title: ADAR1 controls the miR-381-3p-mediated expression of MRP4 by regulating the production of circHIPK3 in human renal cell

first: Satoru

last: Koyanagi

state: Fukuoka

address: 3-1-1 Maidashi, Higashi-ku

department: Pharmaceutics

institute: Kyushu University

summary: Multidrug resistance-associated protein 4 (MRP4), a member of the C subfamily of ATP-binding cassette transporters, is highly expressed in the kidney of mammals and responsible for renal elimination of various drugs. Adenosine deaminase acting on RNA 1 (ADAR1) has been reported to regulate gene expression through catalyzing adenosine-to-inosine (A-to-I) RNA editing. In this study, we found that the down-regulation of ADAR1 increased the expression of MRP4 in human renal cells at post-transcriptional level. The results of luciferase reporter assays and microarray analysis revealed that down-regulation of ADAR1 decreased the levels of miR-381-3p, which led to the up-regulation of MPR4 expression. Circular RNAs (circRNAs) are a kind of closed loop endogenous non-coding RNAs that play a critical role of gene expression by acting as miRNA sponges. ADAR1 repressed the biogenesis of circular RNA circHIPK3 by catalyzing A-to-I RNA editing, which changed the secondary structure of precursor of circHIPK3. In silico analysis suggested that circHIPK3 acted as a sponge of miR-381-3p. Indeed, overexpression of circHIPK3 up-regulated the expression of MRP4 through interfering with miR-381-3p. Our results provide the novel point of view for regulating mechanism of the expression of xenobiotic transporters through mediating the control of circRNA expression by RNA editing enzyme ADAR1.

overall_design: The down-regulation of ADAR1 induced microRNA expression in human renal proximal tubular epithelial cells were measured. The cells were infected with lentiviral particles expressing shRNA against the human ADAR1 gene (sc-37657-V; Santa Cruz Biotechnology) or empty lentiviral to construct mock-transduced RPTECs for the control.

first: Yuji

last: Omata

first: Maseri

last: Okawa

first: Akito

last: Tsuruta

first: Naoya

last: Matsunaga

first: Shigehiro

last: Ohdo


title: Jurkat T cell exposure to short hypergravity on a ground-based facility

status: Public on Jul 27 2022

city: Zurich

first: Cora

middle: S.

last: Thiel

address: Winterthurerstrasse 190

department: Institute of Anatomy

country: Switzerland

institute: University of Zurich

type: Expression profiling by high throughput sequencing

summary: Jurkat T cells have been lysed after exposure to 3 or 15 minutes of 9g hypergravity in a ground-based pipette centrifuge. The RNA samples were analyzed with RNA-Seq transcriptomics.

overall_design: 1 short hyptergravity condition (12 minutes of 1g + 3 minutes of 9g), 1 long hypergravity condition (15 minutes of 9g), 1 ground control condition (15 minutes of 1g). 4 samples per condition.

first: Christian

last: Vahlensieck

first: Oliver

last: Ullrich


title: Expression data in PAX6 depleted corneal epithelial cells

city: Kyoto

first: Koji

last: Kitazawa

state: Kyoto

address: 465 Kajiicho Kamigyoku

department: Ophthalmology

country: Japan

institute: Kyoto Prefectural University of Medicine

summary: PAX6, a paired box transcription factor, is necessary for eye development. However, how it regulates thecell identity of human corneal epithelial cells (CECs) is not well understood. We aimed to clarify thefunction of PAX6 in human CECs using gene knockout via the clustered regularly interspaced shortpalindromic repeats (CRISPR) and CRISPR associated protein 9 (Cas9) system. We designed guide RNAsfor different targets in PAX6. PAX6-depleted CECs maintained the epithelial morphology, but becamelarger. Global analyses using microarray revealed that down-regulated genes were primarily CEC-specificand included keratin 12, keratin 3, clusterin (CLU), aldehyde dehydrogenase 3 family member A1(ALDH3A1), angiopoietin-like 7 (ANGPTL7) and transketolase (TKT), while up-regulated genes wereprimarily epidermis-related and included keratin 10, keratin 1, involucrin (IVL), filaggrin (FLG). Thesefindings suggest that PAX6 maintains CEC identity by regulating differentiation.

overall_design: Human primary corneal epithelial cells depleted PAX6 with CRISPR/Cas9

first: Masahiro

last: Nakamura


title: ZCCHC4 Interacts with AL133467.2 and gamma H2AX to Promote Chemoresistance in Hepatocellular Carcinoma

city: Shanghai

first: Ha

last: Zhu

address: 800 Xiangyin Road

department: Institute of Immunology

country: China

institute: Second Military Medical University

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

overall_design: Refer to individual Series


title: NFIA determines the cis-effect of genetic variation on adipocyte browning in mice [HiC]

city: Tokyo

first: Yuta

last: Hiraike

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

institute: The University of Tokyo

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Thermogenic brown and beige adipocytes counteract obesity by enhancing energy dissipation via uncoupling proein-1 (Ucp1). However, the effect of genetic variation on these cells, a major source of disease susceptibility, has been less well studied. Here we examined beige adipocytes from obesity-prone C57BL/6J (B6) and obesity-resistant 129X1/SvJ (129) mouse strains and identified a cis-regulatory variant rs47238345 that is responsible for differential Ucp1 expression. The alternative T allele of rs47238345 at the Ucp1 -12kb enhancer in 129 facilitates the allele-specific binding of nuclear factor I-A (NFIA) to mediate allele-specific enhancer-promoter interaction and Ucp1 transcription. We also identified Lim homeobox protein 8 (Lhx8), whose expression is higher in 129 than in B6, as a trans-acting regulator of Ucp1 in mice and humans. These results demonstrate the cis- and trans-acting effects of genetic variation on Ucp1 expression that underlie phenotypic diversity.

overall_design: HiC analysis of beige adipocytes from F1 offspring of obesity prone C57BL/6J and obesity-resistant 129X1/SvJ (129).

first: Shuichi

last: Tsutsumi

first: Satoshi

last: Ota

first: Misato

last: Oguchi

first: Hiroyuki

last: Aburatani

first: Hironori

last: Waki

first: Toshimasa

last: Yamauchi


title: NFIA determines the cis-effect of genetic variation on adipocyte browning in mice [WGS]

overall_design: Whole genome-seq analysis of beige adipocytes from obesity-resistant 129X1/SvJ (129).


title: NFIA determines the cis-effect of genetic variation on adipocyte browning in mice [ChIP-Seq]

overall_design: ChIP-seq analysis of beige adipocytes from F1 offspring of obesity prone C57BL/6J and obesity-resistant 129X1/SvJ (129).


title: Next Generation Sequencing identifies differentially translated genes regulated by PM2.5 exposure in BEAS-2B cells [Ribo-seq]

city: Shenzhen

first: Rihong

last: Zhai

state: Guangdong

address: 1066 Xueyuan Ave.

institute: Shenzhen University School of Medicine

summary: We report the application of Ribosome sequencing for high-throughput profiling of tanslation efficiency in BEAS-2B cells after exposure to PM2.5.

overall_design: Comparison of tanslation efficiency between  BEAS-2B cells exposed to PM2.5  and control cells.

first: Qianqian

last: Chen


title: Unraveling the metabolic mechanisms of pioneer bacteria during the utilization of fresh macroalgae

city: Roscoff

first: Francois

last: Thomas

address: Place George Teissier

department: UMR8227, CNRS-UPMC

country: France

institute: Station Biologique de Roscoff

summary: We cultivated the flavobacterium Zobellia galactanivorans DsijT with fresh brown macroalgae with distinct chemical compositions. Its capacity to use macroalgae as the sole carbon source via the secretion of extracellular enzymes, leading to extensive tissue damages, highlights a sharing pioneer degrader behavior. RNA-seq transcriptome analysis revealed a metabolic shift toward the utilization of brown algal polysaccharides during tissue degradation. A subset of genes was specifically induced in cells grown with intact algae compared to purified polysaccharides. It notably includes genes involved in protection against oxidative burst, type IX secretion system proteins and novel uncharacterized Polysaccharides Utilization Loci (PULs). Comparative growth experiments and genomics between Zobellia members brought out putative genetic determinants of the pioneer behavior of Z. galactanivorans, whose in vitro role could be further characterized. This work constitutes the first investigation of the metabolic mechanisms of bacteria mediating fresh macroalgae breakdown, and will help unravel the role of marine microbes in the fate of macroalgal biomass.

overall_design: RNAseq profiles of Zobellia galactanivorans DsijT when grown with different carbon sources. Profiles of free-living cells were assessed with Laminaria digitata, Fucus serratus, Ascophyllum nodosum, Maltose, Alginate or Fucose-containing sulfated polysaccharides (FCSP) as the sole carbon source. Profiles of algae-attached cells were assessed with Laminaria digitata and Fucus serratus as the sole carbon source. Experiments were done in triplicates for each condition (except for free-living cells with F. serratus and algae-attached cells where n=2). 21 samples in total. Maltose condition was used as a control.

first: François

first: Maéva

last: Brunet


title: Granulocytic myeloid-derived suppressor cells to prevent and treat murine immune-mediated bone marrow failure

city: Bethesda

first: Shouguo

last: Gao

state: MD

address: 9000 Rockville Pike

department: NHLBI

country: USA

institute: National Institutes of Health

summary:
Background and methods: Myeloid-derived suppressor cells (MDSCs) are immature myeloid cells which originate in the bone marrow (BM) and have immunoregulatory functions. MDSCs have been implicated in the pathogenesis of several autoimmune diseases but not in immune aplastic anemia (AA). We examined the roles of granulocytic-MDSCs (G-MDSCs) in murine models of human AA and bone marrow failure (BMF). To perform Totalseq, bone marrow mononuclear cells were FACS sorted to obtain alive cells based on FSC and SSC from five bone marrow failure control mice and five G-MDSC-treated mice, mRNA profiles of single cells were generated and sequenced on an Illumina Novaseq System.
Results: As both prophylaxis and therapy, BM-derived G-MDSCs improved pancytopenia and BM cellularity and decreased BM T cell infiltration in major histocompatibility (MHC)-matched CB10 BMF mice. Single cell RNA sequencing demonstrated that G-MDSCs downregulated cell cycle related pathways in BM infiltrated T cells, consistent with suppression of T cell proliferation by G-MDSCs.
Conclusion: Our results demonstrate that BM-derived G-MDSCs improved pancytopenia and BM cellularity and decreased BM T cell infiltration in major histocompatibility (MHC)-matched CB10 BMF mice, but not in MHC-mismatched CByB6F1 BMF model. Therapeutic efficacy of G-MDSCs are immune context-dependent.
Bone marrow mononuclear cells were FACS sorted to obtain alive cells based on FSC and SSC from five bone marrow failure control mice and five G-MDSC-treated mice.

overall_design: We characterized transcriptomes in different cell populations based on their surface protein markers and marker genes in the bone marrow mononuclear cells from five C.B10 BM failure control mice and five bone marrow failure mice treated with G-MDSCs, and described gene expression of these cells.

first: Xingmin

last: Feng


title: NFIA determines the cis-effect of genetic variation on adipocyte browning in mice [RNA-Seq]

overall_design: RNA-seq analysis of beige adipocytes from obesity prone C57BL/6J (B6), obesity-resistant 129X1/SvJ (129) and F1 offspring.


title: Differentially expressed and translated genes regulated by PM2.5 exposure in BEAS-2B cells


title: ZCCHC4 Interacts with AL133467.2 and gamma H2AX to Promote Chemoresistance in Hepatocellular Carcinoma [HepG2_ZCCHC4 KO OXA]

summary: Purpose: We performed RNA sequencing (RNA-seq) analysis to investigate the role of ZCCHC4 in regulating OXA-induced genes in HepG2 cells. The goal of this study  is to investigate the biological effect of ZCCHC4 in HCC progression and prognosis, and we have found that ZCCHC4 could promote chmoresistance of HCC to DNA damage agents including OXA, we conducted RNA-seq to figure out more clues for deep mechanisms.

overall_design: Wild type cells and ZCCHC4 KO cells are seed into 6 well plate, and then treated with 62.5µM OXA for 12h.  Then cells are subjected for RNA-seq. Each group has two samples.

first: Xuetao

last: Cao


title: ZCCHC4 Interacts with AL133467.2 and gamma H2AX to Promote Chemoresistance in Hepatocellular Carcinoma [HepG2_ZCCHC4 KO]

summary: Purpose: We performed RNA sequencing (RNA-seq) analysis of ZCCHC4 KO1 cells and wild type cells to find differentially expressed genes regulated by ZCCHC4 in HCC cells. The goal of this study is to investigate the biological effect of ZCCHC4 in HCC progression and prognosis.

overall_design: Wild type cells and ZCCHC4 KO cells are seeded into 6 well plate and cultured until 80% confluence, and then subjected for RNA-seq. Each group has two repetitions.


title: ZCCHC4 Interacts with AL133467.2 and gamma H2AX to Promote Chemoresistance in Hepatocellular Carcinoma [UV-CLIP_ZCCHC4]

summary: Purpose: We performed UV-CLIP-seq to investigate the RNAs interacting with ZCCHC4. The goal of this study is to investigate the role of ZCCHC4 in regulating the progression and prognosis of HCC. We have found that ZCCHC4 could inhibit DNA damage agent induced DNA damage and apoptosis of HCC, and promote chemoresistance. We proposed that ZCCHC4 could interact with RNAs to regulate chemoresistance.

overall_design: 2×10^7 HepG2 cells transfected with Flag-tagged ZCCHC4 recombinant vectors were subjected to crosslinking with 0.15J/cm2 of 254nm UV light in a crosslinker HL-2000 (UVP). Cells were harvested and lysed with CLB for 1h at 4℃ to obtain the protein extract. The extract was then treated with RNase T1 (1U/ml) at 22℃ for 15min followed by transferring to ice for 5min. The lysates supplemented with cocktail, PMSF and RNase inhibitor were incubated with anti-Flag M2 Magnetic Beads for 7h at 4℃. The beads were washed with NTEN 900 buffer (1mM EDTA, 0.5%NP40, 20mM Tris-HCl (pH8.0), 900mM NaCl) for once, NTEN 300 buffer (1mM EDTA, 0.5%NP40, 20mM Tris-HCl (pH8.0), 300mM NaCl) for twice. The NTEN buffer mentioned was added with cocktail, PMSF and RNase inhibitor. Then beads were linked with biotin-labeled L3 linker, and separated on a 4–12% NuPAGE gel (Invitrogen). The protein-RNA complexes were transferred to nitrocellulose filter membrane and detected by chemiluminescent kit. The target protein-RNA complexes were cut and digested by Protease K. Finally, RNA was isolated and subjected to high-throughput sequencing using Illumina HiSeq 3000 with SE50 strategy.


title: Single-cell transcriptomic analysis of dermal macrophage from PDGFRa-lineage origin under atopic dermatitis

city: Osaka

first: Yu-Tung

last: Li

address: 2-2 Yamada-oka, Suita

institute: Osaka University

summary: We analyzed dermal macrophage repertoire derived from PDGFRa-lineage or non-PDGFRa-lineage origin in atopic dermatitis (AD) with single-cell RNA sequencing. PDGFRa-lineage tracing mice aged between 7- and 14-week old were used to label cells of PDGFRa-lineage with tdTomato. AD was induced by topic application of MC903 bidaily or tridaily to skin of female mice for six times. Inflamed skin was excised on day 14 and single cells were prepared. Target cells were sorted as single cells for sequencing. We identified multiple subtypes in both PDGFRa-lineage or non-PDGFRa-lineage macrophage and the proportion differed by PDGFRa-lineage origin in AD skin.

overall_design: Transcriptomic profiling of F4/80+ MHCII+ dermal macrophage of different PDGFa-lineage origin from AD skin

first: Yuya

last: Ouchi

first: Tomomi

last: Kitayama


title: Differentially expressed genes in HNRNPC knockdown MHCC97H cells

city: Wuhan

first: Danfei

last: Liu

state: China

address: Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Institute of Liver and Gastrointestinal Diseases, Department of Gastroenterology, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology

department: Department of Gastroenterology

summary: HNRNPC plays an important role in HCC metastasis, HNRNPC knockdown by specific shRNA (HNRNPC-shRNA) significantly inhibited the migration and invasion of MHCC97H cells, while HNRNPC overexpression exerted the opposite effect. To elucidate the mechanisms by which HNRNPC facilitated HCC metastasis, we performed microarray analysis to compare the transcription profiling between the MHCC97H-shcontrol and MHCC97H-shHNRNPC cells.

overall_design: Microarray analysis was performed using 3 independent replicates. MHCC97H shcontrol is control group, MHCC97H shHNRNPC is experimental group


title: Next Generation Sequencing identifies differentially expressed genes regulated by PM2.5 exposure in BEAS-2B cells [RNA-seq]

summary: We report the application of RNA-sequencing for high-throughput profiling of transcriptomes in BEAS-2B cells after exposure to PM2.5 for 24 hours..

overall_design: Comparison of mRNA expression profiles between PM2.5 exposed BEAS-2B cells  and control cells.


title: NFIA determines the cis-effect of genetic variation on adipocyte browning in mice

first: Yuta

last: Hiraike


title: Effects of PDGFRa-lineage leukocyte extravasation to skin in atopic dermatitis

summary: The circulating leukocyte population contains a fraction of cells derived from progenitors that had transient PDGFRa expression during embryonic development (PDGFRa-lineage). During inflammation, extravasated leukocytes in inflamed tissue modify the tissue-resident leukocyte population and crosstalk with the stromal cells. The current study investigates the effects of extravasated leukocytes derived from PDGFRa-lineage origin on the skin in atopic dermatitis (AD). Lineage- bone marrow progenitors were isolated from PDGFRa-lineage labeling mice which labels cells derived from PDGFRa-lineage with tdTomato. Progenitors derived from PDGFRa-lineage or non-PDGFRa-lineage were transplanted to irradiated EGFP-transgenic mice and allowed for bone marrow reconstitution (BMT). AD was then induced by repeated topical application of MC903 for six times. On day 14, RNA was isolated from inflamed skin to construct library for bulk RNA sequencing. AD skin transcriptomes of PDGFRa-lineage and non-PDGFRa-lineage BMTs were compared. In addition, the obtained dataset were paired with flow cytometric measurement of leukocyte extravasation to compare samples with similar extravasation loads. We found via functional enrichment analyses that extravasated PDGFRa-lineage leukocytes possess intrinsic properties that differ from non-PDGFRa-lineage, coordinate stronger inflammatory responses and modulate the extracellular matrix.

overall_design: Transcriptomic profiling of AD skin derived from EGFP-transgenic mice receiving bone marrow progenitor transplantation of controlled PDGFRa-lineage origin

first: Sho

last: Yamazaki

first: Eiichi

last: Takaki


title: Nuclear Deformation Guides Chromatin Reorganization in Cardiac Development and Disease

city: Boulder

first: Eduard

last: Casas

state: Colorado

address: Porter Biosciences, CU Campus

department: MCDB

institute: CU Boulder

summary: The purpose of this study was to understand the how the supression of H3K9me3 impacts the phenotype of cardiac cells. Therefore, we compared the mRNA expression profiles of cardiac cells isolated from H3K9M (inducible histone H3.3 lysine-to-methionine mutant) and H3WT (inducibly expressed wild-type H3.3) cells.

overall_design: Compared mRNA profiles of H3K9M (inducible histone H3.3 lysine-to-methionine mutant (H3K9M)) and H3WT (inducibly expressed wild-type H3.3) cardiac cells cultured on soft PDMS substrates (13kPa).

first: Benjamin

last: Seelbinder

first: Soham

last: Ghosh

first: Stephanie

middle: E

last: Schneider

first: Adrienne

middle: K

last: Scott

first: Alison

middle: R

last: Swearingen

first: Justin

last: Brumbaugh

first: Corey

middle: P

last: Neu


title: Whole-transcriptomic analysis of circRNA-miRNA-mRNA ceRNA network in 4-month APP/PS1 mouse hippocampus

first: Xiong

last: Wang

state: Hubei

address: Jiefang Ave No.1095

department: Department of Laboratory Medicine

institute: Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology

type: Non-coding RNA profiling by high throughput sequencing

summary: Alzheimer’s disease (AD) is a progressive neurodegenerative disorder, and the molecular mechanisms of AD remain unclear. Accumulating evidence indicates the involvement of non-coding RNAs in AD pathogenesis. Here, we applied RNA-seq to explore the expression changes of circRNA, miRNA, and mRNA simultaneously, and investigate competing endogenous RNA (ceRNA) networks in hippocampus of 4-month APP/PS1 and wild-type mice.

overall_design: Three male APP/PS1 (APPswe and PSEN1dE9) transgenic mice and three wild type littermates were used for RNA-seq.


title: Transcriptomic profiling of cultured macrophages derived from bone marrow monocyte subsets

summary: The bone marrow monocyte population contains subsets expressing differing amount of LFA-1 and Mac-1. The current analysis has profiled the macrophages derived from the LFA-1-hi Mac-1-hi subsets (MOhi2) and the LFA-1-lo Mac-1-lo subset (MOlo2). We found the transcriptome profiles of macrophages derived from MOhi2 (Machi2) differed from that of macrophages derived from MOlo2 (Maclo2). Machi2 and Maclo2 expressed different surface receptor markers expression and exhibited different panels of transcription factor activities. Functional enrichment analyses suggested Machi2 specializes in cell cycle related processes whereas  Maclo2 has enriched expression of genes involved in immune responses.


title: Primary cicatricial alopecias are characterized by dysregulation of shared gene expression pathways

city: NYC

first: Isha

last: Monga

state: NY

address: 1300 York Ave

department: Neurology

institute: weill cornell medicine

summary: To investigate the molecular signatures of the different sub-types of Primary cicatricial alopecia (PCA). We performed high-throughput RNA-sequencing on scalp biopsies of PCA patient. We developed gene expression-based signatures, trained into machine-learning based predictive models and pathways associated with dysregulated gene expression. We performed morphological and cytokine analysis to define the immune cell populations found in PCA sub types. Using bulk RNA sequencing, we identified a common PCA gene signature that was shared between LPP, FFA, and CCCA which revealed a significant over-representation of mast cell signature genes, as well as down regulation of cholesterogenic pathways and up regulation of fibrosis and immune cell signaling genes. Thw Immunohistological analyses revealed an increased presence of mast cells in PCAs lesions.

overall_design: high-throughput RNA-sequencing on scalp biopsies of PCA patients to develop gene expression-based signatures

first: Eddy

middle: H

first: Brigitte

middle: N

last: . Sallee

first: James

middle: C

last: Chen

first: Alexa

last: Abdelaziz

first: Rolando

last: Perez-Lorenzo

first: Lindsey

middle: A

last: Bordone

first: Angela

middle: M

last: Christiano


title: Trancriptome profiling of murine overexpression of p65/RelA mutants

city: lille

first: frédéric

last: leprêtre

address: Boulevard du Pr Leclercq

department: CHU of Lille, CBP

institute: Lille University

summary: Effect of overexpression of murine p65/RelA and D361 mutant and resulting fragments in DA1-3B Bcr-Abl+ murine cell lines

overall_design: Comparisons of genes regulated by murine p65/RelA WT gene, non-cleavable D361E mutant and resulting fragments in DA1-3B Bcr-Abl+ murine cell lines

first: Thierry

last: Idziorek


title: Sex-biased and parental allele-specific gene regulation by KDM6A [RNA-seq]

status: Public on Jul 26 2022

city: Riverside

first: Wenxiu

last: Ma

address: 900 University Ave

institute: University of California Riverside

summary: KDM6A, which regulates gene expression by demethylation of the repressive histone mark H3K27me3, has a higher level in mammalian females than in males because the Kdm6a gene escapes X chromosome inactivation. Here, we report that maternal and paternal alleles of a number of genes throughout the genome are differentially regulated by KDM6A. Knockout of KDM6A in male and female embryonic stem cells derived from F1 hybrid mice results in downregulation of maternal alleles more frequently than paternal alleles. This parent-of-origin preference for regulation of gene expression by KDM6A was observed for subsets of maternally expressed non-imprinted and imprinted genes. By ATAC-seq downregulated genes showed a concomitant loss of chromatin accessibility on maternal but not on paternal alleles. Surprisingly, enrichment in H3K27me3 was observed on downregulated paternal but not maternal alleles. These results suggest parent-of-origin mechanisms of gene regulation by KDM6A, which may be histone demethylation-dependent and -independent.

sample_organism: Mus musculus musculus x Mus musculus castaneus

overall_design: Gene expression changes were analyzed in hybrid male and female ES cells following KDM6A CRISPR/cas9 knockout. Male wild type controls were compared to six CRISPR targeted clones, four with CRISPR deletions in an exonic region and two clones with CRISPR deletions at the promoter of Kdm6a. These include cells derived from reciprocal crosses. Female cells include two wt cell lines.

first: J

middle: B

last: Berletch

first: W


title: Sex-biased and parental allele-specific gene regulation by KDM6A

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

platform_organism: Mus musculus musculus x Mus musculus castaneus

overall_design: Refer to individual Series


title: Sex-biased and parental allele-specific gene regulation by KDM6A [ChIP-seq]

overall_design: H3K27me3 occupancy changes were analyzed in male ES cells following KDM6A CRISPR/cas9 knockout. Wild type controls were compared to exonic CRISPR Kdm6a KO cells.


title: Sex-biased and parental allele-specific gene regulation by KDM6A [ATAC-seq]

overall_design: Changes in chromatin accessibility were analyzed in male ES cells following KDM6A CRISPR/cas9 knockout. Wild type controls were compared to exonic CRISPR Kdm6a KO cells.


title: Heart mRNA profiles of TAC 8-weeks  wild type (WT) and miR-27b-3p knockout mice

city: Beijing

first: li

middle: guo

last: qi

state: Chaoyang

address: Anzhen number 2 road

institute: Beijing Institute of Heart Lung and Blood Vessel Diseases

summary:
Aim: The heart undergoes pathological remodelling under increased stress and neuronal imbalance. MicroRNAs (miRNAs) are involved in post-transcriptional regulation of genes in cardiac physiology and pathology. However, the mechanisms underlying miRNA-mediated regulation of pathological cardiac remodelling remain to be studied. This study aims to explore the function of endogenous microRNA-27b-3p (miR-27b-3p) in pathological cardiac remodelling.
Methods and results: We found that miR-27b-3p expression was elevated in heart of patients with cardiac hypertrophy and in transverse aortic constriction (TAC)-induced cardiac hypertrophy mouse model. MiR-27b-3p-knockout mice showed significantly attenuated cardiac hypertrophy, fibrosis, and inflammation induced by two independent pathological cardiac hypertrophy models, TAC and Angiotensin II (Ang II) perfusion. Transcriptome sequencing analysis revealed that miR-27b-3p deletion significantly downregulated TAC-induced cardiac hypertrophy, fibrosis, and inflammatory genes. We identified fibroblast growth factor 1 (FGF1) as a novel miR-27b-3p target gene in the heart, which was upregulated in miR-27b-3p-null mice.
Conclusions: Our study has demonstrated that miR-27b-3p induces pathological cardiac remodelling and suggests that inhibition of endogenous miR-27b-3p or administration of FGF1 might have the potential to suppress cardiac remodelling in a clinical setting.

overall_design: heart mRNA profiles of TAC 8-weeks  wild type (WT) and miR-27b-3p knockout mice

first: Guoqi

last: Li

first: Yihui

last: Shao


title: Transcriptome and Methylome analysis of flowering branches building of Citrus plants induced by light drought (LD) condition

city: Taizhou

first: Bei

last: Huang

state: Zhejiang

address: Daqiao street No.157

institute: Zhejiang citrus research institute

type: Methylation profiling by high throughput sequencing


title: Transcriptome profiling of murine overexpression of p65/RelA mutants III


title: Transcriptome profiling of murine overexpression of p65/RelA mutants II

summary: Effect of overexpression of murine p65/RelA and D361 mutant and resulting fragments in B16 Bcr-Abl+ murine cell lines

overall_design: Comparisons of genes regulated by murine p65/RelA WT gene, non-cleavable D361E mutant and resulting fragments inB16 Bcr-Abl+ murine cell lines


title: Methylome analysis of flowering branches building of Citrus plants induced by light drought (LD) condition [Bisulfite-Seq]

summary:
The changes of golbal DNA methylation level are relative to phenotypes transition of plant, expecially during producetive growth program. Therefore, we detect the grolbal DNA methlation and transcription level of stems after  LD treated and CK group to compare the DNA methylomes difference between CK and LD group.
The increase in DNA methylation level of LD group was correlated with decreased expression of DNA demethylase genes.There was a strong negative correlation between the genes expression level and methylation level of the flowering induction/flower development genes.

overall_design: Globbal DNA methylation comparetive analysis of CK and LD group

last: huang

first: Peng


title: Transcriptome analysis of flowering branches building of Citrus plants induced by light drought (LD) condition [RNA-seq]

summary:
To investigate the cooperation of light drought  with flower branches building and flower bud formation in Citrus, we set two groups including  75 days light drought (LD) and CK to uncover which target genes relatived to flower bud and branches building have been influenced by LD.
We then performed gene expression profiling analysis using data obtained from RNA-seq of two different treatment.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for flowering relative genes and methylation relative genes

last: Wang


title: Exosomal-microRNA transcriptome profiling of mice endothelial cells in response to high phosphorus treatment

city: Changsha

first: Su-Kang

last: Shan

address: 139 Middle Renmin Road

institute: Central South University

summary: Using the highly sensitive miRNA array, we screened 3100 microRNAs abundant in the high phosphorus-treated endothelial cells derived exosome and we explored the functions of these miRNAs.

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus

overall_design: In this study, exosome samples from normal and high concentrations of inorganic phosphate-induced ECs were extracted to acquire the miRNA expression profiling. And the function of the abudant miRNAs were analyzed,which may provide potential therapeutic targets for arterial calcification in ESRD patients.

first: Xiao

last: Lin


title: miR-23a regulates T cellular Redox metabolism in juvenile idiopathic arthritis

city: Aachen

first: Bernd

last: Denecke

state: NRW

address: Pauwelsstrasse 30

department: IZKF Aachen

country: Germany

institute: RWTH Aachen University

summary: Juvenile idiopathic arthritis (JIA) is a chronic rheumatic disease with altered transcriptional signatures at the site of inflammation. mRNA transcription and translation are amongst other epigenetic mechanisms tightly regulated by specific miRNA expression. To determine the roles of different miRNAs within JIA pathogenesis we performed a global miRNA expression analysis in parallel in cells from the arthritic joint and peripheral blood of JIA patients, which demonstrates a different composition of miRNA expression at the site of inflammation. Bioinformatic analysis of predicted miRNA target genes suggests a huge overrepresentation of genes involved in metabolic and oxidative stress pathways in the inflamed joint.  On the cellular level enhanced reactive oxygen species (ROS) and signs of highly activated metabolism in JIA T cells are present. Despite enhanced ROS levels within the local inflammatory milieu, JIA T cells are hyperproliferative and reveal a TNFa dependent overexpression of miR-23a, which is an inhibitor of PPIF, the regulator of mitochondrial ROS escape. TNFa blockade reduces miRNA-23a, rescues PPIF expression and ROS shuttling and thereby inhibits hyperproliferation.  Our data show a novel mechanism of T cell proliferation and metabolism in JIA, which is mediated by miRNA dependent mitochondrial ROS shuttling.

first: Kim

last: Ohl

first: Klaus

last: Tenbrock


title: RNA-Seq and ChIP-Seq gene profiling of retinal ganglion cells in Math5Cre-driven Knockout of Ezh2 and G9a in murine retinal ganglion cells at P0

city: Boston

first: Dong Feng

last: Chen

state: Massachusetts

address: 20 Staniford St

institute: Schepens Eye Research Institute

summary: Epigenetic mark deposition during embryonic development contribute to postnatal homeostasis and tissue stability. Previously, we found out that Ezh2 contributes critically to the function and postnatal cell survival in bipolar cells but not in retinal ganglion cells in the retina. (Yan et al. Postnatal onset of retinal degeneration by loss of embryonic Ezh2 repression of Six1. Sci Report. doi:10.1038/srep33887; (Cheng L, Wong LJ, Yan N, Han RC et al. Ezh2 does not mediate retinal ganglion cell homeostasis or their susceptibility to injury. PLoS One 2018;13(2):e0191853.). In this study, we used RNA-seq to define up- and down regulated genes in both Ezh2 and G9a deficient (Math5Cre; Ezh2f/fG9af/+; dKO) retinal ganglion cells (RGC) to evaluate the hypothesis of Ezh2 and G9a interaction that has been discussed in other tissues but in the retina. ChIP-Seq was applied to evaluate H3K27me3 histone marks in retinal ganglion cells in wild type (WT), Ezh2 (Math5Cre; Ezh2-/-, sKO) and combined G9a-Ezh2 (Math5Cre; G9a+/-Ezh2-/-, dKO) knockout mutant mice at P1.

overall_design: mice pups (Math5Cre+;Ezh2f/fG9a+/- [dKO] or wild type [WT]) were sacrificed at P0 and the retina was harvested immediately. After enzymatic digestion, retinal ganglion cells (RGC) were purified from other retinal cells using magnetic labelling with anti-CD90-antibody which binds specifically to RGC. After elution, samples were immediately proceed to RNA extraction. We collected triplicates for each cell samples. Library was prepared with NEBNext Poly A, Sequencing was done with Mid-Output single read 75 cycles flow cell.

first: Lucy

last: Wong


title: Expression profiling of ethanol-treated and EPZ5676-treated mouse DBA2 SSCs

city: Philadelphia

first: Yemin

last: Lan

state: PA

address: 3400 Civic Center Blvd

institute: University of Pennsylvania

summary: We repport the effect of EPZ5676 (DOT1L inhibiotr) on the transcriptome of cultured mouse DBA2 spermatogonial stem cells (SSCs). SSCs were cultured in the presence of 2 uM EPZ5676 or 0.2% ethanol (control) for 2 weeks. We find a number of differentially expressed genes between control and EPZ5676-treated SSCs.

overall_design: RNA-seq of ethanol-treated and EPZ5676-treated mouse DBA2 SSCs in biological triplicates (NovaSeq 6000)

first: Huijuan

first: Marisa

middle: S

last: Bartolomei

first: Mengcheng

last: Luo

first: Jeremy


title: RNA-binding protein ELAVL4/HuD ameliorates Alzheimer's disease-related molecular changes in human iPSC-derived neurons

city: Nijmegen

first: Geert

last: Poelmans

country: Netherlands

institute: Radboud UMC

summary:
We generated ELAVL4 knockout (KO), overexpression (OE), and rescue human induced pluripotent stem cell-derived neurons to study the effect that ELAVL4 has on AD-related cellular phenotypes.
To gain insight into the molecular cascades involved in neuronal ELAVL4 signaling, we then performed gene expression profiling analysis using data obtained from RNA-seq using triplicate samples for each condition

overall_design: Comparative gene expression analysis of RNA-seq data for ELAVL4 KO, OE, and rescue in induced neurons.

first: Robert

middle: J

last: van der Linden

first: Jacqueline

last: Gerritsen

first: Meichen

last: Liao

first: Joanna

last: Widomska

first: Richard

middle: V

last: Pearse II

first: Forest

last: White

first: Barbara

last: Franke

first: Tracy

middle: L

last: Young-Pearse


title: PKCα RNA-seq in t(4;14) cells

city: Singapore

first: Phyllis

last: Chong

address: 14 Medical Drive #12-01

country: Singapore

institute: Cancer Science Institute of Singapore

summary: Multiple myeloma (MM) cells undergo metabolic reprogramming in response to a hypoxic and nutrient-deprived bone marrow microenvironment. However, it is unclear whether primary oncogenes in recurrent translocations drive metabolic heterogeneity that can present new vulnerabilities for therapeutic targeting. t(4;14) translocation leads to the universal overexpression of histone methyltransferase MMSET II that promotes plasma cell transformation through a global increase in H3K36me2. We identified PKCα as a novel epigenetic target that contributes to the oncogenic potential of MMSET II. RNA-sequencing of t(4;14) cell lines revealed a significant enrichment in the regulation of metabolic processes by PKCα, and the glycolytic gene, hexokinase 2 (HK2), is transcriptionally regulated by PKCα in a PI3K/Akt-dependent manner. Loss of PKCα displaces mitochondria-bound HK2 and reversed sensitivity towards the glycolytic blocker 3-Bromopyruvate. Additionally, we observed a metabolic shift to a less energetic state through the reduction in oxidative and glycolytic fluxes, resulting in an overall decrease in ATP production. We employed metabolomics and lactate emerged as a differential metabolite associated with PKCα. This conferred PKCα with immunomodulatory drug (IMiDs) resistance in a cereblon-independent manner and could be phenocopied by either overexpression of HK2 or direct supplementation of lactate. Altogether, we revealed novel insights into the epigenetic and metabolism crosstalk in MM and the opportunity for therapeutic intervention that leverages on the distinct metabolic program in t(4;14) myeloma.

overall_design: t(4;14) cell lines KMS18 and KMS28BM with stable knockdown of PKCα


title: mRNA expression levels in Jurkat cell lines treated with or without IFN-alpha and with shaking or static

city: Minato-ku

first: Kei

last: Sato

state: Tokyo

address: 4-6-1 Shiroganedai

department: Department of Microbiology and Immunology

institute: The Institute of Medical Science, The University of Tokyo

summary: Throuth RNA sequencing analyses, we report that shaking did not affect transcriptome in Jurkat cells and differential expressed genes by IFN-alpha were detected.

overall_design: mRNA expression profiles in the Jurkat T-cell lines in shaking culture without IFN-alpha (n=3), static culture without IFN-alpha  (n=3), shaking culture with IFN-alph treatment for 24h (n=3) and static culture with IFN-alpha treatment for 24h (n=3) were generated by RNA sequencing. RNA was extracted using RNeasy Mini kit (Qiagen). RNA sequencing was conducted in Medical & Biological Laboratories, co (Nagoya, Japan).

first: Ryuichi

last: Kumata

first: Yusuke

last: Kakizoe

first: Shinji

last: Nakaoka

first: Shingo

last: Iwami


title: Next Generation Sequencing (NGS) Facilitates Quantitative Analysis of Wildtype and Zmynd8-Overexpressing Transcriptomes in E14 Mouse Embryonic Stem Cells (mESCs)

city: Worcester

first: Aimin

last: Yan

state: MA

address: 55 N Lake Ave

institute: University of Massachusetts Medical School

summary: Purpose: The goal of this study is to identify Zmynd8-regulated genes.

overall_design: Expression profiles of parental E14 mESCs, E14 mESCs expressing low exogenous levels of Zmynd8, and E14m ESCs expressing high exogenous leves of Zmynd8 levels were generated by RNA-Seq, in triplicates, using Illumina Nova 6000.

first: William

last: Hardy

first: Michael

last: Green


title: Characterization of long non-coding RNA profile in RD and SH-SY5Y cells infected by CV-B5 using RNA sequencing

city: Kunming

first: Wei

last: Chen

address: No. 727, Southern Jingming Road, Chenggong District

institute: Medical School

summary: The long noncoding RNAs (lncRNAs) act as pivotal factors in regulating and participating in virus-host interactions.Therefore, we used the RNA sequencing to determine the expression profiles of lncRNAs in  Coxsackievirus B5 (CV-B5) infected human rhabdomyosarcoma (RD) cell and SH-SY5Y cell. Our results identified that in the differentially expressed lncRNAs a total of 508 up-regulated and 760 down-regulated lncRNAs in RD cell, with 46.2% were lincRNAs, 28.6% were anti-sense lncRNAs, 24.1% were sense overlapping lncRNAs, and 1.0% were sense intronic lncRNAs. Moreover, 792 lncRNAs were significantly increased and 811 lncRNAs were greatly decreased in SH-SY5Y cell including 48.6% were lincRNAs, 34.7% were anti-sense lncRNAs, 16.0% were sense overlapping lncRNAs, and 0.8% were sense intronic lncRNAs. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway showed that the differentially expressed lncRNAs participated in the occurrence of disease in RD cell and associated with signaling pathway in SH-SY5Y cell after CVB5 infection respectively.Our results reveal that lncRNAs can become a possible novel molecular target for the prevention and treatment of CV-B5 infection, and provided information for distinguishing neurogenic CV-B5 disease.

overall_design: lncRNA expression profiles with CV-B5 infected RD and SHSY-5Y cells

first: PeiYing

last: Teng

first: Heng

last: Yang

first: Jing

last: Li

first: Fan


title: RNA-sequencing analysis gene expression changes in response to ischemia reperfusion and upon manipulation of miR-483-5p in PC12 highly differentiated cells

status: Public on Jul 25 2022

city: shenzhen

first: Qiang

last: Zhang

address: 628 Zhenyuaan Rd.

department: Emergency medicine

institute: The seventh Affiliated Hospital of Sun Yat sen University

summary: The consequences of cardiac arrest are often fatal, including brain injury after resuscitation. It has been reported that few people patients can recover to the neurological state before cardiac arrest. MiRNAs are short non-protein-coding RNA molecules that are evolutionarily conserved and ubiquitously expressed. Numerous pieces of research have reviewed the role of miRNAs in regulating neuronal apoptosis, regeneration, and plasticity of neurons, and inflammatory after cardiac arrest . As the stability of miRNAs in the bloodstream and the function in the regulation of neurological impairment after ischemia-reperfusion injury, microRNAs have been the most potential new biomarkers and therapeutic targets after cardiac arrest to alleviate neurological impairment . In this work, we found that the level of miR-483-5p is correlated to the prognosis of neurological function. To investigate the function of miR-483-5p on neurons after ischemia-reperfusion injury,we established  highly differentiated PC12 cell lines in which miR-483-5p was  overexpressed by  transfection with miR-483-5p mimcis.We then performed gene expression profiling analysis using data obtained from RNA-seq of  PC12 cells in different groups.

overall_design: Highly differentiated PC12 cells were used as the research objects.Comparative gene expression profiling analysis of RNA-seq data for PC12 cells ,PC12 cells after oxygen glucose deprivation/reperfusion treatment and PC12  cells transfected with miR-483-5p mimcis after OGD/R treatment .There are three duplicate samples in each group. The divided experimental groups was as follows: control rep1 ,control rep2,control rep3,OGD/R rep1,OGD/R rep2, OGD/R rep3, OGD/R +miR-483-5p mimcis rep1, OGD/R +miR-483-5p mimcis rep2,OGD/R +miR-483-5p mimcis rep3.

first: Xiaoxing

last: liao


title: RNA-seq analysis of MCF-10A human mammary epithelial cells with NF1 deficiency

city: Grand Rapids

first: Ian

last: Beddows

state: MI

address: 333 Bostwick

institute: Van Andel Institute

summary: RNAseq analysis of NF1 loss of function in immortalized, nontumorigenic human breast epithelial cell line MCF10A.  CRISPR guides targeting exon 21 within the GRD domain were constructed and used either as single or dual-guide RNAs with Cas9 nuclease. We established three cell lines (i.e., g1, g2, g1/2) and NF1 loss was validated by PCR and Western blot analysis (Figure S6B).

overall_design: 15 samples derived from the human MCF10 cell line. The samples are divided into 5 genotypes, each with 3 samples. The genotypes are parental MCF10,  empty vector control, and three NF1 mutants: guide RNA 1, guide RNA 2, and guide RNA 1 and 2.

first: Beddows

last: Ian

first: Graveel

last: Carrie

first: Tovar

last: Elizabeth

first: Steensma

last: Matt


title: Systematic comparison of pancreatic ductal adenocarcinoma models identifies a conserved highly plastic basal cell state

city: New York

first: Simon

last: Joost

address: 1275 York Avenue

department: Cell Biology and Genetics

institute: Memorial Sloan Kettering Cancer Center

summary: Pancreatic ductal adenocarcinoma (PDAC) portends a dire prognosis. Intra-tumoral heterogeneity and cellular plasticity have emerged as hallmarks of cancer, including PDAC. Yet, our understanding of the mechanisms underpinning cellular diversity in PDAC remains limited. Here, we investigate cellular heterogeneity of PDAC cancer cells across a range of in vitro and in vivo growth conditions using single-cell genomics. We find heterogeneity contracts significantly in 2D and 3D cell culture models but becomes restored upon orthotopic transplantation. Orthotopic transplants reproducibly acquire cell states identified in autochthonous PDAC tumors, including a basal state exhibiting co-expression and co-accessibility of epithelial and mesenchymal genes. Using linage-tracing combined with single-cell transcriptomics, we demonstrate basal cells display high plasticity in situ. This work defines the impact of cellular growth conditions on phenotypic diversity and uncovers a highly plastic cell state with the capacity to facilitate state transitions and promote intra-tumoral heterogeneity in PDAC.

overall_design: Single-cell RNA-sequencing data of pancreatic ductal adenocarcinoma was generated on the 10X Chromium platform from either autochthonous  KPCT mice or from orthotopic pancreas transplants. Autochthonous KPCT mice were generated by crossing previously published KrasLSL-G12D/+ , Trp53flox/flox , Pdx1-Cre, and Rosa26LSL-tdTomato mice. For Lgr5 co-expression studies, the KPCT mice above were crossed with Lgr5GFP-IRES-CreER/+ reporter mice. To generate various orthotopic PDAC transplant models we have implanted into pancreas of NSG recipient mice either: ~3mm PDAC fragments generated from KPCT primary tumors; or  tumor cells derived from KPCT primary PDAC tumors.

first: Ken

last: Pitter

first: Olivera

last: Grbovic-Huezo

first: Tuomas

last: Tammela


title: The dural innate immune barrier protects the CNS from systemic virus invasion [CD45_10X]

city: Daejeon

first: Ji Hoon

last: Ahn

address: 291 Daehak-ro, Yuseong-gu

country: South Korea

institute: Institute for Basic Science

summary: To investigate cellular landscape of dural immune cells, dural immune cells from 30 P28 male mice and 30 P7 male mice were FACS sorted and single-cell RNA seqs were performed

overall_design: CD45+ immune cells from 30 P28 male mice and 30 P7 male mice were sorted and single-cell libraries were made

first: Gou

middle: Y

last: Koh

first: Ji

first: Young-Chan

last: Kim

first: Myung

first: Seon

last: Hong


title: The dural innate immune barrier protects the CNS from systemic virus invasion

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

overall_design: Refer to individual Series


title: The dural innate immune barrier protects the CNS from systemic virus invasion [MHCII_10X]

summary: To investigate heterogeneity of MHCII high CNS border-associated mononuclear phagocytes (BAMPs), MHCII high BAMPs from 30 adult male mice were FACS sorted and single-cell RNA seqs were performed

overall_design: MHCII high CNS BAMPs from 30 adult male mice were sorted and single-cell libraries were made

last: Yang


title: miR-181 regulates colonic inflammation

first: Monica

last: Jimenez

address: 3800 Spruce Street

summary: The intestinal epithelium is a key physical interface that integrates dietary and microbial signals to regulate nutrient uptake and mucosal homeostasis. Intestinal epithelial cells (IECs) have a high turnover rate driven by the death of terminally differentiated cells with concurrent stem cell proliferation, a process critical for maintaining intestinal homeostasis and protecting against mucosal inflammation. The transcriptional programs that regulate IEC quiescence, proliferation, and differentiation have been well-characterized. However, how gene expression networks critical for IEC functions are regulated at the post-transcriptional level during homeostasis or inflammatory disease remains poorly understood. Herein, we show that a conserved family of microRNAs, miR-181, is significantly downregulated in IECs from patients with inflammatory bowel disease and mice with chemical-induced colitis. Strikingly, we showed that miR-181 expression within IECs, but not the hematopoietic system, is required for protection against the development of severe colonic inflammation in response to epithelial injury in mice. Mechanistically, we showed that miR-181 expression increases the proliferative capacity of IECs, likely through the regulation of Wnt signaling, independently of gut microbiota composition. As epithelial reconstitution is crucial for restoring intestinal homeostasis after injury, the miR-181 family represents a potential novel therapeutic target in IECs for protection against severe intestinal inflammation.

overall_design: Percoll-enriched colonic epithelial cells from baseline or DSS-treated WT and miR-181a1-b1; miR-181a2-b2 double KO mice

middle: T


title: Human 5-lipoxygenase regulates transcription by association to euchromatin

city: Frankfurt am Main

first: Marius

last: Kreiss

address: Max-von-Laue-Str. 9

department: Pharmaceutical Chemistry

institute: Goethe-University


title: HDAC1 and PRC2 mediate combinatorial control in SPI1/PU.1-dependent gene repression in murine erythroleukaemia [763_4C-seq]

city: VILLEJUIF

first: Christel

last: GUILLOUF

address: 114 rue Edouard vaillant

institute: Gustave Roussy

summary: Although originally described as transcriptional activator, SPI1/PU.1, a major player in haematopoiesis whose alterations are associated with haematological malignancies, has the ability to repress transcription. Here, we investigated the mechanisms underlying gene repression in the erythroid lineage, in which SPI1 exerts an oncogenic function by blocking differentiation. We show that SPI1 represses genes by binding active enhancers that are located in intergenic or gene body regions. HDAC1 acts as a cooperative mediator of SPI1-induced transcriptional repression by deacetylating SPI1-bound enhancers in a subset of genes, including those involved in erythroid differentiation. Enhancer deacetylation impacts on promoter acetylation, chromatin accessibility and RNA pol II occupancy. In addition to the activities of HDAC1, polycomb repressive complex 2 (PRC2) reinforces gene repression by depositing H3K27me3 at promoter sequences when SPI1 is located at enhancer sequences. Moreover, our study identified a synergistic relationship between PRC2 and HDAC1 complexes in mediating the transcriptional repression activity of SPI1, ultimately inducing synergistic adverse effects on leukaemic cell survival. Our results highlight the importance of the mechanism underlying transcriptional repression in leukemic cells, involving complex functional connections between SPI1 and the epigenetic regulators PRC2 and HDAC1.

overall_design: 3D genomic interactions of Alas2_enhancer and St3gal6_TSS in TgSpi1 erythroleukemic cells overexpressing SPI1 or not (dox inducible shRNA anti-Spi1).

first: Sebastian

last: Gregoricchio

first: Lélia

last: Polit

first: Michela

last: Esposito

first: Jérémy

last: Berthelet

first: M'Boyba

last: Diop

first: Laure

last: Delestré

first: Emilie

last: Evanno

first: Isabelle

last: Gallais

first: Hanna

last: Aleth

first: Mathilde

last: Poplineau

first: Wilbert

last: Zwart

first: Frank

last: Rosenbauer

first: Fernando

last: Rodrigues-Lima

first: Estelle

last: Duprez

first: Valentina

last: Boeva

last: Guillouf


title: Decoding YAP dependent transcription in the liver [HepG2_RNASeq]

city: milano

first: stefano

last: campaner

address: via adamello 16

department: Center for Genomic Science

country: Italy

institute: fondazione Istituto italiano di tecnologia

summary: In this study we aimed to address how YAP elicits profound biological changes in murine liver, such as proliferation, regeneration and dedifferentiation. We demonstrated that YAP is a master regulatori of liver functions, that reshapes the enhancer landscape  to control transcription of genes involved in metabolism, proliferation and inflammation.

overall_design: In total 5 conditions from HEPG2 pSLIKK YAPs127a cells were analyzed in triplicate:not treated (NT) and YAPS127A induced cells for 48h (48h_doxy); control (siCTRL) and two different HNF4a siRNA (siNHF4a_1/2)

first: Stefano

last: Campaner

first: Francesca

last: Biagioni

first: Ottavio

last: Croci


title: Transcriptome analysis of wildtype elmo3+/+ and homozygous elmo3-/- knockout zebrafish larvae at 120 hpf through next generation RNA sequencing [dataset 3]

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

department: ZMF

institute: University Heidelberg

summary: Elmo3 is one member of the Elmo protein family. In our study we addressed the question if the functions of Elmo1, Elmo2 and Elmo3 ware consistent or if they differ. With the CRISPR/Cas9 system we generated single knockout mutants of elmo1, elmo2 and elmo3 in the zebrafish. To assess the impact of the loss of one of the proteins on the transcriptome of a developing organism, we did RNA sequencing and transcriptome analysis with elmo1+/+ and elmo1-/-, elmo2+/+ and elmo2-/- and elmo3+/+ and elmo3-/- zebrafish larvae at 120 hours post fertilization. Here we provide the sequencing data of elmo3+/+ and elmo3-/-.

overall_design: Total RNA profiles of wildtype and homozygous elmo3 knockout zebrafish larvae samples

first: Mike

last: Boger

first: Jens

last: Kroll


title: Human 5-lipoxygenase regulates transcription by association to euchromatin [ChIP-seq]

first: Marius

last: Kreiss

summary: Human 5-lipoxygenase (5-LO) is the key enzyme of leukotriene biosynthesis,  mostly expressed in leukocytes and thus a crucial component of the innate  immune system.   In this study, we show that 5-LO, beside its canonical function as a  metabolizing enzyme, is also a regulator of gene expression in the monocytic  cell line Mono Mac 6 (MM6). Using RNA-Seq, we identified 5-LO regulated  genes which could be clustered to several biological functions, e.g.  immune/defense response, cell adhesion, transcription and  growth/developmental processes. Thereby, the majority of genes were  upregulated by 5-LO KO. By conducting a ChIP-Seq analysis,  we proved an  association of 5-LO to DNA.   In summary, we demonstrate an additional noncanonical function of 5-LO as a  direct transcriptional regulator in MM6 cells that presumably regulates  specific genes in dependence on histone acetylation.

overall_design: Three independent repeats of ChIP-Seq from MonoMac 6 cells (MM6) after 72h treatment with  TGF-β/1,25(OH)2D3 and with or without 2h LPS stimulation, using antibody against 5-Lipoxygenase (5-LO).

first: Oberlis

last: Julia

first: Sabine

last: Seuter

first: Iris

last: Bischoff-Kont

first: Duran

last: Sürün

first: Dominique

last: Thomas

first: Tamara

last: Göbel

first: Tobias

last: Schmid

first: Robert

last: Fürst

first: Ann-Kathrin

last: Haefner

first: Dieter

last: Steinhilber


title: Transcriptome analysis of WT and homozygous elmo knockout zebrafish larvae at 120 hpf through next generation RNA sequencing


title: The dural innate immune barrier protects the CNS from systemic virus invasion [EC_10X]

first: Ji Hoon

last: Ahn

summary: To investigate heterogeneity of CNS border vasculatures, endothelial cells (EC) from 30 adult male mice were FACS sorted and single-cell RNA seqs were performed

overall_design: CNS border ECs from 30 adult male mice were sorted and single-cell libraries were made

first: Gou

last: Koh

first: Ji

first: Young-Chan

last: Kim

first: Myung

last: Yang

first: Seon

last: Hong


title: Effect of CD33 and/or CD123 KO in the NPM1-mutated AML cell line OCI-AML3

city: Perugia

first: Vincenzo

last: Perriello

address: Piazzale Menghini 8/9

department: Department of Medicine

institute: University of Perugia

summary: To reveal which pathways linked to CD33 and CD123 overexpression could be involved in leukemic proliferation, we performed unbiased bulk RNA sequencing comparison between OCI-AML3 wt and CD123 and or CD33 KO clones

overall_design: Statistically significant DEGs (adjusted p-value<0.05 and absolute log Fold Change (logFC) > 1.5) were identified for each comparison (OCI-AML3 wt vs -CD33KO, vs -CD123KO and vs -CD33/123KO) using edgeR R studio package.

first: Valentina

last: Tini

first: Marcella

last: Sabino

first: Sarah

last: Tettamanti


title: Transcriptome analysis of wildtype elmo2+/+ and homozygous elmo2-/- knockout zebrafish larvae at 120 hpf through next generation RNA sequencing [dataset 2]

first: Carsten

last: Sticht

summary: Elmo2 is one member of the Elmo protein family. In our study we addressed the question if the functions of Elmo1, Elmo2 and Elmo3 are consistent or if they differ. With the CRISPR/Cas9 system we generated single knockout mutants of elmo1, elmo2 and elmo3 in the zebrafish. To assess the impact of the loss of one of the proteins on the transcriptome of a developing organism, we did RNA sequencing and transcriptome analysis with elmo1+/+ and elmo1-/-, elmo2+/+ and elmo2-/- and elmo3+/+ and elmo3-/- zebrafish larvae at 120 hours post fertilization. Here we provide the sequencing data of elmo2+/+ and elmo2-/-.

overall_design: Total RNA profiles of wildtype and homozygous elmo2 knockout zebrafish larvae samples

first: Mike

last: Boger

first: Jens

last: Kroll


title: HDAC1 and PRC2 mediate combinatorial control in SPI1/PU.1-dependent gene repression in murine erythroleukaemia [722_4C-seq]

first: Christel

last: GUILLOUF

first: Sebastian

last: Gregoricchio

first: Lélia

last: Polit

first: Michela

last: Esposito

first: Jérémy

last: Berthelet

first: M'Boyba

last: Diop

first: Laure

last: Delestré

first: Emilie

last: Evanno

first: Isabelle

last: Gallais

first: Hanna

last: Aleth

first: Mathilde

last: Poplineau

first: Wilbert

last: Zwart

first: Frank

last: Rosenbauer

first: Fernando

last: Rodrigues-Lima

first: Estelle

last: Duprez

last: Boeva

last: Guillouf


title: Transcriptome analysis of wildtype elmo1+/+ and homozygous elmo1-/- knockout zebrafish larvae at 120 hpf through next generation RNA sequencing [dataset 1]

first: Carsten

last: Sticht

summary: Elmo1 is one member of the Elmo protein family. In our study we addressed the question if the functions of Elmo1, Elmo2 and Elmo3 are consistent or if they differ. With the CRISPR/Cas9 system we generated single knockout mutants of elmo1, elmo2 and elmo3 in the zebrafish. To assess the impact of the loss of one of the proteins on the transcriptome of a developing organism, we did RNA sequencing and transcriptome analysis with elmo1+/+ and elmo1-/-, elmo2+/+ and elmo2-/- and elmo3+/+ and elmo3-/- zebrafish larvae at 120 hours post fertilization. Here we provide the sequencing data of elmo1+/+ and elmo1-/-.

overall_design: Total RNA profiles of wildtype and homozygous elmo1 knockout zebrafish larvae samples

first: Mike

last: Boger

last: Kroll


title: Investigating the role of cholesterol in regulation of expression using RNA-seq and ATAC-seq

city: Bristol

first: Alexander

last: Moorhouse

address: Biomedical Sciences Building, University Walk,

department: Cell and Molecular Medicine

country: United Kingdom

institute: University of Bristol

summary: Our work demonstrates that nuclear cholesterol plays a direct role in transcriptional regulation through its interaction with BASP1.

overall_design: Investigating the role of BASP1 and its interaction with cholesterol in transcriptional regulation and chromatin reorganisation using high-throughput sequencing assays for differential gene expression and chromatin accessibility. Experiments were performed in triplicate from culture replicates for K562 cells, K562 cells expressing wild type BASP1 and K562 cells expressing the BASP1 mutant BASP1-G2A.

first: Stefan

middle: G

last: Roberts


title: Human 5-lipoxygenase regulates transcription by association to euchromatin [FAIRE-seq]

first: Marius

last: Kreiss

overall_design: Three independent replicates of Formaldehyde Assisted Isolation of Regulatory Elemens (FAIRE)-Seq from MonoMac 6 cells (MM6) with and without 5-Lipoxygenase knockout after 72h treatment with  TGF-β/1,25(OH)2D3 and with or without 2h LPS stimulation.

first: Oberlis

last: Julia

first: Sabine

last: Seuter

first: Iris

last: Bischoff-Kont

first: Duran

last: Sürün

first: Dominique

last: Thomas

first: Tamara

last: Göbel

first: Tobias

last: Schmid

first: Robert

last: Fürst

first: Ann-Kathrin

last: Haefner

first: Dieter

last: Steinhilber


title: Human 5-lipoxygenase regulates transcription by association to euchromatin [RNA-seq]

overall_design: Total RNA profiling of three independent replicates of MonoMac 6 wildtype (WT), 5-lipoxygenase knockout (5-LO KO) and 5-Lipoxygenase knockin (5-LO KI) cells with two single cell clones each with and without TGF-β/1,25(OH)2D3 differentiation and LPS stimulation.


title: TRIM37 augments AP-2γ transcriptional activity and cellular localization via K63-linked polyubiquitination to drive breast cancer progression [RNA-seq]

city: Macau

first: Edwin

middle: Chong Wing

last: CHEUNG

state: Macau

address: Avenida da Universidade, Taipa

department: Faculty of Health Sciences

institute: University of Macau

summary: Using a proteomics approach, we identified the Tripartite Motif Containing 37 (TRIM37) as a novel transcriptional coactivator of AP-2γ. We demonstrate TRIM37 facilitates AP-2γ chromatin binding to regulate the AP-2γ mediated transcriptional program directly. We provide evidence that TRIM37 achieves this by stimulating K63-chain-linked polyubiquitination of AP-2γ, promoting protein localization from the cytoplasm to the nucleus. In clinical analyses, we find TRIM37 is upregulated in multiple breast cancer datasets, supporting our findings that TRIM37-AP-2γ interaction is essential for breast cancer tumor growth. Overall, our work revealed that TRIM37 is an oncogenic coactivator of AP-2γ in breast cancer and provides a novel therapeutic target for treating the disease.

overall_design: RNA-seq following TRIM37 or AP-2γ knockdown in MCF-7 cells

last: Cheung

first: Guimei

last: Cui

first: Nitin

last: Narwade


title: RNA binding protein RBMS3 is a common effector of EMT program that promotes Triple-Negative Breast Cancer Progression by Regulation of PRRX1 mRNA Stability

city: Detroit

first: Guojun

last: Wu

address: 4100 John R

department: Oncology

institute: Karmanos Cancer Institute

summary: The epithelial-to-mesenchymal transition (EMT) has been recognized as a driving force for tumor progression in breast cancer. Recently, our group identified the RNA Binding Motif Single Stranded Interacting Protein 3 (RBMS3) to be significantly associated with an EMT transcriptional program in breast cancer. Additional expression profiling demonstrated that RBMS3 was consistently upregulated by multiple EMT transcription factors and correlated with mesenchymal gene expression in breast cancer cell lines. Functionally, RBMS3 was sufficient to induce EMT in two immortalized mammary epithelial cell line. In triple-negative breast cancer (TNBC) models, RBMS3 was necessary for maintaining the mesenchymal phenotype and invasion and migration in vitro. Loss of RBMS3 significantly impaired both tumor progression and spontaneous metastasis in vivo. Using a genome-wide approach to interrogate mRNA stability, we found that ectopic expression of RBMS3 upregulates many genes that are resistant to degradation following transcriptional blockade by actinomycin D. Specifically, RBMS3 was shown to interact with the mRNA of EMT transcription factor PRRX1 and promote PRRX1 mRNA stability. PRRX1 is required for RBMS3-mediated EMT and is partially sufficient to rescue the effect of RBMS3 knockdown in TNBC cell lines. Together, this study identifies RBMS3 as a novel and common effector of EMT, which could be a promising therapeutic target for triple-negative breast cancer treatment.

overall_design: RBMS3 is a protein that binds to RNA and contributes to RNA stability. However, what genes stability are controlled by RBMS3 remains unknown. The treatment of Actinomycin D (ACTD) is expected to result in RNA degradation. We treated the HMLE/LacZ (control/reference) and HMLE/RBMS3 (over-expression) cell models with ACTD at four different time points (0, 90, 180 and 360 minutes), three replicates for each, and tried to identify the genes whose stability is controlled by RBMS3.

first: C

last: Block

first: Allison

last: Mitchell

first: Ling

first: James

last: Glassbrook

first: Douglas

last: Craig

first: Wei

last: Chen

first: Gregory

last: Dyson

first: Donald

last: DeGracia

first: Lisa

last: Polin

first: Manohar

last: Ratnam

first: Heather

last: Gibson


title: Transcriptional signatures of bone marrow mononuclear cell-mediated resolution of synovitis

city: Lexington

first: Shavahn

last: Loux

state: KY

address: 1400 Nicholasville

department: Veterinary Science

institute: University of Kentucky

summary: synovial macrophages through joint injection with bone marrow mononuclear cells (BMNC) induces lasting synovial inflammation  resolution. To uncover mechanisms by which BMNC may affect resolution, in this study, differential transcriptional signatures of  BMNC in response to normal (SF) and inflamed synovial fluid (ISF) were analyzed. We demonstrate the temporal behavior of  co-expressed gene networks associated with traits from our previous in vivo and in vitro studies. We also identified activated  and inhibited signaling pathways and upstream regulators, further determining their protein expression in the synovium of  inflamed joints treated with BMNC or DPBS controls. BMNC responded to ISF with an early pro-inflammatory response  characterized by a short spike in the expression of a NF-ƙB- and mitogen-related gene network. This response was associated  with sustained increased expression of another gene network comprising known drivers of resolution (IL-10, IGF-1, PPARG,  isoprenoid biosynthesis). This network was common to SF and ISF, but more highly expressed in ISF and. Similarly, most highly  activated pathways in ISF included the super pathway of cholesterol biosynthesis and PPAR‐γ signaling, with pro‐resolving functional  annotations that improve mitochondrial metabolism and deactivate NF-ƙB signaling. Higher expression of the PPAR‐γ c0‐activator  1-ɑ in synovium from inflamed joints treated with BMNC, and equivalent IL‐1β staining between BMNC‐ and DPBS‐treated joints,  emphasize the intricate balance of pro- and anti-inflammatory mechanisms required for resolution. Combined, our data suggest  that BMNC-mediated resolution is characterized by constitutively expressed homeostatic mechanisms, whose expression are  enhanced following tissue damage. These mechanisms translate into macrophage proliferation optimizing their capacity to  counteract inflammatory damage and improving their general and mitochondrial metabolism to endure oxidative stress while  driving tissue repair. Such effect is largely achieved through the synthesis of several lipids that mediate recovery of homeostasis.  Our study reveals candidate mechanisms by which BMNC provide lasting improvement in patients with OA and suggests further  investigation on the effects of PPAR‐γ signaling enhancement for the treatment of arthritic conditions.

overall_design:
Samples used in the current report were obtained from two previous studies using the same horses. These in vitro (Menarim et al, FASEB J, 2020) and in vivo (Menarim et al, FASEB J, 2021) studies were counterparts of a larger project assessing the effects of BMNC on joint inflammation resolution. Briefly, eight skeletally mature Thoroughbred horses (3-9 years old, median 5 years; 2 females and 6 castrated males) free of OA or systemic inflammation were used under IACUC approval and oversight. General and musculoskeletal health were confirmed by clinical, hematological and orthopedic evaluations. Following sternal bone marrow aspiration for BMNC isolation, synovitis was induced in both radiocarpal joints, as a way of producing more homogeneous inflammation and inflamed synovial fluid (ISF)  than could be acquired from naturally occurring OA. Normal synovial fluid (SF) was collected from healthy middle carpal joints. BMNC from each horse were cultured independently (not pooled) in neat (100%) autologous SF or ISF and harvested at 0 (uncultured), 48 and 96 hours, and 6 and 10 days for RNA isolation. RNA-seq was used to identify transcriptional signatures of BMNC in response to acute joint inflammation. The transcriptome of BMNC was assessed over time within the same group (SF or ISF), as well as comparatively between groups at each time point (Figure 1). The expression of 7 potential upstream regulator genes identified following bioinformatical analysis was assessed by immunohistochemistry in the synovium of inflamed joints from the same horses, 6 days after treatment with BMNC or Dulbecco’s phosphate buffered saline (DPBS).
There are 4 supplementary files and there will be a 5th after reanalysis.

first: Bruno

last: Menarim

first: Hossam

last: El-Sheikh Ali

first: Shavan

first: Kirsten

last: Scoggin

first: Ted

last: Kalbfleisch

last: MacLeod

first: Linda

last: Dahlgren


title: TRIM37 augments AP-2γ transcriptional activity and cellular localization via K63-linked polyubiquitination to drive breast cancer progression [ChIP-seq]

first: Edwin

last: CHEUNG

overall_design: ChIP-seq for TRIM37 and AP-2γ in MCF-7 cells

last: Cheung

first: Guimei

last: Cui

first: Nitin

last: Narwade


title: Constitutive expression of JASMONATE RESISTANT 1 elevates content of several jasmonates and primes Arabidopsis thaliana to better withstand drought

city: Bonn

first: Ute

middle: C.

last: Vothknecht

address: Kirschallee 1

department: IZMB

institute: University of Bonn

summary:
Purpose: In this study we investigated the role of JASMONATE RESISTANT 1 (JAR1) and JAR1 mediated JA-Ile formation in drought stress tolerance in Arabidopsis thaliana.
Methods:  Global transcriptional changes in  a newly generated over-expression line (JAR1-OE; 35S::JAR1-1-YFP)),  a T-DNA insertion line in the JAR1 locus (jar1-11;SALK_034543), and wild-type Col-0 were investigated by RNA-seq analyses of rosette leaves from 32 day-old plant that were either well-watered (control) or not watered after day 18 (drought). Plants were grown on soil under long-day conditions
Results: Under control conditions, using a stringent cut-off (DESeq, adjusted to FDR < 0.01 and LogFC ≥ 1), we found only four differentially expressed genes (DEGs) between jar1-11 and Col-0,  all of them  downregulated. By contrast, we found 339 DEGs between JAR1-OE and Col-0, of which 134 were downregulated and 205 were upregulated. A comparison of the RNA-seq data from Col-0 between control and drought conditions revealed 3401 DEGs, of which 2023 were down- and 1378 upregulated. By comparison, jar1-11 plants, which were most heavily affected by drought stress, showed a much higher number (6139 in total; 2616 up- and 3523 down-regulated) of DEGs, while the more drought-tolerant JAR1-OE line displayed a lower number (2025 in total; 971 up- and 1054 down-regulated) of DEGs.  2411 DEGs were found between Col-0 and jar1-11 under drought  among which 966 genes showed a higher and 1445 genes a lower expression level in jar1-11. On the other hand, out of 998 DEGs found between Col-0 and JAR1-OE under drought, 737 genes showed a higher and 261 genes a lower expression level in JAR1-OE. Moreover, we found 391 DEGs counter-regulated between jar1-11 and JAR1-OE.
Conclusion:RNA-seq analysis and additional experiments of plants under control and drought stress conditions provided insight into the molecular reprogramming caused by the alteration in JA-Ile content.

overall_design: Rosette leaf samples from 32 days old wild-type (Col-0), jar1-11 and JAR1-OE plants grown under well-watered (control) and drough conditions (14 days of water withholding).

first: Sakil

last: Mahmud

first: Annika

last: Kortz

first: Peng

last: Yu


title: HDAC1 and PRC2 mediate combinatorial control in SPI1/PU.1-dependent gene repression in murine erythroleukaemia [722_ChIP-seq]

first: Christel

last: GUILLOUF

overall_design: Genome-wide maps of H3K4me1 and H3K27ac in TgSpi1 erythroleukemic cells (#722) overexpressing SPI1 or not (dox inducible shRNA anti-Spi1).

first: Sebastian

last: Gregoricchio

first: Lélia

last: Polit

first: Michela

last: Esposito

first: Jérémy

last: Berthelet

first: M'Boyba

last: Diop

first: Laure

last: Delestré

first: Emilie

last: Evanno

first: Isabelle

last: Gallais

first: Hanna

last: Aleth

first: Mathilde

last: Poplineau

first: Wilbert

last: Zwart

first: Frank

last: Rosenbauer

first: Fernando

last: Rodrigues-Lima

first: Estelle

last: Duprez

first: Valentina

last: Boeva

last: Guillouf


title: TRIM37 augments AP-2γ transcriptional activity and cellular localization via K63-linked polyubiquitination to drive breast cancer progression.

first: Edwin

last: CHEUNG

overall_design: Refer to individual Series


title: HDAC1 and PRC2 mediate combinatorial control in SPI1/PU.1-dependent gene repression in murine erythroleukaemia [763_ChIP-seq]

first: Christel

last: GUILLOUF

overall_design:
Genome-wide maps of SPI1, RNApolII and H3K4me1, H3K27ac, H3K27me3 in TgSpi1 erythroleukemic cells (#763) overexpressing SPI1 or not (dox inducible shRNA anti-Spi1) or treated with Entinostat or DMSO.
Please note that the *rep1-2.bed/bw data is linked to the corresponding *rep1 sample records.

last: Gregoricchio


title: HDAC1 and PRC2 mediate combinatorial control in SPI1/PU.1-dependent gene repression in murine erythroleukaemia [763_ATAC-seq]

overall_design: Chromatin accessibility  in TgSpi1 erythroleukemic cells (#763) overexpressing SPI1 or not (54h-dox inducible shanti-Spi1)

first: Sebastian

last: Polit

last: Esposito


title: HDAC1 and PRC2 mediate combinatorial control in SPI1/PU.1-dependent gene repression in murine erythroleukaemia [722_RNA-seq]

overall_design: Whole transcriptome of blasts in TgSpi1 erythroleukemic cells (#722) overexpressing SPI1 or not (dox-inducible shRNA anti-Spi1).

first: Lélia

last: Berthelet

last: Diop


title: Colorectal cancer lncRNA/mRNA expression

city: SHENYANG

first: ZHIDONG

last: YANG

state: LIAONING

address: 155, nanjingbei str.

institute: The First Affiliated Hospital of China Medical University

summary: CapitalBio Technology Human LncRNA Array v4, 4x180K was used to detect lncRNA expression in CRC tissues compared with their matched non-tumoral tissues. Here we report significantly up-regulated as well as down-regulated lncRNAs in CRC tissues compared with their matched non-tumoral tissues.

overall_design: Examination of LncRNA/mRNA Expression difference between 5 pairs of colorectal tumor tissues and normal tissues

first: S

last: Juanjuan

first: C

last: Chen


title: Human perilymph miRNA

city: Kansas City

first: Hinrich

last: Staecker

state: KS

address: Rainbow Blvd.

department: Otolaryngology Head and Neck Surgery

institute: University of Kansas School of Medicine

summary: Human inner ear perilymph was sampled during cochlear implantation or stapes surgery

overall_design: Analysis of miRNA expression in perilymph.


title: HDAC1 and PRC2 mediate combinatorial control in SPI1/PU.1-dependent gene repression in murine erythroleukaemia [763_CUT&Tag]

overall_design: HDAC1 chromatin occupancy in TgSpi1 pre-leukemic erythroid cells (#763) by CUT&Tag

first: Michela

first: Jérémy

first: M'Boyba

first: Laure

last: Delestré

first: Emilie

last: Evanno

last: Gallais

last: Aleth

last: Poplineau

last: Zwart


title: Genome-wide mRNA expression analyses of liver cells upon YAP induction (time series; Liver_RNAseq_LSL)

first: stefano

last: campaner

summary:
YAP1 is a transcriptional co-activator regulated by the Hippo pathway, mechano-transduction, G-protein coupled receptors and WNT signaling. YAP1 activity depends on its stabilization and its nuclear localization. Once in the nucleus, YAP1 can regulate gene expression by interacting with transcription factors with DNA binding capability. While YAP1 main transcriptional partners belong to the TEAD family, several reports indicate that YAP1 can also associate with SMADs, RUNX and other transcription factors. YAP1 acts as a broad regulator of cell growth and differentiation, thus playing a pivotal role in regeneration, re-programming and cancer. How YAP1 may control such a large number of cellular processes is still to be fully understood.
To identify how YAP1 controls transcription and to define gene expression programs directly regulated by YAP1, we conducted a genome wide investigation in the mouse liver. Integrated analyses of ChIP-seq and RNA-seq data indicated that YAP1 can act both as an activator and as a repressor in a context dependent way, and allowed the dissection of transcriptional mechanisms. Longitudinal analysis by ChIP-seq and RNA-seq highlighted differences in genome binding and transcriptional control which allowed the identification of acute and tonic YAP1 dependent responses. While during acute activation YAP1 supported cell cycle and signal transduction programs, its prolonged activation sustained a feedforward loop that potentiated and expanded YAP1 dependent transcription thus leading to the direct engagement of cell identity programs.
Overall this study provides a genome scale understanding of how YAP1 controls gene expression and reveals principles in gene regulation which account for YAP1 ability to orchestrate development, regeneration and cell reprogramming.

overall_design: RNAseq analyses were performed on livers of ROSA26-rtTA-IRES-EGFP-WT (wild-type controls) and ROSA26-rtTA-IRES-EGFP-tetYAP mice. To induce YAP, mice were treated with doxycycline for either 3 days or 7 days.

first: Stefano

last: Campaner

first: Francesca

last: Biagioni

first: Ottavio

last: Croci


title: Single cell transcripional analysis of murine adult hepatocytes following YAP induction [Liver_scRNAseq_perfused]

overall_design: Single cell RNA-seq was performed on hepatocytes isolated from  LaptTA and LaptTA-tet-YAP mice


title: Genome-wide chromatin analyses and RNA-seq of liver cells upon YAP induction

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: Wheat transcriptomic changes in response to Trichoderma harzianum and/or nitrogen supplies

city: Villamayor

first: Marta

last: Montero-Barrientos

state: Salamanca

address: Río Duero 12

country: Spain

institute: CENIT SUPPORT SYSTEMS

summary:
We used microarrays to detail the Triticum aestivum response to T34 in the presence of different CN concentrations as nitrogen source.
Affymdetrix wheat genome array (platform GPL3802) was used.

overall_design: Eight samples were analyzed as follows: Triticum aestivum grown in the presence or not of Trichoderma harzianum T34 and with or without CN as nitrogen source at different concentrations.Two replicates for each sample were performed.

first: Belen

middle: R

last: Perez

first: Rosa

last: Prieto

first: Enrique

last: Vazquez


title: Profiling non-small cell lung carcinoma cell line PC9 treated with erlotinib, KDM5A inhibitor, or viruses expressing KDM5 shRNAs or cDNA

city: Chicago

first: Elizaveta

last: Benevolenskaya

state: IL

address: 900 S. Ashland Ave.

department: Biochemistry and Molecular Genetics

institute: University of Illinois at Chicago

summary: The non-small cell lung carcinoma (NSCLC) PC9 cell line is an established preclinical model for tyrosine kinase inhibitors. Recent evidence suggests that KDM5A protein is required for emerging drug-resistant cell population. To better understand the dependence of cell survival on KDM5A, we treated EGFR-mutant PC9 cells with erlotinib, KDM5A inhibitor or KDM5A and KDM5B shRNAs and performed Drop-seq. We were able to clearly distinguish cells with KDM5A knockdown from cells with KDM5A overexpression. We were able to identify specific biomarkers associated with varying dose of KDM5A, for each cell population. The results of this study will address clinical usefulness of KDM5A-targeted strategies in overcoming drug resistance, particularly in NSCLC.

overall_design: Examining drug resistant cell populations using single cell RNA-seq

first: Alexandre

middle: F

last: Aissa

first: Abul

last: Islam


title: Co-culture of iPSC-derived microglia and spinal motor neurons as a novel model for amyotrophic lateral sclerosis

status: Public on Jul 24 2022

city: Oxford

first: Kevin

last: Talbot

address: John Radcliffe Hospital, Headley Way

department: Nuffield Department of Clinical Neurosciences

institute: University of Oxford

summary: Amyotrophic lateral sclerosis is a fatal neurodegenerative disorder primarily characterized by motor neuron degeneration with additional involvement of non-neuronal cells, in particular, microglia. In our previous work, we have established protocols for the differentiation of iPSC-derived spinal motor neurons and microglia. Here, we combine both cell lineages and establish a novel co-culture of iPSC-derived motor neurons and microglia, which is compatible with motor neuron identity and function. Co-cultured microglia express key microglial markers and transcriptomically resemble primary human microglia, have highly dynamic ramifications, are phagocytic, release various cytokines and respond to stimulation. Further, they express key amyotrophic lateral sclerosis-associated genes and release disease-relevant biomarkers. This novel and authentic human model system facilitates the study of physiological motor neuron-microglia crosstalk and permits the investigation of non-cell-autonomous phenotypes in amyotrophic lateral sclerosis.

overall_design: We sequenced a total of 12 samples, with 2 sequence runs per sample. The samples included 3 different cell types: iPSC macrophage precursors, iPSC microglia grown in monoculture and iPSC microglia grown in co-culture with iPSC motor neurons and extracted using CD11b MACS. Each cell type was generated from four different healthy control lines.

first: Björn

last: Vahsen

first: Jakub

last: Scaber


title: Analaysis of global effect of the glucocorticoid fluocinolone acetonide on gene expression in human REDD1 KO HaCaT  keratinocytes in comparison to  Cas9 HaCaT cells

status: Public on Jul 23 2022

city: Tempe

first: Ben

last: Readhead

state: AZ

address: 797 E. Tyler Street

institute: ASU-Banner Neurodegenerative Disease Research Center

summary: REDD1 is required for full amplitude activation of the glucocorticoid receptor. In keratinocytes lacking REDD1  both gene  activation and repression by glucocorticoid fluocinolone acetonide was significantly blunted.

overall_design: HaCaT REDD1 KO (IB11 and IB12)  and HaCaT Cas9 control cells (IB9 and IB10) grown in DMEM supplemented with 10% FBS, were switched to DMEM with Charcoal stripped Fetal Bovine Serum and 1 X Pen/Strep overnight, and then  were treated with vehicle control (0.1% acetone, IB9 and IB11) or 1 μM of FA for 24 h (IB10 and IB12). RNA was extracted and used for Illumina gene expression array.

first: Irina

last: Budunova


title: Genome-wide chromatin analyses of liver cells upon YAP induction [time series; Liver_ChIPseq_LSL]

overall_design:
ChIPseq analyses were performed on livers of ROSA26-rtTA-IRES-EGFP-WT (wild-type controls) and ROSA26-rtTA-IRES-EGFP-tetYAP mice. To induce YAP, mice were treated with doxycycline for either 3 days or 7 days.

Please note that the processed data generated from all replicates is linked to the corresponding 'rep 1' sample records and indicated in the associated sample description field.


title: HDAC1 and PRC2 mediate combinatorial control in SPI1/PU.1-dependent gene repression in murine erythroleukaemia.

first: Christel

last: GUILLOUF


title: Genome-wide chromatin analyses of liver cells upon YAP induction [Liver_ChIPSeq_LapTTA]

first: stefano

last: campaner

overall_design:
ChIPseq and ATAC seq analyses were performed on liver of LaptTA-WT (wild type control) or LaptTA-tetYAP mice activated for 4 weeks (4W)

Please note that the processed data generated from all replicates is linked to the corresponding 'rep 1' sample records and indicated in the associated sample description field.

first: Serena

last: De Fazio


title: Spinal astrocytic MeCP2 regulates Kir4.1 for the maintenance of chronic hyperalgesia in neuropathic pain

city: Chengdu

first: Yali

last: Chen

address: No.37 Guoxue Alley, Wuhou District

department: Anesthesiology

institute: West China Hospital of Sichuan University

summary: Previous studies have suggested that astrocyte activation in the spinal dorsal horn may play an important role in the development of chronic neuropathic pain; but the mechanisms involved in astrocyte activation and their modulatory effects remain unknown. The inward rectifying potassium channel protein 4.1 (Kir4.1) is the most important background K+ channel in astrocytes. However, how Kir4.1 is regulated and contributes to behavioral hyperalgesia in chronic pain is unknown. In this study, single-cell RNA sequencing analysis indicated that the expression of Kir4.1 and Methyl-CpG-binding protein 2 (MeCP2) were both decreased in spinal astrocytes after chronic constriction injury (CCI) in a mouse model. Conditional knockout of the Kir4.1 channel in spinal astrocytes led to hyperalgesia; and overexpression of the Kir4.1 channel in spinal cord relieved CCI-induced hyperalgesia. Expression of spinal Kir4.1 after CCI was regulated by MeCP2. Electrophysiological recording in spinal slices showed that knockdown of Kir4.1 significantly regulated the excitability of astrocytes and then functionally changed the firing patterns of neurons in dorsal spinal cord. Therefore, targeting spinal Kir4.1 maybe an underlying treatment for hyperalgesia in chronic neuropathic pain.

overall_design: The spinal cords of adult C57BL/6 J mice at 7 and 14 days after chronic constriction injury of sciatic nerve were analyzed by scRNA-seq.

first: Mengchan

last: Ou

first: Jin

last: Liu

first: Donghang

last: Zhang

first: Yaoxin

last: Yang

first: Jiefei

last: Shen

first: Changhong

last: Miao

first: Daniel

middle: K

last: Mulkey

first: Tao

last: Zhu

first: Cheng

last: Zhou


title: Mint-ChIP-seq from HCT116 (ENCSR743HTN)

status: Public on Jul 22 2022

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

institute: ENCODE DCC

summary: For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Regulatory functions of cellular energy sensor SnRK1 for nitrate signaling through NLP7 repression

city: Qingdao

first: Honglei

last: Wang

state: Shandong

address: BinHai Street

department: School of Life Sciences

institute: Shandong University

summary: Coordinated metabolism of carbon and nitrogen is essential for optimal plant growth and development. Nitrate is an important molecular signal for plant adaptation to changing environmental conditions, but how nitrate regulates plant growth under carbon deficiency conditions remains unclear. Here, we show that the evolutionarily conserved energy sensor SnRK1 negatively regulates the nitrate signaling pathway. Nitrate promoted plant growth and downstream gene expression, but such effects were significantly repressed when plants were grown under carbon deficiency conditions. Mutation of KIN10, the α-catalytic subunit of SnRK1, partially suppressed the inhibitory effects of carbon deficiency on nitrate-mediated plant growth. KIN10 phosphorylated NLP7, the master regulator of nitrate signaling pathway, to promote its cytoplasmic localization and degradation. Furthermore, nitrate depletion induced KIN10 accumulation, whereas nitrate treatment promoted KIN10 degradation. Such KIN10-mediated NLP7 regulation allows carbon and nitrate availability to control the optimal nitrate signaling and ensures the coordination of carbon and nitrogen metabolism in plants.

overall_design: To determine whether KIN10 is involved in nitrate signaling to regulate downstream gene expression,we performed the RNA-sequencing (RNA-Seq) experiments with the roots of wild-type and KIN10 overexpression plants that were grown on MGRL medium containing 5 mM nitrate for 7 days, subjected to nitrogen-free medium for 2 days, and then treated with 5 mM KCl or 5 mM KNO3 for 1 h. To examine the effects of KIN10 on NLP7 functions, we performed the RNA-Seq experiment using the protoplast transient expression system, in which GFP, NLP7-GFP or NLP7-GFP and KIN10-Myc were transformed into the Arabidopsis mesophyll protoplast.Total RNA was extracted with Trizaol RNA extraction kit (Transgene), and the mRNA sequencing libraries construction and sequencing on the BGISEQ-500 platform were performed at Beijing Geonomics institute (BGI). The sequence reads were mapped to the Arabidopsis genome using HISAT and Bowtie2 software, and differential gene expression was analyzed using Noiseq software. Differentially expressed genes were defined by a 2-fold expression difference with a possibility >0.8.

first: Chao

last: Han

first: Mingyi

last: Bai


title: HDAC1 and PRC2 mediate combinatorial control in SPI1/PU.1-dependent gene repression in murine erythroleukaemia [763_RNA-seq]

city: VILLEJUIF

first: Christel

last: GUILLOUF

address: 114 rue Edouard vaillant

institute: Gustave Roussy

summary: Although originally described as transcriptional activator, SPI1/PU.1, a major player in haematopoiesis whose alterations are associated with haematological malignancies, has the ability to repress transcription. Here, we investigated the mechanisms underlying gene repression in the erythroid lineage, in which SPI1 exerts an oncogenic function by blocking differentiation. We show that SPI1 represses genes by binding active enhancers that are located in intergenic or gene body regions. HDAC1 acts as a cooperative mediator of SPI1-induced transcriptional repression by deacetylating SPI1-bound enhancers in a subset of genes, including those involved in erythroid differentiation. Enhancer deacetylation impacts on promoter acetylation, chromatin accessibility and RNA pol II occupancy. In addition to the activities of HDAC1, polycomb repressive complex 2 (PRC2) reinforces gene repression by depositing H3K27me3 at promoter sequences when SPI1 is located at enhancer sequences. Moreover, our study identified a synergistic relationship between PRC2 and HDAC1 complexes in mediating the transcriptional repression activity of SPI1, ultimately inducing synergistic adverse effects on leukaemic cell survival. Our results highlight the importance of the mechanism underlying transcriptional repression in leukemic cells, involving complex functional connections between SPI1 and the epigenetic regulators PRC2 and HDAC1.

overall_design: Whole transcriptome of blasts in TgSpi1 erythroleukemic cells (#763) overexpressing SPI1 or not (dox-inducible shRNA anti-Spi1) additionally or not  to  Entinostat or DMSO

first: Sebastian

last: Gregoricchio

first: Lélia

last: Polit

first: Michela

last: Esposito

first: Jérémy

last: Berthelet

first: M'Boyba

last: Diop

first: Laure

last: Delestré

first: Emilie

last: Evanno

first: Isabelle

last: Gallais

first: Hanna

last: Aleth

first: Mathilde

last: Poplineau

first: Wilbert

last: Zwart

first: Frank

last: Rosenbauer

first: Fernando

last: Rodrigues-Lima

first: Estelle

last: Duprez

first: Valentina

last: Boeva

last: Guillouf


title: Mint-ChIP-seq from CD8-positive, alpha-beta memory T cell (ENCSR919UFE)

first: ENCODE

last: DCC

summary:
H3K27me3 Mint-ChIP-seq on human CD8-positive, alpha-beta memory T cell.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Mint-ChIP-seq from dendritic cell (ENCSR753RMT)


title: TF ChIP-seq from HepG2 (ENCSR678KUJ)

summary:
ChIP-Seq on HepG2

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Whole ganglia RNA sequencing of C57 BL/6J mice

city: Baton Rouge

first: Rui

last: Zhang

state: Louisiana

address: 6400 Perkins Road

institute: Pennington Biomedical Research Center

summary: The study goal is to identify the gene expression profile of iBAT-related ganglia (SG/T1 & T3) and iWAT-related ganglia (T13/L1 & L2). RNA sequencing demonstrated clear separation of gene expression between brown adipose tissue related ganglia (SG and T3) and white adipose tissue related ganglia (T13/L1 and L2). Each sample type also showed clear separation from each other. No significant separation was observed in different genders.

overall_design: All mice were fed with chow (LabDiet Rodent 5001) at room temperature. Ganglia SG, T3, T13/L1, L2 and ganglia fat were isolated from 4 male and 4 female C57 BL/6J mice, followed by RNA extraction. 40 samples were analyzed. There are 8 SG, 8 T3, 8 T13/L1, 8 L2, and 8 ganglia fat samples from 4 males and 4 females.

first: Heike

last: Muenzberg

first: Sanho

last: Yu

first: Clara

last: Huesing

first: Nathan

last: Lee

first: Richard

last: Carmouche

first: Sara

last: Webb

first: Susan

last: Newman

first: Michael

last: Salbaum


city: Shanghai

first: Jiajun

last: Qiu

address: West BeiJing Road

institute: Shanghai Children’s Hospital, Shanghai Institute of Medical Genetics, Shanghai Jiao Tong University School of Medicine

summary: Down syndrome (DS) is the most common genetic condition that causes intellectual disability in humans. The molecular mechanisms behind the DS phenotype remain unclear. Therefore, in the present study, induced pluripotent stem cells (iPSCs) from a patient with DS and a normal control (NC) patient were differentiated into iPSCs‐derived neural stem cells (NSCs). Single-cell RNA sequencing was performed to achieve a comprehensive single-cell level differentiation roadmap for DS-iPSCs. The results demonstrated that iPSCs can differentiate into NSCs in both DS and NC samples. Furthermore, 19,422 cells were obtained from iPSC samples (8,500 cells for DS and 10,922 cells for the NC) and 16,506 cells from NSC samples (7,182 cells for DS and 9,324 cells for the NC), which had differentiated from the iPSCs. A cluster of DS-iPSCs, named DS-iPSCs-not differentiated (DSi-PSCs-ND), which had abnormal expression patterns compared with NC-iPSCs, were demonstrated to be unable to differentiate into DS-NSCs. Further analysis of the differentially expressed genes revealed that inhibitor of differentiation family members, which exhibited abnormal expression patterns throughout the differentiation process from DS-iPSCs to DS-NSCs, may potentially have contributed to the neural differentiation of DS-iPSCs. Moreover, abnormal differentiation fate was observed in DS-NSCs, which resulted in the increased differentiation of glial cells, such as astrocytes, but decreased differentiation into neuronal cells. Furthermore, functional analysis demonstrated that DS-NSCs and DS-NPCs had disorders in axon and visual system development. Biological experiments were also performed to validate these results and the present study provided a new insight into the pathogenesis of DS.

overall_design:
Burlk and single cell RNA sequencing of neural stem cells derived from human trisomic iPSCs
This submission contains scRNA-Seq data.

first: Yanna

last: Liu

first: Hao

last: Wei

first: Fanyi

last: Zeng

first: Jingbin

last: Yan


title: Mint-ChIP-seq from dendritic cell (ENCSR748IOD)


title: TF ChIP-seq from WTC11 (ENCSR127NBZ)

summary:
eGFP-ERG ChIP-seq on human WTC11

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf