title: Transcriptomics analysis of proliferation and differentiation of Guangxi  cattle muscle stem cells

status: Public on Jun 12 2021

city: Nanning

first: Ruimen

last: Zhang

address: NO.100 University Road,Xi xiang tang

institute: Guangxi University

summary: More and more studies have shown that mRNAs and non-coding RNAs are involved in human diseases and various biological processes of animals, and play an important functional role in animal muscle growth and development.  In this study, the expression levels of myogenic marker molecules MYOD1, MYOG, and MyHC increased after cattle muscle stem cells transition from proliferation to differentiation, which promoted the differentiation and maturation of cells. Then, we used RNA sequencing and bioinformatics to analyze the RNA expression of muscle stem cell proliferation phase (GM) and differentiation phase (DM). The results showed that 19,341 protein-coding RNAs (mRNAs) and 12,920 non-coding RNAs participated in the proliferation and differentiation of cattle muscle stem cells. And there were 2,148 differential mRNAs and 888 non-coding RNAs, including 113 miRNAs, 662 lncRNAs, and 113 circRNAs. These differentially expressed mRNAs are enriched in ECM receptor function, cell cycle, TGF-beta, PI3K-Akt and other signaling pathways, covering biological processes such as cell proliferation, invasion, differentiation, and autophagy. At the same time, we verified the expression levels of 7 mRNAs, 3 miRNAs, 2 lncRNAs, and 12 circRNAs by real-time quantitative PCR analysis, and selected circUBE2Q2 for functional verification. The expression profiling analysis showed that circUBE2Q2 was expressed in multiple tissues, and its expression in muscle stem cell differentiation phase was significantly higher than that in proliferation phase. In vitro cell experiments, circUBE2Q2 significantly promoted the differentiation and apoptosis of MuSCs and had no effect on proliferation. It indicates that circRNA plays a role in the muscle development of Guangxi cattle.   Our research revealed the role of RNA expression in the proliferation and differentiation of Guangxi cattle muscle stem cells. These results provide new clues for the analysis of the mechanism by which mRNAs and non-coding RNAs regulate the proliferation and differentiation of Guangxi cattle muscle stem cells.

overall_design: Profiles of mRNAs and non-coding RNAs during the proliferation (GM) and differentiation (DM) of Guangxi Cattle muscle stem cells

first: Sufang

last: Yang

first: Yanfei

last: Dend

first: Yingming

last: Wei


title: RNA/WES/ATAC/scRNA sequencing of murine melanoma primary and LN metastases

status: Public on Jun 14 2021

city: Palo Alto

first: Nathan

middle: Edward

last: Reticker-Flynn

state: CA

address: 3373 Hillview Ave

department: Pathology

country: USA

institute: Stanford University

type: Expression profiling by high throughput sequencing

type: Genome binding/occupancy profiling by high throughput sequencing

summary: The purpose of this study is to identify transcriptional, mutational, andepigenetic differences between LN metastases from primary tumors. Using in vivo serial passaging of the minimally metastatic syngeneic murine melanoma cell line B16-F0, we have generated nearly 300 unique cell lines spanning nine generations of in vivo passaging, derived from LNs, and exhibiting varying degrees of metastatic potential to LNs. Here, we perform mRNAseq on 30 of the lines representing a range of anatomical locations (distinct LNs), generations, and phylogenetic lineages. The subsequent differential expression analysis reveals a marked upregulation of immune-related genes. Additionally, we perform WES to identify differences in particular mutations, total mutational burden, and predicted neoantigen burden. Additionally, we perform ATAC-seq to assess changes in chromatin accessibility hat correlate with LN metastasis. We also perform scRNA-seq on dissociated LNs from mice with and without LN metastases.

overall_design:
mRNA profiles were generated from 30 cell lines derived from the various LN lines and parental. The parental was sequenced in triplicate where each replicate was harvested at distinct passage numbers to account for variability in the profile due to culture. Samples were sequenced on an Illumina HiSeq 2500 to a depth of 50M reads. Following quality filtering, transcript abundance was quantified using Salmon and differential gene expression analysis was performed using DESeq2. LN lines from later generations were compared to the parental or early generation lines.

For WES, 10 cell lines were analyzed. These data are accessible directly from SRA at Accession PRJNA820881.
For ATAC-seq, 3 samples each from parental, LN3, and LN7 generations were analyzed.
For scRNAseq, a LN from tumor naive, parental (non-metastatic) tumor, and LN6 (LN-metastatic) tumor mice each were analyzed.

middle: E

first: Edgar

middle: G

last: Engleman


title: Methylation of Q105 on histone H2A is part of a dynamic regulatory mechanism integrating metabolism with ribosome biogenesis through recruitment of Nhp2

status: Public on Jun 08 2021

city: Cologne

first: Jennifer

last: Maßen

address: Joseph-Stelzmann-Straße 9B

country: Germany

institute: MPI Biology of Ageing

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

overall_design: Refer to individual Series


title: Skin single cell universe identifies IL-1B/IL23A co-producing CD14+ type 3 dendritic cells in psoriasis

status: Public on Jun 10 2021

city: Singapore

first: Florent

last: Ginhoux

address: 8A Biomedical Grove, Immunos Building, Level 3

country: Singapore

institute: Singapore Immunology Network (SIgN), A*STAR

summary: Inflammatory skin diseases including atopic dermatitis (AD) and psoriasis (PSO) are underpinned by dendritic cell- (DC) mediated T cell responses. Currently, the heterogeneous human cutaneous DC population is incompletely characterized, and its contribution to these diseases remains unclear. Here, we performed index-sorted single-cell flow cytometry and RNA-sequencing of lesional and non-lesional AD and PSO skin to identify macrophages and all DC subsets, including the newly-described mature LAMP3+BIRC3+ DC enriched in immunoregulatory molecules (mregDC) and DC3. By integrating our indexed data with published skin datasets, we generated a myeloid cell universe of DC and macrophage subsets in healthy and diseased skin. Importantly, we found that CD14+ DC3 were increased in PSO lesional skin and co-produced IL1B and IL23A, which are pathologic in PSO. Our study comprehensively describes the molecular characteristics of macrophages and DC subsets in AD and PSO at single-cell resolution, and identifies CD14+ DC3 as potential promotors of inflammation in PSO.

overall_design: We collected skin biopsies from two patients with AD and two with PSO, from both non-lesional and lesional areas, and prepared single cell suspensions by enzymatic digestion.

first: Satoshi

last: Nakamizo

first: Charles-Antoine

last: Dutertre

first: Ahad

last: Khalilnezhad

first: Xiao

middle: M

first: Shawn

last: Lim

first: Josephine

last: Lum

first: Geraldine

last: Koh

first: Charlene

middle: F

last: Shu Fen

first: Pearly

middle: A

last: Yong

first: Kahbing

middle: J

last: Tan

first: Reiko

last: Sato

first: Kaori

last: Tomari

first: Laurent

last: Yvan-Charvet

first: Helen

last: He

first: Emma

last: Guttman-Yassky

first: Benoit

last: Malleret

first: Rintaro

last: Shibuya

first: Masashi

last: Iwata

first: Baptiste

last: Janela

first: Tsuyoshi

last: Goto

first: Siyun

middle: L

first: Mark

middle: Y

last: Tang

first: Colin

last: Theng

first: Valerie

last: Julia

first: Feriel

last: Hacini-Rachinel

first: Kenji

last: Kabashima


title: HyDrop: droplet-based scATAC-seq and scRNA-seq using dissolvable hydrogel beads

status: Public on Jun 04 2021

city: Leuven

first: Stein

last: Aerts

state: Vlaams-Brabant

address: O&N4 Herestraat 49 PO Box 602

country: Belgium

institute: KU Leuven

summary: We developed HyDrop, a new droplet microfluidic single-cell sequencing protocol for single-cell ATAC-seq and single-cell RNA-seq. We applied HyDrop-ATAC to flash-frozen mouse cortex and generated 7996 single-cell chromatin accessibility profiles. We applied HyDrop-RNA to flash-frozen mouse cortex and generated 9508 single-cell transcriptomes. We also applied HyDrop-RNA to a small population of FAC-sorted neurons from the Drosophila brain to demonstrate the protocol's applicability to low-input samples. The data available in this repository can be used to replicate all the figures in our manuscript using our data analysis tutorial available here: https://github.com/aertslab/hydrop_data_analysis

sample_organism:
Drosophila melanogaster
Homo sapiens
Mus musculus

overall_design: HyDrop-ATAC on mixed species cell lines and mouse cortex nuclei. HyDrop-RNA on mixed-species cell lines, mouse cortex nuclei and FAC-sorted drosophila neurons.

first: Florian

last: De Rop

first: Joy

last: Ismail

first: Carmen

last: Bravo González-Blas

first: Gert

last: Hulselmans

first: Christopher

last: Flerin

first: Jasper

last: Janssens

last: Christiaens

first: Suresh

last: Poovathingal


title: Methylation of Q105 on histone H2A is part of a dynamic regulatory mechanism integrating metabolism with ribosome biogenesis through recruitment of Nhp2 [RNA-Seq]

first: Jennifer

last: Maßen

summary: Ribosome biogenesis is an essential cellular process that requires integration of extracellular cues, such as metabolic state, with intracellular signaling, transcriptional regulation and chromatin accessibility at the ribosomal DNA. Here, we demonstrate that the recently identified histone modification, methylation of H2AQ105, is an integral part of a dynamic chromatin network at the rDNA locus. Its deposition depends on a functional mTor signaling pathway as well as acetylation of histone H3 at position K56, thus integrating signals from cell cycle, metabolic and proliferative states. Furthermore, we identify a first epigenetic reader of this modification, the ribonucleoprotein Nhp2, which specifically recognizes the methylation on H2AQ105. Based on functional and proteomic data we suggest that Nhp2 functions as an adapter to bridge the rDNA chromatin with components of the small subunit processome to efficiently coordinate transcription of rRNA with its post-transcriptional processing. We support this by showing that an H2AQ105A mutant has a mild defect in early processing of the rRNA.

overall_design: RNA sequencing of four genotypes with 4 replicates each to investigate expression changes

first: Julia

middle: S

last: Mawer

last: Massen

first: Christina

last: Reichert

first: Niklas

last: Grabenhorst

first: Constantine

last: Mylonas

first: Peter

last: Tessarz


title: RNA sequencing reveals novel LncRNAs/mRNAs network associated with puerarin-mediated inhibition of cardiac hypertrophy in mice

status: Public on Jun 09 2021

city: Guangzhou

first: Shan

last: Ye

state: Guangdong

address: 250 Changgang East Road

department: Department of Geriatrics

country: China

institute: the Second Affiliated Hospital of Guangzhou Medical University

type: Non-coding RNA profiling by high throughput sequencing

summary: Although current studies have demonstrated that lncRNAs play an important part in the pathophysiological process of cardiac disease, whether lncRNAs are associated with the protective role of puerarin in myocardial hypertrophy remains unknown. In the present study, RNA sequencing (RNA-seq) was performed to systematically understand the function of lncRNAs in the pharmacological action of puerarin in myocardial hypertrophy.

overall_design: RNA sequencing (RNA-seq) was carried out to systematically analyze global gene expression among the sham group, transverse aortic constriction (TAC) group and TAC + Puerarin (PUE) groups.


title: CHMP2A regulates tumor sensitivity to natural killer cell-mediated cytotoxicity [RNA-seq]

status: Public on Jun 02 2021

city: La Jolla

first: Davide

last: Bernareggi

address: 9500 Gilman Drive

institute: UCSD

summary: We report the application of a two-cell -type whole genome KO CRISPR screen to find new moecular targets that increase the sensitivity or resistance to NK cells  cytotoxixity in glioblastoma stem cells and head and neck squamous cells carcinoma cells. Here we report the RNA sequencing for the CHMP2A KO glioblastoma stem cells CW468 and 387

overall_design: This section reports the RNA sequencing on CW468 and 387 glioblastoma stem cell lines KO for CHMP2A

first: Qi

last: Xie

first: Briana

middle: C

last: Prager


title: CHMP2A regulates tumor sensitivity to natural killer cell-mediated cytotoxicity


title: RRBS-based quantitative methylation analysis define 100% methylation fidelity CpG sites

city: Shanghai

first: Jianing

last: Wang

address: Dongchuan Road

institute: Shanghai JiaoTong University

type: Methylation profiling by high throughput sequencing

summary: Stable maintenance of cytosine methylation is essential for mammalian biological processes such as gene transcription. This study introduced a RRBS-based quantitative method to identify CpG sites of high methylation fidelity (especially those 100% methylation fidelity sites). To separate the 100% methylation fidelity sites , we cultured the ARPE-19, Jurkat and SW1353 cells for lasting 10 generations, and we detected the methylation level of each CpG sites in the 20th generation and the 30th generation by performing reduced representation bisulfite sequencing (RRBS), to obtain the 100% methylation fidelity sites. The result shows that the number of overlapped fidelity methylation CpG sites of the two different time is smaller than number of each generation. Our results also showed that the proportion of high-fidelity 100% methylated sites in Jurkat and ARPE-19 cells is about 4.4% and 8.9%, and the proportion in SW1353 cells is 1.98%. The fidelity methylation sites obtained by the comparison of the two different time periods are the truly unchanged CpG sites during cell passage, which improves the reliability of the fidelity methylation sites. In summary, we provide new insights into the DNA methylation fidelity study.

overall_design: Using RRBS to detect the methylation level of two generation cells.

first: Yulan

last: Qin

first: Yani

last: Kang

first: Daniel

last: Czajkowsky

first: Hua

last: Li

first: Zhifeng

last: Shao


title: The ISR activation confers vulnerability to mitoribosome-targeting antibiotics in melanoma

status: Public on Jul 15 2021

first: Eleonora

last: Leucci

address: Herestraat 49, bus 818 room 06.423

department: Oncology

summary: We report the changes in translatome of a commercially available melanoma line upon acquisition of therapy resistance

overall_design: The ribosome-bound RNAs of a melanoma line in control condition or upon activation of the ISR were compared

first: Yvessa

last: Verheyden


title: PGC-1a overexpression in SH-SY5Y cells

status: Public on May 31 2021

city: Birmingham

first: Rita

last: Cowell

state: AL

address: 2000 9th Avenue South

department: Neuroscience

institute: Southern Research

summary: SH-SY5Y cells were transfected with either GFP control or PGC-1a overexpression adenovirus and RNA was isolated after 48 hours and sequenced in order to understand what genes are differentially expressed with the presence of PGC-1a in neuron like cells. This experiment shows that genes related to neuron health and mitochondiral function are controlled by PGC-1a. We also analyze the promoter of upregualted genes found here to figure out potential partners that co-regulate with PGC-1a.

overall_design: Examination of gene expression resulting from PGC-1a expression in SH-SY5Y cells.

first: Kaval

last: Patel

first: David

last: Crossman

first: Kathlene

last: Joyce

first: Laura

last: McMeekin


title: Epigenetic analysis of Paget’s disease of bone identifies differentially methylated loci that predict disease status

status: Public on Jun 03 2021

city: Doha

first: Omar

middle: M E

last: Albagha

address: Luqta Street, Education City

department: Health and Life Sciences

country: Qatar

institute: Hamad Bin Khalifa University

summary: This study demonstrated that PDB has an epigenetic signature in the blood and that differentially methylated sites in white blood cells may be used as predictive markers of the disease. Many of the identified changes in DNA methylation were associated with genes that regulate osteoclast function, immune responses, host reponse to viral infection, pain pathways and pathways involved in mechanosensing.

overall_design: The study was conducted in 253 cases with clinical and radiological evidence of PDB and 280 controls who were spouses of PDB cases (n=135) or subjects who had been referred for investigation of osteoporosis but had normal bone density upon examination by dual energy X-ray absorptiometry (n=131)

first: Ilhame

last: Diboun

first: Stuart

middle: H

last: Ralston

first: Sachin

last: Wani


title: NOX4 links metabolic regulation in pancreatic cancer to endoplasmic reticulum redox vulnerability and dependence on PRDX4

status: Public on May 25 2021

city: Toronto

first: Jason

last: Moffat

state: ON

address: 686 Bay Street, Room 13.9705

department: Molecular Genetics

country: Canada

institute: University of Toronto

summary: PDAC cells acquire metabolic changes that augment NADPH production and cytosolic redox homeostasis. Here we show that high NADPH levels drive activity of NADPH oxidase 4 (NOX4) expressed in the endoplasmic reticulum (ER) membrane. NOX4 produces H2O2 metabolized by Peroxiredoxin 4 (PRDX4) in the ER lumen. Using functional genomics and subsequent in vitro and in vivo validations, we find that PDAC cell lines with high NADPH levels are dependent on PRDX4 for their growth and survival. PRDX4 addiction is associated with increased reactive oxygen species, a DNA-PKcs-governed DNA damage response and radiosensitivity, which can be rescued by depletion of NOX4 or NADPH. As such, this study has identified NOX4 as a protein which paradoxically converts the reducing power of the cytosol to an ER-specific oxidative stress vulnerability in PDAC that may be therapeutically exploited by targeting PRDX4.

overall_design: Pancreatic ductal adenocarcinoma cell lines were grown in tissue culture and profiled by RNA sequencing to determine global gene expression profiles.

first: Kevin

middle: R

last: Brown

first: Anna

last: Dvorkin-Gheva

first: Marianne

last: Koritzinsky


title: DNA methylation in skeletal muscle of patients with hypertension and diabetes undergoing coronary artery bypass grafting surgery

status: Public on May 09 2021

city: Providence

first: Alexey

middle: V

last: Fedulov

state: Rhode Island

address: 593 Eddy St.

department: RIH / Surgical Research

institute: Alpert Medical School of Brown University

type: Methylation profiling by genome tiling array

summary:
Patients with hypertension alone, hypertension plus controlled diabetes and hypertension plus uncontrolled diabetes, and control patients without these conditions underwent coronary artery bypass grafting surgery.
Skeletal muscle biopsy specimens were taken at the beginning ('pre-operative') and at the end ('post-operative') of the surgery.

overall_design: 4 patients per each of the 4 groups: control, hypertension only, hypertension plus controlled diabetes and hypertension plus uncontrolled diabetes. Each patient was sampled twice: before and after surgery.

first: Ghazal

last: Aghagoli

first: Naohiro

last: Yano

first: Andrew

last: Del Re

first: Zhiqi

last: Zhang

first: Ahmad

last: Gheit

first: Ronald

last: Phillips

first: Frank

last: Sellke


title: Comparison of the transcriptional changes in dorsal root ganglion between paclitaxel and oxaliplatin induced peripheral neuropathic pain in rats

status: Public on May 12 2021

city: Shenzhen

first: SHAO

middle: MIN

last: YANG

state: guangdong

address: Nanshan

department: Shenzhen Nanshan People's Hospital and the 6th Affiliated Hospital of Shenzhen University Health Science Center

institute: Department of Pain Medicine and Shenzhen Municipal Key Laboratory for Pain Medicine

summary: In this study, we screened the differentially expressed genes (DEGs) in dorsal root ganglion between paclitaxel and oxaliplatin induced peripheral neuropathic pain in rats.

overall_design: Paclitaxel (2.0 mg/kg dissolved in DMSO and serially diluted in saline, Dalian Meilun Biology Technology Co. Ltd, China) and Oxaliplatin (2.4 mg/kg dissolved in 5.0% glucose solution, Dalian Meilun Biology Technology Co. Ltd., China) was injected intraperitoneally to induce peripheral neuropathic pain.

first: Shaomin

last: Yang


title: Next Generation Sequencing Facilitates Quantitative Analysis of control group and IL34-overexpresion group

status: Public on May 01 2021

city: tianjin

first: lv

middle: xiao

last: qian

address: nanjinglu

institute: Tsinghu university

summary: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goal of this study is  to reveal functional and phenotypic diversity of control group and IL34-overexpresion group.

overall_design: Explore the differential mechanisms of transcriptome expression in Acute monocytic leukemia cells overexpressing IL34

first: GuoGuang

last: Zheng

first: XiaoQian

last: Lv

first: YuTing

last: Hu


title: Genome wide analysis of important transcription factors and histone modifications for prostate cancer progression

city: Itabashi-ku

first: Ken-ichi

last: Takayama

address: Sakaecho

country: Japan

institute: Tokyo Metropolitan Institute of Gerontology

summary: Prostate cancer is the most common cancer in men and androgen receptor (AR) downstream signalings promote prostate cancer progression. Although androgen deprivation therapy is effective for treating prostate cancer, most tumors relapsed as castration-resistant prostate cancer (CRPC). We performed ChIP-seq analysis to investigate the role of important transcription factors and histone modifications using AR positive prostate cancer cells, LNCaP, CRPC model cells, 22Rv1 and DU145 cells.

overall_design: ChIP-sequence analysis of transcription factors (FOXM1, NRF1, NRF2 and OCT4) and histone modifications in CRPC cells.


title: Comparative transcriptome analysis implicates IL1R8-associated upregulation of myeloid leukocyte pathways in latent HCMV infection

status: Public on Apr 26 2021

city: St. Louis

first: Jinsheng

last: Yu

state: MO

address: 660 S. Euclid Ave.

department: Genetics

institute: Washington University School of Medicine

summary: Latent human cytomegalovirus (HCMV) in myeloid cells can be reactivated during cell differentiation and by inflammatory mediators. Expression level of immune regulator IL1R8 has been associated with the differentiation status of myeloid cells. As far, little is known about the role of IL1R8 in the association between reactivation of latent HCMV and differentiation of myeloid cells. To gain additional insights into IL1R8 and latency, a comparative transcriptome analysis was carried out through a unique bioinformatics approach that integrated IL1R8-correlated genes with differentially expressed genes to identify IL1R8-associated significant pathways. The Metascape pathway tool was utilized to perform enrichment analysis. The initial analysis revealed a significant inverse correlation between IL1R8 and viral counts (r = -0.42, z-score = -4.69) at single cell level in HCMV-infected monocytes at 4-14 days postinfection. In contrast to the majority of pathway analysis studies presenting unilateral up- or down-regulation, the current study discovered a number of bilaterally regulated key immune pathways in both lytic and latent infections. Notably, a ~3-fold predominant downregulation of the high-level adaptive immune system pathway was followed by a modestly predominant downregulation of mid-level Lymphocyte and low-level T cell activation pathways in latent infection. More interestingly, a unilateral upregulation pattern was identified exclusively in latent infection for Myeloid leukocyte activation, differentiation, and migration, in which upregulated genes were in concord with IL1R8 negatively correlated genes. The findings in the present study provided a comprehensive view of immunological alterations and a better understanding on the potential role of IL1R8 in the association between HCMV reactivation and myeloid cell differentiation in HCMV infection. The current study, for the first time, presented unique evidence supportive of a IL1R8-associated unilateral upregulation of myeloid leukocyte pathways in latent infection.

overall_design: THP-1 cells were infected with HCMV Towne strain (or Mock) at a multiplicity of infection (MOI) of 5. To ensure a latent infection, total RNA from THP-1 cells was extracted at day 4 post-infection without any differentiation stimulation (namely HCMV and Mock samples) using Trizol reagent (Invitrogen, USA).

first: Xiaoqun


title: Immune transcriptomes of highly exposed SARS-CoV-2 asymptomatic seropositive versus seronegative individuals from the Ischgl community

city: Bethesda

first: Hye Kyung

last: Lee

state: MD

address: 8 CENTER DR RM 107

department: National Institute of Diabetes and Digestive and Kidney (NIDDK)

institute: National Institutes of Health (NIH)

summary: SARS-CoV-2 infection ranges from asymptomatic to severe with lingering symptomatology in some. This prompted investigation of whether or not asymptomatic disease results in measurable immune activation post-infection. Immune activation following asymptomatic SARS-CoV-2 infection was characterized through a comparative investigation of the immune cell transcriptomes from 43 asymptomatic seropositive and 52 highly exposed seronegative individuals from the same community four to six weeks following a superspreading event. Few of the 95 individuals had underlying health issues. One seropositive individual reported Cystic Fibrosis and one individual reported Incontinentia pigmenti. No evidence of immune activation was found in asymptomatic seropositive individuals with the exception of the Cystic Fibrosis patient. There were no statistically significant differences in immune transcriptomes between asymptomatic seropositive and highly exposed seronegative individuals. Four positive controls, mildly symptomatic seropositive individuals whose blood was examined three weeks following infection, showed immune activation. Negative controls were four seronegative individuals from neighboring communities without COVID19. All individuals remained in their usual state of health through a five-month follow-up after sample collection. In summary, whole blood transcriptomes identified individual immune profiles within a community population and showed that asymptomatic infection within a super-spreading event was not associated with enduring immunological activation.

overall_design: RNA-seq were performed with peripheral blood mononuclear cells (PBMCs) of 43 asymptomatic COVID-19 patients (A_sample#), 52 highliy exposed seronegative subjects (B_sample#), 5 healthy controls (C_sample#), 4 non-Ischgl COVID-19 patients with mild symtoms (D_sample#) and 4 highly exposed seronegative non-Ischgl subjects (E_sample#).

first: Ludwig

last: Knabl


title: The DLK1-DIO3 C/D box snoRNA SNORD113-6/AF357425 plays a dual role in pre-mRNA processing and 2'O-ribose methylation in integrin signalling and arterial fibroblast function

status: Public on Apr 23 2021

city: Leiden

first: Hailiang

last: Mei

address: Einthovenweg 20

department: Sequencing Analysis Support Core

country: Netherlands

institute: Leiden University Medical Center

summary: We have previously shown that C/D box snoRNAs transcribed from the DLK1-DIO3 locus on human chromosome 14 (14q32) are associated with cardiovascular disease. DLK1-DIO3 snoRNAs are ‘orphan snoRNAs’ that have no known targets. We aimed to identify RNA targets and elucidate the mechanism-of-action of human SNORD113-6 (AF357425 in mice). As AF357425-knockout cells were non-viable, we induced overexpression or inhibition of AF357425 in primary murine fibroblasts and performed RNA-Seq. We identified several premRNAs with conserved AF357425/SNORD113-6 D’-seed binding sites in the last exon/3’UTR, which directed pre-mRNA processing and splice-variant specific protein expression. We also pulled down the snoRNA-associated methyltransferase fibrillarin from AF357425-High vs. AF357425-Low fibroblast lysates, followed by RNA isolation, rRNA depletion and RNA-Seq. Identifying mostly mRNAs, we subjected these to PANTHER pathway analysis and observed enrichment for genes in the integrin pathway. We confirmed 2’O-ribose methylation in 6 integrin pathway mRNAs (MAP2K1, ITGB3, ITGA7, PARVB, NTN4 and FLNB). Methylation and mRNA expression were decreased while mRNA degradation was increased under AF357425/SNORD113-6 inhibition in both murine and human primary fibroblasts, but effects on protein expression were more ambiguous. Integrin signalling is crucial for cell-cell and cell-matrix interactions, and correspondingly, we observed altered human primary arterial fibroblast barrier function upon SNORD113-6 inhibition.

overall_design: RNA-seq on whole cell lysates of primary murine ear cells with AF357425 overexpression (AF357425-High) or inhibition (AF357425-Low), and on RNA from fibrillarin pulldown of AF357425-High and AF357425-Low fibroblast lysates.

first: Eva

last: van Ingen

first: Daphne

last: Homberg

first: .L

last: van der Bent

first: Nikolina

last: Papac-Milicevic

first: Veerle

last: Kremer

first: Reinier

last: Boon

first: Paul

last: Quax

first: Johann

last: Wojta

first: A

last: Nossent


title: Gene Transcriptional Variation of Hepatic Progenitor Cells after TGF-𝛽1-Induced EMT Transition and EGF-Induced MET Reversion

city: Beijing

first: Ping

last: Wang

address: Yong An Road No.95

institute: Beijing Friendship Hospital

summary: TGF-b1 induces hepatic progenitor cells experience an epithelial-mesenchymal transition, and EGF could reverse this process via mesenchymal-epithelial transition. Yet, the mechanism underline these EMT and MET processes are not clear. The aim of this study is to reveal the genes with significant difference during these EMT and MET process in hepatic progenitor cells.

overall_design: In vitro cultured rat hepatic progenitor cells were incubated with TGF-b1 (1ng/mL) for 16 days as EMT cells, and EGF (1ng/ml) was administrated for 7 days to reverse the phenotype of 16-day TGF-b1-treated cells as MET cells.

first: Dong

last: Zhang

first: Jidong

last: Jia

first: You

last: Hong


title: RNA-seq analyses for control and nicotinamide treated TNBC cells

status: Public on Apr 22 2021

city: Seoul

first: Yebin

last: Im

address: 504-302, 1, Gwanak-ro, Gwanak-gu,

department: Biological Sciences

country: South Korea

institute: Seoul National University

summary: In this study, we investigated how nicotinamide (NAM) affects cellular metabolism in TNBC cells and also such altered cellular metabolism by NAM is linked to cytotoxic functions through an integrated analysis of proteome and transcriptome data generated from three different TNBC cell lines, BT20, MB468, and MB231. By analyzing mRNA-seq data from control and NAM treated TNBC cells (3 replicates in each of 3 cell lines), we identified differentially expressed genes (DEGs), and associated cellular process. The up-regulated genes were associated with the processes related to cell death (programmed cell death, autophagy, and apoptotic mitochondrial changes) and mitochondria (organization, pH reduction/oxidation-reduction/NADP metabolism, response to starvation, respiratory chain, and lipid/oxoacid metabolism). On the other hand, the processes related to immune response (NF-kB and MAPK signaling, cell adhesion/migration, and response to cytokine) and cell proliferation were down-regulated consistently in the three TNBC cells.

overall_design: BT20/NAM treated BT20/ MDA-MB-468/NAM treated MDA-MB-468

first: Han

last: Ryu

first: Daehee

last: Hwang


title: Single-cell transcriptomic resolution of human pancreatic islets reveals cellular states and intercellular interactions associated with type 1 diabetes

status: Public on Apr 03 2021

city: Philadelphia

first: Maria

last: Fasolino

address: 324 BRB II/III, 421 Curie Blvd

institute: University of Pennsylvania

summary: Our transcriptomic phenotyping of pancreatic cell types provides novel insights into pancreas biology, as well as the initial pathogenic events in T1D.

overall_design: We employed single-cell transcriptomics (10x Genomics Platform) on 35,134 cells from pancreatic islets of organ donors representing three disease states: those with T1D, those with autoantibodies (AAbs) towards pancreatic islet proteins but without a medical history of T1D (referred to as ‘AAB+’ donors), and donors without relevant AAbs or a history of diabetes (referred to as ‘Control’ donors)

first: Golnaz

last: Vahedi


title: CHMP2A regulates tumor sensitivity to natural killer cell-mediated cytotoxicity [CRISPR]

first: Davide

last: Bernareggi

summary: We report the application of a two-cell -type whole genome KO CRISPR screen to find new moecular targets that increase the sensitivity or resistance to NK cells  cytotoxixity in glioblastoma stem cells and head and neck squamous cells carcinoma cells.

overall_design: tumor cells have been transduced with a whole genome KO lentiviral library and after antibiotic selection cells has been challenged with NK cells. The genomic DNA has been sequenced and the abundance of sgRNAs has been ranked.

first: Qi

last: Xie

first: Briana

last: Prager


title: RNA-seq analysis of CNE1 cells based on LMP1 expression

status: Public on Apr 08 2021

city: changsha

first: jiang

last: he

address: 87 Xiangya Road

institute: xiangya hospital

summary: Epstein-Barr virus (EBV) and human papillomavirus (HPV) infection are the risk factors for nasopharyngeal carcinoma and cervical carcinoma, respectively. However, clinical analyses demonstrate that EBV or HPV is associated with improved response of patients, although underlying mechanism remains unclear. Here, we found DNA tumor viruses, such as EBV and HPV, inhibited antioxidant activity and increased oxidative stress of tumor through analyzing RNA-seq data of clinical samples. Further, we found the oncoproteins of DNA tumor viruses, such as LMP1 of EBV and E7 of HPV, interacted with PERK through a conserved motif, which inhibited PERK-Nrf2 signaling and increased the level of reactive oxygen species (ROS). This inhibition of PERK-Nrf2 signaling in LMP1- or E7- positive cancer cells exhibited an increased sensitivity to chemotherapy in vivo. Meanwhile, LMP1- or E7-induced ROS promoted tumor growth. Consistently, disruption of viral oncoprotein-PERK interactions attenuated tumor growth and efficacy of chemotherapy in tumor-bearing mouse models. Our findings uncovered a paradoxical effect of DNA tumor virus oncoproteins on tumors and highlighted that targeting PERK-Nrf2 signaling might be an attractive strategy for the treatment of NPC and cervical carcinoma.

overall_design: mRNA profiles of CNE1 cells stably expressing LMP1

first: He

last: Jiang

first: Lunquan

last: Sun


title: Gene expression profile of Skov3 cells cultured with DMSO (Control) or GA-017 in 3D condition

status: Public on Apr 01 2021

city: Shiraoka

first: Ayako

last: Otani

state: Saitama

address: 1470 Shiraoka

department: Medical Materials group

institute: Nissan Chemical Industries

summary:
3D cell culture models are recognized for representing the physiological microenvironment and exhibiting higher concordance with in vivo conditions, when compared to a conventional 2D cell culture model. However, cells grown in 3D cultures are likely to exhibit slower growth than those in 2D cultures. We found that addition of a novel small molecule named GA-017 to culture media promotes the cell proliferation particularly under 3D conditions.
Gene microarrays were used to observe the global gene expression in Skov3 cells cultured under 3D condition with DMSO or GA-017 and identified distinct classes of up or down-regulated genes.

overall_design: Skov3 cells were cultured for 24 hours with DMSO or GA-017.

last: Aihara


title: Functional genome and microbiome in blood of goats affected by the gastrointestinal pathogen Haemonchus contortus

status: Public on Mar 26 2021

city: Langston

first: Yonathan

last: Tilahun

state: OK

address: 100 Success Dr.

department: Extension

institute: Langston University

summary: The Alpine goat Capra aegagrus hircus is parasitized by the barber pole worm (Haemonchus contortus). This relationship results in changes that affect the gene expression of the host, the pest, and the microbiome of both. Hematological parameters indicating genes that are expressed and/or the % Composition of abundant and diverse microbial flora are reflective of infestation.  We identified responses to barber pole worms using blood-based analysis of transcripts and the microbiome. Seven (7) days post-inoculation (dpi) we identified 7,627 genes associated with different treatment types.

overall_design: We explored the similarity/dissimilarity between and among blood samples of non-infected, infected, infected zoledronic acid-treated, and infected antibody (anti-γσ Т cells) treated wethers under controlled conditions.

first: Qunhui

last: Yang

first: Jessica

last: Quijada Pinango

first: Felicia

last: Johnson

first: Kayla

last: Smith

first: Charles

last: Lett

first: Terry

last: Gipson

first: Arthur

last: Goetsch

first: Malcolm

last: McCallum

first: Peter

last: Hoyt

first: Andrew

last: Tritt

first: Zaisen

last: Wang


title: Analysis of inguinal fat from male and female control and adipocyte-specific STAT5 knockout mice

city: Baton Rouge

first: Carrie

last: Elks

state: LA

address: 6400 Perkins Road

institute: Pennington Biomedical Research Center

summary: To determine the transcriptomic effects of STAT5 loss on adipose tissue gene expression, we assessed inguinal white adipose tissue of 6-week old male and female control and adipocyte-specific STAT5 knockout mice using a Quant-Seq strategy.

overall_design: Inguinal fat pads were dissected from 6 male & 6 female wild-type and 6 male & 6 female adipocyte-specific STAT5 knockout mice at 6 weeks of age, followed by isolation of total RNA and messenger RNA quantification via Quant-Seq.

first: Allison

last: Richard

first: Jacqueline

last: Stephens


title: Molecular roadmap of the healthy stress response in the mouse hippocampus (single-nucleus)

status: Public on Mar 25 2021

city: Zürich

first: Lukas

middle: Matthias

last: von Ziegler

address: Winterthurerstrasse 190

department: D-HESZ

country: Switzerland

institute: ETH Zürich

summary: The acute stress response mobilizes energy to meet situational demands and re-establish homeostasis. Here, we used a brief forced swim exposure to trigger a strong stress response in mice. Using multiomic profiling we characterize the stress-induced molecular events in the dorsal (dHC) and ventral (vHC) hippocampus over time, across molecular scales, and down to the level of cell types and single cells.

overall_design: Here, we used a brief (6min) forced swim exposure and profiled the hippocampus using single-nucleus RNA-seq 45min after initiation of the experiment.

first: Pierre-Luc

last: Germain

first: Amalia

last: Florio-Servou

first: Rebecca

last: Waag

first: Johannes

last: Bohacek

first: Fridolin

last: Gross


title: The RNA Atlas expands the catalog of human non-coding RNAs

status: Public on Apr 15 2021

city: Badalona

first: LUCIA

last: LORENZI

state: Barcelona

address: Ctra de Can Ruti, Camí de les Escoles s/n

country: Spain

institute: Josep Carreras Research Institute

summary: The human transcriptome consists of various RNA biotypes including multiple types of non-coding RNAs (ncRNAs). Current ncRNA compendia remain incomplete partially because they are almost exclusively derived from the interrogation of small- and polyadenylated RNAs. Here, we present a more comprehensive atlas of the human transcriptome that is derived from matching polyA-, total-, and small-RNA profiles of a heterogenous collection of nearly 300 human tissues and cell lines. We report thousands of novel RNA species across all major RNA biotypes, including a hitherto poorly-cataloged class of non-polyadenylated single-exon long non-coding RNAs. In addition, we exploit intron abundance estimates from total RNA-sequencing to predict the regulatory potential of various non-coding RNAs. Our study represents a substantial expansion of the current catalogue of human ncRNAs and their regulatory interactions. All data and results are accessible through the R2 webtool and serve as a basis to further explore RNA biology and function.

overall_design: We applied three complementary RNA-seq methods on a heterogeneous collection of 300 human samples, including 45 tissues, 162 cell types, and 93 cell lines. From these samples, we generated strand-specific small RNA (298 samples), polyA (295 samples) and total RNA (296 samples) libraries that were sequenced at a median depth of 13 M, 60 M paired-end, and 125 M paired-end reads respectively, resulting in a total of 125 Billion reads.

first: Lucia

last: Lorenzi

first: Hua-Sheng

last: Chiu

first: Francisco

last: Cobos

first: Stephen

first: Pieter-Jan

last: Volders

first: Robrecht

last: Cannoodt

first: Justine

last: Nuytens

first: Katrien

last: Vanderheyden

first: Jasper

last: Anckaert

first: Steve

last: Lefever

first: Aidan

middle: P

last: Tay

first: Eric

last: de Bony

first: Wim

last: Trypsteen

first: Fien

last: Gysens

first: Marieke

last: Vromman

first: Tine

last: Goovaerts

first: Thomas

middle: B

last: Hansen

first: Scott

last: Kuersten

first: Nele

last: Nijs

first: Tom

last: Taghon

first: Karim

last: Vermaelen

first: Ken

last: Bracke

first: Yvan

last: Saeys

first: Tim

last: De Meyer

first: Nandan

last: Deshpande

first: Govardhan

last: Anande

first: Ting-Wen

last: Chen

first: Marc

last: Wilkins

first: Ashwin

last: Unnikrishnan

first: Katleen

last: De Preter

first: Jørgen

last: Kjems

first: Jan

last: Koster

first: Gary

last: Schroth

first: Jo

last: Vandesompele

first: Pavel

last: Sumazin

first: Pieter

last: Mestdagh


title: Expression data from D. melanogaster intestinal stem cell with suppression of Imd in progenitors

status: Public on Mar 29 2021

city: Edmonton

first: Edan

last: Foley

state: Alberta

address: 116 st and 85 ave

department: Medical Microbiology and Immunology

institute: University of Alberta

summary: We used RNA-seq to examine transcriptional profiles of midgut progenitor cells with suppression of Imd in progenitors. We found significant differences between the contributions of progenitor IMD to intestinal homeostasis.

overall_design: Genotype control flies and flies with Imd inhibition were raised on regular food (Bloomington standard food) for 10 days at 29C after eclosion. Guts were dissected for RNA extraction and total RNA, in triplicate, sent to Lunenfeld-Tanenbaum Research Institute for library construction and sequencing.

first: Minjeong

last: Shin


title: Lnc453774.1 mediated gene expression in human HK-2 cells

status: Public on Mar 10 2021

city: Changsha

first: Xiangcheng

last: Xiao

state: Hunan

address: No. 87, Xiangya Road, Kaifu District

department: Department of Nephrology

institute: Xiangya Hospital, Central  South University

summary: Long noncoding RNAs (lncRNAs) have been proposed to be engaged in the pathogenesis of renal fibrosis. The current study aims to determine the role of lnc453774.1 in the development of renal fibrosis and its underlying mechanism.Transforming growth factor-β1 (TGF-β1)-induced cell model of renal fibrosis was constructed. RNA sequencing was performed to identify DEGs targeted by lnc453774.1 in TGF-β1-induced renal fibrosis. Dataset GSE23338 was adopted to identify DEGs in 48 h TGF-β1-stimuated human kidney epithelial cells, and these DEGs were interested with genes in the key module using a WGCNA to generate key genes associated with renal fibrosis. Miranda software was adopted to predict miRs that have targeting relationship with keys genes and lnc453774.1, and key genes that have targeting relationship with these miRs were regarded as important genes. A PPI network among lnc453774.1, important genes and reported genes related to autophagy, oxidative stress, and cell adhesion was constructed to select key target genes by lnc453774.1. Twenty key genes regulated by lnc453774.1 was yielded by intersecting genes in key module (turquoise) and dataset GSE23338. Fourteen miRs have targeting relationship with lnc453774.1 and key genes, and 8 important genes targeted by these 14 miRs were identified. FBN1, IGF1R and KLF7 were identified to be associated with autophagy, oxidative stress, and cell adhesion and were upregulated in the lnc453774.1-overexpressing in TGF-β1-induced cells. These results show FBN1, IGF1R and KLF7 serve as downstream targets of lnc453774.1 and protect against renal fibrosis by regulating autophagy, oxidative stress, and cell adhesion.

overall_design: Human renal proximal tubular epithelial cells (HK-2 cells) were cultured in dulbecco's modified eagle medium (DMEM)/F12 supplemented with 10% fetal bovine serum (FBS) at 37°C, 5% CO2, and passaged upon 70-80% confluence. TGF-β1 at a concentration of 5ng/ml for 24 h was adopted to stimulate HK-2 cells to prepare a cell model of renal fibrosis. Lentiviral vector containing (LV)-lnc453774.1 and short hairpin RNA (shRNA)-lnc453774.1 plasmids were prepared, and infected into HK-2 cells of renal fibrosis using liposome 2000 [the overexpressed (OE) group and the knockdown (KD) group]. TGF-β1-stimulated HK-2 cells with no-load vector was used as the control group. The total RNA was extracted from the 3 control, 3 OE group and 3 KD groups for sequencing library construction.

first: Xiangning

last: Yuan

first: Wenbin

last: Tang

first: Ling

last: Peng

first: Yusa

first: Shumei

first: Huipeng

last: Ge

first: Xiufen

last: Wang


title: Ancestral Plastics Exposure Induces Transgenerational Disease Specific Sperm Epigenome-Wide Association Biomarkers Methylation Epimutation Biomarkers for Specific Transgenerational Disease

status: Public on Mar 16 2021

city: Pullman

first: Michael

middle: K

last: Skinner

state: WA

address: Abelson 507

department: SBS

institute: WSU

summary: Plastic derived compounds are one of the most frequent daily world-wide exposures. Previously a mixture of plastic derived toxicants involving bisphenol A (BPA), Bis(2-ethylhexyl) phthalate (DEHP), and dibutyl phthalate (DBP) at lower dose exposures of a gestating female rat were found to promote the epigenetic transgenerational inheritance of disease to the offspring (F1 generation), grand-offspring (F2 generation) and great-grand-offspring (F3 generation). Epigenetic analysis of the male sperm was found to result in differential DNA methylation regions (DMRs) in the transgenerational F3 generation male sperm. The current study is distinct and was designed to identify potential sperm DNA methylation biomarkers for specific transgenerational diseases. Observations show disease specific DMRs called epimutations in the transgenerational F3 generation great-grand-offspring rats ancestrally exposed to plastics. The epigenetic DMR biomarkers were identified for testis disease, kidney disease, and multiple (≥2) diseases. These disease sperm epimutation biomarkers were found to be predominantly disease specific. The genomic locations and features of these DMRs were identified. Interestingly, the disease specific DMR associated genes were previously shown to be linked with each of the specific diseases. Therefore, the germline has ancestrally derived epimutations that potentially transmit transgenerational disease susceptibilities. Epigenetic biomarkers for specific diseases could be used as diagnostics to facilitate clinical management of disease and preventative medicine.

overall_design:
Analysis of the transgenerational actions of multiple pesticide chemicals used outbred Sprague Dawley female rats (F0 generation) transiently exposed to the plastic compound mixture (BPA 25 mg/kg BW/day, DEHP 375 mg/kg BW /day, and DBP 33mg/kg BW/day)during days 8 to 14 of gestation. The F1 generation animals (direct fetal exposure) were bred to generate the F2 generation (direct germline exposure), which were bred to generate the F3 generation (transgenerational so no direct exposure).  The plastics lineage animals were aged to 1 year and euthanized for pathology and sperm epigenetic analysis. No sibling or cousin breedings (crosses) were used to avoid any inbreeding artifacts. Generally 6–8 founder gestating females from different litters were bred and 25–50 individuals of each sex obtained for each generation.
Several samples are not included in the processed data files. These samples were not included in the DMR analyses due to not having relevant diseases. However, they are part of the project and a future reanalysis may require them.

first: Jennifer

last: Thorson

first: Daniel

last: Beck

first: Millissia

last: Ben Maamar

first: Eric

middle: E

last: Nilsson


title: Quantitative analysis of transscriptomes from rat OPCs treated with DMSO or ZJU-37

status: Public on May 20 2021

city: Hangzhou

first: Jingwei

last: Zhao

address: 866 Yuhangtang Road

institute: Zhejiang University

summary: Our previous data showed ZJU-37 promotes OPCs proliferation both in vitro and in vivo, the results of RNA-Seq indicated that up-regulation of cell cycle related genes may be related to it.

overall_design: mRNA profiles of primary cultured OPCs from P0 rats treated with DMSO or ZJU-37, 3 replications per group.

first: Hongguang

last: Xia

first: Xiaoru

last: Ma

first: Shuying

last: Yang


title: IL-17A Promotes HIV-1 Dissemination/Replication and abrogates the Interferon-Mediated Antiviral Immunity in Intestinal Epithelial Cells

status: Public on Mar 01 2021

city: Montréal

first: Jean-Philippe

last: Goulet

state: Québec

address: C.P. 6128, succursale Centre-ville

institute: Université de Montréal

summary: The crosstalk between intestinal epithelial cells (IEC) and Th17-polarized CD4+ T-cells is critical for mucosal homeostasis, with HIV-1 causing major alterations in people living with HIV (PLWH) despite antiretroviral therapy (ART). Here, we used a model of IEC:T-cell co-culture to investigate the effects of IL-17A and TNF, two cytokines produced by Th17-cells, in regulating IEC ability to promote de novo infection and viral outgrowth from reservoir cells. Our results demonstrated that IL-17A in the presence/absence of TNF acts on IEC to increase HIV capture and trans infection of CD3/CD28-activated T-cells from uninfected individuals. Also, IL-17A-exposed IEC significantly increased HIV replication and outgrowth in CD3/CD28-activated T-cells infected with HIV in vitro and isolated from ART-treated PLWH, respectively. Exposure of IEC to IL-17A resulted in decreased type I IFN levels, as measured using the 293T-KEK cell based assay. Illumina RNA sequencing performed on cytokine-activated IEC before/after co-culture with T-cells of ART-treated PLWH revealed a molecular signature associated with IL-17A-mediated proviral effects. This signature includes decreased expression of transcripts linked to type I IFN production/response (DDX60, IRF7, STAT1) and HIV restriction (IFITM1, TRIM5, IF2AK2, MX1, MX2, IFIT1,3,5, PARP12, HERC6, ISG15, viperin, BST2, OAS2/3), and increased expression of Th17-attracting chemokines (CCL20).

overall_design: 3 patients + IEC cell line , 4 conditions: Medium. TNF, IL17, TNF + IL17

first: Tomas

last: Wiche Salinas

first: Annie

last: Gosselin

first: Olivier

last: Tasted

first: Yuwei

last: Zhang

first: Laurence

last: Marchand

first: Dragos

last: Vlad

first: Hanane

last: Touil

first: Jean-Pierre

last: Routy

first: Mariana

middle: G

last: Bego

middle: A

last: Cohen

first: Cecile

last: Tremblay

first: Petronela

last: Ancuta


title: Cancer - immune cell interactions drive transitions to mesenchymal-like states in glioblastoma

city: Rehovot

first: Rony

last: Chanoch

state: Israel

address: Weizmann Institute of Science, 234 Herzl Street

country: Israel

institute: Weizmann Instititue

summary: To understand the diversity of expression states in model systems of Glioblastomas, we profiled 949 single cells from 13 mice at different timepoints by single-cell RNA sequencing, as well as 3483 cells from GBM celllines,  576 cells from OSM-treated vs control-treated mice, 2767 cells from OSM-treated vs control treated cell lines (MGG23, MGG75), 290 macrophage cells from mice OE OSM, and bulk RNA seq from triplicates after treatment with siRNA for 8 TFs known to regulate mesenchymal program.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: From the mice model, tumors were dissociated, sorted into GFP+ single cells, and profiled by Smart-seq2, and for the celllines and OSM-treated experiments, cells were profiled with 10x.

first: Itay

last: Tirosh


title: Initial HCV infection of adult hepatocytes triggers a temporally structured transcriptional program containing diverse pro- and anti-viral elements

status: Public on Mar 02 2021

city: Hannover

first: Birthe

middle: Maren

last: Tegtmeyer

address: Feodor-Lynen-Str. 7

institute: TWINCORE - Centre for Experimental and Clinical Infection Research

summary: Transcriptional profiling provides global snapshots of virus-mediated cellular reprogramming, which can simultaneously encompass pro- and antiviral components. To determine early transcriptional signatures associated with HCV infection of authentic target cells, we performed ex vivo infections of adult primary human hepatocytes (PHHs) from seven donors. Coordinated sampling identified minimal gene dysregulation at six hours post infection (hpi) in PHHs. In contrast, at 72 hpi, massive increases in the breadth and magnitude of HCV-induced gene dysregulation were apparent, affecting gene classes associated with diverse biological processes. Comparison with HCV-induced transcriptional dysregulation in Huh-7.5 cells identified limited overlap between the two systems. Of note, in PHHs, HCV infection initiated broad upregulation of canonical interferon (IFN)-mediated defense programs, limiting viral RNA replication and abrogating virion release. In addition, we confirm that constitutive expression of IRF1 in PHHs maintains a steady-state antiviral program in the absence of infection which can further reduce HCV RNA replication. We also detected infection-induced signatures of translational shutoff in PHHs - downregulation of ~90 genes encoding components of the EIF2 translation initiation complex and ribosomal subunits. As HCV polyprotein translation occurs independently of the EIF2 complex, this process is pro-viral: only translation initiation of host transcripts is arrested. The combination of antiviral intrinsic and inducible immunity, balanced against pro-viral programs, including translational arrest, maintains HCV replication at a low-level in PHHs. This may ultimately keep HCV under the radar of extra-hepatocyte immune surveillance while initial infection is established, promoting tolerance, preventing clearance and facilitating progression to chronicity.

overall_design: Primary human hepatocytes (PHHs) were isolated from livers of seven donors undergoing partial hepatectomy. Plated PHHs and Huh-7.5 were infected with HCV (strain Jc1) or treated with conditioned medium, and incubated (6 or 72 hours) prior to RNA extraction and RNA-seq.  PHH of donors 4-7 were also treated with UV-inactivated HCV. Huh-7.5 experiments were repeated three times for 6 hours and six times for 72 hours. HCV infection rates were determined using viral RT-qPCR, immunofluorescence staining of viral NS5A antigen and quantification of virion secretion via TCID50. JAK/STAT inhibitor ruxolitinib was used to rescue HCV virion replication and release in PHHs.  Determination of the IRF1-regulon was achived via ecotopic expression in Huh-7.5 cells from three replicates, prior to RNA extraction and RNA-seq. HCV replication inhibitor 2’CMA was used to confirm IRF1 mediated restriction of both HCV replication and translation. All RNA-seq data generated were mapped to the Hg38 genome scaffold and raw count data were normalised  (RPKM) for individual genes. For Diffferential Expression of Genes (DEG) analyses, p-values and fold changes in expression were calculated for individual gene comparisons. Genes identified in DEG analyses were used for subsequent Gene ontology analyses, Transcriptional Regulator analyses and Ingenuity Pathway Analyses.

first: Gabrielle

last: Vieyres

first: Richard

middle: J

last: Brown


title: Combinatorial optimization of mRNA structure, stability, and translation for RNA-based therapeutics

city: Stanford

first: Rhiju

last: Das

state: California

address: 279 Campus Dr, B419 Beckman Center

department: Biochemistry

institute: Stanford University School of Medicin

summary: Therapeutic mRNAs and vaccines are being developed for a broad range of human diseases, including COVID-19. However, their optimization is hindered by mRNA instability and inefficient protein expression. Here, we describe design principles that overcome these barriers. We develop a new RNA sequencing-based platform called PERSIST-seq to systematically delineate in-cell mRNA stability, ribosome load, as well as in-solution stability of a library of diverse mRNAs. We find that, surprisingly, in-cell stability is a greater driver of protein output than high ribosome load. We further introduce a method called In-line-seq, applied to thousands of diverse RNAs, that reveals sequence and structure-based rules for mitigating hydrolytic degradation. Our findings show that “superfolder” mRNAs can be designed to improve both stability and expression that are further enhanced through pseudouridine nucleoside modification. Together, our study demonstrates simultaneous improvement of mRNA stability and protein expression and provides a computational-experimental platform for the enhancement of mRNA medicines.

sample_organism:
Homo sapiens
synthetic construct

platform_organism:
Homo sapiens
synthetic construct

overall_design:
For polysome profiling experiments, 16 polysome fractions were collected and sequenced.
For RNA degradation experiments in cells, 5 timepoints with 3 replicates each were collected. For RNA degradation experiments in solution, 10 timepoints were collected.
For directed evolution experiments, two RNA pools were subject to five cycles of selection. For both pools, the input and selection results of cycles 0, 1, and 5 were sequenced. The selected results of cycles 2, 3, 4 were also sequenced.
For RNA chemical mapping experiments, Yellowstone, Lineardesign constructs were probed with 1M7, DMSO, DMS, and NM (water). For P4P6 control, treatment was done with DMS and NM (water).
For in-line-seq degradation experiments, 45-50 pmol of RNA was subject to four conditions: 1) 50 mM Na-CHES buffer (pH 10.0) at room temperature without added MgCl2 ; 2) 50 mM Na-CHES buffer (pH 10.0) at room temperature with 10 mM MgCl2 ; 3) phosphate buffered saline (PBS, pH7.2; Thermo Fisher Scientific-Gibco 20012027) at 50°C without added MgCl2  ; and 4) PBS (pH7.2) at 50°C with 10 mM MgCl2. For degradation reactions containing MgCl2, RNA was collected at 0 and 24 hour time points. For reactions without MgCl2, timepoints were collected at 0 and 7 days.
In-line-seq RNA libraries were also probed for structure with the addition of 1M7 or no 1M7 (negative control)

first: Kathrin

last: Leppek

first: Gun

middle: W

last: Byeon

first: Wipapat

last: Kladwang

first: Hannah

last: Wayment-Steele

first: Craig

last: Kerr

first: Adele

middle: F

last: Xu

first: Do-Soon

last: Kim

first: Ved

last: Topkar

first: Christian

last: Choe

first: Daphna

last: Rothschild

first: Gerald

last: Tiu

first: Roger

last: Wellington-Oguri

first: Kotaro

last: Fuji

first: Eesha

last: Sharma

first: Andrew

middle: M

last: Watkins

first: John

last: Nicol

first: Jonathan

last: Romano

first: Bojan

last: Tunguz

first: Eterna

last: Participants

first: Maria

last: Barna


title: RIF1 is necessary to maintain the global epigenetic state in human cells.

city: Tallahassee

first: David

last: Gilbert

state: FL

address: 319 Stadium Drive

department: Department of Biological Science

institute: Florida State University

summary: DNA is replicated in a defined temporal order termed the replication timing (RT) program, which is correlated with genome compartmentalization with early replicating chromatin located mainly in the A compartment and late replicating chromatin in the B compartment (Dixon et al 2012, Moindrot et al 2012, Ryba et al 2010, Yaffe et al 2010). Similarly, active histone modifications and transcriptional permissiveness are associated with early replication while a repressive chromatin state is associated with late replication (Hiratani et al 2009, Riveria-Mulia et al 2015, Lubelsky et al 2014). However, the mechanistic interplay between RT, chromatin state, and genome compartmentalization is largely unknown. Here we report RT is upstream of epigenome formation and compartmentalisation in human embryonic stem cells (hESCs) and the cancer cell line HCT116. Knockout (KO) of the conserved RT control factor RIF1, rather than causing discrete RT switches, leads to dramatically increased cell to cell heterogeneity of RT genome wide, despite RIF1’s enrichment in late replicating chromatin. RIF1 KO hESCs have a nearly random RT program, unlike any other cell type to date, yet cells self-renew without signs of differentiation. Those regions that do retain RT consist of large H3K9me3 domains, which are prevalent in HCT116 but rare in hESCs, revealing two independent mechanisms of RT regulation that are used to different extents in different cell types. RIF1 KO cells also showed genome wide downregulation of H3K27ac peaks and enrichment of H3K9me3 at large domains that remained late replicating, while H3K27me3 and H3K4me3 were also re-distributed genome wide but in a cell type specific manner. Histone modification changes correlated with gene expression changes and global reorganisation of genome compartments. Some RT/compartment shifts were associated with specific TAD boundary shifts, but overall we observed a genome wide strengthening of TAD structures. Our findings support a model in which RT controlled by RIF1 plays a key role in establishing epigenetic state and genome architecture in human cells.

overall_design: Examination of E/L repli-seq, high resolution repli-seq, ChIP-seq of 4 different histone modifications, Hi-C, RNA-seq, and single cell RNA-seq of two cell lines both WT and RIF1 KO with two replicates each. Single cell repli-seq of WT and RIF1 KO for one other cell line.

first: Kyle

middle: N

last: Klein

first: Peiyao

last: Zhao


title: Transcriptomic analysis and competing endogenous RNA network in the human endometrium between proliferative and mid-secretory phases

status: Public on Feb 24 2021

city: Daejeon

first: Seong-Lan

last: Yu

address: Gasuwon-dong

department: Myunggok Medical Research Institute

institute: Konyang university

summary: To identify differentially expressed transcripts (long-noncoding RNAs [lncRNAs], microRNAs [miRNAs], and mRNAs) and competing endogenous RNA (ceRNA) networks closely connected with endometrial receptivity, we analyzed gene expression profiles between the proliferative and mid-secretory endometria in fertile women.

overall_design: Profiles between the proliferative and mid-secretory endometria in fertile women

first: Tae-Hyun

last: Kim

first: Jaeku

last: Kang

first: Seok-Rae

last: Park


title: Lineage-specific selection and the evolution of virulence in Candida albicans

status: Public on Mar 31 2021

city: San Francisco

first: Sheena

middle: D.

last: Singh-Babak

state: CA

address: 600 16th Street

department: Microbiology & Immunology

institute: University of California San Francisco

summary: This data was generated to compare genome-wide expression differences between a major fungal pathogen of humans, Candida albicans and its less pathogenic relative, Candida dubliniensis, using interspecies hybrids to systematically identify cis-regulatory adaptations.

sample_organism:
Candida dubliniensis
Candida albicans x Candida dubliniensis

overall_design: RNA-Seq data generated in this study for allele-specific expression experiments and overexpression experiments. Samples were grown in culture media (planktonic) to mid-log phase and RNA was extracted using the Ambion RiboPure RNA Purification Kit for Yeast. Every experiment was performed in duplicate (represented by A and B appended to the file names). For the Experiments in the hybrid organism (ASE), the experiments are internally controlled without need for an external control. For the overexpression RNA-Seq experiments, the controls are the Empty vector samples.

middle: D

first: Tomas

last: Babak

first: Hunter

last: Fraser

first: Alexander

last: Johson


title: Single nucleus multi-omics regulatory atlas of the murine pituitary [scRNA-Seq]

status: Public on Feb 23 2021

city: Los Angeles

first: Michel

last: Zamojski

address: 8700 Beverly Boulevard

department: Regenerative Medicine Institute

institute: Cedars-Sinai Medical Center

summary: The pituitary regulates growth, reproduction and other endocrine systems. To investigate transcriptional network epigenetic mechanisms in this gland, we generated paired single nucleus (sn) transcriptome and chromatin accessibility profiles in single mouse pituitaries, and genome-wide sn methylation datasets. Our analysis provided insight into cell type epigenetics, regulatory circuit and gene control mechanisms. Latent variable transcriptome and accessibility data representation resolved both inter-sexual and inter-individual variation in gene control programs. Multi-omics analysis of cell type-specific gene regulatory networks distinguished distinct mechanisms. Particularly, the FoxL2 gonadotrope network is controlled both by FoxL2 expression and by target gene epigenetic status. Co-accessibility analysis comprehensively identified putative regulatory regions, including a region that overlapped the fertility-linked rs11031006 human polymorphism. In vitro CRISPR-deletion at this locus increased Fshb levels, supporting this domain’s predicted regulatory role. The public pituitary atlas [link] is a resource for elucidating cell-type specific gene regulatory mechanisms and principles of transcription circuit control.

overall_design: Single cell transcriptome profiling of adult mouse pituitaries by single cell GEM RNA-seq, using Illumina

first: Frederique

last: Ruf-Zamojski

first: Zidong

last: Zhang

first: Gregory

last: Smith

first: Natalia

last: Mendelev

first: Hanqing

last: Liu

first: German

last: Nudelman

first: Mika

last: Moriwaki

first: Hanna

last: Pincas

first: Rosa

last: Castanon

first: Yongchao

last: Ge

first: Venugopalan

last: Nair

first: Nitish

last: Seenarine

first: Mary-Anne

middle: S

last: Amper

first: Xiang

last: Zhou

first: Luisina

last: Ongaro

first: Chirine

last: Toufaily

first: Gauthier

last: Schang

first: Joseph

middle: R

last: Nery

first: Anna

last: Bartlett

first: Andrew

last: Aldridge

first: Nimisha

last: Jain

first: Gwen

middle: V

last: Childs

first: Olga

last: Troyanskaya

last: Ecker

first: Judith

middle: L

last: Turgeon

first: Corrine

last: Welt

first: Daniel

last: Bernard

first: Stuart

middle: C

last: Sealfon


title: Single nucleus multi-omics regulatory atlas of the murine pituitary [snRNA-seq ]

first: Michel

last: Zamojski

overall_design: Single nucleus transcriptome profiling of adult mouse pituitaries by single nuclei GEM RNA-seq, using Illumina

first: Frederique

last: Ruf-Zamojski

first: Zidong

last: Zhang

first: Gregory

last: Smith

first: Natalia

last: Mendelev

first: Hanqing

last: Liu

first: German

last: Nudelman

first: Mika

last: Moriwaki

first: Hanna

last: Pincas

first: Rosa

last: Castanon

first: Yongchao

last: Ge

first: Venugopalan

last: Nair

last: Seenarine

middle: K


title: Molecular roadmap of the healthy stress response in the mouse hippocampus (small RNA)

first: Lukas

middle: Matthias

last: von Ziegler

overall_design: Here, we used a brief (6min) forced swim exposure and profiled the hippocampus using small RNA sequencing 45min after initiation of the experiment.

first: Pierre-Luc

last: Germain

first: Amalia

last: Florio-Servou

first: Katharina

last: Gapp

first: Johannes

last: Bohacek


title: Discovery of new imprinted genes by genome-wide DNA methylation comparison between human androgenetic and parthenogenetic induced pluripotent stem cells

status: Public on Feb 22 2021

city: Seoul

first: Kinarm

last: Ko

address: 120, Neungdong-ro, Gwangjin-gu

institute: Konkuk University

summary: Genomic imprinting is an epigenetic phenomenon in which the expression of a gene is determined in a parent-of-origin-dependent manner. Imprinted genes play an important role in the normal growth and development of mammals, and mutations at the imprinting sites result in gene dysfunction and many genetic disorders. To identify new human imprinted differentially methylated regions (DMRs), we compared the global levels of DNA methylation in androgenetic induced pluripotent stem cells and parthenogenetic induced pluripotent stem cells using DNA methyl-capture sequencing analysis.

overall_design: We have analyzed human androgenetic, parthenogenetic, biparental induced pluripotent stem cells and their parental fibroblast.

last: Choi


title: Unsupervised cell interaction profiling based on multiplet RNA sequencing reveals major architectural differences between small intestinal and colonic epithelium.

city: Stockholm

first: Martin

last: Enge

address: CCK, Z4

department: Dep of Oncology-Pathology

country: Sweden

institute: Karolinska Institute

summary: Cellular identity in complex multicellular organisms is strictly maintained over the course of life. This control is achieved in part by the organ structure itself, such that neighboring cells influence each other’s identity. However, large-scale investigation of the cellular interactome has been technically challenging. Here, we develop CIM-seq, an unsupervised and high-throughput method to analyze direct physical cell interactions between every cell type in a given tissue. CIM-seq is based on RNA sequencing of incompletely dissociated cells, followed by computational deconvolution of these into their constituent cell types using particle swarm optimization. We use CIM-seq to define the cell interaction landscape of the mouse small intestinal and colonic epithelium uncovering both known and novel interactions. Specifically, we find that the general architecture of the stem cell niche is radically different between the two tissues. In small intestine, the stem-paneth cell interaction forms an exceptionally strong and exclusive niche, in which paneth cells provide Wnt ligands1. In colonic epithelium, no similar compartment exists to support stem cells, and Wnt signaling is provided by a mesenchymal cell layer. However, colonic stem cells are associated with a subset of goblet cells expressing the wound healing marker Plet1, suggesting an additional level of structural control in the colon. These results identify novel cellular interactions specific for the colonic stem cell niche and shed light on a previously unappreciated complexity of the tissue organization and biology of the colon. CIM-seq is broadly applicable to studies that aim to simultaneously investigate the constituent cell types and the global interaction profile in a specific tissue.

overall_design: Singlet and multiplet RNAseq data from C57BL/6J mouse colon, small intestine and spleen

first: Jason

middle: T

last: Serviss

first: Nathanael

last: Andrews

first: Agneta

middle: B

last: Andersson

first: Ewa

last: Dzwonkowska

first: Rosan

last: Heijboer

first: Marco

last: Gerling

first: Natalie

last: Geyer


title: Towards 3D-bioprinting of an endocrine pancreas: A building block concept for bioartificial insulin-secreting tissue

status: Public on Feb 19 2021

city: Heidelberg

first: Gabriel

middle: Alexander

last: Salg

address: Im Neuenheimer Feld 420

department: General-, Visceral-, and Transplantation Surgery

institute: University Hospital Heidelberg

summary:
Background & Aims: 3D Bioprinting of an endocrine pancreas is a promising future curative treatment for selected patients with insulin secretion deficiency. In this study we present an end-to-end integrative, scalable concept extending from the molecular to the macroscopic level.
Methods: A hybrid scaffold device was manufactured by 3D (bio)printing. INS-1 cells with/without endothelial cells were bioprinted in gelatin methacrylate blend hydrogel. Polycaprolactone was 3D-printed and heparin-functionalized as structural scaffold component. In vitro evaluation was performed by viability and growth assays, total mRNA sequencing, and glucose-stimulated insulin secretion. In vivo, xenotransplantation to fertilized chicken eggs was used to investigate vascularization and function, and finite element analysis modeling served to detect boundary conditions and applicability for human islets of Langerhans.
Results: Insulin-secreting pseudoislets were formed and resulted in a viable and proliferative experimental model. Transcriptomics revealed upregulation of proliferative and ß-cell-specific signaling cascades, downregulation of apoptotic pathways, and overexpression of extracellular matrix proteins and VEGF induced by pseudoislet formation and 3D culture. Co-culture with human endothelial cells created a natural cellular niche resulting in enhanced insulin response after glucose stimulation. Survival and function of the pseudoislets after explantation and extensive scaffold vascularization of both the hydrogel and heparinized polycaprolactone components were demonstrated in ovo. Computer simulations of oxygen, glucose, and insulin flows were used to evaluate scaffold architectures and Langerhans islets at a future transplantation site along neurovascular structures.
Conclusion: A defined end-to-end process for multidisciplinary bioconvergence research on a bioartificial endocrine pancreas was developed. A modular, patient-specific device architecture is proposed for future research studies.

overall_design: mRNA profile of 3D-bioprinted INS-1 cells in comparison with 2D-monolayer culture as control (total 4 samples, 2 biological replicates per group)

middle: A

first: Eric

last: Poisel

first: Matthias

last: Neulinger-Munoz

first: Nathalia

last: Giese

first: Thilo

last: Hackert

first: Hannes

middle: G

last: Kenngott


title: Kdm2b promotes cell viability by enhancing DNA damage response in canine hemangiosarcoma

status: Public on Feb 11 2021

city: Sapporo

first: Keisuke

last: Aoshima

state: Hokkaido

address: Kita 18 Nishi 9

department: Faculty of Veterinary Medicine

institute: Hokkaido University

summary: We found that lysine-specific demethylase 2b (Kdm2b) was highly expressed in HSA cell lines compared to normal canine endothelial cells. Silencing of Kdm2b in HSA cells resulted to increased cell death in vitro by inducing apoptosis through the inactivation of the DNA repair pathways and accumulation of DNA damage. Kdm2b silencing in tumor xenografts results to decreased tumor sizes compared to the control. Treatment of GSK-J4, a histone demethylase inhibitor, also induced apoptosis and cell death. In addition, GSK-J4 treatment decreases tumor sizes. Therefore, we demonstrate that Kdm2b acts as an oncogene in HSA by enhancing the DNA damage response. Moreover, we show that histone demethylase inhibitor GSK-J4 can be used as a therapeutic alternative to doxorubicin for HSA treatment.

overall_design: mRNA expression profiles of normal canine endothelial cells and a canine hemangiosarcoma cell line with/without Kdm2b knockdown.

first: Kevin

last: Gulay


title: BABEL enables cross-modality translation between multi-omic profiles at single-cell resolution

status: Public on Feb 16 2021

middle: Eric

last: Wu

address: 353 Jane Stanford Way

department: Computer Science

institute: Stanford University

overall_design: Single cell multiome ATAC + gene expression profiling of GM12878 cells.

middle: E

first: Kathryn

last: Yost

first: Howard

middle: Y

last: Chang

first: James

last: Zou


title: Poll II ChIP-Seq in miR-34a transfectant

status: Public on Feb 01 2021

city: Shinjuku-ku

first: Shin-ichiro

last: Ohno

state: Tokyo

address: 6-1-1 Shinjuku

department: Molecular Pathology

institute: Tokyo Medical University

summary: To investigate the behavior of RNA Pol II during RNA activation by miR-34a,the ChIP-Seq analysis of RNA Poll II in NCI-H1299 cell line was performed. This experiment analyzes how RNA pol II is activated by the introduction of miR-34a in some genes whose transcription is induced by miR-34a. From the analysis of this data, the purpose is to clarify the molecular mechanism of RNA activation by miR-34a.

overall_design: Poll II ChIP was performed on nuclear lysate from non-treated and miR-34a-treated H1299 cell lines. Then, DNA sequence of ChIP samples were analyzed by deep sequencing, using Illumina NextSeq 500.


title: Broad transcriptional firing represses bactericidal activity in human airway neutrophils

city: Atlanta

first: Diego

last: Moncada

state: Georgia

address: 201 Dowman Dr

department: Pediatrics

institute: Emory University

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

overall_design: Refer to individual Series


title: Molecular roadmap of the healthy stress response in the mouse hippocampus

city: Zürich

first: Lukas

last: von Ziegler

address: Winterthurerstrasse 190

institute: ETH Zürich

summary: The acute stress response mobilizes energy to meet situational demands and re-establish homeostasis. Here, we used a brief forced swim exposure to trigger a strong stress response in mice. Using multiomic profiling we characterize the stress-induced molecular events in the dorsal (dHC) and ventral (vHC) hippocampus over time, across molecular scales, and down to the level of cell types and single cells.

overall_design: Examining the effect of acute swim stress (6min at 18°C) on the transcriptome and translatome of the mouse hippocampus at multiple time-points (all data: Stressome_GeneCounts.txt). This series contains data from multiple experiments investigating this. Following sub-experiments were conducted: TimeSeriesFST (TimeSeriesFST_GeneCounts.txt): Experiment to assess stress induced transcriptional changes in the hippocampus at multiple time points (45min, 1h30min, 2h, 3h, 4h) vs controls in the dorsal (dHC) and ventral hippocampus (vHC). FSTFemale45min4h (SwimFemale45min4h_GeneCounts.txt): Experiment replicating two time points (45min and 4h) from the time-series with female and male mice to investigate sex effects in the vHC. LeftvsRight (LeftvsRight_GeneCounts.txt): Experiment to assess differences in the acutes stress response (45min) between left and right hemisphere in both dHC and vHC. CMVTRAP (CMVTRAP_GeneCounts.txt): Experiment to assess changes in ribosome occupancy (active translation) in a ubiquitous TRAP assay (all cell types) at 45minutes in the vHC in both pre- and post-IP fractions. CAMK2A-TRAP (CAMK2A-TRAP_GeneCounts.txt)/CAMK2A-TRAP-2 (CAMK2A-TRAP_Exp2_GeneCounts.txt): Two experiments to assess translation changes in excitatory neurons after acute stress in the dHC and vHC at 45min and 1h30min. VIAAT-TRAP (VIAAT-TRAP_GeneCounts.txt): Experiment to assess translation changes in inhibitory neurons after acute stress in the dHC and vHC at 45min

middle: M

first: Pierre-Luc

last: Germain

first: Amalia

last: Florio-Servou

first: Johannes

last: Bohacek


title: Validation of Baboon Pluripotent Cells as a Model for Translational Stem Cell Research

status: Public on Jan 21 2021

city: Yiwu

first: keren

last: cheng

state: Zhejiang

address: 1575 chouzhou bei road

department: School of Medicine

institute: Zhejiang University


title: Expression profiling in samples with gastric intestinal metaplasia without concurrent gastric cancer

status: Public on Feb 28 2021

city: East Melbourne

first: Rita

middle: Ann

last: Busuttil

state: VIC

address: St Andrews Pl

department: Research

country: Australia

institute: Peter MacCallum Cancer Centre

summary: Genome wide mRNA expression profiling of 14 gastric IM samples derived from an Australian based cohort was performed.

overall_design: Profiling of 14 gastric intestinal metaplasia samples were profiled on Affymetrix GeneChip Human Genome U133 Plus 2.0 Arrays. All samples were collected with approvals from Peter MacCallum Cancer Center, Australia; the Research Ethics Review Committee; and signed informed patient consent.

first: Alex

last: Boussioutas

first: Athanasios

last: Koulis


title: Multi-omics analysis of dynamic dose-response in macrophages recapitulates multi-walled carbon nanotube -induced lung fibrosis [methylation]

status: Public on Mar 05 2021

city: Tampere

first: Dario

last: Greco

address: Arvo ylpön Katu 34

department: Faculty of Medicine and Health Technology

country: Finland

institute: Tampere University

summary: Toxicogenomics approaches are increasingly applied to gain mechanistic insight into the toxicity of engineered nanomaterials (ENMs). These emerging technologies have been shown to aid the translation of in vitro experimentation into relevant information on real-life exposures. Furthermore, integrating multiple layers of molecular alteration can improve the systemic understanding of the toxicological insult. While evidence of the immunotoxic effects of several ENMs is arising, the mechanisms are less characterized, and the dynamics of the molecular adaptation of the immune cells are still largely unknown.  Here, we carried out a multi-omics approach characterizing the dynamic dose-dependent (DDD) molecular alterations in a model of human macrophages. THP-1 macrophages were exposed to increasing concentrations of rigid multiwalled carbon nanotubes (rCNTs) and the genome-wide alterations in the transcriptome and gene promoter methylation were assessed at three consecutive time points. The results suggest dynamic patterns of molecular alterations with a rapid response in the gene expression and contribution of DNA methylation in the long-term adaptation. Moreover, our analytical approach is able to highlight patterns of molecular alteration in vitro that recapitulate several elements of pathogenesis of pulmonary fibrosis, a known long-term effect of rCNTs exposure in vivo.

overall_design: DNA methylation profiles of THP-1 macrophages exposed to three concentrations (5, 10 or 20 µg/mL) of rigid multi-walled carbon and untreated controls were profiled at 24, 48 and 72 hours. Exposures were performed as triplicates, untreated controls with four replictes.

first: L

last: Saarimaki

first: P

last: Kinaret

first: A

last: Federico

first: G

last: del Giudice

last: Scala

last: Serra

first: D


title: Skeletal Muscle Transcriptome in Healthy Aging

status: Public on Jan 08 2021

city: Baltimore

first: Supriyo

last: De

state: Maryland

address: 251 Bayview Blvd

department: Laboratory of Genetics and Genomics

institute: NIA-IRP, NIH

summary: Healthy human skeletal muscle samples were processed and analyzed to infer age associated skeletal muscle changes

overall_design: Total RNA-seq of human skeletal muscle biopsies across different ages

first: Robert

last: Tumasian III

first: Abhinav

last: Harish

first: Gautam

last: Kundu

first: Jen-Hao

last: Yang

first: Ceereena

last: Ubaida-Mohien

first: Marta

last: Gonzalez-Freire

first: Mary

last: Kaileh

first: Linda

last: Zukley

first: Chee

middle: W

last: Chia

first: Alexey

last: Lyashkov

first: William

middle: H

last: Wood III

first: Yulan

last: Piao

first: Christopher

last: Coletta

first: Jun

last: Ding

first: Myriam

last: Gorospe

first: Ranjan

last: Sen

first: Luigi

last: Ferrucci


title: Interplay of BAF and MLL4 promotes enhancer activation

status: Public on Jan 07 2021

city: Bethesda

first: Kai

last: Ge

state: MD

address: 50 South Dr Rm 4154

department: NIDDK

institute: NIH

summary: Cell type-specific enhancers are activated by coordinated actions of lineage-determining transcription factors (LDTFs) and chromatin regulators. The SWI/SNF complex BAF and the histone H3K4 methyltransferase MLL4 (KMT2D) are both implicated in enhancer activation. However, the interplay between BAF and MLL4 in enhancer activation remains unclear. Using adipogenesis as a model system, we identify BAF as the major SWI/SNF complex that colocalizes with LDTFs and MLL4 on active enhancers during cell differentiation. Similar to MLL4, BAF is required for cell type-specific gene induction in adipogenesis. In contrast, another SWI/SNF complex PBAF is enriched on promoters and is dispensable for adipogenesis. By depleting BAF subunits SMARCA4 (BRG1) and SMARCB1 (SNF5) as well as MLL4 in cells, we show that BAF and MLL4 reciprocally regulate each other’s binding on active enhancers before and during adipogenesis. By focusing on enhancer activation by the adipogenic transcription factor C/EBPβ without inducing cell differentiation, we provide direct evidence to support an interdependent relationship between BAF and MLL4 in activating cell type-specific enhancers. Together, these findings suggest that the interplay of BAF and MLL4 promotes LDTF-dependent activation of cell type-specific enhancers.

overall_design: Expression profiling by RNA-Seq at D-3, D2 or D7 of adipogenesis in culture, and ChIP-Seq profiling of BAF subunits (Brg1, SS18, Arid1a), PBAF subunit BAF200, GBAF subunit Brd9, MLL4, CBP, histone modifications (H3K4me1 and H3K27ac) by ChIP-seq, profiling of chromatin accessibility by ATAC-Seq at D-3 or D2 of adipogenesis in culture.

first: Young-Kwon

last: Park

first: Ji-Eun

last: Lee

first: Weiqun

last: Peng


title: Broad transcriptional firing represses bactericidal activity in human airway neutrophils [Transcriptional_Blockage_CFASN_Neutrophils]

first: Diego

last: Moncada

summary: Neutrophils are often considered terminally differentiated and poised for bacterial killing. In chronic diseases such as cystic fibrosis (CF), an unexplained paradox pits massive neutrophil presence against prolonged bacteria infections. Here, we show that neutrophils recruited to CF airways in vivo and in an in vitro transmigration model display rapid and broad transcriptional firing, leading to an upregulation of survival and anabolic genes, and a downregulation of antimicrobial genes. Newly transcribed RNAs are mirrored by the appearance of corresponding proteins, confirming active translation in these cells. Remarkably, treatment by the RNA polymerase II and III inhibitor Alpha-amanitin restored expression of key antimicrobial genes, and increased bactericidal capacity of CF airway neutrophils in vitro and in short-term sputum cultures ex vivo. Broadly, our findings show that neutrophil plasticity is regulated at the terminal organ via RNA and protein synthesis, leading to adaptations that profoundly impact their canonical functions (i.e., bacterial clearance).

overall_design: To investigate a potential causal relationship between de novo transcription and neutrophil fate acquisition, we transmigrated neutrophils in the model for 2 hours into CFASN and then treated them with the RNA polymerase II and III-specific transcriptional blocker 𝛼-amanitin.

first: Camilla

last: Margaroli

last: Moncada Giraldo

first: Rabindra

last: Tirouvanziam


title: TRIM3 depletion in MCF-7 cells

status: Public on Jan 01 2021

city: Wu han

first: Le

last: Wu

state: Hu bei

address: No.1,Shizishan Street · Hongshan District · Wuhan

institute: HuaZhong Agricultural university

summary: We depleted TRIM3 in MCF-7 cells to check the change of the overall genomic profiling

overall_design: siControl vs siTRIM3


title: ChIP-seq analysis of genome-edited MCF7 and T47D ESR1 mutant cell models

city: Boston

first: Zheqi

last: Li

state: Massachusetts

address: 450 Brookline Avenue, Smith Building SM1006

institute: Dana-Farber Cancer Institute

summary: This study is designed to comprehensively characterize the cistromes of Y537S and D538G mutated ER versus WT ER in breast cancer cells. Genome-edited MCF7 and T47D cells were hormone deprived and treated with or without E2 for 45 minuts. Chromatin DNA was then extracted from each sample. The immunoprecipitation was performed using ERα (Santa Cruz Biotechnologies, sc543)  antibody. Pooled DNA samples from individual clones were sent to sequencing with Illumina Hiseq 2500 Platform. ChIP-seq reads were aligned to either hg38 genome assembly using Bowtie 2.0, and peaks were called using MACS2.0 with p value below 10E-5. DiffBind was used to perform principle component analysis, identify differentially expressed binding sites and analyze intersection ratios with other data sets. Genomic feature distribution were called using ChIPseeker.

overall_design: Individual clones of genome-eidted MCF7 and T47D cell lines with knock-in of WT/Y537S/D538G ER were hromone deprived and treated with veh or 1 nM E2 for 45 minutes. Chromatin DNA was then extracted from each sample. The immunoprecipitation was performed using ERα (sc543) antibody (Santa Cruz Biotechnologies). Pooled DNA samples from individual clones were sent to sequencing with Illumina Hiseq 2500 Platform.

first: Amir

last: Bahreini

first: Steffi

last: Oesterreich


title: Unravelling Heterogeneity of Amplified Human Amniotic Fluid Stem Cells Sub-Populations

status: Public on Jan 13 2021

city: Padova

first: Mattia

last: Forcato

address: Via Ugo Bassi, 58/B

country: Italy

institute: University of Padova

summary: Human amniotic fluid stem cells (hAFSCs) are broadly multipotent immature progenitor cells with high self-renewal and no tumorigenic properties. These cells, even amplified, present very variable morphology, density, intracellular composition and stemness potential, and this heterogeneity can hinder their characterization and potential use in regenerative medicine. Celector® (Stem Sel ltd.) is a new technology that exploits the Non-Equilibrium Earth Gravity Assisted Field Flow Fractionation principles to characterize and label-free sort stem cells based on their solely physical characteristics without any manipulation. Viable cells are collected and used for further studies or direct applications. In order to understand the intrapopulation heterogeneity, various fractions of hAFSCs were isolated using the Celector® profile and live imaging feature. The gene expression profile of each fraction was analysed using whole-transcriptome sequencing (RNAseq). Gene Set Enrichment Analysis identified significant differential expression in pathways related to Stemness, DNA repair, E2F targets, G2M checkpoint, hypoxia, EM transition, mTORC1 signalling, Unfold Protein Response and p53 signalling. These differences were validated by RT-PCR, immunofluorescence and differentiation assays. Interestingly, the different fractions showed distinct and unique stemness properties. These results suggest the existence of deep intra-population differences that can influence the stemness profile of hAFSCs. This study represents a proof-of-concept of the importance of selecting certain cellular fractions with the highest potential to use in regenerative medicine.

overall_design: Amplified hASCs from 8 different patients were sorted using Celector technology in different fractions based on sample’s morphological features and named according to their sorting order (F1 is the firt sorted fraction, F4 is the last sorted fraction). The number of  the sorted fractions was dependent on samples characteristics. Unfractioned cells (Ftot) were used as control for each patient sample

first: Francesca

last: Casciaro

first: Silvia

last: Zia

first: Tullia

last: Maraldi

first: Marco

last: Demaria


title: PolyA-sequencing in Jurkat cells upon CDK12 depletion.

status: Public on Jan 05 2021

first: Ruben

last: Dries

address: 360 Longwood Ave

department: Computational Biology

country: USA

institute: DFCI

summary: We analyzed the 3' end of polyadenylated transcripts in Jurkat cells treated with either THZ531 (vs. DMSO) or the CDK12 degrader BSJ-4-116 (vs. BSJ-4-116NC).

overall_design: Expression of polyA transcripts in Jurkat cells treated with 250 nM THZ531 (vs. DMSO control) or 50 nM BSJ-4-116 (vs. BSJ-4-116NC) for 8h using the RNA-seq library kit (QuantSeq 3’ mRNA Sequencing REV, Lexogen) in triplicate, for a total of 12 individual samples.

first: Nathanael

middle: S

last: Gray


title: Androgen Receptor splice variant V7 (AR-V7) mediates AR signalling in castration resistant prostate cancer (CRPC)

city: Houston

first: Basil

last: Paul

address: 1515 Holcombe Blvd

institute: MD Anderson Cancer Center


title: Transcriptional profile of organ fibroblasts from adult mice

city: Clayton

first: Hieu

middle: Tri

last: Nim

address: Monash University Clayton Campus, Wellington Rd

department: Australian Regenerative Medicine Institute

institute: Monash University

summary: Organ fibroblasts are essential components of homeostatic and diseased tissues, as they participate in sensing the microenvironment and communicating with other resident cells. They are also involved in pathological remodeling and fibrosis, caused by excessive deposition of connective tissue after injury, which impairs organ function. It is estimated that 45% of deaths in developed countries are linked to chronic fibrosis, yet current drugs on the market are both inefficient and non-specific to this condition [1]. We have previously shown that cardiac fibroblasts display a unique cardiogenic identity, important for cardiac pathological remodeling. To determine whether fibroblasts from other organ systems display a molecular signature unique to their organ of origin, we characterized fibroblasts isolated from the adult mouse skin, lung, kidney, gonad and liver, and documented a molecular positional and organ signature that is likely a remnant from embryonic development. This information opens novel opportunities for the treatment of fibrotic diseases in a more precise, organ-specific manner.

overall_design: Comparative trancriptional profile of organ fibroblast samples (heart, kidney, liver, skin, lung) isolated from adult mice.

first: Mirana

last: Ramialison

first: Milena

last: Furtado


status: Public on Dec 31 2020

city: Kingston

first: Dasith

last: Perera

state: Rhode Island

address: Flagg Rd

institute: University of Rhode Island

summary: Identify DEGs in H. parainfluenzae in monoculture vs coculture with S. mitis aerobically on BHI-YE HP at 37.C and 5% CO2

sample_organism:
Haemophilus parainfluenzae
Streptococcus mitis

overall_design: Gene expression of H. parainfluenzae in monoculture and coculture with S. mitis, 2 reps for each condition


title: BAP1 mutant uveal melanoma is stratified by metabolic phenotypes with distinct vulnerability to metabolic inhibitors

status: Public on Feb 08 2021

city: Philadelphia

first: Andrew

last: Aplin

state: PA

address: 233 South 10th St.

institute: Thomas Jefferson University

summary: Inactivating mutations of BAP1 are linked with an increased risk of developing metastasis in UM, but the roles of BAP1 in UM progression is unclear. To characterize BAP1’s functions in UM, we performed RNA sequencing on BAP1 wild-type and mutant UM cell lines. Gene set enrichment analysis showed that there is metabolic heterogeneity in BAP1 mutant UM cells based on their oxidative phosphorylation gene signature.

overall_design: RNA were obtained from BAP1 wild-type (MM66) and mutant (MP38, MP46, MP65 and PDX4) UM cell lines.

first: Anna

last: Han

first: Timothy

middle: J

last: Purwin


title: A single-cell chromatin accessibility map of pulmonary alveologenesis in humans and mice

city: La Jolla

first: Thu

last: Duong

address: 9500 Gilman Dr.

institute: University of California San Diego

summary: Regulation of lung responses to air breathing and continued alveolar development shape ex-utero and adult respiratory health.  Applying single-cell transposome hypersensitive site sequencing (scTHS-seq) to human and mouse lung, we assembled a regulatory atlas of postnatal lung development and analyzed over 80,000 single-cells.  From day of life 1, we characterized cell types and cell-cell interactions driving alveoli generation.  We elucidated key transcription factor-gene accessibility modules (TF-GAM) guiding alveolar epithelial cell differentiation and epithelial-mesenchymal interactions involved in alveolar septation and mechanotransduction.  Incorporating GWAS causal variants, we identified lung pathogenic risk units enriched in specific cell types.  Our regulatory map and analysis model provide an effective resource to investigate age-dependent and species-specific control of critical developmental processes.  Furthermore, this resource complements single-cell atlas efforts to advance our understanding of lung health and disease across the human lifespan.

overall_design:
Single DAPI+ nuclei (according to Samples list) were isolated from 4 separate postmortem human and 4 mouse distal lung parenchymal samples and processed for single-cell transposome hypersensitive site sequencing (scTHS-seq).
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Submitter declares that the raw data will be submitted to dbGaP (https://www.ncbi.nlm.nih.gov/gap) because of patient privacy concerns.

first: Yan

last: Wu

first: Brandon

last: Sos

first: Weixiu

last: Dong

first: Siddarth

last: Limaye

first: James

last: Hagood

first: Kun

last: Zhang