title: Microglial metabolism mediated by BACH1 orchestrates astrogenesis during brain development

status: Public on Mar 25 2023

first: Jianwei

last: Jiao

state: Beijing

address: 1 Beichen West Road

department: State Key Laboratory of Reproductive Biology

institute: Institute of Zoology, Chinese Academy of Sciences

summary: Purpose: To gain futher insight into how microglia-derived BACH1 regulates microglial metabolism and astrogenesis, RNA-seq was used to analyze the genome-wide changes resulting from isolated microglia of E16 microglial BACH1 conditional knock out mice and littermate wild-type. Methods: mRNA from E16 isolated microglia of Bach1fl/fl and Bach1cKO-Cx3 mice was extracted. Specifically, Agilent 2100 Bioanalyze was used to quality controlled and quantified. then, mRNA was converted to cDNA and bound the library. RNA-sequencing analysis was used by the Illumina HiSeq 2500 platform in Annoroad Genomics. Results: Approximately one thousand transcripts showed differential expression between the Bach1fl/fl and Bach1cKO-Cx3 mice brain microglia, with a fold change ≥3 and p value <0.05. Geneontology analysis of the downregulated genes were enriched in terms related to cell proliferation, glial cell differentiation and cell communication and upregulated genes were enriched in terms related to negative regulation of cell proliferation, negative regulation of astrocyte differentiation and glial cell fate commitment. These results reflected microglia BACH1 plays roles in cortex development. Conclusions: Microglia BACH1 RNA-seq would provide a overall understanding how microglia-derived BACH1regulates astrogenesis during brain development.

overall_design: mRNA profiles of E16 Bach1fl/fl and Bach1cKO-Cx3 mice were generated by deep sequencing, in triplicate,  using Illumina HiSeq 2500.

first: Yanyan


title: Endothelial cells mediated by STING signaling regulate oligodendrogenesis and myelination during brain development

city: Beijing

country: China

type: Expression profiling by high throughput sequencing

summary: To gain  futher insight into how endothelial STING regulates oligodendrogenesis ,RNA-seq was used to analyze the genome-wide changes resulting from isolated endothelial cells of E18 endothelial STING conditional knock out mice and littermate wild-type.mRNA from  E18 isolated endothelial cells of wild-type(WT) and STINGf/f;Tie2-cre mice was extracted. Specifically, Agilent 2100 Bioanalyze was used to quality controlled and quantified. then, mRNA was converted to cDNA and bound the library. RNA-sequencing analysis was used by the Illumina HiSeq 2500 platform in Annoroad Genomics

overall_design: mRNA profiles of E18 wild type (WT) and STINGECKO mice were generated by deep sequencing, in triplicate,  using Illumina HiSeq 2500.

first: Wenwen

last: Wang


title: Characterization of estrogen and the endocrine-disrupting chemical-induced mouse mammary gland reorganization via bulk RNA-sequencing

status: Public on Mar 24 2023

city: Duarte

first: Shiuan

last: Chen

state: CA

address: 1500 E Duarte Rd

department: Cancer Biology-BRI

country: USA

institute: City of Hope National Medical Center

summary: Similar to the scRNA-Seq data (GSE125272), a surgical menopausal (ovariectomized) mouse model was used to assess how mammary gland tissue was affected by both 17β-estradiol (E2) and polybrominated diphenyl ethers (PBDEs). The PBDE treatments include three analyzed flame retardants: BDE-47, BDE-100 and BDE-153.  Bulk RNA-Seq data was created with treatment conditions lasting 1 week.  Gene expression changes for PBDE treatment are relatively small compared to E2 treatment.  However, along with other studies and experiments, this data is meant to contribute to greater understanding of the interaction of PBDE exposure and estrogen signaling.

overall_design: RNA-sequencing was done on RNA extracted from the fourth mouse mammary gland without the lymph node (vehicle, n = 3; PBDE, n = 3; E2, n = 6; and E2 + PBDE, n = 6)

first: Noriko

last: Kanaya


title: Microarray analysis of choline-deficient L-amino acid-defined (CDAA) diet-induced NAFLD animal model.

city: Takatsuki

first: Tatsuya

last: Ishigure

state: Osaka

address: 1-1 Murasaki-cho

country: Japan

institute: Japan Tobacco Inc.

summary: Nonalcoholic Fatty Liver Disease (NAFLD) is a broad spectrum of liver disorders ranging from simple steatosis to nonalcoholic steatohepatitis, cirrhosis and hepatocellular carcinoma. The choline-deficient L-amino acid-defined (CDAA) diet-induced NAFLD animal model has traditionally been used to understand the molecular mechanisms of disease development and progression. Although this animal model shows a similar course of disease progression to human NAFLD, it does not develop comorbidities such as obesity and type 2 diabetes. Therefore, its relevance to human NAFLD (what aspects of the disease etiology are recapitulated in this model?) is not fully understood. We applied microarray analysis to characterize its pathophysiology, and evaluate the similarity across species.

overall_design: Gene expression in liver tissue was measured after 1, 2, 4, 9 weeks dietary intervention. There are 40 samples in the study which belonged to 8 groups, and each group contains 5 different samples.

first: Koji

last: Edamura


title: Sex and Molecular Differences in Cardiovascular Parameters at Peak Influenza Infection in Mice

city: Jackson

first: Michael

middle: R.

last: Garrett

state: MISSISSIPPI

address: 2500 N State Street, Department of Pharmacology and Toxicology

department: Pharmacology and Toxicology

institute: University of Mississippi Medical Center

summary: Female and male C57BL/6J mice were obtained from The Jackson Laboratory (Bar Harbor, ME, USA) at 16 weeks age. Mice were intranasal infected with a sublethal does of 7.5×104 EID50 A/Puerto Rico/8/34 influenza virus (PR8; Charles River, Wilmington, MA, USA) or mock infected  (naïve) with 1X PBS. After euthanasia at 7 days post infection lung and nasal septum were collected from animals to perform transcriptome analysis by RNA sequencing.

overall_design: RNA was isolated by TRIzol Reagent (Invitrogen Life Technologies, Grand Island, NY, USA) and purified with RNeasy Mini Kit (QIAGEN; Hilden, Germany) according to manufacturer’s instructions. RNAseq was used to analyze lung and nasal septum transcriptomes between females (naïve [n = 6] and infected [n = 6]) and males (naïve [n = 6] and infected [n = 6]). RNA was evaluated for quality (Qubit fluorimeter) and fidelity using Qiagen QIAxcel Advanced System, with all sample demonstrating and RIS > 8. Libraries were generated with TruSeq stranded mRNA kit (Illumina; San Diego, CA, USA), indexed with TruSeq RNA CD indexes (Illumina; San Diego, CA, USA), and sequenced with NextSeq 2000 P3 (PE100) flow cell (Illumina; San Diego, CA, USA)

first: Brigitte

middle: E

last: Martin

first: Erin

middle: B

last: Taylor

first: Esinam

middle: M

last: Attipoe

first: David

last: Stec

first: Kurt

middle: C

last: Showmaker

middle: R


title: Ancient ubiquitous protein 1 (AUP1) is a prognostic biomarker connected with TP53 mutation and the inflamed microenvironments in glioma

city: Taipei

first: YAO FENG

last: LI

address: No.161, Sec. 6, Minquan E. Rd., Neihu Dist., Taipei City 11490, Taiwan

department: Pathology

country: Taiwan

institute: National Defense Medical Center

summary: To investigate the changes of the transcriptome and relevent signalling between control and siAUP1 treated glioblastoma cell line, U87MG.

overall_design: We then performed gene expression profiling analysis using data obtained from RNA-seq of 3 U87MG control verus 3 U87MG treated siAUP1

first: Y

middle: F

last: Li

first: P

last: Chang


title: Retina-Specific Laminin 523 Drives Differentiation of Human Pluripotent Stem Cells to Photoreceptors

status: Public on Mar 26 2023

city: Singapore

first: Jing

last: Guo

state: State...

address: 8 Collage Road, DUKE-NUS Medical School, level 5

department: Center for Computational Biology

country: Singapore

institute: Duke-NUS Medical School

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

overall_design: Refer to individual Series


title: Characterization of estrogen and the endocrine-disrupting chemical-induced mouse mammary gland reorganization

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: Mechanisms of gut epithelial barrier impairment caused by food emulsifiers polysorbate 20 and polysorbate 80

city: Davos-Wolfgang

first: Ismail

last: Ogulur

address: Herman-Burchard-Strasse 9

country: Switzerland

institute: Swiss Institute of Allergy and Asthma Research (SIAF)

summary: We investigated the effects of polysorbate 20 and polysorbate 80 on cytotoxicity, barrier function and the transcriptome in gastrointestinal epithelial cells. RNA-seq was used for checking transcriptome.

overall_design: Monolayered Caco-2 cells were treated with polysorbate 20 and polysorbate 80 at 0.05% concentration for 24 hours. Then, RNA samples were isolated, RNA-seq performed and comparative gene expression analysis done.

first: Elif

middle: N

last: Bingöl


title: Neurulation of the cynomolgus monkey embryo achieved from 3D blastocyst culture [RNA-Seq]

first: Fan

address: 1 Beichen West Road, Chaoyang District

department: The State Key Laboratory of Stem Cell and Reproductive Biology

summary:
To further reveal the major cell types of developing pIVC embryos and underlying epigenetic dynamics, the optimized single-cell based multi-omics sequencing method scChaRM-seq was performed (Yan et al., 2021b). After stringent filtration, 3,682 single cells RNA-seq datasets were further analyzed
We then performed multi-omics profiling analysis using data obtained from9 pIVC embryos at 8 sequential developmental stages.

overall_design: Expression profiling by high throughput sequencing

first: Jinglei

last: Zhai

first: Yanhong

last: Xu

first: Rui

last: Yan

first: Hongmei

last: Wang


title: Neurulation of the cynomolgus monkey embryo achieved from 3D blastocyst culture [Bisulfite-Seq]

type: Methylation profiling by high throughput sequencing

summary:
To further reveal the major cell types of developing pIVC embryos and underlying epigenetic dynamics, the optimized single-cell based multi-omics sequencing method scChaRM-seq was performed (Yan et al., 2021b).  1,862 single cells Bisulfite-seq datasets were further analyzed.
We then performed multi-omics profiling analysis using data obtained from9 pIVC embryos at 8 sequential developmental stages.


title: Evaluation of broad anti-coronavirus activity of autophagy-related compounds using human airway organoids

city: Kyoto

first: Kazuo

last: Takayama

state: Kyoto

address: Shogoin Kawaharacho 53, Sakyo-ku

department: Center for iPS Cell Research and Application

institute: Kyoto University

summary: To deal with the broad spectrum of coronaviruses, including severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), that threatens human health, it is essential to develop not only drugs that target viral proteins but also consider drugs that target host proteins/cellular processes to protect them from being hijacked for viral infection and replication. To this end, it has been reported that autophagy is deeply involved in coronavirus infection. In this study, we used airway organoids to screen a chemical library of autophagic modulators to identify compounds that could potentially be used to fight against infections by a broad range of coronaviruses. Among the 80 autophagy-related compounds tested, cycloheximide and thapsigargin reduced SARS-CoV-2 infection efficiency in a dose-dependent manner. Cycloheximide treatment reduced the infection efficiency of not only six SARS-CoV-2 variants but also human coronavirus (HCoV)-229E and HCoV-OC43. Cycloheximide treatment also reversed viral infection-induced innate immune responses. However, even low dose (1 μM) cycloheximide treatment altered the expression profile of ribosomal RNAs, thus side effects such as inhibition of protein synthesis in host cells must be considered. These results suggest that cycloheximide has broad-spectrum anti-coronavirus activity in vitro and warrants further investigation.

overall_design: The human iPS cell-derived bronchioalveolar organoids were mechanically recovered from the culture plates, and then total RNA was collected and RNA-seq was performed.


title: Staphylococcus Aureus and Streptococcus Pyogenes Induce Psoriasis-Related Transcriptomes in Human Keratinocytes Augmented by IL-17A and TNF-α

city: New York

first: James

last: Krueger

state: NY

address: 1230 York Avenue

department: Center for Clinical and Translational Science

institute: The Rockefeller University

summary: This study aims to define the interactions that SA or SP may have with IL-17A and TNF-α in human keratinocytes, as well as the similarity to psoriasis vulgaris

overall_design: We cultured keratinocytes with SA, SP, IL-17A, and TNF-α. Psoriasis-related key immune biomarkers were measured by quantitative real-time PCR and Olink multiplex assay. Further analysis was performed by microarray to define broader responses in both bacteria and cytokines

first: Shunsuke

last: Miura

first: Yohei

last: Ichimura

first: Sandra

last: Garcet


title: Psoriasis Improvements and Inflammatory Biomarker Normalization With Secukinumab: The Randomized ObePso-S Study

summary: To investigate treatment effects of secukinumab on clinical signs and psoriatic inflammation markers over 52 weeks in patients with psoriasis.

overall_design: Patients with psoriasis were randomized 2:1 to receive secukinumab 300 mg (n=54) or placebo (n=28), stratified by body weight (<90 or ≥90 kg), for 52 weeks. At Week 12, patients receiving placebo were switched to secukinumab. Gene expression profiles were evaluated in lesional and non-lesional skin biopsies collected at baseline, Week 12, and Week 52.

middle: G

first: Andrew

last: Blauvelt


title: H3K4me3 associated chromatin by CUT&RUN on c-kit+ cells from chimeras

city: BOSTON

first: Julie

last: Ng

state: MA

address: 75, Francis Street

institute: Brigham and Women's Hospital

summary: Sequencing of chromatin associated with H3K4me3 histone marks in live c-kit+ cells isolated by CUT&RUN from chimeras after transplantation with Ctrl-BM, MSC-BM and CpG-BM.

overall_design: 6 samples representing 3 groups in duplicate with 1 IgG control (reference sample) was analyzed.


title: Neurulation of the cynomolgus monkey embryo achieved from 3D blastocyst culture


title: Deletion of Tfam in Prx1-Cre expressing limb mesenchyme results in spontaneous bone fractures

city: Toon

first: Yuuki

last: Imai

state: Ehime

address: Shitsukawa

department: Proteo-Science Center

institute: Ehime University

summary: Osteoblasts require substantial amounts of energy to synthesize bone matrix and coordinate the mineralization of the skeleton. This study analyzed the effect of mitochondrial dysfunction on bone formation in mouse limbs. The limb mesenchyme-specific Tfam knockout (Tfamf/f;Prx1-Cre: Tfam-cKO) mice were analyzed morphologically, and histologically and gene expression in the limb bones were assessed by in situ hybridization, quantitative real-time PCR and RNA sequencing. Moreover, we analyzed mitochondrial function of osteoblasts in Tfam-cKO mice by mitochondrial membrane potential assay and transmission electron microscopic (TEM) observations. We investigated the pathogenesis of spontaneous bone fractures by immunohistochemical analysis, TEM observations and biomechanical examination. The forelimbs in Tfam-cKO mice were significantly shortened from birth and occurred spontaneous fractures within the first week after birth, resulting in severe limb deformities. Histologically, bone hypoplasia with decrease of matrix mineralization was apparent, and the expressions of type Ⅰ collagen and osteocalcin were decreased in the osteoblasts of Tfam-cKO mice although Runx2 expression was unchanged. Decreased type Ⅰ collagen deposition and mineralization in the matrix of the limb bones in Tfam-cKO mice was associated with marked mitochondrial dysfunction. Biomechanical analysis showed significantly lower Young’s modulus and hardness due to poor apatite orientation in the bone tissue of Tfam-cKO mice. The mice with limb mesenchyme-specific Tfam deletion exhibited spontaneous limb bone fractures, resulting in severe limb deformities. Their bone fragility was caused by poor apatite orientation due to impaired osteoblasts differentiation and maturation.

overall_design: mRNA profiles of humeral bone obtained from 6-day old control and Tfam-cKO mice were generated by deep sequencing, in triplicate, using Illumina Miseq.

first: Haruhiko

last: Akiyama

first: Hiroki

last: Yoshioka


title: Epigenomic mapping identifies a super-enhancer repertoire that regulates cell identity in bladder cancers through distinct transcription factor networks [siZBED2_siFOXA1]

city: paris

first: Elodie

last: chapeaublanc

address: 26 rue d'ulm

department: UMR 144

country: France

institute: Institut Curie

summary: RNA-seq Series of bladder carcinoma cell lines RT112 and SCaBER treated by siZBED2 and FOXA1.

overall_design: RT112 and SCaBER bladder cancer cell lines were treated with siRNA against ZBED2 and FOXA1.

first: Hélène

last: Neyret-Kahn

first: François

last: Radvanyi

first: Isabelle

last: Bernard-Pierrot

last: Chapeaublanc


title: Epigenomic mapping identifies a super-enhancer repertoire that regulates cell identity in bladder cancers through distinct transcription factor networks [CrispR_FOXA1]

summary: RNA-seq Series of Bladder carcinoma cell lines RT112 and SD48 mutated for FOXA1 by CrispR.

overall_design: RT112 and SD48 CRispR mutated for FOXA1 and controls.


title: Epigenomic mapping identifies a super-enhancer repertoire that regulates cell identity in bladder cancers through distinct transcription factor networks


title: Epigenomic mapping identifies a super-enhancer repertoire that regulates cell identity in bladder cancers through distinct transcription factor networks [siFOXA1]

summary: RNA-seq Series of bladder carcinoma cell lines RT112 and SCaBER treated by siFOXA1.

overall_design: RT112 and SCaBER bladder cancer cell lines were treated with siRNA against FOXA1 or Control.


title: Transcriptomic analysis of KDM4B-mediated gene in C4-2B prostate cancer cells

city: Hsinchu city

first: Meng-Chen

last: Wu

address: 101, Section 2 Kuang Fu Road

department: Institute of Molecular and Cellular Biology

institute: National Tsing Hua University

summary: Histone lysine demethylase KDM4B is often overexpressed in prostate cancer and links to poor survival outcome. Recent evidence suggests that KDM4B serves as a potential therapeutic target. The global transcriptomic analysis between control and KDM4B-knockdown C4-2B cells reveals the metabolic genes involved in Warburg effect are downregulated after knocking down the expression of KDM4B, indicating its role in tumor growth.

overall_design: KDM4B control and knockdown cell lines were established in C4-2B cells based on the lentivirus system: LKO (control) and shKDM4B (shRNA-specific RNA) lines. Global expression analysis was then performed (pLKO vs. KDM4B-knockdown). Microarray analysis was conducted by the National Health Research Institutes, using Affymetrix GeneChip Human Gene 2.0 ST Array (Affymetrix, Santa Clara, California, USA).

first: Ying-Yuan

last: Liu

first: Wen-Ching


title: Poly(I:C)-induced long-term behavioral deficits are accompanied by epigenetic changes in microglia of male mice

city: Freiburg

first: Ori

last: Staszewski

address: Breisacher Str. 64

department: Institute of Neuropathology

country: Germany

institute: University Medical Center Freiburg

type: Genome binding/occupancy profiling by high throughput sequencing


title: Poly(I:C)-induced long-term behavioral deficits are accompanied by epigenetic changes in microglia of male mice (ChIP-seq)

summary: While the exact mechanisms for a sex bias in the development of neuropsychiatric disorders remain only vaguely understood, there is increasing evidence that an early life immune activation contributes to the disease pathogenesis. By administering the double stranded RNA analogue polyriboinosinic:polyribocytidilic acid (poly(I:C)) we mimicked an early viral infection in neonatal female and male mice. As a consequence, male adolescent mice presented long-term behavioral deficits including impaired social behavior and defective spatial working and recognition memory. Notably, behavioral changes were completely absent in female mice. In male mice, poly(I:C) led to an increased number of infiltrating T cells in the brain parenchyma, an enhanced interferon-g (IFNg) signaling, and an epigenetic reprogramming of microglial cells. These reprogrammed microglial cells showed increased phagocytic activity, which resulted in the excessive loss of dendritic spines in male mice only. We corroborated these findings in a murine neonatal infection of mice with murine cytomegalovirus (MCMV) and found sustained aversive behavioral effects and a lower number of excitatory synapses within the hippocampal brain region in young adult male, but not in female mice. Together, our results highlight the crucial role of the early postnatal period for normal brain development: identical immune stimulation during this period led to distinct sex-specific long-term behavioral deficits, indicating that sex is potentially an underappreciated factor when investigating neuropsychiatric disorders.

overall_design: We evaluated H3k4me3 and H3k9ac in microglia isolated from P40 male and female mice, which were poly(I:C) or vehicle-injected at P2-P6. There were 3 samples as a single replicate per group with input DNA as control. The sequencing was performed as a paired end design.

first: Thomas

last: Blank


title: The Adult T-Cell Leukemia/Lymphoma Cell Line KK1 +/- RhoH Reconstitution

status: Public on Mar 23 2023

city: lille

first: frédéric

last: leprêtre

address: Boulevard du Pr Leclercq

department: CHU of Lille, CBP

institute: Lille University

summary: The adult T-cell leukemia/lymphoma cell line KK1 with low RhoH expression was stably transfected with either an empty expression vector or this same vector expressing human RhoH. The transcriptomes of these two daughter lines were then compared by differential microarray analysis

overall_design: Differential microarray analysis of the adult T-cell leukemia/lymphoma cell line KK1 +/- RhoH reconstitution

first: Carl

middle: S

last: Shelley

first: Sylvie

last: Galiègue-Zouitina


title: PBMC single cell transcriptomics of COVID-19 patients

city: Muenster

first: Hyun-Woo

last: Jeong

state: NRW

department: Dept. Tissue Morphogenesis

institute: Max-Planck-Institute for Molecular Biomedicine

summary: The COVID-19 is a mild to moderate respiratory tract infection in the majority, but also can cause life-threatening respiratory failure or persistent debilitating symptoms in a subset of patients. However, the mechanism of protective immunity in mild cases and the pathogenesis of severe COVID-19 remain unclear. On the other hand, it has been proposed that the potent anti-inflammatory effects of corticosteroids are beneficial to decrease the fatality rate in severe COVID-19 patients but its specific mechanism is still in debate.

overall_design:
We have investigated PBMC single cell whole transcriptome analysis of COVID-19 patients. Considering the drastic variation of symptoms, we proposed massive prospective as well as retrospective cohort designs in three independent medical centers in South Korea. In a total of 171 precious clinal samples, we aimed to determine immune cell composition and molecular changes in 1) patient groups of different disease severity, 2) longitudinal analysis of patients during the disease progress, 3) the functional analysis of corticosteroid treatment at the single cell resolution.
***Raw data not available due to patient privacy concerns***

first: Seok

last: Chung

first: Ji

middle: H

last: Yang


title: scRNAseq studies of pMHCII-NP-induced Tet+ cells with different epitope specificities

status: Public on Mar 27 2023

city: Barcelona

first: Pere

last: Santamaria

address: C/Rosselló 149-153

country: Spain

institute: IDIBAPS

summary: SMARTseq2 scRNAseq analysis was performed on Tet+ induced with 3 different epitope specificities (BDC2.5mi/IAg7, FLA2(462-472)/IAb and FLA2(501-515)/IAb) to study transcriptional homogeneity and clonality to different pMHCII-NPs and in different genetic backgrounds (NOD, B6)

overall_design: Treatment of NOD mice with BDC2.5mi/IAg7-NPs or B6 mice with FLA2(462-4742)/IAb- or FLA2(501-515)/IAb-NPs to induce Tet+ cells and perform scRNAseq studies

first: Santamaria

middle: V

last: Pere

first: Solé

last: Patricia

first: Josep

last: Garnica


title: CircRNA expression patterns in human DOXCM and control heart tissues

city: Beijing

first: Dong

last: Han

address: 28 Fuxing street

institute: Chinese PLA general hospital

type: Non-coding RNA profiling by high throughput sequencing

summary: CircRNA profiling of 3 samples of human heart with doxorubicin-induced cardiomyopathy(DOXCM) and 3 healthy hearts

overall_design: To screen the potentially involved circRNAs in doxorubicin-induced cardiotoxicity(DOXIC) pathogenesis, ribosomal and linear RNA-depleted circular RNA sequence was performed to profile circRNA expression in 3 hearts from autopsy specimens of cancer patients suffered from doxorubicin-induced cardiomyopathy and 3 non-diseased healthy donor hearts.

first: Feng

last: Cao

first: Yongjun

last: Wang


title: Transcription factor induction of vascular blood stem cell niches in vivo [scRNA-Seq.Whole-tail]

city: Boston

first: Leonard

last: Zon

address: 1 Blackfan Circle

department: Oncology/Hematology

institute: Boston Children's Hospital

summary: We report single cell gene expression data for caudal tail tissue cells collected from embryos at 72 hours post fertilization (hpf).

overall_design: Wild type embryos were homogenized, filtered, and then 25,000 live cells were FACS sorted into PBS. 5,000 cells were then encapsulated using the inDrops method and libraries were prepared for sequencing.

first: Elliott

middle: J

last: Hagedorn

first: Song

middle: I


title: Selective inhibition of the second bromodomain of BET family proteins results in robust antitumor activity in preclinical models of acute myeloid leukemia

city: North Chicago

first: Josh

last: Plotnik

state: IL

address: 1 North Waukegan Rd, AP10/210A

institute: AbbVie Inc.

summary: Selective inhibition of the second bromodomain of BET family proteins is efficacious in preclinical models of AML

overall_design: BRD4 ChIP-Seq under three different treatment conditions, H3K27Ac ChIP-Seq control conditions only.

first: Emily

last: Faivre

first: Joshua


title: Transcription factor induction of vascular blood stem cell niches in vivo [scRNA-Seq.Embryo-Niche]

summary: We report single cell gene expression data for FACS-isolated zebrafish kdrl(flk1):mCherry and mrc1a.125:GFP double positive cells collected from whole embryos at 72 hours post fertilization (hpf).

overall_design: kdrl:mCherry and mrc1a.125:GFP double positive transgenic embryos were homogenized, filtered, and then 25,000 GFP+ cells were FACS sorted into PBS. 3,000 cells were then encapsulated using the inDrops method and libraries were prepared for sequencing.


title: Transcription factor induction of vascular blood stem cell niches in vivo [ATAC-Seq 2]

summary: We report accessible chromatin genomic regions using ATAC-sequencing of zebrafish double transgenic for kdrl(flk1):mCherry and sele:GFP from FACS-isolated double positive, single positive, and double negative cells collected from whole embryos at 72 hours post fertilization (hpf).

overall_design: kdrl:mCherry and sele:GFP double positive transgenic embryos were homogenized, filtered, and then up to 50,000 cells from each transgene permutation were FACS sorted into PBS. 12,000-50,000 cells were then lysed and nuclei subjected to Tn5 transposase and libraries were prepared for sequencing.


title: The change of  gene expression between late- and early stage lin-5 nodules

city: changsha

first: FENG

middle: zhan

last: Gao

state: hunan

address: no

department: College of Biology

institute: Hunan university

summary: To investigate the function LIN in the regulation of the symbiosome formation, we established the gene expression level between 4 wpi and 2 wpi lin-5 nodule samples

overall_design: comparing gene expression level between 4 wpi and 2 wpi lin-5 nodule samples

first: Fengzhan

first: Huairong

last: Pan


title: Transcription factor induction of vascular blood stem cell niches in vivo [scRNA-Seq.Adult-Kidney]

summary: We report single cell gene expression data for FACS-isolated zebrafish kdrl(flk1):mCherry or kdrl(flk1):GFP positive cells collected from adult kidneys.

overall_design: kdrl:mCherry or kdrl:GFP positive transgenic adult kidneys were dissected, homogenized, filtered, and then 25,000 mCherry+ or GFP+ cells were FACS sorted into PBS. 2,000-3,000 cells were then encapsulated using the inDrops method and libraries were prepared for sequencing.


title: Compound screen identifies inhibitor of apoptosis proteins (IAP) antagonist as an inducer of T cell proliferation after cross-presentation by dendritic cells (Human)

city: Amsterdam

first: PETROS

last: DIMITRIADIS

email: p.dimitriadis@nki.nl, d.rao@nki.nl

state: Noord-Holland

address: Plesmanlaan 121

country: Netherlands

institute: NETHERLANDS CANCER INSTITUTE - NKI

summary: Cross-presentation of tumor antigens by dendritic cells (DCs) is crucial to prime and (re-) stimulate CD8+ T cells. This process is important in initiating and maintaining an anti-tumor response. Here, we show that tumor presence of conventional type 1 DCs (cDC1), a subtype that excels in cross-presentation, correlates with response to neoadjuvant immune checkpoint blockade (ICB) in melanoma. This led us to hypothesize that patients failing to respond to ICB could benefit from enhanced cross-presentation of tumor antigens. We therefore established a cross-presentation assay to screen over 5,500 compounds for enhancers of DC cross-presentation using induced T cell proliferation as readout. We identified 145 enhancers, including AZD5582, an antagonist of inhibitor of apoptosis proteins (IAPs) cIAP1, cIAP2 and XIAP. AZD5582 treatment led to DC activation of the non-canonical nuclear factor kappa B (NF-kB) pathway, enhanced antigen import from endolysosomes into the cytosol and increased expression of genes involved in cross-presentation. Furthermore, it upregulated expression of CD80, CD86, MHC class II, CD70 and secretion of TNF by DCs. This enhanced DC activation and maturation program was observed also in tumor-bearing mice upon AZD5582 treatment, culminating into an increased frequency of systemic tumor antigen-specific CD8+ T cells. Our results merit further exploration of AZD5582 to increase antigen cross-presentation for improving the clinical benefit of ICB in unfavorable patients.

overall_design: GM-CSF DCs ('moDCs') (n=3 biological replicates) and FLT3L + GM-CSF DCs ('cDC1') (n=3 biological replicates) were treated with different contrations of AZD5582 for 24 hours (0.05-1 uM). A time point 0 and DMSO treated control are included.

first: Esmée

middle: P

last: Hoefsmit

first: Paula

middle: T

last: van Royen

first: P

last: Dimitriadis

first: Daniel

last: Peeper

first: Christian

middle: U

last: Blank


title: Compound screen identifies inhibitor of apoptosis proteins (IAP) antagonist as an inducer of T cell proliferation after cross-presentation by dendritic cells (Mouse)


title: Acidity-mediated induction of FoxP3+ regulatory T cells

summary: Regulatory T cells (Tregs) are known to maintain survival and suppressive function in the presence of high levels of extracellular lactic acid. However, the effect of lactic acid on Treg induction is not known. We therfore evaluated the effect of lactic acid on Treg induction and observed an increased induction of Tregs in the presence of lactic acid. This increase occurred in a glycolysis-independent, acidity-dependent manner.

overall_design: CD4+ T cells, purified from spleens of FoxP3RFP mice were stimulated (with anti-CD3 and anti-CD28) for 24 or 72h in the presence of TGFb in low glucose condition. During this 10mM lactic acid was added. Cells were sorted after the indicated timepoint based on expression of FoxP3RFP and cell pellets were snap frozen for RNA extraction and further analysis.

first: Petros

first: Disha

last: Rao


title: The reverse transcriptase inhibitor 3TC protects against age-related cognitive dysfunction

city: Fort Collins

first: Devin

last: Wahl

state: Colorado

address: 1582 Campus Delivery, Moby Reception

institute: Colorado State University

summary:
Aging is the primary risk factor for most neurodegenerative diseases, including
Alzheimer's disease. Major hallmarks of brain aging include neuroinflammation/immune activation and reduced neuronal health/function. These processes contribute to cognitive dysfunction (a key risk factor for Alzheimer's disease), but their upstream causes are incompletely understood. Age-related increases in transposable element (TE) transcripts might contribute to reduced cognitive function with brain aging, as the reverse transcriptase inhibitor 3TC reduces inflammation in peripheral tissues and TE transcripts have been linked with tau pathology in Alzheimer's disease. However, the effects of 3TC on cognitive function with aging have not been investigated. Here, in support of a role for TE transcripts in brain aging/cognitive decline, we show that 3TC: (a) improves cognitive function and reduces neuroinflammation in old wild-type mice; (b) preserves neuronal health with aging in mice and Caenorhabditis elegans; and (c) enhances cognitive function in a mouse model of tauopathy. We also provide insight on potential underlying mechanisms, as well as evidence of translational relevance for these observations by showing that TE transcripts accumulate with brain aging in humans, and that these age-related increases intersect with those observed in Alzheimer's disease. Collectively, our results suggest that TE transcript accumulation during aging may contribute to cognitive decline and neurodegeneration, and that targeting these events with reverse transcriptase inhibitors like 3TC could be a viable therapeutic strategy.

overall_design: Total RNA-seq on hippocampus isolated from C57/B6 Mice aged 9 and 20 months.

first: Thomas

last: LaRocca


title: Ectopic expression of NAC094 induces premature nodule senescence in Lotus japonicus.

city: Hefei

first: Longlong

state: Anhui

address: No. 130, Changjiang West Road

department: School of Agronomy

institute: Anhui Agricultural University

summary: To investigate the function of NAC094 in vivo, we overexpressed NAC094 in the infected cells of nodules using an L. japonicus Lb2 expression cassette. To this end, we used a GUS overexpression construct as control and analysed stably transformed plants to detect symbiotic phenotypes. Results show that overexpression of NAC094 causes premature senescence of nodules. To identify the mechanism by which NAC094 regulates nodule senescence, we performed a transcriptome profiling analysis of nodules at 3 wpi. Around 13,850 differentially expressed genes (DEGs) were identified by comparing NAC-OE with control nodules (Log2FC > 1, FDR < 0.05). Of these, 7,516 were up-regulated (NAC-OE-UP) and 6,334 were down-regulated (NAC-OE-DOWN).

overall_design: we performed a transcriptome profiling analysis of nodules at 3 wpi by comparing NAC-OE with control (GUS-OE) nodules, each with three biological replicates.

first: Xian

last: Xin

first: Runhui

last: Li

first: Deqiang

last: Duanmu


title: A time-course transcriptomic study for investigating the genome-wide effects of nitrate on gene expression in mature nodules of Lotus japonicus.

last: Wang

summary: A time-course transcriptomic study was performed on mature nodules of Lotus japonicus MG-20 at 4 weeks post-inoculation (wpi) with Mesorhizobium loti MAFF303099. Plants were exposed to 10 mM KNO3 for six days and then nitrate was removed for five more days.

overall_design: Nodule samples were collected daily during nitrate treatment (T0 to T6) or nitrate removal (R1 to R5), each with three biological replicates.


title: Enhancing HIV-1 latency reversal through regulating the elongating RNA Pol II pause-release by a small-molecule disruptor of PAF1C

city: Chicago

first: Ali

last: Shilatifard

address: 320 E Superior St

department: Department of Biochemistry and Molecular Genetics

institute: Northwestern University Feinberg School of Medicine

summary: The polymerase-associated factor 1 complex (PAF1C) is a key, post-initiation transcriptional regulator of both promoter-proximal pausing and productive elongation catalyzed by RNA Pol II and is also involved in transcriptional repression of viral gene expression during human immunodeficiency virus–1 (HIV-1) latency. Using a molecular docking–based compound screen in silico and global sequencing–based candidate evaluation in vivo, we identified a first-in-class, small-molecule inhibitor of PAF1C (iPAF1C) that disrupts PAF1 chromatin occupancy and induces global release of promoter-proximal paused RNA Pol II into gene bodies. Transcriptomic analysis revealed that iPAF1C treatment mimics acute PAF1 subunit depletion and impairs RNA Pol II pausing at heat shock–down-regulated genes. Furthermore, iPAF1C enhances the activity of diverse HIV-1 latency reversal agents both in cell line latency models and in primary cells from persons living with HIV-1. In sum, this study demonstrates that efficient disruption of PAF1C by a first-in-class, small-molecule inhibitor may have therapeutic potential for improving current HIV-1 latency reversal strategies.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for DLD1_PAF1-AID cells with and without PAF1C inhibition. Comparative precision run-on sequencing (PRO-seq) for DLD1 cells with and without PAF1C inhibition, with or without heat shock. Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for RNA Polymerase II in HCT116 and DLD1 cells, as well as PAF1C in DLD1 cells.

first: Shimaa

last: Soliman

first: William

last: Cisneros

first: Marta

last: Iwanaszko


title: Orphan elements are clustered with allorecognition loci and likely involved in incompatibility and speciation in Neurospora

city: West Haven

first: Francesc

last: Lopez

state: CT

department: Department of Genetics

institute: Yale University

summary: Orphan genes have been attributed to gene duplication followed by fast divergence, horizontal gene transfer, relocation and rearrangement, and to expression of previously non-coding sequences abundant with long repeats. However, their roles are less well described and there is a lack of working hypotheses that would guide the investigation of orphan genes. For 670 Neurospora orphan genes identified in this study, over 63% form clusters that aggregate adjacent to the telomeres and are clustered with up to 61% het-like genes, which regulate self-recognition and define vegetative compatibility groups (VCGs). Based on transcriptomic data from N. crassa grwoth and reproduction under various conditions, 342 orphan genes are dynamically expressed during both the sexual and asexual growth. Among them, 37% respond to common carbon resources, and 64% respond to non-preferred carbon sources such as furfural and HMF — wildfire-produced chemical that are a strong inducer of sexual development in N. crassa. Expression of a significant portion of the orphan genes was sensitive to light and temperature that regulate fungal activities and distributions. Orphan genes and clustered het-like genes respond similarly to mutation in transcription factors adv-1 and pp-1 that regulate cell communications, and expression of a significant portion of the orphan genes was affected in a mating locus mutant. Coordinate expression in orphan-het gene clusters was observed during early hyphal branching. functional interactions between orphan and het-like genes are likely contribute to the vegetative incompatibilit and possibly promote crossings betwen VCG groups guided by sexual incompatibilities. Orphan genes’ involvements in the balance between genome homogeneity and heterogeneity in VCG genotypes as well as in the speciation could be essential and make them potential targets to control fungal growth for good and bad.

overall_design: RNAs were extract from mat 1-2-1 mutant  (FGSC#4564, mat a[m1]s-3B cyh-1) for six-day cultures on synthetic crossing medium (SCM), when protoperithecia were ripen and two hours after crossing with wild type conidia from FGSC#2489. Transcriptome profiles were compared between wildtype strain and mating locus mat 1-2-1 mutant.

first: Zheng

last: Lopez-Giraldez

first: Jeffrey

last: Townsend


title: Neurotrophin signaling is a central mechanism of salivary dysfunction after irradiation that disrupts myoepithelial differentiation

city: San Francisco

first: Alejandro

last: Martinez Chibly

state: CALIFORNIA

address: 330A Guerrero Street

institute: Genentech

summary: The mechanisms that prevent regeneration of irradiated (IR) salivary glands remain elusive. Bulk RNAseq of IR versus non-IR human salivary glands showed that neurotrophin signaling is highly disrupted post-radiation. Moreover, neurotrophin receptors (NTRs) are significantly upregulated in myoepithelial cells (MECs) post-IR, and scRNAseq revealed that MECs are a main source of neurotrophin ligands. Using two ex vivo models, we show that nerve growth factor (NGF) is essential for MEC differentiation during development, whereas upregulation of NTRs in adult MECs is associated with differentiation defects. The latter morphological abnormalities were confirmed in MECs of human IR glands. As MECs are required for proper acinar cell contraction and secretion, we propose that MEC-specific upregulation of NTRs post-IR disrupts MEC differentiation and potentially hinders the ability of the gland to regenerate.

overall_design: Alejandro M. Chibly

first: Vaishali

last: Patel

first: Marit

last: Aure

first: Mary

last: Pasquale

first: Daniel

last: Martin

first: Gemma

middle: E

first: Mousa

last: Ghannam

first: Julianne

last: Andrade

first: Noah

last: Denegre

first: Colleen

last: Simpson

first: David

last: Goldstein

first: Fei-Fei

last: Liu

first: Isabelle

last: Lombaert

first: Matthew

last: Hoffman


title: RNA seq-based transcriptome analysis of eccrine sweat glands from anhidrotic patients

city: nagasaki

first: Naoya

last: Murayama

state: nagasaki

institute: Nagasaki  University

summary: Eccrine sweat glands contribute to the regulation of human body temperature. Acquired idiopathic generalized anhidrosis (AIGA) is extensive anhidrosis of unknown etiology, that causes the fatal heatstroke and skin dryness. Eccrine sweat glands in hidrotic and anhidrotic skin areas were excised from paraffin-embedded skin specimens from AIGA patients, and the gene expression was profiled by RNA-sequencing. We analyzed the RNA samples to clarify the difference in gene expression between hidrotic and anhidrotic skin areas from AIGA patients.

overall_design: Eccrine sweat glands in hidrotic and anhidrotic skin areas were excised from paraffin-embedded skin specimens from four AIGA patients, and the gene expression was profiled by RNA-sequencing. Since RNA could not be extracted from one patient due to a lack of sample material in the anhidrotic lesion, we analyzed the RNA samples derived from 3 hidrotic and 4 anhidrotic lesions.

first: Daisuke

last: Okuzaki

first: Hiroyuki

last: Murota


title: DNMT1 mutant ants develop normally, but have disrupted oogenesis and decreased survival

city: Athens

first: Robert

last: Schmitz

state: GA

address: B416 Davison Life Sciences

department: Genetics

institute: University of Georgia

summary: While DNA methylation is an important gene regulatory mechanism in mammals (Razin and Riggs 1980; Moore, Le, and Fan 2013), its function in arthropods remains poorly understood. Studies in eusocial insects have argued for its role in caste development by regulating gene expression and splicing (Elango et al. 2009; Lyko et al. 2010; Bonasio et al. 2012; Flores et al. 2012; Foret et al. 2012; Li-Byarlay et al. 2013; Marshall, Lonsdale, and Mallon 2019; Shi et al. 2013)(Alvarado et al. 2015; Kucharski et al. 2008). However, such findings are not always consistent across studies, and have therefore remained controversial (Arsenault, Hunt, and Rehan 2018; Cardoso-Junior et al. 2021; Harris et al. 2019; Herb et al. 2012; Libbrecht et al. 2016; Oldroyd and Yagound 2021b; Patalano et al. 2015). Here we use CRISPR/Cas9 to mutate the maintenance DNA methyltransferase DNMT1 in the clonal raider ant, Ooceraea biroi. Mutants have greatly reduced DNA methylation but no obvious developmental phenotypes, demonstrating that, unlike mammals (Brown and Robertson 2007; En Li, Bestor, and Jaenisch 1992; Jackson-Grusby et al. 2001; Panning and Jaenisch 1996), ants can undergo normal development without DNMT1 or DNA methylation. Additionally, we find no evidence of DNA methylation regulating caste development. However, mutants are sterile, while in wildtypes, DNMT1 is localized to the ovaries and maternally provisioned into nascent oocytes. This supports the idea that DNMT1 plays a crucial but unknown role in the insect germline (Amukamara et al. 2020; Arsala et al. 2021; Bewick et al. 2019; Schulz et al. 2018; Ventós-Alfonso et al. 2020; Washington et al. 2020).

overall_design: 4 MethylC-seq of Ooceraea biroi


title: Transcription factor induction of vascular blood stem cell niches in vivo [TOMO-Seq]

first: Leonard

last: Zon

summary: We report RNA tomography (tomo-seq) gene expression data for the tail region of a 72 hpf zebrafish embryo. The portion of the tail containing the caudal hematopoietic tissue (CHT) was isolated by manual dissection, snap froze, and then cryosections (40 in total, 8 µm-thick) were collected along the dorsal-ventral axis. Each cryosection was placed into a tube and the RNA was exctracted and barcoded during a reverse trancription step prior to library synthesis and sequencing.

overall_design: The region of the tail containing the CHT was isolated using a scalpel and then snap-frozen on dry ice. The RNA from individual cryosections was extracted using Trizol reagent and then barcoded during a reverse transcription step prior to library synthesis according to the previously published method (Junker et al., 2014).

first: E

last: Hagedorn

first: Jan

last: Junker

first: S

last: Yang

first: L


title: Transcription factor induction of vascular blood stem cell niches in vivo [RNA-Seq]

summary: We report gene expression data for FACS sorted zebrafish kdrl(flk1):GFP + and kdrl:mCherry+;sele(5.3kb):GFP+ double positive cells collected from whole embryos at 72 hours post fertilization (hpf). We also report gene expression data for the kdrl:GFP negative fraction.

overall_design: kdrl:GFP or kdrl:mCherry;sele:GFP double positive transgenic embryos were homogenized, filtered, and sorted using FACS into PBS, collecting at least 10,000 cells for each group.


title: Transcription factor induction of vascular blood stem cell niches in vivo [scRNA-Seq]

summary: We report single cell gene expression data for FACS-isolated zebrafish kdrl(flk1):GFP positive cells collected from whole embryos at 72 hours post fertilization (hpf).

overall_design: kdrl:GFP positive transgenic embryos were homogenized, filtered, and then 25,000 GFP+ cells were FACS sorted into PBS. 2,000 cells were then encapsulated using the inDrops method and libraries were prepared for sequencing.


title: CD73+ epithelial progenitor cells which contribute to homeostasis and renewal are depleted in eosinophilic esophagitis

status: Public on Mar 22 2023

city: Philadelphia

first: Amanda

last: Muir

state: PA

address: 3401 Civic Center Boulevard

institute: Children's Hospital of Philadelphia

summary: We performed single-cell RNA sequencing on esophageal PDOs from 4 non-EoE control patients to investigate the molecular heterogeneity of human esophageal organoids. Seurat’s unsupervised dimensionality reduction and clustering along with uniform manifold approximation and projection visualization showed 4 distinct cell clusters in esophageal PDOs cultures with or without IL13

overall_design: Patient-derived esophageal organoids from 4 control patients were cultured with or without IL-13 treatment, followed whole cell single cell RNA-seq

first: Hara

last: Takeo

first: Muir

last: Amanda

first: Karakasheva

last: Tatiana

first: Karami

last: Adam


title: Transcription factor induction of vascular blood stem cell niches in vivo

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

overall_design: Refer to individual Series


title: Inositol hexaphosphate enhances chemotherapy by reversing persistent endoplasmic reticulum stress-induced senescence in colorectal cancer

city: Xi 'an

first: Xia

last: Liao

state: Shaanxi

address: 277# West Yanta Road

institute: Department of nutrition


title: Effect of SlNOR-like1 knockout on gene expression related to cuticle metabolism in tomato exocarp

city: beijing

first: zhijian

last: liu

address: Last Olympic Century Center, Xisanqi, Changping

institute: boyunhuakang

summary: To investigate the function of SlNOR-like1 in the regulation of cuticle formation in tomato fruits, we established nor-like1 mutants by CRISPR/Cas9. We then performed gene expression profiling analysis using data obtained from RNA-seq of tomato exocarp of wild type (WT) and nor-like1 mutant at mature green (MG) stage.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for tomato exocarp of WT and nor-like1 mutants at MG stage

first: Gang-Shuai

last: Liu

first: Hua

last: Huang

first: Da-Qi

last: Fu


title: Transcriptome analysis of molecular mechanisms underlying phenotypic variation in Phaseolus vulgaris mutant nts

city: shenyang

first: jun

last: zhang

address: liaoning

institute: Shenyang Agricultural University

summary: Purpose:the goals of this study are to find the candidate genes that control the phenotypic variation of phasbean mutants and provide theoretical basis for phasbean breeding.

overall_design: The apical stem samples in 'A18' were labeled as A18, and the apical stem samples in 'nts' were labeled as nts, respectively. The differences in gene expression were analyzed using base picture segment number per kilobase pair fragment (FPKM) value per million base pair transcript fragment. Among them, genes with expression log2≥2 or ≤-2 and p value ≤0.05 were labeled as differentially significant

first: Limin

last: Yin

first: Zicong

last: Liang

first: Xiaoxu

first: Guojun

last: Feng


title: Inositol hexaphosphate enhances chemotherapy by reversing persistent endoplasmic reticulum stress-induced senescence in colorectal cancer [RNA-seq I]

summary: To investigate if CRC cells treated with CoCl2, brefeldin A, or low glucose for more than 30 days exhibited an increased  senescence.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for HCT 15 cells treated with CoCl2, brefeldin A, or low glucose.

first: Qingan

last: Jia

first: Binghui

last: Xu

first: Yuna

last: Song

first: Tian

last: Fan

first: Lei

last: Mou

first: Chunyu

last: Zhu

first: Zhixian

last: Li

first: Zhen

last: Zhang

first: Kairan

first: Miao

last: Wang

first: Qiangbo


title: Transcription factor induction of vascular blood stem cell niches in vivo [ATAC-Seq]

first: Leonard

last: Zon

summary: We report ATAC-seq data for FACS sorted zebrafish kdrl(flk1):mCherry+;mrc1a(1.3kb):GFP+ double positive cells collected from whole embryos at 72 hours post fertilization (hpf). We also report ATAC-seq data for the single positive fractions and the remaining, transgene negative, portion of the same embryos. The experiment was performed in triplicate.

overall_design: kdrl:mCherry;mrc1a:GFP double positive transgenic embryos were homogenized, filtered, and sorted using FACS into PBS, collecting at least 12,000 cells (max 50,000) for each of the four cell populations.

first: E

last: Hagedorn

first: S

last: Yang

first: L


title: Transcriptional profiling of liver, neutrophils and T cells from a mouse model of NASH-HCC

city: Glasgow

first: Kathryn

last: Gilroy

address: Garscube

country: United Kingdom

institute: CRUK Scotland Institute

summary: Transcriptional profiling by bulk RNA sequencing of murine livers or sorted immune cells, from DEN ALIOS NASH-HCC mouse model.  Mice treated with CXCR2i (AZD5069) monotherapy,  anti-PD1 monotherapy, or combination CXCR2i,  anti-PD1 treatment. Published in doi: 10.1136/gutjnl-2021-326259

overall_design: Expression data from liver and FACS purfied neutrophils and T cells

first: Leo

last: Carlin

first: John

middle: B

last: Mackey


title: Inositol hexaphosphate enhances chemotherapy by reversing persistent endoplasmic reticulum stress-induced senescence in colorectal cancer [RNA-seq II]

first: Xia

last: Liao

summary: To investigate if oxaliplatin resistance contributed to persistent endoplasmic reticulum-induced senescence,

overall_design: Comparative gene expression profiling analysis of RNA-seq data for HCT 15 cells treated with oxaliplatin and sorafenib.

first: Qingan

first: Binghui

last: Liang


title: Identification of NAC094-targeted genes using DNA affinity purification sequencing (DAP-seq)

first: Longlong

summary: To identify binding sites and nodule SAGs that are directly targeted by NAC094, we used DAP-seq, which allows the capture of the NAC094 regulatory targets at the whole-genome scale. A total of 2,819 binding peaks corresponding to 2,721 genes were identified from two repeats of the DAP-seq experiment.

overall_design: Two repeats of the DAP-seq experiments (NAC094-1 and NAC094-2) were performed. Enriched peaks were identified by comparing the results of  NAC094-1 and NAC094-2 with the control (NAC094-input).

first: Xian

last: Xin

first: Runhui

first: Deqiang

last: Duanmu


title: Effect of depletion of Rif1 on gene expression of mouse embryonic stem cells

city: Beijing

first: Wang

address: 167 Beilishi Rd

department: State Key Laboratory of Cardiovascular Disease

institute: Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences

summary:
To explore the molecular basis of phenotypic alterations observed in Rif1-KO mES cells
we profile the global gene expression in Control and Rif1-KO mESCs by RNA-sequencing

overall_design: Comparative gene expression profiling analysis of RNA-seq data for control mES cells and Rif1-KO mES cells.

first: Cheng

last: Liu

first: Peng

last: Yu

first: Fang

last: Yao

first: Li

first: Pishun

first: Quanyi

last: Zhao


title: ALYREF Mediates RNA m5C Modification to Promote Hepatocellular Carcinoma Progression

city: Hangzhou

first: Xue

last: Chen

state: Zhejiang

address: No.79, Qingchun Road, Shangcheng Distric

department: The First Affiliated Hospital

institute: Zhejiang University

summary: The RNA methyltransferase Aly/REF export factor (ALYREF) is considered one type of “reader” protein located in the nucleus that recognizes and binds directly with m5C sites in RNA and facilitates the export of RNA from the nucleus to the cytoplasm. Notably, ALYREF is considered a promising target for diagnosis and prognosis prediction. However, until now, the low number of related studies has limited the understanding of the mechanism of the HCC-promoting effects of ALYREF. To further elucidate the oncogenic roles of ALYREF in hepatocellular carcinoma (HCC), we assessed the expression levels of ALYREF in clinical samples and HCC cell lines and explored the effects of ALYREF deficiency by both in vitro experiments and m5C-methylated RNA immunoprecipitation sequencing (m5C-MeRIP-Seq)

overall_design: The effect of ALYREF deficiency on Huh-7 and HepG2 cells was investigated.   To further explore the potential molecular mechanism of ALYREF in RNA m5C modification. We then performed m5C-MeRIP-Seq on both sh-NC and sh-ALYREF Huh-7 and HepG2 cells. (Three samples and three controls)


title: Overexpression of OsERF106MZ promotes root growth in rice seedlings by relieving the ABA-mediated inhibition of root growth

city: Taipei

first: MenChi

last: Chang

state: Taiwan (R.O.C.)

address: No. 1, Sec. 4, Roosevelt Rd.

department: Agronomy

institute: National Taiwan University

summary:
Background: Roots are essential for plant growth and serve a variety of functions, such as anchoring the plant to the ground and absorbing water and nutrients. OsERF106MZ is a salinity-induced gene that is expressed in germinating seeds and the roots of rice seedlings. However, the roles of OsERF106MZ in root growth remain poorly understood.
Results: Histochemical staining of GUS (β-glucuronidase) activity in transgenic rice seedlings harboring OsERF106MZp::GUS indicated that OsERF106MZ is mainly expressed in the exodermis, sclerenchyma layer, and vascular system of roots. Overexpression of OsERF106MZ in rice seedlings leads to an increase in the length of primary roots (PRs). The expression of the ABA (abscisic acid) biosynthetic gene, OsAO3, is downregulated in OsERF106MZ-overexpressing roots under normal conditions, while the expression of OsNPC3, an AtNPC4 homolog involved in ABA sensitivity, is reduced in OsERF106MZ-overexpressin roots under both normal and NaCl-treated conditions. Under normal conditions, OsERF106MZ-overexpressing roots have a significantly low level of ABA; moreover, exogenous application of 1.0 µM ABA can suppress the OsERF106MZ-mediated promotion of root growth. Meanwhile, OsERF106MZ-overexpressing roots display less sensitivity to the ABA-mediated inhibition of root growth, when they are treated with ABA at 5.0 µM under normal conditions or exposed to NaCl-treated conditions. Chromatin immunoprecipitation (ChIP)-qPCR and luciferase (LUC) reporter assays showed that OsERF106MZ can bind directly to the sequence containing the GCC-box in the promoter region of OsAO3 gene and repress its expression.
Conclusion: OsERF106MZ may play a role in maintaining root growth for resource uptake when rice seeds are sprouted under salinity stress, which is arrived at by alleviating the ABA-mediated inhibition of root growth.

overall_design: For this experiment, the seedlings were transferred to basal medium supplemented with 0 or 150 mM NaCl after growing for 7 days in plastic basins. Twenty-four hours later, the terrestrial parts of the plant were subjected to RNA extraction

first: Hung-Chi

first: Shi-Cheng

last: Huang

first: Yen-Fu

first: Che-Wei

last: Kuo

first: Ying-Hsuan

first: Men-Chi


title: Transcriptomics of rat arteriovenous fistulas treated with periadventitial beta-aminopropionitrile loaded scaffolds

city: Miami

first: Derek

last: Van Booven

state: FL

address: 1501 NW 10th Ave

institute: University of Miami

summary: We report the RNA expression profiles of rat AVF samples obtained 21 days after creation. We perfomed bulk RNA-seq on AVFs treated with beta-aminopropionitrile scaffolds or vehicle scaffolds.

overall_design: This study was designed to evaluate changes in AVF gene expression with periadventitial LOX inhibition.

first: Roberto

last: Vazquez-Padron

first: Laisel

last: Martinez

first: Brandon

last: Applewhite

first: Anthony

last: Griswold


title: Mitochondrial Genetic Background Modulates Phenotype and Nuclear-Mitochondrial Genome Expression in Isolated Adult Cardiomyocytes of Volume Overload

city: Birmingham

first: Mariame Selma

last: Kane

state: Alabama

address: 901 19th Street South

department: Medicine

institute: University of Alabama at Birmingham

summary: To test the hypothesis that mtDNA haplotype influences structure, bioenergetic response, and gene expression in isolated cardiomyocytes subjected to cyclical stretch or ACF.

overall_design: We then performed gene expression profiling analysis using data obtained from RNA-seq of cardiomycytes isolated from mitochondria-nuclear exchange (MNX) mice in which the mitochondria (mt) and nuclear (n) genomes from wild-type C57BL/6J (C57n:C57mt) and C3H/HeN (C3Hn:C3Hmt) mice have been reciprocally exchanged to generate respective MNX mice (C57n:C3Hmt or C3Hn:C57mt) under two conditions: sham and ACF.

first: Louis

last: Dell'Italia

first: Jason

last: Guichard

first: Mariame


title: Attenuation of IFN signaling due to M6A modification of the host epitranscriptome promotes EBV lytic reactivation

first: Erle

last: Robertson

address: 3610 Hamilton Walk

institute: Otorhinolaryngology-Head and Neck Surgery Perelman School of Medicine

summary: N6-methyladenosine (m6A) modification is one of the most abundant post-transcriptional modifications that plays an important role in many pathophysiological conditions including host-pathogen interactions. A number of viruses were previously shown to manipulate the cellular m6A machinery usurping its function to their benefit during the course of their life cycle. Previously, we reported that EBV reprograms the host m6A system to regulate the stability of the viral transcripts and drive viral-mediated tumorigenesis by hijacking the functions of methyltransferase METTL14. We now report that during lytic reactivation EBV targets the RNA methylation system of the host to attenuate the innate immune response by suppressing the interferon response to facilitate a successful lytic replication.

overall_design: LCL and AKATA cells treated with or without TPA and BA were incubated for 30 h before being lysed and total mRNA was extracted. RNA immuno precipitation was done using either m6A specific antibodies or by IgG control. The immunoprecipitated RNAs were processed for RNA sequencing according to the Trueseq RNA processing lit protocol.

first: Dipayan

last: Bose

first: Xiang

last: Lin

first: Le

last: Gao

first: Yonggang

last: Pei

first: Zhi

last: Wei


title: Pancreatic stellate and cancer cell transcriptomes from heterocellular, 3D invasive, cultures

city: London

first: Ed

last: Carter

address: John Vane Science Centre

institute: Barts Cancer Institute

summary: When combined into spheres and embedded in extracellular matrix, hetero-cellular cultures of pancreatic cancer and stellate cells produce invasive, stellate-led, projections. In order to establish what cancer and stellate cells are expressing in this context we generated chimeric spheres of mouse and human cells. Invasive spheroids could then be processed for RNA sequencing, with reads mapped back to parent species and thus cell type.

overall_design: Two sets of human (Miapaca2 and Panc1) and mouse (DT6066, R254) pancreatic cancer cells were combined with mouse and human pancreatic stellate cells, respectively, and formed into hetero-cellular spheres.  Spheres were then embedded in collagen : matrigel hydrogels and cultured for 72 hours at which point invasive projections are evident. Total RNA was obtained through Trizol extraction and processed for sequencing. Cell type specific information was then extracted my matching reads to host species and therefore cell type.

first: Edward

first: Richard

last: Grose


title: The RNA sequencing analysis of nasopharyngeal carcinoma (NPC) cell line  S18 upon circWDR37 knockdown

city: guangzhou

first: Yingqin

last: Li

state: guangdong

address: Guangzhou, 510060, P.R. China

institute: Sun Yat-sen University Cancer Center

summary: Circular RNAs have been demonstrated to play significant roles in multiple biological processes, such as immune responses and tumorigenesis, suggesting it might be potential therapeutic targets. However, the function and mechanisms of circRNAs in nasopharyngeal carcinoma (NPC) metastasis remain largely unknown. In this study, we identified circWDR37 as a metastasis related circRNA. To further explore the underlying mechanism of circWDR37 promoting NPC metastasis, we performed RNA sequencing analysis of NPC cell line S18 upon circWDR37 knockdown.

overall_design: High-throughput RNA sequencing analysis was performed in the human nasopharyngeal carcinoma cell line S18 after transfection with control siRNA or circWDR37 siRNA.

first: Q

first: J

last: Ma

first: Y

middle: Q


title: RNA-seq of Phytophthora sojae WT and pskmt3

city: nanjing

first: Han

last: Chen

state: jiangsu

address: weigang no.1,xuanwu district

institute: Nanjing Agricultural University

summary: Plant pathogens secreted effector proteins to overcome host immunity system and gain access to colonization. Although more than 300 hundred of RxLR effectors were encoded by the devastating soybean pathogen Phytophthora sojae, the patterns of conditionally expressed effector genes were well programmed. However, the effector gene regulation mechanisms were not fully dissected. In this study, we identified the H3K36me3 methyltransferase PsKMT3. Phenotypic assays showed PsKMT3 was involved in regulation of growth, sporulation, zoospore production and pathogenicity. ChIP-seq analysis, together with RNA-seq analysis, showed PsKMT3 controlled a set of RxLR gene expression.  The transcriptome comparison showed large-scale mis-expression of RxLR waves during mycelium, 3 hpi and 6 hpi stages between WT and pskmt3. Our result supports a new RxLR gene regulation mechanisms in which methyltransferase PsKMT3 maintains well programmed RxLR gene expression in P. sojae.

overall_design: Two replicates of  P. sojae mycelium, 3 hpi and 6 hpi  stage samples were performed.


title: Metatranscriptomics of Salmonella superspeader stool

city: Stanford

first: Denise

last: Monack

state: Ca

address: 299 Campus Drive, Fairchild Building D331

department: Microbiology and Immunology

institute: Stanford University

summary: Longitudinal analysis of Salmonella typhimurium mRNA from superspeader mouse cecal content and stool compared to in vitro Salmonella typhimurium mRNA.

sample_organism: Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344

overall_design: Mice were infected with 10^8 colony forming units of Salmonella Typhimurium. 3 mice were euthanized at day 14 and 21 post-infection. Cecal content and feces were collected. RNA was extracted from those cecal contents and feces. In addition, salmonella was grown in LB for 10-16 hours aerobically and anaerobically for RNA extraction. In vivo and in vitro samples were sequenced and differential expression analysis was performed comparing the two sample groups.

first: Sarah

last: Ruddle


title: ChIP-seq of Phytophthora sojae WT and pskmt3

overall_design: Two replicates of  P. sojae mycelium stage samples were performed.


title: Isoginkgetin induces autophagic cell death in hepatocellular carcinoma [ChIP-seq 2]

city: wuhan

first: Jie

last: Yao

state: 湖北

address: wuhan hubei province

institute: wuhan university

summary:
Purpose: Our previous studies have identified isoginkgetin as an inducer of autophagic cell death in hepatocellular carcinoma. We set out to analyze how isoginkgetin regulates the genome-wide enhancer activity in HepG2 cells.
Methods: ChIP-seqs for H3K4me, H4K8ac, H3K27me3 and H3K9ac were performed in HepG2 followed by treatment with 20 μM isoginkgetin for 24 h.
Conclusions: Isoginkgetin treatment reduces the expression of glucose transporters and inhibts SLC2A1 enhancer activity in HepG2 cells.

overall_design: ChIP-seq was performed  in HepG2 cells followed by treatment with 20 μM Isoginkgetin for 24 h.  The genome-wide enhancer activity was studied by H3K4me, H4K8ac, H3K27me3 and H3K9ac ChIP sequencing.

first: Chuan

first: Xiaobin

last: Zeng


title: Fetal hypoxia results in sex- and cell type-specific alterations in postnatal transcription in rat oligodendrocyte precursor cells, microglia, neurons, and oligodendrocytes

city: Loma Linda

first: Isaac

middle: Jacob

last: Kremsky

state: CA

address: 11175 Campus St., Chan Shun Pavilion, Room A1022

department: Basic Sciences

institute: Loma Linda University

summary: Background: Fetal hypoxia causes vital, systemic, developmental malformations in the fetus, particularly in the brain, and increases the risk of diseases in later life.  We previously demonstrated that fetal hypoxia exposure increases the susceptibility of the neonatal brain to hypoxic-ischemic insult. Herein, we investigate the effect of fetal hypoxia on programming of cell-specific transcriptomes in the brain of neonatal rats.

overall_design: Pregnant Sprague-Dawley (SD) rats (Charles River Laboratories, Portage, MI, USA) were randomly divided into two groups: (i) the normoxic control and (ii) hypoxic exposure (10.5% O2) from Day 15 to Day 21 of gestation, as we previously described [11, 34-37]. The pups were sacrificed at postnatal day 7, and the brains were collected for cell sorting. Five types of brain cells (microglia, neurons, astrocytes, oligodendrocytes, A2B5+ glia precursor cells) were sorted from P7 pups using magnetic-activated cell sorting (MACS) technology. Total RNA was isolated from each cell type using the Qiagen miRNeasy kit (Cat # 217004) following manufacturer’s protocol.

first: Qingyi

first: Bo

first: Chiranjib

last: Dasgupta

first: Xin

first: Samir

last: Ali

first: Shawnee

last: Angeloni

first: Charles

last: Wang

first: Lubo

last: Zhang


title: Gene expression profiles in ethylene glycol-induced renal stone formation and phlorizin treatment

city: Sendai

first: Takuo

last: Hirose

state: Miyagi

address: 1-15-1 Fukumuro Miyagino

department: Department of Nephrology and Endocrinology

institute: Tohoku Medical and Pharmaceutical University

summary:
Microarray analysis for total RNA from rat renal cortex and outer meulla.
Nephrolithiasis is a disorder with a poor quality of life due to severe pain and no effective medication. Sodium-glucose cotransporter-2 (SGLT2) inhibitors, an anti-diabetic agent, have diuretic and anti-inflammatory effects, suggesting their benefit in treating nephrolithiasis. However, the effects of SGLT2 inhibition against renal stone formation have not been elucidated. To check gene expression profiles, microarray analysis was performed.

overall_design: To evaluate the relationship between SGLT2 inhibition and renal stone formation, renal stone formation rats were generated and treated with phlorizin. Gene expression profiles in the renal cortex and outer medulla were assessed with Clariom S Assays.

first: Go

last: Anan


title: Characterization of Sox15 binding occupancy and gene expression (RNA-Seq)

city: Boston

first: Shannan

last: Ho Sui

state: Massachusetts

address: 401 Park Drive, Level 3 East

department: Biostatistics

institute: Harvard T.H. Chan School of Public Health

summary: SOX15 and SOX2 are Sox family transcription factors (TFs) enriched in embryonic stem cells (ESCs). The role of SOX2 in activating gene expression programs essential for stem cell self-renewal and acquisition of pluripotency in somatic cells during reprogramming is well-documented. However, the contribution of SOX15 to these processes is unclear and often presumed redundant with SOX2 because both TFs display similar DNA binding specificity. Here, we show that SOX15 contributes to stem cell maintenance by cooperating with ESC-enriched transcriptional coactivators to ensure optimal expression of pluripotency-associated genes. We demonstrate that SOX15 depletion compromises reprogramming of fibroblasts to pluripotency which cannot be compensated by SOX2. Ectopic expression of SOX15 promotes the reversion of a more restricted, post-implantation pluripotent state back to a pre-implantation, ESC-like identity even though SOX2 is expressed in both cell states. We also uncover a role of SOX15 in lineage specification, by showing that loss of SOX15 leads to defects in commitment of ESCs to neural fates. SOX15 promotes neural differentiation by binding to and activating a previously uncharacterized distal enhancer of a key neurogenic regulator, Hes5. Together, these findings identify a multifaceted role of SOX15 in induction and maintenance of pluripotency and neural differentiation.

overall_design: Total RNAs were isolated from wild-type and Sox15 knockout ESCs and subjected to RNA-seq analysis

first: Eun-Bee

last: Choi

first: Munender

last: Vodnala


title: Characterization of Sox15 binding occupancy and gene expression (ChIP-Seq)

overall_design: We performed ChIP-seq in HA-tagged SOX15 and SOX2 knockin mouse ESCs to identify SOX15 and SOX2 binding sites, respectively. We generated Sox15 knockout mouse ESC lines and anlayzed changes in gene expression by RNA-seq.


title: Characterization of Sox15 binding occupancy and gene expression

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

overall_design: Refer to individual Series


title: Fibroblast heterogeneity: a new phenotype associated with photoaging/solar elastosis

city: Lübeck

first: Hauke

last: Busch

state: Schleswig-Holstein

address: Ratzeburger Allee 160

department: Lübeck Institute of Experimental Dermatology

institute: University of Lübeck

summary: We here present a novel subtype of fibroblasts isolated from sun-exposed skin of elderly donors and characterized by its prominent and stable myo-chondrocyte-type differentiation. As we depict a similar chondrocyte-type expression pattern at sites of solar elastosis in human skin, we propose that this fibroblasts phenotype develops in the course of massive and perseverative UV-dependent damage as part of the process terminating in the most severe appearance of photoaging - solar elastosis. Along with the abnormal expression profile, these “old” fibroblasts generate a chondrocyte-type matrix with a layer of myofibroblast-differentiation in close vicinity to the epidermis, when propagated as skin equivalents (SEs) in 3D organotypic cultures. Importantly, these fibroblasts are strongly reduced in their ability to support epidermal growth and differentiation, allowing for rapid/premature epidermal atrophy. Having identified TGFß as an important player in this scenario, we show that the addition of TGFß to normal young fibroblast induces while inhibition of TGFß to the old fibroblast abolishes the myo-chondrogenic expression profile. Accordingly, inhibiting TGFß in the in vivo-like SEs, not only abrogates the aberrant phenotype but allows these fibroblasts to regain their normal mutual interaction with the epidermal keratinocytes and to support epidermal regeneration and longevity. Further, we provide evidence for a role of chronic solar UV radiation in initiating chondrogenic gene expression in young fibroblasts. Concomitantly, we show however, that the same UV treatment abolishes myofibroblast differentiation in the SEs with the “old” chondrogenic fibroblasts, and that this selective inhibition is already sufficient to restore the fibroblasts’ ability for successfully supporting epidermal growth and differentiation. From this it is tempting to suggest, that besides all damaging potential, “mild” solar UV radiation may exert also beneficial effects, e.g. in promoting activation of photoaged skin.

overall_design:
To compare in vitro and in vivo aging of human dermal fibroblasts we cultivated cells in vitro from young donors (21/22 years of age) over 22 passages and compared gene expression to fibroblasts from an old donor (66 years of age).

To compare in vitro and in vivo aging of human dermal fibroblasts we compared the gene expression from a scaffold-based OTC model  (scaOTC), which allows epidermal regeneration for several months (Boehnke et al., 2007; Stark et al., 2004, 2006). sca-OTCs were cultivated from 3 different fibroblast sources (one from a young (22 years) and 2 from old donors  (66 years and   74 years), all co-cultured with the same normal human epidermal keratinocytes. scaOTCs were cultivated for three and 9 weeks and gene expression compared based on the in vivo age of the constitutent fibroblasts. While all fibroblasts were able to promote the establishment of a well-stratified and differentiated epidermis yet epidermal differentiation demonstrated a somewhat impaired epidermal differentiation in 3-week-old scaOTCs , as compared to that seen on young fibroblasts.
In scaOTCs with old fibroblasts, the epithelia became more disorganized and in part atrophic. After 9 weeks, this phenotypic difference was even more aggrevated, leading to a largely atrophic epithelium with hardly any vital keratinocytes, while the young fibroblasts continued to support regeneration of a still perfectly organized epidermis.

first: Melanie

last: Boerries

first: Petra

last: Boukamp

first: Sabrina

last: Bauer

first: Hans-Jürgen

last: Stark


title: RNA transcriptome sequencing of  cutaneous squamous cell carcinoma cell line HSC-1 treated with siNC or siLINP1 oligonucleotides

city: Guangzhou

first: Xiaoting

last: Liang

state: Guangdong

address: School of Public Health, 1023 Shatai South Road, Southern Medical University, Baiyun District, Guangzhou city, Guangdong Province

department: school of public health

institute: southern medical university

summary: To figure out the role of long non-coding RNA LINP1 in cSCC and the underlying mechanism, RNA transcriptome sequencing was performed to globally characterize LINP1-regulated transcriptome changes. LINP1 knockdown by RNA interference in HSC-1 cells. HSC-1 cells treated with siNC served as control.

overall_design: Cutaneous squamous cell carcinoma cell line HSC-1 treated with siNC or siLINP1

first: Xingyuan

last: Liu

first: Jieyu

first: Chunting

first: Liang

last: Zhou


title: Establishing the enhancers/super-enhancers landscape and associated alterations leading to bladder cancer

city: Illkirch

first: Tao

last: YE

address: 1 rue Laurent Fries

institute: IGBMC (CNRS/INSERM/UDS)

summary: Provide a first characterization of the chromatin landscapes of bladder cancers. Using ChIPseq (H3K27ac, H3K27me3, H3K9me3)  in tumors characterized at the genetic, DNA methylation and transcriptomic levels, we will identify active regulatory regions. We will in particular define the super-enhancers active in the different molecular subtypes recently described.

overall_design: H3K27ac, H3K27me3, and H3K9me3  in tumors

first: Helene

last: Neyret-Kahn

first: Jacqueline

last: Fontugne

last: Ye

first: Isabelle

last: Bernard-Pierrot

first: Irwin

last: Davidson

first: François

last: Radvanyi


title: Isoginkgetin induces autophagic cell death in hepatocellular carcinoma [RNA-Seq]

first: Jie

last: Yao

summary:
Purpose: Our previous studies have identified Isoginkgetin as an inducer of autophagic cell death in hepatocellular carcinoma. We set out to analyze how isoginkgetin regulates gene expression in HepG2 cells.
Methods: RNA-seq was performed with two repetitions in HepG2 followed by treatment with DMSO and 20 μM Isoginkgetin for 24 h.
Conclusions: Isoginkgetin treatment reduces the expression of glucose transporters in HepG2 cells.

overall_design: RNA-seq was performed with two repetitions in HepG2 cells followed by treatment with 20 μM Isoginkgetin for 24 h. The gene expression profile was studied by RNA sequencing.

first: Chenyan

last: Shi

first: Xiaobin

last: Zeng


title: A549 NRF NT, mock and knockout RNAseq

city: Kuopio

first: Anna-Liisa

last: Levonen

state: Savonia region

address: Neulaniementie 2

department: A.I. Virtanen Institute

country: Finland

institute: University of Eastern Finland

summary: The NRF2 pathway is frequently activated in various cancer types, yet a comprehensive analysis of its effects across different malignancies is currently lacking. We developed a robust NRF2 activity metric and utilized it to conduct a pan-cancer wide analysis of oncogenic NRF2 signaling. We identified a distinct immunoevasive phenotype where high NRF2 activity is associated with low interferon-gamma (IFNγ), HLA-I expression and T-cell infiltration spanning non-small cell lung cancer (NSCLC) and squamous malignancies of head and neck area, cervix and esophagus. In squamous cell cancers, NRF2 overactive tumors comprise a molecular phenotype with SOX2/TP63 amplification, TP53 mutation and CDKN2A loss. These immune-cold NRF2 hyperactive diseases are associated with upregulation of immunomodulatory NAMPT, WNT5A, SPP1, SLC7A11 and SLC2A1 that represent candidate NRF2 target genes, suggesting direct modulation of the tumor immune milieu. Based on single-cell mRNA data, coupled with a priori information on intercellular ligand-receptor interactions, cancer cells of this subtype exhibit decreased expression of IFNγ responsive ligands, and increased expression of immunosuppressive ligands NAMPT, SPP1 and WNT5A that mediate signaling in intercellular crosstalk. As we observed differential cytokine mRNA expression with IFNγ treatment in NSCLC adenocarcinoma subtype, we explored the cytokine secretome in vitro. We found that secreted neutrophil chemoattractants interleukin-8 (CXCL8) and ENA-78 (CXCL5) are elevated in NRF2 overactive cells, suggesting contribution of immunosuppressive neutrophils in NRF2 driven immune escape. Importantly, as overactive NRF2 is associated with immune-cold characteristics, our results highlight the utility of NRF2 pathway activation as a putative biomarker for stratifying immune-checkpoint blockade responders and non-responders across NSCLC and squamous cancers.

overall_design: RNAseq for A549 parental (NT), mock and NRF2 knockout by CRISPR/Cas9.

first: Jouni

last: Härkönen


title: Isoginkgetin induces autophagic cell death in hepatocellular carcinoma [ChIP-Seq]

summary:
Purpose: Our previous studies have identified isoginkgetin as an inducer of autophagic cell death in hepatocellular carcinoma. We set out to analyze how isoginkgetin regulates the genome-wide enhancer activity in HepG2 cells.
Methods: ChIP-seq for H3K27ac was performed in HepG2 followed by treatment with 20 μM isoginkgetin for 24 h.
Conclusions: Isoginkgetin treatment reduces the expression of glucose transporters and inhibts SLC2A1 enhancer activity in HepG2 cells.

overall_design: ChIP-seq was performed with two repetitions in HepG2 cells followed by treatment with20 μM Isoginkgetin for 24 h.  The genome-wide enhancer activity was studied by H3K27ac ChIP sequencing.


title: RNA Sequencing  Analysis of H1299 cells with Hyperoxia Treatment and Control Cells

city: shanghai

first: Xiucheng

address: zhengmin road 557

institute: Shanghai pulmonary hospital

summary: Purpose: To study the effect of hyperoxia on lung cancer cells, H1299 cells were cultured in 60% O2 for 12 h and 24 h, and RNA-seq was performed.

overall_design: Total RNAs from the H1299 cells treated with hyperoxia treatment (24 h) and control cells were isolated and quantified. The high-throughput RNA sequencing analysis was performed by Shanghai Aksomics Biotech Company Ltd. (Shanghai, China). Briefly, The ribosomal RNA (rRNA) was removed from the total RNA using the NEBNext® rRNA Depletion Kit (New England Biolabs, Inc., Ipswich, MA, USA) following the manufacturer's instructions. RNA libraries were constructed by using NEBNext® Ultra™ II Directional RNA Library Prep Kit (New England Biolabs, Inc., Massachusetts, USA) according to the manufacturer’s instructions. Then, HTSeq software (v0.9.1) was used to obtain the transcript level (lncRNA) raw count as the expression profiling, and edgeR (v3.16.5) was used to perform normalization, and differentially expressed mRNAs were identified by p-value and fold change.

first: Hao

last: Qin


title: Isoginkgetin induces autophagic cell death in hepatocellular carcinoma


title: Nuclear receptor subfamily 4A signaling as a key disease pathway of CD1c+ dendritic cell dysregulation in systemic sclerosis [ChIP-seq]

city: Utrecht

first: Aridaman

last: Pandit

address: Heidelberglaan 100

institute: University Medical Center Utrecht

summary: Objectives: To identify key pathways, transcriptional regulators and epigenetic mechanisms underlying conventional dendritic cell (cDC) alteration in Systemic Sclerosis (SSc).  Methods: Transcriptomic profiling was performed on CD1c+ cDCs isolated from peripheral blood samples obtained from 12 healthy donors and 48 SSc patients with all major disease subtypes. Differential expression analysis comparing the different SSc subtypes and healthy donors was performed to uncover genes dysregulated in SSc. To identify biologically relevant pathways, a gene co-expression network was built using the Weighted Gene Correlation Network Analysis. We validated the role of key transcriptional regulators using ChIP-sequencing and in vitro functional assays.  Results: We identified 17 modules of co-expressed genes in cDCs that correlated with SSc subtypes and key clinical traits. A module of immune regulatory genes was markedly down regulated in patients with the diffuse SSc subtype suffering from severe fibrosis. Gene regulatory network analysis performed on the immune regulatory module predicted NR4A (nuclear receptor 4A) subfamily (NR4A1, NR4A2, NR4A3) genes as the master transcriptional mediators of inflammation. Indeed, ChIP-sequencing analysis of cDCs supported that these NR4A members target numerous differentially expressed genes in SSc cDCs. Inclusion of NR4A receptor agonists in culture-based experiments provided functional proof that dysregulation of NR4As affects cytokine production by cDCs and modulates T-cells activation.   Conclusions: NR4A1, NR4A2 and NR4A3 are important regulators of immunosuppressive and fibrosis-associated pathways in SSc cDCs. Thus, the NR4A family represent novel potential targets to restore cDC homeostasis in SSc.

overall_design: ChIP-sequencing for the transcription factors NR4A1, NR4A2 and NRA3 was performed on stimulated and unstimulated CD1c+ dendritic cells obtained from healthy donors.  For every condition we obtained three biological replicates, for which material from three to four healthy human donors was pooled to obtain enough chromatin for ChIP-seq.

first: Nila

last: Servaas


title: WT1+ parietal epithelial progenitor cells are essential for renal proximal tubule repair and regeneration

first: Liting

last: Chen

address: 1838 North Guangzhou Blvd.

department: Division of Nephrology

institute: Nanfang Hospital, Southern Medical University

summary:
Purpose: We have found that WT1+ parietal epithelial progenitor cells contribute to  renal proximal tubule repair and regeneration by cell lineage tracing and  direct differentiation analysis, but the transcription profile of these WT1+ PECs is largely unkown. Here, we aimed to unveil the transcriptional features of WT1+ PECs through single-cell RNA sequencing (scRNA-seq).
Methods: Single cell suspension was prepared from kidney cortex of WT1CreERT2; Rosa26-tdTfl/+ mice that underwent sham or ischemic reperfusion injury (IRI) 24h .TdT+ cells were enriched by fluorescence activated cell sorter (FACS) and further analyzed with BD Rhapsody platform.
Results: After quality control and cell filtering, 26,759 cells were informative (Dataset S1) and divided into 10 clusters using Harmony algorithm to reduce batch effects. GO analysis and QuSAGE heatmap suggested that WT1+ PECs might promote kidney regeneration after AKI through TGF-β and Notch signaling pathway. Marker gene expression analysis showed that WT1+ PECs shared the characteristics of STCs. Pseudotemporal analysis indicated that that WT1+ PECs developed to PTECs through STCs intermediate stage.
Conclusions: scRNA-seq indicated that the rare, quiescent PECs supplied PTECs through STCs intermediate stage after severe ischemic injury, and this process most likely was regulated through TGF-β and Notch signaling pathway.

overall_design: Single cell mRNA sequence of  kidneys from sham or IRI 24h WT1CreERT2; Rosa26-tdTfl/+ mice and focus on the gene expression profile of WT1+ PECs.

first: Xizhen

last: Hong

last: Nie

first: Fujian

last: Zhang


title: Nuclear receptor subfamily 4A signaling as a key disease pathway of CD1c+ dendritic cell dysregulation in systemic sclerosis [RNA-seq]

overall_design: Transcriptomic profiling was performed for a cohort of SSc patients and healthy controls. Total RNA from 12 heathy controls and 48 SSc patients were subjected to RNA-seq analysis.


title: Nuclear receptor subfamily 4A signaling as a key disease pathway of CD1c+ dendritic cell dysregulation in systemic sclerosis


title: High-throughput RNA sequencing reveals major alterations of inflammatory molecules involved in pathogenesis of peri- lesional psoriasis after NBUVB treatment

city: Bangkok

first: Pinyadapat

last: Vacharanukrauh

address: Sutthisan vinitchai

country: Thailand

institute: CICM Thammasat university,

summary: We report the high-throughput profiling of tissue biopsy in peri- lesion from psoriasis skin before the start of NB-UVB therapy and after treatment.RNA sequencing (RNA-Seq) was conducted to assay the transcriptomes and identify differentially expressed transcripts enriched in major pathway analysis.

overall_design: This study aimed to understand the mechanisms of psoriasis through analyzing differentially expressed genes with RNA-Seq technique by using phototherapy. This research was conducted in patients with moderate to severe plaque-type psoriasis who received NB-UVB treatment.

first: Jitlada

last: Meephansan


title: GM-free immortalization and high yield production of cultured chicken [WGS]

city: Jerusalem

first: Avner

last: Ehrlich

address: Silberman 3-512, Edmond J. Safra Campus (Givat Ram)

department: Bioengineering

country: Israel

institute: The Hebrew University of Jerusalem

summary: Global demand for animal protein is expected to double by 2050 at a time when resource-intensive livestock production is reaching peak capacity. Cellular agriculture offers an opportunity to meet the increasing demand for animal products, but the technology is currently limited by the genetic stability of immortalized cells, low culture yields, and high production costs. Here we demonstrate the spontaneous immortalization and long-term genetic stability of fibroblasts derived from the indigenous Israeli Baladi and the commercial Broiler Ross chicken breeds. Cells were adapted for growth as single-cell suspensions in animal-component free culture medium reaching cell densities of over 100x10^6 cells/mL in ATF perfusion presenting a production yield of over 33% w/v. We show that soy phosphatidylcholine, a major component of lecithin, activates PPAR, driving adipogenesis in immortalized chicken fibroblasts. Harvesting cultured adipocytes and blending them with high moisture extruded soy protein formed cultured chicken strips in which mouth feel and texture were supported by a blend of animal and plant proteins while aroma and flavor were driven by cultured animal fat. Visual and sensory analysis graded the product 4.5 out of 5.0, with over 85% percent of the study group said they are extremely likely to replace their food choice with this cultured meat product. The ability to create immortalized lines without genetic modification and the high yield process for cultured meat production presents an important steppingstone in the market realization of cultured meat.

overall_design: Whole Genome Sequencing (WGS) of 5 Immortalized chicken fibroblasts from 2 different breeds (Broiler Ross 308; Israeli Baladi)

first: Yaakov

last: Nahmias

first: Boaz

last: Gildor

first: Eli

last: Reuveni

first: Merav

last: Cohen

first: Laura

last: Pasitka


title: High-Throughput RNA Sequencing Reveals the Effect of NB- UVB Phototherapy on Major Inflammatory Molecules of Lesional Psoriasis

summary: We report the high-throughput profiling of tissue biopsy from psoriasis skin before the start of NB-UVB therapy and after the last treatment session.RNA sequencing (RNA-Seq) was conducted to assay the transcriptomes and identify differentially expressed transcripts enriched in major pathway analysis. Our results support that clinically effective NB-UVB therapy is based on suppression of a broad range of inflammatory signaling pathways, gene expression of inflammatory cytokines, and increased the expression of anti-inflammatory signaling pathways in psoriatic skin.


title: The change of rhizobium gene expression of symbiosome in medicago mutant debino1 comparing wild type

status: Public on Mar 21 2023

city: changsha

first: FENG

last: Gao

state: hunan

address: no

department: College of Biology

institute: Hunan university

summary: To investigate the function NCR343 in the regulation of the survival of terminal differentiation of bacteroids, we established the rbizobium gene expression level of symbiosome in wild type and debino1 mutant medicago

overall_design: comparing rhizubium gene expression level between symbiosome in wild type and debino1 mutant medicago

first: Fengzhan

first: Huairong

last: Pan


title: Human alveolar hydrogels promote morphological and transcriptional differentiation in iPSC-derived alveolar type 2 epithelial cells

city: Burlington

first: Korin

last: Eckstrom

state: VT

address: 89 Beaumont Ave

institute: University of Vermont

summary: To investigate the role of alveolar extracellular matrix (aECM) hydrogels on iPSC-derived alveolar type 2 epithelial cell (iAT2) morphological and transcriptional differentiation

overall_design: We analyzed RNA collected from iAT2s grown in two different densities of aECM hydrogels (8mg/mL and 30mg/mL) compared to Matrigel at Day 4 and Day 8

first: Evan

last: Hoffman

first: Juan

last: Uriarte

first: Franziska

last: Uhl

first: Alicia

last: Tanneberger

first: Chloe

last: Becker

last: Moulin

first: Loredana

last: Asarian

first: Laertis

last: Ikonomou

first: Darrell

last: Kotton

first: Daniel

last: Weiss


title: Detection of Active Transposable Elements using Mobilome-seq on Poplar WT and ddm1 meristems in water stress conditions

city: PARIS

first: Anne-laure

last: Le gac

address: 26 rue d'ulm

institute: Institut Curie

summary: Long time considered as « junk DNA », the evolutive force of transposable elements (TEs) is now well established and TEs contribute strongly to eukaryote genome plasticity. However, it is difficult to fully characterize the mobile part of a genome, or active mobilome, and tracking TE activity remains challenging. He we have applied the detection of extrachromosomal circular DNA (mobilome-seq) as a diagnostic for plant TE activity on Poplar mersitems from WT and ddm1 RNAi plants grown in normal or hydric stress conditions.

overall_design: Mobilome-seq using Illumina Miseq  (2x250bp)

first: Marie

last: Mirouze

first: Sophie

last: Lanciano

first: Anne-Laure

last: LeGac

first: Stephane

last: Maury


title: Basic characteristics of transcription and expression of mRNA transcriptome (mRNAome) and lncRNA transcriptome (lncRNAome) in rat cortical tissue of MCAO 2 h / R 24 h model

city: Shihezi City

first: Shan

last: Yuan

state: Xinjiang Uygur Autonomous Region

address: North Second Road, Hongshan Street

institute: Shihezi University

summary:
We used deep sequencing technology to find out the basic characteristics of the transcription and expression of the mRNA transcriptome (mRNAome) and lncRNA transcriptome (lncRNAome) in the rat cortical tissue of MCAO 2 h / R 24 h model.
Then, we used it to obtain the basic data of mRNAome and lncRNAome structural variation and gene expression in response to cerebral hypoxic-ischemic stress.

overall_design: Structural variation and gene expression profile of mRNAome and lncRNAome from RNA-seq data of rat cerebral cortex in Sham group and MCAO 2 h / R 24 h group.

first: Sham

first: Yuying

last: Yang

first: Meimei

last: Xv

first: Guangze

last: Hu

first: Rui

last: Gao


title: Tumor microenvironment remodeling after neoadjuvant immunotherapy in non-small cell lung cancer revealed by single-cell RNA sequencing

city: Shanghai

first: Peng

last: Zhang

address: No. 507 Zhengmin Road

institute: Department of Thoracic Surgery, Shanghai Pulmonary Hospital

summary: To address the potential therapy-resistant mechanisms and underly the changes of tumor microenvironment (TME) after immunotherapy, we performed scRNA-seq  and bulk RNA-seq from the patients with resectable non-small cell lung cancer (NSCLC) before and after PD-1 blockade combined with chemotherapy. We found that the combined therapy significantly remodeled the immune cell compartments in the TME. Patients with different pathologic responses had distinct characteristics of malignant cells and immune cell compositions. Our study provided several potential biomarkers for future immunotherapy and novel strategies to improve response.

overall_design:
Transcriptomic dynamics of NSCLC during anti-PD-1 + chemotherapy
Submitter statement concerning raw data: The raw data files have been deposited to Genome Sequence Archive of the BIG Data Center at the Beijing Institute of Genomics, Chinese Academy of Science, under accession number HRA001033.


title: Single cell and spatial transcriptomic profile of whole CLAD and donor control lung tissue

city: Durham

first: Scott

last: Palmer

state: NC

address: 2100 Erwin Road

institute: Duke University

summary: Chronic lung allograft dysfunction (CLAD) is the leading cause of death in lung transplant recipients. CLAD is characterized clinically by a persistent decline in pulmonary function and histologically by the development of airway centered fibrosis known as bronchiolitis obliterans. We performed single-cell sequencing and spatial transcriptomic analysis of explanted tissues from human lung recipients with CLAD and donor control lungs.

overall_design: For the single cell dataset, whole lung tissue segments from four CLAD samples and three donor control samples were used. For the spatial transcriptomic dataset, tissue blocks from three CLAD samples and one donor control sample were used. Donor control tissue was obtained from donor lungs used for transplant that were harvested, perserved, implanted, and then trimmed to fit the recipient chest cavity with excess donor trimming preserved for research. Donor control lung tissue underwent formal pahtology evaluation that confirmed the absence of any significant lung disease.

first: Palmer

last: Scott

first: Khatri

last: Aaditya

first: Jain

last: Vaibhav

first: Todd

last: Jamie