title: Transcriptome of two maize lines seedlings show resistance and susceptible to corn smut during infection of Ustilago maydis

status: Public on Apr 15 2021

city: Nanjing

first: Xinsen

last: Ruan

address: Weigang #1

institute: Nanjing Agricultural University

summary: The biotrophic fungal pathogen Ustilago maydis cause common smut in maize, and lead to gall formation on all aerial organs, especially on maize kernel thus reduce yield. The interaction of U. maydis with maize is a well-established model to study the interaction between maize and biotrophic pathogen. U. maydis infection could activate host immune responses including: ROS accumulation, protease activation, salicylic acid signaling. U. maydis employ several strategies to overcome maize immune response, thus initial the biotrophic interaction with host. It has been suggested that genetic factors of maize host affected the disease severity of U. maydis infection, here we investigated the transcriptome profile of resistance and susceptible maize lines upon U. maydis infection, thus propose candidate maize genes involved in the defense response in maize to corn smut cause by U. maydis.

overall_design: Maize 7 days seedlings of resistance CML326 and susceptible GEMS15 to U. maydis were inject with U. maydis at 1h before the light period as described above. Samples of the stem around inject site were collected at 0 hour (mock), 24 hours, 48 hours, and 96 hours post infection, and quickly frozen in liquid nitrogen. Three biological replicates were conducted, and six plants were sampled for each time point. Each subset of samples were pooled and ground in liquid nitrogen, and the RNA was extracted with TRIZOL (Invitrogen) followed the manufactory instruction. mRNA sequencing was performed with 150bp paired-end reads, approximately 24 million clean reads were obtained per sample.

first: Xiquan

last: Gao


title: ISR target genes in adipose of maP2-Fv2E-PERK

status: Public on Apr 01 2021

city: Tokushima

first: Masato

last: Miyake

state: Tokushima

address: 3-18-15 Kuramoto

department: Institute of Advanced Medical Sciences

country: Japan

institute: Tokushima university

summary: To identify the target genes of integrated stress reponse (ISR) in adipose tissue, we have employed whole genome microarray expression in adipose specific Fv2E-PERK transgenic mice.

overall_design: The mAP2-Fv2E-PERK transgenic mice were injected by AP20187 or mock.

first: M

first: S

last: Oyadomari


title: Identification of downstream effectors of retinoic acid specifying the zebrafish pancreas by integrative genomics [ChIP-seq]

status: Public on Mar 16 2021

city: Pamplona

first: Ana

middle: Rosa

last: López-Pérez

address: Calle Irunlarrea, 3

country: Spain

institute: Navarrabiomed - Fundacion Migues Servet

type: Expression profiling by high throughput sequencing

summary: Retinoic acid (RA) is a key signal for the specification of the pancreas. Still, the gene regulatory cascade triggered by RA in the endoderm remains poorly characterized. In this study, we investigated this regulatory network in zebrafish by combining RNA-seq, RAR ChIP-seq and ATAC-seq assays. By analysing the effect of RA and of the RA receptor (RAR) antagonist BMS439 on the transcriptome and on the chromatin accessibility of endodermal cells, we identified a large set of genes and regulatory regions regulated by RA signalling. RAR ChIP-seq further defined the direct RAR target genes including the known hox genes as well as several pancreatic regulators like mnx1, insm1b, hnf1ba and gata6. Comparison of our zebrafish data with available murine RAR ChIP-seq data highlighted conserved direct target genes and revealed that some RAR sites are under strong evolutionary constraints. Among them, a novel highly conserved RAR-induced enhancer was identified downstream of the HoxB locus and driving expression in the nervous system and in the gut in a RA-dependant manner. Finally, ATAC-seq data unveiled the role of the RAR-direct targets Hnf1ba and Gata6 in opening chromatin at many regulatory loci upon RA treatment.

overall_design: Combination of 12 ATAC-seq samples. Non endodermal cells and endodermal cells (sox17:GFP +) from zebrafish embryos at 3 somites stage treated with DMO (control), retionic acid and BMS493 (RA antagonist)  were generated in triplicates.

middle: R

first: Piotr

middle: J

last: Balwierz

first: Boris

last: Lenhard

first: Ferenc

last: Muller

first: Fiona

middle: C

last: Wardle

first: Isabelle

last: Manfroid

first: Marianne

middle: L

last: Voz

first: Bernard

last: Peers


title: Identification of downstream effectors of retinoic acid specifying the zebrafish pancreas by integrative genomics

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: UBB+1-induced activation of autophagy reduces cytotoxicity of amyloid-β in yeast

status: Public on Mar 12 2021

city: Göteborg

first: Xin

last: Chen

address: Kemigården 4

department: Department of Biology and Biological Engineering

country: Sweden

institute: Chalmers University of Technology

summary: UBB+1 is a mutated version of ubiquitin B caused by a transcriptional frameshift. The accumulation of UBB+1, has been linked to ubiquitin-proteasome system (UPS) dysfunction and neurodegeneration. Alzheimer’s disease (AD) is the most common form of neurodegeneration and accumulation of amyloid β (Aβ) in the brain is a prominent neuropathological feature of AD. In our previous study, we found that low expression of UBB+1 could protect cells against several stresses during chronological aging. Here, we applied the genome-wide expression analyses and found that low UBB+1 expression activated the autophagy pathway. Low UBB+1 expression was shown to upregulate vacuolar activity and promote transport of the ATG8p (autophagic marker) to the vacuole. To further study the effects, we expressed low level of UBB+1 in our humanized yeast Aβ models with the expression of either Aβ42 or Aβ40. Interestingly, the co-expression of UBB+1 with Aβ42 or Aβ40 showed a reduction of intracellular Aβ levels and increased chronological life span. In the autophagy deficient mutant background (atg1∆), the intracellular Aβ levels were not affected by UBB+1 expression. Our findings suggest a mechanism of UBB+1 action in reducing intracellular levels of Aβ.

platform_organism:
Schizosaccharomyces pombe
Saccharomyces cerevisiae

overall_design: The goal of the present study is to evaluate the impact of low expression level of UBB+1 on yeast physiology and transcriptome profiles following the growth phases. Saccharomyces cerevisiae expressing empty plasmid (control strain) and p413 TEF UBB+1 plasmid (LUBB+1 strain) respectively was cultivated in shake flask at 30℃. Samples were taken from duplicate cultures during exponential phase (EX) and day 6 (D6).

last: Muñoz-Arellano

first: Dina

last: Petranovic


title: Identification of downstream effectors of retinoic acid specifying the zebrafish pancreas by integrative genomics [ATAC-seq]


title: Transcriptional deregulation in subcutaneous adipose tissue from severely obese patients is associated with cancer: focus on gender differences and role of type 2 diabetes

status: Public on Mar 10 2021

city: Milan

first: Letizia

last: Messa

address: Piazza Leonardo Da Vinci 32

department: Electronics, Informatics and Bioengineering

country: Italy

institute: Politecnico di Milano

summary: Obesity is a major risk factor for a high number of secondary diseases, including cancer. Specific insights into the role of gender differences and secondary co-morbidities, such as type 2 diabetes (T2D) and cancer risk, are yet to be fully obtained. The aim of this study is thus to find a correlation between the transcriptional deregulation present in the subcutaneous adipose tissue of obese patients and the risk of cancer, in the presence of T2D, and considering gender differences. Through deep RNA-sequencing we highlighted the presence of both coding and non-coding deregulated RNAs, and we subsequently assessed their oncogenic risk. We correlated the oncogenes with anthropometrical parameters, highlighting significant trends. For each analysed condition we assessed the oncogenic pathways deregulated, the specific prognosis for different cancer types and the lncRNAs involvement in oncogenic networks and tissues. Our results provided a comprehensive characterization of oncogenesis correlation in subcutaneous adipose tissue, providing specific insights into the oncogenic prognosis for obese, diabetic or gender-specific differences. These results could shed light on new molecular targets to be specifically modulated in obesity and highlight which cancers should be most looked out for a better prevention in obesity affected patients.

overall_design: Biopsies of SAT collected from a total of 20 subjects: 5 healthy normal weight women (CTRL, age 37 ± 6.7 years, BMI 24.3 ± 0.9 kg/m2), 5 obese women (OBF, age 41 ± 12.5 years, BMI 38.2 ± 4.6 kg/m2), 5 obese women with T2D (OBT2D; age 54.6 ± 14.9 years, BMI 38.1 ± 11.8 kg/m2) and 5 obese men (OBM, age 42.4 ± 6.58 years, BMI 36.9 ± 3.5 kg/m2)

first: Federica

last: Rey

first: Cecilia

last: Pandini

first: Rossella

last: Launi

first: Giancarlo

last: Micheletto

first: Manuela

middle: T

last: Raimondi

first: Simona

last: Bertoli

first: Cristina

last: Cereda

first: Gian

middle: V

last: Zuccotti

first: Raffaella

last: Cancello

first: Stephana

last: Carelli


title: Targeting nuclear pore protein, NUP210, reduces metastasis through heterochromatin-mediated silencing of mechanosensitive genes

status: Public on Mar 05 2021

city: Bethesda

first: Maxwell

last: Lee

state: MD

address: Building 37, Room 5120

department: CCR

country: USA

institute: National Cancer Institute, NIH

summary: Mechanical signals from the extracellular microenvironment have been shown to promote tumor and metastasis progression. It remains unclear how these signals are transmitted to the nucleus to regulate gene expression necessary for metastatic progression. In a genome-wide screen for metastasis-associated polymorphism in the non-coding regulatory region of the genome, we found NUP210, a nuclear pore complex protein as a metastasis susceptibility gene and a cellular mechanosensor. Depletion of NUP210 in metastatic cancer cells significantly reduces lung metastasis in mouse orthotopic transplantation models. Mechanistically, NUP210 interacts with histone H3.1/3.2 (preferentially enriched at the poised/bivalent gene promoters) at the nuclear periphery. To investigate how NUP210 regulates metastasis, we performed combined ChIP-seq and RNA-seq analysis to identify the NUP210-dependent downstream signaling pathways necessary for metastatic progression. Interestingly, RNA-seq analysis revealed that the loss of NUP210 in cancer cells significantly decreased the expression of mechanosensitive, cell adhesion/migration-related pro-metastatic genes. ChIP-seq analysis of H3K4me3 (transcriptional activation mark) and H3K27me3 (transcriptionally repressive, heterochromatin mark) in NUP210 WT/KO cells revealed that NUP210 loss resulted in increased heterochromatinization of mechanosensitive, cell migration-related genes associated at the nuclear periphery. Our results provide a new insight into the role of nuclear pore protein in regulating cellular mechanosensation and metastasis.

overall_design: For RNA-seq, 4T1 cells were grown in tissue culture dishes. After 48 h of incubation, total RNA was isolated using RNeasy mini kit (Qiagen). On-column DNase I treatment was performed to eliminate genomic DNA contamination. For chromatin immunoprecipitation, 4T1 cells were cultured for 48h. Chromatin was prepared using ChIP-IT Express Enzymatic kit (Active Motif) according to manufacturer’s instructions.

first: Amin

last: Ruhul

first: Shukla

last: Anjali

first: Zhu

last: Jacqueline

first: Kim

last: Sohyoung

first: Wang

last: Ping

first: Tian

last: Simon

first: Cappell

last: Steven

first: Burkett

last: Sandra

first: Liu

last: Huaitian

first: Lee

last: Maxwell

first: Tran

last: Andy

first: Kruhlak

last: Michael

first: Hager

last: Gordon

first: Ruan

last: Yijun

first: Kent

last: Hunter


title: The NOTCH3 Downstream Target HEYL Is Required for Efficient Human Airway Basal Cell Differentiation [RNA-Seq]

status: Public on Mar 04 2021

city: Oklahoma City

first: Jonathan

last: Wren

state: OK

address: 825 N.E. 13th Street

department: Genes & Human Disease Research Program

institute: OMRF

summary: Basal cells (BC) are the resident stem/progenitor cells of the adult pseudostratified airway epithelium, whose differentiation program is orchestrated by the NOTCH signaling pathway. NOTCH3 receptor mediated signaling regulates BC to club cell differentiation; however, the downstream responses that regulate this process are largely unknown. In the present study we utilized an in vitro air-liquid interface model of the human pseudostratified airway epithelium to identify the NOTCH3-dependent downstream genes/pathways that regulate human BC to club cell differentiation. Activation of NOTCH3 signaling in BC via lentivirus-mediated over-expression of the active NOTCH3 intracellular domain (NICD3) promoted club cell differentiation. Bulk RNA-seq analysis of control vs NICD3 -transduced cells, identified 692 NICD3 responsive genes enriched for pathways linked to airway epithelial biology and differentiation including Wnt/β-catenin Signaling. Expression of the classical NOTCH target HEYL increased in response to NOTCH3 activation and positively correlated with the club cell marker SCGB1A1. Further, using single-cell RNA-seq, we report that HEYL+ cells primarily clustered with SCGB1A1+ and NOTCH3+ cells. Moreover, HEYL protein co-localized with SCGB1A1 in ALI cultures in vitro and in the human and mouse airway epithelium in vivo. siRNA-mediated knockdown of HEYL in BC led to changes in epithelial structure including altered morphology and significant reductions in transepithelial electrical resistance and expression of tight junction related genes. Finally, HEYL knockdown significantly reduced the number of SCGB1A1+ club cells, along with a corresponding increase in KRT8+ BC-intermediate cells. Overall, our data identifies NOTCH3-HEYL signaling as a key regulator of BC to club cell differentiation.

overall_design: mRNA profiling of primary human bronchial epithelial cells (HBECs) from nonsmokers infected with either Control (empty GFP vector) Lentivirus or Lentivirus expressing NICD3 cultured on air-liquid interface (ALI) for up to 7 days and harvested as a function of time (ALI day 0, 3, 5 and 7)

first: Matthew

middle: S

last: Walters


title: Transcriptional differentiation of Trypanosoma brucei during in vitro acquisition of resistance to acoziborole

status: Public on Mar 07 2021

city: Midlothian

first: Pieter

last: Steketee

address: Easter Bush Campus

department: Division of Infection and Immunity

country: United Kingdom

institute: Roslin Institute, University of Edinburgh

summary:
Purpose: Acoziborole is a recently developed benzoxaborole class compound, currently in clinical trials, for stage 1 and stage 2 treatment of Human African Trypanosomiasis. Recent studies have made significant progress in determining the molecular mode of action of acoziborole. However, less is known about the potential mechanisms leading to acoziborole resistance in trypanosomes. By characterising in vitro drug-resistance, this study aimed to gain a better understanding of the mechanisms involved in acoziborole resistance in the clinicaly relevant Trypanosoma brucei
Methods: Drug resistance was generated in vitro through incremental dosage of acoziborole. RNA was isolated from axenic cultures of drug-resistant and parental drug sensitive cells and submitted for RNA-seq
Results: Transcriptomics analysis revealed widepread downregulation of transcripts associated with mammalian-infective bloodstream-form parasites. Conversely, transcripts associated with insect-stage procyclic form parasites were increased, indicating that the resistant cells had undergone an unspecified "differentiation event", albeit on a transcriptomic level
Conclusions: Trypanosoma brucei resistance to acoziborole can be generated under in vitro axenic conditions, and "transcriptional differentiation" is a mechanism of resistance. However, it is unknown whether this phenomenon is relevant to an in vivo setting

overall_design: Acoziborole resistance generated in vitro by supplementation of incremental drug dosage. Comparison to wild-type parental control and wild-type control passaged in the absence of drug to account for long tem in vitro medium adaptation

first: Isabel

middle: M

last: Vincent

first: Fiona

last: Achcar

first: Nicholas

last: Dickens

first: Liam

last: Morrison

first: Annette

last: MacLeod

first: Michael

middle: P

last: Barrett


title: The NOTCH3 Downstream Target HEYL Is Required for Efficient Human Airway Basal Cell Differentiation [scRNA-Seq]

overall_design: scRNA profiling of primary human bronchial epithelial cells (HBECs) from nonsmokers cultured on air-liquid interface (ALI) for 9 days.


title: The NOTCH3 Downstream Target HEYL Is Required for Efficient Human Airway Basal Cell Differentiation


title: Endothelial TFEB improves glucose intolerance via upregulation of IRS1 and IRS2

status: Public on Mar 01 2021

city: ANN ARBOR

first: Jinjian

last: Sun

state: Michigan

address: 2415 LANCASHIRE DR APT 2B

institute: university of michigan

type: Non-coding RNA profiling by high throughput sequencing

summary: To determine whether endothelial TFEB is critical for glucose metabolism in vivo, we utilized EC-selective TFEB knockout  mice and EC selective TFEB transgenic mice fed a high fat diet (HFD). EC-TFEB knockout mice exhibited significantly impaired glucose tolerance compared with control mice. Consistently, EC-TFEB transgenic mice showed improved glucose intolerance. In primary human ECs, small interfering RNA-mediated TFEB knockdown blunts the Akt signaling. adenovirus-mediated overexpression of TFEB consistently activates Akt signaling and significantly increases glucose uptake in ECs. Mechanically, TFEB upregulates insulin receptor substrate 1 and 2 (IRS1 and IRS2). TFEB increases IRS2 transcription measured by reporter gene and chromatin immunoprecipitation assays. Furthermore, we found that TFEB increases IRS1 protein via downregulation of microRNAs (miR-335, miR-495 and miR548o). In vivo, Akt signaling in the skeletal muscle and adipose tissue was significantly impaired in EC-TFEB knockout mice and consistently improved in EC-TFEB transgenic mice on HFD

overall_design: Comparison of human endothelial small RNA profiles infected with adenovirus encoding LacZ or adenovirus encoding TFEB (4 replicates for each group).

first: Haocheng

last: Lu

first: Yanbo

last: Fan


title: Gene expression individuals at different ages

city: Novato

first: Yingxiang

last: Huang

state: California

address: 8001 Redwood Blvd

institute: Buck Institute

summary: We report a gene expression data on human serum samples for 312 individuals. By examing individuals of different ages. We can have a better understanding of gene expressions associated with aging.

overall_design: Examination of gene expressions for 312 individuals of varying ages

first: David

last: Furman


title: PolyA RNA-seq from whole blood of subjects with Trisomy 21 ± clonal hematopoiesis

city: Aurora

middle: D

last: Galbraith

state: CO

department: Department of Pharmacology; Linda Crnic Institute for Down Syndrome

summary: Analysis of steady-state mRNA levels in trisomy 21 subjects ± clonal hematopoiesis. This dataset is part of the Human Trisome Project run by the Linda Crnic Institute for Down Syndrome at the University of Colorado Anschutz Medical Campus. http://www.trisome.org/

overall_design: Comparison of trisomy 21 subjects: 44 clonal hematopoiesis-negative versus 26 clonal hematopoiesis-positive

first: Keith

last: Smith

first: Kelly

last: Sullivan

first: Joaquin

last: Espinosa


title: Long-RNA sequencing and ribosome profiling of inflamed beta-cells reveal an extensive translatome landscape

status: Public on Feb 23 2021

city: Leiden

first: Hailiang

last: Mei

address: Einthovenweg 20

department: Sequencing Analysis Support Core

country: Netherlands

institute: Leiden University Medical Center

summary: Using a transcriptome-wide profiling approach to map translation initiation start sites in human beta-cells under standard and inflammatory conditions, we identifies non-canonical start sites and translation initiation within lncRNA.

overall_design: EndoC-BH1 cells have been treated 24h with proinflammatory cytokines 1000 U/ml IFNγ and 2 ng/ml IL1β for 24 h. RNA was isolated by TRizol and sequenced by nanopore sequencing to etablish the de novo transcritpome. Upon incubation, cells were treated with 2ug/ml harringtonine for 30 minutes and Cycloheximide (100ug/ml) for ribosome footprint purification.

first: Sofia

last: Thomaidou

first: Jasper

last: Boom

first: Arnaud

last: Zaldumbide


title: Abundant Circular RNA expression in terminal erythropoiesis and megakaryopoiesis shows limited evidence for translation or circRNA-mediated translation regulation [RNA-seq]

city: Amsterdam

first: Monika

last: Wolkers

address: Plesmanlaan 125

department: Hematopoiesis

institute: Sanquin Blood foundation

summary: Erythrocytes and platelets have high production rates, with 1012 cells released daily into the blood stream. This output from bone-marrow residing hematopoietic stem cells is tightly regulated by transcription factors and epigenetic modifications. Whether and how non-coding RNAs such as circular RNAs (circRNAs) contribute to the differentiation and/or identity of hematopoietic cells is to date not well understood. We recently published a circRNA expression map of hematopoietic cells, which showed that erythrocytes and platelets contain the highest levels and numbers of circRNAs. Whether and how circRNA expression alters during differentiation of erythrocytes and platelet precursors is however not known. Therefore, we here provide the first detailed and comprehensive analysis of circRNA expression during red blood cell and megakaryocyte differentiation. CircRNA expression significantly increased during erythroid precursor differentiation into red blood cells, and in differentiating megakaryocytes, in particular upon enucleation. Many functions have been attributed to circRNAs. To dissect their possible function in hematopoietic differentiation, we first focused on translation regulation. We compared circRNA and mRNA expression to ribosomal foot printing data, and found that only 20 (2.6%) circRNAs associated with translation regulation of their mRNA counterparts. We also identified thousands of putative open reading frames in circRNAs, suggesting that circRNAs may also encode proteins. However, deep ribosome-footprinting sequencing data and in-depth mass spectrometry data analysis provided little evidence for translation of endogenously expressed circRNAs in erythroblasts, megakaryocytes and platelets. In conclusion, circRNAs in platelets and red blood cells are highly abundant and alter their expression profile during differentiation, yet their contribution to regulate cellular processes remains enigmatic.

overall_design: RNA-seq analysis of CD42- and CD42+ megakaryocytes

first: Benoit

last: Nicolet

first: Sjoert

middle: B

last: Jansen

first: Esther

last: Heideveld

first: Willem

middle: H

last: Ouwehand

first: Emile

last: van den Akker

first: Marieke

last: von Lindern


title: Expression data from CD103+ CD11b+ cDCs expressing or not hBcl-2 transgene in the mesenteric lymph nodes under control chow diet

status: Public on Feb 17 2021

city: Paris

first: Maharajah

last: Ponnaiah

state: Île-de-France

address: 47-83 Boulevard de l'Hôpital

country: France

institute: Institute for Cardiometabolism and Nutrition

summary:
hBcl-2 transgene under CD11c promotor fosters tolerogenic DCs properties linked to a global downmodulation of genes related to pro-inflammatory pathway and upregulation of tolerogenic ones
We used microarrays to detail the global programme of gene expression underlying the tolerogenic phenotype of hBcl-2 expressing CD103+ CD11b+ cDCs to identify the pathways involved in the promotion of tolerogenic DCs ability

overall_design: We performed a FACS-cell sorting of CD103+CD11b+ cDC from the mesenteric lymph nodes in both, transgenic mice expressing the hBcl-2 transgene under the CD11c promotor and control littermates (8weeks-old- under control chow diet). To obtain homogenous quantity of material, we pooled 2 to 3 samples per genotype.

first: Emelyne

last: Lécuyer

first: Magalie

last: Fradet


title: Macrophages in SHH subgroup medulloblastoma display dynamic heterogeneity that varies with treatment modality

status: Public on Feb 13 2021

city: Philadelphia

first: Michael

last: Gonzalez

state: Pennsylvania

address: 3535 Market St

department: Translational Medicine and Human Genetics

institute: University of Pennsylvania

summary: Using 10xGenomics single cell RNAseq library creation and Illumina sequencing, we generated single cell RNAseq data for 12 samples of myeloid cells in mouse sonic hedgehog medulloblastomas to characterize their heterogeneity in comparison to control peripheral myeloids cells and homeostatic cerebellar myeloid cells from young mice without significant tumors. We then sequenced myeloid cells in tumors that were treated with two modalities, sonic hedgehog inhibition and radiation, to determine the differential recruitment of myeloid cells. Finally we sequenced samples of myeloid cells from irradiated Ccr2 knockout mice to further determine the change in recruitment of myeloid cells and their heterogeneity when monocyte-derived macrophages are reduced.

overall_design: 12 scRNAseq samples were analyzed

first: Mai

last: Dang

first: Fernanda

last: Mafra


title: Ribosome profiling experiments of LRRK2 mouse models

status: Public on Feb 27 2021

city: Berkeley

first: Jungwoo Wren

last: Kim

state: CA

address: Barker Hall, Room 416

department: Molecular and Cell Biology

institute: UC Berkeley

summary: G2019S mutaion of LRRK2 is known to increase mRNA translation. We perform ribosome profiling to study defective translation in mammalian LRRK2 models. We used G2019S LRRK2 transgenic mice, G2019S/D1994A LRRK2 transgenic mice, LRRK2 knockout mice.

overall_design: Mouse: 3 months old. Biological replicates were generated for mouse experiments.

first: Jungwoo

middle: W

first: Ted

last: Dawson

first: Valina


title: Reprogramming of bacterial and plant sulfur metabolisms in Enterobacter sp. SA187-induced plant salt stress tolerance

status: Public on Feb 25 2021

city: Thuwal

first: Prof. Heribert

last: HIRT

address: 4700 KAUST

country: Saudi Arabia

institute: KAUST

summary:
Although some mechanisms are known how plant growth beneficial bacteria help plants to grow under stressful conditions, we still know little how the metabolism of host plants and bacteria is coordinated during the establishment of functional interaction. In the present work, using single and dual transcriptomics, we studied the reprograming of metabolic and signaling pathways of Enterobacter sp. SA187 with Arabidopsis thaliana during the change from free-living to endophytic host-microbe interaction. We could identify major changes in primary and secondary metabolic pathways in both the host and bacteria upon interaction, with an important role of the sulfur metabolism and retrograde signaling in mediating plant resistance to salt stress. Also, we studied the effect of SA187 endogenous compounds and its role on sulfur metabolism and consequently salt tolerance. These data should help future research in the field of beneficial plant-microbe interactions for developing sophisticated strategies to improve agriculture of crops under adverse environmental conditions.
transcriptome of Arabidopsis thaliana organs with beneficial microbe, beneficial microbe endogenous compound, and ethylene precursor

overall_design: Arabidopsis thaliana Col-0 seeds were surface sterilized 10 min in 70% EtOH + 0.05% sodium dodecyl sulfate on a shaker, washed 2 times in 96% EtOH and air dried. Sterilized seeds were sown on half-strength Murashige and Skoog (Murashige and Skoog, 1962) (MS) agar plates (0.9% agar) inoculated with SA187 for SA187 treated samples, and other treatments were directly stratified for 2 days at 4˚C in darkness. After stratification, seeds were germinated vertically for 5 days at 22 °C and 16/8 h light/dark cycle with photon flux density 150 μmol m-2 s-1 during the light cycle. Uniformly germinated seedlings with 1 cm root length were then transferred and grown vertically in 1/2MS with 100 mM NaCl plates, and for ACC (1-aminocyclopropane-1-carboxylic acid, Sigma) and KMBA (2-keto-4-methylthiobutyric acid, Sigma) treatments 100 nM dilutions with water of each substance were added into pre-cooled ½ MS agar medium together with 100 mM NaCl, and all seedlings for all treatments were grown for another 16 days. Six seedlings were transferred to each plate. To prepare the SA187 inoculum, overnight bacterial cultures in LB broth (Sigma) were harvested, centrifuged 15 min at 3,000 rpm, washed twice in liquid MS and resuspended in MS to a final OD600 = 0.2. Plates containing 50 ml of cooled-down 1/2MS were inoculated with 0.1 ml of the bacterial suspension (~10^7 CFU) and let solidify. At the end of the experiment, whole 21 days-old plant organs where collected and immediately submerged in liquid nitrogen, then stored at -80˚C until needed.

first: Hanin

last: Alzubaidy

first: Cristina

last: Andres-Barrao

first: Rewaa

last: Jalal

first: Axel

last: de Zelicourt

first: Maged

last: Saad

first: Ameerah

last: Bokhari

first: Heribert

last: Hirt


title: DNA methylation analysis of synovial fibroblasts from mice undergoing collagen-induced arthritis (CIA) treated, or not, with the the helminth-derived immunomodulator, ES-62

city: Glasgow

first: Margaret

last: Harnett

address: 120 University Place

department: Infection, Immunity & inflammation

institute: University of Glasgow

type: Methylation profiling by high throughput sequencing

summary: Aim: Synovial fibroblasts (SFs) undergo a rewiring of their DNA methylation landscape that is associated with their development of an aggressive pathogenic phenotype during Rheumatoid Arthritis (RA), both in humans and in CIA, a mouse model of this chronic inflammatory disease. The helminth-derived immunomodulator, ES-62 acts to prevent joint destruction in CIA by suppressing pathogenic SF responses. We therefore investigated whether  ES-62 suppressed the changes in DNA methylation observed in SFs from CIA, relative to those from healthy, mice.  Methods: The DNA methylation status of SFs from naïve (no induction of CIA), CIA and ES-62-treated mice undergoing CIA (CIA_ES-62) was compared by Reduced Representation Bilsulphite Sequencing (RRBS) analysis performed by the Active Motif service. Results: Synovial fibroblasts from naive, CIA and CIA_ES-62 mice exhibit differential genomic methylation profiles. Conclusion: ES-62 protection against joint protection in CIA is not associated with prevention of the changes in DNA methylation occurring during rewiring of naive SFs to aggressively pathogenic CIA SFs but rather, reflects generation of a distinct ES-62 phenotype of SF genomic methylation.

overall_design: Comparison of the genomic methylation profiles of SFs from naïve, CIA and ES-62-treated CIA mice.

first: Marlene

last: Corbet

first: Miguel

middle: A

last: Pineda

first: William


title: Single Cell RNA Sequencing of  fetal mouse neurosphere cultures.

status: Public on Feb 10 2021

city: Bryan

first: Rajesh

last: Miranda

address: 8447 Riverside Parkway

institute: Texas A&M University

summary: We performed single-cell RNA sequencing on neurosphere cultures derived from the dorsal telencephalic vesicles of sex segregated gestational day (GD) 12.5 C57BL/6J mouse fetuses.

overall_design: We sequenced 6885 single cells from the female mouse fetus-derived culture and 4317 cells from a male-derived culture.

first: Nihal

last: Salem

first: Andrew

middle: E

last: Hillhouse

first: Kranti

last: Konganti


title: Epigenetic Dysregulation by Polyglutamine-expanded Ataxin-7 In The mouse model of SCA7

status: Public on Feb 04 2021

city: Irvine

first: Pawel

middle: Michal

last: Switonski

address: 1001 Health Sciences Road

department: Department of Pathology & Laboratory Medicine

institute: University of California, Irvine

summary: To determine if STAGA complex dysfunction affects chromatin remodeling in SCA7 cerebellar  degeneration, we pursued unbiased ChIP-Seq analysis of histone 3 lysine 9 acetylation (H3K9ac), as  this histone mark is an established indicator of open chromatin in the transcription regulatory regions of most genes.  We studied SCA7 266Q knock-in mice which faithfully recapitulate a  severe, rapidly progressive neurodegenerative phenotype involving the cerebellum.  We  detected altered H3K9ac in the promoter regions of 777 genes in the cerebellum of SCA7 266Q  knock-in mice and wild-type littermate control mice, and noted that the vast majority of these chromatin alterations corresponded to markedly increased H3K9 promoter acetylation in genes expressed in the cerebellum of SCA7 model mice.

overall_design: Examination of H3K9ac histone modification in cerebella of symptomatic SCA7 266Q knock-in mice and wild type littermates.

first: Joe

last: Delaney

first: Chenchen

last: Niu

first: Albert

last: La Spada


title: Estrogen Receptor 1 is a Central Regulator of Hepatocarcinogenesis through Inhibition of Wnt/β-catenin Signaling

status: Public on Feb 22 2021

city: Toronto

first: Marc

last: Angeli

state: Ontario

address: 101 College street

department: Multi Organ Transplant

country: Canada

institute: University Health Network

summary: A genetic mouse model of HCC was generated through the injection of proto-oncogene-coding plasmids, then given a 5 week treatment of either ESR1 agonist or antagonist.

overall_design: HCC was generated through hydrodynamic tail vein injection of proto-oncogene-coding plasmids in 8-10-week-old Male and Female FVB/N mice; 2 weeks post-injection mice where given a 5-week treatment of the following: 1) ESR1 agonist Propyl pyrazole triol (PTT) subcutaneously at 1mg/kg (Sigma-Aldrich H6036) N=6; 2) ESR1 antagonist methyl-piperidino-pyrazole (MPP) given subcutaneously at 200ug/kg

first: Mamatha

last: Bhat


title: Targeted transcriptome sequencing reveals the in vivo M. tuberculosis transcriptome and host interaction during early infection in a murine model

status: Public on Jan 27 2021

city: Cuernavaca

first: Fernanda

last: Cornejo

address: Av Universidad 2001

country: Mexico

institute: Instituto de Biotecnología UNAM

summary: We describe a differential cellular lysis strategy, followed by a biotynilated probe-based ribosomal depletion, to simultaneously obtain the gene expression of Mycobacterium tuberculosis infecting BALB/c mouse lungs

overall_design: RNAseq from M. tuberculosis infected mice lungs.

last: Cornejo-Granados

first: Gamaliel

last: Lopez-Leal

first: Dulce

last: Mata-Espinosa

first: Jorge

last: Barrios-Payan

first: Edgar

last: Equihua-Medina

first: Zyanya

last: Zatarain-Barron

first: Camilo

last: Molina-Romero

first: Rogelio

last: Hernandez-Pando

first: Adrian

last: Ochoa-Leyva


title: Cooperative herbivory between two important pests of rice

status: Public on Feb 28 2021

city: Xinyang

first: Qingsong

last: Liu

state: Henan

address: No. 237, Nanhu road

country: China

institute: Xinyang Normal University

summary: To explore the molecular mechanisms underlying the rice plant-mediated interaction between  brown planthopper (BPH) and striped stem borer (SSB), gene expression changes in rice plant response to infestation by SSB, BPH or both and control were analyzed by RNA-seq.

overall_design: We compared gene expression in rice stems after being infestation by different insect pests for 48 hr.

first: Yunhe

last: Li


title: Transcriptome analysis and 3‘-end detection of total RNA from Rhodobacter sphaeroides 2.4.1 wildtype, polynucleotide phosphorylase (pnp) mutant and RNase III (rnc) mutant strain

status: Public on Feb 16 2021

city: Gießen

first: Gabriele

last: Klug

address: Heinrich-Buff-Ring 26-32

department: Molecular- and Microbiology

country: Germany

institute: Justus-Liebig University Gießen

summary: The polynucleotide phosphorylase (PNPase) is conserved among both Gram-positive and Gram-negative bacteria. As a core part of the degradosome, the PNPase is involved in maintaining proper RNA levels within the bacterial cell. It plays a major role in RNA homeostasis and decay since it acts as a 3’- to 5’-exoribonuclease. Furthermore PNPase can catalyze the reverse reaction by elongating RNA molecules in 5’- to 3’-end direction which finally has a destabilizing effect on the prolonged RNA molecule. RNA degradation can be initiated by an endonucleolytic cleavage and then by further promoted by exoribonucleolytic decay. In this study, we analyzed the importance of the Rhodobacter sphaeroides PNPase regarding the physiology and sRNA homeostasis. Moreover, we developed a pipeline to globally identify differential RNA 3’-ends in RNA NGS sequencing data obtained from PNPase, RNase E and RNase III mutants. The Rhodobacter sphaeroides PNPase mutant exhibits several phenotypical characteristics, including diminished adaption to low temperature, reduced resistance to organic peroxide induced stress and altered growth behavior. Furthermore, the transcriptome composition differs in the pnp mutant strain, resulting in a decreased abundance of most tRNAs and rRNAs. In addition, the PNPase has a major influence on the half-lives of several regulatory sRNAs and can have both a stabilizing or a destabilizing effect. The RNA 3’-end analysis reveals that 82% of all differential 3’-ends are enriched in the pnp mutant and are mostly located in coding sequences or untranslated regions (UTR). A fair percentage of these ends was also identified as differential RNA 3’-end in RNase E and RNase III mutant strains. The PNPase has a major influence in RNA processing and maturation and thus modulates the transcriptome. This includes regulatory sRNAs, stressing the role of PNPase in cellular homeostasis and its importance in regulatory networks. The 3’-end analysis indicates a sequential processing of UTR- and non-UTR derived sRNAs by several ribonucleases. Moreover, we provide a modular pipeline which greatly facilitates the identification of RNA 5’/3’-ends. It is publicly available on GitHub and is distributed under ICS licence.

overall_design: This data includes the transcriptome data of three different exponentially growing strains each in triplicates: Rhodobacter sphaeroides 2.4.1 (wildtype), R. sphaeroides 2.4.1 pnp mutant (lacking C-terminal KH and S1 domains) and  R. sphaeroides 2.4.1 RNase III mutant.  Total RNA of all strains was isolated and sequenced.

first: Daniel-Timon

last: Spanka

first: Carina

last: Reuscher


title: Characterization of HEK293T-SPINDOC KO vs WT by RNA-Seq profiling

status: Public on Feb 24 2021

city: Smithville

first: Bin

state: TX

address: 1808 Park Road 1C

department: Epigenetics and Molecular Carcinogenesis

institute: University of Texas MD Anderson Cancer Center

summary: Background: SPIN1 is a known histone code effector protein, which is composed of three Tudor domains. With its second Tudor domain, it reads the H3K4me3 mark, which is the canonical signal for transcriptional activation. It also has the ability to recognize combinatorial marks like H3R8me2a and H3K9me3 through its first Tudor domain, when they occur in the presence of K3K4me3. We identified SPINDOC as a stable component of the SPIN1 protein complex. SPINDOC referred to its ability to dock with SPIN1, which was previously called C11orf84 before it was functionally deorphanized. Objective:  To investigate the biological function of SPINDOC, we generated SPINDOC KO by CRISPR technology in HEK293T cell lines and performed RNA sequencing. Conclusion:Our data represent the first detailed analysis of SPINDOC associated transcriptome, with biologic replicates, generated by RNA-seq technology. Comprehensive RNA-seq analysis demonstrated that 1005 genes were differentially regulated, including 459 up-regulated genes and 546 down-regulated genes.

overall_design: Two pairs cell lines HEK29T-SPINDOC KO-1/WT-1 and HEK29T-SPINDOC-KO-2/WT-2

first: Fen

last: Yang

first: Jianjun

last: Shen

first: Mark

last: Bedford


title: Genome-wide Translocation Analysis in the 266Q Knock-in Mouse Model of SCA7

first: Pawel

last: Switonski

summary: To determine whether a predisposition to DNA damage exists in SCA7 and how extensive the predilection to DNA damage might be in SCA7, we used LAM-HTGTS, a powerful high throughput next generation sequencing technique developed for monitoring of DNA double-strand break formation.  We modified the LAM-HTGTS protocol by utilizing CRISPR-Cas9 to create the double-strand DNA break at a specific site and also added a step with a 5’ methyl  cytosine modified primer to promote LpnPI endonuclease cleavage of sealed breaks to enrich for  translocation events. Our unbiased native chromosome DNA repair experimentation revealed that expression of polyglutamine-expanded ataxin-7 yielded greatly reduced translocations in comparison to normal ataxin-7, which is consistent with retained canonical NHEJ repair, decreased HDR activity, and decreased SSA repair in SCA7 cells, as the classical NHEJ pathway is known to prevent translocation by ligating broken double-strand breaks.

overall_design: Examination of translocation events with genome-wide translocation assay in Neuro-2A cells transiently expressing mutant (92Q) or normal (10Q) ataxin-7. Double strand DNA breaks were introduced by co-expression of Cas9 and sgRNAs targeting two selected genomic loci. For the quality control experiment, only the CRISPR-Cas9 plasmid co-expressing site 2 targeted sgRNA or non-targeted sgRNA were used.  Three independent transfection replicates per condition were pooled prior sequencing.

first: Joe

last: Delaney

first: Albert

last: La Spada


title: Abundant Circular RNA expression in terminal erythropoiesis and megakaryopoiesis shows limited evidence for translation or circRNA-mediated translation regulation [Ribo-seq]

first: Monika

last: Wolkers

overall_design: Ribo-seq analysis of CD42- and CD42+ megakaryocytes

first: Benoit

last: Nicolet

first: Sjoert

last: Jansen

first: Esther

last: Heideveld

first: Willem

last: Ouwehand

first: Emile

last: van den Akker

first: Marieke

last: von Lindern


title: A pan-cancer single-cell landscape of tumor-infiltrating myeloid cells

city: Beijing

first: Sijin

last: Cheng

state: Beijing

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

department: School of Life Science

institute: Peking University

summary: Tumor-infiltrating myeloid cells (TIMs) have emerged as key regulators in tumor progression, however, the similarity and discrepancy of the fundamental properties of these cells across different cancer types remain elusive. Here, we performed a pan-cancer analysis of TIM sub-populations in multiple human cancer types. Our comprehensive analyses provide valuable insights for understanding the TIM properties across multiple tumors.

overall_design: We generated  scRNA-seq data from 48 patients to investigate tumor-infiltrating myeloid cells across multiple cancer types. The sequencing data have been uploaded to Genome Sequence Archive (accession number PRJCA001702), and the data disclosure permissions are currently being requested.

first: Ziyi

last: Li

first: Ranran

last: Gao

first: Yunong

first: Peng

last: Du

last: Zhang

first: Yue

first: Baocai

last: Xing

first: Xianwen

last: Ren

first: Xueda

last: Hu

first: Zhaode

last: Bu

first: Jiafu

last: Ji

first: Zemin


title: Circular RNAs exhibit limited evidence for translation, or translation regulation of the mRNA-counterpart in terminal hematopoiesis

first: Monika

last: Wolkers

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

overall_design: Refer to individual Series


title: Next Generation Sequencing Facilitates Quantitative Analysis of oral epithelial cells from SPF 8 weeks and 1 week old Wild Type mice

status: Public on Jan 21 2021

city: Jerusalem

first: Khaled

last: Zubeidat

address: Faculty of Medicine, Ein-Kerem

country: Israel

institute: The Hebrew University of Jerusalem

summary: Purpose: RNAseq analysis to identify differentiatlly expressed genes due to development

overall_design: Oral epithelial cells mRNA profile of SPF WT 8 weeks and 1 week old mice, 4 animals in each group.

first: Avi-Hai

last: Hovav


title: Next Generation Sequencing Facilitates Quantitative Analysis of oral epithelial cells from SPF and germ free (GF) Wild Type mice

summary: Purpose: RNAseq analysis to identify differentiatlly expressed genes due to the presnce of microbiota

overall_design: Oral epithelial cells mRNA profile of adult germ free and SPF mice, 4 animals in each group.


title: Convergent evolution of resistance pathways during early stage breast cancer treatment with combination cell cycle (CDK) and endocrine signalling inhibitors

status: Public on Feb 09 2021

city: Houston

first: Jeffrey

last: Chang

address: 6431 Fannin St

institute: University of Texas

summary: Samples were taken from ER+ breast cancer patients treated with neoadjuvant endocrine therapy (letrozole) with or without CDK4/6 inhibitor (ribociclib) at the beginning of treatment, 14 days after starting treatment, or after 180 days. Nuclei were isolated and single-nucleus RNA sequencing (snRNA-seq) was performed using 10X or iCell8 technologies.

overall_design:
Single-nucleus RNA sequencing of 41 ER+ breast cancer patients undergoing neoadjuvant therapy.
----------------------------------------------------
Submitters state "we cannot upload the raw data to GEO due to patient privacy issues".  Thus, this dataset is incomplete.

first: Jinfeng

last: Chen

first: Patrick

last: Cosgrove

first: Jason

last: Griffiths

first: Qamar

last: Khan

first: Andrea

last: Bild


title: RNAseq of perivascular adipose tissue from mesenteric arteries from normotensive and hypertensive Dahl S rats

status: Public on Jan 23 2021

city: East Lansing

first: G. Andres

last: Contreras

state: MI

address: 736 Wilson Road Room D202, Michigan State University

department: Large Animal Clinical Sciences

institute: Michigan State University

summary: We report the results from RNA-seq analysis of perivascular adipose tissues (PVAT) collected from mesenteric arteries from Dahl S rats. Animals were on a control or a high fat diet for 24 weeks. At the moment of collection, rats fed high fat diet were hypertensive. In contrast, rats on the control diet were normotensive.

overall_design: RNAseq performed on mesenteric PVAT from Dahl S fed a control (normotensive) or a high fat diet (Hypertensive).

first: Ramya

last: Kumar

first: Yongliang

last: Yang

first: Andres

first: Hannah

last: Garver

first: Sudin

last: Bhattacharya

first: Gregory

last: Fink

first: Cheryl

last: Rockwell

first: Stephanie

last: Watts


title: Molecular profiling of stem cell-derived retinal pigment epithelial cell differentiation established for clinical translation

city: Lausanne

first: Gioele

last: La Manno

state: Vaud

address: Station 19

department: BMI

country: Switzerland

institute: EPFL

summary: Human embryonic stem cell-derived retinal pigment epithelial cells (hESC-RPE) are a promising cell source to treat age-related macular degeneration (AMD). Despite several ongoing clinical studies, a detailed mapping of transient cellular states during in vitro differentiation has not been performed. Here we conduct single-cell transcriptomic profiling of a hESC-RPE differentiation protocol that has been developed for clinical use. Differentiation progressed through a culture diversification recapitulating early embryonic development, in which cells rapidly acquired a rostral embryo patterning signature, before converging towards the RPE lineage. At intermediate steps, we identified and examined the potency of a NCAM1+ retinal progenitor population and showed the ability of the protocol to suppress non-RPE fates. We demonstrated that the method produces a pure RPE pool capable of maturing further after subretinal transplantation in a large-eyed animal model. Our evaluation of hESC-RPE differentiation supports the development of safe and efficient pluripotent stem cell-based therapies for AMD.

sample_organism:
Homo sapiens
Oryctolagus cuniculus

platform_organism:
Homo sapiens
Oryctolagus cuniculus

overall_design:
hESC lines HS980 and KARO1 were previously derived and cultured under xeno-free and defined conditions (Rodin et al. 2014). Donors gave their informed consent for the derivation and subsequent use of hESC lines (Swedish Ethical Review Authority: 2011/745:31/3). The hESC line E1C3 (NN GMP0050E1C3) was provided as a research cell bank of the clinical GMP cell line by NovoNordisk (UCSF IRB:1518222, for RPE differentiation Projekt-ID: H-18016740, Anmeldelsesnr.: 73105). All hESCs maintain a normal karyotype and trilineage differentiation potential, and they are routinely tested for mycoplasma. Cells were maintained by clonal propagation on hrLN-521-coated plates and on iMatrix-511 for the E1C3 line (0.25 μg/cm2, Nippi, T303) in NutriStem hPSC XF medium (Biological Industries) and a 5% CO2/5% O2 incubator.

All cells were transported at 4°C to the Eukaryotic Single Cell Genomics Facility (ESCG, SciLifeLab, Stockholm, Sweden) where a 3’ cDNA library was prepared for single cell RNA sequencing (scRNA-seq) using the 10X Genomics platform and NovaSeq 6000 software. Cell Ranger 2.1.1 was used to convert Illumina base call files to FASTQ format. Cell Ranger 3.1.0 was used to map FASTQ sequencing reads to the human GRCh38 reference transcriptome with the STAR aligner and to generate feature-barcode count matrices.

A step-by-step protocol describing the differentiation procedure has been reported previously (doi 10.1038/s41467-020-15326-5 and doi 10.21203/rs.3.pex-635/v1). hESCs were plated at a cell density of 2.4x104 cells/cm2 on hrLN-521 (20 μg/mL) using NutriStem hPSC XF medium. A Rho-kinase inhibitor (Millipore, Y-27632) at a concentration of 10 μM was added during the first 24h, while cells were kept at 37°C, 5% CO2/5% O2. After 24h, hPSC medium was replaced with differentiation medium NutriStem hPSC XF without bFGF and TGFβ and cells were placed at 37°C, 5% CO2/21%O2. From day 6 after plating, 100 ng/mL of Activin A was added to the media. Cells were fed three times a week and kept for 30 days. Monolayers were then trypsinized using TrypLE Select for 10 min at 37°C, 5% CO2. The enzyme was carefully removed and the cells were collected in fresh pre-warmed NutriStem hPSC XF medium without bFGF and TGFβ by gentle pipetting to obtain a single cell suspension. Cells were centrifuged at 300 g for 4 min, the pellet was resuspended, passed through a cell strainer and seeded on laminin coated dishes at different cell densities ranging from 1.4x106 to 1.4x104 cells/cm2. Replated cells were fed three times a week during the subsequent 30 days with NutriStem hPSC XF medium without bFGF and TGFβ. Single cell RNA-sequencing was performed on undifferentiated hESCs and at days 7, 14, 30, 38, 45, and 60 of this protocol.

hESC-RPE monolayers were washed with DPBS, incubated with TrypLE and dissociated to single cell suspension as described above. Cells were counted in a Neubauer hemocytometer chamber using 0.4% trypan blue, centrifuged at 300g for 4 min, and the cell pellet was resuspended in freshly filter-sterilized DPBS to a final concentration of 1000 cells/μL. The cell suspension was then aseptically aliquoted into 600 μL units and kept on ice until surgery.

After approval by the Northern Stockholm Animal Experimental Ethics Committee (DNR N56/15), two female New Zealand white albino rabbits aged 5 months and weighing 3.5 to 4.0 kg were used in this study. All experiments were conducted in accordance with the Statement for the Use of Animals in Ophthalmic and Vision Research.

Animals were put under general anesthesia by intramuscular administration of 35 mg/kg ketamine and 5 mg/kg xylazine, and the pupils were dilated with a mix of 0.75% cyclopentolate / 2.5% phenylephrine. Microsurgeries were performed on both eyes using a 2-port 25G transvitreal pars plana technique. 25G trocars were inserted 1 mm from the limbus and an infusion cannula was connected to the lower temporal trocar. The cell suspension was drawn into a 1 mL syringe connected to an extension tube and a 38G polytip cannula. Without infusion or prior vitrectomy the cannula was inserted through the upper temporal trocar. After proper tip positioning, ascertained by a focal whitening of the retina, 50 μL of hESC-RPE cell suspension (equivalent to 50,000 cells) was injected slowly subretinally, approximately 6 mm below the inferior margin of the optic nerve head, forming a uniform bleb that was clearly visible under the operating microscope

Human post-mortem research-consented donor eyes were obtained from the cornea bank at St. Erik Eye Hospital, Stockholm, Sweden. The use of human tissue was in accordance with the tenets of the Declaration of Helsinki and was approved by the Swedish legislative and ethical committee (#2019-02032) for the use of human donor material for research. Donors did not present any clinical diagnosis of ocular disease, and samples were anonymized and processed under the general data protection regulation. Two human eyes from the same donor were used (45-year-old male, 32 hours post-mortem). The lens was dissected out and the rest of the retina, except the sclera, was chopped in several small pieces mixed together in 500 uL of digestion buffer (described below). Two embryonic eyes from the same embryo were used from a 7.5 post-conception week embryo (Table S1). The optic cups were dissected out and chopped in several small pieces to facilitate dissociation in 500 uL of digestion buffer (described below). Donors (deceased, family for adult human eyes, or couples for the embryos) gave their informed consent for the donation and subsequent use for research purposes. The embryonic eyes were acquired from a clinical routine abortion after informed consent by the pregnant woman, in accordance with permissions from the regional ethical review board and the Swedish National Board of Health and Welfare (“Socialstyrelsen” #8.1-11692/2019) and the Swedish Ethical Review Authority (“EPN” #2007/1477-31/3).

Two rabbit eyes (from different animals) with 30-day integrated hESC-RPE were enucleated and pigmented areas including neuroretina, choroid and RPE layer was dissected out, trimmed and mixed together in 500 uL of digestion buffer. Eppendorfs containing the samples were rotated and incubated at 37°C on a thermocycler at 300g for 25 min until samples were homogenized. Samples were pipetted every 5 min to digest the tissue sample into single cells. Digestion was stopped by adding equivalent volume of 10% embryonic bovine serum in PBS, the samples were filtered using a 30µm MACS Smart Strainer followed by Dead Cell Removal kit to remove dead cells and debris. At this stage, one of the rabbit eye cell samples was stained with mouse anti-human HLA-ABC-FITC, and anti-human HLA-ABC-positive cells were FACS-sorted as specified above, collected and resuspended to 1000 cells/uL in 1% BSA in PBS for further scRNA-sequencing. Otherwise, cells were finally resuspended to 1000 cells/uL in 1% BSA in PBS prior to scRNA-seq.

first: Sandra

last: Petrus-Reurer

first: Alex

last: Lederer

first: Laura

last: Baqué-Vidal

first: Iyadh

last: Douagie

first: Belinda

last: Pannagel

first: Irina

last: Khven

first: Monica

last: Aronsson

first: Hammurabi

last: Bartuma

first: Magdalena

last: Wagner

first: Andreas

last: Wrona

first: Paschalis

last: Efstathopoulos

first: Elham

last: Jaberi

first: Hanni

last: Willenbrock

first: Yutaka

last: Shimizu

first: J

last: Villaescusa

first: Helder

last: André

first: Erik

last: Sundström

first: Aparna

last: Bhaduri

first: Arnold

last: Kriegstein

first: Anders

last: Kvanta

first: Fredrik

last: Lanner


title: Epigenetic dysregulation impairs high-fidelity DNA repair to promote cerebellar degeneration in spinocerebellar ataxia type 7

first: Pawel

last: Switonski


title: circEPS15 overexpression in hepatocellular carcinoma modulates tumor invasion and migration

status: Public on Jan 15 2021

first: Yuntao

last: Bing

address: No.49 Huayuan North Road

department: Department of General Surgery

institute: Peking University Third Hospital

summary: This study evaluates the effect circular RNA (circRNA) has on the development of hepatocellular carcinoma (HCC), which has been an area of limited information in the field. Through microarray analysis, we identified and then characterized the circRNA, circEPS15, which is downregulated in HCC tissue compared to noncancerous tissues. Our analysis shows that overexpressing circEPS15 could reduce tumor cell migration through the inhibition of cell cycle signaling pathways, suggesting this circRNA could be a target for novel HCC therapies. Moreover, we show that circEPS15 encodes a functional protein that could contribute to its antitumor effects. We believe that our study makes a significant contribution to the literature because it both clarifies the molecular mechanisms of circRNA in cell growth and development, as well as provides novel marker or target candidates for improving HCC diagnosis and treatment.

overall_design: Total RNAs were digested with RNase R (20 U/μL, Epicentre, Madison, WI, USA) to remove linear RNAs and enrich circular RNAs. The enriched circular RNAs were amplified and transcribed into fluorescent cRNA utilizing a random priming method (Super RNA Labelling Kit; Arraystar, Rockville, MD, USA). The labeled cRNAs were hybridized onto the Human circRNA Array (8 × 15K, Arraystar). The slides were incubated for 17 h at 65°C in a hybridization oven (Agilent Technologies, Santa Clara, CA, USA). CircRNAs, with statistically significant fold-change differential expression between HCC and paired normal tissues (FC ≥ 2 and p ≤ 0.05) were identified by Volcano plot filtering. Hierarchical clustering was performed to determine the distinguishable expression pattern of circRNAs among samples.

first: Maolin

last: Tian

first: Chunhui

last: Yuan


title: Single-cell chromatin accessibility identifies pancreatic islet cell type- and state-specific regulatory programs of diabetes risk

status: Public on Jan 14 2021

city: La Jolla

first: Kyle

last: Gaulton

address: 9500 Gilman Drive

department: Pediatrics

institute: University of California, San Diego

summary: Single-nucleus assay for transposase-accessible chromatin using sequencing (snATAC-seq) creates new opportunities to dissect cell type-specific mechanisms of complex diseases. Since pancreatic islets are central to type 2 diabetes (T2D), we profiled 15,298 islet cells by using combinatorial barcoding snATAC-seq and identified 12 clusters, including multiple alpha, beta and delta cell states. We cataloged 228,873 accessible chromatin sites and identified transcription factors underlying lineage- and state-specific regulation. We observed state-specific enrichment of fasting glucose and T2D genome-wide association studies for beta cells and enrichment for other endocrine cell types. At T2D signals localized to islet-accessible chromatin, we prioritized variants with predicted regulatory function and co-accessibility with target genes. A causal T2D variant rs231361 at the KCNQ1 locus had predicted effects on a beta cell enhancer co-accessible with INS and genome editing in embryonic stem cell-derived beta cells affected INS levels. Together our findings demonstrate the power of single-cell epigenomics for interpreting complex disease genetics.

overall_design: This SuperSeries is composed of the SubSeries listed below. Refer to individual Series for Overall Design.


title: Single-cell chromatin accessibility identifies pancreatic islet cell type– and state-specific regulatory programs of diabetes risk [snATAC-seq]

summary: Single-nucleus assay for transposase-accessible chromatin using sequencing (snATAC-seq) creates new opportunities to dissect cell type–specific mechanisms of complex diseases. Since pancreatic islets are central to type 2 diabetes (T2D), we profiled 15,298 islet cells by using combinatorial barcoding snATAC-seq and identified 12 clusters, including multiple alpha, beta and delta cell states. We cataloged 228,873 accessible chromatin sites and identified transcription factors underlying lineage- and state-specific regulation. We observed state-specific enrichment of fasting glucose and T2D genome-wide association studies for beta cells and enrichment for other endocrine cell types. At T2D signals localized to islet-accessible chromatin, we prioritized variants with predicted regulatory function and co-accessibility with target genes. A causal T2D variant rs231361 at the KCNQ1 locus had predicted effects on a beta cell enhancer co-accessible with INS and genome editing in embryonic stem cell–derived beta cells affected INS levels. Together our findings demonstrate the power of single-cell epigenomics for interpreting complex disease genetics.

overall_design:
Single nucleus ATAC-seq of purified pancreatic islets from 3 human donors and whole pancreas from 1 human donor.

Note: Supplementary files GSE160472_islet_snATAC.cluster_labels.txt.gz and GSE160472_islet_snATAC.merged_sites.bed.gz are results of the analysis only including the 3 islet samples.

first: Joshua

last: Chiou


title: Hsa-miR-375/RASD1 signaling predicts local control in early breast cancer

status: Public on Jan 01 2021

city: Salzburg

first: Elvis

last: Ruznic

state: Salzburg

address: Müllner Hauptstraße 48

department: UK f. Radiotherapie & Radio-Onkologie

country: Austria

institute: Gemeinnützige Salzburger Landeskliniken Betriebsges.m.b.H.

summary: The current analysis was a two phase study. The first step of the pilot phase comprised an in-silico search for potential target molecules in five different databases. The second step was a screen for potential targets in 28 patients (14 with local relapse and 14 matched controls) by means of microarray technology. The combined results formed the basis for the validation phase in an independent set of 53 patients performed with droplet digital PCR (ddPCR).

first: Franz

last: Zehentmayr

first: Barbara

last: Zellinger


title: Human and mouse muscle transcriptomic analyses identify insulin receptor mRNA downregulation in hyperinsulinemia-associated insulin resistance

status: Public on Dec 31 2020

city: Vancouver

first: Howard

last: Cen

state: BC

address: 2350 Health Sciences Mall

institute: University of British Columbia

summary: Hyperinsulinemia is often viewed as compensatory to insulin resistance, but studies have shown that high levels of insulin may contribute to insulin resistance. The precise mechanisms by which hyperinsulinemia contributes to insulin resistance remain poorly defined. To understand direct effects of prolonged exposure to excess insulin in muscle cells, we incubated differentiated C2C12 myotubes with elevated insulin for 16 hours, followed by 6 hours serum starvation, before examining key insulin signaling nodes. Using this model, we found that prolonged high insulin treatment significantly increased the phosphorylation of insulin receptor (INSR) and AKT, but not ERK. After starvation, acute AKT and ERK signaling stimulated by 0.2 - 20 nM insulin was attenuated. INSR protein was significantly downregulated by hyperinsulinemia in a insulin-dose-dependent manner. Surface INSR was reduced proportionally to total INSR levels. Mechanistically, we found that hyperinsulinemia strongly downregulated Insr mRNA, which was correlated with increased threonine 24 phosphorylation of FOXO1. Interestingly, 6h starvation reversed the effects of high insulin on basal phosphorylation of INSR, AKT and FOXO1, and Insr transcription. Using RNAseq, bioinformatics, and follow-up RNAi studies, we identified SIN3A as a negative regulator of Insr mRNA levels and JUND, MAX and MXI as positive regulators of Irs2 mRNA. We validated our in vitro results by determining that INSR levels in mouse skeletal muscle were negatively correlated with circulating insulin in vivo. Together, our findings shed new light on the mechanisms underlying hyperinsulinemia-induced insulin resistance in muscle cells, which are likely to be relevant in the pathogenesis of type 2 diabetes.

overall_design: There are 4 conditions: 0 nM insulin before starvation (BS, 0 nM), 200 nM insulin before starvation (BS, 200 nM), 0nM insulin after starvation (AS, 0nM), 200 nM insulin after starvation (AS, 200 nM). Each condition has 5 biological replicates.

first: Haoning

first: James

last: Johnson


title: FOXA1 suppresses cancer immunity independent of DNA binding

city: Rochester

first: LIGUO

last: WANG

state: MN

address: 200 1st St SW

department: Division of Computational Biology

institute: Mayo Clinic

summary: Exclusion of lymphocytes from tumors is a major barrier for effective immuno- and chemo-therapy of cancer. We found that FOXA1 overexpression inversely correlates with expression of antigen processing and presentation and interferon signaling genes in different cancer types. FOXA1 binds to STAT proteins and inhibits expression of antigen presentation and interferon response genes and tumor immunity independent of the forkhead domain - DNA binding function. Increased FOXA1 also correlates with immunotherapy resistance in murine triple negative breast tumor and bladder cancer in patients and chemo-resistance in breast cancer patients. Our results reveal that FOXA1 is a key immune suppressor, suggesting that FOXA1 overexpression may predict tumor resistance to immuno- and chemo-therapies and that depletion of FOXA1 may therapeutically convert cancers from ‘immune-cold’ to ‘immune-hot’ diseases.

overall_design: To determine the inhibitory effect of FOXA1 variants on the DNA binding ability of STAT2,  cells were expressed of Vetor as control, FOXA1-WT, FOXA1-R261G and FOXA1△αH3, and then the endogenous FOXA1 in LNCaP cells was knocked down by specific siRNA for next STAT2 chromatin immunoprecipitation sequencing (ChIP-seq).

first: Haojie

last: Huang

first: Yundong

last: He

first: Liguo

last: Wang

first: Zhenqing

last: Ye

first: Ting

last: Wei


title: Comparison of gene expression profile among four groups of mice that developed under the different combination of genes and environments

city: Tokyo

first: Shinobu

last: Hirai

address: Setagaya Kamikitazawa 2-1-6

institute: Tokyo Metropolitan Institute of Medical Science

summary: To investigate the mechanisms underlying the emergence of  schizophrenic phenotypes, especially in sucrose fed Glo1 heterozygote mice, we conducted a transcriptome analysis of PFC regions using microarray experiments among the four groups of mice. The coagulation factor V, which is an essential participant in the processes of production of fibrin from fibrinogen, ranked seventh on the list of transcripts that exhibited more than doubled expression levels in sucrose fed Glo1 heterozygote mice compared with the remaining three groups. This result supports our idea that angiopathy with fibrrin deposition is a novel phenotype in schizphrenia.

overall_design: We investigated four groups of mice that were fed two kinds of diets for about 70 days immediately after weaning (from postnatal day 21): wild-type, starch-fed mice (control, CTL); wild-type, sucrose-fed mice; Glo1 heterozygous, starch-fed mice; and Glo1 heterozygous, sucrose-fed mice. Three independent PFC samples were mixed in each group of mice.

first: Yasumasa

last: Nishito

first: Haruo

last: Okado


title: Transcriptional reprogramming of the endophytic bacterium Enterobacter sp. SA187 upon Arabidopsis colonization

status: Public on Jan 04 2021

city: Thuwal

first: Prof. Heribert

last: HIRT

address: 4700 KAUST

institute: KAUST

summary: Enterobacter sp. SA187 is a plant growth-promoting bacterium (PGPB) that promotes growth of the crop plant alfalfa under saline irrigation and desert farming conditions. SA187 also enhances salt tolerance of the model plant Arabidopsis thaliana under in vitro conditions. In the present study, we used a transcriptomic approach to elucidate the mechanisms underlying plant growth promotion by SA187 under salt stress. Compared to free-living SA187, a massive metabolic reprogramming of SA187 occurs upon association with Arabidopsis. This effect was largely independent of the plant growth condition (non-salt or salt stress). Our data revealed pronounced changes in gene expression of proteins involved in cell signaling, chemotaxis, flagella biosynthesis, quorum sensing and biofilm formation. Also, upon plant interaction, a complete reprograming of nutrients acquisition and the central carbon metabolism of SA187 was observed. Moreover, in accordance with the previously identified role of bacterially produced 2-keto-4-methylthiobutyric acid (KMBA) in mediating salt stress tolerance, the sulfur metabolism of SA187 was strongly induced. Overall, our results give a deep insight into the metabolic and signaling pathways involved in the transition from free-living to a plant-associated PGPB life style of SA187.

overall_design: 4 samples, 3 biological replicates

first: Cristina

last: Andrés-Barrao

first: Kiruthiga

middle: G

last: Mariappan

first: Axel

last: de Zélicourt

first: Ameerah

last: Bokhari

first: Maged

last: Saad

first: Heribert

last: Hirt


title: Transcriptome-Wide Combinatorial RNA Structure Probing in Living Cells with icSHAPE and icLASER

city: Irvine

first: Whitney

last: England

address: 2403 Natural Sciences I

department: Pharmaceutical Sciences

institute: University of California Irvine

summary: We design and test a novel di-azido LASER reagent capable enrichment through attachment of biotin with strain-promoted azide alkyne cycloaddition (SPAAC). We term this approach in vivo click LASER or icLASER. Aligned with the goal of extending transcriptome-wide measurements of RNA structure and to develop an approach that takes advantage of combinatorial RNA structure probing,we then use this novel bi-functional probe to interrogate LASER reactivity transcriptome-wide, revealing the first solvent accessibility transcriptome map. We also directly compare icSHAPE (hydroxyl acylation; flexibility) and icLASER (solvent accessibility) to demonstrate the power of utilizing them together to predict RNA-protein interactions and RNA polyadenylation.Our results demonstrate that combinatorial RNA structure probing can be employed to compliment orthogonal methods to better understand RNA structure and processing in cells transcriptome-wide.

overall_design: Fourteen total samples, consisting of three biological replicates each of: in vivo icSHAPE-treated, DMSO icSHAPE control, and two biological replicates each of: in vitro icSHAPE-treated, in vivo icLASER-treated, in vitro icLASER-treated, no-UV icLASER control

first: Dalen

last: Chan

first: Chao

last: Feng

first: Ryan

last: Flynn

first: Yongsheng

last: Shi

first: Robert

last: Spitale


title: A comparative profile of the mRNA and microRNA transcriptome in immature and mature bovine testes

city: Changchun

first: Xibi

last: Fang

address: No. 5333 Xian Road

institute: Jilin University

summary: This study aim to screening potential regulators of fecundity, the bovine testes of immature and mature in Chinese Red Steppes were performed by a genome-wide analysis of mRNAs and miRNAs. Compared with born testicular tissue, 6051 upregulated genes and 7104 downregulated genes in adult bovine testicular tissue were identified as differentially expressed genes (DEGs) (log2FC>1 or <－1 , FDR <0.05). The DEGs were significantly enriched in 808 GO terms (p <0.05), which are involved in sperm biological activity, including male gonad development, male genitalia development, spermatogenesis, sperm motility, spermatid development, sperm chromatin condensation, etc. Moreover, DEGs were also significantly enriched in 105 KEGG pathways (p <0.05), such as focal adhesion, cGMP-PKG signaling pathway and calcium signaling pathway, etc. To explore the miRNA-regulated gene expression network integrated analysis was used between DEGs and differentially expressed miRNAs (DERs). Correlation prediction and analysis found that 896 differentially expressed target genes were negatively correlated with the expression levels of 31 differentially expressed bovine miRNAs. Our results identified novel candidate DEGs and DERs correlated with male reproduction, which will be valuable for future genetic and epigenetic studies of sperm development and maturity, as well as provided valuable insights into the molecular mechanisms of the male fertility and spermatogenesis in cattle.

overall_design: A genome-wide profiling of mRNA and miRNA of Chinese Red Steppes cattle by next-generation sequencing technology in immature and mature testicular tissue

first: Lihong

last: Qin

first: Zhihui

last: Zhao


title: Aly/REF interacting lncRNAs and mRNAs by RNA immunoprecipitation (RIP)-sequencing in human abdominal aortic aneurysm tissue

status: Public on Dec 25 2020

city: Dalian

first: Yanshuo

last: Han

address: No.2 Dagong Load

institute: Dalian University of Technology

summary: We performed a global screening for Aly/REF-binding lncRNAs and mRNAs in an infrarenal abdominal aortic aneurysm patient (maximum aortic diameter=64.3 mm) sample, who have no comorbidity i.e. cancer, drug history, infection, or any other immune-related disease that might have influenced the study. After screening for reads in AAA tissue compare with anti-Aly/REF group relative to IgG as control. The clustered libraries were loaded onto a reagent cartridge and forwarded for sequencing runs on an illumina Hiseq 4000.

overall_design: Human infrarenal abdominal aortic aneurysm sample lncRNA and mRNA profiles of binding interactions with Aly/REF by RNA immunoprecipitation sequencing.

first: Jian

last: Zhang


title: RNA-sequencing of Dot1L-deficient B cell subsets

status: Public on Dec 01 2020

city: Clayton

first: David

middle: Richard

last: Powell

state: VIC

address: Wellington Road

department: Bioinformatics Platform

country: Australia

institute: Monash University

summary: We assessed gene expression differences in B cells from mice in which Dot1L is conditionally deleted in mature B cells

overall_design: RNA-sequencing of CD19+IgD+ and CD19+IgD- B cell subests from Dot1L floxed CD23cre and CD23cre (WT) mice

first: Kim

last: Good-Jacobson


title: RAW264.7 cells:treated with Rhizoma Coptidis extract and its main alkoloids

status: Public on Dec 12 2020

first: Lan

last: Xie

address: School of Medicine B410, Tsinghua University

institute: Tsinghua University

summary: To investigate the differently expressed genes treated with DMSO, extracts of Rhizoma Coptidis and its main alkoids berberine, coptisine and palmatine

overall_design: Total RNAs were extracted from RAW264.7 cells treated with PBS, DMSO, Rhizoma Coptidis, berberine, coptisine and palmatine. Gene-expression profiling was performed on the CapitalBio 32k mouse Genome Array microchips  (Beijing, China). Differentially expressed genes and pathway analysis was based on comparison of different drug treated samples vs. DMSO.

first: Shanshan

first: Xiaoling


title: Spatial RNA sequencing of regenerating mouse hindlimb muscle

status: Public on Dec 02 2020

city: Ithaca

middle: William

last: McKellar

state: NY

address: 237 Tower Rd

department: Biomedical Engineering

institute: Cornell University

summary: We report a series of spatial transcriptomics datasets of regenerating mouse muscle tissue generated with the 10x Genomics Visium platform.

overall_design: Tibialis anterior muscles were injected with notexin and collected two, five, and seven days post-injury. Samples were frozen in OCT. 10 micron tissue sections were assayed using the Visium Spatial Gene Expression Kit (v1). To improve resolution, each spot within the Visium slide was deconvolved using a matched single-cell RNA sequencing reference and BayesPrism (https://github.com/Danko-Lab/TED). Cell type fractions for each spot are included in the metadata files.

first: Benjamin

last: Cosgrove

first: Iwijn

last: De Vlaminck


title: Subcellular sequence tracking of RNA maturation during neuronal differentiation [smallRNA]

status: Public on Nov 18 2020

city: LOS ANGELES

first: Chia-ho

last: Lin

address: 6577 MRL. 675 CHARLES E YOUNG DR. SOUTH

institute: UCLA

summary: We developed an extensive resource of RNAseq data to track mRNA maturation across subcellular locations in multiple cell types. Mouse embryonic stem cells, neuronal progenitor cells, and post-mitotic neurons were separated into chromatin-associated, soluble nucleoplasmic and cytoplasmic fractions, with RNA from each fraction isolated as both polyadenylated, total rRNA-depleted pools, and small RNA pools and sequenced. Genes exhibit disparate patterns of RNA enrichment between subcellular fractions, with some genes maintaining more polyadenylated RNA in the chromatin fraction than in the cytoplasm. These chromatin-associated poly(A)+ RNAs are often incompletely spliced and we devise a simple metric to identify introns whose excision is posttranscriptional. X-means clustering and deep learning methods identified intron groups with four defined regulatory behaviors, including complete cotranscriptional splicing, and complete retention in the cytoplasmic RNA. Two groups display intermediate levels of retention in the RNA in the nucleus but are fully spliced in the cytoplasm. These groups include previously described sets of retained introns, but extend to many new introns, including introns repressed by polypyrimidine track binding protein 1 (PTBP1). We find that the PTBP1 regulated Gabbr1 transcript is highly expressed in mESC without expression of Gabbr1 protein. The bulk of Gabbr1 RNA is incompletely spliced and remains sequestered on chromatin similar to certain long noncoding RNAs. Only after neuronal differentiation does Gabbr1 RNA become fully processed and released to the cytoplasm as mRNA. Thus, splicing repression and the chromatin anchoring of RNA provide a combined mechanism of posttranscriptional regulation over development.  Our datasets provide a rich resource for analyzing many other aspects of mRNA maturation in subcellular locations and across development.

overall_design: mESC line (E14), mNPC line (established in the lab), and mCtx (primary cortical neuron culture) were prepared and performed subcellular fractionation in biological triplicates. After size selection for smaller than 200 nt RNAs, rRNA were removed and subjected to library construction.

first: Douglas

last: Black

first: Kyu-hyeon

last: Yeom


title: Innate and adaptive immune responses to SARS-CoV-2 in Syrian hamsters disclosed by single-cell sequencing and high-throughput proteomics

status: Public on Dec 15 2020

city: Berlin

first: Emanuel

last: Wyler

address: Robert Roessle Str 10

department: Berlin Institute for Medical Systems Biology

institute: Max Delbrück Center for Molecular Medicine

summary:
We describe the cellular response to SARS-CoV-2 infections in lung and blood of Syrian gold hamsters
Single-cell RNA-sequencing and proteomics was performed from lung and blood of infected animals at different time points post infection

overall_design: Bulk and single-cell RNA-sequencing was performed from lung and blood of infected animals at different time points post infection

first: Geraldine

last: Nouailles

first: Peter

last: Pennitz

first: Dylan

last: Postmus

first: Daria

last: Vladimirova

first: Julia

last: Kazmierski

first: Fabian

last: Pott

first: Kristina

last: Dietert

first: Michael

last: Mülleder

first: Vadim

last: Farztdinov

first: Benedikt

last: Obermayer

first: Sandra-Maria

last: Wienhold

first: Sandro

last: Andreotti

first: Thomas

last: Höffler

first: Christian

last: Drosten

first: Leif

last: Sander

first: Norbert

last: Suttorp

first: Markus

last: Ralser

first: Dieter

last: Beule

first: Achim

last: Gruber

first: Christine

last: Goffinet

last: Landthaler

first: Jakob

last: Trimpert

first: Martin

last: Witzenrath


title: Subcellular sequence tracking of RNA maturation during neuronal differentiation [Total]

first: Chia-ho

last: Lin

overall_design: mESC line (E14), mNPC line (established in the lab), and mCtx (primary cortical neuron culture) were prepared and performed subcellular fractionation in biological triplicates. After size selection for longer than 200 nt RNAs, rRNA were removed and subjected to library construction.

first: Douglas

last: Black

first: Kyu-hyeon

last: Yeom

first: Zhicheng

last: Pan


title: Gene-regulatory network analysis of ankylosing spondylitis with a single-cell chromatin accessible assay

city: Shenzhen

first: Haiyan

last: YU

address: No. 1017, North of Dongmen Road

institute: Shenzhen People's Hospital

summary: A detailed understanding of the gene-regulatory network in ankylosing spondylitis (AS) is vital for elucidating the mechanisms of AS pathogenesis. Assaying transposase-accessible chromatin in single cell sequencing (scATAC-seq) is a suitable method for revealing such networks. Thus, scATAC-seq was applied to define the landscape of active regulatory DNA in AS. As a result, there was a significant change in the percent of CD8+ T cells in PBMCs, and 37 differentially accessible transcription factor (TF) motifs were identified. T cells, monocytes-1 and dendritic cells were found to be crucial for the IL-17 signaling pathway and TNF signaling pathway, since they had 73 potential target genes regulated by 8 TF motifs with decreased accessibility in AS. Moreover, natural killer cells were involved in AS by increasing the accessibility to TF motifs TEAD1 and JUN to induce cytokine-cytokine receptor interactions. In addition, CD4+ T cells and CD8+ T cells may be vital for altering host immune functions through increasing the accessibility of TF motifs NR1H4 and OLIG (OLIGI and OLIG2), respectively. These results explain clear gene regulatory variation in PBMCs from AS patients, providing a foundational framework for the study of personal regulomes and delivering insights into epigenetic therapy.

overall_design: Single-cell chromatin accessibility (scATAC) profiles of human peripheral blood mononuclear cells in ankylosing spondylitis

last: Yu

first: Hongwei

last: Wu

first: Yong

last: Dai


title: Subcellular sequence tracking of RNA maturation during neuronal differentiation [Poly]

overall_design: mESC line (E14), mNPC line (established in the lab), and mCtx (primary cortical neuron culture) were prepared and performed subcellular fractionation in biological triplicates. After size selection for longer than 200 nt RNAs, polyadenlayted RNA were subjected to library construction.


title: RNA sequencing of pre-treatment biopsy sampless from BrighTNess phase III study (AFT-04)

status: Public on Jan 08 2021

city: Columbus

first: Daniel

last: Stover

state: OH

address: Biomedical Research Tower, Room 512, 460 W. 12th Avenue

institute: Ohio State University Comprehensive Cancer Center

summary: BrighTNess was a phase III, multicenter, randomized, double-blind, placebo-controlled study that enrolled stage II/III TNBC patients to receive neoadjuvant chemotherapy with paclitaxel followed by doxorubicin/cyclophosphamid (AC), or the same plus carboplatin or carboplatin plus the PARP inhibitor veliparib concurrent with paclitaxel. Whole transcriptome RNA sequencing (RNAseq) was performed on pre-treatment research biopsies.

overall_design:
Whole transcriptome RNA sequencing (RNAseq) was performed on pretreatment research biopsies

*** Submitter declares that they do not have permission to deposit the raw data due to patient privacy concerns ***

first: Otto

last: Metzger


title: TMEM41B is a pan-flavivirus host factor

status: Public on Nov 24 2020

city: New York

first: John

last: Poirier

address: 550 1st Ave

institute: NYU Langone Health

summary: Flaviviruses pose a constant threat to human health. These RNA viruses are transmitted by the bite of infected mosquitoes and ticks and regularly cause outbreaks. To identify host factors required for flavivirus infection we performed full-genome loss of function CRISPR-Cas9 screens. Based on these results we focused our efforts on characterizing the roles that TMEM41B and VMP1 play in the virus replication cycle. Our mechanistic studies on TMEM41B revealed that all members of the Flaviviridae family that we tested require TMEM41B. We tested 12 additional virus families and found that SARS-CoV-2 of the Coronaviridae also required TMEM41B for infection. Remarkably, single nucleotide polymorphisms (SNPs) present at nearly twenty percent in East Asian populations reduce flavivirus infection. Based on our mechanistic studies we propose that TMEM41B is recruited to flavivirus RNA replication complexes to facilitate membrane curvature, which creates a protected environment for viral genome replication.

sample_organism:
Homo sapiens
synthetic construct

platform_organism:
Homo sapiens
synthetic construct

overall_design: Genome-scale CRISPR screens targeting were performed for ZIKV (PRVABC59 strain) and YFV (Asibi strain).

first: Hans-Heinrich

last: Hoffmann

first: William

last: Schneider

first: Kathryn

last: Rozen-Gagnon

first: Linde

last: Miles

first: Felix

last: Schuster

first: Brandon

last: Razooky

first: Eliana

last: Jacobson

first: Xianfang

first: Soon

last: Yi

first: Charles

last: Rudin

first: Margaret

middle: R

last: MacDonald

first: Laura

middle: K

last: McMullan

last: Rice


title: Alternative splicing and the epigenome in CML remission

status: Public on Dec 19 2020

city: Sydney

last: Bailey

state: NSW

address: Missenden Rd, Building 93

institute: Centenary Institute

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

overall_design: Refer to individual Series


title: Expression Data from Young Uteroplacental Insufficiency-induced Low Birth Weight Adult Guinea Pig Offspring

status: Public on Nov 10 2020

city: London

first: Ousseynou

last: Sarr

state: United States

address: 1811 Creekside Street

department: Physiology & Pharmacology

institute: Western universitry

summary:
We aimed to gain mechanistic insights into the impact of uteroplacental insufficiency upon hepatic cholestrol metabolism pathways in young adult offspring.Uterine artery ablation-induced low birth weight (LBW) and normal birth weight (NBW) male and female guinea pig offspring were fed a control diet from weaning until postnatal day 150.
Analysis of whole hepatic transcriptome results identified that between LBW and NBW offspring livers, 51 (29 up-regulated and 22 down-regulated) and 31 (8 up-regulated and 23 down-regulated) genes were differentially expressed in males and females respectively (fold change| >= 2 and p-value < 0.05). KEGG pathway analysis of these differentially expressed genes revealed that “Cholesterol metabolism” was an enriched pathway in LBW males but not females (p<0.05).

overall_design: A whole-Transcript Expression Analysis Gene Titan was conducted (Genome Québec Innovation Centre, QU, Canada) on guinea pig livers of 5 NBW males, 5 LBW males, 5 NBW females and 5 LBW females.

first: Katherine

last: Mathers

first: Christina

last: Vanderboor

first: Aditya

last: Devgan

last: Hardy

first: Lin

last: Zhao

first: Timothy

last: Regnault


title: Nociceptin/orphanin FQ opioid receptor selective ligand MCOPPB as a potent senolytic drug

status: Public on Nov 14 2020

city: S. Giovanni Rotondo (FG)

first: Tommaso

last: Mazza

address: Viale Cappuccini, 1

department: Bioinformatics

institute: IRCCS Casa Sollievo della Sofferenza

summary: Here we used RNA-Seq to gain deep mechanistic insight into the effects of the drug MCOPPB  on C57BL6J mice that were fed with chow diet or that received a low dose of a carcinogen (25 mg/kg diethynitrosamine, DEN) and then fed with high fat diet (HFD). Only in a second step we decided to focus exclusevely on the groups under chow diet. Heatmap analysis of the differentially expressed genes between the two groups revealed a difference in transcriptomic profile of MCOPPB-treated mice compared to the control condition. Genes were considered differentially expressed between groups if their expression values significantly differed by >4 fold. Statistical differences in gene expression were assessed by the ANOVA test. Correction for multiple test was achieved by the Benjamini-Hochberg procedure. The significance threshold was set to 0.05.       Significantly enriched transcripts over-represented in MCOPPB compared to control were implicated in a number of functions and diseases. Specifically,Ingenuity pathway analysis (IPA) identified differences in hepatic fibrosis, oxidative stress,Ephrin A signaling, GP6 signaling pathway, Ephrin B signaling and others categories  between MCOPPB versus CTL. These data suggested a slight pro-fibrotic effect in the liver of MCOPPB.

overall_design: Profiling the transcriptome of C57BL6J mice under chow diet or high fat diet+DEN and treated with MCOPPB, using RNA-Seq.

first: Manlio

last: Vinciguerra


title: Transcriptional analysis on the effect of the overexpression of VvSUC11,VvSUC12,or VvSUC27 in tomato on the growth of fruit

status: Public on Nov 16 2020

city: Beijing

first: Yumeng

last: Cai

state: Be

address: Qinghua Dong Road NO.17,Beijing,China

institute: China Agriculture University

summary:
Purpose: We used transcriptome sequencing to study the regulated mechanism of VvSUC11,VvSUC12,or VvSUC27 on tomato fruit growth.
Methods: the 35S:: VvSUC11, VvSUC12, and VvSUC27 constructs were introduced into transgenic tomatoes (Micro-Tom) by the Agrobacterium-mediated transformation, 5 DPA (days after anthesis) fruit was collected, 3 replicates per group. Extract total RNA, detect RNA quality, library preparation, sequencing, and analyze data.
Results:Reads were obtained for each sample using Illumina Hiseq X Ten sequencing. After discarding the low-quality reads, corresponding to over 40 million clean reads obtained from sequencing were mapped on the reference genome of Solanum lycopersicum. High Pearson's correlation coefficients of FPKM distribution between the three biological replicates for each sample were detected (1> R2 > 0.99, P < 0.001) , reflecting the robustness of our library preparation from tomato RNA samples. Compared with WT lines, there were 2459 DEGs in the VvSUC11-overexpressing lines, of which 1283 genes were upregulated and 1176 genes were downregulated. Whereas, there were 1369 DEGs in VvSUC12-overexpressing lines, including 544 upregulated and 825 downregulated genes. In the meanwhile,there were 1777 DEGs in VvSUC27-overexpressing lines, including 623 upregulated and 1154 downregulated genes.

overall_design: Deep-sequencing using Illumina, in triplicate, yielded 5 DPA tomato fruit mRNA expression profiles from WT lines, VvSUC11-, VvSUC12-,and VvSUC27-overexpressing lines.

first: Yali

last: Zhang


title: Subcellular sequence tracking of RNA maturation during neuronal differentiation

first: Chia-ho

last: Lin


title: Opposing Wnt signals regulate cervical squamocolumnar homeostasis and emergence of metaplasia

status: Public on Dec 26 2020

city: Würzburg

first: Antoine-Emmanuel

last: Saliba

address: Josef-Schneider-Straße 2 / D15

institute: Helmholtz Institute for RNA-based Infection Research

summary: The transition zones (TZs) of the squamous and columnar epithelium constitute hotspots for the emergence of cancers, often preceded by metaplasia, where one epithelial type is replaced by cells of another type. Yet, it remains uncertain how the spatial organization of the epithelia is maintained and how the TZ niche is remodeled during metaplasia. Here, we used single-cell RNA-sequencing to characterize subpopulations of the epithelium as well as the underlying stromal compartment of endo and ectocervix, encompassing the TZ. Mouse lineage tracing, organoid culture and smRNA-ISH revealed that the two epithelia derive from two separate cervix-resident lineage-specific stem cell populations that are regulated by opposing WNT signals from the stroma. Using a mouse model of cervical metaplasia, we further show that the endocervical stroma undergoes remodeling and increased expression of WNT signaling inhibitor Dickkopf-2 (DKK2), promoting the outgrowth of ectocervical stem cells. Thus, homeostasis at the TZ results from divergent stromal signals, driving the differential proliferation of resident epithelial lineages.

overall_design: Balb/c mice were euthanized and the genital tract was extracted. Endocervix, ecto-endo junction and ectocervix were seperated from healthy mice. In addition, a metaplasia sample was processed twice, as a technical replicate, after extraction from an in vivo mouse model of cervical metaplasia.

first: Cindrilla

last: Chumduri

first: Rajendra

last: Gurumurthy

first: Hilmar

last: Berger

first: Oliver

last: Dietrich

first: Naveen

last: Kumar

first: Stefanie

last: Koster

first: Volker

last: Brinkmann

first: Kirstin

last: Hoffmann

first: Marina

last: Drabkina

first: Panagiota

last: Arampatzi

first: Dajung

last: Son

first: Uwe

last: Klemm

first: Hans

middle: J

last: Mollenkopf

first: Hermann

last: Herbst

first: Mandy

last: Mangler

first: Jörg

last: Vogel

first: Antoine

first: Thomas

middle: F

last: Meyer


title: Expression data from endometrial adenocarcinoma cell line ISK with and without EZH2 knockdown

status: Public on Nov 22 2020

city: Nanjing

first: Tao

last: Gui

state: Jiangsu

address: NO.100 Shizi Street, Hongshan Road

institute: Affiliated Hospital of Integrated Traditional Chinese and Western Medicine, Nanjing University of Chinese Medicine

summary:
The findings indicate that EZH2 may act as a important therapeutic target for treatment of EAC. Furherly, EZH2 knockdown couldinduce G2/M phase arrest and resulted in cell proliferation inhibition.
To further investigate how EZH2 overexpression impacted cell proliferation of EAC, Microarray gene expression profiling was performed on ISK cell line with or without EZH2 knockdown.

overall_design: Microarray gene expression profiling was performed on ISK cell line with and without EZH2 knockdown. Stable Scr and EZH2 knockdown cell lines were selected for RNA extraction and hybridization on Affymetrix microarrays. To that end, we prepared 3 biological duplication of Scr and EZH2 knockdown cell lines respectively.

first: Quan

last: Zhao


title: promoter capture Hi-C in ex vivo primary bronchial epithelial cells

status: Public on Oct 31 2020

city: Chicago

first: Carole

last: Ober

state: IL

address: 920 E 58TH ST

department: Human Genetics

institute: The University of Chicago

summary: promoter capture Hi-C in pooled asthma cases and non-asthma controls from freshly isolated primary bronchial epithelial cells

overall_design: Ex vivo, human bronchial epithelial cells were harvested within 24 hours of donor death from the Gift of Hope Regional Organ Bank of Illinois.

first: Britney

last: Helling

first: William

last: Wentworth-Sheilds


title: Transcriptional and Chromatin Changes Reflect Prolonged Inflammatory Responses to Rhinovirus in Bronchial Epithelial Cells from Adults with Asthma


title: ATAC-seq studies of Rhinovirus Response in asthma cases and non-asthma controls

summary: There is a life-long relationship between rhinovirus (RV) infection and the development and clinical manifestations of asthma. In this study we demonstrate that cultured primary bronchial epithelial cells from adults with asthma (n = 9) show different transcriptional and chromatin responses to RV infection compared to those without asthma (n = 9). Both the number and magnitude of transcriptional and chromatin responses to RV were muted in cells from asthma cases compared to controls. Pathway analysis of the transcriptionally responsive genes revealed enrichments of apoptotic pathways in controls but inflammatory pathways in asthma cases. Using promoter capture Hi-C we tethered regions of RV-responsive chromatin to RV-responsive genes and showed enrichment of these regions and genes at asthma GWAS loci. Taken together, our studies indicate a delayed or prolonged inflammatory state in cells from asthma cases and highlight genes that may contribute to genetic risk for asthma.

overall_design: Primary bronchial epithelial cells were grown in culture from nine asthma cases and nine non-asthma controls in triplicate and treated with either RV-A16 or Vehicle (PBS)


title: micro RNA expression analysis in the prefrontal cortex of Fkbp5 deficient mice

city: Seoul

first: Koeul

last: Choi

address: 84, Heukseok-ro

country: South Korea

institute: Chung-Ang university

summary: Psychological stress is a risk factor for several diseases. In particular, stressor exposure has been linked with various psychiatric disorders. Since the hypothalamic-pituitary-adrenal (HPA) axis plays a central role in the regulation of stress responses, it has been implicated in the etiology of stress related disorders such as PTSD. The HPA axis regulate synthesis and release of glucocorticoids and its dysregulation cause abnormal response to stress. FK506-binding protein 51 (FKBP5) is a co chaperone of HSP90 in the glucocorticoid receptor (GR) molecular complex and a key regulator of the sensitivity of GR. In this study, we profiled the miRNAs in the prefrontal cortex of FKBP5 knock out mice compared to the wild type. Subsequently, we profiled target mRNAs for differentially expressed miRNAs in the FKBP5 deficient mice using several tools for sequence-based miRNA target prediction such as miRDB, DIANA tool, miRmap and TargetScan. Gene ontology analysis suggested that differentially expressed miRNAs in the brain of FKBP5 deficient mice may be involved in neuron development, cell motion, endocytosis, and cell-cell adhesion. These results suggest that Nfasc could be a new target for understanding of the pathophysiology of PTSD.

overall_design: miRNA profiles of prefrontal cortex (PFC) from wild type and Fkbp5 deficient mice were generated by small RNA sequencing using Illumina HiSeq 2500.

first: Joonhee

last: Lee

first: HyoJung

last: Kang