title: Conditionally reprogrammed cells from patient-derived xenograft to model neuroendocrine prostate cancer development

city: Vancouver

first: Yuzhuo

state: BC

address: 2660 Oak Street

department: Vancouver Prostate Centre

institute: University of British Columbia

summary: Treatment-emergent neuroendocrine prostate cancer (t-NEPC) is a lethal subtype of advanced prostate cancer that develops via NE transdifferentiation of prostate adenocarcinomas in response to androgen receptor (AR)-inhibition therapy. Study of t-NEPC has been hampered by a lack of clinically relevant models. We previously established a unique and first-in-field patient-derived xenograft (PDX) model of adenocarcinoma (LTL331)-to-NEPC (LTL331R) transdifferentiation. In this study, we applied conditional reprogramming (CR) culture to establish a LTL331 PDX-derived cancer cell line named LTL331_CR_Cell. LTL331_CR_Cells retain the same genomic mutations as the LTL331 parental tumor, can be continuously propagated in vitro, and can be genetically manipulated. Androgen deprivation treatment on LTL331_CR_Cells showed no effect on cell proliferation. Transcriptomic analyses comparing the LTL331_CR_Cell to its parental tumor revealed a profound downregulation of the androgen response pathway and an upregulation of stem and basal cell marker genes. The transcriptome of LTL331_CR_Cells partially resembles that of post-castrated LTL331 xenografts in mice. Notably, when grafted under the renal capsule of male NOD/SCID mice, LTL331_CR_Cells spontaneously give rise to NEPC tumors as manifested by the histological expression of the NE marker CD56 and the loss of adenocarcinoma markers such as PSA. Transcriptomic analyses of the newly developed NEPC tumors further demonstrate marked enrichment of NEPC signature genes and loss of AR signaling genes. This study provides a novel research tool based on a unique PDX model. It allows for the investigation of mechanisms underlying t-NEPC development by enabling gene manipulation ex vivo and subsequent functional evaluation in vivo.

overall_design: mRNA profiles of prostate cancer PDX LTL331 and its castration-resistant relapsed NEPC tumor LTL331R, contionally reprogrammed cell LTL331_CR_Cell and the cell-derived xenograft LTL331_CR_Tumor, were generated by deep sequencing  using Illumina NextSeq 500.

first: Xinpei

last: Ci

first: Anne

last: Haegert


title: Single-cell lineage analysis reveals genetic and epigenetic interplay in glioblastoma drug resistance

status: Public on Jun 18 2020

city: Boston

first: Volker

last: Hovestadt

state: MA

address: 360 Longwood Avenue

department: Pediatric Oncology

country: USA

institute: Dana-Farber Cancer Institute

type: Expression profiling by high throughput sequencing

summary: Drug resistance is a central problem in cancer therapy, yet the underlying mechanisms remain obscure. Cancer cells typically acquire resistance via genetic mutations, but may also adopt reversible epigenetic phenotypes that allow them to persist through drug exposure. In glioblastoma, poor efficacy of receptor tyrosine kinase (RTK) therapies has been alternatively ascribed to genetic heterogeneity or to epigenetic transitions that circumvent signaling blockade.

overall_design: Here we combined cell lineage barcoding and single-cell transcriptomics to trace the emergence of resistance in stem-like glioblastoma (GBM) cells treated with RTK inhibitors. Whereas a broad spectrum of barcoded lineages adopts a Notch-dependent persister phenotype that sustains them through early drug exposure, rare subclones acquire genetic changes that enable their rapid outgrowth over time. Single-cell analyses revealed that these genetic subclones gain copy number amplifications of the IRS1 or IRS2 loci, which activate insulin and AKT signaling programs. Persister-like cells and genomic amplifications of IRS2 and other loci are evident in primary glioblastomas, and may underlie the inefficacy of targeted therapies in this disease.

first: Christine

middle: E

last: Eyler

first: Hironori

last: Matsunaga

first: Samantha

middle: J

last: Vantine

first: Peter

last: van Galen

first: Bradley

last: Bernstein


title: Rph1 coordinates transcription of ribosomal protein gene and ribosomal RNA to control cell growth under nutrient stress conditions

city: Wuhan

first: shu

last: Wenjie

address: East Lake South Road

department: College of Life Sciences

country: China

institute: Wuhan University

type: Genome binding/occupancy profiling by high throughput sequencing

summary:
Coordinated regulation of ribosomal RNA (rRNA) and ribosomal protein gene (RPG) transcription by eukaryotic RNA polymerases (RNAP) is a key requirement for growth control. Although evidence for balance between RNPI-mediated 35S rRNA production and RNAPII-mediated RPG transcription have been described, the molecular basis is obscure. Here, we found that Rph1 modulates the transcription status of both rRNA and RPG in yeast. We show that Rph1 widely associates with RNAPI and RNAPII-transcribed genes. Deletion of RPH1 remarkably alleviates cell slow growth caused by TORC1 inhibition via derepression of rRNA and RPG transcription under nutrient stress conditions. Mechanistically, Rim15 kinase phosphorylates Rph1 upon rapamycin treatment. Phosphorylationmimetic mutant of Rph1 exhibited more resistance to rapamycin treatment, decreased association
with ribosome-related genes, and faster cell growth compared to the wild-type, indicating that Rph1 dissociation from chromatin ensures cell survival upon  nutrient stress. Our results uncover the role of Rph1 in coordination of RNA polymerases-mediated transcription to control cell growth under nutrient
stress conditions.

overall_design: RNA-seq dataset of wild-type and Rph1 deletion yeast treated with or without rapamycin. ChIP-seq dataset of Pol II and FLAG-Rph1  treated with or without rapamycin.

first: Wen-Jie

last: Shu

first: Runfa

last: Chen

first: Zhao-Hong

last: Yin

first: Feng

last: Li

first: Heng

last: Zhang

first: Hai-Ning

last: Du


title: Single-cell transcriptomic analysis of human germinal center B cells

status: Public on Jun 17 2020

city: New York

first: Riccardo

last: Dalla-Favera

state: NY

address: 1130 St Nicholas Avenue

institute: Columbia University

summary: In response to T cell-dependent antigens, mature B cells are stimulated to form germinal centers, which are the place of B cell affinity maturation and selection. Here, we dissected the heterogeneity of germinal center B cells and reconstructed their pathway of differentiation using single-cell transcriptomic analysis.

overall_design: Dark zone, light zone and total germinal center B cells were isolated from two donors and analyzed by single-cell RNAseq. Total germinal center B cells were isolated from a third donor and subject to Cellular Indexing of Transcriptomes and Epitopes by sequencing (CITE-seq).

first: Katia

last: Basso

first: Antony

middle: B

last: Holmes


title: Comparative RNA-Seq transcriptome analyses reveal dynamic time dependent effects of 56Fe, 16O, and 28Si irradiation on the induction of murine hepatocellular carcinoma

city: Galveston

first: Anna

last: Nia

state: TX

address: 301 University Blvd

department: Biochemistry and Molecular Biology

institute: University of Texas Medical Branch

summary: One of the health risks posed to astronauts during deep space flights is exposure to high charge, high-energy (HZE) ions (Z>13) which can lead to induction of hepatocellular carcinoma (HCC). We performed comparative RNA-Seq transcriptomic analysis to assess the carcinogenic effects of 600 MeV/n 56Fe (0.2 Gy), 1 GeV/n 16O (0.2 Gy), and 350 MeV/n 28Si (0.2 Gy) ions in a mouse model for radiation-induced hepatocellular carcinoma. C3H/HeNCrl mice were subjected to total body irradiation to simulate space HZE-irradiation environment and liver tissues were extracted at five different time points post-irradiation to investigate the time-dependent gradual carcinogenic response at the transcriptomic level. Our data demonstrated a clear difference in the effects of these HZE ions, particularly immunological, on the carcinogenic process of HCC, suggesting different molecular mechanisms of tumorigenesis. Also seen in this study was novel unmapped transcripts that were significantly affected by HZE. To investigate the biological functions of these transcripts, we used a machine learning technique known as self-organizing maps (SOMs) to characterize the transcriptome expression profiles of 60 samples (45 HZE-irradiated, 15 non-irradiated control) from liver tissues. A handful of localized modules in the maps emerged as groups of co-regulated and co-expressed transcripts. The functional context of these modules was discovered using overrepresentation analysis. We found that these spots typically contained enriched populations of transcripts related to specific immunological molecular processes. Taken together, these findings not only led to a better understanding of biological mechanisms underlying risks for HCC after HZE irradiation but also have important implications for discovery of potential countermeasures and identification of biomarkers of HZE-induced HCC.

overall_design: C3H/HeNCrl mice purchased from Charles River (Wilmington, MA) were used in this experiment. Mice were used for this study because they have been shown in the past to be a good experimental model for liver carcinogenesis. Strains used were based on previous studies by Weil et al. (2009) demonstrating that C3H/HeNCrl mice are sensitive to the induction of HCC after exposure to a dose of 0.2 Gy of 600 MeV/n 56Fe. Tumor induction studies and studies of molecular changes in the irradiated tissues can only be conducted in whole animals. Conducted studies were approved by the institutional animal care and use committees (IACUCs) that are charged with evaluating the appropriateness of the use of animals in specific experiments and the numbers of animals requested for each group. The numbers of animals used were based on the expected numbers of irradiation-related tumors that would develop if animals were allowed to live out their lifespan. Power calculations for numbers in this study are based on chi-square test for comparing two proportions, controlling two-sided significance level at 0.05 or with 95% confidence about our results, and with 80% power. Computer models or cell culture studies are not possible based on an extensive literature search.  Serial sacrifice study consisted of 15 male mice with 3 mice per time point and five time-points consisting of 30, 60, 120, 270, and 360 days post-exposure to HZE: 56Fe, 16O, and 28Si irradiation. Additionally, 15 mice were used as controls resulting in a total of 60 eight to ten-week-old male mice for this study. The 3 treatment groups were: 600 MeV/n 56Fe (0.2 Gy), 1 GeV/n 16O (0.2 Gy), 350 MeV/n 28Si (0.2 Gy), and no irradiation. The mice were shipped from the vendor to Brookhaven National Laboratories (BNL) and housed at the BNL animal facility until the time of irradiation at the NASA Space Radiation Laboratory (NSRL). Following irradiation, the animals were shipped to the UTMB Animal Resources Center (ARC), quarantined for one month and then maintained in the ARC for the duration of the experiment.  Animals were housed in sterile cages with free access to food and water. Facilities at both BNL and UTMB are fully AAALAC accredited which ensured adequacy of all animal care issues at both animal facilities.  At each of the five time-points, 3 animals from each treatment group were randomly selected and euthanized by using CO2 asphyxiation as per current AVMA guidelines for euthanasia.  Prior to euthanasia animals were weighed and weight recorded.  Post euthanasia tissues of the left lobe of livers were collected, snap-frozen on either dry ice or liquid nitrogen and stored at -80°C until tissues could be extracted for RNA. Livers were sampled by taking two 40-micron thick slices using a cryotome at -20°C.

middle: M

first: Kamil

last: Khanipov

first: Brooke

middle: L

last: Barnette

first: Robert

last: Ullrich

first: George

last: Golovko

first: Mark

middle: R

last: Emmett


title: Naïve human embryonic stem cells can give rise to cells with trophoblast-like transcriptome and methylome

status: Public on Jun 16 2020

city: Haining

first: Yixin

last: Guo

address: 718 East Haizhou Rd.

institute: Zhejiang University

type: Methylation profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: The BET inhibitor CPI203 promotes ex-vivo expansion of long-term repopulating human hematopoietic stem cells and megakaryocyte

status: Public on Jun 29 2020

city: Nanjing

first: Peng

last: Hua

state: Jiangsu

address: 101 Longmiandadao

department: State Key Laboratory of Reproductive Medicine and Offspring Health

institute: Nanjing Medical University

summary: RNA sequencing reveals the transcriptomic differences between cord blood cells expanded by CPI203/cytokines against DMSO/cytokines.

overall_design: Cord blood CD133+ cells were expanded for 5 days in either CPI203/cytokines (B) or DMSO/cytokines (V) conditions. Each experiment starting from cell expansion was performed duplicately using cells from three different biological donors (a1-3).


title: Differentially expression profiling in Hashimoto's thyroiditis (HT), papillary thyroid carcinoma (PTC) with HT in background, PTC without HT in background, micro PTC (mPTC), and three normal thyroid samples (TN).

city: Jeddah

first: Hans-Juergen

last: Schulten

department: Center of Excellence in Genomic Medicine Research

country: Saudi Arabia

institute: King Abdulaziz University

summary: Experiment: Establishment of expression profiles in HT, PTC with HT, PTC without HT, and mPTC in comparison to TN samples. TN samples were downloaded as CEL files from the repository of the microarray vendor. Biostatistical analysis focussed in first instance on identifying genes and biofunctions related to HT and PTC with HT.

overall_design:
We extracted RNA from tumor specimens and RNA with an RIN > 5 (Bioanalyzer, Agilent) or, in exceptional cases, RNA assessed by gel electrophoresis, was processed using the recommended processing kits and hybridized to Affymetrix Human Gene 1.0 ST arrays. Three normal tissue samples were downloaded as CEL files from the data resource center of the vendor (https://www.thermofisher.com/us/en/home/life-science/microarray-analysis/microarray-data-analysis/microarray-analysis-sample-data/gene-st-array-data-set.html): TisMap_Thyroid_01_v1_WTGene1, TisMap_Thyroid_02_v1_WTGene1, TisMap_Thyroid_03_v1_WTGene1. All CEL files were RMA normalized and ANOVA was applied to generate differentially expressed probe sets. Differentially expressed genes that were significantly associated with one or more disease categories were subjected to biofunctional analysis.
The renormalized cases from GSE54958 are included in the current study.

first: Sajjad

last: Karim


title: Assessment of  gene expression levels upon overexpession of Retinitis pigmentosa associated Prp8 mutant proteins in the Drosophila eye antennal imaginal discs

city: Cologne

first: Mirka

last: Uhlirova

state: NRW

address: Joseph-Stelzmann Str. 26

department: Institute for Genetics

country: Germany

institute: CECAD Research Center  Cologne

summary: Retinitis pigmentosa (RP) represents a heterogeneous group of hereditary eye disorders characterized by a progressive loss of vision. Mutations in thirty different genes have been linked to the autosomal dominant form of RP (adRP), with nearly one-quarter of them encoding the core components of the spliceosome, a macromolecular machine that removes introns from nascent pre-mRNAs, generating mature transcripts. Here we establish the Drosophila melanogaster model for RP13 linked to the mutations in the most conserved protein of the spliceosome, PRPF8/Prp8. We demonstrate negative impact of the nine different RP-associated Prp8 mutant proteins on the developmental timing when expressed in the endocrine cells specialized to produce the major insect molting hormone. In the developing eye primordium, actively cycling cells rather than differentiated photoreceptors showed sensitivity to Prp8 malfunction. The overexpression of the two most toxic RP variants Prp8S>F and Prp8H>R induced apoptosis and disturbances of the adult eye morphology. While the affected tissue mounted the stress and cytoprotective response, the genetic programs underlying neuronal function were attenuated. Importantly, the expressivity and penetrance among the RP-Prp8 mutations differed and increased under prp8 heterozygosity.

overall_design: Tissue-specific overexpression of RP-Prp8 mutant proteins (designated as Prp8F>L "Lilac", Prp8H>R "Russet" and Prp8S>F "Fuchsia") and wild-type Drosophila Prp8 (Prp8wt) in Drosophila eye-antennal imaginal discs; tissues were dissected in three replicates, and RNA was extracted for next-generation sequencing

first: Dimitrije

last: Stanković

first: Ann-Katrin

last: Cladius

first: Thomas

last: Schertel

first: Tina

last: Bresser


title: Naïve human embryonic stem cells can give rise to cells with trophoblast-like transcriptome and methylome [Bisulfite-Seq]

summary: Human embryonic stem cells (hESCs) readily differentiate to somatic or germ lineages but have impaired ability to form extra-embryonic lineages such as placenta or yolk sac. Here we demonstrate that hESCs cultured in naïve media conditions can be converted into cells that exhibit the cellular and molecular phenotypes of human trophoblast stem cells (hTSCs) derived from human placenta or blastocyst. The resulting “transdifferentiated” hTSCs show reactivation of core placental genes, acquisition of a placenta-like methylome, and the ability to differentiate to extravillous trophoblasts and syncytiotrophoblasts. Modest differences are observed between transdifferentiated and placental hTSCs, most notably in the expression of certain imprinted loci. These results indicate that naïve hESCs can differentiate to extra-embryonic lineage, and demonstrate a new way of modeling human trophoblast specification and placental methylome establishment.

overall_design: Bisulfite-seq of human trophoblast stem cells and transdifferentiated human trophoblast stem cells

first: William

last: Pastor

first: Wanlu

last: Liu


title: NRF2 is a key regulator of endothelial miRNA expression under pro-atherogenic stimuli

city: Kuopio

first: Minna

last: Kaikkonen-Määttä

country: Finland

institute: A. I. Virtanen Institute

type: Non-coding RNA profiling by high throughput sequencing

summary: Regulation of coding and non-coding genes is studied from primary human aortic endothelial cells (HAECs), venous endothelial cells (HUVECs), aortic smooth muscle cells (HASMCs) and macrophages (CD14+) under pro-atherogenic stimuli (hypoxia, oxPAPC and hypoxia+oxPAPC) by integrating three different sequencing techinques: GRO-seq, miRNA-seq and RNA-seq

overall_design: Three different sequencing techniques (GRO-Seq, RNA-Seq and miRNA-Seq) of four distinct cell types (HAEC, HUVEC, HASMC, CD14+/Macrophages) analysed under 3 stimuli (hypoxia, oxPAPC and hypoxia+oxPAPC)

first: M

last: Bouvy-Liivrand

first: P

last: Moreau

first: E

last: Kansanen

first: A

last: Kivelä


title: Naïve human embryonic stem cells can give rise to cells with trophoblast-like transcriptome and methylome [RNA-Seq]

overall_design: 33 replicates


title: Brainstem organoids from human pluripotent stem cells contain neural crest population

status: Public on Jun 13 2020

city: Horn

first: Joachim

last: Luginbuehl

address: Bürgerstrasse

country: Switzerland

institute: RIKEN

summary: Brainstem controls heartbeat, blood pressure and respiration which are vital for life, therefore, damage to brainstem can be lethal. Brain organoids derived from human pluripotent stem cells recapitulate the course of human brain development and are expected to be useful for medical research on central nervous system disorders. However, existing organoid models have limitations, hampering the elucidation of diseases affecting specific components  of the brain. Here, we developed a method to generate human brainstem organoids (hBSOs), containing neural crest stem cells as well as midbrain/hindbrain progenitors, noradrenergic and cholinergic neurons, and dopaminergic neurons, demonstrated by specific electrophysiological signatures. Single-cell RNA-sequence analysis, together with proteomics and electrophysiology further revealed that the cellular population in the organoids is similar to that of the human brainstem and neural crest, which makes it possible to make use of the hBSOs for modeling and grafting for transplantation.

overall_design: Single-cell RNA-sequencing of human brainstem organoids

first: Eiichiro

last: Mori

first: Jay

middle: W

last: shin


title: UTX Regulates Human Neural Differentiation and Dendritic Morphology by Resolving Bivalent Promoters

status: Public on Jun 15 2020

city: Zibo

first: Dai

middle: Shang

last: Kun

state: Shandong

address: 266 Xincun West Road

department: School of Life Sciences and Medicine

institute: Shandong University of Technology

summary: To gain a deeper insight into roles of UTX in hESCs derived neurons, we performed ChIP-seq and RNA-seq to analyze the genome-wide changes of histone modifications and transcriptome changes after UTX deletion in hESCs-derived neurons.

overall_design: Total RNA was extracted from WT and UTX-KO neurons and generated by deep sequencing, in at least three biological replicates, using novaseq 6000. ChIP-seq was sequenced in one biological replicates using neurons and BGISEQ-500.

last: Shang-Kun


title: Interferons disrupt lung epithelial repair during recovery from respiratory infection

status: Public on Jun 12 2020

city: London

first: Andreas

last: Wack

address: 1 Midland Road

country: United Kingdom

institute: The Francis Crick Institute


title: Transcriptional profiles of human mature B cells from tonsil tissue

first: Riccardo

last: Dalla-Favera

summary: Mature B cells leave the bone marrow  as naïve B cells and migrate to the secondary lymphoid organs where they encounter the antigen for the first time. This interaction stimulates B cells to rapidly grow and form characteristic histological structures called germinal center. In the germinal centers, B cells are targeted by mechanisms of genetic editing of the immunoglobulin loci, namely somatic hypermutation and class switch recombination, undergo selection for high affinity immunoglobulin receptors and are committed to differentiate into memory B cells or plasma cells. GCs display two histological areas the dark and the light zone that have been characterized as functionally distinct compartments through which B cells recycle multiple times during the germinal center reaction.

overall_design: Naïve, total germinal center, and memory B cells were isolated from three independent donors each.  Dark zone and light zone germinal center B cells were isolated from four donors/each.

first: Katia

last: Basso

first: Antony

last: Holmes


title: Interferons disrupt lung epithelial repair during recovery from respiratory infection [RN19197]

summary: Respiratory viral infections cause lung epithelial damage, barrier dysfunction and severe disease. Type I interferons (IFN-a/b) are antiviral cytokines whose therapeutic use is limited by well-characterized pleiotropic effects. Type III IFNs (IFN-λ) are less pro-inflammatory and regarded a superior treatment option. Here, we show that IFN signalling reduces lung epithelial proliferation and differentiation and increases epithelial apoptosis during recovery from viral infection. This delays epithelial repair, increasing disease severity and the risk of bacterial superinfection. IFN-a has least effects, with IFN-b intermediate and IFN-λ strongest action.

overall_design: C57BL/6 (WT) or IFNLR deficient mice were infected or not with influenza, and at XXX time point, epithelial cells (MARKERS) were FACS sorted and lysed into RNA buffer, The indicated number of biological repeats was performed.

first: Jack

last: Major


title: Dynamic Transcriptional and Chromatin Accessibility Landscape of Medaka Embryogenesis

city: Beijing

first: Yongjie

address: No. 1 West Beichen Road, Chaoyang District

institute: Institute of Genetics and Developmental Biology

summary: Chromatin accessibility of nine embryonic samples was profiled using transposase-accessible chromatin with high-throughput sequencing (ATAC-seq) to identify potential regulatory elements.

overall_design: ATAC-seq libraries of 18 medaka embryonic stages.

first: Qiang

last: Tu

first: Yingshu

last: Li


title: Gene regulation in Arabidopsis by isothiocyanates

status: Public on Jun 14 2020

city: Wuerzburg

first: Susanne

last: Berger

address: Julius-von-Sachs-Platz 2

department: Pharmaceutical Biology

institute: Julius-von-Sachs-Institute

summary:
in Brassicaceae isothiocyanates are generated by metabolism of endogenous glucosinulates
regulation of gene expression by subtoxic concentrations of isothiocyanates  was investigated

overall_design: Arabidopsis seedlings were treated with sulforaphane, benzylisothiocyanate or prostaglandine A1 and gene expression was compared to control treaments

first: Martin

last: Müller


title: Gene expression responses in potato tubers treated with 1,4-dimethylnapjhthalene during longterm storage [year 2]

city: Erie

first: Michael

middle: A

last: Campbell

state: PA

address: 4205 College Drive

department: School of Science

institute: Penn State Erie

summary: Commercial storage of potatoes often relies on the use of sprout inhibitors to prolong storage and reduce spoilage. The compound 1,4-dimethylnaphthalene (DMN) has seen increase application as a sprout inhibitor in the potato industry as older chemistries are being phased out. The mode of action of DMN is poorly understood as is the sensitivity of potato tissues to this new class of inhibitor.  During storage potato tubers transition from a state of endo-dormant to eco-dormant and it is not known if the DMN response is consistent across this developmental transition. RNA-seq gene expression profiling was used to establish if stored potato tubers (Solanum tuberosum cv La Chipper) have differential sensitivity to DMN as tubers age. DMN was applied at three different times during storage; just after harvest when tubers are in endo-dormancy, midwinter at early eco-dormancy, and in spring during late eco-dormancy when sprouting was prevented via exposure to cold storage temperatures. Changes in gene expression were lowest during endo-dormancy while midwinter and spring treatments exhibited a greater and more diverse expression response. Functional analysis of differential gene expression demonstrated gene sets associated with DNA replication, cell division, and DNA methylation are suppressed after DMN treatment. However, gene sets associated with salicylic acid, jasmonic acid, abiotic and biotic stress responses are elevated by DMN only after endodormancy terminates. Gene clusters associated with pathogenesis related proteins PR-4 and PR-5 are also upregulated in response to DMN. These results indicate that DMN sensitivity changes as potato tubers age and transition from endo-dormant to eco-dormant in storage and the overall response is a shift in gene classes that regulate growth and response to stress.

overall_design:
Potato tubers were treated with the sprout regulator 1,4-dimethylnaphthalene after harvest (endodormant) again at midwinter (early ecodormancy) and then in spring (late ecodormancy)
Study was conducted in two separate havest years with relication within each year, this is year 2 (2016)


title: Transcriptome profiling of medaka timecourse embryonic samples and adult tissues  samples.

address: No.1 West Beichen Road,Chaoyang District

summary: We collected ten embryonic stages covering cleavage, blastula, gastrula, somite, and late stages until hatching. We also collected two adult tissue samples, including ovary and testis. 13 samples were sequenced using the illumina short-read sequencing platform.

overall_design: Total RNA was extracted from medaka whole embryo samples  of 11 developmental stages and 2 adult tissues. Short-read strand-specific library was constructed and sequenced using Illumina platform.


title: Gene expression responses in potato tubers treated with 1,4-dimethylnapjhthalene during longterm storage [year 1]

overall_design:
Potato tubers were treated with the sprout regulator 1,4-dimethylnaphthalene after harvest (endodormant) again at midwinter (early ecodormancy) and then in spring (late ecodormancy)
Study was conducted in two separate havest years with relication within each year, this is year 1 (2015)


title: An in vivo systematic genetic analysis of tumour progression in Drosophila identifies the cohesin complex as an invasion suppressor

city: Nottingham

first: Marios

last: Georgiou

address: Queen's Medical Centre

department: School of Life Sciences

institute: University of Nottingham

summary:
Metastasis is the leading cause of death for cancer patients. Consequently it is imperative that we improve our understanding of the molecular mechanisms that underlie progression of tumour growth towards malignancy. Advances in genome characterisation technologies have been very successful in identifying commonly mutated or misregulated genes in a variety of human cancers. However the difficulty in evaluating whether these candidate genes drive tumour progression remains a major challenge. Using the genetic amenability of Drosophila melanogaster we generated tumours with specific genotypes in the living animal and carried out a detailed systematic loss-of-function analysis to identify conserved genes that enhance or suppress epithelial tumour progression. This enabled the discovery of functional cooperative regulators of invasion and the establishment of a network of conserved invasion suppressors. This includes constituents of the cohesin complex, which can either promote individual or collective invasion, depending on the severity of effect on cohesin function.
We used Clariom™ S Assay arrays to detail the global programme of gene expression following STAG2 KD to detect DEG involved in regulation of cell motility and cell-cell junction assembly and maintenance.

overall_design: In order to assess the role of STAG2 in invasion, STAG2 was transiently knocked down by siRNA in MCF-7 cells 48h prior to RNA extraction and hybridization on Affymetrix microarrays. 3 independent experiments were performed, each including un-treated cells, cells treated with mock siRNA and cells treated with STAG2 siRNA. The microarray analysis was further conducted in triplicate for each sample.

first: Brenda

last: Canales

first: Marcos

last: Castellanos Uribe


title: High-resolution view at the coding transcriptome and noncoding RNAs of major gut microbe Bacteroides thetaiotaomicron

status: Public on Jun 11 2020

city: Würzburg

first: Lars

last: Barquist

state: Bayern

address: Josef-Schneider-Straße 2 / Bau D15

institute: Helmholtz Institute for RNA-based Infection Research

summary: Gram-negative, obligate anaerobic Bacteroides thetaiotaomicron is emerging as the model organism for gut microbiota research. Colonization of its host niche within the human colon depends to large parts on the extensive metabolic capacity encoded in the Bacteroides genome, but little is known about how its transcription is organized. Here, we transferred differential RNA-seq (dRNA-seq) to B. thetaiotaomicron type strain VPI-5482 to globally map transcription start sites (TSSs). Our screen identified ~4,500 TSSs and we globally determined untranslated regions (UTRs), operon structures, and promoter motifs. In addition, dRNA-seq led to the discovery of ~250 noncoding RNA elements, including 124 novel intergenic small RNAs (sRNAs), several of which we validated experimentally. One of them is the conserved, 145 nt-long sRNA BTnc035, that was highly expressed when B. thetaiotaomicron was grown in the presence of N-acetylglucosamine or glucuronic acid as the sole carbon source. Combining computational predictions with experimental data, we determined the secondary structure of BTnc035 and identified target genes of this sRNA. The emerging model places BTnc035 at the center of a metabolic feedback-loop, wherein sensing of  N-acetyl-D-glucosamine and D-glucuronic acid induces BTnc035, which in turn may contribute to a metabolic switch from polysaccharide biosynthesis to break-down. Together, we compiled a single-nucleotide resolution transcriptome map of B. thetaiotaomicron and provide the first global analysis of noncoding RNAs in this important anaerobic model bacterium. To allow easy interrogation of our transcriptome data, we developed Theta-Base – an intuitive online browser that can be freely accessed at https://www.helmholtz-hiri.de/en/bacteroides.

overall_design: Samples 1-18: Genome-wide mapping of transcription start sites via differential RNA-seq (dRNA-seq) of Bacteroides thetaiotaomicron VPI-5482 (wild type) grown in TYG to early-logarithmic phase (ELP), mid-logarithmic phase (MLP) and stationary phase (stat). Three biological replicates per strain and condition. Samples 19-24: Comparative expression analysis by RNA-seq of B. thetaiotaomicron wild-type (tdk deletion background), ∆BTnc035 (BTnc035 deletion mutant), and BTnc035+ (BTnc035 complementation strain). Two biological replicates per strain.


title: Generation of a Broadly Useful Model for COVID-19 Pathogenesis, Vaccination, and Treatment

city: GuangZhou

first: Jiangping

last: He

address: Kai yuan avenue 190

institute: Guangzhou Institutes of Biomedicine and Health (GIBH), CAS

summary: COVID-19, caused by SARS-CoV-2, is a virulent pneumonia, with >4,000,000 confirmed cases worldwide and >280,000 deaths as of May 13, 2020.  It is critical to develop and evaluate vaccines and therapeutic interventions as rapidly as possible. Mice, the ideal animal for such studies, are resistant to SARS-CoV-2. Here, we overcome this difficulty by exogenous delivery of human ACE2 with a replication-deficient adenovirus (Ad5-hACE2). Ad5-hACE2-sensitized mice developed pneumonia characterized by weight loss, severe pulmonary pathology, and high-titer virus replication in lungs. Type I interferon, T cells and, most importantly, signal transducer and activator of transcription 1 (STAT1) are critical for virus clearance and diminished disease in these mice. Ad5-hACE2-transduced mice enabled rapid assessments of a vaccine candidate, of human convalescent plasma, and of two antiviral therapies (poly I:C and remdesivir). In summary, we describe a murine model of broad and immediate utility to investigate COVID-19 pathogenesis, and to evaluate new therapies and vaccines.

overall_design: We analyzed the gene expression profiles SARS-CoV-2 infected tranduced human ACE2 mouse models

first: Jincun

last: Zhao


title: Interferons disrupt lung epithelial repair during recovery from respiratory infection [RN200717]

first: Andreas

overall_design: Mouse airway epithelial cultures were grown in vitro and exposed to the indicated IFN types for the indicated time periods. Biological triplicates were run for every treatment group.


title: An OTX2-PAX3 signaling axis regulates Group 3 medulloblastoma cell fate [scRNA-seq]

city: Winnipeg

first: Tamra

last: Werbowetski-Ogilvie

state: Manitoba

address: 611-745 Bannatyne Avenue

department: Biochemistry & Medical Genetics

country: Canada

institute: University of Manitoba

summary: scRNA-seq was performed to evaluate the OTX2-PAX3-mTOR signalling axis at the single cell level in heterogeneous Group 3 MB tumorspheres

overall_design: Tumorspheres were generated from 3 Group 3 MB cell lines to examine mTOR signalling and assess similiarity to patient tumors


title: An OTX2-PAX3 signaling axis regulates Group 3 medulloblastoma cell fate

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

overall_design: Refer to individual Series

first: T


title: Gene expression responses in potato tubers treated with 1,4-dimethylnapjhthalene during longterm storage


title: Gene expression analysis of E2A forced homodimer overexpression in mouse embryonic stem cells.

status: Public on Jun 10 2020

city: New York

first: Chandrika

last: Rao

address: 619 West 54th Street, 3rd Floor

institute: New York Stem Cell Foundation Institute

summary: We set out to investigate whether overexpression of the bHLH transcription factor, E2A, is sufficient to drive neural differentiation in mouse embryonic stem cells under non-permissive culture conditions. Having identified that overexpression of specifically E2A homodimers, but not E2A monomers, was sufficient to drive neural differentiation, we sought to identify early downstream targets of E2A during the process of neural commitment using RNA-sequencing.

overall_design: A doxycycline-inducible cell line was used to drive overexpression of a forced homodimer construct of E2A in mouse embryonic stem cells. Cells were induced with 1ug/mL doxcycline for up to 24 hours, and samples were collected for RNA-sequencing at 0h, 18h and 24h time-points. All samples were collected in triplicate (total of 9 samples). Differential analysis was performed using the following comparisons: 0h vs. 18h; 0h vs. 24h; 18 vs. 24h.

first: Sally

last: Lowell


title: An OTX2-PAX3 signaling axis regulates Group 3 medulloblastoma cell fate [RNA-seq]

summary: RNA-seq was carried out to evaluate the molecular mechanisms that contribute to the distinguishing effects of PAX3 and PAX6 GOF on Group 3 MB cells

overall_design: Transcriptional profiles for PAX3-GOF and PAX6-GOF tumorspheres were genreated in triplicate by RNA-seq


title: Murine models of IDH-wild-type glioblastoma exhibit spatial segregation of tumor initiation and manifestation during evolution

city: WASHINGTON

first: Yuan

last: Zhu

state: DC

address: 111 Michigan Ave NW

institute: Childrens National Medical Center

summary:
Primary glioblastoma, representing over 90% of adult glioblastoma, develop rapidly without preexisting lower-grade glioma. We have generated a mouse model of primary glioblastoma driven by a single p53 mutation. These p53-mutant gliomas lose the syntenic region of human chromosome 10q, which is mapped to mouse chr19 and chr7. Loss of mouse chr19, containing Pten, activates PI3K/Akt signaling.
Using serial MRI/3D-reconstruction, whole-genome sequencing and spectral karyotyping-based single-cell phylogenetic tree building, we showed two distinct types of tumor evolution in p53-mutant driven mouse models. Malignant gliomas/GBMs grew as a single mass (Type 1) and multifocal masses (Type 2), respectively, despite both exhibiting loss of Pten/chromosome 19 (chr19) and PI3K/Akt activation with sub-tetraploid/4N genomes. Analysis of early biopsied and multi-segment tumor tissues revealed no evidence of less proliferative diploid/2N lesions in Type 1 tumors. Strikingly, CA-derived relatively quiescent tumor precursors with ancestral diploid/2N genomes and normal Pten/chr19 were observed in the subventricular zone (SVZ), but was distantly segregated from multi-focal Type 2 tumors. Importantly, PI3K/Akt inhibition by Rictor/mTORC2 deletion blocked distant dispersal, restricting glioma growth in the SVZ.

overall_design: In this study we generate mouse models with single p53 mutations. We profiled the resultant tumors, tumor derived cell lines as well as normal forebrain as controls.


title: Longitudinal serum auto-antibody response during HER2-CAR T cell therapy in a child with rhabdomyosarcoma identified using Protein microarray

status: Public on Jun 09 2020

city: Houston

first: Sujith

middle: K

last: Joseph

state: Texas

address: 1102 Bates Avenue Suite 1770

department: Pediatrics Hematology-Oncology

institute: Baylor College of Medicine

summary: Protein microarray was used to identify proteins with elevated interactions with serum autoantibodies in a responding patient with rhabdomyosarcoma before and after multiple doses of HER2 CAR T cell therapy. Elevated signals were observed for multiple proteins interacting with serum autoantibodies following multiple doses of HER2-CAR T cell treatment when compared to pre-treatment serum.

sample_organism:
Homo sapiens
other sequences

overall_design: Serum samples were obtained before start of treatment and subsequent follow up time points after treatment from a child with metastatic rhabdomyosarcoma enrolled in a phase 1 clinical study testing safety of HER2 targeted Chimeric Antigen Receptor (CAR) modified T cells according to Baylor College of medicine IRB approved study protocol H-24489 with the clinical trial registry number NCT00902044. The serum samples (n=6) were probed utilizing one ProtoArray™ Human Protein Microarray per sample along with a negative control.

first: Meenakshi

last: Hegde

first: Nabil

last: Ahmed


title: 3D genome organization, transcription and aberrant DNA replication contribute to genome instability at fragile sites

city: Jerusalem

first: Dan

last: Sarni

address: Givart Ram

country: Israel

institute: The Hebrew University of Jerusalem

summary: Common fragile sites (CFSs) are regions susceptible to replication stress and are hotspots for chromosomal instability in cancer. Several features characterizing CFSs have been associated with their instability, however, these features are prevalent across the genome and do not account for all known CFSs. Here we explored the DNA replication timing (RT) and transcriptional profile under mild replication stress in the context of the 3D genome organization. We report the analysis of DNA replication timing profiling of human fibroblasts (BJ-hTERT), grown with or without aphidicolin, a DNA polymerase inhibitor used to induce CFS expression. We find that aphidicolin treatment affects the RT of a small portion of the genome. However, CFSs are enriched for delayed RT regions under stress. We further study the mechanism leading to recurrent chromosomal instability at CFSs and find that the 3D genome organization underlies fragility at RT delayed large expressed genes. We report a fragility signature at the core of CFSs comprised of delayed replication of large expressed gene spanning over a TAD-boundary. The fragility signature allows for mapping of the core fragile site and the identification of novel fragile sites in BJ cells.

overall_design: Genome-wide replication timing profiles were constructed for immortalized human foreskin fibroblasts (BJ-hTERT) with or without 200nM aphidicolin treatment for 24 hours (4 biological replicates per condition).

first: Takayo

last: Sasaki

first: Karin

last: Miron

first: David

last: Gilbert

first: Batsheva

last: Kerem


title: Discovery of DAP3-binding RNA sites by eCLIP

status: Public on Jun 23 2020

city: Singapore

first: Polly Leilei

last: Chen

address: #12-01, MD6, 14 Medical Drive

department: Department of Anatomy

country: Singapore

institute: Cancer Science Institute of Singapore NUS

summary: eCLIP paired-end sequencing of DAP3 in EC109 cells with two biological replicates. This analysis revealed the genome-wide RNA binding landscape of DAP3, as the supporting data of the main publication.

overall_design: We examined DAP3-binding sites on RNA in EC109 cells by eCLIP-seq. Protein-RNA interactions were covalently linked by UV crosslinking and RNase treatment removed unbound RNA. The crosslinked RNA was immunoprecipitated together with DAP3 using specific antibody targeting DAP3, and converted to double-stranded DNA high-throughput sequencing libraries through adapter ligation and reverse transcription. Two biological replicates of DAP3 eCLIP were performed and an IgG eCLIP served as a control. Each eCLIP experiment has a corresponding size-matched input control experiment.

first: Chen

last: Leilei

first: Han

last: Jian

first: Omer

last: An

first: Gene

last: Yeo

first: Katannya

last: Kapeli

first: Tan

middle: H

last: Qing


title: An OTX2-PAX3 signaling axis regulates Group 3 medulloblastoma cell fate [ChIP-seq]

first: Tamra

last: Werbowetski-Ogilvie

summary: We evaluated changes in active and repressive histone modifications following the silencing of OTX2 in Group 3 medulloblastoma tumorspheres

overall_design: H3K4me3 and H3K27me3 enrichment examined to evaluate the global silencing of transcription factors in Group 3 medulloblastoma


title: GDNF drives rapid tubule morphogenesis in novel 3D in vitro model for ADPKD

status: Public on Jun 08 2020

city: Saint Louis

first: Eryn

last: Dixon

state: MO

address: 600 S Euclid Ave

department: Renal Division/Internal Medicine

institute: Washington University in St. Louis


title: miR-181a initiates and perpetuates oncogenic transformation through the regulation of innate immune signaling

status: Public on Jun 07 2020

city: Ann Arbor

first: Analisa

last: DiFeo

state: MI

address: 1600 Huron Parkway

department: Pathology

institute: The University of Michigan

summary: Genomic instability predisposes cells to malignant transformation, however the molecular mechanisms that allow for the propagation of cells with a high-degree of genomic instability remains unclear. Here we report that miR-181a is able to transform fallopian tube secretory epithelial cells- the precursor cell type for the majority of high-grade serous ovarian cancers- through the inhibition of RB1 and simultaneously drives a cell protective inhibition of the stimulator-of-interferon-genes (STING) in order to maintain a microenvironment conducive to the propagation of cells with a high-degree of genomic instability. We found that miR-181a inhibition of RB1 leads to profound nuclear defects, genomic instability, and nuclear rupture resulting in a persistence of genomic material in the cytoplasm. While normally, this persistence of genomic material in the cytoplasm induces interferon response through STING to drive cell death, miR-181a directly downregulates STING and prevents apoptosis. The most common mechanism by which oncogenic miRNAs promote tumorigenesis is through the direct inhibition of tumor suppressor genes, however our studies highlight a new mechanism of oncomiR transformation through the combination of tumor suppressor gene inhibition and abrogation of immune surveillance that initiates and propagates tumor cell survival. Importantly, we found that miR-181a induction in ovarian patient tumors is tightly associated with decreased IFNg response and downregulation of lymphocyte infiltration amd leukocyte fraction. To date, DNA oncoviruses are the only known inhibitors of STING that allow for cellular transformation thus, our findings are the first to identify a genetic factor, miR-181a, that can downregulate STING expression, suppress activation of the immunosurveillance machinery, and impair signaling in cancer cells creating a survival advantage. Our studies support the notion that the induction of STING-mediated signaling in cancer cells could lead directly to cancer cell death however these effects are abrogated by miR-181a. Given the recent interest in the development of STING agonists as a strategy to harness the immune system to treat cancer, this study introduces novel patient selective biomarker as well as potent therapeutic target for development of the most effective combination treatments.

overall_design: Total RNA was extracted from cell lysates of FT237-001, p181a, and p181a inhibitor in triplicate and submitted for Microarray using Affymetrix Human Clariom S array and the WT Plus chemistry.


title: Optimized CRISPR-Cas12a platform for combinatorial drop-out genetic screening  (RNA-seq)

city: PHILADELPHIA

first: Zhendong

last: Cao

address: BRB Rm620, 421 Curie Blvd

department: Cancer biology

institute: university of pennsylvania

summary: Combinatorial genetic perturbations have been utilized to identify synthetic sick/lethal genetic interactions for cancer drug target discovery. Current methods for high-throughput combinatorial genetic screening are inefficient and cumbersome. Here we developed a simple, robust, and high-performance CRISPR-Cas12a-based approach for unbiased, combinatorial genetic screening in cancer cells.

overall_design: mRNA profiles of Cas12 sgRNA-expressing MLL-AF9 transformed acute myeloid leukemia cells (RN2).

first: Junwei

last: Shi


title: Murine B cell response to immunization with SARS-CoV-2

city: New Haven

first: Steven

last: Kleinstein

state: Ct

address: 300 George St.

institute: Yale University

summary: We performed single-cell gene expression and V(D)J profiling to interrogate the blood plasmablast response in mice immunized with the receptor binding domain of the SARS-CoV-2 spike protein.

overall_design: Examination of one scRNA-seq sample of total antibody-secreting cells sorted from pooled draining lymph nodes of two C57BL/6 mice.

first: Jackson

middle: S

last: Turner

first: Julian

middle: Q

last: Zhou

first: Aaron

last: Schmitz

first: Ali

last: Ellebedy


title: inflammatory response to IL-1b in WT, LDHA KO, NAMPT KO, NFKBIZ KO and FX11 treated chondrocytes

status: Public on Jun 06 2020

first: Yosuef

last: Abu-amer

address: 660 South Euclid Ave

department: Orthopedic Surgery

institute: Washington University School of Medicine

summary: Our goal is to study the impacts of IL-1b treatment on chondrocyte physiology. Furthermore, we knocked out several genes that we believe are important for modulating the inflammatory response. We find that IL-1b treatment induces metabolic reprogramming towards aerobic glycoylsis. We found that inhibition of LDHA using inbhitiro FX11 inhibited the inflammatory response of chondrocytes. We hypothesized that this effect was mediated by interaction with NADH, leading to regulation of IkB-z protein. Thus, deletion of LDHA, NAMPT or NFKBIZ was performed and found to inhibit inflammatory response genes induced by IL-1b, with similar gene expression changes amongst the three suggesting that they may work in the same pathway.

overall_design: Chondrocytes were isolated from sterna of WT animals and treated with IL-1b (10 ng/mL) in the presence or absence of FX11 (40 uM) for 24 hours. For other samples, chondrocytes were isolated from sterna of LDHA flox, NAMPT flox or NFKBIZ flox pups. Chondrocytes were adenovirally transduced with GFP or Cre expressing vectors to delete genes. Cells were then treated with IL-1b for 24 hours. No passaging was perfomred on chondrocytes, all cultures were performed at normoxia.

first: Yousef

last: Abu-Amer

first: Manoj

last: Arra


first: Brian

last: Magnuson

address: 1500 East Medical Center Drive

institute: University of Michigan

summary: Common fragile sites (CFSs) are regions susceptible to replication stress and are hotspots for chromosomal instability in cancer. Several features characterizing CFSs have been associated with their instability, however, these features are prevalent across the genome and do not account for all known CFSs. Here we explored the transcriptional profile and DNA replication timing under mild replication stress in the context of the 3D genome organization. We report the analysis of nascent RNA-seq for high-throughput profiling of gene expression in human fibroblasts (BJ-hTERT), grown with or without aphidicolin, a DNA polymerase inhibitor used to induce CFS expression. We find that aphidicolin treatment does not affect the transcriptional program. However, large expressed genes are susceptible to replication timing delay under stress. We further study the mechanism leading to recurrent chromosomal instability at CFSs and find that the 3D genome organization underlies fragility at large expressed genes. We report a fragility signature at the core of CFSs comprised of a large expressed gene spanning over a TAD-boundary with delayed DNA replication. The fragility signature allows for mapping of the core fragile site and the identification of novel fragile sites in BJ cells.

overall_design: Nascent RNA-seq profiles of immortalized human foreskin fibroblasts (BJ-hTERT) with or without 200nM aphidicolin treatment for 24 hours (2 biological replicates per condition).

first: Dan

last: Sarni

first: Karin

last: Miron

first: Mats

last: Lujngman

first: Batsheva

last: Kerem


title: Multi-omics analysis reveals divergent epigenetic regulation of gene expression and drivers of esophageal squamous cell carcinoma [ChIP-seq]

status: Public on Jun 05 2020

city: San Francisco

first: Wei

last: Wu

state: CA

address: 600 16th street

department: Department of Medicine

institute: University of California, San Franciso

summary: Purpose: Epigenetic landscapes can shape physiologic and disease phenotypes. We used whole genome bisulfite sequencing, RNAseq, and ChIP-seq technologies to understand the methylome profiling, gene expression and regulation via epigenetic alterations on esophageal sequamouse carcinoma comparing to adjacent non-tumor tissues.

overall_design: Methods:  Cultured cells  were used to examine  EZH2 binding regions across genome.


title: Transcriptional profiles of male posterior amygdala

first: Takashi

last: Yamaguchi

state: New York

address: 435 E 30th St

department: Neuroscience Institute

institute: New York University School of Medicine

summary: To investigate whether male MPN- and VMHvl-projecting neurons in posterior amygdala have distinct transcriptional profiles, we conducted RNAseq onto these subpoplations that were microdissected by laser capture microdissection. Our results demonstrate that each subpoplations had largely distinct set of enriched genes.

overall_design: MPN- and VMHvl-projecting neurons in posterior amygdala and basomedial amygdala posterior part of C57BL/6N male mice were microdissected using Laser capture microdissection. Subsequent RNAseq generated transcriptional profiles of the subnucleus.

first: Dayu

last: Lin


title: Long non-coding RNAs and mRNAs profiling of liver tissue during four developmental stages in chickens

city: Chengdu

first: Chunyou

last: Ning

address: No. 211, Huimin road

institute: SICAU

summary: Liver is the major organ of lipid biosynthesis in chicken. In laying hens, the liver synthesizes most of yolk precursors and transports to the developing follicles to produce eggs. However, a systematic and comprehensive investigation of long non-coding RNAs (lncRNAs) and mRNAs transcriptome in chicken liver across different developmental stages remain clearly unknown. Here, we constructed 12 RNA libraries from liver tissue during four developmental stages, including juvenile period (JP, day 60), sexual maturity period (SM, day 133), peak laying period (PL, day 220) and broodiness period (BP, day 400). A total of 16,930 putative lncRNAs and 18,260 mRNAs were identified among these samples. More than half of identified lncRNAs were intergenic lncRNAs (lincRNAs), accounting for 53.70%. The temporal expression pattern showed that lncRNAs were more restricted than mRNAs. We identified numerous differentially expressed lncRNAs (DE lncRNA) and mRNAs (DEGs) by pairwise comparisons between the four developmental stages and found that vitellogenin 2 (VTG2), riboflavin binding protein (RBP), and a novel protein-coding gene were differentially expressed in all stages. Time-series analysis showed that the module with up-regulated genes were enriched in related to lipid metabolism process. Co-expression networks suggested the functional relatedness between mRNAs and lncRNAs and the results showed the DE-lncRNAs also mainly involve in lipid biosynthesis and metabolism process. These results suggest the transcriptome variation of liver in different developmental stages and improve the comparative understandings of molecular mechanisms of liver development in chickens.

overall_design: transcriptome profiles of the chicken liver from 4 developmental stages, differentially expressed genes, Gene Ontology (GO), and KEGG enrichment and co-expression networks were analyzed.

first: Silu

last: Hu

first: Zhongxian

last: Xu

first: Pu

last: Zhang

first: Qing

last: Zhu

first: Diyan

last: Li


title: The regulatory landscape of early maize inflorescence development

city: St. Louis

first: Andrea

last: Eveland

state: Missouri

address: 975 North Warson Road

institute: Donald Danforth Plant Science Center

summary: The functional genome of agronomically important plant species remains largely unexplored, yet presents a virtually untapped resource for targeted crop improvement. Functional elements and regulatory DNA revealed through chromatin accessibility maps can be harnessed for manipulating gene expression to subtle phenotypic outputs that enhance productivity in specific environments. Here, we present a genome-wide view of accessible chromatin and nucleosome occupancy at a very early stage in the development of both pollen- and grain-bearing inflorescences of the important cereal crop maize (Zea mays), using an assay for differential sensitivity of chromatin to micrococcal nuclease (MNase) digestion. Results showed that in these largely undifferentiated tissues, approximately 1.5-4 percent of the genome is accessible, with the majority of MNase hypersensitive sites marking proximal promoters but also 3’ flanks of maize genes. This approach mapped regulatory elements to footprint-level resolution, and through integration of complementary transcriptome and transcription factor occupancy data, we annotated regulatory factors such as combinatorial motifs and long non-coding RNAs that potentially contribute to organogenesis in maize inflorescence development, including tissue-specific regulation between male and female structures. Finally, genome-wide association studies for inflorescence architecture traits based only on functional regions delineated by MNase hypersensitivity, revealed new SNP-trait associations in known regulators of inflorescence development. These analyses provide a first look into the cis-regulatory landscape during inflorescence differentiation in a major cereal crop, which ultimately shapes architecture and influences yield potential.

overall_design: As detailed below, we analyzed 2 different tissue types, maize tassel and ear primordia. Nucleosome bound DNA from these primordia were digested with low (light digest) and high (heavy digest) concentration of micrococcal nuclease enzyme followed by high-throughput sequencing to investigate the chromatin landscape. The differential between light and heavy digests and the different size classes of sequenced reads were used to call nucleosomal and transcription factor footprints. Two biological replicates were used per tissue per micrococcal nuclease enzyme concentration.

first: Rajiv

last: Parvathaneni

first: Edoardo

last: Bertolini

first: Md

last: Shamimuzzaman

first: Daniel

last: Vera

first: Pei-Yau

last: Lung

last: Rice

first: Jinfeng

first: Patrick

last: Brown

first: Alexander

last: Lipka

first: Hank

last: Bass


title: Mouse wound healing [RNA-seq]

city: Bethesda

first: Junji

address: 9000 Rockville Pike

institute: NIH, NIDCR

summary:
Purpose: To explore the changes of genes expression in different time points during mouse wound healing.
Two wounds tissue from one animal were pooled, three animals were used per time point. The wounds tissue was collected on day 0, 1, 3, 5, 7 after cutting. Skin was cleaned of muscle and fat tissue; total RNA was extracted using the RNeasy mini kits (Qiagen), purified using Direct-zol RNA MiniPrep kit (Zymo Research). Next-generation libraries were prepared using the VAHTS TM mRNA-seq V2 Library Prep Kit for Illumina (Vazyme, #NR601). RNA-seq libraries were run on an Illumina HiSeq X-Ten next-generation sequencer. Analysis of RNA-seq data was done using the DESeq package in R.

overall_design: mRNA profiles of genes expression in different time points of mice skin wounds were generated by deep sequencing, in triplicate, using Illumina HiSeq X-Ten next-generation sequencer.

first: Pang-Yen

last: Tseng

first: Lei


title: RNA-sequencing study of global gene expression in haploid yeast Saccharomyces cerevisiae mating type MATa treated with different doses of alpha-pheromone

status: Public on Jun 04 2020

city: Marburg

first: Victor

last: Sourjik

state: Hessen

address: Karl-von-Frisch-Straße 10

department: Systems and Synthetic Microbiology

institute: Max Planc Institute for Terrestrial Microbiology

summary: Yeast cells were treated with different doses of pheromone in order to obtain dose-response profiles for induced genes. Specifically, dose-dependencies of transcriptional feedback regulators of the pheromone-response pathway were quantified.

overall_design: Yeast cells were grown in minal medium with glucose and treated with pheromone at mid-exponential phase. Samples were collected after 60 minutes of incubation with pheromone. Two biological replicates were performed, each with 9, partially overlapping, doses of pheromone. A sample with mock-treatment, i.e., no addition of pheromone, served as a reference for non-treated cells in each experiment.

last: Anders

first: Bhaswar

last: Ghosh

first: Timo

last: Glatter


title: Liver Single-Cell Transcriptome Analysis of Cell-specific Dysregulation of Liver Cell Biology Following Intravenous Administration of AAV Vectors

first: Yael

last: Strulovici-Barel

state: NY

address: 1300 York Avenue

department: Department of Genetic Medicine

institute: Weill Cornell Medical College

summary: Zhu et al. report the application of single-cell RNA-sequencing technology for profiling the cell-specific transgene expression and transcriptome dysregulation in mouse liver following intravenous administration of AAV vectors. By profiling 46,500 mouse liver cells, we have identified 3 separate clusters of hepatocytes (hep1, hep2 and hep3), endothelial cells, Kupffer cells and lymphocytes. Assessment of the AAVrh.10mCherry treated liver demonstrated transgene expression in not only hepatocytes, but in all cell types, with significant cell-type-specific expression heterogeneity. Large numbers of cell type-specific genes were up- and down-regulated in response to the AAV vectors. These observations provide insights into the liver cell-specific consequences of AAV-mediated liver gene transfer, far beyond the well-known organ-specific expression of the vector-delivered transgene.

overall_design: Single-cell RNA-sequencing analysis of livers of wild-type, male, C57BL/6 mice following intravenous injection of PBS, AAVrh.10Null and AAVrh.10mCherry

first: Detu

last: Zhu

first: Mahboubeh

last: Rostami

first: Wu-lin

last: Zuo

first: Philip

last: Leopold

first: Jason

middle: G

last: Mezey

first: Ronald

last: Crystal


city: Manchester

first: Angela

last: Simeone

address: 200 Hathersage Rd

institute: Genomic Services QIAGEN

summary:
Epigenetic homogeneity underlies sperm programming for embryonic transcription
single-ended ChIP-Seq libraries from sperm, egg extract (-geminin) treated sperm, egg extract (+geminin) treated sperm, and St 7 embryos with antibody for H3Kme3, H3K27me3, 3 replicates for each histone modification pull-down

sample_organism:
Xenopus laevis
Homo sapiens

platform_organism:
Xenopus laevis
Homo sapiens

overall_design:
30 samples, paired-ended and single-ended ChIP-Seq libraries from sperm, egg extract (-geminin) treated sperm, egg extract (+geminin) treated sperm, and St 7 embryos with antibody for H3Kme3, H3K27me3, 3 replicates for each histone modification pull-down.
-------------------------------------------------
*The authors state the following regarding the human raw data: "We don't have the required patient consents to deposit them".  Thus, this submission is incomplete.

first: Mami

last: Oikawa

first: Eva

last: Hormanseder

first: Marta

last: Teperek

first: Clive

last: D’Santos

first: Charles

last: Bradshaw

first: Alan

last: O’Doherthy

first: T

last: Freour

first: L

last: David

first: Adrian

middle: T

last: Grzybowski

last: Ruthenburg

first: John

last: Gurdon

first: Jerome

last: Jullien


title: Global expression analysis of the transcriptome from bone marrow cells from wild type (WT) mice and mice with S1P-ablation in the Osterix-lineage (Cko)

first: Debabrata

last: Patra

address: 425 S. Euclid Avenue

department: Orthopaedic Surgery

summary: Comparison of the transcriptome of non-RBC bone marrow cells from WT mice with non-RBC bone marrow cells from mice with S1P-ablation in the Osterix-lineage (Cko).

overall_design: Forelimbs and hindlimbs from mice were crushed in a mortar and pestle in the presence of phosphate buffered saline (PBS) and strained through a 70 micron filter and filtrate stored on ice.  Crushed bones were digested with collagenase at 37 degree celcius for 15 min, strained through a 70 micron filter and pooled with the filtrate from above.  The filtrate/cells were washed with cold PBS, and the RBCs lysed using an RBC lysis buffer (Sigma, R 7757) for 5 min.  Following washings with cold PBS to remove lysed cells and hemoglobin, cells were suspended in 0.1% bovine serum albumin and processed by the 10x Genomics microfluidic platform (www.10xgenomics.com).

first: Eric

last: Tycksen


title: RNA-Seq Analysis of FACS-sorted GFP-expressing and skeletal stem cells (SSC) from the bone marrow of mice with S1P ablation in the Osterix (Osx)-lineage (Cko)

summary: Comparison of the transcriptome of GFP-expressing cells from the bone marrow compartment of Cko mice with the transcriptome of skeletal stem cells (SSC) from the bone marrow compartment of Cko and WT mice (homozygous floxed S1P mice).

overall_design: Forelimbs and hindlimbs from mice were crushed in a mortar and pestle in the presence of phosphate buffered saline (PBS) and strained through a 70 micron filter and filtrate stored on ice.  Crushed bones were digested with collagenase at 37 degree celcius for 15 min, strained through a 70 micron filter and pooled with the filtrate from above.  The filtrate/cells were washed with cold PBS, and the RBCs lysed using an RBC lysis buffer (Sigma, R 7757) for 5 min.  Following washings with cold PBS to remove lysed cells and hemoglobin, cells were suspended in PBS with 0.1% bovine serum albumin and stained with fluorescence-conjugated CD45, Ter-119, CD31, and CD105 antibodies and FACS-sorted for skeletal stem cells (SSC) defined as the population of cells positive for CD105 antigen but triple negative for Ter-119, CD31, and CD45 markers. Single cells were collected directly into 96 well plates from two WT (WT3 and WT5) and two Cko (Cko2 and Cko4) individually, lysed and RNAseq performed from RNA harvested from each well.  Similarly, single GFP-expressing cells were directly FACS-sorted (i.e. without the use of any fluorescence conjugated antibodies) from the pooled bone marrow compartment of two Cko mice (in duplicate).


title: RNA-seq analysis of mouse embryonic stem cells cultured in medium containing MEK and Akt inhibitors

city: Wako

first: Itoshi

last: NIKAIDO

state: Saitama

address: 2-1 Hirosawa

department: Center for Biosystems Dynamics Research

country: Japan

institute: RIKEN

summary: Cell-to-cell heterogeneity in gene expression can even be observed in the same type of cells, present in a similar environment. Transcriptional bursting is thought to be one of contributing factors to the heterogeneity, but it remains elusive how the kinetic properties of transcriptional bursting (e.g. burst size, burst frequency, and noise induced by transcriptional bursting) are regulated in mammalian cells. To unbiasedly identify genes regulating the kinetic properties of transcriptional bursting, we performed large-scale CRISPR/-Cas9 based screening and functional analysis, and found that Akt/MAPK signaling pathways are involved in the regulation of the kinetic properties of transcriptional bursting. To further characterize how these pathways affect mESC gene expression programs, we performed RNA-Seq analysis of mESCs cultured in standard (Std), 2i and Akt/MAPK signal-inhibitor containing medium (PD-MK). We found that expression levels of some genes encoding transcription elongation related factors were upregulated in PD-MK condition.

overall_design: Bulk RNA-Seq was performed by CEL-Seq2 method (Hashimshony et al., 2016) with total RNA amounts were used the range of 30-60 ng. Three biological replicates were prepared.

first: Yasuyuki

last: Ohkawa

first: Akihito

last: Harada

first: Hiroshi

last: Ochiai

last: Nikaido


title: RNA-seq analysis of mESCs cultured on either Laminin-511 or gelatin coated dishes in either Std or 2i medium

summary: Some mouse embryonic stem cell (mESC) lines need to be maintained on feeder cells in gelatin/Std condition. To eliminate the need for feeder cells, we decided to maintain the C57BL6/J mESCs on dishes coated with Laminin-511 (LN511) enabling maintenance of mESCs without feeder cells in Std condition (Domogatskaya et al., 2008). To compare the transcriptomes of mESCs cultured on gelatin-coated dish and those cultured on Laminin-511 coated dish, we performed RNA-Seq analysis. We found that the transcriptomes of mESCs cultured on gelatin-coated dish and those cultured on LN511 coated dish showed no considerable difference in expression patterns.

overall_design: Examination of 2 coating conditions in 2 medium. There are two biological replication in each condition.


title: Genome-wide CRISPR library screening to identify genes involved in the regulation of the kinetic properties of transcriptional bursting

summary: Cell-to-cell heterogeneity in gene expression can even be observed in the same type of cells, present in a similar environment. Transcriptional bursting is thought to be one of contributing factors to the heterogeneity, but it remains elusive how the kinetic properties of transcriptional bursting (e.g. burst size, burst frequency, and noise induced by transcriptional bursting) are regulated in mammalian cells. To unbiasedly identify genes regulating the kinetic properties of transcriptional bursting, we performed large-scale CRISPR/-Cas9 based screening and functional analysis, and found that Akt/MAPK signaling pathways are involved in the regulation of the kinetic properties of transcriptional bursting.

overall_design: Genome-wide CRISPR library screening was performed in Nanog, Dnmt3l, Trim28 knockin cell lines, in which GFP and iRFP reporter separately inserted into the two alleles. There are two technical replication in FACS-sorted sampels.


title: Allele-specific mRNA expression analysis in 129/CAST hybrid mESCs by single-cell full-length total RNA-sequencing

summary: Cell-to-cell heterogeneity in gene expression can even be observed in the same type of cells, present in a similar environment. Transcriptional bursting is thought to be one of contributing factors to the heterogeneity, but it remains elusive how the kinetic properties of transcriptional bursting (e.g. burst size, burst frequency, and noise induced by transcriptional bursting) are regulated in mammalian cells. Here, by using single-cell, full-length total RNA-sequencing, we performed genome-wide analysis of transcriptional bursting in mouse embryonic stem cells (mESCs). We found that the kinetics of transcriptional bursting is gene-specific and is determined by a combination of promoter and gene body binding proteins, including polycomb repressive complex 2 and transcription elongation-related factors.

overall_design: To study kinetic properties of transcriptional bursting genome-wide, we analyzed allele-specific mRNA levels in 129/CAST hybrid mESCs (grown on Laminin-511 (LN511) without feeder cells in G1 phase) by RamDA-Seq - a highly sensitive RNA-Seq method capable of determining the full-length of transcript at single cell level (Hayashi et al., 2018).

first: Tetsutaro

last: Hayashi


title: Genome-wide kinetic properties of transcriptional bursting in mouse embryonic stem cells

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

overall_design: Refer to individual Series


title: Lactate released by inflammatory bone marrow neutrophils induces their mobilization via endothelial GPR81 signaling

status: Public on Jun 03 2020

city: Rehovot

first: Hassan

last: Massalha

address: Herzl St 234

institute: Weizmann Institute of Science

summary: We found different expression between glycolytic enzymes and TCA pathway in bone marrow neutrophils following LPS treatment, using RNAseq. This enable us to uncover the important role of glycolysis in activated neutrophils and the effect of HIF-1alpha on this pathway

overall_design: mRNA profiles from bulk-seq library of sorted bone marrow neutrophils upon LPS treatment (sorted gating on CD45+/CD11b+/Ly6Ghigh cells usingSORP-FACSAria II machine)

first: Eman

last: Khatib-Massalha

first: Suditi

last: Bhattacharya

first: Adi

last: Biram

first: Karin

last: Golan

first: Orit

last: Kollet

first: Anju

last: Kumari

first: Francesca

last: Avemaria

first: Ekaterina

last: Petrovich-Kopitman

first: Shiri

last: Gur-Cohen

first: Tomer

last: Itkin

first: Isabell

last: Brandenburger

first: Asaf

last: Spiegel

first: Ziv

last: Shulman

first: Zachary

last: Gerhart-Hines

first: Shalev

last: Itzkovitz

first: Matthias

last: Gunzer

first: Stefan

last: Offermanns

first: Ronen

last: Alon

first: Amiram

last: Ariel

first: Tsvee

last: Lapidot


title: Gene expression profiles of differentially expressed genes in Enterococcus faecalis 14 ΔBac mutant strain

status: Public on Jun 02 2020

city: Villeneuve d'Ascq

first: Anca

last: Lucau-Danila

address: Cité Scientifique SN2 303

department: Biology

country: France

institute: University of Lille

summary: To explain the particular behavior of the mutant ΔBac strain and the impact of the bacteriocin DD14 on the global regulation and gene expression in Ent. faecalis 14, we performed a  comparative transciptomic analysis of RNA isolated from a derivative strain ΔBac mutant versus the wild-type (WT) , after 6 h of growth in GM17 medium under semi-aerobic conditions.

overall_design: Expression data of the 3 wild-type samples were filtered and the average was calculated for each gene. A fold change (FC) value was calculated between ΔBac individual samples and the mean of WT. Differentially expressed genes (DEGs) were selected for a FC threshold > 2.0 or < 0.5.

first: Rabia

last: Ladjouzi

first: Djamel

last: Drider


title: Dual RNA-seq of Orientia tsutsugamushi in HUVEC cells

city: Würzburg

first: Lars

last: Barquist

address: Josef-Schneider-Straße 2 / Bau D15

institute: Helmholtz Institute for RNA-based Infection Research

summary: Emerging and neglected diseases pose challenges as their biology is frequently poorly understood, and genetic tools often do not exist to manipulate the responsible pathogen. Organism agnostic sequencing technologies offer a promising approach to understand the molecular processes underlying these diseases. Here we apply dual RNA-seq to Orientia tsutsugamushi (Ot), an obligate intracellular bacterium and the causative agent of the vector-borne human disease scrub typhus. Half the Ot genome is composed of repetitive DNA, and there is minimal collinearity in gene order between strains. Integrating RNA-seq, comparative genomics, proteomics, and machine learning, we investigated the transcriptional architecture of Ot, including operon structure and non-coding RNAs, and found evidence for wide-spread post-transcriptional antisense regulation. We compared the host response to two clinical isolates and identified distinct immune response networks that are up-regulated in response to each strain, leading to predictions of relative virulence which were confirmed in a mouse infection model. Thus, dual RNA-seq can provide insight into the biology and host-pathogen interactions of a poorly characterized and genetically intractable organism such as Ot.

overall_design: RNA-seq of Orientia tsutsugamushi strains UT176 and Karp in HUVEC cells with uninfected controls

first: Jeanne

last: Salje


title: Driving Intracellular Metal Ions of Human Induced Pluripotent Stem Cells with Intense Terahertz Pulses

city: Kyoto

first: Ken-ichiro

last: Kamei

state: Kyoto

address: Yoshida-Ushinomiya-cho, Sakyo-ku

department: iCeMS

institute: Kyoto University

summary: Terahertz (THz) radiation has been exploited for biomedical applications for non-invasive manipulation of living cells. Here we describe an apparatus to apply high-field THz excitation on highly environmental sensitive human induced pluripotent stem cells (hiPSCs), and manipulate the gene expression networks associated with zinc-finger (ZNF) transcription factors.

overall_design: We analyzed cDNA library generated from 585A1 hiPSCs treated with THz light.

first: Kamei

last: Ken-ichiro

first: Tachizaki

last: Takehiro

first: Sakaguchi

last: Reiko

first: Hirori

last: Hideki


title: Plant virus diversity in invasive weeds and crop plant varying between plant species and management systems

city: Gödöllő

first: Éva

last: Várallyay

address: 4 Szent-Györgyi Albert Street

department: Agricultural Biotechnology Institute

country: Hungary

institute: National Agricultural Research and Innovation Centre

summary: We conducted field surveys to detect the population density of the most important invasive weed species and their associated virus vectoring aphids in crops grown under high input (HIF) vs low-input (LIF) field conditions, with and without fertilizers and pesticides. The most frequent invasive weed species were Stenactis annua, Erigeron canadensis and Solidago canadensis. These species were hosts predominantly for the aphids Brachycaudus helichrysi and Aulacorthum solani in both management systems. The 13% higher coverage of S. annua under LIF conditions resulted in a 30% higher B. helichrysi abundance and ~85% higher A. solani abundance compared with HIF conditions. To reveal virus infection in crop plants and invasive weeds high-throughput sequencing of small RNAs were carried out. Bioinformatics analysis of the results detected the presence of 16 important plant viruses, but not resulting strikingly different pattern under LIF and HIF. This could suggest that invasive weeds serves as a virus reservoir both under low and high input management systems. The lake of any management increases virus vector aphids abundances, their presence has a great impact on the viromes of the crops.

sample_organism:
Medicago sativa
Solanum tuberosum
Zea mays
Solidago canadensis
Erigeron canadensis
Erigeron annuus

overall_design: Leaf samples were collected from Tusnad and from Segesvar from three different crops: Solanum tuberosum, Medicago sativa and Zea mays and from two weeds species from each place. RNA was extracted by a phenol-chloroform method. RNA pools were prepared mixing equal amounts of RNA originating from different individuals, collection times (in case of the weeds) and from different species (in case of the crops). These pools were used for small RNA library preparation (6 libraries in total) using Truseq Small RNA Library Preparation Kit (Illumina, USA) and our modified protocol. Samples were sequenced using single index on a HiScan2000 by UD Genomed (Debrecen, Hungary) 50 bp, single end.

first: Attila

last: Szabo

first: Janos

last: Balint

first: Hugh

middle: D

last: Loxdale

first: Jozsef

last: Kiss

first: Emese

last: Demian

first: Eva

last: Varallyay

first: Adalbert

last: Balog


title: Genome-wide analyses of chromatin interactions after the loss of Pol I, Pol II and Pol III [Hi-C]

city: Beijing

first: Xiong

last: Ji

address: Haidian District, Beijing Summer Palace Road No. 5

department: School of Life Sciences

institute: Peking University

summary:
Genome binding/occupancy profiling by high throughput sequencing ｜ Expression profiling by high throughput sequencing | Other
We analyzed Hi-C, HiChIP, Ocean-C, RNA-seq, ATAC-seq, ChIP-seq and 4C-seq data to provide the most comprehensive evidence to date to demonstrate that transcription plays a marginal role in organizing the 3D genome in mammalian cells: 1) degraded Pol I, Pol II and Pol III proteins in mESCs, and showed their loss results in little or no changes of global 3D chromatin structures for the first time; 2) selected RNA polymerases high abundance binding sites-associated interactions and found they still persist after the degradation; 3) generated higher resolution chromatin interaction maps and revealed that transcription inhibition mildly alters small loop domains; 4) identified Pol II bound but CTCF and Cohesin unbound loops and disclosed that they are largely resistant to transcription inhibition
Interestingly, we found that Pol II depletion for a longer time significantly affects the chromatin accessibility and Cohesin occupancy, suggesting RNA polymerases are capable of affecting the 3D genome indirectly. So, the direct and indirect effects of transcription inhibition explain the previous confusing effects on the 3D genome. We conclude that Pol I, Pol II, and Pol III loss only mildly alter chromatin interactions in mammalian cells, suggesting the 3D chromatin structures are preestablished and relatively stable.

overall_design: We have finished the Hi-C, HiChIP, Ocean-C, RNA-seq, ATAC-seq, ChIP-seq and 4C-seq to investigate the roles of Pol I, Pol II and Pol III in 3D genome organization and transcription. The V6.5 mouse ES (mES) cell line was used to perform all the high-throughput analysis. Degron mES cells were treated with 1 μg/ml Doxycycline for different hours refer to individual Series.

first: Yongpeng

last: Jiang

first: Jie

last: Huang

first: Kehuan

last: Lun

first: Boyuan

last: Li


title: Genome-wide analyses of chromatin interactions after the loss of Pol I, Pol II and Pol III [Ocean-C ]


title: Genome-wide analyses of chromatin interactions after the loss of Pol I, Pol II and Pol III [4C-seq]

summary:
We analyzed Hi-C, HiChIP, Ocean-C, RNA-seq, ATAC-seq, ChIP-seq and 4C-seq data to provide the most comprehensive evidence to date to demonstrate that transcription plays a marginal role in organizing the 3D genome in mammalian cells: 1) degraded Pol I, Pol II and Pol III proteins in mESCs, and showed their loss results in little or no changes of global 3D chromatin structures for the first time; 2) selected RNA polymerases high abundance binding sites-associated interactions and found they still persist after the degradation; 3) generated higher resolution chromatin interaction maps and revealed that transcription inhibition mildly alters small loop domains; 4) identified Pol II bound but CTCF and Cohesin unbound loops and disclosed that they are largely resistant to transcription inhibition
Interestingly, we found that Pol II depletion for a longer time significantly affects the chromatin accessibility and Cohesin occupancy, suggesting RNA polymerases are capable of affecting the 3D genome indirectly. So, the direct and indirect effects of transcription inhibition explain the previous confusing effects on the 3D genome. We conclude that Pol I, Pol II, and Pol III loss only mildly alter chromatin interactions in mammalian cells, suggesting the 3D chromatin structures are preestablished and relatively stable.

overall_design: We have finished the Hi-C, HiChIP, Ocean-C, RNA-seq, ATAC-seq, ChIP-seq and 4C-seq to investigate the roles of Pol I, Pol II and Pol III in 3D genome organization and transcription. The V6.5 mouse ES (mES) cell line was used to perform all the high-throughput analysis. Degron mES cells were treated with 1 μg/ml Doxycycline for different hours.


title: Genome-wide analyses of chromatin interactions after the loss of Pol I, Pol II and Pol III [HiChIP]


title: Renal gene expression in two mouse strains with different propensity to develop chronic kidney disease after subtotal nephrectomy at different time-points

status: Public on Jun 01 2020

city: Paris

first: Fabiola

last: Terzi

state: Choisir votre état

address: Inserm U1151 CNRS U8253 Paris University, 160 rue de Vaugirard

institute: Inserm

summary: Renal gene expression analysis was performed in mouse strains with different propensity to develop progressive chronic kidney disease (CKD) after subtotal nephrectomy: the FVB strain which is spontaneously highly predisposed to CKD and the C57BL/6 which is spontaneously not predisposed to CKD. Subtotal nephrectomy (Nx) is normally initially compensated by proliferative tissue repair (2 days after nephrectomy). After this initial proliferation follows a quiescent period (28 days after NX). Finally, specifically in the sensitive strain there is lesion onset (53 days after Nx). Gene expression was monitored on RNA from whole kidneys from different mouse strains Sham operated or Nephrectomised at three different time-points.

overall_design: 9 weeks old lesion-predisposed FVB mice or lesion-non-predisposed C57BL/6 mice were subjected either to Subtotal-Nephrectomy (Nx) or sham-operation (S). Gene expression was monitored at three different time points: 2, 28 and 53 days after either Subtotal Nephrectomy or Sham Operation. Gene expression was monitored on whole kidney RNA with Affymetrix microarrays.

first: Mohamad

last: Zaidan

first: Martine

last: Burtin

first: Jitao

last: Zhang

first: Thomas

last: Blanc

first: Pauline

last: Barre

first: Serge

last: Garbay

first: Clément

last: Nguyen

first: Florence

last: Vasseur

first: Lucie

last: Yammine

first: Serena

last: Germano

first: Laura

last: Badi

first: Marie-Claire

last: Gubler

first: Morgan

last: Gallazzini

first: Gérard

last: Friedlander

first: Marco

last: Pontoglio


title: Genome-wide analyses of chromatin interactions after the loss of Pol I, Pol II and Pol III [RNA-seq]

first: Xiong

last: Ji

first: Yongpeng

last: Jiang

first: Jie

last: Huang

first: Kehuan

last: Lun

first: Boyuan

last: Li


title: Genome-wide analyses of chromatin interactions after the loss of Pol I, Pol II and Pol III [ChIP-seq]


title: Circulating microRNAs profile in patients with transthyretin variant amyloidosis

status: Public on May 31 2020

city: Messina

first: M'Hammed

last: Aguennouz

address: Piazza Pugliatti, 1

department: Department of Clinical and Experimental Medicine

country: Italy

institute: University of Messina

summary: Transthyretin variant amyloidosis (ATTRv) is a rare autosomal dominant disease characterized by the accumulation of amyloid in many organs, mostly causing a sensory-motor neuropathy, cardiomyopathy, and dysautonomia. The aim of the study was to report microRNAs (miRNAs) expression profile identified in the blood of ATTRv patients. 10 symptomatic ATTRv patients, 10 asymptomatic carriers of transthyretin variant (TTRv), 10 patients with Charcot-Marie-Tooth (CMT) disease, and 10 healthy controls were studied. Human Schwann cells cultures were used to study the regulatory effects of miR-150-5p on the expression of cAMP response element-binding protein (CREB), brain-derived neurotrophic factor (BDNF), and nerve growth factor (NGF). ATTRv patients had 33 miRNAs up-regulated and 48 down-regulated versus healthy controls; 9 miRNAs were up-regulated and 30 down-regulated versus CMT patients; 19 miRNAs were up-regulated and 38 down-regulated versus asymptomatic TTRv carriers. Twelve out of the 19 upregulated miRNAs had a fold increase higher than 100. The validation experiment indicated miR-150-5p as a valuable biomarker to differentiate ATTRv patients from asymptomatic TTRv carriers (AUC: 0.9728; p<0.0001). Schwann cells culture model demonstrated that miR-150-5p is a powerful negative regulator of CREB, BDNF and NGF genes. Identification of deregulated miRNAs can help in understanding the complex pathomechamism underlying the development of ATTRv and related multisystemic pathology. Further investigations are needed on the role of circulating miR-150-5p to predict the shift of TTRv carriers from an asymptomatic status to symptoms appearance.

overall_design: We investigated serum miRNA expression in 10 symptomatic ATTRv patients, 10 asymptomatic TTRv patients, 10 CMT patients and 10 unaffected controls (CTRL)

first: Gian

last: Vita

first: Francesca

last: Polito

first: Rosaria

last: Oteri

first: Massimo

last: Russo

first: Luca

last: Gentile

first: Cristina

last: Barbagallo

last: Ragusa

first: Carmelo

last: Rodolico

first: Rosa

last: Di Giorgio

first: Antonio

last: Toscano

first: Giuseppe

first: Anna

last: Mazzeo


title: Genome-wide analyses of chromatin interactions after the loss of Pol I, Pol II and Pol III [ATAC-seq]

first: Xiong

last: Ji


title: CAGE sequencing of LASV infected Vero Cells

city: New York

first: Sook Yuin Jessica

last: Ho

address: 1468 Madison Avenue

department: Microbiology

institute: Icahn School of Medicine at Mount Sinai

summary: We report a novel mechanism of gene origination in the segmented negative sense viruses (sNSVs), including IAV and LASV. During replication, these viruses use "snatched" host caps to prime their own transcription (cap-snatching). We show that a proportion of cap-snatched host sequences contain translational start codons (AUGs), that are recognized by the host ribosome. This allows for the translation of host and viral “untranslated regions” (UTRs) to create N-terminally extended viral proteins or entirely novel polypeptides by genetic overprinting.

overall_design: CAGE sequencing of LASV infected Vero cells was used to determine if cap-snatching events in LASV infected cells gave rise to chimeric host-virus RNAs that had upstream AUGs.

first: Jessica

last: Sook

first: Yuin

first: Ivan

last: Marazzi


title: Engineered receptors for human cytomegalovirus that are orthogonal to normal human biology

city: Urbana

first: Erik

last: Procko

state: IL

address: 601 S Goodwin Ave

department: Biochemistry

institute: University of Illinois

summary: A trimeric glycoprotein complex on the surface of human cytomegalovirus (CMV) binds to platelet-derived growth factor (PDGF) receptor α (PDGFRα) to mediate host cell recognition and fusion of the viral and cellular membranes.  Soluble PDGFRα potently neutralizes CMV in tissue culture, and its potential use as an antiviral therapeutic has the benefit that any escape mutants will likely be attenuated.  However, PDGFRα binds multiple PDGF ligands in the human body as part of developmental programs in embryogenesis and continuing through adulthood.  Any therapies with soluble receptor therefore come with serious efficacy and safety concerns, especially for the treatment of congenital CMV.  Soluble virus receptors that are orthogonal to human biology would reduce safety and efficacy concerns.  This engineering problem is solved by deep mutational scanning on the D2-D3 domains of PDGFRα to identify variants that maintain interactions with the CMV glycoprotein trimer in the presence of competing PDGF ligands.

overall_design: Site-saturation mutagenesis was focused on the D2-D3 domains (a.a. D123-E311) of human PDGFRα, thereby creating a library of variants encompassing all possible single amino acid substitutions within the structural elements that form the PDGF binding site. The PDGFRα plasmid library, bearing an extracellular c-myc epitope tag for detection of surface expression, was transfected in to Expi293F cells; this line is a suspension culture derivative of HEK 293.  The transfected culture was incubated with medium from cells expressing soluble CMV trimer (glycoproteins gH-gL-gO, where gO was genetically fused at its C-terminus to superfolder GFP), and co-stained with a fluorescent anti-myc antibody. Trimer binding was readily detected based on GFP fluorescence, and was proportional to PDGFRα expression levels.  In the presence of competing PDGF ligands (25 nM each of PDGF-AA, -BB, -AB, and -CC), a subset of variants in the library maintained high CMV trimer binding.  These variants were collected by fluorescence-activated cell sorting (FACS).  In addition, cells expressing PDGFRα but with low CMV trimer binding were also collected, so that the effects of mutations on receptor expression versus trimer binding could be teased apart.  RNA was extracted from the collected cells, reverse transcribed with a high fidelity polymerase, and relevant coding regions were PCR amplified for sequencing.  Following Illumina sequencing, the frequencies of PDGFRα variants in the transcripts were compared to their frequencies in the naive plasmid library, such that the enrichment or depletion of all sequence variants was determined.


title: Deciphering the regulatory landscape of fetal and adult gd T-cell development at single-cell resolution

city: Freiburg

first: Sagar

address: Hugstetter Straße 55

department: Department of Internal Medicine II

institute: University Medical Center Freiburg

summary: Gamma delta T (gdT) cells with distinct properties develop in the embryonic and adult thymus and have been identified as critical players in a broad range of infections, antitumor surveillance, autoimmune diseases and tissue homeostasis. Despite their potential value for immunotherapy, differentiation of gdT cells in the thymus is incompletely understood. Here, we establish a high-resolution map of gdT cell differentiation from the fetal and adult thymus using single-cell RNA-sequencing. We reveal novel sub-types of immature and mature gdT cells and identify an unpolarized thymic population which is expanded in the blood and lymph nodes. Our detailed comparative analysis reveals remarkable similarities between the gene networks active during fetal and adult gdT cell differentiation. By performing a combined single-cell analysis of Sox13, Maf and Rorc knockout mice, we demonstrate sequential activation of these factors during IL-17-producing gdT cell (gdT17) differentiation. These findings substantially expand our understanding of gdT cell ontogeny in fetal and adult life. Our experimental and computational strategy provides a blueprint for comparing immune cell differentiation across developmental stages.

overall_design: Single cell RNA sequencing was performed on T cell progenitors - DN1, DN2, DN3 as well as cells encompassing various stages of gdT cell differentiation from fetal and adult murine thymus. Furthermore, single cells were also profiled from the Sox13, Maf and Rorc deficient mice in order to gain molecular insights into the regulation of IL-17-producing gdT cell differentiation in the thymus. Single-cell RNA sequencing was performed using the mCEL-Seq2 protocol, an automated and miniaturized version of CEL-Seq2 (Hashimshony et al., 2016; Herman et al., 2018). Note that we had 192 polyT primers containing unique cell barcodes, therefore each count file is demultiplexed into 192 cells. Although only 96 cells were pooled per library so each fastq paired-end file and the corresponding .csv count file contains data from 96 cells and NOT from 192 cells. The remaining 96 columns in the .csv count files are either empty or have very low counts due to spillover or index hopping.

last: Sagar

first: Dominic

last: Gruen


title: Genome-wide analyses of chromatin interactions after the loss of Pol I, Pol II and Pol III


title: cRel Expression Regulates Distinct Transcriptional and Functional Profiles Driving Fibroblast Matrix Production in Systemic Sclerosis

status: Public on May 30 2020

city: Newcastle upon Tyne

first: Graham

last: Smith

address: Framlington Place

department: Bioinformatics Support Unit

institute: Newcastle University

summary: The scope of this project is to investigate transcriptional differences bewteen wild type and Rel-/-  fibroblasts under basal conditions. Mouse fibroblasts were isolated via explant culture from  skin and  lungs of un-challenged mice.

overall_design: Male C57BL/6J and Rel -/- mice (housed in IVC cages) aged 8-10 weeks, mice were euthanized by cervical dislocation and skin (dorsal area) and lung tissues were extracted

first: Julie

last: Worrell

first: Fiona

last: Oakley


title: Effects of repetitive Iodine Thyroid Blocking on the Fetal Brain and Thyroid in rats: a Systems Biology approach [Cortex]

city: Fontenay-aux-Roses

first: Maâmar

last: Souidi

address: 31 Avenue de la Division Leclerc

institute: IRSN

summary: Our group showed that repetitive dose of KI for eight days offers efficient protection against radiation exposure during nuclear accidents without toxic effects in adult rats. However, the effect of repetitive KI on the developing fetus still unknown especially on brain development, but a correlation between the impaired maternal thyroid status and a decrease in intelligence quotient has been observed. In this study, gene expression analysis of the progeny of repetitive KI-administered pregnant rats performed by our group showed distinct gene expression profile from two different organs: thyroid and cortex. To understand how these differentially expressed genes are implicated in the observed behaviour change, a systems biology approach was used to construct networks using three different techniques; Bayesian statistics using ShrinkNet, sPLS-DA on the DIABLO platform using mixOmics and manual construction of a Process Descriptive network. For each organ, we were able to construct gene expression network, to select genes that are most contributing to either control or KI-treated groups, respectively, and to construct the PD network from differentially expressed (DE) gene enriched with data from publications. Furthermore, we were able to connect DE genes from both organs into one network with genes from both organ participating in the same cellular processes that affect mitophagy and neuronal outgrowth.

overall_design: 2 groups: treated and control.


title: Effects of repetitive Iodine Thyroid Blocking on the Fetal Brain and Thyroid in rats: a Systems Biology approach [Thyroid]

overall_design:
The effect of administrated KI to mother rats and its effect on gene expression in the cortex of the progeny rats
2 groups: treated and control


title: Expression profile of COUP-TFII overexpressing mouse ventral midbrain

status: Public on May 29 2020

city: Houston

first: Chung-Yang

last: Kao

address: One Baylor Plaza

department: Molecular & Cellular Biology

institute: Baylor College of Medicine

summary: Elevated COUP-TFII levels are found in Parkinson’s disease. COUP-TFII overexpression in mouse dopaminergic neurons caused neurodegeneration. The goal of this study is to identify molecular mechanisms of COUP-TFII-mediated cell death through RNAseq.

overall_design: We utilized a previously established CAG-S-COUP-TFII allele and crossed it with the Slc6a3-Cre line to overexpress COUP-TFII specifically in dopaminergic neurons. The experimental group is Slc6a3-Cre; CAG-S-COUP-TFII, while the control group is Slc6a3-Cre. Ventral midbrain tissues from two-month-old mice were harvested for molecular profiling.