title: Multiomic analysis of the Arabian camel (Camelus dromedarius) kidney reveals a role for cholesterol in water conservation

status: Public on Jun 18 2021

city: Bristol

first: Fernando

last: Alvira Iraizoz

address: Dorothy Hodgkin Building, University of Bristol, Whitson Street

department: Bristol Medical School

institute: University of Bristol

summary: The one-humped Arabian camel (Camelus dromedarius) is the most important livestock animal in arid and semi-arid regions and continues to provide basic necessities to millions of people. In the current context of global warming, there is renewed interest in the adaptive mechanisms that enable camelids to survive in arid conditions. Recent investigations described genomic signatures that revealed evolutionary adaptations to desert environments. We now present a comprehensive catalogue of the transcriptomes and proteomes of the dromedary kidney and describe how the gene expression profiles of Differentially Expressed Genes (DEGs) are modulated as a consequence of chronic dehydration and subsequent acute rehydration. We performed RNAseq and quantification of peptides in samples from 15 dromedaries (5 controls, 5 dehydrated and 5 rehydrated). Gene Ontology analyses suggested an enrichment of the cholesterol biosynthetic process and an overrepresentation of categories related to ion transmembrane transport in the camel kidney, and RTN analyses confirmed alterations in the transcriptional machinery involved in cholesterol synthesis. These data were validated by RT-qPCR. Based on our hypothesis of a role for cholesterol during dehydration, we identified DEGs with roles in the countercurrent multiplication process which are affected by changes in the level of cholesterol. Thus, we further validated differentially expressed genes with known roles in water conservation which are affected by changes in cholesterol levels. Our datasets suggest that suppression of cholesterol biosynthesis may facilitate water retention in the kidney by indirectly facilitating the AQP2-mediated water reabsorption.

overall_design: Nineteen male dromedary camels aged 4-5 years, body weight range 276-416 kg, were used in the present study. The camels were supplied with alfalfa hay as feed and ranch-housed in the United Arab Emirates. Veterinary supervision was provided throughout the experimental period and no signs of distress or illness were identified. After a short adaptive period, the camels were divided into 3 groups, control (n=5), dehydrated (n=8) and rehydrated (n=6). The control group had free access to food and water during the entire experimental period. The dehydrated group was water-deprived but had ad libitum access to food for 20 days. Meanwhile the rehydrated group was subjected to the same protocol as the dehydrated animals followed by ad libitum water supply for 3 additional days. After the experimental period, the camels were sacrificed in the local central abattoir for human consumption in April 2016. Kidney samples were harvested within 1 hour after killing the animals, immediately frozen in liquid nitrogen and kept at -80°C for later physiological, histological, morphological and molecular analysis. Samples were shipped frozen on dry ice to the University of Bristol under the auspices of a DEFRA Import Licence (TARP/2016/063). This study was approved by the Animal Ethics Committee of the United Arab Emirates University (approval ID: AE/15/38) and the University of Bristol Animal Welfare and Ethical Review Board. Total RNA was extracted from fresh frozen kidney medulla and cortex of 5 control, 5 dehydrated and 5 rehydrated camels (for a total of 30 samples). These 15 animals were randomly selected out of the 19 animals included in the experimental set up while the remaining 4 were used for preliminary analyses only. Frozen tissue was added to a pre-cooled mortar containing a small volume of liquid nitrogen. Tissue was then grounded to a fine powder using a pestle and the nitrogen was allowed to evaporate. The powdered tissue was placed into pre-chilled tubes on dry ice and stored at -80°C. For RNA extraction, 1ml of Qiazol (79306, Qiagen) was added to 100mg of powdered tissue, then immediately vortexed for 2 minutes, then incubated on ice for 10 minutes. Lysed samples were spun at 12000xg for 10 minutes at 4°C and the supernatant was transferred to a new tube. 1/5 volume Chloroform (22711.244, VWR) was added to each sample and vortexed for 15 seconds. Samples were then spun at 12000xg for 15 minutes at 4°C. 350ml of the upper phase was removed and mixed with an equal volume of absolute ethanol. RNA was extracted using ZymoTM Direct-Zol RNA miniprep (Zymo Research) as per the manufacturer’s instructions. Total RNA concentration and 260/280 ratios were measured using a Nanodrop 2000c (Thermo Scientific). Illumina Sequencing was performed by Bristol Genomics Facility, University of Bristol, using the poly-A selection method for library preparation and the Illumina NextSeq500 system. RIN were 8.1 (SD=0.5), 7.7 (SD=0.2) and 7.6 (SD=0.6) for control, dehydrated and rehydrated cortex samples, and 8.5 (SD=0.5), 8.8 (SD=0.2) and 8.7 (SD=0.4) for control, dehydrated and rehydrated medulla samples, respectively.

last: Alvira-Iraizoz

first: Ben

middle: T

last: Gillard

first: David

last: Murphy

first: Michael

last: Greenwood

first: Abdu

last: Adem


title: RFX7, ANKRA2, and p53-regulated transcriptome in RPE-1

status: Public on Jun 20 2021

city: Jena

first: Martin

last: Fischer

state: Thuringia

address: Beutenbergstraße 11

department: Computational Biology

country: Germany

institute: Leibniz Institute on Aging - Fritz Lipmann Institute (FLI)

type: Expression profiling by high throughput sequencing

summary: Identification of the RFX7-regulated transcriptome in Nutlin-3a and DMSO control treated RPE-1 cells

overall_design: RNA-seq (PolyA) from Nutlin-3a and DMSO control treated RPE-1 cells transfected with siControl or siRFX7

first: Konstantin

last: Riege

first: Steve

last: Hoffmann


title: Single cell RNA-seq data comparing lesional (papules) and non-lesional skin biopsies of acne patients

status: Public on May 31 2021

city: Los Angeles

first: Tran

middle: Hue

last: Do

state: CA

address: 615 Charles E Young Dr

country: USA

institute: David Geffen School of Medicine

summary: We performed single-cell RNA seq analysis on skin biopsies from six acne patients with a total of 32,966 cells from lesional skin and 29,202 cells from non-lesional skin using 10X Genomics. Gene expression data derived from cells in both lesional and non-lesional skin were aligned and projected onto a two-dimensional space using UMAP (Uniform Manifold Approximation and Projection). Unsupervised clustering revealed eight major clusters corresponding to seven different cell types lymphocytes, myeloid cells, keratinocytes, fibroblasts, endothelial cells, smooth muscle cells, and melanocytes.

overall_design:
Examine the transcriptomics differences in acne lesional and non-lesional skin

The meta_donorlesional.csv file (containing the average counts of the data separated by donor and lesionality) was added on Mar 5, 2023.

middle: H

first: Feiyang

last: Ma

first: Carol

last: Cheng

first: Jenny

last: Kim

first: Matteo

last: Pellegrini

first: Robert

middle: L

last: Modlin


title: Stem-like cells drive NF1-associated MPNST functional heterogeneity and tumor progression

status: Public on Apr 07 2021

city: New Brunswick

first: Xiyuan

last: Zhang

state: NJ

address: 195 Little Albany St.

department: Pediatric Hematology/Oncology

institute: Rutgers Cancer Institute

summary: NF1-associated malignant peripheral nerve sheath tumors (MPNST) are the major cause of mortality in neurofibromatosis. MPNST arise from benign peripheral nerve plexiform neurofibromas (PN) which originate in the embryonic neural crest cell lineage. Using reporter transgenes that label early neural crest lineage cells in multiple NF1 MPNST mouse models, we discovered and characterized a rare MPNST cell population with stem cell-like properties that is essential for tumor initiation and relapse. Following isolation of these cells we derive a cancer stem cell specific gene expression signature that includes consensus embryonic neural crest genes and we also identify Nestin as a novel marker for the MPNST cell of origin. Finally, application of the mouse cancer stem cell signature to single cell sequencing data from a rare NF1-associated MPNST precursors called atypical neurofibromatosis neoplasms of uncertain biologic potential (ANNUBP), identifies preformed unsupervised gene expression cell clusters. Enrichment of the cancer stem cell signature in cognate human tumors supports the generality and relevance of cancer stem cells to therapy development.

overall_design: Single-cell transcriptomic profiling of human ANNUBP

first: Jack

last: Shern


title: HDAC4 controls senescence and aging by safeguarding the epigenetic identity and  ensuring the genomic integrity

status: Public on Apr 06 2021

city: udine

first: raffaella

last: picco

address: piazzale kolbe 4

department: department of medical and biological sciences

country: Italy

institute: university of Udine

summary:
Purpose: Define HDAC4 signature
Outcome: HDAC4 is required for the repression of a senescence signature. HDAC4 KO promotes the expression of inflammatory genes, the derepression of ERVs and the accumulation of DNA damage. All together these signalling pathways lead to permanent cell-cycle arrest in low grade tumor cells and pre-transformation models, while they weaken the replicative potential of primary normal cells.

overall_design: 6 clones of SK-LMS-1 cells were created. Two controls: one expressing Cas9 as control, the other expressing Cas9 + sgRNA1. 4 HDAC4 KO clones were generated: 76 and 1231 (achieved through sgRNA1); 205 and 1254 (achieved through sgRNA2). Two biological replicates per clone were analyzed.

first: E

last: Di Giorgio

first: H

last: Paluvai

last: Dalla

first: A

last: Renzini

first: V

last: Moresi

first: L

last: Ranzino

last: Cutano

first: R

last: Picco

first: C

last: Brancolini


title: Association with YY1 and the PRC2 complex mediates the transcriptional repressive functions of YAP/TEAD

city: Jupiter

first: Joseph

last: Kissil

state: FL

address: 130 Scripps Way #2C1

department: Department of Cancer Biology

institute: The Scripps Research Institute, Scripps Florida

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Inhibition of cell proliferation through cell-cell contact (contact-inhibition or CI) is a major mechanism regulating development and homeostasis in multicellular organisms. However, the molecular mechanisms mediating CI remain largely unknown. The Hippo pathway has emerged as a central regulator of organ size and tissue homeostasis, by controlling the localization and activity of the transcriptional regulator YAP. As previous studies indicated YAP is regulated by cell-cell contact, we assessed the function of YAP in this context. Here we show that in addition to its function as a transcriptional activator, YAP functions as a repressor of a significant number of genes including the cyclin-dependent kinase (Cdk) inhibitor p27. We find that inhibition of p27 depends on the Ying-Yang 1 (YY1) transcription factor and recruitment of the Polycomb repressive complex (PRC2). Moreover, YAP marks co-localizes with YY1 and EZH2 marks on the genome to transcriptionally repress a network of genes mediating a host of cellular functions, including key regulators of the cell cycle. This work highlights a broad and underappreciated aspect of YAP function as a transcriptional repressor and details a mechanism through which these functions are mediated.

overall_design: YAP, YY1, and EZH2 ChIP-Seq

first: Sany

last: Hoxha

first: Scott

last: Troutman

first: William

middle: W

last: Ja

first: Michael

middle: S

last: Kareta


title: Bariatric surgery reduces obesity associated breast cancer and enhances response to immunotherapy

status: Public on May 21 2021

city: Memphis

first: Liza

last: Makowski

state: Tennessee

address: 19 South Manassas St

department: Medicine- Heme Onc

institute: UTHSC

summary: This SuperSeries is composed of the SubSeries listed below. -GEO GSE174760 (bulk mammary fat pad RNA), GSE174761 (bulk tumor RNA),

overall_design: Refer to individual Series -GEO GSE174760 (bulk mammary fat pad RNA), GSE174761 (bulk tumor RNA),


title: Tumor suppressor p53 employs RFX7 and ANKRA2

status: Public on Jun 17 2021

first: Martin

last: Fischer

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

overall_design: Refer to individual Series


title: Single cell RNA sequencing of CD45.2+ endogenous immune cells following treatment with CAR-T cells

status: Public on Sep 01 2021

city: Philadelphia

first: Lexus

last: Johnson

state: Pennsylvania

address: 421 Curie Blvd, 532

department: Radiation Oncology

institute: University of Pennsylvania

summary: The goal of this study was to assess the consequences of RNA delivery via CAR-T cell on endogenous immune cells within the B16 tumor microenvironment. RN7SL1 RNA-producing CAR-T cells are the relevant experimental condition, while control scramble RNA and No RNA 19BBz CAR-T cells are also included.

overall_design: Single-cell mRNA profiles. 10X 3' v2.0 chemistry utilized.

first: Andy

middle: J

last: Minn

middle: R


title: scRNA-seq profiling of breast cancer tumors, BRCA1 mutant pre-neoplastic mammary gland cells and normal mammary gland cells

status: Public on Mar 19 2021

city: Parkville

first: Gordon

middle: K

last: Smyth

state: Vic

address: 1G Royal Pde

department: Bioinformatics

country: Australia

institute: Walter and Eliza Hall Institute of Medical Research

summary: This study presents a single cell transcriptome map of nearly 430,000 cells encompassing normal breast at different hormonal stages, preneoplastic BRCA1+/- tissue, the major clinical subtypes of breast cancer, and matching pairs of tumors and involved axillary lymph nodes. Comparison of normal tissue specimens according to menopausal status primarily revealed changes in the stroma. Although there were modest changes in the microenvironment of preneoplastic BRCA1+/- versus normal tissue, a profound increase in infiltrating immune cells and a concomitant decrease in fibroblasts accompanied the transition to neoplasia. Single cell profiling of 32 tumors representing treatment-naive ER+, HER2+, triple negative (TN) breast cancers revealed equivalent diversity between tumor cells across the subtypes, each comprising a broad cluster and a prominent subset of cycling cells. In the immune landscape of tumors, highly proliferative T cells characterize TN and HER2+ tumors, whereas cycling tumor-associated macrophages featured in ER+ tumors. Copy number variant and scRNA-seq analysis of paired ER+ tumors and lymph node (LN) samples revealed either collective migration of primary tumor cells into LNs or seeding by genetically distinct clones. This large-scale integration of patient samples provides a high resolution map of cell diversity for normal and cancerous human breast.

overall_design:
The data provides 69 scRNA-seq profiles using the 10X Genomics Chromium platform, comprising a total of 421,761 cells from 52 patients. This includes profiles of 4 TNBCs, 4 BRCA1 TNBCs, 6 HER+ tumors, 19 ER+ tumors and 6 lymph-node metastases of ER+ tumors. It also includes profiles of total mammary gland cells from 13 normal patients without breast cancer, of epithelial mammary gland cells from 11 normal patients, and of total mammary gland cells from 4 preneoplastic patients with BRCA1 mutations.

Detailed cell annotation and downstream Seurat analysis objects are available from Chen et al (Scientific Data, 2022, https://doi.org/10.1038/s41597-022-01236-2 ).

Note from submitter: we are unable to upload the raw data files because of privacy issues with human samples.

first: Yunshun

last: Chen

first: Bhupinder

last: Pal

first: Jane

middle: E

last: Visvader


title: TDP-43 Interactor and Motor Neuron Tagged Ribosome Affinity Purification in a Drosophila Model of ALS

status: Public on Mar 31 2021

city: Phoenix

first: Eric

last: Alsop

state: AZ

address: 445 N 5th St

institute: TGen

summary:
We report the enrichment of mRNAs with motor neuron specific TDP-43 and tagged ribosomes in control as well as multiple models of TDP-43 induced neurodegeneration.

Amyotrophic lateral sclerosis (ALS) is a genetically heterogeneous neurodegenerative disease in which 97% of patients exhibit cytoplasmic aggregates containing the RNA binding protein TDP-43. The goal of this study is to understand the translational consequences of TDP-43 pathology. Using the GAL4-UAS system, we expressed TDP-43WT and TDP-43G298S in the motor neurons of our drosophila to induce ALS-like neurodegeneration. TDP-43 was immunoprecipitated from the larvae at the 3rd instar stage; TDP-43 associated mRNAs, the whole larvae input, and ventral nerve cords of the same genotype were then sequenced. To identify translational changes we conducted TRAP (translating ribosome affinity purifications) in 3rd instar larvae by immunoprecipitating the motor neuron specific tagged ribosomal subunit RpL10-GFP in both ALS models as well as a RpL10-GFP control. The RpL10-GFP associated mRNAs, the whole larval input, and ventral nerve cords of the same genotype. From this data, we identified both compensatory alterations to translation induced by TDP-43 pathology and direct targets of TDP-43 mediated translational inhibition.

overall_design: Examination of mRNA association with TDP-43 and tagged ribosomal subunit RpL10 in motor neurons during TDP-43 induced neurodegeneration. The antibody used for both IPs was rabbit anti-GFP Lifetech A11122.

first: Erik

last: Lehmkuhl


title: Gene expression profiling of mouse embryonic kidney (E12.5) treated with CHIR99021 or DMSO

status: Public on May 01 2021

city: Shenzhen

first: Yifan

last: Li

state: Guangdong

address: No.89 Taoyuan Road, Nanshan District

department: Department of Laboratory Medicine

country: China

institute: Shenzhen Nanshan People's Hospital and the Affiliated Shenzhen Sixth Hospital of Guangdong Medical University

summary: Purpose: To investigate GSK3 inhibitor effect on gene expression during renal development. Methods: mRNA profiles of in-vitro organ culture of mouse embryonic kidney (E12.5) treated with 5 µM CHIR99021 or 0.1% DMSO for 72 hours were generated by deep sequencing in quadruplicate. Results: When comparing CHIR99021 group to DMSO group, in 30890 genes tested, 950 genes were upregulated, and 1,879 genes were downregulated, with a fold change ≥2 and p (padj value) <0.05.

overall_design: mRNA profiles of mouse embryonic kidney (E12.5) treated with 5 µM CHIR99021 (4 samples) or 0.1% DMSO (4 samples) for 72 hours were generated by deep sequencing in quadruplicate


title: Epidermal PPARγ is a key homeostatic regulator of cutaneous inflammation and barrier function in mouse skin

status: Public on Aug 31 2021

city: Indianapolis

first: Raymond

last: Konger

state: IN

address: 975 West Walnut Street

department: Pathology & Laboratory Medicine

institute: Indiana University School of Medicine

summary: Both agonist studies and loss-of-function models indicate that PPARγ plays an important role in cutaneous biology. Since PPARγ has a high level of basal activity, we hypothesized that epidermal PPARγ would regulate normal homeostatic processes within the epidermis.  In this current study, we performed mRNA sequencing and differential expression analysis of epidermal scrapings from knockout mice and wildtype littermates.  Pparg-/-epi mice exhibited a 1.5-fold or greater change in the expression of 11.8% of 14,482 identified transcripts. Up-regulated transcripts included those for a large number of cytokines/chemokines and their receptors, as well as genes associated with inflammasome activation and keratinization. Several of the most dramatically up-regulated pro-inflammatory genes in Pparg-/-epi mouse skin included Igfl3, 2610528A11Rik, & Il1f6.  RT-PCR was performed from RNA obtained from non-lesional full-thickness skin and verified a marked increase in these transcripts, as well as transcripts for Igflr1, which encodes the receptor for Igfl3, and the 2610528A11Rik receptor (Gpr15).  Transcripts for Il4 were detected in Pparg-/-epi mouse skin, but transcripts for Il17 & Il22 were not detected.   Down-regulated transcripts included sebaceous gland markers and a number of genes associated with lipid barrier formation.  The change in these transcripts correlates with an asebia phenotype, increased transepidermal water loss, alopecia, dandruff and the appearance of spontaneous inflammatory skin lesions. Histologically, non-lesional skin showed hyperkeratosis, while inflammatory lesions were characterized by dermal inflammation and epidermal acanthosis, spongiosis, and parakeratosis.   In conclusion, loss of epidermal Pparg alters a substantial set of genes that are associated with cutaneous inflammation, keratinization and sebaceous gland function. This data indicates that epidermal PPARγ plays an important role in homeostatic epidermal function, particularly epidermal differentiation, barrier function, sebaceous gland development and function, and inflammatory signaling.

first: Edward

last: Simpson


title: Pancreatic progenitor epigenome maps prioritize type 2 diabetes risk genes with roles in development

status: Public on Jan 19 2021

city: La Jolla

first: Maike

last: Sander

address: 2880 Torrey Pines Scenic Dr.

institute: UC San Diego

summary: Genetic variants associated with type 2 diabetes (T2D) risk affect gene regulation in metabolically relevant tissues, such as pancreatic islets. Here, we investigated contributions of regulatory programs active during pancreatic development to T2D risk. Interrogation of chromatin maps from developmental precursors throughout pancreatic differentiation of human embryonic stem cells (hESCs) identifies enrichment of T2D variants in pancreatic progenitor-specific stretch enhancers that are not active in islets. Genes associated with progenitor-specific stretch enhancers are predicted to regulate developmental processes, most notably tissue morphogenesis. Through gene editing in hESCs, we demonstrate that progenitor-specific enhancers harboring T2D-associated variants regulate cell polarity genes LAMA1 and CRB2. Knockdown of lama1 or crb2 in zebrafish embryos causes a defect in pancreas morphogenesis and impairs islet cell development. Together, our findings reveal that a subset of T2D risk variants specifically affects pancreatic developmental programs, suggesting that dysregulation of developmental processes can predispose to T2D.

overall_design: Identification and functional characterization of T2D risk loci located in pancreatic progenitor-specific regulatory elements.

first: R

last: Geusz

first: M


title: Long-read transcriptome sequencing reveals abundant promoter diversity in distinct molecular subtypes of gastric cancer

status: Public on Dec 10 2020

city: Singapore

first: Kie Kyon

last: Huang

state: Select State/Province

address: 8 College Road

country: Singapore

institute: Duke-NUS Graduate Medical School

summary: We perform full-length transcriptome analysis across 10 GC cell lines.

overall_design: We combined the Iso-Seq technology with short read methods to survey the full-length GC transcriptome landscape.

first: Patrick

last: Tan


title: miRNA expression of the isolated human platelet-derived microparticle

status: Public on Sep 07 2020

city: Beijing

first: Mingyi

last: Qu

state: Beijing

address: 27 Taiping Road

institute: Institute of Health Service and Transfusion Medicine

summary: To analysis of potential functional components in PMPs to miRNAs, we have employed miRNA microarray expression profiling as a discovery platform to identified the miRNA content of PMPs.Human cord blood from healthy donors was used to isolated platelets and platelet-derived microparticles (PMPs) were isolated from activated platelets. First, for platelet isolation and purification, human platelets were isolated from the supernatant of umbilical cord blood after Ficoll-Hypaque density gradient centrifugation and pelleted by centrifugation at 2,000 × g for 20 min at RT. Second, the platelets were resuspended in saline (pH=7.4) containing 1 mM calcium and 1 U per mL thrombin for 15 min at 37°C. The PMPs were released into the supernatant. Contaminating remnant platelets were removed by centrifugation at 2,000 × g for 20 min at 4°C and filtered through a 0.8 μm filter unit (Millipore, America). Then, the supernatants containing PMPs were centrifuged at 20,000 × g for 120 min at 4°C.182 miRNAs were detected in the isolated human PMPs from five independent donors, although individual differences in miRNA expression were also observed. Thereafter, these miRNAs were ranked by expression level, and those expressed above the median level from each unique subject were considered to be abundantly expressed miRNAs. The intersection of abundantly expressed miRNAs in PMPs from each donor yielded 48 commonly expressed miRNAs in PMPs. Among these 48 miRNAs, miR-4454 ranked number 1, and its level was consistent in all samples examined.

overall_design: Five independent experiments were performed using different donors for this experiment.

first: Xiaoyan

last: Xie


title: Gene expression signatures for PMP treatment

summary: To identify the genes inversely regulated by PMPs, we performed a microarray for global gene expression profiling in CB-MNCs with/without PMP treatment. In MNCs treated with PMPs, 129 genes were downregulated.

overall_design: 1×106 CB-MNCs from three different donors were isolated and cultured in megakaryocytic induction medium supplemented with 20 μL of saline or an equivalent volume of saline containing 2×106 PMPs from another 2 donors.


title: Transcriptional Profiling Uncovers Human Hyalocytes as a Unique Innate Immune Cell Population

status: Public on Oct 05 2020

city: Freiburg

first: Clemens

last: Lange

address: Kilianstraße 5

department: Klinik für Augenheilkunde

institute: Uniklinik Freiburg

summary: Purpose: To decipher the transcriptional signature of macrophages of the human vitreous, also known as hyalocytes, and compare it to the profiles of other myeloid cell populations including human blood-derived monocytes, macrophages and brain microglia.  Methods: This study involves a total of 13 patients with disorders of the vitreoretinal interface undergoing vitrectomy at the University Eye Hospital Freiburg between 2018 and 2019. Vitreal hyalocytes were characterized by fluorescence-activated cell sorting (FACS) and isolated as CD45+CD11b+CX3CR1+Mat-Mac+ cells using a FACS-based sorting protocol. RNA extraction, library preparation and RNA sequencing were performed and the sequencing data was analyzed using the Galaxy web platform. The human hyalocyte transcriptome was compared to the transcriptional profile of human macrophages, brain microglia and blood-derived monocytes obtained from public databases. Protein validation for selected factors was performed by immunohistochemistry on paraffin sections from three human donor eyes.  Results: On average, 383 ± 233 hyalocytes were isolated per patient, resulting in 128 pg/µl ± 76 pg/µl total RNA per sample. RNA sequencing revealed SPP1, FTL and CD74 as the most abundantly expressed genes in hyalocytes, which was confirmed by immunofluorescence. Gene ontology (GO) enrichment analysis showed that biological processes such as “humoral immune response”, “leukocyte migration” and “antigen processing and presentation of peptide antigen” (adjusted p < 0.001) are dominating in vitreal hyalocytes. While the comparison of the gene expression profiles of hyalocytes and other myeloid cell populations, such as brain microglia or blood-derived monocytes, showed an overall strong similarity (R2 > 0.637, p < 0.001), hyalocytes revealed significant differences with respect to common leukocyte-associated factors. In particular, transcripts involved in the immune privilege of the eye, such as POMC, CD46 and CD86, were significantly increased in hyalocytes compared to other myeloid cell subsets.  Conclusion: Human hyalocytes represent a unique and distinct innate immune cell population specialized and adapted for the tissue-specific needs in the human vitreous. Vitreal hyalocytes are characterized by a strong expression of genes related to antigen processing and presentation as well as immune modulation. Thus, hyalocytes may represent a clearly underestimated mediator in vitreoretinal disease and for the immune privilege of the eye.

overall_design: After quality control, 9 hyalocyte samples from 9 patients were included in this study

first: Stefaniya

last: Boneva

first: Julian

last: Wolf

first: Anja

last: Schlecht

first: Gabriele

last: Prinz

first: D

last: Rosmus

first: Ingo

last: Hilgendorf

first: Andreas

last: Stahl

first: Yannik

last: Laich

first: Myriam

last: Boeck

first: Peipei

last: Zhang

first: Thomas

last: Reinhard

first: Hansjürgen

last: Agostini

first: James

last: Bainbridge

first: Peter

last: Wieghofer

first: Günther

last: Schlunck


title: Increased processing of SINE B2 non coding RNAs unveils a novel type of transcriptome de-regulation underlying amyloid beta neuro-pathology

status: Public on Nov 19 2020

city: Winnipeg

first: Athanasios

last: Zovoilis

state: MB

address: 745 Bannatyne Ave

department: Biochemistry and Medical Genetics

country: Canada

institute: University of Manitoba

summary: More than 97% of the mammalian genome is non-protein coding, and repetitive elements account for more than 50% of noncoding space. However, the functional importance of many non-coding RNAs generated by these elements and their connection with pathologic processes remains elusive. We have previously shown that B2 RNAs, a class of non-coding RNAs that belong to the B2 family of SINE repeats, mediate the transcriptional activation of stress response genes (SRGs) upon application of a stimulus. Notably, B2 RNAs bind RNA Polymerase II (RNA Pol II) and suppress SRG transcription during pro-stimulation state. Upon application of a stimulus, B2 RNAs are processed into fragments and degraded, which in turn releases RNA Pol II from suppression and upregulates SRGs. Here, we demonstrate a novel role for B2 RNAs in transcriptome response to amyloid beta toxicity and pathology in mouse hippocampus. In healthy hippocampi, activation of SRGs is followed by a transient upregulation of pro-apoptotic factors, such as p53 and miRNA-34c, which target SRGs creating a negative feedback loop that facilitates return to the pro-stimulation state. Using an integrative RNA genomics approach, we show that in mouse hippocampi with amyloid pathology and in an in vitro cell culture model of amyloid beta toxicity, this regulatory loop is dysfunctional due to increased levels of B2 RNA processing, constitutively elevated SRG expression and high p53 levels. Evidence indicates that Hsf1, a master regulator of stress response, mediates B2 RNA processing in cells, and is upregulated during amyloid toxicity accelerating the processing of SINE RNAs and SRG hyper-activation. This data attributes a role to SINE RNA processing in a pathological process as well as a new function to Hsf1 that is independent of its transcription factor activity. Our study reveals that in mouse, SINE RNAs constitute a novel pathway deregulated in amyloid beta pathology, with potential implications for similar cases in the human brain, such as Alzheimer’s disease (AD).

overall_design: In this study, we employed a transgenic mouse model of amyloid pathology, APP NL−G−F (APP) (Saito et al., 2014) and the respective wild type control C57BL/6J (WT). We have tested three different mouse ages that correspond to different phases of amyloid beta pathology: i) pre-symptomatic stage with undetectable (very low) amyloid plaque load, (3 months - 3m/ APP: 3x mice, WT:2x mice), ii) stage of symptom manifestation (that coincides with the active neurodegeneration phase and appearance of amyloid plaques (6 months - 6m/ APP: 3x mice, WT:3x mice), and iii) terminal stage of the pathology (12 months - 3m/ APP: 3x mice, WT:3x mice). Whole hippocampi, (hippocampi separated from both the left (L) and right (R) hemishere of each mouse and pooled together), represented as hippocampus L+R, were isolated from the above mice, and the extracted RNA from each hippocampus was separated into two samples: one enriched in short-RNAs (sR) and one in long-RNAs  (LR). Each sample was then subjected to  next-generation sequencing (short-RNA-seq and long-RNA-seq, respectively).  We also employed the hippocampal HT-22 cell line  (Davis & Maher, 1994). We treated HT22 cells with either an LNA against Hsf1 (anti-Hsf1) or a scramble LNA (ctrl) followed by incubation with amyloid beta peptides (42/ 1-42 aa) or a control peptide with an inverted amino acid sequence (R/ reverse 42-1). Biological replicates were as follows: 42/Ctrl: x4, R/Ctrl: x4, 42/Anti-Hsf1:x3, R/Anti-Hsf1:x3  Subsequently RNA was extracted, separated into short-RNA and long-RNA samples as above, and subjected to next generation sequencing (short-RNA-seq and long-RNA-seq, respectively).

first: Yubo

last: Cheng

first: Luke

last: Saville

first: Babita

last: Gollen

first: Christopher

last: Isaac

first: Jogender

last: Mehla

first: Majid

last: Mohajerani


title: Macrophage Exosomes Resolve Atherosclerosis by Regulating Hematopoiesis and Inflammation via MicroRNA Cargo

status: Public on Aug 06 2020

first: Eric

last: Alsop

type: Non-coding RNA profiling by high throughput sequencing

summary: Developing strategies that promote the resolution of vascular inflammation and atherosclerosis remains a major therapeutic challenge. Here, we show that exosomes produced by naive bone marrow-derived macrophages (BMDM-exo) contain anti-inflammatory microRNA-99a/146b/378a that are further increased in exosomes produced by BMDM polarized with IL-4 (BMDM-IL-4-exo). These exosomal microRNAs suppress inflammation by targeting NF-kB and TNF-a signaling and foster M2 polarization in recipient macrophages. Repeated infusions of BMDM-IL-4-exo into Apoe_x0001_/_x0001_ mice fed a Western diet reduce excessive hematopoiesis in the bone marrow and thereby the number of myeloid cells in the circulation and macrophages in aortic root lesions. This also leads to a reduction in necrotic lesion areas that collectively stabilize atheroma. Thus, BMDM-IL-4-exo may represent a useful therapeutic approach for atherosclerosis and other inflammatory disorders by targeting NF-kB and TNF-a via microRNA cargo delivery.

overall_design: 14 samples were analyzed. 6 samples were cell lysates (3 controls, 3 stimualted macrophages). 8 samples were extracellular exosomes (4 controls, 4 stimulated macrophages)

first: Robert

last: Raffai

first: Kendall

last: Jensen

first: Laura

last: Bouchareychas


title: Methylation and gene expression data obtained from Dnmt3b+/+, Dnmt3bD/D and Dnmt3bCI/CI MYC induced T-cell lymphomas (MTCLs).

status: Public on Dec 30 2020

city: Gainesville

first: Rene

last: Opavsky

address: 2033 Mowry rd, CGRC r..265

department: Anatomy and cell biology

institute: University of FLORIDA

summary: DNA methylation has suppressive effects on gene transcription and it is involved in a variety of physiologic processes, including development and cancer. As we and others demonstrated, Dnmt3b is a tumor suppressor in oncogene-driven lymphoid and myeloid malignancies in mice. Due to numerous activities such as methylation-dependent and independent repression and accessory functions, it is difficult to pinpoint physiological processes solely dependent on catalytic activity of Dnmt3b. By utilizing our new mouse model expressing catalytically inactive Dnmt3b at physiological levels we identified genome-wide methylation changes and aberrant gene expression profiles that are specific to catalytic activity of DNMT3b.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: We performed WGBS and RNA-seq analysis on Dnmt3b+/+, Dnmt3bD/D and Dnmt3bCI/CI MYC-induced T-cell lymphoma samples isolated from lymph nodes of terminally sick mice. WGBS experiments were performed in biological duplicates, RNA-seq experiments in triplicates. In addition we performed RNA-seq on human peripheral T-cell lymphomas (hPTCLs) and normal human CD8+ and CD4+ T-cells.

first: Katarina

last: Lopusna

first: Pawel

last: Nowialis

first: Jana

last: Opavska

first: Ajay

last: Abraham

first: Alberto

last: Riva


title: Identification and functional analysis of a potential key circRNA in aged mice with perioperative neurocognitive dysfunction

status: Public on Aug 10 2021

city: beijing

first: huihui

last: miao

address: 10th Tieyi road

institute: Capital medical university,Beijing Shijitan Hospital

summary: Perioperative neurocognitive dysfunction (PND) is emerging as a significant complication of surgery in elderly patients. However, the molecular mechanisms of PND are not well known. Here we applied microarray analysis to identify circular RNAs (circRNAs) in hippocampus from a mouse model of PND and control mice. Then, the dysregulated circRNAs were confirmed via quantitative real-time polymerase chain reaction (qRT-PCR). Then, Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were performed to probe the vital functions of dysregulated genes.

overall_design: We randomly selected 6 C57 male mice (age 18 months) and divided them into two groups: control group (n=3) and surgery group (n=3). The surgical procedures of intramedullary fixation for open tibial fracture were performed to simulate a mouse model of POCD. The hippocampal tissues of the surgery and control group mice were harvested on day 3 after the surgery for RNA extraction and hybridization. The RNA labeling and array hybridization were performed by KangChen Bio-tech, Shanghai, PR China.

first: Yu-Qing

last: Wu

first: Qiang

last: Liu

first: Hai-Bi

last: Wang

first: Chen

last: Chen

first: Hui

last: Huang

first: Yi-Man

last: Sun

first: Lin-Hui

last: Ma

first: Jie

last: Wan

first: Yin-Ying

first: Hui-Hui

last: Miao


title: Longitudinal single-cell epitope and RNA-sequencing reveals the immunological impact of type 1 interferon autoantibodies in critical COVID-19

status: Public on Mar 09 2021

city: San Francisco

first: George

middle: Christopher

last: Hartoularos

address: 513 Parnassus Ave S965F

department: Graduate Division

institute: University of California, San Francisco

summary: Type I interferon (IFN-I) neutralizing autoantibodies have been found in some critical COVID-19 patients; however, their prevalence and longitudinal dynamics across the disease severity scale, and functional effects on circulating leukocytes remain unknown. Here, in 284 COVID-19 patients, we found IFN-I autoantibodies in 19% of critical, 6% of severe and none of the moderate cases. Longitudinal profiling of over 600,000 peripheral blood mononuclear cells using multiplexed single- cell epitope and transcriptome sequencing from 54 COVID-19 patients, 15 non-COVID-19 patients and 11 non-hospitalized healthy controls, revealed a lack of IFN-I stimulated gene (ISG-I) response in myeloid cells from critical cases, including those producing anti-IFN-I autoantibodies. Moreover, surface protein analysis showed an inverse correlation of the inhibitory receptor LAIR-1 with ISG-I expression response early in the disease course. This aberrant ISG-I response in critical patients with and without IFN-I autoantibodies, supports a unifying model for disease pathogenesis involving ISG-I suppression via convergent mechanisms.

overall_design: Multiplexed droplet-based single-cell RNA and epitope sequencing from 79 individuals: 54 COVID positive patients, 15 COVID negative patients, and 11 healthy controls. Donor cells were multiplexed into 9 pools (i.e. runs 1, 2, 3, 4, 5, 7, 8, 9, 10) and each pool was distributed to several droplet reactions to yield 50 reactions total.

first: Monique

middle: G

last: van der Wijst

first: Sara

last: Vazquez

middle: C

first: Paul

last: Bastard

first: Tianna

last: Grant

first: Raymund

last: Bueno

first: David

last: Lee

first: John

last: Greenland

first: Yang

first: Richard

last: Perez

first: Anton

last: Ogorodnikov

first: Alyssa

last: Ward

first: Sabrina

middle: A

last: Mann

first: Kara

last: Lynch

first: Cassandra

last: Yun

first: Diane

middle: V

last: Havlir

first: Gabriel

last: Chamie

first: Carina

last: Marquez

first: Bryan

last: Greenhouse

first: Michail

last: Lionakis

first: Philip

last: Norris

first: Larry

last: Dumont

first: Kathleen

last: Kelly

first: Peng

last: Zhang

first: Qian

first: Adrian

last: Gervais

first: Tom

last: Le Voyer

first: Alexander

last: Whatley

first: Yichen

last: Si

first: Ashley

last: Byrne

first: Alexis

last: Combes

first: Yun

last: Song

first: Gabriela

last: Fragiadakis

first: Kirsten

last: Kangelaris

first: Carolyn

last: Calfee

last: Erle

last: Hendrickson


title: Whole transcriptome sequencing of 57 laryngeal squamous cell carcinoma and paired adjacent normal tissues

status: Public on Jun 17 2020

city: Taiyuan

first: Yongyan

last: Wu

state: Shanxi

address: No.85 South Jiefang Road, Taiyuan, Shanxi, China

department: Department of Otolaryngology Head & Neck Surgery, The First Hospital

institute: Shanxi Medical University

summary: Laryngeal squamous cell carcinoma (LSCC) is a common form of head and neck cancer with poor prognosis. However, the mechanism underlying the pathogenesis of LSCC remains unclear. We performed high throughout transcriptome sequencing to identify lncRNA and mRNA that associated with LSCC progression.Transcriptome sequencing were performed on a cohort of LSCC tissues (57 samples) and paired adjacent normal mucosa tissues (57 samples).

overall_design: Expression of lncRNA and mRNA in 57 LSCC and 57 paired adjacent normal mucosa tissues was examination by high throughout sequencing.

first: Wei

last: Gao

first: Binquan

last: Wang

first: Qinli

last: Zhao


title: Real-time quantitative PCR analysis of rat aorta samples after stent deployment

status: Public on Apr 30 2021

city: New York

first: Shiqi

last: Hu

state: NY

address: 3960 Broadway Rm 430

institute: Columbia University

summary: Bare Metal Stents (BMS), Drug Eluting Stent (DES) and Exosomes Eluting Stent (EES) were placed in rat abdominal aorta for one week. Then total RNA of aortas was extracted. We used ScienCell's GeneQuery Rat Macrophage Polarization Markers qPCR Array Kit to quantitate gene expression of macrophage relevant genes.

overall_design: qPCR gene expression profiling. Four rats per group were used and treated with BMS, DES and EES respectively. Equal amount total RNA from each sample was pooled prior to gene expression analysis.

first: Hu

last: Shiqi


title: Genome wide methylation analysis of aged uterus and decidua

status: Public on Mar 02 2020

city: Calgary

first: Myriam

last: Hemberger

state: Alberta

address: 3330 Hospital Dr NW

institute: University of Calgary

type: Methylation profiling by high throughput sequencing

summary: We use MeDIP-sequencing to measure global DNA methylation (5mC) in the uteri of young and aged C57BL/6 mice at day 3.5 (E3.5) of pregnancy, and of young and aged decidua at day 11.5 (E11.5) of pregnancy

overall_design: For E3.5 uterus MeDIP-seq data, we generated biological replicates from 3 young (8-20 week old) and 5 aged (41-49 week old) mice. For E11.5 data, we generated biological replicates of 6 deciduae from 3 litters (2 from each litter) from young mothers (9-10 weeks, n=3) and 10 deciduae from 5 litters of aged mothers (43-47 weeks, 2 deciduae from each litter). Aged E11.5 samples were split into 2 groups: those accompanying embryos that appeared normal (An, n=3) and those with morphologically abnormal embryos (Aa, n=3). One An and one Aa decidua was taken from each litter

first: Laura

last: Woods

first: Vicen

last: Perez-Garcia

first: Natasha

last: Morgan

last: Hembrger


title: The orchestrated cellular and molecular responses of the kidney to endotoxin define a precise sepsis timeline

status: Public on Jun 03 2020

first: Takashi

last: Hato

address: 950 W Walnut Street

department: Nephrology and Hypertension

summary: Utilizing single cell RNA sequencing, we demonstrated multiple time-anchored, cell-type specific events that are key to understand clinical features of sepsis.

overall_design:
Wild type mouse kidneys were harvested and used for single cell RNAseq to examine baseline gene expression patterns across 0,1,4,16,27,36, and 48 hour timepoints after endotoxin (LPS) administration.
Library kit used for this dataset: Chromium Single Cell 3' Reagent Kits V2 was used with read1 L=26 and read2 L=91 configuration.

first: Danielle

last: Janosevic

first: Thomas

last: McCarthy


title: The effects of chromosomal copy number variations (CNV) on transcriptional programs at single cell resolution in multiple myeloma

status: Public on Jan 13 2020

city: Toronto

first: Ali

last: Mahdipour Shirayeh

state: Ontario

address: 101 College St

department: Princess Margater Cancer Centre / Faculty of Medicine

institute: University Health Network / University of Toronto

summary: Chromosome copy number variations (CNV) are a near-universal feature of cancer however their specific effects on cellular function are poorly understood. Single-cell RNA sequencing (scRNA-seq) can reveal cellular gene expression however cannot directly link this to CNVs. Here we report scRNA-seq normalization methods that improve inter-cellular expression alignment, increasing the sensitivity of scRNA-seq for CNV detection. We additionally report sciCNV, a tool for inferring CNVs from scRNA-seq data. Together, these tools enable simultaneous profiling of DNA CNV and RNA within single cells. We apply these tools to multiple myeloma and examine the roles of pan cancer CNVs +8q and +1q. Cells with +8q23-24 upregulate MYC, MYC-target genes, mRNA translation, protein synthesis capacity and DEPTOR; and show reduced transcriptome size. Cells with +1q21-44 reconfigure translation to suppress unfolded protein stress and show increased proliferation, oxidative phosphorylation and MCL1. Overall, we report scRNA-seq methods that can reveal the function of CNVs in cancer.

overall_design: Single cell RNA-seq (10X Genomics) was used to profile the transcriptomes of plasma cells and B cells from the bone marrow of patients with multiple myeloma (MM). FACS was employed to enrich the profiled populations for the B cell - plasma cell lineage. Novel normalization methods (RTAM2) and single cell inferred copy number variation (sciCNV) methods were applied to the data to identify the effect of specific CNVs on transcriptional programs in MM cells. Normal plasma cells were identified by their expression of non-tumor immunoglobulin isotype and by their lack of tumor clone CNVs.

middle: M

last: Shirayeh

first: Rodger

last: Tiedemann


title: Small RNA sequencing of 57 laryngeal squamous cell carcinoma and paired adjacent normal tissues

last: Wu

summary: Laryngeal squamous cell carcinoma (LSCC) is a common form of head and neck cancer with poor prognosis. However, the mechanism underlying the pathogenesis of LSCC remains unclear. We performed high throughout sequencing to identify miRNA that associated with LSCC progression.Small RNA libraries were constructed followed by sequencing on a cohort of LSCC tissues (57 samples) and paired adjacent normal mucosa tissues (57 samples).

overall_design: Expression of miRNA in 57 LSCC and 57 paired adjacent normal mucosa tissues was examination by high throughout sequencing.

first: Xiwang

last: Zheng


title: Transcriptional profiling following knockdown of RNA binding proteins

status: Public on Jun 28 2020

city: Cleveland

first: Daniel

last: McGrail

state: Ohio

address: 9500 Euclid Avenue

department: Center for Immunotherapy and Precision Immuno-Oncology

institute: Cleveland Clinic

summary: Human cancer cell lines were profiled by RNAseq following knockdown of RNA binding proteins, BRCA1, BRCA2, or treatment with siCTRL

overall_design: Samples were run in biological duplicates with 1-2 siRNAs per cell line


title: Peripheral blood mononuclear cells as a source of cold exposure biomarkers

status: Public on Jan 08 2020

city: Wageningen

first: Evert

middle: M.

last: van Schothorst

address: De Elst 1

country: Netherlands

institute: Wageningen University

summary: Male ferrets, aged 3 months, were divided into two group: one group remained at 22 degrees Celsius, while the other group was acclimatized to 4 degrees Celsius for one week. After sacrification, inguinal and periaortic white adipose tissues were dissected, and peripheral blood mononuclear cells (PBMC) were isolated. The three tissues are used for RNA isolation and subsequent global gene expression profiling using custom Agilent ferret-specific 2x400K microarrays. Data analysis indicated that the cold exposure induce a clear gene expression response of some genes in the inguinal and periaortic white adipose tissue as in PBMC. These genes could be defined as a  biomakers of the effect of cold exposure in these cells.

overall_design: Ferrets, male, aged 3 months, were divided into two groups: one group remained at 22 degrees Celsius, while the other group was acclimatized to 4 degrees Celsius for one week. After sacrification, peripheral blood mononuclear cells (PBMC) were isolated and immediately snap frozen in liquid nitrogen. Total RNA was isolated, quantified and qualified, and subsequently used for global gene expression profiling using custom Agilent ferret-specific 2x400K microarrays.

first: Bàrbara

last: Reynés

first: Jaap

last: Keijer

first: Paula

last: Oliver

first: Andreu

last: Palou


title: Kidney organoid reproducibility across multiple human iPSC lines and diminished off target cells after transplantation revealed by single cell transcriptomics

status: Public on Nov 04 2019

city: Cambridge

first: Ayshwarya

last: Subramanian

state: MA

address: 415 Main Street

department: Klarman Cell Observatory

institute: Broad Institute

summary: Human iPSC-derived kidney organoids have the potential to revolutionize discovery, but assessing their consistency and reproducibility across iPSC lines, and reducing the generation of off-target cells remain an open challenge. Here, we used single cell RNA-Seq (scRNA-Seq) to profile 450,118 cells to show that organoid composition and development are comparable to human fetal and adult kidneys. Although cell classes were largely reproducible across iPSC lines, time points, protocols, and replicates, cell proportions were variable between different iPSC lines. Off-target cell proportions were the most variable. Prolonged in vitro culture did not alter cell types, but organoid transplantation under the mouse kidney capsule diminished off-target cells. Our work shows how scRNA-seq can help score organoids for reproducibility, faithfulness and quality, that kidney organoids derived from different iPSC lines are comparable surrogates for human kidney, and that transplantation enhances their formation by diminishing off-target cells.

overall_design: We have 49 organoids in total. We include 4 donors (AS, ThF, N1, N2; 2 males, 2 females) at 4 timepoints: 1 replicate each at the iPSC (Day 0), 1 replicate for 2 donors (N1, N2), 2 for the other two (AS, ThF) at  Day 7, 3 replicates each at Days 15 and 29. For one donor (AS), we include 2 experiments at D15 and D29. For one donor (ThF), we have extended culture experiments at D32 (3 replicates) and D51(1 replicate). For ThF, we generated D29 organoids (3 replicates) from a second protocol. We have 2 transplanted organoids at D29. Organoids were pooled on lanes using a randomized design to ensure that organoids replicates from an individual batch (donor, replicate, condition) were distributed across lanes.


title: Expression data from stratified mads-box (agl67) mutant and wild-type seeds, ABA-treated

status: Public on Dec 31 2019

city: Salamanca

first: Oscar

last: Lorenzo

address: C/ Río Duero, 12 Campus de Villamayor. Parque Científico

department: Dpt. Fisiologia Vegetal, Centro Hispano Luso de Investigaciones Agrarias (CIALE)

country: Spain

institute: Universidad de Salamanca

summary: The mads-box mutant line showed an abscisic acid (ABA)-insensitive phenotype. The AGAMOUS-LIKE 67 (AT1G77950) gene encodes a transcription factor that is nuclear-localized, as observed by transiently transformed epidermal onion cells, specifically expressed in seeds and involved in an ABA signaling pathway during seed germination (Fernández-Arbaizar et al.  2012). SALK_050367 seeds were obtained from the Arabidopsis Biological Resource Center, ABRC.

overall_design: To analyze AGAMOUS-LIKE 67 regulation of gene expression in a developmental time window of ABA responsiveness following breakage of seed dormancy (Lopez Molina et al. 2001, 2002), wild-type Col-0 and mads-box mutant seeds were stratified in water (4ºC, dark) during 3 days, and then transferred to light (22ºC, percival) in the presence of 5μM ABA for 3 hours. Three biological replicates were performed per seed type in order to get consistent results.

last: Osuna

first: Marta

last: Curto-Prieto

first: Luis

last: Sanz


title: Expression data from stratified anac089-2 mutant and wild-type seeds, ABA-treated.

summary: Through a genetic screening in 3μM (+)-S-ABA, we have isolated the anac089-2 mutant, which was obtained from fast neutron-mutagenized Col-0 M2 seeds. This mutant showed ABA-insensitive phenotypes in the transition from dormancy to germination. anac089-2 mutant line was subjected to mapping based on Col/Ler polymorphisms. This mutation was independently mapped to the top arm of Chromosome 5. The anac089-2 mutation is located in a 25 kb region between CAPS markers MWD9/EcoRV and MWD9-25.3/AccI. This 25 kb region contains 8 genes, and sequencing of these genes revealed that anac089-2 mutant contained a mutation in the At5g22290. This gene encodes ANAC089, a nuclear localized NAC transcription factor, with the deduced protein of 340 amino acids. Southern blot analysis suggests that anac089-2 mutation is a ~700 bp deletion that includes the C-terminal region. ANAC089 is involved in an ABA signaling pathway during seed germination and stress responses (Osuna et al., 2011).

overall_design: To analyze ANAC089 regulation of gene expression in a developmental time window of ABA responsiveness following breakage of seed dormancy (Lopez Molina et al 2001, 2002), anac089-2 mutant and wild-type Col-0 (background) seeds were stratified in water (4ºC, dark) during 3 days, and then transfered to light (22ºC, percival) in presence of 5μM ABA for 3 hours. Three biological replicates were performed in order to get consistent results.

first: Alejandro

last: Fernández-Arbaizar

first: Eiji

last: Nambara

first: Pablo

last: Albertos


title: RNA-seq experiment of shControl and shPHF2 NSCs

status: Public on Sep 10 2019

city: Barcelona

first: Marian

last: Martínez-Balbás

state: Barcelona

address: C/ Baldiri Reixac 15-21

department: Molecular Genomics

institute: IBMB-CSIC

summary: Histone H3 lysine 9 methylation (H3K9me) is essential for cellular homeostasis; however, its contribution to development is not well established. Here, we demonstrate that the H3K9me2 demethylase PHF2 is essential for neural progenitor proliferation in vitro and for early neurogenesis in the chicken spinal cord. Using genome-wide analyses and biochemical assays we show that PHF2 controls the expression of critical cell cycle progression genes, particularly those related to DNA replication, by keeping low levels of H3K9me3 at promoters. Accordingly, PHF2 depletion induces R-loop accumulation that leads to extensive DNA damage and cell cycle arrest. These data reveal a role of PHF2 as a guarantor of genome stability that allows proper expansion of neural progenitors during development.

overall_design: RNA-seq of shPHF2 in NSCs was performed using two biological replicates (shPHF2 rep1, shPHF2 rep2). shControl was used as a control

first: Stella

last: Pappa

first: Natalia

last: Padilla

first: Simona

last: Iacobucci

last: Vicioso

first: Elena

last: Alvarez de la Campa

first: Claudia

last: Navarro

first: Elia

last: Marcos

first: Xavier

last: de la Cruz

first: Marian A.

last: Martinez-Balbas


title: Gene expression analysis of inguinal white adipose tissue upon cold exposure in ferrets: mainly metabolism is effected

status: Public on Sep 07 2019

first: Evert

last: van Schothorst

summary: Male ferrets, aged 3 months, were divided into two group: one group remained at 22 degrees Celsius, while the other group was acclimatized to 4 degrees Celsius for one week. After sacrification, inguinal white adipose tissues were dissected, and used for RNA isolation and subsequent global gene expression profiling using custom Agilent ferret-specific 2x400K microarrays. Data analysis indicated that mainly metabolism is significantly upregulated. When we focus on the top 50 significantly upregulated transcripts we identified: 7 genes involved in the structure and actin metabolism; 2 genes involved in lipid metabolism and 5 genes involved in electron transport chain in mitochondria and oxidative phosphorylation, suggesting an increased fatty acid catabolism; 4 genes involved in skeletal muscle or muscle contraction and 6 genes involved in skeletal development and 1 gene involved in brown and white adipose differentiation, suggesting a transformation of the cell population; 6 genes involved in amino acid catabolism; and 19 others genes involved in other processes.

overall_design: Ferrets, male, aged 3 months, were divided into two groups: one group remained at 22 degrees Celsius, while the other group was acclimatized to 4 degrees Celsius for one week. After sacrification, inguinal white adipose tissues were dissected, and immediately snap frozen in liquid nitrogen. Total RNA was isolated, quantified and qualified, and subsequently used for global gene expression profiling using custom Agilent ferret-specific 2x400K microarrays.

first: Bàrbara

last: Reynés

first: Jaap

last: Keijer

first: Paula

last: Oliver

first: Andreu

last: Palou


title: ChIP-seq experiment of PHF2 and H3K9me2 in NSCs

overall_design: ChIP-seq of PHF2 and H3K9me2 were performed in Neural stem cells. Input of PHF2 and H3K9me2 is included.

first: Marta


title: The cold exposure produce a different gene expression pattern in inguinal and periaortic white adipose

summary: Male ferrets, aged 3 months, were divided into two group: one group remained at 22 degrees Celsius, while the other group was acclimatized to 4 degrees Celsius for one week. After sacrification, inguinal and periaortic white adipose tissues were dissected, and used for RNA isolation and subsequent global gene expression profiling using custom Agilent ferret-specific 2x400K microarrays. Data analysis indicated that while the cold exposure induces an increase on metabolism in inguinal white adopose tissue, in periaortic white adipose tissue this stimulus induces a reduction on expression  of genes involved in cell cycle and in immune response.

overall_design: Ferrets, male, aged 3 months, were divided into two groups: one group remained at 22 degrees Celsius, while the other group was acclimatized to 4 degrees Celsius for one week. After sacrification, inguinal and periaortic white adipose tissues were dissected, and immediately snap frozen in liquid nitrogen. Total RNA was isolated, quantified and qualified, and subsequently used for global gene expression profiling using custom Agilent ferret-specific 2x400K microarrays.


title: Transcriptomic Signatures of Kidney Injury in Human Renal Biopsy Specimens

status: Public on Oct 28 2019

city: Indianapolis

first: Michael

middle: T

last: Eadon

address: 950 W Walnut St

institute: Indiana University

summary: The pathogenesis and molecular signature of human acute kidney injury (AKI) remain incompletely understood, in part, owing to the heterogeneity of the disease. Further, the link between animal models and human AKI is not well characterized. Transcript expression of AKI in 39 native human renal biopsy samples was compared to 9 reference nephrectomies. These data demonstrate that the molecular signature segregates patients with AKI in spite of similar pathological and clinical phenotyping. Such molecular characterization will offer advantages in categorizing and understanding the underlying pathogenesis of phenotypically complex and heterogeneous forms of AKI.

overall_design: Bulk 20 um thickness specimens from cross-sectional human kidney biopsies or nephrectomies embedded in OCT underwent RNA sequencing. All biopsy subjects had AKI. Sequencing performed on an Illumina HiSeq 4000.


title: CD8+ T cells expand stem and progenitor cells in favorable but not adverse risk acute myeloid leukemia

status: Public on Apr 04 2019

city: Bern

first: Ramin

last: Radpour

address: Murtenstrasse 35

department: Department for BioMedical Research

country: Switzerland

institute: University of Bern

summary: We performed a comprehensive transcriptomic profiling of BM derived leukemia stem cells (LSCs) and leukemia progenitor cells (LPCs) together with paired CD8+ T cells of AML patients from different molecular risk groups, as well as hematopoietic stem cells (HSCs) and progenitor cells (HPCs) with paired CD8+ T cells of controls. This analysis revealed that epigenetic alterations mainly via histone deacetylation reduced the expression of immune-related genes in bone marrow (BM)-infiltrating CD8+ in AML when compared to CD8+ T cells in normal BM and that silenced gene expression pattern correlated with an improved prognosis. Correlation network modeling indicated that CD8+ T cells regulate leukemia stem/progenitor cells (LSPCs) in favorable risk but not in adverse risk AML.

overall_design: We characterized the molecular signature of well-defined leukemia stem/progenitor cells and paired CD8+ T cells in patients with acute myeloid leukemia (AML) compared to control subjects.

first: Carsten

last: Riether

first: Adrian

middle: F

last: Ochsenbein


title: Loss of PRC2 enforces a mesenchymal neural crest stem cell phenotype in NF1-deficient cancer through activation of core transcription factors [ChIP-seq]

status: Public on Sep 20 2022

city: New Brunswick

first: Xiyuan

last: Zhang

state: NJ

address: 195 Little Albany St.

department: Pediatric Hematology/Oncology

institute: Rutgers Cancer Institute

summary: Genetic alterations that result in the dysregulation of polycomb repressive complex 2 (PRC2) are common features of multiple cancer types. Loss-of-function mutations in the PRC2 genes, SUZ12 or EED, occur at high frequency in malignant peripheral nerve sheath tumors (MPNST), a clinically aggressive sarcoma that arises from NF1-deficient Schwann cells. To define the oncogenic mechanisms mediated by PRC2 loss, we used engineered MPNST model systems that dynamically reassemble a competent PRC2 coupled with single cell sequencing from clinical samples to evaluate the transcriptomic and epigenetic consequences of PRC2 loss. We discovered a two-pronged oncogenic process; first, PRC2 loss leads to remodeling of bivalent chromatin and the enhancer landscape of the tumor cell. These epigenetic changes result in the upregulation of developmentally regulated transcription factors, including FOXC1, which enforce a transcriptional circuit that is a core vulnerability of the cell. Second, PRC2 loss reduces type I interferon signaling and antigen presentation as a downstream consequence of hyperactivated Ras signaling and its crosstalk with STAT and IRF transcription factors. Mapping of the transcriptional program of these PRC2-deficient tumor cells onto a constructed developmental trajectory of the developing neural crest stem cell revealed that changes induced by PRC2 loss enforced a cellular profile characteristic of a primitive mesenchymal neural crest stem cell.

overall_design: Epigenetic and transcriptomic profiling of doxycycline-inducible restoration of a functional PRC2 in human MPNST cells.

first: Jack

last: Shern


title: ChIP-seq of H3K27ac and CTCF in primary glioblastoma cultures

status: Public on Jun 06 2019

city: Houston

first: Marco

last: Gallo

state: TX

address: 1102 Bates Avenue

department: Pediatrics

institute: Baylor College of Medicine

summary: We characterize H3K27ac and CTCF profiles of three primary glioblastoma cultures, and use them to bolster Hi-C datasets.

overall_design: Paired inputs and ChIP experiments in duplicate for CTCF and H3K27ac for three independent cultures.

last: Johnston

first: Ana

last: Nikolic


title: Clinicogenetic Risk Prognostication for First-Line Treatment of Symptomatic Follicular Lymphoma

status: Public on Feb 19 2019

first: Anjali

last: Silva

state: ON

address: 610 University Ave

department: Lymphoid Cancer Research

institute: Princess Margaret Cancer Centre - University Health Network

summary: Background: Follicular lymphoma (FL) is an indolent malignancy of germinal center B cells with highly variable patient outcomes. Recently, a 23-gene predictor score was proposed for predicting progression-free survival. In the past, we had shown that the m7-FLIPI, a clinico-genetic risk model, allows to improve patient stratification compared to clinical risk models alone. The multitude of prognostic tools in FL raises the question whether they identify common biology.   Methods: In this study, we applied a modified risk score (MRS) to an independent gene-expression dataset of FL patients treated with rituximab in combination with chemotherapy.  Results: Using supervised and unsupervised approaches, we showed that the MRS identifies patient groups with diverging outcomes in our dataset. In addition, using gene set enrichment and network identification, we discovered associations between the MRS, the m7-FLIPI, EZH2 mutation status and FOXP1 expression.  Conclusions: Our findings lend support to expression of dark-zone related genes as a key determinant of poor outcome following rituximab and chemotherapy.

overall_design: All RNA samples were derived from formalin-fixed paraffin-embedded tissue blocks and processed using the Illumina Whole-Genome DASL assay. The study includes 137 gene expression samples from the BC Cancer Agency cohort.

first: Robert

last: Kridel


title: Construction of a dynamic gene regulatory network required for cellular reprogramming

status: Public on Feb 14 2019

city: Athens

first: Dimitris

last: Valakos

address: Soranou Ephessiou 4

department: Center of Basic Research

country: Greece

institute: Biomedical Reasearch Foundation Academy of Athens

summary:
The generation of induced Pluripotent Stem Cells (iPSCs) from somatic cells provides an excellent example to study mechanisms of transcription factor-induced global alterations of the genome and the epigenome.  Here, we have investigated the early transcriptional events of cellular reprogramming triggered by the co-expression of OSKM (Oct4, Sox2, Klf4 and c-Myc) in Mouse Embryonic Fibroblasts (MEFs) and mouse Hepatocytes (mHeps) and identified a novel gene regulatory network composed of 9 Transcriptional Regulators (TRs), which are directly targeted by OSKM. Functional studies using single and double shRNA knock-downs of any of these TRs caused disruption of the network and dramatic reductions in reprogramming efficiency, demonstrating that this novel gene regulatory network is essential for the induction and establishment of pluripotency. We demonstrate that that the stochastic co-expression of the 9TRs network components occurs in a remarkably small number of cells approximating the percentage of reprogrammed cells as the result of dynamic molecular events. Thus, the early binding patterns of OSKM and the subsequent stochastic co-expression of pivotal TRs in subpopulations of cells steer the reconstruction of a gene regulatory network crucial for the generation of iPSCs.
In this study, we show that OSKM trigger the gradual establishment of the stemness phenotype by inducing the stochastic reconstruction of a novel 9TRs gene regulatory network that guides the acquisition to pluripotency.

overall_design:
Affymetrix Mouse Genome 430 A 2.0 version was used for gene expression profiling of the reprogramming course. RNA was isolated from mESCs, miPSCs, control (naïve) MEFs and reprogrammable MEFs on day 0.5, 1, 1.5, 2, 2.5, 3, 6, 12, 18 of reprogramming. Additional RNA was isolated from mHeps at days 0, 3 and 6 of reprogramming.

UPDATE: [08-11-2024] The titles and antibodies of the following Sample pairs were swapped:
GSM4667681 and GSM4667683
GSM4667682 and GSM4667684
GSM4667685 and GSM4667687
GSM4667686 and GSM4667688
GSM4667693 and GSM4667694
The raw data and processed data associated with these Sample accession numbers did not change.

last: Thanos

first: Alexandros

last: Polyzos


title: CD47 expression in natural killer cell regulates homeostasis and modulates immune response to lymphocytic choriomeningitis virus

status: Public on Mar 11 2019

city: Bethesda

first: Stefano

last: Marenco

state: MD

address: Building 10, Room 4N306

institute: National Institute of Mental Health

summary: CD47 is a ubiquitous cell surface receptor that limits cell clearance by phagocytes that express its counter-receptor signal-regulatory protein-α and directly regulates T cell immunity by interacting with its inhibitory ligand thrombospondin-1. Murine natural killer (NK) cells express higher levels of CD47 than other lymphocytes, but the role of CD47 in regulating NK cell homeostasis and immune function remains unclear. Cd47-/- mice exhibited depletion of NK precursors in bone marrow, but antisense Cd47 knockdown or gene disruption resulted in a dose dependent accumulation of immature and mature NK cells in spleen. Cd47-/- mice were impaired in controlling chronic Clone-13 lymphocytic choriomeningitis virus (LCMV) infection, which was associated with depletion of splenic NK cells and loss of effector cytokine and interferon response gene expression in Cd47-/- NK cells. These data identify CD47 as a cell-intrinsic and systemic regulator of NK cell homeostasis and NK cell responses to viral infection.

overall_design: Examining natural killer (NK) cell intrinsic role of CD47 during viral infection.

first: Pulak

last: Nath

first: Arunakumar

last: Gangaplara

first: Dragan

last: Maric

first: Ajeet

last: Mandal

first: Margaret

last: Cam

first: Ethan

last: Shevach

first: David

middle: D

last: Roberts


title: Bacterial sepsis triggers an antiviral response that causes translation shutdown

status: Public on Oct 06 2018

first: Takashi

last: Hato

address: 950 W. Walnut St. R2 202

department: Medicine

summary: In response to viral pathogens, the host upregulates antiviral genes that suppress translation of viral mRNAs. However, induction of such antiviral responses may not be exclusive to viruses as the pathways lie at the intersection of broad inflammatory networks that can also be induced by bacterial pathogens. Using a model of Gram-negative sepsis, we show that propagation of kidney damage initiated by a bacterial origin ultimately involves antiviral responses that result in host translation shutdown. We determined that activation of the Eif2ak2-Eif2α axis is the key mediator of translation initiation block in late phase sepsis. Reversal of this axis mitigated kidney injury. Furthermore, temporal profiling of the kidney translatome revealed that multiple genes involved in formation of the initiation complex were translationally altered during bacterial sepsis. Collectively, our findings implicate that translation shutdown is indifferent to the specific initiating pathogen and is an important determinant of tissue injury in sepsis.

overall_design: C57BL/6J male mice were subjected to vehicle (control), LPS (5 mg/kg iv), or LPS and ISRIB (5 mg/kg iv and ip respectively) for indicated durations.


title: RNA-seq analysis of Scn1+/- Dravet mice on susceptible and resistant strains at postnatal days 14 and 24

status: Public on Oct 26 2018

city: Chicago

first: Jennifer

last: Kearney

state: IL

address: 320 East Superior Street, Searle 8-510

department: Pharmacology

institute: Northwestern University

summary: Dravet syndrome is a severe, early-onset epileptic encephalopathy frequently resulting from de novo mutations of SCN1A. Mice with heterozygous deletion of Scn1a (Scn1a+/-) model many features of Dravet syndrome, including spontaneous seizures and premature lethality. Scn1a+/- mice exhibit variable phenotype penetrance and expressivity dependent upon the strain background. On the 129S6/SvEvTac (129) strain, Scn1a+/- mice do not display an overt phenotype. However Scn1a+/- mice on the [129S6xB6]F1 strain (F1.Scn1a+/-) exhibit juvenile-onset spontaneous seizures and premature lethality. QTL mapping identified several modifier loci responsible for strain-dependent differences in survival of Scn1a+/- mice, but these loci do not account for all the observed phenotypic variance. Global RNA-seq analysis was performed to identify additional genes and pathways that may contribute to variable phenotypes. Hippocampal gene expression was analyzed in wild-type (WT) and Scn1a+/- mice on both F1 and 129 strains, at two time points during disease development. There were few gene expression differences between 129.WT and 129. Scn1a+/- mice and approximately 100 genes with small expression differences (6-36%) between F1.WT and F1.Scn1a+/- mice. Strain-specific gene expression differences were more pronounced, with dozens of genes with >1.5-fold expression differences between 129 and F1 strains. Age-specific and seizure-related gene expression differences were most prominent, with hundreds of genes with >2-fold differences in expression were identified between groups with and without seizures, suggesting potential differences in developmental trajectory and/or homeostatic plasticity during disease onset. Global expression differences in the context of Scn1a deletion may account for strain-dependent variation in seizure susceptibility and survival observed in Scn1a+/- mice.

overall_design: Hippocampal mRNA expression profiles of P14 and P24 wild-type and Scn1a+/- mice were generated by deep sequencing of 2-3 replicates using Illumina HiSeq4000

first: Nicole

last: Hawkins

first: Jeffrey

last: Calhoun

first: Alexandra

last: Huffman


title: microRNA profile in the cervical mucus of the cervical neoplasia

status: Public on May 09 2018

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

country: Japan

institute: Toray Industries,Inc.

summary: Cervical mucus was collected from 86 patients with a normal cervix, cervical intraepithelial neoplasia (CIN), squamous cell carcinoma (SCC), or adenocarcinoma (AD). 76 candidates of miRNAs were selected according to criteria such as absolute value of the signal intensity included more than 20 and the ratio of the SCC/normal or AD/normal included more than four.

overall_design: Cervical mucus was collected from 86 patients with a normal cervix, cervical intraepithelial neoplasia (CIN), squamous cell carcinoma (SCC), or adenocarcinoma (AD). The expression level of microRNAs in cervical mucus was compared with normal and cervical neoplasia by microarray including 2588 miRNAs. Cervical mucus was collected from 86 patients with a normal cervix, cervical intraepithelial neoplasia (CIN), squamous cell carcinoma (SCC), or adenocarcinoma (AD). The samples were classified into normal (n = 16), CIN1 (n = 11), CIN3 (n = 29), squamous cell carcinoma (SCC) (n = 19), and adenocarcinoma (AD) (n = 11). 76 candidates of miRNAs were selected according to criteria such as absolute value of the signal intensity included more than 20 and the ratio of the SCC/normal or AD/normal included more than four.

first: Takuma

last: Fujii


title: The co-existence of transcriptional activator and transcriptional repressor MEF2 complexes influences tumor aggressiveness

status: Public on Apr 17 2017

city: udine

first: raffaella

last: picco

address: piazzale kolbe 4

department: department of medical and biological sciences

institute: university of Udine

summary: MEF2 (MEF2A, B, C, D) transcription factors (TFs) regulate many complex biological responses, spanning from differentiation to stress-adaptation. MEF2’s activities are therefore strictly regulated. A family of transcriptional repressors: the class IIa HDACs, which includes HDAC4, 5, 7, 9, is intimately involved in the fine tuning of MEF2 activities. In many cancer types the physiological cycle of turning on and off of MEF2 transcriptional activities is subverted due to mutations or dysregulations. On the basis of loss-of-function experiments, MEF2 factors are classified sometimes as oncogenes and sometimes as tumor suppressors. With this project we aimed to address this apparent paradox. Soft-tissue sarcomas and leiomyosarcomas (LMSs) in particular are tumors characterized by a strong repression of MEF2, which is achieved through an increase in proteasomal-mediated degradation of MEF2 proteins or in the repression exerted by HDAC4 and HDAC9. MEF2 degradation prevails in a cellular model of low-grade tumors (SK-LMS-1 cells), while in a model of high-grade LMSs (SK-UT-1 cells) MEF2 are converted into transcriptional repressors of specific genome loci. In this latter case the knock down of MEF2D and MEF2A causes the de-repression of some MEF2-target genes and, surprisingly, has a tumor suppressive effect. Our results suggest that MEF2 could provide different contributions during tumor progression in relation to the specific cellular microenvironment.

overall_design: 5 clones of each LMS cell line were created: one expressing a shRNA control, two expressing two different shRNAs against MEF2D (#1 and #2), and two expressing two different shRNAs against MEF2A (#4 and #5). The total RNA of the 10 clones were compared under the same growth conditions. For each condition two biological replicates were performed.!Series_contributor = Eros,,Di Giorgio

first: Eros

last: Di Giorgio

first: Elisa

last: Franforte

first: Raffaella

last: Picco

first: Claudio

last: Brancolini


title: Sex Differences in the Late First Trimester Human Placenta Transcriptome

status: Public on Jan 22 2018

city: Charlottesville

first: Alexander

middle: Fritz

last: Koeppel

state: VA

address: 1640 Jefferson Park Avenue

department: School of Medicine

institute: University of Virginia

summary: This study is the first characterization of the first trimester placenta transcriptome, highlighting similarities and differences among the sexes in ongoing human pregnancies resulting in live births. Sexual dimorphism may contribute to pregnancy outcomes, including fetal growth and birth weight, which was seen in our cohort, with males significantly heavier than females at birth. This transcriptome provides a basis for development of early diagnostic tests of placental function that can indicate overall pregnancy heath, fetal-maternal health, and long term adult health.

overall_design: Examination of gene expression in Males vs. Females

first: Tania

middle: L

last: Gonzalez

first: Tianyanxin

last: Sun

first: Bora

last: Lee

first: Erica

last: Wang

first: Charles

last: Farber

first: Stephen

last: Rich

first: Lauren

last: Sundheimer

first: Rae

last: Buttle

first: Yii-Der

middle: I

last: Chen

first: Jerome

last: Rotter

last: Turner

first: John

last: Williams

first: Mark

middle: O

last: Goodarzi

first: Margareta

last: Pisarska


title: Control of Fiber Color in Naturally Colored Cotton by Flavonoid Biosynthesis

status: Public on Nov 28 2017

city: Shanghai

first: Hailiang

last: Liu

address: NO 1239, siping road

institute: Tongji university

summary: Compare the expression profiles of natural brown and green cotton fibers, and white color fiber at 0 and 12 days post-anthesis (DPA) to identify genes involved in pigment synthesis

overall_design: Examination of 3 different color cotton Fibers in 2  time points (0 day and 12 day).

first: Hai-Liang


title: Unique transcriptional architecture in airway epithelial cells and macrophages shapes distinct responses following influenza virus infection ex vivo.

status: Public on Dec 20 2018

city: Parkville

first: Joel

middle: Zhi-Iong

last: Ma

state: Victoria

address: Grattan Street

institute: University of Melbourne

summary: Airway epithelial cells and macrophages differ markedly in their responses to influenza A virus (IAV) infection. To investigate transcriptional responses underlying these differences, purified subsets of type II airway epithelial cells (ATII) and alveolar macrophages (AM) recovered from the lungs of mock- or IAV-infected mice were subjected to RNA sequencing. In the absence of infection, AM predominantly expressed genes related to immunity whereas ATII expressed genes consistent with their physiological roles in the lung. Following IAV infection, AM almost exclusively activated cell-intrinsic antiviral pathways that were dependent on interferon regulatory factor (IRF)3/7 and/or type I interferon (IFN) signaling. In contrast, IAV-infected ATII activated a broader range of physiological responses, including cell-intrinsic antiviral pathways, which were both independent and dependent on IRF3/7 and/or type I IFN. These data suggest that transcriptional profiles hardwired during development could be a major determinant underlying the different responses of ATII and AM to IAV infection.

overall_design: 96 samples were analyzed: (A) 4 replicates of HA+ Alveolar Macrophage (AM) and 4 replicates of CD103+ Dendritic cells (DC) isolated from the lung lobes of C57/BL6 mice on 9 h p.i. with PR8.  4 replicates of mock-infected (HA-) AM and 4 replicates of mock-infected (HA-) CD103+ DC isolated from the lung lobes of mock-infected C57/BL6 mice on 9 h p.i. with allantoic fluid of equal dilution as PR8. 4 replicates of HA+ Airway epithelial cell Type II (ATII) and 4 replicates of HA+ Ciliated Cell (CC) isolated from the lung lobes of C57/BL6 mice on 9 h p.i. with PR8.  4 replicates of mock-infected (HA-) ATII and 4 replicates of mock-infected (HA-) CC isolated from the lung lobes of mock-infected C57/BL6 mice on 9 h p.i. with allantoic fluid of equal dilution as PR8. (B) 4 replicates of HA+ AM and 4 replicates of CD103+ DC isolated from the lung lobes of IFNAR2-/- mice on 9 h p.i. with PR8.  4 replicates of mock-infected (HA-) AM and 4 replicates of mock-infected (HA-) CD103+ DC isolated from the lung lobes of mock-infected IFNAR2-/- mice on 9 h p.i. with allantoic fluid of equal dilution as PR8. 4 replicates of HA+ ATII and 4 replicates of HA+ CC isolated from the lung lobes of IFNAR2-/- mice on 9 h p.i. with PR8.  4 replicates of mock-infected (HA-) ATII and 4 replicates of mock-infected (HA-) CC isolated from the lung lobes of mock-infected IFNAR2-/- mice on 9 h p.i. with allantoic fluid of equal dilution as PR8.  (C) 4 replicates of HA+ AM and 4 replicates of CD103+ DC isolated from the lung lobes of IRF3/7-/- mice on 9 h p.i. with PR8.  4 replicates of mock-infected (HA-) AM and 4 replicates of mock-infected (HA-) CD103+ DC isolated from the lung lobes of mock-infected IRF3/7-/- mice on 9 h p.i. with allantoic fluid of equal dilution as PR8. 4 replicates of HA+ ATII and 4 replicates of HA+ CC isolated from the lung lobes of IRF3/7-/- mice on 9 h p.i. with PR8.  4 replicates of mock-infected (HA-) ATII and 4 replicates of mock-infected (HA-) CC isolated from the lung lobes of mock-infected IRF3/7-/- mice on 9 h p.i. with allantoic fluid of equal dilution as PR8.

middle: Z

first: Wy

last: Ng

first: Luke

last: Zappia

first: Linden

middle: J

last: Gearing

first: Moshe

last: Olshansky

first: Kym

last: Pham

first: Karey

last: Cheong

first: Arthur

last: Hsu

first: Odilia

last: Wijburg

first: Sarah

last: Londrigan

first: Andrew

last: Brooks

first: Patrick

last: Reading


title: Drop-seq of N2a cells transfected with Bsn

status: Public on Apr 03 2019

city: Hamburg

first: Manuel

last: Friese

address: Falkenried 94

department: Institut für Neuroimmunologie und Multiple Sklerose

institute: Universitätsklinikum Hamburg-Eppendorf

summary: During the course of multiple sclerosis (MS), inflammatory insults drive neuro-axonal loss and disability progression. However, pathways that guide neurons toward survival or death during central nervous system (CNS) inflammation are largely unexplored. Here we show that somatic deposition of the presynaptic protein bassoon (Bsn) in inflamed neurons directly contributes to neurodegeneration in MS. By comparing neuron-specific RNA-seq of healthy mice to mice undergoing experimental autoimmune encephalomyelitis (EAE), the animal model of MS, we identified key components of neurodegenerative pathways, including reduced mitochondrial ATP synthesis and increased protein catabolism. These changes were accompanied by neuronal induction and deposition of the intrinsically disordered protein Bsn in both EAE and in patients with MS. Somatic Bsn also accumulated in Bsn-overexpressing Neuro-2a (N2a) cells and single cell RNA-seq revealed dose-dependent repression of energy metabolism and induction of the unfolded protein response, reminiscent of our in vivo findings. Furthermore, Bsn overexpression in N2a cells or in Drosophila melanogaster neurons led to decreased survival and shortened lifespan, respectively. Conversely, genetic disruption of Bsn in mice was neuroprotective, with reduced neuro-axonal injury and clinical disability during EAE, establishing a toxic gain-of-function of Bsn during CNS inflammation. Our study provides systemic insights into neuronal responses to inflammation and identifies protein accumulation as a generic pathomechanism uniting primary and inflammatory neurodegeneration. Moreover, it offers a new explanation and possible treatment strategy to halt disability progression in MS, irrespective of immunotherapies.

overall_design: N2a cells were transfected with eGFP-Bsn (eGFP labeled rat Bsn) and sorted for GFP-positivity were subjected to Drop-seq single-cell RNA sequencing.

first: Max

last: Kaufmann

first: Jan

middle: B

last: Engler

first: Nicola

last: Rothammer


title: Epigenomic Profiling of Primary Gastric Adenocarcinoma Reveals Super-enhancer Heterogeneity [RNA-seq]

status: Public on Sep 28 2016

city: Singapore

first: Aditi

last: Qamra

address: 60 Biopolis Street, Genome, #02-01

institute: GIS

summary: Regulatory elements in cancer remain poorly characterized in primary solid tumors. Here we applied microscale histone modification profiling to delineate the landscape of somatic promoters and super-enhancers in primary gastric adenocarcinoma, analyzing 94 epigenomic  profiles of primary tumors, normal tissues, and cell lines

overall_design: Total RNA extracted from gastric cell lines, tumors and matched gastric non-malignant (normal) tissues was sequenced.

first: Ooi

middle: W

last: Fong

last: Tan


title: DNA methylation-based classification of human central nervous system tumors [validation set]

status: Public on Jan 18 2018

city: Heidelberg

first: Martin

last: Sill

address: Im Neuenheimer Feld 280

department: Division of Pediatric Neurooncology

institute: DKFZ

type: Methylation profiling by genome tiling array

summary: Background: Modern neuropathology is challenged by an increasing number of clinically-relevant CNS tumor subgroups that require assessment of a multitude of molecular markers for classification, as well a highly trained medical staff. Failure to meet this challenge leads to tumor misclassification, which can have severe consequences for affected patients. Methods: We compiled a cohort of genome-wide DNA methylation profiles of 2,682 tumors from 82 histologically and/or molecularly distinct CNS tumor classes across all ages and histologies that served as reference for a Random Forest-based diagnostic classifier. This classifier was used to prospectively investigate a further 1,104 CNS tumor samples in order to determine its clinical utility. Results: The classifier was able to reliably assign tumor samples to a given diagnostic category with a misclassification rate of less than 2%. The system functioned robustly across laboratories and using different DNA methylation profiling techniques. Prospective application to clinical samples resulted in a reclassification of 12% of tumors compared with standard practice alone. A further 12% could not be classified by methylation profiling – this subset was highly enriched for unusual syndrome-associated tumors and likely novel entities. Conclusion: This study represents a proof-of-concept for the application of machine learning approaches in molecular diagnostics using a single, easy-to-use assay. The reference cohort and Random Forest-based classifier are available online as a valuable community tool for improving precision in brain tumor diagnostics. We expect that approaches similar to the one presented herein will rapidly restructure diagnostic practice in neurooncology and across tumor pathology.

overall_design: The Illumina Infinium HumanMethylation450 array (Illumina, San Diego, USA) data from n=2801 patients were used to obtain genome-wide assessment of DNA methylation, according to the manufacturer’s instructions at the Genomics and Proteomics Core Facility of the German Cancer Research Center (DKFZ) as described previously (Sturm et al. Cancer Cell. 2012 Oct 16;22(4):425-37).

first: David

last: Capper

last: Jones

first: Volker

last: Hovestadt

first: Andreas

last: von Deimling

first: Stefan

last: Pfister


title: Bassoon proteinopathy drives neurodegeneration in multiple sclerosis

overall_design: Refer to individual Series


title: TRAP-seq of spinal cord motor neurons in EAE versus healthy mice

overall_design: mRNA of Chat+ spinal cord motor neurons derived from mice undergoing experimental autoimmune encephalomyelitis (EAE) and healthy control mice was enriched by translating ribosome affinity purification (TRAP) and sequenced by RNA-seq.

first: Constantin

last: Volkmann


title: Gene expression in primary erythroid cells and in bone marrow stromal cells following treatment with Sotatercept (ACE-011)

status: Public on Oct 20 2012

city: New York

first: Camelia

last: Iancu-Rubin

address: One Gustave Levy Place Box 1079

department: Hematology and Medical Oncology

institute: Mount Sinai School of Medicine

overall_design: Gene expression profiles of erythroid cells derived from human CD34+ cells generated under standard conditions and in cultures containing conditioned media from bone marrow stromal cells treated in vitro with ACE-011; Gene expression profiles of untreated bone marrow stromal cells and of stromal cells treated with ACE-011.

first: Ronald

last: Hoffman


title: Comparision of Clostridium botulinum type A (HA-/ORFX+ A1) isolates

status: Public on Sep 26 2013

city: Atlanta

first: Brian

middle: H

last: Raphael

state: GA

address: 1600 Clifton Road

department: Enteric Diseases Laboratory Branch

institute: Centers for Disease Control and Prevention

type: Genome variation profiling by genome tiling array

summary: The purpose of this study was to evaluate differences in gene content between tests samples isolated from separate food sources.

overall_design: A single biological sample was used for each test strain examined

first: Kristin

last: Marshall

first: Louis

last: Nowaczyk

first: Guy

middle: E

last: Skinner

first: Rukma

last: Reddy


title: Molecular Hallmarks of Naturally Acquired Immunity to Malaria

status: Public on Nov 08 2013

city: Rockville

first: Ravi

last: Sanka

state: Maryland

address: 9704 Medical Center Drive

institute: JCVI

summary: Immunity to malaria can be acquired through natural exposure to Plasmodium falciparum (Pf), but only after years of repeated infections. Typically, this immunity is acquired by adolescence and confers protection against disease, but not Pf infection per se. Efforts to understand the mechanisms of this immunity are integral to the development of a vaccine that would mimic the induction of adult immunity in children. The current study applies transcriptomic analyses to a cohort from the rural village of Kalifabougou, Mali, where Pf transmission is intense and seasonal. Signatures that correlate with protection from malaria may yield new hypotheses regarding the biological mechanisms through which malaria immunity is induced by natural Pf infection. The resulting datasets will be of considerable value in the urgent worldwide effort to develop a malaria vaccine that could prevent more than a million deaths annually.

overall_design:
108 samples; paired pre- and post-challenge for 54 individuals
198 samples; paired pre- and post-challenge for 99 individuals

first: Ewen

last: Kirkness

first: Peter

last: Crompton


title: Rare cell variability and drug-induced reprogramming as a mode of cancer drug resistance [RNA-seq]

status: Public on Apr 13 2017

city: Philadelphia

first: Sydney

last: Shaffer

state: PA

address: BRB II/III, Room 445, 421 Curie Blvd

institute: University of Pennsylvania

summary: Therapies targeting signaling molecules mutated in cancers can often have striking short-term effects, but the emergence of resistant cancer cells is a major barrier to full cures. Resistance can sometimes result from a secondary mutations in rare cells, but other times, there is no clear genetic cause, raising leaving the possibility of non-genetic rare cell variability. Here, we show that melanoma cells can display profound transcriptional variability at the single cell level that predicts which cells will ultimately resist drug treatment. This variability involves semi-coordinated transcription of a number of resistance markers at high levels in a very small percentage of cells. The addition of drug then induces an epigenetic reprogramming in these cells, converting the transient transcriptional state to a stably resistant state. This reprogramming begins with a progressive process consisting of a loss of SOX10-mediated differentiation followed by activation of new signaling pathways, partially mediated by activity of Jun-AP-1 and TEAD. Our work reveals the multistage nature of the acquisition of drug resistance and provides a framework for understanding resistance dynamics. We find that other cell types also exhibit sporadic expression of many of these same marker genes, suggesting the existence of a general rare-cell expression program.

overall_design: We performed FACS to isolate EGFR-high populations of WM989 melanoma cells at three time points (untreated, 1 week in vemurafenib, 4 weeks in vemurafenib) for RNA sequencing and ATAC sequencing. Each sample has three biological replicates.

first: Arjun

last: Raj


title: Tracking transcript abundance changes of D. vulgaris co-cultures with M. maripaludis in fluctuating resource environment

status: Public on Mar 10 2016

city: Seattle

first: Serdar

last: Turkarslan

state: WA

address: 401 Terry Ave

institute: Institute for Systems Biology

summary: Managing tradeoffs through gene regulation is believed to maintain resilience of a microbial community in a fluctuating resource environment. To investigate this hypothesis we imposed a fluctuating environment that required the sulfate-reducing generalist Desulfovibrio vulgaris to manage tradeoffs associated with repeated ecologically-relevant shifts between retaining metabolic independence (active capacity for sulfate respiration) and becoming metabolically specialized to a mutualistic association with the hydrogen consuming Methanococcus maripaludis. Strikingly, the microbial community became progressively less proficient at restoring the environmentally-relevant physiological state after each perturbation. Most cultures collapsed within 3-7 shifts with only a few collapsing later. We demonstrate that the collapse was caused by conditional gene regulation, which drove precipitous decline in intracellular abundance of essential transcripts and proteins, imposing greater energetic burden of regulation to restore function in a fluctuating environment. The microbial community collapse was rescued by a single regulatory mutation that could then potentially serve as a stepping stone for further adaptive evolution in a variable resource environment.

sample_organism: Nitratidesulfovibrio vulgaris str. Hildenborough

overall_design: Co-culture strains of M. maripaludis wild type and either wild type or DVU0744::Tn5 mutant of D. vulgaris strains were grown anaerobically in replicates. Samples were transitioned between syntrophic and sulfate respiratory growth conditions at early log phases.

first: Christina

last: Arens

first: Nitin

middle: S

last: Baliga


title: Acyclic retinoid targets platelet-derived growth factor signaling in the prevention of hepatic fibrosis and hepatocellular carcinoma development

status: Public on Aug 19 2012

city: Kanazawa

first: Masao

last: Honda

address: Takara-Machi 13-1

department: Gastroenterology

institute: Kanazawa University

summary: Gene expression profiling in non tumor lesion in the liver of patients prior to administering peretinoin was unrelated to the clinical outcome, however, gene expression profiling 8 weeks after starting peretinoin therapy significantly predicted the recurrence of HCC

overall_design: Peretinoin, a member of the acyclic retinoid family, is expected to be an effective chemo preventive drug for HCC.The patients had undergone curative surgical resection or radiofrequency ablation (RFA). They received 300 mg/day or 600 mg/day of peretinoin for 8 weeks and were followed up for 88 weeks with 600 mg/day of peretinoin. Hepatic gene expression profiling obtained from non tumor lesion of these patients prior to administering peretinoin and 8 weeks after starting peretinoin treatment

first: Hikari

last: Okada

first: Jean

last: Campbell

first: Yoshio

last: Sakai

first: Taro

last: Yamashita

first: Tatsuya

first: Kuniaki

last: Arai

first: Eishiro

last: Mizukoshi

first: Akito

first: Hajime

last: Sunakozaka

first: Yuuki

last: Takebuchi

first: Kazuhiro

last: Hata

first: Takayoshi

last: Shirasaki

first: Mikiko

last: Nakamura

first: Takuji

last: Tanaka

first: Nelson

last: Fausto

first: Shuichi

last: Kaneko