title: The translatome of Glioblastoma

status: Public on Aug 01 2023

city: Amsterdam

first: Bart A.

last: Westerman

address: De Boelelaan 1117

department: Cancer Center Amsterdam - Neurosurgery

institute: Cancer Center Amsterdam CCA

summary: To identify new potential therapeutic targets for the treatment of GB we performed ribosome profiling of glioblastoma sphere cultures (GSCs) under normal and radiotherapeutic conditions.

overall_design: Glioma sphere cultures were left untreated (t0), or irradiated and harvested 30 min (t1) or 60 min (t2) after irradiation

first: Fleur

last: Cornelissen

first: Zhaoren

last: He

first: Cornelis

last: Murre

first: Bart


title: Investigating the role of USP22 in reprogramming

status: Public on Jul 31 2023

city: Istanbul

first: Hamzah

last: Syed

address: Rumelifeneri Yolu

department: School of Medicine

country: Turkey

institute: Koç University

type: Expression profiling by high throughput sequencing

summary: Somatic cells can be reprogrammed to induced pluripotent stem cells (iPSCs) by overexpressing OCT4, SOX2, KLF4 and MYC. Although this cell fate transition is a slow and inefficient process, inhibiting several epigenetic barriers has shown to facilitate it. A previously employed epigenetic focused CRISPR-Cas9-mediated knockout screen during reprogramming uncovered novel human somatic cell reprogramming barriers. Here, I showed that USP22, target for gRNAs that were enriched in iPSCs from the screen, is a barrier for reprogramming and its loss is compatible with iPSC generation. Overexpressing wild-type or deubiquitinase mutant (C185A) USP22 in knockout background could rescue the phenotype. Additionally, knocking out other SAGA deubiquitinase subunits, ENY2 and ATXN7L3 did not increase the reprogramming efficiency. Mechanistically, we showed that USP22 loss upregulates an important pluripotency-related transcription factor, SOX2, expression even as early as 3 days after OSKM expression. We hypothesized that USP22 downregulates pluripotency-related gene expression during reprogramming independent from its SAGA integration and deubiquitinase activity. To address this, I will repeat rescuing USP22 knockout phenotype in reprogramming by overexpressing mutant versions of USP22 including K129R (acetyl inhibited) and HHAA (deubiqutinase). Additionally, I will check the expression of pluripotency-related genes at early time points of reprogramming upon USP22 knockout by transcriptome profiling. Lastly, I will generate USP22 knockout iPSC lines to force them to differentiation to observe if they have any problem with pluripotency exit. This work will establish a mechanistic understanding for the role USP22 play on both human somatic cell reprogramming, pluripotency and differentiation.

overall_design: We performed gene expression profiling analysis using data obtained from RNA-seq of 4 samples generated as independent duplicates from 2 different samples.

first: Kenan

last: Sevinç

first: Tamer

last: Önder


title: Protein localisation during chromatin regulator depletion

status: Public on Jun 29 2023

city: Rehovot

first: Naama

last: Barkai

state: --- Select a state ---

address: Herzl St 234

department: Molecular Genetics

country: Israel

institute: Weizmann Institute

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Using ChECseq, we measured the effect of histone regulator depletion on chromatin protein localisation

overall_design: Sensor and anchor-away-system carrying cells were grown to exponential phase and then regualtor depletion was induced using Rapamycin. ChEC-seq was induced at different timepoints after rapamycin addition.

first: Gilad

last: Yaakov

first: Felix

last: Jonas


title: Regulators of histone exchange

summary: Using a recently established histone turnover sensor, we measured the effect of histone regulator depletion on H2B and H3 turnover

overall_design: Sensor and anchor-away-system carrying cells were grown to exponential phase and then regualtor depletion was induced using Rapamycin. Samples were taken before and during the depletion.


title: single-cell transcriptional profiling of human cholestatic livers

status: Public on Jul 22 2023

city: Jinan

first: Detian

last: Yuan

address: Wenhuaxi Road 44

country: China

institute: Shandong University

summary: Cholestatic liver diseases are characterized by excessive accumulation of bile acids in the liver. The involvement of local tissue microenvironment in cholestatic diseases remains poorly understood. Here, we performed a comprehensive analysis of liver single-cell transcriptomic study of human cholestatic liver diseases. Our study involved 9 liver samples obtained from 7 patients diagnosed with hepatatrophia resulting from cholestasis. By utilizing single-cell data, we gained valuable insights into the specific functions of endothelial cells (EC) in response to chenodeoxycholic acid during cholestasis. The findings from our study hold the potential to lay the groundwork for personalized therapeutic approaches in the future, tailored to the individual needs of patients.

overall_design: We conducted single-cell transcriptomic sequencing on liver tissue samples obtained from 7 patients diagnosed with hepatatrophia due to cholestasis. Among these patients, CLD1-CLD7 indicates cholestatic liver tissue samples. Additionally, HL1 represents the healthy liver tissue paired with the CLD5 patient, while HL2 corresponds to the paired liver tissue of the CLD6 patient.

first: Shiyang

last: Li

first: Peng

last: Zhang

first: Xinying


title: Upper respiratory and peripheral blood gene expression profiles of children, adolescents, and adults with SARS-CoV-2 infection

status: Public on Jul 23 2023

city: Durham

first: Matthew

middle: Scott

last: Kelly

state: NC

address: 3 Genome Court, MSRB3, Room 4200

department: Pediatrics

country: USA

institute: Duke University

summary: The goal of this analysis is to evaluate the extent to which transcriptomic profiles associated with SARS-CoV-2 infection differ by age.

overall_design: Gene expression profiling of upper respiratory and peripheral blood samples was performed using nasopharyngeal and peripheral blood samples from individuals with SARS-CoV-2 infection and uninfected controls

first: Kelly

last: Matthew

first: Burke

last: Thomas

first: Hurst

last: Jillian


title: Epigenome analysis of normal and breast cancer(BC) samples

status: Public on Jul 20 2023

first: Tiantian

last: Wang

state: 请选择

address: Beiyuan

institute: The Second Hospital of Shandong University

type: Methylation profiling by genome tiling array

summary: Genome wide DNA methylation profiling of peripheral blood mononuclear cells (PBMCs) in normal and BC samples. The Illumina Infinium 850k Human DNA methylation Beadchip was used to obtain DNA methylation profiles across approximately 820,000 CpGs in PBMC samples. Samples included 50 newly diagnosed BC patients and 30 normal controls.

overall_design: Bisulphite converted DNA from the 80 samples were hybridised to the Illumina Infinium 850k Human Methylation Beadchip.

first: Chuanxin


title: Gene expression profile at single cell level of bulk liver allograft tissue isolated 12 months post-transplant in patients receiving regulatory dendritic cell therapy (STUDY) and reference standard-of-care patients (SOC)

status: Public on Jun 01 2023

city: Pittsburgh

first: Lillian

last: Tran

state: Pennsylvania

address: 200 Lothrop Street

department: Surgery

institute: University of Pittsburgh

summary: Regulatory dendritic cell therapy has shown potential in modulating the effector immune response after liver transplant in precliical models . We used single cell RNA sequencing (scRNA-seq) to analyze the differences in immune cell landscape of liver allograft at 12 months post-transplant in patients infused with regulatory dendritic cell therapy compared to standard-of-care control patients.

overall_design: Non-parenchymal and parenchymal cells from liver allograft biopsy tissue obtained 12 months post-transplant were analyzed using scRNAseq.


title: DNAJB1-PRKACA fusion protein-regulated LINC00473 promotes tumor growth and  alters mitochondrial fitness in fibrolamellar carcinoma

status: Public on May 27 2023

city: Ithaca

first: Praveen

last: Sethupathy

email: as3999@cornell.edu, pr46@cornell.edu

state: NY

address: T7 006D Veterinary Research Tower, Box 17

department: Department of Biomedical Sciences

institute: Cornell University

summary: Fibrolamellar carcinoma (FLC) is a rare liver cancer that disproportionately affects adolescents and young adults. Currently, no standard of care is available and there remains a dire need for new therapeutics. Most patients harbor the fusion oncogene DNAJB1-PRKACA (DP fusion), but clinical inhibitors are not yet developed and it is critical to identify downstream mediators of FLC pathogenesis. Here, we identify long non-coding RNA LINC00473 among the most highly upregulated genes in FLC tumors and determine that it is strongly suppressed by RNAi-mediated inhibition of the DP fusion in FLC tumor epithelial cells. We show by loss- and gain-of-function studies that LINC00473 suppresses apoptosis, increases the expression of FLC marker genes, and promotes FLC growth in cell-based and in vivo models of disease. Mechanistically, LINC00473 plays an important role in promoting glycolysis and altering mitochondrial activity. Specifically, LINC00473 knockdown leads to increased spare respiratory capacity, an indicator of mitochondrial fitness. Overall, we propose that LINC00473 could be a viable target for this devastating disease.

overall_design:
RNA-seq of FLC LINC00473-overexpression (LeGO-473ox) FLC monoclone cell and empty vector (LeGO-Ctl) control FLC monoclone cell samples. Also, RNA-seq of FLC patient samples for Primary & NML tumor samples.

UPDATE: [Mar-25-2025] The title of Sample GSM7402776 was updated to 'FLC NML tumor RNA-seq sample #6'.

first: Rosanna

last: Ma

first: Alexandria

last: Shumway


title: SOX9 ameliorates nonalcoholic steatohepatitis through activating AMPK pathway

status: Public on Jul 16 2023

city: Shanghai

first: xin

last: zhang

address: 415 Fengyang Road

institute: Changzheng hospital

summary: To systemically investigate the mechanism underlying the impact of SOX9 on lipid metabolism in NASH, we performed RNA-seq analysis in liver tissues from Sox9HKO mice and Sox9f/f mice after 6 weeks of MCD feeding.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for liver tissues from Sox9HKO mice and Sox9f/f mice after 6 weeks of MCD feeding.

first: Juan

last: Deng

first: Ding

last: Kai


title: Terminal differentiation and persistence of effector regulatory T cells essential for the prevention of intestinal inflammation

status: Public on Jul 11 2023

city: La Jolla

first: Stanislav

last: Dikiy

state: CA

address: 10550 North Torrey Pines Road

department: Immunology

institute: Scripps Research

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

overall_design: Refer to individual Series


title: Neonatal and maternal dietary interventions in piglets

city: Wageningen

first: Dirkjan

last: Schokker

address: Droevendaalsesteeg 1

department: Wageningen Livestock Research

country: Netherlands

institute: Wageningen UR

summary: Feed additives aiming to improve gastrointestinal health are frequently supplied to piglets after weaning but might be more effective when administered before weaning. In this period, feed additives can either be administered directly to neonates, or indirectly via sow’s feed. It is yet unknown what the effect of the administration route is on gut functionality and health. Therefore, we compared the effect of different dietary interventions on gut functionality after maternal administration (lactation feed) to the neonatal administration route (oral gavage). These feed interventions included medium chain fatty acids (MCFA), beta-glucans (BG), and galacto-oligosaccharides (GOS). We measured intestinal gene expression and microbiota composition after birth (d1) and after weaning (d31). Our results show that the type of intervention and the administration route influence gut functionality (microbiome and gene expression profiles). MCFA administration led to a more differentially orchestrated response when comparing the neonatal and maternal administration route then the other two additives, indicating the route of administration of the feed interventions is determinative for the outcome. This implies that for each nutritional intervention in early life of a pig the optimal route of administration needs to be determined.

overall_design: Thirty-nine Hypor sows were housed in gestation group housing. One week prior to expected farrowing, sows were moved to the farrowing rooms. Sows were allocated to one of three groups: maternal administration, neonatal administration, or the control group. The impact of three feed additives, i.e., medium-chain fatty acids (MCFA), β-glucans (BG), and galacto-oligosaccharides (GOS), on gut functionality of piglets was determined. Feed additives were either administered directly to neonatal piglets, or indirectly via maternal lactation feed. At day 1 after birth and 3 days post-weaning (day 31), piglets of the maternal administration route were sacrificed for necropsy and sample collection. Whereas piglets from the neonatal group were sacrificed at day 31 for necropsy and sample collection.

first: Astrid

last: de Greeff


title: Terminal differentiation and persistence of effector regulatory T cells essential for the prevention of intestinal inflammation [scRNA-seq]

summary: Regulatory T (Treg) cells represent a specialized CD4+ T cell lineage with essential anti-inflammatory functions. Recent studies of the adaptations of Treg cells to non-lymphoid tissues which enable their specialized immunosuppressive and tissue supportive functions raise questions about the underlying mechanisms of these adaptations and whether they represent stable differentiation or reversible activation states. Using novel genetic tools, we characterized the transcriptional programs of distinct colonic effector Treg cell types. We found that attenuated T cell receptor (TCR) signaling and acquisition of substantial TCR independent functionality appears to facilitate the terminal differentiation of a population of colonic effector Treg cells distinguished by stable expression of immunomodulatory cytokine interleukin-10 (IL-10). Functional studies revealed that this subset of effector Treg cells, but not their expression of IL-10, was indispensable for preventing colitis. These findings suggest core features of terminal differentiation of effector Treg cells in non-lymphoid tissues and their function therein.

overall_design: We performed scRNA-seq on Il10 expressing and Il10 non-expressing Treg cells from several tissues (colon, lung) and their draining lymph nodes in order to identify potential subpopulations within each as well as to gain insight into potential differentiation trajectories.

first: Andrew

middle: G

last: Levine

first: Yuri

last: Pritykin

first: Chirag

last: Kirshna

first: Ariella

last: Glasner

first: Christina

middle: S

last: Leslie

first: Alexander

middle: Y

last: Rudensky


title: Impaired histone inheritance promotes tumor progression

status: Public on May 15 2023

city: Shenzhen

first: haiyun

last: gan

address: xueyuan lu 1068

institute: Shenzhen Institute of Advanced Technology

summary: In this study, we constructed a tumor model of impaired inheritance of parental histones by introducing an MCM2 histone-binding domain (HBD) mutation in the breast cancer cell lines MCF-7. In this model, impaired histone inheritance resulted in dramatic epigenetic reprogramming, especially the pattern of the repressive histone mark H3K27me3, and promoted tumor growth and metastasis in vivo.

overall_design: We used breast cancer MCF-7 cell line (Wild type and MCM2-2A mutant cells) in this study. ATAC-seq method was used to evaluate the chromatin accessibility and CUT&Tag-seq and ChIP-seq were adopted to study the chromatin-binding affinity of histones, histone marks and their associated complex members. In both WT and MCM2-2A MCF-7 cells, we employed ATAC-seq, CUT&Tag-seq of H3.3, H3K27me3, H3K27ac, H3K9me3, H3K4me3, H3K4me1, H3K36me3, SUZ12, H2AK119ub and RING1B, as well as ChIP-seq of H3K36me2 and EZH2. H3K27me3 CUT&Tag experiments above were also implemented in POLE3 KO MCF7 cells. In addition, CUT&Tag for H3K27me3, H3K4me3 and H3.3 were performed in WT and MCM2-2A mutant HEK293T cells, as well as in WT and MCM2-90A mutant T47D cells.  Bulk RNA-seq and scRNA-seq in vitro and in vivo were also implememted.

first: Congcong

last: Tian

first: Jiaqi

last: Zhou

first: Xinran

last: Li

first: Haiyun

last: Gan


title: Pseudouridine guides small RNA transport and inheritance via Exportin-t

status: Public on Aug 07 2023

city: Cambridge

first: Tony

last: Kouzarides

address: Wellcome/Cancer Research UK Gurdon Institute, Henry Wellcome Building of Cancer and Developmental Biology, Tennis Court Road

department: Gurdon Institute

country: United Kingdom

institute: University of Cambridge

type: Non-coding RNA profiling by high throughput sequencing

summary: Pseudouridine (Ψ) is an isomer of uridine found in ribosomal, transfer and other structural RNAs as well as in some mRNAs and non-coding RNAs, but is difficult to detect in short RNA sequences.  Using modified techniques we found Ψ in microRNAs (miRNAs) and their precursors from mammalian and plant cells, primarily at the 5ʹ terminus of the mature miRNA. Small RNAs targeting transposons in reproductive cells (piRNA in testis and easiRNA in pollen) were highly enriched for Ψ, indicating a potential role in epigenetic inheritance. In pollen, pseudouridylated small RNAs were produced by RNA polymerase IV and were localized to sperm cells, as were miRNAs with terminal Ψ. We show that pseudouridylated easiRNAs from pollen contribute to imprinting and the triploid block (chromosome dosage-dependent epigenetic lethality) via the activity of PAUSED/HEN5, the plant homolog of Exportin-t. Exportin-t is required for nuclear export of pseudouridylated tRNA, and we found that PSD is required for cell-cell transport of small RNA in the germline.

overall_design: Small RNA-Seq experiment following RNA Immunoprecipation for pseudouridine (psi-IP) in WildType and Pus1 Knock Down 3T3 cells. Samples analysed include RNA following psi-IP as well as control Input samples. Time point analysed include 3 and 6 days after Knock Down of Pus1.

first: Rowan

middle: P

last: Herridge

first: Valentina

last: Migliori

first: Jakub

last: Dolata

first: Cristiane

last: de Santis Alves

first: Filipe

last: Borges

first: Andrea

middle: J

last: Schorn

first: Tommaso

last: Leonardi

first: Alan

last: Hendrick

first: Robert

middle: A

last: Martienssen


title: Mono(2-ethylhexyl) phthalate induces transcriptomic changes in placental cells based on concentration, fetal sex, and trophoblast cell type

status: Public on May 01 2023

city: Seattle

first: Alison

last: Paquette

state: Washington

address: 1900 Ninth Ave.

department: Center for Developmental Biology and Regenerative Medicine

institute: Seattle Childrens

summary: Phthalates are ubiquitous plasticizer chemicals found in consumer products. Exposure to phthalates during pregnancy has been associated with adverse pregnancy and birth outcomes and differences in placental gene expression in human studies. The objective of this research was to evaluate global changes in placental gene expression via RNA sequencing in two placental cell models following exposure to the phthalate metabolite mono(2-ethylhexyl) phthalate (MEHP). HTR-8/SVneo and primary syncytiotrophoblast cells were exposed to three concentrations (1, 90, 180µM) of MEHP for 24 hours with DMSO (0.1%) as a vehicle control. mRNA and lncRNAs were quantified using paired end RNA sequencing, followed by identification of differentially expressed genes (DEGs) and significant KEGG pathways and enriched transcription factors (TFs). MEHP caused gene expression changes across all concentrations for HTR-8/SVneo and primary syncytiotrophoblast cells. Sex-stratified analysis of primary cells identified different patterns of sensitivity in response to MEHP dose by sex, with male placentas being more responsive to MEHP exposure. Pathway analysis identified 11 KEGG pathways significantly associated with at least one concentration in both cell types. Four ligand-inducible nuclear hormone TFs (PPARG, PPARD, ESR1, AR) were enriched in at least three treatment groups. Overall, we demonstrated that MEHP differentially affects placental gene expression based on concentration, fetal sex, and trophoblast cell type. This study confirms prior studies as enrichment of nuclear hormone TFs were concordant with previously published mechanisms of phthalate disruption, and generates new hypotheses, as we identified many pathways and genes not previously linked to phthalate exposure.

overall_design: HTR-8/SVneo Cells: 3-DMSO (0.1%) Biological Replicates for Batch 1, 3- DMSO (0.1%) Biological Replicates for Batch 2, 3- 1uM MEHP Biological Replicates from Batch 2, 3- 90uM MEHP Biological Replicates from Batch 1, 3-180uM MEHP Biological Replicates from Batch 2. For Primary Syncytiotrophoblast Cells: 6-DMSO (0.1%) Biological Replicates (3M, 3F), 5- 1uM MEHP Biological Replicates (3M, 2F), 6- 90uM MEHP Biological Replicates (3M, 3F), 6- 180uM MEHP Biological Replicates (3M, 3F)

first: Samantha

last: Lapehn

first: Scott

last: Houghtaling

first: Kylia

last: Ahuna

first: Leena

last: Kadam

first: James

middle: W

last: MacDonald

first: Theo

middle: K

last: Bammler

first: Kaja

middle: Z

last: LeWinn

first: Leslie

last: Myatt

first: Sheela

last: Sathyanarayana


title: mRNA during Spt6,Spt16 and Rtt106 depletion

first: Naama

last: Barkai

summary: We measured the transcriptome of yeast cells during the depletion of chromatin regulators using anchor away

overall_design: Sensor and anchor-away-system carrying cells were grown to exponential phase and then regualtor depletion was induced using Rapamycin. Sampls for RNA seq were collected ever 10minutes.

first: Gilad

last: Yaakov

first: Felix

last: Jonas


title: Competing endogenous RNA expression profiling in decidua after LPS treatment

status: Public on May 06 2023

city: jinan

first: hai

middle: yan

last: liu

address: huaxianchanglu

institute: bohao

summary: To investigate the competing endogenous RNA expression changes in decidua under the inflammatory reaction, LPS (100 μg/kg body weight) was intraperitoneally injected into the mice at 15 days of pregnancy. Premature births has been found after approximately 48 h of treatment. When bleeding found in vagina, the decidua were selected in asepsis condition, and total RNA was isolated to analyze the expression of competing endogenous RNA compared with cesarean sections.

overall_design: The decidua derived from LPS-treated mice were tested the competing endogenous RNA expression, the decidua derived from cesarean sections as a control.

first: Yuhua

last: Gao

first: Chunyu

last: Bai


title: Control of ciliary transcriptional programs during spermatogenesis  by antagonistic transcription factors

status: Public on Jul 06 2023

city: Wuhan

first: Weihua

last: Wang

state: Hubei

address: No. 8, Sanjiaohu Rd., Wuhan Economic & Technological Development Zone

institute: Jianghan University

summary: Cilia and flagella are dynamicallyregulatedduring development and differentiation.  Coordination of temporal and spatial transcription regulators are essential for ciliogenesis. We here report that XAP5 and XAP5L are two conserved pairs of antagonistic transcription regulators that control ciliary transcriptional programs during spermatogenesis. Male mice lacking either XAP5 or XAP5L display infertility, as a result of meiotic prophase arrest and sperm cilia malformation, respectively. XAP5 positively regulates the ciliary gene expression by activating the key regulators including FOXJ1 and RFX families during the early stage of spermatogenesis. In contrast, XAP5L negatively regulates the expression of ciliary genes via repressing these ciliary transcription factors during the spermiogenesis stage. Taken together, our data provide new insights into the mechanisms by which temporal and spatial transcription regulators are coordinated to control ciliary transcriptional programs during spermatogenesis.

overall_design: To investigate the XAP5L-dependent genes during sperm cilia assembly, we generated XAP5L KO mice using CRISPR/CAS9 system and then performed RNA-seq analysis using postnatal day 56 (D56)  mature sperm collected from the cauda epididymis of WT and XAP5L KO adult mice. To investigate the roles of XAP5 during spermatogenesis, we generated XAP5 male germ cell conditional KO (cKO) mice using XAP5 floxed mice mating with Stra8-EGFPCre mice, and then performed RNA-seq analysis using D16 WT and XAP5 cKO testes samples. Three biological replicates were included for each genotype.

first: Junqiao

last: Xing

first: Xiqi

last: Zhang

first: Zhangfeng

last: Hu


title: Map active enhancer and gene expression at 6 distinct time of the day

status: Public on Apr 24 2023

city: Didcot

first: Akanksha

last: Bafna

address: Harwell Campus

institute: MRC HARWELL


title: Study the gene expression in SCN after lights on (ZT=0) , at 6 distinct time of the day.

summary: To investigate the rhythmic gene expression in the SCN during day.

overall_design: Gene expression profiling analysis of RNA-seq data in SCN at six distinct time-points , ZT3,7,11,15,19,23. Each time-point had 4 biological replicates. Each biological replicate constituted 3-4 individual SCN samples.

first: Gareth

last: Banks

first: Michael

middle: H

last: Hastings

first: Patrick

middle: M

last: Nolan


title: Exosomal miRNA signatures of RAW 264.7 cells

status: Public on Apr 30 2023

summary: To investigate the exosomal miRNA changes under LPS treatment in RAW 264.7 cells, 2 μg/mL LPS were added into complete medium to incubate RAW 264.7 cells. And then The exosomes  were isolated and tested the exosomal miRNAs change using microarray.

overall_design: The exosomes derived from LPS-treated RAW 264.7 cells were tested the miRNAs expression, the exosomes derived from normal cells as a control.


title: MATR3

status: Public on Jun 28 2023

first: Xuan

last: Cao

address: 320 Yueyang Road

institute: Shanghai Institute of Nutrition and Health,  Chinese Academy of Sciences


title: Map active enhancer and gene promoter regions in the SCN

summary:
Histone ChIP-seq was performed at varied time of the day to map the gene promoter and active enhancer sites in the central clock; SCN (suprachiasmatic nuclei).
Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for the histone modifications H3K4me3 and H3K27ac in adult mouse SCN and cortex at distinct time of the day .

overall_design: WT C57Bl/6J mice were used for SCN tissue collection at 6 distinct time-points starting from ZT3 at every 4 hours, where lights on at 7 am (ZT0) and lights off at 7 pm (ZT12). We also collected cortical punches at ZT3 and ZT15 to compare and establish SCN enriched chromatin modifications. For histone chromatin immunoprecipitation two separate biological replicates per time-point per tissue-type was collected where each biological replicate composed of 3-4 individual SCN or cortical punches.


title: Exosomal miRNA signatures of amniotic fluid in mice

summary: To investigate the exosomal miRNA changes under the inflammatory reaction, LPS (100 μg/kg body weight) was intraperitoneally injected into the mice at 15 days of pregnancy. Premature births has been found after approximately 48 h of treatment. When bleeding found in vagina, the uterus and other embryo without breaking water were selected in asepsis condition. The amniotic fluid were selected and isolated exosome to analyze the expression of miRNAs compared with cesarean sections.

overall_design: The exosomes derived from LPS-treated mice were tested the miRNAs expression, the exosomes derived from cesarean sections as a control.


title: Dynamin-like proteins are essential for vesicle biogenesis in Mycobacterium tuberculosis.

status: Public on Jun 22 2023

city: Derio

first: Jose

middle: Luis

last: Lavin

state: Bizkaia

address: Parque Tecnológico de Bizkaia Building 502, Floor 0

country: Spain

institute: CIC bioGUNE

summary: Mycobacterium tuberculosis (Mtb) secretes pathogenicity factors and immunologically active molecules via membrane vesicles. However, nothing is known about the mechanisms involved in mycobacterial vesicle biogenesis. This study investigates molecular determinants of membrane vesicle production in Mtb by analyzing Mtb cells under conditions of high vesicle production: iron limitation and VirR restriction. Ultrastructural analysis showed extensive cell envelope restructuring in association with vesicle release that correlated with downregulation of cell surface lipid biosynthesis and peptidoglycan alterations. Comparative transcriptomics showed common upregulation of the iniBAC operon in association with high vesicle production in Mtb cells. Vesicle production analysis demonstrated that the dynamin-like proteins (DLPs) encoded by this operon, IniA and IniC, are necessary for release of EV by Mtb in culture and in infected macrophages. Isoniazid, a first-line antibiotic, used in tuberculosis treatment, was found to stimulate vesicle release in a DLP-dependent manner. Our results provide a new understanding of the function of mycobacterial DLPs and mechanistic insights into vesicle biogenesis. The findings will enable further understanding of the relevance of Mtb-derived extracellular vesicles in the pathogenesis of tuberculosis and may open new avenues for therapeutic research.

overall_design: Gene expression changes between M.tuberculosis H37Rv wild type stain and the transposon mutant in Rv0431 (virR)

first: Rafel

last: Prados Rosales

first: Jose Luis


title: CTCF-mediated insulation and chromatin environment modulate Car5b escape from X inactivation I

status: Public on May 18 2023

first: Xinxian

last: Deng

state: WA

address: 1959 NE Pacific St.

department: Laboratory Medicine and Pathology

institute: University of Washington

summary: Although the chromatin regulator CTCF is enriched at genes escaping from X-chromosome inactivation (XCI), molecular mechanisms remain elusive. We examined CTCF and epigenetic features at escape genes on the inactive X (Xi) in mouse F1 hybrid cells and tissues. We found that escape genes are located inside topologically insulated domains limited by convergent arrays of CTCF binding sites, suggesting loop formation. Xi-specific deletion of a CTCF right boundary of the escape gene Car5b caused loss of CTCF binding and changes of histone modifications at Car5b and abolished escape, suggesting loss of insulation. This is consistent with Car5b lack of escape in mouse brain showing no CTCF binding at the boundary. Inversion of this boundary had no effect on Car5b escape, suggesting that tandem coiled looping could still function as insulation. To test whether chromatin features of the Xi could affect escape we examined mutants in which the Xi-specific compact structure is disrupted or there is loss of H3K27me3 enrichment. We found that both conditions cause an Xi-specific increase in active marks and gene expression at escape regions, suggesting that the 3D structure and heterochromatic marks of the Xi play a role in modulating escape levels of genes insulated by CTCF.

sample_organism:
Mus musculus
Mus spretus

platform_organism:
Mus musculus
Mus spretus

overall_design: Rad21 ChIP-seq on F1 hybrid wild-type and CRISPR/cas9-modified Patski cells

first: He

last: Fang

first: Christine

last: Disteche


title: Structure-function relationship of ASH1L and histone H3K36 and H3K4 methylation

status: Public on Apr 23 2023

city: New York

first: Rajal

last: Sharma

address: 1425 Madison Ave., Room 16-52

institute: ISMMS

summary: The ASH1L lysine methyltransferase plays a critical role in development and is frequently dysregulated in cancer and neurodevelopmental diseases. ASH1L catalyzes mono- and dimethylation of histone H3K36 and contains a set of uncharacterized domains. Here, we report the structure-function relationships of the C-terminal cassette of ASH1L encompassing a bromodomain (BD), a PHD finger and a bromo-associated homology (BAH) domain and show that ASH1L co-localizes with H3K4me3 but not with H3K36me2 at transcription start sites genome-wide and is involved in embryonic stem cell differentiation and transcriptional regulation of differentiation marker genes. Our crystal and NMR structural data provide mechanistic details for the recognition of H3K4me3 by PHD, the DNA binding activities of BD and BAH, and crosstalk among these domains. We show that the PHD-H3K4me3 interaction is inhibitory to the catalytic activity of ASH1L and that the DNA binding function of BAH is necessary for ASH1L engagement with the nucleosome. Our findings suggest a mechanism by which the C-terminus of ASH1L associates with chromatin and provide molecular and structural insights that are essential in therapeutic targeting of ASH1L.

overall_design: ChIP-Seq of Ash1l and control in Retinoic Acid differentiated mouse ES cells

first: R

first: K

middle: R

last: Vann

first: T

last: Kutateladze


title: Cellular Composition and 5hmC Signature Predict the Treatment Response of AML Patients to Azacitidine Combined with Chemotherapy

status: Public on May 25 2023

city: Bethesda

first: Chuanyuan

last: Chen

state: MD

address: 9000 Rockville Pike, Building 37

department: National Cancer Institute

institute: National Institutes of Health

type: Methylation profiling by high throughput sequencing

summary: Azacitidine (AZA) is a DNA methyltransferase inhibitor and epigenetic modulator that can be an effective agent in combination with chemotherapy for patients with high-risk acute myeloid leukemia (AML). However, biological factors driving the therapeutic response of such hypomethylating agent (HMA)-based therapies remain unknown. Herein, the transcriptome and/or genome-wide 5-hydroxymethylcytosine (5hmC) are characterized for 41 patients with high-risk AML from a phase 1 clinical trial treated with AZA epigenetic priming followed by high-dose cytarabine and mitoxantrone (AZA-HiDAC-Mito). Digital cytometry reveals that responders have elevated Granulocyte-macrophage-progenitor-like (GMP-like) malignant cells displaying an active cell cycle program. Moreover, the enrichment of Natural killer (NK) cells predicts favorable outcome in patients receiving AZA-HiDAC-Mito therapy or other AZA-based therapies. Comparing 5hmC profiles before and after five-day treatment of AZA shows that AZA exposure induces dose-dependent 5hmC changes, the magnitude of which predicts overall survival (p=0.015). An XGBoost machine learning model is developed to predict the treatment response based on 5hmC levels of only 11 genes, achieving an area under the curve (AUC) of 0.860. These results suggest that cellular composition markedly impacts the treatment response, and showcase the prospect of 5hmC signature in predicting the outcomes of HMA-based therapies in AML.

overall_design: A total of 46 patients who received AZA-HiDAC-Mito therapy (AZA epigenetic priming followed by high-dose cytarabine and mitoxantrone) were enrolled in this study, out of which 41 provided usable RNA and/or 5hmC sequencing data. Samples were collected at Day 0 (before treatment) and Day 5 (after 5 days of AZA treatment) from BM and PB. There were 71 samples from 31 patients for RNA-seq and 120 samples from 40 patients for 5hmC-seq. For patients receiving HiDAC-Mito therapy, there were 22 RNA-seq samples and 23 DNA 5hmC samples from 23 AML patients collected before treatment. For patients only receiving AZA treatment, there were 11 RNA-seq samples and 12 5hmC-seq samples collected before treatment.

first: Dali

last: Han

first: Chuan

last: He

first: Qiancheng

last: You

first: Linchen

last: Wang


title: Secretome analysis in CAF-dependent conditioned mediums with FaDu cells

status: Public on Apr 17 2023

city: Daegu

first: Soo hyun

last: Kang

address: 2177 Dalgubeol-daero

country: South Korea

institute: kyungpook university

summary: We co-cultured primary cultured CAF (CAF-P), which promotes progression more actively, and CAF (CAF-D), which have less cancer-promoting properties, with OSCC cells, and analyzed the differential secretion through antibody microarray.

overall_design: To evaluate the differential effect of the two CAF cell types on cisplatin efficacy in OSCC cells, we co-cultured FaDu spheroids (bottom well) with OSCC cells, CAF-P or CAF-D for 48 h in transwells. Antibody arrays were performed for each CM.

first: Soo

first: Su

last: Hong


title: DNA methylation of diabetic and normal human limbal epithelial cells

status: Public on Apr 15 2023

city: Los Angeles

first: Alexander

middle: V

last: Ljubimov

address: 8700 Beverly Blvd.,

department: Biomedical Sciences

institute: Cedars-Sinai Medical Center

summary: Genome wide DNA methylation profiling of primary cultures of normal and diabetic corneolimbal epithelial cells. The Illumina Infinium MethylationEPIC Human DNA methylation Beadchip v1.0 B4 was used to obtain DNA methylation profiles across approximately 850,000 CpGs.

overall_design: Bisulphite converted DNA from 11 samples were hybridized to the Illumina InfiniumEPIC Human Methylation Beadchip v1.0 B4

first: Daniel

last: Weisenberger


title: scRNAseq in a panel of neuroblasoma cell lines

status: Public on Apr 10 2023

city: MEMPHIS

first: Richard

last: Chapple

state: Tennessee

address: 262 Danny Thomas Pl

institute: St Jude Children's Hospital

summary: The similarity of preclinical models to human neuroblastoma tumors was evaluated with scRNAseq.  The 13 NB cell lines represent a cross section of disease risk, clinical subtypes, genomic alterations, and disease phenotypes.

overall_design: Neuroblastoma cell lines were grown under standard culture conditions and were collected for scRNAseq with 10X Genomics platform.

first: Paul

last: Geeleher

first: Sivaraman

last: Natarajan

first: John

last: Easton


title: Regulators of histone exchange and protein localisation during chromatin regulator depletion

status: Public on Jun 29 2023

city: Rehovot

first: Naama

last: Barkai

address: Herzl St 234

institute: Weizmann Institute

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

overall_design: Refer to individual Series


title: Multi-scale chromatin footprinting reveals wide-spread alterations to the structure of DNA regulatory elements [Human BMMC ATAC]

status: Public on Mar 29 2023

first: Jason

last: Buenrostro

state: MA

address: 7 Divinity Ave

institute: Harvard University

summary: Cis-regulatory elements (CREs) are bound by diverse chromatin-associated proteins, cooperate to establish gene expression, and change in structure over time to alter cell fate and function1–3. Here, we develop a footprinting framework that uses deep learning to correct Tn5 sequence bias, improving accuracy and reducing false positives. This framework additionally identifies the interaction of DNA with objects of various sizes. Using these ‘multi-scale footprints’ we find that transcription factor (TF) binding occurs at well-defined distances from nucleosomes. Further, we demonstrate that multi-scale footprints, which include the positions of nucleosomes, enable more accurate inference of TF binding. Using multi-scale footprinting with single-cell multi-omics, we discover wide-spread structural and functional changes of CREs across hematopoiesis, wherein nucleosomes slide, expose DNA for TF binding, and promote gene expression. Finally, we apply this single-cell and footprint approach to characterize age-associated structural changes to CREs within hematopoietic stem cells and identify a spectrum of cells harboring age-associated changes to the epigenome. Interestingly, we find extensive changes to the structure of CREs upon aging, with many age-associated changes altering CRE structure while preserving overall accessibility. Collectively, we reveal the dynamics and functional importance of CRE structure, highlighting changes to gene regulation at single-cell and single-base-pair resolution.

overall_design: SHARE-Seq of bone marrow from 7 human donors

first: Sai

last: Ma

first: Yan

last: Hu


title: Multi-scale chromatin footprinting reveals wide-spread alterations to the structure of DNA regulatory elements [Human BMMC RNA]


title: Multi-scale chromatin footprinting reveals wide-spread alterations to the structure of DNA regulatory elements [scATAC]

overall_design:
10x multi-ome to profile chromatin accessibility in mouse hematopoietic stem cells from different age groups.

UPDATE: [Mar-27-2025] Samples GSM6672046 and GSM6672047 were corrected from "Old" to "Young", and Samples GSM6672048 and GSM6672049 were corrected from "Young" to "Old". The raw and processed data associated with each GSM record did not change.

first: Fabiana

last: Duarte

first: Heidi

last: Kletzien

first: Rojesh

last: Shrestha


title: p53 drives premature neuronal differentiation in response to acute DNA damage during early neurogenesis

status: Public on Mar 31 2023

city: Mol

first: Mohamed

last: Mysara

state: Belgium

address: Boeretang 200

country: Belgium

institute: Belgian nuclear research center (SCK-CEN)

summary:
Purpose: The transcription factor p53 classically regulates the cellular response to DNA damage. Inappropriate activation of p53 during embryonic development can lead to a range of developmental defects such as microcephaly. Here, we studied the cellular and molecular mechanisms underlying microcephaly induced by acute irradiation of mouse fetuses at the onset of neurogenesis. This leads to transient DNA damage followed by apoptosis and premature neuronal differentiation, both of which are p53-dependent as they are reduced in dorsal forebrain-specific Trp53 knockout mice. A functional genomics screen shows that radiation induces the p53-dependent activation of both apoptosis- and differentiation-associated genes. Irradiation furthermore induces an epithelial-to-mesenchymal transition-like process characterized by a reduction of epithelial markers and a disruption of the apical adherens junction belt. Altogether, we have identified a novel function of p53 as an activator of neuronal differentiation in response to acute embryonic DNA damage further demonstrating its importance as a regulator of cell fate.
Methods:  Pregnant mouse dams were (sham-)irradiated at gestational day 11 after which they were sacrificed for dissection of fetuses after 2 h, 6 h and 12 h. Cerebral cortices were removed for transcriptomic analysis via RNA-seq.

overall_design: Mice were coupled during a 2-h time period and the morning of coupling was counted as embryonic day (E) 0. Pregnant dams were (sham-)irradiated at E11 after which they were sacrificed for dissection of fetuses after 2 h, 6 h and 12 h. Cerebral cortices were subsequently removed for transcriptomic analysis. Both wild-type (WT) mice and Emx1-cre;Trp53-LoxP mice (cKO) were used, and (sham)irradiated as described before. For each experimental condition 3 individual fetuses were used from at least 2 different mothers except for cKO_1 Gy_6 h for which all three fetuses were littermates. Fetal cortices were dissected and stored in RLT Plus lysis buffer (Qiagen) at -80°C until further processing.

first: Roel

last: Quintens


title: Multi-scale chromatin footprinting reveals wide-spread alterations to the structure of DNA regulatory elements [BAC]

overall_design: Regions of the human genome are cloned into bacteria artificial chromosomes (BACs). The BAC DNA was purified for Tn5 tagmentation.

first: Ajay

last: Labade


title: Transcriptional single-cell study of Nanoparticle-derived TR1-like cells in NOD.Prdm1 flox/floxCD4-Cre+ mice.

status: Public on Mar 27 2023

city: Barcelona

first: Josep

last: Garnica

address: Rosselló, 149

institute: IDIBAPS

summary:
10X technology single-cell RNA-seq was used on tetramer-sorted CD4+ T cells from nanoparticle-treated control mice (NOD.CD4-Cre+ and NOD.Prdm1 flox/flox)  and NOD.Prdm1 flox/floxCD4-Cre+ mice to study the role of Prmd1 on the differentiation of TFH cells into TR1 cells.
Study evidencies the devolopment linkage between tetramer positive TFH and TR1 based on gene expression gradient. Remarkably, mice lacking Prmd1 fail to develop TR1 cells and their differentation is blocked.

overall_design: 10X Single-cell RNAseq data from control mice (NOD.CD4-Cre+ and NOD.Prdm1 flox/flox)  and NOD.Prdm1 flox/floxCD4-Cre+ mice both treated with nanoparticles.

first: Pere

last: Santamaria

first: Muhammad

last: Uddin


title: ChIP-seq data for Cbp1 and RNA polymerase in Sulfolobus islandicus LAL14/1

status: Public on Mar 24 2023

city: London

first: Finn

last: Werner

address: Gower Street

department: Institute of Structural and Molecular Biology

institute: University College London

summary: Chromatin proteins competes with the transcription machinery for access to genomic DNA and suppress cryptic promoters. CRISPR arrays form the physical memory of CRISPR adaptive immune systems. The incorporation of virus-derived AT-rich DNA into CRISPR arrays renders them prone to harbouring cryptic promoters. Sulfolobales feature extremely long CRISPR arrays spanning several kilobases as well as a CRISPR-specific chromatin protein termed Cbp1. Altered Cbp1 expression affects transcription from CRISPR arrays in multiple ways, but the mechanistic basis remains to be understood. Here, we show that Cbp1 recruits the general chromatin protein Cren7 to form a heteromeric chromatin complex at CRISPR arrays. Cbp1-CreN7 chromatinisation plays a dual role in the transcription of CRISPR array. It suppresses spurious transcription from cryptic CRISPR array-internal promoters via steric occlusion of the transcription machinery while enhancing transcription from promoters in the CRISPR leaders. Our results show that Cbp1-CreN7 chromatinization drives the coordinated transcription of long CRISPR arrays. Additional binding sites of Cbp1 associated with transposases and the leaders of alternative CRISPR arrays hint on a wider regulatory function of Cbp1 linking defense systems and mobile genetic elements.

overall_design: ChIP-seq data for chromatin proteins Cbp1 and RNA polymerase subunits 4/7 in a Sulfolobus islandicus LAL14/1 infected with Sulfolobus islandicus rod-shaped virus 2 (SIRV2)

first: Fabian

last: Blombach

first: Mart

last: Krupovic

first: Diana

last: Baquero


title: Transcriptome analyses reveal antibiotic-resistant pathways in Klebsiella pneumonia

status: Public on Apr 18 2023

city: Baotou

first: Guo

middle: qing

last: Liu

state: Inner Mongolia

address: 7 Arding street

department: School of Life Science and Technology

institute: Inner Mongolia University of Science and Technology

summary: The increasing antibiotic resistance of Klebsiella pneumoniae poses a serious threat to global public health. To investigate the antibiotic resistance mechanism of Klebsiella pneumonia, we performed gene expression profiling analysis using RNA-seq data for clinical isolates of Klebsiella pneumonia, KPN16 and ATCC13883. Our results showed that mutant strain KPN16 is likely to act against the antibiotics through increased increased butanoate metabolism and lipopolysaccharide biosynthesis, and decreased transmembrane transport activity.

overall_design: The K. pneumonia (ATCC13883 and KPN16) isolate was cultured to reach a turbidity of 0.05 at OD600. 2 mL bacterial culture was centrifuged at 12,000 rpm for 2 min for cell collection. Discard the supernatant and store the bacterial collection at -80 ℃. In each group, triplicate samples were prepared under the same experimental conditions. RNA degradation and contamination was monitored on 1% agarose gels. RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA). Total RNA was used as input material for the RNA sample preparations. mRNA was purified from total RNA using probes to remove rRNA. Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer(5X). First strand, and then second strand of cDNA were synthesized. In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system. The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina Novaseq platform and 150 bp paired-end reads were generated.

first: Ying

first: Dezhi

last: Yang

first: Guoqing

first: Jun

last: Chen

last: Zhao


title: ChIP-seq data for Cbp1 and CreN7 in Saccharolobus solfataricus P2

overall_design: ChIP-seq data for chromatin proteins Cbp1 and CreN7 in a Saccharolobus solfataricus P2


title: Anti-GD2 CAR-NKT cells in relapsed or refractory neuroblastoma: updated phase 1 trial interim results

status: Public on Apr 19 2023

city: Houston

first: Antonino

last: Montalbano

state: TX

address: 1102 Bates Ave

institute: Baylor School of Medicine

summary: Vα24-invariant natural killer T cells (NKTs) have antitumor properties that can be enhanced by transgenic expression of tumor-specific receptors. Here, we report the results of the first-in-human clinical evaluation of autologous NKTs co-expressing a GD2-specific chimeric antigen receptor with interleukin (IL)15 (GD2-CAR.15) in 12 children with neuroblastoma (NB) treated on four dose levels (NCT03294954). Objectives included assessing safety, antitumor activity, and immune response. No dose-limiting toxicities occurred, and one patient had grade 2 cytokine release syndrome resolved by tocilizumab. The overall response rate was 25% (3/12) and disease control rate was 58% (7/12) including four patients with stable disease, two partial responses, and one complete response. CD62L+ NKT frequency in infused products correlated with CAR-NKT expansion in patients and was higher in responders than non-responders (71% vs 35.3%, p=0.002). Singe-cell RNA sequencing analysis identified B cell translocation gene 1 (BTG1) as one of the top upregulated genes in GD2-CAR.15-NKTs after in vitro serial tumor challenge. Genetic gain- and loss-of-function experiments revealed that BTG1 is a key driver of hyporesponsiveness in exhausted NKT and T cells. Crucially, NKTs co-expressing GD2-CAR.15 and BTG1-specific shRNA eradicated metastatic NB in mice. These results indicate that CAR-NKTs are safe, produce objective responses in NB patients, and that targeting BTG1 can enhance their therapeutic potency.

overall_design: Single-cell RNA sequencing analysis of differently regulated genes in GD2-CAR.15-NKTs between pre-infusion and post-infusion cells.

first: Andras

last: Heczey

first: Xin

last: Xu

first: Amy

middle: N

last: Courtney

first: Gengwen

last: Tian

first: Gabriel

last: Barragan

first: Linjie

last: Guo

first: Cluadia

last: Martinez Amador

first: Nisha

last: Ghatwai

first: Purva

last: Rathi

first: Michael

last: Wood

first: Yanchuan

last: Li

first: Chunchao

last: Zhang

first: Thorsten

last: Demberg

first: Erica

last: Di Pierro

first: Andrew

middle: C

last: Sher

first: Huimin

first: Birju

last: Mehta

first: Sachin

last: Thakkar

first: Bambi

last: Grilley

first: Tao

last: Wang

first: Brian

middle: D

last: Weiss

first: Meena

last: Subramaniam

first: Chenling

first: Chirag

last: Sachar

first: Daniel

last: Wells

first: Gianpietro

last: Dotti

first: Leonid

last: Metelitsa


title: Undernutrition disrupts cecal microbiota and epithelium interactions and epithelial metabolism and immune response in a pregnant sheep model

status: Public on Mar 22 2023

city: Hefei

first: weibin

last: wu

address: Changjiang Western Road 130

institute: Anhui Agricultural University

summary: In the current study, five late gestation multiparous ewes were restricted to a 30% feeding level to create a model of malnutrition, while five other ewes were fed normally as controls. All ewes were sacrificed and cecal samples were collected for transcriptome sequencing to study metabolic changes.

overall_design: Compare the differences in transcriptome profiles between the cecal sample from CON and TR ovis aries.

first: Weibin

last: Wu

first: Huizhen

last: Lu

first: Shengyong

last: Mao

first: Yanfeng

last: Xue


title: ChIP-exo data for Cbp1 and CreN7 in Saccharolobus solfataricus P2

first: Finn

last: Werner

overall_design: ChIP-exo data for chromatin proteins Cbp1 and CreN7 in a Saccharolobus solfataricus P2

first: Fabian

last: Blombach


title: Transcriptome sequencing in patients with Tetralogy of Fallot and healthy unaffected individuals [LncRNA/mRNA]

status: Public on Mar 13 2023

city: Chongqing

first: Quan

address: Zhongshan 2nd Road

department: Department of Cardiothoracic Surgery

institute: Children’s Hospital of Chongqing Medical University

summary: The right ventricular tissues of 5 children with tetralogy of Fallot and 5 healthy unaffected individuals were collected and sequenced in full transcriptome. Mechanism of tetralogy of fallot and cerna regulatory network were analyzed.

overall_design: Right ventricular transcriptome sequencing from 5 patients with Tetralogy of Fallot with right ventricle and transcriptome sequencing from right ventricle of 5 healthy unaffected individuals.


title: Transcriptome sequencing in patients with Tetralogy of Fallot and healthy unaffected individuals [miRNA]


title: Transcriptome sequencing in patients with Tetralogy of Fallot and healthy unaffected individuals


title: Genetically engineered endothelial niche induces vascularization in human kidney organoids

status: Public on May 22 2023

city: Pittsburgh

first: Joseph

middle: C.

last: Maggiore

state: PA

institute: University of Pittsburgh

summary: Here we developed a method to incorporate a genetically engineered endothelial niche into an established protocol for generating human kidney organoids.

overall_design: Control and vascularized human kidney orgaonids at day 18 were analyzed with snRNAseq

first: Ryan

last: LeGraw

first: Jeremy

last: Velazquez

first: Alex

last: Hill

first: Haojia

first: Benjamin

last: Humphreys

first: Samira

last: Kiani

first: Mo

last: Ebrahimkhani

first: Neil

last: Hukriede


title: Transcriptomic Effects on the Mouse Heart Following 30 Days on the International Space Station

status: Public on Mar 01 2023

city: Loma Linda

first: Lorelei

last: Hughes

address: 11021 Campus

department: Pathology and Human Anatomy

institute: Loma Linda University

summary: Efforts to understand the impact of spaceflight on the human body stem from the growing interest in long-term space travel. Multiple organ systems are affected by micro-gravity and radiation, including the cardiovascular system. Previous transcriptomic studies have sought to reveal the changes in gene expression after spaceflight. However, little is known about the impact of long-term spaceflight on the mouse heart in vivo. This study focused on transcriptomic changes in the hearts of female C57BL/6J mice flown on the International Space Station (ISS) for 30 days. RNA was isolated from the hearts of three flight and three comparable ground control mice and RNA sequencing was performed. Our analysis showed that 1,147 transcripts were significantly regulated after spaceflight. MAPK, PI3K-Akt and GPCR signaling pathways were predicted to be activated. Transcripts related to cytoskeleton breakdown and organization were upregulated, but no significant change in the expression of extracellular matrix (ECM) components or oxidative stress pathway associated transcripts occurred. Our results indicate an absence of cellular senescence, and a significant upregulation of transcripts associated with the cell cycle. Transcripts related to cellular maintenance and survival were most affected by spaceflight, suggesting that the cardiovascular transcriptome initiates an adaptive response to long-term spaceflight

overall_design: comparing transcriptomic diffrerences induced by spaceflight in the murine heart

first: Lana

last: Mamoun

first: Alicia

last: Veliz

first: Richard

last: Vega

first: Jillian

last: Bray

first: Bailey

last: Holmes

first: Andrea

last: Monteon

first: Micheal

last: Pecaut

first: Mary

last: Kearns-Jonker


title: Cbp1-Cren7 chromatinization of CRISPR arrays favours transcription from CRISPR leaders over cryptic promoters.

first: Finn

last: Werner

summary: CRISPR arrays form the physical memory of CRISPR adaptive immune systems by incorporating foreign DNA as spacers that are often AT-rich and derived from viruses. As promoter elements such as the TATA-box are AT-rich, CRISPR arrays are prone to harbouring cryptic promoters. Sulfolobales harbor extremely long CRISPR arrays spanning several kilobases, a feature that is accompanied by the CRISPR-specific transcription factor Cbp1. Aberrant Cbp1 expression modulates CRISPR array transcription, but the molecular mechanisms underlying this regulation are unknown. Here, we characterise the genome-wide Cbp1 binding at nucleotide resolution and characterise the binding motifs on distinct CRISPR arrays, as well as on unexpected non-canonical binding sites associated with transposasons. Cbp1 recruits Cren7 forming together ‘chimeric’ chromatin-like structures at CRISPR arrays. We dissect Cbp1 function in vitro and in vivo and show that the third HTH domain is responsible for Cren7 recruitment, and that Cbp1-Cren7 chromatinization plays a dual role in the transcription of CRISPR arrays. It suppresses spurious transcription from cryptic promoters within CRISPR arrays but enhances CRISPR RNA transcription directed from their cognate promoters in their leader region. Our results show that Cbp1-Cren7 chromatinization drives the productive expression of long CRISPR arrays.

sample_organism:
Saccharolobus solfataricus P2
Saccharolobus islandicus REY15A
Saccharolobus islandicus LAL14/1


title: Cappable-seq data for Sulfolobus islandicus REY15A and cbp1 deletion strains

overall_design: Cappable-seq data  for Sulfolobus islandicus REY15A Δcbp1 strain and the parental strain E234 to map 5'-ends of small (20-200 nt) 5'-triphosphorylated RNAs

first: Fabian

last: Blombach


title: Molecular and genetic insights into human ovarian aging from single-nuclei multi-omics analyses

status: Public on Mar 12 2023

first: Chen

last: Jin

institute: Columbia University Medical Center

summary: The ovary is the first organ to age in the human body, affecting both fertility and overall health. However, the biological mechanisms underlying human ovarian aging remain poorly understood. Here we present a comprehensive single-nuclei multi-omics atlas of four young (ages 23–29 years) and four reproductively aged (ages 49–54 years) human ovaries. Our analyses reveal coordinated changes in transcriptomes and chromatin accessibilities across cell types in the ovary during aging, notably mTOR signaling being a prominent ovary-specific aging pathway. Cell-type-specific regulatory networks reveal enhanced activity of the transcription factor CEBPD across cell types in the aged ovary. Integration of our multi-omics data with genetic variants associated with age at natural menopause demonstrates a global impact of functional variants on gene regulatory networks across ovarian cell types. We nominate functional non-coding regulatory variants, their target genes and ovarian cell types and regulatory mechanisms. This atlas provides a valuable resource for understanding the cellular, molecular and genetic basis of human ovarian aging.

overall_design: The snRNA-seq and snATAC-seq of human young and reproductively old ovaries

first: Yousin

last: Suh


title: ADAD2 facilitates piRNA biogenesis and spermiogenesis in mice

status: Public on Jan 19 2023

city: Kashihara

first: Hisato

last: Kobayashi

state: Nara

address: 840 Shijo-Cho

department: Department of Embryology

country: Japan

institute: Nara Medical University

summary: Adenosine Deaminase Domain Containing 2 (ADAD2) is a testis-specific protein composed of a double-stranded RNA binding domain and a non-catalytic adenosine deaminase domain. A recent study showed that ADAD2 is indispensable for the male reproduction in mice. However, its detailed function remains elusive. The aims of this study are to investigate the cause of male sterility in Adad2 knockout mice and to understand the molecular function of ADAD2. RNA-seq analyses were carried out to analyze the changes in the transcriptome and piRNA population of Adad2 mutant testes.

overall_design: RNA-seq of testis from Adad2-knockout mouse

first: Satomi

last: Kuramochi-Miyagawa


title: Challenges posed to the dermatophyte Trichophyton rubrum by sertraline; a drug predominantly used to treat human depression

status: Public on Feb 23 2023

city: Ribeirão Preto

first: Pablo

middle: Rodrigo

last: Sanches

state: SP

address: Av. Bandeirantes, 3900

department: Genetics

country: Brazil

institute: University of São Paulo

summary:
Purpose: We evaluated T. rubrum transcriptome using high-throughput RNA-sequencing (RNA-seq) technology aiming to identify metabolic pathways modulated by the antidepressive sertraline.
Methods: We employed the next-generation sequencing (RNA-seq) approach to identify the central responsively genes related to SRT effects.
Results: we identified the main effects of sertraline as the disturbance of maintaining the fungal cell wall and plasmatic membrane stability targeting ergosterol biosynthesis. SRT also modulated genes encoding enzymes related to fungal energy metabolism, cellular detoxification, and defense against oxidative stress
Conclusions: Our findings provide insights into a specific molecular network interaction operative for main-taining metabolic stability perturbed by SRT drug showing relevant targets for its strategic use in the dermatophytosis field.

overall_design: We examined at the transcriptomic level the effects of sertraline in Trichophyton rubrum metabolism.

first: Flaviane

last: Galvao-Rocha

first: Carlos

last: Rocha

first: Maíra

middle: P

last: Martins

first: Tamires

last: Bitencourt

first: Matthew

middle: S

last: Sachs

first: Antonio

last: Rossi

first: Nilce

last: Martinez-Rossi


title: Effective extraction of polyribosomes exposes gene expression strategies in primary astrocytes

status: Public on Feb 09 2023

city: Tel Aviv

first: Shir

last: Mandelboum

address: chaim levanon

department: Sagol School of Neuroscience

institute: Tel Aviv University

overall_design: Refer to individual Series


title: Single-cell multi-scale footprinting reveals the modular organization of DNA regulatory elements

status: Public on Mar 28 2023

city: Cambridge

first: Jason

last: Buenrostro

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: PGC 1α Senses the CBC of Pre-mRNA to Dictate the Fate of Promoter-Proximally Paused RNAPII [RIP-seq native]

city: Rochester

first: Lynne

last: Maquat

state: New York

address: 601 Elmwood Ave # 712

institute: University of Rochester

summary: Although PGC 1α is well-established as a transcriptional coactivator for the metabolic adaptation of mammalian cells to diverse physiological stresses, its molecular dynamics at the start and during gene transcription are incompletely understood. Previously, we defined a CBP80-binding motif (CBM) within PGC 1α that binds CBP80 at the 5′-cap of nascent transcripts deriving from PGC 1α-responsive genes. Binding verifies proper 5′-cap assembly, after which gene transcription is somehow promoted. Here, using protein immunoprecipitations, size-exclusion chromatography, PRO-seq, RNA-seq, native RIP-seq, RIP-seq footprinting and CUT&RUN, we report that PGC 1α, serving as a DNA−RNA conduit between promoter-bound ERRα and nascent transcript-bound CBP80, overcomes promoter-proximal pausing of RNAPII by competing against the premature transcription termination complex Integrator and also by recruiting P-TEFb. Using mice homozygous for five amino-acid changes in PGC 1α that destroy CBM function, we demonstrate that efficient differentiation of primary myoblasts to myofibers and effective regeneration of skeletal muscle after injury requires PGC 1α binding to CBP80.

overall_design: Three biological replicates were generated to compare mRNA levels, using RIP-seq, in anti-FLAG IPs using lysates of PGC-1α KD C2C12 MBs (i.e. WT C2C12 MBs stably expressing a PGC-1α-mRNA targeting shRNA) transiently expressing FLAG alone, FLAG-PGC-1α(WT), or FLAG-PGC-1α(CBM5mut)

first: Xavier

last: Rambout

first: Hana

last: Cho

first: Hari

last: Yalamanchili

middle: E


title: PGC 1α Senses the CBC of Pre-mRNA to Dictate the Fate of Promoter-Proximally Paused RNAPII [RNA-seq]

overall_design: Three biological replicates were generated to compare total-cell mRNA levels, using RNA-seq, in PGC-1α KD C2C12 MBs (i.e. WT C2C12 MBs stably expressing a PGC-1α-mRNA targeting shRNA) transiently expressing FLAG alone, FLAG-PGC-1α(WT), or FLAG-PGC-1α(CBM5mut)

middle: K


title: PGC 1α Senses the CBC of Pre-mRNA to Dictate the Fate of Promoter-Proximally Paused RNAPII


first: Finn

last: Werner

overall_design: ChIP-seq data for chromatin proteins Cbp1 and CreN7 in a Sulfolobus islandicus REY15A Δcbp1 strain and the parental strain E234 to conduct a differential binding analysis for CreN7

first: Fabian

last: Blombach


title: PGC 1α Senses the CBC of Pre-mRNA to Dictate the Fate of Promoter-Proximally Paused RNAPII [RIP-seq footprint]

overall_design: Three biological replicates were generated to compare RNA footprints, using RIP-seq footprinting, in anti-FLAG IPs using lysates of PGC-1α KD C2C12 MBs (i.e. WT C2C12 MBs stably expressing a PGC-1α-mRNA targeting shRNA) transiently expressing FLAG alone, FLAG-PGC-1α(WT), or FLAG-PGC-1α(CBM5mut)


title: Multi-scale chromatin footprinting reveals wide-spread alterations to the structure of DNA regulatory elements [scRNA-Seq]

overall_design: 10x multi-ome to profile RNA levels in mouse hematopoietic stem cells from different age groups

first: Fabiana

last: Duarte

first: Heidi

last: Kletzien

first: Rojesh

last: Shrestha

first: Yan

last: Hu


title: High-throughput sequencing in SLE patients PBMC

status: Public on Jan 13 2023

city: Changchun

first: Xiaosong

last: Wang

state: Jilin

address: No.519 Dongminmin Street Changchun 130021, China

institute: Department of Translational Medicine, the First Hospital of Jilin University

summary: High-throughput sequencing was performed on the PBMCs from SLE patients and healthy control. The purpose of the current study is to identify new genes and pathways of interest involved in the pathogenesis of SLE.

overall_design: 20 SLE patients (10 patients with LN and 10 SLE patients without LN were included) and 10 healthy controls were randomly selected for RNA sequencing.

first: Mingyue

last: Yang


title: Modulation of CTCF barrier permeability by ZFP661 enhances protocadherin diversity for proper cortical dendritic projection in mammals

status: Public on May 09 2023

city: Bethesda

first: Jinpu

last: Jin

address: Building 6B, Room 2B-211, 6 Center Drive

institute: NICHD

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


title: PGC 1α Senses the CBC of Pre-mRNA to Dictate the Fate of Promoter-Proximally Paused RNAPII [PRO-seq]

overall_design: Two biological replicates were generated to compare at single-nucleotide resolution, using PRO-seq, the gene localization of transcribing RNAPII in control (CTL) C2C12 myoblasts (MBs) (i.e. WT C2C12 MBs stably expressing a control GFP-mRNA-targeting shRNA) transiently expressing FLAG alone, and in PGC-1α KD C2C12 MBs (i.e. WT C2C12 MBs stably expressing a PGC-1α-mRNA targeting shRNA) transiently expressing FLAG alone, FLAG-PGC-1α(WT), or FLAG-PGC-1α(CBM5mut)

first: Geoffrey

last: Nelson

first: Karen

last: Adelman


title: RNA-seq analysis of young adult daf-18(ok480) and control  worms

status: Public on Jan 11 2023

city: Kaifeng

first: Shanqing

last: Zheng

address: 1 Jinming Avenue North, Longting District,  School of Basic Medical Sciences, Henan University

institute: Henan university

summary: RNA-seq analysis was used to identify the gene expression changes in male and hermaphroditie when daf-18 is lost. Based on these sequencing data, the genes that were up-regulated or down-regulated by at least 2 times (|log2 (folding change) | ≥ 1 and padj ≤ 0.05) were analyzed. The analysis of these differentially expressed genes' pathway and gene ontology (GO) enrichment shows that the influence of different genders after daf-18 deletion is enriched to some signal pathways, including longevity and protein degradation pathway in endoplasmic reticulum, etc.

overall_design: The mRNA profile changes of each sex when daf-18 is lost,  were generated by deep sequencing. Use Illumina Gallx


title: Deciphering the resiquimod induced toll-like receptor signalling pathway in chickens

status: Public on Jan 03 2023

city: Bareilly

first: SARAVANAN

last: RAMAKRISHNAN

state: Uttar Pradesh

address: Izatnagar

country: India

institute: ICAR-Indian Veterinary Research Institute

summary: Resiquimod (R-848) is a synthetic TLR7 agonist.  This study was targeted to understand  the signaling molecules involved in the Resiquimod (R-848) mediated TLR7 stimulation in the chicken and specifically for Th1 and Th2 type of immune responses. For this, transcriptome data (RNA-seq)  was generated from RNA extracted at 24 hour from  spleen tissues (1 each) of both control (untreated) and chicken administered with R-848 (intra muscular route). Upregulated and downregulated genes were identified following using transcriptome analysis pipeline Geo2RNAseq_0.99.9  (https://anaconda.org/xentrics/r-geo2rnaseq). Within the pipeline, the reads were quality checked using FastQC,  quality trimming performed with Trimmomatic (Bolger et al., 2014) and reference genome (Gallus gallus: GRCg6a (GCA_000002315.5)) mapping was carried out using TopHat2 (Kim et al., 2013). Differently expressed genes (DEGs) were identified using baySeq (Hardcastle and Kelly, 2010). Functional annotation of  DEGs were carried out using g:Profiler (Reimandet al., 2016; http://biit.cs.ut.ee/gprofiler/). Among the 5884 DEG, eight genes enriched in biological processes associated to signal transduction (MAPK14, MAP3K8, PIK3CD, STAT1, STAT3, MAPK11 LRRK2, and GATA3) were considered for further validation. Among the eight significant DEGs, MAPK14, MAP3K8, PIK3CD, STAT1 and STAT3 were up-regulated while MAPK11, LRRK2 and GATA3 transcripts were down-regulated in the R-848 treated birds evidenced by transcriptomic data.

overall_design: Chicken spleen RNA profiles of treatment  (post 24 hour R-848 administed)  and control were generated by deep sequencing using Illumina sequencing technology

first: Deepthi

last: Kappala

first: Prasad

last: Thomas

first: R

last: Saravanan


title: Cystic fibrosis causes olfactory system defects by altering progenitor cell proliferation (scRNA-Seq)

status: Public on Dec 31 2022

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

country: France

institute: IPMC/CNRS

summary: A reduced sense of smell has been reported in people with cystic fibrosis (CF). These olfactory defects have largely been attributed to secondary manifestations of the disease, such as inflammation of the nasal mucosa. Here we show that CFTR, the gene responsible for CF, is expressed in proliferating olfactory human cells and that  newborn CFTR null pigs display ultrastructural abnormalities in the olfactory epithelium and olfactory bulbs. In the absence of CFTR, olfactory sensory neurons still produce odor-evoked activity, but mutant animals display defective odor-guided suckling behavior after birth. Consistent with epithelial changes, we found a reduced expression of genes implicated in cell cycle and development in globose basal cells (GBCs), the neurogenic progenitor cells in the olfactory epithelium. Targeted sequencing revealed enhanced CFTR expression in the subpopulation of GBCs that is actively proliferating. Furthermore, CFTR loss caused a global reduction in the number of sensory neurons and altered olfactory receptors expression. Our findings highlight a previously unknown role of CFTR in olfactory system function by regulating progenitor cell proliferation in the olfactory epithelium.

overall_design: The molecular pathology of olfactory loss in CF.

first: Ignacio

last: Caballero

first: Raquel

last: López-Gálvez

first: Yvon

last: Mbouamboua

first: Marie

last: Couralet

first: Isabelle

last: Fleurot

first: Nicolas

last: Pons

first: Marta

last: Barrera-Conde

first: Nayima

last: Quílez-Playán

first: Matthieu

last: Keller

first: Nikolai

last: Klymiuk

first: Patricia

last: Robledo

first: Pascal

last: Barbry

first: Pablo

last: Chamero


title: Cystic fibrosis causes olfactory system defects by altering progenitor cell proliferation


title: Cystic fibrosis causes olfactory system defects by altering progenitor cell proliferation (Bulk RNA-Seq)


title: A dietary change to a high fat diet initiates a rapid adaptation of the intestine

status: Public on Nov 15 2022

city: Chicago

first: Jacob

last: Enriquez

state: IL

institute: University of Chicago

summary: Examine the single cell transcriptional changes during Normal Chow and Acute HFD

overall_design: Duodenum and Jejunum under Normal Chow, 1 Day HFD, 3 Days HFD, and 7 Days HFD

first: James

last: Wells


title: Genomic and Transcriptional Characterisation of Carbapenem and Colistin Resistance Mechanisms in Klebsiella pneumoniae

status: Public on Nov 07 2022

city: Pretoria

first: John

last: Osei Sekyere

state: Gauteng

address: 05 Bopheloweg Off Dr. Savage Road

department: Department of Medical Microbiology

country: South Africa

institute: University of Pretoria

summary: The transcriptional, epigenomic, and genomic profiles of K. pneumoniae isolates were characterised to identify novel colistin and carbapenem resistance mechanisms. The genomic DNA and total RNA of the isolates were isolated and sequenced on PacBio.

sample_organism:
Acinetobacter baumannii
Enterobacter cloacae
Klebsiella pneumoniae
Enterobacter asburiae
Enterobacter bugandensis
Enterobacter cloacae complex sp. R_G8

overall_design: DNA-seq sequenced on PACBIO platform and RNA-seq sequenced on Illumina MiSeq.

first: Masego

last: Mmatli

first: Nontombi

last: Mbelle

first: Tumisho

last: Mmatumelo Seipei Leshaba

first: Busi

last: Lebogang Skosana


title: DNA methylation analysis using Illumina 450K BeadChip of 7 pancreatic ductal adenocarcinoma patients

status: Public on Nov 09 2022

city: Kolkata

first: Nilabja

last: Sikdar

state: West Bengal

address: Plot No, 203, Barrackpore Trunk Rd, Dunlop, Bonhooghly Government Colony, Baranagar, Kolkata, West Bengal 700108

department: Human Genetics Unit

institute: Indian Statistical Institute

summary: Genome-wide DNA methylation profiling of normal and tumor tissue samples of 7 pancreatic ductal adenocarcinoma patients.

overall_design: Bisulphite-converted DNA from the 14 samples were hybridised to the Illumina Infinium 450k Human Methylation BeadChip v1.2.


title: Impact of COP1 silencing on hepatoma and hepatocyte transcriptomics

status: Public on Nov 01 2022

city: Ottawa

first: Ruth

last: McPherson

state: Ontario

address: 40 Ruskin

country: Canada

institute: UOHI

summary: Transfection experiments aimed at understanding the role of COP1 in hepatocytes and hepatoma models

overall_design: HuH-7 cells, HepG2 cells (hepatocyte-derived carcinoma cell line) or a lot of commercial primary hepatocytes (HMCPMS) from ThermoFisher Scientific were transfected for 96 h with 10 nM siRNA targeting either a RFWD2/COP1 or a control (NT1) siRNA.  RNA was then harvested and the transcriptome analyzed by transcription array.  Each file corresponds to a distinct biologic:  the experiment was repeated on 2 -3 distinct occasions.

first: Sebastien

last: Soubeyrand


title: Multiple genes of Candida albicans influencing echinocandin susceptibility in caspofungin-adapted mutants

status: Public on Nov 05 2022

first: Soumyaroop

last: Bhattacharya

state: NY

address: 601 Elmwood Ave Box 703

summary: Expression profiles of five caspofungin adapted candida albicans strains were analysed from their parental strains

overall_design: RNA-seq of Candia albicans caspofungin adapted strains were compaired from their parental strain.

first: Elena

last: Rustchenko

first: Sudisht

last: Sah

first: Anshuman

last: Yadav

first: Farha

last: Husain

first: Aissatou

middle: B

last: Ndiaye

first: Michael

last: Kruppa

first: Jeffrey

middle: J

last: Hayes


title: Charting the development of Drosophila leg sensory organs at single-cell resolution

status: Public on Oct 13 2022

city: Davis

first: Ben

last: Hopkins

state: CA

address: One Shields Avenue

department: Evolution & Ecology

institute: UC Davis

summary: To respond to the world around them, animals rely on the input of a network of sensory organs distributed across the body. A single individual will generally express several distinct classes of sensory organ, each bearing features that appear to enhance the detection of specific stimuli, such as strain, pressure, or light. The features that underlie this specialization relate both to the neurons housed within a sensory organ and to the various accessory cells that they are composed of. This diversity of cell types, both within and between sensory organs, raises two fundamental questions: (1) How is this diversity generated during development? And (2) What makes these cell types distinct from one another? To address these questions, we performed single-cell RNA-sequencing on a region of the pupal male Drosophila melanogaster foreleg that displays a wide variety of functionally and structurally distinct sensory organs: the first tarsal segment. Our work characterizes the cellular landscape in which the sensory organs reside; identifies a novel glia  cell type that appears to contribute towards the construction of the neural lamella; resolves and validates a combinatorial transcription factor code unique to each of mechanosensory, sex comb, and campaniform sensilla neurons, as well as four distinct gustatory receptor neuron classes; matches receptors and membrane channels to specific neurons; and characterizes the transcriptomic differences between and within sensory organ support cell types. Collectively, our work identifies core genetic features of a variety of sensory organs and provides a rich, annotated resource for studying their development and function.

overall_design: First tarsal segment cells from pupal male Drosophila melanogaster (DGRP line RAL-517) were isolated separately at 24h and 30h after puparium formation


title: mtDNA breaks compromise mitochondrial membrane ultrastructure and trigger an integrated stress response

status: Public on Oct 04 2022

city: New York

first: Yi

last: Fu

address: 430 E 67th Street – RRL 1141

institute: MSKCC

summary: Mitochondrial DNA (mtDNA) breaks are deleterious lesions that lead to degradation of mitochondrial genomes and subsequent reduction in mtDNA copy number. The signaling pathways activated in response to mtDNA damage remain ill-defined. Using mitochondrial targeted restriction enzymes, we show that cells with mtDNA breaks exhibit reduced respiratory complexes, loss of membrane potential, and mitochondrial protein import defect. Furthermore, mtDNA damage activates the integrated stress response (ISR) through phosphorylation of eIF2α by the OMA1-DELE1-HRI pathway. Electron microscopy reveals concomitant defects in mitochondrial membranes and cristae ultrastructure. Notably, inhibition of the ISR exacerbates mitochondrial defects and delays the recovery of mtDNA copy number, thereby implicating this stress response in mitigating mitochondrial dysfunction following mtDNA damage. Last, we provide evidence suggesting that ATAD3A, a membrane-anchored protein that interacts with nucleoids, relays the signal from mtDNA breaks to the inner mitochondrial membrane. Altogether, our study fully delineates the sequence of events linking damaged mitochondrial genomes with the cytoplasm and uncovers an unanticipated role for the ISR in response to mitochondrial genome instability.

overall_design: We performed RNA-seq analysis on GFP11 tagged RRBP1 and MTA2 cells subjected to the following treatments: ApaLI* + Dox, ApaLI + Dox, ApaLI + Dox GFP- population, ApaLI + Dox GFP+ population. RNA-seq was done in 2 replicates.

first: Agnel

last: Sfeir


title: An atlas of transcribed human cardiac promoters and enhancers reveals an important role of regulatory elements in heart failure

status: Public on Oct 20 2022

city: Tokyo

first: Ruslan

last: Deviatiiarov

address: Hongo 2-1-1, Bunkyo-ku

department: Intractable Disease Research Center

institute: Juntendo University

summary: In this work we present atlas of human cardiac regulatory elements defined by CAGE (cap analysis of gene expression) technique. The dataset includes right and left atria and ventricles form both healthy and failing samples. The deep sequencing of CAGE libraries on Illumina HiSeq2500, mapping, and signal clustering resulted in identification of 65,458 CAGE peaks, from which 55,204 were robust decomposition peak identifiers (DPIs) and 10,254 bidirectional enhancers. We created comprehensive classification of the peaks by applying machine learning along with annotation from available databases containing cardiac data. Identified CAGE peaks were arranged into non-overlapping 400 bp consensus clusters. Our classification method determined 17,668 promoters and 14,920 enhancers active in the human heart. Differential expression analysis revealed regulatory elements activated or inactivated in healthy or failing states. About 10% of heart related GWAS SNPs were found to be located around heart CAGE clusters. The library of cardiac promoters and enhancers is available in Zenbu reports for browsing and visualization.   Superior and inferior sinoatrial node samples are labeled as sSAN and iSAN, respectively.

overall_design: In total 109 samples from 31 human hearts were freshly collected and were either flash frozen in liquid nitrogen or stored in RNAlater. Total RNA was extracted with RNeasy Fibrous Tissue Mini Kit and CAGE libraries prepared with ssCAGE or nAnT-iCAGE. Libraries were sequenced on Illumina HiSeq2500.

first: Anna

last: Gams

first: Roman

last: Syunyaev

first: Tatiana

last: Tatarinova

first: Ramesh

last: Singh

first: Palak

last: Shah

first: Oleg

last: Gusev

first: Igor

last: Efimov

first: Ivan

last: Kulakovskiy

first: Andrey

last: Buyan

first: Georgy

last: Meshcheryakov


title: Small-molecule inhibition of the acyl-lysine reader ENL as a strategy against acute myeloid leukemia [RNA-Seq]

status: Public on Oct 05 2022

city: Philadelphia

first: Liling

last: Wan

address: 421 Curie Blvd

department: Cancer Biology

institute: University of Pennsylvania

summary: Acute myeloid leukemia (AML) is characterized by dysregulated transcriptional programs and these programs require support from chromatin regulators to maintain their hyperactive state. Recent studies have identified the histone acylation ‘reader’ ENL as being a critical dependency in AML, but the potential of therapeutic applications targeting this chromatin reader remains poorly understood. Here, we present a potent and orally bioavailable small-molecule inhibitor of ENL, TDI-055, which displaces ENL from chromatin by competitively blocking the interaction of its YEATS domain with acylated histones. We show that TDI-055 treatment preferentially inhibited the proliferation of human leukemia cells harboring MLL translocations or NPM1 mutations. Through a CRISPR/Cas9 saturated mutagenesis screen, we uncovered an ENL mutant that could confer cells resistance to TDI-055, thus providing compelling proof for the on-target activity of the compound. Rapid displacement of ENL from chromatin resulted in decreased recruitment of select ENL-associated complexes and impaired RNA polymerase II elongation which, in turn, led to the suppression of critical leukemogenic gene expression programs. Finally, pharmacological inhibition of ENL in vivo led to reduced AML growth and prolonged survival in cell line and patient-derived xenograft (PDX) models. Collectively, these results provide critical evidence and mechanistic insights to establish inhibition of ENL as a potential therapeutic strategy against molecularly defined AML, laying the foundation for rapid clinical translation of this approach.

overall_design: to determine transcriptional changes induced by TDI-055 in MV411 and OCI-AML3 cell lines

first: Yiman

last: Liu

first: Hangpeng

last: Li

first: Qinglan


title: RNA-seq analysis of human placenta to elucidate the pathomechanism of spontaneous preterm birth

status: Public on Oct 24 2022

city: Sheffield

first: Khondoker

middle: Mehedi

last: Akram

state: South Yorkshire

address: Tree Root Walk

department: Oncology and Metabolism

institute: University of Sheffield

summary: The pathogenesis of spontaneous preterm birth (PTB) is largely unknown. We conducted RNA-seq transcriptomic analysis, qRT-PCR and ELISA on fresh placental villous tissue from 20 spontaneous preterm and 20 spontaneous term deliveries, to identify genes and signalling pathways involved in the pathogenesis of PTB. Our differential gene expression, gene ontology and pathway analysis revealed several dysregulated genes, including OCLN, OPTN, KRT7, WNT7A, RSPO4, BAMBI, NFATC4, SLC6A13, SLC6A17, SLC26A8 and KLF8, associated with altered trophoblast functions. We identified dysregulated Wnt, oxytocin and cellular senescence signalling pathways in preterm placentas, where augmented Wnt signalling could play a pivotal role in the pathogenesis of PTB due to its diverse biological functions. We provide fresh molecular insight into the pathogenesis of spontaneous PTB, which may drive further studies to develop new predictive biomarkers and therapeutics.

overall_design: Total RNA was extracted from fresh villous tissue from 20 spontaneous preterm (cases) and 20 term (controls) human placentas. Bulk NGS RNA sequencing was conducted using MinION Oxford Nanopore Technology. Differential gene expression analysis was conducted to identify significantly differentially expressed genes in the preterm placenta. Gene ontology and signalling pathway analyses were conducted using upregulated and downregulated gene sets separately. A sub-group analysis was also conducted to differentiate gene expression profiles of male and female preterm placentas compared to term placentas, to elucidate the influences of fetal sex differences on preterm labour.

first: Neha

last: Kulkarni

first: Abbey

last: Brook

first: Matthew

last: Wyles

first: Dilly

middle: O

last: Anumba


title: XEN state reprogramming into self-organizing trophectoderm-like cells enables the assembly of synthetic embryoids

status: Public on Sep 13 2022

city: Muenster

first: Hyun-Woo

last: Jeong

state: NRW

department: Dept. Tissue Morphogenesis

country: Germany

institute: Max-Planck-Institute for Molecular Biomedicine

summary: We established culture conditions that enable the two fates of blastocysts’ extraembryonic lineages – the primitive endoderm and the trophectoderm – to co-exist in a shared XTE state. The XTE cells exhibit robust self-organization capacity and in combination with ES cells enable the assembly of blastocyst-like embryoids.

overall_design: We use single cell RNA-sequencing to characterise the three lineages (epiblast, primitive endoderm and trophectoderm) of the E4.5 blastocyst and compare transcriptionally these cells with the XTE/ES cells embryoids.

first: Anusha

last: Sathyanarayanan

first: Rui

last: Chen

last: Bedzhov


title: Aberrant MYCN expression drives oncogenic hijacking of EZH2 as a transcriptional activator in peripheral T cell lymphoma

status: Public on Sep 01 2022

city: Leuven

first: Sofie

last: Demeyer

address: Herestraat 49 / bus 912

department: Center for Cancer Biology

institute: KULeuven / VIB

overall_design: Refer to individual Series


title: Small-molecule inhibition of the acyl-lysine reader ENL as a strategy against acute myeloid leukemia


title: Aberrant MYCN expression drives oncogenic hijacking of EZH2 as a transcriptional activator in peripheral T cell lymphoma [RNA-seq]

summary: Peripheral T cell lymphoma (PTCL) is a heterogeneous group of hematological cancers arising from the malignant transformation of mature T cells. In a cohort of 28 PTCL cases, we identified recurrent overexpression of MYCN, a member of the MYC family of oncogenic transcription factors. Approximately half of all PTCL cases was characterized by a MYC expression signature. Inducible expression of MYCN in lymphoid cells in a mouse model caused T cell lymphoma that recapitulated human PTCL with a MYC expression signature. Integration of mouse and human expression data identified EZH2 as a key downstream target of MYCN. Remarkably, EZH2 was found to be an essential co-factor for the transcriptional activation of the MYCN-driven gene expression program, which was independent of methyltransferase activity, but dependent on phosphorylation by CDK1. MYCN-driven T cell lymphoma was sensitive to EZH2 degradation or CDK1 inhibition, which displayed synergy with FDA-approved HDAC inhibitors.

overall_design: 3' end RNA sequencing data of murine MYCN-driven T cell lymphoma, and CD4 T cells (control).

first: Marlies

last: Vanden Bempt

first: Daan

last: Dierickx


title: Aberrant MYCN expression drives oncogenic hijacking of EZH2 as a transcriptional activator in peripheral T cell lymphoma [ChIP-seq]

overall_design: ChIPmentation sequencing of murine thymus cells of MYCN-driven T cell lymphomas with H3K27ac, H3K4me3, H3K27me3, p300, NMYC, EZH2 and SUZ12 antibodies.


title: RNA Post-transcriptional Modifications in Two Large Subunit Intermediates Populated in E.coli Cells Expressing Helicase Inactive R331A DbpA

status: Public on Sep 15 2022

city: El Paso

first: Eda

last: Kocui

address: 500 W. University Avenue

department: Chemistry and Biochemistry

institute: University of Texas at El Paso

summary: 23S ribosomal RNA (rRNA) of Escherichia coli 50S large ribosome subunit contains 26 post-transcriptionally modified nucleosides. Here, we determine the extent of modifications in the 35S and 45S large subunit intermediates, accumulating in cells expressing the helicase inactive DbpA protein, R331A, and the native 50S large subunit. The modifications we characterized are nine pseudouridines, 3-methylpseudouridine, 2-methyladenine, and 5-hydroxycytosine. These modifications were detected using 1-cyclohexyl-(2-morpholinoethyl)carbodiimide metho-p-toluene sulfonate (CMCT) treatment followed by alkaline treatment. In addition, KMnO4 treatment of 23S rRNA was employed to detect 5-hydroxycytosine modification. CMCT and KMnO4 treatment produce chemical changes in modified nucleotides that cause reverse transcriptase misincorporations and deletions, which were detected employing next generation sequencing. Our results show that seven uridines to pseudouridine isomerizations and the 2-methyladenosine modification are present both in the 35S and 45S to similar extents as in the 50S. Hence, the enzymes that perform these modifications, namely RluF, RluB, RlmN, RluA, RluC, and RluA, have already acted in the intermediates. While two uridines to pseudouridines isomerizations, the 3-methylpseudouridine, and 5-hydroxycytosine modifications are significantly less present in the 35S and 45S as compared to the 50S. Therefore, the enzymes that perform these modifications, RluD, RlmH, and RlhA, are in the process of modifying the 35S, and 45S or these enzymes act during the later stages of ribosome assembly. Our study employs a novel high throughput and single nucleotide resolution technique for detection of 2-methyladenine and two novel high throughput and single nucleotide resolution technique for detection of 5-hydroxycytosine.

overall_design: Ribosomal particles treated with CMCT and NaHCO3 , NaHCO3 alone, KMnO4, or no chemical treatment

last: Koculi

first: Samuel

last: Cho


title: Single cell ATAC-seq analysis of the kidney in a murine endotoxemia model

status: Public on Aug 17 2022

city: Indianapolis

first: Takashi

last: Hato

state: IN

address: 950 W. Walnut St. R2 202

department: Medicine

institute: Indiana University

summary: To investigate chromatin accessibility changes after endotoxin exposure in the mouse kidney, single-cell ATACseq was performed (10X Genomics). Low dose endotoxin (0.25 mg/kg) was used to examine the renoprotective effects of endotoxin preconditioning.

overall_design: C57BL/6J male mice (8-10 weeks of age) were subjected to the following condtions: 1) untreated control, 2) 0.25 mg/kg LPS for 4 hrs, 3) 0.25 mg/kg LPS for 24 hrs, 4)  0.25 mg/kg LPS followed 24 hrs later by 5 mg/kg LPS for 24 hrs.  5) 5 mg/kg LPS for 16 hrs.


title: The genomic and immune landscape of long-term survivors of high-grade serous ovarian cancer

status: Public on Aug 26 2022

city: Melbourne

first: Dale

middle: W

last: Garsed

state: VIC

address: 305 Grattan St

country: Australia

institute: Peter MacCallum Cancer Centre

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


title: The genomic and immune landscape of long-term survivors of high-grade serous ovarian cancer [Methylation array]

summary:
Less than half of all patients with advanced-stage high-grade serous ovarian cancers (HGSC) survive more than five years post-diagnosis but those who have an exceptionally long survival could provide new insights into tumor biology and therapeutic approaches. We analyzed 60 patients with advanced-stage, HGSC who survived more than 10 years after diagnosis using whole-genome sequencing, transcriptome, and methylome profiling of their primary tumor samples, comparing this data to 66 short- or moderate-term survivors. Tumors of long-term survivors were more likely to have multiple alterations in genes associated with DNA repair, and more frequent somatic variants resulting in an increased predicted neoantigen load. Patients clustered into survival groups based on genomic and immune cell signatures, including three subsets of patients with BRCA1 alterations with distinctly different outcomes. Specific combinations of germline and somatic gene alterations, tumor cell phenotypes, and differential immune responses appear to contribute to long-term survival in HGSC.
Methylation profiling was done on 58 high grade serous ovarian cancer samples, 53 of which were primary tumors and  and 5 were relapse tumors. 73 primary tumors from GSE65820 were also used as part of the cohort.

overall_design: Genome wide DNA methylation profiling of 53 primary tumors and 5 relapse tumors of long-term survivors of high grade serous ovarian cancer. The Illumina Infinium MethylationEPIC BeadChip was used to obtain DNA methylation profiles across approximately 850,000 CpGs. 73 primary tumors from GSE65820 were also used in the project.

first: Ahwan

last: Pandey

first: David

last: Bowtell


title: ChIP-seq assay in human cancer cells

status: Public on Aug 04 2022

city: La Jolla

first: Yuliang

last: Tan

state: California

address: Room 345, CMM West, 9500 Gilman Drive, Mail Code 0648

department: School of Medicine

institute: University of California, San Diego

summary: ChIP-seq assay was performed for the quantitative detection of  the binding of TFs and histones upon acute stimulations.

overall_design:
MCF7 cells were maintained at 37°C and 5% CO2 in Dulbecco's modified Eagle's medium (DMEM, GIBCO/Invitrogen), supplemented with 10% fetal bovine serum (FBS, GIBCO/Invitrogen). LNCAP cells were maintained at 37°C and 5% CO2 in Advanced RPMI 1640 medium (GIBCO/Invitrogen), supplemented with 10% fetal bovine serum (FBS, GIBCO/Invitrogen).
For hormone treatments, cells were incubated at 37°C and 5% CO2 for at least 3 days in phenol red-free DMEM (GIBCO/Invitrogen) supplemented with 5% charcoal dextran-stripped FBS (GIBCO/Invitrogen). 17-β-Estradiol (E2; Steraloids, Inc.) was added to a final concentration of 100 nM. TNF⍺ (R&D systems) was added to a final concentration of 20 ng/ml. 5α-dihydrotestosterone (DHT, Sigma) was added to a final concentration of 100 nM. The ethanol (EtOH) vehicle control was 0.05% in all samples. For knock-down of Top1 genes, the siTop1_1 (SASI_Hs01_00047440, Sigma, CACAAAGAGAGGAAUGCUA[dT][dT], UAGCAAUCCUCUCUUUGUG[dT][dT]) and siTop1_3 (SASI_Hs02_00335354, Sigma, GACAAGAUCCGGAACCAGU[dT][dT], ACUGGUUCCGGAUCUUGUC[dT][dT]) were employed. For knock-down of Cbx3 genes, the siCbx3_1 (SASI_Hs01_00170890, Sigma, CCAAGAGGAUUUGCCAGAG[dT][dT], CUCUGGCAAAAUCCUCUUGG[dT][dT]) and siCbx3_2 (SASI_Hs01_00196532, Sigma, CCAAGAGGAUUUGCCAGAG[dT][dT], CUCUGGCAAAAUCCUCUUGG[dT][dT]) were employed. For ChIP-seq and PRO-seq experiments, cells were transfected in 10-cm plates in regular DMEM without antibiotics. 20 μl of 20 μM small interfering RNA (siRNAs) and Lipofectamine® 2000 reagent (Invitrogen Cat# 11668-019) were diluted in Opti-MEM I Reduced Serum Medium (Invitrogen Cat# 11058-021), and incubated for 6 h, and then changed to phenol red-free medium.


title: TOP1cc-seq assay in human cancer cells

summary: TOP1cc-seq assay was performed for the quantitative detection of  the transient DNA-protein covalent interactions upon acute stimulations.

overall_design:
MCF7 cells were maintained at 37°C and 5% CO2 in Dulbecco's modified Eagle's medium (DMEM, GIBCO/Invitrogen), supplemented with 10% fetal bovine serum (FBS, GIBCO/Invitrogen). LNCAP cells were maintained at 37°C and 5% CO2 in Advanced RPMI 1640 medium (GIBCO/Invitrogen), supplemented with 10% fetal bovine serum (FBS, GIBCO/Invitrogen).
For hormone treatments, cells were incubated at 37°C and 5% CO2 for at least 3 days in phenol red-free DMEM (GIBCO/Invitrogen) supplemented with 5% charcoal dextran-stripped FBS (GIBCO/Invitrogen). 17-β-Estradiol (E2; Steraloids, Inc.) was added to a final concentration of 100 nM. TNFalpha (R&D systems) was added to a final concentration of 20 ng/ml. 5α-dihydrotestosterone (DHT, Sigma) was added to a final concentration of 100 nM. The ethanol (EtOH) vehicle control was 0.05% in all samples.