title: Subcellular location defines GPCR signal transduction

city: Geneva

first: Miriam

last: Stoeber

state: GE

address: Rue Michel Servet 1

department: PHYM

institute: University of Geneva

summary: G protein-coupled receptors in intracellular organelles can be activated in response to membrane permeant ligands, which contributes to the diversity and specificity of agonist action. The opioid receptors (ORs) provide a striking example, where small molecule opioid drugs activate ORs in the Golgi apparatus within seconds of drug addition. To date, our knowledge on the signaling of intracellular GPCRs remains incomplete and it is unknown if the downstream events triggered by ORs in plasma membrane and Golgi apparatus differ. To address this gap, we analyzed OR-mediated gene expression changes upon treatment with impermeant peptide ligand DPDPE, permeant ligand SNC80 or ICI-SNC80 (Golgi-restricted signaling). We show that DOR activation in the Golgi does not trigger any gene transcription at these two time points as compare to plasma membrane receptors. The study delineates OR signal transduction with unprecedented resolution and reveals that the subcellular location defines the signaling effect promoted by opioid drugs.

overall_design: Comparative analysis of HEK293 gene expression profiles upon activation of OR at plasma membrane or in the Golgi using different ligands combinations. All treatments performed in triplicates.

first: Lucie

last: Oberhauser


title: DNA Methylome and 3D Chromatin Landscape of Cell Types Across the Mouse Brain [BICCN-11D_191031]

status: Public on Apr 24 2023

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

country: USA

institute: HHMI-Salk-Institute

type: Methylation profiling by high throughput sequencing

summary: Illustrating the cellular architecture of the mammalian brain is critical to understanding its diverse functions and complex animal behaviors. With support from NIMH and NINDS as part of the BRAIN Initiative Cell Census Network (BICCN), the Center for Epigenomics of the Mouse Brain Atlas (CEMBA) applied single nucleus methylation sequencing in 117 brain funtional regions across the whole adult male P56 C57BL/6J mouse brain. In each major brain regions, we identified distinct cell clusters and formed them in a hierarchical taxonomy. These clusters include known primary brain cell types and possible sub-types. We use these data to identify the epigenomic characteristics and to define specific regulatory elements for each cell cluster. We integrate the single cell methylome with single cell gene expression and chromatin accessibility profiles from the same brain region to further identify potential enhancers and their corresponding genes for several neuronal cell types. By brain region spacial comparisons, we found spatial specificity among excitatory neuronal clusters within the same cortical layer. We identify brain-region-specific transcription factors that may regulate cortical region development of excitatory neurons. These data define the landscape of cell type and spatial heterogeneity in the mouse brain and the underlining regulatory epigenomic basis.

overall_design: Apply snmC-seq2 to 117 brain functional regions to identify epigenomic landcape of the adult mouse brain, this subseries consists of one single nucleus methylation sequencing experiment of brain region (11D).

first: Hanqing

last: Liu

first: Anna

last: Bartlett

first: Jacinta

last: Lucero

first: Julia

middle: K

last: Osteen

first: Jordan

last: Altshul

first: Mia

last: Kenworthy

first: Rosa

middle: G

last: Castanon

last: Nery

first: Peter

last: Berube

first: Huaming

last: Chen

first: Michael

last: Nunn

first: Jesse

last: Dixon

first: M

middle: M

last: Behrens


title: Generation of ventralized thalamic organoids with inhibitory thalamic reticular nucleus

city: NEW HAVEN

first: Bilal

last: Cakir

state: Connecticut

address: 10 Amistad Street, Ste 214J

institute: Yale University

type: Expression profiling by high throughput sequencing

summary: Single-cell RNA-seq was performed in SHH-treated thalamic organoids

overall_design: Human thalamic organoids (ThOs) resembling the dorsal thalamus by dual SMAD inhibition and insulin-driven caudalization coupled with thalamic patterning (MEK-ERK inhibition and BMP7 activation) from hESCs. The organoids were further guided into ventral identity with SHH treatment.

first: Yoshiaki

last: Tanaka

first: Yangfei

last: Xiang

first: In-Hyun

last: Park


title: DNA Methylome and 3D Chromatin Landscape of Cell Types Across the Mouse Brain [BICCN-11G_210204]

first: Joseph

last: Ecker

overall_design: Apply snmC-seq3 to 117 brain functional regions to identify epigenomic landcape of the adult mouse brain, this subseries consists of one single nucleus methylation sequencing experiment of brain region (11G).

last: Liu


title: DNA Methylome and 3D Chromatin Landscape of Cell Types Across the Mouse Brain [BICCN-11D_191024]

first: Hanqing

last: Bartlett

last: Lucero


title: Next Generation Sequencing Facilitates Quantitative Analysis of  in 14-day-old wt, syd-5 and swi3d-1  seedlings [RNA-seq]

city: Guangzhou

first: yaoguang

last: yu

address: No. 135, Xingang Xi Road

country: China

institute: SUN YAT-SEN UNIVERSITY

summary:
To investigate the cooperative function swi3d-1 and syd-5 in regulating plant development.
We then performed gene expression profiling analysis using data obtained from RNA-seq of 14-day-old wt, syd-5 and swi3d-1  seedlings under long day condition.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for WT and mutants.

first: Wei

last: Fu

first: Yaogaung

last: Yu

first: Chenlong

last: Li


title: DNA Methylome and 3D Chromatin Landscape of Cell Types Across the Mouse Brain [BICCN-11G_210128]

status: Public on Apr 25 2023

first: Anna

first: Jacinta

first: Julia

last: Osteen

first: Jordan

last: Altshul

first: Mia

last: Kenworthy

last: Castanon

last: Nery

last: Berube


title: Integrated Transcriptome and Metabolome Identified Novel Candidate Genes Regulating Anthocyanin Biosynthesis in Colored-Grain Wheat (Triticum aestivum L.)

city: Zhengzhou

first: Liu

last: Xiaoting

address: 100 Science Avenue

institute: Zhengzhou University

summary: Purpose: The present study aimed to investigate the anthocyanin components and identify relevant regulatory genes in  purple wheat grain by carrying out transcriptome analyses.                                                                                Methods: The seeds of purple grain wheat and white grain wheat were collected 30 days after flowering, and three biological replicates were set. Total RNA was isolated and purified using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer's procedure. The RNA amount and purity of each sample was quantified using NanoDrop ND-1000. Then synthesizing the fragmented RNA into cDNA through the action of reverse transcriptase, and finally obtaining acDNA library. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina Novaseq™ 6000 following the vendor's recommended protocol.                                                                              Results: A total of 10440 diferentially expressed genes were signifcantly enriched by RNA sequencing. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses revealed signifcantly enriched flavonoid biosynthesis and anthocyanin biosynthesis in CW_S versus W_S. And the ANS and UFGT genes were predicted as core genes in anthocyanin biosynthesis.                   Conclusions: Our study represents the detailed analysis of wheat grain transcriptomes, with biologic replicates, generated by RNA-seq technology. Through this study, we speculated that ANS and UFGT genes are the core genes of anthocyanin biosynthesis.The significant differences of these genes affect the synthesis of anthocyanins in wheat grains, and thus affect the grain color of wheat.

overall_design: The mRNA profiles of white grain wheat (W_S) and purple grain wheat (CW_S) grains 30 days after flowering.

first: Xiaoting

last: Fang


title: Mesenchymal-epithelial transition in lymph node metastases of oral squamous cell carcinoma is accompanied by ZEB1 expression

city: Essen

first: Jürgen

middle: C

last: Becker

state: NRW

address: Universitätsstraße 1

department: Translational Skin Cancer Research

country: Germany

institute: Deutsches Krebsforschungszentrum

summary:
Background
Oral squamous cell carcinoma (OSCC), an HPV-negative head and neck cancer, frequently metastasizes to the regional lymph nodes but only occasionally beyond. Initial phases of metastasis are associated with an epithelial–mesenchymal transition (EMT), while the consolidation phase is associated with mesenchymal–epithelial transition (MET). This dynamic is referred to as epithelial–mesenchymal plasticity (EMP). While it is known that EMP is essential for cancer cell invasion and metastatic spread, less is known about the heterogeneity of EMP states and even less about the heterogeneity between primary and metastatic lesions.

Methods
To assess both the heterogeneity of EMP states in OSCC cells and their effects on stromal cells, we performed single-cell RNA sequencing (scRNAseq) of 5 primary tumors, 9 matching metastatic and 5 tumor-free lymph nodes and re-analyzed publicly available scRNAseq data of 9 additional primary tumors. For examining the cell type composition, we performed bulk transcriptome sequencing. Protein expression of selected genes were confirmed by immunohistochemistry.

Results
From the 23 OSCC lesions, the single cell transcriptomes of a total of 7263 carcinoma cells were available for in-depth analyses. We initially focused on one lesion to avoid confounding inter-patient heterogeneity and identified OSCC cells expressing genes characteristic of different epithelial and partial EMT stages. RNA velocity and the increase in inferred copy number variations indicated a progressive trajectory towards epithelial differentiation in this metastatic lesion, i.e., cells likely underwent MET. Extension to all samples revealed a less stringent but essentially similar pattern. Interestingly, MET cells show increased activity of the EMT-activator ZEB1. Immunohistochemistry confirmed that ZEB1 was co-expressed with the epithelial marker cornifin B in individual tumor cells. The lack of E-cadherin mRNA expression suggests this is a partial MET. Within the tumor microenvironment we found immunomodulating fibroblasts that were maintained in primary and metastatic OSCC.

Conclusions
This study reveals that EMP enables different partial EMT and epithelial phenotypes of OSCC cells, which are endowed with capabilities essential for the different stages of the metastatic process, including maintenance of cellular integrity. During MET, ZEB1 appears to be functionally active, indicating a more complex role of ZEB1 than mere induction of EMT.

overall_design:
We provide the gene and hashtag oligo expression count matrices for oral squamous cell carcinoma samples from primary tumor, lymph node metastases and unaffected lymph nodes processed using single cell RNA sequencing with 10x Genomics technology. Further we performed whole-transcriptome sequencing on FFPE samples using a quantitative nuclei protection assay with the HTG whole-transcriptome panel.
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Authors state the following:
The raw FASTQ files cannot be uploaded due to privacy concerns. The files contain sequencing data from human patients and can be received upon request from the submitters.

first: Kai

last: Horny

first: Christoph

last: Sproll

first: Lukas

last: Peiffer

first: Frauke

last: Furtmann

first: Patricia

last: Gerhardt

first: Jan

last: Gravemeyer

first: Nikolas

last: Stoecklein

first: Ivelina

last: Spassova


title: Transcriptome analysis of alternative splicing under ABA exposure in osfkbp20-1b mutant compared to wild-type (ZH11) of rice

city: Daejeon

first: Haemyeong

last: Jung

address: 125 Gwahak-ro, Yuseong-gu

department: Plant Systems Engineering Research Center

country: South Korea

institute: KRIBB

summary: To investigate whether observed changes in pre-mRNA splicing led to OsFKBP20-1b depletion, we analyzed RNA-seq to identify the quantitative profiling and alternative splicing

overall_design: RNA was extracted from osfkbp20-1b and WT of 1 week rices and treated with mock or 100 μM ABA for 6 hr

first: Hye Sun

last: Cho

first: Hyun Ji

last: Park


title: Methylation data of serially sorted primary AML patient blasts prior and after treatment with the DNMT inhibitor decitabine (DAC)

city: Freiburg

first: Geoffroy

last: Andrieux

address: Breisacherstr 153

institute: University clinics Freiburg

type: Methylation profiling by genome tiling array

summary: The therapeutic effect of DNA-hypomethylating agents (HMAs) in   AML/MDS is discussed to be via its effects on aberrant gene silencing   by reactivation (e.g. through promoter demethylation). While this has   been broadly studied in cell line models, only very few studies have   addressed the global effects of HMAs in primary blasts serially isolated   from AML patients (pts) undergoing HMA treatment (Claus et al., Leuk.   Res. 2013, Klco et al., Blood 2013, Welch et al., N. Engl. J. Med. 2016).   We therefore conducted prospective serial methylome and   transcriptome analyses on AML blasts from pts of the DECIDER trial   (NCT00867672), hypothesizing that both random and non-random   effects of the HMA may be observed in vivo.

overall_design: Genomic DNA was isolated with the DNeasy Blood & Tissue Kit (Qiagen, Hilden, Germany), bisulfite converted and hybridized to HumanMethylation450 BeadChip arrays (450K arrays; Illumina) according to the manufacturer’s instructions at the DKFZ Genomics and Proteomics Core Facilities (Heidelberg, Germany). To avoid a possible batch effect, samples were randomized across and within plates.

first: Gabriele

last: Greve

first: Nadja

last: Blagitko-Dorfs

first: Melanie

last: Boerries

first: Michael

last: Lübbert


title: MYC induces immunotherapy and interferon-γ resistance through downregulation of JAK2

city: Ramat Gan

first: Ettai

last: Markovits

address: 2 Derech sheba st.

country: Israel

institute: Shaba Medical Center

summary: Immunotherapy revolutionized the treatment of advanced melanoma. As the pathways mediating resistance to immunotherapy are largely unknown, we conducted transcriptome profiling of pre-immunotherapy tumor biopsies from melanoma patients that received PD-1 blockade (n=36) or adoptive cell therapy with tumor infiltrating lymphocytes (n=37). We identified two melanoma-intrinsic mutually exclusive gene programs, which are controlled by interferon-γ and MYC, and determine immunotherapy outcome. MYC-overexpressing melanoma cells exhibited lower interferon-γ responsiveness, which was linked with JAK2 downregulation. Luciferase activity assays under the control of JAK2 promoter demonstrated reduced activity in MYC-overexpressing cells, which was reversible upon mutagenesis of MYC E-box binding sites in the JAK2 promoter. Moreover, silencing of MYC or its co-factor MAX with siRNA increased JAK2 expression and interferon-γ responsiveness of melanomas, while concomitantly enhancing the effector functions of T-cells co-incubated with MYC-overexpressing cells. Thus, we propose that MYC plays a pivotal role in immunotherapy resistance through downregulation of JAK2.

overall_design: RNA-seq from pre-treatment tumor biopsies of advanced melanoma patients treated with PD-1 blockade (n=36) or TIL ACT (n=37)

first: Ran

last: Elkon

first: Michal

middle: J

last: Besser

first: Gal

last: Markel


title: Transcriptome analyses revealed differentially expressed genes in DAF-16 WT and KR mutants.

city: Taipei

first: Ao-Lin

last: Hsu

address: No.155, Sec.2, Linong Street

department: Institute of Biochemistry and Molecular Biology

country: Taiwan

institute: National Yang-Ming University

summary: By using RNA-seq, we have dicovered hypoacetylated DAF-16 (KR) controlled additional subsets of longevity-related genes.

overall_design: Total RNA from Day 1 N2 and daf-16(mu86) worms expressing wild-type and hypoacetylated DAF-16 were subject to Illuina RNA-seq in triplicate.

first: Chung-Yi

last: Liang


title: African swine fever virus tropism for different organ tissues and host transcriptomic responses in experimentally infected pigs

status: Public on Apr 23 2023

city: Wanju-Gun

first: woncheoul

last: park

state: Iseo-Myeon

address: 1500 kongjwipatjwi-Ro

department: Animal genomics and Bioinformatics

institute: National Institute of Animal Science

summary:
Purpose: This goal of this study was to explore the host transcriptomic responses in African swine fever virus  experimentally infected pigs using RNA-Sequencing.
Methods: RNAs acquired from ten different organ tissue samples were sequenced. Sequencing reads were preprocessed, aligned with the reference genome, assembled and expressions were estimated through bioinformatics approaches.
Result: Several uprugulated DEGs were  identified.
Conclusion: We found important candidate genes and pathways for further testing in African swine fever virus infection in pig.

overall_design: Different organ tissues time Series transcriptome profiles of African swine fever virus infection in pig.


title: DNA Methylome and 3D Chromatin Landscape of Cell Types Across the Mouse Brain [12B_190314]

first: Joseph

last: Ecker

overall_design: Apply snmC-seq2 to 117 brain functional regions to identify epigenomic landcape of the adult mouse brain, this subseries consists of one single nucleus methylation sequencing experiment of brain region (12B).

first: Hanqing

last: Liu

first: Anna

last: Bartlett

first: Jacinta

last: Lucero

first: Julia

last: Osteen

first: Jordan

last: Altshul

first: Mia

last: Kenworthy

first: Rosa

last: Castanon

last: Nery

first: Peter

last: Berube

first: Huaming

last: Chen

last: Nunn

first: Jesse

last: Dixon

first: M

last: Behrens


title: Expression profile of microRNA in human serum

city: Guiyang

first: Gu

last: Yan

state: Guizhou

address: Huaxi

institute: Guizhou Medical University

type: Non-coding RNA profiling by high throughput sequencing

summary: Serum microRNA combinations may be a powerful classifier for detecting cancer patients

overall_design: A total of 9 serum microRNA expression profiles were included, including 2 CRC, 4 BRCA, and 3 non cancer controls

first: Xianpeng

last: Wei

first: Yan

last: Gu

first: Yang


title: WGBS of Arabidopsis thaliana COM-edm2 mutant

city: nanjing

first: la

middle: yu

last: mei

address: xuanwu

institute: njau

summary: Here we address that a mutation of EDM2 (Enhanced Downy Mildew 2), which is regarded as regulator of genome DNA methylation patterns, displays abnormal cotyledon number and shorted root length. Further, in early embryogenesis, edm2 shows embryonic developmental abnormalities, including the appearance of asymmetric embryos at the heart stage and unclear boundary between the spherical proembryo and suspensor cells. In addition, dysfunction of EDM2 alters the level of the auxin transporter PINs (PIN-FORMEDs), consistent with disordered distribution of auxin, which maybe the reason for developmental defect. Interestingly, analysis of high-throughput sequencing data show that the loss-of-function EDM2 exhibits the decreased expression of auxin polar transport-related gene PLT1 (PLETHORA 1), while methylation level and H3K9me2 enrichment in gene body are slightly higher than that in wide type. These results advance our understanding of EDM2 in establishment of auxin gradients through epigenetic modification and elucidate the roles of EDM2 in early embryogenesis.

overall_design: BS-seq of COM-edm2

first: Honggui

last: La

first: Qianqian

last: Wang

first: Yumei


title: Transcriptomic profiling of Prostate Cancer

city: Moscow

first: Anastasiya

last: Kobelyatskaya

address: Vavilov str, 32

country: Russia

institute: Engelhardt Institute of Molecular Biology, RAS

summary: This study included primary tumor sequencing data from 197 patients with prostate cancer. All of them did not receive neoadjuvant therapy. Patients belong to the Caucasoid population. For each specimen, extensive information is provided, namely, clinical and pathological criteria, as well as molecular subtype and biochemical relapse status.

overall_design: mRNA and miRNA profiles of primary tumors for patients with prostate cancer


title: Type 1 diabetes and diet-induced obesity predispose C57BL/6J mice to PM2.5-induced lung injury: a comparative study

first: Wen

address: No. 74, 2nd Zhongshan Road

department: Department of Toxicology

institute: School of Public Health, Sun Yat-sen University

summary: Background: Pre-existing metabolic diseases may predispose individuals to particulate matter (PM)-induced adverse health effects. However, the differences in susceptibility of various metabolic diseases to PM-induced lung injury and their underlying mechanisms have yet to be fully elucidated.   Results: Type 1 diabetes (T1D) or diet-induced obesity (DIO) murine models were generated by injection of streptozotocin or feeding a 45% high-fat diet for 10 weeks, respectively, and subjected to 4-week real-ambient PM exposure in Shijiazhuang, China (mean PM2.5 concentration 95.77 μg/m3). Pulmonary and systemic injury was assessed, and the underlying mechanisms were explored through transcriptomics analysis. Compared with normal diet (ND)-fed mice, T1D mice exhibited severe hyperglycemia with a blood glucose of 350 mg/dL, while DIO mice displayed moderate obesity and marked dyslipidemia with a slightly elevated blood glucose of 180 mg/dL. T1D and DIO mice were susceptible to PM-induced lung injury, manifested by inflammatory changes such as interstitial neutrophil infiltration and alveolar septal thickening. Notably, the acute lung injury scores were higher by 79.57% and 48.47%, respectively, than that of ND-fed mice. Lung transcriptome analysis revealed that increased susceptibility to PM exposure was associated with perturbations in multiple pathways including glucose and lipid metabolism, inflammatory responses, oxidative stress, cellular senescence, and tissue remodeling. Functional experiments confirmed that changes in biomarkers of macrophage (F4/80), lipid peroxidation (4-HNE), cellular senescence (SA-β-gal), and airway repair (CCSP) were most pronounced in the lungs of PM-exposed T1D mice. Furthermore, pathways associated with xenobiotic metabolism showed metabolic state- and tissue-specific perturbation patterns. Upon PM exposure, activation of nuclear receptor (NR) pathways and inhibition of the glutathione (GSH)-mediated detoxification pathway were evident in the lungs of T1D mice, and a significant upregulation of NR pathways was present in the livers of T1D mice.   Conclusions: These differences might contribute to differential susceptibility to PM exposure between T1D and DIO mice. These findings provide new insights into the health risk assessment of PM exposure in populations with metabolic diseases.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for PM-exposed lung and liver tissues of T1D, DIO, and ND-fed mice, compared to those of AF (filtred air)-exposed mice (n =3 per group).

first: Shen

first: Miao

last: Li

first: Rui

last: Zhang

first: Lizhu

last: Ye

first: Yue

last: Jiang

first: Xinhang

first: Hui

last: Peng

first: Ziwei

first: Zhanyu

last: Guo

first: Liping

first: Rong

first: Yujie

last: Niu

first: Michael

last: Aschner

first: Daochuan


title: Sex-lethal regulates back-splicing and generation of the sex-differentially expressed circular RNAs

city: Shanghai

first: Zhan

last: Ding

address: 300 Feng Lin Road

institute: CAS Center for Excellence in Molecular Plant Sciences

summary: Conversely to canonical splicing, back-splicing covalently ligates the upstream 3' splice site (SS) with downstream 5'SS and generates exonic circular RNAs (circRNAs) that are widely-identified in eukaryotes and have regulatory functions in gene expression. However, sex-specific back-splicing in Drosophila has not been investigated and its regulation remains unclear. Here, we performed multiple RNA-seq of various sex-specific Drosophila samples including head, body and gonads from both genders, and identified more than ten thousand of circular RNAs, in which hundreds are sex-differentially expressed and back-spliced. Intriguingly, we found that expression of SXL, an RNA-binding protein encoded by Sex-lethal (Sxl), the master Drosophila sex-determination gene which only functionally spliced in females, promotes back-splicing of many female-differentially expressed circRNAs in the male S2 cells, while expression of a SXL mutant did not. Using a monoclonal antibody, we further obtained the transcriptome-wide RNA-binding sites of SXL through a PAR-CLIP approach and revealed that SXL-binding on flanking exons and introns of pre-mRNAs facilitates back-splicing of those circRNAs, whereas SXL-binding on the circRNA exons inhibits the back-splicing. This study provides strong evidence that SXL has a regulatory role in back-splicing to generate sex-specifc circRNAs, as well as in the initiation of Drosophila sex-determination cascade through canoncial forward-splicing.

overall_design: RNA-seq

first: Yu-Jie

last: Fan

first: Yong-Zhen

last: Xu


title: Lamin B1 overexpression alters chromatin organization and gene expression (Cut&Run-seq)

first: Juliana

middle: S

last: Capitanio

state: California

address: 10010 N Torrey Pines Rd

department: molecular and call biology laboratory

institute: The Salk Institute for Biological Studies

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Overexpression of Lamin B1 leads to the redistribution of H3K9me3 heterochromatin away from the nuclear periphery and into heterochromatic DNA foci within the nucleoplasm. These changes in chromatin organization correlate with misregulated gene expression (mRNA-sequencing), but do not correlate with altered H3K9me3 deposition across the genome (Cut&Run).

overall_design: Cut&Run for H3K9me3 in hTERT RPE-1 stable cell lines overexpressing mCherry or mCherry-LmnB1. Samples include two clonal cell lines for each overexpression construct (mCherry_3, mCherry_4, LmnB1_6, LmnB1_16) and two biological replicates per cell line.

first: Jeanae

last: Kaneshiro

first: Martin

middle: W

last: Hetzer


title: Lamin B1 overexpression alters chromatin organization and gene expression (mRNA-seq)

overall_design: Gene expression analysis of mRNA-sequencing data in hTERT RPE-1 stable cell lines overexpressing mCherry or mCherry-LmnB1. Samples include two clonal cell lines for each overexpression construct (mCherry_3, mCherry_4, LmnB1_6, LmnB1_16) and three biological replicates per cell line.


title: Development of an osteosarcoma model with MYCN amplification and TP53 mutation in hiPS cell-derived neural crest cells

city: Kitaadachi-gun

first: Hisanori

last: Takenobu

state: Saitama

address: 818, Komuro, Ina-machi

department: Research Institute for Clinical Oncology

country: Japan

institute: Saitama Cancer Center

summary: Osteosarcoma, derived from mesenchymal stem cells or osteoblasts, is the most common malignant bone tumor and the highly metastatic malignant phenotypes often with poor prognosis are related to modulation of TP53- and cell cycle-related pathways. MYC, which regulates the transcription of cell-cycle modulating genes, e.g. CCNE1, is used as a representative prognostic marker. MYCN, a member of MYC oncoprotein family, is highly expressed in a subset of osteosarcoma, however, its roles in osteosarcoma have not been elucidated extensively. Here, we attempted to make an in vitro tumorigenesis model by using hiPSCs derived neural crest cells, which is a precursor cell of mesenchymal stem cells, by MYCN overexpression in the background of heterozygousTP53 hotspot mutation (c.733G>A; p.G245S). MYCN-expressing transformed clones with TP53 mutation were isolated by soft agar colony formation, and injected subcutaneously and into periadrenal adipose tissue of immune-deficient mice, resulted in development of chondroblastic osteosarcoma. MYCN suppression decreased proliferation in MYCN-induced osteosarcoma cells, suggesting that MYCN seems to be one of the targets of osteosarcoma treatment. Further, comprehensive analysis of gene expression and exome sequencing of the MYCN-induced transformed clones indicated molecular context of osteosarcoma-specific feature such as activation of TGF-β signaling and DNA copy number amplification of GLI1. The model of MYCN-expressing chondroblastic osteosarcoma was developed from hiPSC-based neural crest cells, allowing us to provide useful tool for development of new tumor models using hiPSC-derived progenitor cells with gene modification and in vitro transformation.

overall_design: Total RNA was extracted from LF cNCCs and tumors, and a microarray analysis was performed using the Agilent platform of 8x60 K design ID G4851B (Agilent Single Color. 39494, Agilent Technologies). Two hundred nanograms of total RNA was labeled with Cyanine3 using a Low Input Quick-Amp Labeling Kit (one color, Agilent Technologies) according to the manufacturer’s instructions. Purified labeled total RNA was hybridized to the expression microarray. Hybridization, the scanning of microarrays, and data extraction from scanned images were conducted according to Agilent protocol version 6.9.

first: Takehiko

last: Kamijo

first: Kyosuke

last: Mukae

first: Miki

last: Ohira


title: microRNA array analysis of HTR-8/Svneo cells with BHLHE40 knockdown or not.

city: Changsha

first: MI

middle: CHUN

last: MEI

state: HuNan

address: 138 Tongzipo Road, Yuelu District

department: Department of Obstetrics and Gynecology

institute: The Third Xiangya Hospital, Central South University

summary: Preeclampsia (PE), which results from abnormal placentation, acts as a primary cause of maternal and neonatal morbidity and mortality. However, the cause of abnormal development of placenta remain poorly understood. BHLHE40, a transcript factor, is up-regulated in PE placenta compared to normal placenta probably due to the stimulation by low oxygen, but the implication of BHLHE40 in PE pathogenesis is not elucidated. Therefore, we conducted transcriptional profiling of genes in HTR-8/Svneo cells with BHLHE40 knockdown or not.

overall_design:
RNA was extracted from HTR-8/Svneo cells with BHLHE40 knockdown or not. The miRNA expression profiles of these cells were detected by GeneChip miRNA 4.0 (Affymetrix, Santa Clara, CA).

**CEL files not provided**

first: Chunmei

last: Mi


title: Different expression profiles of mRNAs in preeclampsia and normal placenta (mRNA)

summary: Preeclampsia (PE), which results from abnormal placentation, acts as a primary cause of maternal and neonatal morbidity and mortality. However, the cause of abnormal development of placenta remain poorly understood.Recently, it has been proposed that the genes that are differnetially expressed between PE and normal placenta tissues are associated with PE pathogenesis. To further elucidate the pathogenesis, we conducted transcriptional profiling of mRNA  between PE and normal placenta tissues.

overall_design: Placental biopsies were obtained during Caesarean section from both normotensive patients (n=3) and from those with pre-eclampsia (n = 3) (early onset type; earlier than 31 weeks gestation)


title: DNA Methylome and 3D Chromatin Landscape of Cell Types Across the Mouse Brain [12A_191008]

first: Joseph

last: Ecker

address: 10010 North Torrey Pines Road

institute: HHMI-Salk-Institute

summary: Illustrating the cellular architecture of the mammalian brain is critical to understanding its diverse functions and complex animal behaviors. With support from NIMH and NINDS as part of the BRAIN Initiative Cell Census Network (BICCN), the Center for Epigenomics of the Mouse Brain Atlas (CEMBA) applied single nucleus methylation sequencing in 117 brain funtional regions across the whole adult male P56 C57BL/6J mouse brain. In each major brain regions, we identified distinct cell clusters and formed them in a hierarchical taxonomy. These clusters include known primary brain cell types and possible sub-types. We use these data to identify the epigenomic characteristics and to define specific regulatory elements for each cell cluster. We integrate the single cell methylome with single cell gene expression and chromatin accessibility profiles from the same brain region to further identify potential enhancers and their corresponding genes for several neuronal cell types. By brain region spacial comparisons, we found spatial specificity among excitatory neuronal clusters within the same cortical layer. We identify brain-region-specific transcription factors that may regulate cortical region development of excitatory neurons. These data define the landscape of cell type and spatial heterogeneity in the mouse brain and the underlining regulatory epigenomic basis.

overall_design: Apply snmC-seq2 to 117 brain functional regions to identify epigenomic landcape of the adult mouse brain, this subseries consists of one single nucleus methylation sequencing experiment of brain region (12A).

first: Hanqing

last: Liu

first: Anna

last: Bartlett

first: Jacinta

last: Lucero

first: Julia

last: Osteen

first: Jordan

last: Altshul

first: Mia

last: Kenworthy

first: Rosa

last: Castanon

last: Nery

first: Peter

last: Berube

first: Huaming

last: Chen

last: Nunn

first: Jesse

last: Dixon

first: M

last: Behrens


title: DNA Methylome and 3D Chromatin Landscape of Cell Types Across the Mouse Brain [12A_191017]

first: Michael


title: Lamin B1 overexpression alters chromatin organization and gene expression

first: Juliana

last: Capitanio

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

overall_design: Refer to individual Series


title: A ribosomal assembly stress response governed by the methionine cycle extends lifespan in C. elegans mutant with defective de novo proline biogenesis

city: Koln

first: Jorge

last: Boucas

address: Joseph-Stelzmann-Str. 9b

department: Bioinformatics

institute: Max Planck Institute for Biology of Ageing

summary: We compared the ratio of polysome-associated mRNAs (>3 ribosomes/mRNA) normalized to total mRNA levels between WT and pycr-1(wrm22) mutants. While mRNA translation as measured by polysome profiling was not affected in pycr-1 mutants, we detected significant changes in the translation of mRNAs involved in ribogenesis. Ribosomal stress can activate HSF-1 and indeed a transcriptome analysis of pycr-1 mutants revealed a significant change in HSF-1 target gene expression.

overall_design: Polysome and total RNA sequencing was performed to compare pycr-1(wrm22) to wildtype worms.

first: Felix

middle: A

last: Mayr

first: Maxime

last: Derisbourg

first: Gabriel

last: Guerrero

first: Martin

last: Denzel


title: Gene expression profile at single cell level of Lineage- Sca1+ c-Kit+ cells (LSKs)  from the bone marrow of normal  C57BL/6J mice with or without 5.0 Gy total body irradiation.

status: Public on Apr 22 2023

first: Qiancheng

last: Xiao

address: Building 25, No. 1188, LIANHANG Road, Pujiang Town, Minhang District, Shanghai

institute: Shanghai OE Biotech Co., Ltd

summary: Lineage- Sca1+ c-Kit+ cells (LSKs) are considered as a homogeneous population in the bone marrow. We used single cell RNA sequencing (scRNA-seq) to analyze the diversity of LSKs in the bone marrow.

overall_design: LSKs from the bone marrow of control (CTL) and irradiated (IR) mice (at day 15 after 5.0 Gy total body irradiation) were isolated by Fluorescence-activated cell sorting (FACS) according to three surface markers including Lineage, Sca1 and c-Kit and analyzed using scRNAseq.

first: Mengjia

last: Hu


title: Transcriptome analysis indicates the involvement of herbicide-responsive and plant–pathogen interaction pathways in the development of resistance to ACCase inhibitors in Apera spica-venti

city: Poznań

first: Aleksandra

last: Obrepalska-Steplowska

address: 20 Władysława Węgorka

country: Poland

institute: Institute of Plant Protection - National Research Institute

summary:
Background: The continuous use of the herbicides contributes to the emergence of the resistant populations of numerous weed species that are tolerant to multiple herbicides with different modes of action (multiple resistance) which is provided by non-target-site resistance mechanisms. In this study, we addressed the question of rapid acquisition of herbicide resistance to pinoxaden (acetyl CoA carboxylase inhibitor) in Apera spica-venti, which endangers winter cereal crops and has high adaptation capabilities to inhabit many rural locations. To this end, de novo transcriptome of Apera spica-venti was assembled and RNA-sequencing analysis of plants resistant and susceptible to pinoxaden treated with this herbicide was performed.

Results: The obtained data showed that the prime candidate genes responsible for herbicide resistance were those encoding 3-ketoacyl-CoA synthase 12-like, UDP-glycosyltransferases (UGT) including UGT75K6, UGT75E2, UGT83A1-like, and glutathione S-transferases (GSTs) such as GSTU1 and GSTU6. Also, such highly accelerated herbicide resistance emergence may result from the enhanced constitutive expression of a wide range of genes involved in detoxification already before herbicide treatment and may also influence response to biotic stresses, which was assumed by the detection of expression changes in genes encoding defence-related proteins, including receptor kinase-like Xa21. Moreover, alterations in the expression of genes associated with methylation in non-treated herbicide-resistant populations were identified.

Conclusion: The obtained results indicated genes that may be involved in herbicide resistance. Moreover, they provide valuable insight into the possible effect of resistance on the weed interaction with the other stresses by indicating pathways associated with both abiotic and biotic stresses.

overall_design: RNA isolated from two susceptible and two resistant to multiple herbicides A. spica-venti populations. Four biological replicates for each condition, with 3 plants per biological replicate were harvested.

first: Barbara

last: Wrzesińska-Krupa

last: Obrępalska-Stęplowska


title: Transcriptome analysis indicates the involvement of herbicide-responsive and plant-pathogen interaction pathways in the development of resistance to ACCase inhibitors in Apera spica-venti

overall_design: RNA isolated from susceptible and resistant to multiple herbicides A. spica-venti plants that were subjected to de novo assembly. There were 2 samples described as S (susceptible) and R (resistant).

first: Tomasz

last: Szmatoła


title: RNA-seq analysis of brain tissue treated by VEGFC in BDL-induced cirrhotic rat with hepatic encephalopathy

city: New Haven

first: Chihao

last: Zhang

state: CT

address: 300 Cedar Street

department: Internal Medicine

institute: Yale University

summary:
Aims: Hepatic encephalopathy (HE) is a serious neurological complication in patients with liver cirrhosis. Nothing is known about the role of the meningeal lymphatic system in HE. We tested our hypothesis that enhancement of meningeal lymphatic drainage could decrease neuroinflammation and ameliorate HE.
Methods: A 4-week bile duct ligation (BDL) model was used to develop cirrhosis with HE in rats. Brain inflammation in patients with HE was evaluated using archived GSE41919. Motor  function of rats was assessed by the rotarod test. AAV8-VEGF-C was injected into the cisterna  magna of BDL rats one day after surgery to induce meningeal lymphangiogenesis.
Results: Cirrhotic rats with HE showed significantly increased microglia activation in the middle  region of the cortex (p<0.001) as well as increased neuroinflammation as indicated by significant increases in IL-1, INF, TNF and Iba1 expression in at least one of the three  regions of the cortex. Motor function was also impaired in rats with HE (p<0.05). Human brains of cirrhotic patients with HE also exhibited upregulation of pro-inflammatory genes (NF-κβ, Iba1, TNFα and IL-1β) (n=6). AAV8-VEGF-C injection significantly increased meningeal lymphangiogenesis (p=0.035) and tracer dye uptake in the anterior and middle regions of the cortex (p=0.006 & 0.003, respectively), their corresponding meninges (p=0.086 & 0.006, respectively) and the draining lymph nodes (p=0.02). Further, AAV8-VEGF-C decreased microglia activation (p<0.001) and neuroinflammation, and ameliorated motor dysfunction (p=0.024).
Conclusion: Promoting meningeal lymphatic drainage and enhancing waste clearance improves HE. Manipulation of meningeal lymphangiogenesis could be a new therapeutic  strategy for the treatment of HE.

overall_design: Transcriptomic profile of middle brain tissues from three male Sprague–Dawley rats with bile duct ligation (BDL) , three sham rats as controls, three BDL rats treated with AAV-GFP as well as three BDL rats treated with AAV-VEGFC

first: Yasuko

last: Iwakiri


title: Investigating microRNA Profiles in Prostate Cancer Bone Metastases

status: Public on Apr 21 2023

city: UMEÅ

first: Pernilla

last: Wikström

address: Department of Medical biosciences, Buildning 6M, 2nd floor

department: Medical biosciences, Pathology

country: Sweden

institute: Umeå University

summary: The aim of this small screening study was to identify differentially expressed miRNAs in clinical PC bone metastasis (n=14) in comparisson to beinging postate (n=7) and localized PC (n=7). Short RNA from 28 tissue samples were analyzed on 3D-Gene® microarray platform (Toray Industries, Tokyo, Japan).

overall_design: RNA was isolated from fresh-frozen tissue samples of benign prostate (n=7), localized PC (n=7), and PC bone metastasis (n=14) using Allprep RNA/DNA/Protein Isolation Kit (Qiagen, Hildenm Germany) followed by Rneasy MinElute Cleanup Kit (Qiagen, Hildenm Germany) to enrich for short RNAs.

first: Helena

last: Järemo

first: Julius

last: Semenas

first: Sofia

middle: H

last: Bergström

first: Marie

last: Lundholm

first: Elin

last: Thysell

first: Anders

last: Widmark

first: Sead

last: Crnalic

first: Erik

middle: B

last: Ylitalo

last: Bergh

first: Maria

last: Brattsand


title: Transcriptomics of the racematic Praziquantel: R-PZQ versus S-PZQ in male Schistosoma mansoni

city: Albuquerque

first: Charles

last: Cunningham

state: New Mexico

address: 1 University of New Mexico

department: Biology

institute: University of New Mexico

summary: Schistosomiasis affects over 250 million people worldwide and is caused by trematodes of the genus Schistosoma including the species Schistosoma mansoni. Praziquantel (PZQ) is the most widely available and implemented drug for this disease, and is produced as an racematic mixture composed of the enantiomers, R-PZQ and S-PZQ. In this study we examined the gene expression profiles of 49 day male S. mansoni after 18 hour treatment with R-PZQ, S-PZQ or control (1% DMSO). These results provide insight into the effect of PZQ enantiomers against male S. mansoni.

overall_design: Examination of the enantiomers of praziquantel, R-PZQ and S-PZQ, in 49 day old male Schistosoma mansoni, in quadruplicate, using Illumina NextSeq 500.

first: Melissa

last: Sanchez


title: The SEQC2 epigenomics quality control (EpiQC) study [methylation array]

city: Uppsala

first: Jessica

last: Nordlund

address: Box 1432, BMC

department: Department of Medical Sciences

institute: Uppsala University

summary: We present a multi-platform assessment and a global resource for epigenetics research from the FDA's Epigenomics Quality Control (EpiQC) Group. The study design leverages seven human cell lines that are designated as reference materials and publicly available from the National Institute of Standards and Technology (NIST) and Genome in a Bottle (GIAB) consortium. These samples were subject to a variety of genome-wide methylation interrogation approaches across six independent laboratories, with a primary focus on 5-methylcytosine modifications.

overall_design: Microarray experiments were run at three different labs, denoted labs A, B, and C. The resulting dataset contains 30 samples, with each of the seven cell lines (HG001-HG007) having between three and six replicates (biological or technical). Two technical replicates were generated for each cell line at lab A, one replicate from each cell line was generated at lab B, and three technical replicates were generated for the Han Chinese family trio cell lines (HG005-HG007) at lab C.

first: Jonathan

last: Foox

first: Claudia

last: Lalancette

first: Ting

last: Gong

first: Michelle

last: Lacey

first: Christopher

last: Mason

first: Youping

last: Deng


title: Broader functions of TIR domains in Arabidopsis immunity

city: Carrboro

first: Dor

last: Russ

state: NORTH CAROLINA

address: 222 Old Fayetteville Rd, Apt. L103

institute: UNC Chapel Hill


title: Broader functions of TIR domains in Arabidopsis immunity [NAM]

summary: Characterization of the impact of nicotinamide on TIR function

overall_design: We performed transcriptomic analyses on control Col-0 plants and TIR signaling impaired eds1-12 mutants, infected or not by Pseudomonas syringae DC3000 empty vector or expressing avrRps4, in the presence or not of 50mM nicotinamide. Samples consisted of two leaf discs from two plants. We collected six samples from three independent experiments for each genotype/treatment.

first: Pierre

last: Jacob

first: Junko

last: Hige

first: Lijiang

last: Song

first: Adam

last: Bayless

first: Vera

last: Bonardi

first: Farid

last: El-Kasmi

first: Lisa

last: Wünsch

first: Yu

last: Yang

first: Connor

last: Fitzpatrick

first: Brock

last: Mckinney

first: Marc

middle: T

last: Nishimura

first: Murray

last: Grant

first: Jeffery

middle: L

last: Dangl


title: Broader functions of TIR domains in Arabidopsis immunity [DV]

summary: Characterization of ADR1-L2 D484V suppressor mutants

overall_design: We performed transcriptomic analyses on control Col-0 plants, on ADR1-L2 D484V plants and compared it to suppressor mutant ADR1-L2 D484V 26.6 and 30.4. Samples consisted of two leaves from at least two plants. We collected three samples from three independent experiments for each genotype.


title: Single-cell transcriptomic analysis reveals the developmental trajectory and transcriptional regulatory networks of pigment glands in Gossypium bickii

city: Hangzhou

first: Yue

last: SUN

state: Zhejiang

address: Yuhangtang Rd

institute: Zhejiang University


title: Single-cell transcriptomic analysis reveals the developmental trajectory and transcriptional regulatory networks of pigment glands in Gossypium bickii [bulk RNA-seq]

summary: Comprehensive utilization of cottonseeds is limited by the presence of pigment gland and its inclusion gossypol. The ideal cotton is glandless-seeds and glanded-plant, a trait found in only few Australian wild cotton species, including Gossypium bickii. Introgressing the trait to cultivated species is proved to be difficult. Understanding the biological processes towards pigment gland morphogenesis and the associated underlying molecular mechanisms will facilitate breeding cultivated cotton varieties with the trait of glandless-seeds and glanded-plant. Single-cell RNA sequencing (scRNA-seq) was performed on 12,222 protoplasts isolated from cotyledons of germinating G. bickii seeds 48-hours after imbibition. Clustered into 14 distinct clusters unsupervisedly, these cells could be grouped into eight cell populations with the assistance of known cell marker genes. The pigment gland cells were well separated from others, and could be separated into pigment gland parenchyma cells, secretory cells, and apoptotic cells. In this study, integrating pigment gland cells developmental trajectory, transcription factors regulatory networks, and core transcription factors functional validation, a relatively complete model was proposed for pigment gland formation. Light and gibberellin were verified to promote the formation of pigment glands. Besides, three novel genes, GbiERF114 (ETHYLENE RESPONSE FACTOR 114), GbiZAT11 (ZINC FINGER OF ARABIDOPSIS THALIANA 11) and GbiNTL9 (NAC TRANSCRIPTION FACTOR-LIKE 9), were found to affect pigment gland formation. These findings shed new insights into pigment gland morphogenesis and lay the cornerstone for future cotton scRNA-seq investigations.

overall_design: Comparative gene expression profiling analysis of bulk RNA-seq data along the germination and under the treatments of dark and light of G. bickii cotyledons

last: Sun

first: Yifei

last: Han

first: Kuang

last: Sheng

first: Shuijin

last: Zhu

first: Tianlun

last: Zhao


title: Complex regulation of Eomes levels mediated through distinct functional features of the Meteor long non-coding RNA locus (RNA-Seq)

city: Rehovot

first: Igor

last: Ulitsky

address: Hertzl St.

institute: Weizmann Institute of Science

summary: Long non-coding RNAs (lncRNAs) are diverse transcription products emanating from thousands of loci in mammalian genomes, implicated in a wide array of cellular processes including transcriptional regulation, differentiation, cellular reprogramming, and many others. While a large majority of functional lncRNAs have been proposed to act in cis to their sites of transcription, an in-depth understanding of the functional features within such lncRNA loci, as well as their mechanisms of action, is currently lacking. Further insights are hindered by the heavy dependencies of observed phenotypes on the perturbation techniques employed. Here, we study Meteor, a lncRNA transcribed nearby the gene encoding for Eomes, a pleiotropic transcription factor with highly regulated spatiotemporal expression patterns throughout early development and in adult tissues. Using a wide array of perturbation techniques, we show that transcription elongation through the Meteor locus is required for Eomes activation in naive mouse embryonic stem cells (mESCs), with Meteor repression linked to a reduction in cells potentiated to differentiate to the mesoderm lineage. We further demonstrate that a distinct functional feature of the locus – namely, the underlying DNA element – is required for suppressing Eomes expression following neuronal differentiation of mESCs. Our results demonstrate the complex regulation that can be conferred by a single lncRNA locus, and emphasize the importance of careful selection of perturbation techniques for the study of lncRNA loci.

overall_design: RNA-seq of either mESCs or NPCs of various genotypes (WT, Meteor promoter KO, Meteor promoter inversion) or perturbations (Ctrl, Meteor CRISPR/Cas9 KD).

first: Noa

last: Gil


title: Exploring the molecular mechanism of Bushen Huoxue Fang on premature ovarian failure based on transcriptomics and systems biology

first: Kailin

state: Hunan

address: Xueshi Road No. 300

institute: Hunan University of Chinese Medicine

summary: Objective: To Explore the mechanism of autophagy in mice with immune premature ovarian failure (POF) and the effect of Bushen Huoxue Fang (BSHXF)  Method: POF mice were treated with BSHXF, and estradiol valerate. Then, the ovaries were used for transcriptome sequencing.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for POF mice and BSHXF treated mice

first: Huiping

last: Liu

first: Guomin

last: Zhang


title: DNA Methylome and 3D Chromatin Landscape of Cell Types Across the Mouse Brain [11K_201022]

city: La Jolla

first: Joseph

last: Ecker

overall_design: Apply snmC-seq3 to 117 brain functional regions to identify epigenomic landcape of the adult mouse brain, this subseries consists of one single nucleus methylation sequencing experiment of brain region (11K).

first: Hanqing

first: Anna

last: Bartlett

first: Jacinta

last: Lucero

first: Julia

last: Osteen

first: Jordan

last: Altshul

first: Mia

last: Kenworthy

first: Rosa

last: Castanon

last: Nery

first: Peter

last: Berube

first: Huaming

last: Chen

first: Michael

last: Nunn

first: Jesse

last: Dixon

first: M

last: Behrens


title: DNA Methylome and 3D Chromatin Landscape of Cell Types Across the Mouse Brain [11K_201015]


title: DNA Methylome and 3D Chromatin Landscape of Cell Types Across the Mouse Brain [11J_210204]

overall_design: Apply snmC-seq3 to 117 brain functional regions to identify epigenomic landcape of the adult mouse brain, this subseries consists of one single nucleus methylation sequencing experiment of brain region (11J).


title: Transcriptome profiling of Drosophila adults from multiple generations including flies with genetically-ablated insulin-producing cells as founders.

city: New Delhi

first: Abhay

last: Sharma

state: Delhi

address: Sukhdev Vihar, Mathura Road

country: India

institute: CSIR-Institute of Genomics and Integrative Biology

summary: Transgenerational epigenetic inheritance is a subject of immense current interest. In a newly developed Drosophila model in the laboratory, genetic ablation of insulin-producing cells (IPCs) was found to affect whole -body triglyceride levels not only in the ablated flies but also in their male-line derived, non-ablated future generations. To further characterize this genetic-factor-induced transgenerational inheritance model, we have now performed whole body microarray gene expression profiling of adult males and females with genetically ablated IPCs, and of three consecutive, paternally derived non-ablated generations of adult males and females originating from ablated males. Interestingly, like altered levels of triglycerides, transcriptomic alterations are found not only in the ablated flies but also in their male-line-derived, non-ablated future generations.

overall_design: Test and control line Drosophila cultures were grown at 250C in parallel, with whole body RNA isolated from adults used in gene expression profiling of at least three biological replicates. Adult males and females of the genotype rpr/cyo; dilp3/ser in w1118 background served as F0 test, and that isolated from w1118 background strain as F0 control. F0 test males were mated to F0 control females to generate test line F1 males and females, with the genotypes rpr/+; ser/+, rpr/+; dilp3/+, cyo/+; ser/+, and cyo/+; dilp3/+. All these genotypes were expression profiled. On the other hand, F0 control males mated to F0 control females produced F1 individuals, which were not profiled but used in crosses as described below. F1 test males of the genotype rpr/+; ser/+ were mated to control line F1 females to generate F2 individuals, of which only balancer-free flies were used further. Similarly, F1 control males and females were mated to generate F2 controls. Next, balancer-free F2 test males were crossed to F2 control females to generate F3 individuals. Similarly, mating between F2 control males and females yielded F3 controls.

first: Ameek

last: Bhalla


title: Human induced pluripotent stem cell culture on a non-coated dish using medium supplemented with milk fat globule epidermal growth factor 8

status: Public on Apr 20 2023

city: Kyoto

first: Yoshiki

last: Nakashima

state: Kyoto

address: Kyoto Research Park KISTIC Building Room 501, 5th floor, KISTIC building,  134 Chudoji Minami-cho, Shimogyo-ku

department: Research and Development Center

institute: Kyoto University Center for iPS Cell Research and Application Foundation (CiRA Foundation)

summary:
201B7 cells were cultured on iMatrix-511 for 4 days after cell seeding in Stem Fit AK03 medium or CTS Essential 8 medium (2 samples each), and separately, different 201B7 cells (2 samples each) were cultured in Stem Fit AK03 medium or gelatin solution (10%) + MFGE 8 (2 µg/mL) in CTS Essential 8 medium for 4 days from cell seeding. A hierarchical cluster analysis of the 10 cell types is shown (Figure 2A).
The 5,919 probes with variable expression are shown in a heatmap. Comparisons between samples based on 'human ES cell' were made using a hierarchical cluster analysis, and 4,825 probes with variable expression in each of the four comparisons are shown in the heatmap (Figure 2B). Comparisons between samples based on 'human iPSC N116213' were performed using a hierarchical cluster analysis, and 4,886 probes with variable expression in each of the four comparisons are also shown in a heatmap (Figure 2C).

overall_design: Data from public databases of iPS and ES cells were used as controls. iPS cells (201B7 line) cultured for 4 days in two different media and two different scaffold materials were used as samples (n = 2).


title: A novel mouse model of hepatocellular carcinoma mediated by hepatitis B virus-specific CD8+ T cells [bulk RNA-seq]

city: Hefei

first: Xiaolei

last: Hao

state: Anhui

address: huangshan Road 443

institute: Institute of Immunology, USTC

summary: We used immunocompetent Fah-/- mice as the recipients and adoptively transferred HBsAg+ hepatocytes from HBs-Tg mice to replace the recipient hepatocytes (HBs-HepR). HBs-HepR mice maintained persistent HBsAg expression with chronic hepatitis and spontaneous liver fibrosis, and eventually developed HCC with a prevalence of 100%.

overall_design: Liver tissue  mRNA profiles of B6-HepR and  HBs-HepR mice after 6 months and 12 months post transfer were generated by deep sequencing using Illumina

first: Zhigang

last: Tian


title: BORIS/CTCFL-mediated chromatin accessibility alterations promote a pro-invasive transcriptional signature in melanoma cells

city: Montreal

first: Sanne

middle: Marlijn

last: Janssen

state: Quebec

address: 3755 Chemin de la Côte-Sainte-Catherine

department: Pathology

country: Canada

institute: Lady Davis Institute for Medical Research

summary: Melanoma is the deadliest form of skin cancer, due to its tendency to metastasize early. Brother of Regulator of Imprinted Sites (BORIS), also known as CCCTC binding factor-Like (CTCFL), is a transcription regulator that becomes ectopically expressed in melanoma. We recently showed that BORIS contributes to melanoma phenotype switching by altering the gene expression program of proliferative melanoma cells in favor of a more invasive phenotype. However, how BORIS alters the transcriptome remains unclear. Here, ATAC-seq was used to study BORIS-mediated chromatin accessibility alterations in proliferative melanoma cells. Genes that gained promoter accessibility following ectopic BORIS expression, were enriched for melanoma-specific invasive genes as well as invasion-associated biological processes, while promoters of genes associated with proliferation show reduce accessibility. Integration of ATAC-Seq and RNA-Seq data demonstrates that increased chromatin accessibility is associated with transcriptional upregulation of genes involved in tumor progression processes, and the aberrant activation of oncogenic transcription factors, while reduced chromatin accessibility and downregulated genes, were associated with repressed activity of tumor suppressors. Together, these findings indicate that BORIS mediates transcriptional reprogramming in melanoma cells by altering chromatin accessibility and gene expression, shifting the cellular transcription landscape of proliferative melanoma cells towards a pro-invasive genetic signature.

overall_design: Assay for Transposase-Accessible Chromatin followed by sequencing (ATAC-Seq) on MM057 melanoma cells expressing doxycycline-inducible empty vector control or human BORIS

first: Roy

last: Moscona

first: Mounib

last: Elchebly

first: Andreas

middle: I

last: Papadakis

first: Eitan

last: Rubin

first: Alan

last: Spatz


title: Effect of CDDO-2P-Im Treatment in Fibroblast Cells

city: Cleveland

first: George

last: Luo

state: OH

address: 2103 Cornell Rd. Wolstein Research Bldg/Rm 3501

institute: Case Western Reserve University

summary: Primary Dermal Fibroblasts (PDF) were treated with various concentrations of CDDO-2P-Im for 6 hours and then RNA was extracted for gene expression changes

overall_design: 5 x 10^5 cells were treated with Control (DMSO), 0.1μM CDDO-2P-Im, or 0.4 μm CDDO-2P-Im for 6 hours. Groups were compared between each other.

first: John

last: Letterio


title: Senotherapeutic peptide treatment reduces biological age and senescence burden in human skin models

city: Rio de Janeiro

first: Mariana

last: Boroni

state: RJ

address: Rua André Cavalcanti 37

country: Brazil

institute: Instituto Nacional de Câncer

summary: this work shows the safe reduction of the biological age of ex vivo human skins by a senomorphic peptide.

overall_design: DNA samples included control, 5 days treatment with 12.5 μM Pep 14, and 5 days treatment with 100 nM Rapamycin, 3 independent replicates each.

first: Alessandra

last: Zonari


title: Impact of K pneumoniae infection and/or exogenous surfactant protein-A2 (1A0) on alveolar macrophage miRNome in SP-A-knockout mice.

city: hershey

first: Nithyananda

last: Thorenoor

state: PA

address: 500 University Drive

department: Pediatrics

institute: Penn State University College of Medicine

summary: Human SP-A1 and SP-A2, encoded by SFTPA1 and SFTPA2 and their genetic variants differentially impact alveolar macrophage (AM) functions and regulation, including the miRNome.  single dose of SP-A exogenous treatment of SP-A-KO mice prior to infection, after infection, or at the time of infection significantly improved survival.  we investigated the role of exogenous SP-A protein treatment on the regulation of AM miRNome in SP-A-KO mice at the time of infection.  Towards this, SP-A-KO male and female mice were infected with K. pneumoniae alone or in combination with exogenous SP-A2 (1A0) protein for 6 h, and the expression levels of AM miRNAs, target mRNAs of the significant miRNAs, and pathways involved were studied.  We found (i) significant differences in AM miRNome of KO in terms of sex and exposure; (ii) the expression of the overwhelming majority of miRNA targets in KO males were increased in response to infection and exogenous SP-A2 (1A0) protein treatment at the time of infection; (iii) miRNA-mRNA targets were involved in the pro-inflammatory response, anti-apoptosis, cell cycle, cellular growth and proliferation pathways.  These data may assist in studying molecular mechanisms of exogenous SP-A mediated the AM miRNome regulation and potentially identify novel therapeutic targets for K. pneumoniae infection.

overall_design: Twelve-week-old, SP-A-knockout (KO) mice, were used in this study. The male and female mice used in this study were raised and maintained in a pathogen-free environment. The females were synchronized with regards to the estrous cycle by group housing and exposure to the bedding from male mice. A total of 28 mice (16 for miRNA analysis and 12 for target gene validation by qRT-PCR analysis) were used in the present study.  All the procedures involving animals  were approved by The Penn State Hershey Medical Center Institutional Animal Care and Use Committee (IACUC). SP-A (KO) male and female mice (n = 4/group for miRNA analysis and 3/group for qRT-PCR validation) were anesthetized with a mixture of ketamine and xylazine and infected with K. pneumoniae (~ 450 CFU/mouse) in 50 μl of PBS oropharyngeal.   SP-A-KO male and female mice were anesthetized and the mice were infected with K. pneumoniae (~450 CFU/mouse) as described above, and/or in combination with 10 µg of purified SP-A2 (1A0) protein expressed by stably transfected CHO cells as described [50] in 50 µl of PBS oropharyngeal.  The mice were monitored for 6 h after infection.  Mouse AM were obtained from both male and female mice by bronchoalveolar lavage (BAL) at 6 h, after infection alone and/or in combination with SP-A2(1A0) protein.Total RNA extraction from AM cells, library construction, and sequencing were performed.  The differentially expressed miRNAs between infection alone and/or in combination with SP-A2 (1A0) protein in males and females were identified by using the edgeR and the TCC v1.14.0 R package with false discovery rate (FDR) adjusted P-value of 0.1 as a significance cutoff.

first: Joanna

last: Floros


title: Epigenome analysis of normal skin and hypertrophic scar samples

city: Xi'an

first: huayu

last: Zhu

address: No. 28 Road

institute: Fourth

summary: Hypertrophic scarring (HS) is characterized by excessive extracellular matrix deposition, matrix metalloprotein gene activation, and fibroblast invasive growth. However, the methylation level of hypertrophic scarring is poorly understood. Genome wide DNA methylation profiling of normal skin and hypertrophic scar. The Illumina Infinium Methylation EPIC BeadChip (850K) was used to obtain DNA methylation profiles across approximately 853,307 CpGs in liquid based scar samples. Samples included 6 normal skin, and 6 hypertrophic scar.

overall_design: HS tissue samples and matched normal skin (NS) tissue samples were collected from patients who received surgeries.

first: Huayu

first: Hongtao

last: Wang


title: Effect of Gas6/Axl on HCC cell line gene expression

city: Vienna

first: Wolfgang

last: Mikulits

address: Borschkegasse 8A

country: Austria

institute: Medical University of Vienna

summary: We adressed the impact of the receptor tyrosine  kinase Axl and ist ligand Gas6 on gene expression in cellular HCC models, including cells harbouring Axl KO and exogenous reexpression.

overall_design: Differential gene expression analysis was performed based on RNA-seq data of HLF, HLF-nickase, HLF-Axl-KO and HLF-Axl-KO-wt-Axl cells stimulated with Gas6. Analysis was done in technical triplicates for each cell line.

first: Viola

last: Hedrich

first: Doris

last: Chen


title: Effect of CDDO-2P-Im Treatment in Ovarian Cells

summary: OVCAR-8 Cells were treated with various concentrations of CDDO-2P-Im for 6 hours and then RNA was extracted for gene expression changes

overall_design: 500,000 cells were treated with Control (DMSO), 0.4μM CDDO-2P-Im, or 0.8 μm CDDO-2P-Im for 6 hours. Groups were compared between each other.

first: Ahmed

last: Soloman

first: Haider

last: Mahdi


title: Effect of KEAP1 knockout and CDDO-2P-Im Treatment in ARH-77 Cells

summary: ARH-77 cells were genetically editted with CRISPR-Cas9 to knock out KEAP1 and treated with various doses of CDDO-2P-Im or DMSO.

overall_design: WT and KEAP1 KO cells were extracted for RNA.  In addition, 500,000 KEAP1 knockout cells were treated with DMSO, 0.1μM CDDO-2P-Im, or 0.4 μm CDDO-2P-Im for 6 hours. Groups were compared between each other.


title: Effect of CDDO-2P-Im Treatment in DIPG Cells

summary: SF8628 Cells were treated with various concentrations of CDDO-2P-Im for 6 hours and then RNA was extracted for gene expression changes

overall_design: 500,000 cells were treated with Control (DMSO), 0.3 μM CDDO-2P-Im, or 0.7 μm CDDO-2P-Im for 6 hours. Groups were compared between each other.

first: Kristin

last: Alridge


title: Cardiomyocyte peroxisome proliferator-activated receptor α prevents septic cardiomyopathy via improving mitochondrial function

city: Beijing

first: Xinxin

address: 10 You’anmen Outer West 1st Street

department: Department of Physiology and Pathophysiology

institute: Capital medical university

summary: Clinically, cardiac dysfunction is a key component of sepsis-induced multi-organ failure. Mitochondrial function is essential for cardiomyocyte homeostasis as disrupted mitochondrial dynamics enhances mitophagy and apoptosis. However, therapies targeted to improve mitochondrial function in septic patients have not been explored. Our research is helpful to understand the role of cardiomyocyte PPARα in LPS-induced cardiac dysfunction

overall_design: In this study, we isolated heart tissue from PBS- or LPS- treated Ppara-Flox and cardiomyocyte PPARα deficient mice (4 samples each) were subjected to RNA sequencing.

first: Qi

last: Zhang

first: Yuner

first: Aijuan

last: Qu


title: Gene expression profiling of asthma

city: Taipei

first: Yungling

middle: Leo

last: Lee

address: Sec. 2, Academia Rd.

department: Institute of Biomedical Sciences

institute: Academia Sinica

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

overall_design: Refer to individual Series


title: Li-Fraumeni Syndrome-associated dimer-forming mutant p53 promotes transactivation-independent mitochondrial cell death [RNA2]

city: New York

first: Joshua

last: Choe

state: NY

address: 816 Fairchild Center, MC 2422

department: Department of Biological Sciences

institute: Columbia University

summary: Mutations that occur within the oligomerization domain (OD) of the tumor suppressor p53 generally abolish p53 tetramerization and are associated with increased cancer susceptibility in Li-Fraumeni syndrome (LFS). Despite their prevalence, the impact of OD-mutant p53 proteins in cancer, especially beyond a loss of canonical p53 activity, has not been well elucidated. We sought to delineate the gain-of-function (GOF) vs. loss-of-function (LOF) activities of OD-mutant p53, specifically focusing on the LFS tumor-derived p53(A347D) variant. We obtained LFS patient-derived dermal fibroblasts heterozygous for the mutation and generated an allelic series of U2OS cancer cell lines expressing wild-type p53, heterozygous (p53+/AD) or homozygous (p53AD/AD) mutant p53 or no p53 (p53 KO). In contrast to wild-type p53, mutant p53(A347D) exclusively forms dimers in both fibroblasts and cancer cells and has lost the ability to bind and transactivate the majority of canonical p53 target genes, which yields comparable tumorigenic properties between mutant p53 and p53 KO cells. Mutant p53(A347D), however, displays neomorphic activities. Glycolysis and oxidative phosphorylation pathways are enriched in cells bearing p53(A347D) relative to both wild-type p53 and p53 KO cells. Furthermore, dimeric mutant p53 induces striking mitochondrial network aberration and preferentially associates with mitochondria to drive apoptotic cell death upon topoisomerase II inhibition in the absence of transcription. Ultimately, we describe dimeric mutant p53 as wielding a double-edged sword: driving tumorigenesis through LOF while gaining enhanced apoptogenic activity, thereby providing a potential basis for select therapeutic approaches.

overall_design: We engineered via CRISPR-Cas9 U2OS osteosarcoma cells that harbor wild-type p53 to express either no p53 or are heterozygous (p53+/AD) or homozygous (p53AD/AD) for the A347D mutation. After 24 h of treatment with either DMSO or 20 µM etoposide, cells were harvested for RNA extraction. Osteoblasts generated from patient-derived dermal fibroblasts either wild-type p53 or heterozygous for the p53(A347D) mutation were subjected to RNA-seq.

first: An

last: Xu

first: Aleksandar

middle: Z

last: Obradovic

first: Carol

last: Prives


title: Li-Fraumeni Syndrome-associated dimer-forming mutant p53 promotes transactivation-independent mitochondrial cell death [RNA1]

overall_design: We engineered via CRISPR-Cas9 U2OS osteosarcoma cells that harbor wild-type p53 to express either no p53 or are heterozygous (p53+/AD) or homozygous (p53AD/AD) for the A347D mutation. After 24 h of treatment with either DMSO or 20 µM etoposide, cells were harvested for RNA extraction. Four biological replicates were used for each condition. Cells grown on separate plates were considered biological replicates.


title: Li-Fraumeni Syndrome-associated dimer-forming mutant p53 promotes transactivation-independent mitochondrial cell death [ChIP2]

overall_design: We engineered via CRISPR-Cas9 U2OS osteosarcoma cells that harbor wild-type p53 to express either no p53 or are heterozygous (p53+/AD) or homozygous (p53AD/AD) for the A347D mutation. Osteoblasts were also generated from patient-derived dermal fibroblasts either wild-type p53 or heterozygous for the p53(A347D) mutation. Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) was performed to assess the genome-wide occupancy of mutant p53(A347D) relative to wild-type p53 in both U2OS cells and osteoblasts.


title: Characterization of culprit-coronary artery miRNA expression in acute myocardial infarction male patients

city: Poriya

first: Natalia

last: Volinsky

address: building 26

department: Research Institute

institute: Tzafon Medical Center

summary: Coronary artery disease (CAD) is the leading cause of mortality worldwide. We aimed to compare expression of miRNA in the affected artery of acute myocardial infarction (ST-elevation myocardial infarction) male patients versus healthy individuals (control). Blood samples were collected during coronary catheterization from proximal culprit coronary arteries aimed for the interventions or from a random artery in control samples. RNA isolated from serum was used for miRNA high throughput sequencing.

overall_design: miRNA libraries were prepared from RNA samples of 16 control and 18 STEMI patients, using the QIAseq miRNA Library Kit (Qiagen).  Library concentrations were measured with Qubit dsDNA HS Assay Kit (Molecular Probes Life Technology) and the quality was assessed by Bioanalyzer and TapeStation systems (Agilent).  All miRNA libraries were sequenced using Nextseq 550 (Illumina) with a read length of 75bp. Differential expression analysis was performed using the Qiagen platform.

first: Olga

last: Volodko

first: Offer

last: Amir


title: Integrative analysis of genomic structural variants in human leukemia

city: Memphis

first: Jian

state: Tennessee

address: 262 Danny Thomas Place, MS 345

institute: St. Jude Children's Research Hospital


title: Li-Fraumeni Syndrome-associated dimer-forming mutant p53 promotes transactivation-independent mitochondrial cell death [ChIP 1]

overall_design: We engineered via CRISPR-Cas9 U2OS osteosarcoma cells that harbor wild-type p53 to express either no p53 or are heterozygous (p53+/AD) or homozygous (p53AD/AD) for the A347D mutation. Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) was performed to assess the genome-wide occupancy of mutant p53(A347D) relative to wild-type p53.


title: The molecular grammar of protein disorder guiding genomic binding specificity

first: Naama

last: Barkai

state: --- Select a state ---

address: Herzl St 234

department: Molecular Genetics

institute: Weizmann Institute

summary: Profiling Msn2 IDR sequence variants to reveal the grammar underlying specificity

overall_design: 70 IDR variants were designe, synthesized and constructed using CRIPSR and profiled ChEC-Seq

first: Felix

last: Jonas

first: Miri

last: Carmi

first: Beniamin

last: Krupkin


title: Microarray of 3D cultured basal cells in the presence of TNFa

city: Wuhan

first: Yu

last: Zhou

address: Donghu Road, No. 115, Wuchang District, Wuhan, Hubei Province, P.R. China.

institute: Medical Research Institute, Wuhan University

summary: To investigate the impact of TNFa on mammary basal colony formation in vitro 3D culture.

overall_design: The mammary basal cells were sorted from adult female mammary glands by FACS sorting, and cultured in the presence of 10ng/ml recombinated mouse TNFa  in 3D for 10 days, and harvested for microarray, compared with control.

first: Cheguo

last: Cai


title: AAV-mediated gene augmentation therapy of CRB1-patient derived retinal organoids restores the histological and transcriptional retinal phenotype

city: Leiden

first: Hailiang

last: Mei

address: Einthovenweg 20

department: Sequencing Analysis Support Core

country: Netherlands

institute: Leiden University Medical Center

summary: Retinitis pigmentosa (RP) and Leber congenital amaurosis are inherited retinal dystrophies caused by mutations in, among others, the Crumbs homologue 1 (CRB1) gene. CRB1 is required for organizing apical-basal polarity and adhesion between photoreceptors and Müller glial cells. Using human CRB1 patient induced pluripotent stem cells from RP patients we derived CRB1 retinal organoids, with diminished expression of variant CRB1 protein with immunohistochemical analysis. Single cell RNA-sequencing revealed impact on, among others, the endosomal pathway and cell adhesion and migration in CRB1 patient derived retinal organoids compared to isogenic controls. Adeno-associated viral (AAV) vector-mediated hCRB2 or hCRB1 gene augmentation in Müller glial and photoreceptor cells partially restored the histological and differentially expressed genes phenotype. Altogether, we show proof-of-concept that AAV.hCRB1 or AAV.hCRB2 treatment improved the phenotype of CRB1 patient derived retinal organoids, providing essential information for future gene therapy approaches for patients with mutations in the CRB1 gene.

overall_design: CRB1 patient-derived retinal organoids were treated with AAV5.CMV.GFP and AAV5.CMV.hCRB1 or AAV5.CMV.hCRB2 were analyzed using scRNAseq at differentiation day 230. Samples were multiplexed using cell hashing oligonucleitode (HTO): each run contains 14 HTO with different organoids (multiple organoid lines, and tratments). In run 1, 2, and 3, CRB1 patient-derived retinal organoids P117, P128 and isogenic control of P128 (ISO-P128) with and without AAV.hCRB treatment were sequenced. In run 4 only P116 and ISO-P116 with and without AAV.hCRB treatment were sequenced.

first: Nanda

last: Boon

first: Ioannis

last: Moustakas

first: Jan

last: Wijnholds


title: single cell RNA sequencing of macrophage-depleted mammary gland by clodronate liposome treatment

summary: To investigate the impact of macrophages on cell population of mammary gland, we performed the single cell RNA sequencing of the macrophage-depleted mammary gland compared with control.

overall_design: The mammary single cells were sorted from adult female mammary glands by FACS sorting, which were included CD45+ immune cells and CD31-TER119- cells.


title: Microarray of 3D cultured basal cells co-cultured with M2-like macrophages

summary: To facilitate the research on the interaction between mammary basal cells and M2-like macrophages, we established a co-culture system of mammary basal cells and M2-like macrophages in vitro, and performed microarray of M2-like macrophage co-cultured basal cells comparing with control, for investigating the changes of downstream signals after co-culturing with M2-like macrophages in the basal cells.

overall_design: The mammary basal cells were sorted from adult female mammary glands by FACS sorting, and co-cultured with M2-like macrophages in 3D for 11-14 days, and the co-cultured cells and control cells were harvested for microarray.


title: The effect of macrophage depletion on mammary basal cells

summary:
To investigate the effect of macrophages on mammary basal cells, we established a macrophage depletion mouse model by clodronate liposome (CL) intraperitoneal injection, and the mammary basal cells were collected by FACS sorting.
We then performed RNA-seq analysis on clodronate liposome (CL) treated mammary basal cells compared to control.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for clodronate liposome (CL) treated mammary basal cells and control basal cells (treated with saline).


title: DNA Methylome and 3D Chromatin Landscape of Cell Types Across the Mouse Brain [11C_190620]

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

institute: HHMI-Salk-Institute

summary: Illustrating the cellular architecture of the mammalian brain is critical to understanding its diverse functions and complex animal behaviors. With support from NIMH and NINDS as part of the BRAIN Initiative Cell Census Network (BICCN), the Center for Epigenomics of the Mouse Brain Atlas (CEMBA) applied single nucleus methylation sequencing in 117 brain funtional regions across the whole adult male P56 C57BL/6J mouse brain. In each major brain regions, we identified distinct cell clusters and formed them in a hierarchical taxonomy. These clusters include known primary brain cell types and possible sub-types. We use these data to identify the epigenomic characteristics and to define specific regulatory elements for each cell cluster. We integrate the single cell methylome with single cell gene expression and chromatin accessibility profiles from the same brain region to further identify potential enhancers and their corresponding genes for several neuronal cell types. By brain region spacial comparisons, we found spatial specificity among excitatory neuronal clusters within the same cortical layer. We identify brain-region-specific transcription factors that may regulate cortical region development of excitatory neurons. These data define the landscape of cell type and spatial heterogeneity in the mouse brain and the underlining regulatory epigenomic basis.

overall_design: Apply snmC-seq2 to 117 brain functional regions to identify epigenomic landcape of the adult mouse brain, this subseries consists of one single nucleus methylation sequencing experiment of brain region (11C).

first: Hanqing

last: Liu

first: Anna

last: Bartlett

first: Jacinta

last: Lucero

first: Julia

middle: K

last: Osteen

first: Jordan

last: Altshul

first: Mia

last: Kenworthy

first: Rosa

middle: G

last: Castanon

last: Nery

first: Peter

last: Berube

first: Huaming

last: Chen

first: Michael

last: Nunn

first: Jesse

last: Dixon

first: M

last: Behrens


title: DNA architectural protein CTCF facilitates subset-specific chromatin interactions to limit the formation of memory CD8+ T cells

first: Ananda

last: Goldrath

address: 9500 Gilman Drive

institute: UCSD


title: Expression data from Knockdown of ACTL6A in SNU638 cell line

city: Guangzhou

first: Lekun

last: Fang

address: Yuancunerheng Road

institute: Sun Yat-sen University

summary: Gastric cancer malignant progression depends on the aberrant oncogenic expressions. During tumorigenesis, the oncogeneic genes mutation or expression, following specific sets of genes are up-regulated or down-regulated. Some of them, for instance, control metabolism reprogramming to promote tumor growth and maliganant progression.

overall_design: Gastric cancer cell line SNU638 with ACTL6A high expression was selected for RNA extraction and hybridization on Affymetrix microarrays. We sought to obtain gene expression profiles regulated by ACTL6A in gastric cancer cell. To that end, we transfected SNU638 cells with scramble RNA (scramble-1 and scramble-2) and sh-ACTL6A (shRNA-1 and shRNA-2).

first: Ziqing

last: Yang


title: Effect of elevated glucose on gene expression during foam cell formation.

first: Jie

last: Qi

state: Shaanxi

address: 256 West youyi Rd.

department: Second Department of Cardiovascular Medicine

institute: Shaanxi Provincial People's Hospital

summary: To investigate the intrinsic causes of the high prevalence of atherosclerosis in diabetic patients, we cultured macrophages differentiated from THP-1 in a high-glucose environment and oxidized low-density lipoprotein to induce its transformation into foam cells. We sought the effect of high glucose on gene expression during foam cell formation by transcriptome sequencing.

overall_design: We used untreated macrophages as control, and the rest of the cells were cultured in a high or no glucose medium for induction using oxLDL, respectively. Each group contained two biological replicates. We extracted all genes of the three groups for expression profiling by high-throughput sequencing.

first: Chaofeng

last: Sun


title: Gene expression profiling of Six1-null developing inner ear.

city: Madrid

first: Ignacio

last: Palmero

state: Madrid

address: Arturo Duperier, 4.

country: Spain

institute: CSIC

summary: Six1-null mice display developmental defects in the inner ear associated to aberrant senescence. To understand the molecular basis of this phenotype, here we investigated gene expression profiles of otic vesicles from Six1-null and wild-type embryos at developmental stage E10.5.

overall_design: RNA expression profiles were obtained from otic vesicles dissected from Six1-/- and Six1+/+ E10.5 mouse embryos. For each genotype, three pools of 6 vesicles (from three embryos) were used. Samples were analyzed by RNA-Seq using Illumina HiSeq.

first: Cristina

last: de Lope


title: High-throughput lncRNA sequencing profile of ovarian granulosa cells in polycystic ovary syndrome

city: Jinan

first: Yanjun

last: Zheng

state: Shandong Province

address: Wenhua West Road

institute: Center for Reproductive Medicine, Cheeloo College of Medicine, Shandong University

summary:
Purpose:To examine different expression profiles of lncRNAs and mRNAs in ovarian granulosa cells (GCs) in PCOS patients and controls
Patients:6 GCs samples in each group were subjected to high-thoughput sequencing
Results:54,615 lncRNAs and 123,141 mRNAs were detected in this high-thoughput sequencing, and we identified 1049 differential expressed lncRNAs and 3246 mRNAs (fold-change≧2, P-value<0.05). So far, we found 7 lncRNAs and 3mRNAs were validated consistent with sequence profile which were selected, randomly. There is still a large part that we have not verified yet.
Conclusion: Our study provides the detail analysis of GCs transcriptomes, generated by high-thoughput technology. This report also provides a framework for comparative investigations of PCOS. Our results revealed the expression of lncRNAs, mRNAs and part of circRNAs in PCOS, after more in-depth research in future, it can provide basic datas for studying the pathogenesis of PCOS.

overall_design: The expression profile of mRNAs, lncRNAs in GCs of PCOS patients

first: Yuhua

last: Shi

first: Xiao


title: N-acetyl-D-glucosamine is an oncometabolite modulating mast cell effector functions by chromatin remodeling

city: Marseille

first: Julien

last: Maurizio

address: Centre d’Immunologie de Marseille-Luminy

country: France

institute: INSERM

summary: We investigated the metabolic regulation of mast cell (MC) functions to control them. MCs are sentinels of the immune system with functions involved not only in host defense but also, if not properly controlled, in MC disorders such as systemic mastocytosis (SM). We identified N-acetyl-D-glucosamine (GlcNAc or NAG) as both a circulating biomarker for SM severity and an oncometabolite that promotes uncontrolled degranulation and proliferation of MCs expressing the Kit kinase domain mutant allele, D816V, that is both an oncogene and characterizes patients with SM. Given the known role of GlcNAc-related protein glycosylation in modifying factors involved in epigenetic regulation of gene expression and the effects of GlcNAc on neoplastic MCs effector functions, we asked whether the increased susceptibility of KIT D816V MCs to GlcNAc was due to chromatin state changes.

overall_design: ATAC-Sequencing of two independent experiments on ROSA KIT WT and KIT D816V human mast cells line exposed or not to 20 mM NAG (or GlcNAc) for 24h.

first: Rabie

last: Chelbi

first: Fabienne

last: Brenet


title: miRNA expression in primary ovarian tumors from stressed and non-stressed nude mice

city: Changsha

first: fang

last: zhou

address: 283 Tongzipo Road, Yuelu District,

institute: hunan cancer hospital

summary: Comparison of stress and non-stressed ovarian epithelial tumor tissues in nude mice.

overall_design: We injected ovarian cancer cells SKOV3 into nude mice peritoneal cavity. Tumor tissues with good growth were obtained from nude mice, including 4 non-stressed malignant ovarian tumor tissue samples and 3 stressed malignant ovarian tissue samples. High-throughput profiling of miRNA from the collected ovarian tissue samples. We experimentally stressed animals with a physical restraint system that Anil K Sood designed firstly. The physical restraint system is constructed by polymethylmethacrylate which is either transparent or non-transparent, specifically 50ml centrifuge tubes. Sterilization of the experimental equipment was conducted daily. The physical restraint system had approximately 5 holes (u = 4 mm) at the bottom to ensure adequate ventilation. The mice were reared in a room (specific pathogen-free) with controlled temperature, and 12 h/12 h light / dark, respectively.

last: Tang

first: Le

first: Xiaofang

last: Zhou


title: Metformin promotes in vitro maturation of oocytes from aged mice

city: JINAN

first: Yongzhi

last: Cao

address: NO. 44 Wenhuaxi Road

institute: Shandong University

summary: Our study demonstrates a protective effect for metformin against the decreased quality of aged oocytes to potentially improve ART success rates and illustrates a potential strategy to prevent or delay reproductive aging.

overall_design: The first-line type 2 diabetes treatment metformin has been associated with delayed ageing and reduction of oxidative stress; yet it remains unclear if metformin confers any benefits for aged oocytes, particularly in the context of the assisted human reproductive technology (ART) known as in vitro maturation (IVM). Here, we found that adding metformin into the IVM culture medium of aged oocytes significantly improves both oocyte maturation and early embryonic development.

first: Yueran

last: Zhao

first: Zhao

last: Wang

first: Changming

last: Zhang


title: RNA-sequencing of mouse Lang+ and Lang- migratory dendritic cells (DC) under 2 pathogenic conditions of atopic dermatitis

city: ILLKIRCH

first: Mei

last: Li

address: 1 Rue Laurent Fries

department: Functional Genomics and Cancer

institute: Institut de Génétique et de Biologie Moléculaire et Cellulaire

summary: Comparison of mouse Lang+ and Lang- migratory dendritic cells (DC) under 2 pathogenic conditions of atopic dermatitis (MC903-treated and OVA treated)

overall_design: Lang+ and Lang- migratory DC from ear-draining lymph nodes from non-treated mice, MC903- and OVA-treated LangGFP mice were FACS-sorted and profiled by RNA-sequencing. Three independent replicates were generated for each group.

first: Pierre

last: Marschall

first: Justine

last: Segaud


title: Refine regulatory elements across the genome

city: Shenzhen

first: Qing

address: No 7,Pengfei Road,Dapeng District

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

summary: We develop an experimental method termed as MAE-seq, to identify active enhancer across the genome. Enhancer loci are mapped precisely to 25 bp in different types of cells. In mouse embryonic stem cells, 19,514 active enhancers are identified including 49.25% known and 50.75% de novo ones. In human HEK293T cell , 3,0359 active enhancers are identified.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Examination of active enhancers in 2 cell types.

first: Xiusheng

last: Zhu

first: Lei

last: Huang

first: Yubo


title: Trdmt1-KO Group and Control in Zebrafish

city: Yanghzou

first: Songlei

last: Xue

state: Jiangsu

address: Wenhui Road 48#

institute: Yangzhou University

summary: RNA-seq of 6 samples, 3 of them are Ttdmt1 knockout in zebrafish named ZF-TKO and 3 of them are  control group named ZF-Control.

overall_design: Examination 2 conditions, each with 3 replicates and the function of Trdmt1 in zebrsfish.

first: Hengmi

last: Cui


title: Core and auxiliary functions of one-carbon metabolism in Pseudomonas putida exposed by a systems-level analysis of transcriptional and physiological responses

status: Public on Apr 19 2023

city: Kongens Lyngby

first: Oscar

last: Puiggene

address: Kemitorvet 220

department: DTU Biosustain

country: Denmark

institute: Novo Nordisk Foundation Center for Biosustainability

summary: P. putida is equipped with functions related to one-carbon (C1) compounds (e.g. methanol, formaldehyde and formate) oxidation—yet pathways to assimilate these carbon sources are largely absent. In this work, we adopted a systems-level approach to study the genetic and molecular basis of C1 metabolism in P. putida (both in EM42 and a double mutant of the characterized formate dehydrogenases in this organism.

overall_design: We incubated P. putida in different C1 compounds (namely methanol and formate) in three  biological replicates until expontential phase (OD ca.0.5). For formate, we also tested the double formate dehydrogenase mutant. They were compared to the minimal media with glucose solely. We then performed RNA seq data and gene expression profiling analysis.

last: Turlin

first: Stefano

last: Donati

first: Nicolas

last: Wirth

first: Pablo

last: Nikel


title: Repeat tick exposure elicits distinct immune responses in guinea pigs and mice [guinea pig]

city: New Haven

first: Erol

last: Fikrig

address: 300 Cedar Street

country: USA

institute: Yale University School of Medicine

summary: RNA-seq gene expression analysis of guinea pig and mouse skin after tick bites

overall_design: Guinea pigs were exposed to repeat tick infestations. RNA was isolated from skin biopsies 4 days post tick attachment.

first: Fikrig

last: Erol

first: Mehta

last: Sameet


title: Repeat tick exposure elicits distinct immune responses in guinea pigs and mice [mouse]

overall_design: mice were exposed to repeat tick infestations. RNA was isolated from skin biopsies 4 days post tick attachment.


title: Repeat tick exposure elicits distinct immune responses in guinea pigs and mice

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

sample_organism:
Mus musculus
Cavia porcellus

platform_organism:
Mus musculus
Cavia porcellus

overall_design: Refer to individual Series


title: Identification of differentially expressed fecal miRNA in hepatic encephalopathy

city: Hangzhou

first: Yuchong

last: Wang

address: Xiacheng district

country: China

institute: Zhejiang University

summary: To further identify the fecal miRNAs generated in HE, we conducted an miRNA microarray analysis on feces collected from patients with HE and CHB. The microarray analysis of miRNA expression profiles revealed that the abundance of 10 miRNAs was significantly increased in feces from patients with HE, as compared with that from patients with CHB, whereas the abundance of 8 miRNAs was decreased.

overall_design: RNA was isolated from feces of 2 patients with HE and 2 patients with CHB.

first: Hongyan

last: Diao


title: Dissection of a Down syndrome-associated trisomy to separate the gene dosage-dependent and -independent effects of an extra chromosome

city: BUFFALO

first: Eduardo

last: Cortes

address: ELM AND CARLTON STREETS

department: Biostatistics and Bioinformatics

institute: ROSWELL PARK CANCER INSTITUTE

summary: Trisomy is a form of aneuploidy associated with embryonic and postnatal abnormalities in mammals. Understanding the underlying mechanisms involved in mutant phenotypes is broadly important and may lead to new strategies to treat clinical manifestations in individuals with trisomies, such as trisomy 21 (Down syndrome). While increased gene dosage effects due to a trisomy may account for the mutant phenotypes, there is also the possibility that phenotypic consequences of a trisomy can arise because of the presence of a freely segregating extra chromosome with its own centromere, i.e., a ‘free trisomy’ independent of gene dosage effects. Presently, there are no reports of attempts to functionally separate these two types of effects. To fill this gap, here we describe a strategy that employed two new mouse models of Down syndrome, Ts65Dn;Df(17)2Yey/+ and Dp(16)1Yey/Df(16)8Yey. Both models carry triplications of the same 103 human chromosome 21 gene orthologs; however, only Ts65Dn;Df(17)2Yey/+ mice carry a free trisomy. Comparative analysis of these two models revealed the gene dosage-independent effect of an extra chromosome at the phenotypic level for the first time, as reflected by impairments of Ts65Dn;Df(17)2Yey/+ males in T-maze tests when compared with Dp(16)1Yey/Df(16)8Yey males. Results from the transcriptomic analysis suggest the extra chromosome may play a major role in trisomy-associated expression alterations of disomic genes beyond gene dosage effects. This model system can now be used to deepen our mechanistic understanding of this common human aneuploidy and obtain new insights into the effects of free trisomies in other human diseases such as cancers.

overall_design: RNA-seq-based comparative gene expression profiling analysis for the cerebral cortex samples from Ts65Dn;Df(17)2, Dp(16)1/Df(16)8, and +/+ mice at 6 weeks of age

first: Eugene

last: Yu

last: Cortes Gomez


title: Liver transcriptome of GCKR-P446L-EMI-B6N male and female mice

city: Newcastle upon Tyne

first: Loranne

last: Agius

address: Framlington Place

department: Biosciences Institute

country: United Kingdom

institute: Newcastle University

overall_design:
Male mice: N=4 446PP genotype; N=4 446LL genotype;  Female mice n=5 446PP genotype;  n=5 446LL genotype were maintained on standard rodent diet
At age 14-wk; mice were culled and livers harvested for RNA extraction and sequencing

first: Brian

middle: E

last: Ford


title: Short-term effects of overexpression of GK and/or GKRP on the transcriptome in mouse primary hepatocytes

overall_design:
GKRP-deficient hepatocytes from female GCKR-P446L-EMI-B6N mice (n=3: LL; LL; LP) were cultured in monolayer and treated with adenoviral vectors for GK or GKRP(446P or 446L) expression
Sequences for GKRP vectors were Human: BC130481; Mouse: XM_006503883; GK PMID: 8550593.
After 24h-culture in MEM with 5mM glucose, they were incubated for 4h in medium containing 25mM glucose and then harvested for RNA extraction and sequencing


title: hsa-miR-7704 enriched in feces from patients with hepatic encephalopathy aggravates disease by inhibiting the growth and adhesion of Bifidobacterium longum

summary: We established an experimental mouse model of HE using thioacetamide (TAA) and examined the alterations in the gut microbiome.

overall_design: 16S rRNA analysis of gut microbiota in mice with TAA-induced hepatic encephalopathy.

first: Yuyu

last: Li


title: Expression data from human inflammatory breast cancer biopsy samples

city: Boston

first: Aditi

last: Hazra

state: MA

address: 900 Commonwealth Ave

institute: Brigham and Women's Hospital

summary: We used the Human Transcriptome Array 2.0 expression data to examine quality control, reproducibility, and insights on differential gene expression inflammatory breast cancer biopsy specimens prior to systemic treatment.

overall_design: Inflammatory breast cancer biopsy specimens were selected prior to initiating preoperative systemic treatment for RNA extraction and expression profiling using the Human Transcriptome Array 2.0

first: Filipa

last: Lynce