title: The MT1G gene in LUHMES Neurons is a Sensitive Biomarker of Neurotoxicity

city: Rockville

middle: Lee

last: Gerhold

address: 9800 Medical Center Drive

department: Division of Preclinical Innovation

country: USA

institute: NCATS/NIH

summary: Identification of toxicants that underlie neurological diseases is a neglected area awaiting a valid strategy to identify such toxicants. We sought biomarkers that respond to known neurotoxicants in LUHMES immortalized neurons and evaluated these biomarkers for use in screening libraries of environmental toxicants. LUHMES immortalized human dopaminergic neurons were surveyed by RNA sequencing following challenge with Parkinsonian toxicants rotenone, 6-hydroxydopamine, MPP+, and ziram (zinc dimethyldithiocarbamate; Zn2+DDC2), as well as additional toxicants paraquat, MS275, and methylmercury. The metallothionein gene MT1G was the most dynamic gene expression response to all seven toxicants. Multiple toxicants also increased transcripts for SLC30A1 and SLC30A2 zinc secretion transporters, the SLC7A11 xCT cystine/glutamate antiporter important for glutathione synthesis, DNA damage Inducible Transcript 3 (DDIT3), and secreted growth factors FIBIN and CXCL12, whereas several toxicants decreased expression of the Apelin growth factor (APLN).  These biomarker genes showed advantages in sensitivity by responding to many toxicants at sub-cytotoxic concentrations. Since several of these biomarker genes and prior neurological disease studies implicated disruption of metal distribution, we tested metal chelator thiram (dimethyldithiocarbamate, DDC), Zn2+DDC2, and several other metals and metal chelates for cytoxicity and induction of MT1G expression. Metals and chelators that caused dynamic increases in MT1G expression caused cytotoxicity, whereas Ni2+DDC2 caused MT1G increase, but no cytotoxicity. These results bolster prior work suggesting that neurons are characteristically sensitive to depletion of glutathione or to disruption of cellular metal distribution and provide biomarkers to search for such neurotoxicants in chemical libraries.

overall_design: Dopaminergic neurons differentiated from LUHMES cells were exposed to a vehicle control or one of seven different toxicants. The vehicle control and 7 toxicants were tested on cultured cells in triplicate for a total of 24 biological samples (3 control, 21 toxicant treated samples). Cells were treated for 6 hours prior to initiation of sample prep and RNA extraction.

first: Zhi-Bin

last: Tong

first: John

last: Braisted

first: Pei-Hsuan

last: Chu


title: Distinct Regulatory Programs Control the Latent Regenerative Potential of Dermal Fibroblasts during Wound Healing

status: Public on Aug 04 2020

city: Calgary

first: Jeff

last: Biernaskie

state: Alberta

address: 3330 Hospital Drive NW

department: Comparative Biology and Experimental Medicine

country: Canada

institute: University of Calgary

type: Expression profiling by high throughput sequencing

type: Genome binding/occupancy profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Multiplexed measurement of variant abundance and activity reveals VKOR topology, active site and human variant impact

status: Public on Aug 10 2020

city: Seattle

first: Douglas

last: Fowler

state: WA

address: 3720 15th Ave NE

department: Genome Sciences

institute: University of Washington

summary: Vitamin K epoxide reductase (VKOR) drives the vitamin K cycle, activating vitamin K-dependent blood clotting factors. VKOR is also the target of the widely used anticoagulant drug, warfarin.  Despite VKOR’s pivotal role in coagulation, its structure and active site remain poorly understood. Here, we used multiplexed, sequencing-based assays to measure the effects of 2,695 VKOR missense variants on abundance and 697 variants on activity in cultured human cells.

sample_organism:
Homo sapiens
synthetic construct

platform_organism:
Homo sapiens
synthetic construct

overall_design: Barcoded single amino acid variant libraries of VKOR variants were recombined into HEK293 and HEK293T cells previously engineered to contain a Bxb1 recombination site at the AAVS1 locus. Upon sorting cells for APC or eGFP expression, genomic DNA was extracted. Barcodes were amplified and counted with Illumina sequencing. Barcodes were associated back to the corresponding VKOR by comparison with a barcode-variant map previously created by sequencing the variant library plasmids using Illumina sequencing.

middle: M


title: Central clock components modulate plant shade avoidance by directly repressing transcriptional activation activity of PHYTOCHROME-INTERACTING FACTORS

status: Public on Sep 01 2020

city: Albany

first: Yu

last: Zhang

state: California

address: 800 Buchanan Street

department: Plant and Microbial Biology

institute: UC Berkeley

summary: Light-environment signals, sensed by plant phytochrome (phy) photoreceptors, are transduced to target genes through direct regulation of PHYTOCHROME-INTERACTING FACTOR (PIF) transcription factor abundance and activity. Previous genome-wide DNA-binding and expression analysis has identified a set of genes that are direct targets of PIF transcriptional regulation. However, quantitative analysis of promoter occupancy versus expression level has suggested that unknown “trans factors” modulate the intrinsic transcriptional activation activity of DNA-bound PIF proteins. Here, using computational analysis of published data, we have identified PSEUDO-RESPONSE REGULATORS (PRR5 and PRR7) as displaying a high frequency of co-localization with the PIF proteins at their binding sites in the promoters of PIF Direct Target Genes (DTGs). We show that the PRRs function to suppress PIF-stimulated growth in the light and vegetative shade, and that they repress the rapid PIF-induced expression of PIF-DTGs triggered by exposure to shade. The repressive action of the PRRs on both growth and DTG expression requires the PIFs, indicating direct action on PIF activity, rather than a parallel antagonistic pathway. Protein interaction assays indicate that the PRRs exert their repressive activity by binding directly to the PIF proteins in the nucleus.  These findings support the conclusion that the PRRs function as direct outputs from the core circadian oscillator, to regulate the expression of PIF-DTGs, through modulation of PIF transcriptional activation activity, thus expanding the roles of the multifunctional PIF signaling hub.

relation:
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overall_design:
To examine the relative distributions of published DNA-binding sites of other transcription factors (TFs), with those of the PIF quartet proteins within the promoters of our 338 PIF-DTGs, we compared the published ChIP-defined binding regions for 25 Arabidopsis transcription factors (25 TFs) with those of four core PIFs. For this purpose, we used a BED file, kindly provided by K. Heyndrickx, K. Vandepoele and colleagues, containing the boundaries of genomic regions displaying significant binding of the TF specified. We located these binding regions within the promoters of our 338 PIF-DTGs, using the Integrative Genomics Viewer, and compared them to the binding peaks of all four PIFs. To quantify the extent and proximity of the binding sites of the ’25 TFs’ compared to those of the PIFs, across all PIF-DTG promoter regions, we first determined the overlap (if any) of the binding regions of each of the ’25 TFs’, with the mean of the PIF-bound summits. If the center of a PIF-bound region was located within a ’25-TF’ binding region, the binding was defined as ‘coincident’. The proximity was then defined as the distance between the coincident-TF and PIF binding centers, and was plotted using Mathematica (http://www.wolfram.com/mathematica/).
The re-analyzed sample information and data processing details are provided in the 'README.txt'.

first: Anne

last: Pfeiffer

first: James

last: Tepperman


title: RNA-seq analysis of human NK cells expanded with 221-mIL21 expansion system and K562-mIL21 expansion system

status: Public on Aug 07 2020

city: Newark

first: Dongfang

last: Liu

state: New Jersey

address: 205 S Orange Ave

department: Department of Pathology, Immunology and Laboratory Medicine

institute: Rutgers-The State University of New Jersey

summary: PBMCs were stimulated with irradiated K562-mIL21 and 221-mIL21 feeder cells, respectively, as well as supplemented with IL-2 and IL-15. NK cells were purified from expanded cells using flow cytometry on day 7 and day 14 for RNA sequencing (RNA-Seq).

overall_design: mRNA profiles of NK cells expanded with 221-mIL21 expansion system and K562-mIL21 expansion system on day 7 and day 14 of expansion

first: Yan

last: Yang


title: Genome-wide transcriptomic analysis in pediatric glioblastomas cell lines by RNA-seq.

city: Shanghai

first: jiao

last: fangfang

address: DongAn Road 131

country: China

institute: fudan university

summary: We identified that RACK7 recognizes the histone H3.3G34R mutaion in vitro and in vivo. In order to explore the function of RACK7 and H3.3G34R mutaion, we used three pediatric glioblastomas(pGBM) cell lines. SJ-HGGx6c(R6) and SJ-HGGx42c(R42) have heterozygous  G34R mutation, while SJ-HGGx39c(WT39) has wildtype H3F3A, which encodes H3.3. We next corrected H3.3G34R in R6 and R42 cells to wildtype H3.3 by CRISPR/Cas9 mediated knock-in, and knocked out RACK7 in R6 and R42 cells by CRISPR/Cas9. Finaly, we performed genome-wide transcriptomic analysis in these cell lines by RNA-seq analysis.

overall_design: The mRNA was captured and deep sequenced in the pGBM cell lines on Illumina Hiseq X-Ten with 2×150 bp paired-end sequencing,  two biological repeats for each cell lines were used.

first: Fangfang

last: Jiao

first: Chen

last: He

first: Wenqi

last: Xu

first: Gensheng

first: Suzanne

middle: J

last: Baker

first: Yang

last: Shi

first: Rui

last: Guo


title: Intratumoral injection of TLR4 agonist GLA in A20 tumor model

city: BOTHELL

first: Hailing

last: Lu

institute: Seattle Genetics

summary: The goal of this study was to investigate the effect of intratumoral injection of GLA-SE, a TLR4 agonist in stable emulsion (SE), in Balb/c mice with established A20 lymphoma.

overall_design: Female Balb/c mice with implanted A20 tumors were randomly assigned to each treatment group (N=4 per group): PBS control, GLA-SE (10 ug GLA in 50ul of 2% SE), or control SE alone.  Intratumoral injection was administrated every other day.  After three injections, the tumors were harvested for RNA extraction. Total RNA was extracted using the Qiagen DNA/RNA Allprep kit.  200ug of total RNA was used for nanostring gene expression analysis using the mouse panCancer Immune profiling panel

first: Jan

last: ter Meulen


title: Microarray analysis of lncRNA and mRNA reveals lipogenesis inhibition along with metabolic remodeling in mice infected by the larval Echinococcus granulosus

city: Xuzhou

first: Wei

last: Pan

state: Jiangsu

address: 209 Tongshan Road

institute: Xuzhou Medical University

type:
Expression profiling by array
Non-coding RNA profiling by array

summary: Parasitic infection improves metabolic homeostasis in “western diet” induced-obesity, which partially results from the regulation of adipogenesis. However, the underlying mechanism remains largely unknown. This study investigated the long non-coding RNA（lncRNA）and mRNA profiles of subcutaneous adipose tissues in mice infected by the protoscoleces of Echinococcus granulosus (EgPSC) using a microarray analysis. In comparison with control mice, the infected mice showed decreased mass of adipose tissues and shrunken size of adipocytes. The indirect calorimetry found the alternation of energy metabolism post infection, which was characterized by less CO2 production and O2 consumption, sharp decline of carbohydrate oxidation and a little increase of fat oxidation. A total of 1,052 mRNAs and 220 lncRNAs were differentially expressed in infected subcutaneous adipose tissues (fold change ≥2, P＜0.05). Of them, 541 mRNAs were upregulated and 511 mRNAs were downregulated; 126 lncRNAs were upregulated and 94 lncRNAs were downregulated. The Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis showed that the parasitic infection reprograms a complex metabolic network. Notably, “lipoxygenase” and “Arginine and proline metabolism” pathways were significantly upregulated while “glycolysis”, “Tricarboxylic acid (TCA) cycle”, “denovo lipogenesis” and “lipid droplet” pathways were dramatically downregulated. In addition, several key lncRNAs were linked with insulin resistance and adipocyte differentiation. Overall, this study suggests that E. granulosus infection inhibits the adipogenesis, which provides a novel insight for metabolic homeostasis mediated by parasitic infection, and hypertrophic adipocytes in obesity.

overall_design: Female C57BL/6J mice were intraperitoneally injected with a 200 μl suspension containing 2000 live EgPSC in 0.9% NaCl, and were sacrificed at the 16th week post infection. The lncRNA and mRNA expression patterns in subcutaneous adipose tissues of three EgPSC infected mice and three control mice were detected. The Agilent-085631 was used in this experiment and data analysis of the 6 samples were conducted by OE Biotechnology Co., Ltd., (Shanghai, China).


title: Transcriptomic analyses of Aedes aegypti cultured cells upon heme exposure

status: Public on Aug 03 2020

city: College Station

first: Zach

last: Adelman

state: TX

address: 370 Olsen Blvd

department: Entomology

institute: Texas A&M University

summary: After a bloodmeal, mosquitoes import heme into the midgut epithelium. Heme acts as an essential signal for oogenesis in Aedes aegypti. However, the mechanisms behind heme import in Aedes aegypti are largely unexplored. In this study, RNA sequencing data from 4 different Aedes aegypti cell culture experiments where exposure to an overabundance or deficiency of heme was examined to identify heme-responsive genes. Zinc mesoporphyrin (ZnMP), a heme fluorescent analog, was used to measure changes in heme uptake prior to mRNA sequencing. A soft cluster analysis was performed to identify genes encoding potential membrane bound importers and exporters based on expression profiles across the samples for each experiment. Stronger candidates were obtained by comparing genes in each dataset to each other. When comparing all datasets to each other, 223 candidate genes with expression pattern changes consistent with importers were found to be heme-regulated in only 2 datasets, 46 were heme-regulated in 3 datasets and 2 was heme-regulated in all 4 datasets. In contrast, 114 candidate genes with patterns consistent with exporters were common to only 2 datasets, with just 11 present in 3 of the 4 datasets. A large number of genes containing transmembrane domains were isolated across the 4 datasets which showed downregulation or upregulation in response to heme overexposure conditions indicating the possibility that heme membrane bound import and export genes were identified respectively, with the reverse trend observed in the presence of heme deficiency. However, few transporter candidate genes were identified that showed high differential expression (above 4-fold or below 1/4th fold). Ultimately, as few strong candidates were identified by these studies, we consider the possibility that each cell line could have a redundant system of heme import, whereby multiple transport proteins each contribute to the total heme accumulation in the cell. Alternatively, it is possible that these cells lines do not regulate heme transport at the transcript level, but rather do so post-translationally.

overall_design: 33 samples, 3 replicates of each type of sample. 4 total experiments were performed, 6, 9, 9, and 9 samples in each one. The untreated samples are the reference sample in all experiments

first: Heather

middle: L

last: Eggleston

middle: N


title: Correlation Analysis of Expression Profile and Quantitative iTRAQ-LC-MS/MS Proteomics Reveals Resistance Mechanism Against TuMV in Chinese Cabbage (Brassica rapa ssp. pekinensis)

city: Nanjing

first: Shanwu

last: Lyu

address: Weigang 1

department: College of Horticulture

institute: Nanjing Agriculture University

summary: To better examine the molecular mechanisms behind the virus infection, we conducted a correlation analysis of RNA-Seq and quantitative iTRAQ-LC-MS/MS in TuMV-infected and in healthy Chinese cabbage leaves.

overall_design: The five-leaf stage seedlings were rubbed with the TuMV inoculum by grounding the TuMV-infected Chinese cabbage leaves with phosphate buffer. The plants inoculated only with buffer served as control. At 21 days post-inoculation each of the infected and the control leaves were collected for RNA-Seq.

first: Changwei

last: Zhang

first: Xilin

last: Hou


title: RNAseq analysis of Angiotensin II or PBS perfused Apolipoprotein E deficient mice

city: New York

first: Bhama

last: Ramkhelawon

state: NY

address: 435 East 30th - Science Building 416

department: Surgery

institute: NYU Langone Medical Center

summary: We report the transcriptomic analysis of RNA-seq of aortas isolated from ApoE-/- mice exposed to Ang II or PBS to uncover the mechanisms underlying the undefined role ripk3 in AAA

overall_design: Comparison of mouse aortic samples of Apolipoprotein E deficient mice perfused with Ang II or PBS


title: ARID3a expression in human hematopoietic stem cells is associated with distinct gene patterns in aged individuals

city: Greenville

first: Michelle

last: Ratliff

state: NC

address: 600 Moye Blvd, 132 Biotechnology Building

department: Microbiology and Immunology

institute: East Carolina University

summary: Aging results in altered gene expression patters in HSCs expressing ARID3A transcirpts, with a number of genes downregulated in aged donor ARID3a+ HSCs compared to young donor ARID3a+ HSCs

overall_design: scRNA-seq of isolated peripheral blood HSCs from young and aged donors.

first: Carol

last: Webb


title: Gene expression profiling study by RNA-seq for identifying genes associated with sound vibration in plant

city: Daejeon

first: Seon-Kyu

last: Kim

address: 125 Gwahak-ro, Yuseong-gu, Daejeon 305-806, Korea

department: Personalized Genomic Medicine Research Center

country: South Korea

institute: Korea Research Institutue of Bioscience & Biotechnology

summary: Plant can perceive and respond natural sound vibration (SV). Artificial SV also served as a novel trigger of induced resistance, although approaches for activating such plant innate immunity intensively studied on the use of biological and chemical agents (BCA). Artificial SV pre-treatment protected Arabidopsis thaliana seedlings against insect pests and fungal pathogens. However, SV-mediated epigenetic modulation remains unexplored while CBA-mediated induced resistance is known as a complicated process involving epigenetic regulation. Here, we performed a gene expression profiling basd on RNA-seq experiment to understand the role of 10 kHz SV-mediated epigenetic modification in induced resistance against a soil-borne pathogenic bacterium Ralstonia solanacearum.

overall_design: A group of plants was prepared to be expose to sound vibration (SV, 10 kHz) at 90 dB every 3 h for 10 days. Another group of plants dreched with benzothiadiazole (BTH) were also prepared as a positive control group. The other group of plants with non-treatment were also prepared as a control group. Then, all samples were drenched with a pathogen (R. solanacearum). Transcriptome data were generated by performing RNA-seq analysis of 29 arabidopsis samples, which were obtained at 0d, 1d and 2d after dreching pathogen. Each sample group contains three biological replicates, except for a 10kHz sound wave treated group obtained at 1d after drenching pathogen (4 replicates) and a non-treatment group obtained at 2d after drenching pathogen (4 replicates). Total RNA was isolated from Arabidopsis roots using RNeasy Mini Kit (Qiagen), according to the manufacturer’s instructions. The quality and integrity of total RNA were confirmed by agarose gel electrophoresis and ethidium bromide staining, followed by a visual examination of RNA under ultraviolet light. RNA-seq library was prepared using the TruSeq RNA Sample Prep Kit v2 (Illumina, San Diego, CA, USA) and sequenced on the Illumina Hiseq2500 platform to generate 100 bp paired-end reads.

first: Jeong-Hwan

first: Jihye

last: Jung

first: Choong-Min

last: Ryu


title: Single-cell transcriptomics of Hic1 lineage cells recruited during regenerative and scar-forming skin wound healing.

first: Jeff

last: Biernaskie

summary: Adult mammalian skin wound healing is typically accompanied by fibrotic scar that impairs normal skin function and regeneration of skin appendages. Interestingly, however, in adult mice, large severe skin injuries exhibit de novo formation of HFs following severe skin injuries (a phenomenon termed wound-induced HF neogenesis, WIHN). Understanding the competent cell types and molecular mechanisms that enable regenerative wound healing will be critical for developing treatments that restore skin function after injury. We described the existence of an adult bipotent hair follicle dermal stem cell (hfDSC) that functions to regenerate the connective tissue sheath and to populate the DP with new cells (Rahmani et al., 2014). Based on this, we hypothesized that the mesenchymal cells comprised within the neogenic HFs might originate from hfDSCs. To test this, we employed αSMACreERT2:ROSAYFP and Hic1CreERT2:TDTmt mice to examine the contribution of hfDSCs or hfDSCs and reticular/hypodermal progenitors, respectively, to the formation of neodermis and regeneration of de novo HFs. Mice received full-thickness excision wounds (>1 cm2) and then harvested at 18-140 days post-wounding (dpw). αSMA+ve and Hic1-lineage cells were activated upon wounding, migrated into the wound, and contributed to both DP and DS in almost all de novo-formed HFs. Surprisingly, hfDSCs contributed only a minority of cells (20%) to nascent DP cells, whereas Hic1-lineage cells generated >90% of the neogenic DP cells. In both cases, cells integrating into neogenic HF mesenchyme appeared to restore the hfDSC pool, since they repopulated the neogenic mesenchyme over successive regenerative hair cycles. Finally, using an ex vivo HF formation assay, we found that prospectively isolated extrafollicular Hic-lineage cells could participate in HF formation when exposed to a permissive environment. Our data reveal that despite their origin in the reticular/hypodermis, Hic1-lineage dermal progenitors are able to adopt a regenerative response during wound healing if provided with a permissive local environment.

overall_design: To isolate cells comprising the wound neodermis, we created small (8 mm diameter) and large (1.5 cm diameter) full-thickness skin wounds on P.24-26 Hic1Cre:tdTomato+ve mice treated with tamoxifen as pups (P.4-5). We FACS collected viable Hic1tdTomato+ve cells 14 dpw from four separate cell populations in parallel. These included: 1) cells recruited in small (scar-forming) wounds, 2) cells recruited to outside (scar-forming portion) of large wound, 3) cells recruited to center (regenerative portion) of large wounds, and 4) cells within the intact (uninjured) skin. All four samples were processed according to 10X Genomics ChromiumTM Single Cell 3’ Reagent Guidelines v2 Chemistry as per the manufacturer’s protocol. In brief, single cells were sorted into 0.1% BSA–PBS and partitioned into Gel Bead-In-EMulsions (GEMs) using 10xTM GemCodeTM Technology. This process lysed cells and enabled barcoded reverse transcription of RNA, generating full-length cDNA from poly-adenylated mRNA. DynaBeads® MyOneTM Silane magnetic beads were used to remove leftover biochemical reagents, then cDNA was amplified by PCR over 10 cycles. Quality control size gating was used to select cDNA amplicon size prior to library construction. Read 1 primer sequences were added to cDNA during GEM incubation. P5 primers, P7 primers, i7 sample index, and Read 2 primer sequences were added during library construction. Quality control and cDNA quantification was performed using Agilent High Sensitivity DNA Kit. Sequencing was performed first using Illumina MiSeq SR50 to approximate the number of recovered cells in each sample. We recovered 4061, 3776, 2604, and 3293 cells for Samples 1-4, respectively, with an estimated doublet rate of ≈3%. Based on this, we determined lane distributions for sequencing using Illumina HiSeq 4000 PE (75 bp paired-end reads) with a targeted sequencing depth of ~115,000 reads/cell.

first: Sepideh

last: Abbasi

first: Sarthak

last: Sinha

first: Prajay

last: Shah

first: Jo

last: Stratton

first: Andrew

last: Hagner

first: Anowara

last: Islam


title: Identifying genes associated with sound vibration in plant

type: Non-coding RNA profiling by high throughput sequencing


title: Expression profiling by small RNA-seq for identifying miRNA associated with sound vibration in plant

summary: Plant can perceive and respond natural sound vibration (SV). Artificial SV also served as a novel trigger of induced resistance, although approaches for activating such plant innate immunity intensively studied on the use of biological and chemical agents (BCA). Artificial SV pre-treatment protected Arabidopsis thaliana seedlings against insect pests and fungal pathogens. However, SV-mediated epigenetic modulation remains unexplored while CBA-mediated induced resistance is known as a complicated process involving epigenetic regulation. Here, we performed an expression profiling basd on small RNA-seq experiment to understand the role of 10 kHz SV-mediated epigenetic modification in induced resistance against a soil-borne pathogenic bacterium Ralstonia solanacearum.

overall_design: A group of plants was prepared to be expose to sound vibration (SV, 10 kHz) at 90 dB every 3 h for 10 days. The other group of plants with non-treatment were also prepared as a control group. Then, all samples were drenched with a pathogen (R. solanacearum). miRNA quantification data were generated by performing small RNA-seq analysis of 18 arabidopsis samples, which were obtained at 0d, 1d and 2d after dreching pathogen. Total RNA was isolated using the mirVana miRNA isolation kit (Ambion). Small RNAs (20 - 30 nt) were purified from 15% Novex TBE-Urea gel (Invitrogen) and ligated first with the 5’ RNA adaptor and then with the 3’ RNA adaptor provided by Illumina TruSeq small RNA sample preparation protocol. In each step, the ligated product was PAGE-gel purified. After first-strand synthesis and 11 cycles of PCR amplification, the product was PAGE-gel purified. Sequencing was performed in single end reads (75 bp) using NextSeq 500 platform (Illumina).


title: ChIP-seq for identifying molecules associated with sound vibration in plant

summary: Plant can perceive and respond natural sound vibration (SV). Artificial SV also served as a novel trigger of induced resistance, although approaches for activating such plant innate immunity intensively studied on the use of biological and chemical agents (BCA). Artificial SV pre-treatment protected Arabidopsis thaliana seedlings against insect pests and fungal pathogens. However, SV-mediated epigenetic modulation remains unexplored while CBA-mediated induced resistance is known as a complicated process involving epigenetic regulation. Here, we performed a ChIP-seq analysis to understand the role of 10 kHz SV-mediated epigenetic modification in induced resistance against a soil-borne pathogenic bacterium Ralstonia solanacearum.

overall_design: A group of plants was prepared to be expose to sound vibration (SV, 10 kHz) at 90 dB every 3 h for 10 days. The other group of plants with non-treatment were also prepared as a control group. Then, all samples were drenched with a pathogen (R. solanacearum). ChIP-seq analysis was performed on 36 arabidopsis samples, which were obtained at 0d and 1d after dreching pathogen. Cells were fixed using 1% formaldehyde, lysed and sonicated using a Bioruptor (Diagenode Inc.). Immunoprecipitation was performed with anti-H3k36ac(Millipore, 07-540) or anti-H3k27me3(07-449, Milipore). 250-400 bp genomic libraries were generated from the input and immunoprecipitated DNA and sequenced using Illumina HiSeq2500 to generate 100 bp paired-end reads.


title: The Chloroplast RNA Binding Protein CP31A Has a Preference for mRNAs Encoding the Subunits of the Chloroplast NDH Complex and is Required for Their Accumulation

status: Public on Aug 01 2020

city: Berlin

first: Benjamin

last: Lenzen

address: Philippstr. 13, House 22

department: Institute of Biology

country: Germany

institute: Humboldt University of Berlin

summary: Chloroplast RNA processing requires a large number of nuclear-encoded RNA binding proteins (RBPs) that are imported post-translationally into the organelle. Most of these RBPs are highly specific for one or few target RNAs. By contrast, members of the chloroplast ribonucleoprotein family (cpRNPs) have a wider RNA target range. We here present a quantitative analysis of RNA targets of the cpRNP CP31A using digestion-optimized RNA co-immunoprecipitation with deep sequencing (DO-RIP-seq). This identifies the mRNAs coding for subunits of the chloroplast NDH complex as main targets for CP31A. We demonstrate using whole-genome gene expression analysis and targeted RNA gel blot hybridization that the ndh mRNAs are all down-regulated in cp31a mutants. This diminishes the activity of the NDH complex. Our findings demonstrate how a chloroplast RNA binding protein can combine functionally related RNAs into one post-transcriptional operon.

overall_design: RIP-seq of CP31A in Arabidopsis thaliana WT plants with 3 replicates

first: Thilo

last: Rühe

first: Marie-Kristin

last: Lehniger

first: Ayako

last: Okuzaki

first: Mathias

last: Labs

first: Jose

last: Muino

first: Uwe

last: Ohler

first: Dario

last: Leister

first: Christian

last: Schmitz-Linneweber


title: Novel insights into the oxidative stress response of Salmonella enterica serovar Enteritidis revealed by the next generation sequencing approach

status: Public on Jul 31 2020

city: Saint Paul

first: Sinisa

last: Vidovic

state: MN

address: 1971 Commonwealth Avenue

institute: University of Minnesota

summary: We report our results of RNA-seq analysis on the wild type Salmonella enterica serovar Enteritidis with and without H2O2 treatment

sample_organism: Salmonella enterica subsp. enterica serovar Enteritidis

overall_design: RNA was isolated from cultures of the wild type Salmonella enterica serovar Enteritidis exposed to H2O2 and without exposure to H2O2. Libraries were created using standard Illumina reagents and analyzed using a HiSeq 2500 Illumina.

first: Juan

middle: E

last: Abrahante


title: Regulation of dynamic pigment cell states at single-cell resolution

city: Providence

first: nathalie

last: oulhen

state: RI

address: 185 meeting street

institute: Brown university

summary: Pigment cells bear molecules with diverse physiological roles across phylogeny and are often under strict evolutionary selection. Thus, the mechanisms of regulating these cells, and the pigments within them, are of critical importance. Here, we explore the regulation of pigment cells in the purple sea urchin Strongylocentrotus purpuratus, an emerging model  for understudied pigments at a molecular level. Sea urchins display a variety of pigments in both embryos and adults, but how the pigment cells form during development has not been resolved, nor has their breadth of biological significance been revealed. Known genes expressed by embryonic pigment cells are the transcriptional factor glial cells missing (gcm),  and the enzymes pks1 and fmo1,2 and 3 (polyketide synthase1, flavin-dependent monooxygenase 1, 2, 3 respectively). In this study, we took advantage of single cell RNA-seq technology to interrogate the cell state of emerging pigment cells, and to test their diversity in fate and function.

overall_design: Eggs and sperm of S.purpuratus were spawned by injection of 0.5M KCl into the adult coelomic cavity. Embryos were cultured in filtered (0.2micron) sea water collected at the Marine Biological laboratories in Woods Hole MA, until the appropriate stage for dissociation (48 and 72 hours post fertilization). To test the function of gcm, eggs were dejelled before fertilization by washing in pH4.0 seawater, and injected post fertilization in presence of 1mM 3-AT with either a control morpholino or the gcm morpholino used at a concentration of 0.5mM. The resulting wild type controls and albino embryos were collected at 48 hpf. These 4 samples (non injected 48 and 72 hpf, control morpholino injected 48 hpf and gcm morpholino injected 48 hpf embryos) were used for single cell RNA seq. Briefly, the collected embryos were washed twice with calcium-free sea water, and then suspended hyalin-extraction media (HEM) for 10-15 minutes, depending on the stage of dissociation. When cells were beginning to dissociate, the embryos were collected and washed in 0.5M NaCl, gently sheared with a pipette, run through a 40micron Nitex mesh, counted on a hemocytometer, and diluted to reach the appropriate concentration for the single cell RNA-seq protocol using the 10X Chromium technology (v3 Chemistry).

first: Margherita

last: Perillo

first: Nathalie

last: Oulhen

first: Stephany

last: Foster

first: Maxwell

last: Spurrell

first: Cristina

last: Calestani

first: Gary

last: Wessel


title: Transcriptomic analysis of Aedes aegypti midgut epithelial cells upon heme exposure

first: Zach

last: Adelman

summary: The female mosquito Aedes aegypti requires amino acids and other nutrients like heme and iron from a blood meal to initiate vitellogenesis. Heme is a pro-oxidant molecule that acts as a nutrient, signaling molecule and in large quantities, as a toxin. Ae. aegypti has developed a few strategies to handle heme toxicity, as during a typical meal ~10mM is released into the midgut lumen. These strategies include heme aggregation to the peritrophic matrix and the degradation of heme by heme oxygenase in the cytosol of the midgut epithelium. However, despite the importance of heme as a nutrient and toxin, the mechanism of entry into the midgut epithelial cells is not currently known. As no heme transport proteins in have been identified in any dipteran, heme fluorescent analog studies were performed to visualize changes in expression caused by heme followed by global expression analyses performed in midgut tissues using NGS-based RNA sequencing with the end goal to identify the gene(s) that encode the membrane bound heme import proteins responsible for heme uptake during blood digestion. Examination of differential expression of mRNA transcripts at the gene level, found 65 significant DE genes at the adjusted p-value cut off of 0.0001, 38 of which are TM containing and only 2 of which showed high expression changes, AAEL019570 (-2.04 log2, ~0.243), unknown function, and AAEL000717 (3.91 log2, ~15.03), a protocadherin. This list was further reduced to 16 genes with potential heme import function and 7 genes with potential heme export function by examination of differential expression, number of TM domains and function relating to transport. As very few highly differentially expressed genes were found in the analysis, heme import may be controlled by a redundant system of multiple transport proteins instead of a single highly expressed one. Alternatively, heme transport in Ae. aegypti could be regulated post-translationally.

overall_design: 8 samples total, with 4 replicates of each sample type. The 0µM heme sample was the reference sample.

first: Heather

last: Eggleston


title: EDF1 binds collided ribosomes and facilitates recruitment of translational repressors GIGYF2/EIF4E2 and initiates JUN-mediated transcriptional response

status: Public on Aug 02 2020

city: Baltimore

first: Boris

last: Zinshteyn

state: Maryland

address: 725 N Wolfe St, PCTB 714

department: Molecular Biology and Genetics

institute: Johns Hopkins University School of Medicine

summary: RNA-seq analyses of wild-type and DEDF1 cell lines show that the immediate-early JUN-dependent transcriptional response to collisions is dependent on EDF1.

overall_design: RNA-seq of WT or EDF1Δ cells treated with emetine.

first: Niladri

last: Sinha

first: Rachel

last: Green


title: Macrophage Secretion of miR-106b-5p Causes Renin-Dependent Hypertension

city: Indianapolis

first: Scot

last: Matkovich

state: IN

address: Lilly Corporate Center

institute: Eli Lilly and Company

summary: We generated myeloid cells lacking VDR (KODMAC) by crossing Vdrfl/fl mice with lysosome-M-promoter-driven Cre mice (Lyz2Cre) in the Ldlr-/-background (a model of diet-induced metabolic syndrome), as previously described13 and compared them to Vdrfl/flLdlr-/- littermates (control).  Unbiased miRNA expression analyses using media from KODMAC or control peritoneal macrophages identified 361 differentially expressed miRNAs with p<0.05

overall_design: Supernatants were obtained from 9 independent cultures of wild-type peritoneal macrophages (wt) or of KODMAC (vitamin D receptor knockout in the macrophage lineage) (vdrko)

first: Carlos

last: Bernal-Mizrachi


title: Transcriptome Analyses in BV2 microglial cells following treatment with amino-terminal fragments of apolipoprotein E

city: Boise

first: Troy

last: Rohn

state: ID

address: 1910 W University Dr

department: Department of Biology

institute: Boise State University

summary: This study assessed the effects of amino terminal ApoE4 fragments (residues 1-151) on modulating the transcriptome of BV2 microglial cells. Treatment with amino terminal ApoE4 fragments caused the upregulation of nearly four-thousand genes, and further analysis revealed a significant upregulation of genes related to the inflammatory immune response. As a control, an amino terminal ApoE3 fragment was tested and produced a similar but reduced level of upregulation of an identical set of genes.  This set of genes affected pathways including Toll receptor signaling, chemokine/cytokine signaling and apoptosis signaling. Additionally, each treatment regulated a unique set of genes. Amino terminal ApoE3 fragments uniquely regulated 14 times as many genes (1,674), many of which are involved in physiological functions within microglia.  Amino terminal ApoE4 fragments uniquely upregulated 119 genes, with many of the top upregulated genes having unknown functions. Our results suggest that while amino terminal ApoE3 fragments may serve a more physiological role in microglia amino terminal ApoE4 fragments may activate genes with a more pathological purpose. These data support the hypothesis that the link between harboring the APOE4 allele and dementia risk could be enhanced inflammation through activation of microglia.

overall_design: Total RNA-sequencing was performed to assess transcriptional changes that occurred in BV2 microglial cells following treatment with amino-terminal fragment (residues 1-151) of ApoE4 or ApoE3.

first: Tanner

middle: B

last: Pollock

first: Noail

middle: F

last: Isho

first: Giovan

last: Cholico

middle: T


title: Genome-wide Identification of Transcription Start Sites in Two Alphaproteobacteria

city: Madison

first: Kevin

middle: S

last: Myers

state: WI

address: 5127 WEI, 1552 University Ave

department: Great Lakes Bioenergy Research Center

institute: University of Wisconsin - Madison

summary: The alphaproteobacteria have metabolic activities and lifestyles of societal and industrial importance that differ from those in many other bacteria. Here we report the genome-wide identification of transcription start sites (TSSs) from two alphaproteobacteria grown under conditions that result in significant changes in gene expression. TSSs that were identified as present in one condition or both will be an important resource for future studies of these, and possibly other, alphaproetobacteria.

sample_organism:
Novosphingobium aromaticivorans
Cereibacter sphaeroides 2.4.1

overall_design: Transcription start site data of three biological replicates Rhodobacter sphaeroides grown aerobically or photosynthetically and Novosphingobium aromaticivorans grown in glucose plus or minus vanillic acid.

first: Jessica

last: Vera

first: Kimberly

middle: C

last: Lemmer

first: Alexandra

last: Lindz

first: Robert

last: Landick

first: Daniel

middle: R

last: Noguera

first: Timothy

last: Donohue


title: Non-neuronal expression of SARS-CoV-2 entry genes in the olfactory system suggests mechanisms underlying COVID-19-associated anosmia (scRNA-seq: olfactory mucosa)

status: Public on Jul 30 2020

city: Boston

first: David

last: Brann

state: MA

address: 220 Longwood Ave

department: Neurobiology

institute: Harvard Medical School

summary: A subset of COVID-19 patients exhibit altered olfactory function. Here we analyze bulk and single cell RNA-Seq datasets to identify cell types in the olfactory epithelium and olfactory bulb that express cell entry molecules that mediate infection by SARS-CoV-2 (CoV-2), the causal agent in COVID-19. We find that samples from whole olfactory mucosa in species including mouse and human express two key genes involved in CoV-2 entry, ACE2 and TMPRSS2. However, neither olfactory sensory neurons nor olfactory bulb neurons express these genes, which are instead expressed in support cells, stem cells, and perivascular cells. These findings suggest that CoV-2 infection of non-neuronal cell types leads to anosmia and related disturbances in odor perception in COVID-19 patients.

overall_design: Eight 15 min Drop-seq runs from dissociated whole olfactory mucosa from five adult male C57BL/6 mice (8–12 weeks-old). Additional Drop-Seq data from the olfactory bulb can be found in GSE148360.

middle: H

first: Tatsuya

last: Tsukahara

first: Sandeep

last: Datta


title: iPS-derived early oligodendrocyte progenitor cells from SPMS patients reveal deficient in vitro cell migration stimulation

city: Granada

first: Jordi

last: Martorell-Marugan

address: Avenida de la Ilustración 114

department: Bioinformatics Unit

country: Spain

institute: GENyO

summary: Secondary progressive multiple sclerosis (SPMS) most challenging aspect is the lack of efficient regenerative response for remyelination, which is carried out by the endogenous population of adult oligoprogenitor cells (OPCs) after proper activation. OPCs must proliferate and migrate to the lesion and then differentiate into mature oligodendrocytes. To investigate the OPC cellular component in SPMS we developed iPSCs from SPMS affected donors and age matched controls (CT). We confirmed their efficient and similar OPC differentiation capacity, although we reported SPMS-OPCs are transcriptional distinguishable from their CT counterparts. Analysis of OPC-generated conditioned media (CM) also evidenced differences in protein secretion. We further confirmed SPMS-OPC CM presents a deficient capacity to stimulate OPC in vitro migration that can be compensated by exogenous addition of specific components. Our results provide an SPMS-OPC cellular model and encouraging venues to study potential cell communication deficiencies in the progressive form of MS for future treatment strategies.

overall_design: Four biological replicates from SPMS adult donors (01-04) and three biological replicates from adult healthy donors (01-03) were used for analysis, iPSC reprogramming and OPC differentiation.

first: Lidia

last: Lopez-Caraballo

last: Martorell-Marugán

first: Pedro

last: Carmona-Sáez

first: Elena

last: Gonzalez-Munoz


title: DNA methylome analysis of leader cells and follower cells derived from the H1299 NSCLC cell line

city: Atlanta

first: Emily

middle: Rose

last: Summerbell

state: GA

address: Winship Cancer Institute, 1701 Uppergate Dr NE, C4060- Marcus Lab

institute: Emory University

type: Methylation profiling by genome tiling array

summary: Tumor heterogeneity drives disease progression, treatment resistance, and patient relapse, yet remains largely under-explored in invasion and metastasis. Here, we investigated heterogeneity within collective cancer invasion by integrating DNA methylation and gene expression analysis in rare purified lung cancer leader and follower cells. Our results showed global DNA methylation rewiring in leader cells and revealed the filopodial motor MYO10 as a critical gene at the intersection of epigenetic heterogeneity and 3D collective invasion. We further identified JAG1 signaling as a novel upstream activator of MYO10 expression in leader cells. Using live cell imaging, we discovered that MYO10 drives filopodial persistence necessary for micropatterning extracellular fibronectin into linear tracks at the edge of 3D collective invasion exclusively in leaders. Our data fit a model where epigenetic heterogeneity and JAG1/Notch signaling jointly drive collective cancer invasion through MYO10 upregulation in epigenetically permissive leader cells, which induces filopodia dynamics necessary for linearized fibronectin micropatterning.

overall_design: Using the H1299 NSCLC cell line, parental cells, follower cells, and leader cells were isolated from collectively invading spheroids in Matrigel as previously described (Konen et al., Nat Comm, 2017; doi: 10.1038/ncomms15078). DNA methylation status was assessed in triplicate samples of H1299 parental, leader and follower cells. Bisulphite converted DNA from the 9 samples were hybridized to the Illumina Infinium MethylationEPIC array.

first: Janna

middle: K

last: Mouw

first: Joshua

last: Bell

first: Christina

last: Knippler

first: Brian

last: Pedro

first: Jamie

last: Arnst

first: Tala

middle: O

last: Khatib

first: Rachel

last: Commander

first: Benjamin

middle: G

last: Barwick

last: Konen

first: Bhakti

last: Dwivedi

first: Sandra

last: Seby

first: Jeanne

last: Kowalski

first: Paula

last: Vertino

first: Adam

middle: I

last: Marcus


title: Host transcriptional response to porcine reproductive and respiratory syndrome virus persistent infection

city: Lincoln

first: Jean-Jack

middle: M.

last: Riethoven

state: NE

address: 1901 Vine Street

department: Beadle Center for Biotechnology

institute: University of Nebraska-Lincoln

summary: Both virulent and live-attenuated PRRSV strains can establish persistent infection in lymphoid tissues of pigs. To investigate the mechanisms of PRRSV persistence, we performed transcriptional analysis of inguinal lymphoid tissue of pigs experimentally infected with an attenuated PRRSV strain. A total of 6,404 differentially expressed genes (DEGs) were detected of which 3,690 DEGs were upregulated and 2,444 DEGs were downregulated. Specifically, genes involved in innate immune responses and chemokine and receptors associated with T cell homing to lymphoid tissues were down regulated. As a result, homing of virus-specific T cells to lymphoid tissues seems to be ineffective, evidenced by the lower frequencies of virus-specific T cells in lymphoid tissue than in peripheral blood. Genes associated with T cells exhaustion were upregulated. Likewise, genes involved in the anti-apoptotic pathway were upregulated. Collectively, the data suggested that PRRSV establishes a pro-survival microenvironment in lymphoid tissue by suppressing innate immune responses, T cell homing and preventing cell apoptosis.

overall_design: For both control (mock) and infected pigs the transcriptome of the lymphoid tissue was sequenced with five biological replicates each.

first: Jayeshbhai

last: Chaudhari

first: Chia

last: Liew

first: Aspen

last: Workman

middle: M

first: Davis

last: Steffen

first: Sarah

last: Sillman

first: Hiep

middle: X

last: Vu


title: RNA-seq in mouse CD8+ T cells cultured with medium with or without methionine

city: Ann Arbor

first: Yingjie

last: Bian

state: MI

address: 109 Zina Pitcher Pl

institute: University of Michigan

summary: Abnormal epigenetic patterns correlate with effector T cell malfunction in tumors. However, their causal link is unknown. Here, we show that tumor cells disrupt methionine metabolism in CD8+ T cells, thereby lowering intracellular methionine levels and the methyl donor S-adenosylmethionine (SAM), resulting in loss of H3K79me2. Consequently, loss of H3K79me2 impaired T cell immunity. Our work reveals a novel mechanistic connection between methionine metabolism, histone patterns, and T cell immunity in the tumor microenvironment.

overall_design: CD8+ T cells were cultured with fresh medium without methionine (fresh-), fresh medium with methionine (fresh+), B16F10 supernatants (Sup-), and B16F10 supernatants with methionine supplementation (Sup+) for 36h, quadruplicate per group.

first: Wei

last: Li

first: Weiping

last: Zou


title: Transcriptome analysis of brown fat in young or old mice in cold exposure

city: Los Angeles

first: Claudio

last: Villanueva

state: CA

address: 610 Charles E. Young Drive East Box 957239

department: Integrative Biology and Physiology

institute: UCLA

summary:
Purpose: We investigated the transcriptomic change in brown fat of young and old mice (wild type) through high-throughput RNA-sequencing (RNA-Seq) analysis when the mice were exposed to cold room or room temperatur.
Methods: We prepared 10 of young (3 months) mice and 9 of old (24 months) mice, and kept them in cold room (4°c) or room temperature (24°c) for 24 hours. Then, we sacrified mice and extracted RNA from brown fat tissue (BAT) for RNA-seq experiment.
Results: BAT of Young mice showed increased carbohydrate metabolism and glycolytic flux during cold exposure
Conclusions: The thermogenesis function of BAT is accelerated on cold exposure.

overall_design: Five young (3 months) male mice were exposed to cold room (4°c); five young male mice were exposed to room temperature (24°c); four old (24 months) male mice were expposed to cold room (4°c); five old male mice were exposed to room temperature. After 24 hours for exposure, mice were sacrificed and BAT was extracted from between the shoulder blades.


title: Cancer SLC43A2 alters T cell methionine metabolism and histone methylation

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

overall_design: Refer to individual Series


title: RNA-seq of Bacillus subtilis WT W168 treated with the amphotericin B (10 µg ml-1) compared to untreated control

city: Dresden

first: Thorsten

last: Mascher

address: Zellescherweg 20b

institute: TU Dresden

summary: To obtain global cellular response of Bacillus subtilis WT W168 when treated with amphotericin B, we performed RNA-seq experiments. For this, we added 10 µg ml-1 amphotericin B to logarithmic phase growing cells and harvested cells after 10 min exposure. Experiments were performed in triplicates and non-induced Bacillus subtilis WT W168 was used as reference condition.

sample_organism: Bacillus subtilis subsp. subtilis str. 168

overall_design: Examination of amphotericin B induced Bacillus subtilis WT cells compared to non-induced Bacillus subtilis WT cells

first: Ainhoa

last: Revilla-Guarinos


title: Prm2 deficiency triggers a Reactive Oxygen Species (ROS)-mediated destruction cascade during epididymal sperm maturation in mice

status: Public on Jul 29 2020

city: Madrid

first: Lena

last: Arévalo

state: Madrid

address: Avda. Puerta de Hierro, 18

department: Animal Reproduction

institute: INIA-CSIC

summary: Protamines are the safeguards of the paternal sperm genome. They replace most of the histones during spermiogenesis, resulting in DNA hypercondensation, thereby protecting its genome from environmental noxa. Impaired protamination has been linked to male infertility in mice and humans in many studies. Apart from impaired DNA integrity, protamine-deficient human and murine sperm show multiple secondary effects, including decreased motility and aberrant head morphology. In this study, we use a Prm2-deficient mouse model in combination with label-free quantitative proteomics to decipher the underlying molecular processes of these effects. We show that loss of the sperm`s antioxidant capacity, indicated by downregulation of key proteins like SOD1 and PRDX5, ultimately initiates an oxidative stress-mediated destruction cascade during epididymal sperm maturation. This is confirmed by an increased level of 8-OHdG in epididymal sperm, a biomarker for oxidative stress-mediated DNA damage. Prm2-deficient testicular sperm are not affected and initiate the proper development of blastocyst stage preimplantation embryos in vitro upon intracytoplasmic sperm injection (ICSI) into oocytes. Our results provide new insight into the role of Prm2 and its downstream molecular effects on sperm function and present an important contribution to the investigation of new treatment regimens for infertile men with impaired protamination.

overall_design: Testicular mRNA of wildtype, Prm2-deficient and Prm2-heterozygous mice

first: Simon

last: Schneider

first: Farhad

last: Shakeri

first: Christian

last: Trötschel

first: Alexander

last: Kruse

first: Andreas

last: Buness

first: Ansgar

last: Poetsch

first: Klaus

last: Steger

first: Hubert

last: Schorle


title: RNA-array in DOT1L knockout and wild type CD8+ T cells

summary:
Disruptor of telomeric silencing 1-like (DOT1L) is the specific and sole methyltransferase for H3K79. However, the role of Dot1l in T cells is not well determined. Here, used CD4-Cre/Dot1lflox/flox mice to specifically delete DOT1L in T cells. The genes characteristics were determined by RNA array and compared to wild type cells.
We used microarrays to detail the global gene expression in Dot1l knockout and wild type CD8+ T cells.

overall_design: Dot1l knockout or wild type CD8+ T cells were separated by the EasySep™ Mouse CD8+ T Cell Isolation Kit (STEMCELL Technologies Inc., Cambridge, MA, USA) in the peripheral and spleen of mice. The RNA was isolated by using Direct-zolTM RNA miniprep Plus kit (ZOMO research).


title: Comparison of transcriptome profiles of human embryo cultured in either closed or standard incubator

city: Chongqing

first: Jingyu

address: #64, Jintang street

institute: Chongqing Reproductive and Genetics Institute

type: Methylation profiling by high throughput sequencing

summary: Measuring transcriptomic profiles of human embryos cultured in time-lapse imaging (TLI) incubator and standard incubator (SI) is crucial for studying whether the closed culture system has a positive impact on embryos. Here we used RNA-sequencing (RNA-Seq) to characterize and compare the gene expression profiles of TLI and SI cultured 8-cell embryos with the same quality grade. A total of 580,952,620 fragments were sequenced for zygote, SI and TLI groups. The global transcriptomic profiles of embryos from TLI group were similar to SI group, with a high distinct to zygotes. However, wo also detected 539 genes showing differential expression between the TLI and SI group with false discovery rate (FDR) < 0.05. Using GO enrichment analysis, we found that the high expressed genes in SI tend to execute functions, including transcription, RNA splicing and DNA repair, and the high expressed genes in TLI were enriched in the cell differentiation and methyltransferase activity pathway. This study provides the first comparison between SI and TLI via transcriptome analysis, and will serve as a basis for assessing the safety of TLI application in assisted reproductive technology.

overall_design: In total, we analyzed the transcriptomes of 3 groups of embryos in human: zygote, standard and time-lapse monitoring incubators produced 8-cell embryos using RNA-Seq technology. Pools of 5 embryos in one sample, 3 replicates in each group.

first: J

middle: Y

first: G

middle: N

last: Huang


title: Bulk RNA-seq data to assess an improved zebrafish transcriptome annotation

status: Public on Jul 28 2020

city: Worcester

first: Nathan

middle: D.

last: Lawson

address: 364 Plantation Street

department: Molecular, Cell, and Cancer Biology

institute: University of Massachusetts Medical School

summary: oligo-dT and random primed RNA-seq libraries were used to test an improved annotation of the zebrafish transcriptome

overall_design: RNA-seq was performed on transgene-positive cells isolated by FACS


title: Evolutionary co-option of a Drosophila enhancer of the yellow gene through shared chromatin accessibility input

city: Planegg-Martinsried

first: Nicolas

last: Gompel

address: Grosshaderner Str. 2

department: Faculty of Biology

institute: Ludwig Maximilian University of Munich

summary: The diversity of forms in multicellular organisms originates largely from the spatial redeployment of genes expressed during development. Several scenarios explain the emergence of cis-regulatory elements that govern novel aspects of a gene expression pattern. One scenario, enhancer co-option, holds that a DNA sequence producing an ancestral regulatory activity also becomes the template for a new regulatory activity and shares regulatory information. While enhancer co-option might fuel morphological diversification, it has rarely been documented and the regulatory mechanisms underlying this evolutionary process are elusive. Here we show how a novel enhancer of the Drosophila pigmentation gene yellow, the spot enhancer, has co-opted the ancestral wing blade enhancer. We mapped the sequences driving each regulatory activity, ancestral and derived, and identified a shared core element necessary for DNA accessibility in this regulatory region. Our results suggest a model where a new enhancer emerges by co-opting accessibility information intrinsic to an older enhancer, and gaining transcription factor binding sites that diversify its spatial activity.

overall_design: Using DNA accessibility profiling to assess the effect caused by a particular mutation on the cis-regulatory region

first: Liucong

last: Ling

first: Yaqun

last: Xin


title: Effect of Particulate Matter (PM10) on innate immunity upon H5N1 infection

city: Bhopal

first: Himanshu

last: Kumar

state: MADHYA PRADESH

address: Indore bypass road

department: Biological Sciences

country: India

institute: IISER Bhopal

summary: Comparative transcriptomic analysis of A549 cell after H5N1 infection alone and H5N1 infection with PM10 exposure respectively

overall_design: We exposed cells with PM10 and infected with H5N1 virus in one group of cells and in other group of cells were infected with H5N1 virus alone, total RNA was isolated and whole transcriptomic sequencing was done.

first: Richa

last: Mishra


title: Non-neuronal expression of SARS-CoV-2 entry genes in the olfactory system suggests mechanisms underlying COVID-19-associated anosmia (scRNA-seq: olfactory bulb)

first: David

last: Brann

overall_design: Two 15 min Drop-seq runs from a single dissociation of the olfactory bulbs were obtained from 2 mice. Two such dissociations were performed, giving 4 total replicates. Additional Drop-Seq data from the olfactory mucosa can be found in GSE151346.

first: Tatsuya

last: Tsukahara

first: Sandeep

last: Datta


title: FUS-mediated dysregulation of Sema5a, an autism-related gene, in FUS mice with hippocampus-dependent cognitive deficits

city: Singapore

first: Shuo-Chien

state: Singapore

address: 12 Science Drive 2, MD1, 16-03-H

department: Physiology

country: Singapore

institute: National University of Singapore

summary: Pathological FUS inclusions are found in 10% of patients with frontotemporal dementia (FTD) and those with amyotrophic lateral sclerosis (ALS) carrying FUS mutations. Current work indicates that FUS mutations may incur gain-of-toxic functions to drive ALS pathogenesis. However, how FUS dysfunction may affect cognition remains elusive.  Using a mouse model expressing wild-type human FUS mimicking the endogenous expression pattern and level within the central nervous system, we found that they developed hippocampus-mediated cognitive deficits accompanied by an age-dependent reduction in spine density and long-term potentiation (LTP) in their hippocampus. However, there were no apparent FUS aggregates, nuclear envelope defects and cytosolic FUS accumulation. These suggest that these proposed pathogenic mechanisms may not be the underlying causes for the observed cognitive deficits. Unbiased transcriptomic analysis identified expression changes in a small set of genes with preferential expression in the neurons and oligodendrocyte lineage cells. Of these, we focused on Sema5a, a gene involved in axon guidance, spine dynamics, Parkinson’s disease and autism spectrum disorders. Critically, FUS binds directly to Sema5a mRNA and regulates Sema5a expression in a FUS-dose-dependent manner. Taken together, our data suggest that FUS-driven Sema5a deregulation may underlie the cognitive deficits in FUS transgenic mice.

overall_design: Differential gene expression analysis of 12-month-old prnp-hFUSWT mice hippocampus

first: Yun

last: Wan

first: Jer-Cherng

last: Chang

first: Sheue-Houy

last: Tyan

first: Yi-Chun

last: Yen

first: Kenneth

last: Lim

first: Bernice

last: Tan

first: Jolynn

last: Ong

first: Greg

last: Tucker-Kellogg

first: Peiyan

last: Wong

first: Edward

last: Koo


title: Cell type- and replication stage-specific influenza virus responses in vivo

status: Public on Jul 24 2020

city: MINNEAPOLIS

first: Ryan

last: Langlois

institute: University of Minnesota

summary: We used two different influenza viruses lacking either PB1 or HA to differentiate the antiviral responses generated from primary transcription and full replication, respectively.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: We infected mice with influenza viruses lacking either PB1 or HA  and sorted out AT-I, AT-II and ciliated epithelial cells. We also used wt A549 cells, non targeting control A549 cells and A549 cells deficient in RIG-I, MAVS and MDA5. We primariy used polyA based transcriptomics but also did a time course in A549s for both positive and negative sense influenza virus RNA.

first: Elizabeth

middle: J

last: Fay

first: Stephanie

last: Aron

first: Marissa

last: Macchietto

first: Matthew

middle: W

last: Markman

first: Michael

last: Gale Jr

first: Steven

last: Shen

middle: A


title: Understanding seasonal weight loss tolerance in dairy goats: a transcriptomics approach

city: Lisboa

first: Andre

middle: Martinho

last: de Almeida

address: Tapada da Ajuda

department: DCEB

country: Portugal

institute: Instituto Superior de Agronomia / University of Lisbon

summary:
Seasonal weight loss is one of the most important limitations to ruminant production in drought-prone regions. In these regions and under the dry season, animals may lose up to 30% of their body weight, conditioning production performance. It is of the utmost importance to understand the physiological basis of tolerance to SWL, particularly by contrasting breeds that are susceptible and tolerant to SWL.
In this study, transcriptomics was used to describe the gene expression effects of feed restriction in dairy goat of two breeds with different SWL tolerance: Majorera (tolerant) and Palmera (susceptible). Two control and two restricted groups per breed were established: Majorera Control (adequately fed; MC; n=4), Palmera Control (adequately fed; PC; n=6), Majorera Restricted (feed restricted; ME; n=5) and Palmera Restricted (feed restricted; PE; n=4). On day 22 of the trial, mammary gland biopsies were collected for transcriptomics analysis. Results were obtained using Next Generation RNA sequencing and validation using qPCR.

overall_design: Twelve mRNA libraries were constructed, 3 biological replicates per group were created. Comparison between control vs. underfed groups. The groups are MC – Majorera Control; PC – Palmera Control; ME – Majorera Restricted; PE – Palmera Restricted

first: André

last: Almeida

first: José

last: Parreira

first: Susana

middle: S

last: Araújo

first: Noemi

last: Castro

first: Anastasio

last: Arguello

first: Juan

last: Capote

first: Lorenzo

last: Hernandez-Castellano


title: Transcriptome response of metallicolous and a non-metallicolous ecotypes of Noccaea goesingensis to nickel excess

status: Public on Jul 25 2020

city: Kraków

first: Agnieszka

middle: Małgorzata

last: Domka

address: Gronostajowa 7a

department: Małopolska Centre of Biotechnology

country: Poland

institute: Jagiellonian University

summary: Root transcriptomic profile was comparatively studied in a serpentine (TM) and a non-metallicolous (NTM) population of Noccaea goesingensis in order to investigate possible features of Ni hyperaccumulation. The exposure to Ni altered the expression of 403 and 534 probe sets in roots of NTM and TM ecotypes respectively. Only 19 genes were commonly regulated in roots of both ecotypes.

overall_design: Plants of non-metallicolous population (NTM) and from serpentinite area (TM) were grown in control media and under Ni exposure. The treatment with Ni lasted three weeks, after this time plants were harvested and weighed. 15 plants from each experimental group were frozen in liquid nitrogen for RNA extraction. Total RNA Mini Kit (Bio-Rad, USA) was used for total RNA extraction from roots (from 5 plants per sample). Sequencing was conducted with the use of Ion PI Hi‐Q Sequencing 200 Kit (ThermoFisher Scientific, USA) and Ion PI Chip Kit v3 (ThermoFisher Scientific, USA) on the Ion Proton System (ThermoFisher Scientific, USA) according to standard protocol provided by the manufacturer.

first: Piotr

last: Rozpądek

first: Rafał

last: Ważny


title: Genome-wide maps of ZCWPW1 in HEK293T cells with or without PRDM9, plus DMC1 ChIP-seq in ZCWPW1 KO mouse

city: Oxford

first: Simon

last: Myers

address: Roosevelt Drive

department: Wellcome Center for Human Genetics

country: United Kingdom

institute: University of Oxford

summary: During meiosis, homologous chromosomes pair (synapse) and recombine, enabling balanced segregation and generating genetic diversity. In many vertebrates, recombination initiates with double-strand breaks (DSBs) within hotspots where PRDM9 binds, and deposits H3K4me3 and H3K36me3. However, no protein(s) recognising this unique combination of histone marks have yet been identified.  We identified Zcwpw1, which possesses H3K4me3 and H3K36me3 recognition domains, as highly co-expressed with Prdm9. In this study we used ChIP-sequencing in human HEK293T cells (co)-transfected with HA tagged ZCWPW1 (and human or chimp PRDM9). This enabled us to determine that PRDM9 causes the recruitment of ZCWPW1 to its binding sites, and to determine the general binding properties of ZCWPW1 including a preference for CpG sites. We also performed SSDS ChIP-sequencing of mice testis that are homozygous KO for ZCWPW1, revealing that double strand breaks occour at completely normal positions in the ZCWPW1 KO, but with persistant DMC1 at many hotspots, particularly those more strongly bound by PRDM9.

overall_design:
ChIP-sequencing of HA-tagged ZCWPW1 in HEK293T cells (either alone or with co-transfection of either human or chimp PRDM9). Additionally SSDS DMC1 ChIP-sequencing in ZCWPW1 KO mice testis

***Please note that the series includes re-analysis of GSE99407 (Mapping PRDM9 binding and its effects in transfected HEK293T cells).
The 'GSE99407_re-processed_readme.xls' includes the source of the sequence data accession numbers (GSMnnnn/SRRnnnn) and the re-analysis data processing details/output.
The re-processed 'SingleBasePeaks.NA15* and ForceCalledPeaks_NA15* bed.gz' files are linked as Series supplementary files.

first: Daniel

last: Wells

first: Emmanuelle

last: Bitoun

first: Daniela

last: Moralli

first: Gang

last: Zhang

first: Anjali

last: Hinch

first: Peter

last: Donnelly

first: Catherine

last: Green

middle: R


title: Landscape of Cohesin-Mediated Chromatin Loops in the Human Genome (RNA-Seq)

status: Public on Jul 23 2020

city: Stanford

first: Fabian

last: Grubert

address: 300 Pasteur Drive

institute: Stanford University

summary: Physical interactions between distal regulatory elements in the genome play a key role in regulating gene expression, yet the extent to which these interactions vary between cell types and contribute to cell type-specific gene expression patterns remains unclear. To address this question we have mapped cohesin-bound chromatin loops in 24 diverse human cell types at high resolution using the chromatin interaction analysis by paired-end tag (ChIA-PET) sequencing approach. We combined a total of ~9.6 billion reads across all samples to generate a compendium of 124,830 loops, the most extensive resource currently available. We find that 39% of all chromatin loops vary across cell types, and such changes are effective at grouping cell types based on their tissue of origin, indicating commonalities in three-dimensional (3D) genome architecture amongst related cell types. In contrast, different cell types derived from the same individual show markedly different patterns of interactions indicating that the observed differences are mainly caused by epigenetic changes. Variation in chromatin loops correlates with changes in gene expression, especially for long-range contacts linking cell type-specific enhancers to promoters; moreover, genes contained within the same loop show coordinated co-expression changes in expression across cell types. We further find that loops specific to either blood or embryonic cell lines harbor distinct sets of genes relevant to cell type-specific function, and are enriched for lineage determining transcription factors, indicating a possible mechanism for the assembly of variable loops. Finally, we demonstrate that genetic variants identified in GWAS are enriched in variable loops in disease relevant cell types. Our results provide important insights in how changes in 3D chromatin organization potentially regulate cell type-specific functions.

overall_design: To identify chromatin loops which vary in interaction frequency across cell lines we mapped cohesin (Rad21)-mediated loops in 24 different cell lines. These cell lines span both primary and cancer cell lines from a variety of tissues, and more over span all three germ layers. We further generated both RNA and H3K27ac data in 22 out of 24 cell lines to study the interplay between looping, enhancer activity, and gene expression.

first: Rohith

last: Srivas

first: Damek

middle: V

last: Spacek

first: Maya

last: Kasowski

first: Marian

last: Velasco

first: Nasa

last: Sinnott-Armstrong

first: Peyton

last: Greenside

first: Anil

last: Narasimha

first: Qing

last: Liu

first: Benjamin

last: Geller

first: Akshay

last: Sanghi

first: Michael

last: Kulik

first: Silin

last: Sa

first: Marlene

last: Rabinovitch

first: Anshul

last: Kundaje

first: Stephen

last: Dalton

first: Judith

last: Zaugg

middle: P

last: Snyder


title: Landscape of Cohesin-Mediated Chromatin Loops in the Human Genome

first: Fabian

last: Grubert


title: In vivo antiviral host response to SARS-CoV-2 by viral load, sex, and age [dataset III]

status: Public on Jul 21 2020

city: Seattle

first: Nicole

middle: A P

last: Lieberman

state: WA

address: 850 Republican St S130

department: Laboratory Medicine

institute: University of Washington

summary: We examined host gene expression as a function of time in SARS-CoV-2-infected individuals.

overall_design:
Examination of differential expression of host genes during SARS-CoV-2 infection
Submitter declares that the raw data have not been submitted due to patient privacy concerns and the University of Washington IRB's strict prohibitions.

first: Alex

last: Greninger


title: In vivo antiviral host response to SARS-CoV-2 by viral load, sex, and age [dataset II]

summary: We examined host gene expression in human airway epithelial cells following infection at 3 or 7 days post infection (DPI) with SARS-CoV-2

overall_design:
Examination of differential expression of host genes in response to SARS-CoV-2 infection
Submitter declares that the raw data have not been submitted due to patient privacy concerns and the University of Washington IRB's strict prohibitions.


title: Massively parallel and time-resolved RNA sequencing in single cells with scNT-Seq

city: Philadelphia

first: Peng

last: Hu

state: PA

address: 415 Curie Blvd, 545 CRB

department: Genetics

institute: University of Pennsylvanian

summary: Single-cell RNA sequencing offers snapshots of whole transcriptomes but obscures the temporal RNA dynamics. Here we present single-cell metabolically labeled new RNA tagging sequencing (scNT-Seq), a method for massively parallel analysis of newly-transcribed and pre-existing mRNAs from the same cell. This droplet microfluidics-based method enables high-throughput chemical conversion on barcoded beads, efficiently marking newly-transcribed mRNAs with T-to-C substitutions. With scNT-Seq, we jointly profiled new and old transcriptomes in ~55,000 single cells. These data revealed time-resolved transcription factor activities and cell state trajectories at single-cell level in response to neuronal activation. We further determined rates of RNA biogenesis and decay to uncover RNA regulatory strategies during stepwise conversion between pluripotent and rare totipotent two-cell-embryo-like (2C-like) stem cell states. Finally, integrating scNT-Seq with genetic perturbation identifies DNA methylcytosine dioxygenases as an epigenetic barrier into 2C-like cell state. Time-resolved single-cell transcriptomic analysis thus opens new lines of inquiry regarding cell-type-specific RNA regulatory mechanisms.

overall_design: Single-cell metabolically labeled new RNA tagging sequencing

first: Qi

last: Qiu

first: Xiaojie

first: Kiya

last: Govek

first: Pablo

last: Gonzalez-Camara

first: Hao

last: Wu


title: The Human Integrator Complex Facilitates Transcriptional Elongation by Endonucleolytic Cleavage of Nascent Transcripts

city: Miami

first: Felipe

last: Beckedorff

state: FL

address: 1501 NW 10th Avenue room 731.G , Miami, FL

institute: University of Miami

summary: Transcription by RNA polymerase II (RNAPII) is pervasive in the human genome. However, the mechanisms controlling transcription at promoters and enhancers remain enigmatic. Here, we demonstrate that Integrator subunit 11 (INTS11), the catalytic subunit of the Integrator complex, regulates transcription at these loci through its endonuclease activity. Promoters of genes require INTS11 to cleave nascent transcripts associated with paused RNAPII and induce their premature termination in the proximity of the +1 nucleosome. The turnover of RNAPII permits the subsequent recruitment of an elongation-competent RNAPII complex, leading to productive elongation. In contrast, enhancers require INTS11 catalysis not to evict paused RNAPII but rather to terminate enhancer RNA transcription beyond the +1 nucleosome. These findings are supported by the differential occupancy of negative elongation factor (NELF), SPT5, and tyrosine-1-phosphorylated RNAPII. This study elucidates the role of Integrator in mediating transcriptional elongation at human promoters through the endonucleolytic cleavage of nascent transcripts and the dynamic turnover of RNAPII.

overall_design: Pro-seq of INTS11-depleted or control in  HeLa sshINTS11, shGFP, WT and E203Q mutant INTS11 cells in duplicates.

first: Ezra

last: Blumenthal

first: Lucas

last: Ferreira daSilva

first: Yuki

last: Aoi

first: Pradeep

last: Cingaram

first: Jingyin

last: Yue

first: Anda

last: Zhang

first: Sadat

last: Dokaneheifard

first: Monica

middle: G

last: Valencia

first: Gabriel

last: Gaidosh

first: Ali

last: Shilatifard

first: Ramin

last: Shiekhattar


title: Expression data from KYSE-150-shCtrl and KYSE-150-shCDKL3 cells

city: Linhai

first: suna

last: zhou

state: zhejiang

address: No. 150 Ximen Street

institute: The Affiliated Taizhou Hospital, Wenzhou Medical University

summary:
ESCC tumor tissues possessed a significantly higher expression of CDKL3 than matched adjacent normal tissues. CDKL3 acts as a new oncogene in ESCC cell line TE-1. However, the molecular mechanisms and biological effects of CDKL3 in esophageal squamous cell carcinoma (ESCC) remain unknown.
We used microarrays to elucidate the molecular mechanisms through which CDKL3 promotes the proliferation of ESCC cancer cells.

overall_design: KYSE-150 cells at the logarithmic growth phase were transfected with the recombinant lentiviral vector (LV) named as KD (KYSE-150-shCDKL3 cells) labeled with green fluorescent or NC(KYSE-150-shCtrl) labeled with green fluorescent. We analyzed the gene expression profiles of 3 pairs of KYSE-150-shCtrl and KYSE-150-shCDKL3 cells by GeneChip® PrimeView™ Human Gene Expression Array.

first: Suna

last: Zhou


title: In vivo antiviral host response to SARS-CoV-2 by viral load, sex, and age

first: Nicole

last: Lieberman

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

overall_design: Refer to individual Series


title: DNA Binding Signatures of the Myocyte Enhancer Factor-2B

city: Los Angeles

first: Remo

last: Rohs

address: 1050 Childs Way

department: Molecular and Computational Biology

institute: University of Southern California

summary: DNA binding function of the myocyte enhancer factor-2B (MEF2B) is achieved through its unique capability of binding to target sites with a degenerate motif, while still functioning as a gene-specific transcriptional regulator. MEF2B-DNA recognition likely involves elements beyond the sequence of letters, aspects that are crucial to understand, particularly given recent evidence suggesting MEF2B regulatory role across a number of tissues and involvement with B-cell lymphoma. By coupling structural information, SELEX-seq and computational analysis, we were able to deduce sequence and shape determinants of MEF2B target sites at a high-throughput scale in vitro, based on which modeling binding affinities further exposed sequence-dependent shape patterns. The resulting binding signature of MEF2B reveals intricacies of DNA recognition mechanisms that, different from other TFs, sets it as a unique TF that combines base readout at the edges and shape readout at the center of its degenerate core-binding site.

overall_design: SELEX-seq was performed for the transcription factor MEF2B according to as described in Dantas et al. (to be submitted). Briefly, a DNA library 5’-GAGTTCTACAGTCCGACGATCCGC[N16]CCTGGAATTCTCGGGTGCCA-3’ , containing fixed sites and a random region of 16 base pairs (bp) (N16) was used in a binding reaction. Bound fragments were separated by electrophoretic mobility assay (EMSA), followed by isolation of DNA fragments and amplification by PCR. Two rounds of selection were performed. Final sequencing libraries were prepared using a 4-cycle PCR.

first: Lin

last: Chen

first: Ana Carolina

last: Dantas Machado

first: Xiao

last: Lei

first: Brendon

last: Cooper


title: Cytokines gene signatures on primary human cells

status: Public on Jul 18 2020

city: Brussels

first: Grégoire

last: de Streel

state: Woluwe-Saint-Lambert

address: 75 Avenue Hippocrate

department: de Duve Institute

country: Belgium

institute: UCLOUVAIN

summary: We derived gene set signature for GSEA investigation study from primary cell culture derived from healthy patients. Cells were exposed or not to cytokine for 24H before RNA collection and microarray analysis

overall_design: IFNg, TNFa, IL-1b and TGFb gene signatures were established on primary culture of keratinocytes, endothelial cells, fibroblasts and melanocytes by incubating cells for 24h in presence of either IFNg, TNFa, IL-1b, TGFb or without cytokine

first: Nicolas

last: Van Baren

first: Marjorie

last: Mercier

first: Francis

last: Brasseur


title: Simple inheritance, complex regulation: supergene-mediated fire ant social polymorphism

city: Griffin

first: Brendan

middle: G.

last: Hunt

address: 125 Redding Building, Griffin Campus, 1109 Experiment Street

department: Entomology

institute: University of Georgia

summary: Using an organ-specific RNA-sequencing approach, we explore the role of supergene genotype and social environment on unmated, reproductive females Solenopsis invicta ants as they depart on their mating flights.

overall_design: Quantification of gene expression in gynes from monogyne and polygyne colonies and of all possible supergene genotypes.

first: Kenneth

last: Ross


title: RNA sequencing of primary mouse ileal organoids treated with bile acid pools with various compositions

status: Public on Jul 19 2020

city: New York

first: Rebecca

last: Haeusler

state: NY

address: 1150 Saint Nicholas Ave Room 303A

department: Pathology and Cell Biology

institute: Columbia University

summary: Bile acids act as ligands for several nuclear receptors expressed in the small intestine, especially the terminal ileum. Bile acid pool composition can be influenced by health and disease states. Here, we used RNA-seq to investigate the effects of altering bile acid pool composition on gene expression in ileal organoids.

overall_design: Primary mouse ileal organoids were treated with vehicle or a designer bile acid pool for 24h. 4 distinct bile acid pools were used, which varied based on the species we modeled (human or mouse) and the proportion of 12a-hydroxylated bile acids (10% or 90%). 3 samples from each treatment group were submitted for RNA sequencing.

first: Tiara

last: Ahmad


title: Modulating the transcriptional landscape of SARS-CoV-2 as an effective method for developing antiviral compounds

status: Public on Jul 17 2020

first: Avi

last: Ma'ayan

address: One Gustave L. Levy Place, Box 1603

department: Pharmacological Sciences

institute: Icahn School of Medicine at Mount Sinai

summary: The pandemic of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has imposed a significant burden on the human population. To understand the virus and the disease it causes we sought to interfere with the transcriptional response of the infected host. Utilizing the expression pattern of SARS-CoV-2-infected cells, we identified a region in gene expression space that was unique to virus infection and inversely proportional to the transcriptional footprint of known compounds characterized in the Library of Integrated Network-based Cellular Signatures (LINCS). Here we demonstrate the successful identification of compounds that display efficacy in blocking SARS-CoV-2 replication based on their ability to counteract the virus-induced transcriptional landscape.  These compounds were found to potently reduce viral load despite having no impact on viral entry or modulation of the host antiviral response in the absence of virus. RNA-Seq profiling implicated the induction of the cholesterol biosynthesis pathway as the underlying mechanism of inhibition and suggested that targeting this aspect of host biology may significantly reduce SARS-CoV-2 viral load.

overall_design: Independent biological triplicates of transformed lung alveolar (A549) transduced with a vector expressing human ACE2, or pancreatic organoids created from hESCs, were mock treated or infected with SARS-CoV-2 (USA-WA1/2020) with or without DMSO, berbamine, terfenadine, loperamide, trifluoperazine, amlodipine, and RS-504393. The drugs were applied at 10uM.

first: Daisy

last: Hoagland

first: Benjamin

last: tenOever


title: Master stress response gene ATF4 & other oncogenes are translated by DENR-dependent reinitiation

city: Heidelberg

first: Jonathan

last: Bohlen

address: Im Neuenheimer Feld 581

institute: DKFZ

summary: Translation efficiency varies 1000-fold between different mRNAs, thereby strongly impacting protein expression. Translation of the master stress response gene ATF4 increases in response to stress, but the molecular mechanisms are not well understood. We discover here that translation initiation factors DENR, MCTS1 and eIF2D are absolutely required to induce ATF4 translation upon stress, by promoting translation reinitiation on the ATF4 5’UTR. Hence DENR and MCTS1 are important players in the cellular Integrated Stress Response. We find DENR and MCTS1 promote reinitiation after long uORFs with specific penultimate codons, due to the tRNA that remains attached to 40S ribosomes after translation termination. This provides a model for how DENR and MCTS1 promote translation reinitiation. Since cancer cells are exposed to many stresses, they require ATF4 for survival and proliferation. We find a strong correlation between DENR•MCTS1 expression and ATF4 activity across cancers. Additional oncogenes including a-Raf, c-Raf and Cdk4 have long uORFs and are translated in a DENR•MCTS1 dependent manner. This explains in part why DENR and MCTS1 are oncogenes.

overall_design: We created a DENR KO Hela Cell line and carried out ribosome footprinting to determine translational targets of the DENR-MCTS1 complex.

first: Aurelio

last: Teleman


first: Felipe

last: Beckedorff

overall_design:
ChIP-seq of RNAPII and INTS11 in INTS11-depleted in HeLa shINTS11 cells in duplicates.
ATAC-seq in HeLa shINTS11 cells in duplicates.
Total RNA-seq of INTS11-depleted in  HeLa shINTS11 cells in duplicates.
small RNA-seq INTS11-depleted or control in  HeLa shINTS11, shGFP, WT and E203Q mutant INTS11 cells in duplicates.
CAGE-seq control in  HeLa shGFP cells in duplicates.
ChIP-seq of RNAPII and INTS11 in INTS11-depleted in HeLa shINTS11 cells in duplicates.
ATAC-seq in HeLa shINTS11 cells in duplicates.
Total RNA-seq of INTS11-depleted in  HeLa shINTS11 cells in duplicates.
small RNA-seq INTS11-depleted or control in  HeLa shINTS11, shGFP, WT and E203Q mutant INTS11 cells in duplicates.
CAGE-seq control in  HeLa shGFP cells in duplicates.

first: Ezra

last: Blumenthal

first: Lucas

last: Ferreira Da Silva

first: Yuki

last: Aoi

first: Pradeep

last: Cingaram

first: Jingyin

last: Yue

first: Anda

last: Zhang

first: Sadat

last: Dokaneheifard

first: Monica

last: Valencia

first: Gabriel

last: Gaidosh

first: Ali

last: Shilatifard

first: Ramin

last: Shiekhattar


title: Modeling SHH-driven medulloblastoma with patient iPS cell-derived neural stem cells

status: Public on Jul 16 2020

city: Stockholm

first: Margareta

last: Wilhelm

address: Nobels väg 16

department: Microbiology, Tumor and Cell biology (MTC)

country: Sweden

institute: Karolinska Institutet

summary: Medulloblastoma is the most common malignant brain tumor in children. Here we describe a medulloblastoma model  using  iPS  cell-derived  human  neuroepithelial  stem  (NES)  cells generated from a Gorlin syndrome patient carrying a germline mutation in the Sonic hedgehog (SHH) receptor PTCH1. We found that Gorlin NES cells formed tumors in mouse cerebellum mimicking human medulloblastoma. Re-transplantation of tumor-isolated NES (tNES) cells resulted in accelerated tumor formation, cells with reduced growth factor  dependency, enhanced neurosphere formation in vitro, and increased sensitivity to Vismodegib. Using our model we identified LGALS1 to be a GLI target gene that is upregulated in both Gorlin tNES cells and SHH-subgroup of  medulloblastoma patients. Taken together, we demonstrate that NES cells derived from Gorlin patients can be used as a resource to model medulloblastoma initiation and progression, and to identify novel putative targets.

overall_design: Examination of RNA expression in parental cells and cells derived from 3 primary tumors and 3 secondary tumors.

first: Evelyn

last: Susanto

first: Anders

last: Sundström


title: Role of  EI24 in ESCC cells

status: Public on Jul 15 2020

city: Xi'an

first: Lili

last: Duan

state: Shaanxi

address: 169 Changle West Road

institute: Fourth military medical university


title: Expression data from EI24 overexpression in ESCC cells

summary:
Analysis of EC109 cells following overexpression of EI24 and control vector. Etoposide induced 2.4 kb transcript (EI24), also known as p53-induced gene 8 (PIG8), is located on human chromosome 11q23. Serving as a p53 responsive pro-apoptotic factor, EI24 plays a pivotal role in inhibiting cell growth and activating autophagy and  is associated with drug resistance.
Results provide insight into the role of EI24 in cell proliferation and drug resistance of ESCC cells.

overall_design: To examine the cellular pathways that result from EI24 overexpression, we performed microarray expression analysis between the EI24-overexpression EC109 cell line and the empty virus control cell line. Their respective RNA was extracted for Affymetrix microarrays.

first: Duan

last: Lili

first: Hong

last: Liu


title: Expression data from EI24 knockdown in ESCC cells

summary:
Analysis of TE-1 cells following knockdown of EI24 and control vector. Etoposide induced 2.4 kb transcript (EI24), also known as p53-induced gene 8 (PIG8), is located on human chromosome 11q23. Serving as a p53 responsive pro-apoptotic factor, EI24 plays a pivotal role in inhibiting cell growth and activating autophagy and  is associated with drug resistance.
Results provide insight into the role of EI24 in cell proliferation and drug resistance of ESCC cells.

overall_design: To examine the cellular pathways that result from EI24 knockdown, we performed microarray expression analysis between the TE-1 cell line with CRISPR/Cas9 mediated deletion of EI24  and the empty virus control cell line. Their respective RNA was extracted for Affymetrix microarrays.


title: Whole transcriptome analysis of coding and non-coding RNAs associated with RBSDV infection in Laodelphax striatellus (Fallén) midgut

status: Public on Jul 22 2020

city: Jinan

first: jianhua

last: zhang

address: gongyebei street No. 23788

institute: Shandong Academy of Agricultural Sciences

summary: We report the application of whole transcriptome sequencing technology for high-throughput profiling of coding and non-coding RNAs associated with RBSDV infection in Laodelphax striatellus (Fallén) midgut. Over 20 and 21 million clean reads from virus free (VF) and RBSDV infected (RB) libraries were obtained, respectively. Q30 base percentages of each sequencing sample were no less than 93.89%. More than 50.37% of the clean reads were perfectly mapped to the L. striatellus genome. The uniquely mapping ratio was ranged from 48.03% to 52.08%. A total of 35,316 mRNAs and 13,927 novel lncRNAs were identified from VF and RB libraries. 169 mRNAs and 176 lncRNAs were differentially expressed during RBSDV infection. RNA-seq data had a linear relationship with qRT–PCR results. Our study represents the first detailed transcriptomes analysis of L. striatellus midgut during RBSDV infection, with biologic replicates, generated by RNA-seq technology. Our data contribute to the understanding of the function of coding and non-coding RNAs in the regulation of viral infection.

overall_design: Examination of mRNA, lncRNA and circRNAs associated with RBSDV infection in Laodelphax striatellus (Fallén) midgut.

first: Qiufang

last: Xu

first: Jianhua


title: Transcriptome profiling from Arabidopsis thaliana overexpressing Jatropha curcas ERFVII2

city: Chatuchak

first: Piyada

last: Juntawong

state: Bangkok

address: 50 Ngamwongwan rd.

country: Thailand

institute: Kasetsart University

summary: Gene expression analysis by high-throughtput RNA-sequencing from Arabidopsis seedlings (10 d.o.) overexpressing Jatropha curcas (Jc) ERFVII-2 in wildtype (MC) or stablized (MA) forms.

overall_design: 6 samples, 1 condition (aerobic) and 2 independent biological replicates


title: Hepatic transcriptomic alterations for bis(2-ethylhexyl) tetrabromophthalate (TBPH) after 5-day exposure in rats

city: RTP

first: Keith

last: Shockley

state: NC

address: 111 TW Alexander Drive

institute: NIEHS

summary:
To identify liver transcripts differentially expressed due to treatment with bis(2-ethylhexyl) tetrabromophthalate (TBPH), we collected RNA from male Harlan Sprague Dawley rats exposed to 0, 0.07, 0.71, 7.06, 70.6 or 706 mg/kg TBPH, 5 days after exposure for animals 7 weeks of age.  These samples were interrogated with the Affymetrix Rat Genome 230 2.0 GeneChip array.
A total of 0,0,0,0, and 0 gene transcripts were differentially expressed due to TBPH treatment after exposure to 0.07, 0.71, 7.06, 70.6 or 706 mg/kg TBPH (false discovery rate (FDR) < 0.05).

overall_design: There were 6 groups and 6x replication for each group, for 36 total samples. The groups were (1) TBPH-0mg/kg, (2) TBPH-0.07mg/kg, (3) TBPH-0.71mg/kg, TBPH-7.06mg/kg, TBPH-70.6mg/kg, and TBPH-706mg/kg. We compared vehicle control (0mg/kg) vs dose using the R/maanova package. The differentially expressed transcripts were identified based on a statistical significance threshold of FDR<5%.

first: June

middle: K

last: Dunnick


title: Hepatic transcriptomic alterations for tetrabromobisphenol A-bis(2,3-dibromopropyl ether)  (TBBPA-DBPE) after 5-day exposure in rats

summary:
To identify liver transcripts differentially expressed due to treatment with tetrabromobisphenol A-bis(2,3-dibromopropyl ether) (TBBPA-DBPE), we collected RNA from male Harlan Sprague Dawley rats exposed to 0, 0.1, 0.94, 9.4, 94.3 or 943 mg/kg TBBPA.DBPE, 5 days after exposure for animals 7 weeks of age.  These samples were interrogated with the Affymetrix Rat Genome 230 2.0 GeneChip array.
A total of 0,0,0,0,0, and 0 gene transcripts were differentially expressed due to TBBPA.DBPE treatment after exposure to 0.1, 0.94, 9.4, 94.3 or 943 mg/kg TBBPA.DBPE (false discovery rate (FDR) < 0.05).

overall_design: There were 6 groups and 6x replication for each group, for 36 total samples. The groups were (1) TBBPA.DBPE-0mg/kg, (2) TBBPA.DBPE-0.1mg/kg, (3) TBBPA.DBPE-0.94mg/kg, TBBPA.DBPE-9.4mg/kg, TBBPA.DBPE-94.3mg/kg, and TBBPA.DBPE-943mg/kg. We compared vehicle control (0mg/kg) vs dose using the R/maanova package. The differentially expressed transcripts were identified based on a statistical significance threshold of FDR<5%.


title: Hepatic transcriptomic alterations for polybrominated diphenyl ether 47 (PBDE47) after 5-day exposure in rats

summary:
To identify liver transcripts differentially expressed due to treatment with polybrominated diphenyl ether 47 (PBDE47), we collected RNA from male Harlan Sprague Dawley rats exposed to 0, 0.0485, 0.485, 4.85, 48.5 or 485 mg/kg PBDE47, 5 days after exposure for animals 7 weeks of age.  These samples were interrogated with the Affymetrix Rat Genome 230 2.0 GeneChip array.
A total of 44,28,111,999, and 3195 gene transcripts were differentially expressed due to PBDE47 treatment after exposure to 0.0485, 0.485, 4.85, 48.5 or 485 mg/kg PBDE47 (false discovery rate (FDR) < 0.05).

overall_design: There were 6 groups and 6x replication for each group, for 36 total samples. The groups were (1) PBDE47-0mg/kg, (2) PBDE47-0.0485mg/kg, (3) PBDE47-0.485mg/kg, PBDE47-4.85mg/kg, PBDE47-48.5mg/kg, and PBDE47-485mg/kg. We compared vehicle control (0mg/kg) vs dose using the R/maanova package. The differentially expressed transcripts were identified based on a statistical significance threshold of FDR<5%.


title: Hepatic transcriptomic alterations for hexachlorocyclopentadienyl-dibromocyclooctane  (HCDBCO) after 5-day exposure in rats

summary:
To identify liver transcripts differentially expressed due to treatment with hexachlorocyclopentadienyl-dibromocyclooctane (HCDBCO), we collected RNA from male Harlan Sprague Dawley rats exposed to 0, 0.05, 0.54, 5.41, 54.1 or 541 mg/kg HCDBCO, 5 days after exposure for animals 7 weeks of age.  These samples were interrogated with the Affymetrix Rat Genome 230 2.0 GeneChip array.
A total of 0,0,0,12, and 19 gene transcripts were differentially expressed due to HCDBCO treatment after exposure to 0.05, 0.54, 5.41, 54.1 or 541 mg/kg HCDBCO (false discovery rate (FDR) < 0.05).

overall_design: There were 6 groups and 6x replication for each group, for 36 total samples. The groups were (1) HCDBCO-0mg/kg, (2) HCDBCO-0.05mg/kg, (3) HCDBCO-0.54mg/kg, HCDBCO-5.41mg/kg, HCDBCO-54.1mg/kg, and HCDBCO-541mg/kg. We compared vehicle control (0mg/kg) vs dose using the R/maanova package. The differentially expressed transcripts were identified based on a statistical significance threshold of FDR<5%.