapped about 45 million sequence reads per sample to the human genome in the WT and AS2 cell lines Hisat2 (v2.0.1). RNA-seq data confirmed stable expression of the known housekeeping genes, and these genes were validated with qRT–PCR. RNA-seq data had a linear relationship with qRT–PCR for more than a goodness of fit (R2) of 0.9. Approximately 4.2% of the transcripts showed significantly differential expression between the WT and AS2 cell lines, with a log2 fold change ≥1.0 and p value <0.05. Altered expression of 5 genes was confirmed with qRT–PCR, demonstrating the high degree of sensitivity of the RNA-seq method.
Conclusions: Our study represents the first detailed transcriptomes analysis of ASGR1 knock down in Huh7 cells, with biologic replicates, generated by RNA-seq technology. The optimized data analysis workflows reported here should provide a framework for comparative investigations of expression profiles. Our results show that NGS offers a comprehensive and more accurate quantitative and qualitative evaluation of mRNA content within the WT and AS2 cell. We conclude that RNA-seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions.

overall_design: transcriptome profiles of siRNA targeting scramble (WT) or ASGR1 (AS2) for 72 hours in Huh7 cells.

first: Ju-Qiong

last: Wang

first: Bao-Liang

last: Song


title: H3K4 demethylase KDM5B regulates epigenetic plasticity and cancer cell identity [RNA-seq]

city: Detroit

first: Benjamin

last: Kidder

state: MI

address: 4100 John R St

department: Oncology

institute: Wayne State University

summary: The H3K4 demethylase KDM5B is overexpressed in multiple cancer types, but the underlying mechanistic contribution of dysregulated H3K4 demethylation in cancer is poorly understood. Here, we show that depletion of KDM5B in multiple types of cancer cells leads to increased proliferation, decreased heterogeneity, and phenotype changes consistent with a de-differentiated or stem cell-like phenotype. Our results also support a role for KDM5B in regulating epigenetic plasticity, where loss of KDM5B in cancer cell lines with elevated KDM5B expression leads to permissive or repressive chromatin states, which facilitate activation or repression of alternative transcriptional programs. KDM5B depleted cancer cells exhibited altered epigenetic and transcriptional profiles resembling a more primitive cellular state. Genome-wide maps of H3K4me3 across a compendium of KDM5B-depleted cancer cell lines revealed altered distributions of canonical and broad H3K4me3 domains at promoters of tumor suppressors. Genes with altered H3K4me3 in KDM5B-depleted cancer cells were enriched with tumor suppressors and housekeeping genes. While high expression of KDM5B is associated with poor clinical outcomes, findings from this study suggest that targeted inhibition of KDM5B as a therapeutic strategy may not be sufficient to inhibit growth of cancer cells as KDM5B regulates H3K4 methylation at a wide range of genes, but does so in a context-dependent manner. This study also provides a resource for evaluating associations between alterations in epigenetic patterning of H3K4 methylation and transcriptome profiles in a diverse set of cancer cells.

overall_design: RNA-Seq of shLuc and shKdm5b cancer cells


title: GRHL2 enhances phosphorylated estrogen receptor DNA binding and regulates ER-mediated transcriptional activation and repression [Cut&Run]

first: Elaine

last: Alarid

overall_design:
CUT&RUN for ER, pS118-ER, and GRHL2 in MCF7 cells depleted of GRHL2 with siRNA and treated with estrogen (E2).
Please note that each processed data file is the result of merging all replicate bams for a given condition together and is linked to the corresponding *Rep 1 sample records.

first: Rebecca

last: Reese


title: H3K4 demethylase KDM5B regulates epigenetic plasticity and cancer cell identity [ChIP-seq]

overall_design: ChIP-Seq of human cancer cells


title: Bulk RNA-seq analysis of developing ocular anterior segments from wildtype and Col4a1 mutant mice

city: San Francisco

first: Douglas

last: Gould

address: Room 235, 10 Koret Way

department: Ophthalmology

institute: UCSF

summary:
COL4A1 mutations cause Gould syndrome, a multi-system disorder which is characterized by a broad range of cerebrovascular, ocular, muscular, renal, or cardiac manifestations. To investigate the patheogenic mechanism of Col4a1 mutations in ocular anterior segment dysgenesis, we used a Col4a1 mutant mouse model that recapitulate many aspects of the pathophysiological hallmarks of Gould syndrome including anterior segment dysgenesis.
We then isolated developing anterior segments from wildtype and mutant mice and performed differntial expression analysis using bulk RNAseq.

overall_design: Anterior segments (cornea, iris, ciliary body and ocular drainage structures) were dissected from P0 Col4a1+/+ (wildtype) and Col4a1+/G1344D (mutant) eyes and comparative gene expression profiling analysis were performed.

first: Mao

last: Mao

first: Cassandre

last: Labelle-Dumais

first: Sara

last: Tufa

last: Keene


title: The long noncoding RNA Malat1 regulates CD8+ T cell differentiation by mediating epigenetic repression (GRID-Seq)


title: The long noncoding RNA Malat1 regulates CD8+ T cell differentiation by mediating epigenetic repression (ChIP-Seq)


title: BCL6-dependent TCF-1+ progenitor cells maintain effector and helper CD4 T cell responses to persistent antigen  [ATAC-Seq]

city: Stanford

first: Ansuman

last: Satpathy

address: 240 Pasteur Drive

institute: Stanford University

summary: Shortly after priming, the fate of activated CD4 T cells is segregated into BCL6+ follicular helper T (Tfh) and BCL6– effector (Teff) cells. However, it remains unknown how these subsets are sustained in the presence of chronic antigen stimulation. Using a combination of single cell- and population-based approaches, we show that in chronic viral infection, activated CD4 T cells differentiate into BCL6-dependent TCF-1+ progenitor cells with superior capacity to expand and give rise to both Teff and Tfh. They share properties with progenitor-exhausted CD8 T cells and are required for the continued generation of Teff cells as antigen persists. In response to tumors, an analogous CD4 T cell population develops in draining lymph nodes. Our study reveals the heterogeneity and plasticity of CD4 T cells upon encountering persistent antigen and highlights their population dynamics through a stable bipotent intermediate state.

overall_design: CD4+PD1+ T splenocytes were sorted and subjected to single-cell ATAC-seq on the 10x Genomics platform.

first: Yu

last: Xia

first: Katalin

last: Sandor

first: Joy

last: Pai

first: Bence

last: Daniel

first: Saravanan

last: Raju

first: Renee

last: Wu

first: Sunnie

last: Hsiung

first: Yanyan

last: Qi

first: Tenzin

last: Yangdon

first: Mariko

last: Okamoto

first: Chun

last: Chou

first: Kamir

last: Hiam-Galvez

first: Robert

middle: D

last: Schreiber

first: Kenneth

last: Murphy

first: Takeshi

last: Egawa


title: BCL6-dependent TCF-1+ progenitor cells maintain effector and helper CD4 T cell responses to persistent antigen


title: The long noncoding RNA Malat1 regulates CD8+ T cell differentiation by mediating epigenetic repression (scRNA-Seq)

first: John

last: Chang

first: Jad

last: Kanbar


title: Expression data from isolated endothelial cells from glioblastoma and normal brain cultured as monolayer on gelatin

city: Cleveland

first: Candece

last: Gladson

state: OH

address: 9500 Euclid Ave.

institute: Cleveland Clinic

summary:
We compared gene expressions between CD31-positive cells from glioblastoma (TECs) and endothelial cells from normal brain (NECs)
In this dataset, expression data obtained from Affymetrix Human Genome U219 Array (HG-U219) are presented.

overall_design: 9 samples in total  were analyzed: 6 TECs and 3 NECs

first: Eunnyung

last: Bae

first: Ping

last: Huang

first: Nicholas

last: Marko


title: Expression data from isolated endothelial cells from glioblastoma and normal brain cultured on Matrigel

overall_design: 6 samples in total  were analyzed: 3 TECs and 3 NECs


title: Expression data from isolated endothelial cells from glioblastoma and normal brain cultured as monolayer on gelatin and on Matrigel


title: Nanostring Glial Profiling Panel of whole brain RNA from CD73ko and control mice subjected to tMCAO

status: Public on May 17 2022

city: Hamburg

first: Björn

last: Rissiek

state: Hamburg

address: Martinistraße 52

department: Department of Neurology

country: Germany

institute: University Medical Center Hamburg-Eppendorf

summary: CD73ko and control mice were subjected to transient middle cerebral artery occlusion (tMCAO) for 50min or subjected to equally long sham surgery. Whole brain RNA was isolated and analyzed with the NanoString nCounter® mouse glial profiling panel.

overall_design: 12 samples from individual mice were analyzed, consisting of 4x shamed CD73flox mice (control) and 4x CD73floxed / 4x CD73ko mice that underwent tMCAO surgery.

first: Ines

last: Schädlich


title: Immune transcriptome in adult-onset Still’s disease with mild flare following administration of mRNA vaccine BNT162b2

city: Bethesda

first: Hye Kyung

last: Lee

state: MD

address: 8 CENTER DR RM 107

department: National Institute of Diabetes and Digestive and Kidney (NIDDK)

institute: National Institutes of Health (NIH)

summary: Adult-onset Still’s disease (AOSD) patients represent a population for which vaccination can induce disease flare1. The COVID-19 pandemic vaccination programs presented these patients and their health care providers with a critical decision. Previously it has been described that AOSD patients can experience disease flare with COVID-19 vaccination but no one has yet reported their immune transcriptional and antibody response. Here we present the transcriptional response and anti-spike antibody profile of a 58-year-old male after vaccination with BNT162b2 who experienced a mild AOSD flare following the second vaccine.

overall_design: RNA-seq were performed with peripheral blood mononuclear cells (PBMCs) from AOSD patient who had received the BNT162b2 mRNA vaccine.

first: Hye

middle: K

first: Ludwig

last: Knabl


title: Chromatin accessibility in neonatal and adult naïve CD4 T cells

city: Iowa City

first: Jennifer

middle: Rachelle

last: Bermick

state: IA

address: 431 Newton Road, 505 EMRB

department: Pediatrics

institute: University of Iowa

summary: Adult naïve CD4 T cells demonstrate differences in chromatin accessibility with increased chromatin accessibility in T cell receptor signaling pathways compared to neonatal cells.

overall_design: ATAC-seq was performed on adult peripheral blood naïve CD4 T cells and term neonatal umbilical cord blood naïve CD4 T cells.


title: BCL6-dependent TCF-1+ progenitor cells maintain effector and helper CD4 T cell responses to persistent antigen [TCR-seq]

first: Ansuman

last: Satpathy

overall_design: CD4+ T splenocytes were sorted with I-Ab-LCMV-gp66 tetramer and subjected to paired single-cell RNA- and TCR-sequencing on the 10x Genomics platform.

first: Yu

last: Xia

first: Katalin

last: Sandor

first: Joy

last: Pai

first: Bence

last: Daniel

first: Saravanan

last: Raju

first: Renee

last: Wu

first: Sunnie

last: Hsiung

first: Yanyan

last: Qi

first: Tenzin

last: Yangdon

first: Mariko

last: Okamoto

first: Chun


title: BCL6-dependent TCF-1+ progenitor cells maintain effector and helper CD4 T cell responses to persistent antigen [scRNA-Seq]

last: Chou

first: Kamir

last: Hiam-Galvez

first: Robert

last: Schreiber

first: Kenneth

last: Murphy

first: Takeshi

last: Egawa


title: Spatial sequencing of Foreign body granuloma

city: Seoul

first: YOON-SEOB

last: KIM

state: Korea (the Republic of)

address: Banpodaero 222

country: South Korea

institute: The Catholic University of Korea

summary: Although macrophage-epithelioid cell (EPC)-giant cell (GC) differentiation is acknowledged in foreign body reaction (FBR), the exact molecular features remain elusive. To discover the molecular profiles of EPC and GC, we analyzed mouse sponge and silk FBRs by integrating single-cell RNA-sequencing (scRNA-seq) and spatial sequencing.

overall_design: After adjusting tissue permeabilization time to 18 min, we performed spatial sequencing library construction using Visium Spatial Gene Expression Reagent Kits (10x Genomics), according to the manufacturer’s instructions.

first: Yoon-Seob

last: Kim

first: Sun

last: Shin

first: Yeun-Jun

last: Chung

first: Sug Hyung

last: Lee


title: Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and delta-RRE Liver Transcriptomes

city: Minato City

first: Satoshi

last: Kawakami

address: 4-6-1 Shirokanedai

department: The Institute of Medical Science

institute: The University of Tokyo

summary: In mammals, the circadian clock consists of transcriptional and translational feedback loops through DNA cis-elements such as E-box and RRE. In this study, we established mutant mice deficient for rhythmic transcription of Bmal1 gene by deleting its upstream RRE elements.  We observed apparently normal circadian rhythms in the mutant, but the circadian period and amplitude of the mutants were more susceptible to disturbance of CRY1 protein rhythm.  Our findings demonstrate that the RRE-mediated feedback regulation of Bmal1 underpins the E-box-mediated rhythm in cooperation with CRY1-dependent posttranslational regulation of BMAL1 protein, thereby conferring the perturbation-resistant oscillation and chronologically organized output of the circadian clock.

overall_design: Circadian mRNA profiles of wild type (WT) and delta-RRE mouse liver

first: Yasuko

middle: O

last: Abe

first: Hikari

last: Yoshitane

first: Yoshitaka

last: Fukada


title: POLH ChIP-seq data in HEK293T cells

status: Public on May 16 2022

city: Riverside

first: feng

last: tang

address: 26861 Campus Point Dr., Moreno Valley

department: chemistry

institute: University of California, riverside

summary: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for Pol η in HEK293T cells.

overall_design: Genome editing-based integration of three tandem repeats of the FLAG epitope tag (3×FLAG tag) into endogenous Pol η was conducted. Then we crosslinked DNA and proteins in chromatin, fragmented DNA, immunoprecipitated endogenous Pol η and its associated genomic DNA using anti-FLAG M2 beads, and subjected the resulting DNA fragments for next-generation sequencing analysis.

first: Feng

last: Tang

first: Yinsheng

last: Wang


title: Spontaneous DIPG Modeling Reveals Novel H3.3 K27M-Mediated Oncogenic Mechanisms Acting Through Epigenetic Effects

city: Memphis

first: Suzanne

last: Baker

state: TN

address: 262 Danny Thomas Place

department: Developmental Neurobiology

institute: St Jude Children's Research Hospital

summary: A mouse knock-in model engineered for Cre recombinase-activated expression of the endogenous mouse H3f3a allele generating an epitope-tagged H3.3 equipped with or without a K27M mutation to investigate H3.3 K27M effects on brain cell and tumor growth, gene expression and epigenetics. These samples are matched with H3K27me3 ChIPseq and RNAseq in GSE108364.

overall_design: ChIP-seq for FLAG and H3K4me3 in neural stem cells from a mouse knock in model of H3f3a K27M (samples also appear in SuperSeries GSE108364).

first: L

last: Kasper

first: S


title: Single cell 3' RNA sequencing of Foreign body granuloma

overall_design: Chromium Single Cell 3ʹ (10x Genomics, Pleasanton, CA, USA) was used for library preparation of scRNA-seq according to the manufacturer’s protocol.


title: Derivation of functional trophoblast stem cells from human primed pluripotent stem cells [scRNA-seq]

first: Robert

last: Morey

address: 2880 Torrey Pines Scenic Dr

department: Pathology

institute: UCSD

summary: Trophoblast stem cells (TSC) have recently been derived from human embryos, and early first trimester placenta; however, aside from ethical challenges, the unknown disease potential of these cells limits their scientific utility. We have previously established a BMP4-based two-step protocol for differentiation of primed human pluripotent stem cells (hPSC) into functional trophoblast; however, those trophoblast could not be maintained in a self-renewing TSC-like state.  Here, we use the first step from this protocol, followed by a switch to a newly-developed TSC media, to derive bona-fide TSC.  We show that these cells resemble placenta- and naïve hPSC-derived TSC, based on their transcriptome, as well as in vitro and in vivo differentiation potential.  We conclude that primed hPSC can be used to generate functional TSC, through a simple protocol which can be applied to a widely-available set of existing hPSC, including induced pluripotent stem cells derived from patients with known birth outcomes.

overall_design: We differentiated primed PSC into TE-like cells by treatment with BMP4/IWP2 and collected cells at 12h, 24h and 4 days (96h) of treatment. We also collected primed H9 hESC-derived TSC. Single cell libraries were created using the 10x Genomics technology with a target cell number of 1000/cells per sample, pooled and submitted for sc RNA-seq.

first: Francesca

last: Soncin

first: Tony

last: Bui

first: Daniela

last: Requena Gilbert

first: Virginia

middle: C

last: Cheung

first: Sampada

last: Kallol

first: Ryan

last: Kittle

first: Omar

last: Farrah

first: Morgan

last: Meads

first: Donald

last: Pizzo

first: Mariko

last: Horii

first: Kathleen

last: Fisch

first: Mana

middle: M

last: Parast


title: Derivation of functional trophoblast stem cells from human primed pluripotent stem cells

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

overall_design: Refer to individual Series


title: The long noncoding RNA Malat1 regulates CD8+ T cell differentiation by mediating epigenetic repression

first: John

last: Chang


title: H3K4me3 patterning in neonatal and adult naïve CD4 T cells

first: Jennifer

last: Bermick

summary: Adult naïve CD4 T cells demonstrate differences in H3K4me3 patterning with H3K4me3 enrichment in T cell activation pathways compared to neonatal cells.

overall_design: H3K4me3 ChIP-seq was performed on adult peripheral blood naïve CD4 T cells and term neonatal umbilical cord blood naïve CD4 T cells.


title: Nfkbid-overexpression and -ablation enhances thymic deletion of autoreactive AI4 CD8 T-cells

city: Bar Harbor

first: David

middle: V

last: Serreze

state: ME

address: 600 Main St

institute: The Jackson Laboratory

summary:
Purpose: Analyze genes involved in the negative selection of CD4CD8 double positive thymocytes from NOD-AI4 control mice, NOD-AI4-Nfkbid-/- (KO) and NOD-AI4-60A undergoing negative selection.
Methods: RNA-Seq based gene expression analyses were used to identify differentially expressed genes in CD4CD8 double positive thymocytes from NOD-AI4 (control), NOD-AI4-Nfkbid-/- (KO) and NOD-AI4-60A undergoing negative selection.

overall_design: mRNA profiles of CD4CD8 double positive thymocytes from 6-7-week-old NOD-AI4 (control, CTL), NOD-AI4-Nfkbid-/- (knockout, KO) and NOD-AI4-60A (Nfkbid transgenic) mice

last: Dwyer

first: Jeremy

last: Racine

first: Harold

last: Chapman

first: Anna

last: Quinlan

first: Maximiliano

last: Presa

first: Grace

last: Stafford

first: Ingo

last: Schmitz


title: Gene expression profiles of Semaphorin 3G stimulated macrophages [RNA-seq]

city: Chiba

first: Shigeru

last: Tanaka

address: 1-8-1 Inohana

department: Allergy and Clinical Immunology

institute: Chiba University

summary: Although Semaphorin 3G has some roles in the development of  vessels, the roles in immune system are not characterized. We aimed to study how Semaphorin 3G affects the function of macrophages.

overall_design: Bone marrow cells were obtained from C57BL6/J mice and the cells were cultured in the presence of 50ng/ml M-CSF. Adhered cells were considered as macrophages. These macrophages were stimulated with 100ng/ml LPS overnight. Activated macrophages were further cultured with or without 100ng/ml recombinant Semaphorin 3G

first: Jumpei

last: Shoda

first: Hiroshi

last: Nakajima


title: Calorie restriction and calorie dilution have different impacts on body fat, metabolism, behavior and hypothalamic gene expression

city: Beijing

middle: Roger

last: Speakman

address: No. 1 West Beichen Road

institute: Institute of Genetics and Developmental Biology, Chinese Academy of Sciences

summary: Caloric restriction is a robust intervention to increase life span. Giving less food (CR), or allowing free access to diluted diet with indigestible components (CD) are two methods to impose restriction. CD does not generate the same lifespan effect as CR. We compared responses of C57BL/6 mice to equivalent levels of CR and CD. Our study calorie restriction and calorie two restriction methods different effect on hypothamic gene expression pattern, RNA-seq was performed using hypothalamus of mice with 2 methods treatment as well as control group.

overall_design: There are three groups in total,control group (CT), calorie restriction group (CR) and dietary dilution group (CD) were exposed to the corresponding experimental diets for 3 months. All animals used in this study were C57BL/6J male mice that were purchased at age 8 weeks from Charles River Laboratories. The mice were single housed in a specific pathogen free facility at 60% humidity with a 12-hour light /12-hour dark circle (light, 7:30 am to 7:30 pm). All the mice were under ad libitum access to water and standard diet (D12450B) in the first 30 days as the baseline period.Afterwards, mice were divided into 3 groups - control group (CT) (D12450B diet), calorie restriction group (CR) and dietary dilution group (CD) were exposed to the corresponding experimental diets for 3 months. CR mice were pair fed the baseline diet to the absorbed intake of ad lib fed CD mice fed the high cellulose diet. The energy intake of CD group was calculated daily by weighing the food that went missing from the hopper (plus any food items recovered from the bedding). This was calculated for each mouse. We then provided paired mice from the CR group with the corresponding amount of standard diet  adjusted for the absorption efficiency and dilutent. The food was provided just before lights off on that day in the evening. CT mice were under ad libitum supply of the baseline diet throughout. In the end of the experiment, mice were sacrificed and hypothalamus part were collected for RNA extraction and sequencing.

first: Xue

last: Liu

first: Zengguang

last: Jin

first: Stephanie

last: Summers

first: Davina

last: Derous

first: Min

last: Li

first: Baoguo

first: Li


title: Long non-coding RNA DARS-AS1 promotes tumor progression by suppressing PACT-mediated PKR activation

status: Public on May 15 2022

first: Kequan

last: Lin

address: Qinghua Yuan #1

institute: Tsinghua University

summary: Cancer cells evolve various mechanisms to overcome cellular stresses and maintain progression. Protein kinase R (PKR) and its protein activator (PACT) are the initial responders in monitoring diverse stress signals and lead to cell proliferation inhibition and cell apoptosis in consequence. However, the regulation of PACT-PKR pathway in cancer cells is largely unknown. Herein, we identify that the long non-coding RNA (lncRNA) aspartyl-tRNA synthetase antisense RNA 1 (DARS-AS1) is directly involved in the inhibition of the PACT-PKR pathway and promotes cancer cell proliferation. Using large-scale CRISPRi functional screening of 971 cancer-associated lncRNAs, we find that DARS-AS1 is associated with significantly enhanced cancer cell proliferation. Accordingly, knocking down DARS-AS1 inhibits cell proliferation of multiple cancer cell lines and promotes cancer cell apoptosis in vitro and significantly reduces tumor growth in vivo. Mechanistically, DARS-AS1 directly binds to the activator domain of PACT and prevents PACT-PKR interaction, thereby decreasing PKR activation, eIF2α phosphorylation and inhibiting apoptotic cell death. Clinically, DARS-AS1 is broadly expressed across multiple cancers and the increased expression of this lncRNA indicates poor prognosis. This study elucidates the lncRNA DARS-AS1 directed cancer-specific modulation of the PACT-PKR pathway and provides a novel target for cancer prognosis and therapeutic treatment.

overall_design: The pool of sgRNA oligos was synthesized at CustomArray, Inc. (Bothewell, WA) and cloned into a pgRNA-humanized plasmid (Addgene #44248). To produce virus particles, 12 μg pooled pgRNA-humanized plasmids, 7.2 μg psPAX2, and 4.8 μg pMD2.G were co-transfected into 5×106 HEK293T cells in a 10 cm dish using DNAfect transfection reagent (CWBIO, Beijing, China), by following the manufacturer’s instructions. Virus particles were harvest at 48 hr and 72 hr after transfection and filtered through 0.45 μm filter membrane. For screening, SW620 cells expressing dCas9/KRAB fusion proteins were generated by viral transduction. Modified SW620 cells were infected with the viral library in four independent infection experiments at MOI 0.1-0.3 and selected with 2 μg/mL puromycin (Sigma, St. Louis, MO) over 2 days. After, cells were in vitro cultured for 18 days at minimum library coverage of 500 cells/sgRNA for screening.

first: Liuqing

last: Yang

first: Dong

last: Wang


title: Single-cell gene expression of tumor-specific CD4  T cells

first: Thomas

last: Ciucci

summary: Single-cell gene expression of GP66 CD4+ T cells responding to MC38_GP tumor was determined by scRNAseq

overall_design: C57Bl6 were injected subcutaneously with MC38 colon carcinoma expressing GP protein. GP66+ CD4+ T cells were sorted 13 days later from the draining lymph or tumor and gene expression was determined by scRNAseq

first: Santiago

last: Carmona

first: Remy

last: Bosselut


title: Single-cell RNA-seq of sorted E11.5 AGM HSCs

city: Edinburgh

first: Katrin

last: Ottersbach

address: 5 Little France Drive

department: Centre for Regenerative Medicine

institute: University of Edinburgh

summary: The aim of this study was to analyse the heterogeneity within the first haematopoietic stem cells generated during mouse development using single-cell RNA-Seq. Freshly dissected aorta-gonads-mesohenphros (AGM) regions from E11.5 mouse embryos were dissociated by collagenase and the cells stained for the cell surface markers EPCR and CD45. EPCR+CD45+ cells were index-sorted as single cells into 96-well plates and processed based on the SmartSeq2 protocol. PCA and tSNE analyses identified 2 main subpopulations which are segregated based on differences in cell cycle. Known HSC markers such as Gata2 and Runx1 show little correlation.

overall_design: EPCR+CD45+ E11.5 AGM cells, which contain all HSCs, were analysed by single-cell RNA-Seq to generate HSC2 cells. Freshly dissected aorta-gonads-mesohenphros (AGM) regions from E11.5 mouse embryos were dissociated by collagenase and the cells stained for the cell surface marker Ngfr. Ngfr+Pdgfrb- cells were index-sorted as single cells into 96-well plates and processed based on the SmartSeq2 protocol. This was done separately for Ngfr+Pdgfrb- cells isolated from the ventral side of the dorsal aorta and from the dorsal side of the aorta, but the two data sets were analysed together. This generated Dorsal and Ventral cell populations. tSNE analysis identified 6 subpopulations which differentially express markers that define specific maturation steps, thus allowing a reconstruction of the differentiation pathway. Pdgfrb+Ngfr- E11.5 AGM cells, which were isolated from the ventral side of the aorta and which contain subaortic mesenchymal cells, were analysed by single-cell RNA-Seq. This population are the Mesenchymal cell population.

first: Chrysa

last: Kapeni

first: Simon

last: Fitch

first: Ying


title: Disrupted control of origin activation promotes genomic instability upon loss of POLE4 and disfunction of the TRP53-CDKN1A/P21 tumour suppressor axis.

city: Shanghai

first: Wei

last: Wu

state: Shanghai

address: 320 yueyang road

department: Center for Excellence in Molecular Cell Science

summary: The maintenance of genome stability relies on the coordinated control of origin activation and replication fork progression. How the interplay between these processes impacts human genetic disease and cancer remains incompletely characterized. Here we initially show that mouse cells lacking Pole4 and featuring Pole instability exhibit impaired genome-wide activation of DNA replication origins, in a origin location-independent manner. Lack of POLE4 leads to proteasome-dependent Pole degradation prior to CMG (CDC45/MCM2-7/GINS) helicase formation and origin activation. Strikingly, Trp53 ablation in primary Pole4 knock-out cells increased Pole levels and origin activation and reduced DNA damage levels in a transcription-dependent manner. Transcriptome analysis of primary Trp53 knock out cells revealed that the TRP53-CDKN1A/P21 axis maintains appropriate levels of replication initiation factors and CDK activity during unchallenged S-phase. Loss of this control mechanism deregulates origin activation, perturbs genome-wide replication fork progression and induces fork stalling and DNA damage. Thus, while our data support an impaired origin activation model for genetic diseases affecting CMG formation, we propose that loss of the TRP53-CDKN1A/P21 tumour suppressor axis induces inappropriate origin activation and deregulates genome wide fork progression. This phenomenon has broad implications for genetic instability and therapeutic targeting in cancer.

overall_design: Examination of the role of POLE4 in maintaining genome stability

first: Roberto

last: Bellelli


title: Stromal remodeling regulates dendritic cell abundance and activity in the tumor microenvironment

city: La Jolla

first: Fotis

last: Asimakopoulos

address: 3855 Health Sciences Drive

department: Moores Cancer Center

summary: Stimulatory type 1 conventional dendritic cells (cDC1s) engage in productive interactions with CD8+ effectors along tumor-stroma boundaries. The paradoxical accumulation of “poised” cDC1s within stromal sheets is unlikely to simply reflect passive exclusion from tumor cores. Drawing parallels with embryonic morphogenesis, we hypothesized that invasive margin stromal remodeling generates developmentally conserved cell fate cues that regulate cDC1 behavior. We find that, in human T cell-inflamed tumors, CD8+ T cells penetrate tumor nests, whereas cDC1s are confined within adjacent stroma that recurrently displays site-specific proteolysis of the matrix proteoglycan versican (VCAN), an essential organ-sculpting modification in development. VCAN is necessary, and its proteolytic fragment (matrikine) versikine is sufficient for cDC1 accumulation. Versikine does not influence tumor-seeding pre-DC differentiation; rather, it orchestrates a distinctive cDC1 activation program conferring exquisite sensitivity to DNA sensing, supported by atypical innate lymphoid cells. Thus, peritumoral stroma mimicking embryonic provisional matrix remodeling regulates cDC1 abundance and activity to elicit T cell-inflamed tumor microenvironments.

overall_design: The role of versikine in shaping tumor immmune microenvironment


title: Inflammation accelerates BCR-ABL1+ B-ALL development through upregulation of Aid

city: Xi’an

first: Yanhong

last: Ji

address: No.76 Yanta West Road

institute: Xi’an Jiaotong University

summary: To investigate the mechanism driving BCR-ABL1+ B-ALL progression involves inflammatory stimulation in murine model. We then performed gene expression profiling analysis using data obtained from RNA-seq of  3 different bone marrow cells derived from BCR-ABL1+ B-ALL mice with lipopolysaccharide  treatment

overall_design: Comparative gene expression profiling analysis of RNA-seq data for bone marrow cells derived from the leukemic mice transplanted with PBS-treated Aid WT BCR-ABL1+ B-ALL cells, the leukemic mice transplanted with LPS-treated Aid WT BCR-ABL1+ B-ALL cells , and the leukemic mice transplanted with LPS-treated Aid KO BCR-ABL1+ B-ALL cells

first: Ping

last: Zhang

first: Mengting

last: Qin

first: Yang


title: Genome-wide gene expression Streptococcus mutans under Aralia continentalis extracts such as acanthoic acid, continentalic acid and kaurenoic acid

status: Public on May 14 2022

city: Busan

first: Keumok

last: Moon

address: 2, Busandaehak-ro 63beon-gil, Geumjeong-gu

institute: Pusan national university

summary: The goals of this study are to compare NGS-derived transcriptome profiling (RNA-seq) of S. mutans upon the treatment of three types of diterpenoid

overall_design: mRNA from S. mutans incubated with/without acanthoic acid, continentalic acid and kaurenoic acid

first: Sungmin

last: Hwang

first: Jaeho

last: Cha

first: Jeong

middle: N

last: Kim


title: Meg-01 cell line expression data after propionate stimulation

city: Erlangen

first: Michael

last: Frech

address: Ulmenweg 18

department: Department of Internal Medicine 3 - Rheumatology and Immunology

institute: University Hospital Erlangen

summary: Platelets are produced by megakaryocytes, deriving from megakaryocyte erythrocyte progenitors (MEP) in the bone marrow. Increased megakaryocyte expansion across common autoimmune diseases was shown for rheumatoid arthritis (RA), systemic lupus erythematosus (SLE) and primary Sjögren’s syndrome (pSS). In this context, we evaluated the role of the microbial-derived short chain fatty acid (SCFA) propionate on megakayriocytes in vitro. Using RNA sequencing we characterized the consequences of propionate exposure on the megakaryoblast cell line Meg-01.

overall_design: The megakaryoblast cell line Meg-01 was stimulated with 500 µM sodium propionate for 48 hours and untreated cells served as controls. RNA was extracted using a RNeasy Mini kit (qiagen, USA) according to the manufacturer's instructions. The Illumina RNA sequencing (RNAseq) analysis was performed by Novogene Sequencing – Europe (UK, Cambridge Sequencing Center). Sequencing libraries were generated using NEBNext® Ultra TM RNA Library Prep Kit for Illumina® (NEB, USA) and sequenced on an Illumina platform.

first: Kerstin

last: Dürholz

first: Eva

last: Schmid

first: Mario

last: Zaiss


title: Decreased serine biosynthesis identifies a subgroup of platinum resistant ovarian cancers and novel actionable metabolic vulnerabilities

city: Amsterdam

first: Pierre-Rene

last: Körner

address: Plesmanlaan 121

department: Oncogenomics

country: Netherlands

institute: Netherlands Cancer Institute (NKI)

summary: Resistance to platinum-based chemotherapy represents a major clinical challenge for many tumors, particularly epithelial ovarian cancer. After initial response, patients often experience several response-relapse events, until tumors start to resist the treatment. Resistant patients have low response rate to other chemotherapy regimens, with life expectancy of 12-15 months. Despite improved knowledge of the molecular determinants of platinum resistance, the lack of clinical applicability limits exploitation of many potential targets, and no novel drugs have been approved for resistant disease. By investigating the functional link between metabolic adaptations and resistance, we discovered that resistant cells modify their serine metabolism and acquire a specific NAD+ generating phenotype, which allows them to sustain PARP activity under treatment. Our findings reveal a novel metabolic vulnerability of resistant tumors that might have an immediate clinical implication, showing that ex vivo patient derived resistant models can be re-sensitized to platinum by combining it with PARP inhibition.

overall_design: RNA sequencing of A2780 and cisplatin-resistant A2780 cells.

first: Tom

last: Van Nyen

first: Mélanie

last: Planqu

first: Lilian

last: van Wagensveld

first: Joao

last: Duarte

first: Esther

last: Zaal

first: Ali

last: Talebi

first: Matteo

last: Rossi

first: Pierre

first: Lara

last: Rizzotto

first: Stijn

last: Moens

first: Wout

last: De Wispelaere

first: Guy

last: Eelen

first: Emanuele

last: Berardi

first: Johannes

last: Swinnen

first: Celia

last: Berkers

first: Peter

last: Carmeliet

first: Diether

last: Lambrechts

first: Ben

last: Davidson

first: Reuven

last: Agami

first: Sarah

last: Fendt

first: Daniela

last: Annibali

first: Frédéric

last: Amant


title: Selective CDK9 inhibition by natural compound toyocamycin in cancer cell

city: Nutley

first: Ying

last: Wang

state: NJ

address: 111 Ideation Way

institute: Hackensack Meridian Health Center for Discovery and Innovation

summary: Aberrant transcription in cancer cells is characterized by silencing of tumor suppressor genes (TSG) and activation of oncogenes. Transcriptomic changes are associated with epigenomic alterations such as DNA hypermethylation, histone deacetylation, and chromatin condensation in promoter regions of silenced TSG. To discover novel drugs that trigger tumor suppressor genes reactivation in cancer cells, we used a GFP reporter system whose expression is silenced by promoter DNA hypermethyation and histone deacetylation. After screening a natural product drug library, we identified toyocamycin, an adenosine analog that induced potent GFP reactivation and loss of clonogenicity in human colon cancer cells. Toyocamycin induced a downregulation in gene pathways involved in RNA pol II transcription regulation. Connectivity mapping analysis revealed that toyocamycin produced a pharmacological signature mimicking cyclin-dependent kinase (CDK) inhibitors. Using RNA-sequencing, we showed that toyocamycin transcriptomic signature closely resembled the profile of a specific CDK9 inhibitor (HH1). Specific inhibition of RNA pol II phosphorylation level and enzymatic kinase assays confirmed that toyocamycin inhibits specifically CDK9 (IC50 = 79nM) with a greater efficacy than other CDKs (IC50 values between 0.67-15µM). Molecular docking showed that toyocamycin binds efficiently CDK9 catalytic site with a different pose than in other CDKs, which was explained by the binding contribution of specific amino acids within the catalytic pocket and the backbone of the protein. Altogether, we demonstrated that toyocamycin exhibits specific CDK9 inhibition in cancer cells, highlighting its potential for cancer chemotherapy.

overall_design: YB5 cells were treated with either DMSO or Toyocamycin (250 nM) for various time points. Cells were harvested posy incubation with the drug and RNA was extracted and sent for sequencing.

first: Somnath

last: Pandey

first: Rahinatou

last: Djibo

first: Anaïs

last: Darracq

first: Gennaro

last: Calendo

first: Hanghang

last: Zhang

first: Ryan

last: Henry

first: Andrew

last: Andrews

first: Steven

last: Baylin

first: Jozef

last: Madzo

first: Rafael

last: Najmanovich

first: Jean-Pierre

last: Issa

first: Noël

last: Raynal


title: Global transcriptional profiles of plantar epidermal basal cells from normal diet-fed, HFD-fed, and aged mice

city: Bunkyo-ku

first: Fumiko

last: Toyoshima

state: Tokyo

address: 1-5-45 Yushima

department: Medical Research Laboratory

institute: Institute of Science Tokyo

summary: We report global transcriptional profiles of epidermal basal cells from plantar skin of control mice, high fat diet-fed (HFD) mice and aged mice. By RNA-sequencing of FACS-isolated interfollicular epidermal (IFE) basal cells, we revealed that calcium signal-associated genes, which regulate differentiatin of keratinocytes,were enriched in the plantar skin of HFD and aged mice.

overall_design: For RNAseq, mRNA profiles of FACS-isolated interfollicular basal cells (CD49f+, CD34-) from plantar skin of control (nomal diet fed) mice, high fat diet fed (HFD) mice and aged mice were generated by deep sequencing, in triplicate, using Illumina NextSeq500. For scRNAseq, after dissociation of the dermis into single cells, we generated chromium single cell 3′ v2 libraries from randomly captured dermal cells and sequenced them using Illumina NextSeq500. We profiled 13,584 cells (Cont: 4,775 cells; HFD: 4,184 cells; Aged: 4,625 cells) with a range of 20,000–40,000 mean reads per cell for each sample, whereby approximately 1,400–1,600 median genes per cell for each sample were detected.

first: Ryo

last: Ichijo

first: Mio

last: Kabata

first: Takuya

last: Yamamoto


title: ATAC-seq Optimization for Cancer Cells

city: Grand Forks

first: Archana

last: Dhasarathy

state: ND

address: 1301 N. Columbia Road, STOP 9061, STOP 9037

department: Biomedical Sciences

institute: UNIVERSITY OF NORTH DAKOTA

summary: ATAC-seq has been used for mapping open chromatin regions. Here we summarize our optimization methods.

overall_design: ATAC seq experiment is optimized using different cancer cell lines. Moreover, it is optimized using different cell numbers of mouse mammary gland epithelial cell line NMuMG

first: Atrayee

last: Ray

first: Mikhala

last: Cooper

first: Motoki

last: Takaku


title: Derivation of functional trophoblast stem cells from human primed pluripotent stem cells [bulk RNA-seq]

first: Robert

last: Morey

state: CA

summary: Trophoblast stem cells (TSC) have recently been derived from human embryos, and early first trimester placenta; however, aside from ethical challenges, the unknown disease potential of these cells limits their scientific utility. We have previously established a BMP4-based two-step protocol for differentiation of primed human pluripotent stem cells (hPSC) into functional trophoblast; however, those trophoblast could not be maintained in a self-renewing TSC-like state.  Here, we use the first step from this protocol, followed by a switch to a newly-developed TSC media, to derive bona-fide TSC.  We show that these cells resemble placenta- and naïve hPSC-derived TSC, based on their transcriptome, as well as in vitro and in vivo differentiation potential.  We conclude that primed hPSC can be used to generate functional TSC, through a simple protocol which can be applied to a widely-available set of existing hPSC, including induced pluripotent stem cells derived from patients with known birth outcomes.

overall_design: We differentiated primed PSC into TE-like cells by treatment with BMP4/IWP2 for 4 days followed by adaptation in TSC media for at least 6 passages. Starting and final cells as well as various intermediate cell types were profiled by RNA-seq.

first: Francesca

last: Soncin

first: Tony

last: Bui

first: Daniela

last: Requena Gilbert

first: Virginia

last: Cheung

first: Sampada

last: Kallol

last: Kittle

first: Omar

last: Farrah

first: Morgan

last: Meads

first: Donald

last: Pizzo

first: Mariko

last: Horii

first: Kathleen

last: Fisch

first: Mana

last: Parast


title: An ancient founder mutation located between ROBO1 and ROBO2 is responsible for increased microtia risk in Amerindigenous populations

city: Boston

first: Daniel

last: Quiat

address: 300 Longwood Ave

department: Cardiology

institute: Boston Children's Hospital

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

overall_design: Refer to individual Series


title: Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and non-antibiotic pharmaceuticals stressed E. coli K-12 LE392, P. putida KT2440, and RP4 plasmid Transcriptomes [experiment 2]

city: Brisbane

first: Jianhua

last: Guo

address: Research Road, Level 4 Gehrmann Building

department: Australian Centre for Water and Environmental Biotechnology

country: Australia

institute: University of Queensland

summary: The goals of this study are to use Next-generation sequencing (NGS) to detect bacterial mRNA profiles of E. coli K-12 LE392, P. putida KT2440 and IncPα RP4 plasmid, and their mRNA response under the exposure of CuO NPs and Cu2+. The concentrations were 5 μmol/L for CuO NPs and Cu2+. The group without dosing CuO NPs or Cu2+ was the control group. Each concentration was conducted in triplicate. By comparing the mRNA profiles of experimental groups and control group, the effects of these CuO NPs and Cu2+ on transcriptional levels can be revealed. Illumina HiSeq 2500 was applied. The NGS QC toolkit (version 2.3.3) was used to treat the raw sequence reads to trim the 3’-end residual adaptors and primers, and the ambiguous characters in the reads were removed. Then, the sequence reads consisting of at least 85% bases were progressively trimmed at the 3’-ends until a quality value ≥ 20 were kept. Downstream analyses were performed using the generated clean reads of no shorter than 75 bp. The clean reads of each sample were aligned to the E. coli reference genome (NC_000913), P.putida reference genome (NC_002947), and IncPα plasmid reference genome (NC_00) using SeqAlto (version 0.5). Cufflinks (version 2.2.1) was used to calculate the strand-specific coverage for each gene, and to analyze the differential expression in triplicate bacterial cell cultures. The statistical analyses and visualization were conducted using CummeRbund package in R (http://compbio.mit.edu/cummeRbund/). Gene expression was calculated as fragments per kilobase of a gene per million mapped reads (FPKM, a normalized value generated from the frequency of detection and the length of a given gene.

sample_organism:
Plasmid RP4
Escherichia coli K-12
Pseudomonas putida KT2440

overall_design: Bacterial mRNA profiles of wild-type E. coli K-12 LE392, P. putida KT2440, and IncPα RP4 plasmid in the pressure of CuO NPs or Cu2+ at 5 μmol/L  for 2 hours, bacteria and plasmid without CuO NPs or Cu2+ are the control group, in triplicate, using Illumina HiSeq 2500

first: Shuai

last: Zhang

first: Yue

last: Wang

first: Hailiang

last: Song

first: Ji

last: Lu

first: Zhiguo

last: Yuan


title: An ancient founder mutation located between ROBO1 and ROBO2 is responsible for increased microtia risk in Amerindigenous populations (scRNA-Seq)

summary: Microtia is a congenital malformation that encompasses mild hypoplasia to complete loss of the external ear, or pinna. Although contribution of genetic variation and environmental factors to microtia remains elusive, Amerindigenous populations have the highest reported incidence. Here, using both transmission disequilibrium tests (TDT) and association studies in microtia trios (parents and affected child) and microtia cohorts enrolled in Latin America, we map a ~10 kb microtia locus (OR 4.7; p=6.78e-18) to the intergenic region between Roundabout 1 (ROBO1) and Roundabout 2 (ROBO2) (chr3: 78546526-78555137).  While alleles at the microtia locus significantly increase the risk of microtia, their penetrance is low (<1%).  We demonstrate that the microtia locus contains a polymorphic complex repeat element that is expanded in affected individuals.  The locus is located near a chromatin loop region that regulates ROBO1  and ROBO2 expression in induced pluripotent stem cell-derived neural crest cells. Furthermore, we use single nuclear RNA sequencing (snRNAseq) to demonstrate ROBO1 and ROBO2 expression in both fibroblasts and chondrocytes of the mature human pinna. Because the microtia allele is enriched in Amerindigenous populations and shared by some East Asian subjects with craniofacial malformations, we propose both populations share a mutation that arose in a common ancestor prior to the ancient migration of Eurasian populations into the Americas, and that the high incidence of microtia among Amerindigenous populations reflects the population bottleneck that occurred during the migration out of Eurasia.

overall_design:
Comparative gene expression profiling analysis of RNA-seq data for undifferentiated iPSC and iPSC-derived neural crest cells (NCC) with 40 and 100kb deletions of an intergenic region between ROBO1 and ROBO2 genes
----------------------------------------
Authors state "raw data for single cell sequencing cannot be supplied due to IRB".

first: Quiat

last: Daniel

first: Seidman

last: Jon


title: Polycomb-mediated genome architecture enables long-range spreading of H3K27 methylation [RNA-Seq]

status: Public on May 13 2022

city: Stanford

first: Howard

middle: Y

last: Chang

address: CCSR 2130, 269 Campus Drive

department: Center for Personal Dynamic Regulomes

institute: Stanford University

summary: Polycomb-group proteins play critical roles in gene silencing through the deposition of histone H3 lysine 27 trimethylation (H3K27me3) and chromatin compaction. This process is essential for embryonic stem cells (ESCs) pluripotency, differentiation, and development. Polycomb repressive complex 2 (PRC2) can both read and write H3K27me3, enabling processive spread of H3K27me3 on linear genome and epigenetic memory. Long-range Polycomb-associated DNA contacts have also been described, but their regulation and role in gene silencing remains unclear. Here, we develop H3K27me3 HiChIP and apply optical reconstruction of chromatin architecture to reveal long-range Polycomb-associated DNA loops that span tens to hundreds of megabases and across multiple topological associated domains in mouse ESCs and human induced pluripotent stem cells. H3K27me3 loop anchors are enriched for Polycomb nucleation points and coincide with key developmental genes, such as Hmx1, Wnt6 and Hoxa. Genetic deletion of H3K27me3 loop anchors causes spatially proximal partner chromosomal loci to break apart, and alters H3K27me3 deposition, both locally and megabases away on the same chromosome. A selective EZH2 mutant deficient in RNA binding but intact H3K27me3 enzymatic activity leads to global alteration in H3K27me3 loops, decreased spatial proximity, and failure to spread Polycomb from PRC2 nucleation points to partner loci at developmental genes. Together, these results suggest PRC2 acts as a “genomic wormhole”, using RNA binding to enhance long range chromosome folding and H3K27me3 spreading. Developmental gene loci have novel roles in Polycomb spreading, emerging as key architectural elements of the epigenome.

overall_design: RNA-seq of CRISPR-Cas9 edited mouse embryonic stem cells (mESCs).

first: Katerina

last: Kraft

first: Kathryn

last: Yost

first: Sedona

last: Murphy

first: Andreas

last: Magg

first: Yicheng

last: Long

first: M

last: Corces

first: Jeffrey

last: Granja

first: Stefan

last: Mundlos

first: Thomas

last: Cech

first: Alistair

last: Boettiger


title: An ancient founder mutation located between ROBO1 and ROBO2 is responsible for increased microtia risk in Amerindigenous populations (RNA-Seq)

first: Daniel

last: Quiat

overall_design: Comparative gene expression profiling analysis of RNA-seq data for undifferentiated iPSC and iPSC-derived neural crest cells (NCC) with 40 and 100kb deletions of an intergenic region between ROBO1 and ROBO2 genes

first: Jon

last: Seidman


title: Discovery of a dual PROTAC for degrading WDR5 and Ikaros oncoproteins as therapeutics [GRO-Seq]

city: Chapel Hill

first: Gang Greg

last: Wang

state: NORTH CAROLINA

address: 405 West Drive

department: UNC Lineberger Comprehensive Cancer Center; Department of Biochemistry and Biophysics

institute: University of North Carolina at chapel hill

summary: WD repeat domain 5 (WDR5), a chromatin regulator associated with MLL complex and MYC oncoproteins, was shown to be critical for oncogenesis in human cancers and represents an attractive drug target. Inhibitors for targeting protein-protein interaction interfaces (PPIs) within WDR5 were developed; however, they inhibited only a part of WDR5-mediated functional interactions, exerting rather limited antitumor effects. We report a cereblon (CRBN)-based proteolysis targeting chimera (PROTAC) of WDR5, MS40, which is capable of selectively degrading cellular WDR5 and the well-established IMiDs:CRBN targets such as Ikaros (IKZF1). MS40-induced WDR5 degradation caused disassociation of MLL complex off chromatin, resulting in a decrease of global H3K4me2. Transcriptomic profiling revealed that gene targets of WDR5 and IMiDs:CRBN were both repressed by MS40. In MLL-rearranged acute leukemias, which exhibit high IKZF1 expression and IKZF1 dependency, co-suppression of WDR5 and IKZF1/3 by MS40 is superior at suppressing tumor growth not only to WDR5 PPI inhibitors but also to a matched VHL-based WDR5 PROTAC, MS169, which selectively targets WDR5 only. Furthermore, MS40 suppressed growth of primary leukemia patient cells in vitro and patient-derived xenografts (PDX) in vivo. Collectively, we report the discovery of a dual WDR5 and Ikaros degrader as anti-cancer therapeutic.

overall_design: Examination of nascent RNA profiling using GRO-seq in MV4;11 cells after the treatment with either DMSO or MS40 (a WDR5 and Ikaros degrader).

first: Dongxu

last: Li

first: Zhao

last: Zhang

first: Zhijie

last: Liu

first: Greg


title: Developmental cues license emergency megakaryopoiesis in hematopoietic stem cells

city: Lund

first: Jonas

last: Ungerback

address: Klinikgatan 26

department: Division of Molecular Hematology

institute: Lund University


title: Developmental cues license emergency megakaryopoiesis in hematopoietic stem cells [bulk RNA-seq & ATAC-seq]

summary: The fetal to adult switch in mouse hematopoietic stem cell (HSC) behavior is characterized by entry into quiescence and alterations in lineage output. Here we identify the ability of HSCs to undergo emergency megakaryopoiesis following acute inflammatory insult as an outcome of this developmental switch. Single cell accessibility mapping of fetal and adult HSCs resolves a heterogeneous chromatin landscape consistent with a two-step megakaryocyte lineage priming process. Importantly, we demonstrate that the accumulation of megakaryocyte primed HSCs is under the control of the developmentally restricted Lin28b RNA binding protein. Persistent Lin28b protein expression in postnatal HSCs delays the formation of a primed HSC pool and limits emergency megakaryopoiesis. Taken together, we identify Lin28b as a negative regulator of a megakaryocyte primed HSC state that is enforced at the chromatin level during unperturbed organismal development. These findings highlight the ontogenically timed onset of inflammatory responsiveness, with important implications for the delicate balance between host protection and tissue damage during neonatal life.

overall_design: Bulk RNA- and ATAC-seq was used to compare E14.5 fetal liver and adult bone marrow hematopoietic stem cells(HSC) and lymphoid primed multipotent progenitors (LMPP). Biological replicates (n) as follows:  RNA-seq ABM HSC (n=3), RNA-seq FL HSC (n=2), RNA-seq ABM LMPP (n=3), RNA-seq FL LMPP (n=3), ATAC-seq ABM HSC (n=2), ATAC-seq FL HSC (n=2), ATAC-seq ABM LMPP (n=2), ATAC-seq FL LMPP (n=2).

first: Trine

last: Kristiansen

last: Ungerbäck

first: Joan

last: Yuan


title: RNA-seq from the liver, ileum, muscle, fat of SPF or GF mice on ND, WD

city: Corvallis

first: Andrey

last: Morgun

state: OR

address: 1601 SW Jefferson Way

institute: Oregon State University

summary:
RNA seq from the liver, ileum, muscle, fat of SPF or GF mice on ND, WD.
"Microbiota and adipocyte mitochondrial damage in type 2 diabetes are linked by Mmp12+ macrophages"

overall_design: Liver, ileum, muscle, fat of SPF or GF mice on ND, WD

first: Natalia

last: Shulzhenko


title: Developmental cues license emergency megakaryopoiesis in hematopoietic stem cells [scATAC-seq]

overall_design: Single cell ATAC-seq was used to compare megakaryocyte priming between E14.5 fetal liver and adult bone marrow hematopoietic stem cells. FL CD41- HSC: CD3-Gr1-B220-ter119-7AAD-cKit+Sca1+CD48-CD150+Flt3-CD41-, ABM CD41- HSC: CD3-Gr1-B220-ter119-CD11b-7AAD-cKit+Sca1+CD48-CD150+Flt3-CD41-,  ABM CD41int HSC: CD3-Gr1-B220-ter119-CD11b-7AAD-cKit+Sca1+CD48-CD150+Flt3-CD41+, ABM MkP: :CD3-Gr1-B220-ter119-CD11b-7AAD-cKit+Sca1-CD150+CD41+.


title: Polycomb-mediated genome architecture enables long-range spreading of H3K27 methylation [4C-seq]

first: Howard

last: Chang

overall_design: 4C-seq of wild-type and RNA-binding deficient EZH2 mutant human induced pluripotent stem cells (iPSCs).

first: Katerina

last: Kraft

first: Kathryn

last: Yost

first: Sedona

last: Murphy

first: Andreas

last: Magg

first: Yicheng

last: Long

first: M

last: Corces


title: Flattened circadian glucocorticoid oscillations cause obesity due to increased lipid turnover and lipid uptake

city: New York

first: Mary

last: Teruel

state: NY

address: 1300 York Avenue, Room A-403

institute: Weill-Cornell Medical College, Cornell University

summary: Chronic stressors flatten circadian glucocorticoid (GC) oscillations, which has been correlated with negative health outcomes including obesity. How such flattened circadian GC oscillations affect metabolism and fat storage remains unknown. Here we investigated the consequences in mice and found that flattening of GC oscillations results not only in body weight gain, mainly due to increases in white fat depot mass, but also leads to hyperinsulinemia and fat accumulation in brown adipose tissue. Global analysis of the transcriptome of WAT and BAT revealed alterations in gene expression dependent on flattened GC oscillations and point to increased lipid turnover and lipid uptake in both fat depots.

overall_design: To elucidate how gene expression is globally affected by flattening of glucocorticoid oscillations as a potential cause for the expansion of fat depots, we performed RNAseq analysis of vWAT and BAT. Mice were subcutaneously implanted with corticosterone pellets to flatten their corticosterone oscillations and compared to mice inplanted with a placebo pellet. The fat depots (vWAT and BAT) were harvested 0, 3, 7, and 14 days after pellet implantation. To control that observed changes in gene expression are due to flattening of diurnal corticosterone oscillations and not caused by the amount of corticosterone released by the corticosterone pellet, a similar RNAseq analysis was performed, in which mice were injected with the same amount of corticosterone released by the corticosterone pellet per day in one single injection, thereby increasing the peak amplitude of corticosterone in the evening phase. Also these fat depots (vWAT and BAT) were harvested 0, 3, 7, and 14 days after start of injection.

first: Stefan

last: Tholen

first: Kyle

last: Kovary

first: Atefeh

last: Rabiee

first: Agnieszka

last: Agas

first: Wenting

last: Yang

first: Roma

last: Patel

first: Fredric

middle: B

last: Kraemer


title: Effect of MMP12 inhibitor on gene expression

first: Andrey

last: Morgun

summary:
Identifying changes in fat tissue gene expression in mice treated with or without mmp12 inhibitor.
"Microbiota and adipocyte mitochondrial damage in type 2 diabetes are linked by Mmp12+ macrophages"

overall_design: Adult male C57BL/6J SPF mice were first fed with the western diet for 4 weeks to induce glucose intolerance then divided into 2 groups accordingly. Afterward, mice were injected intraperitoneally with an MMP12 selective inhibitor MMP408 (3.5 mg/kg, dissolved in PBS containing 10% DMSO) or vehicle every day for 2-3 weeks while continuing western diet feeding. All mice were housed individually. The experiment was done twice. RNA-seq data provided here.


title: Transcriptome profiles of differentiated wt1-SAM brown adipocytes treated with different sgRNA encoding plasmids and stimulated with isoproterenol

status: Public on May 12 2022

city: Odense

first: Jan

middle: Wilhelm

last: Kornfeld

address: Campusbej 50

department: Biochemistry and Molecular Biology

country: Denmark

institute: University of Southern Denmark

summary: Cold and nutrient activated brown adipose tissue (BAT) is capable of increasing systemic energy expenditure via uncoupled respiration and secretion of endocrine factors thereby protecting mice against diet-induced obesity and improving insulin response and glucose tolerance in men. Long non-coding RNAs (lncRNAs) have recently been identified as fine tuning regulators of cellular function. While certain lncRNAs have been functionally characterised in adipose tissue, their overall contribution in the activation of BAT remains elusive. We identified lncRNAs correlating to inter- scapular brown adipose tissue (iBAT) function in high fat diet (HFD) and cold stressed mice. We focused on Gm15551 which has an adipose tissue specific expression profile, is highly upregulated during adipogenesis and downregulated by β-adrenergic activation in mature adipocytes. Albeit we performed comprehensive transcriptional and adipocyte physiology profiling in vitro and in vivo, we could not detect an effect of gain or loss of function of Gm15551.

overall_design: polyA RNA profiles of brown adipocytes (wt1-SAM) differentiated for 7 days, reverse transfected with different sgRNAs at day 4 of differentiation and stimulated for 24 h with isoproterenol before harvesting were generated by deep sequencing in triplicate.

first: Christoph

last: Engelhard

first: Chien

last: Huang

first: Sajjad

last: Khani

first: Petr

last: Kasparek

last: Procházka

last: Rozman

first: David

middle: P

last: Reguera

first: Radislav

last: Sedláček

first: Jan-Wilhelm


title: RNA seq on tumors from two groups of mice (cancer-collagen1 knockout group and control group)

city: Houston

first: Yang

last: Chen

state: Texas

address: 1881 East Road

department: Cancer Biology

institute: UT-MD Anderson Cancer Center

summary: RNA sequencing analysis on tumor samples from two groups of mice (1) KPPC;Col1pdxKO cancer-collagen1 knockout group and (2) KPPC control group

overall_design: A total of 9 RNA samples from tumors from two groups of age-matched mice (1) KPPC;Col1pdxKO cancer-collagen1 knockout group, 5 mice; and (2) KPPC control group, 4 mice.


title: Adipose tissue poly RNA profiles of C57BL/6N-ΔGm15551 mice.

overall_design: PolyA RNA profiles of different adipose tissues from 12-week old  ∆Gm15551 and wild type litter mate mice.


title: Effect of insulin on 3T3L1 cell line gene expression

summary:
Identifying changes in gene expression in 3T3L1 cell line treated with or without insulin.
"Microbiota and adipocyte mitochondrial damage in type 2 diabetes are linked by Mmp12+ macrophages"

overall_design: RNA seq from the 3T3L1 cell lines treated with or without insulin

first: Natalia

last: Shulzhenko


title: Inactivation of Sirt6 ameliorates muscular dystrophy in mdx mice by releasing suppression of utrophin expression

city: Bad Nauheim

first: Carsten

last: Kuenne

address: Ludwigstrasse 43

department: Bioinformatics

institute: Max Planck Institute for Heart and Lung Research

summary: In this study, Pax7-Cre mediated inactivation of Sirt6 in mdx mice resulted in profound improvement of the mdx phenotype at the functional level. To study the underlying molecular mechanisms and identify specific Sirt6 targets irrespectively to mdx mutation, we performed RNA-seq of freshly isolated muscle stem cells from control and Sirt6mKO mice.

overall_design: Transcriptome profiling of MuSCs from control (wild type) and Sirt6mKO mice

first: Angelina

last: Georgieva

first: Stefan

last: Günther


title: Acinetobacter baumannii ATCC 17978 Transcriptome Sequencing 37ºC Light/Dark

city: Oxford

first: Luis

last: Actis

address: E High St

department: Microbiology

institute: Miami University

summary: We performed RNA sequencing analysis with differential expression analysis to compare the expression of genes between A. baumannii 17978 wildtype strain grown in the light and the dark. The purpose was to determine any genes whose expression was mediated by light at 37ºC, a temperature at which the currently best studied photoreceptor for A. baumannii BlsA, is unfunctional.

overall_design: Compared gene expression between 3 biological samples of cells grown in illumination and cells grown in darkness at 37ºC.

first: Mariah

middle: S

last: Squire

first: Hope

last: Townsend


title: Whole genome bisulfite sequencing of 3T3-L1 preadipocytes and adipocytes

city: Seoul

first: Jae Bum

last: Kim

address: Bldg 105-Rm. 333, Seoul National University, San 56-1, Sillim Dong, Kwanak-Gu

department: Biological Sciences

institute: Seoul National University

type: Methylation profiling by high throughput sequencing

summary: Examination of 2 samples derived from 3T3-L1 preadipocytes and adipocytes

first: Jeu

last: Park

first: A

first: Yoon

middle: J

first: Jae