title: Comparative bulk RNAseq analysis of CXCL12-deficient bone marrow stromal cells (BMSCs), Cxcl12-GFP+ BMSCs versus CXCL12-deficient Cxcl12-GFP+ BMSCs.

status: Public on Oct 27 2020

city: Houston

first: Noriaki

last: Ono

state: Texas

department: School of Dentistry

institute: University of Texas Health Science Center at Houston

summary: We revealed the unique molecular signature characterizing CXCL12-deficient Cxcl12-GFP+ bone marrow stromal cells.

overall_design: Control: GFP+ cells were FACS-isolated from postnatal day 21 (P21) femurs of Cxcl12(GFP/fl); R26R-tdTomato mice. ∆CXCL12: GFP+tdTomato+ cells were FACS-isolated from P21 femurs of Col2a1-cre; Cxcl12(GFP/fl); R26R-tdTomato mice. mRNA were amplifed by SMARTer mRNA-seq kit (Clonetech/Takara) before deep-sequenced by Illumina HiSeq4000.


title: SWI/SNF inactivation in the endometrial epithelium leads to loss of epithelial integrity [ChIP-seq]

status: Public on Oct 20 2020

city: Grand Rapids

first: Ronald

middle: L.

last: Chandler

state: MI

department: Obstetrics, Gynecology and Reproductive Biology

country: USA

institute: Michigan State University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Although ARID1A mutations are a hallmark feature, mutations in other SWI/SNF (SWItch/Sucrose Non-Fermentable) chromatin remodeling subunits are also observed in endometrial neoplasms. Here, we interrogated the roles of Brahma/SWI2-related gene 1 (BRG1, SMARCA4), the SWI/SNF catalytic subunit, in the endometrial epithelium. BRG1 loss affects more than one-third of all active genes and highly overlaps with the ARID1A gene regulatory network. Chromatin immunoprecipitation studies revealed widespread subunit-specific differences in transcriptional regulation, as BRG1 promoter interactions are associated with gene activation, while ARID1A binding is associated with gene repression. However, we identified a physiologically relevant subset of BRG1 and ARID1A co-regulated epithelial identity genes. Mice were genetically engineered to inactivate BRG1 specifically in the endometrial epithelium. Endometrial glands were observed embedded in uterine myometrium, indicating adenomyosis-like phenotypes. Molecular similarities were observed between BRG1 and ARID1A mutant endometrial cells in vivo, including loss of epithelial cell adhesion and junction genes. Collectively, these studies illustrate overlapping contributions of multiple SWI/SNF subunit mutations in the translocation of endometrium to distal sites, with loss of cell integrity being a common feature in SWI/SNF mutant endometrial epithelia.

overall_design: Wild-type Human 12Z endometriotic epithelial cells were assayed by chromatin immunoprecipitation (ChIP) for BRG1 followed by sequencing.

first: Jake

middle: J

last: Reske

first: Mike

middle: R

last: Wilson

middle: L


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

status: Public on Oct 31 2020

city: Chicago

first: Carole

last: Ober

state: IL

address: 920 E 58TH ST

department: Human Genetics

institute: The University of Chicago

type: Expression profiling by high throughput sequencing

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

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

first: Britney

middle: A

last: Helling

first: William

last: Wentworth-Sheilds


title: SWI/SNF inactivation in the endometrial epithelium leads to loss of epithelial integrity

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: Identification of hormone interactions important for mammary gland proliferation and gene expression

status: Public on Oct 25 2020

city: Davis

first: Russell

last: Hovey

state: CA

address: 1 Shields Ave

department: Animal Science

institute: University of California Davis

summary:
Using our unique and authentic animal model, the pig, we determined which genes in the normal mammary gland are regulated in response to different combinations of the ovarian hormones estrogen and progesterone and the pituitary hormone prolactin. We surgically removed ovaries from 32 pigs to deplete endogenous estrogen and progesterone, and administered bromocriptine to suppress endogenous prolactin. Pigs were treated with all combinations of estrogen, progesterone and bromocriptine and/or haloperidol (to induce prolactin secretion), in a factorial design. Affymetrix arrays were used to analyze RNA from the mammary glands of these pigs and we found that estrogen, prolactin and the interaction of estrogen*prolactin were the primary regulators of gene expression in the mammary gland.  This is in contrast to rodents where progesterone has an important role in ductal elongation and branching.  Functional enrichment analyses suggest that estrogen promotes cell division while prolactin stimulates elements of fatty acid metabolism and an inflammatory response (in addition to milk protein genes).  These results concur with phenotypic changes where estrogen, prolactin and estrogen*prolactin were the most important regulators of morphological development, cell proliferation and steroid receptor expression.
Regression analysis of expression data against the rate of cell proliferation in all 32 pigs identified 1669 genes correlated with proliferation (FDR a=0.01). Regression analysis of expression data against proliferation in the 16 pigs treated with E identified 71 genes correlated with proliferation. 29 genes were common to both lists and also regulated by estrogen, and of these 16 have known functions in the cell cycle while the other 13 have never been associated with estrogen regulated mammary gland growth or cell proliferation. Twenty six of these genes were more highly correlated with proliferation than MKI67 (Ki67).

overall_design: Thirty six porcine mammary gland RNA samples were analyzed.  Four were from sham-operated saline treated controls.  All hormone treatment combinations were given to four pigs

first: Josephine

middle: F

last: Trott

middle: C


title: Histone H3.3 G34 mutations promote aberrant PRC2 activity and drive tumor progression [ChIP-Seq]

status: Public on Oct 12 2020

city: Madison

first: Peter

middle: W

last: Lewis

state: Wisconsin

address: 330 N Orchard Street

department: Department of Biomolecular Chemistry

institute: University of Wisconsin-Madison

summary: A remarkably high frequency of pediatric gliomas and bone tumors harbor monoallelic, missense mutations in genes encoding histone variant H3.3 at Glycine 34. We find that G34 mutations distinctly impede H3K36 methylation by SETD2. Consequently, the reduction of H3K36 methylation leads to high levels of PRC2-mediated H3K27me3 on G34 mutant nucleosomes. We find that H3.3G34W expression in murine mesenchymal stem cells (mMSCs) promotes aberrant gain of H3K27me2/3 and loss of H3K27ac at active enhancers containing SETD2. mMSCs expressing H3.3G34W display a unique transcriptional program that is dependent on PRC2 activity *in cis* and exhibit enhanced tumor development *in vivo*. Altogether, we demonstrate that H3.3G34 oncohistones selectively promote PRC2 activity by interfering with SETD2-mediated H3K36 methylation. We propose that PRC2-mediated silencing of enhancers involved in cell differentiation represents a potential mechanism that drives these malignancies.

overall_design:
To understand the chromatin profile alterations caused by oncogenic H3.3G34W mutation
Cells expressing H3.3WT or G34W mutations were probed for changes in chromain modification profiles.

first: Siddhant

middle: U

last: Jain


title: Expression data for 1) pear host resistance allowed by transgenic expression of apple Rvi6 resistance gene and 2) nonhost resistance against scab

status: Public on Oct 08 2020

city: BEAUCOUZE

first: Emilie

last: VERGNE

address: 42 rue Georges MOREL

country: France

institute: INRAE

summary: Comparative analyze at the transcriptomic level 1) of Venturia pyrina pear host resistance via the major apple resistance gene Rvi6, in Rvi6 overexpressing transgenic pear versus ‘conference’ susceptible variety; 2) of Venturia inaequalis pear nonhost resistance, in ‘Conference’ variety, 24 and 72 hours post inoculation.

overall_design: For host resistance analyses, sampling concerned the youngest expanded leaf of each plant labeled the day of the inoculation with Venturia pyrina VP102 strain. Each sample is a pool of leaves from three different plants. Two biological repeats (genotype x treatment x time) were collected during two independent scab inoculation tests. Leaf samples taken just before inoculation (T0) and at 8, 24 and 72 hours post inoculation of these two biological repeats are used to perform transcriptomics analyses. At each time, the ‘Conference’ variety is used as a susceptible reference and compare to the resistant Rvi6 overexpressing transgenic line 60AU. For nonhost resistance analyses, sampling concerned the youngest expanded leaf of each ‘Conference’ plant labeled the day of the inoculation with Venturia inaequalis EUB04 strain. Each sample is a pool of leaves from three different plants and two biological repeats (n=2) have been made by condition (genotype x treatment x time). Leaf samples taken just before inoculation (T0) and at 24 and 72 hours post inoculation are used to perform transcriptomics analyses: T0 versus 24hpi and T0 versus 72 hpi.

last: Vergne

first: Laure

last: Perchepied

first: Elisabeth

last: Chevreau

first: Elisa

last: Ravon

first: Sandrine

last: Balzergue

first: Muriel

last: Bahut

first: Sandra

last: Pelletier

first: Sylvain

last: Gaillard


title: Expression data for apple Rvi6 host resistance and nonhost resistance against scab

summary: Comparative analyze at the transcriptomic level 1) of Venturia inaequalis apple host resistance via the major resistance gene Rvi6, in Rvi6 overexpressing transgenic apple versus ‘Gala’ susceptible variety; 2) of Venturia pyrina apple nonhost resistance, in ‘Gala’ variety, 24 and 72 hours post inoculation.

overall_design: For host resistance analyses, sampling concerned the youngest expanded leaf of each plant labeled the day of the inoculation with Venturia inaequalis EUB04 strain. Each sample is a pool of leaves from three different plants. Two biological repeats (genotype x treatment x time) were collected during two independent scab inoculation tests. Leaf samples taken just before inoculation (T0) and at 8, 24 and 72 hours post inoculation of these two biological repeats are used to perform transcriptomics analyses. At each time, the ‘Gala’ variety is used as a susceptible reference and compare to the resistant Rvi6 overexpressing transgenic line GalaRvi6. For nonhost resistance analyses, sampling concerned the youngest expanded leaf of each ‘Gala’ plant labeled the day of the inoculation with Venturia pyrina VP102 strain. Each sample is a pool of leaves from three different plants and two biological repeats (n=2) have been made by condition (genotype x treatment x time). Leaf samples taken just before inoculation (T0) and at 24 and 72 hours post inoculation are used to perform transcriptomics analyses: T0 versus 24hpi and T0 versus 72 hpi.


title: Precise Genome Editing in vivo with Single, Canonical AAV Vectors. Encoding Guide RNA, Cas9, and Homologous Repair Donor

status: Public on Oct 19 2020

city: Worcester

first: Athma

last: Pai

state: MA

address: 368 Plantation Street, ASC5-2057

department: RNA Therapeutics Institute

institute: University of Massachusetts Medical School

summary: Adeno-associated virus (AAV) vectors are important delivery platforms for therapeutic genome editing but are severely constrained by cargo limits, especially for large effectors like Cas9s. Simultaneous delivery of multiple vectors can limit dose and efficacy and increase safety risks. The use of compact effectors has enabled single-AAV delivery of Cas9s with 1-3 guides for edits that use end-joining repair pathways, but many precise edits that correct disease-causing mutations in vivo require homology-directed repair (HDR) templates. Here, we describe  single-vector, ~4.8-kb AAV platforms that express Nme2Cas9 and either two sgRNAs to produce segmental deletions, or a single sgRNA with an HDR template. We also examine the utility of Nme2Cas9 target sites in the vector for self-inactivation. We demonstrate that these platforms can effectively treat two disease models [type I hereditary tyrosinemia (HT-I) and mucopolysaccharidosis type I (MPS-I)] in mice. These results will enable single-vector AAVs to achieve diverse therapeutic genome editing outcomes.

overall_design: This study consists of 59 samples total. FAH and HPD were the gene targets for our samples, which include multiple replicates for each sample and also negative controls (PBS, scramble guide RNA, and scramble donor DNA). Libraries were made for the following mice: 3 PBS treated Fahneo/neo, 8 dual-sgRNA Design 1 treated Fahneo/neo, 8 dual-sgRNA Design 4 treated Fahneo/neo, 3 healthy C57BL/6, 4 dual-sgRNA Design 1 treated C57BL/6, 4 dual-sgRNA Design 4 treated C57BL/6, 3 PBS treated FahPM/PM, 3 rAAV:HDR:FahDonor:ncSpacer treated FahPM/PM, 3 rAAV:HDR:ncDonor:FahSpacer treated FahPM/PM, 10 rAAV:HDR:uncleaved treated FahPM/PM, and 10 rAAV:HDR:cleaved treated FahPM/PM

first: Raed

last: Ibrahim

first: Eraj

last: Khokhar

first: Nida

last: Javeed


title: Scar-free healing and axon regeneration after spinal cord injury in neonatal mice is orchestrated by microglia

status: Public on Oct 07 2020

city: Los Angeles

first: Riki

last: Kawaguchi

address: 760 Westwood Plaza, Room 37-420

department: Department of Neurology and Department of Psychiatry

institute: University of California Los Angeles

summary: By utilizing single-cell analysis at different times after P2 injury(0, 3, and 5 dpi), we discovered that neonatal microglia undergo a transient activation and play at least two critical roles in scar-free healing. First, they transiently secrete fibronectin and its binding proteins, to form extracellular matrix bridges that ligate the severed ends. Second, neonatal, but not adult, microglia express a number of extracellular and intracellular peptidase inhibitors, along with other molecules involved in inflammatory resolution.

overall_design: Five 10X genomics chromium samples from neonatal mice microglia cells with 3 conditions (0, 3, and 5 dpi).

first: Yi

last: Li

first: Xuelian

last: He

first: Yu

last: Zhang

first: Qing

last: Wang

first: Aboozar

last: Monavarfeshani

first: Huyan

last: Meng

first: Zhiyun

last: Yang

first: Vivek

last: Swarup

first: Phillip

last: Popovich

first: Dan

last: Geschwind

first: Zhigang


title: Microphysiological System Modeling of Ochratoxin A-Associated Nephrotoxicity

status: Public on Oct 22 2020

city: Seattle

first: James

middle: William

last: MacDonald

state: WA

address: 4225 Roosevelt Way NE

department: Environmental and Occupational Health Sciences

institute: University of Washington

summary: Ochratoxin A (OTA) is one of the most abundant mycotoxin contaminants in food stuffs and possesses carcinogenic, nephrotoxic, teratogenic and immunotoxic properties.  Especially, severe nephrotoxicity is of great concern, as characterized by degeneration of epithelial cells of the proximal tubules and interstitial fibrosis.  However, its mechanism of toxicity, hazard identification as well as genetic risk factors contributing to OTA toxicity in humans has been elusive due to the lack of adequate models that fully recapitulate kidney function in vitro.  The present study attempts to evaluate dose-response relationships, identify the contribution of active transport proteins that govern renal disposition of OTA, and determine the role of metabolism in bioactivation and detoxification of OTA using a 3D human kidney proximal tubule microphysiological system (kidney MPS).  We demonstrated that IC50 values of OTA in kidney MPS culture (0.375 – 1.21 µM) were in good agreement with clinical toxic concentrations of OTA in urine.  Surprisingly, no enhancement of kidney injury biomarkers was evident in the effluents of kidney MPS after OTA exposure despite significant toxicity observed by LIVE/DEAD staining, rather these biomarkers were decreased in OTA concentration-dependent manner.   Furthermore, the effect of 1-aminobenzotriazole (ABT) and 6-(NBD-4-ylthio-) hexanol (NBDHEX), pan-inhibitor of P450 and GST enzymes, respectively, on the OTA-induced toxicity in kidney MPS was examined, which resulted in significant enhancement of OTA-induced toxicity by NBDHEX  (3 µM) treatment whereas ABT (1 mM) treatment decreased OTA-induced toxicity, suggesting the roles of GSTs and P450 enzymes in the detoxification and bioactivation of OTA, respectively.  Additionally, OTA transport studies using kidney MPS in the presence and absence of inhibitor of organic anion transporter(s), probenecid (1 mM), revealed the role of organic anionic membrane transporter(s) in the kidney specific disposition of OTA.  Our findings provide a better understanding of the mechanism of OTA-induced kidney injury which may support changes in risk assessment, regulatory agency policies on allowable exposure levels and determination of genetic factors in high-risk populations against OTA nephrotoxicity.

overall_design: Human kidney proximal tubule epithelial cells (PTEC) from two donors were seeded into a total of 34 kidney chips, and effluents of kidney MPS were exposed to 0 to 100 µM OTA  for 72 or 168 hours.

first: Tomoki

last: Imaoka

first: Jade

first: Lu

first: Matthew

middle: G

last: McDonald

first: Zahra

last: Afsharinejad

first: Theo

middle: K

last: Bammler

first: Kirk

last: Van Ness

first: Catherine

last: Yeung

first: Allan

middle: E

last: Rettie

first: Jonathan

last: Himmelfarb

first: Edward

last: Kelly


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

state: Cantabria

address: PCTCAN - Cl. Albert Einstein, 22

country: Spain

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

last: Jones

first: Camilla

last: Luni

first: Cecilia

last: Laterza

first: Silvia

last: Perin

first: Hannah

middle: T

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

middle: S

last: Li

first: Simon

last: Eaton

first: Nikhil

last: Thapar

first: Davide

last: Cacchiarelli

first: Nicola

last: Elvassore

first: Paolo

last: De Coppi


title: Effects of proto-Y chromososomes and temperature on house fly gene expression

status: Public on Sep 01 2020

first: Richard

last: Meisel

state: TX

address: 3455 Cullen Blvd

department: Biology and Biochemistry

institute: University of Houston

summary:
Purpose: House fly has a stable polygenic sex determination system. The male determining factor (Mdmd) is commonly found on the Y chromosome (Y^M) or the third chromosome (III^M). These proto-Y chromosomes are clinally distributed, with Y^M found most commonly in northern latitudes and III^M most commonly found at southern latitudes, hinting at possible genotype-by-temperature interactions that maintain the polymorphism. If this distribution is maintained by temperature-dependent selection pressures, we expect the fitness of III^M and Y^M flies to vary across developmental temperatures. These temperature-dependent effects could be driven by differential gene expression in III^M and Y^M males at different temperatures. Here, we performed RNA-seq experiments to study how genotype-by-temperature interactions affect gene expression in male houseflies carrying different proto-Y chromosomes.
Methods: We raised a Y^M strain known as IsoCS and a III^M strain known as CSrab at 18°C and 29°C for two generations. We dissected 5 heads and 15-20 pairs of testes for each of three replicates of each genotype-by-temperature combination. We carried out RNA-seq on these tissues.
Results: We identified 247 genes whose expression in testis and 50 genes whose expression in head depends on genotype-by-temperature  interactions.

overall_design: We carried out RNA-seq on head and testis from two isogenic strains differing only in their proto-Y chromosomes, raised at two different developmental temperatures. We used three biological replicates for each tissue type at each temperature.

first: Kiran

last: Adhikari

middle: P


title: Robust mitotic regeneration by hidden progenitors after ablation of Lgr5+ cochlear cells

status: Public on Aug 01 2020

city: Baltimore

first: yang

last: song

state: MD

address: HSF-3, 3rd Floor; 670 W Baltimore St.

department: Department: Institute for Genome Sciences

institute: University of Maryland in Baltimore

summary: We identified a subpopulation within the Lgr5+ cells serving as progenitor cells for supporting cell regeneration in the inner ear.

overall_design: Gene expression pattern of undamaged and DTR-damaged Glast-Cre+ cells in the mouse inner ear was assessed at P4 using the RiboTag model.

first: Alan

last: Cheng

first: Tomokatsu

last: Udagawa

first: Beatrice

last: Milon

first: Patrick

last: Atkinson

first: Yang

last: Song

first: Elvis

middle: H

last: Najarro

first: Mirko

last: Scheibinger

first: Ronna

last: Hertzano


title: Global landscape of RNA editing in hematopoiesis

status: Public on Sep 29 2020

city: Beijing

first: Jiahuan

last: HE

state: Beijing

address: Dong dan san tiao wu hao xie he ji chu suo

department: Department of Biochemistry and Molecular Biology

country: China

institute: Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College

summary: Adenosine-to-inosine (A-to-I) RNA editing plays a vital role in many biological processes. Our previous study has demonstrated that the hematopoietic stem and progenitor cells (HSPCs) deficient in RNA editing cannot reconstitute the irradiated recipients in vivo. However, the overall profile of RNA editome in hematopoiesis has not been established and the underlying mechanism is poorly understood. Here, we sorted 12 murine adult hematopoietic cell populations, and performed deep RNA and DNA sequencing. We depicted the first landscape of RNA editing in hematopoietic cells and identified 30,796 editing sites in total. Although total editing frequency was stable across the 12 hematopoietic populations, we identified stage-specific and group-specific editing genes, and uncovered multiple famous hematopoietic regulators were dynamically edited. By charactering group specific editing genes, we found that the Azin1 (antizyme inhibitor 1) was highly edited in HSPCs, which was required for HSPCs differentiation. A-to-I editing of Azin1 transcript resulted in serine-to-glycine substitution at residue 367 of AZIN1, induced its translocation from cytoplasm to nucleus, enabled its higher binding affinity with DDX1 (DEAD box polypeptide 1) in nucleus further to alter the chromatin distribution of DDX1, resulting in multiple hematopoietic regulators expression change. Collectively, this study provided the first landscape of RNA editing in hematopoietic cascade and uncovered the mechanism of A-to-I editing of Azin1 in regulating HSPCs function.

overall_design: (1)LSK+ HSPC DNA-seq were generated by deep sequencing, in duplicate. (2) mRNA profiles of LT-HSC / ST-HSC / MPP / CMP / MEP / GMP / MK / Ery-A / Ery-B / monocyte / macrophage / granulocyte were generated by deep sequencing, in duplicate. (3) mRNA profiles of overexpression of Azin1-TC/Azin1-G in c-Kit+ cell were generated by deep sequencing, in duplicate. (4)mRNA profiles of Ddx1 knock down / normal control in c-Kit+ cell were generated by deep sequencing, in duplicate. (5)Ddx1 ChIP-seq with input in 32D cells were generated by deep sequencing, in duplicate.

first: Fengjiao

last: Wang

last: He

first: Yanni

last: Ma

first: Siqi

last: Liu

first: Hui

first: Jia

last: Yu

first: Tao


title: Integrated mRNA/miRNA-seq of Caco-2 and HT-29 cells under chemical hypoxia (cobalt chloride, oxyquinoline)

city: Moscow

first: Stepan

last: Nersisyan

address: Vavilova str 7

department: Faculty of Biology and Biotechnology

country: Russia

institute: HSE University

type: Non-coding RNA profiling by high throughput sequencing

summary: To uncover hypoxia-induced miRNA-mRNA interactions landscape in colorectal cancer cell lines we performed integrated miRNA/mRNA sequencing of Caco-2 and HT-29 cells. Hypoxia was chemically induced via 24 h cobalt(II) chloride and oxyquinoline treatments.

overall_design: The experiment included CoCl2-treated, oxyquinoline-treated and control Caco-2, HT-29 cells, three biological replicated per group were used.


title: Next Generation Sequencing Facilitates Quantitative Analysis of Papillary Thyroid Carcinoma

status: Public on Aug 16 2020

first: Fan

last: Yang

address: No.2 Anzhen Street

institute: Beijing Anzhen Hospital, Capital Medical University

summary: Our study aims to investigate the molecular variance of PTC in human PTC tumor sample and normal tissue sample, and to identifiy potential genes as  diagnostic markers for PTC.

overall_design: RNA sequencing was performed in tumor and normal thyroid tissue samples for patients with papillary thyroid carcinoma

first: Jugao

last: Fang

first: Meng

last: Lian

first: Hongzhi

first: Ling

last: Feng

first: Xixi

last: Shen

first: Bo

first: Huan

last: Zhuang

first: Jiaming

last: Chen


title: Long and short-read single cell RNA-seq profiling of human lung adenocarcinoma cell lines using 10X version 2 chemstry.

status: Public on Jul 22 2020

city: Parkville

first: Matthew

last: Ritchie

state: Victoria

address: 1G Royal Parade

department: Epigenetics and Development Division

country: Australia

institute: The Walter and Eliza Hall Institute of Medical Research

summary: Single cell RNA-seq was used to profile gene expression in 5 human lung adenocarcinoma cell lines.

overall_design: Single cells from five human lung adenocarcinoma cell lines (H2228, H1975, A549, H838 and HCC827) were mixed in equal proportions and processed using the Chromium 10X platform, then sequenced using both short-read (Illumina) and long-read (Nanopore) technologies.

first: Luyi

last: Tian

first: Jafar

last: Jabbari

first: Azadeh

last: Seidi


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

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: Transcriptome analysis of a heat-resistant jujube cultivar response to high temperature stress

status: Public on Oct 02 2020

city: WuHan

first: Guosong

last: Jiang

state: Hubei Province

address: Jiefang Road, No. 1277

department: Department of Urology

institute: Union Hospital, Tongji Medical College, Huazhong University of Science and Technology

summary: We found a heat-resistant jujube cultivar in our previous study, but the molecular mecanism of heat-resistantance remained investigated. In the current study, we made this seedlings of jujube cultivar to be under heat stress (45°C) for 0, 1, 3, 5 and 7 days respectively. After checking the phenotypic and physiological features, the leaf samples (HR0, HR1, HR3, HR5 and HR7) were collected accordingly. RNA-seq transcriptome comparisons were performed, showing that 2266, 4907, 6120 and 2894 differentially expressed genes (DEGs) were identified among HR1 vs. HR0, HR3 vs. HR0, HR5 vs. HR0, and HR7 vs. HR0 respectively. Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses of the DEGs from these comparisons. it revealed that a series of biological processes involved in photosynthesis, protein processing in endoplasmic reticulum and metabolism, suggesting that lowering or upregulating these processes may contribute to improved heat resistance in this jujube cultivar.

overall_design: Transcriptome analysis for a jujuebe heat-resistant cultivar under heat stress,in triplicate, using Illumina HiSeq X-ten.

first: Lei

last: Yang

first: Jianxin

last: Niu


title: Long and short-read single cell RNA-seq profiling of mouse muscle stem cells

first: Matthew

last: Ritchie

summary: Single cell RNA-seq was used to identify the gene expression signatures and transcript isoforms that distinguish quiescent and activated muscle stem cells in mouse.

overall_design: Quiescent skeletal muscle stem cells isolated from uninjured muscles and activated muscle stem cells isolated post injury were profiled using the Chromium platform (10x Genomics) with sequencing from both short-read (Illumina) and long-read (Nanopore) technologies.

first: C

last: Ly

first: Luyi

last: Tian

first: Jafar

last: Jabbari

first: Gordon

last: Lynch

first: James

last: Ryall


title: Expression analysis of white adipose, brown adipose tissue and gastrocnemius muscle isolated from tumor bearing mice treated with control IgG1 or anti-GFRAL 3P10

status: Public on Jul 20 2020

city: South San Francisco

first: Joshua

last: Lichtman

address: 333 Oyster Point Boulevard

department: Translational Science

institute: NGM Biopharmaceuticals

summary: RNA sequencing of white adipose, brown adipose tissue and gastrocnemius muscle isolated from non-tumor bearing and HT1080 tumor-bearing mice treated with control IgG1 or anti-GFRAL 3P10

overall_design: Tissues from non-tumor bearing (NTB) and HT1080 tumor bearing animals treated with IgG1 or 3P10 (3mg/kg, weekly starting Day 0) were harvested 21 days post inoculation. Gastrocnemius muscle (GN), white and brown adipose were flash frozen prior to RNA isolation.  RNA was prepared using the Qiagen RNAeasy kit with on column DNAse treatment.  Brown adipose RNA was prepared for sequencing using the UMI second strand synthesis module for QuantSeq 3’ mRNA-Seq Library Prep Kit FWD for Illumina (Lexogen) and sequenced on an Illumina NovaSeq 6000 (100bp single-end reads and 5-10 million reads were generated for each sample). White adipose and gastrocnemius muscle RNA were prepared for sequencing using the TailorMix Directional RNA Sample Preparation Kit (SeqMatic) and sequenced on an Illumina NovaSeq 6000 (100bp single-end reads and 30-50 million reads were generated for each sample).

first: Rowena

last: Suriben

first: Michael

last: Chen

first: Jared

last: Higbee

first: Julie

last: Oeffinger

first: Richard

last: Ventura

first: Betty

first: Kalyani

last: Mondal

first: Zhengyu

last: Gao

first: Dina

last: Ayupova

first: Pranali

last: Taskar

first: Diana

first: Shelley

last: Starck

first: Harry

first: Michelle

last: McEntee

first: Subhash

last: Katewa

first: Van

last: Phung

first: Marilyn

last: Wang

first: Avantika

last: Kekatpure

first: Damodharan

last: Lakshminarasimhan

first: Andre

last: White

first: Andrea

last: Olland

first: Raj

last: Haldankar

first: Mark

last: Solloway

first: Jer-Yuan

last: Hsu

first: Yan

first: Jie

last: Tang

first: Darrin

last: Lindhout

first: Bernard

middle: B

last: Allan


title: RNA-seq after CD95 gene knockout in 4T1 cells

status: Public on Jul 19 2020

first: Zhe

last: Ji

state: ILLINOIS

address: 303 E Superior St, Lurie 6-107

institute: Northwestern University

summary: We examine the differential RNA expression after knocking out CD95/Fas gene in 4T1 cells

overall_design: 2 control samples, and 2 CD95ko samples

first: Hongbin

first: Emily

last: Stroup

first: Marcus

last: Peter


title: Impact of Microbiome on Hepatic Drug Processing Genes in Mice during Pregnancy

status: Public on Aug 26 2020

first: James

last: MacDonald

summary: While microbiome and pregnancy are known to alter drug disposition, the interplay of the two physiological factors to impact expression and/or activity of drug processing genes (DPGs) has yet to be elucidated. This study aimed to investigate the effects of microbiome on host hepatic DPGs during pregnancy using conventional (CV) and germ-free (GF) mice. Four groups of female mice were used, namely CV non-pregnant (CVNP), GF non-pregnant (GFNP), CV pregnant (CVP), and GF pregnant (GFP) mice. Pregnant mice examined were on gestation day 15. Transcriptomic and targeted proteomics of hepatic DPGs were profiled using a multi-omics approach. Plasma bile acid and steroid hormone levels were quantified using LC-MS/MS. Cyp3a activities were measured by mouse liver microsome incubations. While the overall trend in pregnancy-induced changes in the expression or activity of hepatic DPGs in CV and GF mice was similar, significant differences in the magnitude of changes were observed. For certain genes, we noticed opposite effects of pregnancy on mRNA and protein expression of DPGs in both CV and GF mice. For instance, the mRNA levels of Cyp3a11, the murine homolog of human CYP3A4, were decreased by 1.7-fold and 3.3-fold by pregnancy in CV and GF mice, respectively. However, the protein levels of Cyp3a11 were increased similarly ~2-fold by pregnancy in both CV and GF mice. Yet, microsome incubations revealed a marked induction of Cyp3a activity by pregnancy that was >5-fold greater in CV mice than that in GF mice. Plasma bile acid and steroid hormone levels were also significantly altered by microbiome and pregnancy, respectively, which may contribute to the differential effects of pregnancy in CV and GF mice. This is the first study to show that microbiome can alter hepatic DPGs in pregnancy.

overall_design: Four groups of female mice were used, namely conventional non-pregnant (CVNP), germ-free non-pregnant (GFNP), conventional pregnant (CVP), and germ-free pregnant (GFP) C57BL/6  mice. Liver tissues from 6 CVNP, 5 CVP, 6 GFNP, and 5 GFP mice were collected.

first: Lyrialle

last: Han

first: Lu

first: Yuanyuan

last: Shi

first: Joseph

last: Dempsey

first: Olesya

middle: V

last: Pershutkina

first: Moumita

last: Dutta

first: Theo

last: Bammler

first: Julia

middle: Y

last: Cui

first: Qingcheng

last: Mao


title: Heat shock protein gp96 induces  Foxp3 expression in Regulatory T Cells via interaction with TLRs for treatment of Auto-immune Diseases

status: Public on Jul 11 2020

first: Songdong

last: Meng

address: NO.1 Beichen West Road, Chaoyang District

institute: nstitute Of Microbiology Chinese Academy of Sciences

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

overall_design: Refer to individual Series


title: Human-chimpanzee hybrid cells reveal gene regulatory evolution underlying skeletal divergence

status: Public on Oct 09 2020

city: Jerusalem

first: David

last: Gokhman

address: Givat Ram, Safra Campus

country: Israel

institute: The Hebrew University of Jerusalem

summary: Gene regulatory divergence is thought to play a central role in determining human-specific traits. However, our ability to link divergent regulation to divergent phenotypes is limited. Here, we utilized human-chimpanzee hybrid induced pluripotent stem cells to study divergent gene expression separating these species. The hybrid cells allowed us to separate cis- from trans-regulatory effects, and to control for non-genetic factors that often confound comparative studies. We differentiated these cells into cranial neural crest cells (CNCCs), the primary cell type giving rise to the face, and used the hybrid cells to generate a catalogue of divergent cis-regulatory gene expression between humans and chimpanzees. We found that cis-regulatory divergence is tightly linked to phenotypic divergence, enabling the identification of candidate genes associated with several divergent traits. Specifically, we find support for lineage-specific selection acting on the cis-regulation of the hedgehog signaling pathway. This pathway includes EVC2 (LIMBIN), whose cis-regulation is among the most divergent in the genome, resulting in 6-fold down-regulation along the human lineage. We found that inducing a similar reduction in EVC2 levels substantially reduces Hh signaling output. Mice and humans lacking functional EVC2 show striking parallels to many human-chimpanzee phenotypic differences, particularly in the skull and face, suggesting that the regulatory divergence of Hh signaling may have contributed to the unique craniofacial morphology of humans. In sum, our results suggest that human-chimpanzee hybrid cells can serve as a valuable resource to study the evolution of gene regulation and its impact on phenotypic divergence. SRA/fastq files include Illumina adapters (GATCGGAAGAGCACACGTCT and GATCGGAAGAGCGTCGTGTA).

sample_organism:
Pan troglodytes
Homo sapiens

platform_organism:
Pan troglodytes
Homo sapiens

overall_design: RNA sequencing of iPSC-derived cranial neural crest cells (CNCCs) from three triplicates of human, chimpanzee and human-chimpanzee hybrid

first: Hunter

last: Fraser


title: Heat shock protein gp96 induces  Foxp3 expression in Regulatory T Cells via interaction with TLRs for treatment of Auto-immune Diseases [FFoxp3-GFP-hCre]

summary: Upregulate and stabilize Foxp3 expression in Treg are essential for manipulating Treg cell function and immune homeostasis. Here, we examined the potential role and mechanism of gp96 protein in regulating FoxP3 transcription and Treg activation in vivo.

overall_design: We analyzed gene-expression profiles of FoxP3-GFP+ Tregs from Foxp3-GFP-hCre mice immunized with gp96 and pbs.

first: Xin

last: Li

first: Yuxiu

last: Xu


title: Heat shock protein gp96 induces  Foxp3 expression in Regulatory T Cells via interaction with TLRs for treatment of Auto-immune Diseases [Foxp3Cre Myd88fl/fl]

overall_design: We analyzed gene-expression profiles of CD4+FoxP3-GFP+ Tregs from Foxp3Cre Myd88fl/fl mice immunized with gp96 and pbs.


title: FoxM1 insufficiency hyperactivates Ect2-RhoA-mDia1 signaling to drive cancer

status: Public on Jul 09 2020

city: Rochester

first: Hu

state: MN

address: 200 First Street, Gonda Building G19-408

department: Molecular Pharmacology & Experimental Therapeutics

institute: Mayo Clinic

summary: FoxM1 activates genes that regulate S-G2-M cell-cycle progression and, when overexpressed, is associated with poor clinical outcome in multiple cancers. Here we identify FoxM1 as a tumor suppressor in mice that, through its N-terminal domain, binds to and inhibits Ect2 to limit the activity of RhoA GTPase and its effector mDia1, a catalyst of cortical actin nucleation. FoxM1 insufficiency impedes centrosome movement through excessive cortical actin polymerization, thereby causing the formation of non-perpendicular mitotic spindles that missegregate chromosomes and drive tumorigenesis in mice. Importantly, low FOXM1 expression correlates with RhoA GTPase hyperactivity in multiple human cancer types, indicating that suppression of the newly discovered Ect2-RhoA-mDia1 oncogenic axis by FoxM1 is clinically relevant. Furthermore, by dissecting the domain requirements through which FoxM1 inhibits Ect2 GEF activity, we provide mechanistic insight for the development of pharmacological approaches that target protumorigenic RhoA activity.

overall_design: FoxM1 non-transcriptionally suppresses cortical actin-mediated tumorigenesis

first: Jan

last: van Deursen


title: Synergistic alterations in multilevel chromatin structure anchor dysregulated genes in small cell lung cancer

status: Public on Jul 10 2020

first: hebing

last: chen

address: taiping road 27

institute: Institute of Health Service  and Transfusion Medicine

summary: Small cell lung cancer (SCLC) is an aggressive form of lung cancer withunique change in chromosomal structure while the basis of the aberrant gene expression in SCLC remains largely unclear. Topologically associated domains (TADs) are structural and functional units of the human genome. Genetic and epigenetic alterations in the cancer genome can lead to disruption of TAD boundaries and may cause gene dysregulation. To understand thepotentialregulatoryroleofthisprocess in SCLC, we developed TAD boundary alteration-related gene identification in tumour (TARGET), a computational framework that,forthefirsttime, enables a systematic identificationof candidate dysregulated genes associated with altered TAD boundaries. Using TARGET to compare gene expression profiles between SCLC and normal human lung fibroblast celllines, we have identified over one hundredgenes in this catagory, amongwhich 24 were further verified in SCLC patient samples using NanoString. Further, analysis revealed a synergistic chromatin structure alteration at both the AB compartment level and TAD boundary level that underlie aberrant gene expression in SCLC. Therefore, TARGET serves as a novel and powerful method could be used to explore the relationship of chromatin structure alteration and gene dysregulation relatedto tumorigenesis, progression, and prognosis of SCLC.

overall_design: Examination chromatin structure and gene expression in  two human lung carcinoma cell lines and fibroblast cell

first: Dan

last: Guo

first: Qiu

last: Xie

first: Shuai

last: Jiang

first: Hebing

last: Chen

first: Zhiyong

last: Liang


title: Long noncoding RNA profiles in plasma exosomes of patients with gastric high-grade intraepithelial neoplasia

status: Public on Jun 29 2020

city: changchun

first: Feng

last: Hu

state: jilin

address: No. 3302, Jilin Dadu

department: Department of Hepatology and Gastroenterology

institute: The Second Part of First Hospital of Jilin University

summary: The sensitivity and specificity of traditional non-invasive diagnostic markers for gastric cancer are insufficient. Long-chain noncoding RNAs (lncRNAs) in circulating exosomes are a new class of promising cancer biomarkers. However, the expression profile of long-chain noncoding RNAs (lncRNAs) in exosomes derived from gastric high-grade intraepithelial neoplasia (GHGIN) has not been reported.The aim of this study was to investigate the expression profile of long non-coding RNAs (lncRNAs) in the plasma exosomes of patients with gastric high-grade intraepithelial neoplasia. Peripheral blood samples were collected from five patients with GHGIN and five healthy donors, and the exosomes were isolated. We used high-throughput sequencing to detect differently expressed lncRNAs (DE lncRNAs) in these individuals. Real-time quantitative polymerase chain reaction (RT-qPCR) assay was performed to verify the sequencing results. The potential roles of the DE lncRNAs in GHGIN were speculated by performing Gene ontology (GO) and Kyoto Encyclopedia of Gene and Genome (KEGG) analysis. We constructed a lncRNAs–miRNA–mRNA network diagram and performed association analyses to explore the underlying molecular mechanisms. A total of 25145 lncRNAs were identified in all samples; 83 lncRNAs that showed significant differential expression were further screened, including 76 up‐regulated and 7 down‐regulated lncRNAs. RT-qPCR further confirmed these results. GO and KEGG analyses predicted that these lncRNAs played important roles in protein and macromolecule glycosylation, regulation of protein ubiquitination, and renin-angiotensin system and MAPK signaling pathways. We further constructed a lncRNA–miRNA–mRNA interaction network. This study may help in discovering new molecular changes, enrich the expression profile of lncRNAs in human GHGIN, and help us better understand the molecular mechanisms of GHGIN and gastric cancer.

overall_design:
We used high-throughput sequencing to detect lncRNAs  and mRNAs in plasma exosomes of patients with gastric high-grade intraepithelial neoplasia and  healthy controls
contributor: cloudseq


title: Alternative splicing and the epigenome in CML remission [RNA-Seq]

status: Public on Jun 30 2020

city: Sydney

first: Charles

last: Bailey

state: NSW

address: Missenden Rd, Building 93

institute: Centenary Institute

summary: Transcriptomic and epigenomic profiling of matched CML diagnosis/remission samples revealed a reconfiguration of gene expression and DNA methylation at remission exhibiting patterns similar to those observed in healthy individuals. In contrast, alternative splicing retains chronic phase-like abnormal patterns. Most dramatic dissimilarities between remission and healthy control samples were observed in intron retention. While reduced DNA methylation around splice sites could explain increased intron retention at diagnosis, maintenance of high intron retention levels at remission has other causes, such as reduced splicing factor expression and histone modifications.

overall_design: mRNA sequencing was performed on 16 CML diagnosis and 11 matched remission samples as well as 6 control samples.

first: Ulf

last: Schmitz

first: Jaynish

last: Shah

first: Bijay

last: Dhungel

first: Geoffray

last: Monteuuis

first: Phuc

middle: L

last: Luu

first: Veronika

last: Petrova

first: Cynthia

last: Metierre

first: Shalima

last: Nair

first: Ali

last: Turhan

first: Susan

last: Branford

first: Timothy

last: Hughes

last: Clark

first: Justin

middle: J

last: Wong

first: John

last: Rasko


title: Transcriptomic Response of Brain Tissue to Focused Ultrasound-Mediated Blood-Brain Barrier Disruption Depends Strongly on Anesthesia - Bulk RNA-seq

status: Public on Jun 11 2020

city: Charlottesville

first: Alexander

last: Mathew

state: VA

address: 415 Lane Road

institute: University of Virginia

summary: Focused ultrasound (FUS) mediated blood brain barrier disruption (BBBD) is a promising strategy for the targeted delivery of systemically-administered therapeutics to the central nervous system (CNS). Pre-clinical investigations of BBBD have been performed on different anesthetic backgrounds; however, the potential influence of the choice of anesthetic on the molecular response to BBBD is unknown, despite its potential to critically affect interpretation of experimental therapeutic outcomes. Here, using bulk RNA sequencing approaches, we comprehensively examined the transcriptomic response of both normal brain tissue and brain tissue exposed to FUS-induced BBBD in mice anesthetized with either Isoflurane with medical air (Iso) or Ketamine/Dexmedetomidine (KD). In normal murine brain tissue, Iso alone elicited minimal differential gene expression (DGE) and repressed pathways associated with neuronal signaling. KD alone, however, led to massive DGE and enrichment of pathways associated with protein synthesis. In brain tissue exposed to BBBD (1 MHz, 0.5 Hz pulse repetition frequency, 0.4 MPa peak-negative pressure), we systematically evaluated the relative effects of anesthesia, microbubbles, and FUS on the transcriptome. Of particular interest, we observed that gene sets associated with sterile inflammatory responses and cell-cell junctional activity were induced by BBBD, regardless of the choice of anesthesia. Meanwhile, gene sets associated with metabolism, platelet activity, tissue repair, and signaling pathways, were differentially affected by BBBD, with a strong dependence on the anesthetic. We conclude that the underlying transcriptomic response to FUS-mediated BBBD may be powerfully influenced by anesthesia. These findings raise considerations for the translation of FUS-BBBD delivery approaches that impact, in particular, metabolism, tissue repair, and intracellular signaling.

overall_design: Groups of 3 mice were treated with sham, isoflurane in medical air (iso), ketamine/dexmedetomidine (KD), iso+microbubbles (MB), KD+MB, iso+MB+FUS, or KD+MB+FUS. At either 6 hours following FUS activation of plasmid-bearing MBs, the front right quadrant of the brain was harvested and processed for bulk mRNA sequencing followed by bioinformatics analyses.

first: Richard

last: Price


title: Comparative RNA-Seq analysis reveals potentially resistance-related genes in response to Bacterial canker of tomato

status: Public on Jun 13 2020

city: SAN LUIS POTOSI

first: Cesaré

last: Ovando-Vázquez

state: SAN LUIS POTOSI

address: Camino a la Presa de San José 2055. Lomas 4 sección

department: CNS

country: Mexico

institute: CONACyT IPICyT

summary: Tomato is one of the most important crops for human consumption. Unfortunately, its production is affected by diseases caused by pathogens such as the actynomicete Clavibacter michiganensis subsp. michiganens (Cmm). This pathogen is the causal agent of the bacterial canker of tomato, considered one of the most devastating tomato diseases. To date, there are not resistant varieties of commercial tomato against Cmm. However, there are wild tomato species resistant to Cmm. Using massive sequencing, we obtained the transcriptomes of the wild tomato species Solanum arcanum LA2157 and the commercial tomato Solanum lycopersicum cv. Ailsa Craig at 8 and 24 hours after Cmm challenge. We identified potential tomato tolerance-related genes by three approaches: mapping the reads to S. lycopersicum reference genome SL3.0, performing a semi de novo transcriptome assembly and a de novo transcriptome assembly. Some functional groups such as oxylipin biosynthetic process response to wounding, response to cytokinin among others, were enriched in both tomato species, suggesting a similar response, however, genes that encode proteins such as the Polyphenol oxidase E, Ankyrin and Leucine Rich Repeat receptors were overexpressed mainly in the wild tomato species, suggesting a possible role in the defense response. Here, we uncovered new candidate genes potentially related to bacterial canker tomato defense.

sample_organism:
Solanum lycopersicum
Solanum arcanum

platform_organism:
Solanum lycopersicum
Solanum arcanum

overall_design: Comparison of two Solanum species, wild type and commercial, during 24 hours post-infection with Clavibacter michiganensis subsp. michiganensis (Cmm).

first: Leonardo

middle: I

last: Pereyra-Bistraín

first: Alejandra

last: Rougon-Cardoso

first: Ángel

last: Alpuche-Solís


title: Comprehensive comparison and biologic activity of novel therapeutic agents in NPM1 mutated Acute Myeloid Leukemia (AML)

status: Public on Jun 01 2020

city: Paris

first: Marc

last: Delord

address: Hopital Saint-Louis, 1 avenue Claude Vellefaux

department: Recherche clinique

institute: Centre hospitalier de Versailles

summary: Acute Myeloid Leukemia (AML) is frequently associated with mutations of NPM1 (NPM1c+) and even if considered to be of better prognosis for younger patients, relapse is frequent and outcome remains poor for elder patients with a need for novel treatment strategies. Differentiation-based therapy by all trans retinoic acid (ATRA) combined with arsenic trioxide (ATO) induce proteasomal degradation of NPM1c protein, NPM1 nuclear re localization, differentiation and apoptosis in NPM1c+ cells and blast clearance in relapsed/refractory AML patients. In line, the XPO1 inhibitor Selinexor showed similar results in vitro associated with down regulation of a specific HOX gene signature. BET inhibitors (BETi) OTX015 (MK-8628) and JQ1 yield antileukemic activity and here we demonstrate their effects in NPM1c+ leukemia cells compared to ATO+ATRA and Selinexor. Compared to ATO+ATRA and Selinexor, BRDi induced TP53 independent apoptosis, differentiation, proteasomal NPM1c degradation and nuclear relocalization in NPM1c+ OCI-AML3 cell line and to different extend in patient derived blast cells. As ATO+ATRA and Selinexor had significant biological activity in NPM1c+ cell line IMS-M2, these cells were resistant to BETi exposure, except for nuclear re localization of NPM1 which is a general phenomenon upon treatment with all three drug types. Gene profiling revealed that BRDi downregulate a BRD specific core gene signature in OCI-AML3 and IMS-M2 cells but IMS-M2 cells yield a transcriptional resistance signature including upregulation of the Wnt/beta-catenin pathway. HOX gene clusters in OCI-AML3 cells and IMS-M2 cells are heterogeneously regulated by BETi and are down regulated by ATO+ATRA in line with results reported for Selinexor treatment. Taken together, our preclinical results encourage clinical testing of ATO+ATRA, Selinexor and BRDi in NPM1c+ AML patients.

overall_design: Comparison of drugs ATO+ATRA, ATO, ATRA, JQ1, OTX015 and DMSO in IMS-M2 and OCI AML3 leukemic cell lines

first: Hanene

last: Djamai

first: Jeannig

last: Berrou

first: Mélanie

last: Dupont

first: Marie-Magdelaine

last: Coudé

first: Emmanuelle

last: Clappier

first: Anna

last: Kaci

first: Emmanuel

last: Raffoux

first: Raphaël

last: Itzykson

first: Caroline

last: Berthier

first: Hugues

last: de Thé

first: André

last: Baruchel

first: Claude

last: Gardin

first: Hervé

last: Dombret

first: Thorsten

last: Braun


title: Cell-intrinsic Innate Immune Responses against Chikungunya Virus in a Human Ex Vivo Synovial Fibroblast Model

status: Public on Jun 19 2020

city: Berlin

first: Fabian

last: Pott

state: Berlin

address: Charitéplatz 1

department: Institute for Virology

country: Germany

institute: Charité - Universitaetsmedizin Berlin

summary:
Purpose: Human primary synovial fibroblasts extracted from the knee were established as an ex vivo infection model for Chikungunya Virus. The cell-intrinsic immune response was determined using RNA-seq of infected and uninfected fibroblasts from healthy donors and donors with an osteoarthritic background.
Methods: Fibroblasts of four osteoarthritic and two healthy donors were infected with CHIKV strain LR2006-OPY at an MOI of 10 in the presence or absence of the CHIKV neutralizing antibody C9 and total RNA was extracted at 24 hours post infection. Deep sequencing with paired-end reads was performed using an Illumina platform and data was analyzed with CLC Genomics Workbench 12 (QIAGEN) by mapping the human reads onto the hg19 reference genome scaffold (GCA_000001405.28). Unmapped reads not matching the human genome were subsequently mapped onto the CHIKV genome LR2006_OPY (DQ443544.2).
Results: For osteoartritic fibroblasts ~25-35 Mio reads per sample, for healthy donor fibroblasts ~50-60 Mio reads per sample were achieved. Analysis revealed no major differences in the resting or infection-induced transcriptome (R2 = 0.9085 and 0.9086, respectively), yet some non-inflammation related pathways were significantly different regulated as determined by Gene Ontology analysis.
Conclusion: Osteoarthritic fibroblasts were found to be an accessible source of primary cells suitable for studying CHIKV infection and pathophysiology. The cells did not majorly differ from the rarely avaiblabe healthy donor fibroblasts on the transcriptomic level, and did not show signs of pre-activation or inflammation in the absence of infection.

overall_design: Human synovial fibroblast mRNA profiles of CHIKV- or mock-infected samples.

first: Richard

last: Brown

first: Elena

last: Neumann

first: Thomas

last: Pietschmann

first: Christine

last: Goffinet

first: Dylan

last: Postmus

first: Emanuel

last: Wyler

first: Markus

last: Landthaler


title: Phase separation of RNA-binding protein promotes polymerase binding and transcription

status: Public on May 12 2020

first: Hai

last: Qi

address: Zhongguancun North Street

department: School of Medicine

institute: Tsinghua University

summary: An RNA-involved phase-separation model has been proposed for transcription control. Yet, the molecular links that connect RNA to the transcription machinery remain missing. Here we find RNA-binding proteins (RBPs) constitute half of the chromatin proteome in embryonic stem cells (ESCs), and some are colocalized with RNA polymerase (Pol) II at promoters and enhancers. Biochemical analyses of representative RBPs show that the paraspeckle protein PSPC1 inhibits the RNA-induced premature release of Pol II, and  makes use of RNA as multivalent molecules to enhance the formation of transcription condensates and subsequent phosphorylation and release of Pol II. This synergistic interplay enhances polymerase engagement and activity via the RNA-binding and phase-separation activities of PSPC1. In ESCs, auxin-induced acute degradation of PSPC1 leads to genome-wide defects in Pol II binding and nascent transcription. We propose that promoter-associated RNAs and their binding proteins synergize the phase separation of polymerase condensates to promote active transcription.

overall_design: Pol II ChIP-seq and TT-seq were used to chracterize the changes of Ser5 or Ser2 phosphorylated Pol II occupancy and transcription rate upon PSPC1 acute degradation. RBP ChIP-seq were used to charaterize the binding of different RBPs on chromatin. Pol II ChIP-seqs rescued with different forms of PSPC1 proteins were used to characterize whether the changes of Ser2 phosphorylated Pol II occupancy upon PSPC1 acute degradation is dependent on PSPC1 protein. ChIP-seqs of PSPC1 mutants were used to charaterize the binding of different PSPC1 mutants on chromatin. PSPC1 CLIP-seq was used to detect RNA targets of PSPC1. EU-seq was used to detect change of transcription level upon PSPC1 acute depletion.

first: Wen

last: Shao

first: Xiaohua

last: Shen


title: Patient-derived xenograft culture-transplant system for investigation of human breast cancer metastasis

status: Public on Jul 07 2020

city: Irvine

first: Devon

last: Lawson

state: CA

address: 839 Health Sciences Rd

department: Physiology and Biophysics

institute: University of California, Irvine

summary: We report a new method for culturing patient breast tumor cells in vitro, for subsequent transplantation in vivo for experimental metastasis assays. RNA sequencing shows that tumor spheres formed in culture maintain the fundamental properties of native tumor cells.

overall_design: Comparison of uncultured and cultured cells of two patient-derived xenograft models (HCI010 and HCI002). 6 biological replicates of uncultured cells (n=3 HCI010, n=3 HCI002), and paired cultured cells (n=3 HCI010, n=3 HCI002).

middle: A

first: Dennis

last: Ma

first: Grace

last: Hernandez

first: Kerrigan

last: Blake

first: Justice

last: Williams


title: Single cell human melanocytes

status: Public on May 29 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 report single cell transcriptomes from human skin samples that have been enriched for melanocytes using FACS. This work revealed anatomical site-specific melanocyte expression programs. In addition, by surveying melanocytes at different stages of development, we identified development-associated expression programs that are reflected in the dedifferentiation of melanomas.

overall_design: Single cell RNA-seq of human skin from multiple sites and ages

first: Daniel

middle: D

last: Le

first: Rachel

last: Belote

first: Spyros

last: Darmanis


title: Small RNA sequencing of msh1 memory line and with isogenic Col-0 wild-type control in Arabidopsis

status: Public on Apr 03 2020

city: University Park

first: Hardik

last: Kundariya

state: PA

address: 361 N. Frear

institute: The Pennsylvania State University

summary: Col-0 plants were transformed with MSH1 RNAi construct. Transgene positive plant was self pollinated and transgene was segregated in subsequent  generation, and screened for presence of transgene using PCR assay. Of transgene null plants, 20% plants displayed delayed in flowering, smaller in size, and lighter green termed as memory phenotype.

overall_design: Two memory plants, four Col-0 wild-type plants were sequenced.

first: Xiaodong

last: Yang

first: Sally

last: Mackenzie


title: Integrated analysis of sea cucumber ambient temperature and dissolved oxygen responsive lncRNAs and mRNAs

status: Public on Apr 22 2020

city: Qingdao

first: Da

last: HUO

address: No. 7 Nanhai Road, Qingdao, China

institute: Institute of Oceanology,Chinese Academy of Science

summary: In this work, identification of differentially expressed (DE) genes, including lncRNAs and mRNAs, in sea cucumber response to multiple environmental stress, such as thermal, hypoxic and the combined treatment.

overall_design: RNA-seq for respiratory tree in sea cucumber Apostichopus japonicus under thermal, hypoxic and the combined stress.

last: Huo

first: Lina

last: Sun


title: S100A4 mRNA-protein relationship uncovered by measurement noise reduction

status: Public on Mar 26 2020

city: VIENNA

first: Angelos

middle: Theodoros

last: Athanasiou

address: Veterinärplatz 1

country: Austria

institute: University of Veterinary Medicine Vienna

summary: Intrinsic biological fluctuation and/or measurement error can obscure the association of gene expression patterns between RNA and protein levels. Appropriate normalisation of reverse-transcription quantitative PCR (RT-qPCR) data can reduce technical noise in transcript measurement, thus uncovering such relationships. The accuracy of gene expression measurement is often challenged in the context of cancer due to its genetic instability and ‘splicing weakness’. Here we sequenced the poly(A) cancer transcriptome of canine osteosarcoma using mRNA-Seq. Expressed sequences were resolved at the level of two consecutive exons to enable the design of exon-border spanning RT-qPCR assays and ranked for stability based on the coefficient of variation (CV). Using the same template type for RT-qPCR validation, i.e. poly(A) RNA, avoided skewing of stability assessment by circular RNAs (circRNAs) and/or rRNA deregulation. The strength of the relationship between mRNA expression of the tumour marker S100A4 and its proportion score of quantitative immunochemistry (qIHC) was introduced as an experimental read-out to fine-tune the normalisation choice. Together with the essential logit transformation of qIHC scores, this approach reduced the noise of measurement as demonstrated by uncovering a highly significant, strong association between mRNA and protein expressions of S100A4 (Spearman's coefficient r = 0.72 (p = 0.006)).

overall_design: mRNA profiles of canine osteosarcoma were generated by deep sequencing using Illumina HiSeq 2000.

first: Thomas

last: Nussbaumer

first: Stefan

last: Kummer

first: Martin

last: Hofer

first: Iain

last: Johnston

first: Moritz

last: Staltner

first: Daniela

middle: M

last: Allmer

first: Milcah

middle: C

last: Scott

first: Claus

last: Vogl

first: Joelle

last: Fenger

first: Jaime

middle: F

last: Modiano

first: Ingrid

last: Walter

first: Ralf

last: Steinborn


title: Identification of circular RNA specifically expressed in oral cancer.

status: Public on Feb 21 2020

city: chiba

first: Toshiaki

last: Ando

state: chiba

address: 1-8-1 inohana chuo-ku

department: Grad. Sch. Med

country: Japan

institute: Chiba Univ

summary: Three types of oral cancer cell lines (HSC3,Sa3 and SAS) and human normal oral keratinocytes(HNOKs) were used to identify a circular RNA specifically. expressed in oral cancer

overall_design: Comparison of expression levels of circular RNA between untreated HSC3, Sa3, SAS and HNOKs.

first: Hideki

last: Tanzawa


title: LSD1-mediated enhancer silencing enables endocrine cell development through attenuation of retinoic acid signaling

status: Public on Mar 02 2020

city: La Jolla

first: Maike

last: Sander

address: 2880 Torrey Pines Scenic Dr.

institute: UC San Diego

summary: Developmental progression depends on temporally defined changes in gene expression mediated by transient exposure of lineage intermediates to signals in the progenitor niche. To identify a possible contribution of cell-intrinsic epigenetic mechanisms to signal-induced transcriptional responses, we manipulated the signaling environment and activity of the histone demethylase LSD1 during stepwise differentiation of gut tube intermediates into pancreatic endocrine cells. Analysis of enhancer and transcriptome landscapes revealed that lineage progression and endocrine cell differentiation requires LSD1-mediated silencing of transiently active retinoic acid (RA)-induced enhancers. In the absence of LSD1, early RA-responsive enhancers remain partially active despite RA removal, resulting in perduring expression of RA-induced genes, and failure to progress in development. Our findings identify LSD1-mediated enhancer silencing as a cell-intrinsic epigenetic feedback mechanism by which the duration of the transcriptional response to a developmental signal is limited. Given LSD1’s requirement in numerous developmental contexts, the here-described mechanism would be broadly relevant.

overall_design: Inhibition of LSD1 during pancreatic differentiation of hESCs followed by ChIP- and RNA-seq at milestone stages of differentiation.

first: Vinckier

last: Nicholas


title: Investigating Relationship between Plant Hormones and Important Substances in Harvested Tea Leaves Before Withering

status: Public on Jan 31 2020

city: Hangzhou

first: Xu

last: Ping

state: Zhejiang

address: 866 Yuhangtang Road

department: Tea Research Institute

institute: Zhejiang University

summary: Senescence is initiated immediately in harvested tea leaves, and leads to physiological and biochemical changes, and could affects the final tea products. In the present work, we investigated the relationship between hormones and critical components in harvested tea leaves before withering, changes in hormones including abscisic acid (ABA), salicylic acid (SA), jasmonic acid (JA), and critical components like catechins, theanine, and caffeine were analyzed. Significant changes in these substances were identified and ABA correlated with catechin in harvested tea leaves before withering. RNA-seq transcriptome analysis revealed dramatic differences between tea samples at 1 h and 2 h compared with those at 0 h. The patterns of these three critical components correlated with the expression profiles of differentially expressed genes (DEGs). Weighted correlation network analysis of co-expressed genes revealed that genes in the mediumpurple2 module correlated with ABA and catechins. The results of this study suggest that harvested tea leaves before withering undergo significant hormonal changes (ABA, JA, and SA) and ABA may participate in regulating catechin biosynthesis.

overall_design: mRNA profiles of tea leaves at 0, 1 and 2 hours after harvested


title: mRNA sequencing of msh1 memory line and non-memory (normal looking) sibling plants with isogenic Col-0 wild-type control in Arabidopsis

first: Hardik

last: Kundariya

summary: Col-0 plants were transformed with MSH1 RNAi construct. Transgene positive plant was self pollinated and transgene was segregated in subsequent  generation, and screened for presence of transgene using PCR assay. Of transgene null plants, 20% plants displayed delayed in flowering, smaller in size, and lighter green termed as memory phenotype. Memory plants were self pollinated for six generations and plants from generation 1 and 5 were sequenced for RNASeq.

overall_design: Three of each memory, non-memory, and Col-0 wild-type plants from generation 1 and 5 were sequenced.

first: Xiaodong

last: Yang

first: Sally

last: Mackenzie


title: microRNAs Restrain Proliferation in BRAFV600E Melanocytic Nevi [miRNA-Seq, RNA-Seq]

status: Public on May 22 2020

first: Robert

last: Judson-Torres

summary: We conducted small RNA sequencing on low passage human melanocytes derived from melanocytic nevi and normal skin.

overall_design: 8 normal skin derived melanocyte cultures and 6 nevus derived melanocyte cultures were sequenced.

first: Andrew

last: McNeal


title: The IRE1 Pathway Regulates Honey Bee Unfolded Protein Response Gene Expression

status: Public on Mar 28 2020

city: New York

first: Jonathan

middle: W.

last: Snow

state: New York

address: 3009 Broadway

department: Biology

institute: Barnard College

summary: Our molecular understanding of honey bee cellular stress responses is incomplete. Previously, we sought to identify and began functional characterization of the components of the UPR in honey bees. We observed that UPR stimulation resulted in induction of target genes upon and IRE1 pathway activation, as assessed by splicing of Xbp1 mRNA. However, were not able to determine the relative role of the various UPR pathways in gene activation. Our understanding of honey bee signal transduction and transcriptional regulation has been hampered by a lack of tools. After using RNAseq to expand the known UPR targets in the bee, we use the Drosophila melanogaster S2 cell line and honey bee trans and cis elements to investigate the role of the IRE-1 pathway in the transcriptional activation of one of these targets, the honey bee Hsc70-3 gene. Using a luciferase reporter, we show that honey bee hsc70 promoter activity is inducible by UPR activation. In addition, we show that this activation is IRE1-dependent and relies on specific cis regulatory elements. Experiments using exogenous honey bee or fruit fly XBP1S proteins demonstrate that both factors can activate the Hsc70-3 promoter and further support a role for the IRE-1 pathway in control of its expression in the honey bee. By providing foundational knowledge about the UPR in the honey bee and demonstrating the usefulness of a heterologous cell line for molecular characterization of honey bee pathways, this work stands to improve our understanding of this critical species.

overall_design: Six Samples, 3 controls and 3 fed solution containing Tunicamycin

middle: W

first: Tara

middle: R

last: Adames

first: Nicole

last: Rondeau

first: Mosammed

last: Kabir

first: Brittany

last: Johnston

first: Henry

last: Truong


title: Transcriptomes of different developmental stages of Zeugodacus cucurbitae

status: Public on Jan 02 2020

city: Beibei

first: Dong

last: Wei

state: Chongqing

address: Tiansheng

institute: Southwest University

summary: Functional studies of the genes associated with development and reproduction during different life stages are limited in Zeugodacus cucurbitae. There have yet to be comprehensive transcriptomic resources for genetic and functional genomic studies to identify the molecular mechanisms related to its development and reproduction.

overall_design:
we comprehensively sequenced the transcriptomes of four different developmental stages: egg, larva, pupa, and adults.
SRA Study accession (SRP220120) and BioProject accession (PRJNA562032)

first: Jin-Jun

last: Wang

first: Hui-Qian

last: Xu


title: The kinesin KIF1C transports APC-dependent mRNAs to cell protrusions

status: Public on Nov 13 2020

city: MONTPELLIER

first: Xavier

last: Pichon

state: herault

address: 1919 route de Mende

department: IGMM

institute: CNRS

summary:
Transcriptome analysis of specific mRNA interacting with KIF1C-GFP in HeLa Cells.
RNA localization and local translation are involved in a wide range of cellular functions. In mammals, a class of mRNAs localize to cytoplasmic protrusions in an APC dependent manner, with important roles during cell migration. Here, we investigated this localization mechanism. We found that the KIF1C motor interacts with many APC-dependent mRNAs and is required for their localization. Live cell imaging of localizing mRNAs further revealed rapid, active transport of single mRNAs over long distances, and showed that this requires both microtubules and KIF1C. Moreover, two color imaging directly revealed single mRNAs transported by single KIF1C motors, with the 3’UTR of localized mRNAs being sufficient to trigger KIF1C-dependent RNA transport and localization. These results reveal a general RNA transport pathway in mammalian cells, in which the KIF1C motor transports RNAs to cytoplasmic protrusions. Interestingly, KIF1C also transported its own mRNA suggesting a possible feedback loop acting at the level of mRNA transport.

overall_design: In total 4 samples; 2 control IP, 2 GFP-KIF1C IP. We performed RNA immunoprecipitation using the Affymetrix Human Transcriptome Array 2.0 chip on an Affymetrix platform (Thermo Fisher). Experiments were performed in duplicates, data were normalized and averaged,

first: Konstadinos

last: Moissoglu

first: Tianhong

first: Emeline

last: Coleno

first: Arthur

last: Imbert

first: Marion

last: Peter

first: Racha

last: Chouaib

first: Kazem

last: Zibara

first: Florian

last: Mueller

first: Thomas

last: Walter

first: Edouard

last: Bertrand

first: Stavroula

last: Mili


title: Imatinib-induced changes in expression profile of microRNA in plasma of mice - comparison with doxorubicin

status: Public on Jan 01 2020

city: Prague 10

first: Veronika

last: Boušková

address: Srobarova 48

country: Czech Republic

institute: National Institute of Public Health

summary: Cardiotoxicity is serious adverse reaction of cancer chemotherapy and may lead to critical heart damage. Imatinib mesylate (IMB), a selective tyrosine kinase inhibitor, is sometimes accompanied by severe cardiovascular complications. To minimize the risk, early biomarkers of such complications are of utmost importance. MicroRNAs (miRNAs) are, nowadays intensively studied as potential biomarkers of many pathological processes. Many miRNAs appear to be specific in some tissues, including heart. Here, we have explored the potential of specific miRNAs to be early markers of IMB-induced cardiotoxicity. Doxorubicin (DOX), an anthracycline with well-known cardiotoxicity, was used for comparison. NMRI mice were treated with IMB or DOX for nine days in doses corresponding to the highest recommended doses in oncological patients. Then, plasmatic levels of miRNAs were analyzed by miRNA microarrays and selected cardio-specific miRNAs were quantified using qPCR. The plasmatic level of miR-1a, miR-133a, miR-133b, miR-339, miR-7058, miR-6236 and miR-6240 were the most different between IMB-treated and control mice. Interestingly, most of the miRNAs affected by DOX were also affected by IMB with the same trends. Concerning selected microRNAs in hearts of individual mice, only miR-34a was significantly increased after DOX treatment and only miR-205 was significantly decreased after IMB and DOX treatment. However, changes in any miRNA expression did not correlate with level of troponin T, classical marker of heart injury.

overall_design: Mice were randomly divided in three groups. The animals in the first group  (n=9) were treated p.o. with IMB (distilled water solution) in daily dose 100 mg/kg of body weight for 9 consecutive days. The animals in the second group (n=9) were treated i.v. (tail vein) with DOX in saline solution (one dose 3mg/kg, 4 doses, application every other day). The mice in control group (n=6) were treated with the solvents only. The next day after the last dose of drugs, mice were sacrificed by cervical spine dislocation. Blood from aorta was collected into K2EDTA-coated tubes and centrifuged to get plasma samples. Total RNA was isolated from 300 μl of plasma (pooled sample of 3 treated mice as a biological replicate) by miRNeasy Serum/Plasma Kit (Qiagen) according to manufactures’ protocol.

first: Barbora

last: Hanousková

first: Mikuláš

last: Skála

last: Brynychová

last: Skarková

first: Petra

last: Kazimírová

first: Tomáš

last: Zárybnický

first: Pavel

last: Souček

first: Lenka

last: Skálová

last: Matoušková


title: Targeted next generation sequencing of transcriptomes from human treatment-naïve patient-derived prostate tissues, organoids, and organoid-derived cells (unaffected and tumor counterparts)

status: Public on Apr 21 2020

city: Beirut

first: Wassim

last: Abou-Kheir

address: Bliss St. DTS Bldg.

department: Department of Anatomy, Cell Biology, and Physiological Sciences

country: Lebanon

institute: American University of Beirut

summary: Human prostate mRNA profiles of organoids, cells, and tissues were generated by targeted next generation sequencing from three patients using Illumina® TruSeq Stranded mRNA prep kit.

overall_design: Purpose: To examine the genome-wide expressions using targeted next generation sequencing (NGS) in novel patient-derived organoids and organoid-derived cells versus their corresponding human tissue specimens and whole-transcriptome sequencing on a number of prostate cancer patients. We aim to compare the novel patient-derived organoids and organoid-derived cells with their corresponding tissues (unaffected and tumor parts) to demonstrate the faithfulness of this model. In addition, we aim to explore the genomic profiles that exemplify the molecular landscape of Lebanese prostate cancer patients and identify lead targets that could be implemented for personalized treatments of this disease.

first: Mohamed

last: Al-Sayegh

first: Hisham

last: Bahmad


title: Integrative analysis of Hydra head regeneration reveals activation of distal enhancer-like elements [ChIP-seq]

status: Public on Dec 31 2019

first: Ali

last: Mortazavi

state: California

address: 2300 Biological Sciences III

department: Developmental & Cell Biology

institute: University of California Irvine

summary: The cnidarian model organism Hydra has long been studied for its remarkable ability to regenerate its head, which is controlled by a head organizer located near the hypostome. Cnidarians and bilaterians diverged about 600 millions years ago but the gene contents of species of both phyla are surprisingly similar despite divergent morphologies and functions. While little is known about the role of cis-regulatory elements in cnidarians, understanding gene regulatory mechanisms in cnidarians can potentially shed light on metazoan evolution. The canonical Wnt pathway plays a central role in head organizer function during regeneration and during bud formation, which is the asexual mode of reproduction in Hydra. However, it is unclear how shared the developmental programs of head organizer genesis are in budding and regeneration. Time-series analysis of gene expression changes during head regeneration and budding revealed a set of 298 differentially expressed genes during the 48-hour head regeneration and 72-hour budding time-courses. In order to understand the regulatory elements controlling hydra head regeneration, we first identified 27,137 open-chromatin elements that are open in one or more sections of organism. We used histone modification ChIP-seq to identify 9998 candidate proximal promoter and 3018 candidate enhancer-like regions respectively. We show that a subset of these regulatory elements is dynamically remodeled during head regeneration and identify a set of transcription factor motifs that are enriched in the enhancer regions activated during head regeneration. Our results show that Hydra displays complex gene regulatory structures of developmentally dynamic enhancers, which suggests that the evolution of complex developmental enhancers predates the split of cnidarians and bilaterians.

overall_design: ChIP-seq of three histone modifications (H3K4me2, H3K4me3, and H3K27ac) in head regeneration time course and body map in Hydra Vulgaris. All experiments were done in duplicates.

first: Mortazavi

last: Ali

first: Murad

last: Rabi


title: Transcriptional Profiling of Leiomyosarcoma Cell Lines

status: Public on Jan 22 2020

city: Worcester

first: Matthew

last: Hemming

state: MA

address: 364 Plantation Street

institute: UMass Medical School

summary: Leiomyosarcoma (LMS) is a mesenchymal neoplasm with complex copy number alterations and characteristic loss of tumor suppressor genes without known recurrent activating oncogenic mutations. Clinical management of advanced LMS relies on cytotoxic chemotherapy and complementary palliative approaches, and research efforts to date have had limited success identifying clinically actionable biomarkers or targeted therapeutic vulnerabilities. To explore the distinctive biological underpinning of LMS, we evaluated gene expression patterns of LMS cell lines and correlated results with primary tumor samples.

overall_design: RNA-seq from LMS cell lines


title: Integrative analysis of Hydra head regeneration reveals activation of distal enhancer-like elements [RNA-seq]

overall_design: Gene expression profiles of budding and head regeneration time courses as well as body map in Hydra Vulgaris using RNA-seq. All experiments were done in duplicates.


title: Integrative analysis of Hydra head regeneration reveals activation of distal enhancer-like elements

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

overall_design: Refer to individual Series


title: Integrative analysis of Hydra head regeneration reveals activation of distal enhancer-like elements [ATAC-seq]

overall_design: Open chromatin profiling of head regeneration time course and body map in Hydra Vulgaris using ATAC-seq. All experiments were done in duplicates.


title: BRCAness, SLFN11 and RB1 loss predict response to topoisomerase I inhibitors in triple negative breast cancers

status: Public on Dec 28 2019

first: Tatiana

last: Popova

state: Veuillez choisir

address: 26 rue d'Ulm

institute: Institut Curie

summary: Expression data from patient-derived xenografts of human triple-negative breast cancers

overall_design: We used GeneChip Human 1.1 ST arrays  to identify the genes differentially expressed in PDX with different responses to irinotecan treatment

first: Elisabetta

last: Marangoni


title: Designing a single cell ATAC-Seq (scATAC-Seq) dataset to validate long read RNA-Seq isoforms and benchmark scATAC-Seq analysis methods

status: Public on Dec 19 2019

city: Clayton

first: Shanika

last: Amarasinghe

state: VIC

address: 15 Innovation Walk

department: Monash Biomedicine Discovery Institute

institute: Monash Unviersity

summary: Single cell sequencing technology has been widely used for understanding the heterogeneity of complex tissue and for identifying novel cell types or cell states. Previous efforts of single cell profiling are mostly performed by measuring transcriptomes using single cell RNA sequencing (scRNA-seq). scRNA-seq is relatively well developed and around 500 analysis tools are currently available for performing different tasks. In the past five years, assays for profiling the single cell chromatin accessibility landscape have emerged and provide extra information about gene regulation at the epigenetic level. Due to its simplicity and sensitivity, single cell Assays for Transposase-Accessible Chromatin using sequencing (scATAC-seq) is widely used to obtain chromatin accessibility. This data will be used to comprehensively evaluate scATAC-seq data analysis tools and gaps in analysis workflows together with publicly available bulk ATAC-Seq and scATAC-seq data using optimised universal evaluation metrics. Furthermore, this data will be used to validate novel isoforms identified from long-read scRNA-Seq study.

overall_design: our experiment utilized the 5 human lung adenocarcinoma cell lines H2228, H1975, A549, H838 and HCC827. For the single cell designs, the five cell lines were mixed equally and processed by 10X chromium, referred to as sc_10X_5cl in the analysis that follows.

first: Luyi

last: Tian

first: Jafar

middle: S

last: Jabbari

first: Matt

last: Ritchie


title: Sonoselective Transfection of Cerebral Vasculature without Blood-Brain Barrier Disruption - Bulk RNA seq

status: Public on Dec 11 2019

city: Charlottesville

first: Alexander

last: Mathew

address: 415 Lane Road

institute: University of Virginia

summary: Treatment of many pathologies of the brain could be improved markedly by the development of non-invasive therapeutic approaches that elicit robust, endothelial cell-selective, gene expression in specific brain regions that are targeted under MR image-guidance. While focused ultrasound (FUS) in conjunction with gas-filled microbubbles (MBs) has emerged as a non-invasive modality for MR image-guided gene delivery to the brain, it has been used exclusively to transiently disrupt the blood-brain barrier (BBB), which may induce a sterile inflammation response. Here, we introduce a new MR image-guided FUS method that elicits endothelial-selective transfection of the cerebral vasculature (i.e. “sonoselective” transfection), without opening the BBB. We first determined that activating circulating, cationic plasmid-bearing, MBs with pulsed low-pressure (0.1 MPa) 1.1 MHz FUS facilitates sonoselective gene delivery to the endothelium without MRI-detectable disruption of the BBB. The degree of endothelial selectivity varied inversely with the FUS pressure, with higher pressures (i.e. 0.3 MPa and 0.4 MPa FUS) consistently inducing BBB opening and extravascular transfection. Bulk RNA sequencing analyses revealed that the sonoselective low pressure regimen does not upregulate inflammatory or immune responses. Single cell RNA sequencing indicated that the transcriptome of sonoselectively transfected brain endothelium was unaffected by the treatment. The approach developed here permits targeted gene delivery to blood vessels and could be used to promote angiogenesis, release endothelial cell-secreted factors to stimulate nerve regrowth, or recruit neural stem cells.

overall_design: Groups of 3 - 4 mice were treated with 0.1 MPa, 0.2 MPa, 0.4 MPa, or 0.0 MPa (Anesthesia + Cationic microbubbles only) for harvest at both 6 h and 24 h post treatment, for a total of 8 groups. At either 6 or 24 hours following FUS activation of plasmid-bearing MBs, the front right quadrant of the brain was harvested and processed for bulk mRNA sequencing followed by bioinformatics analyses.


title: Amplification of Oocytes through Parthenogenesis

status: Public on Nov 28 2019

city: Munich

first: Chenglei

address: Ingolstädter Landstraße 1

institute: Helmholtz Munich

summary: We asked whether oocyte number could be amplified through parthenogenesis of mouse oocytes, without requiring creation of a paternal genome and a genetically unique genome. Parthenotes develop to a blastocyst-like stage, and from this parthenogenetic ESCs (pESCs) can be derived with high efficiency. Like ESCs, pESCs maintain unlimited self-renewal and pluripotency, as well as germline competence. Further, we demonstrate that their expression pattern of imprinted maternal genes resembles that observed in oocytes. pESCs can be directed to differentiate into primordial germ cell-like cells (PGCLCs) and form oocytes that produce fertile pups and reconstitute ovarian endocrine functions. The transcriptome and imprinting pattern of PGCLCs differentiated from pESCs more closely approximate those of in vivo produced embryonic PGCs, than PGCLCs produced from ESCs. Parthenogenesis offers a promising route for deriving PGCLCs and amplifying oocytes by faithfully maintaining maternal genes, without fertilization.

overall_design: We used ESC and pESC to do RNA-seq for analysis the gene expression of pluripotent genes, X-linked genes and imprinting genes; and then used pESC-PGCLC, ESC-PGCLC and PGCs to do RNA-seq for analysis the germ cell marker genes and imprinting genes expression.


title: Landscape and Dynamics of Single Immune Cells in Hepatocellular Carcinoma

status: Public on Nov 13 2019

city: Beijing

first: Yao

last: He

state: Haidian District

address: Room 307A, Intergrated Science Building 2, Peking University,, No.5 Yiheyuan Road

institute: BIOPIC

summary: The immune microenvironment of hepatocellular carcinoma (HCC) is poorly characterized. Combining two single-cell RNA sequencing technologies, we produced transcriptomes of CD45+ immune cells for HCC patients from five immune-relevant sites: tumor, adjacent liver, hepatic lymph node (LN), blood, and ascites.A cluster of LAMP3+ dendritic cells (DCs) appeared to be the mature form of conventional DCs and possessed the potential to migrate from tumors to LNs. LAMP3+ DCs also expressed diverse immune-relevant ligands and exhibited potential to regulate multiple subtypes of lymphocytes. Of the macrophages in tumors that exhibited distinct transcriptional states, tumor-associated macrophages (TAMs) were associated with poor prognosis, and we established the inflammatory role of SLC40A1 and GPNMB in these cells. Further, myeloid and lymphoid cells in ascites were predominantly linked to tumor and blood origins, respectively. The dynamic properties of diverse CD45+ cell types revealed by this study add new dimensions to the immune landscape of HCC.

overall_design:
The immune microenvironment of hepatocellular carcinoma (HCC) is poorly characterized. Combining two single-cell RNA sequencing technologies, we produced transcriptomes of CD45+ immune cells for HCC patients from five immune-relevant sites: tumor, adjacent liver, hepatic lymph node (LN), blood, and ascites.
*** Raw sequence data access provided at:  China Genomic Sequence Archive (GSA)  (under accession HRA000069 https://bigd.big.ac.cn/gsa-human/browse/HRA000069).

first: Qiming

last: Zhang

first: Zemin

first: Xianwen

last: Ren

first: Kang

last: Liu


title: Transcriptome data of rat bladder tissues of chronic bladder ischemia injury mediated detrusor underactive animal model

status: Public on Nov 19 2019

city: Seoul

first: DONG-MYUNG

last: SHIN

address: Pungnap-2 dong, Songpa-gu

department: Department of Biomedical Sciences

country: South Korea

institute: University of Ulsan College of Medicine

summary: Detrusor underactivity (DUA) is defined as reduced detrusor contraction strength and/or duration, resulting in prolonged bladder emptying and/or a failure to achieve complete bladder emptying within a normal time span. DUA is a frustrating diagnosis for clinicians as well as patients since no effective pharmacological treatment is available. The prevalence of urodynamically confirmed DUA in elderly patients with lower urinary tract symptoms (LUTS) is known to be approximately 28% (40.2% in male and 13.3% in female), and the prevalence of DUA increases with age 65. Vascular endothelial damage (VED) also occurs during the human aging process and is an independent risk factor for atherosclerosis and hypertension. Pelvic arterial insufficiency, a common clinical problem in the elderly population, may lead to impaired lower urinary tract perfusion and have an important role in voiding dysfunction, such as DUA or detrusor overactivity (DO). Thus, to establish a reliable detrusor underactivity (DUA) rat model and to investigate the pathophysiology of chronic bladder ischemia (CBI) on voiding behavior and bladder function.

overall_design: 16 weeks Sprague–Dawley (SD) rats were used. The iliac arterial injury (AI) was made by endothelial injury of the iliac arteries (AI-30, 30 times of injury at each iliac artery) for bladder ischemia and received a 2% cholesterol diet for atherosclerosis. The sham group underwent sham operation and received 2% cholesterol diet. After 8 weeks, gene expression analysis was done.

first: Dong-Myung

last: Shin

first: Myung-Soo

last: Choo

first: Hwan

last: Yu

first: Hyein

last: Ju


title: The evolution of DNA methylation inheritance and programming in animals

status: Public on Nov 17 2019

city: beijing

first: jiang

last: liu

address: NO.1 Beichen West Road, Chaoyang District

institute: Beijing Institute of Genomics, Chinese Academy of Sciences

type: Methylation profiling by high throughput sequencing

summary: DNA methylation has been found throughout animal kingdom, but it is still unclear whether this epigenetic mechanism affects the evolution of genomic elements in animals. Here, we compare the DNA methylomes of gametes and embryos from 7 representative animal species. We find that parental methylomes are propagated to the progeny without significant changes during embryogenesis in cnidarians and insects, but undergo substantial reprogramming in echinoderms, and the reprogramming become more dramatic during deuterostome evolution. Interestingly, young gene promoters in mammals tend to be reprogrammed, usually have low CpG density, don’t contain CpG Islands (CGIs) and are hypermethylated, and the hypermethylated status correlates to lower transcription. Unexpectedly, an evolutionary trend of CpG accumulation in promoters is observed only during vertebrate evolution. Most of ancient gene promoters in mammals form CGIs, which are generally unmethylated and associate with higher transcription. Thus, to gain unmethylated pattern to facilitate transcription, nature selection should be in favor of the formation of CGIs in promoters. Our data suggest that the formation of CGIs in promoters is driven by DNA methylation during mammalian evolution.

sample_organism:
Apis mellifera
Strongylocentrotus purpuratus
Nematostella vectensis
Ciona savignyi

overall_design: MethylC-seq were performed with  gametes and early developmental embryos in four species, including honey bee, sea anemone, sea urchin and ciona. We compared the inheritance and programming of parental CpG methylation of animal species including cnidarian, protostome and deuterostome.

first: Xiaocui

last: Xu

first: Guoqiang

last: Li

first: Congru

first: Jing

first: Jiang