title: A white to opaque like phenotypic switch in the yeast Torulaspora microellipsoides

city: Vancouver

first: thomas

last: sierocinski

state: BC

address: 2389 east mall

country: Canada

institute: Renaissance Bioscience

summary: Torulaspora microellipsoides is a unicellular budding yeast of the Saccharomycetaceae family and is primarily associated with viticulture, however it has not been studied with regards to growth morphology or phenotypic switching. We discovered that T. microellipsoides undergoes a low-frequency morphological switch from small budding haploid (white) yeast to larger, higher ploidy (opaque) yeast. Genome sequencing of both cell types did not reveal any conspicuous differences, but comparison of transcriptomes by mRNA-seq revealed 511 differentially regulated genes, with white cells having greater expression of genes involved in stress resistance and complex carbohydrate utilization, and opaque cells up-regulating genes involved in ribosome biogenesis. Growth experiments showed that white cells are in general physiologically more resistant to stationary phase conditions and oxidative stress than opaque cells, but the latter performed better under some conditions and are more tolerant to cold temperatures. Opaque cells are also phenotypically more unstable than white cells and give rise to derivatives with diverse phenotypes and different total DNA content.  We propose that ability of T. microellipsoides to switch phenotype is an ecological adaptation to specific niches, as has been suggested for similar morphological switching phenomena in distantly related species such as C. albicans, and suggest switching of this nature may be a more a more broadly utilized biological strategy among yeasts than previously thought.

overall_design: DNA or RNA was extracted from triplicate matched log-phase samples of each cell type (verified to the pure by plating and microscopy), extracted using standard methods, and sequencing libraries prepared using standard methods.

first: Cedric

middle: A

last: Brimacombe

first: Thomas

last: Sierocinski

first: Matthew

last: Dahabieh


title: DNA methylation alternations in the offspring liver from inulin early intervention dams

status: Public on Jan 10 2020

city: Beijing

first: Qian

last: Zhang

address: No. 1 Shuaifuyuan, Dongcheng District

country: China

institute: Peking Union Medical College Hospital

type: Methylation profiling by genome tiling array

summary: Maternal high fat diet may disturb susceptibility in offspring. liver from maternal inulin early intervention has  CpG  sites that exhibit differential DNA methylationregulated compared to high fat diet.

overall_design: We performed DNA methylation array analyses of offspring liver from inulin early intervention dams and high fat diet dams (n=3 per group).

first: Xinhua

last: Xiao

first: Jia

last: Zheng

first: Ming

last: Li

first: Miao

last: Yu

first: Fan

last: Ping

first: Tong

last: Wang

first: Xiaojing


title: Myeloid Dendritic Cells from People Living with HIV have Altered Gene Expression Not Restored by Anti-Retroviral Therapy

city: Seattle

first: Shannon

last: Murray

state: WA

address: 1100 Fairview Ave N

country: USA

institute: Fred Hutchinson Cancer Research Center

summary: Myeloid dendritic cells (mDC) were isolated from antiretroviral therapy (ARV)-treated and untreated people living with HIV (PLWH), and from HIV uninfected Individuals. The results indicate that mDC are altered in genes expression from PLWH. Some RNA transcriptional changes are not completely restored by ARV. This provides more data on myeloid cells, an understudied cell type, and alterations in PLWH.

overall_design: Peripheral blood mononuclear cells were enriched and flow cytometry-sorted to obtain purified myeloid dendritic cells from each of the donor groups. mRNA was isolated from the myeloid dendritic cells for each donor group, which included ART-treated (n=3) and Treatment-naive (n=3) PLWH, and HIV uninfected (n=4) persons. All samples were sorted with at least 2 technical replicates and microarray analyses were performed.

middle: M

first: Daniel

middle: C

last: Douek

first: Rafick

middle: P

last: Sekaly


title: Analysis of gene expression modulated by autophagy during bleomycin induced lung injury from mouse lung alveolar progenitor cells

status: Public on Jan 08 2020

city: Tianjin

first: Xue

address: 890, Jingu Road

institute: Tianjin University Haihe Hospital

type: Expression profiling by high throughput sequencing

summary: Autophagy is a cellular catabolic process that supports metabolism in response to stress. To identify gene expression that are modulated by autophagy in AT2 cells during BLM-induced lung injury, RNA-seq profiling were carried out with AT2 cells from Atg5f/f mice treated with PBS (AT2-PBS), Nkx2.1Cre; Atg5f/f mice treated with PBS (Atg5−/− AT2-PBS), Atg5f/f mice treated with BLM (AT2-BLM), and Nkx2.1Cre; Atg5f/f mice treated with BLM (Atg5−/− AT2-BLM) at day 14. We found the glycolytic and pentose phosphate pathways were promoted, but that the synthesis of fatty acids was repressed in mouse AT2 cells during BLM injury. Autophagy may serve as a switch between these two metabolic pathways during lung injury. These data highlight an essential role for autophagy in reprogramming the metabolism of alveolar progenitor cells to meet energy needs for alveolar epithelial regeneration.

overall_design: 12 samples were analyzed. Each RNA-seq group with 3 biological replicates. Alveolar type 2 cells were sorted from Atg5f/f mice treated with PBS (AT2-PBS), Nkx2.1Cre; Atg5f/f mice treated with PBS (Atg5−/− AT2-PBS), Atg5f/f mice treated with BLM (AT2-BLM), and Nkx2.1Cre; Atg5f/f mice treated with BLM (Atg5−/− AT2-BLM) by FACS.

first: Huaiyong

last: Chen


title: Transcriptomic profiling of PBDE-exposed HepaRG cells unveils critical lncRNA-  PCG pairs involved in intermediary metabolism

first: Julia Yue

last: Cui

address: 4225 Roosevelt Way NE

department: Department of Environmental and Occupational Health Sciences

institute: University of Washington

type: Non-coding RNA profiling by high throughput sequencing

summary:
Purpose: The goal of this study was to investigate how PBDEs regulate both PCGs and lncRNAs in a PXR/CAR ligand-dependent and independent manner
Methods:  HepaRG cells, which are human-derived hepatic cells that accurately represent gene expression profiles of human liver tissue, were exposed to BDE-47 and BDE-99 at a dose of 25 μM for 24 hours. Differentially expressed lncRNA-PCG pairs were identified through DESeq2 and HOMER; significant canonical pathways were determined through Ingenuity Pathway Analysis (IPA). LncTar was used to predict the binding of 19 lncRNA-PCG pairs with known roles in drug-processing pathways.
Results: Genome annotation revealed that the majority of the differentially expressed lncRNAs map to PCG introns. PBDEs regulated overlapping pathways with PXR and CAR such as protein ubiqutination pathway and peroxisome proliferator-activated receptor alpha-retinoid X receptor alpha (PPARα-RXRα) activation but also regulate distinctive pathways involved in intermediary metabolism. PBDEs uniquely down-regulated GDP-L-fucose biosynthesis, suggesting its role in modifying important pathways involved in intermediary metabolism such as carbohydrate and lipid metabolism.
Conclusion: There is strong evidence that PBDEs regulate both PCGs and lncRNAs in a PXR/CAR ligand-dependent and independent manner

overall_design: The fully differentiated HepaRG cells were then treated with vehicle control (0.1% DMSO), CITCO (1 µM, Sigma-Aldrich), RIF (10 µM, Sigma-Aldrich), BDE-47 (25 µM, Chem Service Inc., West Chester, PA, Catalog No.), or BDE-99 (25 µM, AccuStandard Inc., New Haven, CT, Catalog No.) in triplicates for 24 hours

first: Angela

first: Cindy

middle: Y

first: Edward

middle: J

last: Kelly

first: Lianne

last: Sheppard

first: Julia


title: Circadian analysis of the mouse retinal pigment epithelium transcriptome

city: Atlanta

first: Gianluca

last: Tosini

state: GA

address: 720 Westview Dr. SW

department: Pharmacology and Toxicology

institute: Morehouse School of Medicine

summary:
Purpose: The presence of a phagocytic peak of photoreceptor outer segments by the retinal pigment epithelium (RPE) one or  two hours after the onset of light has been reported for several diurnal and nocturnal species. This peak in phagocytic  activity also persists under constant lighting conditions (i.e., constant light or dark) thus demonstrating that the timing  of this peak is driven by a circadian clock. The aim of this study was to investigate the change in RPE whole  transcriptome at two different circadian times (CT; 1 hour before (CT23) and 1 hour after (CT1) subjective light onset)
Methods: C57BL/6J male mice were maintained in DD for three days and euthanized under red light (< 1 lux) at CT23 and CT1.  RPE was isolated from whole eyes for RNA library preparation and sequencing on an Illumina HiSeq4000 platform.
Results: 14,083 mouse RPE transcripts were detected in common between CT23 and CT1. 12,005 were protein coding  transcripts and 2078 were non-protein coding transcripts. 2421 protein coding transcripts were significantly  upregulated whereas only 3 transcripts were significantly downregulated and 12 non-protein coding transcripts were  significantly upregulated and 31 non-protein coding transcripts were significantly downregulated at CT1 when  compared to CT23 (p < 0.05, fold change ≥±2.0). Of the protein coding transcripts, a majority of them were classified  as: enzymes, kinases, and transcriptional regulators with a large majority of activity in the cytoplasm, nucleus, and  plasma membrane. Non-protein coding transcripts included classes such as long-non coding RNAs and pseudogenes.  Gene ontology analysis and ingenuity pathway analysis revealed that differentially expressed transcripts were  associated with integrin signaling, oxidative phosphorylation, protein phosphorylation, and actin cytoskeleton  remodeling suggesting that these previously identified phagocytic pathways are under circadian control.
Conclusions: Our analysis  identified new pathways (e.g., increased mitochondrial respiration via increased oxidative phosphorylation) that may  be involved in the circadian control of phagocytic activity. In addition, our dataset suggests a possible regulatory role  for the identified non-protein coding transcripts in mediating the complex function of RPE phagocytosis. Finally, our  results also indicate, as seen in other tissues, about 20 % of the whole RPE transcriptome may be under circadian  clock regulation.

overall_design: Retinal pigment epithelium enriched samples isolated from whole eyes from 8-10 week old male C57BL/6J mice at 2 different circadian timepoints in triplicate

first: Christopher

last: DeVera


title: The histone demethylase JMJD2B regulates endothelial-to-mesenchymal transition

city: Frankfurt

first: David

last: John

state: Hessen

address: Theodor-Stern-Kai 7

country: Germany

institute: Institute for Cardiovascular Regeneration

type: Genome binding/occupancy profiling by high throughput sequencing

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: PRC1 catalytic activity is central to Polycomb system function. [CaptureC ]

city: Oxford

first: Nadezda

last: Fursova

address: South Parks Rd

department: Department of Biochemistry

country: United Kingdom

institute: University of Oxford

summary: The Polycomb repressive system is an essential chromatin-based regulator of gene expression. Despite being extensively studied, how it selects its target genes is poorly understood and whether its histone modifying activities are required for transcriptional repression remains controversial. Here, we directly test the requirement for PRC1 catalytic activity in Polycomb system function. To achieve this, we develop a new inducible mutation system in embryonic stem cells that completely removes PRC1 catalytic activity. Using this system, we demonstrate that catalysis by PRC1 is important for Polycomb chromatin domain formation and long-range chromatin interactions. Furthermore, we show that variant PRC1 complexes with DNA-binding activities occupy target sites independently of Polycomb chromatin domain formation, providing a putative mechanism for Polycomb target site selection. Finally, we discover that Polycomb-mediated gene repression requires PRC1 catalytic activity. Together these discoveries provide compelling new evidence that PRC1 catalysis is central to Polycomb system function and gene regulation.

overall_design: Tir1 expressing mouse embryonic stem cells (Control) and cells in which PRC1 (PRC1DEG) or specifically PRC1 catalytic activity (PRC1CPM) can be conditionally removed, were profiled for interactions between canonical polycomb target sites by CaptureC.

first: Neil

last: Blackledge

first: Angelika

last: Feldmann

first: Robert

last: Klose


title: ISX-9 manipulates endocrine progenitor fate revealing conserved intestinal lineages in mouse and human

city: London

first: Patricia

last: Fonseca Pedro

state: I am not in the U.S. or Canada

address: Hodgkin Building, 2nd Floor, Newcomen Street

institute: King's College London

summary: Objective: Enteroendocrine cells (EECs) survey the gut luminal environment and co-ordinate hormonal, immune and neuronal responses to it. They exhibit well characterized physiological roles ranging from the control of local gut function to whole body metabolism, but little is known regarding the regulatory networks controlling their differentiation, especially in human gut. The small molecule Isoxazole-9 (ISX-9) has been shown to stimulate neuronal and pancreatic beta-cell differentiation, both closely related to EEC differentiation. Our aim was to use ISX-9 as a tool to explore EEC differentiation.  Methods: We investigated the effects of ISX-9 on EEC differentiation in mouse and human intestinal organoids, using real time quantitative PCR, fluorescent activated cell sorting, immunostaining and single cell RNA sequencing.  Results: ISX-9 increased the number of neurogenin3 (Ngn3) positive endocrine progenitor cells and upregulated NeuroD1 and Pax4, transcription factors which play roles in mouse EEC specification. Single cell analysis revealed induction of Pax4 expression in a developmentally late Ngn3+ population of cells and potentiation of genes associated with progenitors biased towards serotonin-producing enterochromaffin (EC) cells.  This coincided with enrichment of organoids with functional EC cells which was partly dependent on stimulation of calcium signalling in a population of cells residing outside the crypt base. Inducible Pax4 overexpression, in ileal organoids, uncovered its importance as a component of early human endocrine specification and highlighted the potential existence of two major endocrine lineages, the early appearing enterochromaffin lineage and the later developing peptidergic lineage which contains classical gut hormone cell types.  Conclusion: Our data provide proof-of-concept for the controlled manipulation of specific endocrine lineages with small molecules, whilst also shedding new light on human EEC differentiation and its similarity to mouse. Given their diverse roles, understanding endocrine lineage plasticity and its control could have multiple therapeutic implications.

overall_design: Single-cell RNA-seq data from mouse Ngn3-RFP small intestine organoids (Control and ISX-9 treated)

first: Anastasia

last: Tsakmaki

first: Polychronis

last: Pavlidis

first: Bu’Hussain

last: Hayee

first: Gavin

last: Bewick


title: Budesonide induced transcriptional activity in control and Gs-knockdown human airway smooth muscle cells

city: Irvine

first: Moom

middle: R

last: Roosan

state: CA

address: 9401 Jeronimo Rd

department: Pharmacy Practice

institute: Chapman University School of Pharmacy

summary: Budesonide alter cell function through gene expression changes that occur via activation of ubiquitously expressed intracellular glucocorticoid receptors. However, a number of recent studies suggest that budesonide also activate rapid alterations in various signaling processes that appear to be non-genomic in nature, and likely dependent on Gs. Here, we investigate the Gs dependent non-genomic transcriptional activity due to 24 hours of budesonide treatment.

overall_design: Investigation of budesonide induced activity in control and Gs-knockdown human airway smooth muscle cells from six patients

first: Francisco

last: Nunez

first: Rennolds

middle: S

last: Ostrom

first: Timothy

middle: B

last: Johnstone


title: PRC1 catalytic activity is central to Polycomb system function. [RNA]

overall_design: Mouse embryonic stem cells in which all PRC1 complexes (PRC1CKO) or specifically PRC1 catalytic activity (PRC1CPM) can be conditionally removed, were profiled for gene expression using spike-in calibrated RNA-seq.


title: Transcriptome of whole antennae of control and programmed cell death (PCD)-blocked Drosophila.

city: Lausanne

first: Karolina

last: Bojkowska

address: Unil, Genopode

country: Switzerland

institute: University of Lausanne

summary: Here, we tested the possibility that Drosophila peripheral olfactory system cells fated to die might represent a reservoir of potential neurons. Inhibition of PCD is sufficient to generate many new cells in the antenna that express neural markers. Transcriptomic and in situ analyses reveal that these “undead” neurons express a subset of olfactory receptor genes, including some normally only expressed in other sensory organs.

overall_design: Two groups of flies: control (peb-Gal4/+;Or49a-GFP/+) and PCD-blocked (peb-Gal4/+;Or49a-GFP/UAS-p35) with three biological replicates per group; each replicate consisting of antennae from approximately 350 animals; paired design.

first: Ana

middle: F

last: Silbering

first: Steeve

last: Cruchet

first: Sylvain

last: Pradervand

first: Richard

last: Benton


title: Characterization of the Wheat-Psathyrostachys huashania 2Ns/2D Substitution Line H139: A Novel Germplasm with Enhanced Resistance to Wheat Take-all

status: Public on Jan 07 2020

city: YangLing

first: bai

middle: sheng

last: sheng

state: ShaanXi

address: Xi Nong Road

department: College of Agronomy

institute: 西北农林科技大学

summary:
Take-all is a devastating soil-borne disease that affects wheat production. The continuous generation of disease-resistance germplasm is an important aspect of the management of this pathogen.
In this study, we characterized the wheat-Psathyrostachys huashania Keng-derived progeny H139 that exhibits significantly improved resistance to wheat take-all disease compared with its susceptible parent 7182. GISH) and  mc-FISH analyses revealed that H139 is a stable wheat-P. huashania disomic substitution line lacking wheat chromosome 2D.EST-STS marker and Wheat Axiom 660K Genotyping Array analysis further revealed that H139 was a novel wheat-P. huashania 2Ns/2D substitution line, and that the P. huashania 2Ns chromosome shares high sequence similarity to wheat chromosome 2D. These results indicate that H139, with its enhanced wheat take-all disease resistance and desirable agronomic traits, provides valuable genetic resources for wheat chromosome engineering breeding.

overall_design: To further clarify the chromosome composition of H139, the Wheat Axiom 660K Genotyping Array was used for genotyping. A total of one sample (H139) was genotyped by wheat Axiom 660K Genotyping Array, which is due to the data of one sample enough to revealed that H139 was a novel wheat-P. huashania 2Ns/2D substitution line.

first: Bai

last: Shengsheng

first: Chen

last: Xinhong


title: A psychological stressor conveyed by appetite-linked neurons

status: Public on Jan 06 2020

first: Linda

last: Buck

state: Washington

address: 1100 fairview ave North

department: Basic Sciences

institute: Fred Hutchinson Cancer Research Centre

summary: We report RNA sequencing of individual neurons producing corticotropin-releasing hormone (CRH), which are the master regulators of blood levels of stress hormones. Analyses of individual transcriptomes reveal a large variety of neurotransmitter and neuromodulator receptors. Using the ligand information for different receptors expressed on CRHNs, we mapped the locations of upstream neurons expressing different ligands.

overall_design: Receptor assisted mapping of upstream neurons


title: TF ChIP-seq from transverse colon (ENCSR907BES)

city: Stanford

first: ENCODE

last: DCC

address: 300 Pasteur Dr

institute: ENCODE DCC

summary: For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Polycomb Mediated Chromatin Organization Reveals Transcriptional Silencers Required for Embryonic Development

city: Farmington

first: Chia-Lin

last: Wei

state: CT

address: 10 Discovery Drive

department: Genome Technologies

institute: The Jackson Laboratory

summary: Polycomb repressive complex 2 (PRC2), a key regulator of metazoan development, induces transcriptional silencing by organizing repressive chromatin structures. To understand PRC2 associated genome topology, we performed chromatin interaction analyses focusing on three core subunits of PRC2 in embryonic stem cells (ESCs). Our comprehensive and high-resolution PRC2 interactome reveals connectivity networks manifested by the extensive looping between distal regulatory elements (DREs) and genes controlling differentiation. The deletion of these non-coding DREs in mice results in transcriptional de-repression and embryonic lethality. While functioning as silencers in ESCs, these DREs can transition into active enhancers during development, suggesting their dual regulatory activities. Integrative analysis of the three dimensional genome organization and spatial clusters of PRC2-chromatin hubs reveals the compact, peripheral assembly as the structural basis of the silencing compartments. Our study uncovers the molecular identity of PRC2 silencers, their associated genome architectures, and offers the exciting possibility of targeted re-activation of epigenetically silenced genes.

overall_design:
1. Chromatin interaction analyses focusing on three core subunits of PRC2 (Eed, Ezh2, Suz12) in embryonic stem cells (ESCs) were performed to understand PRC2 associated genome topology and identify the distal regulatory elements (DREs).
2. Regulation activities of the DREs studied with the deletion of non-coding DREs in mice.

first: Chew

last: Ngan

first: Harianto

last: Tjong

first: Chee-Hong

last: Wong


title: Collaborative interactions of heterogenous ribonucleoproteins contribute to transcriptional regulation of sterol metabolism

city: Los Angeles

first: Zhengyi

last: Zhang

address: Westwood

institute: UCLA

summary: Heterogeneous nuclear ribonucleoproteins (hnRNPs) are a group of functionally versatile proteins that play critical roles in the biogenesis, cellular localization and transport of RNA. Although several lines of evidence link hnRNP abnormalities to neurodegenerative diseases and cancer their contribution to metabolic control remains unexplored. Here, we outline a role for hnRNPs in regulatory circuits controlling sterol homoeostasis. Specifically, we find that tissue-selective loss of the conserved hnRNP RALY enriches for metabolic pathways arguing that hnRNPs can discriminately influence regulated gene expression programs. Liver-specific deletion of RALY alters hepatic lipid content and serum cholesterol level. In vivo interrogation of chromatin architecture and genome-wide RALY binding pattern reveal insights into its cooperative interactions and mode of action in regulating cholesterogenesis. Interestingly, we find that RALY binds the promoter region of the master metabolic regulator Srebp2 and show that it directly interacts with coactivator NFY to influence cholesterogenic gene expression. Our work offers new insights into mechanisms orchestrating selective promoter activation in metabolic control and a model by which hnRNPs can impact metabolic health and disease states.

overall_design: RALY KO and  histone-DNA complexes

first: Tamer

last: Sallam


title: Inference and effects of barcode multiplets in droplet-based single-cell assays

city: New York

first: Caleb

last: Lareau

state: New York

address: 417 E 68th St, Zuckerman - ZRC 1132

institute: Memorial Sloan Kettering

summary: A widespread assumption for single-cell analyses specifies that one cell’s nucleic acids are predominantly captured by one oligonucleotide barcode. However, we show that ~13-21% of cell barcodes from the 10x Chromium scATAC-seq assay may have been derived from a droplet with more than one oligonucleotide sequence, which we call “barcode multiplets”. We demonstrate that barcode multiplets can be derived from at least two different sources. First, we confirm that  approximately 4% of droplets from the 10x platform may contain multiple beads. Additionally, we find that approximately 5% of beads may contain detectable levels of multiple oligonucleotide barcodes. We show that this artifact can confound single-cell analyses, including the interpretation of clonal diversity and proliferation of intra-tumor lymphocytes. Overall, our work provides a conceptual and computational framework to identify and assess the impacts of barcode multiplets in single-cell data.

overall_design: Peripheral blood mononuclear cells were obtained from a healthy individual and processed with 10x scATAC-seq to determine the rate of barcode multiplets

first: Sai

last: Ma

first: Fabiana

last: Duarte

first: Jason

last: Buenrostro


title: Histone ChIP-seq from esophagus muscularis mucosa (ENCSR805OCD)


title: microRNA-seq from C2C12 (ENCSR808LQW)

summary:
RNA Evaluation C2C12 microRNA-seq from Mortazavi

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Histone ChIP-seq from esophagus muscularis mucosa (ENCSR894MOX)


title: TF ChIP-seq from ascending aorta (ENCSR846JKO)


title: Astrocytic trans-differentiation completes a multicellular paracrine feedback loop required for medulloblastoma tumor growth

city: Charlottesville

first: Kevin

middle: A.

last: Janes

state: VA

address: Box 800759 Health System

department: Department of Biomedical Engineering

institute: University of Virginia

summary: We used RNA-sequencing technology for high-throughput profiling of tumor-derived astrocytes. Laser capture microdissection of individual cells was performed on an ArcturusXT LCM system (Applied Biosystems) with an infrared laser using CapSure HS LCM caps after optimization of laser power and duration. For each sample, 250 cells were microdissected per LCM cap and split into five 50-cell technical replicates (as a control, one replicate did not undergo reverse transcription) after elution from the cap. Reamplified cDNA (~500 bp 3’ ends) was purified away from primer concatemers by two rounds of purification with 0.7x volume of AMPure XP beads (Beckman) according to the manufacturer’s recommendations, and purified cDNA was quantified by Qubit assay (Life Technologies). For each sample, 1 ng was tagmented with the Nextera XT kit (Illumina) and sequenced as 75 bp paired-end reads on a NextSeq instrument using v2 reagents (Illumina).  14–22 million reads per sample were filtered for signal to noise (chastity filtered), assessed for overall quality with FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/), and then mapped with STAR (Dobin et al., 2013) against the mouse genome build mm10.

overall_design: Comparing the gene profile of tumor derived astrocytes with normal astrocytes and tumor cells (TuGNPs)

first: Hui

last: Zong

first: Maojin

last: Yao


title: microRNA-seq from GM12878 (ENCSR770HBF)

summary:
RNA Evaluation GM12878 microRNA-seq from Mortazavi, using 5' adaptor set 1 and 2 for reps 1 and 2.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Systematic identification of silencers in human cells

status: Public on Jan 09 2020

city: Palo Alto

first: Baoxu

last: Pang

state: CALIFORNIA

address: 3165 Porter Drive

department: Genetics

institute: Stanford University

summary: The majority of the human genome does not encode proteins. Many of these noncoding regions contain important regulatory sequences that control gene expression. To date, most studies have focused on activators such as enhancers, but regions that repress gene expression⎯silencers⎯have not been systematically studied. We have developed a system that identifies silencer regions in a genome-wide fashion based on silencer-mediated transcriptional repression of caspase 9. We found that silencers are widely distributed and may function in a tissue-specific fashion. These silencers harbor unique epigenetic signatures and are associated with specific transcription factors. Silencers also act at multiple genes, and at the level of chromosomal domains and long-range interactions. Deletion of silencer regions linked to the drug transporter genes ABCC2 and ABCG2 caused chemo-resistance. Overall, our study demonstrates that tissue-specific silencing is widespread throughout the human genome and likely contributes significantly to the regulation of gene expression and human biology.

overall_design: A high-throughput ReSE lenti-viral screen system was designed to systematically discover silencer regions in the human genome.

first: Michael

last: Snyder


title: microRNA-seq from right lobe of liver (ENCSR783JQT)

summary:
RNA Evaluation human tissue W63 right lobe liver microRNA-seq from Mortazavi

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Histone ChIP-seq from upper lobe of left lung (ENCSR759RTY)


title: microRNA-seq from heart left ventricle (ENCSR792MDW)

summary:
RNA Evaluation human tissue left ventricle microRNA-seq from Mortazavi

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: microRNA-seq from HFFc6 (ENCSR750ZGO)

summary:
RNA Evaluation HFFc6 microRNA-seq from Mortazavi

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: microRNA-seq from pancreas (ENCSR701ZTJ)

summary:
RNA Evaluation human tissue W80 pancreas microRNA-seq from Mortazavi

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: TF ChIP-seq from tibial nerve (ENCSR689VEF)


title: microRNA-seq from ovary (ENCSR684FLE)

summary:
RNA Evaluation human tissue W61 ovary microRNA-seq from Mortazavi

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: microRNA-seq from mucosa of descending colon (ENCSR664CDH)

summary:
RNA Evaluation human tissue W80 mucosa descending colon microRNA-seq from Mortazavi

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Histone ChIP-seq from prostate gland (ENCSR748RBT)


title: Histone ChIP-seq from heart left ventricle (ENCSR613PPL)


title: microRNA-seq from myocyte (ENCSR613OJJ)

summary:
RNA Evaluation C2C12 differentiated for 72 hours microRNA-seq from Mortazavi

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Histone ChIP-seq from esophagus muscularis mucosa (ENCSR674WSL)


title: Predicting Human Clinical Outcomes using Mouse Multi-Organ Transcriptome

city: Seika-cho, Soraku-gun

first: Thomas

middle: N.

last: Sato

state: Kyoto

address: 2-2-2 Hikaridai

country: Japan

institute: Karydo TherapeutiX, Inc.

summary: Approximately 90% of pre-clinically validated drugs fail in clinical trials due to unanticipated clinical outcomes, costing over several hundred million US dollars per drug. Despite such critical importance, translating pre-clinical data to clinical outcomes remain a major challenge. Herein, we designed a modality-independent and unbiased approach to predict clinical outcomes of drugs. The approach exploits their multi-organ transcriptome patterns induced in mice and a unique mouse-transcriptome database “humanized” by machine learning algorithms and human clinical outcome datasets. The cross-validation with small-molecule, antibody and peptide drugs shows effective and efficient identification of the previously known outcomes of 5,519 adverse events and 11,312 therapeutic indications. In addition, the approach is adaptable to deducing potential molecular mechanisms underlying these outcomes. Furthermore, the approach identifies previously unsuspected repositioning targets. These results, together with the fact that it requires no prior structural or mechanistic information of drugs, illustrate its versatile applications to drug development process.

overall_design: mRNA profiles of drug-treated or no-treated mice were generated by deep sequencing in duplicate or quadruplicate using Illumina NextSeq 500.

first: Satoshi

last: Kozawa

first: Fumihiko

last: Sagawa

first: Satsuki

last: Endo

first: Glicia

last: Almeida

first: Yuto

last: Mitsuishi

middle: N


title: Histone ChIP-seq from prostate gland (ENCSR763IDK)

first: ENCODE

last: DCC


title: microRNA-seq from K562 (ENCSR569QVM)

summary:
RNA Evaluation K562 microRNA-seq from Mortazavi, using 5' adaptor sets 3 and 4 for rep 1 and 2.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Histone ChIP-seq from esophagus muscularis mucosa (ENCSR708BMV)

summary: For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: microRNA-seq from adrenal gland (ENCSR649MMJ)

summary:
RNA Evaluation human tissue adrenal gland 1-2 microRNA-seq from Mortazavi

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: TF ChIP-seq from ascending aorta (ENCSR555DCD)


title: Histone ChIP-seq from tibial nerve (ENCSR464TRM)


title: Histone ChIP-seq from esophagus muscularis mucosa (ENCSR543UBL)


title: microRNA-seq from adrenal gland (ENCSR407OAH)

summary:
RNA Evaluation adrenal gland C57BL6 WT female microRNA-seq from Mortazavi

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: TF ChIP-seq from thoracic aorta (ENCSR549TXG)


title: TF ChIP-seq from coronary artery (ENCSR447ANW)


title: Histone ChIP-seq from ovary (ENCSR242AHB)


title: TF ChIP-seq from right atrium auricular region (ENCSR401KRN)


title: TF ChIP-seq from upper lobe of left lung (ENCSR224WWI)


title: Histone ChIP-seq from gastroesophageal sphincter (ENCSR316LNO)


title: Histone ChIP-seq from gastrocnemius medialis (ENCSR453MSI)


title: microRNA-seq from left lung (ENCSR183LLK)

summary:
RNA Evaluation human tissue W62 left lung microRNA-seq from Mortazavi

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Histone ChIP-seq from tibial artery (ENCSR187SVM)


title: microRNA-seq from HL-60 (ENCSR157VHD)

summary:
RNA Evaluation HL60 microRNA-seq from Mortazavi

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: TF ChIP-seq from prostate gland (ENCSR230ORT)


title: microRNA-seq from left lung (ENCSR151ZUP)

summary:
RNA Evaluation human tissue W76 left lung microRNA-seq from Mortazavi

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Histone ChIP-seq from prostate gland (ENCSR133QBG)


title: Histone ChIP-seq from esophagus muscularis mucosa (ENCSR030NGB)


title: Histone ChIP-seq from gastrocnemius medialis (ENCSR283BRU)


title: microRNA-seq from spleen (ENCSR086SWA)

summary:
RNA Evaluation human tissue W80 spleen microRNA-seq from Mortazavi

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Histone ChIP-seq from esophagus squamous epithelium (ENCSR049FUB)


title: TF ChIP-seq from thyroid gland (ENCSR033KMZ)


title: microRNA-seq from adrenal gland (ENCSR014LFG)

summary:
RNA Evaluation adrenal gland C57BL6 WT male microRNA-seq from Mortazavi

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Transcriptome analysis and quantification of microaerobic growth of Geobacter sulfurreducens

status: Public on Jan 02 2020

city: Braunschweig

first: Rebekka

last: Biedendieck

address: Rebenring 56

department: Institute of Microbiology

institute: Technische Universtität Braunschweig

summary: Geobacter sulfurreducens was originally considered a strict anaerobe. However, this bacterium was later shown to not only tolerate but also to use oxygen as terminal electron acceptor. Research performed has so far only revealed the general ability of G. sulfurreducens to reduce oxygen, but the oxygen consumption rate has not been quantified, nor has evidence been provided as to how the bacterium achieves oxygen consumption. The microaerobic growth of G. sulfurreducens under more controlled operating conditions was investigated here and a transcriptome analysis was performed to elucidate possible metabolic mechanisms important for oxygen consumption in G. sulfurreducens. The experiments revealed that growth with oxygen is possible to the same extent as with fumarate when a maximum oxygen load per cell of 95 mgO2gcdw-1h-1 is applied. When oxygen concentrations are too high, growth is completely inhibited and there is no partial consumption. Transcriptome analysis suggests a menaquinol oxidase to be the enzyme responsible for oxygen reduction. Transcriptome analysis has further revealed three different survival strategies, depending on the oxygen concentration present. When prompted with small amounts of oxygen, G. sulfurreducens will try to escape the microaerobic area; if concentrations are higher cells will focus on rapid and complete reduction; and ultimately cells will form protective layers if a complete reduction becomes impossible. The results presented here have important implications for understanding how G. sulfurreducens survives exposure to oxygen.

overall_design: Geobacter sulfurreducens was grown in minimal medium containing 10 mM acetate under anaerobic and aerobic conditions. Cultivations were performed with three biological replicates. Samples were taken during the late growth phase from cultures exposed to 1%, 3% or 5% of oxygen. Reference for transcriptome analysis were samples taken from anaerobic cultivations.

first: Christina

last: Engel

first: David

last: Vorländer

first: Katrin

last: Dohnt

first: Rainer

last: Krull


title: tRNA 2’-O-methylation by a duo of TRM7/FTSJ1 proteins modulates small RNA silencing in Drosophila.

status: Public on Jan 03 2020

first: Jean-Yves

last: Roignant

address: genopode building

summary: 2’-O-methylation (Nm) represents one of the most common RNA modifications. Nm affects RNA structure and function with crucial roles in various RNA-mediated processes ranging from RNA silencing, translation, self versus non-self recognition to viral defense mechanisms. Here, we identify two novel Nm methyltransferases (Nm-MTases) in Drosophila melanogaster (CG7009 and CG5220) as functional orthologs of yeast TRM7 and human FTSJ1. Genetic knockout studies together with MALDI-TOF mass spectrometry and RiboMethSeq mapping revealed that CG7009 is responsible for methylating the wobble position in tRNAPhe, tRNATrp and tRNALeu, while subsequently, CG5220 methylates position C32 in the same tRNAs and targets also additional tRNAs. CG7009 or CG5220 mutant animals were viable and fertile but exhibited various phenotypes such as life span reduction, small RNA pathways dysfunction and increased sensitivity to RNA virus infections. Our results provide the first detailed characterization of two TRM7 family members in Drosophila and uncover a molecular link between enzymes catalysing Nm at specific tRNAs and small RNA-induced gene silencing pathways.

overall_design: Knockdown of methyltransferase CG7009 using dsRNA and control knockdown using double stranded RNA for LacZ. The experiment was performed in duplicates for the control and triplicates CG7009 in S2R+ cells.

first: Nastasja

last: Kreim


title: Genome-wide map of H3K27Ac chromatin state in CRISPR/Cas9 negative control and AP-1 depleted human uterine smooth muscle cells (HUtSMCs).

status: Public on Jan 01 2020

city: Chicago

first: Debabrata

last: Chakravarti

state: IL

address: 303 E Superior St.

institute: Northwestern University

summary: We report that the loss of AP-1 subunit gene expression leads to alterations in enhancer H3K27Ac enrichment. Altered distal enhancer regions are shown to overlap significantly with AP-1 DNA binding motifs.

overall_design: Examination of the genome-wide histone modification H3K27Ac signal in AP-1 depleted human uterine smooth muscle cells (HUtSMCs).

first: Mthabisi

last: Moyo


title: Quantitative analysis of AP-1 dependent gene expression in CRISPR/Cas9 negative control and AP-1 depleted human uterine smooth muscle cells (HUtSMCs).

summary: Down-regulation of genes belonging to the JUN, FOS, and ATF families of transcription factors has previously been described. In this study, we demonstrate that the loss of AP-1 subunit gene expression leads to a decrease in AP-1 enhancer occupancy. CRISPR/Cas9 mediated depletion of AP-1 subunits demonstrates that loss of AP-1 subunit gene expression results in a perturbation of extracellular matrix-associated gene expression. This work establishes AP-1 as an important transcription factor in uterine leiomyoma gene transcription.

overall_design: RNA profiles of CRISPR/Cas9 mediated control and AP-1 depleted human uterine smooth muscle cells (HUtSMCs) were generated by deep sequencing.


title: DNA-PKcs has KU-dependent function in rRNA processing and hematopoiesis

status: Public on Jan 05 2020

first: Ryan

middle: Alexander

last: Flynn

address: 380 Roth Way, Room 265

summary: The DNA-dependent protein kinase (DNA-PK), composed of the KU heterodimer and the catalytic subunit (DNA-PKcs), is a classical non-homologous end-joining (cNHEJ) factor1. KU binds to DNA ends, initiates cNHEJ, and recruits and activates DNA-PKcs. Beyond DNA, KU also binds to RNA, with unknown significance in mammals. Using mouse models, we uncovered an unexpected role for DNA-PK in ribosomal RNA (rRNA) biogenesis and hematopoiesis. Expression of kinase-dead (KD) DNA-PKcs (DNA-PKcsKD/KD) abroagates cNHEJ2. But DNA-PKcsKD/KDTp53-/- mice develop myeloid disease rather than pro-B cell lymphoma, like other cNHEJ/Tp53-deficient mice3. DNA-PKcs is its own the best substrate. Blocking DNA-PKcs phosphorylation at the T2609, but not the S2056 cluster leads to KU-dependent 18S rRNA processing defects, compromises global protein synthesis in hematopoietic cells and causes bone marrow failure in mice. KU drives assembly of DNA-PKcs on a broad array of cellular RNAs, including the U3 small nucleolar RNA (snoRNA), which is essential for 18S rRNA processing4. U3 activates purified DNA-PK and triggers T2609 phosphorylation. DNA-PK, but not other cNHEJ factors, resides in nucleoli in an rRNA-dependent manner and is co-purified with the small subunit (SSU) processome. Together our data show that DNA-PK has RNA-dependent, but cNHEJ-independent, functions during ribosome biogenesis that require DNA-PKcs’ kinase activity and T2609 cluster’s phosphorylation.

overall_design: irCLIP with anti-DNA-PKCs or anti-Ku86 antibody in HeLa cells.

first: Shan

last: Zha

first: Eliezer

last: Calo


title: Single-cell Transcriptomes Reveal Diverse Regulatory Strategies for Olfactory Receptor Expression and Axon Targeting

status: Public on Jan 04 2020

city: Houston

first: Hongjie

last: Li

state: TX

address: one Baylor Plaza

institute: Baylor College of Medicine

summary: Using single-cell RNA-sequencing, we comprehensively characterized the transcriptomes of Drosophila olfactory receptor neurons (ORNs) from middle pupal stage antennae. These ORNs are from 3 genotypes: nSyb-GAL4 labels 44 ORN types, 85A10-GAL4 labels 5 ORN types, and AM29-GAL4 labels 2 ORN types.

overall_design: Single-cell RNA-seq


title: Greb1 is required for axial elongation and segmentation in vertebrate embryos

first: Ravindra

last: Prajapati

address: 123 Coldharbour Lane

institute: King's college London

summary: This study presents transcription profiles for mouse axial progenitors, presomitic mesoderm and tailbud mesoderm. During vertebrate embryonic development, the formation of axial structures is driven by a population of stem-like cells (axial progenitors) that reside in a region of the tailbud called the chordoneural hinge (CNH) where. We have compared the CNH transcriptome with those of surrounding tissues and shown that the CNH and tailbud mesoderm are transcriptionally similar, and distinct from the presomitic mesoderm. Amongst CNH-enriched genes are several that are required for axial elongation, including Wnt3a, Cdx2, Brachyury/T and Fgf8, and androgen/estrogen receptor nuclear signalling components such as Greb1.

overall_design: Chordoneural hinge, tailbud mesoderm, and presomitic mdesoderm were dissected from E10.5 wildtype mouse embryos. These microdissected tissues were used to extract total RNA for microarray study.

first: Richard

last: Mitter

first: Annalisa

last: Vezzaro

first: Valerie

last: Wilson

last: Ish-Horowicz


title: Artificial escape from XCI by DNA methylation editing of the CDKL5 gene

city: Sacramento

first: Julian

last: Halmai

address: 2921 Stockton Blvd

department: Department of Neurology

institute: UC Davis

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

overall_design: Refer to individual Series


title: Intricate structure of the interphase chromocenter revealed by proximity based biotinylation

city: Munich

first: Tamas

last: Schauer

address: Feodor-Lynen-Straße 21

department: Institute of Epigenetics and Stem Cells

institute: Helmholtz Zentrum München

summary: During interphase centromeres often coalesce into a small number of chromocenters, which can be visualized as distinct, DAPI dense nuclear domains. Intact chromocenters play a major role in maintaining genome stability as they stabilize the transcriptionally silent state of repetitive DNA while ensuring centromere function. Despite its biological importance, relatively little is known about the molecular composition of the chromocenter or the processes that mediate chromocenter formation and maintenance. To shed light on this, we performed confocal and super resolution microscopy and proximity based biotinylation experiments of three proteins associated with the chromocenter in Drosophila: the centromeric H3 variant dCenpA, the heterochromatin protein HP1a and the speciation factor HMR. Our work revealed an intricate internal structure of the chromocenter suggesting a complex multilayered structure of this intranuclear domain.

overall_design: ChIP-seq experiments of HMR ChIP in dCenpC knock-down (RNAi) and control (GST RNAi) as well as CAPH2 ChIP in HMR+LHR over-expression (induced) and control induced condition in 2 biological replicates.

first: Natalia

last: Kochanova

first: Axel

last: Imhof


title: Artificial escape from XCI by DNA methylation editing of the CDKL5 gene [methylation array]

summary: A significant number of X-linked genes escape from X-chromosome inactivation and are associated with a distinct epigenetic signature. One epigenetic modification that strongly correlates with X-escape is reduced DNA methylation in promoter regions. Here, we sought to create an artificial escape by editing DNA methylation on the promoter of CDKL5, a gene causative for an infantile epilepsy, from the silenced X-chromosomal allele in human neuronal-like cells. We identify that a fusion of the catalytic domain of TET1 to dCas9 targeted to the CDKL5 promoter using three guide RNAs causes significant reactivation of the inactive allele in combination with removal of methyl groups from CpG dinucleotides. Strikingly, we demonstrate that co-expression of TET1 and a VP64 transactivator have a synergistic effect on the reactivation of the inactive allele to levels above 60% of the active allele. We further used a multi-omics assessment to determine potential off-targets on the transcriptome and methylome. We find that synergistic delivery of dCas9 effectors is highly selective for the target site. Our findings further elucidate a causal role for reduced DNA methylation associated with escape from X-chromosome inactivation. Understanding the epigenetics associated with escape from X-chromosome inactivation has potential for those suffering from X-linked disorders.

overall_design:
850K MethylationEPIC to identify differentially methylated promoters (DMP) in cells transduced with dCas9 effectors.
Bisulfite converted DNA from the 8 samples were hybridized to the Illumina Infinium EPIC Array.


title: Artificial escape from XCI by DNA methylation editing of the CDKL5 gene [RNA-seq]

overall_design: We analysed CRISPR off-targets with at least two biological replicates per sample group. The control groups were mock-treated SH-SY5Y or cells transduced with dC. Treatment groups included dC-V, dC-T and a combination of dC-V and dC-T.


title: microRNA-seq from colonic mucosa (ENCSR128VGG)

first: ENCODE

last: DCC

summary:
RNA Evaluation human tissue W61 colon mucosa microRNA-seq from Mortazavi

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Long-term programming of CD8 T cell immunity by perinatal exposure to stress hormone

city: Seoul

first: Jaechul

last: Lim

address: 1 Gwanak-ro, 1 Gwanak-gu

country: South Korea

institute: Seoul National University


title: Histone ChIP-seq from transverse colon (ENCSR069EGE)

summary:
Pipeline ran using replicate 1 and 3, replicate 2 raw data was archived.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Long-term programming of CD8 T cell immunity by perinatal exposure to stress hormone [RNA-seq]

summary: Early life environmental exposure, particularly during perinatal period, can have a lifelong impact on organismal development and physiology. The biological rationale for this phenomenon is to promote physiological adaptation to the anticipated environment based on early life experience. However, perinatal exposure to adverse environments can also be associated with adult-onset disorders. Multiple environmental stressors  induce glucocorticoids, which prompted us to investigate their role in developmental programming. Here, we report that perinatal glucocorticoid exposure had long-term consequences and resulted in diminished CD8 T cell response in adulthood and impaired control of tumor growth and bacterial infection. We found that perinatal glucocorticoid exposure resulted in persistent alteration of the hypothalamic-pituitaryadrenal (HPA) axis. Consequently, the level of the hormone in adults was significantly reduced, resulting in decreased CD8 T cell function. Our study thus demonstrates that perinatal stress can have long-term consequences on CD8 T cell immunity by altering HPA axis activity.

overall_design: Three replicates of naive or stimulated CD8 T cells from Control and DEX mice, respectively.

first: Jun

last: Hong

first: Ruslan

last: Medzhitov


title: Identification of tissue regulatory T cell precursors in lymphoid organs [bulk RNA-Seq]

city: Mainz

first: Michael

last: Delacher

state: Rhineland-Palatinate

address: Langenbeckstrasse 1

department: Institute for Immunology

institute: University Medical Center of the Johannes Gutenberg-University Mainz

summary: Regulatory T (Treg) cells maintain self-tolerance in lymphoid tissues, and specialized Treg cells accumulate and perform homeostasis and regenerative functions in non-lymphoid tissues. A common differentiation pathway of homeostasis-promoting Treg cells in non-lymphoid tissues from a putative precursor remains elusive. By using novel reporter mice and single-cell RNA-sequencing, we identified precursor stages of the IL-33 receptor ST2-expressing non-lymphoid tissue Treg population in spleen and lymph nodes. Molecular profiling of these precursors versus mature tissue Treg cells revealed their sequence of differentiation on a single-cell level. Global chromatin profiling of non-lymphoid tissue Treg cells and progenitor populations revealed a stepwise acquirement of open chromatin accessibility at tissue Treg genes. Mechanistically, we identified and validated the basic leucine zipper transcription factor, ATF-like (Batf) as a driver of the molecular tissue Treg program. Understanding this tissue program will help to harness regenerative properties of tissue Treg cells for therapy.

overall_design: RNA-seq on FACS purified T cell subpopulatinos from different organs

first: Charles

middle: D

last: Imbusch

first: Christian

last: Schmidl

first: Markus

last: Feuerer


title: Identification of tissue regulatory T cell precursors in lymphoid organs [ATAC-Seq]

overall_design: ATAC-seq on FACS purified T cell subpopulatinos from different organs


title: Effect of expression of a  PI3-Kinase Dp110 dominant-negative (Dp110-DN) trangene on gene expression in fly fat body

city: London

first: Eugene

last: Schuster

address: 123 Old Brompton Road

department: Breast Cancer Research

institute: Institute of Cancer Research

summary: Gene expression pattern in fat bodies of flies expressing (or not) a dominant-negative form of the PI3K Dp110 (UAS-Dp110-DN, D954A) driven from a constitutive fat body-specific driver  (FB-GAL4).

overall_design: Fat bodies were dissected from flies (5 per sample) expressing the Dp110DN transgene (FB-Dp110DN) or control flies expressing only the driver (FB-GAL4). 3 samples were prepared in total, each on a different date.

first: Lazaros

last: Foukas


title: Identification of tissue regulatory T cell precursors in lymphoid organs [scTCR-seq]

overall_design: RNA-seq and scRNA-seq on FACS purified T cell subpopulatinos from different organs


title: Effect of inhibition of PI3-Kinase p110alpha on saturated fatty acid-induced gene expression alterations in murine 3T3-L1 adipocytes

summary: Gene expression pattern in murine 3T3-L1 adipocytes treated with saturated fatty acid (palmitate) in the presence or absence of PI3K p110alpha-selective inhibitor A66.

overall_design: Differentiated 3T3-L1 adipocytes were treated with p110alpha inhibitor (A66) or palmitate or a combination or both. Gene expression alterations were compared to untreated adipocytes.


title: Quantitative analysis of AP-1 dependent gene expression in negative control and AP-1 knockdown myometrium primary cells derived from 2 patient tissue samples.

first: Debabrata

last: Chakravarti

summary: Down-regulation of genes belonging to the JUN, FOS, and ATF families of transcription factors has previously been described. In this study, we demonstrate that the loss of AP-1 subunit gene expression leads to a decrease in AP-1 enhancer occupancy. Knockdown of AP-1 subunits demonstrates that loss of AP-1 subunit gene expression results in a perturbation of extracellular matrix-associated gene expression. This work establishes AP-1 as an important transcription factor in uterine leiomyoma disease pathogenesis.

overall_design: RNA profiles of negative control and AP-1 knockdown in myometrium primary cells derived from 2 patient tissue samples were generated by deep sequencing.

first: Mthabisi

last: Moyo


title: Expression data from CTCF RNAi experiments in LNCaP cell line

city: Darlinghurst

first: Amanda

last: Khoury

state: NSW

address: 384 Victoria St.

country: Australia

institute: Garvan Institute

summary: This study aimed to ascertain the effect of CTCF RNAi on gene expression, chromatin conformation and the chromatin environment in prostate cancer cell line, LNCaP

overall_design: We measured changes to gene expression following 24hrs, 72hrs and 144hrs of CTCF RNAi. The following comparisons were made for each of the time points. Untransfected to Non-target control RNAi, Untransfected to CTCF RNAi, Non-target control RNAi to CTCF RNAi. Genes were deemed significantly up- or down-regulated if the Benjamini-Hochberg adjusted P-value was < 0.05. Experiments were performed in duplicate.

first: Susan

last: Clark


title: Altered chromatin landscape and enhancer engagement underlie transcriptional dysregulation in MED12 mutant uterine leiomyomas


title: Profiling of Myometrium and Leiomyoma transcriptomes in 15 leiomyoma (MED12 G44 mutant) and 15 matched normal myometrium (WT) patient tissue samples.

summary: Through comprehensive profiling of transcribed genes in myometrium and leiomyoma tissue samples, we demonstrate two distinct gene expression profiles for myometrium and leiomyoma. This study shows that transcriptional dysregulation, and not post-transcriptional dysregulation, is primarily responsible for the perturbations of key biological processes in leiomyomas such as the extracellular matrix organization.

overall_design: RNA expression profiles of myometrium (WT) and leiomyoma (G44 mutant) patient tissue samples were generated by deep sequencing.


title: RNA-seq analysis of doxycycline-inducible BORIS/CTCFL expression in the metastatic melanoma cell line MM057

city: Montreal

first: Sanne

middle: Marlijn

last: Janssen

state: Quebec

address: 3755 Chemin de la Côte-Sainte-Catherine

department: Pathology

institute: Lady Davis Institute for Medical Research

summary: Brother of Regulator of Imprinted Sites (BORIS) is a DNA binding protein with high similarity to CCCTC binding factor (CTCF), a multifunctional transcription factor that plays an important role in genome organization. Like CTCF, BORIS plays a role in transcriptional regulation. BORIS becomes aberrantly expressed in melanoma with a higher frequency in metastatic tumors compared to primary tumors, which indicates a role for BORIS in melanoma progression. Currently, little is known about the role of BORIS in melanoma. To gain insight into the functional role of BORIS in melanoma we established doxycycline-inducible BORIS expression in the MM057 melanoma cell line that harbors a proliferation-associated transcriptome. Next, we used RNA-seq to investigate BORIS-mediated transcriptional changes. We show that differentially expressed genes are enriched among invasion-related processes and gene signatures, indicating that BORIS expression contributes to an EMT-like switch from a proliferation to invasion-associated transcriptome. In agreement with these findings, we demonstrate that BORIS overexpression leads to reduced proliferation and increased migration and invasion. Taken together, these data indicate that expression of BORIS promotes a switch from a proliferative to invasive state at both the transcriptional and phenotypic level in melanoma cell lines.

overall_design: MM057 cells were stably infected with the lentiviral doxycycline-inducible vector pI20 (empty vector; EV) or with the same vector carrying full length human BORIS (BOR). Cell lines were grown for 5 days either with (EVpos and BORpos) or without (EVneg and BORneg) 50ng/ml doxycycline to induce expression and RNA was extracted for RNA-seq (3 biological replicates).

first: Roy

last: Moscona

first: Mounib

last: Elchebly

first: Andreas

middle: I

last: Papadakis

first: Margaret

last: Redpath

first: Hangjun

last: Wang

first: Eitan

last: Rubin

first: Leon

last: van Kempen

first: Alan

last: Spatz


title: Transcriptional Profiling of Black and White Skins Reveals Expression Patterns of mRNA and lncRNA changes for lacking melanocyte in Bama pig

city: Chengdu

first: LiRui

last: Zhao

state: Sichuan

address: HuiMing road

department: College of Animal Science and Technology

institute: Sichuan Agricultural University

summary: Skin is the largest organ of body, and one function of skin is protecting underly organs away from ultraviolet (UV) radiation damage. Loss of melanocyte will reduce ability of skin to against UV radiation damage. We found Bama Pig can be an ideal model studying loss of melanocyte. In this study, we performed transcriptome profiling of mRNA and long noncoding RNA in Bama pig white skin (absence of melanocyte) and black skin (existence of melanocyte) to provide dataset for clinical researches. Total of 14,900 mRNAs and 7,566 lncRNAs were expressed in the study. Results of hierarchical cluster analysis and principal component analysis (PCA) demonstrated expression of mRNAs and lncRNAs varied greatly between two color skins. 2,342 mRNA were identified as being differentially expressed, including 1,309 genes that were down-regulated in white skin and 1,033 gene that were up-regulated in white skin (P <0.05; |log2(fold change)| > 1). The genes down-regulated in white skin were associated with melanocyte biology, melanocyte function and keratin, while genes up-regulated in white skin were main associated with metabolism pathway, oxidative phosphorylation and citrate cycle (TCA cycle). In addition, we identified 120 differentially expressed lncRNAs. In those lncRNAs, 4 lncRNAs may function in skin biology (TCONS_00019024 and TCONS_00077733) or metabolic (TCONS_00042201 and TCONS_00060772). Our research provides Bama pig skins datasets and could promote clinical researches utilizing Bama pig as model.

overall_design: Three two-year-old female Bama pigs (without relationship) were used to investgate mechanism of 'two end black'. skin samples (8mm of deepth) of two different colour were collected respectively (white skin in back and black skin in buttock) and separated into two groups. Each collected sample was put into 1.5 ml tube with 1ml Trizol reagent and cut up immediately.Finally, the tubes were placed in liquid nitrogen and stored in -80℃ until required for RNA extraction, sequencing and transcriptome analysis.

first: Lirui

first: Silu

last: Hu

first: Long

last: Jin

first: Qianzi

last: Tang

first: Mingzhou

last: Li


title: Hi-C following CTCF RNAi in LNCaP cells to determine changes to topological domains

first: Amanda

overall_design: We performed Hi-C-seq following 144hrs of Non-Target or CTCF RNAi in LNCaP cells.


title: Whole brain delivery of an instability-prone Mecp2 transgene improves behavioral and molecular pathological defects in mouse models of Rett syndrome

city: Milano

first: Luca

last: Massimino

state: MI

address: Via Olgettina, 58

department: Gastroenterology

country: Italy

institute: Ospedale San Raffaele

summary: Rett syndrome is an incurable neurodevelopmental disorder caused by mutations in the gene encoding for methyl-CpG binding-protein 2 (MeCP2). Gene therapy for this disease presents inherent hurdles since MECP2 is expressed throughout the brain and its duplication leads to severe neurological conditions as well. Herein, we use the AAV-PHP.eB to deliver an instability-prone Mecp2 (iMecp2) transgene cassette which, increasing RNA destabilization and inefficient protein translation of the viral Mecp2 transgene, limits supraphysiological Mecp2 protein levels. Intravenous injections of the PHP.eB-iMecp2 virus in symptomatic Mecp2 mutant mice significantly improved locomotor activity, lifespan and gene expression normalization. Remarkably, PHP.eB-iMecp2 administration was well tolerated in female Mecp2 mutant or in wild-type animals. In contrast, we observed a strong immune response to the transgene in treated male Mecp2 mutant mice that was overcome by immunosuppression. Overall, PHP.eB-mediated delivery of iMecp2 provided widespread and efficient gene transfer maintaining physiological Mecp2 protein levels in the brain.

overall_design: 3⨯ WT mice, 3⨯ MECP2 KO mice, 3⨯ gene therapy-treated WT mice, 3⨯ gene therapy-treated KO mice

first: Vania

last: Broccoli

first: Mirko

last: Luoni

first: Serena

last: Giannelli


title: Back-spliced RNA from Retrotransposon Binds to Centromere and Regulates Centromeric Chromatin Loops in Maize

city: Wuhan

first: Handong

last: Su

state: Hubei

address: No.1,Shizishan Street · Hongshan District

institute: Huazhong Agricultural University

summary: In most plants, centromeric DNA contains highly repetitive sequences, including tandem repeats and retrotransposons; however, the roles of these sequences in the structure and function of the centromere are unclear. Here, we found that retrotransposon-derived back-spliced RNA can bind to the centromere through R-loops and regulate the formation of centromeric chromatin loops. Multiple RNA sequences from centromeric retrotransposons (CRMs) were enriched in maize (Zea mays) centromeres and back spliced RNA from CRM1 were detected. We identified three types of circular CRM1 RNAs with the same back-splicing site based on the back-spliced sequences. These circular RNAs bound to the centromere through R-loops. Two R-loop sites inside a single circular RNA promoted the formation of chromatin loops in CRM1 regions. When RNAi was used to target the back-spliced site of the circular CRM1 RNAs, the levels of R-loops and chromatin loops formed by these circular RNAs decreased, while the levels of R-loops produced by linear RNAs with similar binding sites increased. Linear RNAs with only one R-loop site could not promote chromatin loop formation. Higher levels of R-loops and lower levels of chromatin loops in the CRM1 regions of RNAi plants led to a reduced localization of the centromeric H3 variant (CENH3). Our work reveals that centromeric chromatin organization by circular CRM1 RNAs via R-loops and chromatin loops. R-loops are integral components of centromeric chromatin. Proper centromere structure is essential for CENH3 localization. CRM1 elements may have helped to build a suitable chromatin environment during centromere evolution.

sample_organism:
Triticum urartu
Zea mays

platform_organism:
Triticum urartu
Zea mays

overall_design: Young leaves were cross-linked in 0.4 M sucrose, 10 mM Tris-HCl (pH = 8), 1 mM EDTA, 1 mM PMSF and 1% formaldehyde in a vacuum for 30 min, after which the reaction was terminated by adding 2 M glycine. The leaves were washed three times with RNase-free water, and Kimwipes (Kimberly-Clark Professional) were used to remove water drops from the leaves. The leaves were then transferred to liquid nitrogen and ground into a fine powder. The following experiment was carried out using the native ChIP protocol as previously described with slight modification. The chromatin was digested into single nucleosomes using 0.02 U/μl DNase I (RNase-free) at 37°C. Dynabeads Protein A (ThermoFisher, Cat#:10001D) was used for binding the anti-CENH3 antibody. After washing the beads incubated with the antibody and chromatin fragments, the beads were eluted twice at 65°C for 15 min using elution buffer containing 50 mM Tris-HCl (pH = 7.5), 10 mM EDTA, 200 mM NaCl and 1% SDS. The eluted fractions were combined, and Proteinase K (Invitrogen, Cat#: 25530-49) was added to relieve cross-linking at 37°C overnight after which the RNA was extracted using TRIzol reagent, and the residual DNA was removed using RNase-free DNase I (NEB, Cat#: M0303S). The cDNA libraries of RIP samples were prepared using the standard manual provided in the NEB Next Ultra RNA Library Prep Kit for Illumina (NEB, Cat#: E7530S). The samples were applied to the Illumina HiSeq 2500 sequencing system, generating ~37 million 125-bp paired-end reads.

first: Fangpu

last: Han


title: Genome-wide maps of chromatin state, transcription factor and cofactor occupancy in 5 leiomyoma (MED12 G44 mutant) and 5 matched normal myometrium (WT) patient tissue samples.

first: Debabrata

last: Chakravarti

summary: We report the application of high resolution MNase ChIP for high-throughput profiling of H3K27Ac and RNAPII in uterine fibroid tumors. Analysis revealed H3K27Ac remodeling at distal enhancer regions, highlighting the enrichment of AP-1 complex DNA binding motifs. ChIP-sequencing of AP-1 subunits JUN and FOS revealed differential occupancy of AP-1 at enhancer sites. In addition, ChIP-seq of CDK8 submodule subunits CDK8 and MED12 demonstrate differential CDK8 submodule occupancy consistent with remodelled enhancer regions.

overall_design: Examination of the genome-wide histone modification H3K27Ac signal as well as RNAPII occupancy in fibroid tumors and matched normal myometrium. Genome-wide occupancy of AP-1 complex transcription factors JUN and FOS was investigated. In addition, CDK8 submodule factors CDK8 and MED12 were also analyzed in fibroid tumors and matched normal myometrium.

first: Mthabisi

last: Moyo


title: Genome-wide chromatin interaction maps of enhancer-promoter and promoter-promoter contacts in 5 leiomyoma (MED12 G44 mutant) and 5 matched normal myometrium (WT) patient tissue samples.

summary: Through promoter capture Hi-C performed directly from patient tissue samples, we report the near-native characterization of intradomain chromatin architecture changes in uterine leiomyomas. This study identifies altered enhancer-promoter interactions and differential enhancer usage of enhancers associated with extracellular matrix-associated genes.

overall_design: Chromatin interactome profiles of myometrium (WT) and leiomyoma (G44 mutant) patient tissue samples were generated by deep sequencing.


title: Promoter capture Hi-C identifies long-range promoter contact dynamics in response to diet and the development of non-alcoholic fatty liver disease

city: Research Triangle Park

first: Paul

middle: A

last: Wade

state: NC

address: 111 TW Alexander Drive

department: Laboratory of Molecular Carcinogenesis

institute: NIEHS

summary: We profiled the chromatin interactions in liver from mice fed either an obesogenic or control diet.

overall_design: Examination of chromatin interactions, histone modification, gene expression and transcription factors binding in mice liver samples

first: Yufeng

last: Qin

first: John

last: Roberts

first: Sara

last: Grimm

first: Kaliopi

last: Chrysovergis


title: Long-term programming of CD8 T cell immunity by perinatal exposure to stress hormone [ATAC-seq]

first: Jaechul

last: Lim

overall_design: Three replicates of naive CD8 T cells from Control and DEX mice, respectively.

first: Jun

last: Hong

first: Ruslan

last: Medzhitov


title: Single cell transcriptome sequencing of gastric cancer cell lines

status: Public on Dec 31 2019

city: Stanford

first: Hanlee

last: Ji

state: CA

address: 269 Campus Drive

department: Division of Oncology

institute: Stanford University

summary: We report the integrative analysis of single cell genome and transcriptome characteristics of gastric cancer cell lines

overall_design: Examination of transcriptomes and genomes at single cell resolution


title: Transcriptional Programming of Human Mechanosensory Neuron Subtypes from Pluripotent Stem Cells

city: Bethesda

first: Minh

middle: Q

last: Nguyen

state: MARYLAND

address: 9000, Rockville Pike

institute: NIDCR/NIH

summary: In vitro generation of human peripheral sensory neurons may provide a framework for novel drug screening platforms and disease models of touch and pain. However, derivation of a functionally pure sensory neuron population remains a major unmet challenge. We discovered that, by expressing the transcription factors NGN2 and BRN3A, human pluripotent stem cells can be induced to differentiate into a surprisingly homogenous culture of cold- and mechano-sensing neurons. Although such a neuronal subtype has not been reported in mice, we found molecular evidence of its existence in adult human sensory ganglia. Combining NGN2 and BRN3A programming with neural crest patterning, we produced two additional populations of sensory neurons, including a more specialized mechanosensory neuron subtype. Finally, we applied this system to model a rare inherited sensory disorder, characterized by profound impairment of touch sensation and proprioception, caused by inactivating mutations in PIEZO2. Together these findings establish an approach to specify distinct sensory neuron subtypes in vitro, underscoring the utility of stem cell technology to capture human-specific features of physiology and disease.

overall_design: Two distinct populations of peripheral sensory neuron were generated from human pluripotent stem cells, through a neural crest intermediate stage. The morphology, protein expression, and RNA transcriptomes of these two populations were analyzed.

first: Alec

last: Nickolls

first: Carsten

middle: G

last: Bönnemann


title: RNA-seq of Aspergillus sydowii growing in three different salinity conditions

city: Cuernavaca

first: Maria

middle: del Rayo

last: Sanchez-Carbente

state: Morelos

address: Universidad 1001. Col Chamilpa

department: Center for Research on Biotechnology

country: Mexico

institute: Autonomous University of the State of Morelos

summary: The mechanisms of cellular and molecular adaptation of fungi to salinity have been commonly drawn from halotolerant strains, although some exceptions in basidiomycete fungi can be found. These studies have been conducted in settings where cells are subjected to stress, either hypo or hyperosmotic, which can be a confounding factor in describing physiological mechanisms related to salinity. Here, we have studied transcriptomic changes in Aspergillus sydowii, a halophilic species, when growing in three different salinity conditions (No salt, 0.5M and 2.0M NaCl). In this fungus salinity related responses occur under high salinity (2.0M NaCl) and not when cultured under optimal conditions (0.5M NaCl), suggesting that in this species, most of the mechanisms described for halophilic growth are a consequence of saline stress response and not an adaptation to saline conditions.

overall_design: A. sydowii grown on wheat straw without NaCl or with 0.5M NaCl and 2.0M NaCl

first: Yordanis

last: Perez-Llano

middle: d


title: Human and mouse single-nucleus transcriptomics reveal TREM2-dependent and -independent cellular responses in Alzheimer’s disease [15 months]

first: Maxim

last: Artyomov

state: MO

address: 660 S. Euclid Avenue, Campus Box 8118

department: Immunology&Pathology

institute: Washington University in St.Louis

summary: Glia have been implicated in Alzheimer’s disease (AD) pathogenesis. Variants of the microglia receptor TREM2 increase AD risk and activation of “disease-associated microglia” (DAM) is dependent on TREM2 in mouse models of AD. We surveyed gene expression changes associated with AD pathology and TREM2 in 5XFAD mice and human AD by snRNA-seq. We confirmed the presence of Trem2-dependent DAM and identified a novel Serpina3n+C4b+ reactive oligodendrocyte population in mice. Interestingly, remarkably different glial phenotypes were evident in human AD. Microglia signature was reminiscent of IRF8-driven reactive microglia in peripheral nerve injury. Oligodendrocyte signatures suggested impaired axonal myelination and metabolic adaptation to neuronal degeneration. Astrocyte profiles indicated weakened metabolic coordination with neurons. Notably, the reactive phenotype of microglia was less palpable in TREM2 R47H and R62H carriers than in non-carriers, demonstrating a TREM2 requirement in both mouse and human AD, despite the marked species-specific differences.

overall_design:
Droplet-based 3′ end massively parallel single-cell RNA sequencing was performed by isolating single nuclei from flash-frozen mouse brains through sucrose gradient and libraries were prepared using Chromium Single Cell 3′ Reagent Kits according to manufacturer’s protocol (10x Genomics). The generated scRNAseq libraries were sequenced using Illumina sequencers.
Cells from 3 mice per genotype were pooled for sequencing.

first: Yingyue

last: Zhou

first: Wilbur

middle: M

last: Song

first: Prabhakar

last: Andhey

first: Amanda

last: Swain

first: Tyler

last: Levy

first: Kelly

middle: R

last: Miller

first: Pietro

middle: L

last: Poliani

first: Manuela

last: Cominelli

first: Shikha

last: Grover

first: Susan

last: Gilfillan

first: Marina

last: Cella

middle: K

last: Ulland

first: Konstantin

last: Zaitsev

first: Akinori

last: Miyashita

first: Takeshi

last: Ikeuchi

first: Makoto

last: Sainouchi

first: Akiyoshi

last: Kakita

first: David

last: Bennett

first: Julie

last: Schneider

first: Michael

last: Nichols

first: Sean

last: Beausoleil

first: Jason

last: Ulrich

last: Holtzman

first: Marco

last: Colonna


title: Human and mouse single-nucleus transcriptomics reveal TREM2-dependent and -independent cellular responses in Alzheimer’s disease [7 months]

first: Maxim

last: Artyomov

overall_design:
Droplet-based 5′ end massively parallel single-cell RNA sequencing was performed by isolating single nuclei from flash-frozen mouse brains through sucrose gradient and libraries were prepared using Chromium Single Cell 5′ Reagent Kits according to manufacturer’s protocol (10x Genomics). The generated scRNAseq libraries were sequenced using Illumina sequencers.
3 biologically independent mice per genotype were individually procesed and sequenced.

first: Yingyue

last: Zhou

first: Wilbur

last: Song

first: Prabhakar

middle: S

last: Andhey

first: Amanda

last: Swain

first: Tyler

last: Levy

first: Kelly

last: Miller

last: Poliani

last: Cominelli


title: Human and mouse single-nucleus transcriptomics reveal TREM2-dependent and -independent cellular responses in Alzheimer’s disease

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

overall_design: Refer to individual Series


title: miRNA Analysis of lungs of LCPUFA-treated asthmatic C57BL/6 mice and respective controls

city: Fulda

first: Daniela

last: Fussbroich

address: Leipziger Str. 123

institute: University of Applied Sciences Fulda

summary:
Next generation sequencing (NGS) results demonstrate the modulative capacity of LCPUFAs on dysregulated miRNA expression in asthma.
Methods: Sequencing of miRNA was performed by NGS from lung tissue of asthmatic and control mice with normal diet, as well as of LCPUFA supplemented asthmatic mice using Illumina miSeq.
Conclusion: Our results demonstrate the modulative capacity of LCPUFAs on dysregulated miRNA expression in asthma.

sample_organism:
Homo sapiens
Mus musculus
synthetic RNA

platform_organism:
Homo sapiens
Mus musculus
synthetic RNA

overall_design: Lungs of LCPUFA-treated asthmatic C57BL/6 mice and respective controls were analyzed with n=4-5 via NGS

first: Caroline

last: Kohnle

first: Teresa

last: Schwenger

first: Christine

last: Driessler

first: Ruth

middle: P

last: Dücker

first: Olaf

last: Eickmeier

first: Gabriele

last: Gottwald

first: Silvija

last: Jerkic

first: Stefan

last: Zielen

first: Hermann

last: Kreyenberg

first: Christopher

last: Beermann

first: Andreas

last: Chiocchetti

first: Ralf

last: Schubert


title: Genome-wide profiling of non-small cell lung cancer derived cells

city: Barcelona

first: Anna

last: Esteve-Codina

address: Carrer Baldiri Reixac 4-8

country: Spain

institute: CNAG-CRG

summary: We established patient-derived cancer cell (PDC) cultures from metastatic non-small cell lung cancer, including two pairs of matched EGFR-mutant PDCs pre-treatment and after resistance to tyrosine-kinase inhibitors (TKIs), and then performed whole-exome and RNA sequencing to delineate their genomic architecture. For validation, we analyzed independent cohorts of primary NSCLC.

overall_design:
RNA sequencing from NSCLC patient-derived cancer cell cultures (PDC). PDC (n=15; 13 patients) were established in our laboratory from malignant pleural effusions, collected by thoracentesis, from patients diagnosed with metastatic NSCLC.

Samples PDC4 and PDC5 are pre-treatment and PDC4.2 and PDC.5 are TKI-resistant.

first: Montse

last: Sanchez-Cespedes


title: Enhancer profiling in Esrrb-/- ES cells

first: Ed

last: Curry

address: Hammersmith Hospital, Du Cane Road

institute: Imperial College London


title: Expression data of BCPAP cells with LRRC34 knockdown

city: Columbus

first: Albert

last: de la Chapelle

address: 460 W. 12th Avenue

institute: The Ohio State University Wexner Medical Center

summary: A recent genome-wide association study (GWAS) in thyroid cancer discovered 3q26 as one of five loci implicated in thyroid cancer predisposition. The tag SNP, rs6793295, is located in exon 7 of LRRC34. However, there are genetically distinct, but population-specific signals upstream of LRRC34 that demonstrate allele-specific expression. In order to reveal the regulatory gene network of LRRC34 in thyroid cells, microarray analysis was performed in the BCPAP cell line treated with siRNA against LRRC34.

overall_design: BCPAP cells were seeded in 6-well-plate and grown to 75% confluence at the time of transfection. 40 uM siLRRC34 or siNS were transfected into BCPAP cells using 7.5 ul Lipofectamine RNAiMAX (Thermo Fisher Scientific). After transfection for 72 hours, cells were harvested and total RNA was extracted by using RNeasy (Qiagen) then treated by DNase I (Ambion) to eliminate DNA contamination. Experiments described above were performed at four different time points in order to obtain four biological replicates for expression analysis.

first: Daniel

middle: F

last: Comiskey


title: Enhancer profiling in Esrrb-/- ES cells [4C-seq]

summary: We uncover a pivotal role for ESRRB in demarcating ESC-specific enhancer units, and propose that ESRRB’s developmentally-regulated extinction precipitates their decommissioning with impact on the rewiring of the pluripotency transcriptional programme upon embryo implantation.

overall_design: Profiling chromatin interactions at Klf4 enhancer locus with 4C-seq.

first: Veronique

last: Azuara

first: Wout

last: Megchelenbrink


title: Role of Cyp2b in diet-induced nonalcoholic steatohepatitis (NASH)

city: Clemson

first: William

last: Baldwin

state: South Carolina

address: 230 Parkway Dr

department: Biological Sciences

institute: Clemson University

summary: To investigate the role of hepatic CYP2B in diet-induced nonalcoholic steatohepatitis (NASH), a Cyp2b triple knockout mouse lacking Cyp2b9, Cyp2b10, and Cyp2b13 was developed using CRISPER/Cas9. Wildtype (WT) and Cyp2b-null mice were fed a normal diet (ND) or a choline-deficient, L-amino acid-defined high-fat diet (CDAHFD), containing 0.1% methionine and 62% fat for 8 weeks. RNA was extracted from the livers of female and male mice from all treatment groups and used for RNA seqencing. RNAseq data demonstrated that a lack of Cyp2b was protective in female but more harmful in male mice. Hepatic gene expression revealed a higher number of phase I-III xenobiotic metabolism and inflammatory response genes were down-regulated in CDAHFD-fed WT female and Cyp2b-null male mice.

overall_design: Use RNA-sequencing to investigate the role of Cyp2b in diet-induced NASH on a transcriptomic level, by comparing the livers of WT and Cyp2b-null mice fed a CDAHFD for 8 weeks using Illumina technology.

first: Melissa

last: Heintz

first: Rooksana

middle: E

last: Noorai


title: RNA-seq analysis of the transcriptional profile of SiHa cells with CNN3 interference.

city: Hangzhou

first: Lili

last: Xia

address: No.1 Xueshi Road

institute: Zhejiang University

summary: Transcriptome variation of SiHa cells transfected with si-CNN3  or si-NC were detected by RNA-seq.

overall_design: mRNA profiles of SiHa cells transfected with si-CNN3  or si-NC were generated by deep sequencing, in triplicate, using IlluminaHiSeq

first: Xing

last: Xie


title: Single-cell RNA sequencing of zebrafish thyroid cells

city: Greater Noida

first: Sumeet

middle: Pal

last: Singh

state: Uttar Pradesh

address: NH91, Tehsil Dadri

department: Life Sciences

country: India

institute: Shiv Nadar Institution of Eminence

summary: The thyroid gland is responsible for supplying the thyroid hormones to the body. The gland is an endocrine organ with an intricate structure enabling production, storage and release of the thyroid hormones. The gland is composed of numerous spherical follicles of varying sizes, surrounded by thyroid follicular epithelial cells, or thyrocytes. The thyrocytes surrounding the follicles generate the thyroid hormones in a multi-step process. Though the machinery responsible for the production of thyroid hormones by thyrocytes is well established, it remains unknown if all the thyrocytes resident in the thyroid gland are equally capable of generating thyroid hormones. In other words, the extent of molecular homogeneity between individual thyrocytes has not yet been investigated. To obtain an unbiased picture into the molecular heterogeneity present in zebrafish thyrocytes, we performed droplet based next-generation sequencing of individual thyrod gland cells. Using unsupervised clustering, we could identify all the major cell types present in the thyroid gland. Moreover, we could define sub-populations within the major cell-types, demonstrating the presence of molecular heterogeneity within nominally homogenous cell-populations.

overall_design: We used 10x Genomics to profile thyroid cells from zebrafish. Thyroid gland was enzymatically dissociated and single-cell library prepared using 10x Genomics Chromium pipeline. Sequencing was performed on llumina NextSeq 550 machine using a HighOutput flowcell in paired-end mode (R1: 26 cycles; I1: 8 cycles; R2: 57 cycles), thus generating ~45 mio fragments. The raw sequencing data was then processed with the ‘count’ command of the Cell Ranger software (v2.1.0) provided by 10X Genomics with the option ‘--expect-cells’ set to 6000 (all other options were used as per default). To build the reference for Cell Ranger, zebrafish genome (GRCz10) as well as gene annotation (Ensembl 87) were downloaded from Ensembl and the annotation was filtered with the ‘mkgtf’ command of Cell Ranger (options: ‘--attribute=gene_biotype:protein_coding --attribute=gene_biotype:lincRNA –attribute=gene_biotype:antisense’). Genome sequence and filtered annotation were then used as input to the ‘mkref’ command of Cell Ranger to build the appropriate Cellranger Reference.


title: Circular extrachromosomal DNA drives massive oncogene expression and chromatin accessibility

city: La Jolla

first: Paul

last: Mischel

address: 9500 Gilman Dr.

institute: Ludwig Institute for Cancer Research

summary: Oncogenes are commonly amplified on extrachromosomal DNA particles (ecDNA) in cancer, but our understanding of the structure of ecDNA and its impact on gene regulation is limited. We integrated ultrastructural imaging, long range-optical mapping, and computational analysis of whole genome sequencing to demonstrate unequivocally that ecDNA is circular. Pan-cancer analyses reveal that the oncogenes encoded on ecDNA are among the most highly expressed genes in the transcriptome of tumours, linking elevated copy with very high levels of transcription. Quantitative assessment of the chromatin state, including ATAC-seq to map the accessible genome and ATAC-see to examine spatial distribution of open chromatin, reveal that while ecDNA is chromatinized, it lacks higher order compaction typical of chromosomes. In fact, ecDNA contains the most accessible DNA in the tumour genome. Using chromosome conformation capture technologies and CRISPR interference, we reveal the differential organization of active chromatin in cancer that is dictated by the circular shape of ecDNA. Lastly, we develop comprehensive maps that provide new insight into how circular ecDNA structure determines oncogene function, bridging ecDNA biology with modern cancer genomics and epigenetics.

overall_design: Quantitative assessment of the chromatin state, including ATAC-seq to map the accessible genome and ATAC-see to examine spatial distribution of open chromatin.

first: Sihan

last: Wu


title: A systematic dissection of whole transcriptome profiling in the APP/PS1 mouse brain

city: BEIJING

first: MA

address: haidian

institute: peking university

summary: This study is the first to provide a systematic dissection of whole transcriptome profiling in the APP/PS1 mouse brain. The identified ceRNA networks may provide insight into the diagnosis and therapy of AD in the future.

overall_design: we used deep RNA sequencing (RNA-seq) to examine whole transcriptome profiling in the brain of APP/PS1 mice (which express APP695swe and PS1-dE9 mutations) and wild-type control mice at the 6-month-old and 9-month-old stage.

first: Jun

last: Wan

first: Nana

last: Ma


title: Hypoxic gene expression in med25-1

city: Antwerpen

first: Gerrit

last: Beemster

state: Antwerpen

address: Groenenborgerlaan 171

department: Biology

country: Belgium

institute: University of Antwerp

summary: Plants as obligate aerobic organisms are severely affected by flooding-induced oxygen restriction. As a consequence, they suffer from energy deficits which are counterbalanced by activation of anaerobic metabolism genes through subgroup VII ETHYLENE-RESPONSE FACTOR (ERFVII) transcription factors. Despite the crucial role of ERFVIIs in regulating transcript responses to hypoxia in multiple plant species, it is not understood how these factors mechanistically initiate hypoxic gene expression. Here, we show that the Arabidopsis ERFVIIs RELATED TO APETALA 2.12 (RAP2.12) and RAP2.2 recruit the Mediator complex, present in all higher eukaryotes, in order to convey stress signals to RNA polymerase II. This is achieved by specific interaction with Mediator subunit 25 (AtMED25). Both RAP2.12 and RAP2.2 require AtMED25 for full activity and subsequent induction of target hypoxia core genes. Our findings support an interplay of multiple coactivators under hypoxia and underline the flexible nature of the Mediator complex composition, which both help to meet specific cellular demands under (hypoxic) stress conditions.

overall_design: 1 control, 1 treatment (3h 1% O2), wildtype and med25-1 plants, 3 biological replicates per genotype and treatment)

first: Alina

last: Rosinski

first: Jos

middle: H

last: Schippers

first: Lisa

last: Häger

first: Stephanie

last: Frohn

first: Christian

last: Hammerschmid

first: Frauke

last: Augstein

last: Beling

first: Katharina

last: Winkels

first: Brigitta

last: Ehrt

first: Patricia

middle: D

last: Martins

first: Katrien

last: Sprangers

middle: T

first: Joost

last: van Dongen

first: Romy

last: Schmidt


title: Oncogenic KIT mutations induce STAT3-dependent autophagy to support cell proliferation in acute myeloid leukemia

city: Strassen

first: Tony

last: KAOMA

address: 1 A-B Rue Thomas Edison

department: Quantitative Biology Unit

country: Luxembourg

institute: Luxembourg Institute of Health

summary: Autophagy is associated with both survival and cell death in myeloid malignancies. Therefore, deciphering its role in different genetically defined subtypes of acute myeloid leukemia (AML) is critical. Activating mutations of the KIT receptor tyrosine kinase are frequently detected in core-binding factor AML and are associated with a greater risk of relapse. Herein, we report that basal autophagy was significantly increased by the KITD816V mutation in AML cells and contributed to support their cell proliferation and survival. Invalidation of the key autophagy protein Atg12 strongly reduced tumor burden and improved survival of immunocompromised NSG mice engrafted with KITD816V TF-1 cells. Downstream of KITD816V, STAT3, but not AKT or ERK pathways, was identified as a major regulator of autophagy. Accordingly, STAT3 pharmacological inhibition or downregulation inhibited autophagy and reduced tumor growth both in vitro and in vivo. Taken together, our results support the notion that targeting autophagy or STAT3 opens up an exploratory pathway for finding new therapeutic opportunities for patients with CBF-AML or others malignancies with KITD816V mutations.

overall_design: TF-1 cells expressing either the wild type or the mutated form of KIT (KITD816V) were grown and treated for RNA extraction and hybridization on Affymetrics microarrays. We sought to obtain gene signature specific of the constitutive activation of the KITD816V mutant.

first: Clément

last: Larrue

first: Quentin

last: Heydt

first: Estelle

last: Saland

first: Héléna

last: Boutzen

last: Kaoma

first: Jean-Emmanuel

last: Sarry

first: Carine

last: Joffre

last: Récher


title: The poly(A) polymerase PAPS1 interacts with the RNA-directed DNA methylation pathway in sporophyte and pollen development [small RNA]

city: Potsdam

first: Michael

last: Lenhard

address: Karl-Liebknecht-Str. 24-25, Haus 26

department: Institut für Biochemie und Biologie

institute: Universität Potsdam

summary: RNA-based processes play key roles in the regulation of eukaryotic gene expression. This includes both the processing of pre-mRNAs into mature mRNAs ready for translation and RNA-based silencing processes, such as RNA-directed DNA methylation (RdDM). Polyadenylation of pre-mRNAs is one important step in their processing and is carried out by three functionally specialized canonical nuclear poly(A) polymerases in Arabidopsis thaliana. Null-mutations in one of these, termed PAPS1, result in a male gametophytic defect. Using a fluorescence-labelling strategy, we have characterized this defect in more detail using RNA and small-RNA sequencing. In addition to global defects in expression of pollen-differentiation genes, paps1 null mutant pollen show a strong overaccumulation of transposable-element transcripts, yet a depletion of 21- and particularly 24-nucleotide long short interfering RNAs (siRNAs) and microRNAs (miRNAs) targeting the corresponding transposable elements. Double-mutant analyses support a specific functional interaction between PAPS1 and components of the RdDM pathway, as evident from strong synergistic phenotypes in mutant combinations involving paps1, but not paps2 paps4 mutations. In particular, the double mutant of paps1 and rna-dependent rna polymerase 6 (rdr6) shows a synergistic developmental phenotype disrupting the formation of the transmitting tract in the female gynoecium. Thus, our findings in A. Thaliana uncover a potentially general link between canonical poly(A) polymerases as components of mRNA processing and RdDM, reflecting an analogous interaction in fission yeast.

overall_design: Small RNA in mutant and wild type pollen.

first: Yunming

last: Zhang

first: Anna

last: Ramming

first: Lisa

last: Heinke

first: Lothar

last: Altschmied

first: R

last: Slotkin

first: Jörg

last: Becker

last: Kappel


title: The poly(A) polymerase PAPS1 interacts with the RNA-directed DNA methylation pathway in sporophyte and pollen development


title: The poly(A) polymerase PAPS1 interacts with the RNA-directed DNA methylation pathway in sporophyte and pollen development [RNA-seq]

overall_design: Differential gene expression between mutant and wild-type pollen.

first: Christian


title: Enhancer profiling in Esrrb-/- ES cells [ChIP-seq]

city: London

first: Ed

last: Curry

summary: We uncover a pivotal role for ESRRB in demarcating ESC-specific enhancer units, and propose that ESRRB’s developmentally-regulated extinction precipitates their decommissioning with impact on the rewiring of the pluripotency transcriptional programme upon embryo implantation

overall_design: Profiling H3K27ac and Med1 occupancy through ChIP-seq

first: Veronique

last: Azuara

first: Wout

last: Megchelenbrink


title: Transcriptome analysis of bovine uninucleated trophoblast cells (UTC) and Trophoblast Giant Cells (TGC)

city: Dummerstorf

first: Rainer

last: Fuerbass

address: Wilhelm-Stahl-Allee

institute: Leibniz Institute for Farm Animal Biology

summary: In the bovine placenta, intimate fetomaternal contacts are confined to multiple discrete structures termed placentomes. In the placentomes, widely ramified fetal chorionic villi interdigitate with corresponding maternal caruncular crypts.  The trophoblast covering the chorionic villi is composed of uninucleate trophoblast cells (UTCs) and binucleate trophoblast giant cells (TGCs). TGCs are weakly invasive and capable of migrating toward the caruncular epithelium where they eventually fuse with single epithelial cells to form short-living trinucleate fetomaternal hybrid cells. Thereby, molecules of fetal origin are transported into the maternal compartment. The loss of TGCs due to fetomaternal hybrid cell formation is compensated by differentiation of UTCs into TGCs. We performed a genome-wide gene expression study of virtually pure UTCs and TGCs to to identify genes which are associated with trophoblast cell differentiation

overall_design: Bovine placentomes were obtained from three pregnant cows from days 118 to 130 of gestation. UTCs and TGCs were isolated by an optimized fluorescence activated cell sorting (FACS) procedure.  RNA was isolated and subjected to mRNA microarray analysis using Bovine Gene 1.0 ST Arrays (Affymetrix, St. Clara, CA, USA).

first: Marina

last: Polei

first: Dirk

last: Koczan

last: Fürbass