title: Expression data from stroke patients brain samples

status: Public on Dec 31 2021

city: Barcelona

first: Laura

last: Ramiro

state: Barcelona

address: Passeig De La Vall D'hebrón 119-129, Edificio Mediterránea, Laboratorio 120

institute: Vall d'Hebron Institute of Research

summary:
Stroke is still a major cause of death and disability worldwide. A better comprehension of stroke pathophysiology is fundamental to reduce its dramatic outcome.
Our aim was to identify and verify gene expression changes that occur in the human brain after ischemia.

overall_design: Six ischemic stroke patients who died during hospitalization in the Vall d’Hebron Hospital (Barcelona, Spain) were included. Tissue collection was done under the supervision of an experienced neuropathologist. Brain pieces from the infarct core (IC) and the healthy contralateral (CL) areas were gathered within the first hours after death, snap-frozen in liquid nitrogen and stored at -80ºC. Total RNA was isolated from frozen brain samples using the Fatty Tissue RNA Purification kit (Norgen Biotek Corp., Canada), following manufacturer’s instructions. DNase treatment was performed in solution with the DNA-free DNA removal kit (Ambion, ThermoFisher). All RNAs were kept at -80ºC.  The integrity of the isolated RNA was determined using the Bioanalyzer 2100 platform (Agilent, UK), with an average integrity number of 6.4 ± 1.5.

first: Teresa

last: García-Berrocoso

first: Joan

last: Montaner


title: Single cell RNA sequencing of mouse brain hematopoietic cells after brain ischemia model

status: Public on Dec 22 2021

city: Tsukuba

first: Akira

last: Shibuya

state: Ibaraki

address: 1-1-1 Tennodai

department: Immunology

country: Japan

institute: University of Tsukuba

type: Expression profiling by high throughput sequencing

summary: We performed scRNA-seq of brain CD45+ hematopoietic cells from the brain of Cd300a-fl/fl and Cd300a-fl/fl Lys2-Cre mice 0, 1 and 3 hrs after the reperfusion of middle cerebral artery occlusion (MCAO).

overall_design: Brain PI-CD45+ hematopoietic cells were sorted by flow cytometry from Cd300a-fl/fl and Cd300a-fl/fl Lys2-Cre mice 0, 1 and 3 hrs after the reperfusion of MCAO. Three brains were pooled per each sample. Re-staining of PI of sorted samples were measured by flow cytometry, and the viability of all samples were more than 85%. Single cells were processed through the Chromium Single Cell Platform using the Chromium Single Cell 3’ Library and Gel Bead Kit v3 (10X Genomics, PN-1000092) and the Chromium Single Cell B Chip Kit (10X Genomics, PN-1000074) as per the manufacturer’s protocol. The sequencing of libraries was performed at Macrogen Japan (Kyoto, Japan) using an Illumina HiSeq X. Processed files were generated from Cell Ranger (10X Genomics) pipeline.

first: Kazumasa

last: Kanemaru

first: Chigusa

last: Oda

first: Yuta

last: Nakazawa

first: Fumie

last: Abe


title: M-CSF-responsive immortal macrophages are a new model for studying macrophage function

status: Public on Dec 11 2021

city: Brookings

first: Natalie

last: Thiex

state: SD

address: 1066 Campanile Ave, Box 2022A ookings

department: Biology and Microbiology

country: USA

institute: South Dakota State University

summary: We generated non-senescent, macrophage colony stimulating factor (M-CSF) dependent macrophages from murine fetal livers. These fetal liver macrophages (FLM-M) resemble bone marrow macrophage (BMM) morphology and express similar macrophage surface markers as BMM. In comparison to granulocyte monocyte-colony stimulating factor (GM-CSF) derived FLM (FLM-G), FLM-M have higher surface expression of CD11b, CD68, CD14 and CD64, and lower expression of CD11c. BMM, FLM-M and FLM-G all produce TNFα and IL-6 in response to lipopolysaccharide activation. BMM and FLM-M cells have similar phagocytic properties with 99.3% of BMM and FLM-M actively phagocytosing opsonized sheep erythrocytes and a phagocytic efficiency of 0.9. The average number of internalized erythrocytes per cell was higher (13.1±10.0) in BMM than in FLM-M (7.6±2.9). FLM-G had fewer actively phagocytic cells (86%), lower phagocytic efficiency (0.7) and fewer internalized erythrocytes per macrophage (4.2±2.1) than BMM or FLM-M. Principal component analysis and hierarchical clustering demonstrated mRNA expression profiles were more similar between BMM and FLM-M cells than FLM-G. Transcriptome comparison to the ImmGen tissue atlas shows cultured BMM and FLM-M cluster with macrophage progenitors and bone marrow macrophages. In conclusion, FLM-M cell cultures share major morphological, phenotypic and functional properties of BMM except for senescence, and can be an effective substitute to BMM. These new cells will facilitate study of macrophage biology by enabling experiments requiring long-term culture or genetic modifications.

overall_design: Comparison of 3 different murine macrophage cell cultures.

middle: W

first: Padmapriya

last: Swaminathan

first: Jason

last: Kerkvliet

first: Maxim

middle: I

last: Lebedev

first: H

middle: C

last: Eisenbeisz

first: Lisa

middle: M

last: Martinez

first: Xijin

last: Ge

first: Anne

last: Fennell

first: Adam

middle: D

last: Hoppe


title: Genome-wide gene expression Haloferax volcanii under oxidative stress

status: Public on May 25 2022

city: Seoul

first: Sungmin

last: Hwang

address: Hwarangno 14-gil 5, Seongbuk-gu

country: South Korea

institute: Korea Institute of Science and Technology

summary: The goals of this study are to compare NGS-derived transcriptome profiling (RNA-seq) of H. volcanii upon treatment of NaOCl.

overall_design:
mRNA from H. volcanii wt and oxsR deletion strains incubated with/without 1.5 mM of NaOCl.

Grant ID: NSF-1642283
Grantee First Name: Julie
Grantee Last Name: Maupin-Furlow
Grant title: Remodelling Replication Roadblocks: Regulatory Systems that Integrate DNA Replication, Recombination and Protein Modification
Name of the funding source: National Science Foundation

Grant ID: DE-FG02-05ER15650
Grantee First Name: Julie
Grantee Last Name: Maupin-Furlow
Grant title: Ubiquitin-like Proteins in Protein-conjugation and Sulfur-transfer in Archaea
Name of the funding source: US Department of Energy

Grant ID: NIH-5R01GM057498
Grantee First Name: Julie
Grantee Last Name: Maupin-Furlow
Grant title: Ubiquitin-like Proteins and Proteasomes of Archaea
Name of the funding source: National Institutes of Health

Grant ID: NSF-1651117
Grantee First Name: Amy
Grantee Last Name: Schmid
Grant title: Elucidating cell cycle regulatory networks across the tree of life.
Name of the funding source: National Science Foundation

Grant ID: NSF-1936024
Grantee First Name: Amy
Grantee Last Name: Schmid
Grant title:  Causes and consequences of regulatory network rewiring under extreme environmental selection
Name of the funding source: National Science Foundation

first: Paula

last: Mondragon

first: Amy

middle: K

last: Schmid

first: Julie

middle: A

last: Maupin-Furlow


title: Effect of long-term adaptation of an acetogenic bacterium Clostridium sp. AWRP under acetate stress

status: Public on Jun 26 2022

city: Busan

first: Soo Jae

last: Kwon

address: KIOST, 385, Haeyang-ro, Yeongdo-gu, Busan Metropolitan City, KOREA

institute: KIOST

summary:
Acetate is a simple carboxylic acid that is synthesized in various microorganisms. Although acetate toxicity and tolerance have been studied in many microorganisms, little is known about the effects of exogenous acetate on the cell growth of acetogenic bacteria. In this study, we report the phenotypic changes that occurred in the acetogenic bacterium Clostridium sp. AWRP as a result of an adaptive laboratory evolution under acetate challenge. When compared with the wild-type strain, the acetate-adapted strain displayed a tolerance to acetate up to 10 g L-1 and higher biomass yields in batch cultures, although the metabolite profiles greatly varied depending on culture conditions. Interestingly, genome sequencing revealed that the adapted strain harbored three point mutations in the genes encoding an electron-bifurcating hydrogenase, which is crucial to its autotrophic growth on CO2 + H2, in addition to one in the dnaK gene. Transcriptome analysis revealed the global change in the gene expression profile of the acetate-adapted strain. Strikingly, most genes involved in CO2-fixing Wood-Ljungdahl pathway and auxiliary pathways for energy conservation (e.g., Rnf complex, Nfn, etc.) were significantly down-regulated. In addition, we observed that a couple of metabolic pathways associated with dissimilation of nucleosides and carbohydrates were significantly up-regulated in the acetate-adapted strain as well as several amino acid biosynthetic pathways, indicating that the strain might increase its fitness by utilizing organic substrates in response to the down-regulation of carbon fixation. Further investigation into the carbon fixation degeneration of the acetate-adapted strain will provide practical implications in CO2 + H2 fermentation using acetogenic bacteria for long-term continuous fermentation.
The transcriptome profiles of the wild-type Clostridium sp. AWRP and its acetate-tolerant derivative 46T-a were compared.

overall_design: Two strains were cultivated using bioreactors with continous gas flow. The samples were taken at exponential and stationary phases and subjected to transcriptome analysis.

first: HyunSook

last: Lee

first: Joungmin

first: SooJae


title: Stroke induces disease-specific myeloid cells in the brain parenchyma and pia

status: Public on Nov 26 2021

city: Muenster

first: Michael

last: Heming

address: Albert-Schweitzer-Campus 1, Bldg A1

department: Department of Neurology with Institute of Translational Neurology

country: Germany

institute: University Hospital Muenster

summary:
Inflammation triggers secondary brain damage after stroke. The meninges and other CNS border compartments serve as invasion sites for leukocyte influx into the brain thus promoting tissue damage after stroke. However, the post-ischemic immune response of border compartments compared to brain parenchyma remains poorly characterized .
Here, we deeply characterize tissue-resident leukocytes in meninges and brain parenchyma by flow cytometry, histology, and single cell transcriptomics after experimental stroke and discover that leukocytes respond differently to stroke depending on their site of residence. We thereby discover a unique phenotype of myeloid cells exclusive to the brain after stroke. These stroke-associated myeloid cells partially resemble neurodegenerative disease-associated microglia. They are mainly of resident microglial origin, partially conserved in humans and exhibit a lipid-phagocytosing phenotype. Blocking markers specific for these cells partially ameliorates stroke outcome thus providing a potential therapeutic target. The injury-response of myeloid cells in the CNS is thus compartmentalized, adjusted to the type of injury and may represent a therapeutic target.

overall_design: Single-cell RNA profiling of CD45iv-CD45+ TRL sorted from the brain parenchyma, pia and dura at 24h and 72h after transient middle cerebral artery occlusion compared to healthy control animals.

first: Carolin

last: Beuker

first: David

last: Schafflick

first: Jan-Kolja

last: Strecker

first: Gerd

last: Meyer zu Hörste

first: Jens

last: Minnerup


title: On/Off targets INDEL analysis  by Next Generation Sequencing

status: Public on Nov 11 2021

city: Santander

first: Lucio

last: Di Filippo

address: PCTCAN - Cl. Albert Einstein, 22

country: Spain

institute: IBBTEC

summary: SpCas9 INDEL frequency was evaluated at both the on- and off-target sites of guideRNA targeting either the murine Rhodopsin or Albumin by Next Generation Sequencing. Minimal INDELs were found at the off target sites evaluted, while SpCas9 activity was predominantly on-target.

overall_design: Three gRNA- and 2 scramble control-treated samples of either retina or liver were used to amplify the gRNA on-target and the top 10 off-target sites.

first: Patrizia

last: Tornabene

first: Rita

last: Ferla

first: Anna

last: Manfredi

last: Difilippo


title: HITI and INDEL analysis by next-generation sequencing

summary: SpCas9 INDEL frequency and HITI was evaluated at the on-target site of guide RNA targeting either the mouse or pig rhodopsin by next-generation sequencing.

sample_organism:
Sus scrofa
Mus musculus

platform_organism:
Sus scrofa
Mus musculus

overall_design: Two gRNA-treated samples of either mouse or pig were used to amplify the gRNA on-target site with forward primer that anneals to the mRho/pRho sequence and two reverse primers, one that anneals to mRho/pRho and the other to DsRed on the donor DNA.


title: 3D ECM-rich environment sustains the identity of naïve human iPSCs [Bulk RNA-seq in triplicate after 1, 4, and 7 days of culture]

summary: The establishment of in vitro naïve human pluripotent stem cell cultures opened new perspectives for the study of early events in human development. In the last 5 years the signalling environment promoting human naïve pluripotency has been extensively investigated. However, little is known about the role exerted by the extracellular matrix and three-dimensional organization in naïve maintenance. Here, by using an unbiased and integrated approach we found that naïve, but not primed, hiPSC colonies are characterized by an extracellular matrix-rich microenvironment, and by a specific extracellular matrix fingerprint at transcriptional, proteomic and secretome levels. Based on this, we developed a 3D culture system which supports robust long-term feeder-free expansion of naïve hiPSCs. In this same 3D ECM-rich environment, we can recapitulate timely developmental morphogenesis simply by modulating the signalling environment. Our study opens new perspectives for future applications of naïve hiPSCs to study critical stages of human development in three-dimensions starting from a single cell.

overall_design: Bulk RNA-seq in triplicate after 1, 4, and 7 days of culture. Microfluidic and standard plate culture of human fibroblasts (HFF-1), naïve iPSCs (isogenic, HFF-1-derived), and induced primed (isogenic, naïve iPSCs-derived) .

first: Elisa

last: Cesare

last: Urciuolo

first: Hannah

last: Stuart

first: Erika

last: Torchio

first: Cecilia

last: Laterza

first: Onelia

last: Gagliano

first: Sebastian

last: Martewicz

first: Meihua

last: Cui

last: Sabatelli

first: Stefano

last: Squarzoni

first: Irene

last: Zorzan

first: Graziano

last: Martello

first: Davide

last: Cacchiarelli

first: Camilla

last: Luni

first: Nicola

last: Elvassore


title: Single-Cell RNA-Seq reveals cellualr heterogeneity and gene expression difference between ischemic and hemorrhagic stroke brain

status: Public on Oct 31 2021

city: Shanghai

first: Xiaojing

last: Shi

state: Please Select

address: 1954 Huashan Rd.

country: China

institute: Shanghai Jiao Tong University

summary: Cluster analysis using nonlinear dimensionality reduction ([tSNE]) revealed the differences in global gene expression profiles of healthy and injured striatum, and identified clusters of cells with unique genetic signatures in both ischemic brain and hemorrhagic brain. Genes with p-value < 0.05 and fold change ≥1.5 were regarded as differentially expressed genes (DEGs). For astrocytes, 135 DEGs were downregulated in hemorrhagic stroke compared to ischemic stroke. The secondary profiling of astrocytic subtypes yielded 10 different subtypes with distinct functional cell identities. For microglia, tSNE map indicated the distribution and proportion of microglia/macrophage were very similar in in the ischemic and hemorrhagic stroke models.  We obtained 75 DEGs in total (hemorrhagic stroke vs. ischemic stroke, 54 were upregulated, 21 were downregulated) .

overall_design: comparison of gene exprssion difference between ischemic and hemorrhagic brain in mice

first: Yaohui

last: Tang

first: Guo-yuan

last: Yang


title: 3D ECM-rich environment sustains the identity of naïve human iPSCs

first: Lucio

last: Di Filippo

overall_design: Bulk RNA-seq. Microfluidic 3-day culture of human naïve iPSCs on MEF feeder layer (3 replicates) and on Vitronectin coating (3 replicates).

last: Cesare

first: Anna

last: Urciuolo

last: Manfredi

first: Patrizia


title: C57BL/6J tMCAO brain scRNAseq data

city: Ulju-gun

first: Wonhyo

last: Lee

state: Ulsan

address: Unist-gil 50

department: Biological Sciences

institute: UNIST

summary: Single Cell RNA sequencing data from C57BL/6J mouse brain hemisphere after 24hours and 48hours after tMCAO surgery.

overall_design: examination of Prdx1 effects on ischemia-reperfusion stroke in mus musculus with transient middle cerebral artery occlusion model

first: Sinai

last: Kim

first: Sung

middle: H

last: Park

first: Goo

middle: T

last: Oh


title: Developmental dynamics of sea urchin and sea star cis-regulation and the evolution of echinoderm genome organization

status: Public on Oct 24 2021

city: Seville

first: Marta

middle: Silvia

last: Magri

address: Carretera de Utrera km1

institute: Centro Andaluz de Biología del Desarrollo

type: Genome binding/occupancy profiling by high throughput sequencing

summary: We identified cis-regulatory elements based on their dynamic chromatin accessibility during the gastrula-larva stages of sea urchin and sea star and studied their evolution in these echinoderm species

overall_design: ATAC-seq assays in wild-type sea urchin embryos, at 48 hpf developmental stage

middle: S

first: Danila

last: Voronov

first: Maria

last: Arnone

first: Igniacio

last: Maeso

first: José

middle: L

last: Gómez-Skarmeta


title: Single-cell RNA sequencing identifies macrophage transcriptional heterogeneities in granulomatous diseases

status: Public on Sep 27 2021

city: Aurora

first: Ivana

state: CO

address: 1635 Aurora Ct

institute: University of Colorado

summary:
Purpose: Using single-cell RNA sequencing to explore the common and unique pathways between progressive (SarcP) and remitting (SarcR) sarcoidosis as well as chronic beryllium disease (CBD) and sarcoidosis, focusing on macrophages and macrophages subpopulations (recruited vs. resident).
Methods: We used scRNA-seq to analyze BAL cells from SarcP (N=2), SarcR (N=2), and CBD (N=3) compared to beryllium sensitized non-diseased subjects (BeS; N=2) or healthy control (Con; N=4). The controls were from Mould KJ, et al. Airspace Macrophages and Monocytes Exist in Transcriptionally Distinct Subsets in Healthy Adults. Am J Respir Crit Care Med 2020. We used the R package Seurat to project cells unto Uniform Manifold Approximation and Projection (UMAP) 2D space, identify cell clusters, and detect differentially expressed (DE) genes.
Results: We focused our analysis on macrophages (excluding cell clusters going through the cell cycle). We first compared disease groups to healthy control Using False Discovery Rate (FDR) adjusted p<0.05 and absolute log fold change (log FC)>0.25. We identified 191, 242, and 234 DE genes within all macrophages for the comparisons of SarcP vs. Con, SarcR vs. Con, and CBD vs. Con, respectively, with 82 genes common to all three comparisons; 47 out of the 82 genes were common to all comparisons in regards to recruited macrophages.
Conclusions: We focused this first single-cell transcriptome study in granulomatous lung disease on macrophages. This study offers investigators cell-specific transcriptional changes (genes and networks/pathways) to consider mechanisms of granulomatous disease and as potential drug targets.

overall_design:
Single-cell RNA-seq for granulomatous disease.

**Submitter declares that the raw data were not submitted due to patient privacy concerns**

first: Shu

middle: Y

last: Liao


title: Testing different rRNA removal methods in 4 species of model halophilic archaea

status: Public on Apr 14 2022

city: Durham

first: Amy

last: Schmid

state: NC

address: 125 Science Dr.

department: Biology

institute: Duke University

summary: We tested a number of rRNA removal methods (Illumina RiboZero Plus, NEBNext, NEB Core Depletion Set with custom probes, siTools Panarchaea, siTools RiboPool) on 4 model halophile species: Halobacterium salinarum, Haloferax volcanii, Haloferax meditteranei, Haloarcula hispanica). It was found that methods using custom probes (NEB Core Depletion set with HVO probes, siTools RiboPool with HVO probes) efficiently remove rRNA in species they are targeted to, and that Panarchaea efficiently removes rRNA in all 4 tested species.

sample_organism:
Halobacterium salinarum
Haloferax volcanii
Haloferax mediterranei
Haloarcula hispanica

overall_design: Cells were grown to mid-exponential phase and cell pellets were extracted and immediately frozen in liquid N2. After 1-7 days at -80C, total RNA was extracted from frozen cell pellets using the Absolutely RNA Miniprep kit made by Agilent, with additional DNase treatment as necessary. 1-10ng of total RNA was used as input for rRNA removal methods, for which we followed manufacturer's protocols (with the exception of longer RNase digestion of 120 minutes instead of 30 minutes, for some samples of HBT treated with NEB Core Depletion set, labeled NEB_HVO_120). dsDNA libraries were created using NEBMultiplex Oligos (part of the NEBNext protocol for the relevant samples). They were quantified and quality-checked using DNA High Sensitivity Chip for the Agilent Bioanalyzer and were sent for sequencing to the Duke Center for Genomic and Computational Biology, where they were sequenced on Illumina NovaSeq 6000.

first: Mar

last: Martinez-Pastor

first: Saaz

last: Sakrikar


title: Single-cell RNA-seq reveals the transcriptional landscape in ischemic stroke

status: Public on Sep 24 2021

city: Tianjin

first: Kai

last: Zheng

address: No.154 Anshan Road, Heping District

institute: Tianjin Medical University General Hospital

summary: Here, we employed single-cell RNA sequencing (scRNA-seq) to comprehensively map the cell populations in the mouse model of MCAO (middle cerebral artery occlusion).

overall_design: Single cell suspension was prepared from mouse brain tissues at 24 h after MCAO or sham-operations.

first: Junwei

last: Hao


title: High Glucose Macrophage Exosomes Enhance Atherosclerosis by Driving Cellular Proliferation & Hematopoiesis

status: Public on Aug 18 2021

city: Phoenix

first: Eric

last: Alsop

state: AZ

address: 445 N. Fifth Street

institute: TGen

type: Non-coding RNA profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: SARS-CoV-2 infection and replication in human  gastric organoids

status: Public on Sep 20 2021

first: Lucio

last: Di Filippo

summary: COVID-19 typically manifests as a respiratory illness but several clinical reports described gastrointestinal (GI) symptoms. This is particularly true in children, whom GI symptoms are frequent and viral shedding outlasts viral clearance from the respiratory system. These observations raise the question of whether the virus can replicate within the stomach. Here we show the novel derivation of gastric organoids from fetal, pediatric and adult biopsies and prove their value as in vitro models for SARS-CoV-2 infection. To facilitate infection, we induced a reversed polarity in our organoids (RP-GOs). The pediatric RP-GOs are fully susceptible to infection with SARS-CoV-2, while the viral replication is significantly lower in organoids of fetal and adult origin. Transcriptomic analysis shows a moderate innate antiviral response and the lack of differentially expressed genes belonging to the interferon family. Collectively, we show how the virus can efficiently infect gastric epithelium, suggesting that the stomach might have an active role in fecal-oral SARS-CoV-2 transmission.

overall_design: Transcriptomic analysis of organoids derived from fetal, pediatric and adult gastric samples infected by SARS-CoV-2 virus at MOI 1, and paired negative controls.

first: Giovanni

middle: G

last: Giobbe

first: Francesco

last: Bonfante

first: Elisa

last: Zambaiti

first: Onelia

last: Gagliano

first: Brendan

last: Jones

first: Camilla

last: Luni

first: Cecilia

last: Laterza

first: Silvia

last: Perin

first: Georg

last: Busslinger

first: Hannah

last: Stuart

first: Matteo

last: Pagliari

first: Alessio

last: Bortolami

first: Eva

last: Mazzetto

first: Anna

last: Manfredi

first: Chiara

last: Colantuono

first: Alessandro

last: Pellegata

first: Vivian

last: Li

first: Simon

last: Eaton

first: Nikhil

last: Thapar

first: Davide

last: Cacchiarelli

first: Hans

last: Clevers

first: Nicola

last: Elvassore

first: Paolo

last: De Coppi


title: High Glucose Macrophage Exosomes Enhance Atherosclerosis by Driving Cellular Proliferation & Hematopoiesis [RNA-Seq]

first: Eric

last: Alsop

summary: Hyperglycemia is a recognized risk factor for cardiovascular complications in diabetes. While hyperglycemia is known to cause microRNA dysregulation that contributes to cellular activation, whether it can do so through intercellular communication via extracellular vesicles (EVs) is not known. We investigated whether EVs produced under hyperglycemic conditions could communicate signaling to drive atherosclerosis. We did so by treating Apoe−/−mice with exosomes produced by bone marrow‐derived macrophages (BMDM) exposed to high glucose (BMDM–HG-exo) or control. Repeated infusion of BMDM–HG-exo led to a robust increase in hematopoiesis leading to augmented circulating myeloid cell numbers. Four weeks of BMDM–HG-exo infusions increased atherosclerotic lesion sizes with an accumulation of macrophage and apoptotic cells in the aortic root. Transcriptome-wide analysis of naïve cultured macrophages treated with BMDM–HG-exo showed an upregulation of genes associated with cell proliferation. Furthermore, BMDM–HG-exo reprogramed energy metabolism in recipient macrophages with an upregulation of glycolytic activity. Plasma EVs isolated from human subjects with type II diabetes exerted similar cell signaling when incubated with cultured human macrophages. Lastly, profiling microRNA in BMDM–HG-exo and human diabetic plasma EVs converged on miR-486 as commonly enriched. In conclusion, our findings show that EVs serve to communicate detrimental

overall_design: RNA-Seq

first: Bouchareychas

last: Laura

first: Alsop

last: Eric

first: Jensen

last: Kendall

first: Raffai

last: Robert


title: High Glucose Macrophage Exosomes Enhance Atherosclerosis by Driving Cellular Proliferation & Hematopoiesis [miRNA-Seq]

overall_design: miRNA-Seq


title: RNA Sequencing facilitates quantitative Analysis of differently expressed genes with negative control (NC) and siLINK-A treatment in rheumatoid fibroblast-like synoviocytes

status: Public on Aug 10 2021

city: Guangzhou

first: Jingnan

last: Wang

state: Guangdong

address: Zhongshan 2nd Road

institute: Department of Rheumatology and Immunology, The First Affiliated Hospital, Sun  Yat-sen University


title: RNA Sequencing facilitates quantitative analysis of lncRNA and mRNA expression in fibroblast-like synoviocytes from rheumatoid arthritis patients and trauma patients [microarray]

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

summary: Fibroblast-like synoviocytes (FLS), the active resident cell component in synovial intimal lining, play a critical role in aggressive action of synovial pannus tissue. The underlying mechanism of FLSs  in the progression of RA is still unknown. To evaluate the expression pattern of lncRNA and mRNA, we preformed microarray to determine its expression profiles in FLS separated from RA patients and trauma patients.

overall_design: FLSs were seperated from synovial tissues and cutured until passage 4. Total RNA was prepared using TRIzol from HC FLS (n=5) and RA FLS (n=5) and quantified by NanoDrop ND-1000.

first: J

first: C

last: Shen

first: R


title: Targeting tumor-macrophage interaction via the Notch2-Jag1 axis reverses tumor resistance to paclitaxel

status: Public on Jun 29 2021

city: Hefei

first: Fazhi

last: Yu

address: huangshan road 443

institute: USTC

summary: Taxanes are widely used in chemotherapy, but intrinsic and acquired resistance limit the clinical outcomes. Studies showed tumor interaction with suppressive macrophages plays a key role in taxane resistance, yet therapeutic strategies that deplete or repolarize macrophages are challenging. Here we uncovered a novel tumor-macrophage interaction via Notch2-Jag1 justacrine signaling that can be targeted to sensitize paclitaxel response without affecting the broad macrophage functions. Using translatome profiling, we identified Notch2 upregulation during taxol-induced prolonged mitosis. Notch2 was subsequently activated in the post-mitotic G1 phase by Jag1 expressed on neighboring macrophages, which promoted tumor cell survival by upregulating p38 and anti-apoptotic proteins. Notch2 also upregulated cytokines that further recruited Jag1-expressing macrophages. By targeting this Notch2-Jag1 interaction with a pan-Notch inhibitor, RO4929097, taxol resistance was significantly attenuated in multiple mouse tumor models. Our results point to combining Notch inhibitor with taxane as an effective strategy to selectively disrupt tumor-macrophage interaction underlying chemoresistance.

overall_design:
For ribosome profiling, HeLa cells were synchronized by double thymidine (2 mM, Sigma). Then the dishes were washed three times with PBS to release the cells in complete DMEM again. 9h later, DMSO and 5nM Taxol were added to each group, respectively. The mitosis cells were collected by shake-off. And the mitosis cells from DMSO and Taxol treatment were defined as mitosis(M) and prolonged mitosis(pM) cells, respectively. Mitotic (M) and prolonged mitotic (pM) HeLa cells were lysed in lysis buffer (20 mM Tris pH 7.5, 150 mM KCl, 5 mM MgCl2, 1 mM dithiothreitol, 8% glycerol) supplemented with 0.5% Triton X-100, 30 U/ml Turbo DNase (Ambion, Life Technologies, CA, United States) and 100 μg/ml cycloheximide (Sigma Aldrich, MO, United States). Ribosome protected fragments were then isolated and sequenced as previously described (PMID: 22056041). The resulting mRNAs were modestly fragmented by partial hydrolysis in bicarbonate buffer so that the average size of fragments was ∼80 bp. The fragmented mRNAs were separated by denaturing PAGE and fragments of 26–34 nt were selected. The sequencing libraries were prepared and sequenced as previously described (PMID: 22056041).The differential gene translation profile between M and pM were analyzed.
The differential gene expression profile between wild type and Notch2 knockdown OVCAR8 cell lines were analyzed. RNA was extracted from OVCAR8 cells using Trizol Reagent (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s protocol. Subsequently, total RNA was quantified using a Nano Drop and Agilent 2100 bioanalyzer (Thermo Fisher Scientific, MA, USA). The Beijing Genomics Institute (BGI, Shenzhen, China) performed the RNA integrity checking, library preparation and sequencing.Each group was performed in two replicates. Notch2 knockdown OVCAR8 cells were established using plko.1 lentivirus system and two shRNAs target different sequences on Notch2 mRNA were used. Subsequently, we confirmed the RNAseq result in ovarian cancer cells by qPCR (data not included).

first: Jing

last: Guo

first: Zhenye

last: Yang


title: Long noncoding RNA TP53TG1 suppresses the growth and metastasis of hepatocellular carcinoma by regulating the PRDX4/β-catenin pathway

status: Public on Jun 14 2021

city: wuhan

first: Baiyang

last: Chen

address: donghu road 169

institute: wuhan university

summary: Hepatocellular carcinoma (HCC) is a leading cause of cancer mortality worldwide. Resection, transplantation, locoregional therapy, targeted agents and immunotherapy have expanded treatment options, yet late presentation, recurrence, intrahepatic dissemination and drug resistance continue to limit durable benefit. The persistent mortality burden of liver cancer motivates the identification of molecular dependencies that can be validated mechanistically and, ultimately, exploited therapeutically. We identified TP53TG1 as a promising tumor suppressor LncRNA. To understand TP53TG1 target genes and the regulatory mechanisms, we performed RNA expression profiling in TP53TG1-overexpressed Huh7 cells and in control cells.

overall_design: Huh7 cells were transfected with TP53TG1 plasmid and empty vector respectively.  And then they were subjected to gene expression profiling.

first: Jianwei

last: Lan

first: Yusha

last: Xiao

first: Pengpeng

last: Liu


title: RNA-SEQ OF 24H TIME COURSE OF MOUSE FIBROBLASTS ENTRAINED WITH DIFFERENT CYCLIC METABOLIC  ENTRAINMENTS

status: Public on Jun 10 2021

first: Lucio

last: Di Filippo

summary: In our daily routine we are continually exposed to feeding ang fasting cycles, and it is important to take into consideration the overall coherence between metabolism and circadian rhythms. The loss of such a coherence, translating in a misalignment, may contribute to the weakening or desynchronization of oscillators.   In this study we asked whether the synchronization between the feeding-fasting cycles and the cell-autonomous clock affects the entire transcriptome of mouse fibroblasts in vitro. We found that in the metabolic entrainment proposed in this work and based on sustained 3 days of feeding and fasting cycles (HL, LH, HH), RNA-sequencing data from this work show a significant number of oscillating genes (N=500) belong to the transcriptome in all the dietary regimes. This result could be the consequence of the cyclical nature of the metabolic perturbations implemented in our study.    Moreover, our investigation has also shown that the fasting phase is important to have a phase polarization of the transcriptome, that is completely missing in the HH condition where the cells were always kept in high level of nutrients. It is worth mentioning that the misalignment leads to a polarized expression of ECM protein which is a typical mechanism of stimulated fibroblasts that is frequently associated with fibrosis. It was observed that this polarization involves different pools of genes and as consequence is enriched for different metabolic functions. All these findings confirm that regulation of metabolism by the circadian clock and its components is reciprocal, attesting that metabolism and circadian clocks are tightly interlocked: clocks drive metabolic processes, and various metabolic parameters affect clocks, producing complex feedback relationships.

overall_design: Comparison of the different effects of metabolic oscillations  on the transcrioptome entrainment

first: Onelia

last: Gagliano

first: Camilla

last: Luni

first: Yan

last: Li

first: Francesco

last: Panariello

first: Davide

last: Cacchiarelli

first: Joseph

last: Takahashi

first: Nicola


title: Single-cell and spatial mapping identify cell types and signaling networks in the human ureter

status: Public on Mar 31 2022

city: Houston

first: Angela

last: Ting

state: Tx

address: 1881 East Road

department: Epigenetics and Molecular Carcinogenesis

institute: The University of Texas MD Anderson Cancer Center


title: Noncanonical mRNA decay by the endoplasmic-reticulum stress sensor IRE1-alpha promotes cancer cell survival [GRO-seq]

status: Public on Jun 01 2021

city: South San Francisco

first: Thomas

middle: D.

last: Wu

state: CA

address: 1 DNA Way

institute: Genentech, Inc.

summary: Eukaryotic IRE1 mitigates endoplasmic-reticulum (ER) stress by orchestrating the unfolded-protein response (UPR). IRE1 spans the ER membrane, and signals through a cytosolic kinase-endoribonuclease module. The endoribonuclease generates the transcription factor XBP1s by intron excision between similar RNA stem-loop endomotifs, and depletes select cellular mRNAs through regulated IRE1-dependent decay (RIDD). Paradoxically, mammalian RIDD seemingly targets only mRNAs with XBP1-like endomotifs, while in flies RIDD exhibits little sequence restriction. By comparing nascent and total IRE1α-controlled mRNAs in human breast cancer cells, we discovered not only canonical endomotif-containing RIDD substrates, but also many targets lacking recognizable motifs—degraded by a process we coin RIDDLE, for RIDD lacking endomotif. IRE1α displayed two basic endoribonuclease modalities: endomotif-specific cleavage, minimally requiring dimers; and endomotif-independent promiscuous processing, requiring phospho-oligomers. An oligomer-deficient mutant that did not support RIDDLE failed to rescue cancer-cell viability. These results link IRE1α oligomers, RIDDLE, and cell survival, advancing mechanistic understanding of the UPR.

overall_design: GROseq in MDAMB231 cells WT and IRE1 KO, during triggered ER stress (Thapsigargin for 8h). This dataset is used to identified genome wide IRE1 RIDD targets (n=3 per group).

first: Adrien

last: Le Thomas

first: Elena

last: Ferri

first: Scot

last: Marsters

first: Jonathan

last: Harnoss

first: Zora

last: Modrusan

first: Weihan

first: Joachim

last: Rudolph

first: Weiru

last: Wang

first: Peter

last: Walter

first: Avi

last: Ashkenazi


title: Noncanonical mRNA decay by the endoplasmic-reticulum stress sensor IRE1-alpha promotes cancer cell survival


title: Noncanonical mRNA decay by the endoplasmic-reticulum stress sensor IRE1-alpha promotes cancer cell survival [RNA-seq]

overall_design: RNAseq in MDAMB231 cells WT and IRE1 KO, during triggered ER stress (Thapsigargin for 8h). This dataset is used to identified genome wide IRE1 RIDD targets (n=3 per group).


title: Regulatory T Cell-Microglia Crosstalk Promotes White Matter Repair after Ischemic Stroke through Osteopontin [scRNA-seq]

status: Public on May 19 2021

city: Pittsburgh

first: Xiaoming

last: Hu

state: PA

address: 200 lothrop street

department: Neurology

institute: University of Pittsburgh

summary: CD45high infiltrating immune cells were sorted from ischemic mouse brains at 5 days (5d) and 14 days (14d) after transient (60 min) middle cerebral artery occlusion (tMCAO) and subjected to scRNAseq.

overall_design: Ischemic hemispheres were harvested at 5 or 14 days after tMCAO. The CD45high cells were sorted by FACSAriaTM and send to scRNAseq.


title: Regulatory T Cell-Microglia Crosstalk Promotes White Matter Repair after Ischemic Stroke through Osteopontin


title: Differential gene expression and pathway analysis by RNA sequencing in human OPTN(E50K) astrocytes

status: Public on Apr 23 2021

city: INDIANAPOLIS

first: Xiaoyu

last: Lu

state: IN

address: 410W 10TH ST

department: school of medicine

institute: INDIANA UNIVERSITY

summary: Retinal ganglion cell (RGC) degeneration is a primary characteristic of glaucoma, although non-cell autonomous mechanisms have been implicated in RGC dysfunction. Astrocytes closely associate with RGCs in the nerve fiber layer of the retina and optic nerve, where they can contribute to RGC neurodegeneration. However, the mechanisms by which astrocytes promote neurotoxicity and contribute to glaucoma remain unclear. Here we present data describing disease phenotypes in astrocytes and their ability to modulate RGC health.

overall_design: Examination the differential gene expression from mRNA in human pluripotent stem cell-derived astrocytes underlying OPTN E50K mutation in comparison with wild-type OPTN

first: Catia

last: Gomes

first: Kirstin

last: VanderWall

first: Jason

last: Meyer


title: Sex differences in transcriptome profiles in hypothalamic and extrahypothalamic nuclei of rats impacted by adolescent stress

status: Public on Jun 06 2021

city: oxford

first: Haifei

last: Shi

state: OH

address: 700 E High Street

institute: Miami University

summary: In order to generate data worthy of translatability to known sex differences in human stress-induced maladies, adolescent male and female rats underwent chronic restraint stress (stress) or not (nonstress, control) from postnatal day (PD)32-PD44. Specific brain nuclei (PVN, VMH, ARC, BLA, CEA, CA1, CA3, DG, and OFC) were analyzed for genome-wide transcriptome using RNA sequencing (RNA-Seq). Global transcriptome profiles were generated, and genes differentially expressed (DE) due to stress were identified for each nuclear subregion listed. Canonical pathway analyses identified DE genes that are likely crucial for causing well-known stress-induced sex differences.

overall_design: adolescent male and female rats underwent stress or nonstress for 1 hour each day from  PD32-PD44. Specific brain nuclei (PVN, VMH, ARC, BLA, CEA, CA1, CA3, DG, and OFC) were analyzed for genome-wide transcriptome using RNA sequencing (RNA-Seq). Differential Expression transcriptional analyses between stress and nonstress for each sex and brain region were performed.

first: Kristen

middle: N

last: Krolick

first: Jingyi

last: Cao

first: Andor

middle: J

last: Kiss


title: Chronic social instability stress during adolescence does not change the acute stress response in adult male mice

status: Public on Apr 21 2021

city: Zürich

first: Lukas

middle: Matthias

last: von Ziegler

address: Winterthurerstrasse 190

department: D-HESZ

country: Switzerland

institute: ETH Zürich

summary: Chronic stress exposure in adolescence can lead to a lasting change in stress responsiveness later in life and is associated with increased mental health issues in adulthood. Here we investigate whether the Chronic Social Instability (CSI) paradigm in mice influences the molecular response to novel acute stressors

overall_design: Mice were either subjected to a chronic social instability (CSI) (random weekly chagemate changes for 7 weeks) paradigm, or kept as control animals (no cagemate changes). Then, a subset of both groups was subjected to a novel acute stressor in the form of restraint stress (30 min). 45min after onset of restraint stress animals were sacrificed and ventral hippocampi dissected and the transcriptome alanyzed with next generation sequecing

first: Oliver

last: Sturman

first: Johannes

last: Bohacek


title: RNA-seq and ATAC-sequencing of esophageal cells after HH pathway activation

status: Public on Apr 20 2021

city: Anderlecht

first: Alizee

last: Vercauteren Drubbel

address: 808 route de Lennik

country: Belgium

institute: Université Libre de Bruxelles


title: Single cell mRNA sequencing on esophageal cells after HH pathway activation

summary: In this study we used single cell mRNA sequencing to explore heterogeneity of the fate induced by hedgehog (HH) pathway activation in esophageal cells. We merged the data from the two samples and filtered the merged data to work only with cells expressing the SmoM2-YFP protein (2,413 cells). Using UMAP reduction, we observed 10 clusters with a resolution set at 0.3. Among these clusters, we identified clusters of squamous esophagus epithelial cells but also one cluster enriched for many columnar markers. These results show that activation of the HH pathway in esophageal keratinocytes leads to multiple cell phenotypes including a columnar epithelial one in a minority of keratinocytes.

overall_design: Oesophageal single cell mRNA profiles of Krt5SmoM2 mice by deep sequencing using 10x genomic and Illumina

first: Benjamin

last: Beck

first: Alizée


title: mRNA sequencing of esophageal cells and columnar cells from different tissues

summary: In this study, we used RNA sequencing to characterize esophageal progenitors following activation of the hedgehog (HH) pathway in vivo. We observed two main fates following activation of the HH pathway in the squamous epithelium: one population is in an intermediate state between squamous and columnar epithelium, and another achieves a full columnar conversion. We compared these 2 populations to different FACS sorted epithelial cells from different tissues of the gastro-intestinal tract (adult esophagus, embryonic esophagus, transition epithelium from the stomach,  corpus of the stomach and small intestine). Our results suggest a multistep process in which esophageal progenitors first turn on a transcriptomic program that resembles the one from embryonic esophagus, then, a subset of these dedifferentiated cells can turn on a columnar differentiation program that shares similarities with intestinal cells. Collectively, these data demonstrate that some esophageal cells can be reprogrammed to generate columnar cells in vivo.

overall_design: Oesophageal mRNA profiles of wild type (WT), K5SmoM2 and K5SmoM2-K8YFP mice by deep sequencing using Illumina


title: ATAC sequencing of esophageal cells from wild type and Krt5SmoM2 mice

summary: In this study, we used ATAC sequencing to compare the chromatin landscape of esophageal cells in which hedgehog (HH) pathway has been activated (K5SmoM2), to control esophageal cells (WT). We identified more than 50% of the peaks differentially opened in both conditions. Among these differentially opened peaks in EpHI cells, we identified chromatin regions in key columnar markers. Taken together these results show that HH pathway activation triggers chromatin landscape remodeling to facilitate transcommitment.

overall_design: Examination of chromatin modifications in esophageal cells from wild type (WT) and Krt5SmoM2 mice by deep sequencing using Illumina


title: TDP-43 Interactor and Motor Neuron Tagged Ribosome Affinity Purification in a Drosophila Model of ALS

status: Public on Mar 31 2021

first: Eric

last: Alsop

summary:
We report the enrichment of mRNAs with motor neuron specific TDP-43 and tagged ribosomes in control as well as multiple models of TDP-43 induced neurodegeneration.

Amyotrophic lateral sclerosis (ALS) is a genetically heterogeneous neurodegenerative disease in which 97% of patients exhibit cytoplasmic aggregates containing the RNA binding protein TDP-43. The goal of this study is to understand the translational consequences of TDP-43 pathology. Using the GAL4-UAS system, we expressed TDP-43WT and TDP-43G298S in the motor neurons of our drosophila to induce ALS-like neurodegeneration. TDP-43 was immunoprecipitated from the larvae at the 3rd instar stage; TDP-43 associated mRNAs, the whole larvae input, and ventral nerve cords of the same genotype were then sequenced. To identify translational changes we conducted TRAP (translating ribosome affinity purifications) in 3rd instar larvae by immunoprecipitating the motor neuron specific tagged ribosomal subunit RpL10-GFP in both ALS models as well as a RpL10-GFP control. The RpL10-GFP associated mRNAs, the whole larval input, and ventral nerve cords of the same genotype. From this data, we identified both compensatory alterations to translation induced by TDP-43 pathology and direct targets of TDP-43 mediated translational inhibition.

overall_design: Examination of mRNA association with TDP-43 and tagged ribosomal subunit RpL10 in motor neurons during TDP-43 induced neurodegeneration. The antibody used for both IPs was rabbit anti-GFP Lifetech A11122.

first: Erik

last: Lehmkuhl


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

status: Public on Apr 15 2021

city: Lund

first: Petter

last: Storm

address: Sölvegatan 19, BMC A11

department: Developmental and Regenerative Neurobiology

country: Sweden

institute: Lund University

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

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

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

first: Catharina

last: Svanborg

first: Ines

last: Ambite


title: CDK7 inhibitor THZ1 induces the cell apoptosis of B-cell acute lymphocytic leukemia by perturbing cellular metabolism

status: Public on Feb 20 2021

city: Shanghai

first: duan

middle: cai

last: wen

address: 1678 dongfang road

institute: Shanghai Children's Medical Center

summary:
Purpose:CDK7 is a potential drug target for the treatment of tumors. THZ1 is the first selective and covalent CDK7 inhibitor, which shows anti-tumor effects in various cancers by inhibiting cell proliferation and inducing apoptosis. However, whether THZ1 has an inhibitory effect on B-ALL cells and the underlying mechanism remains unclear. To address this question, we collected THZ1- and DMSO-treated cells for RNA sequencing
Methods:Nalm6 cells were seeded at a density of 1× 10e6 cells/ml and treated with 500nm THZ1or DMSO for 24h.
Results:THZ1 perturbed the cellular metabolic pathways of B-ALL cells in vitro.

overall_design: Nalm6 total mRNA profiles treated with 500nm THZ1 or DMSO for 24h.

first: Tuersunayi

last: Abudureheman

first: Jing

last: Xia

first: Ming-Hao

last: Li

first: Kai

last: Qing

first: Cai-Wen

last: Duan


title: Transcripts identified by microarray analysis that were deregulated in E10.5 Pax2-cre;Tbx2(fl/fl);Tbx3(fl/fl) (Tbx2/3cDKO) otocysts.

status: Public on Apr 04 2021

city: Hannover

first: Mark-Oliver

last: Trowe

address: Carl-Neuberg-Str. 1

department: Molekularbiologie

institute: Medizinische Hochschule Hannover

summary: Evaluation of the transcriptional changes in E10.5 otocysts upon loss of Tbx2 and Tbx3 in the otic epithelium.

overall_design: Total RNA from dissected otocysts of E10.5 Tbx2/3cDKO and control embryos was analyzed by microarray analysis.

first: Andreas

last: Kispert


title: single cell RNA-sequencing on triple negative G422-glioma(G422TN)

status: Public on Feb 11 2021

city: Wuhan

first: Liu

last: Feng

state: Hubei

address: 13 Hangkong Road, Hankou

department: School of Basic Medicine

institute: Huazhong University of Science and Technology

summary: The aim was to reveal cellular heterogeneity of orthotropic G422TN-glioma

overall_design: Control group:The seventh day after G422TN(5*104) inoculation into the brain, brain tumor tissue was taken for single cell isolation. LTS group: After combined therapy, the mice survived for more than 100 days, and the contralateral side of the brain received the same tumor inoculation again. The tumor-bearing mice survived again for more than 100 days. At this time, on the 7th day after tumor inoculation, the tumor tissue was obtained for single cell sequencing.

first: Xiao-qian

last: Chen

first: Feng

last: Liu


title: Post-transcriptional regulation of redox homeostasis by the small RNA SHOxi in haloarchaea

status: Public on Dec 08 2020

city: Baltimore

first: Diego

middle: Rivera

last: Gelsinger

state: MD

address: 910 Light Street, Apartment 2

institute: The Johns Hopkins Univeristy

summary: Oxidative stress responsive small non-coding RNAs (sRNAs) have been reported in the model archaeon, Haloferax volcanii, but targets and mechanisms of actions have not been elucidated. While haloarchaea are highly resistant to oxidative stress, a comprehensive understanding of the mechanisms regulating this remarkable response is lacking. Here, using a combination of high throughput and reverse molecular genetic approaches we elucidated the functional role of the most up-regulated intergenic sRNA during oxidative stress in H. volcanii, aptly named Small RNA in Haloferax Oxidative Stress (SHOxi). We demonstrated that SHOxi is a functional non-coding RNA that plays gene regulatory roles in the oxidative stress response of an extremophilic archaeon. We found that SHOxi likely regulates redox homeostasis during oxidative stress by the post-transcriptional destabilization of malic enzyme mRNA. The decrease in the NAD+/NADH ratio resulting from the direct RNA-RNA interaction between SHOxi and its trans-target is instrumental in the survival of H. volcanii. The regulatory effects of SHOxi provides evidence that the fine-tuning of metabolic cofactors could be a core strategy to mitigate damage from oxidative stress and confer resistance. This study is the first to establish the regulatory effects of sRNAs on mRNAs during the oxidative stress response in Archaea.

overall_design: H. volcanii auxotrophic strain H53 (Δpyre2, ΔtrpA) and H98 (Δpyre2, ΔthyH) were used for all experiments. Culturing in liquid and solid media was done in rich medium (Hv-YPC) or selection medium (Hv-Cab), at 42°C and with shaking at 220 rpm (Amerix Gyromax 737) (Dyall-Smith, 2009). Uracil, tryptophan, thymidine, and hypoxanthine were added to a final concentration of 50 µg/mL, each. H. volcanii liquid cultures were exposed to H2O2 as previously described (Gelsinger & DiRuggiero, 2018b). In brief, cultures were grown in 160 mL of Hv-YPC or Hv-Cab under optimal conditions to an OD of 0.4 (mid exponential phase). 2 mM H2O2 was directly added to the cultures followed by an hour incubation at 42 °C with shaking at 220 rpm. Cultures were then rapidly cooled down, centrifuged at 5,000 x g for 5 minutes and the pellets resuspended in 18% sea water. The cell suspensions were then transferred to a 1 mL tube and centrifuged at 6,000 x g for 3 minutes, the pellets were flash frozen and stored at -80 °C until ready for RNA extraction.  Total RNA was extracted using the Zymo Quick-RNA Miniprep kit with the following modifications: H. volcanii liquid culture is slimy and viscous thus to increase cellular lysis a 23 G needle and syringe were used to break down the cell pellet after addition of RNA lysis buffer to the frozen pellets to insure complete cell lysis. Total RNA was then extracted following the standard kit protocol. Total RNA was DNase I (NEB) treated (37 °C for 2 hours) as previously described (ref). Total RNA was then rRNA-depleted using the Ribo-zero Bacteria kit (Illumina). Strand-specific libraries were prepared using the SMART-seq Ultralow RNA input kit (Takara), insert sizes checked with the Bioanalyzer RNA pico kit (Agilent), and either paired-end sequenced (2 x 150 bp) or single-end sequenced (100 bp) on the Illumina HiSeq 2500 platform at the Johns Hopkins University Genetic Resources Core Facility (GRCF). We used a read count-based differential expression analysis to identify putative targets of SHOxi that were differentially expressed during oxidative stress and in ΔSHOxi. The program featureCounts was used to rapidly count reads that map to the NCBI H. volcanii annotation. featureCounts was run with strand-specific options on, paired-end mode on or off, multi-mapping off. The read counts were then used in the R differential expression software package DESeq2 (ref). Briefly, read counts were converted into a data matrix and normalized by sequencing depth and geometric mean. Differential expression was calculated by finding the difference in read counts between the SHOxi knockout oxidative stress state to the normalized read counts from the wild-type oxidative stress normalized read counts. The differentially expressed mRNAs were filtered based on the statistical parameter of False Discovery Rate (FDR) under 5%. In addition, only mRNAs with converse differential expression levels (FDR < 5%) in our previous wild type no challenge/oxi stress differential expression comparison (Gelsinger & DiRuggiero, 2018b) were labeled as specific putative targets of SHOxi.

middle: R

first: Rahul

last: Reddy

first: Kathleen

last: Whittington

first: Sara

last: Debic

first: Jocelyne

last: DiRuggiero


title: DNA methylation profiles of F1 mice sperm of the control group and arsenic group II

city: Tsukuba

first: Keiko

last: Nohara

address: 16-2 Onogawa

department: Center for Health and Environmental Risk Research

institute: National Institute for Environmental Studies

type: Methylation profiling by high throughput sequencing

summary: Pregnant C3H mice were given tap water (control group) and tap water containing 85 ppm sodium arsenite from gestational day 8 to 18 (arsenic group), respectively. The DNA methylomes of sperm of F1 mice were investigated by RRBS method. The results showed that gestational arsenic exposure increased hypomethylated cytosines in active retrotransposon subfamilies. The present study has indicated environmental impacts on sperm DNA methylome establishment.

overall_design: Five DNA samples of purified sperm were prepared from F1 mice (17-19 weeks of age) born to the control dams and gestationally arsenite exposed dams, respectively, and subjected to RRBS analysis.


title: CDK9 inhibitor induces the apoptosis of acute lymphocytic leukemia by inhibiting c-Myc-mediated glycolytic metabolism

status: Public on Feb 09 2021

first: duan

last: wen

summary:
Purpose:the inhibitory effect of CDK9i on the energy metabolism of B-ALL cells remains unclear. To address this question, we collected SNS-032- and DMSO-treated cells for RNA sequencing
Methods:REH cells were seeded at a density of 1× 106 cells/ml and treated with 200nm SNS_032 or DMSO for 24h.
Results:CDK9i perturbs the glycolytic metabolism of B-ALL cells in vitro.

overall_design: REH total mRNA profiles treated with 200nm SNS_032 or DMSO for 24h.

first: Wen-Li

last: Huang

first: Sa

last: Guo

first: Gang

last: Yin


title: Genome-wide occupancy of conditionally-expressed wild-type and Lys120-to-Arg (K120R) p53 in H1299 cells.

status: Public on Dec 02 2020

city: New York

first: Manoj

last: Kandpal

state: NY

address: 1230 York Ave

department: Hospital Bioinformatics

institute: Rockefeller University

summary: The tumor suppressor p53 integrates stress response pathways, triggering the appropriate cell fate by selectively engaging one of a diverse set of transcriptomes (e.g., cell cycle arrest, apoptosis). Foundational to this process is the binding of tetrameric p53 to response elements (REs) in the genome, of the consensus sequence (RRRCWWGYYYN0-13RRRCWWGYYY). This unusually long and degenerate RE provides a potential mechanism for contextually activating distinct sets of downstream targets. However, the RE code underlying this selectivity remains undeciphered. p53 REs exhibit the highest sequence variability at the triplets RRR/YYY, which flank the core (CWWG) sequence, and p53 tetramers interact with REs at those bases via Arg248 from the DNA minor groove and Lys120 from the DNA major groove. This set of observations triggered our hypothesis that the interplay of Lys120 and Arg248 residues with variable sequences of REs might be a potential source of p53 selectivity. To gain insight into the role of Lys120 integrity in the recognition of specific RE sequences, we performed a ChIP-seq experiment and analyzed genome-wide occupancy of conditionally-expressed wild-type (WT) and K120R forms of p53 in isogenic human cell lines that are null for endogenous p53. Using an optimized data analysis workflow, we mapped about 35 million unique sequence reads per sample to the human genome, and the number of significantly enriched peaks in each replicate was detected by setting an enrichment cutoff of 0.3 counts per million reads. This study presents a foundation for analysis of differences in sequences between K120R-sensitive and K120R-insensitive p53 binding sites.

overall_design: ChiP-seq profiles of WT and K120R-p53 forms in untreated [Tet(-)] and Tetracycline treated [(Tet(+)] 1299 cells.

first: Marina

last: Farkas

first: Yingtao

last: Bi

first: Ramana

middle: V

last: Davuluri

first: Adam

last: Ertel


title: Identification of Hepatic Genes Regulated by ATF3 using Next Generation Sequencing

status: Public on Nov 26 2020

city: Phoenix

first: Yanqiao

last: Zhang

address: 475 N 5th Street

institute: University of Arizona COM - Phoenix

summary: This study aimed to investigate how many genes were regulated by hepatocyte ATF3. C57BL/6J mice were injected intravenously with adeno-associated virus (AAV) expressing human activating transcription factor 3 (ATF3) under the control of an albumin promoter (AAV8-ALB-ATF3) or AAV8-ALB-Null). After 8 weeks, liver samples were used for RNA sequencing using Illumina NextSeq 500. Over 3000 genes were found to be up- or down-regulated by ATF3.

overall_design: Ten weeks old C57BL/6J mice were intravenoulsy injected with AAV8-ALB-ATF3 or AAV8-ALB-Null (control) (n=8 per group). After 8 weeks, total RNA was extracted and cDNA libraries were prepared. RNA sequencing was carried out using Next-Seq 500. Data were analyzed using Illumina Softwares in BaseSpace.

first: Yingdong

last: Zhu

first: Yanyong

last: Xu


title: Mirc11 role in myeloid differentiation

status: Public on Nov 18 2020

city: South Bend

first: Richard

last: Dahl

address: Harper Hall 227, 1234 Notre Dame Ave.

department: Microbiology and Immunology

institute: Indiana University School of Medicine, South Bend

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

overall_design: Refer to individual Series


title: Gene expression of Mirc11-/- hematopoietic myeloid progenitors

summary: Compared gene expression between Lin-Sca1-cKit+ myeloid progenitors isolated from the bone marrow of 6-8 week old wildtype and Mirc11-/- mice. Previously observed that overexpression of Mirc11 in hematopoietic progenitors increased myeloid differentiation whereas loss of Mirc11 decreased myeloid differentiation. Performed RNA-seq to identify potential genes involved in myeloid differentiation regulated by Mirc11.  Gene expression analysis of Mirc11 deficient myeloid progenitors revealed a decrease in Toll like receptor and interferon signaling. This anti-inflammatory phenotype was further observed in mature cells as Mirc11-/- bone marrow derived macrophages (BMDMs) have an attenuated response to inflammatory lip-opolysaccharide (LPS).

overall_design: Sequenced total RNA obtained from Lin-Sca1-cKit+ bone marrow cells obtained from cohorts of wildtype and Mirc11 deleted mice.

first: Austin

last: Boucher


title: Scalable pooled CRISPR screens with single cell chromatin accessibility profiling.

status: Public on Nov 07 2020

first: Neville

last: Sanjana

address: 101 Avenue of the Americas

institute: New York Genome Center

summary: A scalable, cost-effective method that combines CRISPR perturbations with a single-cell indexing assay for transposase-accessible chromatin (CRISPR-sciATAC). This method links genome-wide chromatin accessibility to genetic perturbations through simultaneous capture of ATAC-seq fragments and CRISPR guide RNAs from single cells using a 96-well plate combinatorial indexing approach.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Single cell ATAC-seq and CRISPR sgRNA capture for K562 cells and a mixture of NIH3T3 cells and HEK293T cells.

first: Noa

last: Liscovitch-Brauer

first: Antonino

last: Montalbano

first: Jiale

last: Deng

first: Alejandro

last: Méndez-Mancilla

first: Hans-Hermann

last: Wessels

first: Nicholas

last: Moss

first: Chia-Yu

last: Kung

first: Akash

last: Sookdeo

first: Xinyi

first: Evan

last: Geller

first: Suma

last: Jaini

first: Peter

last: Smibert

middle: E


title: Chromatin occupancy assessment an AML cell line treated with vehicle control, BETi, MDM2i, or a drug combination (BRD4-bound profiles)

status: Public on Nov 04 2020

city: La Jolla

last: Adams

address: 10901 North Torrey Pines Road

department: Cancer Genome and Epigenetics Program

institute: Sanford Burnham Prebys Medical Discovery Institute

summary:
BRD4 chromatin occupancy changes in human OCI-AML3 cells treated with DMSO (vehicle control), the BET inhibitor CPI-203, the MDM2 inhibitor Nutlin-3a, or a combination of both drugs, were compared.
Method: Genomic DNA from the OCI-AML3 cell line treated for 24 hrs with either DMSO, CPI-203, Nutlin-3a or a combination of both drugs was extracted, BRD4-bound chromatin was immunoprecipitated, then DNA was sequenced with an Illumina NextSeq 500 sequencer. Sequence reads passing the quality control filters were aligned using Bowtie2 and then analysed with SICER.

overall_design: BRD4-bound chromatin profiles from drug-treated human OCI-AML3 cells were generated, in duplicate, using an Illumina NextSeq 500 sequencer.

first: Ashley

last: Newcombe

middle: D

first: Kathryn

last: Gilroy


title: The miR-23a~27a~24-2 microRNA cluster promotes inflammatory polarization of macrophages

first: Richard

last: Dahl

summary:
Purpose: RNA-sequencing was performed to identify gene expression changes between bone marrow derived macrophages isolated from wildtype and mirn23a-/- (Mirc11-/-) mice that were either M1 or M2 polarized.
Results: Diferential gene expression was examined between wildtype and mirn23a-/- M1 polarized macrophages and wildtype and mirn23a-/- M2 polarized macrophages. The number of genes with significant (p<0.05) 2-fold changes in our M1 dataset is 4-fold higher than the 2-fold changed genes in our M2 dataset. 43 unique genes were differentially expressed over 2-fold in M1 mutant macrophages compared to wildtype with 29 upregulated and 14 downregulated. 10 genes (8 downregulated/ 2 upregulated)were differentially expressed in mirn23a-/- M2 macrophages by at least 2-fold compared to wildtype.

overall_design: Wildtype and mirn23a-/- (Mirc11-/-) bone marrow derived macrophage gene expression profiles after 24h of polarization (M1 or M2 conditions).

first: Sridhar

last: Rao

first: Kirthi

last: Pulakanti


title: Chromatin occupancy assessment an AML cell line treated with vehicle control, BETi, MDM2i, or a drug combination (p53-bound profiles)

summary:
p53 chromatin occupancy changes in human OCI-AML3 cells treated with DMSO (vehicle control), the BET inhibitor CPI-203, the MDM2 inhibitor Nutlin-3a, or a combination of both drugs, were compared.
Method: Genomic DNA from the OCI-AML3 cell line treated for 24 hrs with either DMSO, CPI-203, Nutlin-3a or a combination of both drugs was extracted, p53-bound chromatin was immunoprecipitated, then DNA was sequenced with an Illumina NextSeq 500 sequencer. Sequence reads passing the quality control filters were aligned using Bowtie2 and then analysed with MACS.

overall_design: p53-bound chromatin profiles from drug-treated human OCI-AML3 cells were generated, in quadruplicate, using an Illumina NextSeq 500 sequencer.

first: Anne-Louise

last: Latif


title: Deep sequencing of an AML cell line, with and without p53, treated with vehicle control, BETi, MDM2i, or a drug combination

summary:
Gene expression changes were compared in human OCI-AML3 cells, with or without p53 knock down, that were treated with DMSO (vehicle control), the BET inhibitor CPI-203, the MDM2 inhibitor Nutlin-3a, or a combination of both drugs. compared.
Method: OCI-AML3 cells were transduced with either empty vector or vector expressing an shRA targeting p53. Cells were then treated for 24 hrs with either DMSO, CPI-203, Nutlin-3a or a combination of both drugs. PolyA mRNA was extracted, in triplicate, then sequenced with an Illumina NextSeq 500 sequencer. Sequence reads passing the quality control filters were aligned using Tophat2 and then analysed with Cufflinks.

Keywords: Expression profiling by high throughput sequencing

overall_design: polyA mRNA profiles from drug-treated human OCI-AML3 cells with or without p53 were generated, in triplicate, using an Illumina NextSeq500 sequencer.


title: Deep sequencing of an AML cell line treated with vehicle control, BETi, MDM2i, or a drug combination

summary:
Gene expression changes in human OCI-AML3 cells treated with DMSO (vehicle control), the BET inhibitor CPI-203, the MDM2 inhibitor Nutlin-3a, or a combination of both drugs, were compared.
Method: poly-A mRNA from the OCI-AML3 cell line treated for 24 hrs with either DMSO, CPI-203, Nutlin-3a or a combination of both drugs was extracted, in triplicate, then sequenced with an Illumina NextSeq500 sequencer. Sequence reads passing the quality control filters were aligned using Tophat2 and then analysed with Cufflinks.

overall_design: polyA mRNA profiles from drug-treated human OCI-AML3 cells were generated, in triplicate, using an Illumina GAIIx sequencer.


title: Dissecting esophageal squamous-cell carcinoma ecosystem by single-cell transcriptomic analysis

status: Public on Oct 29 2020

city: Beijing

first: Xiannian

last: Zhang

address: 10 YouAnMen Xitoutiao, Fengtai District

department: Department of neurology

institute: Captital Medical University

summary: Esophageal squamous-cell carcinoma (ESCC), one of the most prevalent and lethal malignant disease, has a complex but unknown tumor ecosystem. Here, we decipher for the first time the full compositions of ESCC tumor based on analyzing 208,659 single-cell transcriptomes in ESCC derived from 60 individuals. We identify 8 essential expression programs from malignant epithelial cells and discovered 43 cell types including 26 immune cell and 17 nonimmune stromal cell subtypes in the tumor microenvironment (TME), and also explicate the interactions between cancer cells and other cells and the interactions among different cell types in the TME. Moreover, we have linked the cancer cell transcriptomes to the somatic mutations and identified several markers significantly associated with survival time in patients, which may be relevant to precision cares of ESCC patients. These results renew our understanding of ESCC and provide a valuable example and resource for investigating other types of solid tumor.

overall_design:
We performed scRNA-seq on 60 ESCC tumor and 4 adjacent normal tissue samples obtained from 60 individuals using 10X Genomics platform.
Raw data is available at https://bigd.big.ac.cn/gsa-human/ under the accession ID of HRA000195.

For the details or customized demand of Raw and Processed data, please feel free to contact Prof Zhang (xiannian@ccmu.edu.cn). We are glad to help.

first: Linna

last: Peng

first: Yingying

last: Guo

first: Wenjia

first: Jiacheng

last: Yao

first: Mingming

last: Shao

first: Wenyi

last: Fan

first: Yamei

last: Chen

first: Qionghua

last: Cui

first: Yiyi

last: Xi

first: Yanxia

last: Sun

first: Xiangjie

last: Niu

first: Xuan

last: Zhao

first: Liping

first: Yuqian

last: Wang

first: Yachen

last: liu

first: Jianbin

first: Chen

last: Wu

first: Dongxin

last: Lin


title: Single cell analysis reveals onset of multiple progression associated transcriptomic remodellings in prostate cancer

status: Public on Oct 22 2020

city: Chengdu

first: Guanghui

last: Zhu

state: Sichuan

address: 8 Linyin Street

institute: Sichuan University

summary: Dissecting heterogeneity of prostate tumors is a clinical imperative. Here, we analyzed the transcriptomes of 36,424 single-cells from 13 prostate tumors, and identified lineage specific epithelial cells underlying disease aggressiveness. Activation of various progression-associated transcriptomic programs exists in the tumor microenvironment (TME). Notably, we observed promiscuous KLK3 expression in TME and validated the ability of tumor-derived exosomes in altering T cell transcriptomes. Single-cell profiling of a high-risk patient tumor and lymph nodes provided evidence that KLK3 ectopic expression is associated with micrometastases. Close cell-cell communication exists among tumor and TME cells. We identified an endothelial subset harboring active communication (aEC) with tumor cells. Together with sequencing of an additional 11 samples, we showed that aECs are enriched in castration-resistant prostate cancer and promote cancer cell invasion. Finally, we created a user-friendly web interface (www.pradcellatlas.com) for the sequenced data as a resource for the research community.

overall_design:
The 13 prostate tumor samples used in this study were collected from patients who had undergone radical prostatectomy at Shanghai Changhai Hospital. Single cell RNA sequencing was performed with 10XGenomics.

>>>Submitter states that raw data are not available due to patient privacy concerns<<<

first: Shancheng

last: Ren


title: Human fetal and pediatric primary gastric samples and organoids derived from them

status: Public on Oct 01 2020

city: Santander

first: Lucio

last: Di Filippo

address: PCTCAN - Cl. Albert Einstein, 22

institute: IBBTEC

summary: Reliable modelling of human stomach development and in vitro derivation of mature subsets of gastric epithelial cells has been challenging to achieve in 3D cultures. We derived fetal gastric organoid cultures from 8-20 post-conception week (PCW) stomachs, and post-natal controls from pediatric biopsies.

overall_design: mRNA profiles of human primary gastric tissues and cultured organoid derived from fetal and pediatric gastric tissues of different stages.

first: Giovanni

last: Giobbe

first: Francesco

last: Bonfante

first: Elisa

last: Zambaiti

first: Onelia

last: Gagliano

first: Brendan

middle: C

last: Jones

first: Camilla

last: Luni

first: Cecilia

last: Laterza

first: Silvia

last: Perin

first: Hannah

last: Stuart

first: Matteo

last: Pagliari

first: Alessio

last: Bortolami

first: Eva

last: Mazzetto

first: Anna

last: Manfredi

first: Chiara

last: Colantuono

first: Alessandro

last: Pellegata

first: Vivian

last: Li

first: Simon

last: Eaton

first: Nikhil

last: Thapar

first: Davide

last: Cacchiarelli

first: Nicola

last: Elvassore

first: Paolo

last: De Coppi


title: SARS-CoV-2 infection and replication in human fetal and pediatric gastric organoids

first: Lucio

last: Di Filippo

summary: Coronavirus disease 2019 (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection is a global public health emergency. COVID-19 typically manifests as a respiratory illness but an increasing number of clinical reports describe gastrointestinal (GI) symptoms. This is particularly true in children in whom GI symptoms are frequent and viral shedding outlasts viral clearance from the respiratory system. By contrast, fetuses seem to be rarely affected by COVID-19, although the virus has been detected in placentas of affected women. These observations raise the question of whether the virus can infect and replicate within the stomach once ingested. Moreover, it is not yet clear whether active replication of SARS-CoV-2 is possible in the stomach of children or in fetuses at different developmental stages. Here we show the novel derivation of fetal gastric organoids from 8-21 post-conception week (PCW) fetuses, and from pediatric biopsies, to be used as an in vitro model for SARS-CoV-2 gastric infection. Gastric organoids recapitulate human stomach with linear increase of gastric mucin 5AC along developmental stages, and expression of gastric markers pepsinogen, somatostatin, gastrin and chromogranin A. In order to investigate SARS-CoV-2 infection with minimal perturbation and under steady-state conditions, we induced a reversed polarity in the gastric organoids (RP-GOs) in suspension. In this condition of exposed apical polarity, the virus can easily access viral receptor angiotensin-converting enzyme 2 (ACE2). The pediatric RP-GOs are fully susceptible to infection with SARS-CoV-2, where viral nucleoprotein is expressed in cells undergoing programmed cell death, while the efficiency of infection is significantly lower in fetal organoids. The RP-GOs derived from pediatric patients show sustained robust viral replication of SARS-CoV-2, compared with organoids derived from fetal stomachs. Transcriptomic analysis shows a moderate innate antiviral response and the lack of differentially expressed genes belonging to the interferon family. Collectively, we established the first expandable human gastric organoid culture across fetal developmental stages, and we support the hypothesis that fetal tissue seems to be less susceptible to SARS-CoV-2 infection, especially in early stages of development. However, the virus can efficiently infect gastric epithelium in pediatric patients, suggesting that the stomach might have an active role in fecal-oral transmission of SARS-CoV-2.

overall_design: Transcriptomic analysis of organoids derived from fetal and pediatric gastric samples infected by SARS-CoV-2 virus at MOI 1, and paired negative controls.

first: Giovanni

last: Giobbe

first: Francesco

last: Bonfante

first: Elisa

last: Zambaiti

first: Onelia

last: Gagliano

first: Brendan

last: Jones

middle: T


title: Rice domestication-associated miRNA 397 targets laccases to facilitate lignin biosynthesis and yield-related traits [Degradome]

status: Public on Sep 30 2020

city: Bangalore

first: Shivaprasad

last: Padubidri V.

address: GKVK Campus, Bellary road

department: Plant epigenetics

country: India

institute: National Center for Biological Sciences

summary: MicroRNAs (miRNAs) are a class of 21 nt non-coding small RNAs (sRNAs) produced from endogenously expressed MIR genes. MiRNAs are mostly involved in development and disease resistance. To know the involvement of miRNAs during domestication of rice, sRNA sequencing of two wild species (O. nivara and O. rufipogon), one landrace (O. sativa chomala) and one cultivated species of rice (O. sativa indica Pusa Basmati-1) was carried out. Analysis of sRNA datasets revealed a surprisingly higher abundance of 22nt sRNAs originating from a loci on Chromosome 2 in wild rice species. This locus codes for a 22 nt miRNA named as miR397. Studies in Arabidopsis and O. sativa japonica nipponbare have shown that miR397 targets a group of proteins called laccases, which are involved in secondary metabolite (lignin) production. The expression of these targets also differs across the species shown through RNA-Seq analysis. Although a functional significance of this interaction between the miRNA and laccase has not been understood. In the current study we attempt to explain the functional relevance of the miRNA in domestication of rice.

sample_organism:
Oryza nivara
Oryza sativa Indica Group

platform_organism:
Oryza nivara
Oryza sativa Indica Group

overall_design: We have performed degradome sequencing of 4-week old seedling and, flagleaf and panicle of two rice species.

first: Padubidri

last: Shivaprasad

first: Swetha

last: Chenna


title: Macrophage Exosomes Resolve Atherosclerosis by Regulating Hematopoiesis and Inflammation via MicroRNA Cargo

status: Public on Aug 06 2020

first: Eric

last: Alsop

address: 445 N. Fifth Street

institute: TGen

summary: Developing strategies that promote the resolution of vascular inflammation and atherosclerosis remains a major therapeutic challenge. Here, we show that exosomes produced by naive bone marrow-derived macrophages (BMDM-exo) contain anti-inflammatory microRNA-99a/146b/378a that are further increased in exosomes produced by BMDM polarized with IL-4 (BMDM-IL-4-exo). These exosomal microRNAs suppress inflammation by targeting NF-kB and TNF-a signaling and foster M2 polarization in recipient macrophages. Repeated infusions of BMDM-IL-4-exo into Apoe_x0001_/_x0001_ mice fed a Western diet reduce excessive hematopoiesis in the bone marrow and thereby the number of myeloid cells in the circulation and macrophages in aortic root lesions. This also leads to a reduction in necrotic lesion areas that collectively stabilize atheroma. Thus, BMDM-IL-4-exo may represent a useful therapeutic approach for atherosclerosis and other inflammatory disorders by targeting NF-kB and TNF-a via microRNA cargo delivery.

overall_design: 14 samples were analyzed. 6 samples were cell lysates (3 controls, 3 stimualted macrophages). 8 samples were extracellular exosomes (4 controls, 4 stimulated macrophages)

first: Robert

last: Raffai

first: Kendall

last: Jensen

first: Laura

last: Bouchareychas


title: Intersectional analysis of chronic mild stress-induced lncRNA-mRNA interaction networks in rat hippocampus reveals potential anti-depression/anxiety drug targets

status: Public on Aug 21 2020

city: Chongqing

first: Jian

last: Zhou

state: China

address: 1 Yixueyuan Road, Yuzhong District

department: Institute of Neuroscience

institute: Chongqing Medical University

summary: Despite studies providing insight into the neurobiology of chronic stress, depression and anxiety, long noncoding RNA (lncRNA)-mediated mechanisms underlying the common and distinct pathophysiology of these stress-induced disorders remain nonconclusive. In a previous study, we used the chronic mild stress paradigm to separate depression-susceptible, anxiety-susceptible and insusceptible rat subpopulations. In the current study, lncRNA and messenger RNA (mRNA) expression was comparatively profiled in the hippocampus of the three stress groups using microarray technology. Groupwise comparisons identified distinct sets of lncRNAs and mRNAs associated with the three different behavioral phenotypes of the stressed rats. To investigate the regulatory roles of the dysregulated lncRNAs upon mRNA expression, correlations between the differential lncRNAs and mRNAs were first analyzed by combined use of weighted gene coexpression network analysis and ceRNA theory-based methods. Subsequent functional analysis of strongly correlated mRNAs indicated that the dysregulated lncRNAs were involved in various biological pathways and processes to specifically induce rat susceptibility or resiliency to depression or anxiety. Further intersectional analysis of phenotype-associated and drug-associated lncRNA-mRNA networks and subnetworks assisted in identifying 16 hub lncRNAs as potential targets of anti-depression/anxiety drugs. Collectively, our study established the molecular basis for understanding the similarities and differences in pathophysiological mechanisms underlying stress-induced depression or anxiety and stress resiliency, revealing several important lncRNAs that represent potentially new therapeutic drug targets for depression and anxiety disorders.

overall_design: After the tests, animals were decapitated, and the entire brain was rapidly removed. Then, we separated hippocampal tissues from the brain. After weighing the brains, we froze them rapidly in liquid N2 and stored them at a temperature of −80°C. Total RNA was extracted from tissues with TRIzol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer’s instructions. Moreover, we measured RNA quality and quantity with a NanoDrop ND-1000. Then, we evaluated RNA integrity using standard electrophoresis.the hippocampus tissues were prepared for microarray data analysis

first: Ming-zhong

last: Xiao

first: Yu

last: Chen


title: The Effect of Compound Kushen Injection on Cancer Cells: Integrated Identification of Candidate Molecular Mechanisms

status: Public on Aug 05 2020

city: Pittsburgh

last: Cui

address: Assembly building, 5051 Centre Ave

department: Department of Immunology

institute: University of Pittsburgh

summary: Compound Kushen Injection (CKI) is a TCM fomula  has been in use in hospitals in China for over twenty years for the integrated treatment of cancer.There is little evidence based medicine supporting such complex mixture. Because TCM preparations are often combinations of multiple herbs containing hundreds of compounds, they have been difficult to study.  The development of high throughput -omics methods has allowed better characterization of TCM. We have applied high-throughput transcriptome data in two additional cancer cell lines and integrated our differential expression results across cell lines to identify a reduced set of differentially expressed (DE) candidate genes as well as a reproducible set of candidate pathways that are perturbed by CKI. In our results,CKI induced cell-cycle arrest and apoptosis. We identified 363 core candidate genes that were associated with cell cycle, apoptosis, DNA replication/repair and various cancer pathways. Of these, 7 are known to be clinically relevant to cancer diagnosis or therapy and 14 are cell cycle regulators, and most of these 21 candidates are downregulated by CKI. Comparison of our core candidate genes to a database of plant medicinal compounds and their effects on gene expression identified one-to-one, one-to-many and many-to-many regulatory relationships between compounds in CKI and DE genes.By identifying a number of promising candidate pathways and genes associated with CKI based on our transcriptome based analysis, we have shown this type of approach is useful for the systematic analysis of molecular changes resulting from complex mixtures of bioactives in the context of cancer therapy.

overall_design: High-depth paired-end RNA-seq from HEPG2 and MDA-MB-231 cell lines. Each sample contains 3 biological replicates.

first: David

last: Adelson


title: Comprehensive analysis of the complexity and heterogeneity of the lncRNAs transcriptome in multiple myeloma

city: Pamplona

first: Xabier

last: Agirre

state: Navarra

address: Pio XII, 55

department: Oncology

institute: CIMA

summary: ssRNA-seq analysis of the transcriptional landscape of 38 multiple myeloma patients

overall_design: Bone marrow aspiration specimens from 38 newly diagnosed MM patients were obtained. MM plasma cells were purified by CD138+ positive magnetic separation using AutoMACS system. Total RNA was isolated using TRIzol® Reagent extraction method.

first: Felipe

last: Prosper

first: Teresa

last: Ezponda

first: Arantxa

last: Carrasco-Leon


title: The Tumor Microenvironment and Inflammation Influence toxicity in patients with Large B Cell Lymphoma Treated with Axicabtagene Ciloleucel [RNA-Seq]

status: Public on Jul 27 2020

city: Tampa

first: Marco

last: Davila

state: FL

address: 12902 Usf Magnolia Dr

department: BMT-CI

institute: Moffitt Cancer Center and Research Institute

summary: We aimed to identify factors that place patients with Large B Cell Lymphoma at higher risk of developing severe immune mediated toxicities after CAR T infusion. Tumor biopsies were taken within one month prior to CAR T infusion for evaluation of gene expression. In pre-treatment patient tumor biopsies, we found that gene expression of  myeloid markers was associated with higher toxicity.

overall_design:
Tumor biopsies were taken within one month of CAR T infusion in a cohort of 25 patients and prospectively snap-frozen. We compared gene expression of the pre-treatment biopsy samples  of patients who developed severe immune mediated toxicities ( Grade > 3 neurotoxicity) vs. those with grade 0-2 toxcities after CAR T infusion.

We compared patients who went on to have a durable response (DR) to those with a non-durable response (NDR) in patients that had sufficient follow up (minimum 6 months post-CAR T infusion).

first: Michael

last: Jain

first: Rawan

last: Faramand


title: The Tumor Microenvironment and Inflammation Influence toxicity in patients with Large B Cell Lymphoma Treated with Axicabtagene Ciloleucel

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

overall_design: Refer to individual Series


title: Single-cell RNA-sequencing of carotid artery ,vein graft and vena cava in mouse models

status: Public on Jul 06 2020

city: London

first: Zhichao

last: Ni

address: 125 Coldharbour Lane, James Black Centre, King's College London

country: United Kingdom

institute: King's College London

summary: We reported the transcriptional profiling of cells in a mouse model of vein grafts by single-cell RNA sequencing.

overall_design: This entry contains 10X Single-cell RNA-seq data of cells of  carotid artery , 4 weeks vein graft and vena cava

first: Ni

last: Zhichao

first: Deng

last: Jiacheng

first: Gu

last: Wenduo

first: Xu

last: Qingbo


title: Role of FTO in ovarian cancer

status: Public on Jul 01 2020

first: Manoj

last: Kandpal


title: Role of FTO in ovarian cancer (RNA-Seq)

summary: RNA methylation plays an important role fine tuning translation and subsequently regulating cellular responses and cell fate. The fat mass- and obesity-associated protein (FTO) was recognized as an m6A demethylase and described as an oncogenic factor in leukemia and brain tumors. FTO expression levels are suppressed in ovarian tumors and ovarian cancer stem cells (CSCs). FTO induce cyclic AMP activity through targeting PDE4B and PDE1C by down-regulation of m6A levels in the mRNA transcript. In all or findings point to a tumor suppressor function of FTO in high grade serous OC. FTO induce cyclic AMP activity through targeting PDE4B and PDE1C by down-regulation of m6A levels in the mRNA transcript. In all or findings point to a tumor suppressor function of FTO in high grade serous OC

overall_design:
GFP (control) or FTO-GFP (treatment) over-expression in OVCAR-5 cells
3 biological replicates for GFP and 3 biological replicates for FTO-GFP in RNA-seq

first: Kandpal

last: Manoj

first: Hao

last: Huang

first: Daniela

last: Matei


title: Role of FTO in ovarian cancer (MeRIP-Seq)

summary: RNA methylation plays an important role fine tuning translation and subsequently regulating cellular responses and cell fate. The fat mass- and obesity-associated protein (FTO) was recognized as an m6A demethylase and described as an oncogenic factor in leukemia and brain tumors. FTO expression levels are suppressed in ovarian tumors and ovarian cancer stem cells (CSCs). FTO induce cyclic AMP activity through targeting PDE4B and PDE1C by down-regulation of m6A levels in the mRNA transcript. In all or findings point to a tumor suppressor function of FTO in high grade serous OC

overall_design:
GFP (control) or FTO-GFP (treatment) over-expression in OVCAR-5 cells
3 biological replicates for IgG input for GFP, 3 biological replicates for m6A pull-down for GFP, 3 biological replicates for IgG input for FTO-GFP, and 3 biological replicates for m6A pull-down for FTO-GFP


title: Deep sequencing of human fibroblastic cell line IMR90, either proliferating or senescent,  expressing either empty vector or Parkin, with or without CCCP treatment

status: Public on Jun 30 2020

first: Peter

last: Adams

summary:
Gene expression changes were compared in proliferating and senescent human IMR90 cells, with either empty vector, Parkin, or Parkin+CCCP.
Method: RNA was extracted, in triplicate, then sequenced with an Illumina NextSeq 500 sequencer. Sequence reads passing the quality control filters were aligned using Tophat2 and then analysed with Cufflinks.

overall_design: polyA mRNA profiles from proliferating or senescent human IMR90 cells, with either empty vector, parkin, or parkin plus CCCP, were generated, in triplicate, using an Illumina NextSeq 500 sequencer.

first: Maria-Grazia

last: Vizioli

first: Kathryn

last: Gilroy


title: Cell Senescence


title: Next Generation Sequencing timecourse of murine hepatocytes with or without paracetamol treatment

summary:
Untreated mice or mice treated with paracetamol, in the presence or absence of TSA, were culled after 14 hrs or 24 hrs of treatment, and RNAseq was performed.
Method: RNA was extracted, in triplicate, then sequenced with an Illumina NextSeq 500 sequencer. Sequence reads passing the quality control filters were aligned using Tophat2 and then analysed with Cufflinks.

overall_design: Quadruplicate polyA mRNA profiles from mouse hepatocytes were generated following various drug treatment protocols, using an Illumina NextSeq 500 sequencer.


title: Deep sequencing of human fibroblastic cell line IMR90, either proliferating or senescent,  with or without TSA treatment.

summary:
Gene expression changes were compared in proliferating and senescent human IMR90 cells, with or without TSA treatment.
Method: RNA was extracted, in triplicate, then sequenced with an Illumina NextSeq 500 sequencer. Sequence reads passing the quality control filters were aligned using Tophat2 and then analysed with Cufflinks.

overall_design: polyA mRNA profiles from proliferating or senescent human IMR90 cells, with or without TSA, were generated, in triplicate, using an Illumina NextSeq 500 sequencer.


title: RNA sequencing of miRNA in plasma from myocardial ischemia and reperfusion mice and sham mice

status: Public on Apr 18 2020

first: Sheng

last: Wang

address: 660 W Redwood Street, Howard Hall 564

department: Anesthesiology

institute: University of Maryland Baltimore

summary:
Purpose: The aim of this study is to compare the plasma miRNA profile between mice subject to myocardial ischemia and reperfusion and mice subject to sham operation.
Methods: 8 to 10-week old C57BL/6 mice underwent myocardial ischemia and reperfusion (MIR) or Sham operation. Plasma RNA was isolated using Trizol LS reagent 4h post-surgery. NGS cDNA libraries were prepared using Norgen Biotek Small RNA Library Prep Kit. Library quality was validated prior to sequencing on an Illumina NextSeq 500 platform.

overall_design: 8 to 10 weeks old male C57BL/6 mice were subject to myocardial ischemia and reperfusion (8 mice) or sham surgery (6 mice). Plasma was collect for RNA isolation 4 hour post-surgery. cDNA librarues were sequenced using Illumina NextSeq 500 platform.

first: Yang

last: Yang

first: Wei

last: Chao


title: Single-cell RNA-sequencing of CD45+ cells isolated from mouse dura mater or brain after photothrombotic injury

status: Public on May 18 2020

city: Daejeon

first: Bong Ihn

last: Koh

address: 291 Daehakro

institute: Korea Advanced Institute of Science and Technology

summary: To further elucidate molecular differences in immune cells and identify potential sources of Vegfa in response to photothrombotic injury, we performed single-cell RNA-sequencing of CD45+ cells isolated from the mouse dura mater or brain after photothrombotic injury.

overall_design: 3 days after photothrombotic injury on 8-week-old mice, CD45+ cells of the dura mater or brain were isolated by FACS and subjected to single-cell RNA-sequencing using the 10X Chromium system.

first: Bong

middle: I


title: Gene expression profile at single cell level of human melanoma cell lines, normal human melanocytes and human nevus cells (bulk RNAseq)

status: Public on May 22 2020

city: Salt Lake City

first: Robert

last: Judson-Torres

state: Utah

address: 2000 Circle of Hope

department: Dermatology

institute: Huntsman Cancer Institute at the University of Utah

summary: We generated a live reporter for tumor-initiating cells in the 501MEL human melanoma line. We conducted mRNA sequencing of reporter high and reporter low expressing cells.

overall_design: Reporter high and low populations were sorted directly into trizol. RNA was harvested and sequenced.


title: TAK-418-418, a LSD1 inhibitor, can rescue the genome wide chromatin abnormality in hippocapmus tissue in KMT2D+/bGeo mice  after 2 week treatment

status: Public on Mar 11 2020

city: Ellicott city

first: Li

last: Zhang

state: Maryland

address: 733N Broadway

department: Department of Human Genetics

institute: The Johns Hopkins University


title: TAK-418-418, a LSD1 inhibitor, can rescue the genome wide chromatin abnormality in hippocapmus tissue in KMT2D+/bGeo mice  after 2 week treatment [RNA-seq]

summary: Mutation in KMT2D, a histone-lysine N-methyl transferase, is responsible for majority of Kabuki syndrome in human. A mouse model of Kabuki syndrome with heterzygous mutation of KMT2D, KMT2D+/bGeo was created to understand the disease mechanism and for drug discovery. TAK-418-418, a lysine-specific histone demethylase (LSD1) inhibitor, was tested on these mice for therapeutic treatment of the disease. Differences between expression levels among different experimental conditions was evaluated by high throughput RNA sequencing (RNA-Seq).

overall_design: Wild type mice and KMT2D+/bGeo mice were treated with either TAK-418-418 (3-4 per group) or vehicle control (3-4 per group) starting at age of 2-week  old. Hippacampi were harvested at the end of 2-week treatment. Global chromatin changes were investigated by high throughput CHIPSEQ of H3K4me1 and H3K4me3.

first: Hans

last: Bjornsson