title: Genomic and epigenomic responses to aspirin in human colonic organoids

first: Sonia

middle: S

last: Kupfer

department: Human Genetics

institute: University of Chicago

summary:
Background & Aims: Aspirin (ASA) is a proven chemoprotective agent for colorectal cancer; yet, mechanisms underlying these effects are incompletely understood. Human organoids are an ideal system to study genomic and epigenomic host-environment interactions. Here, we utilize human colonic organoids to profile ASA responses on genome-wide gene expression and chromatin accessibility.
Methods: Human colonic organoids from one individual were cultured and treated in triplicate with 3mM ASA or vehicle control (DMSO) for 24 hours. Gene expression and chromatin accessibility were measured using RNA- and ATAC-sequencing, respectively. Differentially expressed genes were analyzed using DESeq2. Gene set enrichment was performed by SetRank. Differentially accessible peaks were analyzed using DiffBind and EdgeR. Motif enrichment was determined using HOMER and diffTF.
Results: The results yielded strong transcriptional responses to ASA treatment with significant enrichment for fatty acid oxidation and PPAR signaling in the normal colonic epithelium that were validated in independent organoid lines. A large number of differentially accessible chromatin regions were found in response to ASA treatment with significant enrichment for Fos, Jun and Hnf transcription factor motifs. Integrated analysis of epigenomic and genomic treatment responses highlighted genes and regulatory regions that could mediate ASA’s specific effects in the colon including those involved in chemoprotection and/or toxicity.
Conclusions: Assessment of chromatin accessibility and transcriptional responses to ASA yielded new observations about genome-wide effects in the colon facilitated by application of human colonic organoids. This framework can be applied to study colonic ASA responses between individuals and populations in future.

overall_design: Gene expression (RNA-seq) and chromatin accessibility (ATAC-seq) data from three replicates of aspirin and vehicle control (DMSO) treated human colonic organoids from one individual.

first: David

last: Witonsky

first: Margaret

last: Bielski

first: Jinchao

last: Li

first: Kristi

last: Lawrence

first: Ishmael

last: Mendoz

first: Hina

last: Usman


title: Inhibition of the epigenetic regulator Ezh2 redistributes bivalent domains within transcriptional regulators associated with Wnt and Hedgehog pathways

status: Public on Jan 01 2023

city: Rochester

first: Asha

last: Nair

address: 200 1ST ST SW

country: USA

institute: Mayo Clinic

type: Expression profiling by high throughput sequencing

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Osteoporosis is characterized by bone loss, reduced bone strength, and increased fracture risk. Studies have shown that epigenetic mechanisms play a role during bone formation and bone-related disorders, including osteoporosis.  However, the contribution of bivalent domains, which are chromatin regions that are co-occupied by the gene activating Histone 3 lysine 4 trimethylation (H3K4me3) and the gene suppressive Histone 3 lysine 27 trimethylation (H3K27me3) marks, has not been elucidated during osteogenesis. Previous work demonstrated that the enhancer of zeste homolog 2 (Ezh2), a histone 3 lysine 27 (H3K27) methyltransferase, suppressed differentiation of osteogenic progenitor cells and that a small molecule inhibitor of Ezh2 (GSK126) enhanced osteogenic commitment of osteoblast progenitors in vitro and bone formation in vivo. Tazemetostat (or EPZ6438) is an Ezh2 inhibitor (iEzh2) that is FDA approved for the treatment of epithelioid sarcoma and might be repurposed to mitigate bone loss. The present study aimed to elucidate mechanisms by which Tazemetostat-mediated H3K27me3 reduction regulates bivalent domain associated enhancers critical for bone formation. Tazemetostat enhanced the expression of bone-related genes (e.g., Runx2-p57, Bglap, Ibsp) as measured by qPCR analysis and stimulated extracellular matrix deposition as revealed by alizarin red staining of cell cultures. Western blotting analysis revealed that Tazemetostat reduced H3K27me3 levels and concomitantly enhanced H3K27Ac, as well as increased protein levels of the osteoblastic master regulator Runx2. Integrative analysis of RNA-seq and ChIP-seq datasets revealed that upregulation of group of genes that are associated with bivalent domains. Importantly, gene ontology analysis showed that genes associated with Wnt, Pth and Hh signaling pathways are enriched within these up-regulated genes. Follow-up mechanistic-based studies revealed that the pro-osteogenic effects induced by Ezh2 inhibition are attenuated by inhibition of Hh signaling and enhanced by disruption of Wnt signaling. Our data demonstrate that the genes controlled by bivalent domains are associated with key osteogenic signaling pathways and are induced upon Ezh2 inhibition and subsequent H3K27me3 reduction. Our data also demonstrate that iEzh2-induced osteogenic differentiation is modulated by Wnt and Hh signaling pathways.

overall_design: MC3T3-E1 subclone 4 cells Passage 9 were maintained in ?-minimal essential medium without ascorbic acid (Gibco) containing 10% fetal bovine serum (Atlanta Biologicals), 100 units/ml penicillin and 100 ?g/ml streptomycin (Gibco). Cells were seeded in maintenance medium at a density of 10,000 cells/cm2. Next day, cells were treated with vehicle (DMSO) or 2.5µM EPZ6438 (MedChem, HY-13803) in osteogenic medium (maintenance medium supplemented with 50?g/ml ascorbic acid (Sigma) and 10mM ?-glycerol phosphate (Sigma). Three day later, the cells were harvested by trypsin and analyzed by ChIP assay using H3K27me3 (H3K27me3, Cell Signaling, #9733 Lot 8) and H3K4me3 (H3K4me3, Abcam, ab8580 Lot GR3264490-1) antibodies. DNA fragments were isolated using QIAquick PCR Purification Kit (Qiagen). Total RNA was isolated on days three of osteogenic differentiation using the Direct-zol? RNA kit (Zymo Research) and TRIzol reagent (Invitrogen)

first: Andre

middle: J

last: van Wijnen

first: Margarita

middle: E

last: Carrasco Jeldres

first: Amel

last: Dudakovic

first: Gino

last: Nardocci


title: Idiopathic pulmonary fibrosis (IPF)

city: Giessen

first: Jochen

last: Wilhelm

state: Hessen

address: Aulweg 132

department: Institute for Lung Health

country: Germany

institute: Justus-Liebig University Giessen

summary: Idiopathic pulmonary fibrosis (IPF) is a disease related to AT2 cell. We used flow cytometry to analyze the epithelial component of donor and IPF lungs. From the live cells, we first excluded the CD31PosCD45Pos and then selected the EPCAMPos cells for further analysis using the human AT2 cell marker HTll-280 and the surface marker PD-L1. Our data indicate that, the bona fide differentiated AT2 cells (HTll-280High PD-L1Neg), were drastically reduced in the context of IPF. More interestingly, the number of HTll-280Low/Neg PD-L1High was drastically increased, suggesting that HTll-280Low PD-L1High epithelial cells could represent a pool of progenitors linked to the deficient AT2 lineage. The aim of this experiment is further characterization of AT2 and PDL1+ cells in donor and IPF.

overall_design: 4 groups, each with 2 biological replicates

first: Negah

last: Ahmadvand

first: Saverio

last: Bellusci


title: Expression data for mouse skin-in atopy DNCB model

city: Hongcheon

first: Aziz

last: Ghaderpour

state: Gangwon-do

address: 101 Dabyeonbat-gil, Hwachon-myeon,

department: biomedical

country: South Korea

institute: Seoul national university

summary:
Atopic dermatitis (AD) is the most common chronic inflammatory skin disorder, characterized by intense itch and recurrent eczematous lesions. Due to lack of proper therapy, the strategies of T cell modulators in combination with targeting keratinocytes and/or myeloid cells might hold promise for achieving disease control in AD patients better than T cell modulators alone.
we used microarrays to detail the global programme of gene expression underlying cellularisation and identified distinct classes of up-regulated genes during HY209 treatment in mouse skin

overall_design: DNCB was applied on the dorsal skin of Balb/c mice for 15 days and treated with vehicle or 5% HY209-PEG gel for the last 7 days. The skin samples were collected for RNA and the gene expression analysis.

first: Seung-Yong

last: Seong


title: A volatile from skin microbiota of flavivirus-infected host promotes mosquito attractiveness

city: Beijing

first: Yibin

last: Zhu

address: Tsinghua, Beijing, China

country: China

institute: Tsinghua University

summary: We performed whole-transcriptome RNA sequencing (RNA-Seq) to compare transcript abundances in the skin of DENV- or ZIKV-infected AG6 mice to those in the skin of uninfected mice.

overall_design: As a step toward understanding how flavivirus infection regulates skin microbiota, we examined the immune responses in the skin.

first: Gong

last: Cheng


title: Integrative nascent RNA methods to reveal cell-type specific transcription programs in peripheral blood and its derivative cells

city: Ithaca

first: Hojoong

last: Kwak

state: NY

address: 516 Campus Rd Biotechnology Bldg

department: Molecular Biology and Genetics

institute: Cornell University

summary: Nascent RNA sequencing is a powerful method to measure transcription with high resolution, sensitivity, and directional information, which gives distinctive information about transcription from other methods such as chromatin immunoprecipitation or mRNA sequencing. We present an integrated package of nascent RNA-seq methods - ultrafast Precision Run On (uPRO) combined with computational procedures to discover cell type specific enhancers, promoters, and transcription factor networks. uPRO is composed of adaptor ligation and reverse transcription reactions, which is reduced to a one-day procedure and makes nascent RNA-seq more feasible and flexible for a widespread use. We generated genome-wide profiles of nascent transcription in human blood derived cell lines and clinical samples of ~1 ml of untreated whole blood. We integrated these data into deep learning and hierarchical network analysis to detect enhancers, promoters, and co-expression networks to define cell-type specific transcription programs. We found conservation of position but variation of expression in cell type specific enhancers and transcription start sites. Transcription factors (TFs) such as TCF-3 and OCT1 were pivotally associated with TF-enhancer-gene networks across cell types. Intriguingly, we also discovered that TFs related to cell stress and inflammation - such as SRF, ATF, CHOP, and NF-kB - are associated with inter-individual variation of leukocyte transcription in whole blood. Our integration of experimental and computational nascent RNA methods will provide an efficient strategy to identify specific transcriptional programs, both in cell-type and patient/disease-associated, with minimal sample requirements.

overall_design: Nascent RNA sequencing of peripheral blood and derived cell lines

first: Samantha

last: Kim

first: Eunyoo

first: Aileen

last: Kimm


title: Mouse testicular gene expression profile after KIFC1 inhibition

city: Shanghai

first: Xinrui

last: Wang

address: 197 Ruijin Rd II

institute: Rui-Jin Hospital affiliated to Shanghai Jiao Tong University School of Medicine

summary:
Purpose: Kinesin-14 KIFC1 proteins are highly expressed in testes and function in male spermatogenesis, especially acrosome biogenesis. However, the mechanisms of KIFC1 during acrosomal vesicles transportation and vesicle fusion are still unknown. This study revealed the in vivo functions of KIFC1 proteins in mouse spermiogenesis using two KIFC1 specific inhibitors, AZ82 and CW069.
Methods: Testicular mRNA profiles of male mice PBS (Control), AZ82 and CW069 injected groups were progressed with deep sequencing, in triplicate through Illumina sequencing platform (HiSeqTM 2500). Genes with adjusted P-value < 0.05 and foldChange > 1.2 were defined as differentially expressed genes (DEGs) and subjected to the following GO and KEGG enrichment. qRT-PCR was performed to validate several essential genes using QuantStudio 5 (Thermo Fisher) and SYBR Green assays.
Results: We have mapped over 40 million sequence reads to the mice genome in each specimen. Only a few genes showed significant differences in our gene expression profile of KIFC1 inhibition groups compared with the control. The transcriptome of testes in the AZ82 treatment group reflected the defects in protein maturation. CW069 activated apparent drug responses. In results, AZ82 and CW069 reduced cell viability with an enhanced apoptosis signal and excessive oxidation. Comparing the GO enrichment data, we confirmed the role of KIFC1 in actin filament organization and intercellular adhesion. KEGG enrichment showed a series of lipid, organic acid and steroid metabolism disorders after KIFC1 inhibition, resulting in fatty acid degradation and lipid oxidation.
Conclusions: Our study confirmed that KIFC1 functioned in the microfilament organization and proacrosomal vesicle transportation. The acrosin could not accumulate on the nuclear surface with fatty acid degradation. The RNA-seq results were consistent with our in vivo experiments which proved that KIFC1 plays an essential role in mouse acrosome biogenesis.

overall_design: Mouse testicular mRNA profiles of PBS, AZ82 and CW069 injection groups.

first: Yalan

last: Wei

first: Zhenyu

last: She


title: Transcriptome analysis of sweet1 seeds upon treatments during germination

city: Urbana

first: Xueyi

last: Xue

state: Illinois

address: 1201 W. Gregory Dr.

department: Department of Plant Biology

institute: University of Illinois at Urbana-Champaign

summary:
Purpose: The goals of this study are to compare the transcriptome profiling between wild type and sweet1 under the treatments of either the glucose, ABA or both during germination.
Methods: After 3-day imbibition, sweet1 seeds were sown on ½ MS medium and grown under constant light, 22 °C for 24 hours. Seeds were transferred to ½ MS liquid medium supplemented with either 60 mM Glc, 5 µM ABA or both for 6 hours. Four biological replicates were collected for each treatment. Total RNA was extracted by RNeasy PowerPlant Kit (13500-50, Qiagen), The libraries were prepared from 1 µg total RNA using KAPA mRNA Hyper Prep kit (KK8581, Roche) with KAPA Dual-indexed Adapter kit (KK8722, Roche). The libraries were sequenced by Hiseq 2500 (Illumina) with paired-end reads.
Results: Gene expression level was quantified using Kallisto v 0.44.0 by mapping to Arabidopsis thaliana (version 11) primary transcript sequences. Samples were evaluated based on pair-wise comparison between different conditions and outliers within each treatment were removed for the further analysis based on PCA results. Candidates with more than 10 counts per million reads in at least 50% samples, |b| ≥ 0.2 and q-value < 0.05 were identified as differentially expressed genes (DEGs) using Sleuth program. Hierarchical clustering of DEGs uncovered several pathways that may contribute to glucose antagonizing ABA function.
Conclusions: This study represents the detailed analysis of transcriptome in germinating seeds under ABA+Glc treatment. Our study provides a new perspective on the interaction between ABA and Glc in response to external stimuli to control the seed germination.

overall_design: Seed transcript profiles in sweet1 under glucose, ABA and ABA+glucose treatments in 30 hours after imbibition.

first: Li-Qing

last: Chen


title: Next Generation Sequencing Facilitates Quantitative Analysis of shPLKO- and shPSPH-Cancer Cell Transcriptomes

city: Guangzhou

first: ZHIPENG

last: PENG

state: Guangdong

address: Xin Gang Xi Lu 135#

institute: Sun Yet-sen university

summary: We report the Phosphoserine Phosphatase (PSPH) would impair influence the Chemokines expression in TNF-A condition, Gene enrichment analysis of the transcriptome profiles of shPSPH-transfected hepatoma cells or shPLKO-transfected control cells could discover which changes in signaling pathways affect chemokine expression.PLC/PRF/5 and SNU449 were stimulated with human recombinant TNFα for 24 hours. RNA of the cells was extracted by TRIzol method.

overall_design: Cancer cell line (PLC/PRF/5, SNU449) mRNA profiles of shPLKO (Contral) and shPSPH cell

first: Zhi-Peng

last: Peng

first: Limin

last: Zheng

first: Yan

last: Wu


title: RNF6 enhances chemo-resistance by transcriptionally activating PCNA expression and attenuating DNA damage in lung adenocarcinoma.

first: Yile

last: SUN

address: HuaiHai west road

institute: Shanghai chest hospital

summary: To elucidate whether RNF6 plays a role in development of lung adenocarcinma, a RNA-seq analysis was performed to compare the gene expression profiles of RNF6 shRNA and control shRNA transfectants.

overall_design: RNA-seq was performed in H3255 lung cancer cells after RNF6 knock down

first: Hongmiao

first: Mengqiao

last: PAN

first: Zhiwei

last: CHEN


title: Screening for eukaryotic motives in Legionella pneumophila reveals bacterial LPC_1677 as functional host histone de-acetylase

city: Marburg

first: Wilhelm

last: Bertrams

address: Hans-Meerwein-Str. 2

department: Institute for Lung Research

institute: Philipps University Marburg

summary:
Purpose: The interaction between Legionella pneumophila and its host cell is not completly understood. The aim of this study was to identify eukaryotic-like bacterial factors which manipulate the host cell.
Method: A stable overexpression of LPC_1677 was performed in THP-1 cells. The LPC_1677 overexpressing cells were infected with L.p. and RNA sequencing was performed. Key pro-inflammatory markers were validated via qPCR and ELISA.
Results: Bioinformatic screening for eukaryotic-like motives in L.p. took us to LPC_1677 which deacetylates host histones and thereby attenuating gene transcription.
Conclusion: This study demonstrated that the eukaryotic-like bacterial factor LPC_1677 de-acetylates Histones in the host cell.

overall_design: THP-1 control cells as well as LPC_1677 overexpressing cells were infected with L.p. (MOI 1) for 3 hours or left uninfected.

first: Stefanie

middle: M

last: Herbel

first: Bernd

last: Schmeck


title: The transcription factor Zic4 promotes tentacle formation and prevents epithelial transdifferentiation in Hydra.

city: Geneva

first: Celine

last: Delucinge

address: 1 rue Michel Servet

department: iGE3 Genomics Platform

country: Switzerland

institute: University of Geneva

summary: A Zic4-dependent switch in Hydra turns tentacle into foot cells.

overall_design: The experiments have been designed to analyze the effect of the transcription factor Zic4 in different tissues of Hydra (head and body column).

first: Matthias

middle: C

last: Vogg

first: Jaroslav

last: Ferenc

first: Wanda

last: Buzgariu

first: Chrystelle

last: Perruchoud

first: Paul

middle: G

last: Layague Sanchez

first: Leonardo

last: Beccari

first: Clara

last: Nunninger

first: Youn

last: Le Cras

first: Céline

last: Delucinge-Vivier

first: Panagiotis

last: Papasaikas

first: Stéphane

last: Vincent

first: Brigitte

last: Galliot

first: Charisios

middle: D

last: Tsiairis


title: Fate restricted stromal fibroblasts and adipocytes demonstrate multi-modal responses to tissue injury

city: Biberach

first: Meshal

last: Ansari

address: Birkendorfer Straße 65

institute: Boehringer Ingelheim

summary: Adult connective tissues rearrange themselves during injury, disease, and aging. This response is widely considered to involve cross-lineage conversion between two differentiated stromal cell types: fibroblasts and adipocytes. Here, we directly explore the potential plasticity of these cells after injury in the skin. Using single-cell transcriptomics we confirm that adipocyte and fibroblast lineages undergo separate differentiation pathways after injury, avoiding cross-lineage conversion. We performed Single-Cell RNA-seq experiments and employed a fibroblast-lineage specific reporter (En1Cre), labeling a sub-population of fibroblasts termed EPFs (Engrailed-lineage positive fibroblasts). Mature adipocytes were tracked using an adiponectin lineage-specific reporter (AdipoqCre). The two lineage-specific transgenic lines were individually crossed to a double-color fluorescent reporter (R26mTmG), thereby marking mature adipocytes and fibrogenic cells with membrane-bound green. Sorted populations were subjected to SCRB-seq analysis.

overall_design: Single-cell transcriptomics on mouse stromal cells after injury in the skin

first: Shruthi

last: Kalgudde Gopal

first: Anna

last: Stefanska

first: Herbert

middle: B

last: Schiller

first: Yuval

last: Rinkevich


title: Intronic Circular RNA hsa_circ_0092339 Plays as Molecular Sponge in Castration-resistance Prostate Cancer by hsa-mir-940/C-MYC Axis

city: Tianjin

first: Hanlin

last: Li

state: Tianjin

address: 23, Pingjiang Rd, Hexi District

institute: Tianjin Medical University

summary: Generally, only exonic circular RNA is believed to play the role as molecular sponge, while the main function of intronic circular RNA is regulating the expression of its parental gene. We aimed to find out whether intronic circular RNA could also act as molecular sponge in castration-resistance prostate cancer. Gene chip of castration-resistant and hormone-sensitive prostate cancer cell lines was sequenced to identify the differentially expressed circular RNA. We demonstrated that intronic circular RNA hsa_circ_0092339, located in the nucleus, was highly expressed in castration-resistance prostate cancer (CRPC) cell lines by using high throughput RNA sequencing. By knocking down hsa_circ_0092339, we found that this intronic circular RNA did not regulate the expression of its parental gene. By RIP and RNA pull-down experiment, we further found hsa_circ_0092339 realized its function by acting as molecular sponge. Hsa_circ_0092339 prevented degradation of C-MYC by absorbing hsa-mir-940 and preventing it enter the cytoplasm from nucleus. The combination of hsa-mir-940 and C-MYC was certified by dual-luciferase assay. In addition, we proved this axis was also effective in CRPC xenografted model. The effectiveness of this pathway in tissues was verified by animal experiments.

overall_design: RNA-sequencing after hsa_circ_0092339 was knocking down in LNCaP-AI cell line

first: Zhiqun

last: Shang

first: Yuanjie

last: Niu


title: FOXK2 transcriptionally activating VEGFA induces apatinib resistance in anaplastic thyroid cancer through VEGFA/VEGFR1 pathway (RNA-seq)

first: Weihua

last: Qiu

address: Ruijin 2 road

institute: Ruijin Hospital, Shanghai Jiao Tong University School of Medicine

summary: To identify differentially expressed genes caused by FOXK2 overexpression, RNA-seq was performed on(Anaplastic thyroid cancer cell line) CAL62/oeFOXK2 and CAL62/Vector cells (N = 3 biological replicates).

overall_design: RNA-seq was performed on (Anaplastic thyroid cancer cell line) CAL62/oeFOXK2 and CAL62/Vector cells (N = 3 biological replicates).


title: FOXK2 transcriptionally activating VEGFA induces apatinib resistance in anaplastic thyroid cancer through VEGFA/VEGFR1 pathway

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

overall_design: Refer to individual Series


title: FOXK2 transcriptionally activating VEGFA induces apatinib resistance in anaplastic thyroid cancer through VEGFA/VEGFR1 pathway (ChIP-seq)

summary: Chromatin immunoprecipitation -seq analysis of FOXK2 was performed on(Anaplastic thyroid cancer cell line) CAL-62 cells(WT).

overall_design: Chromatin immunoprecipitation -seq analysis of FOXK2 (ILF-1) was performed on(Anaplastic thyroid cancer cell line) CAL62 cells(WT).


title: Astragaloside IV attenuates macrophage-derived exosomes induced peritoneal fibrosis after inflammatory injury through the miR-204-5p/Foxc1 pathway

city: Nanjing

first: Yun

last: Shan

address: No.138 Xianlin Avenue, Qixia District

institute: Nanjing University of Chinese Medicine

type: Non-coding RNA profiling by high throughput sequencing

summary: Peritoneal dialysis (PD) is a successful renal replacement therapy for end-stage renal disease that effectively improves the quality of life. Long-term PD causes epithelial mesenchymal transformation (MMT) of peritoneal mesothelial cells, leading to peritoneal fibrosis which reduces the efficiency of PD. Macrophages are considered players in the onset and perpetuation of peritoneal injury. Yet, the mechanisms employed by macrophage-mesothelial cells communication to regulate peritoneal fibrosis are not fully elucidated resulting in lack of disease-modified drugs. This study analyzes the role of macrophage-mesothelial cell communication by intraperitoneal injection of macrophage derived exosomes in PD model rats. These results show that macrophages secrete exosomal miR-204-5p that directly targets Foxc1, leading to the activation of MMT in mesothelial cells. The data also shows that intraperitoneal injection of dissolved AS-IV can improve MMT by altering macrophage derived exosomal miRNAs. This study indicates that intercellular crosstalk between peritoneal macrophages and mesothelial cells is mediated by macrophage derived miR-204-5p-containing exosomes that control the MMT progression, providing AS-IV for prevention and treatment of PD induced peritoneal fibrosis. Our results demonstrate, for the first time, a novel role of the AS-IV on miR-204-5p/Foxc1/β-catenin axis in improving peritoneal fibrosis in vivo and vitro.

overall_design:
The high-throughput miRNA sequencing from macrophage derived exosomes
Exosomes from rat peritoneal macrophage stimulated by Control, LPS or LPS+AS-IV were collected and dissolved in 100ul PBS. Exosomal RNA was extracted for small RNA sequencing analysis.

first: Manshu

last: Yu

first: Lei

last: Tang

first: Huimin

last: Cao

first: Jun

last: Shi

first: Xiaolin

last: Zhu

first: Li

last: Sheng

first: Junyi

last: Zhao

first: Meixiao


title: Characterizing the molecular-physiological basis of pollen abortion upon prolonged high temperature stress

city: Nijmegen

first: Ivo

last: Rieu

state: Gelderland

address: Heyendaalseweg 135

department: Plant Systems & Physiology

country: Netherlands

institute: Radboud University

summary: We evaluated the transcriptomic response of developing tomato anthers to long-term mild heat (LTMH-) stress. Our results indicated changes in HSR-, carbohydrate-, and phytohormone-related gene expression and a delayed reduction in tapetum-related gene expression.

overall_design: mRNA profiles of tetrad stage-, free microspore stage-, and polarized microspore stage tomato anthers after exposure to long-term mild heat stress

first: Stuart

last: Jansma

first: Wilco

last: Ligterink


title: Effect of Insulin receptor deletion in hepatocytes on liver gene expression at three distinct time points in male mice (C57BL/6J) fed ad libitum a chow diet

city: Toulouse

first: Hervé

last: Guillou

address: 180 Chemin de Tournefeuille

department: ToxAlim

country: France

institute: INRAE

summary: To assess the consequences of IR deletion on gene expression using microarray and its contribution of IR to the control of nocturnal and diurnal liver activity, we analyzed liver gene expression during the day (ZT8), at day-night transition (ZT12) and at night (ZT16).

overall_design: To generate tamoxifen-inducible hepatocyte-specific IR knockout mouse line (IRhep-/-) and their control (IRhep+/+), animals carrying LoxP sites flanking the fourth exon of the IR gene (IRlox/lox stock number: 006955; Jackson Laboratory, Bar Harbor, ME, USA) were intercrossed with C57BL/6J mice, which specifically express Cre recombinase in the liver under the transthyretin promoter (TTR-CreTam mice), as previously described (Nemazanyy et al., 2015; Smati et al., 2020). Total liver RNA was extracted using TRI Reagent (Molecular Research Center, Inc., Cincinnati, OH, USA). Gene expression profiles were obtained at the GeT‐TRiX facility (GenoToul, Genopole Toulouse Midi-Pyrénées) using Agilent Sureprint G3 Mouse GE v2 microarrays (8x60K, design 074809) following the manufacturer's instructions.

first: Tiffany

last: Fougeray

first: Arnaud

last: Polizzi

first: Marion

last: Régnier

first: Anne

last: Fougerat

first: Anne-Françoise

last: Burnol

first: Catherine

last: Postic

first: Alexandra

last: Montagner

first: Claire

last: Naylies

first: Yannick

last: Lippi


title: Transcriptome analysis and differentially expressed gene screening for hypoxic-ischemic brain damage in rats treated with acupuncture

first: Xin

last: Jiang

address: No.232 Waihuandong Road, Panyu District, Guangzhou

institute: Guangzhou University of Chinese Medicine

summary:
Purpose: Hypoxic-ischemic brain damage (HIBD) is one of the most common critical diseases in neonates and has high mortality and disability rates. Increasing evidence shows that long non-coding RNAs(lncRNA) plays an important role in the development of HIBD. Recently, acupuncture therapy has been found to be effective in the treatment of HIBD. However, the mechanism of lncRNA in acupuncture treatment of HIBD is still unclear.
Method: In this study, a whole transcriptometric RNA-sequencing technique was applied to investigate transcriptome changes caused by acupuncture in PFC.
Results: A total of 48 mRNAs (7 up-regulated and 41 down-regulated) and 65 lncRNAs (17 up-regulated and 48 down-regulated) was identified relate to acupuncture group and model group. According to Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO) analysis, we found several lncRNAs and their target mRNAs were related to PI3K-Akt signaling pathway, TNF signaling pathway and NOD-like receptor signaling pathway, etc.
Conclusion: we found several significant lncRNAs whose corresponding target genes might be the targets of acupuncture therapy for HIBD. The results of our study may provide new perspectives on the mechanism of acupuncture and affect the diagnosis and therapy of HIBD

overall_design: Prefrontal mRNA, lncRNA and circRNA profiles of SD rats in normal, model (HIBD) and acupuncture groups.

first: Weixun

last: Qin

first: Junyan

last: Wu


title: Integrative single-cell RNA and T-cell receptor analyses reveal transcriptional features of antigen-reactive tumor-infiltrating regulatory T cells in patients with lung cancer

city: Boston

first: JAE WON

last: CHO

state: MA

address: 60 Fenwood Road

department: Neurology

institute: Brigham and Women's Hospital

summary: Background: T-cell receptor (TCR) stimulation is essential to complete differentiation of tumor-infiltrating regulatory T cells (T-Tregs). Therefore, elucidation of TCR-dependent regulatory network involved in activation and proliferation of T-Tregs will facilitate discovery of novel antitumor remedy. Here, we investigated transcriptional features specific for antigen-reactive Tregs by harnessing single-cell RNA and TCR analyses of human Tregs derived from patients with non-small cell lung cancer (NSCLC).  Methods: Assuming Tregs undergo clonal expansion in response to antigens, we sought for transcriptional features specific for antigen-reactive Tregs by comparing gene expression of Tregs with unique TCR clonotypes and those with expanded TCR clonotypes. To verify the identified molecule, multiplex immunohistochemistry and flow cytometry were used.  Results: We found that the proportion of Tregs with expanded clonotypes was much higher in the tumor than in the periphery blood. We also found that T-Tregs with shared clonotypes were transcriptionally more similar to each other than to those with different clonotypes. Finally, we identified SYNGR2, TNFRSF18, DUSP4, and CTLA4 as core signature genes for T-Tregs with expanded clonotypes and confirmed their existences expressed on human T-Tregs. Interestingly, T-Treg-specific co-regulatory network revealed that SYNGR2, TNFRSF18 and DUSP4 are potential coordinators between TCR-dependent activation and cell proliferation.  Conclusions: Our study shed light on regulatory insights of TCR-dependent Treg activation and differentiation in tumor and therapeutic strategies for patients with NSCLC.

overall_design: The study is composed of 4 samples from 4 human non-small-cell lung cancer patients, respectively. Each sample is composed of tumor-infiltrating Treg, blood-Treg, and blood-naïve-Treg. From each sample, scRNA-seq, CITE-seq ,and scVDJ-seq were performed

first: Hye

middle: R

last: Kim

first: Jae-Won

last: Cho

first: Haydn

middle: T

last: Kissick

first: Se

last: Im

first: Maria

middle: A

last: Cardenas

first: Jennifer

middle: W

last: Carlisle

first: Suresh

last: Ramalingam

first: Yun

last: Chang

first: Gamin

first: Sunhye

last: Shin

first: Seong

middle: Y

last: Park

first: Sang-Jun

last: Ha

first: Insuk

last: Lee

first: Ahmed

last: Rafi


title: Gene expression changes in human non-transformed breast epithelial cell lines with ARID1A knockdown.

first: Jie

last: Wang

address: 416 Rm., MingdaoBldg., 131 Dongan Rd., Shanghai 200032, P.R.China

institute: Fudan University

summary: We measured changes in gene expression using human non-transformed breast epithelial cell lines with ARID1A knockdown.

overall_design: HMEC-pLKO.1, HMEC-sh-ARID1A, MCF10A-pLKO.1, and MCF10A-sh-ARID1A cells in 6cm plates were subjected. Total RNA were amplified, labeled and purified using GeneChip 3’IVT Express  Kit (Cat#901229, Affymetrix, Santa Clara, CA, US) and subjected to analysis by microarray using the Affymetrix Human U133plus2.0 chip.

first: J

first: H

last: Yan

first: Q

last: Zhang

first: Y

last: Jiang

first: P

last: Yang

first: F

last: Liu


title: Transcriptome analysis of Artemisia annua L. seedlings under UV-B radiation

city: shanghai

first: yongp

last: li

address: shanghai

institute: shanghai jiaotong university

summary:
Purpose: UV-B radiation is a pivotal photomorphogenic signal and positively regulates plant growth and metabolite biosynthesis. In order to elucidate the transcriptional regulation mechanism underlying UV-B-induced artemisinin and flavonoid biosynthesis in Artemisia annua, the transcriptional response of A. annua leaves to UV-B radiation was analyzed using the Illumina transcriptome sequencing.
Methods: For UV-B treatment, six-week-old A. annua seedlings growing under normal growth condition were supplemented with extra narrowband UV-B lamps (Philips TL20W/01RS; 1.5 μmol·m-2·s-1)(Yin et al. 2016). The most recently expanded leaf for each A. annua seedling was collected at 0, 2, 4 and 6 hours after exposure to UV-B radiation.
Results: A total of 10706 differentially expressed genes including 533 transcription factors, were identified. Based on the expression trends of the differentially expressed factors as well as artemisinin and flavonoid biosynthesis genes, we speculated that transcription factors belonging to 6 clusters were most likely to be involved in the regulation of artemisinin and/or flavonoid biosynthesis. The regulatory relationship between transcription factors and artemisinin/flavonoid biosynthetic genes was further studied. Dual-LUC assays results showed that AaMYB6 is a positive regulator of AaLDOX, which belongs to flavonoid biosynthesis pathway. In addition, we identified a R2R3MYB transcription factor, AaMYB4 which positively mediated both artemisinin and flavonoid biosynthesis pathways by activating the expression of AaADS and AaDBR2 in artemisinin biosynthesis pathway and AaUFGT in flavonoid biosynthesis pathway.
Conclusions: our findings provide fundamental knowledge for the further analysis of the parallel transcriptional regulation of artemisinin and flavonoid biosynthesis in A. annua L. under UV-B radiation.

overall_design: Six-week-old A. annua seedlings growing under normal growth condition were supplemented with extra narrowband UV-B lamps (Philips TL20W/01RS; 1.5 μmol·m-2·s-1). The most recently expanded leaf for each A. annua seedling was collected at 0, 2, 4 and 6 hours after exposure to UV-B radiation.

first: Yongpeng

last: Li

first: Kexuan

last: Tang


title: Discovery of TF-gene regulatory interactions identifies new targets in CRLF2-overexpressing B-ALL

city: New York

first: Jane

last: Skok

address: 550 First Ave

department: Pathology

institute: NYU School of Medicine

summary: We analyzed the impact of CRLF2 overexpression on transcriptional and chromatin accessibility landscape in primary patient samples and cell lines in B-cell leukemia.

overall_design: RNA-seq and ATAC-seq in B-cell leukemia patients and cell lines.

first: Sana

last: Badri


title: A single-cell genomic strategy for alternative TSSs identification

city: Shenzhen

first: Yanling

last: Peng

address: Pengfei Road 7, Dapeng new distinct

department: Animal Functional Genomics Group

institute: Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences


title: Development of gene expression signatures for barrier recovery phase in epidermis from acute barrier disruption

city: Sapporo

first: Takashi

last: Teramura

address: North 15 West 7, Kita-ku

country: Japan

institute: Hokkaido University

summary: The skin barrier consists of multiple lipid-enriched layers. Sodium lauryl sulfate is a well-known substance that can disrupt the skin barrier. The mechanisms underlying the barrier repair process, especially the influence of topical sodium lauryl sulfate treatment  in the barrier recovery phase remain unresolved. To understand the process of reconstruction of the intercellular lipid layer of the skin after acute barrier disruption by sodium lauryl sulfate treatment in vivo.

overall_design: Female hairless mice were treated with 3% sodium lauryl sulfate. Gene expression analysis were performed from 1 to 288 h after the topical application of 3% sodium lauryl sulfate.


title: A single-cell genomic strategy for alternative TSSs identification [scTSS-seq]

summary: Alternative transcription start sites (TSSs) usage plays a critical role in gene transcription regulation in mammals. However, precisely identifying alternative TSSs remains challenging at the genome-wide level. Here, we report a single-cell genomic technology for alternative TSSs annotation and cell heterogeneity detection. Here, we utilize Fluidigm C1 system to capture individual cells of interest, SMARTer cDNA synthesis kit to recover full-length cDNA, then dual priming oligonucleotide system to specifically enrich 5’-end tags for genomic analysis.

overall_design: Apply single-cell TSS-seq in a genome-wide study of alternative TSSs identification in IFN-β stimulated mouse fibroblast cells (MEFs).

first: Yubo


title: RNA sequencing results of wild type and knockout USP11 in E13.5 or E18.5 of cortex based on IlluminaNovaSeq 6000 platform

city: Taipei

first: Shang Yin

last: Chiang

address: 6F.-602, IBC, No.128, Sec. 2, Academia Rd., Nangang Dist.

department: Institute of Biological Chemistry

country: Taiwan

institute: Academia Sinica

summary: We found that USP11 expression perturbed neurogenesis.

overall_design: Gene expression profiles of knockout USP11 mice in E13.5 and E18.5 cortex were generated by Illumna RNA sequencing and compared to profiles derived from wild type cortex.

first: Shang-Yin

first: Ruey-Hwa

last: Chen


title: Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type CD8a+ Dendritic cells upon pIC stimulation

city: Bhubaneswar

first: Sunil

middle: Kumar

last: Raghav

state: Odisha

address: Nalco Square

department: Infectious Disease Biology

country: India

institute: Institute of Life Sciences

summary: Purpose: The goals of this study to understand gene expression at the transcriptional level in CD8a+ Dendritic cells after TLR3 activation by pIC.

overall_design: Methods: mRNA expression of  Empty vector transduced cells followed by pIC activation were generated by deep sequencing, in duplicate, using Illumina HiSeq 2000 platform. The sequencing reads that passed quality filters were analyzed at the transcript level with two methods:TopHat followed by Cufflinks.

first: Abdul

last: Ahad

first: Shuchi

last: Smita

first: Gyan

middle: P

last: Mishra

first: Viplov

middle: K

last: Biswas

first: Kaushik

last: Sen

first: Bhawna

last: Gupta

first: Dominique

last: Garcin

first: Hans

last: Acha-Orbea


title: Next-Generation Sequencing Facilitates Quantitative Analysis of Interferon-Stimulated MEFs Transcriptomes [RNA-Seq]

summary: Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare NGS-derived interferon-stimulated MEF cells transcriptome profiling (RNA-seq).

overall_design: mRNA profiles of interferon-stimulated MEF cells derived from H3.3-HA knock-in mice were generated by deep sequencing, using Illumina HiSeq2000.

last: Zhang


title: Regulation of actin cytoskeleton signaling pathways improves egg-production through up-regulation of integrin beta family genes expression in ducks

city: Longyan

first: Yanfa

last: Sun

state: Fujian

address: Dongxiao North Road No. 1, Xinluo District

department: College of Life Science

institute: Longyan University

summary: Ovaries transcriptomic profiling between of egg of three high number of laying eggs (HEN) and three low number of laying eggs (LEN) in Longyan Shan-ma duck at 71 weeks were sequenced using Illumina Hiseq 2500 technology.

overall_design: At 71 weeks, three duck with the high egg number (HEN) and three duck with the low egg number (LEN) from full-sib family were weighed and the number of laying egg, average egg weight and total egg weight were calculated. The ducks were killed by stunning and exsanguination, 12 h after feed was withheld. Samples from the ovarian tissue were separated and snap-frozen in liquid nitrogen until RNA sequencing and analysis of relative mRNA expression

first: Min


title: TfR1 binding with H-ferritin nanocarrier achieves prognostic diagnosis and enhances the therapeutic efficacy in clinical gastric cancer

city: BEIJING

first: XJ

last: Cheng

state: BEIJING

address: 52 FUCHENG ROAD

institute: Beijing Cancer Hospital

summary: H-ferritin (HFn) nanocarrier is emerging as a promising theranostic platform for tumor diagnosis and therapy, which can specifically target tumor cells via binding transferrin receptor 1 (TfR1). This led us to investigate the therapeutic function of TfR1 in GC. The clinical significance ofTfR1 was assessed in 178 GC tissues using a magneto-HFn nanoparticle-based immunohistochemistry method. Therapeutic effects of doxorubicin-loaded HFn nanocarriers evaluated on TfR1 positive GC patient-derived xenograft (GC-PDX) models. The biological function of TfR1 was investigated through in vitro and in vivo assays. TfR1 was upregulated (73.03%) in GC tissues and reversely correlated with patient outcome. TfR1 negative sorted cells exhibited tumor-initiating feature, which enhanced tumor formation in vitro and in vivo, migration/invasion, whereas TfR1 positive sorted cells showed significant proliferation ability. Knockout of TfR1 in GC cells also enhanced cell invasion. TfR1 deficient cells displayed immune escape by upregulating PD-L1, CXCL9 and CXCL10, when disposed by IFN-γ. Western blot results demonstrated that knockout of TfR1 in GC cells upregulated Akt and STAT3 signaling. Moreover, in TfR1 positive GC-PDX models, HFn-Dox group significantly inhibited tumor growth and increased mouse survival compared with that of free-Dox group. TfR1 could be a potential prognostic and therapeutic biomarker for GC: (i) TfR1 reversely correlated with patient outcome and its negative cells possess tumor aggressive features; (ii) TfR1 positive cells can be killed by H-ferritin nanocarrier. Given the heterogeneity of GC, HFn nanocarrier combined with other therapies towards TfR1 negative cells (such as: small molecule or immunotherapy etc.) will be new options for GC treatment.

overall_design: Detection of 2 different mRNA results by deep sequencing in 2 TfR1 negative (NG) and positive (PS) cells sorted by FACS.

first: Xiaojing

first: Kelong

last: Fan

first: Jiafu

last: Ji

first: Xiyun

last: Yan


title: Transcriptome comparison of adipose tissue in Iranian fat and thin-tailed sheep breeds using RNA-seq technique

city: Tabriz

first: Sana

last: Farhadi

address: Golgasht street

country: Iran

institute: Tabriz University

summary: An essential tissue involved in the development and regulation of lipid metabolism in animals is adipose tissue. The “fat-tail” can supply energy for sheep during migration and winter when a low amount of dry matter intake is available. Tail fat content affects meat quality and varies significantly among the different breeds of sheep. Ghezel (fat-tailed) and Zel (thin-tailed) are two important local Iranian sheep breeds that show different patterns of fat storage. The current study presents the transcriptome characterization of tail fat using RNA-sequencing in order to get a better comprehension of the molecular mechanism of lipid storage in the two sheep breeds. The results of sequencing were analyzed with bioinformatics methods, including differentially expressed genes (DEGs) identification, functional enrichment analysis, structural classification of proteins, protein–protein interaction (PPI), network analysis and module analysis. The results revealed a total of332 DEGs between the Zel and Ghezel breed, with78 up-regulated and 254 down-regulated DEGs in the Zel breed. Identification of differential genes showed that some DEGs, such as IL-6, LIPG, SAA1, SOCS3 and HIF-1α, with the largest fold change had close association with lipid deposition. Also, important lipid storage genes such as FASN and SCPEP1 had high levels of expression. Furthermore, functional enrichment analysis revealed some pathways associated with fat deposition, such as “Fatty acid metabolism”, “Fatty acid biosynthesis” and“HIF-1 signaling pathway”. In addition, structural classification of proteins showed major DEGs in transcription factor classes such as JUNB, NR4A3, FOSL1, MAFF, NR4A1, CREB3L1 and ATF3 were up-regulated in the Zel breed. IL-6, JUNB, and related DEGs were up-regulated in the PPI network.HMGCS1, SUCLA2 and STT3B and related DEGs were down-regulated in the PPI network and had high topology scores as hub genes. This implies the DEGs of these modules are important candidate genes for tail fat metabolism and, therefore, can be further studied.

overall_design: Fat subcutaneous mRNA profiles of 7-month old fat and thin tail sheep breeds were generated by deep sequencing, in duplicate using Illumina Hiseq 2000

first: Jalil

last: Shodja

first: Esmail

last: Ebrahimie

first: Karim

last: Hasanpour

first: Abolghasem

last: Mohammadi


title: RNA-seq analysis about MuERVL knocked down samples

city: Tainjin

first: Weiyu

address: No.38 Tongyan Road, Jinnan District

institute: Nankai University

summary: Endogenous retrovirus MERVL is specifically expressed in a minority of embryonic stem cells and 2-cell embryos. To determine the function of MERVL transcripts, we knocked down MuERVL and analyzed the effect on the expression of MERVL and its targeting genes. It turns out the downregulation of MuERVL would lead to downregulation of MERVL nearby genes. This study extends our understandings of the machanism by which MERVL regulates its neatby genes.

overall_design: We knocked down MuERVL in E14 by shRNA. We performed RNA-seq analysis in order to exam the transcriptome after MuERVL knockdown.

first: Ruiqing

last: Chen


title: Comprehensive transcriptome study of salinity stress of salt-tolerant  and sensitive genotypes rice at seedling stage

city: Düsseldorf

first: Andreas

middle: PM

last: Weber

address: Universitätsstr. 1

department: Institute for Plant Biochemistry

institute: Heinrich-Heine-University

summary: In order to understand molecular mechanisms of salt stress tolerance in rice several researches have been reported, however there are still unclear processes involved in salt tolerance. For reaching to a better perspective of the molecular mechanisms, we designed a comprehensive transcriptome study consisting contrasting genotypes, different tissues and different sampling time points. Two contrasting genotypes were selected and grown in Yoshida hydroponic medium for 14 days under controlled conditions. For salinity stress half of the seedlings were under 150 mM NaCl and after 6 and 54 h the treated and untreated samples were harvested in three replications from roots and shoots separately

overall_design: 48 samples were used for sequencing including two contrasting genotypes (CSR28 and IR28), two treatments (control and 150 mM salinity), two tissues (root and shoot) and two sampling time points (6 h and 54 h) in three biological replications

first: Mojdeh

last: Lelekami

first: Dominik

last: Brilhaus

first: Samantha

last: Flachbart


title: ChIP-Sequencing experiment for N1IC and β-Catenin in Jurkat T-ALL cells.

city: Barcelona

first: Christos

last: Gekas

address: Carrer del Doctor Aiguader 88, Lab277

country: Spain

institute: Centre for Genomic Regulation (CRG)

summary: Notch activation is instrumental in the development of most T-cell acute lymphoblastic leukemia (T-ALL) cases, yet Notch mutations alone are not sufficient to recapitulate the full human disease in animal models. Using multiple in vivo and in vitro T-ALL models we here demonstrate that β-Catenin is essential for Notch-driven T-cell leukemic initiation. Transcriptome analyses of leukemic initiating cells revealed a switch in β-Catenin activity that was Notch-context dependent. Moreover, ChIP-seq coupled with RNA-Seq in human Notch-active T-ALL showed that leukemic β-Catenin was independent of canonical LEF/TCF partners, and instead depended on direct association with Notch or ZBTB33/Kaiso for gene activation. The functional relevance of this mechanism is exemplified by the MYC 3´enhancer that requires β-Catenin and Notch1 recruitment to induce MYC expression. Finally, we demonstrate that pharmacological inhibition of β-Catenin with PKF115-584 prevented and partially reverted leukemogenesis induced by active Notch1.

overall_design: Examination of chromatin immunprecipitated with antibodies against 2 transcription factors (N1IC and β-Catenin) in Jurkat T-ALL cells.


title: Non-conventional β-catenin activity is essential for Notch1-driven T-cell leukemia

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: Gene expression analyses of GFP+ sorted, lineage depleted (Lin-) bone marrow (BM) cells from wild-type or VavCre+β-Catenin-KO mice infected with pMIG-GFP (control) or pMIG-N1IC-GFP retrovirus.

summary:
Notch activation is instrumental in the development of most T-cell acute lymphoblastic leukemia (T-ALL) cases, yet Notch mutations alone are not sufficient to recapitulate the full human disease in animal models. Using multiple in vivo and in vitro T-ALL models we here demonstrate that β-Catenin is essential for Notch-driven T-cell leukemic initiation. Transcriptome analyses of leukemic initiating cells revealed a switch in β-Catenin activity that was Notch-context dependent. Moreover, ChIP-seq coupled with RNA-Seq in human Notch-active T-ALL showed that leukemic β-Catenin was independent of canonical LEF/TCF partners, and instead depended on direct association with Notch or ZBTB33/Kaiso for gene activation. The functional relevance of this mechanism is exemplified by the MYC 3´enhancer that requires β-Catenin and Notch1 recruitment to induce MYC expression. Finally, we demonstrate that pharmacological inhibition of β-Catenin with PKF115-584 prevented and partially reverted leukemogenesis induced by active Notch1.
These microarray data show the transcriptional activities of N1IC and β-Catenin in wild-type or leukemic initiating cell (LIC) contexts in N1IC-transduced adult Lineage-depleted BM cells.

overall_design: Study is based on biological triplicates. Total RNA from 500-2500 transduced BM Lin- GFP+ sorted cells was isolated with RNEasy Mini or Micro kits (QIAgen). RNA quality was assessed with the Bioanalyzer 2100 PicoChip (Agilent Technologies, Palo Alto, CA) and only RNA samples with RIN >6 was used for microarrays. RNAs were amplified using the Ovation™ Pico WTA System (NuGEN Technologies, San Carlos, CA) and sense transcript cDNA (ST-cDNA) was generated using the WT-Ovation™ Exon Module (NuGEN Technologies). After, ST-cDNA was fragmented and labelled with the FL-Ovation™ cDNA Biotin Module V2 (NuGEN Technologies), and the biotinylated cDNA were hybridized to Affymetrix GeneChip® Mouse Gene 1.0 ST arrays as biological triplicates. Following hybridization, the arrays were washed, stained and scanned to generate CEL files for each array. CEL files were analyzed in R (v3.1.2) with the oligo (v1.30.0) and limma (v3.22.4) packages from Bioconductor, data were normalized using RMA (Robust Multi-array Average) and expression values log2-transformed.


title: Adaptation of the circadian clock during the evolution of C4 photosynthesis

sample_organism:
Flaveria bidentis
Flaveria robusta

platform_organism:
Flaveria bidentis
Flaveria robusta

overall_design: RNA was extracted from leaves harvested every for hours from Flaveria bidentis (C4) and Flaveria robusta (C3) plants (2 biological replicates) grown for two days under entrained (10 hr light, 14 hr dark) and two days under free-running (constant light) conditions

first: Thea

last: Pick


title: RNA profile of nuclei isolated from neurons coexpressing VAChT and VGlut or VAChT and VGAT

status: Public on Dec 31 2022

city: Waltham

first: Albert

middle: Dayuan

last: Yu

address: 415 South St.

department: Molecular and Cell Biology

institute: Brandeis University

summary:
The concept of neurotransmitter identity, once considered singular and immutable for mature neurons, has been broadened by the recognition that many neurons release multiple neuro-active substances.
In order to demonstrate the extent of neurotransmitter co-expression, we labelled neuronal nuclei with UNC84-GFP using VAChT and either Vglut or VGAT split-GAL4s and isolated them with the isolation of nuclei tagged in specific ell types (INTACT) method
From the isolated nuclei, we isolated and sequenced Poly(A) RNA and examined the relative expression levels of glutamatergic, GABAergic, or cholinergic genes in each population.

overall_design: Comparative gene expression profiling analysis of RNA-Seq data from INTACT purified nuclei from VAChT:Vglut split Gal4/UAS-UNC84-GFP and VAChT:VGAT split Gal4/UAS-UNC84-GFP flies

first: Yunpeng

last: Zhang

first: Nannan

first: Emmanuel

last: River-Rodriguez

first: Michael

last: Hobin

last: Rosbash

first: Leslie

last: Griffith


title: Gene expression analyses of E14.5 fetal liver Lin-Sca1+ckit+ (LSK) cells from wild-type, β-Catenin-KO, N1IC+ and N1IC+β-Catenin-KO embryos.

summary:
Notch activation is instrumental in the development of most T-cell acute lymphoblastic leukemia (T-ALL) cases, yet Notch mutations alone are not sufficient to recapitulate the full human disease in animal models. Using multiple in vivo and in vitro T-ALL models we here demonstrate that β-Catenin is essential for Notch-driven T-cell leukemic initiation. Transcriptome analyses of leukemic initiating cells revealed a switch in β-Catenin activity that was Notch-context dependent. Moreover, ChIP-seq coupled with RNA-Seq in human Notch-active T-ALL showed that leukemic β-Catenin was independent of canonical LEF/TCF partners, and instead depended on direct association with Notch or ZBTB33/Kaiso for gene activation. The functional relevance of this mechanism is exemplified by the MYC 3´enhancer that requires β-Catenin and Notch1 recruitment to induce MYC expression. Finally, we demonstrate that pharmacological inhibition of β-Catenin with PKF115-584 prevented and partially reverted leukemogenesis induced by active Notch1.
These microarray data show the transcriptional activities of N1IC and β-Catenin in wild-type or leukemic initiating cell (LIC) contexts in E14.5 FL LSK cells.

overall_design: Study is based on biological triplicates. Total RNA from 5-50k sorted FL LSK cells was isolated with RNEasy Mini or Micro kits (QIAgen). RNA quality was assessed with the Bioanalyzer 2100 PicoChip (Agilent Technologies, Palo Alto, CA) and only RNA samples with RIN >6 was used for microarrays. RNAs were amplified using the Ovation™ Pico WTA System (NuGEN Technologies, San Carlos, CA) and sense transcript cDNA (ST-cDNA) was generated using the WT-Ovation™ Exon Module (NuGEN Technologies). After, ST-cDNA was fragmented and labelled with the FL-Ovation™ cDNA Biotin Module V2 (NuGEN Technologies), and the biotinylated cDNA were hybridized to Affymetrix GeneChip® Mouse Gene 2.0 ST arrays as biological triplicates. Following hybridization, the arrays were washed, stained and scanned to generate CEL files for each array. CEL files were analyzed in R (v3.1.2) with the oligo (v1.30.0) and limma (v3.22.4) packages from Bioconductor, data were normalized using RMA (Robust Multi-array Average) and expression values log2-transformed.


title: RNA-seq analysis on thymic epitherial cells from Prmt5-cKO mice

city: Tokyo

first: Ryunosuke

last: Muro

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

department: Department of Immunology,

institute: Graduate School of Medicine and Faculty of Medicine, The University of Tokyo

summary: Thymic epithelial cells play the important role in the development of T cells. We performed RNA sequencing (RNA-seq) on thymic epithelial cells (mTEChi, mTEClo and cTEC)  isolated from control or Prmt5-cKO (Foxn1cre Prmt5flox/flox) or Aire-KO mice.

overall_design: RNA-seq analysis on thymic stromal cells isolated from WT or LTbR-deficient mice.


title: Targeted pseudouridylation: A novel approach for suppressing nonsense mutations in disease genes

city: Rochester

first: Paul

middle: L.

last: Boutz

address: 601 Elmwood Ave.

department: Biochemistry & Biophysics

institute: University of Rochester School of Medicine

summary: A large number of genetic diseases are caused by various mutations in specific disease genes. A significant proportion (~15%) of these mutations are nonsense mutations that create a premature termination codon (PTC). Consequently, the Nonsense-mediated mRNA Decay (NMD) surveillance pathway degrades a large fraction of PTC-containing mRNA. Translation of the remaining un-degraded PTC-containing mRNA terminates at the PTC, leading to no full-length protein production and hence disease. Therefore, suppressing NMD and translation termination at PTCs becomes an attractive strategy for combating these diseases. This work presents a novel approach, namely targeted PTC pseudouridylation, to suppress nonsense mutations in human cells. By co-transfecting human cells with a PTC-reporter gene and a designer box H/ACA guide RNA gene targeting the PTC, we show that targeted pseudouridylation suppresses both NMD and translation termination at PTCs in the contexts of various disease gene sequences. Furthermore, targeted pseudouridylation exhibits a level of suppression comparable to that of antibiotic treatments, and the suppressive effect is long-lasting in the cell. When targeted pseudouridylation is combined with the antibiotic treatment, a much higher level of suppression is observed. Remarkably, by transfecting a disease model cell line (carrying a chromosomal PTC) with a designer guide RNA gene alone targeting the PTC, we also observe nonsense suppression, suggesting the high potential of this novel approach in treating PTC-associated diseases. Finally, one of the restored full-length proteins is further tested to be functional. Targeted pseudouridylation appears to be the first RNA-directed gene-specific therapeutic approach that suppresses NMD and concurrently promotes PTC read-through.

overall_design: HEK293T cells were transfected with sgRNA expression plasmid to direct targeted pseudouridylation (psU samples), or mock transfected (wt samples), RNA was harvested and modified Pseudoseq was performed.

first: Yi-Tao


title: Effect of high and low FGF21 expression on metabolic, inflammatory and antioxidative stress-related parameters in early lactating dairy cows

city: Giessen

first: Denise

last: Gessner

address: Heinrich-Buff-Ring

department: Animal Physiology and animal nutrition

institute: JLU Giessen

summary: Studies in rodent models have shown that fibroblast growth factor 21 (FGF21) is a liver-derived metabolic regulator that is induced in response to different stress conditions, such as energy and nutrient deprivation, inflammation and metabolic disorders. Recently, it has been shown that FGF21 expression in liver is dramatically induced in dairy cows during early lactation. However, the physiologically role of FGF21 in dairy cows has not been established so far. Therefore, the aim of this study was to gain knowledge about the physiological role of FGF21 in cows during this period. For this end, out of 30 cows, 8 cows with the highest FGF21 expression in the liver were compared to 8 cows with the lowest FGF21 expression.

overall_design: 16 liver total RNA samples were included in the microarray analysis. 8 cows with the highest FGF21 expression in the liver at wk 1 pp were compared to 8 cows with the lowest FGF21 expression out of 30 cows.

first: Lena

last: Sandrock

first: Erika

last: Most

first: Christian

last: Koch

first: Robert

last: Ringseis

first: Klaus

last: Eder


title: Transcriptomic profiling of Bone Marrow Derived Macrophages (BMDM) treated with KN93 by RNA sequencing

city: wuhan

first: Xiaomeng

last: Dai

address: Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China

summary: Studies have revealed that TAMs can promote tumor immune escape, tumor growth, angiogenesis, and metastasis. Targeting TAMs to reset M2 towards the anti-tumor M1 phenotype is considered as a promising strategy in cancer immunotherapy. Interestingly, we found in the current investigation that the expression level of CAMKII mRNA in M2 was much higher than that in M1 . Based on this finding, the CAMKII specific inhibitor KN93 was used to explore the effect on bone marrow-derived macrophages. Strikingly, KN93 significantly increased the expression of CD86 (M1 marker) and reduced CD206 (M2 marker) expression in a concentration-dependent manner by the flow cytometry. To further verify whether KN93 could affect the polarization of BMDMs at the transcriptome level, we cultured BMDMs with KN93 (5 μM or 10 μM) or PBS for 24 h and analyzed the global transcriptional profile in cells through RNA sequencing. Compared with control cells, KN93-treated BMDMs expressed significantly higher levels of M1-related transcriptional factors, cytokines and other molecules and lower levels of M2-associated transcriptional factors, cytokines and other molecules. Conclusively, these results demonstrate that targeting CAMKII reprogramed M2 toward the M1 phenotype in vitro.

overall_design: Total RNA was extracted from mice BMDMs treated with PBS or KN93 at different concentrations using a TRIzol reagent

first: Jingshu

last: Meng

first: Suke

last: Deng

first: Lingling

first: Chao

last: Wan

first: Lisen

last: Lu

first: Jing

last: Huang

first: Yan

last: Hu

first: Zhanjie

first: Jonathan

middle: F

last: Lovell

first: Gang

last: Wu

first: Kunyu

last: Yang

first: Honglin

last: Jin


title: Clonal replacement sustains long-lived germinal centers primed by respiratory viruses

first: Tiago

last: Castro

state: New York

address: 1230 York Avenue

institute: The Rockefeller University

summary: Germinal centers (GCs) form in secondary lymphoid organs in response to infection and immunization and are the source of affinity-matured B cells. The duration of GC reactions spans a wide range, and long-lasting GCs (LLGCs) are potentially a source of highly mutated B cells. We show that, rather than consisting of continuously evolving B cell clones, LLGCs elicited by influenza virus or SARS-CoV-2 infection in mice are sustained by progressive replacement of founder clones by naïve-derived invader B cells that do not detectably bind viral antigens. Rare founder clones that resist replacement for long periods are enriched in clones with heavily mutated immunoglobulins, including some with very high affinity for antigen, that can be recalled by boosting. Our findings reveal underappreciated aspects of the biology of LLGCs generated by respiratory virus infection and identify clonal replacement as a potential constraint on the development of highly mutated antibodies within these structures.

overall_design: Total GC B cells from lymph nodes were fate-mapped at 8 and 3 weeks post infection, pooled with controls  and sequenced using the 10x sequencing platform.

first: Carvalho

middle: V

last: Renan

first: Ersching

last: Jonatan

first: Barbulescu

last: Alexandru

first: Hobbs

last: Alvaro

first: Castro

last: Tiago

first: Mesin

last: Luka

first: Jacobsen

last: Johanne

first: Phillips

last: Brooke

first: Hoffman

last: Hans-Heinrich

first: Parsa

last: Roham

first: Canesso

last: Maria Cecilia

first: Nowosad

last: Carla

first: Feng

last: Allan

first: Leist

last: Sarah

first: Baric

middle: S

last: Ralph

first: Yang

last: Emily

first: Utz

middle: J

last: Paul

first: Victora

last: Gabriel


title: small RNA sequencing of human endothelial cells (HUVECs)

city: Newcastle Upon Tyne

first: Konstantinos

last: Stellos

state: England

address: Central Parkway, Centre for Life

department: Faculty of Medical Sciences

country: United Kingdom

institute: Newcastle University

summary: We report that ADAR2 regulates small RNAs (miRNAs) expression in human endothelial cells.

overall_design: Evaluation of small RNA expression in endothelial cell transcriptome after ADAR2 knockdown.

first: Aikaterini

last: Gatsiou


title: Effects of PFKFB4 deletion on transcriptional reprogramming in breast cancer cells

city: Buffalo

first: Subhamoy

last: Dasgupta

address: Elm and Carlton Streets

institute: Roswell Park Comprehensive Cancer Center

summary: To explore the mechanisms by which PFKFB4 promotes breast cancer metastasis, we CRISPR-Cas knock-out PFKFB4 in two breast cancer lines for RNA-seq to identify downstream target genes that are regulated by PFKFB4

overall_design: Single-end mRNA sequencing was performed from wild-type (WT) or PFKFB4-knock-out (PFKFB4-KO) mouse EMT6 and human MDA-MB-231 breast cancer cells

first: Tao

last: Dai


title: Gene expression in the development of C3 and C4 Atriplex and C3 Atriplex prostrata x C4 Atriplex rosea F1 hybrids

first: Andreas

last: Weber

summary: Elucidating the genetic control of development of C3 and C4 photosynthesis. Atriplex rosea (C4) and Atriplex prostrata (C3) were studied along a leaf developmental gradient to compare development between C3 and C4. C3 Atriplex prostrata x C4 Atriplex rosea F1 hybrid were studied along the same developmental gradient and will aid in identifying regulatory elements involved in C3 and C4 leaf development.

sample_organism:
Atriplex rosea
Atriplex prostrata
Atriplex prostrata x Atriplex rosea

overall_design:
Atriplex plants [Atriplex rosea and Atriplex prostrata] were grown in biological triplicates and C3 Atriplex prostrata x C4 Atriplex rosea F1 hybrids were all grown at ~500umol photons m^-2 s^-1 under 17 hr light / 7 hr dark. Samples for RNASeq were taken at equivalent developmental stages (according to the leaf plastochron index) two hours after the onset of light. If leaves were longer than 10mm, they were cut in half and analyzed separately for (a) bottom of the leaf and (b) top of the leaf.

Please note that, since part of the analysis is still in progress, the 'SupplementalDataset*.txt' does not yet contain results for all samples. The dataset will be updated as soon as the results are available.

first: Stefanie

last: Sultmanis

first: Udo

last: Gowik

first: Peter

last: Westhoff

first: Tammy

last: Sage


title: Reduced LYNX1 and epilepsy phenotype-related changes in transcriptome of human iPSC-derived neural progenitors modeling fragile X syndrome

city: Helsinki

first: Maija

last: Castrén

address: P.O.BOX 63

department: Faculty of Medicine/Physiology

country: Finland

institute: University of Helsinki

summary:
Transcriptome analysis of RNA samples collected from human control and FXS iPS cell-derived neural progenitors at day 1 and day 7 of differentiation
Lack of fragile X mental retardation protein results in fragile X syndrome (FXS), which is the most common inherited intellectual disability syndrome and serves as an excellent model disease to study molecular mechanisms behind neuropsychiatric comorbidities. We compared the transcriptomes of human neural progenitors (NPCs) generated from patient-derived induced pluripotent stem cells (iPSCs) of three FXS and three control male donors. Altered expression of RAD51C, PPIL3, GUCY1A2, MYD88, TRAPPC4, LYNX1, and GTF2A1L in FXS NPCs suggested changes related to triplet repeat instability, RNA splicing, testes development, and pathways previously shown to be affected in FXS. LYNX1 is a cholinergic break of tissue plasminogen activator (tPA)-dependent plasticity, and its reduced expression was consistent with augmented tPA-dependent radial glial process growth in NPCs derived from FXS iPSC lines. An analysis of gene expression in LYNX1-related signaling pathways revealed that NPCs derived from an FXS male with concomitant epilepsy differed from the other FXS NPCs. The differently expressed genes comprised several epilepsy-related genes, including genes shown to cause the auditory epilepsy phenotype in the murine model of FXS. Functional enrichment analysis highlighted regulation of insulin-like growth factor pathway in human NPCs modeling FXS with epilepsy. Our results link early gene expression changes of FXS NPCs with the pathogenesis of FXS and comorbid epilepsy.

overall_design: In this study, we analyzed gene expression profile of human iPS cell-derived neural progenitors reprogrammed from somatic cells of 3 healthy subjects and 3 patients diagnosed with FXS using the Affymetrix ClariomTM D Human array.

first: Karo

last: Talvio

first: Rimante

last: Minkeviciene

first: Padraic

last: Corcoran


title: Evolving a novel AAV variant for efficient gene delivery to murine T lymphocytes

city: durham

first: Jonathan

last: Ark

address: 3 genome ct

institute: Duke University

summary: Evolved an AAV6 capsid library on Murine T-cells.

overall_design: High throughput sequencing of evolved AAV6 capsid libraries

first: William

last: Nyberg

first: Justin

last: Eyquem

first: Aravind

last: Asokan


title: Resistance of MMTV-NeuT/ATTAC mice to anti-PD-1 immune checkpoint therapy is associated with activation of the Wnt pathway

city: Washington

first: Lu

last: Jin

address: 3970 Reservoir Rd NW

department: Oncology

institute: Georgetown University

summary: One of the central challenges for cancer therapy is the identification of factors in the tumor microenvironment that increase tumor progression and immune tolerance. In breast cancer, fibrosis is a histopathologic criterion for invasive cancer and poor survival that results from inflammatory factors and remodeling of the extracellular matrix to produce an immune tolerant microenvironment.

overall_design: To test whether this is associated with the immune checkpoint, Programmed Cell Death 1 (PD-1), NeuT/ATTAC mice, a conditional model of mammary fibrosis that we recently developed, were administered a murine-specific anti-PD-1 mAb related to pembrolizumab, and drug response was monitored in tumor gene expression by RNAseq.

first: Hongyan

last: Yuan

first: Changyan

last: Zhou

first: Robert

middle: I

last: Glazer


title: Gene expression in C3 and C4 Atriplex leaves, roots, and stem, and C3xC4 F1 and F3 hybrid

first: Andreas

last: Weber

summary: Elucidating the genetic control of C3 and C4 photosynthesis. Atriplex rosea (C4) and Atriplex prostrata (C3) were at maturity to compare expression between C3 and C4 in leaves, stems, and roots. Their F1 hybrid leaf was studied at maturity and will aid in identifying regulatory elements involved in C3 and C4 leaf development. Two C3 Atriplex prostrata x C4 Atriplex rosea F3 hybrids (F3003 and F3036) were sequenced at a mature leaf stage.

platform_organism:
Atriplex rosea
Atriplex prostrata
Atriplex prostrata x Atriplex rosea

overall_design:
Atriplex plants [Atriplex rosea, Atriplex prostrata, and C3 A. prostrata x C4 A. rosea F1 hybrid] were grown in biological triplicates at ~500umol photons m^-2 s^-1 under 17 hr light / 7 hr dark. Samples for RNASeq were taken from the middle of the leaf at mature leaf stage two hours after the onset of light.  Stem material were taken from the most recently elongated node on the main stem. Roots were cleaned and excised from the plant.

Please note that, since part of the analysis is still in progress, the 'SupplementalDataset*.txt' does not yet contain results for all samples. The dataset will be updated as soon as the results are available.


title: A temporal classifier predicts histopathology state and parses acute-chronic phasing in inflammatory bowel disease patients

city: New York city

first: Zhi

last: Chai

address: 1425 Madison Ave

institute: Icahn School of Medicine at Mount Sinai

summary: We characterized the transcriptional landscape of acute and chronic models of dextran sodium sulfate (DSS) and adoptive transfer (AT) colitis murine models to derive novel temporal gene expression and splicing signatures in blood and colonic tissue in order to capture dynamics of colitis remission and relapse. We show that colitis induces robust expression of minor isoforms and using machine learning, demonstrate that specific temporal gene expression and splicing signatures are highly predictive of tissue histopathology spanning blood and colonic tissue as well as various experimental sites and protocols. Finally, we identified sub networks of patient-derived causal networks that were enriched in these temporal signatures to distinguish acute and chronic disease components within the broader molecular landscape of IBD.

overall_design: Case-control differential gene-expression with temporal interaction

first: Bojun

last: Losic

first: Lauren

last: Peters


title: Inhibiting Androgen Receptor Splice Variants with Cysteine-Selective Irreversible Covalent Inhibitors to Treat Prostate Cancer

city: Memphis

first: Daniel

middle: Lee

last: Johnson

state: Tennessee

address: 71 S Manassas

department: Molecular Informatics Core

institute: UTHSC

summary: Prostate cancer (PCa) affects over 250,000 men in the US. Androgen Receptor (AR) signaling inhibitors are the mainstay therapeutics for PCa. Advanced PCa that expresses AR splice variants (AR-SVs) does not respond to current therapeutic strategies. In this manuscript, we uncovered the physicochemical properties of the intrinsically-disordered transactivation domain of AR and AR-SV and developed novel AR irreversible covalent antagonists (SARICA) to the transactivation domain for the treatment of advanced PCa. SARICAs were also used to identify a potential binding region in the AR and AR-SV transactivation domain.

overall_design: 22RV1 ATAC-Seq and RNA-Seq and LNCaP ATAC-Seq

first: Ramesh

last: Narayanan


title: Gene expression profiles of renal tubules in the kidney of fibrosis model rat produced by allopurinol.

city: Tonomachi, Kawasaki-ku, Kawasaki City, Kanagawa, JAPAN

first: Kohei

last: Matsushita

institute: National Institute of Health Sciences

summary: The aim of this study is to investigate the gene expression profiles of renal tubules during maladaptive repair.

overall_design: n = 4/group. 2 groups (Total n = 8). Control group and renal fibrosis group.


title: Expression data from rodents following ischemic injury, permanent middle cerebral artery occlusion (MCAO) Neuregulin-1 treatment.

city: Riverside

first: Byron

last: Ford

state: CA

address: 900 University Ave

institute: University of California-Riverside

summary: We used gene expression profiling to understand the early cellular and molecular mechanisms of NRG1’s effects after the induction of ischemia.

overall_design: Cortical brain tissues were collected three hours following MCAO and NRG1 treatment, RNA extracted and hybrdized to an Affymetrix microarray chip.

first: Monique

last: Surles-Zeigler

first: Yonggang

last: Li


title: Activation of Epidermal Growth Factor Receptor Pathway in Slow-Flow Vascular Malformations

city: Kuopio

first: Minna

middle: U

last: Kaikkonen

department: A.I. Virtanen Institute, Department of Biotechnology and Molecular Medicine

institute: University of Eastern Finland

summary: Sporadic venous malformations (VM) and angiomatosis of soft tissue (AST) are benign, congenital slow-flow vascular anomalies that have no available targeted therapies. Depending on the size and location of the lesion, symptoms vary from motility disturbances to pain and disfigurement. In this work, we analyzed tissue samples from 36 patients with VM or AST. Additionally, patient-derived endothelialCD31+ and intervascular stromalCD31-, vimentin+ cells were used. Majority of the samples had a somatic mutation in either TEK or PIK3CA gene. Activation of ErbB1/EGFR pathway and expression of a pro-angiogenic ligand, transforming growth factor A, was found in both VM and AST samples. Activation of EGFR pathway led to the secretion of a major angiogenic factor VEGF-A. Intriguingly, patient-derived intervascular stromal cells were able to induce angiogenesis of genotypically normal endothelial cells via paracrine signaling. Significant decrease in endothelial sprouting and VEGF-A production were observed after treatment with a pan-ErbB inhibitor afatinib. To conclude, our data demonstrate that intervascular stromal cells play a role in the pathogenesis of AST and VM by producing pro-angiogenic factors that activate EGFR. Activation of EGFR pathway was not associated with a genetic cause but is likely caused by hypoxia. EGFR targeted therapy of both intervascular stromal cells and endothelial cells could be beneficial for the treatment of a subpopulation of AST and VM lesions expressing EGFR ligands.

overall_design:
Strand specific RNA-Seq of Human saphenous vein endothelial cells, Human umbilical vein endothelial cells and Human CD31+ endothelial cells extracted from vascular malformation

***Please note that, due to EU GDPR (EU2016/679) on personal data protection and legislation,and directives pertinent to the management of human data, only processed data is available for GSM3754280-GSM3754284. ***

first: Johanna

last: Laakkonen


title: Gene expression profile at single cell level of HaCaT cells exposed to ionizing radiation

city: suzhou

first: zhang

middle: shu

last: yu

address: No. 199, Ren'ai Road

department: soochow university

institute: Soochow University

summary: HaCaT cell line is a kind of keratinocyte from human skin. We used single cell RNA sequencing (scRNA-seq) to analyze the influnce of fractionated 2 Gy or single 20 Gy irradiation on HaCaT cells.

overall_design: HaCaT cells were administrated with 5 or 10 times fractionated 2 Gy irradiation, and meanwhile at the end of last time fractionated irradiation, a single 20 Gy irradiation was given for cells in another cultrue dish (PF1 for 0 Gy,PF2 for 2 Gy×5,PF3 for 2 Gy×10 and PF4 for 20 Gy). And three days after last time irradiation, cells were collected and analyzed using scRNAseq to investigate the change of cluster profiles.

first: Shuyu

last: Zhang


title: Transcriptomic profiling of KMT2A-rearranged infant acute lymphoblastic leukemia (ALL) cells after treatment witith azacitidine and decitabine.

city: perth

first: Carlos

middle: A

last: Aya-bonilla

state: WA

address: 32 kinship street

country: Australia

institute: Telethon Kids Institute

summary: Transcriptomic profiling was performed on six cell lines derived from infants with KMT2A-rearranged ALL following treatment with two hypomethylating drugs (azacitidine and decitabine) administered at low doses for 72 hours in vitro. We identified changes in gene expression following treatment with hypomethylating agents, with decitabine exerting a greater effect than azacitidine.

overall_design: Total RNA (500 ng) for each cell line and condition was used as input for library preparation using the Illumina Stranded mRNA Prep kit (Illumina). A total of 54 poly A stranded libraries (6 controls, 6 azacitidine-treated and 6 decitabine-treated cell lines in triplicate) were sequenced to a depth of >20 million paired-end reads (150 bp) per sample using a NovaSeq 6000 (Illumina). Raw data was demultiplexed, underwent quality control, aligned and mapped to the trancriptome (hg38). Differential expression analysis was performed to identify differentially expressed genes comparing treatment with untreated control for each cell line.

last: Aya-Bonilla

first: Rishi

last: Kotecha

first: Laurence

middle: C

last: Cheung


title: Preclinical efficacy of azacitidine and venetoclax for infant KMT2A-rearranged ALL reveals a new therapeutic strategy

type: Genome binding/occupancy profiling by genome tiling array

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

overall_design: Refer to individual Series


title: Single-cell transcriptomics of hypoxic WT and Vegfr2Y949F mouse lungs

city: Guangzhou

first: lei

last: zeng

address: No. 74, Zhongshan 2nd Road, Yuexiu District

institute: SUN YAT-SEN UNIVERSITY

summary: We report a comprehensive cell atlas of the lungs from mice that were housed under hypoxia (10% oxgyen) for 6 weeks.

overall_design: The mouse lung tissue blocks from WT and Vegfr2Y949F mice with 6-week hypoxia exposure were dissected and dissociated to yeild single cell suspension. Each suspension contained cells from lung tissues of 2 WT or 2 Vegfr2Y949F mice.  Single cells RNAseq was performed using the 10X Genomic system, followed by analyses of cell clusters, and specific gene expression patterns

first: Feng

first: Yangxin

last: Chen

first: Weibin

last: Zhou

first: Keli

last: Liu

first: Lei

last: Zeng


title: Gene expression profile at single cell level of infiltrated macrophages from ischemic brain after stroke

first: Mengyan

last: Hu

address: Tianhe Road

institute: Sun Yat-sen University

summary: Macrophages play an important role in the pathological process of stroke. We used single cell RNA sequencing (scRNA-seq) to analyze the diversity of infiltrated macrophages from ischemic brain after stroke.

overall_design: Infiltrated macrophages from ischemic brain of Foxp3Egfp mice were isolated by Fluorescence-activated cell sorting (FACS) according to low sorting of CD45+CD11b+CD3-F4/80+ cells signal and analyzed using scRNAseq.

first: Wei

last: Cai

first: Zhengqi

last: Lu


title: Foxp3 promotes macrophage phagocytosis in AIS


title: Analysis of Foxp3 binding DNA in mouse bone marrow derived macrophages stimulated with brain derived DAMPs

summary:
Treg-specific transcription factor Foxp3 is also expressed in macrophages. Macrophages play an important role in the pathological process of stroke, and their Foxp3 is significantly up-regulated after stroke, and the underlying mechanism is still unclear. The purpose of this study was to investigate the function of Foxp3 as a transcription factor in macrophages. Ten million bone marrow-derived macrophages were treated with mouse brain-derived danger-associated molecular patterns, and experiments were performed 2 hours later using CST's Cut&Run kit and Foxp3 antibody. The obtained DNA was subjected to sequencing analysis. Our findings suggest that the expression of foxp3 is associated with the phagocytosis and digestion of macrophages, and the molecular may be a potential target for stroke.
CUT & RUN and DNA product sequencing for Foxp3 in bone marrow-derived macrophages (BMDMs)

first: Quenti

first: Yan


title: Dihydrofolate reductase metabolic activity controls neurogenic transitions in the developing human and mouse neocortex

city: Toulouse

first: Alice

last: Davy

address: 118 route de Narbonne

department: MCD, CBI

institute: CNRS


title: Dihydrofolate reductase metabolic activity controls neurogenic transitions in the developing human and mouse neocortex [ChIP-seq]

summary: To identify whether DHFR deficiency affects neurogenesis by modulating H3K4me3 methylation marks.

overall_design: ChIP-seq analysis of H3K4me3 in NPC from E13.5 mice.

first: Mohamad

last: Fawal

first: Tao

last: Ye

first: Sulov

last: Saha

first: Thomas

last: Jungas

first: Christophe

last: Audouard

first: David

last: Ohayon


title: ChIP-Seq of DNA lesions from irradiated and non-irradiated HaCaT cells

first: zhang

last: yu

summary: This study aims to investigate the binding DNA lesions of AIM2 in HaCaT cells exposed to 0Gy and 20Gy by ChIP-Seq. In this study, HaCaT cells were maintained in DMEM. All culture media were supplemented with 10% fetal bovine serum (FBS; Biological Industries, Kibbutz Beit-Haemek, Israel). Cells were grown at 37 °C in 5% CO2 incubators. Cells were exposed to 20Gy of ionizing radiation using X-ray linear accelerator (Rad Source, Suwanee, GA) at a fixed dose rate of 1.15 Gy/min.Four hours after irradiation, specific antibody against AIM2 was used to pull down AIM2 and the binding DNA lesions, which was then analyzed through ChIP-Seq.

overall_design: The feature of AIM2 binding DNA lesions were compared through ChIP-Seq in HaCaT cells exposed to ionizing radiation or not.

first: Shuyu

last: Zhang


title: Dihydrofolate reductase metabolic activity controls neurogenic transitions in the developing human and mouse neocortex [RNA-seq]

summary: To identify how DHFR deficiency affects neurogenesis by modulating neocortical gene expression at E12.5.

overall_design: RNA-seq analysis of E12.5 neocortical tissues isolated from WT and DHFR+/Δ mice.


title: Comparative Computational RNA Analysis of Cardiac-Derived Progenitor Cells and Their Extracellular Vesicles [miRNA-seq]

city: Atlanta

first: Michael

last: Davis

state: GA

address: 2015 Uppergate Dr

institute: Emory University

summary: We aimed to examine differences between c-kit+ progenitor cells (CPCs) and CPC-derived extracellular vesicles (EV) RNA content. We isolated CPCs from cardiac biopsies of patients with congenital heart disease using magnetic bead sorting. We expanded CPCs, reduced serum for 24hrs, and collected secreted EVs from conditioned media with sequential ultracentrifugation. We isolate RNA from CPCs and CPC-EVs and sequence total RNA and miRNA. Sequencing was performed in at two different facilities: "E" and "N".

overall_design: Examination of CPC and CPC-derived EV small RNA content.

first: Jessica

middle: R

last: Hoffman

first: Hyun

last: Park

middle: E


title: Double-haploid induction induces extensive variation in DNA methylation in Arabidopsis

city: Gatersleben, Stadt Seeland, Germany

first: Hua

last: Jiang

address: Corrensstraße 3

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

type: Methylation profiling by high throughput sequencing

summary: Doubled haploids (DHs) fix traits from hybrids in one generation. DH induction includes two changes in ploidy levels typically associated with variation in DNA methylation. However, DNA methylation patterns in DH plants and their biological significance are largely unknown. We generated three DH lines in Arabidopsis thaliana by crossing a haploid inducer to the accession Col-0, thus removing tissue culture and hybridization as a variable. DH induction produced thousands of differentially DNA methylated regions (DMRs), most of which were stochastic. Both haploidization and colchicine-induced genome duplication produced DMRs; the former mainly yielded DMRs at non-CG contexts, whereas the latter affected differential gene body methylation. Spontaneous genome doubling of haploid plants also induced DMRs in greater numbers than self-propagation. Our results provide the first evidence that haploid induction and genome doubling result in differential DNA methylation, offering a novel approach to induce epialleles.

overall_design: We compared the transcriptomes and genome profiles of DNA methylation in DH Arabidopsis.

first: Ewa

last: Piskorz

first: Linhao

last: Xu

first: Yingrui

last: Ma


title: Comparative Computational RNA Analysis of Cardiac-Derived Progenitor Cells and Their Extracellular Vesicles [RNA-Seq]

overall_design: Examination of CPC and CPC-derived EV RNA content

first: Hyun-Ji


title: Transcriptomic profile of murine macrophage RAW264.7 in response to Salmonella flagellin

city: Yangzhou

first: Li

last: Song

state: Jiangsu

address: 48 East Wenhui Road

institute: Yangzhou University

summary: Macrophages are an important component of the innate immune system. Flagellin has been extensively studied for its adjuvant activity owing to its TLR5 and NLRC4 binding sites. However, few studies have comprehensively investigated the effects of flagellin in macrophages using transcriptome sequencing. In this study, RNA sequencing (RNA-seq) was used to analyze the expression patterns of RAW264.7 cells induced by flagellin (FliC) of Salmonella typhimurium compared with unstimulated cells, to identify novel transcriptomic signatures in macrophages.

overall_design: The murine macrophage cell line RAW264.7 were stimulated with flagellin (FliC). After 5 h of stimulation, total RNA from FliC stimulated and unstimulated RAW264.7 cells (three samples each group) was sent to Novogene Co., Ltd. for RNA-seq.

first: Xinan

last: Jiao

first: Zhiming

last: Pan


title: 10X Gemonics Single-cell RNA sequence of ovaries at P1,P14,W8,M8 and M12

city: Beijing

first: Wenjie

last: Shu

address: Taiping Road 27

institute: Beijing Institute of Radiation Medicine

summary: 1 day-, 14-day-, 8-week-, 8-month- and 12-month-old mice ovaries were collected for single-cell RNA sequencing. The developmental stage-specific somatic cells were defined and analyzed with the dynamics of cell-cell communication networks to reveal their association with ovarian development and senescence. These results provide strong support for further research on the supporting role and regulation mechanism of somatic cells to follicles.

overall_design: Single cell transcriptome landscape of mouse ovary from fetal to aged mouse: total 9 samples of 10xGenomic Single cell RNA sequencing of ovary at 5 different ages, including  postnatal 1 day(P1, 1sample,germ cell and somatic cell),14-day-old(2 samples,somatic cell), 8-week-old(2 samples,somatic cell), 8-month-old(2 samples,somatic cell) and 12-month-old(2 samples,somatic cell) were produced.

first: Shu

last: wenjie

last: jing


first: Carlos

last: Aya-bonilla

type: Methylation profiling by genome tiling array

summary: Genome-wide methylation profiling was performed on six cell lines derived from infants with KMT2A-rearranged ALL following treatment with three hypomethylating drugs (azacitidine, decitabine and zebularine) administered at low doses for 72 hours in vitro. We identified drug-specific and common differentially methylated regions and validated differentially expressed genes located within such regions, indicating commonalities in pathways targeted by azacitidine and decitabine in KMT2A-rearranged infant ALL. Of the three drugs, the most significant degree of hypomethylation was induced by decitabine followed by azacitidine, whereas zebularine did not exert a significant hypomethylating effect.

overall_design:
Genome-wide methylation profiling of KMT2A-rearranged infant Acute Lymphoblastic Leukemia (ALL) cells after treatment with azacitidine, decitabine and zebularine
Genomic DNA (750 ng) for each cell line and condition was treated with sodium bisulfite using the Zymo EZ DNA Methylation kit (Irvine). DNA was then hybridized to the Infinium MethylationEPIC BeadChip (Illumina). QC and data was filtered and quantile normalised in R. Following quality control checks, 773,929 probes were taken forward for downstream analyses.  Differential methylation analysis of CpG sites was performed using limma, adjusting for pairing by cell line. Differential methylation analysis of regions was performed using DMRcate where CpGs were annotated and differentially methylated regions were identified.

last: Aya-Bonilla

first: Rishi

last: Kotecha

first: Laurence

last: Cheung


title: Integrated Transcriptomic-Proteomic Analysis Revealed the Diagnostic and Potential Therapeutic Targets of Colorectal Cancer

city: Nanjing

first: qiu

last: chengchao

address: Moling Street

institute: Nanjing University of Aeronautics and Astronautics

summary: To identify the potential biomarkers related to the development of colorectal cancer.we established an inflammation-induced colorectal cancer disease model in mice.

overall_design: We then performed gene expression profiling analysis using data obtained from RNA-seq of 12 different mice serum.

first: Chengchao

last: Qiu

first: Jingjing

last: Liu


title: Gene expression data from muscle-invasive bladder cancer samples

city: Bangor

first: Tim

last: Smith

address: Dean Street

department: School of Computer Science and Engineering

institute: University of Bangor

summary:
Gene signatures based on the median expression of a preselected set of genes can provide prognostic and treatment outcome prediction and so be valuable clinically.
Different health care services use different gene expression platforms to derive gene expression data. Here we have derived gene expression data using a microarray platform.

overall_design: RNA extracted from FFPE blocks from patients with muscle-invasive bladder cancer and full transcriptome analysis on Clariom S microarray platform.  Sample blocks were collected for platform comparison and a heterogeneity gene signature study without any associated patient information.

first: Brian

last: Lane

first: Elisabet

last: More

first: Helen

last: Valentine

first: Sapna

last: Lunj

first: J

last: Irlam-Jones

first: Kimberley

last: Reeves

first: Peter

last: Hoskin

first: Ananya

last: Choudhury

first: Catharine

middle: M

last: West


title: Role of Axl in target organ inflammation and damage due to hypertensive aortic remodeling

city: Nashville

first: Wei

last: Chen

state: TN

address: 2213 Garland Ave

department: Medicine

institute: VUMC

summary:
Aortic remodeling is a cause and consequence of hypertension. It increases workload on the heart and enhances arterial pulsatility in the microcirculation. We have shown that excessive endothelial stretch leads to release of Growth Arrest Specific 6 (GAS6), which in turn activates the tyrosine kinase receptor Axl on monocytes, and causes immune activation and inflammation. We hypothesized that GAS6/Axl blockade would reduce renal and vascular inflammation and lessen renal dysfunction in the setting of chronic aortic remodeling. We characterized a model aortic remodeling in mice following a 2-week infusion of angiotensin II (ang II).
Aortas demonstrated increased mural collagen and mechanical testing revealed a marked loss of Windkessel function or energy storage that persisted for 6 months following ang II. Renal function studies showed a reduced ability to excrete a volume load, a progressive increase in albuminuria and tubular damage as estimated by Periodic Acid Schiff (PAS) staining. Treatment with the Axl inhibitor R428 beginning 2 months after ang II infusion had minimal effect on aortic remodeling 2 months later, but reduced the infiltration of T cells, g/d T cells and macrophages into the aorta and kidney, and improved renal excretory capacity, reduced albuminuria, and reduced evidence of renal tubular damage. We conclude that brief episodes of hypertension can induce chronic aortic remodeling which in turn associates with a low-grade inflammation of the aorta and kidneys and evidence of renal dysfunction. These events are mediated at least in part by GAS6/Axl signaling and are improved with Axl blockade.

overall_design: Comparative gene expression profiling analysis of RNA-seq data aortas 2, 4 and 6 months after a 2 week episode of hypertension

first: David

middle: G

last: Harrison


title: RNAseq for WT and xip mutant in mock, HU and BLM treatment

city: Shanghai

first: Yan

last: Zhu

address: 2005, Songhu Road

department: Biochemistry

institute: Fudan University, School of life sciences

summary: XIP interact with g-H2A.X and mediate the DNA damage response in Arabidopsis.

overall_design: WT and xip mutant in 3 growth conditions with 2 replicates

first: Tianyi

last: Fan

first: Huijia

last: Kang

first: Ji

last: Qi


title: Effect of Insulin receptor deletion in hepatocytes on liver gene expression at different time point in mice either fed ad libitum or upon day-restricted feeding

first: Hervé

last: Guillou

address: 180 Chemin de Tournefeuille

department: ToxAlim

institute: INRAE

summary: To assess the consequences of IR deletion on gene expression using microarray and its contribution of IR to the control of rythmic liver gene expression, wild-type (IRhepWT) and KO (IRhepKO) mice were either fed ad libitum or submitted to day-restricted feeding (as described by Damiola et al., 2000).  Liver samples were collected around the clock (ZT0, ZT04, ZT08, ZT12, ZT16, ZT20).

overall_design: To generate tamoxifen-inducible hepatocyte-specific IR knockout mouse line (IRhep-/-) and their control (IRhep+/+), animals carrying LoxP sites flanking the fourth exon of the IR gene (IRlox/lox stock number: 006955; Jackson Laboratory, Bar Harbor, ME, USA) were intercrossed with C57BL/6J mice, which specifically express Cre recombinase in the liver under the transthyretin promoter (TTR-CreTam mice), as previously described (Nemazanyy et al., 2015; Smati et al., 2020). Mice were either fed ad libitum (AdLib) or fed only during the day (RF= restricted feeding) for two weeks as previsouly described (Damiola et al., 2000). Total liver RNA was extracted using TRI Reagent (Molecular Research Center, Inc., Cincinnati, OH, USA). Gene expression profiles were obtained at the GeT‐TRiX facility (GenoToul, Genopole Toulouse Midi-Pyrénées) using Agilent Sureprint G3 Mouse GE v2 microarrays (8x60K, design 074809) following the manufacturer's instructions.

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