title: Hyaluronic acid ameliorates the proliferative ability of human amniotic epithelial cells through activation of TGF-β/BMP signaling

city: Zunyi

first: Nuo-Xin

last: Wang

state: Guizhou

address: 149 Dalian Road

institute: Affiliated Hospital of Zunyi Medical University

summary: This study investigated the mechanism by which 300 kDa HA (1 mg/mL) promotes the proliferation of hAECs. P1 hAECs in logarithmic growth phase were harvested, inoculated into 6-well plates at 3×105/well, and cultured with 5% CO2 at 37 °C. The medium was changed after 3 days, and then the cells were cultured for 18 or 36 h in the presence and absence of HA (300 kDa, 1 mg/mL). The total RNA was purified using the RNeasy MinElute kit (Qiagen, Valencia, CA, USA) according to the manufacturer’s instructions. cDNA was synthesized using a SuperScript III Reverse Transcriptase Kit (Invitrogen, Shanghai, China). Real-time PCR was conducted, and the 2–∆∆Ct method was used to quantify gene expression levels. The signal was collected by Agilent Feature Extraction software and analyzed by Agilent GeneSpring GX software.

overall_design: qPCR gene expression profiling.  hAECs from three samples were used and treated separately as indicated in the summary. Equal amount total RNA from each donor was pooled prior to gene expression analysis.

first: Ya-Bing

last: Tian

first: Yan

last: Xu

first: Chang-Yin

last: Yu

first: Ru-Ming

last: Liu

first: Yi

last: Luo

first: Jian-Hui

last: Xiao


title: The Atoh7 shadow enhancer provides transcriptional robustness during retinal ganglion cell development

status: Public on Aug 25 2020

city: Davis

first: Tom

last: Glaser

address: One Shields Ave

country: USA

institute: University of California Davis

type: Genome binding/occupancy profiling by high throughput sequencing

summary: The retinal ganglion cell (RGC) competence factor ATOH7 is dynamically expressed during retinal histogenesis. ATOH7 transcription is controlled by a promoter-adjacent primary enhancer and a remote shadow enhancer (SE). Deletion of the ATOH7 human SE causes non‑syndromic congenital retinal non-attachment (NCRNA) disease, characterized by optic nerve aplasia and total blindness. We used genome editing to model NCRNA in mice. Deletion of the murine SE reduces Atoh7 mRNA >5-fold, but does not recapitulate optic nerve loss; however, SEdel/KO (knockout) trans heterozygotes have thin optic nerves. By analyzing Atoh7 mRNA and protein levels, RGC development and survival, and chromatin landscape effects, we show how the SE ensures robust Atoh7 transcriptional output. Combining SE deletion, KO and wild-type alleles in a genotypic series, we determined the amount of Atoh7 needed to produce a normal complement of adult RGCs, and the secondary consequences of graded reductions in Atoh7 dosage. Together these data reveal the workings of an evolutionary fail-safe, a duplicate enhancer mechanism hard-wired in the machinery of vertebrate retinal ganglion cell genesis.

overall_design: ATAC-seq open chromatin profiling of E14.5 wild type and Atoh7 shadow enhancer mutant retinas.  There were 3 biological replicates per genotype, which consisted of pooled retinal pairs from individual animals and 50,000 cells from each pair per replicate.

first: Joel

middle: B

last: Miesfeld


title: Gene expression of mouse lung CD11b+ dendritic cells before and after ex vivo culture

city: RTP

first: Rick

middle: David

last: Fannin

state: NC

address: 111 Tw Alexander Dr, MD D204

department: NIEHS/NIH

institute: Mr.

summary: Conventional dendritic cells (cDCs) in the lung drive effector T cell differentiation, and initiate allergic responses upon inhalation of allergens. However, CD11b+ cDCs are composed Ly-6C+ and Ly-6C– subpopulations, and the specific function of each subpopulation has been elusive. Since Ly-6C+ CD11b+ cDCs lost the surface display of Ly-6C upon ex vivo culture, we hypothesized that Ly-6C+ cDCs are precursors of Ly-6C– cDCs. To determine whether 2 CD11b+ cDC subpopulations become the same cell types after maturation, we compared their transcriptomes after ex vivo cultue. As controls, we also compared transcriptomes of freshly isolated Ly-6C+ and Ly-6C– cDCs. Their transcriptomes were also compared with another CD103+ cDCs and monocytes.

overall_design: C57BL/6 mice were inhaled house dust extract together with ovalbumin. Ly-6C+CD11b+, Ly-6C– CD11b+, and CD103+ cDCs and monocytes were purified by flow cytometric sorting. Purified lung cDCs and monocytes were cultured for 2 days. mRNA expression  isolated from freshly isolated or cultured cellswas examined by the NanoString platform.

first: Hideki

last: Nakano

first: Gentaro

last: Izumi

first: Donald

middle: N

last: Cook


title: CRISPR repair in a preclinical model of Noonan syndrome associated cardiomyopathy

city: Goettingen

first: Gabriela

last: Salinas

state: Lower-Saxony

address: Kreuzbergring 57

department: Department of Pathology

country: Germany

institute: Universitaetsmedizin Goettingen

type: Expression profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Gene Expression Analysis of WT and dnTCF4-expressing Short-Term Hematopoietic Stem Cells (ST-HSC)

city: Prague

first: Petr

last: Danek

address: Videnska 1083

department: Laboratory of Hemato-oncology

country: Czech Republic

institute: Institute of Molecular Genetics of the CAS

summary: The canonical Wnt signaling pathway is mediated by interaction of b-catenin with the TCF/LEF transcription factors and subsequent transcriptional activation of Wnt-target genes. In the hematopoietic system, the function of the pathway has been mainly investigated by genetic manipulation of b-catenin. However, this approach does not allow to discriminate between TCF/LEF dependent or independent b-catenin activity. Here, we employed a transgenic mouse model expressing a truncated dominant negative form of the human TCF4 transcription factor (dnTCF4) which abrogates activation of Wnt target genes even when b-catenin is stabilized and translocated into the nucleus while preserving its TCF/LEF independent activities. The disruption of the b-catenin-TCF/LEF interaction results in reduced granulocytic differentiation accompanied with an accumulation of short-term hematopoietic stem cells (ST-HSC) and granulocytic progenitors. In order to investigate the mechanism responsible for the insufficient production of granulocytes, we performed a transcriptomic analysis of ST-HSC from dnTCF4-expressing and control WT mice.

overall_design: ST-HSC, defined as Lin- ckit+ CD48+ CD150- cells, were sorted from BM of 3 WT and 3 dnTCF4-expressing mice. PolyA enriched sequencing libraries were constructed using SMARTer Universal Low Input RNA Kit and Nextera XT DNA Library Prep Kit and sequenced (paired-end sequencing) on NextSeq 500 instrument from Illumina.

first: Miroslava

middle: K

last: Adamcova

first: Lucie

last: Janeckova

first: Vladimir

last: Korinek

first: Carlos

middle: L

last: Asencio

first: Touati

last: Benoukraf

first: Roberto

middle: T

last: Magallanes

first: Qiling

last: Zhou

first: Daniel

middle: G

last: Tenen

first: Meritxell

last: Alberich-Jorda


title: Cartilaginous and osteochondral tissue formation by human mesenchymal stem cells on three-dimensionally woven scaffolds

city: Cambridge

first: Charles

middle: Arthur

last: Whittaker

state: MA

institute: Koch Institute

summary: The development of mechanically functional cartilage and bone tissue constructs of clinically relevant size, as well as their integration with native tissues, remain important challenges for regenerative medicine. The objective of this study was to assess of adult human mesenchymal stem cells (MSC) in large, three dimensionally woven poly(-caprolactone) (PCL) scaffolds in proximity to viable bone, both in a nude rat subcutaneous pouch model and under simulated conditions in vitro. In Study I, various scaffold permutations: PCL alone, PCL-bone, “point-of-care” seeded MSC-PCL-bone, and chondrogenically pre-cultured Ch-MSC-PCL-bone constructs were implanted in a dorsal, ectopic pouch in a nude rat. After eight weeks, cells in the PCL scaffold exhibited both chondrogenic and osteogenic gene expression profiles. Notably, while both tissue profiles were present, constructs that had been chondrogenically pre-cultured prior to implantation showed a loss of glycosaminoglycan (GAG) as well as the presence of mineralization along with the formation of trabeculae-like structures. In Study II of the study, the GAG loss and mineralization observed in Study I in vivo were recapitulated in vitro by the presence of either nearby bone or osteogenic culture medium additives but were prevented by a continued presence of chondrogenic medium additives. These data suggest conditions under which adult human stem cells in combination with polymer scaffolds synthesize functional and phenotypically distinct tissues based on the environmental conditions, and highlight the potential influence that paracrine factors from adjacent bone may have on MSC fate, once implanted in vivo for chondral or osteochondral repair.

sample_organism:
Homo sapiens
Bos taurus
Rattus norvegicus

overall_design: Three replicates of chondrogenically pre-cultured adult human mesenchymal stem cells (hMSC) seeded on poly(ε-caprolactone) scaffolds (3D woven PCL) sutured to bovine bone and implanted into info nude rats for 8 weeks follwed by RNA isolation.

first: Benjamin

last: Larson

first: Sarah

last: Yu

first: Hyoungshin

last: Park

first: Bradley

last: Estes

first: Franklin

last: Moutos

first: Cameron

middle: J

last: Bloomquist

first: Patrick

last: Wu

first: Jean

middle: F

last: Welter

first: Robert

last: Langer

first: Farshid

last: Guilak

first: Lisa

middle: E

last: Freed


title: RNAseq analysis of bone marrow aspirates from Plasmodium vivax patients in the Amazon State, Brazil

city: Brasília

first: Taina

last: Raiol

state: DF

address: Av. L3 Norte, Campus Universitário Darcy Ribeiro

department: Fiocruz Brasília (GEREB)

country: Brazil

institute: Oswaldo Cruz Foundation - Fiocruz

summary: We analyzed bone marrow aspirates from seven patients with vivax malaria and RNAseq analysis identified genes assoviated with erythropoietic defects

overall_design: Bone marrow aspirates from three patients obtained during the acute attack and 42 days after drug cure treatment

first: Marcus

middle: V

last: Lacerda

first: Hernando

middle: A

last: del Portillo


title: A single genetic locus senses and protects the beneficial oral bacterium Streptococcus sp. A12 from a spectrum of antimicrobial peptides

status: Public on Aug 24 2020

city: Gainesville

first: Kyulim

last: Lee

address: 1395 Center Drive

institute: University Florida

summary:
BACKGROUND: While substantial advances have been made to understand the nature and significance of interspecies interaction in oral microbial communities, much remains to be learned about how commensal species contribute to the maintenance of health-associated biofilm communities. We report that successful competition of Streptococcus sp. A12 with the dental pathogen Streptococcus mutans requires many different factors. While A12 can directly inhibit the growth of S. mutans, A12 harbors several genes (i.e. pcfFEGRK) that are required to be able to tolerate antagonistic factors of S. mutans, and these gene products are critical to the competitive fitness of A12. Here, we delve deeper in the role of the pcfFEG, a predicted lantibiotic immunity transporter, and the pcfRK, its genetically-linked two-component system (TCS) in A12.
METHODS: RNA-Seq was utilized to compare the transcriptomes of A12 wild-type strain and A12 lacking the response regulator (pcfR) or histidine kinase (pcfK) of pcfRK, a TCS directly regulating pcfFEG. Each strains were prepared in 3 biological replicates. Strains were grown to OD600 nm = 0.4 in BHI medium before harvest. Deep sequencing was performed at the University of Florida ICBR facilities (Gainesville, FL). Approximately 15 million short-reads were obtained for each sample. After removing adapter sequences from each short-read and trimming of the 3’-ends by quality scores, the resulting sequences were mapped onto the reference genome of strain Streptococcus sp. A12 (NCBI Reference Sequence: NZ_CP013651.1) using the short-read aligner.  Mapped short-read alignments were then converted into readable formats using SAMTOOLS.
RESULTS: Using an optimized data analysis workflow, we mapped 13-16 million reads per sample to the genome of A12. For viewing of the mapped reads aligned to the genome, .bam files were uploaded into the Integrative Genomics Viewer (IGV – version 2.3.55). A .csv file containing raw read counts for each replicate (3) was then uploaded to Degust (http://degust.erc.monash.edu/) and edgeR analysis performed to determine Log2 fold change and a false discovery rate (FDR). When compared to the wild-type A12 strain, 61 genes were differentially expressed in A12 lacking pcfR and 35 genes were differentially expressed in A12 lacking pcfK (Log2 fold change > (-)1.5, -log10 P-value > 4). Interestingly, a subset of the same genes was found to be upregulated in both pcfR and pcfK deletion strains, including ATM98_04215, ATM98_04220 and ATM98_03625, annotated as a protease, a dipeptidase (both co-transcribed), and an aminopeptidase, respectively. Another interesting finding was a cluster of genes predicted to be the mannose PTS system was downregulated in the pcfK mutant strain, and a two-component ABC transporter annotated as ABC-type CcmA multidrug resistance system was found to be upregulated in the pcfR mutant strain. The pcfK mutant strain showed an upregulation of the pcfFEG genes and the cognate response regulator gene, pcfR. In the pcfR mutant, pcfK was also upregulated, compared to the parental A12 strain.
CONCLUSIONS: Transcriptional profiling of pcfR and pcfK mutant strains revealed the scope of the pcfRK regulon. When supplemented with functional genomics, we uncovered additional genes shown to function independently or cooperatively with PcfFEGRK in tolerating the lantibiotic nisin. Together these results highlight additional mechanisms beneficial species may be utilizing to remain competitive when existing in complex microbial communities.

overall_design: Transcriptional profiling of wild-type strain A12 and A12 lacking the response regulator (pcfR) or histidine kinase (pcfK) of pcfRK, a TCS directly regulating pcfFEG, a LanFEG-type ABC transporter shown to enhance tolerance to bacteriocins


title: Transcriptome Analysis of Candida albicans Biofilms Grown in the Presence of Arachidonic Acid and Fluconazole

city: Bloemfontein

first: Oluwasegun

middle: Olalekan

last: Kuloyo

address: 200 Nelson mandela drive, Park west

department: Microbial Biochemical and Food Biotechnology

country: South Africa

institute: University of the Free State

summary: Candida albicans is a commensal yeast within the human microbiota with significant medical importance because of its pathogenic potential. The yeast produces biofilms, which are highly resistant to available antifungals. High level of antifungal resistance by C. albicans biofilms has resulted in the need for alternative treatment. Polyunsaturated fatty acids such as arachidonic acid has been reported to increase the susceptibility of C. albicans biofilms to azole. However, the underlining mechanism is unknown. To unravel the mechanism behind this phenomenon, identification of differentially regulated genes in C. albicans biofilms grown in the presence of arachidonic acid, fluconazole, and the combination of both compounds was conducted using RNAseq.

overall_design: Investigation in triplicate three treatment conditions and a control

middle: O

first: Ruan

last: Fourie

first: Jacobus

last: Albertyn

first: Carolina

middle: H

last: Pohl


title: Deep sequencing of small RNAs from neurosurgical extracellular vesicles substantiate miR-486-3p as a circulating biomarker that distinguishes glioblastoma from lower-grade astrocytoma patients

city: Sydney

first: Susannah

last: Hallal

state: NSW

address: 119-143 Missenden Road

department: Neurosurgery

country: Australia

institute: Chris O'Brien Lifehouse

type: Non-coding RNA profiling by high throughput sequencing

summary: Neurosurgical aspirate fluids captured during tumour resections are a rich source of glioma extracellular vesicles (EVs) isolated directly from tumour microenvironments. The sncRNA contents of EVs derived from 17 neurosurgical aspirates were  profiled using the Illumina® NextSeqTM 500 NGS System.

overall_design: Using density gradient ultracentrifugation, EVs were purified from cavitron ultrasonic surgical aspirate (CUSA) washings from glioblastoma (GBM; n=12) and astrocytoma II-III (GII-III, n=5) surgeries. The sncRNA contents of surgically captured EVs were profiled using the Illumina® NextSeqTM 500 NGS System.

first: Saeideh

last: Ebrahim Khani

first: Heng

last: Wei

first: Maggie

middle: Y

first: Hao-Wen

last: Sim

first: Joanne

last: Sy

first: Brindha

last: Shivalingam

first: Michael

last: Buckland

first: Kim

last: Kaufman


title: Transcriptome-wide m6A profiles analysis in response to hypoxia

city: Guangzhou

first: Yan-Jie

last: Wang

address: 107, West Yanjiang Road

country: China

institute: Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University

summary: Recently, many studies have focused on the epigenetics such as histone modification and DNA methylation upon hypoxic stress. However, little is known about the the m6A epitranscriptome in response to hypoxia. In this study, we report that hypoxia systematically inhibit the m6A pathway through reducing the total m6A level and the expression of m6A readers. Deep m6A transcriptome sequencing revealed a drastic reprogramming of m6A epitranscriptome during cellular hypoxia. Integration m6A epitranscriptome with RNA-Seq or LC-MS/MS based proteome analysis of cells upon hypoxic stress revealed that the reprogramming of m6A epitranscriptome remodels the transcriptome and proteome to support the efficient generation of energy for adaption to hypoxia. Taken together, our studies indicated that the crosstalk between m6A and HIF1 pathway was essential for the cellular response to hypoxia, and provided profound insights into the molecular mechanism underlying the hypoxic responsive process.

overall_design: meRIP-seq, RNA-seq for the human HeLa cervical cancer cells under the normoxia vs. hypoxia(6h, 12h, 24h, 1% oxygen) conditions

first: Jian-You

last: Liao


title: Pre-existing tumoral B cell infiltration and impaired genome maintenance correlate with response to chemoradiotherapy in locally advanced rectal cancer (LARC)

city: Buenos Aires

first: Juan

middle: Martín

last: Sendoya

state: Buenos Aires

address: Avenida Patricias Argentinas 435

department: Laboratory of Molecular and Cellular Therapy

country: Argentina

institute: Fundación Instituto Leloir

summary: Using Human Genome 4x44 two-color Agilent microarrays, we established the expression profiling of 39 LARC pretreatment tumor samples to elucidate the molecular features associated with response to treatment after neoadjuvant chemoradiotherapy (nCRT).

overall_design:
Two color microarrays where Cy5= tumor sample and Cy3= Stratagene Universal Human RNA Reference. This dataset comprises the transcriptomic profiling of 39 consecutive eligible LARC patients who underwent therapy at the Oncology Unit at Bonorino Udaondo Hospital (Buenos Aires, Argentina) from November 2015 to September 2018. This study was approved by the Udaondo Hospital Ethics Committee and the Instituto Leloir Institutional Review Board. All patients signed the approved Informed Consent.  All patients were assigned to standard pelvic long course radiotherapy (LCRT: 50.4 Gy in 28 fractions of three-dimensional conformal radiotherapy, 1.8 Gy per fraction, per day) with concurrent capecitabine (825 mg/m2/bid for 28 days), termed hereafter CRT. Patients with a high risk of systemic relapse (EMVI, high mesorectal node burden and LLND) underwent TNT, which comprises pre-treatment before the CRT with three cycles of CAPOX (130 mg/m² of oxaliplatin on day 1 and capecitabine 1000 mg/m²/bid, days 1-14 every 3 weeks). Two cycles of capecitabine monotherapy (850 mg/m²/bid, days 1-14 every 3 weeks) was then administered until response assessment for all patients. Together, TNT and CRT are referred to as nCRT. Response to nCRT was evaluated on the surgical specimen by the  pathological tumor regression (pTRG) score proposed by  the seventh edition manual of the American Joint Committee on Cancer (AJCC), except for cases where pTRG was unavailable due to complete clinical response or unresectability. pTRG=0-1 and complete clinical responders were considered good responders, while pTRG=2-3 and unresectable patients were considered poor responders. The most relevant clinical variables are summarized in the metadata file; in case you require further information, do not hesitate to contact the authors.
contributor: GENUIT consortium

middle: M


title: Whole transcriptome analysis for blue light-induced eye damage in mice

city: Weifang

first: Guohui

last: wang

address: baotong west street 7166

institute: department of cell biology，Weifang Medical University

summary: We identified 737 differentially expressed genes, including 430 upregulated genes and 307 downregulated genes, by calculating the gene FPKM in each sample and conducting differential gene analysis. Gene ontology analysis and KEGG pathway enrichment analysis suggested that blue light influenced visual perception, sensory perception of light stimulus, phototransduction, and JAK-STAT signaling pathways. Differential lncRNA, circRNA and miRNA analysis suggested that blue light exposure affected pathways for retinal cone cell development and phototransduction, among others.

overall_design: Kunming mice into an experimental group that was exposed to blue light and a control group that was exposed to natural light

first: Xiaoyun

last: Dong

first: Xinli

last: Ouyang

first: Boyu

last: Chen

first: Yongfang

last: Xie


title: Translational repression of G3BP in cancer and germ cells suppresses stress granules and enhances stress tolerance

city: Memphis

first: Yong-Dong

state: TN

address: 262 Danny Thomas Pl, MS1135

institute: St. Jude Children's Research Hospital

summary: Stress granules (SG) are membrane-less ribonucleoprotein condensates that form in response to various stress stimuli via phase separation. SG act as a protective mechanism to cope with acute stress, but persistent SG have cytotoxic effects that are associated with several age-related diseases. Here, we demonstrate that the testis-specific protein, MAGE-B2, increases cellular stress tolerance by suppressing SG formation through translational inhibition of the key SG nucleator G3BP. MAGE-B2 reduces G3BP protein levels below the critical concentration for phase separation and suppresses SG initiation. Importantly, knockout of the MAGE-B2 mouse ortholog confers hypersensitivity of the male germline to heat stress in vivo. Thus, MAGE-B2 provides cytoprotection to maintain mammalian spermatogenesis, a highly thermo-sensitive process that must be preserved throughout reproductive life. These results demonstrate a mechanism that allows for tissue-specific resistance against stress through fine-tuning phase separation and could aid in the development of male fertility therapies

overall_design: RNA-Seq using Illumina sequencing in WT and KO animals’ whole testes with and without heat stress to characterize how loss of Mageb4 affects the transcriptome

first: Anna

last: Lee

first: Jonathon

last: Klein

first: Ryan

last: Potts


title: Identification and characterization of microRNAs (miRNAs) and their transposable element origins in the saltwater crocodile, Crocodylus porosus

city: Lubbock

first: ARNAB

last: GHOSH

state: Texas

address: 2500 Broadway

department: Biology

institute: Texas Tech University

summary: MicroRNAs (miRNAs) are 18-24 nucleotide autonomous regulatory RNA molecules found in all eukaryotes. They are involved in the regulation of a multitude of genetic and biological pathways through post transcriptional gene silencing and/or translational repression. Previous data has suggested a slow evolutionary rate for the saltwater crocodile (Crocodylus porosus) over the past several million years when compared to its closest extant relatives, the birds. Understanding genome regulation, adaptive capabilities and physiological features in the saltwater crocodile in the context of relatively slow genomic change thus holds significant potential for the investigation of genomics, evolution and adaptive studies. Utilizing eleven different tissue types and sixteen small RNA libraries, we report a catalog of 644 miRNAs in the saltwater crocodile with > 78% of miRNAs being potentially novel to crocodilians. We also predicted and identified targets for the miRNAs as well as analyzed the relationship of the miRNA repertoire to transposable elements (TEs)  in the saltwater crocodile that showed an increased association of DNA transposons with miRNA biogenesis when compared to retrotransposons. Phylogenetic analysis of C. porosus miRNA expectedly revealed highest number of miRNAs in sister crocodilian clades of the American Alligator and the Indian Gharial. This work reports the first comprehensive analysis of miRNAs in Crocodylus porosus for and addresses the potential impacts of miRNAs in regulating the genome in the saltwater crocodile as well as supporting the role of TEs as a source for miRNAs, adding to the increasing evidence that TEs play a significant role in the evolution of gene regulation.

overall_design: Construction of Illumina Deep sequening small RNA libraries in 11 different tissue typoes in the C porosus and bioinformatic analysis to predict C porosus known and novel miRNAs, their targets, expression profiles and other genomic features of the miRNAs in the C porosus

first: Arnab

last: Ghosh

first: Roy

middle: N

last: Platt

middle: W

last: Vandewege

first: Sally

middle: R

last: Isberg

first: Travis

middle: C

last: Glenn

first: Daniel

last: Peterson

first: Chuan-Yu

last: Hsu

first: John

last: Finger

first: Troy

last: Kieran

first: Jaime

last: Gongora

first: Rabia

last: Tabassum

first: David

last: Ray


title: Transient in vivo base editing with no detectable RNA- and DNA off-target mutations

city: Zurich

first: Weihong

last: Qi

address: Winterthurerstr. 190

department: FGCZ

country: Switzerland

institute: ETHZ

summary: RNA-programmable deaminases, known as base editors (BEs), enable precise single base conversions on genomic DNA and hold great promise for therapeutic application in patients. Recent studies, however, have raised serious concern with regard to off-target effects, questioning translatability of BEs to the clinic. Here we analyze transcriptome- and genome-wide off-target effects following AAV-mediated delivery of cytosine base editors (CBEs) in vivo in an unbiased manner. We show that low expression of CBEs allows sufficient on-target editing to cure a disease phenotype with no increase in off-target effects compared to untreated controls. To further improve safety of in vivo base editing, we developed a lipid nanoparticle (LNP)-mediated delivery system to transiently express BEs. We reach up to 21% on-target editing with no detectable transcriptome- or genome-wide off-target effects, and are able to reverse the disease phenotype of a phenylketonuria mouse model. These results have important implications, underlining the feasibility of transient in vivo base editing for therapeutic use in patients.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: RNA-seq experiment for the evaluation of in-vivo off-target deamination by saKKH-CBE and determination of dose dependency

first: Tanja

last: Rothgangl

first: Gerald

last: Schwank


title: Nrg1/ErbB4 signaling contributes to the effects of the ketogenic diet on GABAergic activity and seizures

city: Gangzhou

first: jin

last: wang

address: Xinzao Panyu District

institute: Guangzhou Medical University

summary: The ketogenic diet (KD) has been used as an effective therapy to treat epilepsy. Previous studies indicate an elevated level of GABA in the brain by KD treatment. However, the underlying mechanisms remain to be elucidated. Here we report that KD treatment suppresses seizures in both acute and chronic seizure models and enhances presynaptic GABA release probability in the hippocampus. By screening molecular targets that potentially linked to GABAergic activity with transcriptome analysis, we identify that KD treatment dramatically increased the Nrg1 gene expression in the hippocampus. Disruption of Nrg1 signaling by genetically deleting its receptor-ErbB4 or blocking ErbB4 kinase activity abolishes KD’s effects on GABAergic activity and seizures. Mechanistically, KD treatment increases Nrg1 expression via up-regulating histone acetylation. Our findings suggest a critical role of Nrg1/ErbB4 signaling in mediating KD’s effects on GABAergic activity and seizures, which sheds light on the development of new therapeutic interventions to seizure control.

overall_design: Hippocampal mRNA profiles of 2-3 month-old male C57BL/6J mice that were fed with control diet or the ketogenic diet for three weeks.

first: Xiang-Dong

last: Sun


title: Comparison of Regulatory Type of Macrophages and PCMO Cells from perspective of RNAseq data.

city: Kuopio

first: Tuija

last: Kekarainen

state: Northern Savonia

address: Microkatu 1

department: Cell Therapy Unit

country: Finland

institute: Kuopio Center for Gene and Cell Therapy

summary: Gene expression plasticity is central for macrophages? timely responses to cues from the microenvironment permitting phenotypic adaptation from pro-inflammatory (M1) to wound healing and tissue-regenerative (M2, with several subclasses). Regulatory macrophages (Mreg) are a distinct macrophage type, partially sharing some functionalities with both M1 and M2 cells. Mreg possess immunoregulatory, anti-inflammatory, and angiogenic properties, and are considered as a potential allogeneic cell therapy product to treat clinical conditions, e.g., non-healing diabetic foot ulcers. In this study we characterized clinically relevant regulatory macrophages, Mreg and Mreg_UKR, programmable cells of monocytic origin (PCMO) and comparator macrophages (M1, M2a and M0) using flow-cytometry, RT-qPCR, phagocytosis and secretome measurements, and finally RNA-Seq. We demonstrate that conventional phenotyping has a limited potential in deciphering all classes of produced cells. This limitation was ameliorated when global transcriptome characterization by RNA-Seq was employed. Using this approach we prove that macrophage manufacturing processes can result in a highly reproducible cell phenotype. At the same time, minor changes introduced in a protocol can consistently effect the phenotype of the end product as well. Additionally, we have identified a novel constellation of potential process specific biomarkers, which will not only support further clinical product development, but will lead to a better understanding of macrophage biology, differentiation and polarized activation.

overall_design: There are 7 immune cell types, comprised of 1 reference (CD14) and 6 differentiated types: M0, M1, M2a, Mreg, Mreg_UKR, and PCMO. There are 9 anonymized human donors, with a minimum of 3 donors per cell type. The donors act as biological replicates for the purpose of differential expression statistics.

first: Olga

middle: L

last: Gurvich

first: Katja

last: Puttonen

first: Aubrey

last: Bailey

first: Anssi

last: Kailaanmäki

first: Vita

last: Skirdenko

first: Minna

last: Sivonen

first: Sanna

last: Pietikanen


title: Millet can be infected with several viruses if grown as a weed on crop fields

city: Gödöllő

first: Éva

last: Várallyay

address: 4 Szent-Györgyi Albert Street

department: Agricultural Biotechnology Institute

country: Hungary

institute: National Agricultural Research and Innovation Centre

summary: Millet is a dangerous weed in Hungary. Lack of seed dormancy helps it to spread easily and be present at maize, wheat and other crop fields. Our previous report revealed the possibility that millet can also play a role as a virus reservoir. In that study we detected the presence of several viruses in millet using DAS ELISA. Because serological methods can only detect the presence of the investigated particular pathogens, we suspected that other, previously unknown viruses can also be present in this weed. To investigate this theory, we randomly sampled two locations and collected millets showing stunting, chlorosis, and striped leaves and investigated the presence of viruses using small RNA HTS as a diagnostic method. Our result confirmed the widespread presence of wheat streak mosaic virus at both locations. Moreover, barley yellow striate mosaic virus and barley virus G were also identified, which have not been described from Hungary before. As these viruses can cause severe diseases on wheat, their presence on a weed mean a potential infection risk. Our study indicates that the presence of millets on the fields needs a special control in order to prevent emergence of new diseases at crop fields.

overall_design: 2 libraries from symptomatic Panicum miliaceum from two different areas

first: György

last: Pasztor

first: Zsuzsanna

last: Galbacs

first: Tamas

last: Kossuth

first: Emese

last: Demian

first: Erzsebet

last: Nadasy

first: Andras

middle: P

last: Takacs

first: Eva

last: Varallyay


title: WT/AtohKO/TNFdARE Ileum

city: Nashville

first: Ken

last: Lau

address: 2215 Garland Ave. MRBIV10475

department: Cell and Developmental Biology

institute: Vanderbilt University

summary: An inverse correlation between countries endemic for helminth infestation and Crohn's disease (CD) incidences has been reinforced by anecdotal but successful cases of helminth therapy for CD. Recent studies have revealed that tuft cells in the small intestine are critical for sensing helminths and directing a type 2 immune response to counteract colonization. Here, we establish an inverse relationship between chemosensory tuft cells and local tissue inflammation in CD patients as well as an established mouse model of TNF-á-induced Crohn's-like ileitis (TNFÄARE). Using a combination of mouse and organoid models, single-cell RNA-sequencing, multiplex immunofluorescence, computational analysis, metabolite mass spectrometry, and microbiome sequencing and manipulation, we identified Atonal Homolog 1 (ATOH1)-independent tuft cells, as opposed to ATOH1-dependent tuft cells, to be responsive to the commensal microbiome through the tricarboxylic acid (TCA) cycle metabolite succinate. To evaluate the ability of the malleable, ATOH1-independent tuft cell population to suppress intestinal inflammation, we administered succinate to TNFÄARE animals post onset of ileal inflammatory disease. We observed significantly reduced pathology that is exquisitely dependent on succinate-induced tuft cell specification in the disease model, leading to an anti-helminth response previously shown to suppress inflammation. Inflammation suppression was triggered by cytokines critical to anti-helminthic response, such as IL-22, IL-25, and IL-13. We provide evidence implicating the modulatory role of intestinal tuft cells in chronic intestinal inflammation, which could enable the development of CD therapies around leveraging this rare and elusive cell type.

overall_design: Ileum Biological Replicates Collected from WT/AtohKO/TNFdARE Mice; 7 WT vs. 3 AtohKO vs. 3 TNFdARE

first: Amrita

last: Banerjee

first: Alan

middle: J

last: Simmons


title: Ileum/colon treated with succinate

overall_design: WT Ileum or Colon Biological Replicates Collected from WT Mice treated with succinate


title: WT/AtohKO Ileum w/ antibiotics

overall_design: Ileum Biological Replicates Collected from WT/AtohKO Mice treated with antibiotics; 2 WT vs 2 AtohKO (both with antibiotics)


title: Ileal single-cell analysis in the context of inflammation focused on tuft cells

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

overall_design: Refer to individual Series


title: LncRNA-mRNA expression profiles and functional networks of hyposalivation in the submandibular gland in hypertension

city: Beijing

first: Jinghua

last: Yang

address: 32 North Third Ring Road West, Haidian District, Beijing

institute: Beijing Zhiyun data technology co. LTD

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

summary: Hyposalivation is a complication of hypertension. Although the lncRNA have recently been identified to play a role in the pathogenesis of hypertension, the specific effects of lncRNAs on hyposalivation caused by hypertension remain unclear. The aim of the current study was to construct and systematically analyze the lncRNA-miRNA-mRNA network and reveal its potential roles in hyposalivation.

overall_design: We use high-throughput technologies to screen the lncRNAs and mRNAs in the submandibular gland (SMG) tissues from SHR rats (n=5) compared with WKY rats (n=5). Differential expression lncRNAs and mRNAs were confirmed by qRT-PCR. We constructed a CNC and ceRNA network to reveal the core genes in hyposalivation.

first: Hongzhi

last: Xie

first: Zhujun

last: Shen

first: Yechen

last: Han

first: Yining

last: Wang


title: Colonic Crohn's left and right colon

summary: Colonic Crohn's Disease from a single patient in remission with mild disease index

overall_design: Single patient with left and right colonic biopsy

first: Elizabeth

last: Scoville


title: Heparin anticoagulant for human bone marrow does not influence in vitro-performance of human mesenchymal stromal cells

city: Hannover

first: Oliver

last: Dittrich-Breiholz

address: Carl-Neuberg-Str. 1

department: Research Core Unit Genomics

institute: Medical School Hannover

summary: Background: Mesenchymal stromal cells (MSCs) are a promising cell source for tissue engineering and regenerative medicine. In our lab, we found that cell preparations from bone marrow of many donors had a limited capacity for in vitro-differentiation into the osteogenic and chondrogenic lineages although this is a capacity claimed to be inherent to this kind of cells. Therefore the current study was designed to test the hypothesis whether the amount of heparin used as anti-coagulant during bone marrow harvest has inhibitory influence on the in vitro-differentiation capacity of the isolated MSCs.   Methods: Bone marrow was obtained from twelve donors with good physical condition during preparation of the femoral cavity for the implantation of the femoral stem for a total hip arthroplasty in the absence or presence of heparin. Isolated MSCs were characterized by plastic adhesion, morphology, population doubling times, expression of cell surface antigens and in vitro-differentiation into the adipogenic, osteogenic and chondrogenic lineages. In addition, transcriptome analyses were performed.  Results: Bone marrow prepared in the absence of heparin showed a comparable processability as bone marrow in the presence of heparin. Notably, no coagulation was observed. The number of mononuclear cells retrieved from the density gradient was independent of heparin addition. Moreover, none of the phenotypic or functional parameters assessed correlated with the addition of heparin. Transcriptome and quantitative realtime PCR analyses demonstrated that some selected genes were up- or downregulated in the cells isolated with the addition of heparin. However, this statement held true for only some but not all of the donors investigated in the present study.   Conclusions: No correlation with heparin addition was observed with respect to the parameters assessed in the present study. This implies the absence of consequences both for the results of in vitro-investigations and also during in vivo-application, thereby ruling out heparin as a potential source of disparate results that are described in the literature.

overall_design: Mesenchymal stromal cells from bone marrow of three donors were treated with heparin or were left untreated. Accordingly, six samples were processed and finally analyzed by use of single color microarray technology.

first: Yvonne

last: Roger

first: Andrea

last: Hoffmann

first: Laura

last: Burmeister

first: Anika

last: Hamm

first: Kirsten

last: Elger

first: Thilo

last: Flörkemeier


title: WT colonic scRNA-seq experiment [re-analysis]

summary: The GSE114044 data was re-mapped and re-analyzed. Duplicated sample records were created for the convenient retrieval of the complete raw data from SRA.

overall_design: 3 colon from different  WT mice in single sequencing run;


title: Set1/COMPASS repels heterochromatin invasion at euchromatic sites by disrupting Suv39/Clr4 activity and nucleosome stability

city: San Francisco

first: Bassem

last: Al-Sady

state: CA

address: 513 Parnassus Ave HSW1501

institute: UC San Francisco

summary: We report global occupancy of H3K9me2 and H3K4me3 in wild-type S. pombe and two mutant backgrounds - the deletion of heterochromatin antagonist epe1 and the double mutant absent epe1 and the H3K4 methyltransferase set1

overall_design: ChIP-Seq was performed for two histone modifications in three genotypes

first: R

last: Greenstein


title: Biofilms of non-tuberculous mycobacteria display distinct expression patterns and form an extracellular matrix

city: Seattle

first: Eliza

last: Peterson

state: WA

address: 401 Terry Ave N

institute: Institute for Systems Biology

summary: Comparison of  transcriptional differences (RNA-seq) between biofilm and planktonic cultures of Mycobacterium chelonae

overall_design: For pellicle samples, cultures of Mycobacterium chelonae were grown in 75cm2 cap-vented culture flasks in a 30 degrees C static incubator for 5 (t1) or 10 (t2) days. For planktonic samples, M. chelonae was cultured in the same way as pellicle samples, but tyloxapol was added to a final concentration of 0.05%. Samples were collected from pellicle and planktonic cultures from four independent experiments.  The sequence reads that passed quality filters were aligned with Bowtie2 and processed using the R package DuffyNGS.


title: Analysis of HIV-1 transcriptome in different cell models with nanopore sequencing [KHI-1_A2019]

city: PARIS

first: Stephane

last: Le Crom

address: 46 rue Ulm

department: Genomic Core Facility

country: France

institute: IBENS

summary: To explore in depth and in a quantitative manner the complexity of the HIV-1 splicing landscape we used nanopore long-read cDNA (ONT) sequencing in NL4-3 HIV-1 infected primary CD4+ T cells and transfected/infected HeLa cells. Mean read lengths were between 1286 and 2626 nucleotides with maximum sizes of up to 9182 nucleotides, sufficiently long to span all possible splice junctions and to be assigned to a total of 229 exon combinations. Seventy isoforms were above the threshold of 5 copies in infected T cells and a core of 36 isoforms were found in common in infected T cells, infected HeLa cells and transfected HeLa cells. Quantification of both all viral isoforms as well as splice site (SS) usage were compiled to build “splice trees”, a quantitative representation of the splicing pathways leading to the different viral isoforms.  This approach allowed visualizing the complete rewiring of SS usages upon perturbation of SS D2, using over-expression of U1 D2UpEx snRNA in transfected HeLa cells and its impact on viral RNA expression. Furthermore, we produced the first dynamic picture of the cascade of events occuring between 12 and 24 hours of CD4+ T cells HIV-1 infection. In particular, our data highlighted the importance of non-coding exons in viral RNA transcriptome regulation. Altogether, our results show that ONT sequencing allows one to grasp the dynamic of splicing events modulating the viral RNA landscape in infected cells.

overall_design: To assess the ability of ONT sequencing to follow the expression of viral isoforms during an infection, CD4+ T cells were isolated from one donor and infected with VSVg pseudotyped NL4-3 HIV-1. Total RNA was extracted at 12/14/16/20/24 hours post-infection.

first: Nam

last: Quang

first: Sophie

last: Goudey

first: Emmanuel

last: Ségéral

first: Ammara

last: Mohammad

last: Lemoine

first: Corinne

last: Blugeon

first: Margaux

last: Versapuech

first: Jean-Christophe

last: Paillart

first: Clarisse

last: Berlioz-Torrent

first: Stéphane

last: Emiliani

first: Sarah

last: Gallois-Montbrun


title: Analysis of HIV-1 transcriptome in different cell models with nanopore sequencing [HIVTCD4_A2018]

overall_design: To assess the ability of ONT sequencing to explore HIV-1 transcriptome, CD4+ T cells were isolated from 3 donors and infected with VSVg pseudotyped NL4-3 HIV-1. Total RNA was extracted 24h post-infection


title: Analysis of HIV-1 transcriptome in different cell models with nanopore sequencing


title: Analysis of HIV-1 transcriptome in different cell models with nanopore sequencing [HIVEXTA_A2018]

overall_design: To assess the ability of ONT sequencing to follow changes in NL4-3 HIV-1 transcriptome, we artificially perturbed HIV-1 splicing by transfecting HeLa cells with a mutant of U1 snRNA increasing D2 splice site usage (pNL4-3 and pU1D2UpEx) or with the WT U1 (pNL4-3 and pUC13-U1). Total RNA was extracted 24h post-transfection (3 biological replicates per condition).


title: Identification of plant PKG in GA signaling via fine-tuning GAMYB nuclear localization

city: Wuhan

first: Qingwen

last: Shen

state: Hubei

address: Huazhong Agriculture University

department: Lipid metabolism

institute: National Key Laboratory of Crop Genetic Improvement

summary: Through transcriptomic profiling, we compared differentially expressed genes between WT and pkg mutant treated with Br-cGMP, we found that PKG as primary receptor mediated cGMP signaling in rice.

overall_design: Total RNA samples were extracted from 14-day-old seedlings of WT and pkg mutant treated with or without 10 μM Br-cGMP for 5 h. Each line contains three biological repetitions.

first: Yueyun

last: Hong


title: Analysis of HIV-1 transcriptome in different cell models with nanopore sequencing [HIVTA_A2017]

overall_design: To assess the ability of ONT sequencing to compare the viral transcriptome in different HIV-1 expressing models, total RNA was extracted from 2 samples of non-infected HeLa cells, 2 samples of HeLa cells infected with VSVg pseudotyped NL4-3 HIV-1 (24h post-infection) and 2 samples of HeLa cells transfected with pNL4-3 (24h post-transfection).


title: SmallRNA analysis of simulated microgravity sensitized endothelial cells.

city: Madras Institute of Technology, Chrompet

first: Suvro

last: Chatterjee

state: Tamil Nadu

address: Vascular Biology Laboratory

country: India

institute: AU-KBC Research Centre, Anna University

summary: SmallRNAs are proposed as key regulators in many cellular processes including angiogenesis, suggested candidates for future therapeutic applications. But, regulation and modulation of smallRNAs in pathology conditions and normal conditions are poorly recognized, supremely in wound care management. Current study focused to identify the smallRNA regulatory network in simulated microgravity sensitized Human Umbilical Cord Vein Endothelial cells (HUVECs) and gravity (1g) as a background. HUVECs were purchased from Lonza (Cat.No) and cultured in EGM2 medium (Cat.No CC3162) supplemented with 10% Fetal Bovine, 1% penicillin-streptomycin (W/V). Cells were cultured in RPM (Randomized positioned machine) for 2 hours at 37°C.

overall_design: small RNAs expression in simulated microgravity sensitized endothelial cells (ug) and control (gravity) were analyzed by Next-Gen Sequencing.

first: Dharanibalan

last: Kasiviswanathan

first: Rajadurai

last: Perumal

first: Manuel

last: Philip


title: Butyrate, but not Propionate, Rescues Maternal Diet-Induced Neurocognitive Deficits in Offspring

city: chongqing

first: yu

last: linchao

address: No.136 Zhongshan Second Road, Yuzhong District, Chongqing

institute: children's hospital of chongqing medical university

summary: Fiber diet plays a beneficial role in neurocognitive disorders, like dementia and Alzheimer’s Disease. However, insufficient fiber consumption in public increases the concern about public health, particularly about neurocognitive diseases. To survey the association between fiber dietary and neurocognitive performances, mice were subjected to normal-fiber diet or low-fiber diet during gestation, and the neurocognitive functions of the offspring were assessed. We found that maternal low-fiber diet impaired the cognitive functions, and the impairments can be reversed by butyrate, rather than propionate intake. Mechanism studies showed that HDAC4 might become the most potential mediator in butyrate-dependent neurocognitive improvement. Besides, using human maternal serum and paired umbilical cord blood samples, we demonstrated that the SCFA levels in offspring are positively correlated with levels in maternal serum. Those results provide a solid basis for not only maternal fiber diet regulates neurocognitive functions in offspring through altering SCFA levels, but clinical practice in SCFAs-dependent maternal intervention for offspring health.

overall_design: Examination of intestinal microbiota in normal mice and low-fiber mice using 16S rDNA.

first: Linchao

last: Yu

first: Yuan

last: Shi


title: Immune differentiation regulator p100 tunes NF-kB responses to TNF

status: Public on Aug 22 2020

city: Baltimore

first: Supriyo

last: De

state: Maryland

address: 251 Bayview Blvd

department: Laboratory of Genetics and Genomics

institute: NIA-IRP, NIH

summary: Stringent regulation of TNF signaling prevents aberrant inflammation. TNF engages the canonical NF-kB pathway for activating the RelA:p50 heterodimer, which mediates specific expressions of pro-inflammatory and immune response genes. Importantly, the NF-kB system discriminates between time-varied TNF inputs. Negative feedback regulators of the canonical pathway, including IkBa, thought to ensure transient RelA:p50 responses to brief TNF stimulations. The noncanonical NF-kB pathway controls a separate RelB activity associated with immune differentiation. In a systems modeling approach, we uncovered an unexpected role of p100, a constituent of the noncanonical pathway, in TNF signaling. Brief TNF stimulation of p100-deficient cells produced an additional late NF-kB activity composed of the RelB:p50 heterodimer, which distorted the TNF-induced gene-expression program. Periodic TNF pulses augmented this RelB:p50 activity, which was reinforced by NF-kB-dependent RelB synthesis. In sum, the NF-kB system seems to engage distantly related molecular species for enforcing dynamical and gene controls of immune-activating TNF signaling.

overall_design: There are 9 samples in total. Every time point has two replictes. The Input sample is the control and it is the combined input sample from the two replicates.

first: Mingming

last: Zhao

first: Amit

last: Singh

first: Jaimy

last: Joy

first: Ranjan

last: Sen


title: Innate, non-cytolytic CD8+ T cell-mediated suppression of HIV replication by MHC-independent inhibition of virus transcription

status: Public on Aug 23 2020

city: Atlanta

first: Gregory

middle: K

last: Tharp

state: GA

address: 954 Gatewood Dr

department: Developmental and Cognitive Neuroscience

institute: Yerkes National Primate Research Center

summary: MHC-I-restricted, virus-specific cytotoxic CD8+ T cells control HIV/SIV replication via the recognition and killing of productively infected CD4+ T cells. Several studies in SIV-infected macaques suggest that CD8+ T cells may also decrease virus production by suppressing viral transcription. RNA sequencing is used to identify candidate cellular pathways that are involved in the virus-silencing mediated by these CD8+ T cells.

overall_design: Peripheral blood mononuclear cells (PBMCs) from 8 donors were obtained using Ficoll-Hypaque density gradient centrifugation. CD4+ and CD8+ T cells were purified by negative selection (Miltenyi Biotec) and stimulated with human CD3/CD28/CD2 antibody-coated beads (Miltenyi Biotec) at 1:1 bead-to-cell ratio, in the presence of 50 IU/ml of rhIL-2 (Miltenyi Biotec) for three days. A replication-competent and an Envelope (Env)-defective NL4-3 reporter virus expressing eGFP under control of the HIV- 1 LTR were kindly provided by F Kirchhoff58 (Ulm University Medical Center, Ulm, Germany). Envelope (Env)-defective NL4-3_eGFP was then complemented in trans with a dual-tropic Env (pSVIII-92HT593.1) obtained through the NIH-NIH AIDS Reagent Program from Dr. Beatrice Hahn (cat# 3077). A variant of the (Env)-defective NL4-3 IRES-eGFP reporter virus encoding the short-lived D2eGFP version of the protein was generated as previously described32 by inserting the protein-destabilizing mouse ornithine decarboxylase (MODC) domain at the Emory Custom Cloning Core Division using standard cloning techniques.  Viral stocks were produced by single or co-transfection of Lenti-X 293T cells with the respective HIV-1 constructs, using FuGene6 (Promega) in OptiMEM (Thermo Fisher). For the dual-color co-culture assays, target CD4+ T cells were labelled with CellTrace Violet dye (Vio) prior to infection. Briefly, TCR-activated CD4+ T cells were labelled with 5 μM of CellTrace Violet dye (Vio) (Thermo Fisher) per 10x106 cells and were subsequently infected by spinoculation (2h, 37°C, 2,500 rpm) using 100 l of virus stock/0.6x106 cells in flat-bottom 96-well plates. Autologous TCR-activated CD8+ T cells were labelled with 5 μM of CellTrace Red dye (Red) (Thermo Fisher) per 10x106 cells and added to the Vio+CD4+ T cells at 1:1 and 5:1 effector-to-target cell (E:T) ratios in the presence of 50 IU/ml of rhIL-2 after infection in 48-well plates.

first: Michelle

last: Zanoni

first: David

last: Palesch

first: Claudia

last: Pinacchio

first: Mirko

last: Paiardini

first: Ann

last: Chahroudi

first: Steven

last: Bosinger

first: Deanna

last: Kulpa

first: Guido

last: Silvestri


title: Effect of nitric oxide on the reversal of adriamycin resistance in NCI/ADR-RES tumor cells

city: RTP

first: NIEHS

last: Microarray Core

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

summary: To understand how nitric oxide is involved in reversal of resistance and investigate mechanisms of Pgp-dependent efflux and genes in involved in drug resistance.

overall_design: NCI/ADR-RES cells were treated with Adriamycin, DETNO or combinations of Adriamycin and DETNO for 24 hours.

first: Birandra

last: Sinha


title: Integrated analysis of a compendium of RNA-Seq data reveals putative master splicing factors underlying Rett syndrome and thermogenesis

city: Chengdu

first: Peng

last: Yu

state: Sichuan

address: No.37 Guoxue Alley, Wuhou District

department: West China Biomedical Big Data Center, West China School of Medicine (West China Hospital)

institute: Sichuan University

summary: Cold exposed mice were studied to investigate the genes changed in cold-induced thermogenesis.

overall_design: Brown adipose tissue and subcutaneous WAT were dissected from mice that were treated in thermo-neutral (30 C) and cold temperature (4 degrees) for 72 hours. Total 12 samples with three replicates for each condition.

first: Jin

last: Li

first: Nolwenn

last: Joffin

first: Philipp

middle: E

last: Scherer


title: RNA-seq of porcine parthenogenetic embryos and wild-type controls

status: Public on Aug 21 2020

city: Columbus

first: Jinsoo

last: Ahn

state: OH

address: 2029 Fyffe Rd

institute: The Ohio State University

summary: The objective of this study was to, using porcine parthenogenetic embryos, investigate imprinting status of genes within the genomic region spans between the CALCR and ASB4 genes in chromosome 9.

overall_design: Examination of paternal or maternal gene expression patterns in porcine embryos.

first: Seongsoo

last: Hwang

first: Kichoon

last: Lee


title: Changes of gene expression patterns of mouse in vivo and TC-1 cell lines

city: Daejeon

first: Galam

last: Leem

address: 291 Daehakro Yusunggu

country: South Korea

institute: KAIST

overall_design: Refer to individual Series


title: Genome-wide maps of histone lactylation in ocular melanoma

city: Shanghai

first: Peiwei

last: Chai

address: No.833 Zhizaoju Road

institute: Shanghai Jiao Tong University school of medcine

summary: For the first time, we investigated the role of histone lactylation in tumorgenesis of ocular melanoma.

overall_design: Examination of histone lactylation in ocular melanoma cells.

first: Jie


title: Transcriptome analysis after glycolysis inhibitors treatment in ocular melanoma cella

summary: In order to study the mechanism of histone lactylation, we used glycolysis inhibitors to reduce histone lactylation and applied RNA-seq and ChIP-seq to identify its target genes in ocular melanoma.

overall_design: Examination the target genes of histone lactylation in ocular melanoma cells.


title: Gene expression profiling data following HIF-1α or HIF-2α knockdown in SW1353 cells

city: Seoul

first: Jin-Hong

last: Kim

address: 1 Gwanak-ro, Gwanak-gu

institute: Seoul National University

summary: Chondrosarcomas, malignant cartilaginous neoplasms, are capable of transitioning to highly aggressive, metastatic, and treatment-refractory states, resulting in significant patient mortality. We aimed to uncover the transcriptional program directing such tumor progression in chondrosarcomas. Here, we conducted weighted correlation network analysis (WGCNA) to extract a characteristic gene module underlying chondrosarcoma malignancy. We identified hypoxia-inducible factor-2α (HIF-2α, encoded by EPAS1) as an upstream regulator that governs the malignancy gene module. HIF-2α was upregulated in high grade chondrosarcoma biopsies and HIF-2α gene amplification was associated with the poor prognosis of patients with chondrosarcoma. Using tumor xenograft mouse models, we demonstrated that HIF-2α confers chondrosarcomas the capacities required for tumor growth, local invasion, and metastasis. Pharmacological inhibition of HIF-2α in conjunction with the chemotherapy agents synergistically enhanced chondrosarcoma cell apoptosis and abolished malignant signatures of chondrosarcoma in mice. We expect that our insights into the pathogenesis of chondrosarcoma will provide guidelines for the development of novel molecular-targeted therapeutics for chondrosarcoma.

overall_design: Gene expression profiling of SW1353 cells were transfected with HIF1A, EPAS1 siRNA or control siRNA. Three biological replicates were used for each group.

first: Hyeonkyeong

first: Yongsik

last: Cho


title: Whole genome bisulfite sequencing (WGBS) of porcine parthenogenetic embryos and wild-type controls.

type: Methylation profiling by high throughput sequencing

overall_design: Examination of paternal or maternal hypermethylation in porcine embryos.


title: Circulation of gut pre-activated naïve CD8+ T cells enhances anti-tumor immunity in B cell defective mice

city: Kyoto

first: Kenji

last: Chamoto

state: Kyoto

address: Yoshida Konoe-cho, Sakyo-ku

department: Department of Immunology and Genomic Medicine

country: Japan

institute: Graduate School of Medicine, Kyoto University

summary: The gut microbiome has garnered attention as an effective target to boost immunity and improve cancer immunotherapy. We found that B cell defective (BCD) mice, such as µ membrane tail deletion (µMT), have elevated anti-tumor immunity under specific-pathogen-free condition, depending on CD8+ T cells. Further studies suggest that microbiota-dependent upregulation of type-I IFN inducible genes, including Sca-1, in CD8+ T cells underlies the strong anti-tumor response of BCD mice.   Of the CD8+ T cell subpopulations, the most significant difference in Sca-1 expression between wild-type (WT) and BCD mice was seen in naïve CD8+ T cells (CD44lowCD62Lhigh) in peripheral lymphoid and spleen. To further explore whether the upregulation of Sca-1 expression in peripheral CD8+ T cells of BCD mice associates with a unique gene profile, transcriptomic analysis was performed in peripheral CD8+ T cell populations in WT and µMT mice at the single cell level, providing the evidence that among peripheral CD8+ T cells, naïve CD8+ T cells are the most distinct subpopulation between WT and BCD mice.

overall_design: Peripheral CD8+ T cell populations derived from WT and B cell defective (µMT) strains each were labeled with oligo DNA-tagged antibodies against CD44 and CD62L (TotalSeq-A provided from BioLegend) and used for the single cell transcriptome analysis.

first: Maryam

last: Akrami

first: Rosemary

last: Menzies

first: Michio

last: Miyajima

first: Ryuji

last: Suzuki

first: Hiroyuki

last: Sato

first: Akiko

last: Nishii

last: Tomura

first: Sidonia

last: Fagarasan

first: Tasuku

last: Honjo


title: Changing expression profiles of mRNA, miRNA, lncRNA, and circRNA reveal the key regulators and interaction networks of ceRNA in pulmonary fibrosis

city: JiNan

first: Xue

last: Liu

state: ShangDong

address: Wenhua West Road

institute: The Affiliated Hospital of Shandong University of TCM

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


title: Changing expression profiles of mRNA, miRNA, lncRNA, and circRNA reveal the key regulators and interaction networks of ceRNA in pulmonary fibrosis [ncRNA-seq]

summary: Pulmonary fibrosis is a kind of interstitial lung disease with architectural remodeling of tissues and excessive matrix deposition. Apart from mRNA, microRNA, long non-coding RNA (lncRNA) and circular RNA (circRNA) could also play important roles in the regulatory processes of occurrence and progression of pulmonary fibrosis. In the present study, whole transcriptome sequencing analysis was applied to investigate the expression profiles of mRNAs, lncRNAs, circRNAs and miRNAs. After comparing bleomycin-induced pulmonary fibrosis model lung samples and controls, 286 lncRNAs, 192 mRNAs, 605 circRNAs, and 32 miRNAs were found to be differentially expressed. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were performed to investigate the potential functions of these DE mRNAs and ncRNAs. Various related GO-BP terms such as “inflammatory response”, “positive regulation of interleukin-2 biosynthetic process”, “Regulation of actin cytoskeleton”, “Notch signaling pathway”, “negative regulation of cellular response to vascular endothelial growth factor stimulus”, and KEGG signal pathways such as “Wnt signaling pathway”, “TNF signaling pathway”, “MAPK signaling pathway”, “Regulation of actin cytoskeleton” were enriched implying potential roles in regulatory process. In addition, two co-expression networks (lncRNA-miRNA-mRNA, circRNA-miRNA-mRNA) were also constructed to understand the internal regulating relationships of these mRNAs and ncRNAs. Our study provides a systematic perspective on the potential functions of these DE mRNAs and ncRNAs during PF process, and could help pave the way for effective therapeutics for this devastating and complex disease.

overall_design: Six samples, 3 bleomycin-induced pulmonary fibrosis model and 3 controls.

first: Wei

last: Zhang

first: Huaman

first: Xinhua

last: Jia

first: Rong

last: He


title: Changes of gene expression patterns of mouse lung epithelial cells in response to IL-15 whether or not they have MCMV-memory CD8 T cells [mouse in vivo]

first: Galam

last: Leem

summary: We report the differences of gene expression pattern of 4 different groups of mouse lung epithelial cells (Naive mouse without IL-15, Naive mouse with IL-15, MCMV-infected mouse without IL-15, and MCMV-infected mouse with IL-15). We found that mouse with MCMV-memory CD8 T cells response to IL-15 and the behaviors of cancer were changed compared to other groups.

overall_design: Compare gene expression patterns among 4 different groups of mouse lung epithelial cells (Naive mouse without IL-15, Naive mouse with IL-15, MCMV-infected mouse without IL-15, and MCMV-infected mouse with IL-15)

first: Eui-Cheol

last: Shin


title: The site and nature of terminal bronchiolar destruction in chronic obstructive pulmonary disease (COPD).

city: VANCOUVER

first: FENG

last: XU

state: BC

address: Suite 110, 6309 Larkin Dr, 110

department: Department of Pathology and Lab Medicine

country: Canada

institute: UBC

summary:
Previous studies have reported progressive reductions of terminal bronchioles in chronic obstructive pulmonary disease (COPD).
Based on micro-CT and Microarray profiling, this study determines the exact site of terminal bronchiole reduction and begins to investigate the gene expression patterns associated with the reduction in COPD.

overall_design: Systematic uniform random (SUR) sampling provided 120 samples (8/lung) from 10 explanted lungs of patients with very-severe (Global Initiative for Obstructive Lung Disease, GOLD 4) COPD treated by lung transplantation, and 5 unused donor control lungs. After quality control, three samples were removed from the panel. Thus, this dataset contains the Microarray profiling of 117 samples that includes 77 COPD samples and 40 control samples.

first: Feng

last: Xu

first: Drago

last: Vasilescu

first: Daisuke

last: Kinose

first: Naoya

last: Tanabe

first: Kevin

last: Ng

first: Harvey

last: Coxson

first: Joel

middle: D

last: Cooper

first: Tillie-Louise

last: Hackett

first: Stijn

last: Verleden

first: Bart

last: Vanaudenaerde

first: Christopher

middle: S

last: Stevenson

first: Marc

last: Lenburg

first: Avrum

last: Spira

first: Don

last: Sin

first: Raymond

first: James

last: Hogg


title: Changes of gene expression patterns of Mouse TC-1 cell lines responding to Interferon-gamma [TC-1 cell line]

first: Galam

last: Leem

summary: We report the differences of gene expression pattern of Mouse TC-1 cell lines responding to Interferon-gamma. TC-1 cell lines were treated with 20ng/ml of Interferon-gamma for 72 hours and gathered for RNA seq. We found that in response to Interferon-gamma, TC-1 cell lines expressed increased amounts of RNA related to immune responses.

overall_design: Compare gene expression patterns between Interferon-gamma treated TC-1 cell lines and untreated TC-1 cell lines

first: Eui-Cheol

last: Shin


title: Gaucher Disease Renders Resistance Against Viral Infection of the CNS

city: Ness-Ziona

first: Einat

middle: B.

last: Vitner

state: Israel

address: Ness-Ziona

country: Israel

institute: Israel institute for Biological Research

summary:
Purpose: In order to describe how non- genetic factors may contribute to emergence of additional neurodegenerative disorders in mice with neuronal Gaucher Disease (nGD), full transcript mRNA sequencing was implemented with half brain in order to study differential gene expression between experimental groups: (Untreated) Control, CBE (Conduritol β epoxide ), SVNI (Sindbis virus), and CBE + SVNI
Methods: Full transcript mRNA sequencing was implemented with half brain in order to study differential gene expression between experimental groups (biologilal triplicates in each group). We mapped 20 million sequence reads per sample to the mouse genome (GRCm38) and identified 16,903 transcripts. .  All subjects were 28 days old. Half of the bisected brains were flash-frozen in liquid nitrogen and stored in -80C conditions until use. RNA was isolated using a RNeasy mini kit (Qiagen, Hilden, Germany). Extraction of RNA was performed at the Israeli Institute for Biological Research and the RNA was then transferred to the Weizmann Institute of Science for further analysis. Quality was examined with the Agilent 2200 TapeStation system (Agilent Technologies); RIN values of each sample were determined satisfactory for use in sequencing. Expression of mRNA was quantified using DESeq following normalization of library size with Pipeline. Gene lists were created by criteria based on an absolute linear fold change ≥ 2.0, *p ≤ 0.05. Enriched pathways in the resulting gene lists were analyzed with Ingenuity Pathway Analysis (IPA).
Results: Our study represents the first full RNA transcriptome analysis of brains from of CBE-treated mice, with biological triplicates generated by RNA-seq technology. The CBE and CBE+SVNI conditions boast remarkably similar genetic profiles with no differentially expressed genes changed between them (fold change ≥ 2.0, *p ≤ 0.05). In CBE, SVNI, and CBE + SVNI conditions respectively, 501, 1724, and 554 genes were significantly upregulated compared to the control, while 5, 333, and 40 genes were significantly downregulated respectively (Fig. 2B). Surprisingly, 476 upregulated genes in the CBE condition were shared with SVNI, while only 25 genes were uniquely upregulated. No downregulated genes were shared between the two conditions (Fig. 2C). Here, we conclude that CBE and CBE+SVNI demonstrate nearly identical mRNA profiles while SVNI boasted highly differential genes compared to all other conditions.
Conclusion: Half brain mRNA profiles of 28-day old untreated (Control), CBE-treated, SVNI-treated, and SVNI + CBE-treated mice were generated by deep sequencing, in triplicate, using Illumina Hiseq.

overall_design: full transcript mRNA sequencing was implemented with half brain: (Untreated) Control, CBE (Conduritol β epoxide ), SVNI (Sindbis virus), and CBE + SVNI

first: Deborah

last: Rothbard


title: Direct DNA crosslinking with CAP-C uncovers transcription-dependent chromatin organization at high resolution

city: Farmington

first: Youzhi

last: Cheng

state: Connecticut

address: 400 Farmington Avenue

department: Genetics and Genome Sciences

country: USA

institute: University of Connecticut Health Center

summary: We introduce Chemical-crosslinking Assisted Proximity Capture (CAP-C), a method that utilizes multi-functional chemical crosslinkers with defined physical sizes to directly assess spatial distances between nuclear genomic sequences. CAP-C avoids limitations caused by extensive protein-DNA crosslinking in most in situ methods, and thus generates chromatin contact maps at high resolution with low background noise.

sample_organism:
Drosophila melanogaster
Homo sapiens
Mus musculus

overall_design: CAP-C utilizes a multifunctional PAMAM dendrimer platform instead of DNA-bound proteins to crosslink spatially adjacent DNA sequences, followed by restriction digestion and proximal ligation and high-throughput sequencing. We develop this method to examine the chromatin architecture of mouse embryonic stem cell F123, human HCT116 and drosophila S2 cell lines.

first: Qiancheng

last: You

first: Anthony


title: Genome-wide structure changes during neuronal differentiation drive gene regulatory networks

city: Singapore

first: Yue

last: Wan

address: 60 Biopolis Street

country: Singapore

institute: Genome Institute of Singapore

summary: RNAs structures play central roles in various cellular processes, and can be remodeled upon binding to cellular factors such as RNA binding proteins (RBP). However, how widespread this remodeling is and whether structural changes can serve as additional regulatory steps for other regulators remains under-explored. Here, we assayed RNA structural dynamics, gene expression, translation and decay during different stages of human neuronal differentiation to understand the impact of RNA structures in stem cell regulation. RBP binding resulted in wide-spread RNA structure changes during early neuronal differentiation.  Structure changes act as a common mechanism for RBPs to modulate the binding of additional RBPs and miRNAs to coordinate gene expression temporally.  In particular, we showed that PUM2 binding on LIN28A resulted in RNA structure changes that enabled miR-30 binding, leading to downregulation of LIN28A. Compensatory mutagenesis experiments that lock specific structural states confirmed the importance of PUM2-induced structure changes in miR-30 regulation. This systematic study broadens our understanding of RNA structural dynamics during human neuronal differentiation and illustrates the wide-spread and complex role of RBPs in regulating RNA structures for gene regulation during human development.

overall_design: High throughput RNA structure probing experiments in vivo using icSHAPE, as well as RNA sequencing, ribosome profiling and RNA decay experiments in hESCs (Day 0, D0), neuronal precursor cells (Day 7, D7), early neurons (Day 8, D8) and neurons (Day 14, D14).

first: Jiaxu

last: Wang

first: Tong

last: Zhang


title: Transcriptome profiling of WT and Cav-1- mouse peritoneal mesothelial cells grown in static and stretching conditions

city: Madrid

first: Manuel

last: Gomez

state: Madrid

address: Melchor Fernández Almagro, 3

country: Spain

institute: CNIC

summary: RNA-Seq was used to characterize the changes induced by mechanical stretching on the gene expression profile of mouse peritoneal mesothelial cells with WT and Cav-1- genetic backgrounds.

overall_design: RNA-Seq of WT and Cav-1- (B6.Cg-CAV1tm1mls/J) mouse peritoneal mesothelial cells cultured in static or stretching conditions.

first: R

last: Strippoli

last: Moreno-Vicente

first: M

middle: A

last: del Pozo


title: Transcriptome profiling of human peritoneal mesothelial cells grown in static and stretching conditions

summary: RNA-Seq was used to characterize the changes induced by mechanical stretching on the gene expression profile of human peritoneal mesothelial cells.

overall_design: RNA-Seq of primary human peritoneal mesothelial cells (HPMCs) obtained from the omentum of abdominal surgery patients.


title: Caveolin1 and YAP drive mechanically-induced mesothelial-to-mesenchymal transition and fibrosis

summary:
Despite their emerging relevance to fully understand disease pathogenesis, we have as yet a poor understanding as to how biomechanical signals are integrated with specific biochemical pathways to determine cell behaviour. Mesothelial-to-mesenchymal transition (MMT) markers colocalized with TGF-beta1-dependent signalling and yes-associated protein (YAP) activation across biopsies from different pathologies exhibiting peritoneal fibrosis, supporting mechanotransduction as a central driving component of these class of fibrotic lesions and its crosstalk with specific signaling pathways. Transcriptome and proteome profiling of the response of mesothelial cells (MCs) to linear cyclic stretch revealed molecular changes compatible with bona fide MMT, which (i) overlapped with established YAP target gene subsets, and (ii) were largely dependent on endogenous TGF-beta1 signaling. Importantly, TGF-beta1 blockade blunts the transcriptional upregulation of the se gene signatures, but not the mechanical activation and nuclear translocation of YAP per se. We studied the role therein of caveolin-1 (Cav1), a plasma membrane mechanotransducer. Exposure of Cav1-deficient MCs to cyclic stretch led to a robust upregulation of MMT-related gene programs, which was blunted upon TGF-beta1 inhibition. Conversely, Cav1 depletion enhanced both TGF-beta1 and TGFBRI expression. Cav1 genetic deficiency exacerbated MMT and PA fibrosis in an experimental model of peritoneal ischaemic buttons. Taken together, these results support that Cav1-YAP/TAZ fine-tune the fibrotic response through the modulation of MMT, onto which TGF-beta1-dependent signaling coordinately converges. Our findings reveal a cooperation between biomechanical and biochemical signals in the triggering of MMT, representing a novel potential opportunity to intervene mechanically-induced disorders coursing with peritoneal fibrosis, such as post-surgical adhesions.

This SuperSeries is composed of the SubSeries listed below.


title: A distinct subpopulation of follicular helper T (Tfh) cells promotes Tfr cell differentiation by producing Sostdc1

city: Beijing

first: Huiping

last: Lu

address: Tsinghua university

institute: Tsinghua university

summary: By using RNA-sequencing assay on sorted Sostdc1-EGFP- Tfh, Sostdc1+ Tfh and Non-Tfh cells and single cell RNA-seq assay on sorted CD4+CD44+T cells from Sostdc1-EGFP reporter mice, support the conclusion that Sostdc1+ Tfh cells are a distinct subpopulation of Tfh cells.After performing the RNA-seq assessment and ATAC-seq on Tfr and Treg cells from WT and Sostdc1 KO mice,demonstrated that Sostdc1 ablation predominantly augmented β-catenin-controlled transcriptome, which in turn resulted in Tfr cell failure.

overall_design: We conducted RNA-seq assay on sorted Sostdc1-EGFP- Tfh, Sostdc1+ Tfh, and Non-Tfh cells with two biological replicates per group.CXCR5+PD1+ GITRhi Tfr and CXCR5- PD1- GITRhi Treg cells were sorted from WT and Sostdc1 KO mice and then subjected to RNA-seq and ATAC-seq assessment. CD44+CD4+ T cells were sorted from heterozygous Sostdc1-EGFP reporter mice  and then analyzed by single cell RNA-seq (10xgenomics).

first: Xindong

last: Liu

first: Xin

last: Wu

first: Rui

last: Huang


title: Gene expression data of colon tissues derived from DSS-ttreated Uhrf1fl/flLyz2-Cre and WT mice

city: Wuhan

first: Qi

last: shanshan

address: 1277 Jiefang Avenue

department: Union Hospital

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

summary: To identify the idea that deficiency of Uhrf1 in macrophages aggravated the intestinal inflammation, We compared the mRNA expression profiles of colon tissues derived from DSS-treated WT and Uhrf1fl/flLyz2-Cre mice.

overall_design: WT mice(n=4) and Uhrf1fl/flLyz2-Cre mice(n=3) were treated with 2.5% DSS in drinking water for 5 days. The total RNA were isolated from colitis colons and subjected to RNA sequencing.

first: Shanshan

last: Qi

first: Yongkui

last: Li


title: Changing expression profiles of mRNA, miRNA, lncRNA, and circRNA reveal the key regulators and interaction networks of ceRNA in pulmonary fibrosis [miRNA-seq]

first: Xue

first: Wei

first: Huaman

first: Xinhua

last: Jia

first: Rong

last: He


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

city: Chongqing

first: Jian

last: Zhou

state: China

address: 1 Yixueyuan Road, Yuzhong District

department: Institute of Neuroscience

institute: Chongqing Medical University

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

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

first: Ming-zhong

last: Xiao

first: Yu

last: Chen


title: Developmental patterns in the hippocampal transcriptome of the vervet monkey

city: Los Angeles

first: Ivette

last: Zelaya

address: 695 Young Drive South, Rm 1524 Gonda

institute: University of California, Los Angeles

summary: Elucidating the developmental patterns of gene expression across brain regions is a critical step toward understanding brain development and disease. We previously studied the transcriptome of multiple brain regions and peripheral tissues across development in the vervet monkey, and identified transcripts related to hippocampal size in 59 animals across 10 developmental timepoints, ranging between 7 days to 9 years of age. Here, we extended this analysis with a focus on transcriptomic changes in hippocampus across early development in vervet neonates and infants under 1 year of age. We combined this dataset with the previously analyzed data. We identified groups of transcripts with age-related patterns, which correlated well with existing human resources. Additionally, expression quantitative trait locus (eQTL) analysis identified two further genes, RAB31 and CHMP1B, associated with hippocampal volume, refining the previously identified locus. This dataset provides unique developmental expression data in the hippocampus of a non-human primate, and expands our catalog of local and distant eQTL in this brain region.

overall_design: Examination of developmental transcriptome changes in vervet hippocampus.

first: Anna

last: Jasinska

first: Fuying

last: Gao

first: Matthew

last: Jorgensen

first: Scott

last: Fears

first: Roger

last: Woods

first: Nelson

last: Freimer

first: Giovanni

last: Coppola


title: Transcriptional profiling of hepatocyte, reprogrammed hepatocyte, and biliary cells

status: Public on Aug 27 2020

city: New York

first: Jinyang

state: New York

address: 1230 York Ave

institute: The Rockefeller University

summary: Following liver injury, a subset of hepatocytes adopt features of biliary epithelial cells (BECs) in a process known as biliary reprogramming. The aim of this study is to elucidate the molecular events accompanying this dramatic shift in cellular identity. Wild type hepatocytes, wild type biliary cells, DDC-treated hepatocytes, DDC-treated biliary cells, and DDC-treated reprogrammed cells were isolated by FACS, RNA isolated, and sequenced.

overall_design: Transcriptional profiling of liver cell populations by RNA-seq in control and DDC-treated mice

first: Allyson

last: Merrell

first: Ben

last: Stanger


title: Profound discrepancies between cell autonomous and systemic Akt isoform deletions have uncovered new roles for Akt isoforms in breast cancer development and metastasis

city: Chicago

first: Elizaveta

middle: V

last: Benevolenskaya

state: IL

address: 900 S. Ashland Ave.

department: Biochemistry and Molecular Genetics

institute: University of Illinois at Chicago

summary: Here we study the effect on cell autonomous and systemic Akt isoform deletions in breast cancer

overall_design: Investigating role of Akt isoforms in breast cancer using single cell RNA-seq

first: Nissim

last: Hay

first: Majd

last: Ariss

first: Xinyu

first: Abul

middle: B

last: Islam


title: Inhibition of Gli2 suppresses tumorigenicity in glioblastoma stem cells derived from a de novo murine brain cancer model

status: Public on Aug 20 2020

city: Kyoto city

first: Seisuke

last: Tanigawa

address: 465 Kajii-cho,Kawaramachi-Hirokoji

department: Neurosurgery

institute: Kyoto prefectural university of medicine

summary: Prognosis of glioblastoma remains poor despite a great deal of research. In glioblastoma, the existence of glioblastoma stem cells (GSCs) has been shown, which are responsible for tumorigenesis, invasive capacity, and therapy resistance. One of cancer stem cell markers, Leucine-rich repeat-containing G-protein coupled receptor (Lgr5) plays a role in maintenance of GSCs, however, properties of the Lgr5 positive GSCs have not been fully understood. We applied the Sleeping-Beauty transposon-induced glioblastoma model to the Lgr5-GFP transgenic mice and sorted the GFP-positive cells from the neurosphere cultures derived from the mouse glioblastoma tissues. We found that the GFP-positive GSCs exhibited higher expression of Gli2 using a global gene expression analysis. Gli2 knockdown using lentiviral-mediated shRNA downregulates both the Hedgehog- and Wnt signaling pathway-related genes including Lgr5, suppresses tumor cell proliferation and invasion capacity, and induces apoptosis. Pharmacological Gli inhibition by GANT61 also suppresses tumor cell proliferation. Furthermore, the orthotopic transplantation model revealed that silencing of Gli2 suppresses tumorigenicity of GSCs in vivo. These findings demonstrate that Gli2 affects not only Hh pathway but also Wnt pathway and plays an important role in the GSC maintenance, suggesting that Gli2 may be a potential therapeutic target for glioblastoma treatment.

overall_design: To test the effect of suppression of Gli2 on the gene expression, murine GSC was tranducted with lentiviral non-target (control) or Gli2 shRNA. Gli2-knockdown GSCs were compared to control cells.

first: Mitsugu

last: Fujita

first: Chiami

last: Moyama

first: Shota

last: Ando

first: Hiromi

last: Li

first: Eishi

last: Ashihara

first: Yasushi

last: Kojima

first: Teruaki

last: Fujishita

first: Masahiro

last: Aoki

first: Hayato

last: Takeuchi

first: Takumi

last: Yamanaka

first: Yoshinobu

last: Takahashi

first: Naoya

last: Hashimoto

first: Susumu

last: Nakata


title: poly A+ RNA sequencing of quiescent and early serum stimulated control and MIR222HG-depleted WI-38s

city: Urbana

first: Prasanth Kumar

middle: Vijayan

last: Kannanganattu

state: Illinois

address: 601S, Goodwin Avenue

institute: University of Illinois at Urbana-Champaign

summary: We performed paired-end poly A+ RNA sequencing using total RNA isolated  from serum-starved and serum-released (6-hour) control and MIR222HG-depleted WI-38 cells

overall_design: Control and MIR222HG-depleted WI-38 cells in quiescence or at 6-hour serum stimulation were collected for RNA-seq. Two biological replicates were included

first: Sun

last: Qinyu

first: Prasanth


title: Cardiac-tbx20 overexpression enhances heart regeneration by promoting cardiomyocytes dedifferentiation and endocardial activation

city: Shanghai

first: Tao

middle: Peter

last: Zhong

address: No.2005, Songhu Road

department: School of Life Sciences

institute: Fudan University

summary: The goal of this study is to understand the function of cardiac tbx20 during heart regeneration. By high-throughput sequencing, molecular variations of tbx20-cardiac specific inducing heart in response to heart injury compared with control hearts were demonstrated. We collected the injured heart apex tissue at 7 days post injury and sequenced the transcriptome.

overall_design: RNA was extracted from ventricular apical portions at 7 days post injury from control hearts and tbx20-cardiac-specific inducing hearts. Tissue from 6-8 zebrafish were collected in each control group or cardiac-tbx20-overexpressing group, three replications were carried out.

first: Yabo

last: Fang

first: Kaa

last: Lai

first: Wufan

last: Tao


title: CRISPR-Cas9 knockdown of RBM48 in K562 cells

city: Gainesville

first: William

middle: Bradley

last: Barbazuk

state: Florida

address: UF-CGRC Room 407 2033 Mowry Rd

department: Biology

institute: University of Florida

summary: U12-type or minor (U12) introns are spliced by a distinct minor spliceosome and are found in the vast majority of multicellular eukaryotes, including plants and animals. Although U12 introns constitute less than 0.5% of all introns in many species, minor intron containing genes (MIGs) are important for organismal growth, development and pathology. We recently reported that maize RNA Binding Motif Protein 48 (RBM48) is required for U12-type intron splicing. Maize rbm48 mutants have genome-wide defects of U12 intron splicing, leading to abnormal endosperm cell differentiation and proliferation. To investigate whether RBM48 mediated U12 splicing is conserved between maize and humans, we generated a CRISPR/Cas9-mediated RBM48 functional knockout of the human RBM48 ortholog (RBM48 FunKO) in human K-562 cells.

overall_design: The mRNA profiles of RBM48 knockout and Vector Control K562 cells were generated by deep sequencing, in triplicate, using Illumina HiSeq platform

first: Lal

last: Shailesh


title: poly A+ RNA sequencing of quiescent and early serum stimulated WI-38s

department: Cell and Developmental Biology

summary: We performed paired-end poly A+ RNA sequencing using total RNA isolated  from serum starved and serum released WI-38 cells

overall_design: Quiescent WI-38s were induced by serum starvation (0.1% FBS) for 3 days, and collected for RNA extraction. Serum stimulation was performed in quiescent cells by changing back to 10% FBS contained medium. Cells at early serum release time points at 3 hour and 6 hour were collected for RNA extraction.

first: Qinyu

last: Sun

first: Kannanganattu

last: Prasanth


title: Loss of CBX2 induces genome instability and senescence-associated chromosomal rearrangements

city: Athens

first: Claudia

last: Baumann

address: 501 DW Brooks Drive

department: Physiology and Pharmacology

institute: University of Georgia

summary: Polycomb group proteins play important roles in developmental and cell proliferation processes. We demonstrate that the PRC1 protein CBX2 is critical for heterochromatin homeostasis, chromosome stability and the prevention of premature cellular senescence. Purpose: Use of Next-generation sequencing (NGS) to assess transcriptional (RNAseq) profiles and changes in chromatin accessibility in WT and Cbx2-/- fibroblasts prior to the onset of premature senescence.

overall_design:
Methods: RNA-seq and ATAC-seq profiles of Passage 2 mouse embryonic fibroblasts (MEFs) from wild-type (WT) and Cbx2 knockout (Cbx2-/-) mice were maintained in high glucose DMEM (Gibco/Thermo Fisher, Waltham, MA, USA) supplemented with 10% FBS (Hyclone, GE Healthcare, Chicago, IL, USA), 1/100 (v/v) sodium pyruvate, 1/100 (v/v) L-Glutamine and 1/100 (v/v) Penicillin/Streptomycin (all Gibco/Thermo Fisher) before cell collection for ATAC-seq and RNAseq.
Results: Integrative transcriptome analysis and ATAC-seq revealed a significant dysregulation of transcripts involved in DNA repair, chromocenter formation and tumorigenesis in addition to changes in chromatin accessibility of genes involved in amyotrophic lateral sclerosis, basal transcription factors and folate metabolism.
Conclusions: The presence of transcriptional dysregulation and altered chromatin accessibility at key loci in Cbx2-/- cells combined with extensive centromere and telomere defects suggest a prominent role for CBX2 in heterochromatin homeostasis and the regulation of nuclear architecture.

first: Xiangyu

last: Zhang

first: Rabindranath

last: De La Fuente


title: Global transcriptomic changes in aged mouse kidney podocytes

city: Box

first: Stuart

last: Shankland

state: WA

address: 1959 NE Pacific Avenue

department: Nephrology

institute: University of Washington, Seattle

summary: Like many cell types, the mechanisms and pathways underlying healthy aged-related changes to podocytes are not fully understood. Candidate pathways include oxidative stress, epigenetic changes, senescence, sirtuins, reduced autophagy and increased apoptosis, although detailed mechanisms underlying each pathway is not well defined. While detailed gene analysis has been undertaken on whole portions of the aging kidney, transcriptomic changes specific to podocytes in the aged kidney are not known. To address this, we used an inducible podocyte specific reporter mouse in which a cohort of podocytes are permanently labeled over the life time of the animal. RNA-seq was then used to measure transcriptional changes in genes in labeled podocytes in mice with advanced age, compared to podocytes from a cohort of young reporter mice.

overall_design: We did RNA-seq of aged and young podocytes from male and female mice. Aged female: 5 biological replicates; young female: 4 replicates; aged male: 3 replicates; young male: 4 replicates

first: Yuliang

last: Wang


title: Salicylic Acid Suppresses Apical Hook Formation via NPR1-Mediated Repression of EIN3/EIL1 in Arabidopsis

city: Shenzhen

first: Bosheng

last: Li

state: Guangdong

address: SUStech Huiyuan #1 406

department: MCDB

institute: SUSTC (current, may different with previous institution )

summary: Salicylic acid (SA) and ethylene (ET) are two important plant hormones that regulate numerous plant growth, development, and stress response processes. Previous studies have suggested functional interplay of SA and ET in defense response, but precisely how these two hormones co-regulate plant growth and development processes remains unclear. The present findings reveal an antagonism between SA and ET in apical hook formation, a process that ensures successful soil emergence of dicotyledonous etiolated seedlings. Exogenous SA inhibited the ET-induced expression of HOOKLESS1 (HLS1) in a manner dependent on ETHYLENE INSENSITIVE3 (EIN3)/EIN3-LIKE1 (EIL1), the core transcription factors in the ET signaling pathway. We found that SA-activated NONEXPRESSER OF PR GENES1 (NPR1) physically interacted with EIN3 and interfered with the direct binding of EIN3 to target gene promoters, including the HLS1 promoter. Transcriptomic analysis further revealed that NPR1 and EIN3/EIL1 coordinately regulated subsets of genes that mediate plant growth and stress responses, suggesting that the interaction between NPR1 and EIN3/EIL1 might be an important mechanism for integrating the SA and ET signaling pathways in multiple physiological processes. Taken together, our findings shed light on the molecular mechanism underlying SA regulation of apical hook formation as well as the antagonism between SA and ET in early seedling establishment and possibly other physiological processes.

overall_design: The 3.5-day-old etiolated seedlings of Col-0, ein3-1 eil1-1, and npr1-1 were treated with MS liquid supplemented with or without 500 μM SA for 4 hrs before tissue collection. Three biological replicates were prepared for detection and whole seedlings was used for RNA extraction. Total RNA was extracted using the RNeasy Plant Mini Kit (Qiagen). Magnetic beads with Oligo (dT) are used to isolate mRNA. Agilent 2100 Bioanaylzer and ABI StepOnePlus Real-Time PCR System are used in quantification and qualification of the sample library. mRNA-seq was performed by the Beijing Genomics Institute (BGI) using the Illumina HiSeq X Ten system.

first: Peixin

last: Huang

first: Zhi

last: Dong

first: Pengru

last: Guo

first: Xing

first: Yuping

last: Qiu

first: Yichuan

first: Hongwei


title: Expression data from MDA-MB-231 cells treated or not with AsiDNA

city: Paris

first: Pierre

last: de la Grange

address: 29, rue du Faubourg Saint-Jacques

department: Paris Biotech Santé

institute: GenoSplice technology

summary:
Transcriptome analysis revealed a major change in gene expression with a large excess of genes down regulated in 3 independent AsiDNA-treated “evolved” populations as compared to three independent not-treated “naïve” populations
The Achilles heel of anticancer treatments is intrinsic or acquired resistance. Among many targeted therapies, the  DNA repair inhibitors show limited efficacy due to rapid emergence of resistance. We examined evolution of  cancer cells and tumors treated with AsiDNA, a new DNA repair inhibitor targeting all DNA break repair pathways.  Effects of AsiDNA or Olaparib were analyzed in various cell lines. Frequency of AsiDNA- and olaparib-resistant  clones was measured after 2 weeks of continuous treatment in KBM7 haploid cells. Cell survivals were also  measured after one to six cycles of 1-week treatment and 1-week recovery in MDA-MB-231 and NCI-H446.  Transcriptomes of cell populations recovering from cyclic treatments or mock treatment were compared. MDAMB-  231 xenografted models were treated with three cycles of AsiDNA to monitor the effects of treatment on  tumor growth and transcriptional modifications. No resistant clones were selected after AsiDNA treatment  (frequency b 3x10−8) in treatment conditions that generate resistance to olaparib at a frequency of 7.2x10−7  resistant clones per treated cell. Cyclic treatments promote cumulative sensitivity characterized by a higher  mortality of cells having undergone previous treatment cycles. This sensitization was stable, and transcriptome  analysis revealed a major gene downregulation with a specific overrepresentation of genes coding for targets of  DNA-PK. Such changes were also detected in tumor models which showed impaired growth after cycles of  AsiDNA treatment.

overall_design: MDA-MB-231 cells were treated or not with AsiDNA during 3 cycles of 1week treatement/1week release (6 total weeks), RNA was then extracted and hybridyzed on Affymetrix Human Gene 2.1 Arrays, 3 independant AsiDNA treated populations and 3 independant not-treated populations were analyzed.

first: Wael

last: Jdey


title: Sexually dimorphic crosstalk at the maternal-fetal interface

first: Margareta

last: Pisarska

state: CA

address: 8700 Beverly Blvd

department: OB/GYN, Div REI

institute: Cedars Sinai Medical Center

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

overall_design: Refer to individual Series