title: Distinct and additive effects of calorie restriction and rapamycin in aging skeletal muscle [CR data set]

city: Basel

first: Anastasiya

last: Boersch

address: Klingelbergstrasse 50 / 70

department: Biozentrum

institute: University of Basel

summary: As global life expectancy continues to climb, maintaining skeletal muscle function is increasingly essential to ensure a good life quality for aging populations. Calorie restriction (CR) is the most potent and reproducible intervention to extend health and lifespan, but is largely unachievable in humans. Therefore, identification of “CR mimetics” has received much attention. Since CR targets nutrient-sensing pathways centering on mTORC1, rapamycin, the allosteric inhibitor of mTORC1, has been proposed as a potential CR mimetic and counteracts age-related muscle loss. Therefore, we tested whether rapamycin acts via similar mechanisms as CR to slow muscle aging. Contrary to our prediction, long-term CR and rapamycin-treated geriatric mice display distinct skeletal muscle gene expression profiles despite both conferring benefits to aging skeletal muscle. Furthermore, CR improved muscle integrity in a mouse with nutrient-insensitive sustained muscle mTORC1 activity and rapamycin provided additive benefits to CR in aging mouse muscles. Therefore, RM and CR exert distinct, compounding effects in aging skeletal muscle, opening the possibility of parallel interventions to counteract muscle aging.

overall_design: Skeletal muscle mRNA profiles of 30 months-old mice subjected to calorie restriction (70% of AIN93M diet with 1.43x(vitamins + minerals)) for 15 months from the age of 15 months were generated by next-generation sequencing.

first: Daniel

last: Ham

last: Börsch

first: Mihaela

last: Zavolan

first: Nitish

last: Mittal

first: Markus

middle: A

last: Rüegg


title: Wild-type Heterogeneity Contributes to Clonal Variability in Genome-Edited Cells

status: Public on Feb 18 2022

city: Freiburg

first: Yong

last: Li

address: Hugstetter Str. 49

department: Institute of Genetic Epidemiology

country: Germany

institute: Medical Center - University of Freiburg

type: Expression profiling by high throughput sequencing

summary: Phenotypic variability among different knockout clones of the same gene is a common problem confounding the establishment of robust genotype-phenotype correlations. Optimized genome editing protocols to enhance reproducibility include measures to reduce off-target effects. However, even if current state-of-the-art protocols are applied phenotypic variability is frequently observed. Here we identify heterogeneity of wild-type cells as an important and often neglected confounding factor in genome-editing experiments. We demonstrate that isolation of individual wild-type clones from an apparently homogenous stable cell line uncovers significant phenotypic differences between clones. Strikingly, we observe hundreds of differentially regulated transcripts when comparing two populations of wild-type cells. Heterogeneity of wild-type cells thus contributes to variability in genome-edited cells when these are generated through isolation of clones. We show that the generation of monoclonal isogenic wild-type cells prior to genomic manipulation reduces phenotypic variability.

overall_design: Expression profiling of polyclonal vs. monoclonal mIMCD-3 wild-type cells and expression profiling of monoclonal vs. subclone mIMCD-3 cells. Data of polyclonal wild-type cells have been analyzed in a different context before (GSE179947).

first: Burulca

last: Göcmen

first: Lukas

last: Westermann

first: Michael

last: Köttgen

first: Tilman

last: Busch


title: Hybrid sequencing characterizes expression and function of mouse pseudogenes

city: Wuhan

first: Zhen-Xia

last: Chen

state: Hubei

address: No.1 Shizishan Street

department: College of Life Science and Technology

country: China

institute: Huazhong Agricultural University

summary: Pseudogenes are defined as regions of the genome that resemble functional genes but contain disabling mutations and lack regulatory elements needed for transcription or translation. They are excellent markers for genome evolution and are emerging as crucial regulators of the development and disease, especially cancer. However, systematic functional characterization and evolution of pseudogene remain largely unexplored. In particular, the contribution of pseudogene to organ development is still unknown. Meanwhile, studies of pseudogene transcription, which is the first step for generating functional RNA, is precluded by the limited capacity of short-read sequencing. To address these issues, we systematically inferred the origin time and characterized the evolution pattern of pseudogenes. We leveraged PacBio full-length sequencing in combination with deep Illumina data as well as public developmental time-course RNA-seq, we dramatically expanded the analyzed samples and profiled genome-wide pseudogene expression paradigm. Additionally, we prioritized functional pseudogenes at multiple regulatory layers and determined their implications in disease and cancer biology.

overall_design: Identification of full-length pseudogene transcripts and subsequent quantification.

first: Lu

first: Sheng

middle: H

last: Qian


title: Inhibition of mitochondrial translocase SLC25A5 and histone deacetylation is an effective combination therapy in neuroblastoma

status: Public on Feb 05 2022

city: Melbourne

first: Janith

last: Seneviratne

state: VIC

address: Peter MacCallum Cancer Centre, 305 Grattan Street

country: Australia

institute: Peter MacCallum Cancer Centre

summary: Mitochondria are gatekeepers of apoptotic processes and mediate drug resistance to several chemotherapy agents used to treat cancer. Neuroblastoma is a common solid cancer in young children with poor clinical outcomes following conventional chemotherapy. We sought druggable mitochondrial protein targets in neuroblastoma cells. Among mitochondria-associated gene targets, we found that high expression of the mitochondrial adenine nucleotide translocase 2 (SLC25A5/ANT2), was a strong predictor of poor neuroblastoma patient prognosis and contributed to a more malignant phenotype in pre-clinical models. Inhibiting this transporter with PENAO reduced cell viability in a panel of neuroblastoma cell lines in a TP53-status-dependent manner. We identified the histone deacetylase inhibitor, suberanilohydroxamic acid (SAHA), as the most effective drug in clinical use against mutant TP53 neuroblastoma cells. SAHA and PENAO synergistically reduced cell viability, and induced apoptosis, in neuroblastoma cells independent of TP53-status. The SAHA and PENAO drug combination significantly delayed tumour progression in pre-clinical neuroblastoma mouse models, suggesting that these clinically advanced inhibitors may be effective in treating the disease.

overall_design:
We use gene expression microarrays to profile the transcriptome of SH-SY5Y cells treated with either a DMSO control, SAHA, PENAO or the combination of drugs after 8 hours of drug exposure.
Treated SH-SY5Y cells were subject to RNA extraction and hybridization on Affymetrix gene expression microarrays.

first: Belamy

middle: B

last: Cheung

first: Glenn

middle: M

last: Marshall


title: Aberrant M1 polarization of macrophages in Behcet’s disease

status: Public on Mar 17 2022

city: Beijing

first: Wenjie

last: Zheng

address: No1 ShuaiFuYuan，Dong Cheng District ，Beijing, Beijing, CN

institute: Peking Union Medical College Hospital

summary: Macrophages are key inflammatory immune cells in Behcet’s disease (BD) and BD serum may contribute to macrophages’ hyperactivation in BD. To further investigate the role of BD serum on the phenotypes and functions of macrophages, we performed next generation sequencing-based genome-wide transcriptional profiling on BD serum or healthy control (HC) serum treated macropahges.

overall_design: Transcriptional profiling of BD serum treated macropahges (n=4) and HC serum treated macropahges (n=4).

first: Xiuhua

last: Wu

first: Zhimian

last: Wang

first: Jing

last: Shi

first: Xin

last: Yu

first: Chaoran

first: Jinjing

last: Liu

first: Fengchun

last: Zhang

first: Hua


title: RBCK1 is an Endogenous Inhibitor for Triple Negative Breast Cancer via Hippo/YAP axis

city: Xinxiang

first: Zhongbo

last: li

state: Henan

institute: Xinxiang medical university

summary: Triple negative breast cancer (TNBC) is one of the most lethal breast cancer subtypes. Due to a lack of effective therapeutic targets, chemotherapy is still the main medical treatment for TNBC patients. Thus, it is important and necessary to identify novel therapeutic targets for TNBC. Recent genomic studies implicated the hyper-activation of Hippo/YAP signaling in TNBC, manifesting its critical roles in TNBC carcinogenesis and cancer progression. RBCK1 was firstly identified as an important component for linear ubiquitin assembly complex (LUBAC) and facilitates NFKB signaling in immune response. Further studies showed RBCK1 also facilitated luminal type breast cancer growth and endocrine resistance via trans-activation estrogen receptor alpha. Interestingly, our data revealed an opposite function for RBCK1 in TNBC progression. RBCK1 over-expression inhibited TNBC cell progression in vitro and in vivo, while RBCK1depletion promoted TNBC cell invasion. The whole genomic expression profiling showed that RBCK1 depletion activated Hippo/YAP axis. RBCK1 depletion increased YAP protein level and Hippo target gene expression in TNBC. The molecular biology studies showed that RBCK1 could associate with YAP protein and enhance YAP protein stability via promoting YAP K48-linked poly-ubiquitination at several YAP lysine sites (K76, K204 and K321). Our study revealed the multi-faced RBCK1 function in different subtypes of breast cancer patients and a promising therapeutic target for TNBC treatment.

overall_design: Breast cancer cell mRNA samples were summarized in six samples, divided into two groups, siControl and siRBCK1

first: Ting

last: Zhuang

last: Li

first: Jian

last: Zhu

first: Shu

last: Zhuo


title: RNA-sequencing analysis of effect of miR-155 overexpression in human CD14+ monocytes

status: Public on Feb 07 2022

city: London

first: Leonie

last: Taams

state: london

address: CIBCI, 1.26, New Hunts House

country: United Kingdom

institute: King's College London

summary: We report the application of bulk RNA-Sequencing to assess the effect of miR-155 overexpression by profiling gene expression following transfection of miR-155 mimic compared against negative control mimic in human peripheral blood CD14+ monocytes. Isolated human CD14+ monocytes were transfected for 24 hours and mRNA profiles of miR-155 and negative control mimic were generated by bulk RNA-Sequencing in 5 donors. The sequence reads passed quality checks and were analysed using DeSeq2. We mapped the sequence reads to the human genome (build hg38) and identified 16,014 transcripts.

overall_design: Comparing gene expression in human peripheral blood CD14+ monocytes transfected with a miR-155 or negative control mimic

first: Anton

last: Olsson

middle: S


title: A20 governs fibrosis susceptibility in bleomycin-induced mouse scleroderma model

status: Public on Feb 01 2022

city: Ann Arbor

first: Swati

last: Bhattacharyya

state: MI

address: 1150 W. Medical Center Drive

country: USA

institute: University of Michigan

summary: In addition to autoimmune and inflammatory diseases, variants of the TNFAIP3 gene encoding A20 are also associated with systemic sclerosis (SSc). However, it remains unclear how genetic factors contribute to fibrosis in SSc, and which cell types drive disease due to SSc-specific genetic alterations. We characterized the expression and function of A20, and its negative transcriptional regulator DREAM, in patient with SSc. We found that levels of A20 were significantly reduced in SSc skin and lung biopsies, while DREAM was elevated and showed anti-correlation with A20. Mice haploinsufficient for A20, or harboring fibroblasts-specific A20 deletion, recapitulated major pathological and genomic features of SSc, whereas DREAM-null mice showed elevated A20 expression and were protected from fibrosis. In fibroblasts, A20 mitigated ex vivo profibrotic responses. An anti-fibrotic small molecule targeting the adiponectin receptors stimulated A20 expression in vitro in wildtype but not A20-deficient fibroblasts, and in bleomycin-treated mice. Thus, A20 has a novel function in negative regulation of fibroblast responses, and together with DREAM, constitutes a critical regulatory network governing the fibrotic process in SSc, suggesting that A20 and DREAM represent novel druggable targets.

overall_design: We have generated A20+/- mice, by crossing A20fl/fl mice with EIIa-Cre mice generating mice with a single A20 allele, and displaying ~50% decrease in levels of A20 in multiple tissues. At 6-8 weeks of age, four female A20 +/- mice and four female wildtype mice were randomized to start treatment with s.c. bleomycin, a fibrosis inducing agent (5 mg/kg/day), or PBS given for 10 days (5 days/week). Mice were then sacrificed at day 22 and skin tissues were harvested RNA isolation and RNA sequencing.

first: Wenxia

first: Jun

last: Wei

first: Hiam

last: Abdala-Valencia

first: Sergejs

last: Berdnikovs

first: John

last: Varga


title: RNF186/EPHB2 axis is essential for colorectal tumorigenesis by regulating TNFα signalling in colorectal epithelial cells

status: Public on Mar 06 2022

first: Huazhi

address: Luoyu Road

institute: Huazhong University of Science and Technology

summary: We provide evidence that the EPHB2-RNF186-TAB2-TAK1 signalling cascade plays an essential role in TNFα-mediated signal transduction in colorectal epithelial cells and the carcinogenesis of CRC, which may provide potential targets for the treatment of colorectal cancer.

overall_design: The differentially expressed genes from control Ls174t cells or RNF186-overexpressed Ls174t cells were analysised by transcriptomes sequence .

first: Chenhui

last: Wang

first: Zhihui

last: Cui

first: Huijun

last: Hu


title: Rixosomal RNA degradation contributes to silencing of Polycomb target genes

status: Public on Jan 26 2022

city: boston

first: Danesh

last: Moazed

state: MA

address: 240 longwood avenue

department: cell biology

institute: Harvard medical school

summary: Polycomb Repressive Complex (PRC) 1 and 2 are histone-modifying and chromatin-binding complexes that are required for silencing of developmental regulatory and other genes. Their silencing functions are thought to involve chromatin compaction and condensate formation but whether other mechanisms contribute to silencing is unknown. Here we show that the rixosome, a conserved RNA degradation complex with roles in ribosomal RNA processing and heterochromatic RNA degradation in fission yeast, associates with human PRC complexes, is recruited to promoters of Polycomb target genes in differentiated cell lines and embryonic stem cells, and is required for efficient silencing of Polycomb target genes. These findings reveal an unanticipated role for RNA degradation in Polycomb-mediated gene silencing.

overall_design: PRO-seq analysis of histone modifications and chromatin associated proteins

first: Haining

last: zhou


title: Single-cell transcriptional profiling informs efficient reprogramming of human somatic cells to cross-presenting dendritic cells

status: Public on Mar 05 2022

city: Lund

first: Ilia

last: Kurochkin

state: Skane

address: BMC A12, Sölvegatan 17

country: Sweden

institute: Lund University

summary: Type-1 conventional dendritic cells (cDC1s) are rare immune cells critical for the induction of antigen-specific cytotoxic CD8+ T-cells. The genetic program driving human cDC1 specification remains largely unexplored. We have previously identified PU.1, IRF8 and BATF3 transcription factors as sufficient to induce cDC1 fate in mouse fibroblasts but reprogramming of human somatic cells was limited by low efficiencies. Here, we investigated single-cell transcriptional dynamics during human cDC1 reprogramming. Human induced cDC1s (hiDCs) generated from embryonic fibroblasts gradually acquire a global cDC1 transcriptional profile and activate antigen presentation signatures. Importantly, other DC subsets are not induced at the single-cell level. We extracted gene modules associated with successful reprogramming and identified inflammatory signaling and the cDC1-inducing transcription factor network as key drivers of the process. Combining IFN-γ, IFN-β and TNF-α with constitutive expression of cDC1-inducing transcription factors lead to improvement of reprogramming efficiency by 190-fold. hiDCs uptake dead cells, secrete inflammatory cytokines and perform antigen cross-presentation, a key cDC1 function. This approach allowed efficient hiDC1 generation from adult fibroblasts and mesenchymal stromal cells. Mechanistically, PU.1 shows dominant and independent chromatin targeting at early phases of reprogramming, recruiting IRF8 and BATF3 to shared binding sites. The cooperative binding at open enhancers and promoters leads to silencing of fibroblast genes and activation of a cDC1 program. These findings provide mechanistic insights into human cDC1 specification and reprogramming and represent a platform for generating patient-tailored cDC1s, a long-sought DC subset for vaccination strategies in cancer immunotherapy.

overall_design: RNAseq profiling on single cells, generated after transduction of human embryonic fibroblasts (HEFs) or human dermal fibroblasts (HDFs) with PU.1, IRF8, BATF3, at day 3 and day 9, generated in the presence or absence of IFN-γ, IFN-β and TNF-α. Single cell RNAseq profiling of HEFs, HDFs, and freshly isolated peripheral blood Dendritic cells type 1 (HLA-DR+CD11C+CD141+), Dendritic cells type 2 (HLA-DR+CD11C+CD141-CD1C+) and plasmacytoid dendritic cells (HLA-DR+CD11C-CD123+) were used as controls.

first: Fábio

middle: F

last: Rosa

first: Cristiana

last: Pires

first: Carlos-Filipe

last: Pereira


title: RNA-seq of whole maize seedlings

status: Public on Jan 27 2022

city: Athens

first: Brad

last: Nelms

state: GA

address: 120 E Green St

institute: University of Georgia

summary: RNA-seq from whole V3 maize seedlings (roots and shoots) for the B73 inbred line and A188 x B73 hybrid.

overall_design: RNA-seq of whole maize seedlings. Libraries were constructed with a modified version of CelSeq2.

first: Virginia

last: Walbot


title: A Single Cell Transcriptome Atlas of The Domestic Pig

status: Public on Jan 21 2022

city: Aarhus

first: Lin

last: Lin

address: Høegh-Guldbergs Gade 10

department: Department of Biomedicine

country: Denmark

institute: Aarhus University

summary: By leveraging single-cell/nuclei RNA sequencing, we generate the first single-cell transcriptome atlas of over 200,000 pig cells from 20 tissues/organs.

overall_design:
In this study, we report the generation of a single-cell transcriptome atlas of 222,526 cells across twenty tissues of the domestic pig by using scRNA-seq and single-nuclei RNA-sequencing (snRNAseq).

Please note that the processed data files have been replaced and 3 samples (GSM6605687-GSM6605689) added on Sep 29, 2022.
In the previous files, the mitochondria gene name in the gene matrix were with the "MT-" prefix. To be consistent with the pig Sus_scrofa11.1 genome assembly, the matrix has been updated with "MT-" prefix removed for the pig mitochondria genes.

first: Dongsheng

last: Chen

first: Yonglun

last: Luo

first: Fei


title: Mapping Human Hematopoietic Stem Cells From Hemogenic Endothelium To Birth

status: Public on Jan 20 2022

city: Los Angeles

first: Feiyang

last: Ma

state: CA

address: 610, Charles Young Dr East, TLSB 3000C

department: Molecular Biology Institute

institute: UCLA

summary: Human hematopoietic stem cell (HSC) ontogeny is poorly defined due to the inability to identify HSCs as they emerge and mature in different hematopoietic sites. We created a single-cell transcriptome map of human hematopoietic tissues from 1st trimester to birth and found that HSC signature RUNX1+HOXA9+MLLT3+MECOM+HLF+SPINK2+ distinguishes HSCs from progenitors throughout gestation. In addition to the AGM (aorta-gonad-mesonephros) region, nascent HSCs populated the placenta and yolk sac before colonizing the liver at 6 weeks. Comparison of HSCs from different maturation stages revealed the establishment of HSC transcription factor machinery upon HSC emergence, whereas their surface phenotype evolved throughout development. HSC transition to the liver marked a molecular shift evidenced by suppression of surface antigens, reflecting nascent HSC identity, and acquisition of HSC maturity markers PROM1/CD133 and HLA-DR. HSC origin was tracked to ALDH1A1+KCNK17+ hemogenic endothelial (HE) cells, which arose from IL33+ALDH1A1+ arterial endothelial subset, termed pre-HE. Spatial transcriptomics and immunofluorescence visualized this process in ventrally located intra-aortic hematopoietic clusters. The in vivo map of human HSC ontogeny validated the generation of AGM-like definitive HSPCs from human pluripotent stem cells, and serves as a guide to improve their maturation to functional HSCs.

overall_design:
Single cell RNA sequencing of human HSC in different tissues at different timepoints to track the development of human HSC.

Spatial transcriptomics of various transverse section of a human embryo (5 weeks, CS15).

first: Vincenzo

last: Calvanese

first: Sandra

last: Capellera-Garcia

first: Matteo

last: Pellegrini

first: Hanna

last: Mikkola


title: Single-cell Transcriptome Analysis of Chronic Antibody-mediated Rejection after Renal Transplantation

status: Public on Jan 12 2022

first: Yan

last: Xiong

address: donghu road

institute: Zhongnan Hospital of Wuhan University

summary: Renal transplantation is currently the most effective treatment for end-stage renal disease. However, chronic antibody-mediated rejection (cABMR) remains a serious obstacle for the long-term survival of patients with renal transplantation and a problem to be solved. At present, the role and mechanism underlying immune factors such as T- and B- cell subsets in cABMR after renal transplantation remain unclear. In this study, single-cell RNA sequencing (scRNA-seq) of peripheral blood monocytes (PBMCs) from cABMR and control subjects was performed to define the transcriptomic landscape at single-cell resolution. A comprehensive scRNA-seq analysis was performed. The results indicated that most cell types in the cABMR patients exhibited an intense interferon response and release of proinflammatory cytokines. In addition, we found that the expression of MT-ND6, CXCL8, NFKBIA, NFKBIZ, and other genes were up-regulated in T- and B-cells and these genes were associated with pro-inflammatory response and immune regulation. GO and KEGG enrichment analyses indicated that the overexpressed genes in T- and B-cells were mainly enriched in inflammatory pathways, including the TNF, IL-17, and Toll-like receptor signaling pathways. Additionally, MAPK and NF-κB signaling pathways were also involved in the occurrence and development of cABMR. Trajectory analysis assembled the T-cell subsets into three differentiation paths with distinctive phenotypic and functional prog rams. CD8 effector T cells and γδ T cells showed three different differentiation trajectories, while CD8_MAI T cells and naive T cells primarily had two differentiation trajectories. Cell-cell interaction analysis revealed strong T/B cells and neutrophils activation in cABMR. Thus, the study offers new insight into pathogenesis and may have implications for the identification of novel therapeutic targets for cABMR.

overall_design:
PBMCs from 2 control patients and 2 chronic antibody-mediated rejection after renal transplantation patients were obtained and analyzed by single-cell transcriptome sequencing.

#### Please note that GSM5719952 raw data is not provided #######

first: Qifa

last: Ye

first: Shaoiun

first: Fanhua

last: Kong


status: Public on Jan 25 2022

first: Danesh

last: Moazed

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Polycomb Repressive Complexes 1 and 2 (PRC1 and PRC2) are histone-modifying and -binding complexes that mediate the formation of facultative heterochromatin and are required for silencing of developmental genes and maintenance of cell fate1-3. Multiple pathways of RNA decay work together to establish and maintain heterochromatin in fission yeast, including a recently identified role for a conserved RNA degradation complex called the rixosome or RIX1 complex4,5. Whether RNA degradation also plays a role in the stability of mammalian heterochromatin remains unknown. Here we show that the rixosome contributes to silencing of many Polycomb targets in human cells. The rixosome associates with human PRC complexes and is enriched at promoters of Polycomb target genes. Importantly, depletion of either the rixosome or Polycomb results in accumulation of paused and elongating RNA polymerase at Polycomb-target genes. We identify point mutations in the RING1B subunit of PRC1 that disrupt the interaction between PRC1 and the rixosome and result in diminished silencing, suggesting that direct recruitment of the rixosome to chromatin is required for silencing. Finally, we show that the RNA endonuclease and kinase activities of the rixosome and the downstream XRN2 exoribonuclease, which degrades RNAs with 5’ mono-phosphate groups generated by the rixosome, are required for silencing. Our findings suggest that rixosome-mediated degradation of nascent RNA is conserved from fission yeast to human, although in human cells the rixosomal RNAe degradation activity is primarily associated withes RNA in facultative rather than constitutive heterochromatin.

overall_design: Refer to individual Series


title: Genome wide DNA methylation of pediatric acute myeloid leukemia

status: Public on Jan 01 2022

city: Setagaya

first: Tomoko

last: Kawai

state: Tokyo

department: Department of Maternal-Fetal Biology

country: Japan

institute: National Research Institute for Child Health and Development

summary: Genome wide DNA methylation profiling of pediatric acute myeloid leukemia obtained from bone marrow. The Illumina EPIC methylation beadchip array was used to obtain DNA methylation profiles across approximately 850,000 CpG dinucleotide methylation loci in DNA isolated from leukemia. Samples include 64 patients.

overall_design: DNA methylation was assessed in 64 periatric acute myeloid leukemia using the Illumina HumanMethylation EPIC array.

first: G

last: Yamato

first: T

first: N

last: Shiba

first: Y

last: Hara

first: K

last: Ohki

last: Kaburagi

last: Yoshida

last: Shiraishi

first: S

last: Miyano

last: Kiyokawa

first: D

last: Tomizawa

first: A

last: Shimada

first: M

last: Sotomatsu

first: H

last: Arakawa

last: Adachi

last: Taga

last: Horibe

last: Ogawa

last: Hata

last: Hayashi


title: Transcriptome of ex vivo-sorted and in vitro-grown Cryptococcus neoformans cells

city: Salt Lake City

first: Jessica

middle: CS

last: Brown

state: Utah

address: 15 N Medical Drive East

department: Pathology

institute: University of Utah

summary: We compared the transcriptome of subpopulations of Cryptococcus neoformans cells within the lungs and C. neoformans cells cultured in capsule repressing medium, capsule inducing medium, and capsule inducing medium with the addition of 10% conditioned medium from cells grown in capsule repressing medium. The aim of the study was to identify genes that regulate C. neoformans cell body and capsule size reductions.

overall_design: Transcriptomic profiles of the smallest, middle, and largest Cryptococcus neoformans cells found in muring lungs 14 days post-intranasal inoculation. mRNA profiles of cells grown for 24 hours in capsule inducing medium, capsule inducing medium, or capsule repressing medium supplemented with 10% conditioned medium (filtered supernatant of cells grown in capsule repressing medium. Each sample was sequenced twice.

first: Steven

middle: T

last: Denham

middle: C


title: Differential analysis of chromatin accessibility and gene expression profiles identifies cis-regulatory elements in rat adipose and muscle

city: New York

first: Venugopalan

last: Nair

state: NY

address: 1468 Madison Avenue

department: Neurology

institute: Icahn School of Medicine at Mount Sinai

summary: Chromatin accessibility is a key factor influencing gene expression. We developed a modified protocol, ruptor-ATAC, which together with RNA-seq was used to investigate regulatory elements underlying tissue-specific gene expression in rat white adipose and skeletal muscle, two tissues with contrasting metabolic functions. While promoter accessibility correlated with RNA expression, integration of the two datasets identified tissue-specific differentially accessible regions (DARs) that predominantly localized in intergenic and intron regions. DARs mapped to differentially expressed genes that were enriched in distinct biological processes in each tissue. Motif enrichment analysis on tissue-specific DARs predicted binding sites for transcription factors (TFs), several of which were up-regulated in the corresponding tissue. Positive relationship between DARs and target gene expression further supported a functional role for these TF binding motifs. Our study identifies cis-regulatory regions that likely play a major role in the regulation of tissue-specific gene expression in adipose and muscle.

overall_design: ATAC-seq was performed on 9 abdominal white adipose tissue (WAT) and 9 gastrocnemius muscle (skeletal muscle) tissue samples obtained from Fischer 344 rats. Tissue samples were either collected from individual animals, or represented pulverized aliquots of tissues pooled from 15 males.

middle: D

first: Mital

last: Vasoya

first: Vishnu

first: Gregory

middle: R

last: Smith

first: Hanna

last: Pincas

first: Yongchao

last: Ge

first: Collin

last: Douglas

first: Karyn

last: Esser

first: Stuart

last: Sealfon


title: RNA-seq on ZNF417/587 double KO K562

status: Public on Dec 31 2021

city: Guangzhou

first: Bo

last: Yang

state: Guangdong

address: Guangzhou, 510150, Guangdong Province, China.

institute: The Third Affiliated Hospital of Guangzhou Medical University

summary: To verify ZNF417 and ZNF587 knock out whether leads to HERV-K element reactivation, we performed RNA-seq on ZNF417/ZNF587  double knock out (DKO) K562 cell lines. We observed a dozen of genes were upregulated in KO cells, and some of them possessed PBS-Lys sites near their promoters that can be directly targeted by ZNF417 and ZNF587, such as MS4A clusters. We also measured the expression levels of repetitive elements in ZNF417 ZNF587 dKO cells, which exhibited only some ERVs reactivation indirectly.

overall_design: Two DKO cell lines and two control KO cell lines were used to perform RNA-seq.


title: The effects of phoenixin-14 on the hypothalamic-pituitary-gonadal (HPG) axis and spawning in green-spotted puffer (Dichotomyctere nigroviridis)

status: Public on Mar 01 2022

city: Gainesville

first: Christopher

last: Martyniuk

state: FL

address: 8891 SW 79th Avenue

institute: University of Florida

overall_design: Pufferfish hypothalami and whole ovaries were compared for gene expression changes 24 hours following intramuscular injections with puffer-specific phoenixin-14 (PNX-14).  Six fish were injected with 100 ng/g body weight PNX-14, while a second set were injected with saline (n = 6, control group).  All fish were female (approximately 15 g body weight) and exhibited vitellogenic ovaries prior to treatment.  Final dataset included six PNX-treated hypothalami (HT group), six control hypothalami (HC), five PNX-treated ovaries (OT), and five control ovaries (OC).

first: Timothy

last: Breton

first: Chris

first: Matthew

last: DiMaggio

first: Casey

last: Murray


title: Alternative spliced genes downstream of EMT enhance phenotypic plasticity and malignant behaviour in colon cancer

status: Public on Jan 04 2022

city: Rotterdam

first: Mathijs

last: Verhagen

address: Doctor Molewaterplein 40

country: Netherlands

institute: Erasmus Medical Center

summary: CD44s and CD44v6 overexpressed RNAseq profiles of colon cancer cell lines HCT116 and SW480

first: T

last: Xu

first: M

middle: P

first: R

last: Fodde


title: ChIP-seq on Zfp961 GFP flox/flox mESCs to verify Zfp961 binding capacity at PBS-Lys elements.

status: Public on Feb 10 2022

summary: We performed ChIP-seq assay with anti-GFP antibodies on Zfp961-GFPflox/flox ESCs.We found PBS-Lys-containing endogenous virus K subgroup repeats (ERV-K) were significantly enriched in the strong peak regions (40%, 165 out of 413), compared to their abundance in the mouse genome (~5%), suggesting Zfp961 binding preference towards ERV-K regions. And Zfp961 has a PBS-Lys motif. We performed H3K9me3 ChIP on Zfp961 WT or KO mESCs. We found that Zfp961 recruits H3k9me3 modification at ERVKs, and H3K9me3 level showed a moderate decrease upon Zfp961 deletion.

overall_design: We used two replicates of each ChIP reaction. Basically, two Zfp961-GFP floxed mESCs cell lines treated with 4-OHT or etOH as control were used for anti-GFP ChIP and anti-H3K9me3 ChIP.


title: mRNA sequencing of PBMCs from one THES2 patient and two healthy controls

city: DALLAS

last: Yan

state: TEXAS

address: 6000 Harry Hines Blvd

institute: UT Southwestern Medical Center

summary: To identify differentially epxressed mRNAs in THES2 patient's PBMCs

overall_design: PBMCs from one THES2 patient and two health controls

first: Kun


title: De novo analysis of bulk RNA-seq data at spatially resolved single-cell resolution

status: Public on Jan 09 2022

city: Hangzhou

first: Xin

last: Shao

state: Zhejiang

address: #866 Yuhangtang Rd.

institute: Zhejiang University

summary: We developed a spatially resolved RNA-seq protocol based on laser capture microdissection (LCM) and spatial barcoding strategy termed Spatial-seq. Here, we provide the demo transcriptomic data derived from mouse hypothalamus and isocortex regions for applications of our newly proposed spatial deconvolution algorithm termed Bulk2Space. We want to reveal the spatial heterogeneity and cellular diversity within the bulk brain region.

overall_design: We performed laser capture microdissection to isolate the hypothalamus and isocortex regions of mouse brain sections from the sagittal direction. The brain sections were first registered to the Allen Brain Atlas, and each main region was annotated. The annotated region outline was then imported into LCM. The hypothalamus and isocortex regions were cut by LCM and followed with RNA-seq to obtain the gene expression matrix.

first: Jie

last: Liao

first: Jingyang

last: Qian

first: Yang

last: Hu

first: Xiaoyan

last: Lu


title: Early life stress leads to gene expression down-regulation in prefrontal cortex [microarray]

city: Kensington

first: Irina

last: Voineagu

state: NSW

address: High St

department: Biotechnology and Biomolecular Sciences

institute: The University of New South Wales

summary: Early life stress (ELS) is associated with adverse mental health outcomes including anxiety, depression and addiction-like behaviours. While ELS is known to affect the developing brain by leading to increased stress responsiveness and increased glucocorticoid levels, the molecular mechanisms underlying the detrimental effects of ELS remain incompletely characterised. Rodent models have been instrumental in beginning to uncover the molecular and cellular underpinnings of ELS. Limited nesting (LN), an ELS behavioural paradigm with significant improvements over maternal separation, mimics human maternal neglect. We have previously shown that LN leads to anxiety like-behaviours in rats. Here we assessed gene expression changes induced by ELS in rat prefrontal cortex by RNA-sequencing. We show that LN leads primarily to transcriptional repression and identify a molecular signature of LN in rat PFC that is robust to the behavioural paradigm and replicable across rodent species (mouse and rat).

overall_design: RNA-seq from prefrontal cortex of 5 control and 5 early life stress rats

first: Nicole

last: Green

first: Jayanthi

last: Maniam

first: Jessica

last: Riese

first: Margaret

last: Morris

last: Voinegu


title: Peripheral blood gene expression profiling predicts response to mycophenolate in systemic sclerosis related interstitial lung disease

city: Houston

first: Shervin

last: Assassi

state: TX

address: 6431 Fannin

department: Division of Rheumatology

institute: The University of Texas Health Science Center at Houston

summary: PBC RNA samples from 134 baseline and 98 month-12 visits, corresponding to the active treatment period of both arms in Scleroderma Lung Study II, along with 45 healthy controls were investigated by global RNA sequencing. The objective was to examine the peripheral blood cell (PBC) gene expression changes ensuing from mycophenolate mofetil (MMF) or cyclophosphamide (CYC) treatment and to determine the predictive significance of baseline PBC transcript scores for response to immunosuppression in systemic sclerosis (SSc) related interstitial lung disease (ILD).

overall_design: Whole blood samples were collected in PAXgene tubes.  PBC RNA was extracted according to the manufacturer’s protocol. RNA integrity was measured on an Agilent 2100 Bioanalyzer (Agilent Technologies).  mRNA was enriched from total RNA using oligo(dt) beads (NEBNext Ultra II RNA Kit following the poly(A) enrichment workflow). The mRNA was subsequently fragmented randomly in fragmentation buffer, and reverse transcribed to cDNA.  The cDNAs were converted to double stranded cDNAs, then subjected to end-repair, A-tailing, and adapter ligation, size selection and PCR enrichment. Library concentration was first quantified using a Qubit 2.0 fluorometer (Life Technologies), and then diluted to 1 ng/ul before checking insert size on an Agilent 2100 and quantifying to greater accuracy by quantitative PCR (q-PCR) (library activity >2 nM). Libraries are pooled into Novaseq6000 machines according to molarity and expected data volume. A paired-end 150 bp sequencing strategy was used to generate an average of 99 million reads per sample.

first: Elizabeth

last: Volkman

first: Wenjin

middle: J

last: Zheng

first: Xuan

last: Wang

first: Holly

last: Wilhalme

first: Marka

last: Lyons

first: Michael

last: Roth

first: Donald

last: Tashkin


title: Single-cell RNA and protein profiling of immune cells from the mouse brain and its border tissues

status: Public on Dec 23 2021

city: Brussels

first: Daliya

last: Kancheva

address: Laarbeeklaan 103, Building E

country: Belgium

institute: Vrije Universiteit Brussel - VIB

summary: Brain-immune crosstalk and neuroinflammation critically shape brain physiology in health and disease. A detailed understanding of the brain immune landscape is essential for developing new treatments for many neurological disorders. Single-cell technologies offer an unbiased assessment of the heterogeneity, dynamics and functions of immune cells. Here, we provide a protocol that outlines all the steps involved for performing single-cell multi-omic analysis of the brain immune compartment. This includes a step-by-step description on how to micro-dissect the border regions of the mouse brain, together with dissociation protocols tailored to each of these tissues. These combine a high-yield with minimal dissociation-induced gene expression changes. Next, we outline the steps involved for droplet-based single-cell RNA sequencing (scRNA-seq), Cellular Indexing of Transcriptomes and Epitopes by Sequencing (CITE-seq), or high-dimensional flow cytometry. Each of these single-cell modalities has specific strengths and limitations, but they are highly complementary. Importantly, we detail how to implement CITE-seq with large antibody panels to obtain unbiased protein-expression screening coupled to transcriptome analysis. Finally, we describe the main steps involved in the analysis and interpretation of the data. This optimized workflow allows for a detailed assessment of immune cell heterogeneity and activation in the whole brain or specific border regions, at RNA and protein level. The wetlab workflow can be completed by properly trained researchers (with basic proficiency in cell and molecular biology) and takes between 6 and 11 hours, depending on the chosen procedures. The computational analysis requires a background in bioinformatics and programming in R.

overall_design: Sample of WT mouse dura mater (pooled from 6 mice)

first: Isabelle

last: Scheyltjens

first: Hannah

last: Van Hove

first: Karen

last: De Vlaminck

first: Jonathan

last: Bastos

first: Mónica

last: Vara Perez

first: Ana

last: Pombo Antunes

first: Liesbet

last: Martens

first: Charlotte

last: Scott

first: Jo

last: Van Ginderachter

first: Yvan

last: Saeys

first: Martin

last: Guilliams

first: Niels

last: Vandamme

first: Kiavash

last: Movahedi


title: Loss of FSTL1 in the Myf5 lineage causes brown adipose tissue atrophy

city: Minneapolis

first: Hai-Bin

last: Ruan

state: MN

department: Integrative Biology and Physiology

institute: University of Minnesota

summary: Aim to investigate the role of FSTL1 in brown adipose tissue (BAT) development and function

overall_design: Bulk RNA sequencing of the total interscapular BAT depot from newborn wildtype and Myf5-Fstl1 KO mice

first: Zan

last: Huang


title: Early life stress leads to gene expression down-regulation in prefrontal cortex [RNA-seq]

first: Irina

last: Voineagu

first: Nicole

last: Green

first: Jayanthi

last: Maniam

first: Jessica

last: Riese

first: Margaret

last: Morris


title: RNA-sequencing of iPSC-derived blood-brain barrier cell types across microenvironments

status: Public on Jan 30 2022

city: BALTIMORE

first: Peter

last: Searson

state: MD

address: 3400 North Charles Street

institute: Johns Hopkins University

summary: The blood-brain barrier (BBB) is lined by brain microvascular endothelial cells (BMECs) which regulate transport into and out of the brain.  We used human induced pluripotent stem cell (iPSC)-derived cell types to model BBB function within 2D and 3D in vitro models. We compare gene expression between different iPSC-derived cell types, and specifically profile the response of iPSC-derived BMEC-like cells (iBMECs) to differentiation media volume, microenvironmental cues, and cytokines.

overall_design: 24 total samples were analyzed, across 5 cell types: (1) induced pluripotent stem cells (iPSCs), (2) iPSC-derived brain microvascular endothelial cell-like cells (iBMECs), (3) iPSC-derived pericyte-like cells (iPCs), (4) primary human dermal microvascular endothelial cells (HDMECs), and iPSC-derived endothelial cells (iECs). Differentiations of iBMECs were conducted across two source iPSCs (WTC and BC1), across media volumes (1 mL and 2 mL), across microenvironments (2D and 3D), and across cytokine exposures (with and without TNFa).

first: Raleigh

last: Linville


title: Bacterial growth in multicellular aggregates leads to the emergence of complex lifecycles

status: Public on Dec 10 2021

city: Cambridge

first: Julia

last: Schwartzman

address: 15 Vassar St

department: Civil and Environmental Engineering

institute: MIT

summary:
In response to environmental stresses such as starvation, many bacteria facultatively aggregate into multicellular structures that can attain new metabolic functions and behaviors.
Despite the ubiquity and relevance of this form of collective behavior, we lack an understanding of how the spatiotemporal dynamics of aggregate development emerge from cellular physiology.
Here, we study the development of multicellular aggregates by the marine bacterium Vibrio splendidus when it grows on the polysaccharide alginate.
Transcriptional profiling was used to define genes differentially expressed at stages of aggregate morphogenesis, and between cell sub-populations, which included genes encoding a putative type IV pillus and carbon storage granules.
Combined with measurements of in situ cellular physiology, we show that the coupling between growth and spatial gradient formation leads to the emergence of a complex lifecycle.

overall_design: Comparison of samples taken from early and late stages of aggregate development. Late stage taken after structures rupture, and represents 'shell' and released inner 'core' contents.

first: Ali

last: Ebrahimi

first: Grayson

last: Chadwick

first: Yuya

last: Sato

first: Benjamin

last: Roller

first: Victoria

last: Orphan

first: Otto

middle: X

last: Cordero


title: Translation rescue by targeting Ppp1r15a upstream open reading frame in vivo

status: Public on Dec 22 2021

city: Indianapolis

first: Takashi

last: Hato

state: IN

address: 950 W. Walnut St. R2 202

department: Medicine

institute: Indiana University

summary: The eIF2 initiation complex is central to maintaining a functional translation machinery. Extreme stress such as life-threatening sepsis exposes vulnerabilities in this tightly regulated system, resulting in an imbalance between the opposing actions of kinases and phosphatases on the main regulatory subunit eIF2α. Here, we report that translation shutdown is a hallmark of established sepsis-induced kidney injury brought about by excessive eIF2α phosphorylation and sustained by blunted expression of the counterregulatory phosphatase subunit Ppp1r15a. We determined that the blunted Ppp1r15a expression persists because of the presence of an upstream open reading frame (uORF). Overcoming this barrier with genetic approaches enabled the derepression of Ppp1r15a, salvaged translation and improved kidney function in an endotoxemia model. We also found that the loss of this uORF has broad effects on the composition and phosphorylation status of the immunopeptidome that extended beyond the eIF2α axis. Collectively, our findings define the breath and potency of the highly conserved Ppp1r15a uORF and provide a paradigm for the design of uORF-based translation rheostat strategies. The ability to accurately control the dynamics of translation during sepsis will open new paths for the development of therapies at codon level precision.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Mice were subjected to a single-dose, 5 mg/kg LPS tail vein i.v. injection or vehicle saline and kidney tissues were harvested at indicated timepoints (0, 1, 4, or 16 hrs). Indicated cell lines with 60-80% confluency were harvested at baseline or 16 hrs after poly(I:C) transfection using lipofectamine 2000 (final working concentration 1.0 µg/mL).


title: Ptbp1 deletion does not induce glia-to-neuron conversion in adult mouse retina and brain.

status: Public on Dec 07 2021

city: Baltimore

first: Dong Won

middle: Thomas

last: Kim

state: Maryland

address: 733 N.Broadway, MRB building (Rm 332)

department: Neuroscience

summary: Purpose: scRNA-Seq was performed to profile changes in adult retina Muller glia cells and brain astrocytes after Ptbp1 deletion

overall_design: Tissues (retina, cerebral cortices, striatum, and midbrain) were dissected into Hibernate-A media with a 2% B-27 and GlutaMAX supplement (0.5 mM final). Tissues were dissociated in papain (Worthington). Cells were then loaded into 10x Genomics Chromium Single Cell System (10x Genomics) and libraries were generated using v3.1 chemistry following the manufacturer’s instructions.  Libraries were sequenced on Illumina NovaSeq. Sequencing data were first processed through the Cell Ranger (v.6.0.1, 10x Genomics) with default parameters, aligned to the mm10 genome (refdata-gex-mm10-2020-A), and matrix files were used for subsequent bioinformatic analysis.

first: Thanh

last: Hoang

first: Dong

middle: W

first: Seth

last: Blackshaw


title: PRC1 Sustains the Memory of Neuronal Fate Independent of PRC2 Function

status: Public on Jan 10 2022

city: New York City

first: Alireza

last: Khodadadi-Jamayran

address: 550 1st Ave, MSB 304

department: Division of Advanced Research Technologies (DART)

institute: New York University, NYU Langone Medical Center

summary: Polycomb repressive complexes (PRCs) 1 and 2 maintain stable cellular memories of early developmental patterning programs by establishing heritable patterns of gene repression. PRCs repress transcription through histone modifications and chromatin compaction, but their roles in neuronal subtype diversification are poorly defined. We unexpectedly found that PRC2 is dispensable to preserve the Hox transcription factor-dependent positional identity of spinal motor neurons (MNs), while PRC1 is essential for the specification of segmentally-restricted subtypes. Mutation of the core PRC1 component Ring1 leads to increased chromatin accessibility and ectopic expression of a broad variety of fates determinants, including Hox genes, while general features of MNs are maintained. Loss of MN subtype-specific fates in Ring1 mutants is due to the suppression of Hox networks by derepressed caudal Hox genes. These results indicate that PRC1 can function independently of de novo PRC2-dependent methylation to maintain chromatin topology and transcriptional identity at the time of differentiation.

overall_design: RNAseq and ATACseq of brachial thoracic and lumbar motor neurons in Ring1 mutants. RNAseq of ESC-derived motor neurons expressing Hoxc13.

first: Ayana

last: Sawai

first: Sarah

last: Pfennig

first: Milica

last: Bulaji

first: Alexander

last: Miller

first: Esteban

middle: O

last: Mazzoni

first: Jeremy

last: Dasen


title: Early life stress leads to gene expression down-regulation in prefrontal cortex

first: Irina

last: Voineagu

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

overall_design: Refer to individual Series


title: Inactivation of phosphate transporters alters gene expression in T. gondii

status: Public on Dec 04 2021

city: Wuhan

first: Bang

last: Shen

address: No. 1 SHizishan St

institute: Huazhong Agricultural University

summary:
Purpose:This study was aimed to profile the transcriptome changes of Toxoplasma after loss of phosphate transporters. For this purpose, phosphate transporter TgPiT and TgPT2 mutants were constructed by using direct knockout or conditional knockdown methods in RH or TATi parasite strain, respectively. The transcriptome changes  were captured by RNA-seq analyses.
Methods: Transcriptomic profiles of mutants (Δpit and iKD-PT2+ATc, respectively) and controls (RH and iKD-PT2-ATc,respectively) were generated by deep sequencing, in triplicate, using Illumina HiSeq xten. The sequence reads that passed quality filters were analyzed at the transcript level with TopHat (v2.1.1) followed by RSEM (v1.3.3). The differential expression genes were identified by DESeq2 (v1.24.0) analyses (mutant samples versus control samples).
Results: Using an optimized data analysis workflow, More than 30 million paired-end reads were generated for each sample and about 90% of the clean reads were mapped to GT1 reference genome. RNA-seq data indicated deletion of TgPiT caused modest transcriptome changes in Toxoplasma. Within the 61 DEGs, several genes are typically increased during transition from tachyzoites to bradyzoites, were upregulated in the Δpit mutant, thus suggest stress response in Toxoplasma due to inactivation of TgPiT. While more than 900 genes (fold change ≥2 and adjusted p value <0.05) were significantly regulated in TgPT2 knockdown mutant. Enrichment of the differentially expressed genes using cluster of orthologous group indicate that these DEGs were enriched in pathways like genetic information processing (such as protein translation, transcription, RNA processing and modification, DNA replication and repair, chromatin structure regulation), nutrient transport and metabolism, signal transduction, intracellular trafficking, protein secretion and vesicular transport etc. 24 of 61 DEGs in Δpit strain were also found in DEGs of TgPT2 deficient parasites. The similar gene expression changes caused by inactivation of TgPiT and TgPT2 suggest that the two proteins have overlapping functions.
Conclusions: Our study  revealed the transcriptome changes in Toxoplasma due to phosphate transporters deficiency with biologic replicates, generated by RNA-seq technology. The optimized data analysis workflows reported here provide the overall transcripts changes in TgPiT and TgPT2 defect strains, respectively. The results showed the unique and overlapping impacts of TgPiT and TgPT2 on Toxoplasma. These widen our understanding of phosphate requirements and potential transport pathway in Toxoplasma.

overall_design: The transcriptome expression patterns in phosphate transporter deficient Toxoplasma and wild type parasites  were generated by deep sequencing, in triplicate, using Illumina HiSeq xten.

first: Jianmin

last: Cui


title: Transcriptional profiling of mouse eosinophils identifies distinct gene signatures following cellular activation

city: Tel Aviv

first: Guy

last: Shapira

address: Chaim Levanon 30

country: Israel

institute: Tel Aviv University

summary:
Purpose: we aimed to characterized the transcriptional profile of mouse eosinophils in response to stimuli that are associated with Type 1 and Type 2 environments
Methods: Eosinophils were purified from the peritoneal cavity of Il5Tg mice and stimulated with IL-4 (i.e. type 2 activated eosinophils), IFN-γ, and a combination of lipopolysaccharide (LPS, i.e. type 1 activated eosinophils) in the presence of IFN-γ. Thereafter, RNA was obtained and the transcriptome signature following each stimulation was determined using RNA sequencing. Raw sequencing reads were trimmed and filtered using fastp, then aligned to mouse genome assembly (GRCm38) using STAR 2.7.2a. Normalization and differential expression analysis were performed in R 4.0.3 using the package DESeq2. Finally, gene ontology annotations were obtained from Ensembl and pathway graphs were obtained from KEGG.
Results: RNAseq analysis revealed marked differences, which were driven by the different stimulating conditions
Conclusion: We demonstrate that eosinophils are polarized to distinct phenotypes following distinct stimuli. These findings contribute to the growing understanding regarding the heterogeneity of eosinophils and their possible roles in different diseases.

overall_design: RNAseq of eosinophils following activation with stimuli that are associated with Type 1 and Type 2 environments


title: FoxP3 associates with enhancer-promoter loops to regulate Treg-specific gene expression

status: Public on Dec 03 2021

city: Boston

first: CBDM

last: Lab

state: MA

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

institute: Harvard Medical School


title: Alteration of gene expression by diallyl trisulfide (DATS) administration in chemically-induced rat mammary tumors

city: Pittsburgh

first: Shivendra

middle: V

last: Singh

state: PA

address: 5117 Centre Avenue UPMC HCC Research Pavilion Suite 2.32A

department: Pharmacology and Chemical Biology

institute: University of Pittsburgh

summary: We report altered gene expression profiles by DATS in chemically-induced rat mammary tumors

overall_design: Examination of DATS-regulated transcriptome in chemically-induced rat mammary tumors


title: Transcriptomic reprograming during the involution of brown adipose tissue in rabbits

first: Hai-Bin

last: Ruan

summary: Brown adipose tissue (BAT) in rabbits undergoes rapid involution, i.e. transforming to white adipose tissue (WAT), similarly to what happens in humans. We aim to profile the transcriptomic changes of total BAT and the stromal vascular fraction (SVF) that contains adipocyte progenitors at the global and single-cell levels.

overall_design: Bulk- and single cell-RNA sequencing of total and/or the SVF of the interscapular and/or subscapular BAT depots from rabbits at ages of 1 day, 3 weeks, 6 weeks, and 12 weeks.

first: Zan

last: Huang


title: Krab-ZFPs Inhibit Retrovirus by Targeting PBS Sites

status: Public on Dec 01 2021

city: Guangzhou

first: Bo

last: Yang

address: Guangzhou, 510150, Guangdong Province, China.

institute: The Third Affiliated Hospital of Guangzhou Medical University


title: ChIP-seq on Znf417 and Znf587 overexpression 293T to verify Znf417 and Znf587 binding capacity at PBS-Lys elements.

summary: The ChIP-seq experiments using GFP antibody on ZNF417/ZNF587-GFP overexpressing 293T cells revealed that ZNF417/ZNF587 preferred to bind a PBS-Lys-containing HERVs. Further motif calling analysis showed that both ZNF417 and ZNF587 bind to HERVK PBS-resembled motif.

overall_design: We used two replicates of each ChIP reaction and used ZNF417/587 overexpression 293T input as control.


title: Transcriptional responses of primary murine macrophages to four Candida species

status: Public on Nov 28 2021

first: Michael

last: Lorenz

institute: UTHealth Houston

summary: Candidiasis is an infection caused by yeasts of the genus Candida that ranges in severity from debilitating mucosal infections to disseminated disease with high mortality rates. C. albicans is the most common cause of infection, but non-albicans species collectively represent a significant disease burden. Disseminated disease rarely affects immunocompetent individuals, largely due to the action of innate immune cells, including macrophages, in controlling infection. The interaction of C. albicans with macrophages has been subject to extensive study, but there has been little investigation of the macrophage response to non-albicans Candida species. Here, we used RNA-seq to investigate global transcriptional changes within primary murine macrophages after one hour in response to four species: C. albicans, C. parapsilosis, C. tropicalis and Clavispora lusitaniae. We identified a strong pro-inflammatory response to C. albicans that was largely independent of fungal variability and found that this was highly correlated with the response to C. parapsilosis and C. tropicalis. In contrast, C. lusitaniae elicited a broadly weaker response, including reduced induction of cytokine genes. Several chemokine genes also showed weaker induction in response to both C. lusitaniae and C. parapsilosis than to C. albicans, although significantly reduced secretion of CCL3 protein was only evident in response to C. lusitaniae. These data indicate a high degree of similarity in early macrophage recognition of multiple important Candida pathogens, but also suggest that weaker recognition of C. lusitaniae by immune cells may aid immune evasion by this species.

overall_design: Macrophages were differentiated from murine bone marrows using 10 ng/ml macrophage colony stimulating factor (M-CSF) for seven days, before being distributed into 12-well plates and incubated overnight. Macrophages were then stimulated with medium only, live Candida (C. albicans, C. lusitaniae, C. parapsilosis, C. tropicalis) or UV-killed C. albicans (all in a 3:1 Candida:macrophage ratio). For the LPS/IFN-gamma condition, macrophages were treated overnight with 100 U/ml IFN-gamma, then during the experiment were stimulated with 100 ng/ml LPS. After 1 hr treatment, macrophage RNA was isolated using the Qiagen RNeasy Micro kit. RNA samples were obtained from macrophages derived from three individual mice. Sequencing and library preparation was performed by Macrogen, Inc.

first: Andrew

last: Pountain


title: Evaluation of reliable reference genes for the lung of neonatal C57BL/6 mice under consideration of biological, technical and experimental variables

status: Public on Nov 30 2021

city: Braunschweig

first: Prof. Hamid

last: Hossain

state: Lower Saxony

address: Celler Str. 38

department: Microbiology

institute: Klinikum Braunschweig

summary: A pool of reference gene candidates was first gathered by reviewing previous studies and a commercial panel as well as using Genevestigator, analysis software for published microarray experiments. In the next step, the expression of the potential reference gene candidates was evaluated by the present microarray from the neonatal C57BL/6 mice with otherwise physiologic conditions and through this process, the 24 final reference gene candidates were chosen. Then, RT-qPCR validation of the 24 reference gene candidates and data analysis by GeNorm and Normfinder were completed, so that reliable reference genes specific for biological, technical and experimental conditions were suggested.

overall_design: Microarray experiment was performed in the lung tissue of three neonatal (5-7-day-old) C57BL/6 mice from physiologic conditions (FiO2=0.21). Each mouse was investigated in two technical replicates.

first: Hamid

first: Anne

last: Hilgendorff


title: RNA sequencing of Wild type and Gpr109a-/- CD4+ T cells

status: Public on Dec 11 2021

city: Duarte

first: Anastasia

middle: I

last: Kousa

state: CA

address: 1500 E Duarte Rd

department: Hematology / HCT

institute: City of Hope

summary: We report minimal differences between CD4+ T cells isolated from WT C57BL/6 mice and Gpr109a-/- mice

overall_design: Splenic CD4+ T cells were FACS-sorted and submitted for RNA sequencing analysis

first: Melissa

last: Docampo

first: Marcel

last: van den Brink


title: SP-C BRICHOS mutation mouse model

status: Public on Nov 26 2021

city: Philadelphia

first: Apoorva

last: Babu

address: SCTR, 3400 Civic Center Blvd

department: Cardiovascular Institute

institute: University of Pennsylvania


title: Single Cell sequencing analysis of adult SP-C BRICHOS mice lung epithelium

summary: We report the single cell RNA sequencing of the lung epithelium of mice expressing the SP-C BROCHOS mutation (SP-C C121G) at 3 and 7 days after tamoxifen induced mutation expression. The control sample for this experiment are mice hypomorphic for the SP-C mutation (SP-C C121Gneo). This study allow for the identification of unique lung epithelial cell states that emerge following SP-C mutation expression

overall_design: EPCAM+ sort of whole lung single cell suspensions was loaded into 10x genomic platform for single cell RNA sequencing

first: Katzen

last: Jeremy

first: Beers

last: Michael

first: Babu

last: Apoorva


title: Morphological, molecular and functional cardiac study during aging in animals submitted to gestational protein restriction

status: Public on Nov 17 2021

city: campinas

first: Marina

middle: Silva

last: Folguieri

state: são paulo

address: rua cinco de junho, 350

department: Fisiopatologia Médica

country: Brazil

institute: Universidade Estadual de Campinas, UNICAMP

summary:
Purpose: In this study, we used RNA-Seq to characterize differences in the Left ventricle expression profiles rats with 62-week old submited to gestational protein restricion (LP) compared to normal protein (NP) offspring during de gestacional.
Methods: Total RNA was extracted from left heart (rats with 62-week old submited to gestational protein restricion (LP) (n=5) compared to normal protein (NP) offspring during de gestacional) (n=5) using the Trizol methods. RNA concentration was quantitated using the NanoDrop. A library was built for each sample, using the TruSeq Stranded mRNA kit (illumina) and submitted to sequencing.
Results: By genomic sequencing analysis, we verified changes in the expression of 137 genes; After gene to gene biological evaluation and relevance, the present study demonstrated significant differences in genes linked to inflammatory activity, oxidative stress, apoptosis process, autophagy and, in hypertrophy and fibrosis pathways resulting heart function disorders.
Conclusion:  The present study suggests that maternal protein restriction may lead to early heart disorders in the LP offspring compared to the NP group. We may hypothesize that rapid heart dysfunction is associated with heart fibrosis, myocardial cell hypertrophy and multiple gene expression abnormalities in the LP offspring.

overall_design: Left ventricle mRNA profiles of Wistar Rat

first: Patricia

middle: A

last: Boer

first: José-Antonio

last: Gontijo

first: André

last: Vieira


title: Comparative transcriptomic analysis of the response of CUG-clade Candida species to phagocytosis

city: Houston

summary: Pathogenic Candida fungi are a leading cause of opportunistic, hospital-associated bloodstream infections with high mortality rates, typically in immunocompromised patients. Several species, including C. albicans, the most prevalent cause of infection, belong to the monophyletic CUG clade of yeasts. Much is known about the interaction of C. albicans with innate immune cells, which are crucial for controlling infection. Phagocytosis of C. albicans elicits transcriptional induction of several pathways involved in catabolism of non-glucose carbon sources that are important for virulence, termed alternative carbon metabolism. However, the response of other CUG clade species has not been characterized. Here, we analyzed the transcriptional responses to macrophage phagocytosis by seven Candida species across a range of virulence and clinical importance. We observed a strikingly high degree of conservation even in species that rarely cause infection and defined a core induced response linked to alternative carbon metabolism. Many of these genes showed convergence to the same level of expression upon phagocytosis. Some differences were observed, however, including notably deficient expression of heat shock protein HSP21 in common pathogen C. parapsilosis that may be linked to reduced thermotolerance in this species. In contrast, C. parapsilosis showed a more robust induction of metabolite transporters compared to the related L. elongisporus, which rarely causes infection. This study significantly broadens our understanding of host interactions in CUG clade species and shows that while metabolic plasticity is an important attribute in pathogenic Candida species, it is neither an adaptation to, nor sufficient for, virulence.

sample_organism:
Candida albicans
Candida parapsilosis
Candida tropicalis
Mus musculus
Clavispora lusitaniae
Lodderomyces elongisporus
Candida dubliniensis

overall_design: The transcriptional responses of six Candida species (C. albicans, C. dubliniensis, C. tropicalis, C. parapsilosis, Lodderomyces elongisporus and Clavispora lusitaniae) to phagocytosis was analysed by incubating fungal cells in mammalian medium in the presence or absence of primary macrophages for 1 hour, followed by RNA extraction and sequencing. This experiment was performed in duplicate.

first: John

last: Collette


title: RNAseq data of duck liver after feeding choline chloride

city: Shenzhen

first: Xingzheng

last: Li

address: Pengfei campus

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

summary: We aim to study the unusual TMA metabolism mechanism of ducks, and further explore the hidden reasons that led to the weakening TMA metabolism ability. To achieve this, transcriptome, proteome, and metagenome analyses were integrated based on the constructed duck populations with high TMA metabolism ability and low TMA metabolism ability. In addition, further experiments were followed to validate the hypothesis on the limited flavin-containing monooxygenase 3 (FMO3) metabolism ability of ducks. The study demonstrated that both cecal microbe, including Akkermansia and Mucispirillum, and liver FMO3 participated in the TMA metabolism process of ducks. The limited oxidation ability of FMO3 explained the weakening TMA metabolism ability of ducks. Nevertheless, it contributed to the duck’s survival and reproduction during the evolutional adaption process.

overall_design: A population of 294 ducks (Jingjiang, 72 wks) was fed a diet containing 4000 mg/kg choline chloride (TMA precursor), 6 liver samples with low egg TMA levels, 6 liver samples with high egg TMA levels, and 16 random liver samples were selected for RNAseq sequencing

first: Jiangxia

last: Zheng


title: RNA-seq on Zfp961 GFP flox/flox mESCs to verify ERVKs repression by Zfp961.

first: Bo

last: Yang

summary: To investigate the functional consequences in the absence of ZFP961 in mESCs, we treated the Zfp961-GFPflox/flox cells with 4-OHT to deplete the ZFP961 alleles, and then performed RNA-seq on three independent Zfp961-GFPflox/flox ESC lines before and after Cre mediated excision. Considerate that stable DNA methylation may remain upon Zfp961 absent, therefore ERVKs could still be repressed, we then treated Zfp961-GFPflox/flox cells with 5aza, which a inhibitor of DNA methylation, 24h before Zfp961 deletion with 4-OHT addition. After 4-OHT treatment，we performed RNAseq again, and this time we observed a ETnERV2-int, with belongs to ERVK elements, was upregulated after Zfp961 deletion.

overall_design: Basically, three Zfp961-GFP floxed mESCs cell lines treated with 4-OHT or EtOH as control and two cell lines treated with 5AZA for 24h and then treated with 4-OHT or EtOH. RNA of these cell lines was isolated and sequenced.


title: Transcriptome-wide maps of subcutaneous adipose tissues and visceral adipose tissues in cancer-associated cachexia patients

status: Public on Oct 26 2021

city: Shanghai

first: Zuoyou

last: Ding

state: Shanghai

address: 180, Fenglin Road

institute: ZhongShan  Hospital affiliated Fudan University

summary: In order to identify differentially expressed RNAs among subcutaneous and visceral adipose tissue of cachxtic patients, we recruited three colon cancer patients with remarkable weight lose. We harvested adipose tissue from abdomen of patients at time of surgery and completed transcriptome sequencing using Illumina platform.

overall_design: Subcutaneous and visceral adipose tissues of 3 cancer-associated cachexia patients.

first: Han

last: Jun


title: LPS causes a transcriptional shift in iPSC-microglia similar to an activated state from genetic mouse models of AD

status: Public on Oct 23 2021

city: Cardiff

first: Jimena

last: Monzón-Sandoval

address: Maindy Road

institute: UK Dementia Research Institute at Cardiff University

summary: Alzheimer’s disease (AD) is the most common form of dementia and risk-influencing genetics implicates microglia and neuroimmunity in the pathogenesis of AD. iPSC-microglia are increasingly used as a model of AD but the relevance of common immune stimuli to model AD is unclear. We performed a detailed cross-comparison over time on the effects of combinatory stimulation of iPSC-microglia, and in particular their relevance to AD. We used single cell RNA-seq to measure the transcriptional response of iPSC-microglia after 24 and 48h of stimulation with PGE2 or LPS+IFN-γ either alone or in combination with ATPγS. We observed a shared core transcriptional response of iPSC-microglia to ATPγS and to LPS+IFN-γ, suggestive of a convergent mechanism of action. Across all conditions we observed a significant overlap and functional links to genes that change their expression levels in human microglia from AD patients. Using a data-led approach, we identify a common axis of transcriptomic change across AD genetic mouse model microglia and show that only LPS provokes a transcriptional response along this axis in mouse microglia and LPS+IFN-γ in human iSPC-microglia.

overall_design: Single cell expression profiles for iPSC derived microglia from 4 biological replicates across 8 different conditions. iPSC- microglia were exposed to individual and combined stimuli and their transcriptional profiled measured after 24 or 48 hours. The eight conditions included Control, ATPgS 24h, LPS+IFNg 24h, PGE2 24h, LPS+IFNg 48h, PGE2 48h, LPS+IFN 48h ATPgS 24h, PGE2 48h ATPgS 24h.

first: Elena

last: Burlacu

first: Devika

last: Agarwal

first: Adam

middle: E

last: Handel

last: Davis

first: Sally

last: Cowley

first: M

middle: Z

last: Cader

first: Caleb

last: Webber


title: Bromodomain protein 9 (BRD9) regulates interferon-stimulated genes during macrophage activation via cooperation with BET protein BRD4

city: San Diego

first: Diana

middle: C.

last: Hargreaves

address: 10010 North Torrey Pines Road

institute: The Salk Institute for Biological Studies

summary: Macrophages induce a number of inflammatory response genes in response to stimulation with microbial ligands. In response to endotoxin Lipid A, lineage-defining and stimulation-responsive transcription factors cooperate to induce a gene activation cascade of primary followed by secondary response genes. Epigenetic state is an important regulator of the kinetics, specificity, and mechanism of gene activation of these two classes. In particular, the SWI/SNF chromatin remodeling complex is required for the activation secondary response genes, but not primary response genes, which generally exhibit open chromatin. Here we show that a recently discovered variant of the SWI/SNF complex, the non-canonical BAF complex (ncBAF), regulates secondary response genes in the interferon (IFN) response pathway. Inhibition of bromodomain-containing protein 9 (BRD9), a subunit of the ncBAF complex, with BRD9 bromodomain inhibitors (BRD9i) or a degrader (dBRD9), led to reduction in a number of interferon-stimulated genes (ISGs) following stimulation with endotoxin lipid A. BRD9-dependent genes overlapped highly with a subset of genes differentially regulated by BET protein inhibition with JQ1 following endotoxin stimulation. We find that the BET protein BRD4 is co-bound with BRD9 in unstimulated macrophages and co-recruited upon stimulation to ISG promoters along with STAT1, STAT2, and IRF9, components of the ISGF3 complex activated downstream of IFNAR stimulation. In the presence of BRD9i or dBRD9, STAT1, STAT2, and IRF9 binding is reduced, in some cases with reduced binding of BRD4. These results demonstrate a specific role for BRD9 and the ncBAF complex in ISG activation and identify an activity for BRD9 inhibitors and degraders in dampening endotoxin- and IFN-dependent gene expression.

overall_design:
RNA-seq of BRDi-treated bone-marrow derived macrophages (BMDMs) in 0h, 1h, or 4h Lipid A stimulation; ChIP-seq of BRD4, BRD9, BRD2 in RAW 264.7 macrophage cell line in 0h or 4h Lipid A stimulation; ChIPseq of BRD9 in 0h or 4h Lipid A stimulation; ChIPseq of IRF9, STAT1, and STAT2 in BRDi treatment in 0h or 4h Lipid A; ChIPseq of BRD4 in BMDMs in BRD9i in 4h Lipid A.
RNA-seq of BRDi-treated bone-marrow derived macrophages (BMDMs) in 0h or 4h Interferon-alpha stimulation; ChIP-seq of BRD4 in 0h or 4h Lipid A stimulation with treatment with JQ1; ChIPseq of BRD9 in 0h or 4h Lipid A stimulation with treatment with vehicle, BI9564, dBRD9, IBRD9, JQ1; ChIPseq of IRF9, STAT1, and STAT2 4h Lipid A with vehicle or BI9564.

first: Nasiha

last: Ahmed

first: Jovylyn

last: Gatchalian


title: RNA-seq on ZNF417/587 double KO 293T

summary: To verify Znf417 and Znf587 knock out whether leads to HERV-K element reactivation, we performed RNA-seq on Znf417/Znf587  double knock out (DKO) 293T cell lines. We did not find any significant changes in HERVK expression.

overall_design: Two DKO cell lines and two WT cell lines were used to perform RNA-seq.


title: Raw single-cell RNA sequencing data of adult rumen tissues

status: Public on Oct 21 2021

city: Hangzhou

first: Jiajin

last: Wu

address: Yuhangtang road

institute: Zhejiang University

summary: We performed single-cell RNA-sequencing on the rumen epithelium of dairy cows to construct an epithelial single-cell map of the rumen.

overall_design: Single-cell RNA sequencing for 3 samples of rumen tissues of lactating dairy cow.

first: Jia-Jin

first: Senlin

last: Zhu

first: Hui-Zeng

last: Sun


title: Transcriptome-wide Profiling of N6‑Methyladenosine via a Selective Chemical Labeling Method

status: Public on Oct 15 2021

first: Yalun

last: Xie

state: Hubei

address: Ba Yi Road

institute: Wuhan University

type: Methylation profiling by high throughput sequencing

summary: We present a chemical method (m6A-ORL-Seq) for transcriptome-wide m6A profiling , and compared its results with MeRIP-seq.

overall_design: Transcriptome-wide Mapping of N6‑Methyladenosine on HEK-293T by a chemical method (m6A-ORL) and an antibody-based method (MeRIP-seq), then analyzed and compared the performance of those two methods. M6A-ORL aslo provides four thousands of high-confidence m6A sites based on chemical modified m6A induced RT truncation.

first: Xiang

last: Zhou


title: ATOH8 and SMAD3 form a transcriptional complex to induce an anti-cell cycle signature and prevent cell cycle progression [ChIP-seq]

status: Public on Dec 05 2021

first: Ximeng

last: Liu

address: Zhongshan Road No.2 Yuexiu district

institute: SUN YAT-SEN UNIVERSITY

summary: To identify ATOH8 and SMAD3 form a novel transcriptional complex, we performed chromatin immunoprecipitation followed by sequencing (ChIP-seq). Analyses of their genome occupancy profiling reveals that their genome-wide binding patterns are highly similar and they co-occupy a number of same genes. CCNE2 and CDK1 are their common downstream target genes.

overall_design: ChIP-seq was generated to identify ATOH8 and SMAD3 transcriptional program in ATOH8 overexpressing A549.


title: Monoclonal Antibody Targeting Pear1 for Pulmonary Fibrosis Therapy [bulk RNA-seq]

status: Public on Oct 20 2021

city: Charlottesville

first: Yong

last: Huang

state: VA

address: 1340 Jefferson Park Ave

institute: University of Viginia

summary: Pulmonary fibrosis (PF) is a chronic interstitial lung disease that causes irreversible and progressive lung scarring and respiratory failure. Activation of fibroblasts (FBs) play a central role in progression of PF. Here we report that platelet endothelial aggregation receptor 1 (Pear1) in FBs is a new molecular target for PF therapy. Pear1 deficiency spontaneously caused respiratory function decline and alveolar collagens accumulation in old mice. The degree of PF and mortality induced by bleomycin were significantly enhanced in Pear1 deficient mice. FB Mesenchyme-specific Pear1 deficiency aggravated bleomycin-induced PF, confirming that Pear1 modulates PF progression probably byvia regulation of FBs function. Single cell RNA-seq analysis of pulmonary FB and functional enrichment analysis revealed drastic expansion of Aactivated- FB clusters and enrichment of activated FB marker genes in extracellular matrix (ECM) development and pulmonary fibrosis in Pear1-/- fibrotic lungs. CD140+ bulk tissue RNA-seq analysis further confirmed that multiple mesenchyme development pathways especially epithelial mesenchymal transition (EMT) are enriched with up-regulated genes involving FB mediated ECM organization and development in in Pear1-/- fibrotic lungs. We further found that Pear1 associated with Protein Phosphatase 1 to suppress fibrotic factors such as TGFß, FGF or PDGF-induced intracellular signalling and FB activation. Intratracheal aerosolization of monoclonal antibody activating Pear1 greatly ameliorates PF in both wild-type mice and Pear1-humanized mice, suggesting that targeting Pear1 may serve as a new therapeutic strategy for PFand significantly improves their survival rate.

overall_design: Fresh lung tissues were harvested from mouse bleomycin model. We used flow cytometry to sort out Cd140+ cells from total lung cells. Total RNA were isolated from the cells and used for RNA-seq assay.

first: Xuemei

last: Fan

first: Yan

last: Geng

first: Lin

last: Li

first: Imre

last: Noth

first: Junling


title: Monoclonal Antibody Targeting Pear1 for Pulmonary Fibrosis Therapy [scRNA-seq]

summary: Pulmonary fibrosis (PF) is a chronic interstitial lung disease that causes irreversible and progressive lung scarring and respiratory failure. Activation of fibroblasts (FBs) play a central role in progression of PF. Here we report that platelet endothelial aggregation receptor 1 (Pear1) in FBs is a new molecular target for PF therapy. Pear1 deficiency spontaneously caused respiratory function decline and alveolar collagens accumulation in old mice. The degree of PF and mortality induced by bleomycin were significantly enhanced in Pear1 deficient mice. FB Mesenchyme-specific Pear1 deficiency aggravated bleomycin-induced PF, confirming that Pear1 modulates PF progression probably byvia regulation of FBs function. Single cell RNA-seq analysis of pulmonary FB and functional enrichment analysis revealed drastic expansion of Aactivated- FB clusters and enrichment of activated FB marker genes in extracellular matrix (ECM) development and pulmonary fibrosis in Pear1-/- fibrotic lungs. CD140+ bulk tissue RNA-seq analysis further confirmed that multiple mesenchyme development pathways especially epithelial mesenchymal transition (EMT) are enriched with up-regulated genes involving FB mediated ECM organization and development in in Pear1-/- fibrotic lungs. We further found that Pear1 associated with Protein Phosphatase 1 to suppress fibrotic factors such as TGFß, FGF or PDGF-induced intracellular signalling and FB activation. Intratracheal aerosolization of monoclonal antibody activating Pear1 greatly ameliorates PF in both wild-type mice and Pear1-humanized mice, suggesting that targeting Pear1 may serve as a new therapeutic strategy for PF.

overall_design: Cellular suspensions were loaded on a Chromium Controller instrument (10x Genomics) to generate single-cell Gel-Bead-in-Emulsions (GEMs) and perform single cell partitioning and barcoding.


title: Next generation sequencing facilitates quantitative analysis of  oncogene induced transcriptomes

status: Public on Oct 11 2021

city: Groningen

first: Marcel

last: van Vugt

state: Groningen

address: Hanzeplein 1

department: Department of Medical Oncology

institute: UMCG

summary: Expression of CDC25A, CCNE1, or MYC in MDA-MB-231, BT549, HCC1806, RPE1-TP53wt, and RPE1-TP53mut cells was induced using 1 µg/mL of doxycycline. Cells were harvested and frozen at -80°C at 48 hours and 120 hours after doxycycline induction. Next, RNA was isolated using the mirVANA kit (Ambion, AM1561). To determine RNA quality, RNA was separated by electrophoresis on microfluidic sipper chips and detected by fluorescence (LabChip GX, Caliper LifeSciences). RNA Quality Scores (RQS) were based on electropherogram features (total and fast region areas, 28S, and 18S height), and ranged from 0-10. Only samples with RQS scores above 5 were included for analysis. To generate cDNA libraries suitable for next-generation sequencing (NGS), the QuantSeq RNAseq 3' mRNA kit (Lexogen) was employed. Briefly, the poly-A tail from total RNA was bound to oligo-dT primers to synthesize the first cDNA strand. After RNA removal, a second cDNA strand was synthesized by random priming. The double-stranded cDNA library was purified, and PCR amplified with Illumina sequencing adapters. The libraries were sequenced with 65 base-pair reads on a NextSeq 500 sequencer (Illumina) and generated 7.2 to 19.8 million of reads per sample.

last: Vugt

first: Rudolf

middle: S

last: Fehrmann

first: Sergi

middle: G

last: Llobet

first: Arkajyoti

last: Bhattacharya

first: Marieke

last: Everts

first: Klaas

last: Kok

first: Bert

last: van der Vegt


title: Single-cell RNA sequencing data of stem cell-derived microfluidic human embryoids, NODAL-KO human embryoids and chimpanzee embryoids

status: Public on Oct 13 2021

city: Syracuse

first: Yi

last: Zheng

state: New York

address: 900 S Crouse Ave

department: Biomedical and Chemical Engineering

institute: Syracuse University

summary: Transcriptome at the single-cell level of a human embryoid model, which recapitulates aspects of lineage diversification and three-dimensional tissue architecture of the human embryo from the implantation to the onset of gastrulation, was profiled at different time points. Similarly, chimpanzee embryoids were generated and profiled to reveal transcriptome dynamics during the early post-implantation chimpanzee development. Our comparative transcriptome analyses reveal a critical role of NODAL signaling in human mesoderm specification, which is functionally validated by generating embryoids with NODAL-knockout (KO) hPSCs.

sample_organism:
Pan troglodytes
Homo sapiens

platform_organism:
Pan troglodytes
Homo sapiens

overall_design:
We applied single-cell mRNA sequencing technique to examine the transcriptomes of microfluidic embryoids.
The .Rd files can be loaded into RStudio using "load ("file_name.Rd")", and analyzed using the Seurat R package (https://satijalab.org/seurat/). In case of difficulties accessing the data, please contact Dr. Yi Zheng (zhengum@umich.edu)

first: Jianping

last: Fu


title: GFI1 tethers the nucleosome-remodeling and histone-deacetylase (NuRD) complex to open and transcriptionally active chromatin in myeloid progenitors

city: Montréal

first: Tarik

last: Moroy

state: Québec

address: 110 Avenue des Pins

country: Canada

institute: Institut de recherches cliniques de Montréal (IRCM)

summary:
Purpose: The goals of this study are to identify sites in genomic DNA that are occupied by GFI1 and the NurD complex, represented by its member the chromodomain helicase CHD4 or by a complex of GFI1 and CHD4 in myeloid precursors cells and to determined the effect on gene expression.
Methods: Granulocytic-monocytic precursors (GMPs) as well as pre neutrophils and mature neutrophils were sorted by flow cytometry from murine bone marrow and sujected to RNA-seq and Chromatin-immuno-precipitation and sequencing (ChIP-Seq) and ATAC-seq procedures. Ch-IP seq experiments were done with antibodies against GFI1, CHD4 or different histone H3 modifications as indicated.
Results: GFI1 and GFI1/CHD4 complexes occupies both promoter and enhancers of genes that are down or upregulated during the formation of preNeu and matNeu cells from GMPs
Conclusions: Myeloid precursors required GFI1 to tether the NuRD complex to a specific set of target genes that are either transcriptionally active or poised to enable their transcriptional regulation during neutrophil differentiation by chromatin remodeling

overall_design: RNA-Seq with GMPs, preNeu, matNeu cells sorted from murine bone marrow, GMPs, preNeu, matNeu cells sorted from murine bone marrow

first: Anne

last: Helness

first: Charles

last: Joly-Beauparlant

first: Arnaud

last: Droit


title: Early anteroposterior regionalization of human neural crest is shaped by a pro-mesodermal factor

status: Public on Sep 18 2021

city: Sheffield

first: Anestis

last: Tsakiridis

address: Western Bank

department: Biomedical Science

institute: University of Sheffield

summary: We employed ATAC-seq to interrogate the chromatin accessibility landscape in neuromesodermal progenitor (NMP)-like cells derived from a human embryonic stem cell (hESC) line engineered to exhibit shRNA-mediated, tetracycline (Tet)-inducible knockdown of TBXT expression. TBXT shRNA hESCs were differentiated toward NMPs following a three day treatment in the presence of WNT and FGF agonists in the presence or absence of tetracycline and +/-Tet treated samples were harvested and analysed by ATAC-seq.

overall_design: ATAC-seq analysis on samples obtained from +/-Tet TBXT shRNA sOPTiKD hESC-derived NMPs


title: Spatial transcriptome of Nematostella vectensis apical organ reveals its molecular signature and associated cells

status: Public on Oct 01 2021

city: Plymouth, Devon

first: vengamanaidu

last: modepalli

address: The Laboratory,Citadel Hill

department: Cell and Molecular

institute: Marine Biological Association of the UK

summary: The spatial transcriptome data has allowed us to explore the differential gene expression among the oral-aboral domains and provided new insights into the apical organ signalling pathways for future mechanistic studies and genes associated with oral/aboral differentiation. This resource identifies numerous candidates for elucidating the functional role of the apical organ and to address the evolution of the metazoan larval nervous system.

overall_design: Here, we uncovered the molecular signature of the apical organ in N. vectensis through spatial transcriptomics. We performed microdissection on N. vectensis larvae and carefully separated the aboral tissue from the rest of the larval body at the planula and late planula development stages.We acquired transcriptome data from both the aboral tissue and the rest of the body separately to perform differential gene expression (DGE) analysis.

first: Eleanor

last: Gilbert

first: Callum

last: Teeling

first: V

last: Modepalli


title: aCGH from cells derived from adult individuals with acute lymphoblastic leukemia

status: Public on Oct 31 2021

city: Guadalajara

first: Adriana

middle: Del Carmen

last: Aguilar Lemarroy

state: Jalisco

address: Sierra Mojada 800, Independencia Oriente, 44340 Guadalajara, Jal.

department: División de Inmunología

country: Mexico

institute: Centro de Investigación Biomédica de Occidente

type: Genome variation profiling by genome tiling array

summary:
Chromosomal instability is a characteristic of cancer, in acute lymphoblastic leukemia, several genes with aberrations have been reported that are currently used as diagnostic tools, prognostics and are even part of the treatment.
The CGH microarrays performed in ten adult individuals with ALL, and the JURKAT and CEM cell lines, show that there are regions of shared loss on chromosomes 2, 9 and 14 and of gain on chromosomes 13 and 17 that are maintained in more than five of the samples.

overall_design: Identification of regions of loss or gain in adult individuals with ALL and the JURKAT and CEM cell lines.

last: Aguilar-Lemarroy

first: Jessica

last: Zapata-García


title: Profiling and functional characterization of maternal mRNA translation in mouse maternal-to-zygotic transition

city: Boston

last: Zhang

address: 200 Longwood Avenue WAB 149

department: PCMM

institute: Boston Children's Hospital / Harvard Medical School

summary: Translational regulation plays an important role in gene expression and function. Although the transcriptional dynamics of mouse pre-implantation embryos has been well characterized, the global mRNA translation landscape and the master regulators of zygotic genome activation (ZGA) remain unknown. Here, by developing and applying a low-input ribosome profiling (LiRibo-seq) technique, we profiled the mRNA translation landscape in mouse pre-implantation embryos and revealed the translational dynamics during mouse pre-implantation development. We identified a dramatic translational transition from MII oocytes to zygotes, and demonstrated that active translation of maternal mRNAs is essential for maternal-to-zygotic transition (MZT). We further showed that two maternal factors, Smarcd2 and Cyclin T2, whose translation is activated in zygotes, are required for chromatin reprogramming and ZGA, respectively. Our study thus not only filled in a knowledge gap on translational regulation during mammalian pre-implantation development, but also revealed new insights into the critical function of maternal mRNA translation in MZT.

overall_design: In this study, we modified RiboLace sequencing method to achieve mRNA translation profiling using as few as 100-250 oocytes or embryos. Using this low-input ribosome sequencing (LiRibo-seq) method, we have generated mRNA translation profiling of mouse MII oocytes and preimplantation embryos from 1-cell to blastocyst stage, revealing the dynamics of mRNA translation during the natural developmental process. We constructed a total of 14 LiRibo-seq datasets, including: two 5k ESC libraries, two MII oocyte libraries, two 1-cell embryo libraries, two 2-cell embryo libraries, two 4-cell embryo libraries, two morula libraries, two blastocyst embryo libraries. 12 total RNA-seq datasets were generated including two MII oocyte libraries, two 1-cell embryo libraries, two 2-cell embryo libraries, two 4-cell embryo libraries, two morula libraries, two blastocyst embryo libraries. 16 polyA RNA-seq datasets were generated including two MII oocyte libraries, two 1-cell embryo libraries, two DMSO and CHX treated zygote libraries, two DMSO and AMA treated zygote libraries, two siRNA control and Ccnt2 KD 2-cell embryo libraries. 8 ATAC-seq datasets were generated including two DMSO and CHX zygotes libraries, two siRNA control and Smarcd2 KD 1-cell embryo libraries.

first: Chunxia

first: Meng

last: Wang

first: Yisi

last: Li


title: Single-cell RNA-sequencing reveals pervasive but highly cell type-specific genetic ancestry effects on the response to viral infection

city: Chicago

first: Luis

middle: B

last: Barreiro

address: 900 E 57th Street

institute: University of Chicago

summary: Humans show remarkable variation in susceptibility to infectious diseases as well as chronic inflammatory and autoimmune disorders. This heterogeneity arises partially from variation in the immune response, which is responsible for preventing and controlling infection. To better understand the major factors driving antiviral immune response differences, we used single-cell RNA-sequencing to measure the effects of genetic ancestry and cis-regulatory variation on the transcriptional response to influenza infection in various immune cell types in 90 European and African American individuals. We show that monocytes are the most responsive to infection but that all cell types engage a conserved, type I IFN response, which is stronger in European individuals. Further, we detect directional, polygenic differences in expression phenotypes between populations that are under cis-genetic control and show that recent positive selection has acted on putatively causal risk loci associated with common autoimmune disorders. Our findings establish genetic ancestry and common cis-regulatory variants as important determinants governing the antiviral immune response, thus improving our understanding of the factors that contribute to differences in infectious and complex disease susceptibility.

overall_design: Multiplexed single-cell RNA expression profiles of control (mock-infected) and influenza A virus (IAV)-infected peripheral blood mononuclear cells (PBMCs) collected from African and European American individuals

first: Haley

last: Randolph

middle: K

last: Fiege

first: Beth

last: Thielen

first: Mari

last: Cobb

first: João

last: Batista-Barroso

first: Ryan

last: Langlois


title: A Single-cell Transcriptomic Atlas of Human Intervertebral Disc

status: Public on Aug 20 2021

city: Beijing

first: Jian

last: He

address: DongDaJie #8

institute: the Fifth Medical Center of the PLA General Hospital

summary: Using high-precision transcriptomics to systematically map the atlas of human intervertebral disc (IVD) at single-cell resolution. Consequently, we found remarkable cellular diversity in the human IVD and identified a set of signature markers to recognize the cell types spatially. Furthermore, we deciphered a biological classification of chondrocyte subclusters with distinct role in the ECM homeostasis.Notably, the critical clues were also discovered for progenitor cells with bi-lineage differentiation trajectories in the nucleus pulposus, which discriminatively marked by the ancestry molecules PDGFRA and PROCR and highly enriched PDGF network. Finally, we uncovered the potential vital factors maintaining the IVD homeostasis from the intercellular crosstalk based on the signaling network landscape of the IVD microenvironment.

overall_design: Single-cell sequencing of 91,295 IVD cells from 3 nucleus pulposus, 2 cartilage endplate and 2 annulus fibrosus in IVD using the 10X genomics Kit.

first: Yibo

last: Gan

first: Bing

last: Liu

first: Peng


title: Genomic and epigenetics guided identification of tissue-specific genomic safe harbor sites for gene therapy

status: Public on Sep 13 2021

city: Memphis

first: Yong

last: Cheng

state: Tennessee

address: 262 Danny Thomas Pl

department: Department of Hematology

institute: St. Jude Children's Research Hospital

summary: One common strategy in gene and cell therapies requires the integration and stable transcription of transgenes into the host cell genomes. Genomic safe harbors (GSHs) are regions of the genome that can maintain the expression of transgenes without disrupting the transcriptome of host cells. With recent advances in genome editing technology, GSHs play an increasingly important role in improving the efficiency and safety of genome engineering. However, limited candidate GSHs have been identified. In addition, many parameters currently used to identify GSHs are not knowledge based and none of the current available GSHs meet all the ideal safety requirement. In this study, we use the polymorphic mobile element insertions (pMEIs) that naturally occur among healthy human populations to facilitate GSHs searching. By integrating pMEIs with epigenomic signatures and 3D chromatin organization information, we developed a framework to map cell typespecific GSHs. We applied our framework to pMEIs identified in the 1000 Genomes project and GTEX projects and identified novel GSHs Candidates in blood and brain cells. We further validated that a transgene cassette integrated in one novel GSH can be stably transcribed without affecting normal proliferation and differentiation of host cells. We also developed a user-friendly program to search for GSHs in different population and cell types.

overall_design: Candidate Genomic safe harbor sites are predicted using data from the 1000 Genome and GTEx projects. GFP expression cassette was integrated into four (three identified in blood and one in brain)  safe harbor site, and two random site in HUDEP2 cells. RNA-seq assays were performed in all GFP integrated and  wild-type HUDEP2 cells..

first: Dewan

last: Shrestha


title: Mechanisms Governing Target Search and Binding Dynamics of Hypoxia-Inducible Factors [ChIP-seq]

status: Public on Oct 29 2021

city: Berkeley

first: Robert

last: Tjian

address: University of California, Berkeley 450 Li Ka Shing #3370

department: MCB

institute: UC Berkeley

summary: We performed ChIP-seq to compare genome-wide HIF-1b and HIF-2a occupancy in wild type 786-O cells to 786-O cells with either HIF-1b or HIF-2a endogenously tagged with a V5-Halo moiety.

overall_design: We performed ChIP-seq in WT 786-O cells and in 786-O cells with either HIF-1b or HIF-2a endogenously tagged with a V5-Halo moiety using no antibody (input samples) or anti-HIF-1b, anti-HIF-2a and anti-V5 antibodies (3 cell types, 3 antibodies plus inputs for a total of 12 libraries).

first: Claudia

last: Cattoglio

first: Yu

last: Chen

first: Gina

last: Dailey

first: Qiulin

last: Zhu

first: Xavier

last: Darzacq