title: Bladder cancer therapy using a conformationally fluid tumoricidal peptide complex

status: Public on Apr 15 2021

city: Lund

first: Petter

last: Storm

address: Sölvegatan 19, BMC A11

department: Developmental and Regenerative Neurobiology

institute: Lund University

summary: Partially unfolded alpha-lactalbumin forms the oleic acid complex HAMLET, with potent tumoricidal activity. Here we define a peptide-based molecular approach for targeting and killing tumor cells and evidence of its clinical potential (ClinicalTrials.gov NCT03560479). A 39-residue alpha-helical peptide from alpha-lactalbumin is shown to gain lethality for tumor cells by forming oleic acid complexes (alpha1-oleate). In a single center, placebo controlled, double blinded Phase I/II interventional clinical trial of non-muscle invasive bladder cancer, all primary end points of safety and efficacy of alpha1-oleate treatment are reached, as evaluated in an interim analysis. Intra-vesical instillations of alpha1-oleate triggers massive shedding of tumor cells and the tumor size is reduced but no drug-related side effects are detected (primary endpoints). Shed cells contain alpha1-oleate, treated tumors show evidence of apoptosis and the expression of cancer-related genes is inhibited (secondary endpoints). The results are especially encouraging for bladder cancer, where therapeutic failures and high recurrence rates create a great, unmet medical need.

overall_design:
RNA-seq of bladder tumour biposies from a clinical trial of alpha1-oleate

>>>Submitter states that raw data are unavailable due to patient privacy concerns<<<

first: Catharina

last: Svanborg

first: Ines

last: Ambite


title: Using small RNA-Seq to verify that 5' tRNA-fMet1 half is over-expressed in outer membrane vesicles (OMVs)

status: Public on Sep 12 2021

city: Hanover

first: Zhongyou

last: Li

state: NH

address: 504 Remsen

country: USA

institute: Geisel School of Medicine at Dartmouth

type: Non-coding RNA profiling by high throughput sequencing

summary: 5′ tRNA-fMet1 half (5′- CGCGGGGTGGAGCAGTCTGGTAGCTCGTCGGGCTC-3′) was cloned into the arabinose-inducible expression vector pMQ70.  PA14 was transformed with the tRNA-fMet1 half expression vector or empty vector via electroporation. Characterization of the sRNA content of OMVs secreted by 5' tRNA-fMet1 half over-expression clone and empty vector control clone.

overall_design: over-expression OMVs (tRNA1-OMVs) and empty vector ctrl OMVs (V-OMVs) from 3 separate preparations.

first: Katja

last: Koeppen

first: Bruce

middle: A

last: Stanton


title: Single cell RNA sequencing study of Lung epithelial cells with Il33 KO cells

status: Public on Jul 29 2021

city: St Louis

first: Samantha

last: Morris

state: Missouri

address: 660 S. Euclid Avenue

department: Department of Developmental Biology, Washington University School of Medicine

institute: Washington University in St Louis

type: Expression profiling by high throughput sequencing

summary: Epithelial cells are charged with protection at barrier sites, but whether this normally beneficial response might sometimes become dysfunctional still needs definition. Here we identify a pattern of imbalance marked by basal epithelial cell growth and differentiation that replaces normal airspaces in a mouse model of progressive post-viral lung disease due to Sendai virus. Single-cell and lineage-tracing technologies identify a distinct subset of basal epithelial stem cells (basal- ESCs) that extend into gas-exchange tissue to form long-term bronchiolar-alveolar remodeling regions. Moreover, this cell subset is selectively expanded by crossing a cell growth and survival checkpoint linked to the nuclear-localized alarmin IL-33 that is independent of IL-33-receptor signaling and instead connected to autocrine chromatin accessibility. This mechanism creates an activated stem-progenitor cell lineage with potential for physiological or pathological function. Thus, conditional loss of Il33 gene function in basal epithelial cells disrupts homeostasis of the epithelial barrier at skin and gut sites but also markedly attenuates post-viral disease in the lung based on down-regulation of remodeling and inflammation. We thereby identify a basal-ESC strategy to deploy innate-immune machinery that appears to overshoot the primordial goal of self- defense. The findings reveal new targets to stratify and correct chronic and often deadly post-viral disease.

overall_design: This dataset consists of 6 10x Genomics scRNA-seq libraries, including 3 experimental conditions for each WT sample Il33KO sample.

first: Kangyun

last: Wu

first: Kenji

last: Kamimoto

first: Yong

last: Zhang

first: Kuangying

last: Yang

first: Shamus

middle: P

last: Keeler

first: Benjamin

last: Gerovac

first: Eugene

last: Agapov

first: Stephen

last: Austin

first: Jennifer

last: Yantis

first: Kelly

last: Gissy

first: Derek

middle: E

last: Byers

last: Alexander-Brett

first: Christy

middle: M

last: Hoffmann

first: Matthew

last: Wallace

first: Michael

last: Hughes

first: Erika

last: Crouch

middle: J

last: Holtzman


title: The transcriptomic landscapes of rice cultivars with diverse root system architectures grown in upland field conditions

status: Public on Mar 07 2021

city: Tsukuba

first: Taiji

last: Kawakatsu

state: Ibaraki

address: 3-1-3 Kan-nondai

country: Japan

institute: National Agriculture and Food Research Organization

type: Genome binding/occupancy profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: The transcriptomic landscapes of rice cultivars with diverse root system architectures grown in upland field conditions [DAP-seq]

summary: Genomic diversity is a source of transcriptomic and phenotypic diversities. Although genomic variations in rice (Oryza sativa) accessions have been extensively analyzed, information of transcriptomic and phenotypic variations, especially for below-ground variations, are limited. Here, we report the diversities of above- and below-ground traits and transcriptomes in highly diversified 61 rice accessions grown in the upland-field. We found that phenotypic variations were explained by four principal components and that tiller numbers and crown root diameters could summarize admixture groups. Transcriptome analysis revealed that admixture-group-associated differentially expressed genes were enriched with stress response related genes, suggesting that admixture groups have distinct stress response mechanisms. Root growth was negatively correlated with auxin inducible genes, suggesting the association between auxin signaling and mild drought stress. Negative correlation between crown root diameters and stress response related genes suggested that thicker crown root diameter is associated with mild drought stress tolerance. Finally co-expression network analysis implemented with DAP-seq analysis identified phytohormone signaling network and key transcription factors negatively regulating crown root diameters. Our datasets would serve as an important resource for understanding genomic and transcriptomic basis of phenotypic variations under the upland-field condition.

overall_design: DAP-seq of two rice bZIP transcription factors.


title: The CLASSY family controls tissue-specific DNA methylation patterns in Arabidopsis [ncRNA-seq]

status: Public on Mar 01 2021

city: La Jolla

first: Julie

middle: Ann

last: Law

state: CA

address: 10010 North Torrey Pines Rd

department: PLANT MOLECULAR AND CELLULAR BIOLOGY LABORATORY

institute: The Salk Institute for Biological Studies

summary: DNA methylation alters the epigenetic landscape of the genome, plays critical roles in regulating gene expression, and ensures transposon silencing. As evidenced by the numerous defects associated with aberrant DNA methylation landscapes, establishing proper tissue-specific methylation patterns is critical. Yet, how such differences arise remains a largely open question in both plants and animals. Here we demonstrate that four CLASSY proteins (CLSY1-4), which are differentially expressed during plant development, play major roles in controlling tissue-specific DNA methylation patterns. Depending on the tissue, the genetic requirements for specific CLSYs differ significantly and on a global scale, certain clsy mutants are sufficient to largely shift the epigenetic landscape between tissues. Together, these findings not only reveal substantial epigenetic diversity between tissues, but assign these changes to specific CLSY proteins, revealing how locus-specific targeting combined with tissue-specific expression enables the CLSYs to generate epigenetic diversity during plant development.

overall_design: smRNA-seq libraries were sequenced.

first: Ming

last: Zhou


title: RFX7 DNA binding landscape in U2OS

status: Public on Jun 17 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)

summary: Identification of the DNA binding landscape of the transcription factor regulatory factor X 7 (RFX7) in Nutlin-3a and DMSO control treated U2OS cells.

overall_design: RFX7 ChIP-seq in Nutlin-3a and DMSO control treated U2OS cells

first: Konstantin

last: Riege

first: Steve


title: Fasting/fed/refeeding RNAseq experiment conducted on mice with xenografted human livers.

status: Public on Jan 06 2021

city: Bethesda

first: Haiming

last: Cao

state: MD

address: 9000 Rockville Pike

department: NHLBI

institute: NIH

summary: Human hepatic gene regulations by fasting and refeeding in a mouse model with humanized liver generated from a single donor were reported.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Examination of three metabolic conditions in xenografted human liver cells

first: Ping

last: Li

first: Xiangbo

last: Ruan

first: Yi

last: Chen

first: Chengfei

last: Jiang

first: Yonghe

last: Ma


title: Single cell RNA-seq and machine learning reveal novel subpopulations and regulatory sequences in low-grade inflammatory monocytes

status: Public on Jan 29 2021

city: Blacksburg

first: Song

state: VA

address: 185 Ag-Quad Lane

institute: Virginia Tech

summary: We report the application of single-cell RNA sequencing(scRNA-seq) in mouse monocyte cells by integrating scRNA-seq, transcriptionfactor binding motifs, and ATAC-seq data using machine learning. We generated scRNA-seqdata from mouse monocytes treated with PBS, SD-LPS, 4-PBA, and SD-LPS + 4-PBA tounderstand the gene regulatory networks of monocytes under the low-grade inflammatorycondition and the mechanism of action for 4-PBA. We find two novelsubpopulations of monocyte cells in response to SD-LPS. We show that 4-PBApotently reprograms an anti-inflammatory monocyte phenotype and masks theeffects of subclinical low dose LPS. Together with TF binding motifs and ATAC-seqdata, a machine learning method, using guided, regularized random forest (GRRF)and feature selection was developed to select the best candidate TFs that areinvolved in the activation of monocytes within different clusters. Our results suggestthat our new machine learning method can select candidate regulatory genes aspotential targets for developing new therapeutics against low-gradeinflammation.

overall_design: Analysis of gene expression of mouse monocytes treated with PBS, SD-LPS, 4-PBA, and SD-LPS + 4-PBA at the single cell level

first: Jiyoung

last: Lee

first: Shuo

last: Geng

first: Liwu


title: Transcription profiles of tomato (Solanum lycopersicum) seedlings response to drought and heat stress

status: Public on Dec 30 2020

city: YangLin

first: WANG

middle: QI

last: QI

address: No.3，TaiCheng Road

country: China

institute: Northwest A&F University

summary: A total of 18 RNA samples over 6 time points under heat stress treatment and 21 RNA samples at 7 time points under drought condition were sequenced on Illumina HiSeq2500. After quality assessment and data clearance, a total of 288 Gb of data with average Q30 values 95.85% were obtained.

overall_design: In this research, S. lycopersicum cv. M82, a heat-sensitive and drought-sensitive tomato cultivar, was investigated by transcriptome sequencing under progressive heat stress with recovery and drought stress with recovery individually.

first: Qiqi

last: Wang

first: Tixu

last: Hu

first: Xiangqiang

last: Zhan


title: Estrogen-Sensitive Medial Preoptic Area Neurons Coordinate Hypothermia and Hypometabolism in Mice

status: Public on Oct 29 2020

city: Los Angeles

first: John

middle: Edward

last: van Veen

address: 610 Charles E young Dr

department: Integrative Biology and Physiology

institute: UCLA

summary: Homeotherms maintain a stable internal body temperature despite changing environments. During energy deficiency, some species can cease to defend their body temperature and enter a hypothermic and hypometabolic state known as torpor. Despite recent advances in our understanding of thermoregulation, the precise neurons that coordinate these profound thermoregulatory and metabolic changes remain largely unknown. Here, we demonstrate that estrogen-sensitive neurons in the medial preoptic area (MPA) are key drivers of hypothermia and hypometabolism in mice. We find that selectively activating estrogen-sensitive MPA neurons was sufficient to drive a coordinated depression of metabolic rate and body temperature similar to torpor, as measured by body temperature, physical activity, indirect calorimetry, heart rate, and brain activity. Inducing torpor with a prolonged fast revealed larger and more variable calcium transients from estrogen-sensitive MPA neurons during bouts of hypothermia. Finally, selective ablation of estrogen-sensitive MPA neurons demonstrated that these neurons are required for the full expression of fasting-induced torpor. Together, these findings suggest a role for estrogen-sensitive MPA neurons in directing the thermoregulatory and metabolic responses to energy deficiency.

overall_design: Patch-seq to compare transcriptomes of heat responsive and heat non-responsive Esr1 positive neurons in the MPA

first: Zhi

last: Zhang

first: Yanlin

last: He

first: J

first: Yong

last: Xu

first: Stephanie

last: Correa


title: Drug Combination Signatures for Prediction and Mitigation of Toxicity.

status: Public on May 21 2021

city: New York

first: Ravi

last: Iyengar

state: NY

address: 1425 Madison Avenue, Room 12-70C

department: Pharmacological Sciences

institute: Icahn School of Medicine at Mount Sinai

summary: Baseline transcriptomic signatures of cardiomyocytes differentiated from hiPSC lines generated from clinically well-characterized, diverse healthy human individuals. We provide mRNAseq data of various replicate samples of cardiomyocytes differentiated from 6 hiPSC lines.

overall_design: The overall goal of the drug signatures for prediction and mitigation of toxicity study is to use genomic and proteomic high-throughput measurements as the basis for computational analysis that integrates network analyses with structural constraints and dynamical models in multiple cell types to identify signatures that predict toxicity induced by 55 FDA-approved chemotherapeutic drugs and potential mitigation of this toxicity.  For this purpose, we have generated human induced pluripotent cell (hiPSC) lines from established fibroblast lines of forty clinically healthy racially diverse male and female study participants who ranged in age from 22 and 61 years. One clone from each of the forty hiPSC line was fully characterized for normal karyotype, short-tandem repeat matching to the original fibroblast line (authentication), pluripotency by select pluripotent marker expression via immunocytochemistry and by mRNAseq-based PluriTest analysis, and whole-genome sequencing. In order to establish hiPSC line-specific baseline (vehicle/control treatment) drug toxicity trasncriptomic signatures, cardiomyocytes were differentiated from 6 (3 male and 3 female) hiPSC lines using an established protocol, purified to 95% purity (SIRPA+CD90-) using a metabolic switch protocol, reseeded and treated for 48 hrs with DMSO (14.1 mM) before mRNAseq was performed on various replicate samples (biological/independent differentiations as well as technical/independent wells).


title: Prior activation state shapes the microglia response to anti-human TREM2 in a mouse model of Alzheimer's disease

status: Public on Dec 08 2020

city: South San Francisco

first: Daniel

middle: C

last: Ellwanger

address: 1120 Veterans Blvd

department: Genome Analysis Unit

institute: Amgen Inc

summary: Triggering receptor expressed on myeloid cells 2 (TREM2) sustains microglia response to brain injury stimuli including apoptotic cells, myelin damage, and amyloid β (Aβ). Alzheimer’s Disease (AD) risk is associated with the TREM2R47H variant, which impairs ligand binding and consequently microglia responses to Aβ pathology. Here we tested whether TREM2 engagement by an agonistic mAb, hT2AB, designated as a surrogate ligand facilitates microglia responses in 5XFAD transgenic mice that accumulate Aβ and express either the common TREM2 variant (TREM2CV) or TREM2R47H. scRNA-seq of microglia from TREM2CV-5XFAD mice treated once with control IgG exposed trajectories representative of activated microglial populations including disease-associated microglia (DAM), interferon-responsive (IFN-R), cycling (Cyc-M), and MHC-II expressing (MHC-II) microglia. All of these were underrepresented in TREM2R47H-5XFAD mice, suggesting that TREM2 ligand engagement is required for microglia transitions. Moreover, Cyc-M and IFN-R microglia were better represented in female than male TREM2CV-5XFAD mice, likely reflecting a greater Aβ load in female 5XFAD mice. A single systemic injection of hT2AB replenished the Cyc-M, IFN-R, and MHC-II pools in TREM2R47H-5XFAD mice. In TREM2CV-5XFAD mice, however, hT2AB brought the representation of male Cyc-M and IFN-R microglia closer to that of females, in which microglia transitions in response to Aβ had already reached their peak. Repeated treatment with a murinized version mT2AB over a 10 days period increased brain content of chemokines in TREM2R47H-5XFAD mice, consistent with microglia expansion and shifts in gene expression patterns. Thus, the impact of hT2AB on microglia responses is shaped by the extent of TREM2 endogenous ligand engagement and basal microglia activation.

overall_design: Single-cell RNA-Seq profiles of CD45+ cells from brain cortices of 8-month-old female and male TREM2CV-5XFAD or TREM2R47H-5XFAD transgenic mice, and female Trem2–/– mice assayed 48 hours after single dose injections of hT2AB or control IgG.

first: Shoutang


title: In vitro gene exoression comparison between the ST217 serotype 1 strain A42174 and the serotype 2 strain D39.

status: Public on Nov 12 2020

city: Dublin

first: Karsten

last: Hokamp

address: College Green

department: Smurfit Institute of Genetics

country: Ireland

institute: Trinity College Dublin

summary: Streptococcus pneumoniae is a frequent coloniser of the human nasopharynx and a major cause of life-threating invasive infections such as pneumonia, meningitis and sepsis. Over 1 million people die every year due to invasive pneumococcal disease (IPD), mainly in developing countries. Serotype 1 is a common cause of IPD; however, unlike other serotypes, it is rarely found in the carrier state in the nasopharynx, which is often considered a prerequisite for disease. The aim of this study was to understand this dichotomy.    We used murine models of carriage and IPD to characterise the pathogenesis of African serotype 1 (Sequence Type 217) pneumococcal strains obtained from the Queen Elizabeth Central Hospital in Blantyre, Malawi. We found that ST217 pneumococcal strains were highly virulent in a mouse model of invasive pneumonia, but in contrast to the generally accepted assumption, can also successfully establish nasopharyngeal carriage. Interestingly, we found that co-colonising serotypes may proliferate in the presence of serotype 1, suggesting that acquisition of serotype 1 carriage could increase the risk of developing IPD by other serotypes. RNAseq analysis confirmed that key virulence genes associated with inflammation and tissue invasiveness were upregulated in serotype 1. These data reveal important new insights into serotype 1 pathogenesis, with implications for carriage potential and risk of invasive disease through interactions with other co-colonising serotypes; an often overlooked factor in transmission and disease progression.

overall_design: A total of 6 samples were analysed. These samples were from 3 different growth phases and two different bacterial strains (ST217 serotype 1 strain A42174 and serotype 2 strain D39). No replicates were used.

first: Laura

last: Bricio-Moreno

first: Chrispin

last: Chaguza

first: Reham

last: Yahya

first: Rebecca

middle: K

last: Shears

first: Jennifer

last: Cornick

first: Marie

last: Yang

middle: R

last: Neill

first: Neil

last: French

first: Jay

middle: D

last: Hinton

first: Dean

middle: B

last: Everett

first: Aras

last: Kadioglu


title: Dynamic Shifts in the Composition of Resident and Recruited Macrophages Influence Tissue Remodeling in NASH

status: Public on Dec 31 2020

first: Maxim

middle: N.

last: Artyomov

state: MO

address: 660 S. Euclid Avenue, Campus Box 8118

department: Immunology&Pathology

institute: Washington University in St.Louis

summary: NASH is associated with signficant changes in liver macrophage composition.  To gain insight into this heterogenity we performed scRNA on liver myeloid cells from mice fed a HFD for 16 weeks.

overall_design: Three C57CL/6 male mice were fed High fat, high sucrose diet (Research Diets -cat# D12492) for 16 weeks after which immune cells were isolated from the liver using portal vein perfusion and a percoll gradient protocol. The cells underwent flow sorting on live singlet cells and were gated on CD11bhi, F4/80int and CD11bint, F4/80hi populations.  Eosinophils and neutrophils were removed using Ly6G and siglecF exlusion. Samples of these macrophages were mixed 1:1 and the 3 mouse samples were pooled to create a signal sample for scRNA seq.

first: Sabine

last: Daemen

first: Anastasiia

last: Gainullina

first: Gowri

last: Kalugotla

first: Li

last: He

first: Mandy

last: Chan

first: Joseph

middle: W

last: Beals

first: Kim

middle: H

last: Liss

first: Samuel

last: Klein

first: Ariel

last: Feldstein

middle: N

first: Brian

last: Finck

first: Joel

last: Schilling


title: Defining the Teratoma as a Model for Multi-Lineage Human Development

status: Public on Nov 04 2020

first: Yan

last: Wu

state: California

address: 9500 Gilman Drive

department: Bioengineering

institute: UCSD

summary: Studying early human developmental processes requires access to a model system that is easy to perturb, either genetically or chemically, genetically tractable and recapitulates key features of organogenesis. We propose that the teratoma, a recognized standardused for for validating pluripotency in stem cells, could be a promising platform for modeling human development. Teratomas differentiate to all germ layers, have regions of complex tissue-like organization with internal vasculature, and are relatively easy to generate and thus accessible, especially in comparison to human fetal tissue. Teratomas, however, have not been characterized rigorously to determine their suitability to model human developmental processes the diversity and identities of the cell types present, and their level of maturity in comparison to human developmental cell types. We thus systematically analyzed, perturbed, and engineered human pluripotent stem cell (PSC)-derived teratomas. Usingused histology, RNA in situ hybridization, and single cell RNA-seq (scRNA-seq) of 179,632 cells across 23 teratomas generated from 4 cell lines, we observed  to find that teratomas reproducibly contain approximatelyat least 20 cell types across all three germ layers, and the cell type heterogeneity between teratomas was comparable to that found in organoid systems. We found that a significant fraction of injected PSCs engrafted, suggestingused lentiviral barcoding to determine there is minimalno bottlenecking during teratoma formation. Additionally, we mapped our teratoma data to published human fetal data and showed that the teratoma gut and brain cell types correspond well to existing fetal gut and brain scRNA-seq datasetscells. We then performed a CRISPR-Cas9 knockout screen in teratomas targeting key genes known to be embryonic lethal, and found that TWIST1, RUNX1, ASCL1, CDX2, and KLF6 knockouts resulted in assessed shifts in lineage abundance.  using scRNA-seq. We found that TWIST1, RUNX1, ASCL1, CDX2, and KLF6 knockouts resulted in reproducible shifts in lineage abundance consistent with known biology.  All of these  These knockouts had effects on cell types from multiple germ layers, showing that the teratoma can serve as a platform to studymodel all major human lineages of human development simultaneously. Additionally, we ran a CRISPR-Cas9 screen targetingWe also knocked out the genes underlying Rett, Pitt-Hopkins, and L1 Syndromes and identified cell type specific shifts in gene expression. Finally, we engineered a novel miRNA-regulated suicide gene circuit that enriches for tissues in the teratoma that express a specific miRNA that selectively depletes cells that do not express a tissue-specific endogenous miRNA, allowing us to enrich for desired lineages in the teratoma, which we demonstrated using miR-124 to enrich for neuro-ectoderm. Specifically, we used miR-124 to successfully enrich for neuro-ectoderm. Taken together, we believe the teratoma is a promising platform for modeling multi-lineage human development, functional genetic screening, and cellular engineering

overall_design: We first characterized 7 teratomas generated from H1 stem cells, with 3 of those teratomas containing lentiviral barcodes for additional lineage tracing. We characterized one teratoma each from H9, HUES62, and PGP1 stem cells to assess heterogeneity across cell lines. We ran 2 replicate CRISPR-KO screens targeting embryonic lethal genes. We generated 3 teratomas (with 2 x 10X runs for each teratoma) per screen. We then ran a CRISPR-KO screen targeting genes known to cause neural diseases using 2 teratomas (again with 2 x 10X runs per teratoma). Finally, we created a miRNA circuit that enriches for neuro-ectoderm cells expressing miR-124. We generated 4 GCV+ teratomas, 2 that used intratumoral injections of GCV, and 2 that used both intratumoral and intraperitoneal injections. We generated one GCV- miR-124 teratoma as a control.

first: Daniella

last: McDonald

first: Amir

last: Dailamy

first: Justin

last: Tat

first: Udit

last: Parekh

first: Dongxin

last: Zhao

first: Michael

last: Hu

first: Ann

last: Tipps

first: Kun

last: Zhang

first: Prashant

last: Mali


title: Direct induction of retinal ganglion cell-like neurons

status: Public on Sep 30 2020

city: Guangzhou

first: Shuyi

last: Chen

address: #7 Jinsui Rd, Zhujiang Newtown

institute: Zhongshan Ophthlamic Center

summary: Mouse embryonic fibroblasts were reprogrammed into retinal ganglion cell-like neurons by overexpressing Ascl1/Brn3b/Isl1 transcription factor combination in 13 days.

overall_design: Cells were collected on day 0 (MEF), 2, 4, 7, 9 13 of reprogramming, and processed using 10X Genomics Chrominum to prepare scRNA-seq libraries.


title: Single-cell Transcriptomics Identifies Transcriptional Networks Driving Differentiation and Tumorigenesis in the Human Fallopian Tube

status: Public on Apr 19 2021

city: San Antonio

first: Kate

last: Lawrenson

address: 7703 Floyd Curl Dr.

institute: Cedars Sinai Medical Center

summary: The human fallopian tube harbors the cell-of-origin for the majority of high-grade serous “ovarian” cancers (HGSCs), but its cellular composition, particularly of the epithelial component, is poorly characterized. We subjected 12 fallopian specimens from 8 patients to single-cell transcriptomic profiling, analyzing around 53,000 individual cells to map the major immune, fibroblastic and epithelial cell types present in this organ. We identified 10 epithelial sub-populations, characterized by diverse transcriptional programs including SOX17 (enriched in secretory epithelial cells), TTF3 and RFX3 (enriched in ciliated cells) and NR2F2 (enriched in early, partially differentiated secretory cells). Based on transcriptional signatures, we reconstructed a trajectory whereby secretory cells differentiate into ciliated cells via a RUNX3high intermediate. Computational deconvolution of the cellular composition of advanced HGSCs based on epithelial subset signatures identified the ‘early secretory’ population as a likely precursor state for the majority of HGSCs. The signature of this rare population of cells comprised both epithelial (EPCAM, KRT) and mesenchymal (THY1, ACTA2) features, and was enriched in mesenchymal-type HGSCs (P = 6.7 x 10e-27), a group known to have particularly poor prognoses. This cellular and molecular compendium of the human fallopian tube in cancer-free women is expected to advance our understanding of the earliest stages of fallopian epithelial neoplasia.

overall_design: Single-cell RNA sequencing (scRNA-Seq) analysis of 12 fresh primary fallopian tube specimens from 8 patients

first: Huy

middle: Q

last: Dinh

first: Xianzhi

last: Lin

first: Forough

last: Abbasi


title: Global genome decompaction leads to stochastic activation of gene expression as a first step toward fate commitment in human hematopoietic cells [scRNA-seq]

status: Public on Aug 25 2020

city: Paris

first: Andràs

last: Pàldi

state: Ile de France

address: 19 rue Chaligny

department: Centre de Recherche de Saint Antoine

country: France

institute: Ecole Pratique des Hautes Etudes

summary: When human cord blood derived CD34+ cells are induced to differentiate in vitro, they undergo rapid and dynamic morphological and molecular transformation that are critical for the fate commitment. Using ATAC-seq and single-cell RNA sequencing we detected two phases of this process. We show that a rapid and widespread chromatin opening - that makes most of the gene promoters in the genome accessible - precedes the high and unrestrained transcription of a large variety of genes. This phase results in a quasi-random gene expression profile unique to each cell. During the second phase, slow chromatin closing precedes the downregulation of transcription and the emergence of coherent expression profiles. Transcription factors may play a role in the maintenance of the transcription activity of their target genes rather than in their initial activation. These observations are consistent with a model based on the spontaneous probabilistic organization of the cellular process of fate commitment.

overall_design: Evolution of single cell mRNA profile and DNA accessibility profile of HSC after cytokine stimulation

first: Romuald

last: Parmentier

first: Alice

last: Moussy

first: Sophie

last: Chantalat


title: The transcriptomic landscapes of rice cultivars with diverse root system architectures grown in upland field conditions [RNA-seq]

first: Taiji

last: Kawakatsu

overall_design: RNA-seq from root tips and leaves of 61 highly diversified rice accessions grown in the upland field.


title: The Innate Immune Factor IRF3 Reduces Adipose Thermogenesis via ISG15-mediated Reprogramming of Cellular Metabolism

status: Public on Jul 24 2020

city: Boston

first: NORC

last: Boston

state: MA

address: 3 Blackfan Circle, CLS0733

institute: Beth Israel Deaconess Medical Center

summary:
Purpose: Interferon regulatory factor 3 (IRF3) is activated by pro-inflammatory cytokines, but its role in regulating adaptive thermogenesis and energy expenditure remains unclear. Here, we report that IRF3 as a negative transcription regulator of adaptive thermogenesis. Adipocyte-specific IRF3 knockout (FI3KO) attenuates HFD-induced obesity by increasing energy expenditure; further studies show that IRF3 suppresses adaptive thermogenesis through ISG15-mediated inhibition of glycolysis in adipocytes. Conversely, overexpression of IRF3 in adipocytes causes reduced thermogenesis gene expression, energy expenditure, and more persistent to HFD-induced obesity. Moreover, Isg15-/- increases adipose thermogenesis and protects mice from HFD-induced obesity and glucose intolerance. Taken together, these data indicate that IRF3 as a transcriptional regulator connecting between inflammatory signaling pathway and energy homeostasis
Methods: primary adipocyte mRNA profiles of 8-week-old wild-type (WT) and FI3OE mice were generated by deep sequencing.  The sequence reads that passed quality filters were analyzed at the transcript isoform level. qRT–PCR validation was performed using RT-PCR.
Conclusions: Our study represents the first detailed analysis of adipocyte transcriptomes from WT and FI3OE iWAT, with biologic replicates, generated by RNA-seq technology. The optimized data analysis workflows reported here should provide a framework for comparative investigations of expression profiles. Our results show that Irf3 adipocyte-speficic overrxpression markedly increases the expression of Isg15 and Herc6, which play important role in regulation of glycolysis.

overall_design: primary adipocyte mRNA profiles of 8-week-old old wild type (WT) and FI3OE mice

first: Shuai

last: Yan

first: Evan

last: Rosen


title: Integration of M. tuberculosis phenotype with single cell RNA-seq to interrogate host macrophage heterogeneity in vivo.

status: Public on Apr 28 2021

city: Ithaca

first: Davide

last: Pisu

address: 930 Campus Road

department: Microbiology and Immunology

institute: Cornell University

summary: Over the last several years, scRNA-seq has proven an invaluable tool for dissecting the role of the immune environment in many diseases. However, for infectious disease studies, the absence of information regarding the transcriptional status of the infecting agent reduces our functional appreciation of the roles of different immune effector cells in determining control versus progression of disease. In this study we detail a novel approach that combines bacterial fitness fluorescent reporter strains with scRNA-seq to simultaneously acquire the host transcriptome, surface marker expression and bacterial phenotype for each infected cell. This approach facilitates the dissection of the functional heterogeneity of M. tuberculosis-infected alveolar (AMs) and interstitial macrophages (IMs) in vivo and identifies clusters of pro-inflammatory AMs associated with stressed bacteria, in addition to three different populations of IMs with heterogeneous bacterial phenotypes. Finally, we show that the main macrophage populations in the lung are epigenetically constrained in their response to infection, while inter-species comparison reveals that most AMs subsets are conserved between mice and humans. Our approach is readily transferable to other infectious disease agents with the potential for a better understanding of the role that different host-cell populations play during the course of an infection.

overall_design: scRNA-seq analysis of Mtb-infected and uninfected mice lungs at 3 wpi (weeks post-infection); scRNA-seq of BAL (bronchoalveolar lavage) recovered from the lung of 3 healthy human volunteers; Bulk Dual RNA-seq analysis of M.tuberculosis transcriptome from hspx-high and hspx-low bacteria at 3 wpi; Bulk ATAC-seq analysis of BCG infected and uninfected mouse AM and IM populations 4 wpi.

first: Vipin

last: Narang

first: Lu

last: Huang

first: Monique

last: Theriault

first: Gabrielle

last: Le-Bury

first: Bernett

last: Lee

first: Agnes

last: Lakudzala

first: David

middle: T

last: Mzinza

middle: V

last: Mhango

first: Steven

last: Mitini-Nkhoma

first: Kondwani

last: Jambo

first: Amit

last: Singhal

first: Henry

last: Mwandumba

middle: G

last: Russell


title: Expression of circRNAs in gastrointestinal stromal tumor

status: Public on Jun 22 2020

city: changsha

first: Fangwen

last: Zou

state: hunan

institute: Central south univ

summary: To determine the circRNA expression profile in gastrointestinal stromal tumor and matched non-tumor tissues, we used circRNA microArray analysis from Arraystar to examine the expression of circRNAs in gastrointestinal stromal tumor and matched non-tumor tissues.

overall_design: Surgical specimen were distributed into two experimental groups: normal tissue group and tumor tissue group, then perform circRNAs chips by Arraystar Human circRNAs chip (Arraystar).

first: Ding

last: Cao


title: The transcriptional elongation rate regulates alternative polyadenylation in yeast

status: Public on Sep 01 2020

first: Zarmik

last: Moqtaderi

address: 240 Longwood Avenue C2-355

department: BCMP

institute: Harvard Medical School

summary: Yeast cells undergoing the diauxic response show a striking upstream shift in poly(A) site utilization, with increased use of ORF-proximal poly(A) sites resulting in shorter 3’ mRNA isoforms for most genes.  This altered poly(A) pattern is extremely similar to that observed in cells containing Pol II derivatives with slow elongation rates.  Conversely, cells containing derivatives with fast elongation rates show a subtle downstream shift in poly(A) sites. Polyadenylation patterns of many genes are sensitive to both fast and slow elongation rates, and a global shift of poly(A) utilization is strongly linked to increased purine content of sequences flanking poly(A) sites.  Pol II processivity is impaired in diauxic cells, but strains with reduced processivity and normal Pol II elongation rates have normal polyadenylation profiles.   Thus, Pol II elongation speed is important for poly(A) site selection and for regulating poly(A) patterns in response to environmental conditions.

overall_design:
mRNA isoform-specific sequencing to determine polyadenylation site usage in mutant strains and under various growth conditions

Please note that the *ABmerged_RelCountsByPosition 1 to 400.txt file was generated from both rep A and rep B samples, and is linked to the corresponding 'rep A' sample records.

first: Joseph

last: Geisberg

first: Kevin

last: Struhl


title: Global genome decompaction leads to stochastic activation of gene expression as a first step toward fate commitment in human hematopoietic cells.

first: Andràs

last: Pàldi

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

overall_design: Refer to individual Series


title: Next Generation Sequencing Facilitates Quantitative Analysis of Solanum lycopersicum bud and flower Transcriptomes

status: Public on Feb 27 2021

city: Harbin

first: Jian

last: Wang

address: 600 Changjiang Road

institute: Northeast Agricultural University

overall_design: RNA sequencing  in tomato for detect mRNA expression of Solanum lycopersicum.The two cultivars (monomaker, raceme) of bud and flower for transcriptome sequencing

first: Huanhuan

last: Yang


title: Maturational changes in mouse cutaneous touch and Piezo2-mediated mechanotransduction

status: Public on Jul 21 2020

city: Goettingen

first: Gabriela

last: Salinas

state: Lower-Saxony

address: Kreuzbergring 57

department: Department of Pathology

institute: Universitaetsmedizin Goettingen


title: Dysregulation of brain and choroid plexus cell types in severe COVID-19

status: Public on Oct 22 2020

city: Saarbrücken

first: Fabian

middle: Michael

last: Kern

state: Saarland

address: Campus E2 1

department: Center for Bioinformatics

institute: Saarland University

summary: Though SARS-CoV-2 primarily targets the respiratory system, patients and survivors can suffer neurological symptoms. Yet, an unbiased understanding of the cellular and molecular processes affected in the brains of COVID-19 patients is still missing. Here, we profile 65,309 single-nucleus transcriptomes from 30 frontal cortex and choroid plexus samples across 14 control (including 1 terminal influenza) and 8 COVID-19 patients. While a systematic analysis yields no molecular traces of SARS-CoV-2 in the brain, we observe broad cellular perturbations which predict that choroid plexus barrier cells sense and relay peripheral inflammation into the brain and show that peripheral T cells infiltrate the parenchyma. We discover COVID-19 disease-associated microglia and astrocyte subpopulations that share features with pathological cell states reported in human neurodegenerative disease. Synaptic signaling of upper-layer excitatory neurons—evolutionarily expanded in humans and linked to cognitive function—are preferentially affected in COVID-19. Across cell types, COVID-19 perturbations overlap with those in chronic brain disorders and reside in genetic variants associated with cognition, schizophrenia, and depression. Our findings and public dataset provide a molecular framework to understand COVID-19 related neurological disease observed now and which may emerge later.

overall_design:
Single-nuclei RNA transcriptomes of prefrontal cortex and choroid plexi tissue obtained from post-mortem brains of COVID-19, Influenza, and non-viral control patients using the 10x Genomics Drop-seq gene expression kit (v3.1).

Samples were sequenced at 150 bps paired-end configuration on a NovaSeq system. Index 1 contains sample indices (8 nts). Read 1 contains 10x cell barcode + UMI (28 nts). Read 2 contains the fragment insert (91 nts).

first: Andrew

first: Patricia

middle: M

last: Losada

first: Christina

middle: A

last: Maat

first: Georges

middle: P

last: Schmartz

first: Tobias

last: Fehlmann

first: Nicholas

last: Schaum

first: Davis

last: Lee

first: Kruti

last: Calcuttawala

first: Ryan

last: Vest

last: Gate

first: Daniela

last: Berdnik

first: Windy

last: McNerney

first: Inma

last: Cobos

first: Nicole

last: Ludwig

first: Walter

middle: J

last: Schulz-Schaeffer

first: Andreas

last: Keller

first: Tony

last: Wyss-Coray

first: Mayaan

last: Agam

first: Julian

last: Stein

first: Nannan

last: Lu

first: Oliver

last: Hahn

first: Divya

last: Channappa


title: RNA-Seq analysis of the retinal pigment epithelial cell line, ARPE19, during a time course of serum deprivation.

status: Public on May 13 2020

first: Katherine

middle: MacLean

last: Peterson

address: Building 6 Room 107B

institute: NEI, NIH

summary: ARPE19 cells, derived from human retinal pigment epithelium (RPE), were cultured in serum supplemented media, then the serum was removed, and culture continued in serum free media.  We use this culture system as a model for the early stages of Age-related macular degeneration.  RNA-Seq was performed on RNAs from seven time points: day0 (serum supplemented), day1, 3, 4, 5, 6, and 9 serum deprived samples.

overall_design: RNA sequencing was performed on samples from serum deprived ARPE19 cells from days 0, 1, 3, 4, 5, 6, and 9 with three biological replicates for each time point.

first: Graeme

last: Wistow

first: Sanghamitra

last: Mishra

first: Yiwen

last: He

first: John

last: Powell

first: Esther

last: Asaki


title: Anti-human TREM2 induces microglia proliferation and reduces pathology in an Alzheimer's Disease model

first: Meer

last: Mustafa

address: 131 Oyster Point Blvd, Ste 600

institute: Alector

summary: TREM2 is a receptor for lipids expressed in microglia. The R47H variant of human TREM2 impairs ligand binding and increases Alzheimer’s Disease (AD) risk. In mouse models of amyloid b (Ab) accumulation, defective TREM2 function affects microglial response to Ab plaques exacerbating tissue damage, whereas TREM2 overexpression attenuates pathology. Thus, AD may benefit from TREM2 activation. Here, we examined the impact of an anti-human TREM2 agonistic mAb, AL002c, in a mouse AD model expressing either the common variant (CV) or the R47H variant of TREM2. Single cell RNA-seq of microglia after acute systemic administration of AL002c showed induction of proliferation in both CV- and R47H-transgenic mice. Prolonged administration of AL002c reduced filamentous plaques and neurite dystrophy, impacted behavior and tempered glial inflammatory response. We further showed that a variant of AL002c has been given safely in a first-in-human phase I clinical trial and engages TREM2 based on CSF biomarkers. We conclude that AL002c is a promising candidate for AD therapy.

overall_design: Single-cell RNA-seq on whole brains from an AL002c acute dose in common variant (CV) and R47H human TREM2 variant BAC transgenic 5XFAD mice


status: Public on May 26 2020

first: Xuemei

last: Xie

address: 811 Enders Building, 320 Longwood Ave.

department: Transfusion Medicine

institute: Boston Children's Hospital

overall_design:
Refer to individual Series

The GitHub analysis code link to our study "Single-cell transcriptome profiling reveals neutrophil heterogeneity in homeostasis and infection": https://github.com/ChengLiLab/Neutrophil_NI_paper.


title: scRNA-seq of electrophysiologically characterized DRG neurons reveals subtype-specific and maturational differences in gene expression

first: Gabriela

last: Salinas

summary: Cultured dorsal root ganglia neurons of 4 and 12 weeks old C57Bl/6 mice were first characterized as mechanosensitive (showed  rapidly adapting mechanically actived currents in whole-cell votage clamp or not (non-responders)) and as either mechanoreceptors or nociceptors (evoked action potential waveform in whole-cell current clamp). Next, cells were subjected to RNA-seq and sequences were analyzed bioinformatically. We found maturatinal changes comprising subtype-specific and age-dependent differential gene expression in these somatosensory neurons. See Michel, Niklas and Narayanan, Pratibha and Shomroni, Orr and Schmidt, Manuela, Cutaneous Touch and Piezo2-Mediated Mechanotransduction Decline Throughout Mouse Maturation Until Adulthood. CELL-REPORTS-D-20-00425. Available at SSRN: https://ssrn.com/abstract=3536401 or http://dx.doi.org/10.2139/ssrn.3536401

overall_design: 31 Single DRG neuron RNA profiles of 4 and 12 weeks old male WT C57Bl/6J mice, grouped by age and their electrophysiological profile

first: Michel

last: Niklas

first: Narayanan

last: Pratibha

first: Shomroni

last: Orr

first: Schmidt

last: Manuela


title: Transcriptional profiling of endothelial cells lacking Flvcr2

status: Public on May 06 2020

city: Rancagua

first: Nicolas

last: Santander

address: Libertador Bernardo O'Higgins 611

country: Chile

institute: Universidad de O´Higgins

summary: Flvcr2 is a putative heme transporter expressed in endothelial cells of the brain. Mutations in this gene in humans is the cause of Fowler syndrome, in which newborns show malformed brain blood vessels. We generated a mouse model of this disease by knocking out the mouse ortholog of the gene (Flvcr2). These mouse mutants recapitulate the human phenotype. To understand the molecular changes associated with Flvcr2 deletion, we defined the transcriptional profile of heterozygous and mutant endothelial cells. We observed changes in gene expression consistent with altered angiogenesis and metabolic pathways necessary for endothelium homeostasis.

overall_design: Endothelial cells were isolated from E14.5 embryonic brains using fluorescent-activated cell sorting. Since the mutation in the Flvcr2 gene leads to expression of GFP, we sorted GFP+ CD31+ cells. Total RNA was extracted from 2000 – 5000 cells to synthesize PolyA+ libraries for sequencing in a HiSeq4000 using SE50. More than 40 million reads were obtained for each sample.

first: Carlos

last: Lizama

first: Thomas

last: Arnold


title: Transcriptome profiling of lettuce plants exposed to low temperature (4°C)

status: Public on Apr 13 2020

city: Beltsville

first: Sunchung

last: Park

address: 10300 Baltimore ave, Bldg001

department: ARS-NEA

institute: USDA -ARS

overall_design: mRNA profiles for lettuce plants exposed to low temperature for 0h, 4h, 24h, or 7d were generated in triplicate by Illumina RNA sequencing

first: Beiquan

last: Mou


title: Genome wide analysis of the changes in gene expression following co-culture of A431 cancer cells and stromal fibroblasts

status: Public on Mar 31 2020

city: London

first: Erik

last: Sahai

address: 1 Midland Road

country: United Kingdom

institute: Francis Crick Institute

summary:
This experiment tested the hypothesis that distinct changes in gene expression are triggered in response to direct contact between cancer cells and fibroblasts, as
opposed to co-cultures in which the cells are physically separated by membrane that permits diffusion

overall_design: A431-GFP or VCAF2b-mCherry were cultured in either mono-cultures, co-cultures separated by a 0.4micron filter, or direct co-cultures followed by FACS purification.

first: Stefanie

last: Derzsi

last: Arwert


title: Identification of mecciRNAs and their roles in the mitochondrial entry of proteins

status: Public on Jan 23 2020

city: Hefei

first: Ge

last: Shan

state: Anhui

address: 443 Huangshan Road

department: School of Life Sciences

institute: University of Science and Technology of China

summary: To identify mitochondrial RNAs, we isolated mitochondria and performed RNA sequencing. Differential expression of mRNAs and circRNAs were then analyzed.

sample_organism:
Danio rerio
Homo sapiens
Mus musculus

platform_organism:
Danio rerio
Homo sapiens
Mus musculus

overall_design: RNA-seq of Mitochondria

first: Liu

last: Xu


title: Transcriptional profiling of endothelial cells lacking Tgfbr2

summary: Tgfbr2 controls signal transduction after binding activated Tgfb1. Inactivation of this receptor in endothelium results in vascular dysplasia and severe hemorrhage. Here, we define the transcriptional profile of endothelial cells lacking Tgfbr2.

overall_design: Endothelial cells were isolated from E14.5 embryonic brains using fluorescent-activated cell sorting. We used the Ai14 allele to induce expression of TdTomato in recombined cells, facilitating cell sorting by detecting TdTomato fluorescence. Total RNA was extracted from 2000 – 5000 cells to synthesize PolyA+ libraries for sequencing in a HiSeq4000 using SE50.


title: Whole blood transcriptomic analysis of beef cattle at arrival identifies potential predictive molecules and mechanisms that indicate animals that naturally resist bovine respiratory disease

status: Public on Jan 14 2020

city: Canyon

first: Matthew

middle: Adam

last: Scott

state: TX

address: 3201 Russell Long Blvd

department: Large Animal Clinical Sciences

institute: Texas A&M University

summary:
Objectives: Identify gene products that characterize the biological status of typical calves which have been recently weaned, transported, and co-mingled prior to arrival at stocker facilities in order to identify gene products associated with BRD resistance.
Methods: Whole blood RNA profiles were generated via NGS approach, using an Illumina HiSeq 3000. Individual samples were processed using an adaptation of the Revised Tuxedo Suite protocol (Tuxedo 2), then analyzed in R using edgeR and DESeq2 with likelihood-ratio testing. Genes were considered differentially expressed with an FDR cutoff of 0.10. qRT-PCR validation was performed using a SYBR green assay.
Results: 135 differentially expressed genes were identified between healthy and BRD animals; 36 were shared between edgeR and DESeq2. Biological processes, using the 36 DEGs, were identified to be involved with inflammation, defense response, macrophage function, and lipoxin metabolism/biosynthesis. Enriched pathways of the 36 DEGs were involving SPM synthesis and angiotensinogen metabolism to angiotensins. Genes increased in diseased animals had known function towards anitmicrobial activity.
Conlusions: Our analysis has provided, for the first time, a list of whole blood molecular biomarkers that may predict disease risk in the first 28 days of stocker cattle arrival. We identified pathways related to immune response, inflammatory mediation, metabolic processes, and stress regulation. Using whole blood transcriptomic analysis, this study provides an insight to host immunity in response to BRD.

overall_design: Whole blood mRNA of stocker cattle at facility arrival were generated through next-generation sequencing utilizing an Illumina HiSeq 3000.


title: RNA-seq and Mass spectrometry analysis reveals the  roles of YTHDF1 in aging

city: Shenzhen

first: yuan

last: meng

address: College avenue 1066#

department: Department of Medicine

institute: Shenzhen University

type: Methylation profiling by high throughput sequencing

summary:
To understand the functional roles of YTHDF1 in cellular senescence and aging,  we lead the RNA sequence in WT or Ythdf1 deficiency colon epithelial cells. The results showed that the cholesterol biosynthesis related genes were upregulated in Ythdf1 KO mice. We also purified FLAG-YTHDF1 protein in HEK293T cells and did protein mass spectrometry, and found that the mTORC1 and TSC complex constituents mTOR, RPTOR, and TSC1/2 were identified in the YTHDF1-complex.
Methylated RNA immunoprecipitation(MeRIP) with specific m6A antibody and used for library construction and the next generation sequencing, to identify m6A modified transcripts in WT or Ythdf1 deficiency colon epithelial cells after DSS treatment

overall_design:
FLAG-YTHDF1 IP MASS spectrometry
2 WT vs 2 Ythdf1 KO
2 WT_DSS vs 2 Ythdf1 KO_DSS

first: Zhen

last: Zhang

first: Baohua

last: Liu

first: Chenzhong

first: Yuan

last: Meng


title: Translational profiling of microglia

status: Public on Jan 06 2020

summary: Several mouse lines  have been developed to target microglia genetically; however, they lack specificity. Here, we use ribosome tagging and immunoprecipitation coupled to RNA-Seq in our newly developed mouse line to define the true microglial translatome.

overall_design: Ribosome-mRNA complexes were isolated from whole brains from P2ry12-CreER; RPL22HA mice by immunoprecipitation. Transcript enrichment was evaluated by RNA-Seq of transcripts in the input and in the immunoprecipitated fractions.

first: Gabriel

last: McKinsey


title: Investigating cone photoreceptor development using patient-derived NRLnull retinal organoids

status: Public on Jan 15 2020

city: Baltimore

first: Alyssa

last: Kallman

state: Maryland

address: 400 N Broadway

institute: Johns Hopkins University, School of Medicine

summary: Photoreceptor loss is a leading cause of blindness, but mechanisms underlying photoreceptor degeneration are not well understood.  Treatment strategies would benefit from an improved understanding of gene-expression patterns directing photoreceptor development, as many genes are implicated in both development and degeneration.  Neural retina leucine zipper (NRL) is critical for rod photoreceptor genesis and degeneration, with NRL mutations known to cause enhanced S-cone syndrome and retinitis pigmentosa.  While murine Nrl loss has been characterized, studies of human NRL can identify important insights for human retinal disease.  Here we utilized human organoid models of retinal development to molecularly define developmental alterations in a human model of NRL loss.  Consistent with the function of NRL in rod fate specification, human retinal organoids lacking NRL develop S-opsin dominant photoreceptor populations.  We report generation of two distinct S-opsin expressing populations in NRL null retinal organoids and identify MEF2C as a candidate regulator of cone development.

overall_design: single cell RNA sequencing via Dropseq of retinal organoids at d100 (4 wild type and 4 NRL null) and at d170 (3 wild type and 6 NRL null)

first: Donald

last: Zack

first: David

last: Gamm


title: Therapeutic IDOL reduction ameliorates amyloidosis and improves cognitive function in APP/PS1 mice

status: Public on Dec 24 2019

city: Los Angeles

first: Russell

last: Littman

state: Ca

address: 610 Charles E Young Dr S

institute: UCLA

summary: An antisense oligonucleotide (ASO) against E3 ubiquitin ligase IDOL in the brain significantly decreased Aβ pathology, and improved spatial learning and memory in APP/PS1 mice.

overall_design: Drop-Seq was performed on 6 B6.Cg-Tg( APPswe,PSEN1dE9) 85Dbo/Mmjax (005864) mice. 3 mice were treated with ASO, and 3 treated with PBS.

first: Jie

last: Gao

first: Xia

last: Yang

first: Peter

last: Tontonoz


title: Massively parallel characterization of regulatory dynamics during neural induction [RNA-seq II]

status: Public on Oct 23 2019

city: Berkeley

first: Anat

last: Kreimer

address: 378 Stanley Hall

institute: University of California, Berkeley

summary: The molecular components governing neural induction remain largely unknown. Here, we used a suite of genomic and computational tools to comprehensively identify these components. We performed RNA-seq, ChIP-seq (H3K27ac, H3K27me3) and ATAC-seq on human embryonic stem cells (hESCs) at seven early neural differentiation time points (0-72 hours) and identified thousands of induced genes and their putative regulatory regions. We analyzed the function of ~2,500 selected regions using massively parallel reporter assays at all time points. We found numerous temporal enhancers that correlated with similarly timed epigenetic marks and gene expression. Development of a prioritization method that incorporated all genomic data identified key transcription factors (TFs) involved in neural induction. Individual overexpression of eleven TFs and several combinations in hESCs found novel neural induction regulators. Combined, our results provide a comprehensive map of genes and functional regulatory elements involved in neural induction and identify master regulator TFs that are instrumental for this process.

overall_design: RNA-seq (3 replicates), ChIP-seq (H3K27ac, H3K27me3 - 2 replicates) and ATAC-seq (3 replicates) were preformed on human embryonic stem cells (hESCs) at seven early neural differentiation time points (0-72 hours). Moreover, the function of ~2,500 selected regions was analyzed using massively parallel reporter assays at all time points (3 replicates). Additionally, RNA-seq (3 replicates) was performed on hESCs at 14 hours after overexpression of candidte TFs and controls.

first: Fumitaka

last: Inoue

first: Nadav

last: Ahituv

first: Nir

last: Yosef


title: Massively parallel characterization of regulatory dynamics during neural induction

overall_design: Refer to individual Series


title: Global genome decompaction leads to stochastic activation of gene expression as a first step toward fate commitment in human hematopoietic cells [ATAC-seq]

status: Public on Aug 25 2020

first: Andràs

last: Pàldi

address: 19 rue Chaligny

institute: Ecole Pratique des Hautes Etudes

summary: When human cord blood derived CD34+ cells are induced to differentiate in vitro, they undergo rapid and dynamic morphological and molecular transformation that are critical for the fate commitment. Using ATAC-seq and single-cell RNA sequencing we detected two phases of this process. We show that a rapid and widespread chromatin opening - that makes most of the gene promoters in the genome accessible - precedes the high and unrestrained transcription of a large variety of genes. This phase results in a quasi-random gene expression profile unique to each cell. During the second phase, slow chromatin closing precedes the downregulation of transcription and the emergence of coherent expression profiles. Transcription factors may play a role in the maintenance of the transcription activity of their target genes rather than in their initial activation. These observations are consistent with a model based on the spontaneous probabilistic organization of the cellular process of fate commitment.

overall_design: Evolution of single cell mRNA profile and DNA accessibility profile of HSC after cytokine stimulation

first: Romuald

last: Parmentier

first: Alice

last: Moussy

first: Sophie

last: Chantalat


title: Massively parallel characterization of regulatory dynamics during neural induction [MPRA]

overall_design: RNA-seq (3 replicates), ChIP-seq (H3K27ac, H3K27me3 - 2 replicates) and ATAC-seq (2 replicates) were preformed on human embryonic stem cells (hESCs) at seven early neural differentiation time points (0-72 hours). Additionally, the function of ~2,500 selected regions was analyzed using massively parallel reporter assays at all time points (3 replicates).


title: Fasting Fed RNA sequencing experiment of mice with humanized livers

status: Public on Oct 04 2019

city: Bethesda

first: Haiming

last: Cao

address: 9000 Rockville Pike

department: NHLBI

institute: NIH

summary: We report the RNA sequencing results of four fasting mice with humanized livers and four fed mice with humanized livers.

overall_design:
RNA sequencing profiles were generated for fasting and fed humanized mice.
The humanized livers are generated by engrafting human hepatocytes in immunodeficient mice.


title: Single-cell RNA seq reveals the transcriptional landscape and heterogeneity of macrophages in murine gut tissues

status: Public on Oct 16 2019

city: Tianjin

first: Ming

last: Wei

address: 94 Weijin road

department: Department of Immunology, Nankai University School of Medicine

institute: Nankai University

summary: CD11b+ cell populations, especially macrophages are highly heterogeneous tissue resident immune cells in both mice and human. Exact subsets and their phenotype remain unknown. We here analyzed gut CD11b+ cell populations using scRNA-seq in normal, inflamed and Nlrc4 deficient mice. There existed twelve CD11b+ cell populations and subsets in SPF mice. These CD11b+ subsets were changeable dependent on inflammation and gut environment. We found consistent high expression of Ly6C, Cd62L, previously undescribed Trem1 and Ccr7 in Ly6Chigh macrophages and Cd206 and Cx3cr1 in Ly6Clow/neg cell population in different mice. However, signature genes showed that resident macrophages but not inflammatory macrophages were highly conserved in normal and inflamed mice. Gut microbiota play a role in accumulation and differentiation of gut macrophages. Both Ly6Chigh and Ly6Clow macrophages in intestine and colon tissues are similar. These uncover the transcriptional landscape and phenotypic heterogeneity of CD11b+ cells, especially macrophages in gut tissues.

overall_design: 10X Genomics scRNA-seq was performed to better assess immune cell heterogeneity in gut lamina propria (LP).

first: Wei

last: Chen

first: Yazheng

first: Jianmei

first: Houbao

last: Qi

first: Yuan

last: Zhang

first: Rongcun


title: Massively parallel characterization of regulatory dynamics during neural induction [ChIP-seq]


title: Massively parallel characterization of regulatory dynamics during neural induction [RNA-seq]


title: Massively parallel characterization of regulatory dynamics during neural induction [ATAC-seq]


title: Human Tolerogenic Dendritic Cells Regulate Immune Responses through Lactate Synthesis

status: Public on Oct 18 2019

city: Nantes

first: Aurelie

last: Moreau

address: 30 bd Jean Monnet

institute: INSERM U1064

summary: Transcriptome analysis of different populations of human monocyte-derived myeloid cells: Autologous Tolerogenic Dendritic Cells (ATDCs), Monocyte-derived Dendritic Cells (MoDCs) and Monocyte-derived Macrophages (MoMacro)

overall_design: CD14+ sorted monocytes from 6 different donors were used to differentiate ATDCs, MoDCs and MoMacro from the same samples. We analyzed transcriptomic profiles from these monocytes-derived cells using Agilent whole genome oligo Microarrays (8x60K).

first: James

middle: I

last: Hutchinson

first: Edward

last: Geissler

first: Maria-Cristina

last: Cuturi

first: Paloma

last: Riquelme

first: Natasa

last: Obermajer


title: Comparison of Cortical Organoids to Human Cortex Identifies Cellular Identity and Maturation Differences

status: Public on Jun 14 2019

city: Santa Cruz

first: Christopher

last: Villarreal

address: 1156 Hight Street, Engineering-2 Rm. 501, MS: GENOMICS INSTITUTE

department: Genomics Institute

summary: Direct Comparisons Between Cortical Organoids Generated with 3 Distinct Protocols and Primary Developing Human Cortex

overall_design: Single-cell sequencing of cortical organoids using 10X Chormium v2 and NovaSeq S2. The primary developing human cortex samples will be available through dbGaP. Project name: A Cellular Resolution Census of the Developing Human Brain

first: Aparna

last: Bhaduri


title: Affymetrix SNP array data (Oncoscan CNV) for Fudan University Shanghai Cancer Center Triple Negative Breast Cancer (FUSCCTNBC) project

status: Public on Mar 09 2019

city: Shanghai

first: Zhi-Ming

last: Shao

address: 270 Dong An Road, Build 7, RM304

institute: Fudan University Shanghai Cancer Center

type: Genome variation profiling by genome tiling array

summary: We comprehensively analyzed clinical, genomic and transcriptomic data of a cohort of 465 primary triple-negative breast cancer (TNBC). PIK3CA mutations and copy number gains of chromosome 22q11 were more frequent in our Chinese cohort than in The Cancer Genome Atlas. We classified TNBCs into four transcriptome-based subtypes: 1) luminal androgen receptor (LAR), 2) immunomodulatory (IM), 3) basal-like immune-suppressed (BLIS), and 4) mesenchymal (MES). Putative therapeutic targets or biomarkers were identified among each subtype. Importantly, the LAR subtype showed more ERBB2 somatic mutations, infrequent mutational signature 3 and frequent CDKN2A loss. The comprehensive profile of TNBCs provided here will serve as a reference to further advance the understanding and precision treatment of TNBC.

overall_design: Copy number analysis of Affymetrix Oncoscan (Oncoscan CNV) SNP arrays was performed for samples from 401 primary triple negative breast cancer patients treated at Fudan University Shanghai Cancer Center. There are also 23 randomly selected white blood cell samples from the mentioned patients, which were used as references for eliminating potential recurrent germline CNV and/or recurrent false positive calls.

first: Yi-Zhou

last: Jiang

first: Ding

last: Ma


title: Expression profiling of microglia lacking Tgfbr2

status: Public on Jan 10 2019

first: Nicolas

last: Santander

summary: Microglia contribute to maintaining brain homeostasis by interacting with neurons and macroglial cells through different signaling molecules. Here, we investigate the transcriptional profile of microglia lacking TGFbeta signaling given by inactivation of the Tgfbr2 gene, at three different stages of development. These microglia show a signature consistent with increased activation and impaired maturation, representing a state commonly associated with neurological pathologies.

overall_design: Microglia lacking one or the two copies of the Tgfbr2 gene were FACS-sorted for RNA extraction at E16.5, P15, and P60. Three animals per genotype were used at E16.5 and P15, and 4 animals per genotype were used at P60.

first: Carlos

last: Lizama

first: Thomas

last: Arnold


title: A novel fate-mapping approach allows intratumoral profiling of hypoxic cells

status: Public on Feb 16 2019

first: Daniele

middle: Marie

last: Gilkes

address: 1650 N Orleans St, CRB1 128, None

department: Oncology

institute: Johns Hopkins

summary: We designed a novel approach to fate-map hypoxic cells in order to determine their cellular response to physiological O2 gradients. Our system causes a change in the expressing fluorescent protein upon hypoxic exposure (DsRed -> GFP). We generated hypoxia fate-mapping tumors using MDA-MB-231 cells expressing our system. Tumors were resected 2 weeks post-implantation, mechanically disrupted and digested with collagenase to obtain a cell suspension. The cell suspension was enriched using magnetic-activated cell sorting (MACS) and DsRed+ cells were isolated from GFP+ cells by fluorescence-activated cell sorting (FACS) directly into Tris Reagent (Zymo Research). Total RNA was extracted from cells using TRIzol (Invitrogen) and purified using Direct-zol RNA mini kit (Zymo Research) with DNase I treatment. After RNA purification, samples were confirmed to have a RIN value > 9.0 when measured on an Agilent Bioanalyzer. Libraries for RNA-Seq were prepared with KAPA Stranded RNA-Seq Kit. The workflow consisted of mRNA enrichment, cDNA generation, end repair to generate blunt ends, A-tailing, adaptor ligation and 12 cycles of PCR amplification. Unique adaptors were used for each sample in order to multiplex samples into several lanes. Sequencing was performed on Illumina Hiseq 4000 with a 150bp pair-end run. A data quality check was done on Illumina SAV. Demultiplexing was performed with Illumina Bcl2fastq2 v 2.17 program.

overall_design: In order to permanently mark hypoxic cells upon exposure to hypoxia, we generated a dual-vector hypoxia fate-mapping system delivered by a lentiviral approcah. Vector 1 expresses a red fluorescent reporter protein (DsRed) with a stop codon flanked by tandem loxP sites (“floxed”) and located in front of a gene encoding a green fluorescent protein (GFP). Vector 2 contains an altered Cre gene modified by the addition of an oxygen-dependent degradation domain (ODD) that is under the transcriptional control of a synthetic HIF-DNA binding sequence (HRE). HIF stabilization causes the activation of vector 2 by binding to hypoxia-dependent DNA response elements (HREs). Vector 2 activation causes the production of a genetically modified Cre protein that is only stable under hypoxia, leading to the cleavage of DsRed and permanent GFP expression. DsRed+ and GFP+ cells were sorted from MDA-MB-231 hypoxia fate-mapping tumors.


title: Chromatin structure dynamics during human cardiomyocyte differention reveals a role of HERV-H in demarcating TAD boundaries.

status: Public on Jul 09 2019

city: La Jolla

first: Bing

last: Ren

address: 9500 Gilman Drive

institute: University of California, San Diego

summary: The three-dimensional chromatin architecture plays a critical role in the establishment of cell-type-specific gene regulatory networks in eukaryotic cells.  How pluripotent stem cells (PSC) alter their chromatin architecture to direct cell fate specification remains to be elucidated.  Here, using a human PSC cardiomyocyte differentiation model, we analyze the dynamic reorganization of chromatin structure and gene regulatory networks during key transitional stages of cardiomyocyte development.  We show that many human PSC-specific topologically associating domains (TADs) are driven by active transcription of the primate-specific retroviruses HERVH.  These HERVH are silenced at the earliest stages of differentiation , accompanied by loss of TAD borders and subsequent merging of cognate TADs during differentiation, which leads to repression of gene expression within these domains .  In line with these findings, deletion of select HERVHs results in elimination of corresponding TAD boundaries in human PSCs. We further discovered developmental stage-specific chromatin loop interactions that predict target genes of cardiac-related trait/disease non-coding genetic variants.  Overall, our results not only highlight a novel role for endogenous retroviruses in shaping species-specific PSC chromatin architecture during evolution but also provide a genomic blueprint for understanding the impact of non-coding variants in congenital and adult heart disease/traits.

sample_organism:
Callithrix jacchus
Pan paniscus
Pan troglodytes
Homo sapiens

overall_design: hESCs are differentiated into cardiomyocyte. We used a transgenic H9 hESC line expressing a H2B-GFP fusion protein under control of the ventricular cardiomyocyte specific MYL2 promoter. We collected samples at six critical time points during differentiation: human embryonic stem cells (hESC) (Day 0), hESC mesodermal cells (Day 2), hESC-cardiac mesodermal cells (Day 5), hESC-cardiac progenitor cell (Day 7), hESC-primitive cardiomyocytes (Day 15) and hESC-ventricular cardiomyocytes (Day 80). We performed HiC, ATAC-seq, RNA-seq, and ChIP-seq for H3K27ac, H3K27me3, H3K4me1, H3K4me3, H3K9me3 and CTCF for every time point, each with two biological replicates. We also made CRISPR edited deletion at two HERV-H loci and performed RNA-seq and Hi-C, each with two replicates.

first: Neil

last: Chi

first: Yanxiao

first: Sebastian

last: Preissl

first: Eugin

last: Destici

first: Ting

last: Li

first: Hongbo

last: Yang

first: Jonathan

last: Grinstein

first: Ah-Yong

last: Lee

first: Sora

last: Chee

first: Zhen

last: Ye

first: Kaiyue

last: Tedeschi

first: Samantha

last: Kuan

first: Jennifer

last: Vevers

first: Sylvia

last: Evans


title: Apical progenitors remain multipotent throughout cortical neurogenesis

status: Public on Jun 28 2019

city: Geneva

first: Denis

last: Jabaudon

address: Rue Michel-Servet 1

country: Switzerland

institute: University of Geneva

summary: We used FlashTag, a method to pulse-label and isolate APs in the mouse neocortex with high temporal resolution, to fate-map neuronal progeny following heterochronic transplantation of APs into younger embryos. We find that unlike differentiated IPs, which lose the ability to generate deep layer neurons when transplanted into a younger host, APs are temporally uncommitted and become molecularly respecified to generate normally earlier-born neuron types. These results indicate that AP temporal identity progression occurs in the absence of detectable fate restriction and reveal that differentiation status, rather than embryonic age, is the core determinant of temporal plasticity in the mammalian neocortex.

overall_design: Patch-seq RNA sequencing of apical progenitors transplanted into a younger host.

first: Polina

last: Oberst

first: Sabine

last: Fièvre

first: Natalia

last: Baumann


title: The cell fate regulator NUPR1 is induced by Mycobacterium leprae via type I interferon in human leprosy

status: Public on Jan 31 2019

first: Priscila

middle: Ribeiro

last: Andrade

state: CALIFORNIA

address: 615 Charles E Young Drive South, room 246

department: Medicine

summary: The initial interaction between a microbial pathogen and the host immune response influences the outcome of the battle between the host and the foreign invader. Leprosy, caused by the obligate intracellular pathogen Mycobacterium leprae, provides a model to study relevant human immune responses. Previous studies have adopted a targeted approach to investigate host response to M. leprae infection, focusing on the induction of specific molecules and pathways. By measuring the host transcriptome triggered by M. leprae infection of human macrophages, we were able to detect a host gene signature 24–48 hours after infection characterized by specific innate immune pathways involving the cell fate mechanisms autophagy and apoptosis. The top upstream regulator in the M. leprae-induced gene signature was NUPR1, which is found in the M. leprae-induced cell fate pathways. The induction of NUPR1 by M. leprae was dependent on the production of the type I interferon (IFN), IFN-β. Furthermore, NUPR1 mRNA and protein were upregulated in the skin lesions from patients with the multibacillary form of leprosy. Together, these data indicate that M. leprae induces a cell fate program which includes NUPR1 as part of the host response in the progressive form of leprosy

overall_design: RNA sequencing of human monocyte differentiated macrophages infected with Mycobacterium leprae at a multiplicity of infection of 10 from one heathy donor for 0h (uninfected control), 1, 2, 24 and 48h

middle: R

first: Manali

last: Mehta

first: Robert

middle: L

last: Modlin


title: Genome-wide stability of DNA replication program in single mammalian cells

status: Public on Dec 13 2018

city: Kobe

first: Ichiro

last: Hiratani

state: Hyogo

address: 2-2-3 Minatojima-minamimachi, Chuo-ku

department: Center for Developmental Biology

institute: RIKEN

summary: We report the establishment of a single-cell DNA replication sequencing method, scRepli-seq, which is a simple genome-wide methodology that measures copy number differences between replicated and unreplicated DNA. Using scRepli-seq, we demonstrate that replication domain organization is conserved among individual mouse embryonic stem cells (mESCs). Differentiated mESCs exhibited distinct replication profiles, which were conserved from cell to cell. Haplotype-resolved scRepli-seq revealed similar replication timing profiles of homologous autosomes, while the inactive X chromosome was clearly replicated later than its active counterpart. However, a small degree of cell-to-cell replication timing heterogeneity was present, and we discovered that developmentally regulated domains are a source of such variability, suggesting a link between cell-to-cell heterogeneity and developmental plasticity. Together, our results form a foundation for single-cell-level understanding of DNA replication regulation and provide insights into 3D genome organization.

overall_design:
BrdUIP Repli-seq, Population Repli-seq, 100-cells Repli-seq and single-cell Repli-seq experiments in hTERT-RPE1, female mouse embryonic stem cells (CBMS1 mESCs) and 7-day differentiated mESCs. We only deposited single-cell data sets which passed our filtering steps.
RNA-Seq: CBMS1 mESCs sample with 3 individual replicates

first: Hisashi

last: Miura

first: Saori

last: Takahashi

first: Shin-ichiro

last: Takebayashi


title: Expression data from D2.OR Derivatives

status: Public on Aug 30 2017

city: Cleveland

first: William

last: Schiemann

state: OH

address: 2103 Cornell Rd Rm 2404

institute: Case Western Reserve University

summary:
BORG elicits the metastatic outgrowth of nonmetastatic breast cancer cells by promoting the localization and transcriptional repressive activity of TRIM28, which binds BORG and induces substantial alterations in carcinoma in the proliferation and survival
We sought to assess genome-wide transcriptomic profiles governed by BORG in a TRIM28-dependent and -independent manner in latent D2.OR breast cancer cells

overall_design: We propagated parental, BORG-, and BORG/sgTRIM28-expressing D2.OR cells in 3D-culture for 7 days, at which point total RNA was isolated and subsequently subjected to Affymetrix GeneChip Mouse Gene 2.0 ST Array analysis

first: Alex

last: Gooding


title: Studies of modern Italian dog populations reveal multiple patterns for domestic breed evolution

status: Public on Oct 10 2018

first: Alexander

middle: Christian

last: Harris

address: 50 South Drive

department: National Human Genome Research Institute

institute: National Institutes of Health

type:
Genome variation profiling by SNP array
SNP genotyping by SNP array

summary: Through thousands of years of breeding and strong human selection, the dog (Canis lupus familiaris) exists today within hundreds of closed populations throughout the world, each with defined phenotypes. A singular geographic region with broad diversity in dog breeds presents an interesting opportunity to observe potential mechanisms of breed formation. Italy claims 14 internationally recognized dog breeds, with numerous additional local varieties. To determine the relationship among Italian dog populations, we integrated genetic data from 263 dogs representing 23 closed dog populations from Italy, seven Apennine gray wolves. Using 142,840 genome-wide SNPs, this dataset was used in the identification of breed development routes for the Italian breeds that included divergence from common populations for a specific purpose, admixture of regional stock with that from other regions, and isolated selection of local stock with specific attributes.

overall_design: 273 canid samples representing 21 Italian breeds and seven Apennine gray wolves

first: Dayna

last: Dreger

first: Andrea

last: Talenti

first: S

last: Frattini

first: M

last: Polli

last: Marelli

first: A

middle: C

first: L

last: Liotta

first: R

last: Cocco

middle: N

last: Hogan

first: D

last: Bigi

last: Caniglia

first: H

last: Parker

first: G

last: Pagnacco

first: E

last: Ostrander

first: P

last: Crepaldi


title: Single cell RNA-seq analysis of human embryonic cortex

status: Public on Jun 29 2018

city: Beijing

first: Ji

last: Dong

address: Yiheyuan 5#

institute: Peking University

summary: Many studies have been launched to investigate cellular and molecular regulation regarding human neural system development, yet there is hardly any regional characterization on the whole developmental human cerebral cortex. We found that inhibitory neuron subtypes possibly originated from MGE and CGE. The molecular regulation of excitatory neuron maturation in vivo showed differences to that in rodent. Different regions appeared to have distinct cell type diversities with pons proceeding to show astrocyte explosion. Generally neurons of the same subtype were more uniform in gene expression inside each region except for those in parietal lobe.

overall_design:
Here we performed single cell RNA-seq analysis for human embryonic cortex, covering the developmental stages of 22-23 weeks after gestation female and male human embryos

Each sample includes data for 96 single cells. The cell barcode information is available in the file "Region_Sample_Barcode_Information.xls" at the foot of this page.

first: Xiaoying

last: Fan

first: Xiaoqun

last: Wang

first: Jie

last: Qiao

first: Fuchou

last: Tang


title: DNA methylation analysis in head and neck cancer cells

status: Public on May 10 2018

city: Chiba

first: Masaki

last: Fukuyo

address: 1-8-1 Inohana, Chuo-ku

department: Department of Molecular Oncology

institute: Chiba University

summary: DNA methylation analysis in oropharyngeal squamous carcinoma(OPSCC) samples, oropharyngeal non-cancerous mucosa samples and head and neck cancer cell lines, FaDu and UMSCC47  before and after 5-aza'2-deoxycytidine(Aza)/trichostatin A(TSA) treatment. Infinium HumanMethylation450 BeadChip was used to obtain DNA methylation profiles across 485,577 CpG sites. Samples included 13 OPSCC samples, 4 non-cancerous mucosa samples and 2 FaDu with and without Aza/TSA treatment and 2 UMSCC47  with and without Aza/TSA treatment.

overall_design: Bisulphite converted DNA from the 21 samples were hybridised to the Infinium HumanMethylation450 BeadChip.

first: Takuya

last: Nakagawa

first: Atsushi

last: Kaneda


title: Divergent mechanisms of EZH1 regulation of heart development and regeneration [ChIP-Seq]

status: Public on Jul 26 2017

city: Chicago

first: Yong

last: Peng

state: IL

address: 929 E 57th Street

department: Department of Chemistry

institute: University of Chicago

summary: Through EZH1, H3K27me3 and H3K27ac ChIP-seq and RNA-seq data in P13 EZH1 and GFP overexpressing heart (AAVEzh1 and AAVGFP respectively) suffered MI at P10, we surprisingly found that EZH1 can active the expression of regenerating relevant genes by directly binding to the promoter of targeted genes and through a mechanism independent of H3K27me3 deposition.

overall_design: EZH1, H3K27me3 and H3K27ac occupancy in P13 mice heart suffered MI at P10 and injected with AAV9 expressing Ezh1 or GFP

first: Shanshan

last: Ai

first: Xianhong

last: Yu

first: Yumei

last: Li

first: Yanzhu

last: Yue

first: Chen

first: Aibin

last: He


title: SNP genotyping of ǂKhomani San

status: Public on May 20 2017

city: Stony Brook

first: Shyamalika

last: Gopalan

address: 100 Nicolls Road

institute: Stony Brook University

summary: 48 ǂKhomani San living in the South African Kalahari were genotyped using the Illumina OmniExpress, OmniExpress Plus, and HumanHap550 arrays

overall_design: Genomic DNA was hybridized to the Illumina OmniExpress, OmniExpress Plus, and HumanHap550 arrays

first: Brenna

last: Henn


title: Genome-wide DNA methylation and SNP genotyping of ǂKhomani San

type:
Methylation profiling by array
SNP genotyping by SNP array

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

overall_design: Refer to individual Series


title: RNA-seq and DNA methylation analysis in head and neck cancer cells and cell lines


title: SNP genotyping of various breeds

status: Public on Dec 06 2018

first: Heidi

last: Parker

state: MD

address: 50 South Dr. Rm 5347

department: CGB

institute: NHGRI

type:
SNP genotyping by SNP array
Genome variation profiling by SNP array

summary: SNP of new dog breeds improves the validity of population clustering and breed based phylogenies.

overall_design: DNA was collected from pedigreed dogs of multiple breeds. SNPs were genotyed using the Illumina CanineHD SNP chip. These SNPs were analyzed using distance measures and haplotype sharing to build a cladogram of breeds and show across-breed hybridization.

first: Elaine

last: Ostrander


title: Genome-wide DNA methylation of ǂKhomani San

status: Public on May 18 2017

summary: Genome-wide DNA methylation profiling was conducted in two batches for 56 ǂKhomani San living in the South African Kalahari using the Illumina 450k array on saliva-derived DNA

overall_design: Bisulphite converted DNA was hybridized to the Illumina Infinium HumanMethylation450 BeadChip


title: Chromatin accessibility maps of human primary pancreatic cell types

status: Public on Aug 21 2018

city: Stanford

first: Seung

last: Kim

state: CA

address: 279 Campus Dr B303

department: Developmental Biology

institute: Stanford University

summary: To obtain comprehensive maps of human pancreatic chromatin states, we performed genome-wide open chromatin and histone modification assays from primary human pancreatic cells.

overall_design: For this study, we purified primary human pancreatic cells from several donors and analyzed the chromatin landscape using ATAC-Seq and ChIP-Seq assays.

first: Efsun

last: Arda

first: Jennifer

last: Tsai


title: Lipid engineering reveals regulatory roles for membrane fluidity in yeast flocculation and oxygen-limited growth

status: Public on Jan 31 2017

city: Emeryville

first: Itay

last: Budin

address: 5885 Hollis

institute: UC Berkeley

summary: Analysis of gene expression changes in S. cerevisiae in response to OLE1 repression, SPT23 and MGA2 p90 expression, and hypoxic growth

overall_design: 9 samples (comprising 5 pairwise comparisons), three biological replicates per sample

first: I

first: T

last: de Rond

first: D

last: Degreif


title: Genomic analyses reveal the influence of geographic origin, migration and hybridization on modern dog breed development

status: Public on Mar 17 2017

summary: Analysis of genotypes at 150,000 SNPs reveals patterns of allele and haplotype sharing that describes the breed relationships and development of 161 breeds of dog.

overall_design:
DNA was collected from pedigreed dogs of multiple breeds. SNPs were genotyed using the Illumina CanineHD SNP chip. These SNPs were analyzed using distance measures and haplotype sharing to build a cladogram of breeds and show across-breed hybridization.

The processed and raw data is also provided in a plain text file (*matrix.txt and *signal.txt, respectively). The associated files are indicated iin the corresponding sample description field.


title: Whole genome sequence, SNP chips and pedigree structure

status: Public on Nov 24 2016

first: Dayna

last: Dreger

department: NHGRI

summary: Building demographic profiles in domestic dog breeds to optimize genetic trait mapping study design

sample_organism:
Canis lupus
Canis lupus familiaris

overall_design: 795 dogs representing 89 breeds, plus wolf

first: Maud

last: Rimbault

first: Brian

middle: W

last: Davis

first: Adrienne

last: Bhatnagar


title: A novel fate-mapping approach allows intratumoral profiling of hypoxic cells II

status: Public on Aug 27 2019

city: Baltimore

first: Daniele

last: Gilkes

summary: We designed a novel approach to fate-map hypoxic cells in order to determine their cellular response to physiological O2 gradients. Our system causes a change in the expressing fluorescent protein upon hypoxic exposure (DsRed -> GFP). We generated hypoxia fate-mapping tumors using MDA-MB-231 cells expressing our system. Metastatic lungs were resected 2 weeks after primary tumor removal, mechanically disrupted and digested with collagenase to obtain a cell suspension. The cell suspension was enriched using magnetic-activated cell sorting (MACS) and DsRed+ cells were isolated from GFP+ cells by fluorescence-activated cell sorting (FACS) directly into Tris Reagent (Zymo Research). Total RNA was extracted from cells using TRIzol (Invitrogen) and purified using Direct-zol RNA mini kit (Zymo Research) with DNase I treatment. After RNA purification, samples were confirmed to have a RIN value > 9.0 when measured on an Agilent Bioanalyzer. Libraries for RNA-Seq were prepared with KAPA Stranded RNA-Seq Kit. The workflow consisted of mRNA enrichment, cDNA generation, end repair to generate blunt ends, A-tailing, adaptor ligation and 12 cycles of PCR amplification. Unique adaptors were used for each sample in order to multiplex samples into several lanes. Sequencing was performed on Illumina Hiseq 3000/4000 with a 150bp pair-end run. A data quality check was done on Illumina SAV. Demultiplexing was performed with Illumina Bcl2fastq2 v 2.17 program.

overall_design: In order to permanently mark hypoxic cells upon exposure to hypoxia, we generated a dual-vector hypoxia fate-mapping system delivered by a lentiviral approcah. Vector 1 expresses a red fluorescent reporter protein (DsRed) with a stop codon flanked by tandem loxP sites (“floxed”) and located in front of a gene encoding a green fluorescent protein (GFP). Vector 2 contains an altered Cre gene modified by the addition of an oxygen-dependent degradation domain (ODD) that is under the transcriptional control of a synthetic HIF-DNA binding sequence (HRE). HIF stabilization causes the activation of vector 2 by binding to hypoxia-dependent DNA response elements (HREs). Vector 2 activation causes the production of a genetically modified Cre protein that is only stable under hypoxia, leading to the cleavage of DsRed and permanent GFP expression. DsRed+ and GFP+ cells were sorted from metastatic lungs of mice bearing MDA-MB-231 hypoxia fate-mapping tumors.


title: Studies of canine breed development on the island of Sardinia recapitulate genomic features of human population isolates [CANE]

status: Public on Jun 10 2016

summary: The Italian island of Sardinia is well known in studies of human population isolates. It is also home to the Fonni's Dog, a breed of canine whose development was reliant on the functionality of the dog. Using genome-wide variant and sequence analyses, we have characterized the Fonni's Dog relative to 27 other dog breeds from the Mediterranean region. We determine introgression events relevant to Mediterranean breed development and describe how the Fonni's dog presents an intriguing model demonstrating the characteristics of traditional human population isolates and, in particular, exhibiting the unique demographic composition of the people of Sardinia.

overall_design: 4 canine samples representing 1 dog breed

first: Raffaella

last: Cocco

first: Sara

last: Sechi

first: Alessandro

last: DiCerbo

middle: G

first: Michele

last: Polli

first: Stefano

last: Marelli

first: Paola

last: Crepaldi


title: Gene expression profiling of hip cartilage with necrosis of femoral head

status: Public on Jun 01 2016

city: Xi'an

first: Feng

last: Zhang

address: Yanta West Road 76

institute: Xi'an Jiaotong University

summary: The pathogenesis of necrosis of femoral head (NFH) remains elusive now. Limited studies were conducted to investigate the molecular mechanism of hip articular cartilage damage of NFH. We conducted a genome-wide gene expression profiling of hip articular cartilage with NFH.

overall_design: Hip articular cartilage specimens were collected from 12 NFH patients and 12 healthy controls. Gene expression profiling of NFH articular cartilage was carried out by Agilent Human 4x44K Gene Expression Microarray chip. Differently expressed genes were identified using the Significance Analysis of Microarrays (SAM) software.

first: Liu

last: Ruiyu


title: Multiparameter functional diversity of human C2H2 zinc finger proteins

status: Public on Oct 25 2016

city: Montreal

first: Hamed

middle: S

last: Najafabadi

state: QC

address: 740 Dr. Penfield Avenue, Room 7202

department: Human Genetics

country: Canada

institute: McGill University


title: Studies of canine breed development on the island of Sardinia recapitulate genomic features of human population isolates

city: Bethesda


title: Hepatitis B virus-mediated alterations to the primary hepatocyte transcriptome

status: Public on Jan 20 2016

city: Philadelphia

first: James

middle: M

last: Wilson

state: Pennsylvania

address: 125S 31st St

institute: University of Pennsylvania


title: Identification of in vivo binding sites of human GFP-tagged C2H2-ZF proteins

summary: The largest and most diverse class of eukaryotic transcription factors contain Cys2-His2 zinc fingers (C2H2-ZFs), each of which typically binds a DNA nucleotide triplet within a larger binding site. Frequent recombination and diversification of their DNA-contacting residues suggests that these zinc fingers play a prevalent role in adaptive evolution. Very little is known about the function and evolution of the vast majority of C2H2-ZFs, including whether they even bind DNA. We determined in vivo binding sites of 39 human C2H2-ZF proteins, and correlated them with potential functions for these proteins.

overall_design: We expressed GFP-tagged C2H2-ZF proteins in stable transgenic HEK293 cells. Chromatin immunoprecipitation was performed as described before (Schmidt et al., Methods, 2009), and ChIP samples along with several control samples from different experimental batches were sequenced on Illumina HiSeq 2000. Reads were mapped to hg19 (GRCh37) assembly, and peaks were identified by MACS using an experiment-specific background that controls for various biases, such as the Sono-Seq effect as well as potential co-purification of targets of other (interacting) proteins.

first: Frank

last: Schmitges

first: Ernest

last: Radovani

first: Jack

last: Greenblatt

first: Timothy

last: Hughes


title: Hepatitis B virus-mediated alterations to the primary hepatocyte transcriptome [24 and 48 h]

status: Public on Jan 15 2016

summary:
Purpose:  Chronic infection with hepatitis B virus is the leading global risk factor for the development of liver cancer.  A large body of research has shown the many effects an HBV infection has on cellular physiology, particularly on pathways that may be involved in the development of HBV-associated diseases.  Unfortunately, a significant portion of this research has been done in systems that may not mimic what is seen in a primary hepatocyte, and is not done on a transcriptome-wide scale.  Because of this, we performed an RNA-seq analysis of primary rat hepatocytes expressing HBV to determine the global changes HBV has on primary hepatocyte physiology.
Methods: To do this RNA-seq analysis, triplicate samples of total RNA were collected from cultured primary rat hepatocytes infected with adenovirus expressing GFP alone (AdGFP) or GFP along with a greater than unit length copy of the HBV genome (AdHBV).  Samples were collected either 24h or 48h after infection.  cDNA libraries were sequenced two times using the Illumina HiSeq or Illumina NextSeq platform to generate either 1x50bp or 1x75bp reads.  Reads from each sequencing run were mapped using the STAR aligner, and output BAMs were merged into a single BAM for each sample.  The merged BAM was further analyzed in R using the GenomicAlignments package to quantify number of reads per transcript and DESeq2 to determine differential expression. Reads per kilobase transcript per million total reads (RPKM) was calculated by dividing reads per transcript by the transcript length and then normalizing to the total number of reads in the sample.
Results: Following this pipeline, we were able to identify a number of HBV-mediated differentially expressed transcripts at 24h and 48h post-infection.  Further pathway analysis of these differentially expressed transcripts identified many important cellular pathways, including those involved with cell cycle regulation and metabolism, as being differentially regulated by HBV in primary hepatocytes.

overall_design: mRNA profiles of HBV-expressing and non-expressing primary rat hepatocytes were generated, in triplicate, 24h and 48h post-infection using Illumina HiSeq 2500 and NextSeq 500 instruments.

first: Jason

last: Lamontagne

first: Michael

last: Bouchard